test_clickhouse_JSONAsObject.ndjson

{"title":"Mesothelioma_52413","status":"Public on Dec 23 2022","submission_date":"2022-08-05","last_update_date":"2022-12-23","type":"genomic","anchor":null,"contact":{"city":"Nagoya","name":{"first":"Shinya","middle":"","last":"Toyokuni"},"email":"akatsuka@med.nagoya-u.ac.jp","state":"Aichi","address":"65 Tsuruma-Cho, Showa-Ku","department":"Pathology","country":"Japan","web_link":null,"institute":"Nagoya University","zip_postal_code":null,"phone":null},"description":null,"accession":"GSM6433302","biosample":null,"tag_count":null,"tag_length":null,"platform_id":"GPL10451","hyb_protocol":"The labeled DNA was hybridized with Agilent SurePrint G3 Mouse CGH 4x180k microarray at 67°C for 24 hours according to the manufacturer's protocol (Version 8.0).","channel_count":2,"scan_protocol":"The slides were scanned in an Agilent DNA microarray scanner with SureScan High-Resolution Technology (G2565CA).","data_row_count":174012,"library_source":null,"overall_design":null,"sra_experiment":null,"data_processing":"The scanned images were analyzed with Agilent Feature Extraction Software 10.7 using default parameters (CGH_107_Sep09 protocol).","supplemental_files":["ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6433nnn/GSM6433302/suppl/GSM6433302_CCGHarray_52413.txt.gz"],"channels":[{"label":"Cy3","taxid":[10116],"molecule":"genomic DNA","organism":"Rattus norvegicus","source_name":"normal kidney cortex","label_protocol":"The extracted genomic DNA was labeled using Aagilent Sure tag DNA labeling kit according to the manufacturer's protocol (Version 8.0).","growth_protocol":null,"extract_protocol":"Genomic DNA was extracted using DNeasy Blood & Tissue Kit (QIAGEN).","treatment_protocol":"Male and female wild-type and BRCA1+/- rats at 5,6,7 weeks of age were injected intraperitoneally with 3,3,4 mg crocidolite or chrysotile. The rats were euthanized when they were dying.","characteristics":[{"tag":"genotype","value":"Jcl:SD BRCA1+/-"},{"tag":"Sex","value":"Male"},{"tag":"Sex","value":"Male"}]},{"label":"Cy5","taxid":[10116],"molecule":"genomic DNA","organism":"Rattus norvegicus","source_name":"Mesothelioma_52413","label_protocol":"The extracted genomic DNA was labeled using Aagilent Sure tag DNA labeling kit according to the manufacturer's protocol (Version 8.0).","growth_protocol":null,"extract_protocol":"Genomic DNA was extracted using DNeasy Blood & Tissue Kit (QIAGEN).","treatment_protocol":"Male and female wild-type and BRCA1+/- rats at 5,6,7 weeks of age were injected intraperitoneally with 3,3,4 mg crocidolite or chrysotile. The rats were euthanized when they were dying.","characteristics":[{"tag":"treatment","value":"Untreated"},{"tag":"genotype","value":"Jcl:SD BRCA1+/-"},{"tag":"treatment","value":"Chrysotile, 10mg"}]}],"contributor":[]}
{"title":"Tcells_PBS_3","status":"Public on Dec 23 2022","submission_date":"2021-12-13","last_update_date":"2022-12-23","type":"RNA","anchor":null,"contact":{"city":"Freiburg","name":{"first":"Geoffroy","middle":"","last":"Andrieux"},"email":null,"state":null,"address":"Breisacherstr 153","department":null,"country":"Germany","web_link":null,"institute":"University clinics Freiburg","zip_postal_code":null,"phone":null},"description":null,"accession":"GSM5732107","biosample":null,"tag_count":null,"tag_length":null,"platform_id":"GPL23038","hyb_protocol":"Labeled fragments were hybridized to Affymetrix Clariom S Mouse arrays for 16h at 45°C with 60 rpm in an Affymetrix Hybridization oven 645.","channel_count":1,"scan_protocol":"After washing and staining, the arrays were scanned with the Affymetrix GeneChip Scanner 3000 7G. CEL-files were produced from the raw data with Affymetrix GeneChip Command Console Software.","data_row_count":22203,"library_source":null,"overall_design":null,"sra_experiment":null,"data_processing":"CEL files were analysed using the oligo R package. RMA method, log2 transformed were used to normalized the probe intensities.","supplemental_files":["ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5732nnn/GSM5732107/suppl/GSM5732107_N11_PBS.CEL.gz"],"channels":[{"label":"Biotin","taxid":[10090],"molecule":"total RNA","organism":"Mus musculus","source_name":"T cells, PBS, 48h","label_protocol":"We used the Affymetrix WT Pico kit for cDNA synthesis, amplification, and second-cycle cDNA synthesis, as well as fragmentation and labeling with Biotin, as described by the manufacturer.","growth_protocol":"Spleens were isolated from 4 wildtype (WT) C57BL/6 mice and meshed through a 100 µM cell strainer into a PBS filled dish. T cells were isolated using the Pan T cell isolation kit (Miltenyi). 200 000 CD4/CD8 T cells were cultured in 96-well format in 200µL RPMI+10%FCS per well.","extract_protocol":"Total RNA was isolated using the miRNeasy Mini Kit (Qiagen) according to the manufacturer's protocol.","treatment_protocol":"T cells were stimulated with anti-CD3/anti-CD28 microbeads in a 1:1 bead-to-cell ratio. PBS or hBD-2 (60µL/mL) were added, respectively. Cells were cultured for 48h at 37°C, 5% CO2.","characteristics":[{"tag":"cell type","value":"splenic CD4/CD8 T cells"},{"tag":"tissue","value":"spleen"},{"tag":"genotype","value":"C57BL/6 wildtype"},{"tag":"gender","value":"male"},{"tag":"treatment","value":"PBS"}]}],"contributor":[]}
{"title":"Tcells_hBD-2_4","status":"Public on Dec 23 2022","submission_date":"2021-12-13","last_update_date":"2022-12-23","type":"RNA","anchor":null,"contact":{"city":"Freiburg","name":{"first":"Geoffroy","middle":"","last":"Andrieux"},"email":null,"state":null,"address":"Breisacherstr 153","department":null,"country":"Germany","web_link":null,"institute":"University clinics Freiburg","zip_postal_code":null,"phone":null},"description":null,"accession":"GSM5732112","biosample":null,"tag_count":null,"tag_length":null,"platform_id":"GPL23038","hyb_protocol":"Labeled fragments were hybridized to Affymetrix Clariom S Mouse arrays for 16h at 45°C with 60 rpm in an Affymetrix Hybridization oven 645.","channel_count":1,"scan_protocol":"After washing and staining, the arrays were scanned with the Affymetrix GeneChip Scanner 3000 7G. CEL-files were produced from the raw data with Affymetrix GeneChip Command Console Software.","data_row_count":22203,"library_source":null,"overall_design":null,"sra_experiment":null,"data_processing":"CEL files were analysed using the oligo R package. RMA method, log2 transformed were used to normalized the probe intensities.","supplemental_files":["ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5732nnn/GSM5732112/suppl/GSM5732112_N16_hBD2.CEL.gz"],"channels":[{"label":"Biotin","taxid":[10090],"molecule":"total RNA","organism":"Mus musculus","source_name":"T cells, hBD-2, 48h","label_protocol":"We used the Affymetrix WT Pico kit for cDNA synthesis, amplification, and second-cycle cDNA synthesis, as well as fragmentation and labeling with Biotin, as described by the manufacturer.","growth_protocol":"Spleens were isolated from 4 wildtype (WT) C57BL/6 mice and meshed through a 100 µM cell strainer into a PBS filled dish. T cells were isolated using the Pan T cell isolation kit (Miltenyi). 200 000 CD4/CD8 T cells were cultured in 96-well format in 200µL RPMI+10%FCS per well.","extract_protocol":"Total RNA was isolated using the miRNeasy Mini Kit (Qiagen) according to the manufacturer's protocol.","treatment_protocol":"T cells were stimulated with anti-CD3/anti-CD28 microbeads in a 1:1 bead-to-cell ratio. PBS or hBD-2 (60µL/mL) were added, respectively. Cells were cultured for 48h at 37°C, 5% CO2.","characteristics":[{"tag":"cell type","value":"splenic CD4/CD8 T cells"},{"tag":"tissue","value":"spleen"},{"tag":"genotype","value":"C57BL/6 wildtype"},{"tag":"gender","value":"male"},{"tag":"treatment","value":"hBD-2"}]}],"contributor":[]}
{"title":"Mesothelioma_52416","status":"Public on Dec 23 2022","submission_date":"2022-08-05","last_update_date":"2022-12-23","type":"genomic","anchor":null,"contact":{"city":"Nagoya","name":{"first":"Shinya","middle":"","last":"Toyokuni"},"email":"akatsuka@med.nagoya-u.ac.jp","state":"Aichi","address":"65 Tsuruma-Cho, Showa-Ku","department":"Pathology","country":"Japan","web_link":null,"institute":"Nagoya University","zip_postal_code":null,"phone":null},"description":null,"accession":"GSM6433307","biosample":null,"tag_count":null,"tag_length":null,"platform_id":"GPL10451","hyb_protocol":"The labeled DNA was hybridized with Agilent SurePrint G3 Mouse CGH 4x180k microarray at 67°C for 24 hours according to the manufacturer's protocol (Version 8.0).","channel_count":2,"scan_protocol":"The slides were scanned in an Agilent DNA microarray scanner with SureScan High-Resolution Technology (G2565CA).","data_row_count":174012,"library_source":null,"overall_design":null,"sra_experiment":null,"data_processing":"The scanned images were analyzed with Agilent Feature Extraction Software 10.7 using default parameters (CGH_107_Sep09 protocol).","supplemental_files":["ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6433nnn/GSM6433307/suppl/GSM6433307_CCGHarray_52416.txt.gz"],"channels":[{"label":"Cy3","taxid":[10116],"molecule":"genomic DNA","organism":"Rattus norvegicus","source_name":"normal kidney cortex","label_protocol":"The extracted genomic DNA was labeled using Aagilent Sure tag DNA labeling kit according to the manufacturer's protocol (Version 8.0).","growth_protocol":null,"extract_protocol":"Genomic DNA was extracted using DNeasy Blood & Tissue Kit (QIAGEN).","treatment_protocol":"Male and female wild-type and BRCA1+/- rats at 5,6,7 weeks of age were injected intraperitoneally with 3,3,4 mg crocidolite or chrysotile. The rats were euthanized when they were dying.","characteristics":[{"tag":"genotype","value":"Jcl:SD wild-type"},{"tag":"Sex","value":"Male"},{"tag":"Sex","value":"Male"}]},{"label":"Cy5","taxid":[10116],"molecule":"genomic DNA","organism":"Rattus norvegicus","source_name":"Mesothelioma_52416","label_protocol":"The extracted genomic DNA was labeled using Aagilent Sure tag DNA labeling kit according to the manufacturer's protocol (Version 8.0).","growth_protocol":null,"extract_protocol":"Genomic DNA was extracted using DNeasy Blood & Tissue Kit (QIAGEN).","treatment_protocol":"Male and female wild-type and BRCA1+/- rats at 5,6,7 weeks of age were injected intraperitoneally with 3,3,4 mg crocidolite or chrysotile. The rats were euthanized when they were dying.","characteristics":[{"tag":"treatment","value":"Untreated"},{"tag":"genotype","value":"Jcl:SD wild-type"},{"tag":"treatment","value":"Crocidolite, 10mg"}]}],"contributor":[]}
{"title":"Mesothelioma_62401","status":"Public on Dec 23 2022","submission_date":"2022-08-05","last_update_date":"2022-12-23","type":"genomic","anchor":null,"contact":{"city":"Nagoya","name":{"first":"Shinya","middle":"","last":"Toyokuni"},"email":"akatsuka@med.nagoya-u.ac.jp","state":"Aichi","address":"65 Tsuruma-Cho, Showa-Ku","department":"Pathology","country":"Japan","web_link":null,"institute":"Nagoya University","zip_postal_code":null,"phone":null},"description":null,"accession":"GSM6433306","biosample":null,"tag_count":null,"tag_length":null,"platform_id":"GPL10451","hyb_protocol":"The labeled DNA was hybridized with Agilent SurePrint G3 Mouse CGH 4x180k microarray at 67°C for 24 hours according to the manufacturer's protocol (Version 8.0).","channel_count":2,"scan_protocol":"The slides were scanned in an Agilent DNA microarray scanner with SureScan High-Resolution Technology (G2565CA).","data_row_count":174012,"library_source":null,"overall_design":null,"sra_experiment":null,"data_processing":"The scanned images were analyzed with Agilent Feature Extraction Software 10.7 using default parameters (CGH_107_Sep09 protocol).","supplemental_files":["ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6433nnn/GSM6433306/suppl/GSM6433306_CCGHarray_62401.txt.gz"],"channels":[{"label":"Cy3","taxid":[10116],"molecule":"genomic DNA","organism":"Rattus norvegicus","source_name":"normal kidney cortex","label_protocol":"The extracted genomic DNA was labeled using Aagilent Sure tag DNA labeling kit according to the manufacturer's protocol (Version 8.0).","growth_protocol":null,"extract_protocol":"Genomic DNA was extracted using DNeasy Blood & Tissue Kit (QIAGEN).","treatment_protocol":"Male and female wild-type and BRCA1+/- rats at 5,6,7 weeks of age were injected intraperitoneally with 3,3,4 mg crocidolite or chrysotile. The rats were euthanized when they were dying.","characteristics":[{"tag":"genotype","value":"Jcl:SD BRCA1+/-"},{"tag":"Sex","value":"Female"},{"tag":"Sex","value":"Female"}]},{"label":"Cy5","taxid":[10116],"molecule":"genomic DNA","organism":"Rattus norvegicus","source_name":"Mesothelioma_62401","label_protocol":"The extracted genomic DNA was labeled using Aagilent Sure tag DNA labeling kit according to the manufacturer's protocol (Version 8.0).","growth_protocol":null,"extract_protocol":"Genomic DNA was extracted using DNeasy Blood & Tissue Kit (QIAGEN).","treatment_protocol":"Male and female wild-type and BRCA1+/- rats at 5,6,7 weeks of age were injected intraperitoneally with 3,3,4 mg crocidolite or chrysotile. The rats were euthanized when they were dying.","characteristics":[{"tag":"treatment","value":"Untreated"},{"tag":"genotype","value":"Jcl:SD BRCA1+/-"},{"tag":"treatment","value":"Chrysotile, 10mg"}]}],"contributor":[]}
{"title":"Prostate tumor_nTKO_Rep1","status":"Public on Dec 23 2022","submission_date":"2022-02-02","last_update_date":"2022-12-23","type":"RNA","anchor":null,"contact":{"city":"South Bend","name":{"first":"Xin","middle":"Lu","last":"Lu"},"email":"xlu@nd.edu","state":"Indiana","address":"113 Galvin Life Science Center","department":"Biological Department","country":"USA","web_link":null,"institute":"University of notre dame","zip_postal_code":null,"phone":null},"description":"mouse id 471842","accession":"GSM5856795","biosample":null,"tag_count":null,"tag_length":null,"platform_id":"GPL1261","hyb_protocol":"Affymetrix protocol","channel_count":1,"scan_protocol":"Affymetrix protocol","data_row_count":45037,"library_source":null,"overall_design":null,"sra_experiment":null,"data_processing":"The data were analyzed with Transcriptome Analysis Console, Summarization Method: RMA","supplemental_files":["ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5856nnn/GSM5856795/suppl/GSM5856795_02_nTKO_471842.CEL.gz"],"channels":[{"label":"biotin","taxid":[10090],"molecule":"total RNA","organism":"Mus musculus","source_name":"Probasin PtenL/L/Smad4L/LPygo2L/L prostate tumor cells","label_protocol":"Affymetrix protocol","growth_protocol":"NA","extract_protocol":"total RNA was extracted using RNeasy Kit (Qiagen) according to the manufacturer's instructions.","treatment_protocol":"All the procedure including tumor dissociation and tumor cell purification were performed on ice","characteristics":[{"tag":"strain","value":"C57BL/6"},{"tag":"tissue","value":"Prostate"},{"tag":"genotype","value":"PtenL/L/Smad4L/LPygo2L/L"},{"tag":"age","value":"31.43 week"}]}],"contributor":[]}
{"title":"Mesothelioma_60212","status":"Public on Dec 23 2022","submission_date":"2022-08-05","last_update_date":"2022-12-23","type":"genomic","anchor":null,"contact":{"city":"Nagoya","name":{"first":"Shinya","middle":"","last":"Toyokuni"},"email":"akatsuka@med.nagoya-u.ac.jp","state":"Aichi","address":"65 Tsuruma-Cho, Showa-Ku","department":"Pathology","country":"Japan","web_link":null,"institute":"Nagoya University","zip_postal_code":null,"phone":null},"description":null,"accession":"GSM6433305","biosample":null,"tag_count":null,"tag_length":null,"platform_id":"GPL10451","hyb_protocol":"The labeled DNA was hybridized with Agilent SurePrint G3 Mouse CGH 4x180k microarray at 67°C for 24 hours according to the manufacturer's protocol (Version 8.0).","channel_count":2,"scan_protocol":"The slides were scanned in an Agilent DNA microarray scanner with SureScan High-Resolution Technology (G2565CA).","data_row_count":174012,"library_source":null,"overall_design":null,"sra_experiment":null,"data_processing":"The scanned images were analyzed with Agilent Feature Extraction Software 10.7 using default parameters (CGH_107_Sep09 protocol).","supplemental_files":["ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6433nnn/GSM6433305/suppl/GSM6433305_CCGHarray_60212.txt.gz"],"channels":[{"label":"Cy3","taxid":[10116],"molecule":"genomic DNA","organism":"Rattus norvegicus","source_name":"normal kidney cortex","label_protocol":"The extracted genomic DNA was labeled using Aagilent Sure tag DNA labeling kit according to the manufacturer's protocol (Version 8.0).","growth_protocol":null,"extract_protocol":"Genomic DNA was extracted using DNeasy Blood & Tissue Kit (QIAGEN).","treatment_protocol":"Male and female wild-type and BRCA1+/- rats at 5,6,7 weeks of age were injected intraperitoneally with 3,3,4 mg crocidolite or chrysotile. The rats were euthanized when they were dying.","characteristics":[{"tag":"genotype","value":"Jcl:SD BRCA1+/-"},{"tag":"Sex","value":"Female"},{"tag":"Sex","value":"Female"}]},{"label":"Cy5","taxid":[10116],"molecule":"genomic DNA","organism":"Rattus norvegicus","source_name":"Mesothelioma_60212","label_protocol":"The extracted genomic DNA was labeled using Aagilent Sure tag DNA labeling kit according to the manufacturer's protocol (Version 8.0).","growth_protocol":null,"extract_protocol":"Genomic DNA was extracted using DNeasy Blood & Tissue Kit (QIAGEN).","treatment_protocol":"Male and female wild-type and BRCA1+/- rats at 5,6,7 weeks of age were injected intraperitoneally with 3,3,4 mg crocidolite or chrysotile. The rats were euthanized when they were dying.","characteristics":[{"tag":"treatment","value":"Untreated"},{"tag":"genotype","value":"Jcl:SD BRCA1+/-"},{"tag":"treatment","value":"Chrysotile, 10mg"}]}],"contributor":[]}
{"title":"Mesothelioma_52805","status":"Public on Dec 23 2022","submission_date":"2022-08-05","last_update_date":"2022-12-23","type":"genomic","anchor":null,"contact":{"city":"Nagoya","name":{"first":"Shinya","middle":"","last":"Toyokuni"},"email":"akatsuka@med.nagoya-u.ac.jp","state":"Aichi","address":"65 Tsuruma-Cho, Showa-Ku","department":"Pathology","country":"Japan","web_link":null,"institute":"Nagoya University","zip_postal_code":null,"phone":null},"description":null,"accession":"GSM6433299","biosample":null,"tag_count":null,"tag_length":null,"platform_id":"GPL10451","hyb_protocol":"The labeled DNA was hybridized with Agilent SurePrint G3 Mouse CGH 4x180k microarray at 67°C for 24 hours according to the manufacturer's protocol (Version 8.0).","channel_count":2,"scan_protocol":"The slides were scanned in an Agilent DNA microarray scanner with SureScan High-Resolution Technology (G2565CA).","data_row_count":174012,"library_source":null,"overall_design":null,"sra_experiment":null,"data_processing":"The scanned images were analyzed with Agilent Feature Extraction Software 10.7 using default parameters (CGH_107_Sep09 protocol).","supplemental_files":["ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6433nnn/GSM6433299/suppl/GSM6433299_CCGHarray_52805.txt.gz"],"channels":[{"label":"Cy3","taxid":[10116],"molecule":"genomic DNA","organism":"Rattus norvegicus","source_name":"normal kidney cortex","label_protocol":"The extracted genomic DNA was labeled using Aagilent Sure tag DNA labeling kit according to the manufacturer's protocol (Version 8.0).","growth_protocol":null,"extract_protocol":"Genomic DNA was extracted using DNeasy Blood & Tissue Kit (QIAGEN).","treatment_protocol":"Male and female wild-type and BRCA1+/- rats at 5,6,7 weeks of age were injected intraperitoneally with 3,3,4 mg crocidolite or chrysotile. The rats were euthanized when they were dying.","characteristics":[{"tag":"genotype","value":"Jcl:SD BRCA1+/-"},{"tag":"Sex","value":"Male"},{"tag":"Sex","value":"Male"}]},{"label":"Cy5","taxid":[10116],"molecule":"genomic DNA","organism":"Rattus norvegicus","source_name":"Mesothelioma_52805","label_protocol":"The extracted genomic DNA was labeled using Aagilent Sure tag DNA labeling kit according to the manufacturer's protocol (Version 8.0).","growth_protocol":null,"extract_protocol":"Genomic DNA was extracted using DNeasy Blood & Tissue Kit (QIAGEN).","treatment_protocol":"Male and female wild-type and BRCA1+/- rats at 5,6,7 weeks of age were injected intraperitoneally with 3,3,4 mg crocidolite or chrysotile. The rats were euthanized when they were dying.","characteristics":[{"tag":"treatment","value":"Untreated"},{"tag":"genotype","value":"Jcl:SD BRCA1+/-"},{"tag":"treatment","value":"Crocidolite, 10mg"}]}],"contributor":[]}
{"title":"Prostate tumor_nDKO_Rep3","status":"Public on Dec 23 2022","submission_date":"2022-02-02","last_update_date":"2022-12-23","type":"RNA","anchor":null,"contact":{"city":"South Bend","name":{"first":"Xin","middle":"Lu","last":"Lu"},"email":"xlu@nd.edu","state":"Indiana","address":"113 Galvin Life Science Center","department":"Biological Department","country":"USA","web_link":null,"institute":"University of notre dame","zip_postal_code":null,"phone":null},"description":"mouse id 490761","accession":"GSM5856794","biosample":null,"tag_count":null,"tag_length":null,"platform_id":"GPL1261","hyb_protocol":"Affymetrix protocol","channel_count":1,"scan_protocol":"Affymetrix protocol","data_row_count":45037,"library_source":null,"overall_design":null,"sra_experiment":null,"data_processing":"The data were analyzed with Transcriptome Analysis Console, Summarization Method: RMA","supplemental_files":["ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5856nnn/GSM5856794/suppl/GSM5856794_01_nDKO_490761.CEL.gz"],"channels":[{"label":"biotin","taxid":[10090],"molecule":"total RNA","organism":"Mus musculus","source_name":"Probasin PtenL/L/Smad4L/L prostate tumor cells","label_protocol":"Affymetrix protocol","growth_protocol":"NA","extract_protocol":"total RNA was extracted using RNeasy Kit (Qiagen) according to the manufacturer's instructions.","treatment_protocol":"All the procedure including tumor dissociation and tumor cell purification were performed on ice","characteristics":[{"tag":"strain","value":"C57BL/6"},{"tag":"tissue","value":"Prostate"},{"tag":"genotype","value":"PtenL/L/Smad4L/L"},{"tag":"age","value":"10.71 week"}]}],"contributor":[]}
{"title":"p53","status":"Public on Dec 23 2022","submission_date":"2022-02-10","last_update_date":"2022-12-23","type":"SRA","anchor":null,"contact":{"city":"South Bend","name":{"first":"Xin","middle":"Lu","last":"Lu"},"email":"xlu@nd.edu","state":"Indiana","address":"113 Galvin Life Science Center","department":"Biological Department","country":"USA","web_link":null,"institute":"University of notre dame","zip_postal_code":null,"phone":null},"description":null,"accession":"GSM5885381","biosample":"SAMN25841795","tag_count":null,"tag_length":null,"platform_id":"GPL16417","hyb_protocol":null,"channel_count":1,"scan_protocol":null,"data_row_count":0,"library_source":"genomic","overall_design":null,"sra_experiment":"SRX14128914","data_processing":"Library strategy: CUT&RUN\nAll the data analysis were performed in https://usegalaxy.org/\nThe reads were first mapped using the module Bowtie2 in galaxy.\nThe unaligned reads then were filtered using the module samtool_filter2 in galaxy.\nPeaks were called using MACS2 module in galaxy with the following setting: input were used as control, not buld shiftting model, shift size 100bp, use the default for all the other parameters.\nGenome_build: mm10 (GRCm38)\nSupplementary_files_format_and_content: bigwig files were generated using CONVERTER_bedgraph_to_bigwig module in galaxy using the wig file generated in peak calling.","supplemental_files":["ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5885nnn/GSM5885381/suppl/GSM5885381_p53.bigwig"],"channels":[{"label":null,"taxid":[10090],"molecule":"genomic DNA","organism":"Mus musculus","source_name":"Mouse prostate Pten/Smad4 KO (PS) cell line","label_protocol":null,"growth_protocol":"DMEM:F12 supplemented with FBS (5%), penicillin/streptomycin (1%), EGF (10 ng/ml), adenine (20 μg/ml), HEPES (15 mM), insulin (5 μg/ml), hydrocortisone (0.32 μg/m) and ROCK inhibitor (10 μ M Y-27632).","extract_protocol":"The samples are prepared according to the instruction of CUT&RUN Assay Kit (CST #86652). The input samples were sonicated for 12min with Covaris S220 Ultrasonicator System to get the fragment size between 150-300bp.\nLibrary were prepared according to the instruction of SimpleChIP® ChIP-seq DNA Library Prep Kit for Illumina® (CST #56795).","treatment_protocol":"No treatment.","characteristics":[{"tag":"cell line","value":"PS"},{"tag":"cell type","value":"Prostate tumor cell line established from pDKO tumor"},{"tag":"strain","value":"C57BL/6"},{"tag":"treatment","value":"untreated"},{"tag":"antibody","value":"p53 (CST, #2524S)"}]}],"contributor":[]}