|
| Status |
Public on Jul 20, 2017 |
| Title |
SCZ164G |
| Sample type |
SRA |
| |
|
| Source name |
Glial Progenitor Cell
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Brain
facs marker: hPDGFRa
subject: Schizophrenic Patient
subject age: 14
subject ethnicity: African American
subject gender: Female
source: hiPSC
cell type: GPC
|
| Growth protocol |
The GPC differentiation from human iPS cells is published in Wang et al. "Human iPSC-Derived Oligodendrocyte Progenitor Cells Can Myelinate and Rescue a Mouse Model of Congenital Hypomyelination" in Cell Stem Cell Volume 12, Issue 2, 2013
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Human iPS cells were derived from fibroblasts obtained from schizophrenic patients and controls. The iPS cells were then differentiated into Glial Progenitor Cells (GPCs) which were than purified by FACS with PDGFRa (aka CD140a) as cell surface marker. The PDGFRa-positive GPC population was used in RNA isolation and sequencing.
RNA libraries were prepared for sequencing using Illumina's TruSeq RNA V2 library preparation kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
mRNA sequencing in Illumina HiSeq 2500 platform for approximately 45 million 1x100 bp reads per sample
Trimming of adapter sequences and low-quality bases with Trimmomatic (version 0.32), parameters: "SLIDINGWINDOW:4:20 TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 MINLEN:15"
Read alignment to human genome build GRCh38 with Subread (version 1.4.6-p3), parameters: "-T 12 --gzFASTQinput --BAMoutput -H"
Feature counting with featureCounts (version 1.4.6-p3) with grouping exons into genes, parameters: "-t exon -g gene"
Genome_build: GRCh38
Supplementary_files_format_and_content: counts
|
| |
|
| Submission date |
Oct 13, 2016 |
| Last update date |
Nov 10, 2021 |
| Contact name |
Steven Goldman |
| Organization name |
University of Rochester Medical Center
|
| Department |
Center for Translational Neuromedicine
|
| Lab |
Goldman Lab
|
| Street address |
601 Elmwood Ave
|
| City |
Rochester |
| State/province |
NY |
| ZIP/Postal code |
14642 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE86906 |
Human iPSC glial mouse chimeras reveal glial contributions to schizophrenia |
|
| Relations |
| Reanalyzed by |
GSM5685573 |
| BioSample |
SAMN05907642 |
| SRA |
SRX2243159 |
