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| Status |
Public on Dec 26, 2018 |
| Title |
morula |
| Sample type |
SRA |
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| Source name |
morula stage embryo
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| Organism |
Bubalus bubalis |
| Characteristics |
developmental stage: morula
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| Extracted molecule |
total RNA |
| Extraction protocol |
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Description |
T07
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| Data processing |
Illumina Hiseq Xten platform and paired-end reads were generated
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v4-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq Xten platform and paired-end reads were generated.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
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. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
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| Submission date |
Dec 27, 2017 |
| Last update date |
Dec 26, 2018 |
| Contact name |
F.M Chen |
| E-mail(s) |
gxchenfumei@163.com
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| Phone |
15296575023
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| Organization name |
Guangxi University
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| Department |
Animal Science and Technology
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| Lab |
State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources
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| Street address |
No. 100, East University Road
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| City |
Nanning |
| State/province |
GuangXi |
| ZIP/Postal code |
530004 |
| Country |
China |
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| Platform ID |
GPL24447 |
| Series (1) |
| GSE108578 |
Maternally Expressed Genes Identified by Single-cell RNA Sequencing in Pre-implantation Development of Buffalo Parthenogenesis |
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| Relations |
| BioSample |
SAMN08271821 |
| SRA |
SRX3517698 |
| 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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