Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Epitope tags

Cell type

Cell type Class
Uterus
Cell type
Endometriotic lesions
NA
NA

Attributes by original data submitter

Sample

source_name
Endometriotic Lesions
strain
C57BL/6
gender
female
tissue
lesion
chip antibody
FLAG M2 agarose (Sigma, A2220)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Tissue was submersed in PBS + 1% formaldehyde, cut into small pieces and incubated at room temperature for 15 minutes. Fixation was stopped by the addition of 0.125 M glycine. The tissue pieces were then treated with a TissueTearer and spun down and washed 2x in PBS. Chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. For each ChIP reaction, 50 ug of precleared chromatin was mixed with Flag M2 Agarose and incubated for 3 hr. Immune complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on NextSeq 500.

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
55515746
Reads aligned (%)
97.3
Duplicates removed (%)
23.0
Number of peaks
18891 (qval < 1E-05)

mm9

Number of total reads
55515746
Reads aligned (%)
97.2
Duplicates removed (%)
23.1
Number of peaks
18892 (qval < 1E-05)

Base call quality data from DBCLS SRA