whole genomic shotgun sequence data  (Zymo Research)

Journal: Cell reports

Article Title: Conserved and divergent DNA recognition specificities and functions of R2 retrotransposon N-terminal domains

doi: 10.1016/j.celrep.2024.114239

Figure Lengend Snippet: (A and B) Images of EMSA native PAGE gels. NBoMo proteins (A) and NDroSi proteins (B) were tested with 100-bp duplex target site (−50 to +50). (C and D) Images of denaturing PAGE gels for DNase I footprinting using 100-bp duplex target site (−50 to +50) with NBoMo ZF1-Myb (C) or NDroSi ZF1-Myb (D). G + A denotes a Maxam-Gilbert sequencing ladder with target-site DNA fragmented at guanosines and adenosines. Numbering on the left indicates target-site DNA position using the numbering scheme of . Circles outlined with dashed or solid lines indicate 125 or 625 nM protein, respectively. Regions of protection are indicated to the right of each gel. (E) Schematic of DNase I footprints of NBoMo ZF1-Myb and NDroSi ZF1-Myb. The consensus target site for B. mori and D. simulans is displayed using International Union of Pure and Applied Chemistry (IUPAC) notation.

Article Snippet: Illumina whole genome shotgun sequencing data , This manuscript , NCBI Sequence Read Archive (SRA): SRR24873001, SRR24873002, SRR24873003.

Techniques: Clear Native PAGE, Footprinting, Sequencing

Journal: Cell reports

Article Title: Conserved and divergent DNA recognition specificities and functions of R2 retrotransposon N-terminal domains

doi: 10.1016/j.celrep.2024.114239

Figure Lengend Snippet: (A and B) Images of EMSA native PAGE gels. NTrCasB proteins (A) and NZoAl proteins (B) were tested with upstream target half-site DNA (−50 to −1). (C and D) Quantifications of (A) and (B) with technical replicates ( n = 3). The x axis is on a logarithmic scale. Mean ± SEM is plotted. (E and F) Images of denaturing PAGE gels for DNase I footprinting using upstream target half-site DNA (−50 to −1) with NTrCasB proteins (E) or NZoAl proteins (F). See also . (G) Schematic of DNase I footprints of NTrCasB Myb and NZoAl ZF1-Myb. The consensus target-site sequence for T. castaneum and Z. albicollis is displayed using IUPAC notation.

Article Snippet: Illumina whole genome shotgun sequencing data , This manuscript , NCBI Sequence Read Archive (SRA): SRR24873001, SRR24873002, SRR24873003.

Techniques: Clear Native PAGE, Footprinting, Sequencing

Journal: Cell reports

Article Title: Conserved and divergent DNA recognition specificities and functions of R2 retrotransposon N-terminal domains

doi: 10.1016/j.celrep.2024.114239

Figure Lengend Snippet:

Article Snippet: Illumina whole genome shotgun sequencing data , This manuscript , NCBI Sequence Read Archive (SRA): SRR24873001, SRR24873002, SRR24873003.

Techniques: Produced, Virus, Recombinant, Protease Inhibitor, Staining, Transfection, Bicinchoninic Acid Protein Assay, Purification, Shotgun Sequencing, Sequencing, Cell Culture, Plasmid Preparation, Software, Membrane

Journal: Scientific Data

Article Title: Marine picoplankton metagenomes and MAGs from eleven vertical profiles obtained by the Malaspina Expedition

doi: 10.1038/s41597-024-02974-1

Figure Lengend Snippet: The Malaspina expedition microbial picoplankton vertical profiles. ( a ) Schematics of a typical vertical profile sampling event. Water samples were collected at seven depths from the surface to the ocean bottom or 4,000 m deep, targeting 3 layers from the photic and dark ocean: epipelagic, including surface and DCM, mesopelagic and bathypelagic. (b) Map showing the sampling stations of the Malaspina Expedition presented in this data set, along the tropical and sub-tropical global Ocean, and the depths from where water was collected for metagenomic sequencing of the 0.2–3 µm plankton size fraction.

Article Snippet: This resource consists on: (i) primary data in the form of 1.66 Tbp of environmental whole genome shotgun sequencing data (Illumina 2 × 101 pair-end reads), distributed over 76 samples (Fig. ) corresponding to 7 depths in 11 vertical profiles (108.1 ± 2.8 million read pairs, mean ± sd, and 21.8 ± 0.6 Gbp per sample), collected along the track of R/V Hespérides across tropical and sub-tropical regions of the global ocean during the Malaspina Expedition in 2010–2011.

Techniques: Sampling, Sequencing

Journal: PLoS Computational Biology

Article Title: Microbiome-based disease prediction with multimodal variational information bottlenecks

doi: 10.1371/journal.pcbi.1010050

Figure Lengend Snippet: (A) The raw data, i.e., shotgun metagenomic sequencing data of the human gut microbiome. (B) For pre-processing, we leverage MetaPhlAn2 and MetAML to extract species-relative abundances and strain-level markers. We consider two pre-processing schemes to produce two different dataset collections, default (D) and joint (J). (C) A high-level representation of the probabilistic encoders of the MVIB model. (D) The Product of Experts computes a single joint posterior i.e. z ; the joint posterior z is sampled with the reparametrisation trick . (E) A logistic regression decoder estimates the probability of whether a subject is affected by a certain disease. (F, G) The gradients of the output class are computed with respect to (w.r.t) the input vectors and used to compute saliency maps.

Article Snippet: We downloaded whole-genome shotgun metagenomic sequencing data from the bioproject repositories of the National Center for Biotechnology Information (NCBI).

Techniques: Sequencing