|
| Status |
Public on Apr 01, 2024 |
| Title |
CAP-H_Halo_CDK1as(biol rep1)_CENP-A_ChIP |
| Sample type |
SRA |
| |
|
| Source name |
Bursa
|
| Organism |
Gallus gallus |
| Characteristics |
tissue: Bursa
cell line: DT40
cell type: lymphoblast
Sex: female
chip antibody: custome made anti CENP-A antibody
|
| Treatment protocol |
asynchronous growth mainting the concentration between 0.2-1 X10^6/ml
|
| Growth protocol |
DMEM, 10% FBS, 1% Chicken serum, betamercaptoethanol, penicillin and streptmycin. Cells were culutured at 38C at 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
A nuclear fraction of cells was digested with MNase and solubulised with 0.5M NaCl. CENP-A containing nucleosomes were immunoprecipitated with custom-made CENP-A antibody.
ChIP-seq libraries were prepared either using NEBNext Ultra II prep (WT, SMC2, SMC3) or KAPA Hyper prep (CAP-H, CAP-H2).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
101 bp x 101 bp
|
| Data processing |
Remove adapters with Cutadapt-1.18 --minimum-length 20 --nextseq-trim=20
Align to galGal7b reference with bwa mem
Convert to coverage file with deeptools bamCoverage -bs 1 --normalizeUsing BPM
Assembly: GRCg7b
Supplementary files format and content: BigWig
|
| |
|
| Submission date |
Jan 25, 2024 |
| Last update date |
Apr 01, 2024 |
| Contact name |
Shaun Michael Webb |
| E-mail(s) |
shaun.webb@ed.ac.uk
|
| Organization name |
University of Edinburgh
|
| Department |
Wellcome Trust Centre for Cell Biology
|
| Lab |
Bioinformatics Core Facility
|
| Street address |
2.21 Swann Building, Kings Buildings
|
| City |
Edinburgh |
| ZIP/Postal code |
EH9 3JR |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL26853 |
| Series (2) |
| GSE254181 |
Centromeric chromatin in mitosis reorganizes into a functional structure stabilized by cohesin [CENPA-ChIP-seq] |
| GSE254182 |
Centromeric chromatin in mitosis reorganizes into a functional structure stabilized by cohesin |
|
| Relations |
| BioSample |
SAMN39610094 |
| SRA |
SRX23389019 |
