Project description:The expression profile and sequence variants of 476 early stage urothelial carcinoma were studied using whole transcriptome sequencing. RNA-Seq libraries were prepared by Ribo-Zero treatment of total-RNA (to reduce the rRNA content) followed by library preparation using ScriptSeq. RNA-Seq libraries were paired-end sequenced (2x 101 bp) on Illumina HiSeq 2000 and the resulting fastq files were processed using tools from the Genome Analysis Toolkit (GATK and from the Tuxedo suite. Access to the sequence data (bam and vcf files), containing person identifying information, needs signature on a controlled access form, and can be accessed at The European Genome-phenome Archive (EGA) using the study ID EGAS00001001236 following request. An expression matrix of FPKM values are available without restriction at ArrayExpress.

2016-06-17 | E-MTAB-4321 | biostudies-arrayexpress

Pilot Experiment for Cell-specific Translatome: AP1 Domain vs. Whole Flower

Project description:A pilot experiment for an RNA-seq dataset (SRP003234). This experiment compares AP1 domain-specific translating RNA with total flower translating mRNA.

2010-08-25 | GSE23777 | GEO

CTCF ChIP-seq of human acute leukemias

Project description:CTCF ChIP-seq of 39 primary samples derived from human acute leukemias, namely AML, T-ALL and mixed myeloid/lymphoid leukemias with CpG Island Methylator Phenotype (CIMP). Due to patient confidentiality considerations, the raw data files for this dataset have been deposited to the EGA controlled-access archive under the accession numbers EGAS00001007094 (study); EGAD00001011059 (dataset).

2023-08-31 | E-MTAB-13117 | biostudies-arrayexpress

H3K27ac ChIP-seq of human acute leukemias and healthy donors

Project description:H3K27ac ChIP-seq of 79 primary samples derived from human acute leukemias, namely AML, T-ALL and mixed myeloid/lymphoid leukemias with CpG Island Methylator Phenotype (CIMP). In addition, 4 samples derived from CD34+ cord blood cells of healthy donors were included. Due to patient confidentiality considerations, the raw data files for this dataset have been deposited to the EGA controlled-access archive under the accession numbers EGAS00001007094 (study); EGAD00001011060 (dataset).

2023-08-31 | E-MTAB-13119 | biostudies-arrayexpress

Geuvadis RNA-seq five individual pilot

Project description:Pilot RNA-seq dataset created by the Geuvadis consortium (www.geuvadis.org)

2010-04-14 | E-GEUV-4 | biostudies-arrayexpress

Processed small RNA sequencing data of plasma samples from patients with esophageal adenocarcinoma or precursor lesions

Project description:In the past decades, the incidence of esophageal adenocarcinoma has increased dramatically in Western populations. Better understanding of disease etiology along with the identification of novel prognostic and predictive biomarkers are urgently needed to improve the dismal survival probabilities. Here, we performed comprehensive RNA (both coding and non-coding) profiling in various samples from 17 patients diagnosed with esophageal adenocarcinoma, high-grade dysplastic or non-dysplastic Barrett’s esophagus. Per patient, a blood plasma sample, and a healthy esophageal and disease tissue sample were included. In total, this comprehensive dataset consists of 102 RNA-seq libraries from 51 samples. The raw data for this study have been deposited to the controlled access archive EGA under submission EGAS00001004939.

2022-01-01 | E-MTAB-10004 | biostudies-arrayexpress

Processed polyA+ RNA sequencing data of tissue samples from patients with esophageal adenocarcinoma or precursor lesions

2022-01-01 | E-MTAB-10005 | biostudies-arrayexpress

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