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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 18, 2018 |
| Title |
PE RNA rep2 |
| Sample type |
SRA |
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| Source name |
human ES cells
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| Organism |
Homo sapiens |
| Characteristics |
strain: H1 ES differentiate
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| Treatment protocol |
Pancreatic differentiation was following previous published protocol (Schulz et al., 2012; Xie et al., 2013). Differentiation employed a suspension-based format using rotational culture. Aggregates of undifferentiated hESC were generated by resuspending dissociated cells in hESC media at 1 × 106 cells/mL and culturing them overnight in six-well ultra-low attachment plates (Costar) with 5.5ml per well on an orbital rotator (Innova2000, New Brunswick Scientific) at 95 rpm. The following day undifferentiated aggregates were washed in RPMI media and then differentiated using a multi-step protocol with daily media feeding except on day 10 and continued orbital rotation at either 95 rpm or at 105 rpm on days 4 to 8. In addition to GlutaMAX™ and penicillin/streptomycin, RPMI media (Mediatech) was supplemented with 0.2% (vol/vol) FBS (HyClone) and DMEM High Glucose media (HyClone) was supplemented with 0.5X B-27® supplement (Life Technologies). Human activin, mouse Wnt3a, human KGF, human Noggin, and human EGF were purchased from R&D systems. Other media components included TGFb R1 kinase inhibitor IV (EMD Bioscience), KAAD-Cyclopamine (Toronto Research Chemicals), the retinoid analog TTNPB (Sigma Aldrich), and Insulin-Transferrin-Selenium (ITS; Life Technologies). For some differentiations, 50ng/mL Noggin was also included on days 8 to 12.
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| Growth protocol |
Human embryonic stem cells (H1) was cultured in hESC culture media (mTeSR1, Stem Cell Technologies) following manufactures instruction. Every 3-4 days, cells were passaged using AccutaseTM (Innovative Cell Technologies) supplied with 10% (vol/vol) human AB serum (Valley Biomedical) included in the hESC media the day of passage.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using Qiagen RNeasy mini kit.
RNA library was constructed according to illumina Trueseq kit protocol
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Removed the low quality reads; Bowtie2 was used to map RNAseq to hg19 with default parameters.
DESeq2 was used to count the raw reads number fail in genes and call differential expressed genes
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file include the RPKM for each gene in each sample
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| Submission date |
Apr 19, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jia Li |
| E-mail(s) |
jiali@tamu.edu
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| Organization name |
Texas A&M U Health Science Center
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| Department |
CEDP
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| Lab |
Jia Li Lab
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| Street address |
2121 W HOLCOMBE BLVD
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| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77030 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE97990 |
5hmC dynamically correlated with enhancer's activities during hES-to-Pancreatic endoderm cell differentiation (RNA-Seq) |
| GSE97992 |
5hmC dynamically correlated with enhancer's activities during hES-to-Pancreatic endoderm cell differentiation |
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| Relations |
| BioSample |
SAMN06767333 |
| SRA |
SRX2747194 |
| 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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