|
| Status |
Public on Mar 05, 2024 |
| Title |
CD8_Prf1_UnRx_3 2511407_06 |
| Sample type |
SRA |
| |
|
| Source name |
Blood
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6 Prftm1Sdz/J
tissue: Blood
cell type: CD8+ T cells
genotype: Prf1-/-
treatment: LCMV untreated
time: Day 9
|
| Treatment protocol |
CD8 T cells and CD11b+ Ly6C+Ly6G- monocytes were sort-purified from the spleens of mice collected on day 9 post-infection, 1 hour after receiving an 11th dose of JAK inhibitor or vehicle via oral gavage (3 mice per treatment group)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from sorted cell populations using the RNeasy Micro Kit (Qiagen, Germantown, Maryland). The quality and quantity of the initial RNA was determined by using the Agilent 2100 Bioanalyzer with the Eukaryote Total RNA Pico kit.
For each good quality sample, 2.5-25 nanograms of total RNA was used in the Tecan Ovation RNA sequencing system v2 protocol as written to create SPIA (single primer isothermal amplification)-cDNA. Once the cDNA was purified, five hundred nanograms of each sample was sheared using the Covaris LE220 focused ultra sonicator. The shearing plate used was the 96 microtube-50 AFA fiber plate and the target base pair size was 300. The settings for the shearing were the following: Peak incident Power (W) of 450, duty factor of 15%, cycles per burst 1000 with a 100 second treatment time. Once the cDNA was sheared, libraries were created using the KAPA Hyper-Prep kit from Roche.
Based on the starting cDNA input amount, the Kapa Hyper protocol recommended four pcr cycles for the amplification step while the rest of the protocol was followed as described. The indexes used were the UDI DNA indexes from Illumina. Eukaryote Total RNA Pico kit (catalog: 5067-1513) Tecan (formally NuGen) Ovation RNA sequencing system v2 (catalog: 7102-32) Covaris 96 tube plate (catalog:520168) KAPA Hyper-Prep (catalog: KK8504) UDI DNA Indexes from Illumina (catalog: 20022370)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
CD8_Prf1_UnRx_3
CD8_Prf1_UnRx_3
|
| Data processing |
Total stranded RNA sequencing data were processed by the internal AutoMapper pipeline. The raw reads were firs trimmed (Trim-Galore version 0.60), mapped to mouse genome assembly (mm10) (STAR v2.7). The gene level expression values were quantified (RSEM v1.31) based on GENCODE annotation (M22 [mm10]).
Assembly: GRCm38
Supplementary files format and content: coutns matrix, RSEM counts
|
| |
|
| Submission date |
Apr 27, 2023 |
| Last update date |
Mar 05, 2024 |
| Contact name |
Kim Nichols |
| E-mail(s) |
kim.nichols@stjude.org
|
| Organization name |
St. Jude Children's Research Hospital
|
| Department |
Oncology
|
| Lab |
Nichols Lab
|
| Street address |
262 Danny Thomas Pl
|
| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE230771 |
Differential Effects of JAK1 vs. JAK2 Inhibition in Mouse Models of Hemophagocytic Lymphohistiocytosis |
|
| Relations |
| BioSample |
SAMN34405349 |
| SRA |
SRX20119108 |
