ChIP-seq of Atlantic salmon (Salmo salar) gill exposed to varying winter length
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina NovaSeq 6000
ORGANISM(S): Salmo salar
SUBMITTER: Gareth Gillard
PROVIDER: E-MTAB-11091 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:The anadromous Atlantic salmon undergo preparatory physiological transformations before seawater entry, referred to as smoltification. Little is known about the photoperiod-influence and genome regulatory processes driving smoltification such as the large scale changes in lipid metabolism and energy homeostasis in the developing smolt liver. To shed light on this, we performed a smoltification trial using contrasting photoperiod regimes and generate a transcriptome data from livers throughout smoltification and after seawater transfer. In this experiment two groups of Atlantic salmon were reared for a total of 46 weeks from the parr stage, through smoltification, and seawater transfer. After 21 week from first feeding, the experiment group was given artificial winter photoperiod (8 hours light, 16 hours dark) for 8 weeks to induce smoltification before returning to constant light. The second control group received constant light throughout the experiment. Liver tissue was sampled from individuals first at week 1, 21 weeks after first feeding, then again at week 10, after the winter period, at week 19, after the expected smoltification time, and lastly at week 25, after transfer to seawater.
2022-05-16 | E-MTAB-11746 | biostudies-arrayexpress
Project description:The anadromous Atlantic salmon undergo preparatory physiological transformations before seawater entry, referred to as smoltification. Little is known about the photoperiod-influence and genome regulatory processes driving smoltification such as the large scale changes in lipid metabolism and energy homeostasis in the developing smolt liver. To shed light on this, we performed a smoltification trial using contrasting photoperiod regimes and generate ATAC-seq data from livers throughout smoltification and after seawater transfer to assess the differences in chromatin accessibility. In this experiment Atlantic salmon were reared for a total of 46 weeks from the parr stage, through smoltification, and seawater transfer. After 21 week from first feeding, the group was given artificial winter photoperiod (8 hours light, 16 hours dark) for 8 weeks to induce smoltification before returning to constant light. Liver tissue was sampled from individuals first at week 1, 21 weeks after first feeding, then again at week 10, after the winter period, at week 19, after the expected smoltification time, and lastly at week 25, after transfer to seawater.
2024-02-02 | E-MTAB-13743 | biostudies-arrayexpress
Project description:This experiment is intended to provide information about transcriptional changes in the gill of Atlantic salmon during smoltification, in comparison with juvenile salmon not given the appropriate photoperiodic stimuli. Also, transcriptional changes due to osmotic stress (24H salt water challenged) will be recorded. This to better understand the transformation of the gill from a fresh water-type to a salt water-type, and possibly identify novel and important genes that are dependent upon a specific photoperiodic history for their expression. Additionally the data can be used to observe the shift in salt water response as the juvenile salmon goes through smoltification. Experimental workflow: All fish started on 24H light (LL), after one week, half of the fish were moved to short photoperiod (8:16, SP). The rest remained on LL throughout. After eight weeks, half of the fish on short photoperiod were moved back onto 24H light (SPLL). Remaining fish continued under 8:16. After another eight weeks the experiment was ended. Fish were sampled on days 0, 32, 53, 68, 89 and 110. On each sampling occasion fish were sampled directly from fresh water (FW), and from a 24H salt water (SW) stay, transferred the previous day. Weight and length was noted. Gill tissue was the taken and placed in RNAlater. Additionally plasma for measuring hypoosmoregulatory capacity was taken.
2019-09-12 | E-MTAB-8276 | biostudies-arrayexpress
Project description:Atlantic salmon (Salmo salar) pre-smolt optic tectum, saccus vasculosus and gill tissues were collected over a light:dark (LD, 8:16) cycle, constant light (LL) and constant dark (DD) time series at a four hour resolution Total RNA was extracted, RNA quality was assessed using BIORAD Experion, then submitted to a bespoke clock gene NanoString CodeSet
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Project description:One hundred ninety wildtype male C57BL/6J mice age 7-10 weeks were purchased from Jackson Laboratory and entrained to a 12:12 light:dark cycle for 2 weeks. Mice were placed in light-tight boxes on a 12:12 LD cycle for 4 weeks, then released into constant darkness. Starting 30 hours after entry into DD (CT18), tissues from 5 (skeletal muscle) or 10 (liver or SCN) wildtype mice were collected every 4 hours for 48 hours, for a total of 12 timepoints. At timepoints 34 through 58 hours in DD, tissues from age-matched male C57BL/6J Clock/Clock homozygous mutant mice that had been treated with the same light entrainment protocol as the wildtype were collected. Tissues were collected from 5 Clock/Clock mutants at each timepoint except for 34 and 46 hours after the onset of DD, when tissues from 10 Clock/Clock mice were collected and run as independent replicates. Mice were sacrificed by cervical dislocation, and the optic nerves were severed in complete darkness; brain dissection was performed using illumination from an infrared viewer (FJW Industries, Palatine, IL). SCNs were dissected out, pooled at a density of 5 per tube in 100 ul RNAlater (Ambion, Austin, TX), frozen on dry ice, and stored at â80 degrees C until use. Keywords: SuperSeries This reference Series links data in the following related Series: GSE3746 Circadian skeletal muscle_wt and Clock mutants GSE3748 Circadian liver_wt and Clock mutants
2010-06-12 | E-GEOD-3751 | biostudies-arrayexpress
Project description:One hundred ninety wildtype male C57BL/6J mice age 7-10 weeks were purchased from Jackson Laboratory and entrained to a 12:12 light:dark cycle for 2 weeks. Mice were placed in light-tight boxes on a 12:12 LD cycle for 4 weeks, then released into constant darkness. Starting 30 hours after entry into DD (CT18), the left leg muscle from 5 wildtype mice, and the right leg muscle from the same wildtype mice were collected every 4 hours for 48 hours, for a total of 12 timepoints. Total RNA from each side (left or right) were separately pooled to make a single sample for amplification and hybridization. Therefore, duplicate arrays (from left and right side) were performed at each time point. At timepoints 34 through 58 hours in DD, tissues from age-matched male C57BL/6J Clock/Clock homozygous mutant mice that had been treated with the same light entrainment protocol as the wildtype were collected. Tissues were collected from 5 Clock/Clock mutants at each timepoint except for 34 and 46 hours after the onset of DD, when tissues from 10 Clock/Clock mice were collected. As for the wildtype mice, right and left sides were collected, prepared, amplified, and hybridized in separate pools. Mice were sacrificed by cervical dislocation, and the optic nerves were severed in complete darkness; brain dissection was performed using illumination from an infrared viewer (FJW Industries, Palatine, IL). SCNs were dissected out, pooled at a density of 5 per tube in 100 ?l RNAlater (Ambion, Austin, TX), frozen on dry ice, and stored at â80?C until use. duplicates consisted of pools from independent mice
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