Multiple Displacement Amplification:Article Title: An omic and multidimensional spatial atlas from serial biopsies of an evolving metastatic breast cancer
Article Snippet: .. Participant ID: HTA9_1; https:// idp.tissue-atlas.org/ Experimental models: Cell lines Human MCF7 Characterized Cell Line Core (MDACC) https://www.atcc.org/products/ all/HTB-22.aspx; RRID: CVCL_0031 Human MDA-MB-468 Characterized Cell Line Core (MDACC) https://www.atcc.org/products/ all/HTB-132.aspx; RRID: CVCL_0419 Human MDA-MB-231 ATCC https://www.atcc.org/products/ all/HTB-26.aspx#generalinformation; RRID: CVCL_0062 Human BT474 ATCC https://www.atcc.org/products/ all/HTB-20.aspx; RRID: CVCL_0179 Human HCC1954 ATCC https://www.atcc.org/products/crl-2338; RRID: CVCL_1259 Human SKBR3 ATCC RRID: CVCL_0033; https://www.atcc.org/ products/htb-30 HCC1143 ATCC RRID: CVCL_1245; https://www.atcc.org/ products/crl-2321 HCC3153 UT-Southwestern RRID: CVCL_3377 T47D ATCC RRID: CVCL_0553; https://www.atcc.org/ products/htb-133 AU565 ATCC RRID: CVCL_1074; https://www.atcc.org/ products/crl-2351 (Continued on next page) e4 Cell Reports Medicine 3, 100525, February 15, 2022 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER MDAMB436 ATCC RRID: CVCL_0623; https://www.atcc.org/ products/htb-130 Oligonucleotides See Table S2 This paper N/A Software and algorithms LabVantage LabVantage Solutions Inc. https://www.labvantage.com/ LabKey 74 https://www.labkey.com/ Removal of Unwanted Variation (RUV-III) 111 https://cran.r-project.org/package=ruv Removal of Unwanted Variation (RUVSeq) 105 https://bioconductor.org/packages/ release/bioc/html/RUVSeq.html MATLAB MathWorks https://www.mathworks.com/ products/matlab.html syngo.via Siemens Healthcare GmbH https://www.siemens- healthineers.com/en-us/ molecular-imaging/pet-ct/syngo-via Horos Nimble Co LLC https://horosproject.org/download-horos/ Cluster 3.0 110 http://bonsai.hgc.jp/ mdehoon/software/ cluster/software.htm TreeView 109 http://jtreeview.sourceforge.net/ MATLAB, Computer vision toolbox MathWorks https://www.mathworks.com/help/vision/ SURF algorithm (for MATLAB) 113 https://www.mathworks.com/help/vision/ ref/detectsurffeatures.html ImageJ 81 https://imagej.nih.gov/ij/ RGB to CMYK (FIJI Plugin) 81 https://imagej.net/tutorials/rgb-to-cmyk CellProfiler 3.0 114 https://cellprofiler.org/ FCS Express Image Cytometry RUO DeNovo Software https://denovosoftware.com/ mpileup (Samtools) 90 http://samtools.sourceforge.net/ BWA-MEM 87 http://bio-bwa.sourceforge.net/ GATK 88 https://gatk.broadinstitute.org/hc/en-us Galaxy 75 https://galaxyproject.org/ ape 91 http://ape-package.ird.fr/ CNVkit 92 https://github.com/etal/cnvkit Trim Galore Babraham Institute https://www.bioinformatics. babraham.ac.uk/projects/trim_galore/ Kallisto 101 https://github.com/pachterlab/kallisto tximport 103 https://bioconductor.org/packages/ release/bioc/html/tximport.html SVA/Combat 106 https://bioconductor.org/packages/ release/bioc/html/sva.html GSVA 17 https://www.bioconductor.org/ packages/release/bioc/html/GSVA.html Pathway Commons 24 https://www.pathwaycommons.org/ Transcriptional Regulator Analysis This work. https://dx.doi.org/10.5281/zenodo.
Article Title: An omic and multidimensional spatial atlas from serial biopsies of an evolving metastatic breast cancer.
Article Snippet: .. Participant ID: HTA9_1; https:// idp.tissue-atlas.org/ Experimental models: Cell lines Human MCF7 Characterized Cell Line Core (MDACC) https://www.atcc.org/products/ all/HTB-22.aspx; RRID: CVCL_0031 Human MDA-MB-468 Characterized Cell Line Core (MDACC) https://www.atcc.org/products/ all/HTB-132.aspx; RRID: CVCL_0419 Human MDA-MB-231 ATCC https://www.atcc.org/products/ all/HTB-26.aspx#generalinformation; RRID: CVCL_0062 Human BT474 ATCC https://www.atcc.org/products/ all/HTB-20.aspx; RRID: CVCL_0179 Human HCC1954 ATCC https://www.atcc.org/products/crl-2338; RRID: CVCL_1259 Human SKBR3 ATCC RRID: CVCL_0033; https://www.atcc.org/ products/htb-30 HCC1143 ATCC RRID: CVCL_1245; https://www.atcc.org/ products/crl-2321 HCC3153 UT-Southwestern RRID: CVCL_3377 T47D ATCC RRID: CVCL_0553; https://www.atcc.org/ products/htb-133 AU565 ATCC RRID: CVCL_1074; https://www.atcc.org/ products/crl-2351 (Continued on next page) e4 Cell Reports Medicine 3, 100525, February 15, 2022 .. REAGENT or RESOURCE SOURCE IDENTIFIER MDAMB436 ATCC RRID: CVCL_0623; https://www.atcc.org/ products/htb-130 Oligonucleotides See Table S2 This paper N/A Software and algorithms LabVantage LabVantage Solutions Inc. https://www.labvantage.com/ LabKey 74 https://www.labkey.com/ Removal of Unwanted Variation (RUV-III) 111 https://cran.r-project.org/package=ruv Removal of Unwanted Variation (RUVSeq) 105 https://bioconductor.org/packages/ release/bioc/html/RUVSeq.html MATLAB MathWorks https://www.mathworks.com/ products/matlab.html syngo.via Siemens Healthcare GmbH https://www.siemens- healthineers.com/en-us/ molecular-imaging/pet-ct/syngo-via Horos Nimble Co LLC https://horosproject.org/download-horos/ Cluster 3.0 110 http://bonsai.hgc.jp/ mdehoon/software/ cluster/software.htm TreeView 109 http://jtreeview.sourceforge.net/ MATLAB, Computer vision toolbox MathWorks https://www.mathworks.com/help/vision/ SURF algorithm (for MATLAB) 113 https://www.mathworks.com/help/vision/ ref/detectsurffeatures.html ImageJ 81 https://imagej.nih.gov/ij/ RGB to CMYK (FIJI Plugin) 81 https://imagej.net/tutorials/rgb-to-cmyk CellProfiler 3.0 114 https://cellprofiler.org/ FCS Express Image Cytometry RUO DeNovo Software https://denovosoftware.com/ mpileup (Samtools) 90 http://samtools.sourceforge.net/ BWA-MEM 87 http://bio-bwa.sourceforge.net/ GATK 88 https://gatk.broadinstitute.org/hc/en-us Galaxy 75 https://galaxyproject.org/ ape 91 http://ape-package.ird.fr/ CNVkit 92 https://github.com/etal/cnvkit Trim Galore Babraham Institute https://www.bioinformatics. babraham.ac.uk/projects/trim_galore/ Kallisto 101 https://github.com/pachterlab/kallisto tximport 103 https://bioconductor.org/packages/ release/bioc/html/tximport.html SVA/Combat 106 https://bioconductor.org/packages/ release/bioc/html/sva.html GSVA 17 https://www.bioconductor.org/ packages/release/bioc/html/GSVA.html Pathway Commons 24 https://www.pathwaycommons.org/ Transcriptional Regulator Analysis This work. https://dx.doi.org/10.5281/zenodo.
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