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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 08, 2024 |
| Title |
Paw skin bulk RNA-seq 16d post-PTX female, rep1 |
| Sample type |
SRA |
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| Source name |
Non-neuronal cells
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| Organism |
Mus musculus |
| Characteristics |
cell type: Non-neuronal cells
genotype: WT
treatment: Chemotherapy (Pacletaxol) treatment
time: Day 16
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| Treatment protocol |
Mice were treated by injecting systemically with PTX (6mg/kg) at day -6, -3 and 0
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| Growth protocol |
None
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| Extracted molecule |
total RNA |
| Extraction protocol |
Dissection of hind paw skin and DRG
Approximately 500ng Total RNA was used for RNA-seq library preparation by following TruSeq stranded mRNA-seq library preparation kit ( Cat. No: 20020595, Illumina, USA). Following mRNA enrichment by oligodT beads, the RNA was fragmented into small pieces using divalent cautions under elevated temperature and magnesium. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This was followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP in the Second Strand Marking Mix (SMM). The incorporation of dUTP in second strand synthesis effectively quenches the second strand during amplification, since the polymerase used in the assay will not incorporate past this nucleotide. These cDNA fragments then went through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products were then purified and enriched with PCR to create the final RNA-Seq library for sequencing by 50bp single-end protocol with Illumina HiSeq 3000 platform.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Illumina bcl2fastq software used for base-calling
All RNA-seq FastQ reads were aligned with the reference genome (UCSC mouse genome build mm9) using TopHat2 default settings (Trapnell et al., 2012).
The BAM files obtained after alignment were processed using HTSeq-count to obtain the counts per gene in all samples (Anders et al., 2015).
Assembly: UCSC mouse genome build mm9
Supplementary files format and content: The processed data files are in tabular format. The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count
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| Submission date |
Aug 11, 2023 |
| Last update date |
Aug 08, 2024 |
| Contact name |
YI ZOU |
| E-mail(s) |
zou@uthscsa.edu
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| Organization name |
UTHSA-GCCRI
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| Street address |
8403 Floyd Curl Drive
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| City |
SAN ANTONIO |
| State/province |
TX |
| ZIP/Postal code |
78229 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE240708 |
Degenerative and regenerative peripheral processes are associated with persistent painful chemotherapy-induced neuropathies in males and females |
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| Relations |
| BioSample |
SAMN36949835 |
| SRA |
SRX21346025 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7708091_PTX_Si_Paw_16d_F1_Genes_ReadCount.txt.gz |
94.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
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