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Series GSE135799 Query DataSets for GSE135799
Status Public on Feb 18, 2020
Title Simple differentiation method using FBS identifies DUSP6 as a marker for fine-tuning of FGF-ERK signaling activity in human pluripotent stem cells
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Assessment of differentiation potential is a basic requirement to obtain qualified human pluripotent stem cells (hPSCs). Here, we report a simple differentiation method using fetal bovine serum (FBS) to estimate differentiation potential and propensity of hPSCs. PluriTest using RNA-sequencing showed that cells differentiated after treatment with 5% FBS. Expression patterns of three germ layer markers revealed that cells cultured in Knockout Serum Replacement-containing medium (KSR) with mouse feeder cells had higher differentiation potential than cells cultured in a chemically defined medium (E8) with recombinant matrix proteins, especially into the mesoderm and endoderm lineages. Analysis of differentially expressed genes between KSR and E8 identified DUSP6 as a marker for where cells had been cultured. Expression of DUSP6 correlated with FGF-ERK signaling activity. Fine-tuning of FGF-ERK signaling activity to a range that can shut down DUSP6 transcription but sustain NANOG transcription partially increased the differentiation potential. Our data suggest that differentiation with 5% FBS is good to estimate differentiation potential and propensity at the early stage, and that DUSP6 is an excellent marker to monitor ERK signaling activity.
Overall design Two biological replicates were analyzed for each point of differentiation of human pluripotent stem cells cultured in two widely used media. For differentiation with 5% FBS, hFSiPS1 cells were cultured KSR and E8 media for 3 weeks and differentiated with 5% FBS. Cells were harvested after 1, 2, 3 weeks. For culture media, hPSCs, hFSiPS1, hFmiPS2, SNUhES31, H9, were cultured for 13 weeks and harvested at 3 weeks and 13 weeks.
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Contributor(s) Yoo D, Im Y, Jo E, Kim B, Jo H, Park M, Koo S, Kim Y
Citation(s) 31668921
Submission date Aug 13, 2019
Last update date Feb 18, 2020
Contact name Yong-Ou Kim
Phone 82-43-249-2510
Organization name Korea National Institute of Health
Street address Osongsangmyeong 2ro
City Cheongju
State/province Chungchung buk do
ZIP/Postal code 28160
Country South Korea
Platforms (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (65)
GSM4030336 hFSiPS1_KSR_undiff_rep1
GSM4030337 hFSiPS1_KSR_undiff_rep2
GSM4030338 hFSiPS1_KSR_5%FBS_1W_rep1
BioProject PRJNA560087
SRA SRP218264

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Supplementary file Size Download File type/resource
GSE135799_RNA-seq_FPKM_5_FBS_.csv.gz 1.7 Mb (ftp)(http) CSV
GSE135799_RNA-seq_FPKM_KSR_E8VN_E8LN_.csv.gz 1.8 Mb (ftp)(http) CSV
GSE135799_RNA-seq_FPKM_PD03_5_FBS_.csv.gz 1.3 Mb (ftp)(http) CSV
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Raw data are available in SRA
Processed data are available on Series record

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