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Sample GSM5128808 Query DataSets for GSM5128808
Status Public on May 17, 2021
Title IL4-positive lymph node 2 [LR_1; IonXpress_025]
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:
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
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
BioSample SAMN18110396
SRA SRX10207311

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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