title: Root Cortex Cells_Hypoxia+MCP vs Hypoxia_Replicate 2

description: Biological replicate 2 of 3. Root Cortex Cells, Hypoxia+MCP, harvested after 12h MCP pretreatment + 12h Waterlogging treatment


title: Coregonus_dwarf_individual21, Sample 39

status: Public on Aug 01 2010

type: RNA

city: Quebec

first: Sébastien

last: Renaut

state: qc

address: 1030 Avenue de la Médecine

department: Biology

country: Canada

institute: Université Laval

description:
Lake whitefish.
One sexually undifferentiated individual - sampling at 280-288 degree days post fertilisation.

hyb_protocol: Microarray were hybridized using Cy3/Cy5 dyes (Genisphere) as detailed  in http://web.uvic.ca/grasp/microarray/protocols/Genisphere_Array_50_Protocol_Revised_v.5.pdf

scan_protocol: Microarrays were scanned using a ScanArray™ Express scanner (Packard Bioscience, Wellesley, MA) and spots were located and quantified using the histogram method in QuantArray 3.0 (Perkin Elmer, Waltham, USA).

data_processing: Data were exported in text format and then analysed in R using MAANOVA package. Data were Lowess normalized. Channels were analyzed independently.

molecule: total RNA

organism: Coregonus clupeaformis

source_name: Frozen individual in toto, dwarf

label_protocol: For each sample, 20µg total RNA was retro-transcribed and the cDNA samples labelled using Genisphere 3DNA Array 50 Kit, Invitrogen's Superscript II retro transcriptase and Cyanine-3 and Cyanine-5 fluorescent dyes (Genisphere), following the procedures at http://web.uvic.ca/cbr/grasp/ (Genisphere Array 50 Protocol).

growth_protocol: Whole individuals were stored at -80°C in RNAlater prior to any sampling

extract_protocol: Total RNA was extracted using the Trizol Reagent protocol (Invitrogen, Carlsbad, CA). A pool of five whole embryos preserved in RNA later was homogenized using a bead mill (Qiagen, Germantown, MD) for each sample hybridized on the array. Total RNA was eluted in pure water supplemented with Superase-In™ RNase Inhibitor (Ambion), quantified and quality checked using ExperionTM RNA StdSens Analysis Kit (Bio-Rad, Hercules, CA), then stored at -80°C.

treatment_protocol: Samples were treated with DNAse enzyme prior to labeling.

tag: tissue

value: whole body

tag: develomental stage

value: embryo

tag: type

value: dwarf

tag: sexual differentiation

value: undifferentiated

tag: incubation time

value: 280-288 degree days post fertilisation

tag: individual


title: Coregonus_normal_individual28, Sample 42

source_name: Frozen individual in toto, normal

value: normal


title: Root Cortex Cells_Aerated vs Hypoxia_Replicate 3

city: Chikusa-ku

first: Mikio

last: Nakazono

state: Nagoya

address: Furo-cho

department: Graduate School of Bioagricultural Sciences

country: Japan

institute: Nagoya University

description: Biological replicate 3 of 3. Root Cortex Cells, Hypoxia, harvested after 12h Waterlogging treatment

hyb_protocol: Gene Expression Hybridization kit part No. 5188-5242

scan_protocol: Agilent scanner model G2505C

data_processing: Data was analyzed by Feature Extraction Software (Version 10.5.1.1, Agilent)

organism: Zea mays

source_name: Root Cortex Cells, Hypoxia, 12 h

label_protocol: Quick Amp Labeling Kit, two-color (Agilent)

growth_protocol: Maize (Zea mays, inbred line B73) kernels were placed on germination paper, rolled-up in the paper, and placed in a flask. Water was added to the flask to keep the paper moist, but not enough to submerge the roots. Seedlings were germinated and grown at 28°C under constant light in a growth chamber for 3 days

extract_protocol: Total RNA was extracted from the LM-isolated cortex cells using the PicoPure™ RNA isolation kit (Molecular Devices) according to the manufacturer’s protocol.

treatment_protocol: For the waterlogging treatments, the primary root (but not the shoots) was waterlogged. Two and half day-old-seedlings were pre-treated with an inhibitor of ethylene perception 1-methylcyclopropene (1-MCP; 1 ppm) for 12 hours before the waterlogging treatment. Three-day-old seedlings were growing under aerated conditions at the same time with other treatments as a control. For all experiments we were using segment from the primary root, 0.5 cm long: from 1.5 to 2 cm from the junction shoot-root. Cortex part of the root was collected using Veritas Laser Microdissection System LCC170 (Molecular Devices)

tag: cultivar

value: inbred line B73

tag: sample

value: Root Cortex Cells from the segment of the primary root, 0.5 cm long:from 1.5 to 2 cm from the junction shoot-root.

tag: treatment

value: Waterlogging treatment for 12 h

source_name: Root Cortex Cells, Aerated, 12 h

value: Aerated treatment for 12 h

tag: samples


title: Coregonus_bc-moribund_individual16, Sample 40

source_name: Frozen individual in toto, bc-moribund

value: backcross-moribund


title: Root Cortex Cells_Hypoxia+MCP vs Hypoxia_Replicate 1

description: Biological replicate 1 of 3. Root Cortex Cells, Hypoxia+MCP, harvested after 12h MCP pretreatment + 12h Waterlogging treatment

source_name: Root Cortex Cells, MCP+Hypoxia, 12 h

value: MCP pretreatment for 12 h + Waterlogging treatment for 12 h


title: Root Cortex Cells_Aerated vs Hypoxia_Replicate 1

description: Biological replicate 1 of 3. Root Cortex Cells, Hypoxia, harvested after 12h Waterlogging treatment


title: Root Cortex Cells_Hypoxia+MCP vs Hypoxia_Replicate 3

description: Biological replicate 3 of 3. Root Cortex Cells, Hypoxia+MCP, harvested after 12h MCP pretreatment + 12h Waterlogging treatment


title: ColorSwap_Root Cortex Cells_Hypoxia vs Aerated_Replicate 1

description: Color Swap replicate 1 of 3. Root Cortex Cells, Hypoxia, harvested after 12h Waterlogging treatment


title: ColorSwap_Root Cortex Cells_Hypoxia vs Aerated_Replicate 3

description: Color Swap replicate 3 of 3. Root Cortex Cells, Hypoxia, harvested after 12h Waterlogging treatment


title: ColorSwap_Root Cortex Cells_Hypoxia vs Hypoxia+MCP_Replicate 2

description: Color Swap replicate 2 of 3. Root Cortex Cells, Hypoxia+MCP, harvested after 12h MCP pretreatment + 12h Waterlogging treatment


title: Coregonus_bc-moribund_individual15, Sample 36


title: Coregonus_normal_individual26, Sample 35


title: Coregonus_normal_individual26, Sample 34


title: Coregonus_normal_individual27, Sample 32


title: Coregonus_bc-healthy_individual8, Sample 33

source_name: Frozen individual in toto, bc-healthy

value: backcross-healthy


title: Coregonus_dwarf_individual21, Sample 38


title: Coregonus_bc-healthy_individual1, Sample 37


title: Coregonus_bc-healthy_individual1, Sample 30


title: Coregonus_bc-moribund_individual16, Sample 31


title: Coregonus_normal_individual27, Sample 29


title: Coregonus_bc-moribund_individual15, Sample 27


title: Coregonus_dwarf_individual20, Sample 28


title: Coregonus_bc-moribund_individual14, Sample 24


title: Coregonus_bc-healthy_individual8, Sample 26


title: Coregonus_dwarf_individual19, Sample 22


title: H929 1X

status: Public on Aug 20 2010

type: genomic

city: Research Triangle Park

first: Deepak

last: Mav

state: NC

address: 2 Davis Drive

country: USA

institute: Sciome LLC

description: MIRA-chip from H929

hyb_protocol: Samples were hybridized onto a NimbleGen 2.1M Deluxe Human Promoter Array following NimbleGen’s protocol.

scan_protocol: The microarray slides were scanned using the Agilent G2565BA DNA Microarray Scanner.  Images were processed using the NimbleScan software.

data_processing: The log2(Cy5) values were normalized using loess curve fitting conditioning on GC content as described in BMC Bioinformatics 2009, 10:173 doi:10.1186/1471-2105-10-173. These signal values were further quantile normalized to adjust for between sample variations. This method accounts for CG effect and also incorporates cy3 data as following. First we bin all probes according to their GC content defined as a ratio of number of C and G nucleotides to the total number of nucleotides in the probe sequence. We used overall variability in GC content values to compute bin width according to zero-stage rule described by Wand (1997). The bins with fewer probes are then merged to make sure that each bin contains at least 500 probes.  Within each bin we use loess regression to predict log2(cy5) values as a smooth function of log2(cy3) values. The residuals (difference between observed and predicted value) from this loess fit are then divided by their mean absolute deviations to compute normalized signal.

molecule: genomic DNA

organism: Homo sapiens

source_name: MIRA-enriched DNA

label_protocol: Input and methylated CpG DNA fragments were amplified (WGA2, Sigma), labeled with Cy3 and Cy5 random nonomers (Trilink Biotechnologies) following NimbleGen’s protocol.

growth_protocol: DMEM + 10% FBS

extract_protocol: Genomic DNA was purified from Raji and H929 were sonicated using a Bioruptor (Diagenode) to generate 200-500 bp fragments.  Methylated CpG DNA fragments were enriched from 200 ng of sonicated DNA using the MethylCollector Ultra Kit (Actif Motif) following the manufacturer’s protocol.

tag: cell type

value: H929 methylated DNA fraction

tag: cycles

value: 1X WGA

tag: cell line

source_name: Input DNA

value: H929 input DNA


title: Coregonus_dwarf_individual19, Sample 23


title: CO:KM12 Replication 2

city: Bethesda

first: Hongfang

last: Liu

state: MD

address: 9000 Rockville Pike

institute: National Cancer Institute

description: CO:KM12 Replication 2

hyb_protocol: Hybridization following the Agilent Technologies One-Color Microarray-Based Gene Expression Analysis Protocol version 5.5.

scan_protocol: Scanned following the Agilent Technologies One-Color Microarray-Based Gene Expression Analysis Protocol version 5.5 using Agilent Scanner G2505B.

data_processing: After data extraction with Feature Extraction (version 9.5, Agilent Technologies), the data quality was confirmed using the Agilent quality control metrics. Intensity data on all mRNA probes processed using GeneSpring GX by (i) setting any gProcessedSignal (mRNA_Agilent) value less than 5 to 5; (ii) transforming the gProcessedSignal or gTotalGeneSignal to Logbase 2; and (iii) normalizing per array to the 75th scaling normalization.

label_protocol: Labeled following the Agilent Technologies One-Color Microarray-Based Gene Expression Analysis Protocol version 5.5 with a total RNA input of 200 ng.

growth_protocol: Frozen stocks of the NCI-60 were obtained from the NCI Developmental Therapeutics program (NCI DTP). The cells were cultured and then thawed, placed in RPMI 1640 (Lonza Walkersville, Inc.) containing 5% fetal calf serum (Atlantic Biologicals) and 2 mM glutamine (Invitrogen Corporation). For compatibility with our other profiling studies, we used the same batch of serum used by DTP, and the procedures were done or overseen by the same researcher (Dr. William Reinhold).

extract_protocol: The total RNA was extracted using the RNeasy purification kit (Qiagen, Inc.) according to the manufacturer's instructions.

tag: tissue-of-origin

value: Colon

tag: age

tag: gender

value: F

tag: histology

value: Adenocarcinoma-md


title: CO:SW-620 Replication 2

description: CO:SW-620 Replication 2

value: Adenocarcinome-pd


title: Coregonus_bc-moribund_individual14, Sample 19

tag: tissue

value: whole body

value: embryo

value: undifferentiated


title: CO:SW-620 Replication 1

description: CO:SW-620 Replication 1


title: Coregonus_bc-healthy_individual7, Sample 21

tag: develomental stage

value: 280-288 degree days post fertilisation


title: Coregonus_normal_individual24, Sample 18

tag: type

value: normal


title: Coregonus_bc-healthy_individual6, Sample 17

tag: sexual differentiation


title: LC:HOP-92 Replication 2

description: LC:HOP-92 Replication 2

value: Non-Small Cell Lung

value: adenocarcinoma-ud


title: Coregonus_dwarf_individual20, Sample 25

value: dwarf

tag: incubation time


title: Coregonus_dwarf_individual18, Sample 16

tag: individual


title: LC:NCI-H522 Replication 1

description: LC:NCI-H522 Replication 1

value: M

value: Large Cell Carcinoma-ud


title: LC:NCI-H23 Replication 2

description: LC:NCI-H23 Replication 2

value: Squamous cell carcinoma-vpd


title: LC:NCI-H322M Replication 2

description: LC:NCI-H322M Replication 2

value: Adenocarcinoma-ud


title: Coregonus_normal_individual25, Sample 20


title: CO:KM12 Replication 1

description: CO:KM12 Replication 1


title: Raji 2X

description: MIRA-chip from Raji

value: Raji methylated DNA fraction

value: 2X WGA

value: Raji

value: Raji input DNA


title: Coregonus_bc-moribund_individual13, Sample 15

value: backcross-moribund


title: LC:NCI-H522 Replication 2

description: LC:NCI-H522 Replication 2


title: CO:HT29 Replication 4

description: CO:HT29 Replication 4

value: Colon

value: F

value: Adenocarcinoma-md


title: H929 2X

description: MIRA-chip from H929

value: H929 methylated DNA fraction

value: H929 input DNA


title: Coregonus_bc-healthy_individual6, Sample 14

value: whole body

value: embryo

value: backcross-healthy

value: undifferentiated

value: 280-288 degree days post fertilisation


title: Coregonus_dwarf_individual18, Sample 13

value: dwarf


title: BR:MDB-MB-231 Replication 2

description: BR:MDB-MB-231 Replication 2

value: Breast

value: Adenocarcinoma-mammary gland; breast; epithelial; metastatic site:pleural effusion;


title: Coregonus_normal_individual24, Sample 11

value: normal


title: CNS:SNB-75 Replication 2

description: CNS:SNB-75 Replication 2

value: CNS

value: Astrocytoma


title: Coregonus_normal_individual25, Sample 9


title: Raji 1X

description: MIRA-chip from Raji

value: Raji methylated DNA fraction

value: 1X WGA

value: Raji

value: Raji input DNA


title: BR:T47D Replication 2

description: BR:T47D Replication 2

value: F

value: infiltrating ductal carcinoma


title: CO:HCT-116 Replication 4

description: CO:HCT-116 Replication 4

value: Colon

value: carcinoma


title: BR:BT-549 Replication 2

description: BR:BT-549 Replication 2

value: Papillary infiltrating ductal carcinoma-mammary gland; breast


title: Coregonus_bc-moribund_individual13, Sample 12

value: whole body

value: embryo

value: backcross-moribund

value: undifferentiated


title: 24K562

city: Boston

first: Zhe

last: Li

state: MA

department: Division of Hematology/Oncology

institute: Children's Hospital Boston

description: Gene expression data from a erythroleukemia cell line.

hyb_protocol: The fragmented cRNA was added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to U133 Plus 2.0 chips overnight at 45°C. The chips were then transferred to a fluidics instrument that performs washes to remove cRNA that had not hybridized to its complementary oligonucleotide probe. The bound cRNA was then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors were then added using biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: Each cRNA bound at its complementary oligonucleotide was excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions were captured.

data_processing: The raw CEL files were imported into dChip and normalized with dChip. After normalization, the model-based expression values were calculated by dChip and exported.

label: biotin

source_name: Erythroleukemia cell line K562

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

growth_protocol: Cell lines were grown in RPMI1640+15%FCS.

extract_protocol: Trizol extraction of total RNA followed by cleaning up using columns from the Promega SV total RNA isolation kit.

tag: cell description

value: Erythroleukemia cell line


title: CO:HCT-116 Replication 3

description: CO:HCT-116 Replication 3


title: ColorSwap_Root Cortex Cells_Hypoxia vs Hypoxia+MCP_Replicate 1

description: Color Swap replicate 1 of 3. Root Cortex Cells, Hypoxia+MCP, harvested after 12h MCP pretreatment + 12h Waterlogging treatment

tag: cultivar

value: inbred line B73

tag: sample

value: Root Cortex Cells from the segment of the primary root, 0.5 cm long:from 1.5 to 2 cm from the junction shoot-root.

value: MCP pretreatment for 12 h + Waterlogging treatment for 12 h

value: Waterlogging treatment for 12 h


title: Coregonus_bc-healthy_individual7, Sample 10

value: backcross-healthy

value: 280-288 degree days post fertilisation


title: Coregonus_dwarf_individual17, Sample 7

value: dwarf


title: Coregonus_bc-dead_individual12, Sample 8

source_name: Frozen individual in toto, bc-dead

value: backcross-dead


title: 23M07

description: Gene expression data from a non-DS AMKL cell line.

source_name: AMKL cell line M07

value: AMKL cell line


title: CO:HCC-2998 Replication 2

description: CO:HCC-2998 Replication 2

value: Colon

value: M

value: carcinoma-vpd


title: Coregonus_normal_individual23, Sample 6

value: whole body

value: normal


title: CNS:U251 Replication 2

description: CNS:U251 Replication 2

value: CNS

value: Glioblastoma,ud


title: CNS:SF-539 Replication 2

description: CNS:SF-539 Replication 2

value: F

value: Glial cell neoplasm


title: CO:HCC-2998 Replication 1

description: CO:HCC-2998 Replication 1


title: 19CMK

description: Gene expression data from a DS-AMKL cell line.

source_name: DS-AMKL cell line CMK

value: CMK

value: DS-AMKL cell line


title: CNS:SF-295 Replication 2

description: CNS:SF-295 Replication 2

value: Glioblastoma, ud


title: ColorSwap_Root Cortex Cells_Hypoxia vs Aerated_Replicate 2

description: Color Swap replicate 2 of 3. Root Cortex Cells, Hypoxia, harvested after 12h Waterlogging treatment

value: inbred line B73

value: Root Cortex Cells from the segment of the primary root, 0.5 cm long:from 1.5 to 2 cm from the junction shoot-root.

tag: treatment

value: Waterlogging treatment for 12 h

value: Aerated treatment for 12 h

tag: samples


title: Coregonus_bc-moribund_individual12, Sample 5

value: embryo

value: backcross-moribund

value: undifferentiated

value: 280-288 degree days post fertilisation


title: 22Meg01

source_name: AMKL cell line Meg01

value: AMKL cell line


title: BR:BT-549 Replication 1

description: BR:BT-549 Replication 1

value: Breast

value: Papillary infiltrating ductal carcinoma-mammary gland; breast


title: Coregonus_bc-healthy_individual5, Sample 3

value: whole body

value: backcross-healthy


title: BR:HS578T Replication 2

description: BR:HS578T Replication 2

value: F

value: Carcinosarcoma-mammary gland; breast


title: CNS:SNB-19 Replication 1

description: CNS:SNB-19 Replication 1

value: CNS

value: M


title: CNS:SNB-19 Replication 2

description: CNS:SNB-19 Replication 2

value: Glioblastoma, ud


title: Non-DS AMKL02

description: Gene expression data from sorted primary leukemic cells.

source_name: Non-DS AMKL sample 2, sorted blasts

tag: cell type

value: megakaryocytic leukemia blasts

tag: disease

value: AMKL

value: FACS sorted leukemic blasts from patients


title: Coregonus_normal_individual23, Sample 1

value: embryo

value: normal


title: 16UT-7

source_name: Non-DS AMKL cell line UT-7

tag: cell line


title: Coregonus_dwarf_individual17, Sample 4

value: dwarf

value: undifferentiated


title: CNS:SF-295 Replication 1

description: CNS:SF-295 Replication 1

tag: tissue-of-origin

tag: age


title: 17CMK

value: CMK

value: DS-AMKL cell line


title: 18UT-7

value: AMKL cell line


title: Non-DS AMKL05

source_name: Non-DS AMKL sample 5, sorted blasts


title: Non-DS AMKL03

source_name: Non-DS AMKL sample 3, sorted blasts


title: BR:MCF7 Replication 4

description: BR:MCF7 Replication 4

value: Breast

tag: gender

tag: histology

value: Adenocarcinoma- mammary gland; breast; metastatic site:pleural effusion;


title: Non-DS AMKL04

source_name: Non-DS AMKL sample 4, sorted blasts


title: Coregonus_bc-healthy_individual5, Sample 2

tag: tissue

value: whole body

tag: develomental stage

value: backcross-healthy

value: 280-288 degree days post fertilisation


title: Non-DS AMKL01

source_name: Non-DS AMKL sample 1, sorted blasts


title: CNS:SF-268 Replication 2

description: CNS:SF-268 Replication 2

value: CNS

value: F


title: DS-AMKL04

source_name: DS-AMKL sample 4, sorted blasts

value: megakaryocytic leukemia blasts

value: Down Syndrome-AMKL


title: CO:HCT-116 Replication 2

description: CO:HCT-116 Replication 2

value: Colon

value: M

value: Adenocarcinoma


title: CNS:SF-539 Replication 1

description: CNS:SF-539 Replication 1

value: Glial cell neoplasm


title: DS-AMKL06

source_name: DS-AMKL sample 6, sorted blasts

value: FACS sorted leukemic blasts from patients


title: DS-AMKL03

source_name: DS-AMKL sample 3, sorted blasts


title: DS-AMKL02

source_name: DS-AMKL sample 2, sorted blasts


title: CNS:U251 Replication 1

description: CNS:U251 Replication 1

value: Glioblastoma,ud


title: CO:HCT-116 Replication 1

description: CO:HCT-116 Replication 1


title: DS-AMKL05

source_name: DS-AMKL sample 5, sorted blasts


title: BR:MCF7 Replication 3

description: BR:MCF7 Replication 3


title: DS-AMKL01

source_name: DS-AMKL sample 1, sorted blasts


title: BR:MCF7 Replication 2

description: BR:MCF7 Replication 2


title: BR:MDB-MB-231 Replication 1

description: BR:MDB-MB-231 Replication 1

value: Adenocarcinoma-mammary gland; breast; epithelial; metastatic site:pleural effusion;


title: BR:MCF7 Replication 1

description: BR:MCF7 Replication 1


title: BR:T47D Replication 1

description: BR:T47D Replication 1

value: infiltrating ductal carcinoma


title: RE:CAKI-1 Replication 4

description: RE:CAKI-1 Replication 4

value: Renal

value: Clear cell carcinoma


title: BR:HS578T Replication 1

description: BR:HS578T Replication 1

value: Breast

value: Carcinosarcoma-mammary gland; breast


title: OV:NCI/ADR-RES Replication 2

description: OV:NCI/ADR-RES Replication 2

value: Ovarian

value: Adenocarinoma


title: CNS:SF-268 Replication 1

description: CNS:SF-268 Replication 1

value: CNS

value: F

value: Glioblastoma, ud


title: RE:CAKI-1 Replication 3

description: RE:CAKI-1 Replication 3


title: OV:OVCAR-4 Replication 2

description: OV:OVCAR-4 Replication 2

value: Adenocarcinoma-md


title: OV:IGROV1 Replication 2

description: OV:IGROV1 Replication 2

value: Cystoadenocarcinoma-pd


title: CNS:SNB-75 Replication 1

description: CNS:SNB-75 Replication 1

value: Astrocytoma


title: PR:PC-3 Replication 2

description: PR:PC-3 Replication 2

value: Prostate

value: M

value: Adenocarcinoma- prostate; metastatic site:bone;


title: RE:ACHN Replication 2

description: RE:ACHN Replication 2

value: Renal cell carcinoma-p/md


title: PR:DU-145 DTP Replication 2

description: PR:DU-145 DTP Replication 2

source_name: PR:DU-145 DTP

value: PR:DU-145 DTP

value: prostate; metastatic site:brain; carcinoma (patient with metastatic carcinoma of the prostate and a 3 year history of lymphocytic leukemia.)


title: OV:OVCAR-8 Replication 2

description: OV:OVCAR-8 Replication 2

value: Carcinoma-ud


title: PR:PC-3 Replication 1

description: PR:PC-3 Replication 1


title: RE:ACHN Replication 1

description: RE:ACHN Replication 1

value: Renal


title: PR:DU-145 DTP Replication 1

description: PR:DU-145 DTP Replication 1


title: RE:A498 Replication 2

description: RE:A498 Replication 2

value: Adenocarcinoma


title: RE:SN12C Replication 2

description: RE:SN12C Replication 2

value: Renal cell carcinoma-pd


title: OV:IGROV1 Replication 1

description: OV:IGROV1 Replication 1

value: Ovarian


title: RE:786-0 Replication 2

description: RE:786-0 Replication 2


title: OV:NCI/ADR-RES Replication 1

description: OV:NCI/ADR-RES Replication 1

value: Adenocarinoma


title: RE:CAKI-1 Replication 2

description: RE:CAKI-1 Replication 2

value: Clear cell carcinoma


title: RE:A498 Replication 1

description: RE:A498 Replication 1


title: RE:RXF-393 Replication 2

description: RE:RXF-393 Replication 2

value: hypernephroma-pd


title: RE:RXF-393 Replication 1

description: RE:RXF-393 Replication 1


title: OV:OVCAR-3 Replication 2

description: OV:OVCAR-3 Replication 2

value: F

value: Adenocarcinoma-md


title: OV:OVCAR-4 Replication 1

description: OV:OVCAR-4 Replication 1


title: OV:OVCAR-8 Replication 1

description: OV:OVCAR-8 Replication 1


title: RE:786-0 Replication 1

description: RE:786-0 Replication 1


title: RE:UO-31 Replication 2

description: RE:UO-31 Replication 2

value: Renal cell carcinoma-vpd


title: OV:OVCAR-3 Replication 1

description: OV:OVCAR-3 Replication 1


title: RE:CAKI-1 Replication 1

description: RE:CAKI-1 Replication 1


title: LE:MOLT-4 Replication 2

description: LE:MOLT-4 Replication 2

value: Leukemia

value: ALL (cells were taken when patient was in relapse)


title: LE:RPMI-8226 Replication 2

description: LE:RPMI-8226 Replication 2

value: M

value: Myeloma


title: ME:SK-MEL-28 Replication 2

description: ME:SK-MEL-28 Replication 2

value: Melanoma

value: Malignant melanotic melanoma


title: ME:MALME-3M Replication 2

description: ME:MALME-3M Replication 2


title: RE:SN12C Replication 1

description: RE:SN12C Replication 1


title: RE:TK-10 Replication 1

description: RE:TK-10 Replication 1

value: Renal Spindle cell carcinoma


title: LE:K-562 Replication 4

description: LE:K-562 Replication 4

value: CML


title: RE:TK-10 Replication 2

description: RE:TK-10 Replication 2

value: Renal


title: RE:UO-31 Replication 1

description: RE:UO-31 Replication 1


title: ME:MDA-MB-435 d Replication 2

description: ME:MDA-MB-435 d Replication 2

source_name: ME:MDA-MB-435 d

value: ME:MDA-MB-435 d

value: Ductal carcinoma- mammary gland; breast; duct; metastatic site:pleural effusion;


title: LE:MOLT-4 Replication 1

description: LE:MOLT-4 Replication 1


title: ME:UACC-257 Replication 2

description: ME:UACC-257 Replication 2

value: Melanotic melanoma


title: ME:MDA-MB-435 d Replication 1

description: ME:MDA-MB-435 d Replication 1


title: LE:SR Replication 2

description: LE:SR Replication 2

value: Lymphoma


title: ME:LOXIMVI Replication 2

description: ME:LOXIMVI Replication 2

value: Malignant amelanotic melanoma


title: ME:M14 Replication 2

description: ME:M14 Replication 2


title: ME:UACC-257 Replication 1

description: ME:UACC-257 Replication 1


title: ME:SK-MEL-5 Replication 2

description: ME:SK-MEL-5 Replication 2

value: F


title: ME:SK-MEL-2 Replication 4

description: ME:SK-MEL-2 Replication 2


title: LE:K-562 Replication 3

description: LE:K-562 Replication 3


title: ME:UACC-62 Replication 1

description: ME:UACC-62 Replication 1


title: ME:UACC-62 Replication 2

description: ME:UACC-62 Replication 2


title: LE:SR Replication 1

description: LE:SR Replication 1


title: ME:MDA-N d Replication 2

description: ME:MDA-N d Replication 2

source_name: ME:MDA-N d

value: ME:MDA-N d


title: ME:SK-MEL-5 Replication 1

description: ME:SK-MEL-5 Replication 1


title: LE:RPMI-8226 Replication 1

description: LE:RPMI-8226 Replication 1


title: ME:MDA-N d Replication 1

description: ME:MDA-N d Replication 1


title: ME:SK-MEL-2 Replication 3

description: ME:SK-MEL-2 Replication 1


title: ME:LOXIMVI Replication 1

description: ME:LOXIMVI Replication 1


title: ME:SK-MEL-2 Replication 2

description: ME:SK-MEL-2 Replication 2


title: ME:MALME-3M Replication 1

description: ME:MALME-3M Replication 1


title: LE:K-562 Replication 1

description: LE:K-562 Replication 1


title: ME:M14 Replication 1

description: ME:M14 Replication 1


title: LE:K-562 Replication 2

description: LE:K-562 Replication 2


title: ME:SK-MEL-28 Replication 1

description: ME:SK-MEL-28 Replication 1


title: LC:NCI-H23 Replication 1

description: LC:NCI-H23 Replication 1

value: Non-Small Cell Lung

value: Squamous cell carcinoma-vpd


title: ME:SK-MEL-2 Replication 1

description: ME:SK-MEL-2 Replication 1


title: LC:A549-ATCC Replication 2

description: LC:A549-ATCC Replication 2

value: Colon

value: Carcinoma-ud


title: LC:EKVX Replication 2

description: LC:EKVX Replication 2

value: M

value: Adenocarcinoma-p/md


title: LC:HOP-92 Replication 1

description: LC:HOP-92 Replication 1

value: adenocarcinoma-ud


title: CO:HCT-15 Replication 2

description: CO:HCT-15 Replication 2

value: carcinoma-vpd


title: LC:EKVX Replication 1

description: LC:EKVX Replication 1


title: LE:HL-60 Replication 1

description: LE:HL-60 Replication 1

value: Leukemia

value: Pro myelocytic leukemia


title: CO:HT29 Replication 3

description: CO:HT29 Replication 3

value: Adenocarcinoma-md


title: CO:HT29 Replication 2

description: CO:HT29 Replication 2

value: Adenocarcinoma p/md


title: LE:HL-60 Replication 2

description: LE:HL-60 Replication 2


title: CO:HCT-15 Replication 1

description: CO:HCT-15 Replication 1


title: LE:CCRF-CEM Replication 2

description: LE:CCRF-CEM Replication 2

value: ALL


title: CO:HT29 Replication 1

description: CO:HT29 Replication 1


title: LC:A549-ATCC Replication 1

description: LC:A549-ATCC Replication 1


title: blood C57BL/6J 12hours rep3

city: Durham

first: Lindsay

last: Cowell

address: 2424 Erwin Road

institute: Duke University

hyb_protocol: Labeled cDNA was hybridized to the arrays for 16 hours at 45°C following the manufacturer’s instruction. The arrays were then washed and labeled with streptavidinphycoerythrin (strep-PE), and the signal was amplified using biotinylated antistreptavidin followed by another round of staining with strep-PE.

scan_protocol: Labeled gene chips were scanned using an Affymetrix Genechip Scanner 7G (Affymetrix).

data_processing: Preprocessing was conducted using the Robust Multichip Analysis (RMA) (PMID: 12925520) implementation in the Bioconductor “affy” package (http://www.bioconductor.org/), with an additional step to account for differences in probe hybridization resulting from single nucleotide polymorphisms (SNP) between A/J and C57BL/6J mice.  The additional step is referred to as SNP masking (PMID:17762873) and is applied after background correction and quantile-quantile normalization but prior to the determination of probeset expression values.  Genomic locations hybridized by each probe were obtained from the Ensembl database (http://www.ensembl.org/index.html), and these genomic locations were compared to the locations of SNPs for which A/J and C57BL/6J mice have different alleles.  Probes that hybridize to such SNPs within the target transcripts were excluded from the determination of probeset expression values.  Statistically significant differences in expression between A/J and C57BL/6J mice were determined using a standard ANOVA with model terms for batch, strain, and time post-infection, with uninfected mice coded as 0 hours post-infection.

label: Biotin

organism: Mus musculus

source_name: blood C57BL/6J mouse strain blood taken 12 hours after infection with S. aureus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA (Affymetrix).

growth_protocol: S. aureus strain Sanger 476 was used in this study. For preparation of S. aureus for injection, an overnight bacterial culture of S. aureus was diluted with fresh tryptic soy broth (TSB) and incubated (37°C) with aeration to log-phase growth (optical density at wavelength 600 nm (O.D.600) of ~1.0) (Rice 2003). S. aureus was harvested by centrifugation, rinsed, and resuspended in saline.

extract_protocol: Total RNA was prepared using the Mouse RiboPure Blood RNA isolation kit (Ambion) following the manufacturer’s instruction. Globin mRNA was removed from whole blood RNA samples using the Globinclear kit (Ambion).

treatment_protocol: To mimic the natural course of S. aureus infection in humans, which typically arises from a primary focus of infection and disseminates to other sites, we employed an intraperitoneal (i.p.) route of infection in our animal model. For experiments involving RNA analysis, blood was collected by intracardiac puncture and stored in RNAlater at -20oC.

tag: strain

tag: infection

value: Staphylococcus aureus

tag: time point

value: 12 hours


title: blood C57BL/6J 4hours rep4

source_name: blood C57BL/6J mouse strain blood taken 4 hours after infection with S. aureus

value: 4 hours


title: LC:NCI-H322M Replication 1

description: LC:NCI-H322M Replication 1

value: Adenocarcinoma-ud


title: blood C57BL/6J 12hours rep4


title: blood C57BL/6J 2hours rep4

source_name: blood C57BL/6J mouse strain blood taken 2 hours after infection with S. aureus

value: 2 hours


title: LC:NCI-H460 Replication 1

description: LC:NCI-H460 Replication 1

value: Non-Small Cell Lung

value: Small cell Bronchioalveolar Carcinoma


title: LC:NCI-H460 Replication 2

description: LC:NCI-H460 Replication 2


title: blood C57BL/6J 6hours rep3

source_name: blood C57BL/6J mouse strain blood taken 6 hours after infection with S. aureus

value: 6 hours


title: LE:CCRF-CEM Replication 1

description: LE:CCRF-CEM Replication 1

value: F


title: blood C57BL/6J 2hours rep3


title: OV:SKOV3 Replication 2

description: OV:SKOV3 Replication 2

value: Ovarian

value: Adenocarcinoma-vpd


title: blood C57BL/6J 0hours rep4

source_name: blood C57BL/6J mouse strain NOT infected with S. aureus


title: OV:SKOV3 Replication 1

description: OV:SKOV3 Replication 1


title: blood C57BL/6J 0hours rep3


title: LC:NCI-226 Replication 1

description: LC:NCI-226 Replication 1

value: M

value: Large cell-ud


title: blood A/J 12hours rep4

source_name: blood A/J mouse strain blood taken 12 hours after infection with S. aureus

value: A/J


title: LC:NCI-226 Replication 2

description: LC:NCI-226 Replication 2


title: OV:OVCAR-5 Replication 2

description: OV:OVCAR-5 Replication 2

value: Adenocarcinoma-wd


title: blood A/J 6hours rep4

source_name: blood A/J mouse strain blood taken 6 hours after infection with S. aureus


title: blood C57BL/6J 6hours rep4


title: CO:COLO205 Replication 2

description: CO:COLO205 Replication 2

value: Colon

value: carcinoma-vpd


title: LC:HOP-62 Replication 2

description: LC:HOP-62 Replication 2

value: Adenocarcinoma-md


title: blood A/J 4hours rep3

source_name: blood A/J mouse strain blood taken 4 hours after infection with S. aureus

value: Staphylococcus aureus


title: OV:OVCAR-5 Replication 1

description: OV:OVCAR-5 Replication 1


title: blood A/J 4hours rep4

value: 4 hours


title: blood A/J 12hours rep3

value: 12 hours


title: blood A/J 2hours rep3

source_name: blood A/J mouse strain blood taken 2 hours after infection with S. aureus

value: 2 hours


title: LC:HOP-62 Replication 1

description: LC:HOP-62 Replication 1

value: Non-Small Cell Lung


title: blood A/J 2hours rep4


title: blood C57BL/6J 6hours rep2


title: blood A/J 12hours rep2


title: blood A/J 6hours rep3


title: blood C57BL/6J 2hours rep2


title: blood A/J 0hours rep4

source_name: blood A/J mouse strain NOT infected with S. aureus


title: CO:COLO205 Replication 1

description: CO:COLO205 Replication 1


title: blood C57BL/6J 4hours rep2


title: blood A/J 0hours rep3


title: blood C57BL/6J 12hours rep2


title: blood C57BL/6J 0hours rep2


title: blood A/J 4hours rep2


title: blood A/J 6hours rep2


title: blood C57BL/6J 0hours rep1


title: blood A/J 6hours rep1


title: blood C57BL/6J 6hours rep5


title: blood C57BL/6J 6hours rep1


title: blood A/J 2hours rep2


title: blood C57BL/6J 12hours rep1


title: blood C57BL/6J 12hours rep5


title: blood C57BL/6J 4hours rep5


title: blood A/J 2hours rep1


title: blood A/J 0hours rep2


title: blood C57BL/6J 4hours rep1


title: blood A/J 4hours rep1


title: blood A/J 6hours rep5


title: blood C57BL/6J 0hours rep5


title: T6(6)_leukemia_Tripz_Dox

description: Gene expression data from T6(6) leukemic cells without Igf1r knockdown.

hyb_protocol: The fragmented cRNA was added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to MOE 430.2 chips overnight at 45°C. The chips were then transferred to a fluidics instrument that performs washes to remove cRNA that had not hybridized to its complementary oligonucleotide probe. The bound cRNA was then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors were then added using biotinylated anti-streptavidin antibody and additional SAPE.

source_name: T6(6) leukemic cells infected with the empty Tripz vector, with Dox, control (no Igf1r knockdown)

growth_protocol: Cells were grown in IMDM+10%FCS+IL3 or Tpo.

treatment_protocol: Doxycycline was or was not added to the culture medium.

value: leukemic cells derived from Gata1s mutant fetal progenitors

tag: igf1r knockdown

value: no


title: T6(6)_leukemia_Tripz-shIgf1r_No Dox

source_name: T6(6) leukemic cells infected with Tripz-shIgf1r, no Dox, control (no Igf1r knockdown)


title: blood A/J 4hours rep5


title: blood C57BL/6J 2hours rep1


title: blood A/J 12hours rep5


title: blood A/J 12hours rep1


title: T6(6)_leukemia_Tripz-shIgf1r_Dox3

description: Gene expression data from T6(6) leukemic cells with Igf1r knockdown.

source_name: T6(6) leukemic cells infected with Tripz-shIgf1r, with Dox, Igf1r knockdown, replicate 3

value: yes


title: T6(6)_leukemia_Tripz-shIgf1r_Dox2

source_name: T6(6) leukemic cells infected with Tripz-shIgf1r, with Dox, Igf1r knockdown, replicate 2


title: T6(6)_leukemia_Tripz-shIgf1r_Dox1

source_name: T6(6) leukemic cells infected with Tripz-shIgf1r, with Dox, Igf1r knockdown, replicate 1


title: blood A/J 0hours rep1


title: blood A/J 0hours rep5


title: blood A/J 2hours rep5


title: M7_leukemia_splenocyte_rep2

description: Gene expression data from GFP+ leukemic blasts.

source_name: GFP+ T6(6) leukemic blasts from spleen, mouse 2

growth_protocol: These were primary leukemic cells isolated directly from mice.

value: spleen

value: leukemic cells derived from Gata1 mutant fetal progenitors


title: T6(6)_leukemia_Tripz_No Dox

source_name: T6(6) leukemic cells infected with the empty Tripz vector, no Dox, control (no Igf1r knockdown)


title: M7_leukemia_peripheral_blood_rep2

source_name: GFP+ T6(6) leukemic blasts from peripheral blood, mouse 2

value: peripheral blood


title: blood C57BL/6J 2hours rep5


title: M7_leukemia_splenocyte_rep1

source_name: GFP+ T6(6) leukemic blasts from spleen, mouse 1


title: cell line2_Plag1_KT_subline2_B

description: Gene expression data from cell line2 transduced with Plag1.

source_name: Cell line2 transduced with Plag1, subline 2, replicate B

growth_protocol: These cells were grown in DMEM+10%FCS+Tpo+KL.

value: Immortalized cell line2

tag: transduced vector


title: cell line2_Plag1_KT_subline1_B

source_name: Cell line2 transduced with Plag1, subline 1, replicate B


title: cell line2_Vector_KT_subline2_A

description: Gene expression data from cell line2 transduced with the empty vector.

source_name: Cell line2 transduced with empty vector, subline 2, replicate A

value: empty


title: cell line2_Vector_KT_subline1_B

source_name: Cell line2 transduced with empty vector, subline 1, replicate B


title: T6(6)-GATA1ER_leukemia_48hr_b-est_rep2

description: Gene expression data from Gata1-rescued leukemic cells.

source_name: Gata1-ER transduced T6(6) leukemic cells 48hrs after adding beta-estradiol

growth_protocol: Gata1-ER transduced leukemic cells were grown in IMDM+10%FCS+IL3 or Tpo.

treatment_protocol: Gata1-ER transduced leukemic cells were treated with or without 10e-7 M beta-estradiol.

value: mutant M7

value: beta-estradiol


title: T6(6)-GATA1ER_leukemia_48hr_control_rep2

description: Gene expression data from untreated leukemic cells.

source_name: Gata1-ER transduced T6(6) leukemic cells at time point 48hrs, untreated control

value: untreated


title: T6(6)-GATA1ER_leukemia_24hr_control_rep1

source_name: Gata1-ER transduced T6(6) leukemic cells at time point 24hrs, untreated control


title: T6(6)-GATA1ER_leukemia_24hr_control_rep2


title: T6(6)-GATA1ER_leukemia_24hr_b-est_rep2

source_name: Gata1-ER transduced T6(6) leukemic cells 24hrs after adding beta-estradiol


title: M7_leukemia_peripheral_blood_rep1

source_name: GFP+ T6(6) leukemic blasts from peripheral blood, mouse 1


title: T6(6)-GATA1ER_leukemia_8hr_b-est

source_name: Gata1-ER transduced T6(6) leukemic cells 8hrs after adding beta-estradiol


title: T6(6)-GATA1ER_leukemia_24hr_b-est_rep1


title: cell line2_Plag1_KT_subline2_A

source_name: Cell line2 transduced with Plag1, subline 2, replicate A


title: T6(6)-GATA1ER_leukemia_48hr_control_rep1


title: cell line2_Vector_KT_subline2_B

source_name: Cell line2 transduced with empty vector, subline 2, replicate B


title: T6(6)-GATA1ER_leukemia_0hr_control_rep2

source_name: Gata1-ER transduced T6(6) leukemic cells at time point 0, untreated control


title: T6(6)-GATA1ER_leukemia_48hr_b-est_rep1


title: BMP4 treated AHF explants 24hr after plating

city: Rehovot

first: Amit

last: Zeisel

address: Weizmann Institute

department: Physics of complex systems

country: Israel

institute: Weizmann Institute of Science

hyb_protocol: According to Affymetrix manual

scan_protocol: According to Affymetrix manual

data_processing: MAS5+lowess normalization

organism: Gallus gallus

label_protocol: According to Affymetrix manual

growth_protocol: culture on a collagen drop covered with 0.5 ml of dissection medium (10% Fetal Calf Serum, chick embryo extract 2.5% and pen/strep 0.5% in MEM medium) in a four-well plate

extract_protocol: QIAGEN miniRNA extraction kit was used.

tag: time point (hours)

tag: agent

value: human recombinant BMP4


title: BMP4 treated AHF explants 12hr after plating, B


title: T6(6)-GATA1ER_leukemia_0hr_control_rep1

tag: treatment


title: untreated AHF explants 12hr after plating, B


title: cell line2_Vector_KT_subline1_A

source_name: Cell line2 transduced with empty vector, subline 1, replicate A


title: untreated AHF explants 24hr after plating


title: cell line2_Plag1_KT_subline1_A

source_name: Cell line2 transduced with Plag1, subline 1, replicate A


title: BMP4 treated AHF explants 12hr after plating, A


title: blood C57BL/6J 4hours rep3

source_name: blood C57BL/6J mouse strain blood taken 4 hours after infection with S. aureus

value: Staphylococcus aureus


title: untreated AHF explants 3hr after plating


title: untreated AHF explants

source_name: untreated AHF explants


title: untreated AHF explants 12hr after plating, A


title: BMP4 treated AHF explants 3hr after plating


title: CVS 9 methylated CpG dinucleotides

status: Public on Jul 31 2010

city: Pittsburgh

first: Tianjiao

last: Chu

state: PA

address: 204 Craft Ave

institute: Magee Womens Research Institute

hyb_protocol: Standard Illumina protocol used, See Methylation InfiniumMethylation UserGuides

data_processing: Illumina Bead Studio

label: cy3, cy5

source_name: chorionic villus

extract_protocol:
The standard Illumina protocol for the Infiniuam Humanmethylation27 arrays was used. 500ng genomic DNA was bisulphite converted before labeling.
DNA Extraction from CVS: CVS samples were obtained between gestational weeks 11 and 13 from the Magee-Womens Hospital Cytogenetic Laboratory.  Samples were dissected under a microscope and separated from any decidua or flecks of blood.  The culture media was removed and the tissue placed in 1.5 -2.0mL microcentrifuge tubes before freezing at -80oC until DNA was extracted.  To extract the DNA, one 5mm stainless steel bead and 180*L buffer ATL (from Qiagen’s DNeasy Blood and Tissue kit) were added to each CVS sample. The samples were placed in the TissueLyser (Qiagen) Adaptor set 2 x 24, and the TissueLyser was operated for 20 seconds at 30Hz.  The DNA was then purified using the DNeasy Blood and Tissue kit as per the manufacturer’s protocol.
DNA Extraction from MBC: MBCs were obtained between gestational weeks 11 and 13 from the Magee Women’s Hospital Prenatal Screening lab. DNA was extracted from the MBC’s using a modified protocol previously described by Iovannisci, et al., 2006 (Iovannisci et al., 2006), using reagents from the MasturePure DNA Purification Kit (Epincentre Technologies, Madison, WI, Cat. No. MCD85201).  Briefly, clotted blood (approximately 1mL) was mixed with an equal volume (1mL) of 2X Tissue and Cell Lysis Solution, votexed for 10s and combined with 2mL Tissue and Cell Lysis Solution (MasturePure kit) containing 25ng/*L proteinase K. 2mL of MPC Protein Precipitation Reagent was added to the total volume (4mL) of the lysed sample and vortex vigorously for 10-15 sec, after which samples were cooled on ice for * 1 hour. Cell debris were then pelleted by centrifugation (x2) for at least 30 min at * 2000g and supernatants transferred to a new 50mL conical tube.  DNA was precipitated in 2 volumes of isoproponal, purified by phenol/chloroform extraction and resuspended in 50*L DNAse/RNAse free water.

value: placenta


title: CSV 12 unmethylated CpG dinucleotides

scan_protocol: Standard Illumina protocol used, See Methylation InfiniumMethylation UserGuides


title: CSV 11 methylated CpG dinucleotides

label_protocol: Standard Illumina protocol used, See Methylation InfiniumMethylation UserGuides


title: CSV 11 unmethylated CpG dinucleotides


title: CVS10 unmethylated CpG dinucleotides


title: CSV 12 methylated CpG dinucleotides


title: CVS10 methylated CpG dinucleotides


title: Δisw2 trf4, Replicate 3

type: mixed

city: Seattle

first: Toshio

last: Tsukiyama

state: WA

address: 1100 Fairview Ave N

department: Basic Science

institute: Fred Hutchinson Cancer Research Center

description:
DV25_isw2trf4_3866_227896

Biological replicate of isw2 trf4 Rep 1, isw2 trf4 Rep 4.
Technical replicate of isw2 trf4 Rep 2

hyb_protocol: According to NimbleGen manufacturer's suggested protocol.

data_processing: Biweight mean-adjusted log2 ratios (Cy5/Cy3) were generated using NimbleScan software (NimbleGen) for each hybridization.

organism: Saccharomyces cerevisiae

source_name: Δisw2 trf4

label_protocol: 25 μg total RNA and 12 μg random hexamers were placed in 40 μl H2O.  The reaction was incubated at 70°C for 5 min, 25°C for 5 min, and 4°C for 5 min.  0.5 μL of 1 mg ml-1 Actinomycin D, 20 μl of 5X SuperScript III Buffer (Invitrogen), 8 μl of 0.1 M DTT, 1 μl of 40 U μl-1 RNase Inhibitors (Roche), 4 μL of dNTP mix (10 mM dATP, 10 mM dGTP, 10 mM dCTP, 8.5 mM dTTP, and 1.5 mM dUTP), 4 μl of 200 U μl-1 SuperScript III (Invitrogen), and 20 μL H2O were added, and the reaction was incubated at 25°C for 10 min, 48°C for 90 min, and 70°C for 10 min.  2 μl of 0.1 mg ml-1 RNaseA and 2 μl of 5,000 U μl-1 RNaseH (NEB) were added and incubated at 37°C for 30 min.  The reaction was stopped by phenol:chloroform extraction and unincorporated random hexamers were removed with a gel filtration spin column.  cDNA was ethanol precipitated and the pellet was suspended in 80 μl H2O.

extract_protocol: Total RNA was isolated by standard hot acid phenol extraction.

value: congenic to S288C background

tag: genotype

value: Δisw2 trf4

source_name: Input Genomic DNA from WT

label_protocol: Purified genomic DNA was fragmented with DNaseI to an average size ~25-75 bp.  Fragmented DNA (30 ng) was heated at 70°C for 5 min.  Then, 5 μl Buffer #4 (NEB), 5 μl of 2.5 mM CoCl2 (NEB), 5 μl of 1 mM Cy3-dUTP (GE Healthcare), and 5 μl of 20,000 U ml-1 terminal deoxytransferase (NEB) were added to a total volume of 50 μl.  The reaction was incubated at 37°C for 3 hours.  50 μl H2O was added and labeled DNA was purified with a gel filtration spin column and ethanol precipitation.  The pellet was suspended in a final volume of 50 μl H2O.

extract_protocol: Input genomic DNA was isolated from WT cells with Qiagen Genomic DNA columns according to the manufacturer's protocols.

value: WT


title: Δtrf4, Replicate 1

description:
AY186_trf4_3812_251486.2

Biological replicate of trf4 Rep 2, trf4 Rep 4.
Technical replicate of trf4 Rep 3.

scan_protocol: According to NimbleGen manufacturer's suggested protocol.


title: Δisw2 trf4, Replicate 1

description:
AY202_isw2trf4_3868_319926.3

Biological replicate of isw2 trf4 Rep 2, isw2 trf4 Rep 3.
Technical replicate of isw2 trf4 Rep 4


title: WT, Replicate 4

description:
DV2_WT_3775_145502.1

Biological replicate of WT Rep 3.
Technical replicate of WT Rep 1, WT Rep 2.

source_name: WT


title: Δtrf4, Replicate 2

description:
AY202_trf4_3811_319930.2

Biological replicate of trf4 Rep 1, trf4 Rep 3.
Technical replicate of trf4 Rep 4.


title: CVS 9 unmethylated CpG dinucleotides


title: Δisw2 rrp6, Replicate 2

description:
AY_vs_.190_isw2rrp6_4340_253178

Biological replicate of isw2 rrp6 Rep 3.
Technical replicate of isw2 rrp6 Rep 1.

source_name: Δisw2 rrp6

value: Δisw2 rrp6


title: Δrrp6, Replicate 3

description:
DV28_rrp6_4336_250392

Biological replicate of rrp6 Rep 1, rp6 Rep 2.


title: Δisw2 trf4, Replicate 2

description:
AY_vs_.187_isw2trf4_3866_251802

Biological replicate of isw2 trf4 Rep 1, isw2 trf4 Rep 4.
Technical replicate of isw2 trf4 Rep 3.


title: CVS 6 methylated CpG dinucleotides


title: Δrrp6, Replicate 2

description:
DV27_rrp6_4334_252346

Biological replicate of rrp6 Rep 3.
Technical replicate of rrp6 Rep 1.


title: CVS 5 methylated CpG dinucleotides


title: Δisw2, Replicate 3

description:
DV3_isw2_3858_145605.1

Technical replicate of isw2 Rep 1, isw2 Rep 2.


title: WT, Replicate 3

description:
DV16_WT_3776_145605.3

Biological replicate of WT Rep 1, WT Rep 2, WT Rep 4.


title: Δtrf4, Replicate 4

description:
DV4_trf4_3811_145489.1

Biological replicate of trf4 Rep 1, trf4 Rep 3.
Technical replicate of trf4 Rep 2.


title: CVS 5 unmethylated CpG dinucleotides


title: Δrrp6, Replicate 1

description:
AY202_rrp6_4334_319926.2

Biological replicate of rrp6 Rep 3.
Technical replicate of rrp6 Rep 2.


title: Δisw2, Replicate 1

description:
AY195_isw2_3858_251802.2

Technical replicate of isw2 Rep 2, isw2 Rep 3.


title: Δisw2, Replicate 2

description:
AY202_isw2_3858_319894

Technical replicate of isw2 Rep 1, isw2 Rep 3.


title: CVS 6 unmethylated CpG dinucleotides


title: Δisw2 rrp6, Replicate 1

description:
AY202_isw2rrp6_4340_319894.2

Biological replicate of isw2 rrp6 Rep 3.
Technical replicate of isw2 rrp6 Rep 2.


title: Δtrf4, Replicate 3

description:
Biological replicate of trf4 Rep 2, trf4 Rep 4.
Technical replicate of trf4 Rep 1.


title: WT, Replicate 2

description:
AY201_WT_3775_2_319926

Biological replicate of WT Rep 3.
Technical replicate of WT Rep 1, WT Rep 4.


title: CVS 8 unmethylated CpG dinucleotides


title: WT, Replicate 1

description:
AY201_WT_3775_1_319930

Biological replicate of WT Rep 3.
Technical replicate of WT Rep 2, WT Rep 4.


title: Δisw2 trf4, Replicate 4

description:
DV5_isw2trf4_3868_146746.1

Biological replicate of isw2 trf4 Rep 2, isw2 trf4 Rep 3.
Technical replicate of isw2 trf4 Rep 1


title: CVS 8 methylated CpG dinucleotides


title: CVS 7 methylated CpG dinucleotides


title: CVS 3  methylated CpG dinucleotides


title: CVS 2 methylated CpG dinucleotides


title: CVS 4 unmethylated CpG dinucleotides


title: CVS 3 unmethylated CpG dinucleotides


title: CVS 4 methylated CpG dinucleotides


title: Δisw2 rrp6, Replicate 3

description:
DV29_isw2rrp6_4338_251486

Biological replicate of isw2 rrp6 Rep 1, isw2 rrp6 Rep 2.


title: CL_24h post PG_day 11_replicate5

city: East Lansing

first: juan

middle: p

last: steibel

state: MI

address: 1205 I Anthony Hall

institute: Michigan State University

description: Day_11_24 hour post PG

hyb_protocol: Labeled cRNA was hybridized to GeneChip Bovine Genome Arrays (Affymetrix, Santa Clara, CA) containing 24,072 25-mer probe sets with hybridization and washing conditions as recommended by the manufacturer

scan_protocol: Affymetrix Genearray scanner 3000, with 7G upgrade

data_processing: R/Bioconductor RMA. Linear fixed effects model with effect of treatment, shrinkage and permutation analysis implemented through MAANOVA

organism: Bos taurus

source_name: Corpus luteum tissue 24h post PG on day 11

label_protocol: Total RNA was subjected to reverse transcription for synthesis of cDNA, which served as a template for synthesis of full length biotin labeled cRNA using the GeneChip HT One-Cycle Target Labeling and Controls Kit (Affymetrix, Santa Clara, CA).  Labeled cRNA was then fragmented to ~ 1000 base fragments prior to hybridization.

extract_protocol: Total RNA was isolated from luteal tissue using the PerfectPure RNA Cell and Tissue kit according to the manufacturer's instructions.

treatment_protocol: Corpora lutea were collected  from thirty Angus crossbred heifers assigned to one of six treatments (n = 5 per treatment) at 0 (control), 4 or 24 h following injection of saline (control) or prostaglandin F2α on d 4 or d 11 of the estrous cycle.

value: Corpus luteum

tag: breed

value: Angus


title: CL_0h post PG_day 4_replicate5

description: Day_4_0 hour post PG

source_name: Corpus luteum tissue 0h post PG on day 4


title: CL_4h post PG_day 11_replicate5

description: Day_11_4 hour post PG

source_name: Corpus luteum tissue 4h post PG on day 11


title: CL_4h post PG_day 4_replicate5

description: Day_4_4 hour post PG

source_name: Corpus luteum tissue 4h post PG on day 4


title: CVS 2 unmethylated CpG dinucleotides


title: CL_24h post PG_day 4_replicate5

description: Day_4_24 hour post PG

source_name: Corpus luteum tissue 24h post PG on day 4


title: CL_24h post PG_day 4_replicate4

description: Day_4_24 hour post PG


title: CVS 1 unmethylated CpG dinucleotides


title: CVS 1 methylated CpG dinucleotides


title: CL_0h post PG_day 11_replicate5

description: Day_11_0 hour post PG

source_name: Corpus luteum tissue 0h post PG on day 11


title: MBC 12 methylated CpG dinucleotides

source_name: maternal blood cells

value: maternal blood cells


title: MBC 12 unmethylated CpG dinucleotides


title: CL_4h post PG_day 4_replicate4

description: Day_4_4 hour post PG


title: CVS 7 unmethylated CpG dinucleotides


title: MBC 10 unmethylated CpG dinucleotides


title: CL_24h post PG_day 11_replicate4

description: Day_11_24 hour post PG


title: MBC 11 unmethylated CpG dinucleotides


title: CL_0h post PG_day 11_replicate4

description: Day_11_0 hour post PG


title: MBC 11 methylated CpG dinucleotides


title: CL_0h post PG_day 4_replicate4

description: Day_4_0 hour post PG


title: MBC 9 methylated CpG dinucleotides


title: CL_4h post PG_day 4_replicate3

description: Day_4_4 hour post PG


title: CL_24h post PG_day 4_replicate3

description: Day_4_24 hour post PG


title: MBC 8 unmethylated CpG dinucleotides


title: MBC 7 methylated CpG dinucleotides


title: MBC 10 methylated CpG dinucleotides


title: MBC 8 methylated CpG dinucleotides


title: CL_0h post PG_day 4_replicate3

description: Day_4_0 hour post PG


title: MBC 9 unmethylated CpG dinucleotides


title: MBC 5 methylated CpG dinucleotides


title: MBC 6 unmethylated CpG dinucleotides


title: MBC 3 methylated CpG dinucleotides


title: CL_0h post PG_day 4_replicate2

description: Day_4_0 hour post PG


title: CL_24h post PG_day 4_replicate2

description: Day_4_24 hour post PG


title: MBC 6 methylated CpG dinucleotides


title: CL_4h post PG_day 4_replicate2

description: Day_4_4 hour post PG


title: CL_24h post PG_day 4_replicate1

description: Day_4_24 hour post PG


title: CL_4h post PG_day 4_replicate1

description: Day_4_4 hour post PG


title: MBC 4 methylated CpG dinucleotides


title: CL_4h post PG_day 11_replicate3

description: Day_11_4 hour post PG


title: CL_0h post PG_day 4_replicate1

description: Day_4_0 hour post PG


title: MBC 3 unmethylated CpG dinucleotides


title: CL_0h post PG_day 11_replicate3

description: Day_11_0 hour post PG


title: MBC 2 methylated CpG dinucleotides


title: CL_24h post PG_day 11_replicate2

description: Day_11_24 hour post PG


title: CL_0h post PG_day 11_replicate2

description: Day_11_0 hour post PG


title: MBC 5 unmethylated CpG dinucleotides


title: CL_4h post PG_day 11_replicate2

description: Day_11_4hour post PG


title: CL_24h post PG_day 11_replicate1

description: Day_11_24 hour post PG


title: MBC 7 unmethylated CpG dinucleotides


title: CL_24h post PG_day 11_replicate3

description: Day_11_24 hour post PG


title: MBC 4 unmethylated CpG dinucleotides


title: MBC 1 methylated CpG dinucleotides


title: MBC 1 unmethylated CpG dinucleotides


title: CL_0h post PG_day 11_replicate1

description: Day_11_0 hour post PG


title: CL_4h post PG_day 11_replicate1

description: Day_11_4 hour post PG


title: MBC 2 unmethylated CpG dinucleotides


title: iris differentiated 3

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

description: RMA expression value derived from GeneSpring GX software; core-exon analysis

hyb_protocol: Samples were hybridized with GeneChip Human Gene 1.0 ST Arrays (Affymetrix) and scanned in Affymetrix 7G workstation with genechip operating software at Vision Research Foundation Sankara nethralaya.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing:
Raw data was analyzed using GeneSpring GX v 10.0.1 software from Agilent. Normalization of the data was done in GeneSpring GX using the recommended Quantile normalization.
Summarization Algorithm: ExonRMA16
Transcript level: CORE
Technology: Affymetrix.ExonExprChip.HuGene-1_0-st-v1
Normalization: Quantile
Baseline Transformation: median of all samples

source_name: iris differentiated

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: All the samples were collected in DMEM and processed immediately or stored in liquid nitrogen for later processing

extract_protocol: RNA was isolated from pellet of cells with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions. Obtained total RNA was quantified using nanodrop and the quality was analysed by Agilent Bioanalyser on RNA Nano chips and the samples with RIN<7.0 was used for further processing.

treatment_protocol: Primary cells were collected as such by scraping form the tissue, these primary cells were grow under neurosphere culture conditions and further under differentiation conditions.

value: cadeveric eye

tag: cell type

value: Primary cultured cells


title: iris differentiated 2


title: retina 1

source_name: retina


title: Liver_hyperglycima_no.8

city: Kanazawa

first: Hirofumi

last: Misu

address: 13-1 Takaramachi

institute: Kanazawa University

description: Gene expression data from human liver.

hyb_protocol: Ten micrograms of labelled and fragmented cRNA was hybridised onto a Human Genome U133 Plus 2.0 Array (Affymetrix) for 16 h at 45°C.

scan_protocol: Chips were scanned by using GeneChip Scanner3000, Affymetrix.

data_processing: A scanned image was quantified using GCOS version 1.1.1 (GeneChip Operating Software; Affymetrix) with the default parameters for the statistical algorithm and all probe sets scaled to a target intensity of 100.

source_name: Liver, fasting

label_protocol: A total of 100 ng of total RNA was labelled according to the small sample labelling protocol recommended by the manufacturer.

growth_protocol: Hepatic tissues were obtained with percutaneous needle liver biopsy, and immediately frozen in liquid nitrogen and stored at −80°C until use.

extract_protocol: Total RNA was extracted with a kit (Micro RNA Isolation Kit; Stratagene, La Jolla, CA, USA), purified with RNeasy MiniElute Cleanup Kit (Qiagen, Hilden, Germany).

treatment_protocol: Patients with type 2 diabetes were treated with diet therapy alone or insulin; no patients were receiving any oral hypoglycaemic agent. Participants receiving statins, ACE inhibitors or angiotensin II receptor blockers were excluded.

value: liver

value: female

tag: disease status

value: type 2 diabetes


title: retina 2


title: iris neurospheres 3

source_name: iris neurospheres


title: ciliary neurospheres 3

source_name: ciliary neurospheres


title: iris differentiated 1


title: iris neurospheres 2


title: ciliary differentiated 3

source_name: ciliary differentiated


title: ciliary differentiated 1


title: Liver_hyperglycima_no.5

description: Gene expression data from human liver.

value: male


title: Liver_hyperglycima_no.10

description: Gene expression data from human liver.


title: iris neurospheres 1


title: N-terminal G3BP overexpression vs Mock

city: Nankoku

first: Keisuke

last: Taniuchi

address: Kohasu, Oko

institute: Kochi University Medical School

hyb_protocol: Cy3- and Cy5-conjugated cDNA targets were then purified by QIAquick PCR purification columns, combined, vacuum-concentrated, and diluted to 55 µl with hybridization solution containing final concentrations of 50% formamide, 4.1x Denhardts, and 4.4x SSC.  To reduce nonspecific hybridization, the hybridization solution also contained final concentrations of 15 µg human Cot1 DNA (Invitrogen), 12µg poly-deoxyadenylate, and 5 µg of yeast tRNA (Sigma).  After clarification by centrifugation, the cDNA/hybridization solution was applied to DNA microarrays and incubated at 42ºC for 16-20 h.

scan_protocol: After hybridization, microarray slides were washed by immersion in 2X SSC, 0.1%SDS for 5 min at room temperature, 1X SSC, 0.01% SDS for 5 min at room temperature, and 0.2X SSC for 2 min at room temperature.  The microarrays were dried by centrifugation for 5 min at 1000 rpm and scanned immediately with a ScanArray 4000 confocal laser system (Perkin-Elmer).

data_processing: Fluorescent intensities were background subtracted, and normalization and filtering of the data were performed using the QuantArray software package (Perkin-Elmer). Total background subtracted intensities for each channel were used for normalization. Differential expression was defined as those genes exhibiting a 2-fold up or down average ratio in signal intensity (after normalization).

source_name: Mock

label_protocol: To generate fluorescently-labeled single-stranded cDNA target, 40µg of total RNA was incubated with 2µg of anchored oligodeoxythymidylate primer in a total volume of 30µl at 70ºC for 10 min and chilled on ice.  To each sample was added 10X first strand buffer (6µl), 0.1M DTT (6µl), 20X aminoallyl-dNTP mix (3µl; 10mM dATP, 10mM dCTP, 10mM dGTP, 6mM dTTP, and 4mM aminoallyl-dUTP), RNase inhibitor (0.5µl) (RNasin, Promega), and StrataScript reverse transcriptase (3µl; 50U/µl).  After incubation at 48ºC for 60 min, an additional 50 units (1µl) of StrataScript was added to the samples and incubated for an additional 60 min. The reaction was stopped by adding 12 µl of 0.5M EDTA (pH 8).  Residual RNA was hydrolyzed by adding 12 µl of 1M NaOH to the mixture followed by incubation at 65ºC for 15 min and cooled to room temperature.  The reaction was neutralized with 16.8µl of 1N HCl.  First-strand cDNA was purified from unicorporated amino allyl-dUTPs on QIAquick PCR purification columns (Qiagen) according to manufacuter’s protocols, except that QIAquick wash buffer was replaced with 5 mM potassium phosphate buffer (pH 8.5) containing 80% ethanol, and cDNA was eluted with 4 mM potassium phosphate buffer (pH 8.5) and vacuum-dried.  cDNA was resuspended in 10 µl 0.05 M Na2CO3 buffer (pH 9), mixed with either Cy3 or Cy5 monofunctional NHS-ester (Amersham Pharmacia), and incubated for 90 min in the dark at room temperature.

extract_protocol: Total RNA was extracted from control and N-terminal G3BP overexpressed S2-013 cells using the RNeasy kit with DNase I treatment.

tag: tissue type

value: primary pancreatic cancer

value: pancreatic cancer cell line (S2-013)

source_name: overexpression of N-terminal G3BP


title: ciliary neurospheres 2


title: Liver_hyperglycima_no.6

description: Gene expression data from human liver.

tag: gender


title: Liver_hyperglycima_no.9

description: Gene expression data from human liver.


title: ciliary neurospheres 1


title: ciliary 3

source_name: ciliary

value: Primary cells


title: iris 3

source_name: iris


title: Liver_hyperglycima_no.2

description: Gene expression data from human liver.


title: Liver_hyperglycima_no.4

description: Gene expression data from human liver.


title: iris 2


title: iris 1


title: Liver_hyperglycima_no.7

description: Gene expression data from human liver.


title: Liver_hyperglycima_no.3

description: Gene expression data from human liver.


title: Liver_hyperglycima_no.1

description: Gene expression data from human liver.


title: ciliary differentiated 2


title: ciliary 1


title: Tricellular pollen 11447_1

city: Shanghai

first: Weihua

last: Tang

address: 300 Fenglin Rd

country: China

institute: Shanghai Inst. Plant Phys. & Eco.

description: default protocol, available at www.agilent.com

data_processing:
Use the Feature Extraction to obtain raw data.
Data was processed by using Genespring

organism: Oryza sativa

extract_protocol: Arcturus Picopure RNA isolation kit

value: tricellular pollen

value: Nipponbare

tag: age

value: one week-old

tag: developmental stage

value: seedling


title: ciliary 2

tag: tissue


title: CL_4h post PG_day 11_replicate4

description: Day_11_4 hour post PG


title: Tricellular pollen 11447_2

hyb_protocol: default protocol, available at www.agilent.com

value: triccellular pollen

tag: strain


title: Pollen mother cells 11447_4

scan_protocol: default protocol, available at www.agilent.com

value: pollen mother cells


title: Pollen mother cells 11447_3

label_protocol: default protocol, available at www.agilent.com


title: LSL833

status: Public on Jul 30 2010

city: London

first: Bartlomiej

middle: Przemyslaw

last: Przychodzen

address: Coldharbour Lane

department: Department of Haematology

country: United Kingdom

institute: King's College

hyb_protocol: Affymetrix standard procedure

scan_protocol: Affymetrix standard procedure

data_processing: Copy numbers were estimated using CNAG v3.0.3 analysis suite and further screened in Chromosome Analysis Suite for overlap with known copy number variants using the .chp files.

source_name: MDS TET2LSL833

label_protocol: Affymetrix standard procedure

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from mononuclear cell preparations of leukemic blasts obtained from peripheral blood or bone marrow at diagnosis using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

tag: chromosomal aberration status

value: chromosomal aberrations found

tag: mutation

value: no

tag: who

value: RAEB II

tag: aml transformation

value: No

tag: iPSs


title: WGA_LSL822

source_name: MDS TET2WGA_LSL822

value: no chromosomal aberrations found

value: RCMD


title: WGA_LSL2583

source_name: MDS TET2WGA_LSL2583

value: RCMD Srcmd


title: WGA_LSL3179

source_name: MDS TET2WGA_LSL3179

value: yes


title: LSL957_2

source_name: MDS TET2LSL957_2


title: LSL961

source_name: MDS TET2LSL961

value: YES


title: WGA_LSL2244

source_name: MDS TET2WGA_LSL2244

value: Saml


title: LSL915

source_name: MDS TET2LSL915

value: AML M4


title: WGA_LSL2375

source_name: MDS TET2WGA_LSL2375

value: RA


title: LSL836

source_name: MDS TET2LSL836

value: MDS/MPD

value: Yes


title: LSL671

source_name: MDS TET2LSL671

value: AML M1


title: WGA_LSL2344

source_name: MDS TET2WGA_LSL2344

value: rcmd-RS


title: LSL682

source_name: MDS TET2LSL682

value: RAEB I


title: LSL3147

source_name: MDS TET2LSL3147

value: chromosomal aberrations found

value: RAEB I/RCMD


title: WGA_LSL2007

source_name: MDS TET2WGA_LSL2007

value: no


title: LSL953

source_name: MDS TET2LSL953

value: No


title: LSL887

source_name: MDS TET2LSL887

value: no chromosomal aberrations found

value: RAEB-II


title: WGA_LSL3217

source_name: MDS TET2WGA_LSL3217

value: RCMD


title: WGA_LSL688

source_name: MDS TET2WGA_LSL688

value: RAEB-I


title: LSL955

source_name: MDS TET2LSL955


title: WGA_LSL2018

source_name: MDS TET2WGA_LSL2018


title: WGA_LSL1884

source_name: MDS TET2WGA_LSL1884


title: WGA_LSL1854

source_name: MDS TET2WGA_LSL1854

value: Normal


title: LSL3104

source_name: MDS TET2LSL3104

value: RAEB II


title: LSL704

source_name: MDS TET2LSL704


title: LSL654

source_name: MDS TET2LSL654


title: LSL2984

source_name: MDS TET2LSL2984

value: yes


title: LSL3513

source_name: MDS TET2LSL3513

value: sRAEB I


title: WGA_LSL1681

source_name: MDS TET2WGA_LSL1681


title: LSL2859_2

source_name: MDS TET2LSL2859_2


title: LSL2470

source_name: MDS TET2LSL2470


title: LSL2844

source_name: MDS TET2LSL2844


title: LSL2218_2

source_name: MDS TET2LSL2218_2


title: LSL2841

source_name: MDS TET2LSL2841

value: Saml


title: LSL2066

source_name: MDS TET2LSL2066

value: RAEB 1


title: LSL2404

source_name: MDS TET2LSL2404


title: LSL2306_2

source_name: MDS TET2LSL2306_2


title: LSL2692

source_name: MDS TET2LSL2692

value: MDS MPD


title: LSL2762_2

source_name: MDS TET2LSL2762_2


title: LSL2236_2

source_name: MDS TET2LSL2236_2


title: LSL2251

source_name: MDS TET2LSL2251


title: LSL2719

source_name: MDS TET2LSL2719

value: Yes


title: LSL2750

source_name: MDS TET2LSL2750

value: systemic mastocytosis


title: LSL2596

source_name: MDS TET2LSL2596


title: LSL2063

source_name: MDS TET2LSL2063

value: RAEB -I


title: LSL1899

source_name: MDS TET2LSL1899

value: chromosomal aberrations found

value: RAEB I


title: LSL2222

source_name: MDS TET2LSL2222

value: No


title: LSL2029

source_name: MDS TET2LSL2029

value: no


title: LSL2337

source_name: MDS TET2LSL2337

value: MDS/MPD


title: LSL2214

source_name: MDS TET2LSL2214

value: no chromosomal aberrations found


title: LSL1932

source_name: MDS TET2LSL1932

value: RCMD


title: LSL2531

source_name: MDS TET2LSL2531


title: LSL2025

source_name: MDS TET2LSL2025


title: LSL1782

source_name: MDS TET2LSL1782


title: LSL1684_2

source_name: MDS TET2LSL1684_2


title: LSL2799

source_name: MDS TET2LSL2799


title: LSL1874

source_name: MDS TET2LSL1874

value: CMML-II


title: LSL1740

source_name: MDS TET2LSL1740


title: LSL2392

source_name: MDS TET2LSL2392


title: LSL1665

source_name: MDS TET2LSL1665

value: AML M6


title: LSL1625

source_name: MDS TET2LSL1625

value: yes


title: LSL1449

source_name: MDS TET2LSL1449

value: RAEB II


title: LSL1619

source_name: MDS TET2LSL1619


title: LSL1490

source_name: MDS TET2LSL1490


title: LSL1586

source_name: MDS TET2LSL1586


title: LSL1444

source_name: MDS TET2LSL1444


title: LSL1825_2

source_name: MDS TET2LSL1825_2

value: sAML


title: osmpk6 complemented ethanol rep3

city: Tsukuba

first: Hirohiko

last: Hirochika

state: Ibaraki

address: 2-1-2 Kannondai

department: Division of Genome and Biodiversity Research

institute: National Institute of Agrobiological Sciences

description: gene expression after 12h in ethanol treated cell

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ml of 2x GE buffer was added to the fragmentation mixture and hybridized to Agilent Rice Oligo Microarrays (G2519F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with SSPE Buffer  and 1 minute with 37°C SSPE buffer 2, then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software v9.5 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 015241_D_F_20061020) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: osmpk6 complemented line, ethanol treatment, 12h, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.4 ug RNA using the Low RNA Input Linear Amplification/Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Calli of O. sativa L. cv. Nipponbare were suspension-cultured at 25℃ in N6D liquid medium and subcultured in fresh medium every 7days. For the treatment, suspension cell cultures were subcultured for 3 days in a fresh medium.

extract_protocol: RNA was prepared using the Isogen (Nippongene) and RNeasy Plnat Mini kit (Qiagen) following the manufacturer's recommendations.  The protocol includes an on-column DNase digestion.  RNA was quantified using a NanoDrop ND-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Suspension cultured cells were transferred to 60 mm dishes (0.4 g cells, 5 ml fresh medium) and maintained in suspension for O.N. at 25˚C with gentle shaking at 100 rpm. Incubations with shaking were continued for various lengths of time after treatments. Dexamethasone (DEX) was used at 10 mM, starting from a 10 mM stock solution in ethanol.

tag: sample type

value: suspension cultured cell

tag: cultivar

value: Nipponbare


title: LSL1326

source_name: MDS TET2LSL1326

value: Yes


title: osmpk6 complemented DEX rep3

description: gene expression after 12h in DEX treated cell

source_name: osmpk6 complemented line, DEX treatment, 12h, replicate 3

tag: genotype


title: LSL1121

source_name: MDS TET2LSL1121

value: tMDS


title: MR knockout, corticosterone stimulated, biological rep2

city: ann arbor

first: mort

last: lab

address: 1150 W Med Ctr Dr

department: Physiology

institute: University of Michigan

description: Gene expression data from mineralocorticoid receptor knockout mouse peritoneal macrophages stimulated with corticosterone

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on Affymetrix Mouse Genome 430 2.0, washed and stained per manufacturer's instructions

scan_protocol: GeneArray scanner

data_processing: I used the affy and affycoretools package of Bioconductor version 2.2 for RMA normalization and log2 transformation with R version 2.7.

source_name: Cort Stimulated MRKO murine peritoneal macrophages

label_protocol: RNA was biotinylated using the Ovation Biotin Labeling system from NuGen, Inc.

growth_protocol: Mouse peritoneal macrophages were isolated 4 days after an intra-peritoneal injection of aged 3% Brewer’s thioglycolate. Macrophages were then cultured in media containing 10% FBS and isolated by differential adherence.

extract_protocol: Total RNA was isolated using an RNeasy kit (QIAGEN) following on-column DNase digestion.

treatment_protocol: Peritoneal macrophages were subsequently treated in the presence or absence of 1 µM Corticosterone for 24 hours.

value: peritoneal macropahges

value: male

tag: genotype/variation

value: MR fl / fl, LysM cre

tag: treatment

value: 24 hours of 1 µM Corticosterone


title: LSL1143

source_name: MDS TET2LSL1143

value: no

value: AML M4

value: No


title: LSL1310

source_name: MDS TET2LSL1310

value: chromosomal aberrations found


title: osmpk6 complemented DEX rep2

source_name: osmpk6 complemented line, DEX treatment, 12h, replicate 2


title: LSL1229

source_name: MDS TET2LSL1229

value: no chromosomal aberrations found

value: Saml


title: MR knockout, corticosterone stimulated, biological rep1

tag: cell type


title: LSL1614

source_name: MDS TET2LSL1614


title: osmpk6 complemented ethanol rep2

source_name: osmpk6 complemented line, ethanol treatment, 12h, replicate 2


title: osmpk6 complemented DEX rep1

source_name: osmpk6 complemented line, DEX treatment, 12h, replicate 1


title: G3345

source_name: MDS TET2G3345

value: RAEB-t

value: yes


title: Floxed Control, corticosterone stimulated, biological rep2

description: Gene expression data from floxed control mouse peritoneal macrophages stimulated with corticosterone

source_name: Cort Stimulated FC murine peritoneal macrophages

value: MR fl / fl


title: LSL1242

source_name: MDS TET2LSL1242

value: RAEB II


title: Floxed Control, corticosterone stimulated, biological rep1


title: Floxed Control, untreated, biological rep2

description: Gene expression data from floxed control mouse peritoneal macrophages

source_name: Unstimulated FC murine peritoneal macropahges

value: No treatment


title: Floxed Control, untreated, biological rep1


title: LSL1040

source_name: MDS TET2LSL1040

value: RCMD


title: LSL1078

source_name: MDS TET2LSL1078


title: osmpk6 DEX rep3

source_name: osmpk6, DEX treatment, 12h, replicate 3

value: suspension cultured cell

value: Nipponbare


title: G3242

source_name: MDS TET2G3242

value: CMML II


title: osmpk6 complemented ethanol rep1

source_name: osmpk6 complemented line, ethanol treatment, 12h, replicate 1


title: LSL1104

source_name: MDS TET2LSL1104

value: sAML M6


title: LSL1060

source_name: MDS TET2LSL1060

value: RAEB-I


title: osmpk6 ethanol rep3

source_name: osmpk6, ethanol treatment, 12h, replicate 3


title: G3279

source_name: MDS TET2G3279

value: no

value: RA


title: osmpk6 DEX rep2

source_name: osmpk6, DEX treatment, 12h, replicate 2


title: TSC2-/- p53-/-, biological replicate 2, treated, time course 2 hours

city: Cambridge

first: Pichai

last: Raman

address: 220 Massachusetts Avenue

institute: Novartis Institutes for BioMedical Research, Inc.

description: Gene Expression Data from TSC2 Deficient Mouse Embryonic Fibroblasts rapamycin treated for 2 hours

hyb_protocol: Resulting biotin-labeled cRNA was fragmented and hybridized to the Affymetrix Mouse 430_2 oligonucleotide microarray chip for 16 h at 45°C

scan_protocol: Affymetrix GCS 3000 GeneArray Scanner

data_processing: The raw data for microarray results were normalized using RMA from the R/Bioconductor package ‘affy’ and transformed (the Log2 Ratio was calculated over the median of the TSC2 Wild Type at 0 Hours). All treatments were compared back to the 0 h time point and WT was compared to both the 0 and 24 h time points. Fold Changes and P-values for array comparisons were calculated using the R/Bioconductor package ‘Limma’.

source_name: TSC2 Deficient Mouse Embryonic Fibroblasts, biological replicate 2, treated, time course 2 hours

label_protocol: Linear amplification with T7-RNA polymerase and biotin labeling were performed by in vitro transcription

growth_protocol: Tsc1 and Tsc2 wild-type and null MEFs were grown to 70% confluence in 10 cm plates.

extract_protocol: For each replicate, RNA was isolated using an RNeasy Mini Kit (Qiagen)

treatment_protocol: Cells were serum starved for 24 h in the presence of vehicle (DMSO) for 24 h or rapamycin (20 nM) for 2, 6, 12, or 24 h.

tag: cell line

value: Embryonic Fibroblasts

value: TSC2 Deficient

tag: time point

value: 2 hours

tag: agent

value: Rapamycin


title: LSL1147

source_name: MDS TET2LSL1147

value: no chromosomal aberrations found

value: No


title: LSL1280

source_name: MDS TET2LSL1280


title: TSC1-/-, biological replicate 1, treated, time course 6 hours

description: Gene Expression Data from TSC1 Deficient Mouse Embryonic Fibroblasts rapamycin treated for 6 hours

source_name: TSC1 Deficient Mouse Embryonic Fibroblasts, biological replicate 1, treated, time course 6 hours

value: TSC1 Deficient

value: 6 hours


title: TSC1-/-, biological replicate 2, treated, time course 2 hours

description: Gene Expression Data from TSC1 Deficient Mouse Embryonic Fibroblasts rapamycin treated for 2 hours

source_name: TSC1 Deficient Mouse Embryonic Fibroblasts, biological replicate 2, treated, time course 2 hours


title: TSC1-/-, biological replicate 2, treated, time course 6 hours

source_name: TSC1 Deficient Mouse Embryonic Fibroblasts, biological replicate 2, treated, time course 6 hours


title: TSC1-/-, biological replicate 2, treated, time course 12 hours

description: Gene Expression Data from TSC1 Deficient Mouse Embryonic Fibroblasts rapamycin treated for 11 hours

source_name: TSC1 Deficient Mouse Embryonic Fibroblasts, biological replicate 2, treated, time course 12 hours

value: 12 hours


title: osmpk6 DEX rep1

source_name: osmpk6, DEX treatment, 12h, replicate 1


title: osmpk6 ethanol rep2

source_name: osmpk6, ethanol treatment, 12h, replicate 2


title: TSC2-/- p53-/-, biological replicate 1, treated, time course 2 hours

source_name: TSC2 Deficient Mouse Embryonic Fibroblasts, biological replicate 1, treated, time course 2 hours


title: TSC2-/- p53-/-, biological replicate 1, treated, time course 6 hours

description: Gene Expression Data from TSC2 Deficient Mouse Embryonic Fibroblasts rapamycin treated for 6 hours

source_name: TSC2 Deficient Mouse Embryonic Fibroblasts, biological replicate 1, treated, time course 6 hours


title: TSC2-/- p53-/-, biological replicate 2, treated, time course 12 hours

description: Gene Expression Data from TSC2 Deficient Mouse Embryonic Fibroblasts rapamycin treated for 12 hours

source_name: TSC2 Deficient Mouse Embryonic Fibroblasts, biological replicate 2, treated, time course 12 hours


title: G3216

source_name: MDS TET2G3216

value: RAEB II


title: MR knockout, untreated, biological rep2

description: Gene expression data from mineralocorticoid receptor knockout mouse peritoneal macrophages

source_name: Unstimulated MRKO murine peritoneal macrophages

value: peritoneal macropahges

tag: gender

value: male

value: MR fl / fl, LysM cre

value: No treatment


title: TSC2-/- p53-/-, biological replicate 1, treated, time course 12 hours

source_name: TSC2 Deficient Mouse Embryonic Fibroblasts, biological replicate 1, treated, time course 12 hours

tag: tissue


title: MR knockout, untreated, biological rep1

tag: strain


title: osmpk6 ethanol rep1

source_name: osmpk6, ethanol treatment, 12h, replicate 1

value: suspension cultured cell

value: Nipponbare


title: TSC1-/-, biological replicate 1, treated, time course 24 hours

description: Gene Expression Data from TSC1 Deficient Mouse Embryonic Fibroblasts rapamycin treated for 14 hours

source_name: TSC1 Deficient Mouse Embryonic Fibroblasts, biological replicate 1, treated, time course 24 hours

value: 24 hours


title: G2348

source_name: MDS TET2G2348

tag: chromosomal aberration status

value: chromosomal aberrations found

value: no

value: RAEB-t

value: yes


title: H9_feeder_d0-C [miRNA]

city: San Diego

first: Andrew

last: Hinton

state: CA

address: 3525 John Hopkins Ct.

department: Pediatrics

institute: UC, San Diego

description: miRNA expression data from pluripotent hESCs

hyb_protocol: Hybridization, washing, staining, imaging and signal extraction were performed according to Affymetrix-recommended procedures, excet that the 20X GeneChip Eikaryotic Hybridization Control cocktail was omitted from the hybridization.

scan_protocol: Affymetrix GeneChip® 3000 7G scanner

data_processing: The signal processing implemented for the Ambion miRCHIP is a multi-step process involving probe specific signal detection calls, background estimate and correction, constant variance stabilization and either array scaling or global normalization. For each probe, an estimated background value is subtracted that is derived from the median signal of a set of G-C matched anti-genomic controls. Arrays within a specific analysis experiment were normalized together according to the variance stabilization methods described by Huber et al. (Huber et al., 2002). Detection calls were based on a Wilcoxon rank-sum test of the miRNA probe signal compared to the distribution of signals from GC-content matched anti-genomic probes.  For statistical hypothesis testing, a two-sample t-Test, with assumption of equal variance, was applied.  One-way ANOVA was used for experimental designs with more than two experimental groupings or levels of the same factor.  These tests define which probes are considered to be significantly differentially expressed, or significant, based on a default p-value of 0.001 and log2 difference > 1.

source_name: H9 cells, day 0 of differentiation (pluripotent ESCs)

label_protocol: The 3' ends of the RNA molecules were tailed and biotin-labeled using the mirVana miRNA Labeling Kit (Ambion Inc., Austin, TX). The kit's dNTP mixture in the tailing reaction was replaced with a proprietary nucleotide mixture containing biotin-modified nucleotides (PerkinElmer, Waltham, MA).

growth_protocol: H9 were plated on feeder layer of mouse embryonic fibroblasts (MEFs) and grown in DMEM/F12 supplemented with 20% knockout serum replacement, 4 ng/mL basic FGF, and 10ng/mL activin A

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. The miRNA-enriched fraction of small RNAs was purified from total RNA by polyacrylamide gel electrophoresis using Ambion’s flashPAGE™ kits

treatment_protocol: For differentiation, growth medium was replaced with RPMI with 0% serum, 100ng/mL activin A and 25 ng/mL Wnt3A for 1 day, followed by RPMI with 0.2% serum and 100ng/mL Activin A for 2 days, followed by RPMI with 2% serum and 100ng/mL Activin A for 1 days.

value: H9 human embryonic stem cell line

tag: growth protocol

value: feeder layer

tag: time

value: 0 days


title: TSC1-/-, biological replicate 2, treated, time course 24 hours

source_name: TSC1 Deficient Mouse Embryonic Fibroblasts, biological replicate 2, treated, time course 24 hours

value: Embryonic Fibroblasts

value: TSC1 Deficient

value: Rapamycin


title: H9_feeder_d4-C [miRNA]

description: miRNA expression data from hESCs differentiated 4 days

source_name: H9 cells, day 4 of differentiation  (DE)

value: 4 days


title: TSC1-/-, biological replicate 3, no treatment

description: Gene Expression Data from TSC1 Deficient Mouse Embryonic Fibroblasts treated with vehicle for 24 hours

source_name: TSC1 Deficient Mouse Embryonic Fibroblasts, biological replicate 3, vehicle treated

value: DMSO


title: H9_feeder_d4-A [miRNA]


title: TSC1-/-, biological replicate 2, no treatment

source_name: TSC1 Deficient Mouse Embryonic Fibroblasts, biological replicate 2, vehicle treated


title: H9_feeder_d4-B [miRNA]


title: H9_feeder_d0-B [miRNA]


title: Cyt49_feeder_d4-B [miRNA]

source_name: Cyt49 cells, day 4 of differentiation  (DE)

growth_protocol: Cyt49 were plated on feeder layer of mouse embryonic fibroblasts (MEFs) and grown in DMEM/F12 supplemented with 20% knockout serum replacement, 4 ng/mL basic FGF, and 10ng/mL activin A

value: Cyt49 human embryonic stem cell line


title: TSC1-/-, biological replicate 1, treated, time course 2 hours

source_name: TSC1 Deficient Mouse Embryonic Fibroblasts, biological replicate 1, treated, time course 2 hours

value: 2 hours


title: TSC2-/- p53-/-, biological replicate 1, no treatment

description: Gene Expression Data from TSC2 Deficient Mouse Embryonic Fibroblasts treated with vehicle for 24 hours

source_name: TSC2 Deficient Mouse Embryonic Fibroblasts, biological replicate 1, vehicle treated

value: TSC2 Deficient


title: TSC2-/- p53-/-, biological replicate 1, treated, time course 24 hours

description: Gene Expression Data from TSC2 Deficient Mouse Embryonic Fibroblasts rapamycin treated for 24 hours

source_name: TSC2 Deficient Mouse Embryonic Fibroblasts, biological replicate 1, treated, time course 24 hours


title: TSC1-/-, biological replicate 1, no treatment

source_name: TSC1 Deficient Mouse Embryonic Fibroblasts, biological replicate 1, vehicle treated


title: TSC2-/- p53-/-, biological replicate 2, no treatment

source_name: TSC2 Deficient Mouse Embryonic Fibroblasts, biological replicate 2, vehicle treated


title: TSC2-/- p53-/-, biological replicate 2, treated, time course 24 hours

source_name: TSC2 Deficient Mouse Embryonic Fibroblasts, biological replicate 2, treated, time course 24 hours


title: LSL1063

source_name: MDS TET2LSL1063

tag: mutation

tag: who

value: RCMD

tag: aml transformation

value: Yes


title: Cyt49_feeder_d0-B [miRNA]

source_name: Cyt49 cells, day 0 of differentiation (pluripotent ESCs)


title: Cyt49_feeder_d0-C [miRNA]


title: TSC2-/- p53-/-, biological replicate 3, no treatment

source_name: TSC2 Deficient Mouse Embryonic Fibroblasts, biological replicate 3, vehicle treated


title: LSL1544

source_name: MDS TET2LSL1544

value: no chromosomal aberrations found

value: RAEB II

tag: iPSs


title: Cyt49_feeder_d4-A [miRNA]


title: TSC2-/- p53-/-, biological replicate 2, treated, time course 6 hours

source_name: TSC2 Deficient Mouse Embryonic Fibroblasts, biological replicate 2, treated, time course 6 hours

value: 6 hours


title: TSC2+/+ p53-/-, biological replicate 3, no treatment

description: Gene Expression Data from TSC Wild Type Mouse Embryonic Fibroblasts treated with vehicle for 24 hours

source_name: Wild Type Mouse Embryonic Fibroblasts, biological replicate 3, vehicle treated

value: Wild Type


title: LSL1602

source_name: MDS TET2LSL1602

value: chromosomal aberrations found

value: no

value: sRCMD

value: No


title: TSC2+/+ p53-/-, biological replicate 2, no treatment

source_name: Wild Type Mouse Embryonic Fibroblasts, biological replicate 2, vehicle treated

value: Embryonic Fibroblasts


title: TSC2+/+ p53-/-, biological replicate 1, no treatment

source_name: Wild Type Mouse Embryonic Fibroblasts, biological replicate 1, vehicle treated


title: Cyt49_feeder-free_d4-A [miRNA]

growth_protocol: Cyt49 were plated on BD matrigel and cultured MEF conditioned medium, containing DMEM/F12 supplemented with 20% knockout serum replacement, 4 ng/mL basic FGF, and 10ng/mL activin A

value: feeder-free conditions


title: Cyt49_feeder-free_d4-C [miRNA]

value: 4 days


title: Cyt49_feeder_d0-A [miRNA]

value: feeder layer

value: 0 days


title: Cyt49_feeder-free_d2-C [miRNA]

description: miRNA expression data from hESCs differentiated 2 days

source_name: Cyt49 cells, day 2 of differentiation

value: Cyt49 human embryonic stem cell line

value: 2 days


title: Cyt49_feeder-free_d2-A [miRNA]


title: Cyt49_feeder-free_d2-B [miRNA]


title: Cyt49_feeder-free_d0-C [miRNA]

value: 0 day


title: Psoas major_female_Low feeding level_animal8

city: Madrid

first: Ana

middle: I

last: Fernandez

state: Madrid

address: Ctra. Coruña Km 7.5

department: Mejora Genética Animal

country: Spain

institute: INIA

description:
Psoas major 23
Psoas major sample at 211 days, female, low.

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: GCOS.

data_processing: Bioconductor, GCRMA.

organism: Sus scrofa

source_name: Psoas major, 211 days, female, low

growth_protocol: Pigs were fed twice daily with the same pelleted diet until feeding restriction treatment.

extract_protocol: RiboPure RNA isolation kit.

treatment_protocol: Diaphragm and Psoas major muscles were maintained at -80ºC.

tag: breed

value: Iberian

value: female

tag: age

value: 211 days

value: psoas major

tag: diet

value: restricted level


title: Psoas major_female_High feeding level_animal7

description:
Psoas major 22
Psoas major sample at 211 days, female, high.

source_name: Psoas major, 211 days, female, high

value: high level


title: Psoas major_female_Low feeding level_animal5

description:
Psoas major 20
Psoas major sample at 211 days, female, low.


title: Psoas major_female_High feeding level_animal6

description:
Psoas major 21
Psoas major sample at 211 days, female, high.


title: Psoas major_male_High feeding level_animal4

description:
Psoas major 17
Psoas major sample at 211 days, male, high.

source_name: Psoas major, 211 days, male, high

value: male


title: Psoas major_male_Low feeding level_animal2

description:
Psoas major 15
Psoas major sample at 211 days, male, low.

source_name: Psoas major, 211 days, male, low


title: Cyt49_feeder-free_d0-B [miRNA]


title: Cyt49_matrigel_d4-B [mRNA]

description:
Gene expression data from hESCs differentiated 4 days
4210857018_F

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: Cyt49 cells, day 4 of differentiation  (DE)

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

growth_protocol: Cyt49 cells were plated on BD matrigel and grown in cultured MEF conditioned medium, containing DMEM/F12 supplemented with 20% knockout serum replacement, 4 ng/mL basic FGF, and 100 ng/mL activin A

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (Invitrogen, Carlsbad, CA) followed by DNAse treatment (Turbo DNAse, Ambion, Austin, TX), extraction in phenol/chloroform and ethanol precipitation.

treatment_protocol: For differentiation, growth medium was replaced with RPMI with 0% serum, 100ng/mL activinA and 25 ng/mL Wnt3A for 1 day, followed by RPMI with 0.2% serum and 100 ng/mL activin A for 2 days, followed by RPMI with 2% serum and 100ng/mL activinA for 1 day

value: matrigel


title: Diaphragm_female_Low feeding level_animal8

description:
Diaphragm 23
Diaphragm sample at 211 days, female, low.

source_name: Diaphragm, 211 days, female, low

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

value: diaphragm


title: Psoas major_male_High feeding level_animal1

description:
Psoas major 14
Psoas major sample at 211 days, male, high.


title: Diaphragm_female_High feeding level_animal7

description:
Diaphragm 22
Diaphragm sample at 211 days, female, high.

source_name: Diaphragm, 211 days, female, high


title: Cyt49_matrigel_d4-C [mRNA]

description:
Gene expression data from hESCs differentiated 4 days
4210857026_C


title: Cyt49_matrigel_d2-C [mRNA]

description:
Gene expression data from hESCs differentiated 2 days
4210857026_B


title: Cyt49_matrigel_d4-A [mRNA]

description:
Gene expression data from hESCs differentiated 4 days
4210857018_E


title: LSL1048

source_name: MDS TET2LSL1048

value: no chromosomal aberrations found

value: no

value: RCMD

value: No


title: TCS1-/-, biological replicate 1, treated, time course 12 hours

description: Gene Expression Data from TSC1 Deficient Mouse Embryonic Fibroblasts rapamycin treated for 11 hours

source_name: TSC1 Deficient Mouse Embryonic Fibroblasts, biological replicate 1, treated, time course 12 hours

value: Embryonic Fibroblasts

tag: genotype/variation

value: TSC1 Deficient

value: 12 hours

value: Rapamycin


title: Cyt49_matrigel_d2-B [mRNA]

description:
Gene expression data from hESCs differentiated 2 days
4210857018_D

tag: cell line

value: Cyt49 human embryonic stem cell line

value: 2 days


title: G2834

source_name: MDS TET2G2834

value: RAEB II

value: yes


title: Psoas major_male_Low feeding level_animal3

description:
Psoas major 16
Psoas major sample at 211 days, male, low.

value: Iberian

value: 211 days

value: psoas major

value: restricted level


title: Diaphragm_female_Low feeding level_animal5

description:
Diaphragm 20
Diaphragm sample at 211 days, female, low.

value: female

value: diaphragm


title: Diaphragm_male_Low feeding level_animal3

description:
Diaphragm 16
Diaphragm sample at 211 days, male, low.

source_name: Diaphragm, 211 days, male, low

value: male


title: Diaphragm_male_High feeding level_animal4

description:
Diaphragm 17
Diaphragm sample at 211 days, male, high.

source_name: Diaphragm, 211 days, male, high

value: high level


title: G3231

source_name: MDS TET2G3231

value: no chromosomal aberrations found

value: no

value: RCMD


title: Diaphragm_male_Low feeding level_animal2

description:
Diaphragm 15
Diaphragm sample at 211 days, male, low.


title: Cyt49_matrigel_d2-A [mRNA]

description:
Gene expression data from hESCs differentiated 2 days
4210857018_C

value: matrigel


title: Spleen-severe

city: New Haven

first: Pramod

middle: K

last: Mistry

state: CT

address: 333 Cedar Street

institute: Yale University

description: disease spleen severe enlarge

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). Transfer 200μl of hyb solution to each array, then tape holes and parafilm. Hybridize 16 hours at 45° at 60rpm. Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using Partek Genomic Suite software v7.3. GC-RMA normalization was applied to normalize gene level intensity.
probe group file: MoGene-1_0-st-v1.r4.pgf
meta-probeset file: MoGene-1_0-st-v1.r4.mps

source_name: Spleen-severe

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

growth_protocol: Livers and spleens were remove from euthanized mice and acutely frozen on dry ice and subsequently stored in -80C freever.

extract_protocol: Qiagen lipid mini tissue kit was used for the Total RNA extraction

value: mixed 129svj and C57 BL/6 background

value: spleen

tag: disease status

value: severe splenomegaly


title: Cyt49_matrigel_d0-C [mRNA]

description:
Gene expression data from pluripotent hESCs
4210857026_A

source_name: Cyt49 cells, day 0 of differentiation (pluripotent ESCs)

value: Cyt49 human embryonic stem cell line

value: 0 day


title: Cyt49_matrigel_d0-B [mRNA]

description:
Gene expression data from pluripotent hESCs
4210857018_B


title: Spleen-disease-no-enlarge

description: disease spleen without enlarge

source_name: Spleen-disease-no-enlarge

value: splenomegaly (not enlarged)


title: Spleen-disease-moderate

description: disease spleen moderate enlarge

source_name: Spleen-disease-moderate

value: moderate splenomegaly


title: Cyt49_feeder_d4-C [miRNA]

description: miRNA expression data from hESCs differentiated 4 days

value: feeder layer

value: 4 days


title: Liver-severe

description: disease liver severe stage

source_name: Liver-severe

value: severe hepatomegaly


title: Liver-control

description: normal liver tissue

source_name: Liver-control

value: liver

value: control


title: Liver-mild

description: disease liver mild stage

source_name: Liver-mild

value: mild hepatomegaly


title: Diaphragm_male_High feeding level_animal1

description:
Diaphragm 14
Diaphragm sample at 211 days, male, high.

value: Iberian

value: male

value: 211 days

value: diaphragm

value: high level


title: Cyt49_matrigel_d0-A [mRNA]

description:
Gene expression data from pluripotent hESCs
4210857018_A

value: matrigel