|
| Status |
Public on Jun 04, 2024 |
| Title |
SG-29-Rep2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Seeds at 21 DAF
|
| Organism |
Brassica napus |
| Characteristics |
sample type: tissue
tissue: development seeds
|
| Treatment protocol |
The developing seeds at 21 days post-anthesis were collected from B. napus lines grown under field conditions at the AAFC Saskatoon Research Farm in 2009. This time point was selected because approximately 20 days after flowering ( DAF) had previously been identified as a critical stage for cell proliferation and oil deposition (O’Hara et al., 2002; Dong et al., 2004).
|
| Growth protocol |
The B. napus lines used in this study include the two parental lines DH12075, a Canadian spring-type doubled haploid canola line (generated by Dr. Gerhard Rakow and Dr. Ginette Séguin-Swartz, Agriculture and Agri-Food Canada), and PSA12, a resynthesised B. napus line (generated by Dr. Monica Beschorner and Dr. Derek Lydiate, Agriculture and Agri-Food Canada), and 96 doubled haploid segregating (SG) lines generated from the cross of these two parental lines. PSA12 was developed from an interspecific cross between B. oleracea ssp. alboglabra line A12DH and B. rapa line Parkland Sunshine, and DH12075 was derived from a cross between varieties Cresor and Westar (Mayerhofer et al., 2005).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the developing seeds using a method modified from that of Oñate-Sánchez and Vicente-Carbajosa (2008) and described in detail by Parkin et al. (2010). Seeds from field grown plants from two trials (2009 and 2010) were harvested for seed quality analysis.
|
| Label |
Cy5
|
| Label protocol |
cRNAs were amplified from total RNA samples (2 µg) and labeled with either cy3 or cy5 using the Quick Amp labeling kit, Two Color (Agilent, Catalogue: 5190-0444) according to the manufacturer’s instructions, followed by purification with the Qiagen RNeasy Mini Kit (Qiagen, Catalogue 74104) and quantification with a NanoDrop ND-1000.
|
| |
|
| Channel 2 |
| Source name |
Seeds at 21 DAF
|
| Organism |
Brassica napus |
| Characteristics |
sample type: tissue
tissue: development seeds
|
| Treatment protocol |
The developing seeds at 21 days post-anthesis were collected from B. napus lines grown under field conditions at the AAFC Saskatoon Research Farm in 2009. This time point was selected because approximately 20 days after flowering ( DAF) had previously been identified as a critical stage for cell proliferation and oil deposition (O’Hara et al., 2002; Dong et al., 2004).
|
| Growth protocol |
The B. napus lines used in this study include the two parental lines DH12075, a Canadian spring-type doubled haploid canola line (generated by Dr. Gerhard Rakow and Dr. Ginette Séguin-Swartz, Agriculture and Agri-Food Canada), and PSA12, a resynthesised B. napus line (generated by Dr. Monica Beschorner and Dr. Derek Lydiate, Agriculture and Agri-Food Canada), and 96 doubled haploid segregating (SG) lines generated from the cross of these two parental lines. PSA12 was developed from an interspecific cross between B. oleracea ssp. alboglabra line A12DH and B. rapa line Parkland Sunshine, and DH12075 was derived from a cross between varieties Cresor and Westar (Mayerhofer et al., 2005).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the developing seeds using a method modified from that of Oñate-Sánchez and Vicente-Carbajosa (2008) and described in detail by Parkin et al. (2010). Seeds from field grown plants from two trials (2009 and 2010) were harvested for seed quality analysis.
|
| Label |
Cy3
|
| Label protocol |
cRNAs were amplified from total RNA samples (2 µg) and labeled with either cy3 or cy5 using the Quick Amp labeling kit, Two Color (Agilent, Catalogue: 5190-0444) according to the manufacturer’s instructions, followed by purification with the Qiagen RNeasy Mini Kit (Qiagen, Catalogue 74104) and quantification with a NanoDrop ND-1000.
|
| |
|
| |
| Hybridization protocol |
Purified cRNAs (2 µg) were fragmented and hybridized to the Agilent 4x44K Brassica arrays (Parkin et al., 2010) for 17 h at 65°C with a rotation of 10 rpm according to the manufacturer’s protocol.
|
| Scan protocol |
Arrays were washed with the Agilent Gene Expression Washing buffers according to the manufacturer’s protocol and scanned with GenePix 4000B as described by Parkin et al. (2010). Four and two biological replications were performed for the parental lines and the SG lines, respectively, with dye-swaps applied to the biological replicates to minimize dye effects from the two colour systems (Lee et al., 2004).
|
| Description |
SG-172-cy3 vs SG-29-cy5(2).gpr
Biological replicate 2
|
| Data processing |
The raw array datasets were extracted with Gene Pix Pro 6.0, and were firstly normalized by the lowess LOWNESS (Yang et al., 2002) method within arrays, followed by the quantile (Bolstad et al., 2003) method between arrays, using the R/Bioconductor software (available at http://www.r-project.org/). R package Limma (Smyth, 2005).
|
| |
|
| Submission date |
May 30, 2024 |
| Last update date |
Jun 04, 2024 |
| Contact name |
wentao zhang |
| E-mail(s) |
wentao.zhang@nrc-cnrc.gc.ca
|
| Organization name |
NRC-Canada
|
| Street address |
110 Gymnasium Pl
|
| City |
Saskatoom |
| State/province |
SK |
| ZIP/Postal code |
S7N 0W9 |
| Country |
Canada |
| |
|
| Platform ID |
GPL15739 |
| Series (1) |
| GSE268725 |
A systems genomics and genetics approach to identify the genetic regulatory network for lignin content in Brassica napus seeds |
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