|
| Status |
Public on Jun 22, 2022 |
| Title |
cells_water_H3K27ac_2 |
| Sample type |
SRA |
| |
|
| Source name |
hippocampus
|
| Organism |
Mus musculus |
| Characteristics |
tissue: hippocampus
cell type: isolated hippocampal cells
chip antibody: H3K27ac (Abcam, #ab4729)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tagmented DNA was extracted using MinElute PCR Purification Kit (Qiagen, # 28004)
Library preparation was conducted according to the protocol using Nextera primers (Illumina, #FC-131-2001) and post-PCR clean-up using SPRI bead slurry (Beckmann Coulter, #B23317).
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
cells water H3K27ac
|
| Data processing |
Libraries were sequenced on an Illumina HiSeq 4000 sequencer as paired-end 100 base reads. Image analysis and base calling were performed using RTA version 2.7.7 and bcl2fastq version 2.20.0.422.
Data were preprocessed with Cutadapt (Martin 2011) v1.18 to trim adapter sequences (Nextera Transposase Sequence) from 3’ end of reads. Cutadapt was used with the following parameters ‘-a CTGTCTCTTATA -A CTGTCTCTTATA -m 25:25’. Reads were mapped to Mus musculus genome (assembly mm10) using Bowtie2 (Langmead and Salzberg 2012) v2.2.8 with default parameters except for “–end-to-end –very-sensitive –no-mixed –no-discordant -I 10 -X 700”.
Assembly: mm10
Supplementary files format and content: BigWig files were generated using Homer (Heinz et al. 2010) makeUCSCfile v4.11.0 with default parameters except for “-norm 10e6 -fragLength 200”.
|
| |
|
| Submission date |
Apr 04, 2022 |
| Last update date |
Oct 27, 2023 |
| Contact name |
David Blum |
| E-mail(s) |
[email protected]
|
| Organization name |
Inserm
|
| Department |
Lille Neurosience & Cognition
|
| Lab |
Alzheimer & Tauopathies
|
| Street address |
1 place de Verdun
|
| City |
Lille |
| State/province |
Cedex |
| ZIP/Postal code |
59045 |
| Country |
France |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE167123 |
Genomewide effects of regular caffeine intake on hippocampal metabolism and learning-dependent transcription |
| GSE200156 |
Genomewide effects of regular caffeine intake on hippocampal metabolism and learning-dependent transcription [Cut & Tag] |
|
| Relations |
| BioSample |
SAMN27293877 |
| SRA |
SRX14733292 |
