|
| Status |
Public on Jul 15, 2022 |
| Title |
CD4 T cells, Control Day 0 rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
Spleen
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
treatment: control
time point: Day 0
tissue: spleen
cell type: CD4 T cell
|
| Extracted molecule |
total RNA |
| Extraction protocol |
CD4 T cells were isolated using immunomagnetic negative selection. T cells were then pelleted and RNA was extracted using a commercial kit (Macherey-Nagel)
100ng RNA was used to prepare libraries for sequencing using Nugen Mouse RNA-seq kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
S14
|
| Data processing |
Illumina BaseSpace software (bcl2fastq v2.20.0.422) used for basecalling.
Sequenced reads were trimmed for adaptor sequence with cutadapt (https://doi.org/10.14806/ej.17.1.200) (version 1.8.1), and mapped to mm10 reference genome using star v2.5.3a with default settings.
Uniquely mapped reads were counted at gene-level by HTSeq (version 0.6.1) using Gencode vM21 annotations for mouse
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file includes normalized gene count for each sample
|
| |
|
| Submission date |
Sep 08, 2021 |
| Last update date |
Jul 15, 2022 |
| Contact name |
Rebecca Hesterberg |
| E-mail(s) |
[email protected]
|
| Organization name |
Moffitt Cancer Center
|
| Street address |
12902 Magnolia Dr.
|
| City |
Tampa |
| ZIP/Postal code |
33612 |
| Country |
USA |
| |
|
| Platform ID |
GPL30172 |
| Series (1) |
| GSE183693 |
Gene expression profiling of CD4 T cells in a mouse model of B-cell Lymphoma |
|
| Relations |
| BioSample |
SAMN21357963 |
| SRA |
SRX12105577 |
