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CLUSTER DAC

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Ms Sandra Ng
s.ng@qmul.ac.uk

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This DAC controls 8 datasets

Dataset ID	Description	Technology	Samples
EGAD50000001455	This is the RNAseq CD4 dataset (paired FASTQ files, n = 86 paired files) generated from pre-methotrexate treatment JIA patients cohort samples. CD4 cells were sorted from isolated total PBMC by cell sorter (BD FACSAriaTM III, BD Biosciences). Clinical metadata is also included in this dataset. Samples were sequenced on the NovaSeq6000 instrument (Illumina, San Diego, US) at 300pM, using a 100bp paired read run with corresponding 8bp dual sample index and 5bp or 8bp unique molecular index reads. Run data were demultiplexed and converted to FASTQ files using Illumina’s BCL Convert Software v3.75.	Illumina NovaSeq 6000	416
EGAD50000001456	This is the RNAseq CD8 dataset (paired FASTQ files, n = 85 paired files) generated from pre-methotrexate treatment JIA patients cohort samples. CD8 cells were sorted from isolated total PBMC by cell sorter (BD FACSAriaTM III, BD Biosciences). Clinical metadata is also included in this dataset. Samples were sequenced on the NovaSeq6000 instrument (Illumina, San Diego, US) at 300pM, using a 100bp paired read run with corresponding 8bp dual sample index and 5bp or 8bp unique molecular index reads. Run data were demultiplexed and converted to FASTQ files using Illumina’s BCL Convert Software v3.75.	Illumina NovaSeq 6000	416
EGAD50000001457	This is the RNAseq PBMC dataset (paired FASTQ files, n = 82 paired files) generated from pre-methotrexate treatment JIA patients cohort samples. Total PBMC were isolated from pre-treated blood of JIA patients and clinical metadata is also included in this dataset. Samples were sequenced on the NovaSeq6000 instrument (Illumina, San Diego, US) at 300pM, using a 100bp paired read run with corresponding 8bp dual sample index and 5bp or 8bp unique molecular index reads. Run data were demultiplexed and converted to FASTQ files using Illumina’s BCL Convert Software v3.75.	Illumina NovaSeq 6000	416
EGAD50000001458	This is the RNAseq CD14 dataset (paired FASTQ files, n = 80 paired files) generated from pre-methotrexate treatment JIA patients cohort samples. CD14 cells were sorted from isolated total PBMC by cell sorter (BD FACSAriaTM III, BD Biosciences). Clinical metadata is also included in this dataset. Samples were sequenced on the NovaSeq6000 instrument (Illumina, San Diego, US) at 300pM, using a 100bp paired read run with corresponding 8bp dual sample index and 5bp or 8bp unique molecular index reads. Run data were demultiplexed and converted to FASTQ files using Illumina’s BCL Convert Software v3.75.	Illumina NovaSeq 6000	416
EGAD50000001459	This is the RNAseq CD19 dataset (paired FASTQ files, n = 83 paired files) generated from pre-methotrexate treatment JIA patients cohort samples. CD19 cells were sorted from isolated total PBMC by cell sorter (BD FACSAriaTM III, BD Biosciences). Clinical metadata is also included in this dataset. Samples were sequenced on the NovaSeq6000 instrument (Illumina, San Diego, US) at 300pM, using a 100bp paired read run with corresponding 8bp dual sample index and 5bp or 8bp unique molecular index reads. Run data were demultiplexed and converted to FASTQ files using Illumina’s BCL Convert Software v3.75.	Illumina NovaSeq 6000	416
EGAD50000001616	CLUSTER consortium RNA sequencing dataset from UK JIA patient cohort with documented uveitis status. Peripheral blood mononuclear cells (PBMCs) were isolated from blood samples and cryopreserved. Samples were subsequently thawed and flow-sorted for CD19+ B cells prior to RNA sequencing. Clinical metadata includes patient demographics and uveitis status at time of sampling.	Illumina NovaSeq 6000	133
EGAD50000002169	Samples were sequenced with NovaSeq6000 and the sequencing files were processed using the RSSnextflow workflow (https://gitlab.com/b8307038/rssnextflow). The raw read counts from all batches were combined. Analysis-ready batch-corrected read counts were generated using ComBat-seq.	Illumina NovaSeq 6000	97
EGAD50000002170	Samples were sequenced with NovaSeq6000 and the sequencing files were processed using the RSSnextflow workflow (https://gitlab.com/b8307038/rssnextflow). The raw read counts from all batches were combined. Analysis-ready batch-corrected read counts were generated using ComBat-seq. Read counts normalisation for DGE analysis was performed with limma-voom function (log2 CPM) as seen in the pipeline.	Illumina NovaSeq 6000	97