Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K27me3

Cell type

Cell type Class
Kidney
Cell type
Podocytes
MeSH Description
Highly differentiated epithelial cells of the visceral layer of BOWMAN CAPSULE of the KIDNEY. They are composed of a cell body with major CELL SURFACE EXTENSIONS and secondary fingerlike extensions called pedicels. They enwrap the KIDNEY GLOMERULUS capillaries with their cell surface extensions forming a filtration structure. The pedicels of neighboring podocytes interdigitate with each other leaving between them filtration slits that are bridged by an extracellular structure impermeable to large macromolecules called the slit diaphragm, and provide the last barrier to protein loss in the KIDNEY.

Attributes by original data submitter

Sample

source_name
Terminally Differentiated Podocyte
cell type
Immortalized Mouse Podocyte
passage
23-28
chip antibody
H3K27me3 (Cell Signaling, 9733S, Lot 8)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were processed using Magna ChIP™ A - Chromatin Immunoprecipitation Kit, Millipore,Cat No. 7-408, Lot No.2500615 to obtain the Chip DNA using H3K27me3 antibody Libraries from the immunoprecipitated and whole cell lysate DNA were prepared using the NEBNext® ChIP-Seq Library Prep Reagent Set for Illumina (NEB, Cat. No. E6200S). In brief, immunoprecipitated DNA was first end-repaired, followed by a dA-Tailing of End Repaired DNA using NEBNext dA-Tailing reaction mixture (NEB, Cat No. E6053), and ligated to custom adapters with NEBNext adaptor (NEB E7500) having Oligos for Illumina. Fragments of 150 to 700 (+120 bp) bp of adaptor-ligated DNA were size-selected using AMPure XP Beads followed by ligation-mediated PCR amplification of the adaptor-ligated DNA using Phusion DNApolymerase.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
17759255
Reads aligned (%)
80.3
Duplicates removed (%)
1.9
Number of peaks
1463 (qval < 1E-05)

mm9

Number of total reads
17759255
Reads aligned (%)
80.2
Duplicates removed (%)
1.9
Number of peaks
1452 (qval < 1E-05)

Base call quality data from DBCLS SRA