Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

D14a6dab-fa4c-4c2c-9a8d-6286e2dd9ff0 - samples

ABSTRACT: Content: 60 GB patient tumours and 4 normal brain samples combined in pairs by region (x2=8 total input samples). RNAseq: 1 lane per sample, total strand-specific rRNA-depleted (normal samples were combined = 2 lanes/samples per brain region). WGBS: 2 lanes per sample (normal samples were combined = 2 lanes/samples per brain region). ChIPseq (histone mark): a subset of 20 GB samples were profiled. For the same modification were multiplexed and sequenced on 4 lanes each (H3K27ac, H3K4me1) or a single lane (all others). WGS: used as matching input control for the 20 ChIPseq samples. Data type and technology: RNA-seq: PE 100bp sequenced on HiSeq2000. WGBS: PE 100bp sequenced on HiSeq2000/4000. ChIPseq: SE 50bp sequenced on HiSeq2000/4000. WGS: PE 150bp sequenced on HiSeq X.

PROVIDER: EGAD00001005492 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Similar Datasets

aaaf5e5f-dfc0-42e3-8e4a-f117f938fb5d - samples

Project description:Content: 2 GB RTK I cell lines (LN229, ZH487) in two conditions (NT control and shSOX10). RNAseq: single replicates per condition, polyA+ RNA sequencing, SE. ATACseq: biological replicates per condition, SE. ChIPseq (histone H3 modifications, LN229 only): all marks for each condition were pooled and sequenced on two lanes for each pool. ChIPseq (BRD4 and SOX10): SOX10 libraries were sequenced on single lanes. BRD4 samples were multiplexed and sequenced in two lanes. ChIPseq input samples are also included. Data type and technology: RNAseq: SE 50bp sequenced on HiSeq2000/4000. ATACseq: SE 50bp sequenced on HiSeq2000/4000. ChIPseq: SE 50bp sequenced on HiSeq2000/4000.

| EGAD00001005493 | EGA

RNAseq data of two week-old soybean leaves response to cold stress

Project description:Transcriptome analysis of cold-treated leaves (unifoliates) of soybean seedlings were performed. RNAseq analysis was performed using two lanes on a Illumina HiSeq2000 and sequenced on a 100bp, paired-end run.

2018-07-27 | GSE117686 | GEO

Genome-wide identiﬁcation of circular RNAs in Arabidopsis thaliana

Project description:To exlore more circRNAs involved in Arabidopsis thaliana, we deeply sequenced 14 samples including whole plants from four developmental stages (rosette leaves > 1 mm in length; rosette growth complete; 50% of flowers to be produced have opened; first silique shattered), aerial part of plants from four stress treatments (control, drought, salinity and heat), five organs (roots, stems, leaves, flowers and siliques) and a mixed sample from whole plants across the lifespan (cotyledons emergence, rosette leaves﹥1 mm, rosette growth complete, first flower open, flourishing florescence, first silique shattered, senescence). The total RNA was purified by rRNA-depletion and linear RNA removal with RNAseR, and paired-end (PE) sequenced by Illumina HiSeq 2500 (read length, PE125, the mixed sample) and Illumina Hiseq X Ten (read length, PE150, 13 independent samples) platforms. We obtained 181.97 Gb raw data (151.37 Gb from 13 samples and 30.6 Gb from a mixed sample) and identified 5861 circRNAs with expression quantity. We annotated the parent genes of these circRNAs and predicted their target sites of microRNAs.

2016-09-01 | GSE77672 | GEO

A benchmark of hemoglobin blocking during library preparation for mRNA-Sequencing of human blood samples

Project description:Background: RNA-Sequencing (RNA-Seq) of peripheral blood can be a valuable source of information for investigating the status and mechanism of diseases. However, blood contains mostly unwanted hemoglobin (Hb) transcripts. A recent method for Illumina RNA-Seq features a ‘Globin Block’ (GB) module that depletes Hb transcripts during library preparation. Here, we aimed to assess GB’s effectiveness, and we checked for technical biases attributable to GB. Results: We sequenced 91 pairs of GB and non-blocked samples (noGB) and 8 GB and noGB technical replicates from whole blood total RNA samples of 91 healthy individuals. GB reduced the fraction of Hb transcripts from 43 % to 8.0 %. From GB samples we detected 1,397 more expressed genes at approximately 11 million reads per RNA-isolate. Using correlation analyses we showed that GB and noGB samples could be assigned to the same RNA isolate with 89.8 % accuracy. Interestingly, lane and platform bias influenced accuracy stronger than GB. Gene expressions distinguishing between GB and noGB could not be enriched for sequence similarity or molecular function. Conclusions: Lexogen’s GB RNA-Seq module is a valuable addition during mRNA-Seq library preparation. GB facilitates the detection of low abundant transcripts and yields more non-hemoglobin reads, while preserving biological information.

2020-04-14 | GSE133758 | GEO

RNA-seq Files : The Hypoxia Response Pathway Promotes PEP Carboxykinase And Gluconeogenesis In C. elegans

Project description:RNA was isolated from L4 stage animals for the following genotypes: N2, hif-1(ia4), egl-9(sa307), hif-1(ia4);egl-9(sa307) grown at 20C. Total RNA was isolated and used to prepare libraries using the Illumina Truseq with polyA selection. Libraries were sequenced across two lanes on an Illumina HiSeq2000 (GeneWiz) or an Illumina HiSeq 2500 in Rapid Run Mode (RUCDR).

2022-09-19 | GSE173580 | GEO

Analyses of lncRNA profiling during the development from pre-receptive to receptive phases in goat endometrium

Project description:In the present study, RNA-seq technique was used to compare the expression profiles of lncRNAs from goat endometrium samples at gestational day 5 (pre-receptive endometrium, PE) and day 15 (receptive endometrium, RE). This yielded 18 gigabases (Gb) of sequence, representing approximately seven times the size of the genome (2.66 Gb). A total of 120 million raw reads were produced from the Illumina HiSeq 2500 platform. After discarding adaptor sequences and low-quality sequences, 90 to 97 million clear reads per sample were obtained, and the percentage of clean reads among raw tags in each library ranged from 75.79–81.03 %. A total of 668 lncRNAs were found to differ significantly in terms of expressional levels (P< 0.05) between the PE and RE libraries,98.35% of the DELs were mapped to “u” (Unknown, intergenic transcript).Our results included 76,844 lncRNAs that corresponded to 42,933 protein-coding genes within a range of 1-100 kb. It deserved to note that 783 target genes of the 200 DELs that were annotated to 153 GO terms meeting our designated criteria of P-values< 0.05, KEGG pathway annotation showed 242 target genes of the DELs were annotated for 146 KEGG pathways.

2019-09-10 | GSE86816 | GEO

A clinically applicable connectivity signature for glioblastoma includes the tumor network driver CHI3L1

Project description:Tumor microtubes (TMs) connect glioma cells to a network with considerable relevance for tumor progression and therapy resistance. The determination of TM-interconnectivity in individual tumors has been challenging and the impact on patient survival unresolved. Here, a connectivity signature from single-cell RNA-sequenced (scRNA-Seq) xenografted primary glioblastoma (GB) cells has been established using a dye uptake methodology, confirmed with recording of cellular calcium epochs and validated with clinical correlations. Astrocyte-like and mesenchymal-like GB cells have the highest connectivity signature scores in scRNA-sequenced patient-derived xenografts and patient samples. In large GB cohorts, network connectivity correlated with the mesenchymal subtype and dismal patient survival. CHI3L1 has been identified and validated as a robust molecular marker of connectivity with functional relevance. The connectivity signature allows novel insights into brain tumor biology, provides a proof-of-principle that tumor cell TM-connectivity is relevant for patients’ prognosis, and serves as a robust prognostic biomarker.

2023-11-27 | PXD044001 | Pride

Whole Genome Bisulfite sequencing for liver DNA methylation analysis of rat exposed to 0.05% Pb

Project description:We generated 4 Gb of high-quality sequencing data (~1 Gb per sample). The NCD+0.05%Pb group had hypermethylation at the whole genome level, compared to NCD. Difference analysis in gene methylation aimed at TSS region indicated that a total of 2733 genes experienced DNA methylation changes, with 2320 hypermethylated genes and 413 hypomethylated genes of the NCD+0.05%Pb group compared with the NCD group.

2016-11-17 | GSE89919 | GEO

Transcriptomics analysis of gene expression in normal and METTL3 or WTAP deficient Human HeLa cells

Project description:RNA was isolated from and METTL3，WTAP deficient Human HeLa cells using the TRIzol (Invitrogen) reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN (RNA integrity number) of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2000 (Illumina) in single-read mode, creating reads with a length of 50 bp. Sequencing chemistry v2 (Illumina) was used and samples were multiplexed in two samples per lane.

2014-01-16 | GSE50582 | GEO

Transcriptomics analysis of gene expression in normal and Smg6 deficient mouse ES cells

Project description:RNA was isolated from control and Smg6 deficient ES cells using the TRIzol (Invitrogen) reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN (RNA integrity number) of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2000 (Illumina) in single-read mode, creating reads with a length of 50 bp. Sequencing chemistry v2 (Illumina) was used and samples were multiplexed in two samples per lane.

2013-08-14 | GSE49844 | GEO

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