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| Status |
Public on Sep 08, 2023 |
| Title |
IVC2_11 |
| Sample type |
SRA |
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| Source name |
Embryo
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| Organism |
Bos taurus |
| Characteristics |
tissue: Embryo
cell line: Embryonic cells
cell type: Blastocyst
treatment: IVC2
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| Extracted molecule |
total RNA |
| Extraction protocol |
Prior to dissociation and single cell collection, embryos were manipulated to remove approximately half of the TE to enrich the cell population for ICM cells
The RNA-seq libraries were generated from individual cells by using the Smart-seq2 v4 Ultra Low Input RNA Kit and Nextera XT DNA Library Prep Kit and multiplexed by Nextera XT indexes (Illumina).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
TPM.txt
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| Data processing |
Multiplexed sequencing reads that passed filters were trimmed to remove low quality reads and adaptors. The quality of reads after filtering was examined using fastQC, followed by alignment to the bovine reference genome by STAR (2.5.3a) with default parameters. Individual mapped reads were quantified to calculate TPM (transcript per Million) values using RefSeq genes as reference. Data was analyzed using principal component analysis, Leiden clustering analysis, UMAP plotting.
Assembly: ARS-UCD1.2
Supplementary files format and content: tab-delimited text files include TPM values for each Sample
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| Submission date |
Oct 13, 2022 |
| Last update date |
Sep 08, 2023 |
| Contact name |
Zongliang Jiang |
| E-mail(s) |
[email protected]
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| Organization name |
University of Florida
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| Department |
Animal Sciences
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| Street address |
2033 Mowry Rd
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| City |
Gainesville |
| State/province |
FL |
| ZIP/Postal code |
32610 |
| Country |
USA |
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| Platform ID |
GPL26012 |
| Series (1) |
| GSE215409 |
Single cell RNA sequencing of bovine blastocysts: Early cellular differentiation |
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| Relations |
| BioSample |
SAMN31270217 |
| SRA |
SRX17878229 |
| 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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