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Sample GSM4078571 Query DataSets for GSM4078571
Status Public on Mar 11, 2020
Title H4K16ac Heat shock rep1
Sample type SRA
 
Source name S2 cell line
Organism Drosophila melanogaster
Characteristics heat shock: yes
recovery: no
antibody: H4K16ac
Treatment protocol Control: Cells were incubated at 27˚C; Heat shock: Cells were incubated 1 h at 37˚C; 2h recovery: Cells were incubated 1 h at 37˚C. Then cold medium was added to decrease the temperature to 27˚C and cells were incubated for 2 h at 27˚C.
Growth protocol S2 cells were grown in Schneider media supplemented with 1% penicillin/straptomycin and 10% heat-inactivated FBS at 27˚C until density of 4 million cells/ml.
Extracted molecule genomic DNA
Extraction protocol Cells were washed with PBS and crosslinked with 1% formaldehyde for 5 min. Formaldehyde was quenched with glycine and incubated for 5 min. Cells were lysed and centrifuged to isolate nuclei. Nuclei were lysed and sheared with Covaris S220 to ~300 bp fragment sizes. SDS was quenched with Triton X-100 and extract was cleared by centrifugation. For IP, 2 µg of anti-H4K16ac Ab (Millipore, 07-329) was added per 1 ml of extract and incubated over night Complexes were captured on Protein G DynaBeads and washed with Low salt, High salt, LiCl and TE buffer. Complexes were eluted with proteinase K treatment followed by over night decrosslinking at 65˚C. DNA was isolated using PCR purification kit (Quiagen).
Libraries were constructed according to Bowman et al. (2012, BMC Genomics)
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NovaSeq 6000
 
Data processing Adaptor sequences were removed using Cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -m 3
Reads were aligned to reference genome using bowtie2
Aligned reads were filtered for MAPQ > 2 woth samtools
Sample enrichment over input was calcualted using MACS2
Enrichment bedgraph files were converted to bigWig format
Genome_build: dm6
Supplementary_files_format_and_content: bigWig files contain track of sample enrichemnt over input
 
Submission date Sep 13, 2019
Last update date Mar 12, 2020
Contact name Matthew D Simon
E-mail(s) matthew.simon@yale.edu
Phone 2037373274
Organization name Yale University Chemical Biology Instiute
Department Molecular Biophysics & Biochemistry
Lab Simon Lab
Street address 600 West Campus Dr. MIC312
City West Haven
State/province CT
ZIP/Postal code 06516
Country USA
 
Platform ID GPL25244
Series (2)
GSE120220 Harnessing enhanced nucleotide chemistry and toehold nanotechnology to reveal lncRNA spreading on chromatin
GSE137401 ChIP of H4K16ac
Relations
BioSample SAMN12742372
SRA SRX6845079

Supplementary file Size Download File type/resource
GSM4078571_Sample_MM1906093_S9_L003_FE.bigWig 274.1 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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