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| Status |
Public on Nov 02, 2015 |
| Title |
SNL_rep2 |
| Sample type |
SRA |
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| Source name |
nervous system
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague-Dawley
tissue: Dorsal root ganglion (DRG)
treatment: Experiment, Spinal nerve Ligated, left side
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| Extracted molecule |
total RNA |
| Extraction protocol |
DRGs were removed, flash frozen on dry ice, andtotal RNA wasextracted using either Trizol reagent(Life Technologies) or RNeasy (Qiagen). Illumina TruSeq Stranded Total RNA with Ribo-zero Gold kits (RS-122-2301 was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Experiment, Spinal nerve Ligated, left side
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| Data processing |
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were aligned to the rn4 genome assembly using TopHat 2.0.9 with these parameters: -p 28 --b2-fast -G /UCSC/rn4/Annotation/Genes/genes.gtf --segment-length 20
Fragments Per Kilobase of exon per Megabase of library size (FPKM) and DE genes were calculated using cuffdiff v 2.1.1 with default parameters
Genome_build: rn4
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...
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| Submission date |
Jul 02, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
matteo cesaroni |
| Organization name |
Temple University
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| Street address |
3307 N. Broad S, Rm 220, PAHB
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| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19140 |
| Country |
USA |
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| Platform ID |
GPL18694 |
| Series (1) |
| GSE59043 |
G9a is essential for epigenetic silencing of K+ channel genes in acute-to-chronic pain transition |
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| Relations |
| BioSample |
SAMN02900661 |
| SRA |
SRX644932 |
| 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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