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Status |
Public on Oct 23, 2013 |
Title |
H23387-DC |
Sample type |
RNA |
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|
Source name |
human embryonic limb tissue
|
Organism |
Homo sapiens |
Characteristics |
tissue: Differentiated 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.
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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.
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|
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Hybridization protocol |
n/a
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Scan protocol |
n/a
|
Description |
Differentiated chondrocytes, replicate 2
|
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.
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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 |
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