|
| Status |
Public on Nov 30, 2022 |
| Title |
High-Throughput Transcriptome Profiling of Single Nuclei and Single Synapses Using Single-Cell Total-RNA-Seq [Hs] |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
|
| Summary |
We developed the first droplet-based single-cell total-RNA-seq method. We refer to this platform as Multiple Annealing and Tailing-based Quantitative scRNA-seq in Droplet (MATQ-Drop). With the detection of nascent RNA species, we showed that the cell atlas of human brain samples could be effectively constructed based on nascent RNA species. Furthermore, we observed that only lncRNA species are sufficient to construct the cell atlas, suggesting that MATQ-Drop allows a large-scale identification of the cell-type-specific lncRNA species. Beyond total-RNA profiling for single nuclei, we also showed that MATQ-Drop could be used to profile the transcripts in different neuronal sub-compartments. Based on transcriptome profiling, we were able to determine different types of sub-compartments—in particular, synapses. Here we have referred to the transcriptome of individual synapses as the synaptome, and we identified different subtypes of pre-synapses and post-synapses. Furthermore, between pre-synapses and post-synapses, as well as between pre-synapses and the nuclei, we were able to identify different functional enrichments. Our result unveils unprecedented new insights about gene expression in individual synapses. It also demonstrates the feasibility of using MATQ-drop to profile the transcriptome of sub-cellular compartments.
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| |
|
| Overall design |
MATQ-Drop single-cell total-RNA-seq of Hoechst-positive nuclei and Hoechst-negative subneuronal compartments isolated from frozen human brain tissues
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| |
|
| Contributor(s) |
Niu M, Zong C |
| Citation(s) |
36646931 |
| Submission date |
May 11, 2021 |
| Last update date |
Mar 01, 2023 |
| Contact name |
Chenghang Zong |
| E-mail(s) |
chenghang.zong@bcm.edu
|
| Organization name |
Baylor College of Medicine
|
| Lab |
Zong Lab
|
| Street address |
1 Baylor Plaza
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
| GPL19415 |
Illumina NextSeq 500 (Homo sapiens; Mus musculus) |
|
| Samples (47)
|
|
| This SubSeries is part of SuperSeries: |
| GSE199346 |
High-Throughput Transcriptome Profiling of Single Nuclei and Single Synapses Using Single-Cell Total-RNA-Seq |
|
| Relations |
| BioProject |
PRJNA729162 |
| SRA |
SRP319587 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE174293_Combined_5818h_sorted_NC_transcript_counts_rRNA_MT_filtered.tsv.gz |
136.4 Kb |
(ftp)(http) |
TSV |
| GSE174293_Combined_5818h_sorted_PP_transcript_counts_rRNA_MT_filtered.tsv.gz |
1.5 Mb |
(ftp)(http) |
TSV |
| GSE174293_P5818_Hippo_nucleus_exon_count.tsv.gz |
4.6 Mb |
(ftp)(http) |
TSV |
| GSE174293_P5818_Hippo_nucleus_intron_count.tsv.gz |
9.0 Mb |
(ftp)(http) |
TSV |
| GSE174293_P5818_Hippo_nucleus_transcript_count.tsv.gz |
11.0 Mb |
(ftp)(http) |
TSV |
| GSE174293_P5818_Hippo_nucleus_transcript_lncRNA_count.tsv.gz |
1.0 Mb |
(ftp)(http) |
TSV |
| GSE174293_P5818_Hippo_synapse_exon_count.tsv.gz |
3.4 Mb |
(ftp)(http) |
TSV |
| GSE174293_P5818_Hippo_synapse_intron_count.tsv.gz |
518.8 Kb |
(ftp)(http) |
TSV |
| GSE174293_P5818_Hippo_synapse_transcript_count.tsv.gz |
3.6 Mb |
(ftp)(http) |
TSV |
| GSE174293_P5818_PFC_nucleus_exon_count.tsv.gz |
2.4 Mb |
(ftp)(http) |
TSV |
| GSE174293_P5818_PFC_nucleus_intron_count.tsv.gz |
4.0 Mb |
(ftp)(http) |
TSV |
| GSE174293_P5818_PFC_nucleus_transcript_count.tsv.gz |
4.9 Mb |
(ftp)(http) |
TSV |
| GSE174293_P5818_PFC_nucleus_transcript_lncRNA_count.tsv.gz |
523.4 Kb |
(ftp)(http) |
TSV |
| GSE174293_P5818_PFC_synapse_exon_count.tsv.gz |
2.4 Mb |
(ftp)(http) |
TSV |
| GSE174293_P5818_PFC_synapse_intron_count.tsv.gz |
503.2 Kb |
(ftp)(http) |
TSV |
| GSE174293_P5818_PFC_synapse_transcript_count.tsv.gz |
2.6 Mb |
(ftp)(http) |
TSV |
| GSE174293_P5844_Hippo_nucleus_exon_count.tsv.gz |
4.2 Mb |
(ftp)(http) |
TSV |
| GSE174293_P5844_Hippo_nucleus_intron_count.tsv.gz |
7.3 Mb |
(ftp)(http) |
TSV |
| GSE174293_P5844_Hippo_nucleus_transcript_count.tsv.gz |
9.2 Mb |
(ftp)(http) |
TSV |
| GSE174293_P5844_Hippo_nucleus_transcript_lncRNA_count.tsv.gz |
882.4 Kb |
(ftp)(http) |
TSV |
| GSE174293_P5844_Hippo_synapse_exon_count.tsv.gz |
1.7 Mb |
(ftp)(http) |
TSV |
| GSE174293_P5844_Hippo_synapse_intron_count.tsv.gz |
444.9 Kb |
(ftp)(http) |
TSV |
| GSE174293_P5844_Hippo_synapse_transcript_count.tsv.gz |
1.9 Mb |
(ftp)(http) |
TSV |
| GSE174293_P5844_PFC_synapse_exon_count.tsv.gz |
1.2 Mb |
(ftp)(http) |
TSV |
| GSE174293_P5844_PFC_synapse_intron_count.tsv.gz |
329.5 Kb |
(ftp)(http) |
TSV |
| GSE174293_P5844_PFC_synapse_transcript_count.tsv.gz |
1.4 Mb |
(ftp)(http) |
TSV |
| GSE174293_RAW.tar |
4.6 Mb |
(http)(custom) |
TAR (of TSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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