|
| Status |
Public on Jan 01, 2014 |
| Title |
2nd_NPC_rna_seq |
| Sample type |
SRA |
| |
|
| Source name |
NPC
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: NPC
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated from cells using the miRNeasy Kit (Qiagen) according to the manufacturer’s protocol. An additional DNAse1 digestion step was performed to ensure that the samples were not contaminated with genomic DNA. RNA purity was assessed using the Agilant 2100 Bioanalyzer (Beijing Genomics Institute). Each RNA sample had an A260:A280 ratio above 1.8, a RIN>9, and a A260:A230 ratio above 2.2. Briefly, total RNA was converted to cDNA, which was then used for Illumina sequencing library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
RNA-Seq reads were aligned to the human genome (GRCh37/hg19) using the software TopHat (version 1.3.2 )
The resulting alignment data from Tophat were then fed to an assembler, Cufflinks (version 1.3.0) to assemble aligned RNA-Seq reads into transcripts
the program Cuffdiff was used to define differential expression
Genome_build: hg19
Supplementary_files_format_and_content: excel files include FPKM for each sample and some statistics
|
| |
|
| Submission date |
Aug 12, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Herb Lachman |
| E-mail(s) |
herb.lachman@einstein.yu.edu
|
| Organization name |
Albert Einstein College of Medicine
|
| Department |
Psychiatry
|
| Lab |
Behavioral Genetics
|
| Street address |
1300 Morris Park Ave., F103
|
| City |
Bronx |
| State/province |
NY |
| ZIP/Postal code |
10461 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE43143 |
RNA-Seq analysis of neurons derived from induced pluripotent stem cells reprogrammed from dental pulp |
|
| Relations |
| BioSample |
SAMN02315669 |
| SRA |
SRX333643 |
