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Series GSE174293 Query DataSets for GSE174293
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.
Overall design MATQ-Drop single-cell total-RNA-seq of Hoechst-positive nuclei and Hoechst-negative subneuronal compartments isolated from frozen human brain tissues
Contributor(s) Niu M, Zong C
Citation(s) 36646931
Submission date May 11, 2021
Last update date Mar 01, 2023
Contact name Chenghang Zong
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)
GSM5970701 Cell line nucleus species mixing experiment (Mixed_nuclei_0830_D200)
GSM5970702 5818_Hippo_nucleus_1
GSM5970703 5818_Hippo_nucleus_2
This SubSeries is part of SuperSeries:
GSE199346 High-Throughput Transcriptome Profiling of Single Nuclei and Single Synapses Using Single-Cell Total-RNA-Seq
BioProject PRJNA729162
SRA SRP319587

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
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)
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Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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