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| Status |
Public on Jun 11, 2021 |
| Title |
2_month_old_fractured 3 |
| Sample type |
SRA |
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| Source name |
Day 10 fracture callus
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
tissue: Femur
cell: mSSC
age: 2 months
treatment: NA
gating strategy: CD45-TER119-TIE2-ITGAV+THY1-6C3-CD105-
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| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA extraction of mSSCs, 500 to 1,000 cells were FAC-sorted directly into 1 mL TRIzol LS (Invitrogen, Cat#10296028).
Bulk mRNA was processed and sequenced as described before (PMID: 32792541). Briefly, RNA was isolated with Qiagen miRNeasy kit (Cat. 1071023), cDNA was prepared using the Clontech Smarter Ultra Low Input RNA kit (Takara Bio, Cat. 634848), and libraries were generated with the Clontech Low Input Library Prep kit (Takara Bio, Cat. 634947). The barcoded samples were pooled and then sequenced on four lanes of NextSeq 500 (Illumina) to obtain 2x76 base pair paired-end reads (average no. of mapped reads per sample: ~45 million).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Bulk mRNA sequencing data was analyzed as described before (PMID: 32792541). Briefly, raw FASTQ reads from each lane were merged and then aligned to the GENCODE vM20 mouse reference transcripts (GRCm38.p6) with Salmon (PMID: 28263959) v0.12.0 using the --seqBias, --gcBias, --posBias, --useVBOpt, --rangeFactorizationBins 4, and --validateMappings flags and otherwise default parameters for paired-end mapping. Salmon results were merged into a single gene-level transcripts per million (TPM) matrix using the R package, tximport (PMID: 26925227) v1.10.1 and log2-normalized.
Genome_build: GENCODE vM20 mouse reference transcripts (GRCm38.p6)
Supplementary_files_format_and_content: Excel spreadsheet containing log2-and-TPM-normalized gene expression matrix
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| Submission date |
Feb 09, 2021 |
| Last update date |
Jun 11, 2021 |
| Contact name |
Thomas H Ambrosi |
| E-mail(s) |
[email protected]
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| Phone |
9162983241
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| Organization name |
UC Davis
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| Street address |
2700 Stockton Blvd
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| City |
Sacramento |
| State/province |
California |
| ZIP/Postal code |
95817 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE166441 |
Aged skeletal stem cells during fracture healing |
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| Relations |
| BioSample |
SAMN17841229 |
| SRA |
SRX10058315 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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