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Ena-DATASET-MUG-25-01-2020-09:58:43:375-169 - samples

ABSTRACT: Paired end shallow whole genome sequencing (sWGS) data of tumor tissue from RCC patients (DAIMOND cohort)

PROVIDER: EGAD00001005815 | EGA |

REPOSITORIES: EGA

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ena-DATASET-MUG-25-01-2020-09:55:51:618-168 - samples

Project description:Paired end shallow whole genome sequencing (sWGS) data of cell-free DNA from plasma and urine from RCC patients (DAIMOND cohort)

| EGAD00001005814 | EGA

ena-DATASET-MUG-23-01-2020-15:19:23:857-102 - samples

Project description:Paired end shallow whole genome sequencing (sWGS) data for the identification of somatic copy number alterations (SCNA) and the estimation of tumor fractions in plasma DNA of renal cell carcinoma (RCC) patients (MonRec Cohort)

| EGAD00001005804 | EGA

ena-DATASET-MUG-23-01-2020-15:27:37:770-103 - samples

Project description:Paired end shallow whole genome sequencing (sWGS) data of cell-free DNA from plasma from self-reporting healthy individuals (MonRec Cohort)

| EGAD00001005805 | EGA

ena-DATASET-MUG-01-09-2020-10:55:42:997-687 - samples

Project description:Shallow whole-genome sequencing (sWGS) data for the identification of somatic copy number alterations (SCNA) and the estimation of tumor fractions in plasma DNA of metastatic colorectal cancer patients (mCRC).

| EGAD00001006384 | EGA

ena-DATASET-MUG-25-01-2021-19:08:23:000-259 - samples

Project description:Paired end shallow whole genome sequencing (sWGS) data for the identification of somatic copy number alterations (SCNA) and the estimation of tumor fraction and ploidy sorted malignant CD3+/Vb+ T-cells and corresponding CD19+ non-malignant B-cells

| EGAD00001006901 | EGA

ena-DATASET-MUG-04-05-2020-16:04:36:243-580 - samples

Project description:Paired end (47/98) and single end (51/98) shallow whole genome sequencing (sWGS) data for the identification of somatic copy number alterations (SCNA) and the estimation of tumor fractions in plasma DNA of colorectal cancer (CRC) patients.

| EGAD00001006101 | EGA

ena-DATASET-MUG-25-01-2020-09:49:23:596-166 - samples

Project description:Whole exome sequencing (WES) of tumor tissues from RCC patients (DIAMOND cohort)

| EGAD00001005812 | EGA

ena-DATASET-MUG-02-12-2021-20:16:00:427-345 - samples

Project description:Paired end shallow whole genome sequencing (sWGS) data for the identification of genomewide somatic copy number alterations (SCNA) and the estimation of tumor fractions.

| EGAD00001008397 | EGA

ena-DATASET-MUG-25-01-2020-09:52:56:047-167 - samples

Project description:A 2.077Mb (57306 probes) personalised capture panel [Tailored Panel Sequencing (TAPAS)] was designed based upon the somatic SNVs identified by WES of RCC patient FF and FFPE tissue samples and applied to cfDNA in plasma and urine.

| EGAD00001005813 | EGA

Antibody against TDP-43 phosphorylated at serine 375 suggests conformational differences of TDP-43 aggregates among FTLD-TDP subtypes.

Project description:Aggregation of hyperphosphorylated TDP-43 is the hallmark pathological feature of the most common molecular form of frontotemporal lobar degeneration (FTLD-TDP) and in the vast majority of cases with amyotrophic lateral sclerosis (ALS-TDP). However, most of the specific phosphorylation sites remain to be determined, and their relevance regarding pathogenicity and clinical and pathological phenotypic diversity in FTLD-TDP and ALS-TDP remains to be identified. Here, we generated a novel antibody raised against TDP-43 phosphorylated at serine 375 (pTDP-43S375) located in the low-complexity domain, and used it to investigate the presence of S375 phosphorylation in a series (n = 44) of FTLD-TDP and ALS-TDP cases. Immunoblot analysis demonstrated phosphorylation of S375 to be a consistent feature of pathological TDP-43 species, including full-length and C-terminal fragments, in all FTLD-TDP subtypes examined (A-C) and in ALS-TDP. Of particular interest, however, detailed immunohistochemical analysis showed striking differences in the immunoreactivity profile of inclusions with the pTDP-43S375 antiserum among pathological subtypes. TDP-43 pathology of ALS-TDP, FTLD-TDP type B (including cases with the C9orf72 mutation), and FTLD-TDP type C all showed strong pTDP-43S375 immunoreactivity that was similar in amount and morphology to that seen with an antibody against TDP-43 phosphorylated at S409/410 used as the gold standard. In stark contrast, TDP-43 pathology in sporadic and genetic forms of FTLD-TDP type A (including cases with GRN and C9orf72 mutations) was found to be almost completely negative by pTDP-43S375 immunohistochemistry. These data suggest a subtype-specific, conformation-dependent binding of pTDP-43S375 antiserum to TDP-43 aggregates, consistent with the idea of distinct structural TDP-43 conformers (i.e., TDP-43 strains) as the molecular basis for the phenotypic diversity in TDP-43 proteinopathies.

| S-EPMC7547034 | biostudies-literature

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