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Sample GSM4029569 Query DataSets for GSM4029569
Status Public on Feb 07, 2020
Title RA5103K3-4N: Newly diagnosed Rheumatoid Arthritis patient CD4nai 3.2
Sample type SRA
 
Source name CD4+ naïve t cell
Organism Homo sapiens
Characteristics tissue: CD4+ naïve t cell
library prep kit: Diagenode mRRBS
disease state: Newly diagnosed Rheumatoid Arthritis
replicate: 1
Extracted molecule genomic DNA
Extraction protocol RNA/DNA/Protein Purification Kit (Norgen Biotek Corp)
Diagenode RRBS, In house mRRBS
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection Reduced Representation
Instrument model Illumina HiSeq 3000
 
Description MSP1 fragmented DNA
Data processing Primary base calling and quality scoring was performed using BSMAP v.2.90 (-p4, -D C-CGG, -v2, -n1, -q28)
getting methylation ratios in methratio.py with samtools
Getting CGs: grep -c "CG" sorted_*.txt
Methratio format to RnBeads format were transformed with a custom R-script
Call methylation differences: RnBeads v.1.10.8 No SNPs, cov treshold=10, min.group.size=5, no sex chromosomes)
Genome_build: hg19
 
Submission date Aug 13, 2019
Last update date Feb 08, 2020
Contact name Kari Guderud
E-mail(s) kari.guderud@gmail.com
Organization name University of Oslo
Department Medical Genetics
Street address Kirkeveien 166
City Oslo
ZIP/Postal code 0450
Country Norway
 
Platform ID GPL21290
Series (1)
GSE135770 Rheumatoid arthritis patients, both newly diagnosed and methotrexate treated, show more DNA methylation differences in CD4+ memory than in CD4+ naïve T cells
Relations
BioSample SAMN12566909
SRA SRX6708512

Supplementary file Size Download File type/resource
GSM4029569_RA5103K3_4N_RnBeads2.bed.gz 31.5 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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