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Sample GSM2144500 Query DataSets for GSM2144500
Status Public on Jan 02, 2018
Title VirIEC01
Sample type SRA
 
Source name epithelial isolates_viremic untreated
Organism Homo sapiens
Characteristics subject status: viremic untreated
tissue type: Intestinal Rectosigmoid Biopsies
cell type: Intestinal Epithelial Cell
sample storage: EDTA-Isolated, Stored in Trizol
Extracted molecule total RNA
Extraction protocol Phenol:Chloroform Extraction, Cleanup with Zymo IC Column
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 SAMN04961519
SRA SRX1748431

Supplementary file Size Download File type/resource
GSM2144500_VirIEC01.genes.results.txt.gz 1.3 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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