|
|
GEO help: Mouse over screen elements for information. |
|
Status |
Public on Feb 09, 2017 |
Title |
UMSCC103 |
Sample type |
SRA |
|
|
Source name |
Human cell-line
|
Organism |
Homo sapiens |
Characteristics |
cell line: UMSCC103
|
Extracted molecule |
total RNA |
Extraction protocol |
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit 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 2500 |
|
|
Data processing |
Illumina Casava1.8.2 software used for basecalling. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 genome using the Tophat algorithm v2.0.7 with parameters -G -p 8 and default settings [Trapnell C, et al. (2012) Nat Protoc Mar 1;7(3):562-78.] Fragments Per Kilobase of exon per Million fragments mapped (FPKM) were calculated using the Cufflinks algorithm (v2.1.1). [Trapnell C, et al. (2012) Nat Protoc Mar 1;7(3):562-78.] Genome_build: hg19 Supplementary_files_format_and_content: Tab-delimited text files include FPKM values
|
|
|
Submission date |
May 14, 2015 |
Last update date |
May 15, 2019 |
Contact name |
SATRAJIT SINHA |
E-mail(s) |
SSINHA2@BUFFALO.EDU
|
Organization name |
SUNY AT BUFFALO
|
Street address |
701 ELLICOTT STREET
|
City |
BUFFALO |
ZIP/Postal code |
14203 |
Country |
USA |
|
|
Platform ID |
GPL16791 |
Series (1) |
GSE68872 |
RNA-Seq analysis of Head and Neck Squamous cell carcinoma cell-lines |
|
Relations |
BioSample |
SAMN03658157 |
SRA |
SRX1027576 |
Supplementary file |
Size |
Download |
File type/resource |
GSM1684868_UMSCC103_Rep1_transcripts.gtf.gz |
6.0 Mb |
(ftp)(http) |
GTF |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
|
|
|
|
|