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| Status |
Public on Oct 24, 2014 |
| Title |
Non-PD-1_1 |
| Sample type |
SRA |
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| Source name |
iPS cell-derived neuronal samples
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| Organism |
Homo sapiens |
| Characteristics |
cell type: iPS cell-derived neuronal samples
diferentiation day: ~ day 33
disease: Healthy
genotype: GBA +/N370S
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using RNeasy Micro Kit (QIAGEN). Quality control of the RNA was carried out with the Agilent Bio-analyzer, Qubit 2.0 at the MPSR of Columbia University. 100 ng of RNA with RIN ≥ 9 were used for generating mRNA-focused libraries.
RNA libraries were prepared using TruSeq RNA Sample Preparation Kit v2
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
SA003
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| Data processing |
The reads were mapped to a reference genome (Human: NCBI/build37.2) using Tophat (version 2.0.4) with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10). The relative abundance (aka expression level) of genes and splice isoforms were evaluated using cufflinks (version 2.0.2) with default settings. We test for differentially expressed genes under various conditions using DEseq. The differential expression signature and differential pathways enrichment were identified with a statistical significance (P < 0.01). To specifically discover the profile of genes involved in DA synthesis, storage, release, re-uptake, metabolism, and PD pathogenesis in both twins, the average FPKM (Fragments Per Kilobase Of Exon Per Million Fragments Mapped) value from four biological replicates of each twin and their ratio of FPKM (affected twin vs. unaffected twin) were calculated. Positive/negative fold change mean an up-regulation and a down-regulation, respectively. 2-fold change was used as an arbitrary cut- off point in this analysis.
Genome_build: Human: NCBI/build37.2
Supplementary_files_format_and_content: csv files include FPKM values for each Sample
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| Submission date |
Oct 23, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Aiqun Li |
| E-mail(s) |
leeaiqun@hotmail.com
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| Phone |
2128515422
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| Organization name |
The New York Stem Cell Foundation
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| Department |
Research Institute
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| Street address |
3960 Broadway
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE62642 |
RNA-Seq Analysis in purified iPS cell-derived neuronal samples |
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| Relations |
| BioSample |
SAMN03140161 |
| SRA |
SRX739115 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1530728_SA003_genes.csv.gz |
949.8 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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