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| Status |
Public on Oct 06, 2011 |
| Title |
iPS1-C3 day 10 |
| Sample type |
SRA |
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| Source name |
neurons
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| Organism |
Homo sapiens |
| Characteristics |
cell type: hiPSCs-derived neurons
passages: 5
clone: 3
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| Treatment protocol |
To support glutamatergic differentiation, adherent colonies were treated on day 10 with WNT3A (100ng/ml) (R&D Systems, Minneapolis, MN) in neural induction medium. Cells were fed every other day for 2 weeks. On day 25, medium was changed to neuronal differentiation medium, which consists of Neurobasal medium, 1X N2 supplement, 2X B27, 0.1 mM NEAA, supplemented with cAMP (1 μM), BDNF, GDNF, and IGF1 (10 ng/ml each, PeproTech, Rocky Hill, NJ). The concentration of WNT3A was reduced to 10ng/ml.
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| Growth protocol |
Stem cell lines were maintained on irradiated mouse embryonic fibroblasts (MEFs) in hES medium consisting of knockout (KO)-DMEM, 1mM pen/strep, 1 mM Gluta-MAX, 1X nonessential amino acids (NEAA), 55 μM β-mercaptoethanol (β-ME) (Gibco, Carlsbad, CA), 10% Knockout (KO) serum replacement (Invitrogen, Carlsbad, CA), 10% plasmanate (Talecris Biotherapeutics, Research Triangle Park, NC), and 10 ng/ml FGF2 (R&D Systems Inc., Minneapolis, MN).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA (25 ng) was converted to cDNA using the NuGEN Ovation RNA-Seq System according to the manufacturer's protocol (NuGEN, San Carlos, CA, USA). The protocol employs a single primer isothermal amplification (SPIA) method to amplify RNA target into double stranded cDNA under standardized conditions that markedly deplete rRNA without preselecting mRNA. cDNA was then used for Illumina sequencing library preparation using Encore NGS Library System I. NuGEN-amplified double-stranded cDNA was fragmented into ,300 base pair (bp) using a Covaris-S2 system. DNA fragments (200 ng) were then end-repaired to generate blunt ends with 59 phosphatase and 39 hydroxyls and adapters were ligated for paired end sequencing on Illumina HiSeq 2000. The average fragment length is 250bp and the standard deviation is 50bp.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
amplified cDNA (The average fragment length : 250bp, the standard deviation : 50bp)
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| Data processing |
iPS cell and neuron RNA-Seq reads were separately aligned to the human genome (GRCh37/hg19) using the software TopHat (version 1.2.0).
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| Submission date |
Oct 05, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Mingyan Lin |
| E-mail(s) |
mingyan.lin@phd.einstein.yu.edu
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| Organization name |
Albert Einstein college of medicine
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| Street address |
1300 Morris Park Avenue
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| City |
bronx |
| State/province |
ny |
| ZIP/Postal code |
10461 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE32625 |
RNA-Seq of human neurons derived from iPS cells Reveals candidate long non-coding RNAs Involved in neurogenesis and neuropsychiatric disorders. |
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| Relations |
| SRA |
SRX099712 |
| BioSample |
SAMN00736192 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM808735_iPS1-C3day10.hg19.tophat.bam |
9.4 Gb |
(ftp)(http) |
BAM |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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