GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1062432 Query DataSets for GSM1062432
Status Public on Jul 09, 2013
Title GBD22_naïve_AcH2B_ChIPseq
Sample type SRA
Source name naïve_AcH2B_ChIPseq
Organism Mus musculus
Characteristics strain: C57/DBA F1 hybrid
gender: female
age: 3 month
treatment group: Naïve
tissue: hippocampus
chip antibody: AcH2B (in-house made rabbit whole antiserum)
Treatment protocol Experiments were performed in 3 month old animals and in all cases the mice used as control were littermates of the treated mice. Trichostatin A (TSA) 2.4 mg/kg in DMSO/Saline solution (1:4) was administered by intraperitoneal injection. The brains were removed 30 min after treatment, and hippocampi rapidly dissected, minced in small pieces and crosslinked by addition of 1/10 volume of fresh 11% formaldehyde solution.
Growth protocol Mice were C57/DBA F1 hybrid. Mice were group-housed in single-sex cages on a light:dark cycle (12/12 h) with food and water available ad limitum.
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to standard Illumina's protocols and sequenced on the Genome Analyzer II or HiSeq2000 following the manufacturer's protocols.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
Description Sample 5
Data processing Basecalls performed using: GAPipeline-1.0rc4 (GA-II) (samples 1-3) (Read size: 32 bp), CASAVA version 1.8.2 (HiSeq2000) (Samples 4-15) (Read size: 50 bp)
ChIP-seq reads were aligned to the mm9 genome assembly using BWA version 0.5.9. BWA was used to map reads with a maximun of 2 mismatches in the first 32 bases of the sequences, and a maximun of n mismatches in total.
To subset uniquelly mapped reads, the produced BAM files where then parsed using the SAMTOOLS and all mapped with a mapping quality greater than 0 were exported.
Peaks were called using SICER version 1.1 (program settings are described in the methods sections of the manuscript).
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using IGV tools and normalized by using Wigreader library ( Scores represent normalized (RPM) read density.
Submission date Jan 11, 2013
Last update date Sep 16, 2019
Contact name Angel Barco
Organization name Instituto de Neurociencias (UMH-CSIC)
Street address Av. Santiago Ramón y Cajal
City Sant Joan d'Alacant
State/province Alicante
ZIP/Postal code 03550
Country Spain
Platform ID GPL13112
Series (2)
GSE43439 Genomic topography of HDACi-induced hyperacetylation of hippocampal chromatin [ChIP-Seq]
GSE44868 Genomic targets, and histone acetylation and gene expression profiling of neural HDAC inhibition
SRA SRX216303
BioSample SAMN01886022

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data not provided for this record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap