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Rapid Acceleration of Diagnostics - Underserved Populations (RADx-UP): LITE CONNECT: Addressing Testing Gaps and Epidemiologic Disparities of COVID- 19 Among Transgender People in the United States

ABSTRACT: Rapid Acceleration of Diagnostics - Underserved Populations (RADx-UP): LITE CONNECT: Addressing Testing Gaps and Epidemiologic Disparities of COVID- 19 Among Transgender People in the United States

PROVIDER: PRJNA773171 | ENA |

REPOSITORIES: ENA

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Rapid Acceleration of Diagnostics - Underserved Populations (RADx-UP): LITE CONNECT: Addressing Testing Gaps and Epidemiologic Disparities of COVID- 19 Among Transgender People in the United States

Project description:Rapid Acceleration of Diagnostics - Underserved Populations (RADx-UP): LITE CONNECT: Addressing Testing Gaps and Epidemiologic Disparities of COVID- 19 Among Transgender People in the United States

| PRJNA773172 | ENA

Sequence and expression analysis of human chromosome 20 gaps

Project description:The finished human genome-assemblies comprise several hundred un-sequenced euchromatic gaps, which may be rich in long polypurine/polypyrimidine stretches. Human chromosome 20 currently has three remaining un-sequenced gaps on its q-arm. All three gaps are within gene-dense regions, or overlap loci associated with human disorders, including one gap, which is at DLGAP4. In this study we sequenced, determined the complete sizes and assessed epigenetic landscapes of all three un-sequenced gaps on human chromosome 20 using a methodological approach involving Sanger sequencing, mate-pair paired-end high-throughput sequencing and chromatin and methylation analysis. We found histone H3K27me3 to be distributed across all three gaps in immortalized B-lymphocytes. We found five novel CpG islands in one gap to be highly hypermethylated in genomic DNA from both peripheral blood lymphocytes and human cerebellum. One of these CpG islands was differentially methylated and paternally hypermethylated. Furthermore, computational analyses predicted the presence of structured non-coding RNAs (ncRNAs) in all three chromosome 20 gaps. We verified expression for thirteen candidate ncRNAs, some of which showed tissue-specificity. Four ncRNAs expressed within the gap at DLGAP4 show elevated expression particularly in the human brain. Our data suggests that un-sequenced human genome gaps may comprise functional elements. Mate-pair paired end sequencing using genomic DNA from human translocation carriers having chromosomal rearrangments of chromosomes other than chromosome 20 and chromatin, DNA methylation analysis using human peripheral blood lymphocytes and/or human cerebellum tissue. Analysis done for three remaining human chromosome 20 un-sequenced gap regions.

2012-04-17 | E-GEOD-35405 | biostudies-arrayexpress

Six months of gender affirming hormone treatment modifies the methylome in the transgender population

Project description:The main objective was to carry out a prospective global CpG (cytosine-phosphate-guanine) methylation analysis before vs. after six months of gender affirming hormone treatment (GAHT), in a transgender population vs. a cisgender population.

2021-05-03 | GSE173717 | GEO

Microbiome Transgender

Project description:The vaginal microbiome of transgender men receiving gender affirming hormonal therapy in comparison to cisgender woman

| PRJEB71387 | ENA

Sequence and expression analysis of human chromosome 20 gaps

2012-04-17 | GSE35405 | GEO

Hordeum vulgare cultivar:AAC Connect

Project description:Hordeum vulgare cultivar:AAC Connect Genome sequencing

| PRJNA1076538 | ENA

RNA-seq of human Tregs from healthy cisgender and transgender individuals and patients with juvenile-onset systemic lupus erythematosus (JSLE)

Project description:Sexual dimorphisms, which vary depending on age group and pubertal status, have been described across both the innate and adaptive immune system. We explored the influence of sex hormones on Treg differential gene expression in the context of adolescent health (cisgender and transgender individuals) and autoimmunity (juvenile-onset SLE).

2022-09-01 | E-MTAB-11919 | biostudies-arrayexpress

Closing Gaps in the Human Genome with Fosmid Resources Generated from Multiple Individuals

Project description:The published finished human genome contained 340 gaps including 250 gaps in the euchromatic region. The reasons for these gaps were not fully understood, although subsequent analysis revealed that presence of segmentally duplicated sequences were a good predictor for the presence of gaps. However, not all segmentally duplicated regions contained gaps. We made a systemic effort to close euchromatic gaps and understand the nature of gap closing sequences. Our studies clearly demonstrate that the gap closing sequences analyzed were over 2.3-fold more enriched in segmental duplications and that about 40% of the gap closing sequences were structurally variant. The structural variant nature of gap closing sequences was verified by aCGH analysis, and by paired-end-sequence and fingerprint analysis of gap spanning clones from recently available human genome fosmid libraries from eight individuals. Identification and characterization of gap closing sequences provides an effective approach for closing the remaining euchromatic gaps in the human genome. Keywords: comparative genomic hybridization

2007-12-23 | GSE9075 | GEO

CBLL1 is hypomethylated and correlates with cortical thickness in transgender men before gender affirming hormone treatment

Project description:We measured whole-genome DNA methylation by the Illumina Infinium Human Methylation 850 array and reported its correlation with cortical thickness (CTh) in 22 transgender men (TM) experiencing GD versus 25 cisgender men (CM) and 28 cisgender women (CW). With respect to the methylation analysis, TM vs. CW showed significant differences in 35 CpGs, while 2,155 CpGs were found when TM vs. CM were compared. With respect to correlation analysis, TM showed differences in methylation of CBLL1 and DLG1 genes that correlated with global and left hemisphere CTh. Both genes were hypomethylated in TM compared to the cisgender groups. Early onset TM showed a positive correlation between CBLL1 and several cortical regions in the frontal (left caudal middle frontal), temporal (right inferior temporal, left fusiform) and parietal cortices (left supramarginal and right paracentral). This is the first study relating CBLL1 methylation with CTh in transgender persons and supports a neurodevelopmental hypothesis of gender identity

2023-11-03 | GSE237955 | GEO

Characterization of a Distinct Rectal Mucosal Transcriptome among Transgender Women utilizing Cross-Sex Hormone Therapy

Project description:A comparison of rectal mucosal RNA transcriptome findings between transgender women using feminizing hormone therapy, men who have sex with men engaging in receptive anal intercourse, and males who had never engaged in anal intercourse demonstrates differential gene expression involving pathways critical for mucosal inflammation, suggesting the urgent need for further exploration into the immunologic effects of cross-sex hormone therapy in the rectal mucosa and the potential impact on HIV transmission risk at this site.

2023-03-21 | GSE141785 | GEO

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