|
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 |