SRX319086 The Western diet alters offspring immunity - pup from breeders fed high omega-6 diet - 062 SRP026657 The samples are surgically/sterilely resected stool from the cecum of 5-7 week old pups. The pups came from breeders that were exposed to different diets. The breeders were placed on the diets one day before placement in breeding cages and remained on the diets throughout the study. All pups from all breeders were weaned onto the low fat control diet. The samples were from pups that thus, were exposed to these diets in utero and during nursing. Therefore, the variable under investigation in the study involving these cecal content samples was the dietary exposure from the breeders/parents during gestation and lactation. The omega-6 group (O6) came from pups who's breeding parents were fed a diet with 40% kcal from fat, most of which from omega-6. DNA was extracted from sterilely excised cecal stool pellets using QIAamp DNA stool mini kit (Qiagen). For sequencing of 16S rDNA, amplicon libraries were prepared from sample DNA using Accuprime High Fidelity Taq polymerase (Invitrogen) and universal primers flanking variable regions V1 (primer 27F; 5’-AGAGTTTGATCCTGGCTCAG-3’) and V3 (primer 534R; 5’- ATTACCGCGGCTGCTGG-3’). For each sample, the universal primers were tagged with unique sequences ("barcodes") to allow for multiplexing/demultiplexing. PCR products were then purified using the Agencourt Ampure XP Kit (Beckman Counter Genomics) and quantitated using the QuantIT dsDNA High-Sensitivity Assay Kit (Invitrogen). Approximately equivalent amounts of each PCR product were then pooled and purified with a Qiagen minElute column (Qiagen) into 30 microliter TE buffer prior to sequencing at the NIH Intramural Sequencing Center. Sequencing was done on a 454 FLX instrument using Titanium chemistry. Flowgrams were processed using the 454 Basecalling pipeline. SRS455911 O62 AMPLICON METAGENOMIC PCR 0 0 Technical Read Adapter 1 1 Application Read Forward 5 454 GS FLX Titanium 454 Basecalling pipeline 2.6 SRX319104 The Western diet alters offspring immunity - pup from breeders fed high omega-6 diet - 061 SRP026657 The samples are surgically/sterilely resected stool from the cecum of 5-7 week old pups. The pups came from breeders that were exposed to different diets. The breeders were placed on the diets one day before placement in breeding cages and remained on the diets throughout the study. All pups from all breeders were weaned onto the low fat control diet. The samples were from pups that thus, were exposed to these diets in utero and during nursing. Therefore, the variable under investigation in the study involving these cecal content samples was the dietary exposure from the breeders/parents during gestation and lactation. The omega-6 group (O6) came from pups who's breeding parents were fed a diet with 40% kcal from fat, most of which from omega-6. DNA was extracted from sterilely excised cecal stool pellets using QIAamp DNA stool mini kit (Qiagen). For sequencing of 16S rDNA, amplicon libraries were prepared from sample DNA using Accuprime High Fidelity Taq polymerase (Invitrogen) and universal primers flanking variable regions V1 (primer 27F; 5’-AGAGTTTGATCCTGGCTCAG-3’) and V3 (primer 534R; 5’- ATTACCGCGGCTGCTGG-3’). For each sample, the universal primers were tagged with unique sequences ("barcodes") to allow for multiplexing/demultiplexing. PCR products were then purified using the Agencourt Ampure XP Kit (Beckman Counter Genomics) and quantitated using the QuantIT dsDNA High-Sensitivity Assay Kit (Invitrogen). Approximately equivalent amounts of each PCR product were then pooled and purified with a Qiagen minElute column (Qiagen) into 30 microliter TE buffer prior to sequencing at the NIH Intramural Sequencing Center. Sequencing was done on a 454 FLX instrument using Titanium chemistry. Flowgrams were processed using the 454 Basecalling pipeline. SRS455928 O61 AMPLICON METAGENOMIC PCR 0 0 Technical Read Adapter 1 1 Application Read Forward 5 454 GS FLX Titanium 454 Basecalling pipeline 2.6 SRX319105 The Western diet alters offspring immunity - pup from western diet breeders cohoused with pups from low fat breeders WDCoH3-2 SRP026657 The samples are surgically/sterilely resected stool from the cecum of 5-7 week old pups. The pups came from breeders that were exposed to different diets. The breeders were placed on the diets one day before placement in breeding cages and remained on the diets throughout the study. All pups from all breeders were weaned onto the low fat control diet. The samples were from pups that thus, were exposed to these diets in utero and during nursing. Therefore, the variable under investigation in the study involving these cecal content samples was the dietary exposure from the breeders/parents during gestation and lactation. The Western Diet co-housed (WDCoH) pups came from parents fed with 40% kcal from fat, much from saturated fat with an over-representation of omega-6, breeders weaned in to the same cage, all fed the low fat control diet for 4 weeks. DNA was extracted from sterilely excised cecal stool pellets using QIAamp DNA stool mini kit (Qiagen). For sequencing of 16S rDNA, amplicon libraries were prepared from sample DNA using Accuprime High Fidelity Taq polymerase (Invitrogen) and universal primers flanking variable regions V1 (primer 27F; 5’-AGAGTTTGATCCTGGCTCAG-3’) and V3 (primer 534R; 5’- ATTACCGCGGCTGCTGG-3’). For each sample, the universal primers were tagged with unique sequences ("barcodes") to allow for multiplexing/demultiplexing. PCR products were then purified using the Agencourt Ampure XP Kit (Beckman Counter Genomics) and quantitated using the QuantIT dsDNA High-Sensitivity Assay Kit (Invitrogen). Approximately equivalent amounts of each PCR product were then pooled and purified with a Qiagen minElute column (Qiagen) into 30 microliter TE buffer prior to sequencing at the NIH Intramural Sequencing Center. Sequencing was done on a 454 FLX instrument using Titanium chemistry. Flowgrams were processed using the 454 Basecalling pipeline. SRS455929 WDCoH3 AMPLICON METAGENOMIC PCR 0 0 Technical Read Adapter 1 1 Application Read Forward 5 454 GS FLX Titanium 454 Basecalling pipeline 2.6 SRX319143 The Western diet alters offspring immunity - pup from western diet breeders cohoused with pups from low fat breeders - WDCoH2 SRP026657 The samples are surgically/sterilely resected stool from the cecum of 5-7 week old pups. The pups came from breeders that were exposed to different diets. The breeders were placed on the diets one day before placement in breeding cages and remained on the diets throughout the study. All pups from all breeders were weaned onto the low fat control diet. The samples were from pups that thus, were exposed to these diets in utero and during nursing. Therefore, the variable under investigation in the study involving these cecal content samples was the dietary exposure from the breeders/parents during gestation and lactation. The Western Diet co-housed (WDCoH) pups came from parents fed with 40% kcal from fat, much from saturated fat with an over-representation of omega-6, breeders weaned in to the same cage, all fed the low fat control diet for 4 weeks. DNA was extracted from sterilely excised cecal stool pellets using QIAamp DNA stool mini kit (Qiagen). For sequencing of 16S rDNA, amplicon libraries were prepared from sample DNA using Accuprime High Fidelity Taq polymerase (Invitrogen) and universal primers flanking variable regions V1 (primer 27F; 5’-AGAGTTTGATCCTGGCTCAG-3’) and V3 (primer 534R; 5’- ATTACCGCGGCTGCTGG-3’). For each sample, the universal primers were tagged with unique sequences ("barcodes") to allow for multiplexing/demultiplexing. PCR products were then purified using the Agencourt Ampure XP Kit (Beckman Counter Genomics) and quantitated using the QuantIT dsDNA High-Sensitivity Assay Kit (Invitrogen). Approximately equivalent amounts of each PCR product were then pooled and purified with a Qiagen minElute column (Qiagen) into 30 microliter TE buffer prior to sequencing at the NIH Intramural Sequencing Center. Sequencing was done on a 454 FLX instrument using Titanium chemistry. Flowgrams were processed using the 454 Basecalling pipeline. SRS455962 WDCoH2 AMPLICON METAGENOMIC PCR 0 0 Technical Read Adapter 1 1 Application Read Forward 5 454 GS FLX Titanium 454 Basecalling pipeline 2.6 SRX319144 The Western diet alters offspring immunity - pup from western diet breeders cohoused with pups from low fat breeders - WDCoH1 SRP026657 The samples are surgically/sterilely resected stool from the cecum of 5-7 week old pups. The pups came from breeders that were exposed to different diets. The breeders were placed on the diets one day before placement in breeding cages and remained on the diets throughout the study. All pups from all breeders were weaned onto the low fat control diet. The samples were from pups that thus, were exposed to these diets in utero and during nursing. Therefore, the variable under investigation in the study involving these cecal content samples was the dietary exposure from the breeders/parents during gestation and lactation. The Western Diet co-housed (WDCoH) pups came from parents fed with 40% kcal from fat, much from saturated fat with an over-representation of omega-6, breeders weaned in to the same cage, all fed the low fat control diet for 4 weeks. DNA was extracted from sterilely excised cecal stool pellets using QIAamp DNA stool mini kit (Qiagen). For sequencing of 16S rDNA, amplicon libraries were prepared from sample DNA using Accuprime High Fidelity Taq polymerase (Invitrogen) and universal primers flanking variable regions V1 (primer 27F; 5’-AGAGTTTGATCCTGGCTCAG-3’) and V3 (primer 534R; 5’- ATTACCGCGGCTGCTGG-3’). For each sample, the universal primers were tagged with unique sequences ("barcodes") to allow for multiplexing/demultiplexing. PCR products were then purified using the Agencourt Ampure XP Kit (Beckman Counter Genomics) and quantitated using the QuantIT dsDNA High-Sensitivity Assay Kit (Invitrogen). Approximately equivalent amounts of each PCR product were then pooled and purified with a Qiagen minElute column (Qiagen) into 30 microliter TE buffer prior to sequencing at the NIH Intramural Sequencing Center. Sequencing was done on a 454 FLX instrument using Titanium chemistry. Flowgrams were processed using the 454 Basecalling pipeline. SRS455963 WDCoH1 AMPLICON METAGENOMIC PCR 0 0 Technical Read Adapter 1 1 Application Read Forward 5 454 GS FLX Titanium 454 Basecalling pipeline 2.6 SRX319181 The Western diet alters offspring immunity - pup from low fat breeders cohoused with pups from western diet breeders SRP026657 The samples are surgically/sterilely resected stool from the cecum of 5-7 week old pups. The pups came from breeders that were exposed to different diets. The breeders were placed on the diets one day before placement in breeding cages and remained on the diets throughout the study. All pups from all breeders were weaned onto the low fat control diet. The samples were from pups that thus, were exposed to these diets in utero and during nursing. Therefore, the variable under investigation in the study involving these cecal content samples was the dietary exposure from the breeders/parents during gestation and lactation. The Low Fat Diet co-housed (LFCoH) pups came from parents fed with 10% kcal from fat and a healthy balance of omega-3 to omega-6, breeders weaned in to the same cage, all fed the low fat control diet for 4 weeks. DNA was extracted from sterilely excised cecal stool pellets using QIAamp DNA stool mini kit (Qiagen). For sequencing of 16S rDNA, amplicon libraries were prepared from sample DNA using Accuprime High Fidelity Taq polymerase (Invitrogen) and universal primers flanking variable regions V1 (primer 27F; 5’-AGAGTTTGATCCTGGCTCAG-3’) and V3 (primer 534R; 5’- ATTACCGCGGCTGCTGG-3’). For each sample, the universal primers were tagged with unique sequences ("barcodes") to allow for multiplexing/demultiplexing. PCR products were then purified using the Agencourt Ampure XP Kit (Beckman Counter Genomics) and quantitated using the QuantIT dsDNA High-Sensitivity Assay Kit (Invitrogen). Approximately equivalent amounts of each PCR product were then pooled and purified with a Qiagen minElute column (Qiagen) into 30 microliter TE buffer prior to sequencing at the NIH Intramural Sequencing Center. Sequencing was done on a 454 FLX instrument using Titanium chemistry. Flowgrams were processed using the 454 Basecalling pipeline. SRS455972 LFCoH2 AMPLICON METAGENOMIC PCR 0 0 Technical Read Adapter 1 1 Application Read Forward 5 454 GS FLX Titanium 454 Basecalling pipeline 2.6 SRX319182 The Western diet alters offspring immunity - pup from low fat breeders cohoused with pups from western diet breeders - LFCoH1 SRP026657 The samples are surgically/sterilely resected stool from the cecum of 5-7 week old pups. The pups came from breeders that were exposed to different diets. The breeders were placed on the diets one day before placement in breeding cages and remained on the diets throughout the study. All pups from all breeders were weaned onto the low fat control diet. The samples were from pups that thus, were exposed to these diets in utero and during nursing. Therefore, the variable under investigation in the study involving these cecal content samples was the dietary exposure from the breeders/parents during gestation and lactation. The Low Fat Diet co-housed (LFCoH) pups came from parents fed with 10% kcal from fat and a healthy balance of omega-3 to omega-6, breeders weaned in to the same cage, all fed the low fat control diet for 4 weeks. DNA was extracted from sterilely excised cecal stool pellets using QIAamp DNA stool mini kit (Qiagen). For sequencing of 16S rDNA, amplicon libraries were prepared from sample DNA using Accuprime High Fidelity Taq polymerase (Invitrogen) and universal primers flanking variable regions V1 (primer 27F; 5’-AGAGTTTGATCCTGGCTCAG-3’) and V3 (primer 534R; 5’- ATTACCGCGGCTGCTGG-3’). For each sample, the universal primers were tagged with unique sequences ("barcodes") to allow for multiplexing/demultiplexing. PCR products were then purified using the Agencourt Ampure XP Kit (Beckman Counter Genomics) and quantitated using the QuantIT dsDNA High-Sensitivity Assay Kit (Invitrogen). Approximately equivalent amounts of each PCR product were then pooled and purified with a Qiagen minElute column (Qiagen) into 30 microliter TE buffer prior to sequencing at the NIH Intramural Sequencing Center. Sequencing was done on a 454 FLX instrument using Titanium chemistry. Flowgrams were processed using the 454 Basecalling pipeline. SRS455973 LFCoH1 AMPLICON METAGENOMIC PCR 0 0 Technical Read Adapter 1 1 Application Read Forward 5 454 GS FLX Titanium 454 Basecalling pipeline 2.6 SRX319188 The Western diet alters offspring immunity - pup from breeders fed western diet - WD4 SRP026657 The samples are surgically/sterilely resected stool from the cecum of 5-7 week old pups. The pups came from breeders that were exposed to different diets. The breeders were placed on the diets one day before placement in breeding cages and remained on the diets throughout the study. All pups from all breeders were weaned onto the low fat control diet. The samples were from pups that thus, were exposed to these diets in utero and during nursing. Therefore, the variable under investigation in the study involving these cecal content samples was the dietary exposure from the breeders/parents during gestation and lactation. The Western Diet (WD) group came from pups who's breeding parents were fed a diet with 40% kcal from fat, much from saturated fat with an over-representation of omega-6. DNA was extracted from sterilely excised cecal stool pellets using QIAamp DNA stool mini kit (Qiagen). For sequencing of 16S rDNA, amplicon libraries were prepared from sample DNA using Accuprime High Fidelity Taq polymerase (Invitrogen) and universal primers flanking variable regions V1 (primer 27F; 5’-AGAGTTTGATCCTGGCTCAG-3’) and V3 (primer 534R; 5’- ATTACCGCGGCTGCTGG-3’). For each sample, the universal primers were tagged with unique sequences ("barcodes") to allow for multiplexing/demultiplexing. PCR products were then purified using the Agencourt Ampure XP Kit (Beckman Counter Genomics) and quantitated using the QuantIT dsDNA High-Sensitivity Assay Kit (Invitrogen). Approximately equivalent amounts of each PCR product were then pooled and purified with a Qiagen minElute column (Qiagen) into 30 microliter TE buffer prior to sequencing at the NIH Intramural Sequencing Center. Sequencing was done on a 454 FLX instrument using Titanium chemistry. Flowgrams were processed using the 454 Basecalling pipeline. SRS455975 WD4 AMPLICON METAGENOMIC PCR 0 0 Technical Read Adapter 1 1 Application Read Forward 5 454 GS FLX Titanium 454 Basecalling pipeline 2.6 SRX319189 The Western diet alters offspring immunity - pup from breeders fed western diet - WD3 SRP026657 The samples are surgically/sterilely resected stool from the cecum of 5-7 week old pups. The pups came from breeders that were exposed to different diets. The breeders were placed on the diets one day before placement in breeding cages and remained on the diets throughout the study. All pups from all breeders were weaned onto the low fat control diet. The samples were from pups that thus, were exposed to these diets in utero and during nursing. Therefore, the variable under investigation in the study involving these cecal content samples was the dietary exposure from the breeders/parents during gestation and lactation. The Western Diet (WD) group came from pups who's breeding parents were fed a diet with 40% kcal from fat, much from saturated fat with an over-representation of omega-6. DNA was extracted from sterilely excised cecal stool pellets using QIAamp DNA stool mini kit (Qiagen). For sequencing of 16S rDNA, amplicon libraries were prepared from sample DNA using Accuprime High Fidelity Taq polymerase (Invitrogen) and universal primers flanking variable regions V1 (primer 27F; 5’-AGAGTTTGATCCTGGCTCAG-3’) and V3 (primer 534R; 5’- ATTACCGCGGCTGCTGG-3’). For each sample, the universal primers were tagged with unique sequences ("barcodes") to allow for multiplexing/demultiplexing. PCR products were then purified using the Agencourt Ampure XP Kit (Beckman Counter Genomics) and quantitated using the QuantIT dsDNA High-Sensitivity Assay Kit (Invitrogen). Approximately equivalent amounts of each PCR product were then pooled and purified with a Qiagen minElute column (Qiagen) into 30 microliter TE buffer prior to sequencing at the NIH Intramural Sequencing Center. Sequencing was done on a 454 FLX instrument using Titanium chemistry. Flowgrams were processed using the 454 Basecalling pipeline. SRS455976 WD3 AMPLICON METAGENOMIC PCR 0 0 Technical Read Adapter 1 1 Application Read Forward 5 454 GS FLX Titanium 454 Basecalling pipeline 2.6 SRX319190 The Western diet alters offspring immunity - pup from breeders fed western diet - WD2 SRP026657 The samples are surgically/sterilely resected stool from the cecum of 5-7 week old pups. The pups came from breeders that were exposed to different diets. The breeders were placed on the diets one day before placement in breeding cages and remained on the diets throughout the study. All pups from all breeders were weaned onto the low fat control diet. The samples were from pups that thus, were exposed to these diets in utero and during nursing. Therefore, the variable under investigation in the study involving these cecal content samples was the dietary exposure from the breeders/parents during gestation and lactation. The Western Diet (WD) group came from pups who's breeding parents were fed a diet with 40% kcal from fat, much from saturated fat with an over-representation of omega-6. DNA was extracted from sterilely excised cecal stool pellets using QIAamp DNA stool mini kit (Qiagen). For sequencing of 16S rDNA, amplicon libraries were prepared from sample DNA using Accuprime High Fidelity Taq polymerase (Invitrogen) and universal primers flanking variable regions V1 (primer 27F; 5’-AGAGTTTGATCCTGGCTCAG-3’) and V3 (primer 534R; 5’- ATTACCGCGGCTGCTGG-3’). For each sample, the universal primers were tagged with unique sequences ("barcodes") to allow for multiplexing/demultiplexing. PCR products were then purified using the Agencourt Ampure XP Kit (Beckman Counter Genomics) and quantitated using the QuantIT dsDNA High-Sensitivity Assay Kit (Invitrogen). Approximately equivalent amounts of each PCR product were then pooled and purified with a Qiagen minElute column (Qiagen) into 30 microliter TE buffer prior to sequencing at the NIH Intramural Sequencing Center. Sequencing was done on a 454 FLX instrument using Titanium chemistry. Flowgrams were processed using the 454 Basecalling pipeline. SRS455977 WD2 AMPLICON METAGENOMIC PCR 0 0 Technical Read Adapter 1 1 Application Read Forward 5 454 GS FLX Titanium 454 Basecalling pipeline 2.6 SRX319191 The Western diet alters offspring immunity - pup from breeders fed western diet - WD1 SRP026657 The samples are surgically/sterilely resected stool from the cecum of 5-7 week old pups. The pups came from breeders that were exposed to different diets. The breeders were placed on the diets one day before placement in breeding cages and remained on the diets throughout the study. All pups from all breeders were weaned onto the low fat control diet. The samples were from pups that thus, were exposed to these diets in utero and during nursing. Therefore, the variable under investigation in the study involving these cecal content samples was the dietary exposure from the breeders/parents during gestation and lactation. The Western Diet (WD) group came from pups who's breeding parents were fed a diet with 40% kcal from fat, much from saturated fat with an over-representation of omega-6. DNA was extracted from sterilely excised cecal stool pellets using QIAamp DNA stool mini kit (Qiagen). For sequencing of 16S rDNA, amplicon libraries were prepared from sample DNA using Accuprime High Fidelity Taq polymerase (Invitrogen) and universal primers flanking variable regions V1 (primer 27F; 5’-AGAGTTTGATCCTGGCTCAG-3’) and V3 (primer 534R; 5’- ATTACCGCGGCTGCTGG-3’). For each sample, the universal primers were tagged with unique sequences ("barcodes") to allow for multiplexing/demultiplexing. PCR products were then purified using the Agencourt Ampure XP Kit (Beckman Counter Genomics) and quantitated using the QuantIT dsDNA High-Sensitivity Assay Kit (Invitrogen). Approximately equivalent amounts of each PCR product were then pooled and purified with a Qiagen minElute column (Qiagen) into 30 microliter TE buffer prior to sequencing at the NIH Intramural Sequencing Center. Sequencing was done on a 454 FLX instrument using Titanium chemistry. Flowgrams were processed using the 454 Basecalling pipeline. SRS455978 WD1 AMPLICON METAGENOMIC PCR 0 0 Technical Read Adapter 1 1 Application Read Forward 5 454 GS FLX Titanium 454 Basecalling pipeline 2.6 SRX319196 The Western diet alters offspring immunity - pup from breeders fed lowfat diet - LF5 SRP026657 The samples are surgically/sterilely resected stool from the cecum of 5-7 week old pups. The pups came from breeders that were exposed to different diets. The breeders were placed on the diets one day before placement in breeding cages and remained on the diets throughout the study. All pups from all breeders were weaned onto the low fat control diet. The samples were from pups that thus, were exposed to these diets in utero and during nursing. Therefore, the variable under investigation in the study involving these cecal content samples was the dietary exposure from the breeders/parents during gestation and lactation. The Low Fat (LF) groups came from pups who's parents were fed a diet with 10% kcal from fat and a healthy balance of omega-3 to omega-6. DNA was extracted from sterilely excised cecal stool pellets using QIAamp DNA stool mini kit (Qiagen). For sequencing of 16S rDNA, amplicon libraries were prepared from sample DNA using Accuprime High Fidelity Taq polymerase (Invitrogen) and universal primers flanking variable regions V1 (primer 27F; 5’-AGAGTTTGATCCTGGCTCAG-3’) and V3 (primer 534R; 5’- ATTACCGCGGCTGCTGG-3’). For each sample, the universal primers were tagged with unique sequences ("barcodes") to allow for multiplexing/demultiplexing. PCR products were then purified using the Agencourt Ampure XP Kit (Beckman Counter Genomics) and quantitated using the QuantIT dsDNA High-Sensitivity Assay Kit (Invitrogen). Approximately equivalent amounts of each PCR product were then pooled and purified with a Qiagen minElute column (Qiagen) into 30 microliter TE buffer prior to sequencing at the NIH Intramural Sequencing Center. Sequencing was done on a 454 FLX instrument using Titanium chemistry. Flowgrams were processed using the 454 Basecalling pipeline. SRS455981 LF5 AMPLICON METAGENOMIC PCR 0 0 Technical Read Adapter 1 1 Application Read Forward 5 454 GS FLX Titanium 454 Basecalling pipeline 2.6 SRX319204 The Western diet alters offspring immunity - pup from breeders fed lowfat diet - LF4 SRP026657 The samples are surgically/sterilely resected stool from the cecum of 5-7 week old pups. The pups came from breeders that were exposed to different diets. The breeders were placed on the diets one day before placement in breeding cages and remained on the diets throughout the study. All pups from all breeders were weaned onto the low fat control diet. The samples were from pups that thus, were exposed to these diets in utero and during nursing. Therefore, the variable under investigation in the study involving these cecal content samples was the dietary exposure from the breeders/parents during gestation and lactation. The Low Fat (LF) groups came from pups who's parents were fed a diet with 10% kcal from fat and a healthy balance of omega-3 to omega-6. DNA was extracted from sterilely excised cecal stool pellets using QIAamp DNA stool mini kit (Qiagen). For sequencing of 16S rDNA, amplicon libraries were prepared from sample DNA using Accuprime High Fidelity Taq polymerase (Invitrogen) and universal primers flanking variable regions V1 (primer 27F; 5’-AGAGTTTGATCCTGGCTCAG-3’) and V3 (primer 534R; 5’- ATTACCGCGGCTGCTGG-3’). For each sample, the universal primers were tagged with unique sequences ("barcodes") to allow for multiplexing/demultiplexing. PCR products were then purified using the Agencourt Ampure XP Kit (Beckman Counter Genomics) and quantitated using the QuantIT dsDNA High-Sensitivity Assay Kit (Invitrogen). Approximately equivalent amounts of each PCR product were then pooled and purified with a Qiagen minElute column (Qiagen) into 30 microliter TE buffer prior to sequencing at the NIH Intramural Sequencing Center. Sequencing was done on a 454 FLX instrument using Titanium chemistry. Flowgrams were processed using the 454 Basecalling pipeline. SRS455983 LF4 AMPLICON METAGENOMIC PCR 0 0 Technical Read Adapter 1 1 Application Read Forward 5 454 GS FLX Titanium 454 Basecalling pipeline 2.6 SRX319205 The Western diet alters offspring immunity - pup from breeders fed lowfat diet - LF3 SRP026657 The samples are surgically/sterilely resected stool from the cecum of 5-7 week old pups. The pups came from breeders that were exposed to different diets. The breeders were placed on the diets one day before placement in breeding cages and remained on the diets throughout the study. All pups from all breeders were weaned onto the low fat control diet. The samples were from pups that thus, were exposed to these diets in utero and during nursing. Therefore, the variable under investigation in the study involving these cecal content samples was the dietary exposure from the breeders/parents during gestation and lactation. The Low Fat (LF) groups came from pups who's parents were fed a diet with 10% kcal from fat and a healthy balance of omega-3 to omega-6. DNA was extracted from sterilely excised cecal stool pellets using QIAamp DNA stool mini kit (Qiagen). For sequencing of 16S rDNA, amplicon libraries were prepared from sample DNA using Accuprime High Fidelity Taq polymerase (Invitrogen) and universal primers flanking variable regions V1 (primer 27F; 5’-AGAGTTTGATCCTGGCTCAG-3’) and V3 (primer 534R; 5’- ATTACCGCGGCTGCTGG-3’). For each sample, the universal primers were tagged with unique sequences ("barcodes") to allow for multiplexing/demultiplexing. PCR products were then purified using the Agencourt Ampure XP Kit (Beckman Counter Genomics) and quantitated using the QuantIT dsDNA High-Sensitivity Assay Kit (Invitrogen). Approximately equivalent amounts of each PCR product were then pooled and purified with a Qiagen minElute column (Qiagen) into 30 microliter TE buffer prior to sequencing at the NIH Intramural Sequencing Center. Sequencing was done on a 454 FLX instrument using Titanium chemistry. Flowgrams were processed using the 454 Basecalling pipeline. SRS455984 LF3 AMPLICON METAGENOMIC PCR 0 0 Technical Read Adapter 1 1 Application Read Forward 5 454 GS FLX Titanium 454 Basecalling pipeline 2.6 SRX319207 The Western diet alters offspring immunity - pup from breeders fed lowfat diet - LF2 SRP026657 The samples are surgically/sterilely resected stool from the cecum of 5-7 week old pups. The pups came from breeders that were exposed to different diets. The breeders were placed on the diets one day before placement in breeding cages and remained on the diets throughout the study. All pups from all breeders were weaned onto the low fat control diet. The samples were from pups that thus, were exposed to these diets in utero and during nursing. Therefore, the variable under investigation in the study involving these cecal content samples was the dietary exposure from the breeders/parents during gestation and lactation. The Low Fat (LF) groups came from pups who's parents were fed a diet with 10% kcal from fat and a healthy balance of omega-3 to omega-6. DNA was extracted from sterilely excised cecal stool pellets using QIAamp DNA stool mini kit (Qiagen). For sequencing of 16S rDNA, amplicon libraries were prepared from sample DNA using Accuprime High Fidelity Taq polymerase (Invitrogen) and universal primers flanking variable regions V1 (primer 27F; 5’-AGAGTTTGATCCTGGCTCAG-3’) and V3 (primer 534R; 5’- ATTACCGCGGCTGCTGG-3’). For each sample, the universal primers were tagged with unique sequences ("barcodes") to allow for multiplexing/demultiplexing. PCR products were then purified using the Agencourt Ampure XP Kit (Beckman Counter Genomics) and quantitated using the QuantIT dsDNA High-Sensitivity Assay Kit (Invitrogen). Approximately equivalent amounts of each PCR product were then pooled and purified with a Qiagen minElute column (Qiagen) into 30 microliter TE buffer prior to sequencing at the NIH Intramural Sequencing Center. Sequencing was done on a 454 FLX instrument using Titanium chemistry. Flowgrams were processed using the 454 Basecalling pipeline. SRS455986 LF2 AMPLICON METAGENOMIC PCR 0 0 Technical Read Adapter 1 1 Application Read Forward 5 454 GS FLX Titanium 454 Basecalling pipeline 2.6 SRX319208 The Western diet alters offspring immunity - pup from breeders fed lowfat diet - LF1 SRP026657 The samples are surgically/sterilely resected stool from the cecum of 5-7 week old pups. The pups came from breeders that were exposed to different diets. The breeders were placed on the diets one day before placement in breeding cages and remained on the diets throughout the study. All pups from all breeders were weaned onto the low fat control diet. The samples were from pups that thus, were exposed to these diets in utero and during nursing. Therefore, the variable under investigation in the study involving these cecal content samples was the dietary exposure from the breeders/parents during gestation and lactation. The Low Fat (LF) groups came from pups who's parents were fed a diet with 10% kcal from fat and a healthy balance of omega-3 to omega-6. DNA was extracted from sterilely excised cecal stool pellets using QIAamp DNA stool mini kit (Qiagen). For sequencing of 16S rDNA, amplicon libraries were prepared from sample DNA using Accuprime High Fidelity Taq polymerase (Invitrogen) and universal primers flanking variable regions V1 (primer 27F; 5’-AGAGTTTGATCCTGGCTCAG-3’) and V3 (primer 534R; 5’- ATTACCGCGGCTGCTGG-3’). For each sample, the universal primers were tagged with unique sequences ("barcodes") to allow for multiplexing/demultiplexing. PCR products were then purified using the Agencourt Ampure XP Kit (Beckman Counter Genomics) and quantitated using the QuantIT dsDNA High-Sensitivity Assay Kit (Invitrogen). Approximately equivalent amounts of each PCR product were then pooled and purified with a Qiagen minElute column (Qiagen) into 30 microliter TE buffer prior to sequencing at the NIH Intramural Sequencing Center. Sequencing was done on a 454 FLX instrument using Titanium chemistry. Flowgrams were processed using the 454 Basecalling pipeline. SRS455987 LF1 AMPLICON METAGENOMIC PCR 0 0 Technical Read Adapter 1 1 Application Read Forward 5 454 GS FLX Titanium 454 Basecalling pipeline 2.6