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Status |
Public on Sep 17, 2024 |
Title |
p23098-s001_Mouse-1 |
Sample type |
SRA |
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Source name |
Lymph node
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Organism |
Mus musculus |
Characteristics |
strain: C57BL6 Sex: Female tissue: Lymph node cell type: CD4 T cells treatment: Skin-graft rejection
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Extracted molecule |
total RNA |
Extraction protocol |
Cells were FACS sorted and used to generate single cell suspensions. Samples were loaded onto the 10X Genomics Chromium Controller according to manufacturer's protocol. Library construction was performed using the Chromium Single Cell 5’ Library Construction Kit
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Library strategy |
OTHER |
Library source |
transcriptomic |
Library selection |
other |
Instrument model |
Illumina MiSeq |
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Description |
VDJ TCR
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Data processing |
VDJ TCR alignment and filtering for single-cell TCR sequencing samples were performed using Cell Ranger v3.1 VDJ TCR alignment and filtering for non-paired TCR sequencing samples were performed using MIXCR Assembly: A genome build is generally not required for TCR sequencing, as it focuses on the rearranged TCR genes using V(D)J reference libraries Supplementary files format and content: The processed data for single-cell TCR sequencing samples include filtered contig annotations, consensus annotations, clonotypes, and all contig annotations. For bulk TCR sequencing, the processed data contain clonotype information for both TCRα and TCRβ chains. Library strategy: VDJ TCR
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Submission date |
Sep 12, 2024 |
Last update date |
Sep 17, 2024 |
Contact name |
Christian Larsen |
E-mail(s) |
clarsen@emory.edu
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Organization name |
Emory University
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Department |
Department of Surgery
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Lab |
Larsen Lab
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Street address |
101 Woodruff Circle
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City |
Atlanta |
State/province |
Georgia |
ZIP/Postal code |
30328 |
Country |
USA |
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Platform ID |
GPL16417 |
Series (1) |
GSE277075 |
Identification of rejection-associated indirect CD4 T cell epitopes provides a target for donor-specific transplant tolerance |
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Relations |
BioSample |
SAMN43750297 |
SRA |
SRX26070527 |
Supplementary file |
Size |
Download |
File type/resource |
GSM8513547_p23098-s001_Mouse-1_S1_L001.clones_TRAD.tsv.gz |
467.6 Kb |
(ftp)(http) |
TSV |
GSM8513547_p23098-s001_Mouse-1_S1_L001.clones_TRB.tsv.gz |
409.4 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
Raw data are available in SRA |
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