Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Validation of Nextera dual index kits on MiSeq platform

PROVIDER: PRJDB9704 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	DRR223361_1.fastq.gz	Fastqsanger.gz
	DRR223361_2.fastq.gz	Fastqsanger.gz
	DRR223362_1.fastq.gz	Fastqsanger.gz
	DRR223362_2.fastq.gz	Fastqsanger.gz
	DRR223363.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 7

Similar Datasets

Next Generation Metatranscriptome Sequencing of an Anaerobic Hexadecane-Degrading Microbial Consortia

Project description:Purpose: Identification of transcriptionally active genes in the unculturable community constituent, Smithella, during hexadecane degradation; Differential gene expression analysis of hexadecane-relevant genes acoss three different conditions; Extension of metatranscriptomic datasets to other community constituents to identify interspecies relationships. mRNA profiles were generated for this community across three different conditions (hexadecane-, butyric acid-, caprylic acid-degrading conditions) using a modified version of Nextera and sequenced using Illumina's Miseq platform.

2013-10-29 | E-GEOD-49830 | biostudies-arrayexpress

RNA-seq of butyrate micelle or control treated murine Ly6Chi CD11b+ myeloid cells

Project description:We aimed to study the impact of bacteria-derived metabolites in solid organ transplantation. The short-chain fatty acid butyrate was administered using a new drug-delivery method developed by Wang et al. (https://doi.org/10.1038/s41551-022-00972-5). This system is based on a micelle platform that carries and protects butyrate (ButM) from degradation in the upper gastrointestinal tract, to lower distal portions of the gut. Mice (adult B6 females) were treated for 21 days with ButM (100mg/mL) or 1x PBS. Splenic Ly6Chi CD11b+ monocytes were sorted for bulk RNAseq using the Takara SMART-Seq mRNA LP and Unique Dual Index kits. Libraries were sequenced using the Illumina NovaSeq 6000 platform.

2024-04-05 | E-MTAB-13931 | biostudies-arrayexpress

16S rRNA sequencing analysis of bacteiral community composition in antibiotic-treated mouse fecal sample

Project description:Purpose: This study aims to compare and analyze the differences in bacterial community composition in fecal samples from mice treated with Control(DW), Vancomycin (VAN), Ampicillin (AMP), Neomycin (NEO), Metronidazole (MET), and a combination of all antibiotics (ALL, VANM) using 16S rRNA sequencing. Methods: Each antibiotics treated mice's fecal samples were collected and stored -80'c until analyzation. DNA was extracted using the NucleoSpin DNA Stool Kit (MACHEREY-NAGEL) following the manufacturer’s protocol. Metagenomic sequencing was performed on an Illumina MiSeq platform (Illumina), targeting the V3 and V4 regions of the 16S rRNA gene according to the manufacturer's instructions. PCR products were purified using AMPure XP beads, and sequencing adapters were added using the Nextera XT Index Kit (Illumina). The library was further purified with AMPure XP beads and quantified using automated electrophoresis with the TapeStation System (Agilent). Sequencing was performed using the MiSeq v3 reagent kit (Illumina), following the manufacturer’s protocol. Results: QIIME2 (v2023.02) was used to process and analyze 16S rRNA gene amplicon sequencing data, from sequence preprocessing to taxonomic classification. Paired-end sequences were merged and quality-filtered using Deblur. The resulting amplicon sequence variants (ASVs) were used for downstream analyses. Conclusions: Our study presents a comparative analysis of bacterial community composition in fecal samples from antibiotic-treated mice. We observed that microbiota composition varied distinctly depending on the type of antibiotic administered.

2026-01-28 | GSE291841 | GEO

Single cell RNA-Seq of dengue seronegative and seropositive individuals

Project description:Single cell RNA-seq was conducted on peripheral blood mononuclear cells (PBMCs) collected from study participants that were dengue seronegative (n=3) or dengue seropositive (n=3). Baseline single cell gene expression profiling was conducted using 10x Genomics Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index).

2025-09-08 | E-MTAB-13441 | biostudies-arrayexpress

Dual-index pollen meta-barcoding

Project description:Increased throughput for meta-barcoding of mixed pollen samples using a dual-index approach with the Illumina MiSeq platform

| PRJEB8640 | ENA

Homo sapiens

Project description:Endocrine Sensitivity Index Validation Dataset

| PRJNA118415 | ENA

Whole-exome sequencing (WES) of single glands from opposite side of two colorectal tumors and WES of colorectal cancer xenografts derived from single cell culture to study tumor growth dynamics

Project description:Single Gland Whole-exome sequencing: building on our prior description of multi-region WES of colorectal tumors and targeted single gland sequencing (E-MTAB-2247), we performed WES of multiple single glands from different sides (right: A and left: B) of two tumors in this study (tumor O and U) on the illumina platform using the Agilent SureSelect 2.0 or illumina Nextera Rapid Capture Exome kit (SureSelect or NRCE, as indicated in the naming of fastq files). Colorectal Cancer Xenograft Whole-exome sequencing: The HCT116 and LoVo Mismatch-Repair-deficient colorectal adenocarcinoma cell lines were obtained from the ATCC and cultured under standard conditions. For both cell lines, a single âfoundingâ cell was cloned and expanded in vitro to ~6M cells. Two aliquots of ~1M cells were subcutaneously injected into opposite flanks (right and left) of a nude mouse and tumors allowed to reach a size of ~1B cells (1cm3) before the animal was sacrificed. Tumor tissue was collected separately from the right and left lesions and DNA was extracted for WES using the illumina TruSeq Exome kit or Nextera Rapid Capture Exome expanded Kits (Truseq or NRCEe), as was DNA from the first passage population (a polyclonal tissue culture for HCT116 and a polyclonal xenograft sample for LoVo), which were employed as a control to study mutation accumulation in culture and post xenotransplantation.

2017-05-01 | E-MTAB-5547 | biostudies-arrayexpress

Comparison of DNA extraction kits for MiSeq sequencing

Project description:Comparison of DNA extraction kits for MiSeq sequencing

| PRJEB10820 | ENA

ATAC-seq in Arabidopsis thaliana Col and hcr2 mutant

Project description:ATAC-seq of Col and hcr2 mutant from seedling and bud sample. Tagmentation was performed using the Tag DNA enzyme & buffer kit (Illumina, 20034210). Nextera DNA CD Index primers were used for library construction. The indexed libraries were subjected to paired-end 50-bp sequencing using an Illumina HiSeqX instrument (Microgen, Korea).

2022-03-23 | E-MTAB-10790 | biostudies-arrayexpress

human metagenome

Project description:An Improved Dual-Indexing Approach for Multiplexed 16S Microbial Sequencing on the Illumina MiSeq Platform

| PRJNA203369 | ENA