|
Status |
Public on Dec 08, 2016 |
Title |
HBBx2 |
Sample type |
SRA |
|
|
Source name |
IRI negative_post-reperfusion
|
Organism |
Homo sapiens |
Characteristics |
transplant stage: post-reperfusion ischemia reperfusion injury (iri): negative tissue: Liver
|
Extracted molecule |
total RNA |
Extraction protocol |
2mm core needle biopsies placed in RNAlater (ThermoFisher) and RNA was enriched for mRNA with NEBNext Poly(A) mRNA Magnetic isolation kit, then put on IntegenX Apollo 324 system for automated library preparation using IntegenX PrepX RNA-Seq Library reagent kit for Illumina. RNA libraries were prepared for sequencing using standard Illumina protocols.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
|
|
Data processing |
Demultiplexing was performed with Illumina CASAVA 1.8.2. Demultiplexed FASTQ files were checked with FASTQC. Reads were trimmed with Cutadapt to remove adapters and low-quality ends Alignment to the hg38 human genome assembly was performed using STAR 2.5.1b. Unmapped reads, multi-mappers and low-quality alignments were removed with Samtools. Reads mapping gene exons were counted using featureCounts Counts were imported in R version 3.2.3 for analysis using the edgeR and ggplot2 packages. A negative binomial generalized log-linear model was fitted to the read counts for each gene. Genome_build: human NCBI genome build 38 Supplementary_files_format_and_content: tab-delimited text files include counts for each sample
|
|
|
Submission date |
Sep 29, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Rebecca A. Sosa |
E-mail(s) |
rsosa@mednet.ucla.edu
|
Organization name |
UCLA
|
Department |
Pathology & Lab Medicine
|
Lab |
Elaine F. Reed
|
Street address |
1000 Veteran Ave
|
City |
Los Angeles |
State/province |
California |
ZIP/Postal code |
90095 |
Country |
USA |
|
|
Platform ID |
GPL11154 |
Series (1) |
GSE87487 |
Genes encoding cognate receptors for IRI-related recipient cytokines are expressed in donor livers |
|
Relations |
BioSample |
SAMN05852466 |
SRA |
SRX2199846 |