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| Status |
Public on Feb 26, 2024 |
| Title |
ESIG_IL1B |
| Sample type |
SRA |
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| Source name |
Equine embryonic stem cell-derived tenocytes
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| Organism |
Equus caballus |
| Characteristics |
tissue: Equine embryonic stem cell-derived tenocytes
genotype: WT
treatment: Interleukin 1 beta
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| Treatment protocol |
Embryonic stem cell-derived tenocytes were seeded in type 1 collagen gels (bovine; Advanced Biomatrix, California, USA) to generate a three-dimensional matrix and stimulated with IL-1ß (1 nM) or control for 14 days, with fresh media changes every 3-4 days before harvesting at day 14.
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| Growth protocol |
Embryonic stem cell-derived tenocytes were cultured in Dulbecco’s modified eagle medium (DMEM)/F-12 with high glucose (4.5 g/L), 15% fetal bovine serum, 2 mM L-glutamine, 1% none-essential amino acids, 1 mM sodium pyruvate, and 0.1 mM 2-mercaptoethanol (all from Invitrogen, Renfrewshire, UK) with mechanical passaging every 5-7 days.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Tri-reagent (Sigma), purified using an RNeasy mini Kit (Qiagen, Manchester, UK) and contaminating genomic DNA removed using Ambion DNA-free (Life Technologies, Paisley, UK). RNA concentration was measured using a Nanodrop (ThermoFisher, Loughborough, UK) and a Qubit (ThermoFisher). RNA integrity was confirmed on a Tapestation (Agilent, Milton Keynes, UK).
mRNA libraries were prepared using a TruSeq stranded mRNA kit (Illumina, Cambridge, UK)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
ESIG IL1B
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| Data processing |
RNA sequencing was performed on a NovaSeq6000 (Illumina) by external providers (Oxford Genomics, Oxford, UK & Novagene, Cambridge, UK).
30.7 – 38 million reads of 150 base pair paired-end data were generated per sample.
Resulting FASTQ files generated were quality control (QC) checked using FASTQC and MultiQC (Babraham Bioinformatics, Cambridge, UK).
QC checked reads were then aligned to the Ensemble version v95 EquCab 3.0 transcriptome using the pseudoaligner Salmon in Quasi-mapping based mode with GC-bias correction (-gcBias).
The tximport package (v.1.24; Soneson et al 2015) was used to import the quantified gene-level abundance data into R (v.4.2.1) and differential expression analysis conducted using R/Bioconductor DESeq2 (v.1.36) as described in Love et al., 2014.
Assembly: Genes with adjusted pvalue of less than 0.05 and log2 fold change of ± 1 were considered as differentially expressed.
Supplementary files format and content: Ensemble version v95 EquCab 3.0
Supplementary files format and content: A text document (.txt) includes the raw counts for each of the three biological replicates under both experimental conditions.
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| Submission date |
Jul 20, 2023 |
| Last update date |
Feb 26, 2024 |
| Contact name |
Ross Eric Beaumont |
| E-mail(s) |
robeaumont@rvc.ac.uk
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| Phone |
07312130009
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| Organization name |
Royal Veterinary College
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| Department |
Clinical science and services
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| Lab |
Skeletal biology group
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| Street address |
Hawkshead Ln
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| City |
Hatfield |
| State/province |
Hertfordshire |
| ZIP/Postal code |
AL97TA |
| Country |
United Kingdom |
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| Platform ID |
GPL26749 |
| Series (1) |
| GSE237821 |
Impact of exogenous IL-1ß stimulation on equine embryonic stem cell-derived tenocytes in three-dimensional culture |
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| Relations |
| BioSample |
SAMN36651811 |
| SRA |
SRX21102376 |
| 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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