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Series GSE140227 Query DataSets for GSE140227
Status Public on Nov 13, 2019
Title RNA sequencing of lesional and nonlesional skin from patients with atopic dermatitis
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Purpose: To determine the transcriptional differences between lesional skin and nonlesional skin from patients with atopic dermatitis
Methods: Skin biopsies of lesional and non-lesional sites on atopic dermatitis patients were obtained and stored in RNA Later. Ribosomal RNA was removed and cDNA was generated with the SMARTer kit (CloneTech) with 10 ng of total RNA per sample.
Samples were sequenced to an average depth of 34 million 1x50 reads on a HiSeq3000 (Illumina). Reads were aligned to Ensembl release 76 using STAR, gene counts were determined with Subread:featureCount, and sequence performance was assessed with RSeQC.
Overall design Six atopic dermatitis patients
Contributor(s) Mack MR, Kim BS
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Submission date Nov 12, 2019
Last update date Nov 20, 2019
Contact name Ting-Lin Yang
Organization name Washington University of St Louis
Lab Brian Kim
Street address 660 S. Euclid Ave., CB 8123
City Saint Louis
State/province Missouri
ZIP/Postal code 63110
Country USA
Platforms (1)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Samples (12)
GSM4156922 AD pt1 lesional
GSM4156923 AD pt1 nonlesional
GSM4156924 AD pt2 lesional
BioProject PRJNA588999
SRA SRP229587

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE140227_RAW.tar 14.7 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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