|
| Status |
Public on Nov 11, 2018 |
| Title |
Myod1 reprogrammed MEFs, biological replicate 1, technical replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Reprogrammed MEFs with Myod1, day 7
|
| Organism |
Mus musculus |
| Characteristics |
strain: ICR
internal sample id: BL16
cell type: reprogrammed MEF
infection: mixed sample (non-demultiplexed)
|
| Treatment protocol |
MEFs were pooled infected with two retroviral vectors (Myod1 and empty vector) to induce expression of Myod1. Another MEF sample was infected with empty retroviral vector. Both infected MEFs were incubated 7 days and mixed together before library prep. The cells were washed with DPBS and trypsinized into a single cell suspension. Cells were spun at 500X G for 5 minutes at 4˚C and resuspended in cold growth media.
|
| Growth protocol |
MEFs were maintained in high glucose DMEM supplemented with 10% FBS and 1X penicillin/streptomycin and incubated at 37˚C in 5% CO2.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Single cell suspension was washed with 1X PBS (0.04% BSA) before 10x Genomics procedure. The concentration of single cell suspension was adjusted to about 500 to 1000 cells/µL and was loaded on the 10x Genomics’ Chromium™ system (10x Genomics, Pleasanton, CA) with the aim of 6000 to 10000 cells per channel (Chromium™ Single Cell 3' Library & Gel Bead Kit v2, catalog number 120237).
Single cell RNA sequencing libraries were constructed following the manufacturer’s instructions (Zheng et al., 2017).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
This record represents two infected MEFs samples mixed together before sequencing library prep. One MEF sample was pooled infected with two retroviral vectors (one vector is Myod1, the other is empty vector), the other MEF sample was infected with an empty vector. These two infected MEF samples were mixed together.
|
| Data processing |
BCL files generated by Illumina sequencing systems were demultiplexed and converted to standard FASTQ files using mkfastq function from Cell Ranger pipeline (version 2.1.0).
Reads were processed to generate expression (UMI count) matrices using Cell Ranger pipeline (version 2.1.0) with default parameters, except the parameter of expected number of cells, which was adjusted based on individual experiment.
For 10X Genomics, the first 1-16 bp are cell barcode and 17-26 bp are UMI in read 1.
Genome_build: mm10
Supplementary_files_format_and_content: Raw UMI count matrix representing gene expression values (comma-separated) generated as described above. Each column represents a single cell, each row represents a single gene.
|
| |
|
| Submission date |
Aug 09, 2018 |
| Last update date |
Nov 12, 2018 |
| Contact name |
Gary Hon |
| Organization name |
UT Southwestern
|
| Department |
Department of Obstetrics and Gynecology
|
| Lab |
Hon Lab
|
| Street address |
5323 Harry Hines Blvd.
|
| City |
Dallas |
| ZIP/Postal code |
75390 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE117795 |
Reprogram-Seq: A platform for single-cell combinatorial reprogramming |
| GSE118368 |
Reprogram-Seq: A platform for single-cell combinatorial reprogramming [IX] |
|
| Relations |
| BioSample |
SAMN09788128 |
| SRA |
SRX4525365 |
