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Flycatcher genome and transcriptome sequencing

ABSTRACT: Whole genome sequencing and de novo assembly of the collared flycatcher. Population resequencing of additional 9 collared flycatchers and 10 pied flycatchers. Transcriptome sequencing of male/female samples, 9 tissues and embryos of collared and pied flycatchers.

PROVIDER: PRJEB409 | ENA |

REPOSITORIES: ENA

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Project description:Whole genome sequencing and de novo assembly of the collared flycatcher. Population resequencing of additional 9 collared flycatchers and 10 pied flycatchers

| PRJEB2984 | ENA

Proteome Plasticity in Drosophila Hybrids

Project description:This submission contains 3 different datasets: - series A: D. melanogaster female ? D. simulans male embryos vs internal standard of pooled D. simulans and D. melanogaster (1:1) embryos - series B: D. simulans female ? D. melanogaster male embryos vs internal standard of pooled D. simulans and D. melanogaster (1:1) embryos - series E: D. melanogaster female ? D. simulans male adult heads vs internal standard of pooled D. simulans and D. melanogaster (1:1) adult heads Each dataset is in triplicates. Quantitation was performed with isobaric isotopologues labelling.

| MSV000081535 | MassIVE

Watanabe2018_Simple markov model

Project description:Simple Markov model. There are 3 disease states: Healthy, Sick, and Dead, where the Dead state is terminal. The yearly transition probabilities are: Healthy to Dead: 0.01; Healthy to Sick: 0.2 for Male and 0.1 for Female; Sick to Healthy: 0.1; Sick to Dead: 0.3. The transition probability now depends on the cohort (Male or Female) and can be expressed as a function of a Boolean covariate Male. Initial conditions: Healthy = (50 Male, 50 Female), Sick = (0,0) and Dead = (0,0). Output: Number of men and women in each disease state for years 1-10.

2019-01-30 | MODEL1803120004 | BioModels

mRNA-Seq of male and female embyos of the honeybee (Apis mellifera)

Project description:Transcriptional profiling of male and female honeybee embryos 10-15 h, 25-40 h, 55-70 h after egg laying was performed by RNA-SEQ. The sex specific expressed and spliced genes were examined comparing male and female embryos.

2021-01-01 | GSE159387 | GEO

Watanabe2018_State Transition Model with Treatment and Costs

Project description:Model with functions depending on Age, Male, BP (Blood Pressure). There are 3 disease states: Healthy, Sick, and Dead, where the Dead state is terminal. The yearly transition probabilities are: Healthy to Dead: Age/1000; Healthy to Sick: According to function F1 depending on Age and Male and BP; Sick to Healthy: 0.1; Sick to Dead: according to function F2 depending on Age and Male. Pre-Transition Rules: Age increased by 1 and BP by Age/10 each simulation cycle. Post-Transition Rules: Treatment = BP>140 , becomes 1 when BP crosses 140 threshold; BP =BP-Treatment*10 , meaning a drop of 10 once treatment is applied; CostThisYear = Age + \Treatment*10 , cost depends on age and if treatment was taken; Cost= Cost + CostThisYear , it accumulates cost over time. Initial conditions: Healthy = (50 Male, 50 Female with Age =1,2,...,50 for each individual), BP =120, Sick = (0,0) and Dead = (0,0). Output: Number of men and women in each disease state for years 1-10 and their ages and costs in each state. A stratified report by male and female and young – up to age 30 and old above age 30 is produced.

2019-01-30 | MODEL1803120006 | BioModels

Plasma proteomic profile by regular training in male and female basketball players: a preliminary study

Project description:Aim of the present study is to identify sex-related sport adaptation proteins in female and male basketball players using proteomics approach on plasma samples withdraw from athletes during in-season training period but far from a competition. A cohort of 20 professional basketball players, 10 females (BF) and 10 males (BM), and 20 sedentary males (10 CM) and females (10 CF) as control, of comparable age and BMI were involved in this study. Protein profiles of plasma samples obtained from BM, BF, CM and CF were analysed by 2-DE. Differentially expressed proteins were identified by mass spectrometry. The computational 2-DE gel image analysis pointed out 33 differentially expressed protein spots (ANOVA p-value<0.05) and differences between male and female are more evident among the players than controls. The expression profile of 54.5% of the total proteins is affected by the sport activity. 14 proteins are differentially expressed in basket female players in comparison with their relative controls while 7 are differentially expressed in basket male players in comparison with their controls. In conclusion, we identify in female athletes a reduction in proteins related to transcription regulation, most of these modulate chronic inflammation confirming the anti-inflammatory effect of regular training in female muscle metabolism. In male and female athletes, we found a decrease in Transthyretin involved in muscle homeostasis and regeneration and Dermcidin a stress-induced myokine linked to inflammatory and it will be interesting to fully understand the role of its different isoforms in male and female skeletal muscle contraction.

2022-05-20 | PXD031050 | Pride

Whole Genome Sequencing and Haplotyping of Blastocyst Biopsies

Project description:Current methods available for pre-implantation genetic diagnosis (PGD) of in vitro fertilized (IVF) embryos do not detect de novo. Detection of these types of mutations requires whole genome sequencing (WGS). In this study advanced massively parallel WGS was performed on three 5-10 cell biopsies from two blastocyst-stage embryos. Overall, greater than 95% of each genome was called and experimentally derived haplotypes and barcoded read data were used to detect and phase up to 82% of de novo single base mutations with a false positive rate of ~1 error per Gb. These results suggest that phased WGS using barcoded DNA could be used in the future as part of the PGD process to maximize comprehensiveness in detecting disease causing mutations and reduce the incidence of genetic diseases.

| phs000858 | dbGaP

Array based comparative genomic hybridisation analysis of 1 Mb resolution of 21 follicular lymphomas (FL), 31 transformed diffuse large B-cells lymphomas (DLBCL), 29 de novo DLBCL (10 of GC and 19 non-GC related immunophenotype).

Project description:Follicular lymphoma (FL) is one of the most common types of indolent B-cell lymphoma in Western countries. FL commonly transforms to more aggressive diffuse large B-cell lymphoma (DLBCL) at reported frequencies between 15 - 60%. We have used microarray comparative genomic hybridisation (aCGH) at 1 Mb resolution to study copy number changes in paired tumor samples (primary FL and a subsequent tDLBCL) as well as de novo DLBCL cases to outline genetic mechanisms of transformation from follicular lymphoma to diffuse large B-cell lymphoma. Single hybridization per case. 21 FL, 31 transformed DLBCL, 29 de novo DLBCL (10 GC and 19 non-GC DLBCL). Tumor labelled with Cy5 and reference with Cy3. Mixture of 20 normal male or female genomic DNA was used in sex-mismatched hybridization.

2014-04-18 | E-GEOD-56884 | biostudies-arrayexpress

Transcriptome of the chicken chorioallantoic membrane from male and female embryos, after 11 and 15 days of incubation

Project description:The aim the the sequencing project was to investigate differentially expressed genes between fertilized eggs incubated during 11 or 15 days of incubation (EID11 and EID15). At each stage (EID11 and EID15), chorioallantoic membranes from 10 male embryos and 10 females embryos were collected and processed for RNA extraction and RNAseq analysis (n=40 in total). Thus, the design of the protocol also allowed comparison of differentially expressed genes in the chorioallantoic membrane between male and female embryos

2023-01-20 | GSE199780 | GEO

Transcription profiling of mouse prospermatogonia, pachytene oogonia, and gonadal somatic cells from 15 day post-conceptus fetuses and pachytene spermatocytes from adults

Project description:RNA expression microarray analysis of prospermatogonia in 15 day post-conceptus (dpc) fetuses, a stage when they are undergoing rapid de novo DNA methylation. For comparison, we also analysed 15 dpc pachytene oogonia, 15 dpc female and male gonadal somatic cells, and adult pachytene spermatocytes.

2008-12-16 | E-TABM-412 | biostudies-arrayexpress

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