title: FT-3-PC-a
organism: Salmo salar
description: Protocols: Four fish (Atlantic salmon, approx. 7 months old, 26-28 g) were killed with a sharp blow to the head. Liver and brain were removed, washed with PBS and perfused to remove as much blood as possible. Small pieces of tissue was either placed directly into cold lysis buffer (fresh tissue) or frozen in cryotubes placed on dry ice (slow frozen) Fresh and slow frozen tissues (50 mg) followed the omni-ATAC protocol for frozen tissues (1). The nuclei were counted on an automated cell counter (TC20 BioRad, range 4-6 um) and assessed under microscope. 50 000 nuclei followed transposition for 30 minutes at 37 °C, in a shaker at 200 rpm. The samples were subsequently purified with the MinElute PCR purification kit (Qiagen) and eluted in 12 μl of Elution Buffer. (1) Corces MR, Trevino AE, Hamilton EG, Greenside PG, Sinnott-Armstrong NA, Vesuna S, et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods. 2017 Oct;14(10):959-962. qPCR was used to determine the appropriate number of PCR cycles for library preparation by finding the cycle number that is 1/4th of the maximum fluorescent intensity based on the protocol of Buenrostro et al. (2). The total number of cycles determined for library preparation ranged from 8 - 10 cycles. Libraries were made with Nextera DNA Library Prep Kit (Illumina) and short fragments (primer dimers) or fragments longer than 1000 bp were removed using AMPure XP beads (Beckman Coulter, Inc.) purification. The fragment length distributions were determined on a 2100 Bioanalyzer using the High Sensitivity Kit (Agilent) and the library concentration was determined with Qbit HS Kit (Thermo Scientific) before submitting the samples to The Norwegian Sequencing Centre (NSC).
attributes.tag: ENA-FIRST-PUBLIC
attributes.value: 2020-05-08T04:03:57Z
attributes.tag: ENA-LAST-UPDATE
attributes.value: 2020-04-28T16:58:34Z
attributes.tag: External Id
attributes.value: SAMEA6806949
attributes.tag: INSDC center name
attributes.value: Center for Integrative Genetics, Department of Animal and Aquacultural Sciences Faculty of Biosciences, Norwegian University of Life Sciences
attributes.tag: INSDC first public
attributes.value: 2020-05-08T04:03:57Z
attributes.tag: INSDC last update
attributes.value: 2020-04-28T16:58:34Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-9001:FT-3-PC-a
attributes.tag: age
attributes.value: 7
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: common name
attributes.value: Atlantic salmon
attributes.tag: developmental stage
attributes.value: adult
attributes.tag: individual
attributes.value: 3
attributes.tag: organism part
attributes.value: pyloric caeca
attributes.tag: sample name
attributes.value: E-MTAB-9001:FT-3-PC-a
attributes.tag: scientific_name
attributes.value: Salmo salar
attributes.tag: sex
attributes.value: female
attributes.tag: specimen with known storage state
attributes.value: fresh
attributes.tag: strain
attributes.value: Aquagen