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Sample GSM1062438 Query DataSets for GSM1062438
Status Public on Jul 09, 2013
Title GBD20_Veh_AcH4K12_ChIPseq
Sample type SRA
Source name Veh_AcH4K12_ChIPseq
Organism Mus musculus
Characteristics strain: C57/DBA F1 hybrid
gender: female
age: 3 month
treatment group: vehicle; DMSO/Saline solution (1:4)
tissue: hippocampus
chip antibody: AcH4K12; Anti-Histone H4 (acetylated) (acetyl K12) antibody
chip antibody vendor: abcam
chip antibody cat. #: ab46983
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 11
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 SRX216309
BioSample SAMN01886028

Supplementary file Size Download File type/resource
GSM1062438_gbd20_X_SICER-W200-G600-FDR.00000001-islandfiltered.wig.normalized.wig.gz 21.0 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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