|
| Status |
Public on Oct 30, 2009 |
| Title |
C57BL/6J XY gonad H3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
e11.5 XY mouse gonads (1 pair)
|
| Organism |
Mus musculus |
| Characteristics |
tissue: gonad
sex: XY
developmental stage: e11.5 d
strain: C57BL/6J
|
| Treatment protocol |
Gonads were dissected away from mesonephroi in sterile PBS and stored in RNAlater RNA stabilization solution (Ambion) at -80C.
|
| Growth protocol |
C57BL/6J (stock# 000664) and 129S1/SvImJ (stock# 002448) mice were obtained from The Jackson Laboratory. Timed matings were established, embryos were collected from pregnant mothers at embryonic day 11.5 (e11.5), where e0.5 is defined as noon on the day a mating plug was detected. Embryos were staged more precisely by counting tail somites distal to the hindlimbs according to Hacker et al (1995). Embryos that fell within a 17-21 tail somite window were included in this study.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA isolated from e11.5 XY gonads (separated from mesonephroi) using Trizol reagent according to standard protocols optimized in lab. Glycogen was added (10ug) as a carrier molecule to improve RNA yield.
|
| Label |
Cy5
|
| Label protocol |
200-450ng total RNA from each sample was amplified into cRNA using the Low RNA Input Linear Amplification kit (Agilent) and labeled with 1.5uL Cy5-CTP according to protocols established by Agilent and modified by us (see Syed and Threadgill 2006).
|
| |
|
| Channel 2 |
| Source name |
pooled gonads and whole mouse embryos e11.5
|
| Organism |
Mus musculus |
| Characteristics |
tissue: gonads and whole embryos
sex: pooled XY and XX samples
developmental stage: e11.5 d
strain: Sox9-ECFP(C57BL/6J) x CD-1
|
| Treatment protocol |
Gonads were dissected away from mesonephroi in sterile PBS and stored in RNAlater RNA stabilization solution (Ambion) at -80C.
|
| Growth protocol |
C57BL/6J (stock# 000664) and 129S1/SvImJ (stock# 002448) mice were obtained from The Jackson Laboratory. Timed matings were established, embryos were collected from pregnant mothers at embryonic day 11.5 (e11.5), where e0.5 is defined as noon on the day a mating plug was detected. Embryos were staged more precisely by counting tail somites distal to the hindlimbs according to Hacker et al (1995). Embryos that fell within a 17-21 tail somite window were included in this study.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA isolated from e11.5 XY gonads (separated from mesonephroi) using Trizol reagent according to standard protocols optimized in lab. Glycogen was added (10ug) as a carrier molecule to improve RNA yield.
|
| Label |
Cy3
|
| Label protocol |
200-450ng total RNA from each sample was amplified into cRNA using the Low RNA Input Linear Amplification kit (Agilent) and labeled with 1.5uL Cy5-CTP according to protocols established by Agilent and modified by us (see Syed and Threadgill 2006).
|
| |
|
| |
| Hybridization protocol |
To each array, 900ng each of Cy5-labeled experimental and Cy3-labeled reference cRNA were co-hybridized at 65C for 17h according to Syed and Threadgill 2006.
|
| Scan protocol |
Microarrays were scanned using an Agilent scanner, and raw data were collected using feature extraction software (Agilent).
|
| Description |
Reference sample includes 4 pairs of e11.5 XY gonads, 3 pairs of e11.5 XX gonads, 4 e11.5 XY whole embryos, and 2 e11.5 XX whole embryos.
|
| Data processing |
Probe level data were imported into BRB-ArrayTools software (version 3.7.0), and normalized using the Lowess smoother function.
|
| |
|
| Submission date |
Jul 01, 2009 |
| Last update date |
Jul 01, 2009 |
| Contact name |
Steven C Munger |
| E-mail(s) |
steven.munger@jax.org
|
| Organization name |
The Jackson Laboratory
|
| Lab |
Steven Munger
|
| Street address |
600 Main Street
|
| City |
Bar Harbor |
| State/province |
ME |
| ZIP/Postal code |
04609 |
| Country |
USA |
| |
|
| Platform ID |
GPL4134 |
| Series (1) |
| GSE16917 |
Strain differences in e11.5 XY gonad transcriptome suggest a mechanism for the sensitivity of C57BL/6J to sex reversal |
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