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Status |
Public on Feb 28, 2019 |
Title |
WT |
Sample type |
SRA |
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Source name |
Peritoneal cavity cells
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Organism |
Mus musculus |
Characteristics |
strain: C57BL/6 condition: germ-free genotype: WT
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
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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).
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Submission date |
Jan 02, 2019 |
Last update date |
Mar 02, 2019 |
Contact name |
Niklas Krupka |
E-mail(s) |
niklas.krupka@gmail.com
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Organization name |
Brigham and Women's Hospital
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Department |
Medicine - Gastroenterology
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Lab |
Blumberg Lab
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Street address |
77 Avenue Louis Pasteur
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City |
Boston |
State/province |
MA |
ZIP/Postal code |
02115 |
Country |
USA |
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Platform ID |
GPL17021 |
Series (1) |
GSE124562 |
Epithelial endoplasmic reticulum stress orchestrates a protective IgA response II |
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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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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