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| Status |
Public on May 31, 2021 |
| Title |
activated |
| Sample type |
SRA |
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| Source name |
iNKT cells
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
chip antibody: PPAR-gamma1+2 (Abcam, ab41928)
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| Treatment protocol |
Expanded iNKT cells were activated by immobilized anti-CD3 plus anti-CD28 in the presence or absence of T007 (2 mg/ml)
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| Growth protocol |
To expand iNKT cells in vitro, splenocytes from Va14 Tg mice were cultured with 100 U/ml human recombinant IL-2 and 100 ng/ml aGC for 3 days, then were cultured for another 7 days with only 100 U/ml human recombinant IL-2.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select DNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer.At last,PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Frist at all, we use FastQC performs basic statistics on the quality of the raw reads. Then,those read sequences produced by the Illumina pipeline in FASTQ format were pre-processed through Trimmomatic software which can be summarized as below:(1) Remove low-quality reads: The reads that mean quality value less than 20 were removed.(2) Remove the reads that contain more than 15 percent N bases.(3) Remove adapters. Remove the reads that alignment with the adapter sequence.(4) Drop reads blow the 18 bases long after trimming.(5) The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last,we use FastQC performs basic statistics on the quality of the clean reads.
Index of the reference genome was built using BWA v0.7.12 and clean reads were aligned to the reference genome using BWA mem v 0.7.12.
After mapping reads to the reference genome, we used the MACS2 version 2.1.0 (model-based analysis of ChIP-seq) (Zhang et al., 2008) peak finding algorithm to indentify regions of IP enrichment over background. A q value threshold of enrichment of 0.05 was used for all data sets. Then, the distribute of chromosome distribution, peak width, fold enrichment, significant level and peak summit number per peak were all displayed.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig
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| Submission date |
May 29, 2019 |
| Last update date |
May 31, 2021 |
| Contact name |
Sicheng Fu |
| E-mail(s) |
1072693906@qq.com
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| Organization name |
USTC
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| Street address |
Huangshan road
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| City |
Hefei |
| ZIP/Postal code |
233100 |
| Country |
China |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE131908 |
ChIP-Seq analysis of PPARγ binding sites in iNKT cells |
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| Relations |
| BioSample |
SAMN11883513 |
| SRA |
SRX5924727 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3827173_activated.bigwig |
127.6 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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