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Sample GSM2041274 Query DataSets for GSM2041274
Status Public on Jul 24, 2016
Title RNA-seq-PGT2
Sample type SRA
 
Source name hESC-derived primitive gut tube
Organism Homo sapiens
Characteristics cell type: hESC-derived primitive gut tube
Treatment protocol GECs, hiMEP-Heps, Fetal-Heps, DE, PGT and PFG were collected after trypsinized with TrypLE. The hiMEPs were collected by manual picking.
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).
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
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
 
Submission date Jan 18, 2016
Last update date May 15, 2019
Contact name Jinhua Qin
E-mail(s) qinjinhuarhea@126.com
Organization name Beijing Institute of Transfusion
Street address Taiping Road
City Beijing
ZIP/Postal code 100850
Country China
 
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
Relations
BioSample SAMN04420285
SRA SRX1533895

Supplementary file Size Download File type/resource
GSM2041274_PGT2.count.txt.gz 109.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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