Analysis of ER stress-induced three-dimensional enhancer network in wild-type and transcription facotr-knockout HCT116 cells [ChIP-Seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 94 samples
- What it is
- ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
- Organism
- Homo sapiens (human)
- Samples
- 94 samples: 47 conditions, mostly in duplicateGroups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
- Paper
- ATF4 and CHOP coordinate endoplasmic reticulum stress-responsive gene programs through enhancer activation and chromatin loopingNucleic acids research · 2026
Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.
Processed table
The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE324343_RAW.tar (it can run to tens of gigabytes).
Raw sequencing reads
The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.
What the files usually look like: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.
Also filed as BioProject PRJNA1434447 and SRA study SRP682323. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 94 samples.
How we read this: 47 replicated groups read from 94 sample titles; they account for 94 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.
- GSM9573965 Input_rep1 Input
- GSM9573966 Input_rep2 Input
- GSM9573967 WT_Con_H3K27ac_SET1_rep1 WT_Con_H3K27ac_SET1
- GSM9573968 WT_Con_H3K27ac_SET1_rep2 WT_Con_H3K27ac_SET1
- GSM9573969 WT_Con_H3K27ac_SET2_rep1 WT_Con_H3K27ac_SET2
- GSM9573970 WT_Con_H3K27ac_SET2_rep2 WT_Con_H3K27ac_SET2
- GSM9573971 ATF4_KO_Con_H3K27ac_SET2_rep1 ATF4_KO_Con_H3K27ac_SET2
- GSM9573972 ATF4_KO_Con_H3K27ac_SET2_rep2 ATF4_KO_Con_H3K27ac_SET2
- GSM9573973 ATF6_KO_Con_H3K27ac_SET2_rep1 ATF6_KO_Con_H3K27ac_SET2
- GSM9573974 ATF6_KO_Con_H3K27ac_SET2_rep2 ATF6_KO_Con_H3K27ac_SET2
- GSM9573975 XBP1_KO_Con_H3K27ac_SET2_rep1 XBP1_KO_Con_H3K27ac_SET2
- GSM9573976 XBP1_KO_Con_H3K27ac_SET2_rep2 XBP1_KO_Con_H3K27ac_SET2
- GSM9573977 WT_Con_H3K27ac_SET3_rep1 WT_Con_H3K27ac_SET3
- GSM9573978 WT_Con_H3K27ac_SET3_rep2 WT_Con_H3K27ac_SET3
- GSM9573979 CHOP_KO_Con_H3K27ac_SET3_rep1 CHOP_KO_Con_H3K27ac_SET3
- GSM9573980 CHOP_KO_Con_H3K27ac_SET3_rep2 CHOP_KO_Con_H3K27ac_SET3
- GSM9573981 WT_Con_H3K27ac_SET4_rep1 WT_Con_H3K27ac_SET4
- GSM9573982 WT_Con_H3K27ac_SET4_rep2 WT_Con_H3K27ac_SET4
- GSM9573983 CEBPB_KO_Con_H3K27ac_SET4_rep1 CEBPB_KO_Con_H3K27ac_SE…
- GSM9573984 CEBPB_KO_Con_H3K27ac_SET4_rep2 CEBPB_KO_Con_H3K27ac_SE…
- GSM9573985 WT_Con_H3K27ac_SET5_rep1 WT_Con_H3K27ac_SET5
- GSM9573986 WT_Con_H3K27ac_SET5_rep2 WT_Con_H3K27ac_SET5
- GSM9573987 NFIL3_KO_Con_H3K27ac_SET5_rep1 NFIL3_KO_Con_H3K27ac_SE…
- GSM9573988 NFIL3_KO_Con_H3K27ac_SET5_rep2 NFIL3_KO_Con_H3K27ac_SE…
- GSM9573989 WT_Tm_H3K27ac_SET1_rep1 WT_Tm_H3K27ac_SET1
- GSM9573990 WT_Tm_H3K27ac_SET1_rep2 WT_Tm_H3K27ac_SET1
- GSM9573991 WT_Tm_H3K27ac_SET2_rep1 WT_Tm_H3K27ac_SET2
- GSM9573992 WT_Tm_H3K27ac_SET2_rep2 WT_Tm_H3K27ac_SET2
- GSM9573993 ATF4_KO_Tm_H3K27ac_SET2_rep1 ATF4_KO_Tm_H3K27ac_SET2
- GSM9573994 ATF4_KO_Tm_H3K27ac_SET2_rep2 ATF4_KO_Tm_H3K27ac_SET2
- GSM9573995 ATF6_KO_Tm_H3K27ac_SET2_rep1 ATF6_KO_Tm_H3K27ac_SET2
- GSM9573996 ATF6_KO_Tm_H3K27ac_SET2_rep2 ATF6_KO_Tm_H3K27ac_SET2
- GSM9573997 XBP1_KO_Tm_H3K27ac_SET2_rep1 XBP1_KO_Tm_H3K27ac_SET2
- GSM9573998 XBP1_KO_Tm_H3K27ac_SET2_rep2 XBP1_KO_Tm_H3K27ac_SET2
- GSM9573999 WT_Tm_H3K27ac_SET3_rep1 WT_Tm_H3K27ac_SET3
- GSM9574000 WT_Tm_H3K27ac_SET3_rep2 WT_Tm_H3K27ac_SET3
- GSM9574001 CHOP_KO_Tm_H3K27ac_SET3_rep1 CHOP_KO_Tm_H3K27ac_SET3
- GSM9574002 CHOP_KO_Tm_H3K27ac_SET3_rep2 CHOP_KO_Tm_H3K27ac_SET3
- GSM9574003 WT_Tm_H3K27ac_SET4_rep1 WT_Tm_H3K27ac_SET4
- GSM9574004 WT_Tm_H3K27ac_SET4_rep2 WT_Tm_H3K27ac_SET4
+ 54 more — browse all 94 samples with per-sample file links →
- GSE324342 Analysis of ER stress-induced three-dimensional enhancer network in wild-type and transcription facotr-knockout HCT116 cells [ATAC-Seq] 4 samples shares hct116, three-dimensional, facotr-knockout, stress-induced, transcription, wild-type, enhancer
- GSE324345 Analysis of ER stress-induced three-dimensional enhancer network in wild-type and transcription facotr-knockout HCT116 cells [RNA-Seq] 66 samples shares hct116, three-dimensional, facotr-knockout, stress-induced, transcription, wild-type, enhancer
- GSE262938 ChIP-seq of BRD4 of HCT116 cells treated with MZ1 or PDD00017273 6 samples shares hct116, chip-seq
- GSE305298 RNA-seq data from human HCT116 wild-type cells, HCT116 DNMT1 hypomorphs, and HCT116 UHRF1 hypomorphs. 8 samples shares hct116, wild-type
- GSE223052 TFIIIC and MYCN link the three-dimensional chromatin structure of promoters to transcription termination of stalled RNA polymerase (ChIPseq CnR) 32 samples shares three-dimensional, transcription
- GSE260528 Three-dimensional regulatory hubs support oncogenic programs in glioblastoma [ChIP-seq] 20 samples shares three-dimensional, chip-seq
- GSE246285 Pseudogenes contribute to the evolution of topological domains across species via forming three-dimensional genome [ChIP-seq] 8 samples shares three-dimensional, chip-seq
- GSE202020 HNF1B induced three-dimensional genome analysis of patient-derived pancreas neoplasm organoids [ChIP-seq] 6 samples shares three-dimensional, chip-seq
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.