Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

12 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of human non-small-cell lung cancer cell line A549 treated with Feiyanning

ABSTRACT: We performed RNA seq to elucidate differential gene expression in A549 treated with Feiyanning (FYN). A549 cells were treated with FYN, then cultured for 24 h. Total RNA were extracted using TrizoI, and mRNA were retain using Oligotex mRNA Mini kit. The mRNA were fragmented into small fragments and reverse transcripted into cDNA. Next, the cDNA fragments were purified with Ampure beads, end repaired, poly(A) added, and ligated to Illumina sequencing adapters. Then User enzyme was used to digest the second-strand cDNA. The products were amplified, and sequenced.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Homo sapiens

SUBMITTER: chenyangchChen Yang Wang

PROVIDER: E-MTAB-10821 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Ribosome sequencing of the effect of control lentivirus and AARS2 overexpression lentivirus on neonatal rat cardiomyocyte translation

Project description:Ribo-seq was performed by Novogene. Briefly, use RNase I to digest the unprotected RNA, leaving only the ribosome-protected mRNA fragments, and sequencing libraries were constructed and carried out on an Illumina Novaseq 6000 SE50.

2024-03-01 | E-MTAB-13767 | biostudies-arrayexpress

Comprehensive analysis of transcriptomic changes in cutaneous squamous cell carcinoma

Project description:Purpose: We report the coding and non-coding transcriptomic changes in primary cutaneous squamous cell carcinoma Methods: 4 mm punch biopsies were collected from 7 unmatched healthy and 9 cSCC patients and snap frozen. The library preparation was done using Illumina TruSeq® Stranded Total RNA (with Ribo-Zero Gold) preparation kit. 100 ng of total RNA was depleted of rRNAs using ribo-zero gold magnetic bead based capture-probe system (Illumina Inc.). The remaining RNA was subsequently purified (RNAcleanXP, Beckman Coulter) and fragmented using enzymatic fragmentation. Then first strand synthesis and second strand synthesis were performed and the double stranded cDNA was purified (AMPure XP, Beckman Coulter). The cDNA was end repaired, 3’ adenylated and Illumina sequencing adaptors ligated onto the fragments ends, and the library was purified (AMPure XP). The stranded libraries were amplified with PCR and purified (AMPure XP). The libraries size distribution was validated and quality inspected on a Bioanalyzer. Sequencing was performed on NextSeq 500 instrument using v2 reagent kits according to the manufacturer instructions (Illumina Inc.). Results: On average 49.8 million 100 base pair (bp) paired-end reads were obtained from each sample and genome mapping was on average 55% for all samples. Altered expression of 5,352 protein-coding genes, 908 lncRNAs and 55 circular RNAs was identified. Conclusions: Here, we report the coding and non-coding transcriptomic changes from cSCC samples, along with identification of skin specific transcripts and novel deregulated circRNAs.

2020-03-09 | GSE139505 | GEO

RNA-SEQ assay for wild type and CRISPR induced endoglin knockout human pulmonary artery smooth muscle cells (PASMC)

Project description:The goal of this study is to investigate the differential transcripted genes affected by CRISPR induced endoglin knockout in PASMC cells. Total RNA was purified from NTC or ENG-/- PASMC cells using RNeasy Mini Kit (Qiagen, Hilden, Germany). RNA quality and concentration were assessed with Agilent Tapestation 200 (Agilent Technologies) and Qubit 2.0 (ThermoFisher Scientific). ~250-500 ng RNA were used for library construction. The NGS libraries were constructed using the KAPA Stranded mRNA-Seq Kits (KapaBioSystems). mRNA was captured using magnetic oligo-dT beads and 1st strand cDNA was synthesized using random priming. In order to preserve strand-specificity, 2nd strand synthesis, which converts the cDNA:RNA hybrid to double-stranded cDNA (dscDNA), was marked by dUTP incorporation. cDNA framents were A-tailed by adding dAMP to the 3'-ends of the dscDNA library fragments. dsDNA Illumina TruSeq "forkedâ adapters 3'-dTMP overhangs were then ligated to A-tailed library insert fragments. Each of the six libraries were ligated with a unique Truseq 6bp barcode. Library fragments were amplified using the KAPA HiFi HotStart polymerase. The strand marked with dUTP was not amplified, allowing strand-specific sequencing. Fragment length and library quality was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit (Agilent Technologies). Libraries were diluted to 10nM and pooled at equimolar ratios. The pool was then diluted to 2nM and denatured in NaOH following Illumina recommendations. 10pM of denatured library pool was loaded in one HiSeq lane and flowcell was clustered on the Illumina C-bot. 5% PhiX control was spiked-in. The flowcell was sequenced on a HiSeq 2500 V4 chemistry with 50bp Single read protocol. Data was demultiplexed and Fastq files were generated using BcptoFastq 1.8.4 script provided by Illumina.

2017-05-16 | E-GEOD-78271 | biostudies-arrayexpress

Human RNase 4 Improves mRNA Sequence Characterization by LC-MS/MS.

Project description:With the rapid growth of synthetic messenger RNA (mRNA)-based therapeutics and vaccines, the development of analytical tools for characterization of long, complex RNAs has become essential. Tandem liquid chromatography-mass spectrometry (LC-MS/MS) permits direct assessment of the mRNA primary sequence and modifications thereof without conversion to cDNA or amplification. It relies upon digestion of mRNA with site-specific endoribonucleases to generate pools of short oligonucleotides that are then amenable to MS-based sequence analysis. Here, we showed that the uridine-specific human endoribonuclease hRNase 4 improves mRNA sequence coverage, in comparison with the benchmark enzyme RNase T1, by producing a large population of uniquely mappable cleavage products. Furthermore, we deployed hRNase 4 to characterize mRNAs fully substituted with 1-methylpseudouridine (m1Ψ) or 5-methoxyuridine (mo5U), as well as mRNAs selectively depleted of uridine–two key strategies to reduce synthetic mRNA immunogenicity. Lastly, we demonstrated that hRNase 4 enables direct assessment of the 5′ cap incorporation in in vitro synthesized mRNA. Collectively, this study highlights the power of hRNase 4 to interrogate mRNA sequence, identity, and modifications by LC-MS/MS.

2022-07-26 | PXD033334 | Pride

ASC-J9 blocks STAT3 signaling, cell proliferation, collagen synthesis, inflammation, and ROS generation in keloid fibroblasts

Project description:The purified RNA from NFs (n=1) and KFs (n=1) treated with DMSO or ASC-J9 was used for the preparation of the sequencing library by the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s recommendations. Briefly, mRNA was purified from total RNA (1 µg) by oligo(dT)-coupled magnetic beads and fragmented into small pieces under elevated temperature. The first-strand cDNA was synthesized using reverse transcriptase and random primers. After the generation of double-strand cDNA and adenylation on the 3’ ends of DNA fragments, the adaptors were ligated and purified with the AMPure XP system (Beckman Coulter, Beverly, USA). The quality of the libraries was assessed by the Agilent Bioanalyzer 2100 system and a real-time PCR system. The qualified libraries were then sequenced on an Illumina NovaSeq 6000 platform with 150-bp paired-end reads generated by Genomics BioSci & Tech Co., Ltd.

2022-06-01 | GSE198095 | GEO

Transcriptome analysis of human blastocysts with different levels of chromosomal mosaicism after preimplantation genetic testing.

Project description:An inner cell mass biopsy and the remaining trophectoderm were separately collected from 14 blastocysts with preimplantation genetic testing result into RNAse-free PCR tubes containing 2 µl of 10X reaction buffer (SMART-Seq v4 Ultra-Low Input RNA kit for Sequencing, Takara Bio, USA). cDNA was obtained from mRNA with 3′SMART-Seq CDS primer II (Takara Bio, USA) and PCR-amplified (17 cycles) from 10 pg of RNA. Amplified cDNA was purified using AMPure XP magnetic beads (Illumina, USA). After confirming cDNA integrity on a 2100 Bioanalyzer (Agilent Technologies, USA), 1 ng of cDNA per sample were fragmented, and libraries were constructed using NexteraXT DNA sample preparation (Illumina, USA). Samples were quantified using Qubit dsDNA Quantitation Assay (Thermo Fisher Scientific, USA), and 3 samples were excluded due to poor cDNA quality. An RNA pool was generated with 25 samples using equal concentration (5 nM) of RNA per sample. Sequencing was performed in duplicate in a single run using an Illumina NovaSeq 6000 S1 platform (Illumina, USA) with a 200-nucleotide read length in a paired-end design (100-bp fragments). FastQC was used for checking the quality of the raw sequence data. Fragments that did not meet quality requirements were trimmed using Trimmomatic. Alignment and quantification were performed using the Salmon algorithm (reference genome GRCh38). Raw counts were directly used for differential gene expression analysis.

2022-01-31 | GSE194306 | GEO

Authentic single cell RNA-Seq by measuring the transcriptome of an individual cell twice

Project description:We developed a novel single-cell RNA-Seq technique that can directly measure the technical noises for each individual gene by splitting a single cell into two equal halves and measuring their transcriptomes separately (Measure a single cell twice by RNA-Seq, MAST-Seq).The MAST-Seq protocol was developed from the single cell RNA-Seq technique we previously developed (Tang et al. 2010). We first lysated the cell to release the RNA from the cell, then reverse transcripted the mRNA into cDNA, added polyA to the 3' end of cDNA, synthesized the second strand of cDNA used designed primer, and at last PCR amplified the double strand cDNA to get enough amount of DNA to construct the cDNA libraries.

2018-01-01 | GSE65160 | GEO

Transcriptional profiling of wild type Neurospora crassa cells treated with novel antifungal agents

Project description:Purpose: Evaluate the transcriptional profile of Neurospora crassa cells treated with a group of novel antifungal compounds Methods: Conidial suspensions were obtained and 1 x 106 cells/ml incubated in minimal medium for 6 hours (26ÂºC, 140 rpm, constant light) followed by the addition of the indicated compound (or DMSO) and growth for 1 more hour. Cells were harvested using 0.45 Î¼m filters and immediately frozen in liquid nitrogen. Total RNA was isolated by the Trizol-Phenol-Chloroform method. After digestion of 25 Î¼g RNA with TURBO DNAse (Life Technologies), mRNA was purified using Dynabeads oligo(dT) magnetic beads (Life Technologies). The mRNA was chemically fragmented using the Ambion RNA fragmentation kit (Life Technologies). First and second strand cDNA synthesis was achieved using appropriate kits (Life Technologies). The illumina TruSeq kit was employed to generate the cDNA libraries with indexing adapters essentially following the manufacturerâs protocol. After purification of the libraries with AMPure XP beads (Roche), the quality of the libraries was analysed in a Agilent 2100 Bioanalyzer. The cDNA libraries were sequenced in a illumina HiSeq2000 and single reads of 50 bp were obtained. Sequencing data was handled essentially with Tophat, Cufflinks and Cuffdiff. Expression levels are presented as Fragments Per Kilobase of transcript per Million mapped reads (FPKM). Results: XP13 promoted a particularly active transcriptional response. Functional enrichment analysis of the genes with altered expression revealed novel pathways that are affected by these compounds. Conclusions: These compounds are active in Neurospora crassa and we anticipate that this and future studies will ascertain their potential as antifungal agents. The transcriptional profile of Neurospora crassa wild type cells exposed with a group of novel compounds with antifungal activity was analysed using illumina HiSeq2000 and single reads of 50 bp.

2015-11-25 | E-GEOD-53040 | biostudies-arrayexpress

Ultra-low levels of CpG Island methylation control tissue-specific expression and hypermethylation in cancer.

Project description:We analyzed levels of 5-methyl cytosine CCCGGG target sites by sequential restriction digest by SmaI and XmaI enzymes, ligating Illumina adaptors to the restriction fragments and reading methylation-specific signatures at the ends of restriction fragments by paired ends Illumina high throughput sequencing.

2019-06-02 | GSE82205 | GEO

DNA methylation drift as a marker of lifespan in mammals [monkey]

Project description:We analyzed levels of 5-methyl cytosine at CCCGGG target sites by sequential restriction digest by SmaI and XmaI enzymes, ligating Illumina adaptors to the restriction fragments and reading methylation-specific signatures at the ends of restriction fragments by paired ends Illumina high throughput sequencing.

2017-07-10 | GSE75496 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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