|
| Status |
Public on Nov 19, 2019 |
| Title |
iPS_RAG1_1 |
| Sample type |
SRA |
| |
|
| Source name |
human induced pluripotent stem cells
|
| Organism |
Homo sapiens |
| Characteristics |
experiment #: 1
differentiation day: 20
representative population: early_RAG1
sort parameters: RAG1:GFP+
|
| Growth protocol |
Induced pluripotent stem cell lines were differentiated as embryoid bodies (EBs) for 8 days in presence of appropriate supplements. The EBs were then transferred onto Corning transmembranes to grow in air liquid interface system until the end of experiments.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
iPSC derived RAG1:GFP+ purified cells were submitted to the Australian Genome Research Facility (AGRF) for single cell RNA sequencing using 10x Genomics Chromium system.
The sequencing and data generation was performed using AGRF- Illumina bcl2fastq pipeline version 2.20.0.422, via generation of 100bp Paired End reads and sequencing through Illumina HiSeq platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
10X single cell software (Cell Ranger) was used to preform secondary analysis including generation of Cell Ranger mkfastq and Cell Ranger count on each of the samples. This process produced filtered feature-barcode matrices MEX.
Genome_build: hg_38
Supplementary_files_format_and_content: The processed data files presented here are the output files generated via the cell ranger pipeline. The output “filtered_gene_bc_matrices” (only includes cellular barcodes) component was used for this study. This folder included 3 files; matrix.mtx file which contains the number of unique molecular identifiers (UMIs) associated with a gene (rows) and a cell (barcodes, columns), barcodes.tsv and genes.tsv files corresponding columns and rows of the mtx file, respectively.
|
| |
|
| Submission date |
Dec 20, 2018 |
| Last update date |
Nov 23, 2019 |
| Contact name |
Ali Motazedian |
| E-mail(s) |
ali.motazedian@mcri.edu.au
|
| Organization name |
Murdoch Children's Research Institute
|
| Department |
Stem Cell Technology
|
| Street address |
Royal Children's Hospital
|
| City |
Parkville |
| State/province |
Victoria |
| ZIP/Postal code |
3052 |
| Country |
Australia |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE124172 |
RAG1+ multipotent progenitors emerge directly from hemogenic endothelium of human PSC derived haemopoietic organoids [single cell RNA-Seq] |
|
| Relations |
| BioSample |
SAMN10619269 |
| SRA |
SRX5169362 |
