|
| Status |
Public on Jan 17, 2013 |
| Title |
PGC_E13_F3-Control_biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Primordial germ cell from E13 days old F3 control lineage rat embryo
|
| Organism |
Rattus norvegicus |
| Characteristics |
treatment: F3 control lineage
cell preparation date batch: 1
genetic background: Sprague-Dawley rat
gender: Male
cell type: Primordial germ cell
developmental stage: E13
|
| Treatment protocol |
Gestating outbred Sprague-Dawley mother rats were given intraperitoneal injections of Vinclozolin (100mg/kg/day) or vehicle (DMSO, Control) from embryonic day 8-14 (E8-E14) of gestation (i.e. F0 generation) [Cupp AS, et al., 2003]. Subsequent F2 and F3 generations wee obtained from F1 rats.
|
| Growth protocol |
Primordial germ cell were isolated from male embryos age E13 and E16 of F3 generation of vinclozolin and control lineages rats as described before [. Kafri T, Ariel M, Brandeis M, Shemer R, Urven L, et al. (1992) Developmental pattern of gene-specific DNA methylation in the mouse embryo and germ line. Genes Dev 6: 705-714.]. Male sex of gonads was confirmed by PCR for male specific SRY gene.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from primordial germ cells after lysis in 1 ml Trizol™ reagent (Sigma-Aldritch, USA), according to manufacturer’s instructions.
|
| Label |
biotin
|
| Label protocol |
Biotin-labeled ssDNA were prepared according to the standard Affymetrix protocol from at least 300 ng total RNA (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual, 2005-2209, Affymetrix).
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| |
|
| Hybridization protocol |
Following fragmentation, ssDNA were hybridized on Affymetrix Rat Gene 1.0 ST Array according to standard Affymetrix protocol. Chips were washed and stained in the Affymetrix Fluidics Station 4500.
|
| Scan protocol |
GeneChips were scanned using Affymetrix GeneChip® Scanner 3000.
|
| Description |
Male gonads from embryonic day E13 rat
Gene expression data from embryonic day E13 male gonads of F3 control lineage rat
For each mRNA microarray replica, PGC from 7-20 different male embryos were combined.
|
| Data processing |
The data were analyzed with Partek Genomic Suite 6.6 beta software (Partek Inc., St. Louis, MO) using RMA, GC-content adjusted algorithm background correction, quintile normalization, median polish methods for probesets summarization, and log values of probes signals using base 2. Cell preparation date batch effect was removed.
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| |
|
| Submission date |
Jan 16, 2013 |
| Last update date |
Jan 17, 2013 |
| Contact name |
Michael K Skinner |
| E-mail(s) |
skinner@mail.wsu.edu
|
| Organization name |
WSU
|
| Department |
SBS
|
| Street address |
Abelson 507
|
| City |
Pullman |
| State/province |
WA |
| ZIP/Postal code |
99163 |
| Country |
USA |
| |
|
| Platform ID |
GPL6247 |
| Series (2) |
| GSE43559 |
Environmentally Induced Transgenerational Epigenetic Reprogramming of Primordial Germ Cells and Subsequent Germline [Affymetrix] |
| GSE59511 |
Environmentally Induced Transgenerational Epigenetic Reprogramming of Primordial Germ Cells and Subsequent Germline |
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