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Sample GSM5965763 Query DataSets for GSM5965763
Status Public on Mar 23, 2023
Title FCTWC3
Sample type RNA
 
Source name frontal cortexes
Organism Mus musculus
Characteristics stain: CD-1
gender: Female
Treatment protocol Detection of a vaginal plug was considered day 0.5 of pregnancy. Pregnant CD-1 mice were then housed individually and continuously treated with E3 (50┬Ál of 0.46mg/ml in DMSO to approximate human exposure) or vehicle control (DMSO) via a mini-osmotic pump (Alzet model # 1002) beginning on Day 9 of gestation for 7 days.We began each experiment by treating pregnant mice with E3, and ended by analyzing their offspring.
Growth protocol CD-1 mice were obtained from Charles River Laboratories (Wilmington, MA, USA). Animals were housed in a 12 hr day/night cycle. All experiments were conducted in accordance with Yale University Animal Care Committee Guidelines. Eight-week-old CD-1 female mice were bred to male mice of the same strain and examined every 12 hours until the presence of a vaginal plug was detected.
Extracted molecule total RNA
Extraction protocol The tissue intended for mRNA analysis was placed in 1 mL TRIzol per 100 mg tissue (Invitrogen, Carlsbad, CA, USA). Tissue was homogenized on ice, and total RNA was isolated using methodology described by the manufacturer.
Label biotin
Label protocol High quality total RNA is used as starting material to obtain labeled cRNA. In the first step, single stranded cDNA is synthesized by reverse transcription using the poly (A) RNA present in the starting total RNA sample. Single stranded cDNA is then converted into double stranded cDNA and purified using the Affymetrix Cleanup Module. An in vitro transcription (IVT) reaction is then carried out overnight in the presence of biotinylated
 
Hybridization protocol Samples are hybridized to arrays for 16 hours at 45C. The standard array is then washed and stained using the fluidics station and then scanned. The images are analyzed using Affymetrix Command Console Viewer and metric analyses are carried out according to the instructions provided by Affymetrix using the Affymetrix Expression Console.
Scan protocol GeneChips were scanned using GeneChip Scanner 3000 with Autoloader.
Data processing The data were analyzed with Expression Console using the following paramaters:
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = MTA-1_0
program-version = 1.4.1.46
 
Submission date Mar 22, 2022
Last update date Mar 24, 2023
Contact name Yuping Zhou
E-mail(s) joezhouyp@gmail.com
Organization name Yale
Department OB/GYN
Lab Taylor Lab
Street address 310 cedar street
City new haven
State/province CT
ZIP/Postal code 06511
Country USA
 
Platform ID GPL20775
Series (2)
GSE199174 The steroid hormone estriol (E3) regulates epigenetic programming of fetal mouse brain and reproductive tract [Affymetrix]
GSE199214 The steroid hormone estriol (E3) regulates epigenetic programming of fetal mouse brain and reproductive tract

Data table header descriptions
ID_REF
VALUE Quantification

Data table
ID_REF VALUE
AFFX-BkGr-GC03_st 6.19641
AFFX-BkGr-GC04_st 6.04431
AFFX-BkGr-GC05_st 5.46474
AFFX-BkGr-GC06_st 4.74945
AFFX-BkGr-GC07_st 4.11417
AFFX-BkGr-GC08_st 3.87674
AFFX-BkGr-GC09_st 3.48499
AFFX-BkGr-GC10_st 3.42181
AFFX-BkGr-GC11_st 3.21172
AFFX-BkGr-GC12_st 3.09069
AFFX-BkGr-GC13_st 2.93383
AFFX-BkGr-GC14_st 2.83388
AFFX-BkGr-GC15_st 2.7952
AFFX-BkGr-GC16_st 2.85547
AFFX-BkGr-GC17_st 2.90477
AFFX-BkGr-GC18_st 3.02686
AFFX-BkGr-GC19_st 3.30236
AFFX-BkGr-GC20_st 3.46819
AFFX-BkGr-GC21_st 3.65309
AFFX-BkGr-GC22_st 4.28201

Total number of rows: 72688

Table truncated, full table size 1859 Kbytes.




Supplementary file Size Download File type/resource
GSM5965763_FCTWC3_MTA-1_0_.CEL.gz 25.3 Mb (ftp)(http) CEL
GSM5965763_FCTWC3_MTA-1_0_.sst-rma-gene-full.chp.gz 481.7 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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