Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: raw sequence reads of Gallus gallus small RNA sequencing

PROVIDER: PRJNA674336 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR12972236.fastq.gz	Fastqsanger.gz
	SRR12972237.fastq.gz	Fastqsanger.gz
	SRR12972238.fastq.gz	Fastqsanger.gz
	SRR12972239.fastq.gz	Fastqsanger.gz
	SRR12972240.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 12

Similar Datasets

Morus alba Raw protein sequence reads

Project description:Morus alba L. Raw protein sequence reads and sequence

2024-02-08 | PXD049451 |

Sequencing of siRNA from soybean containing silencing vectors and empty vectors

Project description:A cDNA library was constructed by Novogene (CA, USA) using a Small RNA Sample Pre Kit, and Illumina sequencing was conducted according to company workflow, using 20 million reads. Raw data were filtered for quality as determined by reads with a quality score > 5, reads containing N < 10%, no 5' primer contaminants, and reads with a 3' primer and insert tag. The 3' primer sequence was trimmed and reads with a poly A/T/G/C were removed

2021-07-21 | GSE180131 | GEO

Quantitative profiling of differentially expressed miRNAs in siCTL- and siOASL-transfected HUVECs

Project description:Purpose: The goal of this study is to compare endothelial small RNA transcriptome to identify the target of OASL under basal or stimulated conditions by utilizing miRNA-seq. Methods: Endothelial miRNA profilies of siCTL or siOASL transfected HUVECs were generated by illumina sequencing method, in duplicate. After sequencing, the raw sequence reads are filtered based on quality. The adapter sequences are also trimmed off the raw sequence reads. rRNA removed reads are sequentially aligned to reference genome (GRCh38) and miRNA prediction is performed by miRDeep2. Results: We identified known miRNA in species (miRDeep2) in the HUVECs transfected with siCTL or siOASL. The expression profile of mature miRNA is used to analyze differentially expressed miRNA(DE miRNA). Conclusions: Our study represents the first analysis of endothelial miRNA profiles affected by OASL knockdown with biologic replicates.

2022-09-06 | GSE186354 | GEO

Gallus gallus

Project description:Gallus gallus 16 purebred and crossbred small RNA Raw sequence reads

| PRJNA859020 | ENA

Genome-wide miRNA turnover profile in HDMYZ cells after transcription inhibition

Project description:HDMYZ cells were treated with 2ug/ml ActD for 0, 4 and 12 hours. Small RNAs of 15-40 bases were gel-purified from 10 ug total RNA, and subjected to multiplex Illumina small RNA library preparation. Small RNA libraries were sequenced on a HiSeq2000 (Illumina) with 3 samples per lane. To quantify miRNA and isoform abundance, sequence reads were processed by the miRDeep2 package, with the following modifications. First, to remove adaptor sequence, we removed both the main adaptor sequence present in the sequencing reads, as well as the second most abundant adaptor variant. In addition, we did not restrict the size of small RNAs during adaptor removal. Second, we used miRBase v18 for mapping the reads. Third, for quantifying miRNA and isoform frequency, we limited reads to more or equal to 15 bases in length with zero mis-match during mapping. The number of reads that were mapped to known miRNAs was used to normalize read frequencies for each miRNA or each miRNA isoform. For quantification purposes, we only considered miRNAs or isoforms that had frequency >= 1x10e-6 in samples without ActD treatment, which correspond to ~21-30 reads in raw count. These miRNAs or isoforms were referred to as reliably quantifiable.To analyze mapping to the genome, we removed reads that mapped to miRNA precursors. The rest of the reads were then mapped to the genome with Bowtie.

2017-09-02 | GSE46968 | GEO

Project description:raw sequence reads of Gallus gallus RNA sequencing

| PRJNA674456 | ENA

Transcriptomic analyses of co-treatment of AFB1 and curcumin in chicken liver

Project description:Purpose:In order to assess the toxicity of AFB1 in chicken liver and the mechanism of curcumin alleviating AFB1-induced liver toxicity in chicken, we established a co-administered model to investigate LncRNA and mRNA profiles of chicken liver. Methods: RNA extracted by Total RNA Extractor (Trizol) was utilized to construct the final library. Libraries were pooled and sequenced on a 150-bp paired-end Illumina HiSeq™ 2000 run. The sequencing data obtained from Illumina Hiseq™ was filtered to get clean reads using Trimmomatic. The reads themselves and their matching reads which length was less than 35nt were removed. Clean reads were aligned to the reference sequence (Gallus_gallus-5.0, NCBI) using HISAT2. Results: Sampling directly from the liver yielded sufficient quantities of RNA to assess transcripts from each chicken and mapped to 24,883 Gallus gallus genes. Conclusions: We used the method of RNA-seq to find the target genes and related signaling pathways involved in the co-administered (AFB1 and curcumin) and their underlying mechanisms.

2022-04-02 | GSE148014 | GEO

Genome-wide identification and characterization of transfer RNA-derived small RNAs in Plasmodium falciparum

Project description:In this study, we performed deep sequencing and bioinformatics analyses of short RNAs from Plasmodium falciparum parasites to identify and characterize novel type of small RNAs. A total of 14,828,877 raw reads were produced from small RNA libraries. We detected a new type of small RNA from tranfer RNA known as tRFs.

2019-01-23 | GSE119771 | GEO

MicroRNA Profiling of Rhesus Macaque Embryonic Stem Cells

Project description:We established three new rhesus embryonic stem cells lines and conducted their microRNA profilings by Solexa sequencing. Sequencing of small RNA libraries yielded 12.66 million, 13.12 million and 11.57 million raw reads from IVF1.2, IVF3.2 and IVF3.3, respectively. After filtering, we obtained 10.89 million (IVF1.2), 10.60 million (IVF3.2) and 9.26 million (IVF3.3) clean reads (18-30nt).

2011-06-20 | GSE27886 | GEO

Gallus gallus

Project description:Gallus gallus Raw single-cell RNA sequence reads

| PRJNA1053748 | ENA