dCas9 level on chromatin to validate the specificity of CRISPRi-sgRNAs
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 21 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
- 21 samples: 21 samples, each with a distinct title — no replicated groupsGroups 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.
- Paper
- Disruption of TAD hierarchy promotes LTR co-option in cancerNature genetics · 2025
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 GSE295495_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 PRJNA1254965 and SRA study SRP581145. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 21 sample titles: 21 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.
- GSM8951404 ChIP_501mel_set1_dCas9_ALK_sgCtrl1_Cas9
- GSM8951405 ChIP_501mel_set2_dCas9_ALK_sgCtrl1_Cas9
- GSM8951406 ChIP_501mel_set1_dCas9_ALK_sgCtrl2_Cas9
- GSM8951407 ChIP_501mel_set2_dCas9_ALK_sgCtrl2_Cas9
- GSM8951408 ChIP_501mel_set1_dCas9_sgGFP_Cas9
- GSM8951409 ChIP_501mel_set2_dCas9_sgGFP_Cas9
- GSM8951410 ChIP_501mel_set1_dCas9_ALK_sgint4_Cas9
- GSM8951411 ChIP_501mel_set2_dCas9_ALK_sgint4_Cas9
- GSM8951412 ChIP_501mel_set1_dCas9_ALK_sgint19_Cas9
- GSM8951413 ChIP_501mel_set2_dCas9_ALK_sgint19_Cas9
- GSM8951414 ChIP_501mel_set1_dCas9_NOsg_Cas9
- GSM8951415 ChIP_501mel_set2_dCas9_NOsg_Cas9
- GSM8951416 501mel_dCas9_input
- GSM8951417 ChIP_501mel_set1_dCas9_ULK4_sgCtrl1_Cas9
- GSM8951418 ChIP_501mel_set2_dCas9_ULK4_sgCtrl1_Cas9
- GSM8951419 ChIP_501mel_set1_dCas9_ULK4_sgCtrl2_Cas9
- GSM8951420 ChIP_501mel_set2_dCas9_ULK4_sgCtrl2_Cas9
- GSM8951421 ChIP_501mel_set1_dCas9_ULK4_sgint30_Cas9
- GSM8951422 ChIP_501mel_set2_dCas9_ULK4_sgint30_Cas9
- GSM8951423 ChIP_501mel_set1_dCas9_ULK4_sgint31_Cas9
- GSM8951424 ChIP_501mel_set2_dCas9_ULK4_sgint31_Cas9
- GSE256207 Accessible chromatin profiles (ATAC) at single-cell level of human post-mortem brain tissue from the orbitofrontal cortex 92 samples shares chromatin, level
- GSE262518 Acute multi-level response to defective de novo chromatin assembly in S-phase 72 samples shares chromatin, level
- GSE142751 Genome-wide maps of chromatin state in 142 cancer cell lines [cell line] 855 samples shares chromatin
- GSE327821 Single-molecule, single-cell profiling of linked chromatin states [Single_cell_CoCUT&Tag] 200 samples shares chromatin
- GSE215328 Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [hESC_H9_d049_ChIP_Seq] 135 samples shares chromatin
- GSE273054 Differential chromatin accessibility analysis elucidates mechanisms of coronary artery disease-associated genetic variation 119 samples shares chromatin
- GSE296190 Hypoxic regulation of chromatin and gene transcription [ChIP-seq] 84 samples shares chromatin
- GSE334008 CTCF regulates wild-type and recombinant AAV gene expression by shaping viral chromatin [CUT&Run] 47 samples shares chromatin
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.