Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
FOS

Cell type

Cell type Class
Uterus
Cell type
Myometrium
MeSH Description
The smooth muscle coat of the uterus, which forms the main mass of the organ.

Attributes by original data submitter

Sample

source_name
Uterine muscle tissue
tissue
Myometrium
chip antibody
FOS (Millipore, cat # 06-341)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Myometrium and leiomyoma tissue samples were cryopulverized into a fine powder and immediately formaldehyde cross-linked with 1% formaldehyde for 10min at room temperature with rotation and then quenched with 0.15M glycine for 10min at room temperature with rotation. Cross-linked tissue samples were dounce homogenized in ChIP lysis buffer 1 (50mM HEPES-KOH [pH 7.6], 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% IGEPAL CA-630, 0.25% Triton X-100, 1X Protease inhibitor cocktail [Roche, cat # 4693132001]) followed by end-over-end rotation at 4°C for 15min and then low speed centrifugation at 4°C. Samples were resuspended in ChIP lysis buffer 2 (10mM Tris-HCl [pH 8.0], 200mM NaCl, 1mM EDTA, 0.5mM EGTA, 1X Protease inhibitor cocktail [Roche, cat # 4693132001]) followed again by end-over-end rotation at 4°C for 15min and sample recovery by low speed centrifugation at 4°C. Samples were then resuspended in MNase digestion buffer (20mM Tris-HCl [pH 8.0], 150mM NaCl, 2mM EDTA, 1% Triton X-100, 0.1% SDS, 125U MNase [Worthington, cat # LS004798]) and incubated at 37°C until 75% mononucleosomal chromatin profile is observable by gel electrophoresis of purified MNase digested DNA. Digestion was quenched with MNase quenching buffer (10mM EDTA, 20mM EGTA) after which samples were briefly sonicated (Misonix, setting 6 [~6 W power output], 3 cycles of 15sec on and 45sec off). Collagen and cell debris was removed by centrifugation at 20,000 x g at 4°C for 20min. Solubilized chromatin was incubated overnight with antibody at 4°C with end-over-end rotation. KAPA Hyper Prep kit (Kapa Biosystems, cat # KK8502) was used for end-repair, A-tailing, and adapter ligation with TruSeq index adapters, all according to manufacturer's instructions. A 1.1X-1.8X AMPure XP bead (Beckman Coulter, cat # A63881) size selection was carried out after adapter ligation to enrich for sub-nucleosomal DNA fragments followed by 10-12 cycles of PCR amplification. For H3K27Ac ChIP, a 0.6X-1.0X AMPure XP bead size selection was performed to enrich for mono-nucleosomal DNA fragments.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
15644035
Reads aligned (%)
87.2
Duplicates removed (%)
7.8
Number of peaks
3323 (qval < 1E-05)

hg38

Number of total reads
15644035
Reads aligned (%)
88.4
Duplicates removed (%)
7.0
Number of peaks
3285 (qval < 1E-05)

Base call quality data from DBCLS SRA