Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
GATA1

Cell type

Cell type Class
Blood
Cell type
Erythroid progenitors
NA
NA

Attributes by original data submitter

Sample

source_name
erythroid progenitors (E-Prog)
cell type
human HSPC-derived early erythroid progenitors
tissue
Human umbilical cord blood
antibody
GATA1 (ab11852, Abcam)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin from E-Prog and E-Prec was prepared after cross-linking for 10' at RT with 1% formaldehyde-containing medium. Nuclear extracts were sonicated using the Bioruptor Pico Sonication System (Diagenode) to obtain DNA fragments around 150-200 bp in length. For histone modifications, chromatin obtained from 107 cells was immunoprecipitated overnight with 10 µg of antibody. For transcription factors, chromatin obtained from 3x107 cells was immunoprecipitated overnight with 30 µg of antibody. ChIP assay was performed as previously described (Romano, Sci Reports, 2016; Cui et al., 2009). ChIP-seq libraries for E-Prog and E-Prec were prepared from 1 ng of immunoprecipitated DNA (IP) and 5 ng of control DNA (Input: non-immunoprecipitated chromatin fragments) following the Diagenode Microplex Library preparation kit. Libraries were checked by capillary electrophoresis by Tape Station Agilent with the High sensitivity D1000 assay and quantified by Real Time q-PCR using the kit from KAPA Biosystems (Roche). Each library was sequenced in one MiSeq Illumina RUN and 50 bp single-end reads were generated.

Sequencing Platform

instrument_model
Illumina MiSeq

hg19

Number of total reads
24757963
Reads aligned (%)
67.8
Duplicates removed (%)
25.4
Number of peaks
9927 (qval < 1E-05)

hg38

Number of total reads
24757963
Reads aligned (%)
69.1
Duplicates removed (%)
24.5
Number of peaks
9759 (qval < 1E-05)

Base call quality data from DBCLS SRA