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Sample GSM5602678 Query DataSets for GSM5602678
Status Public on Sep 30, 2021
Title L2.peri.sham.rat.3
Sample type RNA
 
Source name peri.sham
Organism Rattus rattus
Characteristics strain background: Sprague Dawley
sample group: controls (Sham)
tissue: Striatum
Extracted molecule total RNA
Extraction protocol Qiagen miRNeasy kit was used for total RNA extraction following manufacturer's protocol.
Label Cy5
Label protocol Microarray assay was performed using a service provider (LC Sciences). Total RNA sample (2 µg) were 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining. Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies) (1). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://mirbase.org) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. (1) (a) Gao, X., Gulari, E., and Zhou, X. (2004) In situ synthesis of oligonucleotide microarrays. Biopolymers 73, 579-596; (b) Zhu, Q., Hong, A., Sheng, N., Zhang, X., Jun, K.-Y., Srivannavit, O., Gulari, E., Gao, X., and Zhou, X. (2007) Microfluidic biochip for nucleic acid and protein analysis. in Methods Mol. Biol. Ed. Rampal, J. B. 382:287-312.
 
Hybridization protocol Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://miRBase.org) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.
Scan protocol The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 mL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C. After RNA hybridization, tag-conjugating Alexa Fluor®546 dye was circulated through the microfluidic chip for dye staining. Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).
Data processing Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression) (2). (2) Bolstad, B. M., Irizarry, R. A., Astrandand, M., Speed, T. P. (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinfo. 19, 185-193.
 
Submission date Sep 29, 2021
Last update date Sep 30, 2021
Contact name Antonio Vinciguerra
E-mail(s) winwar1985@yahoo.it
Phone 3487949766
Organization name Università Politecnica delle Marche
Street address via Pasquale Circelli 130
City San Bartolomeo in Galdo
State/province Benevento
ZIP/Postal code 82028
Country Italy
 
Platform ID GPL30677
Series (1)
GSE184975 Rattus norvegicus brain tissue samples: Sham-operated vs. Remote limb postconditioning (PostC) and Sham-operated vs. transient middle cerebral artery occlusion (tMCAO)

Data table header descriptions
ID_REF
VALUE LOWESS normalized signal

Data table
ID_REF VALUE
rno-let-7a-1-3p 158.93
rno-let-7a-2-3p 80.30
rno-let-7a-5p 6417.17
rno-let-7b-3p 52.75
rno-let-7b-5p 5808.14
rno-let-7c-1-3p 8.35
rno-let-7c-5p 8443.97
rno-let-7d-3p 401.77
rno-let-7d-5p 4402.57
rno-let-7e-3p 32.62
rno-let-7e-5p 1840.63
rno-let-7f-1-3p 185.58
rno-let-7f-2-3p 52.86
rno-let-7f-5p 4915.46
rno-let-7g-3p 15.15
rno-let-7g-5p 11168.91
rno-let-7i-3p 9.52
rno-let-7i-5p 10238.68
rno-miR-1-3p 197.23
rno-miR-1-5p 0.01

Total number of rows: 810

Table truncated, full table size 16 Kbytes.




Supplementary file Size Download File type/resource
GSM5602678_L2.peri.sham.rat.3.txt.gz 93.3 Kb (ftp)(http) TXT
Processed data included within Sample table

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