title: White_hypertensive_pool_replicate_1

description: Sample name: WHT


title: AA_normotensive_pool_replicate_3

status: Public on Nov 16 2016

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: BNHT 3

hyb_protocol: Exiqon miCURY 7th generation LNA microRNA arrays were hybridized for 16 hours at 56oC using the Agilent SureHyb chamber and gasket slide kit, as per the manufacturer's protocol.

scan_protocol: Arrays were scanned on an Agilent scanner at 10 micron resolution.

data_processing: Spot evaluation and data extraction was done using Agilent Feature Extraction software without background subtraction as per the manufacturer's protocol. Any spots at or below the background were filtered out. 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.

molecule: total RNA

organism: Homo sapiens

source_name: Blood

label_protocol: One microgram total RNA containing small RNA species was pooled from three-four individuals, such that forty individuals were sampled via three replicate pools for each of the four disease state x ethnicity comparisons. This pooled RNA was labeled according to the manufacturer's protocol, directly incorporating the Hy3-flourescent label

growth_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). This study was approved by the Institutional Review Board of the National Institute of Environmental Health Sciences (NIEHS), NIH and all participants provided written informed consent. Age-matched AA and white females that were either normotensive (NT) or hypertensive (HT). Hypertension was defined as an average SBP ≥140 mmHg or DP ≥90 mmHg or use of previously prescribed antihypertensive medications (diuretics, beta blockers, ACE inhibitors, angiotensin II blockers, calcium channel blockers, or vasodilators) and/or prior diagnosis of hypertension. We excluded participants with documented Hepatitis B, Hepatitis C, or human immunodeficiency virus (HIV) infection and current or former smokers.

extract_protocol: Total RNA from PMBCs was isolated using the miRVana miRNA Isolation Kit with enrichment for small RNAs according to the manufacturer’s protocol (Life Technologies). RNA quality was measured by a Nanodrop 2000 and Agilent Bioanalyzer and all RNA was stored at -80°C.

tag: ethnicity

value: African American

tag: gender

value: Female

tag: hypertension status

value: Normotensive


title: AA_hypertensive_pool_replicate_2

description: Sample name: BHT 2

value: Hypertensive


title: AA_normotensive_pool_replicate_1

description: Sample name: BNHT


title: White_hypertensive_pool_replicate_3

description: Sample name: WHT 3

value: Caucasian


title: White_normotensive_pool_replicate_1

description: Sample name: WNHT


title: White_normotensive_pool_replicate_2

description: Sample name: WNHT 2


title: AA_hypertensive_pool_replicate_3

description: Sample name: BHT 3


title: White_normotensive_pool_replicate_3

description: Sample name: WNHT 3


title: AA_normotensive_pool_replicate_2

description: Sample name: BNHT 2


title: HEK293T_Exosome depleted_Replicate_3

status: Public on Oct 23 2016

description: Sample name: Exosome-depleted_FBS-3

hyb_protocol: Standard Illumina protocol. In short, a total of 0.75 μg of biotin-labeled cRNA was hybridized at 58°C for 16 hours to Illumina's HumanHT-12 V4.0 Expression Bead Chips (Illumina, San Diego, CA). Each BeadChip has 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. 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 0.54 μm using the Illumina iScan scanner.

data_processing: Data was extracted using the Illumina GenomeStudio software V2011.1, Gene expression module 1.9.0. 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 is supplied.

source_name: HEK293T_Exosome depleted

label_protocol: Standard Illumina protocol using Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791) In short, 0.5 μg 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: HEK293T cells (5x105) were grown on a 10 cm dish for 24 hours. Medium was replaced with fresh media containing EVR or UC-EVD serum, and following 48 hours of growth.

extract_protocol: RNA was extracted using Trizol (Trizol Reagent, Invitrogen) according to manufacturer’s instructions. RNA integrity was assessed by Agilent Bioanalyzer RNA 6000 Chip (Agilent, Santa Clara, CA).

tag: cell line


title: HEK293T_Exosome enriched_Replicate_2

description: Sample name: Exosome-enriched_FBS-2

source_name: HEK293T_Exosome enriched


title: HEK293T_Exosome enriched_Replicate_1

description: Sample name: Exosome-enriched_FBS-1


title: HEK293T_Exosome depleted_Replicate_2

description: Sample name: Exosome-depleted_FBS-2


title: HEK293T_Exosome depleted_Replicate_4

description: Sample name: Exosome-depleted_FBS-4


title: HEK293T_Control_Replicate_1

description: Sample name: Control_FBS-1


title: HEK293T_Control_Replicate_2

description: Sample name: Control_FBS-2


title: HEK293T_Exosome enriched_Replicate_3

description: Sample name: Exosome-enriched_FBS-3


title: HEK293T_Exosome depleted_Replicate_1

description: Sample name: Exosome-depleted_FBS-1


title: HEK293T_Control_Replicate_3

description: Sample name: Control_FBS-3


title: HEK293T_Exosome enriched_Replicate_4

description: Sample name: Exosome-enriched_FBS-4


title: HEK293T_Control_Replicate_4

description: Sample name: Control_FBS-4


title: GM_MYF5_replicate4

status: Public on Aug 08 2016

hyb_protocol: Standard Illumina protocol. In short, all biotin-labeled cRNA was hybridized at 58 degrees C for 16 hours to Illumina's Mouse-Ref8 v2 Expression Bead Chips (Illumina, San Diego, CA). Each BeadChip has ~25,600 well-annotated RefSeq transcripts . 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 0.53um using the Illumina iScan beadarray reader.

data_processing: Data was extracted using the Illumina GenomeStudio software V2011.1, Gene expression module 1.9.0. 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.  Z-score = (raw value - avg)/std.  All data were log2-transformed and normalised by Robust Spline Normalisation using the lumi software package in Bioconductor. 18,185 nucleotide probes were filtered from 25,697 total using an Illumina detection P value of α = 0.05. Significant genes were selected by a one-way ANOVA or t-test (FDR = 0.05) for further analysis. GSEA software was used to select differentially expressed (DE) genes by calculating out a ‘score’ using the Kolmogorov-Smirnov (KS) test. The score indicates how a gene relates with genotype, where positive values relate to up-regulation and negative values relate to down-regulation. Only transcripts with a KS score > |0.15| were considered DE. Transcripts demonstrating greater than 1.2-fold change in expression were processed using Ingenuity Pathway Analysis software (Ingenuity Systems, CA, USA) to identify networks and canonical pathways overrepresented in enriched genes.Complete data including detection scores is supplied.

organism: Mus musculus

source_name: C2C12_Growth medium_MYF5 IP

label_protocol: Standard Illumina protocol using Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791): RIP 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: Proliferating C2C12 myoblasts cells were cultured in growing medium [(GM), Dulbecco's modified Eagle's medium (Invitrogen) supplemented with 10% fetal bovine serum (Gibco), antibiotics, and antimycotics (Life Technologies)].  Growing, subconfluent C2C12 cultures were induced to differentiate by replacing the GM with differentiation medium [(DM) DMEM with 2% horse serum].

extract_protocol: RNA was extracted using TRIzol according to the manufacturer’s protocol.

treatment_protocol: Cytoplasmic extracts from growing (GM) and differentiated (DM)  C2C12 cells were prepared by lysing the cells in polysome extraction buffer (PEB, 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 the supernatant was collected by centrifugation (15,000 × g for 10 min at 4°C).  The supernatants were incubated with protein A sepharose beads coated with anti-MYF5 (sc-302, Santa Cruz Biotechnology) or with control IgG (Santa Cruz Biotechnology) antibodies for 2 h at 4°C.  After washes with NT2 buffer (50 mM Tris-HCl [pH 7.5], 150 mM NaCl, 1 mM MgCl2, 0.05% NP-40), MYF5 or control IgG immunoprecipitated RNA was extracted using TRIzol.

tag: tissue

value: Myoblast cell line


title: DM_MYF5_replicate2

source_name: C2C12_Differentiation medium_MYF5 IP


title: DM_MYF5_replicate3


title: DM_IgG_replicate3

source_name: C2C12_Differentiation medium_IgG IP


title: GM_IgG_replicate3

source_name: C2C12_Growth medium_IgG IP


title: GM_MYF5_replicate1


title: Exendin4 Post-TBI_replicate 4

status: Public on Aug 05 2016

description:
INJ_BL_DRUG_4
Hippocampus_Exendin4 Post-TBI_replicate 4

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-Ref8 v3 Expression Bead Chips (Illumina, San Diego, CA). Each BeadChip has ~22,000 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.

label: biotin

source_name: Hippocampus_EX-4 PostTBI_Day 3

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: Male ICR mice weighing 30-40 g were kept five per cage under a constant 12-h light/dark cycle, at room temperature (22 +/-2°C). Food and water were available ad libitum. Each mouse was used for one experiment and for one time point only. The Ethics Committee of the Sackler Faculty of Medicine approved the experimental protocol (M-11-086), in compliance with the guidelines for animal experimentation of the National Institutes of Health (DHEW publication 85-23, revised, 1995). The numbers of animals per treatment group for the assessment of neurodegeneration; gene expression and animal cognition were selected based upon experience from prior studies. All attempts were made to minimize both the numbers of mice used for our studies and their suffering. All experimental manipulations were conducted during the light phase of the light/dark cycle. At the time of animal euthanasia, a two stage method approved by the Sackler Faculty of Medicine Ethics Committee was employed; animals were terminally anesthetized with Isoflurane, followed by decapitation.

extract_protocol: RNA was extracted from dissected hippocampi using the RNeasy kit (Qiagen, Valencia, CA) using the standard manufactures protocol. Samples were assessed for quality and quantity using an Agilent 2100 Bioanlyzer with RNA 6000 Nano Chips, (Aligent technologies).

treatment_protocol: Hippocampal brain gene expression was examined on day 3 and day 14 (Experiment GSE44625) after male ICR mice (30-40 g) underwent a blast traumatic brain injury (B-TBI) or sham procedure. Animals received 3.5 pM/kg/min (21ug/kg/day) Exendin-4 using Alzet micro-osmotic pumps either as a pre-treatment to the blast injury 48 hours before (Ex-4 pre-TBI) or as a post-treatment 2 hours after the blast injury (Ex-4 post-TBI) and were evaluated at Day 3 post-blast. Animals in a previous data set on Day 14 (GSE44625) were administered Ex-4 as a pre-treatment.

tag: strain

value: ICR

value: Male

value: Brain

value: Hippocampus


title: GM_IgG_replicate2


title: Exendin4 Post-TBI_replicate 3

description:
INJ_BL_DRUG_3
Hippocampus_Exendin4 Post-TBI_replicate 3


title: DM_IgG_replicate4


title: DM_MYF5_replicate1


title: GM_IgG_replicate4


title: Exendin4 Post-TBI_replicate 2

description:
INJ_BL_DRUG_2
Hippocampus_Exendin4 Post-TBI_replicate 2


title: DM_IgG_replicate1


title: Exendin4 Pre-TBI_replicate 4

description:
DRUG_INJ_BL_4
Hippocampus_Exendin4 Pre-TBI_replicate 4

source_name: Hippocampus_EX-4 PreTBI_Day 3


title: DM_MYF5_replicate4


title: Exendin4 Pre-TBI_replicate 1

description:
DRUG_INJ_BL_1
Hippocampus_Exendin4 Pre-TBI_replicate 1


title: GM_MYF5_replicate2


title: GM_IgG_replicate1


title: Exendin4 Pre-TBI_replicate 3

description:
DRUG_INJ_BL_3
Hippocampus_Exendin4 Pre-TBI_replicate 3


description:
INJ_BL_2
Hippocampus_Traumatic blast injury (TBI)_replicate 2

source_name: Hippocampus_TBI_Day 3


title: GM_MYF5_replicate3


description:
INJ_BL_3
Hippocampus_Traumatic blast injury (TBI)_replicate 3


description:
INJ_BL_4
Hippocampus_Traumatic blast injury (TBI)_replicate 4


title: DM_IgG_replicate2


title: Exendin4 Post-TBI_replicate 1

description:
INJ_BL_DRUG_1
Hippocampus_Exendin4 Post-TBI_replicate 1


title: Exendin4 Pre-TBI_replicate 2

description:
DRUG_INJ_BL_2
Hippocampus_Exendin4 Pre-TBI_replicate 2


description:
INJ_BL_5
Hippocampus_Traumatic blast injury (TBI)_replicate 5


description:
INJ_BL_1
Hippocampus_Traumatic blast injury (TBI)_replicate 1


title: Exendin4 Pre-TBI_replicate 5

description:
DRUG_INJ_BL_5
Hippocampus_Exendin4 Pre-TBI_replicate 5


title: Exendin4_replicate 5

description:
DRUG_5
Hippocampus_Exendin4_replicate 5

source_name: Hippocampus_EX-4_Day 3


title: C57_liver_Male_ CR40_replicate_6

status: Public on Jun 27 2016

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

label_protocol: Standard Illumina protocol using Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791) In short, IP 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: Male and female C57BL/6J and DBA2/J mice were obtained from the Jackson Laboratory (Bar Harbor, ME) and then bred in house at the National Institute on Aging (Baltimore, MD) in order to obtain sufficient number of mice per group. Litters were maintained with approximately eight pups to minimize the potential confounding effect of a crowded litter. Mice were housed in cages of three to four with ad libitum access to water at the Gerontology Research Center in Baltimore, MD. All animal protocols were approved by the National Institute on Aging Animal Care and Use Committee (405-LEG-2012, 405-TGB-2015, 405-TGB-2019) of the National Institute on Aging.

extract_protocol: Total RNA was isolated from mouse livers with Trizol® (Invitrogen) according to the manufacturers instructions.

treatment_protocol: Mice were fed house chow (2018 Teklad Global 18% Protein Rodent Diet, Harlan Teklad, Indianapolis, IN) either ad libitum (AL) or at 20% or 40% CR starting at 6 months of age for the remainder of their lives. A gradual stepwise reduction in food intake by increments of 10% per week was carried out for CR mice. Body weight and food intake were monitored biweekly. CR mice were fed daily between 7.30am ± 1 h and food was placed onto the floor of the cage. AL mice were fed in the hopper. Animal rooms were maintained at 20–22ºC with 30–70% relative humidity and a 12-h light/dark cycle. In March 2013, all animals were moved to the new NIA Biomedical Research Center (across the road), and for the next two weeks, no change in food consumption, bodyweight or unexpected increase in mortality of mice was recorded. All animal protocols were approved by the National Institute on Aging Animal Care and Use Committee (405-LEG-2012, 405-TGB-2015, 405-TGB-2019) of the National Institute on Aging. At 23-24 months of age (17-18 months of dietary intervention), 6 mice per diet group were sacrificed over three consecutive days from 8am to 12pm. Mice were euthanized by cervical dislocation and tissues were rapidly collected, weighed and then snap frozen in liquid nitrogen or processed for further analyses as detailed below. All mice were sacrificed between 7-11am. On the day of the sacrifice mice were not fasted (mice on a CR diet were not fed their daily ration, while AL mice were allowed to eat ad libitum until sacrifice).

value: Liver

tag: mouse strain

tag: diet

value: 40% Caloric Restriction


title: C57_liver_Male_ CR40_replicate_5


title: C57_liver_Male_ CR40_replicate_1


title: C57_liver_Male_ CR40_replicate_3


title: Exendin4_replicate 4

description:
DRUG_4
Hippocampus_Exendin4_replicate 4


title: C57_liver_Male_ CR20_replicate_6

value: 20% Caloric Restriction


title: Control_replicate 2

description:
CTR_2
Hippocampus_Control_replicate 2


title: Control_replicate 4

description:
CTR_4
Hippocampus_Control_replicate 4


title: Exendin4_replicate 1

description:
DRUG_1
Hippocampus_Exendin4_replicate 1


title: Exendin4_replicate 3

description:
DRUG_3
Hippocampus_Exendin4_replicate 3


title: Control_replicate 5

description:
CTR_5
Hippocampus_Control_replicate 5


title: Control_replicate 1

description:
CTR_1
Hippocampus_Control_replicate 1


title: C57_liver_Male_ CR20_replicate_5


title: C57_liver_Male_ AL_replicate_5

value: Ad libitum


title: C57_liver_Male_ AL_replicate_1


title: C57_liver_Male_ AL_replicate_2


title: C57_liver_Male_ AL_replicate_4


title: Control_replicate 3

description:
CTR_3
Hippocampus_Control_replicate 3


title: C57_liver_Male_ CR40_replicate_4


title: C57_liver_Male_ CR20_replicate_4


title: Exendin4_replicate 2

description:
DRUG_2
Hippocampus_Exendin4_replicate 2


title: C57_liver_Male_ CR20_replicate_2


title: C57_liver_Female_ CR40_replicate_5


title: C57_liver_Male_ AL_replicate_3


title: C57_liver_Male_ CR20_replicate_3


title: C57_liver_Male_ CR20_replicate_1


title: C57_liver_Female_ CR40_replicate_6


title: C57_liver_Female_ CR40_replicate_4


title: C57_liver_Male_ CR40_replicate_2


title: C57_liver_Female_ CR40_replicate_3


title: C57_liver_Female_ CR20_replicate_5


title: C57_liver_Female_ CR20_replicate_2


title: C57_liver_Female_ AL_replicate_3


title: C57_liver_Female_ AL_replicate_1


title: C57_liver_Female_ CR20_replicate_4


title: C57_liver_Female_ CR20_replicate_3


title: DBA_liver_Male_ CR40_replicate_6


title: C57_liver_Female_ CR40_replicate_1


title: C57_liver_Female_ AL_replicate_4


title: DBA_liver_Male_ CR40_replicate_5


title: DBA_liver_Male_ CR20_replicate_3


title: DBA_liver_Male_ CR20_replicate_1


title: C57_liver_Female_ CR20_replicate_1


title: DBA_liver_Male_ CR40_replicate_4


title: C57_liver_Female_ AL_replicate_6


title: C57_liver_Female_ CR40_replicate_2


title: C57_liver_Female_ AL_replicate_2


title: DBA_liver_Male_ CR40_replicate_2


title: DBA_liver_Male_ CR40_replicate_1


title: DBA_liver_Male_ CR20_replicate_2


title: C57_liver_Female_ AL_replicate_5


title: DBA_liver_Male_ CR40_replicate_3


title: DBA_liver_Male_ CR20_replicate_6


title: DBA_liver_Male_ CR20_replicate_4


title: DBA_liver_Male_ CR20_replicate_5


title: C57_liver_Female_ CR20_replicate_6


title: DBA_liver_Male_ AL_replicate_6


title: DBA_liver_Male_ AL_replicate_5


title: Total RNA-Frag-Seq rep2

status: Public on Jun 03 2016

type: SRA

city: Göttingen

first: Björn

last: Schwalb

address: Fassberg 11

country: Germany

institute: MPI

library_source: transcriptomic

data_processing:
Sequencing data processing. Paired-end 50 base reads with additional 6 base reads of barcodes were obtained for each of the samples, i.e. total RNA (RNA-Seq), total fragmented RNA (RNA-Frag-Seq), labeled RNA (4sU-Seq), labeled fragmented RNA (TT-Seq) and ChIP-Seq samples (N20 and S2P). Reads were demultiplexed and mapped with STAR 2.3.0 (for RNA-Seq) (Dobin and Gingeras, Current protocols in bioinformatics, 2015) and Bowtie 2.1.0. (Langmead and Salzberg, Nat Methods, 2012) (for ChIP-Seq) to the hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium). Samtools (Li et al., Bioinformatics, 2009) was used to quality filter SAM files, whereby alignments with MAPQ smaller than 7 (-q 7) were skipped and only proper pairs (-f99, -f147, -f83, -f 163) were selected. Further processing of the RNA-Seq data was carried out using the R/Bioconductor environment. For visualization purposes piled-up read counts for every genomic position were summed up over replicates, size factors for each condition were calculated as described in (Anders and Huber, Genome Biol, 2010) and used to correct for library size and sequencing depth variations.
Genome_build: hg20/hg38 (GRCh38)
Supplementary_files_format_and_content: The file binned_count_table.txt gives the fragment counts for all experiments using the binning_anno.txt annotation file
Supplementary_files_format_and_content: The Series file README.txt includes information about the contents of the processed data files.

source_name: K562 cells

growth_protocol: K562 cells were acquired from DSMZ (Braunschweig, Germany). Cells were grown in RPMI 1640 medium (Gibco) supplemented with 10% heat-inactivated FBS (Gibco) and 1% Penicillin/Streptomycin (100x, PAA) at 37°C under 5% CO2

extract_protocol:
RNA was extracted using TRIzol (Life Technologies), 4sU-labeled RNA was exctracted according to Dolken et al., RNA, 2008.
fragmentation: yes; BioRuptor Next Gen (Diagenode) at high power for one cycle of 30’’/30’’ ON/OFF
NuGEN Human Whole Blood RNA-Seq System

treatment_protocol: Cells  were labeled in media for 5 min with 500 μM 4-thiouridine (4sU, Sigma-Aldrich) and harvested through centrifugation for 2 min at 3,000 rpm.

tag: passage


title: DBA_liver_Male_ AL_replicate_3


title: TT-Seq rep1


title: DBA_liver_Male_ AL_replicate_4


title: Total RNA-Frag-Seq rep1


title: TT-Seq rep2


title: DBA_liver_Female_ CR40_replicate_1


title: DBA_liver_Female_ CR40_replicate_5


title: DBA_liver_Male_ AL_replicate_2


title: DBA_liver_Female_ CR40_replicate_2


title: DBA_liver_Female_ CR40_replicate_4


title: DBA_liver_Female_ AL_replicate_6


title: DBA_liver_Female_ CR40_replicate_6


title: DBA_liver_Female_ CR20_replicate_4


title: C57_liver_Male_ AL_replicate_6


title: DBA_liver_Female_ CR20_replicate_1


title: DBA_liver_Male_ AL_replicate_1


title: DBA_liver_Female_ CR20_replicate_3


title: DBA_liver_Female_ CR20_replicate_5


title: DBA_liver_Female_ AL_replicate_5


title: DBA_liver_Female_ AL_replicate_2


title: DBA_liver_Female_ CR40_replicate_3


title: DBA_liver_Female_ CR20_replicate_6


title: DBA_liver_Female_ AL_replicate_1


title: DBA_liver_Female_ AL_replicate_3


title: DBA_liver_Female_ AL_replicate_4


title: DBA_liver_Female_ CR20_replicate_2


title: UACC-1273  Cells_Cultured with Old Fibroblasts_replicate 2

status: Public on Apr 08 2016

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.

label: Streptavidin-Cy3 bound to biotin labeled cRNA.

source_name: UACC-1273  Cells_Cultured for 96hr with Old Fibroblasts

growth_protocol:
M93-047, UACC-903 and UACC-1273 cells were maintained in RPMI (Invitrogen, Carlsbad, CA), supplemented with 10% FBS, 100 units/ml penicillin and streptomycin and 4 mM L-glutamine.
Fibroblasts were maintained in DMEM, supplemented with 10% FBS, 100 units/ml penicillin and streptomycin and 4 mM L-glutamine.

extract_protocol: Total RNA extraction was done using TRIzol as per manufacturer’s protocol.  Quality and quantity of the total RNA was tested using the Agilent 2100 Bio-Analyzer and RNA 6000 nano kits.

treatment_protocol: Dermal fibroblasts from young medium or aged individuals were co-cultured with the three different melanoma cell lines (UACC1273, M93-047 and UACC903) using transwell chambers. After 96 h of co-culture, fibroblasts in the upper well were removed, and melanoma cells (lower chamber) were harvested and used for microarray analysis.

value: UACC-1273  melanoma cell line

tag: treatment

value: Cells co-cultured with dermal fibroblasts from old (>55 years) individuals using transwell chambers for 96 hr.


title: UACC-1273  Cells_Cultured with Old Fibroblasts_replicate 1


title: UACC-1273  Cells_Cultured with Medium aged Fibroblasts_replicate 3

source_name: UACC-1273  Cells_Cultured for 96hr with Medium aged Fibroblasts

value: Cells co-cultured with dermal fibroblasts from medium aged individuals using transwell chambers for 96 hr.


title: UACC-1273  Cells_Cultured with Medium aged Fibroblasts_replicate 1


title: UACC-1273  Cells_Cultured with Old Fibroblasts_replicate 3


title: UACC-1273  Cells_Cultured with Medium aged Fibroblasts_replicate 2


title: UACC-1273  Cells_Cultured with Young Fibroblasts_replicate 3

source_name: UACC-1273  Cells_Cultured for 96hr with Young Fibroblasts

value: Cells co-cultured with dermal fibroblasts from young (<35 years) individuals using transwell chambers for 96 hr.


title: UACC-903  Cells_Cultured with Old Fibroblasts_replicate 3

source_name: UACC-903  Cells_Cultured for 96hr with Old Fibroblasts

value: UACC-903  melanoma cell line


title: UACC-903  Cells_Cultured with Young Fibroblasts_replicate 3

source_name: UACC-903  Cells_Cultured for 96hr with Young Fibroblasts


title: UACC-903  Cells_Cultured with Old Fibroblasts_replicate 1

source_name: UACC-903  Cells_Cultured for 96hr with Old Fibroblast


title: UACC-1273  Cells_Cultured with Young Fibroblasts_replicate 2


title: UACC-903  Cells_Cultured with Old Fibroblasts_replicate 2


title: UACC-903  Cells_Cultured with Medium aged Fibroblasts_replicate 3

source_name: UACC-903  Cells_Cultured for 96hr with Medium aged Fibroblasts


title: M93-047 Cells_Cultured with Young Fibroblasts_replicate 3

source_name: M93-047 Cells_Cultured for 96hr with Young Fibroblasts

value: M93-047 melanoma cell line


title: UACC-903  Cells_Cultured with Young Fibroblasts_replicate 1


title: M93-047 Cells_Cultured with Young Fibroblasts_replicate 2


title: UACC-903  Cells_Cultured with Young Fibroblasts_replicate 2


title: M93-047 Cells_Cultured with Old Fibroblasts_replicate 2

source_name: M93-047 Cells_Cultured for 96hr with Old Fibroblasts


title: UACC-903  Cells_Cultured with Medium aged Fibroblasts_replicate 2


title: M93-047 Cells_Cultured with Medium aged Fibroblasts_replicate 2

source_name: M93-047 Cells_Cultured for 96hr with Medium aged Fibroblasts


title: M93-047 Cells_Cultured with Old Fibroblasts_replicate 1


title: M93-047 Cells_Cultured with Young Fibroblasts_replicate 1


title: UACC-903  Cells_Cultured with Medium aged Fibroblasts_replicate 1


title: M93-047 Cells_Cultured with Old Fibroblasts_replicate 3


title: Tumor biopsy [P-310_re-analysis]

status: Public on Mar 29 2016

city: Oslo

first: Heidi

last: Lyng

address: Montebello

department: Department of Radiation Biology

country: Norway

institute: Oslo University Hospital

description: Reanalysis of GSM1668715

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation in BeadStudio 3.1.3.0

source_name: Cervical tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol

growth_protocol: 1-4 tumor samples wer collected from each patient at the time of diagnosis

extract_protocol: In cohort 1, RNA was extracted with Trizol reagent, followed by double precipitation with isopropanol and final precipitation with 5M lithium chloride. In cohort 2, RNA was extracted by use of the miRNeasy mini kit. RNA from different biopsies of the same tumor was pooled. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: The samples were immediately snap-frozen in liquid nitrogen and stored at -80 C until used for analysis.

tag: histology

value: Squamous cell carcinoma

tag: gene-based hypoxia

value: Less hypoxic

tag: imaging-based hypoxia

tag: combined hypoxia biomarker

tag: figo stage

tag: hypoxia classifier

tag: cohort

value: Cohort 2


title: M93-047 Cells_Cultured with Medium aged Fibroblasts_replicate 3


title: Tumor biopsy [P-269_re-analysis]

description: Reanalysis of GSM1668708

value: More hypoxic


title: Tumor biopsy [P-300_re-analysis]

description: Reanalysis of GSM1668714


title: UACC-1273  Cells_Cultured with Young Fibroblasts_replicate 1


title: Tumor biopsy [P-297_re-analysis]

description: Reanalysis of GSM1668712


title: Tumor biopsy [P-267_re-analysis]

description: Reanalysis of GSM1668707


title: Tumor biopsy [P-262_re-analysis]

description: Reanalysis of GSM1668703


title: Tumor biopsy [P-255_re-analysis]

description: Reanalysis of GSM1668702


title: Tumor biopsy [P-266_re-analysis]

description: Reanalysis of GSM1668706


title: M93-047 Cells_Cultured with Medium aged Fibroblasts_replicate 1


title: Tumor biopsy [P-254_re-analysis]

description: Reanalysis of GSM1668701


title: Tumor biopsy [P-211_re-analysis]

description: Reanalysis of GSM1668696


title: Tumor biopsy [P-097_re-analysis]

description: Reanalysis of GSM1668690


title: Tumor biopsy [P-207_re-analysis]

description: Reanalysis of GSM1668695


title: Tumor biopsy [P-243_re-analysis]

description: Reanalysis of GSM1668700


title: Tumor biopsy [P-060_re-analysis]

description: Reanalysis of GSM1668688


title: Tumor biopsy [P-167]


title: Tumor biopsy [P-090]

value: Adenocarcinom

value: Adeno


title: Tumor biopsy [P-052]


title: Tumor biopsy [P-008_re-analysis]

description: Reanalysis of GSM1668685


title: Tumor biopsy [P-015]


title: Tumor biopsy [P-029]


title: Tumor biopsy [P-104]


title: Tumor biopsy [P-185]


title: Tumor biopsy [P-147]


title: Tumor biopsy [P-201_re-analysis]

description: Reanalysis of GSM1668693


title: Tumor biopsy [P-003_re-analysis]

description: Reanalysis of GSM1668684


title: Tumor biopsy [P-119]


title: Tumor biopsy [P-044]


title: Tumor biopsy [P-041_re-analysis]

description: Reanalysis of GSM1668687


title: Tumor biopsy [P-206]


title: Tumor biopsy [P-122]

value: Adenosquamous


title: Tumor biopsy [P-179_re-analysis]

description: Reanalysis of GSM1668692


title: SRSF7_iCLIP_mm9_Rep5

status: Public on Mar 07 2016

city: Frankfurt am Main

first: Michaela

last: Müller-McNicoll

address: Max-von-Laue-Str. 13

department: Institute for Cell Biology and Neuroscience

institute: Goethe University Frankfurt

description:
processed data file: mSRSF7_iCLIP_all_mm9_iCLIP_tags.bed
processed data file: mSRSF7_iCLIP_all_mm9_iCLIP_tag_clusters.bed

data_processing:
Basecalls performed using CASAVA version 1.4
For detail on data processing see: König et al. (2010): iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959
Genome_build: mm9
Supplementary_files_format_and_content: .bed files containing the genomic coordinates for significant CLIP tags for individual replicates or combined replicates (3-6 replicates).
Supplementary_files_format_and_content: .bed files containing the genomic coordinates for significant CLIP tag clusters from combined replicates.

growth_protocol: Cells were grown in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal calf serum and pennicilin/streptomycin antibiotics at 37˚C with 5% CO2.

extract_protocol:
Cells were lysed and treated with RNase I. GFP-tagged proteins were immunoprecipitated with Gamma binding beads coupled to goat anti-EGFP antibody (D. Drechsel, MPI-CBG).
After stringent washing, RNA was dephosphorylated and ligated to a 3' linker. Protein-RNA complexes were resolved by denaturing gel electrophoresis and transfered to nitrocellulose membrane. A membrane region above the expected size of the protein was cut and RNA was released by Proteinase K treatment. RNA was reverse transcribed using reverse primer containing a barcode sequence. cDNA was separated into 3 size fractions by denaturing gel electrophoresis and circularized by ssDNA circligase. A specific oligonukelotide was annealed to create a restriction site for BamHI and cDNA was linearized by digest with BamHI. Linearized cDNA was PCR amplifiied with Solexa sequencing primers to create the final libraries. For more details see: König et al. (2010): iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959

treatment_protocol: Cells were washed with PBS and irradiated with 254 nm UV light to crosslink proteins to nucleic acids.

value: P19 embryonal carcinoma cell line

tag: fusion protein expression

tag: antibody

value: anti-EGFP (D. Drechsel, MPI-CBG)

tag: barcode sequence

value: TGGC


title: Tumor biopsy [P-088]


title: SRSF7_iCLIP_mm9_Rep6

tag: cell line

value: CCAC


title: Tumor biopsy [P-001]


title: SRSF7_iCLIP_mm9_Rep3

value: CAAT


title: SRSF7_iCLIP_mm9_Rep2

value: GGTT


title: SRSF7_iCLIP_mm9_Rep1


title: Tumor biopsy [P-163_re-analysis]

description: Reanalysis of GSM1668691


title: SRSF3_iCLIP_mm9_Rep3

description:
processed data file: mSRSF3_iCLIP_all_mm9_iCLIP_tags.bed
processed data file: mSRSF3_iCLIP_all_mm9_iCLIP_tag_clusters.bed

value: CCGG


title: SRSF7_iCLIP_mm9_Rep4


title: Metazome_Tardigrade_timecourse_sample_0126

status: Public on Feb 18 2016

city: Haifa

first: Itai

last: Yanai

address: Technion City

department: Biology

country: Israel

institute: Technion - Israel Institute of Technology

data_processing:
Libraries were sequenced on the Illumina HiSeq2000 according to standard, paired-end sequencing, protocols. Primary analysis done in RTA 1.17.20,1.13.48
Conversion from BCL to FASTQ and deumltiplexing using CASAVA-1.8 (configureBclToFastq.pl--fastq-cluster-count 1234567890 --mismatches 0 --use-bases-mask Y15n,I6n,Y35n)
Filter and read trimming (barcode minimum quality of 10. trimming of read2 to 35 bases - not required).
CEL-Seq (Hashimshony, et a. 2012l) demultiplexing of second mate, using first mate barcode, allowing no mismatches in barcode.
bowtie2, version 2.1.0, against Hduj_transcriptome_v1
Read counting with htseq-count version 0.5.4p3.
Genome_build: Hduj_transcriptome_v1 (NCBI BioProject PRJNA271450)
Supplementary_files_format_and_content: tabular expression matrix

molecule: polyA RNA

organism: Hypsibius dujardini

source_name: single embryo 126

growth_protocol: Hypsibius dujardini starting cultures were provided by Bob Goldstein (University of North Carolina at Chapel Hill) and were grown as previously described (Gabriel et al. 2007). Small cultures of tardigrades were kept in 60 mm glass Petri dishes in commercial bottled spring water until gravid animals were visible. Tardigrades lay 2-5 eggs during molting, with the embryos deposited in their exuvia, the shed exoskeleton. Soon after the adult crawled out of the exuvia, it was cut open using a scalpel on a microscope-cavity-slide to release embryos into the medium. Embryos were observed using a standard binocular and when reaching two-cell stage were deposited in a 10 ul drop mineral water on the cap of an 1.5 ml Eppendorf tube. Tubes were closed and incubated for respective periods at 20°C. For 4.5 days every hour past two-cell stage embryos were inspected for viability and excessive water was removed using a micro-mouth pipette. The embryo was then quick-frozen in liquid nitrogen.

extract_protocol:
Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps.
The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used.

tag: time (minutes after fertilization)


title: SRSF3_iCLIP_mm9_Rep2

value: GGCG


title: Metazome_Tardigrade_timecourse_sample_0125

source_name: single embryo 125


title: SRSF3_iCLIP_mm9_Rep1

value: GGTC


title: Metazome_Tardigrade_timecourse_sample_0124

source_name: single embryo 124


title: Metazome_Tardigrade_timecourse_sample_0122

source_name: single embryo 122


title: Metazome_Tardigrade_timecourse_sample_0123

source_name: single embryo 123


title: Metazome_Tardigrade_timecourse_sample_0121

source_name: single embryo 121


title: Metazome_Tardigrade_timecourse_sample_0120

source_name: single embryo 120


title: Metazome_Tardigrade_timecourse_sample_0117

source_name: single embryo 117


title: Metazome_Tardigrade_timecourse_sample_0116

source_name: single embryo 116


title: Metazome_Tardigrade_timecourse_sample_0119

source_name: single embryo 119


title: Metazome_Tardigrade_timecourse_sample_0118

source_name: single embryo 118


title: Metazome_Tardigrade_timecourse_sample_0110

source_name: single embryo 110


title: Metazome_Tardigrade_timecourse_sample_0115

source_name: single embryo 115


title: Metazome_Tardigrade_timecourse_sample_0109

source_name: single embryo 109


title: Metazome_Tardigrade_timecourse_sample_0108

source_name: single embryo 108


title: Metazome_Tardigrade_timecourse_sample_0105

source_name: single embryo 105


title: Metazome_Tardigrade_timecourse_sample_0114

source_name: single embryo 114


title: Metazome_Tardigrade_timecourse_sample_0113

source_name: single embryo 113


title: Metazome_Tardigrade_timecourse_sample_0104

source_name: single embryo 104


title: Metazome_Tardigrade_timecourse_sample_0106

source_name: single embryo 106


title: Metazome_Tardigrade_timecourse_sample_0103

source_name: single embryo 103


title: Metazome_Tardigrade_timecourse_sample_0111

source_name: single embryo 111


title: Metazome_Tardigrade_timecourse_sample_0101

source_name: single embryo 101


title: Metazome_Tardigrade_timecourse_sample_0102

source_name: single embryo 102


title: Metazome_Tardigrade_timecourse_sample_0100

source_name: single embryo 100


title: Metazome_Tardigrade_timecourse_sample_0099

source_name: single embryo 99


title: Metazome_Tardigrade_timecourse_sample_0098

source_name: single embryo 98


title: Metazome_Tardigrade_timecourse_sample_0096

source_name: single embryo 96


title: Metazome_Tardigrade_timecourse_sample_0097

source_name: single embryo 97


title: Metazome_Tardigrade_timecourse_sample_0094

source_name: single embryo 94


title: Metazome_Tardigrade_timecourse_sample_0112

source_name: single embryo 112


title: Metazome_Tardigrade_timecourse_sample_0107

source_name: single embryo 107


title: Metazome_Tardigrade_timecourse_sample_0092

source_name: single embryo 92


title: Metazome_Tardigrade_timecourse_sample_0091

source_name: single embryo 91


title: Metazome_Tardigrade_timecourse_sample_0086

source_name: single embryo 86


title: Metazome_Tardigrade_timecourse_sample_0093

source_name: single embryo 93


title: Metazome_Tardigrade_timecourse_sample_0089

source_name: single embryo 89


title: Metazome_Tardigrade_timecourse_sample_0085

source_name: single embryo 85


title: Metazome_Tardigrade_timecourse_sample_0090

source_name: single embryo 90


title: Metazome_Tardigrade_timecourse_sample_0083

source_name: single embryo 83


title: Metazome_Tardigrade_timecourse_sample_0088

source_name: single embryo 88


title: Metazome_Tardigrade_timecourse_sample_0084

source_name: single embryo 84


title: Metazome_Tardigrade_timecourse_sample_0078

source_name: single embryo 78


title: Metazome_Tardigrade_timecourse_sample_0081

source_name: single embryo 81


title: Metazome_Tardigrade_timecourse_sample_0080

source_name: single embryo 80

value: 2 cells


title: Metazome_Tardigrade_timecourse_sample_0079

source_name: single embryo 79

value: 1 cell


title: Metazome_Tardigrade_timecourse_sample_0082

source_name: single embryo 82


title: Metazome_Tardigrade_timecourse_sample_0076

source_name: single embryo 76


title: Metazome_Tardigrade_timecourse_sample_0077

source_name: single embryo 77


title: Metazome_Tardigrade_timecourse_sample_0075

source_name: single embryo 75


title: Metazome_Tardigrade_timecourse_sample_0072

source_name: single embryo 72


title: Metazome_Tardigrade_timecourse_sample_0095

source_name: single embryo 95


title: Metazome_Tardigrade_timecourse_sample_0074

source_name: single embryo 74


title: Metazome_Tardigrade_timecourse_sample_0073

source_name: single embryo 73


title: Metazome_Tardigrade_timecourse_sample_0071

source_name: single embryo 71


title: Metazome_Tardigrade_timecourse_sample_0069

source_name: single embryo 69


title: Metazome_Tardigrade_timecourse_sample_0067

source_name: single embryo 67


title: Metazome_Tardigrade_timecourse_sample_0068

source_name: single embryo 68


title: Metazome_Tardigrade_timecourse_sample_0087

source_name: single embryo 87


title: Metazome_Tardigrade_timecourse_sample_0065

source_name: single embryo 65


title: Metazome_Tardigrade_timecourse_sample_0066

source_name: single embryo 66


title: Metazome_Tardigrade_timecourse_sample_0064

source_name: single embryo 64


title: Metazome_Tardigrade_timecourse_sample_0062

source_name: single embryo 62


title: Metazome_Tardigrade_timecourse_sample_0061

source_name: single embryo 61


title: Metazome_Tardigrade_timecourse_sample_0059

source_name: single embryo 59


title: Metazome_Tardigrade_timecourse_sample_0058

source_name: single embryo 58


title: Metazome_Tardigrade_timecourse_sample_0055

source_name: single embryo 55


title: Metazome_Tardigrade_timecourse_sample_0060

source_name: single embryo 60


title: Metazome_Tardigrade_timecourse_sample_0056

source_name: single embryo 56


title: Metazome_Tardigrade_timecourse_sample_0052

source_name: single embryo 52


title: Metazome_Tardigrade_timecourse_sample_0051

source_name: single embryo 51


title: Metazome_Tardigrade_timecourse_sample_0048

source_name: single embryo 48


title: Metazome_Tardigrade_timecourse_sample_0050

source_name: single embryo 50


title: Metazome_Tardigrade_timecourse_sample_0054

source_name: single embryo 54


title: Metazome_Tardigrade_timecourse_sample_0057

source_name: single embryo 57


title: Metazome_Tardigrade_timecourse_sample_0053

source_name: single embryo 53


title: Metazome_Tardigrade_timecourse_sample_0049

source_name: single embryo 49


title: Metazome_Tardigrade_timecourse_sample_0070

source_name: single embryo 70


title: Metazome_Tardigrade_timecourse_sample_0043

source_name: single embryo 43


title: Metazome_Tardigrade_timecourse_sample_0042

source_name: single embryo 42


title: Metazome_Tardigrade_timecourse_sample_0045

source_name: single embryo 45


title: Metazome_Tardigrade_timecourse_sample_0044

source_name: single embryo 44


title: Metazome_Tardigrade_timecourse_sample_0063

source_name: single embryo 63


title: Metazome_Tardigrade_timecourse_sample_0041

source_name: single embryo 41


title: Metazome_Tardigrade_timecourse_sample_0040

source_name: single embryo 40


title: Metazome_Tardigrade_timecourse_sample_0038

source_name: single embryo 38


title: Metazome_Tardigrade_timecourse_sample_0037

source_name: single embryo 37


title: Metazome_Tardigrade_timecourse_sample_0039

source_name: single embryo 39


title: Metazome_Tardigrade_timecourse_sample_0047

source_name: single embryo 47


title: Metazome_Tardigrade_timecourse_sample_0033

source_name: single embryo 33


title: Metazome_Tardigrade_timecourse_sample_0035

source_name: single embryo 35


title: Metazome_Tardigrade_timecourse_sample_0034

source_name: single embryo 34


title: Metazome_Tardigrade_timecourse_sample_0023

source_name: single embryo 23


title: Metazome_Tardigrade_timecourse_sample_0032

source_name: single embryo 32


title: Metazome_Tardigrade_timecourse_sample_0030

source_name: single embryo 30


title: Metazome_Tardigrade_timecourse_sample_0024

source_name: single embryo 24


title: Metazome_Tardigrade_timecourse_sample_0025

source_name: single embryo 25


title: Metazome_Tardigrade_timecourse_sample_0027

source_name: single embryo 27


title: Metazome_Tardigrade_timecourse_sample_0022

source_name: single embryo 22


title: Metazome_Tardigrade_timecourse_sample_0021

source_name: single embryo 21


title: Metazome_Tardigrade_timecourse_sample_0046

source_name: single embryo 46


title: Metazome_Tardigrade_timecourse_sample_0026

source_name: single embryo 26


title: Metazome_Tardigrade_timecourse_sample_0036

source_name: single embryo 36


title: Metazome_Tardigrade_timecourse_sample_0031

source_name: single embryo 31


title: Metazome_Tardigrade_timecourse_sample_0017

source_name: single embryo 17


title: Metazome_Tardigrade_timecourse_sample_0016

source_name: single embryo 16


title: Metazome_Tardigrade_timecourse_sample_0018

source_name: single embryo 18


title: Metazome_Tardigrade_timecourse_sample_0015

source_name: single embryo 15


title: Metazome_Tardigrade_timecourse_sample_0012

source_name: single embryo 12


title: Metazome_Tardigrade_timecourse_sample_0014

source_name: single embryo 14


title: Metazome_Tardigrade_timecourse_sample_0010

source_name: single embryo 10


title: Metazome_Tardigrade_timecourse_sample_0028

source_name: single embryo 28


title: Metazome_Tardigrade_timecourse_sample_0029

source_name: single embryo 29


title: Metazome_Tardigrade_timecourse_sample_0008

source_name: single embryo 8


title: Metazome_Tardigrade_timecourse_sample_0006

source_name: single embryo 6


title: Metazome_Tardigrade_timecourse_sample_0005

source_name: single embryo 5


title: Metazome_Tardigrade_timecourse_sample_0003

source_name: single embryo 3


title: Metazome_Tardigrade_timecourse_sample_0004

source_name: single embryo 4


title: Metazome_Tardigrade_timecourse_sample_0001

source_name: single embryo 1


title: Metazome_Tardigrade_timecourse_sample_0002

source_name: single embryo 2


title: Young

status: Public on Feb 08 2016

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
The samples were annotated with Ensembl hg19 (v62)
Genome_build: hg19
Supplementary_files_format_and_content: The processed data file contain the FPKM values, fold changes, p-values and q-values in tab-delimited TXT format.

source_name: Lung diploid fibroblasts

growth_protocol: WI-38 cells in DMEM

extract_protocol:
Trizol (Invitrogen) was used to extract total RNA from proliferating and senescent cells according to the manufacturer's protocol. Total RNA was used for gene expression analysis by reverse transcription (RT) followed by quantitative (q)PCR analysis or by RNA deep sequencing (RNA-Seq). RT was performed using random hexamers and reverse transcriptase (Maxima Reverse Transcriptase; Fermentas, Pittsburgh, PA, USA), and qPCR was carried out using gene-specific primers and SYBR green master mix (Kapa Biosystems, Woburn, MA, USA) in an Applied Biosystems 7300 instrument (Applied Biosystems, Life Technologies, Grand Island, NY, USA).
100 ng of RNA was used for first-strand and second-strand cDNA synthesis followed by single-primer isothermal amplification 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, Denville, NJ, USA) to an average size of 250–450 bases. The sequencing library was prepared using Illumina kits according to the manufacturer's protocol (Illumina, San Diego, CA, USA).

treatment_protocol: Replicative senescence


title: Metazome_Tardigrade_timecourse_sample_0013

source_name: single embryo 13


title: Metazome_Tardigrade_timecourse_sample_0009

source_name: single embryo 9


title: Metazome_Tardigrade_timecourse_sample_0019

source_name: single embryo 19


title: Metazome_Tardigrade_timecourse_sample_0007

source_name: single embryo 7


title: Senescent


title: CTX_28_RUN_40

status: Public on Dec 21 2015

description:
Mouse ID: RUN-40-CTX
Streptavidin-Cy3

hyb_protocol: The standard Illumina hybridization protocol was followed.

scan_protocol: Arrays were scanned at a resolution of 0.8 um using the Illumina BeadArray Reader.

data_processing: Data was extracted using the Illumina GenomeStudio software (version 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 non-normalized data including detection scores are included in the supplemental file linked to the Series record.

source_name: Lateral entorhinal cortex, RUN, day 28

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep RNA Amplification kit for Illumina arrays.

growth_protocol: One-month-old C57BL/6J male mice (Jackson Laboratory, Bar Harbor, ME) were individually housed in standard conditions with food and water ad libitum, and were maintained in accordance with the National Institutes of Health guidelines. All protocols for procedures were approved by the NIA’s Institutional Animal Care and Use Committee.

extract_protocol: Total RNA was extracted using the Trizol reagent (Life Technologies, Frederick, MD) according to the manufacturer’s protocol using chloroform extraction. Quantity and quality of the RNA were assessed using the Agilent 2100 Bioanalyzer with RNA 6000 Nano Chips.

treatment_protocol: One-month-old C57BL/6J male mice were divided into 3 groups - control (CTR), AICAR-treated (ACR) or voluntary running (RUN). ACR mice received a daily intraperitoneal injection (IP) of 5-aminoimidazole-4-carboxamide-1-β-D-ribofuranoside (AICAR, Toronto Research Chemicals Inc., Canada) of 500 mg/kg/day, dissolved in saline; CTR and RUN animals received IP saline vehicle; RUN animals had free access to running wheels. Animals were sacrificed after deep anesthesia with isofluorane (Henry Schein Animal Health, OH) after 7, 14 or 28 days, and the dentate gyrus (DG) and lateral entorhinal cortex (LEC) were collected and immediately frozen and stored at -80ºC.

tag: strain/background

tag: gender

value: male

tag: tissue

value: lateral entorhinal cortex

tag: intervention

value: voluntary running

tag: timepoint

value: day 28

tag: replicate


title: CTX_14_ACR2_73

description:
Mouse ID: ACR-73-CTX
Streptavidin-Cy3

source_name: Lateral entorhinal cortex, AICAR, day 14

value: AICAR

value: day 14


title: CTX_14_ACR2_75

description:
Mouse ID: ACR-75-CTX
Streptavidin-Cy3


title: CTX_28_RUN_41

description:
Mouse ID: RUN-41-CTX
Streptavidin-Cy3


title: CTX_28_CTRL_37

description:
Mouse ID: CTRL-37-CTX
Streptavidin-Cy3

source_name: Lateral entorhinal cortex, CTR, day 28

value: saline vehicle


title: CTX_14_CTRL2_70

description:
Mouse ID: CTRL-70-CTX
Streptavidin-Cy3

source_name: Lateral entorhinal cortex, CTR, day 14


title: CTX_14_RUN_31

description:
Mouse ID: RUN-31-CTX
Streptavidin-Cy3

source_name: Lateral entorhinal cortex, RUN, day 14


title: CTX_14_RUN_30

description:
Mouse ID: RUN-30-CTX
Streptavidin-Cy3


title: CTX_7_ACR_25

description:
Mouse ID: ACR-25-CTX
Streptavidin-Cy3

source_name: Lateral entorhinal cortex, AICAR, day 7

value: day 7


title: CTX_28_CTRL_35

description:
Mouse ID: CTRL-35-CTX
Streptavidin-Cy3


title: CTX_14_CTRL2_68

description:
Mouse ID: CTRL-68-CTX
Streptavidin-Cy3


title: CTX_14_RUN_33

description:
Mouse ID: RUN-33-CTX
Streptavidin-Cy3


title: CTX_28_RUN_39

description:
Mouse ID: RUN-39-CTX
Streptavidin-Cy3


title: CTX_28_CTRL_36

description:
Mouse ID: CTRL-36-CTX
Streptavidin-Cy3


title: CTX_14_CTRL_27

description:
Mouse ID: CTRL-27-CTX
Streptavidin-Cy3


title: CTX_14_CTRL_28

description:
Mouse ID: CTRL-28-CTX
Streptavidin-Cy3


title: CTX_7_ACR_23

description:
Mouse ID: ACR-23-CTX
Streptavidin-Cy3


title: CTX_7_RUN_20

description:
Mouse ID: RUN-20-CTX
Streptavidin-Cy3

source_name: Lateral entorhinal cortex, RUN, day 7


title: CTX_7_RUN_21

description:
Mouse ID: RUN-21-CTX
Streptavidin-Cy3


title: CTX_7_RUN_19

description:
Mouse ID: RUN-19-CTX
Streptavidin-Cy3


title: CTX_7_ACR_22

description:
Mouse ID: ACR-22-CTX
Streptavidin-Cy3


title: CTX_14_CTRL_26

description:
Mouse ID: CTRL-26-CTX
Streptavidin-Cy3


title: CTX_7_CTRL_17

description:
Mouse ID: CTRL-17-CTX
Streptavidin-Cy3

source_name: Lateral entorhinal cortex, CTR, day 7


title: CTX_7_CTRL_14

description:
Mouse ID: CTRL-14-CTX
Streptavidin-Cy3


title: CTX_7_CTRL_16

description:
Mouse ID: CTRL-16-CTX
Streptavidin-Cy3


title: CTX_14_CTRL2_69

description:
Mouse ID: CTRL-69-CTX
Streptavidin-Cy3


title: HIPP_28_RUN_41

description:
Mouse ID: RUN-41-HIPP
Streptavidin-Cy3

source_name: Dentate gyrus, RUN, day 28

value: dentate gyrus


title: CTX_28_CTRL_34

description:
Mouse ID: CTRL-34-CTX
Streptavidin-Cy3


title: HIPP_28_CTRL_37

description:
Mouse ID: CTRL-37-HIPP
Streptavidin-Cy3

source_name: Dentate gyrus, CTR, day 28


title: HIPP_14_ACR2_74

description:
Mouse ID: ACR-74-HIPP
Streptavidin-Cy3

source_name: Dentate gyrus, AICAR, day 14


title: HIPP_14_CTRL2_68

description:
Mouse ID: CTRL-68-HIPP
Streptavidin-Cy3

source_name: Dentate gyrus, CTR, day 14


title: HIPP_14_ACR2_73

description:
Mouse ID: ACR-73-HIPP
Streptavidin-Cy3


title: HIPP_28_CTRL_36

description:
Mouse ID: CTRL-36-HIPP
Streptavidin-Cy3


title: HIPP_14_RUN_33

description:
Mouse ID: RUN-33-HIPP
Streptavidin-Cy3

source_name: Dentate gyrus, RUN, day 14


title: HIPP_28_RUN_39

description:
Mouse ID: RUN-39-HIPP
Streptavidin-Cy3


title: HIPP_7_ACR_25

description:
Mouse ID: ACR-25-HIPP
Streptavidin-Cy3

source_name: Dentate gyrus, AICAR, day 7


title: HIPP_14_CTRL_26

description:
Mouse ID: CTRL-26-HIPP
Streptavidin-Cy3


title: HIPP_7_ACR_24

description:
Mouse ID: ACR-24-HIPP
Streptavidin-Cy3


title: HIPP_14_CTRL2_70

description:
Mouse ID: CTRL-70-HIPP
Streptavidin-Cy3


title: HIPP_14_RUN_32

description:
Mouse ID: RUN-32-HIPP
Streptavidin-Cy3


title: HIPP_7_ACR_22

description:
Mouse ID: ACR-22-HIPP
Streptavidin-Cy3


title: HIPP_14_CTRL2_69

description:
Mouse ID: CTRL-69-HIPP
Streptavidin-Cy3


title: HIPP_7_RUN_18

description:
Mouse ID: RUN-18-HIPP
Streptavidin-Cy3

source_name: Dentate gyrus, RUN, day 7


title: HIPP_14_RUN_31

description:
Mouse ID: RUN-31-HIPP
Streptavidin-Cy3


title: HIPP_28_CTRL_35

description:
Mouse ID: CTRL-35-HIPP
Streptavidin-Cy3


title: HIPP_14_ACR2_75

description:
Mouse ID: ACR-75-HIPP
Streptavidin-Cy3


title: HIPP_7_RUN_19

description:
Mouse ID: RUN-19-HIPP
Streptavidin-Cy3


title: HIPP_28_RUN_38

description:
Mouse ID: RUN-38-HIPP
Streptavidin-Cy3


title: HIPP_7_CTRL_17

description:
Mouse ID: CTRL-17-HIPP
Streptavidin-Cy3

source_name: Dentate gyrus, CTR, day 7


title: age40.1

status: Public on Nov 16 2015

description:
Circular RNA
RNase R treated total RNA

data_processing:
Base-Calling: Illumina-RTA 1.18.54
BCL conversion: BCLtoFastq 1.8.4
Sequenced reads were trimmed for adaptor sequence using cutadapt, and the sequences were aligned to the Macaca mulatta (rheMac2) genome with TopHat2 (v2.0.14) and Bowtie2 (v2.2.4), first for linear RNA, and then by searching for fusion transcripts using the reads which did not align to the linear RNA with default parameters using tophat-fusion.
RNA was assembled into linear transcripts using Cufflinks (v2.2.1) using default parameters (except for assembled transfrags are supported by 5 fragments or more were reported) and was annotated using rheMac2 and Ensembl v78.
The circExplorer program was run with the fusion transcripts obtained from TopHat2 using the annotated combined transcripts obtained from the assembled linear RNA for characterizing and annotating circular RNAs.
Genome_build: rheMac2
Supplementary_files_format_and_content: Tab-delimited text in bed12 format (with additional columns at the end) of circRNA splice sites with number of supporting junctional reads in the read_number column for each sample.

organism: Macaca mulatta

growth_protocol: Monkeys were housed individually in standard nonhuman primate caging on a 12 h light/12 h dark cycle, at room temperature (25.5 ± 0.5 °C), humidity at 60 ± 20%.  Monkeys were monitored minimally 3 times daily by trained animal care staff.  All monkeys were given normal diets (TestDiet® #5038 Purina Mills, Richmond, IN) and were fed ad libitum.  Skeletal muscle tissues (vastus lateralis) were obtained from young (Y), middle-aged (MA), and old (O) monkeys from an ongoing NIA longitudinal study on dietary manipulation and aging that began in 1987

extract_protocol:
Tissues were homogenized in Trizol (Invitrogen, NY) and used to isolate total RNA according to the manufacturer's protocol.  Total RNA (5 μg) was treated with 20 U of RNase R (RNR07250, Epicenter) for 15 min at 37⁰C and the digested RNA was isolated using acidic phenol-chloroform (5:1) and ethanol precipitation.  CircRNA sequencing was performed at the Genomics Research Center, University of Rochester; 24 samples (one per monkey) were sequenced initially at a depth of approximately 20 million reads (paired-end), and two samples were subsequently sequenced in-depth (at approximately 100 million reads) to assess sample saturation.
Modified TruSeq RNA.  Briefly, quantitation and quality of RNA was determing with NanoDrop and Agilent Bioanalyzer 2100, respectively.  PolyA capture with oligo-dT beads was omitted and each library was generated from 40ng RNA input with a fragmentation time of 5 minutes at 94C. First-strand cDNA synthesis was performed with random hexamer priming followed by second-strand cDNA synthesis. End repair and 3` adenylation was then performed on the double stranded cDNA. Illumina adaptors were ligated to both ends of the cDNA, purified by gel electrophoresis and amplified with PCR primers specific to the adaptor sequences to generate amplicons of approximately 200-400bp in size. The amplified libraries were hybridized to the Illumina pair end flow cell and amplified using the cBot

tag: age in years

tag: age classification

value: Old

value: skeletal muscle


title: S31_age12

description:
Circular RNA
RNase R treated total RNA

source_name: Skeletal muscle tissues (vastus lateralis)

value: Middle Age


title: HIPP_7_CTRL_15

description:
Mouse ID: CTRL-15-HIPP
Streptavidin-Cy3


title: age005

description:
Circular RNA
RNase R treated total RNA

value: Young


title: S30_age14.4

description:
Circular RNA
RNase R treated total RNA


title: S24_age30.1

description:
Circular RNA
RNase R treated total RNA


title: S28_age15.43

description:
Circular RNA
RNase R treated total RNA


title: Metazome_Tardigrade_timecourse_sample_0011

source_name: single embryo 11


title: HIPP_7_CTRL_16

description:
Mouse ID: CTRL-16-HIPP
Streptavidin-Cy3


title: S20_age12.48

description:
Circular RNA
RNase R treated total RNA


title: HIPP_7_RUN_21

description:
Mouse ID: RUN-21-HIPP
Streptavidin-Cy3


title: S29_age11.3

description:
Circular RNA
RNase R treated total RNA


title: S19_age25.7

description:
Circular RNA
RNase R treated total RNA


title: S21_age0.003

description:
Circular RNA
RNase R treated total RNA


title: S16_age40.9

description:
Circular RNA
RNase R treated total RNA


title: S13_age13.5

description:
Circular RNA
RNase R treated total RNA


title: S15_age2.8

description:
Circular RNA
RNase R treated total RNA


title: S12_age28.7

description:
Circular RNA
RNase R treated total RNA


title: S11_age14.4

description:
Circular RNA
RNase R treated total RNA


title: S07_age0.03

description:
Circular RNA
RNase R treated total RNA


title: S05_age27

description:
Circular RNA
RNase R treated total RNA


title: S08_age13

description:
Circular RNA
RNase R treated total RNA


title: S01_age0.005

description:
Circular RNA
RNase R treated total RNA


title: S03_age6

description:
Circular RNA
RNase R treated total RNA


title: S17_age16.93

description:
Circular RNA
RNase R treated total RNA


title: S02_age4.06

description:
Circular RNA
RNase R treated total RNA


title: S18_age32

description:
Circular RNA
RNase R treated total RNA


title: S04_age14.7

description:
Circular RNA
RNase R treated total RNA


title: S06_age13.6

description:
Circular RNA
RNase R treated total RNA


title: S10_age40.1

description:
Circular RNA
RNase R treated total RNA


title: HIPP_14_CTRL_28

description:
Mouse ID: CTRL-28-HIPP
Streptavidin-Cy3


title: Cortical neuron_IgG RIP_replicate 4

status: Public on Nov 06 2015

description:
IgG3_0
IP RNA

organism: Rattus norvegicus

source_name: Cortical neuron_E18_cultured 9 days

extract_protocol:
Endogenous mRNA-protein complexes were immunoprecipitated (RIP) as described previously. Briefly, the high density cortical cultures (~1.2 x 108 neurons) were homogenized in polysome lysis buffer (PLB) consisting of 100 mM KCl, 5 mM MgCl2, 10 mM HEPES (pH 7.0), 0.5% Nonidet P-40, 1 mM dithiothreitol (DTT), 100 U/ml RNase OUT (Invitrogen) and a protease inhibitor cocktail (Roche). Lysates were incubated (1 hour at 4°C) with 100 ml of a 50% (v/v) suspension of protein-A Sepharose beads precoated with 20 g each of polyclonal anti-TRF2-S (Santa Cruz, H300) or rabbit IgG. Beads were washed with NT2 buffer consisting of 50 mM Tris-HCl (pH 7.4), 150 mM NaCl, 1 mM MgCl2 and 0.05% NP-40, and then incubated with 100 ml of NT2 buffer containing RNase-free DNase I (20 U, 15 minutes at 30°C), washed with NT2 buffer and further incubated in 100 ml NT2 buffer containing 0.1% SDS and 0.5 mg/ml Proteinase K (15 minutes at 55°C) to digest proteins bound to the beads.
RNA was extracted using phenol/chloroform extraction and precipitated in the presence of glycoblue.

treatment_protocol: [Experimental protocol] Cerebral cortical neurons isolated from 18 day-old rat embryos were plated at a density of 2-6 x 105 cells/well and grown in Neurobasal medium and harvested at culture day 9 before RNA immunoprecipitation.

tag: strain

value: Sprague-Dawley

value: Brain

tag: tissue region

value: Cerebral cortex

tag: cell type

value: Cortical neuron

tag: developmental stage

tag: ip antibody

value: anti-IgG


title: Cortical neuron_TRF2-S RIP_replicate 1

description:
TRF2-1
IP RNA


title: Cortical neuron_IgG RIP_replicate 2

description:
IgG2
IP RNA


title: Cortical neuron_TRF2-S RIP_replicate 2

description:
TRF2-2
IP RNA


title: Cortical neuron_IgG RIP_replicate 3

description:
IgG3
IP RNA


title: Cortical neuron_IgG RIP_replicate 1

description:
IgG1
IP RNA


title: Metazome_Tardigrade_timecourse_sample_0020

source_name: single embryo 20


title: Cortical neuron_IgG RIP_replicate 5

description:
IgG3_1x
IP RNA


status: Public on Aug 07 2015

description:
Cell Line FS-7_Poorly_Invasive
Irradiated_1Day
Cell Line FS-7_Poorly_Invasive_Irradiated_1Day
FS_7_D1_IR

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 ver3. Expression BeadChips (Illumina, San Diego, CA). Each BeadChip has ~48,000 well-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.

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.
ID_REF = Unique identifiers from GPL6947-21367
Z_VALUE = Z transformation of the natural log of the raw intensity values
Detection_Pval = Detection Pvalue from Illumina GenomeStudio software, ver 1.1.1.

source_name: Patient Derived Cell Line FS-7_Irradiated_1Day

growth_protocol: FS cell lines were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (Invitrogen, Carlsbad, CA). The media was supplemented with 100 U/ml penicillin and streptomycin and 4 mM L-glutamine. All cells were cultured at 37°C in 5% CO2.

extract_protocol: RNA was extracted from the cells of each time point using Trizol (Invitrogen) and an RNeasy Mini kit (Qiagen) according to the manufactures standard protocols.

treatment_protocol: Both the highly invasive and poorly invasive cell lines were treated with y-irradiation, and RNA was taken at 1 hour, 24 hours and 5 days after irradiation. Control cells from each group were not treated with radiation and RNA was isolated after 24 hours.

tag: treatment

value: Irradiated

tag: phenotype

value: Poorly Invasive

tag: time


description:
Cell Line FS-7_Poorly_Invasive
Irradiated_5Day
Cell Line FS-7_Poorly_Invasive_Irradiated_5Day
FS_7_D5_IR

source_name: Patient Derived Cell Line FS-7_Irradiated_5Day

tag: cell line


title: SUDHL6_NS3 overexpression_replicate 2

status: Public on Oct 14 2015

hyb_protocol: Standard Illumina protocol. In short, 750 ug biotin-labeled cRNA was hybridized at 58 degrees C for 16 hours to Illumina's Sentrix Human-Ref8 v3 Expression Bead Chips (Illumina, San Diego, CA). Each BeadChip has ~22,000 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 GenomeStudio software V2011.1, Gene expression module 1.9.0. 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 is supplied.
Z_VALUE = Z transformation of the natural log of the raw intensity values
Detection_Pval = Detection Pvalue from Illumina GenomeStudio software V2011.1, Gene expression module 1.9.0.

label_protocol: The Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791) and the standard Illumina labeling protocol was used.  In short, immunoprecipitated RNA was 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: Stably transfected SUDHL6 cells were lysed and HuR-binding mRNAs immunoprecipitated (IP) using a HuR-antibody. Phenol and chlororform were used to extract RNA from the IP material in the presence of GlycoBlue.

tag: transduced with

value: lentivirus encoding HCV NS3/4A (NS3_S6_8_2_x)

tag: rnp ip antibody

value: HuR-antibody

tag: molecule subtype

value: HuR-IP mRNAs


description:
Cell Line FS-7_Poorly_Invasive
Irradiated_1Hour
Cell Line FS-7_Poorly_Invasive_Irradiated_1Hour
FS_7_1HR_IR

source_name: Patient Derived Cell Line FS-7_Irradiated_1Hour


description:
Cell Line FS-9_Highly_Invasive
Irradiated_5Day
Cell Line FS-9_Highly_Invasive_Irradiated_5Day
FS_9_D5_IR

source_name: Patient Derived Cell Line FS-9_Irradiated_5Day

value: Highly Invasive


title: SUDHL6_NS3 overexpression_replicate 3


description:
Cell Line FS-13_Poorly_Invasive
Irradiated_5Day
Cell Line FS-13_Poorly_Invasive_Irradiated_5Day
FS_13_D5_IR

source_name: Patient Derived Cell Line FS-13_Irradiated_5Day


title: SUDHL6_NS3 overexpression_replicate 1


title: SUDHL6_Control_replicate 1

value: lentivirus encoding vector control (CTR_S6_532_x)


title: SUDHL6_Control_replicate 2


title: SUDHL6_Control_replicate 3


description:
Cell Line FS-9_Highly_Invasive
Irradiated_1Day
Cell Line FS-9_Highly_Invasive_Irradiated_1Day
FS_9_D1_IR

source_name: Patient Derived Cell Line FS-9_Irradiated_1Day


description:
Cell Line FS-7_Poorly_Invasive
Not_Irradiated_1Day
Cell Line FS-7_Poorly_Invasive_Not_Irradiated_1Day
FS_7_D1_None

source_name: Patient Derived Cell Line FS-7_Not_Irradiated_1Day

value: Not Irradiated


description:
Cell Line FS-9_Highly_Invasive
Irradiated_1Hour
Cell Line FS-9_Highly_Invasive_Irradiated_1Hour
FS_9_1HR_IR

source_name: Patient Derived Cell Line FS-9_Irradiated_1Hour


description:
Cell Line FS-13_Poorly_Invasive
Irradiated_1Hour
Cell Line FS-13_Poorly_Invasive_Irradiated_1Hour
FS_13_1HR_IR

source_name: Patient Derived Cell Line FS-13_Irradiated_1Hour


title: CTX_14_ACR2_74

description:
Mouse ID: ACR-74-CTX
Streptavidin-Cy3

source_name: Lateral entorhinal cortex, AICAR, day 14

tag: strain/background

tag: gender

value: male

tag: tissue

value: lateral entorhinal cortex

tag: intervention

value: AICAR

value: day 14


description:
Cell Line FS-13_Poorly_Invasive
Not_Irradiated_1Day
Cell Line FS-13_Poorly_Invasive_Not_Irradiated_1Day
FS_13_D1_None

source_name: Patient Derived Cell Line FS-13_Not_Irradiated_1Day


description:
Cell Line FS-12_Poorly_Invasive
Irradiated_5Day
Cell Line FS-12_Poorly_Invasive_Irradiated_5Day
FS_12_D5_IR

source_name: Patient Derived Cell Line FS-12_Irradiated_5Day


description:
Cell Line FS-9_Highly_Invasive
Not_Irradiated_1Day
Cell Line FS-9_Highly_Invasive_Not_Irradiated_1Day
FS_9_D1_None

source_name: Patient Derived Cell Line FS-9_Not_Irradiated_1Day


description:
Cell Line FS-13_Poorly_Invasive
Irradiated_1Day
Cell Line FS-13_Poorly_Invasive_Irradiated_1Day
FS_13_D1_IR

source_name: Patient Derived Cell Line FS-13_Irradiated_1Day


description:
Cell Line FS-12_Poorly_Invasive
Irradiated_1Day
Cell Line FS-12_Poorly_Invasive_Irradiated_1Day
FS_12_D1_IR

source_name: Patient Derived Cell Line FS-12_Irradiated_1Day


description:
Cell Line FS-11_Highly_Invasive
Not_Irradiated_1Day
Cell Line FS-11_Highly_Invasive_Not_Irradiated_1Day
FS_11_D1_None

source_name: Patient Derived Cell Line FS-11_Not_Irradiated_1Day


title: Human UCMSC co-cultured with MDA-231 cells_48hr_rep2

status: Public on Aug 06 2015

description:
Sample name: HUC + MDA-2
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 HumanRef-8 v2.0 Expression BeadChip (Illumina, San Diego, CA). Each BeadChip has ~22,000 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 BeadStudio software, ver 3.3.7. 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 is supplied.

source_name: human UCMSC co-cultured with MDA-231 cells, 48hrs

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: Human UCMSC (5x10^4 cells) were seeded in defined medium in the bottom of a 6-well Transwell culture dish and allowed to settle for 24 hours. The human biological samples were sourced ethically with no donor-identifying information and their research use was approved by the Kansas State University Institutional Review Board (Protocol # 3515).

extract_protocol: RNA was extracted from naïve and MDA-231 co-cultured UCMSC cells 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: MDA-231 cells (5x10^5 cells) were added in Transwell inserts for 48 hours.

value: umbilical cord matrix mesenchymal stem cells (UCMSC)

tag: co-culture

value: MDA-231 breast carcinoma cells


title: Naïve human UCMSC_48hr_rep1

description:
Sample name: HUC_new-1
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: naïve human UCMSC, 48hrs


description:
Cell Line FS-11_Highly_Invasive
Irradiated_1Hour
Cell Line FS-11_Highly_Invasive_Irradiated_1Hour
FS_11_1HR_IR

source_name: Patient Derived Cell Line FS-11_Irradiated_1Hour


title: Human UCMSC co-cultured with MDA-231 cells_48hr_rep1

description:
Sample name: HUC + MDA-1
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Human UCMSC co-cultured with MDA-231 cells_48hr_rep3

description:
Sample name: HUC + MDA-3
Streptavidin-Cy3 bound to biotin-labeled cRNA.


description:
Cell Line FS-11_Highly_Invasive
Irradiated_1Day
Cell Line FS-11_Highly_Invasive_Irradiated_1Day
FS_11_D1_IR

source_name: Patient Derived Cell Line FS-11_Irradiated_1Day


title: Naïve human UCMSC_48hr_rep2

description:
Sample name: HUC_new-2
Streptavidin-Cy3 bound to biotin-labeled cRNA.


description:
Cell Line FS-12_Poorly_Invasive
Irradiated_1Hour
Cell Line FS-12_Poorly_Invasive_Irradiated_1Hour
FS_12_1HR_IR

source_name: Patient Derived Cell Line FS-12_Irradiated_1Hour


description:
Cell Line FS-11_Highly_Invasive
Irradiated_5Day
Cell Line FS-11_Highly_Invasive_Irradiated_5Day
FS_11_D5_IR

source_name: Patient Derived Cell Line FS-11_Irradiated_5Day


description:
Athymic female nude mice (SWISS nu+/nu+) were obtained from Charles Rivers (L’Arbresle, France) and maintained under pathogen-free conditions with a 12 h light/12 h dark cycle. Animals were fed ad libitum with normal chow.
C6 glioma xenografts, (R,R’)-4-methoxy-1-naphthylfenoterol (MNF)  treated, replicate #4, cohort #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 Rat Ref-12 v1 Expression BeadChips (Illumina, San Diego, CA). Each BeadChip has ~22,000 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 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.
Detection_Pval = Detection Pvalue from Illumina GenomeStudio software, ver 1.6.0.

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: The rat-derived C6 glioma cell line was obtained from the American Type Culture Collection (Manassas, VA). The cells were routinely maintained in DMEM supplemented with L-glutamine, 1% penicillin/streptomycin solution, and 10% FBS in a humidified CO2 incubator at 37 ºC.  Athymic female nude mice (SWISS nu+/nu+) were obtained from Charles Rivers (L’Arbresle, France) and maintained under pathogen-free conditions with a 12 h light/12 h dark cycle. Animals were fed ad libitum with normal chow.  Nude mice were inoculated subcutaneously with 100µl of culture medium containing 0.5 x 106 C6 glioma cells in the left flank.  The mice were monitored up to 19 days after MNF injection or euthanized earlier if the tumor size was superior to 2 cubic cm or the mouse was lethargic, sick and unable to feed, which caused the body weight to drop below 20% of initial weight. The mice were euthanized by cervical extension, and tumor masses were removed, weighed and washed with cold PBS before being snap-frozen in liquid nitrogen.

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: Starting 3 days after tumor cell inoculation, mice received daily intraperitoneal injection of either (10 µl.g-1 bw) of vehicle or MNF (2 mg.kg-1) in 100µM ascorbic acid in saline (vehicle) five days a week for 19 days.

tag: host strain

value: SWISS nu+/nu+

tag: tumor cell type

tag: tumor inoculation

tag: treatment of mice

value: 3 days after cell inoculation, mice received daily intraperitoneal injection of MNF (2 mg.kg-1) in 100µM ascorbic acid in saline five days a week for 19 days.

tag: isolation of tumor cells


description:
Athymic female nude mice (SWISS nu+/nu+) were obtained from Charles Rivers (L’Arbresle, France) and maintained under pathogen-free conditions with a 12 h light/12 h dark cycle. Animals were fed ad libitum with normal chow.
C6 glioma xenografts, vehicle treated, replicate #6, cohort #2

value: The rat-derived C6 glioma cell line was obtained from the American Type Culture Collection (Manassas, VA). The cells were routinely maintained in DMEM supplemented with L-glutamine, 1% penicillin/streptomycin solution, and 10% FBS in a humidified CO2 incubator at 37 ºC.

value: Nude mice were inoculated subcutaneously with 100µl of culture medium containing 0.5 x 106 C6 glioma cells in the left flank.

value: 3 days after cell inoculation, mice received daily intraperitoneal injection (10 µl.g-1 bw) of vehicle (100µM ascorbic acid in saline) five days a week for 19 days.

value: The mice were monitored up to 19 days after MNF injection or euthanized earlier if the tumor size was superior to 2 cubic cm or the mouse was lethargic, sick and unable to feed, which caused the body weight to drop below 20% of initial weight. The mice were euthanized by cervical extension, and tumor masses were removed, weighed and washed with cold PBS before being snap-frozen in liquid nitrogen


description:
Athymic female nude mice (SWISS nu+/nu+) were obtained from Charles Rivers (L’Arbresle, France) and maintained under pathogen-free conditions with a 12 h light/12 h dark cycle. Animals were fed ad libitum with normal chow.
C6 glioma xenografts, (R,R’)-4-methoxy-1-naphthylfenoterol (MNF)  treated, replicate #1, cohort #1

source_name: The rat-derived C6 glioma cell line was obtained from the American Type Culture Collection (Manassas, VA).


description:
Athymic female nude mice (SWISS nu+/nu+) were obtained from Charles Rivers (L’Arbresle, France) and maintained under pathogen-free conditions with a 12 h light/12 h dark cycle. Animals were fed ad libitum with normal chow.
C6 glioma xenografts, vehicle treated, replicate #3, cohort #1


description:
Athymic female nude mice (SWISS nu+/nu+) were obtained from Charles Rivers (L’Arbresle, France) and maintained under pathogen-free conditions with a 12 h light/12 h dark cycle. Animals were fed ad libitum with normal chow.
C6 glioma xenografts, vehicle treated, replicate #5, cohort #2


title: Naïve human UCMSC_48hr_rep3

description:
Sample name: HUC_new-3
Streptavidin-Cy3 bound to biotin-labeled cRNA.

tag: cell type


title: Rat UCMSC co-cultured with Mat B III cells_48hr_rep1

description:
Co_MAT-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 Rat Ref-12 v1 BeadChips (Illumina, San Diego, CA). Each BeadChip has ~22,000 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 3.4.0. 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 is supplied.

source_name: rat UCMSC co-cultured with Mat B III cells, 48hrs

growth_protocol: Rat UCMSC (1x10^5 cells) were seeded in defined medium in the bottom of a 10 cm Transwell culture dish and allowed to settle for 24 hours.

extract_protocol: RNA was extracted from naïve and Mat B III co-cultured UCMSC cells 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 (Aligent Technologies).

treatment_protocol: Mat B III cells (1.5x10^6 cells) were added in Transwell inserts for 48 hours.

value: Mat B III breast carcinoma cells


title: Rat UCMSC co-cultured with Mat B III cells_48hr_rep3

description:
Co_MAT-3
Streptavidin-Cy3 bound to biotin-labeled cRNA.


description:
Athymic female nude mice (SWISS nu+/nu+) were obtained from Charles Rivers (L’Arbresle, France) and maintained under pathogen-free conditions with a 12 h light/12 h dark cycle. Animals were fed ad libitum with normal chow.
C6 glioma xenografts, (R,R’)-4-methoxy-1-naphthylfenoterol (MNF)  treated, replicate #3, cohort #1


description:
Athymic female nude mice (SWISS nu+/nu+) were obtained from Charles Rivers (L’Arbresle, France) and maintained under pathogen-free conditions with a 12 h light/12 h dark cycle. Animals were fed ad libitum with normal chow.
C6 glioma xenografts, vehicle treated, replicate #4, cohort #2


title: Naïve rat UCMSC_48hr_rep3

description:
MAT-3
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: naïve rat UCMSC, 48hrs


description:
Athymic female nude mice (SWISS nu+/nu+) were obtained from Charles Rivers (L’Arbresle, France) and maintained under pathogen-free conditions with a 12 h light/12 h dark cycle. Animals were fed ad libitum with normal chow.
C6 glioma xenografts, (R,R’)-4-methoxy-1-naphthylfenoterol (MNF)  treated, replicate #5 cohort #2


description:
Athymic female nude mice (SWISS nu+/nu+) were obtained from Charles Rivers (L’Arbresle, France) and maintained under pathogen-free conditions with a 12 h light/12 h dark cycle. Animals were fed ad libitum with normal chow.
C6 glioma xenografts, vehicle treated, replicate #1, cohort #1


description:
Athymic female nude mice (SWISS nu+/nu+) were obtained from Charles Rivers (L’Arbresle, France) and maintained under pathogen-free conditions with a 12 h light/12 h dark cycle. Animals were fed ad libitum with normal chow.
C6 glioma xenografts, vehicle treated, replicate #2, cohort #1


description:
Athymic female nude mice (SWISS nu+/nu+) were obtained from Charles Rivers (L’Arbresle, France) and maintained under pathogen-free conditions with a 12 h light/12 h dark cycle. Animals were fed ad libitum with normal chow.
C6 glioma xenografts, (R,R’)-4-methoxy-1-naphthylfenoterol (MNF)  treated, replicate #2, cohort #1


description:
Athymic female nude mice (SWISS nu+/nu+) were obtained from Charles Rivers (L’Arbresle, France) and maintained under pathogen-free conditions with a 12 h light/12 h dark cycle. Animals were fed ad libitum with normal chow.
C6 glioma xenografts, (R,R’)-4-methoxy-1-naphthylfenoterol (MNF)  treated, replicate #6, cohort #2


title: Rat UCMSC co-cultured with Mat B III cells_48hr_rep2

description:
Co_MAT-2
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Naïve rat UCMSC_48hr_rep1

description:
MAT-1
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: B16F10 cells_Mice_CR fed, replicate #1

description: B16F10 melanoma cells allowed to proliferate in CR fed mice, replicate #1

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 v1.1 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 Inc. BeadStudio version 1.5.0.34.  Any spots at or below the background were filtered out using an Illumina detection value of 0.98 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 data file.

label: Streptavidin-Cy3 bound to biotin labeled cRNA

source_name: B16F10 cells_Mice_CR fed

growth_protocol:
Male C57BL/6 mice (3 month old) were single-housed in duplex caging in a room maintained at a constant temperature (20-22 °C) and humidity (30-70%) in a light:dark 12:12-h schedule, according to established animal protocols and NIH guidelines.  They were fed on either a standard purified mouse diet (NIH-31) ad libitum (AL; n=10) or maintained on a 40% calorie restriction regimen (CR; n=10) during six weeks.
B16F10 melanoma cells (ATCC® CRL-6475™) were purchased from American Type Culture Collection (Manassas, VA); they were cultured in Dulbecco's Modified Essential Medium (DMEM) supplemented with 10% fetal bovine serum and penicillin/streptomycin (Gibco, Gaithersburg, MD) under standard cell culture conditions.

extract_protocol:
Tumor cells were harvested, washed and collected for RNA isolation using Rneasy mini Kits from Qiagen. Quality and quantity of the RNA samples was tested with the Agilent bioanalyzer using the RNA 6000 Nano Chips.
Cultured cells were harvested, washed and collected for RNA isolation using Rneasy mini Kits from Qiagen.  Quality and quantity of the RNA samples was  tested with the Agilent bioanalyzer using the RNA 6000 Nano Chips.

treatment_protocol:
One month into the study, 5 mice from each diet group were injected with 1x106 B16F10 melanoma cells in the periscapular region. Fourteen days later, animals were euthanized and tumors were excised and frozen for RNA isolation.
Cells were incubated in media with 10% serum from either AL- or CR-fed rats for 96 hours.  Serum was obtained from overnight fasted, anesthetized 6-month-old male Fisher 344 rats.

value: B16F10 mouse melanoma cell line

tag: treatment

value: B16F10 cells allowed to proliferate in CR fed mice for 14 days

tag: tissue collection

value: Cells were harvested, washed and collected for RNA isolation.

tag: host

value: male C57BL/6 mice (3 month old)


title: B16F10 cells_10% serum_CR fed Rats_replicate #2

description: B16F10 melanoma cells grown in culture supplemented with 10% serum from CR fed Rats, replicate #2

source_name: B16F10 cells_10% Rat serum_CR fed Rats

tag: cell line

value: B16F10 cells grown in culture and supplemented with 10% serum from CR fed Rats

value: Cells were grown for 96 hours before being harvested, washed and collected for RNA isolation.


title: B16F10 cells_Mice_CR fed, replicate #3

description: B16F10 melanoma cells allowed to proliferate in CR fed mice, replicate #3


title: B16F10 cells_Mice_CR fed, replicate #2

description: B16F10 melanoma cells allowed to proliferate in CR fed mice, replicate #2


title: Naïve rat UCMSC_48hr_rep2

description:
MAT-2
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: SAMP8_Astrocytes_CR_Diet_ Replicate_2

status: Public on Jun 23 2015

description: 10-P8-CR B

data_processing:
Data was extracted using the Illumina Bead Studio software, ver 3.3.7  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;
Detection_Pval = Detection Pvalue from Illumina Bead Studio software (ver 3.3.7)

growth_protocol: Primary cultures enriched in astrocytes were obtained from cerebral cortical tissue from 2-day-old SAMP8 and SAMR1 mice.  Astrocyte cultures were established and experiments were routinely carried out after 21 days in culture.  Established astrocyte cultures of both SAMR1 and SAMP8 consisted of 85–90% astrocytes, 10–15% microglia and 0.1–1% oligodendroglia.

extract_protocol: RNA was extracted from astrocyte cultures using TRIzol reagent following the manufacturer’s instructions (Invitrogen, Carlsbad, CA, USA).  Quality and quantity were checked with the Agilent Bio-Analyzer using RNA 6000 Nano Chips.

treatment_protocol: Sera from rats subjected to ad libitum (AL) diet and to CR were obtained as described for the establishment of the CR in vitro model (de Cabo et al., 2003). Serum was heat inactivated at 56°C prior to use in astrocyte culture experiments. Treatment in vitro was performed by adding 10% volume CR or AL serum onto the astrocyte culture medium for 48 h.

tag: strain

value: senescence-accelerated prone 8 (SAMP8) mouse

tag: mouse age

value: 2 days

tag: tissue origin

value: cerebral cortical tissue

value: Primary astrocyte cultures

tag: cell culture age

value: 21 days

tag: treated with

value: 10% Rat serum subjected to an CR Diet for 48hrs


title: SAMP8_Astrocytes_AdLib_Diet_ Replicate_3

description: 11-P8-AL C

value: 10% Rat serum subjected to an AdLib Diet for 48hrs


title: B16F10 cells_10% serum_CR fed Rats_replicate #1

description: B16F10 melanoma cells grown in culture supplemented with 10% serum from CR fed Rats, replicate #1


title: SAMP8_Astrocytes_CR_Diet_ Replicate_3

description: 12-P8-CR C


title: SAMR1_Astrocytes_CR_Diet_ Replicate_3

description: 06-R1-CR C

value: senescence-resistant 1 (SAMR1) control mouse


title: B16F10 cells_Mice_Ad Lib fed, replicate #1

description: B16F10 melanoma cells allowed to proliferate in Ad Lib fed mice, replicate #1

source_name: B16F10 cells_Mice_Ad Lib fed

value: B16F10 cells allowed to proliferate in Ad Lib fed mice for 14 days


title: B16F10 cells_Mice_Ad Lib fed, replicate #3

description: B16F10 melanoma cells allowed to proliferate in Ad Lib fed mice, replicate #3


title: B16F10 cells_10% serum_CR fed Rats_replicate #3

description: B16F10 melanoma cells grown in culture supplemented with 10% serum from CR fed Rats, replicate #3


title: B16F10 cells_10% serum_Ad Lib fed Rats_replicate #3

description: B16F10 melanoma cells grown in culture supplemented with 10% serum from Ad Lib fed Rats, replicate #3

source_name: B16F10 cells_10% Rat serum_Ad Lib fed Rats

value: B16F10 cells grown in culture and supplemented with 10% serum from Ad Lib fed Rats


title: SAMR1_Astrocytes_CR_Diet_ Replicate_2

description: 04-R1-CR B


title: SAMR1_Astrocytes_AdLib_Diet_ Replicate_3

description: 05-R1-AL C


title: SAMP8_Astrocytes_AdLib_Diet_ Replicate_1

description: 07-P8-AL A


title: SAMP8_Astrocytes_CR_Diet_ Replicate_1

description: 08-P8-CR A


title: SAMR1_Astrocytes_AdLib_Diet_ Replicate_1

description: 01-R1-AL A


title: B16F10 cells_10% serum_Ad Lib fed Rats_replicate #1

description: B16F10 melanoma cells grown in culture supplemented with 10% serum from Ad Lib fed Rats, replicate #1


title: SAMP8_Astrocytes_AdLib_Diet_ Replicate_2

description: 09-P8-AL B


title: B16F10 cells_Mice_Ad Lib fed, replicate #2

description: B16F10 melanoma cells allowed to proliferate in Ad Lib fed mice, replicate #2


title: Cerebellum_WT_Saline-Replicate-2

status: Public on Jun 04 2015

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.

data_processing: Data was extracted using the Illumina BeadStudio 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.  Complete data including detection scores will be included in the supplemental file.

growth_protocol: Mice carrying WT, or CX (Csa-/-/Xpa-/-) alleles in a C57BL/6 background were maintained under standard laboratory conditions at Harvard School of Public Health and allowed free access to water and control casein pelleted diet (Research Diets D12450B).

extract_protocol: On day 15, mice were sacrificed and half of a cerebellum was harvested for purification of mitochondria, with the left half snap-frozen, homogenized, and aliquoted for RNA isolation.  Total RNA extraction was done using a TRIzol Plus RNA purification kit as per manufacturer’s protocol.  Quality and quantity of the total RNA was tested using the Agilent 2100 Bio-Analyzer and RNA 6000 nano kits.

treatment_protocol: CX and WT (C57BL/6) mice of 3 months of age were given subcutaneous interscapular injections of 500 mg NR/kg body weight/day or the equivalent volume of saline for a consecutive of 14 days at 4:00 pm

value: C57BL/6 WT 3 months old

value: WT mice of 3 months of age were given subcutaneous interscapular injections of the equivalent volume of saline for 14 consecutive days at 4:00 pm.

tag: gender

value: male

value: On day 15, the mice were sacrificed and half of the cerebellum was harvested for purification of mitochondria, with the left half snap-frozen, homogenized, and aliquoted for western blotting, microarray, and detection of ATP and NAD+.


title: SAMR1_Astrocytes_AdLib_Diet_ Replicate_2

description: 03-R1-AL B


title: B16F10 cells_10% serum_Ad Lib fed Rats_replicate #2

description: B16F10 melanoma cells grown in culture supplemented with 10% serum from Ad Lib fed Rats, replicate #2

value: B16F10 mouse melanoma cell line

value: male C57BL/6 mice (3 month old)


title: SAMR1_Astrocytes_CR_Diet_ Replicate_1

description: 02-R1-CR A


title: Cerebellum_WT_Saline-Replicate-3


title: Cerebellum_WT_NR-Replicate-3

source_name: Cerebellum_WT_Nicotinamide riboside

value: WT mice, 3 months old were given subcutaneous interscapular injections of Nicotinamide riboside, 500 mg /kg body weight/day for 14 consecutive days at 4:00 pm.


title: Cerebellum_WT_NR-Replicate-2