|
| Status |
Public on Dec 20, 2017 |
| Title |
aH3K4me3_STAT4KO_UNSTIM_1_CHIP |
| Sample type |
SRA |
| |
|
| Source name |
splenic NK cells
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Stat4KO
chip antibody: anti-H3K4me3 (Millipore, 07473, lot# 2207275)
condition: unstim
cell type: splenic NK cells
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Protein was cross-linked to DNA with 0.75% formaldehyde. Clarified supernatant from sonicated nuclei were applied to antibody-bound beads. After de-crosslinking and elution, DNA was isolated using Qiagen Gel Extraction Kit. Input samples were clarified supernatant that were not applied to antibody-bound beads.
Immunoprecipitated DNA was quantified by Picogreen and size was evaluated on a HighSense BioAnalyzer chip. When possible, fragments between 100 and 600 bp were size selected and Illumina Hiseq libraries were prepared using the Kapa DNA library preparation chemistry (Kapa Biosystems) using 12-15 cycles of PCR. Adaptors were diluted 1/10 or 1/50 depending on the starting amount of material available. Barcoded libraries were run on Hiseq 2500 1T in a 50bp/50bp Paired end run, using the TruSeq SBS Kit v3 (Illumina). An average of 57 million paired reads were generated per sample.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
BCL files were converted to fastq using bcl2fastq (v1.8.3 and v1.8.4)
ChIP-seq reads were trimmed for quality and adaptors using Trimmomatic (v.0.36) and aligned to the mm10 genome assembly using Bowtie2 (v2.2.9).
Peak-calling was done on concordantly aligned paired reads using MACS2 (2.1.1.20160309).
BigWig files were generated by converting BAM files to size-normalized BEDGRAPH files using bedtools (v2.26.0) and converted to bigWig using UCSC's bedGraphToBigWig (v4).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files normalized by size factors calculated by DESeq2 among all ChIP (non-input) samples in peak regions or flank regions (see manuscript)
|
| |
|
| Submission date |
Oct 25, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Colleen Lau |
| Organization name |
Cornell University
|
| Department |
Microbiology & Immunology
|
| Street address |
930 Campus Road
|
| City |
Ithaca |
| State/province |
New York |
| ZIP/Postal code |
14850 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE106137 |
Transcriptional and epigenetic regulation of adaptive NK cell responses [ChIP-Seq] |
| GSE106139 |
Regulation of natural killer cells during MCMV infection |
|
| Relations |
| BioSample |
SAMN07833660 |
| SRA |
SRX3324128 |
