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Sample GSM8003786 Query DataSets for GSM8003786
Status Public on Jun 12, 2024
Title WT, snRNAseq
Sample type SRA
 
Source name Colon
Organism Mus musculus
Characteristics tissue: Colon
cell type: all cell nuclei from colon
genotype: wild type (WT)
Extracted molecule total RNA
Extraction protocol To isolate single nuclei from mouse colon, Sigma’s Nuclei EZ Prep Kit (Sigma, Cat #NUC-101) was used. Briefly, snap frozen mouse colon samples were firstly cut into 2mm pieces and homogenized using gentleMACS Dissociator (m_intestine_01 mode 2x, C Tubes) in 4 ml of ice-cold EZ Prep buffer (supplemented with 0.2 U/µl RNAse inhibitor, Clontech #2313A) and incubated on ice for 5 min. subsequently, nuclei were filtered through a 20-μm Pre-Separation Filter (Miltenyi Biotech, 130-101-812) and centrifuged at 500 × g for 5 min at 4 °C. After centrifugation, the nuclei were washed in 4 ml suspension buffer (1× PBS supplemented with 0.01% BSA and 0.2 U/µl RNase inhibitor (Clontech, Cat #2313A)). Isolated nuclei were resuspended in 1 ml suspension buffer, filtered through a 20-μm Pre-Separation Filter (Miltenyi Biotech, 130-101-812) and counted. A final concentration of 1000 nuclei per µl was used for 10x Genomics Chromium loading. Considering a 10–20% loss, we pipetted 9.9 μl single nuclei suspension (concentration of ~1000 nuclei/μl, ~9,900 nuclei), targeting the recovery of ~6,000 nuclei. A single nuclei suspension targeting 6000 cells per sample was loaded into 10x Genomics Chromium Single Cell Controller and barcoded with unique molecular identifiers.
Single-nuclei RNA-seq libraries were obtained following the 10x Genomics recommended protocol, using the reagents included in the Chromium Single Cell 3′v3.1 Reagent Kit Libraries.
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description 10x Genomics
Data processing RNA velocity was estimated by velocity python module ((La Manno et al., 2018)). Briefly, to generate loom files, spliced and unspliced reads were annotated by velocyto.py with CellRanger (version 7.0.1) output files. The loom files were then loaded to jupyter notebook (Python version 3.9.13). The calculation of RNA velocity values for each cell and embedding RNA velocity vector to UMAP were done by following the scvelo python pipeline.
Assembly: mm10
Supplementary files format and content: loom, CellRanger output files (barcodes.tsv, features.tsv, matrix.mtx)
 
Submission date Jan 05, 2024
Last update date Jun 12, 2024
Contact name Zheng Fan
Organization name University of Zurich
Department Anatomy Institute
Street address Winterthurerstrasse 190
City Zurich
ZIP/Postal code CH-8057
Country Switzerland
 
Platform ID GPL19057
Series (1)
GSE252602 Expression of the transcription factor HIF-1α in NKp46+ innate lymphoid cells limits inflammation and fibrosis upon chronic colitis
Relations
BioSample SAMN39272852
SRA SRX23110306

Supplementary file Size Download File type/resource
GSM8003786_WT_barcodes.tsv.gz 25.4 Kb (ftp)(http) TSV
GSM8003786_WT_features.tsv.gz 284.1 Kb (ftp)(http) TSV
GSM8003786_WT_matrix.mtx.gz 25.8 Mb (ftp)(http) MTX
GSM8003786_colon_snRNA_WT.loom.gz 41.4 Mb (ftp)(http) LOOM
SRA Run SelectorHelp
Raw data are available in SRA

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