NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM8047988 Query DataSets for GSM8047988
Status Public on Apr 01, 2024
Title SMC2au_M_P3_rep1
Sample type SRA
 
Source name Bursa
Organism Gallus gallus
Characteristics tissue: Bursa
cell line: DT40
cell type: lymphoblast
genotype: female (ZW)
treatment: Oligo pool 3
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
12_SMC2au_M_P3
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 SAMN39682136
SRA SRX23456752

Supplementary file Size Download File type/resource
GSM8047988_12_SMC2au_M_captured_normalizedpileup_chrZ_12a_P3.bedGraph.gz 14.9 Kb (ftp)(http) BEDGRAPH
GSM8047988_12_SMC2au_M_captured_normalizedpileup_chrZ_15a_P3.bedGraph.gz 5.7 Kb (ftp)(http) BEDGRAPH
GSM8047988_12_SMC2au_M_captured_normalizedpileup_chrZ_18a_P3.bedGraph.gz 5.8 Kb (ftp)(http) BEDGRAPH
GSM8047988_12_SMC2au_M_captured_normalizedpileup_chrZ_21a_P3.bedGraph.gz 10.5 Kb (ftp)(http) BEDGRAPH
GSM8047988_12_SMC2au_M_captured_normalizedpileup_chrZ_24a_P3.bedGraph.gz 12.9 Kb (ftp)(http) BEDGRAPH
GSM8047988_12_SMC2au_M_captured_normalizedpileup_chrZ_27a_P3.bedGraph.gz 15.0 Kb (ftp)(http) BEDGRAPH
GSM8047988_12_SMC2au_M_captured_normalizedpileup_chrZ_30a_P3.bedGraph.gz 17.1 Kb (ftp)(http) BEDGRAPH
GSM8047988_12_SMC2au_M_captured_normalizedpileup_chrZ_33a_P3.bedGraph.gz 18.4 Kb (ftp)(http) BEDGRAPH
GSM8047988_12_SMC2au_M_captured_normalizedpileup_chrZ_37a_P3.bedGraph.gz 18.1 Kb (ftp)(http) BEDGRAPH
GSM8047988_12_SMC2au_M_captured_normalizedpileup_chrZ_3a_P3.bedGraph.gz 14.6 Kb (ftp)(http) BEDGRAPH
GSM8047988_12_SMC2au_M_captured_normalizedpileup_chrZ_6a_P3.bedGraph.gz 18.7 Kb (ftp)(http) BEDGRAPH
GSM8047988_12_SMC2au_M_captured_normalizedpileup_chrZ_9a_P3.bedGraph.gz 12.9 Kb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap