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Status |
Public on Aug 19, 2023 |
Title |
Sample 2 GEX |
Sample type |
SRA |
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Source name |
Spleen
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Organism |
Mus musculus |
Characteristics |
tissue: Spleen cell type: T cell condition: NP-OVA immunization library type: mRNA hto: None
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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
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Library strategy |
RNA-Seq |
Library source |
transcriptomic single cell |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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Description |
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript poly-A RNA
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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
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Submission date |
Aug 14, 2023 |
Last update date |
Aug 19, 2023 |
Contact name |
Thiago Y Oliveira |
E-mail(s) |
toliveira@rockefeller.edu
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Organization name |
The Rockefeller University
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Department |
Immunology, Virology and Microbiology
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Lab |
Laboratory of Molecular Immunology
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Street address |
1230 YORK AVE
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City |
NEW YORK |
State/province |
New York |
ZIP/Postal code |
10065 |
Country |
USA |
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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. |
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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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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