|
| Status |
Public on Dec 19, 2018 |
| Title |
Control_1 |
| Sample type |
RNA |
| |
|
| Source name |
Healthy subject
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: iPS cell-derived neural progenitors
disease state: healthy
|
| Growth protocol |
Human iPS cell clusters were grown as neurospheres in neuronal differentiation medium. After 6 weeks, neurospheres were plated on poly-D-lysin/laminin coated plates and allowed to differentiate for 1 day. Following day cells were scraped in PBS and the cell pellet was collected.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNA Purification Kit (Norgen Biotek Corp.) according to the manufacturer’s instructions.
|
| Label |
Biotin
|
| Label protocol |
Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip WT Plus reagent Kit, Manual Target Preparation for GeneChip Whole Transcript Expression Arrays, P/N 703174 Rev.5, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 5.2 ug of cRNA was hybridized for 16 hr at 45oC on Affymetrix Human Clariom D arrays. The Clariom D arrays were washed and stained in the Affymetrix Fluidics Station 450 (GeneChip Expression Wash, Stain and Scan User Manual for Cartridge Arrays, P/N 702731 Rev. 4, Affymetrix).
|
| Scan protocol |
Clariom D arrays were scanned using the Hewlett-Packard GeneChip Scanner 3000 (GCS3000).
|
| Description |
SST-RMA expression value derived from Affymetrix Expression Console Software
HEL11.4
|
| Data processing |
The CEL files were processed and normalized using Expression Console Software using Affymetrix default analysis settings to perform Gene Level Analysis (Gene Level-SST-RMA). Gene level data files (sst-rma-gene-full.chp) were then loaded into Affymetrix’s Transcriptome Analysis Console software to perform gene level analysis.
|
| |
|
| Submission date |
Sep 18, 2017 |
| Last update date |
Dec 19, 2018 |
| Contact name |
Maija L Castrén |
| E-mail(s) |
maija.castren@helsinki.fi
|
| Organization name |
University of Helsinki
|
| Department |
Faculty of Medicine/Physiology
|
| Street address |
P.O.BOX 63
|
| City |
Helsinki |
| State/province |
Helsinki |
| ZIP/Postal code |
00014 |
| Country |
Finland |
| |
|
| Platform ID |
GPL23126 |
| Series (1) |
| GSE103965 |
Functional changes of AMPA responses in human induced pluripotent stem cell-derived neural progenitors in fragile X syndrome |
|
