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Sample GSM2371025

Query DataSets for GSM2371025

Status

Public on Jun 19, 2017

Title

arthralgia tissue 6

Sample type

SRA

Source name

synovial biopsy

Organism

Homo sapiens

Characteristics

Sex: F
age: 33
disease: Arthralgia
acpa positivity: Positive

Treatment protocol

n/a

Growth protocol

n/a

Extracted molecule

total RNA

Extraction protocol

Total RNA was extracted from RA synovial samples and the quality of all RNA samples was evaluated using an Agilent Bioanalyzer
Sequencing libraries were prepared using TruSeq Stranded Total RNA RiboZero protocol from Illumina. Libraries were pooled and sequenced with an Illumina HiSeq 2000 with paired-end 100 bp flow cells. Raw read quality was evaluated using FastQC.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Data processing

Reads were trimmed for adaptors and sequence quality. The average number of clusters (post-trimming) per sample was 89 million.
Trimmed reads were aligned to human b37.3 reference genome using the STAR v2.4 aligner (Dobin et al., 2013).
Aligned reads were quantified using RSEM v1.2.14 algorithm (Li and Dewey, 2011) with UCSC transcriptome model (accessed on 03/17/2014) that included lincRNAs from Ensembl v75. This transcriptome model has a total of 34495 genes and 88933 isoforms
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited processed data matrix file contains feature counts for all samples and features

Submission date

Nov 01, 2016

Last update date

May 15, 2019

Contact name

Alice Walsh

E-mail(s)

awalsh17@its.jnj.com

Organization name

Janssen R&D

Department

Immunology