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Sample GSM3037399

Query DataSets for GSM3037399

Status

Public on Sep 28, 2018

Title

KO_RNAseq_Rep1

Sample type

SRA

Source name

mouse embryo

Organism

Mus musculus

Characteristics

strain: FVB/N
developmental stage: E8.5
tissue: embryo
genotype/variation: Tip55 knockout

Extracted molecule

total RNA

Extraction protocol

RNA was isolated from E8.5 embryos using a Direct-zol RNA MicroPrep kit (Zymo research).
These libraries are not strand specific. Enrichment of mRNA, library preparation, and sequencing were performed at BGI, using the BGI-seq format.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

BGISEQ-500

Data processing

Reads were mapped to the mm10 genome and quantified using RSEM (Li and Dewey, 2011). Identification of differentially expressed genes was performed using a combined RSEM-EBseq pipeline (Leng et al., 2013)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with fold change values and differential expression probabilities. PPEE means “posterior probability of equal expression”, PPDE means “posterior probability of differential expression”, PostFC means “posterior fold change” and RealFC means "Real Fold Change". It was made using the “rsem-run-ebseq” command in RSEM.

Submission date

Mar 12, 2018

Last update date

Sep 28, 2018

Contact name

Thomas Fazzio

E-mail(s)

Thomas.Fazzio@umassmed.edu

Organization name

UMMS

Street address

364 Plantation street