|
| Status |
Public on Oct 19, 2021 |
| Title |
14837 CM |
| Sample type |
SRA |
| |
|
| Source name |
PDAC Tumor
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: mouse PDAC 14837
treatment: treated with 14837 conditional medium
|
| Treatment protocol |
14837 PDAC cells were treated with conditional medium for 48h.
|
| Growth protocol |
14837 PDAC cells were maintained at 37℃ and 5% CO2 in DMEM with 10% (v/v) FBS and 100U/ml penicillin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent.2 ug of total RNA is used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standrad Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Normal sequence Illumina Novaseq
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.1.0 with parameters hisat2 -p 8 --dta -x -1 -2 -S.
Transcript assembly and quantification with StringTie. Analysis of RNA-seq experiments requires accurate reconstructions of all the isoforms expressed from each gene, as well as estimates of the relative abundance of those isoforms. Use parameters as stringtie –e –B -p 8 -G -o.
Fragments per kilobase of transcript per million mapped reads (FPKM) were calculated using Ballgown from Pertea M et al., Nature Protocols, 2016. In short, differential expression analysis proceeds using a linear model. The FPKM values attached to transcripts are typically highly skewed; thus, to stabilize the variance, Ballgown’s builtin functions apply a log transformation and then fit standard linear models that can be used to test for differential expression.
Genome_build: mm10
Supplementary_files_format_and_content: text files include FPKM values for each Sample ...
|
| |
|
| Submission date |
Oct 12, 2021 |
| Last update date |
Oct 19, 2021 |
| Contact name |
YU ZHANG |
| E-mail(s) |
1410305236@pku.edu.cn
|
| Phone |
01082805861
|
| Organization name |
Peking Univ.
|
| Street address |
XUEYUANLU No.38 Haidian District, PKUHSC Anatomy Building
|
| City |
北京 |
| State/province |
non-US Resident |
| ZIP/Postal code |
100191 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE185750 |
Pancreatic Tumor Microenvironment Maintains Tumor Growth through Nucleosides Secretion |
|
| Relations |
| BioSample |
SAMN22228205 |
| SRA |
SRX12579829 |
