|
| Status |
Public on Dec 20, 2022 |
| Title |
CK2: BFRTV0d miRNAseq |
| Sample type |
SRA |
| |
|
| Source name |
Ear fibroblasts
|
| Organism |
Capra hircus |
| Characteristics |
tissue: Ear fibroblasts
induction time: 0d
|
| Treatment protocol |
GEFs were seeded at a density of 5×104 cells per well of a 4-well plate or 5×105 cells per 60 mm dish and cultured in the incubator at 37.5°C in a humidified atmosphere of 5% CO2 with fibroblast culture medium. The next day, the fibroblast medium was replaced by BFRTV induction medium. The culture was continued for 8 days, and the induction medium was refreshed every 2 days. On day 8, those induced cells with primary colonies were named BFRTV-8d cells/CiMECs-P0 and were further passaged at a ratio of 1:3 every 3-4 days; the cells were cultured in the incubator at 37.5°C in a humidified atmosphere of 5% CO2 with goat MEC culture medium changed every 2 days. The culture plates or dishes were precoated with Matrigel® Matrix (Corning, 356230).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Extract total RNA from each sample,then total RNA was separated by 15% agarose gels to extract the small RNA (18-30 nt).
After ethanol precipitation and small RNA sample enrichment by centrifugation, the libraries were prepared according to the method and process of the Small RNA Sample Preparation Kit (Illumina, RS-200-0048).The main contents are as follows: First,connecting the 3' adaptor and 5' adaptor to the separated small RNA.Then RT-PCR.Finally,recycling strips of 145-160bp (22-30nt RNA).
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Illumina seqencing reads were cleaned and adapter-removed for quality control and tested the results using FastQC(version0.10.1).
High-quality reads were mapped to the refer genome to obtain SAM files using Bowtie(v1.1.2)
Known miRNA and Novel miRNA were identified by miRDeep2(v2.0.0.5) software,also obtained the read count of each sample and the Reads Per Million(RPM) was then calculated for downstream analysis.
Differential expression analysis was performed using DESeq2 (v1.16.1) with read count,target genes detection and function enrichment were performed.
Genome_build: CaprahircusARS1
Supplementary_files_format_and_content: count and RPM values for each Sample
|
| |
|
| Submission date |
Dec 27, 2019 |
| Last update date |
Dec 20, 2022 |
| Contact name |
ben huang |
| E-mail(s) |
benhuang@gxu.edu.cn
|
| Organization name |
School of Animal Science and Technology, Guangxi University
|
| Street address |
NO.100. DAXUE EAST RD, Nanning
|
| City |
Guangxi |
| ZIP/Postal code |
530004 |
| Country |
China |
| |
|
| Platform ID |
GPL21299 |
| Series (2) |
| GSE142551 |
Direct Reprogramming of Fibroblasts into Functional Mammary Epithelial cells by small molecules |
| GSE142659 |
Direct Reprogramming of Fibroblasts into Functional Mammary Epithelial cells by small molecules (miRNAseq) |
|
| Relations |
| BioSample |
SAMN13690830 |
| SRA |
SRX7449429 |
