Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

57fd780e-ce9a-4c69-843e-a8afb4a3f8d8 - samples

ABSTRACT: This dataset contains 56 fastq files of paired-end RNA sequencing of a IlluminaÃ‚Â® TrueSeq stranded mRNA library of 28 renal cell carcinoma PDX samples.

PROVIDER: EGAD00001008766 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Similar Datasets

f10c1ad3-cb5a-44db-b52f-58b3e25f0164 - samples

Project description:This dataset contains 46 fastq files of paired-end RNA sequencing of an IlluminaÃ‚Â®Ã¯Â¸Â TrueSeq stranded mRNA library of 23 glioblasoma PDX samples.

| EGAD00001010196 | EGA

656d00d5-0e2e-44f3-b6ce-e8787de9b107 - samples

Project description:To investigate the mode of action and potential side-effects we analyzed differential gene expression in Postmitotic C9orf72 iPSC-Neurons by RNAseq. The cells were treated in a 2 dose regime at 10 Ã‚Âµm in 0.1 % DMSO for 9 days. Compound treated iPSC-Neurons were washed with PBS, frozen on dry ice and stored at -80Ã‚Â°C until RNA isolation. The RNA was isolated using miRNA Mini Kit (Qiagen) using 700 ÃŽÂ¼l of Qiazol. A total of 250 ng of RNA per sample was processed for mRNA library preparation as per the manufacturerÃ¢Â€Â™s instructions for IlluminaÃ‚Â® Stranded mRNA Prep Ligation to be used with the IDTÃ‚Â® for IlluminaÃ‚Â® RNA UD Indexes Set B and sequenced using NextSeq 500/550 High Output Kit v2.5 (Illumina) on NextSeq 550 (Illumina). The data was processed and analyzed using CLC genomics workbench (Version 21.0.3, Qiagen)

| EGAD00001008674 | EGA

Covid19 RNAseq Fastq files

Project description:RNA Sequencing using IlluminaÃ¢Â€Â™s TruSeq Stranded Total RNA with RiboZero Globin depletion library pre kit and sequencing on the NovaSeq 6000.

| EGAS00001007022 | EGA

Covid19 RNAseq BAM files

Project description:RNA Sequencing using IlluminaÃ¢Â€Â™s TruSeq Stranded Total RNA with RiboZero Globin depletion library pre kit and sequencing on the NovaSeq 6000.

| EGAS00001007050 | EGA

Targeted next generation sequencing of transcriptomes from human treatment-naïve patient-derived prostate tissues, organoids, and organoid-derived cells (unaffected and tumor counterparts)

Project description:Human prostate mRNA profiles of organoids, cells, and tissues were generated by targeted next generation sequencing from three patients using Illumina® TruSeq Stranded mRNA prep kit.

2020-04-21 | GSE148937 | GEO

RNA-Seq of chicken breast samples treated with chronic heat stress

Project description:To study the effect of chronic heat stress on producing laying type hens, RNA-Seq was performed on breast samples during a 4-week heat stress experiment. RNA-Seq samples were collected 3-hour, 2-weeks, and 4-weeks post heat from both control (unheated) and treatment (heated) birds. RNA was extracted from the tissues with RNAqueous Total RNA Isolation Kit, treated with DNase, and mRNA cDNA libary were prepared with Illumina TrueSeq Stranded mRNA Library Prep Kit. Sequencing was done on 4 lanes with 12 libraries per lane on Illumina HiSeq 3000 platform.

2019-03-01 | E-MTAB-7479 | biostudies-arrayexpress

RNA-Seq of chicken liver samples treated with chronic heat stress

Project description:To study the effect of chronic heat stress on producing laying type hens, RNA-Seq was performed on liver samples during a 4-week heat stress experiment. RNA-Seq samples were collected 3-hour, 2-weeks, and 4-weeks post heat from both control (unheated) and treatment (heated) birds. RNA was extracted from the tissues with mirVana miRNA Isolation Kit, treated with DNase, and mRNA cDNA libary were prepared with Illumina TrueSeq Stranded mRNA Library Prep Kit. Sequencing was done on 4 lanes with 12 libraries per lane on Illumina HiSeq 3000 platform.

2019-03-01 | E-MTAB-7480 | biostudies-arrayexpress

RNA-Seq of chicken cecal tonsil samples treated with chronic heat stress

Project description:To study the effect of chronic heat stress on mature laying type hens, RNA-Seq was performed on cecal tonsil samples during a 4-week heat stress experiment. RNA-Seq samples were collected 3-hour, 2-weeks, and 4-weeks post heat from both control (unheated) and treatment (heated) birds. RNA was extracted from the tissues with RNAqueous Total RNA Isolation Kit, treated with DNase, and mRNA cDNA libary were prepared with Illumina TrueSeq Stranded mRNA Library Prep Kit. Sequencing was done on 2 lanes with 12 libraries per lane on Illumina HiSeq 3000 platform.

2019-05-01 | E-MTAB-7865 | biostudies-arrayexpress

RNA-Seq of ALDH positive and ALDH negative cells from patient-derived xenograft models of colon cancer

Project description:Colon cancer patient-derived xenograft (PDX) models were processed to single cells and sorted by FACS (BD FACS Aria II) for ALDH activity (Aldefluor assay) and DAPI. ALDH Negative and ALDH Positive cells from each PDX model were collected and lysed in RLT buffer and processed for RNA using the RNeasy Mini Plus RNA extraction kit (Qiagen). Samples were processed using Illumina’s TrueSeq RNA protocol and sequenced on an Illumina HiSeq 2500 machine as 2x125nt paired-end reads. Reads were mapped to the human reference genome (assembly hg19) using the STAR aligner (version 2.4.2a). Total read counts per gene were computed using the program “featureCounts” (version 1.4.6-p2) in the “subread” package, with the gene annotation taken from Gencode (version 19).

2021-01-11 | E-MTAB-8927 | biostudies-arrayexpress

Study of the molecular stability of patient-derived tumor xenograft (PDX) for human renal cell carcinoma (RCC) in nude mice during subsequent passages in mice

Project description:We established a large panel of preclinical models of human RCC directly from patients, faithfully reproducing the biological features of the original tumor. RCC tissues were collected for 8 years from 336 patients undergoing surgery, xenografted subcutaneously in nude mice, and serially passaged into new mice up to 13 passages. Tissue samples from the primary tumor and tumors grown in mice through passages were analyzed at the histology, genetic and for of them at the molecular levels for biological tissue stability. We established a large panel of 30 RCC models and 5 them of the clear cell type (clear cell renal cell carcinoma, CCC) were characterized at the mRNA expression level. We used Affymetrix whole genome microarrays to analyze the stability of the PDX models comparing the primary tumor (P0) with the subsequent passages in mice (P1 â¦).

2016-06-29 | E-GEOD-83820 | 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