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Series GSE199344 Query DataSets for GSE199344
Status Public on Nov 30, 2022
Title High-Throughput Transcriptome Profiling of Single Nuclei and Single Synapses Using Single-Cell Total-RNA-Seq [Mm]
Organism 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.
 
Overall design MATQ-Drop single-cell total-RNA-seq of Hoechst-positive nuclei and Hoechst-negative subneuronal compartments isolated from WT and 5XFAD mouse hippocampus
 
Contributor(s) Niu M, Zong C
Citation(s) 36646931
Submission date Mar 24, 2022
Last update date Mar 01, 2023
Contact name Chenghang Zong
E-mail(s) [email protected]
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 (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (40)
GSM5970760 417_nucleus_1
GSM5970761 417_nucleus_2
GSM5970762 417_nucleus_3
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 PRJNA819431

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE199344_Combined_778syn_transcript_counts_rRNA_MT_filtered.tsv.gz 3.2 Mb (ftp)(http) TSV
GSE199344_P417_Hippo_nucleus_exon_count.tsv.gz 5.0 Mb (ftp)(http) TSV
GSE199344_P417_Hippo_nucleus_intron_count.tsv.gz 9.1 Mb (ftp)(http) TSV
GSE199344_P417_Hippo_nucleus_transcript_count.tsv.gz 10.8 Mb (ftp)(http) TSV
GSE199344_P417_Hippo_nucleus_transcript_lncRNA_count.tsv.gz 540.1 Kb (ftp)(http) TSV
GSE199344_P417_Hippo_synapse_exon_count.tsv.gz 3.9 Mb (ftp)(http) TSV
GSE199344_P417_Hippo_synapse_intron_count.tsv.gz 1.2 Mb (ftp)(http) TSV
GSE199344_P417_Hippo_synapse_transcript_count.tsv.gz 4.4 Mb (ftp)(http) TSV
GSE199344_P418_Hippo_nucleus_exon_count.tsv.gz 4.5 Mb (ftp)(http) TSV
GSE199344_P418_Hippo_nucleus_intron_count.tsv.gz 7.5 Mb (ftp)(http) TSV
GSE199344_P418_Hippo_nucleus_transcript_count.tsv.gz 8.9 Mb (ftp)(http) TSV
GSE199344_P418_Hippo_nucleus_transcript_lncRNA_count.tsv.gz 480.9 Kb (ftp)(http) TSV
GSE199344_P418_Hippo_synapse_exon_count.tsv.gz 4.6 Mb (ftp)(http) TSV
GSE199344_P418_Hippo_synapse_intron_count.tsv.gz 1.0 Mb (ftp)(http) TSV
GSE199344_P418_Hippo_synapse_transcript_count.tsv.gz 5.0 Mb (ftp)(http) TSV
GSE199344_P480_Hippo_nucleus_exon_count.tsv.gz 2.1 Mb (ftp)(http) TSV
GSE199344_P480_Hippo_nucleus_intron_count.tsv.gz 3.4 Mb (ftp)(http) TSV
GSE199344_P480_Hippo_nucleus_transcript_count.tsv.gz 3.9 Mb (ftp)(http) TSV
GSE199344_P480_Hippo_nucleus_transcript_lncRNA_count.tsv.gz 237.2 Kb (ftp)(http) TSV
GSE199344_P480_Hippo_synapse_exon_count.tsv.gz 3.1 Mb (ftp)(http) TSV
GSE199344_P480_Hippo_synapse_intron_count.tsv.gz 559.2 Kb (ftp)(http) TSV
GSE199344_P480_Hippo_synapse_transcript_count.tsv.gz 3.3 Mb (ftp)(http) TSV
GSE199344_P514_Hippo_nucleus_exon_count.tsv.gz 4.2 Mb (ftp)(http) TSV
GSE199344_P514_Hippo_nucleus_intron_count.tsv.gz 6.8 Mb (ftp)(http) TSV
GSE199344_P514_Hippo_nucleus_transcript_count.tsv.gz 8.1 Mb (ftp)(http) TSV
GSE199344_P514_Hippo_nucleus_transcript_lncRNA_count.tsv.gz 450.7 Kb (ftp)(http) TSV
GSE199344_P514_Hippo_synapse_exon_count.tsv.gz 2.7 Mb (ftp)(http) TSV
GSE199344_P514_Hippo_synapse_intron_count.tsv.gz 461.0 Kb (ftp)(http) TSV
GSE199344_P514_Hippo_synapse_transcript_count.tsv.gz 2.8 Mb (ftp)(http) TSV
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