Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Pacbio sequencing of bacteria from one colony from a urine of a patient with a urinary tract infection

ABSTRACT: Pacbio library preparation and sequencing was carried-out by BGI on one of the technical samples of the Microcolony-seq experiment (UTI_30). A SMRTbell library was prepared and sequenced in a Pacbio Revio machine. The assembled genome was used for mapping the Microcolony-seq experiment

INSTRUMENT(S): PacBio RS

ORGANISM(S): mixed sample

SUBMITTER: Raya Faigenbaum-Romm

PROVIDER: E-MTAB-13944 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Whole genome sequencing of urinary tract infection (UTI) microcolonies used for Microcolony-seq

Project description:Urine from a patient with a urinary tract infection was plated on LB agar plate. Microcolonies appeared ~8h after plating. Microcolonies were picked and subjected to Microcolony-seq and to whole-genome sequencing. Genomic DNA of each UTI microcolony was extracted from 1 mL of bacteria using the DNeasy Blood & Tissue Kit (Qiagen). Library preparation and sequencing was carried out by BGI company, China. Concentration of samples was detected by fluorometer or Microplate Reader (Qubit Fluorometer, Invitrogen). Sample integrity and purity were detected by Agarose Gel Electrophoresis. 1μg genomic DNA was randomly fragmented by Covaris. The fragmented genomic DNA were selected by Agencourt AMPure XP-Medium kit to an average size of 200-400bp. Fragments were end repaired and then 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated fragments. PCR products were purified by the Agencourt AMPure XP-Medium kit. The double stranded PCR products were heat denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) were formatted as the final library. Samples were deep-sequenced with the DNBseq G400 machine using the 150-cycles paired-end with 350 bp insert size. At least 150X sequencing depth for each nucleotide in each sample was targeted.

2025-08-27 | E-MTAB-13941 | biostudies-arrayexpress

PacBio Iso-Seq transcriptome sequencing data of multiplexed maize cDNA

Project description:Full-Length cDNA transcriptome (Iso-Seq) data sequenced on the PacBio Sequel system using 2.1 chemistry. Multiplexed cDNA library of 12 samples (3 tissues x 4 strains). Tissues: root, embryo, endosperm. Strains: B73, Ki11, B73xKi11, Ki11xB73.

2020-02-25 | E-MTAB-7837 | biostudies-arrayexpress

Whole genome sequencing of EPEC microcolonies from anaerobic conditions

Project description:Bacteria from anaerobic Microcolony-seq condition that were kept at the -80C were regrown in liquid LB at 37C for 5 hours. DNA was extracted from 1 mL of bacteria using the DNeasy Blood & Tissue Kit (Qiagen). Library preparation and sequencing was carried out by the Genomics Applications Laboratory, Core Research Facility, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel. DNA libraries for sequencing were prepared using the kit (ILMN DNA LP (M) Tagmentation (24 Samples, IPB) 20060060) (Illumina, Inc., USA) according to manufacturing instructions. At least 100X sequencing depth for each nucleotide in each sample was targeted. Samples were deep-sequenced with the Nextseq500 machine using the 150-cycle mid output kit (Illumina, Inc., USA) from the forward read direction.

2025-08-04 | E-MTAB-13428 | biostudies-arrayexpress

Methylome of Salmonella enterica subsp. Enterica serovar Javiana str. CFSAN001992 by PacBio SMRT Sequencing

Project description:Single-molecule read technologies allow for detection of epigenomic base modifications during routine sequencing by analysis of kinetic data during the reaction, including the duration between base incorporations at the elongation site (the "inter-pulse duration.") Methylome data associated with a closed de novo bacterial genome of Salmonella enterica subsp. enterica serovar Javiana str. CFSAN001992 was produced and submitted to the Gene Expression Omnibus. Single-sample sequencing and base modification detection of cultured isolate of a foodborne pathogen.

2013-03-15 | E-GEOD-45178 | biostudies-arrayexpress

Long-read ONT-dRNA and PacBio Kinnex full-length RNA sequencing of UPF1 depletion in human colorectal adenocarcinoma cell line HCT116 via the auxin-inducible degron (AID) system

Project description:UPF1 is a multi-domain RNA helicase that constantly monitors the transcriptome by non-specifically binding to mRNAs, dissociating from non-target transcripts, and initiating degradation on selected target RNAs via multiple proposed pathways such as nonsense-mediated decay (NMD). NMD is a translation-coupled mechanism that targets mRNAs harboring a premature stop codon (PTC) for degradation, thereby serving as a quality control and gene regulatory pathway ensuring transcriptome integrity. The UPF1 gene is essential in cultured human cells and previous studies relied mostly on RNA interference to downregulate UPF1. Here we established an auxin-inducible UPF1 degron system in the human colorectal adenocarcinoma cell line HCT116 by first inserting the auxin receptor F-box protein-encoding AtAFB2-mCherry in the AAVS1 locus, followed by tagging UPF1 at the N-terminus with an V5-AID-tag (AID = miniIAA7 = AtIAA7 amino acids 37–104). With this cell line and using long-read sequencing approaches (ONT-direct RNA sequencing [ONT-dRNA] and PacBio Kinnex full-length RNA sequencing) we wanted to explore the changes in transcript isoform composition upon rapid depletion of UPF1. To this end, depletion of UPF1 was induced with 500 µM indole-3-acetic acid (IAA) for 12h. As control untreated cells were used.

2025-06-01 | E-MTAB-14725 | biostudies-arrayexpress

Iso-Seq analysis of Miscanthus sinensis plants

Project description:Iso-Seq (PacBio) sequencing was performed to generate a reference transcriptome library of M. sinensis.

2025-11-21 | E-MTAB-15228 | biostudies-arrayexpress

Iso-seq seuqencing of leukemic pooled samples

Project description:2 samples have been prepared for ISO-seq sequencing. CD34+ blast cells from 5 MDS patients before 5-AZA treatment (GEO531A16, GEO531A13, GEO531A5, GEO531A11, GEO531A3) were pooled to generate one sample and 2 AML non-treated and 2 CMML non-treated cells (GEO531A2, GEO531A9, GEO531A6, GEO531A7) were pooled for second sample.

2019-12-10 | E-MTAB-8195 | biostudies-arrayexpress

PacBio Sequel WGS of Tursiops Aduncus

Project description:This data and additional 10x Genomics Chromium data were collected from the same individual for a de-novo genome assembly

2022-01-01 | E-MTAB-7308 | biostudies-arrayexpress

Methylome sequencing of Burkholderia pseudomallei strains Bp33 and Bp35

Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of DNA methylations in Burkholderia pseudomallei. SMRTbell™ sequencing

2014-09-15 | E-GEOD-55168 | biostudies-arrayexpress

Iso-Seq analysis of cell suspension culture and plantlets of Hypericum perforatum

Project description:Iso-Seq (PacBio) sequencing was performed to generate a reference library of H. perforatum. We generated genome-wide transcriptome data from in vitro cell suspensions and shoot cultures of H. perforatum.

2022-12-31 | E-MTAB-11423 | biostudies-arrayexpress

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