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Sample GSM3671471 Query DataSets for GSM3671471
Status Public on Dec 01, 2019
Title PCOS 2
Sample type SRA
 
Source name endometrial organoids
Organism Homo sapiens
Characteristics source tissue: endometrium
patient age: 41
Treatment protocol A stepwise estradiol treatment was used to treat endometrial organoids within agarose 3D Petri Dishes® to mimic the 14 days of follicular phase of human menstrual cycle with the addition of testosterone. The normal hormone treatment was 0.1 nM E2 + 0.8 nM testosterone (day 0–7), 1 nM E2 + 0.8 nM testosterone (day 7–13) and 1 nM E2 + 1.25 nM testosterone (day 13–14). The PCOS hormone treatment was 0.1 nM E2 + 3 nM testosterone (day 0–7) and 1 nM E2 + 3 nM testosterone (day 7–14). Media was changed every second day.
Growth protocol Endometrial epithelial and stromal cells were isolated from endometrial biopsies from premenopausal women undergoing routine hysterectomy for benign uterine conditions. Both epithelial and stromal cells were seeded in 1.5% agarose 3D Petri Dishes®at 3:1 ratio by volume. Cells were let form organoids in complete MammoCult human medium for 7 days before hormone treatments.
Extracted molecule total RNA
Extraction protocol All endometrial organoids were harvested from 3D Petri Dishes® by pipetting. Total RNA was extracted from organoids using Tri Reagent (Sigma Aldrich, 93289) and Direct-zol™ RNA MicroPrep (Zymo Research, R2060) with an additional step of DNase I treatment to remove any contaminating DNA.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description PCOS hormone treatment
Data processing Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned to mm10 using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited file with read counts per gene
 
Submission date Mar 14, 2019
Last update date Dec 01, 2019
Contact name Julie Kim
E-mail(s) j-kim4@northwestern.edu
Phone 312-503-5377
Organization name Northwestern University
Department Obstetrics and Gynecology
Lab Lurie 4-250
Street address 303 E. Superior St
City Chicago
State/province IL
ZIP/Postal code 60611
Country USA
 
Platform ID GPL20301
Series (1)
GSE128328 Gene expression profile in endometrial organoids cultured in normal follicular phase vs PCOS-like hormone profile
Relations
BioSample SAMN11128488
SRA SRX5523397

Supplementary file Size Download File type/resource
GSM3671471_PCOS2.txt.gz 95.6 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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