Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gut metagenome/FR 2002 (Salosensaari et al. Nature Comms 2021)

ABSTRACT: The main goal of the project is the study the associations between the gut metagenome and human health. The dataset contains data for n=7211 FINRISK 2002 participants who underwent fecal sampling. Demultiplexed shallow shotgun metagenomic sequences were quality filtered and adapter trimmed using Atropos (Didion et al., 2017), and human filtered using Bowtie2 (Langmead and Salzberg, 2012).

PROVIDER: EGAS00001005038 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Similar Datasets

Gut metagenome/FINRISK 2002 (Salosensaari et al. Nature Comms 2021)

Project description:The main goal of the project is the study the associations between the gut metagenome and human health. The dataset contains data for n=7211 FINRISK 2002 participants who underwent fecal sampling. Demultiplexed shallow shotgun metagenomic sequences were quality filtered and adapter trimmed using Atropos (Didion et al., 2017), and human filtered using Bowtie2 (Langmead and Salzberg, 2012).

| EGAS00001005020 | EGA

69f9e234-85f6-4145-9c85-d364c4bcb278 - samples

Project description:The dataset contains data for n=7211 FINRISK 2002 participants who underwent fecal sampling. Demultiplexed shallow shotgun metagenomic sequences were quality filtered and adapter trimmed using Atropos (Didion et al., 2017), and human filtered using Bowtie2 (Langmead and Salzberg, 2012). The files are in FASTQ format.

| EGAD00001007035 | EGA

Next Generation Sequencing analysis of KSHV lytic replication in TREx-BCBL1-RTA cells

Project description:Purpose: miR-Seq was utilised to identify miRNAs which are altered during the course of KSHV lytic replication at 0, 16 and 24 hours post reactivation in TREx-BCBL1-RTA cells. Methods: Virus lytic replication was induced via addition of 2 µg/mL doxycycline hyclate (Sigma-Aldrich). Total RNA was extracted from TREx-BCBL-1s at 0, 16 and 24 hours post lytic induction. Small RNA libraries were prepared using the TruSeq Small RNA Library Prep Kit (Illumina). Quality filtered (Q < 20), and adapter trimmed reads (Trimmomatic v0.39) [59] were aligned to the GRCh38/hg38 assembly of the human genome using Bowtie2 (V 2.4.2).

2022-02-09 | GSE186652 | GEO

KDM5 Lysine Demethylases Are Involved in Maintenance of 3'UTR Length [RNA-Seq]

Project description:We discovered that the Saccharomyces cerevisiae lysine demethylase, Jhd2 (also known as KDM5), recruits 3'UTR processing machinery and promotes alteration of 3'UTR length in a demethylase-dependent manner. Interaction of Jhd2 with both chromatin and RNA suggests that Jhd2 affects selection of polyadenylation sites through a transcription-coupled mechanism. For 3'READs analysis, wild-type yeast or yeast with JHD2 deleted were grown to mid-log phase and RNA was extracted as mentioned above. cDNA libraries enriched for 3'UTRs were prepared as previously published and as noted in Figure 4a [28]. Samples were then subjected to RNA sequencing on the Illumina Hiseq 2000 using 50bp single end reads. Data was analyzed as previously [Hoque M] with the following modifications: The adapter sequences were trimmed off the single-ended reads. The remaining reads longer than 15 bp were mapped to yeast genome SacCer3 using bowtie2 [Langmead B 2012] with the setting '-5 4 --local', trimming off 4bp from 5' and allowing soft clipping (S) at both ends. The alignments were then filtered by 1) MAPQ>=10, 2) mismatches <= 5%, 3) unaligned 5' Ts >=2 to get the PASS reads. The last aligned positions of the PASS reads were grouped to pA clusters with a clustering size of 24 bp. Each pA cluster was assigned to one of the genes defined by SGD [Cherry JM]. The 3' end of a gene was extended 1000bp from the end of CDS until it overlaps with another gene in the same direction. The pA Clusters were then filtered by contains 1) >= 3 PASS reads 2) >= 5% of all PASS reads mapped to the gene.

2016-03-23 | E-GEOD-67163 | biostudies-arrayexpress

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

ChIP-sequencing fragment coverage

Project description:Raw sequencing reads from H3K27ac ChIP and input DNA from lymphoblastoid cells of three TET2 mutation carriers and two wild-type family members were quality and adapter trimmed with cutadapt version 1.16 in Trim Galore version 0.3.7 using default parameters. Trimmed reads were aligned to hs37d5 reference genome using Bowtie2 (version 2.1.0). Duplicate reads were removed with samtools rmdup (v1.7). Fragment coverage of paired-end reads was calculated from bam files with BEDtools genomecov (v2.26.0).

| EGAD00010001671 | EGA

Inactivation of ARID1A-SWI/SNF Complex Alters Chromatin Compactness at Enhancer Regions and Affects Transcription of Key Tumor Signaling Circuitry [ChIP-Seq]

Project description:For ATAC-seq data processing, we used the ENCODE ATAC-seq pipeline (https://www.encodeproject.org/atac-seq/). In detail, for each sample, ATAC-seq reads were first checked for adaptor contamination. Then, adaptor trimmed reads were aligned to hg19 using Bowtie2 under paired-end mode with parameter “-X2000”, which permits 2000 bp for the maximum allowable insert size between two paired ends of each read. Using the ENCODE ATAC-seq pipeline, duplicated reads were properly filtered out. ATAC-seq enriched peaks were called using MACS2 (Zhang et al., 2008) based on remaining unique reads with parameters “-f BAMPE -q 0.05 --nomodel”. In total, we collected 45,569 peaks for the ARID1AWT sample and 27,480 peaks for the ARID1AKO sample.

2020-06-08 | GSE106660 | GEO

genes regulated by mitoflash

Project description:we examine the genes expression after activation of mitoflash. The MEF were expressed with CypD or treated with paraquat and mastoparan. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.RNA libraries were prepared for sequencing using standard Illumina protocols.Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie2-2.2.5 with parameters -p 8 --bowtie2 -sensitivity-level very_sensitive.

2015-09-26 | E-MTAB-3875 | biostudies-arrayexpress

ncRNA-Seq of human blood with different disease state of COVID-19

Project description:To analyse gene expression pattern in different disease state of COVID-19 patients. Experimental workflow: 1) rRNA was removed by using RNase H method, 2) QAIseq FastSelect RNA Removal Kit was used to remove the Globin RNA, 3) The purified fragmented cDNA was combined with End Repair Mix, then add A-Tailing Mix, mix well by pipetting, incubation, 4) PCR amplification, 5) Library quality control and pooling cyclization, 6) The RNA library was sequenced by MGI2000 PE100 platform with 100bp paired-end reads. Analysis steps: 1) RNA-seq raw sequencing reads were filtered by SOAPnuke (Li et al., 2008) to remove reads with sequencing adapter, with low-quality base ratio (base quality < 5) > 20%, and with unknown base (’N’ base) ratio > 5%. 2) Reads aligned to rRNA by Bowtie2 (v2.2.5) (Langmead and Salzberg, 2012) were removed. 3) The clean reads were mapped to the reference genome using HISAT2 (Kim et al., 2015). Bowtie2 (v2.2.5) was applied to align the clean reads to the transcriptome. 4)Then the gene expression level (FPKM) was determined by RSEM (Li and Dewey, 2011). Genes with FPKM > 0.1 in at least one sample were retained.

2021-03-24 | E-MTAB-10298 | biostudies-arrayexpress

Identifying crossover locations in an Arabidopsis thaliana Col x Di-G F2 population using genotyping by sequencing

Project description:Genomic DNA from 239 Col x Di-G F2 individuals was extracted using CTAB and used to generate sequencing libraries as described (Rowan et al; Yelina et al), with the following modifications. DNA was extracted from 3 rosette leaves of 5 week old plants and 150 ng of DNA used as input for each library. DNA shearing was carried out for 20 minutes at 37°C with 0.4U of DNA Shearase (Zymo research). Each set of 96 libraries was sequenced on one lane of an Illumina NextSeq500 instrument (300-cycle Mid Output run). The barcoded adapter sequences were trimmed and bases with quality lower than 19 were filtered using Cutadapt. Sequencing data was analysed to identify crossovers as previously reported, using the TIGER pipeline.

2024-08-19 | E-MTAB-14382 | 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