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Sample GSM2232861 Query DataSets for GSM2232861
Status Public on Feb 09, 2017
Title RAG1-/- (L1)
Sample type SRA
Source name RAG1-/-, lung
Organism Mus musculus
Characteristics genotype/variation: RAG1-/-
tissue: normal-looking lung
Treatment protocol No experimental treatment was applied
Growth protocol all mice were maintained to 12 months of age
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from normal-looking lung tissues using Trizol reagent.
Libraries were prepared according to Illumina's instructions accompanying the RNA TruSeq V2 Library construction kit. Libraries were sequenced on the Illumina MiSeq following the manufacturer's protocols.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina MiSeq
Description L1
Data processing Genesifter software was used for base-calling and alignment.
BWA Paired-End (GATKv3) pipeline was used to align with Mus musculus (build 37.2) genome. Pairwise and Cluster analyses were done using Genesifter software and differential gene lists were exported as tab delimited files.
Pairwise settings were as follows: normalize to mapped reads, statistical analysis using EdgeR differential genes narrowed to 2 fold min for final analysis, data correct using Benjamini Hochberg method.
Pairwise analysis was done using RPKMs and determination of fold significance using EdgeR with a significance value (p value) cutoff of 0.05. Then fold cutoff was set to 2.0-fold for identifying differentially expressed genes and for subsequent pathway analysis.
Genome_build: Mus musculus build 37.2 (MGSCv37)
Supplementary_files_format_and_content: [.txt] RPKMs and differentially expressed genes
Submission date Jul 14, 2016
Last update date May 15, 2019
Contact name Hiroshi Y Yamada
Organization name OUHSC
Department Medicine
Street address 975 NE 10th st. BRC1207
City Oklahoma City
State/province Oklahoma
ZIP/Postal code 73104
Country USA
Platform ID GPL16417
Series (1)
GSE84383 NGS-mRNA in lung tissues in RAG1-/- and in RAG1-/- Sgo1-/+ mice
BioSample SAMN05390875
SRA SRX1948850

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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