Semi-pure petrobactin analyzed for metal-binding (mzML files for personal use)
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive HF
ORGANISM(S): Methylobacterium Aquaticum (ncbitaxon:270351)
SUBMITTER: 
Allegra Aron
PROVIDER: MSV000098913 | MassIVE | Fri Aug 22 09:02:00 BST 2025
REPOSITORIES: MassIVE
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Project description:Intervention name : S-1 (tegafur + gimeracil + oteracil potassium)
INN of the intervention : S-1: tegafur, gimeracil, oteracil potassium
Dosage And administration of the intervention : 40-60 mg bid day 1 (evening) - day 15 (morning). Repeat cycles every 3 weeks
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INN of the intervention : oxaliplatin
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INN of the intervention : bevacizumab
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Control intervention name : 5-FU (Fluorouracil)
INN of the control intervention : fluorouracil
Dosage And administration of the control intervention : 400 mg/m2 IV bolus on day 1, followed by 2400 mg/m2 over 46 hours. Repeat cycles every 2 weeks.
Control intervention name : l-LV (Levofolinate calcium)
INN of the control intervention : folic acid
Dosage And administration of the control intervention : 200 mg IV on day 1. Repeat cycles every 2 weeks.
Control intervention name : L-OHP (Oxaliplatin)
INN of the control intervention : oxaliplatin
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Project description:This repository contains all the FASTQ files for the five data modalities (scRNA-seq, scATAC-seq, Multiome, CITE-seq+scVDJ-seq, and spatial transcriptomics) used in the article \\"An Atlas of Cells in The Human Tonsil,\\" published in Immunity in 2024. Inspired by the TCGA barcodes, we have named each fastq file with the following convention: [TECHNOLOGY].[DONOR_ID].[SUBPROJECT].[GEM_ID].[LIBRARY_ID].[LIBRARY_TYPE].[LANE].[READ].fastq.gz which allows to retrieve all metadata from the name itself. Here is a full description of each field: - TECHNOLOGY: scRNA-seq, scATAC-seq, Multiome, CITE-seq+scVDJ-seq, and spatial transcriptomics (Visium). We also include the fastq files associated with the multiome experiments performed on two mantle cell lymphoma patients (MCL). - DONOR_ID: identifier for each of the 17 patients included in the cohort. We provide the donor-level metadata in the file \\"tonsil_atlas_donor_metadata.csv\\", including the hospital, sex, age, age group, cause for tonsillectomy and cohort type for every donor. - SUBPROJECT: each subproject corresponds to one run of the 10x Genomics Chromium™ Chip. - GEM_ID: each run of the 10x Genomics Chromium™ Chip consists of up to 8 \\"GEM wells\\" (see https://www.10xgenomics.com/support/software/cell-ranger/getting-started/cr-glossary): a set of partitioned cells (Gel Beads-in-emulsion) from a single 10x Genomics Chromium™ Chip channel. We give a unique identifier to each of these channels. - LIBRARY_ID: one or more sequencing libraries can be derived from a GEM well. For instance, multiome yields two libraries (ATAC and RNA) and CITE-seq+scVDJ yields 4 libraries (RNA, ADT, BCR, TCR). - LIBRARY_TYPE: the type of library for each library_id. Note that we used cell hashing () for a subset of the scRNA-seq libraries, and thus the library_type can be \\"not_hashed\\", \\"hashed_cdna\\" (RNA expression) or \\"hashed_hto\\" (the hashtag oligonucleotides). - LANE: to increase sequencing depth, each library was sequenced in more than one lane. Important: all lanes corresponding to the same sequencing library need to be inputed together to cellranger, because they come from the same set of cells. - READ: for scATAC-seq we have three reads (R1, R2 or R3), see cellranger-atac's documentation. While we find these names to be the most useful, they need to be changed to follow cellranger's conventions. We provide a code snippet in the README file of the GitHub repository associated with the tonsil atlas to convert between both formats (https://github.com/Single-Cell-Genomics-Group-CNAG-CRG/TonsilAtlas/). Besides the fastq files, cellranger (and other mappers) require additional files, which we also provide in this repository: - cell_hashing_metadata.csv: as mentioned above, we ran cell hashing (10.1186/s13059-018-1603-1) to detect doublets and reduce cost per cell. This file provides the sequence of the hashtag oligonucleotides in cellranger convention to allow demultiplexing. - cite_seq_feature_reference.csv: similar to the previous file, this one links each protein surface marker to the hashtag oligonucleotide that identified it in the CITE-seq experiment. - V10M16-059.gpr and V19S23-039.gpr: these correspond to the two slides of the two Visium experiments performed in the tonsil atlas. They are needed to run spaceranger. - [GEM_ID]_[SLIDE]_[CAPTURE_AREA].jpg: 8 images associated with the Visium experiments. Here, GEM_ID refers to each of the 4 capture areas in each slide. - [TECHNOLOGY]_sequencing_metadata.csv: the GEM-level metadata for each technology. It includes the relationship between subproject, gem_id, library_id, library_type and donor_id. These are the other repositories associated with the tonsil atlas: - Expression and accessibility matrices: https://zenodo.org/records/10373041 - Seurat objects: https://zenodo.org/records/8373756 - HCATonsilData package: https://bioconductor.org/packages/release/data/experiment/html/HCATonsilData.html - Azimuth: https://azimuth.hubmapconsortium.org/ - Github: https://github.com/Single-Cell-Genomics-Group-CNAG-CRG/TonsilAtlas
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Project description:Interventions: investigational material(s)
Generic name etc : S-1 (tegafur + gimeracil + oteracil potassium)
INN of investigational material : S-1: tegafur, gimeracil, oteracil potassium
Therapeutic category code : 422 Antimetabolic agents
Dosage and Administration for Investigational material : 40-60 mg bid day 1 (evening) - day 15 (morning). Repeat cycles every 3 weeks
Generic name etc : L-OHP (Oxaliplatin)
INN of investigational material : oxaliplatin
Therapeutic category code : 429 Other antitumor agents
Dosage and Administration for Investigational material : 130 mg/m2 IV on day 1. Repeat cycles every 3 weeks
Generic name etc : BV (Bevacizumab)
INN of investigational material : bevacizumab
Therapeutic category code : 429 Other antitumor agents
Dosage and Administration for Investigational material : 7.5 mg/kg IV on day 1. Repeat cycles every 3 weeks
control material(s)
Generic name etc : 5-FU (Fluorouracil)
INN of investigational material : fluorouracil
Therapeutic category code : 422 Antimetabolic agents
Dosage and Administration for Investigational material : 400 mg/m2 IV bolus on day 1, followed by 2400 mg/m2 over 46 hours. Repeat cycles every 2 weeks.
Generic name etc : l-LV (Levofolinate calcium)
INN of investigational material : folic acid
Therapeutic category code : 392 Antidotes
Dosage and Administration for Investigational material : 200 mg IV on day 1. Repeat cycles every 2 weeks.
Generic name etc : L-OHP (Oxaliplatin)
INN of investigational material : oxaliplatin
Therapeutic category code : 429 Other antitumor agents
Dosage and Administration for Investigational material : 85 mg/m2 IV on day 1. Repeat cycles every 2 weeks.
Generic name etc : BV (Bevacizumab)
INN of investigational material : bevacizumab
Therapeutic category code : 429 Other antitumor agents
Dosage
Primary outcome(s): Progression free survival(PFS)
Study Design: Randomized, open-label, comparative study
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