|
| Status |
Public on Dec 27, 2023 |
| Title |
3d_post_IR_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
MK, 3dpi
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Bone marrow
cell type: megakaryocyte (MK)
gender: male
treatment: 3 day post IR
|
| Treatment protocol |
With or without exposed to IR.
|
| Growth protocol |
All mice used were randomized, background-matched. All mice used were housed in individually ventilated specific pathogen-free (SPF) conditions and fed with autoclaved water and food.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from sorted mMKs using a TRIzol Plus reagent (TaKaRa, Shiga, Japan).
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse Gene Expression v2 8x60K Microarray for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).
|
| Description |
Gene expression of MKs from mice at 3 day post IR
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained
|
| |
|
| Submission date |
Jan 10, 2023 |
| Last update date |
Dec 27, 2023 |
| Contact name |
Weinian Liao |
| E-mail(s) |
[email protected]
|
| Phone |
15111956240
|
| Organization name |
Army Medical University
|
| Street address |
Gaotanyan street 30
|
| City |
Chongqing |
| ZIP/Postal code |
400038 |
| Country |
China |
| |
|
| Platform ID |
GPL33010 |
| Series (1) |
| GSE222512 |
Gene expression signatures of megakaryocytes post-IR |
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