 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 01, 2023 |
| Title |
S852 BiSulfite-seq |
| Sample type |
SRA |
| |
|
| Source name |
Isolated CD4+ cells
|
| Organism |
Homo sapiens |
| Characteristics |
age: 20
Sex: M
case control: Dis
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Resection or mucosal biopsies of the terminal ileum and CD4+ cells were isoloated for RNA-seq and RRBS
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina’s RTA version 1.13.48.
RRBS reads were aligned to the hg19 genome assembly using the internal SAAP-RRBS pipeline
RRBS was performed at the Mayo Clinic Genotyping Shared Resource facility as previously described. Briefly, DNA (250ng) was digested with Msp1 (New England Biolabs, Catalog Number: R0106M) and purified using Qiaquick Nucleotide Removal Kit (Qiagen, Catalog Number: 28004). End-repair A tailing was performed (New England Biolabs, Catalog Numbers: M0212L) and TruSeq methylated indexed adaptors (Illumina, Catalog Number: 15025064) were ligated with T4 DNA ligase (New England Biolabs, Catalog Number: M0202L). Size selection was performed with Agencourt AMPure XP beads (Beckman Coulter, Catalog Number: A63882). Bisulfite conversion was performed using EZ-DNA Methylation Kit (Zymo Research, Catalog Number: D5001) as recommended by the manufacturer with the exception that incubation was performed using 55 cycles of 95 ̊C for 30 sec and 50°C for 15 min. Following bisulfite treatment, the DNA was purified as directed and amplified using Pfu Turbo C Hotstart DNA Polymerase (Agilent Technologies, Catalog Number: 600414). Library quantification was performed using Qubits dsDNA HS Assay Kit (Life Technologies, Catalog Number: Q32854) and the Bioanalyzer DNA 1000 Kit (Agilent Technologies, Catalog Number: 5067-1504).
Genome_build: hg19
Supplementary_files_format_and_content: methylation ratio file (text)
|
| |
|
| Submission date |
Sep 16, 2021 |
| Last update date |
Sep 01, 2023 |
| Contact name |
ZHIFU SUN |
| Organization name |
Mayo Clinic
|
| Department |
Quantitative Health Sciences
|
| Street address |
200 1st St SW
|
| City |
ROCHESTER |
| State/province |
Minnesota |
| ZIP/Postal code |
55905 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE184312 |
DNA methylation landscape and signature of CD4+ lymphocytes of lamina propria in Crohn's patients by reduced representation and bisulfite sequencing [BiSulfite-seq] |
| GSE184314 |
DNA methylation landscape and signature of CD4+ lymphocytes of lamina propria in Crohn's patients by reduced representation and bisulfite sequencing |
|
| Relations |
| BioSample |
SAMN21465547 |
| SRA |
SRX12215279 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5583871_S852.txt.gz |
15.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
