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Sample GSM8513547 Query DataSets for GSM8513547
Status Public on Sep 17, 2024
Title p23098-s001_Mouse-1
Sample type SRA
 
Source name Lymph node
Organism Mus musculus
Characteristics strain: C57BL6
Sex: Female
tissue: Lymph node
cell type: CD4 T cells
treatment: Skin-graft rejection
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
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina MiSeq
 
Description VDJ TCR
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
 
Submission date Sep 12, 2024
Last update date Sep 17, 2024
Contact name Christian Larsen
E-mail(s) clarsen@emory.edu
Organization name Emory University
Department Department of Surgery
Lab Larsen Lab
Street address 101 Woodruff Circle
City Atlanta
State/province Georgia
ZIP/Postal code 30328
Country USA
 
Platform ID GPL16417
Series (1)
GSE277075 Identification of rejection-associated indirect CD4 T cell epitopes provides a target for donor-specific transplant tolerance
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 SelectorHelp
Raw data are available in SRA

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