Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

1cc14008-e4e2-4ca7-8bc3-b23f66e85760 - samples

ABSTRACT: This dataset contains single-cell RNA sequencing data from patients with thyroid cancer (n=7), multinodal Goiter (n=3) and healthy individuals (n=5). Mononuclear cells were taken from both the peripheral blood and the bone marrow compartments. We used a pooled single-cell design where multiple individuals were pooled in a single sample for sequencing (NextSeq 500-V2) and later demultiplexed using their genotype data. Associated metadata contains information on the phenotypes per individual, the pooling design and the linkage between the supplied files and sequenced pools. Due to limitations from EGA in uploading single-cell data, the raw fastq files were processed as follows: (i) I1/I2/R1/R2 fast files were concatenated over the different lanes. (ii) Concatenated I1 and I2 files were interleaved, as were the concatenated R1 and R2 files to generate two fastq files per pool containing all the information. To interleave the fastq files, the BBmap tool bbmap/reformat.sh was used, which can also be used to de-interleave the files.

PROVIDER: EGAD00001008108 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Similar Datasets

Role of Bcl3 in Dendritic cell function in the context of Toxoplasma gondii infection

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

554dd5bd-a656-41fb-82c8-1e6d002d0638 - samples

Project description:Single cell RNA-sequencing of treatment naÃƒÂ¯ve PDAC patient samples. We have 10 samples, sequenced using the 10X genomics chromium platform with 3 prime chemistry. We are submitting FASTQ files representing the index files (I1), Read1 (R1) and Read2 (R2).

| EGAD00001008961 | EGA

e9bc4a5b-d4f6-4bea-b043-78924e5886a8 - samples

Project description:Single-cell RNAseq dataset of paired normal and tumor human prostate biopsies from n=10 participants. Fastq files corresponding to R1, R2 and I1 are uploaded and were generated from cellranger mkfastq. Data was sequenced on Illumina HiSeq 4000.

| EGAD00001008340 | EGA

9163c19f-69f7-43d4-859f-bdec62f381bd - samples

Project description:This dataset contains raw sequencing files associated with the paper "Neutrophils and emergency granulopoiesis drive immune suppression and an extreme response endotype during sepsis" (https://doi.org/10.1038/s41590-023-01490-5). It is composed of two experiments, which are as follows: 1. Single-cell profiling of whole blood leukocytes: This experiment comprises sequencing files generated using the BD Rhapsody single-cell multi-omics profiling (RNA + protein) platform. This platform was used to profile the whole blood leukocyte population in a cohort of sepsis patients, cardiac surgery controls and healthy controls. There are 48 samples and four files per sample: two paired-end FASTQ files (R1 and R2) corresponding to the RNA-seq library, and two paired-end FASTQ files (R1 and R2) corresponding to the protein profiling (ADT-based AbSeq) library. 2. Single-cell profiling of circulating HSPCs: This experiment comprises sequencing files generated using the 10X single-cell multi-omics (RNA-seq + ATAC-seq) profiling platform. This platform was used to profile circulating HSPCs in a cohort of sepsis patients and healthy controls. There are 5 samples (or plexes), each of which consists of a pool of individuals for whom cells were multiplexed and sequenced as a single sample. There are four files per sample: two paired-end FASTQ files (R1 and R2) corresponding to the RNA-seq library, and two paired-end FASTQ files (R1 and R2) corresponding to the ATAC-seq library. Because these samples consists of multiplexed pools, index files are also provided. These can be used for sample deconvolution using the Cell Ranger pipeline. NOTE: Due to EGA's constrains in the number of files permitted per sample, index files (I1 and I2) for the HSPC data set are provided as a separate experiment named "FASTQ index files (I1 and I2) for deconvolution of 10X single-cell multiomics libraries".

| EGAD00001010927 | EGA

0c903f58-2e89-4994-932f-a802828f8767 - samples

Project description:The dataset includes 12 paired FASTQ files (6 samples) with single cell transcriptome sequencing data of normal breast luminal cells from ducts and TDLUs derived from reduction mammoplasties from three patients. Chromium Single Cell 3Ã¢Â€Â™ Reagent Kit v2 or v3 (10x Genomics) were used for processing of cells, whereafter sequencing was performed using the IlluminaÃ‚Â® NextSeq500/550 High Output Kit v2. Cell Ranger was used for generating FASTQ files and files from different lanes were concatenated prior to uploading the data to EGA. "R1" files include the feature barcodes and UMIs, while "R2" files include the reads.

| EGAD00001008499 | EGA

977e192e-cfe4-495d-8125-60fa1b5eefde - samples

Project description:The dataset contains 200 fastq files of Illumina 5'end RNA sequencing data of 50 PBMC samples. The paired-end data includes 100 fastq files (R1 and R2) of 50 full-length cDNA sequencing libraries and 100 fastq files (R1 and R2) of 50 HLA amplicon sequencing libraries.

| EGAD00001006838 | EGA

Integrated genomics of Crohn’s disease risk variant identifies a role for CLEC12A in antibacterial autophagy

Project description:Using integrated genomics we identify a role for CLEC12A in antibacterial autophagy. Clec12a-/- mice are more susceptible to bacterial infection and CLEC12A deficient cells exhibit impaired antibacterial autophagy. We used transcriptional profilinf to understand the role of CLEC12A in the response to Salmonella and Listeria. Bone marrow-derived macrophages from WT or Clec12a-/- mice were infected with Salmonella enterica serovar Typhimurium or Listeria monocytogenes. Cells were harvested at 0,3,6, and 24hours post-infection for RNA analysis. Please note that single-end sequencing was performed but two files: R1 files that contained the sample barcodes (19 or 17bp reads) and R2 files that contained the single-end-sequenced 46bp cDNA reads were generated. Since the barcode info is mostly redundant, only R2 reads were submitted (described in 'raw_file_readme.txt').

2015-06-30 | E-GEOD-69132 | biostudies-arrayexpress

Transcriptional regulation of germinal center B and plasma cell fates by dynamical control of IRF4 (ChIP-seq)

Project description:Temporal analysis of Irf4 and PU.1 genome binding during B cell activation and differentiation in vitro using antigen (NP-Ficoll) CD40L and IL-2/4/5 cytokines (see Molecular Systems Biology 7:495 for details of cellular system). The results provide insight in the target genes and binding specificity of IRF4 and PU.1 during coordination of different programs of B cell differentiation. Regrettably three of the FASTQ raw sequence files in our study were corrupted during storage. FASTQ data from our experimental and control groups are available for download via GEO SRA; however, two groups are missing select raw sequence files. These include one PU.1 Day 3 group file (Sample GSM1133499) and two of four input files used to generate a concatenated “super” input file (Sample GSM1133490); the raw data provided for input consists of the two input files recovered. Importantly, FASTA sequences for both of these datasets are available as supplementary data through GEO, and we can make available upon request (rsciamma@uchicago.edu) all files in our study in the ELAND-extended alignment format. Please note that GEO no longer supports this format.

2013-05-04 | GSE46607 | GEO

Immune Transcriptome Study of Human Nucleated Erythroid Cells from Different Tissues by Single-Cell RNA-Sequencing

Project description:Purpose: studying of immunity-related genes in CD235a erythroid cell in order to validate previous findings on the subject using single cell RNA sequencing (scRNA-seq) and its benefits such as mRNA co-localization in a single cell and cell specific marker gating of populaions of interest. Methods: we extracted mononuclear cells from the fetal liver, the fetal thymus, the cord blood and the adult bone marrow, performed magnetic separation of CD235a (Erythroid) cells, marked magnetically separated cells with BD Sample Tags, loaded the cells on a BD Rhapsody cartridge, lysed the cells, performed reverse transcription, cDNA library preparation, QC of final cDNA libraries by BioAnalyzer 2000 and Qubit 4, pooled the final cDNA libraries, sequenced them on a Illumina NextSeq 550 sequencer. Then, we processed FASTQ R1 and R2 files using the BD Pipeline V1.9 and got final metrics in a mols_per_cell.tsv file. Results: in this work, we investigated other possible immunity-related functions on a single cell level using RNA sequencing of adult bone marrow, cord blood and fetal liver NECs and found that NECs from every studied origin expressed ARG1, CXCL5, CXCL8, DEFA3, DEFA4, IL1B, IL15, IL18, IGHE (secreted), LGALS3, LAGLS9, TGFB3 and VEGFA. Conclusions: our study allows to access new potential immunological roles of CD235a erythroid cells, both validated and discarded previous results regarding cytokine and chemokine gene expression in erythroid cells.

2022-05-04 | GSE199230 | GEO

f7575ebd-d0b5-4c67-801a-1f3868f5baf4 - samples

Project description:scRNA-seq dataset on a patient (P_IKZF2-het) presenting with immune dysregulation. This dataset contains raw and processed files from scRNA-seq performed on samples using the 10x Genomics Chromium Controller with the Chromium Single Cell 3Ã¢Â€Â² Reagent Kit (v3 chemistry). There are three paired-end (75 bp) fastq files (I1, R1, R2) and three processed files generated with 10x Genomics Cell Ranger v3.0.2 software against GRCh38 human reference transcriptome (scrnaseq_P_IKZF2-het_barcodes.tsv.gz, scrnaseq_P_IKZF2-het_features.tsv.gz, scrnaseq_P_IKZF2-het_matrix.mtx.gz).

| EGAD00001008443 | EGA

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data