EGAD00001003235 |
Raw exome sequence data(fastq) for the GATCI project |
unspecified |
172 |
EGAD00001003236 |
Raw whole genome sequence data(fastq) for the GATCI project |
HiSeq X Ten |
10 |
EGAD00001003589 |
Ultra-Fast Patient-Derived Xenografts Identify Functional and Spatial Tumour Heterogeneities that Drive Therapeutic Resistance - WXS mapped reads |
|
27 |
EGAD00001003590 |
Ultra-Fast Patient-Derived Xenografts Identify Functional and Spatial Tumour Heterogeneities that Drive Therapeutic Resistance - WXS unaligned reads |
Illumina HiSeq 2500 |
27 |
EGAD00001004126 |
Sequence data in fastq format was aligned to the GRCH38 reference genome. Aligned sequence was preprocessed with GATK for Indel Realignment and Base Quality Score Recalibration. Duplicates were marked with Picard Mark Duplicates. Aligned sequence is in bam format. Details of the alignment can be found int he bam header. In total, data generated from 174 tumour samples 102 matched blood normal controls was aligned. Tumour samples were classified as Anaplastic Thyroid, Poorly-differentiated or well-differentiated cancers. |
|
264 |
EGAD00001004127 |
Sequence was aligned to the GRCH38 reference genome. Aligned sequence was analyzed with GATK Haplotype Caller, to generate germline variant calls across the SureSelect All Exon V5+UTR target region. Variant calls are in VCF format. In total there are samples from 173 donors. 101 donors have calls generated from both normal and tumour samples tumour samples, 94 of which have a matched normal. Details for the call can be found in the vcf headers. |
|
263 |
EGAD00001004128 |
Sequence was aligned to the GRCH38 reference genome. Aligned sequence was analyzed with SomaticSniper. Somatic variant calls are in VCF format. In total there are 94 tumour samples, each with a matched normal. |
|
178 |
EGAD00001004129 |
Sequence was aligned to the GRCH38 reference genome. Aligned sequence was analyzed with GATK/MuTect, to generate somatic variant calls across the SureSelect All Exon V5+UTR target region. Somatic variant calls are in VCF format. In total there are 166 tumour samples, 94 of which have a matched normal. Somatic variants for tumours without a matched normal, were called against a panel of normals. Details for the mutect call can be found in the vcf header. |
|
250 |
EGAD00001005791 |
Whole exome sequence data in fastq format was aligned to the GRCH38 reference genome. Aligned sequence was preprocessed with GATK for Indel Realignment and Base Quality Score Recalibration. Duplicates were marked with Picard Mark Duplicates. Aligned sequence is in bam format. Details of the alignment can be found in he bam header. Tumour samples were classified as Anaplastic Thyroid, Poorly-differentiated or well-differentiated cancers. |
|
264 |
EGAD00001005808 |
Raw whole exome sequencing data (fastq) for the GATCI project |
unspecified |
264 |
EGAD00001005810 |
Raw RNA sequence data (fastq) for the GATCI project |
unspecified |
30 |
EGAD00001005817 |
Sequence data in fastq format was aligned to the GRCh38 reference genome with BWA-MEM and preprocessed with GATK for indel realignment and base quality score recalibration. Aligned sequence was analyzed with GATK HaplotypeCaller to generate germline variant calls. Variant calls are in VCF format. In total, there are 60 tumour samples from 38 patients, all with matched normal. Further details can be found in the vcf headers |
|
98 |
EGAD00001005818 |
Sequence data in fastq format was aligned to the GRCh38 reference genome with BWA-MEM and preprocessed with GATK for indel realignment and base quality score recalibration. Aligned sequence was analyzed with SomaticSniper to generate somatic variant calls. Variant calls are in VCF format. In total, there are 60 tumour samples from 38 patients, all with matched normal. Further details can be found in the vcf headers |
|
98 |
EGAD00001005822 |
Sequence data in fastq format was aligned to the GRCh38 reference genome with BWA-MEM and preprocessed with GATK for indel realignment and base quality score recalibration. Aligned sequence was analyzed with MuTect to generate somatic variant calls. Variant calls are in VCF format. In total, there are 60 tumour samples from 38 patients, all with matched normal. Further details can be found in the vcf headers. |
|
98 |
EGAD00001005914 |
Sequence data in fastq format was aligned to the GRCh38 reference genome with BWA-MEM. Aligned sequence was preprocessed with GATK for Indel Realignment and Base Quality Score Recalibration. Duplicates were marked with Picard Mark Duplicates. Aligned sequence is in bam format. Details of the alignment can be found in the bam header |
|
97 |
EGAD00001005916 |
Exome sequences were aligned to the GRCH38 reference genome. Aligned sequence was analyzed with GATK Haplotype Caller to generate germline variant calls. Variant calls are in VCF format. Details for the call can be found in the VCF header |
|
263 |
EGAD00001005917 |
Exome sequences were aligned to the GRCH38 reference genome. Aligned sequence was analyzed with GATK/MuTect, to generate somatic variant calls. Somatic variant calls are in VCF format. Details for the mutect call can be found in the vcf header. |
|
250 |
EGAD00001005918 |
Exome sequences were aligned to the GRCH38 reference genome. Aligned sequence was analyzed with GATK/SomaticSniper, to generate somatic variant calls. Somatic variant calls are in VCF format. Details for the mutect call can be found in the vcf header. |
|
178 |
EGAD00001005926 |
Raw whole genome sequencing data (fastq) for the GATCI project |
HiSeq X Ten,unspecified |
104 |
EGAD00010001540 |
Oncoscan CHP files for the Mesothelemia Project |
Illumina Oncoscan Array |
100 |
EGAD00010001579 |
This dataset contains files generated from Affymetrix Oncoscan Arrays. For each sample there are two paired cel files containing the raw data from AT and GT channels. Raw data has been transfromed to OSCHP signal files also within this dataset. |
Oncoscan Array |
157 |
EGAD00010001626 |
mpMRI visible prostate tumour samples (PI-RADSv2 5) |
OncoScan |
20 |
EGAD00010001627 |
mpMRI invisible prostate tumour samples |
OncoScan |
20 |