ISB-CGC Migration to Project isb-cgc-bq Release NotesΒΆ

December 15, 2020

Existing TCGA hg19 DNA Methylation tables in the isb-cgc project were copied to the isb-cgc-bq project, TCGA and TCGA_versioned data sets. Corresponding TCGA tables in the isb-cgc project were deprecated.

BigQuery tables created

  • isb-cgc-bq.TCGA.DNA_methylation_chrY_hg19_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_chrY_hg19_gdc_2017_01
  • isb-cgc-bq.TCGA.DNA_methylation_chrX_hg19_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_chrX_hg19_gdc_2017_01
  • isb-cgc-bq.TCGA.DNA_methylation_chr22_hg19_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_chr22_hg19_gdc_2017_01
  • isb-cgc-bq.TCGA.DNA_methylation_chr21_hg19_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_chr21_hg19_gdc_2017_01
  • isb-cgc-bq.TCGA.DNA_methylation_chr20_hg19_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_chr20_hg19_gdc_2017_01
  • isb-cgc-bq.TCGA.DNA_methylation_chr19_hg19_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_chr19_hg19_gdc_2017_01
  • isb-cgc-bq.TCGA.DNA_methylation_chr18_hg19_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_chr18_hg19_gdc_2017_01
  • isb-cgc-bq.TCGA.DNA_methylation_chr17_hg19_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_chr17_hg19_gdc_2017_01
  • isb-cgc-bq.TCGA.DNA_methylation_chr16_hg19_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_chr16_hg19_gdc_2017_01
  • isb-cgc-bq.TCGA.DNA_methylation_chr15_hg19_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_chr15_hg19_gdc_2017_01
  • isb-cgc-bq.TCGA.DNA_methylation_chr14_hg19_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_chr14_hg19_gdc_2017_01
  • isb-cgc-bq.TCGA.DNA_methylation_chr13_hg19_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_chr13_hg19_gdc_2017_01
  • isb-cgc-bq.TCGA.DNA_methylation_chr12_hg19_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_chr12_hg19_gdc_2017_01
  • isb-cgc-bq.TCGA.DNA_methylation_chr11_hg19_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_chr11_hg19_gdc_2017_01
  • isb-cgc-bq.TCGA.DNA_methylation_chr10_hg19_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_chr10_hg19_gdc_2017_01
  • isb-cgc-bq.TCGA.DNA_methylation_chr9_hg19_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_chr9_hg19_gdc_2017_01
  • isb-cgc-bq.TCGA.DNA_methylation_chr8_hg19_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_chr8_hg19_gdc_2017_01
  • isb-cgc-bq.TCGA.DNA_methylation_chr7_hg19_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_chr7_hg19_gdc_2017_01
  • isb-cgc-bq.TCGA.DNA_methylation_chr6_hg19_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_chr6_hg19_gdc_2017_01
  • isb-cgc-bq.TCGA.DNA_methylation_chr5_hg19_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_chr5_hg19_gdc_2017_01
  • isb-cgc-bq.TCGA.DNA_methylation_chr4_hg19_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_chr4_hg19_gdc_2017_01
  • isb-cgc-bq.TCGA.DNA_methylation_chr3_hg19_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_chr3_hg19_gdc_2017_01
  • isb-cgc-bq.TCGA.DNA_methylation_chr2_hg19_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_chr2_hg19_gdc_2017_01
  • isb-cgc-bq.TCGA.DNA_methylation_chr1_hg19_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_chr1_hg19_gdc_2017_01
  • isb-cgc-bq.TCGA.DNA_methylation_hg19_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_hg19_gdc_2017_01

December 11, 2020

Existing TCGA hg38 DNA Methylation tables in the isb-cgc project were copied to the isb-cgc-bq project, TCGA and TCGA_versioned data sets. Corresponding TCGA tables in the isb-cgc project were deprecated.

BigQuery tables created

  • isb-cgc-bq.TCGA.DNA_methylation_chrY_hg38_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_chrY_hg38_gdc_2017_01
  • isb-cgc-bq.TCGA.DNA_methylation_chrX_hg38_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_chrX_hg38_gdc_2017_01
  • isb-cgc-bq.TCGA.DNA_methylation_chr22_hg38_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_chr22_hg38_gdc_2017_01
  • isb-cgc-bq.TCGA.DNA_methylation_chr21_hg38_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_chr21_hg38_gdc_2017_01
  • isb-cgc-bq.TCGA.DNA_methylation_chr20_hg38_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_chr20_hg38_gdc_2017_01
  • isb-cgc-bq.TCGA.DNA_methylation_chr19_hg38_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_chr19_hg38_gdc_2017_01
  • isb-cgc-bq.TCGA.DNA_methylation_chr18_hg38_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_chr18_hg38_gdc_2017_01
  • isb-cgc-bq.TCGA.DNA_methylation_chr17_hg38_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_chr17_hg38_gdc_2017_01
  • isb-cgc-bq.TCGA.DNA_methylation_chr16_hg38_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_chr16_hg38_gdc_2017_01
  • isb-cgc-bq.TCGA.DNA_methylation_chr15_hg38_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_chr15_hg38_gdc_2017_01
  • isb-cgc-bq.TCGA.DNA_methylation_chr14_hg38_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_chr14_hg38_gdc_2017_01
  • isb-cgc-bq.TCGA.DNA_methylation_chr13_hg38_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_chr13_hg38_gdc_2017_01
  • isb-cgc-bq.TCGA.DNA_methylation_chr12_hg38_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_chr12_hg38_gdc_2017_01
  • isb-cgc-bq.TCGA.DNA_methylation_chr11_hg38_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_chr11_hg38_gdc_2017_01
  • isb-cgc-bq.TCGA.DNA_methylation_chr10_hg38_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_chr10_hg38_gdc_2017_01
  • isb-cgc-bq.TCGA.DNA_methylation_chr9_hg38_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_chr9_hg38_gdc_2017_01
  • isb-cgc-bq.TCGA.DNA_methylation_chr8_hg38_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_chr8_hg38_gdc_2017_01
  • isb-cgc-bq.TCGA.DNA_methylation_chr7_hg38_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_chr7_hg38_gdc_2017_01
  • isb-cgc-bq.TCGA.DNA_methylation_chr6_hg38_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_chr6_hg38_gdc_2017_01
  • isb-cgc-bq.TCGA.DNA_methylation_chr5_hg38_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_chr5_hg38_gdc_2017_01
  • isb-cgc-bq.TCGA.DNA_methylation_chr4_hg38_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_chr4_hg38_gdc_2017_01
  • isb-cgc-bq.TCGA.DNA_methylation_chr3_hg38_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_chr3_hg38_gdc_2017_01
  • isb-cgc-bq.TCGA.DNA_methylation_chr2_hg38_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_chr2_hg38_gdc_2017_01
  • isb-cgc-bq.TCGA.DNA_methylation_chr1_hg38_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_chr1_hg38_gdc_2017_01
  • isb-cgc-bq.TCGA.DNA_methylation_hg38_gdc_current
  • isb-cgc-bq.TCGA_versioned.DNA_methylation_hg38_gdc_2017_01

December 4, 2020

Existing pancancer_atlas tables in the isb-cgc project were copied to the isb-cgc-bq project. Corresponding tables in the isb-cgc project were deprecated.

BigQuery tables created

The following tables were created under the isb-cgc-bq:pancer-altas data set:

  • Original_TCGA_RPPA_pancan_clean
  • Original_pancanMiRs_EBadjOnProtocolPlatformWithoutRepsWithUnCorrectMiRs_08_04_16
  • Original_jhu_usc_edu_PANCAN_merged_HumanMethylation27_HumanMethylation450_betaValue_whitelisted
  • Original_jhu_usc_edu_PANCAN_HumanMethylation450_betaValue_whitelisted
  • Original_jhu_usc_edu_PANCAN_HumanMethylation27_betaValue_whitelisted
  • Original_EBpp_AdjustPANCAN_IlluminaHiSeq_RNASeqV2_genExp
  • Original_clinical_PANCAN_patient_with_followup
  • Filtered_TCGA_RPPA_pancan_clean
  • Filtered_pancanMiRs_EBadjOnProtocolPlatformWithoutRepsWithUnCorrectMiRs_08_04_16
  • Filtered_MC3_MAF_V5_one_per_tumor_sample
  • Filtered_jhu_usc_edu_PANCAN_merged_HumanMethylation27_HumanMethylation450_betaValue_whitelisted
  • Filtered_jhu_usc_edu_PANCAN_HumanMethylation450_betaValue_whitelisted
  • Filtered_jhu_usc_edu_PANCAN_HumanMethylation27_betaValue_whitelisted
  • Filtered_EBpp_AdjustPANCAN_IlluminaHiSeq_RNASeqV2_genExp
  • Filtered_clinical_PANCAN_patient_with_followup
  • Filtered_all_CNVR_data_by_gene
  • merged_sample_quality_annotations
  • TCGA_CDR
  • Whitelist_ParticipantBarcodes
  • BarcodeMap

November 13, 2020

Existing methylation annotation and liftover tables in the isb-cgc project were copied to the isb-cgc-bq project. Corresponding tables in the isb-cgc project were deprecated.

BigQuery tables created

  • isb-cgc-bq.annotations.methylation_annotation_hg19_illumina_current
  • isb-cgc-bq.annotations_versioned.methylation_annotation_hg19_illumina_2015_06
  • isb-cgc-bq.annotations.methylation_annotation_hg38_gdc_current
  • isb-cgc-bq.annotations_versioned.methylation_annotation_hg38_gdc_2016_11
  • isb-cgc-bq.annotations.liftover_hg19_to_hg38_current
  • isb-cgc-bq.annotations_versioned.liftover_hg19_to_hg38_2016_08
  • isb-cgc-bq.annotations.methylation_liftover_hg19_illumina_to_hg38_current
  • isb-cgc-bq.annotations_versioned.methylation_liftover_hg19_illumina_to_hg38_2016_08

November 9, 2020

Existing GENCODE tables in the isb-cgc project were copied to the isb-cgc-bq project. Corresponding GENCODE tables in the isb-cgc project were deprecated.

BigQuery tables created

  • isb-cgc-bq.GENCODE_versioned.annotation_gtf_hg19_v19
  • isb-cgc-bq.GENCODE_versioned.annotation_gtf_hg38_v22
  • isb-cgc-bq.GENCODE_versioned.annotation_gtf_hg38_v23
  • isb-cgc-bq.GENCODE_versioned.annotation_gtf_hg38_v24

October 22, 2020

Existing TARGET tables in the isb-cgc project (data sets TARGET_bioclin_v0 and TARGET_bioclin_v0) were copied to the isb-cgc-bq project, TARGET and TARGET_versioned data sets. Corresponding TARGET tables in the isb-cgc project were deprecated.

BigQuery tables created

  • isb-cgc-bq.TARGET_versioned.per_sample_file_metadata_hg38_gdc_r14
  • isb-cgc-bq.TARGET_versioned.miRNAseq_isoform_hg38_gdc_r11
  • isb-cgc-bq.TARGET.miRNAseq_isoform_hg38_gdc_current
  • isb-cgc-bq.TARGET_versioned.miRNAseq_isoform_hg38_gdc_r14
  • isb-cgc-bq.TARGET_versioned.miRNAseq_hg38_gdc_r11
  • isb-cgc-bq.TARGET_versioned.miRNAseq_hg38_gdc_r14
  • isb-cgc-bq.TARGET_versioned.RNAseq_hg38_gdc_2017_12
  • isb-cgc-bq.TARGET.biospecimen_gdc_current
  • isb-cgc-bq.TARGET_versioned.biospecimen_gdc_2017_04
  • isb-cgc-bq.TARGET_versioned.clinical_gdc_2019_06
  • isb-cgc-bq.TARGET_versioned.clinical_gdc_2017_04

October 07, 2020

Existing TCGA tables (except for DNA Methylation) in the isb-cgc project were copied to the isb-cgc-bq project, TCGA and TCGA_versioned data sets. Corresponding TCGA tables in the isb-cgc project were deprecated.

BigQuery tables created

  • isb-cgc-bq.TCGA.annotations_gdc_current
  • isb-cgc-bq.TCGA_versioned.annotations_gdc_2017_04
  • isb-cgc-bq.TCGA.biospecimen_gdc_current
  • isb-cgc-bq.TCGA_versioned.biospecimen_gdc_2017_02
  • isb-cgc-bq.TCGA_versioned.clinical_gdc_2018_06
  • isb-cgc-bq.TCGA_versioned.clinical_gdc_2019_06
  • isb-cgc-bq.TCGA.slide_images_gdc_current
  • isb-cgc-bq.TCGA_versioned.slide_images_gdc_r17
  • isb-cgc-bq.TCGA.radiology_images_tcia_current
  • isb-cgc-bq.TCGA_versioned.radiology_images_tcia_2018_06
  • isb-cgc-bq.TCGA_versioned.per_sample_file_metadata_hg19_gdc_r14
  • isb-cgc-bq.TCGA_versioned.per_sample_file_metadata_hg38_gdc_r14
  • isb-cgc-bq.TCGA_versioned.somatic_mutation_hg19_MC3_2017_02
  • isb-cgc-bq.TCGA_versioned.somatic_mutation_hg19_DCC_2017_02
  • isb-cgc-bq.TCGA_versioned.somatic_mutation_hg38_gdc_r6
  • isb-cgc-bq.TCGA_versioned.somatic_mutation_hg38_gdc_r7
  • isb-cgc-bq.TCGA.somatic_mutation_hg38_gdc_current
  • isb-cgc-bq.TCGA_versioned.somatic_mutation_hg38_gdc_r10
  • isb-cgc-bq.TCGA.miRNAseq_hg19_gdc_current
  • isb-cgc-bq.TCGA_versioned.miRNAseq_hg19_gdc_2017_03
  • isb-cgc-bq.TCGA.miRNAseq_hg38_gdc_current
  • isb-cgc-bq.TCGA_versioned.miRNAseq_hg38_gdc_r14
  • isb-cgc-bq.TCGA.protein_expression_hg19_gdc_current
  • isb-cgc-bq.TCGA_versioned.protein_expression_hg19_gdc_2017_02
  • isb-cgc-bq.TCGA.protein_expression_hg38_gdc_current
  • isb-cgc-bq.TCGA_versioned.protein_expression_hg38_gdc_2017_02
  • isb-cgc-bq.TCGA.miRNAseq_isoform_hg19_gdc_current
  • isb-cgc-bq.TCGA_versioned.miRNAseq_isoform_hg19_gdc_2017_02
  • isb-cgc-bq.TCGA.miRNAseq_isoform_hg38_gdc_current
  • isb-cgc-bq.TCGA_versioned.miRNAseq_isoform_hg38_gdc_r14
  • isb-cgc-bq.TCGA.RNAseq_hg19_gdc_current
  • isb-cgc-bq.TCGA_versioned.RNAseq_hg19_gdc_2017_02
  • isb-cgc-bq.TCGA.RNAseq_hg38_gdc_current
  • isb-cgc-bq.TCGA_versioned.RNAseq_hg38_gdc_2017_12
  • isb-cgc-bq.TCGA_versioned.copy_number_segment_masked_hg38_gdc_2017_02
  • isb-cgc-bq.TCGA.copy_number_segment_masked_hg19_gdc_current
  • isb-cgc-bq.TCGA_versioned.copy_number_segment_masked_hg19_gdc_2017_02
  • isb-cgc-bq.TCGA.copy_number_segment_masked_hg38_gdc_current
  • isb-cgc-bq.TCGA_versioned.copy_number_segment_masked_hg38_gdc_r14

September 3, 2020

Existing CCLE tables in the isb-cgc project were copied to the isb-cgc-bq project, CCLE and CCLE_versioned data sets. Corresponding CCLE tables in the isb-cgc project were deprecated.

BigQuery tables created

  • isb-cgc-bq.CCLE_versioned.clinical_2019_06
  • isb-cgc-bq.CCLE.clinical_current
  • isb-cgc-bq.CCLE_versioned.biospecimen_2019_04
  • isb-cgc-bq.CCLE.biospecimen_current
  • isb-cgc-bq.CCLE_versioned.sample_information_hg19_2016_02
  • isb-cgc-bq.CCLE.sample_information_hg19_current
  • isb-cgc-bq.CCLE_versioned.RMA_expression_hg19_2016_02
  • isb-cgc-bq.CCLE.RMA_expression_hg19_current
  • isb-cgc-bq.CCLE_versioned.copy_number_segment_hg19_2016_02
  • isb-cgc-bq.CCLE.copy_number_segment_hg19_current
  • isb-cgc-bq.CCLE_versioned.somatic_mutation_hg19_2016_02
  • isb-cgc-bq.CCLE.somatic_mutation_hg19_current
  • isb-cgc-bq.CCLE_versioned.file_metadata_hg19_2016_03
  • isb-cgc-bq.CCLE_versioned.fastqc_metrics_hg19_2016_03
  • isb-cgc-bq.CCLE.fastqc_metrics_hg19_current
  • isb-cgc-bq.CCLE_versioned.per_sample_file_metadata_hg19_gdc_r14

Have feedback or corrections? Please email us at feedback@isb-cgc.org.