|
| Status |
Public on May 17, 2017 |
| Title |
HSPC from hiPSC_RS7 |
| Sample type |
SRA |
| |
|
| Source name |
HSPC from hiPSC
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Hematopoietic stem/progenitor cells
cell type derived from: human induced pluripotent stem cells
|
| 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 with RNeasy Micro kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Adaptor sequences were removed using a Cutadapt tool (Martin, 2011) allowing some mismatches (The specific parameters we used were -n 2 -e 0.1 –O 15 --quality-base=33).
The cleaned reads were aligned to the human genome/transcriptome (hg19 and corresponding UCSC gene model, hg19_UCSC_knownGene) using TopHat2 software (Kim et al., 2013).
To estimate expression levels for each gene, aligned reads per gene were counted using a htseq-count tool (Anders et al., 2015) on refGene gene model.
Counts were then normalized and converted to RPKM values (Reads Per Kilobase per Million) utilizing an edgeR package (Robinson et al., 2010).
Genome_build: hg19
Supplementary_files_format_and_content: [.txt] tab-delimited text file includes RPKM values for each Sample.
|
| |
|
| Submission date |
Aug 31, 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) |
| GSE83719 |
Transcriptome profiling 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 |
SAMN05717702 |
| SRA |
SRX2069763 |
