Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Embryo
Cell type
Embryonic liver
NA
NA

Attributes by original data submitter

Sample

source_name
embryonic fetal liver
strain background
C57Bl/6
genotype/variation
Pcl2 -/-
developmental stage
E14.5
tissue source
embryonic fetal liver
sorted fraction
Ter119minus; CD71+Ter119-/lo
chip antibody
Rabbit IgG
chip antibody vendor
Santa Cruz

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
FL cells from e14.5 Pcl2+/+ and Pcl2-/- mice were isolated and CD71+Ter119-/lo and CD71+Ter119high fractions were sorted using a MoFlo sorter For ChIP-seq, sorted cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature. Samples were sheared using a Covaris sonicator until DNA reached a final size of 75-700bp. 10ug of antibody (anti-Pcl2, Genway; anti-H3K27me3, Millipore) was bound to pre-blocked Protein A magnetic beads (Millipore), combined with sonicated DNA and incubated overnight. After incubation, beads were collected and DNA-antibody complexes were eluted at 65oC. Crosslinks were reversed overnight at 65oC. Samples were treated with Proteinase K and RNase A and DNA was purified using phenol-chloroform. 500,000 cells per sample were used for both IP and control (IgG, SantaCruz).

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
144955335
Reads aligned (%)
63.4
Duplicates removed (%)
57.4
Number of peaks
5708 (qval < 1E-05)

mm9

Number of total reads
144955335
Reads aligned (%)
63.2
Duplicates removed (%)
57.4
Number of peaks
6338 (qval < 1E-05)

Base call quality data from DBCLS SRA