|
Status |
Public on Oct 18, 2022 |
Title |
MHC+ DP transcripts (file prefix: PDP_) |
Sample type |
SRA |
|
|
Source name |
Thymocytes developing for 9 days in vitro from stem cells
|
Organism |
Mus musculus |
Characteristics |
strain: C57BL/6 cell line: hematopoietic stem cells
|
Growth protocol |
Wild-type hematopoietic stem cells isolated from fetal liver were cultured on stromal support cells expressing MHC (OP9-DL4) or not expressing MHC (OP9-DL4-Tap2/B2m-KO) for 9d
|
Extracted molecule |
total RNA |
Extraction protocol |
Following growth cells were separated by surface phenotype using FACS into DN3a, DN3b, DN4 and DP cells Cell separation protocol: Isolated cells were washed, assessed for viability, and loaded onto a 10X Chromium instrument (10X Genomics) per the manufacturer’s instructions. Single-cell RNA libraries were generated using the Single Cell 5’ Reagent Kit (10X Genomics) per user guide together with the 5' V(D)J Kit (10X Genomics)for parallel determination of single cell TCR alpha and beta chains representation
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
scRNA-Seq
|
Data processing |
For the thymocyte scRNA-Seq analysis, all raw sequencing reads were processed using the 10X Genomics CellRanger bioinformatics pipeline v3.0.2. For the thymocyte scRNA-Seq analysis, all analysis was performed using the 10x Loupe browser v4.2 (for Gene expression) and the 10x Single-cell V(D)J browser v3.0.0 (for TCR clonotypic analysis). For the Gene Expression analysis of the stromal support cells expressing MHC (OP9-DL4) or not expressing MHC (OP9-DL4-Tap2/B2m-KO), all initial processing (Quality control: Error Rate Distribution, GC content distribution and data filtering), mapping to mouse reference genome, and normalized gene expression quantification, was performed by the sequencing facility at Novogene using standard procedures. Genome_build: mm10
|
|
|
Submission date |
Oct 18, 2021 |
Last update date |
Oct 18, 2022 |
Contact name |
Jonathan S. Duke-Cohan |
E-mail(s) |
Jonathan_Duke-Cohan@dfci.harvard.edu
|
Phone |
+1-617-632-3122
|
Organization name |
Dana-Farber Cancer Institute
|
Department |
Medical Oncology
|
Lab |
Immunobiology
|
Street address |
450 Brookline Avenue JF517
|
City |
Boston |
State/province |
MA |
ZIP/Postal code |
02215 |
Country |
USA |
|
|
Platform ID |
GPL19057 |
Series (1) |
GSE186049 |
Pre-T cell receptor Self-MHC Sampling Restricts Thymocyte Dedifferentiation |
|
Relations |
BioSample |
SAMN22369467 |
SRA |
SRX12673896 |