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Status |
Public on Feb 04, 2021 |
Title |
WT rep1 [WT_1694] |
Sample type |
SRA |
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Source name |
WT_liver
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Organism |
Mus musculus |
Characteristics |
strain background: C57BL/6 genotype/variation: wild type age: 12 weeks tissue: liver
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
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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
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Submission date |
Jul 18, 2019 |
Last update date |
Feb 04, 2021 |
Contact name |
Lubov Nathanson |
E-mail(s) |
lnathanson@nova.edu
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Organization name |
Nova Southeastern University
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Department |
INIM
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Street address |
3321 College Ave.
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City |
Fort Lauderdale |
State/province |
Florida |
ZIP/Postal code |
33314 |
Country |
USA |
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Platform ID |
GPL21103 |
Series (1) |
GSE134466 |
INPP4B protects from metabolic disease and obesity associated prostate neoplasia. |
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Relations |
BioSample |
SAMN12308522 |
SRA |
SRX6460133 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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