Journal: Silence

Article Title: Experimental design, preprocessing, normalization and differential expression analysis of small RNA sequencing experiments

doi: 10.1186/1758-907X-2-2

Figure Lengend Snippet: Flowchart of typical data-handling steps for small RNA (sRNA) libraries . Flowchart depicting the steps involved in creating, processing and normalizing next-generation sequencing libraries. In this article, we focus on sRNA data, but the methods for analyzing other RNA-based or even chromatin immunoprecipitation sequencing data are similar.

Article Snippet: Illumina's first-generation sRNA library preparation kits used T4 RNA ligase 1 for the ligation of both the 5'- and 3'-adapters, but their Small RNA version 1.5 and TrueSeqTM RNA Sample Preparation kits use the truncated form of T4 RNA ligase 2 for the ligation of the 3'-adapter.

Techniques: Next-Generation Sequencing, ChIP-sequencing

Journal: Silence

Article Title: Experimental design, preprocessing, normalization and differential expression analysis of small RNA sequencing experiments

doi: 10.1186/1758-907X-2-2

Figure Lengend Snippet: Comparison of next-generation sequencing technologies a

Article Snippet: Illumina's first-generation sRNA library preparation kits used T4 RNA ligase 1 for the ligation of both the 5'- and 3'-adapters, but their Small RNA version 1.5 and TrueSeqTM RNA Sample Preparation kits use the truncated form of T4 RNA ligase 2 for the ligation of the 3'-adapter.

Techniques: Comparison, Next-Generation Sequencing, Sequencing, Ligation

Journal: Silence

Article Title: Experimental design, preprocessing, normalization and differential expression analysis of small RNA sequencing experiments

doi: 10.1186/1758-907X-2-2

Figure Lengend Snippet: Sample file formats for small RNA libraries . Illumina machines generate .bcl files, which are in binary form and are not human-readable. These files are converted into .qseq files, which record the most likely sequence and a quality score for each read. Scripts are available to convert files in .qseq format into .fastq or SCARF format (Solexa Compact ASCII Read Format). Files in these formats are often converted to a "tag count" format so that they can be easily stored and analyzed.

Article Snippet: Illumina's first-generation sRNA library preparation kits used T4 RNA ligase 1 for the ligation of both the 5'- and 3'-adapters, but their Small RNA version 1.5 and TrueSeqTM RNA Sample Preparation kits use the truncated form of T4 RNA ligase 2 for the ligation of the 3'-adapter.

Techniques: Sequencing

Journal: Silence

Article Title: Experimental design, preprocessing, normalization and differential expression analysis of small RNA sequencing experiments

doi: 10.1186/1758-907X-2-2

Figure Lengend Snippet: Small RNA (sRNA) reads derived from structural RNA versus other sRNA-generated loci . (A) The number of total and distinct reads for all genomic sequences divided into those derived from ribosomal RNA, transfer RNA (tRNA), small nuclear RNA (snRNA) or other "structural" noncoding RNA-derived and other categories for each size class from 18 to 34 nt across 51 publicly available Arabidopsis sRNA libraries. We typically refer to the sRNA from nonstructural loci as "good" sRNA. (B) The percentage of tRNA-derived reads for each size class from 18 to 34 nt across 24 publicly available wild-type Arabidopsis libraries. Because of variations in sequencing read lengths among libraries, some libraries are missing data for sizes above 27 nt or 31 nt.

Article Snippet: Illumina's first-generation sRNA library preparation kits used T4 RNA ligase 1 for the ligation of both the 5'- and 3'-adapters, but their Small RNA version 1.5 and TrueSeqTM RNA Sample Preparation kits use the truncated form of T4 RNA ligase 2 for the ligation of the 3'-adapter.

Techniques: Derivative Assay, Generated, Genomic Sequencing, Sequencing

Journal: Silence

Article Title: Experimental design, preprocessing, normalization and differential expression analysis of small RNA sequencing experiments

doi: 10.1186/1758-907X-2-2

Figure Lengend Snippet: Repetitiveness of small RNA (sRNA) reads measured across sizes . The number of total reads for all uniquely and nonuniquely mapping genomic sequences divided into ribosomal RNA- or transfer RNA-derived and other (also known as "good") categories for each size class from 18 to 34 nt across 51 publicly available Arabidopsis sRNA libraries. For each size class, structural RNA-derived reads are more likely to map nonuniquely mapping genomic sequences (that is, to more than one genomic location), whereas good reads are more likely to map uniquely mapping genomic sequences (that is, to one genomic location).

Article Snippet: Illumina's first-generation sRNA library preparation kits used T4 RNA ligase 1 for the ligation of both the 5'- and 3'-adapters, but their Small RNA version 1.5 and TrueSeqTM RNA Sample Preparation kits use the truncated form of T4 RNA ligase 2 for the ligation of the 3'-adapter.

Techniques: Genomic Sequencing, Derivative Assay

Journal: Silence

Article Title: Experimental design, preprocessing, normalization and differential expression analysis of small RNA sequencing experiments

doi: 10.1186/1758-907X-2-2

Figure Lengend Snippet: Comparison of sRNA normalization methods a

Article Snippet: Illumina's first-generation sRNA library preparation kits used T4 RNA ligase 1 for the ligation of both the 5'- and 3'-adapters, but their Small RNA version 1.5 and TrueSeqTM RNA Sample Preparation kits use the truncated form of T4 RNA ligase 2 for the ligation of the 3'-adapter.

Techniques: Comparison, Control