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Sample GSM6663300 Query DataSets for GSM6663300
Status Public on Oct 25, 2022
Title SA-NucPr-2_GEX
Sample type SRA
Source name Lymph node
Organism Mus musculus
Characteristics tissue: Lymph node
strain: C57BL/6
cell type: Follicular T cells
genotype: WT
Extracted molecule polyA RNA
Extraction protocol Single Cell 5' R2-only
Single cell libraries were generated using the 10x Genomics Chromium Controller with Immune Profiling reagents following the manufacturer’s protocol (10x Genomics)
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description 10x Genomics
Data processing 10x Genomics CellRanger-6.1.2
The single cell RNA-seq libraries were prepared at the University of Michigan Advanced Genomics Core using the 10X Genomics Chromium Next GEM Single Cell 5′ R2 only following the manufacturer’s protocol.
The libraries were run on the PerkinElmer LabChip GX Touch HT for library quality control before sequencing.
Libraries were sequenced on a NovaSeq6000 with the following run configuration: R1 - 28, Index1-10, R2 - 150. The total number of cells recovered was 15514. 
Assembly: comma-separated values file that is a delimited text files include FPKM values for each sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: html file containing summary of the processed data
Submission date Oct 20, 2022
Last update date Oct 28, 2022
Contact name Irina Grigorova
Organization name University of Michigan
Department Microbiology and Immunology
Street address 1150 W MEDICAL CENTER DR
City Ann Arbor
ZIP/Postal code 48109
Country USA
Platform ID GPL24247
Series (1)
GSE216236 Gene expression and VDJ TCR profile of follicular T cells from immunized with nuclear proteins and control mice
BioSample SAMN31392789
SRA SRX17971670

Supplementary file Size Download File type/resource
GSM6663300_Sample_5077-FK-4_GEX_processed.tar.gz 70.0 Mb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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