Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 1000

GNPs Testing Samples Groups by BSN

ABSTRACT: Testing GNPs from raw data samples Nudibranchia and Achantostrongylophora.

INSTRUMENT(S): GCT

ORGANISM(S): Achantostrongylophora Ingens Nudibranchia (ncbitaxon:70849)

SUBMITTER: Berlian Safriana Nuraulia

PROVIDER: MSV000088261 | MassIVE | Sun Oct 24 00:37:00 BST 2021

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

GNPs Testing 2 Samples BSN October

Project description:Testing GNPs again with the same samples in 6th of October 2021

2021-10-06 | MSV000088195 | MassIVE

GNPS Testing Samples Groups by BSN

Project description:Testing GNPs from raw data samples Nudibranchia and Achantostrongylophora.

2021-10-24 | MSV000088261 | GNPS

Testing data

Project description:Testing data

| PRJNA562298 | ENA

Testing

Project description:Testing

| PRJEB12736 | ENA

Testing

Project description:Testing

| PRJEB34844 | ENA

Gnps stage 1 molecular network training

Project description:analyze the lc-ms raw data with molecular networking using gnps

2024-11-18 | MSV000096464 | MassIVE

Integrating whole blood transcriptomic collection procedures into the current anti-doping testing system, including long-term storage and re-testing of anti-doping samples

Project description:Recombinant human erythropoietin administration studies involving transcriptomic approaches have demonstrated a gene-expression signature that could aid detection of blood doping. However, current anti-doping testing does not involve blood collection into tubes with RNA preservative. This study investigated if whole blood in long-term storage and whole blood leftover from standard haematological testing in short-term storage could be used for transcriptomic analysis despite lacking RNA preservative. Whole blood samples were collected from thirteen and fourteen healthy males, for long-term and short-term storage experiments. Long-term storage: whole blood collected into Tempus™ tubes and K2EDTA tubes and subjected to long-term (i.e., −80°C) storage and RNA extracted. After storage, K2EDTA tubes were thawed and extracted using GeneJET RNA Purification Kit (Thermo Fisher Scientific, Vilnius, Lithuania) or Tempus™ Spin RNA Isolation Kit (Life Technologies, Carlsbad, CA, USA). RNA quality and purity was sufficient for gene expression analysis. Principle Component Analysis of microarray and RNA-seq gene expression data for long-term storage: When comparing gene expression between blood tubes with and without RNA preservation, 6% (4058 transcripts) were differentially expressed. RNA quantity, purity and integrity was not significantly compromised from long-term storage in blood storage tubes lacking RNA preservative, indicating that transcriptomic analysis could be conducted using anti-doping samples collected or biobanked without RNA preservation.

2021-08-13 | GSE181970 | GEO

Transcriptome analysis of human blastocysts with different levels of chromosomal mosaicism after preimplantation genetic testing.

Project description:An inner cell mass biopsy and the remaining trophectoderm were separately collected from 14 blastocysts with preimplantation genetic testing result into RNAse-free PCR tubes containing 2 µl of 10X reaction buffer (SMART-Seq v4 Ultra-Low Input RNA kit for Sequencing, Takara Bio, USA). cDNA was obtained from mRNA with 3′SMART-Seq CDS primer II (Takara Bio, USA) and PCR-amplified (17 cycles) from 10 pg of RNA. Amplified cDNA was purified using AMPure XP magnetic beads (Illumina, USA). After confirming cDNA integrity on a 2100 Bioanalyzer (Agilent Technologies, USA), 1 ng of cDNA per sample were fragmented, and libraries were constructed using NexteraXT DNA sample preparation (Illumina, USA). Samples were quantified using Qubit dsDNA Quantitation Assay (Thermo Fisher Scientific, USA), and 3 samples were excluded due to poor cDNA quality. An RNA pool was generated with 25 samples using equal concentration (5 nM) of RNA per sample. Sequencing was performed in duplicate in a single run using an Illumina NovaSeq 6000 S1 platform (Illumina, USA) with a 200-nucleotide read length in a paired-end design (100-bp fragments). FastQC was used for checking the quality of the raw sequence data. Fragments that did not meet quality requirements were trimmed using Trimmomatic. Alignment and quantification were performed using the Salmon algorithm (reference genome GRCh38). Raw counts were directly used for differential gene expression analysis.

2022-01-31 | GSE194306 | GEO

Comparison between Nestin+ and Nestin- Ptch1 deficient GNPs

Project description:The intermediate filament protein Nestin serves as a biomarker for stem cells and has been used to identify subsets of cancer stem-like cells. However, the mechanistic contributions of Nestin to cancer pathogenesis are not understood. Here we report that Nestin binds the hedgehog pathway transcription factor Gli3 to mediate the development of medulloblastomas of the hedgehog subtype. In a mouse model system, Nestin levels increased progressively during medulloblastoma formation resulting in enhanced tumor growth. Conversely, loss of Nestin dramatically inhibited proliferation and promoted differentiation. Mechanistic investigations revealed that the tumor-promoting effects of Nestin were mediated by binding to Gli3, a zinc finger transcription factor that negatively regulates hedgehog signaling. Nestin binding to Gli3 blocked Gli3 phosphorylation and its subsequent proteolytic processing, thereby abrogating its ability to negatively regulate the hedgehog pathway. Our findings show how Nestin drives hedgehog pathway-driven cancers and uncover in Gli3 a therapeutic target to treat these malignancies. Nestin+ and Nestin- GNPs (granule neuron precursors) were purified from Nestin-CFP/Math1-Cre/Ptch1-loxp cerebella at postnatal day 4 by FACs, and total RNA from these two cell populations were extracted, and then labeled and hybridized to Affymetrix Mouse Genome 430 2.0 arrays.

2016-08-09 | E-GEOD-84392 | biostudies-arrayexpress

EURL reference testing

Project description:EURL reference testing

| PRJEB18618 | ENA