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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 31, 2021 |
| Title |
MYB+/-YFP-ve_day6rep2 |
| 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: 48-55
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 |
16D6-neg2
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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 |
SAMN10833325 |
| SRA |
SRX5299994 |
| 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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