Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

716568ed-48eb-41ce-8d8f-ef2ce053b6a0 - samples

ABSTRACT: RNA sequencing from MSTO-211H cell line cultures treated for 72h with vehicle solution, palbociclib 250nM, or abemaciclib 250nM (N = 3, each). RNA-seq prepared using TruSeq Stranded mRNA libraries and sequenced with Illumina HiSeq 4000. Data is in raw fastq format, paired end. Some samples have been split in two lanes, with a final count of 24 fastq files.

PROVIDER: EGAD00001007737 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Similar Datasets

54d657ed-ca5d-4c5d-87a0-24ae0ac28f3e - samples

Project description:RNA sequencing from 12 xenografts implanted using MSTO-211H cell line and treated with vehicle solution, cisplatin + pemetrexed, or palbociclib (N = 4, each). RNA-seq prepared using TruSeq Stranded mRNA libraries and sequenced with Illumina HiSeq 4000. Data is in raw fastq format, paired end. Some samples have been split in two lanes, with a final count of 34 fastq files.

| EGAD00001007739 | EGA

Transcriptomic differences between euryhaline and stenohaline malaria vector sibling species in response to salinity stress [set2]

Project description:We use RNA-Seq to explore the reaction norm of gene expression of larval Anopheles coluzzii and An. merus to a gradient of salinity. After rearing in freshwater, separate pools of 18 h post-hatch larval instars of An. merus and An. coluzzii were briefly (6 h) exposed to one of six water salinities: 0%, 10%, 20%, 30%, 40%, or 50% the salinity of seawater. The last sample (G-50-RC) was split across 5 lanes for sequencing, resulting in total 10 fastq files associated with subparts G-50-RCa, G-50-RCb, G-50-RCc, G-50-RCd, G-50-RCe.

2016-03-09 | E-GEOD-74819 | biostudies-arrayexpress

Gene expression profiles between the palbociclib monotherpy versus palbociclib alternating with ICI182,780 treatment in breast cancer cells at 10 weeks.

Project description:We examined differential gene expression profiles between MCF7 human breast cancer cells treated with vehicle alone (control), palbociclib monotherapy, palbociclib alternating with ICI182,780 treatment, and palbociclib resistant cells. For this, we used gene microarray expression profiling to identify significantly changed genes under different treatment conditions.

2023-04-10 | GSE229002 | GEO

The effect of sample splitting and technical replication on mRNA-seq and sRNA-seq quantification

Project description:RNA sequencing (RNA-seq) is a widely used method for quantifying RNA levels across the environmental, biological and medical sciences. The accuracy of the output from an RNA-seq experiment is known to vary due to sequencing biases or errors in quantification. These have the potential to lead to false calls of differential expression (DE), and hence, to affect the accuracy of the biological inference. A proposed solution to reduce the number of false positives and increase confidence in the quality of results from such experiments is to increase the number of biological replicates. In addition, more recent suggestions are to create additional technical replicates within biological replicates (i.e. to split samples across sequencing lanes). The optimal strategy for analysing and normalizing such data, and for maximising accuracy as a function of cost, biological and technical replication is important to understand, yet currently unclear. The aim of this study was to test the effect of technical replication and sample splitting on the overall outcome of gene expression profiling for RNA-seq data.

2018-12-15 | GSE85806 | GEO

H. sapiens First trimester placental villous explant 0conditioned media; galectin-7/BSA treatment; 2% O2

Project description:Identification of factors in conditioned media of first-trimester placental villous explants. Explants were cultured under hypoxia (2% O2), 5% CO2 in serum-free DMEM/F12 and treated with recombinant galectin-7 (1ug/ml) or vehicle control (BSA) for 72h. Identification of factors in conditioned media of first-trimester placental villous explants. Explants were cultured under superoxia (20% O2), 5% CO2 in serum-free DMEM/F12 and treated with recombinant galectin-7 (1ug/ml) or vehicle control (BSA) for 72h.

2021-04-20 | PXD019331 | Pride

Human benign adrenocortical tumors miRNome

Project description:Small RNAs (<100 bases in length) were purified from total RNA samples using the miRNeasy kit (Qiagen), and multiplexed miRNA libraries were prepared using a previously described protocol and sequenced on a HiSeq 2000 (Illumina). Image analysis, base calling, demultiplexing and conversion of BCL to FASTQ format were carried out using CASAVA 1.8.2 software (Illumina). Adaptor sequences were removed using mirExpress software. Fastq were 3p-adaptor trimmed. The sequences were then aligned on hg19 (GRCh37) human reference genome with STAR (v.2.5.2a), allowing no mismatch with reference. Reads were counted using HTSeq-count (HTSeq v 0.6.1p1 Python package) using “intersection-strict” mode, to count mature miRNA abundance according to miRbase v.20.

2020-08-12 | E-MTAB-6553 | biostudies-arrayexpress

Single cell RNA-seq and TCR-seq of coding RNA from single cells in the mouse lung using 10x Chromium Single Cell 5' Reagent Kits User Guide (v2 Chemistry Dual Index)

Project description:Single-cell RNA-seq and TCR-seq were conducted using coding RNA of single cells isolated from mouse lung MNCs with or without 7DW8-5 according to the manufacturer’s instructions. In brief, single cells from the mouse lung MNCs were incubated with mouse Fc block and then stained by anti-mouse CD45+ antibody and DAPI. Sorted viable CD45+DAPI- single cells were loaded into 10x genomics ChromiumTM controller (samples were split into 4 lanes, Saline1 and Saline2 without 7DW8-5 treatment, and 7DW1 and 7DW2 with 7DW8-5 treatment) to make nanoliter-scale droplets with uniquely barcoded 5’ gel beads called GEMs. After GEM-RT and the following some cDNA amplification steps, cDNAs derived from cellular mRNA were pooled for downstream processing and library preparation according to the manufacturer’s instructions. The 5’ transcript library and TCR library were sequenced with Illumina Novaseq. Fastq files from RNA-seq and TCR-seq can be processed through cellranger and vdjranger by 10xgenomics. The datasets include the data of the samples Saline1, Saline2, 7DW1, and 7DW2.

2023-06-06 | E-MTAB-11770 | biostudies-arrayexpress

dcc4e242-ffa2-4244-aa8b-89f604f524d2 - samples

Project description:scRNAseq dataset of colonic epithelium from distal colon biopsies from 4 patients with ulcerative colitis and 4 healthy individuals. Includes 11 samples split into three conditions: healthy, healthy margin and ulcerated. Dataset includes raw Fastq files and processed csv count matrices. Fastq files are divided into 4 lanes and into index (I1) and read (R1, R2) files. Count matrices contain comma-separated values with cell barcodes as column names and gene names as row names. Cell Ranger (v3.0.1) software from 10x Genomics was used to process the output and align the reads. The refdata-cellranger-GRCh38-3.0.0 reference was downloaded from the 10x Genomics website. First, cellranger mkfastq function was used to demultiplex raw base call files into FASTQ files. Then, the FASTQ files were aligned and filtered with cellranger count function.

| EGAD00001010167 | EGA

Transcriptome analysis of human iPSC-neurons treated with cardiac glycosides

Project description:To investigate the molecular mechanisms of cardiac glycosides’ neuroprotection, we profiled transcriptomes of human iPSC-neurons after 72h of treatment with increasing doses of digoxin, oleandrin, proscillaridin A or vehicle alone (0.1% DMSO) using RNA sequencing.

2023-10-19 | GSE228348 | GEO

Sequencing of the non-ribosomal transcriptome allows the simultaneous identification of protein-coding and non-protein-coding RNAs

Project description:Deep Sequencing of protein-coding and non-protein-coding RNAs from mouse differentiated embryonic stem cells and 14.5dpc mouse fetal head Analysis of Ribominus RNA from mouse differentiated embryonic stem cells and 14.5dpc mouse fetal head There are no processed data files for GSM566806-GSM566811. There are no fastq raw data files for GSM566812 and GSM566813 since these samples are the combined reads from all sequence lanes.

2011-12-06 | E-GEOD-22959 | 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