characteristics: ERC000011
characteristics: ENA-CHECKLIST
characteristics: 2022-10-01T16:26:11Z
characteristics: ENA-FIRST-PUBLIC
characteristics: 2022-10-01T16:26:11Z
characteristics: ENA-LAST-UPDATE
characteristics: SAMEA110114526
characteristics: External Id
characteristics: IOWA STATE UNIVERSITY
characteristics: INSDC center name
characteristics: 2022-10-01T16:26:11Z
characteristics: INSDC first public
characteristics: 2022-10-01T16:26:11Z
characteristics: INSDC last update
characteristics: public
characteristics: INSDC status
characteristics: ERS12213342
characteristics: SRA accession
characteristics: E-MTAB-11815:Sample 44
characteristics: Submitter Id
characteristics: 14
characteristics: month
characteristics: age
characteristics: Hereford
characteristics: breed
characteristics: ArrayExpress
characteristics: broker name
characteristics: cattle
characteristics: common name
characteristics: Protocols: Adult tissue collections. Procedures for tissue collection followed the Animal Care and Use protocol (#18464) approved by the Institutional Animal Care and Use Committee (IACUC), University of California, Davis (UCD). Four cattle (2 males and 2 females) were slaughtered at UCD using captive bolt under USDA inspection at 14 months old and were intact male and female Line 1 Herefords that had the same sire, provided by Fort Keogh Livestock and Range Research Lab (Tixier-Boichard et al. 2021). Tissue samples were flash frozen in liquid nitrogen then stored at -80 °C until further assay processing. Fetal tissue collections. Fetal sample collection and tissue collection were approved by the Institutional Animal Care and Use Committee (IACUC), University of Idaho (2017-67). Four pregnant females Line 1 Herefords were slaughtered at UI meats lab using captive bolt under USDA inspection. Animals were provided by Fort Keogh Livestock and Range Research Lab (Tixier-Boichard et al. 2021). Tissue samples were flash frozen in liquid nitrogen then stored at -80 °C until further assay processing. Adult tissue collections. Procedures for tissue collection followed the Animal Care and Use protocol (#18464) approved by the Institutional Animal Care and Use Committee (IACUC), University of California, Davis (UCD). Four cattle (2 males and 2 females) were slaughtered at UCD using captive bolt under USDA inspection at 14 months old and were intact male and female Line 1 Herefords that had the same sire, provided by Fort Keogh Livestock and Range Research Lab (Tixier-Boichard et al. 2021). Tissue samples were flash frozen in liquid nitrogen then stored at -80 °C until further assay processing. Fetal tissue collections. Fetal sample collection and tissue collection were approved by the Institutional Animal Care and Use Committee (IACUC), University of Idaho (2017-67). Four pregnant females Line 1 Herefords were slaughtered at UI meats lab using captive bolt under USDA inspection. Animals were provided by Fort Keogh Livestock and Range Research Lab (Tixier-Boichard et al. 2021). Tissue samples were flash frozen in liquid nitrogen then stored at -80 °C until further assay processing. Frozen tissue samples (Additional file18) were pulverized under liquid nitrogen using mortar and pestle. Permeabilized nuclei were obtained by resuspending pulverized tissue (5-15 mg) in 250 µL Nuclear Permeabilization Buffer [0.2% IGEPAL-CA630 (I8896, Sigma), 1 mM DTT (D9779, Sigma), Protease inhibitor (05056489001, Roche), and 5% BSA (A7906, Sigma) in PBS (10010-23, Thermo Fisher Scientific)], and incubating for 10 min on a rotator at 4°C. Nuclei were then pelleted by centrifugation for 5 min at 500 xg at 4°C. The pellet was resuspended in 25 µL ice-cold Tagmentation Buffer [33 mM Tris-acetate (pH = 7.8) (BP-152, Thermo Fisher Scientific), 66 mM K-acetate (P5708, Sigma), 11 mM Mg-acetate (M2545, Sigma), 16% DMF (DX1730, EMD Millipore) in molecular biology grade water (46000-CM, Corning)]. An aliquot was then taken and counted by hemocytometer to determine nuclei concentration. Approximately 50,000 nuclei were resuspended in 20 µL ice-cold Tagmentation Buffer and incubated with 1 µL Tagmentation enzyme (FC-121-1030; Illumina) at 37 °C for 30 min with shaking at 500 rpm. The tagmentated DNA was purified using MinElute PCR purification kit (28004, Qiagen). The libraries were amplified using NEBNext High-Fidelity 2X PCR Master Mix (M0541, NEB) with primer extension at 72°C for 5 min, denaturation at 98°C for 30 s, followed by 8 cycles of denaturation at 98°C for 10 s, annealing at 63°C for 30 s and extension at 72°C for 60 s. Amplified libraries were then purified using MinElute PCR purification kit (28004, Qiagen), and two size selection steps were performed using SPRIselect bead (B23317, Beckman Coulter) at 0.55X and 1.5X bead-to-sample volume ratios, respectively. ATAC-seq libraries were sequenced on an Illumina Nextseq 500 platform using Nextra V2 sequencing chemistry to generate 2 × 75 paired-end reads.
characteristics: description
characteristics: adult
characteristics: developmental stage
characteristics: wild type genotype
characteristics: genotype
characteristics: Bos taurus
characteristics: organism
characteristics: Bos taurus
characteristics: organism
characteristics: ruminant reticulum
characteristics: organism part
characteristics: Bos taurus
characteristics: scientific_name
characteristics: male
characteristics: sex
characteristics: Sample 44
characteristics: title