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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 01, 2024 |
| Title |
Healthy skin, vehicle control, replicate 3 |
| Sample type |
SRA |
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| Source name |
healthy skin
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| Organism |
Homo sapiens |
| Characteristics |
tissue: healthy skin
treatment: vehicle (DMSO)
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Fibrous Tissue Mini Kit (Qiagen) per manufacturer’s instructions.
Libraries were generated with Ribo-Zero Plus rRNA Depletion Kit (Illumina).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
HS_Veh_3
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| Data processing |
Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software
The fastq files were trimmed for adaptor sequences using trimmomatic version 0.36 in paried end mode with parameters - minimal read length option set to 35 base pairs, trailing set to 5 and sliding window set to 4:15.
After trimming, the data was aligned using STAR. Human samples were aligned to the human genome (hg38) and mouse samples aligned to the mouse genome (mm10/GRCm38).
The featureCounts program was used to generate raw counts for each gene.
Assembly: hg38/mm10 for human/mouse respectively
Supplementary files format and content: tab-delimited text files, include raw counts for each sample. human_raw_counts contains all raw counts for human samples and mouse_raw_counts contains all raw counts for mouse samples.
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| Submission date |
Jul 19, 2023 |
| Last update date |
Apr 01, 2024 |
| Contact name |
Shruti Naik |
| Organization name |
NYU Langone Health
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| Department |
Pathology
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| Lab |
Naik Lab
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| Street address |
435 E 30th St
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| City |
NYC |
| ZIP/Postal code |
10016 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE237767 |
Epithelial-Immune Metabolic Codependency Fuels Inflammatory Disease [Bulk RNA-seq] |
| GSE237772 |
Epithelial-Immune Metabolic Codependency Fuels Inflammatory Disease |
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| Relations |
| BioSample |
SAMN36618294 |
| SRA |
SRX21081800 |
| 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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