AKAP95 condensates regulate transcription and can be targeted in MLL-fusion driven oncogenesis
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 49 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
- 49 samples: 36 distinct titles, 9 of them repeatedGroups 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 GSE271858_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 PRJNA1133755 and SRA study SRP518849. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 49 sample titles: 36 distinct titles with little repetition. 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.
- GSM8387177 DMSO
- GSM8387178 High_ActD
- GSM8387179 Low_ActD
- GSM8387180 WT_INPUT
- GSM8387181 KO_INPUT
- GSM8387182 WT_H3K4Me1
- GSM8387183 KO_H3K4Me1
- GSM8387184 WT_H3K4Me3
- GSM8387185 KO_H3K4Me3
- GSM8387186 WT_H3K27Ac
- GSM8387187 KO_H3K27Ac
- GSM8387188 AKAP_WT_ChIP
- GSM8387189 AKAP_KI_ChIP
- GSM8387190 PSmut_PolII_CHIP
- GSM8387191 WT_PolII_CHIP
- GSM8387192 ZFmut_PolII_CHIP
- GSM8387193 PSmut_S2P_CHIP
- GSM8387194 WT_S2P_CHIP
- GSM8387195 ZFmut_S2P_CHIP
- GSM8387196 AKAP_WT_CLIP
- GSM8387197 AKAP_KI_CLIP
- GSM8387201 WT_MA9_Rep1
- GSM8387202 WT_MA9_Rep2
- GSM8387203 WT_MA9_Rep3
- GSM8387204 KO_MA9_Rep1
- GSM8387205 KO_MA9_Rep2
- GSM8387206 KO_MA9_Rep3
- GSM8387207 Hela_Scr_Rep1
- GSM8387208 Hela_Scr_Rep2
- GSM8387209 Hela_Scr_Rep3
- GSM8387210 Hela_KD_Rep1
- GSM8387211 Hela_KD_Rep2
- GSM8387212 Hela_KD_Rep3
- GSM8387213 Hela_PSmut_Rep1
- GSM8387214 Hela_PSmut_Rep2
- GSM8387215 Hela_Wt_Rep1
- GSM8387216 Hela_Wt_Rep2
- GSM8387217 Hela_Zfmut_Rep1
- GSM8387218 Hela_Zfmut_Rep2
- GSM9141743 KD-rescued with AKAP-WT-PRO-Seq
+ 9 more — browse all 49 samples with per-sample file links →
- GSE292300 A core transcriptional regulatory circuitry controls super-enhancer-driven activation of LGR5 in colorectal cancer: ChIP-seq 76 samples shares transcription, driven
- GSE266391 Suppressing Aberrant Hedgehog Pathway and Overcoming Resistance to Smoothened Antagonists via Targeting Super-enhancer-driven Transcriptional Dependencies 74 samples shares transcription, driven
- GSE188412 The PAF1 Complex Regulates Transcriptional Termination and Reinitiation [CUT&Tag] 71 samples shares transcription, regulate
- GSE266389 Suppressing Aberrant Hedgehog Pathway and Overcoming Resistance to Smoothened Antagonists via Targeting Super-enhancer-driven Transcriptional Dependencies [RNA-seq] 60 samples shares transcription, driven
- GSE292302 A core transcriptional regulatory circuitry controls super-enhancer-driven activation of LGR5 in colorectal cancer: RNA-seq 42 samples shares transcription, driven
- GSE245173 APE1 regulates the transcription of urea cycle genes through stabilizing DNA G-quadruplexes in lung adenocarcinoma 38 samples shares transcription, regulate
- GSE302338 Transcriptional landscape of MYCN-driven liver tumors 38 samples shares transcription, driven
- GSE303605 Rbm5 Sustains Leukemia Stem Cells Through a Myc-driven Transcriptional Circuitry 15 samples shares transcription, driven
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.