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

Journal: Nucleic Acids Research

Article Title: SETDB1 activity is globally directed by H3K14 acetylation via its Triple Tudor Domain

doi: 10.1093/nar/gkae1053

Figure Lengend Snippet: SETDB1 is recruited to H3K14ac containing target loci. ( A ) Scheme of the cell HCT116 derived lines generated in this study by SETDB1 KO followed by reconstitution with SETDB1 WT or mutants and by HBO1 KO. ( B and C ) H3K9me3 (B) and H3K14ac (C) ChIP-qPCR at known SETDB1 target regions ( , ) showing changes in the histone modification as indicated upon SETDB1 KO and reconstitution with WT SETDB1 of its catalytically inactive mutant H1224K or the 3TD mutant F332A. Moreover, HBO1 KO cells were investigated. ChIP was performed on mononucleosomes isolated from two individual biological replicates from each cell line (represented as dots). Averages of the individual measurements are represented as bars.

Article Snippet: For each region of interest, a master mix was prepared with 7.5 μl of 2X ORATM See qPCR Probe Mix (highQu), 0.4 μl forward primer, 0.4 μl reverse primer and 5.7 μl ddH 2 O.

Techniques: Derivative Assay, Generated, ChIP-qPCR, Modification, Mutagenesis, Isolation

Journal: Cell

Article Title: Biology and clinical implications of the 19q13 aggressive prostate cancer susceptibility locus

doi: 10.1016/j.cell.2018.06.003

Figure Lengend Snippet: DATA AND SOFTWARE AVAILABILITY

Article Snippet: Quanti tech probe PCR mix , QIAGEN , Cat#204343.

Techniques: Software, Virus, Recombinant, Protease Inhibitor, Transfection, Membrane, Reverse Transcription, Luciferase, Purification, Microarray, Gene Expression, Genome Wide, CRISPR, Control, Negative Control, Functional Assay, Binding Assay, Plasmid Preparation, Blocking Assay