title: Subject 23

description:
raw_data.csv - Sample 23
Serum samples were run in triplicate against rubella nine rubella virus proteins/polypeptides (i.e., E1, E2, and C rubella virus proteins, three spots of overlapping polypeptides/fragments for P150 [i.e., P150s1, P150s2, and P150s3], and three spots for P90 [i.e., P90s1, P90s2, and the whole P90] on the proteome microarray chip (Antigen Discovery, Inc., Irvine, CA). No DNA(expressed protein) spots were used for negative control for each serum sample.


title: Subject 22

status: Public on Sep 23 2017

type: protein

city: Rochester

first: Gregory

middle: A.

last: Poland

state: MN

address: 200 1st St SW

country: USA

institute: Mayo Clinic

description:
raw_data.csv - Sample 22
Serum samples were run in triplicate against rubella nine rubella virus proteins/polypeptides (i.e., E1, E2, and C rubella virus proteins, three spots of overlapping polypeptides/fragments for P150 [i.e., P150s1, P150s2, and P150s3], and three spots for P90 [i.e., P90s1, P90s2, and the whole P90] on the proteome microarray chip (Antigen Discovery, Inc., Irvine, CA). No DNA(expressed protein) spots were used for negative control for each serum sample.

hyb_protocol: Bound antibodies were detected by incubation with streptavidin-conjugated SureLight® P3 (Columbia Biosciences; Columbia, MD).

scan_protocol: The array slides were scanned using a GenePix® 4300 Microarray Scanner (Molecular Devices; San Diego, CA) and quantified using GenePix® Pro 7 Microarray Acquisition and Analysis Software (Molecular Devices; Sunnyvale, CA) with spot-specific background correction.

data_processing: All samples were run in triplicate against nine proteins/polypeptides and the median values were calculated and normalized for background effects.

label: Biotin

molecule: protein

organism: Homo sapiens

source_name: Blood - Serum

label_protocol: After the overnight incubation, microarray slides were incubated in Fc������-specific Biotin-SP-Conjugated Affini-Pure Goat Ant-Human IgG secondary Ab (Jackson ImmunoResearch, Inc.; West Grove, PA).

extract_protocol:
Serum samples were diluted 1:100 in Protein Array Blocking Buffer (Whatman, Inc.; Sanford, ME) supplemented with 10% DH5-α Escherichia coli lysate (Antigen Discovery, Inc.), incubated for 30 minutes, and probed on arrays overnight at 4°C. Chips were developed by PCR amplification of cDNA for all rubella virus proteins, as previously described (Davies DH et al., 2005; Luevano M et al., 2010; Kalantari-Dehaghi M et al., 2012). The amplicons were inserted into pXi T7-based exvectors, expressed in coupled in-vitro transcription-translation (IVTT) reactions, and printed onto the microarray slides.
cDNAs were created by RT-PCR from Rubella virus/RV (strain RA27/3, Taxonomy ID) infected cells (total RNAs were extracted using the Qiagen RNeasy Plus mini kit and PCR was performed using the Novagen’s KOD Hot Start DN Polymerase kit/Cat # 71086). The following RV-specific primers were used: for envelope glycoprotein 1/E1 RubE1-F gaggaggctttcacctacctctgca and RubE1-R gcgcggcgctatagcgc; for envelope glycoprotein 2/E2 RubE2-F gggctccagccccgcgct and RubE2-R gccataggcgggggggttgt ; for capsid protein/CP RubC-F atggcttctactacccccatcaccatgga and RubC-R ggcgcgcgcggtgcc ; for nonstructural protein P150 Rub150-F atggagagactcctagatgaggttc and Rub150-R gacagggggaccgcg ; for nonstructural protein P90 RubP90-F cggggcggtggcacc and RubP90-R tagtcagcgtcgtggagattggc. PCR amplicons were verified by sequencing. The amplicons were inserted into pXi T7-based exvectors, and the products were expressed in coupled in-vitro transcription-translation (IVTT) reactions as described previously (Doolan DL et al., Proteomics. 2008 Nov;8(22):4680-94) and printed onto microarray slides as protein/polypeptide spots representing the individual rubella virus proteins/polypeptides. Larger genes (P150 and P90) were amplified in segments overlapping by 150 nucleotides and expressed on the chip as three spots of overlapping polypeptides/fragments for P150 (i.e., P150s1, P150s2, and P150s3), and three spots for P90 (i.e., P90s1, P90s2, and the whole P90). Glycoproteins E1 and E2, and the capsid C protein were expressed on the chip as single spots.

tag: high/low antibody responder to rubella vaccination

value: Low

tag: Sex

value: Male

tag: age

tag: time from last vaccination to  enrollment (years)


title: Subject 21

description:
raw_data.csv - Sample 21
Serum samples were run in triplicate against rubella nine rubella virus proteins/polypeptides (i.e., E1, E2, and C rubella virus proteins, three spots of overlapping polypeptides/fragments for P150 [i.e., P150s1, P150s2, and P150s3], and three spots for P90 [i.e., P90s1, P90s2, and the whole P90] on the proteome microarray chip (Antigen Discovery, Inc., Irvine, CA). No DNA(expressed protein) spots were used for negative control for each serum sample.

value: High

value: Female


title: Subject 18

description:
raw_data.csv - Sample 18
Serum samples were run in triplicate against rubella nine rubella virus proteins/polypeptides (i.e., E1, E2, and C rubella virus proteins, three spots of overlapping polypeptides/fragments for P150 [i.e., P150s1, P150s2, and P150s3], and three spots for P90 [i.e., P90s1, P90s2, and the whole P90] on the proteome microarray chip (Antigen Discovery, Inc., Irvine, CA). No DNA(expressed protein) spots were used for negative control for each serum sample.


title: Subject 20

description:
raw_data.csv - Sample 20
Serum samples were run in triplicate against rubella nine rubella virus proteins/polypeptides (i.e., E1, E2, and C rubella virus proteins, three spots of overlapping polypeptides/fragments for P150 [i.e., P150s1, P150s2, and P150s3], and three spots for P90 [i.e., P90s1, P90s2, and the whole P90] on the proteome microarray chip (Antigen Discovery, Inc., Irvine, CA). No DNA(expressed protein) spots were used for negative control for each serum sample.


title: Subject 19

description:
raw_data.csv - Sample 19
Serum samples were run in triplicate against rubella nine rubella virus proteins/polypeptides (i.e., E1, E2, and C rubella virus proteins, three spots of overlapping polypeptides/fragments for P150 [i.e., P150s1, P150s2, and P150s3], and three spots for P90 [i.e., P90s1, P90s2, and the whole P90] on the proteome microarray chip (Antigen Discovery, Inc., Irvine, CA). No DNA(expressed protein) spots were used for negative control for each serum sample.


title: phdepi17

type: RNA

city: paris

first: veronique

last: PELLOUX

address: 50-52 bld Vincent Auriol

department: UMR 1166 eq 6

country: France

institute: INSERM

description:
SAMPLE 26
9703982025_F

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation and without subtract Background with Genome Studio (Illumina software)

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: mouse CIH+_epidydimal adipose tissue

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

extract_protocol: RNA was extracted followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: exposed to

value: chronic intermittent hypoxia (CIH) for 14 days

tag: tissue

value: epidydimal adipose tissue


title: phdepi7

description:
SAMPLE 22
9703982022_D

source_name: mouse control_epidydimal adipose tissue

value: normoxia (controls) for 14 days


title: phdepi22

description:
SAMPLE 31
9703982031_C


title: phdepi18

description:
SAMPLE 27
9703982025_G


title: Subject 16

description:
raw_data.csv - Sample 16
Serum samples were run in triplicate against rubella nine rubella virus proteins/polypeptides (i.e., E1, E2, and C rubella virus proteins, three spots of overlapping polypeptides/fragments for P150 [i.e., P150s1, P150s2, and P150s3], and three spots for P90 [i.e., P90s1, P90s2, and the whole P90] on the proteome microarray chip (Antigen Discovery, Inc., Irvine, CA). No DNA(expressed protein) spots were used for negative control for each serum sample.


title: Subject 15

description:
raw_data.csv - Sample 15
Serum samples were run in triplicate against rubella nine rubella virus proteins/polypeptides (i.e., E1, E2, and C rubella virus proteins, three spots of overlapping polypeptides/fragments for P150 [i.e., P150s1, P150s2, and P150s3], and three spots for P90 [i.e., P90s1, P90s2, and the whole P90] on the proteome microarray chip (Antigen Discovery, Inc., Irvine, CA). No DNA(expressed protein) spots were used for negative control for each serum sample.


title: phdepi21

description:
SAMPLE 30
9703982031_B


title: phdepi19

description:
SAMPLE 28
9703982025_H


title: phdepi8

description:
SAMPLE 23
9703982022_E


title: phdepi15

description:
SAMPLE 24
9703982025_D


title: phdepi16

description:
SAMPLE 25
9703982025_E


title: phdepi20

description:
SAMPLE 29
9703982031_A


title: phdepi5

description:
SAMPLE 20
9703982022_B


title: Subject 14

description:
raw_data.csv - Sample 14
Serum samples were run in triplicate against rubella nine rubella virus proteins/polypeptides (i.e., E1, E2, and C rubella virus proteins, three spots of overlapping polypeptides/fragments for P150 [i.e., P150s1, P150s2, and P150s3], and three spots for P90 [i.e., P90s1, P90s2, and the whole P90] on the proteome microarray chip (Antigen Discovery, Inc., Irvine, CA). No DNA(expressed protein) spots were used for negative control for each serum sample.


title: Subject 13

description:
raw_data.csv - Sample 13
Serum samples were run in triplicate against rubella nine rubella virus proteins/polypeptides (i.e., E1, E2, and C rubella virus proteins, three spots of overlapping polypeptides/fragments for P150 [i.e., P150s1, P150s2, and P150s3], and three spots for P90 [i.e., P90s1, P90s2, and the whole P90] on the proteome microarray chip (Antigen Discovery, Inc., Irvine, CA). No DNA(expressed protein) spots were used for negative control for each serum sample.


title: phdepi4

description:
SAMPLE 19
9703982022_A


title: Subject 17

description:
raw_data.csv - Sample 17
Serum samples were run in triplicate against rubella nine rubella virus proteins/polypeptides (i.e., E1, E2, and C rubella virus proteins, three spots of overlapping polypeptides/fragments for P150 [i.e., P150s1, P150s2, and P150s3], and three spots for P90 [i.e., P90s1, P90s2, and the whole P90] on the proteome microarray chip (Antigen Discovery, Inc., Irvine, CA). No DNA(expressed protein) spots were used for negative control for each serum sample.


title: phdepi6

description:
SAMPLE 21
9703982022_C


title: phdepi2

description:
SAMPLE 17
9703982021_G


title: phdfoie22

description:
SAMPLE 15
9703982021_E

source_name: mouse CIH+_liver

value: liver


title: phdepi1

description:
SAMPLE 16
9703982021_F


title: phdfoie21

description:
SAMPLE 14
9703982021_D


title: phdfoie20

description:
SAMPLE 13
9703982021_C


title: phdepi3

description:
SAMPLE 18
9703982021_H


title: Subject 11

description:
raw_data.csv - Sample 11
Serum samples were run in triplicate against rubella nine rubella virus proteins/polypeptides (i.e., E1, E2, and C rubella virus proteins, three spots of overlapping polypeptides/fragments for P150 [i.e., P150s1, P150s2, and P150s3], and three spots for P90 [i.e., P90s1, P90s2, and the whole P90] on the proteome microarray chip (Antigen Discovery, Inc., Irvine, CA). No DNA(expressed protein) spots were used for negative control for each serum sample.


title: Subject 10

description:
raw_data.csv - Sample 10
Serum samples were run in triplicate against rubella nine rubella virus proteins/polypeptides (i.e., E1, E2, and C rubella virus proteins, three spots of overlapping polypeptides/fragments for P150 [i.e., P150s1, P150s2, and P150s3], and three spots for P90 [i.e., P90s1, P90s2, and the whole P90] on the proteome microarray chip (Antigen Discovery, Inc., Irvine, CA). No DNA(expressed protein) spots were used for negative control for each serum sample.


title: phdfoie19

description:
SAMPLE 12
9703982021_B


title: HCC827-RB2-rep1

city: Monterotondo (Roma)

first: Giovina

last: Ruberti

address: Via E. Ramarini, 32

country: Italy

institute: Institute of Cell Biology and Neurobiology, National Research Council

hyb_protocol: Microarray hybridizations were carried out in Agilent’s SureHyb Hybridization Chambers containing 600 ng of Cyanine 3-labelled cRNA per hybridization. The hybridization reactions were performed at 65°C for 17 hours using Agilent’s Gene Expression Hybridization Kit (5188-5242). After hybridization, slides were washed with Agilent Gene Expression Wash Buffer 1, Gene Expression Wash Buffer 2 and Acetonitrile for one minute at room temperature.

scan_protocol: Chips were scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: The raw signal intensity data were background corrected (normexp method) and quantile normalised using limma package of Bioconductor in R program.

source_name: HCC827 derived cell line

label_protocol: 500ng of Poly A+RNA were labelled, using Cyanine 3-CTP  (Perkin Elmer)  with the Agilent Low Imput Linear Amplification Kit and purified with Qiagen’s RNeasy mini spin columns

growth_protocol: The NSCLC cell lines were grown in RPMI 1640 (BioWhittaker, Lonza, USA) supplemented with 10 mM Hepes pH 6.98-7.30, 1 mM L-glutamine, 100 U/ml penicillin/streptomycin (BioWittaker, Lonza) and heat inactivated 10% fetal bovine serum (FBS) (Sigma-Aldrich). All cells were cultured at 37°C in a 5% CO2 humidified incubator.

extract_protocol: Total RNA was isolated using a total RNA purification kit (Norgen Biotek, Thorold, ON, Canada). RNA quantity was determined by absorbance at 260 nm using a NanoDrop ND-1000 UV-VIS spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, USA). The quality and integrity of each sample were confirmed using a BioAnalyzer. RNA sample replicates for each cell line were labeled and assayed by using SurePrint G3 Human Gene Expression 8x60K v2 (G4851B - 039494) one-color microarray kit of Agilent Technologies. Microarray hybridization was performed according to the Agilent standard protocols.

treatment_protocol: The Erlotinib-resistant NSCLC cell lines were derived by by exposing HCC827 and HCC4006 cell lines (parental) to erlotinib for 5–6 months as previously described (D. Presutti et al,  PLoS One. 2015 Nov 18;10(11):e0143333. doi: 10.1371/journal.pone.0143333. eCollection 2015.)

tag: cell type

value: NSCLC

tag: erlotinib response

value: Resistant


title: Subject 12

description:
raw_data.csv - Sample 12
Serum samples were run in triplicate against rubella nine rubella virus proteins/polypeptides (i.e., E1, E2, and C rubella virus proteins, three spots of overlapping polypeptides/fragments for P150 [i.e., P150s1, P150s2, and P150s3], and three spots for P90 [i.e., P90s1, P90s2, and the whole P90] on the proteome microarray chip (Antigen Discovery, Inc., Irvine, CA). No DNA(expressed protein) spots were used for negative control for each serum sample.


title: Subject 9

description:
raw_data.csv - Sample 9
Serum samples were run in triplicate against rubella nine rubella virus proteins/polypeptides (i.e., E1, E2, and C rubella virus proteins, three spots of overlapping polypeptides/fragments for P150 [i.e., P150s1, P150s2, and P150s3], and three spots for P90 [i.e., P90s1, P90s2, and the whole P90] on the proteome microarray chip (Antigen Discovery, Inc., Irvine, CA). No DNA(expressed protein) spots were used for negative control for each serum sample.


title: Subject 7

description:
raw_data.csv - Sample 7
Serum samples were run in triplicate against rubella nine rubella virus proteins/polypeptides (i.e., E1, E2, and C rubella virus proteins, three spots of overlapping polypeptides/fragments for P150 [i.e., P150s1, P150s2, and P150s3], and three spots for P90 [i.e., P90s1, P90s2, and the whole P90] on the proteome microarray chip (Antigen Discovery, Inc., Irvine, CA). No DNA(expressed protein) spots were used for negative control for each serum sample.


title: Subject 5

description:
raw_data.csv - Sample 5
Serum samples were run in triplicate against rubella nine rubella virus proteins/polypeptides (i.e., E1, E2, and C rubella virus proteins, three spots of overlapping polypeptides/fragments for P150 [i.e., P150s1, P150s2, and P150s3], and three spots for P90 [i.e., P90s1, P90s2, and the whole P90] on the proteome microarray chip (Antigen Discovery, Inc., Irvine, CA). No DNA(expressed protein) spots were used for negative control for each serum sample.


title: Subject 8

description:
raw_data.csv - Sample 8
Serum samples were run in triplicate against rubella nine rubella virus proteins/polypeptides (i.e., E1, E2, and C rubella virus proteins, three spots of overlapping polypeptides/fragments for P150 [i.e., P150s1, P150s2, and P150s3], and three spots for P90 [i.e., P90s1, P90s2, and the whole P90] on the proteome microarray chip (Antigen Discovery, Inc., Irvine, CA). No DNA(expressed protein) spots were used for negative control for each serum sample.


title: Subject 4

description:
raw_data.csv - Sample 4
Serum samples were run in triplicate against rubella nine rubella virus proteins/polypeptides (i.e., E1, E2, and C rubella virus proteins, three spots of overlapping polypeptides/fragments for P150 [i.e., P150s1, P150s2, and P150s3], and three spots for P90 [i.e., P90s1, P90s2, and the whole P90] on the proteome microarray chip (Antigen Discovery, Inc., Irvine, CA). No DNA(expressed protein) spots were used for negative control for each serum sample.


title: Subject 3

description:
raw_data.csv - Sample 3
Serum samples were run in triplicate against rubella nine rubella virus proteins/polypeptides (i.e., E1, E2, and C rubella virus proteins, three spots of overlapping polypeptides/fragments for P150 [i.e., P150s1, P150s2, and P150s3], and three spots for P90 [i.e., P90s1, P90s2, and the whole P90] on the proteome microarray chip (Antigen Discovery, Inc., Irvine, CA). No DNA(expressed protein) spots were used for negative control for each serum sample.


title: Subject 2

description:
raw_data.csv - Sample 2
Serum samples were run in triplicate against rubella nine rubella virus proteins/polypeptides (i.e., E1, E2, and C rubella virus proteins, three spots of overlapping polypeptides/fragments for P150 [i.e., P150s1, P150s2, and P150s3], and three spots for P90 [i.e., P90s1, P90s2, and the whole P90] on the proteome microarray chip (Antigen Discovery, Inc., Irvine, CA). No DNA(expressed protein) spots were used for negative control for each serum sample.


title: phdfoie8

description:
SAMPLE 8
9703982004_H

source_name: mouse control_liver


title: phdfoie17

description:
SAMPLE 10
9703982014_H


title: phdfoie7

description:
SAMPLE 7
9703982004_G


title: Subject 6

description:
raw_data.csv - Sample 6
Serum samples were run in triplicate against rubella nine rubella virus proteins/polypeptides (i.e., E1, E2, and C rubella virus proteins, three spots of overlapping polypeptides/fragments for P150 [i.e., P150s1, P150s2, and P150s3], and three spots for P90 [i.e., P90s1, P90s2, and the whole P90] on the proteome microarray chip (Antigen Discovery, Inc., Irvine, CA). No DNA(expressed protein) spots were used for negative control for each serum sample.


title: phdfoie4

description:
SAMPLE 4
9703982004_D


title: phdfoie5

description:
SAMPLE 5
9703982004_E


title: phdfoie2

description:
SAMPLE 2
9703982004_B


title: phdfoie16

description:
SAMPLE 9
9703982014_G


title: phdfoie6

description:
SAMPLE 6
9703982004_F


title: phdfoie18

description:
SAMPLE 11
9703982021_A


title: sde2-ts 37C Rep1

status: Public on Sep 22 2017

city: Ithaca

first: Jeffrey

middle: A

last: Pleiss

state: NY

address: 451 Biotech

department: Molecular Biology and Genetics

institute: Cornell University

description: sde2-ts vs. WT at 37C

hyb_protocol: Labelled cDNA was hybridized according to Inada, M & Pleiss, JA. Methods in Enzymology, 2010 (PMID 20946806).

scan_protocol: Arrays were scanned on GenePix 4000B scanner and images were quantified GenePix Pro 6.1 software.

data_processing: Background subtraction and median normalization was applied according to Inada, M & Pleiss, JA. Methods in Enzymology, 2010 (PMID 20946806).

organism: Schizosaccharomyces pombe

source_name: sde2-ts at 37C for 15min

label_protocol: Total RNA was reverse transcribed and labelled according to Inada, M & Pleiss, JA. Methods in Enzymology, 2010 (PMID 20946806).

growth_protocol: Cells were inoculated at an OD~0.05 in 25mL YES media and after reaching mid-log growth (OD~0.5) were either collected by vacuum filtration, or shifted to a 37C water bath for 15 minutes and then collected by vacuum filtration.

extract_protocol: Total RNA was isolated by Acid-phenol extraction followed by ethanol precipitation and resuspension in 50uL TE buffer.

tag: genotype/variation

tag: temperature

source_name: WT at 37C for 15min

value: WT


title: sde2-ts 37C Rep2

description: WT vs. sde2-ts at 37C


title: sde2-ts 30C Rep2

description: WT vs. sde2-ts at 30C

source_name: WT at 30C

source_name: sde2-ts at 30C


title: sde2-ts 30C Rep1

description: sde2-ts vs. WT at 30C


title: Subject 1

description:
raw_data.csv - Sample 1
Serum samples were run in triplicate against rubella nine rubella virus proteins/polypeptides (i.e., E1, E2, and C rubella virus proteins, three spots of overlapping polypeptides/fragments for P150 [i.e., P150s1, P150s2, and P150s3], and three spots for P90 [i.e., P90s1, P90s2, and the whole P90] on the proteome microarray chip (Antigen Discovery, Inc., Irvine, CA). No DNA(expressed protein) spots were used for negative control for each serum sample.


title: phdfoie1

description:
SAMPLE 1
9703982004_A


title: phdfoie3

description:
SAMPLE 3
9703982004_C


title: Endolymphatic_sac-E16.5_Slc26a4DeltaDelta-rep3

city: Manhattan

first: Philine

last: Wangemann

state: KS

address: 1600 Dension Avenue

department: Anatomy and Physiology

institute: Kansas State University

description: Starting material: 6.0 ng total RNA with RIN= 9.2 (RIN=RNA Integrity Number provided by Agilent Bioanalyzer)

hyb_protocol: Following fragmentation and labeling, 6 µg of cDNA was hybridized (GeneChip Hybridization Oven 640, Affymetrix) to gene arrays (Mouse Genome 430 2.0 GeneChip, Affymetrix), washed and stained (GeneChip Fluidics Station 450, Affymetrix) according to manufacturer’s procedures.

scan_protocol: Gene chips were scanned and *.cel and pivot files were generated (K-State Integrated Genomics Facility).  Normalization quality controls, including scaling factors, average intensities, present calls, background intensities, noise, and raw Q values were all within acceptable limits.

label_protocol: Total RNA was reverse transcribed into cDNA, amplified, fragmented and labelled following manufacturers procedures (Ovation Pico WTA System V2 and Encore Biotin, Nugen).

growth_protocol: Developmental time points were generated by harvesting embryos from time-pregnant dams.  Time-pregnant dams were deeply anesthetized with 4% tri-bromo-ethanol (0.014 ml/g body weight, i.p.) and embryos were harvested by laparotomy.  Dams and embryos were sacrificed by decapitation.  All procedures involving animals were performed according to protocols approved by the Animal Care and Use Committees at Kansas State University.

extract_protocol: Microdissection of endolymphatic sacs was carried out in cooled (4 C) physiologic salt solution containing (in mM): 150 NaCl, 1.6 K2HPO4, 0.4 K2HPO4, 0.75 CaCl2, 1.0 MgCl2 and 5 glucose, pH 7.4.   Endolymphatic sacs were isolated, freed of connective tissue, and freed from endolymphatic ducts by manual micro-dissection under a high-power stereo microscope using custom-made forceps.  Clean dissection solutions were maintained during dissection to prevent contamination of endolymphatic sacs.  Total RNA was extracted from micro-dissected endolymphatic sacs following the manufacturer’s procedures (RNeasy Plus Micro, Qiagen).  Na-citrate (RNA storage solution, Applied Biosystems/Ambion) was added to 0.33 mM.  Quantity and quality of total RNA was evaluated by RT-PCR of 18S and by microfluidic electrophoresis (2100 Bioanalyzer, RNA 6000 Pico) according to manufacturer’s procedures.  The RNA integrity number (RIN), which judges RNA quality on a scale from 1 (most degraded) to 10 (most intact) was used to evaluate the quality of total RNA.  Total RNA from multiple extractions was combined and concentrated (Speed Vac).  RNA samples forwarded to target preparation consisted of 3.5 to 6.0 ng of total RNA, depending on the developmental time point.  Samples were prepared in a volume of 5 µl containing a final Na-citrate concentration of 0.2 to 2.1 mM and ranging in RIN number between 8.7 to 9.8.

value: Endolymphatic sac

tag: genotype

tag: developmental stage

value: Embryonic day 16.5


title: Endolymphatic_sac-E16.5_Slc26a4DeltaPlus-rep3

description: Starting material: 6.0 ng total RNA with RIN= 8.8 (RIN=RNA Integrity Number provided by Agilent Bioanalyzer)


title: Endolymphatic_sac-E13.5_Slc26a4DeltaPlus-rep2

description: Starting material: 4.1 ng total RNA with RIN= 9.2 (RIN=RNA Integrity Number provided by Agilent Bioanalyzer)

value: Embryonic day 13.5


title: Endolymphatic_sac-E13.5_Slc26a4DeltaDelta-rep3

description: Starting material: 4.0 ng total RNA with RIN= 9.7 (RIN=RNA Integrity Number provided by Agilent Bioanalyzer)


title: Endolymphatic_sac-E17.5_Slc26a4DeltaDelta-rep3

description: Starting material: 6.0 ng total RNA with RIN= 9.4 (RIN=RNA Integrity Number provided by Agilent Bioanalyzer)

value: Embryonic day 17.5


title: Endolymphatic_sac-E13.5_Slc26a4DeltaPlus-rep3

description: Starting material: 4.0 ng total RNA with RIN= 9.8 (RIN=RNA Integrity Number provided by Agilent Bioanalyzer)


title: Endolymphatic_sac-E17.5_Slc26a4DeltaPlus-rep3

description: Starting material: 6.0 ng total RNA with RIN= 9.6 (RIN=RNA Integrity Number provided by Agilent Bioanalyzer)


title: Endolymphatic_sac-E14.5_Slc26a4DeltaPlus-rep3

description: Starting material: 4.0 ng total RNA with RIN= 8.7 (RIN=RNA Integrity Number provided by Agilent Bioanalyzer)

value: Embryonic day 14.5


title: Endolymphatic_sac-E17.5_Slc26a4DeltaDelta-rep2

description: Starting material: 5.8 ng total RNA with RIN= 9.6 (RIN=RNA Integrity Number provided by Agilent Bioanalyzer)


title: Endolymphatic_sac-E16.5_Slc26a4DeltaPlus-rep2

description: Starting material: 5.6 ng total RNA with RIN= 9.2 (RIN=RNA Integrity Number provided by Agilent Bioanalyzer)


title: Endolymphatic_sac-E17.5_Slc26a4DeltaPlus-rep1

description: Starting material: 4.6 ng total RNA with RIN= 9.6 (RIN=RNA Integrity Number provided by Agilent Bioanalyzer)


title: Endolymphatic_sac-E16.5_Slc26a4DeltaDelta-rep2

description: Starting material: 5.6 ng total RNA with RIN= 9.1 (RIN=RNA Integrity Number provided by Agilent Bioanalyzer)


title: Endolymphatic_sac-E14.5_Slc26a4DeltaPlus-rep2


title: Endolymphatic_sac-E14.5_Slc26a4DeltaDelta-rep3

description: Starting material: 4.0 ng total RNA with RIN= 9.3 (RIN=RNA Integrity Number provided by Agilent Bioanalyzer)


title: Endolymphatic_sac-E13.5_Slc26a4DeltaDelta-rep2

description: Starting material: 4.0 ng total RNA with RIN= 9.0 (RIN=RNA Integrity Number provided by Agilent Bioanalyzer)


title: Endolymphatic_sac-E17.5_Slc26a4DeltaPlus-rep2

description: Starting material: 5.9 ng total RNA with RIN= 9.6 (RIN=RNA Integrity Number provided by Agilent Bioanalyzer)


title: Endolymphatic_sac-E17.5_Slc26a4DeltaDelta-rep1

description: Starting material: 4.6 ng total RNA with RIN= n/a (RIN=RNA Integrity Number provided by Agilent Bioanalyzer)


title: Endolymphatic_sac-E14.5_Slc26a4DeltaDelta-rep2

description: Starting material: 4.0 ng total RNA with RIN= 9.1 (RIN=RNA Integrity Number provided by Agilent Bioanalyzer)


title: Endolymphatic_sac-E14.5_Slc26a4DeltaDelta-rep1

description: Starting material: 3.4 ng total RNA with RIN= 9.6 (RIN=RNA Integrity Number provided by Agilent Bioanalyzer)


title: Endolymphatic_sac-E13.5_Slc26a4DeltaPlus-rep1

description: Starting material: 3.5 ng total RNA with RIN= 9.6 (RIN=RNA Integrity Number provided by Agilent Bioanalyzer)


title: Endolymphatic_sac-E15.5_Slc26a4DeltaPlus-rep1

description: Starting material: 5.1 ng total RNA with RIN= 9.4 (RIN=RNA Integrity Number provided by Agilent Bioanalyzer)


title: Cerevisiae_cdc20_340min_rep2_reanalyzed

city: Durham

first: Steven

middle: B

last: Haase

state: NC

department: Biology

institute: Duke University

description: Cell cycle gene expression data from CDK on yeast synchronized by elutration

hyb_protocol: DNA microarray hybridization was performed according to standard Affymetrix protocols by the Duke Micorarray Core Facility.

scan_protocol: Array scanning was carried by the Duke Micorarray Core Facility using standard Affymetrix protocols.

data_processing: The new samples in this study and re-analyzed samples from GSE8799, GSE32974, and GSE49650 were normalized together using the dChip implementation with default parameters from the affy package within R/Bioconductor. S. pombe probes are removed before analysis.

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae culture cdc20 340min

label_protocol: biotin

growth_protocol: YEPDextrose/1M sorbitol at 30c

extract_protocol: RNA was extracted using standard yeast methods.

treatment_protocol: synchronous G1 populations collected by elutration.

tag: strain


title: Cerevisiae_cdc20_360min_rep2_reanalyzed

source_name: S. cerevisiae culture cdc20 360min


title: Cerevisiae_cdc20_200min_rep2_reanalyzed

source_name: S. cerevisiae culture cdc20 200min


title: Cerevisiae_cdc20_320min_rep2_reanalyzed

source_name: S. cerevisiae culture cdc20 320min


title: Cerevisiae_cdc20_220min_rep2_reanalyzed

source_name: S. cerevisiae culture cdc20 220min


title: Cerevisiae_cdc20_300min_rep2_reanalyzed

source_name: S. cerevisiae culture cdc20 300min


title: Endolymphatic_sac-E14.5_Slc26a4DeltaPlus-rep1

description: Starting material: 3.5 ng total RNA with RIN= 8.8 (RIN=RNA Integrity Number provided by Agilent Bioanalyzer)


title: Cerevisiae_cdc20_240min_rep2_reanalyzed

source_name: S. cerevisiae culture cdc20 240min


title: Cerevisiae_cdc20_260min_rep2_reanalyzed

source_name: S. cerevisiae culture cdc20 260min


title: Cerevisiae_cdc20_160min_rep2_reanalyzed

source_name: S. cerevisiae culture cdc20 160min


title: Cerevisiae_cdc20_120min_rep2_reanalyzed

source_name: S. cerevisiae culture cdc20 120min


title: Cerevisiae_cdc20_180min_rep2_reanalyzed

source_name: S. cerevisiae culture cdc20 180min


title: Cerevisiae_cdc20_280min_rep2_reanalyzed

source_name: S. cerevisiae culture cdc20 280min


title: Endolymphatic_sac-E16.5_Slc26a4DeltaDelta-rep1

description: Starting material: 5.2 ng total RNA with RIN= 9.6 (RIN=RNA Integrity Number provided by Agilent Bioanalyzer)


title: Endolymphatic_sac-E13.5_Slc26a4DeltaDelta-rep1

description: Starting material: 3.5 ng total RNA with RIN= 9.7 (RIN=RNA Integrity Number provided by Agilent Bioanalyzer)


title: Cerevisiae_cdc20_60min_rep2_reanalyzed

source_name: S. cerevisiae culture cdc20 60min


title: Cerevisiae_cdc20_40min_rep2_reanalyzed

source_name: S. cerevisiae culture cdc20 40min


title: Cerevisiae_cdc20_20min_rep2_reanalyzed

source_name: S. cerevisiae culture cdc20 20min


title: Cerevisiae_cdc20_220min_rep1_reanalyzed


title: Cerevisiae_cdc20_240min_rep1_reanalyzed


title: Cerevisiae_cdc20_140min_rep2_reanalyzed

source_name: S. cerevisiae culture cdc20 140min


title: Cerevisiae_cdc20_160min_rep1_reanalyzed


title: Cerevisiae_cdc20_180min_rep1_reanalyzed


title: Cerevisiae_cdc20_200min_rep1_reanalyzed


title: Cerevisiae_cdc20_80min_rep2_reanalyzed

source_name: S. cerevisiae culture cdc20 80min


title: Cerevisiae_cdc20_100min_rep2_reanalyzed

source_name: S. cerevisiae culture cdc20 100min


title: Cerevisiae_cdc20_300min_rep1_reanalyzed


title: Cerevisiae_cdc20_140min_rep1_reanalyzed


title: Cerevisiae_cdc20_260min_rep1_reanalyzed


title: Cerevisiae_cdc20_280min_rep1_reanalyzed


title: Cerevisiae_cdc20_120min_rep1_reanalyzed


title: Cerevisiae_cdc20_60min_rep1_reanalyzed


title: Cerevisiae_cdc20_100min_rep1_reanalyzed


title: Cerevisiae_cdc20_40min_rep1_reanalyzed


title: wild-type, 37 degrees, t=225_reanalyzed

source_name: S. cerevisiae culture wildtype 225min

growth_protocol: Cells were grown at 25°C in YEPD to a final concentration of 3-5x107 cells/mL. Small daughter cells were collected by centrofugal elutriation. The synchronized population was resuspended in YEPD prewarmed to 37°C at time=0. Samples were taken at each time indicated.

extract_protocol: Total RNA was extracted using a standard hot acid phenol protocol and cleaned with a Qiagen RNeasy MinElute Cleanup Kit.

value: BF264-15DU; mat a; bar1


title: wild-type, 37 degrees, t=165_reanalyzed

source_name: S. cerevisiae culture wildtype 165min


title: wild-type, 37 degrees, t=210_reanalyzed

source_name: S. cerevisiae culture wildtype 210min


title: wild-type, 37 degrees, t=195_reanalyzed

source_name: S. cerevisiae culture wildtype 195min


title: wild-type, 37 degrees, t=135_reanalyzed

source_name: S. cerevisiae culture wildtype 135min


title: wild-type, 37 degrees, t=150_reanalyzed

source_name: S. cerevisiae culture wildtype 150min


title: wild-type, 37 degrees, t=180_reanalyzed

source_name: S. cerevisiae culture wildtype 180min


title: wild-type, 37 degrees, t=105_reanalyzed

source_name: S. cerevisiae culture wildtype 105min


title: wild-type, 37 degrees, t=120_reanalyzed

source_name: S. cerevisiae culture wildtype 120min


title: Cerevisiae_cdc20_80min_rep1_reanalyzed


title: wild-type, 37 degrees, t=90_reanalyzed

source_name: S. cerevisiae culture wildtype 90min


title: wild-type, 37 degrees, t=75_reanalyzed

source_name: S. cerevisiae culture wildtype 75min


title: wild-type, 37 degrees, t=15_reanalyzed

source_name: S. cerevisiae culture wildtype 15min


title: wild-type, 37 degrees, t=30_reanalyzed

source_name: S. cerevisiae culture wildtype 30min


title: wild-type, 37 degrees, t=60_reanalyzed

source_name: S. cerevisiae culture wildtype 60min


title: Cerevisiae_CyclinMutant_254min_rep2_reanalyzed

source_name: S. cerevisiae culture CyclinMutant 254min

growth_protocol: YEPDextrose /1M Sorbitol at 30c

value: BF264-15DU MATa; clb1::URA3; clb2::LEU2; clb3::TRP1; clb4::HIS2; clb5::ARG4; clb6::APE1; GAL1-CLB1:LEU2


title: wild-type, 37 degrees, t=45_reanalyzed

source_name: S. cerevisiae culture wildtype 45min


title: Cerevisiae_CyclinMutant_238min_rep2_reanalyzed

description: Cell cycle gene expression data from B-cyclin mutant yeast synchronized by elutration

source_name: S. cerevisiae culture CyclinMutant 238min


title: HeLaS3_EV_p

city: Chiba

first: Kazuyoshi

last: Kobayashi

address: 1-8-1 Inohana, Chuo-ku

department: Medical Mycology Research Center (MMRC)

country: Japan

institute: Chiba University

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v3; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were  normalized by the quantile algorithm with the Bioconductor.

source_name: HelaS3, empty vector, TNF+

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

growth_protocol: Cells were grown in Dulbeco's modified Eagle`s mudium containing 10% fetal calf serum.

extract_protocol: Total RNA was prepared using a mirVana miRNA isolation kit (Ambion) and DNA was removed by a TURBO DNA-free™ kit (Ambion) according to the manufacturer’s instructions. The quality of all RNA samples was measured using a 2200 TapeStation (Agilent). RNA samples with RNA integrity numbers higher than 9.0 were used for gene expression analysis.

treatment_protocol: Cells transduced with a dominant negative mutant of d4-family protein (CT1) or empty vector (Control) were grown in the absence or presence (10 ng/ml) of TNF-alpha for 1 hour at 37 ºC in a humidified incubator with 5% CO2.

tag: cell line


title: HeLaS3_DPF3_CT1_p

source_name: HelaS3, DPF3, CT1, TNF+


title: Cerevisiae_CyclinMutant_222min_rep2_reanalyzed

source_name: S. cerevisiae culture CyclinMutant 222min


title: Cerevisiae_CyclinMutant_206min_rep2_reanalyzed

source_name: S. cerevisiae culture CyclinMutant 206min


title: Cerevisiae_CyclinMutant_190min_rep2_reanalyzed

source_name: S. cerevisiae culture CyclinMutant 190min


title: Cerevisiae_CyclinMutant_174min_rep2_reanalyzed

source_name: S. cerevisiae culture CyclinMutant 174min


title: Cerevisiae_CyclinMutant_110min_rep2_reanalyzed

source_name: S. cerevisiae culture CyclinMutant 110min


title: HeLaS3_DPF3_CT1_m

source_name: HelaS3, DPF3, CT1, TNF-


title: Cerevisiae_CyclinMutant_78min_rep2_reanalyzed

source_name: S. cerevisiae culture CyclinMutant 78min


title: A549_EV_m

source_name: A549, empty vector, TNF-


title: Cerevisiae_CyclinMutant_142min_rep2_reanalyzed

source_name: S. cerevisiae culture CyclinMutant 142min


title: Cerevisiae_CyclinMutant_126min_rep2_reanalyzed

source_name: S. cerevisiae culture CyclinMutant 126min


title: Cerevisiae_CyclinMutant_62min_rep2_reanalyzed

source_name: S. cerevisiae culture CyclinMutant 62min


title: Cerevisiae_CyclinMutant_158min_rep2_reanalyzed

source_name: S. cerevisiae culture CyclinMutant 158min


title: A549_DPF3_CT1_m

source_name: A549, DPF3, CT1, TNF-


title: A549_DPF3_CT1_p

source_name: A549, DPF3, CT1, TNF+


title: Cerevisiae_CyclinMutant_46min_rep2_reanalyzed

source_name: S. cerevisiae culture CyclinMutant 46min


title: A549_EV_p

source_name: A549, empty vector, TNF+


title: HeLaS3_EV_m

source_name: HelaS3, empty vector, TNF-


title: Cerevisiae_CyclinMutant_30min_rep2_reanalyzed

source_name: S. cerevisiae culture CyclinMutant 30min


title: Cerevisiae_CyclinMutant_262min_rep1_reanalyzed

source_name: S. cerevisiae culture CyclinMutant 262min


title: Cerevisiae_CyclinMutant_198min_rep1_reanalyzed

source_name: S. cerevisiae culture CyclinMutant 198min


title: Cerevisiae_CyclinMutant_214min_rep1_reanalyzed

source_name: S. cerevisiae culture CyclinMutant 214min


title: Cerevisiae_CyclinMutant_230min_rep1_reanalyzed

source_name: S. cerevisiae culture CyclinMutant 230min


title: Cerevisiae_CyclinMutant_182min_rep1_reanalyzed

source_name: S. cerevisiae culture CyclinMutant 182min


title: Cerevisiae_CyclinMutant_150min_rep1_reanalyzed

source_name: S. cerevisiae culture CyclinMutant 150min


title: Cerevisiae_CyclinMutant_166min_rep1_reanalyzed

source_name: S. cerevisiae culture CyclinMutant 166min


title: Cerevisiae_CyclinMutant_102min_rep1_reanalyzed

source_name: S. cerevisiae culture CyclinMutant 102min


title: Cerevisiae_CyclinMutant_118min_rep1_reanalyzed

source_name: S. cerevisiae culture CyclinMutant 118min


title: Cerevisiae_CyclinMutant_134min_rep1_reanalyzed

source_name: S. cerevisiae culture CyclinMutant 134min


title: Cerevisiae_CyclinMutant_70min_rep1_reanalyzed

source_name: S. cerevisiae culture CyclinMutant 70min


title: Cerevisiae_CyclinMutant_38min_rep1_reanalyzed

source_name: S. cerevisiae culture CyclinMutant 38min


title: Cerevisiae_WildType_262min_rep2_reanalyzed

description: Cell cycle gene expression data from wild type yeast synchronized by elutration

source_name: S. cerevisiae culture WildType 262min

value: BF264-15DU MATa; bar1


title: Cerevisiae_CyclinMutant_54min_rep1_reanalyzed

source_name: S. cerevisiae culture CyclinMutant 54min


title: Cerevisiae_WildType_246min_rep2_reanalyzed

source_name: S. cerevisiae culture WildType 246min


title: Cerevisiae_WildType_198min_rep2_reanalyzed

source_name: S. cerevisiae culture WildType 198min


title: Cerevisiae_WildType_230min_rep2_reanalyzed

source_name: S. cerevisiae culture WildType 230min


title: Cerevisiae_WildType_214min_rep2_reanalyzed

source_name: S. cerevisiae culture WildType 214min


title: Cerevisiae_CyclinMutant_86min_rep1_reanalyzed

source_name: S. cerevisiae culture CyclinMutant 86min


title: Cerevisiae_WildType_86min_rep2_reanalyzed

source_name: S. cerevisiae culture WildType 86min


title: Cerevisiae_WildType_102min_rep2_reanalyzed

source_name: S. cerevisiae culture WildType 102min


title: Cerevisiae_WildType_182min_rep2_reanalyzed

source_name: S. cerevisiae culture WildType 182min


title: Cerevisiae_WildType_150min_rep2_reanalyzed

source_name: S. cerevisiae culture WildType 150min


title: Cerevisiae_WildType_166min_rep2_reanalyzed

source_name: S. cerevisiae culture WildType 166min


title: Cerevisiae_WildType_118min_rep2_reanalyzed

source_name: S. cerevisiae culture WildType 118min


title: Cerevisiae_WildType_38min_rep2_reanalyzed

source_name: S. cerevisiae culture WildType 38min


title: Cerevisiae_WildType_70min_rep2_reanalyzed

source_name: S. cerevisiae culture WildType 70min


title: Cerevisiae_WildType_54min_rep2_reanalyzed

source_name: S. cerevisiae culture WildType 54min


title: Cerevisiae_WildType_254min_rep1_reanalyzed

source_name: S. cerevisiae culture WildType 254min


title: Cerevisiae_CyclinMutant_94min_rep2_reanalyzed

source_name: S. cerevisiae culture CyclinMutant 94min


title: Cerevisiae_WildType_238min_rep1_reanalyzed

source_name: S. cerevisiae culture WildType 238min


title: Cerevisiae_WildType_222min_rep1_reanalyzed

source_name: S. cerevisiae culture WildType 222min


title: Cerevisiae_WildType_134min_rep2_reanalyzed

source_name: S. cerevisiae culture WildType 134min


title: Cerevisiae_CyclinMutant_246min_rep1_reanalyzed

source_name: S. cerevisiae culture CyclinMutant 246min


title: Cerevisiae_WildType_206min_rep1_reanalyzed

source_name: S. cerevisiae culture WildType 206min


title: Cerevisiae_WildType_158min_rep1_reanalyzed

source_name: S. cerevisiae culture WildType 158min


title: Cerevisiae_WildType_174min_rep1_reanalyzed

source_name: S. cerevisiae culture WildType 174min


title: Cerevisiae_WildType_190min_rep1_reanalyzed

source_name: S. cerevisiae culture WildType 190min


title: Cerevisiae_WildType_142min_rep1_reanalyzed

source_name: S. cerevisiae culture WildType 142min


title: Cerevisiae_WildType_30min_rep1_reanalyzed

source_name: S. cerevisiae culture WildType 30min


title: Cerevisiae_WildType_46min_rep1_reanalyzed

source_name: S. cerevisiae culture WildType 46min


title: Cerevisiae_WildType_78min_rep1_reanalyzed

source_name: S. cerevisiae culture WildType 78min


title: Cerevisiae_WildType_94min_rep1_reanalyzed

source_name: S. cerevisiae culture WildType 94min


title: Cerevisiae_WildType_62min_rep1_reanalyzed

source_name: S. cerevisiae culture WildType 62min


title: Cerevisiae_WildType_110min_rep1_reanalyzed

source_name: S. cerevisiae culture WildType 110min


title: cdc15-2_144min

description: Gene expression levels during cell-cycle arrest

source_name: S. cerevisiae culture, cdc15-2, 144 min

growth_protocol: Standard YEP medium with 2% dextrose

extract_protocol: Standard acid phenol method

treatment_protocol: Cells were collected on filters and then flash-frozen in liquid nitrogen.

value: BF264-15D MATa bar1 cdc15-2


title: cdc15-2_180min

source_name: S. cerevisiae culture, cdc15-2, 180 min


title: cdc15-2_132min

source_name: S. cerevisiae culture, cdc15-2, 132 min


title: cdc15-2_156min

source_name: S. cerevisiae culture, cdc15-2, 156 min


title: cdc15-2_96min

source_name: S. cerevisiae culture, cdc15-2, 96 min


title: cdc15-2_108min

source_name: S. cerevisiae culture, cdc15-2, 108 min


title: cdc15-2_168min

source_name: S. cerevisiae culture, cdc15-2, 168 min


title: cdc15-2_120min

source_name: S. cerevisiae culture, cdc15-2, 120 min


title: Cerevisiae_WildType_126min_rep1_reanalyzed

source_name: S. cerevisiae culture WildType 126min


title: cdc15-2_24min

source_name: S. cerevisiae culture, cdc15-2, 24 min


title: cdc15-2_36min

source_name: S. cerevisiae culture, cdc15-2, 36 min


title: cdc15-2_84min

source_name: S. cerevisiae culture, cdc15-2, 84 min


title: cdc15-2_48min

source_name: S. cerevisiae culture, cdc15-2, 48 min


title: cdc15-2_60min

source_name: S. cerevisiae culture, cdc15-2, 60 min


title: cdc15-2_12min

source_name: S. cerevisiae culture, cdc15-2, 12 min


title: cdc15-2_72min

source_name: S. cerevisiae culture, cdc15-2, 72 min


title: cdc15-2_0min

source_name: S. cerevisiae culture, cdc15-2, 0 min


title: cdc14-3_228min

source_name: S. cerevisiae culture, cdc14-3, 228 min

value: BF264-15D MATa bar1 cdc14-3


title: cdc14-3_240min

source_name: S. cerevisiae culture, cdc14-3, 240 min


title: cdc14-3_192min

source_name: S. cerevisiae culture, cdc14-3, 192 min


title: cdc14-3_204min

source_name: S. cerevisiae culture, cdc14-3, 204 min


title: cdc14-3_216min

source_name: S. cerevisiae culture, cdc14-3, 216 min


title: cdc14-3_180min

source_name: S. cerevisiae culture, cdc14-3, 180 min


title: cdc14-3_168min

source_name: S. cerevisiae culture, cdc14-3, 168 min


title: cdc14-3_156min

source_name: S. cerevisiae culture, cdc14-3, 156 min


title: cdc14-3_144min

source_name: S. cerevisiae culture, cdc14-3, 144 min


title: cdc14-3_132min

source_name: S. cerevisiae culture, cdc14-3, 132 min


title: B-ALL-88, 6h

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

institute: Eurac Researc

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-88, 6h.

hyb_protocol: Resulting targets, fragmented and labeled RNA, were hybridized to the Affymetrix GeneChip Human Genome U133 Plus 2.0 in an Affymetrix Fluidic Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix scanner 3000.

data_processing: Quality assessment and preprocessing of the microarrays was done in R version 3.0.2 by utilizing the Bioconductor packages affyPLM version 1.38.0, GCRMA version 2.34.0 and frma version 1.14.0. Normalization parameters for frozen RMA and parameters for GCRMA background adjustment were estimated on the reference normalization set and applied to all microarrays.

label_protocol: 1.5 ug of high-quality RNA per sample were processed to generate biotinylated hybridization targets using the appropriate standard protocols and reagents from Affymetrix.

extract_protocol: Total RNA was extracted using the standard TRIZOL protocol.

treatment_protocol: Individuals were treated according to the Berlin-Frankfurt-Muenster (BFM) protocol.

tag: disease status

value: childhood acute lymphoblastic leukemia (ALL)

value: lymphoblasts

tag: treatment

value: glucocorticoid (GC) mono-therapy

tag: treatment time point

value: M

tag: all subtype by clustering

tag: all subtype for analysis

tag: prednisone poor responder

value: FALSE

tag: hyb year

tag: normalization set


title: B-ALL-94, 6h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-94, 6h.

tag: age

tag: Sex

value: F


title: T-ALL-86, 24h

description: Expression profile of lymphoblasts from childhood ALL patient: T-ALL-86, 24h.

tag: cell type

value: T-ALL

value: TRUE


title: B-ALL-94, 24h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-94, 24h.


title: B-ALL-88, 0h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-88, 0h.


title: T-ALL-86, 0h

description: Expression profile of lymphoblasts from childhood ALL patient: T-ALL-86, 0h.


title: T-ALL-86, 6h

description: Expression profile of lymphoblasts from childhood ALL patient: T-ALL-86, 6h.


title: B-ALL-94, 0h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-94, 0h.


title: B-ALL-88, 24h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-88, 24h.


title: T-ALL-84, 24h

description: Expression profile of lymphoblasts from childhood ALL patient: T-ALL-84, 24h.


title: cdc14-3_108min

source_name: S. cerevisiae culture, cdc14-3, 108 min


title: cdc14-3_60min

source_name: S. cerevisiae culture, cdc14-3, 60 min


title: cdc14-3_120min

source_name: S. cerevisiae culture, cdc14-3, 120 min


title: cdc14-3_96min

source_name: S. cerevisiae culture, cdc14-3, 96 min


title: cdc14-3_72min

source_name: S. cerevisiae culture, cdc14-3, 72 min


title: cdc14-3_84min

source_name: S. cerevisiae culture, cdc14-3, 84 min


title: cdc14-3_48min

source_name: S. cerevisiae culture, cdc14-3, 48 min


title: T-ALL-84, 0h

description: Expression profile of lymphoblasts from childhood ALL patient: T-ALL-84, 0h.


title: cdc14-3_36min

source_name: S. cerevisiae culture, cdc14-3, 36 min


title: cdc14-3_24min

source_name: S. cerevisiae culture, cdc14-3, 24 min


title: B-ALL-85, 24h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-85, 24h.


title: T-ALL-84, 6h

description: Expression profile of lymphoblasts from childhood ALL patient: T-ALL-84, 6h.


title: cdc14-3_0min

source_name: S. cerevisiae culture, cdc14-3, 0 min


title: cdc14-3_12min

source_name: S. cerevisiae culture, cdc14-3, 12 min


title: B-ALL-85, 6h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-85, 6h.


title: 1561 PAX 5hr prefreeze 17hr thaw Tube2

city: Thousand Oaks

first: Dan

last: Baker

state: CA

address: 1 Amgen Center Drive

department: Molecular Sciences

institute: Amgen Inc.

description:
1561-5-17b
raw data file (Cy3): 101807_251485023262_S01_GE2-v5_95_Feb07_Feature_Extraction_1_3.txt
raw data file (Cy5): 101807_251485023262_S01_GE2-v5_95_Feb07_Feature_Extraction_1_2.txt

hyb_protocol: Overnight hybridizations at 65C per manufacturer’s instructions

scan_protocol: All arrays were scanned on the Agilent Surescaner Scanner (Agilent p/n G2600D). Agilent Scan Control Software version 9.1.5.1 was used for array scanning. Array files were processed using Agilent Feature Extraction software 11.0.1.1.

data_processing:
Extracted feature intensities for each channel on each array were processed separately by subtracting the lower 0.1th percentile from all intensities and then taking the log base 2. The transformed intensities were mapped using a non-linear function to a proprietary target density to ensure the distributions of the intensities were comparable between arrays and channels. Replicates of any identical sequences on the array were averaged to produce values called gene intensities.
Normalized log base 2 intensities in sereis supplementary file processed_data.txt

source_name: Blood

label_protocol: Samples were labeled using the Agilent Low RNA Input Linear Amplification Kit PLUS, Two-Color (Agilent Cat # 5188-5340) per manufacturer’s instructions.

extract_protocol: Total RNA was isolated from PAXgene whole blood tubes (BD Cat # 762165) using the PAXgene RNA Kit. (Qiagen Cat # 762164) on the Qiacube automated sample prep system

tag: donor id

tag: prefreeze (h)

tag: thaw (h)

tag: tube

value: PAXgene


title: 1561 PAX 5hr prefreeze 2hr thaw Tube2

description:
1561-5-2-b
raw data file (Cy3): 101807_251485023261_S01_GE2-v5_95_Feb07_Feature_Extraction_1_3.txt
raw data file (Cy5): 101807_251485023261_S01_GE2-v5_95_Feb07_Feature_Extraction_1_2.txt


title: 1561 PAX 5hr prefreeze 2hr thaw Tube1

description:
1561-5-2-a
raw data file (Cy3): 101807_251485023259_S01_GE2-v5_95_Feb07_Feature_Extraction_1_2.txt
raw data file (Cy5): 101807_251485023259_S01_GE2-v5_95_Feb07_Feature_Extraction_1_1.txt


title: 1561 PAX 24hr prefreeze 2hr thaw Tube2

description:
1561-24-2-b
raw data file (Cy3): 101807_251485023261_S01_GE2-v5_95_Feb07_Feature_Extraction_1_4.txt
raw data file (Cy5): 101807_251485023261_S01_GE2-v5_95_Feb07_Feature_Extraction_1_3.txt


title: 1561 EDTA 30' Tube2

description:
1561-2a
raw data file (Cy3): 101807_251485023260_S01_GE2-v5_95_Feb07_Feature_Extraction_1_4.txt
raw data file (Cy5): 101807_251485023262_S01_GE2-v5_95_Feb07_Feature_Extraction_1_4.txt

value: EDTA


title: 1561 PAX 5hr prefreeze 17hr thaw Tube1

description:
1561-5-17a
raw data file (Cy3): 101807_251485023260_S01_GE2-v5_95_Feb07_Feature_Extraction_1_2.txt
raw data file (Cy5): 101807_251485023260_S01_GE2-v5_95_Feb07_Feature_Extraction_1_1.txt


title: B-ALL-85, 0h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-85, 0h.


title: B-ALL-81, 0h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-81, 0h.

value: Hyperdiploid

value: others


title: B-ALL-6, 0h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-6, 0h.

value: BCR/ABL


title: 1561 PAX 24hr prefreeze 2hr thaw Tube1

description:
1561-24-2-a
raw data file (Cy3): 101807_251485023259_S01_GE2-v5_95_Feb07_Feature_Extraction_1_3.txt
raw data file (Cy5): 101807_251485023259_S01_GE2-v5_95_Feb07_Feature_Extraction_1_2.txt


title: 1561 PAX 24hr prefreeze 17hr thaw Tube2

description:
1561-24-17b
raw data file (Cy3): 101807_251485023262_S01_GE2-v5_95_Feb07_Feature_Extraction_1_4.txt
raw data file (Cy5): 101807_251485023262_S01_GE2-v5_95_Feb07_Feature_Extraction_1_3.txt


title: 1561 PAX 24hr prefreeze 17hr thaw Tube1

description:
1561-24-17a
raw data file (Cy3): 101807_251485023260_S01_GE2-v5_95_Feb07_Feature_Extraction_1_3.txt
raw data file (Cy5): 101807_251485023260_S01_GE2-v5_95_Feb07_Feature_Extraction_1_2.txt


title: B-ALL-83, 6h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-83, 6h.

value: reference


title: B-ALL-83, 24h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-83, 24h.


title: B-ALL-82, 0h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-82, 0h.


title: B-ALL-82, 24h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-82, 24h.


title: B-ALL-19, 24h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-19, 24h.


title: B-ALL-81, 24h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-81, 24h.


title: 1561 PAX 2hr prefreeze 2hr thaw Tube2

description:
1561-2-2-b
raw data file (Cy3): 101807_251485023261_S01_GE2-v5_95_Feb07_Feature_Extraction_1_2.txt
raw data file (Cy5): 101807_251485023261_S01_GE2-v5_95_Feb07_Feature_Extraction_1_1.txt


title: B-ALL-19, 8h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-19, 8h.


title: B-ALL-83, 0h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-83, 0h.


title: B-ALL-82, 6h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-82, 6h.


title: B-ALL-81, 6h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-81, 6h.


title: 1561 PAX 2hr prefreeze 2hr thaw Tube1

description:
1561-2-2-a
raw data file (Cy3): 101807_251485023259_S01_GE2-v5_95_Feb07_Feature_Extraction_1_1.txt
raw data file (Cy5): 101807_251485023219_S01_GE2-v5_95_Feb07_Feature_Extraction_1_4.txt


title: 1561 PAX 2hr prefreeze 17hr thaw Tube1

description:
1561-2-17a
raw data file (Cy3): 101807_251485023260_S01_GE2-v5_95_Feb07_Feature_Extraction_1_1.txt
raw data file (Cy5): 101807_251485023259_S01_GE2-v5_95_Feb07_Feature_Extraction_1_4.txt


title: 1561 PAX 2hr prefreeze 17hr thaw Tube2

description:
1561-2-17b
raw data file (Cy3): 101807_251485023262_S01_GE2-v5_95_Feb07_Feature_Extraction_1_2.txt
raw data file (Cy5): 101807_251485023262_S01_GE2-v5_95_Feb07_Feature_Extraction_1_1.txt


title: 1561 EDTA 30' Tube1

description:
1561-1a
raw data file (Cy3): 101807_251485023219_S01_GE2-v5_95_Feb07_Feature_Extraction_1_3.txt
raw data file (Cy5): 101807_251485023260_S01_GE2-v5_95_Feb07_Feature_Extraction_1_3.txt


title: B-ALL-80, 0h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-80, 0h.


title: 1561 PAX No prefreeze 2hr thaw Tube2

description:
1561-0-2-b
raw data file (Cy3): 101807_251485023261_S01_GE2-v5_95_Feb07_Feature_Extraction_1_1.txt
raw data file (Cy5): 101807_251485023260_S01_GE2-v5_95_Feb07_Feature_Extraction_1_4.txt


title: 1561 PAX No prefreeze 2hr thaw Tube1

description:
1561-0-2-a
raw data file (Cy3): 101807_251485023219_S01_GE2-v5_95_Feb07_Feature_Extraction_1_4.txt
raw data file (Cy5): 101807_251485023219_S01_GE2-v5_95_Feb07_Feature_Extraction_1_3.txt


title: 1561 PAX No prefreeze 17hr thaw Tube2

description:
1561-0-17b
raw data file (Cy3): 101807_251485023262_S01_GE2-v5_95_Feb07_Feature_Extraction_1_1.txt
raw data file (Cy5): 101807_251485023261_S01_GE2-v5_95_Feb07_Feature_Extraction_1_4.txt


title: 1561 PAX No prefreeze 17hr thaw Tube1

description:
1561-0-17a
raw data file (Cy3): 101807_251485023259_S01_GE2-v5_95_Feb07_Feature_Extraction_1_4.txt
raw data file (Cy5): 101807_251485023259_S01_GE2-v5_95_Feb07_Feature_Extraction_1_3.txt


title: 1553 PAX 5hr prefreeze 17hr thaw Tube2

description:
1553-5-17.2
raw data file (Cy3): 111307_251485024188_S01_GE2-v5_95_Feb07_Feature_Extraction_1_1.txt
raw data file (Cy5): 111307_251485024187_S01_GE2-v5_95_Feb07_Feature_Extraction_1_4.txt


title: 1553 PAX 5hr prefreeze 2hr thaw Tube2

description:
1553-5-2.2
raw data file (Cy3): 111307_251485024187_S01_GE2-v5_95_Feb07_Feature_Extraction_1_1.txt
raw data file (Cy5): 111307_251485024186_S01_GE2-v5_95_Feb07_Feature_Extraction_1_4.txt


title: 1553 PAX 5hr prefreeze 2hr thaw Tube1

description:
1553-5-2.1
raw data file (Cy3): 103007_251485023276_S01_GE2-v5_95_Feb07_Feature_Extraction_1_4.txt
raw data file (Cy5): 103007_251485023276_S01_GE2-v5_95_Feb07_Feature_Extraction_1_3.txt


title: 1553 PAX 5hr prefreeze 17hr thaw Tube1

description:
1553-5-17.1
raw data file (Cy3): 111307_251485023432_S01_GE2-v5_95_Feb07_Feature_Extraction_1_4.txt
raw data file (Cy5): 111307_251485023432_S01_GE2-v5_95_Feb07_Feature_Extraction_1_3.txt


title: B-ALL-80, 24

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-80, 24.


title: B-ALL-55, 6h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-55, 6h.


title: B-ALL-78, 0h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-78, 0h.


title: B-ALL-78, 24h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-78, 24h.


title: B-ALL-79, 6h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-79, 6h.


title: B-ALL-79, 24h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-79, 24h.


title: B-ALL-76, 24h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-76, 24h.


title: 1553 PAX 24hr prefreeze 2hr thaw Tube2

description:
1553-24-2.2
raw data file (Cy3): 111307_251485024187_S01_GE2-v5_95_Feb07_Feature_Extraction_1_2.txt
raw data file (Cy5): 111307_251485024187_S01_GE2-v5_95_Feb07_Feature_Extraction_1_1.txt


title: 1553 PAX 24hr prefreeze 2hr thaw Tube1

description:
1553-24-2.1
raw data file (Cy3): 111307_251485023432_S01_GE2-v5_95_Feb07_Feature_Extraction_1_1.txt
raw data file (Cy5): 103007_251485023276_S01_GE2-v5_95_Feb07_Feature_Extraction_1_4.txt


title: 1553 PAX 24hr prefreeze 17hr thaw Tube2

description:
1553-24-17.2
raw data file (Cy3): 111307_251485024188_S01_GE2-v5_95_Feb07_Feature_Extraction_1_2.txt
raw data file (Cy5): 111307_251485024188_S01_GE2-v5_95_Feb07_Feature_Extraction_1_1.txt


title: B-ALL-79, 0h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-79, 0h.


title: 1553 PAX 2hr prefreeze 17hr thaw Tube2

description:
1553-2-17.2
raw data file (Cy3): 111307_251485024187_S01_GE2-v5_95_Feb07_Feature_Extraction_1_4.txt
raw data file (Cy5): 111307_251485024187_S01_GE2-v5_95_Feb07_Feature_Extraction_1_3.txt


title: 1553 PAX 24hr prefreeze 17hr thaw Tube1

description:
1553-24-17.1
raw data file (Cy3): 111307_251485024186_S01_GE2-v5_95_Feb07_Feature_Extraction_1_1.txt
raw data file (Cy5): 111307_251485023432_S01_GE2-v5_95_Feb07_Feature_Extraction_1_4.txt


title: 1553 PAX 2hr prefreeze 2hr thaw Tube2

description:
1553-2-2.2
raw data file (Cy3): 111307_251485024186_S01_GE2-v5_95_Feb07_Feature_Extraction_1_4.txt
raw data file (Cy5): 111307_251485024186_S01_GE2-v5_95_Feb07_Feature_Extraction_1_3.txt


title: 1553 PAX 2hr prefreeze 2hr thaw Tube1

description:
1553-2-2.1
raw data file (Cy3): 103007_251485023276_S01_GE2-v5_95_Feb07_Feature_Extraction_1_3.txt
raw data file (Cy5): 103007_251485023276_S01_GE2-v5_95_Feb07_Feature_Extraction_1_2.txt


title: B-ALL-75, 6h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-75, 6h.


title: B-ALL-76, 0h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-76, 0h.


title: T-ALL-74, 24h

description: Expression profile of lymphoblasts from childhood ALL patient: T-ALL-74, 24h.


title: 1553 EDTA 30min Tube1

description:
1553-1.1
raw data file (Cy3): 103007_251485023276_S01_GE2-v5_95_Feb07_Feature_Extraction_1_1.txt
raw data file (Cy5): 111307_251485024186_S01_GE2-v5_95_Feb07_Feature_Extraction_1_1.txt


title: 1553 PAX 2hr prefreeze 17hr thaw Tube1

description:
1553-2-17.1
raw data file (Cy3): 111307_251485023432_S01_GE2-v5_95_Feb07_Feature_Extraction_1_3.txt
raw data file (Cy5): 111307_251485023432_S01_GE2-v5_95_Feb07_Feature_Extraction_1_2.txt


title: B-ALL-55, 0h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-55, 0h.


title: 1553 PAX No prefreeze 2hr thaw Tube2

description:
1553-0-2.2
raw data file (Cy3): 111307_251485024186_S01_GE2-v5_95_Feb07_Feature_Extraction_1_3.txt
raw data file (Cy5): 111307_251485024186_S01_GE2-v5_95_Feb07_Feature_Extraction_1_2.txt


title: T-ALL-74, 6h

description: Expression profile of lymphoblasts from childhood ALL patient: T-ALL-74, 6h.


title: T-ALL-46, 0h

description: Expression profile of lymphoblasts from childhood ALL patient: T-ALL-46, 0h.


title: T-ALL-46, 24h

description: Expression profile of lymphoblasts from childhood ALL patient: T-ALL-46, 24h.


title: T-ALL-46, 6h

description: Expression profile of lymphoblasts from childhood ALL patient: T-ALL-46, 6h.


title: B-ALL-75, 0h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-75, 0h.


title: T-ALL-74, 0h

description: Expression profile of lymphoblasts from childhood ALL patient: T-ALL-74, 0h.


title: B-ALL-76, 6h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-76, 6h.


title: B-ALL-71, 6h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-71, 6h.


title: 1553 PAX No prefreeze 17hr thaw Tube2

description:
1553-0-17.2
raw data file (Cy3): 111307_251485024187_S01_GE2-v5_95_Feb07_Feature_Extraction_1_3.txt
raw data file (Cy5): 111307_251485024187_S01_GE2-v5_95_Feb07_Feature_Extraction_1_2.txt


title: B-ALL-19, 0h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-19, 0h.


title: 1512 PAX 5hr prefreeze 2hr thaw Tube2

description:
1512-5-2-b
raw data file (Cy3): 101807_251485023218_S01_GE2-v5_95_Feb07_Feature_Extraction_1_1.txt
raw data file (Cy5): 101807_251485023217_S01_GE2-v5_95_Feb07_Feature_Extraction_1_4.txt


title: 1553 PAX No prefreeze 17hr thaw Tube1

description:
1553-0-17.1
raw data file (Cy3): 111307_251485023432_S01_GE2-v5_95_Feb07_Feature_Extraction_1_2.txt
raw data file (Cy5): 111307_251485023432_S01_GE2-v5_95_Feb07_Feature_Extraction_1_1.txt


title: 1512 PAX 5hr prefreeze 2hr thaw Tube1

description:
1512-5-2-a
raw data file (Cy3): 101807_251485023215_S01_GE2-v5_95_Feb07_Feature_Extraction_1_4.txt
raw data file (Cy5): 101807_251485023215_S01_GE2-v5_95_Feb07_Feature_Extraction_1_3.txt


title: 1553 EDTA 30min Tube 2

description:
1553-2.2
raw data file (Cy3): 111307_251485024186_S01_GE2-v5_95_Feb07_Feature_Extraction_1_2.txt
raw data file (Cy5): 111307_251485024188_S01_GE2-v5_95_Feb07_Feature_Extraction_1_2.txt


title: 1553 PAX No prefreeze 2hr thaw Tube1

description:
1553-0-2.1
raw data file (Cy3): 103007_251485023276_S01_GE2-v5_95_Feb07_Feature_Extraction_1_2.txt
raw data file (Cy5): 103007_251485023276_S01_GE2-v5_95_Feb07_Feature_Extraction_1_1.txt


title: B-ALL-71, 24h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-71, 24h.


title: B-ALL-62, 24h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-62, 24h.


title: 1512 PAX 5hr prefreeze 17hr thaw Tube2

description:
1512-5-17b
raw data file (Cy3): 101807_251485023219_S01_GE2-v5_95_Feb07_Feature_Extraction_1_1.txt
raw data file (Cy5): 101807_251485023218_S01_GE2-v5_95_Feb07_Feature_Extraction_1_4.txt


title: 1512 PAX 5hr prefreeze 17hr thaw Tube1

description:
1512-5-17a
raw data file (Cy3): 101807_251485023216_S01_GE2-v5_95_Feb07_Feature_Extraction_1_4.txt
raw data file (Cy5): 101807_251485023216_S01_GE2-v5_95_Feb07_Feature_Extraction_1_3.txt


title: B-ALL-24, 24h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-24, 24h.


title: 1512 EDTA 30' Tube2

description:
1512-2a
raw data file (Cy3): 101807_251485023217_S01_GE2-v5_95_Feb07_Feature_Extraction_1_2.txt
raw data file (Cy5): 101807_251485023219_S01_GE2-v5_95_Feb07_Feature_Extraction_1_2.txt


title: 1512 PAX 24hr prefreeze 2hr thaw Tube2

description:
1512-24-2-b
raw data file (Cy3): 101807_251485023218_S01_GE2-v5_95_Feb07_Feature_Extraction_1_2.txt
raw data file (Cy5): 101807_251485023218_S01_GE2-v5_95_Feb07_Feature_Extraction_1_1.txt


title: T-ALL-25, 6h

description: Expression profile of lymphoblasts from childhood ALL patient: T-ALL-25, 6h.


title: B-ALL-62, 6h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-62, 6h.


title: 1512 PAX 24hr prefreeze 2hr thaw Tube1

description:
1512-24-2-a
raw data file (Cy3): 101807_251485023216_S01_GE2-v5_95_Feb07_Feature_Extraction_1_1.txt
raw data file (Cy5): 101807_251485023215_S01_GE2-v5_95_Feb07_Feature_Extraction_1_4.txt


title: B-ALL-24, 6h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-24, 6h.


title: B-ALL-24, 0h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-24, 0h.


title: B-ALL-71, 0h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-71, 0h.


title: B-ALL-62, 0h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-62, 0h.


title: T-ALL-61, 24h

description: Expression profile of lymphoblasts from childhood ALL patient: T-ALL-61, 24h.


title: 1512 PAX 24hr prefreeze 17hr thaw Tube2

description:
1512-24-17b
raw data file (Cy3): 101807_251485023219_S01_GE2-v5_95_Feb07_Feature_Extraction_1_2.txt
raw data file (Cy5): 101807_251485023219_S01_GE2-v5_95_Feb07_Feature_Extraction_1_1.txt


title: T-ALL-61, 6h

description: Expression profile of lymphoblasts from childhood ALL patient: T-ALL-61, 6h.


title: T-ALL-61, 0h

description: Expression profile of lymphoblasts from childhood ALL patient: T-ALL-61, 0h.


title: T-ALL-54, 24h

description: Expression profile of lymphoblasts from childhood ALL patient: T-ALL-54, 24h.


title: CD1c+_polyIC_3

city: Woolloongabba

first: Kristen

last: Radford

address: Translational Research Institute, 37 Kent St

country: Australia

institute: Mater Research Institute – University of Queensland

description:
3998755170_H
CD1c DC from Flt3L humanised mouse bone marrow polyIC 2h in vivo

hyb_protocol: Not provided

scan_protocol: Not provided

data_processing: The data were background corrected, log2 tranformed and quantile normalised using lumi (version 1.1.0)

source_name: HuMouse CD1c, polyIC 2hr

label_protocol: Not provided

growth_protocol: Cord blood was obtained with informed consent from the Queensland Cord Blood Bank with approval from the Mater Adult Hospital Human Ethics Committee. CD34+ haematopoietic progenitor cells were isolated by density gradient enrichment followed by a positive selection using a CD34+ isolation kit (Miltenyi Biotec). NSG-A2 mice (stock no. 014570 ) were purchased from Jackson Laboratories. Two – five day old NSG-A2 pups received 10Gy total body irradiation 4hr prior to intrahepatic injection of human CD34+ cells. Engraftment of human CD45+ cells was confirmed 10-12 weeks later, after which hu mice received 2 s.c. doses of human recombinant huFLT3-L (BioXcell) 4 days apart prior to experimentation.

extract_protocol: Human DCs were enriched from single cell BM suspensions by first labelling with Ab specific for human CD3, CD14, CD19, CD20, CD34, and mouse CD45 and Ter119 followed by depletion of bound cells using sheep anti-rat IgG Dynabeads (Invitrogen). Cells were then labelled with Live Dead® aqua, anti-mouse CD45 PerCP Cy5.5, anti-human CD45 APC Cy7, CD19/20 Pacific blue, HLA DR PE Cy7, CD123 PE or PerCP Cy5.5, CD1c FITC, and CD141 APC and sorted using a Moflo Astrios (Beckman Coulter)

treatment_protocol: Engrafted mice were injected retroorbitally with poly IC (50µg, (Invivogen)) or R848 (20µg, (Invivogen)) alone or in combination and mice were euthanased 2h later.

tag: tissue

value: FLT3L humanised mouse bone marrow

value: CD1c+ dendritic cells

value: polyIC


title: CD1c+_R848_2

description:
3998755170_G
CD1c DC from Flt3L humanised mouse bone marrow R848 2h in vivo

source_name: HuMouse CD1c, R848 2hr


title: CD141+_polyIC_3

description:
3998755170_F
CD141 DC from Flt3L humanised mouse bone marrow polyIC 2h in vivo

source_name: HuMouse CD141, polyIC 2hr

value: CD141+ dendritic cells


title: CD141+_R848_3

description:
3998755170_J
CD141 DC from Flt3L humanised mouse bone marrow R848 2h in vivo

source_name: HuMouse CD141, R848 2hr


title: CD141+_R848_2

description:
3998755170_E
CD141 DC from FLT3L humanised mouse bone marrow R848 2h in vivo


title: CD141+_polyIC+R848_3

description:
3998755170_I
CD141 DC from Flt3L humanised mouse bone marrow polyIC+R848 2h in vivo

source_name: HuMouse CD141, polyIC_R848 2hr


title: CD1c+_untreated_3

description:
3998755170_D
CD1c DC from Flt3L humanised mouse bone marrow

source_name: HuMouse CD1c, untreated

value: untreated


title: 1512 PAX 2hr prefreeze 2hr thaw Tube2

description:
1512-2-2-b
raw data file (Cy3): 101807_251485023217_S01_GE2-v5_95_Feb07_Feature_Extraction_1_4.txt
raw data file (Cy5): 101807_251485023217_S01_GE2-v5_95_Feb07_Feature_Extraction_1_3.txt


title: 1512 PAX 24hr prefreeze 17hr thaw Tube1

description:
1512-24-17a
raw data file (Cy3): 101807_251485023217_S01_GE2-v5_95_Feb07_Feature_Extraction_1_1.txt
raw data file (Cy5): 101807_251485023216_S01_GE2-v5_95_Feb07_Feature_Extraction_1_4.txt


title: CD1c+_R848_3

description:
3998755170_L
CD1c DC from Flt3L humanised mouse bone marrow R848 2h in vivo


title: CD141+_untreated_3

description:
3998755170_B
CD141 DC from Flt3L humanised mouse bone marrow

source_name: HuMouse CD141, untreated


title: CD1c+_polyIC_1

description:
3998755167_K
CD1c DC from Flt3L humanised mouse bone marrow polyIC 2h in vivo


title: CD1c+_polyIC+R848_3

description:
3998755170_K
CD1c DC from Flt3L humanised mouse bone marrow polyIC+R848 2h in vivo

source_name: HuMouse CD1c, polyIC_R848 2hr


title: CD141+_untreated_2

description:
3998755167_J
CD141 DC from Flt3L humanised mouse bone marrow


title: B-ALL-725, 24h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-725, 24h.

value: childhood acute lymphoblastic leukemia (ALL)

value: lymphoblasts

value: glucocorticoid (GC) mono-therapy


title: CD1c+_polyIC+R848_2

description:
3998755167_H
CD1c DC from Flt3L humanised mouse bone marrow polyIC+R848 2h in vivo


title: CD141+_polyIC_1

description:
3998755167_I
CD141 DC from Flt3L humanised mouse bone marrow polyIC 2h in vivo


title: CD1c+_polyIC_2

description:
3998755170_C
CD1c DC from Flt3L humanised mouse bone marrow polyIC 2h in vivo


title: T-ALL-54, 6h

description: Expression profile of lymphoblasts from childhood ALL patient: T-ALL-54, 6h.

value: M

value: FALSE


title: CD1c+_untreated_1

description:
3998755167_G
CD1c DC from Flt3L humanised mouse bone marrow


title: T-ALL-54, 0h

description: Expression profile of lymphoblasts from childhood ALL patient: T-ALL-54, 0h.

value: T-ALL


title: 1512 PAX 2hr prefreeze 2hr thaw Tube1

description:
1512-2-2-a
raw data file (Cy3): 101807_251485023215_S01_GE2-v5_95_Feb07_Feature_Extraction_1_3.txt
raw data file (Cy5): 102307_251485023263_S01_GE2-v5_95_Feb07_Feature_Extraction_1_2.txt

value: PAXgene


title: 1512 PAX 2hr prefreeze 17hr thaw Tube2

description:
1512-2-17b
raw data file (Cy3): 101807_251485023218_S01_GE2-v5_95_Feb07_Feature_Extraction_1_4.txt
raw data file (Cy5): 101807_251485023218_S01_GE2-v5_95_Feb07_Feature_Extraction_1_3.txt


title: B-ALL-725, 6h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-725, 6h.


title: CD141+_polyIC+R848_2

description:
3998755167_F
CD141 DC from Flt3L humanised mouse bone marrow polyIC+R848 2h in vivo


title: CD1c+_R848_1

description:
3998755167_D
CD1c DC from Flt3L humanised mouse bone marrow R848 2h in vivo


title: 1512 PAX 2hr prefreeze 17hr thaw Tube1

description:
1512-2-17a
raw data file (Cy3): 101807_251485023216_S01_GE2-v5_95_Feb07_Feature_Extraction_1_3.txt
raw data file (Cy5): 101807_251485023216_S01_GE2-v5_95_Feb07_Feature_Extraction_1_2.txt


title: 1512 PAX No prefreeze 2hr thaw Tube1

description:
1512-0-2-a
raw data file (Cy3): 102307_251485023263_S01_GE2-v5_95_Feb07_Feature_Extraction_1_2.txt
raw data file (Cy5): 101807_251485023215_S01_GE2-v5_95_Feb07_Feature_Extraction_1_1.txt


title: B-ALL-725, 0h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-725, 0h.


title: 1504 PAX 5hr prefreeze 2hr thaw Tube2

description:
1504-5-2.2
raw data file (Cy3): 121307_251485024165_S01_GE2-v5_95_Feb07_Feature_Extraction_1_1.txt
raw data file (Cy5): 121307_251485024164_S01_GE2-v5_95_Feb07_Feature_Extraction_1_4.txt


title: 1512 EDTA 30' Tube1

description:
1512-1a
raw data file (Cy3): 101807_251485023215_S01_GE2-v5_95_Feb07_Feature_Extraction_1_1.txt
raw data file (Cy5): 101807_251485023217_S01_GE2-v5_95_Feb07_Feature_Extraction_1_1.txt

value: EDTA


title: 1512 PAX No prefreeze 17hr thaw Tube1

description:
1512-0-17a
raw data file (Cy3): 101807_251485023216_S01_GE2-v5_95_Feb07_Feature_Extraction_1_2.txt
raw data file (Cy5): 101807_251485023216_S01_GE2-v5_95_Feb07_Feature_Extraction_1_1.txt


title: 1504 PAX 5hr prefreeze 2hr thaw Tube1

description:
1504-5-2.1
raw data file (Cy3): 121307_251485024162_S01_GE2-v5_95_Feb07_Feature_Extraction_1_4.txt
raw data file (Cy5): 121307_251485024162_S01_GE2-v5_95_Feb07_Feature_Extraction_1_3.txt


title: 1512 PAX No prefreeze 2hr thaw Tube2

description:
1512-0-2-b
raw data file (Cy3): 101807_251485023217_S01_GE2-v5_95_Feb07_Feature_Extraction_1_3.txt
raw data file (Cy5): 101807_251485023217_S01_GE2-v5_95_Feb07_Feature_Extraction_1_2.txt


title: 1504 PAX 5hr prefreeze 17hr thaw Tube2

description:
1504-5-17.2
raw data file (Cy3): 122007_251485019986_S01_GE2-v5_95_Feb07_Feature_Extraction_1_1.txt
raw data file (Cy5): 121307_251485024165_S01_GE2-v5_95_Feb07_Feature_Extraction_1_4.txt


title: 1504 PAX 5hr prefreeze 17hr thaw Tube1

description:
1504-5-17.1
raw data file (Cy3): 121307_251485024163_S01_GE2-v5_95_Feb07_Feature_Extraction_1_4.txt
raw data file (Cy5): 121307_251485024163_S01_GE2-v5_95_Feb07_Feature_Extraction_1_3.txt


title: 1512 PAX No prefreeze 17hr thaw Tube2

description:
1512-0-17b
raw data file (Cy3): 101807_251485023218_S01_GE2-v5_95_Feb07_Feature_Extraction_1_3.txt
raw data file (Cy5): 101807_251485023218_S01_GE2-v5_95_Feb07_Feature_Extraction_1_2.txt


title: 1504 PAX 24hr prefreeze 2hr thaw Tube1

description:
1504-24-2.1
raw data file (Cy3): 121307_251485024163_S01_GE2-v5_95_Feb07_Feature_Extraction_1_1.txt
raw data file (Cy5): 121307_251485024162_S01_GE2-v5_95_Feb07_Feature_Extraction_1_4.txt


title: B-ALL-739, 6h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-739, 6h.

value: F

value: Hyperdiploid


title: 1504 PAX 24hr prefreeze 17hr thaw Tube2

description:
1504-24-17.2
raw data file (Cy3): 122007_251485019986_S01_GE2-v5_95_Feb07_Feature_Extraction_1_2.txt
raw data file (Cy5): 122007_251485019986_S01_GE2-v5_95_Feb07_Feature_Extraction_1_1.txt


title: CD141+_polyIC+R848_1

description:
3998755167_A
CD141 DC from FLT3L humanised mouse bone marrow polyIC + R848 2h in vivo


title: B-ALL-739, 0h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-739, 0h.


title: B-ALL-715, 24h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-715, 24h.


title: B-ALL-715, 0h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-715, 0h.


title: B-ALL-52, 0h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-52, 0h.


title: B-ALL-699, 6h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-699, 6h.

value: TRUE


title: 1504 PAX 2hr prefreeze 2hr thaw Tube2

description:
1504-2-2.2
raw data file (Cy3): 121307_251485024164_S01_GE2-v5_95_Feb07_Feature_Extraction_1_4.txt
raw data file (Cy5): 121307_251485024164_S01_GE2-v5_95_Feb07_Feature_Extraction_1_3.txt


title: 1504 PAX 2hr prefreeze 2hr thaw Tube1

description:
1504-2-2.1
raw data file (Cy3): 121307_251485024162_S01_GE2-v5_95_Feb07_Feature_Extraction_1_3.txt
raw data file (Cy5): 121307_251485024162_S01_GE2-v5_95_Feb07_Feature_Extraction_1_2.txt


title: 1504 PAX 2hr prefreeze 17hr thaw Tube2

description:
1504-2-17.2
raw data file (Cy3): 121307_251485024165_S01_GE2-v5_95_Feb07_Feature_Extraction_1_4.txt
raw data file (Cy5): 121307_251485024165_S01_GE2-v5_95_Feb07_Feature_Extraction_1_3.txt


title: B-ALL-52, 6h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-52, 6h.

value: reference


title: B-ALL-715, 6h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-715, 6h.


title: B-ALL-699, 0h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-699, 0h.


title: 1504 EDTA 30min Tube 2

description:
1504-2.2
raw data file (Cy3): 121307_251485024164_S01_GE2-v5_95_Feb07_Feature_Extraction_1_2.txt
raw data file (Cy5): 122007_251485019986_S01_GE2-v5_95_Feb07_Feature_Extraction_1_2.txt


title: 1504 PAX 24hr prefreeze 2hr thaw Tube2

description:
1504-24-2.2
raw data file (Cy3): 121307_251485024165_S01_GE2-v5_95_Feb07_Feature_Extraction_1_2.txt
raw data file (Cy5): 121307_251485024165_S01_GE2-v5_95_Feb07_Feature_Extraction_1_1.txt


title: B-ALL-699, 24h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-699, 24h.


title: B-ALL-52, 24h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-52, 24h.


title: B-ALL-739, 24h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-739, 24h.


title: 1504 PAX 24hr prefreeze 17hr thaw Tube1

description:
1504-24-17.1
raw data file (Cy3): 121307_251485024164_S01_GE2-v5_95_Feb07_Feature_Extraction_1_1.txt
raw data file (Cy5): 121307_251485024163_S01_GE2-v5_95_Feb07_Feature_Extraction_1_4.txt


title: 1504 PAX No prefreeze 2hr thaw Tube1

description:
1504-0-2.1
raw data file (Cy3): 121307_251485024162_S01_GE2-v5_95_Feb07_Feature_Extraction_1_2.txt
raw data file (Cy5): 121307_251485024162_S01_GE2-v5_95_Feb07_Feature_Extraction_1_1.txt


title: 1504 PAX No prefreeze 17hr thaw Tube2

description:
1504-0-17.2
raw data file (Cy3): 121307_251485024165_S01_GE2-v5_95_Feb07_Feature_Extraction_1_3.txt
raw data file (Cy5): 121307_251485024165_S01_GE2-v5_95_Feb07_Feature_Extraction_1_2.txt


title: 1504 PAX 2hr prefreeze 17hr thaw Tube1

description:
1504-2-17.1
raw data file (Cy3): 121307_251485024163_S01_GE2-v5_95_Feb07_Feature_Extraction_1_3.txt
raw data file (Cy5): 121307_251485024163_S01_GE2-v5_95_Feb07_Feature_Extraction_1_2.txt


title: 1504 PAX No prefreeze 17hr thaw Tube1

description:
1504-0-17.1
raw data file (Cy3): 121307_251485024163_S01_GE2-v5_95_Feb07_Feature_Extraction_1_2.txt
raw data file (Cy5): 121307_251485024163_S01_GE2-v5_95_Feb07_Feature_Extraction_1_1.txt


title: B-ALL-689, 0h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-689, 0h.


title: B-ALL-704, 0h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-704, 0h.


title: B-ALL-704, 6h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-704, 6h.


title: B-ALL-685, 0h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-685, 0h.


title: B-ALL-704, 24h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-704, 24h.


title: B-ALL-685, 6h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-685, 6h.


title: B-ALL-689, 6h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-689, 6h.


title: B-ALL-677, 24h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-677, 24h.


title: 1504 EDTA 30min Tube1

description:
1504-1.1
raw data file (Cy3): 121307_251485024162_S01_GE2-v5_95_Feb07_Feature_Extraction_1_1.txt
raw data file (Cy5): 121307_251485024164_S01_GE2-v5_95_Feb07_Feature_Extraction_1_1.txt


title: 1504 PAX No prefreeze 2hr thaw Tube2

description:
1504-0-2.2
raw data file (Cy3): 121307_251485024164_S01_GE2-v5_95_Feb07_Feature_Extraction_1_3.txt
raw data file (Cy5): 121307_251485024164_S01_GE2-v5_95_Feb07_Feature_Extraction_1_2.txt


title: B-ALL-677, 6h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-677, 6h.


title: B-ALL-44, 6h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-44, 6h.


title: B-ALL-43, 0h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-43, 0h.


title: B-ALL-44, 0h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-44, 0h.


title: iFIPC-derived SOs and BOs (2)

city: Fukuoka

first: Atsushi

last: Suzuki

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: Division of Organogenesis and Regeneration

institute: Medical Institute of Bioreguration, Kyushu University

description: cells composed of spheroids and organoids derived from induced fetal intestinal progenitor cells

hyb_protocol: cRNA was hybridized to a 44K 60-mer oligomicroarray (Whole Mouse Gene Expression Microarray 4x44K v1; Agilent Technologies) according to the manufacturer's instructions.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

source_name: iFIPC-derived spherical organoids (SOs) and budding organoids (BOs)

label_protocol: cRNA was amplified and labelled using a Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: Total RNA was isolated from tissues using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)

tag: strain

tag: cell/tissue type

value: spheroids and organoids

tag: cell source


title: FI-derived SOs and BOs (2)

description: cells composed of spheroids and organoids derived from fetal intestinal progenitor cells

source_name: FI-derived spherical organoids (SOs) and budding organoids (BOs)

value: fetal intestinal progenitor cells


title: B-ALL-44, 24h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-44, 24h.

tag: disease status

tag: treatment

tag: treatment time point


title: iFIPC-derived SOs and BOs (3)

value: induced fetal intestinal progenitor cells


title: B-ALL-43, 24h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-43, 24h.

tag: all subtype by clustering

tag: all subtype for analysis

tag: prednisone poor responder


title: FI-derived SOs and BOs (3)


title: FI-derived SOs and BOs (1)


title: B-ALL-38, 6h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-38, 6h.

tag: age

tag: hyb year

tag: normalization set


title: B-ALL-677, 0h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-677, 0h.

tag: cell type

tag: Sex


title: B-ALL-685, 24h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-685, 24h.


title: iFIPC-derived SOs and BOs (1)


title: iISC-derived BOs (1)

description: cells composed of organoids derived from induced intestinal stem cells

source_name: iISC-derived budding organoids (BOs)

value: organoids

value: induced intestinal stem cells


title: B-ALL-38, 24h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-38, 24h.

value: childhood acute lymphoblastic leukemia (ALL)


title: Crypt-derived BOs (2)

description: cells composed of organoids derived from adult intestinal crypts

source_name: Crypt-derived budding organoids (BOs)

value: adult intestinal crypts


title: B-ALL-38, 0h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-38, 0h.

value: lymphoblasts


title: B-ALL-39. 24h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-39. 24h.

value: glucocorticoid (GC) mono-therapy

value: M


title: Crypt-derived BOs (3)


title: iISC-derived BOs (3)


title: B-ALL-43, 6h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-43, 6h.

value: FALSE


title: T-ALL-2, 0h

description: Expression profile of lymphoblasts from childhood ALL patient: T-ALL-2, 0h.

value: T-ALL


title: iISC-derived BOs (2)


title: Crypt-derived BOs (1)


title: B-ALL-39, 6h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-39, 6h.


title: T-ALL-20, 24h

description: Expression profile of lymphoblasts from childhood ALL patient: T-ALL-20, 24h.


title: T-ALL-2, 24h

description: Expression profile of lymphoblasts from childhood ALL patient: T-ALL-2, 24h.


title: iHep (4α3)-MEF [re-analysis]

description:
induced hepatocyte-like cells derived from MEFs
GSM737104

value: induced hepatocyte-like cells


title: B-ALL-39, 0h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-39, 0h.


title: T-ALL-2, 8h

description: Expression profile of lymphoblasts from childhood ALL patient: T-ALL-2, 8h.


title: MEF-1 [re-analysis]

description:
embryonic fibroblasts
GSM737099
MEF(1) of PMID: 28943029

source_name: mouse embryonic fibroblasts

value: embryonic fibroblasts


title: MEF-3 [re-analysis]

description:
embryonic fibroblasts
GSM737101
MEF(2) of PMID: 28943029


title: iHep (4α2)-MEF [re-analysis]

description:
induced hepatocyte-like cells derived from MEFs
GSM737103


title: iHep (4α1)-MEF [re-analysis]

description:
induced hepatocyte-like cells derived from MEFs
GSM737102


title: B-ALL-40, 0h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-40, 0h.

value: BCR/ABL


title: B-ALL-40, 24h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-40, 24h.


title: T-ALL-20, 0h

description: Expression profile of lymphoblasts from childhood ALL patient: T-ALL-20, 0h.


title: B-ALL-13, 0h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-13, 0h.


title: MEF-2 [re-analysis]

description:
embryonic fibroblasts
GSM737100
MEF(3) of PMID: 28943029


title: B-ALL-40, 6h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-40, 6h.


title: B-ALL-31, 6h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-31, 6h.

value: F

value: Hyperdiploid


title: B-ALL-13, 8h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-13, 8h.

value: reference


title: T-ALL-20, 8h

description: Expression profile of lymphoblasts from childhood ALL patient: T-ALL-20, 8h.


title: B-ALL-17, 0h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-17, 0h.

value: BCR/ABL, Hyperdiploid


title: B-ALL-6, 8h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-6, 8h.

value: TRUE


title: B-ALL-31, 0h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-31, 0h.


title: B-ALL-6, 24h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-6, 24h.


title: B-ALL-31, 24h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-31, 24h.


title: B-ALL-33, 0h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-33, 0h.


title: B-ALL-32, 0h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-32, 0h.


title: B-ALL-17, 8h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-17, 8h.


title: B-ALL-33, 24h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-33, 24h.


title: B-ALL-13, 24h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-13, 24h.


title: B-ALL-17, 24h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-17, 24h.


city: Beijing

first: Xiaolei

last: Li

address: #28 Fuxing Road,

country: China

institute: Institute of Basic Medicine, Chinese PLA General Hospita

description: Gene expression in SW480 cells_Stably transfected with LRP16 treated with ETO for 3 hours 2#

hyb_protocol: 1.5 ug 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 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°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 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Colon cancer cell SW 480, transfected with LRP16, treated with 50 μM etoposide for 3 hours, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) 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.

extract_protocol: Total RNA of colon cancer cells stably transfected with vector control and LRP16 treated with or without etoposide (50 mM) for the indicated periods was isolated and purified using RNeasy Kit (Qiagen, Hilden, Germany). Integrity of RNA was assessed by using an Agilent BioAnalyser 2100 (Agilent Technologies).

treatment_protocol: SW 480 cells were cultured with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum, and cells were treated with etoposide for the indicated periods

value: Colon

tag: gender

value: Male


description: Gene expression in SW480 cells_Stably transfected with LRP16 treated with ETO for 3 hours 1#

source_name: Colon cancer cell SW 480, transfected with LRP16, treated with 50 μM etoposide for 3 hours, replicate 1


title: B-ALL-33, 6h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-33, 6h.

value: childhood acute lymphoblastic leukemia (ALL)


description: Gene expression in SW480 cells_Stably transfected with LRP16 treated with ETO for 3 hours 3#

source_name: Colon cancer cell SW 480, transfected with LRP16, treated with 50 μM etoposide for 3 hours, replicate 3


title: B-ALL-32, 24h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-32, 24h.


title: B-ALL-32, 6h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-32, 6h.


title: B-ALL-37, 24h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-37, 24h.


title: T-ALL-25, 0h

description: Expression profile of lymphoblasts from childhood ALL patient: T-ALL-25, 0h.


title: T-ALL-25, 24h

description: Expression profile of lymphoblasts from childhood ALL patient: T-ALL-25, 24h.


description: Gene expression in SW480 cells_Stably transfected with LRP16 treated with ETO for 1 hour 1#

source_name: Colon cancer cell SW 480, transfected with LRP16, treated with 50 μM etoposide for 1 hour, replicate 1


description: Gene expression in SW480 cells_Stably transfected with LRP16 untreated2#

source_name: Colon cancer cell SW 480, transfected with LRP16, untreated with etoposide, replicate 2


description: Gene expression in SW480 cells_Stably transfected with pc3.1 untreated 3#

source_name: Colon cancer cell SW 480, transfected with pc3.1, untreated with etoposide, replicate 3


description: Gene expression in SW480 cells_Stably transfected with LRP16 treated with ETO for 1 hour 2#

source_name: Colon cancer cell SW 480, transfected with LRP16, treated with 50 μM etoposide for 1 hour, replicate 2


description: Gene expression in SW480 cells_Stably transfected with pc3.1 treated with ETO for 3 hours 1#

source_name: Colon cancer cell SW 480, transfected with pc3.1, treated with 50 μM etoposide for 3 hours, replicate 1


title: B-ALL-37, 6h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-37, 6h.


description: Gene expression in SW480 cells_Stably transfected with pc3.1 treated with ETO for 3 hours 3#

source_name: Colon cancer cell SW 480, transfected with pc3.1, treated with 50 μM etoposide for 3 hours, replicate 3


title: B-ALL-37, 0h

description: Expression profile of lymphoblasts from childhood ALL patient: B-ALL-37, 0h.


description: Gene expression in SW480 cells_Stably transfected with pc3.1 treated with ETO for 1 hour 1#

source_name: Colon cancer cell SW 480, transfected with pc3.1, treated with 50 μM etoposide for 1 hour, replicate 1


description: Gene expression in SW480 cells_Stably transfected with LRP16 treated with ETO for 1 hour 3#

source_name: Colon cancer cell SW 480, transfected with LRP16, treated with 50 μM etoposide for 1 hour, replicate 3


description: Gene expression in SW480 cells_Stably transfected with LRP16 untreated3#

source_name: Colon cancer cell SW 480, transfected with LRP16, untreated with etoposide, replicate 3


description: Gene expression in SW480 cells_Stably transfected with pc3.1 treated with ETO for 3 hours 2#

source_name: Colon cancer cell SW 480, transfected with pc3.1, treated with 50 μM etoposide for 3 hours, replicate 2


description: Gene expression in SW480 cells_Stably transfected with LRP16 untreated1#

source_name: Colon cancer cell SW 480, transfected with LRP16, untreated with etoposide, replicate 1


description: Gene expression in SW480 cells_Stably transfected with pc3.1 treated with ETO for 1 hour 3#

source_name: Colon cancer cell SW 480, transfected with pc3.1, treated with 50 μM etoposide for 1 hour, replicate 3


description: Gene expression in SW480 cells_Stably transfected with pc3.1 treated with ETO for 1 hour 2#

source_name: Colon cancer cell SW 480, transfected with pc3.1, treated with 50 μM etoposide for 1 hour, replicate 2


description: Gene expression in SW480 cells_Stably transfected with pc3.1 untreated1#

source_name: Colon cancer cell SW 480, transfected with pc3.1, untreated with etoposide, replicate 1


description: Gene expression in SW480 cells_Stably transfected with pc3.1 untreated 2#

source_name: Colon cancer cell SW 480, transfected with pc3.1, untreated with etoposide, replicate 2