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Status |
Public on May 20, 2022 |
Title |
Sox9 directs divergent epigenomic states in brain tumor subtypes (ChIP-Seq) |
Organisms |
Homo sapiens; Mus musculus |
Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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Summary |
The goal of this study was to profile active H3K27ac marks between autochthonous mouse models of high-grade glioma (HGG) and ependymoma (EPN). Furthermore, with the objective of how transcription factor Sox9 affect H3K27ac states in these two models, we also profiled H3K27ac status between HGG and EPN after Sox9 overexpression (Sox9-GOF) or deletion (Sox9-LOF) in each of these models. In addition, we extended our studies to evaluate both H3K27ac and Sox9 states in human HGG and mouse EPN derived tumor cells.
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Overall design |
Chromatin immunoprecipitation (ChIP-seq) for H3K27ac in tumors from mouse models HGG, EPN and human HGG; ChIP-Seq for Sox9 in human HGG; ChIP-Seq for Sox9 from mouse EPN derived tumor cells. All experiments performed in independent biological replicates except for human HGG and mouse EPN derived cells.
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Contributor(s) |
Sardar D, Chen H, Lozzi B, Varadharajan S, Mack S, Deneen B |
Citation missing |
Has this study been published? Please login to update or notify GEO. |
Submission date |
May 13, 2022 |
Last update date |
May 20, 2022 |
Contact name |
Debosmita Sardar |
E-mail(s) |
sardar@bcm.edu
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Organization name |
Baylor College of Medicine
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Street address |
1 Baylor Plaza
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City |
Houston |
ZIP/Postal code |
77030 |
Country |
USA |
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Platforms (3) |
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Samples (25)
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GSM6139233 |
mouse HGG, control, ChIP-H3K27ac, rep2 |
GSM6139234 |
mouse EPN, control, Input, rep1 |
GSM6139235 |
mouse EPN, control, ChIP-H3K27ac, rep1 |
GSM6139236 |
mouse EPN, control, Input, rep2 |
GSM6139237 |
mouse EPN, control, ChIP-H3K27ac, rep2 |
GSM6139238 |
mouse HGG, Sox9-LOF, Input, rep1 |
GSM6139239 |
mouse HGG, Sox9-LOF, ChIP-H3K27ac, rep1 |
GSM6139240 |
mouse HGG, Sox9-LOF, Input, rep2 |
GSM6139241 |
mouse HGG, Sox9-LOF, ChIP-H3K27ac, rep2 |
GSM6139242 |
mouse HGG, Sox9-GOF, Input, rep1 |
GSM6139243 |
mouse HGG, Sox9-GOF, ChIP-H3K27ac, rep1 |
GSM6139244 |
mouse HGG, Sox9-GOF, Input, rep2 |
GSM6139245 |
mouse HGG, Sox9-GOF, ChIP-H3K27ac, rep2 |
GSM6139246 |
mouse EPN, Sox9-GOF, Input, rep1 |
GSM6139247 |
mouse EPN, Sox9-GOF, ChIP-H3K27ac, rep1 |
GSM6139248 |
mouse EPN, Sox9-GOF, Input, rep2 |
GSM6139249 |
mouse EPN, Sox9-GOF, ChIP-H3K27ac, rep2 |
GSM6139250 |
human HGG, Input1 |
GSM6139251 |
human HGG, ChIP-H3K27ac |
GSM6139252 |
human HGG, Input2 |
GSM6139253 |
human HGG, ChIP-Sox9 |
GSM6139254 |
mouse EPN cells, ChIP-Sox9 |
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This SubSeries is part of SuperSeries: |
GSE202961 |
Sox9 directs divergent epigenomic states in brain tumor subtypes |
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Relations |
BioProject |
PRJNA837888 |
Supplementary file |
Size |
Download |
File type/resource |
GSE202960_EPN-GOF1_H3K27ac_Normalized.bw |
263.0 Mb |
(ftp)(http) |
BW |
GSE202960_EPN-GOF2_H3K27ac_Normalized.bw |
248.8 Mb |
(ftp)(http) |
BW |
GSE202960_EPN-control1_H3K27ac_Normalized.bw |
259.3 Mb |
(ftp)(http) |
BW |
GSE202960_EPN-control2_H3K27ac_Normalized.bw |
260.7 Mb |
(ftp)(http) |
BW |
GSE202960_HGG-GOF1_H3K27ac_Normalized.bw |
265.3 Mb |
(ftp)(http) |
BW |
GSE202960_HGG-GOF2_H3K27ac_Normalized.bw |
264.0 Mb |
(ftp)(http) |
BW |
GSE202960_HGG-LOF1_H3K27ac_Normalized.bw |
240.5 Mb |
(ftp)(http) |
BW |
GSE202960_HGG-LOF2_H3K27ac_Normalized.bw |
265.8 Mb |
(ftp)(http) |
BW |
GSE202960_HGG-control1_H3K27ac_Normalized.bw |
259.9 Mb |
(ftp)(http) |
BW |
GSE202960_HGG-control2_H3K27ac_Normalized.bw |
272.6 Mb |
(ftp)(http) |
BW |
GSE202960_humanHGG_H3K27ac_Normalized.bw |
271.5 Mb |
(ftp)(http) |
BW |
GSE202960_humanHGG_Sox9_Normalized.bw |
225.8 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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