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| Status |
Public on Dec 01, 2022 |
| Title |
AT2 Mock infection replicate r4 Input control |
| Sample type |
SRA |
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| Source name |
AT2 Mock infection replicate r4 Input control
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| Organism |
Homo sapiens |
| Characteristics |
cell line: lung avleolar type 2 cells
treatment: Mock infection
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Following infection, cells were fixed in 4% PFA for 30 minutes, followed by freezing, lysis, sonication, and ChIP agains the hPTMs H3K27ac, H3K27me3, H3K9ac, H3K9me3
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 550 |
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then aligned to hg38 whole genome using bowtie2, followed by peak calling using MACS2
MACS2 was used for calling peaks for each replicate and hPTM indivdually
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited bed files of per-replicate individual peak calls for hPTMs
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| Submission date |
Dec 23, 2020 |
| Last update date |
Dec 01, 2022 |
| Contact name |
Karl Michael Glastad |
| E-mail(s) |
[email protected]
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| Organization name |
University of Pennsylvania
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| Department |
CDB
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| Lab |
Berger
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| Street address |
3400 Civic Center Blvd, Bldg 421
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| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
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| Platform ID |
GPL21697 |
| Series (1) |
| GSE163774 |
profiling of histone modifications in SARS-CoV-2 infected cells |
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| Relations |
| BioSample |
SAMN17147507 |
| SRA |
SRX9724178 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data not provided for this record |
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