LINE1 RNA demethylation represses chromatin accessibility and sensitizes cancer cells to blockage of DNA damage repair [ATAC-seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 20 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
- 20 samples: 10 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.
Read the full summary ↓
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 GSE285742_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 PRJNA1205742 and SRA study SRP554984. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 20 samples.
How we read this: 10 replicated groups read from 20 sample titles; they account for 20 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.
- GSM8707981 LOVO_shControl_rep1 LOVO_shControl
- GSM8707982 LOVO_shControl_rep2 LOVO_shControl
- GSM8707983 LOVO_shMETTL3_rep1 LOVO_shMETTL3
- GSM8707984 LOVO_shMETTL3_rep2 LOVO_shMETTL3
- GSM8707985 LOVO_shControl_batch2_rep1 LOVO_shControl_batch2
- GSM8707986 LOVO_shControl_batch2_rep2 LOVO_shControl_batch2
- GSM8707987 LOVO_OLA_shControl_rep1 LOVO_OLA_shControl
- GSM8707988 LOVO_OLA_shControl_rep2 LOVO_OLA_shControl
- GSM8707989 LOVO_OLA_shMETTL3_rep1 LOVO_OLA_shMETTL3
- GSM8707990 LOVO_OLA_shMETTL3_rep2 LOVO_OLA_shMETTL3
- GSM8707991 RKO_shControl_rep1 RKO_shControl
- GSM8707992 RKO_shControl_rep2 RKO_shControl
- GSM8707993 RKO_shMETTL3_rep1 RKO_shMETTL3
- GSM8707994 RKO_shMETTL3_rep2 RKO_shMETTL3
- GSM8707995 RKO_shControl_batch2_rep1 RKO_shControl_batch2
- GSM8707996 RKO_shControl_batch2_rep2 RKO_shControl_batch2
- GSM8707997 RKO_OLA_shControl_rep1 RKO_OLA_shControl
- GSM8707998 RKO_OLA_shControl_rep2 RKO_OLA_shControl
- GSM8707999 RKO_OLA_shMETTL3_rep1 RKO_OLA_shMETTL3
- GSM8708000 RKO_OLA_shMETTL3_rep2 RKO_OLA_shMETTL3
- GSE285741 LINE1 RNA demethylation represses chromatin accessibility and sensitizes cancer cells to blockage of DNA damage repair ChIP-seq 32 samples shares line1, demethylation, accessibility, sensitizes, represses, chromatin, blockage
- GSE291386 Chromatin accessibility profiling of HSPC-derived erythroblast differentiation [ATAC-seq] 165 samples shares accessibility, chromatin, atac-seq
- GSE318082 BAF complexes maintain accessibility at stimulus-responsive chromatin and are required for transcriptional stimulus responses [ATAC-seq] 63 samples shares accessibility, chromatin, atac-seq
- GSE316389 Chromatin accessibility and gene expression profiling of primary and metastatic ER+ breast cancer [ATAC-seq] 36 samples shares accessibility, chromatin, atac-seq
- GSE256317 SWI/SNF complex-mediated ZNF410 cooperative binding maintains chromatin accessibility and enhancer activity [ATAC-Seq] 32 samples shares accessibility, chromatin, atac-seq
- GSE203251 Mapping genotypes to chromatin accessibility profiles in single cells [scATAC-seq; Pt01-19;Pt-02 DOGMAseq] 28 samples shares accessibility, chromatin, atac-seq
- GSE269112 Notch induces transcription by stimulating release of paused RNA Pol II without increasing chromatin accessibility [ATAC-seq] 28 samples shares accessibility, chromatin, atac-seq
- GSE240183 HBV-driven host chromatin accessibility changes affect liver metabolic pathways, iron homeostasis and promote a preneoplastic phenotype [ATAC-seq] 22 samples shares accessibility, chromatin, atac-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.