IRRI SERVICE LABORATORIES
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4.A Submit samples to GSL
4.A Submit samples to GSL
• Submit DNA samples
• Submit DNA samples
5.1 Submit files for sample quality check
5.1 Submit files for sample quality check
Before you submit the physical samples, GSL will email a Microsoft Excel file where you can provide gel pictures and nanodrop readings of your samples to be checked for quality.
Before you submit the physical samples, GSL will email a Microsoft Excel file where you can provide gel pictures and nanodrop readings of your samples to be checked for quality.
GSL_DNA QC_InternalClient_2019July.xlsx- On the left, indicate your samples’ names, 260/280 nm ratio, and concentrations.
- On the right, replace the example gel pictures with those of your samples.
- Once satisfied with the pictures, save the Excel file and send it back to GSL via email.
Caution: Samples must be arranged column-wise & includes a standard of 50 ng/µL Lambda DNA in each plate.
Caution: Samples must be arranged column-wise & includes a standard of 50 ng/µL Lambda DNA in each plate.
After GSL reviews your samples’ quality, they will send an email informing you if it meets their requirements. If your samples do not meet GSL standards, it is advised that you resubmit samples (see Section 5. Resubmit samples). Otherwise, proceed to the next steps in preparing your sample quality and quantity for genotyping.
After GSL reviews your samples’ quality, they will send an email informing you if it meets their requirements. If your samples do not meet GSL standards, it is advised that you resubmit samples (see Section 5. Resubmit samples). Otherwise, proceed to the next steps in preparing your sample quality and quantity for genotyping.
5.2 Prepare sample quality & quantity
5.2 Prepare sample quality & quantity
Samples must be RNAse-treated & have nanodrop readings of 1.8-2.0 at 260/280 to pass the quality check.
Samples must be RNAse-treated & have nanodrop readings of 1.8-2.0 at 260/280 to pass the quality check.
The amount of DNA samples needed depends on the genotyping platform. Refer to the table below for the required concentration and volumes per platform.
The amount of DNA samples needed depends on the genotyping platform. Refer to the table below for the required concentration and volumes per platform.
Note: DNA extracted through quick & dirty methods (e.g.TPS) are not accepted due to its effect on data quality.
Note: DNA extracted through quick & dirty methods (e.g.TPS) are not accepted due to its effect on data quality.
5.3 Plate the DNA samples
5.3 Plate the DNA samples
Your samples must be submitted in a 96-well polypropylene plate, arranged column-wise to match the layout in your B4R request.
Your samples must be submitted in a 96-well polypropylene plate, arranged column-wise to match the layout in your B4R request.
5.4 Label the plates
5.4 Label the plates
1. Label each plate according to this format:
1. Label each plate according to this format:
GSL Code_Plate #_Date of Sample Preparation (DD-MMM-YYYY)
GSL Code_Plate #_Date of Sample Preparation (DD-MMM-YYYY)
Example: 2020-1_INF_Plate1_20FEB2020
Example: 2020-1_INF_Plate1_20FEB2020
2. Hand in the complete set of samples to the Genotyping Services Laboratory.
2. Hand in the complete set of samples to the Genotyping Services Laboratory.
• Submit leaf samples
• Submit leaf samples
5.1 Identify the appropriate leaves for sampling
5.1 Identify the appropriate leaves for sampling
Your samples should be collected from tagged plants 20-35 days after transplanting. Refer to Section 3. Prepare plants for sampling on how to do this.
Your samples should be collected from tagged plants 20-35 days after transplanting. Refer to Section 3. Prepare plants for sampling on how to do this.
5.2 Collect the leaves
5.2 Collect the leaves
- Collect two leaves per sample with length and width dimensions of 152.4 mm (6.0 in) by 6 mm (0.24 in) respectively.
2. Place the leaves in ¼-size glassine bags with lengths and width dimensions of 51 mm (2.0 in) by 145 mm (5.71 in) respectively.
2. Place the leaves in ¼-size glassine bags with lengths and width dimensions of 51 mm (2.0 in) by 145 mm (5.71 in) respectively.
3. Label the bags using the GSL provided barcodes which indicate the B4R Sample Names.
3. Label the bags using the GSL provided barcodes which indicate the B4R Sample Names.
5.3 Store the samples for submission
5.3 Store the samples for submission
- Bundle or group together the glassine bags per plate according to the sequence indicated in the B4R request.
- Place the bundle of samples in a sealable plastic bag, which should then be immediately put inside a cooler filled with ice.
Note: Ensure that the samples are completely covered in ice. Replenish the ice as needed to avoid the leaves rolling due to hot weather.
Note: Ensure that the samples are completely covered in ice. Replenish the ice as needed to avoid the leaves rolling due to hot weather.
3. Store the samples in -80°C while you are on standby for freeze drying.
3. Store the samples in -80°C while you are on standby for freeze drying.
4. Once all samples are freeze-dried, submit them to the Genotyping Services Laboratory.
4. Once all samples are freeze-dried, submit them to the Genotyping Services Laboratory.
• Submit seed samples
• Submit seed samples
5.1 Identify the appropriate seeds for sampling
5.1 Identify the appropriate seeds for sampling
Samples should be taken from seeds that are filled, non-diseased, and were harvested no longer than 2.5 months beforehand.
Samples should be taken from seeds that are filled, non-diseased, and were harvested no longer than 2.5 months beforehand.
5.2 Collect the seeds
5.2 Collect the seeds
- Collect two grams of seeds per sample (threshed). Alternatively, a single panicle of seeds can be collected.
- Place the seeds in #4 coin envelopes with lengths and width dimensions of 231 mm (9.1 in) by 145 mm (5.7 in) respectively.
- Label the bags using the GSL-provided barcodes which indicate the B4R Sample Names.
- Bundle or group together the glassine bags per plate according to the sequence indicated in the B4R request.
- Hand in the complete set of samples to the Genotyping Services Laboratory.
After GSL reviews your samples, you will be sent a confirmation email that informs you whether your samples have been accepted or rejected. If accepted, then GSL will proceed with the requested service. If rejected, then GSL will provide guidelines on how to resubmit samples.
After GSL reviews your samples, you will be sent a confirmation email that informs you whether your samples have been accepted or rejected. If accepted, then GSL will proceed with the requested service. If rejected, then GSL will provide guidelines on how to resubmit samples.