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Sample GSM3581885 Query DataSets for GSM3581885
Status Public on May 17, 2021
Title IL-4-negative Lung
Sample type SRA
Source name CD4 T cell from lung
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Lung
treatment: N. brasiliensis infection
day post infecton: Day 9
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.
Single cell RNA sequencing was performed using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 (10x Genomics) according to the manufacturer’s protocol using the Chromium Controller. Single cell libraries were sequenced on an Illumina Novaseq 6000.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description 10x_rawData.txt
Data processing Raw FASTQ files were demultiplixed, mapped, and quantified using CellRanger (verison 2.1.0, )
All post-quantification quality control and analysis was performed using the Seurat analysis suite. For each cell, we quantified four library/sequencing quality metrics: the number of genes for which at least one read was mapped, the total number of UMIs, the % of total UMIs which mapped to mitochondrial genes, and % of total UMIs which mapped to ribosomal genes. All cells which had between 500 and 4500 unique expressed genes, between 1000 and 30000 UMIs, less than 5% mitochondrial UMIs, and greater than 20% ribosomal UMIs were used for downstream analysis. Expression values Ei,j for gene i in cell j were calculated by dividing UMI count values for gene i by the sum of the UMI counts in cell j, to normalize for differences in coverage, and then multiplying by 10,000 to create TPM-like values, and finally calculating log2(TPM+1) values.
Genome_build: mm10
Supplementary_files_format_and_content: Text files containing gene counts and metatadata describing the sample time for each cell
Submission date Jan 28, 2019
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 GPL24247
Series (1)
GSE125788 Transcription profiling of IL-4-expressing CD4 T cells in the lung and lung-draining lymph nodes
BioSample SAMN10835335
SRA SRX5301672

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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