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datasets available to search
ShareScore release 0.9.0
Dataset results
16 results for “gtf”
Customized gtf file from Ensembl version 109 GRCz11 (danRer11)
<p>The gtf from Ensembl version 109 GRCz11 (danRer11) was filtered to remove transcripts on alternative chromosomes, readthrough transcripts and all non-coding transcripts from a protein-coding gene. In addition, all genes with the same gene name which overlaps were merged under the same gene id to avoid ambiguous reads.<br>The procedure to generate the gtf is described in the bash file attached.<br> </p>
Customized gtf file from Ensembl version 102 mm10
<p>The gtf from Ensembl version 102 (mm10) was filtered to remove readthrough transcripts and all non-coding transcripts from a protein-coding gene. In addition, all genes with the same gene name which overlaps were merged under the same gene id to avoid ambiguous reads.<br> In this new version, genes on contigs have been kept as well as CDS information. The procedure to generate the gtf is described in the bash file attached.<br> The version used in Amandio et al. 2021 is the previous version of this record available <a href="https://zenodo.org/record/4596490">here</a>.</p>
customized gtf file from Ensembl version 93 mm10
<p>The gtf from Ensembl version 93 was filtered to remove readthrough transcripts and all non-coding transcripts from a protein-coding gene. In addition, all genes with the same gene name which overlaps were merged under the same gene to avoid ambiguous reads.</p>
customized gtf file from Ensembl version 92 mm10
<p>The gtf from Ensembl version 92 was filtered to remove readthrough transcripts and all non-coding transcripts from a protein-coding gene.</p>
WSB fa and gtf files (with human APP/PS1 genes)
<p>WSB_EiJ with human APP/PS1 genes</p>
Extended gtf based on a customized gtf file from Ensembl version 102 mm10 for Gastruloid
<p>This gtf has been generated based on https://doi.org/10.5281/zenodo.7510406 and extends 3' of genes using RefSeq and bulk RNA-seq from GSE106225, GSE113885 and time-course samples from GSE205781. All command lines can be found at <a href="https://github.com/lldelisle/extendMouseGTFUsingGastruloidData">https://github.com/lldelisle/extendMouseGTFUsingGastruloidData</a>.</p>
Customized gtf file from Ensembl version 99 galGal6
<p>The gtf from Ensembl version 99 (galGal6) was filtered to remove readthrough transcripts and all non-coding transcripts from a protein-coding gene. In addition, all genes with the same gene name which overlaps were merged under the same gene id to avoid ambiguous reads.</p>
gencode v25 tRNAs gtf file chr22 only
<p>Gencode predicted tRNA genes annotation gtf file--CHR (https://www.gencodegenes.org/releases/25.html) truncated to only contain chromosome 22 entries. </p>
Extended gtf based on a customized gtf file from Ensembl version 108 mm39 for Gastruloid
<p>This gtf has been generated based on https://doi.org/10.5281/zenodo.7510797 and extends 3' of genes using RefSeq and bulk RNA-seq from GSE106225, GSE113885 and time-course samples from GSE205781. All command lines can be found at <a href="https://github.com/lldelisle/extendMouseGTFUsingGastruloidData">https://github.com/lldelisle/extendMouseGTFUsingGastruloidData</a>.</p>
Customized gtf file from Ensembl version 108 mm39
<p>The gtf from Ensembl version 108 (mm39) was filtered to remove readthrough transcripts and all non-coding transcripts from a protein-coding gene. In addition, all genes with the same gene name which overlaps were merged under the same gene id to avoid ambiguous reads.<br> The procedure to generate the gtf is described in the bash file attached.<br> </p>
Gene annotation for TAMU_BisBis3 in GTF format and biallelic population SNV in VCF format
<p class="MsoNormal"><span>We developed a highly contiguous chromosome-level reference genome for North American bison to provide a platform to evaluate the conservation, ecological, evolutionary, and population genomics of this species. Generated from an F1 hybrid between a North American bison dam and a domestic cattle bull, completeness and contiguity exceed that of other published bison genome assemblies</span><span>. To </span><span>demonstrate the utility for genome-wide variant frequency estimation, we compiled a genomic variant database consisting of three true albino bison and 45 wild-type pelage color bison. Through the examination of genomic </span>variants fixed in the albino cohort and absent in the controls<span>, we identified a nonsynonymous</span> single nucleotide polymorphism (SNP) <span>mutation on chromosome 29 </span>in exon 3 of the tyrosinase gene (c.1114C>T). A TaqMan SNP Genotyping Assay was developed to genotype this SNP in a total of 283 animals across 29 herds. This assay confirmed the absence of homozygous variants in all animals except 7 true albino bison included in this study. In addition, the only heterozygous animals identified were 2 wild-type pelage color dams of albino offspring. Therefore, we propose that this new high-quality bison genome assembly and incipient variant database provide a highly robust and informative resource for <span>genomics </span>investigations for this iconic North American species.</p>
Gene annotation for TAMU_BisBis3 in GTF format and biallelic population SNV in VCF format
Open the record for dataset details and reuse information.
GTF
<p><strong>protein_coding.gtf</strong></p> <p><strong>noisy.gtf</strong></p> <p><strong>piquant.txt</strong></p>
Transcription Initiation Platforms and GTF recruitment at tissue-specific enhancers and promoters
GEO Series GSE29362. Mus musculus. 20 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing.
customized gtf file from Ensembl version 99 mm10
<p>The gtf from Ensembl version 99 (mm10) was filtered to remove readthrough transcripts and all non-coding transcripts from a protein-coding gene. In addition, all genes with the same gene name which overlaps were merged under the same gene id to avoid ambiguous reads.</p>
Halobacterium NRC-1 Growth curve and GTF perturbation
GEO Series GSE6776. Halobacterium salinarum NRC-1. 322 samples. Type: Expression profiling by array.
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