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Sample GSM7911151 Query DataSets for GSM7911151
Status Public on Dec 01, 2023
Title Cxcl12-GFP P6
Sample type SRA
 
Source name Mandibular molars
Organism Mus musculus
Characteristics tissue: Mandibular molars
cell type: CXCL12-GFP+ mesenchymal cells in tooth bud
genotype: Cxcl12-GFP/+
Extracted molecule total RNA
Extraction protocol Mandibular molars were extracted, dental pulp and periodontium were enzymatically dissociated and GFP+, tdTomato+ or GFP+tdTomato+ cells were FACS-isolated. ~10,000 cells were loaded onto 10X Genomic Chromium platform
10X Genomic Chromium Single Cell 3' v3 Libraries
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description Postnatal day 6
Data processing The sequencing data was first pre-processed using the 10X Genomics Cell Ranger software.
For alignment purposes, we generated and used a custom genome fasta and index file by including the sequences of eGFP and tdTomato_WPRE to the mouse genome (mm10).
Further downstream analysis steps were performed using the Seurat R package.
We filtered out cells with less than 1000 genes per cell and with more than 15% mitochondrial read content.
The downstream analysis steps include normalization, identification of highly variable genes across the single cells, scaling based on number of UMI, dimensionality reduction (PCA, and UMAP), unsupervised clustering, and the discovery of differentially expressed cell-type specific markers.
Assembly: mm10_trans_nono
Supplementary files format and content: barcodes.tsv, genes.tsv & matrix.mtx for Sample 1, barcodes.tsv.gz, features.tsv.gz & matrix.mtx.gz for Sample 2, barcodes.tsv.gz, features.tsv.gz & matrix.mtx.gz for Sample 3,
 
Submission date Nov 20, 2023
Last update date Jan 06, 2024
Contact name Mizuki NAGATA
E-mail(s) Mizuki.Nagata@uth.tmc.edu
Phone 7134862658
Organization name UTHealth
Department Orthodontics
Lab Ono lab
Street address 7500 Cambridge St
City Houston
State/province TX
ZIP/Postal code 77054
Country USA
 
Platform ID GPL21103
Series (1)
GSE248300 Single-cell RNAseq analysis of CXCL12+ mesenchymal cells of the murine molar
Relations
BioSample SAMN38335757
SRA SRX22587213

Supplementary file Size Download File type/resource
GSM7911151_scRNA-seq-1_Cxcl12GFP+_cells_at_P6_barcodes.tsv.gz 29.6 Kb (ftp)(http) TSV
GSM7911151_scRNA-seq-1_Cxcl12GFP+_cells_at_P6_genes.tsv.gz 212.8 Kb (ftp)(http) TSV
GSM7911151_scRNA-seq-1_Cxcl12GFP+_cells_at_P6_matrix.mtx.gz 68.0 Mb (ftp)(http) MTX
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Raw data are available in SRA

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