|
| Status |
Public on May 29, 2023 |
| Title |
Cultured normal human epidermal keratinocytes at 37 degrees C (miRNA) |
| Sample type |
SRA |
| |
|
| Source name |
Epidermis
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: epidermis
cell: keratinocytes (YF29)
|
| Treatment protocol |
100 nM Rapamycin was added into medium which are inchubated at 37 degrees C from day0 to end of cell culture
|
| Growth protocol |
Cells were cultured with 3T3J2 feeder cells in cFAD medium at each temprature (32, 35, 36, 37 and 38 degrees C)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Followed a protocol of miRNAeasy mini kit (QIAGEN)
RNA libraries were prepared for sequencing by using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technology, CA, USA) in Novogen Experimental Department
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
cells are cultured at 37 degrees C
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts. In this step, clean data (clean reads) were obtained by removing reads containing ploy-N, with 5’ adapter contaminants, without 3’ adapter or the insert tag, containing ploy A or T or G or C and low quality reads from raw data. At the same time, Q20, Q30, and GC-content of the raw data were calculated. Then, chose a certain range of length from clean reads to do all the downstream analyses.
The expression of known and unique miRNAs in each sample are statistically analyzed and normalized by TPM (Zhou et al., 2010).
Assembly: Homo Sapiens(GRCh38)
Supplementary files format and content: tab-delimited text files include TPM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Mar 15, 2022 |
| Last update date |
May 29, 2023 |
| Contact name |
Jun-Ichi Sakabe |
| E-mail(s) |
sakabe.junichi@sgh.com.sg
|
| Phone |
91003620
|
| Organization name |
Singapore General Hospital (SGH)
|
| Department |
Plastic Reconstructive and Aesthetic Surgery
|
| Lab |
Skin Bank Unit
|
| Street address |
Blk4 Lv3, Outram Rd
|
| City |
Singapore |
| ZIP/Postal code |
169608 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE198696 |
Low temperature and mTOR inhibition favor stem cell maintenance in human keratinocyte cultures [miRNA-seq] |
| GSE199523 |
Low temperature and mTOR inhibition favor stem cell maintenance in human keratinocyte cultures |
|
| Relations |
| BioSample |
SAMN26677624 |
| SRA |
SRX14468568 |
