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Sample GSM3895613 Query DataSets for GSM3895613
Status Public on Nov 01, 2021
Title third day
Sample type SRA
 
Source name fracture tissues
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: bone fracture tissues( bone and bone marrow)
time point: 3 days
Treatment protocol By constructing mouse fracture model, and extracting bone fracture end tissue at different time ( 0day, 3days, 7days, 14days),and extracting single cells by digestion
Extracted molecule total RNA
Extraction protocol To obtain bone and bone marrow cells for scRNA-seq, mice were sacrificed via CO2 asphyxia. 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
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Description zuoer
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% < 20%;  Cell Gene Number < Median Gene Number * 2;  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: mm10
Supplementary_files_format_and_content: TXT file contain counts for each sample
 
Submission date Jun 18, 2019
Last update date Nov 01, 2021
Contact name Renkai Wang
E-mail(s) jfsdfgjh@126.com
Organization name changhai hospital
Street address 168 Changhai Road,
City shanghai
ZIP/Postal code 200433
Country China
 
Platform ID GPL21273
Series (1)
GSE132884 Single-cell RNA-seq analysis reveals two specific endothelial cells promote fracture healing
Relations
BioSample SAMN12084342
SRA SRX6085363

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

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