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Sample GSM1430016 Query DataSets for GSM1430016
Status Public on Dec 02, 2014
Title Twist ChIP-seq (Drosophila embryos) Rep 1
Sample type SRA
Source name Oregon-R_embryo
Organism Drosophila melanogaster
Characteristics tissue: whole-embryo
time point: 02 to 04 h AEL
chip antibody: anti-Twist rabbit polyclonal, custom (Covance)
strain: Oregon-R
Growth protocol D. melanogaster embryos were collected and aged on yeasted apple juice plates at 25C and 60 % humidity
Extracted molecule genomic DNA
Extraction protocol embryos were cross-linked in 1.8% formaldehyde. Embryos were then dounced to break down cells and extract nuclei. Chromatin was sonicated by bioruptor to an average size of 300~500 bp. 300 ul soluble chromatin from ~100 mg embryos was used
DNA-protein-complexes were isolated with specific antibodies. Sequencing libraries were prepared following Illumina's instructions: 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 were ligated to the adenylated fragments, and after a size-selection step using AmPure beads (200-250 bp) the adapter modified DNA was PCR-amplified. Following cluster generation on the flowcell surface, the sequencing libraries were sequenced following Illumina's protocol.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
Description dmel_embryo_twi_chipseq_01
Illumina multiplex barcode: ACAGTG
Data processing Base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings
Reads were trimmed to 50 bp and aligned to the reference genome using bowtie v1.0.0, retaining only uniquely aligning reads with a maximum of 2 mismatches
Aligned reads were extended to each library's estimated insert size
Genome-wide coverage counts were calculated and saved in BigWig format
Genome_build: UCSC dm3
Supplementary_files_format_and_content: BigWig files contain pileup counts for each base
Submission date Jul 08, 2014
Last update date May 15, 2019
Contact name Julia Zeitlinger
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
BioSample SAMN02904901
SRA SRX2009293
Named Annotation

Supplementary file Size Download File type/resource 54.6 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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