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Sample GSM1348731 Query DataSets for GSM1348731
Status Public on Nov 10, 2014
Title SuUR_Input
Sample type SRA
 
Source name third instar salivary gland from SuUR
Organism Drosophila melanogaster
Characteristics strain: SuUR
chip antibody: NA
developmental stage: third instar
tissue: salivary gland
Treatment protocol Salivary glands were hand dissected from committed wandering third instar larvae directly into EBR medium and frozen within less than 30 min in liquid nitrogen. When enough were collected, ChIP was performed with either anti gamma-H2Av antibody (Rockland) or rabbit IgG (Abcam)
Growth protocol Drosophila were grown on standard cornmeal, molasses agar media.
Extracted molecule genomic DNA
Extraction protocol Salivary glands 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 SuUR 3SG Input
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 MACS v1.4 with the following setting; -tsize=40 --wig --space=25 --mfold=10,30 --pvalue=1e-5. Peaks were further filtered based on the FDR. Peaks with a FDR of <5% were included in the analysis
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 Mar 14, 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 SAMN02689382
SRA SRX490732

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data not provided for this record

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