Journal: Biology of Reproduction

Article Title: What has single-cell RNA-seq taught us about mammalian spermatogenesis?

doi: 10.1093/biolre/ioz088

Figure Lengend Snippet: Mouse spermatogenesis single-cell RNA-seq datasets.

Article Snippet: scRNA-seq Chemistry/Method , 3′ sequencing and full length sequence (SMART-seq2) , 3′ sequencing and barcoding (10x Genomics) , 3′ sequencing and barcoding (Oliginal Drop-seq) , 3′ sequencing and barcoding (10x Genomics) , 3′ sequencing and barcoding (SMART-seq2 and Microwell-seq) , full length sequence (Fluidigm C1), 3′ sequencing and barcoding (10x Genomics) , 3′ sequencing and barcoding (10x Genomics) , 3′ sequencing and barcoding (10x Genomics) , full length sequence (Fluidigm C1) , full length sequence (Fluidigm C1) , 3′ sequencing and barcoding (10x Genomics) , 3′ sequencing and barcoding (10x Genomics) , full length sequence (Fluidigm C1).

Techniques: Biomarker Discovery, Knock-Out, RNAscope, Transplantation Assay, Sequencing

Journal: Biology of Reproduction

Article Title: What has single-cell RNA-seq taught us about mammalian spermatogenesis?

doi: 10.1093/biolre/ioz088

Figure Lengend Snippet: Human spermatogenesis single-cell RNA-seq datasets.

Article Snippet: scRNA-seq Chemistry/Method , 3′ sequencing and full length sequence (SMART-seq2) , 3′ sequencing and barcoding (10x Genomics) , 3′ sequencing and barcoding (Oliginal Drop-seq) , 3′ sequencing and barcoding (10x Genomics) , 3′ sequencing and barcoding (SMART-seq2 and Microwell-seq) , full length sequence (Fluidigm C1), 3′ sequencing and barcoding (10x Genomics) , 3′ sequencing and barcoding (10x Genomics) , 3′ sequencing and barcoding (10x Genomics) , full length sequence (Fluidigm C1) , full length sequence (Fluidigm C1) , 3′ sequencing and barcoding (10x Genomics) , 3′ sequencing and barcoding (10x Genomics) , full length sequence (Fluidigm C1).

Techniques: Biomarker Discovery, Sequencing

Journal: iScience

Article Title: Lineages of embryonic stem cells show non-Markovian state transitions

doi: 10.1016/j.isci.2021.102879

Figure Lengend Snippet:

Article Snippet: ESCs were labeled using ClonTracer library ( , Addgene #67267).

Techniques: Next-Generation Sequencing, Recombinant

Journal: bioRxiv

Article Title: Interface-guided phenotyping of coding variants in the transcription factor RUNX1 with SEUSS

doi: 10.1101/2023.08.03.551876

Figure Lengend Snippet: An interface-guided Perturb-seq assay for coding variant phenotyping of RUNX1. a. 3D crystal structure of transcription factor CBF, consisting of RUNX1 Runt domain (purple) and CBFB (blue), interacting with DNA (yellow and pink strands) (PDB: 1h9d). b. Amino acid residue map of the RUNX1 Runt domain. Columns represent amino acid residues, while rows represent interaction partners of RUNX1. At each row, interface residues involved in interaction to the partner are highlighted black. Rows are hierarchically clustered. On top: 3D location annotations of each residue (core, intermediate, and surface), followed by VEST and FoldX scores of most damaging mutations targeting the residue. The darker the color, the more damaging (VEST) or destabilizing (FoldX) the mutation is. c. Schematic of lentiviral ORF vector containing the RUNX1 variant (WT, mutated, or GFP) and a 12 base pair barcode sequence unique to each variant for identification during single cell transcriptome sequencing. d. Experimental and computational overview: ORF variant library design, transduction, single cell RNA-sequencing of all 117 library elements, bulk RNA and ATAC-sequencing of 12 selected library elements, and computational analysis.

Article Snippet: The gene overexpression vector was generated from a modified lentiviral vector (Addgene #120426).

Techniques: Variant Assay, Mutagenesis, Plasmid Preparation, Sequencing, Transduction, RNA Sequencing Assay

Journal: Cell reports

Article Title: High-Throughput Screens of PAM-Flexible Cas9 Variants for Gene Knockout and Transcriptional Modulation

doi: 10.1016/j.celrep.2020.02.010

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: pCC_01 - lenti-hU6-sgRNA{F+E)-EFS-Gas9-NLS-2A-Puro , This study , Addgene, plasmid #139086.

Techniques: Virus, Recombinant, DNA Extraction, DNA Purification, Staining, Plasmid Preparation, Software