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| Status |
Public on Apr 28, 2017 |
| Title |
Liver differentiation day 0 (hESC cells) |
| Sample type |
SRA |
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| Source name |
hESCs
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| Organism |
Homo sapiens |
| Characteristics |
day: 0
treatment: None
presumed cell type: hESCs
cell line: H1
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| Treatment protocol |
For hepatic differentiation, we established a serum-free protocol based on previously described protocols with minor modifications (Si-Tayeb et al., 2010; Song et al., 2009). Briefly, cells were cultured for 3 days in RPMI/B27 medium (Insulin minus, Gibco, A18956-01) supplemented with 100 ng/ml Activin A (Peprotech, A120-14E), followed by 4 days with 20 ng/ml BMP2 (Peprotech, 120-02)and 30 ng/ml FGF-4 (Peprotech, 100-31) in RPMI/B27(complete with Insulin, Gibco,17504-044) medium, then 6 days with 20 ng/ml HGF (Peprotech, 100-39) and KGF (Peprotech, 100-19) in RPMI/B27 (complete with Insulin), then 8 days with 20 ng/ml Oncostatin-M (R&D Systems, 295-OM/CF) in Hepatocyte Culture Media (Lonza, cc-3198) supplemented with SingleQuots (without EGF).
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| Growth protocol |
Undifferentiated human H1 ES cells were maintained in monolayer culture on Matrigel (BD Biosciences, 354277) in mTeSR1 medium (Stemcell Technologies, 05850) at 37°C with 5% CO2. Cells were manually passaged at 1:4 to 1:6 split ratios every 3 to 5 days.
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| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol
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 MiSeq |
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| Description |
Human embryonic stem cells
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| Data processing |
rsem v1.2.17/bowtie2 v2.2.0 was used to align to the ensembl transcriptome (mm10, v76)
transcripts with more than 25 sequence tags in 2 or more timepoints were kept for further analysis
mapping tag counts were GC normalised using EDASeq v2.0.0
Genome_build: hg19
Supplementary_files_format_and_content: tab delimeted text file containing ensembl transcript accession, gene name and normalised abundance estimates for each transcript
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| Submission date |
Jul 10, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Andrew P Hutchins |
| E-mail(s) |
andrewh@sustech.edu.cn
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| Organization name |
Southern University of Science and Technology
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| Department |
Bioinformatics
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| Lab |
Bioinformatics and Genomics
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| Street address |
1088 Xueyuan Rd
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| City |
Shenzhen |
| ZIP/Postal code |
518055 |
| Country |
China |
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| Platform ID |
GPL15520 |
| Series (1) |
| GSE70741 |
Differentiation of human embryonic stem cells towards hepatocytes |
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| Relations |
| BioSample |
SAMN03854048 |
| SRA |
SRX1091576 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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