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| Status |
Public on Jan 26, 2022 |
| Title |
NK92_HSF1_IP |
| Sample type |
SRA |
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| Source name |
NK-92 MI cells
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| Organism |
Homo sapiens |
| Characteristics |
antibody: HSF1
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| Growth protocol |
NK-92 MI were maintained in αMEM without ribonucleosides and deoxyribonucleosides (Gibco) but containing 1.5 g/L sodium bicarbonate, 12.5% (v/v) horse serum (Gibco), 12.5% (v/v) FBS, 1% (v/v) GlutaMAX (Gibco), 0.2 mM inositol (Sigma), 0.1 mM β-mercaptoethanol (Gibco), and 0.02 mM folic acid (Sigma).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were washed in 1XPBS and fixed with 1% formaldehyde for 10 min at room temperature. Subsequent steps until elution used 1x protease inhibitor. Nuclei were isolated on ice using nuclei isolation buffer for 5 minutes, with additional 5 min incubation with NP-40 0.3%. The cell pellet was lysed on ice using nuclei lysis buffer. Samples were sonicated using Covaris sonication. Clarified samples were transferred to Eppendorf tubes and diluted 1:10 with IP dilution buffer. Samples were precleared with 25 µl Protein A by rotation at 4°C for 1h. Supernatants were transferred to fresh tubes, and antibody was added and incubated overnight at 4°C. The next day, 25 µl of Protein A Dynabeads were added and samples were rotated at 4°C for 3 hours. After bead captures, beads were washed twice sequentially in each of. The following buffers: low salt wash buffer, high salt wash buffer, LiCl wash buffer, and TE. Samples were eluted and treated with RNase at 37°C for 30 minutes. Crosslinks were reversed overnight with the addition of proteinase K 0.5 mg/ml and 0.5% SDS. DNA was isolated using phenol/chloroform extraction followed by precipitation with ethanol and glycogen.
Libraries were prepared using the Swift biosciences DNA low-input library 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 |
Reads were aligned to the Mus musculus genome (mm10/GRCm38) using the Bowtie2 aligner (Langmead et al., 2009) (v2.3.4.1).
Duplicate reads were removed using sambamba markdup.
Peaks were determined algorithmically using Model-based Analysis of ChIP-Seq 2 algorithm (v1.4.2) with q < 0.05.
Peak annotation was performed using ChipSeeker (Yu et al., 2015).
Genome_build: hg38
Supplementary_files_format_and_content: Bed files of genomic regions of HSF1 peaks and summits
Supplementary_files_format_and_content: Annotated peak files of genomic regions of HSF1 peaks and summits
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| Submission date |
Jan 25, 2022 |
| Last update date |
Jan 26, 2022 |
| Contact name |
Kathryn Grace Hockemeyer |
| Organization name |
NYU Langone Health
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| Department |
Pathology
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| Lab |
Aifantis
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| Street address |
550 1st Avenue
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| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10016 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE167552 |
The stress response regulator HSF1 modulates natural killer cell anti-tumour immunity |
| GSE194364 |
The NK cell stress response status modulates anti-tumor immunity [ChIP-seq] |
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| Relations |
| BioSample |
SAMN25243265 |
| SRA |
SRX13898238 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5834091_NK92_HSF1_IP.peaks.bed.gz |
224.3 Kb |
(ftp)(http) |
BED |
| GSM5834091_NK92_HSF1_IP.peaks.tsv.gz |
763.7 Kb |
(ftp)(http) |
TSV |
| GSM5834091_NK92_HSF1_IP.summits.bed.gz |
204.1 Kb |
(ftp)(http) |
BED |
| GSM5834091_NK92_HSF1_IP.summits.tsv.gz |
704.9 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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