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| Status |
Public on Feb 07, 2020 |
| Title |
RA5108B-4N: Newly diagnosed Rheumatoid Arthritis patient CD4nai 8.1 |
| Sample type |
SRA |
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| Source name |
CD4+ naïve t cell
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| Organism |
Homo sapiens |
| Characteristics |
tissue: CD4+ naïve t cell
library prep kit: Diagenode mRRBS
disease state: Newly diagnosed Rheumatoid Arthritis
replicate: 1
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
RNA/DNA/Protein Purification Kit (Norgen Biotek Corp)
Diagenode RRBS, In house mRRBS
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiSeq 3000 |
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| Description |
MSP1 fragmented DNA
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| 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
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| Submission date |
Aug 13, 2019 |
| Last update date |
Feb 08, 2020 |
| Contact name |
Kari Guderud |
| E-mail(s) |
kari.guderud@gmail.com
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| Organization name |
University of Oslo
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| Department |
Medical Genetics
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| Street address |
Kirkeveien 166
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| City |
Oslo |
| ZIP/Postal code |
0450 |
| Country |
Norway |
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| 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 |
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| Relations |
| BioSample |
SAMN12566902 |
| SRA |
SRX6708519 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4029576_RA5108B_4N_RnBeads2.bed.gz |
33.5 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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