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Sample GSM1956887 Query DataSets for GSM1956887
Status Public on Dec 01, 2016
Title HH21_whole_Input_r1
Sample type SRA
 
Source name chicken embryos
Organism Gallus gallus
Characteristics tissue: whole embryo
developmental stage: HH21
chip antibody: none
Growth protocol Fertilized chicken eggs (Gallus gallus, White Leghorn) were incubated at 38°C.
Extracted molecule genomic DNA
Extraction protocol Embryonic samples were dissected and dispersed by 0.05% trypsin (Gibco, 25300054) for 5 min at 37 oC. After adding an equal amount of FBS to stop the enzyme reaction, the cells were filtered using a cell strainer (BD Falcon, 352360). At least 5 x106 cells were used for the subsequent process. The cell lysates were sonicated 20 times (pulsed for 30 sec with 30 sec interval) using a Bioruptor (Cosmo Bio, UCD-300) at high power setting. Alternatively, we sonicated the lysates 17 times (pulsed for 15 sec with 60 sec interval) used a Vibra-Cell (Sonics & Materials, VCX130PB) at 20 % amplification setting. The samples were divided into four aliquot and added 10 µg of antibodies
For single ChIP enriched DNA or control DNA samples, ~10 ng genomic DNA per sample was end-repaired. Then the blunt ends fragments were treated with Klenow fragments and dATP to yield a protruding 3'-dA overhang. After adapter ligation, removal of unligated adapter and size selection, library fragments of 100~300 bp were purified from an agarose gel.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description 2 lane
Data processing The sequencing reads of each sample were aligned to the chicken genome by BWA.
After removing PCR duplicates by samtools and removing singletons, we chose uniquely mapped reads to assess the signal-to-noise ratios for each sample using the SPP package.
The input samples of the same condition were merged, and ChIP-seq peaks for each sample were identified by the MACS2 with broad peaks mode (p<0.05).
To obtain the final peak set for each condition, we counted the aligned reads in the peak regions from each of the two replicate samples, and applied quantile normalization on the aligned reads to comparing these values across samples. We only kept reproducible intersected peaks that had an average coverage of >=1 in both replicates for each condition.
Genome_build: galgal3
Supplementary_files_format_and_content: BedGraph files were fold enrichment tracks generated by MACS2 bdgcmp; Bed files were the final peak files.
 
Submission date Nov 30, 2015
Last update date May 15, 2019
Contact name Jun Wu
Organization name University of Texas Southwestern Medical Center
Lab Jun Wu Lab
Street address Main buliding,Beishan Industrial Zone,Yantian District
City Dallas
ZIP/Postal code 5323
Country USA
 
Platform ID GPL16133
Series (1)
GSE75480 Functional roles of Aves class specific cis-regulatory elements on macroevolution of bird-specific features
Relations
BioSample SAMN04301846
SRA SRX1456173

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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