Ontology highlight
ABSTRACT:
PROVIDER: PRJNA318686 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR3397076_1.fastq.gz | Fastqsanger.gz | |||
| SRR3397076_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 2 of 2 |
Similar Datasets
Project description:Whole genome sequencing of 10 HCLc tumor and matched-germline T cells. Genomic DNA from highly purified HCLc tumor and T cell populations were utilized for library preparation using NEBNext Ultra DNA library prep kit. Sequencing was performed as 150 bp paired end sequencing using four lanes of an Illumina HiSeq4000 to an average depth of 12X. Reads from each library were aligned to the human reference genome GRCh37 using BWA-MEM (v0.7.12). The analysis of somatic genetic alterations in WGS data from tumor-germline pair HCLc samples was divided based on the nature of the mutation, as follow: single-nucleotide variants (SNVs), indels, CNAs and SVs. Moreover, COSMIC mutational signatures and subclonal architecture was inferred for each tumor.
2023-01-01 | E-MTAB-12046 | biostudies-arrayexpress
Project description:A map of open chromatin in WT beige ME3 preadipocytes cells on days 0, 1 and 7 of adipogenic differentiation. 100.000 cells were collected in duplicates at each timepoint by trypsination. Cells were slowly frozen at -80C in culture media containing 5% DMSO before shipping on dry ice to Active Motif for open chromatin profiling. In brief, chromatin was isolated from the cells followed by Tn5 transposase-mediated insertion of sequencing primers into open chromatin regions. After library preparation, high-throughput sequencing (Illumina) was performed and reads were then aligned to the mm10 genome using Bowtie2 (Version 2.3.4.3)..
2025-05-16 | E-MTAB-13520 | biostudies-arrayexpress
Project description:We compared 3 small RNA library prep kits (CleanTag, NEXTflex, QIAseq) and two RNA extraction methods (miRNeasy and MagnaZol) on plasma. We report that library preparation has a significant effect upon the miRNA profile detected, with QIAseq libraries exhibiting the least sequencing bias of the three library kits. RNA extraction methods also contribute, to a lesser extent, to the miRNA profile detected, with MagnaZol RNA extraction increasing the percentage of reads mapping to miRNAs and the number of individual miRNAs detected.
2019-05-21 | GSE118125 | GEO
Project description:Small RNA sequencing (tRF-seq) was performed on A375 human melanoma cells with CRISPR/Cas9-mediated knockout of DUS1L and wild-type control cells, with three biological replicates per group. Small RNA libraries were prepared using the NEBNext Small RNA Library Prep Set for Illumina and sequenced on an Illumina NextSeq 500 platform to generate single-end FASTQ files. Sequencing quality was assessed using FastQC, and 3' adaptor sequences were trimmed with cutadapt. Clean reads were aligned to the human tRNA genome using MINTmap to obtain read count-based expression profiles of tRNA-derived fragments (tRFs).
2025-12-12 | GSE312812 | GEO
Project description:<p>Exome sequencing of matched pairs of tumor / normal genomic DNA was performed from high risk localized prostate cancer or lethal, metastatic, castrate resistant prostate cancer (CRPC). Exome libraries were prepared using Illumina Paired_End Genome DNA Sample Prep Kit and captured using Agilent SureSelect Capture Library or Roche EZ Exome capture library. Sequencing was performed on Illumina GAII and HiSeq 2000 platforms in paired end mde, with 80 base pair reads from the final library fragments. Copy number alterations and somatic mutations were identified.</p>
| phs000554 | dbGaP
Project description:Massively parallel DNA sequencing of thousands of samples in a single machine-run is now possible, but the preparation of the individual sequencing libraries is expensive and time-consuming. Tagmentation-based library construction, using the Tn5 transposase, is efficient for generating sequencing libraries but currently relies on undisclosed reagents, which severely limits development of novel applications and the execution of large scale projects. Here, we present simple and robust procedures for Tn5 transposase production and optimized reaction conditions for tagmentation-based sequencing library construction. We further show how molecular crowding agents both modulate library lengths and enable efficient tagmentation from sub-picogram amounts of cDNA. Comparison of single-cell RNA-sequencing libraries generated using produced and commercial Tn5 demonstrated equal performances in terms of gene detection and library characteristics. Finally, as naked Tn5 can be annealed to any oligonucleotide of choice, for example molecular barcodes in single-cell assays or methylated oligonucleotides for bisulfite sequencing, custom Tn5 production and tagmentation enables innovation in sequencing-based applications.
2014-07-14 | GSE58652 | GEO
Project description:To investigate whether Aramchol might reduce liver fibrosis in part directly inhibiting HSCs, we treated LX-2 cells with Aramchol, 10 µM for 24 or 48 hours, then performed RNA sequencing. Sequencing libraries were made with the TruSeq Stranded mRNA Library Prep Kit by manufacturers suggestions. Sequencing parameters are as follows: poly-A RNA enrichment, 175 bp paired reads ran on HiSeq2500 Illumina instrument. Mapping of raw sequencing reads was performed using STAR (2.4.0c) to the UCSC GRCh37/hg19 reference genome.
2021-05-19 | E-MTAB-9870 | biostudies-arrayexpress
Project description:To quantify the contribution of specific transcription factor binding versus chromatin context in chromatin opening, we inserted libraries containing hundreds of CREs into a landing pad within a neutral chromatin environment, devoid of activating or repressive chromatin modifications, in mESCs using Recombination-Mediated Cassette Exchange (RMCE). Chromatin accessibility of the inserted fragments was then profiled by targeted SMF using PCR primers that anneal to a synthetic flanking sequence, allowing unambiguous differentiation of the ectopic site from its endogenous counterpart. The dataset generated includes amplicon-based SMF data from the ectopic site under steady-state conditions, in mouse cells (i.e., TC-1 knock-out of the three DNA methyl transferases (DNMT TKO) mESCs). Two biological replicates were generated. In summary, cells were collected for SMF, which marks accessible cytosines via recombinant methyltransferases, followed by bisulfite sequencing to infer protein-DNA interactions and chromatin accessibility at single-molecule resolution. The sequencing library was prepared using the NEBNext DNA Ultra II Library Prep Kit and sequenced on an Illumina platform, using either a MiSeq 250 bp paired-end run, a MiSeq i100 250 bp paired-end run, or a NextSeq 2000 P1 300 bp paired-end run. Reads were pre-processed with TrimGalore and a custom R script was used to trim the plasmid backbone from the reads. After, pre-processed reads were aligned using QuasR. Further analyses were conducted using custom scripts available at https://github.com/Krebslabrep/TF-chromatin.git.
2026-05-21 | E-MTAB-16658 | biostudies-arrayexpress
Project description:To directly test how individual TFs combine their functions to open chromatin at specific loci, we used synthetic DNA sequences. We generated a library containing all combinations of TF-motif deletions for three CREs: a CTCF-bound region as a positive control (found in \"MutLib1\"), an enhancer with five KLF4 motifs (found in \"MutLib2\"), and a promoter with YY1, NRF1, and MYC motifs (found in \"MutLib1\"). We then inserted the library into a landing pad within a neutral chromatin environment, devoid of activating or repressive chromatin modifications, in mESCs using Recombination-Mediated Cassette Exchange (RMCE). Chromatin accessibility of the inserted fragments was then profiled by targeted SMF using PCR primers that anneal to a synthetic flanking sequence, allowing unambiguous differentiation of the ectopic site from its endogenous counterpart. The dataset generated includes amplicon-based SMF data from the ectopic site under steady-state conditions, in mouse cells (i.e., TC-1 knock-out of the three DNA methyl transferases (DNMT TKO) mESCs). Two biological replicates were generated. In summary, cells were collected for SMF, which marks accessible cytosines via recombinant methyltransferases, followed by bisulfite sequencing to infer protein-DNA interactions and chromatin accessibility at single-molecule resolution. The sequencing library was prepared using the NEBNext DNA Ultra II Library Prep Kit and sequenced on an Illumina platform, using either a MiSeq 250 bp paired-end run, a MiSeq i100 250 bp paired-end run, or a NextSeq 2000 P1 300 bp paired-end run. Reads were pre-processed with TrimGalore and a custom R script was used to trim the plasmid backbone from the reads. After, pre-processed reads were aligned using QuasR. Further analyses were conducted using custom scripts available at https://github.com/Krebslabrep/TF-chromatin.git.
2026-05-21 | E-MTAB-16657 | biostudies-arrayexpress
Project description:The experiment was designed to look into changes in key transcription factors (TFs) binding sites during cell cycle progression in human embryonic stem cells (hESCs). For this, 1 million FUCCI hESCs are sorted in Early G1 (EG1), Late G1 (LG1), and S/G2/M phases in duplicates for each experiment, and chromatin immunoprecipitation was performed for the TFs CTCF, OCT4, NANOG, SOX2, RING1B. Library preparation and sequencing were performed at the Wellcome Trust Sanger Institute next-generation sequencing facility. Size selection was applied, and fragments between 100bp and 400bp (average length of 200bp) were used to prepare barcoded sequencing libraries using NEBNext Sample Prep Kit1 (NEB) following manufacturer’s instructions. Equimolar amounts of each library were pooled, and 10 samples/lane were multiplexed on Illumina HiSeq 2000, 2 X 75bp paired-end reads.
2023-06-24 | E-MTAB-8358 | biostudies-arrayexpress