|
| Status |
Public on Apr 01, 2024 |
| Title |
wt_M_P2_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Bursa
|
| Organism |
Gallus gallus |
| Characteristics |
tissue: Bursa
cell line: DT40
cell type: lymphoblast
genotype: female (ZW)
treatment: Oligo pool 2
|
| Treatment protocol |
Cells were maintained at the concentration between 0.1-1 X10^6/ml. In order to block cells at G2, cells were treated with 2µM 1NMPP1 for 13 h. Prometaphase cells were collected at 30 min except for SMC2-AID cells which was 45 min after washout of 1NMPP1. In order to deplete either SMC2 or SMC3, 125-150 µM auxin were added for the last 3h of 1NMPP1 treatment and then after until haresting cells. Nocodazole was added in release media at 0.5 µg/ml if required. Cells were crosslinked with 1% formaldehyde for 10 min, quenched with glycine, rinced with PBS. Cell pellets were frozen down with dryice.
|
| Growth protocol |
RPMI 10% FBS, 1% Chicken serum. Cells were culutured at 39C at 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were lyse with SDS, washed, and triton X100 is used to sequester the SDS. Then genomic DNA was digedted with DpnII.
NEBNext Ultra II DNA library prep kit for Illumina protocol
NG-Capture-C. 3C library constructed above were double-hybridized with oligo pools to enrich the fragments coverirng Z or 5 centromere regions.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
150 bp x 150 bp
23_wt_M_P2
|
| Data processing |
library strategy: Capture-C
CapC-MAP was used for data processing, genomedigest was used to create a restriction site map for GRCg7b.
Target files for each oligo pool were generated with capClocation2fragment.
Reads were trimmed using cutadapt(v2.5) and mapped with bowtie(v1.2.2) CapC-MAP also uses samtools(v1.9) for processing and replicates were combined with combinereps.
Directionality analysis (min 3kb,max 250kb) used capturec-tools with captured_normalizedpileups as input and custom scripts used for plotting.
Assembly: GRCg7b
Supplementary files format and content: captured_normalizedpileup bedgraph files show piled-up intrachromosomal interaction counts for each target normalised to reads per million.
|
| |
|
| Submission date |
Jan 30, 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 |
GPL19005 |
| Series (2) |
| GSE254182 |
Centromeric chromatin in mitosis reorganizes into a functional structure stabilized by cohesin |
| GSE254659 |
Centromeric chromatin in mitosis reorganizes into a functional structure stabilized by cohesin [NG-Capture-C] |
|
| Relations |
| BioSample |
SAMN39682125 |
| SRA |
SRX23456763 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8047999_23_wt_M_captured_normalizedpileup_chrZ_11a_P2.bedGraph.gz |
20.2 Kb |
(ftp)(http) |
BEDGRAPH |
| GSM8047999_23_wt_M_captured_normalizedpileup_chrZ_14a_P2.bedGraph.gz |
18.8 Kb |
(ftp)(http) |
BEDGRAPH |
| GSM8047999_23_wt_M_captured_normalizedpileup_chrZ_17a_P2.bedGraph.gz |
15.5 Kb |
(ftp)(http) |
BEDGRAPH |
| GSM8047999_23_wt_M_captured_normalizedpileup_chrZ_20a_P2.bedGraph.gz |
17.3 Kb |
(ftp)(http) |
BEDGRAPH |
| GSM8047999_23_wt_M_captured_normalizedpileup_chrZ_23a_P2.bedGraph.gz |
15.8 Kb |
(ftp)(http) |
BEDGRAPH |
| GSM8047999_23_wt_M_captured_normalizedpileup_chrZ_26a_P2.bedGraph.gz |
16.6 Kb |
(ftp)(http) |
BEDGRAPH |
| GSM8047999_23_wt_M_captured_normalizedpileup_chrZ_29a_P2.bedGraph.gz |
16.4 Kb |
(ftp)(http) |
BEDGRAPH |
| GSM8047999_23_wt_M_captured_normalizedpileup_chrZ_2a_P2.bedGraph.gz |
18.4 Kb |
(ftp)(http) |
BEDGRAPH |
| GSM8047999_23_wt_M_captured_normalizedpileup_chrZ_32a_P2.bedGraph.gz |
16.3 Kb |
(ftp)(http) |
BEDGRAPH |
| GSM8047999_23_wt_M_captured_normalizedpileup_chrZ_36a_P2.bedGraph.gz |
12.5 Kb |
(ftp)(http) |
BEDGRAPH |
| GSM8047999_23_wt_M_captured_normalizedpileup_chrZ_5a_P2.bedGraph.gz |
22.2 Kb |
(ftp)(http) |
BEDGRAPH |
| GSM8047999_23_wt_M_captured_normalizedpileup_chrZ_8a_P2.bedGraph.gz |
20.9 Kb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
