|
| Status |
Public on Mar 14, 2018 |
| Title |
rep2_wt_aPDL1 [Lexogen_38] |
| Sample type |
SRA |
| |
|
| Source name |
Tumour infiltrating lymphocytes
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: Tumour infiltrating lymphocytes
genotype: wild type
treatment: aPDL1
|
| Treatment protocol |
Ab treatment with 0.5 mg anti-mouse PD-L1 (Clone10F.9G2; BE0101) or control Ab IgG2b (LTF-2; BE0090) was injected i.p. starting on d3 twice a week.
|
| Growth protocol |
5×10^5 B16-OVA tumor cells were injected s.c. into wild-type or Nr2f6-deficient mice.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the RNeasy® Mini Kit. (205113, Qiagen). RNA integrity was verified with the Agilent Bioanalyzer. Ion TorrentTM compatible libraries were generated from 20 ng total RNA input
QuantSeq 3' mRNA-Seq Library Prep Kit from Lexogen was used for library construction
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
therapy_normalized_counts.txt
Lexogen_38
|
| Data processing |
The reads were first preprocessed through a high stringency quality control pipeline consisting of adapter removal with Cutadapt and quality trimming with Trimmomatic to remove bases with bad quality scores. All reads shorter than 22 nucleotides were removed.
The quality-trimmed reads were mapped to the mm10 reference genome using a two-step alignment method; alignment with STAR followed by alignment of the unmapped reads with Bowtie2.
Gene-specific read counts were calculated using HTSeq-count. Differential expression analyses were performed using the R package DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: count matrix with normalized counts, where rows are genes and columns are samples
|
| |
|
| Submission date |
Mar 13, 2018 |
| Last update date |
Mar 14, 2018 |
| Contact name |
Dietmar Rieder |
| E-mail(s) |
dietmar.rieder@i-med.ac.at
|
| Phone |
+43512900371402
|
| Organization name |
Innsbruck Medical University
|
| Department |
Biocenter
|
| Lab |
Division of Bioinformatics
|
| Street address |
Innrain 80
|
| City |
Innsbruck |
| ZIP/Postal code |
6020 |
| Country |
Austria |
| |
|
| Platform ID |
GPL18635 |
| Series (1) |
| GSE111796 |
Nuclear Receptor NR2F6 as an Alternative Cancer Immune Checkpoint in the T Cell Compartment |
|
| Relations |
| BioSample |
SAMN08706789 |
| SRA |
SRX3786386 |
