|
| Status |
Public on Aug 17, 2015 |
| Title |
H4K12ac ChIP-Seq (Sample 15) |
| Sample type |
SRA |
| |
|
| Source name |
Neuronal nuclei from 10 month old APP/PS1-21 SAHA-treated animals
|
| Organism |
Mus musculus |
| Characteristics |
cellular population: neuronal
strain: Tg(Thy1-APPSw,Thy1-PSEN1*L166P)21Jckr
chip antibody: Anti-Histone H4 (acetyl K12) antibody (Abcam, catalog# ab61238, lot# GR38757-5)
age: 10 months
genotype: APP/Ps1-21 transgenic
drug treatment: SAHA: (18g cyclodextrin + 0.67g SAHA)/L water
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were fixed, extracted in RIPA buffer, and sonicated to achieve an average fragment size of ~300bp. For ChIP 0.5µg of antibody were used with 500ng of chromatin
Libraries were constructed according to standard Illumina protocols using NEB's kits Ultra DNA Library Prep Kit (Ref: E7370L) and Multiplex Oligos for Illumina Index Primer Set (E7335L)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8.2
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2 with default options
Coverage was calculated from -2000 to +2000 from the TSS of all genes using the function coverage within R's package Iranges
Coverage was normalized to total aligned read counts in the library
Genome_build: mm10
Supplementary_files_format_and_content: Normalized coverage files
|
| |
|
| Submission date |
Dec 08, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Eva Benito Garagorri |
| E-mail(s) |
eva.benito@dzne.de
|
| Organization name |
DZNE Goettingen
|
| Department |
Epigenetics of Aging
|
| Lab |
Andre Fischer
|
| Street address |
Von Siebold Strasse 3A
|
| City |
Goettingen |
| State/province |
Niedersachsen |
| ZIP/Postal code |
37075 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE63942 |
Genome-wide analysis of H4K12 acetylation in neuronal and non-neuronal nuclei in young animals treated with vehicle, WT littermates of APP/PS1-21 animals treated with vehicle and aged and APP/PS1-21 animals treated with oral vehicle or SAHA for 4 weeks |
| GSE63945 |
Reinstating transcriptome plasticity and memory function in mouse models for cognitive decline |
|
| Relations |
| BioSample |
SAMN03254980 |
| SRA |
SRX799001 |
