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| Status |
Public on Feb 10, 2015 |
| Title |
WKY KO rep3 |
| Sample type |
SRA |
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| Source name |
macrophages
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: wistar kyoto
genotype/variation: Cyp2j4 kO
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from rat (Wild type Wistar-Kyoto strain, n=3; Cyp2j4-/-, n=3) and mice (commercially outbred mice; n=4) bone marrow derived macrophages (BMDMs) and human monocytes-derived macrophages (n=3 healthy donors) using Trizol (Invitrogen) according to manufacturer's instructions with an additional purification step by on-column DNase treatment using the RNase-free DNase Kit (Qiagen) to ensure elimination of any genomic DNA.
The integrity and quantity of total RNA was determined using a NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific) and Agilent 2100 Bioanalyzer (Agilent Technologies). 1μg of total RNA from each species was used to generate RNA-seq libraries using TruSeq RNA sample preparation kit (Illumina) according to the manufacturer's instructions. Briefly, RNA was purified and fragmented using poly-T oligo-attached magnetic beads using two rounds of purification followed by the first and second cDNA strand synthesis.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
WKY KO macrophages rep3
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| Data processing |
fastq files were mapped using Tophat2
Mapped files were summarised to count level using 'union' model from Htseq
Genome_build: rn4
Supplementary_files_format_and_content: text file containing raw count data
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| Submission date |
Feb 09, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jacques Behmoaras |
| E-mail(s) |
[email protected]
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| Organization name |
Imperial College
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| Department |
Centre for Complement and Inflammation Research (CCIR),
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| Street address |
Du Cane road
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| City |
London |
| ZIP/Postal code |
W12 0NN |
| Country |
United Kingdom |
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| Platform ID |
GPL18694 |
| Series (1) |
| GSE65715 |
Macrophage epoxygenase determines a pro-fibrotic transcriptomesignature |
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| Relations |
| BioSample |
SAMN03333385 |
| SRA |
SRX869231 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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