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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 24, 2021 |
| Title |
C3H/HeJ AA mice - JAK2i #1 |
| Sample type |
SRA |
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| Source name |
skin biopsies
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| Organism |
Mus musculus |
| Characteristics |
strain: C3H/HeJ AA
tissue: skin
treatment: JAK2i
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| Treatment protocol |
The JAK inhibitors were first dissolved in a small volume of DMSO (catalog D12345, Thermo Scientific) and further were diluted with polyethylene glycol 300 (catalog 202371, MilliporeSigma). For topical treatment, C3H/HeJ AA mice were topically treated with 2% (w/w) various JAKis in Aquaphor (Aquaphor) twice daily, or vehicle control.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total cellular RNA was extracted using RNeasy Plus Micro Kit (catalog 74034, QIAGEN) from skin homogenates of indicated JAKi treated mice or control. RNA quality and quantity were determined using an Agilent BioAnalyzer (Agilent Technologies).
Libraries were constructed, pooled and sequenced on an Illumina HiSeq Mid Output run to generate 16-23 million 75-bp paired-end reads per sample at GENEWIZ (South Plainfield, NJ, GENEWIZ).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
DZ13
processed_data-Raw_gene_counts_JAKi_AA-mice.xlsx
processed_data-ALADIN_CTL_signature_genes-JAKi_AA-mice.xlsx
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| Data processing |
Pooled and sequenced on an Illumina HiSeq 4000 Output run to generate 16-23 million 75-bp paired-end reads per sample at GENEWIZ (South Plainfield, NJ, GENEWIZ). The FASTQ files were aligned to the mouse reference genome (mm10) with Subread aligner (Rsubread_1.28.1, R version: 3.4.4, Platform: x86_64-pc-linux-gnu (64-bit)). Raw counts were generated using the same package, Subread aligner (Rsubread_1.28.1, R version: 3.4.4, Platform: x86_64-pc-linux-gnu (64-bit)).
Differential expression (DE) analysis was performed using DESeq2 package (v1.18.1) of R. DE was defined using a significance of FDR<0.05 comparing each treated cohort to the vehicle-treated cohort. Unsupervised hierarchical clustering and gene adjacency matrices were generated using Multiple Experiment Viewer (MeV).
To visualize the difference in expression in the ALADIN genes, the z-score normalized hit counts of the ALADIN genes were inputs for clustering.
Clustering results in this study were done naïve to the treatment status of each sample, and unblinded at the end.
iPathwayGuide (https://www.advaitabio.com) and ClusterProfiler package (v3.6.0) of R was used for the pathway analysis.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: processed_data-Raw_gene_counts_JAKi_AA-mice.xlsx: Excel file includes raw counts.
Supplementary_files_format_and_content: processed_data-ALADIN_CTL_signature_genes-JAKi_AA-mice.xlsx: Excel file includes abundance measurements.
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| Submission date |
Feb 23, 2021 |
| Last update date |
Feb 25, 2021 |
| Contact name |
Zhenpeng Dai |
| E-mail(s) |
zd2148@cumc.columbia.edu
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| Phone |
2128514853
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| Organization name |
Columbia University
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| Department |
Dermatology
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| Street address |
1150 St. Nicholas Ave
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10025-2075 |
| Country |
USA |
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| Platform ID |
GPL21103 |
| Series (1) |
| GSE167360 |
RNA-seq of C3H/HeJ AA mice skin biopsies treated with JAK-selective inhibitors |
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| Relations |
| BioSample |
SAMN18039476 |
| SRA |
SRX10157458 |
| 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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