Photoproximity labeling of c-Myc reveals SLK as a cancer-specific co-regulator
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 47 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
- 47 samples: 9 conditions, mostly in triplicateGroups 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 GSE331167_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 PRJNA1467359 and SRA study SRP619195. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 24 samples.
How we read this: 9 replicated groups read from 47 sample titles; they account for 24 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.
- GSM9231891 WPMY1 cells, replicate A
- GSM9231892 WPMY1 cells, replicate B
- GSM9231893 WPMY1 cells, replicate C
- GSM9231894 LNCaP cells, replicate A
- GSM9231895 LNCaP cells, replicate B
- GSM9231896 LNCaP cells, replicate C
- GSM9231897 PC3 cells, replicate A PC3 cells, replicate A
- GSM9231898 PC3 cells, replicate B PC3 cells, replicate B
- GSM9231899 PC3 cells, replicate C PC3 cells, replicate C
- GSM9231900 PC3 cells, c-Myc-V5-6xHis transfection, replicate A
- GSM9231901 PC3 cells, c-Myc-V5-6xHis transfection, replicate B
- GSM9231902 PC3 cells, c-Myc-V5-6xHis transfection, replicate C
- GSM9231903 PC3 cells, c-Myc-CfaN transfection, replicate A
- GSM9231904 PC3 cells, c-Myc-CfaN transfection, replicate B
- GSM9231905 PC3 cells, c-Myc-CfaN transfection, replicate C
- GSM9724226 PC-3 WT, c-Myc ChIP, Replicate 1 PC-3 WT, c-Myc ChIP,
- GSM9724227 PC-3 WT, c-Myc ChIP, Replicate 2 PC-3 WT, c-Myc ChIP,
- GSM9724228 PC-3 WT, c-Myc ChIP, Replicate 3 PC-3 WT, c-Myc ChIP,
- GSM9724229 PC-3 WT, RNA Pol II ChIP, Replicate 1 PC-3 WT, RNA Pol II ChI…
- GSM9724230 PC-3 WT, RNA Pol II ChIP, Replicate 2 PC-3 WT, RNA Pol II ChI…
- GSM9724231 PC-3 WT, RNA Pol II ChIP, Replicate 3 PC-3 WT, RNA Pol II ChI…
- GSM9724232 PC-3 WT, IgG Control, Replicate 1 PC-3 WT, IgG Control,
- GSM9724233 PC-3 WT, IgG Control, Replicate 2 PC-3 WT, IgG Control,
- GSM9724234 PC-3 WT, IgG Control, Replicate 3 PC-3 WT, IgG Control,
- GSM9724235 PC-3 WT, Input Control, Replicate 1
- GSM9724236 PC-3 PSD10 (SLK-KO), c-Myc ChIP, Replicate 1 PC-3 PSD10 (SLK-KO), c-…
- GSM9724237 PC-3 PSD10 (SLK-KO), c-Myc ChIP, Replicate 2 PC-3 PSD10 (SLK-KO), c-…
- GSM9724238 PC-3 PSD10 (SLK-KO), c-Myc ChIP, Replicate 3 PC-3 PSD10 (SLK-KO), c-…
- GSM9724239 PC-3 PSD10 (SLK-KO), RNA Pol II ChIP, Replicate 1 PC-3 PSD10 (SLK-KO), RN…
- GSM9724240 PC-3 PSD10 (SLK-KO), RNA Pol II ChIP, Replicate 2 PC-3 PSD10 (SLK-KO), RN…
- GSM9724241 PC-3 PSD10 (SLK-KO), RNA Pol II ChIP, Replicate 3 PC-3 PSD10 (SLK-KO), RN…
- GSM9724242 PC-3 PSD10 (SLK-KO), IgG Control, Replicate 1 PC-3 PSD10 (SLK-KO), Ig…
- GSM9724243 PC-3 PSD10 (SLK-KO), IgG Control, Replicate 2 PC-3 PSD10 (SLK-KO), Ig…
- GSM9724244 PC-3 PSD10 (SLK-KO), IgG Control, Replicate 3 PC-3 PSD10 (SLK-KO), Ig…
- GSM9724245 PC-3 PSD10 (SLK-KO), Input Control, Replicate 1
- GSM9724246 PC3 cells, replicate A PC3 cells, replicate A
- GSM9724247 PC3 cells, replicate B PC3 cells, replicate B
- GSM9724248 PC3 cells, replicate C PC3 cells, replicate C
- GSM9724249 PC3 cells, replicate D
- GSM9724250 PC3 SLK-KO cells, replicate A
+ 7 more — browse all 47 samples with per-sample file links →
- GSE330345 Photoproximity labeling of c-Myc reveals SLK as a cancer-specific co-regulator [ChIP-Seq] 20 samples shares slk, cancer-specific, photoproximity, co-regulator, labeling, c-myc
- GSE307813 Photoproximity labeling of c-Myc reveals SLK as a cancer-specific co-regulator [total RNA-seq] 15 samples shares slk, cancer-specific, photoproximity, co-regulator, labeling, c-myc
- GSE330346 Photoproximity labeling of c-Myc reveals SLK as a cancer-specific co-regulator [RNA-Seq] 12 samples shares slk, cancer-specific, photoproximity, co-regulator, labeling, c-myc
- GSE320561 Effect of eIF5B silencing on KSHV-reactivated human iSLK.219 cells from 0-72 Hours reactivation 24 samples shares slk
- GSE259446 The effect of ORF57 knockout (KO) on host expression in iSLK/Bac16 cells. 16 samples shares slk
- GSE255775 Transcriptomic Profiling of Plasma Extracellular Vesicles Enables Reliable Annotation of the Cancer-specific Transcriptome and Molecular Subtype 319 samples shares cancer-specific
- GSE328578 CBFA2T3-GLIS2 fusion-mediated mSWI/SNF chromatin remodeler disruption generates cancer-specific dependencies in AMKL 156 samples shares cancer-specific
- GSE259422 Transcriptomic Profiling of Plasma Extracellular Vesicles Enables Reliable Annotation of the Cancer-specific Transcriptome and Molecular Subtype (plasma_cancer) 156 samples shares cancer-specific
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.