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Sample GSM3042984 Query DataSets for GSM3042984
Status Public on Jan 07, 2019
Title Lung_ILC2_Cbfb-het-PLZF-Cre_RNA-seq_rpt_1
Sample type SRA
 
Source name Lung ILC2
Organism Mus musculus
Characteristics strain: C57BL/6
genotype: Cbfb+/f_PLZF-Cre
tissue: Lung
cell type: Group 2 innate lymphoid cells (ILC2s)
chip antibody: N/A
Growth protocol ILC2s were sorted from the lung for RNA-seq ex vivo. For RNA-seq of activated ILC2s, lung ILC2s were stimulated with IL-2 and IL-33 in vitro. For ChIP-seq, lung ILC2s were cultured with IL-2 and IL-7 in vitro for 2 weeks and stimulated together with IL-33 for 4 days.
Extracted molecule total RNA
Extraction protocol RNA was purified by Trizol first and then by RNeasy micro kit for RNA-seq. Lysates were purified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
RNA libraries were prepared for sequencing using standard Illumina protocols. ChIP-seq libraries were created from the DNA with NEBNext ChIP-seq Library Prep Master Mix set for Illumina Kit (NEB).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Basecalls performed using CASAVA version 1.8.2.
RNA-seq and ChIP-seq sequences were aligned on mm9 using TopHat and bowtie2 (version 2.1.0) with default parameter, respectively.
Cufflinks to calculate RPKM values of RNA-seq data. Homer to call peaks of ChIP-seq and generate bedgraph files of ChIP-seq data.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files including RPKM values for each RNA-seq sample. Bedgraph files for read histograms normalized to 10,000,000 reads for ChIP-seq data.
 
Submission date Mar 15, 2018
Last update date Jan 07, 2019
Contact name Takashi Ebihara
E-mail(s) tebihara@med.akita-u.ac.jp
Phone 81-188846080
Organization name Akita University Graduate School of Medicine
Department Department of Medical Biology
Street address 1-1-1 Hondo
City Akita City
ZIP/Postal code 010-8543
Country Japan
 
Platform ID GPL17021
Series (1)
GSE111871 Runx/Cbfβ complexes protect ILC2s from exhaustion during allergic airway inflammation
Relations
BioSample SAMN08716757
SRA SRX3796538

Supplementary file Size Download File type/resource
GSM3042984_RNA-seq_Cbfb-het_PLZF_rpt_1.txt.gz 188.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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