|
| Status |
Public on Jul 29, 2019 |
| Title |
XBP1 ChIPseq in AtT-20 cells |
| Sample type |
SRA |
| |
|
| Source name |
AtT-20 cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: pituitary corticotroph cell
passages: 17
cell line: AtT-20
chip antibody: XBP1 M-186 Santa Cruz (Sc-7160)
|
| Growth protocol |
AtT-20 cells were plated on adherent culture dishes to obtain about 70% confluence after 3 days. They are cultured in DMEM + 10% FBS.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei lysates were sonicated and protein-DNA complexes were isolated with specific antibodies. Fragments of 200-400bp were kept for library preparation
The libraries and flowcells were prepared at the IRCM Molecular Biology Core facility following Illumina recommendations (Illumina, San Diego, CA) and then sequenced on Hiseq 2000 at the Génome Québec Innovation Centre.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
normal (non Tg) AtT-20 cells
|
| Data processing |
Sequence reads were trimmed for adapter sequences.
The resulting 36bp (XBP1) or 50bp (flag-Creb3l2) reads were trimmed to obtain high quality reads and then mapped to the mm9 mouse genome build using Bowtie with the following parameter: -t -p 4 --trim5 1 --best mm9 –S
Peaks were identified by comparing Creb3I2 to flag ( GSM2324113) and XBP1 to IgG (GSM2324114) using MACS callpeak function with the parameters: --bw 250 -g mm --mfold 7,20 -p 1e-5 ; the parameter -f BAMPE was added for Creb3I2
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files were generated using HOMER
Supplementary_files_format_and_content: Text files were generated with MACS peak caller
|
| |
|
| Submission date |
Jun 06, 2019 |
| Last update date |
Jul 29, 2019 |
| Contact name |
Amandine Bemmo |
| E-mail(s) |
[email protected]
|
| Organization name |
IRCM
|
| Lab |
Dr. Drouin
|
| Street address |
110 Avenue des Pins
|
| City |
Montreal |
| State/province |
QC |
| ZIP/Postal code |
H2W 1R7 |
| Country |
Canada |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE132320 |
Cell-autonomous transcriptional mechanism for enhancement of translation capacity in secretory cells [ChIP-Seq] |
| GSE132324 |
Cell-autonomous transcriptional mechanism for enhancement of translation capacity in secretory cells |
|
| Relations |
| BioSample |
SAMN11970555 |
| SRA |
SRX5982666 |
