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Sample GSM3536577 Query DataSets for GSM3536577
Status Public on Feb 28, 2019
Title WT
Sample type SRA
 
Source name Peritoneal cavity cells
Organism Mus musculus
Characteristics strain: C57BL/6
condition: germ-free
genotype: WT
Extracted molecule polyA RNA
Extraction protocol For each sample, equal cell numbers of 4 male mice of the same genotype were pooled. 8700 cells of each pooled sample were encapsulated into droplets using Chromium Controller (10X Genomics).
Libraries were prepared using Chromium Single Cell 3′ Library Kits v2 (10x Genomics) according to the manufacturer’s protocol. Equal quantities of each library were pooled and sequenced over two lanes of a HiSeq 2500 Rapid Run Flow Cell (Illumina) using custom parameters: Read 1, 26 cycles; i7, 8 cycles; i5, 0 cycles; Read 2, 98 cycles.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Illumina RTA software was used for basecalling.
Cellranger mkfast (v2.2.0, 10X genomics) was used for demultiplexing the Illumina base call files (BCLs).
Cellranger count (v2.2.0, 10X genomics) was used to generate single cell feature counts for each sample.
Cellranger aggr (v2.2.0, 10X genomics) was used to aggregate samples.
Potential doublets were filtered out using DoubletFinder.
Seurat v2.3.0 was used for clustering analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Three processed data files are provided for each sample (output of cellranger count function): barcodes.tsv (filtered barcode sequences and their corresponding GEM groups), genes.tsv (gene ID and gene names), matrix.mtx (feature-barcode matrix in Market Exchange Format).
 
Submission date Jan 02, 2019
Last update date Mar 02, 2019
Contact name Niklas Krupka
E-mail(s) niklas.krupka@gmail.com
Organization name Brigham and Women's Hospital
Department Medicine - Gastroenterology
Lab Blumberg Lab
Street address 77 Avenue Louis Pasteur
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL17021
Series (1)
GSE124562 Epithelial endoplasmic reticulum stress orchestrates a protective IgA response II
Relations
BioSample SAMN10680143
SRA SRX5199618

Supplementary file Size Download File type/resource
GSM3536577_wt_barcodes.tsv.gz 24.7 Kb (ftp)(http) TSV
GSM3536577_wt_genes.tsv.gz 217.5 Kb (ftp)(http) TSV
GSM3536577_wt_matrix.mtx.gz 40.2 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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