Ontology highlight
ABSTRACT:
PROVIDER: PRJNA871056 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR21134672_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR21134673_subreads.fastq.gz | Fastqsanger.gz |
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2022-08-12 | PXD027178 | Pride
Project description:We have completed the high quality reference genome for domestic sheep (Oar v3.1). Early-stage Illumina GA sequence platform sequenced less reads in high GC content regions than in other regions. To read through higher GC content regions, we generated 2 Gb MeDIP-seq data for filling gaps in sheep reference genome assembly.
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Project description:High-quality genome sequence of Monomorium pharaonis
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Project description:Purpose: The goals of this study are to obtain the lncRNA landscape in 6 distinct germ cell types during mouse spermatogenesis. Methods: RNA-seq data of lncRNAs from 6 distinct cell types were generated by deep sequencing using Illumina HiSeq 2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. qRT-PCR validation was performed using SYBR Green assays. Results: Using the rRNA minus strategy, we generated a total of 1100.65 Gb paired and sequence reads with a length of 150 bp. Next, we trimmed the adaptor sequence and filtered the sequence data for low-quality reads at a high stringency with an average Phred quality score less than 20, which resulted in a total of 745.67 Gb high-quality sequence reads. After filtering the reads, almost all sequence reads had a Phred quality score higher than 20, and the percentage of Ns in the reads was nearly zero. By using unique whole-genome alignment (mouse genome (mm10)), a total of 14587 mRNA genes and 6921 lncRNA genes were expressed as fragments per kilobase of exon per million reads mapped (FPKM)>0.1 in at least one sample. In addition, to obtain fingerprint lncRNAs during spermatogenesis, we first identified 2327 differentially expressed lncRNAs between every two adjacent stages. Furthermore, we identified 437 fingerprint lncRNAs that were expressed at a FPKM > 10 of its highly expressed stage. Conclusions: Our RNA-seq dataset comprehensively dissects the dynamic expression mode of lncRNAs during mouse spermatogenesis and generated 28 relatively robust potential lncRNA candidates in spermatogenesis.
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Project description:Hong2004 - Genome-scale metabolic network of
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This model is described in the article:
The genome sequence of the
capnophilic rumen bacterium Mannheimia succiniciproducens.
Hong SH, Kim JS, Lee SY, In YH, Choi
SS, Rih JK, Kim CH, Jeong H, Hur CG, Kim JJ.
Nat. Biotechnol. 2004 Oct; 22(10):
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Abstract:
The rumen represents the first section of a ruminant
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important four-carbon industrial chemical.
This model is hosted on
BioModels Database
and identified by:
MODEL1507180025.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2015-07-30 | MODEL1507180025 | BioModels
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