Journal: Biology Direct

Article Title: Deep transcriptome-sequencing and proteome analysis of the hydrothermal vent annelid Alvinella pompejana identifies the CvP-bias as a robust measure of eukaryotic thermostability

doi: 10.1186/1745-6150-8-2

Figure Lengend Snippet: Size distribution of cDNA contigs and predicted protein sequences in three A. pompejana datasets. ( A ) Histograms representing the number of contigs in the different size-ranges for the MPI (black), MPI + JGI + Genoscope (red) and JGI + Genoscope (cyan) assemblies. ( B ) Histograms representing the number of predicted proteins in the different size-ranges for the MPI (black), MPI + JGI + Genoscope (red) and JGI + Genoscope (cyan) datasets.

Article Snippet: However, they also contained a larger number of long contigs (>1,500 bp) than the JGI + Genoscope dataset (7,269 in MPI and 9,639 in MPI + JGI + Genoscope compared to 3,634 in JGI + Genoscope).

Techniques:

Journal: PLoS ONE

Article Title: Transcriptome and Proteome Data Reveal Candidate Genes for Pollinator Attraction in Sexually Deceptive Orchids

doi: 10.1371/journal.pone.0064621

Figure Lengend Snippet: Cross-validation of NGS data sets.

Article Snippet: Solexa-only contigs ( O. sph. ) , 42 493 , 454 reads (3 spp .) , 16 255 , 38.3%.

Techniques:

Journal: G3: Genes|Genomes|Genetics

Article Title: Reference genomes for BALB/c Nude and NOD/SCID mouse models

doi: 10.1093/g3journal/jkad188

Figure Lengend Snippet: Basic genome assembly statistics.

Article Snippet: To further improve the continuity of the assembled HIFI contigs, we used Bionano optical maps as anchors for scaffolding.

Techniques:

Journal: G3: Genes|Genomes|Genetics

Article Title: Reference genomes for BALB/c Nude and NOD/SCID mouse models

doi: 10.1093/g3journal/jkad188

Figure Lengend Snippet: Identification of reference features that are absent in BALB/c Nude and NOD/SCID mice. a) Circular visualization of annotated reference features that could not be identified in the genome assemblies of BALB/c Nude and NOD/SCID strains. The organization of chromosomes is similar to that in , except that the slices representing the 5 chromosomes with most number of missing protein-coding features were enlarged for clarity. Color codes indicate types of features. b) Close-up view of the highlighted region containing members of the defensin alpha cluster on chromosome 8 (21,859,396-21,942,429; GRCm39). HIFI reads of one representative NOD/SCID (sample 3, upper panel) and BALB/c Nude (sample 6, lower panel) individual aligned to GRCm39 genome using minimap2 and visualized in IGV (Integrative Genomics Viewer) browser in upper and lower panels, respectively. Mismatch coloring was deactivated for clarity.

Article Snippet: To further improve the continuity of the assembled HIFI contigs, we used Bionano optical maps as anchors for scaffolding.

Techniques:

Journal: G3: Genes|Genomes|Genetics

Article Title: Reference genomes for BALB/c Nude and NOD/SCID mouse models

doi: 10.1093/g3journal/jkad188

Figure Lengend Snippet: Identification of reference features that are specifically absent in BALB/c Nude strain. a) GRCm39 features that are absent specifically in BALB/c Nude genome assembly were plotted similarly to that in . b) Close-up view of Klra genes region on chromosome 6 (129,982,946-130,193,356; GRCm39). HIFI reads of one representative NOD/SCID (sample 3, upper panel) and BALB/c Nude (sample 6, lower panel) individual were aligned to GRCm39 genome using minimap2 and visualized similarly to that in .

Article Snippet: To further improve the continuity of the assembled HIFI contigs, we used Bionano optical maps as anchors for scaffolding.

Techniques:

Journal: The Plant Cell

Article Title: Is It Ordered Correctly? Validating Genome Assemblies by Optical Mapping ^[OPEN]

doi: 10.1105/tpc.17.00514

Figure Lengend Snippet: Recent Results of Physical Maps Aligned to Their Respective Reference Genomes

Article Snippet: Bionano contigs are illustrated as cyan bars with a light blue coverage plot and many dark blue vertical BssSI matches to the genome sequence.

Techniques: Sequencing

Journal: The Plant Cell

Article Title: Is It Ordered Correctly? Validating Genome Assemblies by Optical Mapping ^[OPEN]

doi: 10.1105/tpc.17.00514

Figure Lengend Snippet: An Illustration of Bionano Contigs Likely Spanning Centromeric Regions in the G. herbaceum Reference.

Article Snippet: Bionano contigs are illustrated as cyan bars with a light blue coverage plot and many dark blue vertical BssSI matches to the genome sequence.

Techniques:

Journal: The Plant Cell

Article Title: Is It Ordered Correctly? Validating Genome Assemblies by Optical Mapping ^[OPEN]

doi: 10.1105/tpc.17.00514

Figure Lengend Snippet: Sequence Contigs from G. herbaceum Chromosome 4 Ordered and Oriented into Pseudomolecules by the Hi-C Methodology (as Assembled by PhaseGenomics).

Article Snippet: Bionano contigs are illustrated as cyan bars with a light blue coverage plot and many dark blue vertical BssSI matches to the genome sequence.

Techniques: Sequencing, Hi-C