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91 results for “Intergenic”
Intergenic sequences of Mesocricetus auratus
<p>Intergenic sequences created with the 16 libraries of Mesocricetus auratus that will be used for Bgee 15.0</p>
Intergenic RNAPII Atlas : input data
<p>This Zenodo record refers to the <strong>"input data" </strong>used in the manuscript titled "<a href="https://doi.org/10.1101/2023.03.24.534112">Characterising intergenic transcription at RNA polymerase II binding sites in normal and cancer tissues</a>" by de Langen <em>et al.</em> </p> <p>This Zenodo record allows to replicate the results presented in the manuscript, please refer to the instructions available on Github at <a href="https://github.com/benoitballester/Pol2Atlas">https://github.com/benoitballester/Pol2Atlas</a>. </p> <p>The results presented in the manuscript can be accessed at <a href="https://zenodo.org/record/7740073">https://zenodo.org/record/8091826</a>.</p> <p><strong>In short :</strong> </p> <ul> <li><strong>Data "in" :</strong> this record</li> <li><strong>Data "out"</strong> : <a href="https://zenodo.org/record/7740073">https://zenodo.org/record/8091826</a></li> <li><strong>Github Code</strong> : <a href="https://github.com/benoitballester/Pol2Atlas">https://github.com/benoitballester/Pol2Atlas</a></li> </ul> <pre><code class="language-bash"># uncompress the gz files $ cat repro_data.gz.part* | gunzip -c > repro_data.gz</code></pre> <p> </p>
Intergenic sequences of Solenopsis invicta
<p>Intergenic sequences created as part of the Solenopsis ATLAS project.</p>
Data from: Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis
Long intergenic noncoding RNAs (lincRNAs) transcribed from intergenic regions of yeast and animal genomes play important roles in key biological processes. Yet, plant lincRNAs remain poorly characterized and how lincRNA biogenesis is regulated is unclear. Using a reproducibility-based bioinformatics strategy to analyze 200 Arabidopsis transcriptome datasets, we identified 13,230 intergenic transcripts of which 6,480 can be classified as lincRNAs. Expression of 2,708 lincRNAs was detected by RNA-seq experiments. Transcriptome profiling by custom microarrays revealed that the majority of these lincRNAs are expressed at a level between those of mRNAs and pri-miRNAs. A subset of lincRNA genes show organ-specific expression whereas others are responsive to biotic and/or abiotic stresses. Further analysis of transcriptome data in 11 mutants uncovered SERRATE, CBP20, and CBP80 as regulators of lincRNA expression and biogenesis. RT-PCR experiments confirmed these 3 proteins are also needed for splicing of a small group of intron-containing lincRNAs.
Association of SNPs in Long Intergenic Noncoding RNA 00511 (LINC00511) With Breast Cancer Among the Egyptian Population
ClinicalTrials.gov study NCT06357689. IPD Sharing: UNDECIDED. Countries: 1. Publications: 17.
Data from: Characterization of an intergenic polymorphic site (pp-hC1A_5) in Wolbachia pipientis (wPip)
Open the record for dataset details and reuse information.
Data from: Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis
Open the record for dataset details and reuse information.
Data from: Dealing with the adaptive immune system during de novo evolution of genes from intergenic sequences
Open the record for dataset details and reuse information.
Fig. 1 in Mitochondrial Intergenic Spacer in Fairy Basslets (Serranidae: Anthiinae) and the Simultaneous Analysis of Nucleotide and Rearrangement Data
Fig. 1. Illustration of partial H1 in anthiine sea basses that (A) lack or (B) have evolved the intergenic spacer (IGS 5 intergenic spacer, V 5 tRNAVal) with overlapping primer pairs used to amplify DNA mapped.
Intergenic RNAPII Atlas : output data
<p>This dataset represents the RNAPII (RNAP2) Atlas of potentially transcribed intergenic regions of the human genome by integrating 906 high quality human Chromatin-ImmunoPrecipitation sequencing (ChIP-seq) biosamples targeting the RNA Polymerase II, obtained from public data warehouses. </p> <p><strong>Github Code available here : </strong><a href="https://github.com/benoitballester/Pol2Atlas">https://github.com/benoitballester/Pol2Atlas</a> </p> <p><strong>The dataset consists of 5 zipped folders described below: </strong></p> <p><strong>./pol2_consensuses/:</strong><br> consensuses.bed:<br> Location of intergenic RNAP2 consensuses in bed format for the hg38 assembly. <br> First three columns are genomic locations, 4th column is consensus ID, <br> 5th column is the number of datasets with RNAP2 observed at this RNAP2 consensus,<br> 6th column is strand (not used), 7-8th columns is consensus centroid.<br> consensusesHg19.bed:<br> Location of intergenic RNAP2 consensuses in hg19 assembly. ~1000 are missing due to liftover.<br> Consensus ID is matching with the hg38 one.<br> matrix.mtx:<br> RNAP2 occupancy consensus-dataset binary matrix in sparse matrix market format.<br> Corresponding row annotation are RNAP2 consensuses.<br> Corresponding column annotation are datasets stored in dataset.txt.<br> datasets.txt:<br> See matrix.mtx<br> clusterConsensuses_Labels.txt:<br> Assigned cluster for each RNAP2 consensus.<br> intersectIntergPol2.tsv:<br> RNAP2 consensuses with cluster ID and intersections with reference databases.<br> cluster_bed/:<br> consensuses.bed splitted per cluster.<br> saf_files/:<br> Files typically used for read counting with featureCounts. Suffixes:<br> _500 : RNAP2 consensuses standardized to 1kbp.<br> _all : All RNAP2 consensuses including genic.<br> Hg19 : Intergenic RNAP2 Lifted to Hg19.</p> <p> </p> <p><strong>./rnap2_all_peaks/:</strong><br> all_peaks.bed.gz:<br> Concatenated bed file with all POLR2A peaks from all experiments, genome wide, for the hg38 assembly. <br> Peaks are filtered with a MACS2 qvalue > 1e-5, datasets with less than 100 peaks in intergenic regions are removed.<br> First three columns are genomic locations, 4th column contains sample of origin of the peak, 5th column is the<br> MACS2 q-value, 6th column is dna strand (not used), 7-8th are peak "summit". 9th column contains an r,g,b value<br> corresponding to the biotype of origin (Blood / Immune, Brain, Embryo...) for easy visualization in a genome browser.<br> Legend is available in legend.png. Conversion table between rgb values and biotype in palette.csv.<br> Note that singletons are removed when creating consensus peaks.<br> all_peaks_interg.bed.gz:<br> Same as above, but for intergenic regions only (excluding 1kb before TSS and 1kb after TES).</p> <p> </p> <p><strong>./count_tables_rnaseq/:</strong><br> ENCODE/:<br> counts.mtx.gz:<br> Count table in sparse matrix market format. Row corresponds to samples, columns to Pol II probes (Pol2_500.saf).<br> samples.csv.gz:<br> Matching row annotation for count matrix.<br> encode_total_rnaseq_annot.tsv.gz:<br> Sample annotation (not ordered!).<br> GTEx/:<br> counts.mtx.gz:<br> Count table in sparse matrix market format. Row corresponds to samples, columns to Pol II probes (Pol2_500.saf).<br> samples.csv.gz:<br> Matching row annotation for count matrix.<br> sample_annot.tsv.gz:<br> Sample annotation (not ordered!).<br> TCGA/:<br> counts.mtx.gz:<br> Count table in sparse matrix market format. Row corresponds to samples, columns to Pol II probes (Pol2_500.saf).<br> samples.csv.gz:<br> Matching row annotation for count matrix.<br> annotation_table.tsv.gz:<br> Sample annotation (not ordered!).<br> </p> <p><br> <strong>./cancer_markers/:</strong><br> bed/:<br> DE_Tumor_vs_Normal/:<br> TCGA-*/:<br> allWithStats.bed:<br> FDR, mean difference in pearson residuals and log2(FC) for each RNAP2 probe. Warning: probes are prefiltered to have > 1 read in 3 samples, make sure to use row index to match <br> with RNAP2 consensuses.<br> allDE.bed:<br> All DE (cancer vs normal) probes in bed format for this cancer. <br> 5th column has been replaced by enrichment p-value.<br> DE_downreg.bed:<br> Downregulated (cancer vs normal) probes in bed format for this cancer. <br> 5th column has been replaced by enrichment p-value.<br> DE_upreg.bed:<br> Upregulated (cancer vs normal) probes in bed format for this cancer. <br> 5th column has been replaced by enrichment p-value.<br> classifier_TCGA-*:<br> Performance of a machine learning tumor-normal tissues classifier using Pol II probes as input.<br> globally_DE.bed:<br> Probes DE in 7+ cancers (FPR permutation threshold). Last column indicates the number of cancers this probe is DE in.<br> globally_Down regulated.bed:<br> Probes DE in 6+ cancers (FPR permutation threshold). Last column indicates the number of cancers this probe is Down regulated in.<br> globally_Up regulated.bed:<br> Probes DE in 5+ cancers (FPR permutation threshold). Last column indicates the number of cancers this probe is Up regulated in.<br> subtypes/:<br> BRCA/:<br> allWithStats_BRCA.*.bed:<br> FDR, mean difference in pearson residuals and log2(FC) for each RNAP2 probe for DE test of sample from this subtype against normal samples. <br> Warning: probes are prefiltered to have > 1 read in 3 samples, make sure to use row index to match <br> with RNAP2 consensuses.<br> bed_BRCA.*.bed:<br> All DE (subtype vs normal) probes in bed format for this cancer. <br> bed_uniqueDE_BRCA.*.bed:<br> All DE (subtype vs normal) probes in bed format for this cancer and not DE in any other subtype. </p> <p> TCGA_survival/:<br> TCGA-*/:<br> prognostic.bed:<br> All probes associated with survival for this cancer. <br> 5th column has been replaced by p-value.<br> stats.csv:<br> Cox linear model statistics for each Pol II probe. <br> Warning: probes are prefiltered to have > 1 read in 3 samples, make sure to use row index to match <br> with RNAP2 consensuses.<br> globally_prognostic.bed:<br> Probes associated with survival in 5+ cancers (FPR permutation threshold). 5th column has been replaced with <br> the number of cancers this probe is associated with survival in.<br> tabular/:<br> Same as above but stored in a tabular binary format for DE and survival.</p> <p> </p> <p><strong>./metacluster_markers/:</strong><br> bed/:<br> allPol2_datasetCount:<br> For each tissue, all Pol II consensuses, with 5th column indicating the number of<br> datasets (RNAP2, GTEx, ENCODE, TCGA tumour and normal) in which the RNAP2 consensus is<br> considered a marker.<br> robust_2_datasets_per_tissue:<br> For each tissue, Pol II consensuses considered marker in 2+ datasets out of 5 <br> (RNAP2, GTEx, ENCODE, TCGA tumour and normal).<br> tabular/:<br> Each Pol II consensus with marker information stored in a binary format.<br> </p>
Heat shock-induced ribosomal intergenic spacer RNA
GEO Series GSE115731. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
Intergenic DNA organization in the mammalian nervous system
GEO Series GSE154532. Mus musculus. 2 samples. Type: Expression profiling by high throughput sequencing.
Modulation of gene expression in U251 glioblastoma cells by binding of mutant p53 to intronic and intergenic sequences
GEO Series GSE13991. Homo sapiens. 4 samples. Type: Expression profiling by array.
Long Intergenic Noncoding RNA MIAT Contributes to Human Th17 Cell Differentiation
GEO Series GSE183664. Homo sapiens. 72 samples. Type: Expression profiling by high throughput sequencing.
Expression of intergenic regions of Synechococcus WH 7803 under environmentally relevant stresses
GEO Series GSE28263. Synechococcus sp. WH 7803. 24 samples. Type: Expression profiling by genome tiling array.
H2A.Z Demarcates Intergenic Regions of the Plasmodium falciparum Epigenome That Are Dynamically Marked by H3K9ac and H3K4me3
GEO Series GSE23787. Plasmodium falciparum 3D7. 29 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Other.
Myc target gene, long intergenic noncoding RNA, Linc00176 in hepatocellular carcinoma regulates cell cycle and cell survival by titrating tumor suppressor microRNAs.
GEO Series GSE93548. Homo sapiens. 1 samples. Type: Expression profiling by array.
Large intergenic non-coding RNAs as novel modulators of reprogramming
GEO Series GSE24182. Homo sapiens. 43 samples. Type: Expression profiling by array; Non-coding RNA profiling by genome tiling array.
CPSF1 inhibition promotes widespread use of intergenic polyadenylation sites and impairs glycolysis in prostate cancer cells [PAC-seq]
GEO Series GSE263384. Homo sapiens. 27 samples. Type: Other; Expression profiling by high throughput sequencing.
Systematically characterizing dysfunctional long intergenic non-coding RNAs in multiple brain regions of major psychosis
GEO Series GSE78936. Homo sapiens. 82 samples. Type: Expression profiling by high throughput sequencing.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.