NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2748535 Query DataSets for GSM2748535
Status Public on Jul 01, 2020
Title TTC_SC_147
Sample type SRA
 
Source name WT
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: tail tendon
genotype: WT
age: 4-wk-old
Treatment protocol Tail tendons from 4-wk-old wild-type or Mkx-/- mice was minced into desired pieces and digested in 0.2% collagenase I diluted in low-glucose Dulbecco’s modified Eagle’s medium solution at 37°C for 2 hours. Then the cell suspension was filtered using 40 μm strainer to remove the incompletely digested clumps and adjusted to a concentration of 4×10^5 cells/ml.
Extracted molecule total RNA
Extraction protocol Single-cell capture, RNA extraction and cDNA synthesis were performed following the methods described in the Fluidigm protocol(PN 100-9886)
The cDNA reaction products were quantified using the Qubit and were then diluted to a final concentration of 0.2 ng/ μl using C1 Harvest Reagent. The diluted cDNA reaction products were then converted into mRNA-seq libraries using the Nextera XT DNA Sample Preparation Kit (Illumina, FC-131-1096, -2001 and -2002) following the manufacturer’s instructions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Data processing Single-cell RNA sequence reads were evaluated by AfterQC. Bad reads were detected automatically and removed. Bases at 3' end of the read were further timmed by NGSQCToolkit if their PHRED quality score were less than.
The reads were mapped to the mouse genome(mm10) using bowtie2.
The mapped reads for genes were counted via featureCounts. Gene expression was represented by CPM (tags per million).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include count values for each sample
 
Submission date Aug 22, 2017
Last update date Jul 01, 2020
Contact name HONGWEI OUYANG
E-mail(s) hwoy@zju.edu.cn
Phone 13958108337
Organization name Zhejiang University
Street address 866 Yu Hang Tang Road,Hangzhou, Zhejiang, P.R.China.
City Hangzhou
State/province Zhejiang
ZIP/Postal code 310058
Country China
 
Platform ID GPL21273
Series (2)
GSE102929 Divergent cell differentiation trajectory in normal and heterotopic ossified soft connective tissues
GSE102931 Alteration of transcriptomic and epigenetic landscapes in normal and heterotopic ossified tendons
Relations
BioSample SAMN07533688
SRA SRX3111158

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap