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| Status |
Public on Apr 07, 2020 |
| Title |
Cell and molecular transitions during efficient dedifferentiation: single cell RNAseq |
| Organism |
Dictyostelium discoideum |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Transcriptomic analysis of dedifferentiation in Dictyostelium discoideum by single cell RNAseq
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| Overall design |
scRNAseq of cells during the first 6 h of dedifferentiation in liquid growth media. Dedifferentiation cultures with staggered start times were harvested simultaneously at 0, 1, 2, 3, 4, 5 and 6 h of dedifferentiation and pooled together for sequencing using the 10x Chromium platform. Cells from different timepoints were pooled before barcoding. Two biological replicates were collected. In each biological replicate, the input cells were split between two Chromium 10x chip inlets (technical replicates) with data from each technical replicate pooled after mapping for downstream analysis. In biological replicate 1, 967 libraries passed UMI filtering by CellRanger v2.2.0 with median of around 25000 total molecular counts. In biological replicate 2, 2961 libraries passed filtering,with a median of around 18000 total molecular counts.
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| Contributor(s) |
Nichols JM, Antolovic V, Reich J, Brameyer S, Paschke P, Chubb JR |
| Citation(s) |
32255425 |
| |
| Submission date |
Feb 06, 2020 |
| Last update date |
May 07, 2020 |
| Contact name |
Jonathan Chubb |
| E-mail(s) |
j.chubb@ucl.ac.uk
|
| Organization name |
University College London
|
| Department |
MRC Laboratory for Molecular Cell Biology
|
| Street address |
Gower Street
|
| City |
London |
| ZIP/Postal code |
WC1E 6BT |
| Country |
United Kingdom |
| |
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| Platforms (1) |
| GPL26360 |
Illumina NextSeq 500 (Dictyostelium discoideum) |
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| Samples (4)
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| This SubSeries is part of SuperSeries: |
| GSE144892 |
Cell and molecular transitions during efficient dedifferentiation |
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| Relations |
| BioProject |
PRJNA605214 |
| SRA |
SRP247604 |
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