About file location

As the EGA is co-managed by the EMBL-EBI and CRG, files could be located in the UK and/or Spain, as indicated by their respective flags.

Alternatively, files could be located in one of the international Federated EGA nodes, as indicated next to the node's flag.
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RNA-Seq Read Counts from the CheckMate-9ER Clinical Trial

RNA-sequencing was performed on formalin-fixed, paraffin-embedded tumor samples obtained at baseline (pretreatment). Whole-transcriptome RNA-seq libraries were prepared using TruSeq Stranded Total RNA Kit with Ribo-Zero (Illumina) following a validated standard operating procedure. Libraries were sequenced using NovoSeq (Illumina) following 2 × 100 paired-end sequencing, targeting a depth of 80 million reads. Raw RNA-seq reads were aligned and filtered using STAR v2.6.0c.10 After removing microbial contaminants, sequences were aligned to the human reference genome GRCh38 using the Ensembl 91 gene model, and read counts were quantified using RSEM. Read counts are provided.

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DUO:0000026
version: 2021-02-23

user specific restriction

This data use modifier indicates that use is limited to use by approved users.

DUO:0000027
version: 2021-02-23

project specific restriction

This data use modifier indicates that use is limited to use within an approved project.

Requests for access the BMS accession numbers in EGA a request must be submitted through the “Request Data” button on the EGA website.

Access to this data is restricted. Data access requests must be submitted through the “Request Data” button on the EGA website. Upon receipt of a request, the BMS Data Sharing team will coordinate execution of a Data Access Agreement. Access to the data will be granted only after the agreement has been fully executed. We are committed to providing you with answers to your questions and concerns. Please contact us using the information below, and we will respond to your inquiry as quickly as possible. Technical Support: RDD_DataSpecimenRequests@bms.com

Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.

Study ID Study Title Study Type
EGAS50000001905 Cancer Genomics

This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.

ID File Type Size Quality Report
Located in
i
EGAF50000904662 csv 85.0 MB
1 File (85.0 MB)