Tag: Biosample

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…

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‘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…

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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…

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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.,…

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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…

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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…

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