NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4257718 Query DataSets for GSM4257718
Status Public on Dec 31, 2020
Title Female TCDD 1000 ng/kg rep7
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): 71B-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 PB57
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 7.377775356
100036582_at 2.24803944
100036765_at 4.881051297
100049583_at 8.111641226
100124593_at 4.90034162
100125361_at 3.794867378
100125362_at 5.213116721
100125363_at 2.53342205
100125364_at 7.716200539
100125367_at 5.435150152
100125370_at 10.20059943
100125371_at 6.161652677
100125372_at 7.627836156
100125373_at 8.267517496
100125374_at 5.252970148
100125378_at 7.443793877
100125385_at 7.925068295
100125595_at 4.200525067
100126231_at 4.27629871
100137086_at 6.121198416

Total number of rows: 21569

Table truncated, full table size 464 Kbytes.




Supplementary file Size Download File type/resource
GSM4257718_RaGene2_051115H_PB57_57.CEL.gz 8.1 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap
External link. Please review our privacy policy.