Spatial-CITE-seq: spatially resolved high-plex protein and whole transcriptome co-mapping
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Abstract
We present spatial-CITE-seq for high-plex protein and whole transcriptome co-mapping, which was firstly demonstrated for profiling 189 proteins and transcriptome in multiple mouse tissue types. It was then applied to human tissues to measure 273 proteins and transcriptome that revealed spatially distinct germinal center reaction in tonsil and early immune activation in skin at the COVID-19 mRNA vaccine injection site. Spatial-CITE-seq may find a range of applications in biomedical research.
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SciScore for 10.1101/2022.04.01.486788: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication Authentication: Fluorescent staining of human tonsil: Multiplex immunolabeling on FFPE human tonsil sections was performed by sequential IF staining on COMET™ using the FFeX technology previously described by Lunaphore Technologies13, 20. Table 2: Resources
Antibodies Sentences Resources DNA oligos and antibody-derived DNA tags: DNA oligos used were all synthesized by Integrated DNA Technologies with HPLC purification. antibody-derived DNAsuggested: NoneAntibody-derived DNA tags for membrane proteins were purchased from Biolegend and listed in … SciScore for 10.1101/2022.04.01.486788: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication Authentication: Fluorescent staining of human tonsil: Multiplex immunolabeling on FFPE human tonsil sections was performed by sequential IF staining on COMET™ using the FFeX technology previously described by Lunaphore Technologies13, 20. Table 2: Resources
Antibodies Sentences Resources DNA oligos and antibody-derived DNA tags: DNA oligos used were all synthesized by Integrated DNA Technologies with HPLC purification. antibody-derived DNAsuggested: NoneAntibody-derived DNA tags for membrane proteins were purchased from Biolegend and listed in Table S5. Antibody-derived DNA tagssuggested: NoneSoftware and Algorithms Sentences Resources The product was purified with 1.6X SPRI beads and then quantified with QuBit and BioAnalyzer. BioAnalyzersuggested: (BioAnalyzer 2100, RRID:SCR_019715)Data preprocessing: For cDNAs derived from mRNAs, the raw fastq file of Read 2 containing the UMI, barcode A and barcode B regions, were first reformatted into the standard input format required by ST pipeline v1.7.2 21 using customized python script. pythonsuggested: (IPython, RRID:SCR_001658)Using recommended ST pipeline parameters, the read 1 was STAR mapped to either the mouse genome (GRCm38) or the human genome (GRCh38). STARsuggested: (STAR, RRID:SCR_004463)All the heatmap was plotted using ggplot2. scRNA-seq and spatial data integration: The cell types of skin biopsy section were annotated through integration analysis using the matched scRNA-seq data as the reference. ggplot2suggested: (ggplot2, RRID:SCR_014601)Results from OddPub: Thank you for sharing your code.
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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