Tag: Biosample
Apply for samples
BioResource biobanking We extract DNA from blood or saliva donated by our participants. The DNA is quality controlled, banked and then analysed to study genetic variation by genotyping. We also store plasma and serum from blood samples. All samples are sent to the NIHR-funded National Biosample Centre (NBC) in Milton Keynes, for processing,…
Sample GenBank Record / Visual abstracts made easy with Mind the Graph
This page presents an annotated sample GenBank record (accession number U49845) in its GenBank Flat File format. You can check the corresponding alive record for U49845, and seeexamples of other records the show a range of biological features. SITE SCU49845 5028 bp DNA PLN 21-JUN-1999 DEFINITION Saccharomyces cerevisiae TCP1-beta gene,…
Evidence of international transmission of mobile colistin resistant monophasic Salmonella Typhimurium ST34
Three samples of S. 4,[5],12:i:-, all isolated in 2010, harbored mcr-3.1. Two were from human stool and the other was from ready-to-eat frozen food. Phenotypic characterization confirmed that all three isolates were resistant to colistin, all with MIC and MBC of 8 µg/ml. WGS of H1-012, H1-014 and H1-120 were analyzed…
Coming Soon! Including Sample Location and Collection Date and Time for Sequences Submitted to GenBank and SRA – NCBI Insights
As previously announced, in collaboration with our partners at the International Nucleotide Sequence Database Collaboration (INSDC), we will begin to systematically gather ‘location of collection’ and ‘date and time of collection’ for sequence data submitted to GenBank and the Sequence Read Archive (SRA). Gathering information about where and when a…
esearch|elink|esummary|xtract randomly skip some accession
esearch|elink|esummary|xtract randomly skip some accession 0 Hello Everyone, I have a total of ~130.000 SRA accession from which I need to retrieve the isolation source and the location. $head -n 10 SRAyk.txt DRR095581 SRR11035504 SRR9016627 SRR5826819 SRR11032323 SRR6801753 SRR10144785 SRR12961276 SRR5927939 ERR2563030 Here is the bash loop for i in…
Parkinson’s cure ‘inevitable’ after biomarker breakthrough
The Michael J. Fox Foundation for Parkinson’s Research (MJFF) has announced what it says is the ‘most significant breakthrough yet’ in the search for a Parkinson’s biomarker: a biological test for Parkinson’s disease. The test demonstrates high diagnostic accuracy, differentiates molecular subtypes and detects disease in individuals before cardinal movement…
Genomic comparison of two Streptococcus suis serotype 1 strains recovered from porcine and human disease cases
Identification of S. suis serotype 1 Using a novel multiplex PCR test13, we first retyped the 46 strains in our collection previously identified using multiplex PCR14 as serotype 1 or 14. Among them, 2 strains were confirmed as serotype 1 by the new multiplex PCR13, PCR–RFLP of the cpsK locus15…
Ethical Questions To Settle Ahead Of ‘Genetic Revolution’
A genetic revolution is coming. It’s time the medical community and policymakers discuss it. As technology advances and the price for genetic testing decreases, it is likely that within the next five years, DNA sequence information will be part of a patient’s medical records. Such a move would revolutionize the…
djghjc
djghjc 1 hi, does anyone know how to find the sample_id for srr? bioinf • 130 views Using EntrezDirect: $ esearch -db sra -query SRX19366692 | elink -target biosample | esummary | xtract -pattern DocumentSummary -element Identifiers BioSample: SAMN33293805; SRA: SRS16763294; EDLB-CDC: PNUSAE127503 Login before adding your answer. Read more…
bioinformatics – How do I download a large number of GenBank sequences using entrez_fetch in R?
I am trying to download sequence data from 1283 records in GenBank using rentrez. I’m using the following code, first to search for records fitting my criteria, then linking across databases, and finally fetching the sequence data: # Search for sequence ids in biosample database search <- entrez_search(db = “biosample”,…
python – eQTL data extraction from database JSON file
It’s a little hard to know what your goal is here based on the sample code, but I do find that your JSON snippet does not match any spec. I was able to edit it to add brackets to make the entries elements of a list: [ { “biosample_ontology”: {…
Batch-effect detection, correction and characterisation in Illumina HumanMethylation450 and MethylationEPIC BeadChip array data | Clinical Epigenetics
Experimental design and processing steps For the EpiSCOPE study [20], DHA supplementation and gender were balanced as much as possible across the 12 450K BeadChips on each glass slide, with these factors also randomly distributed over the 6 rows and 2 columns of 31 slides (Additional file 1: Fig. S1). Blood…
Summary of Fusobacterium nucleatum MJR7757B, version 26.0
Summary of Fusobacterium nucleatum, Strain MJR7757B, version 26.0 Tier 3 Uncurated Database Summary: This Pathway/Genome Database (PGDB) was generated on 27-May-2018 from the annotated genome of Fusobacterium nucleatum MJR7757B, as obtained from RefSeq (annotation date: 04-APR-2017). The PGDB was created computationally by the PathoLogic component of the Pathway Tools software…
Petabase-scale sequence alignment catalyses viral discovery
Serratus alignment architecture Serratus (v0.3.0) (github.com/ababaian/serratus) is an open-source cloud-infrastructure designed for ultra-high-throughput sequence alignment against a query sequence or pangenome (Extended Data Fig. 1). Serratus compute costs are dependent on search parameters (expanded discussion available: github.com/ababaian/serratus/wiki/pangenome_design). The nucleotide vertebrate viral pangenome search (bowtie2, database size: 79.8 MB) reached processing rates…
Submit sequence data to NCBI
Data provision and standards. GEO sequence submission procedures are designed to encourage provision of MINSEQE elements: Thorough descriptions of the biological samples under investigation, and procedures to which they were subjected. Thorough descriptions of the protocols used to generate and process the data. Request updates to accessioned records per the…
‘Can’t connect to eutils.ncbi.nlm.nih.gov:443’
‘Can’t connect to eutils.ncbi.nlm.nih.gov:443′ 0 Using an AWS AMI to predict small RNA targets. Getting following error. =========Prepping RefSeq Files==================== [Wed Sep 8 08:34:12 UTC 2021] 500 Can’t connect to eutils.ncbi.nlm.nih.gov:443 No do_post output returned from ‘https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=NZ_CP039025&rettype=native&retmode=text&edirect=6.00&tool=edirect&email=ubuntu@ip-172-31-26-35.ec2.internal‘ Result of do_post http request is $VAR1 = bless( { ‘_msg’ => ‘Can’t…
Transcription Factor Functions
Transcription Factor Functions 1 I have been wondering if there is a database that contains information about whether a transcription factor has a repressive or an activating or a context-dependent function. factor database transcription • 71 views If you performed a whole-genome FIMO scan, selecting those hits that match your…
Frontiers | DNA Methylation and RNA-Sequencing Analysis Show Epigenetic Function During Grain Filling in Foxtail Millet (Setaria italica L.)
Introduction Gene expression is not only controlled by DNA sequences but also by epigenetic marks in eukaryotes. DNA methylation as one of the important epigenetic modifications has been demonstrated as closely related to gene expression in biological processes, such as transcriptional activity, developmental regulation, and environmental responses (Maunakea et al.,…
SRA splitting for each metagenome-assembled genome
Job:SRA splitting for each metagenome-assembled genome 0 Hi everybody, we obtained viruses from water and sequenced them with Illumina. we formed different metagenomic-assembled genomes and get a Bioproject number and Biosample numbers (for each of them). Now, i should do SRA submission. But i cannot submit for my all genomes…
Python fast way to get ONLY MAIN metadata for GSE ? (not walking through thousands underlying GSM-samples : slow or even endless)
Not Python but using EntrezDirect you can get: $ esearch -db bioproject -query “GSE118723” | esummary | xtract -pattern DocumentSummary -element Project_Description Quantification of gene expression levels at the single cell level has revealed that gene expression can vary substantially even across a population of homogeneous cells. However, it…
