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| Status |
Public on Nov 01, 2021 |
| Title |
control group_scRNA-seq |
| Sample type |
SRA |
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| Source name |
fracture tissues
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| Organism |
Homo sapiens |
| Characteristics |
tissue: bone fracture tissues (bone and bone marrow)
time: 0 day (control group)
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| Treatment protocol |
Obtained the bone marrow and bone tissue of the patient through the ethics committee review, and extracting bone fracture end tissue at different time ( 0day,30 days),and extracting single cells by digestion
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| Growth protocol |
No growth are needed
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| Extracted molecule |
total RNA |
| Extraction protocol |
To obtain bone and bone marrow cells for scRNA-seq.Bone fracture tissues (including bones and bone marrow 0.5cm from the fracture end) were dissected from mice and placed in DMEM/F12(Gibco), and cut bone fracture tissues into small fragments and digested them with 0.1mg/ml collagenase II (Invitrogen) for 2h at 37℃. After digestion, the obtained cells were filtered through a 70μm filter and collect it into a collection tube, and erythrocytes lysed in ACK-lysis buffer.
RNA libraries were generated by BD Rhapsody singel cell RNA-seq and prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
WRK-GU-NC_BKDL190818112-1a
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| Data processing |
Basecalls performed using CASAVA version 1.8
Umi-tools was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:
MT% < 40%;
Cell Gene Number < 5000;
Cell Gene Number > 200.
PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: TSV file contain counts for each sample
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| Submission date |
Dec 31, 2019 |
| Last update date |
Nov 01, 2021 |
| Contact name |
Renkai Wang |
| E-mail(s) |
jfsdfgjh@126.com
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| Organization name |
changhai hospital
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| Street address |
168 Changhai Road,
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| City |
shanghai |
| ZIP/Postal code |
200433 |
| Country |
China |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE142786 |
Single-cell RNA-seq analysis reveals reduction of B cells in the bone marrow promote fracture healing |
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| Relations |
| BioSample |
SAMN13703130 |
| SRA |
SRX7483444 |
| 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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