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Sample GSM7708458 Query DataSets for GSM7708458
Status Public on Aug 19, 2023
Title Sample 2 GEX
Sample type SRA
 
Source name Spleen
Organism Mus musculus
Characteristics tissue: Spleen
cell type: T cell
condition: NP-OVA immunization
library type: mRNA
hto: None
Extracted molecule polyA RNA
Extraction protocol Single cell suspensions were prepared from OVA immunized popliteal lymph nodes of SellCreERT2 ROSAtdT mice on day 17 post immunization and 7 days post tamoxifen delivery. Samples were indexed with TotalSeqC (BioLegend) cell surface antibodies and CD4 + , CD62 low , CD44 hi , PD1 hi , CXCR5 high , tdTomato+ and - Tfh cells were purified by flow cytometry, pooled and loaded onto a Chromium Controller (10x Genomics).
Library was performed according to the manufacter’s instructions (single cell 5’ v2 protocol, 10x Genomics). Briefly, T cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropriated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences were added.
V(D)J libraries were generated with 350 the Chromium Single Cell 5′ Library & Gel Bead Kit and 351 Chromium Single Cell V(D)J Enrichment Kit
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description 5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly-A RNA
Data processing The demultiplexing, barcode processing, gene counting and aggregation, and the TCR clonotype assembly were performed using the 10x Genomics Cell Ranger software v6.0.1
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz and airr_rearrangement.tsv
 
Submission date Aug 14, 2023
Last update date Aug 19, 2023
Contact name Thiago Y Oliveira
E-mail(s) toliveira@rockefeller.edu
Organization name The Rockefeller University
Department Immunology, Virology and Microbiology
Lab Laboratory of Molecular Immunology
Street address 1230 YORK AVE
City NEW YORK
State/province New York
ZIP/Postal code 10065
Country USA
 
Platform ID GPL24247
Series (1)
GSE240730 Germinal centers continually recruit naïve T cells that alter the balance between follicular T helper and follicular regulatory T cells.
Relations
BioSample SAMN36984018
SRA SRX21361438

Supplementary file Size Download File type/resource
GSM7708458_Sample2_GEX_barcodes.tsv.gz 20.3 Kb (ftp)(http) TSV
GSM7708458_Sample2_GEX_features.tsv.gz 284.1 Kb (ftp)(http) TSV
GSM7708458_Sample2_GEX_matrix.mtx.gz 34.2 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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