|
| Status |
Public on Dec 13, 2016 |
| Title |
DcKOE17.5 Replicate 2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
DcKOE17.5FP (mRNA)
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL6
developmental stage: E17.5
cell type: Dicer cKO
tissue: footpad skin
individual identifier: 251508710968 Array A2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
E16.5 and E17.5 mouse embryos from timed-mating were euthanized and footpad skin was dissected out under a dissection microscope and were frozen on dry ice immediately, and were kept in -80C until use. The frozen footpads were pooled (3-5 embryos for one replicate), and total RNAs were isolated with TRizol reagent (Invitrogen) according to manufacturer’s standard protocol. Isolated RNAs were precipitated with LiCl, and kept in -80C freezer until use.
|
| Label |
Cy3
|
| Label protocol |
Total RNA was labeled using the Agilent Low RNA Input Fluorescent Linear Amplification kit according to the manufacturer's instructions.
|
| |
|
| Channel 2 |
| Source name |
Universal Mouse Reference
|
| Organism |
Mus musculus |
| Characteristics |
sample type: Referecne
|
| Biomaterial provider |
Invitrogen
|
| Extracted molecule |
total RNA |
| Extraction protocol |
E16.5 and E17.5 mouse embryos from timed-mating were euthanized and footpad skin was dissected out under a dissection microscope and were frozen on dry ice immediately, and were kept in -80C until use. The frozen footpads were pooled (3-5 embryos for one replicate), and total RNAs were isolated with TRizol reagent (Invitrogen) according to manufacturer’s standard protocol. Isolated RNAs were precipitated with LiCl, and kept in -80C freezer until use.
|
| Label |
Cy5
|
| Label protocol |
Total RNA was labeled using the Agilent Low RNA Input Fluorescent Linear Amplification kit according to the manufacturer's instructions.
|
| |
|
| |
| Hybridization protocol |
standard Agilent protocol
|
| Scan protocol |
Slides were scanned with an Agilent DNA Microarray Scanner (model G2505-64120) at 100% and 10% PMT in both channels, with a scan resolution of 5um.
|
| Description |
Biological replicate 2 of 2, Cy3 is mouse RNA and Cy5 is mouse reference
DicerE17.5KO_rep2
|
| Data processing |
Data are extracted with Agilent Feature Extraction Software. The data were further processed with NIA ANOVA tool utilities. See http://lgsun.grc.nia.nih.gov/ANOVA for details.
The data is normalized with the following method:
(1) Take values from the columns gDyeNormSignal, rDyeNormSignal in the raw files and log-transform them using: log10(max(x,10)). These values will be referenced below as Xgi and Xri, where i is array number.
(2) Take average of Xri's for the oligo among 8 arrays in the series: AverXr = average(Xri).
(3) For each array, estimate Yi = Xgi-Xri+AverXr (adjust to UMR).
The result Yi is used as the normalized VALUE. More detailed information with error correction can be found at: http://lgsun.grc.nia.nih.gov/ANOVA/help.html#arrayjoin
|
| |
|
| Submission date |
Aug 31, 2016 |
| Last update date |
Dec 14, 2016 |
| Contact name |
Minoru S.H. Ko |
| E-mail(s) |
kom@mail.nih.gov
|
| Phone |
410-558-8359
|
| Organization name |
NIH
|
| Department |
National Institute on Aging
|
| Lab |
Lab of Genetics
|
| Street address |
251 Bayview Blvd, Suite 100, 10C
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21224 |
| Country |
USA |
| |
|
| Platform ID |
GPL6867 |
| Series (2) |
| GSE86294 |
miRNAs are required for post-induction stage sweat gland development [mRNA] |
| GSE86296 |
miRNAs are required for post-induction stage sweat gland development |
|
