 |
 |
GEO help: Mouse over screen elements for information. |
|
| 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 |
http://celltag.org/
|
| |
|
| 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 |
| R21 HG009750 |
SINGLE-CELL ANALYSIS OF PIONEER BINDING AND FUNCTION DURING LINEAGE REPROGRAMMING |
WASHINGTON UNIVERSITY |
Samantha Annette Morris |
|
| Submission date |
Jun 12, 2017 |
| Last update date |
Feb 07, 2023 |
| Contact name |
Samantha Morris |
| E-mail(s) |
s.morris@wustl.edu
|
| 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 |
| GSM2664150 |
Reprogramming timecourse 1, timepoint 3 |
| GSM2664151 |
Reprogramming timecourse 1, timepoint 4 |
| GSM2664152 |
Reprogramming timecourse 2, timepoint 0 |
| GSM2664153 |
Reprogramming timecourse 2, timepoint 1 |
| GSM2664154 |
Reprogramming timecourse 2, timepoint 2 |
| GSM2664155 |
Reprogramming timecourse 2, timepoint 3 |
| GSM2664156 |
Reprogramming timecourse 2, timepoint 4 |
| GSM3191810 |
10x Reprogramming timecouse 1, day 0 |
| GSM3191811 |
10x Reprogramming timecouse 1, day 3 |
| GSM3191812 |
10x Reprogramming timecouse 1, day 6 |
| GSM3191813 |
10x Reprogramming timecouse 1, day 9 |
| GSM3191814 |
10x Reprogramming timecouse 1, day 12 |
| GSM3191815 |
10x Reprogramming timecouse 1, day 15 |
| GSM3191816 |
10x Reprogramming timecouse 1, day 21 |
| GSM3191817 |
10x Reprogramming timecouse 1, day 28 |
| GSM3191818 |
10x Reprogramming timecouse 2, day 0 |
| GSM3191819 |
10x Reprogramming timecouse 2, day 3 |
| GSM3191820 |
10x Reprogramming timecouse 2, day 6 |
| GSM3191821 |
10x Reprogramming timecouse 2, day 9 |
| GSM3191822 |
10x Reprogramming timecouse 2, day 12 |
| GSM3191823 |
10x Reprogramming timecouse 2, day 15 |
| GSM3191824 |
10x Reprogramming timecouse 2, day 21 |
| GSM3191825 |
10x Reprogramming timecouse 2, day 28 |
| GSM3191826 |
10x Reprogramming Foxa1-Hnf4a |
| GSM3191827 |
10x Reprogramming Foxa1-Hnf4a-Mettl7a1 |
|
| Relations |
| BioProject |
PRJNA390078 |
| SRA |
SRP108986 |
| 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 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
Less...
More...