Cell type-specific loops linked to RNA polymerase II elongation in human neural differentiation
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 27 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
- 27 samples: 21 distinct titles, 3 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.
- Paper
- Cell-type-specific loops linked to RNA polymerase II elongation in human neural differentiationCell genomics · 2024
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 GSE220103_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 PRJNA908804 and SRA study SRP411365. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 27 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.
- GSM6788424 NPC_HiC
- GSM6788425 iPSC_HiC
- GSM6788426 NPC_RNAPII_IP
- GSM6788427 iPS_RNAPII_IP
- GSM6788428 NPC_RNAPII_Input
- GSM6788429 iPS_RNAPII_Input
- GSM6788430 NPC_H3K27ac_IP
- GSM6788431 iPSC_H3K27ac_IP
- GSM6788432 NPC_CTCF_IP
- GSM6788433 iPS_CTCF_IP
- GSM6788437 NPC_CTCF_H3K27ac_Input
- GSM6788438 iPSC_CTCF_H3K27ac_Input
- GSM7688212 Neuron_HiC
- GSM7688213 Neuron_RNAPII_IP
- GSM7688214 Neuron_RNAPII_Input
- GSM7688215 Neuron_H3K27ac_IP
- GSM7688216 Neuron_CTCF_IP
- GSM7688217 Neuron_CTCF_H3K27ac_Input
- GSM7699780 iPSC_RNAseq, rep1
- GSM7699781 iPSC_RNAseq, rep2
- GSM7699782 iPSC_RNAseq, rep3
- GSM7699783 NPC_RNAseq, rep1
- GSM7699784 NPC_RNAseq, rep2
- GSM7699785 NPC_RNAseq, rep3
- GSM7699786 Neuron_RNAseq, rep1
- GSM7699787 Neuron_RNAseq, rep2
- GSM7699788 Neuron_RNAseq, rep3
- GSE220318 Splicing Factor RBM22 Broadly Affects RNA Polymerase II 5' Pausing, Elongation Rate and Termination and Prevents Genome Instability 70 samples shares polymerase, elongation
- GSE265883 Tripartite phosphorylation of SPT5 by CDK9 times pause release and tunes elongation rate of RNA polymerase II (CUT&RUN) 68 samples shares polymerase, elongation
- GSE280208 A CDK11-dependent RNA polymerase II pause-release checkpoint precedes CDK9-mediated transition to transcriptional elongation [ChIP-Seq] 33 samples shares polymerase, elongation
- GSE228346 The TFIIH kinase CDK7 governs RNA polymerase II initiation, elongation, termination, and RNA processing 30 samples shares polymerase, elongation
- GSE306294 An RNA polymerase III tissue and tumor atlas uncovers context-specific activities linked to 3D epigenome regulatory mechanisms 24 samples shares polymerase, linked
- GSE273681 NDF-FACT phase separation condensates are required for RNA Polymerase II transcription elongation through chromatin [RNA-Seq] 12 samples shares polymerase, elongation
- GSE280113 Progenitor effects and unique transcriptomic signatures linked to differentiation phenotype in clonally expanded antigen-specific CD8 T memory stem cells (TSCM) 509 samples shares linked
- GSE283619 Single-cell multi-omics analysis identifies metabolism-linked epigenetic reprogramming as a driver of therapy-resistant medulloblastoma [Multiome] 30 samples shares linked
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.