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| Status |
Public on Sep 24, 2020 |
| Title |
DNase-seq from UC Davis FAANG chicken adipose rep A |
| Sample type |
SRA |
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| Source name |
Adipose
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| Organism |
Gallus gallus |
| Characteristics |
tissue: adipose
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNase-seq datasets were generated by the Stam Lab at University of Washington using a previously published protocol. Briefly, cryopreserved nuclei were slowly defrosted on ice, pelleted at 500g, and resuspended in 37°C DNase I digestion buffer (13.5 mM Tris-HCL pH 8.0, 87 mM NaCl, 54 mM KCl, 6 mM CaCl2, 0.9 mM EDTA, 0.45 mM EGTA, 0.45 mM spermidine). After a 3 minute incubation, the reaction was stopped with 2x stop buffer (50 mM Tris-HCl pH 8.0, 100 mM NaCl, 0.1% SDS, 100 mM EDTA pH 8.0, 1 mM spermidine, 0.3 mM spermine). Samples were treated with RNase for 1 hour at 37°C, then an additional hour at 55°C with proteinase K.
DNA fragments were isolated, libraries prepared, and sequenced on Illumina’s Hiseq 2500 with 50bp paired-end sequencing.
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| Library strategy |
DNase-Hypersensitivity |
| Library source |
genomic |
| Library selection |
DNAse |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
SAMEA4454500
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| Data processing |
Reads were trimmed with Trim Galore! 0.4.5 with the default arguments
Reads were aligned with BWA mem 0.7.17 to the galGal6 genome
Alignments were filtered with Samtools 1.10 using arguments -F 1804 -q 30
Duplicates were removed with Picard toolkit 2.18.17
Genome_build: galGal6
Supplementary_files_format_and_content: bam file, aligned reads generated by data processing steps
Supplementary_files_format_and_content: bed file, peak calls using Macs 2.1.1 -q 0.05 --broad
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| Submission date |
Sep 23, 2020 |
| Last update date |
Sep 24, 2020 |
| Contact name |
Colin Kern |
| Organization name |
UC San Diego
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| Street address |
9500 Gilman Dr
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
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| Platform ID |
GPL19005 |
| Series (2) |
| GSE158417 |
Comparative functional genome annotation of livestock species identifies core amniote regulatory features and avian enhancer versatility (DNase-Hypersensitivity) |
| GSE158430 |
Comparative functional genome annotation of livestock species identifies core amniote regulatory features and avian enhancer versatility |
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| Relations |
| BioSample |
SAMN16245434 |
| SRA |
SRX9176872 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4799703_DNaseSeq_Adipose_A_Peaks.bed.gz |
970.5 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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