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Sample GSM3949161 Query DataSets for GSM3949161
Status Public on Feb 04, 2021
Title Inpp4b-/- rep3 [IN_1675]
Sample type SRA
 
Source name Inpp4b-/-_liver
Organism Mus musculus
Characteristics strain background: C57BL/6
genotype/variation: Inpp4b-/-
age: 12 weeks
tissue: liver
Extracted molecule total RNA
Extraction protocol Livers were removed, and total RNA was extracted using Tri Reagent (Molecular Research Center, Cincinnati, OH).
rRNA was removed using the Ribo-Zero kit. Libraries were prepared using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Data processing Sequenced reads were trimmed for adaptor sequence, reads containing N>10% were removed, reads with Q-score<=5 were removed.
Reads were mapped to GRCm38 using HISAT2
Mapped reads were quantified using HTSeq. For differential expression analysis only genes with counts > 0 in all samples in at least one group. Bioconductor/R package DESeq2 was used for normalization and differential gene expression analysis.
Genome_build: GRCm38
Supplementary_files_format_and_content: raw count values for each gene that had counts >0 for each sample in at least one group; normalized counts
 
Submission date Jul 18, 2019
Last update date Feb 04, 2021
Contact name Lubov Nathanson
E-mail(s) lnathanson@nova.edu
Organization name Nova Southeastern University
Department INIM
Street address 3321 College Ave.
City Fort Lauderdale
State/province Florida
ZIP/Postal code 33314
Country USA
 
Platform ID GPL21103
Series (1)
GSE134466 INPP4B protects from metabolic disease and obesity associated prostate neoplasia.
Relations
BioSample SAMN12308524
SRA SRX6460131

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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