|
| Status |
Public on Oct 22, 2018 |
| Title |
PDLSC 1 |
| Sample type |
RNA |
| |
|
| Source name |
periodontal ligament stem cells (PDLSCs)
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: PDLSC
|
| Treatment protocol |
NCCs were passaged in TeSR-E7 basic medium supplemented with 0.5-1 µM CHIR99021 (CHIR), 10 ng/ml SB431542 (R&D Systems) and 100 μg/ml Primocin. All other cell types were passaged in alpha-modification of Eagle’s medium (Gibco/Invitrogen) supplemented with 10% FBS, 1 mM L-glutamine (Gibco/Invitrogen), and 100 μg/ml Primocin for 2-3 passages before RNA extraction for microarray analysis.
|
| Growth protocol |
Undifferentiated hiPSCs were maintained on Matrigel (Corning) coated 6-well plates in TeSR-E8 medium (STEMCELL Technologies) with 100 μg/ml Primocin (1:500 dilution, Invivogen) in a 37°C incubator with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested from wells and RNA was extracted using using QIAshredder columns (QIAGEN, 79656) and the RNeasy Plus Mini Kit (QIAGEN, 74136) according to the QIAGEN manual instructions. Purified RNA was eluted in 30 µl nuclease-free water.
|
| Label |
biotin
|
| Label protocol |
Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.
|
| |
|
| Hybridization protocol |
The labeled, fragmented DNA was hybridized to the Affymetrix Human Gene 2.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.
|
| Scan protocol |
After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.
|
| Description |
Gene expression data from primary periodontal ligament stem cells (PDLSCs).
|
| Data processing |
Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray hugene20sthsentrezg R package (version 17.0.0).
|
| |
|
| Submission date |
Apr 18, 2018 |
| Last update date |
Jun 25, 2019 |
| Contact name |
Boston University Microarray and Sequencing Resource |
| E-mail(s) |
msrdata@bu.edu
|
| Organization name |
Boston University
|
| Department |
Microarray and Sequencing Resource
|
| Street address |
72 East Concord Street, E631
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02118 |
| Country |
USA |
| |
|
| Platform ID |
GPL17930 |
| Series (1) |
| GSE113297 |
Derivation and characterization of putative craniofacial mesenchymal stromal cells from human induced pluripotent stem cells |
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