|
| Status |
Public on Sep 25, 2020 |
| Title |
1ct_day7_control |
| Sample type |
SRA |
| |
|
| Source name |
Colonic Epithelial Cells cultured transfected with shRNA specific for a scrambled control after 7 days
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCEC
cell type: Human colonic epithelial progenitor cells
time point: day7
shRNA: shScramble
|
| Treatment protocol |
For retrovirus transduction, we cultured HCEC 1CT cells in above condition with 1 μg/ml of puromycin after transduction. shAPC and shScrambled cells were harvested at 3-and 7-days after transduction, and stored on ice in PBS before the single cell library preparation.
|
| Growth protocol |
shAPC and shScramble cells stably expressed in HCEC 1CT were routinely cultured in HCEC culture media (DMEM:M199=4:1) supplemented with EGF (20 ng/mL), hydrocortisone (1ug/mL), insulin (10 ug/mL), Sodium selenite (5nM), transferrin (2 ug/mL), and 2% FBS at 37°C in 5% CO2.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Single cells were lysed in droplets using the 10X Chromium instrument Reverse transcription was performed in droplet and library construction was performed according to the 10X Chromium Single Cell 3' ver 2 Reagent Kit User Guide Rev A
RNA libraries were prepared for sequencing using Single Cell 3' Reagent Kit v2 (10x genomics).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
Single-cell RNAseq data
|
| Data processing |
The Cell Ranger 3.0.2 Single-Cell Software Suite (10x Genomics) was implemented to process the raw sequencing data from the Illumina HiSeq X run.
This pipeline performed de-multiplexing, alignment (GRCh38/STAR), and barcode processing to generate gene-cell matrices used for downstream analysis.
Genome_build: GRCh38
26 bp Read1 (10x cell barcode and UMI), 8 bp i7 Index (sample index), and 98 bp Read2 (insert)
Supplementary_files_format_and_content: cell ranger count matrix for single cells in each sample
|
| |
|
| Submission date |
Jun 18, 2020 |
| Last update date |
Sep 27, 2020 |
| Contact name |
Jeong-Ryeol Gong |
| E-mail(s) |
jrgong@kaist.ac.kr
|
| Organization name |
KAIST
|
| Lab |
SBIE
|
| Street address |
291, Daehak-ro
|
| City |
Yuseong-gu |
| State/province |
Daejeon |
| ZIP/Postal code |
34141 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL20795 |
| Series (2) |
| GSE152745 |
Transcriptomic analysis of APC knock down HCEC 1CT cells compared to the wild type HCEC 1CT cells. |
| GSE152746 |
APC knock down HCEC 1CT cells compared to the wild type HCEC 1CT cells |
|
| Relations |
| BioSample |
SAMN15314082 |
| SRA |
SRX8573315 |
