Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Rad21

Cell type

Cell type Class
Embryo
Cell type
Embryonic limb
NA
NA

Attributes by original data submitter

Sample

source_name
Limb
genotype
deltaCTCF i4i5ZRS
embryonic stage
Embryonic day 10.5
strain
G4
chip antibody
Rad21 (Abcam:ab992)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Histone modifications were immunoprecipitated with the respective antibody (Lee et al., 2006, Jerkovic et al., 2017) and trascription factor ChIPs were performed with the iDeal ChIP-seq kit for Transcription Factors (Cat. No. C01010055) according to guidelines. We sheared chromatin using Bioruptor until reaching a fragment size of 200-500bp. 10-15μg of chromatin was then used for each replicate chromatin modification ChIP and 20μg for CTCF and RAD21 ChIP. ChIP for H3K27ac (Diagenode: C15410174), H3K36me3 K3K36me3 (Abcam:ab9050), CTCF (Diagenode:C15410210) and RAD21 (Abcam: ab992) was then performed as in Lee et al., 2006. Libraries were prepared using the Nextera adaptors and sequenced 50 or 75bp reads.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

mm10

Number of total reads
31400686
Reads aligned (%)
93.4
Duplicates removed (%)
23.6
Number of peaks
10286 (qval < 1E-05)

mm9

Number of total reads
31400686
Reads aligned (%)
93.3
Duplicates removed (%)
23.7
Number of peaks
10277 (qval < 1E-05)

Base call quality data from DBCLS SRA