|
| Status |
Public on Sep 01, 2023 |
| Title |
S115 RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
Isolated CD4+ cells
|
| Organism |
Homo sapiens |
| Characteristics |
age: 69
Sex: F
case control: Ctr
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Resection or mucosal biopsies of the terminal ileum and CD4+ cells were isoloated for RNA-seq and RRBS
total RNA was extracted from purified CD4+ cells using Exiqon’s miRCURY RNA Isolation Kit. Illumina TruSeq un-stranded RNA library preparation protocol was used for RNA-seq library preparation. The pair end sequencing was carried out using the Illumina HiSeq 2000 sequencer at 50bps (3-4 samples per lane), which generated 42-113 million pair-end reads for each sample. Raw data was processed using MAPR-Seq pipeline
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina’s RTA version 1.13.48.
RNA-seq reads were aligned to the hg19 genome assembly using the internal MAPR-seq pipeline
The paired end reads were aligned by TopHat 2.0.6
Gene counts were generated using HTseq (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html)
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
Genome_build: hg19
Supplementary_files_format_and_content: gene expression count matrix (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) |
| GSE184307 |
DNA methylation landscape and signature of CD4+ lymphocytes of lamina propria in Crohn's patients by reduced representation and bisulfite sequencing [RNA-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 |
SAMN21463069 |
| SRA |
SRX12214164 |
