Project description:Genome editing was conducted on a t(3;8) K562 model to investigate the effects of deleting different modules or CTCF binding sites within the MYC super-enhancer. To check mutations after targeting with CRISPR-Cas9 we performed amplicon sequencing using the Illumina PCR-based custom amplicon sequencing method using the TruSeq Custom Amplicon index kit (Illumina). The first PCR was performed using Q5 polymerase (NEB), the second nested PCR with KAPA HiFi HotStart Ready mix (Roche). Samples were sequenced paired-end (2x 250bp) on a MiSeq (Illumina).

2021-07-26 | E-MTAB-9937 | biostudies-arrayexpress

KACST_test

Project description:the Ecoli fastq file

| PRJEB13962 | ENA

SRiD- A facile DNA barcode generation and management system for high throughput screening

Project description:20 random DNA barcodes were designed in silico and transfected into PC3 cells. Barcodes were sequenced using Illumina-Miseq technology to find the sequence and their respective copy numbers. Current file contains the raw data of these DNA barcodes in fastq format Validating an algorithm called SRiD that generates random DNA barcodes that do not match a genome of interest, in this case human genome. 20 DNA barcodes were used for this validation.

2016-03-31 | E-GEOD-67441 | biostudies-arrayexpress

peat metagenome

Project description:Illumina MiSeq paired end sequencing

| PRJDB12674 | ENA

The influence of nt-LNA on cell composition and phenotypees in the atherosclerotic lesion.

Project description:Raw fastq files from paired-end, Illumina-based sequencing on NovaSeq6000

2021-11-01 | GSE160791 | GEO

High-throughput RNA Sequencing of THP-1 macrophages treated with or without native LDL for 24h.

Project description:Raw fastq files from paired-end, Illumina-based sequencing on NovaSeq6000

2021-11-01 | GSE160615 | GEO

Direct Selection of an Allosteric RNA-Cleaving DNAzyme for a Protein Target: A Specific DNAzyme for Eosinophil Peroxidase to Monitor Airway Eosinopilia

Project description:In this project, in vitro selection was carried out to generate DNAzymes for Eosinophil peroxidase using a synthetic DNA library. Total 15 rounds of selections were carried out. The DNA molecules obtain in round 15, was applied in Illumina MiSeq deep sequencing which provided fastq files. Sequencing samples were prepared from each parallel SELEX experiment by PCR tagging with Illumina sequencing primers. Samples were size purified by agarose gel electrophoresis prior to being quantified by measuring absorbance at 260 nm. Tagged samples were pooled and paired-end sequenced on an Illumina MiSeq high-throughput DNA sequencer. Sequence data processing was performed on a Windows 10 computer running Ubuntu 20.04 under WSL2. Raw paired-end reads were trimmed of sequencing and library primers using cutadapt 3.4. Trimmed paired-end reads were then: 1) merged into a consensus sense read; 2) dereplicated; and, 3) clustered at 90% identity using USEARCH v11.0.667_i86linux32. Sequence frequencies and ranking lists were generated using custom Python scripts. Multiple sequence alignments were performed using MUSCLE v3.8.1551 and converted to sequence logos using WebLogo 3.7.8. Processed sequencing data and cluster linkage data were stored on a MySQL 8.0.22 database. Analysis of sequence copy number, frequency, cluster linkage and data plots were performed using the database and Microsoft Excel Top 20 sequences were tested for cleavage performance. The most active DNAzyme was characterized and optimized. At the end, fluorescence and lateral flow assays were developed and evaluated in real patients' sputums.

2023-11-15 | GSE217946 | GEO

Project description:Making and breaking DMS by salt marsh microbes (Illumina MiSeq 250bp)

| PRJEB1929 | ENA

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