Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Illumina HiSeq Sequencing on Breast cancer PDX samples

ABSTRACT: RNAseq was done on Breast cancer PDX samples uisng Library protocol =llumina TruSeq Stranded Total RNA Kit with Ribo-Zero Gold , HiSeq 50 Cycle Single-Read Sequencing v4

ORGANISM(S): Homo sapiens

PROVIDER: GSE113986 | GEO | 2019/03/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

RNAseq of Breast cancer PDX samples

Project description:RNAseq was done on Breast cancer PDX samples uisng Library protocol =llumina TruSeq Stranded Total RNA Kit with Ribo-Zero Gold , HiSeq 125 Cycle Paired-End Sequencing v4

2018-05-24 | GSE113476 | GEO

Sheep Tissue Atlas

Project description:Sheep total RNA was extracted from embryonic and adult tissues. Sequencing libraries were prepared from the RNA using the Illumina TruSeq stranded total RNA with the Ribo Zero gold option for the rRNA removal. The fragmentation in the standard protocol was modified to increase the average insert size in the library. Sequencing with 151 base paired end reads was performed on an Illumina HiSeq 2500 in rapid mode.

2014-12-04 | E-MTAB-3838 | biostudies-arrayexpress

Transcriptome of the liver in 15-day-old C3H/HeJ mice

Project description:Male C3H/HeOuJ mice are susceptible to spontaneous liver neoplasms. We collected liver samples from young, tumour-free mice for control experiments. Liver tissue samples were snap frozen in liquid nitrogen and total RNA was extracted using the AllPrep 96 DNA/RNA Kit (Qiagen) according to the manufacturer’s instructions. Libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina) and sequenced in an Illumna HiSeq4000 to produce 150bp paired-end reads.

2018-07-29 | E-MTAB-6972 | biostudies-arrayexpress

Whole-transcriptome of the liver in 15-day-old C3H/HeOuJ and CAST/EiJ mice.

Project description:Male C3H/HeOuJ and CAST/EiJ mice were treated with diethylnitrosamine to induce liver tumours. We collected liver samples from untreated P15 mice for control experiments. Liver tissue samples were snap frozen in liquid nitrogen and total RNA was extracted using the AllPrep 96 DNA/RNA Kit (Qiagen) according to the manufacturer’s instructions. Libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina) and sequenced on an Illumna HiSeq4000 to produce 150bp paired-end reads.

2020-06-18 | E-MTAB-8518 | biostudies-arrayexpress

Transcriptome profiles of C3H/HeJ mouse liver tumours

Project description:Male C3H/HeOuJ mice are susceptible to spontaneous liver neoplasms. We aged a cohort of mice for up to 76 weeks and isolated liver tumours. Tumours were bisected: one half was snap frozen in liquid nitrogen for RNA extraction and the other half of the tumour was processed for histological examination. Total RNA was extracted using the AllPrep 96 DNA/RNA Kit (Qiagen) according to the manufacturer’s instructions. Libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina) and sequenced in an Illumina HiSeq4000 to produce 50bp paired-end reads.

2018-07-29 | E-MTAB-6971 | biostudies-arrayexpress

Multiparameter functional diversity of human C2H2 zinc finger proteins [RNA-Seq]

Project description:C2H2 zinc finger proteins represent the largest and most enigmatic class of human transcription factors. Their C2H2 arrays are highly variable, indicating that most will have unique DNA binding motifs. However, most of the binding motifs have not been directly determined. We have determined the binding sites and motifs of 119 C2H2 zinc finger proteins and the expression pattern of 80 cell lines overexpressing C2H2 zinc finger proteins in order to study the role of C2H2 zinc finger proteins in gene regulation. We expressed GFP-tagged C2H2-ZF proteins in stable transgenic HEK293 cells. Total RNA was isolated using Trizol and sequencing libraries were constructed using TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold or TruSeq RNA Library Preparation Kit v2.

2016-10-25 | E-GEOD-76495 | biostudies-arrayexpress

ena-DATASET-MCGILL-EDCC-12-01-2017-18:11:29:150-25 - samples

Project description:RNA sequencing of 31 patient-derived fibroblast cell lines from patients with inborn errors of cobalamin (vitamin B12) metabolism, and 7 control samples. The RNA seq library was prepared using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina RS-122–2301) including Ribo-Zero Gold depletion to remove ribosomal RNA. Sequencing was done via llumina Hi-Seq2000 sequencer, using 100bp paired end reads.

| EGAD00001003142 | EGA

20954cf8-64d5-4cbc-9c3f-de6457577afc - samples

Project description:RNA-sequencing of human hepatocellular carcinoma biopsies (n=14), 44 HCC xenografts derived from 11 HCC biopsies and 3 lymphoma xenografts derived from 3 HCC biopsies. RNA-sequencing was performed using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (lllumina). SR126 sequencing was performed on an Illumina HiSeq 2500 using v4 SBS chemistry according to the manufacturerÃ¢Â€Â™s guidelines.

| EGAD00001004541 | EGA

RNA-Seq of Drosophlia adult mid-gut with the induction of RNAi against the largest subunit of RNA polymerase III.

Project description:TIGS>dC160RNAi females were fed RU486 from day 2 of adulthood to induce the RNAi expression, 10 guts were dissected per sample (the dissections were batched), RNA extracted with TRIZOL, cleaned up with Quiagen RNEasy with on-column DNase treatment, rRNA depleted (Ribo Zero Gold) and sequenced on the Illumina platform

2017-11-29 | E-MTAB-5252 | biostudies-arrayexpress

Transcriptome analysis of CPSF5 dependent starvation response

Project description:Purpose: transcriptome analysis of CPSF5 dependent starvation response Methods: Total RNA was extracted from larval fat body using TRIzol® reagent (Invitrogen). After assessing RNA quality with an Agilent Bioanalyzer, libraries constructed with an Illumina TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold were sequenced using an Illumina HiSeq 4000 at the Columbia Genome Center (http://systemsbiology.columbia.edu/genome-center). Results: Using an optimized data analysis workflow, we identified 1933 genes responding to starvation and 585 genes were found to be CPSF5-dependent. The gene set enrichment analyses and qPCR confirmation further suggested autophagy, changes of lipid, protein and energy metabolism is requlated by CPSF5 during starvation. Conclusions: our study identified the regulatory role of CPSF5 in autophagy and metabolisms during starvation.

2017-06-01 | GSE99509 | 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