Total RNA was isolated using TRIzol reagent (Life Technologies, Grand Island, NY, USA) and checked for integrity on a Bioanalyzer 2200 (RIN ≥ 7.40). Libraries for sequencing were prepared according to a standard protocol for the SOLiD 5500 system (Life Technology). Sequencing was performed using the SOLiD 5500 W platform. Raw reads of 75 bp in length were mapped to the S. lycopersicum build 2.40 reference using ITAG2.4 as the gene model in colour space with the Maxmapper algorithm implemented in Lifescope software (Life Technologies, Ltd). RNA content was assessed using a whole-transcriptome workflow with the quality threshold set to 10, resulting in an assignment probability of greater than 90. The raw sequencing data with corresponding metadata are available in the NCBI Gene Expression Omnibus (GEO) repository under accession number GSE108421. Analytical comparison between BABA and the control treatments was performed using the DESeq package [89 (link)].
Maxmapper
Manufactured by Thermo Fisher Scientific
The Maxmapper is a modular software platform designed for automated microscopy imaging. It offers seamless integration with various microscope systems, enabling efficient data acquisition and analysis workflows.
Automatically generated - may contain errors
2 protocols using maxmapper
1
Transcriptome Analysis of Tomato Response to BABA
2
RNA-Seq Analysis of Smoking Status
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Raw reads were color-space mapped to the human genome hg19 reference using a Maxmapper algorithm implemented in Lifescope software version 2.5.1 (Life Technologies Corporation, Carlsbad, California). Mapping to multiple locations was permitted. The quality threshold was set at 10, providing a mapping confidence of >90. Reads with a Phred score <10 were filtered out. The mean mapping quality was 30. RNA content and genebased annotation were analyzed with whole-transcriptome workflow. Raw sequencing data with appropriate experimental information are available from the Gene Expression Omnibus repository (www.ncbi.nlm.nih.gov/geo; accession number GSE68549).
We analyzed RNA samples of blood from 24 smokers and 24 never-smokers with SOLiD 5500xl RNA sequencing technology. There were three main groups: smokers (n Z 16), ex-smokers (n Z 8) and individuals who had never
We analyzed RNA samples of blood from 24 smokers and 24 never-smokers with SOLiD 5500xl RNA sequencing technology. There were three main groups: smokers (n Z 16), ex-smokers (n Z 8) and individuals who had never
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