Virus:Article Title: Challenging the Control through a Single-Cell Perspective on Normal Adjacent Tissue in Colorectal Cancer
Article Snippet: .. Jo urn al Pr e-p roo f Key resources table REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Bacterial and virus strains Biological samples Patient-derived CRC organoids Dr. Margarete FischerBosch Institute of Clinical Pharmacology, Bosch Health Campus N/A Chemicals, peptides, and recombinant proteins Critical commercial assays Deposited data Bulk RNAseq data Gene Expression Omnibus (GEO) database GSE95132, GSE158164 Microarray data Gene Expression Omnibus (GEO) database GSE90627 Jo urn al Pr e-p roo f scRNAseq data Gene Expression Omnibus (GEO) database GSE214695, GSE132465, GSE178341, GSE231993 Experimental models: Cell lines Human CRC cell line HCT116 ATCC CCL-247 Human CRC cell line HT29 ATCC HTB-38 Human CRC cell line Colo205 ATCC CCL-222 Experimental models: Organisms/strains Oligonucleotides Primer: RNA18SN1 forward 5’- ACTGCCATTAAGGGTGTGGG-3’ This paper N/A Primer: RNA18SN1 reverse 5’- CAGGTCTTCACGGAGCTTGT-3’ This paper N/A Primer: RPS19 forward 5’- GCCTGGAGTTACTGTAAAAGACG-3’ This paper N/A Primer: RPS19 reverse 5’- CCCATAGATCTTGGTCATGGAGC-3’ This paper N/A Primer: RPL30 forward 5’- TACGTCCTGGGGTACAAGCA-3’ This paper N/A Primer: RPL30 reverse 5’- AAAGCTGGGCAGTTGTTAGC-3’ This paper N/A Primer: RPS18 forward 5’- TGTGGTGTTGAGGAAAGCA-3’ This paper N/A Primer: RPS18 reverse 5’- CTTCAGTCGCTCCAGGTCTT-3’ This paper N/A Primer: RPS27A forward 5’- CTGGAAGATGGACGTACTTTGTC-3’ This paper N/A Primer: RPS27A reverse 5’- CGACGAAGGCGACTAATTTTGC-3’ This paper N/A Recombinant DNA Software and algorithms Jo urn al Pr e-p roo f edgeR (v3.38.4). .. Yunshun Chen https://bioconductor. org/packages/releas e/bioc/html/edgeR.ht ml DESeq2 (v1.36.0 and v2.11.40.8) Michael Love https://bioconductor. org/packages/releas e/bioc/html/DESeq2. html GSEABase (v1.58.0) Martin Morgan https://bioconductor. org/packages/releas e/bioc/html/GSEABa se.html ggplot2 (v3.4.0 and v3.4.1 and v3.4.3) Wickham H https://ggplot2.tidyve rse.org/ MuSiC (v1.0.0) Wang et al. (2019)28 Fan et al. (2022)29 https://github.com/xu ranw/MuSiC FastQC (v0.74) Andrews S https://github.com/sandrews/FastQC FASTQ Trimmer (v1.1.5) Gordon A https://github.com/au erlab/fastq-trim fastp (v0.23.2) Shifu Chen https://github.com/O penGene/fastp RNA STAR (v2.7.10b) Alexander Dobin https://github.com/al exdobin/STAR?tab=r eadme-ov-file htseq-count (v0.9.1) Anders S https://htseq.readthe docs.io/en/release_0 .10.0/overview.html Galaxy Project Europe platform Afgan E https://github.com/ga laxyproject RStudio (v4.2.1) R project https://github.com/rst udio/rstudio RColorBrewer (v1.1-3) Erich Neuwirth https://cran.rproject.org/web/pack ages/RColorBrewer/i ndex.html PCAtools (v2.8.0).
Recombinant:Article Title: Challenging the Control through a Single-Cell Perspective on Normal Adjacent Tissue in Colorectal Cancer
Article Snippet: .. Jo urn al Pr e-p roo f Key resources table REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Bacterial and virus strains Biological samples Patient-derived CRC organoids Dr. Margarete FischerBosch Institute of Clinical Pharmacology, Bosch Health Campus N/A Chemicals, peptides, and recombinant proteins Critical commercial assays Deposited data Bulk RNAseq data Gene Expression Omnibus (GEO) database GSE95132, GSE158164 Microarray data Gene Expression Omnibus (GEO) database GSE90627 Jo urn al Pr e-p roo f scRNAseq data Gene Expression Omnibus (GEO) database GSE214695, GSE132465, GSE178341, GSE231993 Experimental models: Cell lines Human CRC cell line HCT116 ATCC CCL-247 Human CRC cell line HT29 ATCC HTB-38 Human CRC cell line Colo205 ATCC CCL-222 Experimental models: Organisms/strains Oligonucleotides Primer: RNA18SN1 forward 5’- ACTGCCATTAAGGGTGTGGG-3’ This paper N/A Primer: RNA18SN1 reverse 5’- CAGGTCTTCACGGAGCTTGT-3’ This paper N/A Primer: RPS19 forward 5’- GCCTGGAGTTACTGTAAAAGACG-3’ This paper N/A Primer: RPS19 reverse 5’- CCCATAGATCTTGGTCATGGAGC-3’ This paper N/A Primer: RPL30 forward 5’- TACGTCCTGGGGTACAAGCA-3’ This paper N/A Primer: RPL30 reverse 5’- AAAGCTGGGCAGTTGTTAGC-3’ This paper N/A Primer: RPS18 forward 5’- TGTGGTGTTGAGGAAAGCA-3’ This paper N/A Primer: RPS18 reverse 5’- CTTCAGTCGCTCCAGGTCTT-3’ This paper N/A Primer: RPS27A forward 5’- CTGGAAGATGGACGTACTTTGTC-3’ This paper N/A Primer: RPS27A reverse 5’- CGACGAAGGCGACTAATTTTGC-3’ This paper N/A Recombinant DNA Software and algorithms Jo urn al Pr e-p roo f edgeR (v3.38.4). .. Yunshun Chen https://bioconductor. org/packages/releas e/bioc/html/edgeR.ht ml DESeq2 (v1.36.0 and v2.11.40.8) Michael Love https://bioconductor. org/packages/releas e/bioc/html/DESeq2. html GSEABase (v1.58.0) Martin Morgan https://bioconductor. org/packages/releas e/bioc/html/GSEABa se.html ggplot2 (v3.4.0 and v3.4.1 and v3.4.3) Wickham H https://ggplot2.tidyve rse.org/ MuSiC (v1.0.0) Wang et al. (2019)28 Fan et al. (2022)29 https://github.com/xu ranw/MuSiC FastQC (v0.74) Andrews S https://github.com/sandrews/FastQC FASTQ Trimmer (v1.1.5) Gordon A https://github.com/au erlab/fastq-trim fastp (v0.23.2) Shifu Chen https://github.com/O penGene/fastp RNA STAR (v2.7.10b) Alexander Dobin https://github.com/al exdobin/STAR?tab=r eadme-ov-file htseq-count (v0.9.1) Anders S https://htseq.readthe docs.io/en/release_0 .10.0/overview.html Galaxy Project Europe platform Afgan E https://github.com/ga laxyproject RStudio (v4.2.1) R project https://github.com/rst udio/rstudio RColorBrewer (v1.1-3) Erich Neuwirth https://cran.rproject.org/web/pack ages/RColorBrewer/i ndex.html PCAtools (v2.8.0).
RNA sequencing:Article Title: Challenging the Control through a Single-Cell Perspective on Normal Adjacent Tissue in Colorectal Cancer
Article Snippet: .. Jo urn al Pr e-p roo f Key resources table REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Bacterial and virus strains Biological samples Patient-derived CRC organoids Dr. Margarete FischerBosch Institute of Clinical Pharmacology, Bosch Health Campus N/A Chemicals, peptides, and recombinant proteins Critical commercial assays Deposited data Bulk RNAseq data Gene Expression Omnibus (GEO) database GSE95132, GSE158164 Microarray data Gene Expression Omnibus (GEO) database GSE90627 Jo urn al Pr e-p roo f scRNAseq data Gene Expression Omnibus (GEO) database GSE214695, GSE132465, GSE178341, GSE231993 Experimental models: Cell lines Human CRC cell line HCT116 ATCC CCL-247 Human CRC cell line HT29 ATCC HTB-38 Human CRC cell line Colo205 ATCC CCL-222 Experimental models: Organisms/strains Oligonucleotides Primer: RNA18SN1 forward 5’- ACTGCCATTAAGGGTGTGGG-3’ This paper N/A Primer: RNA18SN1 reverse 5’- CAGGTCTTCACGGAGCTTGT-3’ This paper N/A Primer: RPS19 forward 5’- GCCTGGAGTTACTGTAAAAGACG-3’ This paper N/A Primer: RPS19 reverse 5’- CCCATAGATCTTGGTCATGGAGC-3’ This paper N/A Primer: RPL30 forward 5’- TACGTCCTGGGGTACAAGCA-3’ This paper N/A Primer: RPL30 reverse 5’- AAAGCTGGGCAGTTGTTAGC-3’ This paper N/A Primer: RPS18 forward 5’- TGTGGTGTTGAGGAAAGCA-3’ This paper N/A Primer: RPS18 reverse 5’- CTTCAGTCGCTCCAGGTCTT-3’ This paper N/A Primer: RPS27A forward 5’- CTGGAAGATGGACGTACTTTGTC-3’ This paper N/A Primer: RPS27A reverse 5’- CGACGAAGGCGACTAATTTTGC-3’ This paper N/A Recombinant DNA Software and algorithms Jo urn al Pr e-p roo f edgeR (v3.38.4). .. Yunshun Chen https://bioconductor. org/packages/releas e/bioc/html/edgeR.ht ml DESeq2 (v1.36.0 and v2.11.40.8) Michael Love https://bioconductor. org/packages/releas e/bioc/html/DESeq2. html GSEABase (v1.58.0) Martin Morgan https://bioconductor. org/packages/releas e/bioc/html/GSEABa se.html ggplot2 (v3.4.0 and v3.4.1 and v3.4.3) Wickham H https://ggplot2.tidyve rse.org/ MuSiC (v1.0.0) Wang et al. (2019)28 Fan et al. (2022)29 https://github.com/xu ranw/MuSiC FastQC (v0.74) Andrews S https://github.com/sandrews/FastQC FASTQ Trimmer (v1.1.5) Gordon A https://github.com/au erlab/fastq-trim fastp (v0.23.2) Shifu Chen https://github.com/O penGene/fastp RNA STAR (v2.7.10b) Alexander Dobin https://github.com/al exdobin/STAR?tab=r eadme-ov-file htseq-count (v0.9.1) Anders S https://htseq.readthe docs.io/en/release_0 .10.0/overview.html Galaxy Project Europe platform Afgan E https://github.com/ga laxyproject RStudio (v4.2.1) R project https://github.com/rst udio/rstudio RColorBrewer (v1.1-3) Erich Neuwirth https://cran.rproject.org/web/pack ages/RColorBrewer/i ndex.html PCAtools (v2.8.0).
Gene Expression:Article Title: Challenging the Control through a Single-Cell Perspective on Normal Adjacent Tissue in Colorectal Cancer
Article Snippet: .. Jo urn al Pr e-p roo f Key resources table REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Bacterial and virus strains Biological samples Patient-derived CRC organoids Dr. Margarete FischerBosch Institute of Clinical Pharmacology, Bosch Health Campus N/A Chemicals, peptides, and recombinant proteins Critical commercial assays Deposited data Bulk RNAseq data Gene Expression Omnibus (GEO) database GSE95132, GSE158164 Microarray data Gene Expression Omnibus (GEO) database GSE90627 Jo urn al Pr e-p roo f scRNAseq data Gene Expression Omnibus (GEO) database GSE214695, GSE132465, GSE178341, GSE231993 Experimental models: Cell lines Human CRC cell line HCT116 ATCC CCL-247 Human CRC cell line HT29 ATCC HTB-38 Human CRC cell line Colo205 ATCC CCL-222 Experimental models: Organisms/strains Oligonucleotides Primer: RNA18SN1 forward 5’- ACTGCCATTAAGGGTGTGGG-3’ This paper N/A Primer: RNA18SN1 reverse 5’- CAGGTCTTCACGGAGCTTGT-3’ This paper N/A Primer: RPS19 forward 5’- GCCTGGAGTTACTGTAAAAGACG-3’ This paper N/A Primer: RPS19 reverse 5’- CCCATAGATCTTGGTCATGGAGC-3’ This paper N/A Primer: RPL30 forward 5’- TACGTCCTGGGGTACAAGCA-3’ This paper N/A Primer: RPL30 reverse 5’- AAAGCTGGGCAGTTGTTAGC-3’ This paper N/A Primer: RPS18 forward 5’- TGTGGTGTTGAGGAAAGCA-3’ This paper N/A Primer: RPS18 reverse 5’- CTTCAGTCGCTCCAGGTCTT-3’ This paper N/A Primer: RPS27A forward 5’- CTGGAAGATGGACGTACTTTGTC-3’ This paper N/A Primer: RPS27A reverse 5’- CGACGAAGGCGACTAATTTTGC-3’ This paper N/A Recombinant DNA Software and algorithms Jo urn al Pr e-p roo f edgeR (v3.38.4). .. Yunshun Chen https://bioconductor. org/packages/releas e/bioc/html/edgeR.ht ml DESeq2 (v1.36.0 and v2.11.40.8) Michael Love https://bioconductor. org/packages/releas e/bioc/html/DESeq2. html GSEABase (v1.58.0) Martin Morgan https://bioconductor. org/packages/releas e/bioc/html/GSEABa se.html ggplot2 (v3.4.0 and v3.4.1 and v3.4.3) Wickham H https://ggplot2.tidyve rse.org/ MuSiC (v1.0.0) Wang et al. (2019)28 Fan et al. (2022)29 https://github.com/xu ranw/MuSiC FastQC (v0.74) Andrews S https://github.com/sandrews/FastQC FASTQ Trimmer (v1.1.5) Gordon A https://github.com/au erlab/fastq-trim fastp (v0.23.2) Shifu Chen https://github.com/O penGene/fastp RNA STAR (v2.7.10b) Alexander Dobin https://github.com/al exdobin/STAR?tab=r eadme-ov-file htseq-count (v0.9.1) Anders S https://htseq.readthe docs.io/en/release_0 .10.0/overview.html Galaxy Project Europe platform Afgan E https://github.com/ga laxyproject RStudio (v4.2.1) R project https://github.com/rst udio/rstudio RColorBrewer (v1.1-3) Erich Neuwirth https://cran.rproject.org/web/pack ages/RColorBrewer/i ndex.html PCAtools (v2.8.0).
Microarray:Article Title: Challenging the Control through a Single-Cell Perspective on Normal Adjacent Tissue in Colorectal Cancer
Article Snippet: .. Jo urn al Pr e-p roo f Key resources table REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Bacterial and virus strains Biological samples Patient-derived CRC organoids Dr. Margarete FischerBosch Institute of Clinical Pharmacology, Bosch Health Campus N/A Chemicals, peptides, and recombinant proteins Critical commercial assays Deposited data Bulk RNAseq data Gene Expression Omnibus (GEO) database GSE95132, GSE158164 Microarray data Gene Expression Omnibus (GEO) database GSE90627 Jo urn al Pr e-p roo f scRNAseq data Gene Expression Omnibus (GEO) database GSE214695, GSE132465, GSE178341, GSE231993 Experimental models: Cell lines Human CRC cell line HCT116 ATCC CCL-247 Human CRC cell line HT29 ATCC HTB-38 Human CRC cell line Colo205 ATCC CCL-222 Experimental models: Organisms/strains Oligonucleotides Primer: RNA18SN1 forward 5’- ACTGCCATTAAGGGTGTGGG-3’ This paper N/A Primer: RNA18SN1 reverse 5’- CAGGTCTTCACGGAGCTTGT-3’ This paper N/A Primer: RPS19 forward 5’- GCCTGGAGTTACTGTAAAAGACG-3’ This paper N/A Primer: RPS19 reverse 5’- CCCATAGATCTTGGTCATGGAGC-3’ This paper N/A Primer: RPL30 forward 5’- TACGTCCTGGGGTACAAGCA-3’ This paper N/A Primer: RPL30 reverse 5’- AAAGCTGGGCAGTTGTTAGC-3’ This paper N/A Primer: RPS18 forward 5’- TGTGGTGTTGAGGAAAGCA-3’ This paper N/A Primer: RPS18 reverse 5’- CTTCAGTCGCTCCAGGTCTT-3’ This paper N/A Primer: RPS27A forward 5’- CTGGAAGATGGACGTACTTTGTC-3’ This paper N/A Primer: RPS27A reverse 5’- CGACGAAGGCGACTAATTTTGC-3’ This paper N/A Recombinant DNA Software and algorithms Jo urn al Pr e-p roo f edgeR (v3.38.4). .. Yunshun Chen https://bioconductor. org/packages/releas e/bioc/html/edgeR.ht ml DESeq2 (v1.36.0 and v2.11.40.8) Michael Love https://bioconductor. org/packages/releas e/bioc/html/DESeq2. html GSEABase (v1.58.0) Martin Morgan https://bioconductor. org/packages/releas e/bioc/html/GSEABa se.html ggplot2 (v3.4.0 and v3.4.1 and v3.4.3) Wickham H https://ggplot2.tidyve rse.org/ MuSiC (v1.0.0) Wang et al. (2019)28 Fan et al. (2022)29 https://github.com/xu ranw/MuSiC FastQC (v0.74) Andrews S https://github.com/sandrews/FastQC FASTQ Trimmer (v1.1.5) Gordon A https://github.com/au erlab/fastq-trim fastp (v0.23.2) Shifu Chen https://github.com/O penGene/fastp RNA STAR (v2.7.10b) Alexander Dobin https://github.com/al exdobin/STAR?tab=r eadme-ov-file htseq-count (v0.9.1) Anders S https://htseq.readthe docs.io/en/release_0 .10.0/overview.html Galaxy Project Europe platform Afgan E https://github.com/ga laxyproject RStudio (v4.2.1) R project https://github.com/rst udio/rstudio RColorBrewer (v1.1-3) Erich Neuwirth https://cran.rproject.org/web/pack ages/RColorBrewer/i ndex.html PCAtools (v2.8.0).
Software:Article Title: Challenging the Control through a Single-Cell Perspective on Normal Adjacent Tissue in Colorectal Cancer
Article Snippet: .. Jo urn al Pr e-p roo f Key resources table REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Bacterial and virus strains Biological samples Patient-derived CRC organoids Dr. Margarete FischerBosch Institute of Clinical Pharmacology, Bosch Health Campus N/A Chemicals, peptides, and recombinant proteins Critical commercial assays Deposited data Bulk RNAseq data Gene Expression Omnibus (GEO) database GSE95132, GSE158164 Microarray data Gene Expression Omnibus (GEO) database GSE90627 Jo urn al Pr e-p roo f scRNAseq data Gene Expression Omnibus (GEO) database GSE214695, GSE132465, GSE178341, GSE231993 Experimental models: Cell lines Human CRC cell line HCT116 ATCC CCL-247 Human CRC cell line HT29 ATCC HTB-38 Human CRC cell line Colo205 ATCC CCL-222 Experimental models: Organisms/strains Oligonucleotides Primer: RNA18SN1 forward 5’- ACTGCCATTAAGGGTGTGGG-3’ This paper N/A Primer: RNA18SN1 reverse 5’- CAGGTCTTCACGGAGCTTGT-3’ This paper N/A Primer: RPS19 forward 5’- GCCTGGAGTTACTGTAAAAGACG-3’ This paper N/A Primer: RPS19 reverse 5’- CCCATAGATCTTGGTCATGGAGC-3’ This paper N/A Primer: RPL30 forward 5’- TACGTCCTGGGGTACAAGCA-3’ This paper N/A Primer: RPL30 reverse 5’- AAAGCTGGGCAGTTGTTAGC-3’ This paper N/A Primer: RPS18 forward 5’- TGTGGTGTTGAGGAAAGCA-3’ This paper N/A Primer: RPS18 reverse 5’- CTTCAGTCGCTCCAGGTCTT-3’ This paper N/A Primer: RPS27A forward 5’- CTGGAAGATGGACGTACTTTGTC-3’ This paper N/A Primer: RPS27A reverse 5’- CGACGAAGGCGACTAATTTTGC-3’ This paper N/A Recombinant DNA Software and algorithms Jo urn al Pr e-p roo f edgeR (v3.38.4). .. Yunshun Chen https://bioconductor. org/packages/releas e/bioc/html/edgeR.ht ml DESeq2 (v1.36.0 and v2.11.40.8) Michael Love https://bioconductor. org/packages/releas e/bioc/html/DESeq2. html GSEABase (v1.58.0) Martin Morgan https://bioconductor. org/packages/releas e/bioc/html/GSEABa se.html ggplot2 (v3.4.0 and v3.4.1 and v3.4.3) Wickham H https://ggplot2.tidyve rse.org/ MuSiC (v1.0.0) Wang et al. (2019)28 Fan et al. (2022)29 https://github.com/xu ranw/MuSiC FastQC (v0.74) Andrews S https://github.com/sandrews/FastQC FASTQ Trimmer (v1.1.5) Gordon A https://github.com/au erlab/fastq-trim fastp (v0.23.2) Shifu Chen https://github.com/O penGene/fastp RNA STAR (v2.7.10b) Alexander Dobin https://github.com/al exdobin/STAR?tab=r eadme-ov-file htseq-count (v0.9.1) Anders S https://htseq.readthe docs.io/en/release_0 .10.0/overview.html Galaxy Project Europe platform Afgan E https://github.com/ga laxyproject RStudio (v4.2.1) R project https://github.com/rst udio/rstudio RColorBrewer (v1.1-3) Erich Neuwirth https://cran.rproject.org/web/pack ages/RColorBrewer/i ndex.html PCAtools (v2.8.0).
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