The reparative immunologic consequences of stem cell transplantation as a cellular therapy for refractory Crohn’s disease

Single cell isolations were processed using the 10x Genomics Chromium Single Cell 3’ v3.1 kit

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Single cell isolations were processed using the 10x Genomics Chromium Single Cell 3’ v3.1 kit

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Final libraries were sequenced on the Illumina NovaSeq 6000

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Assembly: GRCh38

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samples at baseline and 6 months post-SCT were analysed with scRNA-seq

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Adults with CD with active clinical and endoscopic disease

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Adults with CD with active clinical and endoscopic disease who failed available medical therapies were enrolled in a phase II study of SCT for refractory CD (n=19).

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Adults with CD with active clinical and endoscopic disease

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Paired blood and intestinal tissue samples were obtained at baseline and 6 months post-SCT and additional blood samples were taken longitudinally.

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19 patients were enrolled from 2018 to 2023

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Patients with medically refractory CD were enrolled in the MASCT-CD trial.

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At 6 months post-transplant 10/14 patients had an endoscopic remission

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barcodes.tsv.gz

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Data are available in a public, open access repository.

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Supplementary files format and content: tab-separated value files and matrix files

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Supplementary files format and content: tab-separated value files and matrix files

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GSE284677_RAW.tar

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Single cells were clustered and annotated using known sets of marker genes and reference data sets

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FASTQ files underwent processing through the Cellranger Count v6.1.1 pipeline for quality control

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"source_name": {"blood": 25, "ileum": 9, "jejunum": 2}

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patients with histological inflammation had persistent suppression of CD14 + populations

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"n_samples": 36

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"title": "PT19 blood stem cell collection"

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Samples of tissue from endoscopic biopsies, peripheral blood and peripheral mobilized stem cells were collected

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