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Status |
Public on Jan 07, 2019 |
Title |
Lung_ILC2_Cbfb-homo-PLZF-Cre_RNA-seq_rpt_1 |
Sample type |
SRA |
|
|
Source name |
Lung ILC2
|
Organism |
Mus musculus |
Characteristics |
strain: C57BL/6 genotype: Cbfbf/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).
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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.
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|
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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 |
SAMN08716754 |
SRA |
SRX3796541 |