|Public on Apr 03, 2015
|siTFE3 construct2 rep2
|8988T PDA Cell Line
cell line: 8988T
cell type: pancreatic ductal adenocarcinoma
|8988T cells were transfected with siCTRL and 2 different siRNA targeting TFE3, 24 and 48hrs post-plating. RNA was collected 48hrs following siRNA transfection.
|8988T cells were cultured in DMEM supplemented with 10% FBS
|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)
|Illumina HiSeq 2500
|8988T PDA cells treated with siRNA against TFE3 (construct 2, replicate 2)
|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.
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
|Oct 06, 2014
|Last update date
|May 15, 2019
|Kenneth N Ross
|Dana-Farber Cancer Institute
|450 Brookline Ave., Rm M640
|RNA-Seq Samples of siTFE3 in 8988T PDA Cell Line to Investigate Transcriptional Control of the Autophagy-Lysosome System