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Sample GSM7173765

Query DataSets for GSM7173765

Status

Public on May 24, 2023

Title

HEL Ita 4h - 2

Sample type

SRA

Source name

HEL

Organism

Homo sapiens

Characteristics

cell line: HEL
treatment: Itacitinib

Extracted molecule

total RNA

Extraction protocol

Total RNA from cell lines was extracted with RNeasy Mini Kit (Qiagen, Hilden, Germany) with DNAse treatment following the manufacturer's protocol.
Samples were then indexed, pooled, and sequenced by Illumina NovaSeq 6000 following standard Illumina protocol.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Data processing

Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a.
TMM normalization size factors in EdgeR were calculated to adjust for samples for differences in library size.
Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis.
Assembly: GrCh38
Supplementary files format and content: TSV of raw counts.

Submission date

Apr 14, 2023

Last update date

May 24, 2023

Contact name

Tim Kong

E-mail(s)

timkong@wustl.edu

Organization name

Washington University School of Medicine

Street address

CSRB 8838