|
| Status |
Public on Dec 20, 2022 |
| Title |
0705_DF6_5i_4d: BFRTV4d |
| Sample type |
SRA |
| |
|
| Source name |
Ear fibroblasts induced by BFRTV for 4d
|
| Organism |
Capra hircus |
| Characteristics |
tissue: Ear fibroblasts induced by BFRTV for 4d
induction time: 4d
|
| 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 use Ribo-Zero™ Gold Kits（Human/Mouse/Rat） to delete rRNA
RNA fragmentation and short RNA strands were carried out by NEBNext First Strand Synthesis Reaction Buffer under elevated temperature. Subsequently， First cDNA strand was synthesized using random hexamer primers and RNA fragments as template. Second strand cDNA synthesis was subsequently performed using buffer, dNTPs, DNA polymerase I and RNase H. The library fragments were purified with QiaQuick PCR kits and elution with EB buffer, then terminal repair、 add poly(A)and adapter were implemented. Libraries were sequenced on Illumina HiSeq 2500
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Illumina seqencing reads were cleaned for quality control and tested the results using FastQC(version0.10.1).
Ribosome RNA were removed again from clean reads
High-quality reads were mapped to the refer genome to obtain BAM files
the read count for each gene in each sample was counted by HTSeq, and the fragments per kilobase of million mapped reads (FPKM) was then calculated
Differential expression analysis was performed using DESeq2 (v1.16.1) with read count
Genome_build: CaprahircusARS1
Supplementary_files_format_and_content: xls files include FPKM values for each Sample ...
|
| |
|
| Submission date |
Dec 23, 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 |
GPL27106 |
| Series (2) |
| GSE142548 |
Direct Reprogramming of Fibroblasts into Functional Mammary Epithelial cells by small molecules (RNAseq) |
| GSE142551 |
Direct Reprogramming of Fibroblasts into Functional Mammary Epithelial cells by small molecules |
|
| Relations |
| BioSample |
SAMN13673593 |
| SRA |
SRX7435223 |
