 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 18, 2021 |
| Title |
Vector-1 |
| Sample type |
SRA |
| |
|
| Source name |
Tumor tissue
|
| Organism |
Homo sapiens |
| Characteristics |
mouse strain: NOD/SCID
injected cell line: PANC-1
treatment: lentivirus overexpressing Vector
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from tumor samples 4 weeks after injection using Trizol reagent (Invitrogen, USA). Agilent 2100 Bioanalyzer (Agilent Technologies, USA) was used to evaluate the RNA quality.
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 include FPKM values for each Sample.
|
| |
|
| Submission date |
Dec 13, 2020 |
| 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) |
| GSE163101 |
RNA-Seq analysis SIRT1 overexpression effect on pancreatic tumor tissue in NOD/SCID mice |
|
| Relations |
| BioSample |
SAMN17071942 |
| SRA |
SRX9679508 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4972105_V1.txt.gz |
226.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
