Pseudogenes contribute to the evolution of topological domains across species via forming three-dimensional genome
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 22 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
- 22 samples: 9 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 GSE246663_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 PRJNA1034081 and SRA study SRP468541. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 18 samples.
How we read this: 9 replicated groups read from 22 sample titles; they account for 18 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.
- GSM7866214 hESC cells, WT, input rep1 hESC cells, WT, input
- GSM7866215 hESC cells, WT, CTCF, ChIP rep1 hESC cells, WT, CTCF, C…
- GSM7866216 hESC cells, WT, input rep2 hESC cells, WT, input
- GSM7866217 hESC cells, WT, CTCF, ChIP rep2 hESC cells, WT, CTCF, C…
- GSM7866218 hESC cells, TUBBP2 KO, input rep1 hESC cells, TUBBP2 KO, …
- GSM7866219 hESC cells,TUBBP2 KO, CTCF, ChIP rep1
- GSM7866220 hESC cells, TUBBP2 KO, input rep2 hESC cells, TUBBP2 KO, …
- GSM7866221 hESC cells, TUBBP2 KO, CTCF, ChIP rep2
- GSM7866222 hESC cells, WT rep1 hESC cells, WT
- GSM7866223 hESC cells, WT rep2 hESC cells, WT
- GSM7866224 hESC cells, TUBBP2 KO rep1 hESC cells, TUBBP2 KO
- GSM7866225 hESC cells, TUBBP2 KO rep2 hESC cells, TUBBP2 KO
- GSM7866226 hESC cells, ALOX KO rep1 hESC cells, ALOX KO
- GSM7866227 hESC cells, ALOX KO rep2 hESC cells, ALOX KO
- GSM7866228 hESC cells, WT-KRT18P37 rep1
- GSM7866229 hESC cells,WT-KRT18P37 rep2
- GSM7866230 hESC cells, KRT18P37 KO rep1 hESC cells, KRT18P37 KO
- GSM7866231 hESC cells, KRT18P37 KO rep2 hESC cells, KRT18P37 KO
- GSM7874165 hESC cells, WT, Hi-C, rep1 hESC cells, WT, Hi-C,
- GSM7874166 hESC cells, WT, Hi-C, rep2 hESC cells, WT, Hi-C,
- GSM7874167 hESC cells, TUBBP2 KO, Hi-C rep1 hESC cells, TUBBP2 KO, …
- GSM7874168 hESC cells, TUBBP2 KO, Hi-C rep2 hESC cells, TUBBP2 KO, …
- GSE341599 CTCFL(BORIS) contributes to the transcriptional program of ovarian cancer by relaxing CTCF-mediated three-dimensional genome organization 32 samples shares three-dimensional, contribute
- GSE186599 TULIPs decorate the three-dimensional genome of PFA ependymoma 160 samples shares three-dimensional
- GSE328048 Single-cell transcriptome reveals keratinocyte subclusters that contribute to altered differentiation and inflammatory responses in atopic dermatitis 116 samples shares contribute
- GSE254942 The pluripotency factor NANOG contributes to mesenchymal plasticity and is predictive for outcome in esophageal adenocarcinoma 106 samples shares contribute
- GSE274836 Two unrelated distal genes activated by a shared enhancer benefit from localizing inside the same small topological domain 97 samples shares topological
- GSE324343 Analysis of ER stress-induced three-dimensional enhancer network in wild-type and transcription facotr-knockout HCT116 cells [ChIP-Seq] 94 samples shares three-dimensional
- GSE236415 Topological regulation of the estrogen transcriptional response by ZATT-mediated inhibition of TOP2B activity 89 samples shares topological
- GSE306993 Transcriptional and epigenetic targets of MEF2C in human microglia contribute to cellular functions related to autism risk and age-related disease. 76 samples shares contribute
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.