title: Patient 10_047T

value: Intestinal

value: IIIC


title: Patient 8_040T

status: Public on Mar 01 2014

type: RNA

city: Goyaongsi

first: Charny

last: Park

state: Gyeonggi-do

address: 323 Ilsan-ro,

country: South Korea

institute: National Cancer Center

hyb_protocol: Fragmented cyanine 3-labeled cRNA were loaded on to the gasket slide for hybridization and incubated at 65℃, 10 rpm for 17 hours, See manufactor's manual (http://www.chem.agilent.com/library/usermanuals/Public/G4140-90040_GeneExpression_OneColor_6.6.pdf) for detail

scan_protocol: Microarray slides were scanned on an Agilent C Scanner using the Profile AgilentG3_GX_1Color for 8x60K microarrays.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent). Gene expression data analysis was subsequently conducted in R-project (build 2.11.1). The raw data were normalized by using Quantile method. Paired t-test using Algorithm Limma were performed to select differentially expressed genes (DEG) between normal and tumor tissues in EBV(+)GC and EBV(-)GC. DEGs were clustered based by Cluster 3.0 and Tree View software.

molecule: total RNA

organism: Homo sapiens

source_name: Advanced gastric carcinoma patient

label_protocol: See the manufactor's manual (http://www.chem.agilent.com/library/usermanuals/Public/G4140-90040_GeneExpression_OneColor_6.6.pdf). Briefly, total RNA was converted to ds cDNA1 using One-Color Spike Mix. complementary RNA was amplified with T7 promtoer primers and cyanine 3-CTP. Amplified cRNA was purified with Qiagen’s RNeasy mini spin columns and quantified using NanoDrop ND-1000 (Thermo Scientific).

extract_protocol: Total RNA was isolated from tissue by using RNeasy Mini Kit (Qiagen, Hilden, Germany). Quantity and quality of isolated RNA were measured by Nanodrop ND-1000 (Thermo Scientific, Waltham, MA).

tag: tissue

value: Gastric tumor

tag: ebv

value: EBV+

tag: histology

value: CA

tag: lauren type

tag: age

tag: Sex

value: F

tag: tumor stage


title: Breast Organoids:ORG 009

type: genomic

city: Baltimore

first: leslie

last: cope

state: MD

address: 550 N. Broadway

country: USA

institute: leslie cope

description: Genomic DNA from Breast Organoids

hyb_protocol: Illumina HumanMethylation 27 BeadChip Protocols

data_processing: Six ml serum from women with metastatic breast cancer or healthy volunteers was digested with proteinase K, DNA extracted, and bisulfite treated (EZ DNA Methylation kit, Zymo Research, Orange, CA) as directed.  Bisulfite-converted DNA was processed for the Infinium HumanMethylation27 BeadChip (Illumina, Inc., San Diego, CA; WG-311-1202).  Methylation was measured as β-value, ranging from 0-1 (low to high, respectively). Differential methylation analyses were accomplished using GenomeStudio (Illumina).   Probes were selected with: 1) the most reproducible performance (probe detection p-value <0.00001; 97%, 26759/27578 probes), 2) ≥ 2-fold more methylation in serum from cancer versus normal controls (902/26759 probes), 3) ≥ 1.5-fold more methylation in tissues from breast cancer (n = 103) versus normal breast (n = 21), data from our previous study, and leukocyte DNA (n = 4 pools); all individual normal samples were required to have low methylation (≤ 0.15 β-value methylation) (232/902 probes). Finally, a subgroup of 13 genes was selected consisting of markers with a frequency of ≥ 30% methylation among cancer samples, as well as those associated with outcome in our previous study.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Breast Organoids

extract_protocol: Phenol chloroform extraction of serum DNA

treatment_protocol: Sodium bisulfite converted genomic DNA.

tag: gender

value: Female

value: Breast Organoids


title: 0987V091311_LPS_20121202_n107_01_08.RCC

city: Cambridge

first: Nir

last: Hacohen

state: MA

address: 7 Cambridge Center

institute: Broad Institute

hyb_protocol: Lysates in Qiagen RLT buffer were hybridized for 12-24 hours with custom nCounter Gene Expression CodeSets.

scan_protocol: Nanostring nCounter system (Nanostring; Seattle, WA) was used to digitally count transcripts in a multiplex reaction.

data_processing: The raw data is first scaled by positive spike-ins, shifted by negative spike-ins, and a negative binomial is fit using DESeq based on the scale parameter estimated from the positive spike-ins

growth_protocol: Monocyte-derived dendritic cells from each donor were cultured for 7 days in RPMI supplemented with 10% FBS, 100 ng/mL GM-CSF and 40 ng/mL IL-4.

extract_protocol: Total RNA was isolated using Qiagen RNeasy columns.

treatment_protocol: MoDCs were stimulated with 15 ng/mL LPS for 2.5 h or 5 h, influenza virus for 10 h, 100 U/mL IFNβ for 6.5 h, or left unstimulated.

tag: stimulation

value: LPS

tag: hours

tag: plate

tag: cartridge

tag: lane

tag: date of visit

tag: time of visit

value: M

tag: age (years)

tag: ethnicity

value: Caucasian

tag: million pbmc

tag: million dcs

tag: height (cm)

tag: weight (kg)

tag: systolic/diastolic

tag: bmi


title: Breast Organoids:ORG 109

description: Genomic DNA from Breast Organoids

scan_protocol: Illumina HumanMethylation 27 BeadChip Protocols

tag: tissue


title: 1090V090811_LPS_20121202_n107_01_11.RCC

tag: gender

value: MULTI-RACIAL


title: Breast Organoids:ORG 147

description: Genomic DNA from Breast Organoids

label_protocol: Illumina HumanMethylation 27 BeadChip Protocols


title: Breast Organoids:ORG 006

description: Genomic DNA from Breast Organoids


title: 1229V062811_LPS_20121202_n107_01_06.RCC

tag: stimulation


title: 1421V091311_LPS_20121202_n107_01_07.RCC

tag: hours

value: African-American


title: 1640V012612_LPS_20121203_n109_01_09.RCC

tag: plate

value: East Asian


title: Pooled Leukocytes:LEUK POOL 4

description: Genomic DNA from Pooled Leukocytes

source_name: Pooled Leukocytes

value: Gender unknown

tag: cell type

value: pooled leukocytes


title: 1168V062811_LPS_20121202_n107_01_05.RCC

tag: cartridge

tag: lane


title: 1344V062811_LPS_20121202_n107_01_04.RCC

tag: date of visit

tag: time of visit


title: Clone 8_Replicare 2

city: Singapore

first: Jingli

last: Zhuo

address: MD 6, 14 Medical Drive

country: Singapore

institute: National University of Singapore

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized each chip to the 50th Percentile of the measurements taken from that chip using GeneSpring GX 7.3 software

label: biotin

source_name: Clone 8_Replicare 2

label_protocol: Biotinylated cRNA were prepared with Enzo Diagnostics, USAbiotin labelled cRNA synthesis, in vitro transcription reaction was performed in the presence of T7 RNA polymerase and biotinylated ribonucleotides (Enzo Diagnostics, USA).

extract_protocol: Cells were subjected to appropriate treatment and the total RNA was extracted (RNeasy Kit, Qiagen). Double stranded cDNA was synthesised from 5 μg of total RNA using Superscript system (Invitrogen, USA) primed with T7- (dT)-24 primer.

tag: treatment

value: stable gelsolin-overexpressing C8

tag: replicate

tag: cell line


title: Pooled Leukocytes:LEUK POOL 3

description: Genomic DNA from Pooled Leukocytes


title: Patient 9_044N

value: Gastric normal

tag: ebv

value: EBV-

tag: histology

tag: lauren type

tag: age

tag: Sex

tag: tumor stage


title: Patient 7_038N

tag: tissue


title: Patient 8_040N


title: Pooled Leukocytes:LEUK POOL 2

description: Genomic DNA from Pooled Leukocytes

tag: gender


title: Normal Breast Tissue:9N

description: Genomic DNA from Normal Breast Tissue Adjacent to Tumor

source_name: Normal Breast Tissue

value: Normal Breast Tissue Adjacent to Tumor


title: 1222V062311_LPS_20121202_n107_01_03.RCC

tag: stimulation

tag: hours

tag: plate

tag: age (years)

tag: ethnicity

tag: million pbmc

tag: million dcs

tag: height (cm)

tag: weight (kg)

tag: systolic/diastolic

tag: bmi


title: Pooled Leukocytes:LEUK POOL 1

description: Genomic DNA from Pooled Leukocytes

tag: cell type


title: Patient 7_038T

value: Gastric tumor

tag: ebv

value: EBV+

tag: histology

tag: lauren type

value: Intestinal

tag: age

value: IIB


title: Patient 5_024T

tag: tissue

value: CA

tag: Sex

value: F

tag: tumor stage

value: IIIC


title: Normal Breast Tissue:8N

tag: gender

value: Female


title: Patient 6_036N

value: M


title: Patient 6_036T

value: CLR

value: Diffuse

value: IIIA


title: Patient 5_024N


title: 0668V062311_LPS_20121202_n107_01_01.RCC

tag: stimulation

value: LPS

tag: hours

tag: plate

tag: cartridge

tag: lane

tag: date of visit

tag: time of visit

tag: age (years)

value: Caucasian


title: Patient 4_014T

value: LELC


title: Normal Breast Tissue:5N


title: Patient 4_014N

value: Gastric normal

value: EBV-


title: 1361V062311_LPS_20121202_n107_01_02.RCC

tag: ethnicity

tag: million pbmc

tag: million dcs

tag: height (cm)

tag: weight (kg)

tag: systolic/diastolic

tag: bmi


title: Patient 3_007T

tag: tissue

value: Gastric tumor

tag: ebv

tag: histology

tag: lauren type

tag: age

tag: Sex

tag: tumor stage

value: ⅢA


title: Normal Breast Tissue:6N

tag: gender

value: Normal Breast Tissue Adjacent to Tumor


title: Normal Breast Tissue:7N


title: Patient 3_007N


title: 1475V013112_unstim_20121202_n106_01_09.RCC

tag: stimulation

value: unstim

tag: hours

tag: plate

tag: cartridge

tag: lane

tag: date of visit

tag: time of visit


title: 0498V013112_unstim_20121202_n106_01_10.RCC

tag: age (years)

tag: ethnicity

tag: million pbmc

tag: million dcs

tag: height (cm)

tag: weight (kg)

tag: systolic/diastolic


title: 0773V062111_LPS_20121202_n106_01_12.RCC

value: African-American

tag: bmi


title: 1663V012612_unstim_20121202_n106_01_07.RCC

value: F

value: East Asian


title: 1640V012612_unstim_20121202_n106_01_06.RCC


title: 1669V013112_unstim_20121202_n106_01_11.RCC


title: Patient 19_100T

tag: tissue

tag: ebv

tag: histology

value: CA

tag: lauren type

value: Intestinal

tag: age

tag: Sex

tag: tumor stage

value: ⅢB


title: 0310V012612_unstim_20121202_n106_01_05.RCC

tag: stimulation

tag: hours

tag: plate

tag: cartridge

tag: lane

tag: date of visit

tag: gender


title: 1363V012512_unstim_20121202_n106_01_04.RCC

tag: time of visit

tag: age (years)

tag: ethnicity

tag: million pbmc

tag: million dcs

tag: height (cm)

tag: weight (kg)


title: Gene expression in DND-41 persister, rep2

city: Boston

first: Jiang

last: Zhu

address: 185 Cambridge Street

institute: Massachusetts General Hospital, Harvard Medical School and Broad Institute

hyb_protocol: Following fragmentation, cRNA was hybridized according to the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned according to the standard Affymetrix protocol.

data_processing: Data were processed using GenePattern GC-RMA (v.2.30.0) with standard parameters for normalization and scaling.

source_name: DND-41 persister cells

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

growth_protocol: The human T-cell leukemia cell lines DND-41 and KOPT-K1 were grown in RPMI 1640 containing 10% FCS at 37°C with 5% CO2. Cells were maintained between a density of 5 x 105 cells/ml and 2 x 106 cells/ml.

extract_protocol: Total RNA was extracted using Trizol according to the manufacturer's instructions.

treatment_protocol: Persister cells were established by treating DND-41 or KOPT-K1 cells with 1 microM GSI for at least 7 weeks, replenishing the inhibitor every 3 - 4 days (Compound E, EMD4 Biosciences).

tag: cell line

tag: cell type

value: T-cell acute lymphoblastic leukemia

tag: treated with

value: 1 uM gamma Secretase inhibitor over 7 weeks


title: Patient 2_006N

tag: tissue

tag: ebv

tag: histology

tag: lauren type

tag: age

tag: Sex

value: M

tag: tumor stage


title: Normal Breast Tissue:10N

tag: gender

value: Female


title: Gene expression in DND-41 naïve, rep2

source_name: DND-41 naïve cells

value: vehicle (control)


title: Patient 1_005N

value: Gastric normal


title: Gene expression in DND-41 persister, rep1


title: Gene expression in KOPT-K1 persister, rep2

source_name: KOPT-K1 persister cells


title: Gene expression in DND-41 naïve, rep1


title: 1621V013112_unstim_20121202_n106_01_08.RCC

tag: stimulation

tag: hours

tag: plate

tag: cartridge

tag: lane

tag: date of visit

tag: time of visit

tag: age (years)

value: MULTI-RACIAL

tag: systolic/diastolic

tag: bmi


title: Gene expression in KOPT-K1 persister, rep1

tag: cell line

tag: cell type

tag: treated with


title: 0448V012512_unstim_20121202_n106_01_03.RCC

tag: ethnicity

value: Caucasian

tag: million pbmc

tag: million dcs

tag: height (cm)

tag: weight (kg)


title: 1528V012512_unstim_20121202_n106_01_02.RCC

tag: stimulation

tag: hours

tag: gender


title: 1667V012512_unstim_20121202_n106_01_01.RCC

tag: plate

tag: cartridge

tag: lane


title: 1057V100411_unstim_20121202_n105_01_12.RCC

tag: date of visit

tag: time of visit

tag: age (years)


title: 1479V092911_unstim_20121202_n105_01_09.RCC

tag: systolic/diastolic

tag: bmi


title: 1417V092911_unstim_20121202_n105_01_10.RCC


title: 1442V100411_unstim_20121202_n105_01_11.RCC


title: Patient 2_006T

tag: tissue

value: Gastric tumor

tag: ebv

value: EBV-

tag: histology

tag: lauren type

value: Diffuse

tag: age

tag: Sex

tag: tumor stage

value: ⅢA


title: 0412V092911_unstim_20121202_n105_01_08.RCC

tag: stimulation

value: unstim

tag: hours

tag: ethnicity

tag: million pbmc

tag: million dcs

tag: height (cm)

tag: weight (kg)


title: Gene expression in KOPT-K1 naïve, rep2

source_name: KOPT-K1 naïve cells

tag: cell line

tag: cell type

tag: treated with


title: Gene expression in KOPT-K1 naïve, rep1


title: 1483V092811_unstim_20121202_n105_01_07.RCC

tag: plate

tag: cartridge

tag: lane

tag: date of visit

tag: time of visit

tag: gender

tag: age (years)

tag: systolic/diastolic

tag: bmi


title: MCF-7 untreated biological replicate 1

city: Galway

first: Charles

last: Spillane

state: Galway

address: University Road

department: Botany and Plant Science

country: Ireland

institute: National University of Ireland, Galway

description: Gene expression data from MCF-7 following transfections

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000

data_processing: The raw data were analyzed with R/Bioconductor RMA normaliztion

source_name: MCF7 breast cancer cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: MCF-7 cells were grown in DMEM medium supplemented with 10% v/v fetal bovine serum, 1% v/v Pen/Strep, 1% v/v L-Glutamtine

extract_protocol: 24 hours post-transfection, cells were harvested and total RNA was isolated using Nucleospin miRNA kit (Macherey-Nagel, Germany) according to manufacturer's protocol.

treatment_protocol: anti-ctr or anti-21 oligos were transfected with lipofectamine 2000 reagent (final concentrations of 50nM)

tag: transfection

value: untreated


title: 1469V092811_unstim_20121202_n105_01_06.RCC

tag: stimulation

tag: hours

value: F

tag: ethnicity

value: East Asian

tag: million pbmc


title: MCF-7 anti-21 treated biological replicate 2

tag: cell line

value: anti-21 with lipofectamine 2000


title: MCF-7 untreated biological replicate 2


title: 1345V092811_unstim_20121202_n105_01_05.RCC

tag: million dcs

tag: height (cm)

tag: weight (kg)


title: MCF-7 anti-21 treated biological replicate 1


title: 1499V092711_unstim_20121202_n105_01_04.RCC

tag: plate

tag: cartridge

value: African-American


title: MCF-7 anti-control treated biological replicate 2

value: anti-control with lipofectamine 2000


title: 1449V092711_unstim_20121202_n105_01_03.RCC

tag: lane

tag: date of visit

value: M


title: 1458V092711_unstim_20121202_n105_01_02.RCC

tag: time of visit

tag: gender


title: 0430V092211_unstim_20121202_n105_01_01.RCC

tag: age (years)

tag: systolic/diastolic


title: 45Xp, biological rep9

city: Bethesda

first: Clara

last: Cheng

address: 10 Center Drive

institute: NICHD/NIH

description: Gene expression in PBMC from 45X Turner patient with paternal X chromosome

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 42C on GeneChip Human U133 2.0 Plus (Affymetrix).

scan_protocol: GeneChips were scanned in a GeneChip Scanner 3000.

data_processing: The data were extracted using the GeneChip Operating System 1.2 (Affymetrix).  An estimate of signal for each transcript was clculated using the Robust Multi-Array Average (RMA) using Expression Console Version 1.1 (Affymetrix) for normalization and background adjustment.

source_name: peripheral blood mononuclear cells

label_protocol: Biotinylated cRNA were prepared using the In Vitro Transcription kit (Affymetrix)  from 2 ug total RNA.

extract_protocol:
Monosomic 45X TS patients were identified by 100% of peripheral WBC (50 cells tested) with G-banding karyotype missing a complete second sex chromosome.
Parential origin of the single X chromosome was determined by comparing 8 highly polymorphic miscrosatellite markers distributed along the X chormosome between patient and her parents.
Total RNA was isolated from PBMC using the Qiagen RNeasy mini kit (Qiagen)

value: Female

tag: karyotype


title: 45Xp, biological rep10


title: 45Xp, biological rep8


title: 45Xp, biological rep6


title: 1423V092211_unstim_20121201_n104_01_11.RCC

tag: stimulation

tag: bmi


title: 1088V060911_unstim_20121201_n104_01_12.RCC

tag: hours

tag: ethnicity


title: 45Xp, biological rep7


title: 1476V092211_unstim_20121201_n104_01_10.RCC

tag: million pbmc


title: MCF-7 anti-control treated biological replicate 1

tag: cell line

tag: transfection


title: 1142V092111_unstim_20121201_n104_01_09.RCC

tag: million dcs

tag: height (cm)

tag: weight (kg)


title: 1439V092111_unstim_20121201_n104_01_08.RCC

tag: plate

tag: cartridge

tag: lane


title: 1432V092111_unstim_20121201_n104_01_07.RCC

tag: date of visit

tag: time of visit

tag: gender


title: 0182V092011_unstim_20121201_n104_01_06.RCC

tag: age (years)

tag: systolic/diastolic


title: 45Xp, biological rep3

tag: karyotype


title: 45Xm, biological rep16

description: Gene expression in PBMC from 45X Turner patient with maternal X chromosome


title: 45Xm, biological rep15


title: 45Xm, biological rep13


title: 45Xp, biological rep1


title: 45Xm, biological rep12


title: 45Xm, biological rep14


title: 45Xp, biological rep5


title: 45Xm, biological rep11


title: 45Xp, biological rep4


title: 45Xp, biological rep2


title: 45Xm, biological rep9


title: M12, Transgenic Mosaic 1

city: Moscow

first: Maia

middle: J

last: Benner

state: Idaho

address: 875 Perimeter Drive

department: Biological Sciences

institute: University of Idaho

hyb_protocol: Samples were hybridized on four 12-plex chips in conjunction with another zebrafish experiment and spread randomly across chips. An 18-hour hybridization was conducted at 42 degrees in a NimbleGen Hybridization System 4 chamber (NimbleGen, Madison, WI).

scan_protocol: The chips were washed and then scanned on a Roche MS200 scanner.

data_processing: The NimbleGen 12-plex zebrafish microarrays used in this study were designed based on the Sanger Zv7 zebrafish genome build. To improve the analysis of our microarray experiment, we created a custom NimbleGen Design File (NDF) that was based on the most current zebrafish genome build (Sanger Zv9), using a custom R script. Probe sequences from the NimbleGen microarray (113,549 probes) were aligned to Ensembl Zv9 transcripts (53,067) using the Sequence Search and Alignment by Hashing Algorithm (SSAHA2; parameters -kmer 13, -skip 2, -seeds 2, -score 12, -cmatch 9, -ckmer 6) [87]. Alignments were filtered based on the following conditions: (probe length – number of mismatches) ≤ 4, no gapped alignments, common strand per transcript (+/-), probes had only one matching gene, ≥ 3 probes per transcript, and only canonical transcripts (15,650 remaining transcripts). NimbleScan software (NimbleGen; Madison, WI) was used to align a chip-specific grid to control features and extract raw intensity data for each probe and each array. Chip images were then visually checked for each array and verified not to contain any significant spatial artifacts. Raw intensity data was then read into the R statistical computing environment and checked for quality. Further, chip intensity distributions, boxplots and hierarchical clusters were compared and checked for any unusual global patterns. Each array was then background corrected and normalized using the quantile normalization procedure and finally each probeset was summarized using the median polish procedure as described with the robust multichip average (RMA) procedure. The median Polish procedure is a robust method for summarizing all probes contained within each probeset to a single expression value for each gene taking into account individual probe effects. Probesets with low levels of expression variation across all samples (Interquartile range: IQR < 0.5) were removed from further analysis, reducing the overall number of statistical tests to be performed (6,635 total genes).

organism: Danio rerio

source_name: Adult female zebrafish, midbrain, control, T strain

label_protocol: Double-stranded cDNAs were synthesized using Invitrogen's SuperScript cDNA Synthesis Kit with the standard protocol using random hexanucleotide primers (Invitrogen, Carlsbad, CA). cDNAs were fluorescently labeled with Cy3 using the standard NimbleGen Gene Expression Analysis protocol.

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

treatment_protocol: Midbrain and telencephalon brain region samples were collected from 1-year-old sexually mature adult zebrafish from four populations varying in domestication history (Wild: Nadia and Pargana, and Domesticated: Scientific Hatchery and Transgenic Mosaic 1). Samples were mixed sex (Male and Female).

tag: strain/background

value: Transgenic Mosaic 1 (T)

tag: domestication

value: domesticated

tag: tissue

value: midbrain (M)

tag: age

value: 1 year (sexually mature adult)

tag: Sex

value: female

tag: treatment

value: control


title: M119, Scientific Hatchery

source_name: Adult female zebrafish, midbrain, control, S strain

value: Scientific Hatchery (S)


title: 45Xm, biological rep8


title: 45Xm, biological rep6


title: M109, Transgenic Mosaic 1


title: 45Xm, biological rep10


title: M140, Pargana North

source_name: Adult male zebrafish, midbrain, control, P strain

value: Pargana North (P)

value: wild

value: male


title: M21, Pargana North

source_name: Adult female zebrafish, midbrain, control, P strain


title: M47, Scientific Hatchery


title: 46XX, biological rep9

description: Gene expression in PBMC from normal female volunteer


title: M63, Transgenic Mosaic 1

source_name: Adult male zebrafish, midbrain, control, T strain


title: 45Xm, biological rep3


title: M130, Nadia

source_name: Adult female zebrafish, midbrain, control, N strain

value: Nadia (N)


title: M123, Scientific Hatchery


title: M13, Pargana North


title: 45Xm, biological rep7


title: 45Xm, biological rep4


title: M57, Scientific Hatchery

source_name: Adult male zebrafish, midbrain, control, S strain


title: 45Xm, biological rep2


title: 45Xm, biological rep5


title: 46XX, biological rep10


title: M98, Nadia

source_name: Adult male zebrafish, midbrain, control, N strain


title: 46XX, biological rep8


title: M85, Pargana North


title: M7, Nadia


title: 46XX, biological rep7


title: 46XX, biological rep6


title: M99, Transgenic Mosaic 1


title: T106, Nadia

source_name: Adult male zebrafish, telencephalon, control, N strain

value: telencephalon (T)


title: T109, Transgenic Mosaic 1

source_name: Adult female zebrafish, telencephalon, control, T strain


title: 46XX, biological rep4


title: 46XX, biological rep5


title: T123, Scientific Hatchery

source_name: Adult female zebrafish, telencephalon, control, S strain


title: 46XX, biological rep3


title: 46XX, biological rep2


title: 46XX, biological rep1


title: T13, Pargana North

source_name: Adult female zebrafish, telencephalon, control, P strain


title: Patient 1_005T

source_name: Advanced gastric carcinoma patient

value: Gastric tumor

tag: ebv

value: EBV+

tag: histology

value: CLR

tag: lauren type

value: Diffuse

tag: tumor stage

value: IIB


title: T21, Pargana North


title: T130, Nadia

source_name: Adult female zebrafish, telencephalon, control, N strain


title: T140, Pargana North

source_name: Adult male zebrafish, telencephalon, control, P strain


title: hTERT_control_1

city: Milwaukee

first: Joseph

middle: C

last: Besharse

state: WI

address: 8701 Watertown Plank Rd

department: Cell Biology, Neurobiology and Anatomy,

institute: Medical College of Wisconsin

hyb_protocol: Affymetrix Wash and Stain Kit

scan_protocol: After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner

data_processing: Image data were analyzed with Affymetrix Expression Console™ software and normalized with Robust Multichip Analysis (RMA; www.bioconductor.org/)  to determine signal log ratios. The mean fold change was calculated from the 3 independent technical replicates for each of the two experimental conditions (6 arrays total).

source_name: hTERT control

label_protocol: Affymetrix 3' IVT Express Kit

growth_protocol: Cells were grown in DMEM:F12 with 10% FCS to confluence in 100mm plates

extract_protocol: Trizol

treatment_protocol: Cells were washed with PBS and scraped off in Trizol

tag: cell


title: T12, Transgenic Mosaic 1

value: Transgenic Mosaic 1 (T)


title: T63, Transgenic Mosaic 1

source_name: Adult male zebrafish, telencephalon, control, T strain

value: domesticated


title: hTERT+MFRP_1

source_name: hTERT + MFRP


title: hTERT_control_3


title: T47, Scientific Hatchery


title: hTERT_control_2


title: hTERT+MFRP_3


title: T98, Nadia


title: T7, Nadia


title: T85, Pargana North


title: hTERT+MFRP_2


title: T57, Scientific Hatchery

source_name: Adult male zebrafish, telencephalon, control, S strain


title: T99, Transgenic Mosaic 1


title: 11331TX

city: La Jolla

first: Sunil

last: Kurian

state: CA

address: 10550 N Torrey Pines Road

department: Molecular and Experimental Medicine

institute: The Scripps Research Institute

hyb_protocol: Standard Affymetrix 49 Format Hybridization with 15mg of fragmented cRNA

scan_protocol: Affymetrix EukGE-WS2v4 protocol

data_processing: RMAExpress

source_name: Peripheral Blood

label_protocol: Ambion MessageAmp Biotin II Enhanced

growth_protocol: Peripheral Blood collected in Paxgene tubes

extract_protocol: RNA was extracted using the Paxgene RNA system

value: Peripheral Blood

tag: phenotype

value: Well-functioning kidney transplant

tag: subtype

value: TX


title: 10990TX


title: 10995TX


title: 10905TX


title: 10953TX


title: 10992TX


title: 10898TX


title: 10555TX


title: 10848TX


title: 10950TX


title: 10877TX


title: 10482TX


title: 10695TX


title: M106, Nadia

value: midbrain (M)

value: 1 year (sexually mature adult)

value: control


title: 10408TX


title: C25m normal whole venous blood sample

city: Gainesville

first: Connie

last: Mulligan

state: Florida

address: 2033 Mowry Road

department: Department of Anthropology

institute: University of Florida

description: normal whole venous blood sample

hyb_protocol: Standard Illumina Protocol

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

data_processing: Raw data were processed through Illumina's GenomeStudio V2011.1 Methylation Module v1.9.0 for cross array normalization and output of average Beta estimates and detection p-values

label: Cy3 and Cy5

source_name: venous whole blood

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was isolated using Qiagen QIAamp DNA Midi Kits (Qiagen, Valencia, CA) according to the manufacturerÍs instructions

tag: gender

value: Female

tag: birth weight-lbs

value: normal whole venous blood


title: 10698TX


title: 10850TX


title: 45Xm, biological rep1

source_name: peripheral blood mononuclear cells


title: 10777AR

value: Acute Kidney Rejection

value: Borderline


title: 10774AR

value: IIA


title: 10419AR

value: IA


title: 10535AR


title: C23m normal whole venous blood sample

description: normal whole venous blood sample


title: C22m normal whole venous blood sample

description: normal whole venous blood sample


title: 10503AR


title: C18m normal whole venous blood sample

description: normal whole venous blood sample


title: 10536AR


title: 10484AR

value: IB


title: C24m normal whole venous blood sample

description: normal whole venous blood sample


title: C19m normal whole venous blood sample

description: normal whole venous blood sample


title: 10437AR


title: 10438AR


title: 10481AR


title: 10208AR


title: C20m normal whole venous blood sample

description: normal whole venous blood sample


title: C14m normal whole venous blood sample

description: normal whole venous blood sample


title: C13m normal whole venous blood sample

description: normal whole venous blood sample


title: C17m normal whole venous blood sample

description: normal whole venous blood sample


title: C9m normal whole venous blood sample

description: normal whole venous blood sample


title: C11m normal whole venous blood sample

description: normal whole venous blood sample


title: 10883AR


title: C12m normal whole venous blood sample

description: normal whole venous blood sample


title: C7m normal whole venous blood sample

description: normal whole venous blood sample


title: Mesenteric white adipose 6deg (S0510F016)

city: London

first: Myrsini

last: Kaforou

address: Norfolk Place

country: United Kingdom

institute: Imperial College London

description: Gene expression data from mesenteric white adipose tissue of a 10wks old female mouse kept at 6 degrees for 10 days

hyb_protocol: Hybridization, Washing, Staining and Scanning of Labelled cDNA: The resultant fragmented and labelled cDNA was added to the hybridization cocktail in accordance with the NuGEN™ guidelines for hybridization onto Affymetrix GeneChip® arrays. Following the hybridization for 16-18 hours at 45°C in an Affymetrix GeneChip® hybridization Oven 640, the array was washed and stained on the GeneChip® Fluidics Station 450 using the appropriate fluidics script, before being inserted into the Affymetrix autoloader carousel and scanned using the GeneChip® Scanner 3000.

scan_protocol: GeneChip® Scanner 3000

data_processing: The data were analyzed with R programming language, using Bioconductor packages

organism: Mus musculus

source_name: Mesenteric white adipose 6deg

label_protocol: Fragmentation and Labelling of Amplified Single-Stranded cDNA protocol: The appropriate amount of amplified single-stranded cDNA was fragmented and labelled using the FL-Ovation™ cDNA Biotin Module V2. The enzymatically and chemically fragmented product (50-100 nt) was labelled via the attachment of biotinylated nucleotides onto the 3'-end of the fragmented cDNA.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Eukaryotic Target Preparation  protocol: All eukaryotic target preparations using the project-appropriate NuGEN™ RNA Amplification System in combination with the FL-Ovation™ cDNA Biotin Module V2 were performed in accordance with the guidelines detailed in the corresponding NuGEN™ technical manual.
Amplification of Total RNA protocol: Total RNA was amplified using the NuGEN™ Ovation™ RNA Amplification System V2. First-strand synthesis of cDNA was performed using a unique first-strand DNA/RNA chimeric primer mix, resulting in cDNA/mRNA hybrid molecules. Following fragmentation of the mRNA component of the cDNA/mRNA molecules, second-strand synthesis was performed and double-stranded cDNA was formed with a unique DNA/RNA heteroduplex at one end. In the final amplification step, RNA within the heteroduplex was degraded using RNaseH, and replication of the resultant single-stranded cDNA was achieved through DNA/RNA chimeric primer binding and DNA polymerase enzymatic activity. The amplified single-stranded cDNA was purified for accurate quantitation of the cDNA and to ensure optimal performance during the fragmentation and labelling process. The single stranded cDNA was assessed using spectrophotometric methods in combination with the Agilent Bioanalyzer.

treatment_protocol: Mice were exposed to either 6 or 28 C for 10 days and white and brown fat collected

tag: strain

value: female

value: BAT

tag: temperature

value: 10 weeks


title: C10m normal whole venous blood sample

description: normal whole venous blood sample


title: C8m normal whole venous blood sample

description: normal whole venous blood sample


title: Brown adipose 28deg (S0510F017)

description: Gene expression data from brown adipose tissue of a 10wks old female mouse kept at 28 degrees for 10 days

source_name: Brown adipose 28deg

value: MES


title: 10821AR

value: Peripheral Blood


title: C15m normal whole venous blood sample

description: normal whole venous blood sample


title: Mesenteric white adipose 6deg (S0510F015)

value: WAT


title: 910_Tumor_1

city: Oklahoma City

first: Elizabeth

middle: A

last: Wellberg

state: Oklahoma

address: 975 NE 10th St, BRC 309

department: Pathology

institute: University of Oklahoma HSC

hyb_protocol: Samples were hybridized using the Gene Atlas Microarray System (Affymetrix) hybridization chamber; 20 hours at 48 C

scan_protocol: Samples were scanned and imaged using the Gene Atlas Microarray System Fludics and Imaging equipment (Affymetrix)

data_processing: CEL files were processed in Partek Genomic Suite using RMA Quantile normalization; intensity values were scaled by log2 transformation

source_name: MMTV-Neu mice

label_protocol: Fragmented ssDNA was labeled with the Affymetrix WT Terminal Labeling and Hybridization kit according to the instructions, using Affymetrix proprietary biotinylated labeling reagent.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) and the RNEasy mini kit (Qiagen) with on-column DNAse digestion was used following Trizol extraction.  100ng total RNA per sample was used for array analysis.

value: FVB/N

tag: genotype/variation

value: Neu

tag: tissue type

value: mammary tumor


title: Brown adipose 6deg (S0510F014)

description: Gene expression data from brown adipose tissue of a 10wks old female mouse kept at 6 degrees for 10 days

source_name: Brown adipose 6deg

tag: tissue


title: 10885AR


title: 911_Tumor_2


title: Mesenteric white adipose 6deg (S0510F018)

tag: age


title: C4m normal whole venous blood sample

description: normal whole venous blood sample


title: C16m normal whole venous blood sample

description: normal whole venous blood sample


title: 10703AR


title: C5m normal whole venous blood sample

description: normal whole venous blood sample


title: Mesenteric white adipose 28deg (S0510F013)

description: Gene expression data from mesenteric white adipose tissue of a 10wks old female mouse kept at 28 degrees for 10 days

source_name: Mesenteric white adipose 28deg


title: C3m normal whole venous blood sample

description: normal whole venous blood sample


title: 906_Tumor_2


title: 10641AR


title: 906_Tumor_1


title: Mesenteric white adipose 28deg (S0510F012)


title: 10434AR


title: 10429AR


title: C2m normal whole venous blood sample

description: normal whole venous blood sample


title: C25p normal placenta tissue sample

description: normal placenta tissue sample

source_name: placenta tissue

value: Male

value: normal placenta tissue


title: C6m normal whole venous blood sample

description: normal whole venous blood sample

value: Female

value: normal whole venous blood


title: C22p normal placenta tissue sample

description: normal placenta tissue sample


title: C24p normal placenta tissue sample

description: normal placenta tissue sample


title: C23p normal placenta tissue sample

description: normal placenta tissue sample


title: Subcutaneous white adipose 28deg (S0510F009)

description: Gene expression data from subcutaneous white adipose tissue of a 10wks old female mouse kept at 28 degrees for 10 days

source_name: Subcutaneous white adipose 28deg

value: 6 C


title: C1m normal whole venous blood sample

description: normal whole venous blood sample


title: 844_Tumor_1

source_name: MMTV-Neu/MMTV-Spot14 mice


title: 10426AR

value: Acute Kidney Rejection


title: 10418AR

value: Borderline


title: 827_Tumor_2


title: 838_Tumor_1


title: 904_Tumor_2


title: Subcutaneous white adipose 6deg (S0510F010)

description: Gene expression data from subcutaneous white adipose tissue of a 10wks old female mouse kept at 6 degrees for 10 days

source_name: Subcutaneous white adipose 6deg


title: 10411AR


title: Subcutaneous white adipose 6deg (S0510F007)


title: 10410AR

value: IB


title: 828_Tumor_1


title: 10404AR

value: IA


title: Subcutaneous white adipose 28deg (S0510F008)

value: female


title: Brown adipose 28deg (S0510F006)

value: 10 weeks


title: 10407AR


title: C20p normal placenta tissue sample

description: normal placenta tissue sample


title: 904_Tumor_1


title: C19p normal placenta tissue sample

description: normal placenta tissue sample


title: Brown adipose 6deg (S0510F011)

value: MES


title: C17p normal placenta tissue sample

description: normal placenta tissue sample


title: 826_Tumor_1


title: C16p normal placenta tissue sample

description: normal placenta tissue sample


title: 11599TX

value: Peripheral Blood

value: Well-functioning kidney transplant

value: TX


title: C18p normal placenta tissue sample

description: normal placenta tissue sample


title: Subcutaneous white adipose 6deg (S0510F001)

value: BAT


title: Brown adipose 28deg (S0510F005)


title: Brown adipose 6deg (S0510F003)

value: WAT


title: Mesenteric white adipose 28deg (S0510F002)


title: 821_Tumor_1

value: FVB/N

value: Neu

value: mammary tumor


title: Subcutaneous white adipose 28deg (S0510F004)


title: C13p normal placenta tissue sample

description: normal placenta tissue sample

value: Female

value: normal placenta tissue


title: 813_Tumor_1


title: 11593AR

value: Acute Kidney Rejection


title: 11450AR


title: C14p normal placenta tissue sample

description: normal placenta tissue sample

value: Male


title: 596_Tumor_1


title: 11448AR


title: 15_day5_unbound

type: other

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

institute: IGMM MRC Human Genetics Unit

description:
Extracted molecule: polysomal RNA
Amplification protocol
Target Amplified manufacturer/kit: NuGen WT-Ovation RNA Amplification kit
Target Amplified protocol: NuGEN
Rounds of amplification: 1

hyb_protocol: Amount labeled target hybridization to array: 2.5 µg

scan_protocol: Probe arrays were scanned using an Affymetrix GeneChip Scanner 3000 7G and Affymetrix scanning software AGCC version 1.1 for the Genechip operating software.

data_processing: MATLAB R2011b (7.13.0.564) software and the Bioinformatics Toolbox.

molecule: other

source_name: Peri/FibroTRAP (unbound) WT kidney medulla, day 5

label_protocol: Encore Biotin Module

extract_protocol: Humphreys protocol: TRAP, modified (Based on published protocol: M Heiman, Cell 2008, 135 (4):738-48).

tag: Sex

value: both

value: kidney medulla

tag: time

value: day 5

tag: thelier stage

tag: developmental stage

tag: specimen mutation

tag: mutation notes

value: Construct generated in Ben Humphreys lab. A fusion transgene encoding eGFP and the ribosomal protein L10a was inserted downstream of the collagen1α1 promoter/enhancer element.

tag: url

tag: experimental design

value: Col1a1-eGFPL10a mice were subject to Sham or unilateral ureteral obstruction surgery. Sham kidneys were collected at day 0, and UUO kidneys were collected at day 2 or day 5 for TRAP.


title: 595_Tumor_1


title: 11520AR

value: Peripheral Blood

tag: phenotype

tag: subtype

value: IB


title: 11449AR

value: IA


title: C15p normal placenta tissue sample

description: normal placenta tissue sample

tag: gender

tag: birth weight-lbs


title: 456_Tumor_1

tag: strain


title: 401_Tumor_1

tag: genotype/variation


title: 504_Tumor_1

tag: tissue type


title: 10553TX

tag: tissue

value: Well-functioning kidney transplant

value: TX


title: C12p normal placenta tissue sample

description: normal placenta tissue sample


title: 11018AR


title: 11_day5_bound

source_name: Peri/FibroTRAP (bound) WT kidney pericytes, day 5

value: kidney pericytes (periarterial fibroblasts of inner and outer medulla)


title: 10_day5_bound


title: 10310AR


title: 821_Tumor_2

value: FVB/N

value: Neu


title: C8p normal placenta tissue sample

description: normal placenta tissue sample

value: Female


title: C11p normal placenta tissue sample

description: normal placenta tissue sample

value: normal placenta tissue


title: 10275AR

value: Acute Kidney Rejection


title: C10p normal placenta tissue sample

description: normal placenta tissue sample

value: Male


title: 10266AR

value: Borderline


title: C9p normal placenta tissue sample

description: normal placenta tissue sample


title: 045_Tumor_1

value: mammary tumor


title: C4p normal placenta tissue sample

description: normal placenta tissue sample


title: 7_day2_bound

source_name: Peri/FibroTRAP (bound) WT kidney pericytes, day 2

value: both

value: day 2


title: 13_day5_unbound

value: kidney medulla

value: day 5

value: Construct generated in Ben Humphreys lab. A fusion transgene encoding eGFP and the ribosomal protein L10a was inserted downstream of the collagen1α1 promoter/enhancer element.

value: Col1a1-eGFPL10a mice were subject to Sham or unilateral ureteral obstruction surgery. Sham kidneys were collected at day 0, and UUO kidneys were collected at day 2 or day 5 for TRAP.


title: 10306AR

value: Peripheral Blood


title: C3p normal placenta tissue sample

description: normal placenta tissue sample


title: 8_day2_bound


title: 10309AR

value: IA


title: 6_day0_unbound

source_name: Peri/FibroTRAP (unbound) WT kidney medulla, day 0

value: day 0


title: 5_day0_unbound


title: C5p normal placenta tissue sample

description: normal placenta tissue sample


title: 4_day0_unbound


title: 11349AR


title: C2P normal placenta tissue sample

description: normal placenta tissue sample


title: 11162TX

value: Well-functioning kidney transplant

value: TX


title: C1P normal placenta tissue sample

description: normal placenta tissue sample

value: Female


title: C25c normal whole cord blood sample

description: normal whole cord blood sample

source_name: cord whole blood

value: normal whole cord blood


title: 1_day0_bound

description:
Extracted molecule: polysomal RNA
Amplification Protocol
Target Amplified manufacturer/kit: NuGen WT-Ovation RNA Amplification kit
Target Amplified protocol: NuGEN
Rounds of amplification: 1

source_name: Peri/FibroTRAP (bound) WT kidney pericytes, day 0

value: kidney pericytes (periarterial fibroblasts of inner and outer medulla)


title: 2_day0_bound


title: C23c_2 normal whole cord blood sample

description: normal whole cord blood sample


title: C7p normal placenta tissue sample

description: normal placenta tissue sample

value: normal placenta tissue


title: 11021TX

source_name: Peripheral Blood


title: 11158TX


title: 10847AR

value: Acute Kidney Rejection

value: IIA


title: 3_day0_bound

value: both


title: 11421AR


title: C22c normal whole cord blood sample

description: normal whole cord blood sample

value: Male


title: C6p normal placenta tissue sample

description: normal placenta tissue sample


title: C19c normal whole cord blood sample

description: normal whole cord blood sample


title: 11384AR

value: Borderline


title: 14_day5_unbound

value: kidney medulla

value: day 5


title: 11382AR


title: mixed liver samples from five transgenic mice at 11 months

city: Shanghai

first: wang

last: feng

address: 320 Yue Yang Road

country: China

institute: Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

description: Gene expression data of tumoral liver tissues from WHV/c-myc transgenic C57/BL6 mice bearing primary liver tumors at 11 months of age, the signals represent mean expression of five separate samplings.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16hr at 45℃, 60rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 400. Midi-euk2 washing script was used.

scan_protocol: GeneChips were scanned using Affymetrix Gene Array Scanner 3000.

data_processing: The data were analyzed with GeneChip® Operating Software 1.2 (GCOS1.2) using Affymetrix default analysis settings. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: liver tissues obtained from WHV⁄c-myc transgenic mice at the age of 11 months

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocols (Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: Mice were housed in LD 12:12 light cycles, maintained in a pathogen-free facility and had free access to food and water.

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

treatment_protocol: Mice were examined at weekly interval and euthanized when presenting with abdominal broadening. Tumors and non-tumoral livers were collected and snap-frozen in liquid nitrogen and kept at -80℃.

tag: age

value: 11 months

value: WHV/c-myc transgenic


title: mixed liver samples from five transgenic mice at 5 months

description: Gene expression data of non-tumorous liver tissues from WHV/c-myc transgenic C57/BL6 mice at 5 months of age, the signals represent mean expression of five separate samplings.

source_name: liver tissues obtained from WHV⁄c-myc transgenic mice at the age of 5 months

value: 5 months


title: mixed liver samples from five normal mice at 11 months

description: Gene expression data of normal liver tissues from wild-type C57/BL6 mice at 11 months of age, the signals represent mean expression of five separate samplings.

source_name: liver tissues obtained from wild-type C57/BL6 mice at the age of 11 months

value: wild-type


title: pRRL IRES2-EGFP

city: Groningen

first: JJ

last: Schuringa

address: Hanzeplein 1

department: Experimental Hematology

country: Netherlands

institute: UMCG

description: pRRL IRES2-EGFP_Signal

hyb_protocol: Standard Illumina scanning protocol

scan_protocol: Illumina i-Scan reader

data_processing: All samples were corrected for background using Illumina GenomeStudio and then jointly forced to positive values, normalized and transformed using the R packages Bioconductor (21) and Lumi (22). Probes with a detection p-value larger than 0.01 in all samples, as provided by GenomeStudio, were deleted. Log2 transformation and quantile normalization were applied. As a measure of quality control we performed a principal component analysis (PCA) on the correlation matrix of all 147 samples (23). The first component was removed from the data (24).To ensure reliability and reproducibility of the results we used multivariate permutations (MP) to determine the significance of our results using a False Discovery Rate (FDR) of 0,4. For further details, please see Bonardi et al, Mol Cell Proteomics. 2013 Mar;12(3):626-37. Afther these procedures, 33221 normalized ID_REFs out of a possible 47323 ID_REFs present in the raw dataset were used for the analyses.

source_name: cord blood

label_protocol: Standard Illumina hybridization protocol

growth_protocol: CB CD34+ cells were isolated by Miltenyi miniMACS column. Cells were prestimulated in HPGM with 100 ng/ml KITL, FLT#L and TPO for 48 hrs. Cells were transduced with control pRRL-IRES2-EGFP lentiviral vectors or vectors expressing HIF1α(P402A,P564A) or HIF2α(P405A,P531A) in one or two  rounds of 12 hrs each. 24 hrs later transduced cells were sorted after which RNA was isolated. 5 independent CB CD34+ batches were isolated, transduced and sorted, and isolated RNA was combined and used for Illumina beadhchip arrays HT12 v4

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: cord blood

tag: cell type

tag: transduced with

value: control pRRL-IRS2-EGFP lentiviral vectors


title: 593_Tumor_1

value: FVB/N

value: mammary tumor


title: pRRL HIF2α(P405A,P531A)-IRES2-EGFP

description: pRRL HIF2α_P405A,P531A_-IRES2-EGFP_Signal

value: lentiviral vectors expressing HIF2α(P405A,P531A)


title: C18c normal whole cord blood sample

description: normal whole cord blood sample

value: Female

value: normal whole cord blood


title: R11ΔS15_rep2

city: Los Angeles

first: Siavash

middle: K

last: Kurdistani

address: 615 Charles E Young Dr South

department: Biological Chemistry

institute: UCLA

hyb_protocol: manufacturer's protocol

scan_protocol: manufacturer's protocol

data_processing: MAS5 by Affymetrix's AGCC version 3.2

label: R-Phycoerythrin

organism: Saccharomyces cerevisiae

source_name: H2A R11ΔS15

label_protocol: manufacturer's protocol

growth_protocol: YPD - starter culture was diluted to OD600 0.2 and grown to OD600 0.8

extract_protocol: hot acid phenol RNA extraction method followed by poly A purification

treatment_protocol: no treatment

value: expressing histone H2A with lysine inserted in position 11 and serine 15 deleted

tag: rna extracted from

value: log phase culture


title: C17c normal whole cord blood sample

description: normal whole cord blood sample

value: Male


title: 455_Tumor_1

source_name: MMTV-Neu mice

value: Neu


title: pRRL HIF1α(P402A,P564A)-IRES2-EGFP

description: pRRL HIF1α_P402A,P564A_-IRES2-EGFP _Signal

value: lentiviral vectors expressing HIF1α(P402A,P564A)


title: 11279TX

value: Peripheral Blood

value: Well-functioning kidney transplant

value: TX


title: mixed liver samples from five normal mice at 5 months

description: Gene expression data of normal liver tissues from wild-type C57/BL6 mice at 5 months of age, the signals represent mean expression of five separate samplings.

source_name: liver tissues obtained from wild-type C57/BL6 mice at the age of 5 months

value: 5 months


title: C24c normal whole cord blood sample

description: normal whole cord blood sample


title: R11ΔS15_rep1


title: 11027AR

value: Acute Kidney Rejection

value: IB


title: ΔS15_rep2

source_name: H2A ΔS15

value: expressing histone H2A with serine 15 deleted


title: CB CD34+ normoxia

description: CB CD34+ normoxia

data_processing: All samples were corrected for background using Illumina GenomeStudio and then jointly forced to positive values, normalized and transformed using the R packages Bioconductor (21) and Lumi (22). Probes with a detection p-value larger than 0.01 in all samples, as provided by GenomeStudio, were deleted. Log2 transformation and quantile normalization were applied. As a measure of quality control we performed a principal component analysis (PCA) on the correlation matrix of all 147 samples (23). The first component was removed from the data (24).To ensure reliability and reproducibility of the results we used multivariate permutations (MP) to determine the significance of our results using a False Discovery Rate (FDR) of 0,4. For further details, please see Bonardi et al, Mol Cell Proteomics. 2013 Mar;12(3):626-37. After these procedures, 33221 normalized ID_REFs out of a possible 47323 ID_REFs present in the raw dataset were used for the analyses.

growth_protocol: CB CD34+ cells were isolated by Miltenyi miniMACS column. Cells were prestimulated in HPGM with 100 ng/ml KITL, FLT3L and TPO for 3 days after which cells were placed either at normoxia or hypoxia (1% O2 for an additional 24 hrs). 5 independent CB CD34+ batches were used and isolated RNA was combined and used for Illumina beadhchip arrays HT12 v4

value: cord blood

value: CD34+ cells

tag: exposed to

value: normoxia


title: C15c_2 normal whole cord blood sample

description: normal whole cord blood sample

value: Female


title: 10982AR

value: IA


title: 9_day2_bound

tag: Sex

value: both

value: kidney pericytes (periarterial fibroblasts of inner and outer medulla)

tag: time

value: day 2

tag: thelier stage

tag: developmental stage

tag: specimen mutation

value: Construct generated in Ben Humphreys lab. A fusion transgene encoding eGFP and the ribosomal protein L10a was inserted downstream of the collagen1α1 promoter/enhancer element.

value: Col1a1-eGFPL10a mice were subject to Sham or unilateral ureteral obstruction surgery. Sham kidneys were collected at day 0, and UUO kidneys were collected at day 2 or day 5 for TRAP.


title: ΔS15_rep1

value: log phase culture


title: C16c normal whole cord blood sample

description: normal whole cord blood sample

value: Male

value: normal whole cord blood


title: CB CD34+ hypoxia

description: CB CD34+ hypoxia

value: hypoxia (1% O2)


title: U87-HBMEC Coculture Rep 3

city: Ann Arbor

first: Michael

middle: Dale

last: Brooks

state: Michigan

address: 2800 Plymouth Rd Building 26 Rm 329S

department: Internal Medicine

institute: University of Michigan

scan_protocol: scanned on an Illumina BeadArray Reader

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

label: Biotin

source_name: Human glioma cocultured with endothelial cells

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

extract_protocol: Trizol Extraction

tag: cell line


title: C14c_2 normal whole cord blood sample

description: normal whole cord blood sample

tag: gender


title: K11_rep1

source_name: H2A K11

value: expressing histone H2A with lysine inserted in position 11


title: U87-HBMEC Coculture Rep 2


title: 10886AR

value: Peripheral Blood

tag: phenotype

value: Acute Kidney Rejection

tag: subtype


title: U87-HBMEC Coculture Rep 1


title: C13c normal whole cord blood sample

description: normal whole cord blood sample

tag: birth weight-lbs


title: C12c normal whole cord blood sample

description: normal whole cord blood sample


title: 11019AR

value: IB


title: 10882AR

value: Borderline


title: C11c normal whole cord blood sample

description: normal whole cord blood sample


title: HBMEC Monoculture Rep 3

source_name: Human brain microvascular endothelial cell line

value: HBMEC


title: R11_rep1

source_name: H2A R11

tag: genotype/variation

value: expressing histone H2A with arginine inserted in position 11


title: 12_day5_bound

source_name: Peri/FibroTRAP (bound) WT kidney pericytes, day 5

tag: strain

tag: tissue

value: day 5

tag: mutation notes

tag: url

tag: experimental design


title: 10843TX

value: Well-functioning kidney transplant

value: TX


title: WT_rep3

source_name: WT H2A

value: expressing WT histone H2A

tag: rna extracted from


title: C10c normal whole cord blood sample

description: normal whole cord blood sample

source_name: cord whole blood


title: 10879AR


title: C9c normal whole cord blood sample

description: normal whole cord blood sample


title: HBMEC Monoculture Rep 2


title: HBMEC Monoculture Rep 1


title: R11_rep2


title: 10502AR


title: C8c normal whole cord blood sample

description: normal whole cord blood sample

value: Female


title: U87 Monoculture Rep 2

source_name: Human glioma cell line


title: E207 v control

status: Public on Feb 25 2014

city: Oxford

first: Eric

last: Belfield

state: England

address: South Parks Road

department: Plant Sciences

institute: Oxford University

description:
Sample 5
mutant deletion size (bp): 4
5 x DELLA deficient mutant (gai-t6, rga-t2, rgl1-1, rgl2-1 and rgl3-4)

hyb_protocol: NimbleGen custon array service (http://www.nimblegen.com/support/dna-microarray-support.html)

data_processing:
per standard NimbleGen protocol (http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf)
The "RATIO_CORRECTED" column in the *matrix.txt file reports log2 of the Cy3/Cy5 signal.

organism: Arabidopsis thaliana

source_name: Genomic DNA E207 plant

label_protocol: Cy3/5 labeling per standard NimbleGen protocol (http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf)

extract_protocol: DNeasy Mini Kit (Qiagen)

tag: ecotype

value: Ler background

value: max2 mutant (5 x DELLA KO)

value: Whole plant

source_name: Genomic DNA E207 control plant

value: E207 control


title: FN1148 v control

description:
Sample 2
mutant deletion size (bp): 523

scan_protocol: NimbleGen custon array service (http://www.nimblegen.com/support/dna-microarray-support.html)

source_name: Genomic DNA FN1148 plant

value: Col-0 background

value: hkt1 mutant

source_name: Genomic DNA FN1148 control plant

value: FN1148 control


title: E124 v control

description:
Sample 3
mutant deletion size (bp): 104
5 x DELLA deficient mutant (gai-t6, rga-t2, rgl1-1, rgl2-1 and rgl3-4)

source_name: Genomic DNA E124 plant

value: phyB mutant (5 x DELLA KO)

source_name: Genomic DNA E124 control plant

value: E124 control


title: E99 v control

description:
Sample 4
mutant deletion size (bp): 28
5 x DELLA deficient mutant (gai-t6, rga-t2, rgl1-1, rgl2-1 and rgl3-4)

source_name: Genomic DNA E99 plant

value: hy1 mutant (5 x DELLA KO)

source_name: Genomic DNA E99 control plant

value: E99 control


title: WT_rep2

value: log phase culture


title: ga1-3 v control

description:
Sample 1
mutant deletion size (bp): 5051

source_name: Genomic DNA ga1-3 plant

value: ga1-3 mutant

source_name: Genomic DNA ga1-3 control plant

value: ga1-3 control


title: K11_rep2

source_name: H2A K11

value: expressing histone H2A with lysine inserted in position 11


title: 10439AR

source_name: Peripheral Blood

value: Peripheral Blood

value: Acute Kidney Rejection

value: IB


title: C7c_2 normal whole cord blood sample

description: normal whole cord blood sample

value: Female

value: normal whole cord blood


title: 11160TX

value: Well-functioning kidney transplant

value: TX


title: C6c normal whole cord blood sample

description: normal whole cord blood sample

value: Male


title: U87 Monoculture Rep 1


title: WT_rep1

value: expressing WT histone H2A


title: 10730AR


title: 10427AR

value: IA


title: Tumor #20_2

status: Public on Feb 01 2014

city: Buffalo

first: Qiang

last: Hu

state: NY

address: Elm & Carlton Streets

institute: Roswell Park Cancer Institute

hyb_protocol: 750ng of the biotin labeled cRNA probes were mixed with hybridization reagents and hybridized overnight to the HumanHT-12 v4 BeadChips.

scan_protocol: Following washing and staining, the BeadChips were imaged using the Illumina iScan Reader to measure fluorescence intensity at each probe.

data_processing: BeadChip data files were analyzed with Illumina’s GenomeStudio gene expression module (v1.8.0)

source_name: Breast tumor with high FAK, triple-negative

label_protocol: Initially, 500ng total RNA was converted to cDNA, followed by an in vitro transcription step to generate biotin labeled cRNA using the Ambion Illumina Total Prep RNA Amplification Kit (Ambion, Austin, TX) as per manufacturer’s instructions.

extract_protocol: Total RNA from 10-20 mg fresh frozen tissues were prepared using the RNeasy mini kits (Qiagen, Valencia, CA) following manufacturer’s instructions. After elution, RNA samples were concentrated by EtOH precipitation at –20oC overnight, and resuspended in nuclease-free water.  Before labeling, RNA samples were quantitated using a ND-1000 spectrophotometer (NanoDrop Wilmington, DE) and evaluated for degradation using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).  Samples were required to have a RIN >6.5, an OD 260:280 of 1.9-2.1, an OD 260/230 >1.5 and >1.5 28S:18S ratio of the ribosomal bands for gene expression array analysis.

value: breast tumor


title: Tumor #11

source_name: Breast tumor, high FAK


title: Tumor #11_2


title: C5c normal whole cord blood sample

description: normal whole cord blood sample


title: Tumor #20


title: Tumor #6

source_name: Breast tumor with low FAK


title: Tumor #9_2


title: C3c normal whole cord blood sample

description: normal whole cord blood sample

source_name: cord whole blood


title: C4c normal whole cord blood sample

description: normal whole cord blood sample


title: Streptococcus mutans UA159 100 mM Glucose Replicate 3

status: Public on Dec 03 2013

city: Gainesvile

first: Zachary

middle: Daniel

last: Moye

address: 1395 Center Dr. Box 100424

department: Oral Biology

hyb_protocol: The Cy3-labeled experimental samples were mixed in equal quantity to the Cy5-labeled reference RNA and hybridized to the microarray slides using a Maui four-chamber hyrbidization system (BioMicro Systems) for 16 h at 42°C.  The slides were washed according to the TIGR protocol.

scan_protocol: The slides were scanned using a GenePix scanner (Axon Instruments). The scanned images were loaded into TIGR Spotfinder software and overlaid. A spot grid was created according to TGIR specifications and adjusted manually to fit all spots to the grid and intensity for each spot determined.

data_processing:
Data was normalized using Microarray Data Analysis Software (MIDAS) by using LOWESS and iterative log mean centering with default settings, followed by in-slide replicate anaylsis.
IA corresponds to cells grown with TV plus 10 mM glucose (samples 1-3) or 100 mM glucose (samples 4-6) while IB refers to the reference RNA isolated from cells grown in BHI.

organism: Streptococcus mutans UA159

label_protocol: 2 ug of RNA was primed with 6 ug of random hexamer primer (Invitrogen) at 70°C for 10 mins and reverse transcribed at 42°C overnight using SuperScript III (Invitrogen ) and 2:1 dTTP:aminoacyl-dUTP and 100mM dATP, dCTP, dGTP, dTTP.  Purified cDNA samples were coupled with Cy3 or Cy5.

growth_protocol: Experimental samples were grown in continuous chemostat culture at a dilution rate of 0.3 hr. using TV medium supplemented with either 10 mM or 100 mM glucose. Reference RNA was collected from cells of Streptococcus mutans UA159 grown to mid-exponential phase in BHI media.

extract_protocol: Total RNA was extracted using phenol (pH 4.3), DNase I treated and purified using RNAse mini kit (Qiaigen)

treatment_protocol: Cells were harvested and treated with RNA protect reagent (Qiagen)

tag: growth condition

value: 100 mM Glucose

source_name: Reference S. mutans UA159 RNA

value: mid-exponential phase in BHI media


title: Tumor #6_2


title: C2c_2 normal whole cord blood sample

description: normal whole cord blood sample


title: Streptococcus mutans UA159 100 mM Glucose Replicate 2


title: Tumor #26_2

source_name: Breast tumor with low FAK, triple-negative


title: 10906AR

value: Borderline


title: #483_4EGI-1_2

status: Public on Jan 01 2014

city: Hannover

first: Adrian

last: Schwarzer

address: Carl-Neuberg-Str. 1

country: Germany

institute: Hannover Medical School

description: Polysome fraction from 4EGI-1 TREATED #483 T-ALL CELLS

hyb_protocol: amplified, fragmented, biotin labeled cDNA was hybridized for 18 hr at 45C on Mouse GeneChip1.0 ST Arrays. Chips were washed and stained in the Affymetrix Fluidics Station 450 using protocol FS450_0007

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing: RMA (Robust Multichip Average; Bioconductor)

source_name: # 483 T-ALL clone + 4EGI-1

label_protocol: RNA was amplified by the Applause WT-Amp ST System (NuGEN Technologies, Bemmel, The Netherlands), amplified cDNA was fragmented and biotin labeled using the Encore Biotin Module (NuGEN Technologies)

extract_protocol: polysome fractions were collected and supplied with 0.1 volume of 3 M sodium acetate (pH 5.2) and 1 volume of isopropanol for overnight precipitation at -20 °C. RNA was purified using Nucleospin RNAII tubes (Macherey & Nagel). For microarray analysis RNA from polysome fractions were pooled, precipitated by adding LiCl to a final concentration of 2 M and resolubilized in 15 µl of RNase-free water.

treatment_protocol: #483 were treated with 4EGI-1 or DMSO. Polysomal fractions were prepared via sucrose density gradients and subjected to Microarray analysis.

tag: fraction

value: polysome


title: #483_untreated_1

description: Polysome fraction from untreated #483 T-ALL CELLS

source_name: # 483 T-ALL clone


title: #483_untreated_3


title: Tumor #21


title: #483_4EGI-1_3


title: Streptococcus mutans UA159 100 mM Glucose Replicate 1


title: #483_untreated_2


title: Streptococcus mutans UA159 10 mM Glucose Replicate 2

value: 10 mM Glucose


title: Streptococcus mutans UA159 10 mM Glucose Replicate 3


title: Streptococcus mutans UA159 10 mM Glucose Replicate 1


title: #483_4EGI-1_1


title: Tumor #21_2


title: U87 Monoculture Rep 3

hyb_protocol: Standard Illumina hybridization protocol

source_name: Human glioma cell line


title: Tumor #9


title: Tumor #26


title: iPS cells #26, technical replicate 2

status: Public on Nov 17 2013

city: Houston

first: Bruno

last: Di Stefano

state: TX

address: 1 Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description: iPS cells derived from B cells, replicate 2

hyb_protocol: 600ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human Gene Expression 8x60K arrays (G4851A-028004)  for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent)

scan_protocol: Scanned on an Agilent G2539A scanner at 3um resolution and 100%PMT. The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing: Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng RNA using the LowInputQuick Amp Labeling kit (Agilent 5190-2305) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: ESCs and iPSCs were cultured on mitomycin C treated MEF feeder cells in KO-DMEM (Invitrogen) supplemented withL-glutamine, penicillin/streptomycin, nonessential amino acids, β-mercaptoethanol, 1,000 U/ml LIF (ESC medium) and 15% fetal bovine serum (FBS, Invitrogen). MEF cultures were established by trypsin digestion of mouse embryos (embryonic day 13.5) and the resulting cells cultured in DMEM supplemented with 10% FBS, L-glutamine and penicillin/streptomycin. CD19+ pro-B and pre-B cells were isolated from bone marrow using monoclonal antibodies to CD19 (1D3), obtained from BD Pharmingen, using MACS (Miltenyi Biotech). After isolation B cells were grown in RPMI medium supplemented with 10% FBS and IL-7. cell reprogramming experiments were conducted in gelatinized plates seeded with a feeder layer of the OP9 stromal cell line, using ESC medium supplemented with 2μg/ml of doxycycline and 15% FBS. For the reprogramming of B cells, IL-4 (10ng/ml), IL-7 (10ng/ml) and IL-15 (2ng/ml) were added to the medium.

extract_protocol: RNA isolation  was done with the miRNeasy Mini kit

treatment_protocol: Cells were trypsinized and FACS-sorted to remove feeder and dead cells.

value: iPS cells

tag: treatment

value: iPS cells derived from B cells


title: ES cells Bruce, technical replicate 2

description: ES cells, replicate 2

source_name: bruce

value: ES cells


title: iPS cells #26, technical replicate 1

description: iPS cells derived from B cells, replicate 1


title: aiPS cells #22, technical replicate 2

description: iPS cells derived from B cells infected with C/EBPa, replcate 2


title: ES cells Bruce, technical replicate 1

description: ES cells, replicate 1


title: B cells, time 192, technical replicate 2

description: B cells induced with OSKM for 192hrs  replicate 2

value: primary B cells

tag: time point

value: 196 hrs

value: B cells induced with OSKM for 192hrs


title: Rrm3 npl3∆ exp2

status: Public on Nov 15 2013

city: Seville

first: Andrés

last: Aguilera

address: Av. Américo Vespucio 24

department: Genome BIology

country: Spain

institute: CABIMER, Universidad de Sevilla

description:
Asynchronous cultures growing in rich YPD medium
test CEL file: Rrm3-npl3-2_IP.CEL
control CEL file: Rrm3-npl3-2_SUP.CEL
processed data file: Rrm3-npl3_pvalue.bed
processed data file: Rrm3-npl3_signal.bar
processed data file: Rrm3-npl3_pvalue.bar

hyb_protocol: Approximately 5 μg of DNA was hybridzed per array using the Affymetrix hybridization kit. The arrays were hybridized for 16 hours at 45° at 60 rpm using an Affymetrix hybridization oven. The probe was removed from these arrays and reused to hybridize the remaining three arrays.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G

data_processing:
Primary data analyses were carried out using the Affymetrix TAS 1.1.02 software to obtain hybridization intensity, signal log2 ratio value and change P-value for each locus. For the discrimination of positive and negative signals for the binding, we compared the chromatin-immunprecipitated fraction with the supernatant fraction by using two criteria. First, the reliability of binding ratio was judged by change P-value (P ≤ 0.01). Second, clusters consisting of at least twenty-five contiguous probe-sets (positive signal, max. gap 250bp, min run. 100bp) that filled the above criteria were selected.
Locus identification, raw signal intensity, detection signal log ratio, and change p-value was obtained using the Affymetrix TAS 1.1.02 software.

source_name: Rrm3-Flag ChIP DNA from N3RBb-4B, asynchronous culture

label_protocol: Chromatin-immunprecipitated DNA was purified and amplified by random priming as described (Katou et al. 2003): A total of 5 μg of amplified DNA was digested with DNaseI to a mean size of 100 bp and purified, and the fragments were end-labeled with biotin-N6-ddATP.

growth_protocol: Yeast cells were grown in YPD to mid-log phase at 30°C

extract_protocol: ChIP was carried out as previously described (Katou et al. 2003, 2006): We disrupted 1.5 × 107  cells by Multi-beads shocker (MB400U, Yasui Kikai) using glass beads. Anti-c-Myc monoclonal antibody (Clontech) was used for ChIP.

value: MATa ade2-1 can1-100 trp1-1 his3-11,15 leu2-3,112 ura3::URA3/GPD-Tk(7x) Rrm3::FLAG bar1ΔHphMX npl3::KanMX

tag: cell cycle stage

value: asynchronous

source_name: Input DNA from N3RBb-4B


title: ES cells R1, technical replicate 1

description: ES cells


title: B cells,time 96, technical replicate 2

description: B cells induced with OSKM for 96hrs  replicate 2

value: 96 hrs

value: B cells induced with OSKM for 96hrs


title: B cells, time 144, technical replicate 1

description: B cells induced with OSKM for 144hrs  replicate 1

value: 144 hrs

value: B cells induced with OSKM for 144hrs


title: B cells, time 192, technical replicate 1

description: B cells induced with OSKM for 192hrs  replicate 1


title: B cells, time 48, technical replicate 1

description: B cells induced with OSKM for 48hrs  replicate 1

value: 48 hrs

value: B cells induced with OSKM for 48hrs


title: B cells, time 48, technical replicate 2

description: B cells induced with OSKM for 48hrs  replicate 2


title: 18hrs pulse B cells,time 96, technical replicate 1

description: B cells pulsed for 18hrs with C/EBPa, induced for 96 hrs with OSKM, replicate 1


title: B cells, time 0, technical replicate 1

description: B cells uninduced, replicate 1

value: 0 hrs

value: B cells uninduced


title: 18hrs pulse B cells,time 144, technical replicate 1

description: B cells pulsed for 18hrs with C/EBPa, induced for 144 hrs with OSKM, replicate 1


title: B cells, time 144, technical replicate 2

description: B cells induced with OSKM for 144hrs  replicate 2


title: B cells, time 96, technical replicate 1

description: B cells induced with OSKM for 96hrs  replicate 1


title: 18hrs pulse B cells, time 96, technical replicate 2

description: B cells pulsed for 18hrs with C/EBPa, induced for 96 hrs with OSKM, replicate 2


title: 18hrs pulse B cells, time 192, technical replicate 2

description: B cells pulsed for 18hrs with C/EBPa, induced for 192 hrs with OSKM, replicate 2


title: B cells, time 0, technical replicate 2

description: B cells uninduced, replicate 2


title: 18hrs pulse B cells,time 192, technical replicate 1

description: B cells pulsed for 18hrs with C/EBPa, induced for 192 hrs with OSKM, replicate 1


title: aiPS cells #8, technical replicate 1

description: iPS cells derived from B cells infected with C/EBPa


title: 18hrs pulse B cells, time 0, technical replicate 1

description: B cells pulsed for 18hrs with C/EBPa, replicate 1

value: B cells pulsed for 18hrs with C/EBPa


title: 18hrs pulse B cells, time 144, technical replicate 2

description: B cells pulsed for 18hrs with C/EBPa, induced for 144 hrs with OSKM, replicate 2


title: 18hrs pulse B cells, time 48, technical replicate 1

description: B cells pulsed for 18hrs with C/EBPa, induced for 48 hrs with OSKM, replicate 1


title: 18hrs pulse B cells,time 48, technical replicate 2

description: B cells pulsed for 18hrs with C/EBPa, induced for 48 hrs with OSKM, replicate 2


title: Rrm3 npl3∆ exp1

description:
Asynchronous cultures growing in rich YPD medium
test CEL file: Rrm3-npl3-1_IP.CEL
control CEL file: Rrm3-npl3-1_SUP.CEL
processed data file: Rrm3-npl3_pvalue.bed
processed data file: Rrm3-npl3_signal.bar
processed data file: Rrm3-npl3_pvalue.bar


title: Rrm3-Flag WT exp2

description:
Asynchronous cultures growing in rich YPD medium
test CEL file: Rrm3-WT-2_IP.CEL
control CEL file: Rrm3-WT-2_SUP.CEL
processed data file: Rrm3-WT_pvalue.bed
processed data file: Rrm3-WT_signal.bar
processed data file: Rrm3-WT_pvalue.bar

source_name: Rrm3-Flag ChIP DNA from WRBb-9B, asynchronous culture

value: MATa ade2-1 can1-100 trp1-1 his3-11,15 leu2-3,112 ura3::URA3/GPD-Tk(7x) Rrm3::FLAG bar1Δ

source_name: Input DNA from WRBb-9B


title: Rrm3-Flag WT exp1

description:
Asynchronous cultures growing in rich YPD medium
test CEL file: Rrm3-WT-1_IP.CEL
control CEL file: Rrm3-WT-1_SUP.CEL
processed data file: Rrm3-WT_pvalue.bed
processed data file: Rrm3-WT_signal.bar
processed data file: Rrm3-WT_pvalue.bar


title: WT, biological rep. 3

description:
Microarray_WT-3
Gene expression data from mid-log yeast cells in YPD medium

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Yeast Genome 2.0 Array. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 according to GeneChip® Expression Analysis Technical Manual, 2004, Affymetrix.

scan_protocol: Microarrays were scanned using GeneChip® Scanner 3000 7G

data_processing: The data were normalized by RMA (Robust Microarray Average) to allow direct comparison between expression values in different experiments. Statistical analysis was performed by LIMMA (Linear Models for Microarray Analysis) using the program affylmGUI. Genes showing at least 1.5-fold expression change compared to wild-type strain with a p-value FDR < 0.01, were considered as altered. Expression values were obtained with the anti-log of RMA values

source_name: Total RNA from W303 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA One-Cycle Target Labeling Assays (GeneChip® Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: Each strain was grown to mid-log phase in liquid YPAD medium

extract_protocol: Total RNA was isolated with the Rneasy Midi kit (QIAGEN)

value: W303-1A bar1∆

value: MATa ade2-1 can1-100 trp1-1 his3-11,15 leu2-3,112 ura3-1 bar1ΔHphMX


title: npl3∆, biological rep. 3

description:
Microarray_npl3-3
Gene expression data from mid-log yeast cells in YPD medium

source_name: Total RNA from W303 npl3∆ cells

value: MATa ade2-1 can1-100 trp1-1 his3-11,15 leu2-3,112 ura3-1 bar1ΔHphMX npl3::KanMX


title: npl3∆, biological rep. 2

description:
Microarray_npl3-2
Gene expression data from mid-log yeast cells in YPD medium


title: npl3∆, biological rep. 1

description:
Microarray_npl3-1
Gene expression data from mid-log yeast cells in YPD medium


title: Npl3-Myc ChIP

description:
Asynchronous cultures growing in rich YPD medium
test CEL file: Npl3_IP.CEL
control CEL file: Npl3_SUP.CEL
processed data file: Npl3_pvalue.bed
processed data file: Npl3_signal.bar
processed data file: Npl3_pvalue.bar

source_name: Npl3-Myc ChIP DNA from YAM535, asynchronous culture

value: MATα NPL3-myc:URA3 ade2 ade8 ura3 leu2 his3 lys1

source_name: Input DNA from YAM535


title: WT, biological rep. 2

description:
Microarray_WT-2
Gene expression data from mid-log yeast cells in YPD medium


title: 18hrs pulse B cells, time 0, technical replicate 2

description: B cells pulsed for 18hrs with C/EBPa, replicate 2

value: primary B cells


title: Day 28 High dose TiO2 Treated 5

status: Public on Nov 01 2013

city: Ottawa

first: Mainul

last: Husain

address: 50 Colombine Driveway

country: Canada

institute: Health Canada

description: Biological replicate 5 of high dose sample, harvested 28 day post-instillation

hyb_protocol: Each experimental cRNA sample was mixed with an equimolar amount of reference cRNA and was hybridized to Agilent mouse 4×44 oligonucleotide microarrays (Agilent Technologies Inc., Mississauga, ON, Canada) for 17 h in a hybridization chamber at 60C with a rotation speed of 10 rpm.

scan_protocol: Arrays were washed according to manufacturer’s protocols (Agilent Technologies Inc., Mississauga, ON, Canada) and scanned on an Agilent G2505B scanner.

data_processing: Data from the scanned images were extracted using Agilent Feature Extraction software version 9.5.3.1. Data were normalized using LOWESS method and the normalized data represent the log2 of the ratios (sample(Cy5)/reference(Cy3)) of the median signal intensities.

source_name: Agilent Universal Mouse Reference RNA (UMRR)

label_protocol: Total RNA (250 ng) samples from individual mice (n = 6 per experimental and control group) and from universal reference total RNA (Agilent Technologies, Inc., Mississauga, ON, Canada) were used to synthesize double-stranded cDNA and cyanine labelled cRNA using Quick Amp Labeling Kit (Agilent Technologies Inc., Mississauga, ON, Canada) according to the manufacturer’s instruction. Control and nano-TiO2 treated cRNAs were labelled with Cyanine 5-CTP, and reference RNAs were labelled with Cyanine 3-CTP using a T7 RNA polymerase in vitro transcription kit (Agilent Technologies Inc., Mississauga, ON, Canada) and purified using RNeasy Mini kits (Qiagen, Mississauga, ON, Canada).

growth_protocol: Five-to-seven week old female C57BL/6 mice were purchased from Taconic (Ry, Denmark) and were acclimatized for 1-3 weeks prior to the commencement of the experiment. Mice were maintained in groups in polypropylene cages with sawdust bedding and enrichment, at 20-22°C room temperature and relative humidity of 40-60% with a 12 h light-to-dark cycle. All mice received food and water ad libitum throughout the experiment. All animal experiments were approved by the Danish “Animal Experiments Inspectorate” and performed according to their guidelines for ethical conduct and care of animals in research.

extract_protocol: Total RNA was isolated from random sections of the left lungs (n = 5-6 per group) using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and purified using RNeasy Plus Mini kits (Qiagen, Mississauga, ON, Canada) according to the manufacturer’s instruction. Total RNA concentration was measured using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific Inc., Wilmington, DE, USA) and RNA quality and integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Mississauga, ON, Canada) according to the manufacturer’s instruction. Samples with RNA integrity numbers of 7 and above were used to conduct microarray and qPCR experiments.

treatment_protocol: Naïve C57BL/6 mice were flushed twice with 0.6 ml of 0.9% NaCl to obtain approximately 1 ml of bronchoalveolar lavage fluid (BAL). BAL was centrifuged at 400 g for 10 min at 4°C to remove cells. The supernatant was used in the dispersant liquid. A total of 4.05 mg of nano-TiO2 was suspended in 1 ml of MilliQ water containing 0.9% NaCl and 10% v/v acellular BAL. Particle suspensions were prepared by sonicating the samples using a S-450D sonifier (Branson Ultrasonics Corp., Danbury, CT, USA) at 10% amplitude for a total of 16 minutes on ice with alternating 10 s pulses and pauses. Three different dilutions of nano-TiO2 were prepared and used in this experiment: 162 µg, 54 µg (1:3 dilution of the 162 µg) and 18 µg (1:3 dilution of the 54 µg). Control vehicle solutions were prepared without the nano-TiO2 (MilliQ water containing 90% of 0.9% NaCl and 10% acellular BAL fluid). The doses 18, 54 and 162 μg/mouse equal 1.5, 5 and 15 working days at the Danish occupational exposure level for TiO2 (6.0 mg Ti/m3 ~ 9.75 mg TiO2/m3), respectively. Each treatment group consisted of a minimum of 5 animals. Mice in the experimental groups received a single intratracheal instillation of 18 (low dose), 54 (medium dose) or 162 µg (high dose) of nano-TiO2 in a 40 µl suspension, followed by 150 μl air with a 250 µl SGE glass syringe (250F-LT-GT, MicroLab, Aarhus, Denmark). Intratracheal instillation was performed at 37 ºC on heating plates, under anesthesia using Hypnorm® (fentanyl citrate 0.315 mg/ml and fluanisone 10 mg/ml from Janssen Pharma) and Dormicum® (Midazolam 5 mg/mL from Roche). Control mice received 40 µl of dispersant vehicle only. Following instillation, mice were under observation until they recovered from anaesthesia. Mice were allowed to recover for 24 hours, 3 days and 28 days following instillation before sacrificing under anaesthesia (Hypnorm/Dormicum). Blood, BAL fluid and tissues were collected. Lung tissues from each experimental and control mice were cut into small pieces, and stored in cryogenic vials and snap frozen immediately in liquid nitrogen. All tissues were stored at -80C until analysis.

tag: reference

value: 11 mouse cell lines

source_name: Lung

value: Lung

tag: replicate

value: Biological replicate 5

value: high dose sample

tag: time

value: harvested 28 day post-instillation


title: Day 28 High dose TiO2 Treated 2

description: Biological replicate 2 of high dose sample, harvested 28 day post-instillation

value: Agilent Universal Mouse Reference RNA (UMRR)

value: Biological replicate 2


title: Day 28 High dose TiO2 Treated 4

description: Biological replicate 4 of high dose sample, harvested 28 day post-instillation

value: Biological replicate 4


title: aiPS cells #22, technical replicate 1

description: iPS cells derived from B cells infected with C/EBPa, replicate 1

value: iPS cells


title: WT, biological rep. 1

description:
Microarray_WT-1
Gene expression data from mid-log yeast cells in YPD medium


title: Day 28 Low dose TiO2 Treated 3

description: Biological replicate 3 of low dose sample, harvested 28 day post-instillation

value: Biological replicate 3

value: low dose sample


title: Day 28 Medium dose TiO2 Treated 6

description: Biological replicate 6 of medium dose sample, harvested 28 day post-instillation

value: Biological replicate 6

value: medium dose sample


title: Day 28 Low dose TiO2 Treated 5

description: Biological replicate 5 of low dose sample, harvested 28 day post-instillation


title: Day 28 Control 2

description: Biological replicate 2 of control sample, harvested 28 day post-instillation

value: control sample


title: Day 28 High dose TiO2 Treated 3

description: Biological replicate 3 of high dose sample, harvested 28 day post-instillation


title: Day 28 Medium dose TiO2 Treated 4

description: Biological replicate 4 of medium dose sample, harvested 28 day post-instillation


title: Day 28 High dose TiO2 Treated 1

description: Biological replicate 1 of high dose sample, harvested 28 day post-instillation

value: Biological replicate 1


title: Day 28 Medium dose TiO2 Treated 1

description: Biological replicate 1 of medium dose sample, harvested 28 day post-instillation


title: Day 28 Low dose TiO2 Treated 1

description: Biological replicate 1 of low dose sample, harvested 28 day post-instillation


title: Day 28 Control 3

description: Biological replicate 3 of control sample, harvested 28 day post-instillation


title: Day 28 Control 5

description: Biological replicate 5 of control sample, harvested 28 day post-instillation


title: Day 28 Medium dose TiO2 Treated 3

description: Biological replicate 3 of medium dose sample, harvested 28 day post-instillation


title: Day 28 Low dose TiO2 Treated 4

description: Biological replicate 4 of low dose sample, harvested 28 day post-instillation


title: Day 28 Medium dose TiO2 Treated 2

description: Biological replicate 2 of medium dose sample, harvested 28 day post-instillation


title: Day 3 High dose TiO2 Treated 2

description: Biological replicate 2 of high dose sample, harvested 3 day post-instillation

value: harvested 3 day post-instillation


title: Day 28 Medium dose TiO2 Treated 5

description: Biological replicate 5 of medium dose sample, harvested 28 day post-instillation


title: Day 3 High dose TiO2 Treated 4

description: Biological replicate 4 of high dose sample, harvested 3 day post-instillation


title: Day 28 Low dose TiO2 Treated 2

description: Biological replicate 2 of low dose sample, harvested 28 day post-instillation


title: Day 28 Control 1

description: Biological replicate 1 of control sample, harvested 28 day post-instillation


title: Day 28 Control 4

description: Biological replicate 4 of control sample, harvested 28 day post-instillation


title: Day 3 High dose TiO2 Treated 1

description: Biological replicate 1 of high dose sample, harvested 3 day post-instillation


title: Day 3 High dose TiO2 Treated 5

description: Biological replicate 5 of high dose sample, harvested 3 day post-instillation


title: Day 3 High dose TiO2 Treated 3

description: Biological replicate 3 of high dose sample, harvested 3 day post-instillation


title: Day 3 High dose TiO2 Treated 6

description: Biological replicate 6 of high dose sample, harvested 3 day post-instillation


title: Day 3 Control 2

description: Biological replicate 2 of control sample, harvested 3 day post-instillation


title: Day 3 Control 4

description: Biological replicate 4 of control sample, harvested 3 day post-instillation


title: Day 3 Low dose TiO2 Treated 1

description: Biological replicate 1 of low dose sample, harvested 3 day post-instillation


title: Day 3 Low dose TiO2 Treated 5

description: Biological replicate 5 of low dose sample, harvested 3 day post-instillation


title: Day 3 Medium dose TiO2 Treated 2

description: Biological replicate 2 of medium dose sample, harvested 3 day post-instillation


title: Day 1 High dose TiO2 Treated 6

description: Biological replicate 6 of high dose sample, harvested 1 day post-instillation

value: harvested 1 day post-instillation


title: Day 3 Control 3

description: Biological replicate 3 of control sample, harvested 3 day post-instillation

value: 11 mouse cell lines


title: Day 3 Medium dose TiO2 Treated 4

description: Biological replicate 4 of medium dose sample, harvested 3 day post-instillation

value: Lung


title: Day 3 Medium dose TiO2 Treated 3

description: Biological replicate 3 of medium dose sample, harvested 3 day post-instillation


title: Day 3 Medium dose TiO2 Treated 5

description: Biological replicate 5 of medium dose sample, harvested 3 day post-instillation

value: Biological replicate 5


title: Day 1 Medium dose TiO2 Treated 3

description: Biological replicate 3 of medium dose sample, harvested 1 day post-instillation


title: Day 1 Medium dose TiO2 Treated 4

description: Biological replicate 4 of medium dose sample, harvested 1 day post-instillation


title: Day 1 High dose TiO2 Treated 3

description: Biological replicate 3 of high dose sample, harvested 1 day post-instillation

value: high dose sample


title: Day 3 Medium dose TiO2 Treated 6

description: Biological replicate 6 of medium dose sample, harvested 3 day post-instillation


title: Day 3 Control 5

description: Biological replicate 5 of control sample, harvested 3 day post-instillation


title: Day 1 High dose TiO2 Treated 4

description: Biological replicate 4 of high dose sample, harvested 1 day post-instillation


title: Day 1 Medium dose TiO2 Treated 5

description: Biological replicate 5 of medium dose sample, harvested 1 day post-instillation


title: Day 3 Low dose TiO2 Treated 2

description: Biological replicate 2 of low dose sample, harvested 3 day post-instillation


title: Day 3 Medium dose TiO2 Treated 1

description: Biological replicate 1 of medium dose sample, harvested 3 day post-instillation


title: Day 3 Control 1

description: Biological replicate 1 of control sample, harvested 3 day post-instillation


title: Day 1 High dose TiO2 Treated 5

description: Biological replicate 5 of high dose sample, harvested 1 day post-instillation


title: Day 1 High dose TiO2 Treated 2

description: Biological replicate 2 of high dose sample, harvested 1 day post-instillation


title: Day 1 Medium dose TiO2 Treated 6

description: Biological replicate 6 of medium dose sample, harvested 1 day post-instillation


title: Day 3 Low dose TiO2 Treated 4

description: Biological replicate 4 of low dose sample, harvested 3 day post-instillation


title: Day 3 Low dose TiO2 Treated 3

description: Biological replicate 3 of low dose sample, harvested 3 day post-instillation


title: Day 1 High dose TiO2 Treated 1

description: Biological replicate 1 of high dose sample, harvested 1 day post-instillation


title: Day 1 Medium dose TiO2 Treated 1

description: Biological replicate 1 of medium dose sample, harvested 1 day post-instillation


title: slt2 pH 2.5

status: Public on Oct 18 2013

city: Recife

first: Rodrigo

middle: Mendonça

last: Lucena

state: Pernambuco

address: Av. Jorn. Aníbal Fernandes

department: Genetics

country: Brazil

institute: Federal University of Pernambuco

hyb_protocol: RNA from lab strain BY4741 was labelled with Cy3 and mixed with Cy5-labelled RNA from hog1 and slt2 mutants. Target and reference cRNA samples were mixed and the hybridizations were performed on yeast gene expression 8x15K spots slides (cat. nr. G4813A-016322, Agilent, USA) at 65 ºC for 17 hours at 10 r.pm. in the Microarray Hybridization Oven (cat. nr. G2545A, Agilent, USA).

scan_protocol: The slides were placed into the High-Resolution Microarray Scanner (cat. nr. G2505-60502, Agilent, USA). The fluorescence data were extracted (.txt files) for each spot  by using Scan Control 8.5.1 software (Agilent, USA)

data_processing: Data were then analyzed using specific packages from the R statistical language [20] with the specific LIMMA and MArray  packages. Background correction was done with normexp method. Robust spline and quantile methods were used for normalization within and between arrays, respectively. A list of differentially expressed genes was generated by applying adjusted p-values for multiple tests [20]. Groups of genes with statistical significance (Adj.p<0.05) were utilized.

source_name: slt2 pH 2.5

label_protocol: Synthesis of cDNA and labelling was performed by Two-Color Low Input Quick Amp Labeling Kit (cat. nr. 5190-2306, Agilent, USA), with Two-Color RNA spike-in kit for internal control (cat. nr. 5188-5279, Agilent, USA). For yeast samples, 100 ng of purified RNA was used for labelling.

growth_protocol: Cell from BY4741 strain (EUROSCARF collection) and their derivate mutants hog1∆ and slt2∆ were growth overnight and were transferred to fresh neutral YPD medium (20 g/l glucose, 20 g/l yeast extract and 10 g/l peptone) at 30ºC and 150 rpm in a rotatory shaker  at an initial cell density of OD600 0.1 and cultivated to OD600 0.5.

extract_protocol: total RNA in the lysates was purified by using RNAspin Mini RNA Isolation Kit (cat. nr. 25-0500-71, GE HealthCare, USA) following manufacturer´s instructions and suspended in 25 μl nuclease-free water.

treatment_protocol: The cultures were centrifuged and each one was re-suspended with YPD medium pH 2.5 adjusted with sulfuric acid. After incubation for 1 h at 30°C with orbital agitation (150 rpm), the cells were recovered by centrifugation and immediately used to RNA extraction

value: Lab strain BY4741 (EUROSCARF collection)

value: slt2∆ mutant

value: stress YPD pH 2.5 sulfuric acid

source_name: Lab strain BY4741

value: wild type (reference)


title: Day 1 Medium dose TiO2 Treated 2

description: Biological replicate 2 of medium dose sample, harvested 1 day post-instillation

value: Agilent Universal Mouse Reference RNA (UMRR)

value: Biological replicate 2


title: Day 1 Low dose TiO2 Treated 5

description: Biological replicate 5 of low dose sample, harvested 1 day post-instillation

value: low dose sample


title: Day 1 Low dose TiO2 Treated 4

description: Biological replicate 4 of low dose sample, harvested 1 day post-instillation

value: Biological replicate 4


title: Day 1 Low dose TiO2 Treated 3

description: Biological replicate 3 of low dose sample, harvested 1 day post-instillation

value: Biological replicate 3


title: Day 1 Control 5

description: Biological replicate 5 of control sample, harvested 1 day post-instillation

value: control sample


title: Day 1 Control 2

description: Biological replicate 2 of control sample, harvested 1 day post-instillation


title: hog1 pH 2.5

source_name: hog1 pH 2.5

value: hog1∆ mutant


title: Day 1 Low dose TiO2 Treated 1

description: Biological replicate 1 of low dose sample, harvested 1 day post-instillation

value: Biological replicate 1


title: Day 1 Control 3

description: Biological replicate 3 of control sample, harvested 1 day post-instillation

value: harvested 1 day post-instillation


title: Oct3/4KO Day3 biological rep1

status: Public on Oct 17 2013

city: Wako

first: Itoshi

last: NIKAIDO

state: Saitama

address: 2-1 Hirosawa

department: Center for Biosystems Dynamics Research

country: Japan

institute: RIKEN

description: On MEF feeders, with FGF4/heparin/Activin A

hyb_protocol: Samples were hybridized, stained, and washed according to the Expression Analysis Technical Manual (Affymetrix).

data_processing:
The expression values were summarized and normalized by the robust multiarray analysis and quantile normalization method using by Expression Console(tm) software (Affymetrix).
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.r2.dt1.mod.mm9.mps

source_name: ZHBTc4 ES cells, +Tet, Day 3

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: ES cells were maintained in GMEM supplemented with 10% FBS and 1,000 U/ml LIF on gelatin-coated dishes.

extract_protocol: Total RNA was isolated using QuickGene RNA cultured cell HC kit S (Fuji Film).

treatment_protocol: TS cells were induced in GMEM/10% FBS supplemented with 1 ug/ml Tet, 50 ng/ml human FGF4, 2 ug/ml heparin, 10 ng/ml human Activin A and 2 mM L-glutamine on MEF feeders.

tag: cell line

value: Tet

value: 3 days


title: Oct3/4KO Day3 biological rep3


title: Oct3/4KO Day2 biological rep2

source_name: ZHBTc4 ES cells, +Tet, Day 2

value: 2 days


title: Oct3/4KO Day4 biological rep1

source_name: ZHBTc4 ES cells, +Tet, Day 4

value: 4 days


title: Oct3/4KO Day4 biological rep3


title: Oct3/4KO Day0 biological rep2

description: On MEF feeders

source_name: ZHBTc4 ES cells, untreated

value: control

value: 0 day


title: Oct3/4KO Day0 biological rep3

description: On MEF feeders


title: Oct3/4KO Day0 biological rep1

description: On MEF feeders


title: Oct3/4KO Day4 biological rep2


title: Oct3/4KO Day2 biological rep3


title: Oct3/4KO Day1 biological rep3

source_name: ZHBTc4 ES cells, +Tet, Day 1

value: 1 day


title: Oct3/4KO Day1 biological rep1


title: HS578T, XBP1_ChIPSeq, treated by hypoxia and glucose deprivation, biological replicate 1

status: Public on Sep 26 2013

type: SRA

city: Boston

first: Xiaole

middle: Shirley

last: Liu

address: 450 Brookline Avenue, CLS 11007

department: Department of Biostatistics and Computational Biology

institute: Dana-Farber Cancer Institute, Harvard School of Public Health

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 0.12.7 with the following parameters: bowtie -S -m 1 *.fastq  *.sam.
Sam format files were converted to bed format; mapped reads of treat and input files were randomly sampled to the same depth.
Peaks were called using MACS with p-value cutoff of 1e-7.
Genome_build: hg19
Supplementary_files_format_and_content: Wig files were generated using MACS; scores represent tag pileup over each position.Bed files of peak positions were also generated by MACS.

source_name: breast cancer cells

growth_protocol: All breast cancer cells were cultured according to Neve et al. (Cancer Cell 2006). Following retroviral or lentiviral infection, cells were maintained in the presence of puromycin (2 ug/ml) (Sigma).

extract_protocol:
ChIP was performed as previously described by Chen et al. (Cell 2008).
The ChIP-seq library was prepared using ChIP-Seq DNA Sample Prep Kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: For all hypoxia experiments, cells were maintained in an anaerobic chamber (Coy laboratory) with 0.1% O2. For glucose deprivation experiments, cells were maintained in DMEM without glucose medium (Gibco) with 10% FBS (Gibco) and 50 units/ml of penicillin/streptomycin.

tag: cell type

value: triple negative breast cancer cells

tag: chip antibody

value: XBP1 (Biolegend, 619502)


title: MDA-MB-231, XBP1_ChIPSeq, untreated, biological replicate 1

description: untreated


title: MDA-MB-231, XBP1_ChIPSeq, treated by hypoxia and glucose deprivation, biological replicate 1


title: Oct3/4KO Day3 biological rep2

tag: strain