Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome and translatome profiles of Streptomyces species in different growth phases

ABSTRACT: Trimmed read fastq files and mapped read bam files of four streptomyces species. Raw read fastq files could be found in GEO or ENA database as follows: - S. avermitilis RNA, Ribo : GSE118597 - S. clavuligerus RNA, Ribo : GSE128216 - S. venezuelae RNA : PRJEB34219 - S. venezuelae Ribo : GSE138278 - S. tsukubaensis RNA, Ribo : GSE97637

PROVIDER: PRJEB36893 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR3949730.fastq.gz	Fastqsanger.gz
	ERR3949740.fastq.gz	Fastqsanger.gz
	ERR3949750.fastq.gz	Fastqsanger.gz
	ERR3949760.fastq.gz	Fastqsanger.gz
	ERR3949770.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 112

Similar Datasets

Strand-specific RNA-seq analysis of three streptomycetes

Project description:We report the mRNA and small RNA transcriptomes of Streptomyces coelicolor, Streptomyces avermitilis, and Streptomyces venezuelae. We identified dozens of new conserved sRNAs and antisense RNAs, including a prominent group of antisense RNAs termed ‘cutoRNAs’ that result from overlap of the 3′ ends of convergently transcribed mRNAs. In addition, we observed abundant unique ncRNAs, including many within secondary metabolic gene clusters. For each of the three species (S. coelicolor, S. avermitilis, S. venezuelae) two libraries were created. The first was a long-read library, where total RNA was depleted of rRNA. The second was a short read library, where total RNA was size selected (40-300 nucleotides) prior to library creation. The long-read library allowed the profiling of mRNAs and asRNAs, while the short-read library was enriched for small RNAs (sRNAs).

2013-08-01 | E-GEOD-46008 | biostudies-arrayexpress

AmpliSeq transcriptome profiling of human adipose tissue senescent progenitor cells

Project description:Transcriptomic profile of human adipose tissue progenitor cells was performed as follows. For AmpliSeq transcriptome sequencing library construction, AmpliSeq™ Library PLUS, AmpliSeq Transcriptome Human Gene Expression Panel and AmpliSeq CD indexes SetA kits were purchased from Illumina and sequencing libraries were constructed as described in AmpliSeq for Illumina Transcriptome Human Gene Expression Panel reference guide (Illumina). Equimolar concentrations of libraries were pooled at 4 nM and denatured and diluted as described in Denature and Dilute Libraries Guide (Illumina) and adjusted to final concentration of 1.4 pM. Resulting library was sequenced on NextSeq 500 using NextSeq 500/550 High Output v2 kit with 2 X 151 bp cycle. Generated raw files were converted to FASTQ files and used for data analysis. AmpliSeq transcriptome FASTQ files were analyzed on Array studio V10.0 (Omicsoft, Qiagen). Following raw read QC, first and last 10 bases were trimmed and mapped to reference genome Human.B38. The read count data was generated using GeneModel RefGene20170606. Resulting data was normalized by DESeq package, transformed to log2 value and used for ANOVA analyses.

2023-01-12 | GSE222749 | GEO

Small RNA sequencing of human LDL

Project description:Adapter trimmed fastq files, non-redundant identical reads and the results of their alignment using the TIGER pipeline.

2021-11-01 | GSE160616 | GEO

Transcriptome sequencing of SLC2A10 knock-down VSMCs

Project description:shRNA was used to knock down SLC2A10 VSMCs. The effectiveness of gene interference was tested by qPCR. Transcriptome sequencing was performed and FASTQ files from RNA- seq experiments were clipped and trimmed. KEGG enrichment analysis on differently expressed genes was performed.

2024-11-24 | GSE190244 | GEO

Strand-specific RNA-seq analysis of three streptomycetes

2013-08-01 | GSE46008 | GEO

Project description:GIAB FASTQ files

| PRJNA1257936 | ENA

LCLF1.0 fastq-Files

Project description:LCLF1.0 fastq-Files

| PRJNA928832 | ENA

LCLF1.0 fastq-Files

Project description:LCLF1.0 fastq-Files

| PRJNA928833 | ENA

Targeted RNA-seq of FTLD-TDP brain samples

Project description:UNC13A features a cryptic exon which is expressed upon loss of nuclear TDP-43. Here, we perform targeted RNA-seq on RNA extracted from 10 FTLD-TDP brain samples, and four control samples, enriching for the cryptic exon via nested PCR. Each FTLD-TDP sample is heterozygous for rs12973192. There are two fastqs for each sample. One uses a sequence-specific reverse transcription primer, and detects both the cryptic-containing and correctly spliced isoforms. The second uses random hexamer primer (with specificity derived from downstream PCR and second strand synthesis) - this approach only detects the isoform containing the cryptic. The fastq files provided are demultiplexed and adaptor trimmed. Unique molecular identifiers have been moved to each read name, after \"rbc:\" (random barcode).

2022-02-28 | E-MTAB-10237 | biostudies-arrayexpress

ChIP-seq of Canis familiaris, Gallus gallus, Mus musculus, Homo sapiens, Monodelphis domestica to investigate CEBPA and HNF4a binding in five vertebrates

Project description:Five-vertebrate ChIP-seq reveals the evolutionary dynamics of trancription factor binding. The SRF files for this experiment can be found in the European Read Archive with study accession number ERP000054. The fastq files can be found in the raw archives and for some assays links to the ENA runs and ENA fastq files are provided.

2010-04-08 | E-TABM-722 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data