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Sample GSM1185648

Query DataSets for GSM1185648

Status

Public on Oct 25, 2013

Title

Sample type

SRA

Source name

thyroid tissue

Organism

Homo sapiens

Characteristics

disease state: Tumor
tissue: thyroid

Extracted molecule

polyA RNA

Extraction protocol

RNA were isolated using Rneasy fibrous tissue kit (Qiagen), respectively, according to standard protocols. RNA quality was determined with an Agilent Bioanalyzer.
cDNA libraries for RNA sequencing were prepared using the mRNA-Seq Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s standard protocol. Briefly, poly-A(+) RNA was purified from 2 µg of total RNA for each sample, fragmented by incubation at 94°C for 5 min in fragmentation buffer, and used for double-stranded cDNA synthesis. After ligation of the PE adapter, a fraction of 250–300bp was gel-purified and amplified with 15 cycles of PCR. The resulting libraries were subjected to paired-end sequencing of 76-bp reads on the Genome Analyzer IIx (GAIIx) (Illumina).

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Data processing

Basecalls performed using CASAVA version 1.8
Gene expression: Paired-end RNA sequencing reads were first mapped to the hg19 genome using Tophat and hg19 refseq annotation. Then samtools and bedtools were used to calculate read count expression level.
Genome_build: hg19
Supplementary_files_format_and_content: Gene read count matrix; gene: Refseq gene symbol; chrom: chromosome; start: gene start poition; end: gene end poition; rest column: Sample N22, T22, N23, T23, N24, T24, N25, T25, N26, T26, T25

Submission date

Jul 13, 2013

Last update date

May 15, 2019

Contact name

Christopher E Mason

E-mail(s)

chm2042@med.cornell.edu

Organization name

Weill Cornell Medical College

Department

Physiology and Biophysics