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| Status |
Public on Feb 09, 2017 |
| Title |
UMSCC29 |
| Sample type |
SRA |
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| Source name |
Human cell-line
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| Organism |
Homo sapiens |
| Characteristics |
cell line: UMSCC29
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| 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
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| 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
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| Submission date |
May 14, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
SATRAJIT SINHA |
| E-mail(s) |
SSINHA2@BUFFALO.EDU
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| Organization name |
SUNY AT BUFFALO
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| Street address |
701 ELLICOTT STREET
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| City |
BUFFALO |
| ZIP/Postal code |
14203 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE68872 |
RNA-Seq analysis of Head and Neck Squamous cell carcinoma cell-lines |
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| Relations |
| BioSample |
SAMN03658158 |
| SRA |
SRX1027577 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1684869_UMSCC29_Rep1_transcripts.gtf.gz |
5.9 Mb |
(ftp)(http) |
GTF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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