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Sample GSM5047149

Query DataSets for GSM5047149

Status

Public on May 31, 2021

Title

RIT1-M90I_1

Sample type

SRA

Source name

RIT1-M90I

Organism

Homo sapiens

Characteristics

cell line: SALE
cell type: lung epithelial
treatment (lentiviral transduction): RIT1 M90I

Extracted molecule

polyA RNA

Extraction protocol

Direct-zol RNA Miniprep plus (Zymo Research)
Illumina TruSeq kit for 50bp paired-end reads, poly-A selection, non-strand-specific

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Data processing

Illumina NovaSeq reads were aligned by STAR v2.5.3a in 2-pass mode to BAM files.
Picard tools v.1.114 used mark duplicate reads, add read group info, and reorder BAMs.
BAMs are indexed using samtools v.0.1.19
FeatureCounts from Subread v.1.5.3 was used to quantify gene transcripts and generate raw counts file
EdgeR v.3.30.3 was used to normalize read counts and obtain CPM and RPKM values.
CPM values were used to filter the gene list down to the 12,887 genes with average log2CPM >0.1 across all samples. RPKM values were converted into TPM values.
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: counts_all.txt is a tab-separated values file with the quantified read counts from FeatureCounts. Each row is a gene transcript. The first six columns describe the gene, and each of the remaing columns correspond to a sample.
transcript_quants_log2TPM.csv is a comma-separated values file of the log2 of TPM values. Each row is a gene transcript and each column is a sample.

Submission date

Jan 27, 2021

Last update date

May 31, 2021

Contact name

Alice Berger

Organization name

Fred Hutchinson Cancer Research Center

Street address

1100 Fairview Ave N

City

Seattle