Experiment / E039Q7IUXOther

ChIP-STARR-seq enhancer activity in naive H9 human embryonic stem cells

Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells

This experiment summarizes ChIP-STARR-seq activity measured in naive H9 hESCs using STARR-seq plasmid libraries generated from naive H9 chromatin, including H3K27ac, H3K4me1, NANOG, OCT4, and input-enriched libraries. For each hg19 scaffold region, the processed RPP value is the region-level activity reported in Table S2, and the table retains both active and inactive regions for comparative enhancer analysis.

Download processed table (CSV)Raw source data API documentation

Processed tables are specific to each experiment. Column names, units, measurements, and table structure are not standardized across the database. Check this experiment’s column definitions and quality-control notes before comparing or combining data.

Organism: Human
Taxonomy ID: NCBITaxon:9606
Biosample: CVCL:9773
Reference genome: GRCh37/hg19
Design focus: Region-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Naive-state induction and maintenance in NHSM medium for more than 10 passages, with LIF, bFGF, TGF-beta1, PD0325901, CHIR99021, SP600125, SB203580, Y-27632, and G06983

Activity is reads per plasmid (RPP), the DESeq2-normalized RNA/plasmid DNA ratio. Replicate RPP values were averaged at matched plasmid positions and the maximum observed value per region was used; the source table aggregates libraries across ChIP targets. The paper used Skewer trimming, Bowtie2 --very-sensitive alignment, and retained properly paired, concordantly aligning, uniquely mapping fragments with MAPQ >= 30. RPP >= 138 was the paper's active-enhancer threshold. Naive libraries were transfected into naive cells for this condition; related naive-library/primed-cell comparison datasets are deposited in GEO but are not represented by this condition-specific table.

ChIP-STARR-seq: ChIP-enriched genomic DNA fragments were cloned en masse into the transcription unit of an episomal STARR-seq plasmid downstream of a minimal promoter and upstream of a poly(A) signal. Transfected H9 cells were enriched by GFP FACS and reporter RNA was sequenced with paired-end reads.

Processed data

50 rows per page. Click a cell to inspect its full value.

Visible columns (12 of 12)

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Page 1 · 50 rows · More results available

Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.

Column dictionary · 12 definitions

element_id: Coordinate-derived region identifier in the form chromosome:start-end.
chromosome: Human hg19 chromosome reported for the scaffold region.
start: Reported hg19 scaffold-region start coordinate.
end: Reported hg19 scaffold-region end coordinate.
oct4: Count of OCT4 ChIP-seq peak calls overlapping the region in the source table.
nanog: Count of NANOG ChIP-seq peak calls overlapping the region in the source table.
h3k27ac: Count of H3K27ac ChIP-seq peak calls overlapping the region in the source table.
h3k4me1: Count of H3K4me1 ChIP-seq peak calls overlapping the region in the source table.
rpp: Naive-cell reads-per-plasmid enhancer activity value from Table S2.
log2_rpp: Derived log2 transform of rpp.
active_enhancer: Binary activity call: 1 when rpp >= 138, otherwise 0, following the paper.
activity_class: Active or Inactive classification using the paper's RPP >= 138 threshold.

Quality control

The paper removed ENCODE-blacklisted overlaps from ChIP/plasmid peak sets, required properly paired and uniquely mapping fragments with MAPQ >= 30, normalized matched plasmid/RNA libraries with DESeq2, and assessed replicate concordance. For this packaged table, rows with missing RPP Naive were excluded (2,478 rows); all 359,880 remaining positive RPP measurements passed the source table's condition-specific QC. The RPP >= 138 enhancer call is a biological activity classification, not an additional QC filter.

Curation notes

H9 is the female WA09 embryonic stem-cell line (Cellosaurus CVCL:9773). The paper's naive culture state is a treatment/culture perturbation rather than a genetic perturbation. This is a region-focused ChIP-STARR-seq enhancer screen, not an allele-comparison MPRA; no variant alleles or rs identifiers are produced. RPP Naive was transcribed from the Table S2 workbook's RPP Naive column.

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