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| Status |
Public on Sep 06, 2023 |
| Title |
FN58, CD participants, pair sample, CD mesenteric fat |
| Sample type |
SRA |
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| Source name |
Mesenteric fat
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Mesenteric fat
Sex: Male
disease: Crohn's disease
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using RNeasy Plus Mini Kit (Qiagen, Tokyo, Japan).
The sequencing libraries were prepared with the Illumina TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Globin (Illumina, San Diego, CA, United States).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
FN58
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| Data processing |
The RNA sequencing reads were trimmed using Cutadapt (v.3.7) in paired-end mode (parameter- Quality : 20 minimum length : 20).
The filtered reads were mapped to the reference genome GRCH38 using STAR software v2.7.9a (parameter- default).
Quantification of the gene expression levels was performed using RNA-SeQC v2.1.2 (parameter- default).
Assembly: GRCH38
Supplementary files format and content: TPM_matrix.txt: Tab-delimited text file includes TPM values for each Sample.
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| Submission date |
Mar 14, 2023 |
| Last update date |
Sep 06, 2023 |
| Contact name |
SoJung Park |
| E-mail(s) |
[email protected]
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| Organization name |
Ulsan medical university
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| Street address |
88, Olympic-ro 43-gil
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| City |
Seoul |
| State/province |
Songpa-gu |
| ZIP/Postal code |
05505 |
| Country |
South Korea |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE227376 |
Transcriptomic analysis reveals the dynamic changes of immune responses during the development of creeping fat in Crohn's disease |
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| Supplementary data files not provided |
| Processed data are available on Series record |
| Raw data not provided for this record |
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