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Sample GSM5629779 Query DataSets for GSM5629779
Status Public on Oct 18, 2022
Title MHC+ DN3a transcripts (file prefix: PDN3a_)
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 SAMN22369470
SRA SRX12673893

Supplementary file Size Download File type/resource
GSM5629779_PDN3a_barcodes.tsv.gz 34.0 Kb (ftp)(http) TSV
GSM5629779_PDN3a_features.tsv.gz 272.8 Kb (ftp)(http) TSV
GSM5629779_PDN3a_matrix.mtx.gz 50.0 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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