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| Status |
Public on Jun 20, 2022 |
| Title |
ATAC_HH35_DS_rep1 |
| Sample type |
SRA |
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| Source name |
White Leghorn
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| Organism |
Gallus gallus |
| Characteristics |
developmental stage: HH35
strain: White Leghorn
genotype: WT
dissection: A portion of dorsal skin tissue micro-was dissected from the neck to the shoulder from one HH35 embryo.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ATAC-seq experiments were performed as described in (Bolt et al., 2022)
ATAC-seq librairies were prepared as described in (Bolt et al., 2022)
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
ATAC HH35 dorsal skin
ATAC
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| Data processing |
All scripts are available on https://gitlab.unige.ch/Aurelie.Hintermann/hintermannetal2022
Sequenced DNA fragments were processed as previously reported in (Amândio et al., 2020) with a minor modification on a local Galaxy server: the BAM file was converted to BED prior to peak calling with bedtools version 2.30.0
Peak calling was done using MACS2 (v2.1.1.20160309) callpeak (--no-model --shift -100 --extsize 200 --call-summits --keep-dup all).
Peak regions for each condition were obtained from the union of the peak region of both replicates with bedtools merge (v2.30.0) and extended by 660 bp each side with bedtools slop.
Each replicate was normalized per million reads mapped in their own peaks, subsetted in the HoxD region (mm10,chr2:73000000-77000000 ; galGal6, chr7:13000000-17000000) and the neq2 coverage is the mean of normalized replicates
Assembly: mm10
Assembly: galGal6
Supplementary files format and content: bigwig: coverage from MACS2
Supplementary files format and content: narrowPeak: narrowPeak from MACS2
Supplementary files format and content: bedgraph: replicates were normalized to the number of million reads falling in their own peaks, subsetted in the HoxD region (mm10,chr2:73000000-77000000 ; galGal6, chr7:13000000-17000000) and averaged.
Supplementary files format and content: bed: narrowPeaks of both replicates were pooled, extended by 660 bp each side and then merged to obtain non-overlapping intervals.
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| Submission date |
May 14, 2022 |
| Last update date |
Aug 18, 2022 |
| Contact name |
Aurelie Hintermann |
| E-mail(s) |
aur.hin@gmail.com
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| Organization name |
University of Geneva
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| Department |
Genetics and Evolution
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| Street address |
30 quai Ernest-Ansermet
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| City |
Geneva |
| ZIP/Postal code |
1205 |
| Country |
Switzerland |
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| Platform ID |
GPL19787 |
| Series (2) |
| GSE195592 |
Developmental and evolutionary comparative analysis of a HoxD regulatory landscape in mammals and birds |
| GSE203031 |
Developmental and evolutionary comparative analysis of a HoxD regulatory landscape in mammals and birds [ATAC-Seq] |
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| Relations |
| BioSample |
SAMN28408801 |
| SRA |
SRX15277825 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6152758_ATAC_HH35_DS_rep1.bigwig |
162.9 Mb |
(ftp)(http) |
BIGWIG |
| GSM6152758_ATAC_HH35_DS_rep1.narrowPeak.gz |
2.7 Mb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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