|
| Status |
Public on Sep 17, 2018 |
| Title |
Mouse HSC, NT, biological rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Mouse HSCs after 16-hours in vitro treatment with vehicle
|
| Organism |
Mus musculus |
| Characteristics |
tissue: FACS-sorted HSC
age: 6-10 weeks
|
| Treatment protocol |
Mouse HSCs were treated with either Eltrombopag (10 µg/ml, Novartis), or vehicle control (sterile H2O) in the liquid culture for 16 hours. Thereafter, cells were collected and lysed with RLT plus buffer (Qiagen, Valencia, CA). Cell lysates were stored in -80 °C until use.
|
| Growth protocol |
Mouse HSCs (Lineage−c-Kit+Sca-1+CD150+CD48−) were sorted, and cultured in Myelocult M5300 medium (Stem Cell Technologies) supplemented with 100 ng/ml rmSCF(Gemini Bio-Products, CA) and 200 µg/ml Primocin (InvivoGen, San Diego, CA).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the RNeasy Micro kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions. Quantity and quality were assessed using Nanodrop 3300 Fluorospectrometer (Thermo Fisher Scientific, Waltham, MA) or Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
|
| Label |
Biotin
|
| Label protocol |
Around 10ng of extracted RNA was amplified and labeled using the GeneChip™ 3' IVT Pico Kit (Affymetrix, Santa Clara, CA), according to the manufacturer's instructions
|
| |
|
| Hybridization protocol |
Following fragmentation, labeled cRNA of each individual sample was hybridized to Affymetrix Mouse Clariom S microarrays (Affymetrix), and stained according to the manufacturer's instructions.
|
| Scan protocol |
Hybridization signals were scanned and analyzed with GeneChip Scanner 3000 7G system (Affymetrix) according to standard protocols.
|
| Description |
Gene expression data from mouse HSCs after 16-hours in vitro treatment with vehicle
|
| Data processing |
For analysis of microarray data, intensity normalization was performed across samples with the CEL files using RMA algorithm of Oligo Bioconductor package. For analysis of differential gene expression, paired, linear modeling of Limma Bioconductor package was used to compare the treated samples versus the matched, non-treated controls. Differential expression was defined as fold change > 1.5 (both up and down in) and p-value < 0.05 as estimated by Limma.
|
| |
|
| Submission date |
Nov 28, 2017 |
| Last update date |
Sep 18, 2018 |
| Contact name |
Britta Will |
| E-mail(s) |
britta.will@einsteinmed.edu
|
| Organization name |
Albert Einstein College of Medicine
|
| Department |
Department of Cell Biology
|
| Lab |
Chanin 401
|
| Street address |
1300 Morris Park Ave
|
| City |
Bronx |
| State/province |
NEW YORK |
| ZIP/Postal code |
10461 |
| Country |
USA |
| |
|
| Platform ID |
GPL23038 |
| Series (2) |
| GSE107429 |
Gene expression profiling of mouse HSCs treated with Eltrombopag |
| GSE107430 |
Gene expression profiling of HSCs treated with Eltrombopag |
|
