PMC:6387395 / 33375-34412 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/6387395","sourcedb":"PMC","sourceid":"6387395","source_url":"https://www.ncbi.nlm.nih.gov/pmc/6387395","text":"4.4. Transcript Abundance Estimation and Differential Expression Analysis\nThe mapped reads of each sample were assembled using StringTie [65]. Then, the transcriptomes from all the samples were merged to reconstruct a comprehensive transcriptome using perl scripts. After the final transcriptome was generated, StringTie and Ballgown [66] were used to estimate the expression levels of the transcripts. StringTie was used to determine expression levels for mRNAs by calculating fragments per kilobase of exon per million reads [67].\nA differential expression analysis between the treatments (three biological replicates per treatment) was performed using the DESeq R package. DESeq provides statistical methods for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The differentially expressed mRNAs and genes were determined with log2 (fold change) \u003e 1 or log2 (fold change) ≤ 1 and with statistical significance (p-value \u003c 0.05) using the Ballgown R package.","divisions":[{"label":"title","span":{"begin":0,"end":73}},{"label":"p","span":{"begin":74,"end":532}}],"tracks":[{"project":"2_test","denotations":[{"id":"30708960-25690850-51842996","span":{"begin":138,"end":140},"obj":"25690850"},{"id":"30708960-25748911-51842997","span":{"begin":335,"end":337},"obj":"25748911"},{"id":"30708960-20436464-51842998","span":{"begin":528,"end":530},"obj":"20436464"},{"id":"T30007","span":{"begin":138,"end":140},"obj":"25690850"},{"id":"T81355","span":{"begin":335,"end":337},"obj":"25748911"},{"id":"T79920","span":{"begin":528,"end":530},"obj":"20436464"}],"attributes":[{"subj":"30708960-25690850-51842996","pred":"source","obj":"2_test"},{"subj":"30708960-25748911-51842997","pred":"source","obj":"2_test"},{"subj":"30708960-20436464-51842998","pred":"source","obj":"2_test"},{"subj":"T30007","pred":"source","obj":"2_test"},{"subj":"T81355","pred":"source","obj":"2_test"},{"subj":"T79920","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#9398ec","default":true}]}]}}