|
| Status |
Public on Mar 01, 2018 |
| Title |
KLRG1- Reporter- OT-I cells (exp2) |
| Sample type |
SRA |
| |
|
| Source name |
OT-I cell subset purified from spleen
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL/6
genotype/variation: wild type
tissue: Spleen
cell type: KLRG1- Reporter- OT-I cells
treatment: Infection with ovalbumin-expressing Listeria monocytogenes (LM-OVA)
day post-infection: 110
|
| Extracted molecule |
total RNA |
| Extraction protocol |
OT-I cell subsets were isolated from spleen, purified by FACS and RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy mini kit. Quality control was performed with Agilent Bioanalyser.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
S06613
processed data file: Matrix_table.txt
|
| Data processing |
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38/mm10 whole genome using TopHat2 version 2.0.8.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks version 2.1.1.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Matrix table.txt: Tab-delimited text file includes FPKM values of all six samples.
|
| |
|
| Submission date |
Feb 14, 2018 |
| Last update date |
Mar 01, 2018 |
| Contact name |
Dietmar Herndler-Brandstetter |
| Organization name |
Medical University of Vienna
|
| Department |
Institute of Cancer Research
|
| Street address |
Borschkegasse 8a
|
| City |
Vienna |
| ZIP/Postal code |
1090 |
| Country |
Austria |
| |
|
| Platform ID |
GPL18480 |
| Series (2) |
| GSE110629 |
Next-generation sequencing of three memory OT-I cell subsets from mice infected with Listeria monocytogenes |
| GSE110707 |
KLRG1+ Effector CD8+ T Cells Lose KLRG1, Differentiate Into All Memory T Cell Lineages, and Convey Enhanced Protective Immunity |
|
| Relations |
| BioSample |
SAMN08536817 |
| SRA |
SRX3700448 |
