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| Status |
Public on Jul 30, 2012 |
| Title |
Young skin 3 |
| Sample type |
SRA |
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| Source name |
skin, young
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| Organism |
Homo sapiens |
| Characteristics |
tissue: skin
age group: <=30 years
gender: female
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| Treatment protocol |
3 broadband light treatments over 3 months using a 515 nm or 560 nm cut-off filter at a single long pulse of 10-20 ms duration, fluences of 8-14 J/cm2. At each treatment session, two or more passes were performed.
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| Growth protocol |
Human subjects.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Fibrous Tissue Mini Kit (Qiagen). 3'-seq was performed as described in Beck AH et al., 2010 (PMID 20098735). In brief, oligo-dT-directed reverse transcription generated cDNAs corresponding to the 3' ends of poly-adenylated transcripts; the cDNAs were then cloned and subjected to deep sequencing on the Illumina GAIIx platform with raw read length of 36bp.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
Y3
3' RNA-seq
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| Data processing |
Basecalls were performed using CASAVA version 1.4.
3' seq reads were aligned to the hg18 genome assembly using "Bowtie" (version 0.12.6).
Reads Per Kilobase of exon per Million mappable reads (RPKM, a direct measure of transcript abundance), as well as the number of raw reads falling on to each gene, were calculated using a self-developed script by K. Qu. Only the reads mapping to the 3' UTR and last exon of the RefSeq transcripts were counted.
Genome_build: hg18
Supplementary_files_format_and_content: bedGraph files were generated using the SeqGene sam2wig module.
Supplementary_files_format_and_content: BBL_3seq_GeneExp.txt, which is linked to the Series record as a supplementary file, includes RPKMs.
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| Submission date |
Jul 06, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Kun Qu |
| E-mail(s) |
kqu@stanford.edu
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| Organization name |
Stanford University
|
| Department |
Dermatology
|
| Lab |
Howard Chang
|
| Street address |
269 Campus Dr. CCSR 2150
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platform ID |
GPL9115 |
| Series (1) |
| GSE39170 |
Molecular Rejuvenation of Gene Expression Pattern of Photoaged and Intrinsically Aged Human Skin by Broadband Light Treatment |
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| Relations |
| SRA |
SRX158092 |
| BioSample |
SAMN01086104 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM957473_Y3.bedGraph.gz |
21.5 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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