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Sample GSM4079647

Query DataSets for GSM4079647

Status

Public on Jul 29, 2020

Title

shCTRL-IFN1

Sample type

SRA

Source name

Brain

Organism

Homo sapiens

Characteristics

genotype/variation: shRNA control
treatment: interferon gamma
cell line: U251
passages: 14-18
cell type: MG Glioblastoma Cell Line

Extracted molecule

total RNA

Extraction protocol

RNA was harvested from cells using RNeasy Mini Kit (Qiagen Cat#74104). Illumina TruSeq stranded mRNA Library Prep Kit 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 NovaSeq 6000

Data processing

The quality of produced data is determined by the phred quality score at each cycle. Box plot containing the average quality at each cycle is created with FastQC.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data. Trimmed reads are mapped to reference genome hg19 with HISAT2
Known genes and transcripts are assembled with StringTie based on reference genome model. After assembly, the abundance of gene/transcript is calculated in the read count and normalized value as FPKM (Fragments Per Kilobase of transcript per Million mapped reads) for a sample.
Genome_build: hg19
Supplementary_files_format_and_content: text files include read count for each Sample

Submission date

Sep 15, 2019

Last update date

Jul 29, 2020

Contact name

Marco Mineo

E-mail(s)

mmineo@bwh.harvard.edu

Phone

6175255656

Organization name

Brigham and Women's Hospital