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Sample GSM5393106

Query DataSets for GSM5393106

Status

Public on Jun 01, 2023

Title

MOUSE KO NIH-3T3 Sample 12

Sample type

SRA

Source name

MOUSE

Organism

Mus musculus

Characteristics

genotype: KO
cell line: NIH-3T3

Extracted molecule

total RNA

Extraction protocol

RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Description

MOUSE.counts.matrix

Data processing

Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19,mm10, dm6, sacCer1, GRCz11
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

Submission date

Jun 20, 2021

Last update date

Jun 01, 2023

Contact name

Lei Gu

E-mail(s)

[email protected]

Organization name

Max Planck Institute for heart and lung research

Street address

parkstreet 1