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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 05, 2021 |
| Title |
HUDEP-2_IgG |
| Sample type |
SRA |
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| Source name |
HUDEP-2 cells
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| Organism |
Homo sapiens |
| Characteristics |
antibody: CUT&RUN with IgG antibody
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated and prepared following the CUT&RUN protocol from Skene PJ, et al. Nat Protoc. 2018, PMID: 29651053.
Libraries were prepared using the NEBNext Ultra™ II DNA Library Prep Kit for Illumina following the protocol from Liu N, et al. Cell 2018, PMID: 29606353.
CUT&RUN, Paired-end 42bp sequencing.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Adapter sequences were trimmed with Trimmomatic.
Trimmed reads were aligned to either the human reference genome hg19 or the mouse reference genome mm10 using bowtie2.
The alignment files (.sam) were converted to sorted, indexed bam files and marked for duplicates using Picard.
Reads were filtered using an alignment score cutoff of 10 with samtools
Peak calling was performed using macs2. Genomic regions annotated as part of the ENCODE project blacklist as problematic regions for alignment of high-throughput functional genomics data were excluded from analysis.
Genome_build: hg19, mm10
Supplementary_files_format_and_content: Excel spreadsheet containing genome-wide regions of ZNF410 chromatin occupancy. Data for each cell type is on a separate sheet of the workbook.
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| Submission date |
Feb 04, 2021 |
| Last update date |
Feb 06, 2021 |
| Contact name |
Divya Vinjamur |
| Organization name |
Boston Children's Hospital
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| Street address |
1 Blackfan Circle
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE166221 |
Genome-wide ZNF410 binding sites identified by CUT&RUN in HUDEP-2, human CD34+ HSPCs and MEL cells. |
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| Relations |
| BioSample |
SAMN17800080 |
| SRA |
SRX10031372 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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