|
| Status |
Public on Apr 15, 2024 |
| Title |
shControl mESCs-2 |
| Sample type |
SRA |
| |
|
| Source name |
shControl mESCs
|
| Organism |
Mus musculus |
| Characteristics |
cell line: E14
cell type: embryonic stem cells
passage: passage 25
treatment: transfected with negtive control plasmids
|
| Treatment protocol |
To generate stable Pdgf-d knockdown mESCs, 1μg pLent-Pdgf-d-4in1-shRNA plasmids were transfected into HEK293T cells together with 2μg lentivirus packing plasmids pSPAX2 and pMD2G using Lipofectamine 2000. Supernatants containing the viral particles was collected and added to the mESCs. New ESC medium was added 6 hours later. Cells were selected by puromycin (2 μg/ml). pLent-4in1-shRNA-GFP-Puro was used as a negative control.
|
| Growth protocol |
Mouse embryonic stem cells (mESCs) were maintained in culture dish coated with 0.1% gelatin in ESC medium, which contained Knockout DMEM medium and supplemented with 15% (v/v) fetal bovine serum , β–mercaptoethanol (0.1µM), GlutaMax-I supplement (2mM), MEM non-essential amino acids (0.1 mM), 1% (v/v) Penicillin-Streptomycin, LIF (1,000 U/ml), and 2 inhibitors (CHIR99021, PD325901 at 3 µM and 1 µM, respectively)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from shControl or shPdgf-d mESCs by Trizol regent. 1 ∼ 2 µg of total RNA was used for the construction of sequencing libraries by KAPA Stranded RNA-Seq Library Prep Kit(Illumina).
RNA libraries for sequencing were prepared following standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Solexa pipeline version 1.8 (Off-Line Base Caller software, version 1.8) used for basecalling.
Sequenced reads were trimmed for adaptor sequence by fastQC, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 mouse genome using Hisat2 software.
Fragments per kilobase of transcript per million mapped reads (FPKM) were calculated using StringTie and R software Ballgown package.
Genome_build: GRCm38
Supplementary_files_format_and_content: An Excel file include FPKM values for all Samples
|
| |
|
| Submission date |
Apr 15, 2021 |
| Last update date |
Apr 15, 2024 |
| Contact name |
Weisi Lu |
| E-mail(s) |
luweisi3@mail.sysu.edu.cn
|
| Organization name |
Zhongshan Ophthalmic Center, Sun Yat-sen University
|
| Department |
State Key Laboratory of Ophthalmology
|
| Lab |
Xuri Li Lab
|
| Street address |
No.7 Jinsui Road
|
| City |
Guangzhou |
| ZIP/Postal code |
510060 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE172117 |
RNA sequencing for the gene expression profile changes of shPdgf-d and shControl mESCs |
|
| Relations |
| BioSample |
SAMN18746704 |
| SRA |
SRX10605636 |
