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| Status |
Public on Sep 24, 2020 |
| Title |
H3K4me3 from UC Davis FAANG pig cerebellum rep P348 |
| Sample type |
SRA |
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| Source name |
Cerebellum
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| Organism |
Sus scrofa |
| Characteristics |
chip antibody: H3K4me3 (Diagenode,#C01010059, lot A17723-0041D)
tissue: cerebellum
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq experiments were performed on frozen tissue using the iDeal ChIP-seq kit for Histones (Diagenode Cat.#C01010059, Denville, NJ) according to the manufacturer’s protocol except for the following changes. 20-30 mg of frozen tissue was powdered using liquid nitrogen in pre-chilled mortar. Cross-linking was performed with 1% formaldehyde which was diluted from 16% methanol-free formaldehyde (Thermo Scientific, Cat.#28906, Waltham, MA) for 8 minutes and quenched with glycine for 10 minutes. Nuclei were harvested by centrifugation at 2000g for 5 minutes and resuspended in iS1 buffer for incubation on ice for 30 minutes. Chromatin was sheared using the Covaris E220 between 6-12 minutes depending on the tissue. For immunoprecipitation experiments, about 1000 ng of sheared chromatin (estimated from DNA extraction) was used as input after which the kit protocol was followed with 1 μg (histone modifications) or 1.5 μg (CTCF) of antibody. The following antibodies used were from Diagenode: H3K4me3 (in kit), H3K27me3 (#C15410069), H3K27ac (#C15410174), H3K4me1 (#C15410037), and CTCF (#15410210). An input (no antibody) was performed for each sample.
NEBNext Ultra DNA library prep kit for Illumina libraries (New England Biolabs #E7645L, Ipswich, MA) was used for library construction, selecting for 150-200 bp (H3K4me3, H3K27ac, CTCF) or 200-400 bp (H3K27me3, H3K4me1) insert fragment sizes using Ampure beads (Beckman Coulter #A63881). Libraries were sequenced on Illumina’s HiSeq 4000 with single-end 50 bp reads.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
SAMEA4454609
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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, Sscrofa11.2, and ARS-UCD1.2 genomes
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,susScr11,bosTau9
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 0.01
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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 |
GPL22475 |
| Series (2) |
| GSE158429 |
Comparative functional genome annotation of livestock species identifies core amniote regulatory features and avian enhancer versatility (H3K4me3 ChIP-Seq) |
| GSE158430 |
Comparative functional genome annotation of livestock species identifies core amniote regulatory features and avian enhancer versatility |
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| Relations |
| BioSample |
SAMN16245864 |
| SRA |
SRX9177273 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4800108_H3K4me3_Cerebellum_P348_Peaks.bed.gz |
1.0 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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