|
| Status |
Public on Dec 30, 2016 |
| Title |
aPDL1 rep2 RNA |
| Sample type |
SRA |
| |
|
| Source name |
tumor cells
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6N
genotype/variation: wild type
age: 8- to 12-week-old
time point: day 14
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted, quality validated with the Agilent Bioanalyzer, and submitted to Lexogen 3’ QuantSeq library preparation, following the manufacturers instructions (Lexogen, Vienna Biocenter, Austria). Resulting libraries were sequenced with the Ion ProtonTM System.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
processed data file:
aPDL1_IgG2b_normalized_counts.txt
|
| Data processing |
The sequencing reads were preprocessed through a quality control pipeline consisting of adapter removal with Cutadapt and quality trimming with Trimmomatic to remove bases with bad quality scores and reads shorter than 22 nucleotides. 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. From the reads that mapped to multiple locations in the genome only the primary alignment was retained. Reads that mapped to ribosomal RNA locations in the genome were removed from further analysis using the split_bam.py script from the quality control package RSeQC. Gene-specific read counts were calculated using HTSeq-count. The R package DESeq2 was used for generating normalized counts.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized counts for each Sample
|
| |
|
| Submission date |
Dec 30, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Mirjana Efremova |
| E-mail(s) |
mirjana.efremova@i-med.ac.at
|
| Organization name |
Medical University of Innsbruck
|
| Street address |
Innrain 80-82
|
| City |
Innsbruck |
| ZIP/Postal code |
6020 |
| Country |
Austria |
| |
|
| Platform ID |
GPL18635 |
| Series (2) |
| GSE93017 |
Immunoediting of the cancer genome during tumor progression and activation of PD-1/PD-L1 axis in a mouse model of carcinoma [RNA-seq] |
| GSE93018 |
Immunoediting of the cancer genome during tumor progression and activation of PD-1/PD-L1 axis in a mouse model of carcinoma |
|
| Relations |
| BioSample |
SAMN06191638 |
| SRA |
SRX2452243 |
