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Series GSE211863 Query DataSets for GSE211863
Status Public on Sep 16, 2022
Title Probing cell identity hierarchies by fate titration and collision during direct reprogramming [scRNA-seq & scATAC-seq]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Collide-seq: A systematic comparison of how different reprogramming transcription factors achieve conversion as well as an in-depth analysis of how cells resolve the conflict when more than one fate is instructed.
Overall design Mouse embryonic fibroblasts were nucleofected with doxycycline inducible constructs for Ascl1, MyoD1 and a DNA binding mutant of Ascl1 (mutAscl1). Cells were expanded for about 10 days and positive cells sorted using FACS. All conditions were pooled and plated together. Transcription factor expression was induced for 72h via the administration of doxycycline. After 72h, cells were collected for scMultiome, i.e., scRNA-seq and scATAC-seq from the same cells
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Contributor(s) Hersbach BA, Fischer DS, Masserdotti G, Deeksha D, Mojžišová K, Waltzhöni T, Rodriques-Terrones D, Heinig M, Theis FJ, Götz M, Stricker SH
Citation(s) 36106915
Submission date Aug 23, 2022
Last update date Sep 18, 2022
Contact name Bob Hersbach
Organization name Helmholtz Zentrum Munich
Department Institute of Stem Cell Research
Street address Großhaderner Str. 9
City Planegg-Martinsried
ZIP/Postal code 82152
Country Germany
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (2)
GSM6504520 Ascl1-mutAscl1-Myod1, 72h ATAC
GSM6504521 Ascl1-mutAscl1-Myod1, 72h scRNA-seq
This SubSeries is part of SuperSeries:
GSE211864 Probing cell identity hierarchies by fate titration and collision during direct reprogramming
BioProject PRJNA872404

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Supplementary file Size Download File type/resource
GSE211863_RAW.tar 899.8 Mb (http)(custom) TAR (of BED, H5, TSV)
GSE211863_ascl1_ascl1mutant_myod1_rnaatac.h5ad.gz 255.4 Mb (ftp)(http) H5AD
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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