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Sample GSM2790126 Query DataSets for GSM2790126
Status Public on Sep 21, 2020
Title siAS1 Unst. Rep1
Sample type SRA
 
Source name PANC-1 (Pancreatic ductal adenocarcinoma cell line)
Organism Homo sapiens
Characteristics cell line: PANC-1
treatment: TNF treatment 0h
transfection: SIK3 siRNA
Treatment protocol Cells were transfected with RNAimay for 72h afterwards, rHuTNF-alpha was added
Growth protocol DMEM 10%FCS 1% P/S
Extracted molecule total RNA
Extraction protocol Rneasy Mini Kit (Qiagen) was used according to manufacturer´s instructions, including DNase I digestion.
Library was generated using the ScriptSeq Complete Kit (Illumina)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Description replicate 1
Data processing 1. Alignment of PE fastq files using STAR (2.05b) using GRCh38 and the following options: STAR --runThreadN 10 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outReadsUnmapped Fastq --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignMatesGapMax 1000000 --alignIntronMax 1000000 --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --outWigType bedGraph --outWigStrand Stranded
2. EdgeR analysis of combined STAR-derived read count tables, including batch effects.
Genome_build: GRCh38
 
Submission date Sep 21, 2017
Last update date Sep 21, 2020
Contact name Claudia GEBHARD
E-mail(s) claudia.gebhard@gmail.com
Organization name UNIVERSITY HOSPITAL REGENSBURG
Street address FRANZ-JOSEF-STRAUSS ALLEE 11
City REGENSBURG
ZIP/Postal code 93042
Country Germany
 
Platform ID GPL21290
Series (2)
GSE104112 Validation of AS1 as novel regulator of tumor resistance to immune cell attack
GSE202305 RNA-seq and ATAC-seq of tumor resistance to immune cell attack
Relations
BioSample SAMN07682425
SRA SRX3203947

Supplementary file Size Download File type/resource
GSM2790126_2B_Scr1_30min_CG_96.ReadsPerGene.txt.gz 292.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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