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DNA
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D.SEQ
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| UID | Name | Scientist | LibraryType | Type | Parent | Protocol | VolumeUnits | ConcUnits | Notes | ConcType | NumPrepCycles | InsertionSize | PeakConcUnits | BarcodeType | Barcode2Type | QC_Instrument |
| DNA-260402BMC-1 | NA12878_gDNA | Vincent Butty | Genomic | Genomic DNA | https://fairdomhub.org/sops/900 | uL | ng/uL | GIAB reference material NA12878 (HG001) obtained from the Coriell Institute. Used as input for all 4 library prep conditions. | ||||||||
| DNA-260402BMC-2 | NA12878_lib_SYBR | Vincent Butty | WGS | Amplified Sequencing Library | DNA-260402BMC-1 | https://fairdomhub.org/sops/900 | uL | ng/uL | Library amplified in presence of SYBR Green I (1X final concentration) on n6tec iconPCR. Dye concentration and cycle count set above standard iconPCR stop-point parameters to provide a stringent mutagenicity test. | Agilent Fragment Analyzer; qPCR | 10 | 150-200 | ng/uL | P5/P7 Illumina-compatible adapters | P5/P7 Illumina-compatible adapters | Agilent Fragment Analyzer; qPCR |
| DNA-260402BMC-3 | NA12878_lib_EvaGreen | Vincent Butty | WGS | Amplified Sequencing Library | DNA-260402BMC-1 | https://fairdomhub.org/sops/900 | uL | ng/uL | Library amplified in presence of EvaGreen (1X final concentration) on n6tec iconPCR. Dye concentration and cycle count set above standard iconPCR stop-point parameters to provide a stringent mutagenicity test. | Agilent Fragment Analyzer; qPCR | 10 | 150-200 | ng/uL | P5/P7 Illumina-compatible adapters | P5/P7 Illumina-compatible adapters | Agilent Fragment Analyzer; qPCR |
| DNA-260402BMC-4 | NA12878_lib_EvaGreenPlus | Vincent Butty | WGS | Amplified Sequencing Library | DNA-260402BMC-1 | https://fairdomhub.org/sops/900 | uL | ng/uL | Library amplified in presence of EvaGreen Plus (1X final concentration) on n6tec iconPCR. Dye concentration and cycle count set above standard iconPCR stop-point parameters to provide a stringent mutagenicity test. | Agilent Fragment Analyzer; qPCR | 10 | 150-200 | ng/uL | P5/P7 Illumina-compatible adapters | P5/P7 Illumina-compatible adapters | Agilent Fragment Analyzer; qPCR |
| DNA-260402BMC-5 | NA12878_lib_NoDye | Vincent Butty | WGS | Amplified Sequencing Library | DNA-260402BMC-1 | https://fairdomhub.org/sops/900 | uL | ng/uL | Library amplified in the absence of dyes on n6tec iconPCR. Cycle count set above standard iconPCR stop-point parameters to control for baseline mutagenicity. Serves as baseline control for all downstream mutation analyses | Agilent Fragment Analyzer; qPCR | 10 | 150-200 | ng/uL | P5/P7 Illumina-compatible adapters | P5/P7 Illumina-compatible adapters | Agilent Fragment Analyzer; qPCR |
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| UID | File_PrimaryData | Parent | Name | Scientist | Protocol | Genome | Link_PrimaryData | Software | Aligner |
| A.ALN-260403BMC-1 | NA12878_SybrGreenI_0.5x_Replicate-1_bwa_GRCh38_GIABv3_mapped.bam | D.SEQ-260403BMC-1 | D25-2344 | Vincent Butty | https://fairdomhub.org/sops/899 | GRCh38_GIABv3_no_alt_analysis_set (GIAB masked decoys) | Bams can be generated by downloading the FASTQs from SRA and following the attached Protocol | bwa mem v0.7.12-r1039 and VN:0.7.17-r1188; samtools v1.3 | bwa mem |
| A.ALN-260403BMC-2 | NA12878_EvaGreenI_1x_Replicate-1_bwa_GRCh38_GIABv3_mapped.bam | D.SEQ-260403BMC-2 | D25-2345 | Vincent Butty | https://fairdomhub.org/sops/899 | GRCh38_GIABv3_no_alt_analysis_set (GIAB masked decoys) | Bams can be generated by downloading the FASTQs from SRA and following the attached Protocol | bwa mem v0.7.12-r1039 and VN:0.7.17-r1188; samtools v1.3 | bwa mem |
| A.ALN-260403BMC-3 | NA12878_EvaGreenPlus_1x_Replicate-1_bwa_GRCh38_GIABv3_mapped.bam | D.SEQ-260403BMC-3 | D25-2346 | Vincent Butty | https://fairdomhub.org/sops/899 | GRCh38_GIABv3_no_alt_analysis_set (GIAB masked decoys) | Bams can be generated by downloading the FASTQs from SRA and following the attached Protocol | bwa mem v0.7.12-r1039 and VN:0.7.17-r1188; samtools v1.3 | bwa mem |
| A.ALN-260403BMC-4 | NA12878_NoDye_Replicate-1_bwa_GRCh38_GIABv3_mapped.bam | D.SEQ-260403BMC-4 | D25-2342 | Vincent Butty | https://fairdomhub.org/sops/899 | GRCh38_GIABv3_no_alt_analysis_set (GIAB masked decoys) | Bams can be generated by downloading the FASTQs from SRA and following the attached Protocol | bwa mem v0.7.12-r1039 and VN:0.7.17-r1188; samtools v1.3 | bwa mem |
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| UID | File_PrimaryData | Link_PrimaryData | Parent | Scientist | Protocol | Checksum_PrimaryData | DataType | Software | Method | Signatures |
| A.MUSP-260415BMC-1 | N6_mutational_signatures.xlsx | https://zenodo.org/records/19595418/files/N6_mutational_signatures.xlsx?download=1&preview=1 | A.VCF-260403BMC-2;A.VCF-260403BMC-4;A.VCF-260403BMC-6;A.VCF-260403BMC-8 | Vincent Butty | https://fairdomhub.org/sops/899 | 3c872ce32475da6cb071d75ac37da004 | Mutational spectra catalogue (absolute) | SigProfilerAssignment (COSMIC v3.4); Signal webservice (signal.mutationalsignatures.com); signature.tools.lib R v4.2.0 | SBS 96-channel + DBS 78-channel + Indel 89-channel signature decomposition | COSMIC v3.4 SBS, DBS, ID signatures |
| A.MUSP-260415BMC-2 | n6_differential_signatures.xlsx | https://zenodo.org/records/19595418/files/n6_differential_signatures.xlsx?download=1&preview=1 | A.MUSP-260415BMC-1 | Vincent Butty | https://fairdomhub.org/sops/899 | 038864997f4a52b809525a23431042d4 | Mutational spectra catalogue (differential) | SigProfilerAssignment (COSMIC v3.4); Signal webservice (signal.mutationalsignatures.com); signature.tools.lib R v4.2.0 | SBS 96-channel + DBS 78-channel + Indel 89-channel signature decomposition | COSMIC v3.4 SBS, DBS, ID signatures |
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| UID | File_PrimaryData | Link_PrimaryData | Parent | Checksum_PrimaryData | Type | Protocol | Notes | Scientist | Software | ReferenceGenome | FilterMethod | FilterSet |
| A.VCF-260403BMC-1 | NA12878_SybrGreen_Replicate-1_call_m_ac1.vcf.gz | https://zenodo.org/records/19595418/files/NA12878_SybrGreen_Replicate-1_call_m_ac1.vcf.gz?download=1&preview=1 | A.ALN-260403BMC-1 | 1ba552b62251a2bce86cf3ef890d7fd9 | raw | https://fairdomhub.org/sops/899 | Raw variant calls for SYBR Green I condition. Unfiltered bcftools mpileup output. | Vincent Butty | bcftools mpileup v1.10.2+htslib-1.10.2 | GRCh38_GIABv3_no_alt_analysis_set (GIAB masked decoys) | ||
| A.VCF-260403BMC-2 | Sybr_not_GIAB_wg.vcf.gz | https://zenodo.org/records/19595418/files/Sybr_not_GIAB_wg.vcf.gz?download=1&preview=1 | A.VCF-260403BMC-1 | da34cdb02de63ad9a1ec797228ca0b22 | filtered | https://fairdomhub.org/sops/899 | Filtered variant calls for SYBR Green I condition. Non-GIAB variants only (bcftools isec against HG001 GRCh38 v4.2.1 benchmark). | Vincent Butty | bcftools mpileup v1.10.2+htslib-1.10.2 | GRCh38_GIABv3_no_alt_analysis_set (GIAB masked decoys) | bcftools isec | GIAB HG001 GRCh38 v4.2.1 benchmark (HG001_GRCh38_1_22_v4.2.1_benchmark.vcf.gz) |
| A.VCF-260403BMC-3 | NA12878_EvaGreen_I_Replicate-1_call_m_ac1.vcf.gz | https://zenodo.org/records/19595418/files/NA12878_EvaGreen_I_Replicate-1_call_m_ac1.vcf.gz?download=1&preview=1 | A.ALN-260403BMC-2 | c04e3dfa47a56eef6cb4929c17d73afa | raw | https://fairdomhub.org/sops/899 | Raw variant calls for EvaGreen condition. Unfiltered bcftools mpileup output. | Vincent Butty | bcftools mpileup v1.10.2+htslib-1.10.2 | GRCh38_GIABv3_no_alt_analysis_set (GIAB masked decoys) | ||
| A.VCF-260403BMC-4 | EvaGreen_I_not_GIAB_wg.vcf.gz | https://zenodo.org/records/19595418/files/EvaGreen_I_not_GIAB_wg.vcf.gz?download=1&preview=1 | A.VCF-260403BMC-3 | 73e030f59f7eccffc16b2bbdb5278f7f | filtered | https://fairdomhub.org/sops/899 | Filtered variant calls for EvaGreen condition. Non-GIAB variants only (bcftools isec against HG001 GRCh38 v4.2.1 benchmark). | Vincent Butty | bcftools mpileup v1.10.2+htslib-1.10.2 | GRCh38_GIABv3_no_alt_analysis_set (GIAB masked decoys) | bcftools isec | GIAB HG001 GRCh38 v4.2.1 benchmark (HG001_GRCh38_1_22_v4.2.1_benchmark.vcf.gz) |
| A.VCF-260403BMC-5 | NA12878_EvaGreen_Plus_Replicate-1_call_m_ac1.vcf.gz | https://zenodo.org/records/19595418/files/NA12878_EvaGreen_Plus_Replicate-1_call_m_ac1.vcf.gz?download=1&preview=1 | A.ALN-260403BMC-3 | fa57155165b09cdf6eac5f85b09f64ca | raw | https://fairdomhub.org/sops/899 | Raw variant calls for EvaGreen Plus condition. Unfiltered bcftools mpileup output. | Vincent Butty | bcftools mpileup v1.10.2+htslib-1.10.2 | GRCh38_GIABv3_no_alt_analysis_set (GIAB masked decoys) | ||
| A.VCF-260403BMC-6 | EvaGreen_Plus_not_GIAB_wg.vcf.gz | https://zenodo.org/records/19595418/files/EvaGreen_Plus_not_GIAB_wg.vcf.gz?download=1&preview=1 | A.VCF-260403BMC-5 | b820b1f074570b779fe12fa431bb9192 | filtered | https://fairdomhub.org/sops/899 | Filtered variant calls for EvaGreen Plus condition. Non-GIAB variants only (bcftools isec against HG001 GRCh38 v4.2.1 benchmark). | Vincent Butty | bcftools mpileup v1.10.2+htslib-1.10.2 | GRCh38_GIABv3_no_alt_analysis_set (GIAB masked decoys) | bcftools isec | GIAB HG001 GRCh38 v4.2.1 benchmark (HG001_GRCh38_1_22_v4.2.1_benchmark.vcf.gz) |
| A.VCF-260403BMC-7 | NA12878_NoDye_Replicate-1_call_m_ac1.vcf.gz | https://zenodo.org/records/19595418/files/NA12878_NoDye_Replicate-1_call_m_ac1.vcf.gz?download=1&preview=1 | A.ALN-260403BMC-4 | 6da279302ba31cf2fc5a738fb1b89f48 | raw | https://fairdomhub.org/sops/899 | Raw variant calls for no-dye control condition. Unfiltered bcftools mpileup output. | Vincent Butty | bcftools mpileup v1.10.2+htslib-1.10.2 | GRCh38_GIABv3_no_alt_analysis_set (GIAB masked decoys) | ||
| A.VCF-260403BMC-8 | NoDye_not_GIAB_wg.vcf.gz | https://zenodo.org/records/19595418/files/NoDye_not_GIAB_wg.vcf.gz?download=1&preview=1 | A.VCF-260403BMC-7 | 0ec0c4e1ddd36ea43202780142f552e0 | filtered | https://fairdomhub.org/sops/899 | Filtered variant calls for no-dye control condition. Non-GIAB variants only (bcftools isec against HG001 GRCh38 v4.2.1 benchmark). | Vincent Butty | bcftools mpileup v1.10.2+htslib-1.10.2 | GRCh38_GIABv3_no_alt_analysis_set (GIAB masked decoys) | bcftools isec | GIAB HG001 GRCh38 v4.2.1 benchmark (HG001_GRCh38_1_22_v4.2.1_benchmark.vcf.gz) |
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| UID | Name | File_PrimaryData | Checksum_PrimaryData | Link_PrimaryData | Scientist | Protocol | File_SecondaryData | Checksum_SecondaryData | Sequencer | SequencingType | F_bp | R_bp | LibraryStrategy | LibrarySource | ExtractedMolecule | LibraryDesign | DataType | TotalReads | Genome | Contamination | QCPlatform | Link_SecondaryData | Parent | LibrarySelection | Repository | RepositoryID | Accession |
| D.SEQ-260403BMC-1 | D25-2344 | 250213BMCA_D25-2344_1_sequence.fastq.gz | a657e2742483858db5b4126f8030e4e8 | https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR37956106/SRR37956106 | Vincent Butty | https://fairdomhub.org/sops/901 | 250213BMCA_D25-2344_2_sequence.fastq.gz | 326e847a4937c91543a2d9278cacb14d | Element AVITI | Paired-End | 75 | 75 | WGS | Genomic | DNA | Paired-End 2x75nt | FASTQ | 93000000-138000000 | GRCh38 | Screened against reference genome collection | Agilent Fragment Analyzer; qPCR | https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR37956106/SRR37956106 | DNA-260402BMC-2 | Random | SRA | PRJNA1449470 | SRR37956106 |
| D.SEQ-260403BMC-2 | D25-2345 | 250213BMCA_D25-2345_1_sequence.fastq.gz | 8cbdf999f2bc99e68433f4c7fb136b02 | https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR37956105/SRR37956105 | Vincent Butty | https://fairdomhub.org/sops/901 | 250213BMCA_D25-2345_2_sequence.fastq.gz | 1a8d268c7c13a821886b77832013de37 | Element AVITI | Paired-End | 75 | 75 | WGS | Genomic | DNA | Paired-End 2x75nt | FASTQ | 93000000-138000000 | GRCh38 | Screened against reference genome collection | Agilent Fragment Analyzer; qPCR | https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR37956105/SRR37956105 | DNA-260402BMC-3 | Random | SRA | PRJNA1449470 | SRR37956105 |
| D.SEQ-260403BMC-3 | D25-2346 | 250213BMCA_D25-2346_1_sequence.fastq.gz | c7c5c1e380b27b338e81f179abc30226 | https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR37956104/SRR37956104 | Vincent Butty | https://fairdomhub.org/sops/901 | 250213BMCA_D25-2346_2_sequence.fastq.gz | 04e1a8b10ccf51c7b43569d98a87d016 | Element AVITI | Paired-End | 75 | 75 | WGS | Genomic | DNA | Paired-End 2x75nt | FASTQ | 93000000-138000000 | GRCh38 | Screened against reference genome collection | Agilent Fragment Analyzer; qPCR | https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR37956104/SRR37956104 | DNA-260402BMC-4 | Random | SRA | PRJNA1449470 | SRR37956104 |
| D.SEQ-260403BMC-4 | D25-2342 | 250213BMCA_D25-2342_1_sequence.fastq.gz | 42d7c9b60121e97d7122fc727925e420 | https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR37956103/SRR37956103 | Vincent Butty | https://fairdomhub.org/sops/901 | 250213BMCA_D25-2342_2_sequence.fastq.gz | 56648c1f9584294f07b0342e7139e36c | Element AVITI | Paired-End | 75 | 75 | WGS | Genomic | DNA | Paired-End 2x75nt | FASTQ | 93000000-138000000 | GRCh38 | Screened against reference genome collection | Agilent Fragment Analyzer; qPCR | https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR37956103/SRR37956103 | DNA-260402BMC-5 | Random | SRA | PRJNA1449470 | SRR37956103 |
