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2017-cicese-metagenomics

2020_scworkshop

Code and data repository for the 2020 physalia course on single cell RNA sequencing.

algo

数据结构和算法必知必会的50个代码实现

appstat2020

assemblies-of-putative-sars-cov2-spike-encoding-mrna-sequences-for-vaccines-bnt-162b2-and-mrna-1273

RNA vaccines have become a key tool in moving forward through the challenges raised both in the current pandemic and in numerous other public health and medical challenges. With the rollout of vaccines for COVID-19, these synthetic mRNAs have become broadly distributed RNA species in numerous human populations. Despite their ubiquity, sequences are not always available for such RNAs. Standard methods facilitate such sequencing. In this note, we provide experimental sequence information for the RNA components of the initial Moderna (https://pubmed.ncbi.nlm.nih.gov/32756549/) and Pfizer/BioNTech (https://pubmed.ncbi.nlm.nih.gov/33301246/) COVID-19 vaccines, allowing a working assembly of the former and a confirmation of previously reported sequence information for the latter RNA. Sharing of sequence information for broadly used therapeutics has the benefit of allowing any researchers or clinicians using sequencing approaches to rapidly identify such sequences as therapeutic-derived rather than host or infectious in origin. For this work, RNAs were obtained as discards from the small portions of vaccine doses that remained in vials after immunization; such portions would have been required to be otherwise discarded and were analyzed under FDA authorization for research use. To obtain the small amounts of RNA needed for characterization, vaccine remnants were phenol-chloroform extracted using TRIzol Reagent (Invitrogen), with intactness assessed by Agilent 2100 Bioanalyzer before and after extraction. Although our analysis mainly focused on RNAs obtained as soon as possible following discard, we also analyzed samples which had been refrigerated (~4 ℃) for up to 42 days with and without the addition of EDTA. Interestingly a substantial fraction of the RNA remained intact in these preparations. We note that the formulation of the vaccines includes numerous key chemical components which are quite possibly unstable under these conditions-- so these data certainly do not suggest that the vaccine as a biological agent is stable. But it is of interest that chemical stability of RNA itself is not sufficient to preclude eventual development of vaccines with a much less involved cold-chain storage and transportation. For further analysis, the initial RNAs were fragmented by heating to 94℃, primed with a random hexamer-tailed adaptor, amplified through a template-switch protocol (Takara SMARTerer Stranded RNA-seq kit), and sequenced using a MiSeq instrument (Illumina) with paired end 78-per end sequencing. As a reference material in specific assays, we included RNA of known concentration and sequence (from bacteriophage MS2). From these data, we obtained partial information on strandedness and a set of segments that could be used for assembly. This was particularly useful for the Moderna vaccine, for which the original vaccine RNA sequence was not available at the time our study was carried out. Contigs encoding full-length spikes were assembled from the Moderna and Pfizer datasets. The Pfizer/BioNTech data [Figure 1] verified the reported sequence for that vaccine (https://berthub.eu/articles/posts/reverse-engineering-source-code-of-the-biontech-pfizer-vaccine/), while the Moderna sequence [Figure 2] could not be checked against a published reference. RNA preparations lacking dsRNA are desirable in generating vaccine formulations as these will minimize an otherwise dramatic biological (and nonspecific) response that vertebrates have to double stranded character in RNA (https://www.nature.com/articles/nrd.2017.243). In the sequence data that we analyzed, we found that the vast majority of reads were from the expected sense strand. In addition, the minority of antisense reads appeared different from sense reads in lacking the characteristic extensions expected from the template switching protocol. Examining only the reads with an evident template switch (as an indicator for strand-of-origin), we observed that both vaccines overwhelmingly yielded sense reads (>99.99%). Independent sequencing assays and other experimental measurements are ongoing and will be needed to determine whether this template-switched sense read fraction in the SmarterSeq protocol indeed represents the actual dsRNA content in the original material. This work provides an initial assessment of two RNAs that are now a part of the human ecosystem and that are likely to appear in numerous other high throughput RNA-seq studies in which a fraction of the individuals may have previously been vaccinated. ProtoAcknowledgements: Thanks to our colleagues for help and suggestions (Nimit Jain, Emily Greenwald, Lamia Wahba, William Wang, Amisha Kumar, Sameer Sundrani, David Lipman, Bijoyita Roy). Figure 1: Spike-encoding contig assembled from BioNTech/Pfizer BNT-162b2 vaccine. Although the full coding region is included, the nature of the methodology used for sequencing and assembly is such that the assembled contig could lack some sequence from the ends of the RNA. Within the assembled sequence, this hypothetical sequence shows a perfect match to the corresponding sequence from documents available online derived from manufacturer communications with the World Health Organization [as reported by https://berthub.eu/articles/posts/reverse-engineering-source-code-of-the-biontech-pfizer-vaccine/]. The 5’ end for the assembly matches the start site noted in these documents, while the read-based assembly lacks an interrupted polyA tail (A30(GCATATGACT)A70) that is expected to be present in the mRNA.

atlas

ATLAS - Three commands to start analyzing your metagenome data

azimuth

Machine Learning-Based Predictive Modelling of CRISPR/Cas9 guide efficiency

barcode_generator

A program that generates barcodes for sequencing adapters

bbk3_wf

Scripts to run biobakery workflow at KU FOOD

bio202

Biology 202 Course Website

bioconda-recipes

Conda recipes for the bioconda channel.

bioscript

A repository for some useful bio-scripts.

bookchapter-rna-seq-analyses

Best practice RNA-Seq analysis pipeline for reference-based RNA-Seq analysis

bwt2map

A snakemake workflow to do alignment with bowtie2, and some down-stream analysis

cl_rna_synthbio

Code to reproduce Angenent-Mari, N. et al 2020. Deep Learning for RNA Synthetic Biology

comprehensive-rust

This is the Rust course used by the Android team at Google. It provides you the material to quickly teach Rust to everyone.

config

The config files for my personal computer and browser plugins

copd_multiomics

This repository contains computer codes for main analyses of the manuscript titled 'Multi-omic Landscape of Airway Microbe-Host Interaction in Chronic Obstructive Pulmonary Disease'.

courses

Course materials for the Data Science Specialization: https://www.coursera.org/specialization/jhudatascience/1

covidpbmc

Multi-omics profiling of peripheral immune system response to SARS-CoV-2 infection

cs-base

图解计算机网络、操作系统、计算机组成、数据库，共 1000 张图 + 50 万字，破除晦涩难懂的计算机基础知识，让天下没有难懂的八股文！🚀 在线阅读：https://xiaolincoding.com

cs-self-learning

计算机自学指南

cv

private colletction of my cv and publications

data-science-learning-resources

A collection of machine learning resources that I've found helpful (I only post what I've read!)

demos

eat_tensorflow2_in_30_days

Tensorflow2.0 🍎🍊 is delicious, just eat it! 😋😋

fmt-donor

This is a script repository for FMT-donor paper.

free-programming-books

:books: Freely available programming books

fucking-algorithm

刷算法全靠套路，认准 labuladong 就够了！English version supported! Crack LeetCode, not only how, but also why.

glados-checkin

GLaDOS-checkin，通过 github action 进行自动签到，每天延时一天，签到一定次数后奖励会变少。