|
| Status |
Public on Dec 01, 2017 |
| Title |
AMY_8hr_treated_1 |
| Sample type |
RNA |
| |
|
| Source name |
amygdala, ethanol vapor treated, 8 hr
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
gender: male
age: adult (10-12 weeks)
tissue: amygdala
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the MagMAX™-96 for Microarrays Total RNA Isolation Kit (Ambion, Austin, TX) using the manufacturer supplied modification to collect both mRNAs and small RNAs. Quality control was performed with the Agilent Tape Station.
|
| Label |
biotin
|
| Label protocol |
Samples were biotin-labeled using the FlashTag Biotin HSR RNA Labeling Kit (Affymetrix, Santa Clara, CA)
|
| |
|
| Hybridization protocol |
21.5 ul of biotin-labeled miRNA was hybridized for 16 hr at 48C to the Affymetrix GeneChip 3.0 miRNA arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the FS450_0003 wash protocol.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GCS3000 scanner and .cel files were generated from .dat files using Affymetrix AGCC v3 software.
|
| Description |
microRNA
Replicate 1
Amy-8hr-etoh-3
|
| Data processing |
Data were background subtracted (DABG algorithm) and RMA-normalize in Gene Expression Console (EC) v1.4 using mouse miRNA (hp and mature) annotations only.
Gene Expression Console (EC) v1.4 was used to identify outliers.
miRbaseTracker.org was used to identify miRbase v21 (currently accepted) microRNAs. Obsolete microRNA probesets were removed.
Data were filtered to include only mature mouse microRNAs with a detection p value <0.06 on 80% of arrays.
DABG-RMA (log2 normalized) signals in supplementary files
|
| |
|
| Submission date |
Nov 28, 2016 |
| Last update date |
Dec 01, 2017 |
| Contact name |
Elizabeth Osterndorff-Kahanek |
| Organization name |
University of Texas at Austin
|
| Street address |
2500 Speedway
|
| City |
Austin |
| State/province |
TX |
| ZIP/Postal code |
78712 |
| Country |
USA |
| |
|
| Platform ID |
GPL16384 |
| Series (1) |
| GSE90608 |
MicroRNA expression data from CIE-vapor treated mice |
|
| Relations |
| Affiliated with |
GSM1484473 |
