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| Status |
Public on Nov 03, 2017 |
| Title |
IV_2282del42282del4_131 |
| Sample type |
SRA |
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| Source name |
skin
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| Organism |
Homo sapiens |
| Characteristics |
disease: ichthyosis vulgaris (IV)
mutation: FLG mutation
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| Treatment protocol |
mutation or wild-type
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| Growth protocol |
samples from the skin
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| Extracted molecule |
total RNA |
| Extraction protocol |
After local anesthesia and under standard aseptic conditions, 4 mm punch biopsies were taken. After subcutaneous fat tissue removal, the skin biopsies were directly snap frozen in liquid nitrogen. To further minimize potential RNA degradation by skin RNAses, biopsies were not stored at -80° C, but directly processed for RNA extraction. Skin biopsies were homogenized in TRIZOL (Ambion, Austin, TX) and thereafter centrifuged to eliminate contaminating fat prior extraction with chloroform. After precipitation using isopropanol at -20°C, RNA was washed twice with ethanol and then re-suspended in Tris-EDTA buffer (Ambion, Austin, TX). Then, samples were incubated at 57°C for 10 min and RNA concentration was determined by using a NanoDrop (Thermoscientific, Waltham, MA). RNA quality was assessed by using a Bioanalyzer chip assay (Agilent technologies, Santa Clara, CA). Samples were stored at -80°C until RNA sequencing.
50 ng of total RNA were amplified by applying Ovation RNA-Seq System V2 (NuGen, Emeryville, CA). The resulting cDNAs were pooled in equal amount and used to prepare the DNA fragment library with SOLiD System chemistry (Life Technologies Corp., Carlsbad, CA). Sequencing was performed using SOLiD 5500W platform and DNA sequencing chemistry (Life Technologies Corp., Carlsbad, CA). Raw reads (75 bp) were color-space mapped to the human genome hg19 reference using Maxmapper algorithm implemented in the Lifescope software (Life Technologies Corp., Carlsbad, CA). Mapping to multiple locations was permitted. Reads with score less than 10 were excluded. Average mapping quality was 30. Analysis of the RNA content and gene-based annotation was done with whole-transcriptome work- flow of Lifescope.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent S5 |
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| Description |
Ion Torrent S5
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| Data processing |
Color-space base calling
Mapping, alignment with Lifescope
Lifescope transcriptome workflow
Genome_build: hg19
Supplementary_files_format_and_content: counts data
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| Submission date |
Aug 14, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Sulev Koks |
| E-mail(s) |
sulev.koks@murdoch.edu.au
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| Phone |
+61864570313
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| Organization name |
Murdoch University
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| Department |
Centre for Molecular Medicine and Innovative Therapeutics
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| Street address |
90 South Street
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| City |
Perth |
| State/province |
Western Australia |
| ZIP/Postal code |
6150 |
| Country |
Australia |
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| Platform ID |
GPL23934 |
| Series (1) |
| GSE102628 |
Transcriptional profiling unravels enhanced xenobiotic metabolism in the skin of patients with atopic dermatitis but not with ichthyosis vulgaris |
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| Relations |
| BioSample |
SAMN07503744 |
| SRA |
SRX3102355 |
| 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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