Genome-wide quantitative enhancer activity maps identified by STARR-seq
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 18 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
- 18 samples: 6 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 GSE40739_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 PRJNA175267 and SRA study SRP015758. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 6 replicated groups read from 18 sample titles; they account for 12 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.
- GSM1000400 S2 STARR-seq biological replicate 1 S2 STARR-seq
- GSM1000401 S2 STARR-seq biological replicate 2 S2 STARR-seq
- GSM1000402 OSC STARR-seq biological replicate 1 OSC STARR-seq
- GSM1000403 OSC STARR-seq biological replicate 2 OSC STARR-seq
- GSM1000404 STARR-seq Input library 5.2
- GSM1000405 STARR-seq Input library 500
- GSM1000406 S2 DHS-seq biological replicate 1 S2 DHS-seq
- GSM1000407 S2 DHS-seq biological replicate 2 S2 DHS-seq
- GSM1000408 S2 DHS-seq Input
- GSM1000409 OSC DHS-seq biological replicate 1 OSC DHS-seq
- GSM1000410 OSC DHS-seq biological replicate 2 OSC DHS-seq
- GSM1000411 OSC DHS-seq Input
- GSM1000412 S2 RNA-seq biological replicate 1 S2 RNA-seq
- GSM1000413 S2 RNA-seq biological replicate 2 S2 RNA-seq
- GSM1000414 OSC RNA-seq biological replicate 1 OSC RNA-seq
- GSM1000415 OSC RNA-seq biological replicate 2 OSC RNA-seq
- GSM1055604 HeLa_BAC_STARRseq
- GSM1055605 HeLa_BAC_STARRseq_input
No close match found for this topic, so these are simply the most-viewed datasets of the same kind.
- GSE31332 Genomic maps of lincRNA occupancy reveal principles of RNA-chromatin interactions. 14 samples
- GSE296812 Histone modification clocks for robust cross-species biological age prediction and elucidating senescence regulation 46 samples
- GSE267892 TBP bookmarks and preserves neural stem cell fate memory by orchestrating local chromatin architecture (CUT&Tag) 32 samples
- GSE223117 Conserved intronic secondary structures with concealed branch sites regulate alternative splicing of poison exons 29 samples
- GSE284058 Histone H4 lysine 20 monomethylation is not a mark of transcriptional silencers 16 samples
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.