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| Status |
Public on Feb 08, 2022 |
| Title |
CH_12h_IP_1 |
| Sample type |
SRA |
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| Source name |
liver tissue of duckling liver collected at 12h after being infected by virulent DHAV-1 CH (CH)
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| Organism |
Anas platyrhynchos |
| Characteristics |
infection: virulent DHAV-1 CH (CH)
time: 12h after being infected
tissue: liver
rip antibody: m6A Antibody (Synaptic systems; catalog# 202003)
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| Treatment protocol |
After one week, the ducks were randomly divided into three groups of 15 and raised in separate isolators. The ducks in the first group received 0.40 ml of the DHAV-CH strain (107.88copies/ml) via intramuscular injection, the ducks in the second group received 0.25 ml of the DHAV-CH60 strain (108.07cop-ies/ml) via intramuscular injection, and ducks in the last group were injected with 0.25 ml of 0.75% physiological normal saline (NS) as a negative control. Three ducklings from each group were killed at 12, 24, 36, 48, 60 and 72 hpi, and their livers and blood were collected
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| Growth protocol |
One-day-old Cherry Valley ducks were purchased from the poultry farm of Sichuan Agricultural University and were raised in isolators
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol Reagent (Ambion) following the manufacturer’s instructions, and mRNA were then purified by GenElute™ mRNA Miniprep Kit (sigma, MRN10).
The polyadenylated mRNAs isolated from total RNA using GenElute™ mRNA Miniprep Kit (sigma, MRN10) were fragmented into 100 nt length by using RNA Fragmentation buffer (0.1M Tris-HCL PH 7.0, 0.1M ZnCl2). Then, 50 and 100 ng fragmented mRNAs were incubated for 2 hours at 4 °C with 12.5 μg of anti-m6A antibody (sysy, 202003) in IP buffer (0.05M Tris-HCL pH 7.4, 0.375M NaCl, 0.5% Igepal CA-630). The mixture was then subjected to immunoprecipitation by incubation with Pierce™ ChIP-grade Protein A/G Magnetic Beads (Thermo, 26162) at 4 °C for 2 hours. After sufficient washing, m6A antibody-bound RNA was eluted from the beads with Elution buffer (1×IP buffer, 7mM m6A, RNase inhibitor), and then ethanol-precipitated. The eluted RNA was resuspended in H2O and used to generate the cDNA library according to RNA-Seq Library Preparation Kit for Transcriptome Discovery–Illumina Compatible, which was then sequenced using the HiSeq 2000 system (Illumina) according to the manufacturer’s instructions.
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| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
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| Data processing |
library strategy: m6A-seq
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniquely mapped reads were remained. One more reads with the same start and end position, only one is considered.
After reads were aligned onto the genome, we analysed the unique reads binding regions on genome using “ABLIRC” strategy.
Genome_build: PekingDuck_PBH1.5
Supplementary_files_format_and_content: tab-delimited text files include peak information for each group.
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| Submission date |
Dec 28, 2020 |
| Last update date |
Feb 08, 2022 |
| Contact name |
dong chen |
| Organization name |
ablife
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| Street address |
GaoXin 2nd Road
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| City |
wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430064 |
| Country |
China |
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| Platform ID |
GPL29169 |
| Series (1) |
| GSE163905 |
Transcriptomic analysis of the duckling liver mRNA methylome following infection by the virulent and attenuated Hepatitis A virus type 1 strains |
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| Relations |
| BioSample |
SAMN17169796 |
| SRA |
SRX9739542 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4990451_CH_12h_IP_1_peak_info.txt.gz |
480.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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