|
| Status |
Public on Nov 05, 2016 |
| Title |
22q1130_dup |
| Sample type |
SRA |
| |
|
| Source name |
neuron cell line
|
| Organism |
Homo sapiens |
| Characteristics |
sample group: patients
tissue: iPSC-derived neuron
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA-seq was carried out on and day 14 neurons at the Columbia Genome Center. 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 using oligo dT, which was then used for Illumina sequencing library preparation.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Paired-end RNA-seq was carried out on an Illumina HiSeq 2000. We obtained 90-101 bp mate-paired reads from cDNA fragments with an average size of 250-bp (standard deviation for the distribution of inner distances between mate pairs is approximately 100 bp). RNA-seq reads were aligned to the human genome (GRCh37/hg19) using the software TopHat (version 2.0.8) [PMID:19289445]. We counted the number of fragments mapped to each gene annotated in the GENCODE database (version 18), which included multiple categories of annotated transcripts, and quantified transcript abundance as FPKM (fragments per kilobase of exon per million fragments mapped).
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: text file including FPKM for each sample
|
| |
|
| Submission date |
Nov 04, 2016 |
| 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) |
| GSE46562 |
RNA-seq in neurons derived from iPSCs in controls and patients with schizophrenia and 22q11 del |
|
| Relations |
| BioSample |
SAMN05981678 |
| SRA |
SRX2327635 |
