|
| Status |
Public on Mar 01, 2021 |
| Title |
Aflibercept-AMG386-aPD-1_3 |
| Sample type |
SRA |
| |
|
| Source name |
Brain microvessels from tumor bearing region from mice treated with Aflibercept-AMG386 and anti-PD1
|
| Organism |
Mus musculus |
| Characteristics |
region: tumor bearing region
agent: Aflibercept-AMG386 and anti-PD1
tissue: Brain microvessels
|
| Treatment protocol |
Brain microvessels were isolated from tumor bearing brain region of treated or untreated mice at 21-day post tumor cell transplanantation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from brain microvessels using the Rneasy plus micro Kit (Qiagen) combined with on-column DNase digestion (DNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA.
100ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Clontech).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Aflibercept-AMG386-aPD-1_3
|
| Data processing |
Reaper version 13-100 was employed to trim reads after a quality drop below a mean of Q20 in a window of 10 nucleotides. Only reads between 30 and 150 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl mouse genome version mm10 (GRCm38) using STAR 2.4.0a with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%.
The number of reads aligning to genes was counted with featureCounts 1.4.5-p1 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Differentially expressed genes were identified using DESeq2 version 1.62
The Ensemble annotation was enriched with UniProt data (release 06.06.2014) based on Ensembl gene identifiers.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include library size normlized counts
|
| |
|
| Submission date |
Apr 25, 2019 |
| Last update date |
Mar 01, 2021 |
| Contact name |
Stefan Günther |
| E-mail(s) |
stefan.guenther@mpi-bn.mpg.de
|
| Organization name |
MPI for heart and lung research
|
| Street address |
ludwigtr. 43
|
| City |
bad nauheim |
| ZIP/Postal code |
61231 |
| Country |
Germany |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE130324 |
RNA sequencing of blood-brain barrier (BBB) microvessels from mice with orthotopic GBM showing the benefit of triple therapy combining anti-immune checkpoint therapy with dual-anti angiogenic therapy. |
|
| Relations |
| BioSample |
SAMN11507135 |
| SRA |
SRX5736058 |
