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Status |
Public on Jun 18, 2021 |
Title |
siSIRT1-2 |
Sample type |
SRA |
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Source name |
Human pancreatic cancer cell line
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Organism |
Homo sapiens |
Characteristics |
cell type: PANC-1 treatment: siSIRT1
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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
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
BGISEQ-500 |
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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
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Submission date |
Mar 30, 2021 |
Last update date |
Jun 20, 2021 |
Contact name |
yan wang |
E-mail(s) |
yanwang@tmu.edu.cn
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Organization name |
National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences
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Street address |
17 panjiayuan nanli, chaoyang district, Beijing, China
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City |
beijing |
ZIP/Postal code |
100021 |
Country |
Zimbabwe |
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Platform ID |
GPL23227 |
Series (1) |
GSE171118 |
RNA-Seq analysis SIRT1 knockdown effect on pancreatic cancer cell line |
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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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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