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Sample GSM3949162

Query DataSets for GSM3949162

Status

Public on Feb 04, 2021

Title

Inpp4b-/- rep4 [IN_1678]

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