|
| Status |
Public on Jul 01, 2020 |
| Title |
TTC_SC_144 |
| 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 |
SAMN07533691 |
| SRA |
SRX3111155 |
