Characterization of the effects of ISX9 treatment on RBPJ target genes.
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 36 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
- 36 samples: 16 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.
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 GSE288501_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 PRJNA1217875 and SRA study SRP560803. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 32 samples.
How we read this: 16 replicated groups read from 36 sample titles; they account for 32 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.
- GSM8767841 RNA_DMSO_12h_1 RNA_DMSO_12h
- GSM8767842 RNA_DMSO_12h_2 RNA_DMSO_12h
- GSM8767843 RNA_DMSO_24h_1 RNA_DMSO_24h
- GSM8767844 RNA_DMSO_24h_2 RNA_DMSO_24h
- GSM8767845 RNA_ISX9_12h_1 RNA_ISX9_12h
- GSM8767846 RNA_ISX9_12h_2 RNA_ISX9_12h
- GSM8767847 RNA_ISX9_24h_1 RNA_ISX9_24h
- GSM8767848 RNA_ISX9_24h_2 RNA_ISX9_24h
- GSM8767849 RNA_ev_1 RNA_ev
- GSM8767850 RNA_ev_2 RNA_ev
- GSM8767851 RNA_RBPJKO_1 RNA_RBPJKO
- GSM8767852 RNA_RBPJKO_2 RNA_RBPJKO
- GSM8767853 ATAC_12h_DMSO_1 ATAC_12h_DMSO
- GSM8767854 ATAC_12h_DMSO_2 ATAC_12h_DMSO
- GSM8767855 ATAC_12h_ISX9_1 ATAC_12h_ISX9
- GSM8767856 ATAC_12h_ISX9_2 ATAC_12h_ISX9
- GSM8768085 K27ac_ChIP_12h_DMSO_1 K27ac_ChIP_12h_DMSO
- GSM8768086 K27ac_ChIP_12h_DMSO_2 K27ac_ChIP_12h_DMSO
- GSM8768087 K27ac_ChIP_12h_ISX9_1 K27ac_ChIP_12h_ISX9
- GSM8768088 K27ac_ChIP_12h_ISX9_2 K27ac_ChIP_12h_ISX9
- GSM8768089 K4me1_ChIP_12h_DMSO_1 K4me1_ChIP_12h_DMSO
- GSM8768090 K4me1_ChIP_12h_DMSO_2 K4me1_ChIP_12h_DMSO
- GSM8768091 K4me1_ChIP_12h_ISX9_1 K4me1_ChIP_12h_ISX9
- GSM8768092 K4me1_ChIP_12h_ISX9_2 K4me1_ChIP_12h_ISX9
- GSM8768093 K4me3_ChIP_12h_DMSO_1 K4me3_ChIP_12h_DMSO
- GSM8768094 K4me3_ChIP_12h_DMSO_2 K4me3_ChIP_12h_DMSO
- GSM8768095 K4me3_ChIP_12h_ISX9_1 K4me3_ChIP_12h_ISX9
- GSM8768096 K4me3_ChIP_12h_ISX9_2 K4me3_ChIP_12h_ISX9
- GSM8768097 Mods_12h_DMSO_Input
- GSM8768098 Mods_12h_ISX9_Input
- GSM8768099 RBPJ_ChIP_ev_1 RBPJ_ChIP_ev
- GSM8768100 RBPJ_ChIP_ev_2 RBPJ_ChIP_ev
- GSM8768101 RBPJ_ChIP_ev_Input
- GSM8768102 RBPJ_ChIP_RBPJKO_1 RBPJ_ChIP_RBPJKO
- GSM8768103 RBPJ_ChIP_RBPJKO_2 RBPJ_ChIP_RBPJKO
- GSM8768104 RBPJ_ChIP_RBPJKO_Input
- GSE262166 Treatment of cholangiocarcinoma using humanized monoclonal antibodies targeting Claudin-1 77 samples shares treatment, target
- GSE331214 Single-cell profiling across treatment stages enables precision targeting of therapy-resistant neuroblastoma 38 samples shares treatment, target
- GSE333617 Targeting JAK1/3-STAT1 signaling attenuates cytotoxic T lymphocytes activation for the treatment in Stevens-Johnson syndrome and toxic epidermal necrolysis 26 samples shares treatment, target
- GSE264573 Single Cell Analysis of Treatment–Resistant Prostate Cancer: Implications of Cell State Changes for Cell Surface Antigen Targeted Therapies 4 samples shares treatment, target
- GSE244832 Multi-Modal Comparison of human Hepatic Stellate Cells identifies novel therapeutic targets for Metabolic Dysfunction-Associated Steatotic Liver Disease 36 samples shares target
- GSE300595 Multiomic sequencing identifies myeloid cell associations with neoadjuvant chemotherapy treatment response in pancreatic adenocarcinoma (PDAC) 24 samples shares treatment
- GSE302154 Restoring Taxane Efficacy in Castration Resistant Prostate Cancer Through Targeting Menin 20 samples shares target
- GSE317503 Reference-guided genome assembly of long non-coding RNA transcripts reveals target genes associated with Crohn’s disease 140 samples shares target
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.