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| Status |
Public on Apr 04, 2022 |
| Title |
Over3720_RNAseq Over37202 |
| Sample type |
SRA |
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| Source name |
Ear marginal tissue
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| Organism |
Capra hircus |
| Characteristics |
tissue: Ear marginal tissue
cell type: GFFs cells
genotype: Overexpress
treatment: transfected with pcDNA3.1(+)-lncRNA3720 using Lipofectamine 3000
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from in vitro fertilization (IVF) goat embryos at the two-cell and eight-cell stages and somatic cell nuclear transfer(SCNT) 8-cell embyos. We used the Qubit® RNA Assay Kit and Qubit® 2.0 Fluorometer (Life Technologies, CA, USA) to detect RNA concentration. RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA) was employed for RNA integrity evaluation, and SMART-SeqTM v4 UltraTM Low RNA Kit for Sequencing (Clontech) was used to obtain the amplified cDNA in accordance with the manufacturer’s instructions.
The Covaris system sheared the cDNA samples prior to library preparation. Moreover, sequencing libraries (IVF-2c IVF-8c and SCNT-8c) were generated using NEBNext® UltraTM DNA Library Prep Kit for Illumina® (NEB, USA) in accordance with the manufacturer’s instructions, and index codes were added to attribute sequences to each sample. Clustering of the index-coded samples was conducted on a cBot Closter Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) in accordance with the manufacturer’s instructions. After cluster generation, library preparations were sequenced on an Illumina HiseqTM 2500 platform, and 125-bp paired-end reads were generated.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
TopHat (version 2.0.12) was used to map the paired-end clean reads to the reference goat genome and to build the index of the reference genome with Bowtie (Version 2.2.3)
Cufflinks (version 2.1.1) was used to assemble the mapped reads from TopHat2 (version 2.0.12)
Cuffdiff was used to calculate FPKM of the lncRNAs and coding genes in all libraries
Assembly: ASM170441v1
Supplementary files format and content: gtf were generated by cufflinks. FPKM were caculated by cuffdiff.
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| Submission date |
Apr 01, 2022 |
| Last update date |
Apr 07, 2022 |
| Contact name |
Miaomiao Jin |
| E-mail(s) |
liujun2013@nwsuaf.edu.cn
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| Phone |
18437958771
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| Organization name |
northwest A&F university
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| Street address |
yangling
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| City |
xian |
| ZIP/Postal code |
712100 |
| Country |
China |
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| Platform ID |
GPL19149 |
| Series (1) |
| GSE199933 |
Single-cell RNA-seq of goat early embyos and GFFs cells |
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| Relations |
| BioSample |
SAMN27177131 |
| SRA |
SRX14711855 |
| 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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