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Sample GSM2809214

Query DataSets for GSM2809214

Status

Public on Oct 13, 2017

Title

Liver_Ctrl4

Sample type

SRA

Source name

control_liver needle biopsy

Organism

Homo sapiens

Characteristics

subject status: Autoimmune hepatitis with sclerosing cholangitis
tissue: Liver

Extracted molecule

polyA RNA

Extraction protocol

RNA extraction of homogenized human liver biopsies was performed using Direct-zol™ RNA MiniPrep (cat. no. R2050, Zymo Research), including on-column DNase I digestion (cat. no. E1009, Zymo Research).
cDNA libraries for all samples were created using the TruSeq® RNA Sample Prep Kit v2–48, Set A (cat. no. RS-122-2001, Illumina®,) as per the TruSeq® RNA Sample Preparation v2 Guide, Low-Throughput Protocol.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Description

RPKM L12_NonAlagillePatient4

Data processing

Reads were aligned using STAR to genomes mm10 and hg19
Reads were separated for different species using S^3 (https://github.com/danielramskold/S3_species-specific_sequencing) with default settings (-Ms 1 -Mu 1 -D 2)
Unique reads were selected using mapping quality threshold 255
Gene expression values were calculated using rpkmforgenes.py (see link above) with options -rmnameoverlap -bothendsceil and using RefSeq annotation from 1 July 2014
MicroRNAs and snoRNAs were removed
RPKM values were TMM normalized
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text of normalised expression values and read counts

Submission date

Oct 12, 2017

Last update date

May 15, 2019

Contact name

Urban Lendahl

Organization name

Karolinska Insttitutet

Street address

Von Eulers vag 3

City

Stockholm