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Series GSE99915 Query DataSets for GSE99915
Status Public on Sep 25, 2018
Title Single-cell mapping of lineage and identity in direct reprogramming
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Direct lineage reprogramming involves the conversion of cellular identity. Single-cell technologies are useful for deconstructing the considerable heterogeneity that emerges during lineage conversion. However, lineage relationships are typically lost during cell processing, complicating trajectory reconstruction. Here we present ‘CellTagging’, a combinatorial cell-indexing methodology that enables parallel capture of clonal history and cell identity, in which sequential rounds of cell labelling enable the construction of multi-level lineage trees. CellTagging and longitudinal tracking of fibroblast to induced endoderm progenitor reprogramming reveals two distinct trajectories: one leading to successfully reprogrammed cells, and one leading to a ‘dead-end’ state, paths determined in the earliest stages of lineage conversion. We find that expression of a putative methyltransferase, Mettl7a1, is associated with the successful reprogramming trajectory; adding Mettl7a1 to the reprogramming cocktail increases the yield of induced endoderm progenitors. Together, these results demonstrate the utility of our lineage-tracing method for revealing the dynamics of direct reprogramming.
Overall design This dataset consists of 10 Drop-seq libraries and 18 10x Genomics libraries, including 4 biological replicates of reprogramming timecourse experiments
Web link
Contributor(s) Morris SA, Biddy BA
Citation(s) 30518857, 36584685
NIH grant(s)
Grant ID Grant title Affiliation Name
R01 GM126112 Dissecting mechanisms of pioneer transcription factor-mediated lineage reprogramming WASHINGTON UNIVERSITY Samantha Annette Morris
Submission date Jun 12, 2017
Last update date Feb 07, 2023
Contact name Samantha Morris
Phone 3147478618
Organization name Washington University in St Louis
Street address Department of Developmental Biology, Washington University School of
City St Louis
State/province Missouri
ZIP/Postal code 63110
Country USA
Platforms (2)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL21493 Illumina HiSeq 3000 (Mus musculus)
Samples (28)
GSM2664147 Reprogramming timecourse 1, timepoint 0
GSM2664148 Reprogramming timecourse 1, timepoint 1
GSM2664149 Reprogramming timecourse 1, timepoint 2
BioProject PRJNA390078
SRA SRP108986

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE99915_README.txt.gz 1021 b (ftp)(http) TXT
GSE99915_iep.tc1.dge.txt.gz 15.1 Mb (ftp)(http) TXT
GSE99915_iep.tc2.dge.txt.gz 17.7 Mb (ftp)(http) TXT
GSE99915_mettl.gfp.dge_barcodes.tsv.gz 77.3 Kb (ftp)(http) TSV
GSE99915_mettl.gfp.dge_genes.tsv.gz 212.8 Kb (ftp)(http) TSV
GSE99915_mettl.gfp.dge_matrix.mtx.gz 124.1 Mb (ftp)(http) MTX
GSE99915_reprogramming.timecourse.dge_barcodes.tsv.gz 383.1 Kb (ftp)(http) TSV
GSE99915_reprogramming.timecourse.dge_genes.tsv.gz 212.8 Kb (ftp)(http) TSV
GSE99915_reprogramming.timecourse.dge_matrix.mtx.gz 934.6 Mb (ftp)(http) MTX
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Raw data are available in SRA
Processed data are available on Series record

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