Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

41 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling of chicken oocyte quality

ABSTRACT: The aim of this study was to assess the impact of oocyte competence on subsequent fertility. Based on knowledge already accessible in mammals and on bioinformatics tools including the chicken genome sequence, we focused on the expression of genes involved in the processes of fertilization and of early embryo development. The study was performed using two complementary approaches: a descriptive study of standard laying hens and then a differential study performed with hens from experimental lines expressing broad variations of achieved fertility (approximately 20 per cent). A differential kinetic study is performed on INRA lines selected on the basis of their fertility potential in purpose of hopefully access gene markers of fertility performance. Experiment Overall Design: All the samples were bissected from the F1 oocyte stage , and DPF+ and DPF- samples were compared in order to find differentially expressed genes that could explain the difference in fertility occuring between the two divergently selected lines. HG+ and HG- samples were compared in order to find differentially expressed genes that could explain the difference in fertility occuring between a single line. Indeed we hypothesize that mechanisms and genes related to fertility between 2 lines or in a single one might be different. Experiment Overall Design: This study had 8 samples (a biological replicate of each sample) : Experiment Overall Design: DPF+ F1 1 and DPF+ F1 2 Experiment Overall Design: DPF- F1 1 and DPF- F1 2 Experiment Overall Design: HG+ F1 1 and HG+ F1 2 Experiment Overall Design: HG- F1 1 and HG F1 2

ORGANISM(S): Gallus gallus

SUBMITTER: sandrine balzergue

PROVIDER: E-GEOD-10231 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

High-throughput sequencing analysis identify miRNAs in 7dpf F1-zebrafish under Î²-diketone antibiotics exposure to F0-zebrafish

Project description:Small RNA high-throughput sequencing technology was used to characterize the miRNAs in F1-zebrafish after 90-day Î²-diketoneÂ antibiotic (DKA) exposure to F0-zebrafish at 6.25 and 12.5 mg/L. The small RNA libraries from 7-dpf F1-zebrafish were constructed. In total, 10,117,347, 9,818,830 and 12,049,949 raw reads were acquired, respectively, under the different DKA-exposure treatments (0, 6.25 mg/L and 12.5mg/L) from the three miRNAs libraries by Illumina sequencing. Low-quality reads were removed, which included 5' contaminants, those missing the 3' primer or insert tag, sequences with a poly A tail, and those shorter than 17 nt and longer than 25 nt. As a result, 8,141,146 (representing 312,735 unique sequences; control), 8,687,210 (representing 251,508 unique sequences; 6.25 mg/L), and 10,569,566 (representing 441,938 unique sequences; 12.5 mg/L) valid reads in the 17 to 25 nt size range were isolated for further analysis. The sRNAs from the three libraries were similar, and the unique sRNA reads were mainly distributed in the 20-24 nt range, among which 22 and 23 nt accounted for 41.8% and 20.0% of total unique sRNA reads, respectively. The 22-nt sRNAs were the most abundant, with the length distribution of counts of sequ-seqs and unique miRNAs displaying a normal distribution. Sample 1: Examination of small RNA in 7-dpf F1-zebrafish after 90-day DKA exposure to F0-zebrafish at 0 mg/L; Sample 2: Examination of small RNA in 7-dpf F1-zebrafish after 90-day DKA exposure to F0-zebrafish at 6.25 mg/L; Sample 3: Examination of small RNA in 7-dpf F1-zebrafish after 90-day DKA exposure to F0-zebrafish at 12.5 mg/L.

2016-07-30 | E-GEOD-85004 | biostudies-arrayexpress

Transcription profiling of chicken oocytes to determine impact of oocyte competence on subsequent fertility

Project description:The aim of this study was to assess the impact of oocyte competence on subsequent fertility. Based on knowledge already accessible in mammals and on bioinformatics tools including the chicken genome sequence, we focused on the expression of genes involved in the processes of fertilization and of early embryo development. A differential kinetic study is performed on INRA lines selected on the basis of their fertility potential in purpose of hopefully access gene markers of fertility performance. We use 4 different hen lines:; - one line of laying hens with 3 different samples: the just ovulated oocyte, the oocyte collected 24 hours before ovulation (F1 stage), and granulosa cells collected at the F1 stage. We could compare different tissue and developmental stages. - one line of hen with rapid growth speed; - two lines of laying hens; For the 3 last lines we used animals with different fertility levels. We collected the oocyte of the largest follicle before ovulation (F1). The aim of the study is to identify genes involved in fertility or early embryo mortality. Experiment Overall Design: 6 arrays - Gallus gallus

2008-11-08 | E-GEOD-7805 | biostudies-arrayexpress

Zebrafish 24hpf whole embryo MZezh2mutant

Project description:Polycomb group (PcG) proteins are transcriptional repressors important to maintain cell identity during embryonic development. Ezh2, the catalytic subunit of the Polycomb Repressive Complex 2, is responsible for placing the epigenetic repressive mark histone H3 lysine 27 trimethylation (H3K27me3). In contrast to results in mouse models, zebrafish embryos mutant for both maternal and zygotic ezh2 (MZezh2) can form a normal body plan at 1 day post fertilization (dpf) but die at 2 dpf, exhibiting pleiotropic phenotypes. To elucidate the specificity of PcG-mediated repression during early zebrafish development, we conducted in depth analysis of the transcriptome, epigenome, and proteome of the MZezh2 mutant embryos at 1 dpf. We found that, despite modifications in the epigenetic landscape, transcriptome and proteome analysis revealed only minor changes in gene and protein expression levels.

2019-09-09 | PXD010922 | Pride

RNA-seq of paired granulosa cells and morulas or blastocysts from naturally and superovulated 3M old mice

Project description:Two major factors contributing to reduced fertility is use of exogenous hormones and old age. We use mouse model to study transcriptional and cell-cell communication changes upon superovulation and ageing in female reproductive cells - oocytes (OC) - and somatic cells - granulosa (GC) - surrounding them. In this experiment, we are testing how different GC transcriptional profiles correlate with embryo quality. 3M old C57BL6/J mice were naturally or superovulated and COCs singularized as described above. Granulosa cells were immediately flash frozen and matched oocytes were divided into individual drops of CARD media under mineral oil for fertilization. The oocytes were incubated in 37oC, 5% CO2 incubator for 30-40 min prior to fertilization. Frozen Mus musculus (C57BL6/J) male sperm straws were thawed and capacitated in Fertiup media for 30 min. Fertilization was achieved by combining 2.5 µl of activated sperm with 20 µl CARD media drop containing a single oocyte and incubated at 37oC, 5% CO2 for 3 hours. Then, oocytes were individually washed in Human Tubal Fluid (HTF) media drops and transferred to 20 µl HFT drops for overnight culture. After 24 hours, fertilization rate was evaluated by 2-cell stage and embryos transferred to G1+ media for further development. Early morula stage embryos were continuously collected based on observation 62-64 h post-fertilization. For late blastocysts, fertilization media was additionally changed to G2+ after 48h post- fertilization and blastocysts collected at 108h post-fertilization. For collection, the embryos were washed in DPBS and flash frozen. Granulosa cells and embryo samples were further processed by Smart-seq2, the cDNA amplification PCR cycle number for embryos was 16-17.

2024-09-22 | E-MTAB-13480 | biostudies-arrayexpress

Ribo-depleted total RNA-seq of oocytes in 3M mice after natural and superovulation

Project description:Two major factors contributing to reduced fertility is use of exogenous hormones and old age. We use mouse model to study transcriptional and cell-cell communication changes upon superovulation and ageing in female reproductive cells - oocytes (OC) - and somatic cells - granulosa (GC) - surrounding them. Here, we are validating the results obtained by a polyA-biased method. Oocytes from naturally and superovulated mice were collected as follows: mice were sacrificed by cervical dislocation and oviducts dissected. Ampullas were torn to release the COCs into a 96 µl M2 media drop under mineral oil at room temperature. Then, 4ul of pre-heated 500 µg/ml hyaluronidase diluted in M2 media (final concentration in the drop 20 µg/ml) was added to separate the COCs into single units. The COCs were incubated for 10-20 min at 37oC and then mechanically separated into individual M2 drops using 115-124 μm glass retransfer pipette. Individual COCs were then washed in M2 once and incubated for less than 5 min with enzymatic mix Accutase at 37oC to further separate granulosa cells from the oocytes. Oocytes were washed twice with M2 media and once with DPBS before collection. Cells were immediately flash frozen in liquid nitrogen in individual 0.2ml thin wall PCR tubes and stored in -80oC until library preparation. SMARTer Stranded Total RNA - Low Input Mammalian kit was used for lysis, cDNA amplification and library preparation with 10 cycles for PCR 1 and 16 cycles for PCR 2. Samples were sequenced as recommended by the manufacturer on Novaseq600 with paired-end sequencing.

2024-09-22 | E-MTAB-13474 | biostudies-arrayexpress

Differentially expressed genes after inhibition of methylation

Project description:Expression microarray of livers from 4 dpf control zebrafish larvae, larvae treated with azacytidine, and ahcy mutant larvae Comparison of expression from livers obtained from ahcy+/+ treated with vehicle, ahcy+/+ treated with azacytidine, and ahcy-/- treated with vehicle. We treated larvae starting at 2 dpf with 1 mM azacytidine or vehicle control. Livers were removed at 4 dpf, RNA isolated, and double amplified.

2013-07-11 | E-GEOD-48804 | biostudies-arrayexpress

Effect of 17 M-NM-2-estradiol on developing zebrafish embryos

Project description:Estrogen signaling is important for vertebrate embryonic development. Here we have used zebrafish (Danio rerio) as a vertebrate model to identify estrogen regulated genes during the first 4 days of development. Zebrafish embryos were exposed to 1 M-BM-5M 17M-NM-2-estradiol from 3 hours post fertilization to 4 days post fertilization, harvested daily and subjected to RNA extraction for transcriptome analysis using microarrays. Estrogen responsive genes were analyzed with hierarchical clustering followed by gene function and tissue expression analysis. Markedly distinct sets of genes were up and down-regulated by estrogen treatment at different time points. Among these genes, only the well-known estrogenic marker vtg1 was co-regulated at all time points. Despite this, the biological functional categories targeted by estrogen were similar throughout zebrafish development. Estrogen responsive genes were enriched mainly in the liver, pancreas and brain. In conclusion, our data shows that in zebrafish distinct cohorts of E2 responsive genes are expressed in a tissue specific manner at different developmental stages. However, the biological pathways that are affected are conserved. 30 embryos were pooled as one sample and exposed to 1 M-NM-<M E2 or vehicle (0.1% DMSO) at approximately 3 hours post fertilization (hpf). At different time points, 1 dpf (24 hpf), 2 dpf (48 hpf), 3 dpf (72 hpf) and 4 dpf (104 hpf), embryos were collected for total RNA extractions. Time points 1 and 2 dpf were performed in biological triplicates of independent pools of RNA while time points 3 and 4 dpf were performed in quadruplicates.

2013-12-31 | E-GEOD-42766 | biostudies-arrayexpress

RNA-seq of wild-type zebrafish embryos developmentally exposed to three addictive drugs

Project description:RNA-seq of wild-type Tüpfel long fin (TLF) zebrafish embryos developmentally exposed to three addictive drugs - 5 µM nicotine, 1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples (6 samples per drug, plus 6 control samples) represents RNA from a pool of seven 5 dpf zebrafish embryos, exposed to the drug between 1 dpf and 5 dpf.

2022-01-24 | E-MTAB-11086 | biostudies-arrayexpress

Early depletion of primordial germ cells in zebrafish promotes testis formation

Project description:The requirement for primordial germ cells (PGCs) during sexual differentiation is variable among vertebrates. It has been shown that in zebrafish complete loss of PGCs in the embryos causes exclusive male development. Further, transplantation of a single PGC into a germline deficient zebrafish embryos generates male exclusively, suggesting PGC number might be important for the ovarian fate.To explore how PGC number might regulate sexual development in zebrafish, we experimentally manipulated its number by injecting dnd MO into embryos to generate fish containing a spectrum of PGC number. The experiment was designed to compare transcriptomes between the developing trunk regions of wild type and dnd morphants at different developmental stages. The dnd MO was microinjected into one cell stage embryos to generate zebrafish with a range of PGC numbers. Transcriptomes of developing trunk regions of wild type and dnd morphants at 14 dpf and 22 dpf were analyzed.

2015-05-08 | E-GEOD-57046 | biostudies-arrayexpress

Transcriptomic analysis reveals the involvement of canonical Wnt signaling in zebrafish gonad differentiation

Project description:Zebrafish males undergo a juvenile ovary to testis type gonadal transformation process. To understand how juvenile ovary-to-testis transformation in zebrafish is genetically regulated, we compared the transcriptomes of juvenile ovary (JO) and juvenile ovotestis (JOT) samples at 35 dpf using the Gonad Uniclone Microarray v1 (ArrayExpress ID: A-MEXP-838). We also analyzed the transcriptomes of the 32 dpf JO, 32 dpf JOT, 34 dpf JOT, and 36 dpf JOT gonads using the slightly modified Gonad Uniclone Microarray v2 and together with the 35 dpf JO and 35 dpf JOT samples, compared the JO samples against the JOT samples to identify genes that could be potentially involved in the gonad transformation process.

2013-12-27 | E-MEXP-3879 | 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