Genome-wide marker data for P1 and P2 and the F1 population of 94 genotypes were obtained using the restriction site-associated DNA sequencing (RAD-seq) method [22 (link)]. Genomic DNA of each plant was extracted using MagExtractor -Plant Genome (TOYOBO). Detailed methods and information for library construction for the RAD-seq have been described in our previous report [23 (link)]. Genomic DNA was treated with 2 restriction enzymes, BglII and MseI. RAD-seq data (26 hundred million bp in total read average and 17 million read in average read numbers) was obtained using the Illumina HiSeq X Ten systems via paired-end sequencing (Illumina, Inc., San Diego, CA, USA). Short reads derived from RAD-Seq were analyzed using the Stacks software following the recommended setting [24 (link)].
Magextractor plant genome
Manufactured by Toyobo
The MagExtractor -Plant Genome is a lab equipment product designed for the extraction and purification of plant genomic DNA. It utilizes magnetic bead technology to efficiently capture and isolate DNA from plant samples.
Automatically generated - may contain errors
Lab products found in correlation
Hiseq x ten system, by Illumina (1 mentions)
T4 dna ligase, by Takara Bio (1 mentions)
Blend taq, by Toyobo (1 mentions)
Takara ex taq, by Takara Bio (1 mentions)
Hybond n membrane, by GE Healthcare (1 mentions)
Illustra gfx pcr dna and gel band purification kit, by GE Healthcare (1 mentions)
Cdp star, by GE Healthcare (1 mentions)
Alkphos direct labelling and detection system, by GE Healthcare (1 mentions)
Las 3000 mini, by Fujifilm (1 mentions)
Hybond, by Cytiva (1 mentions)
4 protocols using magextractor plant genome
1
Genome-wide Marker Analysis via RAD-seq
2
L. racemosus Genome Assembly
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Genomic DNA was extracted from root tissues of 2-week-old L. racemosus plants (control treatment) using MagExtractor™ -Plant Genome- (TOYOBO). The isolated DNA was submitted to generate sequencing library for Illumina MiSeq analysis, and the library construction and sequencing process were achieved by a purchasable service from Macrogen, Japan. A total of ~ 35 M paired-end reads (2 × 151-nt) was obtained from the analysis. Subsequent quality trimming (Q > 30) and artificial sequence elimination steps were achieved manually. The cleaned reads were subjected to build L. racemosus genome contigs utilizing Platanus software (v1.2.4) [59 (link)]. Assemblies with variable k-mers (27, 29, 31, 33, 35, and 37) were conducted in parallel, and the resultants were merged into L. racemosus genome scaffolds of unique and significantly long (> 1000-nt) length. The raw sequence data was deposited in NCBI/EBI/DDBJ short read archive under a specific accession number (SRR5796629).
3
Isolating Unknown Genomic Regions via Inverse PCR
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
To isolate unknown genomic region, inverse PCR was performed. Genomic DNA of 'Yuino' and 'Michael J' was digested with a restriction enzyme (BamHI, HindIII or XbaI).
A 300-ng digested DNA sample was then self-ligated by T4 DNA ligase (Takara Bio Inc.) in a 200-μL volume. Inverse PCR was performed with Blend Taq (Toyobo) or Takara EX Taq (Takara Bio Inc.). To analyse allele composition, allele-specific PCR was performed.
For allele-specific PCR, genomic DNA extracted using MagExtractor -Plant Genome-(Toyobo) from leaves of six bicolor cultivars ('Yuino', 'Matsuribayashi', 'Kazusashiranami', 'Santa Claus', 'OriW1' and 'OriW2') and four single-color cultivars ('Kokucho', 'Ms. Noir', 'Yukino' and 'Michael J') was used. The primers that were used for inverse PCR, sequencing and allele-specific PCR analysis are shown in Table S3.
A 300-ng digested DNA sample was then self-ligated by T4 DNA ligase (Takara Bio Inc.) in a 200-μL volume. Inverse PCR was performed with Blend Taq (Toyobo) or Takara EX Taq (Takara Bio Inc.). To analyse allele composition, allele-specific PCR was performed.
For allele-specific PCR, genomic DNA extracted using MagExtractor -Plant Genome-(Toyobo) from leaves of six bicolor cultivars ('Yuino', 'Matsuribayashi', 'Kazusashiranami', 'Santa Claus', 'OriW1' and 'OriW2') and four single-color cultivars ('Kokucho', 'Ms. Noir', 'Yukino' and 'Michael J') was used. The primers that were used for inverse PCR, sequencing and allele-specific PCR analysis are shown in Table S3.
4
Genomic DNA Extraction and Southern Blot Analysis
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Genomic DNA was extracted from leaves of bicolor and single-color cultivars using MagExtractor® Plant Genome (Toyobo). A 20-μg DNA sample was digested with a restriction enzyme (BamHI or HindIII) and separated on 0.8 % agarose gel in 0.5 ×TAE buffer, and subsequently blotted to a Hybond-N+ membrane (GE Healthcare Japan) in 20 ×SSC buffer. For the probe, the PCR product was purified from agarose gel slices with the illustra™ GFX™ PCR DNA and Gel Band Purification Kit (GE Healthcare Japan), and labelled with the AlkPhos Direct Labelling and Detection System (GE Healthcare Japan). The probe was hybridised to the membrane at 55 ºC overnight. Detection was conducted with CDP-Star® (GE Healthcare) and the chemiluminescence image was obtained using a LAS-3000 Mini (Fujifilm).
About PubCompare
Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.
We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.
However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.
Ready to get started?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
Revolutionizing how scientists
search and build protocols!