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Sample GSM4257706 Query DataSets for GSM4257706
Status Public on Dec 31, 2020
Title Female TCDD 1000 ng/kg rep3
Sample type RNA
 
Source name liver_female_TCDD treated F0_1000 ng/kg
Organism Rattus norvegicus
Characteristics strain: Sprague-Dawley
Sex: female
lineage (f0 dam, f1 male, f2 male, f3): 64B-7-5-3
tcdd dose (f0): 1000 ng/kg
tissue: liver
Treatment protocol Pregnant F0 dams were treated by oral gavage with a single bolus of either TCDD (30, 100, 300 or 1000 ng/kg) dissolved in corn oil vehicle or vehicle alone (5mL/kg) on gestational day 11.
Growth protocol Upon weaning, same-sex littermates were housed in stainless steel, wire-mesh bottom cages with pelleted rat feed (R36, Lactamin, Stockholm, Sweden) and tap water available ad libitum. The housing environment was maintained at 21±0.2°C and relative humidity at 50±3%, with a 12/12h artificial light/dark cycle.
Extracted molecule total RNA
Extraction protocol Total hepatic RNA was isolated for analysis on microarrays. Briefly, 20 mg hepatic tissue was ground to a powder in liquid nitrogen using a mortar and pestle, followed by rapid homogenization using a Brinkmann Polytron (Polytron PT1600E with a PT-DA 1607 generator). RNA was extracted using an RNeasy Mini Plus Kit following the manufacturer’s recommended protocol (Qiagen, Mississauga, Canada).
Label biotin
Label protocol Manufacturer's recommended protocols as followed by the TCAG Facility at the Hospital for Sick Kid's in Toronto, Canada
 
Hybridization protocol Manufacturer's recommended protocols as followed by the TCAG Facility at the Hospital for Sick Kid's in Toronto, Canada
Scan protocol Manufacturer's recommended protocols as followed by the TCAG Facility at the Hospital for Sick Kid's in Toronto, Canada
Description PB45
Data processing Raw array data (CEL files) were loaded into the R statistical environment using the affy package (v1.48.0) of the BioConductor library. Data was investigated for distributional homogeneity, then pre-processed using the RMA algorithm. The custom Probe to Entrez Gene ID map, ragene20strnentrezgcdf (v21.0.0) was used for annotation.
 
Submission date Jan 09, 2020
Last update date Jan 01, 2021
Contact name Stephenie Prokopec
E-mail(s) stephenie.prokopec@oicr.on.ca
Organization name Ontario Institute for Cancer Research
Street address 661 University Avenue, Suite 510
City Toronto
State/province Ontario
ZIP/Postal code M5G 0A3
Country Canada
 
Platform ID GPL26164
Series (2)
GSE143368 Transgenerational epigenetic and transcriptomic effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin exposure in rat [array]
GSE143884 Transgenerational epigenetic and transcriptomic effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin exposure in rat

Data table header descriptions
ID_REF
VALUE RMA-normalized signal intensities

Data table
ID_REF VALUE
100034253_at 7.758136295
100036582_at 1.738294183
100036765_at 5.045785138
100049583_at 8.220925344
100124593_at 4.231501152
100125361_at 4.152999063
100125362_at 4.580029737
100125363_at 2.923916222
100125364_at 7.749314565
100125367_at 5.832561606
100125370_at 10.1399326
100125371_at 6.563214749
100125372_at 8.141463885
100125373_at 8.722960516
100125374_at 5.611106469
100125378_at 7.193355088
100125385_at 7.823838525
100125595_at 3.748171949
100126231_at 4.361080637
100137086_at 6.097641575

Total number of rows: 21569

Table truncated, full table size 464 Kbytes.




Supplementary file Size Download File type/resource
GSM4257706_RaGene2_051115H_PB45_45.CEL.gz 8.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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