Need Help?

scRNA seq and scTCR seq data from 5 melanoma patients

The Chromium Controller and Chromium X platfor of 10X Genomics were used for single cell partitioning and barcoding. Each cell's transcriptome was barcoded during reverse transcription, pooled cDNA was amplified and Single Cell 5' Gene Expression (GEX), V(D)J and Feature Barcode (FB) Libraries were prepared according to the manufacturer's protocols (CG000330 and CG000331, 10X Genomics). All libraries were quantified and normalized on library QC data generated on the Bioanalyzer system according to manufacturer's protocols (G2938-90321 and G2938-90024, Agilent Technologies). Based on the expected target cell counts, a balanced library sub-pool of samples was compsed for SC5'GEX, V(D)J and FB libraries. Library sub-pools were quantified by qPCR, accodring to the KAPA Library Quantification Kit Illumina(R) Platforms protocol (KR0405, KAPA Biosystems). Based on qPCR results a final sequencing pool was composed. Paired end sequencing was performed on a NovaSeq 6000 Instrument (Illumina) using NovaSeq 6000 Reagent Kits v1.5 100 cycles (cat. no. 20028401, 20028319, 20028316 Illumina), using 28 cycles for Read 1, 10 cycles for Read i7, 10 cycles for Read i5 and 90 cycles for Read 2.

Request Access

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
EGAS50000000785 Transcriptome 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 Located in
EGAF50000277430 fastq.gz 5.0 GB
EGAF50000277431 fastq.gz 12.4 GB
EGAF50000277432 fastq.gz 968.3 MB
EGAF50000277433 fastq.gz 2.4 GB
EGAF50000277434 fastq.gz 4.8 GB
EGAF50000277435 fastq.gz 1.9 GB
EGAF50000277436 fastq.gz 776.2 MB
EGAF50000277437 fastq.gz 332.0 MB
EGAF50000277438 fastq.gz 7.8 GB
EGAF50000277439 fastq.gz 19.9 GB
EGAF50000277440 fastq.gz 2.0 GB
EGAF50000277441 fastq.gz 5.0 GB
EGAF50000277442 fastq.gz 3.6 GB
EGAF50000277443 fastq.gz 8.6 GB
EGAF50000277444 fastq.gz 892.4 MB
EGAF50000277445 fastq.gz 2.0 GB
EGAF50000277446 fastq.gz 1.7 GB
EGAF50000277447 fastq.gz 4.1 GB
EGAF50000277448 fastq.gz 2.0 GB
EGAF50000277449 fastq.gz 1.0 GB
EGAF50000277450 fastq.gz 1.7 GB
EGAF50000277451 fastq.gz 916.1 MB
EGAF50000277452 fastq.gz 5.4 GB
EGAF50000277453 fastq.gz 13.1 GB
EGAF50000277454 fastq.gz 2.4 GB
EGAF50000277455 fastq.gz 1.1 GB
EGAF50000277456 fastq.gz 6.4 GB
EGAF50000277457 fastq.gz 15.9 GB
EGAF50000277458 fastq.gz 4.6 GB
EGAF50000277459 fastq.gz 2.0 GB
EGAF50000277460 fastq.gz 4.9 GB
EGAF50000277461 fastq.gz 2.1 GB
EGAF50000277462 fastq.gz 1.1 GB
EGAF50000277463 fastq.gz 490.4 MB
EGAF50000277464 fastq.gz 6.1 GB
EGAF50000277465 fastq.gz 14.8 GB
EGAF50000277466 fastq.gz 1.6 GB
EGAF50000277467 fastq.gz 3.8 GB
EGAF50000277468 fastq.gz 3.0 GB
EGAF50000277469 fastq.gz 7.1 GB
EGAF50000277470 fastq.gz 1.5 GB
EGAF50000277471 fastq.gz 661.3 MB
EGAF50000277472 fastq.gz 7.1 GB
EGAF50000277473 fastq.gz 17.3 GB
EGAF50000277474 fastq.gz 3.9 GB
EGAF50000277475 fastq.gz 1.7 GB
EGAF50000277476 fastq.gz 1.5 GB
EGAF50000277477 fastq.gz 9.4 GB
EGAF50000277478 fastq.gz 4.3 GB
EGAF50000277479 fastq.gz 2.2 GB
EGAF50000277480 fastq.gz 7.1 GB
EGAF50000277481 fastq.gz 17.3 GB
EGAF50000277482 fastq.gz 1.7 GB
EGAF50000277483 fastq.gz 3.8 GB
EGAF50000277484 fastq.gz 7.3 GB
EGAF50000277485 fastq.gz 17.7 GB
56 Files (290.2 GB)