|
| Status |
Public on May 17, 2017 |
| Title |
HSPC from CB_RS2 (single-cell RNA-seq) |
| Sample type |
SRA |
| |
|
| Source name |
HSPC from CB
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Hematopoietic stem/progenitor cells
cell type derived from: cord blood
|
| Treatment protocol |
Hemogenic endothelium was induced with lentiviral vectors encoding transcription factors, followed by transplantation to mouse models.
|
| Growth protocol |
Human iPSCs were differentiated with morphogens and hematopoietic cytokines according to Detadi 2015.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was purified and proccessed for indrop according to the protocol from Klein et al (Cell, 2015, doi:10.1016/j.cell.2015.04.044)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Single-cell RNA-seq
Profiling of same sample as GSM2214011 HSPC from CB_RS2 (bulk RNA-seq)
|
| Data processing |
R2 reads were trimmed for adaptor sequence and poly Ts. Barcodes and UMI(Unique Molecular Identifier) were parsed out and used as cell identifiers and redundant reads indicators, respectively. R1 reads were mapped to human cDNA sequences using bowtie. Alignment results were filtered based on the indrop data processing protocol. We are reporting filtered UMI counts per cell and per gene.
Details on how to demultiplex the multiplexed fastq files: see the README file and two barcode list files.
Genome_build: Homo_sapiens.GRCh38 cDNA
Supplementary_files_format_and_content: [.txt] tab deliminated text files with UMI filtered counts. Each "bc#" column represents a single cell.
|
| |
|
| Submission date |
Aug 02, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Areum Han |
| E-mail(s) |
areum.han@childrens.harvard.edu
|
| Organization name |
Boston Children's Hospital
|
| Lab |
Daley lab
|
| Street address |
Karp Family Building, 7th Floor. 300 Longwood Ave.
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE85111 |
inDrop single cell RNA-seq of hematopoietic cells derived from human pluripotent stem cells |
| GSE85112 |
Hematopoietic Stem and Progenitor Cells from Human Pluripotent Stem Cells via Transcription Factor Conversion of Hemogenic Endothelium |
|
| Relations |
| BioSample |
SAMN05505491 |
| SRA |
SRX1995482 |
