Knock-Out:Article Title: Chronic Opioid Treatment Arrests Neurodevelopment and Alters Synaptic Activity in Human Midbrain Organoids.
Article Snippet: .. On day 0, neuronal induction medium composed of 15% Knockout serum replacement (Gibco), 1% GlutaMax (Gibco), 1% minimum essential media-nonessential amino acids (MEM-NEAA) (Gibco), and 0.1% β- mercaptoethanol (Gibco) in Knockout DMEM/F12 (Gibco) supplemented with 100 nm LDN193189 (Stemgent) and 10 μm SB431542 (Tocris Bioscience) was used. .. On day 2, we changed to the neuronal induction media supplemented with LDN193189, SB431542, 100 ng mL−1 SHH (R&D Systems), and 2 μm purmorphamine (Calbiochem).
other:
Article Title: Development of Nurr1 agonists from amodiaquine by scaffold hopping and fragment growing
Article Snippet: Subsequently, 10.000 cells were seeded in each well of a 96-well v-shaped ultra-low attachment plate (Sbio®) in neuronal induction media (NIC; DMEM/F12 (Thermo Fisher): Neurobasal media (Thermo Fisher) (1:1), 1:100 N2 supplement (Gibco), 1:50 B27 without Vitamin A (Gibco), 1% GlutaMAX (Gibco), 1% minimum essential media-nonessential amino acid (MEM-NEAA) (Gibco), 0.1% ß-mercaptoethanol (Gibco) supplemented with 1 μg/mL heparin (Merck), 10 μM SB431542 (Miltenyi), 200 ng/mL human Noggin (Miltenyi), 0.8 μM CHIR99021 (R&D) and 10 μM Rock inhibitor Y27632 (R&D)).
Recombinant:Article Title: A comprehensive single-cell breast tumor atlas defines epithelial and immune heterogeneity and interactions predicting anti-PD-1 therapy response.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-huCD56 BV605, Clone HCD56 (mouse IgG1k) BioLegend Cat#318334; RRID: AB_2561912 Chemicals, peptides, and recombinant proteins 40,6-Diamidino-2-Phenylindole, Dihydrochloride (DAPI) Invitrogen Cat#D1306 Dimethyl sulfoxide (DMSO) Sigma Aldrich Cat#D2650 Dulbecco0s Phosphate Buffered Saline (DPBS) Sigma Aldrich Cat#D8537 Fetal Bovine Serum (FBS) Corning Cat#35-011-CV Human IL-2 IS, premium grade Miltenyi Biotec Cat#130-097-746 RPMI-1640 Corning Cat#10-040-CV Penicillin-Streptomycin (100X) Cytiva HyClone Cat#SV30010 Sodium Pyruvate (100 mM) Gibco Cat#11360070 Minimum Essential Media (MEM) non-essential amino acids (NEAA) (100X) Gibco Cat11140050 GlutaMAX Supplement Gibco Cat#35050061 2-mercaptoethanol (50 mM) Gibco Cat#21985023 Critical commercial assays UltraComp eBeads Plus Compensation Beads Invitrogen Cat#01-3333-42 Deposited data Primary breast tumor atlas This paper https://doi.org/10.5281/zenodo.10672250 Experimental models: Cell lines NK-92 ATCC Cat#CRL-2407, RRID: CVCL_2142 BT-474 ATCC Cat#HTB-20, RRID: CVCL_0179 MDA-MB-436 ATCC Cat#HTB-130, RRID: CVCL_0623 K-562 ATCC Cat#CCL-243, RRID: CVCL_0004 Software and algorithms limma (v3.50.1) Ritchie et al.90 https://bioconductor.org/packages/release/ bioc/html/limma.html org.Hs.e.g.,.db (v3.14.0) Carlson et al.91 https://bioconductor.org/packages/release/ data/annotation/html/org.Hs.eg.db.html DoubletFinder (v2.0.3) McGinnis et al.92 https://github.com/chris-mcginnis-ucsf/DoubletFinder Seurat (v4.1.0) Hao et al.93 https://satijalab.org/seurat/ MAST (v1.20.0) Finak et al.94 https://www.bioconductor.org/packages/ release/bioc/html/MAST.html SCTransform (v0.3.2.9008) Hafemeister et al.95 https://github.com/satijalab/sctransform UCell (v1.99.1) Andreatta et al.96 https://github.com/carmonalab/UCell clusterProfiler (v4.2.2) Wu et al.97 https://bioconductor.org/packages/release/ bioc/html/clusterProfiler.html msigdbr (v7.5.1) Dolgalev et al.98 https://cran.r-project.org/web/packages/ msigdbr/vignettes/msigdbr-intro.html TCGAbiolinks (v2.18.0) Colaprico et al.99 https://bioconductor.org/packages/release/ bioc/html/TCGAbiolinks.html DESeq2 (v1.34.0) Love et al.100 https://bioconductor.org/packages/release/ bioc/html/DESeq2.html inferCNV (v.0.99.7) Tickle et al.101 https://github.com/broadinstitute/infercnv ROGUE Liu et al.52 https://github.com/PaulingLiu/ROGUE (Continued on next page) e1 Cell Reports Medicine 5, 101511, May 21, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER cola (v2.0.0) Gu et al.102 https://www.bioconductor.org/packages/ release/bioc/html/cola.html NicheNet (v1.1.0) Browaeys et al.103 https://github.com/saeyslab/nichenetr CellChat (v0.0.1) Jin et al.104 https://github.com/jinworks/CellChat BisqueRNA (v1.0.5) Jew et al.105 https://github.com/cozygene/bisque pROC (v1.18.0) Robin et al.106 https://cran.r-project.org/web/packages/ pROC/index.html Other Resource website for the primary breast tumor atlas publication containing dataset and analyses This paper https://github.com/ChanLab-UTSW/ BreastCancer_Integrated Original source dataset of immune cells in primary breast tumors Azizi et al.7 GEO: GSE114727 Original source dataset of primary TNBC tumors Karaayvaz et al.8 GEO: GSE118389 Original source dataset of primary breast tumors Pal et al.9 GEO: GSE161529 Original source dataset of T cells in primary TNBC tumors Savas et al.107 GEO: GSE110686 Original source dataset of primary breast tumors Wu et al.13 GEO: GSE176078 Original source dataset with primary breast tumors Xu et al.14 GEO: GSE180286 Original source dataset with primary breast tumors Qian et al.11 https://lambrechtslab.sites.vib.be/en/ pan-cancer-blueprint-tumourmicroenvironment-0 Original source dataset of primary TNBC tumors Wu et al.12 https://singlecell.broadinstitute.org/ single_cell/study/SCP1106/stromalcell-diversity-associated-withimmune-evasion-in-human-triplenegative-breast-cancer Original source dataset of PD-1 treated primary breast tumors Bassez et al.108 https://lambrechtslab.sites.vib. be/en/single-cell Breast cancer cell line data from DepMap 22Q2 public release Ghandi et al.109 https://depmap.org/portal/download/all/ Spatially resolved data for 6 primary breast tumors Wu et al.12 https://doi.org/10.5281/zenodo.4739739 Spatially resolved data from 5 primary breast tumors 10x Genomics https://www.10xgenomics.com/datasets/human- breast-cancer-ductal-carcinoma-in-situ-invasivecarcinoma-ffpe-1-standard-1-3-0; https://www.10xgenomics.com/datasets/humanbreast-cancer-visium-fresh-frozen-wholetranscriptome-1-standard; https://www.10xgenomics.com/datasets/humanbreast-cancer-block-a-section-1-1-standard-1-1-0; https://www.10xgenomics.com/datasets/humanbreast-cancer-whole-transcriptome-analysis-1standard-1-2-0; https://www.10xgenomics.com/products/xeniumin-situ/preview-dataset-human-breast I-SPY2-990 mRNA and clinical data for I-SPY2 trial Nanda et al.57 GEO: GSE194040 OPEN ACCESS
Saline:Article Title: A comprehensive single-cell breast tumor atlas defines epithelial and immune heterogeneity and interactions predicting anti-PD-1 therapy response.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-huCD56 BV605, Clone HCD56 (mouse IgG1k) BioLegend Cat#318334; RRID: AB_2561912 Chemicals, peptides, and recombinant proteins 40,6-Diamidino-2-Phenylindole, Dihydrochloride (DAPI) Invitrogen Cat#D1306 Dimethyl sulfoxide (DMSO) Sigma Aldrich Cat#D2650 Dulbecco0s Phosphate Buffered Saline (DPBS) Sigma Aldrich Cat#D8537 Fetal Bovine Serum (FBS) Corning Cat#35-011-CV Human IL-2 IS, premium grade Miltenyi Biotec Cat#130-097-746 RPMI-1640 Corning Cat#10-040-CV Penicillin-Streptomycin (100X) Cytiva HyClone Cat#SV30010 Sodium Pyruvate (100 mM) Gibco Cat#11360070 Minimum Essential Media (MEM) non-essential amino acids (NEAA) (100X) Gibco Cat11140050 GlutaMAX Supplement Gibco Cat#35050061 2-mercaptoethanol (50 mM) Gibco Cat#21985023 Critical commercial assays UltraComp eBeads Plus Compensation Beads Invitrogen Cat#01-3333-42 Deposited data Primary breast tumor atlas This paper https://doi.org/10.5281/zenodo.10672250 Experimental models: Cell lines NK-92 ATCC Cat#CRL-2407, RRID: CVCL_2142 BT-474 ATCC Cat#HTB-20, RRID: CVCL_0179 MDA-MB-436 ATCC Cat#HTB-130, RRID: CVCL_0623 K-562 ATCC Cat#CCL-243, RRID: CVCL_0004 Software and algorithms limma (v3.50.1) Ritchie et al.90 https://bioconductor.org/packages/release/ bioc/html/limma.html org.Hs.e.g.,.db (v3.14.0) Carlson et al.91 https://bioconductor.org/packages/release/ data/annotation/html/org.Hs.eg.db.html DoubletFinder (v2.0.3) McGinnis et al.92 https://github.com/chris-mcginnis-ucsf/DoubletFinder Seurat (v4.1.0) Hao et al.93 https://satijalab.org/seurat/ MAST (v1.20.0) Finak et al.94 https://www.bioconductor.org/packages/ release/bioc/html/MAST.html SCTransform (v0.3.2.9008) Hafemeister et al.95 https://github.com/satijalab/sctransform UCell (v1.99.1) Andreatta et al.96 https://github.com/carmonalab/UCell clusterProfiler (v4.2.2) Wu et al.97 https://bioconductor.org/packages/release/ bioc/html/clusterProfiler.html msigdbr (v7.5.1) Dolgalev et al.98 https://cran.r-project.org/web/packages/ msigdbr/vignettes/msigdbr-intro.html TCGAbiolinks (v2.18.0) Colaprico et al.99 https://bioconductor.org/packages/release/ bioc/html/TCGAbiolinks.html DESeq2 (v1.34.0) Love et al.100 https://bioconductor.org/packages/release/ bioc/html/DESeq2.html inferCNV (v.0.99.7) Tickle et al.101 https://github.com/broadinstitute/infercnv ROGUE Liu et al.52 https://github.com/PaulingLiu/ROGUE (Continued on next page) e1 Cell Reports Medicine 5, 101511, May 21, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER cola (v2.0.0) Gu et al.102 https://www.bioconductor.org/packages/ release/bioc/html/cola.html NicheNet (v1.1.0) Browaeys et al.103 https://github.com/saeyslab/nichenetr CellChat (v0.0.1) Jin et al.104 https://github.com/jinworks/CellChat BisqueRNA (v1.0.5) Jew et al.105 https://github.com/cozygene/bisque pROC (v1.18.0) Robin et al.106 https://cran.r-project.org/web/packages/ pROC/index.html Other Resource website for the primary breast tumor atlas publication containing dataset and analyses This paper https://github.com/ChanLab-UTSW/ BreastCancer_Integrated Original source dataset of immune cells in primary breast tumors Azizi et al.7 GEO: GSE114727 Original source dataset of primary TNBC tumors Karaayvaz et al.8 GEO: GSE118389 Original source dataset of primary breast tumors Pal et al.9 GEO: GSE161529 Original source dataset of T cells in primary TNBC tumors Savas et al.107 GEO: GSE110686 Original source dataset of primary breast tumors Wu et al.13 GEO: GSE176078 Original source dataset with primary breast tumors Xu et al.14 GEO: GSE180286 Original source dataset with primary breast tumors Qian et al.11 https://lambrechtslab.sites.vib.be/en/ pan-cancer-blueprint-tumourmicroenvironment-0 Original source dataset of primary TNBC tumors Wu et al.12 https://singlecell.broadinstitute.org/ single_cell/study/SCP1106/stromalcell-diversity-associated-withimmune-evasion-in-human-triplenegative-breast-cancer Original source dataset of PD-1 treated primary breast tumors Bassez et al.108 https://lambrechtslab.sites.vib. be/en/single-cell Breast cancer cell line data from DepMap 22Q2 public release Ghandi et al.109 https://depmap.org/portal/download/all/ Spatially resolved data for 6 primary breast tumors Wu et al.12 https://doi.org/10.5281/zenodo.4739739 Spatially resolved data from 5 primary breast tumors 10x Genomics https://www.10xgenomics.com/datasets/human- breast-cancer-ductal-carcinoma-in-situ-invasivecarcinoma-ffpe-1-standard-1-3-0; https://www.10xgenomics.com/datasets/humanbreast-cancer-visium-fresh-frozen-wholetranscriptome-1-standard; https://www.10xgenomics.com/datasets/humanbreast-cancer-block-a-section-1-1-standard-1-1-0; https://www.10xgenomics.com/datasets/humanbreast-cancer-whole-transcriptome-analysis-1standard-1-2-0; https://www.10xgenomics.com/products/xeniumin-situ/preview-dataset-human-breast I-SPY2-990 mRNA and clinical data for I-SPY2 trial Nanda et al.57 GEO: GSE194040 OPEN ACCESS
Multiple Displacement Amplification:Article Title: A comprehensive single-cell breast tumor atlas defines epithelial and immune heterogeneity and interactions predicting anti-PD-1 therapy response.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-huCD56 BV605, Clone HCD56 (mouse IgG1k) BioLegend Cat#318334; RRID: AB_2561912 Chemicals, peptides, and recombinant proteins 40,6-Diamidino-2-Phenylindole, Dihydrochloride (DAPI) Invitrogen Cat#D1306 Dimethyl sulfoxide (DMSO) Sigma Aldrich Cat#D2650 Dulbecco0s Phosphate Buffered Saline (DPBS) Sigma Aldrich Cat#D8537 Fetal Bovine Serum (FBS) Corning Cat#35-011-CV Human IL-2 IS, premium grade Miltenyi Biotec Cat#130-097-746 RPMI-1640 Corning Cat#10-040-CV Penicillin-Streptomycin (100X) Cytiva HyClone Cat#SV30010 Sodium Pyruvate (100 mM) Gibco Cat#11360070 Minimum Essential Media (MEM) non-essential amino acids (NEAA) (100X) Gibco Cat11140050 GlutaMAX Supplement Gibco Cat#35050061 2-mercaptoethanol (50 mM) Gibco Cat#21985023 Critical commercial assays UltraComp eBeads Plus Compensation Beads Invitrogen Cat#01-3333-42 Deposited data Primary breast tumor atlas This paper https://doi.org/10.5281/zenodo.10672250 Experimental models: Cell lines NK-92 ATCC Cat#CRL-2407, RRID: CVCL_2142 BT-474 ATCC Cat#HTB-20, RRID: CVCL_0179 MDA-MB-436 ATCC Cat#HTB-130, RRID: CVCL_0623 K-562 ATCC Cat#CCL-243, RRID: CVCL_0004 Software and algorithms limma (v3.50.1) Ritchie et al.90 https://bioconductor.org/packages/release/ bioc/html/limma.html org.Hs.e.g.,.db (v3.14.0) Carlson et al.91 https://bioconductor.org/packages/release/ data/annotation/html/org.Hs.eg.db.html DoubletFinder (v2.0.3) McGinnis et al.92 https://github.com/chris-mcginnis-ucsf/DoubletFinder Seurat (v4.1.0) Hao et al.93 https://satijalab.org/seurat/ MAST (v1.20.0) Finak et al.94 https://www.bioconductor.org/packages/ release/bioc/html/MAST.html SCTransform (v0.3.2.9008) Hafemeister et al.95 https://github.com/satijalab/sctransform UCell (v1.99.1) Andreatta et al.96 https://github.com/carmonalab/UCell clusterProfiler (v4.2.2) Wu et al.97 https://bioconductor.org/packages/release/ bioc/html/clusterProfiler.html msigdbr (v7.5.1) Dolgalev et al.98 https://cran.r-project.org/web/packages/ msigdbr/vignettes/msigdbr-intro.html TCGAbiolinks (v2.18.0) Colaprico et al.99 https://bioconductor.org/packages/release/ bioc/html/TCGAbiolinks.html DESeq2 (v1.34.0) Love et al.100 https://bioconductor.org/packages/release/ bioc/html/DESeq2.html inferCNV (v.0.99.7) Tickle et al.101 https://github.com/broadinstitute/infercnv ROGUE Liu et al.52 https://github.com/PaulingLiu/ROGUE (Continued on next page) e1 Cell Reports Medicine 5, 101511, May 21, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER cola (v2.0.0) Gu et al.102 https://www.bioconductor.org/packages/ release/bioc/html/cola.html NicheNet (v1.1.0) Browaeys et al.103 https://github.com/saeyslab/nichenetr CellChat (v0.0.1) Jin et al.104 https://github.com/jinworks/CellChat BisqueRNA (v1.0.5) Jew et al.105 https://github.com/cozygene/bisque pROC (v1.18.0) Robin et al.106 https://cran.r-project.org/web/packages/ pROC/index.html Other Resource website for the primary breast tumor atlas publication containing dataset and analyses This paper https://github.com/ChanLab-UTSW/ BreastCancer_Integrated Original source dataset of immune cells in primary breast tumors Azizi et al.7 GEO: GSE114727 Original source dataset of primary TNBC tumors Karaayvaz et al.8 GEO: GSE118389 Original source dataset of primary breast tumors Pal et al.9 GEO: GSE161529 Original source dataset of T cells in primary TNBC tumors Savas et al.107 GEO: GSE110686 Original source dataset of primary breast tumors Wu et al.13 GEO: GSE176078 Original source dataset with primary breast tumors Xu et al.14 GEO: GSE180286 Original source dataset with primary breast tumors Qian et al.11 https://lambrechtslab.sites.vib.be/en/ pan-cancer-blueprint-tumourmicroenvironment-0 Original source dataset of primary TNBC tumors Wu et al.12 https://singlecell.broadinstitute.org/ single_cell/study/SCP1106/stromalcell-diversity-associated-withimmune-evasion-in-human-triplenegative-breast-cancer Original source dataset of PD-1 treated primary breast tumors Bassez et al.108 https://lambrechtslab.sites.vib. be/en/single-cell Breast cancer cell line data from DepMap 22Q2 public release Ghandi et al.109 https://depmap.org/portal/download/all/ Spatially resolved data for 6 primary breast tumors Wu et al.12 https://doi.org/10.5281/zenodo.4739739 Spatially resolved data from 5 primary breast tumors 10x Genomics https://www.10xgenomics.com/datasets/human- breast-cancer-ductal-carcinoma-in-situ-invasivecarcinoma-ffpe-1-standard-1-3-0; https://www.10xgenomics.com/datasets/humanbreast-cancer-visium-fresh-frozen-wholetranscriptome-1-standard; https://www.10xgenomics.com/datasets/humanbreast-cancer-block-a-section-1-1-standard-1-1-0; https://www.10xgenomics.com/datasets/humanbreast-cancer-whole-transcriptome-analysis-1standard-1-2-0; https://www.10xgenomics.com/products/xeniumin-situ/preview-dataset-human-breast I-SPY2-990 mRNA and clinical data for I-SPY2 trial Nanda et al.57 GEO: GSE194040 OPEN ACCESS
Software:Article Title: A comprehensive single-cell breast tumor atlas defines epithelial and immune heterogeneity and interactions predicting anti-PD-1 therapy response.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-huCD56 BV605, Clone HCD56 (mouse IgG1k) BioLegend Cat#318334; RRID: AB_2561912 Chemicals, peptides, and recombinant proteins 40,6-Diamidino-2-Phenylindole, Dihydrochloride (DAPI) Invitrogen Cat#D1306 Dimethyl sulfoxide (DMSO) Sigma Aldrich Cat#D2650 Dulbecco0s Phosphate Buffered Saline (DPBS) Sigma Aldrich Cat#D8537 Fetal Bovine Serum (FBS) Corning Cat#35-011-CV Human IL-2 IS, premium grade Miltenyi Biotec Cat#130-097-746 RPMI-1640 Corning Cat#10-040-CV Penicillin-Streptomycin (100X) Cytiva HyClone Cat#SV30010 Sodium Pyruvate (100 mM) Gibco Cat#11360070 Minimum Essential Media (MEM) non-essential amino acids (NEAA) (100X) Gibco Cat11140050 GlutaMAX Supplement Gibco Cat#35050061 2-mercaptoethanol (50 mM) Gibco Cat#21985023 Critical commercial assays UltraComp eBeads Plus Compensation Beads Invitrogen Cat#01-3333-42 Deposited data Primary breast tumor atlas This paper https://doi.org/10.5281/zenodo.10672250 Experimental models: Cell lines NK-92 ATCC Cat#CRL-2407, RRID: CVCL_2142 BT-474 ATCC Cat#HTB-20, RRID: CVCL_0179 MDA-MB-436 ATCC Cat#HTB-130, RRID: CVCL_0623 K-562 ATCC Cat#CCL-243, RRID: CVCL_0004 Software and algorithms limma (v3.50.1) Ritchie et al.90 https://bioconductor.org/packages/release/ bioc/html/limma.html org.Hs.e.g.,.db (v3.14.0) Carlson et al.91 https://bioconductor.org/packages/release/ data/annotation/html/org.Hs.eg.db.html DoubletFinder (v2.0.3) McGinnis et al.92 https://github.com/chris-mcginnis-ucsf/DoubletFinder Seurat (v4.1.0) Hao et al.93 https://satijalab.org/seurat/ MAST (v1.20.0) Finak et al.94 https://www.bioconductor.org/packages/ release/bioc/html/MAST.html SCTransform (v0.3.2.9008) Hafemeister et al.95 https://github.com/satijalab/sctransform UCell (v1.99.1) Andreatta et al.96 https://github.com/carmonalab/UCell clusterProfiler (v4.2.2) Wu et al.97 https://bioconductor.org/packages/release/ bioc/html/clusterProfiler.html msigdbr (v7.5.1) Dolgalev et al.98 https://cran.r-project.org/web/packages/ msigdbr/vignettes/msigdbr-intro.html TCGAbiolinks (v2.18.0) Colaprico et al.99 https://bioconductor.org/packages/release/ bioc/html/TCGAbiolinks.html DESeq2 (v1.34.0) Love et al.100 https://bioconductor.org/packages/release/ bioc/html/DESeq2.html inferCNV (v.0.99.7) Tickle et al.101 https://github.com/broadinstitute/infercnv ROGUE Liu et al.52 https://github.com/PaulingLiu/ROGUE (Continued on next page) e1 Cell Reports Medicine 5, 101511, May 21, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER cola (v2.0.0) Gu et al.102 https://www.bioconductor.org/packages/ release/bioc/html/cola.html NicheNet (v1.1.0) Browaeys et al.103 https://github.com/saeyslab/nichenetr CellChat (v0.0.1) Jin et al.104 https://github.com/jinworks/CellChat BisqueRNA (v1.0.5) Jew et al.105 https://github.com/cozygene/bisque pROC (v1.18.0) Robin et al.106 https://cran.r-project.org/web/packages/ pROC/index.html Other Resource website for the primary breast tumor atlas publication containing dataset and analyses This paper https://github.com/ChanLab-UTSW/ BreastCancer_Integrated Original source dataset of immune cells in primary breast tumors Azizi et al.7 GEO: GSE114727 Original source dataset of primary TNBC tumors Karaayvaz et al.8 GEO: GSE118389 Original source dataset of primary breast tumors Pal et al.9 GEO: GSE161529 Original source dataset of T cells in primary TNBC tumors Savas et al.107 GEO: GSE110686 Original source dataset of primary breast tumors Wu et al.13 GEO: GSE176078 Original source dataset with primary breast tumors Xu et al.14 GEO: GSE180286 Original source dataset with primary breast tumors Qian et al.11 https://lambrechtslab.sites.vib.be/en/ pan-cancer-blueprint-tumourmicroenvironment-0 Original source dataset of primary TNBC tumors Wu et al.12 https://singlecell.broadinstitute.org/ single_cell/study/SCP1106/stromalcell-diversity-associated-withimmune-evasion-in-human-triplenegative-breast-cancer Original source dataset of PD-1 treated primary breast tumors Bassez et al.108 https://lambrechtslab.sites.vib. be/en/single-cell Breast cancer cell line data from DepMap 22Q2 public release Ghandi et al.109 https://depmap.org/portal/download/all/ Spatially resolved data for 6 primary breast tumors Wu et al.12 https://doi.org/10.5281/zenodo.4739739 Spatially resolved data from 5 primary breast tumors 10x Genomics https://www.10xgenomics.com/datasets/human- breast-cancer-ductal-carcinoma-in-situ-invasivecarcinoma-ffpe-1-standard-1-3-0; https://www.10xgenomics.com/datasets/humanbreast-cancer-visium-fresh-frozen-wholetranscriptome-1-standard; https://www.10xgenomics.com/datasets/humanbreast-cancer-block-a-section-1-1-standard-1-1-0; https://www.10xgenomics.com/datasets/humanbreast-cancer-whole-transcriptome-analysis-1standard-1-2-0; https://www.10xgenomics.com/products/xeniumin-situ/preview-dataset-human-breast I-SPY2-990 mRNA and clinical data for I-SPY2 trial Nanda et al.57 GEO: GSE194040 OPEN ACCESS
Cell Culture:Article Title: Transformer-based modeling of Clonal Selection and Expression Dynamics (TraCSED) reveals resistance signatures in breast cancer
Article Snippet: .. T-47D (female, adenocarcinoma from pleura) ER+ breast cancer cell lines were cultured using standard aseptic tissue culture techniques at 37°C in RPMI medium supplemented with 10% FBS, 2mM L-Glutamine (Catalog 10440, Sigma), 1X Minimum Essential Media, Non-Essential Amino Acids (MEM NEAA, Catalog No. 11140-0500, Thermo Fisher) and 1X Antibiotic-Antimycotic (Catalog No.15240-112, Thermo Fisher). .. Cell line ancestry was determined using Short Tandem Repeat (STR) profiling using the Promega PowerPlex 16 System.
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