Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Ctcf

Cell type

Cell type Class
Embryo
Cell type
Hindlimb
MeSH Description
Either of two extremities of four-footed non-primate land animals. It usually consists of a FEMUR; TIBIA; and FIBULA; tarsals; METATARSALS; and TOES. (From Storer et al., General Zoology, 6th ed, p73)

Attributes by original data submitter

Sample

source_name
Embryonic Limb Bud
tissue
hindlimb
developmental stages
E10.5
strain
CD1
chip antibody
CTCF (Active motif: 613111)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. 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 30μg for CTCF and RAD21 ChIP. ChIP for H3K4me1 (Abcam: 8898), H3K4me3 (Milipore: 07-473), H3K27Ac (Diagenode: C1540174), H3K27me3 (Milipore: 07-449), CTCF (Active motif: 613111) and RAD21 (Abcam: ab992) was then performed as in Lee et al., 2006. Libraries were prepared using the Nextera adaptors and sequenced.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
26906445
Reads aligned (%)
95.0
Duplicates removed (%)
76.3
Number of peaks
30091 (qval < 1E-05)

mm9

Number of total reads
26906445
Reads aligned (%)
94.7
Duplicates removed (%)
76.5
Number of peaks
30013 (qval < 1E-05)

Base call quality data from DBCLS SRA