|
| Status |
Public on Aug 17, 2020 |
| Title |
D16-_10X |
| Sample type |
SRA |
| |
|
| Source name |
BJ Fibroblasts
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: BJ Fibroblasts
treatment: BJ fibroblasts 16 days post induced viral expression of OSKM
time: D16
tra-1-60 staining: Negative
|
| Growth protocol |
BJ fibroblasts were cultured in 10% Fetal Bovine Serum (Gibco) for expansion and medium was changed every two days. BJ human neonatal fibroblast was routinely tested for Mycoplasma and was negative in all instances. hES cells and iPSCs clones were maintained on irradiated murine embryonic fibroblast (MEFs, Global Stem) and cultured in 20% knockout serum replacement (KSR, Life Technologies), 200mM GlutaMAX (Life Technologies), 1 x minimal essential media (MEM) non-essential amino acids solution (Life Technologies), 8 microgram mL-1 bFGF (Life Technologies), 55 micromolar Beta-mercaptoethanol in DMEM/F12 (Life Technogies).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
cDNA was harvested as per the Chromium Single Cell 3’ Reagent Kits v2 user guide Rev E
Libraries were constructed as per the Chromium Single Cell 3’ Reagent Kits v2 user guide Rev E
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
UMI.csv
|
| Data processing |
Fastq files were generated using mkfastq of cellranger v2.1.0. Gene counting was performed using ‘count’ module of cellranger (v2.1.0).
All librariers were then merged using ‘aggr’ function of cellranger without normalization. The output of ‘aggr’ was used for further analysis with Seurat and Monocle.
Genome_build: hg19
Supplementary_files_format_and_content: Comma-delimited table containing the UMI values of the genes in each single-cell library and Tab-delimited text file containing time-point annotation of the cells.
|
| |
|
| Submission date |
Aug 07, 2018 |
| Last update date |
Aug 17, 2020 |
| Contact name |
Chadi El Farran |
| Organization name |
Institute of Molecular and Cell Biology
|
| Lab |
Epigenetics and Cell Fates Laboratory
|
| Street address |
61 Biopolis Drive
|
| City |
Singapore |
| ZIP/Postal code |
138673 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL21290 |
| Series (2) |
| GSE100345 |
Determination of dynamic changes in gene expression and chromatin accessibility during cellular reprogramming |
| GSE118258 |
Determination of dynamic changes in chromatin accessibility during cellular reprogramming [scRNA-seq 10x] |
|
| Relations |
| BioSample |
SAMN09779970 |
| SRA |
SRX4519078 |
