From 36abeb14dfc5f44ff129410ad776607c6b3b87b0 Mon Sep 17 00:00:00 2001 From: bcorrie Date: Thu, 24 Nov 2022 00:53:07 +0000 Subject: [PATCH] Bring up to data with current curation process. 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"property":{"id":"ENSG:ENSG00000125534", "label":"PPDPF"}, "value":1}, +{"cell_id":"AACGTTGAGTATGACA-1", "property":{"id":"ENSG:ENSG00000197457", "label":"STMN3"}, "value":1}, +{"cell_id":"AACGTTGAGTATGACA-1", "property":{"id":"ENSG:ENSG00000159110", "label":"IFNAR2"}, "value":1}, +{"cell_id":"AACGTTGAGTATGACA-1", "property":{"id":"ENSG:ENSG00000159140", "label":"SON"}, "value":3}, +{"cell_id":"AACGTTGAGTATGACA-1", "property":{"id":"ENSG:ENSG00000241837", "label":"ATP5PO"}, "value":4}, +{"cell_id":"AACGTTGAGTATGACA-1", "property":{"id":"ENSG:ENSG00000243927", "label":"MRPS6"}, "value":1}, +{"cell_id":"AACGTTGAGTATGACA-1", "property":{"id":"ENSG:ENSG00000142197", "label":"DOP1B"}, "value":1}, +{"cell_id":"AACGTTGAGTATGACA-1", "property":{"id":"ENSG:ENSG00000182670", "label":"TTC3"}, "value":2}, +{"cell_id":"AACGTTGAGTATGACA-1", "property":{"id":"ENSG:ENSG00000205581", "label":"HMGN1"}, "value":2}, +{"cell_id":"AACGTTGAGTATGACA-1", "property":{"id":"ENSG:ENSG00000160194", "label":"NDUFV3"}, "value":1}, +{"cell_id":"AACGTTGAGTATGACA-1", "property":{"id":"ENSG:ENSG00000160213", "label":"CSTB"}, "value":1}, +{"cell_id":"AACGTTGAGTATGACA-1", "property":{"id":"ENSG:ENSG00000141959", "label":"PFKL"}, "value":2}, +{"cell_id":"AACGTTGAGTATGACA-1", "property":{"id":"ENSG:ENSG00000184787", "label":"UBE2G2"}, "value":1}, +{"cell_id":"AACGTTGAGTATGACA-1", "property":{"id":"ENSG:ENSG00000184900", "label":"SUMO3"}, "value":3}, +{"cell_id":"AACGTTGAGTATGACA-1", "property":{"id":"ENSG:ENSG00000160255", "label":"ITGB2"}, "value":2}, +{"cell_id":"AACGTTGAGTATGACA-1", "property":{"id":"ENSG:ENSG00000227039", "label":"ITGB2-AS1"}, "value":1}, +{"cell_id":"AACGTTGAGTATGACA-1", "property":{"id":"ENSG:ENSG00000160284", "label":"SPATC1L"}, "value":1} ] diff --git a/test/airr-cell/HC1-vdj_t-gex.json b/test/airr-cell/HC1-vdj_t-gex.json index f847c2b..d62223d 100644 --- a/test/airr-cell/HC1-vdj_t-gex.json +++ b/test/airr-cell/HC1-vdj_t-gex.json @@ -19997,6 +19997,5 @@ {"cell_id":"AAACGGGAGATGGGTC-1", "property":{"id":"ENSG:ENSG00000091164", "label":"TXNL1"}, "value":1}, {"cell_id":"AAACGGGAGATGGGTC-1", "property":{"id":"ENSG:ENSG00000141664", "label":"ZCCHC2"}, "value":1}, {"cell_id":"AAACGGGAGATGGGTC-1", "property":{"id":"ENSG:ENSG00000197971", "label":"MBP"}, "value":2}, -{"cell_id":"AAACGGGAGATGGGTC-1", "property":{"id":"ENSG:ENSG00000197540", "label":"GZMM"}, "value":1}, -{"cell_id":"AACTCCCTCGCAAGCC-1", "property":{"id":"ENSG:ENSG00000198695", "label":"MT-ND6"}, "value":4} +{"cell_id":"AAACGGGAGATGGGTC-1", "property":{"id":"ENSG:ENSG00000197540", "label":"GZMM"}, "value":1} ] diff --git a/test/airr-cell/PRJCA002413_wen_wang_HC1-Cell-GEX-2022-02-15.csv b/test/airr-cell/PRJCA002413_wen_wang_HC1-Cell-GEX-2022-02-15.csv index c4beebb..3c8c2e6 100644 --- a/test/airr-cell/PRJCA002413_wen_wang_HC1-Cell-GEX-2022-02-15.csv +++ b/test/airr-cell/PRJCA002413_wen_wang_HC1-Cell-GEX-2022-02-15.csv @@ -1,5 +1,3 @@ -ir_record_number,repertoire_id,repertoire_name,repertoire_description,study_id,study_title,study_contact,study_type,study_type_id,study_description,inclusion_exclusion_criteria,grants,collected_by,lab_name,lab_address,submitted_by,pub_ids,keywords_study,subject_id,synthetic,species,species_id,sex,age,age_min,age_max,age_unit,age_unit_id,age_event,ancestry_population,ethnicity,race,strain_name,linked_subjects,link_type,study_group_description,disease_diagnosis,disease_diagnosis_id,disease_length,disease_stage,prior_therapies,immunogen,intervention,medical_history,sample_id,sample_type,tissue,tissue_id,anatomic_site,disease_state_sample,collection_time_point_relative,collection_time_point_relative_unit,collection_time_point_relative_unit_id,collection_time_point_reference,biomaterial_provider,tissue_processing,cell_subset,cell_subset_id,cell_phenotype,cell_species,cell_species_id,single_cell,cell_number,cells_per_reaction,cell_storage,cell_quality,cell_isolation,cell_processing_protocol,template_class,template_quality,template_amount,template_amount_unit,template_amount_unit_id,library_generation_method,library_generation_protocol,library_generation_kit_version,pcr_target_locus,forward_pcr_primer_target_location,reverse_pcr_primer_target_location,complete_sequences,physical_linkage,total_reads_passing_qc_filter,ir_curator_count,sequencing_platform,read_length,paired_read_length,sequencing_facility,sequencing_run_id,sequencing_run_date,sequencing_data_id,sequencing_kit,file_type,filename,read_direction,paired_filename,paired_read_direction,software_versions,index_filename,index_length,paired_reads_assembly,quality_thresholds,primer_match_cutoffs,collapsing_method,data_processing_protocols,germline_database,germline_set_ref,ir_sra_run_id,primary_annotation,data_processing_files,sample_processing_id,data_processing_id,analysis_provenance_id -,PRJCA002413-Healthy_Control_1-CELL,,,PRJCA002413,"Wen et al., Immune cell profiling of COVID-19 patients in the recovery stage by single-cell sequencing","Hongyang Wang, hywangk@vip.sina.com",Case-Control Study,NCIT:C15197,An inflammatory immune signature in the early recovery stage of COVID-19 suggests patients are still vulnerable after hospital discharge.,Include: COVID,"National Natural Science Foundation of China, award number 81722034, 81670015, 81830054, 81530028, 91953122, 31871326, 81721003, 81988101; Ministry of Science and Technology Key Program, award number 2018ZX09101002, 2017ZX100203205; Shanghai Pujiang Program, award number 2019PJD059; Guangdong Natural Science Funds for Distinguished Young Scholar, award number 2016A030306006, 2020B1515020057","xiaochuanle@126.com, cw0226@foxmail.com, hywangk@vip.sina.com","National Center for Liver Cancer, Second Military Medical University","Second Military Medical University, 200438 Shanghai, China","Chuanle Xiao, xiaochuanle@126.com",PMID: 32377375,contains_schema_cell,Healthy_Control_1,FALSE,Homo sapiens,NCBITAXON:9606,male,,,,,,,,,,,,,Control (Healthy),,,,,,,,,Healthy_Control_1,peripheral venous puncture,venous blood,UBERON:0013756,,,0,day,UO:0000033,Sample collection,Wuhan Hankou Hospital China,PBMCs isolated from heparinized venous blood using Ficoll-Hypaque density solution; cell viability exceeded 80%,,,,Homo sapiens,NCBITAXON:9606,TRUE,13111,1,FALSE,Viability exceeded 80%,,,RNA,,,,,RT(oligo-dT)+TS(UMI)+PCR,"Single-cell suspensions of samples were converted to barcoded scRNA-seq libraries using the Chromium Single Cell 5′ Library and Gel Bead Kit v2 (PN-120237), Multiplex Kit, and Chip Kit (10x Genomics). Full-length TCR/BCR V(D)J segments were enriched from amplified cDNA from 5′ libraries via PCR amplification using a Chromium Single-Cell V(D)J Enrichment kit (10x Genomics) according to the manufacturer’s protocol.",,,,,partial,none,,6672,Illumina NovaSeq 6000,28,150,,,,,,fastq,"CRR143949_f1.fastq.gz, CRR143950_f1.fastq.gz, CRR143951_f1.fastq.gz, CRR143952_f1.fastq.gz, CRR143953_f1.fastq.gz, CRR143954_f1.fastq.gz, CRR143955_f1.fastq.gz, CRR143956_f1.fastq.gz",,"CRR143949_r2.fastq.gz, CRR143950_r2.fastq.gz, CRR143951_r2.fastq.gz, CRR143952_r2.fastq.gz, CRR143953_r2.fastq.gz, CRR143954_r2.fastq.gz, CRR143955_r2.fastq.gz, CRR143956_r2.fastq.gz",,Cell Ranger multi pipeline (v.6.0.1),,,,,,,"Processing by iReceptor: To create AIRR Cell files, script 10x-vdj2cell.sh was run on b-cells and t-cells. To create AIRR GEX files for b-cells and t-cells: -gunzip $COUNT_MATRIX_DIR/*.gz -tail -n +4 $COUNT_MATRIX_DIR/matrix.mtx > $COUNT_MATRIX_DIR/$SUBJECT-matrix-trimmed.mtx -python3 10x-vdj2GEX.py $VDJ_B_DIR/cell_barcodes.json $COUNT_MATRIX_DIR/barcodes.tsv $COUNT_MATRIX_DIR/features.tsv $COUNT_MATRIX_DIR/$SUBJECT-matrix-trimmed.mtx > $OUT_DIR/$SUBJECT-vdj_b_gex.json",refdata-gex-GRCh38-2020-A,,"CRR143949, CRR143950, CRR143951, CRR143952, CRR143953, CRR143954, CRR143955, CRR143956",TRUE,"HC1-vdj_b-gex.json, HC1-vdj_b-cells.json, HC1-vdj_t-gex.json, HC1-vdj_t-cells.json",PRJCA002413-Healthy_Control_1-CELL,PRJCA002413-Healthy_Control_1, +ir_record_number,repertoire_id,repertoire_name,repertoire_description,study_id,study_title,study_contact,study_type,study_type_id,study_description,inclusion_exclusion_criteria,grants,collected_by,lab_name,lab_address,submitted_by,pub_ids,keywords_study,subject_id,synthetic,species,species_id,sex,age_min,age_max,age_unit,age_unit_id,age_event,ancestry_population,ethnicity,race,strain_name,linked_subjects,link_type,study_group_description,disease_diagnosis,disease_diagnosis_id,,disease_length,disease_stage,prior_therapies,immunogen,intervention,medical_history,sample_id,sample_type,tissue,tissue_id,anatomic_site,disease_state_sample,collection_time_point_relative,collection_time_point_relative_unit,collection_time_point_relative_unit_id,collection_time_point_reference,biomaterial_provider,tissue_processing,cell_subset,cell_subset_id,cell_phenotype,cell_species,cell_species_id,single_cell,cell_number,cells_per_reaction,cell_storage,ir_cell_storage,cell_quality,cell_isolation,cell_processing_protocol,template_class,template_quality,template_amount,template_amount_unit,template_amount_unit_id,library_generation_method,library_generation_protocol,library_generation_kit_version,pcr_target_locus,forward_pcr_primer_target_location,reverse_pcr_primer_target_location,complete_sequences,physical_linkage,total_reads_passing_qc_filter,ir_curator_count,sequencing_platform,read_length,paired_read_length,sequencing_facility,sequencing_run_id,sequencing_run_date,sequencing_kit,file_type,filename,read_direction,paired_filename,paired_read_direction,software_versions,paired_reads_assembly,quality_thresholds,primer_match_cutoffs,collapsing_method,data_processing_protocols,germline_database,germline_set_ref,ir_sra_run_id,sequencing_data_id,index_filename,index_length,primary_annotation,data_processing_files,ir_rearrangement_number,sample_processing_id,data_processing_id,analysis_provenance_id +,PRJCA002413-Healthy_Control_1-TR-CELL,,,PRJCA002413,"Wen et al., Immune cell profiling of COVID-19 patients in the recovery stage by single-cell sequencing","Hongyang Wang, hywangk@vip.sina.com",Case-Control Study,NCIT:C15197,An inflammatory immune signature in the early recovery stage of COVID-19 suggests patients are still vulnerable after hospital discharge.,Include: COVID,"National Natural Science Foundation of China, award number 81722034, 81670015, 81830054, 81530028, 91953122, 31871326, 81721003, 81988101; Ministry of Science and Technology Key Program, award number 2018ZX09101002, 2017ZX100203205; Shanghai Pujiang Program, award number 2019PJD059; Guangdong Natural Science Funds for Distinguished Young Scholar, award number 2016A030306006, 2020B1515020057","xiaochuanle@126.com, cw0226@foxmail.com, hywangk@vip.sina.com","National Center for Liver Cancer, Second Military Medical University","Second Military Medical University, 200438 Shanghai, China","Chuanle Xiao, xiaochuanle@126.com",PMID: 32377375,contains_schema_cell,Healthy_Control_1,FALSE,Homo sapiens,NCBITAXON:9606,male,,,,,,,,,,,,Control (Healthy),,,Control (Healthy),,,,,,,Healthy_Control_1,peripheral venous puncture,venous blood,UBERON:0013756,,,0,day,UO:0000033,Sample collection,Wuhan Hankou Hospital China,PBMCs isolated from heparinized venous blood using Ficoll-Hypaque density solution; cell viability exceeded 80%,T cell,CL:0000084,,Homo sapiens,NCBITAXON:9606,TRUE,13111,1,FALSE,,Viability exceeded 80%,,,RNA,,,,,RT(oligo-dT)+TS(UMI)+PCR,"Single-cell suspensions of samples were converted to barcoded scRNA-seq libraries using the Chromium Single Cell 5′ Library and Gel Bead Kit v2 (PN-120237), Multiplex Kit, and Chip Kit (10x Genomics). Full-length TCR/BCR V(D)J segments were enriched from amplified cDNA from 5′ libraries via PCR amplification using a Chromium Single-Cell V(D)J Enrichment kit (10x Genomics) according to the manufacturer’s protocol.",,,,,partial,none,,6672,Illumina NovaSeq 6000,28,150,,,,,fastq,"CRR143949_f1.fastq.gz, CRR143950_f1.fastq.gz, CRR143951_f1.fastq.gz, CRR143952_f1.fastq.gz, CRR143953_f1.fastq.gz, CRR143954_f1.fastq.gz, CRR143955_f1.fastq.gz, CRR143956_f1.fastq.gz",,"CRR143949_r2.fastq.gz, CRR143950_r2.fastq.gz, CRR143951_r2.fastq.gz, CRR143952_r2.fastq.gz, CRR143953_r2.fastq.gz, CRR143954_r2.fastq.gz, CRR143955_r2.fastq.gz, CRR143956_r2.fastq.gz",,Cell Ranger multi pipeline (v.6.0.1),,,,,"Processing by iReceptor: To create AIRR Cell files, script 10x-vdj2cell.sh was run on b-cells and t-cells. To create AIRR GEX files for b-cells and t-cells: gunzip $COUNT_MATRIX_DIR/*.gz; tail -n +4 $COUNT_MATRIX_DIR/matrix.mtx > $COUNT_MATRIX_DIR/$SUBJECT-matrix-trimmed.mtx; python3 10x-vdj2GEX.py $VDJ_B_DIR/cell_barcodes.json $COUNT_MATRIX_DIR/barcodes.tsv $COUNT_MATRIX_DIR/features.tsv $COUNT_MATRIX_DIR/$SUBJECT-matrix-trimmed.mtx > $OUT_DIR/$SUBJECT-vdj_b-gex.json",refdata-gex-GRCh38-2020-A,,"CRR143949, CRR143950, CRR143951, CRR143952, CRR143953, CRR143954, CRR143955, CRR143956","CRR143949, CRR143950, CRR143951, CRR143952, CRR143953, CRR143954, CRR143955, CRR143956",,,TRUE,"HC1-vdj_t-gex.json, HC1-vdj_t-cells.json",,PRJCA002413-Healthy_Control_1-TR-CELL,PRJCA002413-Healthy_Control_1, +,PRJCA002413-Healthy_Control_1-IG-CELL,,,PRJCA002413,"Wen et al., Immune cell profiling of COVID-19 patients in the recovery stage by single-cell sequencing","Hongyang Wang, hywangk@vip.sina.com",Case-Control Study,NCIT:C15197,An inflammatory immune signature in the early recovery stage of COVID-19 suggests patients are still vulnerable after hospital discharge.,Include: COVID,"National Natural Science Foundation of China, award number 81722034, 81670015, 81830054, 81530028, 91953122, 31871326, 81721003, 81988101; Ministry of Science and Technology Key Program, award number 2018ZX09101002, 2017ZX100203205; Shanghai Pujiang Program, award number 2019PJD059; Guangdong Natural Science Funds for Distinguished Young Scholar, award number 2016A030306006, 2020B1515020057","xiaochuanle@126.com, cw0226@foxmail.com, hywangk@vip.sina.com","National Center for Liver Cancer, Second Military Medical University","Second Military Medical University, 200438 Shanghai, China","Chuanle Xiao, xiaochuanle@126.com",PMID: 32377375,contains_schema_cell,Healthy_Control_1,FALSE,Homo sapiens,NCBITAXON:9606,male,,,,,,,,,,,,Control (Healthy),,,Control (Healthy),,,,,,,Healthy_Control_1,peripheral venous puncture,venous blood,UBERON:0013756,,,0,day,UO:0000033,Sample collection,Wuhan Hankou Hospital China,PBMCs isolated from heparinized venous blood using Ficoll-Hypaque density solution; cell viability exceeded 80%,B cell,CL:0000236,,Homo sapiens,NCBITAXON:9606,TRUE,13111,1,FALSE,,Viability exceeded 80%,,,RNA,,,,,RT(oligo-dT)+TS(UMI)+PCR,"Single-cell suspensions of samples were converted to barcoded scRNA-seq libraries using the Chromium Single Cell 5′ Library and Gel Bead Kit v2 (PN-120237), Multiplex Kit, and Chip Kit (10x Genomics). Full-length TCR/BCR V(D)J segments were enriched from amplified cDNA from 5′ libraries via PCR amplification using a Chromium Single-Cell V(D)J Enrichment kit (10x Genomics) according to the manufacturer’s protocol.",,,,,partial,none,,6672,Illumina NovaSeq 6000,28,150,,,,,fastq,"CRR143949_f1.fastq.gz, CRR143950_f1.fastq.gz, CRR143951_f1.fastq.gz, CRR143952_f1.fastq.gz, CRR143953_f1.fastq.gz, CRR143954_f1.fastq.gz, CRR143955_f1.fastq.gz, CRR143956_f1.fastq.gz",,"CRR143949_r2.fastq.gz, CRR143950_r2.fastq.gz, CRR143951_r2.fastq.gz, CRR143952_r2.fastq.gz, CRR143953_r2.fastq.gz, CRR143954_r2.fastq.gz, CRR143955_r2.fastq.gz, CRR143956_r2.fastq.gz",,Cell Ranger multi pipeline (v.6.0.1),,,,,"Processing by iReceptor: To create AIRR Cell files, script 10x-vdj2cell.sh was run on b-cells and t-cells. To create AIRR GEX files for b-cells and t-cells: gunzip $COUNT_MATRIX_DIR/*.gz; tail -n +4 $COUNT_MATRIX_DIR/matrix.mtx > $COUNT_MATRIX_DIR/$SUBJECT-matrix-trimmed.mtx; python3 10x-vdj2GEX.py $VDJ_B_DIR/cell_barcodes.json $COUNT_MATRIX_DIR/barcodes.tsv $COUNT_MATRIX_DIR/features.tsv $COUNT_MATRIX_DIR/$SUBJECT-matrix-trimmed.mtx > $OUT_DIR/$SUBJECT-vdj_b-gex.json",refdata-gex-GRCh38-2020-A,,"CRR143949, CRR143950, CRR143951, CRR143952, CRR143953, CRR143954, CRR143955, CRR143956","CRR143949, CRR143950, CRR143951, CRR143952, CRR143953, CRR143954, CRR143955, CRR143956",,,TRUE,"HC1-vdj_b-gex.json, HC1-vdj_b-cells.json",,PRJCA002413-Healthy_Control_1-IG-CELL,PRJCA002413-Healthy_Control_1,