|
| Status |
Public on Jan 04, 2024 |
| Title |
Marmoset_PRA_rep3 |
| Sample type |
RNA |
| |
|
| Source name |
parent rearing, aged, replicate 3
|
| Organism |
Callithrix jacchus |
| Characteristics |
cell type: hippocampus tissue
age: aged
treatment: parent rearing
|
| Treatment protocol |
After birth, the marmosets underwent either human hand- or parental rearing for a duration of 3 months. Subsequently, they were housed together with their age-matched peers. To categorize the marmosets based on age, those falling within the age range of 13 to 19 months were classified as Young Marmosets, while those within the age range of 88 to 164 months were designated as Aged Marmosets
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with TRIzol Reagent with the PureLink RNA Mini Kit (Thermo Fisher Scientific, USA) according to the manufacturer's instructions.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
0.6µg of Cy3-labelled cRNA (specific activity >25.0 pmol Cy3/µg cRNA) was fragmented at 60˚C for 30 minutes in a reaction volume of 25µl containing 1x Fragmentation Buffer (Agilent) and 2x Blocking Agent (Agilent) following the manufacturer's instructions. On completion of the fragmentation reaction, 25µl of 2x GE Hybridization Buffer HI-RPM(Agilent) was added to the fragmentation mixture and hybridized to marmoset microarray 8x60K (G4858A #84626, Agilent Technologies) for 17 hours at 65˚C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37˚C GE Wash buffer 2 (Agilent), then dried immediately.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2539A) using one color scan setting for 1 x 60K array slides (Scan Area 61x21.6 mm, Scan resolution 3µm, Dye channel is set to Green and Green PMT is set to 100%).
|
| Description |
Gene expression in parent-reared marmoset at aged stage
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol AgilentG3_GX_1Color and Grid: 084626_D_F_20170124) to obtain background subtracted and spatially detrended Processed Signal intensities.
Data were normalized and filtered with three filters with GeneSpring software 14.9 (Agilent Technologies). In brief, raw data were normalized with their 75 percentile values. In the first filter, when the value of a probe was lower than 20 percentile value in any samples, the probe was excluded. In the second filter, when the flag of a probe was compromised in any samples, the probe was excluded. In the last filter, when the value (log scale) of CV was over 50 percent in both conditions, the probe was excluded. After filtering, control probes were excluded, and log scale values were transformed into normal scale.
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| |
|
| Submission date |
Jul 05, 2023 |
| Last update date |
Jan 04, 2024 |
| Contact name |
Shin-ichi Horike |
| E-mail(s) |
sihorike@staff.kanazawa-u.ac.jp
|
| Phone |
+81-76-265-2775
|
| Organization name |
Kanazawa University
|
| Department |
Research Center for Experimental Modeling of Human Disease
|
| Lab |
HORIKE Lab
|
| Street address |
13-1 Takaramachi
|
| City |
Kanazawa |
| State/province |
Ishikawa |
| ZIP/Postal code |
920-0934 |
| Country |
Japan |
| |
|
| Platform ID |
GPL33550 |
| Series (1) |
| GSE236481 |
Early parental deprivation during primate infancy has a lifelong impact on gene expression in the male marmoset brain |
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