|
| Status |
Public on Dec 21, 2022 |
| Title |
Tumor-bearing mouse injected with PBS, mouse 1 |
| Sample type |
SRA |
| |
|
| Source name |
Omentum of mouse challenged with tumor and injected with saline solution on day 6
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell line: B16-OVA
treatment: saline solution
tissue: Omentum
|
| Treatment protocol |
On day 6 mice were either injected with PBS, or treated with OVA-specific T lymphocytes electroporated with IL-12 mRNA either IP or IV.
|
| Growth protocol |
7-10-old week C57BL/6 mice were injected with 500,000 cells of B16-OVA cell line IP on day 0. On day 6 mice were randomized.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
18h after OT-I T cells injection, mice were euthanized and omenta were extracted and stored in RNAlater solution at -80C. RNA extraction was performed using the RNeasy Mini Kit (Qiagen, Hilden, Germany)
Library preparation was performed using the NEBNext Ultra II Directional RNA Library Prep Kit (NEB) following the manufacturer’s protocol. All sequencing libraries were constructed from 100 ng of total RNA according to the manufacturer's instructions
Briefly, the protocol selects and purifies poly(A) containing RNA molecules using magnetic beads coated with poly(T) oligos. Poly(A)-RNAs are fragmented and reverse transcribed into first cDNA strand using random primers. The second cDNA strand is synthesized in the presence of dUTP to ensure strand specificity. Resulting cDNA fragments are purified with NEBNext purification beads, adenylated at 3′ ends and then ligated with uniquely indexed sequencing adapters. Ligated fragments are purified and PCR amplified to obtain the final libraries. The quality and quantity of the libraries were verified using Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and 4200 Tapestation with High Sensitivity D1000 ScreenTape (Agilent Technologies). Libraries were then sequenced using a NextSeq2000 sequencer (Illumina). 40 million pair-end reads (100 bp; Rd1:51; Rd2:51) were sequenced for each sample and demultiplexed using Cutadapt. RNA-Seq was carried out at the Genomics Unit of the Center for Applied Medical Research (CIMA, Universidad de Navarra).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
Tumor-bearing omentum mouse 1
PBS1
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence, then mapped to mm39 whole genome using STAR v2.7.9
Read summarization were obtained using featureCounts.
Normalization were performed in R statistical environment following the limma-voom pipeline
Genome_build: mm39
Supplementary_files_format_and_content: Tab-delimited text file includee log2(cpm) values for each gene and every Sample
Supplementary_files_format_and_content: Tab-delimited text file with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Feb 28, 2022 |
| Last update date |
Dec 21, 2022 |
| Contact name |
Jose Gonzalez |
| E-mail(s) |
[email protected]
|
| Organization name |
FIMA
|
| Street address |
C/PIO XII s/n
|
| City |
Pamplona |
| State/province |
Navarra |
| ZIP/Postal code |
31008 |
| Country |
Spain |
| |
|
| Platform ID |
GPL30172 |
| Series (1) |
| GSE197612 |
RNA-Seq of mice omenta after intraperitoneal (IP) or systemic delivery (IV) of tumor-specific T cells |
|
| Relations |
| BioSample |
SAMN26314999 |
| SRA |
SRX14319050 |
