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Sample GSM4726696 Query DataSets for GSM4726696
Status Public on Mar 01, 2023
Title background_Ytm1_ChIP6
Sample type SRA
 
Source name wild type
Organism Schizosaccharomyces pombe
Characteristics strain number: 63
genotype/variation: wild type
chip antibody: FLAG magnetic resin, Sigma-Aldrich Anti-FLAG® M2 Magnetic Beads, M8823, lot number SLBD2467V/SLBQ3807V
target molecule: Ytm1 bound DNA
Growth protocol cells were grown in liquid, rich YES medium
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.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 1500
 
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
 
Submission date Aug 13, 2020
Last update date Mar 01, 2023
Contact name Mario Halic
E-mail(s) mario.halic@stjude.org
Organization name St. Jude Children’s Research Hospital
Lab Halic
Street address 262 Danny Thomas Place
City Memphis
ZIP/Postal code TN 38105-3678
Country USA
 
Platform ID GPL22681
Series (1)
GSE156203 Chromatin localization of nucleophosmin determines the sorting and compartmentalization of ribosome biogenesis
Relations
BioSample SAMN15813903
SRA SRX8944374

Supplementary file Size Download File type/resource
GSM4726696_background_Ytm1_ChIP6.tdf 34.4 Mb (ftp)(http) TDF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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