27 Matching Annotations
  1. Jul 2019
    1. differentially expressed genes (DEGs)

      Differentially expressed genes are ones that have higher expression in one condition versus another.

    2. bulk sequencing

      In this context, bulk sequencing refers to the analysis of whole tissue, as opposed to single cells or nuclei.

    3. protoplasmic astrocytes

      Protoplasmic astrocytes are a subset of astrocytes that are located in the gray matter (which consists mostly of cell bodies) in the brain. They have many complex processes that can contact blood vessels and neurons.

    4. unbiased clustering

      Unbiased clustering is a statistical approach to make sense of large sets of data. It allows scientists to group together ("cluster") genes that are similar to one another.

    5. astrocytes

      Astrocytes, like microglia, are cells that facilitate neuronal functions. They mediate neuronal signaling, support the blood brain barrier, and help respond to sites of trauma.

    6. interneurons

      Interneurons are neurons that act as an intermediate between two other neurons.

    7. upper-layer excitatory neurons

      Upper-layer refers to where in the cortex these neurons are located.

      Excitatory neurons are neurons which increases the activity of the cells it's connected to.

    8. Although bulk transcriptomic tissue studies revealed convergence of disease pathology on common pathways (1–3)

      These studies performed RNA sequencing to identify differences in RNA and gene expression in the autistic brain. They found that there are similarities in the kinds of genes that are changed in patients with autism.

    9. The multiplet nuclei capture rate was comparable to single-cell RNA-seq analysis using the 10× platform

      In order to see if they were accidentally capturing more than one nuclei at a time, the authors mixed nuclei from mouse and human samples prior to running snRNA-seq. If they saw mouse RNA mixed with human RNA, this meant there was a multiplet (or, more than one nuclei was captured).

      However, they found that there was very low rates of multiplets, meaning that their experiment is working well.

    10. RNA integrity number

      The RNA integrity number, or RIN, is an index of RNA quality. RNA can sometimes be degraded when it is isolated, so this is a useful way to see if the RNA is still reliable.

    11. We aimed to gain insight into cell type–specific transcriptomic changes by performing unbiased single-nucleus RNA sequencing (snRNA-seq) (4) of 41 postmortem tissue samples

      The authors wanted to see if particular cell types have different gene expression in autistic brains. They also examined two different brain areas to see if there's regional differences.

    12. We generated 104,559 single-nuclei gene expression profiles—52,556 from control subjects and 52,003 from ASD patients (data S2)—and detected a median of 1391 genes and 2213 transcripts per nucleus, a yield that is in agreement with a recent snRNA-seq

      The authors calculated the total number of genes expressed in the single-nuclei data of controls and ASD patients and found it was about the same. The median gene number is lower than the transcript number because a gene can have multiple transcript forms (called isoforms).

    13. 10× Genomics platform

      The 10X Genomic system is a platform that isolates single nuclei and isolates "libraries" (a collection of RNA fragments which can be used to identify particular RNAs) from each nuclei.

    14. 1. I. Voineagu et al., Nature 474, 380–384 (2011).

      In this paper by Voineagu et al., the authors found that there is lower enrichment of prefrontal genes in autistic brains, suggesting that there's dysregulation in this region.

    15. To compare changes in ASD to those in patients with sporadic epilepsy only, we generated additional snRNA-seq data from eight PFC samples from patients with sporadic epilepsy and seven age-matched controls (data S1)

      The authors wanted to make sure that any effects they were seeing were specific to ASD, and not epilepsy, so they included patients with epilepsy alone as an additional control.

    16. (fig. S1A; P > 0.1, Mann-Whitney U test)

      This means that the control and ASD subjects didn't differ in age, sex, or RNA quality. This is important because results can be biased by uncontrolled factors (e.g., what if there's more females in one group, and the effect you're seeing is really due to sex?)

      Mann-Whitney U test is a statistical test that they used to show that there's no signifiant differences between the controls and ASD subjects.

    17. Autism spectrum disorder (ASD) affects 1 of 59 children in the United States

      There has been increasing concern about rising rates of autism, although this is a controversial subject. For more information, see:


    18. postmortem interval

      The postmortem interval is the time between when an individual died and when the tissue was prepared.

    19. anterior cingulate cortex

      The anterior cingulate cortex is the part of the brain associated with higher level functions such as emotion, empathy, and decision making.

    20. prefrontal cortex

      The prefrontal cortex is an area at the front of the brain. It is associated with social behavior, decision making, and personality.

    21. cortico-cortical projection neurons

      Cortico-cortical projection neurons are cortical neurons which project (or connect to) other cortical neurons.

    22. microglia

      Microglia are "helper cells" in the brain. They help mediate neuron responses, clear out dead cells, and control immune responses.

    23. synaptic signaling

      Synaptic signaling refers to how neurons communicate with one another.

      A projection called an axon from the pre-synaptic neuron touches or "synapses on" the dendritic projections of the post-synaptic neuron. Chemicals called neurotransmitters are released from the pre-synaptic neuron and mediate responses in the post-synaptic neuron.

    24. transcriptomic

      The transcriptome refers to the total set of RNA transcribed from DNA.

    25. single-nucleus RNA sequencing

      In single-nucleus RNA sequencing, the nucleus (which contains DNA and nascently transcribed RNA) is isolated from a single cell. The isolated RNA undergoes RNA-sequencing, in which the RNA is broken up into fragments. Using a database, these fragments are then aligned to specific transcripts.

    26. neocortex

      The neocortex is the part of the brain that in humans is associated with higher level functions such as cognition and language.

    27. genetic heterogeneity of autism

      Genetic heterogeneity refers to the ability of a phenotype (in this case, autism) to manifest via genetic mutations in multiple different loci. This means that there isn't one single genetic mutation that's associated with autism.