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| Status |
Public on Jun 06, 2024 |
| Title |
P291_10_10-PSA0 |
| Sample type |
RNA |
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| Source name |
Liver
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| Organism |
Gallus gallus |
| Characteristics |
tissue: Liver
treatment: 0% Pleurotus sapidus (PSA)
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| Treatment protocol |
The broilers were randomly assigned to three different groups (4 broilers/cage, 6 cages/group), with a similar mean initial body weight (38.1 ± 2.9 g; mean ± SD; N = 72) across the groups. The broilers were housed in 2.1 m2 cages with nipple drinkers and feed automates and had free access to feed and water. The floor was covered with hemp-based litter (Hemparada, HempFlax Group B.V., Oude Pekela, Netherlands) which allowed scratching, pecking and dustbathing and was exchanged two times per week during the first two weeks and every two days during the last three weeks of the trial. In addition, broilers were provided with perches in elevated position for resting and sleeping. Light regime followed a schedule of 24 h:0 h, 23 h:1 h, 22 h:2 h, 21 h:3 h, 20 h:4 h, 19 h:5 h (light:dark) at days 1, 2, 3, 4, 5, 6, and 18 h:6 h from day 7 onward and the light intensity was constantly 40 Lux, as recommended by the breeder. The room temperature decreased from 28-29°C on day one, measured at pen height, to 23-24°C on day 35. Infrared lamps (Albert Kerbl GmbH, Buchbach, Germany) were used as additional heat sources during the first 6 days to adjust the temperature at the cage floor to 34°C. Mean relative humidity was 60.0 ± 1.9%. The groups were fed three different nutrient adequate diets containing either 0% (group PSA-0), 2.5% (group PSA-2.5) or 5% (group PSA-5.0) P. sapidus mycelium in a three-phase feeding system (starter diet form day 1-10, grower diet from day 11-21, finisher diet from day 22-35). The composition of the three diets is shown in Table 1. The composition of the diets met the broiler’s requirements of nutrients and energy according to the breeder’s recommendations (Cobb-Vantress, 2022). Diets were provided in crumbled form during the first three days, and in pellet form (2 mm diameter) from day 3 until the end of the trial. On days 1, 10, 21 and 35 body weight (individually) and feed intake (per cage) were determined. The feed:gain ratio was calculated from feed intake and body weight gains on cage basis.
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| Growth protocol |
The five-week feeding trial with 72 male, 1-day-old broiler chickens (Cobb 500, Cobb-Vantress, Weidemar, Germany) was approved by the Animal Welfare Officer of the Justus Liebig University Giessen (approval no.: JLU 843_M). All experimental procedures described followed established guidelines for laboratory animals care and handling.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Aliquots from the liver (20-30 mg) were used for total RNA extraction using TRIzol reagent (Invitrogen, Karlsruhe, Germany) according to the manufacturer´s protocol. Total RNA was analyzed for quantity and quality using an Infinite 200M microplate reader with a NanoQuant plate (both from Tecan, Mainz, Germany). The mean RNA concentration and A260/A280 ratio of all total RNA samples was 385 ± 64 µg/mL and 1.91 ± 0.02 (N = 36 or n = 12/group) for liver.
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| Label |
Biotin
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| Label protocol |
200 ng of total RNA was used to generate double-stranded cDNA. 12 µg of subsequently synthesized cRNA were purified and reverse transcribed into single-stranded (ss) cDNA, whereat unnatural dUTP residues were incorporated. Purified ss cDNA was fragmented using a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) followed by a terminal labeling with biotin.
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| Hybridization protocol |
3.8 µg of fragmented and labeled ss cDNA were hybridized to Applied Biosystems GeneChip Clariom S rat arrays for 16 h at 45°C and 60 rpm in an Applied Biosystems GeneChip hybridization oven 640.
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| Scan protocol |
Hybridized arrays were washed and stained in an Applied Biosystems GeneChip Fluidics Station FS450, and the fluorescent signals were measured with an Applied Biosystems GeneChip Scanner 3000 7G System. Fluidics and scan functions were controlled by the Applied Biosystems GeneChip Command Console v4.3.3 software.
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| Description |
PSA-0
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| Data processing |
Summarized probe set signals in log2 scale were calculated by using the GCCN-SST-RMA algorithm with the Applied Biosystems GeneChip Expression Console v1.4 Software. After exporting into Microsoft Excel, average signal values, comparison fold changes (FC) and significance P-values were calculated.
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| Submission date |
Jun 05, 2024 |
| Last update date |
Jun 06, 2024 |
| Contact name |
Robert Ringseis |
| E-mail(s) |
robert.ringseis@ernaehrung.uni-giessen.de
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| Organization name |
JLU Gießen
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| Department |
Institute of Animal Nutrition and Nutrition Physiology
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| Street address |
Heinrich-Buff-Ring 26-32
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| City |
Gießen |
| ZIP/Postal code |
35390 |
| Country |
Germany |
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| Platform ID |
GPL18368 |
| Series (1) |
| GSE269154 |
Effects of a biotechnologically produced Pleurotus sapidus mycelium on gut microbiome, liver transcriptome and plasma metabolome of broilers |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSM8307158_P291_10_10-PSA0.CEL.gz |
5.3 Mb |
(ftp)(http) |
CEL |
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