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Sample GSM1394606 Query DataSets for GSM1394606
Status Public on Aug 01, 2014
Title Control 1 RNA-Seq rep1
Sample type SRA
 
Source name Control 1_induced neuron_RNA-Seq
Organism Homo sapiens
Characteristics cell type: iPSC-derived neurons
differentiation time: 4 weeks
genotype/variation: control
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.
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).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Ion Torrent Proton
 
Description Sample 1 C3-1
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
 
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
Lab Kosik Lab
Street address 552 University Rd
City Santa Barbara
State/province CA
ZIP/Postal code 93106
Country USA
 
Platform ID GPL17303
Series (1)
GSE57821 Transcriptional dysregulation of synaptic genes in a human iPSC model of major mental disorders
Relations
BioSample SAMN02795852
SRA SRX547290

Supplementary file Size Download File type/resource
GSM1394606_C3-1-R1_genecounts.tsv.gz 159.7 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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