|
| Status |
Public on Sep 17, 2019 |
| Title |
CFPAC1.FOXA1-KDFOXA2-KD.Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
CFPAC1 silenced
|
| Organism |
Homo sapiens |
| Characteristics |
cell line background: CFPAC1
cell type: Pancreatic Ductal Adenocarcinoma (PDAC) cell line
transfected with: FOXA1 siRNA (SANTA CRUZ, sc-37030) and FOXA2 siRNA (SANTA CRUZ, sc-35569)
|
| Treatment protocol |
CFPAC1 cells transfected with FOXA1 siRNA (SANTA CRUZ, sc-37030) and FOXA2 siRNA (SANTA CRUZ, sc-35569)
|
| Growth protocol |
IMDM supplemented with 10% Fetal Bovine Serum, 2mM L-Glutamine and 1% Pen/Strep
|
| Extracted molecule |
total RNA |
| Extraction protocol |
10^6 cells are lysed and processed according to SMART-Seq2 protocol. Briefly, 10 ng of poly-A containing mRNA molecules are copied into first strand cDNA by reverse transcription and template-switching using oligo(dt) primers and LNA-containing template-switching oligo (TSO). cDNA is pre-amplified using limited number of cycles, purified and tagmented with Tn5 transposase. cDNA fragments generated after tagmentation are gap-repaired, enriched by PCR and purified to create the final cDNA library for HiSeq 2000 Illumina sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
processed data file:
CFPAC1.FOXAKD.genes.counts.txt
CFPAC1.FOXA1FOXA2KD.genes.edgeR_results.txt
|
| Data processing |
Reads were pre-processing (filtering, quality trimming and adapter clipping) using Trimmomatic (version 0.38), then single-end reads with a minimum of 36 bp were aligned to human genome build GRCh38/hg38 using TopHat2 (version 2.1.0) with the option “--b2-very-sensitive”. Only uniquely mapped reads were retained.
Gene expression counts were estimated using featureCounts (Rsubread version 1.6.1), summarized across all exons as annotated in the GENCODE v28, with option “largestOverlap”.
Differentially expressed genes in biological triplicates of wild-type vs. FOXA1/2-KD in CFPAC1 cell lines or wild-type vs. FOXA2-KO in PANC1 cell lines were identified using EdgeR R-package v3.2.2.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: *.gene.counts.txt files contain raw read counts for each samples. *.edgeR_results.txt files contain differentially expressed genes for each comparison.
|
| |
|
| Submission date |
Sep 13, 2018 |
| Last update date |
Sep 17, 2019 |
| Contact name |
Chiara Balestrieri |
| E-mail(s) |
balestrieri.c@gmail.com
|
| Organization name |
IRCCS San Raffaele Scientific Institute
|
| Department |
Center for Omics Sciences
|
| Street address |
Via Olgettina 58
|
| City |
Milan |
| ZIP/Postal code |
20132 |
| Country |
Italy |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE119931 |
Cell differentiation grade determines distinct FOXA2 contributions to the cis-regulatory networks of pancreatic cancer cells [RNA-seq] |
| GSE120017 |
Cell differentiation grade determines distinct FOXA2 contributions to the cis-regulatory networks of pancreatic cancer cells |
|
| Relations |
| BioSample |
SAMN10056372 |
| SRA |
SRX4677319 |
