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Sample GSM2137737 Query DataSets for GSM2137737
Status Public on Jul 25, 2016
Title CCR6+Foxp3EGFP+ Il4raR576 Treg 2
Sample type SRA
 
Source name CCR6+Foxp3EGFP+ Il4raR576 Treg
Organism Mus musculus
Characteristics age: 5-7 weeks
gender: female
sensitized and challenged with: ovalbumin (OVA)
tissue: lung; total lung digest
genotype: CCR6+Foxp3EGFP+ Il4raR576
cell type: regulatory T (Treg) cells
Treatment protocol 5- 5-7 week-old female mice were sensitized to ovalbumin (OVA) by intraperitoneal injection of 100 μg of OVA in 100 μL of PBS and then boosted 2 weeks later with a second intraperitoneal injection of OVA in PBS. Starting on day 29, OVA-sensitized mice were challenged with aerosolized OVA at 1% delivered through a Schuco 2000 nebulizer (Allied Health Care Products) for 30 minutes daily for 3 days. Mice were euthanized on day 32 post sensitization and analyzed.
Extracted molecule total RNA
Extraction protocol We purified CCR6+Foxp3EGFP+ Il4raR576 and CCR6–Foxp3EGFP+ Il4raR576 Treg cells from total lung digests of OVA-sensitized and challenged mice, using FACS (Fluorescence Activated Cell Sorting).
RNA was first converted to cDNA using ClonetechÕs SMART-Seq v4 Ultra Low Input RNA kit following standard procedure. After cDNA was measured with Nanodrop, 250 ng in a 50 ul volume was then fragmented to 200-300 bp size using the Covaris M220. All the fragmented DNA was then used with the KAPA Hyper Prep Kit (Illumina platform) to make cDNA libraries. Libraries were quantified using HS DNA Qubit and Agilent HS DNA Bioanalyzer.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Data processing Reads aligned with STAR (version 2.5.1b)
Raw counts quantified with htseq-count (version 0.6.1p1)
Normalized counts generated with DESeq2 (version 1.6.3)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files of normalized counts
 
Submission date Apr 28, 2016
Last update date May 15, 2019
Contact name Matteo Pellegrini
E-mail(s) matteop@mcdb.ucla.edu
Phone 310-825-0012
Organization name UCLA
Street address 610 Charles Young Drive East
City Los Angeles
State/province CA
ZIP/Postal code 90095
Country USA
 
Platform ID GPL21493
Series (1)
GSE80804 A Pro-Asthmatic IL-4 Receptor Allele Promotes Airway Inflammation by Programming TH17 Cell-Like Regulatory T cells
Relations
BioSample SAMN04914164
SRA SRX1736294

Supplementary file Size Download File type/resource
GSM2137737_NormalizedCounts--IL4QCCR6plus2.txt.gz 145.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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