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Sample GSM5128809 Query DataSets for GSM5128809
Status Public on May 17, 2021
Title IL4-negative lymph node 2 [LR_2; IonXpress_026]
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 SAMN18110391
SRA SRX10207312

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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