|
Status |
Public on May 17, 2021 |
Title |
IL4-negative lymph node 5 [LR_14; IonXpress_070] |
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: 139.19-09-18.S5XL-00648.bcmatrix.txt 144.21-09-18.S5XL-00648.bcmatrix.txt 145.21-09-18.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) |
reinhardtl@njhealth.org
|
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 |
SAMN18110890 |
SRA |
SRX10207324 |