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| Status |
Public on Oct 19, 2016 |
| Title |
MPB_pub_121 |
| Sample type |
RNA |
| |
|
| Source name |
Rats treated with methyl paraben from postnatal day 42 to 62
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague-Dawley
Sex: Female
tissue: Caudal mammary tissue
exposure/treatment condition: Methyl paraben
window of exposure: Pubertal
age at sacrifice: Rats sacrificed at postnatal day 63
batch: One
rna extraction kit: Promega
|
| Treatment protocol |
Perinatal animals: five animals were treated in utero daily through oral gavage of their pregnant dams (F0) from gestation day (GD) 1 to GD 20; another five animals were treated daily from post natal day (PND)1 to PND 20 through milk of lactating dams (F0) exposed by oral gavage. One female pup per litter was randomly selected and sacrificed at PND 21. Prepubertal animals: treated daily from PND 21 through breast milk, then by oral gavage from PND 28 to PND 41, and sacrificed at PND 42. Pubertal animals: treated daily by oral gavage from PND 42 to PND 62, and sacrificed at PND 63. Chronic treatment group: animals were treated daily from PND 1 through milk of dams (F0) exposed from parturition. After weaning, the female offspring (F1) were treated through oral gavage 3 times a week. Animals were mated (outbred) at PND 97 and treatments were continued through pregnancy, delivery of pups (F2) and lactation. At the end of lactation at lactating day 28 (PND 146), F1 animals were sacrificed.
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| Growth protocol |
The breeder animals (F0) were weighed weekly to determine treatment dose, starting from gestation for the perinatal group and during lactation for prepubertal, pubertal, and adult groups and the dose to be administered was calculated on the basis of the weekly weight. For the perinatal group, all the F1 pups were housed with their dams until sacrifice (postnatal (PND) 21). F1 pups from all the other groups were housed with their dams (F0) until weaning (PND 28) then separated from the dam, identified by ear punch, weighed individually every week and dosed by gavage following the protocol, based on the weekly mean body weight of each group. Animals were randomized into different treatment groups in order to have minimal differences in body weight among them, with a standard deviation of no more than 10% from the average.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The 5th left and right caudal mammary glands were used for transciptome profiling. Mammary tissues were pulverized in liquid nitrogen and total RNA was extracted using the Maxwell 16 LEV simplyRNA Blood kit (Promega, WI) or the Direct-zol RNA MiniPrep kit (Zymo Research, CA). Total RNA concentration was determined using Nanodrop (Thermo Scientific, MA), and RNA quality was assessed using a 2100 Bioanalyzer (Agilent Technologies, CA); only samples with RNA Integrity Number ≥ 7 were used for microarrays.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (Manual Target Preparation for GeneChip® Whole Transcript (WT) Expression Arrays, Affymetrix 2015).
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| |
|
| Hybridization protocol |
Following fragmentation, 5.2 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Gene 2.0 St arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
Arrays were scanned using the GeneChip Scanner 3000.
|
| Description |
Gene expression data from rat mammary tissues at postnatal day 63 following treatment with methyl paraben from postnatal day 42 to postnatal day 62
|
| Data processing |
The data was preprocessed in Expression Console software (Affymetrix) using RMA-sketch workflow and default settings. Transcriptome results from MPB and TCS treatment during three short term windows – perinatal, prepubertal and pubertal windows – were pre-processed independently to generate two separate datasets (MPB and control - table 1, TCS and control - table 2). Transcriptome data from chronically exposed TCS animals and corresponding controls were pre-processed separately from short term data (Chronic TCS and control - table 3). Batch effects were removed using the ComBat package in R (Leek J. T. et al, 2012) for datasets in table 1 and table 2 (no batch covariate in table 3). Data submitted here have not been corrected for batch effects. Batch information is provided in the sample datasheet.
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| |
|
| Submission date |
Aug 21, 2015 |
| Last update date |
Oct 19, 2016 |
| Contact name |
Kalpana Gopalakrishnan |
| E-mail(s) |
kalpana.gopalakrishnan@mssm.edu
|
| Organization name |
Icahn School of Medicine at Mount Sinai
|
| Street address |
1428 Madison Avenue, Atran Building 03-02
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL17117 |
| Series (1) |
| GSE72276 |
Mammary transcriptome of rats treated with low-dose environmental chemicals at critical developmental windows |
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