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| 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
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| 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.
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| 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.
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| Contributor(s) |
Pang L, Deluca SZ, Zhu H, Urban JM, Spradling AC |
| Citation(s) |
37831064 |
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| Submission date |
Apr 18, 2023 |
| Last update date |
Oct 24, 2023 |
| Contact name |
Allan C Spradling |
| E-mail(s) |
spradling@carnegiescience.edu
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| Phone |
(410) 246-3015
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| Organization name |
Carnegie Institution for Science
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| Department |
HHMI Lab at Embryology
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| Lab |
Spradling
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| Street address |
3520 San Martin Drive
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| City |
Baltimore |
| State/province |
Maryland |
| ZIP/Postal code |
21218 |
| Country |
USA |
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| Platforms (1) |
| GPL19132 |
Illumina NextSeq 500 (Drosophila melanogaster) |
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| Samples (28)
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| GSM7181636 |
NC, 8C, ATAC-seq, rep1 |
| GSM7181637 |
NC, 16C, ATAC-seq, rep1 |
| GSM7181638 |
NC, 32C, ATAC-seq, rep1 |
| GSM7181639 |
NC, 64C, ATAC-seq, rep1 |
| GSM7181640 |
NC, 64C, ATAC-seq, rep2 |
| GSM7181641 |
NC, 64C, ATAC-seq, rep3 |
| GSM7181642 |
NC, 128C, ATAC-seq, rep1 |
| GSM7181643 |
NC, 128C, ATAC-seq, rep2 |
| GSM7181644 |
NC, 128C, ATAC-seq, rep3 |
| GSM7181645 |
NC, 256C, ATAC-seq, rep1 |
| GSM7181646 |
NC, 256C, ATAC-seq, rep2 |
| GSM7181647 |
NC, 256C, ATAC-seq, rep3 |
| GSM7181648 |
NC, 512C, ATAC-seq, rep1 |
| GSM7181649 |
NC, 512C, ATAC-seq, rep2 |
| GSM7181650 |
NC, 512C, ATAC-seq, rep3 |
| GSM7181651 |
NC, 32C, H3K27ac ChIP-seq, rep1 |
| GSM7181652 |
NC, 32C, chromatin input control, rep1 |
| GSM7181653 |
NC, 256C, H3K27ac ChIP-seq, rep1 |
| GSM7181654 |
NC, 256C, chromatin input control, rep1 |
| GSM7181655 |
GSC, H3K9me3 ChIP-seq, rep1 |
| GSM7181656 |
NC, 4C, H3K9me3 ChIP-seq, rep1 |
| GSM7181657 |
NC, 8C, H3K9me3 ChIP-seq, rep1 |
| GSM7181658 |
NC, 4C, chromatin input control, rep1 |
| GSM7181659 |
NC, 8C, chromatin input control, rep1 |
| GSM7181660 |
GSC, chromatin input control, rep1 |
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| 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 |
| 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 Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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