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Series GSE125916 Query DataSets for GSE125916
Status Public on Feb 03, 2020
Title RNA-sequencing of CD56dim NK cells from atopic dermatitis and control patients
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Purpose: To determine the underlying transcriptional differences between CD56dim NK cells from atopic dermatitis patients
Methods: We sort-purified 30-100,000 CD56dim NK cells from freshly thawed, cryopreserved PBMCs of atopic dermatitis patients and patients undergoing Mohs surgeries. 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 5 atopic dermatitis patients and 5 control patients were sorted and sequenced, then their transcriptomes were compared to each other using DESeq2 in R v3.5.1 with a single-variable design. Alpha was set to 0.05
Contributor(s) Mack MR, Kim BS
Citation(s) 32102931
Submission date Jan 30, 2019
Last update date May 06, 2020
Contact name Madison R Mack
Organization name Sanofi
Department Immunology & Inflammation Research
Street address 350 Water St
City Cambridge
State/province Massachusetts
ZIP/Postal code 02141
Country USA
Platforms (1)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Samples (10)
GSM3584918 AD pt1
GSM3584919 AD pt2
GSM3584920 Control pt1
BioProject PRJNA517946
SRA SRP182966

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Supplementary file Size Download File type/resource
GSE125916_RAW.tar 50.5 Mb (http)(custom) TAR (of TXT)
GSE125916_all_genes_RPKM.txt.gz 3.0 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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