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These datasets involve 1) ambient air quality testing, 2) spontaneous combustion fire frequency record, 3) temperature anomalies detected by Landsat, 4) photos of mine waste heap as well as affected environment, 5) estimation of remedial cost, 6) VDO of gas emission from a crack on top of the mine waste heap, and 7) XRD analysis of coal-mine waste
Data Types:
  • Other
  • Image
  • Video
  • Tabular Data
  • Dataset
  • Document
Smoke Test on 17Jul2019 natscilivecustomer (Dataset-1) Smoke Test on 17Jul2019 natscilivecustomer (Dataset-2)
Data Types:
  • Other
  • Software/Code
  • Image
  • Video
  • Tabular Data
  • Dataset
  • Document
  • Text
  • Audio
This project produced the complete chloroplast genome for two Sclerolaena napiformis vouchers. It contains both circular annotated cpDNA sequences and the CDS-based alignment used to generate the phylogeny.
Data Types:
  • Software/Code
  • Sequencing Data
  • Dataset
Primary analysis files for bioRxiv manuscript with id 2019/859603 (https://www.biorxiv.org/content/10.1101/859603v1) to evaluate how common variant effect prediction methods capture effect determined by deep mutational scanning experiments. 'data' contains the deep mutational scanning data in a parsed format. See the manuscript for the original data sources which would then be processed with parseRawDatasets.py, followed by manual sequence mapping (resulting in the mapped_seqs.txt files) and then be processed with parseScores.py to result in the .npz files. 'predictionData' contains predictions from SIFT, PolyPhen-2, SNAP2 and Envision, parsed into .npz files. Additional folders are for dummy methods and while executing the below scripts. 'analysis' will contain most of the output files. See below for sample calls to reproduce e.g. Figure 1 from the paper. The scripts are written in Python3 and require, among others, numpy, pandas, scipy, sklearn, rpy2, svgutils and matplotlib. For all scripts the --normalization-scheme flag describes how the experimental scores are processed to fit on the same scale of values. The scheme used for the final manuscript is 'wt0_del_scaled' for deleterious effect variants and 'wt0_ben_scaled' for beneficial effect variants. For compareBinaryDMSToPredictions.py the --binarization-scheme flag describes how scores are binarized to neutral/effect. Possible values are the schemes outlined in the manuscript 'syn90', 'syn95' and 'syn99'.
Data Types:
  • Other
  • Software/Code
  • Sequencing Data
  • Tabular Data
  • Dataset
  • Text
Video S1 shows the process that the liquid level in the cylinder gradually decreased between 0 and 12 h, while the thickness of the bright thin layer at the bottom increased, which is the supplementary datum of Figure 1a. Video S2 presents that the gel, supported on the filter paper, can be obtained by decanting the upper suspension.
Data Types:
  • Video
  • Dataset
complete genome.fas The sequence of complete genome of the Phauda flammans. We checked by manual proofreading according to its relative species. tree.fas The dateset is what we used in the tree reconstruction.
Data Types:
  • Sequencing Data
  • Dataset
Variant calls for the in vivo and in vitro studies of virus diversity and genetic stability reported in the manuscript, "A new live-attenuated polio vaccine constructed by rational design improves safety by preventing reversion to virulence", by Yeh, et al.
Data Types:
  • Sequencing Data
  • Tabular Data
  • Dataset
Abolition of contractile activity in in vitro neuromuscular junctions within multi-nodal microfluidic chips using alpha-Bungarotoxin. Chips seeded as described above were allowed to mature for 21 days after seeding. Chips were selected for high contractile activity of myotubes that had visual contact with axons (more than 1 contraction per minute over 5 minutes with at least 1 contraction in each minute, the day prior to the experiment). Video of pre-experiment activity was recorded for 1 min followed by counting of the total number of contractions in 10 min. The cells were allowed to recover for 1 h at 37°C, 5% CO2 before addition of 1:100 of α-BTX at a final concentration of 1.25μM or of 0.75μl sterile PBS and incubation of 10 min at 37°C, 5% CO2. The α-BTX was only added to the central well containing the myotubes, which was fluidically isolated by hydrostatic pressure throughout the incubation. Another 1 min video of activity after intervention was recorded before counting the total number of contractions in 10 min. Cells were fixed immediately after the final count. For quantitative analysis the experiment was repeated with 10 min video being recorded as baseline followed by 1 h recovery at 37°C, 5% CO2 and treatment. Another 10 min video was recorded after treatment, and blinded quantification was carried out for both.
Data Types:
  • Video
  • Dataset
Multiple alignments of the nuclear SSU rDNA and plastid rbcL, psaA, psbA and psbC loci sequences built either manually in MEGA6 or using MAFFT v6, applying the Q-INS-i strategy.
Data Types:
  • Sequencing Data
  • Tabular Data
  • Dataset
Sanger sequencing files for ICE and EditR analyses Raw gel images and qPCR data for DTECT
Data Types:
  • Sequencing Data
  • Tabular Data
  • Document
  • Dataset