title: HOP-62_Passage 4 xenograft_R4

description:
HOP-62 P04 T4
Gene expression data from HOP-62 Passage 4 xenograft.

hyb_protocol: Samples were hybridized according to the "Affymetrix Technical Manual" (www.expressionanalysis.com).

scan_protocol: Microarray images were captured using a GeneChip® 3000 Scanner.

data_processing: Affymetrix Expression Console v1.3.

source_name: HOP-62, passage 4 xenograft

label_protocol: The RNA samples were submitted to Expression Analysis, Inc. (Durham, NC) for microarray analysis using the GeneChip® Human U133 Plus 2.0 Array (Affymetrix, Santa Clara, CA). Samples were labeled according to the "Affymetrix Technical Manual" (www.expressionanalysis.com).

growth_protocol: All cell lines were obtained from the Division of Cancer Treatment and Diagnosis Tumor Repository (DTP, FNLCR, Frederick, MD) or American Type Culture Collection (ATCC) (Manassas, Va). In addition, the identities of all cell lines used in this study were confirmed using Identifiler® STR genotyping (Applied Biosystems). All mice used in the study were obtained from the Animal Production Program (FNLCR, Frederick, MD). Tumor cells for inoculation were derived from the 4th in vitro passage from cryopreserved cell stocks. Cells (1 x 10^7 cells/0.1 ml/inoculation) were inoculated subcutaneously into mice (n=10 or more mice depending on the tumor cell line). For comparative purposes, 2-3 samples of in vitro cultivated cells at passage 4 post-cryopreservation were also prepared for microarray analysis (P0). When tumors at P1, P4 and P10 reached approximately 500 mg (10x10 mm), 5 tumors were harvested, cut into small pieces and flash frozen in liquid nitrogen using pre-chilled tubes. Samples were transferred to a -70°C freezer for holding prior to processing. Serial tumor passage was achieved by harvesting donor tumor material (n=2 to 5 donors) at each passage, mincing the tumors (2x2 mm fragments), pooling the samples and inoculating the next recipients subcutaneously using tumor implant trocars. Athymic nude mice (nu/nu NCr) served as the primary host for most xenograft studies. In several instances (particularly with human leukemias and lymphomas) it was difficult to establish and passage tumors in nu/nu NCr mice. In these instances, SCID.NCr or NOD.SCID/NCr mice were assessed for suitability. In general, female mice were used as they are less aggressive, easily group-housed and routinely used in xenograft experiments. Male mice were used for prostate tumors (PC-3, PC-3/M). Finally, in those instances where hormone effects on tumor growth are important (e.g., estradiol-dependent breast), mice were supplemented with estradiol.

extract_protocol: Total RNA was isolated using RNeasy (Qiagen).

value: adenocarcinoma lung


title: Uterine epithelial cells isolated from Stat3 flox control mice on day 4 of pregnancy

status: Public on Jul 01 2013

type: RNA

city: urbana

first: Sandeep

last: Pawar

state: Illinois

address: apt 6

department: Molecular and Integrative Physiology

country: USA

institute: University of Illinois

description: Control epithelial RNA

hyb_protocol: The Affymetrix Alternative Protocol for Eukaryotic Target Hybridization manual P/N 702232 Revision 2 Appendices B and C was utilized for hybridization, washing, and staining.  A cocktail was prepared with 15 micrograms of aRNA, adding biotinylated, fragmented hybridization controls: four prokaryotic antisense RNAs and one synthetic oligonucleotide.  Following a 16-hour hybridization to an Affymetrix GeneChip 3’ Expression Mouse Genome 430A 2.0 Array at 45°C and 60 rpm in a GeneChip model 640 oven, the chip was washed, and stained first with streptavidin-conjugated phycoerythrin dye (Invitrogen Corporation, Carlsbad, CA).  The stain was enhanced with biotinylated goat anti-streptavidin antibody (Vector Laboratories, Burlingame, CA), and  counterstained with additional conjugated phycoerythrin utilizing a GeneChip Fluidics Station model 450 and the GeneChip Command Console (AGCC) Fluidics Control software version 1.0.

scan_protocol: The chip was scanned with a GeneChip Scanner model 3000 7G Plus.  Raw fluorescence signals for pixels within each probe feature in the image (DAT) file were converted to a single feature fluorescence value utilizing the Cell Analysis algorithm incorporated in the AGCC Scan Control version 1.0 to generate a fluorescence intensity (CEL) file.  The quality of the image file was evaluated visually before further processing.

data_processing: The CEL files in each experiment were analyzed with Affymetrix Expression Console version 1.1 utilizing the MAS5 algorithm, selecting the scaling parameter for all probe sets, and an arbitrary target value of 150.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Mouse uterine epithelial cells

label_protocol: Microarrays were processed by the W. M. Keck Center for Comparative and Functional Genomics in the Roy J. Carver Biotechnology Center at the University of Illinois at Urbana-Champaign.  Labeled antisense RNA was prepared utilizing the GeneChip 3' IVT Express Kit Labeling and Control Reagents kit (Affymetrix, Inc., Santa Clara, CA), according to the manufacturer’s manual P/N 702646 Revision 1.  Briefly, 100 nanograms of total RNA was spiked with four prokaryotic polyadenylated sense RNA controls, primed with a T7-(dT) oligonucleotide containing a T7 promoter sequence, and reverse transcribed to synthesize first-strand DNA.  A double-stranded DNA template was then synthesized with DNA polymerase along with RNase H to degrade RNA.  The resulting cDNA was in vitro transcribed with the addition of a biotinylated ribonucleotide analog, and amplified at 40°C for 14 hours.  The resulting biotin-labeled antisense RNA was purified with magnetic beads, quantified, and fragmented to produce lengths of less than 200 nucleotides.

growth_protocol: Uteri were removed from Day 4 or Day 5 pregnant mice. With the aid of a dissecting microscope, each uterine horn was cut transversely into two equal segments. The tissues were then incubated in 10 ml of a solution of 0.5% bovine pancreatic trypsin (Cooper Biomedical, Malvern, PA) in Ca- and Mg-free PBS, pH 7.4 Tissues were first incubated at 4 C for 1 h and then at 37 C for 40 min. After incubation, the uterine tissue was squeezed with forceps dissociating the epithelium from the uterine pieces. The epithelial fragments in the supernatant were collected with a pipette; this procedure was repeated three or four times. The epithelial fragments were collected by centrifugation at 100 X g for 5 min. The resulting cell pellet was subjected to RNA isolation protocol.

extract_protocol: Total RNA was extracted from human endometrial stromal cells using the Qiagen RNAeasy total RNA isolation kit according to the manufacturer's instructions.

treatment_protocol: The uterine epithelial cells isolated from the uteri of mice were directly used for RNA extraction, they were not subjected to any form of treatment.

tag: time

value: day 4 pregnancy

tag: cell type

value: Mouse uterine epithelial cells

tag: genotype

value: control


title: HOP-62_Passage 10 xenograft_R1

city: Frederick

first: Luke

middle: Hunter

last: Stockwin

state: MD

address: Ft. Detrick

department: DTP

institute: NCI Frederick

description:
HOP-62 P10 T1
Gene expression data from HOP-62 Passage 10 xenograft.

label: Biotin

organism: Homo sapiens

source_name: HOP-62, passage 10 xenograft

tag: originating cell line

tag: tumor type

tag: in vivo passage


title: MLO_sham_24hr_rep3

city: Richland

first: Katrina

middle: M

last: Waters

state: WA

address: 902 Battelle Blvd; MSIN J4-18

department: Biological Sciences Division

institute: Pacific Northwest National Laboratory

description: Gene expression data from sham MLO cells

hyb_protocol: Biotin-labeled cRNA (15 µg) was fragmented to a size range between 50-200 bases for array hybridization.  After hybridization, the arrays were washed and stained with streptavidin-phycoerythrin.

scan_protocol: The arrays were scanned at a resolution of 2.5 microns using an Affymetrix GeneChip Scanner 3000.

data_processing: Raw intensity data were quantile normalized by Robust Multi-Array Analysis (RMA) summarization and probes were subject to quality control to measure the efficiency of transcription, integrity of hybridization, and consistency of qualitative calls (GeneSpring version 11.5.).

source_name: MLO-Y4 osteocyte-like cells

label_protocol: Complementary DNA was synthesized from 1 µg of total RNA in the presence of an oligo-dT primer containing a T7 RNA polymerase promoter, and an in vitro transcription reaction was performed in the presence of a mixture of biotin-labeled ribonucleotides to produce biotinylated cRNA from the cDNA template, according to manufacturer’s protocols (Affymetrix One-Cycle Target Labeling Kit).

growth_protocol: MLO-Y4 osteocyte-like cells, courtesy of Dr. Lynda Bonewald (University of Missouri—Kansas City) were maintained in normal growth media (α-MEM [Invitrogen, Grand Island, NY] with 2.5% CS [Hyclone, Logan, UT], 2.5% FBS [Lonza, Walkersville, MD], 1% Penicillin/Streptomycin) throughout all portions of the experiment.  Cells were seeded 48 hours prior to fluid flow on 75 x 38 x 1 mm glass slides coated with Type I Collagen (BD Biosciences, Bedford, MA) at 300 μg/ml.  Cell seeding density was 1.35 x 10^4 cells/cm2 so that upon flow exposure, cells were roughly 60% confluent and interconnected by dendritic processes.

extract_protocol: Total RNA was collected using the RNeasy Kit (Qiagen, Valencia, CA).

treatment_protocol: Samples were subjected to 2 hours of sinusoidally oscillating fluid flow with a peak shear stress of 10 dyn/cm^2 at a frequency of 1 Hz.  Glass slides were assembled within parallel plate flow chambers in sterile conditions and placed within an incubator maintained at 37˚C and 5% CO2.  A rigid-walled inlet tube connected to a Hamilton glass syringe was actuated by a servo pneumatic loading device (EnduraTec, Eden Prairie, MN).  Paired controls were maintained in identical, static chambers.  After two hours treatment, flowed and static cells were either collected immediately (0 hour time point) or glass slides were transferred to culture dishes and incubated for 2, 8, or 24 hours post-flow in 10 ml fresh media.

tag: strain

value: mixed C57B1/6 x BALB/c x DBA2

value: MLO-Y4 osteocyte-like cells

tag: treatment

value: sham


title: MLO_flow_24hr_rep1

description: Gene expression data from MLO cells exposed to fluid flow sheer stress

value: flow


title: MLO_flow_24hr_rep2


title: HOP-62_Passage 4 xenograft_R3

description:
HOP-62 P04 T3
Gene expression data from HOP-62 Passage 4 xenograft.


title: MLO_flow_24hr_rep3


title: HOP-62_Passage 4 xenograft_R5

description:
HOP-62 P04 T5
Gene expression data from HOP-62 Passage 4 xenograft.


title: HOP-62_Passage 10 xenograft_R3

description:
HOP-62 P10 T3
Gene expression data from HOP-62 Passage 10 xenograft.


title: b36

city: St. Lucia

first: Maarten

last: Kooiker

state: QLD

address: 306 Carmody Road

country: Australia

institute: CSIRO Plant Industry

description: Gene expression data from flag leaves at anthesis

hyb_protocol: Hybridization were performed by the microarray service at the Australian Genome Research Facility (Melbourne, Australia)

scan_protocol: Data acquisition of Affymetrix wheat GeneChips were performed by the microarray service at the Australian Genome Research Facility (Melbourne, Australia)

data_processing: The Affymetrix GeneChip data were normalized using GeneChip robust multiarray average (GC-RMA), developed by Wu et al. (2004), using the Affymetrix package within Bioconductor, running within the R statistical programming environment (http://www.r-project.org/).

organism: Triticum aestivum

source_name: Flag Leaf at anthesis

label_protocol: RNA-quality check, cRNA preparation, and labelling were performed by the microarray service at the Australian Genome Research Facility (Melbourne, Australia)

growth_protocol: Plants were grown under 16 hour day/8 hour night conditions at 90%/60% relative humidity and 20 ºC / 16 ºC. At anthesis the flag leaves were harvested and total RNA was extracted.

extract_protocol: Samples were ground in liquid Nitrogen using mortar and pestle. RNA was isolated using Plant RNA Reagent from Invitrogen according to the manufacturer’s intructions. DNA was removed as described by Xue and Loveridge (2004) and the isolated RNA was purified using the RNeasy Plant mini-kit column (Qiagen), following the directions of the kit

treatment_protocol: Bobwhite control plants were compared with transgenic lines that overexpress the transcription factor TaMYB13

tag: tissue

value: flag leaf at anthesis

tag: genotype/variation

value: b36 transgenic line that overexpress TaMYB13


title: MLO_sham_24hr_rep2


title: b2

value: b2 transgenic line that overexpress TaMYB13


title: Skeletal Muscle_FlashFrozen_Suspected Mito Disease_myoclonic epilepsy

city: Philadelphia

first: Marni

middle: J

last: Falk

state: PA

address: 3615 Civic Center Blvd

department: Pediatrics/ Human Genetics

institute: CHOP

hyb_protocol: Following fragmentation, 4.6 ug of aRNA were hybridized for 16 hr at 45C on Affymetrix Human Exon 1.0ST cartridge arrays. The arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, 7G.

data_processing:
Probe-level data in CEL files was normalized by RMA method implemented in the affy package of Bioconductor to get gene-level expression measurements. Alternative CDF file of the HuEx ST1.0 platform was used as library.
probe group file: huex_chop_alt1.cdf
meta-probeset file: annotation.csv

source_name: Skeletal muscle

label_protocol: Biotinylated amplified RNA (aRNA) was prepared from 200 ng total RNA using the standard protocol of the Ambion MessageAmp Premier Kit.

growth_protocol: Residual skeletal muscle biopsy specimens were obtained from Clinical Pathology at The Children’s Hospital of Philadelphia or University of California San Diego following completion of all clinical diagnostic assays with the express participant consent of all living participants and/or families, or from decedents following IRB approval following completion of all clinical diagnostic assays with the express participant consent of all living participants and/or families, or from decedents following IRB approval.

extract_protocol: Total RNA was extracted from liquid nitrogen flash-frozen or isopentane frozen skeletal muscle tissues by Norgen RNA/DNA/Protein purification kit (Norgen Biotek Corporation, Ontario, Canada), with slight modification. 10-20 mg of frozen muscle tissue was transferred into a plastic tube with tight fitting pestle and 300 ul of kit lysis buffer, homogenized, and mixed by vortexing after 600 ul of RNAse free water was added.  Lysates were incubated with intermittent vortexing at 550C x15 min with 20 ul Proteinase K, centrifuged x10 min, supernatants were mixed with equal volumes of 70% alcohol, and RNA extraction was completed per published protocol (Norgen protocol booklet step 1.B.h).  RNA was analyzed by NanoDrop 1000 spectrophotometer and Agilent 2100 Bioanalyzer in the Nucleic Acid and Protein Core Facility at The Children’s Hospital of Philadelphia, with RNA integrity number (RIN) > 8 acceptable (maximum RIN is 10) for microarray and real-time qPCR analyses.

value: Skeletal muscle

tag: respiratory chain complex deficiency

value: No Respiratory Chain Complex Deficiency

tag: gender

value: F

tag: age (years)

tag: informatic analysis group

value: Excluded - poor quality


title: a20

value: a20 transgenic line that overexpress TaMYB13


title: BW45

value: bob white


title: Skeletal Muscle_FlashFrozen_Suspected Mito Disease_myopathy

value: M


title: HOP-62_Passage 1 xenograft_R5

description:
HOP-62 P01 T5
Gene expression data from HOP-62 Passage 1 xenograft.

source_name: HOP-62, passage 1 xenograft

value: adenocarcinoma lung


title: HOP-62_Passage 4 xenograft_R2

description:
HOP-62 P04 T2
Gene expression data from HOP-62 Passage 4 xenograft.


title: BW44


title: MLO_sham_24hr_rep1


title: HOP-62_Passage 4 xenograft_R1

description:
HOP-62 P04 T1
Gene expression data from HOP-62 Passage 4 xenograft.


title: HOP-62_Passage 1 xenograft_R3

description:
HOP-62 P01 T3
Gene expression data from HOP-62 Passage 1 xenograft.


title: MLO_flow_8hr_rep3


title: Skeletal Muscle_FlashFrozen_Definite Mito Disease_Complex I_Developmental Delay

value: Complex I


title: MLO_flow_8hr_rep2


title: Skeletal Muscle_FlashFrozen_Definite Mito Disease_Complex I+IV_Myopathy

value: Complex I and IV

value: Mito Disease Group


title: HOP-62_Passage 1 xenograft_R1

description:
HOP-62 P01 T1
Gene expression data from HOP-62 Passage 1 xenograft.


title: HOP-62_Passage 1 xenograft_R4

description:
HOP-62 P01 T4
Gene expression data from HOP-62 Passage 1 xenograft.


title: MLO_sham_8hr_rep2

value: mixed C57B1/6 x BALB/c x DBA2

value: MLO-Y4 osteocyte-like cells


title: Skeletal Muscle_FlashFrozen_Healthy Control B

value: Control Group


title: Skeletal Muscle_FlashFrozen_Healthy Control D


title: MLO_sham_8hr_rep3

value: sham


title: Skeletal Muscle_FlashFrozen_Healthy Control A


title: MLO_flow_8hr_rep1

value: flow


title: HOP-62_originating cell line_R1

description:
HOP-62 P0 T1
Gene expression data from HOP-62 originating cell line.

source_name: HOP-62, originating cell line


title: Skeletal Muscle_FlashFrozen_Definite Mito Disease_Complex I+IV_Leigh Syndrome

value: Complexes I and IV


title: Skeletal Muscle_FlashFrozen_Healthy Control C

value: Skeletal muscle


title: HOP-62_originating cell line_R3

description:
HOP-62 P0 T3
Gene expression data from HOP-62 originating cell line.


title: Skeletal Muscle_FlashFrozen_Definite Mito Disease_Complex IV_MELAS-like

value: Complex IV


title: HL-60(TB)_Passage 10 xenograft_R5

description:
HL-60(TB) P10 T5
Gene expression data from HL-60(TB) Passage 10 xenograft.

source_name: HL-60(TB), passage 10 xenograft

value: promyelocytic leukemia


title: HOP-62_originating cell line_R2

description:
HOP-62 P0 T2
Gene expression data from HOP-62 originating cell line.


title: BW43

value: flag leaf at anthesis


title: Freeze Resistance (FR); Cold Acclimated Rep 1

city: Brookings

first: Xijin

last: Ge

state: SD

address: SDSU box 2220C

department: Mathematics and Statistics

institute: South Dakota State University

description: Gene expression of FR crown tissue after  cold acclimation

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: Eight samples were analyzed by R/Bioconductor http://www.bioconductor.org). Specifically, Robust Multi-Array Average with help of probe sequence information, which is known as gcRMA was used for microarray background correction and normalization.

source_name: Crown tissue

label_protocol: Affymetrix standard protocol

growth_protocol: FR and FS plants (4 plants/pot) were grown in the green house at 22-28 oC with 14 h photoperiod. Soil water was maintained at 0.3 – 0.44 kg H2O kg-1 and plants transferred to 4 oC cold room for cold acclimation after reaching the fourth leaf stage as described by Kenefick DG et al. in BMC Plant Biol 2002, 2:8.

extract_protocol: Total RNA isolation with Modified GSCN/CsCl Chirgwin method. Total RNA isolation Procedure (based on Chirgwin, 1979 and described in Han Kai MS thesis, South Dakota State University, 1997) Prior to submission for use in microarry analyses, RNA stored in formamide were reprecipitated with standard NaOAc/ethanol procedure, resuspended in depc-treated H2O. All samples were treated with DNase to remove any possible contaminating genomic DNA using the protocol as described for the Qiagen RNeasy kit.

treatment_protocol: Cold acclimation after reaching the fourth leaf stage as described by Kenefick DG et al. in BMC Plant Biol 2002, 2:8.


title: Freeze Susceptible (FS); Cold Acclimated Rep 1

description: Gene expression of FS crown tissue after cold acclimation


title: Freeze Resistance (FR); Cold Acclimated Rep 2


title: Freeze Susceptible (FS); Ctrl Rep 2

description: Gene expression of FS crown tissue before cold acclimation


title: Freeze Susceptible (FS); Ctrl Rep 1


title: MLO_flow_2hr_rep1

description: Gene expression data from MLO cells exposed to fluid flow sheer stress


title: Skeletal Muscle_FlashFrozen_Definite Mito Disease_Complex IV_myopathy

value: F


title: HL-60(TB)_Passage 10 xenograft_R4

description:
HL-60(TB) P10 T4
Gene expression data from HL-60(TB) Passage 10 xenograft.


title: MLO_flow_2hr_rep3


title: MLO_sham_2hr_rep3

description: Gene expression data from sham MLO cells


title: MLO_sham_8hr_rep1


title: Skeletal Muscle_FlashFrozen_Definite Mito Disease_Complex IV_myopathy+CoQ10 deficiency

value: Excluded - poor quality


title: MLO_sham_2hr_rep2


title: MLO_flow_2hr_rep2


title: Freeze Susceptible (FS); Cold Acclimated Rep 2


title: MLO_flow_0hr_rep3


title: Skeletal Muscle_FlashFrozen_Suspected Mito Disease_immune disease

value: No Respiratory Chain Complex Deficiency


title: Skeletal Muscle_FlashFrozen_Definite Mito Disease_Complex IV_autism+regression

value: M


title: HL-60(TB)_Passage 10 xenograft_R3

description:
HL-60(TB) P10 T3
Gene expression data from HL-60(TB) Passage 10 xenograft.


title: Skeletal Muscle_FlashFrozen_Definite Mito Disease_RRM2B

value: Complex IV; 93% mtDNA depletion in muscle


title: HL-60(TB)_Passage 10 xenograft_R2

description:
HL-60(TB) P10 T2
Gene expression data from HL-60(TB) Passage 10 xenograft.


title: MLO_sham_2hr_rep1


title: HL-60(TB)_Passage 4 xenograft_R3

description:
HL-60(TB) P04 T3
Gene expression data from HL-60(TB) Passage 4 xenograft.

source_name: HL-60(TB), passage 4 xenograft


title: Skeletal Muscle_FlashFrozen_Non-Mito Disease_dysautonomia


title: MLO_flow_0hr_rep2


title: Freeze Resistance (FR); Ctrl Rep 1

description: Gene expression of FR crown tissue before cold acclimation


title: Skeletal Muscle_Isopentane_Suspected Mito Disease_leukoencephalopathy


title: MLO_flow_0hr_rep1


title: HL-60(TB)_Passage 10 xenograft_R1

description:
HL-60(TB) P10 T1
Gene expression data from HL-60(TB) Passage 10 xenograft.


title: HL-60(TB)_Passage 4 xenograft_R2

description:
HL-60(TB) P04 T2
Gene expression data from HL-60(TB) Passage 4 xenograft.


title: HL-60(TB)_Passage 4 xenograft_R1

description:
HL-60(TB) P04 T1
Gene expression data from HL-60(TB) Passage 4 xenograft.


title: HL-60(TB)_Passage 1 xenograft_R4

description:
HL-60(TB) P01 T4
Gene expression data from HL-60(TB) Passage 1 xenograft.

source_name: HL-60(TB), passage 1 xenograft


title: HL-60(TB)_Passage 1 xenograft_R5

description:
HL-60(TB) P01 T5
Gene expression data from HL-60(TB) Passage 1 xenograft.


title: MLO_sham_0hr_rep3


title: Meg01-4-14-1

city: Detroit

first: Yubin

state: MI

address: 110 East Warren Ave.

institute: Karmanos Cancer Institute

hyb_protocol: Whole human genome oligonucleotide microarrays (Agilent Technologies, catalog no. G4112A) were hybridized using 0.75 ug of Alexa 555 labeled aRNA and 0.75 ug of Alexa 647 labeled aRNA. Agilent's SureHyb hybridization chambers were used in a hybridization oven and rotation rack for 17 h at 60 °C. After hybridization, the slides were washed per Agilent's SSPE wash protocol.

scan_protocol: Slides were scanned using an Agilent dual laser scanner with extended dynamic range (XDR) at 5 micron resolution.

data_processing: Tiff images were analyzed with Agilent's feature extraction software (v9.5.3.1) using protocol GE2_v5_95_Feb07. Linear and LOWESS normalization were performed.

source_name: Meg01 neg control cells

label_protocol: Alexa555 and Alexa 647 labeled aRNA was prepared from 500ng total RNA using the Epicentre TargetAMP 1-Round Aminoallyl-aRNA Amplification Kit 101 according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Alexa Dye (Invitrogen/Molecular Probes, Eugen OR) incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The parental Meg01 cells and the shRNA stable clones were cultured in RPMI 1640 with 10% fetal bovine serum (Hyclone, Logan, UT) and 2 mM L-glutamine plus 100 U/ml penicillin and 100 µg/ml streptomycin, in a 37 °C humidified atmosphere containing 5% CO2/95% air.

extract_protocol: Total RNAs were extracted from the CMK shRNA stable clones using TRIzol reagent (Invitrogen, Carlsbad, CA). The quality and quantify of the extracted total RNAs were determined on a NanoDrop analyzer.

treatment_protocol: Knockdown of GATA1 in the Meg01 cells was performed using shRNA lentivirus. Two clones designated Meg01-5-13 and Meg01-4-14 were used. A pool of cells from a negative control infection (lentivirus expressing a shRNA with limited homology to any known human genes) was used as the negative control (designated GATA1-neg).

tag: transfection

value: negative control

tag: cell line

tag: clone

source_name: Meg01-4-14 GATA1 shRNA infected cells

value: GATA1 shRNA


title: Skeletal Muscle_Isopentane_PDHc Deficiency_subject 2


title: Meg01-4-14-2


title: MLO_sham_0hr_rep2

value: mixed C57B1/6 x BALB/c x DBA2

tag: time


title: Skeletal muscle_FlashFrozen_Definite Mito Disease_POLG

value: Not measured; 87% mtDNA depletion in muscle

value: Mito Disease Group


title: HL-60(TB)_Passage 1 xenograft_R3

description:
HL-60(TB) P01 T3
Gene expression data from HL-60(TB) Passage 1 xenograft.


title: Skeletal Muscle (Psoas)_Autopsy_Definite Mito Disease_MPV17

value: Complex IV; 70% mtDNA depletion in liver


title: Skeletal Muscle_Isopentane_PC Deficiency

value: Control Group


title: HL-60(TB)_Passage 1 xenograft_R2

description:
HL-60(TB) P01 T2
Gene expression data from HL-60(TB) Passage 1 xenograft.


title: ViRas HFD+butyrate rep.2

city: München

first: Olivia

last: Prazeres da Costa

state: Bavaria

address: Trogerstr. 30

department: Medical Microbiology, Immunology and Hygiene

country: Germany

institute: Technische Universität München

hyb_protocol: Hyb wash and stain kit (Affymetrix article no.: 900720)

scan_protocol: Affymetrix scanner 3000 7g.

data_processing: Affymetrix Expression Console (v.1.1.): RMA normalization.

source_name: K-Ras mutant_high fat diet+butyrate

label_protocol: Total RNA (200 ng) was amplified and labeled following the Affymetrix Whole Transcript Terminal Labeling Kit (Affymetrix article no.: 901524) and WT Expression Kit (Applied Biosystems/Life Technologies article no.: 4411974).

growth_protocol: Mouse facility, diet after 5 weeks of age, sacrificed after 22 weeks of diet

extract_protocol: RNeasy Mini Kit (Quiagen)

treatment_protocol: normal diet or high fat diet or high fat diet + butyrate

tag: strain background

value: mixed

value: K-Ras mutant

tag: age

value: diet after 5 wks of age, sacrificed after 22 wks of diet

tag: diet

value: high fat diet+butyrate

value: duodenum


title: MLO_sham_0hr_rep1

tag: cell type

value: MLO-Y4 osteocyte-like cells

value: sham


title: Meg01-5-13-2

source_name: Meg01-5-13 GATA1 shRNA infected cells


title: Skeletal Muscle_FlashFrozen_PC Deficiency

value: Skeletal muscle

value: No Respiratory Chain Complex Deficiency


title: HL-60(TB)_Passage 1 xenograft_R1

description:
HL-60(TB) P01 T1
Gene expression data from HL-60(TB) Passage 1 xenograft.

tag: originating cell line

tag: tumor type

value: promyelocytic leukemia

tag: in vivo passage


title: Meg01-5-13-1

value: negative control


title: HL-60(TB)_originating cell line_R5

description:
HL-60(TB) P0 T5
Gene expression data from HL-60(TB) originating cell line.

source_name: HL-60(TB), originating cell line


title: ViRas HFD+butyrate rep.1

tag: tissue


title: Skeletal Muscle_Isopentane_PDHc Deficiency_subject 1

value: F


title: CO HFD+butyrate

source_name: wild-type_high fat diet+butyrate

tag: genotype/variation

value: wild-type


title: Undifferentiated keratinocytes#1

city: Chapel Hill

first: Julian

last: Rozenberg

state: NC

address: Brinkhous-Bullitt Bldg., CB#7525

department: Pathology and Lab Medicine

institute: University Of North Carolina

description: Gene expression from Undifferentiated keratinocytes#1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Expression console using Affymetrix default RMA analysis settings.

source_name: FVB P1 mouse

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Primary mouse keratinocytes either undifferentiated or Ca differentiated for 2 days.

extract_protocol: Total RNA was performed according to the Qiagen instructions.

treatment_protocol: After 1 day in culture cells where treated with 5-AZA or A/CEBP expression was induced.

value: Cultured primary mouse keratinocytes

tag: strain

value: FVB

value: Undifferentiated keratinocytes


title: Differentiated keratinocytes #4

description: Gene expression from differentiated keratinocytes #4

value: differentiated keratinocytes


title: ViRas HFD+butyrate rep.3

value: mixed


title: Bone marrow maj367Nsp

type: genomic

city: Badalona

first: Mar

last: Mallo

address: Ctra de Can Ruti, s/n, camí de les escoles. Edifici IMPPC

country: Spain

institute: Josep Carreras Leukaemia Research Institute

description: Hybridized to 250K_Nsp

hyb_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned according to the manufacturer's instructions.

scan_protocol: CEL files, generated by AGCC Viewer. CNCHP and LOHCHP, generated by Genotyping Console (all provided by Affymetrix)

data_processing:
CNCHP (from 6.0 arrays) provide data for copy number and LOH analysis. LOCHP provides data for LOH analysis in case of 250K_Nsp arrays.
Genotyping Console; algorithm-name = CN4

molecule: genomic DNA

source_name: Bone marrow

label_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

extract_protocol: Genomic DNA was extracted from whole bone marrow, whole peripheral blood or CD3 lymphocytes isolated from peripheral blood prior to treatment with lenalidomide, at the individual centers participating in the study. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

value: Bone marrow


title: Bone marrow 35Mac816

description: Hybridized to 250K_Nsp


title: Undifferentiated keratinocytes#2

description: Gene expression from Undifferentiated keratinocytes#2


title: Skeletal Muscle_FlashFrozen_PDHc Deficiency_subject 1

tag: respiratory chain complex deficiency

tag: gender

value: Control Group


title: HL-60(TB)_originating cell line_R2

description:
HL-60(TB) P0 T2
Gene expression data from HL-60(TB) originating cell line.


title: ViRas ND rep.3

source_name: K-Ras mutant_normal diet

value: K-Ras mutant

value: diet after 5 wks of age, sacrificed after 22 wks of diet

value: normal diet


title: Skeletal Muscle_FlashFrozen_Definite Mito Disease_epilepsy

value: Complexes II and III

tag: age (years)

tag: informatic analysis group

value: Mito Disease Group


title: HL-60(TB)_originating cell line_R3

description:
HL-60(TB) P0 T3
Gene expression data from HL-60(TB) originating cell line.


title: Bone marrow 35Mac527

description: Hybridized to 250K_Nsp


title: Differentiated keratinocytes #3

description: Gene expression from differentiated keratinocytes #3


title: Differentiated keratinocytes #2

description: Gene expression from differentiated keratinocytes #2


title: HL-60(TB)_originating cell line_R4

description:
HL-60(TB) P0 T4
Gene expression data from HL-60(TB) originating cell line.


title: ViRas ND rep.2

value: duodenum


title: ViRas ND rep.1


title: Skeletal Muscle_Isopentane_Definite Mito Disease_m.12264C>T

value: Skeletal muscle

value: Complexes I and III

value: M


title: Skeletal Muscle_Isopentane_Definite Mito Disease_m5537_5537insT

value: Complex IV

value: F


title: Differentiated keratinocytes #1

description: Gene expression from differentiated keratinocytes #1

value: Cultured primary mouse keratinocytes

value: FVB


title: Freeze Resistance (FR); Ctrl Rep 2

description: Gene expression of FR crown tissue before cold acclimation

tag: genotype


title: HL-60(TB)_originating cell line_R1

description:
HL-60(TB) P0 T1
Gene expression data from HL-60(TB) originating cell line.

value: promyelocytic leukemia


title: A-C/EBP expressing differentiated keratinocytes #1

description: Gene expression from A-C/EBP expressing differentiated keratinocytes #2


title: A-C/EBP expressing differentiated keratinocytes #2


title: Skeletal Muscle_FlashFrozen_Definite Mito Disease_m.12264C>T


title: Bone marrow 35mac469

description: Hybridized to 250K_Nsp


title: HeLa-Luc_Passage 10 xenograft_R4

description:
HeLa-Luc P10 T4
Gene expression data from HeLa-Luc Passage 10 xenograft.

source_name: HeLa-Luc, passage 10 xenograft

value: HeLa-Luc

value: adenocarcinoma cervical


title: Bone marrow 35mac475

description: Hybridized to 250K_Nsp

value: Bone marrow


title: Skeletal Muscle_Isopentane_Non-Mito Disease_MEF2C deletion

source_name: Skeletal muscle

value: No Respiratory Chain Complex Deficiency

value: Control Group


title: HeLa-Luc_Passage 10 xenograft_R5

description:
HeLa-Luc P10 T5
Gene expression data from HeLa-Luc Passage 10 xenograft.


title: HeLa-Luc_Passage 10 xenograft_R3

description:
HeLa-Luc P10 T3
Gene expression data from HeLa-Luc Passage 10 xenograft.


title: HeLa-Luc_Passage 10 xenograft_R2

description:
HeLa-Luc P10 T2
Gene expression data from HeLa-Luc Passage 10 xenograft.


title: Differentiated keratinocytes treated with 5-AZA #2

description: Gene expression from differentiated keratinocytes treated with 5-AZA #2

value: differentiated keratinocytes

tag: treatment


title: wt100NO3-1

city: Freising

first: Ulrich

last: Guldener

address: Maximus-von-Imhof-Forum 3

department: Chair of genome-oriented bioinformatics

description: This sample is of Fusrium fujikuroi wild-type IMI58289 grown on 120 mM NO3 (100%) medium. It is the first of two biological replicates for this condition in this experiment.

hyb_protocol: Hybridization of microarrays was done at Arrows Biomedical (Münster, Germany) and Roche-Nimblegen (Iceland) following NimbleGen's standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning of microarrays was done at Arrows Biomedical (Münster, Germany) and Roche-Nimblegen (Iceland) following NimbleGen's standard operating protocol. See www.nimblegen.com.

data_processing: Pre-processing steps including background correction, normalization and summarization of probe intensities were performed by employing the oligo R package (Carvalho 2010) and its implementation of the RMA algorithm (Irizarry et al., 2003).

organism: Fusarium fujikuroi

source_name: wild-type IMI58289, mycelium, growth medium: 120 mM NO3 (100%)

label_protocol: Labeling was done at Arrows Biomedical (Münster, Germany) and Roche-Nimblegen (Iceland) following NimbleGen's standard operating protocol. See www.nimblegen.com.

growth_protocol: Starting cultures of Fusarium fujikuroi IMI58289 were grown for 72 hours in 100 mL of Darken media (Darken et al., 1959) in 300 mL Erlenmeyer flasks on a rotary shaker at 180 rpm at 28°C. 100 mL of ICI medium (Geissman et al., 1966) in 300 mL Erlenmeyer flasks was inoculated with 500 µL of the starting culture and incubated on a rotary shaker at 180 rpm at 28°C for 72 hours. The mycelium was harvested via Miracloth in a Büchner funnel, frozen in liquid nitrogen and lyophilized before RNA extraction.

extract_protocol: Total RNA was extracted using the RNAgents total RNA isolation kit (Promega GmbH, Mannheim, Germany), and DNA was removed using DNase I (Roche Diagnostics GmbH, Mannheim, Germany). RNA quality and concentration were measured with a Bioanalyzer (Agilent Technologies Deutschland, Böblingen, Germany).

treatment_protocol: The nitrogen composition of the medium for the different cultures varied (6 mM Gln, 60 mM Gln, 6mM NO3, 120 nM NO3).

value: wild-type

value: mycelium

tag: growth medium


title: wt5NO3-3

description: This sample is of Fusrium fujikuroi wild-type IMI58289 grown on 6 mM NO3 (5%) medium. It is the third of three biological replicates for this condition in this experiment.

source_name: wild-type IMI58289, mycelium, growth medium: 6 mM NO3 (5%)


title: HeLa-Luc_Passage 4 xenograft_R5

description:
HeLa-Luc P04 T5
Gene expression data from HeLa-Luc Passage 4 xenograft.

source_name: HeLa-Luc, passage 4 xenograft


title: wt100NO3-2

description: This sample is of Fusrium fujikuroi wild-type IMI58289 grown on 120 mM NO3 (100%) medium. It is the second of two biological replicates for this condition in this experiment.


title: Differentiated keratinocytes treated with 5-AZA #1

description: Gene expression from differentiated keratinocytes treated with 5-AZA #1


title: HeLa-Luc_Passage 10 xenograft_R1

description:
HeLa-Luc P10 T1
Gene expression data from HeLa-Luc Passage 10 xenograft.


title: PN56_Klf4CN_sample_2

city: Pittsburgh

first: Stephen

middle: Alan Kenneth

last: Harvey

address: 203 Lothrop St

department: Ophthalmology

institute: University of Pittsburgh School of Medicine

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The raw data obtained from microarray analysis were processed using Affymetrix GeneChip Operating Software (GCOS v 1.4) using software defaults, to assess the presence or absence of each transcript target sequence, its expression level, and then to make all relevant pair-wise statistical comparisons among samples. Expression levels were scaled to a target value of 500 using the software default (2% trimmed mean). Prior to scaling, E16.5 lenses were 311 ± 27 and 329 ± 8 for WT and Klf4CN samples respectively (mean ± SD, n = 3). The equivalent signals for the PN56 lenses were 95 and 84 (mean 90) for WT samples; and 127 and 142 (mean 135) for Klf4CN samples. After scaling, rhree redundant panels measuring GAPDH showed coefficients of variation of 7.3% ± 1.0% and 7.5% ± 2.4% for E16.5 and PN56 samples, respectively.

source_name: Whole lens of mouse

label_protocol: Total RNAs were amplified and labeled using a 3' IVT Express Kit (Affymetrix Inc., Santa Clara, CA)

extract_protocol: Total RNA was isolated from dissected lenses using the appropriate RNeasy kit (Qiagen, Valencia, CA)

treatment_protocol: Three independent preparations each used lens pooled from five embryos (E16.5) and two independent preparations each used lens pooled from 3 young adult mice (PN56).

value: Postnatal day 56

value: lens

value: Klf4-conditional null


title: HeLa-Luc_Passage 4 xenograft_R4

description:
HeLa-Luc P04 T4
Gene expression data from HeLa-Luc Passage 4 xenograft.


title: PN56_WT_sample_2

value: wild type


title: wt5NO3-2

description: This sample is of Fusrium fujikuroi wild-type IMI58289 grown on 6 mM NO3 (5%) medium. It is the second of three biological replicates for this condition in this experiment.


title: PN56_Klf4CN_sample_1


title: wt100GLN-6

description: This sample is of Fusrium fujikuroi wild-type IMI58289 grown on 60 mM Gln (100%) medium. It is the fourth of four biological replicates for this condition in this experiment.

source_name: wild-type IMI58289, mycelium, growth medium: 60 mM Gln (100%)


title: PN56_WT_sample_1


title: wt5NO3-1

description: This sample is of Fusrium fujikuroi wild-type IMI58289 grown on 6 mM NO3 (5%) medium. It is the first of three biological replicates for this condition in this experiment.


title: HeLa-Luc_Passage 4 xenograft_R3

description:
HeLa-Luc P04 T3
Gene expression data from HeLa-Luc Passage 4 xenograft.


title: E16.5_Klf4CN_sample_2

value: Embryonic day 16.5


title: E16.5_Klf4CN_sample_3


title: HeLa-Luc_Passage 4 xenograft_R1

description:
HeLa-Luc P04 T1
Gene expression data from HeLa-Luc Passage 4 xenograft.


title: wt100GLN-5

description: This sample is of Fusrium fujikuroi wild-type IMI58289 grown on 60 mM Gln (100%) medium. It is the third of four biological replicates for this condition in this experiment.


title: HeLa-Luc_Passage 4 xenograft_R2

description:
HeLa-Luc P04 T2
Gene expression data from HeLa-Luc Passage 4 xenograft.


title: wt100GLN-4

description: This sample is of Fusrium fujikuroi wild-type IMI58289 grown on 60 mM Gln (100%) medium. It is the second of four biological replicates and the second of two technical replicates used for this condition in this experiment.


title: E16.5_Klf4CN_sample_1


title: wt100GLN-3

description: This sample is of Fusrium fujikuroi wild-type IMI58289 grown on 60 mM Gln (100%) medium. It is the first of four biological replicates and the second of two technical replicates used for this condition in this experiment.


title: HeLa-Luc_Passage 1 xenograft_R5

description:
HeLa-Luc P01 T5
Gene expression data from HeLa-Luc Passage 1 xenograft.

source_name: HeLa-Luc, passage 1 xenograft


title: HeLa-Luc_Passage 1 xenograft_R3

description:
HeLa-Luc P01 T3
Gene expression data from HeLa-Luc Passage 1 xenograft.


title: HeLa-Luc_Passage 1 xenograft_R2

description:
HeLa-Luc P01 T2
Gene expression data from HeLa-Luc Passage 1 xenograft.


title: E16.5_WT_sample_3


title: wt10GLN-4

description: This sample is of Fusrium fujikuroi wild-type IMI58289 grown on 6 mM Gln (10%) medium. It is the second of two biological replicates and the second of two technical replicates used for this condition in this experiment.

source_name: wild-type IMI58289, mycelium, growth medium: 6 mM Gln (10%)


title: HeLa-Luc_Passage 1 xenograft_R1

description:
HeLa-Luc P01 T1
Gene expression data from HeLa-Luc Passage 1 xenograft.


title: HeLa-Luc_Passage 1 xenograft_R4

description:
HeLa-Luc P01 T4
Gene expression data from HeLa-Luc Passage 1 xenograft.


title: E16.5_WT_sample_1


title: E13.5 FL LSK HES1-GFP positive replicate 1

city: Paris

first: Camille

last: Lobry

address: 16 rue de la Grange aux Belles

department: IRSL Inserm U944 / CNRS UMR7212

country: France

institute: Inserm

hyb_protocol: 3.75 mcg of biotin-labeled cDNA were hybridized for 16 hrs onto the GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix)

scan_protocol: Affymetrix 7G GeneArray scanner

data_processing: Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was performed by the RMA algorithm using Genespring GX program. No further adjustments were made to the data in the table.

source_name: Lineage negative, cKit+, Sca1+ foetal liver cells from E13.5 embryo

label_protocol: 5 ng total RNA was amplified by Nugen Ovation RNA amplification system V2 and the resulting cDNA biotin-labeled using the FL-Ovation™ cDNA Biotin Module V2

extract_protocol: Qiagen RNEasy Plus mini Kit  was used to extract total cellular RNA according to the manufacturer's protocol, and the RNA was amplified and converted into cDNA using the Ovation Amplification v2 and Biotin cDNA Biotin systems

value: female

value: Hes1 GFP/WT


title: E16.5_WT_sample_2


title: E13.5 FL LSK HES1-GFP negative replicate 3

value: Lineage negative, cKit+, Sca1+ foetal liver cells from E13.5 embryo


title: wt10GLN-3

description: This sample is of Fusrium fujikuroi wild-type IMI58289 grown on 6 mM Gln (10%) medium. It is the first of two biological replicates and the second of two technical replicates used for this condition in this experiment.


title: HCT-15_Passage 10 xenograft_R5

description:
HCT-15 P10 T5
Gene expression data from HCT-15 Passage 10 xenograft.

source_name: HCT-15, passage 10 xenograft

value: adenocarcinoma colon


title: HCT-15_Passage 10 xenograft_R4

description:
HCT-15 P10 T4
Gene expression data from HCT-15 Passage 10 xenograft.


title: HeLa-Luc_originating cell line_R1

description:
HeLa-Luc P0 T1
Gene expression data from HeLa-Luc originating cell line.

source_name: HeLa-Luc, originating cell line

value: HeLa-Luc


title: E13.5 FL LSK HES1-GFP negative replicate 2


title: adult Myeloerythroid Progenitors (MP) ICN2 positive replicate 2

description: 1 weeks after last polyIC injection

source_name: Lineage negative, cKit+, Sca1- bone marrow cells from 6 weeks old mouse

treatment_protocol: 6 weeks old Mx1-cre+ and Rosa-lsl-ICN2 Mx1-cre+ littermate were injected 3 times with polyIC (20mcg/g of body weight) every other day. Mice were sacrificed and analyzed 1 week after last injection

value: male

value: 6 weeks

value: Rosa-lsl-ICN2 Mx1-cre+


title: HCT-15_Passage 10 xenograft_R2

description:
HCT-15 P10 T2
Gene expression data from HCT-15 Passage 10 xenograft.


title: HCT-15_Passage 10 xenograft_R3

description:
HCT-15 P10 T3
Gene expression data from HCT-15 Passage 10 xenograft.


title: adult Myeloerythroid Progenitors (MP) ICN2 positive replicate 3

description: 1 weeks after last polyIC injection

value: Lineage negative, cKit+, Sca1- bone marrow cells from 6 weeks old mouse


title: E13.5 FL LSK HES1-GFP negative replicate 1


title: adult Myeloerythroid Progenitors (MP) ICN2 positive replicate 1

description: 1 weeks after last polyIC injection


title: adult Myeloerythroid Progenitors (MP) ICN2 negative replicate 3

description: 1 weeks after last polyIC injection


title: HCT-15_Passage 10 xenograft_R1

description:
HCT-15 P10 T1
Gene expression data from HCT-15 Passage 10 xenograft.


title: HeLa-Luc_originating cell line_R2

description:
HeLa-Luc P0 T2
Gene expression data from HeLa-Luc originating cell line.

value: adenocarcinoma cervical


title: Bone marrow mac2128

description: Hybridized to 6.0 Array

data_processing:
CNCHP (from 6.0 arrays) provide data for copy number and LOH analysis.
Genotyping Console; algorithm-name = CN5

value: Bone marrow


title: HCT-15_Passage 4 xenograft_R5

description:
HCT-15 P04 T5
Gene expression data from HCT-15 Passage 4 xenograft.

source_name: HCT-15, passage 4 xenograft


title: CD3 lymphocytes from MD137H

description: Hybridized to 6.0 Array

source_name: CD3 lymphocytes isolated from peripheral blood


title: Brain Replicate 2

city: Tsukuba

first: Rieko

last: Ikeda

state: Ibaraki

address: 3-1-1 Koyadai

department: BioResource Center

country: Japan

institute: RIKEN

description: Biological replicate 2 of 2.

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Slides were scanned after washing on the Agilent Scanner G2505B. Grid used for scan was 013205_D_20050216,  and protocol  GE2_105_Dec08 was used.

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction and Lowess normalization. We used only test data and analyzed as single channel data.

source_name: Brain

label_protocol: 500ng of total RNA were labeled with either Cy3 or Cy5 dye with a low-input  linear amplification kit (Agilent Technologies).

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

value: adult

value: Brain


title: HCT-15_Passage 4 xenograft_R3

description:
HCT-15 P04 T3
Gene expression data from HCT-15 Passage 4 xenograft.


title: adult Myeloerythroid Progenitors (MP) HES1-GFP positive replicate 3


title: adult Myeloerythroid Progenitors (MP) ICN2 negative replicate 2

description: 1 weeks after last polyIC injection


title: Bone marrow 04MO

description: Hybridized to 6.0 Array

source_name: Bone marrow


title: Thymus Replicate 2

description: Biological replicate 2 of 2.

source_name: Thymus

value: Thymus


title: HCT-15_Passage 4 xenograft_R4

description:
HCT-15 P04 T4
Gene expression data from HCT-15 Passage 4 xenograft.


title: Bone marrow MD137H

description: Hybridized to 6.0 Array


title: adult Myeloerythroid Progenitors (MP) ICN2 negative replicate 1

description: 1 weeks after last polyIC injection


title: adult Myeloerythroid Progenitors (MP) HES1-GFP positive replicate 2


title: Brain Replicate 1

description: Biological replicate 1 of 2.


title: Bone marrow 03MO

description: Hybridized to 6.0 Array


title: Bone marrow MD79

description: Hybridized to 6.0 Array


title: Bone marrow 07MO

description: Hybridized to 6.0 Array


title: HCT-15_Passage 4 xenograft_R2

description:
HCT-15 P04 T2
Gene expression data from HCT-15 Passage 4 xenograft.


title: CD3 lymphocytes from 04MO

description: Hybridized to 6.0 Array

value: CD3 lymphocytes isolated from peripheral blood


title: adult Myeloerythroid Progenitors (MP) HES1-GFP positive replicate 1


title: Bone marrow 22MO

description: Hybridized to 6.0 Array


title: CD3 lymphocytes MD79

description: Hybridized to 6.0 Array


title: CD3 lymphocytes from 22MO

description: Hybridized to 6.0 Array


title: CD3 lymphocytes from 03MO

description: Hybridized to 6.0 Array


title: CD3 lymphocytes from 20038

description: Hybridized to 6.0 Array


title: Thymus Replicate 1

description: Biological replicate 1 of 2.


title: adult Myeloerythroid Progenitors (MP) HES1-GFP negative replicate 3


title: HCT-15_Passage 1 xenograft_R5

description:
HCT-15 P01 T5
Gene expression data from HCT-15 Passage 1 xenograft.

source_name: HCT-15, passage 1 xenograft


title: adult Myeloerythroid Progenitors (MP) HES1-GFP negative replicate 2


title: HCT-15_Passage 1 xenograft_R4

description:
HCT-15 P01 T4
Gene expression data from HCT-15 Passage 1 xenograft.


title: adult Myeloerythroid Progenitors (MP) HES1-GFP negative replicate 1


title: PDAC Xenograft serum 3

city: Bochum

first: Stephan

middle: A

last: Hahn

address: Universitaetsstrasse 150

department: MGO

institute: Ruhr-University Bochum

description: miRNA expression

hyb_protocol: The hybridization mixture [10X GE blocking agent (4.5 ul), 2X Hi-RPM hybridization buffer (22.5ul)] along with labeled miRNA sample was heated for 5 min at 100 °C and immediately cooled to 0 °C. Each 45 mL sample was hybridized onto a microarray at 55 °C for 21 h. Slides were washed 5 min in GE wash buffer 1 at RT and again for 5 min in GE wash buffer 2 at 37 °C, followed by an acetonitrile wash for 10 sec at RT to dry the slides completely.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B ) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%, No XDR).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol miRNA_107_Sep09 and Grid:029297_D_F_20101116) to obtain background subtracted and spatially detrended Processed Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: serum from NMRI-nu/nu mice carrying a human tumor

label_protocol: miRNA labeling was performed as described in Agilent miRNA microarray protocol version 2.0 using Agilent miRNA labeling kit. 100 ng of total RNA was dephosphorylated with calf intestine alkaline phosphatase for 30 min at 37°C. Denaturation was performed by adding DMSO and incubating at 100°C for 6 min and immediately transferred to ice water bath. Ligation was performed with pCp-Cy3 at 16 °C for 2 h. The labeled samples were dried completely in a vaccum concentrator and resuspended in 18 ul of nuclease free water.

extract_protocol: RNA from serum was isolated using the mirVana PARIS RNA Isolation Kit (Ambion). In all instances RNA isolation was performed according to the manufacturer’s instructions using 300 ml serum.

tag: sample type

value: serum

tag: host strain

value: NMRI-nu/nu

tag: disease state

value: xenograft tumor derived from human primary pancreatic ductal adenocarcinomas


title: Bone marrow 27MO

description: Hybridized to 6.0 Array

tag: cell type


title: HCT-15_Passage 4 xenograft_R1

description:
HCT-15 P04 T1
Gene expression data from HCT-15 Passage 4 xenograft.

tag: originating cell line


title: PDAC Xenograft serum 6

description: miRNA expression


title: PDAC Xenograft serum 2

description: miRNA expression


title: HCT-15_Passage 1 xenograft_R2

description:
HCT-15 P01 T2
Gene expression data from HCT-15 Passage 1 xenograft.

tag: tumor type


title: Bone marrow 25MO

description: Hybridized to 6.0 Array


title: adult LSK HES1-GFP positive replicate 3

source_name: Lineage negative, cKit+, Sca1+ bone marrow cells from 6 weeks old mouse

tag: age

value: Hes1 GFP/WT


title: Bone marrow 20038

description: Hybridized to 6.0 Array


title: HCT-15_Passage 1 xenograft_R1

description:
HCT-15 P01 T1
Gene expression data from HCT-15 Passage 1 xenograft.

tag: in vivo passage


title: Bone marrow 24MO

description: Hybridized to 6.0 Array


title: PDAC Xenograft serum 1

description: miRNA expression


title: adult LSK HES1-GFP positive replicate 2

value: Lineage negative, cKit+, Sca1+ bone marrow cells from 6 weeks old mouse


title: Bone marrow 02MO

description: Hybridized to 6.0 Array


title: adult LSK HES1-GFP positive replicate 1

value: female


title: CD3 lymphocytes from 01MO

description: Hybridized to 6.0 Array


title: Control Serum 5

description: miRNA expression

source_name: serum from NMRI-nu/nu mice, cancer free

value: control


title: HCT-15_originating cell line_R3

description:
HCT-15 P0 T3
Gene expression data from HCT-15 originating cell line.

source_name: HCT-15, originating cell line

value: adenocarcinoma colon


title: HCT-15_originating cell line_R2

description:
HCT-15 P0 T2
Gene expression data from HCT-15 originating cell line.


title: Bone marrow 30MO

description: Hybridized to 6.0 Array


title: Bone marrow 01MO

description: Hybridized to 6.0 Array


title: Control Serum 4

description: miRNA expression


title: HCT-15_Passage 1 xenograft_R3

description:
HCT-15 P01 T3
Gene expression data from HCT-15 Passage 1 xenograft.


title: Control Serum 6

description: miRNA expression


title: Control Serum 3

description: miRNA expression


title: adult LSK HES1-GFP negative replicate 2

value: male

value: 6 weeks


title: adult LSK HES1-GFP negative replicate 1


title: Bone marrow 26MO

description: Hybridized to 6.0 Array


title: Bone marrow 29MO

description: Hybridized to 6.0 Array


title: adult LSK HES1-GFP negative replicate 3


title: Bone marrow 28MO

description: Hybridized to 6.0 Array


title: PDAC Xenograft serum 5

description: miRNA expression


title: HCT-116_Passage 10 xenograft_R3

description:
HCT-116 P10 T3
Gene expression data from HCT-116 Passage 10 xenograft.

source_name: HCT-116, passage 10 xenograft

value: carcinoma colon


title: Dex + E2 (2h) r1

city: Bethesda

first: Songjoon

last: Baek

address: 41 Library Drive

department: CCR

institute: NCI / NIH

description: GR-ChIP in cells treated with Dex + E2 - replicate 1

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Affymetrix Mouse Genome 430 2.0 array data in CEL files were preprocessed using Affymetrix Expression Console software with ‘RMA’ and its quantile normalization method. Mean expression values from biological duplicates were calculated.

source_name: 7438 cells

label_protocol: Samples were processed, labeled, hybridized, and scanned at the Frederick National Laboratory for Cancer Research Microarray Core using standard procedures.

growth_protocol: For maintenance cells were cultured in DMEM supplemented with 10% calf serum, sodium pyruvate, non-essential amino acids, and 5 ug/ml tetracycline to repress expression of the tet-regulated fusion proteins.

extract_protocol: Cells were harvested in trizol and then extracted with chloroform.  Samples were then further purified using the Qiagen RNA purification kit.

treatment_protocol: Cells were plated for experiments in DMEM growth medium supplemented with 10% charcoal-dextran serum with tetracyline 48 hours prior to conducting the experiment.  Twenty-four hours before hormone treatment, cells were washed three times with phosphate-buffered saline and fresh DMEM with 10% charcoal-dextran serum (no tetracyline) was added to the cells to induce expression of GFP-GR and Ch-ER.  Cells were untreated or induced with 100nM dexamethasone, 100nM estradiol, or 100nM dexamethasone plus 100nM estradiol for 2 hours.

value: mouse mammary cells (express GFP-GR and Cherry-ER under a tet regulated promoter)

value: Dexamethasone + Estradiol for 2 hours

tag: cell line

value: 7438 cells


title: HCT-116_Passage 10 xenograft_R4

description:
HCT-116 P10 T4
Gene expression data from HCT-116 Passage 10 xenograft.

data_processing: Affymetrix Expression Console v1.3.


title: Dex + E2 (2h) r2

description: Cells treated with Dex + E2 - replicate 2


title: HCT-15_originating cell line_R1

description:
HCT-15 P0 T1
Gene expression data from HCT-15 originating cell line.


title: HCT-116_Passage 10 xenograft_R5

description:
HCT-116 P10 T5
Gene expression data from HCT-116 Passage 10 xenograft.


title: Control Serum 2

description: miRNA expression


title: Control Serum 1

description: miRNA expression


title: PDAC Xenograft serum 4

description: miRNA expression


title: E2 (2h) r2

description: GR-ChIP in cells treated with E2 - replicate 2

value: Estradiol for 2 hours


title: HCT-116_Passage 10 xenograft_R1

description:
HCT-116 P10 T1
Gene expression data from HCT-116 Passage 10 xenograft.


title: HCT-116_Passage 10 xenograft_R2

description:
HCT-116 P10 T2
Gene expression data from HCT-116 Passage 10 xenograft.


title: CD3 lymphocytes from 19MO

description: Hybridized to 6.0 Array


title: Dex (2h) r2

description: Cells treated with Dex - replicate 2

value: Dexamethasone for 2 hours


title: E2 (2h) r1

description: Cells treated with E2 - replicate 1


title: HCT-116_Passage 4 xenograft_R5

description:
HCT-116 P04 T5
Gene expression data from HCT-116 Passage 4 xenograft.

source_name: HCT-116, passage 4 xenograft


title: ES_10

city: Kyoto

first: Kazutoshi

last: Takahashi

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: Center for iPS Cell Research and Application

institute: Kyoto University

description: Human embryonic stem cell line 10

hyb_protocol: Manufature's protocol

scan_protocol: Slides were scanned on the G2565CA Microarray Scanner System (Agilent).

data_processing: GeneSpring GX. Signals were normalized to percentile.

source_name: Human embryonic stem cell line 10

label_protocol: Manufature's protocol

growth_protocol: DMEM containing 10% fetal bovine serum (by day 7) or Primate ESC medium (ReproCELL) supplemented with 4 ng/ml bFGF (from day 8 to 28) at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA was prepared using the miRNeasy Purification kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Human somatic cells were transduced with OCT3/4, SOX2, KLF4 and c-MYC using retrovirus. From day 7 to 28, we collected TRA-1-60 positive cells as nascent reprogrammed cells.

value: Undifferentiated human embryonic stem cells


title: Dex (2h) r1

description: Cells treated with Dex - replicate 1


title: HCT-116_Passage 4 xenograft_R4

description:
HCT-116 P04 T4
Gene expression data from HCT-116 Passage 4 xenograft.

hyb_protocol: Samples were hybridized according to the "Affymetrix Technical Manual" (www.expressionanalysis.com).

label_protocol: The RNA samples were submitted to Expression Analysis, Inc. (Durham, NC) for microarray analysis using the GeneChip® Human U133 Plus 2.0 Array (Affymetrix, Santa Clara, CA). Samples were labeled according to the "Affymetrix Technical Manual" (www.expressionanalysis.com).

extract_protocol: Total RNA was isolated using RNeasy (Qiagen).


title: ES_8

description: Human embryonic stem cell line 8

source_name: Human embryonic stem cell line 8


title: ES_9

description: Human embryonic stem cell line 9

source_name: Human embryonic stem cell line 9


title: HCT-116_Passage 4 xenograft_R3

description:
HCT-116 P04 T3
Gene expression data from HCT-116 Passage 4 xenograft.


title: Bone marrow 21MO

description: Hybridized to 6.0 Array

value: Bone marrow


title: CD3 lymphocytes from 21MO

description: Hybridized to 6.0 Array

value: CD3 lymphocytes isolated from peripheral blood


title: CD3 lymphocytes from 16MO

description: Hybridized to 6.0 Array


title: Untreated r2

description: Untreated cells - replicate 2

value: untreated


title: ES_6

description: Human embryonic stem cell line 6

source_name: Human embryonic stem cell line 6


title: HCT-116_Passage 4 xenograft_R2

description:
HCT-116 P04 T2
Gene expression data from HCT-116 Passage 4 xenograft.


title: ES_7

description: Human embryonic stem cell line 7

source_name: Human embryonic stem cell line 7


title: astrocytes, biological rep2

city: Barcelona

first: Joan Marc

last: Servitja

state: Catalonia

address: Rosselló, 153

institute: IDIBAPS

description: Gene expression data from astrocytes

hyb_protocol: Following fragmentation, cRNA were hybridized, washed and stained according to the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned according to the standard Affymetrix protocol (Affymetrix Genechip Command Console program 3.0.0.1214, scanner GCS 3000-7G)

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

source_name: astrocytes

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol through two cycles of cDNA synthesis (50 ng starting total RNA).

growth_protocol: Neuronal tissue was minced and incubated in Ca2+-free Krebs–Ringer buffer containing 0.025% trypsin for 15 min at 37°C. Cells were then dissociated by gentle trituration through a fire-polished Pasteur pipette in the presence of 0.52 mg/ml soybean trypsin inhibitor and 170 units/ml DNase I. The cell suspension was then filtered through a 40-um nylon mesh. Cells were collected by centrifugation at 500 g and plated into 24-well plates in basal medium Eagle supplemented with 10% fetal calf serum, 33 mM glucose, 2 mM glutamine, and antibiotics (50 IU/ml penicillin and 50 g/ml streptomycin).

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

treatment_protocol: Astrocytes were incubated at 37°C in a humidified atmosphere of 5% CO2/95% air. After 24 h, the medium was changed to remove nonadhered cells and then changed every 3–4 days. Regarding neuronal cultures, after 2 h of incubation at 37°C in a humidified atmosphere of 5% CO2/95% air, the medium was changed for basal medium Eagle enriched with 1% fetal calf serum, 19.4 mM glucose, 4 mM glutamine, 20 nM progesterone, 100 nM putrescine, 5 g/ml transferrin, 10 g/ml insulin, 30 nM Na2SeO3, and antibiotics. All assays were carried out on cells grown for 7–8 days in vitro.

tag: tissue

value: cerebral cortical astrocytes

tag: strain

value: C57BL6 mice

value: newborn


title: ES_5

description: Human embryonic stem cell line 5

source_name: Human embryonic stem cell line 5


title: HCT-116_Passage 1 xenograft_R5

city: Frederick

first: Luke

address: Ft. Detrick

description:
HCT-116 P01 T5
Gene expression data from HCT-116 Passage 1 xenograft.

scan_protocol: Microarray images were captured using a GeneChip® 3000 Scanner.

source_name: HCT-116, passage 1 xenograft


title: Untreated r1

description: Untreated cells - replicate 1


title: ES_4

description: Human embryonic stem cell line 4

source_name: Human embryonic stem cell line 4


title: HCT-116_Passage 4 xenograft_R1

description:
HCT-116 P04 T1
Gene expression data from HCT-116 Passage 4 xenograft.


title: ES_3

description: Human embryonic stem cell line 3

source_name: Human embryonic stem cell line 3


title: astrocytes, biological rep1

description: Gene expression data from astrocytes


title: Bone marrow 16MO

description: Hybridized to 6.0 Array

source_name: Bone marrow


title: neurons, biological rep2

description: Gene expression data from neurons

source_name: neurons

value: cerebral cortical neurons

value: 16-day-old fetal embryo


title: ES_2

description: Human embryonic stem cell line 2

source_name: Human embryonic stem cell line 2


title: HCT-116_Passage 1 xenograft_R4

description:
HCT-116 P01 T4
Gene expression data from HCT-116 Passage 1 xenograft.


title: Bone marrow 19MO

description: Hybridized to 6.0 Array


title: neurons, biological rep1

description: Gene expression data from neurons


title: HCT-116_Passage 1 xenograft_R2

description:
HCT-116 P01 T2
Gene expression data from HCT-116 Passage 1 xenograft.


title: CD3 lymphocytes from 14MO

description: Hybridized to 6.0 Array

source_name: CD3 lymphocytes isolated from peripheral blood


title: ES_1

description: Human embryonic stem cell line 1

source_name: Human embryonic stem cell line 1


title: HCT-116_Passage 1 xenograft_R3

description:
HCT-116 P01 T3
Gene expression data from HCT-116 Passage 1 xenograft.


title: HCT-116_Passage 1 xenograft_R1

description:
HCT-116 P01 T1
Gene expression data from HCT-116 Passage 1 xenograft.


title: young islets at T4, biological rep2

description: Gene expression data from young islets at T4 at 11mM

source_name: young mice islets after 4h at 11mM

growth_protocol: Mouse pancreatic islets were isolated from wild-type C57/Bl6J male mice. Islets were allowed to recover for 1 day in RPMI (Invitrogen) containing 11mM glucose supplemented with 10% FCS and penicillin/streptomycin (Invitrogen) at 37°C, 5% CO2.

treatment_protocol: Islets were cultured in supplemented RPMI medium for two days at different glucose concentrations (3 mM, 5.5 mM, 11mM, and 16 mM) before RNA extraction

value: pancreatic islets


title: Bone marrow 15MO

description: Hybridized to 6.0 Array


title: HDF_9

description: Human dermal fibroblast line 9

source_name: Human dermal fibroblast line 9

value: Human dermal fibroblasts


title: young islets at T4, biological rep1


title: Bone marrow 14MO

description: Hybridized to 6.0 Array


title: CD3 lymphocytes from 13MO

description: Hybridized to 6.0 Array


title: HDF_8

description: Human dermal fibroblast line 8

source_name: Human dermal fibroblast line 8


title: young islets at T1, biological rep2

description: Gene expression data from young islets at T1 at 11mM

source_name: young mice islets after 1h at 11mM


title: HCT-116_originating cell line_R3

description:
HCT-116 P0 T3
Gene expression data from HCT-116 originating cell line.

source_name: HCT-116, originating cell line

value: carcinoma colon


title: HCT-116_originating cell line_R2

description:
HCT-116 P0 T2
Gene expression data from HCT-116 originating cell line.


title: young islets at T1, biological rep1


title: Bone marrow 18MO

description: Hybridized to 6.0 Array


title: young islets at T0, biological rep2

description: Gene expression data from young islets at T0 after ON 3mM

source_name: young mice islets at T0 after an ON at 3mM


title: Bone marrow 13MO

description: Hybridized to 6.0 Array


title: young islets at T0, biological rep1


title: HDF_6

description: Human dermal fibroblast line 6

source_name: Human dermal fibroblast line 6


title: HCT-116_originating cell line_R1

description:
HCT-116 P0 T1
Gene expression data from HCT-116 originating cell line.


title: HDF_5

description: Human dermal fibroblast line 5

source_name: Human dermal fibroblast line 5


title: HDF_7

description: Human dermal fibroblast line 7

source_name: Human dermal fibroblast line 7


title: fresh young islets, biological rep2

description: Gene expression data from young islets

source_name: Fresh young mice islets


title: HCC-2998_Passage 10 xenograft_R4

description:
HCC-2998 P10 T4
Gene expression data from HCC-2998 Passage 10 xenograft.

source_name: HCC-2998, passage 10 xenograft


title: fresh young islets, biological rep1

description: Gene expression data from young islets


title: CD3 lymphocytes from 12MO

description: Hybridized to 6.0 Array


title: HDF_3

description: Human dermal fibroblast line 3

source_name: Human dermal fibroblast line 3


title: Bone marrow 12MO

description: Hybridized to 6.0 Array

source_name: Bone marrow


title: Peripheral blood 11MO

description: Hybridized to 6.0 Array

source_name: Peripheral blood

value: Peripheral blood


title: HDF_4

description: Human dermal fibroblast line 4

source_name: Human dermal fibroblast line 4


title: young islets at G16, biological rep2

description: Gene expression data from young islets at 16mM glucose

source_name: young mice islets cultured at 16mM of glucose


title: HCC-2998_Passage 10 xenograft_R5

description:
HCC-2998 P10 T5
Gene expression data from HCC-2998 Passage 10 xenograft.


title: HCC-2998_Passage 10 xenograft_R3

description:
HCC-2998 P10 T3
Gene expression data from HCC-2998 Passage 10 xenograft.


title: HDF_2

description: Human dermal fibroblast line 2

source_name: Human dermal fibroblast line 2


title: Bone marrow 10MO

description: Hybridized to 6.0 Array


title: HCC-2998_Passage 10 xenograft_R1

description:
HCC-2998 P10 T1
Gene expression data from HCC-2998 Passage 10 xenograft.


title: young islets at G16, biological rep1


title: HDF_1

description: Human dermal fibroblast line 1

source_name: Human dermal fibroblast line 1


title: HCC-2998_Passage 10 xenograft_R2

description:
HCC-2998 P10 T2
Gene expression data from HCC-2998 Passage 10 xenograft.


title: HCC-2998_Passage 4 xenograft_R5

description:
HCC-2998 P04 T5
Gene expression data from HCC-2998 Passage 4 xenograft.

source_name: HCC-2998, passage 4 xenograft


title: HDF_Day15_EGFP(-)_TRA(-)

description: Non transduced cells derived from human dermal fibroblast line on day 15 with GFP

source_name: Nascent reprogrammed cells with EGFP, day 15,

value: Nascent reprogrammed cells derived from human dermal fibroblasts


title: CD3 lymphocytes from 11MO

description: Hybridized to 6.0 Array

source_name: CD3 lymphocytes isolated from peripheral blood


title: young islets at G11, biological rep3

description: Gene expression data from young islets at 11mM glucose

source_name: young mice islets cultured at 11mM of glucose


title: HDF_Day15_EGFP(+)_TRA(-)

description: TRA-1-60(-) transduced cells derived from human dermal fibroblast line on day 15 with GFP


title: Bone marrow 09MO

description: Hybridized to 6.0 Array


title: HCC-2998_Passage 4 xenograft_R3

description:
HCC-2998 P04 T3
Gene expression data from HCC-2998 Passage 4 xenograft.


title: HDF_Day15_EGFP_TRA(+)

description: Nascent reprogrammed cells derived from human dermal fibroblast line on day 15 with GFP


title: HCC-2998_Passage 4 xenograft_R2

description:
HCC-2998 P04 T2
Gene expression data from HCC-2998 Passage 4 xenograft.


title: CD3 lymphocytes from SSLMO

description: Hybridized to 6.0 Array


title: HCC-2998_Passage 4 xenograft_R4

description:
HCC-2998 P04 T4
Gene expression data from HCC-2998 Passage 4 xenograft.


title: CD3 lymphocytes from 09MO

description: Hybridized to 6.0 Array


title: young islets at G11, biological rep4


title: young islets at G11, biological rep1


title: Bone marrow 08MO

description: Hybridized to 6.0 Array


title: HDF_Day11_EGFP(-)_TRA(-)

description: Non transduced cells derived from human dermal fibroblast line on day 11 with GFP

source_name: Nascent reprogrammed cells with EGFP, day 11,


title: HCC-2998_Passage 4 xenograft_R1

description:
HCC-2998 P04 T1
Gene expression data from HCC-2998 Passage 4 xenograft.


title: HDF_Day11_EGFP(+)_TRA(-)

description: TRA-1-60(-) transduced cells derived from human dermal fibroblast line on day 11 with GFP


title: CD3 lymphocytes from CGI AGF MO

description: Hybridized to 6.0 Array


title: young islets at G5, biological rep1

description: Gene expression data from young islets at 5.5mM glucose

source_name: young mice islets cultured at 5.5mM of glucose


title: Bone marrow SSLMO

description: Hybridized to 6.0 Array


title: HCC-2998_Passage 1 xenograft_R4

description:
HCC-2998 P01 T4
Gene expression data from HCC-2998 Passage 1 xenograft.

source_name: HCC-2998, passage 1 xenograft


title: CD3 lymphocytes from 15MO

description: Hybridized to 6.0 Array


title: Bone marrow CGI AGF MO

description: Hybridized to 6.0 Array


title: young islets at G3, biological rep2

description: Gene expression data from young islets at 3mM glucose

source_name: young mice islets cultured at 3mM of glucose


title: young islets at G5, biological rep2


title: young islets at G11, biological rep2


title: HDF_Day7_EGFP(+)_TRA(-)

description: TRA-1-60(-) transduced cells derived from human dermal fibroblast line on day 7 with GFP

source_name: Nascent reprogrammed cells with EGFP, day 7,


title: young islets at G3, biological rep1


title: HDF_Day7_EGFP_TRA(+)

description: Nascent reprogrammed cells derived from human dermal fibroblast line on day 7 with GFP


title: HDF_Day11_EGFP_TRA(+)

description: Nascent reprogrammed cells derived from human dermal fibroblast line on day 11 with GFP


title: fresh old islets, biological rep2

description: Gene expression data from fresh old islets

source_name: Fresh old mice islets


title: HDF_Day7_EGFP(-)_TRA(-)

description: Non transduced cells derived from human dermal fibroblast line on day 7 with GFP


title: HDF_D11(+)toD15(+)_3

description: Non-Reverted cells on day 15 derived from reprogrammed cells, replicate 3

source_name: Non-Reverted cells, day 15, sample 3


title: CD3 lymphocytes from 10CD3

description: Hybridized to 6.0 Array


title: HCC-2998_Passage 1 xenograft_R1

description:
HCC-2998 P01 T1
Gene expression data from HCC-2998 Passage 1 xenograft.


title: CD3 lymphocytes from 08MO

description: Hybridized to 6.0 Array


title: Bone marrow 6_35486

description: Hybridized to 6.0 Array

source_name: Bone marrow


title: HCC-2998_originating cell line_R3

description:
HCC-2998 P0 T3
Gene expression data from HCC-2998 originating cell line.

source_name: HCC-2998, originating cell line


title: HCC-2998_Passage 1 xenograft_R2

description:
HCC-2998 P01 T2
Gene expression data from HCC-2998 Passage 1 xenograft.


title: Bone marrow 3_35182_rehib

description: Hybridized to 6.0 Array


title: old islets at G11, biological rep2

description: Gene expression data from old islets at 11mM glucose

source_name: Old mice islets cultured at 11mM of glucose


title: HCC-2998_originating cell line_R2

description:
HCC-2998 P0 T2
Gene expression data from HCC-2998 originating cell line.


title: HDF_D11(+)toD15(+)_2

description: Non-Reverted cells on day 15 derived from reprogrammed cells, replicate 2

source_name: Non-Reverted cells, day 15, sample 2


title: HDF_D11(+)toD15(+)_1

description: Non-Reverted cells on day 15 derived from reprogrammed cells, replicate 1

source_name: Non-Reverted cells, day 15, sample 1


title: old islets at G11, biological rep1


title: old islets at G5, biological rep2

description: Gene expression data from old islets at 5.5mM glucose

source_name: Old mice islets cultured at 5.5mM of glucose


title: HDF_D11(+)toD15(-)_3

description: Reverted cells on day 15 derived from reprogrammed cells, replicate 3

source_name: Reverted cells, day 15, sample 3


title: Bone marrow 5_35086

description: Hybridized to 6.0 Array


title: Bone marrow 2_34957

description: Hybridized to 6.0 Array


title: fresh old islets, biological rep1


title: old islets at G5, biological rep1


title: GTL-16_Passage 10 xenograft_R5

description:
GTL-16 P10 T5
Gene expression data from GTL-16 Passage 10 xenograft.

source_name: GTL-16, passage 10 xenograft

value: adenocarcinoma gastric


title: CD3 lymphocytes from 4_34543

description: Hybridized to 6.0 Array

source_name: CD3 lymphocytes isolated from peripheral blood


title: Bone marrow 3_33490

description: Hybridized to 6.0 Array


title: HCC-2998_Passage 1 xenograft_R5

description:
HCC-2998 P01 T5
Gene expression data from HCC-2998 Passage 1 xenograft.


title: Bone marrow 4_34543

description: Hybridized to 6.0 Array


title: HDF_D11(+)toD15(-)_2

description: Reverted cells on day 15 derived from reprogrammed cells, replicate 2

source_name: Reverted cells, day 15, sample 2


title: CD3 lymphocytes from 5_35086

description: Hybridized to 6.0 Array


title: HDF_D11(+)toD15(-)_1

description: Reverted cells on day 15 derived from reprogrammed cells, replicate 1

source_name: Reverted cells, day 15, sample 1


title: HCC-2998_Passage 1 xenograft_R3

description:
HCC-2998 P01 T3
Gene expression data from HCC-2998 Passage 1 xenograft.


title: GTL-16_Passage 10 xenograft_R4

description:
GTL-16 P10 T4
Gene expression data from GTL-16 Passage 10 xenograft.


title: HCC-2998_originating cell line_R1

description:
HCC-2998 P0 T1
Gene expression data from HCC-2998 originating cell line.


title: old islets at G3, biological rep1

description: Gene expression data from old islets at 3mM glucose

source_name: Old mice islets cultured at 3mM of glucose


title: CD3 lymphocytes 6_32611

description: Hybridized to 6.0 Array


title: HDF_D11(+)toDay20(-)

description: Reverted cells derived on day 20from reprogrammed cells

source_name: Reverted cells, day 20, sample 1


title: HDF_Day28_TRA(+)_2

description: Nascent reprogrammed cells derived from human dermal fibroblast line on day 28, replicate 2

source_name: Nascent reprogrammed cells, day 28, sample 1


title: GTL-16_Passage 10 xenograft_R1

description:
GTL-16 P10 T1
Gene expression data from GTL-16 Passage 10 xenograft.


title: old islets at G3, biological rep2


title: GTL-16_Passage 10 xenograft_R2

description:
GTL-16 P10 T2
Gene expression data from GTL-16 Passage 10 xenograft.


title: ES cells wildtype W4 rep 1

city: Freiburg

first: Marc

middle: P.

last: Stemmler

address: Stuebeweg 51

department: Molecular Embryology

institute: Max-Planck Institute of Immunobiology and Epigenetics

data_processing: Data analysis was performed using the R/Bioconductor Limma software. Quality of the data set was controlled by the simpleaffy package and normalized by quantile normalization with the GCRMA alogrithm.

source_name: embryonic stem cells

label_protocol: standard Affymetrix protocol

growth_protocol: ES cells were grown on diluted EMFI plate prior to isolation in DMEM/15% FCS/10 U/ml Pen/Strep, 0.1 mM NEAA, 2 mM L-glutamin, 0.15 mM β-mercaptoethanol, 500 U Lif

extract_protocol: Trizol extraction followed by a Qiagen Rneasy Kit purification

tag: genotype/variation

value: wild type


title: GTL-16_Passage 4 xenograft_R5

last: Stockwin

institute: NCI Frederick

description:
GTL-16 P04 T5
Gene expression data from GTL-16 Passage 4 xenograft.

source_name: GTL-16, passage 4 xenograft


title: GTL-16_Passage 10 xenograft_R3

description:
GTL-16 P10 T3
Gene expression data from GTL-16 Passage 10 xenograft.


title: HDF_Day28_TRA(+)_1

description: Nascent reprogrammed cells derived from human dermal fibroblast line on day 28, replicate 1


title: CD3 lymphocytes from 1_35178

description: Hybridized to 6.0 Array


title: Bone marrow 2_31465

description: Hybridized to 6.0 Array


title: HDF_Day20_TRA(+)_1

description: Nascent reprogrammed cells derived from human dermal fibroblast line on day 20

source_name: Nascent reprogrammed cells, day 20, sample 1


title: GTL-16_Passage 4 xenograft_R4

description:
GTL-16 P04 T4
Gene expression data from GTL-16 Passage 4 xenograft.


title: ES cells wildtype W4 rep 2


title: Bone marrow 6_32611

description: Hybridized to 6.0 Array

source_name: Bone marrow


title: ES cells NcGFP ki/ki rep 1

value: NcGFP ki/ki


title: GTL-16_Passage 4 xenograft_R3

description:
GTL-16 P04 T3
Gene expression data from GTL-16 Passage 4 xenograft.


title: HDF_Day15_TRA(+)_3

description: Nascent reprogrammed cells derived from human dermal fibroblast line on day 15, replicate 3

source_name: Nascent reprogrammed cells, day 15, sample 3


title: ES cells NcGFP ki/+ rep 2

value: NcGFP ki/+


title: HDF_Day15_TRA(+)_2

description: Nascent reprogrammed cells derived from human dermal fibroblast line on day 15, replicate 2

source_name: Nascent reprogrammed cells, day 15, sample 2


title: whole_time1

city: Houston

first: Hao

last: Hu

state: Texas

address: 1155 Pressler Blvd, Unit 1340

department: Epidemiology

institute: MD Anderson Cancer Center

hyb_protocol: Hybridization was performed on an Agilent Drosophila 44K array using a Agilent SureHyb hybridization oven.

scan_protocol: Hybridized chips were scanned using a Agilent G2505C Microarray Scanner and signal processing accomplished with Agilent Feature Extraction software, v 10.5.

data_processing: The Limma package in R (Smyth and Speed 2003) was used to perform background correction and loess normalization.

organism: Drosophila melanogaster

source_name: Upf2-25G/Y mutant

label_protocol: Labeled cRNA was generated by incorporating cyanine 3-CTP or cyanine 5-CTP into a T7 RNA polymerase reaction using the cDNA as template.

extract_protocol: Whole animals or cells were homogenized in Trizol (Invitrogen, Carlsbad, CA) and total RNA extracted using a standard three phase chloroform technique (Chomczynski and Sacchi 1987).  RNA was purified and concentrated using the RNeasy column (Qiagen Inc., Maryland), including an on-column treatment with DNase I. Random decamer-primed cDNA was prepared using M-MLV reverse transcriptase (RNase H+) as part of the RERTOscript kit (Ambion, Austin, TX).

value: Upf2-25G/Y mutant

value: whole animal

value: 2 hour after heatshock

source_name: Upf2-25G/Y mutant with UAS:Upf2

value: Upf2-25G/Y mutant with UAS:Upf2


title: GTL-16_Passage 4 xenograft_R2

description:
GTL-16 P04 T2
Gene expression data from GTL-16 Passage 4 xenograft.


title: whole_time0

value: 0-min after heatshock


title: Peripheral blood 3_16368

description: Hybridized to 6.0 Array

source_name: Peripheral blood


title: ES cells NcGFP ki/+ rep 1


title: whole_preshock

value: pre-heatshock


title: HDF_Day15_TRA(+)_1

description: Nascent reprogrammed cells derived from human dermal fibroblast line on day 15, replicate 1

source_name: Nascent reprogrammed cells, day 15, sample 1


title: GTL-16_Passage 4 xenograft_R1

description:
GTL-16 P04 T1
Gene expression data from GTL-16 Passage 4 xenograft.


title: HDF_Day11_TRA(+)_3

description: Nascent reprogrammed cells derived from human dermal fibroblast line on day 11, replicate 3

source_name: Nascent reprogrammed cells, day 11, sample 3


title: Control for 2 hours single frequency THz irradiation, biological rep3

city: Los Alamos

first: Boian

middle: S

last: Alexandrov

state: NM

address: Bikini Atoll Road

department: Theoretical Division

institute: LANL

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing: The raw microarray .CEL files were analyzed using R and Bioconductor. More specifically, the robust multi-array (RMA) method included in the affy package was used for preprocessing, background correction, and normalization of the raw data. Probes without Entrez identifiers or gene symbols as well as probes with small standard deviation across samples were filtered out from the analysis. Further, features mapping to the same Entrez identifier were consolidated by leaving the one with largest value and, finally, probes with standard deviation less than 0.5 across samples were filtered out from the analysis. Differentially expressed genes were identified using the Bioconductor limma package and ranked by calculating the B statistics for each gene. Gene annotation was performed using the Bioconductor mouse4302.db package, while the hypergeometric test of the Bioconductor’s GOstats package was used for identifying overrepresentation of differentially expressed genes in gene ontology terms.

source_name: Mouse mesenchymal stem cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA using an oligo dT-primer containing the T7 RNApolymerase promoter site and the One-Cycle Target Labeling Kit (Affymetrix). Biotin-labeled cRNA was purified and the absorbance measured at 260 nm to determine yield (NanoDrop).

growth_protocol: Mouse mesenchymal stem cells (MSCs) (ScienCell Research Laboratories, CA 92011, Catalog Number M7500) were cultured on tissue culture treated plastic T-75 flasks (Corning). Once the cells reached 80-90% confluence, the cells were sub-cultured in supplemented medium (95% α-MEM, 5% FBS, and antibiotics) for THz irradiation treatment. Roziglitazone (1 µM), insulin (5 µg/ml), 3-Isobutyl-1-methylxanthine (100 µM), and dexamethasone (1 µM), were added to the medium again 48 hours prior to irradiation.

extract_protocol: Cellular RNA was extracted using the RNeasy Mini kit (Qiagen) following the manufacturer's instructions.

treatment_protocol: Cells are irradiated for 2 hours with a far-IR optically pumped molecular gas continuous wave THz laser source (Edinburgh Instruments FIRL 100). All experiments with this laser were conducted at frequency 2.52 THz (lambda=118.8 um).

value: mesenchymal stem cells

tag: thz irradiation conditions


title: ES cells NcGFP ki/ki rep 2


title: Bone marrow M6_MO

description: Hybridized to 6.0 Array

value: Bone marrow


title: HDF_Day11_TRA(+)_2

description: Nascent reprogrammed cells derived from human dermal fibroblast line on day 11, replicate 2

source_name: Nascent reprogrammed cells, day 11, sample 2


title: U87R Avastin

first: John

last: de Groot

state: TX

address: 1515 Holcombe Blvd

institute: UT - MD Anderson Cancer Center

description: Gene expression data.

hyb_protocol: Hybridize fragmented, biotin-labeled cRNA to the Affymetrix GeneChip® Array overnight at 45oC for 16 to 18 hours (GeneChip Hybridization Oven 640) according to the manufacturer's recommendations, and then stain and wash (GeneChip Fluidics Station 450, EukGE-WS2v5_450 script).

scan_protocol: Scan (GCS 3000 7G with the GeneChip® AutoLoader) according to the manufacturer's recommendations.

data_processing:
The software used was JMP Genomics 5.0. CEL files were imported and probe values determined based on a custom Chip Definition File (CDF; Brainarray Version 11, hgu133plus2hsentrezg). Background correction was performed using the Kernel Smoothing algorithm (correction applied with smoothing bandwidth multiplier of 1) provided by the software. Data were median normalized to 0 and probsets values determined by median polish. Data is log2 transformed.
Probes were combined into probesets using median polish and were assigned using a custom CDF based on alignment to Entrez Gene.

source_name: Human xenograft derived from U87R cells, Avastin treated

label_protocol: Starting with 1 ug total RNA, produce amplified biotin-labeled cRNA targets using the Enzo Target Labeling method. Calculate cRNA Quality Metrics (i.e., IVT yield, 260/280 ratio) and notify client if metrics fall below EA recommended guidelines.

growth_protocol: Tumor cells were injected into the caudate nucleus of nude mice and allowed to grow until animals became moribund.

treatment_protocol: Bevacizumab was given to mice at 10 mg/kg IP twice a week.

value: tumor tissue extracted from mouse brain

tag: injected cell line

value: bevacizumab (Avastin)


title: U87R Control

description: Gene expression data.

source_name: Human xenograft derived from U87R cells, untreated


title: 2 hours single frequency THz irradiation, biological rep3


title: HDF_Day11_TRA(+)_1

description: Nascent reprogrammed cells derived from human dermal fibroblast line on day 11, replicate 1

source_name: Nascent reprogrammed cells, day 11, sample 1


title: GTL-16_Passage 1 xenograft_R3

description:
GTL-16 P01 T3
Gene expression data from GTL-16 Passage 1 xenograft.

source_name: GTL-16, passage 1 xenograft

growth_protocol: All cell lines were obtained from the Division of Cancer Treatment and Diagnosis Tumor Repository (DTP, FNLCR, Frederick, MD) or American Type Culture Collection (ATCC) (Manassas, Va). In addition, the identities of all cell lines used in this study were confirmed using Identifiler® STR genotyping (Applied Biosystems). All mice used in the study were obtained from the Animal Production Program (FNLCR, Frederick, MD). Tumor cells for inoculation were derived from the 4th in vitro passage from cryopreserved cell stocks. Cells (1 x 10^7 cells/0.1 ml/inoculation) were inoculated subcutaneously into mice (n=10 or more mice depending on the tumor cell line). For comparative purposes, 2-3 samples of in vitro cultivated cells at passage 4 post-cryopreservation were also prepared for microarray analysis (P0). When tumors at P1, P4 and P10 reached approximately 500 mg (10x10 mm), 5 tumors were harvested, cut into small pieces and flash frozen in liquid nitrogen using pre-chilled tubes. Samples were transferred to a -70°C freezer for holding prior to processing. Serial tumor passage was achieved by harvesting donor tumor material (n=2 to 5 donors) at each passage, mincing the tumors (2x2 mm fragments), pooling the samples and inoculating the next recipients subcutaneously using tumor implant trocars. Athymic nude mice (nu/nu NCr) served as the primary host for most xenograft studies. In several instances (particularly with human leukemias and lymphomas) it was difficult to establish and passage tumors in nu/nu NCr mice. In these instances, SCID.NCr or NOD.SCID/NCr mice were assessed for suitability. In general, female mice were used as they are less aggressive, easily group-housed and routinely used in xenograft experiments. Male mice were used for prostate tumors (PC-3, PC-3/M). Finally, in those instances where hormone effects on tumor growth are important (e.g., estradiol-dependent breast), mice were supplemented with estradiol.


title: CD3 lymphocytes from 9295_SP

description: Hybridized to 6.0 Array

source_name: CD3 lymphocytes isolated from peripheral blood


title: Bone marrow M5_MO

description: Hybridized to 6.0 Array


title: 2 hours single frequency THz irradiation, biological rep2


title: U87 Avastin

description: Gene expression data.

source_name: Human xenograft derived from U87 cells, Avastin treated


title: U87 Control

description: Gene expression data.

source_name: Human xenograft derived from U87 cells, untreated


title: NSC11R Avastin

description: Gene expression data.

source_name: Human xenograft derived from NSC11R cells, Avastin treated


title: HDF_Day7_TRA(+)_3

description: Nascent reprogrammed cells derived from human dermal fibroblast line on day 7, replicate 3

source_name: Nascent reprogrammed cells, day 7, sample 3


title: HDF_Day7_TRA(+)_2

description: Nascent reprogrammed cells derived from human dermal fibroblast line on day 7, replicate 2

source_name: Nascent reprogrammed cells, day 7, sample 2


title: Control for 2 hours single frequency THz irradiation, biological rep1


title: GTL-16_Passage 1 xenograft_R2

description:
GTL-16 P01 T2
Gene expression data from GTL-16 Passage 1 xenograft.


title: Control for 2 hours single frequency THz irradiation, biological rep2


title: 2 hours single frequency THz irradiation, biological rep1


title: CD3 lymphocytes from Bone marrow 06414_MO

description: Hybridized to 6.0 Array

value: CD3 lymphocytes isolated from peripheral blood


title: CD3 lymphocytes M6_MO

description: Hybridized to 6.0 Array


title: NSC11R Control

description: Gene expression data.

source_name: Human xenograft derived from NSC11R cells, untreated


title: GTL-16_originating cell line_R2

description:
GTL-16 P0 T2
Gene expression data from GTL-16 originating cell line.

source_name: GTL-16, originating cell line


title: whole_time2

source_name: Upf2-25G/Y mutant

value: 4 hour after heatshock

source_name: Upf2-25G/Y mutant with UAS:Upf2


title: GTL-16_Passage 1 xenograft_R1

description:
GTL-16 P01 T1
Gene expression data from GTL-16 Passage 1 xenograft.


title: HDF_Day3_EGFP(+)_3

description: Nascent reprogrammed cells derived from human dermal fibroblast line on day 3, replicate 3

source_name: Nascent reprogrammed cells , day 3, sample 3

value: Nascent reprogrammed cells derived from human dermal fibroblasts


title: Bone marrow 1_35178

description: Hybridized to 6.0 Array

source_name: Bone marrow


title: GTL-16_Passage 1 xenograft_R4

description:
GTL-16 P01 T4
Gene expression data from GTL-16 Passage 1 xenograft.

value: adenocarcinoma gastric


title: HDF_Day7_TRA(+)_1

description: Nascent reprogrammed cells derived from human dermal fibroblast line on day 7, replicate 1

source_name: Nascent reprogrammed cells, day 7, sample 1


title: Control for 12 hours broadband THz irradiation, biological rep3

source_name: Mouse mesenchymal stem cells

treatment_protocol: Cells are irradiated for 12 hours with high-energy (~1 µJ, pulsewidth 35 fs  i.e. high peak power per pulse ~30 MW), average density power 1mW/cm2, broadband THz radiation  (~10 THz) at a high repetition rate (1 kHz).


title: Peripheral blood 9295_SP

description: Hybridized to 6.0 Array

source_name: Peripheral blood

value: Peripheral blood


title: GTL-16_Passage 1 xenograft_R5

description:
GTL-16 P01 T5
Gene expression data from GTL-16 Passage 1 xenograft.


title: 12 hours broadband THz irradiation, biological rep3

value: 12 hours broadband THz irradiation


title: NSC11 Avastin1

description: Gene expression data.

source_name: Human xenograft derived from NSC11 cells, Avastin treated


title: NSC11 Avastin2

description: Gene expression data.


title: Control for 12 hours broadband THz irradiation, biological rep2


title: GTL-16_originating cell line_R1

description:
GTL-16 P0 T1
Gene expression data from GTL-16 originating cell line.


title: HDF_Day3_EGFP(+)_1

description: Nascent reprogrammed cells derived from human dermal fibroblast line on day 3, replicate 1

source_name: Nascent reprogrammed cells , day 3, sample 1


title: NSC11 control2

description: Gene expression data.

source_name: Human xenograft derived from NSC11 cells, untreated


title: NSC11 control1

description: Gene expression data.


title: Bone marrow 06414_MO

description: Hybridized to 6.0 Array


title: EKVX_Passage 10 xenograft_R4

description:
EKVX P10 T4
Gene expression data from EKVX Passage 10 xenograft.

source_name: EKVX, passage 10 xenograft

value: EKVX

value: adenocarcinoma lung


title: EKVX_Passage 10 xenograft_R5

description:
EKVX P10 T5
Gene expression data from EKVX Passage 10 xenograft.


title: Parental HDF_3

description: Human dermal fibroblast line 3

source_name: Parental Human dermal fibroblast line  for reprogramming 3

value: Human dermal fibroblasts


title: Control for 12 hours broadband THz irradiation, biological rep1


title: EKVX_Passage 10 xenograft_R2

description:
EKVX P10 T2
Gene expression data from EKVX Passage 10 xenograft.


title: 12 hours broadband THz irradiation, biological rep2


title: 12 hours broadband THz irradiation, biological rep1


title: Parental HDF_1

description: Human dermal fibroblast line 1

source_name: Parental Human dermal fibroblast line  for reprogramming 1


title: Control for 2 hours broadband THz irradiation, biological rep3

treatment_protocol: Cells are irradiated for 2 hours with high-energy (~1 µJ, pulsewidth 35 fs  i.e. high peak power per pulse ~30 MW), average density power 1mW/cm2, broadband THz radiation  (~10 THz) at a high repetition rate (1 kHz).


title: EKVX_Passage 10 xenograft_R3

description:
EKVX P10 T3
Gene expression data from EKVX Passage 10 xenograft.


title: HDF_Day3_EGFP(+)_2

description: Nascent reprogrammed cells derived from human dermal fibroblast line on day 3, replicate 2

source_name: Nascent reprogrammed cells , day 3, sample 2


title: EKVX_Passage 10 xenograft_R1

description:
EKVX P10 T1
Gene expression data from EKVX Passage 10 xenograft.


title: HCC-LM3-shASPP2-2

city: Shanghai

first: fang

middle: fang

last: bu

address: Yin Road, New Building 10-11th Floor

department: 1International Joint Cancer Institute

country: China

institute: Second Military Medical University

description: This sample is of HCC-LM3 cells infected with shASPP2. It is the second of three shASPP2 infected biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Labeled cDNA was hybridized in NimbleGen Hybridization System following their standard operating protocol.

scan_protocol: Slides were scanned with the Axon GenePix 4000B microarray scanner following their standard operating protocol.

data_processing: Raw data were extracted as pair files by NimbleScan software (version 2.5). NimbleScan software’s implementation of RMA offers quantile normalization and background correction. The 6 gene summary files were imported into Agilent GeneSpring Software (version11.0) for further analysis.

source_name: HCC-LM3 cells infected with ASPP2 shRNA

label_protocol: cDNA was labeled using a NimbleGen One-Color DNA Labeling Kit following their standard operating protocol.

growth_protocol: HCC-LM3 cell lines were cultured with DMEM containing 10% FBS at 37°C, 5% CO2.

extract_protocol: Total RNAs are harvested using TRIzol (Invitrogen) and the RNeasy kit (Qiagen) according to manufacturer’s instructions, including a DNase digestion step. RNA was measured on the Nanodrop ND-1000.

treatment_protocol: HCC-LM3 cells were infected with Lv-shNon or Lv-shASPP2 for one week.

value: HCC-LM3 cells

value: Hepatocarcinoma cell line

tag: treatment group

value: Infected with shASPP2

value: ASPP2 Knockdown


title: CD3 lymphocytes from Mostra 1 (NM14177) 5q 8

description: Hybridized to 6.0 Array

source_name: CD3 lymphocytes isolated from peripheral blood


title: Parental HDF_2

description: Human dermal fibroblast line 2

source_name: Parental Human dermal fibroblast line  for reprogramming 2


title: Bone marrow Mostra 1 (NM14177) 5q 8

description: Hybridized to 6.0 Array


title: HCC-LM3-shASPP2-1

description: This sample is of HCC-LM3 cells infected with shASPP2. It is the first of three shASPP2 infected biological replicates used in this experiment, each from separate cultures.


title: HCC-LM3-shASPP2-3

description: This sample is of HCC-LM3 cells infected with shASPP2. It is the third of three shASPP2 infected biological replicates used in this experiment, each from separate cultures.