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Sample GSM5091322 Query DataSets for GSM5091322
Status Public on Feb 28, 2021
Title Pcdhb_Rad21Cleaved_rep3
Sample type SRA
 
Source name Primary neuron
Organism Mus musculus
Characteristics genotype: RAD21-TEV cleaved
Extracted molecule genomic DNA
Extraction protocol Neuronal cells were cross-linked in PBS buffer with 1% formaldehyde for 10 min at RT and nuclei were isolated in the lysis buffer containing 10 mM Tris-HCl pH 7.4, 150 mM NaCl, 0.5% NP-40 and 1Ă—protease inhibitors.
After digestion using HindIII, digested products were ligated by T4 DNA ligase. 3C templates were purified and then digested again using a second enzyme, NlaIII. Final 4C sequencing libraries were purified using a Roche High-Pure PCR Product Purification Kit, and then sequenced using an Illumina HiSeq 2500 platform.
4C-seq
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
 
Description Pcdhb_Rad21Cleaved_rep1-4.nearcis.norm.txt.mean.scales.txt.gz
Data processing Basecalls performed using CASAVA-2.17
Sequenced data was analysed using the 4Cseqpipe software suite (Van De Werken, Harmen JG, et al. "Robust 4C-seq data analysis to screen for regulatory DNA interactions." Nature methods 9.10 (2012): 969) with the setting of "-stat_type mean -trend_resolution 40000"
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include normalized contact intensity
 
Submission date Feb 18, 2021
Last update date Mar 01, 2021
Contact name LMS Bioinformatics Core
E-mail(s) bioinformatics@lms.mrc.ac.uk
Organization name MRC London Institute of Medical Sciences
Department Bioinformatics Core
Street address Hammersmith Hospital Campus, Du Cane Road
City London
ZIP/Postal code W12 0NN
Country United Kingdom
 
Platform ID GPL17021
Series (2)
GSE150130 Partial rescue of neuronal genes deregulated in CdLS by cohesin
GSE167044 4C contact profiles of the Pcdh-b enhancers HS18-20
Relations
BioSample SAMN17978629
SRA SRX10125157

Supplementary file Size Download File type/resource
GSM5091322_Pcdhb_Rad21Cleaved_rep3.nearcis.norm.txt.mean.scales.txt.gz 90.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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