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| Status |
Public on Sep 24, 2020 |
| Title |
ATAC-seq from UC Davis FAANG pig cerebral cortex rep P350 |
| Sample type |
SRA |
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| Source name |
Cortex
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| Organism |
Sus scrofa |
| Characteristics |
tissue: cerebral cortex
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cryopreserved nuclei prepared from fresh tissue were slowly thawed on ice, centrifuged for 5 minutes at 500 rcf, and resuspended in cold PBS. Nuclei were then washed once with cold ATAC-seq cell lysis buffer and resuspended with cold PBS for counting on a hemocytometer. Approximately 200K cryopreserved nuclei were centrifuged, supernatant aspirated, then treated with 50μl transposition mix (25μl TD buffer,2.5 μl TDE1, 22.5 μl ddH2O) for 1 hour at 37°C and 300 rpm. DNA was purified using the MinElute PCR purification kit (Qiagen, #28004, Germantown, MD) and diluted with 10μl EB buffer. DNA was amplified with primers whose detailed descriptions are found in Buenrostro et al. (2013).
Libraries were purified using the MinElute PCR purification kit and run on Agilent Bioanalyzer (Agilent, Santa Clara, CA) for quality traces. Size-selection on libraries for 150-250bp fragments was performed on PippinHT system (Sage Science, Beverly, MA). Libraries were sequenced on Illumina’s NextSeq with PE 40bp reads.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
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| Description |
SAMEA4454574
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| Data processing |
Reads were trimmed with Trim Galore! 0.4.5 with the -atac argument
Reads were aligned with BWA mem 0.7.17 to the 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: 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 0.05 --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 |
GPL29175 |
| Series (2) |
| GSE158414 |
Comparative functional genome annotation of livestock species identifies core amniote regulatory features and avian enhancer versatility (ATAC-Seq) |
| GSE158430 |
Comparative functional genome annotation of livestock species identifies core amniote regulatory features and avian enhancer versatility |
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| Relations |
| BioSample |
SAMN16245393 |
| SRA |
SRX9176785 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4799616_ATAC_Cortex_P350_Peaks.bed.gz |
4.0 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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