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Single-Cell RNA-Seq Reveals Developmental Origins and Ontogenetic Stability of Neurexin Alternative Splicing Profiles.

Cell reports | 2019

Neurexins are key synaptic organizers that are expressed in thousands of alternatively spliced isoforms. Because transsynaptic neurexin interactions with different postsynaptic molecules are largely isoform dependent, a cell type-level census of different neurexin isoforms could predict molecular interactions relating to synapse identity and function. Using single-cell transcriptomics to study the origin of neurexin diversity in multiple murine mature and embryonic cell types, we have discovered shared neurexin expression patterns in developmentally related cells. By comparing neurexin profiles in immature embryonic neurons, we show that neurexin profiles are specified during early development and remain unchanged throughout neuronal maturation. Thus, our findings reveal ontogenetic stability and provide a cell type-level census of neurexin isoform expression in the cortex.

Pubmed ID: 31242409 RIS Download

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This is a list of tools and resources that we have found mentioned in this publication.


B6.Cg-Gt(ROSA)26Sortm14(CAG-tdTomato)Hze/J (organism)

RRID:IMSR_JAX:007914

Mus musculus with name B6.Cg-Gt(ROSA)26Sortm14(CAG-tdTomato)Hze/J from IMSR.

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B6;CBA-Tg(Lhx6-icre)1Kess/J (organism)

RRID:IMSR_JAX:026555

Mus musculus with name B6;CBA-Tg(Lhx6-icre)1Kess/J from IMSR.

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Flexbar (software resource)

RRID:SCR_013001

Flexible barcode and adapter removal for sequencing platforms.

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STAR (software resource)

RRID:SCR_015899

Software performing alignment of high-throughput RNA-seq data. Aligns RNA-seq reads to reference genome using uncompressed suffix arrays.

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Trimmomatic (data processing software)

RRID:SCR_011848

Software Java pipeline for trimming tasks for Illumina paired end and single ended data. Flexible Trimmer for Illumina Sequence Data. Pair aware preprocessing tool optimized for Illumina next generation sequencing data. Includes several processing steps for read trimming and filtering. Operating systems Unix/Linux, Mac OS, Windows.

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B6.FVB(Cg)-Tg(Htr3a-cre)NO152Gsat/Mmucd (organism)

RRID:MMRRC_037089-UCD

Mus musculus with name B6.FVB(Cg)-Tg(Htr3a-cre)NO152Gsat/Mmucd from MMRRC.

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HTSeq (software resource)

RRID:SCR_005514

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software Python package that provides infrastructure to process data from high-throughput sequencing assays. While the main purpose of HTSeq is to allow you to write your own analysis scripts, customized to your needs, there are also a couple of stand-alone scripts for common tasks that can be used without any Python knowledge.

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scran (software resource)

RRID:SCR_016944

Software package for low-level analyses of single-cell RNA-seq data. Used for quality control, data exploration and normalization, cell cycle phase assignment, identification of highly variable and correlated genes, clustering into subpopulations and marker gene detection.

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SAMTOOLS (software resource)

RRID:SCR_002105

Original SAMTOOLS package has been split into three separate repositories including Samtools, BCFtools and HTSlib. Samtools for manipulating next generation sequencing data used for reading, writing, editing, indexing,viewing nucleotide alignments in SAM,BAM,CRAM format. BCFtools used for reading, writing BCF2,VCF, gVCF files and calling, filtering, summarising SNP and short indel sequence variants. HTSlib used for reading, writing high throughput sequencing data.

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scikit-learn (software resource)

RRID:SCR_002577

scikit-learn: machine learning in Python

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B6.Cg-Gt(ROSA)26Sortm14(CAG-tdTomato)Hze/J (organism)

RRID:IMSR_JAX:007914

Mus musculus with name B6.Cg-Gt(ROSA)26Sortm14(CAG-tdTomato)Hze/J from IMSR.

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B6;CBA-Tg(Lhx6-icre)1Kess/J (organism)

RRID:IMSR_JAX:026555

Mus musculus with name B6;CBA-Tg(Lhx6-icre)1Kess/J from IMSR.

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