ChIP-Atlas: SRX2512949

SRX2512949
GSM2466772: Stressed GRChIP r1; Rattus norvegicus; ChIP-Seq

Cell type Class: Neural
Cell type: Hippocampus
MeSH Description: A curved elevation of GRAY MATTER extending the entire length of the floor of the TEMPORAL HORN of the LATERAL VENTRICLE (see also TEMPORAL LOBE). The hippocampus proper, subiculum, and DENTATE GYRUS constitute the hippocampal formation. Sometimes authors include the ENTORHINAL CORTEX in the hippocampal formation.

source_name: Whole hippocampus
tissue: Whole hippocampus
gender: male
strain: Sprague-Dawley
age: 9 weeks
chip antibody: anti-GR cocktail (2µg Santa Cruz sc-1004 X, 4µl Thermo PA1-510A, 4µg Thermo PA1-511A)

library_strategy: ChIP-Seq
library_source: GENOMIC
library_selection: ChIP
library_construction_protocol: Hippocampi were fixed from fresh in 1% formaldehyde. Lysates were clarified from sonicated nuclei and GR-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.