The Growing Liberality Observed in Primary Animal and Plant Cultures is Common to the Social Amoeba

Article Information

*Norichika Ogata

1Nihon BioData Corporation, Kawasaki, Japan

*Corresponding Author: Norichika Ogata, Nihon BioData Corporation, Kawasaki, Japan.

Received: 6 November 2022; Accepted: 6 January 2023; Published: 03 February 2023

Citation:

Norichika Ogata. The Growing Liberality Observed in Primary Animal and Plant Cultures is Common to the Social Amoeba. Journal of Bioinformatics and Systems Biology. 6 (2023): 10-17.

View / Download Pdf Share at Facebook

Abstract

Tissue culture environment liberates cells fromordinary laws of multicellular organisms. This liberation enables cells several behaviors, such as proliferation, dedifferentiation, acquisition of pluripotency, immortalization, and reprogramming. Recently, the quantitative value of cellular dedifferentiation and differentiation was defined as “liberality”, which is measurable as Shannon entropy of numerical transcriptome data and Lempel-Zip complexity of nucleotide sequence transcriptome data. The increasing liberality induced by the culture environment had first been observed in animal cells and had reconfirmed in plant cells.The phenomena may be common across the kingdom, also in a social amoeba. We measured the liberality of the social amoeba which disaggregated from multicellular aggregates and transferred into a liquid medium.

Keywords

Genomics, Transcriptome, Social Amoeba, Dictyostelium, Dedifferentiation, Liberality, Primary Culture, Lempel-Ziv Complexity.

Genomics articles; Transcriptome articles; Social Amoeba articles; Dictyostelium articles; Dedifferentiation articles; Liberality articles; Primary Culture articles; Lempel-Ziv Complexity articles

Genomics articles Genomics Research articles Genomics review articles Genomics PubMed articles Genomics PubMed Central articles Genomics 2023 articles Genomics 2024 articles Genomics Scopus articles Genomics impact factor journals Genomics Scopus journals Genomics PubMed journals Genomics medical journals Genomics free journals Genomics best journals Genomics top journals Genomics free medical journals Genomics famous journals Genomics Google Scholar indexed journals Transcriptome articles Transcriptome Research articles Transcriptome review articles Transcriptome PubMed articles Transcriptome PubMed Central articles Transcriptome 2023 articles Transcriptome 2024 articles Transcriptome Scopus articles Transcriptome impact factor journals Transcriptome Scopus journals Transcriptome PubMed journals Transcriptome medical journals Transcriptome free journals Transcriptome best journals Transcriptome top journals Transcriptome free medical journals Transcriptome famous journals Transcriptome Google Scholar indexed journals Social Amoeba articles Social Amoeba Research articles Social Amoeba review articles Social Amoeba PubMed articles Social Amoeba PubMed Central articles Social Amoeba 2023 articles Social Amoeba 2024 articles Social Amoeba Scopus articles Social Amoeba impact factor journals Social Amoeba Scopus journals Social Amoeba PubMed journals Social Amoeba medical journals Social Amoeba free journals Social Amoeba best journals Social Amoeba top journals Social Amoeba free medical journals Social Amoeba famous journals Social Amoeba Google Scholar indexed journals Dictyostelium articles Dictyostelium Research articles Dictyostelium review articles Dictyostelium PubMed articles Dictyostelium PubMed Central articles Dictyostelium 2023 articles Dictyostelium 2024 articles Dictyostelium Scopus articles Dictyostelium impact factor journals Dictyostelium Scopus journals Dictyostelium PubMed journals Dictyostelium medical journals Dictyostelium free journals Dictyostelium best journals Dictyostelium top journals Dictyostelium free medical journals Dictyostelium famous journals Dictyostelium Google Scholar indexed journals Dedifferentiation articles Dedifferentiation Research articles Dedifferentiation review articles Dedifferentiation PubMed articles Dedifferentiation PubMed Central articles Dedifferentiation 2023 articles Dedifferentiation 2024 articles Dedifferentiation Scopus articles Dedifferentiation impact factor journals Dedifferentiation Scopus journals Dedifferentiation PubMed journals Dedifferentiation medical journals Dedifferentiation free journals Dedifferentiation best journals Dedifferentiation top journals Dedifferentiation free medical journals Dedifferentiation famous journals Dedifferentiation Google Scholar indexed journals Liberality articles Liberality Research articles Liberality review articles Liberality PubMed articles Liberality PubMed Central articles Liberality 2023 articles Liberality 2024 articles Liberality Scopus articles Liberality impact factor journals Liberality Scopus journals Liberality PubMed journals Liberality medical journals Liberality free journals Liberality best journals Liberality top journals Liberality free medical journals Liberality famous journals Liberality Google Scholar indexed journals Primary Culture articles Primary Culture Research articles Primary Culture review articles Primary Culture PubMed articles Primary Culture PubMed Central articles Primary Culture 2023 articles Primary Culture 2024 articles Primary Culture Scopus articles Primary Culture impact factor journals Primary Culture Scopus journals Primary Culture PubMed journals Primary Culture medical journals Primary Culture free journals Primary Culture best journals Primary Culture top journals Primary Culture free medical journals Primary Culture famous journals Primary Culture Google Scholar indexed journals Lempel-Ziv Complexity articles Lempel-Ziv Complexity Research articles Lempel-Ziv Complexity review articles Lempel-Ziv Complexity PubMed articles Lempel-Ziv Complexity PubMed Central articles Lempel-Ziv Complexity 2023 articles Lempel-Ziv Complexity 2024 articles Lempel-Ziv Complexity Scopus articles Lempel-Ziv Complexity impact factor journals Lempel-Ziv Complexity Scopus journals Lempel-Ziv Complexity PubMed journals Lempel-Ziv Complexity medical journals Lempel-Ziv Complexity free journals Lempel-Ziv Complexity best journals Lempel-Ziv Complexity top journals Lempel-Ziv Complexity free medical journals Lempel-Ziv Complexity famous journals Lempel-Ziv Complexity Google Scholar indexed journals Tissue culture articles Tissue culture Research articles Tissue culture review articles Tissue culture PubMed articles Tissue culture PubMed Central articles Tissue culture 2023 articles Tissue culture 2024 articles Tissue culture Scopus articles Tissue culture impact factor journals Tissue culture Scopus journals Tissue culture PubMed journals Tissue culture medical journals Tissue culture free journals Tissue culture best journals Tissue culture top journals Tissue culture free medical journals Tissue culture famous journals Tissue culture Google Scholar indexed journals

Article Details

1. Introduction

Tissue culture is performed to maintain isolated portions of multicellular organisms in an artificial milieu that is outside the individual organism and for considerable periods of time [1]. It is known over a century that cells derived from cultured explants are, in general, different from cells of the corresponding tissue in a living organism [2, 3]. In these tissue cultures, cells are liberated from stimulations and prohibition which is ordinary in multi-cellular organisms [4]. This liberation is essential for growth, dedifferentiation, acquisition of pluripotency, immortalization and reprogramming. The proliferations of cultured cells were also considered to be a result of dedifferentiation [2]. In this decade, several studies [5-8] following our research [9] repeatedly measured the degree of cellular dedifferentiation and differentiation as a  Shannon entropy of numerical transcriptome data. The Shannon entropy is a kind of alpha diversity in the ecology [10], and the transcriptome Shannon entropy is simply transcriptome diversity [11]. It is not incorrect to call it the (alpha) diversity of the transcriptome, but that would leave its biological significance undefined, as would each principal component that came up in the principal component analysis. We can quantitatively assess, judge, and define that dedifferentiation is an increase in the Shannon entropy of the transcriptome, it is more accurate to position the value not as a mere bioinformatics measure; however, as a number with obvious biological and bioengineering significance, such as viable cell rate, cell density, specific growth rate, or pcd (pg/cell/day) [12]. Here we call the quantitative value of cellular dedifferentiation and differentiation “liberality,” since a previous study explained the changes were happening to cultured cells as “libère” [13]. The study of cellular liberality has entered a phase in which evidence is being gathered to

strengthen the theory; the degree of cellular dedifferentiation and differentiation is measurable. We previously observed increasing liberality in animal and plant primary cultures [5, 14]. In this study, we measured the liberality of the social amoeba, Dictyostelium discoideum, having a transition from single-celled amoebae to a multicellular organism as a natural part of its life cycle [15]. Dictyostelium dedifferentiation was initiated by disaggregation of multicellular aggregates and transfer of the cells into a HL5 liquid medium in a study [16]. We could not reproduce the mapping used in the study since the referential genome was not clear in the manuscript; There is “Reads were mapped to the Dictyostelium genome (version obtained from Gareth Bloomfield, masking the duplication on chromosome 2) using Tophat v2.0.9”. Therefore, we measured the liberality from the transcriptome data without the referential genome and the reads mapping process. A recent study enabled measuring the liberality as Lempel-Ziv complexity of fastq files [17, 18].

fortune-biomass-feedstock

Figure1: Scatter plot of culture time vs cellular liberality.

The social amoeba cells disaggregated of multicellular aggregates and transferred the cells into a HL5 liquid medium. The Lempel-Ziv complexity of transcriptome were measured in each culture time.

2. Materials and Methods

Transcriptome data set was obtained from DDBJ SRA (SRA1039371) [16]; 30 fastq data ware used (SRR11039842-SRR11039872). In the entry, time course total RNA sampling during cultivation of the amoeba (0, 0.5, 1, 1.5, 2, 2.5, 3, 4, 5, 6, 8, 10, 12, 14 and 18 hours). Each sample has two biological replicates. We downloaded sra compressed fastq data. The file size of decompressed raw textual fastq files and bz2 compressed files were measured. We measured Lempel-Ziv complexity of the fastq files as file size rate between bz2 compressed fastq data and raw textual fastq data. Then we compared the culture time and the Lampel-Ziv complexity.

3. Results

Dictyostelium dedifferentiation is initiated by disaggregation of multicellular aggregates and transfer of the cells into a HL5 liquid media. The liberality immediately increased and reached the peak in 3 hours. This result suggested that dedifferentiation of cells in primary explant culture is a common phenomenon for diverse multi-cellular organisms including social amoeba. After 4 hours of the amoeba disaggregation, the liberality started decreasing. The liberality of the amoeba 18 hours after disaggregation were equal to 0 hours after disaggregation. This liberality decreasing following the liberality increase was observed in the previous study of plants, that was thought to be re-differentiation to construct a new plant. The dedifferentiated amoeba would immediately start re-differentiation to achieve a slightly better position in the new environment. Although, in the Dictyostelium paper the amoeba had been thought to dedifferentiate for 18 hours, our observations of the liberality suggest that amoeba dedifferentiation completed in 4 hours. Indeed, the Dictyostelim paper indicated the importantest change of amoeba at 2~4 hours after disaggregation; two transcription factors, bzpS and mybD showed clear peak of expression (Fig. 3a [16]), the PC1 in a primary component analysis of transcriptome does not change after 4 hours after disaggregation (Fig. 3b [16]), and cell motility showed peak at 3 hours after disaggregation (Fig. 5 [16]). Even plants complete dedifferentiation within 6 hours [14,19], so there is no reason why the amoeba dedifferentiation should be slower than that. We recommend that studies attempting to examine dedifferentiation incorporate measurements of cellular liberality to accurately monitor the state of cellular dedifferentiation [20]. As was evident in the present study, measurement processes that include mapping of reads to a reference genome are less reproducible, making the measurement of liberality based on LZ complexity of nucleotide sequence files [18] more useful.

References

  1. Margaret Ransone Murray GK. A Bibliography of the Research in Tissue culture, 1884-1950. New York: Academic Press (1953): 1741.
  2. Champy C. Quelques résultats de la méthode de culture de tissus. I.Généralités. II. Le muscle lisse. Archives de zoologie expérimentale et générale 53(1913-1914): 42-51.
  3. Carleton HM. Tissue culture: A critical summary. Journal of Experimental Biology 1(1923):131-51.
  4. Canguilhem G. La connaissance de la vie. Paris: Librairie Philosophique J Vrin 5(1965).
  5. Guo M, Bao EL, Wagner M, et al. SLICE: determining cell differentiation and lineage based on single cell entropy. Nucleic Acids Res 45(7) (2017): 54.
  6. Teschendorff AE, Enver T. Single-cell entropy for accurate estimation of differentiation potency from a cell’s transcriptome, Nat Commun 8(2017): 15599.
  7. Wiesner K, Teles J, Hartnor M, et al. Haematopoietic stem cells:entropic landscapes of differentiation. Interface Focus 6(8) (2018): 20180040.
  8. Kannan S, Farid M, Lin BL, et al. Transcriptomic entropy benchmarks stem cell-derived cardiomyocyte maturation against endogenous tissue at single cell level. PloS Comput Biol 17(9) (2021): 1009305.
  9. Ogata N, Yokoyama T, Iwabuchi K. Transcriptome responses of insect fat body cells to tissue culture environment. PLoS One  7(4) (2012): 34940.
  10. Dongmei A, Ruocheng H, Jin W, et al. Integrated metagenomic data analysis demonstrates that a loss of diversity in oral microbiota is associated with periodontitis. BMC Genomics 18(2017): 1041.
  11. Martinez O, Reyes-Valdes MH. Defining diversity specialization and gene specificity in transcriptomes through information theory, Proc. Natl. Acad. Sci. U.S.A. 105(2008): 9709–9714.
  12. Yamano-Adachi N, Ogata N, Tanaka S, et al. Characterization of Chinese hamster ovary cells with disparate chromosome numbers: Reduction of the amount of mRNA relative to total protein, J. Biosci. Bioeng 129(1)(2020):121-128.
  13. Canguilhem G. La connaissance de la vie, Pari: Hachette (1952): 41.
  14. Ogata N. Transcriptome Dedifferentiation Observed in Animal Primary Cultures is Essential to Plant Reprogramming, J. Bioinform. Syst. Biol 5(4) (2022):116-118.
  15. Devreotes P.  Dictyostelium discoideum: a model system for cell-cell interactions in development, Science 245(4922)(1989):1054-8.
  16. Nichols JME, Antolovi? V, Reich JD, et al. Cell and molecular transitions during efficient dedifferentiation. eLife 9(2020): 55435.
  17. Lempel A, Ziv J. On the Complexity of Finite Sequences, IEEE Transactions onf Information Theory. 22(1)(1976).
  18. Ogata N, Hosaka A. Cellular liberality is measurable as Lempel-Ziv complexity of fastq files, in 2022 IEEE 22nd International Conference on Bioinformatics and Bioengineering (BIBE), Taichung, Taiwan 7(2022) 321-326.
  19. Nishiyama T, Miyawaki K, Ohshima M, et al. Digital gene expression profiling by 5'-end sequencing of cDNAs during reprogramming in the moss Physcomitrella patens. PLoS One 7(5) (2012): 36471.
  20. Ogata N, Kozaki T, Yokoyama T, et al. Comparison between the Amount of Environmental Change and the Amount of Transcriptome Change. PLoS One 10(12)(2015): 0144822.

Appendix. Codes obtaining data used in this study.

# GSM4300090: Media 0h rep1; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691764
/SRR11039842/SRR11039842.sra ./

# GSM4300091: Media 0.5h rep1; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691765
/SRR11039843/SRR11039843.sra ./

# GSM4300092: Media 1h rep1; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691766
/SRR11039844

# GSM4300093: Media 1.5h rep1; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691767
/SRR11039846/SRR11039846.sra ./

# GSM4300094: Media 2h rep1; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691768
/SRR11039847/SRR11039847.sra ./

# GSM4300095: Media 2.5h rep1; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691770
/SRR11039848/SRR11039848.sra ./

# GSM4300096: Media 3h rep1; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691771
/SRR11039849/SRR11039849.sra ./

# GSM4300097: Media 4h rep1; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691772
/SRR11039850/SRR11039850.sra ./

# GSM4300098: Media 5h rep1; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691773
/SRR11039851/SRR11039851.sra ./

# GSM4300099: Media 6h rep1; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691774
/SRR11039852/SRR11039852.sra ./

# GSM4300100: Media 8h rep1; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691775
/SRR11039853/SRR11039853.sra ./

# GSM4300101: Media 10h rep1; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691776
/SRR11039854/SRR11039854.sra ./

# GSM4300102: Media 12h rep1; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691777
/SRR11039855/SRR11039855.sra ./

# GSM4300103: Media 14h rep1; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691778
/SRR11039856/SRR11039856.sra ./

# GSM4300104: Media 18h rep1; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691779
/SRR11039857/SRR11039857.sra ./

# GSM4300105: Media 0h rep2; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691780
/SRR11039858/SRR11039858.sra ./

# GSM4300106: Media 0.5h rep2; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691781
/SRR11039859/SRR11039859.sra ./

# GSM4300107: Media 1h rep2; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691782
/SRR11039860/SRR11039860.sra ./

# GSM4300108: Media 1.5h rep2; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691783
/SRR11039861/SRR11039861.sra ./

# GSM4300109: Media 2h rep2; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691784
/SRR11039862/SRR11039862.sra ./

# GSM4300110: Media 2.5h rep2; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691785
/SRR11039863/SRR11039863.sra ./

# GSM4300111: Media 3h rep2; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691786
/SRR11039864/SRR11039864.sra ./

# GSM4300112: Media 4h rep2; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691787
/SRR11039865/SRR11039865.sra ./

# GSM4300113: Media 5h rep2; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691788
/SRR11039866/SRR11039866.sra ./

# GSM4300114: Media 6h rep2; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691801
/SRR11039867/SRR11039867.sra ./

# GSM4300115: Media 8h rep2; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691802
/SRR11039868/SRR11039868.sra ./

# GSM4300116: Media 10h rep2; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691803
/SRR11039869/SRR11039869.sra ./

# GSM4300117: Media 12h rep2; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691804
/SRR11039870/SRR11039870.sra ./

# GSM4300118: Media 14h rep2; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691805
/SRR11039871/SRR11039871.sra ./

# GSM4300119: Media 18h rep2; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691806
/SRR11039872/SRR11039872.sra ./

# GSM4300120: Undifferentiated rep1; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691807
/SRR11039873/SRR11039873.sra ./

# GSM4300121: Undifferentiated rep2; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691808
/SRR11039874/SRR11039874.sra ./

# GSM4300122: Bacteria/Buffer 0h rep1; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691809
/SRR11039875/SRR11039875.sra ./

# GSM4300123: Bacteria 0.5h rep1; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691810
/SRR11039876/SRR11039876.sra ./

# GSM4300124: Bacteria 1h rep1; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691811
/SRR11039877/SRR11039877.sra ./

# GSM4300125: Bacteria 1.5h rep1; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691812
/SRR11039878/SRR11039878.sra ./

# GSM4300126: Bacteria 2h rep1; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691814
/SRR11039879/SRR11039879.sra ./

# GSM4300127: Bacteria 3h rep1; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691815
/SRR11039880/SRR11039880.sra ./

# GSM4300128: Bacteria 4h rep1; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691816
/SRR11039881/SRR11039881.sra ./

# GSM4300129: Bacteria 5h rep1; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691817
/SRR11039882/SRR11039882.sra ./

# GSM4300130: Bacteria 6h rep1; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691818
/SRR11039883/SRR11039883.sra ./

# GSM4300131: Bacteria 8h rep1; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691819
/SRR11039884/SRR11039884.sra ./

# GSM4300132: Bacteria 12h rep1; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691820
/SRR11039885/SRR11039885.sra ./

# GSM4300133: Bacteria 24h rep1; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691821
/SRR11039886/SRR11039886.sra ./

# GSM4300134: Buffer 0.5h rep1; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691822
/SRR11039887/SRR11039887.sra ./

# GSM4300135: Buffer 1h rep1; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691823
/SRR11039888/SRR11039888.sra ./

# GSM4300136: Buffer 2h rep1; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691824
/SRR11039889/SRR11039889.sra ./

# GSM4300137: Buffer 3h rep1; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691825
/SRR11039890/SRR11039890.sra ./

# GSM4300138: Buffer 4h rep1; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691826
/SRR11039891/SRR11039891.sra ./

# GSM4300139: Buffer 6h rep1; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691827
/SRR11039892/SRR11039892.sra ./

# GSM4300140: Bacteria/Buffer 0h rep2; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691828
/SRR11039893/SRR11039893.sra ./

# GSM4300141: Bacteria 0.5h rep2; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691829
/SRR11039894/SRR11039894.sra ./

# GSM4300142: Bacteria 1h rep2; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691830
/SRR11039895/SRR11039895.sra ./

# GSM4300143: Bacteria 1.5h rep2; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691831
/SRR11039896/SRR11039896.sra ./

# GSM4300144: Bacteria 2h rep2; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691832
/SRR11039897/SRR11039897.sra ./

# GSM4300145: Bacteria 3h rep2; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691833
/SRR11039898/SRR11039898.sra ./

# GSM4300146: Bacteria 4h rep2; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691834
/SRR11039899/SRR11039899.sra ./

# GSM4300147: Bacteria 5h rep2; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691835
/SRR11039900/SRR11039900.sra ./

# GSM4300148: Bacteria 6h rep2; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691836
/SRR11039901/SRR11039901.sra ./

# GSM4300149: Bacteria 8h rep2; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691837
/SRR11039902/SRR11039902.sra ./

# GSM4300150: Bacteria 12h rep2; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691838
/SRR11039903/SRR11039903.sra ./

# GSM4300151: Bacteria 24h rep2; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691839
/SRR11039904/SRR11039904.sra ./

# GSM4300152: Buffer 0.5h rep2; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691840
/SRR11039906/SRR11039906.sra ./

# GSM4300153: Buffer 1h rep2; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691841
/SRR11039907/SRR11039907.sra ./

# GSM4300154: Buffer 2h rep2; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691842
/SRR11039908/SRR11039908.sra ./

# GSM4300155: Buffer 3h rep2; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691843
/SRR11039909/SRR11039909.sra ./

# GSM4300156: Buffer 4h rep2; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691844
/SRR11039910/SRR11039910.sra ./

# GSM4300157: Buffer 6h rep2; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691846
/SRR11039911/SRR11039911.sra ./

# GSM4300158: Development 0h rep1; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691847
/SRR11039912/SRR11039912.sra ./

# GSM4300159: Development 2h rep1; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691848
/SRR11039913/SRR11039913.sra ./

# GSM4300160: Development 4h rep1; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691849
/SRR11039914/SRR11039914.sra ./

# GSM4300161: Development 6h rep1; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691850
/SRR11039915/SRR11039915.sra ./

# GSM4300162: Development 8h rep1; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691789
/SRR11039916/SRR11039916.sra ./

# GSM4300163: Development 10h rep1; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691790
/SRR11039917/SRR11039917.sra ./

# GSM4300164: Development 12h rep1; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691791
/SRR11039918/SRR11039918.sra ./

# GSM4300165: Development 14h rep1; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691792
/SRR11039919/SRR11039919.sra ./

# GSM4300166: Development 0h rep2; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691793
/SRR11039920/SRR11039920.sra ./

# GSM4300167: Development 2h rep2; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691794
/SRR11039921/SRR11039921.sra ./

# GSM4300168: Development 4h rep2; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691795
/SRR11039922/SRR11039922.sra ./

# GSM4300169: Development 6h rep2; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691796
/SRR11039923/SRR11039923.sra ./

# GSM4300170: Development 8h rep2; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691797
/SRR11039924/SRR11039924.sra ./

# GSM4300171: Development 10h rep2; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691798
/SRR11039925/SRR11039925.sra ./

# GSM4300172: Development 12h rep2; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691799
/SRR11039926/SRR11039926.sra ./

# GSM4300173: Development 14h rep2; Dictyostelium discoideum; RNA-Seq

wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX769/SRX7691800
/SRR11039927/SRR11039927.sra ./

© 2016-2024, Copyrights Fortune Journals. All Rights Reserved