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Status |
Public on Oct 12, 2022 |
Title |
HDB_15mm_1 |
Sample type |
SRA |
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Source name |
skin tissue
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Organism |
Mus musculus |
Characteristics |
tissue: skin tissue cell line: skin cells and mesenchymal stem cells cell type: skin cells and mesenchymal stem cells genotype: WT treatment: mesenchymal stem cell-laden matrigel microspheres implantation
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Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2 mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA). Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
BGISEQ-500 |
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Data processing |
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format The clean reads were mapped to the reference genome using HISAT2 (v2.0.4) . Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set,then expression level of gene was calculated by RSEM (v1.2.12) Assembly: GRCm38.p6 Supplementary files format and content: tab-delimited csv files include read count values for each Sample
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Submission date |
Oct 05, 2022 |
Last update date |
Oct 12, 2022 |
Contact name |
Shaohua Ma |
E-mail(s) |
ellinfff@gmail.com
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Organization name |
Tsinghua University
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Lab |
Ma' Lab
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Street address |
nanshan street
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City |
Shen Zhen |
State/province |
Guangdong Province |
ZIP/Postal code |
518000 |
Country |
China |
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Platform ID |
GPL23479 |
Series (1) |
GSE214868 |
Mesenchymal stem cell-laden matrigel microspheres printing enables large skin wound regeneration |
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Relations |
BioSample |
SAMN31167736 |
SRA |
SRX17806726 |
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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