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| Status |
Public on Aug 04, 2021 |
| Title |
SI1 |
| Sample type |
SRA |
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| Source name |
Small intestine ILC2
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: 6 weeks old
gender: male
tissue: Small intestine
cell type: Group 2 innate lymphoid cells
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Bone marrow cells were processed by flushing femur and tibia using a syringe. For isolation of mononuclear cells from lung or pancreas, tissues were dissected and blood clots, fat tissues and bronchus were discarded. Lung or pancreas tissues were cut into pieces and digested with 10 ml RPMI 1640 medium (Thermo Fisher Scientific) containing DNase I (50 U/ml for digestion of lung, 250U/ml for digestion of pancreas, Sigma-Aldrich) and collagenase VIII (250 U/ml, Sigma-Aldrich) at 37°C for 1h (for digestion of lung) or 30 minutes (for digestion of pancreas). The digested tissues were homogenized by vigorous shaking and passed through a 70-μm cell strainer. Mononuclear cells were then harvested from the interphase of a 40% and 80% Percoll (GE Healthcare) gradient after a spin at 2500 rpm for 20 minutes at room temperature. For isolation of large and small intestine lamina propria lymphocytes, tissues were dissected. Fat tissues and peyer’s patches in the small intestine were removed. The intestines were then cut into pieces, washed, and shaken in PBS containing 1mM dithiothreitol for 10 minutes at room temperature. Intestines were incubated with shaking at 220 rpm in PBS containing 30 mM ethylenediaminetetraacetic acid (EDTA) at 37°C for 10 minutes for 2 cycles. The tissues were then digested in RPMI 1640 medium containing DNase I (150 ug/ml) and collagenase VIII (150 U/ml) at 37°C in an incubator with 5% CO2 for 1.5h. Mononuclear cells were then harvested from the interphase of a 40% and 80% Percoll gradient after a spin at 2500 rpm for 20 minutes at room temperature.
Library preparation was performed using TruePrepTM DNA Library Prep Kit V2 for Illumina® kit from Vanzyme (Nanjing, China). 1.2×Agencourt AMPure XP beads (Beckman Coulter) were used to purify libraries for sequencing.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
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| Data processing |
ATAC-seq raw sequence reads were initially processed by FastQC (version 0.11.9) for quality control, and then adapter sequences and poor quality reads were removed. Quality filtered reads were then mapped to mouse genome (mm10) using Bowtie2 (version 2.2.9), and only uniquely mapped reads were kept. Sam files were converted to Bam format using Samtools (version 1.8). Peak calling was done using MACS (2.1.1) with an initial threshold q-value of 0.01 as cutoff. Differentially expressed peaks were analyzed using DESeq2. Differentially peaks significantly higher or lower (p<0.05) in one tissue ILC2s compared to other tissue ILC2s through a 1 versus 1 comparison mode were overlapped and were defined as "ILC2 tissue specific open chromatin regions (ILC2 TS OCRs)" or "commonly decreased peaks". To look for large and small intestine ILC2 common OCRs, differentially expressed peaks were firstly identified in large intestine or small intestine ILC2s compared to each of the other 3 tissue ILC2s respectively, and then overlapped peaks were intestine ILC2 specific OCRs.
Genome_build: mm10
Supplementary_files_format_and_content: Visualization of read count data was performed by converting raw bam files to bigwig files using IGV tools.
Supplementary_files_format_and_content: ILC2_tissue_differential_ATACseq_peaks.xlsx
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| Submission date |
May 09, 2020 |
| Last update date |
Aug 04, 2021 |
| Contact name |
Ju Qiu |
| Organization name |
Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
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| Street address |
320 Yueyang Road
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| City |
Shanghai |
| ZIP/Postal code |
200031 |
| Country |
China |
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| Platform ID |
GPL21273 |
| Series (2) |
| GSE150179 |
Tissue microenvironment shapes distinct sets of machineries to regulate ILC2 properties [ATAC-seq] |
| GSE153749 |
Tissue microenvironment shapes distinct sets of machineries to regulate ILC2 properties |
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| Relations |
| BioSample |
SAMN14860115 |
| SRA |
SRX8297504 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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