title: regenerating trout muscle (8 days post-lesion) sample 1

value: 8 days post-lesion; T1


title: regenerating trout muscle (8 days post-lesion) sample 3

status: Public on Jul 01 2016

type: RNA

city: Rennes

first: Aurelie

last: LE CAM

address: Campus de Beaulieu

department: PHASE

country: France

institute: INRA

hyb_protocol: 600 ng of Cy3-cRNA was fragmented and hybridized on a sub-array. Hybridization was carried out for 17 hours at 65°C in a rotating hybridization oven prior to washing

scan_protocol: Microarrays were scanned with an Agilent Scanner (Agilent DNA Microarray Scanner, Agilent Technologies, Massy, France) using the standard parameters for a gene expression 8x60K oligoarray (3µm and 20bits)

data_processing:
Data were then obtained with the Agilent Feature Extraction software (10.7.1.1) according to the appropriate GE protocol (GE1_107_Sep09).
Data were scale-normalized using the median value of each array, then log2 transformed before statistical analysis. Normalization and statistical analysis were performed using GeneSpring software (Agilent).

molecule: total RNA

organism: Oncorhynchus mykiss

label_protocol: Labeling and hybridization steps were performed following the “One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling)”Agilent protocol. Briefly, for each sample, 150 ng of total RNA was amplified and labeled using Cy3-CTP. Yield (>0.825µg cRNA) and specific activity (> 6pmol of Cy3 per µg of cRNA) of Cy3-cRNA produced were checked with the Nanodrop.

growth_protocol: Trout were reared in freshwater tank under a natural photoperiod. The average water temperature was around 7 °C throughout the experimental period.

extract_protocol: RNA samples were extracted using TRI Reagent

treatment_protocol: Lesions were made in 24-month-old anaesthetised trout by repeatedly inserting and withdrawing a syringe needle (1.2 x 40 mm) into trunk muscle, one centimetre beneath the dorsal fin. For sampling, the trout were killed by anaesthetic (2-phénoxyéthanol) overdose and decapitated. Blocks of muscle close to the site of the lesions were then cut for histological analysis and RNA extraction.

tag: time point

value: 8 days post-lesion; T8

tag: tissue

value: regenerating trout muscle


title: regenerating trout muscle (1 day post-lesion) sample 5

value: 1 day post-lesion; T1


title: RT_PCR_HMSC1994_P8_TR1

city: Silver Spring

first: Raj

middle: K

last: Puri

state: Maryland

address: 10903 New Hampshire Ave

country: USA

institute: FDA

data_processing: All genes on the 96 well plate were repeated in triplicate.  The CT value for each gene (per plate) was determined by taking the median of the 3 values.  The genes of interest were then normalized by 8 different methods, where the delta CT value was calculated for each gene by subtracting the normalized CT from the gene of interest.  The 8 methods of normalization are: 1) All Combined (The CT value was calculated from the geometric mean of ACTB, GAPDH, GUSB, NACAD and ST13); 2) ACTB (Gene of interest minus the CT of ACTB); 3) Common Combined (Gene of interest minus the CT which is the geometric mean of ACTB, GAPDH and GUSB); 4) GAPDH (Gene of interest minus the CT of GAPDH); 5) GUSB (Gene of interest minus the CT of GUSB); 6) NACAD (Gene of interest minus the CT of NACAD); 7) New Combined (Gene of interest minus the CT which is the geometric mean of NACAD and ST13); 8) ST13 (Gene of interest minus the CT of ST13). RT-qPCR data were further analyzed by correlation to proliferation data. The file Proliferation_gradients.xlsx contains proliferation gradient (slope) of a regression analysis. Sample tables contain data normalized to ACTB. Data normalized by all methods can be found in the file Normalized_data_all_methods.xlsx, available on the series record.

label: SYBR Green

organism: Homo sapiens

source_name: Multipotent Stromal Cells

label_protocol: RT-qPCR plates containing 30 genes in triplicate with positive/negative controls were purchased from Bio-Rad (Hercules, CA).  Reverse transcription was performed per the manufacturer’s instruction using the 5x iScript cDNA synthesis kit. Quantitative PCR was performed per the manufacturer’s instructions using SsoAdvanced universal SYBR green supermix.  The reaction protocol was 10 seconds at 95oC and 30 seconds at 60oC for 40 cycles on Bio-RAD CFX96.

growth_protocol: All cells were expanded in marrow stromal cell growth medium (Cell Applications, San Diego, CA) under a humidified atmosphere of 5% CO2 at 37oC

extract_protocol: Total RNA was extracted with Qiagen RNeasy Mini Kit followed by DNase I treatment.

tag: cell type

value: Multipotent Stromal Cells

tag: passage

tag: number of replicates


title: MH0146581

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

label: biotin

source_name: cultured cells

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: Both RUCDR and UCLA extracted RNA from the cultured cells with an RNeasy 96 kit (Qiagen, Venlo, Netherlands), employing either a Qiagen BioRobot Universal System (RUCDR) or a manual procedure (UCLA) using up to 5x105 cells (RUCDR) or 106 cells (UCLA) as the starting material. To quantify RNA yield, we used a Quant-iT RiboGreen (Invitrogen, Waltham, MA) and measured RNA integrity number, reflective of sample quality, using a TapeStation (Agilent, Santa Clara, CA).

tag: rnasource

value: RNA from NIMH repository

value: Lymphoblastoid cell lines (LCLs)

tag: fid

tag: iid

tag: gender

value: m

tag: age (yrs)


title: 09C99181


title: 10C111628

value: f


title: RT_PCR_HMSC1994_P4_TR1


title: RT_PCR_HMSC2483_P8_TR1


title: 09C99195


title: RT_PCR_RB14_P8_TR1


title: RT_PCR_RB14_P4_TR1


title: RT_PCR_BM3018_P4_TR1


title: RT_PCR_BM3018_P8_TR1


title: RT_PCR_BM2893_P8_TR1


title: RT_PCR_1F3422_P8_TR1


title: RT_PCR_1F3422_P4_allreps

description: Replicate IDs: 1F3422_P4_TR1, 1F3422_P4_TR2, 1F3422_P4_TR3

data_processing: All genes on the 96 well plate were repeated in triplicate.  The CT value for each gene (per plate) was determined by taking the median of the 3 values.  The genes of interest were then normalized by 8 different methods, where the delta CT value was calculated for each gene by subtracting the normalized CT from the gene of interest.  The 8 methods of normalization are: 1) All Combined (The CT value was calculated from the geometric mean of ACTB, GAPDH, GUSB, NACAD and ST13); 2) ACTB (Gene of interest minus the CT of ACTB); 3) Common Combined (Gene of interest minus the CT which is the geometric mean of ACTB, GAPDH and GUSB); 4) GAPDH (Gene of interest minus the CT of GAPDH); 5) GUSB (Gene of interest minus the CT of GUSB); 6) NACAD (Gene of interest minus the CT of NACAD); 7) New Combined (Gene of interest minus the CT which is the geometric mean of NACAD and ST13); 8) ST13 (Gene of interest minus the CT of ST13). RT-qPCR data were further analyzed by correlation to proliferation data. The file Proliferation_gradients.xlsx contains proliferation gradient (slope) of a regression analysis. Sample tables contain data normalized to ACTB. Data normalized by all methods can be found in the file Normalized_data_all_methods.xlsx, available on the series record.  The samples were repeated in triplicate to obtain an estimate of the variability of these genes using the Bio-RAD platform.  These samples are 1F3422_P4, HMSC2483_P4 and HMSC2618_P8.  After the 8 normalization methods were applied, the median delta CT value per gene for the 3 RT-qPCR plates was used for each sample.  The sample size for only the MSC samples was 16, while the samples size was 20 for both the MSCs and non-MSCs.


title: 09C99197


title: NGL1167

value: RNA from LCL in UCLA


title: regenerating trout muscle (1 day post-lesion) sample 3


title: NGL1168


title: trout muscle before injury  (time 0) sample 4

value: before injury; T0

value: trout muscle before injury


title: 1.0mm-anther-ms6015-fertilesib-Rep4-Cy5

city: Stanford

first: John

middle: F

last: Fernandes

address: 385 Serra Mall

department: Bio Sci

institute: Stanford University

description:
raw data file: US84703594_251604710149_S01_GE2_107_Sep09_1_4.txt
compare 1.0 mm anthers from ms6015-mutant versus ms6015-fertilesib

hyb_protocol: 825 ng of each labeled target cRNA were hybridized for 17 h at 60C.

scan_protocol: Slides were scanned on an Agilent DNA microarray scanner as indicated in the manual.  Images were processed with the Agilent Feature Extraction software.

data_processing:
After removal of spots flagged by Feature Extraction as below background or saturated or outliers, intensities for each channel from Feature Extraction were normalized using lowess.  Average intensities were then calculated for each sample type for comparison.
The limma package of R was used to normalize the median intensities for each channel as follows: within each array using loess and between arrays using quantile method.

organism: Zea mays

source_name: 1.0mm whole anther, Cy5 Rep4, ms6015-fertilesib

label_protocol: Total RNA (50 ng) was amplified & labeled with Cy3 or Cy5 using Agilent Low RNA Input Linear Amplification Kit.

growth_protocol: Plants were grown and dissected at the Stanford field; tissues were collected and frozen in liquid nitrogen immediately.

extract_protocol: For whole anthers, total RNA was extracted from 30 - 60 mg of frozen tissues with TRIzol, digested with DNase I, and cleaned up with Qiagen RNeasy Mini kit.

value: anther


title: regenerating trout muscle (1 day post-lesion) sample 4


title: regenerating trout muscle (1 day post-lesion) sample 2


title: regenerating trout muscle (1 day post-lesion) sample 1


title: 10C107446


title: 10C117217


title: trout muscle before injury (time 0) sample 3


title: RT_PCR_BM2893_P4_TR1


title: 1.0mm-anther-ms6015-mutant-Rep3-Cy5

description:
raw data file: US84703594_251604710149_S01_GE2_107_Sep09_1_3.txt
compare 1.0 mm anthers from ms6015-fertilesib versus ms6015-mutant

source_name: 1.0mm whole anther, Cy5 Rep3, ms6015-mutant


title: MH0129856


title: 10C117216


title: trout muscle before injury (time 0) sample 2


title: trout muscle before injury (time 0) sample 1


title: 1.0mm-anther-ms6015-fertilesib-Rep2-Cy5

description:
raw data file: US84703594_251604710149_S01_GE2_107_Sep09_1_2.txt
compare 1.0 mm anthers from ms6015-mutant versus ms6015-fertilesib

source_name: 1.0mm whole anther, Cy5 Rep2, ms6015-fertilesib


title: 1.0mm-anther-tcl1-fertilesib-Rep3-Cy5

description:
raw data file: US84703594_251604710148_S01_GE2_107_Sep09_1_1.txt
compare 1.0 mm anthers from tcl1-mutant versus tcl1-fertilesib

source_name: 1.0mm whole anther, Cy5 Rep3, tcl1-fertilesib


title: 1.0mm-anther-ms6015-mutant-Rep1-Cy5

description:
raw data file: US84703594_251604710149_S01_GE2_107_Sep09_1_1.txt
compare 1.0 mm anthers from ms6015-fertilesib versus ms6015-mutant

source_name: 1.0mm whole anther, Cy5 Rep1, ms6015-mutant


title: 1.0mm-anther-tcl1-mutant-Rep1-Cy5

description:
raw data file: US84703594_251604710148_S01_GE2_107_Sep09_1_3.txt
compare 1.0 mm anthers from tcl1-fertilesib versus tcl1-mutant

source_name: 1.0mm whole anther, Cy5 Rep1, tcl1-mutant


title: 1.0mm-anther-mtm00-06-fertilesib-Rep3-Cy5

description:
raw data file: US84703594_251604710150_S01_GE2_107_Sep09_1_4.txt
compare 1.0 mm anthers from mtm00-06-mutant versus mtm00-06-fertilesib

source_name: 1.0mm whole anther, Cy5 Rep3, mtm00-06-fertilesib


title: 1.0mm-anther-mtm00-06-mutant-Rep3-Cy5

description:
raw data file: US84703594_251604710150_S01_GE2_107_Sep09_1_3.txt
compare 1.0 mm anthers from mtm00-06-fertilesib versus mtm00-06-mutant

source_name: 1.0mm whole anther, Cy5 Rep3, mtm00-06-mutant


title: 1.0mm-anther-tcl1-fertilesib-Rep4-Cy5

description:
raw data file: US84703594_251604710148_S01_GE2_107_Sep09_1_2.txt
compare 1.0 mm anthers from tcl1-mutant versus tcl1-fertilesib

source_name: 1.0mm whole anther, Cy5 Rep4, tcl1-fertilesib


title: 1.0mm-anther-mtm00-06-fertilesib-Rep2-Cy5

description:
raw data file: US84703594_251604710150_S01_GE2_107_Sep09_1_2.txt
compare 1.0 mm anthers from mtm00-06-mutant versus mtm00-06-fertilesib

source_name: 1.0mm whole anther, Cy5 Rep2, mtm00-06-fertilesib


title: 1.0mm-anther-ms6015-mutant-Rep2-Cy3

source_name: 1.0mm whole anther, Cy3 Rep2, ms6015-mutant


title: 10C116759


title: 1.0mm-anther-ms6015-mutant-Rep4-Cy3

source_name: 1.0mm whole anther, Cy3 Rep4, ms6015-mutant


title: 1.0mm-anther-mtm00-06-mutant-Rep1-Cy5

description:
raw data file: US84703594_251604710150_S01_GE2_107_Sep09_1_1.txt
compare 1.0 mm anthers from mtm00-06-fertilesib versus mtm00-06-mutant

source_name: 1.0mm whole anther, Cy5 Rep1, mtm00-06-mutant


title: 1.0mm-anther-tcl1-mutant-Rep4-Cy3

source_name: 1.0mm whole anther, Cy3 Rep4, tcl1-mutant


title: 1.0mm-anther-tcl1-mutant-Rep3-Cy3

source_name: 1.0mm whole anther, Cy3 Rep3, tcl1-mutant


title: 10C117218


title: 1.0mm-anther-ms6015-fertilesib-Rep1-Cy3

source_name: 1.0mm whole anther, Cy3 Rep1, ms6015-fertilesib


title: 1.0mm-anther-ms6015-fertilesib-Rep3-Cy3

source_name: 1.0mm whole anther, Cy3 Rep3, ms6015-fertilesib


title: 09C82034

source_name: cultured cells


title: 10C114428


title: 1.0mm-anther-tcl1-mutant-Rep2-Cy5

description:
raw data file: US84703594_251604710148_S01_GE2_107_Sep09_1_4.txt
compare 1.0 mm anthers from tcl1-fertilesib versus tcl1-mutant

source_name: 1.0mm whole anther, Cy5 Rep2, tcl1-mutant


title: 1.0mm-anther-tcl1-fertilesib-Rep2-Cy3

source_name: 1.0mm whole anther, Cy3 Rep2, tcl1-fertilesib


title: 10C108285


title: 09C82032


title: 09C82033


title: 1.0mm-anther-tcl1-fertilesib-Rep1-Cy3

source_name: 1.0mm whole anther, Cy3 Rep1, tcl1-fertilesib


title: knee6

type: genomic

city: St. John's

first: Guangju

last: Zhai

state: NL

address: 300 Prince Philip Drive

department: Genetics, Medicine

country: Canada

institute: Memorial University of Newfoundland

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation 450 Bead-Chip microarray

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
R packages minfi (version 1.6.0) and minfiData (version 0.3.4)
Normalized beta value by beta-mixture quantile normalization (BMIQ) method
The non_normalized.txt contains unmethylated and methylated signal intensities

label: cy3, cy5

molecule: genomic DNA

source_name: Osteoarthritic knee cartilage

label_protocol: Standard Illumina Protocol

extract_protocol: The DNA was extracted using Phenol-Chloroform method following TRIzole treatment of the homogenized tissues.

tag: subject status

value: joint replacement patient

tag: disease state

value: Osteoarthritic

value: Female

tag: body mass index

tag: joint

value: Knee

tag: sample type

value: Cartilage specimen from joint replacement surgery


title: RT_PCR_HMSC2618_P8_allreps

description: Replicate IDs: HMSC2618_P8_TR1, HMSC2618_P8_TR2, HMSC2618_P8_TR3

data_processing: All genes on the 96 well plate were repeated in triplicate.  The CT value for each gene (per plate) was determined by taking the median of the 3 values.  The genes of interest were then normalized by 8 different methods, where the delta CT value was calculated for each gene by subtracting the normalized CT from the gene of interest.  The 8 methods of normalization are: 1) All Combined (The CT value was calculated from the geometric mean of ACTB, GAPDH, GUSB, NACAD and ST13); 2) ACTB (Gene of interest minus the CT of ACTB); 3) Common Combined (Gene of interest minus the CT which is the geometric mean of ACTB, GAPDH and GUSB); 4) GAPDH (Gene of interest minus the CT of GAPDH); 5) GUSB (Gene of interest minus the CT of GUSB); 6) NACAD (Gene of interest minus the CT of NACAD); 7) New Combined (Gene of interest minus the CT which is the geometric mean of NACAD and ST13); 8) ST13 (Gene of interest minus the CT of ST13). RT-qPCR data were further analyzed by correlation to proliferation data. The file Proliferation_gradients.xlsx contains proliferation gradient (slope) of a regression analysis. Sample tables contain data normalized to ACTB. Data normalized by all methods can be found in the file Normalized_data_all_methods.xlsx, available on the series record.  The samples were repeated in triplicate to obtain an estimate of the variability of these genes using the Bio-RAD platform. These samples are 1F3422_P4, HMSC2483_P4 and HMSC2618_P8. After the 8 normalization methods were applied, the median delta CT value per gene for the 3 RT-qPCR plates was used for each sample. The sample size for only the MSC samples was 16, while the samples size was 20 for both the MSCs and non-MSCs.

source_name: Multipotent Stromal Cells


title: hip5

source_name: Osteoarthritic hip cartilage

value: Hip


title: 1.0mm-anther-mtm00-06-mutant-Rep3-Cy3

source_name: 1.0mm whole anther, Cy3 Rep3, mtm00-06-mutant


title: 1.0mm-anther-mtm00-06-fertilesib-Rep3-Cy3

source_name: 1.0mm whole anther, Cy3 Rep3, mtm00-06-fertilesib


title: 09C82031


title: 1.0mm-anther-mtm00-06-mutant-Rep2-Cy3

source_name: 1.0mm whole anther, Cy3 Rep2, mtm00-06-mutant


title: control7

source_name: Normal hip cartilage

value: Normal


title: Glioblastoma sample #29

city: Barretos

first: Rui

middle: Manuel

last: Reis

state: SP

address: R. Antenor Duarte Villela, 1331

department: Molecular Oncology Research Center

country: Brazil

institute: Barretos Cancer Hospital

hyb_protocol: Labeled DNAs were purified, mixed with 2ul of 1mg/ml Cot1 human DNA, aCGH blocking agent and hybridiation buffer, and hybridized in 8x60k microarray slides for 16 hours. Slides were sequentially washed in wash buffers 1 and 2, following acetonitrile and stabilization and Drying solution according to Agilent's default protocol.

scan_protocol: Scanned on an Agilent G2505C scanner and images were quantified using Agilent Feature Extraction Software (version 11.0.1.1)

data_processing: Analyss was performed using Bioconductor/LIMMA. Data was bacground subtracted, loess normalized and annotated using hg19. Replicate probes were averaged and data was CBS segmented and smoothed. The data was rescaled in order to obtain MAD=0.1

source_name: Glioblastoma multiforme

label_protocol: 400ug of DNA was AluI and RsaI digested at 37oC for 2 hours, primed with 2.5ul of random primers, and CY3 or CY5 labeled at 37oC for 2 hours according to Agilent's default protocol.

growth_protocol: The glioblastoma primary cell lines  grow in DMEM (Dulbecco´s Modified Eagle Medium - Sigma-Aldrich) supplemented with 10% of FBS (Fetal Bovine Serum - Sigma-Aldrich) and 1% of PS (Penicillin-Streptomycin - Invitrogen) at 37ºC in humidified atmosphere of 5% carbon dioxide in air. The medium was renewed every 48 or 72 hours, depending of the cell growth kinetics.

extract_protocol: Genomic DNA was extracted using Trizol (Invitrogen) for primary cell lines and DNAeasy (Qiagen) for frozen tumor tissue using supplier's protocol (Dry)

tag: tissue type

value: Brain

source_name: Promega commercial genomic DNA P/N G1521

tag: reference


title: NGL1310


title: 09C99194


title: 1.0mm-anther-mtm00-06-fertilesib-Rep1-Cy3

source_name: 1.0mm whole anther, Cy3 Rep1, mtm00-06-fertilesib


title: Glioblastoma sample #40

value: Promega commercial genomic DNA P/N G1521


title: Glioblastoma sample #2

value: Male

source_name: Promega commercial genomic DNA P/N G1471


title: NGL2344

value: Lymphoblastoid cell lines (LCLs)


title: knee4


title: MH0128802

value: RNA from NIMH repository


title: Glioblastoma sample #144


title: Glioblastoma sample #149


title: knee5


title: Primary glioblastoma cell line Barretos Cancer Hospital #40

source_name: Primary glioblastoma cell line

value: Primary cell line


title: Primary glioblastoma cell line Barretos Cancer Hospital #2

value: Promega commercial genomic DNA P/N G1471


title: knee3


title: Primary glioblastoma cell line Barretos Cancer Hospital #149


title: NGL188

value: RNA from LCL in UCLA

value: m


title: MH0127894


title: control6


title: NGL157


title: Primary glioblastoma cell line Barretos Cancer Hospital #144


title: hip4


title: Primary glioblastoma cell line Barretos Cancer Hospital #29


title: NGL193

value: f


title: 24_S111A_Fsk_IR_A1

city: RTP

first: Pierre

middle: Robert

last: Bushel

state: NC

department: Biostatistics and Computational Biology Branch

institute: NIEHS

description: Gene expression from S111A forskolin + ionizing radiation treated

hyb_protocol: Hybridizations were carried out using an Agilent Technologies DNA microarray model #G2565 CA.

scan_protocol: Microarrays were carried out using Agilent SurePrint G3 Mouse Gene Expression 8x60K Microarray 8-plex slides (n=6 embryos per genotype/per condition).

data_processing: The pixel intensity data acquired from the microarrays were quantile normalized and log base 2 transformed. Since the arrays were processed at two dFskferent times (A and B), the data were corrected for this batch effect using ComBat and an empirical Bayes, non-parametric model of the data was performed with genotype and treatment as covariates. The data was then filtered by removing probes Fsk 40 of the 48 arrays had values less than the 5th percentile and missing values subsequently imputed by flooring them at the 5th percentile.

organism: Mus musculus

source_name: S111A, Fsk-IR, Batch A, replicate 1

label_protocol: RNA samples were labeled using the Agilent Low Input Quick Amp Labeling Kit, One-Color.

growth_protocol: Primary mouse embryonic fibroblasts (MEFs) were maintained in Dulbecco's modified Eagle's medium (DMEM) containing 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin.

extract_protocol: RNA was extracted using TRIzol (Invitrogen) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop spectrophotometer.

treatment_protocol: Primary MEFs were treated with Fsk for 90 min, irradiated with 20 Gy IR for 120 min (20 Gy), or treated with 20 Gy IR 30 min prior to Fsk (20 Gy/Fsk) after serum starvation for 16 hours.

value: Embryo

value: Mouse embryonic fibroblasts (MEFs)

tag: genotype

tag: treatment

value: Forskolin-Ionizing radiation

tag: batch

value: A

tag: replicate


title: control3

value: joint replacement patient

value: Female

value: Cartilage specimen from joint replacement surgery


title: control5

value: Normal

value: Hip


title: 22_S111A_Fsk_IR_A1

tag: tissue

tag: cell type


title: 23_S111A_Fsk_IR_A1


title: 23_S111A_Fsk_IR_B2

source_name: S111A, Fsk-IR, Batch B, replicate 2

value: B


title: MH0128354

source_name: cultured cells

tag: rnasource

value: Lymphoblastoid cell lines (LCLs)

tag: fid


title: 21_S111A_IR_B3

description: Gene expression from S111A ionizing radiation treated

source_name: S111A, IR, Batch B, replicate 3

value: Ionizing radiation


title: NGL194

tag: iid

tag: gender


title: knee1

tag: subject status

value: Osteoarthritic

tag: age (yrs)

value: Knee


title: 22_S111A_Fsk_IR_B1

source_name: S111A, Fsk-IR, Batch B, replicate 1


title: 24_S111A_Fsk_IR_B3

source_name: S111A, Fsk-IR, Batch B, replicate 3


title: NGL167

value: RNA from LCL in UCLA


title: knee2

source_name: Osteoarthritic knee cartilage

tag: disease state

tag: body mass index


title: control4

tag: joint

tag: sample type


title: 20_S111A_IR_A2

source_name: S111A, IR, Batch A, replicate 2


title: control2


title: NGL196


title: 19_S111A_IR_A1

source_name: S111A, IR, Batch A, replicate 1


title: hip3

source_name: Osteoarthritic hip cartilage


title: 21_S111A_IR_A3

source_name: S111A, IR, Batch A, replicate 3


title: 20_S111A_IR_B2

source_name: S111A, IR, Batch B, replicate 2


title: 19_S111A_IR_B1

source_name: S111A, IR, Batch B, replicate 1


title: NGL295


title: 18_S111A_Fsk_A3

description: Gene expression S111A from forskolin treated

source_name: S111A, Fsk, Batch A, replicate 3

value: Forskolin


title: 18_S111A_Fsk_B3

source_name: S111A, Fsk, Batch B, replicate 3


title: 17_S111A_Fsk_A2

source_name: S111A, Fsk, Batch A, replicate 2


title: hip2


title: control1

source_name: Normal hip cartilage


title: NGL2349

value: m


title: hip1


title: 15_S111A_Control_B3

description: Gene expression from S111A Control treated

source_name: S111A, Control, Batch B, replicate 3

value: Embryo

value: Control


title: 14_S111A_Control_A2

source_name: S111A, Control, Batch A, replicate 2

value: Mouse embryonic fibroblasts (MEFs)


title: 15_S111A_Control_A3

source_name: S111A, Control, Batch A, replicate 3

value: A


title: 16_S111A_Fsk_B1

source_name: S111A, Fsk, Batch B, replicate 1


title: NGL141

source_name: cultured cells

value: f


title: 12_WT_Fsk_IR_A3

description: Gene expression from WT forskolin + ionizing radiation treated

source_name: WT, Fsk-IR, Batch A, replicate 3

value: Wild Type

value: Forskolin-Ionizing radiation


title: NGL177


title: 13_S111A_Control_B1

source_name: S111A, Control, Batch B, replicate 1


title: 13_S111A_Control_A1

source_name: S111A, Control, Batch A, replicate 1


title: 16_S111A_Fsk_A1

source_name: S111A, Fsk, Batch A, replicate 1


title: 09C99193

value: RNA from NIMH repository


title: 10_WT_Fsk_IR_B1

source_name: WT, Fsk-IR, Batch B, replicate 1


title: 14_S111A_Control_B2

source_name: S111A, Control, Batch B, replicate 2


title: 11_WT_Fsk_IR_A2

source_name: WT, Fsk-IR, Batch A, replicate 2


title: NGL145


title: 10_WT_Fsk_IR_A1

source_name: WT, Fsk-IR, Batch A, replicate 1


title: 11_WT_Fsk_IR_B2

source_name: WT, Fsk-IR, Batch B, replicate 2


title: NGL183


title: 9_WT_IR_B3

description: Gene expression from WT ionizing radiation treated

source_name: WT, IR, Batch B, replicate 3


title: 17_S111A_Fsk_B2

source_name: S111A, Fsk, Batch B, replicate 2


title: NGL296


title: NGL190


title: 12_WT_Fsk_IR_B3

source_name: WT, Fsk-IR, Batch B, replicate 3


title: 09C99192


title: 9_WT_IR_A3

source_name: WT, IR, Batch A, replicate 3


title: 8_WT_IR_A2

source_name: WT, IR, Batch A, replicate 2


title: NGL148


title: 6_WT_Fsk_B3

description: Gene expression WT from forskolin treated

source_name: WT, Fsk, Batch B, replicate 3


title: NGL160


title: 7_WT_IR_B1

source_name: WT, IR, Batch B, replicate 1


title: NGL165

source_name: cultured cells


title: 5_WT_Fsk_B2

source_name: WT, Fsk, Batch B, replicate 2


title: 7_WT_IR_A1

source_name: WT, IR, Batch A, replicate 1


title: 4_WT_Fsk_A1

source_name: WT, Fsk, Batch A, replicate 1


title: NGL2343


title: 6_WT_Fsk_A3

source_name: WT, Fsk, Batch A, replicate 3


title: NGL293


title: MH0127896


title: 3_WT_Control_A3

description: Gene expression from WT Control treated

source_name: WT, Control, Batch A, replicate 3


title: NGL164


title: NGL161


title: NGL140


title: NGL153


title: NGL143


title: 3_WT_Control_B3

description: Gene expression from WT Control treated

source_name: WT, Control, Batch B, replicate 3


title: 2_WT_Control_A2

description: Gene expression from WT Control treated

source_name: WT, Control, Batch A, replicate 2


title: NGL135


title: 5_WT_Fsk_A2

source_name: WT, Fsk, Batch A, replicate 2


title: MH0127897


title: 2_WT_Control_B2

description: Gene expression from WT Control treated

source_name: WT, Control, Batch B, replicate 2


title: 1_WT_Control_A1

description: Gene expression from WT Control treated

source_name: WT, Control, Batch A, replicate 1


title: 8_WT_IR_B2

source_name: WT, IR, Batch B, replicate 2


title: 4_WT_Fsk_B1

source_name: WT, Fsk, Batch B, replicate 1


title: Ly6G+/F4/80- neutrophils

city: Shenzhen

first: Yaojiong

last: Wu

state: Guangzhou

address: Xili unversity town, Nanshan

department: Graduate school at shenzhen

country: China

institute: Tsinghua university

description: Genes expression in Ly6C+/F4/80+ inflammatory macrophages, CX3CR1+/F4/80+ tissue resident macrophages and Ly6G+/F4/80- neutrophils which were isolated from day 3 wounds in C57/B6 mice aged 8 weeks by cell sorting

hyb_protocol: 10 μg labeled cRNA was hybridized at 45 °C for 16 h to mouse genome array

scan_protocol: Processed chips were read by Agilent G2565CA Microarray Scanner.

data_processing: Scanned microarray images were imported into GeneSpring GX Software to generate signal values and absent/present calls

source_name: Neutrophils

label_protocol: CY3 labelled

extract_protocol: Total RNA was extracted from the cells with Trizol (Invitrogen).

tag: strain

value: skin wound

value: Neutrophils

tag: cell markers


title: 1_WT_Control_B1

description: Gene expression from WT Control treated

source_name: WT, Control, Batch B, replicate 1

tag: genotype

tag: treatment

value: B


title: Ly6C+/F4/80+ inflammatory macrophages

source_name: Inflammatory macrophages

value: Inflammatory macrophages


title: CX3CR1+/F4/80+ tissue resident macrophages

source_name: Tissue resident macrophages

value: Tissue resident macrophages


title: NGL134

source_name: cultured cells

value: Lymphoblastoid cell lines (LCLs)


title: 09C82030


title: 11C118645


title: NGL139

value: RNA from LCL in UCLA


title: MH0128351


title: 10C110593


title: MH0131370


title: NGL189


title: MH0128352


title: NGL155


title: 09C82039


title: 09C82038


title: 09C82037


title: MH0127895


title: 09C99182


title: 10C111631


title: MH0130542


title: 10C101734


title: MH0130543


title: NGL10


title: NGL171


title: 09C82036


title: NGL2346


title: NGL187


title: 09C99183


title: 09C99184


title: NGL136


title: MH0146583


title: NGL2347


title: NGL85


title: 09C82035


title: NGL144


title: MH0139953


title: MH0138132


title: NGL126


title: MH0137194


title: MH0130373


title: 8-H-45


title: NGL9


title: MH0138559


title: NGL115


title: NGL28


title: MH0140619


title: MH0138351


title: NGL127


title: NGL118


title: NGL100


title: 8-M-51


title: NGL90


title: NGL5


title: 10C116677


title: 09C81644


title: 10C112678


title: 8-I-43


title: 10C111970


title: 8-T-20


title: 10C117199


title: 10C112339


title: 10C106521


title: 09C85176


title: 10C106839


title: 10C115419


title: 11C118476


title: 10C115231


title: 10C111891


title: 7-RS-1084


title: 003795_003795_72deltaMeq(48)

city: East Lansing

first: sugalesini

last: Subramaniam

state: MI

address: 3606 E Mount Hope Rd

department: CMIB

institute: Michigan State University

hyb_protocol: Biotinylated cRNA was hybridized to the Affymetrix chips (GeneChip Chicken Genome Array). GeneChips were then washed and stained in the Affymetrix Fluidics Station

scan_protocol: Genechips were scanned and the resultant intensities analyzed for levels of transcripts of interest

data_processing: The data were analyzed with Affymetrix using default analysis settings and global scaling as normalization method.

organism: Gallus gallus

label_protocol: High quality RNA was labeled using Affymetrix (Santa Clara, CA) One-Cycle Target Labeling and Control Reagents

growth_protocol: Cells were cultured in Lebowitz's L-15 and McCoy 5A media with 15% inactivated fetal bovine serum, 100 U of penicillin per ml, and maintained at 37 °C.

extract_protocol: Total RNA was extracted using the Absolutely RNA Miniprep Kit (Stratagene, Santa Clara, CA)

value: chicken embryo fibroblast cell line

tag: infection

value: Meq-null MDV

tag: time (h)


title: 10C115420

tag: cell type


title: 003797_003797_72deltaMeq(96)


title: 003798_003798_72deltaMeq(96)


title: 7-RS-437

tag: rnasource


title: 003790_003790_72MDV(96)


title: 003787_003787_72MDV(48)


title: 003788_003788_72MDV(96)


title: 7-RS-436

tag: fid

value: m


title: 003784_003784_72MDV(24)


title: 003791_003791_72deltaMeq(24)


title: 10C116727

tag: iid


title: 7-R-59

tag: gender


title: 7-R-383


title: 09C90746


title: 10C111703


title: 7-R-386


title: 003789_003789_72MDV(96)


title: 003781_003781_63deltaMeq(96)


title: 7-H-037


title: 003778_003778_63deltaMeq(48)


title: 003792_003792_72deltaMeq(24)


title: 003782_003782_72MDV(24)


title: 003794_003794_72deltaMeq(48)


title: 003783_003783_72MDV(24)


title: 003796_003796_72deltaMeq(48)


title: 003799_003799_72deltaMeq(96)


title: 003793_003793_72deltaMeq(24)


title: 003779_003779_63deltaMeq(96)


title: 003786_003786_72MDV(48)


title: 003785_003785_72MDV(48)


title: 003777_003777_63deltaMeq(48)


title: 09C90749


title: 003780_003780_63deltaMeq(96)


title: 003776_003776_63deltaMeq(48)


title: 7-RS-282


title: 003775_003775_63deltaMeq(24)


title: 7-RS-283


title: 003774_003774_63deltaMeq(24)


title: 003773_003773_63deltaMeq(24)


title: 003772_003772_63MDV(96)

value: wild type MDV


title: 003771_003771_63MDV(96)


title: 003768_003768_63MDV(48)


title: 003766_003766_63MDV(24)


title: RP066-reduction

city: San Francisco

first: David

last: Quigley

address: 1450 Third St. Room 207

department: Helen Diller Comprehensive Cancer Center

institute: UCSF

description:
RP66
gene expression from mammaplastic reduction

hyb_protocol: Agilent One-Color Microarray-Based Gene Expression Analysis, Protocol 5.5

scan_protocol: Scanning on Agilent scanner G2505B

data_processing: Expression data were background-corrected and quantile normalized using limma in R. Features flagged as non-uniform or below-background were excluded. Batch effect from Scan Date was corrected using ComBat.

source_name: mammaplastic reduction

extract_protocol: Tissue samples were stabilized with RNAlater at the time of surgery. After surgery, RNAlater was removed and tissue was stored at -80°C. RNA was extracted with TRIzol (Invitrogen, Carlsbad CA) or TRI reagent (Life Technologies, Gaithersburg MD) and further purified on RNeasy columns in combination with the RNeasy Mini Kit (Qiagen, Valenca, CA). RNA was quantified using a NanoDrop ND-1000 spectrophotometer (Thermo Scientific, Wilmington DE) and quality checked with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: sample id

tag: tissue

value: reduction

tag: er

tag: cohort

tag: bmi


title: 003769_003769_63MDV(48)


title: 003767_003767_63MDV(48)


title: RP065-reduction

description:
RP65
gene expression from mammaplastic reduction

label_protocol: Agilent One-Color Microarray-Based Gene Expression Analysis, Protocol 5.5


title: 09C87628

tag: age (yrs)


title: RP067-reduction

description:
RP67
gene expression from mammaplastic reduction


title: RP058-reduction

description:
RP58
gene expression from mammaplastic reduction


title: RP064-reduction

description:
RP64
gene expression from mammaplastic reduction


title: 09C90029


title: 7-RS-276


title: 7-R-98


title: 09C84838


title: 7-R-274


title: RP062-reduction

description:
RP62
gene expression from mammaplastic reduction


title: 09C90748


title: 003765_003765_63MDV(24)


title: RP057-reduction

description:
RP57
gene expression from mammaplastic reduction


title: RP070-reduction

description:
RP70
gene expression from mammaplastic reduction


title: 003770_003770_63MDV(96)


title: 003764_003764_63MDV(24)


title: 09C90747


title: 09C90745


title: RP063-reduction

description:
RP63
gene expression from mammaplastic reduction


title: RP054-reduction

description:
RP54
gene expression from mammaplastic reduction


title: 09C99034


title: RP055-reduction

description:
RP55
gene expression from mammaplastic reduction


title: 09C98613


title: RP047-reduction

description:
RP47
gene expression from mammaplastic reduction


title: RP051-reduction

description:
RP51
gene expression from mammaplastic reduction


title: RP048-reduction

description:
RP48
gene expression from mammaplastic reduction


title: RP053-reduction

description:
RP53
gene expression from mammaplastic reduction


title: 7-R-277


title: 7-R-99


title: GMH5xyw_heart_1week_rep2

city: Claremont

first: Alexander

middle: C

last: Zambon

address: 517 Watson Drive

department: Biopharmaceutical Sciences

institute: Keck Graduate Institute

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: ANOVA interaction P values were computed using LIMMA. Genes were clustered with AltAnalyze. Clusters were analyzed for enrichment of functional terms (Gene Ontology and KEGG pathways) using GO-Elite.

organism: Drosophila melanogaster

source_name: heart, aged to 1 week

label_protocol: cDNA was fragmented and biotin labeled for analysis on Affymetrix GeneChip arrays

growth_protocol: Adult Drosophilae were collected and maintained at 25C on typical food made from molasses, cornmeal, and agar. Aging flies were moved to new food about every 4 days.

extract_protocol: Hearts were homogenized directly in TRIzol (Invitrogen). RNA was purified (Qiagen), reverse transcribed into cDNA, and amplified via the WT-ovation Pico RNA Amplification system (NuGEN), Agencourt RNAClean (Beckman Coulter), and DNA Clean & Concentrator-25s columns (Zymo Research).

treatment_protocol: Drosophila heart tubes were exposed via semi-intact microsurgical methods. Fat and pericardial cells were removed from hearts via suction, and hearts were gently removed.

tag: age

value: adult

tag: development stage

value: female

tag: genotype/variation

tag: aged

value: 1 week

value: heart


title: GMH5xFOXO_heart_5week_rep2

source_name: heart, aged to 5 weeks

value: 5 week


title: 09C99035

value: RNA from NIMH repository

value: f


title: GMH5xFOXO_heart_1week_rep1


title: RP050-reduction

description:
RP50
gene expression from mammaplastic reduction


title: RP046-reduction

description:
RP46
gene expression from mammaplastic reduction


title: GMH5xFOXO_heart_1week_rep2


title: RP038-reduction

description:
RP38
gene expression from mammaplastic reduction


title: GMH5xFOXO_heart_5week_rep1


title: GMH5xyw_heart_5week_rep2


title: RP039-reduction

description:
RP39
gene expression from mammaplastic reduction


title: 7-R-287


title: 7-R-385


title: 7-S-380


title: GMH5xyw_heart_1week_rep1


title: 7-R-381


title: 7-R-382


title: GMH5xyw_heart_5week_rep1


title: RP045-reduction

description:
RP45
gene expression from mammaplastic reduction


title: 7-S-260


title: RP036-reduction

description:
RP36
gene expression from mammaplastic reduction


title: RP040-reduction

description:
RP40
gene expression from mammaplastic reduction


title: RP037-reduction

description:
RP37
gene expression from mammaplastic reduction


title: RP026-reduction

description:
RP26
gene expression from mammaplastic reduction


title: RP035-reduction

description:
RP35
gene expression from mammaplastic reduction


title: RP033-reduction

description:
RP33
gene expression from mammaplastic reduction


title: RP024-reduction

description:
RP24
gene expression from mammaplastic reduction


title: 10C116592


title: 7-C-305


title: 7-H-100


title: 11C125716


title: 7-H-34


title: 7-I-01


title: RP028-reduction

description:
RP28
gene expression from mammaplastic reduction


title: RP023-reduction

description:
RP23
gene expression from mammaplastic reduction


title: 7-H-026


title: RP020-reduction

description:
RP20
gene expression from mammaplastic reduction


title: Gill 18 14d dyes No68

city: Taipei

first: Ming Yi

last: Chou

state: Taiwan

address: 128 Sec. 2 Acdemia Rd.

department: Cellular and Organismic Biology

country: Japan

institute: Acdemia Sinica

description:
The commercial zebrafish 14K oligonucleotides set (MWG
Biotech AG, Ebersbach, Germany) were obtained and were printed on UltraGAPS Coated slide (Corning, New York, NY ) with use of the OmniGrid 100 microarrayer (Genomic Solutions, Ann Arbor, MI) according to the manufacture’s instructions. The 14,067 oligonucleotides represent 9666 genes (7009 singlet genes and 2657 redundant genes), and the redundancy of this chip is 31 %. The detailed description of the oligonucleotides information can be obtained on the Ocimun Biosolution website.

hyb_protocol: The zebrafish 14K OciChip array chip was pretreated with 1% bovine serum albumin (BSA) (fraction V), 4x saline-sodium citrate (SSC), and 1% sodium dodecylsulfate (SDS) at 42 °C for 45 min, and then hybridized overnight in a cocktail containing 5x Denhardt's solution, 6x SSC, 0.5% SDS, 50% formamide, 50 mM sodium phosphate, and 2 µg/µl yeast tRNA. Slides were washed with 2x SSC and 0.1% SDS (5 min), 1x SSC and 0.1% SDS (5 min), 0.5x SSC (5 min), and twice with 0.1x SSC (2 min each).

scan_protocol: Scanning was performed with a Scanarray Gx scanner (PerkinElmer, Waltham, MA). The acquired images were analyzed using ScanArray Express 3.0 (PerkinElmer, Waltham, MA)and Genespring software (Aglient Technologies, Foster City, CA).

data_processing: The measurements of spots were filtered by flags, and the Lowess normalization was performed after subtraction of the median background. Each experiment contained 3 biological replicates (including 1 dye swap) with different samples. The differentially expressed genes were selected from those with at least 2 of 3 significant signals (ratio > 2 or < 0.5), and then the Significant Analysis of Microarray method (SAM 3.02) was used to determine statistical significances.

label: Alexa 647 dye

organism: Danio rerio

source_name: Gill normal temperature treatment for 14 d

label_protocol: cDNA probes were synthesized and purified by reverse transcription of 20 μg total RNA using a SuperScript indirect cDNA labeling system (Invitrogen) and MinElute PCR purification kit (Qiagen) and were labeled with Alexa 647 dye (cold treatment groups).

growth_protocol: The experimental protocols were approved by the Academia Sinica Institutional Animal Care and Utilization Committee (approval no. RFiZOOHP2006083).

extract_protocol: Tissues dissected from 10 individuals were pooled as a sample and then homogenized in 0.8 ml Trizol reagent (Invitrogen, Carlsbad, CA). After chloroform extraction, RNA precipitation and ethanol washing, the RNA samples were purified and treated with DNase1 to remove the genomic DNA by using RNeasy Mini Kit (Qiagen, Huntsville, Alabama). The quantity and quality of total RNA were assessed by spectrophotometry and Bioanalyzer (Aglient Technologies, Foster City, CA).

treatment_protocol: Adult zebrafish were incubated in normal temperature as a control group.

tag: The AB strain of zebrafish (D. rerio) was originally obtained from the University of Oregon, and were kept in the zebrafish stock center at Academia Sinica, Taipei, Taiwan.

label: Alexa 555 dye

source_name: Gill cold treatment for 14 d

label_protocol: cDNA probes were synthesized and purified by reverse transcription of 20 μg total RNA using a SuperScript indirect cDNA labeling system (Invitrogen) and MinElute PCR purification kit (Qiagen) and were labeled with Alexa 555 dye (cold treatment groups).

treatment_protocol: Adult zebrafish were acclimated to 18 C with a gradually reduced temperature at a gradient of 4 C/h in order to prevent temperature shock and reduce mortality.


title: Brain 18 14d dyes No57

source_name: Brain normal temperature treatment for 14 d

source_name: Brain cold treatment for 14 d


title: Brain 18 1d 02 No10

source_name: Brain cold treatment for 1 d

source_name: Brain normal temperature treatment for 1 d


title: Gill 18 14d 01 No92


title: Brain 18 1d 01 No6


title: RP017-reduction

description:
RP17
gene expression from mammaplastic reduction


title: Brain 18 14d 03 No21


title: Gill 18 1d dyes No94

source_name: Gill normal temperature treatment for 1 d

source_name: Gill cold treatment for 1 d


title: Brain 18 14d 01 No13


title: RP022-reduction

description:
RP22
gene expression from mammaplastic reduction


title: Brain 18 1d dyes No91


title: Gill 18 14d 02 No93


title: Gill 18 1d 0002


title: RP016-reduction

description:
RP16
gene expression from mammaplastic reduction


title: RP013-reduction

description:
RP13
gene expression from mammaplastic reduction


title: RP014-reduction

description:
RP14
gene expression from mammaplastic reduction


title: Gill 18 1d 0001


title: RP011-reduction

description:
RP11
gene expression from mammaplastic reduction


title: HPM cells, HPM20_1 biological rep1

city: Bethesda

first: Arnold

last: Kirshenbaum

address: 10 Center Drive

department: NIAID

institute: NIH

description: Gene expression data from HPM cells, HPM20_1 biological rep1, 16-bp duplication (c.1470_1486dup16) in the HPS1 gene

hyb_protocol: For CSAS #13690, 4.4ug cDNA were used for fragmentation, biotin-labeling and hybridization. For CSAS #15193 and 15671, 15ug biotinylated aRNA were used for fragmentation and hybridization.

scan_protocol: GeneChip Scanner 3000 7G System was used for chip scanning.

data_processing: Affymetrix Expression Console was used for mas5 chp file generation. CSAS #13690 samples were normalizationed to 500; CSAS #15193 and 15671 samples were normalized to 150.

source_name: HPM cells, HPM20_1 biological rep1

label_protocol: For CSAS #13690, Nugen WB kit was used for target labeling, 20ng total RNA were used. For CSAS #15193 and 15671, Affymetrix IVT Express kit was used for target labeling, 100ng total RNA were used. All probes are biotinylated.

growth_protocol: Typical HPS-1 HuMC cultures at 5-6 weeks were eventually overgrown by a population of smaller, rapidly dividing cells. HPM clones #3 and #4 cultured in complete SFM alone or supplemented with rhSCF and rhIL-6 over 4 wks were transfected using Amaxa Nucleofector II (Lonza, Allendale, NJ).

extract_protocol: Extraction of RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cultures were expanded and gradually weaned into flasks containing complete SFM without cytokines. Cells were dual-stained, selected for FcεRI+/CD117+ expression, and single-cell cloned. Peripheral blood CD34+ progenitor cells were enriched to 90-95% by using commercially available affinity columns and cultured in serum-free media (SFM).

value: mast cell

tag: genotype


title: 7-R-069

tag: cell type


title: 7-H-025

tag: rnasource


title: 09C81413

tag: fid


title: HPM cells, HPM20_3 biological rep3

description: Gene expression data from HPM cells, HPM20_3 biological rep3, 16-bp duplication (c.1470_1486dup16) in the HPS1 gene

source_name: HPM cells, HPM20_3 biological rep3


title: 7-R-058

tag: iid


title: HPM cells, HPM20_2 biological rep2

description: Gene expression data from HPM cells, HPM20_2 biological rep2, 16-bp duplication (c.1470_1486dup16) in the HPS1 gene

source_name: HPM cells, HPM20_2 biological rep2


title: RP010-reduction

description:
RP10
gene expression from mammaplastic reduction


title: RP004-reduction

description:
RP4
gene expression from mammaplastic reduction


title: RP005-reduction

description:
RP5
gene expression from mammaplastic reduction


title: 7-H-36

tag: gender


title: 09C81414


title: RP003-reduction

description:
RP3
gene expression from mammaplastic reduction

tag: sample id


title: MH0142218


title: MH0133831


title: 09C89306


title: 8 wk old control, CON_3 biological rep3

description: Gene expression data from 8 wk old control, CON_3 biological rep3, without duplication

source_name: 8 wk old control, CON_3 biological rep3

tag: tissue

value: healthy control without duplication


title: RP002-reduction

description:
RP2
gene expression from mammaplastic reduction

tag: er


title: 7-R-67


title: 8 wk old control, CON_1 biological rep1

description: Gene expression data from 8 wk old control, CON_1 biological rep1, without duplication

source_name: 8 wk old control, CON_1 biological rep1


title: MH0142217

source_name: cultured cells


title: 8 wk old control, CON_2 biological rep2

description: Gene expression data from 8 wk old control, CON_2 biological rep2, without duplication

source_name: 8 wk old control, CON_2 biological rep2


title: healthy control, NOR2 biological rep2

description: Gene expression data from healthy control, NOR2 biological rep2, without duplication

source_name: healthy control, NOR2 biological rep2


title: healthy control, NOR3 biological rep3

description: Gene expression data from healthy control, NOR3 biological rep3, without duplication

source_name: healthy control, NOR3 biological rep3


title: 11C122875


title: RP006-reduction

description:
RP6
gene expression from mammaplastic reduction

source_name: mammaplastic reduction

tag: cohort


title: 09C89661


title: CMG15-tumor

description:
CMG15T
gene expression from breast adenocarcinoma

source_name: breast adenocarcinoma

value: tumor

value: pos

tag: bmi


title: CMG23-tumor

description:
CMG23T
gene expression from breast adenocarcinoma


title: CM198-tumor

description:
CM198B
gene expression from breast adenocarcinoma


title: CLL B cells P1 Vehicle

city: Columbus

first: Lianbo

last: Yu

state: OH

address: 1800 Cannon Drive

department: Center for Biostatistics

institute: The Ohio State University

hyb_protocol: Following fragmentation, cRNA was hybridized on GeneChip HG-U133 Plus 2 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station prior to scanning

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G using Command Console.

data_processing: The data were analyzed through Expression Console and R program, RMA method was used as the background-correction, normalization, and probe summarization method.

source_name: B cells treated with DMSO (vehicel) control in culture for 24 hours

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

growth_protocol: 5 x 107 primary B cells from healthy volunteers and from CLL patients were freshly isolated and purified using Stem Cell Technologies B cell negative selection Rosettte kits and ficoll seperation

extract_protocol: Trizol extraction followed by Qiagen Rneasy column clean up

treatment_protocol: Cells were treated with 1 uM 17-DMAG treatment or DMSO control for 24 hours in RMPI media containing 10% FBS, l-glutamine and antibiotics

value: B cells

tag: disease state

value: CCL

tag: treatment


title: CMG43-tumor

description:
CMG43T
gene expression from breast adenocarcinoma


title: CLL B cells P1 17-DMAG

source_name: B cells treated with 17-DMAG in culture for 24 hours

value: 17-DMAG in culture for 24 hours


title: CMG24-tumor

description:
CMG24T
gene expression from breast adenocarcinoma


title: CMG28-tumor

description:
CMG28T
gene expression from breast adenocarcinoma


title: CM175-tumor

description:
CM175T
gene expression from breast adenocarcinoma

value: neg


title: 11C119852

value: Lymphoblastoid cell lines (LCLs)

tag: age (yrs)


title: 11C122874


title: 11C122871

value: m


title: 11C123495


title: 11C123309


title: 11C122617


title: RP001-reduction

description:
RP1
gene expression from mammaplastic reduction

value: reduction


title: CLL B cells P2 17-DMAG


title: Normal B cells

value: normal

value: DMSO (vehicel) control in culture for 24 hours


title: 11C122618


title: CLL B cells P2 Vehicle


title: 09C89305


title: HPS-1 patient, HPS2 biological rep2

description: Gene expression data from HPS-1 patient, HPS2 biological rep2, 16-bp duplication (c.1470_1486dup16) in the HPS1 gene

source_name: HPS-1 patient, HPS2 biological rep2


title: HPS-1 patient, HPS1 biological rep1

description: Gene expression data from HPS-1 patient, HPS1 biological rep1, 16-bp duplication (c.1470_1486dup16) in the HPS1 gene

source_name: HPS-1 patient, HPS1 biological rep1


title: CM170-tumor

description:
CM170T
gene expression from breast adenocarcinoma


title: CM159-tumor

description:
CM159T
gene expression from breast adenocarcinoma


title: healthy control, NOR1 biological rep1

description: Gene expression data from healthy control, NOR1 biological rep1, without duplication

source_name: healthy control, NOR1 biological rep1


title: CM161-tumor

description:
CM161T
gene expression from breast adenocarcinoma


title: HPS-1 patient, HPS3 biological rep3

description: Gene expression data from HPS-1 patient, HPS3 biological rep3, 16-bp duplication (c.1470_1486dup16) in the HPS1 gene

source_name: HPS-1 patient, HPS3 biological rep3


title: CM160-tumor

description:
CM160T
gene expression from breast adenocarcinoma


title: 11C122483


title: IFNg- Treg relicate 8

city: New Haven

first: Margarita

last: Dominguez-Villar

state: CT

address: 300 George St

department: Neurology

institute: Yale University

hyb_protocol: Samples were hybridized on GeneChip® Human Genome U133 Plus 2.0 Array

scan_protocol: Samples were scanned with the GeneChip Scanner 3000 with autoloader

data_processing: Microarrays were analyzed using R and Bioconductor. Microarray data were quantile-normalized (Bioconductor affy package) and log2-transformed. Quality control was performed using ArrayQualityMetrics, and arrays were preprocessed with RMA. Differential expression was calculated using LIMMA package for single channel paired experimental design with Benjamini & Hochberg multiple testing adjustment. Microarray analysis and description was carried out according to Minimum Information About a Microarray Experiment (MIAME) guidelines.

source_name: Sorted Tregs

label_protocol: Biotinylated cRNA were prepared according to the standard protocol with the Ovation Pico WTA System V2 - NuGEN from 50ng total RNA

growth_protocol: Tregs were sorted ex vivo from peripheral blool od healthy individuals as CD4+CD25highCD127neg

extract_protocol: RNeasy Micro kit, QIAGEN

treatment_protocol: Sorted Tregs were stimulated for a total of 4 hours with PMA (30ng/ml) and ionomycin (150 ng/ml). At hour 3, cells were labeled with IFNg detection kit (PE, Miltenyi), incubated for 45 more minutes to allow for IFNg capture and resorted based on PE expression into IFNg+ and IFNg- Tregs.

value: Peripheral Blood

value: Treg

tag: cell markers


title: 11C122873

value: RNA from NIMH repository


title: CM128-tumor

description:
CM128B
gene expression from breast adenocarcinoma


title: 11C122797

value: f


title: IFNg+ Treg relicate 7


title: 11C122482


title: 11C119755


title: IFNg- Treg relicate 6


title: 11C122872


title: 11C122798


title: CM148-tumor

description:
CM148T
gene expression from breast adenocarcinoma


title: CM125-tumor

description:
CM125T
gene expression from breast adenocarcinoma


title: IFNg+ Treg replicate8


title: CM137-tumor

description:
CM137B
gene expression from breast adenocarcinoma


title: CM115-tumor

description:
CM115B
gene expression from breast adenocarcinoma


title: IFNg+ Treg replicate6


title: 11C118916


title: IFNg- Treg relicate 7


title: MH0140254


title: CM114-tumor

description:
CM114T
gene expression from breast adenocarcinoma


title: IFNg+ Treg replicate5


title: MH0133832


title: IFNg+ Treg replicate4


title: IFNg- Treg relicate 4


title: 11C119411


title: IFNg- Treg relicate 5


title: CM110-tumor

description:
CM110T
gene expression from breast adenocarcinoma


title: CM112-tumor

description:
CM112T
gene expression from breast adenocarcinoma


title: IFNg- Treg relicate 3


title: CM081-tumor

description:
CM81T
gene expression from breast adenocarcinoma


title: IFNg+ Treg replicate3


title: IFNg+ Treg replicate2


title: IFNg- Treg relicate 1


title: 11C121993


title: CM064-tumor

description:
CM64B
gene expression from breast adenocarcinoma


title: 11C119409


title: 11C119168


title: CM054-tumor

description:
CM54T
gene expression from breast adenocarcinoma


title: 11C122285


title: IFNg- Treg relicate 2


title: CM065-tumor

description:
CM65B
gene expression from breast adenocarcinoma


title: Treatment at 27 °C, biological rep4

city: Pozzuoli

first: Diego

last: Carrella

state: NAPOLI

address: Via Campi Flegrei 34

country: Italy

institute: TIGEM

description: Gene expression data in human bronchial epithelial cells from cystic fibrosis patients at 27 °C

hyb_protocol: Hybridization and scanning was performed on the Affymetrix platform.

data_processing: The data were analyzed with the Bioconductor package Affy using MAS5.0 method for normalizing and summarizing probe level intensity measurements.

label: phycoerythrin

source_name: human bronchus_27C

label_protocol: Oligo(dT)-primed cDNAs were synthesized using the SuperScript III First-Strand Synthesis SuperMix (Invitrogen, Irvine, CA) following manufacturer’s instructions. For microarray analysis, double-stranded cDNAs were synthesized using the Custom SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) and extracted with phenol-chloroform isoamyl alcohol (25:24:1), ethanol precipitated, and used to prepare cRNAs using the Bioarray High Yield RNA Transcription Kit (Affymetrix, Santa Clara, CA) according to manufacturer’s instructions.

growth_protocol: Primary bronchial epithelial cells first grown in LHC9/RPMI 1640 serum-free medium and then plated on porous Snapwell inserts.  Differentiation was obtained in serum-containing medium enriched with hormones and supplements (Sondo et al., Am J Physiol 301: C872-C885, 2011).

extract_protocol: Total RNA was extracted with RNeasy Mini Kit (Qiagen, Hilden, Germany) according to manufacturer’s instructions.

treatment_protocol: After 10-12 days of differentiation on Snapwell inserts, cells were kept under control conditions or incubated at 27 °C for 24 hours.

value: lung

tag: tissue compartment

value: bronchus

value: bronchial epithelium


title: CM056-tumor

description:
CM56T
gene expression from breast adenocarcinoma

value: tumor


title: CM053-tumor

description:
CM53B
gene expression from breast adenocarcinoma

value: pos


title: CM046-tumor

description:
CM46T
gene expression from breast adenocarcinoma


title: IFNg+ Treg replicate1


title: CM047-tumor

description:
CM47T
gene expression from breast adenocarcinoma


title: 11C118332


title: Treatment at 27 °C, biological rep2

scan_protocol: Hybridization and scanning was performed on the Affymetrix platform.


title: 11C121994


title: 09C89304


title: Treatment at 27 °C, biological rep3


title: 10C113118


title: Treatment at 27 °C, biological rep1


title: Control at 37 °C, biological rep3

description: Gene expression data in human bronchial epithelial cells from cystic fibrosis patients at 37 °C

source_name: human bronchus_37C


title: 11C122219


title: 10C112867


title: 10C114140


title: 10C112510


title: Control at 37 °C, biological rep4


title: CM044-tumor

description:
CM44T
gene expression from breast adenocarcinoma


title: Control at 37 °C, biological rep2


title: CM040-tumor

description:
CM40T
gene expression from breast adenocarcinoma


title: CM041-tumor

description:
CM41T
gene expression from breast adenocarcinoma


title: CM038-tumor

description:
CM38T
gene expression from breast adenocarcinoma


title: Control at 37 °C, biological rep1


title: CM032-tumor

description:
CM32T
gene expression from breast adenocarcinoma


title: CM033-tumor

description:
CM33B
gene expression from breast adenocarcinoma


title: 10C114350


title: CM026-tumor

description:
CM26T
gene expression from breast adenocarcinoma


title: CM031-tumor

description:
CM31T
gene expression from breast adenocarcinoma


title: CM035-tumor

description:
CM35B
gene expression from breast adenocarcinoma


title: 10C116676


title: CM034-tumor

description:
CM34B
gene expression from breast adenocarcinoma


title: 10C116594


title: 10C113849


title: DMD biological rep13

city: Baltimore

first: Susan

middle: G

last: Dorsey

address: 655 West Lombard Street

department: Pain and Translational Symptom Science

institute: University of Maryland Baltimore

description:
DMD_Pos-6UP
gene expression data

hyb_protocol: cRNA hybridization per Affymetrix standard protocol

scan_protocol: Gene arrays were scanned on Affymetrix platform

data_processing: The data were normalized using gcrma R package (v.2.20.0) from Bioconductor.

source_name: DMD_muscle biopsy

label_protocol: Biotinylated cRNA prepared, hybridized, and scanned using Affymetrix standard protocol from 1ug RNA

growth_protocol: biopsy sample in clinic

extract_protocol: Trizol extraction of total RNA per manufacturer

tag: sample type

value: Duchenne muscular dystrophy (DMD) patient

tag: age

value: skeletal muscle


title: DMD biological rep15

description:
DMD_Pos-8UP
gene expression data

value: 3yr 7mo


title: CM021-tumor

description:
CM21B
gene expression from breast adenocarcinoma

value: neg


title: CM023-tumor

description:
CM23B
gene expression from breast adenocarcinoma


title: DMD biological rep10

description:
DMD_Pos-3UP
gene expression data


title: DMD biological rep12

description:
DMD_Pos-5UP
gene expression data

value: 1yr 11mo


title: CM018-tumor

description:
CM18T
gene expression from breast adenocarcinoma


title: DMD biological rep8

description:
DMD_Pos-1UP
gene expression data


title: 10C112511

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

tag: cell type

value: Lymphoblastoid cell lines (LCLs)


title: DMD biological rep14

description:
DMD_Pos-7UP
gene expression data


title: DMD biological rep9

description:
DMD_Pos-2UP
gene expression data


title: CM019-tumor

description:
CM19T
gene expression from breast adenocarcinoma


title: 10C114429

tag: rnasource

value: m


title: DMD biological rep16

description:
DMD_Pos-9UP
gene expression data


title: 10C112868

tag: fid


title: DMD biological rep7

description:
DMD_Pos-17UP
gene expression data


title: 10C113848

tag: iid


title: DMD biological rep11

description:
DMD_Pos-4UP
gene expression data


title: 10C113673

tag: gender


title: CM013-tumor

description:
CM13T
gene expression from breast adenocarcinoma

tag: sample id


title: 10C116725


title: 10C113276


title: 10C116593


title: DMD biological rep6

description:
DMD_Pos-16UP
gene expression data

tag: tissue


title: CM015-tumor

description:
CM15T
gene expression from breast adenocarcinoma

tag: er


title: CM010-tumor

description:
CM10T
gene expression from breast adenocarcinoma

tag: cohort


title: 4-R-44

value: RNA from LCL in UCLA


title: CM009-tumor

description:
CM9T
gene expression from breast adenocarcinoma

tag: bmi


title: DMD biological rep4

description:
DMD_Pos-14UP
gene expression data


title: CMG23-normal

description:
CMG23N
gene expression from breast tissue adjacent to tumor

source_name: breast tissue adjacent to tumor

value: normal


title: 09C87627

source_name: cultured cells


title: DMD biological rep2

description:
DMD_Pos-12UP
gene expression data


title: DMD biological rep5

description:
DMD_Pos-15UP
gene expression data


title: CMG24-normal

description:
CMG24N
gene expression from breast tissue adjacent to tumor


title: DMD biological rep1

description:
DMD_Pos-11UP
gene expression data


title: CMG43-normal

description:
CMG43N
gene expression from breast tissue adjacent to tumor


title: DMD biological rep3

description:
DMD_Pos-13UP
gene expression data

value: 1yr 8mo


title: CM198-normal

description:
CM198N
gene expression from breast tissue adjacent to tumor


title: CM011-tumor

description:
CM11T
gene expression from breast adenocarcinoma


title: CM001-tumor

description:
CM1T
gene expression from breast adenocarcinoma


title: CMG28-normal

description:
CMG28N
gene expression from breast tissue adjacent to tumor


title: MH0129907

value: RNA from NIMH repository


title: MH0129910


title: MH0129880

value: f


title: 4-R-111


title: 4-R-389


title: MH0129883


title: CMG15-normal

description:
CMG15N
gene expression from breast tissue adjacent to tumor


title: MH0133067


title: 11C119853


title: 11C119529


title: CM170-normal

description:
CM170N
gene expression from breast tissue adjacent to tumor


title: 11C121887


title: BMD hep - 1 mon_B2

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description:
Expression after 1 month of transplantation
B2

hyb_protocol: Samples that pass the QC for specific activity were taken for hybridization. 600ng of labeled cRNA were hybridized on the array (AMADID: 28005 & 26986) using the Gene Expression Hybridization kit (Part Number 5190-0404; Agilent) in Sure hybridization Chambers (Agilent) at 65ºC for 16 hours. Hybridized slides were washed using wash buffers (Part No: 5188-5327; Agilent).

scan_protocol: scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D)

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX Version  software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift

source_name: BM derived hepatocytes - 1 month

label_protocol: The samples were labeled using Agilent Quick-Amp labeling kit (Part number: 5190-0442). 500ng of total RNA was reverse transcribed using oligo dT based method. mRNA was primed with oligo dT primer tagged to T7 promoter sequence and converted into double stranded cDNA using MMLV-RT reverse transcriptase. Further, in the same reaction cDNA was in-vitro transcribed to cRNA using T7 RNA polymerase enzyme. During cRNA synthesis, Cy3 labeled Cytosine nucleotide was incorporated into the newly synthesized strands. Labeled cRNA thus obtained was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106). Concentration and amount of dye incorporated were determined using Nanodrop

extract_protocol: RNA isolation was performed using Qiagen RNeasy Mini Kit (CAT# 74106 ) following the manufacturer's recommendations.

value: BM derived hepatocytes

tag: protocol

value: transplantation

tag: time

value: 1 month


title: CM175-normal

description:
CM175N
gene expression from breast tissue adjacent to tumor


title: CM161-normal

description:
CM161N
gene expression from breast tissue adjacent to tumor


title: BMD hep - 1 mon_B1

description:
Expression after 1 month of transplantation
B1


title: CM137-normal

description:
CM137N
gene expression from breast tissue adjacent to tumor


title: 10C112203

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

tag: age (yrs)


title: Lin- BMCs_L3

description:
Negative control
L3

source_name: Lin- BMCs

value: Lin- BMCs


title: CM148-normal

description:
CM148N
gene expression from breast tissue adjacent to tumor

value: pos


title: CM159-normal

description:
CM159N
gene expression from breast tissue adjacent to tumor


title: 11C123730


title: 11C119729


title: CM125-normal

description:
CM125N
gene expression from breast tissue adjacent to tumor


title: CM160-normal

description:
CM160N
gene expression from breast tissue adjacent to tumor


title: CM110-normal

description:
CM110N
gene expression from breast tissue adjacent to tumor


title: 10C110781


title: CM114-normal

description:
CM114N
gene expression from breast tissue adjacent to tumor


title: CM112-normal

description:
CM112N
gene expression from breast tissue adjacent to tumor


title: 4-R-391


title: 10C111137


title: 4-R-388


title: CM065-normal

description:
CM65N
gene expression from breast tissue adjacent to tumor


title: 10C111177


title: 10C112340


title: CM128-normal

description:
CM128N
gene expression from breast tissue adjacent to tumor


title: 10C108421


title: 10C112680


title: 11C123729


title: CM115-normal

description:
CM115N
gene expression from breast tissue adjacent to tumor


title: Lin- BMCs_L4

description:
Negative control
L4


title: 10C108576


title: CM081-normal

description:
CM81N
gene expression from breast tissue adjacent to tumor


title: CM056-normal

description:
CM56N
gene expression from breast tissue adjacent to tumor


title: CM054-normal

description:
CM54N
gene expression from breast tissue adjacent to tumor


title: CM064-normal

description:
CM64N
gene expression from breast tissue adjacent to tumor


title: CM047-normal

description:
CM47N
gene expression from breast tissue adjacent to tumor


title: 4-R-342


title: CM053-normal

description:
CM53N
gene expression from breast tissue adjacent to tumor


title: CM044-normal

description:
CM44N
gene expression from breast tissue adjacent to tumor


title: 4-R-390


title: CM040-normal

description:
CM40N
gene expression from breast tissue adjacent to tumor


title: 09C81643


title: CM038-normal

description:
CM38N
gene expression from breast tissue adjacent to tumor


title: CM041-normal

description:
CM41N
gene expression from breast tissue adjacent to tumor


title: CM046-normal

description:
CM46N
gene expression from breast tissue adjacent to tumor


title: 4-R-335


title: 10C107926


title: 10C106484


title: CM033-normal

description:
CM33N
gene expression from breast tissue adjacent to tumor


title: 4-R-392


title: CM032-normal

description:
CM32N
gene expression from breast tissue adjacent to tumor


title: 4-Tm-54


title: 10C106188


title: 10C111354


title: 09C95104


title: CM035-normal

description:
CM35N
gene expression from breast tissue adjacent to tumor


title: 4-R-333


title: CM034-normal

description:
CM34N
gene expression from breast tissue adjacent to tumor


title: 4-T-339


title: 4-R-346


title: CM031-normal

description:
CM31N
gene expression from breast tissue adjacent to tumor


title: CM019-normal

description:
CM19N
gene expression from breast tissue adjacent to tumor


title: CM026-normal

description:
CM26N
gene expression from breast tissue adjacent to tumor


title: CM023-normal

description:
CM23N
gene expression from breast tissue adjacent to tumor


title: CM015-normal

description:
CM15N
gene expression from breast tissue adjacent to tumor


title: CM018-normal

description:
CM18N
gene expression from breast tissue adjacent to tumor


title: CM013-normal

description:
CM13N
gene expression from breast tissue adjacent to tumor


title: CM021-normal

description:
CM21N
gene expression from breast tissue adjacent to tumor


title: MH0140988


title: 4-R-303


title: 10C103077


title: 10C104920


title: CM011-normal

description:
CM11N
gene expression from breast tissue adjacent to tumor


title: CM009-normal

description:
CM9N
gene expression from breast tissue adjacent to tumor


title: MH0138349


title: MH0138353


title: MH0138504


title: CM010-normal

description:
CM10N
gene expression from breast tissue adjacent to tumor


title: PND4 Glis3KO-Testis Thy1+_rep4

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

department: DIR

description: RNA samples from PND4 Glis3KO2 Thy1+ cells

hyb_protocol: For each sample, 3 ug of Cy3 labeled cDNA was hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v12), using the 1-color defaults for all parameters.

source_name: PND4 Glis3KO2

label_protocol: 1.5 microliters (1.5 ul) of total RNA was amplified as directed in the NuGEN Ovation Pico WTA System and 5 ug of amplified cDNA was enzymatically labeled using the Agilent SureTag DNA Labeling Kit.

growth_protocol: Pups were stayed with their biological mother

extract_protocol: Ambion RNAqueous-Micro Kit

treatment_protocol: Nothing was treated

tag: strain

value: testis spermatogonial progenitor cells

tag: genotype


title: CM001-normal

description:
CM1N
gene expression from breast tissue adjacent to tumor


title: PND4 Glis3KO-Testis Thy1+_rep2


title: 4-P-28

first: Giovanni

last: Coppola

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

extract_protocol: Both RUCDR and UCLA extracted RNA from the cultured cells with an RNeasy 96 kit (Qiagen, Venlo, Netherlands), employing either a Qiagen BioRobot Universal System (RUCDR) or a manual procedure (UCLA) using up to 5x105 cells (RUCDR) or 106 cells (UCLA) as the starting material. To quantify RNA yield, we used a Quant-iT RiboGreen (Invitrogen, Waltham, MA) and measured RNA integrity number, reflective of sample quality, using a TapeStation (Agilent, Santa Clara, CA).


title: 10C103188


title: 4-R-387


title: MH0137119


title: MH0138354


title: MH0142137


title: MH0140989


title: PND4 Glis3KO-Testis Thy1+_rep1


title: PND4 Glis3KO-Testis Thy1+_rep3


title: 4-T-302


title: PND4 WT-Testis Thy1+_rep4

description: RNA samples from PND4 WT Thy1+ cells

source_name: PND4 WT

value: wild type


title: 10C117881


title: PND4 WT-Testis Thy1+_rep1

description: RNA samples from PND4 WT Thy1+ cells


title: 10C117045


title: 11C118874


title: PND4 WT-Testis Thy1+_rep2

description: RNA samples from PND4 WT Thy1+ cells


title: PND4 WT-Testis Thy1+_rep3

description: RNA samples from PND4 WT Thy1+ cells


title: 10C111890


title: 10C111704


title: 4 Week-old Glis3KO2 testis_rep3

description: RNA samples from 4 week-old Glis3KO2

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters.

source_name: 4 week-old Glis3KO2

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

growth_protocol: Pups were stayed with their biological mother.

extract_protocol: Qiagen RNA easy mini kit.

treatment_protocol: Nothing was treated.

value: testis

value: 4 week old


title: 11C118580


title: 10C117200


title: 10C107159


title: 10C108162


title: 4 Week-old Glis3KO2 testis_rep2

description: RNA samples from 4 week-old Glis3KO2


title: 10C113119


title: 10C104600


title: 4 Week-old WT testis_rep2

description: RNA samples from 4 week-old WT

source_name: 4 week-old WT

value: WT


title: 4 Week-old Glis3KO2 testis_rep1

description: RNA samples from 4 week-old Glis3KO2


title: 1 Week-old Glis3KO2 testis_rep4

description: RNA samples from 1 week-old Glis3KO2

source_name: 1 week-old Glis3KO2

value: 1 week old


title: 10C104601

value: Lymphoblastoid cell lines (LCLs)


title: 10C104343

value: m


title: 10C102827


title: 4 Week-old WT testis_rep3

description: RNA samples from 4 week-old WT


title: 4 Week-old WT testis_rep1

description: RNA samples from 4 week-old WT


title: 10C102848


title: 1 Week-old Glis3KO2 testis_rep2

description: RNA samples from 1 week-old Glis3KO2


title: 1 Week-old Glis3KO2 testis_rep1

description: RNA samples from 1 week-old Glis3KO2


title: 10C102285


title: 1 Week-old Glis3KO2 testis_rep3

description: RNA samples from 1 week-old Glis3KO2


title: 1 Week-old WT testis_rep2

description: RNA samples from 1 week-old WT

source_name: 1 week-old WT


title: 10C103919


title: 10C103540


title: 1 Week-old WT testis_rep1

description: RNA samples from 1 week-old WT


title: Glis3KO2 pancreas_rep1

description: Gene expression from pancreas of 1 week-old Glis3KO2

source_name: pancreas from 1 week-old Glis3KO2

growth_protocol: Pups stayed with their biological mother.

value: pancreas


title: Glis3KO2 pancreas_rep3


title: Glis3KO2 pancreas_rep4


title: 10C103539


title: 10C102691


title: Glis3KO2 pancreas_rep2


title: 09C97490


title: 10C103896


title: 1 Week-old WT testis_rep4

description: RNA samples from 1 week-old WT


title: 11C120717


title: 10C103189


title: 09C97123


title: 1 Week-old WT testis_rep3

description: RNA samples from 1 week-old WT


title: 09C99563


title: WT pancreas_rep4

description: Gene expression from pancreas of 1 week-old WT

source_name: pancreas from 1 week-old WT

value: wildtype


title: 09C97491

value: RNA from NIMH repository


title: 09C97126

value: f


title: WT pancreas_rep2


title: 09C99708


title: WT pancreas_rep1


title: 09C97489


title: FAF vs. Conv

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

description:
DD3 vs DD1
Organ

hyb_protocol: Agilent-014868 Whole Mouse Genome 4x44K microarrays were done according to the supplier’s protocol (Agilent Technologies) using the SSC wash protocol.

scan_protocol: Scanning of microarrays was performed with 5 µm resolution using a DNA microarray laser scanner (Agilent Technologies).

data_processing: Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.11.5.1.1, Agilent). The extracted MAGE-ML files were analyzed with the Rosetta Resolver Biosoftware (Rosetta Biosoftware).

source_name: small intestine, FAF diet

label_protocol: RNA labeling was performed with the Quick Amp Labeling Kit (Agilent Technologies) according to supplier's instructions.

growth_protocol: C57BL/6 mice (SPF and GF) at 6-8 weeks of age were used.

extract_protocol: Total RNA was isolated by the Trizol (Invitrogen) method following the manufacturer's protocol.

treatment_protocol: The control group were fed a conventional chow (Conv) (LASQCdietRod16, LASvendi), and food antigen-free (FAF) mice were kept on an amino acid-containing diet up to five generations.

tag: strain/background

value: small intestine

tag: diet

value: food antigen-free amino acids

source_name: small intestine, conv diet

value: conventional


city: Shanghai

first: Taoyong

last: Chen

address: 800 Xiangyin Road

institute: Second Military Medical University

description:
Src-/- + HSV-1
Gene expression data from Src-/- RAW264.7 cells infected with HSV-1.

hyb_protocol: The hybridization was done at the Shanghai Biotechnology Corporation (Shanghai, China). Array hybridization and wash were performed using GeneChip® Hybridization, Wash and Stain Kit (Cat #900720, Affymetrix, Santa Clara, CA, US) in Hybridization Oven 645 (Cat #00-0331-220V, Affymetrix, Santa Clara, CA, US) and Fluidics Station 450 (Cat #00-0079, Affymetrix, Santa Clara, CA, US) following the manufacturer’s instructions.

scan_protocol: The scanning was done at the Shanghai Biotechnology Corporation (Shanghai, China). Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, GeneSpring Software 11.0 (Agilent Technologies, Santa Clara, CA, US). The genes in each Matrix template are arranged according to Affymetrix probe set id.

label: Biotin

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3' IVT Express Kit (Cat #901229, Affymetrix, Santa Clara, CA, US) following the manufacturer’s instructions to obtain biotin labeled cRNA at the Shanghai Biotechnology Corporation (Shanghai, China).

extract_protocol: Total RNA was isolated from the cells using the TRIZOL method (InVitrogen), followed by digestion with RNase-free DNase (Qiagen) and purification on RNeasy spin columns using RNeasy Minikit (Qiagen).

treatment_protocol: Wild type and Src-/- RAW264.7 cells were infected with vesicular stomatitis virus (VSV, MOI=1) or herpes simplex virus 1 (HSV-1, MOI=5) for 6h.

tag: cell line

tag: cell type

value: macrophage

tag: genotype/variation

value: Src-/-

tag: treatment

value: herpes simplex virus 1 (HSV-1)


title: WT pancreas_rep3

tag: age


title: Src-/- RAW264.7 cells, untreated

description:
Src-/-
Gene expression data from Src-/- RAW264.7 cells.

source_name: Src-/- RAW264.7 cells, untreated


title: Conv vs. FAF

description:
DD1 vs DD3
Organ


title: 09C97124

city: Los Angeles

address: 1524 Gonda, 695 Charles Young Drive South

institute: UCLA

tag: rnasource

tag: fid

tag: iid

tag: gender


title: 10C110637


title: Src-/- RAW264.7 cells infected with VSV

description:
Src-/- + VSV
Gene expression data from Src-/- RAW264.7 cells infected with VSV.

source_name: Src-/- RAW264.7 cells infected with VSV

value: vesicular stomatitis virus (VSV) infection


title: 10C110531


title: 10C110532


title: 09C97125


title: Src+/+ RAW264.7 cells infected with HSV-1

description:
Src+/+ + HSV-1
Gene expression data from wild type RAW264.7 cells infected with HSV-1.

value: Src+/+


title: GBM-05-bottom

hyb_protocol: 90 microliters of hybridization sample were incubated in the Affymetrix GeneTitan Hybridization Oven instrument for 16 hours at 48C

scan_protocol: Arrays were processed with the Affymetrix GeneTitan Fluidics Station instrument, using the HuGene-1_1-st-16 fluidics script and GeneTitan Hybridization, Wash, and Stain Kit for WT Array Plates. Arrays were scanned in the Affymetrix GeneTitan Multi-Channel (MC) instrument with the AGCC GeneTitan Instrument Control.

data_processing: Arrays were quantile normalized and log2 transformed

source_name: patient-derived GBM tumorsphere

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA

growth_protocol: primary human GBMs were passaged as intracranial xenografts in athymic nu/nu mice and established as tumorsphere cultures.

extract_protocol: Total RNA was extracted from specimens using RNeasy mini kit (Qiagen) and contaminating RNA was digested using RNase free DNase kit (Qiagen). cDNA was synthesized using 500 ng total RNA using High Capacity cDNA Reverse Transcription Kit (Applied Biosystems) or SuperScript VILO (Life Technologies). The concentration and quality of RNA was determined using Nanodrop followed by use of a RNA 6000 Nano Kit (Agilent) and bioanalyzer chips (Applied Biosystems) to determine RIN values.

treatment_protocol: samples were separated into bottom, middle, or top by continuous density gradient centrifugation. To generate continous density gradients, BactXtractor High Density (Bx-H, Fertipro N.V.) with a starting density of 1.3 g/ml was diluted with phosphate-buffered solution (PBS) to generate a Stock Isotonic BactXtractor (SIB) solution with density 1.13 g/ml. We mixed different ratios of SIB solution and PBS (10:0, 9:1, 8:2, 7:3, 6:4, 5:5, 4:6, 3:7, 2:8, 1:9, 0:10) to optimize density gradients for efficient separation of tumor cells.

value: glioblastoma tumorsphere

tag: density gradient region

value: bottom

tag: patient


title: GBM-43-top

value: top


title: Tie2Cre lineage E12.5 mouse hearts Tie2Cre;Tbx20 -/loxP

city: Utrecht

first: Cornelis

middle: J.

last: Boogerd

address: Uppsalalaan 8

department: Developmental Biology and Stem Cell Research

country: Netherlands

institute: Hubrecht Institute

description: Gene expression data endocardial lineage from E12.5 Tie2Cre;Tbx20 mutant hearts

data_processing: The affymetrix standard protocol was used for the raw data processing and MAS5 method was used for the normalization.

source_name: Tie2Cre lineage E12.5 mouse hearts

label_protocol: standard Affymetrix protocol

extract_protocol: Hearts were harvested in icecold PBS with 0.5 mM EDTA and dissociated using collagenase (10 mg/ml; Worthington) and dispase (10 mg/mL, Invitrogen). Cells were stained for 30 minutes, 4',6-diamidino-2-phenylindole (DAPI, 1:1000) was used to label dead cells. Tie2Cre lineage cells, negative for blood markers CD41, CD45 and Ter119, were sorted on an Influx™ cell sorter (BD Biosciences) and collected in RNA lysis buffer (Agilent RNA nanoprep kit)

value: Tie2Cre;Tbx20 loxP/-

value: embryonic day 12.5


title: Tie2Cre lineage E12.5 mouse hearts Tie2Cre;Tbx20 +/loxP

description: Gene expression data endocardial lineage from E12.5 control hearts

value: Tie2Cre;Tbx20 +/loxP


title: GBM-43-middle

value: middle


title: 09C96295

source_name: cultured cells

value: RNA from NIMH repository

value: Lymphoblastoid cell lines (LCLs)


title: 09C97492

value: f


title: 09C99342

value: m


title: 11C126392


title: MH0141254


title: Src+/+ RAW264.7 cells infected with VSV

description:
Src+/+ + VSV
Gene expression data from wild type RAW264.7 cells infected with VSV.

source_name: Src+/+ RAW264.7 cells infected with VSV


title: GBM-05-top


title: DbAL11-specific CD8, anti-CD4, mouse #2

city: Oxford

first: Nicholas

last: Provine

state: Oxfordshire

address: John Radcliffe Hospital

department: NDM - Experimental Medicine

country: United Kingdom

institute: University of Oxford

hyb_protocol: 5 ug was hybridized following standard Nugen/Affymetrix protocols

scan_protocol: Scanned with Affymetrix using AGCC v. 1.1

data_processing:
Analyzed on Affymetrix Expression Console v. 1.1 using a MAS5.0 algorithm
affymetrix-algorithm-name = ExpressionStat
affymetrix-algorithm-version = 5.0

source_name: DbAL11-specific CD8 T cell_anti-CD4 antibody treated Ad5HVR48-Gag immunized mouse

label_protocol: 1st and 2nd strand synthesis, followed by Spia amplification using the Nugen WT pico kit to generate cDNA. Fragmentation and biotinylation using Nugen cat# 4200 following standard Nugen/Affymetrix protocols

growth_protocol: Mice were immunized intramuscularly with 10^9vp of Ad5HVR48(1-7) expressing SIVmac239 Gag and given anti-CD4 antibody prior to immunization or left untreated (control)

extract_protocol: AL11-specific CD8 T cells were isolated using a BD Biosciences Aria cell sorter. RNA extraction was performed by Phenol/Chloroform followed by Agilent RNA extraction proctol with optional DNase treatment.

treatment_protocol: Day 14 post-immunization, splenic CD8 T cells were enriched by negative selection (MACS), stained for CD8, CD44, and Db/AL11 and sort purified on a BD Biosciences Aria cell sorter.

tag: strain background

tag: mouse id

value: mouse #2

tag: tissue

value: spleen

value: DbAL11-specific CD8 T cell

tag: vaccine

tag: timepoint

value: day 14 post-Ad5HVR48-Gag


title: GBM-43-bottom


title: MH0138577

department: Psychiatry and Neurology

tag: age (yrs)


title: 09C95948


title: GBM-34-bottom


title: GBM-34-top


title: DbAL11-specific CD8, anti-CD4, mouse #3

value: mouse #3


title: GBM-12-top


title: DbAL11-specific CD8, untreated, mouse #4

source_name: DbAL11-specific CD8 T cell_untreated Ad5HVR48-Gag immunized mouse

value: mouse #4

value: untreated


title: Src+/+ RAW264.7 cells, untreated

description:
Src+/+
Gene expression data from wild type RAW264.7 cells.

source_name: Src+/+ RAW264.7 cells, untreated

tag: cell line

value: macrophage

value: Src+/+


title: DbAL11-specific CD8, anti-CD4, mouse #1

value: mouse #1

tag: cell type


title: GBM-14-top

value: glioblastoma tumorsphere

value: top


title: DbAL11-specific CD8, anti-CD4, mouse #4


title: DbAL11-specific CD8, untreated, mouse #2


title: 11C123494


title: GBM-14-bottom

value: bottom


title: 09C97100

value: RNA from NIMH repository


title: 11C123131

value: Lymphoblastoid cell lines (LCLs)


title: DbAL11-specific CD8, untreated, mouse #3


title: MH0127150

value: f


title: 3bKI 12 mo lv 4 normalization 2

first: Lindsey

middle: N

last: Kent

state: oh

address: 460 W 12th Ave

department: CCC

institute: OSU

description:
3bKI_12mo_lv4.CEL
Gene expression data

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Affymetrix GeneChip Scanner 3000 was used for data acquisition

data_processing: Data was processed using Affymetrix Expression and Transcriptome analysis consoles

source_name: liver

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: strain

value: mixed background (FVB/NT, 129S1/Svlmj,C57BL/6NT)

tag: genotype

value: E2F3b knock-in

value: 12 months

value: liver

tag: normalization


title: DbAL11-specific CD8, untreated, mouse #1

value: spleen

value: DbAL11-specific CD8 T cell

value: day 14 post-Ad5HVR48-Gag


title: GBM-12-middle

value: middle


title: GBM-12-bottom


title: 3bKI 12 mo lv 3 normalization 2

description:
3bKI_12mo_lv3.CEL
Gene expression data

tag: age


title: cmr1Δ_Rpb3_2

city: Rochester

first: Chhabi

last: Govind

state: mi

address: 333 Science and Engineering Building

department: Biological Sciences

institute: Oakland University

description:
Sulfometuron methyl
Biological Replicate-2

hyb_protocol: The samples were lableled using BioPrime Array CGH Genomic Labeling Module kit and hybridized according to the Manufacturer's recommended protocol

scan_protocol: Agilent Technologies Scanner G2505B US45102973

data_processing: Data processed on R. Median normalization carried out.

organism: Saccharomyces cerevisiae

source_name: IP

label_protocol: BioPrime Array CGH Genomic Labeling Module was used for labeling and the manufacturer's recommended protocol was followed.

growth_protocol: Chromatin immunoprecipitation experiments were performed as described previously (Govind et al., 2012). Briefly, 100 ml of cells (A600 = 0.6) were cross-linked with 1% formaldehyde for 15 minutes at ambient temperature and quenched with glycine. Chromatin was isolated and fragmented by sonication (Branson450) to an average size of 300-400 base pairs. The soluble fraction of chromatin was used for ChIP using the appropriate antibodies.

extract_protocol: The ChIP and Input DNA was extracted by Phenol:Chloform method after reverse-crosslinking at 65 degree C, and after proteinase K treatment. DNA was fragmented with DNase prior to labeling

treatment_protocol: The cells were grown in SC and induced for Gcn4, by treating cells grown in SC with with 0.65 µM of sulfometuron methyl (SM; Chemservice, cat# N-13254) for 20 minutes and processed for ChIP analysis.

tag: tag

value: untagged

tag: antibodies

value: Rpb3 (Neoclone:W0012)

source_name: input


title: 3bKI 12 mo lv 2 normalization 2

description:
3bKI_12mo_lv2.CEL
Gene expression data


title: gcn4Δ_Cmr1-Myc-2

value: CMR1-Myc tagged


title: MH0126617

tag: rnasource

tag: fid

tag: iid

tag: gender


title: cmr1Δ_Rpb3_1

description:
Sulfometuron methyl
Biological Replicate-1


title: 11C121006


title: gcn4Δ_Cmr1-Myc-1


title: 11C125998


title: 3aKO 12 mo lv 5 normalization 2

description:
3aKO_12mo_lv5.CEL
Gene expression data

value: E2f3a knock-out


title: 3aKO 12 mo lv 4 normalization 2

description:
3aKO_12mo_lv4.CEL
Gene expression data


title: 11C125997


title: 3aKO 12 mo lv 2 normalization 2

description:
3aKO_12mo_lv2.CEL
Gene expression data


title: 3aKO 12 mo lv 3 normalization 2

description:
3aKO_12mo_lv3.CEL
Gene expression data


title: WT_Rpb3_1 (2)

value: WT


title: 3bKI 12 mo lv 1 normalization 2

description:
3bKI_12mo_lv1.CEL
Gene expression data


title: WT_Cmr1-Myc_1


title: 11C121215


title: MH0126580

value: m


title: 09C96216

value: RNA from NIMH repository


title: 11C120915

value: Lymphoblastoid cell lines (LCLs)


title: 11C123130


title: WT_Rpb3_2 (2)


title: 3aKO 12 mo lv 1 normalization 2

description:
3aKO_12mo_lv1.CEL
Gene expression data


title: WT_Cmr1-Myc_2


title: wt 12 mo lv 7 normalization 2

description:
wt_12mo_lv7.CEL
Gene expression data

value: wildtype


title: wt 12 mo lv 6 normalization 2

description:
wt_12mo_lv6.CEL
Gene expression data

value: mixed background (FVB/NT, 129S1/Svlmj,C57BL/6NT)


title: wt 12 mo lv 5 normalization 2

description:
wt_12mo_lv5.CEL
Gene expression data


title: 11C121008

value: f


title: wt 12 mo lv 4 normalization 2

description:
wt_12mo_lv4.CEL
Gene expression data

value: 12 months


title: wt 12 mo lv 1 normalization 2

description:
wt_12mo_lv1.CEL
Gene expression data

value: liver


title: 09C99029


title: 11C123132


title: wt 12 mo lv 3 normalization 2

description:
wt_12mo_lv3.CEL
Gene expression data


title: 11C120895


title: 11C121007


title: wt 12 mo lv 2 normalization 2

description:
wt_12mo_lv2.CEL
Gene expression data


title: 09C96750


title: 09C98209


title: 10C101553


title: 10C101554


title: Non-induced suv4-20h mutant replication timing

city: Paris

first: Jean-Charles

last: Cadoret

address: 15 rue hélène Brion

institute: CNRS/ Université de Paris

hyb_protocol: The hybridization was performed according to the manufacturer instructions on 4× 180K human microarray (SurePrint G3 Human CGH Microarray Kit, 4x180K, AGILENT Technologies, genome reference Hg18) that covers the whole genome with one probe every 13 Kb (11 KB in RefSeq sequences).

scan_protocol: Microarrays were scanned with an Agilent's High-Resolution C Scanner using a resolution of 3 µm and the autofocus option.

data_processing: Feature extraction was performed with the Feature Extraction 9.1 software (Agilent technologies). For each experiment, the raw data sets were automatically normalized by the Feature extraction software. Analysis was performed with the Agilent Genomic Workbench 5.0 software.

source_name: neosynthetized DNA in early S phase

label_protocol: Microarray hybridization requires a minimum of 1000 ng of DNA and to obtain sufficient specific immunoprecipited DNA, whole genome amplification was conducted (WGA, Sigma). To be sure that this step does not introduce bias, an after WGA qPCR was performed to confirm the specific enrichment in each fractions S1 and S2. After amplification, early and late neo-synthesized DNA were labeled with Cy3 and Cy5 ULS molecules (Genomic DNA labeling Kit, Agilent) as recommended by the manufacturer.

growth_protocol: Mouse Embryonic Fibroblasts (MEF) 364.2 grown in Dulbecco’s modified Eagle’s medium (Invitrogen) with 10% fetal bovine serum (Sigma) and cultured in tri-gaz incubator (Panasonic) containing 3% O2 and 5% CO2.

extract_protocol: cells were incubated with BrdU (50µM) for one hour, then collected, washed three times in PBS, fixed in 75% ethanol, and stored at −20°C. Fixed cells were re-suspended in PBS first with RNAse (0.5 mg/ml) and then with propidium iodide (PI) (50 µg/ml) following by an incubation of 30 min at room temperature. 80,000 cells were sorted in two fractions S1 and S2 using INFLUX 500 (Cytopeia purchased by BD Biosciences) corresponding to Early and Late fractions respectively. Neo-synthesized DNA was immunoprecipited by BrdU antibodies (Anti BrdU Pure, BD Biosciences, # 347580) as described by Hiratani et al 2008. To control the quality of enrichment of early and late fractions in S1 and S2, qPCR was performed with BMP1 oligonucleotides (early control) and with Dppa2 oligonucleotides (late control).

treatment_protocol: Deletion of floxed SUV4-20H1 allele in MEF364.2 lines was achieved by treatment with 4-hydroxytamoxifen (1 mM) for 24 hours.

value: MEF 362.2 cell line

tag: genotype/variation

value: Non-induced suv4-20h mutant

tag: cell cycle phase

value: early S phase

tag: molecule subtype

value: neosynthetized DNA

source_name: neosynthetized DNA in late  S phase

value: late  S phase


title: 09C97862


title: 1KI 12 mo lv 4 normalization 1

description:
1KI_12mo_lv4.CEL
Gene expression data

value: E2F1 knock-in

tag: tissue


title: 09C100069

tag: age (yrs)


title: 1KI 12 mo lv 5 normalization 1

description:
1KI_12mo_lv5.CEL
Gene expression data


title: 1KI 12 mo lv 2 normalization 1

description:
1KI_12mo_lv2.CEL
Gene expression data


title: 1KI 12 mo lv 3 normalization 1

description:
1KI_12mo_lv3.CEL
Gene expression data


title: 1KI 12 mo lv 1 normalization 1

description:
1KI_12mo_lv1.CEL
Gene expression data


title: 09C96296


title: induced suv4-20h mutant replication timing

tag: cell line

value: induced suv4-20h mutant


title: KO suv4-20h replication timing

value: deletion of floxed SUV4-20H1 allele


title: 09C95949

tag: cell type


title: 3aKO 12 mo lv 5 normalization 1

description:
3aKO_12mo_lv5.CEL
Gene expression data

tag: strain

value: E2f3a knock-out


title: control MEF 362.2 replication timing

value: control


title: siRNA luc replication timing 1

growth_protocol: Cells were grown in Dulbecco’s modified Eagle’s medium (Invitrogen) with 10% fetal bovine serum (Sigma) at 37°C, 5% CO2 and 5% O2 (standard culture conditions).

treatment_protocol: cell lines were established by transfection  using Lipofectamine2000 followed by Zeocine selection (20µg/ml).

value: U2OS cell line

tag: transfected with

value: siRNA luc


title: siRNA prset-7 replication timing 1

value: siRNA prset-7


title: 09C85428

value: RNA from NIMH repository

value: Lymphoblastoid cell lines (LCLs)


title: wt 12 mo lv 7 normalization 1

description:
wt_12mo_lv7.CEL
Gene expression data

value: mixed background (FVB/NT, 129S1/Svlmj,C57BL/6NT)

tag: genotype

value: wildtype

value: 12 months

tag: normalization


title: 09C82490

value: m


title: MH0140621


title: 3aKO 12 mo lv 2 normalization 1

description:
3aKO_12mo_lv2.CEL
Gene expression data

tag: age

value: liver


title: 3aKO 12 mo lv 4 normalization 1

description:
3aKO_12mo_lv4.CEL
Gene expression data


title: 09C85430

value: f


title: 3aKO 12 mo lv 1 normalization 1

description:
3aKO_12mo_lv1.CEL
Gene expression data


title: 09C85178


title: wt 12 mo lv 6 normalization 1

description:
wt_12mo_lv6.CEL
Gene expression data


title: 3aKO 12 mo lv 3 normalization 1

description:
3aKO_12mo_lv3.CEL
Gene expression data


title: MH0140622


title: wt 12 mo lv 3 normalization 1

description:
wt_12mo_lv3.CEL
Gene expression data


title: MH0140990


title: MH0140830


title: wt 12 mo lv 5 normalization 1

description:
wt_12mo_lv5.CEL
Gene expression data


title: wt 12 mo lv 4 normalization 1

description:
wt_12mo_lv4.CEL
Gene expression data


title: wt 12 mo lv 2 normalization 1

description:
wt_12mo_lv2.CEL
Gene expression data


title: 3bKI 1 mo lv 5 normalization 2

description:
3bKI 1 mo lv 5.CEL
Gene expression data

value: E2F3b knock-in

value: 4 weeks (1 month)


title: 09C86270


title: MH0133572


title: 09C86003


title: MH0133573


title: 09C86271


title: wt 12 mo lv 1 normalization 1

description:
wt_12mo_lv1.CEL
Gene expression data


title: 09C86628


title: 3aKO 1 mo lv 10 normalization 2

description:
3aKO 1 mo lv 10.CEL
Gene expression data


title: 09C85702


title: 09C86923


title: 09C86004


title: 3bKI 1 mo lv 2 normalization 2

description:
3bKI 1 mo lv 2.CEL
Gene expression data


title: 3bKI 1 mo lv 1 normalization 2

description:
3bKI 1 mo lv 1.CEL
Gene expression data


title: 3aKO 1 mo lv 6 normalization 2

description:
3aKO 1 mo lv 6.CEL
Gene expression data


title: 09C87239


title: 3bKI 1 mo lv 4 normalization 2

description:
3bKI 1 mo lv 4.CEL
Gene expression data


title: 3bKI 1 mo lv 3 normalization 2

description:
3bKI 1 mo lv 3.CEL
Gene expression data


title: 3aKO 1 mo lv 8 normalization 2

description:
3aKO 1 mo lv 8.CEL
Gene expression data


title: 3aKO 1 mo lv 9 normalization 2

description:
3aKO 1 mo lv 9.CEL
Gene expression data


title: 3aKO 1 mo lv 5 normalization 2

description:
3aKO 1 mo lv 5.CEL
Gene expression data


title: 3aKO 1 mo lv 4 normalization 2

description:
3aKO 1 mo lv 4.CEL
Gene expression data


title: 09C86627


title: 09C85701


title: 09C85429


title: 09C87240


title: 3aKO 1 mo lv 3 normalization 2

description:
3aKO 1 mo lv 3.CEL
Gene expression data


title: wt 1 mo lv 12 normalization 2

description:
wt 1 mo lv 12.CEL
Gene expression data


title: 3aKO 1 mo lv 7 normalization 2

description:
3aKO 1 mo lv 7.CEL
Gene expression data


title: wt 1 mo lv 11 normalization 2

description:
wt 1 mo lv 11.CEL
Gene expression data


title: wt 1 mo lv 7 normalization 2

description:
wt 1 mo lv 7.CEL
Gene expression data