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| Status |
Public on Sep 13, 2017 |
| Title |
cTag-PAPERCLIP Reveals Alternative Polyadenylation Promotes Cell-Type Specific Protein Diversity and Shifts Araf Isoforms with Microglia Activation |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| Summary |
Alternative polyadenylation (APA) is increasingly recognized to regulate gene expression across different cell-types, but obtaining APA maps from individual cell-types typically requires prior purification, a stressful procedure that can itself alter cellular states. Here, we describe a new platform, cTag-PAPERCLIP, that generates APA profiles from single cell populations in intact tissues; cTag-PAPERCLIP requires no tissue dissociation and preserves transcripts in native states. Applying cTag-PAPERCLIP to profile four major cell-types in the mouse brain revealed common APA preferences between excitatory and inhibitory neurons distinct from astrocytes and microglia, regulated in part by neuron-specific RNA-binding proteins NOVA2 and PTBP2. We further identified a role of APA in switching Araf protein isoforms during microglia activation, impacting production of downstream inflammatory cytokines. Our results demonstrate the broad applicability of cTag-PAPERCLIP and a previously undiscovered role of APA in contributing to protein diversity between different cell-types and cellular states within the brain.
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| Overall design |
Samples GSM2467568-GSM2467582: cTag-PAPERCLIP libraries were generated from brain or liver samples of different mouse strains.
Samples GSM2683273-GSM2683281: RNA-seq libraries were generated from isolated mouse brain microglia or dissected mouse embryonic brain cortex.
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| Contributor(s) |
Hwang H, Darnell RB |
| Citation(s) |
28910620 |
| Submission date |
Jan 25, 2017 |
| Last update date |
Jul 25, 2021 |
| Contact name |
Hun-Way Hwang |
| E-mail(s) |
Hunway.Hwang@pitt.edu
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| Organization name |
University of Pittsburgh
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| Department |
Department of Pathology
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| Lab |
S754 Scaife Hall
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| Street address |
3550 Terrace Street
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| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15261 |
| Country |
USA |
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| Platforms (2) |
| GPL16417 |
Illumina MiSeq (Mus musculus) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
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| Samples (24)
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| GSM2467568 |
cTag-PAPERCLIP for Gfap-Cre; Ctag-PABP mouse cortex, replicate 1 |
| GSM2467569 |
cTag-PAPERCLIP for Gfap-Cre; Ctag-PABP mouse cortex, replicate 2 |
| GSM2467570 |
cTag-PAPERCLIP for Gad2-Cre; Ctag-PABP mouse cortex, replicate 1 |
| GSM2467571 |
cTag-PAPERCLIP for Gad2-Cre; Ctag-PABP mouse cortex, replicate 2 |
| GSM2467572 |
cTag-PAPERCLIP for Camk2a-Cre; Ctag-PABP mouse cortex, replicate 1 |
| GSM2467573 |
cTag-PAPERCLIP for Camk2a-Cre; Ctag-PABP mouse cortex, replicate 2 |
| GSM2467574 |
cTag-PAPERCLIP for Cx3cr1-Cre; Ctag-PABP mouse brain, replicate 1 |
| GSM2467575 |
cTag-PAPERCLIP for Cx3cr1-Cre; Ctag-PABP mouse brain, replicate 2 |
| GSM2467576 |
cTag-PAPERCLIP for Cx3cr1-Cre; Ctag-PABP mouse brain, PBS treatment, replicate 1 |
| GSM2467577 |
cTag-PAPERCLIP for Cx3cr1-Cre; Ctag-PABP mouse brain, PBS treatment, replicate 2 |
| GSM2467578 |
cTag-PAPERCLIP for Cx3cr1-Cre; Ctag-PABP mouse brain, PBS treatment, replicate 3 |
| GSM2467579 |
cTag-PAPERCLIP for Cx3cr1-Cre; Ctag-PABP mouse brain, LPS treatment, replicate 1 |
| GSM2467580 |
cTag-PAPERCLIP for Cx3cr1-Cre; Ctag-PABP mouse brain, LPS treatment, replicate 2 |
| GSM2467581 |
cTag-PAPERCLIP for Cx3cr1-Cre; Ctag-PABP mouse brain, LPS treatment, replicate 3 |
| GSM2467582 |
PAPERCLIP for CL57/B6J liver |
| GSM2683273 |
RNA-seq for isolated mouse brain microglia, PBS group, replicate 1 |
| GSM2683274 |
RNA-seq for isolated mouse brain microglia, PBS group, replicate 2 |
| GSM2683275 |
RNA-seq for isolated mouse brain microglia, PBS group, replicate 3 |
| GSM2683276 |
RNA-seq for isolated mouse brain microglia, LPS group, replicate 1 |
| GSM2683277 |
RNA-seq for isolated mouse brain microglia, LPS group, replicate 2 |
| GSM2683278 |
RNA-seq for isolated mouse brain microglia, LPS group, replicate 3 |
| GSM2683279 |
RNA-seq for Ptbp2-KO mouse, E18.5 brain cortex, replicate 1 |
| GSM2683280 |
RNA-seq for Ptbp2-KO mouse, E18.5 brain cortex, replicate 2 |
| GSM2683281 |
RNA-seq for Ptbp2-KO mouse, E18.5 brain cortex, replicate 3 |
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| Relations |
| BioProject |
PRJNA368676 |
| SRA |
SRP097745 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE94054_RAW.tar |
2.9 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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