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| Status |
Public on Mar 01, 2014 |
| Title |
Rat Skin Control 2 |
| Sample type |
SRA |
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| Source name |
Skin
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Wistar
treatment: Control
tissue: skin
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| Treatment protocol |
Humans: volunteers received 3 MEDs of UVB irradiation to 1cm2 of volar forearm skin using TL01 florescent bulbs. Rats: Anaesthetised rats received 1000mJ/cm2 of UVB to the the plantar surface of the left hind paw
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Skin: total RNA was extracted using a combination of the phenol extraction method and column purification. Briefly, samples were homogenised in Trizol (Invitrogen), mixed with chloroform and spun so that the aqueous liquid phase containing the nucleic acids could be removed. This solution was then placed on Qiagen RNeasy columns and subjected to numerous wash steps to purify the RNA sample. DRG: , total RNA from DRG samples was extracted using the miRNeasy kit (Qiagen). All samples were subjected to on-column DNase digestion (Qiagen) to prevent genomic contamination and subsequently analysed using an RNA 6000 nano chip (Agilent Technologies) to confirm sufficient integrity.
cDNA libraries were prepared using the TruSeqTM RNA Sample Preparation Kit (Illumina), low throughput protocol. 200 ng of total RNA were subjected to poly(A) enrichment using poly(T)-attached magnetic beads. Poly(A)-enriched RNA was subsequently used for reverse transcription and library preparation according to Illumina’s instructions
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Description |
s_4_1_rat.qseq.fastq
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| Data processing |
Low quality reads removed (those that did not pass the Illumina quality filter)
Normalisation – the DESeq method was used for library size normalisation (estimateSizeFactors(), estimateDispersions()), as described in pmid:20979621 and the DESeq vignette (http://www.bioconductor.org/packages/devel/bioc/vignettes/DESeq/inst/doc/DESeq.pdf)
Gene Counting – expression was calculated by counting all reads aligning to the known exons of a given gene, according to Ensembl. Exons for a given gene that overlap with exons from another gene (on the same strand or on opposite strand) were removed
Alignment – fastq files (with low quality reads removed) were aligned to the human genome (version Hg19) or the rat genome (version Rn4) using bowtie, with parameters -m 1 -v 1 -p 8 --best, that is, allowing for 1 mismatch and discarding ambiguous reads
Genome_build: Human: Hg19, downloaded from UCSC. Rat: Rn4, downloaded from UCSC.
Supplementary_files_format_and_content: Tables of normalised counts: matrix with genes (Ensemble gene id) as rows and samples as columns. Separate tables are provided for the different sequencing depths
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| Submission date |
Jan 27, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
James R Perkins |
| E-mail(s) |
jimrperkins@gmail.com
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| Organization name |
Hospital Carlos Haya
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| Department |
Hospital Civil
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| Lab |
Research Laboratory for Allergic Diseases
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| Street address |
Pl. Hosp. Civil
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| City |
Malaga |
| ZIP/Postal code |
29009 |
| Country |
Spain |
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| Platform ID |
GPL10669 |
| Series (1) |
| GSE54413 |
Genome-wide Transcriptional Profiling of Skin and Dorsal Root Ganglia after Ultraviolet-B-Induced Inflammation |
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| Relations |
| BioSample |
SAMN02596637 |
| SRA |
SRX450281 |
| 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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