GSE174588 - PreneoplasticBreastNee10x

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Project short name:

PreneoplasticBreastNee10x

Primary Wrangler:

Arsenios

Secondary Wrangler:

Associated files

• Google Drive: folder

Published study links

• Paper: Preneoplastic stromal cells promote BRCA1-mediated breast tumorigenesis - 10.1038/s41588-023-01298-x
• Accessioned data: GSE174588
• Ingest: 3bb95c61-630d-4970-ae40-8a951bd11cc1

Key Events

• Convert published metadata to HCA spreadsheet
• Manually curate dataset to meet HCA metadata standard
• Collect any matrix and cell-type annotation files
• Are the analysis files suitable for CellxGene? If something is missing get in touch with the authors to request it
• Upload sheet to validate metadata
• Transfer raw files to ingest to validate data files
• Check linking using ingest graph validator
• Ask the Secondary Wrangler for an end-to-end review of the project. Ask the Expertise Wrangler to review specific tabs if needed
• Submit dataset to Production
• Complete the Export SOP
• Convert project data to SCEA format following the SCEA conversion SOP if appropriate

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Using ENA to download bam files and then convert to fastq with bamtofastq.

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hca-util upload area: daf551a8-0658-4282-ab95-4f160af483a6

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id_in_geo_matrices	specimen_id
COH_Patients_CA075_BRCA	BRCA_Pt4
COH_Patients_CA098_BRCA	BRCA_Pt5
COH_Patients_CA1140_Ctrl	NC_Pt4
COH_Patients_CA165_BRCA	BRCA_Pt6
COH_Patients_CA275_Ctrl	NC_Pt5
COH_Patients_CA278_Ctrl	NC_Pt6
COH_Patients_CA287_Ctrl	NC_Pt7
COH_Patients_CA320_BRCA	BRCA_Pt7
COH_Patients_CA460_BRCA	BRCA_Pt10
COH_Patients_CA639_Ctrl	NC_Pt8
COH_Patients_CA719_Ctrl	NC_Pt9
COH_Patients_CA818_BRCA	BRCA_Pt9
COH_Patients_CA843_Ctrl	NC_Pt10
COH_Patients_CB375_Ctrl	NC_Pt11
COH_Patients_CB468_BRCA	BRCA_Pt11
COH_Patients_CB_699_BRCA	BRCA_Pt8
UCI_Patients._BRCA_Ind2_BRCA_Ind2_Epi	BRCA_Pt1
UCI_Patients._BRCA_Ind2_BRCA_Ind2_Stroma	BRCA_Pt1
UCI_Patients._BRCA_Ind3_BRCA_Ind3_Epi	BRCA_Pt3
UCI_Patients._BRCA_Ind3_BRCA_Ind3_Stroma	BRCA_Pt3
UCI_Patients._BRCA_Ind4_BRCA_Ind4_Epi	BRCA_Pt2
UCI_Patients._BRCA_Ind4_BRCA_Ind4_Stroma	BRCA_Pt2
UCI_Patients._Ctrl_Ind10_Ctrl_Ind10_Epi	NC_Pt3
UCI_Patients._Ctrl_Ind10_Ctrl_Ind10_Stroma	NC_Pt3
UCI_Patients._Ctrl_Ind1_Ctrl_Ind1_Epi	NC_Pt1
UCI_Patients._Ctrl_Ind1_Ctrl_Ind1_Stroma	NC_Pt1
UCI_Patients._Ctrl_Ind9_Ctrl_Ind9_Epi	NC_Pt2
UCI_Patients._Ctrl_Ind9_Ctrl_Ind9_Stroma	NC_Pt2

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errors in some extracted fastq files.

ERROR: Error in file /data/d43692c8-e57a-450a-b1c2-05193eec877f/ctrl1_QN_ind1_wd37026_ucsf_normal_basal_luminal_MissingLibrary_1_HY7MKBCXX_S1_L001_I1_001.fastq.gz: line 73: read length too small - 0

Removed empty reads but:

• brca2_QN_ind3_m1161055a_uci_brca_basal_luminal_MissingLibrary_1_HHJ5KBBXX_S1_L001_I1_001.fastq.gz, brca2_QN_ind3_m1161055a_uci_brca_basal_luminal_MissingLibrary_1_HHJ5KBBXX_S1_L002_I1_001.fastq.gz and brca2_QN_ind3_m1161055a_uci_brca_basal_luminal_MissingLibrary_1_HHV2FBBXX_S1_L004_I1_001.fastq.gz had only empty reads, therefore, we removed it from the submission.