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| Status |
Public on Mar 01, 2023 |
| Title |
fkbp39Δ_Ytm1_ChIP2 |
| Sample type |
SRA |
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| Source name |
FLAG-Ytm1, fkbp39Δ
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| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain number: 1318
genotype/variation: FLAG-Ytm1, fkbp39{delta}
chip antibody: FLAG magnetic resin, Sigma-Aldrich Anti-FLAG® M2 Magnetic Beads, M8823, lot number SLBD2467V/SLBQ3807V
target molecule: Ytm1 bound DNA
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| Growth protocol |
cells were grown in liquid, rich YES medium
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP libraries: IP of crosslinked (1% formaldehyde, 15 min) sonycated lysate, followed by decrosslinking and protein and RNA degradation. DNA library construction with NEBNext Ultra II DNA Library Prep Kit for Illumina kit (NEB). Nascent RNA: RNA was labeled with 4 Thiouracil (Sigma), extracted, after removal of DNA was treated EZ-Link HPDP-Biotin (Thermo Scientific). Labeled RNA was recovered using streptavidin beads (Roche). RNA libraries were prepared with NEBnext Ultra Directional RNA Library Prep Kit for Illumina (NEB). Total RNA was isolated applying the hot phenol method. RNA libraries were prepared with NEBnext Ultra Directional RNA Library Prep Kit for Illumina (NEB).
Libraries were prepared using NEBnext Ultra Directional RNA or DNA Ultra II Library Prep Kit for Illumina (NEB), following the manufacturer instruction.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 1500 |
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| Data processing |
base calling with RTA1.18.64
Sequenced reads were trimmed for the adaptor sequence, then mapped to the S.pombe genome with Novoalign (http://www.novocraft.com) randomly assigned.
Reads mapping with two or fewer mismatches were retained.
Enrichment was calculated with our house Perl scripts
Normalization to reads per million
Genome_build: Genome_build: Schizosaccharomyces_pombe.ASM294v1.18
Supplementary_files_format_and_content: Supplementary_files_format_and_content: can be viewed with IGV browser: http://www.broad.mit.edu/igv
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| Submission date |
Aug 13, 2020 |
| Last update date |
Mar 01, 2023 |
| Contact name |
Mario Halic |
| E-mail(s) |
mario.halic@stjude.org
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| Organization name |
St. Jude Children’s Research Hospital
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| Lab |
Halic
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| Street address |
262 Danny Thomas Place
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| City |
Memphis |
| ZIP/Postal code |
TN 38105-3678 |
| Country |
USA |
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| Platform ID |
GPL22681 |
| Series (1) |
| GSE156203 |
Chromatin localization of nucleophosmin determines the sorting and compartmentalization of ribosome biogenesis |
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| Relations |
| BioSample |
SAMN15813931 |
| SRA |
SRX8944406 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4726686_fkbp39del_Ytm1_ChIP2.tdf |
29.0 Mb |
(ftp)(http) |
TDF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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