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Sample GSM3124292

Query DataSets for GSM3124292

Status

Public on Apr 25, 2019

Title

Cancer [CA14]

Sample type

SRA

Source name

Cervix

Organism

Homo sapiens

Characteristics

disease: Cancer
tissue: HPV-positive Cervix tissue
age: 49

Extracted molecule

total RNA

Extraction protocol

Cervical tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) 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 HiSeq 2000

Description

High risk HPV infection was determined by Digene HPV Genotyping Kits
CA14

Data processing

Illumina Casava1.7 software used for basecalling?
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: HG19, GRCh37
Supplementary_files_format_and_content: tab-delimited text files include raw reads values for each Sample

Submission date

May 02, 2018

Last update date

Apr 25, 2019

Contact name

Yanqin Yang

E-mail(s)

yanqin.yang@nih.gov

Organization name

NIH

Street address

10 Center Dr.