title: a034


title: a033

status: Public on Dec 03 2013

type: protein

city: Boston

first: Joshua

middle: WK

last: Ho

state: MA

address: 41 Avenue Louis Pasteur

department: Department of Medicine

country: USA

institute: Brigham and Women's Hospital

description: This array survey leukocyte surface CD markers

hyb_protocol: Briefly, duplicate patterns of anti-CD antibody spots were robotically arrayed onto nitrocellulose membrane coated glass slides (Schleicher and Schuell, Keene, NH), and blocked with skim milk (5% in PBS).

scan_protocol: Cells captured on antibody dots were imaged using a DotScan™ slide reader (Medsaic, NSW, Australia). The number of immobilized cells was proportional to the light scattered at each antibody spot. Binding of PBMCs to each antibody dot was monitored by light scatter and averaged between the duplicate spots on each slide.

data_processing: Data were normalized to a range of 0 to 10 with respect to the spot with the maximum binding density on each slide.

molecule: protein

organism: Homo sapiens

source_name: Peripheral Blood Mononuclear Cells

label_protocol: No labeling

extract_protocol: PBMCs were fractionated from whole blood by Ficoll density gradient centrifugation, washed in PBS, then resuspended in PBS + 1 mM EDTA. A total of 4 × 106 PBMC in 300 mL were applied evenly to the antibody-arrayed nitrocellulose surface for 30 minutes, then unbound cells were gently washed off and the slides fixed in 4% formaldehyde in PBS.

tag: age

tag: gender

value: M

tag: cell type

value: Peripheral Blood Mononuclear Cells


title: KhES1(p30)_undiff_hES

type: RNA

city: Kyoto

first: Shinya

last: Yamanaka

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

country: Japan

institute: Center for iPS Cell Research and Applicaton (CiRA), Kyoto University

hyb_protocol: Agilent standard protocol

scan_protocol: Agilent standard protocol

data_processing: The data were analyzed using the Gene Spring GX 11.5.1 software program (Agilent Technologies).The data processing was performed as follows; (i) Threshold raw signals were set to 1.0, (ii) Log base 2 transformation was performed, (iii) 90th percentile normalization was chosen as the normalized algorithm.

molecule: total RNA

source_name: undifferentiated hES

label_protocol: Agilent standard protocol

extract_protocol: Total RNA was isolated by Trizol reagent (Life Technologies) according to the manufacturer's instruction.

tag: cell origin

value: blastocyst


title: KhES3(p37)_undiff_hES


title: KhES4(p44)_undiff_hES


title: LNCaP cells treated for 8 hours with R1881, experiment 2

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

country: Italy

institute: Eurac Researc

hyb_protocol: Target samples were hybridized to Human Gene 1.0 ST v1 microarrays according to the manufacturer's protocols in a Affymetrix hybridization oven.

scan_protocol: Microarrays were scanned in an Affymetrix 3000 scanner.

data_processing: Raw data was preprocessed using the GCRMA method. For transcript probe set definition a custom CDF package based on a complete re-alignment of the probe sequences to the genome and transcriptome (Ensembl version 68) was used; details on http://bioinfo.i-med.ac.at.

label: biotin

source_name: LNCaP

label_protocol: Target RNA was labeled by addition of biotin-linked deoxynucleotides with terminal deoxynucleotidyl transferase according to the manufacturer's (Affymetrix) protocols. Washing and staining was performed in an Affymetrix 450S fluidics station.

growth_protocol: Cells (LNCaP, VCaP, DuCaP) were grown on polylysine-coated (Sigma) petridishes in RPMI1640 supplemented with 10% charcoal-stripped FCS overnight.

extract_protocol: RNA was extracted using TRI-reagent (Sigma) according to the manufacturer`s protocol. After DNA digestion with DnaseI (Qiagen), RNA was purified using Rneasy kit (Qiagen).

treatment_protocol: Cells were cultured in the absence (EtOH) or presence of 1nM R1881 for 8 and 24 hours, respectively.

tag: treatment

tag: date of experiment

tag: timepoint


title: a032


title: a031

value: F


title: a030


title: LNCaP cells treated for 24 hours with EtOH, experiment 2

value: EtOH


title: ES03(p76)_undiff.hES_SFEBq_good

data_processing: The data were analyzed using the Gene Spring GX 11.5.1 software program (Agilent Technologies).The data processing was performed as follows; (i) Threshold raw signals were set to 1.0, (ii) Log base 2 transformation was performed, (iii) 75th percentile normalization was chosen as the normalized algorithm.

tag: sfebq

value: differentiation good


title: ES04(p90)_undiff.hES_SFEBq_good


title: LNCaP cells treated for 24 hours with R1881, experiment 2


title: ES06(p54)_undiff.hES_SFEBq_good


title: KhES4(p49)_undiff.hES_SFEBq_good


title: KhES5(p43)_undiff.hES_SFEBq_good


title: LNCaP cells treated for 8 hours with EtOH, experiment 1


title: ap2-g vs ap2-g2 3

city: Cambridge

first: Katarzyna

middle: Kinga

last: Modrzynska

address: Genome Campus

department: Malaria program

country: United Kingdom

institute: Wellcome Trust Sanger Institute

description: Sample 8

hyb_protocol: lebelled samples were mixed with the reagents from Gene Expression Hybridisation kit (Agilent Technologies), hybridised overnight and washed according to the manufecturer instructions

scan_protocol: scanned using Agilent DNA Microarray Scanner with Surescan High-resolution Technology

data_processing: Images were processed using Agilent Feature Extraction Software (v10.7.3.1).

organism: Plasmodium berghei

source_name: overnight schizont culture, ap2-g KO line

label_protocol: cDNA aminoallyl labelling as desribed on http://www.molbio1.princeton.edu/labs/llinas/protocols.html

growth_protocol: P.berghei parasites were grown in the rodent host according and  to the schizont stage in overnight culture using the establised procedure (Janse et.al., 2006)

extract_protocol: Trizol whole RNA extraction

tag: genotype/variation

value: ap2-g KO line

tag: sample type

value: overnight schizont culture


title: SA02(p34)_undiff.hES_SFEBq_good


title: ap2-g vs ap2-g2 2

description: Sample 7


title: LNCaP cells treated for 24 hours with EtOH, experiment 1


title: LNCaP cells treated for 24 hours with R1881, experiment 1


title: a029


title: MCF7_cancer cell line

type: genomic

hyb_protocol: bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol.

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

data_processing:
Illumina GenomeStudio software
Unmethylated(Signal_A) and methylated(Signal_B) signal intensities

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Human Breast Adenocarcinoma

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA extraction and purification from cultured cells was carried out using a Gentra Puregene kit (QIAGEN).

value: cancer cell line


title: 201B6(p17)_undiff.hiPS_SFEBq_good

source_name: undifferentiated hiPS

tag: method

value: Retrovirus

value: Fibro (HDF1388)

tag: transduction

value: OSKM


title: a028


title: Jurkat_cancer cell line

source_name: Human Acute T cell Leukemia


title: ap2-g2 vs wt 2

description: Sample 5

source_name: overnight schizont culture, ap2-g2 KO line

value: ap2-g2 KO line

source_name: overnight schizont culture, gfp-luc reference line

value: gfp-luc reference line


title: a027


title: a026


title: ap2-g vs ap2-g2 1

description: Sample 6


title: ap2-g2 vs wt 1

description: Sample 4


title: a025


title: LNCaP cells treated for 8 hours with R1881, experiment 1


title: PBMN-1_soma

source_name: Peripheral Blood Mononuclear cells

value: soma


title: a024


title: HepG2_cancer cell line

source_name: Human hepatocellular Carcinoma


title: PBMN-2_soma


title: ap2-g vs wt 1

description: Sample 1


title: 253G1(p22)_undiff.hiPS_SFEBq_good

value: OSK


title: CB-2_soma

source_name: Cord Blood cells


title: 246G1(p23)_undiff.hiPS_SFEBq_good

value: BJ


title: a023


title: 1375-4f1(p24)_undiff.hiPS_SFEBq_good

value: Fibro (HDF1375)


title: a021

value: M

value: Peripheral Blood Mononuclear Cells


title: a022


title: a020


title: ap2-g vs wt 2

description: Sample 2


title: CB-1_soma


title: a019


title: DP74(p14)_soma

source_name: Dental Pulp cells


title: 2102EP4D3(p28)_hEC

source_name: hEC

value: hEC


title: 711C1(p14)_undiff_hiPS

value: Sendai virus

value: CB CD34+  (donor a)


title: 409B2(p48)_undiff.hiPS_SFEBq_good

value: Episomal plasmid

value: differentiation good


title: a018


title: a016

value: F


title: TIG114-4f1(p15)_undiff.hiPS_SFEBq_good

value: Retrovirus

value: Fibro (TIG114)


title: 253G4(p21)_undiff.hiPS_SFEBq_good

value: Fibro (HDF1388)


title: H1(p57)OH_undiff.hES_SFEBq_good

value: blastocyst


title: a015


title: 665A7(p16)_undiff_hiPS

value: CB CD34+  (donor b)

value: OSKM


title: a014


title: KhES3(p61)_undiff.hES_SFEBq_good


title: HDF1388_soma

source_name: Human Dermal Fibroblast cells

value: soma


title: a013


title: 711A6(p13)_undiff_hiPS


title: ap2-g vs wt 3

description: Sample 3

value: gfp-luc reference line

value: overnight schizont culture

value: ap2-g KO line


title: 414C2(p54)_undiff.hiPS_SFEBq_good


title: TIG120-4f1(p23)_undiff.hiPS_SFEBq_intermediate

value: Fibro (TIG120)

value: differentiation intermediate


title: 201B7(p22)_undiff.hiPS_SFEBq_good


title: KhES1(p26)_undiff.hES_SFEBq_intermediate


title: H9(p47)_undiff.hES_SFEBq_good


title: NTERA2cloneD1(p36)_hEC

value: hEC


title: 711A1(p12)_undiff_hiPS

value: Sendai virus

value: CB CD34+  (donor a)


title: 703A1(p17)_undiff_hiPS

value: PBMN abT (donor x)


title: a012

value: F

value: Peripheral Blood Mononuclear Cells


title: 201B2(p79)_undiff.hiPS_SFEBq_good

value: Retrovirus

value: differentiation good


title: a011

value: M


title: 665A1(p16)_undiff_hiPS

value: CB CD34+  (donor b)


title: 703B1(p17)_undiff_hiPS

value: OSKM


title: a009


title: 1503-4f1(p38)_undiff.hiPS_SFEBq_defective

value: Fibro (HDF1503)

value: differentiation defective


title: a008


title: 610B1(p14)_undiff_hiPS

value: Episomal plasmid


title: a006


title: a007


title: a010


title: HBx_RNA

type: SRA

city: Seoul

first: Sun-Min

last: LEE

address: Shinchon-dong Seodeamun-gu

department: Biochemistry

country: South Korea

institute: Yonsei University

description: mRNA samples from three mice

library_source: transcriptomic

data_processing:
mRNA libraries were sequenced on Illumina genome analyzer and MIRA libraries were sequenced on Illumina HiSeq 2500
Sequenced reads of 51 bp that passed quality control filters(ASCII Qscore Offset 33) were used
Sequence tags were mapped to the mouse genome (UCSC mm9 database based on NCBI Build 37 assembly) using the Bowtie2
We extended the 51-bp reads toward the 3’ end to cover DNA fragments bound by the MBD proteins (200 bp)
We counted overlapping sequence tags at 50-bp resolution.
We then calculated RPKM (reads per million base pairs mapped per kb) at 50-bp resolution
The reads from mRNA-seq were aligned to mm9 using TopHat
Genome_build: mm9

organism: Mus musculus

source_name: liver

extract_protocol:
Genomic DNA from 25-mg liver tissue samples was purified with a DNeasyR Blood & Tissue Kit. Total RNA from 3 livers collected from 3-month-old mice was extracted using Qiagen RNeasy mini kits.
We generated cDNA libraries for sequencing using a Illumina mRNA sample prep kit (Hayward, CA). And TruSeq® DNA sample prep kit were used for generation of MIRA libraries.

tag: strain

value: 3 months after birth

tag: genotype

value: HBx TG mouse


title: 622-E1(p18)_undiff_hiPS

value: PBMN abT (donor y)


title: TIG107-4f1(p24)OH_undiff.hiPS_SFEBq_defective

value: Fibro (TIG107)


title: Normal_RNA

description: mRNA samples from three mice

value: wild type


title: a005


title: a004


title: 606B1(p13)_undiff_hiPS

value: CB CD34+  (donor a)


title: TIG107-3f1(p31)_undiff.hiPS_SFEBq_defective

value: OSK


title: TIG118-4f1(p20)_undiff.hiPS_SFEBq_defective

value: Fibro (TIG118)


title: TIG108-4f3(p24)_undiff.hiPS_SFEBq_defective

value: Fibro (TIG108)

value: OSK(M)


title: 610A2(p14)_undiff_hiPS


title: 604A3(p14)_undiff_hiPS


title: PBMN-2_soma

value: soma


title: 604B1(p13)_undiff_hiPS


title: 606A1(p14)_undiff_hiPS


title: a003

value: M

value: Peripheral Blood Mononuclear Cells


title: Jurkat_cancer cell line

value: cancer cell line


title: CB-2_soma


title: 585B1(p16)_undiff_hiPS

value: PBMN abT (donor x)


title: 604A1(p14)_undiff_hiPS


title: a002


title: HepG2_cancer cell line


title: PBMN-1_soma


title: a001

value: F


title: MCF7_cancer cell line


title: CB-1_soma


title: Plasma cells

city: Madrid

first: Ana

last: Rio-Machin

state: Madrid

address: Calle Melchor Fernandez Almagro 3

department: Human Cancer Genetics

country: Spain

institute: CNIO

description: miRNA purified from total RNA

hyb_protocol: All samples, including control plasma cells, were labeled and hybridized in duplicate to the ‘8-pack’ Human miRNA Oligo Microarray G4472A (Agilent Technologies).

scan_protocol: Hybridization signals were detected with a DNA microarray scanner (Agilent Technologies, CA, USA) and the scanned images were analyzed using Agilent Feature extraction software 9.5.

data_processing: Microarray background subtraction was carried out using normexp method. To normalize the dataset, we performed loess within arrays normalization and quantiles between arrays normalization.  We employed Bioconductor's limma package to perform normalization steps and SAM for differential expression analysis.

source_name: Plasma cells

label_protocol: Micro RNA profiling was carried out by labeling 100 ng of total RNA, as recommended by Agilent Technologies (microRNA Microarray System Protocol v.1.5) and using T4 RNA ligase (Amersham Biosciences (Little Chalfont, Bucks, UK).

growth_protocol: This study is based on the bone marrow aspirates that were obtained using standard diagnostic procedures from 92 patients with de novo MM. Samples were collected from three different hematology or Clinical Genetics laboratories. Plasma cells were purified from the bone marrow samples using CD138 immunomagnetic microbeads (Miltenyi Biotec, Germany). All patients gave their informed consent in accordance with the Declaration of Helsinki. The same molecular cytogenetic characterization was performed in all cases to classify them as subtype nh-MM (normal karyotype and/or positive for presence of IgH translocation) or h-MM (no IgH translocations and at least two trisomies of the most frequently supernumerary chromosomes: 5, 7 or 9). CD138-positive snap frozen plasma cell pellets (ALLCELLS, Emeryville, California) were used as a control.

extract_protocol: Total RNA was extracted using the miRNeasy Mini Kit (Qiagen, CA, USA) according to the manufacturer's instructions for Purification of total RNA, including Small RNAs from Animal Cells. The quality of the samples was assessed using the 2100 Expert Eukaryotic Total RNA Nano assay (Agilent Technologies, CA, USA).

value: plasma cells

tag: mm subtype


title: Non-Hyperdiploid multiple myeloma biological replicate 42

description: miRNA purified from total RNA

source_name: Non-Hyperdiploid multiple myeloma

value: L363 MM cell line

value: nh-MM


title: 585A1(p16)_undiff_hiPS

value: Episomal plasmid


title: Non-Hyperdiploid multiple myeloma biological replicate 41

description: miRNA purified from total RNA

value: KMS28PE MM cell line


title: Non-Hyperdiploid multiple myeloma biological replicate 39

description: miRNA purified from total RNA

value: OPM2 MM cell line


title: Non-Hyperdiploid multiple myeloma biological replicate 40

description: miRNA purified from total RNA

value: KMS28BM MM cell line


title: DP74_soma


title: 414C2(p55)_undiff_hiPS

value: Fibro (HDF1388)


title: 454E2(p48)_undiff_hiPS


title: RPMI8226_Hypoxia_24h_exosome

city: Shinjyuku

first: Tomohiro

last: Umezu

state: Tokyo

address: 6-1-1 Shinjyuku

department: Department of Molecular Pathology

institute: Tokyo Medical University

description: test

data_processing:
RNU6B and a spike control (ath-miR159) were used as an invariant control for the cell and culture medium, respectively. QRT-PCR was carried out on an Applied Biosystems 7900HT thermal cycler using the manufacturer’s recommended program.
All the raw data from each array was retrieved from the 7900HT and was run on Data Assist Software ver.3.1 (Applied Biosystems).

label: TaqMan probe (FAM-MGB)

source_name: exosome derived from MM cell line

label_protocol: A fixed volume of 3 µl of RNA solution from 50 µl of the elute was used as input in each reverse transcription (RT) reaction. An RT reaction and pre-amplification step were set up according to manufacturers’ recommendations. miRNAs were reverse transcribed using the Megaplex Primer Pools (Human Pools A v2.1) from Applied Biosystems (Bedford, MA, USA). RT reaction products from the exosome sample were further amplified using the Megaplex PreAmp Primers (Primers A v2.1).

extract_protocol:
The 5 ml of culture medium of RPMI8226 cells was obtained and centrifuged at 3,000 × g for 15 min. The supernatant was filtered through a 0.22-µm PVDF filter (Millipore). The appropriate volume of Exoquick Exosome Precipitation Solution (System Biosciences, Mountain View, CA, USA) was added to the filtered culture medium and mixed well by inverting. After refrigeration for 12 h, the mixture was centrifuged at 1,500 × g for 30 min and all supernatant was removed by aspiration.
The Cell or exosome pellets were dissolved with 700 µl of QIAzol lysis regent (Qiagen). After a 2-min incubation, 1 µl of 1 nM ath-miR-159 (Hokkaido System Science, Hokkaido, Japan) was added to each aliquot as a spike control for losses in preparation, followed by vortexing for 30 sec and incubation on ice for 10 min. Subsequent phenol extraction and cartridge filtration were carried out according to the manufacturer’s instructions.

treatment_protocol: RPMI8226 cells were seeded at a density of 5 × 10^5 cells/ml, and cultured for 24 hours under hypoxic conditions (1% O2, 5% CO2, 94% N2) in a humidified gas-sorted hypoxic incubator (MCO-5M, Sanyo, Osaka, Japan) using the degassed culture mediums (RPMI8226 cells: AIM-V medium, Invitrogen).

tag: cell line

tag: condition

value: hypoxia (1% O2)

tag: time


title: NTERA2 cloneD1_hEC

value: hEC


title: HDF-1388_soma


title: 451F3(p40)_undiff_hiPS


title: 711A6(p13)_undiff_hiPS

value: Sendai virus

value: CB CD34+  (donor a)

value: OSKM


title: 409B2(p45)_undiff_hiPS


title: 404C2(p48)_undiff_hiPS


title: RPMI8226_Normoxia_24h_exosome

description: control

value: normoxia (20% O2)


title: ATCC 17978 chlorhexidine shock replicate 1

city: North Ryde

first: Karl

middle: Adam

last: Hassan

state: NSW

address: Eastern Rd, Macquarie University

department: Dept. Chemistry and Biomolecular Sciences

country: Australia

institute: Macquarie University

description:
Biological replicate 1
Ramaciotti_252465610001_S01_GE2_105_1_1

hyb_protocol: The Ramaciotti Centre, UNSW, Sydney

scan_protocol: The Ramaciotti Centre, UNSW, Sydney

data_processing: The data obtained from replicate probes per gene was processed using Agilent Genespring GX version 9. The processed data was subseqeuntly analyzed using the Significance Analysis of Micrroarray data (Tusher et al. 2001) with a false discovery rate of less than 5%.

organism: Acinetobacter baumannii

source_name: ATCC 17978 untreated rep 1

label_protocol: Cy3 and Cy5 labelling using Agilent Fairplay Microarray Labelling kit (Stratagene)

extract_protocol: Total RNA was purified using TriZol extraction followed by spin-column purification using the PureLinkTM Micro-to-Midi Total RNA Purification kit (Invitrogen), incorporating an on-column DNAseI (Invitrogen) digestion.

treatment_protocol: A. baumannii ATCC 17978 cells were grown at 37°C with shaking (200rpm) in 35mL cultures in MH broth to OD600=0.75, at which time they were split into 15mL cultures. One 15mL sample was treated with 4µg/mL chlorhexidine (0.5x MIC), whereas the other was not treated and used as a reference. Cultures were allowed to grow for a further 30 mins (to an average final OD600= ~1.35 for untreated cells and 1.25 for chlorhexidine treated samples), when cells were harvested by centrifugation and immediately suspended in Trizol reagent (Invitrogen). Total RNA was extracted using the PureLinkTM Micro-to-Midi Total RNA Purification kit (Invitrogen), incorporating an on-column DNAseI (Invitrogen) digestion.

tag: treated with

value: none (untreated control)

source_name: ATCC 17978 chlorhexidine treated rep 1

value: 4µg/mL chlorhexidine


title: 665A7(p18)_undiff_hiPS

tag: cell type

value: CB CD34+  (donor b)


title: 711A1(p12)_undiff_hiPS

tag: cell origin


title: 711C1(p14)_undiff_hiPS


title: TKCB7-2(p38)_undiff_hiPS

value: Retrovirus


title: 2102EP4D3_hEC


title: ATCC 17978 chlorhexidine shock replicate 3

description:
Biological replicate 3
Ramaciotti_252465610001_S01_GE2_105_1_3

source_name: ATCC 17978 untreated rep 3

source_name: ATCC 17978 chlorhexidine treated rep 3


title: Non-Hyperdiploid multiple myeloma biological replicate 36

description:
36 nh
miRNA purified from total RNA

value: primary case of MM

tag: karyotype and igh status

value: 46 Chromosomes + CCND1 marker


title: Non-Hyperdiploid multiple myeloma biological replicate 38

description: miRNA purified from total RNA

value: JJN3 MM cell line

value: nh-MM


title: Non-Hyperdiploid multiple myeloma biological replicate 37

description: miRNA purified from total RNA

value: K620 MM cell line


title: 665A1(p17)_undiff_hiPS

source_name: undifferentiated hiPS


title: ATCC 17978 chlorhexidine shock replicate 2

description:
Biological replicate 2
Ramaciotti_252465610001_S01_GE2_105_1_2

source_name: ATCC 17978 untreated rep 2

source_name: ATCC 17978 chlorhexidine treated rep 2


title: RPMI8226_Hypoxia_24h_cell

description: test

source_name: Multiple Myeloma-derived cell line


title: ATCC 17978 chlorhexidine shock replicate 4 (dye-swap replicate of rep 1)

description:
Technical, dye-swap replicate
Ramaciotti_252465610001_S01_GE2_105_1_4


title: RPMI8226_Normoxia_24h_cell

description: control

source_name: Multiple Myelima-derived cell line


title: Non-Hyperdiploid multiple myeloma biological replicate 35

description:
35 nh
miRNA purified from total RNA

value: 46 [60%]/44 [40%] Chromosomes + FGFR3 (TACC3) marker


title: TKCBV4-2(p74)_undiff_hiPS


title: SUDHL4_Hypoxia_24h_exosome

description: test

source_name: exosome derived from DLBCL cell line

extract_protocol:
The 5 ml of culture medium of SUDHL4 cells was obtained and centrifuged at 3,000 × g for 15 min. The supernatant was filtered through a 0.22-µm PVDF filter (Millipore). The appropriate volume of Exoquick Exosome Precipitation Solution (System Biosciences, Mountain View, CA, USA) was added to the filtered culture medium and mixed well by inverting. After refrigeration for 12 h, the mixture was centrifuged at 1,500 × g for 30 min and all supernatant was removed by aspiration.
The Cell or exosome pellets were dissolved with 700 µl of QIAzol lysis regent (Qiagen). After a 2-min incubation, 1 µl of 1 nM ath-miR-159 (Hokkaido System Science, Hokkaido, Japan) was added to each aliquot as a spike control for losses in preparation, followed by vortexing for 30 sec and incubation on ice for 10 min. Subsequent phenol extraction and cartridge filtration were carried out according to the manufacturer’s instructions.

treatment_protocol: SUDHL4 cells were seeded at a density of 5 × 10^5 cells/ml, and cultured for 24 hours under hypoxic conditions (1% O2, 5% CO2, 94% N2) in a humidified gas-sorted hypoxic incubator (MCO-5M, Sanyo, Osaka, Japan) using the degassed culture mediums (RPMI8226 cells: AIM-V medium, Invitrogen).


title: Non-Hyperdiploid multiple myeloma biological replicate 34

description:
34 nh
miRNA purified from total RNA


title: 703A1(p17)_undiff_hiPS

value: PBMN abT (donor x)


title: 703B1(p17)_undiff_hiPS


title: SUDHL4_Hypoxia_24h_cell

description: test

source_name: Diffuse large B cell lymphoma-derived cell line

value: hypoxia (1% O2)


title: Non-Hyperdiploid multiple myeloma biological replicate 33

description:
33 nh
miRNA purified from total RNA


title: TKCBV5-6(p72)_undiff_hiPS


title: SUDHL4_Normoxia_24h_exosome

description: control


title: 225C7(p14)_undiff_hiPS

value: Fibro (HDF1419)


title: Non-Hyperdiploid multiple myeloma biological replicate 32

description:
32 nh
miRNA purified from total RNA

value: 50 Chromosomes + CCND1 marker


title: Non-Hyperdiploid multiple myeloma biological replicate 30

description:
30 nh
miRNA purified from total RNA

value: 46 Chromosomes + FGFR3 (TACC3) marker


title: 610B1(p14)_undiff_hiPS

value: Episomal plasmid


title: 622G1(p19)_undiff_hiPS

value: Sendai virus

value: PBMN abT (donor y)

value: OSKM


title: SUDHL4_Normoxia_24h_cell

description: control

value: normoxia (20% O2)


title: 622E1(p18)_undiff_hiPS


title: 246G1(p15)_undiff_hiPS

value: Retrovirus

value: BJ


title: Non-Hyperdiploid multiple myeloma biological replicate 29

description:
29 nh
miRNA purified from total RNA

value: primary case of MM

value: 46 Chromosomes + CCND1 marker


title: Non-Hyperdiploid multiple myeloma biological replicate 31

description:
31 nh
miRNA purified from total RNA

value: nh-MM


title: Non-Hyperdiploid multiple myeloma biological replicate 28

description:
28 nh
miRNA purified from total RNA

value: 47 Chromosomes + FGFR3 (TACC3) marker


title: DP31-4f1(p10)_undiff_hiPS


title: 1488-4f1(p20)_undiff_hiPS

value: Fibro (HDF1488)


title: 1678-4f2(p12)_undiff_hiPS

value: Fibro (HDF1687)


title: 610A2(P14)_undiff_hiPS

value: CB CD34+  (donor b)


title: Non-Hyperdiploid multiple myeloma biological replicate 26

description:
26 nh
miRNA purified from total RNA

value: 46 Chromosomes


title: 622G1(p19)_undiff_hiPS


title: 606B1(P13)_undiff_hiPS

value: CB CD34+  (donor a)


title: 1503-4f1(p28)_undiff_hiPS

value: Fibro (HDF1503)


title: 604A3(P14)_undiff_hiPS

value: Episomal plasmid


title: 606A1(p14)_undiff_hiPS


title: 1377-4f1(p13)_undiff_hiPS

value: Fibro (HDF1377)


title: Non-Hyperdiploid multiple myeloma biological replicate 27

description:
27 nh
miRNA purified from total RNA

value: 46 Chromosomes +IgH marker


title: 1375-4f1(p10)_undiff_hiPS

value: Fibro (HDF1375)

value: OSKM


title: Non-Hyperdiploid multiple myeloma biological replicate 25

description:
25 nh
miRNA purified from total RNA

value: 48 Chromosomes + FGFR3 (TACC3) marker


title: Non-Hyperdiploid multiple myeloma biological replicate 24

description:
24 nh
miRNA purified from total RNA


title: 1392-4f2(p19)_undiff_hiPS

value: Retrovirus

value: Fibro (HDF1392)


title: 604B1(p13)_undiff_hiPS

value: PBMN abT (donor y)


title: 604A1(P14)_undiff_hiPS


title: TIG121-4f4(p28)_undiff_hiPS

value: Fibro (TIG121)


title: 585B1(p16)_undiff_hiPS

value: PBMN abT (donor x)


title: TIG120-4f1(p21)_undiff_hiPS

value: Fibro (TIG120)


title: Non-Hyperdiploid multiple myeloma biological replicate 22

description:
22 nh
miRNA purified from total RNA

value: primary case of MM

value: nh-MM


title: Non-Hyperdiploid multiple myeloma biological replicate 23

description:
23 nh
miRNA purified from total RNA

value: 46 Chromosomes


title: TIG114-4f1(p21)_undiff_hiPS

value: Fibro (TIG114)


title: TIG109-4f1(p21)_undiff_hiPS

value: Fibro (TIG109)


title: 585A1(p16)_undiff_hiPS

value: Episomal plasmid


title: TIG118-4f1(p10)_undiff_hiPS

value: Fibro (TIG118)


title: 454E2(p46)_undiff_hiPS


title: TIG108-4f3(p19)_undiff_hiPS

value: Fibro (TIG108)

value: OSK(M)


title: Non-Hyperdiploid multiple myeloma biological replicate 20

description:
20 nh
miRNA purified from total RNA

value: 46 Chromosomes +IgH marker


title: O24

city: Novato

first: Simon

last: Melov

state: CA

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

description: old

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: We used the lumi/methylumi packages (Bioconductor) to derive the quantile normalized values of methylation (ß values). To derive sites of potential differential methylation (DM), we compared old versus young ß values using a modified t-statistic, where defined DM sites based on statistical significance controlling false discovery rate

source_name: vastus lateralis muscle, non-exercised

label_protocol: Standard Illumina Protocol

growth_protocol: Skeletal muscle biopsies from the vastus lateralis

extract_protocol: DNA was extracted from muscle samples in a randomized fashion with regards to age using a Qiagen Qiacube DNA extraction robot

tag: gender

value: male

tag: age

tag: bmi


title: 451F3(p41)_undiff_hiPS


title: O18

description: old


title: Non-Hyperdiploid multiple myeloma biological replicate 21

description:
21 nh
miRNA purified from total RNA


title: O19

description: old


title: 414C2(p55)_undiff_hiPS

value: Fibro (HDF1388)


title: 107-3f1(p57)_undiff_hiPS

value: Retrovirus

value: Fibro (TIG107)

value: OSK


title: Non-Hyperdiploid multiple myeloma biological replicate 19

description:
19 nh
miRNA purified from total RNA


title: 409B2(p52)_undiff_hiPS


title: Non-Hyperdiploid multiple myeloma biological replicate 18

description:
18 nh
miRNA purified from total RNA


title: Non-Hyperdiploid multiple myeloma biological replicate 17

description:
17 nh
miRNA purified from total RNA

value: 46 [83%]/45 [17%] Chromosomes + CCND1 marker


title: TIG107-4f1(p21)_undiff_hiPS

value: OSKM


title: O17

description: old


title: 253G1(p32)_undiff_hiPS


title: Non-Hyperdiploid multiple myeloma biological replicate 16

description:
16 nh
miRNA purified from total RNA

value: primary case of MM


title: 404C2(p44)_undiff_hiPS


title: Non-Hyperdiploid multiple myeloma biological replicate 15

description:
15 nh
miRNA purified from total RNA

value: nh-MM


title: TIG103-4f4(p8)_undiff_hiPS

value: Fibro (TIG103)


title: 253G4(p30)_undiff_hiPS


title: O23

description: old


title: TKCB7-2(p42)_undiff_hiPS


title: O16

description: old


title: 201B7(p18)_undiff_hiPS


title: TKCBV4-2(p82)_undiff_hiPS


title: 201B6(p25)_undiff_hiPS


title: Non-Hyperdiploid multiple myeloma biological replicate 13

description:
13 nh
miRNA purified from total RNA

value: 46 Chromosomes


title: TKCBV5-6(p73)_undiff_hiPS


title: Non-Hyperdiploid multiple myeloma biological replicate 14

description:
14 nh
miRNA purified from total RNA

value: 46 Chromosomes + MAFB marker


title: O22

description: old


title: 201B2(p67)_undiff_hiPS


title: O15

description: old


title: 246G1(p15)_undiff_hiPS

value: BJ


title: 225C7(p14)_undiff_hiPS

value: Fibro (HDF1419)


title: DP31-4f1(p13)_undiff_hiPS


title: Non-Hyperdiploid multiple myeloma biological replicate 11

description:
11 nh
miRNA purified from total RNA


title: O13

description: old


title: O21

description: old


title: ES06(p41)_undiff_hES

source_name: undifferentiated hES

value: blastocyst


title: O14

description: old


title: Non-Hyperdiploid multiple myeloma biological replicate 10

description:
10 nh
miRNA purified from total RNA


title: O20

description: old


title: O11

description: old


title: O12

description: old


title: 1687-4f2(p12)_undiff_hiPS

value: Fibro (HDF1687)


title: Non-Hyperdiploid multiple myeloma biological replicate 8

description:
8 nh
miRNA purified from total RNA


title: H9(p40)_undiff_hES


title: ES03(p60)_undiff_hES


title: Non-Hyperdiploid multiple myeloma biological replicate 7

description:
7 nh
miRNA purified from total RNA


title: 1392-4f2(p19)_undiff_hiPS

value: Fibro (HDF1392)


title: Non-Hyperdiploid multiple myeloma biological replicate 6

description:
6 nh
miRNA purified from total RNA


title: O09

description: old

value: male


title: 1375-4f1(p10)_undiff_hiPS

value: Fibro (HDF1375)


title: H1(p49)_undiff_hES


title: O08

description: old


title: KhES5(p47)_undiff_hES


title: 1377-4f1(p13)_undiff_hiPS

value: Retrovirus

value: Fibro (HDF1377)


title: SA02(p32)_undiff_hES


title: O07

description: old


title: 1503-4f1(p28)_undiff_hiPS

value: Fibro (HDF1503)


title: O06

description: old


title: Non-Hyperdiploid multiple myeloma biological replicate 12

description:
12 nh
miRNA purified from total RNA


title: KhES4(p44)_undiff_hES


title: Non-Hyperdiploid multiple myeloma biological replicate 9

description:
9 nh
miRNA purified from total RNA

value: 46 Chromosomes +IgH marker


title: Non-Hyperdiploid multiple myeloma biological replicate 4

description:
4 nh
miRNA purified from total RNA

value: 46 Chromosomes + FGFR3 (TACC3) marker


title: ES04(p63)_undiff_hES


title: O05

description: old


title: Non-Hyperdiploid multiple myeloma biological replicate 3

description:
3 nh
miRNA purified from total RNA

value: primary case of MM


title: TIG121-4f4(p16)_undiff_hiPS

value: Fibro (TIG121)

value: OSKM


title: O10

description: old


title: KhES3(p37)_undiff_hES


title: TIG120-4f1(p16)_undiff_hiPS

value: Fibro (TIG120)


title: O02

description: old


title: KhES1(p30)_undiff_hES


title: Non-Hyperdiploid multiple myeloma biological replicate 1

description:
1 nh
miRNA purified from total RNA

value: nh-MM


title: Non-Hyperdiploid multiple myeloma biological replicate 2

description:
2 nh
miRNA purified from total RNA


title: Hyperdiploid multiple myeloma biological replicate 18

description: miRNA purified from total RNA

source_name: Hyperdiploid multiple myeloma

value: MM cell line OH-2

value: h-MM


title: TIG114-4f1(p21)_undiff_hiPS

value: Fibro (TIG114)


title: Hyperdiploid multiple myeloma biological replicate 17

description:
17 h
miRNA purified from total RNA

value: 50 Chromosomes NO IgH marker


title: O03

description: old


title: 1488-4f1(p27)_undiff_hiPS

value: Fibro (HDF1488)


title: DP74_soma

hyb_protocol: Approximately 5.5ug of labeled DNA target was hybridized to the Affymetrix GeneChip Human Exon 1.0 ST Array at 45℃ for 17 hrs according to the manufacturer's recommendation.

scan_protocol: Hybridized arrays were washed and satined on a GeneChip Fluidics Satation 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing:
The exon array data analysis was performed using the Gene Spring GX11.5.1 software. Summarization algorithme:ExonPLIER16 with core and extended probe sets.
probe group file: HuEx-1_0-st-v2_na32_hg19_2011-06-23

source_name: Dental Pulp cells

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

value: soma


title: O01

description: old

value: male


title: H1_undiff.hES_SFEBq_good

value: blastocyst

tag: sfebq

value: differentiation good


title: TIG108-4f3(p16)_undiff_hiPS

value: Retrovirus

value: Fibro (TIG108)

value: OSK(M)


title: TIG118-4f1(p10)_undiff_hiPS

value: Fibro (TIG118)


title: TIG107-3f1(p57)_undiff_hiPS

value: Fibro (TIG107)

value: OSK


title: 253G1_undiff.hiPS_SFEBq_good

value: Fibro (HDF1388)


title: TIG109-4f1(p20)_undiff_hiPS

value: Fibro (TIG109)

value: OSKM


title: Hyperdiploid multiple myeloma biological replicate 16

description:
16 h
miRNA purified from total RNA

tag: sample type

value: primary case of MM

value: h-MM


title: TIG107-4f1(p18)_undiff_hiPS

tag: method


title: 451F3_undiff.hiPS_SFEBq_defective

value: Episomal plasmid

tag: transduction

value: differentiation defective


title: TIG103-4f4(p8)_undiff_hiPS

value: Fibro (TIG103)


title: Hyperdiploid multiple myeloma biological replicate 15

description:
15 h
miRNA purified from total RNA

value: 53 [90%]/54 [10%] Chromosomes NO IgH marker


title: Hyperdiploid multiple myeloma biological replicate 13

description:
13 h
miRNA purified from total RNA

value: 53 Chromosomes NO IgH marker


title: 201B7_undiff.hiPS_SFEBq_good

value: differentiation good


title: TIG108-4f3_undiff.hiPS_SFEBq_defective

value: Retrovirus


title: 253G4(p30)_undiff_hiPS


title: Hyperdiploid multiple myeloma biological replicate 11

description:
11 h
miRNA purified from total RNA

value: 54 [65%]/50 [35%] Chromosomes NO IgH marker


title: 201B7(p18)_undiff_hiPS


title: Y22

description: young

value: male


title: Y23

description: young


title: Y21

description: young


title: 253G1(p32)_undiff_hiPS


title: TKCBV5-6_undiff.hiPS_SFEBq_defective


title: Y20

description: young


title: Hyperdiploid multiple myeloma biological replicate 10

description:
10 h
miRNA purified from total RNA

value: 54 Chromosomes NO IgH marker


title: 201B6(p25)_undiff_hiPS


title: Hyperdiploid multiple myeloma biological replicate 9

description:
9 h
miRNA purified from total RNA

value: 52 Chromosomes NO IgH marker


title: SA02(p32)_undiff_hES

value: blastocyst


title: 201B2(p67)_undiff_hiPS

value: Fibro (HDF1388)


title: Y19

description: young


title: Non-Hyperdiploid multiple myeloma biological replicate 5

description:
5 nh
miRNA purified from total RNA

source_name: Non-Hyperdiploid multiple myeloma

value: nh-MM

value: 46 Chromosomes +IgH marker


title: O04

description: old


title: Hyperdiploid multiple myeloma biological replicate 8

description:
8 h
miRNA purified from total RNA

value: primary case of MM

value: 51 Chromosomes NO IgH marker


title: Hyperdiploid multiple myeloma biological replicate 7

description:
7 h
miRNA purified from total RNA

value: h-MM


title: Y17

description: young


title: Hyperdiploid multiple myeloma biological replicate 6

description:
6 h
miRNA purified from total RNA


title: ES04(p74)_undiff_hES


title: Y24

description: young


title: Y16

description: young


title: Hyperdiploid multiple myeloma biological replicate 5

description:
5 h
miRNA purified from total RNA

value: 54 [80%]/47 [20%]  Chromosomes NO IgH marker


title: Y18

description: young


title: ES06(p43)_undiff_hES


title: Hyperdiploid multiple myeloma biological replicate 14

description:
14 h
miRNA purified from total RNA

value: 48 Chromosomes NO IgH marker


title: H9(p40)_undiff_hES


title: Y13

description: young


title: Y14

description: young


title: H1(p49)_undiff_hES


title: Hyperdiploid multiple myeloma biological replicate 3

description:
3 h
miRNA purified from total RNA


title: Hyperdiploid multiple myeloma biological replicate 2

description:
2 h
miRNA purified from total RNA


title: ES03(p65)_undiff_hES


title: Y12

description: young


title: HDF-1388_soma

source_name: Human Dermal Fibroblast cells

value: soma


title: KhES5(p47)_undiff_hES


title: Y10

description: young


title: Hyperdiploid multiple myeloma biological replicate 1

description:
1 h
miRNA purified from total RNA

value: 47 Chromosomes NO IgH marker


title: KhES4(p44)_undiff_hES


title: Y11

description: young


title: KhES3(p37)_undiff_hES


title: control_RIP_Chip4

city: Toronto

first: Howard

middle: D

last: Lipshitz

state: ON

address: 1 King's College Circle

department: Molecular Genetics

country: Canada

institute: University of Toronto

description:
Sample name: control_04
Drosophila_melanogaster_0-3 hr_embryo_control_RIP_Chip4
control RIP-Chip biological replicate 3

hyb_protocol: Labeled cDNA was used to probe Drosophila 4 x 72K NimbleGen arrays: Expression design for Drosophila melanogaster (Release 4.3) (GEO platform number: GPL13782).

scan_protocol: The arrays were scanned using GenePix4000B microarray scanner system (Molecular Devices, Inc., Sunnyvale, CA, USA)

data_processing: The raw values for the arrays were quantified using Nimblescan (Roche), following the protocol described in the NimbleGen Array User's Guide (Gene Expression Arrays, version 5.0). Arrays were normalized by Robust Multi-array Average (RMA) provided in the Nimblescan software.

organism: Drosophila melanogaster

source_name: Oregon-R wild type 0-3hr embryo control RIP RNA

label_protocol: The cDNAs were prepared following the indirect labeling protocal provided by the Canadian Drosophila Microarray Centre using anchored-oligo-dT primers. Cy3 or Cy5-tagged random nonamers were then used to labeled the cDNA.

growth_protocol: Oregon-R wild-type fly stocks were used. All stocks were maintained at 25 °C.

extract_protocol: Embryos collected at 0-3 hours post-egglaying were dechorionated with 50% bleach and homogenized in a minimal volume of RIP lysis buffer (150 mM KCl, 20 mM HEPES pH 7.4, 1 mM MgCl2, 1 mM DTT, 1x protease inhibitor cocktail (Bioshop)). Extracts were centrifuged for 10min at 4°C, and the supernatant was supplemented with 9 M urea to a final concentration of 2 M. Protein A beads were pre-incubated with either guinea pig anti-Smaug antibody or normal guinea pig serum followed by four washes with RIP lysis buffer supplemented with urea. These beads were then incubated with embryo extract for 2 h at 4°C followed by four washed with RIP lysis buffer supplemented with urea and RNA was extracted from the beads using the Trizol reagent (Invitrogen).

tag: strain

value: Oregon-R

tag: genotype/variation

value: wild type

tag: developmental stage

value: 0-3 hr embryo

tag: temperature

value: 25 °C

tag: rip antibody

value: control


title: Hyperdiploid multiple myeloma biological replicate 12

description:
12 h
miRNA purified from total RNA

tag: mm subtype

value: 54 Chromosomes NO IgH marker


title: K562_Normoxia_24h_exosome

description: control

source_name: exosome derived from CML cell line

extract_protocol:
The 5 ml of culture medium of K562 cells was obtained and centrifuged at 3,000 × g for 15 min. The supernatant was filtered through a 0.22-µm PVDF filter (Millipore). The appropriate volume of Exoquick Exosome Precipitation Solution (System Biosciences, Mountain View, CA, USA) was added to the filtered culture medium and mixed well by inverting. After refrigeration for 12 h, the mixture was centrifuged at 1,500 × g for 30 min and all supernatant was removed by aspiration.
The Cell or exosome pellets were dissolved with 700 µl of QIAzol lysis regent (Qiagen). After a 2-min incubation, 1 µl of 1 nM ath-miR-159 (Hokkaido System Science, Hokkaido, Japan) was added to each aliquot as a spike control for losses in preparation, followed by vortexing for 30 sec and incubation on ice for 10 min. Subsequent phenol extraction and cartridge filtration were carried out according to the manufacturer’s instructions.

treatment_protocol: K562 cells were seeded at a density of 5 × 10^5 cells/ml, and cultured for 24 hours under hypoxic conditions (1% O2, 5% CO2, 94% N2) in a humidified gas-sorted hypoxic incubator (MCO-5M, Sanyo, Osaka, Japan) using the degassed culture mediums (K562 cells: AIM-V medium, Invitrogen).

tag: cell line

value: K562 cells

tag: condition

value: normoxia (20% O2)

tag: time


title: KhES1(p30)_undiff_hES

tag: cell type

tag: cell origin

value: blastocyst


title: Y08

description: young

tag: gender

value: male

tag: age


title: K562_Hypoxia_24h_cell

description: test

source_name: CML-derived cell line

value: hypoxia (1% O2)


title: Y07

description: young

tag: bmi


title: SKOV3 FGFR4 knock down siRNA6

city: Houston

first: Tsz-Lun

last: Yeung

state: TX

address: 1515 Holcombe Blvd. Unit 1362

department: Gynecologic Oncology and Reproductive Medicine

institute: University of Texas MD Anderson Cancer Center

description: Gene expression data from SKOV3 cell line with FGFR4 knock down by siRNA6

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

label: Biotin

source_name: Ovarian cancer cell line SKOV3 transfected with FGFR4 targeting siRNA6 (72 hours post transfection)

label_protocol: Biotinylated cRNA were prepared using the MessageAmp Premier RNA Amplification Kit (Ambion) according to the manufacturer's instruction from 100ng total RNA.

growth_protocol: All cell lines were cultured in humidified incubator at 37C and 5% carbon dioxide. Culture medium RPMI1640 supplemented with 10% Fetal bovine serum was used as growth medium.

extract_protocol: Total RNA extraction was performed using the Purelink RNA mini kit (Invitrogen) according to the manufacturer's instructions.

treatment_protocol: prior to treatment, cells were trypsinized, counted and seeded in 60mm cell culture dishes. 24 hours after cell seeding, according to the treatment group, ovarian cancer cells were transfected with the correspondind siRNA using Lipofectamine (Invitrogen). At 72 hours post transfection, transfected cells were harvested and total RNA was extracted.

value: High grade serous ovarian cancer cell line

tag: knockdown

value: FGFR4 siRNA6


title: control_RIP_Chip3

description:
Sample name: control_03
Drosophila_melanogaster_0-3 hr_embryo_control_RIP_Chip3
control RIP-Chip biological replicate 2


title: K562_Normoxia_24h_cell

description: control


title: control_RIP_Chip2

description:
Sample name: control_02
Drosophila_melanogaster_0-3 hr_embryo_control_RIP_Chip2
control RIP-Chip biological replicate 1 (technical replicate 2)


title: SKOV3 FGFR4 knock down siRNA5

description: Gene expression data from SKOV3 cell line with FGFR4 knock down by siRNA5

source_name: Ovarian cancer cell line SKOV3 transfected with FGFR4 targeting siRNA5 (72 hours post transfection)

value: FGFR4 siRNA5


title: control_RIP_Chip1

description:
Sample name: control_01
Drosophila_melanogaster_0-3 hr_embryo_control_RIP_Chip1
control RIP-Chip biological replicate 1 (technical replicate 1)


title: Y09

description: young


title: Y06

description: young


title: Hyperdiploid multiple myeloma biological replicate 4

description:
4 h
miRNA purified from total RNA

tag: sample type

value: primary case of MM

value: h-MM

tag: karyotype and igh status

value: 50 Chromosomes NO IgH marker


title: Y02

description: young


title: Y03

description: young


title: SKOV3 Control Scramble siRNA

description: Gene expression data from SKOV3 cell line transfected with control siRNA

source_name: Ovarian cancer cell line SKOV3 transfected with scramble siRNA (72 hours post transfection)

value: scramble


title: Smaug_RIP_Chip4

description:
Sample name: Smaug_04
Drosophila_melanogaster_0-3 hr_embryo_Smaug_RIP_Chip4
Smaug RIP-Chip biological replicate 3

source_name: Oregon-R wild type 0-3hr embryo Smaug RIP RNA

tag: strain

value: Oregon-R

value: wild type

value: anti-Smaug


title: OVCA432 FGFR4 knock down siRNA5

description: Gene expression data from OVCA432 cell line with FGFR4 knock down by siRNA5

source_name: Ovarian cancer cell line OVCA432 transfected with FGFR4 targeting siRNA5 (72 hours post transfection)


title: Y04

description: young


title: HeLa_NCsiRNA_sample3

city: Prague

first: David

last: Stanek

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics

hyb_protocol: Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling Assay (P/N 701880 Rev. 5)

scan_protocol: Affymetrix GeneChip Expression Wash, Stain, and Scan User Manual (P/N 702731)

data_processing:
Data were analysed using Partek Genomics Suite 6.4 software (RMA, quantile normalization). Only  ‘core’ meta-probe sets were used to identify alternative splicing events.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: HeLa 48 hrs NC siRNA treatment

growth_protocol: HeLa cells cultured in DMEM supplemented with 10% fetal calf serum, penicillin, and streptomycin.

extract_protocol: Total RNA isolated with TRIzol

treatment_protocol: 48 hrs treatment with Brd2 siRNA or control siRNA

value: HeLa

tag: treated with

value: control siRNA for 48hrs


title: OVCA432 FGFR4 knock down siRNA6

description: Gene expression data from OVCA432 cell line with FGFR4 knock down by siRNA6

source_name: Ovarian cancer cell line OVCA432 transfected with FGFR4 targeting siRNA6 (72 hours post transfection)


title: Y01

description: young


title: K562_Hypoxia_24h_exosome

description: test

value: K562 cells


title: Y05

description: young


title: HeLa_NCsiRNA_sample2

label_protocol: Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling Assay (P/N 701880 Rev. 5)


title: Y15

description: young


title: HeLa_NCsiRNA_sample1


title: Smaug_RIP_Chip2

description:
Sample name: Smaug_02
Drosophila_melanogaster_0-3 hr_embryo_Smaug_RIP_Chip2
Smaug RIP-Chip biological replicate 1 (technical replicate 2)

tag: genotype/variation

tag: developmental stage

value: 0-3 hr embryo

value: 25 °C


title: OVCA432 Control Scramble siRNA

description: Gene expression data from OVCA432 cell line transfected with control siRNA

source_name: Ovarian cancer cell line OVCA432 transfected with scramble siRNA (72 hours post transfection)


title: Smaug_RIP_Chip1

description:
Sample name: Smaug_01
Drosophila_melanogaster_0-3 hr_embryo_Smaug_RIP_Chip1
Smaug RIP-Chip biological replicate 1 (technical replicate 1)

tag: temperature

tag: rip antibody


title: input_reference_total_RNA3

description:
Sample name: input_03
Drosophila_melanogaster_0-3 hr_embryo_expression_profile_input_reference_total_RNA3
wild-type 0-3 hr embryo input reference total RNA technical replicate 3

source_name: Oregon-R wild type 0-3hr embryo input total RNA

value: none (input)


title: donor2_CD34+_d7_MSC

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

country: Germany

institute: RWTH Aachen University

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450 Beadchip using standard Infinium HD Methylation Assay protocol.

scan_protocol: Standard Infinium HD Methylation Assay protocol

data_processing: Initial analysis was performed by the Genomestudio 2010.3 (Modul M Version 1.8.5). Data were normalized with internal controls according to Illumina´s standard procedures. Methylation level at each locus was calculated with the GenomeStudio Methylation module as beta-value (ranging from 0 to 1). The number of beads per feature varies between chips and beta-values were calculated as average of at least three technical replica.

source_name: Hematopoietic stem and progenitor cells from umbilical cord blood

extract_protocol: Genomic DNA was isolated from 10(6) cells using the Qiagen DNA Blood Midi Kit.

treatment_protocol: CD34+ cells were isolated from fresh umbilical cord blood after written consent according to the guidelines specifically approved by the Ethic Committee of RWTH Aachen University (Permit Number: EK187/08) using  the CD34 Micro Bead Kit on a MiniMACS system (Miltenyi Biotec GmbH, Bergisch-Gladbach, Germany). Cells were cultured in StemSpan serum free expansion medium (Stem Cell Technologies, Grenoble, France) supplemented with 10 µg/mL heparin (ratiopharm, GmbH, Ulm, Germany), 20 ng/mL thrombopoietin (TPO; PeproTech GmbH, Hamburg, Germany), 10 ng/mL stem cell factor (SCF; PeproTech), 10 ng/mL fibroblast growth factor 1 (FGF1; PeproTech). Culture was either performed on tissue culture plastic (TCP) or on a confluent layer of mesenchymal stromal cells (MSCs; passage 3 to 6). After seven days, CD34+ and CD34- fractions were again separated as described above.

tag: donor

value: CD34+ fraction

tag: passage

value: 7d on MSC


title: donor1_CD34+_d7_MSC

label_protocol: Standard Infinium HD Methylation Assay protocol


title: SUM149_siTIG1_rep3

first: Naoto

middle: T

last: Ueno

address: 1515 Holcombe Blvd.

department: Breast Medical Oncology

institute: UT MD Anderson Cancer Center

hyb_protocol: The fragmented cRNA was used for hybridization to the Affymetrix HGU133 chip overnight at 45°C with rotation.

scan_protocol: Using a GeneArray Scanner (Hewlett-Pacrkard, Palo Alto, CA, USA).

data_processing: The data pre-processing and statistical analysis were performed in R. As part of the standard quality control(QC) analysis, the data were first quantified using the MAS5 algorithm. The Robust Multiarray Analysis (RMA) algorithm that borrows strength across arrays was used to normalize and quantify the data.

source_name: SUM149 cells transfected with siRNA targeting TIG1 (NM_002888)

label_protocol: The double-stranded cDNA was transcribed into cRNA in the presence of biotin-labeled ribonucleotides using the ENZO BioArray HighYield RNA Transcript Labeling Kit (Affymetrix) as described by the manufacturer.

growth_protocol: SUM149 human IBC cells were cultured in Ham’s F-12 medium supplemented with 5% FBS, 5 µg/ml insulin, and 1 µg/ml hydrocortisone.

extract_protocol: Total RNA was extracted and purified using RNeasy mini kit (Qiagen, Inc.) according to the manufacturer’s instructions.

treatment_protocol: SUM149 cells were transfected with ON-TARGET Plus SMART Pools against TIG1 (NM_002888) and siGENOME Non-Targeting siRNA Pool (control siRNA) at a final concentration of 200 nmol/L by using oligofectamine (Invitrogen) according to the manufacturer’s guidelines.

tag: cell line


title: Smaug_RIP_Chip3

description:
Sample name: Smaug_03
Drosophila_melanogaster_0-3 hr_embryo_Smaug_RIP_Chip3
Smaug RIP-Chip biological replicate 2


title: SUM149_siTIG1_rep2


title: SUM149_siTIG1_rep1


title: donor3_CD34-_d7_TCP

tag: cell type

value: CD34- fraction

value: 7d on TCP


title: HeLa_Brd2siRNA_sample3

source_name: HeLa 48 hrs Brd2 siRNA treatment

value: Brd2 siRNA for 48hrs


title: HeLa_Brd2siRNA_sample2


title: donor3_CD34+_d7_MSC


title: input_reference_total_RNA2

description:
Sample name: input_02
Drosophila_melanogaster_0-3 hr_embryo_expression_profile_input_reference_total_RNA2
wild-type 0-3 hr embryo input reference total RNA technical replicate 2


title: SUM149_siControl_rep3

source_name: SUM149 cells transfected with siGENOME Non-Targeting siRNA Pool (control siRNA)


title: donor2_CD34-_d7_TCP


title: HeLa_Brd2siRNA_sample1


title: SUM149_siControl_rep2


title: input_reference_total_RNA1

description:
Sample name: input_01
Drosophila_melanogaster_0-3 hr_embryo_expression_profile_input_reference_total_RNA1
wild-type 0-3 hr embryo input reference total RNA technical replicate 1


title: mir155WT_Bcell

first: Jin-Wu

last: Nam

address: 222 Wangsimni Seongdong-gu

institute: Hanyang University

description: Gene expression data from mouse Bcells

hyb_protocol: Biotinylated cRNA was hybridized at the Whitehead Institute Genome Technology Core, according to standard Affymetrix protocols.

scan_protocol: Arrays were stained, scanned, and quantified according to standard Affymetrix protocols.

data_processing: Raw data was normalized using the RMAExpress software.

source_name: B Cells in mir155 KO mouse

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix 3' IVT Express Kit manual.

growth_protocol: Haematopoietic progenitors were isolated from wild-type and mir-155 knockout male mice and cultured in media containing granulocyte colony-stimulating factor (G-CSF) and stem cell factor (SCF) for six days before harvesting.

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

treatment_protocol: All samples were treated with cycloheximide (100 ug/ml) for 8 min just before harvesting.

value: B cell

tag: genotype

value: mir155 WT

tag: genetic background

value: C57 (from Jackson Laboratory)


title: U87-3M 1

status: Public on Dec 02 2013

city: Birmingham

last: Turan

address: University of Birmingham, Edgbaston

institute: University of Birmingham

hyb_protocol: RNA was hybridised to Agilent Chicken V1 microarrays (for stroma and CAM) and Human GE v2 microarrays (for tumour) (Agilent Technologies, CA). Due to the proximity of tumour cells to the surrounding chicken cells no attempt was made to separate them, instead pooled RNA from both types of cell were hybridised to chicken and human arrays. CAM cells distant from the tumour were hybridised to chicken arrays.

scan_protocol: Scanning and spot analysis were done according to the manufacturer’s instructions.

data_processing: Controls were removed from the data after scanning. The arrays were log2 transformed and normalised using between arrays quantile normalisation in the R software package preprocessCore from BioConductor

label_protocol: RNA was reverse transcribed (cDNA Synthesis System Kit, Roche Diagnostics), purified and transcribed in the presence of Cy3 and Cy5 labels (Megascript D7 Kit, Ambion, Austin, TX).

growth_protocol: U87 human glioma cells were cultured in DMEM with 10% FBS, antibiotics and L-glutamine. Fertilised chicken eggs were kept and prepared as described in (Hagedorn, M et al. 2002. PMID: 12460903)

extract_protocol: RNA was extracted using Qiagen (Valencia, CA) RNeasy columns

value: human glioma

tag: host


title: TUM D16 MORN 1

source_name: TUM D16 MORN

value: chick CAM (chorioallantoic membranne)


title: SUM149_siControl_rep1


title: donor1_CD34-_d7_TCP


title: U87-3M 3


title: donor3_CD34+_d7_TCP


title: mir155KO_Bcell

description: Gene expression data from mouse Bcells

source_name: B Cells in wildtype mouse

value: mir155 KO


title: donor2_CD34+_d7_TCP


title: TUM D15 EVE 3

source_name: TUM D15 EVE


title: TUM D14 EVE 3

source_name: TUM D14 EVE


title: TUM D15 MORN 1

source_name: TUM D15 MORN


title: U87-3M 2


title: TUM D14 MORN 3

source_name: TUM D14 MORN


title: TUM D15 MORN 2


title: donor1_CD34+_d7_TCP


title: TUM D15 MORN 3


title: TUM D15 EVE 1


title: TUM D13 EVE 1

source_name: TUM D13 EVE


title: TUM D14 MORN 1


title: TUM D15 EVE 2


title: TUM D13 EVE 3


title: TUM D14 MORN 2


title: donor3_CD34+_d0

value: freshly isolated


title: TUM D14 EVE 1


title: TUM D12 MORN 2

source_name: TUM D12 MORN


title: TUM D13 MORN 3

source_name: TUM D13 MORN


title: TUM D13 MORN 2


title: TUM D13 MORN 1


title: TUM D12 EVE 1

source_name: TUM D12 EVE


title: TUM D12 EVE 2


title: TUM D12 EVE 3


title: TUM D11 EVE 2

source_name: TUM D11 EVE


title: TUM D12 MORN 3


title: TUM D12 MORN 1


title: TUM D11 MORN 3

source_name: TUM D11 MORN


title: TUM D11 EVE 3


title: TUM D14 EVE 2


title: KI_TEX_2789_130 lymph node

city: Lund

first: Siker

last: Kimbung

address: Scheelevägen 2

department: Department of Oncology and Pathology, Clinical Sciences, Lund

country: Sweden

institute: Lund University

description:
@52070900803933090410408220339078
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease

hyb_protocol: GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques.  Arrays are hybridized for 18 hours at 45C with vigorous mixing.   Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed.  Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: Data were processed using the QC-RMA algorithm (http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=12582260).

source_name: lymph node

label_protocol:
Samples are processed in parallel in 96-well plates to minimize potential variation.  Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.
The final in vitro transcription incorporates biotin moieties that are later labeled with phycoerythrin.  After amplification, samples are put through a controlled fragmentation to improve hybridization sensitivity and consistency.  The labeled molecules are biotinylated-cRNA.

growth_protocol: Fine-needle biopsies of metastases were immersed into RNAlater immidiately after collection.

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

value: Fine-needle aspirate

tag: tissue

value: breast cancer regional lymph node metastasis


title: donor1_CD34+_d0

source_name: Hematopoietic stem and progenitor cells from umbilical cord blood


title: IN3008, biological rep2

city: Wolverhampton

first: Katherine

last: Karakoula

address: Wulfruna Street

department: Brain Tumour Research Centre

institute: University of Wolverhampton

description: IN3008 U

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG_U133_Plus_2 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to standard manufacturer protocols.

scan_protocol: GeneChips were scanned using the the GeneChip Scanner 3000 7G (Affymetrix) according to standard manufacturer protocols.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The raw intensity values were further assessed by the Robust Multi-array Analysis (RMA-GCRMA algorithm from GeneSpring software version 7.3.1)

source_name: Ependymoma cells untreated

label_protocol: Biotinylated cRNA were prepared using the MessageAmp™ II-Biotin Enhanced Single Round aRNA Amplification Kit  according to the manufacturer's instructions (Ambion, Life Technologies Ltd. UK) from 5 ug total RNA from each sample.

growth_protocol: Ependymoma short-term cell cultures were prepared as described previously (Lewandowicz et al., 2002) and grown in Hams F10 nutrient mix supplemented with 10% selected fetal calf serum (Invitrogen, Paisley, UK) at 37 °C in a non-CO2 incubator.

extract_protocol: Total RNA from treated and mock-treated cells was extracted using the RNeasy Mini Kit according to the manufacturer’s instructions (Qiagen Ltd., UK).

treatment_protocol: Three short-term ependymoma cell cultures were used for whole genome expression analysis following treatment with the demethylating agent 5-Aza-dC. Cells were plated at low passage number (passage 6-8) in T75 cm2 flasks (1 X 106 cells) in media with 10% fetal calf serum and left overnight to attach. 5-Aza-dC (Sigma-Aldrich, Inc) was freshly prepared in distilled water and filter sterilized. Cells were treated with 5 µmol/L 5-Aza-dC or a control volume of vehicle (DMSO final concentration not ≤0.1% v/v; Sigma). Medium and drug or vehicle were replaced every 24 hrs over a 96-hr period.

value: primary brain tumour that recurs

tag: cell culture

tag: treatment


title: TUM D11 EVE 1


title: TUM D11 MORN 2


title: KI_TEX_2941_124 bone

description:
@52070900803933090410408220339075
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease

source_name: bone

tag: sample type

value: breast cancer bone  metastasis


title: IN3008, biological rep1

description: IN3008 U


title: KI_TEX_1648_50 liver

description:
@52070900803933090410408220339081
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease

source_name: liver

value: breast cancer liver metastasis


title: donor2_CD34+_d0

value: CD34+ fraction


title: KI_TEX_2739_24 lymph node

description:
@52070900803933090410408220339072
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: KI_TEX_2935_134 lymph node

description:
@52070900803933090410408220339070
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: KI_TEX_1581_86 lymph node

description:
@52070900803933090410408220339076
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: KI_TEX_2775_173 lymph node

description:
@52070900803930090410408220338919
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: KI_TEX_3001_139 lymph node

description:
@52070900803933090410408220339069
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: TUM D11 MORN 1


title: KI_TEX_1083_49 liver

description:
@52070900803933090410408220339074
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: KI_TEX_1649_53 liver

description:
@52070900803933090410408220339073
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: KI_TEX_2776_68 liver

description:
@52070900803933090410408220339068
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: KI_TEX_2923_116 liver

description:
@52070900803933090410408220339060
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: IN3008 Treated, biological rep1

description: IN3008 T

source_name: Ependymoma cells treated with 5-Aaza-dC

value: 5-Aza-dC (5 µmol/L)


title: IN1638, biological rep1

description: IN1638 U


title: IN1638, biological rep2

description: IN1638 U


title: IN1594, biological rep2

description: IN1594 U


title: KI_TEX_1487_40 liver

description:
@52070900803933090410408220339061
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: KI_TEX_1468_36 lymph node

description:
@52070900803933090410408220339057
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: GM09582 1.5 Gy Gamma vs. GM09582 Mock

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Cultures were maintained in RPMI 1640 media supplemented with 15% fetal bovine serum and L-glutamine.  Cells were plated in T25 flasks and cultured for 2 days prior to exposure to gamma radiation.  Cells were harvested 6 hours after mock irradiation or irradiation with 1.5 Gy gamma radiation.  Harvesting cells consisted of spinning the cells and media and aspirating the supernatant.  Pellets were flash frozen in liquid nitrogen and stored at -80oC.

hyb_protocol: For each two color comparison, equal amounts of Cy3 and Cy5 labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol.  Hybridizations were performed for 17 hours in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol.

scan_protocol: Slides were washed as indicated in the Agilent 60-mer oligo microarray processing protocol and then scanned with an Agilent Scanner. Data was obtained using the Agilent Feature Extraction software, using defaults for all parameters.

data_processing: Data was obtained using the Agilent Feature Extraction software, using defaults for all parameters and loaded into the Rosetta Resolver® system (v6.0) (Rosetta Biosoftware, Kirkland, WA).

source_name: GM09582 1.5 Gy Gamma

label_protocol: Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol.  Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

extract_protocol: Qiagen RNeasy technology following the manufacturer's instructions with the RNeasy Midi Kit

value: GM09582 Human non-fetal EBV-immortalized lymphoblast cells from Coriell Institute for Medical Research

value: 1.5 Gy IR + 6 hr

tag: disease state

value: Ataxia telangiectasia affected individual

tag: age

value: 12 yr old

tag: ethnicity

value: caucasian

tag: gender

value: female

source_name: GM09582 Mock

label_protocol: Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol.  Starting with 500ng of total RNA, Cy5 labeled cRNA was produced according to manufacturer’s protocol.

value: 0 Gy IR + 6 hr


title: KI_TEX_2803_113 lymph node

description:
@52070900803933090410408220339053
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: IN3008 Treated, biological rep2

description: IN3008 T


title: KI_TEX_3010_153 liver

description:
@52070900803933090410408220339065
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: GM03714 1.5 Gy Gamma vs. GM03714 Mock

source_name: GM03714 1.5 Gy Gamma

value: GM03714 Human non-fetal EBV-immortalized lymphoblast cells from Coriell Institute for Medical Research

value: Apparently normal individual

value: 10 yr old

value: caucasian (European)

source_name: GM03714 Mock


title: KI_TEX_1477_54 liver

description:
@52070900803933090410408220339050
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease

value: Fine-needle aspirate


title: IN1638 Treated, biological rep2

description: IN1638 T

value: primary brain tumour that recurs


title: GM03332 Mock vs. GM03332 1.5 Gy Gamma

source_name: GM03332 Mock

value: GM03332 Human non-fetal EBV-immortalized lymphoblast cells from Coriell Institute for Medical Research

value: 13 yr old

value: black

value: male

source_name: GM03332 1.5 Gy Gamma


title: KI_TEX_3003_75 lymph node

description:
@52070900803933090410408220339051
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease

value: breast cancer regional lymph node metastasis


title: IN1594, biological rep1

description: IN1594 U


title: GM03714 Mock vs. GM03714 1.5 Gy Gamma

value: 1.5 Gy IR + 6 hr


title: KI_TEX_2740_27 lymph node

description:
@52070900803929090410408220338894
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: KI_TEX_1542_5 lymph node

description:
@52070900803933090410408220339041
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: IN1594 Treated, biological rep1

description: IN1594 T

value: 5-Aza-dC (5 µmol/L)


title: IN1638 Treated, biological rep1

description: IN1638 T


title: KI_TEX_2931_133 lymph node

description:
@52070900803933090410408220339046
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: GM03299 Mock vs. GM03299 1.5 Gy Gamma

source_name: GM03299 Mock

value: GM03299 Human non-fetal EBV-immortalized lymphoblast cells from Coriell Institute for Medical Research

value: 8 yr old

source_name: GM03299 1.5 Gy Gamma


title: KI_TEX_2909_126 skin

description:
@52070900803933090410408220339044
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease

source_name: skin

value: breast cancer skin  metastasis


title: KI_TEX_500_45 breast

description:
@52070900803933090410408220339038
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease

source_name: breast

value: breast cancer local metastasis in the breast


title: KI_TEX_1522_83 skin local-regional

description:
@52070900803933090410408220339040
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease

source_name: skin local-regional


title: KI_TEX_1664_46 breast

description:
@52070900803933090410408220339036
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: GM03189 Mock vs. GM03189 1.5 Gy Gamma

source_name: GM03189 Mock

value: GM03189 Human non-fetal EBV-immortalized lymphoblast cells from Coriell Institute for Medical Research

value: 0 Gy IR + 6 hr

value: Ataxia telangiectasia affected individual

value: 7 yr old

value: caucasian

source_name: GM03189 1.5 Gy Gamma


title: GM02782 1.5 Gy Gamma vs. GM02782 Mock

source_name: GM02782 1.5 Gy Gamma

value: GM02782 Human non-fetal EBV-immortalized lymphoblast cells from Coriell Institute for Medical Research

value: 5 yr old

value: caucasian (Iranian)

source_name: GM02782 Mock


title: KI_TEX_2929_73 lymph node

description:
@52070900803933090410408220339042
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease

source_name: lymph node

value: Fine-needle aspirate


title: AG15033 Mock vs. AG15033 1.5 Gy Gamma

source_name: AG15033 Mock

value: AG15033 Human non-fetal EBV-immortalized lymphoblast cells from Coriell Institute for Medical Research

value: Apparently normal individual

value: 12 yr old

value: male

source_name: AG15033 1.5 Gy Gamma


title: IN1594 Treated, biological rep2

description: IN1594 T

source_name: Ependymoma cells treated with 5-Aaza-dC

value: primary brain tumour that recurs

value: 5-Aza-dC (5 µmol/L)


title: KI_TEX_1469_34 lymph node

description:
@52070900803933090410408220339034
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease

value: breast cancer regional lymph node metastasis


title: KI_TEX_1446_39 lymph node

description:
@52070900803933090410408220339035
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: GM03189 1.5 Gy Gamma vs. GM03189 Mock

value: 1.5 Gy IR + 6 hr


title: KI_TEX_503_41 bone

description:
@52070900803930090410408220338964
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease

source_name: bone

value: breast cancer bone  metastasis


title: KI_TEX_2693 a_109 lymph node

description:
@52070900803930090410408220338949
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: KI_TEX_1557_91 lymph node

description:
@52070900803930090410408220338945
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: KI_TEX_2742_26 skin local-regional

description:
@52070900803930090410408220338950
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease

value: breast cancer skin  metastasis


title: KI_TEX_1570_15 lymph node

description:
@52070900803931090410408220339019
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: Negative scramble control,  biological rep1

city: Beijing

first: Yan

last: Zhang

state: Not Applicable

address: Dongdajie street

country: China

institute: Beijing institute of Biotechnology

description:
100325-HG-U133_Plus-2-10126A_N1.CEL
Gene expression data from scramble siRNA transfected cells

hyb_protocol: Standard Affymetrix protocol

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. A log base 2 transformation is applied to the data before the arrays are normalized. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: SGC-7901 cells transfected with scramble control siRNA

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

growth_protocol: cells were grown in RPMI1640 medium (Life Technologies, Inc., Gaithersburg,MD) supplemented with 10% fetal bovine serum (FBS, Hyclone, Inc.), penicillin (100 U/ml) and streptomycin (100 μg/ml). Cells grew at 37°C in a humidified atmosphere of 5% CO2.

treatment_protocol: SGC-7901 cells were transiently transfected with HPSE siRNA or scramble control siRNA using lipofectamine 2000(life technology), according to the manufacturer’s instructions.. 24hours later, cells were collected in  Trizol solution (life technology).

value: Gastric adenocarcinoma

value: SGC-7901 gastric cancer cells

tag: genotype/variation

value: control


title: HPSE depleted,  biological rep3

description:
100325-HG-U133_Plus-2-10126A_S3.CEL
Gene expression data from HPSE siRNA transfected cells

source_name: SGC-7901 cells transfected with HPSE siRNA

value: HPSE depletion


title: KI_TEX_2770_67 lymph node

description:
@52070900786105090510408220943472
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: AG15014 1.5 Gy Gamma vs. AG15014 Mock

description: Cultures were maintained in RPMI 1640 media supplemented with 15% fetal bovine serum and L-glutamine.  Cells were plated in T25 flasks and cultured for 2 days prior to exposure to gamma radiation.  Cells were harvested 6 hours after mock irradiation or irradiation with 1.5 Gy gamma radiation.  Harvesting cells consisted of spinning the cells and media and aspirating the supernatant.  Pellets were flash frozen in liquid nitrogen and stored at -80oC.

source_name: AG15014 1.5 Gy Gamma

value: AG15014 Human non-fetal EBV-immortalized lymphoblast cells from Coriell Institute for Medical Research

value: 8 yr old

value: caucasian

source_name: AG15014 Mock

value: 0 Gy IR + 6 hr


title: GM03332 1.5 Gy Gamma vs. GM03332 Mock

source_name: GM03332 1.5 Gy Gamma

value: GM03332 Human non-fetal EBV-immortalized lymphoblast cells from Coriell Institute for Medical Research

value: Ataxia telangiectasia affected individual

value: 13 yr old

value: black

source_name: GM03332 Mock


title: KI_TEX_3014_137 skin local-regional

description:
@52070900803930090410408220338946
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease

value: Fine-needle aspirate


title: HPSE depleted,  biological rep1

description:
100325-HG-U133_Plus-2-10126A_S1.CEL
Gene expression data from HPSE siRNA transfected cells


title: HPSE depleted,  biological rep2

description:
100325-HG-U133_Plus-2-10126A_S2.CEL
Gene expression data from HPSE siRNA transfected cells


title: AG14832 Mock vs. AG14832 1.5 Gy Gamma

source_name: AG14832 Mock

value: AG14832 Human non-fetal EBV-immortalized lymphoblast cells from Coriell Institute for Medical Research

value: Apparently normal individual

value: 7 yr old

value: male

source_name: AG14832 1.5 Gy Gamma


title: AG14832 1.5 Gy Gamma vs. AG14832 Mock

value: 1.5 Gy IR + 6 hr


title: Negative scramble control,  biological rep2

description:
100325-HG-U133_Plus-2-10126A_N2.CEL
Gene expression data from scramble siRNA transfected cells

value: Gastric adenocarcinoma

value: SGC-7901 gastric cancer cells


title: KI_TEX_1607_89 liver

description:
@52070900803930090410408220338944
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease

source_name: liver

value: breast cancer liver metastasis


title: AG14778 1.5 Gy Gamma vs. AG14778 Mock

source_name: AG14778 1.5 Gy Gamma

value: AG14778 Human non-fetal EBV-immortalized lymphoblast cells from Coriell Institute for Medical Research

value: 6 yr old

value: female

source_name: AG14778 Mock


title: KI_TEX_1563_31 skin local-regional

description:
@52070900803931090410408220339020
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease

source_name: skin local-regional

value: breast cancer skin  metastasis


title: KI_TEX_2994_145 breast

description:
@52070900803930090410408220338940
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease

source_name: breast

value: breast cancer local metastasis in the breast


title: KI_TEX_2844_103 lung

description:
@52070900803930090410408220338930
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease

source_name: lung

value: breast cancer lung  metastasis


title: KI_TEX_1546_85 lymph node

description:
@52070900803930090410408220338931
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease

source_name: lymph node

value: breast cancer regional lymph node metastasis


title: KI_TEX_2915_118 skin

description:
@52070900803930090410408220338922
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease

source_name: skin


title: AG15033 1.5 Gy Gamma vs. AG15033 Mock

source_name: AG15033 1.5 Gy Gamma

value: AG15033 Human non-fetal EBV-immortalized lymphoblast cells from Coriell Institute for Medical Research

value: 12 yr old

value: caucasian

source_name: AG15033 Mock

value: 0 Gy IR + 6 hr


title: KI_TEX_1596_21 lymph node

description:
@52070900803930090410408220338937
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease

value: Fine-needle aspirate


title: KI_TEX_1485_4 skin local-regional

description:
@52070900803930090410408220338933
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: Negative scramble control,  biological rep3

description:
100325-HG-U133_Plus-2-10126A_N3.CEL
Gene expression data from scramble siRNA transfected cells

source_name: SGC-7901 cells transfected with scramble control siRNA

value: control


title: KI_TEX_1593_93 lymph node

description:
@52070900803930090410408220338941
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: AG15014 Mock vs. AG15014 1.5 Gy Gamma

value: AG15014 Human non-fetal EBV-immortalized lymphoblast cells from Coriell Institute for Medical Research

value: Apparently normal individual

value: 8 yr old

value: male

source_name: AG15014 1.5 Gy Gamma

value: 1.5 Gy IR + 6 hr


title: KI_TEX_1484_3 lymph node

description:
@52070900803930090410408220338935
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: KI_TEX_3011_138 breast

description:
@52070900803930090410408220338916
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: KI_TEX_2846_102 liver

description:
@52070900803929090410408220338898
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease

value: breast cancer liver metastasis


title: GM13989 1.5 Gy Gamma vs. GM13989 Mock

description: Cultures were maintained in RPMI 1640 media supplemented with 15% fetal bovine serum and L-glutamine.  Cells were plated in T25 flasks and cultured for 2 days prior to exposure to gamma radiation.  Cells were harvested 6 hours after mock irradiation or irradiation with 1.5 Gy gamma radiation.  Harvesting cells consisted of spinning the cells and media and aspirating the supernatant.  Pellets were flash frozen in liquid nitrogen and stored at -80oC.

source_name: GM13989 1.5 Gy Gamma

value: GM13989 Human non-fetal EBV-immortalized lymphoblast cells from Coriell Institute for Medical Research

value: Ataxia telangiectasia affected individual

value: caucasian (Palestinian)

source_name: GM13989 Mock


title: KI_TEX_2775_65 lymph node

description:
@52070900803933090410408220339080
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: KI_TEX_2722_70 breast

description:
@52070900803929090410408220338892
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease

value: breast cancer local metastasis in the breast


title: AG14778 Mock vs. AG14778 1.5 Gy Gamma

value: AG14778 Human non-fetal EBV-immortalized lymphoblast cells from Coriell Institute for Medical Research

value: 6 yr old

value: black

value: female


title: KI_TEX_2948_136 lymph node

description:
@52070900803929090410408220338897
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease

value: breast cancer regional lymph node metastasis


title: KI_TEX_1562_13  skin local-regional

description:
@52070900803929090410408220338902
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease

value: Fine-needle aspirate

value: breast cancer skin  metastasis


title: KI_TEX_1525_42 lymph node

description:
@52070900803930090410408220338921
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: KI_TEX_2752_22 lung

description:
@52070900803929090410408220338872
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease

value: breast cancer lung  metastasis


title: GM02782 Mock vs. GM02782 1.5 Gy Gamma

source_name: GM02782 Mock

value: GM02782 Human non-fetal EBV-immortalized lymphoblast cells from Coriell Institute for Medical Research

value: 0 Gy IR + 6 hr

value: 5 yr old

value: caucasian (Iranian)

source_name: GM02782 1.5 Gy Gamma


title: KI_TEX_1567_28 liver

description:
@52070900803929090410408220338880
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease

value: breast cancer liver metastasis


title: KI_TEX_1597_96 breast

description:
@52070900803929090410408220338886
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: KI_TEX_1576_16 lymph node

description:
@52070900803929090410408220338878
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: KI_TEX_3005_154 bone

description:
@52070900803929090410408220338887
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease

source_name: bone

value: breast cancer bone  metastasis


title: KI_TEX_2925_157 breast

description:
@52070900786089090410408220741439
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: KI_TEX_1578_17 lymph node

description:
@52070900803930090410408220338951
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: KI_TEX_2938_125 liver

description:
@52070900786089090410408220741429
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease

source_name: liver


title: GM09582 Mock vs. GM09582 1.5 Gy Gamma

source_name: GM09582 Mock

value: GM09582 Human non-fetal EBV-immortalized lymphoblast cells from Coriell Institute for Medical Research

value: Ataxia telangiectasia affected individual

value: 12 yr old

value: caucasian

source_name: GM09582 1.5 Gy Gamma

value: 1.5 Gy IR + 6 hr


title: GM03299 1.5 Gy Gamma vs. GM03299 Mock

source_name: GM03299 1.5 Gy Gamma

value: GM03299 Human non-fetal EBV-immortalized lymphoblast cells from Coriell Institute for Medical Research

value: Apparently normal individual

value: 8 yr old

source_name: GM03299 Mock


title: KI_TEX_1549_12 liver

description:
@52070900786089090410408220741435
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease

value: Fine-needle aspirate


title: GM13873 1.5 Gy Gamma vs. GM13873 Mock

source_name: GM13873 1.5 Gy Gamma

value: GM13873 Human non-fetal EBV-immortalized lymphoblast cells from Coriell Institute for Medical Research

value: 6 yr old

value: female

source_name: GM13873 Mock


title: GM13873 Mock vs. GM13873 1.5 Gy Gamma

value: 0 Gy IR + 6 hr


title: KI_TEX_2855_129 skin local-regional

description:
@52070900786089090410408220741417
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease

source_name: skin local-regional

value: breast cancer skin  metastasis


title: KI_TEX_1622_44 lymph node

description:
@52070900786089090410408220741425
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease

source_name: lymph node

value: breast cancer regional lymph node metastasis


title: KI_TEX_1600_92 lymph node

description:
@52070900786089090410408220741432
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: KI_TEX_1447_33 skin local-regional

description:
@52070900786089090410408220741415
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: GM13989 Mock vs. GM13989 1.5 Gy Gamma

description: Cultures were maintained in RPMI 1640 media supplemented with 15% fetal bovine serum and L-glutamine.  Cells were plated in T25 flasks and cultured for 2 days prior to exposure to gamma radiation.  Cells were harvested 6 hours after mock irradiation or irradiation with 1.5 Gy gamma radiation.  Harvesting cells consisted of spinning the cells and media and aspirating the supernatant.  Pellets were flash frozen in liquid nitrogen and stored at -80oC.

value: GM13989 Human non-fetal EBV-immortalized lymphoblast cells from Coriell Institute for Medical Research

value: caucasian (Palestinian)

value: male


title: KI_TEX_2957_156 ascites

description:
@52070900786089090410408220741412
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease

source_name: ascites

value: breast cancer ascite  metastasis


title: KI_TEX_2924_119 bone

description:
@52070900786087090410408220741365
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease

value: breast cancer bone  metastasis


title: KI_TEX_2842_107 lymph node

description:
@52070900786087090410408220741379
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: KI_TEX_2741_111 bone

description:
@52070900786089090410408220741411
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: KI_TEX_2811_99 skin local-regional

description:
@52070900786089090410408220741398
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: KI_TEX_2859_155 lymph node

description:
@52070900803933090410408220339052
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: KI_TEX_2806_66 lymph node

description:
@52070900786087090410408220741377
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: KI_TEX_1580_47 breast

description:
@52070900786087090410408220741373
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease

source_name: breast

value: breast cancer local metastasis in the breast


title: KI_TEX_1612_90 skin local-regional

description:
@52070900786087090410408220741372
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: KI_TEX_2834_79 lymph node

description:
@52070900786087090410408220741368
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: KI_TEX_2788_97 lymph node

description:
@52070900786087090410408220741366
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: KI_TEX_2850_62 lymph node

description:
@52070900786087090410408220741356
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: KI_TEX_1560_10 liver

description:
@52070900786087090410408220741363
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease

value: breast cancer liver metastasis


title: KI_TEX_2782_60 skin

description:
@52070900786087090410408220741364
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease

source_name: skin


title: KI_TEX_2910_147 lymph node

description:
@52070900786087090410408220741374
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: STROMA D16 MORN 1

hyb_protocol: RNA was hybridised to Agilent Chicken (V1) microarrays and Human GE v2 microarrays (Agilent Technologies, CA). Due to the proximity of tumour cells to the surrounding chicken cells no attempt was made to separate them, instead pooled RNA from both types of cell were hybridised to chicken and human arrays. CAM cells distant from the tumour were hybridised to chicken arrays.

organism: Gallus gallus

source_name: STROMA D16 MORN

value: CAM, at site of implantation


title: KI_TEX_1451_81 skin local-regional

description:
@52070900786087090410408220741359
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: KI_TEX_2777_105 skin local-regional

description:
@52070900786087090410408220741358
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: KI_TEX_2917_74 lymph node

description:
@52070900786087090410408220741357
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: KI_TEX_3016_142 breast

description:
@52070900786087090410408220741371
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: STROMA D15 EVE 3

source_name: STROMA D15 EVE


title: KI_TEX_2904_71 skin local-regional

description:
@52070900786087090410408220741354
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: STROMA D15 EVE 1


title: STROMA D15 EVE 2


title: KI_TEX_1467_82 skin local-regional

description:
@52070900786087090410408220741350
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: STROMA D15 MORN 1

source_name: STROMA D15 MORN


title: KI_TEX_1524_35 lymph node

description:
@52070900786087090410408220741344
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: KI_TEX_1583_8 breast

description:
@52070900786087090410408220741341
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: STROMA D15 MORN 3


title: KI_TEX_1594_94 breast

description:
@52070900786087090410408220741340
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: STROMA D14 EVE 3

source_name: STROMA D14 EVE


title: KI_TEX_2987_146 liver

description:
@52070900786087090410408220741338
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: KI_TEX_2791_112 liver

description:
@52070900786087090410408220741335
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease


title: STROMA D14 EVE 2


title: STROMA D15 MORN 2


title: STROMA D14 MORN 3

source_name: STROMA D14 MORN


title: STROMA D13 EVE 3

source_name: STROMA D13 EVE


title: STROMA D13 MORN 2

source_name: STROMA D13 MORN


title: STROMA D14 EVE 1


city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: Gene expression data from_Coxiella treated with acidified citrate cysteine media 2 replicate 2

hyb_protocol: All cRNAs were hybridized to a custom Affymetrix GeneChip

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7GPlus.

data_processing: The data were analyzed with GCOS 1.4 using Affymetrix default analysis with a scale filter for Ft genes setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Coxiella burnetii

label_protocol: Biotin-labeled cRNA was then in vitro transcribed using cDNA as a template. Ten mg of labeled cRNA was fragmented using Ambion 10X fragmentation buffer (Invitrogen) and incubation at 75°C for 15 min.

growth_protocol: Host cell propagation of bacteria was conducted using African green monkey kidney (Vero) fibroblasts (CCL-81; American Type Culture Collection) grown in RPMI medium (Invitrogen) supplemented with 2% (v/v) fetal bovine serum (FBS).

extract_protocol: A MicrobEnrich kit (Applied Biosystems) was used to increase the relative level of C. burnetii RNA. Enriched RNA (~1 μg) was amplified using a MessageAmp II Bacteria kit (Applied Biosystems).

treatment_protocol: For axenic cultivation, C. burnetii was grown in ACCM-1 and ACCM-2

tag: growth medium


description: Gene expression data from_Coxiella treated with acidified citrate cysteine media 2 replicate 3


title: STROMA D13 EVE 1


title: STROMA D14 MORN 2


description: Gene expression data from_Coxiella treated with acidified citrate cysteine media 2 replicate 4


title: STROMA D13 MORN 3


title: STROMA D14 MORN 1


title: Coxiella treated with acidified citrate cysteine media 1 replicate 4

description: Gene expression data from_Coxiella treated with acidified citrate cysteine media1replicate 4


title: STROMA D13 MORN 1


description: Gene expression data from_Coxiella treated with acidified citrate cysteine media 2 replicate 1


title: STROMA D12 EVE 3

source_name: STROMA D12 EVE