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| Status |
Public on Nov 01, 2023 |
| Title |
LPP1_RIP |
| Sample type |
SRA |
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| Source name |
ovary
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| Organism |
Gallus gallus |
| Characteristics |
tissue: ovary
breed: Wuhua yellow-feathered chicken
developmental stage: after sexual maturity
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
The total RNA was isolated from each ovary sample using the TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. The concentration and purity of the RNA were measured using the NanoDrop 2000 (NanoDrop, Wilmington, DE, USA).
The mRNA was enriched from the total RNA using the Dynabeads Oligo (dT) and then fragmented. The fragmented RNAs were then divided into two parts, one for isolation of m6A enriched mRNA and the other used for RNA-seq as the input background. The former part of fragmented RNAs was incubated with the m6A-Dynabeads at room temperature for 1 hour to allow them binding to the beads. Eluted m6A-containing fragments (IP) and untreated input control fragments (the latter part) were then concentrated to generate the final cDNA library.
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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 |
Trimmomatic (v 0.39) software to obtain clean reads
clean reads were then aligned to the chicken reference genome GRCg7b using the HISAT2 (v 2.1.0)
MeTDiff (v 1.1.0) was used to call the peaks of m6A modification in each group with the input data as control (P value < = 0.05, fold change > = 0.05)
annotation of the identified m6A peaks in each group and differential m6A peaks between groups was conducted by ChIPseeker (v 1.12.1)
Assembly: GRCg7b
Supplementary files format and content: txt format,BLP.m6A_site
Supplementary files format and content: txt format, LPP.m6A_site
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| Submission date |
Jul 31, 2023 |
| Last update date |
Nov 01, 2023 |
| Contact name |
Congjun Jia |
| E-mail(s) |
dkjcj@nwafu.edu.cn
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| Organization name |
Guangdong Meizhou Vocational and Technical College
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| Street address |
xueyuan road
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| City |
Meizhou |
| ZIP/Postal code |
514011 |
| Country |
China |
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| Platform ID |
GPL24517 |
| Series (1) |
| GSE239644 |
Transcriptome-wide m6A methylation of Wuhua yellow-feathered chicken ovary revealed potential molecular mechanisms underlying the low egg performance |
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| Relations |
| BioSample |
SAMN36780238 |
| SRA |
SRX21205826 |
| 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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