title: HeLa-Con-miR Replicate-3

description: HeLa-Con-miR Replicate-3


title: HeLa-miR-1248 Replicate-2 REPEAT

status: Public on Oct 09 2013

type: RNA

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

country: USA

institute: NIA-IRP, NIH

description: HeLa-miR-1248 Replicate-2 REPEAT

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.

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

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

label: Streptavidin-Cy3 bound to biotin labeled cRNA.

molecule: total RNA

organism: Homo sapiens

source_name: HeLa-miR-1248-2 REPEAT

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

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

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

tag: cell line

value: HeLa Cells

tag: treatment

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


title: WT_WD146_56

status: Public on Aug 01 2013

description: Human subjects from an age matched control group eating a typical Western diet.

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

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

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

source_name: Percutaneous biopsy specimens of vastus lateralis muscle from aged matched control participants following a Western diet.

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

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

tag: biopsy

value: Percutaneous biopsy specimens of vastus lateralis muscle.


title: WT_WD124_69

treatment_protocol: Percutaneous biopsy specimens of vastus lateralis muscle from aged matched control participants following a Western diet.


title: WT_WD_127_56

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


title: HeLa-Con-miR Replicate-1 REPEAT

description: HeLa-Con-miR Replicate-1 REPEAT

source_name: HeLa-Con-miR-1 REPEAT

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


title: HeLa-miR-1248 Replicate-3

description: HeLa-miR-1248 Replicate-3


title: HeLa-miR-1248 Replicate-3 REPEAT

description: HeLa-miR-1248 Replicate-3 REPEAT

source_name: HeLa-miR-1248-3 REPEAT


title: HeLa-miR-1248 Replicate-2

description: HeLa-miR-1248 Replicate-2


title: HeLa-Con-miR Replicate-3 REPEAT

description: HeLa-Con-miR Replicate-3 REPEAT

source_name: HeLa-Con-miR-3 REPEAT


title: WT_WD143_53


title: WT_WD_148_53


title: HeLa-miR-1248 Replicate-1 REPEAT

description: HeLa-miR-1248 Replicate-1 REPEAT

source_name: HeLa-miR-1248-1 REPEAT


title: CR_CR60_49

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

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


title: Muscle_AICAR-3days_Replicate-3

status: Public on Jan 17 2014

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

data_processing: Data was extracted using the Illumina BeadStudio software(v1.6.0).  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.

organism: Mus musculus

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

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

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

tag: strain

tag: gender

value: female

tag: age

value: 23 months old

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

tag: tissue

value: gastrocnemius muscle


title: WT_WD145_54


title: WT_WD142_50


title: CR_CR73_47

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


title: CR_CR65_58


title: CR_CR78_63


title: CR_CR54_57


title: WT_WD136_60


title: CR_CR130_56


title: CR_CR134_66


title: CR_CR52_39


title: CR_CR123_67


title: CR_CR133_65


title: CR_CR129_54


title: CR_CR53_55


title: WT_CC071207_71


title: CR_CR124_52


title: 7-Old AL

description:
Animals at 27 months of age were sacrificed and the vastus lateralis muscle was flash frozen.
Rattus norvegicus (Fischer-344), vastus lateralis muscle from animals maintained on AL feeding from 2-27 months of age.

hyb_protocol: standard Illumina protocol. In short, a total of 0.75ug of biotin-labeled cRNA was hybridized at 58 degrees C for 16 hours to Illumina's Sentrix Rat Ref-12,v1 Expression BeadChips (Illumina, San Diego, CA). Each BeadChip has 22,000 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 Gene Expression 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 values is included in the supplemental file.

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

organism: Rattus norvegicus

treatment_protocol: 2 month old male Fischer-344 rats were assigned to the ad libitum (AL) group, and fed(AL) throughout their lifespan.  All animals were fed a NIH-31 standard chow (Harlan Teklad, Indianapolis, IN, USA). Rats were singly housed in an environmentally controlled vivarium with unlimited access to water and a controlled photoperiod (12 hr. light;12 hr. dark). Body weights and food intake were recorded biweekly.  All rats were maintained between 68-72°F according to animal protocols and NIH guidelines.

tag: diet

value: AL

value: vastus lateralis muscle


title: 4-Old CR

description:
Animals at 27 months of age were sacrificed and the vastus lateralis muscle was flash frozen.
Rattus norvegicus (Fischer-344), vastus lateralis muscle from animals maintained on 40% CR from 2-27 months of age.

treatment_protocol: 2 month old male Fischer-344 rats were assigned to the caloric restriction(CR) group and were progressively brought down to a 40% CR. Animals were fed a NIH-31 standard chow (Harlan Teklad, Indianapolis, IN, USA). Rats were singly housed in an environmentally controlled vivarium with unlimited access to water and a controlled photoperiod (12 hr. light;12 hr. dark). Body weights and food intake were recorded biweekly.  All rats were maintained between 68-72°F according to animal protocols and NIH guidelines.

value: CR


title: 6-Old AL

source_name: Rattus norvegicus (Fischer-344), vastus lateralis muscle


title: 5-Old CR


title: 3-Old CR


title: 10-Old AL

description: =  Rattus norvegicus (Fischer-344), vastus lateralis muscle from animals maintained on AL feeding from 2-27 months of age.

tag: Animals at 27 months of age were sacrificed and the vastus lateralis muscle was flash frozen.


title: 2-Old CR


title: HeLa-Con-miR Replicate-2 REPEAT

description: HeLa-Con-miR Replicate-2 REPEAT

source_name: HeLa-Con-miR-2 REPEAT


title: 8-Old AL


title: 9-Old AL


title: 22-SD-MET-L

status: Public on Jul 31 2013

description:
supplementary file:GEO_Supplementary_file_AS_Liver 9-14-12
Liver tissue from one-year old male B6C57/J mice maintained on ad libitum AIN-93G SD and supplemented with 0.1% w/w metformin until the end of their life.

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

source_name: liver tissue

extract_protocol: RNA was extracted from liver tissue using 1.0mm glass beads (BioSpec Products, Inc.) in a Precellys 24 Tissue Homogenizer (Bertin Technologies) and Qiagen RNeasy Mini Kits according to manufacturer's specifications. Quality and quantity of the total RNA was checked with the Agilent 2100 bioanalyzer using RNA 6000 Nano chips.

value: Liver

value: one-year old

value: male


title: 21-SD-MET-L

treatment_protocol: Liver tissue from one-year old male B6C57/J mice maintained on ad libitum AIN-93G SD and supplemented with 0.1% w/w metformin until the end of their life.


title: 26-CR-L

description:
supplementary file:GEO_Supplementary_file_AS_Liver 9-14-12
Liver tissue from one-year old male B6C57/J mice were maintained on a 40% calorically restricted diet compared to an ad libitum AIN-93G diet for the rest of their lives.


title: 1-Old CR


title: 29-CR-L

treatment_protocol: Liver tissue from one-year old male B6C57/J mice were maintained on a 40% calorically restricted diet compared to an ad libitum AIN-93G diet for the rest of their lives.


title: 27-CR-L

value: maintained on a 40% calorically restricted diet


title: 25-CR-L


title: 28-CR-L


title: 4-SD-L

description:
supplementary file:GEO_Supplementary_file_AS_Liver 9-14-12
Liver tissue from one-year old male B6C57/J mice maintained on ad libitum AIN-93G SD until the end of their life.


title: 29-CR-M

description:
supplementary file:GEO_Supplementary_file_AS_Muscle 9-14-12
Muscle tissue from one-year old male B6C57/J mice were maintained on a 40% calorically restricted diet compared to an ad libitum AIN-93G diet for the rest of their lives.

source_name: muscle tissue

extract_protocol: RNA was extracted from muscle tissue using 1.0mm glass beads (BioSpec Products, Inc.) in a Precellys 24 Tissue Homogenizer (Bertin Technologies) and Qiagen RNeasy Mini Kits for Fibrous Tissue according to manufacturer's specifications. Quality and quantity of the total RNA was checked with the Agilent 2100 bioanalyzer using RNA 6000 Nano chips.

value: Muscle


title: 20-SD-MET-L

value: maintained on ad libitum AIN-93G SD and supplemented with 0.1% w/w metformin until the end of their life


title: 19-SD-MET-L


title: 3-SD-L

treatment_protocol: Liver tissue from one-year old male B6C57/J mice maintained on ad libitum AIN-93G SD until the end of their life.


title: 23-SD-MET-L


title: 1-SD-L

value: maintained on ad libitum AIN-93G SD until the end of their life


title: 23-SD-MET-M

description:
supplementary file:GEO_Supplementary_file_AS_Muscle 9-14-12
Muscle tissue from one-year old male B6C57/J mice maintained on ad libitum AIN-93G SD and supplemented with 0.1% w/w metformin until the end of their life.


title: 26-CR-M

treatment_protocol: Muscle tissue from one-year old male B6C57/J mice were maintained on a 40% calorically restricted diet compared to an ad libitum AIN-93G diet for the rest of their lives.


title: 2-SD-L


title: 25-CR-M


title: 20-SD-MET-M

treatment_protocol: Muscle tissue from one-year old male B6C57/J mice maintained on ad libitum AIN-93G SD and supplemented with 0.1% w/w metformin until the end of their life.


title: 21-SD-MET-M


title: 5-SD-L


title: 5-SD-M

description:
supplementary file:GEO_Supplementary_file_AS_Muscle 9-14-12
Muscle tissue from one-year old male B6C57/J mice maintained on ad libitum AIN-93G SD until the end of their life.


title: 27-CR-M


title: 3-SD-M

treatment_protocol: Muscle tissue from one-year old male B6C57/J mice maintained on ad libitum AIN-93G SD until the end of their life.


title: 1-SD-M


title: 28-CR-M


title: 4-SD-M


title: 2-SD-M


title: WT_WD144_47


title: 19-SD-MET-M


title: Mus musculus hippocampus tissue_blast-mTBI_rep5

status: Public on Mar 18 2013

data_processing: Data was extracted using the Illumina BeadStudio software(v3.4.0).  Any spots at or below the background were filtered out using an Illumina detection p value of 0.02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below.  Z-score = (raw value - avg)/std; Detection_Pval = Detection Pvalue from Illumina BeadStudio software, (v.3.4.0).

source_name: male ICR_hippocampus_physical-mTBI from a blast exposure

growth_protocol: Male ICR mice weighing 30–40 g were kept five per cage under a constant 12-h light/dark cycle, at room temperature (22+/-2°C). Food (Purina rodent chow) and water were available ad libitum. Each mouse was used for one experiment. The Ethics Committee of the Sackler Faculty of Medicine approved the experimental protocol (M-09-055, M-07-055), in compliance with the guidelines for animal experimentation of the National Institutes of Health (DHEW publication 85–23, revised, 1995).  All experimental manipulations were conducted during the light phase of the cycle.

extract_protocol: After the completion of the behavioral assessments, animals were euthanized and the right hippocampus dissected for total RNA isolation. Total RNA was prepared using the Qiagen RNeasy Mini Kit (Qiagen, Inc. Valencia CA) following the manufacturer's specifications. Quantity and quality of the RNA was assessed using the Agilent 2100 Bioanalyzer with RNA 6000 Nano Chips.

treatment_protocol: Behavioral assessments were initiated 7 days after the animals were exposed to either physical-mTBI, blast-mTBI, or sham-mTBI. This time point was selected based upon prior studies with these models where behavioral deficits were observed to occur from this time point. Mouse cognition and emotional behavior was assessed using the novel object recognition; Y maze; passive avoidance and elevated plus maze paradigms.

value: ICR

tag: weight

tag: exposed to

value: blast-TBI from an explosion

value: hippocampus


title: Mus musculus hippocampus tissue_blast-mTBI_rep4


title: 4T1.2-PE-1

status: Public on Mar 13 2013

description:
4T1.2-PE are 4T1.2 cells rendered non-metastatic using TARC-PE38 chemotoxin.
4T1.2 is a subset 4T1 cells which are a 6-thioguanine resistant cell line selected from the 410.4 tumor without mutagen treatment.  When injected into BALB/c mice, 4T1 spontaneously produces highly metastatic tumors that can metastasize to the lung, liver, lymph nodes and brain while the primary tumor is growing in situ.

hyb_protocol: standard Illumina protocol. In short, a total of 0.75ug of biotin-labeled cRNA was hybridized at 58 degrees C for 16 hours to Illumina's Sentrix MouseRef-8 v1.1 Expression BeadChips (Illumina, San Diego, CA). Each BeadChip has ~24,000 well-annotated RefSeq transcripts with approximately 30-fold redundancy. The arrays were washed, blocked and the biotin labeled cRNA was detected by staining with streptavidin-Cy3.

data_processing: Data was extracted using the Illumina BeadStudio software(v3.1.7).  Any spots at or below the background were filtered out using an Illumina detection p value of 0.02 and above. The natural log of all remaining scores were used to find the avgerage and standard deviation 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: biotin

source_name: 4T1.2 cells, a subset of 4T1 cells, were a gift from Dr. Robin L. Anderson (Peter McCallum Cancer Center, Australia).

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

tag: cell type

tag: agent

value: TARC-PE38 chemotoxin


title: 4T1.2-2

description:
Untreated 4T1.2 Cells
4T1.2 is a subset 4T1 cells which are a 6-thioguanine resistant cell line selected from the 410.4 tumor without mutagen treatment.  When injected into BALB/c mice, 4T1 spontaneously produces highly metastatic tumors that can metastasize to the lung, liver, lymph nodes and brain while the primary tumor is growing in situ.

treatment_protocol: Untreated 4T1.2 Cells

value: Untreated


title: Mus musculus hippocampus tissue_blast-mTBI_rep7


title: 4T1.2-PE-3 rept

description:
4T1.2-PE are 4T1.2 cells rendered non-metastatic using TARC-PE38 chemotoxin, technical replicate of sample 4T1.2-PE-3.
4T1.2 is a subset 4T1 cells which are a 6-thioguanine resistant cell line selected from the 410.4 tumor without mutagen treatment.  When injected into BALB/c mice, 4T1 spontaneously produces highly metastatic tumors that can metastasize to the lung, liver, lymph nodes and brain while the primary tumor is growing in situ.

treatment_protocol: 4T1.2-PE are 4T1.2 cells rendered non-metastatic using TARC-PE38 chemotoxin.


title: Mus musculus hippocampus tissue_blast-mTBI_rep3


title: 4T1.2-PE-3


title: 4T1.2-PE-2


title: 4T1.2-1


title: Mus musculus hippocampus tissue_blast-mTBI_rep6


title: 305_BIA-1

status: Public on Mar 07 2013

description: Calvaria of beta-arrestin 2 knockout ({beta}arr2-KO) mice treated for 8 weeks with bovine (D-Trp12, Tyr34)-PTH(7-34) (40 µg/kg•d).

hyb_protocol: Samples were hybridized to GeneChip® Mouse 430 2.0 arrays in Affymetrix GeneChip® hybridization oven 645, washed and stained in Affymetrix GeneChip®  Fluidics Station 450.

scan_protocol: Arrays scanned with Affymetrix GeneChip® Scanner 7G.

data_processing: RNA samples were hybridized to GeneChip Mouse Genome 430 2.0 arrays (Affymetrix, Santa Clara, CA) in the Duke Microarray Facility of the Duke Institute for Genome Sciences & Policy. Three replicates were performed for each condition. Raw hybridization intensity data were log transformed and normalized to yield Z-scores, which in turn were used to calculate a Z-ratio value for each gene with respect to the control geneset. The Z-ratio was calculated as the difference between the observed gene Z-scores for the experimental and the control comparisons divided by the standard deviation associated with the distribution of these differences.

source_name: Mus musculus, beta-arrestin 2 knockout ({beta}arr2-KO) mice on a C57 BL/6J background.

label_protocol: Hybridization targets were prepared with Affymetrix one cycle kit Cat#900431 from total RNA which creates biotinylated cRNA.

extract_protocol: Total cellular RNA was isolated from the calvaria of mice treated with  bovine (D-Trp12, Tyr34)-PTH(7-34) (40 µg/kg•d). Tissue samples were thawed in TRIzol reagent (Invitrogen, Carlsbad, CA) and homogenized. RNA extraction was performed according to the TRIzol manufacturer’s protocol. The total RNA was analyzed for concentration (ng/uL) and purity (ratios of 260/280 nm and 260/230 nm) using a NanoDrop 1000 Spectrophotometer (Thermo Scientific, Wilmington, DE). RNA integrity was analyzed using the Experion RNA HighSens Analysis Kit (Bio-Rad Laboratories, Inc., Hercules CA).

value: Calvaria

tag: genotype/variation

value: bovine (D-Trp12, Tyr34)-PTH(7-34)


title: 306_BIA-2

treatment_protocol: Calvaria of beta-arrestin 2 knockout ({beta}arr2-KO) mice treated for 8 weeks with bovine (D-Trp12, Tyr34)-PTH(7-34) (40 µg/kg•d).


title: 307_BIA-3

value: beta-arrestin 2 knockout ({beta}arr2-KO)


title: CR_CR809_3_54

value: Percutaneous biopsy specimens of vastus lateralis muscle.


title: Mus musculus hippocampus tissue_blast-mTBI_rep1


title: 4T1.2-3


title: 4T1-PE-3

description:
4T1-PE are 4T1 cells rendered non-metastatic using TARC-PE38 chemotoxin.
4T1 is a 6-thioguanine resistant cell line selected from the 410.4 tumor without mutagen treatment. When injected into BALB/c mice, 4T1 spontaneously produces highly metastatic tumors that can metastasize to the lung, liver, lymph nodes and brain while the primary tumor is growing in situ.

source_name: 4T1 cells (CRL-2539) from the American Type Culture Collection.


title: 4T1.2-2 rept

description:
Untreated 4T1.2 Cells, Technical replicate of sample 4T1.2-2
4T1.2 is a subset 4T1 cells which are a 6-thioguanine resistant cell line selected from the 410.4 tumor without mutagen treatment.  When injected into BALB/c mice, 4T1 spontaneously produces highly metastatic tumors that can metastasize to the lung, liver, lymph nodes and brain while the primary tumor is growing in situ.


title: 304_BPTH-3

description: Calvaria of beta-arrestin 2 knockout ({beta}arr2-KO) mice treated for 8 weeks with Human PTH(1–34) (40 µg/kg•d),

extract_protocol: Total cellular RNA was isolated from the calvaria of mice treated with Human PTH(1–34) (40 µg/kg•d). Tissue samples were thawed in TRIzol reagent (Invitrogen, Carlsbad, CA) and homogenized. RNA extraction was performed according to the TRIzol manufacturer’s protocol. The total RNA was analyzed for concentration (ng/uL) and purity (ratios of 260/280 nm and 260/230 nm) using a NanoDrop 1000 Spectrophotometer (Thermo Scientific, Wilmington, DE). RNA integrity was analyzed using the Experion RNA HighSens Analysis Kit (Bio-Rad Laboratories, Inc., Hercules CA).

value: Human PTH(1–34)


title: Mus musculus hippocampus tissue_blast-mTBI_rep2


title: 302_BPTH-1

treatment_protocol: Calvaria of beta-arrestin 2 knockout ({beta}arr2-KO) mice treated for 8 weeks with Human PTH(1–34) (40 µg/kg•d),


title: 303_BPTH-2


title: 4T1-3

description:
Untreated 4T1 Cells
4T1 is a 6-thioguanine resistant cell line selected from the 410.4 tumor without mutagen treatment. When injected into BALB/c mice, 4T1 spontaneously produces highly metastatic tumors that can metastasize to the lung, liver, lymph nodes and brain while the primary tumor is growing in situ.

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

treatment_protocol: Untreated 4T1 Cells


title: 4T1-2

description:
Untreated 4T1 Cells, technical Replicate of sample 4T1-1.
4T1 is a 6-thioguanine resistant cell line selected from the 410.4 tumor without mutagen treatment. When injected into BALB/c mice, 4T1 spontaneously produces highly metastatic tumors that can metastasize to the lung, liver, lymph nodes and brain while the primary tumor is growing in situ.


title: 4T1-PE-1

treatment_protocol: 4T1-PE are 4T1 cells rendered non-metastatic using TARC-PE38 chemotoxin.


title: 301_BNS-3

description: Calvaria of beta-arrestin 2 knockout ({beta}arr2-KO) mice treated for 8 weeks with vehicle, PBS.

extract_protocol: Total cellular RNA was isolated from the calvaria of mice treated for 8 weeks with vehicle, PBS. Tissue samples were thawed in TRIzol reagent (Invitrogen, Carlsbad, CA) and homogenized. RNA extraction was performed according to the TRIzol manufacturer’s protocol. The total RNA was analyzed for concentration (ng/uL) and purity (ratios of 260/280 nm and 260/230 nm) using a NanoDrop 1000 Spectrophotometer (Thermo Scientific, Wilmington, DE). RNA integrity was analyzed using the Experion RNA HighSens Analysis Kit (Bio-Rad Laboratories, Inc., Hercules CA).

value: vehicle


title: 4T1-1

source_name: 4T1 cells (CRL-2539) from the American Type Culture Collection


title: 300_BNS-2

treatment_protocol: Calvaria of beta-arrestin 2 knockout ({beta}arr2-KO) mice treated for 8 weeks with vehicle, PBS.


title: 4T1-PE-2


title: 299_BNS-1


title: 4T1-1 rept


title: 298_WTIA-3

description: Calvaria of C57 BL/6J mice treated for 8 weeks with bovine (D-Trp12, Tyr34)-PTH(7-34) (40 µg/kg•d).

source_name: Mus musculus, C57 BL/6J

value: wild type


title: 296_WTIA-1

treatment_protocol: Calvaria of C57 BL/6J mice treated for 8 weeks with bovine (D-Trp12, Tyr34)-PTH(7-34) (40 µg/kg•d).


title: 4T1.2-3 rept

description:
Untreated 4T1.2 Cells, Technical replicate of sample 4T1.2-3
4T1.2 is a subset 4T1 cells which are a 6-thioguanine resistant cell line selected from the 410.4 tumor without mutagen treatment.  When injected into BALB/c mice, 4T1 spontaneously produces highly metastatic tumors that can metastasize to the lung, liver, lymph nodes and brain while the primary tumor is growing in situ.


title: 292_WTNS-3

description: Calvaria of C57 BL/6J mice treated for 8 weeks with vehicle, PBS.


title: 293_WTPTH-1

description: Calvaria of C57 BL/6J mice treated for 8 weeks with Human PTH(1–34) (40 µg/kg•d),


title: 294_WTPTH-2

treatment_protocol: Calvaria of C57 BL/6J mice treated for 8 weeks with Human PTH(1–34) (40 µg/kg•d),


title: 295_WTPTH-3


title: 291_WTNS-2

treatment_protocol: Calvaria of C57 BL/6J mice treated for 8 weeks with vehicle, PBS.


title: 297_WTIA-2


title: 290_WTNS-1


title: Case 23 ACC29

status: Public on Dec 31 2012

type: genomic

city: Gotenburg

first: Marta

last: Persson

address: Box 425

country: Sweden

institute: Sahlgrenska Cancer Center

hyb_protocol: Oligoarray control targets (Cot-1 DNA and Blocking agent) and hybridization buffer (Agilent oligo aCGH/ChIP-on-Chip Hybridization Kit) were added, the samples were denatured and applied to microarrays (Agilent Human Genome CGH Microarray 244K 60-mer oligonucleotide arrays) as recommended by the manufacturer. The arrays were enclosed in a rotating hybridization oven at 65°C for 40 h. After hybridization, the slides were sequentially washed and dried.

scan_protocol: The arrays were scanned on an Agilent High-Resolution C Microarray Scanner (G2505B) and the images were quantified using Agilent Feature Extraction Software (v.9.1).

data_processing: Data analysis was carried out using Nexus Copy Number software v.4.1 (BioDiscovery Inc., El Segundo, CA, USA), which uses the Rank segmentation algorithm to define non-random regions of CNAs across the genome. Sex chromosomes were excluded from the analysis. The significance threshold for segmentation was set to p=1.0E-6 and the thresholds of log2 ratio values for gain and loss were 0.25 and −0.2, respectively; the thresholds for high copy number gain/amplification and homozygous deletion were 1.0 and −1.0, respectively.

molecule: genomic DNA

source_name: Adenoid cystic cancer

label_protocol: 2.0 µg of genomic tumor DNA and sex-matched reference DNA (Promega p/n G1471) were digested with AluI and Rsa1 for 2 h at 37 1C. Digested tumor and reference DNAs (1.5 mg of each) were labeled with Cy3-dUTP and Cy5-dUTP (Perkin-Elmer Life and Analytical Sciences Inc., Wellesley, MA, USA), respectively.

extract_protocol: Genomic DNA was isolated from frozen tumour tissue using the QIAampR DNA Mini Kit (Qiagen GmbH, Hilden, Germany) according to the manufacturer instructions.

treatment_protocol: Fresh tumor tissue from 40 ACCs were obtained from surgical resection specimens. The tumors were classified as grade I to III according to the histologic classification of salivary gland tumours by WHO.

value: adenoid cystic carcinoma

tag: tumor site

value: Parotid gland

tag: grade

value: I

value: M

source_name: Normal tissue

tag: sample type


title: Case 24 ACC31

value: NDA

value: F

value: sex-matched reference DNA (Promega p/n G1471)


title: Case 39 ACC10

value: III


title: 22-SD-MET-M

value: Muscle

value: one-year old

value: male

value: maintained on ad libitum AIN-93G SD and supplemented with 0.1% w/w metformin until the end of their life


title: Case 36 C857

value: Submandibular gland


title: Case 29 CG885

value: II


title: Case 30 ACC12

value: Buccal mucosa


title: Case 38 ACC6


title: Case 18 ACC16

value: Nasal mucosa


title: Case 22 ACC24


title: Case 17 ACC15


title: Case 19 ACC18

value: Kidney met


title: Case 27 C1024

value: adenoid cystic carcinoma


title: Case 35 CG688

value: Parotid gland


title: Case 37 ACC2

value: Larynx


title: Case 31 ACC14

value: M


title: Case 15 ACC11

value: I


title: Case 21 ACC21

value: F


title: Case 34 CG581

value: sex-matched reference DNA (Promega p/n G1471)


title: Case 28 CG369

value: Maxilla (recurrence)


title: Case 32 ACC25

value: Salivary gland (unspecified)


title: Case 20 ACC20


title: Case 13 ACC8


title: Case 25 C1384


title: Case 40 ACC42

value: III


title: Case 10 ACC3


title: Case 16 ACC13


title: Case 12 ACC7


title: Case 33 CG337


title: Case 11 ACC4


title: Case 9 ACC1

value: Trachea


title: Case 26 CG964

value: Pelvic bone met


title: Case 6 C1076

value: Submandibular gland


title: Ex-4-mTBI-2

status: Public on Oct 17 2012

description: Hippocampus tissue of mice subjected to mTBI while being treated with EX-4.

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

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

source_name: Mus musculus hippocampus tissue

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

treatment_protocol: Mice were treated for 7 days with the peptide Ex-4 dissolved in an equal volume of saline and dimethyl sulfoxide (DMSO) mixture and delivered from a subcutaneously implanted ALZET Micro-osmotic pump (Model 1007D, Alzet, Cupertino, CA) at a rate of 3.5 pM/kg/min. mTBI was induced on day 3 of treatment.

value: Hippocampus

value: Male

value: ICR

tag: treatment protocol

value: mice subjected to mTBI induced by weight drop injury while being treated with EX-4 (Ex-4/mTBI)

tag: time

value: 14 days following mTBI


title: sham-2

description: Hippocampus tissue of mice while being treated with vehicle only.

treatment_protocol: Mice were treated for 7 days with the just vehicle, a saline and dimethyl sulfoxide (DMSO) mixture and delivered from a subcutaneously implanted ALZET Micro-osmotic pump (Model 1007D, Alzet, Cupertino, CA).  Mice were placed into the mTBI equipment on day 3 but no weight was dropped.

value: vehicle only (sham)


title: Case 7 CG139

value: adenoid cystic carcinoma

value: Parotid gland


title: sham-3


title: sham-4


title: Ex-4-mTBI-4


title: Ex-4-mTBI-1


title: Ex-4-5

description: Hippocampus tissue of EX-4 treated mice.

treatment_protocol: Mice were treated for 7 days with the peptide Ex-4 dissolved in an equal volume of saline and dimethyl sulfoxide (DMSO) mixture and delivered from a subcutaneously implanted ALZET Micro-osmotic pump (Model 1007D, Alzet, Cupertino, CA) at a rate of 3.5 pM/kg/min.


title: Ex-4-3


title: Case 1 C1096

value: Nasal mucosa

value: I


title: mTBI-2

description: Hippocampus tissue of control vehicle treated mice subjected to mTBI.

treatment_protocol: Mice were treated for 7 days with the just vehicle, a saline and dimethyl sulfoxide (DMSO) mixture and delivered from a subcutaneously implanted ALZET Micro-osmotic pump (Model 1007D, Alzet, Cupertino, CA).  mTBI was induced on day 3 of treatment.

value: control vehicle treated mice subjected to mTBI induced by weight drop injury (mTBI)


title: Case 2 C1106

value: Buccal mucosa

value: F

value: sex-matched reference DNA (Promega p/n G1471)


title: Ex-4-1


title: mTBI-1


title: mTBI-4


title: sham-5


title: Case 5 CG1029

value: Auditory meatus


title: Ex-4-4


title: Case 3 CG954

value: Maxilla


title: mTBI-3


title: Ex-4-mTBI-3


title: HD_HD_GLP-1_21

status: Public on Oct 05 2012

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

source_name: male B6C3-Tg(HD82Gln)81Dbo/J (N171-82Q) animals.

extract_protocol: RNA was extracted from frozen hypothalamus tissue using 1.0mm glass beads (BioSpec Products, Inc.) in a Precellys 24 Tissue Homogenizer (Bertin Technologies) and Qiagen RNeasy Mini Kits according to manufacturer's specifications. Quality and quantity of the total RNA was checked with the Agilent 2100 bioanalyzer using RNA 6000 Nano chips.

treatment_protocol: GLP-1-transferrin hybrid molecule (GLP-1Tf, 1mg/kg),  was administered by a once-daily subcutaneous injection. Injections were started when animals were pre-symptomatic (2 months of age) and continued for 5 weeks.

value: Hypothalamus

value: male


title: HD_HD_INS_18

treatment_protocol: Insulin (5Units, Lantus) was administered by a once-daily subcutaneous injection. Injections were started when animals were pre-symptomatic (2 months of age) and continued for 5 weeks.

value: insulin


title: HD_HD_GLP-1_20


title: sham-1

value: Hippocampus

value: Male

value: ICR


title: HD_HD_Ex-4_22

treatment_protocol: Ex-4 (300 µL of 0.1 µmol/L  solution, Bachem, Torrance, CA), was administered by a once-daily subcutaneous injection. Injections were started when animals were pre-symptomatic (2 months of age) and continued for 5 weeks.


title: HD_HD_INS_16


title: Case 4 CG1015

value: Lacrimal gland

value: M


title: HD_HD_CTR_14

treatment_protocol: A saline vehicle treatment (phosphate buffered saline, PBS; Sigma, St. Louis, MO) was administered by a once-daily subcutaneous injection. Injections were started when animals were pre-symptomatic (2 months of age) and continued for 5 weeks.

value: saline


title: HD_WT_INS_5

source_name: male B6/C3 Wt animals.

value: WT


title: HD_HD_INS_17


title: HD_WT_INS_4


title: HD_HD_CTR_15


title: HD_WT_GLP-1_8


title: HD_HD_CTR_13


title: HD_WT_Ex-4_12


title: HD_WT_INS_6


title: HD_WT_Ex-4_11


title: HD_WT_CTR_3


title: HD_WT_CTR_1


title: HD_WT_GLP-1_7


title: Ex-4-2


title: Case 8 CG266

value: adenoid cystic carcinoma

value: I


title: HD_WT_GLP-1_9


title: CMP-BDNF_4H-3

status: Public on Sep 20 2012

description:
sh-sy5y cells were maintained at 37oc in a humidified 5% co2 incubator in amem/f12 supplemented with 10% fbs, 100 units/ml ?penicillin and 100 units/ml streptomycin.  cells were conditioned with either phosphate-buffered saline (pbs) (ctr), or 10nm hydrogen peroxide(cmp) (h2o2: Sigma Aldrich, St Louis MO) for seven days.  Cell growth media and applied hydrogen peroxide treatments were changed daily.
CMP-BDNF_4H-3

hyb_protocol: standard Illumina protocol. In short, a total of 0.75ug of biotin-labeled cRNA was hybridized at 58 degrees C for 16 hours to Illumina's Sentrix Human HT-12 v3 Expression BeadChips (Illumina, San Diego, CA). Each BeadChip has ~48,000 transcripts with approximately 15-fold redundancy. The arrays were washed, blocked and the 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 p-value above 0.02. 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 files.

source_name: SH-SY5Y neural cells, obtained from ATCC (http://www.atcc.org/),

extract_protocol: RNA was extracted from the treated cells using Qiagen RNAeasy Mini kit. Quality and quantity of the total RNA was checked with the Agilent 2100 bioanalyzer using RNA 6000 Nano chips.

treatment_protocol: The chronic minimal peroxide(CMP) SH-SY5Y cells were serum-starved overnight prior to ligand stimulation with 10ng/ml brain derived neurotrophic factor (BDNF: Invitrogen, Carlsbad CA) for 4 hours.  Cells were collected and total RNA was isolated.

tag: treatment

value: hydrogen peroxide, brain derived neurotrophic factor

tag: cell line


title: CMP-BDNF_8H-3

description:
sh-sy5y cells were maintained at 37oc in a humidified 5% co2 incubator in amem/f12 supplemented with 10% fbs, 100 units/ml ?penicillin and 100 units/ml streptomycin.  cells were conditioned with either phosphate-buffered saline (pbs) (ctr), or 10nm hydrogen peroxide(cmp) (h2o2: Sigma Aldrich, St Louis MO) for seven days.  Cell growth media and applied hydrogen peroxide treatments were changed daily.
CMP-BDNF_8H-3

treatment_protocol: The chronic minimal peroxide(CMP) SH-SY5Y cells were serum-starved overnight prior to ligand stimulation with 10ng/ml brain derived neurotrophic factor (BDNF: Invitrogen, Carlsbad CA) for 8 hours.  Cells were collected and total RNA was isolated.


title: HD_HD_GLP-1_19

tag: gender

tag: strain


title: CMP-BDNF_8H-2

description:
sh-sy5y cells were maintained at 37oc in a humidified 5% co2 incubator in amem/f12 supplemented with 10% fbs, 100 units/ml ?penicillin and 100 units/ml streptomycin.  cells were conditioned with either phosphate-buffered saline (pbs) (ctr), or 10nm hydrogen peroxide(cmp) (h2o2: Sigma Aldrich, St Louis MO) for seven days.  Cell growth media and applied hydrogen peroxide treatments were changed daily.
CMP-BDNF_8H-2


title: CMP-BMC_8H-3

description:
sh-sy5y cells were maintained at 37oc in a humidified 5% co2 incubator in amem/f12 supplemented with 10% fbs, 100 units/ml ?penicillin and 100 units/ml streptomycin.  cells were conditioned with either phosphate-buffered saline (pbs) (ctr), or 10nm hydrogen peroxide(cmp) (h2o2: Sigma Aldrich, St Louis MO) for seven days.  Cell growth media and applied hydrogen peroxide treatments were changed daily.
CMP-BMC_8H-3

treatment_protocol: The chronic minimal peroxide(CMP) SH-SY5Y cells were serum-starved overnight prior to ligand stimulation with Beta-methylcholine (Calbiochem, Gibbstown NJ) for 8 hours.  Cells were collected and total RNA was isolated.

value: hydrogen peroxide, beta-methylcholine


title: HD_WT_Ex-4_10

tag: tissue


title: CMP-BDNF_2H-1

description:
sh-sy5y cells were maintained at 37oc in a humidified 5% co2 incubator in amem/f12 supplemented with 10% fbs, 100 units/ml ?penicillin and 100 units/ml streptomycin.  cells were conditioned with either phosphate-buffered saline (pbs) (ctr), or 10nm hydrogen peroxide(cmp) (h2o2: Sigma Aldrich, St Louis MO) for seven days.  Cell growth media and applied hydrogen peroxide treatments were changed daily.
CMP-BDNF_2H-1

treatment_protocol: The chronic minimal peroxide(CMP) SH-SY5Y cells were serum-starved overnight prior to ligand stimulation with 10ng/ml brain derived neurotrophic factor (BDNF: Invitrogen, Carlsbad CA) for 2 hours.  Cells were collected and total RNA was isolated.


title: CMP-BDNF_4H-2

description:
sh-sy5y cells were maintained at 37oc in a humidified 5% co2 incubator in amem/f12 supplemented with 10% fbs, 100 units/ml ?penicillin and 100 units/ml streptomycin.  cells were conditioned with either phosphate-buffered saline (pbs) (ctr), or 10nm hydrogen peroxide(cmp) (h2o2: Sigma Aldrich, St Louis MO) for seven days.  Cell growth media and applied hydrogen peroxide treatments were changed daily.
CMP-BDNF_4H-2


title: CMP-BDNF_2H-3

description:
sh-sy5y cells were maintained at 37oc in a humidified 5% co2 incubator in amem/f12 supplemented with 10% fbs, 100 units/ml ?penicillin and 100 units/ml streptomycin.  cells were conditioned with either phosphate-buffered saline (pbs) (ctr), or 10nm hydrogen peroxide(cmp) (h2o2: Sigma Aldrich, St Louis MO) for seven days.  Cell growth media and applied hydrogen peroxide treatments were changed daily.
CMP-BDNF_2H-3


title: CMP-BDNF_8H-1

description:
sh-sy5y cells were maintained at 37oc in a humidified 5% co2 incubator in amem/f12 supplemented with 10% fbs, 100 units/ml ?penicillin and 100 units/ml streptomycin.  cells were conditioned with either phosphate-buffered saline (pbs) (ctr), or 10nm hydrogen peroxide(cmp) (h2o2: Sigma Aldrich, St Louis MO) for seven days.  Cell growth media and applied hydrogen peroxide treatments were changed daily.
CMP-BDNF_8H-1


title: CMP-BDNF_4H-1

description:
sh-sy5y cells were maintained at 37oc in a humidified 5% co2 incubator in amem/f12 supplemented with 10% fbs, 100 units/ml ?penicillin and 100 units/ml streptomycin.  cells were conditioned with either phosphate-buffered saline (pbs) (ctr), or 10nm hydrogen peroxide(cmp) (h2o2: Sigma Aldrich, St Louis MO) for seven days.  Cell growth media and applied hydrogen peroxide treatments were changed daily.
CMP-BDNF_4H-1


title: CMP-BDNF_2H-2

description:
sh-sy5y cells were maintained at 37oc in a humidified 5% co2 incubator in amem/f12 supplemented with 10% fbs, 100 units/ml ?penicillin and 100 units/ml streptomycin.  cells were conditioned with either phosphate-buffered saline (pbs) (ctr), or 10nm hydrogen peroxide(cmp) (h2o2: Sigma Aldrich, St Louis MO) for seven days.  Cell growth media and applied hydrogen peroxide treatments were changed daily.
CMP-BDNF_2H-2


title: CMP-BMC_4H-1

description:
sh-sy5y cells were maintained at 37oc in a humidified 5% co2 incubator in amem/f12 supplemented with 10% fbs, 100 units/ml ?penicillin and 100 units/ml streptomycin.  cells were conditioned with either phosphate-buffered saline (pbs) (ctr), or 10nm hydrogen peroxide(cmp) (h2o2: Sigma Aldrich, St Louis MO) for seven days.  Cell growth media and applied hydrogen peroxide treatments were changed daily.
CMP-BMC_4H-1

treatment_protocol: The chronic minimal peroxide(CMP) SH-SY5Y cells were serum-starved overnight prior to ligand stimulation with Beta-methylcholine (Calbiochem, Gibbstown NJ) for 4 hours.  Cells were collected and total RNA was isolated.


title: CTR-BDNF_8H-3

description:
sh-sy5y cells were maintained at 37oc in a humidified 5% co2 incubator in amem/f12 supplemented with 10% fbs, 100 units/ml ?penicillin and 100 units/ml streptomycin.  cells were conditioned with either phosphate-buffered saline (pbs) (ctr), or 10nm hydrogen peroxide(cmp) (h2o2: Sigma Aldrich, St Louis MO) for seven days.  Cell growth media and applied hydrogen peroxide treatments were changed daily.
CTR-BDNF_8H-3

treatment_protocol: The control(CTR) SH-SY5Y cells were serum-starved overnight prior to ligand stimulation with 10ng/ml brain derived neurotrophic factor (BDNF: Invitrogen, Carlsbad CA) for 8 hours.  Cells were collected and total RNA was isolated.

value: control, brain derived neurotrophic factor


title: CMP2

description:
sh-sy5y cells were maintained at 37oc in a humidified 5% co2 incubator in amem/f12 supplemented with 10% fbs, 100 units/ml ?penicillin and 100 units/ml streptomycin.  cells were conditioned with either phosphate-buffered saline (pbs) (ctr), or 10nm hydrogen peroxide(cmp) (h2o2: Sigma Aldrich, St Louis MO) for seven days.  Cell growth media and applied hydrogen peroxide treatments were changed daily.
CMP2

treatment_protocol: The chronic minimal peroxide(CMP) SH-SY5Y cells were serum-starved overnight prior to collection and isolation of RNA.

value: hydrogen peroxide


title: CMP3

description:
sh-sy5y cells were maintained at 37oc in a humidified 5% co2 incubator in amem/f12 supplemented with 10% fbs, 100 units/ml ?penicillin and 100 units/ml streptomycin.  cells were conditioned with either phosphate-buffered saline (pbs) (ctr), or 10nm hydrogen peroxide(cmp) (h2o2: Sigma Aldrich, St Louis MO) for seven days.  Cell growth media and applied hydrogen peroxide treatments were changed daily.
CMP3


title: HD_HD_Ex-4_23


title: CTR-BDNF_8H-2

description:
sh-sy5y cells were maintained at 37oc in a humidified 5% co2 incubator in amem/f12 supplemented with 10% fbs, 100 units/ml ?penicillin and 100 units/ml streptomycin.  cells were conditioned with either phosphate-buffered saline (pbs) (ctr), or 10nm hydrogen peroxide(cmp) (h2o2: Sigma Aldrich, St Louis MO) for seven days.  Cell growth media and applied hydrogen peroxide treatments were changed daily.
CTR-BDNF_8H-2


title: CTR-BDNF_4H-3

description:
sh-sy5y cells were maintained at 37oc in a humidified 5% co2 incubator in amem/f12 supplemented with 10% fbs, 100 units/ml ?penicillin and 100 units/ml streptomycin.  cells were conditioned with either phosphate-buffered saline (pbs) (ctr), or 10nm hydrogen peroxide(cmp) (h2o2: Sigma Aldrich, St Louis MO) for seven days.  Cell growth media and applied hydrogen peroxide treatments were changed daily.
CTR-BDNF_4H-3

treatment_protocol: The control(CTR) SH-SY5Y cells were serum-starved overnight prior to ligand stimulation with 10ng/ml brain derived neurotrophic factor (BDNF: Invitrogen, Carlsbad CA) for 4 hours.  Cells were collected and total RNA was isolated.


title: CMP-BMC_2H-2

description:
sh-sy5y cells were maintained at 37oc in a humidified 5% co2 incubator in amem/f12 supplemented with 10% fbs, 100 units/ml ?penicillin and 100 units/ml streptomycin.  cells were conditioned with either phosphate-buffered saline (pbs) (ctr), or 10nm hydrogen peroxide(cmp) (h2o2: Sigma Aldrich, St Louis MO) for seven days.  Cell growth media and applied hydrogen peroxide treatments were changed daily.
CMP-BMC_2H-2

treatment_protocol: The chronic minimal peroxide(CMP) SH-SY5Y cells were serum-starved overnight prior to ligand stimulation with Beta-methylcholine (Calbiochem, Gibbstown NJ) for 2 hours.  Cells were collected and total RNA was isolated.


title: CMP-BMC_2H-3

description:
sh-sy5y cells were maintained at 37oc in a humidified 5% co2 incubator in amem/f12 supplemented with 10% fbs, 100 units/ml ?penicillin and 100 units/ml streptomycin.  cells were conditioned with either phosphate-buffered saline (pbs) (ctr), or 10nm hydrogen peroxide(cmp) (h2o2: Sigma Aldrich, St Louis MO) for seven days.  Cell growth media and applied hydrogen peroxide treatments were changed daily.
CMP-BMC_2H-3


title: CMP-BMC_8H-2

description:
sh-sy5y cells were maintained at 37oc in a humidified 5% co2 incubator in amem/f12 supplemented with 10% fbs, 100 units/ml ?penicillin and 100 units/ml streptomycin.  cells were conditioned with either phosphate-buffered saline (pbs) (ctr), or 10nm hydrogen peroxide(cmp) (h2o2: Sigma Aldrich, St Louis MO) for seven days.  Cell growth media and applied hydrogen peroxide treatments were changed daily.
CMP-BMC_8H-2


title: CTR-BDNF_8H-1

description:
sh-sy5y cells were maintained at 37oc in a humidified 5% co2 incubator in amem/f12 supplemented with 10% fbs, 100 units/ml ?penicillin and 100 units/ml streptomycin.  cells were conditioned with either phosphate-buffered saline (pbs) (ctr), or 10nm hydrogen peroxide(cmp) (h2o2: Sigma Aldrich, St Louis MO) for seven days.  Cell growth media and applied hydrogen peroxide treatments were changed daily.
CTR-BDNF_8H-1


title: CMP-BMC_4H-2

description:
sh-sy5y cells were maintained at 37oc in a humidified 5% co2 incubator in amem/f12 supplemented with 10% fbs, 100 units/ml ?penicillin and 100 units/ml streptomycin.  cells were conditioned with either phosphate-buffered saline (pbs) (ctr), or 10nm hydrogen peroxide(cmp) (h2o2: Sigma Aldrich, St Louis MO) for seven days.  Cell growth media and applied hydrogen peroxide treatments were changed daily.
CMP-BMC_4H-2


title: CMP-BMC_2H-1

description:
sh-sy5y cells were maintained at 37oc in a humidified 5% co2 incubator in amem/f12 supplemented with 10% fbs, 100 units/ml ?penicillin and 100 units/ml streptomycin.  cells were conditioned with either phosphate-buffered saline (pbs) (ctr), or 10nm hydrogen peroxide(cmp) (h2o2: Sigma Aldrich, St Louis MO) for seven days.  Cell growth media and applied hydrogen peroxide treatments were changed daily.
CMP-BMC_2H-1


title: CMP-BMC_4H-3

description:
sh-sy5y cells were maintained at 37oc in a humidified 5% co2 incubator in amem/f12 supplemented with 10% fbs, 100 units/ml ?penicillin and 100 units/ml streptomycin.  cells were conditioned with either phosphate-buffered saline (pbs) (ctr), or 10nm hydrogen peroxide(cmp) (h2o2: Sigma Aldrich, St Louis MO) for seven days.  Cell growth media and applied hydrogen peroxide treatments were changed daily.
CMP-BMC_4H-3


title: CMP1

description:
sh-sy5y cells were maintained at 37oc in a humidified 5% co2 incubator in amem/f12 supplemented with 10% fbs, 100 units/ml ?penicillin and 100 units/ml streptomycin.  cells were conditioned with either phosphate-buffered saline (pbs) (ctr), or 10nm hydrogen peroxide(cmp) (h2o2: Sigma Aldrich, St Louis MO) for seven days.  Cell growth media and applied hydrogen peroxide treatments were changed daily.
CMP1


title: Case 14 ACC9

treatment_protocol: Fresh tumor tissue from 40 ACCs were obtained from surgical resection specimens. The tumors were classified as grade I to III according to the histologic classification of salivary gland tumours by WHO.

value: Buccal mucosa

value: F

value: sex-matched reference DNA (Promega p/n G1471)


title: CTR-BDNF_2H-1

description:
sh-sy5y cells were maintained at 37oc in a humidified 5% co2 incubator in amem/f12 supplemented with 10% fbs, 100 units/ml ?penicillin and 100 units/ml streptomycin.  cells were conditioned with either phosphate-buffered saline (pbs) (ctr), or 10nm hydrogen peroxide(cmp) (h2o2: Sigma Aldrich, St Louis MO) for seven days.  Cell growth media and applied hydrogen peroxide treatments were changed daily.
CTR-BDNF_2H-1

treatment_protocol: The control(CTR) SH-SY5Y cells were serum-starved overnight prior to ligand stimulation with 10ng/ml brain derived neurotrophic factor (BDNF: Invitrogen, Carlsbad CA) for 2 hours.  Cells were collected and total RNA was isolated.


title: CTR-BDNF_4H-1

description:
sh-sy5y cells were maintained at 37oc in a humidified 5% co2 incubator in amem/f12 supplemented with 10% fbs, 100 units/ml ?penicillin and 100 units/ml streptomycin.  cells were conditioned with either phosphate-buffered saline (pbs) (ctr), or 10nm hydrogen peroxide(cmp) (h2o2: Sigma Aldrich, St Louis MO) for seven days.  Cell growth media and applied hydrogen peroxide treatments were changed daily.
CTR-BDNF_4H-1


title: CTR-BDNF_2H-3

description:
sh-sy5y cells were maintained at 37oc in a humidified 5% co2 incubator in amem/f12 supplemented with 10% fbs, 100 units/ml ?penicillin and 100 units/ml streptomycin.  cells were conditioned with either phosphate-buffered saline (pbs) (ctr), or 10nm hydrogen peroxide(cmp) (h2o2: Sigma Aldrich, St Louis MO) for seven days.  Cell growth media and applied hydrogen peroxide treatments were changed daily.
CTR-BDNF_2H-3


title: CTR-BDNF_4H-2

description:
sh-sy5y cells were maintained at 37oc in a humidified 5% co2 incubator in amem/f12 supplemented with 10% fbs, 100 units/ml ?penicillin and 100 units/ml streptomycin.  cells were conditioned with either phosphate-buffered saline (pbs) (ctr), or 10nm hydrogen peroxide(cmp) (h2o2: Sigma Aldrich, St Louis MO) for seven days.  Cell growth media and applied hydrogen peroxide treatments were changed daily.
CTR-BDNF_4H-2


title: CMP-BMC_8H-1

description:
sh-sy5y cells were maintained at 37oc in a humidified 5% co2 incubator in amem/f12 supplemented with 10% fbs, 100 units/ml ?penicillin and 100 units/ml streptomycin.  cells were conditioned with either phosphate-buffered saline (pbs) (ctr), or 10nm hydrogen peroxide(cmp) (h2o2: Sigma Aldrich, St Louis MO) for seven days.  Cell growth media and applied hydrogen peroxide treatments were changed daily.
CMP-BMC_8H-1


title: CTR-BDNF_2H-2

description:
sh-sy5y cells were maintained at 37oc in a humidified 5% co2 incubator in amem/f12 supplemented with 10% fbs, 100 units/ml ?penicillin and 100 units/ml streptomycin.  cells were conditioned with either phosphate-buffered saline (pbs) (ctr), or 10nm hydrogen peroxide(cmp) (h2o2: Sigma Aldrich, St Louis MO) for seven days.  Cell growth media and applied hydrogen peroxide treatments were changed daily.
CTR-BDNF_2H-2


title: CTR-BMC_8H-3

description:
sh-sy5y cells were maintained at 37oc in a humidified 5% co2 incubator in amem/f12 supplemented with 10% fbs, 100 units/ml ?penicillin and 100 units/ml streptomycin.  cells were conditioned with either phosphate-buffered saline (pbs) (ctr), or 10nm hydrogen peroxide(cmp) (h2o2: Sigma Aldrich, St Louis MO) for seven days.  Cell growth media and applied hydrogen peroxide treatments were changed daily.
CTR-BMC_8H-3

treatment_protocol: The control(CTR) SH-SY5Y cells were serum-starved overnight prior to ligand stimulation with Beta-methylcholine (Calbiochem, Gibbstown NJ) for 8 hours.  Cells were collected and total RNA was isolated.

value: control, beta-methylcholine


title: CTR-BMC_4H-2

description:
sh-sy5y cells were maintained at 37oc in a humidified 5% co2 incubator in amem/f12 supplemented with 10% fbs, 100 units/ml ?penicillin and 100 units/ml streptomycin.  cells were conditioned with either phosphate-buffered saline (pbs) (ctr), or 10nm hydrogen peroxide(cmp) (h2o2: Sigma Aldrich, St Louis MO) for seven days.  Cell growth media and applied hydrogen peroxide treatments were changed daily.
CTR-BMC_4H-2

treatment_protocol: The control(CTR) SH-SY5Y cells were serum-starved overnight prior to ligand stimulation with Beta-methylcholine (Calbiochem, Gibbstown NJ) for 4 hours.  Cells were collected and total RNA was isolated.


title: CTR1

description:
sh-sy5y cells were maintained at 37oc in a humidified 5% co2 incubator in amem/f12 supplemented with 10% fbs, 100 units/ml ?penicillin and 100 units/ml streptomycin.  cells were conditioned with either phosphate-buffered saline (pbs) (ctr), or 10nm hydrogen peroxide(cmp) (h2o2: Sigma Aldrich, St Louis MO) for seven days.  Cell growth media and applied hydrogen peroxide treatments were changed daily.
CTR1

treatment_protocol: The control(CTR) SH-SY5Y cells were serum-starved overnight prior to collection and isolation of RNA.

value: control


title: CTR-BMC_4H-3

description:
sh-sy5y cells were maintained at 37oc in a humidified 5% co2 incubator in amem/f12 supplemented with 10% fbs, 100 units/ml ?penicillin and 100 units/ml streptomycin.  cells were conditioned with either phosphate-buffered saline (pbs) (ctr), or 10nm hydrogen peroxide(cmp) (h2o2: Sigma Aldrich, St Louis MO) for seven days.  Cell growth media and applied hydrogen peroxide treatments were changed daily.
CTR-BMC_4H-3


title: CTR-BMC_2H-2

description:
sh-sy5y cells were maintained at 37oc in a humidified 5% co2 incubator in amem/f12 supplemented with 10% fbs, 100 units/ml ?penicillin and 100 units/ml streptomycin.  cells were conditioned with either phosphate-buffered saline (pbs) (ctr), or 10nm hydrogen peroxide(cmp) (h2o2: Sigma Aldrich, St Louis MO) for seven days.  Cell growth media and applied hydrogen peroxide treatments were changed daily.
CTR-BMC_2H-2

treatment_protocol: The control(CTR) SH-SY5Y cells were serum-starved overnight prior to ligand stimulation with Beta-methylcholine (Calbiochem, Gibbstown NJ) for 2 hours.  Cells were collected and total RNA was isolated.


title: CTR-BMC_8H-1

description:
sh-sy5y cells were maintained at 37oc in a humidified 5% co2 incubator in amem/f12 supplemented with 10% fbs, 100 units/ml ?penicillin and 100 units/ml streptomycin.  cells were conditioned with either phosphate-buffered saline (pbs) (ctr), or 10nm hydrogen peroxide(cmp) (h2o2: Sigma Aldrich, St Louis MO) for seven days.  Cell growth media and applied hydrogen peroxide treatments were changed daily.
CTR-BMC_8H-1


title: CTR-BMC_4H-1

description:
sh-sy5y cells were maintained at 37oc in a humidified 5% co2 incubator in amem/f12 supplemented with 10% fbs, 100 units/ml ?penicillin and 100 units/ml streptomycin.  cells were conditioned with either phosphate-buffered saline (pbs) (ctr), or 10nm hydrogen peroxide(cmp) (h2o2: Sigma Aldrich, St Louis MO) for seven days.  Cell growth media and applied hydrogen peroxide treatments were changed daily.
CTR-BMC_4H-1


title: CTR-BMC_2H-3

description:
sh-sy5y cells were maintained at 37oc in a humidified 5% co2 incubator in amem/f12 supplemented with 10% fbs, 100 units/ml ?penicillin and 100 units/ml streptomycin.  cells were conditioned with either phosphate-buffered saline (pbs) (ctr), or 10nm hydrogen peroxide(cmp) (h2o2: Sigma Aldrich, St Louis MO) for seven days.  Cell growth media and applied hydrogen peroxide treatments were changed daily.
CTR-BMC_2H-3


title: CTR3

description:
sh-sy5y cells were maintained at 37oc in a humidified 5% co2 incubator in amem/f12 supplemented with 10% fbs, 100 units/ml ?penicillin and 100 units/ml streptomycin.  cells were conditioned with either phosphate-buffered saline (pbs) (ctr), or 10nm hydrogen peroxide(cmp) (h2o2: Sigma Aldrich, St Louis MO) for seven days.  Cell growth media and applied hydrogen peroxide treatments were changed daily.
CTR3


title: CTR-BMC_8H-2

description:
sh-sy5y cells were maintained at 37oc in a humidified 5% co2 incubator in amem/f12 supplemented with 10% fbs, 100 units/ml ?penicillin and 100 units/ml streptomycin.  cells were conditioned with either phosphate-buffered saline (pbs) (ctr), or 10nm hydrogen peroxide(cmp) (h2o2: Sigma Aldrich, St Louis MO) for seven days.  Cell growth media and applied hydrogen peroxide treatments were changed daily.
CTR-BMC_8H-2


title: HD_HD_Ex-4_24

treatment_protocol: Ex-4 (300 µL of 0.1 µmol/L  solution, Bachem, Torrance, CA), was administered by a once-daily subcutaneous injection. Injections were started when animals were pre-symptomatic (2 months of age) and continued for 5 weeks.

value: Hypothalamus

value: male


title: 4% O2 #1

description:
Cerebral cortices were removed from 6-8-day-old Wistar rats and placed in ice-cold phosphate-buffered solution (PBS) containing: 8mM NaH2PO4, 2.7mM KCl, 138mM NaCl, and 2.7mM KH2PO4.  Multiply-dissected cortices were dispersed into the same buffer containing 0.25 mg/mL trypsin, at 37°C for 15 min.  Digestion was halted by the addition of an equal volume of buffer supplemented with 16µg/mL soy bean trypsin inhibitor (type I-S; Sigma, Poole, Dorset, UK), 20U/mL DNase I (EC 3.1.21.1 type II from bovine pancreas; Sigma) and 1.6mM MgSO4.  The tissue was then pelleted by centrifugation at 1000xg for 1 min and the supernatant was poured off before resuspending the cell pellet in 6.8mL of buffer solution containing 100µg/mL soy bean trypsin inhibitor, 125U/mL DNase I and 10mM MgSO4.  The tissue was subsequently triturated and, after allowing larger pieces of tissue to settle, the cell suspension was pipetted into media (Eagle's minimal essential medium supplemented with 10% fetal calf serum (v/v) and 1% (v/v) penicillin-streptomycin (Gibco, Paisley, UK)).  The cell suspension was then aliquoted into 75cm2 flasks.  Cells were then maintained in a humidified incubator at 37°C (95% air; 5% CO2).  Four to six hours following plating, cells were washed twice with fresh media to remove non-adherent cells.  This resulted in a culture of cortical astrocytes, as confirmed by visual inspection the following day and later by glial fibrillary acidic protein immunohistochemistry.  Any cortical astrocyte culture that was not homogenous was disposed of and not used in this study.
= Rattus norvegicus, cortical astrocytes, cultured at 4% O2.

data_processing: Data was extracted using the Illumina BeadStudio software(v3.4). 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 values is included in the supplemental file.

source_name: Wistar rats, cortical astrocytes

extract_protocol: RNA isolation was carried out using the Qiagen RNeasy Mini Kit for cell extraction (Qiagen, Inc. Valencia CA).  The cells were lysed in the proprietary buffer and then centrifuged.  The supernatant was transferred to a second tube and centrifuged again to clear any remaining cellular debris.  The supernatant was added to 95% ethanol, mixed and added to the proprietary binding columns.  The columns were centrifuged, washed several times and the bound RNA was eluted using water.  The RNA quality and quantity was checked using an Agilent 2100 Bio-analyzer and the RNA 6000 nano-chips (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Culture medium was exchanged every 7 days and cells were grown in culture for up to 14 days.  24hr prior to experimentation cells were transferred to an hypoxic workstation equilibrated with 4% O2, 5% CO2, and the remaining percentage gas N2. Once cortical astrocytes had reached approximately 90% confluence (75cm2 flask) they were subjected to hypoxia as above, washed with PBS, removed from the flask base with 0.05% trypsin-EDTA (Gibco) and then gently centrifuged (500xg).  The cell pellet was then re-suspended in PBS and centrifuged twice more to remove any traces of media.  The cell pellet was then triturated in 8-10 volumes of RNAlater (Applied Biosystems), frozen and stored at -80oC.

value: cortical astrocyte

value: Wistar


title: 9% O2 #3

description:
Cerebral cortices were removed from 6-8-day-old Wistar rats and placed in ice-cold phosphate-buffered solution (PBS) containing: 8mM NaH2PO4, 2.7mM KCl, 138mM NaCl, and 2.7mM KH2PO4.  Multiply-dissected cortices were dispersed into the same buffer containing 0.25 mg/mL trypsin, at 37°C for 15 min.  Digestion was halted by the addition of an equal volume of buffer supplemented with 16µg/mL soy bean trypsin inhibitor (type I-S; Sigma, Poole, Dorset, UK), 20U/mL DNase I (EC 3.1.21.1 type II from bovine pancreas; Sigma) and 1.6mM MgSO4.  The tissue was then pelleted by centrifugation at 1000xg for 1 min and the supernatant was poured off before resuspending the cell pellet in 6.8mL of buffer solution containing 100µg/mL soy bean trypsin inhibitor, 125U/mL DNase I and 10mM MgSO4.  The tissue was subsequently triturated and, after allowing larger pieces of tissue to settle, the cell suspension was pipetted into media (Eagle's minimal essential medium supplemented with 10% fetal calf serum (v/v) and 1% (v/v) penicillin-streptomycin (Gibco, Paisley, UK)).  The cell suspension was then aliquoted into 75cm2 flasks.  Cells were then maintained in a humidified incubator at 37°C (95% air; 5% CO2).  Four to six hours following plating, cells were washed twice with fresh media to remove non-adherent cells.  This resulted in a culture of cortical astrocytes, as confirmed by visual inspection the following day and later by glial fibrillary acidic protein immunohistochemistry.  Any cortical astrocyte culture that was not homogenous was disposed of and not used in this study.
= Rattus norvegicus, cortical astrocytes, cultured at 9% O2.

treatment_protocol: Culture medium was exchanged every 7 days and cells were grown in culture for up to 14 days.  24hr prior to experimentation cells were transferred to an hypoxic workstation equilibrated with 9% O2, 5% CO2, and the remaining percentage gas N2. Once cortical astrocytes had reached approximately 90% confluence (75cm2 flask) they were subjected to hypoxia as above, washed with PBS, removed from the flask base with 0.05% trypsin-EDTA (Gibco) and then gently centrifuged (500xg).  The cell pellet was then re-suspended in PBS and centrifuged twice more to remove any traces of media.  The cell pellet was then triturated in 8-10 volumes of RNAlater (Applied Biosystems), frozen and stored at -80oC.


title: 21% O2 #2

description:
Cerebral cortices were removed from 6-8-day-old Wistar rats and placed in ice-cold phosphate-buffered solution (PBS) containing: 8mM NaH2PO4, 2.7mM KCl, 138mM NaCl, and 2.7mM KH2PO4.  Multiply-dissected cortices were dispersed into the same buffer containing 0.25 mg/mL trypsin, at 37°C for 15 min.  Digestion was halted by the addition of an equal volume of buffer supplemented with 16µg/mL soy bean trypsin inhibitor (type I-S; Sigma, Poole, Dorset, UK), 20U/mL DNase I (EC 3.1.21.1 type II from bovine pancreas; Sigma) and 1.6mM MgSO4.  The tissue was then pelleted by centrifugation at 1000xg for 1 min and the supernatant was poured off before resuspending the cell pellet in 6.8mL of buffer solution containing 100µg/mL soy bean trypsin inhibitor, 125U/mL DNase I and 10mM MgSO4.  The tissue was subsequently triturated and, after allowing larger pieces of tissue to settle, the cell suspension was pipetted into media (Eagle's minimal essential medium supplemented with 10% fetal calf serum (v/v) and 1% (v/v) penicillin-streptomycin (Gibco, Paisley, UK)).  The cell suspension was then aliquoted into 75cm2 flasks.  Cells were then maintained in a humidified incubator at 37°C (95% air; 5% CO2).  Four to six hours following plating, cells were washed twice with fresh media to remove non-adherent cells.  This resulted in a culture of cortical astrocytes, as confirmed by visual inspection the following day and later by glial fibrillary acidic protein immunohistochemistry.  Any cortical astrocyte culture that was not homogenous was disposed of and not used in this study.
= Rattus norvegicus, cortical astrocytes, cultured at 21% O2.

treatment_protocol: Culture medium was exchanged every 7 days and cells were grown in culture for up to 14 days.  24hr prior to experimentation cells were transferred to an hypoxic workstation equilibrated with 21% O2, 5% CO2, and the remaining percentage gas N2. Once cortical astrocytes had reached approximately 90% confluence (75cm2 flask) they were subjected to hypoxia as above, washed with PBS, removed from the flask base with 0.05% trypsin-EDTA (Gibco) and then gently centrifuged (500xg).  The cell pellet was then re-suspended in PBS and centrifuged twice more to remove any traces of media.  The cell pellet was then triturated in 8-10 volumes of RNAlater (Applied Biosystems), frozen and stored at -80oC.


title: 9% O2 #2


title: 9% O2 #1


title: 21% O2 #1


title: 21% O2 #3


title: CTR-BMC_2H-1

description:
sh-sy5y cells were maintained at 37oc in a humidified 5% co2 incubator in amem/f12 supplemented with 10% fbs, 100 units/ml ?penicillin and 100 units/ml streptomycin.  cells were conditioned with either phosphate-buffered saline (pbs) (ctr), or 10nm hydrogen peroxide(cmp) (h2o2: Sigma Aldrich, St Louis MO) for seven days.  Cell growth media and applied hydrogen peroxide treatments were changed daily.
CTR-BMC_2H-1


title: 4% O2 #3


title: 4% O2 #2


title: 1% O2 #3

description:
Cerebral cortices were removed from 6-8-day-old Wistar rats and placed in ice-cold phosphate-buffered solution (PBS) containing: 8mM NaH2PO4, 2.7mM KCl, 138mM NaCl, and 2.7mM KH2PO4.  Multiply-dissected cortices were dispersed into the same buffer containing 0.25 mg/mL trypsin, at 37°C for 15 min.  Digestion was halted by the addition of an equal volume of buffer supplemented with 16µg/mL soy bean trypsin inhibitor (type I-S; Sigma, Poole, Dorset, UK), 20U/mL DNase I (EC 3.1.21.1 type II from bovine pancreas; Sigma) and 1.6mM MgSO4.  The tissue was then pelleted by centrifugation at 1000xg for 1 min and the supernatant was poured off before resuspending the cell pellet in 6.8mL of buffer solution containing 100µg/mL soy bean trypsin inhibitor, 125U/mL DNase I and 10mM MgSO4.  The tissue was subsequently triturated and, after allowing larger pieces of tissue to settle, the cell suspension was pipetted into media (Eagle's minimal essential medium supplemented with 10% fetal calf serum (v/v) and 1% (v/v) penicillin-streptomycin (Gibco, Paisley, UK)).  The cell suspension was then aliquoted into 75cm2 flasks.  Cells were then maintained in a humidified incubator at 37°C (95% air; 5% CO2).  Four to six hours following plating, cells were washed twice with fresh media to remove non-adherent cells.  This resulted in a culture of cortical astrocytes, as confirmed by visual inspection the following day and later by glial fibrillary acidic protein immunohistochemistry.  Any cortical astrocyte culture that was not homogenous was disposed of and not used in this study.
= Rattus norvegicus, cortical astrocytes, cultured at 1% O2.

treatment_protocol: Culture medium was exchanged every 7 days and cells were grown in culture for up to 14 days.  24hr prior to experimentation cells were transferred to an hypoxic workstation equilibrated with 1% O2, 5% CO2, and the remaining percentage gas N2. Once cortical astrocytes had reached approximately 90% confluence (75cm2 flask) they were subjected to hypoxia as above, washed with PBS, removed from the flask base with 0.05% trypsin-EDTA (Gibco) and then gently centrifuged (500xg).  The cell pellet was then re-suspended in PBS and centrifuged twice more to remove any traces of media.  The cell pellet was then triturated in 8-10 volumes of RNAlater (Applied Biosystems), frozen and stored at -80oC.


title: 1% O2 #2


title: Anti-DMC1 Prdm9-/-

status: Public on May 22 2012

type: SRA

city: Bethesda

first: Kevin

last: Brick

state: MD

address: 5/205 Memorial Drive

department: GBB

institute: NIDDK

description: Sample 10

library_source: genomic

data_processing:
For SSDS samples, reads were mapped to the mm9 genome using the modified bwa algorithm (bwa_ra), described in Khil et al., Genome Research 2012. Read pairs originating from type 1 single-stranded DNA were then selected.
Peak calling was performed on pooled SSDS samples for each genetic background.  Potential peak centres were identified using SISSRs. Adjacent (within 100 nt) putative centres were merged. True peak centres were identified as the midpoint between the median of the forward and reverse tag distributions in the 2 Kb region around each putative centre. Final peaks were defined as the 2 Kb region around the centre.
For ChIP-Seq samples, reads were mapped to the mm9 genome using the Illumina Genome Analyzer Pipeline.  Reads with less than two mismatches were not aligned.  MACS was used to define peaks.
The fourth column in each bedGraph file represents the strength of the peak. Peak strength is defined as the number of tags per peak as calculated by the coverageBed algorithm in the BEDTools suite.
Genome Build:
PRDM9_DSB_hotspots.bedGraph: mm9
PRDM9_SSDS_Sample1_Testis_ssDNA_type1.bed: mm9

source_name: Anti-DMC1 Prdm9-/-_testis_SSDS

growth_protocol: Cells were extracted from testis of euthanized mice and subjected to immunoprecipitation.

extract_protocol: Lysates from mouse testis cells were crosslinked, sonicated and immunoprecipitated with anti-DMC1 or anti-RAD51 antibodies. Size selection of library fragments of 150 - 250 bp was performed after PCR amplification. SSDS samples were denatured and quickly renatured before adapter ligation.

value: wild type

value: testis

tag: chip antibody

value: Anti-DMC1 (C-20)

tag: chip antibody vendor

value: Santa Cruz

tag: chip antibody cat. #

tag: sequencing technique

value: Single Stranded DNA Sequencing (SSDS)


title: OVCA R2 cont Si1

status: Public on Sep 19 2012

description: OVCA R2 cont Si1

hyb_protocol: standard Illumina protocol. In short, a total of 0.75ug of biotin-labeled cRNA was hybridized at 58 degrees C for 16 hours to Illumina's Sentrix Human Ref-8 v23 Expression BeadChips (Illumina, San Diego, CA). Each BeadChip has ~22,000 transcripts with approximately 30-fold redundancy. The arrays were washed, blocked and the labeled cRNA was detected by staining with streptavidin-Cy3.

data_processing: Data was extracted using the Illumina BeadStudio software(v1.5.0.34). Any spots at or below the background were filtered out using an Illumina detection value below 0.98. 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 files.

source_name: OVCAR-2 was obtained from Dr. Thomas C. Hamilton, Fox Chase Cancer Center, Philadelphia, PA.

growth_protocol: Ovarian cell line was cultured in McCoy’s 5A growth medium (Invitrogen) supplemented with 10% fetal bovine serum (FBS) and antibiotics (100 units/ml penicillin and 100 mg/ml streptomycin).

extract_protocol: RNA was extracted from the treated cells using Trizol. Quality and quantity of the total RNA was checked with the Agilent 2100 bioanalyzer using RNA 6000 Nano chips.

treatment_protocol: Ovarian cancer line OVCAR-2 cells were cultured in 6-well plates and Transfected with control siRNA #1 (Dharmacon) using Lipofectamine 2000 (Invitrogen). Cells were treated for 72 hours to allow maximum knockdown, after which they were harvested for RNA preparation.


title: OVCA R2 cont Si2

description: OVCA R2 cont Si2


title: OVCA 420 cldn7 Si2

description: OVCA 420 cldn7 Si2

source_name: OVCA420 was obtained from Dr. Robert C Bast, The University of Texas MD Anderson Cancer Center, Houston, TX.

treatment_protocol: Ovarian cancer line OVCA420 cells were cultured in 6-well plates and Transfected with control siRNA #1 (Dharmacon) using Lipofectamine 2000 (Invitrogen) Cells were treated for 72 hours to allow maximum knockdown, after which they were harvested for RNA preparation.


title: OVCA R2 cldn7 Si2

description: OVCA R2 cldn7 Si2

treatment_protocol: Ovarian cancer line OVCAR-2 cells were cultured in 6-well plates and transfected with Claudin-7 specific siRNA oligos duplexes (Ambion, Inc.Austin, TX) using LipofectAMINE 2000 (Invitrogen). Cells were treated for 72 hours to allow maximum knockdown, after which they were harvested for RNA preparation.


title: OVCA 420 cont Si1

description: OVCA 420 cont Si1


title: OVCA 420 cont Si2

description: OVCA 420 cont Si2


title: Cervical tumor biopsy, P-152

status: Public on Aug 16 2012

city: Oslo

first: Heidi

last: Lyng

address: Montebello

department: Department of Radiation Biology

country: Norway

institute: Oslo University Hospital

hyb_protocol: The samples were hybridized to the arrays at 58oC overnight, using the standard Illumina hybridization protocol.

scan_protocol: Scanning was performed with an Illumina BeadArray reader, using the standard Illumina scanning protocol.

data_processing: The data were normalized using quantile normalization in J-Express.

source_name: Cervical tumor, 3B

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

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

extract_protocol: RNA was extracted with Trizol reagent, followed by double precipitation with isopropanol and final precipitation with 5M lithium chloride. RNA from different biopsies of the same tumor was pooled. Quality control was performed with the Agilent Bioanalyzer.

treatment_protocol: The samples were immediately snap-frozen in liquid nitrogen and stored at -80oC until used for analysis. Biopsies with more than 50% tumor cells in HE stained sections from the central part of the specimen were used further.

tag: histology

value: Adenosquamous

tag: gene-based hypoxia

value: Less hypoxic

tag: imaging-based hypoxia

tag: combined hypoxia biomarker

value: cervical tumor

tag: figo stage

tag: cohort (gse36562 study)

value: DCE-MRI cohort

tag: hypoxia score

value: Low


title: 1% O2 #1

tag: cell type


title: Cervical tumor biopsy, P-153


title: Cervical tumor biopsy, P-178


title: OVCA 420 cldn7 Si1

description: OVCA 420 cldn7 Si1


title: OVCA R2 cldn7 Si1

description: OVCA R2 cldn7 Si1


title: 6MEF 92

status: Public on Jun 25 2012

description: Mouse embryonic fibroblasts, passage 2.

hyb_protocol: Standard Illumina protocol. In short, a total of 0.75ug of biotin-labeled cRNA was hybridized at 58 degrees C for 16 hours to Illumina's Sentrix Mouse Ref-8,v1.1 Expression BeadChips (Illumina, San Diego, CA). Each BeadChip has 24,000 well-annotated RefSeq transcripts with approximately 30-fold redundancy. The arrays were washed, blocked and the labeled cRNA was detected by staining with streptavidin-Cy3.

data_processing: Data was extracted using the Illumina BeadStudio software(v1.5). 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 'GSE20503_non-normalized.txt', which is linked to the Series GSE20503 record as a supplementary file.

source_name: mouse embryonic fibroblasts, passage 2

extract_protocol: RNA was extracted from MEF cells using STAT-60 according to manufacturer's specifications. Quality and quantity of the total RNA was checked with the Agilent 2100 bioanalyzer using RNA 6000 Nano chips.

treatment_protocol: Cells were grown in DMEM medium supplemented with 10% FBS, and RNA was extracted from confluent dishes.

value: primary mouse embryo fibroblasts (MEFs)

tag: treatment

value: not Mytomycin C treated

tag: passage

value: passage 2 beyond frozen


title: Cervical tumor biopsy, P-039

source_name: Cervical tumor, 2B


title: 2PA6 P5

description: PA6 cell line, passage 5.

source_name: PA6 cell line, passage 5

extract_protocol: RNA was extracted from PA6 cells using STAT-60 according to manufacturer's specifications. Quality and quantity of the total RNA was checked with the Agilent 2100 bioanalyzer using RNA 6000 Nano chips.

treatment_protocol: Cells were grown in MEM-alpha medium supplemented with 10% FBS, and RNA was extracted from confluent dishes.

tag: cell line

value: stromal cells


title: 1PA6 P4

description: PA6 cell line, passage 4.

source_name: PA6 cell line, passage 4


title: 1MEF P4

description: Mouse embryonic fibroblasts, passage 4.

source_name: mouse embryonic fibroblasts, passage 4

tag: strain

value: passage 4 beyond frozen


title: SKOB

status: Public on Mar 27 2012

description: Stimulated naïve CD4+ T cells, Pbrm1/BAF180 deficient, replicate B

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 HumanRef-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 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 intensity 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 p-values will be included in the supplemental file.

source_name: Resting naïve CD4+ T cells (N) were purified to 95% purity from the spleens and lymph nodes of 4-6 week old BAF180 cKO Balb/c mice (KO), using CD4+CD62L+ T cell Purification Kit II per manufacturer’s instructions (Miltenyi).

growth_protocol: Resting naïve CD4+ T cells from Pbrm1/BAF180 deficient Balb/c mice.

extract_protocol: RNA was isolated using RNeasy Kit (Qiagen). Quality and quantity of the total RNA was checked with the Agilent 2100 bioanalyzer using RNA 6000 Nano chips.

treatment_protocol: Stimulated Naive cells (S) were prepared from resting naive cells by stimulation for 24 hours on anti-CD3 (1ug/ml), anti-CD28 (2 ug/ml) coated plates at 1-2 x 106/ml.

value: Stimulated naïve cells

value: Balb/c

tag: genotype/variation

value: Pbrm1/BAF180 KO


title: SKOC

description: Stimulated naïve CD4+ T cells, Pbrm1/BAF180 deficient, replicate C


title: SWTA

description: Stimulated naïve CD4+ T cells, wild type, replicate A

source_name: Resting naïve CD4+ T cells (N) were purified to 95% purity from the spleens and lymph nodes of 4-6 week old  WT Balb/c mice (Wt), using CD4+CD62L+ T cell Purification Kit II per manufacturer’s instructions (Miltenyi).

growth_protocol: Resting naïve CD4+ T cells from Wt Balb/c mice.

value: wild type


title: SKOA

description: Stimulated naïve CD4+ T cells, Pbrm1/BAF180 deficient, replicate A


title: NWTA

description: Resting naïve CD4+ T cells, wild type, replicate A

treatment_protocol: Resting naïve CD4+ T cells (N) were used.

value: Resting naïve CD4+ T cells


title: SWTC

description: Stimulated naïve CD4+ T cells, wild type, replicate C


title: NWTB

description: Resting naïve CD4+ T cells, wild type, replicate B


title: NKOC

description: Resting naïve CD4+ T cells, Pbrm1/BAF180 deficient, replicate C


title: 2UWTB

description: Resting Th2 cells, wild type, replicate B

source_name: Resting naïve CD4+ T cells (N) were purified to 95% purity from the spleens and lymph nodes of 4-6 week old  WT Balb/c mice (Wt) using CD4+CD62L+ T cell Purification Kit II per manufacturer’s instructions (Miltenyi).

growth_protocol: Resting Th2 cells were prepared from resting naive cells by plating onto anti-CD3 (1ug/ml), anti-CD28 (2 ug/ml) coated plates at 1-2 x 106/ml in the presence of 10ng/ml IL-4, 10ug/ml anti-IFN-gamma. IL-2 (100U/ml) was added 24 hours later. Cultures were expanded in IL-2 (100U/ml) three days after initial culture.

treatment_protocol: Resting Th2 cells (2U) were used.

value: Resting Th2 cells


title: NWTC

description: Resting naïve CD4+ T cells, wild type, replicate C


title: SWTB

description: Stimulated naïve CD4+ T cells, wild type, replicate B


title: NKOA

description: Resting naïve CD4+ T cells, Pbrm1/BAF180 deficient, replicate A


title: NKOB

description: Resting naïve CD4+ T cells, Pbrm1/BAF180 deficient, replicate B


title: 2UWTA

description: Resting Th2 cells, wild type, replicate A


title: 2SWTB

description: Stimulated Th2 cells, wild type, replicate B

treatment_protocol: Stimulated Th2 cells (2S) were prepared from resting Th2 cells by treatment with PMA (50ng/ml) and Ionomycin (500ng/ml) for 1.5 hours.

value: Stimulated Th2 cells


title: 2UKOC

description: Resting Th2 cells, Pbrm1/BAF180 deficient, replicate C

source_name: Resting naïve CD4+ T cells (N) were purified to 95% purity from the spleens and lymph nodes of 4-6 week old BAF180 cKO Balb/c mice, (KO) using CD4+CD62L+ T cell Purification Kit II per manufacturer’s instructions (Miltenyi).


title: 2UKOA

description: Resting Th2 cells, Pbrm1/BAF180 deficient, replicate A


title: 2SKOA

description: Stimulated Th2 cells, Pbrm1/BAF180 deficient, replicate A

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 labeled cRNA was detected by staining with streptavidin-Cy3.


title: 2SWTA

description: Stimulated Th2 cells, wild type, replicate A


title: 2SKOB

description: Stimulated Th2 cells, Pbrm1/BAF180 deficient, replicate B


title: 2SWTC

description: Stimulated Th2 cells, wild type, replicate C


title: 2UKOB

description: Resting Th2 cells, Pbrm1/BAF180 deficient, replicate B


title: 2SKOC

description: Stimulated Th2 cells, Pbrm1/BAF180 deficient, replicate C


title: DMSO3

status: Public on Mar 21 2012

hyb_protocol: The labeled Cy3 probe (825 ng) was applied to the C. elegans 4x44K Oligo Microarray (Agilent Technologies, USA).   Slides were hybridized in a rotating chamber overnight at 60°C, and then washed in 6X SSC, 0.005% Triton X-102 for 10 minutes, and then in 0.1X SSC, 0.005% Triton X-102 for 5 minutes on ice. Slides were dried using a nitrogen-filled air gun, and scanned using an Agilent array scanner.

scan_protocol: Arrays were scanned at a 5um resolution using the extended dynamic range setting on an Agilent Scanner(G2565AA) .

data_processing: Data from the Cy-3 channel was extracted using the Agilent Feature Extractor Software, Version 9.5.1.1, then each array was z-normalized. In short, the natural logs of all raw intensities were used to find the avg and std of each array and the z-score normalization was calculated:  Z-score = (Natural Log raw value - avg)/std.  Complete data on all spots will be included in the supplemental files.

organism: Caenorhabditis elegans

source_name: All C. elegans strains were obtained from the Caenorhabditis Genetic Center, University of Minnesota

label_protocol: Total RNA was used in the labeling reaction with the QuickAmp labeling Kit, (Agilent Technologies, USA) according to manufacturer’s protocols. In short, 1000ng of total RNA was used to generate double stranded cDNA from mRNA and containing a T7 RNA polymerase binding site.  Then Cy-3 labeled cRNA was generated from this cDNA template using T7 RNA polymerase.

extract_protocol: Total RNA was isolated with the Absolutely RNA Miniprep Kit (Agilent Technologies, USA).  RNA concentration and quality was assessed with an Agilent 2100 Bioanalyzer using the RNA 6000 Nano Kit (Agilent Technologies, USA).

treatment_protocol: Approximately 1,000 age-synchronized young adults were treated for two days with 0.2% DMSO as a vehicle control and then washed three times in M9 and flash frozen with dry ice.

value: Bristol N2

tag: genotype

value: wild-type

tag: protocol

value: grown and maintained at room temperature (22 to 24°C) on Nematode Growth Media (NGM) containing 2.1% agar with E. coli strain OP50 as a food source. Age-synchronized populations were obtained by collecting the eggs laid by fertile adults over 5 to 7 hours and allowing them to develop to the young adult stage before transfer to treatment plates

tag: agent

value: DMSO


title: DMSO4

label_protocol: Total RNA was used in the labeling reaction with the QuickAmp labeling Kit, (Agilent Technologies, USA) according to manufacturer’s protocols. In short, 2000ng of total RNA was used to generate double stranded cDNA from mRNA and containing a T7 RNA polymerase binding site.  Then Cy-3 labeled cRNA was generated from this cDNA template using T7 RNA polymerase.


title: PLB3

hyb_protocol: The labeled Cy5 probe (825 ng) was applied to the C. elegans 4x44K Oligo Microarray (Agilent Technologies, USA).   Slides were hybridized in a rotating chamber overnight at 60°C, and then washed in 6X SSC, 0.005% Triton X-102 for 10 minutes, and then in 0.1X SSC, 0.005% Triton X-102 for 5 minutes on ice. Slides were dried using a nitrogen-filled air gun, and scanned using an Agilent array scanner.

data_processing: Data from the Cy-5 channel was extracted using the Agilent Feature Extractor Software, Version 9.5.1.1, then each array was z-normalized. In short, the natural logs of all raw intensities were used to find the avg and std of each array and the z-score normalization was calculated:  Z-score = (Natural Log raw value - avg)/std.  Complete data on all spots will be included in the supplemental files.

label_protocol: Total RNA was used in the labeling reaction with the QuickAmp labeling Kit, (Agilent Technologies, USA) according to manufacturer’s protocols. In short, 1000ng of total RNA was used to generate double stranded cDNA from mRNA and containing a T7 RNA polymerase binding site.  Then Cy-5 labeled cRNA was generated from this cDNA template using T7 RNA polymerase.

treatment_protocol: Approximately 1,000 age-synchronized young adults were treated for two days with 100 µM plumbagin(Sigma-Aldrich Co., St. Louis, MO), washed three times in M9 and flash frozen with dry ice.

value: 100 µM plumbagin


title: DMSO2


title: PLB2


title: CLM_29

description: Muscle tissue from mice that were fed an ad lib diet.

data_processing: Data was extracted using the Illumina GenomeStudio software(v1.1.1).  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: Mus musculus muscle tissue

extract_protocol: RNA was extracted from muscle tissue using 1.0mm glass beads (BioSpec Products, Inc.) in a Precellys 24 Tissue Homogenizer (Bertin Technologies) and Qiagen RNeasy Mini Kits according to manufacturer's specifications. Quality and quantity of the total RNA was checked with the Agilent 2100 bioanalyzer using RNA 6000 Nano chips.

tag: tissue

value: Muscle tissue

value: Balb-c mice

value: fed an ad lib diet


title: 2UWTC

description: Resting Th2 cells, wild type, replicate C


title: SLM_14

description: Muscle tissue from mice that fasted for 48 hours.

value: fasted for 48 hours


title: PLB4

label_protocol: Total RNA was used in the labeling reaction with the QuickAmp labeling Kit, (Agilent Technologies, USA) according to manufacturer’s protocols. In short, 2000ng of total RNA was used to generate double stranded cDNA from mRNA and containing a T7 RNA polymerase binding site.  Then Cy-5 labeled cRNA was generated from this cDNA template using T7 RNA polymerase.


title: CNT_18

description: Subcutaneous 4T1 breast cancer tumor mass from mice that were fed an ad lib diet.

source_name: 4T1-luc murine breast cancer cells were purchased from SibTech (Brookfield, CT).

extract_protocol: RNA was extracted from a subcutaneous 4T1 breast cancer tumor mass using 1.0mm glass beads (BioSpec Products, Inc.) and a Precellys 24 Tissue Homogenizer (Bertin Technologies) and Qiagen RNeasy Mini Kits according to manufacturer's specifications. Quality and quantity of the total RNA was checked with the Agilent 2100 bioanalyzer using RNA 6000 Nano chips.

value: Subcutaneous 4T1 breast cancer tumor mass tissue


title: DMSO1

label_protocol: Total RNA was used in the labeling reaction with the QuickAmp labeling Kit, (Agilent Technologies, USA) according to manufacturer’s protocols. In short, 500ng of total RNA was used to generate double stranded cDNA from mRNA and containing a T7 RNA polymerase binding site.  Then Cy-3 labeled cRNA was generated from this cDNA template using T7 RNA polymerase.


title: SNM_4

treatment_protocol: Muscle tissue from mice that fasted for 48 hours.


title: CNM_19

treatment_protocol: Muscle tissue from mice that were fed an ad lib diet.


title: CLT_28

treatment_protocol: Subcutaneous 4T1 breast cancer tumor mass from mice that were fed an ad lib diet.


title: CRM_24


title: SRM_9


title: CTR2

description:
sh-sy5y cells were maintained at 37oc in a humidified 5% co2 incubator in amem/f12 supplemented with 10% fbs, 100 units/ml ?penicillin and 100 units/ml streptomycin.  cells were conditioned with either phosphate-buffered saline (pbs) (ctr), or 10nm hydrogen peroxide(cmp) (h2o2: Sigma Aldrich, St Louis MO) for seven days.  Cell growth media and applied hydrogen peroxide treatments were changed daily.
CTR2

source_name: SH-SY5Y neural cells, obtained from ATCC (http://www.atcc.org/),

treatment_protocol: The control(CTR) SH-SY5Y cells were serum-starved overnight prior to collection and isolation of RNA.

value: control


title: SRT_8

description: Subcutaneous 4T1 breast cancer tumor mass from mice that were fasted for 48 hours.

extract_protocol: RNA was extracted from a subcutaneous 4T1 breast cancer tumor mass using 1.0mm glass beads (BioSpec Products, Inc.) in a Precellys 24 Tissue Homogenizer (Bertin Technologies) and Qiagen RNeasy Mini Kits according to manufacturer's specifications. Quality and quantity of the total RNA was checked with the Agilent 2100 bioanalyzer using RNA 6000 Nano chips.


title: PLB1

label_protocol: Total RNA was used in the labeling reaction with the QuickAmp labeling Kit, (Agilent Technologies, USA) according to manufacturer’s protocols. In short, 500ng of total RNA was used to generate double stranded cDNA from mRNA and containing a T7 RNA polymerase binding site.  Then Cy-5 labeled cRNA was generated from this cDNA template using T7 RNA polymerase.


title: SLT_13

treatment_protocol: Subcutaneous 4T1 breast cancer tumor mass from mice that were fasted for 48 hours.


title: CNL_17

description: Liver tissue from mice that were fed an ad lib diet.

source_name: Mus musculus liver tissue

extract_protocol: RNA was extracted from liver tissue using 1.0mm glass beads (BioSpec Products, Inc.) in a Precellys 24 Tissue Homogenizer (Bertin Technologies) and Qiagen RNeasy Mini Kits according to manufacturer's specifications. Quality and quantity of the total RNA was checked with the Agilent 2100 bioanalyzer using RNA 6000 Nano chips.

value: Liver tissue


title: CRT_23


title: CRL_22

treatment_protocol: Liver tissue from mice that were fed an ad lib diet.