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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NICHE - Pre-treatment single cell RNA-seq of MMR proficient early stage colon cancers

This dataset includes raw single cell RNA sequencing data from 13 pMMR colon cancer patients treated with neoadjuvant immune checkpoint blockade in the NICHE trial. This dataset comprises pre-treatment colon cancer biopsy samples, which digested to obtain single cell suspensions, sorted for CD45+, labelled with hashtag antibodies, split in 3 cell pools, and distributed in 5 sequencing samples (7654_1-5). 30 FASTQ files were generated, 10 files for scRNAseq gene expression (10X Genomics Chromium Next GEM Single Cell 5' v2), 10 files for single cell TCRseq (10X Genomics Chromium Next GEM Single Cell V(D)J Reagent Kits 5' v2) and 10 files for feature barcodes and hashtag antibodies, with feature reference barcodes provided. Samples were sequenced on Illumina Novaseq 6000 and raw FASTQ files were later processed with Cellranger workflows from 10X Genomics, investigating features of pre-treatment immune tumour cells and associations with neoadjuvant response.

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Netherlands Cancer Institute - Antoni van Leeuwenhoek (NKI-AVL) general policy

Data is available under reasonable request. All data requests will be reviewed by the NKI IRB and must be supported by the Principal Investigator of the study. The researcher will need to sign a data access agreement with the NKI after approval.

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
EGAS50000000856 Exome Sequencing

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
EGAF50000922332 fastq.gz 17.5 GB
EGAF50000922333 fastq.gz 7.6 GB
EGAF50000922334 fastq.gz 3.3 GB
EGAF50000922335 fastq.gz 1.5 GB
EGAF50000922336 fastq.gz 1.5 GB
EGAF50000922337 fastq.gz 3.5 GB
EGAF50000922338 fastq.gz 17.7 GB
EGAF50000922339 fastq.gz 7.6 GB
EGAF50000922340 fastq.gz 7.2 GB
EGAF50000922341 fastq.gz 16.8 GB
EGAF50000922342 fastq.gz 14.4 GB
EGAF50000922343 fastq.gz 6.1 GB
EGAF50000922344 fastq.gz 1.7 GB
EGAF50000922345 fastq.gz 3.5 GB
EGAF50000922346 fastq.gz 1.2 GB
EGAF50000922347 fastq.gz 636.4 MB
EGAF50000922348 fastq.gz 1.1 GB
EGAF50000922349 fastq.gz 2.0 GB
EGAF50000922350 fastq.gz 1.9 GB
EGAF50000922351 fastq.gz 4.0 GB
EGAF50000922352 fastq.gz 1.5 GB
EGAF50000922353 fastq.gz 3.3 GB
EGAF50000922354 fastq.gz 3.1 GB
EGAF50000922355 fastq.gz 1.6 GB
EGAF50000922356 fastq.gz 2.3 GB
EGAF50000922357 fastq.gz 1.2 GB
EGAF50000922358 fastq.gz 2.1 GB
EGAF50000922359 fastq.gz 1.1 GB
EGAF50000922360 fastq.gz 6.1 GB
EGAF50000922361 fastq.gz 14.3 GB
EGAF50000922362 csv 1.9 kB
31 Files (157.3 GB)