Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single Cell RNA Sequencing of neonatal and juvenile mice skin (wound and unwounded)

ABSTRACT: We perform 10X Genomics scRNA-Seq on P2, P21, P2 + 7 days post wound, P21 + 7 days post wound, with 3 bioreplicates for each condition. Fastq files and output folders were generated from Cellranger pipeline. Loom files were generated using Velocyto.py for downstream analysis. Chemistry: V2

ORGANISM(S): Mus musculus

PROVIDER: GSE153596 | GEO | 2020/07/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Human fetal yolk sac scRNA-seq data (sample ID: F158 for Haniffa Lab; 16099 for HDBR)

Project description:Investigating the blood, immune and stromal cells present in a human fetal embryo in a world first single cell transcriptomic atlas. The embryo was dissected into 12 coronal sections, yolk sac, and yolk sac stalk. Live single cells sorted, with cell suspension then undergoing 10x chromium 5 prime scRNA-seq. This accession contains the yolk sac and yolk sac stalk data from this embryo. A matched accession contains the coronal section data. Lane "WS_wEMB12142156" (from yolk sac) was excluded from downstream analysis due to low fraction reads in cells post-CellRanger QC. Termination procedure for this embryo was medical. The F158_[features...barcodes...matrix].[tsv...mtx].gz files attached to this accession represent raw count data from all the 10x lanes in this accession combined, and as output from CellRanger filtered matrices (CellRanger version 6.0.1 using human reference genome GRCh38-2020-A). One set of count matrices relates to the yolk sac data, and one set of count matrices relates to the yolk sac stalk data.

2022-12-07 | E-MTAB-11673 | biostudies-arrayexpress

Comparing the transcriptome of early and late phase wound macrophages in skin

Project description:We inflicted full thickness excisional wounds in the back skin of C57BL/6 wild-type mice. Injury-associated macrophages were isolated from wound tissue during the early inflammatory phase (4 days post injury) and in the late, scar forming phase (14 days post injury), sorted by flow cytometry (CD45+CD11b+F4/80+ wound cells), and subjected to RNAsequencing.

2021-10-21 | GSE157291 | GEO

Real-time quantitative PCR analysis of murine non-ischemic and ischemic wound edge

Project description:Wound edges from a murine bipedicle flap ischemic wound model were collected 3 days post wounding. RNA from ischemic and non-ischemic wound edges was isolated by miRVana RNA isolation kit. Mature miRNAs were then profiled by real-time PCR.

2015-09-24 | GSE73358 | GEO

Transcriptional profiling of macrophages in skin wounds

Project description:Macrophages were isolated from wounded skin 4 and 14 days post wounding. Monocytes were adoptively transferred on days 2 and 12 and traced into the wound.

2021-10-28 | GSE183489 | GEO

Single cell RNA analysis of breast cancer bone metastases

Project description:For single cell RNA sequencing analysis, whole cell population isolated from two breast cancer bone metastases and associated organoid models were analyzed by 10X genomic single cell RNA platform. Raw BCL files from Novaseq6000 was converted to FASTQ files with cellranger (Version: 3.1.0) mkfastq function. Cellranger count function was then applied for read alignment, barcode and UMI counting using GRCh38 as reference. scCB2 and DoubletFinder were used to predict and remove empty droplets and doublets of single cell data. Cells with number of features less 300 and more than 9000 were further filtered out based on the distribution of number of features. For bulk RNA sequencing, RNA were extracted from FFPE preserved primary tumor and bone metastasis. Library was prepared with TruSeq Stranded mRNA for FFPE kit, and sequenced by NextSeq 500 with high output 150 cycle kit.

2022-02-08 | GSE190772 | GEO

Murine dermal burn wound

Project description:Investigation into murine dermal burn wound. Mouse thermal injury induced, and skin excised at 0 hours, 2 hours, 3 days and 14 days post-injury. Keywords: other

2003-06-23 | GSE460 | GEO

Inflammatory proteins and neutrophil extracellular traps increase in burn blister fluid after 24 hours post-burn

Project description:Burn wound blister fluid is a valuable matrix for understanding the biological pathways associated with burn injury. In this study, 152 blister fluid samples collected from paediatric burn wounds at two different hospitals were analysed using mass spectrometry proteomic techniques. The protein abundance profile at different days post-burn indicated that there were more proteins associated with cellular damage/repair in the first 24 hours, whereas after this point there were more proteins associated with antimicrobial defence and inflammation. The inflammatory proteins persisted at a high level in the blister fluid for more than 7 days. This may indicate that removal of burn blisters prior to two days post-burn is optimal to prevent excessive or prolonged inflammation in the wound environment. Additionally, many proteins associated with the neutrophil extracellular trap (NET) pathway were increased post-burn, further implicating NETs in the post-burn inflammatory response. NET inhibitors may therefore be a potential treatment to reduce post-burn inflammation and coagulation pathology and enhance burn wound healing outcomes.

2024-03-04 | PXD050003 | Pride

Gene expression changes in Tulasnella calospora- Serapias vomeracea mycorrhizal protocorms at stage P2 compared to Tulasnella calospora free-living mycelium

Project description:Illumina HiSeq technology was used to generate mRNA profiles from Tulasnella calospora mycorrhizal protocorms at stage P2 compared to free-living mycelium grown on Modified Melin-Norkrans medium with two different N sources, ammonium (AL13M) and glutamine (AL1 G) . Protocorms were harvested at stage P2 and mycelium after 15 days and used for RNA extraction. Reads of 150bp were generated and aligned to Tulasnella calospora transcripts (http://genome.jgi-psf.org/Tulca1) using CLC Genomics Workbench 9.

2016-12-01 | GSE86968 | GEO

Quantitative proteomic characterization of Foreign Body Response towards silicone breast implants identifies chronological disease-relevant biomarker dynamics

Project description:The aim of this work was to enlighten the disease progression from implant insertion and immediate tissue damage response reflected in (a) the acute wound proteome, and (b) the adsorption of chronic inflammatory wound proteins at implant surfaces. An intra-individual relative quantitation TMT-liquid chromatography-tandem mass spectrometry approach was applied to profile wound proteome formed around SMI the first five days post-implantation.

2023-02-24 | PXD039840 | Pride

Transcription profiling of skin excised from thermal injured mouse to investigate the molecular mechanism of murine dermal burn wound.

Project description:Investigation into murine dermal burn wound. Mouse thermal injury induced, and skin excised at 0 hours, 2 hours, 3 days and 14 days post-injury. Transcription profiling of skin excised from thermal injured mouse to investigate the molecular mechanism of murine dermal burn wound.

2007-11-07 | E-GEOD-460 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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