|
| Status |
Public on Feb 29, 2016 |
| Title |
Rib_Chondrocyte_Col10a1mCherry_Sorted-4_RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
Enzyme digested rib chondrocytes_P3
|
| Organism |
Mus musculus |
| Characteristics |
cell type: chondrocytes
tissue: rib
developmental stage: Postnatal day 3
mouse strain: Swiss Webster
genotype: Col10a1mCherry
|
| Growth protocol |
Col10a1mCherry transgenic mice was raised in standard mouse husbandary at USC mouse facility
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Rib cages were isolated from Col10a1mCherry mice by manual dissecting. Dissected rib cages were washed in Dulbecco's Phosphate-Buffer Saline (DPBS) briefly and then disgested in 2 mg/mL Collagenase D (Cat# 11088866001, Roche) in DMEM for 30 minutes in a rotating shaker at 37°C to digest off surface soft tissues. The rib cages were then extensively washed in DPBS for 3 times by votex to remove the digested soft tissues. At this stage, the ribs were free of other tissues and were further digested in 2 mg/mL Collagenase D in DMEM for 3 hours with three changes of fresh Collagenase D solution. Collected cells were pooled together and filtered in 40 uM fiter and centrifuged by 500g to collect for FACS sorting. Total RNA was isolated with RNeasy Micro Kit (RNeasy Micro Kit, Cat#74004; Qiagen, Basel, Switzerland) follwoing FACS sorting.
RNA-seq libraries were constructed with RNA-seq Sample Prep Kit (Cat#RS-122-2101, Illumina, San Diego, CA), according to manufacturer’s instruction. RNA-seq barcoded pooled.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Enzyme digested rib chondrocytes
|
| Data processing |
RNA-seq libraries were sequenced on Illumina Nextseq 500
75nt of single end sequence reads were aligned with tophat2 software to mouse genome version mm9/Build 37
Aligned sequence reads were imported into Partek Genomics Suite software (Partek Inc. St. Louis, Missouri) for mRNA quantification
Genome_build: mouse mm9
Supplementary_files_format_and_content: excel file contains raw read count and RPKM values.
|
| |
|
| Submission date |
Dec 18, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Xinjun He |
| E-mail(s) |
xinjun.he@med.usc.edu
|
| Phone |
323-442-8077
|
| Organization name |
University of Southern California
|
| Department |
BROAD CIRM Center
|
| Street address |
1425 San Pablo St
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90033 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE73372 |
AP-1 family members act at DNA targets in conjunction with Sox9 to promote chondrocyte hypertrophy |
|
| Relations |
| BioSample |
SAMN04351371 |
| SRA |
SRX1492126 |
