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Sample GSM4336572 Query DataSets for GSM4336572
Status Public on Aug 24, 2020
Title wt+antibiotics1
Sample type SRA
 
Source name wt+antibiotics
Organism Mus musculus
Characteristics strain background: C57BL/6
genotype/variation: wild type
treatment: antibiotics
tissue: terminal ileum
cell type: primary epithelial cells
Treatment protocol Microbiome depletion was performed by pre-treatment of Lrig1CreERT2/+;Atoh1fl/fl animals with a broad-spectrum antibiotic cocktail containing kanamycin (4.0 mg/ml), metronidazole (2.15 mg/ml), gentamicin (0.35 mg/ml), colistin sulfate (8500 U/ml), and vancomycin (0.45 mg/ml) in their drinking water for seven days prior to tamoxifen treatment. Mid-dose antibiotics and low-dose antibiotics were 0.75x and 0.25x of the original 1x concentration, respectively. Following tamoxifen administration, Lrig1CreERT2/+;Atoh1fl/fl received either standard or antibiotic-supplemented drinking water for an additional fourteen days.
Growth protocol primary cells
Extracted molecule total RNA
Extraction protocol Mouse epithelial cell suspensions were obtained by EDTA extraction and cold protease dissociation. Cells were encapsulated using the inDrop platform (1CellBio), and RNA was extracted according to the protocol of Klein et al., 2015.
CEL-Seq linear amplification of RNA/cDNA followed by index primer-based amplification
RNA-Seq was performed on NextSeq500 with a 2 x 75 paired-end kit using custom read lengths
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description 2056_AS_1-GCCAAT_S1
Data processing After sequencing, reads were filtered, sorted by their barcode of origin and aligned to the reference transcriptome using inDrops pipeline (https://github.com/indrops/indrops). Mapped reads were quantified into UMI-filtered counts per gene, and barcodes that correspond to cells were retrieved based on previously established methods (the filtering code available at: https://github.com/KenLauLab/scRNAseqQC).
Barcodes were filtered (Liu et al., 2018), resulting in the processed data table. Bcd code can be converted to sequence barcodes within the inDrops pipeline. An example is at https://www.dropbox.com/s/tm9ciucqwgunwip/20190419_2969_AS-1-GCCAAT_pickle_bcd.txt?dl=0
NextSeq:Technical read: read2 - UMI/cell barcode - the oligo barcodes are inDrop Version 2 which is positioned exactly as in (Klein et al. 2015) Biological read: read1 - 3' end
Genome_build: Human: GRCh38.85, Mouse: GRCm38.85 (mixed database)
Supplementary_files_format_and_content: Delimited tables, with cells and genes, as columns and rows
 
Submission date Feb 24, 2020
Last update date Aug 29, 2020
Contact name Ken Lau
E-mail(s) ken.s.lau@vanderbilt.edu
Phone 6159366859
Organization name Vanderbilt University
Department Cell and Developmental Biology
Street address 2215 Garland Ave. MRBIV10475
City Nashville
State/province TN
ZIP/Postal code 37232
Country USA
 
Platform ID GPL19057
Series (2)
GSE145828 WT/AtohKO Ileum w/ antibiotics
GSE145830 Ileal single-cell analysis in the context of inflammation focused on tuft cells
Relations
BioSample SAMN14173734
SRA SRX7794017

Supplementary file Size Download File type/resource
GSM4336572_counts_2056_1.csv.gz 4.2 Mb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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