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Sample GSM1257585 Query DataSets for GSM1257585
Status Public on Nov 02, 2013
Title Folate deficient diet
Sample type genomic
 
Channel 1
Source name 56739802_meDIP
Organism Mus musculus
Characteristics strain: C57BL/6
gender: male
tissue: sperm
age: 2-3 months
chip antibody: 5-methylcytidine (BI-MECY-0100, Eurogentec, 10µg per immunoprecipitation tube)
treatment protocol: Folate deficient diet
Treatment protocol To minimize genetic noise the inbred C57BL/6 strain was used for generation of experimental males and for analysis of the sperm epigenome. Mice were housed under a controlled light/dark cycle and were provided with food and water ad libitum. All animal procedures were approved by the Animal Care and Use Committee of McGill University, Montreal. Dietary exposures began in utero. To generate experimental males, female C57BL/6 were fed either the folate sufficient (FS, 2mg folic acid/kg, n=69) diet (TD.01369, Harlan Laboratories, Madison, WI) or the folate deficient diet (FD, 0.3mg folic acid/kg, n=64) (TD.01546), two weeks prior to breeding with non-experimental C57BL/6 males that were fed regular mouse chow (8640 Rodent diet) (used only for breeding to generate experimental males). To breed C57BL/6 females, C57BL/6 males were brought to the females’ cages at night and removed in the morning in order to limit consumption of the experimental diets by the males. Females were maintained on the experimental diets through pregnancy and lactation. From weaning at PND21, male pups were given the same experimental diet as their in utero exposure until sacrifice as adults.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted with a DNeasy Mini Kit (Qiagen, Mississauga, Canada) from mouse sperm.
Label Cy5
Label protocol Both immunoprecipitated DNA and input DNA from MeDIP were amplified with the GenomePlex Complete Whole Genome Amplification Kit (Sigma, WGA2) according to the manufacturer’s instructions. Cy3-dUTP and Cy5-dUTP were used by Nimblegen to label the input and bound factions, respectively.
 
Channel 2
Source name 56739802_input
Organism Mus musculus
Characteristics strain: C57BL/6
gender: male
tissue: sperm
age: 2-3 months
chip antibody: none
treatment protocol: Folate deficient diet
Treatment protocol To minimize genetic noise the inbred C57BL/6 strain was used for generation of experimental males and for analysis of the sperm epigenome. Mice were housed under a controlled light/dark cycle and were provided with food and water ad libitum. All animal procedures were approved by the Animal Care and Use Committee of McGill University, Montreal. Dietary exposures began in utero. To generate experimental males, female C57BL/6 were fed either the folate sufficient (FS, 2mg folic acid/kg, n=69) diet (TD.01369, Harlan Laboratories, Madison, WI) or the folate deficient diet (FD, 0.3mg folic acid/kg, n=64) (TD.01546), two weeks prior to breeding with non-experimental C57BL/6 males that were fed regular mouse chow (8640 Rodent diet) (used only for breeding to generate experimental males). To breed C57BL/6 females, C57BL/6 males were brought to the females’ cages at night and removed in the morning in order to limit consumption of the experimental diets by the males. Females were maintained on the experimental diets through pregnancy and lactation. From weaning at PND21, male pups were given the same experimental diet as their in utero exposure until sacrifice as adults.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted with a DNeasy Mini Kit (Qiagen, Mississauga, Canada) from mouse sperm.
Label Cy3
Label protocol Both immunoprecipitated DNA and input DNA from MeDIP were amplified with the GenomePlex Complete Whole Genome Amplification Kit (Sigma, WGA2) according to the manufacturer’s instructions. Cy3-dUTP and Cy5-dUTP were used by Nimblegen to label the input and bound factions, respectively.
 
 
Hybridization protocol Array hybridization to the NimbleGen mouse 2.1 deluxe promoter array was carried out by Nimblegen..
Scan protocol Scanning was performed by Nimblegen.
Data processing The value is background subtracted and log2-quantile normalized using the limma Bioconductor package.
 
Submission date Nov 01, 2013
Last update date Nov 02, 2013
Contact name Moshe Szyf
E-mail(s) moshe.szyf@mcgill.ca
Organization name McGill University
Department Pharmacology
Street address McIntyre Medical Building, 3655 Promenade Sir William Osler, Room 1309
City Montreal
State/province Quebec
ZIP/Postal code H3G 1Y6
Country Canada
 
Platform ID GPL17878
Series (1)
GSE52017 Low paternal dietary folate alters the sperm epigenome and is associated with negative pregnancy outcomes

Data table header descriptions
ID_REF
VALUE Normalized log2 ratios (Cy5/Cy3)

Data table
ID_REF VALUE
1 -1.12739187339751
2 -0.203112397152244
3 -0.793687887168792
4 -1.05143970346868
5 -0.364973819669885
6 -1.34325026359161
7 -1.46263293726963
8 -0.776405709250788
9 -1.30863050098567
10 -0.898999782105811
11 -0.489003236294741
12 0.0727263982272373
13 -0.789331818193475
14 -0.352958461522001
15 -0.673316585206725
16 -0.275586748095661
17 -1.66865864823103
18 -1.50265940947993
19 -0.35985069309495
20 -0.676162334787449

Total number of rows: 2064266

Table truncated, full table size 52622 Kbytes.




Supplementary file Size Download File type/resource
GSM1257585_56739802_532.pair.gz 37.8 Mb (ftp)(http) PAIR
GSM1257585_56739802_635.pair.gz 37.5 Mb (ftp)(http) PAIR
Processed data included within Sample table

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