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Sample GSM1955085 Query DataSets for GSM1955085
Status Public on Feb 01, 2016
Title 42-3 RNA-Seq
Sample type SRA
 
Source name 2hr after surgery and tourniquet
Organism Homo sapiens
Characteristics tissue: Muscle biopsy 2hr after surgery and tourniquet
Extracted molecule total RNA
Extraction protocol Lexogen QuantSeq mRNA-seq kit
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Sequencing and basecalling by Illumina HiSeq Control Software 2.2.58
BCL conversion and demultiplexing by Illumina CASAVA 1.8.2
FASTQ files aligned to Homo_sapiens.GRCh38.dna.toplevel.fa genome assembly obtained from ENSEMBL. The Homo_sapiens.GRCh38.78.gtf file from ENSEMBL was used for annotation. Alignments were performed with STAR 2.4.0i.
Gene count tables were generated from STAR-produced SAM files using HTSeq-count 0.6.1
genome build: Homo_sapiens.GRCh38.dna.toplevel.fa
.counts files: Gene count tables generated by HTSeq-count from each .sam file for each sample
 
Submission date Nov 27, 2015
Last update date Aug 30, 2022
Contact name Hans Christian Dreyer
E-mail(s) hcdreyer@uoregon.edu
Organization name University of Oregon
Department Human Physiology
Lab Muscle Physiology
Street address 1240 University of Oregon
City Eugene
State/province Oregon
ZIP/Postal code 97403-1240
Country USA
 
Platform ID GPL18573
Series (1)
GSE75432 Muscle transcriptome analysis following Total Knee Arthroplasty with Tourniquet
Relations
BioSample SAMN04297345
SRA SRX1453170

Supplementary file Size Download File type/resource
GSM1955085_42-3.counts.txt.gz 198.6 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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