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| Status |
Public on Aug 01, 2014 |
| Title |
Patient 1 RNA-Seq rep3 |
| Sample type |
SRA |
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| Source name |
Patient 1_induced neuron_RNA-Seq
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| Organism |
Homo sapiens |
| Characteristics |
cell type: iPSC-derived neurons
differentiation time: 4 weeks
genotype/variation: carrying heterozygous 4bp deletion in DISC1 gene
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| Growth protocol |
iPSCs colonies were detached from the feeder layer with collagenase (1 mg/ml) treatment for 1 hr and suspended in EB medium, consisting of FGF-2-free iPSC medium supplemented with Dorsomorphin (2 µM) and A-83 (2 µM), in non-treated polystyrene plates for 4 days with a daily medium change. After 4 days, EB medium was replaced by neural induction medium (hNPC medium) consisting of DMEM/F12, N2 supplement, NEAA, heparin (2 µg/ml) and cyclopamine (2 µM). The floating EBs were then transferred to matrigel-coated 6-well plates at day 7 to form neural tube-like rosettes. The attached rosettes were kept for 15 days with hNPC medium change every other day. On day 22, the rosettes were picked mechanically and transferred to low attachment plates (Corning) in hNPC medium containing B27. For neuronal differentiation, resuspended neural progenitor spheres were dissociated with Accutase at 37⁰C for 10 min and placed onto Poly-D-Lysine/laminin-coated coverslips in the neuronal culture medium, consisting of Neurobasal medium supplemented with 2 mM L-glutamine, B27, BDNF (10 ng/ml) and GDNF (10 ng/ml). Half of the medium was replaced once a week during continuous culturing.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated using mirVana kit (Invitrogen) according to manufacturer’s instructions, polyA selected
Ion Total RNA-Seq Kit v2 for Whole Transcriptome sequencing following the protocol provided by the manufacturer (Life Technologies, Carlsbad, CA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
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| Description |
Sample 2 D2-3
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| Data processing |
Base-calling performed by Torrent Suite Software 4.0.2
Reads were first aligned to UCSC hg19 with TopHat v2.0.10, default settings
The unmapped reads were subsequently mapped with bowtie2 (v2.1.0) --local --very-sensitive-local -p 8 --mm
Reads mapped by tophat and bowtie were merged
Reads mapping to CDS (excluding UTR) were counted using coverageBed (v2.10.0)
Genome_build: hg19
Supplementary_files_format_and_content: Counts for the CDS of each transcript is provided for each replicate in genecounts.tsv files. These files can be read directly into edgeR
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| Submission date |
May 20, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Kenneth Kosik |
| Organization name |
University of California Santa Barbara
|
| Department |
Neuroscience Research Institute
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| Lab |
Kosik Lab
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| Street address |
552 University Rd
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| City |
Santa Barbara |
| State/province |
CA |
| ZIP/Postal code |
93106 |
| Country |
USA |
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| Platform ID |
GPL17303 |
| Series (1) |
| GSE57821 |
Transcriptional dysregulation of synaptic genes in a human iPSC model of major mental disorders |
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| Relations |
| BioSample |
SAMN02795845 |
| SRA |
SRX547295 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1394611_D2-1-R3_genecounts.tsv.gz |
169.6 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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