|
| Status |
Public on Jul 21, 2022 |
| Title |
Blood, non-pregnant buffalo 1 |
| Sample type |
SRA |
| |
|
| Source name |
blood
|
| Organism |
Bubalus bubalis |
| Characteristics |
tissue: blood
group: non-pregnant
breed: Jianghuai
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
circle RNA
c-buffalo-1
|
| Data processing |
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp.
We used HISAT2 (http://daehwankimlab.github.io/hisat2) to map reads to the reference Bubalus bubalis (Version: GRCh38).
Mapped reads of IP and input libraries were provided for R package exomePeak (https://bioconductor.org/packages/exomePeak), which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software (http://www.igv.org). HOMER (http://homer.ucsd.edu/homer/motif) were used for de novo motif finding followed by localization of the motif with respect to peak summit. Called peaks were annotated by intersection with gene architecture using R package ChIPseeker (https://bioconductor.org/packages/ChIPseeker).
Then StringTie (https://ccb.jhu.edu/software/stringtie) was used to perform expression level for all mRNAs from input libraries by calculating FPKM (total exon fragments /mapped reads (millions) × exon length (kB)).
The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and p value < 0.05 by R package edgeR (https://bioconductor.org/packages/edgeR).
Assembly: Version GRCh38.p10
Supplementary files format and content: count, srpbm
|
| |
|
| Submission date |
Jul 18, 2022 |
| Last update date |
Jul 21, 2022 |
| Contact name |
Zubing Cao |
| E-mail(s) |
[email protected]
|
| Organization name |
Anhui Agricultural University
|
| Department |
Animal Science
|
| Street address |
130 changjiang west road
|
| City |
Hefei |
| State/province |
Anhui |
| ZIP/Postal code |
230036 |
| Country |
China |
| |
|
| Platform ID |
GPL29600 |
| Series (1) |
| GSE208385 |
Expression Profiling of Circular RNAs in Early Pregnant Jianghuai Buffaloes |
|
| Relations |
| BioSample |
SAMN29794775 |
| SRA |
SRX16315082 |
