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Series GSE229943 Query DataSets for GSE229943
Status Public on Aug 16, 2023
Title Chromatin and gene expression changes during female Drosophila germline stem cell development.
Organism Drosophila melanogaster
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Third-party reanalysis
Summary The maintenance and differentiation of highly potent animal stem cells generates an epigenetic cycle that underlies development. Drosophila female germline stem cells (GSC) produce cystoblast daughters that differentiate into nurse cells and oocytes. Developmental chromatin analysis profiling the differentiation of GSCs into cystoblasts and NCs of increasing ploidy shows that cystoblasts start developing by forming heterochromatin while in a transient syncytial state, the germline cyst, reminiscent of early embryonic cells. The open GSC chromatin state is further restricted by Polycomb repression of targets that include testis expressed genes briefly active in early female germ cells. Like other highly potent stem cells, GSC metabolism is reprogrammed and Myc-dependent growth is upregulated by altering mitochondrial membrane transport, gluconeogenesis and other processes. Thus, the animal generational cycle comprises similar but distinct maternal and zygotic stem cell epigenetic cycles. We propose that the pluripotent stem cell state and daughter cell differentiation were shaped by the pressure to resist transposon activity over evolutionary time scales. In this GEO submission, we present data and analyses pertaining to H3K27ac, H3K27me3, and H3K9me3 ChIPseq, ATACseq, and RNAseq of Germline Stem Cells (GSCs) and Nurse Cells (NCs) from Drosophila melanogaster ovaries.
 
Overall design H3K27ac ChIP-seq, H3K27me3 ChIP-seq, H3K9me3 ChIPseq, ATAC-seq, and RNA-seq of Germline Stem Cells (GSCs) and Nurse Cells (NCs) from Drosophila melanogaster ovaries.


Please note that this study includes third-party reanalysis of the previously published GSE145282 (Deluca et al, 2020), PRJNA466150 (Greenblatt and Spradling, 2018). The full details of the third-party reanalysis (including the GSM accession of the Samples reanalyzed, their associated GSE Series, data processing strategy, etc.) are provided in the readme_third-party_reanalysis.txt and the re-analyzed data is linked below as a supplementary files.
 
Contributor(s) Pang L, Deluca SZ, Zhu H, Urban JM, Spradling AC
Citation(s) 37831064
Submission date Apr 18, 2023
Last update date Oct 24, 2023
Contact name Allan C Spradling
E-mail(s) spradling@carnegiescience.edu
Phone (410) 246-3015
Organization name Carnegie Institution for Science
Department HHMI Lab at Embryology
Lab Spradling
Street address 3520 San Martin Drive
City Baltimore
State/province Maryland
ZIP/Postal code 21218
Country USA
 
Platforms (1)
GPL19132 Illumina NextSeq 500 (Drosophila melanogaster)
Samples (28)
GSM7181633 GSC, 2C, ATAC-seq, rep1
GSM7181634 GSC, 4C, ATAC-seq, rep1
GSM7181635 NC, 4C, ATAC-seq, rep1
Relations
Reanalysis of GSM4314133
Reanalysis of GSM4314134
Reanalysis of GSM4314135
Reanalysis of GSM4314139
Reanalysis of GSM4314140
Reanalysis of GSM4314141
Reanalysis of GSM4314165
Reanalysis of GSM4314166
Reanalysis of GSM4314167
Reanalysis of GSM4314172
Reanalysis of GSM4314173
Reanalysis of GSM4314178
Reanalysis of GSM4314179
Reanalysis of GSM4314182
Reanalysis of GSM4314183
Reanalysis of GSM4314184
Reanalysis of GSM4314186
Reanalysis of GSM4314187
Reanalysis of GSM4314192
Reanalysis of GSM4314193
BioProject PRJNA956868

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE229943_AllDataTable.csv.gz 4.6 Mb (ftp)(http) CSV
GSE229943_FC16C_Q10-log10FE-medNorm_forHMM.bedGraph.gz 3.5 Mb (ftp)(http) BEDGRAPH
GSE229943_FC16C_Q10_genes_annotated_with_HMM-state-stats.txt.gz 230.9 Kb (ftp)(http) TXT
GSE229943_FC16C_Q10_hmm-genome-segmentation-final-statepath.bedGraph.gz 1.1 Mb (ftp)(http) BEDGRAPH
GSE229943_GSC_002C_H3K27ac.chr.bw 40.1 Mb (ftp)(http) BW
GSE229943_GSC_H3K27me3.chr.bw 94.2 Mb (ftp)(http) BW
GSE229943_GSC_In.chr.bw 300.3 Mb (ftp)(http) BW
GSE229943_GSC_Q10-log10FE-medNorm_forHMM.bedGraph.gz 3.6 Mb (ftp)(http) BEDGRAPH
GSE229943_GSC_Q10_genes_annotated_with_HMM-state-stats.txt.gz 230.0 Kb (ftp)(http) TXT
GSE229943_GSC_Q10_hmm-genome-segmentation-final-statepath.bedGraph.gz 1.1 Mb (ftp)(http) BEDGRAPH
GSE229943_NC_032C_wGLKD_Pse_H3K27me3.q20.chr.bw 43.5 Mb (ftp)(http) BW
GSE229943_NC_032C_wGLKD_Pse_In.q20.chr.bw 61.1 Mb (ftp)(http) BW
GSE229943_NC_512C_wGLKD_H3K27me3.chr.bw 73.1 Mb (ftp)(http) BW
GSE229943_NC_512C_wGLKD_In.chr.bw 183.2 Mb (ftp)(http) BW
GSE229943_RAW.tar 2.0 Gb (http)(custom) TAR (of BEDGRAPH, BW)
GSE229943_St14NC1.genes.results.txt.gz 347.6 Kb (ftp)(http) TXT
GSE229943_St14NC2.genes.results.txt.gz 347.7 Kb (ftp)(http) TXT
GSE229943_St14NC3.genes.results.txt.gz 347.7 Kb (ftp)(http) TXT
GSE229943_St14NC_defolliculated1.genes.results.txt.gz 335.0 Kb (ftp)(http) TXT
GSE229943_St14NC_defolliculated2.genes.results.txt.gz 331.3 Kb (ftp)(http) TXT
GSE229943_St14NC_defolliculated3.genes.results.txt.gz 336.2 Kb (ftp)(http) TXT
GSE229943_St5NC_Q10-log10FE-medNorm_forHMM.bedGraph.gz 3.5 Mb (ftp)(http) BEDGRAPH
GSE229943_St5NC_Q10_genes_annotated_with_HMM-state-stats.txt.gz 232.0 Kb (ftp)(http) TXT
GSE229943_St5NC_Q10_hmm-genome-segmentation-final-statepath.bedGraph.gz 1.1 Mb (ftp)(http) BEDGRAPH
GSE229943_WholeOvary1.genes.results.txt.gz 345.0 Kb (ftp)(http) TXT
GSE229943_WholeOvary2.genes.results.txt.gz 346.2 Kb (ftp)(http) TXT
GSE229943_WholeOvary3.genes.results.txt.gz 343.0 Kb (ftp)(http) TXT
GSE229943_YoungOvary1.genes.results.txt.gz 357.1 Kb (ftp)(http) TXT
GSE229943_YoungOvary2.genes.results.txt.gz 359.1 Kb (ftp)(http) TXT
GSE229943_YoungOvary3.genes.results.txt.gz 357.1 Kb (ftp)(http) TXT
GSE229943_readme_third-party_reanalysis.txt 46.2 Kb (ftp)(http) TXT
GSE229943_sortedGSC.1.genes.results.txt.gz 365.3 Kb (ftp)(http) TXT
GSE229943_sortedGSC.2.genes.results.txt.gz 363.8 Kb (ftp)(http) TXT
GSE229943_sortedGSC.3.genes.results.txt.gz 368.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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