Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

FSSU-RNAseq

ABSTRACT: Retrieval of a million high-quality, full-length SSU rRNA sequences without primer bias

PROVIDER: PRJEB22259 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other
		Other
	ERR2109470_1.fastq.gz	Fastqsanger.gz
	ERR2109470_2.fastq.gz	Fastqsanger.gz
	ERR2109480_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 42

Similar Datasets

full-length ribosomal SSU sequencing

Project description:Generation of thousands of high-quality, full-length 16S/18S rRNA sequences from complex microbial samples without rRNA primer bias.

| PRJEB17706 | ENA

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

Transcriptome profiling for floral bud development in reblooming cultivar 'High Noon' of Paeonia suffruticosa

Project description:To examine the mechanisms that control flower development, we sequenced the flower bud transcriptomes of ‘High Noon’, a reblooming cultivar of P. suffruticosa × P. lutea. Both full-length isoforms and RNA-seq were sequenced in 3 floral developmental stages. A total of 15.94 Gb raw data and 457.0 million reads were generated in full-length transcript sequencing and RNA-seq.

2019-06-29 | GSE133476 | GEO

Project description:ITS2 amplicon sequencing quality bias

| PRJNA1138067 | ENA

Template switching enables chemical probing of native RNA structures

Project description:RNAs are often studied in non-native sequence contexts to facilitate structural studies. However, seemingly innocuous changes to an RNA sequence may perturb the native structure and generate inaccurate or ambiguous structural models. To facilitate the investigation of native RNA secondary structure by selective 2′ hydroxyl acylation analyzed by primer extension (SHAPE), we engineered an approach that couples minimal enzymatic steps to RNA chemical probing and mutational profiling (MaP) reverse transcription (RT) methods - a process we call template switching and mutational profiling (Switch-MaP). In Switch-MaP, RT templates and additional library sequences are added post-probing through ligation and template switching, capturing reactivities for every nucleotide. For a candidate SAM-I riboswitch, we compared RNA structure models generated by the Switch-MaP approach to those of traditional primer-based MaP, including RNAs with or without appended structure cassettes. Primer-based MaP masked reactivity data in the 5′ and 3′ ends of the RNA, producing ambiguous ensembles inconsistent with the conserved SAM-I riboswitch secondary structure. Structure cassettes enabled unambiguous modeling of an aptamer construct but introduced non-native interactions in the full-length riboswitch. In contrast, Switch-MaP provided reactivity data for each nucleotide in each RNA and enabled unambiguous modeling of secondary structure, consistent with the conserved SAM-I fold. Switch-MaP is an alternative approach to primer-based and cassette-based chemical probing methods that precludes primer masking and the formation of alternative secondary structures due to non-native sequence elements.

2024-12-26 | GSE274121 | GEO

Project description:Full-length transcriptome

| PRJNA859128 | ENA

Molecular signature in human cumulus cells related to embryonic developmental potential

Project description:The objective of the present study was to investigate gene expression profiles of human Cumulus cells isolated from oocytes at metaphase II stage, under controlled ovarian stimulation (COS) cycle and to evaluate the relationship of embryo quality with molecular signatures in Cumulus cells. This study has been performed by microarray analysis in order to identify potential biomarkers related to oocyte developmental potential. For each patient, the CCs were classified into two groups (good quality embryo group and bad quality embryo group) and pooled. From the total of 14 samples, total RNA was purified. After removal of rRNA, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method. The amplified and labelled cRNA were pooled as good quality and bad quality group followed by hybridization, scanning and data analysis.Three independent repetitions were carried out, thus a total of 6 chips were employed in this study.

2014-04-05 | GSE54135 | GEO

marine metagenome

Project description:Primer index bias marine water Raw sequence reads

| PRJNA309692 | ENA

PacBio long-read RNA-sequencing to identify differentially expressed genes and repetitive elements between Wild Type RBM4 KO HAP1 cell line samples

Project description:Since short reads from Illumina RNA-seq data are challenging to map to repetitive elements , we wanted to confirm the bulk RNA-seq findings using an orthogonal method, namely, using the long read technology of Pacific Biosciences (PacBio) full-length transcriptome sequencing. This dataset provided around 1.1 (WT) and 1.3 (RBM4 KO) million sequence reads of 2.6 kb average length mapping to the human genome.

2020-10-20 | GSE147896 | GEO

Project description:Nd full-length transcriptome

| PRJNA1112540 | ENA