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clarification of imaging requirements #20

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clarification of imaging requirements #20

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50 changes: 25 additions & 25 deletions docs/materials/rfc/data_specs.csv
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ParentType,Subtype,Description,Requirement,Levels,Format,PublicNotes,PrivateNotes
DNA,whole genome sequencing,,required,__raw__ OR semi-processed,"raw: FASTQ, unaligned BAM, CRAM | semi-processed: aligned BAM",,
DNA,whole exome sequencing,,required,__raw__ OR semi-processed,"raw: FASTQ, unaligned BAM, CRAM | semi-processed: aligned BAM",,
DNA,SNP microarray,,required,__raw__ AND processed,"raw: CEL, IDAT, tsv (raw values per SNP) & processed: tsv (genotypes per SNP)",,
DNA,immunosequencing,,required,__raw__ OR semi-processed,"vendor-dependent, e.g. ImmunoSEQ and 10XGenomics formats",,
DNA,Sanger sequencing,,optional,processed,,,
RNA expression,RNA sequencing (bulk or single-cell),,required,__raw__ OR semi-processed,"raw: FASTQ, unaligned BAM, CRAM | semi-processed: aligned BAM",,
RNA expression,gene expression microarray,,required,__raw__ AND processed,"raw: CEL, IDAT, tsv (raw values per SNP, copy number, and loss of heterozygosity) & processed: tsv (normalized values and purity/ploidy)",,
RNA expression,qPCR,Quantitative PCR.,optional,processed,csv/tsv (according to template),,
methylation,ATAC sequencing,,required,__raw__ OR semi-processed,"raw: FASTQ, unaligned BAM, CRAM | semi-processed: aligned BAM",,
methylation,methylation array,,required,__raw__ OR semi-processed,"raw: FASTQ, unaligned BAM, CRAM | semi-processed: aligned BAM",,
methylation,bisulfite sequencing,,required,__raw__ OR semi-processed,"raw: FASTQ, unaligned BAM, CRAM | semi-processed: aligned BAM",,
protein,LC-MS,,required,__raw__ AND processed,raw: mzML & processed: protein intensities (csv/tsv),https://www.psidev.info/mzML,https://www.immport.org/docs/standards/Metabolomics_Proteomics_Mass_Spectrometry_Standard.pdf
protein,western blot,,optional,processed,densitometry output (csv/tsv),,
protein,plate-based ELISA,,optional,raw,plate reader output (csv/tsv),,
protein,protein/peptide microarrays,,required,processed,label-free quantification matrix (csv/tsv),,
metabolomics,LC-MS,,required,__raw__ AND processed,raw: mzML or vendor-dependent format & processed: metabolite intensities (csv/tsv),,https://www.immport.org/docs/standards/Metabolomics_Proteomics_Mass_Spectrometry_Standard.pdf
clinical,structured clinical data,"Clinical information such as demographics, lab tests, treatment, etc.",required,processed,csv/tsv or XML with metadata for each variable,key primary and secondary endpoints only,
clinical,EEG,,required,raw,,pending additional comments,
clinical/imaging,MRI or other radiological image,Diagnostic images that also may require controlled-access.,required,raw,"dicom, nifti, minc",,
imaging,immunohistochemistry,,required,raw,"tiff, ome-tiff",,
imaging,immunofluorescence,,required,raw,"tiff, ome-tiff",,
imaging,gross morphology photos (mice),,optional,raw,"tiff, png, jpg",,
in vitro drug screening,plate-based cell viability assay,,required,processed,csv/tsv (according to template),,
other,flow cytometry,,optional,raw,fsc with gating parameters,,
ParentType,Subtype,Description,Requirement,Levels,Format,PublicNotes,PrivateNotes
DNA,whole genome sequencing,,required,__raw__ OR semi-processed,"raw: FASTQ, unaligned BAM, CRAM | semi-processed: aligned BAM",,
DNA,whole exome sequencing,,required,__raw__ OR semi-processed,"raw: FASTQ, unaligned BAM, CRAM | semi-processed: aligned BAM",,
DNA,SNP microarray,,required,__raw__ AND processed,"raw: CEL, IDAT, tsv (raw values per SNP) & processed: tsv (genotypes per SNP)",,
DNA,immunosequencing,,required,__raw__ OR semi-processed,"vendor-dependent, e.g. ImmunoSEQ and 10XGenomics formats",,
DNA,Sanger sequencing,,optional,processed,,,
RNA expression,RNA sequencing (bulk or single-cell),,required,__raw__ OR semi-processed,"raw: FASTQ, unaligned BAM, CRAM | semi-processed: aligned BAM",,
RNA expression,gene expression microarray,,required,__raw__ AND processed,"raw: CEL, IDAT, tsv (raw values per SNP, copy number, and loss of heterozygosity) & processed: tsv (normalized values and purity/ploidy)",,
RNA expression,qPCR,Quantitative PCR.,optional,processed,csv/tsv (according to template),,
methylation,ATAC sequencing,,required,__raw__ OR semi-processed,"raw: FASTQ, unaligned BAM, CRAM | semi-processed: aligned BAM",,
methylation,methylation array,,required,__raw__ OR semi-processed,"raw: FASTQ, unaligned BAM, CRAM | semi-processed: aligned BAM",,
methylation,bisulfite sequencing,,required,__raw__ OR semi-processed,"raw: FASTQ, unaligned BAM, CRAM | semi-processed: aligned BAM",,
protein,LC-MS,,required,__raw__ AND processed,raw: mzML & processed: protein intensities (csv/tsv),https://www.psidev.info/mzML,https://www.immport.org/docs/standards/Metabolomics_Proteomics_Mass_Spectrometry_Standard.pdf
protein,western blot,,optional,processed,densitometry output (csv/tsv),,
protein,plate-based ELISA,,optional,raw,plate reader output (csv/tsv),,
protein,protein/peptide microarrays,,required,processed,label-free quantification matrix (csv/tsv),,
metabolomics,LC-MS,,required,__raw__ AND processed,raw: mzML or vendor-dependent format & processed: metabolite intensities (csv/tsv),,https://www.immport.org/docs/standards/Metabolomics_Proteomics_Mass_Spectrometry_Standard.pdf
clinical,structured clinical data,"Clinical information such as demographics, lab tests, treatment, etc.",required,processed,csv/tsv or XML with metadata for each variable,key primary and secondary endpoints only,
clinical,EEG,,required,raw,,pending additional comments,
clinical/imaging,MRI or other radiological image,Diagnostic images that also may require controlled-access.,required,raw,"dicom, nifti, minc",,
imaging,immunohistochemistry,,sometimes required,raw,"tiff, ome-tiff",Required only if a large dataset (e.g. high-throughput). See "Additional Considerations" for imaging data in the section below,
imaging,immunofluorescence,,sometimes required,raw,"tiff, ome-tiff",Required only if a large dataset (e.g. high-throughput). See "Additional Considerations" for imaging data in the section below,
imaging,gross morphology photos (mice),,optional,raw,"tiff, png, jpg",,
in vitro drug screening,plate-based cell viability assay,,required,processed,csv/tsv (according to template),,
other,flow cytometry,,optional,raw,fsc with gating parameters,,
other,in vivo tumor growth experiments,,optional,__raw__ OR processed,csv/tsv (according to template) where raw: tumor dimensions or other raw measurements & processed: calculated tumor volume/size,,
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