|
| Status |
Public on Apr 03, 2015 |
| Title |
siCTRL rep2 |
| Sample type |
SRA |
| |
|
| Source name |
8988T PDA Cell Line
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: siCTRL
cell line: 8988T
cell type: pancreatic ductal adenocarcinoma
|
| Treatment protocol |
8988T cells were transfected with siCTRL and 2 different siRNA targeting TFE3, 24 and 48hrs post-plating. RNA was collected 48hrs following siRNA transfection.
|
| Growth protocol |
8988T cells were cultured in DMEM supplemented with 10% FBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
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 at the Tufts University Bioinformatics Core (http://tucf-genomics.tufts.edu)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
8988T PDA cells treated with control siRNA (replicate 2)
|
| Data processing |
Reads trimmed with Trimmomatic version 0.30 in single end mode and trimming steps set to ILLUMINACLIP:illuminaAdapters.fa: 2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:35
Reads aligned to human genome with tophat version 2.0.8 using UCSC hg19 gene annotation and default settings.
Aligned reads processed to Fragments Per Kilobase of exon per Million fragments mapped (FPKM) using cufflinks version 2.1.1 (http://cufflinks.cbcb.umd.edu/index.html) with the -G flag to use the hg19 reference annotation to estimate isoform expression and not assemble novel transcripts.
Genome_build: hg19
Supplementary_files_format_and_content: genes.fpkm_tracking files are tab delimited text files output by cufflinks in a generic FPKM tracking format with estimated gene-level expression values in the form of FPKM values
|
| |
|
| Submission date |
Oct 06, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Kenneth N Ross |
| E-mail(s) |
Kenneth.Ross@dfci.harvard.edu
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Pediatric Oncology
|
| Street address |
450 Brookline Ave., Rm M640
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE62077 |
RNA-Seq Samples of siTFE3 in 8988T PDA Cell Line to Investigate Transcriptional Control of the Autophagy-Lysosome System |
|
| Relations |
| BioSample |
SAMN03097391 |
| SRA |
SRX723756 |
