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Sample GSM4041989 Query DataSets for GSM4041989
Status Public on Mar 03, 2020
Title K2
Sample type SRA
 
Source name Left liver lobes
Organism Mus musculus
Characteristics treatment type: 56Fe Irradiated
time: 1 month
biological replicate: 1
strain: C57BL16
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from the liver slices using RNAqueousTM Total RNA Isolation Kit (ThermoFisher Scientific, Waltham, MA)
rRNA was removed via Ribo-ZeroTM rRNA Removal Kit (Illumina, San Diego, CA) prior to library preparation with the Illumina TruSeq RNA Library kit. Samples were sequenced in a paired-end 50 base format on an Illumina HiSeq 1500.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Data processing STAR alignment program, version 2.5.3a, with the recommended ENCODE options (Dobin A, Davis CA, Schlesinger F, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics (Oxford, England) 2013;29(1):15-21 doi: 10.1093/bioinformatics/bts635published Online First: Epub Date]|.) -quantMode GeneCounts option was used to obtain read counts per gene based on the Gencode release M14 annotation file
Genome_build: Genome Reference Consortium Mouse Build 38
Supplementary_files_format_and_content: comma-seperated text file which includes raw transcript expression counts (with corresponding ENSEMBL ID) for each sample
 
Submission date Aug 21, 2019
Last update date Mar 03, 2020
Contact name Anna Nia
E-mail(s) anna.nia@ucla.edu
Organization name University of Texas Medical Branch
Department Biochemistry and Molecular Biology
Lab Mark R. Emmett
Street address 301 University Blvd
City Galveston
State/province TX
ZIP/Postal code 77555
Country USA
 
Platform ID GPL18480
Series (1)
GSE136165 Efficient Identification of Multiple Pathways: RNA-Seq Analysis of Livers from 56Fe Ion Irradiated Mice
Relations
BioSample SAMN12618041
SRA SRX6749782

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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