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Sample GSM2586715 Query DataSets for GSM2586715
Status Public on Apr 14, 2021
Title CochlearLateralWall_YoungAdult_rep1
Sample type RNA
 
Source name Cochlear lateral wall, young adult
Organism Mus musculus
Characteristics tissue: cochlear lateral wall
age: 1-3 month
age type: young
Treatment protocol CBA/CaJ young adult (1-3 months) and aged (1.5 years) mice were used in this study. Mice were euthanized and CLW tissues were micro-dissected from the inner ear. All sample types were prepared in experimental triplicate (n=3).
Growth protocol CBA/CaJ mice were bred in-house in a low-noise environment at the Animal Research Facility of the Medical University of South Carolina (MUSC) with original breeding pairs purchased from The Jackson Laboratory (Bar Harbor, ME). All mice received food and water ad libitum and were maintained on a 12-hour light/dark cycle. Mice of both genders were used in the study. All aspects of the animal research were conducted in accordance with the guidelines of the Institutional Animal Care and Use Committee of the MUSC. Prior to treatment, mice were examined for signs of external ear canal and middle ear obstruction, and mice exhibiting these signs were excluded from the study.
Extracted molecule total RNA
Extraction protocol Microdissected CLW underwent total RNA preparation using the miRNeasy Minikit (Qiagen). RNA preparations were run on an Agilent 2100 Bioanalyzer to ensure that total RNA samples retained small molecular weight RNA and were of sufficient quality for transcripomic analysis.
Label biotin
Label protocol Total RNA (130 ng) was converted into biotin-labeled product using the FlashTag™ Biotin HSR RNA Labeling Kit in accordance with manufacturer protocols.
 
Hybridization protocol Targets (21.5 ul of labeled product) were hybridized to Affymetrix microRNA 3.0 GeneChips according to manufacturer protocols. Post hybridization washing and fluorescence labeling was done in an Affymetrix Fluidics Station 450 in accordance with manufacturer protocols.
Scan protocol Microarrays were scanned using an Affymetrix 7G Scanner.
Description YLW1_microRNA
Data processing CEL files imported into Affymetrix Expression Console software and data were summarized by the RMA+DABG-Mouse_only algorithm to obtain RMA normalized log2 expression values and detection calls for the mouse content on the microarray.
 
Submission date Apr 21, 2017
Last update date Jan 27, 2022
Contact name Jeremy Barth
E-mail(s) barthj@musc.edu
Organization name MUSC
Street address 173 Ashley Ave, BSB 627
City Charleston
State/province SC
ZIP/Postal code 29425-5080
Country USA
 
Platform ID GPL16384
Series (2)
GSE98071 MicroRNAs as Regulators of Aging Processes in the Cochlear Lateral Wall of the Mouse Inner Ear (microRNA data set)
GSE98072 MicroRNAs as Regulators of Aging Processes in the Cochlear Lateral Wall of the Mouse Inner Ear

Data table header descriptions
ID_REF
VALUE log2 RMA signal
ABS_CALL DABG detection call

Data table
ID_REF VALUE ABS_CALL
hp_mmu-let-7a-1_st 0.9773991 A
hp_mmu-let-7a-1_x_st 1.63777 P
hp_mmu-let-7a-2_st 1.62802 A
hp_mmu-let-7b_st 1.483915 P
hp_mmu-let-7b_x_st 1.342317 P
hp_mmu-let-7c-1_st 0.8004757 A
hp_mmu-let-7c-2_st 0.8191835 A
hp_mmu-let-7c-2_x_st 1.499189 A
hp_mmu-let-7d_st 1.122447 P
hp_mmu-let-7e_st 2.191966 P
hp_mmu-let-7f-1_st 0.9894146 A
hp_mmu-let-7f-1_x_st 0.8173437 P
hp_mmu-let-7f-2_st 0.9051692 A
hp_mmu-let-7f-2_x_st 0.9742759 A
hp_mmu-let-7g_st 1.068419 P
hp_mmu-let-7g_x_st 0.971766 P
hp_mmu-let-7i_st 1.081541 A
hp_mmu-mir-100_st 0.8039353 A
hp_mmu-mir-101a_st 1.10124 A
hp_mmu-mir-101a_x_st 1.129008 A

Total number of rows: 1966

Table truncated, full table size 57 Kbytes.




Supplementary file Size Download File type/resource
GSM2586715_YLW1_microRNA.CEL.gz 863.4 Kb (ftp)(http) CEL
Processed data included within Sample table

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