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Sample GSM1519403 Query DataSets for GSM1519403
Status Public on Apr 03, 2015
Title siTFE3 construct2 rep2
Sample type SRA
Source name 8988T PDA Cell Line
Organism Homo sapiens
Characteristics treatment: siTFE3_2
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 (
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Description 8988T PDA cells treated with siRNA against TFE3 (construct 2, 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 ( 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
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
BioSample SAMN03097395
SRA SRX723760

Supplementary file Size Download File type/resource
GSM1519403_RP4TB2.genes.fpkm_tracking.gz 810.1 Kb (ftp)(http) FPKM_TRACKING
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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