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Sample GSM1430013 Query DataSets for GSM1430013
Status Public on Dec 02, 2014
Title Myc ChIP-nexus (Drosophila S2 cells) Rep 2
Sample type SRA
 
Source name Schneider 2
Organism Drosophila melanogaster
Characteristics cell line: Schneider 2 cells
chip antibody: anti-Myc rabbit polyclonal, Santa Cruz Technology, catalog # sc-28207, lot # D-2704
Growth protocol grown at 25C in HyClone SFX-Insect Cell Culture Media with penicillin and streptomycin
Extracted molecule genomic DNA
Extraction protocol cells were cross-linked in 1.0% formaldehyde. Cells were then lysed by lysis buffer to extract nuclei. Chromatin was sonicated by bioruptor to an average size of 300~500 bp. 300 ul soluble chromatin from ~ 20 million cells was used
DNA-protein-complexes were isolated with specific antibodies when still being attached to protein A-dynabeads. DNA was end repaired using T4 DNA polymerase, DNA polymerase I large fragment (Klenow polymerase) and T4 polynucleotide kinase. A single 3'-A overhang was added to the blunted ends using Klenow 3'-5' exo- polymerase. Adapters with single 3'-T overhangs and 5’ overhangs (barcode composed of 5 random nucleotides) were ligated to the adenylated fragments. Ligated fragments were blunted again by Klenow 3'-5' exo- polymerase to fill in the 5’ overhang first and then by T4 DNA polymerase to trim any possible 3’ overhang. Blunted DNA was subsequently digested by lambda exonuclease first and RecJf afterwards. Digested single strand DNA was then eluted, reverse cross-linked and purified prior to self-circularization by Circligase. An oligonucleotide was mixed with circularized single DNA for subsequent BamHI digestion to linearize the single DNA again. Linearized single strand DNA was then PCR-amplified using adaptor sequences and library was purified on 2% agarose gel to remove adaptor-adaptor ligation products. Following cluster generation on the flowcell surface, the sequencing libraries were sequenced following Illumina's protocol.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2000
 
Description dmel_s2_myc_chipnexus_02
Protocol: ChIP-nexus
Illumina multiplex barcode: GCCAAT
Data processing Base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings
Custom barcode sequences were removed from the first 9bp of each read and sequencing adapters were trimmed from the 3' end using cutadapt v1.3
Remaining reads with length >= 22bp were aligned to the reference genome using bowtie v1.0.0, retaining only uniquely aligning reads with a maximum of 2 mismatches
Aligned reads were separated by strand and reduced to a single base at the 5' end
Genome-wide coverage counts were calculated for each strand separately and saved in BigWig format
Genome_build: UCSC dm3
Supplementary_files_format_and_content: BigWig files contain genome coordinates and counts of the first base of aligned reads, separated by alignment strand
 
Submission date Jul 08, 2014
Last update date May 15, 2019
Contact name Julia Zeitlinger
E-mail(s) jbz@stowers.org
Organization name Stowers Institute for Medical Research
Lab Zeitlinger Lab
Street address 1000 E 50th St
City Kansas City
State/province MO
ZIP/Postal code 64110
Country USA
 
Platform ID GPL13304
Series (1)
GSE55306 ChIP-nexus: a novel ChIP-exo protocol for improved detection of in vivo transcription factor binding footprints
Relations
BioSample SAMN02904898
SRA SRX647996
Named Annotation GSM1430013_dmel_s2_myc_chipnexus_02_negative.bw
Named Annotation GSM1430013_dmel_s2_myc_chipnexus_02_positive.bw

Supplementary file Size Download File type/resource
GSM1430013_dmel_s2_myc_chipnexus_02_negative.bw 16.9 Mb (ftp)(http) BW
GSM1430013_dmel_s2_myc_chipnexus_02_positive.bw 16.8 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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