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Sample GSM2345404 Query DataSets for GSM2345404
Status Public on Jan 03, 2017
Title co-culture untreated control Hs+Ms_CNTR_2
Sample type SRA
Source name hiPSC-derived neurons
Organisms Homo sapiens; Mus musculus
Characteristics cell type: forebrain neuron-like, heterogenous
passages: from iPSC passages 30-40
iPSc line: iPS D1
developmental stage: postmitotic
Treatment protocol Bicuculline (50 µM) applied together with 4-aminopyridine (250 µM) (Bic/4AP)
Growth protocol We differentiated iPSCs to NPCs using a slightly modified spin embryoid body protocol (Kim et al., 2011) with dual SMAD inhibition (Chambers et al., 2009). Differentiation of NPCs was initiated by plating 50,000 cells/cm2 on PO/Lam dishes without EGF and FGF2. Neuronal differentiation was allowed to proceed for 7 (co-cultures) or 10 (hiPSCd neuron-only cultures) weeks.
Extracted molecule total RNA
Extraction protocol Total RNA was purified from cultured cells (3.5 cm dish) with RNeasy Mini (hiPSCd neuron/mouse primary neuron co-cultures) or Micro (hiPSCd neuron-only cultures) Kit (Qiagen) along with on-column RNase-Free DNase (Qiagen) digestion of DNA
Poly(A)+ RNA was isolated from total RNA with the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). cDNA libraries were prepared with NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs). NEBNext Multiplex Oligos for Illumina (New England Biolabs) were used.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Description P0 mouse primary neurons were added to hiPSCd neurons for the last 10 days of differentiation.
polyA purified
Data processing Illumina Casava1.7 software used for basecalling.
hiPSCd neuron/mouse primary neuron co-culture sample reads were filtered for human reads as follows. Paired-end reads were aligned independently, without pairing, to the mouse genome assembly GRCm38/mm10 with Bowtie2 version 2.1.0. Unaligned read pairs were joined and split again to eliminate pairs with one aligned read. Then, genome-unaligned paired-end reads were aligned to GRCm38/mm10 transcriptomes (UCSC Genes/knownGene), respectively, with Bowtie2 (2.1.0). The reads not aligned to the mouse genome and transcriptome were handled as reads obtained from hiPSCd neuron-only samples.
Processed mixed-species sample reads and human-cells-only sample reads were aligned to gene model annotations of the human genome assembly GRCh37/hg19 with TopHat version v2.0.9.
Mapped reads per gene were counted strand-specifically with HTSeq-count (HTSeq version 0.6.0 or 0.6.1) in the union overlap resolution mode.
Differentially expressed genes were determined with the DESeq2 package version 1.8.1.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: HTSeq-count read counts per gene.
Submission date Oct 14, 2016
Last update date May 15, 2019
Contact name Priit Pruunsild
Organization name University of Heidelberg
Department Neurobiology
Street address INF 364
City Heidelberg
ZIP/Postal code 69120
Country Germany
Platform ID GPL16512
Series (1)
GSE88773 Networks of cultured iPSC-derived neurons reveal the human synaptic activity-regulated adaptive gene program
BioSample SAMN05908859
SRA SRX2245888

Supplementary file Size Download File type/resource
GSM2345404_Hs+Ms_CNTR_2_counts.tabular.txt.gz 101.2 Kb (ftp)(http) TXT
GSM2345404_Hs+Ms_CNTR_2_techRep_counts.tabular.txt.gz 99.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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