|
| Status |
Public on Jul 09, 2013 |
| Title |
GBD5_TSA_AcH2B_ChIPseq |
| Sample type |
SRA |
| |
|
| Source name |
TSA_AcH2B_ChIPseq
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57/DBA F1 hybrid
gender: female
age: 3 month
treatment group: Trichostatin A (TSA) 2.4 mg/kg
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 Genome Analyzer II |
| |
|
| Description |
processed data file: gbd5_X_SICER-W200-G600-E10-islandfiltered.wig.normalized.wig
Sample 3
|
| 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 (https://github.com/rgejman/wigreader). 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 |
GPL9250 |
| 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 |
|
| Relations |
| SRA |
SRX216301 |
| BioSample |
SAMN01886020 |
