List of Metadata fields

Version: ecceaec
Date: 2021-08-02

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Description and examples

Click on the buttons to display the fieldnames for the schemas.

by_category

Field Name description example used_for category regex
0 SAMPLE_NAME_GPCF Sample ID used within a single ILSe submission for GPCF. Limited to 20 characters. 0001_hgla_w23T14_sk-3 ILSe, ODCF sample [\w-]{1,20}
1 PROJECT ODCF Project Name as registered in OTP OE0538_DO0001 GUIDE sample [\w-]{1,32}
2 PATIENT_ID Individual ID for OTP mmus_01234 GUIDE, Odomlab sample [\w-]{1,32}
3 SPECIES Scientific name of a species. Note that CAST/Ej is a strain of Mus musculus. Mus musculus Odomlab sample [\w-]{1,64}
4 STRAIN Identifier for the strain used. Use EFO, if possible CAST/Ej, C57BL/6, [CAST/EjxC57BL/6]F1 Odomlab sample NaN
5 GENOME Genome used for QC at GPCF mm10 ILSe sample NaN
6 INDIVIDUAL ID for the individual (MOVI Number, Researcher's working ID) None Odomlab sample NaN
7 SAMPLE_TYPE Sample Type used by OTP, describing samples *across* individual. (lowercase and dash(-) only, end with digit) liver01, liver01-test01 GUIDE, Odomlab sample [a-z0-9-]*
8 TISSUE Descriptor of the tissue, if not given it's tried to parse from SAMPLE_TYPE. liver, skin, brain Odomlab sample NaN
9 GENOTYPE Genotype according to EFO. Typically wildtype if not GMO. wild type Odomlab sample NaN
10 PHENOTYPE Description of the phenotype healthy, tumor GUIDE, Odomlab sample NaN
11 SEX Biological sex of the sampled individual. female, male, unknown ILSe, GUIDE, Odomlab sample NaN
12 DATE_OF_BIRTH Birthday of individual (format YYYY-MM-DD) 2020-03-31 Odomlab sample [0-9]{4}-[0-9]{2}-[0-9]{2}
13 DATE_OF_DEATH Date of death (format YYYY-MM-DD) 2020-01-04 Odomlab sample [0-9]{4}-[0-9]{2}-[0-9]{2}
14 WAY_OF_DEATH How was the mouse/animal killed? neck_fracture CO2_neck_fracture isofloran_neck_fracture Odomlab sample NaN
15 TREATMENT Any treatment / pertubation applied to the individual/ cell-line. acetone 25w_DMBA/TPA 10w_DMBA/TPA DMBA/TPA_or_TPA TPA UV Odomlab sample NaN
16 CELL_INPUT[TOTAL_ALIVE CELLS] Number of cell, if available 1234 Odomlab experiment [0-9]*
17 TISSUE_PREP_METHOD Brief description to method of tissue preparation liver_ex Single cell MB RNA/DNATissueLyzerII Single cell C. Ernst 1. Enzymes 2. Trypsin 1. Trypsin 2. Enzymes skinbiopsy Odomlab experiment NaN
18 NA_PREP_METHOD Method (probably a kit) used to extract nucleic acid (NA) Modified Qiagen DNeasy blood&tissue Qiagen Dneasy blood&tissue Qiagen RNeasy micro Odomlab experiment NaN
19 NOTES Any additional notes, comments for the submission None Odomlab experiment NaN
20 LIB_PREP_KIT If using a new Kit, check first with ODCF because they need to register it to their database. Use their descriptor. scRNA_10x_v3, WGS_NEBNext_ULTRA_II, Agilent SureSelect Pre-capture, Agilent SureSelect XT Low input Mouse AllExon, Agilent SureSelect Post-capture, NEBNext RNA Low Input - E6420 GUIDE, Odomlab experiment NaN
21 AVERAGE_FRAGMENT_SIZE Experimentally determined average fragment length (basepairs) if available 500 Odomlab experiment [0-9]*
22 BARCODETYPE Description of barcode used SureSelect 16 Rxn 10X Chromium v3 NEB 96 oligos SureSelect 96 rxn Odomlab experiment NaN
23 BARCODE_WELL_I5 Well position of the barcode A7, N701, SI-GA-A6 Odomlab experiment NaN
24 BARCODE_SEQ_I5 Sequence of the I5 barcode TTACCGAC, TATCCTCT ILSe, Odomlab experiment [ATGC]*
25 BARCODE_WELL_I7 Well position of the barcode A7, S503 Odomlab experiment NaN
26 BARCODE_SEQ_I7 Sequence of the I7 barcode (for 10x-Single Cell, you need enter four rows to supply the barcodes and add a "_a,_b,_c, _d" suffix to the Sample Type) TTACCGAC ILSe, Odomlab experiment [ATGC]*
27 DNA_FRAGMENTATION_METHOD Method used to fragment DNA enzymatic sonicator Odomlab experiment NaN
28 IMAGING_DATASET_ID Imaging dataset for Spatial Transcriptomics DOIMG-00001 Odomlab experiment NaN
29 MULTIPLEX_NAME Your initials followed by the date of submission format(ABYYYYMMDD) MB20190923 ILSe, Odomlab sequencing [A-Z]{2}[0-9]{4}[0-9]{2}[0-9]{2}
30 ILSE_NO ILSE number as provided by GPCF/ILSe 12345 GUIDE, Odomlab sequencing [0-9]{5,}
31 SINGLE_CELL_WELL_LABEL REQUIRED FOR SMARTSEQ2, combination of column and row 1A GUIDE sequencing [0-9]{1,2}[A-Z]
32 ANTIBODY_TARGET Antibody target protein HNF4A, CEBPA Odomlab other NaN
33 ANTIBODY Antibody name, manufacturer etc. None Odomlab other NaN

by_provider

Field Name description example used_for category regex
0 SAMPLE_NAME_GPCF Sample ID used within a single ILSe submission for GPCF. Limited to 20 characters. 0001_hgla_w23T14_sk-3 ILSe, ODCF sample [\w-]{1,20}
1 GENOME Genome used for QC at GPCF mm10 ILSe sample NaN
2 SEX Biological sex of the sampled individual. female, male, unknown ILSe, GUIDE, Odomlab sample NaN
3 BARCODE_SEQ_I5 Sequence of the I5 barcode TTACCGAC, TATCCTCT ILSe, Odomlab experiment [ATGC]*
4 BARCODE_SEQ_I7 Sequence of the I7 barcode (for 10x-Single Cell, you need enter four rows to supply the barcodes and add a "_a,_b,_c, _d" suffix to the Sample Type) TTACCGAC ILSe, Odomlab experiment [ATGC]*
5 MULTIPLEX_NAME Your initials followed by the date of submission format(ABYYYYMMDD) MB20190923 ILSe, Odomlab sequencing [A-Z]{2}[0-9]{4}[0-9]{2}[0-9]{2}
6 PROJECT ODCF Project Name as registered in OTP OE0538_DO0001 GUIDE sample [\w-]{1,32}
7 PATIENT_ID Individual ID for OTP mmus_01234 GUIDE, Odomlab sample [\w-]{1,32}
8 SAMPLE_TYPE Sample Type used by OTP, describing samples *across* individual. (lowercase and dash(-) only, end with digit) liver01, liver01-test01 GUIDE, Odomlab sample [a-z0-9-]*
9 PHENOTYPE Description of the phenotype healthy, tumor GUIDE, Odomlab sample NaN
10 LIB_PREP_KIT If using a new Kit, check first with ODCF because they need to register it to their database. Use their descriptor. scRNA_10x_v3, WGS_NEBNext_ULTRA_II, Agilent SureSelect Pre-capture, Agilent SureSelect XT Low input Mouse AllExon, Agilent SureSelect Post-capture, NEBNext RNA Low Input - E6420 GUIDE, Odomlab experiment NaN
11 ILSE_NO ILSE number as provided by GPCF/ILSe 12345 GUIDE, Odomlab sequencing [0-9]{5,}
12 SINGLE_CELL_WELL_LABEL REQUIRED FOR SMARTSEQ2, combination of column and row 1A GUIDE sequencing [0-9]{1,2}[A-Z]
13 SPECIES Scientific name of a species. Note that CAST/Ej is a strain of Mus musculus. Mus musculus Odomlab sample [\w-]{1,64}
14 STRAIN Identifier for the strain used. Use EFO, if possible CAST/Ej, C57BL/6, [CAST/EjxC57BL/6]F1 Odomlab sample NaN
15 INDIVIDUAL ID for the individual (MOVI Number, Researcher's working ID) None Odomlab sample NaN
16 TISSUE Descriptor of the tissue, if not given it's tried to parse from SAMPLE_TYPE. liver, skin, brain Odomlab sample NaN
17 GENOTYPE Genotype according to EFO. Typically wildtype if not GMO. wild type Odomlab sample NaN
18 TREATMENT Any treatment / pertubation applied to the individual/ cell-line. acetone 25w_DMBA/TPA 10w_DMBA/TPA DMBA/TPA_or_TPA TPA UV Odomlab sample NaN
19 WAY_OF_DEATH How was the mouse/animal killed? neck_fracture CO2_neck_fracture isofloran_neck_fracture Odomlab sample NaN
20 DATE_OF_BIRTH Birthday of individual (format YYYY-MM-DD) 2020-03-31 Odomlab sample [0-9]{4}-[0-9]{2}-[0-9]{2}
21 DATE_OF_DEATH Date of death (format YYYY-MM-DD) 2020-01-04 Odomlab sample [0-9]{4}-[0-9]{2}-[0-9]{2}
22 TISSUE_PREP_METHOD Brief description to method of tissue preparation liver_ex Single cell MB RNA/DNATissueLyzerII Single cell C. Ernst 1. Enzymes 2. Trypsin 1. Trypsin 2. Enzymes skinbiopsy Odomlab experiment NaN
23 CELL_INPUT[TOTAL_ALIVE CELLS] Number of cell, if available 1234 Odomlab experiment [0-9]*
24 NA_PREP_METHOD Method (probably a kit) used to extract nucleic acid (NA) Modified Qiagen DNeasy blood&tissue Qiagen Dneasy blood&tissue Qiagen RNeasy micro Odomlab experiment NaN
25 BARCODETYPE Description of barcode used SureSelect 16 Rxn 10X Chromium v3 NEB 96 oligos SureSelect 96 rxn Odomlab experiment NaN
26 BARCODE_WELL_I5 Well position of the barcode A7, N701, SI-GA-A6 Odomlab experiment NaN
27 BARCODE_WELL_I7 Well position of the barcode A7, S503 Odomlab experiment NaN
28 DNA_FRAGMENTATION_METHOD Method used to fragment DNA enzymatic sonicator Odomlab experiment NaN
29 AVERAGE_FRAGMENT_SIZE Experimentally determined average fragment length (basepairs) if available 500 Odomlab experiment [0-9]*
30 IMAGING_DATASET_ID Imaging dataset for Spatial Transcriptomics DOIMG-00001 Odomlab experiment NaN
31 ANTIBODY Antibody name, manufacturer etc. None Odomlab other NaN
32 ANTIBODY_TARGET Antibody target protein HNF4A, CEBPA Odomlab other NaN
33 NOTES Any additional notes, comments for the submission None Odomlab experiment NaN