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Sample GSM5219092 Query DataSets for GSM5219092
Status Public on Jun 18, 2021
Title siSIRT1-2
Sample type SRA
 
Source name Human pancreatic cancer cell line
Organism Homo sapiens
Characteristics cell type: PANC-1
treatment: siSIRT1
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from the PANC-1 cells using Trizol reagent (Invitrogen). RNA quality was checked by Agilent 2100 Bioanalyzer (Agilent Technologies, USA).
RNA libraries were prepared for sequencing using standard BGI protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model BGISEQ-500
 
Data processing SOAPnuke (version: v1.5.2) was used for filter reads, parameters: -1 15 -q 0.5 -n 0.1.
Bowtie2 (version: v2.2.5) was used to map clean reads to reference gene, parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200.
HISAT (version: v2.0.4) was used to align clean reads to the mouse genome, parameters: -p 8 --phred64 --sensitive -I 1 -X 10000.
RSEM (version: v1.2.12) was used for abundance measurement, parameters: default.
FPKM method was used in calculated expression level.
Genome_build: hg 19
Supplementary_files_format_and_content: tab-delimited text files ChIPseeker
 
Submission date Mar 30, 2021
Last update date Jun 20, 2021
Contact name yan wang
E-mail(s) yanwang@tmu.edu.cn
Organization name National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences
Street address 17 panjiayuan nanli, chaoyang district, Beijing, China
City beijing
ZIP/Postal code 100021
Country Zimbabwe
 
Platform ID GPL23227
Series (1)
GSE171118 RNA-Seq analysis SIRT1 knockdown effect on pancreatic cancer cell line
Relations
BioSample SAMN18534217
SRA SRX10474295

Supplementary file Size Download File type/resource
GSM5219092_siSIRT1_2.txt.gz 302.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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