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Sample GSM5058829 Query DataSets for GSM5058829
Status Public on May 09, 2022
Title CAPAN1_IFN2h_rep_2
Sample type SRA
 
Source name Pancreatic Ductal Adenocarcinoma (PDAC) cell line
Organism Homo sapiens
Characteristics cell type: Bulk population of CAPAN1 cell line
growth protocol: RPMI supplemented with 20% Fetal Bovine Serum, 2mM L-Glutamine and 1% Pen/Strep
treatment: Bulk population treated with 1000 U/ml human IFNbeta for 2 hours
Extracted molecule total RNA
Extraction protocol 10^6 cells are lysed and processed according to SMART-Seq2 protocol. Briefly, 5 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 Illumina sequencing.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description 10^6 cells are lysed and processed according to SMART-Seq2 protocol. Briefly, 5 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 Illumina sequencing.
Data processing Reads were pre-processed (quality trimming and adapter clipping) using Trim Galore v0.6.5, then reads with a minimum of 30 bp were aligned to human genome build GRCh38/hg38 using TopHat2 v2.1.1 with parameter “–b2‐very‐sensitive”. Only uniquely mapped reads were retained.
At the gene level, the expression counts were estimated using summarizeOverlaps() function of GenomicRanges R-package v1.38 with "IntersectionStrict" mode.
Differential expression analysis in biological duplicates or more was performed using the DESeq2 R-package v1.26.
Genome_build: GRCh38/hg38
 
Submission date Feb 01, 2021
Last update date May 09, 2022
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)
GSE165949 Interferon regulatory factor 1 (IRF1) controls the metabolic programmes of low-grade pancreatic cancer cells (RNA-Seq 2)
GSE165950 Interferon regulatory factor 1 (IRF1) controls the metabolic programmes of low-grade pancreatic cancer cells
Relations
BioSample SAMN17730345
SRA SRX10000169

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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