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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 24, 2023 |
| Title |
ATAC_CT26_IFNcon_2 |
| Sample type |
SRA |
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| Source name |
CT26
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| Organism |
Mus musculus |
| Characteristics |
cell line: CT26
cell type: colorectal cancer
genotype: WT
treatment: 20 ng/mL IFN-γ for 24 hours
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Control or Phf8 KO CT26 cells treated with or without 20 ng/mL IFN-γ for 24 hours were dissociated and 50,000 cells were washed twice in cold PBS at 4°C.
ATAC-seq libraries were prepared using the N248, Illumina Nextera Kit (Novoprotein, shanghai, China). Cells were resuspended in 50 μL cell lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.05% NP40) and incubated on ice for 5 min. Samples were then washed with 950 μL cold wash buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.05% NP40, 0.1% Tween 20). Samples were centrifuged at 500 g for 5 min at 4°C and supernatant were removed. The transposase reaction was carried out by titurating in 50 μL per sample in TD Buffer (10 mM Tris-HCl, pH 8, 5 mM Magnesium Chloride) with 4 μL Transposase (N248, Illumina Nextera Kit, Novoprotein, shanghai, China), and incubated at 37°C for 30 min, and 10 μL of 100 mM EDTA was added. Then, samples were incubated at 55°C for 5 min and transferred to ice. Samples and DNA recovered using Tagment DNA extract beads (N245, Illumina Nextera Kit, Novoprotein). Libraries were generated by PCR in 50 μL reaction (35 μL sample, 10 μL 5 x AmpliMix, 2.5 μL of each custom Illumina primers at 10 μM). The PCR reaction followed 72 °C for 3 min, 98°C for 30 s, followed by 9 cycles of 98°C for 15 s, 60°C for 15 s, 72°C for 8 s, followed by 72°C for 2 min. DNA was recovered using DNA clean beads (N240, Illumina Nextera Kit, Novoprotein).
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
CT26 cells treated with IFNγ , replicate2
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| Data processing |
All sequencing data were mapped onto the mm10 mouse genome assembly using bowtie2 (–very-sensitive). Low quality mapped reads were removed using samtools (view –q 35) and only unique reads mapping to a single genomic location and strand were kept.
We removed mitochondrial sequences using ‘grep –v ‘chrM’. Biological replicates were merged, and peaks were called using dfilter (with the settings: -bs = 100 –ks = 60 –refine)
BigWig files were produced using genomeCoverageBed from bedtools (scale = 107/ < each_sample’s_total_unique_reads > ) and then bedGraphToBigWig. Gene ontology and gene expression measures were called by first collecting all TSSs within 10 kb of an ATAC-seq peak. bedtools (scale = 107/ < each_sample’s_total_unique_reads > ) and then bedGraphToBigWig. Gene ontology and gene expression measures were called by first collecting all TSSs within 10 kb of an ATAC-seq peak.
Assembly: mm10
Supplementary files format and content: bigWig files
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| Submission date |
Aug 18, 2022 |
| Last update date |
May 25, 2023 |
| Contact name |
Yanan Liu |
| E-mail(s) |
Lyn19950902@outlook.com
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| Organization name |
East China Normal University
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| Department |
School of Life Sciences
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| Street address |
500 Dongchuan Road, Minhang District, Shanghai, China
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| City |
China |
| ZIP/Postal code |
200241 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE211525 |
PHF8 enables immune evasion by silencing endogenous retroelements [ATAC-seq] |
| GSE211526 |
PHF8 enables immune evasion by silencing endogenous retroelements. |
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| Relations |
| BioSample |
SAMN30383437 |
| SRA |
SRX17132149 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6475160_ATAC_CT26_IFNcon_2.bw |
247.1 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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