Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

10X multiome RNA+ATAC sequencing of pooled samples from 5 locations of the adult lung

ABSTRACT: To capture the transcriptional diversity and epigenetic regulation of single cells across different parts of the lung, we profiled adult lung samples from 5 human donors and 5 locations each (trachea, bronchi, parenchyma lower left lobe, parenchyma upper left lobe, parenchyma and small airways from lower left lobe). The 25 samples have been pooled into 5 pools with distinct donor and location combinations. Three libraries from each of the 5 pools have been sequenced, resulting in 15 samples in total.

INSTRUMENT(S): Chromium Controller (10X), Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

SUBMITTER:

PROVIDER: E-MTAB-14583 | biostudies-arrayexpress |

SECONDARY ACCESSION(S): ERP165838

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche - Visium

Project description:Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).

2022-01-06 | E-MTAB-11640 | biostudies-arrayexpress

RNA-seq of mouse iBAT with local acetate administration

Project description:Acetate, or CFMB (Gpr43 agonist), or saline were administrate to left lobe of interscapular brown adipose tissue (iBAT) by a catheter guided pump. Tissue were harvested after four and seven days of administration.

2021-11-20 | E-MTAB-10680 | biostudies-arrayexpress

Alterations of rat liver tissue and hepatic stellate cells during ageing

Project description:Livers for tissue preparation and HSC isolation were derived from 2 and 22 months old male Wistar rats from Janvier Labs (France). Samples from three different lobes (median lobe, left lateral lobe, right lateral lobe) of each liver were collected and pooled for tissue analysis by gene expression. To isolate HSC, the livers were digested with enzyme solutions and HSC were enriched by density gradient centrifugation. HSC were purified by fluorescence-activated cell sorting using their typical retinoid fluorescence emitted after UV-light excitation. The sorted HSC were collected in IMDM supplemented with 10% FCS and 1 % antibiotic-antimycotic solution and cultured for 24 hours. Total RNA of HSC and whole liver tissue from 3 young and 3 old rats was extracted using the Qiagen RNeasy Mini Kit. RNA samples obtained from cultured HSC and whole liver tissues were sent to IMGM Laboratories (Martinsried, Germany) for gene expression analyses by microarrays (Affymetrix, GeneChip Rat Gene 2.0 ST Array, Thermo Fisher Scientific) in triplicates for each age group. The array data were processed by the Transcriptome Analysis Console 3.0 (Thermo Fisher Scientific).

2020-03-12 | E-MTAB-7423 | biostudies-arrayexpress

Gene expression profiles of MBP-specific T cells during experimental autoimmune encephalomyelitis

Project description:2nd generation sequencing was used to compare expression profiles of MBP-specific T cells retrieved from blood, CSF, spinal cord meninges and parenchyma. The overall expression profiles were found to be very similar.However, genes regulated during T cell activation were found to be upregulated in T cells from spinal cord meninges and parenchyma compared to blood and CSF. 2nd generation sequencing of MBP-specific T cells retrieved from blood and CNS compartments during experimental autoimmune encephalomyelitis

2016-02-12 | E-GEOD-75488 | biostudies-arrayexpress

Transcript Profiling of Soybean Seed Compartments Using Laser Capture Microdissection Coupled With RNA-Seq

Project description:We used laser capture microdissection (LCM) to capture soybean seed compartments and profiled the transcriptomes of several compartments using next-generation sequencing. We profiled the transcriptomes of the embryo-proper and the suspensor region from globular stage embryos and the seed coat parenchyma layer of early maturation stage seeds using the Illumina GAIIx system. Illumina sequencing of transcripts from laser-captured embryo proper and suspensor of globular stage embryo and seed coat parenchyma layer of the early maturation stage seed.

2011-05-10 | E-GEOD-29162 | biostudies-arrayexpress

Spatially resolved multiomics of human cardiac niches - Multiome ATAC

Project description:Using Multiome and previously published sc/snRNA-seq data, we studied eight anatomical regions of the human heart including left and right ventricular free walls (LV and RV), left and right atria (LA and RA), left ventricular apex (AX), interventricular septum (SP), sino-atrial node (SAN) and atrioventricular node (AVN). For the first time, we profile the cells of the human cardiac conduction system, revealing their distinctive repertoire of ion channels, G-protein coupled receptors and cell-cell interactions. We map the identified cells to spatial transcriptomic data to discover cellular niches within the eight regions of the heart.

2023-06-13 | E-MTAB-12919 | biostudies-arrayexpress

Spatially resolved multiomics of human cardiac niches - Multiome GEX

2023-06-13 | E-MTAB-12916 | biostudies-arrayexpress

Temporal neocortex mesial temporal lobe epilepsy

Project description:Ion channel splice array data collected from temporal neocortex brain tissue collected from patients with mesial temporal lobe epilepsy. Temporal cortex samples from control subjects were compared to temporal neocortex of patients with mesial temporal lobe epilepsy

2010-06-11 | E-GEOD-6773 | biostudies-arrayexpress

Identification of pro-fibrotic macrophages populations by scRNA-seq in West Highland white terriers affected with canine idiopathic pulmonary fibrosis

Project description:We used the scRNA-seq to characterize disease-related heterogeneity within cell populations of macrophages/monocytes in the bronchoalveolar lavage fluid from West Highland white terriers either healthy or affected with canine idioapthic pulmonary fibrosis. The disease is still not well understood, occurs in old West Highland white terriers and results from deposition of fibrotic tissue in the lung parenchyma causing respiratory failure.

2020-12-02 | E-MTAB-9623 | biostudies-arrayexpress

Fecal microbiota transplant rescues mice from sepsis

Project description:The aim of this study was to test the hypothesis that replenishing the microbiota with a fecal microbiota transplant (FMT) can rescue a host from an advanced stage of sepsis. We developed a clinically-relevant mouse model of lethal polymicrobial gut-derived sepsis in mice using a 4-member pathogen community (Candida albicans, Klebsiella oxytoca, Serratia marcescens, Enterococcus faecalis) isolated from a critically ill patient. In order to mimic pre-operative surgical patient condition mice were exposed to food restriction and antibiotics. Approximately 18 hours prior to surgery food was removed from the cages and the mice were allowed only tap water. Each mouse received an intramuscular Cefoxitin injection 30 minutes prior to the incision at a concentration of 25 mg/kg into the left thigh. Mice were then subjected to a midline laparotomy, 30% hepatectomy of the left lateral lobe of the liver and a direct cecal inoculation of 200 µL of the four pathogen community. On postoperative day one, the mice were administered rectal enema. Mice were given either 1 ml of fecal microbiota transplant (FMT) or an autoclaved control (AC). This was again repeated on postoperative day two. Mice were then followed for mortality. Chow was restored to the cages on postoperative day two, approximately 45 hours after the operation. The injection of fecal microbiota transplant by enema significantly protected mice survival, reversed the composition of gut microflora and down-regulated the host inflammatory response. The cecum, left lobe of the liver, and spleen were isolated from mice for microarray processing with three or more replicates for six expermental conditions: non-treated control, SAHC POD1, SAHC.AC POD2, SAHC.FMT POD2, SAHC.AC POD7, SAHC.FMT POD7

2015-07-30 | E-GEOD-71530 | biostudies-arrayexpress

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