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| Status |
Public on Jul 24, 2016 |
| Title |
RNA-seq-DE2 |
| Sample type |
SRA |
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| Source name |
hESC-derived definitive endoderm
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| Organism |
Homo sapiens |
| Characteristics |
cell type: hESC-derived definitive endoderm
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| Treatment protocol |
GECs, hiMEP-Heps, Fetal-Heps, DE, PGT and PFG were collected after trypsinized with TrypLE. The hiMEPs were collected by manual picking.
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| Growth protocol |
GECs were cultured in Kubota's medium. The hiMEPs were reprogrammed from GECs under advanced DMEM/F12 with 2μM Bay K 8644, 0.5μM Bix01294 , 0.04μM RG108, 2μM SB431542, with the support of feeder cells. The hiMEP-Heps were induced from hiMEPs under hepatic differentiation conditions and cultured in hepatocyte medium (Sciencell) with 25 ng/ml HGF (R&D), 1 μM Dexamethasone (Sigma), and 10 ng/ml OSM (R&D).Fetal-Heps were cultured in hepatocyte medium (Sciencell).To induce ESCs differentiation to definitive endoderm (DE) cells, 80% confluent ESCs were cultured in RPMI 1640 with 3 μM CHIR99021 and 100 ng/ml Activin A for 1 day. The medium was then changed to RPMI 1640 with 0.2% FBS and 100 ng/ml Activin A for 2 days. To further differentiate to primitive gut endoderm (PGT) cells, the medium was changed to RPMI 1640 with 2% FBS, 50 ng/ml human FGF10, and 0.25 mM KAAD-cyclopamine (Stemgent) for 3 days. To differentiate to posterior foregut (PFG) cells, day3 DE was cultured in RPMI 1640 with 2 μM RA (Sigma) and 1.5 μM Dorsomorphin (Stemgent).
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
total RNA (Qiagen, Cat#: 74004) were extracted according to manufacturer’s instructions.
mRNA was reverse transcribed and amplified by REPLI-g Single Cell Kit (cat#. 150063). The library was sequenced using Illumina HiSeq X ten.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Paired-end reads were mapped against the UCSC GRCh38 reference by Tophat with stringent parameters: --coverage-search --microexon-search --b2-very-sensitive. Only unique mapping reads were retained for normalization purposes. Read counts of each gene were summarized using HTSeq version 0.6.1p1. DESeq2 was used to normalize read counts.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include read counts of each gene for each sample
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| Submission date |
Jan 18, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jinhua Qin |
| E-mail(s) |
[email protected]
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| Organization name |
Beijing Institute of Transfusion
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| Street address |
Taiping Road
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| City |
Beijing |
| ZIP/Postal code |
100850 |
| Country |
China |
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| Platform ID |
GPL20795 |
| Series (2) |
| GSE58557 |
Conversion of Human Gastric Epithelial Cells to Multipotent Endodermal Progenitors using Defined Small Molecules [gene expression] |
| GSE69706 |
Conversion of Human Gastric Epithelial Cells to Multipotent Endodermal Progenitors using Defined Small Molecules |
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| Relations |
| BioSample |
SAMN04420283 |
| SRA |
SRX1533893 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2041272_DE2.count.txt.gz |
109.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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