Journal: The Journal of Biological Chemistry

Article Title: Inhibition of Chemokine (CXC Motif) Ligand 12/Chemokine (CXC Motif) Receptor 4 Axis (CXCL12/CXCR4)-mediated Cell Migration by Targeting Mammalian Target of Rapamycin (mTOR) Pathway in Human Gastric Carcinoma Cells *

doi: 10.1074/jbc.M111.302299

Figure Lengend Snippet: Pearson correlations ( r ) between rapamycin activity (−lgGI 50 ) and gene expression patterns in the NCI-60 cell lines based on data from the Affymetrix HG-U133A chip

Article Snippet: Although the cell line samples in the present study are small, the results obtained provided a clue that mTOR inhibitor may be used for therapy of metastatic gastric cancer expressing high levels of cxcl12 . table ft1 table-wrap mode="anchored" t5 TABLE 1 caption a7 Rank Gene name Gene description r p value 1 CDKN1B Cyclin-dependent kinase inhibitor 1B (p27, Kip1) 0.473 0.0000 2 ATP8A2 ATPase, aminophospholipid transporter-like, class I, type 8A, member 2 0.436 0.0005 3 CYFIP2 Cytoplasmic FMR1-interacting protein 2 0.408 0.0010 4 SOX1 SRY ( s ex determining r egion Y )-box 1 0.402 0.0011 5 C5orf13 Chromosome 5 open reading frame 13 0.399 0.0007 6 CXCL12 Chemokine (CXC motif) ligand 12 (stromal cell-derived factor 1) 0.395 0.0011 7 PIP5K2A Phosphatidylinositol 4-phosphate 5-kinase type II α 0.384 0.0009 8 LOC283567 Hypothetical protein LOC283567 0.382 0.0008 9 MGC16169 Hypothetical protein MGC16169 0.382 0.0010 10 NEK11 NIMA ( n ever i n m itosis gene a )-related kinase 11 0.3792 0.0031 Open in a separate window Pearson correlations ( r ) between rapamycin activity (−lgGI 50 ) and gene expression patterns in the NCI-60 cell lines based on data from the Affymetrix HG-U133A chip

Techniques: Activity Assay, Gene Expression

Journal: Nature Biotechnology

Article Title: Systematic benchmarking of single-cell ATAC-sequencing protocols

doi: 10.1038/s41587-023-01881-x

Figure Lengend Snippet: Estimated costs per experiment of 5,000 cells

Article Snippet: Public mouse scATAC-seq data were downloaded from the following sources: 10x Genomics scATAC-seq v1.0 on Chromium ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/1.2.0/atac_v1_adult_brain_fresh_5k/atac_v1_adult_brain_fresh_5k_fastqs.tar ), 10x Genomics scATAC-seq v1.1 on Chromium ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/2.1.0/8k_mouse_cortex_ATACv1p1_nextgem_Chromium_X/8k_mouse_cortex_ATACv1p1_nextgem_Chromium_X_fastqs.tar ), 10x Genomics scATAC-seq v2 on Chromium X ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/2.1.0/8k_mouse_cortex_ATACv2_nextgem_Chromium_X/8k_mouse_cortex_ATACv2_nextgem_Chromium_X_fastqs.tar ), 10x Genomics scATAC-seq v2 on Chromium ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/2.1.0/8k_mouse_cortex_ATACv2_nextgem_Chromium_Controller/8k_mouse_cortex_ATACv2_nextgem_Chromium_Controller_fastqs.tar ), 10x Genomics Multiome ATAC ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-arc/2.0.0/e18_mouse_brain_fresh_5k/e18_mouse_brain_fresh_5k_fastqs.tar ), Bio-Rad ddSEQ (SRA accession number SRR14494477 ), s3-ATAC (SRA accession number SRX10841853 ) and HyDrop (SRA accession number PRJNA733185 ).

Techniques: Sequencing

Journal: Nature Biotechnology

Article Title: Systematic benchmarking of single-cell ATAC-sequencing protocols

doi: 10.1038/s41587-023-01881-x

Figure Lengend Snippet: a , Schematic overview of the experimental design; CNAG-CRG, Centro Nacional de Análisis Genómico; EPFL, École Polytechnique Fédérale de Lausanne; OHSU, Oregon Health & Science University; MDC, Max Delbrück Center for Molecular Medicine in the Helmholtz Association; UCSF, University of California San Francisco; VIB, Vlaams Instituut voor Biotechnologie. b , Bar chart of the number of experiments performed per technology colored by institute of origin. c , Diagram of the universal PUMATAC data analysis pipeline and further downstream analyses; QC, quality control. d , Distribution of TSS enrichment, FRIP and total unique fragment counts for all barcodes across all technologies. The blue, green and yellow color scale denotes local density. Saturated colors mark barcodes identified as cells. The distributions for individual samples are shown in Extended Data Fig. . e , Stacked bar plot showing the fraction of reads lost across each step of data processing. ‘Unique, in cells, in peaks’ is the final fraction of sequencing reads retained in count matrices. Asterisk among technology names indicates mtscATAC-seq samples performed on PBMC that were viability FAC-sorted prior to tagmentation. f – h , Distributions of unique fragments in peaks ( f ), TSS enrichment ( g ) and fraction of unique fragments in peaks ( h ) in filtered cell barcodes. The scale was shifted to accommodate lower fragment counts in s3-ATAC and HyDrop, indicated by a red line denoting a value of 6,000; n = 178,453 cells (before doublet filtering) examined over 47 independent experiments. Median values are indicated by central white dots, quartiles are indicated by black boxes, and minima/maxima/centers are not indicated.

Article Snippet: Public mouse scATAC-seq data were downloaded from the following sources: 10x Genomics scATAC-seq v1.0 on Chromium ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/1.2.0/atac_v1_adult_brain_fresh_5k/atac_v1_adult_brain_fresh_5k_fastqs.tar ), 10x Genomics scATAC-seq v1.1 on Chromium ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/2.1.0/8k_mouse_cortex_ATACv1p1_nextgem_Chromium_X/8k_mouse_cortex_ATACv1p1_nextgem_Chromium_X_fastqs.tar ), 10x Genomics scATAC-seq v2 on Chromium X ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/2.1.0/8k_mouse_cortex_ATACv2_nextgem_Chromium_X/8k_mouse_cortex_ATACv2_nextgem_Chromium_X_fastqs.tar ), 10x Genomics scATAC-seq v2 on Chromium ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/2.1.0/8k_mouse_cortex_ATACv2_nextgem_Chromium_Controller/8k_mouse_cortex_ATACv2_nextgem_Chromium_Controller_fastqs.tar ), 10x Genomics Multiome ATAC ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-arc/2.0.0/e18_mouse_brain_fresh_5k/e18_mouse_brain_fresh_5k_fastqs.tar ), Bio-Rad ddSEQ (SRA accession number SRR14494477 ), s3-ATAC (SRA accession number SRX10841853 ) and HyDrop (SRA accession number PRJNA733185 ).

Techniques: Control, Sequencing

Journal: Nature Biotechnology

Article Title: Systematic benchmarking of single-cell ATAC-sequencing protocols

doi: 10.1038/s41587-023-01881-x

Figure Lengend Snippet: Datapoints were randomly shuffled before plotting. a , Non-harmony-corrected tSNE of non-downsampled data, colored by technology of origin, cell type and donor identity. b , Harmony-corrected (by technology, considering 10x v1, 1.1, 2 as a single technology) tSNE of non-downsampled data, colored by technology of origin, cell type and donor identity.

Article Snippet: Public mouse scATAC-seq data were downloaded from the following sources: 10x Genomics scATAC-seq v1.0 on Chromium ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/1.2.0/atac_v1_adult_brain_fresh_5k/atac_v1_adult_brain_fresh_5k_fastqs.tar ), 10x Genomics scATAC-seq v1.1 on Chromium ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/2.1.0/8k_mouse_cortex_ATACv1p1_nextgem_Chromium_X/8k_mouse_cortex_ATACv1p1_nextgem_Chromium_X_fastqs.tar ), 10x Genomics scATAC-seq v2 on Chromium X ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/2.1.0/8k_mouse_cortex_ATACv2_nextgem_Chromium_X/8k_mouse_cortex_ATACv2_nextgem_Chromium_X_fastqs.tar ), 10x Genomics scATAC-seq v2 on Chromium ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/2.1.0/8k_mouse_cortex_ATACv2_nextgem_Chromium_Controller/8k_mouse_cortex_ATACv2_nextgem_Chromium_Controller_fastqs.tar ), 10x Genomics Multiome ATAC ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-arc/2.0.0/e18_mouse_brain_fresh_5k/e18_mouse_brain_fresh_5k_fastqs.tar ), Bio-Rad ddSEQ (SRA accession number SRR14494477 ), s3-ATAC (SRA accession number SRX10841853 ) and HyDrop (SRA accession number PRJNA733185 ).

Techniques:

Journal: Nature Biotechnology

Article Title: Systematic benchmarking of single-cell ATAC-sequencing protocols

doi: 10.1038/s41587-023-01881-x

Figure Lengend Snippet: a , Genome tracks of sex-specific DARs in B cells and cytotoxic and naive T cells showing coverage in male and female subpopulations. Coverage uses a common scale across techniques within each cell type and is cell count normalized (cell counts are equal for each sex within techniques); Chr, chromosome. b , Top, t -distributed stochastic neighbor embedding (t-SNE) projection of all 167,000 filtered cells across all 47 experiments colored by technology and cell type. Bottom, batch-corrected t-SNE using technology of origin as the batch variable. Data points were randomly shuffled before plotting. c , First two principal components of all experiments based on 15 basic quality metrics. Red links indicate same day replicate experiments. Caption denotes technique followed by center of sample origin (B for BioRad, Br for Broad, C for CNAG-CRG, E for EPFL, H for Harvard, M for MDC, O for OHSU, Sa for Sanger, St for Stanford, T for 10x Genomics, U for UCSF, and V for VIB), and finally an index (either A or B) to denote the replicate set if more than one set of replicates was performed at the same center. d , Local inverse Simpson index values before and after Harmony batch correction.

Article Snippet: Public mouse scATAC-seq data were downloaded from the following sources: 10x Genomics scATAC-seq v1.0 on Chromium ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/1.2.0/atac_v1_adult_brain_fresh_5k/atac_v1_adult_brain_fresh_5k_fastqs.tar ), 10x Genomics scATAC-seq v1.1 on Chromium ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/2.1.0/8k_mouse_cortex_ATACv1p1_nextgem_Chromium_X/8k_mouse_cortex_ATACv1p1_nextgem_Chromium_X_fastqs.tar ), 10x Genomics scATAC-seq v2 on Chromium X ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/2.1.0/8k_mouse_cortex_ATACv2_nextgem_Chromium_X/8k_mouse_cortex_ATACv2_nextgem_Chromium_X_fastqs.tar ), 10x Genomics scATAC-seq v2 on Chromium ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/2.1.0/8k_mouse_cortex_ATACv2_nextgem_Chromium_Controller/8k_mouse_cortex_ATACv2_nextgem_Chromium_Controller_fastqs.tar ), 10x Genomics Multiome ATAC ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-arc/2.0.0/e18_mouse_brain_fresh_5k/e18_mouse_brain_fresh_5k_fastqs.tar ), Bio-Rad ddSEQ (SRA accession number SRR14494477 ), s3-ATAC (SRA accession number SRX10841853 ) and HyDrop (SRA accession number PRJNA733185 ).

Techniques: Cell Counting

Journal: Nature Biotechnology

Article Title: Systematic benchmarking of single-cell ATAC-sequencing protocols

doi: 10.1038/s41587-023-01881-x

Figure Lengend Snippet: a , Knee plots of RNA component of 10x multiome samples. Minimum UMI thresholds were automatically defined using Otsu’s algorithm. b , Scatterplots of number of genes versus unique fragments in peaks detected in the same multiome cells. c , Venn diagrams showing overlap between cell barcodes identified as cells based on ATAC or RNA components.

Article Snippet: Public mouse scATAC-seq data were downloaded from the following sources: 10x Genomics scATAC-seq v1.0 on Chromium ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/1.2.0/atac_v1_adult_brain_fresh_5k/atac_v1_adult_brain_fresh_5k_fastqs.tar ), 10x Genomics scATAC-seq v1.1 on Chromium ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/2.1.0/8k_mouse_cortex_ATACv1p1_nextgem_Chromium_X/8k_mouse_cortex_ATACv1p1_nextgem_Chromium_X_fastqs.tar ), 10x Genomics scATAC-seq v2 on Chromium X ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/2.1.0/8k_mouse_cortex_ATACv2_nextgem_Chromium_X/8k_mouse_cortex_ATACv2_nextgem_Chromium_X_fastqs.tar ), 10x Genomics scATAC-seq v2 on Chromium ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/2.1.0/8k_mouse_cortex_ATACv2_nextgem_Chromium_Controller/8k_mouse_cortex_ATACv2_nextgem_Chromium_Controller_fastqs.tar ), 10x Genomics Multiome ATAC ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-arc/2.0.0/e18_mouse_brain_fresh_5k/e18_mouse_brain_fresh_5k_fastqs.tar ), Bio-Rad ddSEQ (SRA accession number SRR14494477 ), s3-ATAC (SRA accession number SRX10841853 ) and HyDrop (SRA accession number PRJNA733185 ).

Techniques:

Journal: Nature Biotechnology

Article Title: Systematic benchmarking of single-cell ATAC-sequencing protocols

doi: 10.1038/s41587-023-01881-x

Figure Lengend Snippet: a , Lineplots showing fraction of reads passing the threshold with increasing thresholds. Area under curve (AUC) values for each cell type in figure legends. b , Lineplot showing label transfer agreement between RNA and ATAC modalities of 10x Multiome samples on y axis, and Seurat scores in the ATAC cell.

Article Snippet: Public mouse scATAC-seq data were downloaded from the following sources: 10x Genomics scATAC-seq v1.0 on Chromium ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/1.2.0/atac_v1_adult_brain_fresh_5k/atac_v1_adult_brain_fresh_5k_fastqs.tar ), 10x Genomics scATAC-seq v1.1 on Chromium ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/2.1.0/8k_mouse_cortex_ATACv1p1_nextgem_Chromium_X/8k_mouse_cortex_ATACv1p1_nextgem_Chromium_X_fastqs.tar ), 10x Genomics scATAC-seq v2 on Chromium X ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/2.1.0/8k_mouse_cortex_ATACv2_nextgem_Chromium_X/8k_mouse_cortex_ATACv2_nextgem_Chromium_X_fastqs.tar ), 10x Genomics scATAC-seq v2 on Chromium ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/2.1.0/8k_mouse_cortex_ATACv2_nextgem_Chromium_Controller/8k_mouse_cortex_ATACv2_nextgem_Chromium_Controller_fastqs.tar ), 10x Genomics Multiome ATAC ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-arc/2.0.0/e18_mouse_brain_fresh_5k/e18_mouse_brain_fresh_5k_fastqs.tar ), Bio-Rad ddSEQ (SRA accession number SRR14494477 ), s3-ATAC (SRA accession number SRX10841853 ) and HyDrop (SRA accession number PRJNA733185 ).

Techniques:

Journal: Nature Biotechnology

Article Title: Systematic benchmarking of single-cell ATAC-sequencing protocols

doi: 10.1038/s41587-023-01881-x

Figure Lengend Snippet: a , Dependency of Seurat label transfer scores and average log 2 (fold change) of the top 2,000 DARs in selected cell types on the total number of cells in selected cell types. b , c , Heat map of the number of DARs ( b ) and heat map of the fold change enrichment ( c ) of the top 2,000 DARs sourced from the cell-type fair merged sets for every technique across cell types. Colors are scaled per column; mono, monocytes. d , Fragment coverage within each cell type’s strongest common DAR found in the merged set. Each cell type contains an equal number of cells across technologies. All tracks are scaled to the same absolute coverage. The 10x v1 track is slightly truncated to accommodate j . e , f , Fraction of the top 20% and bottom 20% peaks and DARs found by the merged cell-type fair set recovered in subsets from individual technologies. g , Heat map of the normalized enrichment score of cell-type-specific transcription factor motifs. Colors are scaled per row. h , Scatter plot of median Freemuxlet donor assignment log likelihood difference to second-best guess and median number of unique fragments. i , Scatter plot of the ratio of naive T cells to cytotoxic T cells in male and female subpopulations and median number of unique fragments. In h and i , each point represents one experiment, and points are colored by technique. j , Heat map of the number of sex-specific DARs. Colors are scaled per column. k , Heat map of fold change enrichment of the 200 strongest sex-specific DARs. Colors are scaled per column.

Article Snippet: Public mouse scATAC-seq data were downloaded from the following sources: 10x Genomics scATAC-seq v1.0 on Chromium ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/1.2.0/atac_v1_adult_brain_fresh_5k/atac_v1_adult_brain_fresh_5k_fastqs.tar ), 10x Genomics scATAC-seq v1.1 on Chromium ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/2.1.0/8k_mouse_cortex_ATACv1p1_nextgem_Chromium_X/8k_mouse_cortex_ATACv1p1_nextgem_Chromium_X_fastqs.tar ), 10x Genomics scATAC-seq v2 on Chromium X ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/2.1.0/8k_mouse_cortex_ATACv2_nextgem_Chromium_X/8k_mouse_cortex_ATACv2_nextgem_Chromium_X_fastqs.tar ), 10x Genomics scATAC-seq v2 on Chromium ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/2.1.0/8k_mouse_cortex_ATACv2_nextgem_Chromium_Controller/8k_mouse_cortex_ATACv2_nextgem_Chromium_Controller_fastqs.tar ), 10x Genomics Multiome ATAC ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-arc/2.0.0/e18_mouse_brain_fresh_5k/e18_mouse_brain_fresh_5k_fastqs.tar ), Bio-Rad ddSEQ (SRA accession number SRR14494477 ), s3-ATAC (SRA accession number SRX10841853 ) and HyDrop (SRA accession number PRJNA733185 ).

Techniques: