title: Wt Mouse_cerebellum_Standard diet supplemented with resveratrol_Ad Lib_Replicate-4

description:
Sample name: WT_Resv_5
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Wt Mouse_cerebellum_Standard diet Ad Lib_Replicate-3

status: Public on Dec 22 2014

type: RNA

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

country: USA

institute: NIA-IRP, NIH

description:
Sample name: WT_SD_4
Streptavidin-Cy3 bound to biotin-labeled cRNA.

hyb_protocol: Standard Illumina protocol. In short, a total of 0.75ug of biotin-labeled cRNA was hybridized at 58 degrees C for 16 hours to Illumina's Sentrix MouseRef-8 v2 Expression BeadChips (Illumina, San Diego, CA). Each BeadChip has ~24,000 well-annotated RefSeq transcripts with approximately 30-fold redundancy. The arrays were washed, blocked and the biotin-labeled cRNA was detected by staining with streptavidin-Cy3.

scan_protocol: Arrays were scanned at a resolution of 0.8um using the BeadStation 500 X from Illumina.

data_processing: Data was extracted using the Illumina GenomeStudio software (v1.9.0). Any spots at or below the background were filtered out using an Illumina detection Pvalue of 0.02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below. Z-score = (raw value - avg)/std. Complete data including detection scores are included in the supplemental file.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Wt mouse, cerebellum, standard diet ad lib

label_protocol: Standard Illumina protocol using Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791). In short, 0.5ug of total RNA was first converted into single-stranded cDNA with reverse transcriptase using an oligo-dT primer containing the T7 RNA polymerase promoter site and then copied to produce double-stranded cDNA molecules. The double-stranded cDNA was cleaned and concentrated with the supplied columns and used in an overnight in-vitro transcription reaction where single-stranded RNA (cRNA) was generated and labeled by incorporation of biotin-16-UTP.

growth_protocol: Animal rooms were maintained at ~20°C and a 12-hour light/dark cycle.

extract_protocol: RNA was extracted from the cerebellum tissue using TRIzol® reagent (Invitrogen) using the standard manufacturer's protocol. Samples were assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Nano Chips (Agilent Technologies).

treatment_protocol: 4-month-old WT and Csbm/m mice were fed either a standard AIN-93G diet (SD; carbohydrate:protein:fat ratio of 64:19:17 percent of kcal) ad libitum or at 40% CR, or a SD supplemented with 100 mg/kgchow resveratrol ad libitum, or a high-fat diet ad libitum consisting of AIN-93G with 60% of calories from fat, primarily hydrogenated coconut oil (HFD; carbohydrate:protein:fat ratio of 16:23:61). At one year of age, they were sacrificed and cerebellums were harvested.

tag: strain/background

tag: genotype/variation

value: WT

tag: gender

value: male

tag: tissue

value: cerebellum

tag: age

value: 1 year

tag: treatment

value: standard AIN-93G diet (SD; carbohydrate:protein:fat ratio of 64:19:17 percent of kcal) ad libitum for 8 months


title: Wt Mouse_cerebellum_Caloric restricted diet_Replicate-3

description:
Sample name: WT_CR_5
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: Wt mouse, cerebellum, caloric-restricted diet

value: 40% caloric restriction of SD diet for 8 months


title: Wt Mouse_cerebellum_Caloric restricted diet_Replicate-1

description:
Sample name: WT_CR_3
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Wt Mouse_cerebellum_Standard diet supplemented with resveratrol_Ad Lib_Replicate-2

description:
Sample name: WT_Resv_3
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: Wt mouse, cerebellum, standard diet supplemented with resveratrol ad lib

value: SD supplemented with 100 mg/kgchow resveratrol ad libitum


title: Wt Mouse_cerebellum_Caloric restricted diet_Replicate-2

description:
Sample name: WT_CR_4
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Csbm/m Mouse_cerebellum_Standard diet Ad Lib_Replicate-2

description:
Sample name: CSB_SD_2
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: Csbm/m mouse, cerebellum, standard diet ad lib

value: Csbm/m


title: Csbm/m Mouse_cerebellum_High Fat diet Ad Lib_Replicate-6

description:
Sample name: CSB_HFD_6_(3)
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: Csbm/m mouse, cerebellum, high-fat diet ad lib

value: high-fat diet consisting of AIN-93G with 60% of calories from fat (HFD; carbohydrate:protein:fat ratio of 16:23:61) ad libitum for 8 months


title: Csbm/m Mouse_cerebellum_Standard diet supplemented with resveratrol_Ad Lib_Replicate-4

description:
Sample name: CSB_Resv_4
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: Csbm/m mouse, cerebellum, standard diet supplemented with resveratrol ad lib

value: a SD supplemented with 100 mg/kgchow resveratrol ad libitum


title: Csbm/m Mouse_cerebellum_High Fat diet Ad Lib_Replicate-7

description:
Sample name: CSB_HFD_7
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Csbm/m Mouse_cerebellum_Standard diet supplemented with resveratrol_Ad Lib_Replicate-1

description:
Sample name: CSB_Resv_1
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Csbm/m Mouse_cerebellum_Standard diet Ad Lib_Replicate-3

description:
Sample name: CSB_SD_3
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Csbm/m Mouse_cerebellum_Standard diet Ad Lib_Replicate-4

description:
Sample name: CSB_SD_4
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Csbm/m Mouse_cerebellum_Standard diet Ad Lib_Replicate-6

description:
Sample name: CSB_SD_6
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Csbm/m Mouse_cerebellum_Standard diet Ad Lib_Replicate-5

description:
Sample name: CSB_SD_5
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Csbm/m Mouse_cerebellum_Standard diet supplemented with resveratrol_Ad Lib_Replicate-5

description:
Sample name: CSB_Resv_5
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Csbm/m Mouse_cerebellum_Standard diet supplemented with resveratrol_Ad Lib_Replicate-3

description:
Sample name: CSB_Resv_3
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Csbm/m Mouse_cerebellum_Standard diet supplemented with resveratrol_Ad Lib_Replicate-2

description:
Sample name: CSB_Resv_2
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Csbm/m Mouse_cerebellum_Standard diet supplemented with resveratrol_Ad Lib_Replicate-6

description:
Sample name: CSB_Resv_6
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Csbm/m Mouse_cerebellum_Standard diet Ad Lib_Replicate-1

description:
Sample name: CSB_SD_1
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Csbm/m Mouse_cerebellum_High Fat diet Ad Lib_Replicate-3

description:
Sample name: CSB_HFD_3_(4)
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Csbm/m Mouse_cerebellum_High Fat diet Ad Lib_Replicate-2

description:
Sample name: CSB_HFD_2
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Csbm/m Mouse_cerebellum_High Fat diet Ad Lib_Replicate-4

description:
Sample name: CSB_HFD_4_(5)
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Csbm/m Mouse_cerebellum_Caloric restricted diet_Replicate-6

description:
Sample name: CSB_CR_6
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: Csbm/m mouse, cerebellum, caloric-restricted diet

value: 40% caloric restriction of SD diet


title: Csbm/m Mouse_cerebellum_Caloric restricted diet_Replicate-4

description:
Sample name: CSB_CR_4
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Csbm/m Mouse_cerebellum_Caloric restricted diet_Replicate-5

description:
Sample name: CSB_CR_5
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Csbm/m Mouse_cerebellum_Caloric restricted diet_Replicate-2

description:
Sample name: CSB_CR_2
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Csbm/m Mouse_cerebellum_High Fat diet Ad Lib_Replicate-5

description:
Sample name: CSB_HFD_5_(6)
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Csbm/m Mouse_cerebellum_Caloric restricted diet_Replicate-3

description:
Sample name: CSB_CR_3
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Input DNA Control Day6 Replicate 2

description:
Input RNA Control
Input RNA Control Day6 Replicate 2

hyb_protocol: Standard Illumina protocol. In short, a total of 0.75ug of biotin-labeled cRNA was hybridized at 58 degrees C for 16 hours to Illumina's Sentrix MouseRef-8 v2 Expression BeadChips (Illumina, San Diego, CA). Each BeadChip has ~24,000 well-annotated RefSeq transcripts with approximately 30-fold redundancy. The arrays were washed, blocked and the biotin labeled cRNA was detected by staining with streptavidin-Cy3.

scan_protocol: Arrays were scanned at a resolution of 0.8um using the Beadstation 500 X from Illumina.

data_processing: Data was extracted using the Illumina Genome Studio software, ver 1.6.0.  Any spots at or below the background were filtered out using an Illumina detection p value of 0.02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below.  Z-score = (raw value - avg)/std.  Complete data including detection scores will be included in the supplemental file.

source_name: C2C12 Cells_Day6

label_protocol: Standard Illumina protocol using Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791) In short, 0.5ug of total RNA was first converted into single-stranded cDNA with reverse transcriptase using an oligo-dT primer containing the T7 RNA polymerase promoter site and then copied to produce double-stranded cDNA molecules. The double stranded cDNA was cleaned and concentrated with the supplied columns and used in an overnight in-vitro transcription reaction where single-stranded RNA (cRNA) was generated and labeled by incorporation of biotin-16-UTP.

growth_protocol: C2C12 mouse myoblasts were cultured in Dulbecco's modified Eagle's medium (DMEM; Invitrogen, Carlsbad, CA, USA) supplemented with 10% serum (Invitrogen) and antibiotics (Invitrogen).  Differentiation was induced on sub-confluent cultures by replacing the growth media (GM, DMEM with 10% FBS) with differentiation media (DM, DMEM with 2% horse serum).

extract_protocol: At various time points after differentiation, cells were harvested and RNA was extracted with phenol-chloroform and either saved as input samples for microarrays or subjected to AUF1 or IgG ribonucleoprotein immunoprecipitation.  Total RNA from the various time points was either saved as examples of input RNA, or subjected to AUF1 or IgG ribonucleoprotein immunoprecipitation.  C2C12 cells cultured in GM and DM were lysed in 20 mM Tris-HCl at pH 7.5, 100 mM KCl, 5 mM MgCl2, and 0.5% NP-40 for 10 min on ice and centrifuged at 15,000 × g for 10 min at 4°C.  The supernatants were incubated with protein-A Dynabeads beads coated with anti-AUF1 (Millipore) or with control IgG (Santa Cruz Biotechnology) antibodies for 2 hr at 4°C.  The beads were washed with NT2 buffer (50 mM Tris-HCl [pH 7.5], 150 mM NaCl, 1 mM MgCl2, 0.05% NP-40), followed by incubation with 20 units of RNase-free DNase I for 15 min at 37°C to remove the DNA.  The samples were then incubated for 15 min at 55°C with 0.1% SDS/0.5 mg/ml Proteinase K to digest proteins.  The RNA from the IP samples was extracted using phenol-chloroform, precipitated, and used along with the  RNA from the Input samples for cDNA microarrays.

tag: cell line

tag: cell type

value: myoblast

value: female

tag: time point

value: 6 Day, Differention


title: Input DNA Control Day3 Replicate 4

description:
Input RNA Control
Input RNA Control Day3 Replicate 4

source_name: C2C12 Cells_Day3

value: 3 Day, Differention


title: Input DNA Control Day6 Replicate 4

description:
Input RNA Control
Input RNA Control Day6 Replicate 4


title: Input DNA Control Day6 Replicate 5

description:
Input RNA Control
Input RNA Control Day6 Replicate 5


title: Input DNA Control Day3 Replicate 3

description:
Input RNA Control
Input RNA Control Day3 Replicate 3


title: Input DNA Control Day3 Replicate 1

description:
Input RNA Control
Input RNA Control Day3 Replicate 1

value: 3 Day Differention


title: Input DNA Control Day6 Replicate 3

description:
Input RNA Control
Input RNA Control Day6 Replicate 3


title: Csbm/m Mouse_cerebellum_High Fat diet Ad Lib_Replicate-1

description:
Sample name: CSB_HFD_1
Streptavidin-Cy3 bound to biotin-labeled cRNA.


description:
IgG Control ribonucleoprotein immunoprecipitation
IgG Control RNA Pulldown Day4 Replicate2

source_name: C2C12 Cells_Day4

value: 4 Day, Differention


description:
IgG Control ribonucleoprotein immunoprecipitation
IgG Control RNA Pulldown Day4 Replicate1


title: Input DNA Control Day6 Replicate 1

description:
Input RNA Control
Input RNA Control Day6 Replicate 1


title: Input DNA Control Day3 Replicate 2

description:
Input RNA Control
Input RNA Control Day3 Replicate 2


title: Input DNA Control Day0 Replicate 5

description:
Input RNA Control
Input RNA Control Day0 Replicate 5

source_name: C2C12 Cells_Day0

value: Day 0 Growing Cells


title: Input DNA Control Day0 Replicate 1

description:
Input RNA Control
Input RNA Control Day0 Replicate 1


title: Input DNA Control Day3 Replicate 5

description:
Input RNA Control
Input RNA Control Day3 Replicate 5


title: Input DNA Control Day0 Replicate 3

description:
Input RNA Control
Input RNA Control Day0 Replicate 3


title: Input DNA Control Day0 Replicate 2

description:
Input RNA Control
Input RNA Control Day0 Replicate 2


title: Input DNA Control Day0 Replicate 4

description:
Input RNA Control
Input RNA Control Day0 Replicate 4


description:
IgG Control ribonucleoprotein immunoprecipitation
IgG Control RNA Pulldown Day4 Replicate4


description:
IgG Control ribonucleoprotein immunoprecipitation
IgG Control RNA Pulldown Day4 Replicate3


description:
IgG Control ribonucleoprotein immunoprecipitation
IgG Control RNA Pulldown Day0 Replicate4


description:
IgG Control ribonucleoprotein immunoprecipitation
IgG Control RNA Pulldown Day6 Replicate4


description:
IgG Control ribonucleoprotein immunoprecipitation
IgG Control RNA Pulldown Day0 Replicate1


description:
IgG Control ribonucleoprotein immunoprecipitation
IgG Control RNA Pulldown Day6 Replicate3


description:
IgG Control ribonucleoprotein immunoprecipitation
IgG Control RNA Pulldown Day0 Replicate2


description:
IgG Control ribonucleoprotein immunoprecipitation
IgG Control RNA Pulldown Day0 Replicate3


description:
IgG Control ribonucleoprotein immunoprecipitation
IgG Control RNA Pulldown Day6 Replicate2


description:
IgG Control ribonucleoprotein immunoprecipitation
IgG Control RNA Pulldown Day2 Replicate3

source_name: C2C12 Cells_Day2

value: 2 Day, Differention


description:
IgG Control ribonucleoprotein immunoprecipitation
IgG Control RNA Pulldown Day2 Replicate1


title: AUF1 RNA Pulldown Day6 Replicate2

description:
RIP AUF1, ribonucleoprotein immunoprecipitation to identify AUF1-bound mRNAs
AUF1 RNA Pulldown Day6 Replicate2


description:
IgG Control ribonucleoprotein immunoprecipitation
IgG Control RNA Pulldown Day6 Replicate1


title: AUF1 RNA Pulldown Day6 Replicate3

description:
RIP AUF1, ribonucleoprotein immunoprecipitation to identify AUF1-bound mRNAs
AUF1 RNA Pulldown Day6 Replicate3


description:
IgG Control ribonucleoprotein immunoprecipitation
IgG Control RNA Pulldown Day2 Replicate2


title: AUF1 RNA Pulldown Day6 Replicate4

description:
RIP AUF1, ribonucleoprotein immunoprecipitation to identify AUF1-bound mRNAs
AUF1 RNA Pulldown Day6 Replicate4


title: AUF1 RNA Pulldown Day4 Replicate3

description:
RIP AUF1, ribonucleoprotein immunoprecipitation to identify AUF1-bound mRNAs
AUF1 RNA Pulldown Day4 Replicate3


title: AUF1 RNA Pulldown Day6 Replicate1

description:
RIP AUF1, ribonucleoprotein immunoprecipitation to identify AUF1-bound mRNAs
AUF1 RNA Pulldown Day6 Replicate1


title: AUF1 RNA Pulldown Day4 Replicate2

description:
RIP AUF1, ribonucleoprotein immunoprecipitation to identify AUF1-bound mRNAs
AUF1 RNA Pulldown Day4 Replicate2


title: AUF1 RNA Pulldown Day2 Replicate3

description:
RIP AUF1, ribonucleoprotein immunoprecipitation to identify AUF1-bound mRNAs
AUF1 RNA Pulldown Day2 Replicate3


title: AUF1 RNA Pulldown Day4 Replicate1

description:
RIP AUF1, ribonucleoprotein immunoprecipitation to identify AUF1-bound mRNAs
AUF1 RNA Pulldown Day4 Replicate1


title: AUF1 RNA Pulldown Day0 Replicate4

description:
RIP AUF1, ribonucleoprotein immunoprecipitation to identify AUF1-bound mRNAs
AUF1 RNA Pulldown Day0 Replicate4


title: AUF1 RNA Pulldown Day2 Replicate1

description:
RIP AUF1, ribonucleoprotein immunoprecipitation to identify AUF1-bound mRNAs
AUF1 RNA Pulldown Day2 Replicate1


title: AUF1 RNA Pulldown Day0 Replicate3

description:
RIP AUF1, ribonucleoprotein immunoprecipitation to identify AUF1-bound mRNAs
AUF1 RNA Pulldown Day0 Replicate3


title: AUF1 RNA Pulldown Day0 Replicate1

description:
RIP AUF1, ribonucleoprotein immunoprecipitation to identify AUF1-bound mRNAs
AUF1 RNA Pulldown Day0 Replicate1


title: TLR2_KO+SA_12_HR-1

description: RNA from the S. aureus-stimulated microglia (12 hr) of TLR2-KO mice.

hyb_protocol: Standard Illumina protocol. In short, a total of 0.75ug of biotin-labeled cRNA was hybridized at 58 degrees C for 16 hours to Illumina's SentrixMouse Ref-8, v2 Expression BeadChips (Illumina, San Diego, CA). Each BeadChip has 24,000 well-annotated RefSeq transcripts with approximately 30-fold redundancy. The arrays were washed, blocked and the biotin-labeled cRNA was detected by staining with streptavidin-Cy3.

data_processing: Data was extracted using the Illumina BeadStudio software (v3.4). Any spots at or in the Sample data table. the background were filtered out using an Illumina detection p value of 0.02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented in the Sample data table.  Z-score = (raw value - avg)/std. Complete data including detection p-values is included in the supplementary file that is linked to the Series record.

source_name: microglia, TLR2 KO, 12hr

label_protocol: Standard Illumina protocol using the Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791). In short, 0.5g of total RNA was first converted into single-stranded cDNA with reverse transcriptase using an oligo-dT primer containing the T7 RNA polymerase promoter site and then copied to produce double-stranded cDNA molecules. The double-stranded cDNA was cleaned and concentrated with the supplied columns and used in an overnight in-vitro transcription reaction where single-stranded RNA (cRNA) was generated and labeled by incorporation of biotin-16-UTP.

growth_protocol:
TLR2 KO mice were backcrossed with C57BL/6 animals for a minimum of eight generations prior to use in these studies.
Primary mixed glial cultures were prepared on the same day from the cerebral corticies of neonatal TLR2 KO mice (2-4 days of age). Microglia were harvested from mixed glial cultures using a differential shaking technique with a purity of >98%.

extract_protocol: Total RNA was extracted from the stimulated microglia using Trizol (Invitrogen).  The quality and quantity of total RNA were analyzed by the Agilent 2100 Bioanalyzer using RNA 6000 nano chips (Agilent Technologies, Palo Alto, CA).

treatment_protocol: A USA300 community-acquired methicillin-resistant S. aureus (CA-MRSA) clinical isolate recovered from a patient with a fatal brain abscess was kindly provided by Dr. Costi Sifri (University of Virginia School of Medicine, Charlottesville).  Bacterial strains were heat-inactivated and used to stimulate TLR2-KO microglia at 107 colony forming units (cfu)/well for 6 or 12 hours.

tag: strain

tag: genotype

value: TLR2 knockout

tag: developmental stage

value: neonatal

value: 2-4 days

value: cerebral cortex

value: microglia from primary mixed glial culture

value: Staphylococcus aureus stimulation

tag: time

value: 12 hours


title: WT-SA_12_HR-3

description: RNA from the S. aureus-stimulated microglia (12 hr) of WT C57BL/6 mice.

source_name: microglia, wild type control, 12hr

growth_protocol: Primary mixed glial cultures were prepared on the same day from the cerebral corticies of neonatal WT mice (2-4 days of age). Microglia were harvested from mixed glial cultures using a differential shaking technique with a purity of >98%.

treatment_protocol: A USA300 community-acquired methicillin-resistant S. aureus (CA-MRSA) clinical isolate recovered from a patient with a fatal brain abscess was kindly provided by Dr. Costi Sifri (University of Virginia School of Medicine, Charlottesville).  Bacterial strains were heat-inactivated and used to stimulate WT microglia at 107 colony forming units (cfu)/well for 6 or 12 hours.

value: wild type


title: AUF1 RNA Pulldown Day2 Replicate2

description:
RIP AUF1, ribonucleoprotein immunoprecipitation to identify AUF1-bound mRNAs
AUF1 RNA Pulldown Day2 Replicate2


title: WT-SA_6_HR-3

description: RNA from the S. aureus-stimulated microglia (6 hr) of WT C57BL/6 mice.

source_name: microglia, wild type control, 6hr

value: 6 hours


title: TLR2_KO+SA_12_HR-3


title: TLR2_KO+SA_6_HR-3

description: RNA from the S. aureus-stimulated microglia (6 hr) of TLR2-KO mice.

source_name: microglia, TLR2 KO, 6hr


title: TLR2_KO+SA_6_HR-2


title: TLR2_KO+SA_6_HR-1


title: R09

status: Public on Nov 25 2014

type: SRA

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

country: United Kingdom

institute: Centre for Immunity, Infection and Evolution

library_source: transcriptomic

data_processing:
Primers were trimmed from the raw fastq format sequence data using cutadapt software (v1.3; parameters -O 6 -m 16 -q 20).
Only trimmed reads that contained the adapter, were 16-40 nt in length and were present at 2 or more copies per sample were retained.
Simple scripts were used to generate non-redundant sequence sets (collapsed) in fasta format from each sample.
Genome_build: http://www.nematodes.org/genomes/heligmosomoides_polygyrus/nHp_1_0.fna.gz
Supplementary_files_format_and_content: Processed data files contain the non-redundant sequences from each sample.

organism: Heligmosomoides polygyrus

source_name: Vesicle fraction rep 3

growth_protocol: For collection of H. polygyrus secretion product, CF1 mice are infected with infective-stage larvae by gavage and adult parasites collected from the small intestine 14 days post infection. The worms are maintained in serum-free media in vitro.

extract_protocol:
Total RNA was size selected on 15% denaturing PAGE and libraries prepared from the 18-30 nt fraction using Illumina Small RNA preparation kit version 1.5 and sequenced on the GAIIX, the Hpoly HES sample was pooled with RNA prepared in parallel from 60-90 size selection. For analysis of vesicle and non-vesicle fractions, small RNA libraries were prepared using the TruSeq kit and sequenced on MiSeq platform.
Illumina Small RNA preparation kit v1.5 and TrueSeq Small RNA kit

treatment_protocol: For separation of the vesicle and non-vesicle fractions, filtered secretion produce is ultracentrifuged at 100,000 g for 2 hours followed by 2 washes in PBS.

tag: replicate

tag: sample type

value: Vesicle fraction

tag: kit

value: TrueSeq small RNA preparation kit


title: WT-SA_12_HR-1


title: WT-SA_6_HR-1


title: WT-SA_6_HR-2


title: R08

source_name: Vesicle fraction rep 2


title: Liver_Standard Diet plus SRT1720_Replicate #3

status: Public on Dec 20 2014

data_processing: Data was extracted using the Illumina GenomeStudio software(v1.6.0).  Any spots at or below the background were filtered out using an Illumina detection p value of 0.02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below.  Z-score = (raw value - avg)/std.  Complete data including detection scores will be included in the supplemental file.

source_name: Liver_Standard Diet plus SRT1720

growth_protocol: Male C57BL/6J mice were started on two different diets at 28 weeks of age after randomization into two groups of 100 mice per group. Mice were placed into a standard diet group and a standard diet plus SRT1720 group.  Mice were allowed to live to the end of their lives.

extract_protocol: At the end of their life, muscle and liver tissue was harvested and snap frozen.  RNA was extracted from both tissues using 1.0mm glass beads in a Precellys 24 Tissue Homogenizer and Qiagen RNeasy Mini Kits for the liver tissue or the RNeasy Fibrous Tissue kit for the muscle tissue according to manufacturer's specifications. Quality and quantity of the total RNA was checked with the Agilent 2100 bioanalyzer using RNA 6000 Nano chips.

treatment_protocol: Diets were started at 28 weeks of age after randomization into two groups of 100 mice each. Mice were fed either a standard AIN-93G diet (SD; carbohydrate:protein:fat ratio of 64:19:17 percent of kcal), or a SD supplemented with SRT1720. SRT1720 was added at a dose of 1.33 g drug per kg of chow, formulated to provide daily doses of approximately 100 mg drug per kg body weight to the mice.

value: male

value: Liver

value: Standard Diet plus SRT1720


title: Liver_Standard Diet plus SRT1720_Replicate #2


title: Liver_Standard Diet plus SRT1720_Replicate #4


title: Muscle_Standard Diet plus SRT1720_Replicate #2

source_name: Muscle_Standard Diet plus SRT1720

value: Muscle


title: Liver_Standard Diet plus SRT1720_Replicate #1


title: Muscle_Standard Diet plus SRT1720_Replicate #4


title: Muscle_Standard Diet plus SRT1720_Replicate #3


title: Muscle_Standard Diet plus SRT1720_Replicate #1


title: R07

source_name: Vesicle fraction rep 1


title: AUF1 RNA Pulldown Day0 Replicate2

description:
RIP AUF1, ribonucleoprotein immunoprecipitation to identify AUF1-bound mRNAs
AUF1 RNA Pulldown Day0 Replicate2

value: myoblast

value: female

value: Day 0 Growing Cells


title: HLY-1_eIF4E3_transcriptome_replicate 1

status: Public on Nov 18 2014

description:
Sample name: E3FLW1
Stable cell lines of HLY-1 overexpressing eIF4E3 were generated by retroviral transduction and were selected and maintained with puromycin (2 μg ml-1).
Streptavidin-Cy3 bound to biotin-labeled cRNA.

hyb_protocol: Standard Illumina protocol. In short, a total of 0.75ug of biotin-labeled cRNA was hybridized at 58 degrees C for 16 hours to Illumina's SentrixHumanHT-12 v4 Expression BeadChips (Illumina, San Diego, CA). Each array on the HumanHT-12 v4 Expression BeadChip targets more than 47,000 probes derived from the National Center for Biotechnology Information Reference Sequence (NCBI) RefSeq Release 38 (November 7, 2009) and other sources and offers genome-wide transcriptional coverage of well-characterized genes, gene candidates, and splice variants, with approximately 15-fold redundancy. The arrays were washed, blocked and the biotin-labeled cRNA was detected by staining with streptavidin-Cy3.

data_processing: Data was extracted using the Illumina GenomeStudio software (v1.9.0). Any spots at or below the background were filtered out using an Illumina detection p value of 0.02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below. Z-score = (raw value - avg)/std.

label: Biotin

organism: Homo sapiens

source_name: Diffuse large B-cell lymphoma cell line HLY1 transduced with elF4E3, total RNA

growth_protocol: HLY-1 cells were grown in RPMI-1640 media supplemented with 10% FBS, 100 unit/ml penicillin and 0.1 mg/ml streptomycin at 37 degree C with 5% CO2.

extract_protocol:
RNA extraction was carried out on total RNA to investigate the transcriptome.
RNA was isolated using Trizol reagent and the standard protocol. Quality and quantity of the total RNA was tested using the Agilent 2100 Bio-Analyzer and RNA 6000 nano kits.

treatment_protocol:
Expression plasmids for eIF4E1 and eIF4E3 were cloned into lentiviral-vector system CD513B (System Biosciences, CA). For lentiviral packaging, HEK293T/17 cells were seeded at 40% confluence and transfected the following day with psPAX2 and pMD2.G. Virus-containing medium was concentrated using Amicon Ultra-15 100 kDA centrifugal filters (EMD Millipore) per manufacturer's instruction. HLY-1 and centrifuged for 35 mins. at 800 r.c.f. at 30 degrees C. Cell pellets were resuspended in virus-containing medium for 12 hrs. Cells were selected and maintained with puromycin (2 μg ml-1).
1x10^7 cells were harvested using polysome extraction buffer (150 mM KOAc, 2.5 mM Mg(OAc)2, 20 mM K-N-2-hydroxyethylpiperazine-N′-2-ethanesulfonic acid, pH. 7.5, RNaseOUT, and protease inhibitor cocktail). Lysates were fractionated using a linear sucrose gradient (10-50% sucrose) in a Beckman Coulter SW41 swinging bucket rotor (35,000 r.p.m., 3 hrs, 4 degrees C). Heavy fractions numbers 9, 10 and 11 were isolated for RNA extraction using Trizol.

value: diffuse large B-cell lymphoma cell line

tag: stable transduction

tag: rna

value: total RNA


title: WT-SA_12_HR-2

value: neonatal

value: 2-4 days

value: cerebral cortex


title: HLY-1_eIF4E1_transcriptome_replicate 2

description:
Sample name: E1FL_W2
Stable cell lines of HLY-1 overexpressing eIF4E1 were generated by retroviral transduction and were selected and maintained with puromycin (2 μg ml-1).
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: Diffuse large B-cell lymphoma cell line HLY1 transduced with elF4E1, total RNA


title: HLY-1_eIF4E1_transcriptome_replicate 1

description:
Sample name: E1FL_W1
Stable cell lines of HLY-1 overexpressing eIF4E1 were generated by retroviral transduction and were selected and maintained with puromycin (2 μg ml-1).
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: HLY-1_Empty vector_translatome_replicate 3

description:
Sample name: EV-c
Stable cell lines of HLY-1 were generated by retroviral transduction using an empty vector and were selected and maintained with puromycin (2 μg ml-1).
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: Diffuse large B-cell lymphoma cell line HLY1 transduced with empty vector, polysomal RNA fractions 9-11

extract_protocol:
RNA extraction was carried out on polysomal fractions #9-11 to investigate the translatome.
RNA was isolated using Trizol reagent and the standard protocol. Quality and quantity of the total RNA was tested using the Agilent 2100 Bio-Analyzer and RNA 6000 nano kits.

value: empty vector

value: polysomal RNA fractions 9-11


title: HLY-1_eIF4E3_transcriptome_replicate 3

description:
Sample name: E3FLW3
Stable cell lines of HLY-1 overexpressing eIF4E3 were generated by retroviral transduction and were selected and maintained with puromycin (2 μg ml-1).
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: HLY-1_Empty vector_transcriptome_replicate 3

description:
Sample name: EVW-c
Stable cell lines of HLY-1 were generated by retroviral transduction using an empty vector and were selected and maintained with puromycin (2 μg ml-1).
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: Diffuse large B-cell lymphoma cell line HLY1 transduced with empty vector, total RNA


title: HLY-1_eIF4E1_transcriptome_replicate 3

description:
Sample name: E1FL_W3
Stable cell lines of HLY-1 overexpressing eIF4E1 were generated by retroviral transduction and were selected and maintained with puromycin (2 μg ml-1).
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Total RNA with PDL 15 HuR siRNA

status: Public on Nov 04 2014

description: Total RNA seq

data_processing:
The tags were aligned using Tophat (v2.0.6) with --GTF option and segment length of 20 (all other parameters were at their default values)
The aligned tags were assebled using Cufflinks (v2.0.2) with --GTF-guide option and minimum fragment treshold of 5 (all other parameters were at their default values)
The samples were merged using Cuffcompare
Significant changes were calculated using Cuffdiff using fdr cuttoff of 0.1
Genome_build: hg19
Supplementary_files_format_and_content: The processed data file contain the RPKM values of the isoforms in tab-delimited TXT format.

growth_protocol: Human diploid lung (WI-38) fibroblasts were cultured in DMEM (Invitrogen) supplemented with 10% (v/v) FBS and antibiotics.

extract_protocol:
Trizol from Invitrogen was used for total RNA extraction
100 ng of RNA was used for first-strand and second-strand cDNA synthesis followed by single-primer isothermal amplification (SPIA) using NuGEN Ovation RNA-Seq System V2 kits according to the manufacturer’s protocol. The kit amplified both polyA-tailed and non-polyA-tailed RNA and removed ribosomal RNA. The amplified cDNA was sheared using Bioruptor (Diagenode) to an average size of 250-450 bases. The sequencing library was prepared using Illumina ChIp-Seq kits according to the manufacturer’s protocol (Illumina, San Diego, CA). In short, the ends of the fragments were repaired using T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase), and T4 polynucleotide kinase (PNK) and adenines were added to the 3’ end. Adapters were ligated to the DNA fragments, which were size-selected (250-300 bases) after electrophoresis through a 4% agarose gel. Eighteen cycles of PCR amplification was performed, followed by cluster generation and sequencing with Illumina Genome Analyzer (GA-II).

treatment_protocol: WI-38 cells were collected at PDL 15 and 55 and also transfected with Control siRNA, AUF1 siRNA, HuR siRNA

tag: rna type

value: WI-38 Total RNA

tag: passages

tag: crosslinking

value: not applied

tag: ip protein

value: PDL 15 HuR siRNA


title: Total RNA with PDL 55 fibroblast

description: Total RNA seq


title: Total RNA with PDL 15 AUF1 siRNA

description: Total RNA seq

tag: treatment

value: PDL 15 AUF1 siRNA


title: Ribosome Profiling with Control siRNA

description:
small RNA (20 ~ 35 nt)
Ribosome Profiling seq

data_processing:
Adapter sequences were clipped and trimmed using fastx_clipper and fastx_trimmer respectively and rRNA removed
The tags were aligned using Tophat (v2.0.6) to known transcripts and segment length of 20 (all other parameters were at their default values)
The aligned tags were assebled using Cufflinks (v2.0.2) with --GTF option, fragment mean length of 28 and minimum fragment treshold of 5 (all other parameters were at their default values)
The samples were merged using Cuffcompare
Significant changes were calculated using Cuffdiff using fdr cuttoff of 0.1
Genome_build: hg19
Supplementary_files_format_and_content: The processed data file contain the RPKM values of the isoforms in tab-delimited TXT format.

source_name: HeLa

growth_protocol: Human cervical carcinoma (HeLa) cells were cultured in DMEM (Invitrogen) supplemented with 10% (v/v) FBS and antibiotics.

extract_protocol:
After lysis and Rnase digestion, mono ribosomes were purified by 0.9M sucrose cushion
Small RNA libraries were prepared as described previously (Guo et al., 2010)

treatment_protocol: HeLa cells were transfected with Control siRNA, AUF1 siRNA, or HuR siRNA.

value: HeLa RNA from mono ribosome

value: unknown

tag: cell line

value: HeLa

value: Control siRNA


title: Total RNA with PDL 15 fibroblast

description: Total RNA seq


title: Total RNA with PDL 15 Contro siRNA

description: Total RNA seq

value: PDL 15 Contro siRNA


title: HLY-1_Empty vector_transcriptome_replicate 2

description:
Sample name: EVW-b
Stable cell lines of HLY-1 were generated by retroviral transduction using an empty vector and were selected and maintained with puromycin (2 μg ml-1).
Streptavidin-Cy3 bound to biotin-labeled cRNA.

tag: cell type


title: HLY-1_Empty vector_transcriptome_replicate 1

description:
Sample name: EVW-a
Stable cell lines of HLY-1 were generated by retroviral transduction using an empty vector and were selected and maintained with puromycin (2 μg ml-1).
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: HLY-1_eIF4E3_transcriptome_replicate 2

description:
Sample name: E3FLW2
Stable cell lines of HLY-1 overexpressing eIF4E3 were generated by retroviral transduction and were selected and maintained with puromycin (2 μg ml-1).
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Ribosome Profiling with AUF1 siRNA

value: AUF1 siRNA


title: Total RNA with p37, p40, p42, p45 overexpresion

description: Total RNA seq

growth_protocol: Human embryonic kidney 293 (HEK293) cells were cultured in DMEM (Invitrogen) supplemented with 10% (v/v) FBS and antibiotics.

treatment_protocol: HEK293 cells were transfected with Control siRNA, AUF1 siRNA, Empty Vector, Flag-AUF1 p37, p40, p42, or p45.

value: HEK293 Total RNA

value: p37, p40, p42, p45 overexpresion


title: HLY-1_Empty vector_translatome_replicate 2

description:
Sample name: EV-b
Stable cell lines of HLY-1 were generated by retroviral transduction using an empty vector and were selected and maintained with puromycin (2 μg ml-1).
Streptavidin-Cy3 bound to biotin-labeled cRNA.

value: diffuse large B-cell lymphoma cell line


title: HLY-1_eIF4E1_translatome_replicate 3

description:
Sample name: E1_FL-c
Stable cell lines of HLY-1 overexpressing eIF4E1 were generated by retroviral transduction and were selected and maintained with puromycin (2 μg ml-1).
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: Diffuse large B-cell lymphoma cell line HLY1 transduced with elF4E1, polysomal RNA fractions 9-11


title: HLY-1_Empty vector_translatome_replicate 1

description:
Sample name: EV-a
Stable cell lines of HLY-1 were generated by retroviral transduction using an empty vector and were selected and maintained with puromycin (2 μg ml-1).
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: HLY-1_eIF4E1_translatome_replicate 2

description:
Sample name: E1_FL-b
Stable cell lines of HLY-1 overexpressing eIF4E1 were generated by retroviral transduction and were selected and maintained with puromycin (2 μg ml-1).
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: HLY-1_eIF4E3_translatome_replicate 1

description:
Sample name: E3_FL-1
Stable cell lines of HLY-1 overexpressing eIF4E3 were generated by retroviral transduction and were selected and maintained with puromycin (2 μg ml-1).
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: Diffuse large B-cell lymphoma cell line HLY1 transduced with elF4E3, polysomal RNA fractions 9-11


title: HLY-1_eIF4E3_translatome_replicate 3

description:
Sample name: E3_FL-3
Stable cell lines of HLY-1 overexpressing eIF4E3 were generated by retroviral transduction and were selected and maintained with puromycin (2 μg ml-1).
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: HLY-1_eIF4E3_translatome_replicate 2

description:
Sample name: E3_FL-2
Stable cell lines of HLY-1 overexpressing eIF4E3 were generated by retroviral transduction and were selected and maintained with puromycin (2 μg ml-1).
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Ribosome Profiling with HuR siRNA

value: HuR siRNA


title: Total RNA with p40 overexpresion

description: Total RNA seq

value: p40 overexpresion


title: AUF1 p45 PAR-CLIP

description:
small RNA (20 ~ 35 nt)
PAR-CLIP

data_processing:
Adapter sequences were clipped using fastx_clipper
Sequences were aligned to the genome using bowtie with the following parameters -v 2 -m 10 --best --strata
Aligned reads were analyzed with PARAlyzer software using minimum read count of 5, minimum cluster size of 10, minimum conversion count and location of 2
Genome_build: hg19
Supplementary_files_format_and_content: PARAlyzer program created the CSV file containing information about chromosome, strand, cluster start, cluster end, cluster ID, cluster sequence, read count, mode loacation, mode score, conversion location count, conversion event count and non-conversion event count

extract_protocol:
For AUF1 PAR-CLIP, the cleared cell lysates were treated with 1 U/μl RNase T1 (Fermentas) and AUF1 proteins immunoprecipitated with monoclonal anti-FLAG antibodies (M2, Sigma) bound to Protein G Dynabeads. The RNA residing in the immunoprecipitate was further trimmed with 100 U/ml RNase T1. The beads were washed in lysis buffer and resuspended in one bead volume of dephosphorylation buffer. RNA was dephosphorylated and radioactively labeled with γ-32P-ATP. The protein-RNA complexes were separated by SDS-PAGE, and RNA-protein complexes visualized by autoradiography. The radioactive bands migrating at approximately ~37, 40, 42, and 45 kDa were recovered and the protein-RNA complex was electroeluted from the gel. The protein was removed by digestion in proteinase K buffer in the presence of 0.2 mg/ml proteinase K (Roche).
The RNA was then recovered by acidic phenol/chloroform extraction and ethanol precipitation, converted into a cDNA library as described previously (Hafner et al., 2010)

treatment_protocol: For AUF1 PAR-CLIP, the four isoforms of AUF1 (p37, p40, p42, and p45) tagged with a Flag epitope were expressed in HEK293 cells. One hundred million cells per culture were incubated in medium supplemented with 100 μM 4SU for 16 hours, washed with PBS and irradiated with 0.15 mJ/cm2, 365 nm UV light in a Spectrolinker XL-1500 UV cross linker to crosslink RNA to AUF1, and harvested and lysed in the equivalent of 3 cell pellet volumes of NP40 lysis buffer.

value: HEK293 with Flag IP

value: 4-SU with 365nm

value: Flag - AUF1 p37


title: Total RNA with p42 overexpresion

description: Total RNA seq

value: not applied

value: p42 overexpresion


title: Total RNA with AUF1 siRNA

description: Total RNA seq


title: Total RNA with Empty Vector

description: Total RNA seq

value: Empty Vector


title: Total RNA with Control siRNA

description: Total RNA seq


title: Total RNA with p37 overexpresion

description: Total RNA seq

value: p37 overexpresion


title: Total RNA with p45 overexpresion

description: Total RNA seq

value: unknown

value: p45 overexpresion


title: Csbm/m Mouse_cerebellum_Caloric restricted diet_Replicate-1

description:
Sample name: CSB_CR_1
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: Csbm/m mouse, cerebellum, caloric-restricted diet

tag: strain/background

tag: genotype/variation

value: Csbm/m

tag: gender

value: male

tag: tissue

value: cerebellum

tag: age

value: 1 year

value: 40% caloric restriction of SD diet


title: AUF1 p37 PAR-CLIP

description:
small RNA (20 ~ 35 nt)
PAR-CLIP


title: AUF1 p42 PAR-CLIP

description:
small RNA (20 ~ 35 nt)
PAR-CLIP

value: Flag - AUF1 p42


title: AUF1 p40 PAR-CLIP

description:
small RNA (20 ~ 35 nt)
PAR-CLIP

value: Flag - AUF1 p40


title: HLY-1_eIF4E1_translatome_replicate 1

description:
Sample name: E1_FL-a
Stable cell lines of HLY-1 overexpressing eIF4E1 were generated by retroviral transduction and were selected and maintained with puromycin (2 μg ml-1).
Streptavidin-Cy3 bound to biotin-labeled cRNA.

value: diffuse large B-cell lymphoma cell line

value: polysomal RNA fractions 9-11


title: Muscle_Caloric_Restriction_Replicate #5

status: Public on Sep 22 2014

description: Muscle_Caloric_Restriction_Replicate #5

data_processing:
Data was extracted using the Illumina GenomeStudio software(v1.6.0).  Any spots at or below the background were filtered out using an Illumina detection p value of 0.02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below.  Z-score = (raw value - avg)/std.  Complete data including detection scores will be included in the supplemental file.
Detection_Pval = Detection Pvalue from Illumina GenomeStudio software, ver 1.6.0.

label: Streptavidin-Cy3 bound to biotin labeled cRNA.

growth_protocol: Male C57BL/6J mice were started on three different diets at 28 weeks of age after randomization into three groups. Mice were placed either into a standard diet group, a standard diet plus SRT2104 group or a 40% caloric restriction group.  Mice were allowed to live either to the end of their lives or until they were sacrificed.

extract_protocol: At 41 weeks of age, after 14 weeks on each diet, muscle and liver tissue was harvested and snap frozen.  RNA was extracted from both tissues using 1.0mm glass beads in a Precellys 24 Tissue Homogenizer and Qiagen RNeasy Mini Kits for the liver tissue or the RNeasy Fibrous Tissue kit for the muscle tissue according to manufacturer's specifications. Quality and quantity of the total RNA was checked with the Agilent 2100 bioanalyzer using RNA 6000 Nano chips.

treatment_protocol: Diets were started at 28 weeks of age after randomization into three groups. Mice were fed either a standard AIN-93G diet (SD; carbohydrate:protein:fat ratio of 64:19:17 percent of kcal), or a SD supplemented with SRT2104 at a dose of 1.33 g drug per kg of chow, formulated to provide daily doses of approximately 100 mg drug per kg body weight to the mice, or the SD diet at a 40% caloric restriction.

tag: strain

value: Muscle

value: Standard AIN-93G diet, 40% Caloric restriction (CR)


title: Liver_Caloric_Restriction_Replicate #3

description: Liver_Caloric_Restriction_Replicate #3

value: Liver


title: Liver_Caloric_Restriction_Replicate #4

description: Liver_Caloric_Restriction_Replicate #4


title: Muscle_Caloric_Restriction_Replicate #2

description: Muscle_Caloric_Restriction_Replicate #2


title: Muscle_Caloric_Restriction_Replicate #1

description: Muscle_Caloric_Restriction_Replicate #1


title: Liver_Caloric_Restriction_Replicate #2

description: Liver_Caloric_Restriction_Replicate #2


title: Muscle_Caloric_Restriction_Replicate #4

description: Muscle_Caloric_Restriction_Replicate #4


title: Muscle_Caloric_Restriction_Replicate #3

description: Muscle_Caloric_Restriction_Replicate #3


title: Liver_Caloric_Restriction_Replicate #1

description: Liver_Caloric_Restriction_Replicate #1


title: Liver_Caloric_Restriction_Replicate #5

description: Liver_Caloric_Restriction_Replicate #5


title: Liver_Standard Diet plus SRT2104_Replicate #1

source_name: Liver_Standard Diet plus SRT2104

growth_protocol: Male C57BL/6J mice were started on two different diets at 28 weeks of age after randomization into two groups of 100 mice per group. Mice were placed into a standard diet group and a standard diet plus SRT2104 group.  Mice were allowed to live to the end of their lives.

treatment_protocol: Diets were started at 28 weeks of age after randomization into two groups of 100 mice each. Mice were fed either a standard AIN-93G diet (SD; carbohydrate:protein:fat ratio of 64:19:17 percent of kcal), or a SD supplemented with SRT2104. SRT2104 was added at a dose of 1.33 g drug per kg of chow, formulated to provide daily doses of approximately 100 mg drug per kg body weight to the mice.

value: Standard Diet plus SRT2104


title: Liver_Standard Diet plus SRT2104_Replicate #5


title: Liver_Standard Diet plus SRT2104_Replicate #2


title: Liver_Standard Diet_Replicate #1

description: Liver_Standard Diet_Replicate #1

source_name: Liver_Standard Diet

value: standard AIN-93G diet (SD)


title: Muscle_Standard Diet plus SRT2104_Replicate #1

source_name: Muscle_Standard Diet plus SRT2104


title: Muscle_Standard Diet plus SRT2104_Replicate #3


title: Muscle_Standard Diet plus SRT2104_Replicate #4


title: Liver_Standard Diet_Replicate #3

description: Liver_Standard Diet_Replicate #3


title: Liver_Standard Diet_Replicate #2

description: Liver_Standard Diet_Replicate #2


title: Liver_Standard Diet_Replicate #5

description: Liver_Standard Diet_Replicate #5


title: Liver_Standard Diet plus SRT2104_Replicate #4


title: Liver_Standard Diet_Replicate #4

description: Liver_Standard Diet_Replicate #4


title: Muscle_Standard Diet plus SRT2104_Replicate #2


title: Muscle_Standard Diet plus SRT2104_Replicate #5


title: Liver_Standard Diet plus SRT2104_Replicate #3


title: Muscle_Standard Diet_Replicate #5

description: Muscle_Standard Diet_Replicate #5

source_name: Muscle_Standard Diet


title: Muscle_Standard Diet_Replicate #3

description: Muscle_Standard Diet_Replicate #3


title: Muscle_Standard Diet_Replicate #4

description: Muscle_Standard Diet_Replicate #4


title: Muscle_Standard Diet_Replicate #1

description: Muscle_Standard Diet_Replicate #1


status: Public on Jul 21 2014

description:
Samplename: AR_93N080
Aorta_High Fat-Sugar diet+Resveratrol_ Rep-8

hyb_protocol: Standard Illumina protocol. In short, a total of 0.75ug of biotin-labeled cRNA was hybridized at 58 degrees C for 16 hours to Illumina's SentrixHumanHT-12 v4 Expression BeadChips (Illumina, San Diego, CA).  Each array on the HumanHT-12 v4 Expression BeadChip targets more than 47,000 probes derived from the National Center for Biotechnology Information Reference Sequence (NCBI) RefSeq Release 38 (November 7, 2009) and other sources and offers genome-wide transcriptional coverage of well-characterized genes, gene candidates, and splice variants, with approximately 15-fold redundancy. The arrays were washed, blocked and the biotin labeled cRNA was detected by staining with streptavidin-Cy3.

data_processing: Data was extracted using the Illumina GenomeStudio software(v1.6.0).  Any spots at or below the background were filtered out using an Illumina detection p value of 0.02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below.  Z-score = (raw value - avg)/std.

organism: Macaca mulatta

source_name: Thoracic aorta_High Fat-Sugar diet+Resveratrol_ Rep-8

growth_protocol: Twenty-four adult (7-13 years old) male rhesus monkeys (Macaca mulatta) were housed individually in standard nonhuman primate caging on a 12h light/12h dark cycle, room temperature (78 +/- 2 degrees F), and humidity at 60 +/- 20%. One pairing was maintained throughout the study; all other monkeys had extensive visual, auditory, and olfactory but limited tactile contact with monkeys housed in the same room. Monkeys received 2 meals per day at estimated ad libitum levels throughout the study. Water was always available ad libitum. Monkeys were monitored minimally 3 times daily by trained animal care staff.  During baseline assessments, all monkeys were maintained on a commercially available closed formula monkey chow (TestDiet #5038 Purina Mills, Richmond, IN).

extract_protocol: RNA was isolated from rhesus monkey aorta at 24-months of dietary intervention using Trizol reagent (Invitrogen) and further purified using RNeasy mini columns (Qiagen). Quality and Quantity were tested with an Agilent Bio-Analyzer using RNA 6000-Nano Chips.

treatment_protocol:
After baseline assessment, the twenty four male rhesus monkeys were quasi- randomized into one of three groups: a high fat/high sucrose (HFS) diet (n=10); a HFS diet supplemented with resveratrol (HFS+R) (n=10); or, remaining on the healthy standard diet  (SD) (n=4). The standard diet was a purified biscuit consisting of 13% of kcal in fat and less than 5% sucrose by weight. The HFS diet was a specially formulated purified ingredient diet with 42% of kcal in fat and approximately 27% sucrose by weight (Harlan, Teklad, Madison, WI). The monkeys were gradually switched to the HFS diet over a 3-week period. All groups received 2 meals per day of the specified diet in allotments that represent ad libitum feeding, yet consumption was isocaloric across groups.
Resveratrol was supplied by DSM Nutritional Products (Parsippany, NJ) and the dosing for monkeys was determined to be 40.7 mg. The resveratrol was used to formulate a flavored primate treat (Bi-Serv, Frenchtown, NJ) and given to the monkeys prior to each meal, thus, the monkeys received a total dose of 80 mg per day. All monkeys, regardless of weight, received the same amount of resveratrol. Monkeys in non-resveratrol groups receive a placebo treat. After completion of data collection at the one year time point, the resveratrol dose was increased to 240 mg per day.
After baseline assessment, 10 male rhesus monkeys were begun on a high fat/high sucrose (HFS) diet (n=10) plus Resveratrol; the HFS diet was a specially formulated purified ingredient diet with 42% of kcal in fat and approximately 27% sucrose by weight (Harlan, Teklad, Madison, WI). The monkeys were gradually switched to the HFS diet over a 3-week period. All groups received 2 meals per day of the specified diet in allotments that represent ad libitum feeding, yet consumption was isocaloric across groups.  Resveratrol treatment for the first year was 80mg per day. At the one year time point they were switched to 240mg per day until the end of 2 years of dietary intervention.

tag: developmental stage

value: adult

value: Male

tag: diet

value: high fat/high sucrose (HFS) diet

tag: agent

value: Resveratrol

value: Thoracic aorta


title: Muscle_Standard Diet_Replicate #2

description: Muscle_Standard Diet_Replicate #2

value: male


title: Aorta_High Fat-Sugar diet_ Rep-10

description:
Samplename: AF_TTJ
Aorta_High Fat-Sugar diet_ Rep-10

source_name: Thoracic aorta_High Fat-Sugar diet_ Rep-10

treatment_protocol:
After baseline assessment, the twenty four male rhesus monkeys were quasi- randomized into one of three groups: a high fat/high sucrose (HFS) diet (n=10); a HFS diet supplemented with resveratrol (HFS+R) (n=10); or, remaining on the healthy standard diet  (SD) (n=4). The standard diet was a purified biscuit consisting of 13% of kcal in fat and less than 5% sucrose by weight. The HFS diet was a specially formulated purified ingredient diet with 42% of kcal in fat and approximately 27% sucrose by weight (Harlan, Teklad, Madison, WI). The monkeys were gradually switched to the HFS diet over a 3-week period. All groups received 2 meals per day of the specified diet in allotments that represent ad libitum feeding, yet consumption was isocaloric across groups.
Resveratrol was supplied by DSM Nutritional Products (Parsippany, NJ) and the dosing for monkeys was determined to be 40.7 mg. The resveratrol was used to formulate a flavored primate treat (Bi-Serv, Frenchtown, NJ) and given to the monkeys prior to each meal, thus, the monkeys received a total dose of 80 mg per day. All monkeys, regardless of weight, received the same amount of resveratrol. Monkeys in non-resveratrol groups receive a placebo treat. After completion of data collection at the one year time point, the resveratrol dose was increased to 240 mg per day.
After baseline assessment, 10 male rhesus monkeys were begun on a high fat/high sucrose (HFS) diet (n=10); HFS diet was a specially formulated purified ingredient diet with 42% of kcal in fat and approximately 27% sucrose by weight (Harlan, Teklad, Madison, WI). The monkeys were gradually switched to the HFS diet over a 3-week period. All groups received 2 meals per day of the specified diet in allotments that represent ad libitum feeding, yet consumption was isocaloric across groups.

value: control


description:
Samplename: AR_p48
Aorta_High Fat-Sugar diet+Resveratrol_ Rep-10

source_name: Thoracic aorta_High Fat-Sugar diet+Resveratrol_ Rep-10


description:
Samplename: AR_TEJ
Aorta_High Fat-Sugar diet+Resveratrol_ Rep-7

source_name: Thoracic aorta_High Fat-Sugar diet+Resveratrol_ Rep-7


description:
Samplename: AR_AV7W
Aorta_High Fat-Sugar diet+Resveratrol_ Rep-2

source_name: Thoracic aorta_High Fat-Sugar diet+Resveratrol_ Rep-2


title: Aorta_High Fat-Sugar diet_ Rep-7

description:
Samplename: AF_RQ1956
Aorta_High Fat-Sugar diet_ Rep-7

source_name: Thoracic aorta_High Fat-Sugar diet_ Rep-7


description:
Samplename: AR_P57
Aorta_High Fat-Sugar diet+Resveratrol_ Rep-1

source_name: Thoracic aorta_High Fat-Sugar diet+Resveratrol_ Rep-1


title: Aorta_High Fat-Sugar diet_ Rep-4

description:
Samplename: AF_R40
Aorta_High Fat-Sugar diet_ Rep-4

source_name: Thoracic aorta_High Fat-Sugar diet_ Rep-4


title: Aorta_High Fat-Sugar diet_ Rep-5

description:
Samplename: AF_M83
Aorta_High Fat-Sugar diet_ Rep-5

source_name: Thoracic aorta_High Fat-Sugar diet_ Rep-5


title: Aorta_Control diet_ Rep-2

description:
Samplename: AC_PXT
Aorta_Control diet_ Rep-2

source_name: Thoracic aorta_Control diet_ Rep-2

treatment_protocol:
After baseline assessment, the twenty four male rhesus monkeys were quasi- randomized into one of three groups: a high fat/high sucrose (HFS) diet (n=10); a HFS diet supplemented with resveratrol (HFS+R) (n=10); or, remaining on the healthy standard diet  (SD) (n=4). The standard diet was a purified biscuit consisting of 13% of kcal in fat and less than 5% sucrose by weight. The HFS diet was a specially formulated purified ingredient diet with 42% of kcal in fat and approximately 27% sucrose by weight (Harlan, Teklad, Madison, WI). The monkeys were gradually switched to the HFS diet over a 3-week period. All groups received 2 meals per day of the specified diet in allotments that represent ad libitum feeding, yet consumption was isocaloric across groups.
Resveratrol was supplied by DSM Nutritional Products (Parsippany, NJ) and the dosing for monkeys was determined to be 40.7 mg. The resveratrol was used to formulate a flavored primate treat (Bi-Serv, Frenchtown, NJ) and given to the monkeys prior to each meal, thus, the monkeys received a total dose of 80 mg per day. All monkeys, regardless of weight, received the same amount of resveratrol. Monkeys in non-resveratrol groups receive a placebo treat. After completion of data collection at the one year time point, the resveratrol dose was increased to 240 mg per day.
After baseline assessment, four male rhesus monkeys remained on the healthy standard diet  (SD) (n=4). The standard diet was a purified biscuit consisting of 13% of kcal in fat and less than 5% sucrose by weight.  All groups received 2 meals per day of the specified diet in allotments that represent ad libitum feeding, yet consumption was isocaloric across groups.

value: standard diet  (SD)


description:
Samplename: AR_WEJ
Aorta_High Fat-Sugar diet+Resveratrol_ Rep-3

source_name: Thoracic aorta_High Fat-Sugar diet+Resveratrol_ Rep-3


description:
Samplename: AR_96C228
Aorta_High Fat-Sugar diet+Resveratrol_ Rep-4

source_name: Thoracic aorta_High Fat-Sugar diet+Resveratrol_ Rep-4


title: Aorta_High Fat-Sugar diet_ Rep-9

description:
Samplename: AF_RQ1784
Aorta_High Fat-Sugar diet_ Rep-9

source_name: Thoracic aorta_High Fat-Sugar diet_ Rep-9


title: Aorta_High Fat-Sugar diet_ Rep-3

description:
Samplename: AF_T83
Aorta_High Fat-Sugar diet_ Rep-3

source_name: Thoracic aorta_High Fat-Sugar diet_ Rep-3


description:
Samplename: AR_96C029
Aorta_High Fat-Sugar diet+Resveratrol_ Rep-6

source_name: Thoracic aorta_High Fat-Sugar diet+Resveratrol_ Rep-6


title: Aorta_Control diet_ Rep-1

description:
Samplename: AC_P53
Aorta_Control diet_ Rep-1

source_name: Thoracic aorta_Control diet_ Rep-1


title: Aorta_High Fat-Sugar diet_ Rep-6

description:
Samplename: AF_383
Aorta_High Fat-Sugar diet_ Rep-6

source_name: Thoracic aorta_High Fat-Sugar diet_ Rep-6


title: Aorta_High Fat-Sugar diet_ Rep-2

description:
Samplename: AF_TOK
Aorta_High Fat-Sugar diet_ Rep-2

source_name: Thoracic aorta_High Fat-Sugar diet_ Rep-2


title: Aorta_Control diet_ Rep-3

description:
Samplename: AC_V14
Aorta_Control diet_ Rep-3

source_name: Thoracic aorta_Control diet_ Rep-3


title: Aorta_High Fat-Sugar diet_ Rep-1

description:
Samplename: AF_96C219
Aorta_High Fat-Sugar diet_ Rep-1

source_name: Thoracic aorta_High Fat-Sugar diet_ Rep-1


description:
Samplename: AR_RQ4037
Aorta_High Fat-Sugar diet+Resveratrol_ Rep-9

source_name: Thoracic aorta_High Fat-Sugar diet+Resveratrol_ Rep-9


description:
Samplename: AR_TGF
Aorta_High Fat-Sugar diet+Resveratrol_ Rep-5

source_name: Thoracic aorta_High Fat-Sugar diet+Resveratrol_ Rep-5


title: Aorta_High Fat-Sugar diet_ Rep-8

description:
Samplename: AF_95_E081
Aorta_High Fat-Sugar diet_ Rep-8

source_name: Thoracic aorta_High Fat-Sugar diet_ Rep-8


title: UCI-101 cell line, Indomethacin treatment-1

status: Public on Jun 20 2014

description: serous ovarian adenocarcinoma, UCI-101 cell line, 24 hour treatment with Indomethacin.

hyb_protocol: Standard Illumina protocol. In short, a total of 0.75ug of biotin-labeled cRNA was hybridized at 58 degrees C for 16 hours to Illumina's Sentrix Human Ref-8 v2.0 Expression BeadChips (Illumina, San Diego, CA). Each BeadChip has ~24,000 well-annotated RefSeq transcripts with approximately 30-fold redundancy. The arrays were washed, blocked and the biotin labeled cRNA was detected by staining with streptavidin-Cy3.

data_processing: Data was extracted using the Illumina BeadStudio software(v3.1.7).  Any spots at or below the background were filtered out using an Illumina detection p value of 0.02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below.  Z-score = (raw value - avg)/std.

growth_protocol: The serous ovarian adenocarcinoma cell lines HEY, OVCAR5 and UCI-101 were cultured in McCoy’s 5A culture media supplemented with 10% fetal bovine serum and Pen/Strep (100 units/mL penicillin and 100 mg/mL streptomycin).  Cells were incubated at 37°C in an atmosphere of 5% CO2. All experiments were performed in serum-containing media.

extract_protocol: 24 hours after treatment total RNA was prepared using the Qiagen RNeasy Mini Kit (Qiagen, Inc. Valencia CA) following the manufacturer's specifications. Quantity and quality of the RNA was assessed using the Agilent 2100 Bioanalyzer with RNA 6000 Nano Chips.

treatment_protocol: Serous ovarian adenocarcinoma cell lines were seeded in 60 mm dishes and treated for 24 hours with nothing or 300 mM of either diclofenac or indomethacin.

value: serous ovarian adenocarcinoma, UCI-101 cell line.

tag: growth protocol

value: The serous ovarian adenocarcinoma cell line UCI-101 was cultured in McCoy’s 5A culture media supplemented with 10% fetal bovine serum and Pen/Strep (100 units/mL penicillin and 100 mg/mL streptomycin).  Cells were incubated at 37°C in an atmosphere of 5% CO2. All experiments were performed in serum-containing media.

value: UCI-101 cell lines were seeded in 60 mm dishes and treated for 24 hours with 300 mM diclofenac or indomethacin.


title: UCI-101cell line,Control-1

description: serous ovarian adenocarcinoma, UCI-101 cell line.


title: OVCAR5 cell line, Indomethacin treatment-1

description: serous ovarian adenocarcinoma, OVCAR5 cell line, 24 hour treatment with Indomethacin.

value: serous ovarian adenocarcinoma, OVCAR5 cell line.

value: The serous ovarian adenocarcinoma cell line OVCAR5 was cultured in McCoy’s 5A culture media supplemented with 10% fetal bovine serum and Pen/Strep (100 units/mL penicillin and 100 mg/mL streptomycin).  Cells were incubated at 37°C in an atmosphere of 5% CO2. All experiments were performed in serum-containing media.

value: OVCAR5 cell lines were seeded in 60 mm dishes and treated for 24 hours with 300 mM diclofenac or indomethacin.


title: OVCAR5 cell line,Diclofenac treatment-1

description: serous ovarian adenocarcinoma, OVCAR5 cell line, 24 hour treatment with Diclofenac..


title: UCI-101 cell line, Diclofenac treatment-1

description: serous ovarian adenocarcinoma, UCI-101 cell line, 24 hour treatment with Diclofenac.


title: Hey cell line,Control-1

description: serous ovarian adenocarcinoma, HEY cell line.

value: Serous ovarian adenocarcinoma cell lines HEY were cultured in McCoy’s 5A culture media supplemented with 10% fetal bovine serum and Pen/Strep (100 units/mL penicillin and 100 mg/mL streptomycin).  Cells were incubated at 37°C in an atmosphere of 5% CO2. All experiments were performed in serum-containing media.

value: Hey cell lines were seeded in 60 mm dishes and treated for 24 hours with 300 mM diclofenac or indomethacin.


title: Aorta_Control diet_ Rep-4

description:
Samplename: AC_95_E142
Aorta_Control diet_ Rep-4

source_name: Thoracic aorta_Control diet_ Rep-4


title: Hey cell line, Diclofenac treatment-1

description: serous ovarian adenocarcinoma, HEY cell line, 24 hour treatment with Diclofenac.

value: serous ovarian adenocarcinoma, HEY cell line.


title: OVCAR5 cell line,Control-1

description: serous ovarian adenocarcinoma, OVCAR5 cell line.


title: Hey cell line, Indomethacin treatment-1

description: serous ovarian adenocarcinoma, HEY cell line, 24 hour treatment with Indomethacin.


title: AS-2-3

status: Public on May 16 2014

description: WI-38 cells reverse transfected with MALAT1 antisense oligonucleotide,(AS-2) final concentration 100 nM, Replicate #3

hyb_protocol: Standard Illumina protocol. In short, a total of 0.75ug of biotin-labeled cRNA was hybridized at 58 degrees C for 16 hours to Illumina's Sentrix Human HT-12 v4 Expression BeadChips (Illumina, San Diego, CA). Each BeadChip has ~47,000 annotated RefSeq transcripts with approximately 15-fold redundancy. The arrays were washed, blocked and the biotin labeled cRNA was detected by staining with streptavidin-Cy3.

label: Streptavidin-Cy3 bound to biotin

source_name: WI38 cells / MALAT1 antisense oligonucleotide (AS-2)

label_protocol: Standard Illumina protocol using Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791) In short, 0.5g of total RNA was first converted into single-stranded cDNA with reverse transcriptase using an oligo-dT primer containing the T7 RNA polymerase promoter site and then copied to produce double-stranded cDNA molecules. The double stranded cDNA was cleaned and concentrated with the supplied columns and used in an overnight in-vitro transcription reaction where single-stranded RNA (cRNA) was generated and labeled by incorporation of biotin-16-UTP.

growth_protocol: WI-38 cells were grown in DMEM containing high glucose + 10% FBS, and 1% non-essential amino acid (NEA).

extract_protocol: Total RNA was isolated using RNeasy kit (Qiagen) according to the manufacturer’s instructions. Quality and quantity of the total RNA was checked with the Agilent 2100 bioanalyzer using RNA 6000 Nano chips.

treatment_protocol: WI-38 cells were reverse transfected in triplicate with either control (scrambled antisense oligo) or two independent MALAT1 antisense oligonucleotides(AS-1, AS-2) at a final concentration of 100 nM using Lipofectamine RNAiMax (Invitrogen, USA).

value: WI38 cells (normal human diploid fibroblasts)

tag: growth media

tag: transfected with

value: MALAT1 antisense oligonucleotide (AS-2)


title: AS-2-1

description: WI-38 cells reverse transfected with MALAT1 antisense oligonucleotide,(AS-2) final concentration 100 nM, Replicate #1

value: DMEM containing high glucose + 10% FBS, and 1% non-essential amino acid (NEA)


title: AS-1-1

description: WI-38 cells reverse transfected with MALAT1 antisense oligonucleotide,(AS-1) final concentration 100 nM, Replicate #1

source_name: WI38 cells /  MALAT1 antisense oligonucleotide (AS-1)

value: MALAT1 antisense oligonucleotide (AS-1)


title: AS-1-3

description: WI-38 cells reverse transfected with MALAT1 antisense oligonucleotide,(AS-1) final concentration 100 nM, Replicate #3


title: AS-2-2

description: WI-38 cells reverse transfected with MALAT1 antisense oligonucleotide,(AS-2) final concentration 100 nM, Replicate #2


title: Liver-Ad Lib- Homozygous knockout-replicate 3

status: Public on Apr 25 2014

description: Liver-Ad Lib- Homozygous knockout

data_processing: Data was extracted using the Illumina BeadStudio software(v3.4.0).  Any spots at or below the background were filtered out using an Illumina detection p value of 0.02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below.  Z-score = (raw value - avg)/std.  Complete data including detection scores will be included in the supplemental file.

source_name: Liver-Ad Lib- Homozygous knockout

growth_protocol: 2-5 month old C57BL/6J male mice were housed following 1 of 2 dietary protocols

extract_protocol: RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA) following the manufacturer’s instructions and homogenized using a polytron.  Quantity and quality of the RNA was assessed using the Agilent 2100 Bioanalyzer with RNA 6000 Nano Chips.

treatment_protocol: Mice were feed either a 40% caloric restricted (CR) diet or an ad libitum (AL) diet until they reached 13-16 months at which time they were sacrificed, and the livers were collected and flash frozen.

tag: agender

value: 2-5 months old

tag: agenotype

value: Homozygous knockout  (SIRT1-/-)

value: Ad libitum diet


title: AS-1-2

description: WI-38 cells reverse transfected with MALAT1 antisense oligonucleotide,(AS-1) final concentration 100 nM, Replicate #2


title: CTR_3

description: WI-38 cells reverse transfected with control (scrambled antisense oligo), (CTR) final concentration 100 nM, Replicate #3

source_name: WI38 cells / control (scrambled antisense oligo)

value: control (scrambled antisense oligo)


title: Liver-Caloric Restriction- Homozygous knockout-replicate 3

value: male

tag: treatment

value: 40% Caloric restricted diet


title: 4-26-12 TIC-P1

status: Public on May 31 2014

city: Chapel Hill

first: William

middle: Y.

last: Kim

state: NC

address: 450 West Dr.

department: Medicine and Genetics

institute: University of North Carolina at Chapel Hill

description: PBS Treated CD44+;CD24-;EpCAM+, SUM149 Cells

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-125

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software

data_processing: Data for both channels were Lowess-normalized and then the log(2) ratio was taken

source_name: Universal Human RNA Reference

extract_protocol: Total RNA isolated using Qiagen RNeasy Kit

tag: sample type

value: Universal Human RNA Reference

extract_protocol: Total RNA isolated using Qiagen Rneasy Kit

value: PBS Treated

value: CD44+;CD24-;EpCAM+, SUM149 Cells


title: Liver-Ad Lib- Homozygous knockout-replicate 1

description: Liver-Ad Lib- Homozygous knockout


title: Liver-Ad Lib- Homozygous knockout-replicate 2

description: Liver-Ad Lib- Homozygous knockout


title: Liver-Ad Lib-Wt-replcate 2

description: Liver-Ad Lib-Wt

source_name: Liver-Ad Lib-Wt

value: Wild Type  (SIRT1+/+)


title: CTR_1

description: WI-38 cells reverse transfected with control (scrambled antisense oligo), (CTR) final concentration 100 nM, Replicate #1

tag: cell type


title: Liver-Ad Lib- Heterozygous knockout-replicate 1

description: Liver-Ad Lib- Heterozygous knockout

source_name: Liver-Ad Lib- Heterozygous knockout

value: Heterozygous knockout  (SIRT1+/-)


title: Liver-Ad Lib- Heterozygous knockout-replicate 2

description: Liver-Ad Lib- Heterozygous knockout


title: Liver-Ad Lib-Wt-replcate 1

description: Liver-Ad Lib-Wt


title: CTR_2

description: WI-38 cells reverse transfected with control (scrambled antisense oligo), (CTR) final concentration 100 nM, Replicate #2


title: 4-26-12 TIC-E3

description: EPO Treated CD44+;CD24-;EpCAM+, SUM149 Cells

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-125

value: EPO Treated


title: Liver-Ad Lib- Homozygous knockout-replicate 4

description: Liver-Ad Lib- Homozygous knockout


title: 4-26-12 TIC-E1


title: Liver-Caloric Restriction- Wt-replcate 3

description: Liver-Caloric Restriction- Wt

source_name: Liver-Caloric Restriction- Wt


title: Liver-Ad Lib-Wt-replcate 3

description: Liver-Ad Lib-Wt


title: Liver-Caloric Restriction- Heterozygous knockout-replicate 3


title: Liver-Caloric Restriction- Heterozygous knockout-replicate 2


title: Liver-Caloric Restriction- Heterozygous knockout-replicate 1


title: Liver-Caloric Restriction- Homozygous knockout-replicate 1


title: Liver-Caloric Restriction- Homozygous knockout-replicate 2


title: 4-26-12 TIC-P3


title: Liver-Caloric Restriction- Wt-replcate 2

description: Liver-Caloric Restriction- Wt


title: Subcutaneous_Fat_Time-0_Resv_Rep-9

status: Public on Apr 21 2014

data_processing: Data was extracted using the Illumina GenomeStudio software(v1.9.0).  Any spots at or below the background were filtered out using an Illumina detection p value of 0.02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below.  Z-score = (raw value - avg)/std.

growth_protocol: Twenty-four adult (7-13 years old) male rhesus monkeys (Macaca mulatta) were housed individually in standard nonhuman primate caging on a 12h light/12h dark cycle, room temperature (78 +/- 2 degrees F), and humidity at 60 +/- 20%. One pairing was maintained throughout the study; all other monkeys had extensive visual, auditory, and olfactory but limited tactile contact with monkeys housed in the same room. Monkeys received 2 meals per day at estimated ad libitum levels throughout the study. Water was always available ad libitum. Monkeys were monitored minimally 3 times daily by trained animal care staff.  During baseline assessments, all monkeys were maintained on a commercially available closed formula monkey chow.

extract_protocol: RNA was isolated from rhesus monkey fat samples at both the 0 and 24-month time points of dietary intervention for the subcutaneous fat samples and the 24 month time point only for the visceral fat samples using Trizol reagent (Invitrogen) and further purified using RNeasy Lipid mini columns (Qiagen). Quality and Quantity were tested with an Agilent Bio-Analyzer using RNA 6000-Nano Chips.

treatment_protocol:
After baseline assessment, the twenty four male rhesus monkeys were quasi-randomized into one of three groups: a high fat/high sucrose (HFS) diet (n=10); a HFS diet supplemented with resveratrol (HFS+R) (n=10); or, remaining on the healthy standard diet  (SD) (n=4). The standard diet was a purified biscuit consisting of 13% of kcal in fat and less than 5% sucrose by weight. The HFS diet was a specially formulated purified ingredient diet with 42% of kcal in fat and approximately 27% sucrose by weight (Harlan, Teklad, Madison, WI). The monkeys were gradually switched to the HFS diet over a 3-week period. All groups received 2 meals per day of the specified diet in allotments that represent ad libitum feeding, yet consumption was isocaloric across groups.
Resveratrol was supplied by DSM Nutritional Products (Parsippany, NJ) and the dosing for monkeys was determined to be 40.7 mg. The resveratrol was used to formulate a flavored primate treat (Bi-Serv, Frenchtown, NJ) and given to the monkeys prior to each meal, thus, the monkeys received a total dose of 80 mg per day. All monkeys, regardless of weight, received the same amount of resveratrol. Monkeys in non-resveratrol groups receive a placebo treat. After completion of data collection at the one year time point, the resveratrol dose was increased to 480 mg per day.

value: Subcutaneous Fat

tag: dietary treatment

value: high fat/high sucrose diet + Resveratrol(Resv)

tag: time point

value: Baseline


title: Subcutaneous_Fat_Time-0_Resv_Rep-8

tag: gender


title: Subcutaneous_Fat_Time-24month_HFS_Rep-2

tag: tissue

value: high fat/high sucrose diet (HFS)

value: 24 months


title: Subcutaneous_Fat_Time-0_HFS_Rep-10


title: Subcutaneous_Fat_Time-0_Resv_Rep-7


title: Subcutaneous_Fat_Time-24month_Resv_Rep-3


title: Subcutaneous_Fat_Time-0_Resv_Rep-4


title: Subcutaneous_Fat_Time-0_HFS_Rep-8


title: Subcutaneous_Fat_Time-24month_Resv_Rep-4


title: Subcutaneous_Fat_Time-24month_HFS_Rep-1


title: Subcutaneous_Fat_Time-0_HFS_Rep-4


title: Subcutaneous_Fat_Time-0_SD_Rep-3

value: standard diet  (SD)


title: Subcutaneous_Fat_Time-24month_HFS_Rep-3


title: Subcutaneous_Fat_Time-0_HFS_Rep-6


title: Subcutaneous_Fat_Time-24month_HFS_Rep-5


title: Subcutaneous_Fat_Time-0_Resv_Rep-6


title: Subcutaneous_Fat_Time-0_Resv_Rep-10


title: Subcutaneous_Fat_Time-24month_HFS_Rep-4


title: Subcutaneous_Fat_Time-0_HFS_Rep-5


title: Subcutaneous_Fat_Time-24month_SD_Rep-1


title: Subcutaneous_Fat_Time-0_HFS_Rep-9


title: Subcutaneous_Fat_Time-24month_Resv_Rep-1


title: Subcutaneous_Fat_Time-0_Resv_Rep-5


title: Subcutaneous_Fat_Time-24month_Resv_Rep-2


title: Subcutaneous_Fat_Time-0_SD_Rep-4


title: Subcutaneous_Fat_Time-0_HFS_Rep-7


title: Subcutaneous_Fat_Time-24month_SD_Rep-2


title: Subcutaneous_Fat_Time-0_Resv_Rep-3


title: Subcutaneous_Fat_Time-0_HFS_Rep-1


title: Subcutaneous_Fat_Time-0_HFS_Rep-3


title: Visceral_Fat_Time-24month_Resv_ Rep-4

description: Visceral_Fat_Time-24month_Resv_ Rep-4

data_processing:
Data was extracted using the Illumina GenomeStudio software(v1.9.0).  Any spots at or below the background were filtered out using an Illumina detection p value of 0.02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below.  Z-score = (raw value - avg)/std.
ID_REF = Unique identifiers from GPL10558-11219
Z_VALUE = Z transformation of the natural log of the raw intensity values
Detection_Pval = Detection Pvalue from Illumina GenomeStudio software, ver 1.9.0.

extract_protocol: RNA was isolated from rhesus monkey fat samples at 24-months of dietary intervention using Trizol reagent (Invitrogen) and further purified using RNeasy Lipid mini columns (Qiagen). Quality and Quantity were tested with an Agilent Bio-Analyzer using RNA 6000-Nano Chips.


title: Subcutaneous_Fat_Time-0_HFS_Rep-2


title: Subcutaneous_Fat_Time-0_Resv_Rep-1


title: Visceral_Fat_Time-24month_HFS_ Rep-2

description: Visceral_Fat_Time-24month_HFS_ Rep-2


title: Subcutaneous_Fat_Time-0_SD_Rep-2


title: Visceral_Fat_Time-24month_Resv_ Rep-2

description: Visceral_Fat_Time-24month_Resv_ Rep-2


title: Subcutaneous_Fat_Time-0_SD_Rep-1


title: Visceral_Fat_Time-24month_SD_ Rep-1

description: Visceral_Fat_Time-24month_SD_ Rep-1


title: Visceral_Fat_Time-24month_SD_ Rep-2

description: Visceral_Fat_Time-24month_SD_ Rep-2


title: Visceral_Fat_Time-24month_HFS_ Rep-1

description: Visceral_Fat_Time-24month_HFS_ Rep-1


title: Visceral_Fat_Time-24month_Resv_ Rep-1

description: Visceral_Fat_Time-24month_Resv_ Rep-1


title: Visceral_Fat_Time-24month_HFS_ Rep-3

description: Visceral_Fat_Time-24month_HFS_ Rep-3


title: TG_FT_9W_rep1

status: Public on Apr 11 2014

data_processing:
Data was extracted using the Illumina GenomeStudio software, ver 1.6.0.  Any spots at or below the background were filtered out using an Illumina detection p value of 0.02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below.  Z-score = (raw value - avg)/std.
ID_REF = Unique identifiers from GPL6885-5840
Z_VALUE = Z transformation of the natural log of the raw intensity values
Detection_Pval = Detection Pvalue from Illumina GenomeStudio software, ver 1.6.0.

growth_protocol: Female C57BL6 mice and mogp-TAg transgenic mice (Dr. I. Myoshi/Nagoya University, Japan) were housed under standard conditions with food and water ad libitum.

extract_protocol: Total RNA was prepared using Invitrogen Trizol (Life Technologies, Inc. Carlsbad, CA) following the manufacturer's specifications. Quantity and quality of the RNA was assessed using the Agilent 2100 Bioanalyzer with RNA 6000 Nano Chips.

treatment_protocol: Animals were euthanized and the fallopian tubes dissected for total RNA isolation at either 7, 8 or 9 weeks of age.

tag: genotype

value: mogp-TAg transgenic

tag: genetic background

value: female

value: fallopian tube

tag: age

value: 9 weeks old


title: WT_FT_7W_rep1

value: Wildtype

value: 7 weeks old


title: Visceral_Fat_Time-24month_HFS_ Rep-4

description: Visceral_Fat_Time-24month_HFS_ Rep-4

value: male


title: WT_FT_7W_rep2


title: TG_FT_7W_rep1


title: TG_FT_8W_rep2

value: 8 weeks old


title: WT_FT_9W_rep1

description: WT_Fallopian Tube_9Week

source_name: WT_Fallopian Tube_9Week


title: WT_FT_8W_rep1


title: WT_FT_8W_rep2


title: TG_FT_8W_rep1


title: WT_FT_9W_rep2

description: WT_Fallopian Tube_9Week


title: TG_FT_7W_rep2


title: Visceral_Fat_Time-24month_Resv_ Rep-3

description: Visceral_Fat_Time-24month_Resv_ Rep-3


title: FRTotalI520

status: Public on Mar 19 2014

description: Total RNA of HeLa cells transfected with Pre-miR-520c-3p.

hyb_protocol: Standard Illumina protocol. In short, a total of 0.75ug of biotin-labeled cRNA was hybridized at 58 degrees C for 16 hours to Illumina's Sentrix Human HT-12, v3 Expression BeadChips (Illumina, San Diego, CA). Each BeadChip targets more than 25,000 annotated genes with more than 48,000 probes. Probes were designed using the RefSeq (Build 36.2, Rel 22) and the UniGene (Build 199) databases with an average of 15-fold redundancy. The arrays were washed, blocked and the biotin labeled cRNA detected by staining with streptavidin-Cy3.

data_processing: Data was extracted using the Illumina GenomeStudio software(v1.6.0). Any spots at or below the background were filtered out using an Illumina detection p-value of 0.02 and above. The natural log of all remaining scores was used to find the avg and std of each array and the z-score normalization was calculated and presented below. Z-score = (raw value - avg)/std. Complete data including detection scores will be included in the supplemental file.

label: Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: Human cervical carcinoma (HeLa) cells were cultured in DMEM (Gibco BRL, Gaithersburg, MD) supplemented with 10% FBS.

extract_protocol: Total RNA was extracted from unfractionated cell pellets using Trizol (Invitrogen). Quality and quantity of the total RNA was checked with the Agilent 2100 bioanalyzer using RNA 6000 Nano chips.

treatment_protocol: Transfected HeLa cells with no sucrose gradient fractionation.

tag: cell line

value: HeLa

tag: transfected

value: 50 nM small RNAs Pre-miR-520c-3p


title: FR10IIIC

description: Polysomal fraction #10 of HeLa cells transfected with Pre-miR-Ctrl.

extract_protocol: Total RNA was extracted from fraction #10 using Trizol (Invitrogen). Quality and quantity of the total RNA was checked with the Agilent 2100 bioanalyzer using RNA 6000 Nano chips.

treatment_protocol: Linear sucrose gradient fractionation was performed on the transfected HeLa cells. Briefly, ~ 6 × 106 cells were incubated for 15 min with 100 mg/ml cycloheximide. Cells were lysed in cytoplasmic lysis buffer containing 20 mM Tris-HCl (pH 7.5), 100 mM KCl, 5 mM MgCl2, 0.3% IGEPAL CA-630, RNaseOUT (Invitrogen) and, protease inhibitor cocktail for 5 min on ice and centrifuged (10,000 × g, 10 min, 4°C). Cytoplasmic extracts were loaded onto the 10–50% sucrose gradients and after centrifugation (Beckman SW41, 35,000 rpm, 3 h, 4°C) the material was fractionated into eleven 1 ml aliquots labeled 1-11 using a gradient fractionator (Brandel) and monitored by optical density measurement (A254).

value: control miRNA Pre-miR-Ctrl (Ambion)


title: FR11I520

description: Polysomal fraction #11 of HeLa cells transfected with Pre-miR-520c-3p.

extract_protocol: Total RNA was extracted from fraction #11 using Trizol (Invitrogen). Quality and quantity of the total RNA was checked with the Agilent 2100 bioanalyzer using RNA 6000 Nano chips.


title: FRTotalIIC

description: Total RNA of HeLa cells transfected with miRNA Pre-miR-Ctrl.


title: Liver-Caloric Restriction- Wt-replcate 1

description: Liver-Caloric Restriction- Wt

tag: strain

value: 2-5 months old

value: Wild Type  (SIRT1+/+)

value: 40% Caloric restricted diet


title: FRTotalIC


title: FR11IIIC

description: Polysomal fraction #11 of HeLa cells transfected with Pre-miR-Ctrl.


title: FRTotalIII520


title: FR11III520


title: FR11IC


title: FR10IC


title: FR9IIIC

description: Polysomal fraction #9 of HeLa cells transfected with Pre-miR-Ctrl.

extract_protocol: Total RNA was extracted from fraction #9 using Trizol (Invitrogen). Quality and quantity of the total RNA was checked with the Agilent 2100 bioanalyzer using RNA 6000 Nano chips.


title: FR9III520

description: Polysomal fraction #9 of HeLa cells transfected with Pre-miR-520c-3p.


title: FR9IIC


title: FR7IC

description: Polysomal fraction #7 of HeLa cells transfected with Pre-miR-Ctrl.

extract_protocol: Total RNA was extracted from fraction #7 using Trizol (Invitrogen). Quality and quantity of the total RNA was checked with the Agilent 2100 bioanalyzer using RNA 6000 Nano chips.


title: FR9II520


title: FR8IIIC

description: Polysomal fraction #8 of HeLa cells transfected with Pre-miR-Ctrl.

extract_protocol: Total RNA was extracted from fraction #8 using Trizol (Invitrogen). Quality and quantity of the total RNA was checked with the Agilent 2100 bioanalyzer using RNA 6000 Nano chips.


title: FR8IC


title: TG_FT_9W_rep2


title: FR7IIC


title: FR8II520

description: Polysomal fraction #8 of HeLa cells transfected with Pre-miR-520c-3p.


title: FR8IIC


title: FR8III520


title: FRTotalIIIC


title: FR7III520

description: Polysomal fraction #7 of HeLa cells transfected with Pre-miR-520c-3p.


title: FR7IIIC


title: FR10IIC


title: FR6IIIC

description: Polysomal fraction #6 of HeLa cells transfected with Pre-miR-Ctrl.

extract_protocol: Total RNA was extracted from fraction #6 using Trizol (Invitrogen). Quality and quantity of the total RNA was checked with the Agilent 2100 bioanalyzer using RNA 6000 Nano chips.


title: FR6IIC


title: FR5IIIC

description: Polysomal fraction #5 of HeLa cells transfected with Pre-miR-Ctrl.

extract_protocol: Total RNA was extracted from fraction #5 using Trizol (Invitrogen). Quality and quantity of the total RNA was checked with the Agilent 2100 bioanalyzer using RNA 6000 Nano chips.


title: FR10II520

description: Polysomal fraction #10 of HeLa cells transfected with Pre-miR-520c-3p.


title: FR6III520

description: Polysomal fraction #6 of HeLa cells transfected with Pre-miR-520c-3p.


title: FR5IIC


title: Subcutaneous_Fat_Time-0_Resv_Rep-2

value: Subcutaneous Fat

value: high fat/high sucrose diet + Resveratrol(Resv)

value: Baseline


title: FR6IC


title: FR6II520


title: FR5III520

description: Polysomal fraction #5 of HeLa cells transfected with Pre-miR-520c-3p.


title: FR5IC


title: FR4IIC

description: Polysomal fraction #4 of HeLa cells transfected with Pre-miR-Ctrl.

extract_protocol: Total RNA was extracted from fraction #4 using Trizol (Invitrogen). Quality and quantity of the total RNA was checked with the Agilent 2100 bioanalyzer using RNA 6000 Nano chips.


title: FR4IIIC


title: FR4II520

description: Polysomal fraction #4 of HeLa cells transfected with Pre-miR-520c-3p.


title: FR4III520


title: FR3IIIC

description: Polysomal fraction #3 of HeLa cells transfected with Pre-miR-Ctrl.

extract_protocol: Total RNA was extracted from fraction #3 using Trizol (Invitrogen). Quality and quantity of the total RNA was checked with the Agilent 2100 bioanalyzer using RNA 6000 Nano chips.


title: FR4IC


title: FR3IIC


title: FR2I520

description: Polysomal fraction #2 of HeLa cells transfected with Pre-miR-520c-3p.

extract_protocol: Total RNA was extracted from fraction #2 using Trizol (Invitrogen). Quality and quantity of the total RNA was checked with the Agilent 2100 bioanalyzer using RNA 6000 Nano chips.


title: FR3II520

description: Polysomal fraction #3 of HeLa cells transfected with Pre-miR-520c-3p.


title: FR1IIIC

description: Polysomal fraction #1 of HeLa cells transfected with Pre-miR-Ctrl.

extract_protocol: Total RNA was extracted from fraction #1 using Trizol (Invitrogen). Quality and quantity of the total RNA was checked with the Agilent 2100 bioanalyzer using RNA 6000 Nano chips.


title: FR2IIIC

description: Polysomal fraction #2 of HeLa cells transfected with Pre-miR-Ctrl.


title: FR3I520


title: FR5II520


title: FR2IC


title: FR2IIC


title: FR1II520

description: Polysomal fraction #1 of HeLa cells transfected with Pre-miR-520c-3p.


title: FR1IIC


title: FR3IC


title: FR2III520


title: FR1I520

treatment_protocol: Linear sucrose gradient fractionation was performed on the transfected HeLa cells. Briefly, ~ 6 × 106 cells were incubated for 15 min with 100 mg/ml cycloheximide. Cells were lysed in cytoplasmic lysis buffer containing 20 mM Tris-HCl (pH 7.5), 100 mM KCl, 5 mM MgCl2, 0.3% IGEPAL CA-630, RNaseOUT (Invitrogen) and, protease inhibitor cocktail for 5 min on ice and centrifuged (10,000 × g, 10 min, 4°C). Cytoplasmic extracts were loaded onto the 10–50% sucrose gradients and after centrifugation (Beckman SW41, 35,000 rpm, 3 h, 4°C) the material was fractionated into eleven 1 ml aliquots labeled FR1-FR11 using a gradient fractionator (Brandel) and monitored by optical density measurement (A254).


title: FR2II520


title: Muscle_Saline Control_Replicate-3

status: Public on Jan 17 2014

data_processing: Data was extracted using the Illumina BeadStudio software(v1.6.0).  Any spots at or below the background were filtered out using an Illumina detection p value of 0.02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below.  Z-score = (raw value - avg)/std.  Complete data including detection scores will be included in the supplemental file.

source_name: Muscle_Saline Control

growth_protocol: 23-month old female C57BL/6J mice (Jackson Laboratory, Bar Harbor, ME) were housed under standard conditions, 3 mice per cage, with food and water ad libitum.

extract_protocol: RNA isolation was carried out using the Qiagen RNeasy Mini Kit for animal tissues (Qiagen, Inc., Valencia, CA) following the manufacturer’s instructions.  Quantity and quality of the RNA was assessed using the Agilent 2100 Bioanalyzer with RNA 6000 Nano Chips.

treatment_protocol: Mice were injected intraperitoneally with 5-Aminoimidazole-4-carboxamide-1-a-D-ribofuranoside (AICAR, Toronto Research Chemicals Inc., Canada) dissolved in saline, 500 mg/kg/day for  3 (ACR3), 7 (ACR7) or 14 (ACR14) days or saline vehicle, for 3 (CTR) days.   Thirty-three days after the final injection animals were deeply anesthetized with isofluorane and perfused transcardially with 0.9% NaCl solution.  The gastrocnemius muscle and Hippocampus were quickly removed, frozen on dry ice and stored at −80 °C for RNA isolation and microarray analysis.

value: 23 months old

value: saline vehicle for 3 days.

value: gastrocnemius muscle


title: Muscle_Saline Control_Replicate-1

value: female


title: Muscle_AICAR-7days_Replicate-3

value: 5-Aminoimidazole-4-carboxamide-1-a-D-ribofuranoside dissolved in saline, 500 mg/kg/day for 7 days


title: Muscle_AICAR-3days_Replicate-4

value: 5-Aminoimidazole-4-carboxamide-1-a-D-ribofuranoside dissolved in saline, 500 mg/kg/day for 3 days


title: Muscle_AICAR-7days_Replicate-4


title: Muscle_Saline Control_Replicate-2


title: FR1III520


title: Muscle_AICAR-14days_Replicate-4

value: 5-Aminoimidazole-4-carboxamide-1-a-D-ribofuranoside dissolved in saline, 500 mg/kg/day for 14 days


title: Muscle_AICAR-3days_Replicate-2


title: Muscle_AICAR-3days_Replicate-1


title: Muscle_AICAR-14days_Replicate-2


title: Hippocampus_Saline Control_Replicate-2

source_name: Hippocampus_Saline Control

value: hippocampus


title: Muscle_AICAR-7days_Replicate-2


title: Muscle_AICAR-14days_Replicate-1


title: Hippocampus_AICAR-7days_Replicate-1


title: Muscle_AICAR-7days_Replicate-1


title: Hippocampus_AICAR-7days_Replicate-2


title: SampleNo_949_young

status: Public on Dec 18 2013

description: Small RNA-Seq

data_processing:
llumina adapter sequences were clipped and any short sequence tags of length less than 17 bases were removed
miRNA sequences were aligned to human genome (hg19) with no more than 1 base mismatch in the seed region using mirDeep mapper program which uses the popular bowtie algorithm
miRNAs were identified using the MirDeep2 program using human miRBase-19 database of both mature and miRNA precursors
All matches and predicted novel miRNAs were reported and analyzed further by randfold program to identify the folding free energies
Genome_build: hg19
Supplementary_files_format_and_content: The processed data file contain the counts and the micro-RNA structure of the identified micro-RNAs in PDF format.

source_name: serum

extract_protocol:
Total RNA was isolated from 400 uL of serum from 11 young (30 yrs) and 11 old (64 yrs) or peripheral blood mononuclear cells (one young 30 yr old and one old 64 yr old ) from HANDLS participants using Trizol LS (Life Technologies) according to manufacturer’s instructions with the addition of a second phenol/chloroform extraction prior to RNA precipitation in order to reduce protein and DNA contamination.  Samples were resuspended in 15 mL RNase-free water and frozen at -80oC until further use.
Libraries were prepared for sequencing using the TruSeq small RNA sample prep kit (Illumina) with multiplexing according to manufacturer's instructions

treatment_protocol: Fasting blood samples were obtained from participants in the Healthy Aging in Neighborhoods of Diversity across the Life Span (HANDLS) study of the National Institute on Aging Intramural Research Program (NIA IRP), National Institutes of Health (NIH).  Samples were collected in vials with no additives, centrifuged and serum was collected, aliquoted and immediately frozen at -80oC until use.  PBMCs were isolated as in Noren Hooten et al., PLoS ONE 2010.

tag: age in years

tag: age group

value: young

value: serum


title: SampleNo_1632_young

description: Small RNA-Seq


title: Hippocampus_Saline Control_Replicate-1


title: Hippocampus_AICAR-7days_Replicate-4


title: Hippocampus_AICAR-3days_Replicate-1


title: Muscle_AICAR-14days_Replicate-3


title: Hippocampus_Saline Control_Replicate-3


title: SampleNo_1170_young

description: Small RNA-Seq


title: SampleNo_1306_young

description: Small RNA-Seq


title: Hippocampus_AICAR-3days_Replicate-3


title: Hippocampus_AICAR-7days_Replicate-3


title: Hippocampus_AICAR-3days_Replicate-2


title: SampleNo_1241_young

description: Small RNA-Seq


title: Hippocampus_AICAR-3days_Replicate-4


title: Hippocampus_AICAR-14days_Replicate-4


title: Hippocampus_AICAR-14days_Replicate-1


title: Hippocampus_AICAR-14days_Replicate-3


title: Muscle_Saline Control_Replicate-4


title: Hippocampus_AICAR-14days_Replicate-2


title: SampleNo_1257_young

description: Small RNA-Seq


title: SampleNo_954 Cells_old

description: Small RNA-Seq

source_name: peripheral blood mononuclear cells

value: old

value: peripheral blood mononuclear cells


title: SampleNo_1800_old

description: Small RNA-Seq


title: SampleNo_1254_young

description: Small RNA-Seq


title: SampleNo_1387_young

description: Small RNA-Seq


title: SampleNo_944 Cells_young

description: Small RNA-Seq


title: SampleNo_1181_old

description: Small RNA-Seq


title: SampleNo_1365_young

description: Small RNA-Seq


title: SampleNo_1224_old

description: Small RNA-Seq


title: SampleNo_2724_old

description: Small RNA-Seq


title: SampleNo_307_old

description: Small RNA-Seq


title: SampleNo_2130_old

description: Small RNA-Seq


title: SampleNo_1920_young

description: Small RNA-Seq


title: SampleNo_1470_young

description: Small RNA-Seq


title: SampleNo_632_old

description: Small RNA-Seq


title: SampleNo_954_old

description: Small RNA-Seq


title: SampleNo_2157_old

description: Small RNA-Seq


title: FR7II520

value: HeLa

value: 50 nM small RNAs Pre-miR-520c-3p


title: SampleNo_279_old

description: Small RNA-Seq


title: Hippocampus_Saline Control_Replicate-4


title: SampleNo_2898_old

description: Small RNA-Seq


title: HeLa-Con-miR Replicate-2

status: Public on Oct 09 2013

description: HeLa-Con-miR Replicate-2

data_processing:
Data was extracted using the Illumina GenomeStudio software(v1.9.0).  Any spots at or below the background were filtered out using an Illumina detection p value of 0.02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below.  Z-score = (raw value - avg)/std.
Detection_Pval = Detection Pvalue from Illumina GenomeStudio software, ver 1.9.0.

growth_protocol: HeLa cells were grown in DMEM supplemented with 10% FBS and Pen-Strep.

extract_protocol: Forty eight hours post transfection, total RNA was isolated using the mirVana kit (Invitrogen) according to manufacturer’s procedure.

treatment_protocol: HeLa cells were transfected with 20 nM biotinylated miRIDIAN  miR-1248 mimic (Thermo Scientific) or a negative control, biotinylated miRIDIAN C. elegans miR-Mir-67 (here named Con-miR) using Lipofectamine 2000

value: HeLa Cells

value: transfected with 20 nM of biotinylated miRIDIAN C. elegans miR-Mir-67 a negative control,  (here named Con-miR) using Lipofectamine 2000


title: CR_CR79_62

status: Public on Aug 01 2013

description: Human subjects from a group of 15 middle-aged (58.7±7.4 yrs.), weight-stable members of the Calorie Restriction Society who have been practicing ~30% CR with adequate nutrition (at least 100% of RDI for each nutrient) for an average of 9.6 years

data_processing: Data was extracted using the Illumina GenomeStudio software(v1.6.0). Any spots at or below the background were filtered out using an Illumina detection p-value of 0.02 and above. The natural log of all remaining scores was used to find the avg and std of each array and the z-score normalization was calculated and presented below.  Z-score = (raw value - avg)/std.  Complete data including detection scores will be included in the supplemental file.

source_name: Percutaneous biopsy specimens of vastus lateralis muscle of participants following a CR diet.

label_protocol: standard Illumina protocol using Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791) In short, 0.5g of total RNA was first converted into single-stranded cDNA with reverse transcriptase using an oligo-dT primer containing the T7 RNA polymerase promoter site and then copied to produce double-stranded cDNA molecules. The double stranded cDNA was cleaned and concentrated with the supplied columns and used in an overnight in-vitro transcription reaction where single-stranded RNA (cRNA) was generated and labeled by incorporation of biotin-16-UTP.

extract_protocol: RNA was extracted from skeletal muscle samples using Trizol Reagent (Invitrogen, Carlsbad, CA) following the manufacturer’s instructions.  The RNA quality and quantity was checked using an Agilent 2100 Bio-analyzer and the RNA 6000 nano-chips (Agilent Technologies, Palo Alto, CA).

tag: biopsy

value: Percutaneous biopsy specimens of vastus lateralis muscle.


title: HeLa-miR-1248 Replicate-1

description: HeLa-miR-1248 Replicate-1

value: transfected with 20 nM biotinylated miRIDIAN  miR-1248 mimic (Thermo Scientific) using Lipofectamine 2000


title: HeLa-Con-miR Replicate-1

description: HeLa-Con-miR Replicate-1