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| Status |
Public on Dec 01, 2016 |
| Title |
HH32_whole_H3K27ac_r1 |
| Sample type |
SRA |
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| Source name |
chicken embryos
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| Organism |
Gallus gallus |
| Characteristics |
tissue: whole embryo
developmental stage: HH32
chip antibody: H3K27ac, Active Motif, 39113
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| Growth protocol |
Fertilized chicken eggs (Gallus gallus, White Leghorn) were incubated at 38°C.
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| 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.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
2 lane
HH32_whole_H3K27ac_overlaps.finalPeaks.bed
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| 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.
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| Submission date |
Nov 30, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
CNSA CNGB |
| Organization name |
BGI
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| Street address |
BGI
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| City |
shenzhen |
| ZIP/Postal code |
518083 |
| Country |
China |
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| Platform ID |
GPL16133 |
| Series (1) |
| GSE75480 |
Functional roles of Aves class specific cis-regulatory elements on macroevolution of bird-specific features |
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| Relations |
| BioSample |
SAMN04301856 |
| SRA |
SRX1456183 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1956897_HH32_whole_H3K27ac_r1_FE.bedgraph.gz |
551.1 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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