GEO series
SOX9-BAF multi-omics profiling in human colon cancer cell models
GSE335210
Homo sapiens
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
173 samples
Submitted 2026/06/16
Platform GPL24676
Summary
This study combines matched ATAC-seq, RNA-seq, and CUT&RUN profiling in human colon cancer cell models to track SOX9 degradation/recovery, BAF subunit perturbation, histone-mark occupancy, ARID1A/ARID1B knockdown, and SOX9-variant chromatin accessibility. The main time-course series uses HT29-dTAG cells; the SOX9-variant ATAC-seq subset uses LS180 cells.
This dataset
Download
Direct links to NCBI, no account and no request form: the whole study as GSE335210_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 173 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA1472915 and SRA study SRP705828. Searching any of these in the dataset finder brings you back here.
Study design
20 conditions, mostly in duplicate
Human matched ATAC-seq full time-course sampl… ×2
Human matched ATAC-seq full time-course sampl… ×2
Human matched ATAC-seq full time-course sampl… ×2
Human matched ATAC-seq full time-course sampl… ×2
Human matched ATAC-seq full time-course sampl… ×2
Human matched ATAC-seq full time-course sampl… ×2
Human ARID1A/ARID1B perturbation ATAC-seq sam… ×2
Human ARID1A/ARID1B perturbation ATAC-seq sam… ×2
+12 more
Supports a between-group comparison across 40 samples.
20 replicated groups read from the first 40 of 173 sample titles; they account for 40 of them. Check it against the sample list below before relying on it.
Samples in this study
0 selected
- GSM9808114 Human matched ATAC-seq full time-course sample D10_1
- GSM9808115 Human matched ATAC-seq full time-course sample D10_2
- GSM9808116 Human matched ATAC-seq full time-course sample D13_1
- GSM9808117 Human matched ATAC-seq full time-course sample D13_2
- GSM9808118 Human matched ATAC-seq full time-course sample D2_1
- GSM9808119 Human matched ATAC-seq full time-course sample D2_2
- GSM9808120 Human matched ATAC-seq full time-course sample D4_1
- GSM9808121 Human matched ATAC-seq full time-course sample D4_2
- GSM9808122 Human matched ATAC-seq full time-course sample D7_1
- GSM9808123 Human matched ATAC-seq full time-course sample D7_2
- GSM9808124 Human matched ATAC-seq full time-course sample DMSO_1
- GSM9808125 Human matched ATAC-seq full time-course sample DMSO_2
- GSM9808126 Human ARID1A/ARID1B perturbation ATAC-seq sample ARID1AB_KD_F1
- GSM9808127 Human ARID1A/ARID1B perturbation ATAC-seq sample ARID1AB_KD_F2
- GSM9808128 Human ARID1A/ARID1B perturbation ATAC-seq sample ARID1A_KD_D1
- GSM9808129 Human ARID1A/ARID1B perturbation ATAC-seq sample ARID1A_KD_D2
- GSM9808130 Human ARID1A/ARID1B perturbation ATAC-seq sample ARID1B_KD_E1
- GSM9808131 Human ARID1A/ARID1B perturbation ATAC-seq sample ARID1B_KD_E2
- GSM9808132 Human ARID1A/ARID1B perturbation ATAC-seq sample NTC_C1
- GSM9808133 Human ARID1A/ARID1B perturbation ATAC-seq sample NTC_C2
- GSM9808134 Human ARID1A/ARID1B perturbation ATAC-seq sample Neg_Ctrl_B1
- GSM9808135 Human ARID1A/ARID1B perturbation ATAC-seq sample Neg_Ctrl_B2
- GSM9808136 Human ARID1A/ARID1B perturbation ATAC-seq sample Pos_Ctrl_A1
- GSM9808137 Human ARID1A/ARID1B perturbation ATAC-seq sample Pos_Ctrl_A2
- GSM9808138 Human LS180 SOX9 variant ATAC-seq sample GFP_neg_LS180_1
- GSM9808139 Human LS180 SOX9 variant ATAC-seq sample GFP_neg_LS180_2
- GSM9808140 Human LS180 SOX9 variant ATAC-seq sample GFP_pos_LS180_1
- GSM9808141 Human LS180 SOX9 variant ATAC-seq sample GFP_pos_LS180_2
- GSM9808142 Human LS180 SOX9 variant ATAC-seq sample SOX9_228_LS180_1
- GSM9808143 Human LS180 SOX9 variant ATAC-seq sample SOX9_228_LS180_2
- GSM9808144 Human LS180 SOX9 variant ATAC-seq sample SOX9_303_LS180_1
- GSM9808145 Human LS180 SOX9 variant ATAC-seq sample SOX9_303_LS180_2
- GSM9808146 Human LS180 SOX9 variant ATAC-seq sample SOX9_379_LS180_1
- GSM9808147 Human LS180 SOX9 variant ATAC-seq sample SOX9_379_LS180_2
- GSM9808148 Human LS180 SOX9 variant ATAC-seq sample SOX9_FL_LS180_1
- GSM9808149 Human LS180 SOX9 variant ATAC-seq sample SOX9_FL_LS180_2
- GSM9808150 Human CUT&RUN full time-course SOX9 degradation-recovery sample D10_SMARCC1_1
- GSM9808151 Human CUT&RUN full time-course SOX9 degradation-recovery sample D10_SMARCC1_2
- GSM9808152 Human CUT&RUN full time-course SOX9 degradation-recovery sample D10_SOX9_1
- GSM9808153 Human CUT&RUN full time-course SOX9 degradation-recovery sample D10_SOX9_2
+ 133 more — browse all 173 samples with per-sample file links →
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