|
| Status |
Public on Oct 31, 2018 |
| Title |
MSA101_O16_levothyroxine sodium 1_uM 6_hours 2484-2-A |
| Sample type |
RNA |
| |
|
| Source name |
hiPSC_SZ
|
| Organism |
Homo sapiens |
| Characteristics |
perturbagen: levothyroxine sodium
cell id: 2484-2-A
dosage: 1_uM
batch: MSA101_B
duration: 6_hours
perturbation type: test
well id: O16
plate id: MSA101
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed with cell lysis buffer (110 µL per well), and stored at -80⁰C
|
| Label |
biotin
|
| Label protocol |
mRNA is reverse transcribed and the cDNA product PCR amplified using primers that contain contiguous sequence (barcode) complementary to each L1000 gene; in addition, the upstream primer is biotinylated to enable identification of amplicon-bound beads.
|
| |
|
| Hybridization protocol |
PCR amplicon of each gene is hybridized to barcoded Luminex beads. The barcode incorporated in each amplicon is complementary to a barcode on a Luminex bead, ensuring that each gene from the original lysate mRNA is represented by an amplicon bound to a specific bead.
|
| Scan protocol |
Luminex scanners detect individual beads by color, then measure the fluorescent intensity of the SAPE molecules attached to the biotin label on each amplicon-bound bead
|
| Description |
24 hiPSC-derived NPCs and 8 CCLs were used (total: 32 cell lines). Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: a) phase 1 had 6/79 drugs from pilot, and 73/79 phase 1 test compounds, b) phase 2 had 6 pilot drugs re-tested, 6/73 phase 1 drugs re-tested, and 67/79 phase 2 compounds. 135 unique compounds were tested.
|
| Data processing |
Raw intensity measurements are deconvoluted to provide intensity values for each landmark gene (the 978 directly measured features). Data is then normalized using a calibration curve based on invariant gene sets, and then quantile normalized.
|
| |
|
| Submission date |
Aug 30, 2018 |
| Last update date |
Oct 31, 2018 |
| Contact name |
Ben Readhead |
| E-mail(s) |
ben.readhead@asu.edu
|
| Organization name |
ASU-Banner Neurodegenerative Disease Research Center
|
| Street address |
797 E. Tyler Street
|
| City |
Tempe |
| State/province |
AZ |
| ZIP/Postal code |
85281 |
| Country |
USA |
| |
|
| Platform ID |
GPL25480 |
| Series (2) |
| GSE119275 |
Expression-based drug screening of neural progenitor cells from individuals with schizophrenia [MSA101] |
| GSE119291 |
Expression-based drug screening of neural progenitor cells from individuals with schizophrenia |
|
