631558d7-490b-4791-9a4e-eff69be29ae6 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001009819 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:This dataset contains the raw sequencing data (Runs) from all of the 10x Genomics single-cell Multiome Experiments
| EGAD00001009824 | EGA
Project description:This dataset contains the raw sequencing data (Runs) for all 10x Genomics single-cell RNA-seq Experiments.
| EGAD00001009823 | EGA
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
2024-05-02 | E-MTAB-13687 | biostudies-arrayexpress
Project description:This dataset contains the raw sequencing data (Runs) from all of the 10x Genomics single-cell Visium Experiments, as well as the corresponding imaging data (Analyses).
| EGAD00001009821 | EGA
Project description:This dataset contains the raw sequencing data (Runs) from all of the 10x Genomics single-cell Visium Experiments, as well as the corresponding imaging data (Analyses).
| EGAD00010002379 | EGA
Project description:This experiment contains two mice genotypes – WT and Bcl3 flx/flx Zbtb46 cre knockouts (both C57BL/6 background). These mice were either infected with 15 cysts of Toxoplasma gondii (ME49 strain) or kept uninfected. Spleens were harvested from mice 7 days post infection and splenocytes were isolated. With four experimental groups (KO/WT and infected/uninfected) and two biological replicate mice per group, we have a total of 8 biological samples comprising of single cell suspensions of splenocytes enriched for CD11c. Single cell RNA-seq libraries were prepared from CD11c-enriched single cells using the Chromium Single Cell 3’ Reagent Kits v3 (10X Genomics; Pleasanton, CA, USA). Eight sample libraries were multiplexed and sequenced 100bp paired end in four different runs of Illumina NextSeq2000, followed by demultiplexing that resulted in multiple raw FASTQ files corresponding to paired reads (R1 and R2), index barcodes (I1) and four sequencing runs (Seq1 - Seq4). The main goal of this project was to define Bcl3-associated transcriptional responses in dendritic cells during T. gondii infection.
2022-08-08 | GSE193532 | GEO
Project description:This dataset contains the raw sequencing data (Runs) from all of the 10x Genomics single-cell CITE-seq Experiments, as well as the demultiplexed cell-donor identities matrices which were generated with Vireo (Analysis).
| EGAD00001009820 | EGA
Project description:We used Visium technology (10X Genomics) to infer cell-to-cell communication in ovarian and uterine tissue based on spatial proximity. Organs from 3-month mice in diestrus and 18-month old mice were collected and frozen in OCT. 10 µm thick tissue slices were placed on Visium Spatial Gene Expression Slides (10X Genomics) and stained with Hematoxylin and Eosin (H&E). Libraries were prepared by manufacturer’s recommendations and sequenced on NovaSeq6000. For samples that were sequenced in two runs, both sequencing runs were merged when running spaceranger (10X Genomics). Original nd2 microscopy images and results of scRNA-seq (linked datasets) and spatial transcriptomics analysis are available at Biostudies (S-BIAD482 and S-BSST852).
2024-01-30 | E-MTAB-12105 | biostudies-arrayexpress
Project description:This dataset contains the raw sequencing data (Runs) for all 10x Genomics single-cell ATAC-seq Experiment.
| EGAD00001009822 | EGA
Project description:mouse retina 10x Genomics Multiome ATAC+RNA data
| PRJNA831452 | ENA