|
| Status |
Public on Feb 03, 2015 |
| Title |
13_5_MN_VPA_plus |
| Sample type |
SRA |
| |
|
| Source name |
iPSC derived motor neuron
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: VPA
cell type: iPSC derived motor neuron
|
| Treatment protocol |
samples were treated with or without 1 mM VPA for 6 days by changing half of the medium every two days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted and purified using RNA mini kit (QIAGEN) according to manufacturer’s instruction.
One µg of total RNA was depleted of rRNA using Ribo-Zero gold kit (Epicentre), and then 100 ng of rRNA-depleted RNA fraction was subjected to Illumina’s sequencing library using TruSeq Stranded Total RNA Sample Prep Kit (Illumina). The library was captured on an Illumina flow cell for cluster generation.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Basecalls performed using BCL2FASTQ Conversion Software 1.8.4 in the CASAVA 1.8.2 pipeline.
Data were filtered using Illumina's Quality Filtering and 101th bases in reads were not used.
RNA-seq reads were aligned to the hg19 genome assembly using TopHat version 2.0.8b with default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calcurated using RPKMforGenes, downloaded on 19th, October 2012..
Genome_build: hg19
Supplementary_files_format_and_content: Text files which contain RPKM were calcurated using RPKMforGenes, downloaded on 19th, October 2012.
|
| |
|
| Submission date |
Feb 02, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Megumu Saito |
| E-mail(s) |
msaito@cira.kyoto-u.ac.jp
|
| Organization name |
Kyoto University
|
| Street address |
53, Shogoin-Kawahara
|
| City |
Kyoto |
| ZIP/Postal code |
6068507 |
| Country |
Japan |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE65508 |
Modeling the early phenotype at the neuromuscular junction of spinal muscular atrophy using patient-derived iPSCs (RNA-Seq) |
|
| Relations |
| BioSample |
SAMN03324089 |
| SRA |
SRX863074 |
