|
| Status |
Public on Jan 08, 2020 |
| Title |
S28: CTCFKD1_singleCell |
| Sample type |
SRA |
| |
|
| Source name |
EL4
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell number: Single cell
genotype: CTCF knockdown
tissue: EL4 cells
|
| Treatment protocol |
293T cells were co-transfected with an envelope plasmid (pLP/VSVG) to generate lentiviral particles. The medium containing lentiviral particles was harvested after 48h transfection. EL4 cells were infected with the harvested shLuc and shCTCF retroviral particles packaged in GP2-293.
|
| Growth protocol |
EL4 cells were cultured in DMEM (GIBCO Invitrogen) supplemented with 50 IU/mL penicillin, 50 mg/mL streptomycin (GIBCO Invitrogen) and 10% heat inactivated calf serum (Sigma, USA). Cultures were maintained by replacement of fresh medium every 3 days, and cell density was kept between 1 X 105 and 1 X 106 cells/mL.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Single cell RNA libraries were prepared by Fluidigm C1 Single-Cell Autoprep System
Single cell RNA libraries were prepared by Fluidigm C1 Single-Cell Autoprep System
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
RNA-seq
|
| Data processing |
Basecalls performed using RTA 1.7 or Illumina Casava1.7
Reads were aligned to the mouse genome (Ensemble version GRCm38.89) utilizing STAR
We calculated the TPM of each gene in single cell RNA-seq
Genome_build: GRCm38.89
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample
|
| |
|
| Submission date |
Aug 13, 2019 |
| Last update date |
Jan 08, 2020 |
| Contact name |
Wenfei Jin |
| E-mail(s) |
jinwf@sustech.edu.cn
|
| Phone |
+8675588018478
|
| Organization name |
Southern University of Science and Technology
|
| Department |
Department of Biology
|
| Lab |
Single Cell Precise Medicine
|
| Street address |
1088 Xueyuan Rd #faculty research building 1
|
| City |
Shenzhen |
| State/province |
Guangdong |
| ZIP/Postal code |
518055 |
| Country |
China |
| |
|
| Platform ID |
GPL21493 |
| Series (1) |
| GSE135769 |
Single Cell RNA-Seq Reveals Changing Landscape of Cell-to-Cell Variation Induced by CTCF Knockdown |
|
| Relations |
| BioSample |
SAMN12566489 |
| SRA |
SRX6708183 |
