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Sample GSM3756179 Query DataSets for GSM3756179
Status Public on Sep 13, 2019
Title Knee-joint at E14.5 single-cell RNAseq by 10X Genomics
Sample type SRA
Source name Lgr5-EGFP-IRES-creERT2/+ heterozygous embryos, GFP expressed in Lgr5+ cells in the forming knee joint
Organism Mus musculus
Characteristics genotype: Lgr5-EGFP-IRES-creERT2/+ heterozygous
cell type: GFP expressed in Lgr5+ cells in the forming knee joint
developmental stage: E14.5
strain background: C57bl/6
Growth protocol Lgr5GFP/+ (c57bl6) mice were crossed with c57bl6 wt mice to generate the embryos
Extracted molecule total RNA
Extraction protocol Tissue was digested with 0.2% Collagenase II, 0.1% Dispase and 0.1% Hyaluronidase. Cells were washed twice with HBSS, and filtered through 40um cell strainer twice before loading onto the 10x genomics machine.
Single cell encapsulation and cDNA libraries were prepared by Chromium™ Single Cell 3’ Reagent Kits v2 and Chromium™ Single Cell A Chip Kit. Cells in suspension are counted and loaded into individual wells of 10X Chromium Single Cell chip. Single cells are then encapsulated into Gel in-beads emulsions (GEM) by 10X Chromium Controller. Single Cell 3’ Reagent Kits v2 is used to perform downstream steps, in brief as follows: reverse transcription is performed on GEMs, followed by cDNA clean up and amplification. The double-stranded cDNA will then go through enzymatic fragmentation, adapter ligation, index PCR and SPRIselect size selection per manufacturer’s protocol. Library size and concentration is determined by Qubit and Bioanalyzer assays. The libraries are denatured and diluted to optimal concentration. Cluster generation is performed on the flow cell with HiSeq PE Cluster Kit v4 by cbot. Illumina HiSeq SBS Kit v4 is used for sequencing run at 100 bp for read 1 and read 2.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
Description Knee-joint at E14.5 single-cell RNAseq by 10X Genomics.
Data processing Using software from Illumina (bcl2fastq), sequencing reads were assigned into individual samples. An average of 72% of the bases achieved a quality score1 of Q30 where Q30 denotes the accuracy of a base call to be 99.9%.
The demultiplexed FASTQ files were then processed with cellranger-2.1.0 (10X Genomics, Inc), a proprietary pipeline that perform alignment, quantification, and light-weight analyses in one go.
R1 contains barcode (bp 1-16) and UMI (bp 11-26).
Genome_build: Grcm38(mm10)
Supplementary_files_format_and_content: space-delimited text files containing gene expression table of the cells in sparse format (gene-id, cell-id, number-of-UMIs)
barcodes.tsv: cell barcodes for cells that pass non-background cutoff
genes.tsv: a list of all genes
matrix.mtx: gene expression table in sparse format
Submission date May 08, 2019
Last update date Sep 14, 2019
Contact name Peikai Chen
Phone 852-258315217
Organization name The University of Hong Kong
Department Faculty of Medicine
Street address Sassoon Road 5
City Pok Fu Lam
ZIP/Postal code 10000
Country Hong Kong
Platform ID GPL18480
Series (1)
GSE130919 Lgr5 and Col22a1 mark progenitor cells in the lineage toward juvenile articular chondrocytes
BioSample SAMN11605332
SRA SRX5807396

Supplementary file Size Download File type/resource
GSM3756179_barcodes.tsv.gz 22.7 Kb (ftp)(http) TSV
GSM3756179_genes.tsv.gz 212.7 Kb (ftp)(http) TSV
GSM3756179_matrix.mtx.gz 35.3 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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