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Series GSE140380 Query DataSets for GSE140380
Status Public on Nov 15, 2019
Title Transcriptional differences between skin from patients with atopic dermatitis and control skin obtained from the healthy margins of Mohs surgery patients
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Purpose: To determine the transcriptional differences between skin from patients with atopic dermatitis and control skin obtained from the healthy margins of Mohs surgery patients
Methods: 4 mm skin biopsies of skin from atopic dermatitis patients or deidentified healthy margin surgical tissue were obtained and stored in RNA Later (-80C). Whole tissue RNA was isolated from tissue processed with a bead homogenizer using the QIAGEN RNeasy kit. Following DNase treatment (TurboDNase, Invitrogen), ribosomal RNA was removed (Ribo-zero kit, Illumina). mRNA was then fragmented in buffer containing 40 mM Tris acetate (pH 8.2), 100 mM potassium acetate, and 30 mM magnesium acetate and heated to 94C for 150 s. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Invitrogen, per manufacturer’s instructions) and random hexamers. A second strand reaction was performed to yield dscDNA. cDNA was blunt ended, had an A base added to the 30 ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12 cycles using primers incorporating unique index tags. Fragments were sequenced on an Illumina HiSeq-3000 using single reads extending 50 bases.
Samples were sequenced to an average depth of 32 million 1x50 reads on a HiSeq3000 (Illumina). Reads were aligned to Homo_sapiens reference build Ensembl_R76 using STAR, gene counts were determined with Subread:featureCount, transcript counts were produced by Sailfish, and sequence performance was assessed with RSeQC v2.3.
Overall design 4 AD and 4 control patients
Contributor(s) Mack MR, Kim BS
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Submission date Nov 14, 2019
Last update date Nov 20, 2019
Contact name Brian Kim
Phone 314-362-8159
Organization name Washington University in Stl
Street address 660 S Euclid Ave
City St. Louis
State/province MO
ZIP/Postal code 63110
Country USA
Platforms (1)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Samples (8)
GSM4160338 ad013
GSM4160339 ad014
GSM4160340 ad016
BioProject PRJNA589541
SRA SRP229958

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Supplementary file Size Download File type/resource
GSE140380_RAW.tar 10.3 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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