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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 27, 2024 |
| Title |
c201e4 ovoid female control |
| Sample type |
SRA |
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| Source name |
conceptus
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| Organism |
Bos taurus |
| Characteristics |
tissue: conceptus
cell line: ovoid
genotype: female
treatment: control
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| Treatment protocol |
On day 5 post IVF, recombinant bovine IL6 (100 ng/ml; KingFisher Biotech, St. Paul, MN, USA) or its carrier (SOF-BE1) were administered to embryos. Embryos were kept in their treated culture drops until blastocyst assessment and collection on day 7.5 for embryo transfer or immunofluorescence.
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| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzolâ„¢ and Phasemakerâ„¢ Tubes (ThermoFisher) were used to extract high purity total RNA from whole, individual ovoid (n = 6, IL6-treated; n = 6, non-treated, control) and tubular (n = 4, IL6-treated; n = 4, non-treated, control) conceptuses.
Samples were further processed for RNA sequencing at Vanderbilt Technologies for Advanced Genomics (VUMC, Nashville, TN, USA) using the NEBNext® rRNA Depletion kit (New England BioLabs Inc., Ipswich, MA, USA).
A sequencing assay was carried out in a NovaSeq 6000 System (Illumina, Inc, San Diego, CA) to produce pair-end reads 150 nucleotides long.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Data were generated from each sample submitted for sequencing (n = 12 ovoid, and n = 8 tubular conceptuses)
Paired-end reads were trimmed then aligned to the Bos taurus genome (ARS-UCD1.2 assembly) using HiSat2
Samtools was used to sort the aligned reads and filter out any samples with low quality reads
Picard was used for sorting and indexing aligned reads from samples with quality reads (http://broadinstitute.github.io/picard/).
Featurecounts was used for quantifying aligned reads against the Ensembl gene annotation (Bos taurusARS-UCD1.2.98) with duplicates removed
Assembly: ARS-UCD1.2
Supplementary files format and content: tab delineated read files
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| Submission date |
Mar 15, 2024 |
| Last update date |
Mar 27, 2024 |
| Contact name |
Alan D. Ealy |
| E-mail(s) |
ealy@vt.edu
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| Phone |
5402314425
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| Organization name |
Virginia Tech
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| Street address |
175 W Campus Dr
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| City |
Blacksburg |
| State/province |
VA |
| ZIP/Postal code |
24061 |
| Country |
USA |
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| Platform ID |
GPL26012 |
| Series (1) |
| GSE261707 |
Interleukin-6 supplementation improves bovine conceptus elongation and transcriptomic indicators of developmental competence |
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| Relations |
| BioSample |
SAMN40472392 |
| SRA |
SRX23960500 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8149320_8552-FB-3_.count.txt.gz |
2.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
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