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Sample GSM8125234 Query DataSets for GSM8125234
Status Public on May 16, 2024
Title Perianal11_Fistula_cytoRNA
Sample type SRA
Source name fistula tract lining biopsies
Organism Homo sapiens
Characteristics tissue: fistula tract lining biopsies
procedure: proctectomy
Extracted molecule cytoplasmic RNA
Extraction protocol Single Cell Sampling and Isolation Biopsies for single cell processing were obtained from patients at the time of colonoscopy or upon undergoing abdominoperineal resection (completion proctectomy). At endoscopy, ~4 biopsies per region were collected by the physician for further single cell isolation. From proctectomy specimens, 10-20 biopsies per region were collected by the researcher using an endoscopic forceps prior to pathological grossing. To sample the fistula tract, a cross-section was first excised and then transected to expose the tract lining and facilitate biopsy acquisition. From surgical specimens with patent perianal fistulas, cross sections of the tract were resected with the assistance of the pathologist or pathology PA and preserved in O.C.T. Compound (Sakura) by the Mount Sinai Biorepository Core. FFPE specimens were retrieved from clinical samples previously processed and banked by the Biorepository. Single cell suspensions were prepared from 4-10 biopsies as previously described21. If cell viability was < 70%, dead cells were depleted using the Dead Cell Removal Kit (Miltenyi, 130-090-101). Single cells were loaded onto the 10X Chromium Controller at a targeted concentration of 6000 cells/lane, using the Chromium 3’ v3.1 chemistry (PN-1000121), per manufacturer instructions.
Cells were loaded on a Chromium Next GEM Chip G Single Cell Kit (PN-1000127) with GEMs from the Chromium Next GEM Single Cell 3’ Kit v3.1 (PN-1000268) and indexed using the Dual Index Kit TT Set A (PN-1000215) according to 10x protocol CG000315 Revs B,C.
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description 10x Genomics
Data processing Single Cell Process Illumina sequencing products were demultiplexed by the University of Minnesota Genomic Center (UMGC). Prepared FASTQ files were fed into the cellranger count v6.1.1 pipeline for additional QC, alignment, and matrices generation. Filtered matrix outputs were brought into the Seurat wrapper, coreSC, for broad-scope data cleaning and regularization. Gene expression variance stabilization was conducted using the SCTransform v2 function. Normalized GEX outputs were passed to principal component analysis (PCA) and uniform manifold projection (UMAP) for dimensionality reduction and 2-dimensional projection. Individual samples were combined into a single, integrated object and harmonized for batch effects using the Harmony package. Clusters were annotated by parallel data driven and known marker approaches and validated with CellTypist. Clusters classified as myeloid or stromal were subset from the larger Seurat object and sub-clustered.
Assembly: refdata-gex-GRCh38-2020-A
Supplementary files format and content: MEX compatible cell-associated barcodes list
Supplementary files format and content: MEX compatible gene ID/name list
Supplementary files format and content: MEX format feature-barcode associated UMI count sparse matrix
Submission date Mar 04, 2024
Last update date May 16, 2024
Contact name Judy Cho
Organization name Icahn School of Medicine at Mount Sinai
Department Pathology, Molecular and Cell-Based Medicine
Lab Judy Cho Lab
Street address 1470 Madison Avenue, 8th Fl., Box 1498;
City New York
State/province NY
ZIP/Postal code 10029
Country USA
Platform ID GPL24676
Series (1)
GSE260842 Multimodal single cell analyses reveal mechanisms of perianal fistula in diverse Crohn’s disease [scRNA-seq]
BioSample SAMN40254821
SRA SRX23831478

Supplementary file Size Download File type/resource
GSM8125234_RL36.tar.gz 53.7 Mb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA

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