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{ "title": "Mesothelioma_52413", "status": "Public on Dec 23 2022", "submission_date": "2022-08-05", "last_update_date": "2022-12-23", "type": "genomic", "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", "institute": "Nagoya University" }, "description": null, "accession": "GSM6433302", "biosample": 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, "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" } ] } ]}
{ "title": "Tcells_PBS_3", "status": "Public on Dec 23 2022", "submission_date": "2021-12-13", "last_update_date": "2022-12-23", "type": "RNA", "contact": { "city": "Freiburg", "name": { "first": "Geoffroy", "middle": "", "last": "Andrieux" }, "email": null, "state": null, "address": "Breisacherstr 153", "department": null, "country": "Germany", "institute": "University clinics Freiburg"}, "description": null, "accession": "GSM5732107", "biosample": 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, "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" } ] } ]}
{ "title": "Tcells_hBD-2_4", "status": "Public on Dec 23 2022", "submission_date": "2021-12-13", "last_update_date": "2022-12-23", "type": "RNA", "contact": { "city": "Freiburg", "name": { "first": "Geoffroy", "middle": "", "last": "Andrieux" }, "email": null, "state": null, "address": "Breisacherstr 153", "department": null, "country": "Germany", "institute": "University clinics Freiburg"}, "description": null, "accession": "GSM5732112", "biosample": 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, "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" } ] } ]}
{ "title": "Mesothelioma_52416", "status": "Public on Dec 23 2022", "submission_date": "2022-08-05", "last_update_date": "2022-12-23", "type": "genomic", "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", "institute": "Nagoya University" }, "description": null, "accession": "GSM6433307", "biosample": 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, "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" } ] } ]}
{ "title": "Mesothelioma_62401", "status": "Public on Dec 23 2022", "submission_date": "2022-08-05", "last_update_date": "2022-12-23", "type": "genomic", "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", "institute": "Nagoya University" }, "description": null, "accession": "GSM6433306", "biosample": 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, "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" } ] } ]}
{ "title": "Prostate tumor_nTKO_Rep1", "status": "Public on Dec 23 2022", "submission_date": "2022-02-02", "last_update_date": "2022-12-23", "type": "RNA", "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", "institute": "University of notre dame"}, "description": "mouse id 471842", "accession": "GSM5856795", "biosample": null, "platform_id": "GPL1261", "hyb_protocol": "Affymetrix protocol", "channel_count": 1, "scan_protocol": "Affymetrix protocol", "data_row_count": 45037, "library_source": 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" } ] } ]}
{ "title": "Mesothelioma_60212", "status": "Public on Dec 23 2022", "submission_date": "2022-08-05", "last_update_date": "2022-12-23", "type": "genomic", "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", "institute": "Nagoya University" }, "description": null, "accession": "GSM6433305", "biosample": 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, "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" } ] } ]}
{ "title": "Mesothelioma_52805", "status": "Public on Dec 23 2022", "submission_date": "2022-08-05", "last_update_date": "2022-12-23", "type": "genomic", "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", "institute": "Nagoya University" }, "description": null, "accession": "GSM6433299", "biosample": 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, "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" } ] } ]}
{ "title": "Prostate tumor_nDKO_Rep3", "status": "Public on Dec 23 2022", "submission_date": "2022-02-02", "last_update_date": "2022-12-23", "type": "RNA", "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", "institute": "University of notre dame"}, "description": "mouse id 490761", "accession": "GSM5856794", "biosample": null, "platform_id": "GPL1261", "hyb_protocol": "Affymetrix protocol", "channel_count": 1, "scan_protocol": "Affymetrix protocol", "data_row_count": 45037, "library_source": 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" } ] } ]}
{ "title": "p53", "status": "Public on Dec 23 2022", "submission_date": "2022-02-10", "last_update_date": "2022-12-23", "type": "SRA", "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", "institute": "University of notre dame" }, "description": null, "accession": "GSM5885381", "biosample": "SAMN25841795", "platform_id": "GPL16417", "hyb_protocol": null, "channel_count": 1, "scan_protocol": null, "data_row_count": 0, "library_source": "genomic", "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)" } ] } ]}
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