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Sample GSM1471664 Query DataSets for GSM1471664
Status Public on Aug 11, 2017
Title IMIM-PC2 Resistant Rep2
Sample type SRA
 
Source name Cell line
Organism Homo sapiens
Characteristics cell line: IMIM-PC-2
phenotype: MN58b Resistant
Treatment protocol To generate MN58b-resistant IMIM-PC-2 cells, MN58b was added starting at a 0.1μM. In parallel, IMIM-PC-2 cells were cultured without MN58b. Medium was changed every 48 hours and MN58b concentration was increased by 50% weekly at each passage of the cells (split 1:3 when confluent). The final concentration achieved was 8μM.
Growth protocol Cells were cultured in DMEM (Sigma- Aldrich) supplemented with 10% heat-inactivated fetal bovine serum (FBS), 1% Na pyruvate and 1% penicillin/streptomycin under standard conditions.
Extracted molecule total RNA
Extraction protocol RNA from parental and MN58b-resistant cells was extracted and purified using Trizol, RNA integrity was assayed on an Agilent 2100 Bioanalyzer (range 8.4-10). PolyA+ fractions were purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq Stranded mRNA Sample Preparation Part # 15031047 Rev. D". Adapter- ligated library was completed by 10 cycles of PCR with Illumina PE primers. The resulting purified cDNA library of template molecules was applied to an Illumina flow cell for cluster generation (TruSeq cluster generation kit v5) and sequenced on the Genome Analyzer IIx (GAIIx) with SBS TruSeq v5 reagents following manufacturer's instructions (SingleRead 1x40 bases). Image analysis and per-cycle base calling was performed with Illumina Real Time Analysis software (RTA1.13
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
 
Data processing Image analysis and per-cycle basecalling was performed with Illumina Real Time Analysis software (RTA1.13). Conversion to FASTQ read format was performed with CASAVA-1.8 (Illumina).
Quality check was done via fastqc (v0.9.4, Babraham Bioinformatics). The raw reads were aligned to the reference genome hg19/GRCh37 with tophat1 (version 2.0.4) using the following parameters: -- bowtie1, --max-multihits 5, --genome-read-mismatches 1, --segment-mismatches 1, -- segment-length 19, --splice-mismatches 0, --library-type fr-firststrand.
The gene expression levels (Fragments Per Kilobase of exon per Million fragments, FPKMs) were quantified with cufflinks2 (version 2.0.2), as annotated in Ensembl version GRCh37.65, with the following parameters: -N, --library-type fr-firststrand, -u.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
 
Submission date Aug 11, 2014
Last update date May 15, 2019
Contact name Victor Javier Sanchez-Arevalo Lobo
E-mail(s) vjsanchez.arevalo@gmail.com
Organization name CNIO
Department Cancer Biology
Lab Epithelial Carcinogenesis Group
Street address Melchor Fernandez Almagro, 3
City Madrid
ZIP/Postal code 28029
Country Spain
 
Platform ID GPL10999
Series (1)
GSE60321 Choline kinase alpha (CHKA) as a therapeutic target in pancreatic ductal adenocarcinoma: Expression, predictive value, and sensitivity to inhibitors
Relations
BioSample SAMN02982880
SRA SRX675576

Supplementary file Size Download File type/resource
GSM1471664_Sample_R2.fpkm_tracking.gz 1.4 Mb (ftp)(http) FPKM_TRACKING
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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