title: Cerebellum_CX_Saline-Replicate-3

value: C57BL/6 CX (Csa-/-/Xpa-/-) 3 months old

value: CX 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.


title: Cerebellum_CX_Saline-Replicate-1

status: Public on Jun 04 2015

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

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

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

data_processing: Data was extracted using the Illumina 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.

label: Streptavidin-Cy3 bound to biotin labeled cRNA.

molecule: total RNA

organism: Mus musculus

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: 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

tag: strain

tag: treatment

tag: gender

value: male

tag: tissue collection

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: XPA-deficient (GM04312C) cell line_replicate-2

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

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

organism: Homo sapiens

source_name: XPA-deficient (GM04312C) cell line

growth_protocol: XPA-deficient (GM04312C) and the matched complemented (GM15876A) cells, were maintained in Gibco DMEM medium supplemented with 10% FBS with 1% penicillin-streptomycin (P&S).   Primary fibroblasts, GM969, were cultured in Gibco MEM medium mixed with 15% FBS, 1% P&S, and 1 Х Glutamine. All cells were grown in 20% O2/5% CO2 at 37°C.

extract_protocol: 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: The shRNA vector against XPA was from Sigma-Aldrich.  Lentiviral production was performed by co-transfection of packing plasmid pCMV-dr8.2 DVPR (Addgene plasmid 8455) , envelope vector pCMV-VSV-G (Addgene 8454), and the abovementioned XPA shRNA plasmid or a scrambled plasmid (Addgene 1864) into 293T cells using X-tremeGENE transfection reagents (Roche). For infection, the virus was incubated with GM969 primary fibroblast cells plus 4 µg/ml Polybrene for 2 days followed by 24 ~ 48 h 2ug/ml puromycin selection, cells were then applied for further experiments.

tag: cell line

value: XPA-deficient (GM04312C) cell line from Coriell Cell Repository

value: SV40 transformed XPA-deficient (GM04312C) cell line


title: Cerebellum_WT_NR-Replicate-1

source_name: Cerebellum_WT_Nicotinamide riboside

value: C57BL/6 WT 3 months old

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_CX_NR-Replicate-2

source_name: Cerebellum_CX_Nicotinamide riboside

value: CX 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_CX_NR-Replicate-3


title: Cerebellum_CX_Saline-Replicate-2


title: Cerebellum_WT_Saline-Replicate-1

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.


title: Cerebellum_CX_NR-Replicate-1


title: XPA+_(GM15876A)_cell_line_replicate-4

value: Matched complemented XPA+ (GM15876A) cell line from Coriell Cell Repository


title: XPA+_(GM15876A)_cell_line_replicate-3

value: Matched complemented XPA+ (GM15876A) cell line


title: XPA-deficient (GM04312C) cell line_replicate-4


title: XPA+_(GM15876A)_cell_line_replicate-2


title: XPA+_(GM15876A)_cell_line_replicate-1


title: XPA-deficient (GM04312C) cell line_replicate-3


title: Fibroblast_GM969_scrambled_shXPA_replicate-4

value: Human primary fibroblast GM969

value: Human primary fibroblast GM969 transfected with a scrambled shXPA


title: XPA-deficient (GM04312C) cell line_replicate-1


title: Fibroblast_GM969_scrambled_shXPA_replicate-3


title: Fibroblast_GM969_shXPA_replicate-4

value: Human primary fibroblast GM969 transfected with shXPA


title: Fibroblast_GM969_scrambled_shXPA_replicate-1


title: HEK293 cells 72 hour MOTS-c (10 uM), rep6

status: Public on Mar 07 2015

description:
Sample name: MOTS-c6-72 HRS
Streptavidin-Cy3 bound to biotin-labeled cRNA.
HEK293 cells 72 hour incubation with MOTS (10 μM)_replicate_6.

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 HumanHT-12 V4.0 expression BeadChip (Illumina, San Diego, CA). The arrays were washed, blocked and the biotin-labeled cRNA was detected by staining with streptavidin-Cy3.

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

data_processing: Data was extracted using the Illumina GenomeStudio software 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.

label: biotin

source_name: HEK293, incubation with MOTS-c (10 μM), 72 hours

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 embryonic kidney cells (HEK293 cell line) were cultured in 10-cm dishes in 7 mL of phenol-free DMEM supplemented with 10% FBS.

extract_protocol: RNA was extracted from HEK293 cells using the RNeasy kit (Qiagen, Valencia, CA) 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: Cells were treated with water (controls) or the 16-amino-acid peptide mitochondrial open-reading-frame of the twelve S rRNA-c) (MOTS-c) for 4 or 72 hours prior to RNA extraction.

tag: cell type

value: embryonic kidney cell line

tag: culture condition

value: incubation with MOTS-c (10 μM)

tag: time

value: 72 hours


title: HEK293 cells 72 hour MOTS-c (10 uM), rep5

description:
Sample name: MOTS-c5-72 HRS
Streptavidin-Cy3 bound to biotin-labeled cRNA.
HEK293 cells 72 hour incubation with MOTS (10 μM)_replicate_5.


title: Fibroblast_GM969_shXPA_replicate-2


title: Fibroblast_GM969_scrambled_shXPA_replicate-2


title: Fibroblast_GM969_shXPA_replicate-1


title: Fibroblast_GM969_shXPA_replicate-3


status: Public on Aug 07 2015

description:
Cell Line FS-12_Poorly_Invasive
Not_Irradiated_1Day
Cell Line FS-12_Poorly_Invasive_Not_Irradiated_1Day
FS_12_D1_None

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-12_Not_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.

value: Not Irradiated

tag: phenotype

value: Poorly Invasive


title: HEK293 cells 72 hour control, rep2

description:
Sample name: CTR2-72 HRS
Streptavidin-Cy3 bound to biotin-labeled cRNA.
HEK293 cells 72 hour control_replicate_2.

source_name: HEK293, control incubation, 72 hours

value: control incubation


title: HEK293 cells 72 hour control, rep6

description:
Sample name: CTR6-72 HRS
Streptavidin-Cy3 bound to biotin-labeled cRNA.
HEK293 cells 72 hour control_replicate_6.


title: HEK293 cells 72 hour MOTS-c (10 uM), rep4

description:
Sample name: MOTS-c4-72 HRS
Streptavidin-Cy3 bound to biotin-labeled cRNA.
HEK293 cells 72 hour incubation with MOTS (10 μM)_replicate_4.


title: HEK293 cells 72 hour control, rep4

description:
Sample name: CTR4-72 HRS
Streptavidin-Cy3 bound to biotin-labeled cRNA.
HEK293 cells 72 hour control_replicate_4.


title: HEK293 cells 72 hour MOTS-c (10 uM), rep2

description:
Sample name: MOTS-c2-72 HRS
Streptavidin-Cy3 bound to biotin-labeled cRNA.
HEK293 cells 72 hour incubation with MOTS (10 μM)_replicate_2.


title: HEK293 cells 4 hour MOTS-c (10 uM), rep6

description:
Sample name: MOTS-c6-4 HRS
Streptavidin-Cy3 bound to biotin-labeled cRNA.
HEK293 cells 4 hour incubation with MOTS (10 μM)_replicate_6.

source_name: HEK293, incubation with MOTS-c (10 μM), 4 hours

value: 4 hours


title: HEK293 cells 4 hour MOTS-c (10 uM), rep4

description:
Sample name: MOTS-c4-4 HRS
Streptavidin-Cy3 bound to biotin-labeled cRNA.
HEK293 cells 4 hour incubation with MOTS (10 μM)_replicate_4.


title: HEK293 cells 4 hour control, rep6

description:
Sample name: CTR6-4 HRS
Streptavidin-Cy3 bound to biotin-labeled cRNA.
HEK293 cells 4 hour control_replicate_6.

source_name: HEK293, control incubation, 4 hours


title: HEK293 cells 4 hour control, rep2

description:
Sample name: CTR2-4 HRS
Streptavidin-Cy3 bound to biotin-labeled cRNA.
HEK293 cells 4 hour control_replicate_2.


title: HEK293 cells 72 hour MOTS-c (10 uM), rep1

description:
Sample name: MOTS-c1-72 HRS
Streptavidin-Cy3 bound to biotin-labeled cRNA.
HEK293 cells 72 hour incubation with MOTS (10 μM)_replicate_1.


title: HEK293 cells 72 hour MOTS-c (10 uM), rep3

description:
Sample name: MOTS-c3-72 HRS
Streptavidin-Cy3 bound to biotin-labeled cRNA.
HEK293 cells 72 hour incubation with MOTS (10 μM)_replicate_3.


title: HEK293 cells 4 hour MOTS-c (10 uM), rep2

description:
Sample name: MOTS-c2-4 HRS
Streptavidin-Cy3 bound to biotin-labeled cRNA.
HEK293 cells 4 hour incubation with MOTS (10 μM)_replicate_2.


title: HEK293 cells 72 hour control, rep5

description:
Sample name: CTR5-72 HRS
Streptavidin-Cy3 bound to biotin-labeled cRNA.
HEK293 cells 72 hour control_replicate_5.


title: WT_liver_PTH-Barr_2

status: Public on Mar 05 2015

description:
Mouse ID: WTPB_1-3_liver
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 (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 non-normalized data including detection scores are included in the supplemental file linked to the Series record.

source_name: Liver, wild-type, bPTH(7-34)

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

growth_protocol: Animal protocols were approved by the institutional animal care and use committee at Duke University School of Medicine and were in accordance with the NIH Guide for the Care and Use of Laboratory Animals.

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

treatment_protocol: Eleven-week-old male wild type C57BL/6J or congenic arrestin3-null mice were infused with human 40 µg/kg d PTH(1-34), 40 µg/kg d bovine (D-Trp12, Tyr34)-PTH(7-34), or PBS vehicle via Alzet osmotic minipumps (Model #1004, Durect Corp., Cupertino, CA) for 28 days. Minipumps were implanted subcutaneously in the upper back of anesthetized mice. The pump released 0.25 uL/hr in vehicle of 1 mM acetic acid in sterile PBS. At the end of the infusion period, animals were sacrificed and target tissues: calvarial bone, heart, lung, liver, kidney and aorta, were harvested and stored at -80 ˚C until mRNA isolation.

tag: strain/background

tag: genotype/variation

value: wild-type

value: male

tag: age

value: 15 weeks

tag: tissue

value: liver

tag: intervention treatment

value: beta-arrestin-signaling variant of parathyroid hormone, bPTH(7-34)

tag: replicate


title: WT_liver_PTH-Barr_3

description:
Mouse ID: WTPB_1-5_liver
Streptavidin-Cy3


title: HEK293 cells 4 hour control, rep4

description:
Sample name: CTR4-4 HRS
Streptavidin-Cy3 bound to biotin-labeled cRNA.
HEK293 cells 4 hour control_replicate_4.


title: HEK293 cells 72 hour control, rep3

description:
Sample name: CTR3-72 HRS
Streptavidin-Cy3 bound to biotin-labeled cRNA.
HEK293 cells 72 hour control_replicate_3.


title: HEK293 cells 72 hour control, rep1

description:
Sample name: CTR1-72 HRS
Streptavidin-Cy3 bound to biotin-labeled cRNA.
HEK293 cells 72 hour control_replicate_1.


title: HEK293 cells 4 hour MOTS-c (10 uM), rep5

description:
Sample name: MOTS-c5-4 HRS
Streptavidin-Cy3 bound to biotin-labeled cRNA.
HEK293 cells 4 hour incubation with MOTS (10 μM)_replicate_5.


title: HEK293 cells 4 hour MOTS-c (10 uM), rep3

description:
Sample name: MOTS-c3-4 HRS
Streptavidin-Cy3 bound to biotin-labeled cRNA.
HEK293 cells 4 hour incubation with MOTS (10 μM)_replicate_3.


title: WT_liver_PTH_2

description:
Mouse ID: WTP_1-3_liver
Streptavidin-Cy3

source_name: Liver, wild-type, hPTH(1-34)

value: parathyroid hormone, hPTH(1-34)


title: WT_liver_PTH_3

description:
Mouse ID: WTP_1-5_liver
Streptavidin-Cy3


title: WT_liver_PTH_1

description:
Mouse ID: WTP_1-1_liver
Streptavidin-Cy3


title: HEK293 cells 4 hour MOTS-c (10 uM), rep1

description:
Sample name: MOTS-c1-4 HRS
Streptavidin-Cy3 bound to biotin-labeled cRNA.
HEK293 cells 4 hour incubation with MOTS (10 μM)_replicate_1.


title: HEK293 cells 4 hour control, rep5

description:
Sample name: CTR5-4 HRS
Streptavidin-Cy3 bound to biotin-labeled cRNA.
HEK293 cells 4 hour control_replicate_5.


title: WT_liver_vehicle_3

description:
Mouse ID: WTC_1-5_liver
Streptavidin-Cy3

source_name: Liver, wild-type, vehicle

value: PBS vehicle


title: HEK293 cells 4 hour control, rep3

description:
Sample name: CTR3-4 HRS
Streptavidin-Cy3 bound to biotin-labeled cRNA.
HEK293 cells 4 hour control_replicate_3.


title: HEK293 cells 4 hour control, rep1

description:
Sample name: CTR1-4 HRS
Streptavidin-Cy3 bound to biotin-labeled cRNA.
HEK293 cells 4 hour control_replicate_1.


title: WT_liver_PTH-Barr_1

description:
Mouse ID: WTPB_1-1_liver
Streptavidin-Cy3


title: WT_heart_PTH-Barr_3

description:
Mouse ID: WTPB_1-5_heart
Streptavidin-Cy3

source_name: Heart, wild-type, bPTH(7-34)

value: heart


title: WT_liver_vehicle_1

description:
Mouse ID: WTC_1-1_liver
Streptavidin-Cy3


title: WT_lung_PTH-Barr_3

description:
Mouse ID: WTPB_1-5_lung
Streptavidin-Cy3

source_name: Lung, wild-type, bPTH(7-34)

value: lung


title: WT_lung_vehicle_3

description:
Mouse ID: WTC_1-5_lung
Streptavidin-Cy3

source_name: Lung, wild-type, vehicle


title: WT_lung_PTH_2

description:
Mouse ID: WTP_1-3_lung
Streptavidin-Cy3

source_name: Lung, wild-type, hPTH(1-34)


title: WT_lung_PTH_3

description:
Mouse ID: WTP_1-5_lung
Streptavidin-Cy3


title: WT_lung_PTH-Barr_1

description:
Mouse ID: WTPB_1-1_lung
Streptavidin-Cy3


title: WT_liver_vehicle_2

description:
Mouse ID: WTC_1-3_liver
Streptavidin-Cy3


title: WT_lung_PTH_1

description:
Mouse ID: WTP_1-1_lung
Streptavidin-Cy3


title: WT_heart_PTH-Barr_2

description:
Mouse ID: WTPB_1-3_heart
Streptavidin-Cy3


title: WT_lung_PTH-Barr_2

description:
Mouse ID: WTPB_1-3_lung
Streptavidin-Cy3


title: WT_lung_vehicle_1

description:
Mouse ID: WTC_1-1_lung
Streptavidin-Cy3


title: WT_lung_vehicle_2

description:
Mouse ID: WTC_1-3_lung
Streptavidin-Cy3


title: WT_heart_PTH_3

description:
Mouse ID: WTP_1-5_heart
Streptavidin-Cy3

source_name: Heart, wild-type, hPTH(1-34)


title: WT_heart_PTH-Barr_1

description:
Mouse ID: WTPB_1-1_heart
Streptavidin-Cy3


title: WT_heart_vehicle_3

description:
Mouse ID: WTC_1-5_heart
Streptavidin-Cy3

source_name: Heart, wild-type, vehicle


title: WT_heart_PTH_1

description:
Mouse ID: WTP_1-1_heart
Streptavidin-Cy3


title: WT_heart_PTH_2

description:
Mouse ID: WTP_1-3_heart
Streptavidin-Cy3


title: WT_aorta_PTH-Barr_Replicate3

description:
Mouse ID: WTPB_1-5_aorta
Streptavidin-Cy3

source_name: Aorta, wild-type, bPTH(7-34)

value: aorta


title: WT_aorta_vehicle_Replicate2

description:
Mouse ID: WTC_1-3_aorta
Streptavidin-Cy3

source_name: Aorta, wild-type, vehicle


title: WT_heart_vehicle_2

description:
Mouse ID: WTC_1-3_heart
Streptavidin-Cy3


title: WT_heart_vehicle_1

description:
Mouse ID: WTC_1-1_heart
Streptavidin-Cy3


title: WT_aorta_PTH_Replicate3

description:
Mouse ID: WTP_1-5_aorta
Streptavidin-Cy3

source_name: Aorta, wild-type, hPTH(1-34)


title: WT_aorta_PTH_Replicate2

description:
Mouse ID: WTP_1-3_aorta
Streptavidin-Cy3


title: WT_aorta_vehicle_Replicate3

description:
Mouse ID: WTC_1-5_aorta
Streptavidin-Cy3


title: WT_aorta_PTH-Barr_Replicate1

description:
Mouse ID: WTPB_1-1_aorta
Streptavidin-Cy3


title: WT_kidney_PTH-Barr_Replicate1

description:
Mouse ID: WTPB_1-1_kidney
Streptavidin-Cy3

source_name: Kidney, wild-type, bPTH(7-34)

value: kidney


title: WT_kidney_vehicle_Replicate2

description:
Mouse ID: WTC_1-3_kidney
Streptavidin-Cy3

source_name: Kidney, wild-type, vehicle


title: WT_kidney_PTH-Barr_Replicate3

description:
Mouse ID: WTPB_1-5_kidney
Streptavidin-Cy3


title: WT_kidney_PTH_Replicate3

description:
Mouse ID: WTP_1-5_kidney
Streptavidin-Cy3

source_name: Kidney, wild-type, hPTH(1-34)


title: WT_kidney_PTH-Barr_Replicate2

description:
Mouse ID: WTPB_1-3_kidney
Streptavidin-Cy3


title: WT_kidney_vehicle_Replicate3

description:
Mouse ID: WTC_1-5_kidney
Streptavidin-Cy3


title: Barr2KO_bone_vehicle_Replicate2

description:
Mouse ID: BAC-1-3_bone
Streptavidin-Cy3

source_name: Calvarial bone, beta-arrestin null, vehicle

value: beta-arrestin null

value: calvarial bone


title: WT_bone_PTH_Barr_Replicate3

description:
Mouse ID: WTPB_1-5_bone
Streptavidin-Cy3

source_name: Calvarial bone, wild-type, bPTH(7-34)


title: WT_kidney_vehicle_Replicate1

description:
Mouse ID: WTC_1-1_kidney
Streptavidin-Cy3


title: WT_bone_PTH_Barr_Replicate1

description:
Mouse ID: WTPB_1-1_bone
Streptavidin-Cy3


title: WT_kidney_PTH_Replicate2

description:
Mouse ID: WTP_1-3_kidney
Streptavidin-Cy3


title: Barr2KO_bone_PTH_Barr_Replicate3

description:
Mouse ID: BAPB-1-5_bone
Streptavidin-Cy3

source_name: Calvarial bone, beta-arrestin null, bPTH(7-34)


title: Barr2KO_bone_PTH_Replicate1

description:
Mouse ID: BAP-1-1_bone
Streptavidin-Cy3

source_name: Calvarial bone, beta-arrestin null, hPTH(1-34)


title: Barr2KO_bone_PTH_Replicate2

description:
Mouse ID: BAP-1-3_bone
Streptavidin-Cy3


title: Barr2KO_bone_PTH_Barr_Replicate2

description:
Mouse ID: BAPB-1-3_bone
Streptavidin-Cy3


title: Barr2KO_bone_vehicle_Replicate3

description:
Mouse ID: BAC-1-5_bone
Streptavidin-Cy3


title: Barr2KO_bone_PTH_Replicate3

description:
Mouse ID: BAP-1-5_bone
Streptavidin-Cy3


title: WT_bone_PTH_Barr_Replicate2

description:
Mouse ID: WTPB_1-3_bone
Streptavidin-Cy3


title: WT_bone_PTH_Replicate2

description:
Mouse ID: WTP_1-3_bone
Streptavidin-Cy3

source_name: Calvarial bone, wild-type, hPTH(1-34)


title: Barr2KO_bone_PTH_Barr_Replicate1

description:
Mouse ID: BAPB-1-1_bone
Streptavidin-Cy3


title: WT_bone_PTH_Replicate3

description:
Mouse ID: WTP_1-5_bone
Streptavidin-Cy3


title: WT_kidney_PTH_Replicate1

description:
Mouse ID: WTP_1-1_kidney
Streptavidin-Cy3


title: WT_aorta_PTH-Barr_Replicate2

description:
Mouse ID: WTPB_1-3_aorta
Streptavidin-Cy3


title: WT_bone_PTH_Replicate1

description:
Mouse ID: WTP_1-1_bone
Streptavidin-Cy3


title: WT_bone_vehicle_Replicate1

description:
Mouse ID: WTC_1-1_bone
Streptavidin-Cy3

source_name: Calvarial bone, wild-type, vehicle


title: Barr2KO_bone_vehicle_Replicate1

description:
Mouse ID: BAC-1-1_bone
Streptavidin-Cy3


title: SUDHL-4 (DLBCL) cell line_polysomal fractions_20mM ETOH treatment_Replicate-3

status: Public on Mar 03 2015

description:
EtOH_S4_20_3
Polysomal fractions(9-11)
SUDHL-4 (DLBCL) cell line_polysomal fractions (9-11)_20mM ETOH treatment_Replicate-3
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 HumanHT-12 v4 Expression BeadChip (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 (v1.9.0). Any spots at or below the background were filtered out using an Illumina detection Pvalue of .02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below. Z-score = (raw value - avg)/std. Complete data including detection scores are included in the supplemental file.

label: Biotin

source_name: SUDHL-4 (DLBCL) cell line, polysomal fractions, 20mM ETOH treatment

label_protocol: Standard Illumina protocol using Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791). In short, 0.5ug of polysomal 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: SUDHL-2 and SUDHL-4 diffuse large B-cell lymphoma (DLBCL) cell lines (ATCC) were cultured in RPMI Medium 1640 (Gibco BRL) supplemented with 10% fetal bovine serum (FBS) at 37°C in 5% CO2.

extract_protocol: To create polysomal fractions, cells were lysed in cytoplasmic lysis buffer (5mM Tris, 2.5mM MgCl2, 1.5mM KCl, 1% Triton X-100, 0.5% Sodium Deoxycholate and 2 mM DTT), loaded on 10 - 50% linear sucrose gradients and fractionated. The RNA in each fraction was monitored by optical density measurement (A254) and eleven fractions were collected with a fraction collector (Brandel). RNA from the high molecular weight polysomal fractions with actively translated mRNAs (fractions 9 - 11) were pooled and used for microarray analysis.

treatment_protocol: EtOH-treated cells were cultured in sealed flasks to maintain 20mM EtOH concentrations in the culture medium, water was added to EtOH control wells. INK128-treated cells were treated with INK128 at 40nM (Selleckchem) dissolved in dimethyl sulfoxide (DMSO), 0.01% DMSO was added for the control wells.

value: 20mM ETOH


title: SUDHL-4 (DLBCL) cell line_polysomal fractions_water treatment_Replicate-2

description:
EtOH_S4_c3
Polysomal fractions(9-11)
SUDHL-4 (DLBCL) cell line_polysomal fractions (9-11)_water treatment_Replicate-2
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: SUDHL-4 (DLBCL) cell line, polysomal fractions, water treatment

value: diffuse large B-cell lymphoma (DLBCL) cell line

value: water


title: WT_aorta_PTH_Replicate1

description:
Mouse ID: WTP_1-1_aorta
Streptavidin-Cy3


title: SUDHL-4 (DLBCL) cell line_polysomal fractions_20mM ETOH treatment_Replicate-2

description:
EtOH_S4_20_2
Polysomal fractions(9-11)
SUDHL-4 (DLBCL) cell line_polysomal fractions (9-11)_20mM ETOH treatment_Replicate-2
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: SUDHL-2 (DLBCL) cell line_polysomal fractions_20mM ETOH treatment_Replicate-1

description:
EtOH_S2_20_1
Polysomal fractions(9-11)
SUDHL-2 (DLBCL) cell line_polysomal fractions (9-11)_20mM ETOH treatment_Replicate-1
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: SUDHL-2 (DLBCL) cell line, polysomal fractions, 20mM ETOH treatment


title: SUDHL-2 (DLBCL) cell line_polysomal fractions_20mM ETOH treatment_Replicate-2

description:
EtOH_S2_20_3
Polysomal fractions(9-11)
SUDHL-2 (DLBCL) cell line_polysomal fractions (9-11)_20mM ETOH treatment_Replicate-2
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: SUDHL-2 (DLBCL) cell line_polysomal fractions_water treatment_Replicate-3

description:
EtOH_S2_c2
Polysomal fractions(9-11)
SUDHL-2 (DLBCL) cell line_polysomal fractions (9-11)_water treatment_Replicate-3
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: SUDHL-2 (DLBCL) cell line, polysomal fractions, water treatment


title: SUDHL-4 (DLBCL) cell line_polysomal fractions_water treatment_Replicate-1

description:
EtOH_S4_c1
Polysomal fractions(9-11)
SUDHL-4 (DLBCL) cell line_polysomal fractions (9-11)_water treatment_Replicate-1
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: SUDHL-4 (DLBCL) cell line_polysomal fractions_20mM ETOH treatment_Replicate-1

description:
EtOH_S4_20_1
Polysomal fractions(9-11)
SUDHL-4 (DLBCL) cell line_polysomal fractions (9-11)_20mM ETOH treatment_Replicate-1
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: SUDHL-4 (DLBCL) cell line_polysomal fractions_water treatment_Replicate-3

description:
EtOH_S4_c2
Polysomal fractions(9-11)
SUDHL-4 (DLBCL) cell line_polysomal fractions (9-11)_water treatment_Replicate-3
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: WT_bone_vehicle_Replicate2

description:
Mouse ID: WTC_1-3_bone
Streptavidin-Cy3


title: SUDHL-4 (DLBCL) cell line_polysomal fractions_40nM INK128 treatment_Replicate-3

description:
INK128_S4_40_3
Polysomal fractions(9-11)
SUDHL-4 (DLBCL) cell line_polysomal fractions (9-11)_40nM INK128 treatment_Replicate-3
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: SUDHL-4 (DLBCL) cell line, polysomal fractions, 40nM INK128 treatment

value: 40nM INK128


title: SUDHL-2 (DLBCL) cell line_polysomal fractions_40nM INK128 treatment_Replicate-1

description:
INK128_S2_40_1e
Polysomal fractions(9-11)
SUDHL-2 (DLBCL) cell line_polysomal fractions (9-11)_40nM INK128 treatment_Replicate-1
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: SUDHL-2 (DLBCL) cell line, polysomal fractions, 40nM INK128 treatment


title: SUDHL-4 (DLBCL) cell line_polysomal fractions_40nM INK128 treatment_Replicate-1

description:
INK128_S4_40_1
Polysomal fractions(9-11)
SUDHL-4 (DLBCL) cell line_polysomal fractions (9-11)_40nM INK128 treatment_Replicate-1
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: SUDHL-2 (DLBCL) cell line_polysomal fractions_water treatment_Replicate-2

description:
EtOH_S2_c3
Polysomal fractions(9-11)
SUDHL-2 (DLBCL) cell line_polysomal fractions (9-11)_water treatment_Replicate-2
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: SUDHL-2 (DLBCL) cell line_polysomal fractions_water treatment_Replicate-1

description:
EtOH_S2_c1
Polysomal fractions(9-11)
SUDHL-2 (DLBCL) cell line_polysomal fractions (9-11)_water treatment_Replicate-1
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: SUDHL-4 (DLBCL) cell line_polysomal fractions_0.01% DMSO treatment_Replicate-3

description:
INK128_S4_c3
Polysomal fractions(9-11)
SUDHL-4 (DLBCL) cell line_polysomal fractions (9-11)_0.01% DMSO treatment_Replicate-3
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: SUDHL-4 (DLBCL) cell line, polysomal fractions, 0.01% DMSO treatment


title: SUDHL-4 (DLBCL) cell line_polysomal fractions_0.01% DMSO treatment_Replicate-1

description:
INK128_S4_c1
Polysomal fractions(9-11)
SUDHL-4 (DLBCL) cell line_polysomal fractions (9-11)_0.01% DMSO treatment_Replicate-1
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: SUDHL-4 (DLBCL) cell line_polysomal fractions_40nM INK128 treatment_Replicate-2

description:
INK128_S4_40_2
Polysomal fractions(9-11)
SUDHL-4 (DLBCL) cell line_polysomal fractions (9-11)_40nM INK128 treatment_Replicate-2
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: SUDHL-4 (DLBCL) cell line_polysomal fractions_0.01% DMSO treatment_Replicate-2

description:
INK128_S4_c2
Polysomal fractions(9-11)
SUDHL-4 (DLBCL) cell line_polysomal fractions (9-11)_0.01% DMSO treatment_Replicate-2
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: SUDHL-2 (DLBCL) cell line_polysomal fractions_0.01% DMSO treatment_Replicate-3

description:
INK128_S2_c3
Polysomal fractions(9-11)
SUDHL-2 (DLBCL) cell line_polysomal fractions (9-11)_0.01% DMSO treatment_Replicate-3
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: SUDHL-2 (DLBCL) cell line, polysomal fractions, 0.01% DMSO treatment


title: SUDHL-2 (DLBCL) cell line_polysomal fractions_40nM INK128 treatment_Replicate-3

description:
INK128_S2_40_3
Polysomal fractions(9-11)
SUDHL-2 (DLBCL) cell line_polysomal fractions (9-11)_40nM INK128 treatment_Replicate-3
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: SUDHL-2 (DLBCL) cell line_polysomal fractions_0.01% DMSO treatment_Replicate-1

description:
INK128_S2_c1
Polysomal fractions(9-11)
SUDHL-2 (DLBCL) cell line_polysomal fractions (9-11)_0.01% DMSO treatment_Replicate-1
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: 110286_PBMC_7

status: Public on Jan 26 2015

city: New Haven

first: Hailong

last: Meng

state: CT

address: 300 George Str

institute: Yale University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with lumi in R

source_name: PBMC

label_protocol: Preparation of cDNA, cRNA, and labeling were carried out by the Yale Center for Genomic Analysis using the standard Illumina protocols.   Hybridization buffer from the BeadChip kit (Illumina) was mixed with 1500 ng of biotin-labeled cRNA, heated to 65°C for 5 minutes, and then loaded onto the BeadChip.  The BeadChips were sealed in a hybridization chamber and placed in an oven at 58°C with a rocker for 16-20 hours.  After the hybridization, the BeadChips were washed and stained in a series of washes and stains as outlined in the Illumina protocol.  The BeadChips were scanned on the Illumina Iscan.

extract_protocol: Total RNA from PBMC, T Cell, B Cell samples was extracted using the RNeasy mini kit (Qiagen, CA)

tag: blood draw date

tag: age group

value: Old

value: NR


title: 110286_PBMC_4


title: 110285_PBMC_28


title: 110286_PBMC_28


title: 110285_PBMC_7


title: SUDHL-2 (DLBCL) cell line_polysomal fractions_40nM INK128 treatment_Replicate-2

description:
INK128_S2_40_2
Polysomal fractions(9-11)
SUDHL-2 (DLBCL) cell line_polysomal fractions (9-11)_40nM INK128 treatment_Replicate-2
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: 110286_PBMC_0


title: SUDHL-2 (DLBCL) cell line_polysomal fractions_0.01% DMSO treatment_Replicate-2

description:
INK128_S2_c2
Polysomal fractions(9-11)
SUDHL-2 (DLBCL) cell line_polysomal fractions (9-11)_0.01% DMSO treatment_Replicate-2
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: 110285_PBMC_4


title: 110279_PBMC_7

value: Frail


title: 110283_PBMC_4

value: R


title: 110281_PBMC_28


title: 110282_PBMC_28


title: 110281_PBMC_7


title: 110281_PBMC_0


title: 110279_PBMC_0


title: 110278_PBMC_28


title: 110279_PBMC_28


title: 110281_PBMC_4


title: 110283_PBMC_0


title: 110279_PBMC_4


title: 110283_PBMC_7


title: 110283_PBMC_28


title: 110282_PBMC_0


title: 110282_PBMC_7


title: 110277_PBMC_28

value: BadR


title: 110272_PBMC_28

value: Young


title: 110277_PBMC_0


title: 110277_PBMC_7


title: 110282_PBMC_4


title: 110272_PBMC_7


title: 110272_PBMC_2


title: 110278_PBMC_0


title: 110277_PBMC_2


title: 110278_PBMC_4


title: 110285_PBMC_0


title: 110278_PBMC_7


title: 110271_PBMC_2


title: 110270_PBMC_7


title: 110271_PBMC_7


title: 110270_PBMC_0


title: 110271_PBMC_28


title: 110271_PBMC_0


title: 110268_PBMC_7


title: 110270_PBMC_32


title: 110270_PBMC_2


title: 110268_PBMC_2


title: 110268_PBMC_24


title: 110265_PBMC_7


title: 110267_PBMC_0


title: 110268_PBMC_0


title: 110267_PBMC_7


title: 110267_PBMC_28


title: 110272_PBMC_0


title: 110267_PBMC_2


title: 110264_PBMC_2


title: 110264_PBMC_0


title: 110264_PBMC_7


title: 110265_PBMC_28


title: 110260_PBMC_7


title: 110260_PBMC_28


title: 110265_PBMC_2


title: 110260_PBMC_2


title: 110260_PBMC_0


title: 110264_PBMC_28


title: 110258_PBMC_28


title: 110265_PBMC_0


title: 110258_PBMC_2


title: 110257_PBMC_28


title: 110258_PBMC_0


title: 110258_PBMC_7


title: 110256_PBMC_28


title: 110256_PBMC_2


title: 110257_PBMC_2


title: 110257_PBMC_7


title: 110257_PBMC_0


title: 110256_PBMC_0


title: 110256_PBMC_7


title: 110255_PBMC_28


title: 110255_PBMC_0


title: 110255_PBMC_7


title: 110250_PBMC_28


title: 110244_PBMC_28


title: 110250_PBMC_7


title: 110248_PBMC_0


title: 110244_PBMC_7


title: 110244_PBMC_2


title: WT_bone_vehicle_Replicate3

description:
Mouse ID: WTC_1-5_bone
Streptavidin-Cy3

value: wild-type

value: male

value: 15 weeks

value: PBS vehicle


title: 110244_PBMC_0


title: 110255_PBMC_2


title: 110248_PBMC_7


title: 110250_PBMC_0


title: 110248_PBMC_2


title: 110250_PBMC_2


title: 110248_PBMC_28


title: 110243_PBMC_7


title: 110243_PBMC_2


title: 110216_PBMC_7


title: 110243_PBMC_28


title: 110216_PBMC_28


title: 110216_PBMC_2


title: 110243_PBMC_0


title: 110215_PBMC_28


title: 110215_PBMC_2


title: 110216_PBMC_0


title: 110214_PBMC_28


title: 110215_PBMC_7


title: 110215_PBMC_0


title: 110214_PBMC_0


title: 110214_PBMC_2


title: 110204_PBMC_28


title: 110209_PBMC_0


title: 110210_PBMC_7


title: 110211_PBMC_0


title: 110210_PBMC_0


title: 110209_PBMC_28


title: 110211_PBMC_2


title: 110211_PBMC_7


title: 110210_PBMC_28


title: 110204_PBMC_0


title: 110204_PBMC_7


title: 110202_PBMC_28


title: 110214_PBMC_7


title: 110202_PBMC_7


title: 110209_PBMC_2


title: 110204_PBMC_2


title: 110202_PBMC_2


title: 110209_PBMC_7


title: 110202_PBMC_0


title: 110198_PBMC_2


title: 110192_PBMC_7


title: 110199_PBMC_0


title: 110199_PBMC_7


title: 110199_PBMC_28


title: 110198_PBMC_28


title: 110196_PBMC_28


title: 110196_PBMC_2


title: 110201_PBMC_28


title: 110201_PBMC_0


title: 110195_PBMC_28


title: 110198_PBMC_0


title: 110192_PBMC_28


title: 110201_PBMC_7


title: 110196_PBMC_0


title: 110199_PBMC_2


title: 110201_PBMC_2


title: 110194_PBMC_7


title: 110196_PBMC_7


title: 110195_PBMC_7


title: 110192_PBMC_2


title: 110194_PBMC_28


title: 110195_PBMC_2


title: 110198_PBMC_7


title: 110195_PBMC_0


title: 110194_PBMC_2


title: 110210_PBMC_2


title: 110194_PBMC_0


title: 110192_PBMC_0


title: 101119_PBMC_0


title: 101128_PBMC_0


title: 101107_PBMC_7


title: 101119_PBMC_7


title: 101128_PBMC_4


title: 101115_PBMC_7


title: 101117_PBMC_4


title: 101117_PBMC_28


title: 101117_PBMC_0


title: 101115_PBMC_4


title: 101098_PBMC_7


title: 101128_PBMC_7


title: 101119_PBMC_28


title: 101119_PBMC_4


title: 101107_PBMC_4


title: 101105_PBMC_28


title: 101107_PBMC_28


title: 101105_PBMC_4


title: 101115_PBMC_0


title: 101098_PBMC_0


title: 101115_PBMC_28


title: 101092_PBMC_28


title: 101105_PBMC_0


title: 101098_PBMC_4


title: 101128_PBMC_28


title: 101105_PBMC_7


title: 101107_PBMC_0


title: 101092_PBMC_4


title: 101092_PBMC_0


title: 101082_PBMC_28


title: 101079_PBMC_28


title: 101079_PBMC_4


title: 101082_PBMC_4


title: 101076_PBMC_28


title: 101082_PBMC_7


title: 101079_PBMC_7


title: 110211_PBMC_28


title: 101079_PBMC_0


title: 101065_PBMC_28


title: 101076_PBMC_7


title: 101065_PBMC_4


title: 101082_PBMC_0


title: 101041_PBMC_7


title: 101076_PBMC_4


title: 101028_PBMC_0


title: 101028_PBMC_28


title: 101041_PBMC_0


title: 101054_PBMC_7


title: 101065_PBMC_0


title: 101054_PBMC_4


title: 101028_PBMC_4


title: 101028_PBMC_7


title: 101054_PBMC_28


title: 101065_PBMC_7


title: 101076_PBMC_0


title: 101054_PBMC_0


title: 101022_PBMC_7


title: 101041_PBMC_4


title: 101022_PBMC_28


title: 101021_PBMC_28


title: 101008_PBMC_28


title: 101008_PBMC_0


title: 101022_PBMC_4


title: 101021_PBMC_4


title: 101005_PBMC_0


title: 101005_PBMC_4


title: 101005_PBMC_28


title: 101005_PBMC_7


title: 101022_PBMC_0


title: CD4+T cells_82 year Male_4ºC_Replicate-15

status: Public on Jan 08 2015

description:
Sample name: D4_82BL54M4_47
Replicate-15
1x10^7 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 4ºC (5% CO2 incubator) before RNA isolation.
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 HumanHT-12 v3 Expression BeadChip (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 Pvalue of .02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below. Z-score = (raw value - avg)/std. Complete data including detection scores are included in the supplemental file.

source_name: CD4+ T cells, 82 years old, male, 4ºC

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from heparinized blood using Ficoll-Paque Plus (GE Healthcare, Piscataway, NJ, USA) density gradient centrifugation. CD4+ T cells were obtained by positive selection using anti-human CD4 microbeads (Miltenyi Biotec Auburn, CA, USA).

extract_protocol: After incubation, cells were harvested, washed once with cold PBS and collected by centrifugation. Total cellular RNA was prepared by lysing cell pellet in 350μl RLT buffer and proceeding with the RNeasy protocol (QIAGEN Inc., Valencia, CA, USA).

treatment_protocol: For gene expression studies, 1x10^7 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h either at 37ºC or 4ºC (5% CO2 incubator).

value: 82 years

value: CD4+ T cells

value: incubation at 4ºC for 4h


title: CD4+T cells_72 year Male_4ºC_Replicate-11

description:
Sample name: D4_72BL56M4_41
Replicate-11
1x10^7 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 4ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 72 years old, male, 4ºC

value: 72 years


title: CD4+T cells_63 year Male_4ºC_Replicate-9

description:
Sample name: D4_63BL24M4_23
Replicate-9
1x10^7 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 4ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 63 years old, male, 4ºC

value: 63 years


title: CD4+T cells_74 year Male_4ºC_Replicate-12

description:
Sample name: D4_74BL36M4_33_
Replicate-12
1x10^7 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 4ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 74 years old, male, 4ºC

value: 74 years


title: CD4+T cells_30 year old_Male_50nM rapamycin_37ºC_Replicate-2

description:
Sample name: 37R50_ND555_43R
Replicate-2
Treatment drug+/- and temperature: 5x10^6 CD4+ T cells in 3 ml RPMI 1640 medium plus 50nM rapamycin were incubated for 4h at 37ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 30 years old, male, 50nM rapamycin, 37ºC

treatment_protocol: To test the effects of drug treatment, 5x10^6 CD4+ T cells were treated with varying concentrations of rapamycin and also LY 294002 in 3 ml of RPMI 1640 medium. Control cells were also created without any added drugs. Cells were incubated for 4h in 5% CO2 at both 37°C and 4°C.

value: 30 years

value: 50nM rapamycin, incubation at 37ºC for 4h


title: 101021_PBMC_7

value: Old

value: NR


title: CD4+T cells_62 year Female_4ºC_Replicate-5

description:
Sample name: D4_62BL32F4_27
Replicate-5
1x10^7 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 4ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 62 years old, female, 4ºC

value: 62 years

value: female


title: 101021_PBMC_0


title: 101008_PBMC_4


title: CD4+T cells_76 year Male_4ºC_Replicate-13

description:
Sample name: D4_76BL45M4_35
Replicate-13
1x10^7 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 4ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 76 years old, male, 4ºC

value: 76 years


title: CD4+T cells_56 year Male_4ºC_Replicate-7

description:
Sample name: D4_56BL28M4_17
Replicate-7
1x10^7 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 4ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 56 years old, male, 4ºC

value: 56 years


title: CD4+T cells_70 year old_Male_100nM rapamycin_37ºC_Replicate-1

description:
Sample name: 37R100_ND394_24RR
Replicate-1
Treatment drug+/- and temperature: 5x10^6 CD4+ T cells in 3 ml RPMI 1640 medium plus 100nM rapamycin were incubated for 4h at 37ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 70 years old, male, 100nM rapamycin, 37ºC

value: 70 years

value: male

value: 100nM rapamycin, incubation at 37ºC for 4h


title: CD4+T cells_70 year old_Male_Control_4ºC_Replicate-1

description:
Sample name: 4C_ND394_28C4
Replicate-1
Treatment drug+/- and temperature: 5x10^6 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 4ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 70 years old, male, control, 4ºC

value: no drugs, incubation at 4ºC for 4h


title: CD4+T cells_61 year Male_4ºC_Replicate-8

description:
Sample name: D4_61BL38M4_29
Replicate-8
1x10^7 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 4ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 61 years old, male, 4ºC

value: 61 years

value: CD4+ T cells


title: CD4+T cells_70 year old_Male_50nM rapamycin_37ºC_Replicate-1

description:
Sample name: 37R50_ND394_3R
Replicate-1
Treatment drug+/- and temperature: 5x10^6 CD4+ T cells in 3 ml RPMI 1640 medium plus 50nM rapamycin were incubated for 4h at 37ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 70 years old, male, 50nM rapamycin, 37ºC


title: CD4+T cells_67 year Male_4ºC_Replicate-10

description:
Sample name: D4_67BL30M4_25
Replicate-10
1x10^7 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 4ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 67 years old, male, 4ºC

value: 67 years

value: incubation at 4ºC for 4h


title: CD4+T cells_81 year Female_4ºC_Replicate-7

description:
Sample name: D4_81BL2F4_45A
Replicate-7
1x10^7 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 4ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 81 years old, female, 4ºC

value: 81 years


title: CD4+T cells_54 year Male_4ºC_Replicate-6

description:
Sample name: D4_54BL33M4_19
Replicate-6
1x10^7 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 4ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 54 years old, male, 4ºC

value: 54 years


title: CD4+T cells_30 year old_Male_Control_37ºC_Replicate-2

description:
Sample name: 37C_ND555_48C
Replicate-2
Treatment drug+/- and temperature: 5x10^6 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 37ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 30 years old, male, control, 37ºC

value: 30 years

value: no drugs, incubation at 37ºC for 4h


title: CD4+T cells_73 year Female_4ºC_Replicate-6

description:
Sample name: D4_73BL50F4_39
Replicate-6
1x10^7 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 4ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 73 years old, female, 4ºC

value: 73 years


title: 101092_PBMC_7

source_name: PBMC

value: Young

value: R


title: CD4+T cells_53 year Female_4ºC_Replicate-4

description:
Sample name: D4_53BL53F4_21
Replicate-4
1x10^7 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 4ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 53 years old, female, 4ºC

value: 53 years

value: female


title: CD4+T cells_30 year old_Male_100nM rapamycin_37ºC_Replicate-2

description:
Sample name: 37R100_ND555_44RR
Replicate-2
Treatment drug+/- and temperature: 5x10^6 CD4+ T cells in 3 ml RPMI 1640 medium plus 100nM rapamycin were incubated for 4h at 37ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 30 years old, male, 100nM rapamycin, 37ºC


title: CD4+T cells_30 year old_Male_Control_4ºC_Replicate-2

description:
Sample name: 4C_ND555_61C4
Replicate-2
Treatment drug+/- and temperature: 5x10^6 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 4ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 30 years old, male, control, 4ºC


title: CD4+T cells_52 year Male_4ºC_Replicate-5

description:
Sample name: D4_52BL27M4_15
Replicate-5
1x10^7 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 4ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 52 years old, male, 4ºC

value: 52 years


title: CD4+T cells_79 year Male_4ºC_Replicate-14

description:
Sample name: D4_79BL39M4_43
Replicate-14
1x10^7 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 4ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 79 years old, male, 4ºC

value: 79 years

value: male


title: CD4+T cells_30 year old_Male_20uM LY 294002_37ºC_Replicate-2

description:
Sample name: 37L20_ND555_51L
Replicate-2
Treatment drug+/- and temperature: 5x10^6 CD4+ T cells in 3 ml RPMI 1640 medium plus 20uM LY 294002 were incubated for 4h at 37ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 30 years old, male, 20uM LY 294002, 37ºC

value: 20uM LY 294002, incubation at 37ºC for 4h


title: CD4+T cells_70 year old_Male_20uM LY 294002_37ºC_Replicate-1

description:
Sample name: 37L20_ND394_19L
Replicate-1
Treatment drug+/- and temperature: 5x10^6 CD4+ T cells in 3 ml RPMI 1640 medium plus 20uM LY 294002 were incubated for 4h at 37ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 70 years old, male, 20uM LY 294002, 37ºC

value: 70 years


title: CD4+T cells_49 year Female_4ºC_Replicate-3

description:
Sample name: D4_49BL35F4_11
Replicate-3
1x10^7 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 4ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 49 years old, female, 4ºC

value: 49 years

value: CD4+ T cells


title: CD4+T cells_44 year Male_4ºC_Replicate-4

description:
Sample name: D4_44BL44M4_13
Replicate-4
1x10^7 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 4ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 44 years old, male, 4ºC

value: 44 years

value: incubation at 4ºC for 4h


title: CD4+T cells_40 year Male_4ºC_Replicate-2

description:
Sample name: D4_40ND55M4_7B
Replicate-2
1x10^7 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 4ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 40 years old, male, 4ºC

value: 40 years


title: CD4+T cells_70 year old_Male_Control_37ºC_Replicate-1

description:
Sample name: 37C_ND394_27C
Replicate-1
Treatment drug+/- and temperature: 5x10^6 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 37ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 70 years old, male, control, 37ºC


title: CD4+T cells_64 year Female_Serum+_4ºC_Replicate-2

description:
Replicate-2
Treatment serum+/- and temperature: 5x10^6 CD4+ T cells in 3 ml RPMI 1640 plus serum medium were incubated for 4h at 4ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 64 years old, female, serum+, 4ºC

treatment_protocol: For gene expression studies, 5x10^6 CD4+ T cells in either 3 ml RPMI 1640 medium with serum or AIM V serum-free media were incubated for 4h either at 37ºC or 4ºC (5% CO2 incubator).

value: 64 years

value: serum+ medium, incubation at 4ºC for 4h


title: CD4+T cells_75 year Male_Serum Free_4ºC_Replicate-6

description:
Replicate-6
Treatment serum+/- and temperature: 5x10^6 CD4+ T cells in 3 ml AIM V serum-free medium were incubated for 4h at 4ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 75 years old, male, serum-free, 4ºC

value: 75 years

value: serum-free medium, incubation at 4ºC for 4h


title: CD4+T cells_66 year Male_Serum+_37ºC_Replicate-5

description:
Replicate-5
Treatment serum+/- and temperature: 5x10^6 CD4+ T cells in 3 ml RPMI 1640 plus serum medium were incubated for 4h at 37ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 66 years old, male, serum+, 37ºC

value: 66 years

value: serum+ medium, incubation at 37ºC for 4h


title: CD4+T cells_81 year Female_37ºC_Replicate-3

description:
Sample name: D37_81BL2F37_46A
Replicate-3
1x10^7 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 37ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 81 years old, female, 37ºC

value: 81 years

value: female

value: incubation at 37ºC for 4h


title: CD4+T cells_75 year Male_Serum+_4ºC_Replicate-6

description:
Replicate-6
Treatment serum+/- and temperature: 5x10^6 CD4+ T cells in 3 ml RPMI 1640 plus serum medium were incubated for 4h at 4ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 75 years old, male, serum+, 4ºC

value: male


title: CD4+T cells_79 year Male_37ºC_Replicate-5

description:
Sample name: D37_79BL39M37_44
Replicate-5
1x10^7 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 37ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 79 years old, male, 37ºC

value: 79 years


title: CD4+T cells_32 year Male_Serum Free_4ºC_Replicate-3

description:
Replicate-3
Treatment serum+/- and temperature: 5x10^6 CD4+ T cells in 3 ml AIM V serum-free medium were incubated for 4h at 4ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 32 years old, male, serum-free, 4ºC

value: 32 years


title: CD4+T cells_35 year Female_4ºC_Replicate-2

description:
Sample name: D4_35BL60F4_5
Replicate-2
1x10^7 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 4ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 35 years old, female, 4ºC

value: 35 years


title: CD4+T cells_25 year Male_Serum Free_4ºC_Replicate-1

description:
Replicate-1
Treatment serum+/- and temperature: 5x10^6 CD4+ T cells in 3 ml AIM V serum-free medium were incubated for 4h at 4ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 25 years old, male, serum-free, 4ºC

value: 25 years

value: CD4+ T cells


title: CD4+T cells_66 year Male_Serum Free_4ºC_Replicate-5

description:
Replicate-5
Treatment serum+/- and temperature: 5x10^6 CD4+ T cells in 3 ml AIM V serum-free medium were incubated for 4h at 4ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 66 years old, male, serum-free, 4ºC


title: CD4+T cells_25 year Male_Serum+_4ºC_Replicate-1

description:
Replicate-1
Treatment serum+/- and temperature: 5x10^6 CD4+ T cells in 3 ml RPMI 1640 plus serum medium were incubated for 4h at 4ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 25 years old, male, serum+, 4ºC


title: CD4+T cells_29 year Female_4ºC_Replicate-1

description:
Sample name: D4_29ND60F4_1
Replicate-1
1x10^7 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 4ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 29 years old, female, 4ºC

value: 29 years

value: incubation at 4ºC for 4h


title: CD4+T cells_36 year Male_Serum+_4ºC_Replicate-4

description:
Replicate-4
Treatment serum+/- and temperature: 5x10^6 CD4+ T cells in 3 ml RPMI 1640 plus serum medium were incubated for 4h at 4ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 36 years old, male, serum+, 4ºC

value: 36 years


title: CD4+T cells_82 year Male_37ºC_Replicate-6

description:
Sample name: D37_82BL54M37_48
Replicate-6
1x10^7 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 37ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 82 years old, male, 37ºC

value: 82 years


title: CD4+T cells_34 year Female_Serum Free_4ºC_Replicate-1

source_name: CD4+ T cells, 34 years old, female, serum-free, 4ºC

value: 34 years


title: CD4+T cells_64 year Female_Serum+_37ºC_Replicate-2

description:
Replicate-2
Treatment serum+/- and temperature: 5x10^6 CD4+ T cells in 3 ml RPMI 1640 plus serum medium were incubated for 4h at 37ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 64 years old, female, serum+, 37ºC

value: 64 years


title: CD4+T cells_64 year Female_Serum Free_4ºC_Replicate-2

description:
Replicate-2
Treatment serum+/- and temperature: 5x10^6 CD4+ T cells in 3 ml AIM V serum-free medium were incubated for 4h at 4ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 64 years old, female, serum-free, 4ºC

value: serum-free medium, incubation at 4ºC for 4h


title: CD4+T cells_76 year Male_37ºC_Replicate-4

description:
Sample name: D37_76BL45M37_36
Replicate-4
1x10^7 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 37ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 76 years old, male, 37ºC

value: 76 years


title: CD4+T cells_44 year Male_4ºC_Replicate-3

description:
Sample name: D4_44BL25M4_9
Replicate-3
1x10^7 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 4ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 44 years old, male, 4ºC

value: 44 years


title: CD4+T cells_34 year Female_Serum+_4ºC_Replicate-1

source_name: CD4+ T cells, 34 years old, female, serum+, 4ºC

value: female

value: serum+ medium, incubation at 4ºC for 4h


title: CD4+T cells_32 year Male_Serum+_4ºC_Replicate-3

description:
Replicate-3
Treatment serum+/- and temperature: 5x10^6 CD4+ T cells in 3 ml RPMI 1640 plus serum medium were incubated for 4h at 4ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 32 years old, male, serum+, 4ºC

value: male


title: CD4+T cells_30 year Male_4ºC_Replicate-1

description:
Sample name: D4_30BL10M4_3B
Replicate-1
1x10^7 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 4ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 30 years old, male, 4ºC

value: 30 years


title: CD4+T cells_30 year Male_Serum Free_4ºC_Replicate-2

source_name: CD4+ T cells, 30 years old, male, serum-free, 4ºC


title: CD4+T cells_75 year Male_Serum+_37ºC_Replicate-6

description:
Replicate-6
Treatment serum+/- and temperature: 5x10^6 CD4+ T cells in 3 ml RPMI 1640 plus serum medium were incubated for 4h at 37ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 75 years old, male, serum+, 37ºC

value: 75 years

value: serum+ medium, incubation at 37ºC for 4h


title: CD4+T cells_36 year Male_Serum Free_4ºC_Replicate-4

description:
Replicate-4
Treatment serum+/- and temperature: 5x10^6 CD4+ T cells in 3 ml AIM V serum-free medium were incubated for 4h at 4ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 36 years old, male, serum-free, 4ºC


title: CD4+T cells_30 year Male_Serum+_4ºC_Replicate-2

description:
Replicate-2
Treatment serum+/- and temperature: 5x10^6 CD4+ T cells in 3 ml RPMI 1640 plus serum medium were incubated for 4h at 4ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 30 years old, male, serum+, 4ºC


title: CD4+T cells_36 year Male_Serum+_37ºC_Replicate-4

description:
Replicate-4
Treatment serum+/- and temperature: 5x10^6 CD4+ T cells in 3 ml RPMI 1640 plus serum medium were incubated for 4h at 37ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 36 years old, male, serum+, 37ºC


title: CD4+T cells_30 year Male_Serum+_37ºC_Replicate-2

source_name: CD4+ T cells, 30 years old, male, serum+, 37ºC


title: CD4+T cells_74 year Male_37ºC_Replicate-3

description:
Sample name: D37_74BL36M37_34
Replicate-3
1x10^7 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 37ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 74 years old, male, 37ºC

value: 74 years

value: incubation at 37ºC for 4h


title: CD4+T cells_25 year Male_Serum+_37ºC_Replicate-1

description:
Replicate-1
Treatment serum+/- and temperature: 5x10^6 CD4+ T cells in 3 ml RPMI 1640 plus serum medium were incubated for 4h at 37ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 25 years old, male, serum+, 37ºC

value: 25 years

value: CD4+ T cells


title: CD4+T cells_66 year Male_Serum Free_37ºC_Replicate-5

description:
Replicate-5
Treatment serum+/- and temperature: 5x10^6 CD4+ T cells in 3 ml AIM V serum-free medium were incubated for 4h at 37ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 66 years old, male, serum-free, 37ºC

value: 66 years

value: serum-free medium, incubation at 37ºC for 4h


title: CD4+T cells_75 year Male_Serum Free_37ºC_Replicate-6

description:
Replicate-6
Treatment serum+/- and temperature: 5x10^6 CD4+ T cells in 3 ml AIM V serum-free medium were incubated for 4h at 37ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 75 years old, male, serum-free, 37ºC


title: CD4+T cells_73 year old_Male_Old_Replicate-4

description:
Sample name: B7M73O
Replicate-4
Streptavidin-Cy3 bound to biotin-labeled cRNA.

hyb_protocol: Standard Illumina protocol. In short, a total of 0.75ug of biotin-labeled cRNA was hybridized at 58 degrees C for 16 hours to Illumina's humanRef-8 v2.0 Expression BeadChip (Illumina, San Diego, CA). Each BeadChip has ~20,000 well-annotated RefSeq transcripts with approximately 30-fold redundancy. The arrays were washed, blocked and the biotin-labeled cRNA was detected by staining with streptavidin-Cy3.

data_processing: Data was extracted using the Illumina BeadStudio software (v3.0). Any spots at or below the background were filtered out using an Illumina detection value of 0.98 and below. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below. Z-score = (raw value - avg)/std. Complete data including detection scores are included in the supplemental file.

source_name: CD4+ T cells, 73 years old, male

treatment_protocol: For gene expression studies, 1x10^7 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 37ºC (5% CO2 incubator) before RNA isolation.

value: 73 years


title: CD4+T cells_73 year Female_37ºC_Replicate-2

description:
Sample name: D37_73BL50F37_40
Replicate-2
1x10^7 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 37ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 73 years old, female, 37ºC


title: CD4+T cells_32 year Male_Serum Free_37ºC_Replicate-3

description:
Replicate-3
Treatment serum+/- and temperature: 5x10^6 CD4+ T cells in 3 ml AIM V serum-free medium were incubated for 4h at 37ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 32 years old, male, serum-free, 37ºC

value: 32 years


title: CD4+T cells_55 year old_Female_Young_Replicate-8

description:
Sample name: B8F55Y
Replicate-8
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 55 years old, female

value: 55 years


title: CD4+T cells_36 year Male_Serum Free_37ºC_Replicate-4

description:
Replicate-4
Treatment serum+/- and temperature: 5x10^6 CD4+ T cells in 3 ml AIM V serum-free medium were incubated for 4h at 37ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 36 years old, male, serum-free, 37ºC

value: 36 years


title: CD4+T cells_75 year old_Male_Old_Replicate-5

description:
Sample name: B9M75O
Replicate-5
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 75 years old, male


title: CD4+T cells_30 year Male_Serum Free_37ºC_Replicate-2

description:
Replicate-2
Treatment serum+/- and temperature: 5x10^6 CD4+ T cells in 3 ml AIM V serum-free medium were incubated for 4h at 37ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 30 years old, male, serum-free, 37ºC


title: CD4+T cells_52 year old_Male_Young_Replicate-11

description:
Sample name: N36M52Y
Replicate-11
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 52 years old, male

value: 52 years


title: CD4+T cells_66 year Female_37ºC_Replicate-1

description:
Sample name: D37_66BL51F37_32
Replicate-1
1x10^7 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 37ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 66 years old, female, 37ºC

value: female


title: CD4+T cells_32 year Male_Serum+_37ºC_Replicate-3

description:
Replicate-3
Treatment serum+/- and temperature: 5x10^6 CD4+ T cells in 3 ml RPMI 1640 plus serum medium were incubated for 4h at 37ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 32 years old, male, serum+, 37ºC


title: CD4+T cells_25 year Male_Serum Free_37ºC_Replicate-1

description:
Replicate-1
Treatment serum+/- and temperature: 5x10^6 CD4+ T cells in 3 ml AIM V serum-free medium were incubated for 4h at 37ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 25 years old, male, serum-free, 37ºC


title: CD4+T cells_30 year old_Male_Young_Replicate-10

description:
Sample name: N33M30Y
Replicate-10
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 30 years old, male


title: CD4+T cells_30 year old_Male_Young_Replicate-12

description:
Sample name: B10M30Y
Replicate-12
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: CD4+T cells_71 year old_Female_Old_Replicate-6

description:
Sample name: B6F71O
Replicate-6
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 71 years old, female

value: 71 years


title: CD4+T cells_52 year old_Male_Young_Replicate-9

description:
Sample name: N32M52Y
Replicate-9
Streptavidin-Cy3 bound to biotin-labeled cRNA.

value: male


title: CD4+T cells_34 year Female_Serum Free_37ºC_Replicate-1

source_name: CD4+ T cells, 34 years old, female, serum-free, 37ºC

value: 34 years


title: CD4+T cells_63 year Male_37ºC_Replicate-9

description:
Sample name: D37_63BL24M37_24
Replicate-9
1x10^7 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 37ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 63 years old, male, 37ºC

value: 63 years


title: CD4+T cells_67 year Male_37ºC_Replicate-1

description:
Sample name: D37_67BL30M37_26
Replicate-1
1x10^7 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 37ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 67 years old, male, 37ºC

value: 67 years


title: CD4+T cells_64 year Female_Serum Free_37ºC_Replicate-2

source_name: CD4+ T cells, 64 years old, female, serum-free, 37ºC

value: 64 years


title: CD4+T cells_34 year Female_Serum+_37ºC_Replicate-1

description:
Replicate-1
Treatment serum+/- and temperature: 5x10^6 CD4+ T cells in 3 ml RPMI 1640 plus serum medium were incubated for 4h at 37ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 34 years old, female, serum+, 37ºC

value: serum+ medium, incubation at 37ºC for 4h


title: CD4+T cells_62 year Female_37ºC_Replicate-5

description:
Sample name: D37_62BL32F37_28
Replicate-5
1x10^7 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 37ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 62 years old, female, 37ºC

value: 62 years

value: incubation at 37ºC for 4h


title: CD4+T cells_72 year Male_37ºC_Replicate-2

description:
Sample name: D37_72BL56M37_42
Replicate-2
1x10^7 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 37ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 72 years old, male, 37ºC

value: 72 years

value: CD4+ T cells


title: CD4+T cells_83 year old_Male_Old_Replicate-14

description:
Sample name: 0_83M_B74
Replicate-14
Streptavidin-Cy3 bound to biotin-labeled cRNA.

data_processing: Data was extracted using the Illumina GenomeStudio software (ver 1.6.0). Any spots at or below the background were filtered out using an Illumina detection value of 0.98 and below. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below. Z-score = (raw value - avg)/std. Complete data including detection scores are included in the supplemental file.

source_name: CD4+ T cells, 83 years old, male

value: 83 years


title: CD4+T cells_56 year Male_37ºC_Replicate-7

description:
Sample name: D37_56BL28M37_18
Replicate-7
1x10^7 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 37ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 56 years old, male, 37ºC

value: 56 years


title: CD4+T cells_76 year old_Male_Old_Replicate-11

description:
Sample name: 0_76M_B66
Replicate-11
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 76 years old, male

value: 76 years


title: CD4+T cells_75 year old_Male_Old_Replicate-10

description:
Sample name: 0_75M_B63
Replicate-10
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 75 years old, male


title: CD4+T cells_77 year old_Male_Old_Replicate-12

description:
Sample name: 0_77M_B49
Replicate-12
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 77 years old, male

value: 77 years


title: CD4+T cells_53 year Female_37ºC_Replicate-4

description:
Sample name: D37_53BL53F37_22
Replicate-4
1x10^7 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 37ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 53 years old, female, 37ºC

value: 53 years


title: CD4+T cells_74 year old_Male_Old_Replicate-8

description:
Sample name: 0_74M_B70
Replicate-8
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 74 years old, male

value: 74 years


title: CD4+T cells_83 year old_Male_Old_Replicate-13

description:
Sample name: 0_83M_B64
Replicate-13
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: CD4+T cells_81 year old_Female_Old_Replicate-3

description:
Sample name: B2F81O
Replicate-3
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 81 years old, female

value: 81 years

value: female


title: CD4+T cells_71 year old_Female_Old_Replicate-5

description:
Sample name: N31F71O
Replicate-5
Streptavidin-Cy3 bound to biotin-labeled cRNA.

value: 71 years


title: CD4+T cells_77 year old_Male_Old_Replicate-3

description:
Sample name: B5M77O
Replicate-3
Streptavidin-Cy3 bound to biotin-labeled cRNA.

value: male


title: CD4+T cells_25 year old_Male_Young_Replicate-7

description:
Sample name: N29M25Y
Replicate-7
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 25 years old, male

value: 25 years


title: CD4+T cells_50 year old_Male_Young_Replicate-8

description:
Sample name: B4M60Y
Replicate-8
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 50 years old, male

value: 50 years


title: CD4+T cells_55 year old_Female_Young_Replicate-7

description:
Sample name: B1F55Y
Replicate-7
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 55 years old, female

value: 55 years


title: CD4+T cells_44 year Male_37ºC_Replicate-4

description:
Sample name: D37_44BL44M37_14
Replicate-4
1x10^7 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 37ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 44 years old, male, 37ºC

value: 44 years


title: CD4+T cells_49 year Female_37ºC_Replicate-3

description:
Sample name: D37_49BL35F37_12
Replicate-3
1x10^7 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 37ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 49 years old, female, 37ºC

value: 49 years

value: incubation at 37ºC for 4h


title: CD4+T cells_75 year old_Female_Old_Replicate-4

description:
Sample name: 0_76F_B78
Replicate-4
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 75 years old, female

value: 75 years

value: CD4+ T cells


title: CD4+T cells_44 year Male_37ºC_Replicate-3

description:
Sample name: D37_44BL25M37_10
Replicate-3
1x10^7 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 37ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: CD4+T cells_75 year old_Male_Old_Replicate-9

description:
Sample name: 0_75M_B59
Replicate-9
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: CD4+T cells_73 year old_Male_Old_Replicate-5

description:
Sample name: 0_73M_B58
Replicate-5
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 73 years old, male

value: 73 years


title: CD4+T cells_71 year old_Male_Old_Replicate-3

description:
Sample name: 0_71M_B76
Replicate-3
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 71 years old, male


title: CD4+T cells_68 year old_Female_Old_Replicate-4

description:
Sample name: B3F68O
Replicate-4
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 68 years old, female

value: 68 years


title: CD4+T cells_68 year old_Female_Old_Replicate-3

description:
Sample name: 0_68F_B73
Replicate-3
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: CD4+T cells_52 year Male_37ºC_Replicate-5

description:
Sample name: D37_52BL27M37_16
Replicate-5
1x10^7 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 37ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 52 years old, male, 37ºC

value: 52 years


title: CD4+T cells_54 year Male_37ºC_Replicate-6

description:
Sample name: D37_54BL33M37_20
Replicate-6
1x10^7 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 37ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 54 years old, male, 37ºC

value: 54 years


title: CD4+T cells_72 year old_Male_Old_Replicate-4

description:
Sample name: 0_72M_B56
Replicate-4
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 72 years old, male

value: 72 years


title: CD4+T cells_70 year old_Male_Old_Replicate-2

description:
Sample name: 0_70M_B57
Replicate-2
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 70 years old, male

value: 70 years


title: CD4+T cells_73 year old_Male_Old_Replicate-6

description:
Sample name: 0_73M_B67
Replicate-6
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: CD4+T cells_66 year Male_Serum+_4ºC_Replicate-5

description:
Replicate-5
Treatment serum+/- and temperature: 5x10^6 CD4+ T cells in 3 ml RPMI 1640 plus serum medium were incubated for 4h at 4ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 66 years old, male, serum+, 4ºC

value: 66 years

value: serum+ medium, incubation at 4ºC for 4h


title: CD4+T cells_61 year Male_37ºC_Replicate-8

description:
Sample name: D37_61BL38M37_30
Replicate-8
1x10^7 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 37ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 61 years old, male, 37ºC

value: 61 years

value: male


title: CD4+T cells_73 year old_Male_Old_Replicate-7

description:
Sample name: 0_73M_B68
Replicate-7
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: CD4+T cells_52 year old_Male_Old_Replicate-2

description:
Sample name: B22M72O
Replicate-2
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 52 years old, male


title: CD4+T cells_29 year old_Female_Young_Replicate-6

description:
Sample name: N60F29Y
Replicate-6
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 29 years old, female

value: 29 years

value: female


title: CD4+T cells_35 year old_Female_Young_Replicate-1

description:
Sample name: 0_35F_B60
Replicate-1
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 35 years old, female

value: 35 years


title: CD4+T cells_68 year old_Female_Old_Replicate-2

description:
Sample name: 0_68F_B52
Replicate-2
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: CD4+T cells_62 year old_Female_Young_Replicate-4

description:
Sample name: B20F62Y
Replicate-4
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 62 years old, female

value: 62 years


title: CD4+T cells_41 year old_Female_Young_Replicate-5

description:
Sample name: N58F41Y
Replicate-5
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 41 years old, female

value: 41 years

value: incubation at 37ºC for 4h


title: CD4+T cells_52 year old_Male_Young_Replicate-6

description:
Sample name: N59M52Y
Replicate-6
Streptavidin-Cy3 bound to biotin-labeled cRNA.

value: CD4+ T cells


title: CD4+T cells_40 year Male_37ºC_Replicate-2

description:
Sample name: D37_40ND55M37_8
Replicate-2
1x10^7 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 37ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 40 years old, male, 37ºC

value: 40 years


title: CD4+T cells_35 year Female_37ºC_Replicate-2

description:
Sample name: D37_35BL60F37_6
Replicate-2
1x10^7 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 37ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 35 years old, female, 37ºC


title: CD4+T cells_29 year Female_37ºC_Replicate-1

description:
Sample name: D37_29ND60F37_2
Replicate-1
1x10^7 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 37ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 29 years old, female, 37ºC


title: CD4+T cells_30 year Male_37ºC_Replicate-1

description:
Sample name: D37_30BL10M37_4
Replicate-1
1x10^7 CD4+ T cells in 3 ml RPMI 1640 medium were incubated for 4h at 37ºC (5% CO2 incubator) before RNA isolation.
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 30 years old, male, 37ºC

value: 30 years


title: CD4+T cells_33 year old_Male_Young_Replicate-4

description:
Sample name: 0_33M_N554
Replicate-4
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 33 years old, male

value: 33 years


title: CD4+T cells_55 year old_Male_Young_Replicate-5

description:
Sample name: B21M55Y
Replicate-5
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 55 years old, male

value: 55 years


title: CD4+T cells_66 year old_Male_Old_Replicate-1

description:
Sample name: 0_66M_B61
Replicate-1
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 66 years old, male


title: CD4+T cells_26 year old_Male_Young_Replicate-1

description:
Sample name: 0_26M_N703
Replicate-1
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 26 years old, male

value: 26 years


title: CD4+T cells_43 year old_Male_Young_Replicate-2

description:
Sample name: N53M43Y
Replicate-2
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 43 years old, male

value: 43 years


title: CD4+T cells_63 year old_Male_Young_Replicate-3

description:
Sample name: B18M63Y
Replicate-3
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 63 years old, male

value: 63 years


title: CD4+T cells_70 year old_Male_Old_Replicate-1

description:
Sample name: B17M70O
Replicate-1
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 70 years old, male

value: 70 years


title: CD4+T cells_70 year old_Female_Old_Replicate-2

description:
Sample name: B16F70O
Replicate-2
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 70 years old, female


title: CD4+T cells_40 year old_Male_Young_Replicate-4

description:
Sample name: N55M40Y
Replicate-4
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 40 years old, male


title: CD4+T cells_30 year old_Male_Young_Replicate-3

description:
Sample name: 0_30M_N340
Replicate-3
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 30 years old, male


title: CD4+T cells_60 year old_Male_Young_Replicate-1

description:
Sample name: B12M60Y
Replicate-1
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 60 years old, male

value: 60 years


title: CD4+T cells_61 year old_Female_Young_Replicate-2

description:
Sample name: B19F61Y
Replicate-2
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 61 years old, female

value: 61 years


title: CD4+T cells_28 year old_Male_Young_Replicate-2

description:
Sample name: 0_28M_N691
Replicate-2
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 28 years old, male

value: 28 years

value: male


title: CD4+T cells_57 year old_Female_Young_Replicate-1

description:
Sample name: B11F57Y
Replicate-1
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 57 years old, female

value: 57 years

value: female


title: CD4+T cells_75 year old_Female_Old_Replicate-1

description:
Sample name: B13F75O
Replicate-1
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 75 years old, female

value: 75 years


title: WT_1B_Replicate_4

status: Public on Jan 05 2015

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

source_name: Prefrontal cortex 20- month_Wt

growth_protocol: All mice were maintained on a standard NIH diet with free access to water during a 12 hour light/dark cycle. Animals were group housed where possible through-out the experimental period. 3xTgAD and Pol β (+/-) mice were bred at the National Institute on Aging (Baltimore, Maryland). The original line, 3xTgAD possess APPswe, PS1M146V, and tauP301L mutations. DNA polymerase beta heterozygous mice, Pol β (+/-), were crossed with the 3xTgAD mice to generate the 3xTgAD/Polb+/- mice.

extract_protocol: RNA was extracted from tissue using TRIzol® reagent (Invitrogen) and refined using RNA clean & concentrate™ (Zymo research). Samples were assessed for quality and quantity using a 2100 Bioanlyzer with RNA 6000 Nano Chips, (Aligent technologies).

treatment_protocol: At 20 months of age, mice were euthanized by cervical dislocation, with the brain removed from the skull and dissected into regions of interest, the prefrontal cortex was used for the microarray studies.

tag: strain

value: wild type

value: prefrontal cortex


title: CD4+T cells_66 year old_Female_Old_Replicate-1

description:
Sample name: 0_66F_B75
Replicate-1
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 66 years old, female

value: 66 years

value: CD4+ T cells

tag: treatment

value: incubation at 37ºC for 4h


title: WT_1C_Replicate_5

tag: gender


title: CD4+T cells_40 year old_Female_Young_Replicate-3

description:
Sample name: N57F40Y
Replicate-3
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: CD4+ T cells, 40 years old, female

value: 40 years


title: WT_1D_Replicate_1

source_name: Prefrontal cortex 20 month_Wt


title: WT_1E_Replicate_2


title: PB_POLB_2C_Replicate_3

source_name: Prefrontal cortex 20- month_POLB

value: POLB+/-


title: PB_POLB_2D_Replicate_4

source_name: Prefrontal cortex 20 month_POLB


title: WT_1A_Replicate_3


title: PB_POLB_2B_Replicate_2


title: AD_3XTG_3E_Replicate_2

source_name: Prefrontal cortex 20 month_3XTG


title: ADPB_3XTGPOLB_4E_Replicate_4

source_name: Prefrontal cortex 20 month_3XTGPOLB


title: ADPB_3XTGPOLB_4D_Replicate_3


title: PB_POLB_2A_Replicate_1


title: AD_3XTG_3D_Replicate_1


title: AD_3XTG_3F_Replicate_3


title: AD_3XTG_3B_Replicate_6

source_name: Prefrontal cortex 20- month_3XTG


title: AD_3XTG_3A_Replicate_5


title: ADPB_3XTGPOLB_4B_Replicate_1

source_name: Prefrontal cortex 20- month_3XTGPOLB


title: ADPB_3XTGPOLB_4C_Replicate_2


title: AD_3XTG_3C_Replicate_4


title: Wt Mouse_cerebellum_Young_nicotinamide riboside treatment_Replicate-1

status: Public on Dec 22 2014

description:
Sample name: YOUNG-Wt_NR-13
Streptavidin-Cy3 bound to biotin-labeled cRNA.

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

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

source_name: Wt mouse, cerebellum, young, nicotinamide riboside treatment

growth_protocol: Animal rooms were maintained at ~20°C and a 12-hour light/dark cycle. 4- or 18-month-old Csbm/m or WT male mice were maintained on house chow (Harlan Teklad, Madison WI).

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

treatment_protocol: WT and Csbm/m mice were given daily injections of NR (500 mg/kg/d, ip) or saline for one week, after which the mice were sacrificed and the cerebellum was removed for further experiments.

value: WT

value: cerebellum

value: 4 months

value: daily injections of NR (500 mg/kg/d, ip) for one week


title: Wt Mouse_cerebellum_Young_saline treatment_Replicate-4

description:
Sample name: YOUNG-WT_ctrl-6
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: Wt mouse, cerebellum, young, saline treatment

value: daily injections of saline for one week


title: Wt Mouse_cerebellum_Young_nicotinamide riboside treatment_Replicate-3

description:
Sample name: YOUNG-Wt_NR-4
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Wt Mouse_cerebellum_Young_saline treatment_Replicate-2

description:
Sample name: YOUNG-WT_ctrl-14
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Wt Mouse_cerebellum_Young_nicotinamide riboside treatment_Replicate-2

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


title: Wt Mouse_cerebellum_Young_nicotinamide riboside treatment_Replicate-4

description:
Sample name: YOUNG-Wt_NR-9
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Wt Mouse_cerebellum_Young_saline treatment_Replicate-3

description:
Sample name: YOUNG-WT_ctrl-5
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Wt Mouse_cerebellum_Young_saline treatment_Replicate-1

description:
Sample name: YOUNG-WT_ctrl-10
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Csbm/m Mouse_cerebellum_Young_saline treatment_Replicate-3

description:
Sample name: YOUNG-CSB_ctrl-8
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: Csbm/m mouse, cerebellum, young, saline treatment

value: Csbm/m


title: Csbm/m Mouse_cerebellum_Young_nicotinamide riboside treatment_Replicate-1

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

source_name: Csbm/m mouse, cerebellum, young, nicotinamide riboside treatment

value: male


title: Wt Mouse_cerebellum_Old_nicotinamide riboside treatment_Replicate-3

description:
Sample name: OLD-Wt_NR-25
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: Wt mouse, cerebellum, old, nicotinamide riboside treatment

value: 18 months


title: Csbm/m Mouse_cerebellum_Young_nicotinamide riboside treatment_Replicate-2

description:
Sample name: YOUNG-CSB_NR-11
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Wt Mouse_cerebellum_Old_nicotinamide riboside treatment_Replicate-2

description:
Sample name: OLD-Wt_NR-21
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Wt Mouse_cerebellum_Old_saline treatment_Replicate-3

description:
Sample name: OLD-WT_ctrl-26
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: Wt mouse, cerebellum, old, saline treatment


title: Wt Mouse_cerebellum_Old_nicotinamide riboside treatment_Replicate-4

description:
Sample name: OLD-Wt_NR-27
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Csbm/m Mouse_cerebellum_Young_nicotinamide riboside treatment_Replicate-3

description:
Sample name: YOUNG-CSB_NR-7
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Csbm/m Mouse_cerebellum_Old_nicotinamide riboside treatment_Replicate-1

description:
Sample name: OLD-CSB_NR-15
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: Csbm/m mouse, cerebellum, old, nicotinamide riboside treatment


title: Wt Mouse_cerebellum_Old_nicotinamide riboside treatment_Replicate-1

description:
Sample name: OLD-Wt_NR-18
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Wt Mouse_cerebellum_Old_nicotinamide riboside treatment_Replicate-5

description:
Sample name: OLD-Wt_NR-28
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Csbm/m Mouse_cerebellum_Young_saline treatment_Replicate-1

description:
Sample name: YOUNG-CSB_ctrl-12
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Wt Mouse_cerebellum_Standard diet Ad Lib_Replicate-4

description:
Sample name: WT_SD_5
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: Wt mouse, cerebellum, standard diet ad lib

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

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

value: 1 year

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


title: Csbm/m Mouse_cerebellum_Old_saline treatment_Replicate-2

description:
Sample name: OLD-CSB_ctrl-21
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: Csbm/m mouse, cerebellum, old, saline treatment


title: Csbm/m Mouse_cerebellum_Old_nicotinamide riboside treatment_Replicate-2

description:
Sample name: OLD-CSB_NR-16
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Csbm/m Mouse_cerebellum_Old_saline treatment_Replicate-3

description:
Sample name: OLD-CSB_ctrl-24
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Csbm/m Mouse_cerebellum_Old_nicotinamide riboside treatment_Replicate-3

description:
Sample name: OLD-CSB_NR-20
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Wt Mouse_cerebellum_Old_saline treatment_Replicate-2

description:
Sample name: OLD-WT_ctrl-22
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Csbm/m Mouse_cerebellum_Old_saline treatment_Replicate-1

description:
Sample name: OLD-CSB_ctrl-17
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Csbm/m Mouse_cerebellum_Young_saline treatment_Replicate-2

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


title: Csbm/m Mouse_cerebellum_Old_nicotinamide riboside treatment_Replicate-4

description:
Sample name: OLD-CSB_NR-23
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Wt Mouse_cerebellum_Old_saline treatment_Replicate-1

description:
Sample name: OLD-WT_ctrl-19
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Wt Mouse_cerebellum_Standard diet supplemented with resveratrol_Ad Lib_Replicate-1

description:
Sample name: WT_Resv_2
Streptavidin-Cy3 bound to biotin-labeled cRNA.

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

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


title: Wt Mouse_cerebellum_Standard diet supplemented with resveratrol_Ad Lib_Replicate-3

description:
Sample name: WT_Resv_4
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Wt Mouse_cerebellum_High Fat diet Ad Lib_Replicate-2

description:
Sample name: WT_HFD_4
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: Wt mouse, cerebellum, high-fat diet ad lib

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


title: Wt Mouse_cerebellum_High Fat diet Ad Lib_Replicate-1

description:
Sample name: WT_HFD_3
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Wt Mouse_cerebellum_High Fat diet Ad Lib_Replicate-3

description:
Sample name: WT_HFD_5
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Wt Mouse_cerebellum_High Fat diet Ad Lib_Replicate-4

description:
Sample name: WT_HFD_6
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Wt Mouse_cerebellum_Caloric restricted diet_Replicate-4

description:
Sample name: WT_CR_6
Streptavidin-Cy3 bound to biotin-labeled cRNA.

source_name: Wt mouse, cerebellum, caloric-restricted diet

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


title: Wt Mouse_cerebellum_Standard diet supplemented with resveratrol_Ad Lib_Replicate-5

description:
Sample name: WT_Resv_6
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Wt Mouse_cerebellum_Standard diet Ad Lib_Replicate-2

description:
Sample name: WT_SD_3
Streptavidin-Cy3 bound to biotin-labeled cRNA.


title: Wt Mouse_cerebellum_Standard diet Ad Lib_Replicate-1

description:
Sample name: WT_SD_2
Streptavidin-Cy3 bound to biotin-labeled cRNA.