Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Embryo
Cell type
Embryonic gonad
NA
NA

Attributes by original data submitter

Sample

source_name
embryonic genital tubercle
strain
CD1
tissue
embryonic genital tubercle
age
E14.5
genotype
wildtype
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
After cross-linking in 1% formaldehyde in PBS for 20 minutes, tissues were rinsed and treated with trypsin for 5 min. Samples were then homogenized with a Branson 450 Sonifier (at low amplitude for 30 seconds, 100% duty cycle). The homogenates were sheared in a Bioruptor set to high for 15 cycles (30 seconds on, 30 seconds rest) to generate a chromatin size range of 150–400bp. PureProteomeTM Protein G Magnetic Beads (Millipore) were pre-incubated with 5 μg anti-ISL1 rabbit monoclonal antibody (Abcam #EP4182), and the beads were incubated overnight with 500 μg of the sheared E14.5 GT chromatin. After washing, immune complexes were eluted from the beads, and protein-DNA crosslinks were reversed by incubating at 65 °C overnight. After treatment with RNase followed by Proteinase K, samples were purified over MicroChIP DiaPure columns (Diagenode, Inc.). All ChIP and input chromatin control libraries were produced using the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs, #E7645S) as directed by the manufacturer. Libraries were sequenced at the Georgia Genomic Facility on an Illumina NextSeq 500 to produce 75bp SE reads.

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
63369916
Reads aligned (%)
97.4
Duplicates removed (%)
12.7
Number of peaks
569 (qval < 1E-05)

mm9

Number of total reads
63369916
Reads aligned (%)
97.2
Duplicates removed (%)
12.6
Number of peaks
665 (qval < 1E-05)

Base call quality data from DBCLS SRA