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Series GSE90822 Query DataSets for GSE90822
Status Public on Nov 20, 2017
Title Correlating anatomy and function with gene expression in individual neurons by combining in vivo labeling, patch clamp and single cell RNA-seq
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary The classification of neurons into distinct types is an ongoing effort aimed at revealing and understanding the diversity of the components of the nervous system. Recently available methods allow us to determine the gene expression pattern of individual neurons in the mammalian cerebral cortex to generate powerful categorization schemes. For a thorough understanding of neuronal diversity such genetic categorization schemes need to be combined with traditional classification parameters like position, axonal projection or response properties to sensory stimulation. Here we describe a method to link the gene expression of individual neurons with their position, axonal projection or sensory response properties. Neurons are labeled in vivo based on their anatomical or functional properties and, using patch clamp pipettes, their RNA individually harvested in vitro for RNAseq. With this method we can determine the genetic expression pattern of functionally and anatomically identified individual neurons.
 
Overall design single cortical neurons were patch clamped and the RNA harvested; single neuron mRNA profiles were generated by deep sequencing
 
Contributor(s) Pfeffer CK, Scanziani M
Citation(s) 29249941
Submission date Dec 02, 2016
Last update date May 15, 2019
Contact name Carsten Pfeffer
E-mail(s) cpfeffer10@gmail.com
Organization name UCSD
Street address 9500 Gilman Drive
City La Jolla
State/province CA
ZIP/Postal code 92093
Country USA
 
Platforms (2)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
Samples (927)
GSM2413717 SOM-1
GSM2413718 SOM-2
GSM2413719 SOM-3
Relations
BioProject PRJNA356072
SRA SRP094496

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
GSE90822_CA1d-CA1v_tpm5.txt.gz 2.0 Mb (ftp)(http) TXT
GSE90822_ERCC_UMI_5reads.txt.gz 5.6 Kb (ftp)(http) TXT
GSE90822_ERCC_tpm5.txt.gz 25.8 Kb (ftp)(http) TXT
GSE90822_HS-LS_tpm5.txt.gz 1.5 Mb (ftp)(http) TXT
GSE90822_L2-L3_tpm5.txt.gz 3.1 Mb (ftp)(http) TXT
GSE90822_L2-L6_tpm5.txt.gz 970.7 Kb (ftp)(http) TXT
GSE90822_L2PM-L2AL_tpm5.txt.gz 6.0 Mb (ftp)(http) TXT
GSE90822_L5Cal-L5Front_tpm5.txt.gz 2.1 Mb (ftp)(http) TXT
GSE90822_L6Cal-L6Thal_tpm5.txt.gz 2.0 Mb (ftp)(http) TXT
GSE90822_PV-VIP_tpm5.txt.gz 2.4 Mb (ftp)(http) TXT
GSE90822_SOM-PV_tpm5.txt.gz 4.2 Mb (ftp)(http) TXT
GSE90822_SOM-VIP_tpm5.txt.gz 3.1 Mb (ftp)(http) TXT
GSE90822_V1ALPr-V1PMPr_tpm5.txt.gz 2.3 Mb (ftp)(http) TXT
GSE90822_V1L2Ant-V1L2Post_tpm5.txt.gz 2.5 Mb (ftp)(http) TXT
GSE90822_data_overview_file.txt.gz 10.5 Kb (ftp)(http) TXT
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Processed data are available on Series record
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