slc17a7 probeset  (Molecular Instruments)

Journal: Cell

Article Title: High-throughput mapping of long-range neuronal projection using in situ sequencing

doi: 10.1016/j.cell.2019.09.023

Figure Lengend Snippet: Correlating gene expression and projections using BARseq. (A) Barcode sequencing in Cre-labeled animals. Top: images of Fezf2+ tdTomato expressing cells (left), GFP expressing barcoded cells (middle), and merged image of the two (right). Scale bar = 100 μm. Bottom: sequencing images of the boxed area in the merged image. Arrows indicate tdTomato-expressing barcoded neurons. (B) Projection patterns of all neurons (left) and Fezf2+ neurons (right). Rows indicate neurons and columns indicate projection areas. (C) The cortical depth distribution of barcoded Fezf2+ somata color-coded by projections. (D) Representative images of FISH (left) and sequencing images (right) of the same sample. (E) The expression profile of Slc17a7 and Gad2 and barcode sequences of the neurons boxed in (D). Scale bars = 50 μm. (F) The number of neurons with or without projections (Proj) in cells that did or did not express Slc17a7 (S) and/or Gad2 (G). (G) Mean log normalized expression of each gene averaged over all barcoded (x-axis) and non-barcoded (y-axis) neurons. The gene expression is regressed with a Poisson model to remove the effect of both the percentage of mitochondrial genes and endogenous UMI counts. See also Fig. S2 and Table S2.

Article Snippet: After neutralization of additional crosslinkers with Tris, we proceeded with ViewRNA ISH (Thermo Fisher Scientific) using a class 1 probeset for Slc17a7 and a class 6 probeset for Gad2 according to the manufacturer’s protocol.

Techniques: Expressing, Sequencing, Labeling

Journal: bioRxiv

Article Title: Comprehensive profiling of transcription factors for reprogramming human astrocytes to neuronal cells through endogenous CRISPR-based gene activation

doi: 10.1101/2025.10.11.681828

Figure Lengend Snippet: A. ORF overexpression of annotated INSM1, LHX6, and ZNF276 isoforms. RNA levels of neuron marker genes shown. *p < 0.05, ***p < 0.001 by global one-way ANOVA with Dunnett’s post hoc test comparing all groups to mCherry. B. Immunofluorescence staining of reprogrammed cells to assess MAP2, NeuN, and SLC17A7 expression 25 days after transduction. C. Number of spikes (neuronal firing events) in 5-minute multi-electrode array recording 32 days post-transduction. D. Flow analysis of TUBB3-2A-mCherry expression expression as proxy for early neuronal differentiation 5 days post-transduction of VP64 dSpCas9 VP iPSCs with gRNA. E. Summary of mouse gRNA sublibrary. F. Significance (P adj ) versus fold change in gRNA abundance between MAP2-high and MAP2-low populations in mouse CRISPRa screen. G. Top enriched biological processes for upregulated DEGs (L2FC >1, p adj <0.01 determined by DESeq2 vs mCherry, n=121 genes) from RNA-seq 10 days after INSM1 ORF overexpression. Statistical significance of term enrichment was determined using a two-tailed Fisher’s exact test followed by Benjamini–Hochberg correction.

Article Snippet: SLC17A7 screen: To screen for factors that cooperate with INSM1 to enhance glutamatergic subtype specification, cells were sorted based on abundance of SLC17A7 RNA using HCR-FlowFISH according to the method described in Reilly et al. 2021 with the following modifications: SLC17A7 probeset and buffers were ordered from Molecular Instruments ( https://www.molecularinstruments.com ), and SLC17A7 probeset was used at a final concentration of 8nM overnight.

Techniques: Over Expression, Marker, Immunofluorescence, Staining, Expressing, Transduction, RNA Sequencing, Two Tailed Test

Journal: bioRxiv

Article Title: Comprehensive profiling of transcription factors for reprogramming human astrocytes to neuronal cells through endogenous CRISPR-based gene activation

doi: 10.1101/2025.10.11.681828

Figure Lengend Snippet: A. Schematic of paired CRISPRa screens. B. Summary of TFpaired screening library. C. Scatter plot of z-score of gRNA abundance in the INSM1 MAP2 paired screen and the INSM1 SLC17A7 paired screen. D. Euler diagrams of differentially accessible peaks. Differential peaks (p adj <.01) for each sample were determined by DESeq2 vs. non-targeting gRNA. E. Top enriched biological processes for genes nearest top 1000 differentially accessible peaks by z-score for INSM1 (I), IKZF1 (IK), or peaks unique in only the combination of INSM1-IKZF1 (I+IK). Statistical significance of term enrichment was determined using a two-tailed Fisher’s exact test followed by Benjamini–Hochberg correction. F. Browser tracks of ATAC-seq (reads per kilobase per million mapped reads [RPKM]-normalized BigWig, bin size = 25bp. ‘Diff.peaks’ denotes peak significance between IKZF1-INSM1 and non-targeting using DESeq2. G. ANKS1B and KALRN peak accessibility and RNA expression indicate lack of significance after reprogramming with individual factors but significance after reprogramming with combination. H. Expression level ofANKS1B and KALRN in neural cell types in the Human Protein Atlas Single Cell Type data .

Article Snippet: SLC17A7 screen: To screen for factors that cooperate with INSM1 to enhance glutamatergic subtype specification, cells were sorted based on abundance of SLC17A7 RNA using HCR-FlowFISH according to the method described in Reilly et al. 2021 with the following modifications: SLC17A7 probeset and buffers were ordered from Molecular Instruments ( https://www.molecularinstruments.com ), and SLC17A7 probeset was used at a final concentration of 8nM overnight.

Techniques: Two Tailed Test, RNA Expression, Expressing