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| Status |
Public on Dec 16, 2020 |
| Title |
mRNA-liver-FE-offspring broiler3 [B1d_FOLATE_3] |
| Sample type |
SRA |
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| Source name |
liver sample from offspring broilers whose father fed with diet with extra 5mg/kg folate
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| Organism |
Gallus gallus |
| Characteristics |
breed/age: 1-day-old offspring broilers
treatment: 5 mg/kg folate group
tissue: liver
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| Growth protocol |
Based on a single factor experimental design, 80 1-day-old Arbor Acres breeder roosters with similar genetic background and similar body weight (Beijing Arbor Acres Poultry Breeding Co. Ltd. China. P. R) were randomly assigned to 2 treatments with each 5 replicates and 8 birds per replicate. The breeder roosters from each treatment were fed with a standard diet mainly consisting of corn and soybean meal, with the only difference between treatments being the concentration of folic acid (0.25, 5.00 mg folic acid /kg feed, named as folic acid-control (FCON) and folic acid-excess (FE) groups, respectively). Meanwhile, 600 1-day-old Arbor Acres breeder hens with similar genetic background and similar body weight (Beijing Arbor Acres Poultry Breeding Co. Ltd. China. P. R) were kept in the same environment with roosters and fed with corn-soybean meals containing folic acid, then a total of 160 32-week-old breeder hens with similar body weight and met with the standard body weight were selected for the mating with the roosters. The photoperiod and the supplementation of feed were available according to the recommendations established by Aviagen Broiler Breeders Company, U.S.A. The water was available ad libitum. At 32 weeks of age, one rooster closing to the average weight of each replicate was selected and mated with 16 breeder hens by artificial insemination technology. The artificial insemination sustained for 3 weeks, and at 35 weeks of age, fertile eggs of 5 consecutive days from each replication of each treatment were collected and then artificially hatched. The new-born offspring broilers were grouped according to their paternal diets (five treatment with five replicates per treatment and 8 birds per replicate were randomly selected) and were then raised to 21 days by feeding with corn-soybean meals containing folic acid. The water, diet, and photoperiod were all available ad libitum.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA from 10 sperm samples and 10 liver samples of breeder roosters, and 40 liver samples of 1 day-old offspring broilers from folic acid-control and folic acid-excess groups were extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer’s procedures. The RNA amount and purity of each sample was quantified using NanoDrop ND-2000 (NanoDrop, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number > 7.00, and confirmed by electrophoresis with denaturing agarose gel. 4 RNA samples of four separate 1 day-old broilers’ livers from same replication were mixed equally together as a pooled RNA sample according to the purity and quantity of total RNA.
The mRNAs with poly (A) tails from 1 µM total RNA were isolated and purified with Dynabeads oligo (dT) 25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. The mRNAs were randomly segmented into small fragments using Magnesium RNA Fragmentation Module (NEB, USA) at 94 °C for 5 min. Using random hexamer primers, fragmented mRNAs were used as templates to synthesize first-stand cDNA. Following RNase I treatment, DNA polymerase I was used to synthesize second-strand cDNA. cDNA fragments which Purified by using AMPure XP beads were then ligated with sequencing adapters according to the protocol (Illumina, San Diego, USA). Following PCR amplification, target fragments were obtained by agarose gel electrophoresis to create the cDNA library. Then we performed paired-end sequencing (2 × 150 bp) on an Illumina Novaseq™ 6000 at LC-Bio (Hangzhou, China) following the vendor’s recommended protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
B1d_FOLATE_3_Clean_Data
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| Data processing |
Illumina Casava1.8 software used for basecalling.
Cutadapt software was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases
After removing the low quality bases and undetermined bases, we aligned reads to the reference genome using HISAT2 package, the mapped reads of each sample were assembled using StringTie
All transcriptomes from samples were merged to reconstruct a comprehensive transcriptome using gffcompare software. After the final transcriptome was generated, StringTie and ballgown was used to estimate the expression levels of all genes by calculating fragments per kilobase of transcript per million fragments mapped (FPKM).
Differentially expressed genes (DEGs) were selected with log2 (fold change) > 1 or log2 (fold change) less than -1 with statistical significance (q value < 0.01) by R package.
Genome_build: Gallus_gallus 5.0 (GCF_000002315.4)
Supplementary_files_format_and_content: tab-delimited text file include FPKM values and function annotations of each gene
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| Submission date |
Dec 15, 2020 |
| Last update date |
Dec 19, 2020 |
| Contact name |
Shengru Wu |
| E-mail(s) |
wushengru2013@163.com
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| Phone |
+8618700943648
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| Organization name |
Northwest A&F University
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| Department |
College of Animal Science and Technology
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| Street address |
22 St.XiNong
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| City |
Yangling |
| ZIP/Postal code |
712100 |
| Country |
China |
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| Platform ID |
GPL26853 |
| Series (1) |
| GSE163238 |
Nanopore sequencing reveals the roles of spermatozoal DNA N6-Methyladenine modification in mediating transgenerational lipid metabolism disorder induced by folic acid excessive consumption in chicken [RNA-seq] |
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| Relations |
| BioSample |
SAMN17084447 |
| SRA |
SRX9686543 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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