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| Status |
Public on Nov 27, 2018 |
| Title |
HH28_DFL_WT_H3K27ac |
| Sample type |
SRA |
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| Source name |
Forelimb
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| Organism |
Gallus gallus |
| Characteristics |
breed: White Leghorn
age: HH28
tissues: Distal forelimb
genotype: wild type
antibody: H3K27ac (Abcam, ab4729, Lot: GR184558-1)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin immunoprecipitated experiment was performed as previously described (Beccari et al. 2016). Micro-dissected limb tissues from mouse and chick embryos were cross-linked with 1% formaldehyde/PBS for 15 min at room temperature. Chromatin was sheared and used for each immunoprecipitation with anti-H3K27ac (ab4729, Abcam), anti-H3K27me3 (07-449, Merck Millipore), anti-H3K4me1 (ab8895, Abcam) and anti-CTCF (61311, Active Motif), respectively.
Libraries were prepared with at least 5 ng of purified DNA following Illumina TruSeq ChIP library preparation guide. Sequencing was performed with 100-bp single-end.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
chick HH28 WT distal forelimb H3K27ac
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| Data processing |
Demultiplexed ChIP-seq reads were mapped onto the galGal5 or mm10 using Bowtie (Version 0.12.7) (Langmead et al., 2009), with parameters “-m1 –strata –best” according to the conditions described previously (Riising et al. 2014), and PCR duplicates were removed from mapped reads using samtools (Version 0.1.18) (Li et al., 2009)
By using bamCompare (Version 2.5.0), The ChIP data from H3K27ac, H3K27me3 and H3K4me1 and the input data were normalized and compared to compute the log2 of the number of reads ratio.
The CTCF ChIP data was normalized to obtain 1x depth of coverage by using bamCoverage (Version 2.5.0) (Ramirez et al. 2014, 2016). Peaks of CTCF were called by using MACS2 (Version 2.1.0.20151222) with q-value (0.01) and used for the CTCF motif orientation analysis as previously described (Rodríguez-Carballo et al. 2017)
All analysis was done with our Galaxy server (the Bioteam Appliance Galaxy Edition, https://bioteam.net, https://bioteam.net/products/galaxy-appliance) (Afgan et al. 2016).
Genome_build: mm10 or galGal5
Supplementary_files_format_and_content: bedgraph of log2 of the normalized number of reads ratio histone marks ChIP versus Input; bedgraph of the normalized 1x depth of CTCF coverage; bed of CTCF narrow peaks with q-value=0.01
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| Submission date |
Jun 11, 2018 |
| Last update date |
Jan 25, 2022 |
| Contact name |
Nayuta Yakushiji-Kaminatsui |
| E-mail(s) |
nayuta.yakushiji@riken.jp
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| Phone |
+81 45 503 9690
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| Organization name |
RIKEN Center for Integrative Medical Sciences
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| Lab |
Laboratory for Developmental Genetics
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| Street address |
1-7-22 Suehiro-cho, Tsurumi-ku
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| City |
Yokohama |
| State/province |
Kanagawa |
| ZIP/Postal code |
230-0045 |
| Country |
Japan |
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| Platform ID |
GPL19005 |
| Series (2) |
| GSE115561 |
Similarities and differences in the regulation of HoxD genes during chick and mouse limb development [ChIP-Seq] |
| GSE115563 |
Similarities and differences in the regulation of HoxD genes during chick and mouse limb development. |
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| Relations |
| Alternative to |
GSM5835479 |
| BioSample |
SAMN09390355 |
| SRA |
SRX4191514 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3182462_HH28DFL_H3K27ac.bedgraph.gz |
207.1 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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