|
Status |
Public on Jan 02, 2018 |
Title |
UniTIS01 |
Sample type |
SRA |
|
|
Source name |
whole biopsy_uninfected control
|
Organism |
Homo sapiens |
Characteristics |
subject status: uninfected control tissue type: Intestinal Rectosigmoid Biopsies cell type: Mixed sample storage: RNALater Immediately Upon Biopsy
|
Extracted molecule |
total RNA |
Extraction protocol |
RNA Isolated using Qiagen AllPrep Kit RNA libraries were prepared for sequencing following Illumina protocols. cDNA libraries were diluted to 0.15ng/ul, fragmented with the Nextera XT DNA kit (Illumina PN FC-131-1024), multiplexed, and sequenced on a Hi-Seq4000
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
|
|
Data processing |
Bases were called and reads were demultiplexed with Illumina CASAVA 1.8.2 and read quality assessed using FastQC Reads were aligned to the transcriptome using STAR version 2.4.2a with default parameters as called by RSEM version 1.2.22 Gene expression per sample was modeled with RSEM version 1.2.22 Genome_build: Release GRCh38 of the human genome Supplementary_files_format_and_content: RSEM output files with counts, TPM, and FPKM values
|
|
|
Submission date |
May 06, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Charlie Kim |
E-mail(s) |
cckim47@gmail.com
|
Organization name |
University of California, San Francisco
|
Department |
Medicine
|
Lab |
Kim
|
Street address |
1001 Potrero Ave
|
City |
San Francisco |
State/province |
CA |
ZIP/Postal code |
94110 |
Country |
USA |
|
|
Platform ID |
GPL20301 |
Series (1) |
GSE81198 |
Expression data of intestinal epithelial isolates from rectosigmoid tissue in HIV-infected and control patients. |
|
Relations |
BioSample |
SAMN04961514 |
SRA |
SRX1748426 |