|
| Status |
Public on May 17, 2021 |
| Title |
IL4-positive lymph node 1 [GFP_plus_CD4_LN; IonXpress_089] |
| Sample type |
SRA |
| |
|
| Source name |
CD4 T cells from mediastinal lymph node
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
treatment: N. brasiliensis infection
day post infecton: Day 9
tissue: Mediastinal lymph node
cell type: CD4 T cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
CD4+ T cells were sorted into single cell suspensions and sample RNA was isolated using the Quick-RNA Microprep kit (Zymo Research) according to the manufacturer’s protocol.
Whole genome gene expression data was generated using the Ion Ampliseq Transcriptome Mouse Gene Expression Kit (ThermoFisher Scientific) with 2 nanograms of total RNA according the manufacturer’s protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent S5 |
| |
|
| Description |
processed data file:
124.18-04-18.S5XL-00648.bcmatrix.txt
RawCount_Matrix.txt
countNorm_Matrix.txt
vstNorm_Matrix.txt
|
| Data processing |
Basecalling (Ion Torrent S5)
Alignment (Torrent mapping alignment program)
Quantification (Ion Torrent Ampliseq RNA plugin, unique mapping mode)
Count Normalizaiton (DESeq2)
VST Normalizaiton, blind = TRUE (DESeq2)
Genome_build: AmpliSeq Mouse Transcriptome V1 Reference (based on GRCm38)
Supplementary_files_format_and_content: Count matrices (Raw, Count Normalized, VST Normalized)
|
| |
|
| Submission date |
Mar 02, 2021 |
| Last update date |
May 17, 2021 |
| Contact name |
Richard Lee Reinhardt |
| E-mail(s) |
[email protected]
|
| Organization name |
National Jewish Health
|
| Department |
Biomedical Research
|
| Lab |
Reinhardt
|
| Street address |
1400 Jackson Street, K817A
|
| City |
Denver |
| State/province |
Colorado |
| ZIP/Postal code |
80206 |
| Country |
USA |
| |
|
| Platform ID |
GPL25723 |
| Series (1) |
| GSE125788 |
Transcription profiling of IL-4-expressing CD4 T cells in the lung and lung-draining lymph nodes |
|
| Relations |
| BioSample |
SAMN18110459 |
| SRA |
SRX10207306 |
