|
| Status |
Public on Oct 23, 2013 |
| Title |
H23804-HYP |
| Sample type |
RNA |
| |
|
| Source name |
human embryonic limb tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Hypertrophic chondrocytes
|
| Treatment protocol |
Upon removal from cold storage, the tissue sections were exposed to 30 s incubations in cold 75% ethanol followed by 50% ethanol, 20% ethanol, dH2O, 0.02% Toluidine Blue (prepared in RNAse free H2O), two dH20 washes, 75% ethanol, 95% ethanol and 100% ethanol. Finally, sections were transferred to xylene for 3 min and air-dried.LCM was immediately carried out using the LMD7000 system (Leica Microsystems). The three cartilage regions of interest in each tissue section were selected using the system software resulting in a contact and contamination-free collection of tissue directly into one of the three sterile 0.5 mL Eppendorf caps containing 60 ul of lysis buffer from the RNA isolation kit of choice.
|
| Growth protocol |
Frozen blocks of human embryonic limb tissue were sectioned (20um) onto RNAse-free polyethylene naphthalate (PEN)-coated glass slides (Leica Microsystems) that are specifically designed for laser capture microdissection (LCM).Frozen sections were stored at minus 80oC for up to 48 h before being processed for LCM.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA including small RNAs was isolated using either the Total RNA Purification Micro Kit (Norgen Biotek Corp.) or the mirVanaTM miRNA Isollation kit in accordance with the manufacturer’s protocol.
|
| Label |
FAMTP
|
| Label protocol |
Megaplex ™ RT Primers were used to label the cDNA. Protocol specified in TaqMan(R) OpenArray(R) MicroRNA Panels User Guide June 2011.
|
| |
|
| Hybridization protocol |
n/a
|
| Scan protocol |
n/a
|
| Description |
Hypertrophic chondrocytes, replicate 5
|
| Data processing |
The non-normalized_data.txt file contains the CT values exported from the OpenArray ® Real-Time qPCR Analysis . Data were analyzed with the Applied Biosystems DataAssist ™ Software.CT values normalized to RNU44 using the Applied Biosystems DataAssist ™ Software. Series supplementary file GSE49152_non-normalized.txt reports raw CT values. Series supplementary file GSE49152_fold-change_data.txt reports test/control ratios.
|
| |
|
| Submission date |
Jul 23, 2013 |
| Last update date |
Oct 23, 2013 |
| Contact name |
Nobish Varghese |
| E-mail(s) |
nvarghese@path.wustl.edu
|
| Organization name |
Washington University in St.Louis
|
| Street address |
4444 Forest Park Ave.
|
| City |
StLouis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL17485 |
| Series (1) |
| GSE49152 |
miRNA expression in human chondrocyte subtypes |
|
