The Retinal Determination Gene Network can confer chemoresistant properties to AML [THP1_chip_rna]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 23 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
- 23 samples: 7 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 GSE288498_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 PRJNA1217878 and SRA study SRP560916. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 17 samples.
How we read this: 7 replicated groups read from 23 sample titles; they account for 17 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.
- GSM8769046 non_targeting_72hrs1 non_targeting_72hrs
- GSM8769047 non_targeting_72hrs2 non_targeting_72hrs
- GSM8769048 Knock_out_72hrs1 Knock_out_72hrs
- GSM8769049 Knock_out_72hrs2 Knock_out_72hrs
- GSM8769050 non_targeting_96hrs1 non_targeting_96hrs
- GSM8769051 non_targeting_96hrs2 non_targeting_96hrs
- GSM8769052 Knock_out_96hrs1 Knock_out_96hrs
- GSM8769053 Knock_out_96hrs2 Knock_out_96hrs
- GSM8769054 non_targeting_48hrs1 non_targeting_48hrs
- GSM8769055 non_targeting_48hrs2 non_targeting_48hrs
- GSM8769056 non_targeting_48hrs3 non_targeting_48hrs
- GSM8769057 Knock_out_48hrs1 Knock_out_48hrs
- GSM8769058 Knock_out_48hrs2 Knock_out_48hrs
- GSM8769059 Knock_out_48hrs3 Knock_out_48hrs
- GSM8769060 ChIP isotype
- GSM8769061 ChIP_SIX1-1 ChIP_SIX1
- GSM8769062 ChIP_SIX1-2 ChIP_SIX1
- GSM9325532 ChIP_SIX1-3 ChIP_SIX1
- GSM9325533 ChIP isotype + DOX
- GSM9325534 ChIP_SIX1-1 + DOX
- GSM9325535 ChIP_SIX1-2 + DOX
- GSM9325536 ChIP_SIX1-3 + DOX
- GSM9325537 ChIP_SIX1-4 + DOX
- GSE281475 Transcriptomic changes in THP1 human AML cell line on PHF6 knockout, PHF6R274Q mutation, PHIP knockout, and double knockout of PHF6 and PHIP compared to wildtype cells 21 samples shares thp1, aml
- GSE281624 Transcriptomic changes in PHF6 knockout THP1 human AML cell line on rescue with PHF6 wildtype (with and without PHIP) or rescue with PHF6R274Q mutant 19 samples shares thp1, aml
- GSE281627 Changes in H3K27 acetylation in THP1 human AML cell line on PHF6 knockout, PHF6R274Q mutation, PHIP knockout, and double knockout of PHF6 and PHIP compared to wildtype clones 18 samples shares thp1, aml
- GSE296649 Clonal evolution permits outgrowth of chemoresistant LMPP-like early progenitors in relapsed NPM1c AML [scRNA-Seq] 58 samples shares aml, chemoresistant
- GSE293201 Ectopic MYC Expression Reprograms Epigenetic Landscapes and Transcription Factor Networks to Drive Differentiation Block and Malignant Transformation in AML [ATAC-seq] 35 samples shares aml, network
- GSE296381 Clonal evolution permits outgrowth of chemoresistant LMPP-like early progenitors in relapsed NPM1c AML 20 samples shares aml, chemoresistant
- GSE270894 Molecular Characterization of Chemoresistant Cell Populations Improves Risk Stratification and Therapy Response Prediction in Pediatric AML [pAML Patients scRNA-seq] 20 samples shares aml, chemoresistant
- GSE271134 Molecular Characterization of Chemoresistant Cell Populations Improves Risk Stratification and Therapy Response Prediction in Pediatric AML [pAML PDX Bulk RNA-seq] 14 samples shares aml, chemoresistant
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.