|
| Status |
Public on Jan 07, 2019 |
| Title |
Lung_ILC2_Cbfb-het-PLZF-Cre_IL33_RNA-seq_rpt_3 |
| 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 |
SAMN08716749 |
| SRA |
SRX3796546 |
