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Sample GSM1508404 Query DataSets for GSM1508404
Status Public on Nov 10, 2014
Title OrR_st12-13_Cdc45
Sample type SRA
 
Source name pooled stage 12 and 13 egg chambers
Organism Drosophila melanogaster
Characteristics strain: OrR
chip antibody: Cdc45 (made in-house)
developmental stage: pooled stage 12 and 13
tissue: egg chamber
Treatment protocol Ovaries were dissected into EBR mediumand fixed in 2% formaldehyde. Ovaries were resuspended in LB3 and indiviudal egg chambers were isolated. When enough were collected (600 per ChIP reaction), ChIP was performed with either anti-SUUR, anti-Cdc45 or GP IgG
Growth protocol Drosophila were grown on standard cornmeal, molasses agar media.Females were fattend for two days on wet yeast
Extracted molecule genomic DNA
Extraction protocol Egg chambers were dounced and sonicated using a Biorupto 300 (Diagenode)
Libraries were constrcted using the NEB Next ChIP seq kit (Part # E6200S) according to manufactures recommendations with indexing primers for multiplexing
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description OrR stage 12-13Cdc45 ChIP
Data processing Basecalls performed using CASAVA version 1.5
ChIP-seq reads were aligned to the dm3 genome assembly using BWA using the default parameters with the exception of no gaps allowed (-o 0)
Data were filtered using the following specifications…
Peaks were called using MACS2 default settings and a p value of 10-3.
Genome_build: dm3
Supplementary_files_format_and_content: MACS peak files. Information include: chromosome name, start position of peak, end position of peak, length of peak region, peak summit position related to the start position of peak region, number of tags in peak region, -10*log10(pvalue) for the peak region (e.g. pvalue =1e-10, then this value should be 100), fold enrichment for this region against random Poisson distribution with local lambda, FDR in percentage. Coordinates in .txt is 1-based which is different with BED format.
 
Submission date Sep 19, 2014
Last update date May 15, 2019
Contact name Terry L. Orr-Weaver
E-mail(s) weaver@wi.mit.edu
Phone 617-258-5251
Organization name Whitehead Institute for Biomedical Research
Lab Orr-Weaver
Street address 9 Cambridge Center
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
 
Platform ID GPL13304
Series (2)
GSE55932 ChIP-Seq of gamma-H2Av bound to third instar salivary gland DNA in WT and SuUR mutant Drosophila; ChIP-Seq of SUUR and Cdc45 bound to egg chamber DNA from early and late stage egg chambers
GSE56056 SuUR role in regulation of DNA replication
Relations
BioSample SAMN03074569
SRA SRX706815

Supplementary file Size Download File type/resource
GSM1508404_ORR_st12_13_SUUR_macs2_peaks.txt.gz 254.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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