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| Status |
Public on May 09, 2019 |
| Title |
PE1 |
| Sample type |
SRA |
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| Source name |
pre-receptive endometrium
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| Organism |
Capra hircus |
| Characteristics |
breed: Xinong Saanen
tissue: endometrium
endometrium status: pre-receptive
gestational day: at gestational day 5
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| Treatment protocol |
The first day of mating was considered to be Day 0 of pregnancy. Gestational days 5 and 15 were important time points for the embryo implantation in goats. The experimental goats were observed 3 times daily to ascertained estrous sign and mated naturally twice in estrus. And then the goats were euthanized when the goats lost consciousness caused by intravenous injection of barbiturate (30mg/kg) at gestational day 5 (pre-receptive endometrium) and gestational day 15 (receptive endometrium).
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| Growth protocol |
A total of 20 healthy 24-month-old multiparous dairy goats (Xinong Saanen) were induced to estrous synchronization for this study.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the six samples using the TRIzol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The quantity and purity of total RNA were analyzed with Bioanalyzer 2100 (Agilent, CA, USA) and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number> 7.0. At the same time, a new library was constructed by mixing all the six total RNAs with equal amount, and it was used to decrease false positive dentification of circRNA. Approximately 10 ug of total RNA representing a specic adipose type was used to deplete ribosomal RNA according to the manuscript of the Epicentre Ribo-Zero Gold Kit (Illumina, San Diego, USA). Following purication, the RNAs were treated with RNase R for 20 min at 37 ℃ (Epicentre Technologies, Madison, WI), and then the poly (A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature.
Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the RNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 250 bp (±50 bp). Paired-end sequencing on an Illumina Hiseq2500 (LC Sceiences, USA) following the vendor's recommended protocol.
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
circRNA
Sample name: GE258_C_count
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| Data processing |
Prior to reference genome mapping, the raw data (raw reads) were processed to remove low quality reads.
Firstly the RNA-seq clean reaps (valid data) were mapped to the goat reference genome (http://www.ncbi.nlm.nih.gov/genome/?term=goat) using a publicly available program Tophat 2 (http://ccb.jhu.edu/software/tophat/index.shtml).
Second, TopHat-Fusion (http://ccb.jhu.edu/software/tophat/fusion_index.shtml) is an enhanced version of TopHat with the ability to align reads across fusion points, which results from the breakage and re-joining of two different chromosomes, or from rearrangements within a chromosome. The reads, unmapped with TopHat but mapped with TopHat-Fusion on the same chromosome in a noncolinear ordering (back-spliced ordering), were extracted as candidate back-spliced junction reads.
Last, the circRNAs were identified from back-spliced junction reads based on structural and splice sites characters of circRNAs: (1) the two ends of splice sites must be GU/AG, (2) mismatch≤ 2, (3) back-splice junction reads ≥ 1, (4) if there were more than 2 splice sites, they were on the same chromosome and not too wide apart from each other more than 100 kb.
The aligned read files were processed by Cufflinks, which uses the normalized RNA-seq fragement counts to measure the relative abundances of the transcripts [43], the unit of the measurement is Fragment Per Kilobase of exon per Million fragments mapped (FPKM
Genome_build: http://www.ncbi.nlm.nih.gov/genome/?term=goat
Supplementary_files_format_and_content: excel files with circRNA counts, fpkm (S2 File. circRNA expression in goat endometrium. (XLS).xlsx) and other analysis.
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| Submission date |
Aug 09, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Lei Zhang |
| E-mail(s) |
zhanglei07dongke@163.com
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| Phone |
+8615029965499
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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 |
No.22 Xinong Road, Yangling District
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| City |
Yangling District |
| State/province |
Province, State or Region |
| ZIP/Postal code |
712100 |
| Country |
China |
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| Platform ID |
GPL19149 |
| Series (1) |
| GSE85384 |
Analyses of circRNA profiling during the development from pre-receptive to receptive phases in goat endometrium |
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| Relations |
| BioSample |
SAMN05552902 |
| SRA |
SRX2010181 |
| 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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