|
| Status |
Public on Apr 01, 2024 |
| Title |
WT_CDK1as_CAP-H-Halo_30min(biol rep2)_ChIP-Seq |
| Sample type |
SRA |
| |
|
| Source name |
Bursa
|
| Organism |
Gallus gallus |
| Characteristics |
tissue: Bursa
cell line: DT40
cell type: lymphoblast
time: 30 min
chip antibody: Halo-Trap Agarose affinity beads (Chromotek #ota)
|
| Treatment protocol |
Cells were blocked at G2 with 1NMPP1 (G2). After 1NMPP1 washout, cells were collected at 5 min (early prophase), 7.5 min (late prophase), and 30 min (late prometaphase).
|
| Growth protocol |
RPMI1640, 10% FBS, 1% Chicken serum. Cells were culutured at 39C at 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 1% formaldehyde for 10 minutes. After quenchng and cell lysis, chromatin was shear using Diagenode Biorupter.
ChIP-seq libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB #E7645) AND NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1) (NEB #E7335). 15ng of template was used for library preparation for input and IP samples and amplified using 11 cycle on the thermocycler. Libraries were size selected at 200bp to 500bp length range using SPRIselect bead from Beckman Coulter. Purified libraries were analysed by Agilent 2100 Bioanalyzer by using Agilent High Sensitivity DNA Kit (#5067-4626).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
Normalise ChIP/Input with bamCompare -bs 20 --normalizeUsing BPM --exactScaling
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 |
GPL32831 |
| Series (2) |
| GSE254180 |
Centromeric chromatin in mitosis reorganizes into a functional structure stabilized by cohesin [Halo-ChIP-seq] |
| GSE254182 |
Centromeric chromatin in mitosis reorganizes into a functional structure stabilized by cohesin |
|
| Relations |
| BioSample |
SAMN39605716 |
| SRA |
SRX23388988 |
