|
| Status |
Public on Nov 15, 2018 |
| Title |
CASKI |
| Sample type |
SRA |
| |
|
| Source name |
Cervical_HPV_pos
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: CASKI
cell type: cervical squamous cell carcinoma (CESC) cell line
hpv.status: HPV_pos
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNeasy Plus (Qiagen)
TruSeq Stranded Total RNA Sample Prep Kit (Illumina); 75-bp paired-end (Illumina HiSeq3000)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Alignment was performed using tophat2
Aligment quality was accessed by fastqc, samtools and htseq-qa
Counting reads was using htseq-count with parameters: python -m HTSeq.scripts.count -s no -t exon sortByName.sam.mod REFFILE > OUTFILE
The normalization of raw read counts was performed by edgeR package in R. The procedure was described in limma package in R. The features were first filtered out if the total counts less than 50
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized values for each Sample.
|
| |
|
| Submission date |
Nov 14, 2018 |
| Last update date |
Nov 15, 2018 |
| Contact name |
Curtis Pickering |
| E-mail(s) |
crpickering@mdanderson.org
|
| Organization name |
The University of Texas MD Anderson Cancer Center
|
| Department |
Head and Neck Surgery
|
| Lab |
Pickering Lab
|
| Street address |
1515 Holcombe Blvd
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE122512 |
Gene expression analysis of head and neck squamous cell carcinoma (HNSCC) cell lines. |
|
| Relations |
| BioSample |
SAMN10422338 |
