Journal: Cell reports

Article Title: Distinctive physiology of molecularly identified medium spiny neurons in the macaque putamen

doi: 10.1016/j.celrep.2024.114963

Figure Lengend Snippet: (A) Uniform manifold approximation and projection (UMAP) based on Patch-seq single-cell RNA sequencing (scRNA-seq) data reveals separation of direct and indirect pathway neurons as well as co-clustering of mouse and macaque neurons across species. (B) Heatmap of marker gene expression per cell; genes are grouped by markers for all MSNs, indirect pathway MSNs (iMSNs), and direct pathway MSNs (dMSNs). (C) Aggregated data describing marker gene expression across MSNs. (D and E) Excitability of iMSNs is greater than dMSNs in mouse (D) and macaque (E) (mouse dMSNs versus iMSNs, two-way ANOVA p < 10 −24 ; macaque dMSNs versus iMSNs; two-way ANOVA p < 10 −11 ). (F) First spike latency and firing rate adaptation are different across dMSNs and iMSNs in mouse (one-way ANOVA p < 10 −8 across groups; Student’s t test p < 0.01) but not macaque (Student’s t test p > 0.4). (G) Spike rate adaptation is different across direct and indirect pathways in mouse (one-way ANOVA p < 10 −13 across groups; Student’s t test p < 0.01) but not macaque (Student’s t test p > 0.1) (for Patch-seq comparisons: n = 21 mouse dMSNs; n = 6 mouse iMSNs; n = 22 macaque dMSNs; n = 24 macaque iMSNs; for physiology comparisons: n = 30 mouse dMSNs; n = 33 mouse iMSNs; n = 22 macaque MSNs; n = 19 macaque iMSNs). Center point shows mean, and error bars and boxplots are the standard error of the mean.

Article Snippet: Sample tubes were then transferred to −80C for storage until further processing. cDNA libraries were produced using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (634894, Lot 1709695A; Takara Bio Inc.) according to the manufacturer’s instructions, using 20 PCR cycles for cDNA amplification.

Techniques: RNA Sequencing Assay, Marker, Expressing

Journal: Cell reports

Article Title: Distinctive physiology of molecularly identified medium spiny neurons in the macaque putamen

doi: 10.1016/j.celrep.2024.114963

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Sample tubes were then transferred to −80C for storage until further processing. cDNA libraries were produced using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (634894, Lot 1709695A; Takara Bio Inc.) according to the manufacturer’s instructions, using 20 PCR cycles for cDNA amplification.

Techniques: Sequencing, Software, Single-cell Analysis

Journal: Clinical cancer research : an official journal of the American Association for Cancer Research

Article Title: Characterization of an Immunogenic Mutation in a Patient with Metastatic Triple-Negative Breast Cancer

doi: 10.1158/1078-0432.CCR-16-1423

Figure Lengend Snippet: Identification of RBPJ mutation-reactive TCR. A, 4062-TILs were cocultured with autologous APCs presenting RBPJA611T peptide and sorted on the basis of expression of CD4+/4–1BB+ by FACS. Data are gated on live CD3+ cells. B and C, TCR analysis revealed an oligoclonal population of TCR-α (B) and TCR-β (C) chains. Of note, 42.9% of the TCR-α chains were unresolved. On the basis of the frequency, the two most frequent TCR-α and TCR-β chains were used to synthesize the four possible TCR combinations. PBL transduced with TCRAV05 (the second most frequent alpha chain) and TCRBV07 (the most frequent beta chain) recognized APCs specifically presenting mutRBPJ based on IFNγ ELISPOT (D) and upregulation of 4–1BB (E) in the CD4+ T-cell population (▲, mutRBPJ; △, wtRBPJ; ○, irrelevant peptide). Data are representative of three separate patient TCR-transduced PBL.

Article Snippet: Alternatively, 4–1BB + – sorted cells were subjected to single-cell RNA sequencing (RNA-seq) on the Fluidigm C1, according to the manufacturer’s protocol and paired TCR-alpha and beta sequences were identified and synthesized (Genscript).

Techniques: Mutagenesis, Expressing, Transduction, Enzyme-linked Immunospot