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| Status |
Public on Aug 28, 2018 |
| Title |
SIS-seq, a molecular ‘time machine’, connects single cell fate with gene programs |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Conventional single cell RNA-seq methods are destructive, such that a given cell cannot also then be tested for fate and function, without a time machine. Here, we develop a clonal method SIS-seq, whereby single cells are allowed to divide, and progeny cells are assayed separately in SISter conditions; some for fate, others by RNA-seq. By cross-correlating fate and gene expression within a clone, and doing this for many clones, we can identify the earliest gene expression signatures of dendritic cell subset development. SIS-seq could be used to study other populations harboring clonal heterogeneity, including stem, reprogrammed and cancer cells to reveal the transcriptional origins of fate decisions.
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| Overall design |
Single ubiquitin C-GFP+ Sca1+ ckit+ HSPCs were isolated from BM and cultured amongst a pool of BM filler cells from C57BL/6 mice, and supplemented with Flt3 ligand. After 2.5 days, wells were visually inspected for GFP+ clones, and those with 10 or more cells were mixed by pipetting, followed by equal volume separation into three parts; two replicate wells for further culture to test for fate at day 8, and the remaining fraction for single cell, or small cell number RNA-seq, using CEL-Seq2 to provide a transcriptional 'snapshot' of the clone prior to fate acquisition.
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| Contributor(s) |
Tian L, Schreuder J, Amann-Zalcenstein D, Tran J, Su S, Ritchie ME, Naik SH |
| Citation |
https://www.biorxiv.org/content/early/2018/08/29/403113
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| Submission date |
Aug 27, 2018 |
| Last update date |
Jul 01, 2020 |
| Contact name |
Luyi Tian |
| E-mail(s) |
ltian@broadinstitute.org
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| Phone |
8577779729
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| Organization name |
Broad institute
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| Lab |
Fei Chen Lab
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| Street address |
415 main st Cambridge
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
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| Platforms (2) |
| GPL16417 |
Illumina MiSeq (Mus musculus) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (158)
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| This SubSeries is part of SuperSeries: |
| GSE153676 |
Clonal multi-omics in DC development |
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| Relations |
| BioProject |
PRJNA488094 |
| SRA |
SRP158934 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE119097_gene_counts.csv.gz |
1.5 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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