|
| Status |
Public on Sep 21, 2018 |
| Title |
TAM_B |
| Sample type |
SRA |
| |
|
| Source name |
CT26-Sg-Con implanted tumor
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: BALB/C
genotype/variation: wild type
cell type: Tumor-associated macrophages
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TAMs were isolated from tumors by flow cytometry, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
Libraries were prepared using an MGIEasy™ mRNA kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
processed data file: TAM.gene.fpkm.txt
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase Million (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8 (MGSCv36)
Supplementary_files_format_and_content: TAM.gene.fpkm.txt: Tab-delimited text file includes FPKM values for each Sample.
|
| |
|
| Submission date |
Sep 20, 2018 |
| Last update date |
Sep 21, 2018 |
| Contact name |
Haoran Zha |
| E-mail(s) |
zhahaoran@tmmu.edu.cn
|
| Organization name |
Institute of Cancer, Xinqiao Hospital,Third Military Medical University
|
| Street address |
Shaping Street #31
|
| City |
Chongqing |
| ZIP/Postal code |
400037 |
| Country |
China |
| |
|
| Platform ID |
GPL23479 |
| Series (1) |
| GSE120274 |
Intracellular activation of complement C3 leads to PD-L1 antibody treatment resistance via modulating tumor-associated macrophages |
|
| Relations |
| BioSample |
SAMN10075464 |
| SRA |
SRX4704234 |
