Transcriptomics:Article Title: Nova-ST: Nano-patterned ultra-dense platform for spatial transcriptomics.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Stereo-seq Permeabilization kit BGI STomics Catalog #111KP118 Stereo-seq Chip P (1cm*1cm) BGI STomics Catalog #111CP118 Stereo-seq Transcriptomics T kit BGI STomics Catalog #111KT114 Stereo-seq Chip T (1cm*1cm) BGI STomics Catalog #110CT114 Stereo-seq Library Prep kit BGI STomics Catalog #111KL114 2100 Bioanalyzer – High sensitivity DNA analysis Agilent Technologies Catalog #G2939BA QubitTM dsDNA Quantification Assay Kits Thermo Fisher Scientific Catalog #Q32851 QubitTM ssDNA Assay Kit Thermo Fisher Scientific Catalog #Q10212 innuPREP mini RNA kit Analytik Jena Catalog # AJ 845-KS-2040250 Deposited data Nova-ST Data (Mouse Brain) This study GEO: GSE256318 Stereo-seq (Mouse Brain) This study GEO: GSE256319 Stereo-seq (Mouse Brain) Chen et al. (2022)8 CNGB: CNS0390078 Stereo-seq (Mouse Brain) You et al. (2023)20 https://www.genographix.com Slideseq-v2 (Mouse Hippocampus) Stickels et al. (2021)6 https://singlecell.broadinstitute.org/ single_cell/study/SCP815 10X Genomics and SMART-seq2 (Mouse Brain) Yao et al. (Cell)19 https://portal.brain-map.org/ atlases-and-data/rnaseq/mousewhole-cortex-and-hippocampus-10x Experimental models: Organisms/strains Six to eight weeks old mice (C57BL/6J) JAX MGI:3028467 Oligonucleotides HDMI-DraI32 IDT Technologies (Standard desalted) CAAGCAGAAGACGGCATACGAGA TTCTTTCCCTACACGACGCTCTTCC GATCTNNVNNVNNVNNVNNVNNNN NTCTTGTGACTACAGCACCCTCGA CTCTCGCTTTTTTTTTTTTTTTTTTTT TTTTTTTTTTAAAGACTTTCACCAGT CCATGATGTGTAGATCTCGGTGG TCGCCGTATCATT Read1-DraI32 IDT Technologies (PAGE purification) ATCATGGACTGGTGAAAGTCTTTA AAAAAAAAAAAAAAAAAAAAAAAA AAAAAGCGAGAGTCGAGGGTG CTGTAGTCACAAGA RPE_Randomer IDT Technologies (Standard desalted) TCAGACGTGTGCTCTTCCGA TCTNNNGGNNNB RPEPCR_Fwd IDT Technologies (Standard desalted) TCTTTCCCTACACGACGC*T*C RPEPCR_Rev IDT Technologies (Standard desalted) TCAGACGTGTGCTCTTCC*G*A P5_WTA_TCAAGCGA IDT Technologies (Standard desalted) AATGATACGGCGACCACCGAG ATCTACACTCAAGCGAACACTC TTTCCCTACACGACGCTC TTCCGATCT P5_WTA_ GTAGCTGA IDT Technologies (Standard desalted) AATGATACGGCGACCACCGAGA TCTACACGTAGCTGAACACTCTTT CCCTACACGACGCTCTTCCGATCT P5_WTA_ CCAACCAA IDT Technologies (Standard desalted) AATGATACGGCGACCACCGAGA TCTACACCCAACCAAACACTCTT TCCCTACACGACGCTCTTCCGATCT P5_WTA_ AACGTTGG IDT Technologies (Standard desalted) AATGATACGGCGACCACCGA GATCTACACAACGTTGGACAC TCTTTCCCTACACGACGC TCTTCCGATCT (Continued on next page) e2 Cell Reports Methods 4, 100831, August 19, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER P5_WTA_ ACCAATCG IDT Technologies (Standard desalted) AATGATACGGCGACCACCGAG ATCTACACACCAATCGACACT CTTTCCCTACACGACGCT CTTCCGATCT P7_WTA_ CCGCGGTT IDT Technologies (Standard desalted) CAAGCAGAAGACGGCATACGA GATCCGCGGTTGTGACTGGAG TTCAGACGTGTGCTCTTCC*G*A P7_WTA_ TTATAACC IDT Technologies (Standard desalted) CAAGCAGAAGACGGCATACGA GATTTATAACCGTGACTGGAGT TCAGACGTGTGCTCTTCC*G*A P7_WTA_ GGACTTGG IDT Technologies (Standard desalted) CAAGCAGAAGACGGCATACGA GATGGACTTGGGTGACTGGAG TTCAGACGTGTGCTCTTCC*G*A P7_WTA_ AAGTCCAA IDT Technologies (Standard desalted) CAAGCAGAAGACGGCATACGA GATAAGTCCAAGTGACTGGAG TTCAGACGTGTGCTCTTCC*G*A P7_WTA_ ATCCACTG IDT Technologies (Standard desalted) CAAGCAGAAGACGGCATACGA GATATCCACTGGTGACTGGAG TTCAGACGTGTGCTCTTCC*G*A Software and algorithms Nova-ST Analysis Pipeline/Notebooks This study https://github.com/aertslab/Nova-ST https://doi.org/10.5281/ zenodo.12608945 Carbide Create https://carbide3d.com/ N/A Carbide Motion https://carbide3d.com/ N/A bcl2fastq2 (v2.20.0) Illumina https://emea.support.illumina.com/ downloads/bcl2fastq-conversionsoftware-v2-20.html RRID:SCR_015058 Sequence Analysis Viewer (v3.0) Illumina https://emea.support.illumina.com/ sequencing/sequencing_software/ sequencing_analysis_viewer_sav.html Python (v3.8.10) Python Software Foundation https://www.python.org/ RRID:SCR_008394 OpenCV (v4.2.0) OpenCV Team https://opencv.org/RRID:SCR_015526 STARsolo (2.7.10b) Dobin et al. (2013)24 https://github.com/alexdobin/STAR RRID:SCR_021542 SAW (v6.1) BGI https://github.com/STOmics/SAW RRID:SCR_025001 Stereopy (v0.6.0) BGI https://github.com/STOmics/Stereopy Scanpy (v1.9.1) Wolf et al. (2018)25 https://github.com/scverse/scanpy RRID:SCR_018139 Fiji (v1.54f) Schindelin et al. (2019)26 https://github.com/fiji/fiji RRID:SCR_002285 Cell2location (v0.1.3) Kleshchevnikov et al. (2022)18 https://github.com/BayraktarLab/ cell2location/RRID:SCR_024859 SCope (v.1.8.2) Davie et al. (2018)17 https://github.com/aertslab/SCope Napari (v.0.4.18) N/A https://github.com/napari/napari RRID: SCR_022765
Polyacrylamide Gel Electrophoresis:Article Title: Nova-ST: Nano-patterned ultra-dense platform for spatial transcriptomics.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Stereo-seq Permeabilization kit BGI STomics Catalog #111KP118 Stereo-seq Chip P (1cm*1cm) BGI STomics Catalog #111CP118 Stereo-seq Transcriptomics T kit BGI STomics Catalog #111KT114 Stereo-seq Chip T (1cm*1cm) BGI STomics Catalog #110CT114 Stereo-seq Library Prep kit BGI STomics Catalog #111KL114 2100 Bioanalyzer – High sensitivity DNA analysis Agilent Technologies Catalog #G2939BA QubitTM dsDNA Quantification Assay Kits Thermo Fisher Scientific Catalog #Q32851 QubitTM ssDNA Assay Kit Thermo Fisher Scientific Catalog #Q10212 innuPREP mini RNA kit Analytik Jena Catalog # AJ 845-KS-2040250 Deposited data Nova-ST Data (Mouse Brain) This study GEO: GSE256318 Stereo-seq (Mouse Brain) This study GEO: GSE256319 Stereo-seq (Mouse Brain) Chen et al. (2022)8 CNGB: CNS0390078 Stereo-seq (Mouse Brain) You et al. (2023)20 https://www.genographix.com Slideseq-v2 (Mouse Hippocampus) Stickels et al. (2021)6 https://singlecell.broadinstitute.org/ single_cell/study/SCP815 10X Genomics and SMART-seq2 (Mouse Brain) Yao et al. (Cell)19 https://portal.brain-map.org/ atlases-and-data/rnaseq/mousewhole-cortex-and-hippocampus-10x Experimental models: Organisms/strains Six to eight weeks old mice (C57BL/6J) JAX MGI:3028467 Oligonucleotides HDMI-DraI32 IDT Technologies (Standard desalted) CAAGCAGAAGACGGCATACGAGA TTCTTTCCCTACACGACGCTCTTCC GATCTNNVNNVNNVNNVNNVNNNN NTCTTGTGACTACAGCACCCTCGA CTCTCGCTTTTTTTTTTTTTTTTTTTT TTTTTTTTTTAAAGACTTTCACCAGT CCATGATGTGTAGATCTCGGTGG TCGCCGTATCATT Read1-DraI32 IDT Technologies (PAGE purification) ATCATGGACTGGTGAAAGTCTTTA AAAAAAAAAAAAAAAAAAAAAAAA AAAAAGCGAGAGTCGAGGGTG CTGTAGTCACAAGA RPE_Randomer IDT Technologies (Standard desalted) TCAGACGTGTGCTCTTCCGA TCTNNNGGNNNB RPEPCR_Fwd IDT Technologies (Standard desalted) TCTTTCCCTACACGACGC*T*C RPEPCR_Rev IDT Technologies (Standard desalted) TCAGACGTGTGCTCTTCC*G*A P5_WTA_TCAAGCGA IDT Technologies (Standard desalted) AATGATACGGCGACCACCGAG ATCTACACTCAAGCGAACACTC TTTCCCTACACGACGCTC TTCCGATCT P5_WTA_ GTAGCTGA IDT Technologies (Standard desalted) AATGATACGGCGACCACCGAGA TCTACACGTAGCTGAACACTCTTT CCCTACACGACGCTCTTCCGATCT P5_WTA_ CCAACCAA IDT Technologies (Standard desalted) AATGATACGGCGACCACCGAGA TCTACACCCAACCAAACACTCTT TCCCTACACGACGCTCTTCCGATCT P5_WTA_ AACGTTGG IDT Technologies (Standard desalted) AATGATACGGCGACCACCGA GATCTACACAACGTTGGACAC TCTTTCCCTACACGACGC TCTTCCGATCT (Continued on next page) e2 Cell Reports Methods 4, 100831, August 19, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER P5_WTA_ ACCAATCG IDT Technologies (Standard desalted) AATGATACGGCGACCACCGAG ATCTACACACCAATCGACACT CTTTCCCTACACGACGCT CTTCCGATCT P7_WTA_ CCGCGGTT IDT Technologies (Standard desalted) CAAGCAGAAGACGGCATACGA GATCCGCGGTTGTGACTGGAG TTCAGACGTGTGCTCTTCC*G*A P7_WTA_ TTATAACC IDT Technologies (Standard desalted) CAAGCAGAAGACGGCATACGA GATTTATAACCGTGACTGGAGT TCAGACGTGTGCTCTTCC*G*A P7_WTA_ GGACTTGG IDT Technologies (Standard desalted) CAAGCAGAAGACGGCATACGA GATGGACTTGGGTGACTGGAG TTCAGACGTGTGCTCTTCC*G*A P7_WTA_ AAGTCCAA IDT Technologies (Standard desalted) CAAGCAGAAGACGGCATACGA GATAAGTCCAAGTGACTGGAG TTCAGACGTGTGCTCTTCC*G*A P7_WTA_ ATCCACTG IDT Technologies (Standard desalted) CAAGCAGAAGACGGCATACGA GATATCCACTGGTGACTGGAG TTCAGACGTGTGCTCTTCC*G*A Software and algorithms Nova-ST Analysis Pipeline/Notebooks This study https://github.com/aertslab/Nova-ST https://doi.org/10.5281/ zenodo.12608945 Carbide Create https://carbide3d.com/ N/A Carbide Motion https://carbide3d.com/ N/A bcl2fastq2 (v2.20.0) Illumina https://emea.support.illumina.com/ downloads/bcl2fastq-conversionsoftware-v2-20.html RRID:SCR_015058 Sequence Analysis Viewer (v3.0) Illumina https://emea.support.illumina.com/ sequencing/sequencing_software/ sequencing_analysis_viewer_sav.html Python (v3.8.10) Python Software Foundation https://www.python.org/ RRID:SCR_008394 OpenCV (v4.2.0) OpenCV Team https://opencv.org/RRID:SCR_015526 STARsolo (2.7.10b) Dobin et al. (2013)24 https://github.com/alexdobin/STAR RRID:SCR_021542 SAW (v6.1) BGI https://github.com/STOmics/SAW RRID:SCR_025001 Stereopy (v0.6.0) BGI https://github.com/STOmics/Stereopy Scanpy (v1.9.1) Wolf et al. (2018)25 https://github.com/scverse/scanpy RRID:SCR_018139 Fiji (v1.54f) Schindelin et al. (2019)26 https://github.com/fiji/fiji RRID:SCR_002285 Cell2location (v0.1.3) Kleshchevnikov et al. (2022)18 https://github.com/BayraktarLab/ cell2location/RRID:SCR_024859 SCope (v.1.8.2) Davie et al. (2018)17 https://github.com/aertslab/SCope Napari (v.0.4.18) N/A https://github.com/napari/napari RRID: SCR_022765
Purification:Article Title: Nova-ST: Nano-patterned ultra-dense platform for spatial transcriptomics.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Stereo-seq Permeabilization kit BGI STomics Catalog #111KP118 Stereo-seq Chip P (1cm*1cm) BGI STomics Catalog #111CP118 Stereo-seq Transcriptomics T kit BGI STomics Catalog #111KT114 Stereo-seq Chip T (1cm*1cm) BGI STomics Catalog #110CT114 Stereo-seq Library Prep kit BGI STomics Catalog #111KL114 2100 Bioanalyzer – High sensitivity DNA analysis Agilent Technologies Catalog #G2939BA QubitTM dsDNA Quantification Assay Kits Thermo Fisher Scientific Catalog #Q32851 QubitTM ssDNA Assay Kit Thermo Fisher Scientific Catalog #Q10212 innuPREP mini RNA kit Analytik Jena Catalog # AJ 845-KS-2040250 Deposited data Nova-ST Data (Mouse Brain) This study GEO: GSE256318 Stereo-seq (Mouse Brain) This study GEO: GSE256319 Stereo-seq (Mouse Brain) Chen et al. (2022)8 CNGB: CNS0390078 Stereo-seq (Mouse Brain) You et al. (2023)20 https://www.genographix.com Slideseq-v2 (Mouse Hippocampus) Stickels et al. (2021)6 https://singlecell.broadinstitute.org/ single_cell/study/SCP815 10X Genomics and SMART-seq2 (Mouse Brain) Yao et al. (Cell)19 https://portal.brain-map.org/ atlases-and-data/rnaseq/mousewhole-cortex-and-hippocampus-10x Experimental models: Organisms/strains Six to eight weeks old mice (C57BL/6J) JAX MGI:3028467 Oligonucleotides HDMI-DraI32 IDT Technologies (Standard desalted) CAAGCAGAAGACGGCATACGAGA TTCTTTCCCTACACGACGCTCTTCC GATCTNNVNNVNNVNNVNNVNNNN NTCTTGTGACTACAGCACCCTCGA CTCTCGCTTTTTTTTTTTTTTTTTTTT TTTTTTTTTTAAAGACTTTCACCAGT CCATGATGTGTAGATCTCGGTGG TCGCCGTATCATT Read1-DraI32 IDT Technologies (PAGE purification) ATCATGGACTGGTGAAAGTCTTTA AAAAAAAAAAAAAAAAAAAAAAAA AAAAAGCGAGAGTCGAGGGTG CTGTAGTCACAAGA RPE_Randomer IDT Technologies (Standard desalted) TCAGACGTGTGCTCTTCCGA TCTNNNGGNNNB RPEPCR_Fwd IDT Technologies (Standard desalted) TCTTTCCCTACACGACGC*T*C RPEPCR_Rev IDT Technologies (Standard desalted) TCAGACGTGTGCTCTTCC*G*A P5_WTA_TCAAGCGA IDT Technologies (Standard desalted) AATGATACGGCGACCACCGAG ATCTACACTCAAGCGAACACTC TTTCCCTACACGACGCTC TTCCGATCT P5_WTA_ GTAGCTGA IDT Technologies (Standard desalted) AATGATACGGCGACCACCGAGA TCTACACGTAGCTGAACACTCTTT CCCTACACGACGCTCTTCCGATCT P5_WTA_ CCAACCAA IDT Technologies (Standard desalted) AATGATACGGCGACCACCGAGA TCTACACCCAACCAAACACTCTT TCCCTACACGACGCTCTTCCGATCT P5_WTA_ AACGTTGG IDT Technologies (Standard desalted) AATGATACGGCGACCACCGA GATCTACACAACGTTGGACAC TCTTTCCCTACACGACGC TCTTCCGATCT (Continued on next page) e2 Cell Reports Methods 4, 100831, August 19, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER P5_WTA_ ACCAATCG IDT Technologies (Standard desalted) AATGATACGGCGACCACCGAG ATCTACACACCAATCGACACT CTTTCCCTACACGACGCT CTTCCGATCT P7_WTA_ CCGCGGTT IDT Technologies (Standard desalted) CAAGCAGAAGACGGCATACGA GATCCGCGGTTGTGACTGGAG TTCAGACGTGTGCTCTTCC*G*A P7_WTA_ TTATAACC IDT Technologies (Standard desalted) CAAGCAGAAGACGGCATACGA GATTTATAACCGTGACTGGAGT TCAGACGTGTGCTCTTCC*G*A P7_WTA_ GGACTTGG IDT Technologies (Standard desalted) CAAGCAGAAGACGGCATACGA GATGGACTTGGGTGACTGGAG TTCAGACGTGTGCTCTTCC*G*A P7_WTA_ AAGTCCAA IDT Technologies (Standard desalted) CAAGCAGAAGACGGCATACGA GATAAGTCCAAGTGACTGGAG TTCAGACGTGTGCTCTTCC*G*A P7_WTA_ ATCCACTG IDT Technologies (Standard desalted) CAAGCAGAAGACGGCATACGA GATATCCACTGGTGACTGGAG TTCAGACGTGTGCTCTTCC*G*A Software and algorithms Nova-ST Analysis Pipeline/Notebooks This study https://github.com/aertslab/Nova-ST https://doi.org/10.5281/ zenodo.12608945 Carbide Create https://carbide3d.com/ N/A Carbide Motion https://carbide3d.com/ N/A bcl2fastq2 (v2.20.0) Illumina https://emea.support.illumina.com/ downloads/bcl2fastq-conversionsoftware-v2-20.html RRID:SCR_015058 Sequence Analysis Viewer (v3.0) Illumina https://emea.support.illumina.com/ sequencing/sequencing_software/ sequencing_analysis_viewer_sav.html Python (v3.8.10) Python Software Foundation https://www.python.org/ RRID:SCR_008394 OpenCV (v4.2.0) OpenCV Team https://opencv.org/RRID:SCR_015526 STARsolo (2.7.10b) Dobin et al. (2013)24 https://github.com/alexdobin/STAR RRID:SCR_021542 SAW (v6.1) BGI https://github.com/STOmics/SAW RRID:SCR_025001 Stereopy (v0.6.0) BGI https://github.com/STOmics/Stereopy Scanpy (v1.9.1) Wolf et al. (2018)25 https://github.com/scverse/scanpy RRID:SCR_018139 Fiji (v1.54f) Schindelin et al. (2019)26 https://github.com/fiji/fiji RRID:SCR_002285 Cell2location (v0.1.3) Kleshchevnikov et al. (2022)18 https://github.com/BayraktarLab/ cell2location/RRID:SCR_024859 SCope (v.1.8.2) Davie et al. (2018)17 https://github.com/aertslab/SCope Napari (v.0.4.18) N/A https://github.com/napari/napari RRID: SCR_022765
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