cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.60712/si-id125782.2
title: StrainInfo SI-ID 125782.2

description: StrainInfo dataset 125782 about a strain of Photobacterium iliopiscarium. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125783.2
title: StrainInfo SI-ID 125783.2

description: StrainInfo dataset 125783 about a strain of Streptomyces halstedii. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125784.2
title: StrainInfo SI-ID 125784.2

description: StrainInfo dataset 125784 about a strain of Streptomyces cinnamoneus. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.17909/cdm7-3j25
title: TESS Raw Full Frame Images: Sector 88

description: All raw full frame images from Sector 88.
DOI: 10.60712/si-id125785.2
title: StrainInfo SI-ID 125785.2

description: StrainInfo dataset 125785 about a strain of Propionibacterium freudenreichii. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125787.2
title: StrainInfo SI-ID 125787.2

description: StrainInfo dataset 125787 about a strain of Bacillus pumilus. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.5281/zenodo.14962940
title: Example Data for "Tutorial: annotation and interpretation of mammalian genomes"

description: This dataset is used to perform end-to-end genome annotation using the Genome Annotation Tutorial (https://github.com/BaderLab/GenomeAnnotationTutorial) in a manner that is less resource and time intensive than annotating an entire genome assembly. End-to-end, this pipeline should take ~48 hours to run without any parallelization of jobs. With parallelization (i.e., using a Snakemake pipeline), the workflow with this example data will be under 24 hours.

Abstract from: Tutorial: annotation and interpretation of mammalian genomes.

As DNA sequencing technologies improve, it is becoming easier to sequence and assemble the genomes of non-model organisms. However, before a genome sequence can be used as a reference it must be annotated with genes and other features, which can now be performed by individual labs using public software. Modern genome annotations integrate gene predictions from the assembled DNA sequence with gene homology information from a high-quality reference and functional evidence (e.g. protein sequences, RNA sequencing). Many genome annotation pipelines exist that vary in accuracy and how resource-intensive and user-friendly they are. This tutorial covers a streamlined genome annotation pipeline that can create high-quality mammalian genome annotations in-lab. Our pipeline integrates existing state-of-the-art genome-annotation tools capable of annotating protein-coding and non-coding RNA genes. This tutorial also guides the user on assigning gene symbols and annotating repeat regions. We lastly describe additional tools to assess annotation quality and combine and format the results.

This dataset contains a small chromosome from a recent naked mole rat assembly, short read RNA-seq of three tissues, and ISO-seq data from two tissues. This example dataset was generated to allow users to complete the five major steps of genome annotation: (1) identifying repetitive elements and masking repeats that can interfere with gene finding, (2) identifying protein-coding/messenger RNA (mRNA) gene models, (3) optimizing gene models using multiple lines of evidence, (4) adding non-coding RNA (ncRNA) gene models (5) labelling gene models with the likely gene identity (i.e. gene symbol).

The naked mole-rat assembly and ISO-seq data are derived from:

Sokolowski, D. J., Miclăuș, M., Nater, A., Faykoo-Martinez, M., Hoekzema, K., Zuzarte, P., ... & Wilson, M. D. (2024). An updated reference genome sequence and annotation reveals gene losses and gains underlying naked mole-rat biology. bioRxiv, 2024-11.

The short read RNA-seq data are derived from:

Bens, M., Szafranski, K., Holtze, S., Sahm, A., Groth, M., Kestler, H. A., ... & Platzer, M. (2018). Naked mole-rat transcriptome signatures of socially suppressed sexual maturation and links of reproduction to aging. BMC biology, 16, 1-13.
DOI: 10.5281/zenodo.14962941
title: Example Data for "Tutorial: annotation and interpretation of mammalian genomes"

description: This dataset is used to perform end-to-end genome annotation using the Genome Annotation Tutorial (https://github.com/BaderLab/GenomeAnnotationTutorial) in a manner that is less resource and time intensive than annotating an entire genome assembly. End-to-end, this pipeline should take ~48 hours to run without any parallelization of jobs. With parallelization (i.e., using a Snakemake pipeline), the workflow with this example data will be under 24 hours.

Abstract from: Tutorial: annotation and interpretation of mammalian genomes.

As DNA sequencing technologies improve, it is becoming easier to sequence and assemble the genomes of non-model organisms. However, before a genome sequence can be used as a reference it must be annotated with genes and other features, which can now be performed by individual labs using public software. Modern genome annotations integrate gene predictions from the assembled DNA sequence with gene homology information from a high-quality reference and functional evidence (e.g. protein sequences, RNA sequencing). Many genome annotation pipelines exist that vary in accuracy and how resource-intensive and user-friendly they are. This tutorial covers a streamlined genome annotation pipeline that can create high-quality mammalian genome annotations in-lab. Our pipeline integrates existing state-of-the-art genome-annotation tools capable of annotating protein-coding and non-coding RNA genes. This tutorial also guides the user on assigning gene symbols and annotating repeat regions. We lastly describe additional tools to assess annotation quality and combine and format the results.

This dataset contains a small chromosome from a recent naked mole rat assembly, short read RNA-seq of three tissues, and ISO-seq data from two tissues. This example dataset was generated to allow users to complete the five major steps of genome annotation: (1) identifying repetitive elements and masking repeats that can interfere with gene finding, (2) identifying protein-coding/messenger RNA (mRNA) gene models, (3) optimizing gene models using multiple lines of evidence, (4) adding non-coding RNA (ncRNA) gene models (5) labelling gene models with the likely gene identity (i.e. gene symbol).

The naked mole-rat assembly and ISO-seq data are derived from:

Sokolowski, D. J., Miclăuș, M., Nater, A., Faykoo-Martinez, M., Hoekzema, K., Zuzarte, P., ... & Wilson, M. D. (2024). An updated reference genome sequence and annotation reveals gene losses and gains underlying naked mole-rat biology. bioRxiv, 2024-11.

The short read RNA-seq data are derived from:

Bens, M., Szafranski, K., Holtze, S., Sahm, A., Groth, M., Kestler, H. A., ... & Platzer, M. (2018). Naked mole-rat transcriptome signatures of socially suppressed sexual maturation and links of reproduction to aging. BMC biology, 16, 1-13.
DOI: 10.60712/si-id125788.3
title: StrainInfo SI-ID 125788.3

description: StrainInfo dataset 125788 about a strain of Micromonospora echinospora. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.17909/12aq-x597
title: TESS Calibrated Full Frame Images: Sector 88

description: All calibrated full frame images from Sector 88.
DOI: 10.60712/si-id125789.2
title: StrainInfo SI-ID 125789.2

description: StrainInfo dataset 125789 about a strain of Pseudomonas aeruginosa. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125790.2
title: StrainInfo SI-ID 125790.2

description: StrainInfo dataset 125790 about a strain of Escherichia coli. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.17909/n8pn-yq58
title: TESS Data Validation Files: Sector 88

description: All data validation files from Sector 88.
DOI: 10.60712/si-id125793.3
title: StrainInfo SI-ID 125793.3

description: StrainInfo dataset 125793 about a strain of Saccharomonospora viridis. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125794.2
title: StrainInfo SI-ID 125794.2

description: StrainInfo dataset 125794 about a strain of Streptomyces showdoensis. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125796.2
title: StrainInfo SI-ID 125796.2

description: StrainInfo dataset 125796 about a strain of Amycolatopsis mediterranei. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125797.3
title: StrainInfo SI-ID 125797.3

description: StrainInfo dataset 125797 about a strain of Amycolatopsis rifamycinica. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125798.3
title: StrainInfo SI-ID 125798.3

description: StrainInfo dataset 125798 about a strain of Streptomyces durhamensis. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125800.2
title: StrainInfo SI-ID 125800.2

description: StrainInfo dataset 125800 about a strain of Escherichia coli. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125801.3
title: StrainInfo SI-ID 125801.3

description: StrainInfo dataset 125801 about a strain of Nonomuraea helvata. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125802.3
title: StrainInfo SI-ID 125802.3

description: StrainInfo dataset 125802 about a strain of Streptomyces clavuligerus. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125804.2
title: StrainInfo SI-ID 125804.2

description: StrainInfo dataset 125804 about a strain of Actinokineospora riparia. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125805.2
title: StrainInfo SI-ID 125805.2

description: StrainInfo dataset 125805 about a strain of Streptomyces. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125806.2
title: StrainInfo SI-ID 125806.2

description: StrainInfo dataset 125806 about a strain of Salmonella enterica subsp. enterica. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125843.3
title: StrainInfo SI-ID 125843.3

description: StrainInfo dataset 125843 about a strain of Leclercia adecarboxylata. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125844.2
title: StrainInfo SI-ID 125844.2

description: StrainInfo dataset 125844 about a strain of Lacrimispora saccharolytica. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125847.3
title: StrainInfo SI-ID 125847.3

description: StrainInfo dataset 125847 about a strain of Legionella hackeliae. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125848.3
title: StrainInfo SI-ID 125848.3

description: StrainInfo dataset 125848 about a strain of Legionella jamestowniensis. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125862.3
title: StrainInfo SI-ID 125862.3

description: StrainInfo dataset 125862 about a strain of Thermomonospora umbrina. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125863.3
title: StrainInfo SI-ID 125863.3

description: StrainInfo dataset 125863 about a strain of Actinomadura hibisca. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125865.3
title: StrainInfo SI-ID 125865.3

description: StrainInfo dataset 125865 about a strain of Sanguibacter suarezii. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125866.3
title: StrainInfo SI-ID 125866.3

description: StrainInfo dataset 125866 about a strain of Cutibacterium acnes. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125881.3
title: StrainInfo SI-ID 125881.3

description: StrainInfo dataset 125881 about a strain of Kitasatospora mediocidica. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125883.2
title: StrainInfo SI-ID 125883.2

description: StrainInfo dataset 125883 about a strain of Streptomyces lavendulae subsp. lavendulae. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125886.2
title: StrainInfo SI-ID 125886.2

description: StrainInfo dataset 125886 about a strain of Lactiplantibacillus plantarum. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125888.3
title: StrainInfo SI-ID 125888.3

description: StrainInfo dataset 125888 about a strain of Streptococcus uberis. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125889.2
title: StrainInfo SI-ID 125889.2

description: StrainInfo dataset 125889 about a strain of Streptococcus dysgalactiae subsp. equisimilis. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125895.2
title: StrainInfo SI-ID 125895.2

description: StrainInfo dataset 125895 about a strain of Couchioplanes caeruleus subsp. azureus. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125903.3
title: StrainInfo SI-ID 125903.3

description: StrainInfo dataset 125903 about a strain of Photobacterium damselae subsp. piscicida. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125923.2
title: StrainInfo SI-ID 125923.2

description: StrainInfo dataset 125923 about a strain of Treponema. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125926.3
title: StrainInfo SI-ID 125926.3

description: StrainInfo dataset 125926 about a strain of Dactylosporangium thailandense. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125927.3
title: StrainInfo SI-ID 125927.3

description: StrainInfo dataset 125927 about a strain of Methanosarcina lacustris. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125929.3
title: StrainInfo SI-ID 125929.3

description: StrainInfo dataset 125929 about a strain of Streptomyces coeruleorubidus. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125931.2
title: StrainInfo SI-ID 125931.2

description: StrainInfo dataset 125931 about a strain of Pseudomonas aeruginosa. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125932.3
title: StrainInfo SI-ID 125932.3

description: StrainInfo dataset 125932 about a strain of Lacrimispora indolis. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125933.2
title: StrainInfo SI-ID 125933.2

description: StrainInfo dataset 125933 about a strain of Mycobacterium smegmatis. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125934.3
title: StrainInfo SI-ID 125934.3

description: StrainInfo dataset 125934 about a strain of Haloarcula hispanica. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125938.3
title: StrainInfo SI-ID 125938.3

description: StrainInfo dataset 125938 about a strain of Promicromonospora sukumoe. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125941.3
title: StrainInfo SI-ID 125941.3

description: StrainInfo dataset 125941 about a strain of Sphingopyxis witflariensis. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125942.2
title: StrainInfo SI-ID 125942.2

description: StrainInfo dataset 125942 about a strain of Streptosporangium. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125944.2
title: StrainInfo SI-ID 125944.2

description: StrainInfo dataset 125944 about a strain of Mycobacterium intracellulare. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125945.2
title: StrainInfo SI-ID 125945.2

description: StrainInfo dataset 125945 about a strain of Hydrogenophaga palleronii. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125946.3
title: StrainInfo SI-ID 125946.3

description: StrainInfo dataset 125946 about a strain of Gordonia alkanivorans. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125951.2
title: StrainInfo SI-ID 125951.2

description: StrainInfo dataset 125951 about a strain of Aspergillus niger. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125953.2
title: StrainInfo SI-ID 125953.2

description: StrainInfo dataset 125953 about a strain of Fusarium flocciferum. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125954.2
title: StrainInfo SI-ID 125954.2

description: StrainInfo dataset 125954 about a strain of Aspergillus candidus. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125957.2
title: StrainInfo SI-ID 125957.2

description: StrainInfo dataset 125957 about a strain of Streptosporangium amethystogenes subsp. amethystogenes. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125963.2
title: StrainInfo SI-ID 125963.2

description: StrainInfo dataset 125963 about a strain of Starmerella stellata. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125965.3
title: StrainInfo SI-ID 125965.3

description: StrainInfo dataset 125965 about a strain of Malassezia furfur. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125967.3
title: StrainInfo SI-ID 125967.3

description: StrainInfo dataset 125967 about a strain of Geodermatophilus obscurus. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id125968.2
title: StrainInfo SI-ID 125968.2

description: StrainInfo dataset 125968 about a strain of Clostridium beijerinckii. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.