Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Metatranscriptomics sequencing of DOES incubation samples

ABSTRACT: The extraction of RNA from sediment samples are carried out using the RNeasy® PowerSoil® Total RNA Kit (Qiagen, Germany) according to the manufacturer’s instructions for metatranscriptomics sequencing.

SUBMITTER: Yu Zhang

PROVIDER: OEX00022922 | NODE | 2024-03-03

REPOSITORIES: NODE

ACCESS DATA

Json Xml

Similar Datasets

Induction of meiosis by embryonic gonadal somatic cells differentiated from pluripotent stem cells

Project description:ESCs of bulk RNA-Seq were harvested and total RNA extracted using Qiagen RNeasy Mini kit, according to the manufacturers’ instruction, including a DNAse digestion. Single-cell library was prepared using smart-seq2 or the 10 × Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v2 according to the manufacturer’s instructions.

2022-01-07 | GSE181501 | GEO

Investigation of a Quality Check for Plasma Samples

Project description:Plasma samples from healthy volunteers were used for the microarray analysis. The fresh sample and intentionally hemolyzed one due to negative pressure were examined. Microarray analyses were performed using the 3D-Gene microRNA microarray platform, and RNA extraction was conducted according to the manufacturer’s instructions. Only a very small amount of total RNA was present in the plasma samples; therefore 2 out of the 4 µl of total RNA extracted from 300- µl of plasma samples were used in microarray experiments.

2016-01-20 | GSE76954 | GEO

Methylation status of CD4+ and CD11b+ cells from Dnmt3a+/+ or Dnmt3aR878/+ mice

Project description:Splenic CD11b+ and CD4+ cells were isolated from Dnmt3a+/+ or Dnmt3aR878/+ mice using LS columns on the magnetic field of QuadroMACS Separator according to the manufacturer’s instructions (Miltenyi Biotec), and the High-Molecular-Weight (HMW) DNA of cells were isolated using MagAttract HMW DNA Kit according to the manufacturer’s instructions (Qiagen). WGBS was performed using the Zymo-Seq WGBS Library Kit (Zymo research) according to the manufacturer’s recommendations at the High Throughput Sequencing Core of Children’s Hospital of Philadelphia, PA, USA. The sequence was generated on Illumina NovaSeq 6000 using NovaSeq 6000 S4 Reagent Kit v1.5 (200 cycles) at 40X coverage

2024-06-04 | GSE255947 | GEO

Epigenome analysis of intracranial aneurysm and superficial temporal artery samples

Project description:Genomic DNA of intracranial aneurysm and matched superficial temporal artery from same patient (n=9) was extracted with QIAamp DNA Mini Kit (Qiagen, Valencia, CA). A total of 500 of genomic DNA was bisulfite conversion using the EZ DNA Methylation Gold Kit (Zymo Research, Irvine, CA) and then analyzed on an Infinium HumanMethylation450 BeadChip (Illumina, San Diego, CA) following the manufacturer’s instructions.

2016-12-01 | GSE75434 | GEO

Metformin treatment on Fusobacterium nucleatum

Project description:High throughput RNA sequencing For RNA sequencing, F. nucleatum was incubated with 1 mM or 5 mM metformin for 7 hours, when the bacterium were under logarithmic phase. Total RNA of F. nucleatum was stabilized with RNA protect Bacteria Reagent (QIAGEN, Germany) and extracted using a QIAGEN RNeasy kit (QIAGEN, Germany) following the manufacturer’s instructions.

2024-04-01 | GSE171561 | GEO

RNA sequencing of PD-L1 knock out human MDA-MB231 cells and mouse CT26 cells

Project description:Although membrane-anchored PD-L1 has been well-studied for its engagement with PD-1 on T cells to evade anti-tumor immunity, whether PD-L1 regulate oncogenic signaling pathways in tumor cells remains elusive. Methods: Total RNA from MDA-MB-231 wild type (WT) , MDA-MB-231 PD-L1 knock-out (KO), CT26 WT or CT26 Pd-l1 KO cells was purified using Qiagen RNeasy mini kit (Qiagen) according to the manufacturer’s instructions. Library preparation and sequenceing analysis were performed at the Molecular Genetics Core facility in Dana-Farber Cancer institute. RNA-seq data was aligned using STAR v2.5.4a. Conclusions: Our study indicates that PD-L1 may regulate genes that are involved in immune response regulating pathways.

2020-06-07 | GSE134510 | GEO

Transcriptomic profiling of ex vivo isolated CD3+CD4+ T cells from spleens of colitic Rag-/- mice received naïve ERαfl/fl and CD4CreERαfl/fl CD4+ T cells

Project description:To study the role of estrogen receptor alpha (ERα) in T cell mediated inflammation, colitis was induced in Rag-/- mice by injecting FACS sorted CD4 T cells from control (ERαfl/fl) and ERα deficient (CD4CreERαfl/fl). After 8 weeks of injection, the CD4+ T cells were FACS sorted from Rag-/- spleens. RNA extraction was carried out and libraries were prepared using Illumina TruSeq RNA sample Preparation kit according to the manufacturer’s instructions.

2018-03-23 | GSE107284 | GEO

Transcriptional profiling (RNA-seq) of wild-type and Arhgap35 knockout embryonic motor neurons (E12.5)

Project description:Ventral spinal cord regions micro-dissected from E12.5 Arhgap35 (aka, p190) knockout embryos or control littermates (wild-type or p190+/-) were pulled and dissociated with papain (Worthington Biochemical Cat# LK003153) according to the manufacturer’s instructions. Cells were sorted on a Becton Dickinson FACS Vantage SE DiVa using Coherent Sapphire 488 nm solid state laser and collected directly into RLT lysis buffer containing β-mercaptoethanol (Qiagen). RNA was isolated using the RNeasy Mini Kit (Qiagen) with on-column DNase digestion (Qiagen RNase-Free DNase Set). Each sample contained between 100,000 and 200,000 GFP+ motor neurons isolated from 2-5 spinal cords during a single experimental session. Five p190-/- and five control RNA samples were quantified with Agilent 2200 TapeStation system prior to preparation of mRNA-sequencing libraries (50 bp single-end) using the Illumina TruSeq RNA Library Preparation Kit (v2) according to the manufacturer’s instructions. Libraries were sequenced with Illumina HiSeq 2500 platform. "Negative" samples are from FACS-sorted Hb9:GFP-negative cells.

2019-05-01 | GSE126534 | GEO

Angiogenesis gene expression upon Notch activation in human vascular smooth muscle cells

Project description:VSMCs were cultured on Jag1 or IgG-coated plates as described above. RNA was extracted using RNA isolation kit (Qiagen). Reverse-transcription PCR was done with RNA-to-cDNA kit (Applied Biosystems). cDNA was run on a TaqMan Low-Density Array, human angiogenesis panel (Applied Biosystems , Cat#4378725), amplified on a 7900 HT Fast Real Time PCR system (Applied Biosystems) according to manufacturer’s instructions.

2011-12-01 | GSE34024 | GEO

Hyaluronic acid ameliorates the proliferative ability of human amniotic epithelial cells through activation of TGF-β/BMP signaling

Project description:This study investigated the mechanism by which 300 kDa HA (1 mg/mL) promotes the proliferation of hAECs. P1 hAECs in logarithmic growth phase were harvested, inoculated into 6-well plates at 3×105/well, and cultured with 5% CO2 at 37 °C. The medium was changed after 3 days, and then the cells were cultured for 18 or 36 h in the presence and absence of HA (300 kDa, 1 mg/mL). The total RNA was purified using the RNeasy MinElute kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions. cDNA was synthesized using a SuperScript III Reverse Transcriptase Kit (Invitrogen, Shanghai, China). Real-time PCR was conducted, and the 2–∆∆Ct method was used to quantify gene expression levels. The signal was collected by Agilent Feature Extraction software and analyzed by Agilent GeneSpring GX software.

2020-08-28 | GSE157002 | GEO

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