Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Long and short-read transcriptome profiling of human lung cancer cell lines

ABSTRACT: Purpose: The aim of this study is to compare different long-read sequencing platforms using reference lung adenocarcinoma cell lines and spike-in controls. Methods - Cell Culture: Lung adenocarcinoma cell lines NCI-H1975 and HCC827 from a range of passages (2-4) were grown on 3 separate occasions in Roswell Park Memorial Institute (RPMI) 1640 medium with 10% fetal calf serum and 1% penicillin-streptomycin. Methods - RNA preparation: mRNA was extracted using a Qiagen RNA miniprep kit and purified using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490). Purified mRNA spiked with sequins was used for Next Generation Sequencing library preparation using the NEBNext Ultra II Directional RNA Library Prep Kit (Illumina) and the cRNA-PCR Barcoding (SQK-PCS109 with SQK-PBK004) kit (ONT). Completed libraries were sequenced on NextSeq 500 (Illumina) and PromethION (ONT). Iso-Seq libraries were prepared and sequenced by Novogene on Sequel II (PacBio). Reads were mapped to known genomic features of the GRCH38 reference genome and RNA sequin decoy chromosome combined sequences at the gene-level and single reads were then summarized into gene-level counts using featureCounts software (Liao et al. 2014).

ORGANISM(S): Homo sapiens

PROVIDER: GSE172421 | GEO | 2022/07/20

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Long-read transcriptome profiling of human lung cancer cell lines

Project description:Purpose: The aim of this study is to compare the transcriptome profiles using a mixture design that allows the relative changes of the majority of the genes profiled to be estimated. Methods - Cell Culture: Lung adenocarcinoma cell lines NCI-H1975 and HCC827 were grown in Roswell Park Memorial Institute (RPMI) 1640 medium with 10% fetal calf serum and 1% penicillin-streptomycin. Methods - RNA preparation: mRNA was extracted using a Qiagen RNA miniprep kit and purified using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490). Purified mRNA spiked with sequins was used for the cRNA-PCR Barcoding (SQK-PCS109 with SQK-PBK004) kit (ONT). Completed libraries were sequenced on PromethION (ONT). Reads were mapped to known genomic features of the GrCh38 reference transcriptome and RNA sequin transcriptome combined sequences at the transcript-level and single reads were then summarized into transcript-level counts using salmon software (Patro et al. 2017).

2023-07-14 | GSE227000 | GEO

Transcriptome profiling of human lung cancer cell lines with synthetic "sequin" controls

Project description:Purpose: The aim of this study is to build up a transcriptomic data analysis pipeline and test its performance using synthetic "sequins" controls and lung cancer cell lines. Methods - Cell Culture: Lung adenocarcinoma cell lines NCI-H1975 and HCC827 from a range of passages (2-4) were grown on 3 separate occasions in Roswell Park Memorial Institute (RPMI) 1640 medium with 10% fetal calf serum and 1% penicillin-streptomycin. Methods - RNA preparation: Total RNA was extracted using the TRIzol reagent. 6 ng of sequins were added to 1 ug of total RNA (mix A with H1975, mix B with HCC827). Methods - Library prep: the sequin+total RNA mixtures were subjected to polyA selection (NEBNext PolyA E7490) and library prep (NEBNext Ultra II Directional RNA Library Prep Kit for Illumina) following manufacturer's instructions; we performed 9 PCR cycles

2021-01-12 | GSE164598 | GEO

Evaluation of three small RNA library preparation kits on serum-derived RNA

Project description:We evaluated the effect of the small RNA library preparation method on 5' tRNA-halves and miRNA abundance in libraries prepared from serum RNA using three commercially available small RNA library preparation kits (TruSeq small RNA library preparation kit v2 (Illumina), TailorMix miRNA sample preparation kit v2 (Seqmatic) and the NEBNext Multiplex Small RNA library prep kit (New England Biolabs)). RNA isolated from 100 µl of serum collected from healthy mice was used as input for the preparation of a small RNA library in duplicate and libraries were single end sequenced.

2017-02-22 | GSE88914 | GEO

U1 RAP-RNA-Seq analysis of A2Lox mouse embryonic stem cells treated with a control or Srrt-specific siRNA

Project description:The experiment was carried out to examine the effect of Srrt knockdown on the U1 snRNP/pre-mRNA interaction pattern. A2Lox mouse embryonic stem cells were transfected with either an Srrt-specific or a non-targeting siRNA. 48 hours post transfection the cells were cross-linked using 2% formaldehyde and lysed. RNA was partially fragmented by sonication, hybridized with U1 snRNA-specific biotinilated probes and pulled down. U1-associated RNA sequences were then purified and RNA-seq libraries were generated using a NEBNext® rRNA Depletion Kit and NEBNext® Ultra8482 II Directional RNA Library Preparation kit. Paired-end sequencing was performed using a HiSeq4000 75bp platform.

2019-11-27 | E-MTAB-7635 | biostudies-arrayexpress

Long-read Nanopore sequencing of mouse neural stem cells

Project description:Purpose: The aim of this study is to identify genes that are under the transcriptional control of the epigenetic modifier Smchd1 in mouse neural stem cells. We profiled the transcriptomes of mouse neural stem cells from samples that were either wild-type or contained a null mutation in the epigenetic regulator Smchd1 using Oxford Nanopore Technologies (ONT) direct cDNA sequencing protocol and a PromethION sequencer.

2020-06-18 | GSE151841 | GEO

Nanopore RNA-seq of human cell lines treated with or without nicotinamide adenine dinucleotide (NAD+)

Project description:Investigation of transcriptome changes in four human cell lines (BJ, BJ-5ta, U2OS and HeLa) after treatment for 24 hours with nicotinamide adenine dinucleotide (NAD+). Cells were untreated as the control condition. Nanopore sequencing of cDNA was performed after library preparation with the ONT SQK-PCB109 kit.

2023-09-20 | E-MTAB-13187 | biostudies-arrayexpress

m6A-RIP-seq of mRNA in HeLa cells undergoing EMT

Project description:We report the application of m6A-RIP-seq to indentify the m6A modifications variation in genes invovled in EMT. Briefly, total polyadenylated RNA was isolated from HeLa cells treated with or without 10 ng/ml TGF-β for 3 days by use of TRIZOL reagent followed the using of FastTrack MAGMaxi mRNA isolation kit (Invitrogen). RNA fragmentation, m6A-seq, and library preparation were performed according to instructions of manufacture and the previously published protocol (Wang et al., 2015). NEBNext Ultra Directional RNA Library Prep Kit (New England BioLabs, Ipswich, MA) was used for library preparation. Each experiment was conducted in two biological replicates. m6A-seq data were analyzed according to the protocols described before (Wang et al., 2015). Significant peaks with FDR < 0.05 were annotated to RefSeq database (hg19). Sequence motifs were identified by using Homer. Gene expression was calculated by Cufflinks using the sequencing reads from input samples. Cuffdiff was used to find the DE genes.

2019-03-25 | GSE112795 | GEO

RNA-seq of Acidiphilium sp. C61 culture supplemented with 10 µM 2-Phenethylamine (PEA) against controls

Project description:Acidiphilium sp. C61 cultures were cultivated in APPW+YE+Glucose medium with 0 µM or 10 µM PEA. RNA was extracted and library preparation was done using the NEBNext Ultra II directional RNA library prep kit for Illumina. Data was demultiplied by GATC sequencing company and adaptor was trimmed by Trimgalore. After trimming, data was processed quality control by sickle and mRNA was sorted by SortmeRNA. mRNA transcripts were mapped to the assembled genome of Acidiphilium sp. C61 and read counts table was produced by featurecounts. Differential gene expression analysis was done by edgeR package.

2020-03-01 | E-MTAB-8619 | biostudies-arrayexpress

mRNA-seq of H3.3 mutant (K9A; K27A; K79A) and control mESCs

Project description:Mouse embryonic stem cells (i.e., mESCs; line ESC 129-B13) were genetically modified using CRISPR-Cas9 to mutate the H3f3b locus, in order to carry homozygous lysine-to-alanine substitution of residues K9, K27 or K79. Two control mESC lines carrying knock-out of the H3f3a gene were used as background for the editing. To compare the transcriptional profiles of the H3.3 mutant and control mESC lines, three independent replicates per condition were grown and RNA was extracted. After quality assessment of the RNA, messenger RNA was isolated using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs) and sequencing libraries were prepared using the NEBNext Ultra II RNA Library Preparation Kit for Illumina (New England BioLabs). Sequencing was performed on a NextSeq500 platform in single-end mode (75bp reads).

2024-03-09 | E-MTAB-12866 | biostudies-arrayexpress

LRGASP challenge WTC11 ssCAGE sequencing derived peaks

Project description:The LRGASP challenge encompasses different human, mouse, and manatee samples sequenced using multiple combinations of protocols and platforms. Different challenges will use distinct subsets of the samples for evaluation. The long-read sequencing platforms used in these challenges are the Pacific Biosciences (PacBio) Sequel II, Oxford Nanopore (ONT) MinION and PromethION. Samples will also be sequenced on the Illumina HiSeq 2500. The primary LRGASP library prep protocols are “standard” cDNA sequencing, direct RNA sequencing, R2C2, and CapTrap. Each sample will also include Lexogen SIRV-Set 4 spike-ins. We will also provide simulated PacBio and ONT data as part of the evaluations. This particular study focuses on single strand CAGE sequencing of human iPSCs, defining CAGE peaks from Illumina HiSeq 2500 (SR: 150 cycles) of two biological replicates for use in the LRGASP challenge.

2021-10-27 | GSE185917 | 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