Journal: Nature Communications

Article Title: SPACEL: deep learning-based characterization of spatial transcriptome architectures

doi: 10.1038/s41467-023-43220-3

Figure Lengend Snippet: a Spatial domains identified by Splane in slice S2 and S5 from Wu et al. dataset, slice S10 from Zhao et al. dataset, and slice S11 released by 10X Genomics. b , c Spatial distribution of chromosome 1q&8q copy number gains ( b ) and 1p copy number losses ( c ) of ST spots in slices S11, calculated by inferCNV. Dashed lines represent the tumor domain. d , e CNVs of chromosome 1q & 8q ( d ) and chromosome 1p ( e ) in each spatial domain calculated by inferCNV. CNVs, copy number variations; center line, median value; box limits, upper and lower quartiles; whiskers, 1.5× interquartile range; n = 11 slices. f From left to right: Splane predicted spatial domains in slice S5, distribution of Splane predicted immune domains D7/D8/D9, distribution of Spoint predicted immune cells, and distribution of H&E staining marked immune spots. g Percentage of H&E staining marked immune spots in each domain of slice S1, S2, S5, and S6. The four slices were H&E stained in the original study. Bar height, mean value; whiskers, mean values ± 95% confidence intervals; n = 4 slices. h From left to right: Splane predicted spatial domains in slice S10, distribution of Splane predicted immune domains D7, D8, and D9, distribution of Spoint predicted immune cells, and distribution of CD3 + immunofluorescence (IF) staining marked immune spots. i Percentage of CD3 + IF staining marked immune spots in each domain of slice S10. Source data are provided as a Source Data file.

Article Snippet: The raw data of 11 ST datasets and five paired single-cell/nucleus RNA sequence datasets are available from the following studies: (1) 12 slices of human DLPFC 10X Visium data at http://research.libd.org/spatialLIBD/ ; (2) six slices of human breast cancer 10X Visium data at 10.5281/zenodo.4739739 ; (3) four slices of human breast cancer 10X Visium data: Parent_Visium_Human_BreastCancer, V1_Breast_Cancer_Block_A_Section_1, V1_Breast_Cancer_Block_A_Section_2 and Visium_FFPE_Human_Breast_Cancer at https://support.10xgenomics.com/spatial-gene-expression/datasets ; (4) one slice of human breast cancer 10X Visium data: Invasive Ductal Carcinoma Stained With Fluorescent CD3 Antibody at https://support.10xgenomics.com/spatial-gene-expression/datasets ; (5) Mouse brain STARmap data at https://www.starmapresources.org/data ; (6) 33 slices of Mouse MOp MERFISH data at https://doi.brainimagelibrary.org/doi/10.35077/g.21 ; (7) one slice of mouse E16.5 embryo brain Stereo-seq data, one slice of mouse brain Stereo-seq data, and 13 slices of mouse E16.5 whole embryo Stereo-seq data at https://db.cngb.org/stomics/mosta/download/ ; (8) ten slice of human brain MERFISH data at https://datadryad.org/stash/dataset/doi:10.5061/dryad.x3ffbg7mw ; (9) 75 slice of mouse whole brain Spatial Transcriptomics data are available in the GEO database under accession number GSE147747 ; (10) single-nucleus transcriptomics data across multiple human cortical areas at https://portal.brain-map.org/atlases-and-data/rnaseq/human-multiple-cortical-areas-smart-seq ; (11) single-cell transcriptomics data of human breast cancer data at https://singlecell.broadinstitute.org/single_cell/study/SCP1039 ; (12) single-cell transcriptomics data of mouse embryo brain at http://mousebrain.org/development/downloads.html ; (13) single-cell transcriptomics data of mouse whole cortex and hippocampus at https://portal.brain-map.org/atlases-and-data/rnaseq/mouse-whole-cortex-and-hippocampus-10x ; (14) single-cell transcriptomics data of mouse whole brain at mousebrain.org/adolescent/downloads.html .

Techniques: Staining, Immunofluorescence

Journal: PloS one

Article Title: Reduced selenium-binding protein 1 in breast cancer correlates with poor survival and resistance to the anti-proliferative effects of selenium.

doi: 10.1371/journal.pone.0063702

Figure Lengend Snippet: Figure 1. The Expression of SELENBP1 in Normal and Tumor Breast Tissues. Breast cancer tissue arrays were stained by immunohistochemistry using anti-human SELENBP1 antibody at 1:100 dilution. Positive stained cells are shown in dark brown color. (A) Strong positive staining of SELENBP1 in normal breast tissue under low power view (200X). (B–C) Weak positive to negative staining of SELENBP1 in breast cancer tissues under high power view (400X). (D) The Allred scoring distributions of SELENBP1 expression in normal and tumor tissue groups. Inside lines represent means and standard deviations. *p,0.05. (E) Statistical results for the difference between normal and tumor tissues as analyzed by Kruskal-Wallis test. doi:10.1371/journal.pone.0063702.g001

Article Snippet: Breast Cancer Tissue Array Slides Three sets of breast cancer tissue arrays (including normal, primary tumor, and metastases) were obtained from Imgenex or Biomax Inc.

Techniques: Expressing, Staining, Immunohistochemistry, Negative Staining

Journal: PloS one

Article Title: Reduced selenium-binding protein 1 in breast cancer correlates with poor survival and resistance to the anti-proliferative effects of selenium.

doi: 10.1371/journal.pone.0063702

Figure Lengend Snippet: Figure 2. SELENBP1 Expression is Progressively Reduced in Advancing Clinical Stages in Breast Cancer Tissues. (A) The scoring distributions of SELENBP1 expression in normal tissues and tumor tissues at stage II and stage III. Inside lines represent means and standard deviations. **p,0.01. (B) Statistical results for the difference between normal and tumor tissues as analyzed by Kruskal-Wallis test. (C) Survival curves of breast cancer patients with respect to different SELENBP1 expression levels are shown at stage II and (D) stage III. Blue and red lines represent the SELENBP1-high and SELENBP1-low groups, respectively. doi:10.1371/journal.pone.0063702.g002

Article Snippet: Breast Cancer Tissue Array Slides Three sets of breast cancer tissue arrays (including normal, primary tumor, and metastases) were obtained from Imgenex or Biomax Inc.

Techniques: Expressing

Journal: PloS one

Article Title: Reduced selenium-binding protein 1 in breast cancer correlates with poor survival and resistance to the anti-proliferative effects of selenium.

doi: 10.1371/journal.pone.0063702

Figure Lengend Snippet: Figure 3. The Correlation of SELENBP1 Expression with ER, PR, and TP53 in Breast Cancer Tissues. (A) The scoring distributions of SELENBP1 expression in normal tissues and tumor tissues with ER+ and ER– status. The inside lines represent means and standard deviations. **p,0.01. The difference between normal and ER+ and ER– tumor tissues was analyzed by Kruskal-Wallis test and statistical results are shown (B). Survival curves of breast cancer patients with respect to different SELENBP1 expression are shown in ER+ group in (C). The blue line is the SELENBP1- high group and the red line is the SELENBP1-low group. The scoring distributions of SELENBP1 expression in normal and tumor tissues with PR+/PR–

Article Snippet: Breast Cancer Tissue Array Slides Three sets of breast cancer tissue arrays (including normal, primary tumor, and metastases) were obtained from Imgenex or Biomax Inc.

Techniques: Expressing

Journal: Scientific reports

Article Title: IL-17A and its homologs IL-25/IL-17E recruit the c-RAF/S6 kinase pathway and the generation of pro-oncogenic LMW-E in breast cancer cells.

doi: 10.1038/srep11874

Figure Lengend Snippet: Figure 1. Expression of IL-17 cytokines and receptors in clinical samples. The TissueScan Breast Tissue qPCR array was used to determine transcript levels of the IL-17 cytokines (IL-17A and IL-17E) and their receptors (IL-17 RA, IL-17 RB and IL-17 RC). The breast tissue scan contains 48 tissues covering 4 diseases stages and normal tissues. The target transcript levels were normalized to β -Actin and calibrated to the mean mRNA level (arbitrary value of 1) in normal tissue. Data were compared using student’s t test (*P < 0.05, **P < 0.01, ***P < 0.001).

Article Snippet: The target genes expression was also analyzed in normal and tumoral breast tissues using the TissueScan Breast Tissue qPCR array (BCRT502, OriGene Technologies, Rockville, USA).

Techniques: Expressing