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Status |
Public on Jan 31, 2021 |
Title |
MYB-/-YFP+ve_day6rep1 |
Sample type |
SRA |
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Source name |
in vitro hematopoietic cells
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Organism |
Homo sapiens |
Characteristics |
cell type: hESC-derived hematopoietic progenitors passage: 50-65 day of differentiation: Day 6 genotype: MYB-/-
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Growth protocol |
hESC cells–derived hematopoietic cells were routinely generated using EBs-based hematopoietci development in our established serum-free and cytokine-free hematopoietic system (un-published), with initial mesodermal patterning by BMP4 and VEGF supplimentations.
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Extracted molecule |
total RNA |
Extraction protocol |
Differentiated cells were harvested at different time points, filtered and incubated with cell surface markers on ice. The washed cells were collected into Trizol reagent directly from Aria II-cell sorter. RNA libraries were prepared for sequencing using standard Illumina protocols
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 3000 |
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Description |
14D6-pos1
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Data processing |
Samples were checked with FastQC software with no considerable issues found. Reads were trimmed and filtered with BBduk tool from the Bbmap package (used parameters: qtrim=rl trimq=20 maq=20 minlen=50). This procedure keeps 94.98-97.02% bases and 98.64-99.8% reads per sample. Trimmed reads were mapped to the GRCh38 human genome with Gencode v.24 gene annotation (Harrow 2012) using the --quantMode GeneCounts option of the STAR v.2.5.3ab software (Dobin 2013). After removing of ~15,000 pseudogenes and 552 rRNA genes the STAR output tallies raw read per gene counts, that is total read counts for each of 46,214 transcripts, 19,844 of them representing protein-coding genes. According to the STAR manual, “with --quantMode GeneCounts option STAR will count number reads per gene while mapping. EdgeR was used to convert raw read per gene counts to CPM (counts per million reads) matrices. Genome_build: GRCh38 Supplementary_files_format_and_content: mRNA expression raw counts Supplementary_files_format_and_content: mRNA expression counts per million reads Supplementary_files_format_and_content: description of genes_ntc_expression_raw_cpm_GEO.txt file
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Submission date |
Jan 28, 2019 |
Last update date |
Jan 31, 2021 |
Contact name |
ZAHIR SHAH |
E-mail(s) |
zahir@gibh.ac.cn
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Phone |
13229487422
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Organization name |
GIBH,CAS, China
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Department |
Stem Cells and Regenerative Medicines
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Street address |
190 Kaiyuan avenue, Haungpu district, Guangzhou, China
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City |
Guangzhou |
State/province |
Guangdong |
ZIP/Postal code |
510530 |
Country |
China |
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Platform ID |
GPL21290 |
Series (1) |
GSE125761 |
MYB is an essential regulator of primitive human hematopoiesis in human pluripotent stem cell differentiation cultures. |
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Relations |
BioSample |
SAMN10833337 |
SRA |
SRX5299985 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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