Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Dorsal-ventral inversion in the air-filled organ (lungs, gas bladder) of vertebrates: RNA-sequencing of laser capture microdissected embryonic tissue

ABSTRACT: Dorsal-ventral inversion in the air-filled organ (lungs, gas bladder) of vertebrates: RNA-sequencing of laser capture microdissected embryonic tissue

PROVIDER: PRJNA641133 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR12068800.fastq.gz	Fastqsanger.gz
	SRR12068801.fastq.gz	Fastqsanger.gz
	SRR12068802.fastq.gz	Fastqsanger.gz
	SRR12068803.fastq.gz	Fastqsanger.gz
	SRR12068804.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 36

Similar Datasets

Dorsal-ventral inversion in the air-filled organ (lungs, gas bladder) of vertebrates: RNA-sequencing of laser capture microdissected embryonic tissue

Project description:How modification of gene expression generates novel traits is key to understanding the evolutionary process. Here we investigated the genetic basis for the origin of the piscine gas bladder from lungs of ancestral bony vertebrates. Distinguishing these homologous organs is the direction of budding from the foregut during development; lungs bud ventrally and the gas bladder buds dorsally. We investigated whether this morphological inversion is associated with the molecular inversion of conserved genes regulating lung and gas bladder development. Using laser-capture microdissection and RNA-seq, we assayed transcript abundance and compared expression patterns between dorsal and ventral foregut tissues at three developmental stages spanning gasbladder development. Our focal taxon, bowfin (Amia calva), representing the sistergroup to teleosts, is an early diverging ray-finned fish with a gas bladder. We discovered a number of genes with unknown function during lung development that are differentially expressed during gas bladder development and annotated to functions relevant for organ budding. We also identified several known lung-regulatory genes that exhibit inverted dorsoventral expression during gasbladder development relative to lung development. In particular, we found Tbx5 is strongly expressed in the dorsal mesoderm surrounding the gas bladder during bowfin development, and several interacting genes are co-expressed dorsally with Tbx5. In contrast, in mouse and bichir (Polypterus senegalus), the only ray-finned fish that have lungs, Tbx5 is expressed in the ventral lung mesoderm during lung development. Our data demonstrating dorsoventral inversion of conserved genes suggest that these genes may have contributed to the evolutionary transition between ventral lungs and a dorsal gas bladder in ray-finned fishes.

2021-05-12 | GSE152992 | GEO

Dorsoventral inversion of the air-filled organ (lungs, gas bladder) in vertebrates: RNAsequencing of laser capture microdissected embryonic tissue.

Project description:How modification of gene expression generates novel traits is key to understanding the evolutionary process. We investigated the genetic basis for the origin of the piscine gas bladder from lungs of ancestral bony vertebrates. Distinguishing these homologous organs is the direction of budding from the foregut during development; lungs bud ventrally and the gas bladder buds dorsally.

| S-EPMC8094346 | biostudies-literature

Laser-capture microdissected invasive micropapillary carcinomas of the breast

Project description:The purpose of this study was to identify differentially expressed genes in laser-capture microdissected (LCM) invasive mammary carcinomas (IMCs).

2011-04-25 | GSE28821 | GEO

Expression data from laser microdissected murine intestinal epithelial cells

Project description:Microarray analyses of laser microdissected murine intestinal epithelial cells under the control of maternal inflammation at 17.5 days post conception demonstrates that maternal inflammation differentially regulates 2174 (iWT) and 3345 (iARE) genes in fetal tissue, but these transcriptional profiles were overwritten in the postnatal environment dominated by tissue inflammation at 8 weeks postnatal. We isolated 50 ng total RNA out of laser microdissected fetal and adult intestinal epithelial cells from the distal ileum and performed microarrays to address whether maternal inflammation programs the fetal intestine towards TNF-driven pathology

2014-05-05 | GSE44433 | GEO

Gene expression profiling of laser capture microdissected prostate specimens

Project description:We performed gene expression profiling of laser capture microdissected normal non-neoplastic prostate (cystoprostatectomies) epithelial tissue and compared it to non-transformed and neoplastic low and high grade prostate epithelial tissue from radical prostatectomies, each with its immediately surrounding stroma.

2017-09-12 | GSE97284 | GEO

Laser-capture microdissected invasive micropapillary carcinomas of the breast

Project description:The purpose of this study was to identify differentially expressed genes in laser-capture microdissected (LCM) invasive mammary carcinomas (IMCs). Invasive mammary carcinoma of the breast surgical resection specimens were laser capture microdissected for RNA extraction and hybridization to Affymetrix microarrays.

2011-04-25 | E-GEOD-28821 | biostudies-arrayexpress

Gene expression profiles obtained from laser-microdissected human choroid plexus papilloma cells

Project description:Gene expression profiles generated from human tumor cells laser-microdissected from surgical samples of seven choroid plexus papillomas (Grade I WHO) as eight samples of epithelial cells lasermicrodissected from normal choroid plexus obtained at autopsy.

2009-02-01 | GSE14098 | GEO

Inversion breakpoints in Drosophila

Project description:Inversion evolutionary rates might limit the experimental identification of inversion breakpoints in non-model species

| PRJEB23256 | ENA

Gene expression profiles in 132 laser microdissected colorectal cancer tissues

Project description:Tissues from another series of 132 patients with colorectal cancer were collected by laser micro-dissection with the Leica Laser Microdissection System (Leica Microsystems). Gene expression levels obtained from 132 microdissected colorectal tumors were compared with microdissected normal colon epitheliums. we used the commercially available Human Whole Genome Oligo DNA Microarray Kit (Agilent Technologies). Labeled cRNAs were fragmented and hybridized to an oligonucleotide microarray (Whole Human Genome 4×44K Agilent G4112F). Fluorescence intensities were determined with an Agilent DNA Microarray Scanner and were analyzed using G2567AA Feature Extraction Software Version A.7.5.1 (Agilent Technologies).

2011-08-31 | E-GEOD-21815 | biostudies-arrayexpress

Gene expression profiles in 74 laser microdissected colorectal cancer tissues

Project description:Tissues from another series of 74 patients with colorectal cancer were collected by laser micro-dissection with the Leica Laser Microdissection System (Leica Microsystems). Gene expression levels obtained from 74 microdissected colorectal tumors were compared with 5 microdissected normal colon epitheliums. We used the commercially available Human Whole Genome Oligo DNA Microarray Kit (Agilent Technologies). Labeled cRNAs were fragmented and hybridized to an oligonucleotide microarray (Whole Human Genome 4×44K Agilent G4112F). Fluorescence intensities were determined with an Agilent DNA Microarray Scanner and were analyzed using G2567AA Feature Extraction Software Version A.7.5.1 (Agilent Technologies).

2013-08-31 | E-GEOD-35279 | 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