|
| Status |
Public on Jul 03, 2020 |
| Title |
Macheng3 |
| Sample type |
SRA |
| |
|
| Source name |
Ovarian follicle
|
| Organism |
Capra hircus |
| Characteristics |
breed: Macheng black
tissue: ovarian follicle
treated: Each of three Macheng black goat exhibited normal estrous cycles were treated with 1000 IU PMSG and 500 IU hCG
|
| Extracted molecule |
total RNA |
| Extraction protocol |
A total amount of 5 μg RNA per sample was isolated from each individual sample using TRIzol reagent (Invitrogen, USA). Purity and quantity of total RNA were measured by using Nanodrop equipment. Ribosomal RNAs were depleted using Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
MC4_1
|
| Data processing |
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat2.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene, considering the effect of sequencing depth and gene length for the reads count at the same time.
Genome_build: ASM170441v1 ftp://ftp.ncbi.nlm.nih.gov/genomes/Capra_hircus/Assembled_chromosomes/seq/
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Jul 03, 2017 |
| Last update date |
Jul 03, 2020 |
| Contact name |
Hu Tao |
| E-mail(s) |
woshiap@hotmail.com
|
| Phone |
+8602787680959
|
| Organization name |
Hubei Academy of Agricultural Sciences
|
| Street address |
Shizishan street
|
| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430064 |
| Country |
China |
| |
|
| Platform ID |
GPL22146 |
| Series (1) |
| GSE100773 |
Systematic identification of Circular RNAs in pre-ovulatory ovarian follicles of goats |
|
| Relations |
| BioSample |
SAMN07313084 |
| SRA |
SRX2981075 |
