schultzelab Goto Github PK

aml_classifer

Code and figures of the manuscript by Warnat-Herresthal et al 2019

covid-19-blood-bulk-rna-seq

all script and necessary resources to reproduce the figures

degene-pipeline

dnajc22-regulation

docker

drop-seq-pipe-docker

A simple docker wrapper of the dropSeqPipe https://github.com/Hoohm/dropSeqPipe

flye

De novo assembler for single molecule sequencing reads using repeat graphs

fujii_2020_copd

Scripts for our bulk COPD manuscript

generic-qc

goana

gressier_2022

Github repository for the scRNA-seq and scATAC-seq analyses of Gressier et al. 2022 by Jonas Schulte-Schrepping

hisat2-preprocessing

jsschrepping-embgenbroich_2020

kalafati_2020

Github repository for the scATAC-seq analysis of Kalafati et al., 2020 by Jonas Schulte-Schrepping.

kallisto-qc

r_docker

Docker container for genomics analyses in R.

rna-seq-pipeline-base

rosette-to-lumen-stage-embryoids

In this study Langkabel and Horne et al. present an embryo-like organoid cell culture model termed RtL-embryoids, that can be generated from a solely embryonic stem cell-based starting cell population using cellular reprogramming paradigms. The authors demonstrate that induction of trophoblast- or endoderm- stem cell lineage-specific transgenes in two of the starting embryonic stem cell lines, in 3D co-culture with a third embryonic stem cell line, that remains in a state of pluripotency leads to self-organization into tissues resembling epiblast, extraembryonic ectoderm and visceral endoderm. This study provides a detailed analysis of the interaction between the three tissues comprising RtL-embryoids and their developmental progression, which was demonstrated to recapitulate specific developmental hallmarks of early mouse embryogenesis. The comparison to murine embryos at different development stages by single-cell RNA-Seq analysis reveals the highest similarity to embryos between E4.5 – E5.5, which was confirmed morphologically, as RtL-embryoids are demonstrated to undergo formation of rosettes and subsequent lumenogenesis in epiblast- and extraembryonic ectoderm-like tissues, accompanied by a progression of pluripotency states in cells comprising the epiblast-like compartment.

shiny-seq

Shiny-Seq: A web based interactive pipeline to analyze RNA-Seq data

swarm_learning

Scripts for figures and calculations of the manuscript by Warnat-Herresthal el al. 2020

temba-kullaya-pecht-et-al.-

transmission-of-trained-immunity

Re-sequenced data for the reviewers from the paper "Transmission of trained immunity and heterologous resistance to infections across generations."