|
| Status |
Public on Dec 30, 2015 |
| Title |
Transcriptomic profiling in the heart of C57BL/6J mice at embyronic day 15 |
| Sample type |
RNA |
| |
|
| Source name |
whole heart
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
tissue: heart
age: embryonic day 15
|
| Treatment protocol |
Tissue samples from C56BL/6J mice from the Tri-City Academic Laboratory Animal Centre – Research and Services Centre, Medical University of Gdańsk for hearts form embryonic day 15, 16, 17, 19, 1 day, 7 day and 2 week old mice. Tissue samples form C56BL/6J mice from Jackson Laboratories for hearts fro 8 week old mice. All tissues were collected in RNAlater stabilization reagent (QIAGEN. cat. no. 76104), transported on dry ice and stored at -80 C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The solid tissues were disrupted in liquid nitrogen prior RNA extraction. Total RNAs was purified using the RNeasy Mini Kit (QIAGEN. cat. no. 74104) coupled with on-column DNA digestion following the manufacturer’s protocols.
|
| Label |
Cy3
|
| Label protocol |
First strand cDNA synthesis was performed with Maxima Reverse Transcriptase (ThermoScientificBio. cat. no. EP0742) using 3 µg of total RNA, 400 U of the Maxima Reverse Transcriptase (200 U/ul), 5 x reaction buffer (250 mM Tris-HCl, 375 mM KCl, 15 mM MgCl, 50 mM DTT) and oligo dT15.(200 pmoles) in a total volume of 40 µl. Second strand cDNA was synthesized using cDNA Synthesis System (Roche, cat. no. 11 117 831 001) according to the second strand synthesis manufacturer's protocol.
|
| |
|
| Hybridization protocol |
Probe labeling and hybridization was performed with Roche NimbleGen kit using the standard protocol for eukaryotic RNA samples and NimbleGen mouse gene expression 12x135K array (Roche, cat. no. 05543797001). The cDNA samples were labeled with Cy3 using a NimbleGen One-Color DNA labeling kit (Roche, cat. no. 06370411001), and hybridized to slides using a NimbleGen hybridization system (Roche, cat. no. 05583683001).
|
| Scan protocol |
The slides were scanned using MS200 Scanner (Roche, NimbleGen) at 2 µm resolution by using high-sensitivity and autogain settings.
|
| Description |
transcriptomic profiling performed for the pool of three total RNA samples extracted from three hearts
|
| Data processing |
The data from scanned images were processed and normalized using a robust multi-chip average (RMA) algorithm using NimbleScan (2.6.0.0) software with default settings (Roche)
|
| |
|
| Submission date |
May 04, 2015 |
| Last update date |
Dec 30, 2015 |
| Contact name |
Pawel Sachadyn |
| E-mail(s) |
psach@pg.gda.pl
|
| Phone |
+48 583471605
|
| Organization name |
Gdansk University of Technology
|
| Department |
Molecular Biotechnology and Microbiology
|
| Street address |
Narutowicza 11/12
|
| City |
Gdansk |
| ZIP/Postal code |
80-233 |
| Country |
Poland |
| |
|
| Platform ID |
GPL10192 |
| Series (2) |
| GSE68521 |
Comparative analysis of genome-wide gene expression profiles in hearts of C57B/6J mice |
| GSE68524 |
The transcriptome and methylome of neonatal murine hearts |
|
