|
| Status |
Public on Jun 11, 2024 |
| Title |
GEF cells, BERTV,Day0 [GEF_2] |
| Sample type |
SRA |
| |
|
| Source name |
GEF
|
| Organism |
Capra hircus |
| Characteristics |
cell line: GEF
cell type: Fibroblast cells
genotype: WT
treatment: reprogramming
|
| Treatment protocol |
iMECs from fibroblasts with N2B27 and small molecule compounds cocktail induction medium “VTFBR” (500μg/mL VPA, 10 μM Tranylcypromine, 10 μM Forskolin, 1 μM TTNPB, 10 μM RepSox),the induction culture was continued for 8 days.
|
| Growth protocol |
GEFs were seeded at a density of 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; GMECs were cultured in the incubator at 37.5°C in a humidified atmosphere of 5% CO2 with GMEC culture medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the treated iMECs with BERTV from day 0 and day 8 using TRIzol Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara).
RNA-seq transcriptome library was prepared following TruSeqTM RNA sample preparation Kit from Illumina using 1μg of total RNA.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| 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 (v1.16.0) with read count
Assembly: CaprahircusARS1
Supplementary files format and content: counts
|
| |
|
| Submission date |
Jul 11, 2022 |
| Last update date |
Jun 11, 2024 |
| 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 (1) |
| GSE207893 |
Direct Reprogramming of Fibroblasts into Functional Mammary Epithelial cells by small molecules (bulk miRNA-seq) |
|
| Relations |
| BioSample |
SAMN29630420 |
| SRA |
SRX16114193 |
