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| Status |
Public on Jul 15, 2014 |
| Title |
Day 60 (Replicate 1) |
| Sample type |
SRA |
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| Source name |
induced pluripotent stem cells (differentiation into cardiomyocytes)
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| Organism |
Homo sapiens |
| Characteristics |
time: 60d
replicate: 1
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| Growth protocol |
Briefly, hiPSCs were generated from a human fibroblast cell line via reprogramming through retroviral expression of SOX2, OCT4, NANOG, and LIN28. This hiPSC clone was propagated and maintained in feeder-free culture using mTeSR1® (Stem Cell Technologies, Vancouver, British Columbia, Canada) on a Matrigel™ substrate (Beckton Dickinson, Franklin Lakes, NJ). These hiPSCs were formed into aggregates and cultured in differentiation medium containing 100 ng/mL zebrafish basic fibroblast growth factor and 10% fetal bovine serum prior to the differentiation of cardiac myocytes. On day 14 of differentiation, the cultures were subjected to blasticidin selection (25 μg/mL) to purify the cardiomyocyte population. Following blasticidin selection, cultures were maintained in Dulbecco's modified Eagle's medium containing 10% fetal bovine serum for the duration of the cultures. The differentiation protocol and sample collection were performed in 3 independent replicates as indicated by Run 1, 2, and 3.
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| Extracted molecule |
total RNA |
| Extraction protocol |
10 ng of total RNA from each time point and biological replicate was reverse transcribed to cDNA and amplified by limited PCR according to the protocol supplied with the Ion AmpliSeq™ RNA Library Kit (Life Technologies, Carlsbad, USA, Catalog number 4482335). After primer digestion, adapters and barcodes were ligated to the amplicons followed by magnetic bead purification. The purified library was amplified, purified and stored at -20°C. Amplicon size and DNA concentration was measured using an Agilent High Sensitivity DNA Kit (Agilent Technologies, Waldbronn, Germany) according to the manufacturer's guide.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent PGM |
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| Description |
library stratagy: Ampli-seq
iPSC induced into cardiomyocytes at day 60
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| Data processing |
Base-calling, filtering, and alignment is handled automatically by IonTorrent Server Suite (version 4.0.2)
Amplicon coverage is reported by IonTorrent Server Suite (version 4.0.2) as a tab-delimited file, which was converted into GCT format by in-house scripts.
Genome_build: hg19
Supplementary_files_format_and_content: txt
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| Submission date |
Jun 23, 2014 |
| Last update date |
Jul 15, 2014 |
| Contact name |
Jitao David Zhang |
| E-mail(s) |
jitao_david.zhang@roche.com
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| Phone |
+41616886251
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| Organization name |
F. Hoffmann-La Roche
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| Department |
Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel
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| Lab |
Pharmaceutical Sciences
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| Street address |
Grenzacherstrasse 124
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| City |
Basel |
| ZIP/Postal code |
4070 |
| Country |
Switzerland |
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| Platform ID |
GPL17301 |
| Series (1) |
| GSE58737 |
Highly sensitive amplicon-based transcript quantification by semi-conductor sequencing |
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| Relations |
| BioSample |
SAMN02870003 |
| Supplementary data files not provided |
| Raw data not provided for this record |
| Processed data are available on Series record |
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