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| Status |
Public on Apr 15, 2024 |
| Title |
MDM, untreated, rep2 |
| Sample type |
SRA |
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| Source name |
Peripheral blood mononuclear cells
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Peripheral blood mononuclear cells
cell line: Primary human cell
cell type: Macrophages
genotype: WT
treatment: Mock
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was obtained using Direct-zol™ RNA Miniprep. RNA samples were treated with a DNase I column to remove contaminating genomic DNA. RNA was quantified by spectrophotometry, and 1μg of RNA was used for bulk RNA-Seq.
The sequencing library is prepared by random fragmentation of the DNA or cDNA sample, followed by 5' and 3' adapter ligation. Alternatively, "tagmentation" combines the fragmentation and ligation reactions into a single step that greatly increases the efficiency of the library preparation process. Adapter-ligated fragments are then PCR amplified and gel purified.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
MDM_MOCK_L
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| Data processing |
Clean reads were obtained by removing low-quality adapter, poly N-containing, and shorter-than-70 bp reads using trimmomatic
The location of the reads on the reference genome was determined quickly and precisely by comparing reads with the reference genome using the HISAT2 software
he new transcripts were then assembled using String Tie software and the feature count tool in Subread software
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes raw counts bacth corrected for each sample
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| Submission date |
Apr 01, 2024 |
| Last update date |
Apr 15, 2024 |
| Contact name |
Yordi Sebastián Tamayo Molina |
| E-mail(s) |
ystm0827@gmail.com
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| Organization name |
University of Antioquia
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| Lab |
Inmunovirology
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| Street address |
Street 67 No. 53 - 108
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| City |
Medellin |
| State/province |
Antioquia |
| ZIP/Postal code |
050010 |
| Country |
Colombia |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE262963 |
Transcriptional profile of human monocyte-derived macrophages stimulated with Interleukin 27 |
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| Relations |
| BioSample |
SAMN40710704 |
| SRA |
SRX24120475 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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