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Sample GSM2332520 Query DataSets for GSM2332520
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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