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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 04, 2023 |
| Title |
H3K27me3, Armstrong |
| Sample type |
SRA |
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| Source name |
spleen
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| Organism |
Mus musculus |
| Characteristics |
tissue: spleen
cell type: CD8 T Cell
chip antibody: H3K27me3 (CST, #9733)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA extraction, digestion and purification was performed with the CUT&RUN Assay Kit by CST, #86652
ChIP-seq libraries were prepared using the SimpleChIp ChIp-Seq DNA Library Prep Kit (CST, #567945) input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
Reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.38, discarding reads left with < 25 bp
Reads were aligned to the mouse genome (mm10) using Bowtie version 1.1.2. Parameters: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700
Reads were aligned to the yeast genome (sacCer3) using Bowtie version 1.1.2. Parameters: --local --very-sensitive-local --no-overlap --no-dovetail --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 70
Spike-in normalization. The genomic coverage were then normalized by applying the scaling factor that is calculated from the number of mapped reads to mouse genome and yeast genome
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01, using Callpeak, and compared the sample to corresponding IgG samples using bdgcmp in FE (fold-enrichment) mode.
bigWig files were generated using bdg2bw from the bedgraph output from last step. Score represents the FE values at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak (except for IgG sample)
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| Submission date |
Sep 15, 2022 |
| Last update date |
Jan 05, 2023 |
| Contact name |
Gene W Yeo |
| E-mail(s) |
vincenzojin@gmail.com
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| Phone |
+1-650-695-9262
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| Organization name |
University of California, San Diego
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| Department |
Cellular and Molecular Medicine
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| Street address |
9500 Gilman Dr
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| City |
La Jolla |
| ZIP/Postal code |
92093 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE213467 |
Areas of H3K27 tri-methylation in CD8+ T cells from the spleens of LCMV-Armstrong or LCMV-Clone 13 infected mice |
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| Relations |
| BioSample |
SAMN30875303 |
| SRA |
SRX17596194 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6586821_4-H3K27me3_A2_over_6-IgG_A2_FE.bw |
146.9 Mb |
(ftp)(http) |
BW |
| GSM6586821_4-H3K27me3_A2_over_6-IgG_A2_peaks.sorted.narrowPeak.GeneAnnotations.csv.gz |
2.1 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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