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| Status |
Public on Jul 25, 2022 |
| Title |
Lurie ISF 48 |
| Sample type |
SRA |
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| Source name |
Bone marrow mononuclear cells
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| Organism |
Equus caballus |
| Characteristics |
cell type: Bone marrow mononuclear cells
breed: Thoroughbred
age: Adult
age: 5
name: Lurie
Sex: gelding
treatment: cultured in inflammed equine synovial fluid
time: 48 hours
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| Treatment protocol |
Samples identified as ISF(n,y,z, …i) were cultured in autologous inflamed equine synovial fluid for up to 10 days
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| Growth protocol |
Samples identified as SF(n,y,z, …i) were cultured in autologous normal equine synovial fluid for up to 10 days
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cultured cells were recovered in 10 mM EDTA, centrifuged (12,000g; 10 min; 4°C) and the cell pellet placed in 2 mL guanidinium chloride-phenol (Trizol®, Life Technologies). RNA was purified with on-column DNase digest (DirectZolTM RNA microprep kit, , Zymo Research, I), quantified (Qubit® 3.0 Fluorometer), and stored at -80°C. RNA quality was assessed using a Bioanalyzer 2100, Agilent Technologies, Santa Clara, CA).
cDNA libraries were prepared using TruSeq DNA Library Preparation kits (Illumina, Inc., San Diego, CA).
cDNA libraries were sequenced (NovaSeq 6000 S4, Illumina) to generate an average of 34.5 (range, 24-54) million stranded paired-end reads (2 x 150 nt) per sample
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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 |
mapping (STAR 2.7.2a - STAR --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalU nannotated --alignEndsType Local --chimOutType WithinBAM --twopassMode Basic --t wopass1readsN -1 --quantMode GeneCounts --outSAMunmapped Within --outSAMtype BAM SortedByCoordinate )
quantification (STAR-2.7.2a - GeneCounts - annotation Ensembl v 104)
Normalization (GeTMM via EdgeR; rpk.norm <- DGEList(counts=rpk,group=group) rpk.norm <- calcNormFactors(rpk.norm) norm.counts.rpk_edger <- cpm(rpk.norm))
DEG (EdgeR; glmQLFTest)
Genome_build: EquCab3.0
Supplementary_files_format_and_content: GeTMM gene expression values - csv file
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| Submission date |
Oct 07, 2021 |
| Last update date |
Jul 25, 2022 |
| Contact name |
Shavahn C Loux |
| E-mail(s) |
Shavahn.Loux@uky.edu
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| Organization name |
University of Kentucky
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| Department |
Veterinary Science
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| Street address |
1400 Nicholasville
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| City |
Lexington |
| State/province |
KY |
| ZIP/Postal code |
40546 |
| Country |
USA |
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| Platform ID |
GPL26749 |
| Series (1) |
| GSE185521 |
Transcriptional signatures of bone marrow mononuclear cell-mediated resolution of synovitis |
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| Relations |
| BioSample |
SAMN22133233 |
| SRA |
SRX12515525 |
| 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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