Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Embryo
Cell type
Embryonic erythroblasts
NA
NA

Attributes by original data submitter

Sample

source_name
Fetal Liver
genotype/variation
hemagglutinin-Klf1 (KLF1 is hemagglutinin-tagged)
developmental stage
E13.5
cell markers
Ter119-CD71- and and Ter119-CD71+
chip antibody
none (input)
tissue
liver
cell type
erythroid progenitor

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Library construction was performed using the Illumina ChIP-Seq library preparation kit according to the standard protocol. ChIP-Seq fragments were separated on an agarose gel, and fragments of approximately 200 bp were ligated to Illumina-specific adapters to generate libraries. Six cycles of PCR amplification were used to select for fragments containing both Illumina-specific adapters before bead-based elimination of unligated adapters. ChIP enrichment of HA-EKLF-bound chromatin obtained from fetal liver progenitors and erythroblasts was performed as previously described.9,27,34 Chromatin was processed using the Magna ChIP A kit (#17-610; Millipore) according to the manufacturer’s instructions. Chromatin was immunoprecipitated with monoclonal antibodies against HA (F-7, sc-7329X, Santa Cruz Biotechnology). As a background genomic control, sheared chromatin from E13.5 HA-EKLF fetal liver cells was processed in parallel, minus incubation with the antibodies. Fetal livers were dissociated to single- cell suspension and stained with anti-CD71–FITC and anti-Ter119–PE antibodies (BD Biosciences PharMingen). Cell populations were isolated using a FACSAria flow cytometer running FACSDiva 6.1.3 software (BD Biosciences). Cells were collected as erythroid progenitors (Ter119-CD71- and Ter119-CD71+) or erythroblasts (Ter119+CD71+). At least 3 indepen- dent cell sorts for each population were performed.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

mm10

Number of total reads
12247608
Reads aligned (%)
90.1
Duplicates removed (%)
36.7
Number of peaks
457 (qval < 1E-05)

mm9

Number of total reads
12247608
Reads aligned (%)
89.5
Duplicates removed (%)
36.6
Number of peaks
706 (qval < 1E-05)

Base call quality data from DBCLS SRA