title: VAD-IP-17

source_name: Implant Sample 13


title: VAD-IP-15

status: Public on May 20 2010

type: RNA

city: Bad Oeynhausen

first: Patrick

last: Schwientek

address: Georgstr. 11

department: Klinik f. Thorax- & Kardiovaskularchirurgie

country: Germany

institute: Herz- & Diabeteszentrum NRW

description: Gene expression data from patients suffering end-stage heart-failure

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG-U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Implant Sample 11

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: Myocardial tissue was directly taken from non-failing and failing hearts.

extract_protocol: Samples were pruned from the left ventricle near the apex. RNA extraction has been carried out with TRIzol reagent and tissue was homogenized using a rotor-stator homogenizer. Homogenates were transferred to a Phase Lock Gel (PLG) Heavy tube (Eppendorf), chloroform was added, and the mixture was centrifuged. Supernatants were collected, and isopropanol was added to precipitate the RNA. The RNA pellet was washed with 80% ethanol, then air-dried before dissolving in 100  l of RNase-free H2O. RNA was further purified using the RNeasy Mini protocol according to the manufacturer’s directions (Qiagen).

treatment_protocol: The samples were frozen in liquid nitrogen directly after pruning and defrosted only for microarray analysis.

tag: sample pairs

tag: tissue

value: Myocard

tag: vad status

value: before VAD support

tag: disease status

value: ischemic cardiomyopathy

tag: vad

value: Heartmate I

tag: age

tag: gender

value: m


title: VAD-IP-14

source_name: Implant Sample 10

value: dilated cardiomyopathy

value: DuraHeart

value: f


title: VAD-IP-23

source_name: Implant Sample 17

value: Novacor


title: VAD-IP-9

source_name: Implant Sample 7


title: VAD-IP-18

source_name: Implant Sample 14

value: Thoratec


title: NF-14

description: Gene expression data from non-failing control hearts

source_name: Non-Failing Sample 8

value: unsupported


title: VAD-IP-12

source_name: Implant Sample 9

value: CorAide


title: NF-11

source_name: Non-Failing Sample 7


title: VAD-IP-6

source_name: Implant Sample 4


title: VAD-IP-8

source_name: Implant Sample 6


title: VAD-IP-10

source_name: Implant Sample 8


title: VAD-IP-4

source_name: Implant Sample 3


title: NF-9

source_name: Non-Failing Sample 5


title: VAD-IP-2

source_name: Implant Sample 1


title: VAD-IP-3

source_name: Implant Sample 2


title: NF-10

source_name: Non-Failing Sample 6


title: VAD-IP-7

source_name: Implant Sample 5

value: Thoratec (iVAD)


title: NF-8

source_name: Non-Failing Sample 4


title: NF-3

source_name: Non-Failing Sample 2


title: NF-7

source_name: Non-Failing Sample 3


title: 193s_A

status: Public on May 19 2010

city: Beijing

first: Jin

last: Xu

address: Beijing Institute of Genomics, Chinese Academy of Sciences No.7 Beitucheng West Road, Chaoyang District, Beijing 100029, PR China

country: China

institute: BIG,CAS

description: Gene expression data from testis of sterile line

hyb_protocol: Target hybridization for GeneChips were performed according to the standard protocol in Affymetrix GeneChip expression Analysis Technical Manual

scan_protocol: Target scanning for GeneChips were performed according to the standard protocol in Affymetrix GeneChip expression Analysis Technical Manual

data_processing: GeneChip images were quantified and gene expression values(signal intensity) were calculated by Affymetrix Microarry Sute Version 5.0(MAS 5.0).

organism: Drosophila simulans

source_name: Drosophila simulans sterile males

label_protocol: Label for GeneChips were performed according to the standard protocol outline in th Affymetrix GeneChip expression Analysis Technical Manual and the protocals are avaliable at http://fgf.bsd.uchicago.edu/facility/microarray.htm

growth_protocol: The fertile and sterile introgression lines were constructed and maintained as described in Ting et al.(1998)

extract_protocol: The testes were dissected on ice in RNALater and transferred into TRIzol® Reagent (Invitrogen). The abdomens were separated from whole body in dry ice and immediately homogenized in TRIzol®. Total RNA was isolated according to the manufacture's instruction, further purified with phenol-choroform extraction,and precipitated with isopropanol.

treatment_protocol: We collected on average 150 adult male files aged 3-4 days from each line for testis dissection,and 50 files for abdomen dissection

tag: sex

value: male

value: testis

tag: genotype/variation

value: X chromosome (OdsH locus) S variant from D. mauritiana

tag: fertility status

value: sterile

value: 3-4 days


title: NF-1

source_name: Non-Failing Sample 1

value: Myocard


title: 99F_B

description: Gene expression data from testis of fertile line

source_name: Drosophila simulans fertile males

value: X chromosome (OdsH locus) F variant from D. mauritiana

value: fertile


title: 193s_B


title: 99F_C


title: 193s_C


title: 99F_A


title: FAMA-EAR-48h-1

status: Public on May 12 2010

city: Stanford

first: Dominique

last: Bergmann

state: CA

address: 371 Serra Mall

department: Biological Sciences

country: USA

institute: Stanford University

description: Gene expression data from 7 day-old Arabidopsis seedlings,48h EST induction of a FAMA-EAR construct

hyb_protocol: 20 µg of the resulting cRNA was used to hybridize to each ATH1 Arabidopsis GeneChip (Affymetrix) using the manufacturer’s protocols.

scan_protocol: standard Affymetrix protocol

data_processing: The array images were analyzed with the Affymetrix Microarray Suite 5.0 with the target intensity set to 500.

organism: Arabidopsis thaliana

source_name: Whlole seedling, 48h Estrogen induction

label_protocol: Biotinylated complementary RNA (cRNA) was prepared with the bioarray high yield transcript labeling kit (Enzo)

growth_protocol: Sterilized seeds were sowed on MS + Sucrose plates, then keep at 4C for 3 days. Seedlings were grown on vertically oriented plates in a 22 C incubator under 24 hours light for 5 days.

extract_protocol: After 4h or 48h on new plates, samples were collected, frozen in liquid nitrogen and stored at –80 degree until enough material was obtained to do all RNA extractions in the same week.  The Rneasy Plant Mini Kit (QIAGEN) for RNA isolation,

treatment_protocol: Seedlings were transfered with forcepts to plates conatinin MS + Sucrose + 10 μM estrogen  (or new MS + sucrose plates for controls).

tag: ecotype

value: Columbia

value: Whole seedling

value: 7 day old

tag: time

tag: expression

value: FAMA-EAR repression domain


title: FAMA-EAR-48h-3


title: control_48h-1

description: Gene expression data from 7 day-old Arabidopsis seedlings, No induction

source_name: Whlole seedling, 48h Control, no induction


title: FAMA-EAR-48h-2


title: control_4h-3

description: Gene expression data from 5 day-old Arabidopsis seedlings, No induction

source_name: Whlole seedling, 4h Control, no induction

value: 5 day old


title: FAMA_4h-2

description: Gene expression data from 5 day-old Arabidopsis seedlings, 4h EST induction

source_name: Whlole seedling, 4h Estrogen induction

value: FAMA


title: FAMA_48h-2

description: Gene expression data from 7 day-old Arabidopsis seedlings,48h EST induction


title: control_48h-3


title: FAMA_48h-1


title: control_4h-1


title: control_48h-2


title: coi1-2 JA #1

status: Public on May 11 2010

city: Peking

first: Hongwei

last: Guo

address: No.5 Yiheyuan Road

department: College of life sciences

institute: Peking University

description: Gene expression data from coi1 mutant with 100 uM MeJA

hyb_protocol: This procedure used GeneChip® hybridization, wash, and stain kit, three heating blocks are used: one at 65C, one at 99C, and the  third one at 45C

scan_protocol: GeneChips were scanned using The GeneChip® Scanner 3000 7G, and is controlled by GeneChip® Operating Software (GCOS).

data_processing: By using Expression Console software from Affymetrix performed RMA analysis and got QC report. *.CEL files as input in RMA method and by using Partek GS 6.4 software got RMA Data. Then ANOVA analysis was performed based on RMA Data.

organism: Arabidopsis

source_name: 7-day-old Arabidopsis seedlings under long-day and 23C

label_protocol: Biotinylated total RNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (GeneChip® Whole Transcript Sense Target Labeling Assay Manual).

growth_protocol: Seedlings were grown under long-day and 23 C on MS media

extract_protocol: total RNA was extracted by Trizol method and was performed according to the manufacturer's instructions.

treatment_protocol: 7-day-old seedlings were treated with 100 uM MeJA or Mock (EtOH) for 4 hr

tag: genetic background

tag: genotype

value: coi1 mutant

tag: agent

value: MeJA


title: Col-0 JA #2

description: Gene expression data from WT plant with 100 uM MeJA

value: WT


title: FAMA_48h-3


title: ein3 eil1 mock #2

description: Gene expression data from ein3eil1 double mutant with EtOH

value: ein3eil1 double mutant

value: ETOH


title: FAMA_4h-1


title: ein3 eil1 JA #2

description: Gene expression data from ein3eil1 double mutant with 100 uM MeJA


title: control_4h-2


title: Col-0 JA #1


title: coi1-2 JA #2


title: coi1-2 mock #2

description: Gene expression data from coi1 mutant with EtOH


title: coi1-2 mock #1


title: ein3 eil1 JA #1


title: ein3 eil1 mock #1


title: Col-0 mock #2

description: Gene expression data from WT plant with EtOH


title: Col-0 mock #1


title: Bcl6 -/- BCR-ABL1-transformed B cell precursors - STI571 treated 2

status: Public on May 10 2010

city: Los Angeles

first: Markus

last: Müschen

address: 4650 Sunset Blvd

department: Childrens Hospital Los Angeles

institute: University of Southern California

description: BCR-ABL1-transformed Bcl6 knockout B cell precursors were incubated with 10 µM STI571 (Imatinib) for 16 hours

hyb_protocol: Standard Affymetrix protocols (see GeneChip Expression Analysis Technical Manual)

data_processing: RMA

label: Biotin

organism: Mus musculus

source_name: Extracted bone marrow cells of Bcl6 knockout mouse

label_protocol: Standard Affymetrix protocols (Affymetrix GeneChip Expression Analysis Technical Manual) was used. The complete protocol is available on the manufacturer's web site.

extract_protocol: Extraction Method: Qiagen_RNeasy_Kit

tag: cell type

tag: treatment

value: STI571 treated

value: male

value: bone marrow

value: 4 weeks


title: Bcl6 -/- BCR-ABL1-transformed B cell precursors - STI571 treated 3

scan_protocol: Standard Affymetrix protocols (see GeneChip Expression Analysis Technical Manual)

source_name: Extracted bone marrow cells from Bcl6 knockout mouse

tag: tissue


title: Bcl6 -/- BCR-ABL1-transformed B cell precursors - STI571 treated 1


title: Bcl6 +/+ BCR-ABL1-transformed B cell precursors - STI571 treated 3

description: BCR-ABL1-transformed Bcl6 wildtype B cell precursors were incubated with 10 µM STI571 (Imatinib) for 16 hours

source_name: Extracted bone marrow cells of Bcl6 wildtype mouse

value: female


title: Bcl6 -/- BCR-ABL1-transformed B cell precursors - untreated 3

description: BCR-ABL1-transformed Bcl6 knockout B cell precursors were cultured without STI571 (Imatinib)

value: untreated


title: Bcl6 -/- BCR-ABL1-transformed B cell precursors - untreated 2


title: Bcl6 -/- BCR-ABL1-transformed B cell precursors - untreated 1


title: Bcl6 +/+ BCR-ABL1-transformed B cell precursors - STI571 treated 1


title: Round Spermatid, Wildtype, rep2

status: Public on May 08 2010

city: Rotterdam

first: Eskeatnaf

last: Mulugeta Achame

state: Rotterdam

address: Dr Molewaterplein 50

department: Reproduction and Development

country: Netherlands

institute: Erasmusmc

description: Replicate 2 of 2.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C. GeneChips were washed and stained in the Affymetrix Fluidics Station (Affymetrix hybridization protocol).

scan_protocol: Signal intensities were generated by scanning arrays using the Affymetrix 7G GeneChip scanner.

data_processing: RMA normalisation implemented in R /Bioconductor. Linear models and empirical Bayes methods, implemented in Limma (R /Bioconductor), were used to assess differential expression.

source_name: Testis round spermatid, wildtype

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Affymetrix biotin labeling protocol, Affymetrix).

growth_protocol: All animal experiments were approved by the animal experiments committee DEC-Consult (EUR 897, EUR1168, EUR 1427). To obtain knockout mice, Hr6b+/- mice, obtained from backcrosses of Hr6b+/- mice with FVB mice, were intercrossed to obtain Hr6b-/- females. These were then crossed with Hr6b+/- males derived from backcrosses of Hr6b+/- mice with FVB mice, to yield male Hr6b-/- mice. Hr6b+/+ mice, derived from backcrosses of Hr6b+/- mice with FVB mice, were intercrossed to yield male Hr6b+/+ mice. The crosses to obtain male Hr6b+/+ and male Hr6b-/- mice were set up simultaneously, using animals from the same backcross generation (>20).

extract_protocol: RNA was prepared from the isolated germ cell preparations by Trizol. The purity, integrity and quality of extracted RNA was measured using Nanodrop and Bioanalyzer 2100 (Agilent technologies).

treatment_protocol: Spermatocytes and round spermatids were isolated from 4-5-week-old Hr6b+/+ and Hr6b-/- mouse testes after collagenase and trypsin treatment, followed by sedimentation at unit gravity (StaPut procedure). Subsequently, cells were further purified by density gradient centrifugation through Percol. Cells were snap-frozen in liquid nitrogen and stored at –80 0C . A sample of each isolated fraction was used for hematoxilin-eosin staining on slides, in order asses the purity of the fractions. The purity of the cells was >80%, and not different between wild type and knockout preparations.

tag: background

value: FVB

value: 4-5 weeks

value: testis

value: round spermatid


title: Round Spermatid, HR6B Knockout, rep2

description: Replicate 2 of 2.

source_name: Testis round spermatid, HR6B knockout


title: Round Spermatid, Wildtype, rep1

description: Replicate 1 of 2.


title: Bcl6 +/+ BCR-ABL1-transformed B cell precursors - untreated 2

description: BCR-ABL1-transformed Bcl6 wildtype B cell precursors were cultured without STI571 (Imatinib)

source_name: Extracted bone marrow cells from Bcl6 wildtype mouse

label_protocol: Standard Affymetrix protocols (Affymetrix GeneChip Expression nalysis Technical Manual) was used. The complete protocol is available on the manufacturer's web site.

value: Bcl6 +/+ BCR-ABL1 transformed B cell precursors

value: Female

value: Bone marrow


title: Late Spermatocyte, Wildtype, rep1

description: Replicate 1 of 2.

source_name: Testis late spermatocyte, wildtype

value: late spermatocyte


title: Bcl6 +/+ BCR-ABL1-transformed B cell precursors - STI571 treated 2


title: Late Spermatocyte, HR6B Knockout, rep2

description: Replicate 2 of 2.

source_name: Testis late spermatocyte, HR6B knockout


title: Bcl6 +/+ BCR-ABL1-transformed B cell precursors - untreated 3


title: Bcl6 +/+ BCR-ABL1-transformed B cell precursors - untreated 1


title: NSCLC EMC 2323N

status: Public on May 07 2010

first: Sjaak

last: Philipsen

address: Dr. Molewaterplein 50

department: Cell Biology

institute: Erasmus MC

description: Gene expression data from normal lung

hyb_protocol: Following fragmentation, 20 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 Fluidics 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray scanner 3000

data_processing: The data was normalized by Robust Multi-Array average (RMA) algorithm. Intensities of probe sets lower than 30 were reset to 30.The intensity values of individual probe sets in each sample were then displayed as the log 2 of the deviations to the calculated geometric means for that probe sets.

source_name: frozen tissue

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

tag: tissue type

value: healthy

tag: overall survival

value: Not available

tag: status


title: NSCLC EMC TB0067he

description: Gene expression data from normal lung

tag: gender

value: M


title: NSCLC EMC TB0067tu

description: Gene expression data from primary NSCLC

value: tumor

value: ADC

value: deceased


title: NSCLC EMC TB0066tu

description: Gene expression data from primary NSCLC

value: SCC


title: Late Spermatocyte, HR6B Knockout, rep1

description: Replicate 1 of 2.

value: male

tag: age


title: Late Spermatocyte, Wildtype, rep2

description: Replicate 2 of 2.


title: Round Spermatid, HR6B Knockout, rep1

description: Replicate 1 of 2.


title: NSCLC EMC TB0068he

description: Gene expression data from normal lung


title: NSCLC EMC TB0063tu

description: Gene expression data from primary NSCLC


title: NSCLC EMC TB0050he

description: Gene expression data from normal lung

value: F


title: NSCLC EMC TB0047tu

description: Gene expression data from primary NSCLC

value: alive


title: NSCLC EMC TB0053he

description: Gene expression data from normal lung


title: NSCLC EMC TB0058tu

description: Gene expression data from primary NSCLC


title: NSCLC EMC TB0052tu

description: Gene expression data from primary NSCLC


title: NSCLC EMC TB0068tu

description: Gene expression data from primary NSCLC


title: NSCLC EMC TB0060tu

description: Gene expression data from primary NSCLC

value: LCC


title: NSCLC EMC TB0062tu

description: Gene expression data from primary NSCLC


title: NSCLC EMC TB0045tu

description: Gene expression data from primary NSCLC


title: NSCLC EMC TB0036tu

description: Gene expression data from primary NSCLC


title: NSCLC EMC TB0034tu

description: Gene expression data from primary NSCLC


title: NSCLC EMC TB0038tu

description: Gene expression data from primary NSCLC


title: NSCLC EMC TB0044tu

description: Gene expression data from primary NSCLC


title: NSCLC EMC TB0035tu

description: Gene expression data from primary NSCLC


title: NSCLC EMC TB0037tu

description: Gene expression data from primary NSCLC


title: NSCLC EMC TB0041tu

description: Gene expression data from primary NSCLC


title: NSCLC EMC TB0030tu

description: Gene expression data from primary NSCLC


title: NSCLC EMC TB0033he

description: Gene expression data from normal lung


title: NSCLC EMC TB0036he

description: Gene expression data from normal lung


title: NSCLC EMC TB0028tu

description: Gene expression data from normal lung


title: NSCLC EMC TB0033tu

description: Gene expression data from primary NSCLC


title: NSCLC EMC TB0032tu

description: Gene expression data from primary NSCLC


title: NSCLC EMC TB0031he

description: Gene expression data from normal lung


title: NSCLC EMC TB0031tu

description: Gene expression data from primary NSCLC


title: NSCLC EMC TB0027tu

description: Gene expression data from primary NSCLC


title: NSCLC EMC TB0025tu

description: Gene expression data from primary NSCLC


title: NSCLC EMC TB0022he

description: Gene expression data from normal lung


title: NSCLC EMC TB0019tu

description: Gene expression data from primary NSCLC


title: NSCLC EMC TB0022tu

description: Gene expression data from primary NSCLC


title: NSCLC EMC TB0023tu

description: Gene expression data from primary NSCLC


title: NSCLC EMC TB0017he

description: Gene expression data from normal lung


title: NSCLC EMC TB0015tu

description: Gene expression data from primary NSCLC


title: NSCLC EMC TB0018tu

description: Gene expression data from primary NSCLC


title: NSCLC EMC TB0014tu

description: Gene expression data from primary NSCLC


title: NSCLC EMC TB0009tu

description: Gene expression data from primary NSCLC


title: NSCLC EMC TB0020tu

description: Gene expression data from primary NSCLC


title: NSCLC EMC TB0009he

description: Gene expression data from normal lung


title: NSCLC EMC TB0013tu

description: Gene expression data from primary NSCLC


title: NSCLC EMC TB0010he

description: Gene expression data from normal lung


title: NSCLC EMC TB0011he

description: Gene expression data from normal lung


title: NSCLC EMC TB0008tu

description: Gene expression data from primary NSCLC


title: NSCLC EMC TB0024tu

description: Gene expression data from primary NSCLC


title: NSCLC EMC SCC2318T

description: Gene expression data from primary NSCLC


title: NSCLC EMC TB0006tu

description: Gene expression data from primary NSCLC


title: NSCLC EMC SCC2305N

description: Gene expression data from normal lung


title: NSCLC EMC SCC2321N

description: Gene expression data from normal lung


title: NSCLC EMC SCC2306T

description: Gene expression data from primary NSCLC


title: NSCLC EMC SCC2288T

description: Gene expression data from primary NSCLC


title: NSCLC EMC SCC2341T

description: Gene expression data from primary NSCLC


title: NSCLC EMC SCC2302T

description: Gene expression data from primary NSCLC


title: NSCLC EMC TB0003tu

description: Gene expression data from primary NSCLC


title: NSCLC EMC TB0007tu

description: Gene expression data from primary NSCLC


title: NSCLC EMC SCC2313N

description: Gene expression data from normal lung


title: NSCLC EMC SCC2358T

description: Gene expression data from primary NSCLC


title: NSCLC EMC SCC2301N

description: Gene expression data from normal lung


title: NSCLC EMC SCC2317N

description: Gene expression data from normal lung


title: NSCLC EMC SCC2287N

description: Gene expression data from normal lung


title: NSCLC EMC SCC2268T

description: Gene expression data from primary NSCLC


title: NSCLC EMC SCC2283N

description: Gene expression data from normal lung


title: NSCLC EMC SCC2298T

description: Gene expression data from primary NSCLC


title: NSCLC EMC SCC2280T

description: Gene expression data from primary NSCLC


title: NSCLC EMC SCC2267N

description: Gene expression data from normal lung


title: NSCLC EMC SCC2239N

description: Gene expression data from normal lung


title: NSCLC EMC SCC2299N

description: Gene expression data from normal lung


title: NSCLC EMC SCC2273N

description: Gene expression data from normal lung


title: NSCLC EMC SCC2262T

description: Gene expression data from primary NSCLC


title: NSCLC EMC SCC2266T

description: Gene expression data from primary NSCLC


title: NSCLC EMC SCC2265N

description: Gene expression data from normal lung


title: NSCLC EMC SCC2252T

description: Gene expression data from primary NSCLC


title: NSCLC EMC SCC2261N

description: Gene expression data from normal lung


title: NSCLC EMC SCC2279N

description: Gene expression data from normal lung


title: NSCLC EMC SCC2236T

description: Gene expression data from primary NSCLC


title: NSCLC EMC SCC2235N

description: Gene expression data from normal lung


title: NSCLC EMC SCC2222T

description: Gene expression data from primary NSCLC


title: NSCLC EMC LCC2304T

description: Gene expression data from primary NSCLC


title: NSCLC EMC LCC2282T

description: Gene expression data from primary NSCLC


title: NSCLC EMC SCC2213N

description: Gene expression data from normal lung


title: NSCLC EMC LCC2250T

description: Gene expression data from primary NSCLC


title: NSCLC EMC LCC2327N

description: Gene expression data from normal lung


title: NSCLC EMC LCC2228T

description: Gene expression data from primary NSCLC


title: NSCLC EMC SCC2208T

description: Gene expression data from primary NSCLC


title: NSCLC EMC SCC2214T

description: Gene expression data from primary NSCLC


title: NSCLC EMC LCC2312T

description: Gene expression data from primary NSCLC


title: NSCLC EMC LCC2334N

description: Gene expression data from normal lung


title: NSCLC EMC LCC2217N

description: Gene expression data from normal lung


title: NSCLC EMC LCC2281N

description: Gene expression data from normal lung


title: NSCLC EMC LCC2218T

description: Gene expression data from primary NSCLC


title: NSCLC EMC LCC2249N

description: Gene expression data from normal lung


title: NSCLC EMC LCC2286T

description: Gene expression data from primary NSCLC


title: NSCLC EMC ADC2347T

description: Gene expression data from primary NSCLC


title: NSCLC EMC LCC2311N

description: Gene expression data from normal lung


title: NSCLC EMC LCC2234T

description: Gene expression data from primary NSCLC


title: NSCLC EMC LCC2303N

description: Gene expression data from normal lung


title: NSCLC EMC LCC2349T

description: Gene expression data from primary NSCLC


title: NSCLC EMC ADC2320N

description: Gene expression data from normal lung


title: NSCLC EMC ADC2326T

description: Gene expression data from primary NSCLC


title: NSCLC EMC ADC2348T

description: Gene expression data from primary NSCLC


title: NSCLC EMC ADC2316T

description: Gene expression data from primary NSCLC


title: NSCLC EMC ADC2325N

description: Gene expression data from normal lung


title: NSCLC EMC ADC2340T

description: Gene expression data from primary NSCLC


title: NSCLC EMC LCC2233N

description: Gene expression data from normal lung


title: NSCLC EMC ADC2307N

description: Gene expression data from normal lung


title: NSCLC EMC ADC2308T

description: Gene expression data from primary NSCLC


title: NSCLC EMC ADC2310T

description: Gene expression data from primary NSCLC


title: NSCLC EMC ADC2296T

description: Gene expression data from primary NSCLC


title: NSCLC EMC ADC2295N

description: Gene expression data from normal lung


title: NSCLC EMC ADC2294T

description: Gene expression data from primary NSCLC


title: NSCLC EMC ADC2315N

description: Gene expression data from normal lung


title: NSCLC EMC ADC2270T

description: Gene expression data from primary NSCLC


title: NSCLC EMC ADC2330N

description: Gene expression data from normal lung


title: NSCLC EMC ADC2272T

description: Gene expression data from primary NSCLC


title: NSCLC EMC ADC2277N

description: Gene expression data from normal lung


title: INS4_24h_rep1

city: Birmingham

first: Dongquan

last: Chen

state: AL

address: 1717 11th Ave South

department: Medicine

institute: Univ of Alabama at Birmingham

hyb_protocol: Hybridization of the GeneChips was carried out in the following the manufacturer’s protocol. Briefly, the fragmented biotin labeled cRNA was mixed with 0.05nM control oligonucleotide B2, 20X Eukaryotic hybridization controls (bioB, bioC, bioD, cre), 0.1 mg/mL herring sperm DNA, 0.5 mg/mL BSA, 2X hybridization buffer (1X 100mM MES/1M NaCl/20mM EDTA/0.01% Tween-20) and 10% DMSO.  The hybridization cocktail was incubated at 99oC for 5 minutes to denature the herring sperm DNA and any secondary structure on the cRNA.  The cocktail was then equilibrated to 45oC for 5 minutes prior to addition to the GeneChip.  Hybridiztion was carried out in the Affymetrix Hybridization Oven 640 at 45oC with rotation at 60rpm for 16 hours.  Following the hybridization step the GeneChips were washed and stained in the Affymetrix Fluidics Station 450 following Fluidics Protocol Mini_euk2v3 as recommended by the manufacturer for this Chip type.  The GeneChips were first washed in a non-stringent wash buffer of 6X SSPE/0.01% Tween-20 followed by stringent wash with 100mM MES/0.1M NaCl/0.01% Tween-20.  The first staining of the GeneChips was done in 2X stain buffer (1X 100mM MES/1M NaCl/0.05% Tween-20), 2mg/mL BSA, and 0.01 mg/mL Streptavidin Phycoerythrin (SAPE).  The GeneChips were washed in non-stringent wash buffer.  A second stain comprised of 2X staining buffer, 2mg/mL BSA, 0.1mg/mL Goat IgG, and 0.003mg/mL of biotinylated antibody was conducted immediately followed by a third stain comprised of the SAPE solution (see above).  Finally, the GeneChips were washed in non-stringent wash buffer prior to scanning.

scan_protocol: Scanning of the GeneChips was done using the Affymetrix 3000 7G scanner as described by the manufacturer. The Fluidics station and Scanner were controlled using Affymetrix GeneChip Command Console (AGCC).

data_processing: RMA via ArrayAssist Enterprise (Agilent, CA)

source_name: 24h, treated

label_protocol: The labeling of the RNA was done as per the manufacturers instructions (Affymetrix, Santa Clara, CA).  Briefly, One microgram of total RNA was reverse transcribed using an oligo dT-T7 primer under standard conditions.  The resulting first strand cDNA was incubated with RNAse H, E. coli DNA ligase, and E. coli DNA polymerase, dNTPs and buffer to produce second-stranded cDNA.  The cDNA was purified using spin columns following the manufacturer’s instructions (Qiagen).  The purified cDNA was then used in an in vitro transcription assay to produce the target biotin labeled cRNA for hybridization using the 3’ IVT kit from Affymetrix following the manufacturer’s instructions.  The cRNA was purified using a spin column following the kit’s instructions (Qiagen), and fragmented prior to hybridization onto the GeneChips.

growth_protocol: IGF-1 receptor lacking osteoblasts were cultured to confluency.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Purity and integrity of the isolated RNA was confirmed by BioAnalyzer (Agilent)

treatment_protocol: The cells were serum starved and then treated with 10nM insulin for 6, 12, or 24hr.

value: insulin

value: osteoblast

value: IGF-1 null


title: cholera toxin, biological rep 1

city: La Jolla

first: Nick

last: Webster

address: 9500 Gilman Drive

institute: UCSD

description: Gene expression data cholera toxin treated cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430_2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 scanner

data_processing: The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 2500. Data were then analyzed in VAMPIRE.

source_name: mouse bone marrow dendritic cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.

growth_protocol: Bone marrow derived dendritic cells were derived by culturing bone marrow progenitor cells for six days in the presence of GM-CSF

extract_protocol: Total TNA extracted by Qiagen RNeasy kits

treatment_protocol: DCs treated for 2 h with 1 ug/ml cholera toxin, 10 uM forskolin or control medium

tag: strain

value: cholera toxin


title: forskolin, biological rep 1

description: Gene expression data forskolin treated cells

value: forskolin


title: INS1_con_rep1

source_name: control

value: 0 h

value: control


title: NSCLC EMC ADC2264T

description: Gene expression data from primary NSCLC


title: control medium, biological rep 2

description: Gene expression data control cells

value: control medium


title: NSCLC EMC ADC2257N

description: Gene expression data from normal lung

value: healthy

value: Not available

value: M


title: control medium, biological rep 1

description: Gene expression data control cells


title: forskolin, biological rep 2


title: NSCLC EMC ADC2269N

description: Gene expression data from normal lung


title: NSCLC EMC ADC2293N

description: Gene expression data from normal lung


title: NSCLC EMC ADC2263N

description: Gene expression data from normal lung


title: cholera toxin, biological rep 2


title: NSCLC EMC ADC2278T

description: Gene expression data from primary NSCLC

value: tumor

value: deceased


title: NSCLC EMC ADC2260T

description: Gene expression data from primary NSCLC

value: ADC


title: INS3_12h_rep1

source_name: 12hr, treated


title: INS2_6h_rep1

source_name: 6hr, treated

value: 6 h


title: NSCLC EMC ADC2256T

description: Gene expression data from primary NSCLC

value: alive

value: F


title: NSCLC EMC ADC2248T

description: Gene expression data from primary NSCLC


title: NSCLC EMC ADC2247N

description: Gene expression data from normal lung


title: NSCLC EMC ADC2243T

description: Gene expression data from primary NSCLC


title: NSCLC EMC ADC2246T

description: Gene expression data from primary NSCLC


title: NSCLC EMC ADC2231N

description: Gene expression data from normal lung


title: NSCLC EMC 2420T

description: Gene expression data from primary NSCLC


title: NSCLC EMC 2439T

description: Gene expression data from primary NSCLC


title: NSCLC EMC ADC2245N

description: Gene expression data from normal lung


title: NSCLC EMC 2419N

description: Gene expression data from normal lung


title: NSCLC EMC ADC2255N

description: Gene expression data from normal lung


title: NSCLC EMC 2412T

description: Gene expression data from primary NSCLC

value: SCC


title: NSCLC EMC 2408T

description: Gene expression data from primary NSCLC


title: NSCLC EMC 2410T

description: Gene expression data from primary NSCLC


title: NSCLC EMC 2405N

description: Gene expression data from normal lung


title: NSCLC EMC 2407N

description: Gene expression data from normal lung


title: NSCLC EMC 2394T

description: Gene expression data from normal lung


title: NSCLC EMC 2388T

description: Gene expression data from primary NSCLC


title: NSCLC EMC 2384T

description: Gene expression data from primary NSCLC


title: NSCLC EMC 2411N

description: Gene expression data from normal lung


title: NSCLC EMC 2393N

description: Gene expression data from normal lung


title: NSCLC EMC 2409N

description: Gene expression data from normal lung


title: NSCLC EMC TB0069tu

description: Gene expression data from primary NSCLC

value: LCC


title: NSCLC EMC 2333N

description: Gene expression data from normal lung


title: NSCLC EMC 2382T

description: Gene expression data from primary NSCLC


title: NSCLC EMC 2335N

description: Gene expression data from normal lung


title: NSCLC EMC 2406T

description: Gene expression data from primary NSCLC


title: NSCLC EMC 2387N

description: Gene expression data from normal lung


title: NSCLC EMC 2344T

description: Gene expression data from normal lung


title: NSCLC EMC 2381N

description: Gene expression data from normal lung


title: BC166

status: Public on May 05 2010

city: Marseille

first: Pascal

last: FINETTI

state: BdR

address: 232 Bd Ste Marguerite

department: Centre de cancérologie de Marseille

country: France

institute: Institut Paoli-Calmettes

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: RMA using a quantile normalization

source_name: human breast cancer tumors

label_protocol: Affymetrix standard protocol

extract_protocol: Guanidinium isothiocyanate and centrifugation over a cesium chloride gradient.

tag: age at diagnosis

tag: histology

value: IDC

tag: pt

tag: pn

tag: sbr grade

tag: er ihc

tag: pr ihc

tag: p53 ihc

tag: ki67 ihc

tag: dfs evt

tag: dfs time (months)

tag: molecular subtype

value: Basal

value: breast cancer tumor


title: BC171

value: LuminalB

tag: tissue


title: BC162


title: BC175


title: BC165


title: BC167


title: BC164


title: BC170


title: BC163


title: BC176


title: BC174


title: BC169


title: BC173

value: LuminalA


title: BC172


title: BC160


title: BC158


title: BC153


title: BC152

value: Normal


title: BC159


title: BC155


title: BC157


title: BC150


title: BC151


title: BC168


title: BC148


title: BC161


title: BC154


title: BC156


title: BC144


title: BC143


title: BC149


title: BC147


title: BC146

value: MIX


title: BC138

value: ILC


title: BC129


title: BC131


title: BC132


title: BC139


title: BC141


title: BC135


title: BC142


title: BC133


title: BC127


title: BC128


title: BC124


title: BC125


title: BC130


title: BC119


title: BC122


title: BC121


title: BC116


title: BC117


title: BC113


title: BC109


title: BC112

value: other


title: BC98


title: BC99


title: BC108


title: BC102


title: BC114


title: BC89


title: BC85


title: BC87


title: BC94


title: BC76


title: BC79


title: BC88


title: BC93


title: BC107


title: BC75


title: BC101


title: BC95


title: BC86


title: BC92


title: BC72


title: BC74


title: BC71


title: BC70


title: BC69


title: BC66


title: BC65


title: BC52


title: BC59


title: BC62


title: BC42


title: BC60


title: BC63


title: BC50


title: BC55


title: BC39


title: BC48


title: BC49


title: BC45


title: BC43


title: BC51


title: BC47


title: BC57


title: BC54


title: BC41


title: BC38


title: BC36

value: TUB


title: BC34


title: BC46


title: BC35


title: BC37


title: BC33


title: BC44


title: BC31


title: BC30


title: BC29


title: BC53


title: BC27


title: BC17


title: BC25


title: BC26


title: BC24


title: BC13


title: BC21


title: BC16


title: BC10


title: BC23


title: BC19


title: BC8


title: BC12


title: BC20


title: BC7


title: BC14


title: BC22


title: BC9


title: BC15


title: BC18


title: BC5


title: BC1


title: BC3


title: BC6


title: BC11


title: BC4


title: Pancreatic Cancer Cell Line ASPC-1

city: grand rapids

first: brian

last: haab

state: MI

address: 333 bostwick avenue NE

department: lab of cancer immunodiagnostics

institute: van andel institute

description: Gene expression data from untreated cells

hyb_protocol: Standard Affymetrix Protocol

scan_protocol: Standard Affymetrix protocol using GeneChip Scanner 3000 7G with auto loader

data_processing: The data were normalized using Affymetrix Microarray Suite 5.0 using the global scaling technique. The 95% trimmed mean was set arbitrarily to 500.

source_name: Pancreatic Tumor

label_protocol: Labeled one round cRNA was generated using kits (Gene-Chip One-Cycle Target Labeling and Control Reagent) from Affymetrix.

growth_protocol: The pancreatic cancer cell lines were grown to 80% confluence in DMEM/FBS/PenStrep media and cell pellets isolated.

extract_protocol: Total RNA was isolated from the cell pellets through homogenization in TRIzol (Invitrogen, Stockholm, Sweden) using a conventional rotor-stator homogenizer. Nucleic acid was further separated through centrifugation in the presence of chloroform. RNA was then precipitated with isopropyl alcohol and washed with 75% alcohol. RNA pellets were resuspended in nuclease free water. The RNA was further purified using the silica-gel membrane-based spin-column technology RNeasy Mini-/Micro-KitTM (Qiagen, Valencia, CA). RNA quantity was determined using a Nanodrop Spectrophotometer, and RNA quality was determined using the Agilent 2100 Bioanalyzer lab-on-a-chip technology (Agilent, Foster City, CA).

value: Pancreas

tag: cell type

value: Pancreatic Cancer Cell Line

tag: cell line


title: BC2


title: Pancreatic Cancer Cell Line MiaPaCa-2


title: Pancreatic Cancer Cell Line HS766t


title: Pancreatic Cancer Cell Line Panc-1


title: Pancreatic Cancer Cell Line Panc 2.13

value: Panc 2.13


title: Pancreatic Cancer Cell Line Colo 357

value: Colo 357


title: Pancreatic Cancer Cell Line Panc 3.3

value: Panc 3.3


title: Pancreatic Cancer Cell Line Panc 8.13

value: Panc 8.13


title: Pancreatic Cancer Cell Line Panc 5.04

value: Panc 5.04


title: Reference

city: Helsinki

first: Maija

middle: K

last: Wolf

address: Biomedicum Helsinki 2U, Tukholmankatu 8,

country: Finland

institute: Institute for Molecular Medicine Finland (FIMM)

description: Untreated reference cells in regular growth medium.

hyb_protocol: Biotin-labelled target cRNAs were fragmented and the quality of labelling procedures was assessed with GeneChip Test3 arrays. Hybridizations to U133 Plus 2.0 arrays were performed for 16 hours at 45oC, followed by automated array washing and staining procedures.

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000 (Affymetrix).

data_processing: Basic GeneChip array analysis was performed for the obtained image file. Data preprocessing was done using the MAS5 algorithm implemented in the Bioconductor package “affy” (Gentleman et al.,  Genome Biol 2004, 5:R80).

molecule: polyA RNA

source_name: mRNA from a pooled sample consisting of 16 different cancer cell lines

label_protocol: Biotinylated cRNA was prepared from 3 micrograms of mRNA per sample according to manufacturer's (Affymetrix) instructions.

growth_protocol: Cells were grown in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) and 2mM L-glutamine, and Minimum Essential Medium supplemented with 10% FBS, 2mM L-glutamine, 1% non-essential amino acids and 1% sodium pyruvate, respectively.

extract_protocol: mRNA was isolated from the samples using the FastTrack 2.0 mRNA isolation kit according to manufacturer's instructions.

treatment_protocol: Untreated.

tag: treatment

value: untreated

value: Pool of 16 different cancer cell lines

value: mixed


title: Pancreatic Cancer Cell Line Panc 6.03

value: Panc 6.03


title: Pancreatic Cancer Cell Line Nor-P1


title: Pancreatic Cancer Cell Line Panc 10.05


title: Pancreatic Cancer Cell Line Panc 3.27

value: Panc 3.27


title: Pancreatic Cancer Cell Line Mpanc-96


title: Pancreatic Cancer Cell Line Panc 2.03

value: Panc 2.03


title: NGP

description: Untreated NGP cells in regular growth medium.

source_name: mRNA from NGP

value: NGP

value: neuroblastoma


title: Pancreatic Cancer Cell Line CaPan-2


title: Pancreatic Cancer Cell Line HPAF-II

value: HPAF-II


title: Pancreatic Cancer Cell Line CFPAC

value: CFPAC


title: IMR-32

description: Untreated IMR-32 cells in regular growth medium.

source_name: mRNA from IMR-32


title: Pancreatic Cancer Cell Line BxPC-3

value: Pancreas


title: BC187

value: IDC

value: Basal

value: breast cancer tumor


title: Pancreatic Cancer Cell Line PL45

value: Pancreatic Cancer Cell Line


title: BC191

value: LuminalB


title: Pancreatic Cancer Cell Line L3.6 pl

value: L3.6 pl


title: BC177


title: BC178


title: Pancreatic Cancer Cell Line SU86.86


title: CD-1 P0 Male, hypothalamus and preoptic area

status: Public on May 04 2010

city: Baltimore

first: Seth

last: Blackshaw

state: MD

address: 733 N. Broadway, Suite 351

department: Neuroscience

institute: The Johns Hopkins University

description: Hybridization was performed by the Johns Hopkins Medical Institutions Microarray Core Facility.

hyb_protocol: 16hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual.

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual.

data_processing: Image analysis using GCOS 1.4, using MAS 5.0 algorithm and manufacturer’s specifications. Global scaling of images to a target intensity of 150.

label_protocol: One round amplification protocol for total RNA following Affymetrix’ specifications using T7 promoter oligo dT primer for cDNA synthesis, and ENZO IVT kit (www.affymetrix.com, GeneChip Expression Analysis, Technical Manual).

growth_protocol: Standard chow, 12:12 light:dark cycle.

extract_protocol: RNeasy Kit (QIAGEN).

treatment_protocol: Microdissection into RNAlater (Ambion).

tag: strain

tag: sex

value: male

tag: age

value: postnatal day 0

value: hypothalamus and preoptic area


title: CD-1 P42 Male, hypothalamus and preoptic area

value: postnatal day 42


title: CD-1 P21 Female, hypothalamus and preoptic area

value: female

value: postnatal day 21


title: CD-1 E16 Male, hypothalamus and preoptic area

value: embryonic day 16


title: CD-1 E15 Male, hypothalamus and preoptic area

value: embryonic day 15


title: CD-1 P21 Male, hypothalamus and preoptic area


title: CD-1 P42 Female, hypothalamus and preoptic area


title: CD-1 E14 Male, hypothalamus and preoptic area

value: embryonic day 14


title: CD-1 E18 Female, hypothalamus and preoptic area

value: embryonic day 18


title: CD-1 E17 Female, hypothalamus and preoptic area

value: embryonic day 17


title: CD-1 E17 Male, hypothalamus and preoptic area


title: CD-1 E16 Female, hypothalamus and preoptic area


title: CD-1 E13 Male, hypothalamus and preoptic area

value: embryonic day 13


title: CD-1 E18 Male, hypothalamus and preoptic area


title: CD-1 P0 Female, hypothalamus and preoptic area


title: CD-1 E15 Female, hypothalamus and preoptic area


title: CD-1 E13 Female, hypothalamus and preoptic area


title: CD-1 E11 Male, hypothalamus and preoptic area

value: embryonic day 11


title: CD-1 E12 Female, hypothalamus and preoptic area

value: embryonic day 12


title: CD-1 E12 Male, hypothalamus and preoptic area


title: CD-1 E10 Female, hypothalamus and preoptic area

value: embryonic day 10


title: CD-1 E10 Male, hypothalamus and preoptic area


title: C57Bl/6 P42 Male, hypothalamus and preoptic area


title: CD-1 E11 Female, hypothalamus and preoptic area


title: BC181

tag: age at diagnosis

tag: histology

value: IDC

value: Basal

value: breast cancer tumor


title: C57Bl/6 P0 Male, hypothalamus and preoptic area

value: male

value: postnatal day 0


title: C57Bl/6 P42 Female, hypothalamus and preoptic area

value: postnatal day 42

value: hypothalamus and preoptic area


title: C57Bl/6 E18 Male, hypothalamus and preoptic area


title: C57Bl/6 P21 Male, hypothalamus and preoptic area

value: postnatal day 21


title: C57Bl/6 E17 Male, hypothalamus and preoptic area


title: C57Bl/6 E17 Female, hypothalamus and preoptic area

value: female


title: C57Bl/6 E14 Female, hypothalamus and preoptic area


title: C57Bl/6 P21 Female, hypothalamus and preoptic area


title: C57Bl/6 E16 Male, hypothalamus and preoptic area

value: embryonic day 16


title: C57Bl/6 E13 Female, hypothalamus and preoptic area


title: C57Bl/6 E16 Female, hypothalamus and preoptic area


title: C57Bl/6 E12 Male, hypothalamus and preoptic area


title: C57Bl/6 P0 Female, hypothalamus and preoptic area


title: C57Bl/6 E13 Male, hypothalamus and preoptic area


title: C57Bl/6 E15 Male, hypothalamus and preoptic area

value: embryonic day 15


title: C57Bl/6 E11 Male, hypothalamus and preoptic area


title: C57Bl/6 E18 Female, hypothalamus and preoptic area

value: embryonic day 18


title: C57Bl/6 E11 Female, hypothalamus and preoptic area


title: C57Bl/6 E15 Female, hypothalamus and preoptic area


title: C57Bl/6 E14 Male, hypothalamus and preoptic area

value: embryonic day 14


title: C57Bl/6 E12 Female, hypothalamus and preoptic area


title: CD-1 E14 Female, hypothalamus and preoptic area


title: C57Bl/6 E10 Female, hypothalamus and preoptic area


title: C57Bl/6 E10 Male, hypothalamus and preoptic area

source_name: C57Bl/6 E10 Male


title: mrhl siRNA 3, biological rep3

status: Public on May 03 2010

city: Bangalore

first: Gayatri

last: Ganesan

address: Jakkur

department: MBGU

country: India

institute: JNCASR

description: silenced RNA 44 hrs post transfection

hyb_protocol: Following fragmentation, 12 ug of cRNA were hybridized for 16 hr at 45C on GeneChip mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChip  Scanner 3000

data_processing: GCOS and ARRAY ASSIST software for analysis. PLIER algorithm was used for data preprocessing and to generate the normalized intensity data.

growth_protocol: Mouse spermatogonial cells were grown in DMEM medium containing 10% FBS supplemented with antibiotics

treatment_protocol: 100nM scrambled or siRNA against mrhl

value: spermatoginial cells


title: mrhl siRNA 1, biological rep1

description: silenced RNA 44 hrs post transfection


title: Polg_WT_GN_13mo_1-13M

status: Public on May 01 2010

city: Tokyo

first: Takuya

last: Miyakawa

address: 1-1-1 Yayoi, Bunkyo-ku

country: Japan

institute: The University of Tokyo

description: Affymetrix standard spike controls were used in all experiments (eukaryotic hybridization control kit).

hyb_protocol: Hybridization (hybridization oven 640), and washing and staining (fluidics station 400) (Affymetrix) were accomplished according to the manufacturer’s instructions.

scan_protocol: Arrays were scanned on the GeneChip Scanner 3000 (Affymetrix).

data_processing: Image analysis was performed using GCOS 1.3 (Affymetrix). Each array was scaled (all probe sets) to a target signal of 500 before comparison in GCOS 1.3.

source_name: Polg+/+ mice, gastrocnemius muscle

label_protocol: Labeling (Enzo BioArray IVT kit) was accomplished according to the manufacturer’s instructions.

extract_protocol:
a) Gastrocnemius muscle tissue was dissected and immediately flash-frozen in liquid nitrogen.
b) Total RNA was isolated from cochlea tissues using the TriZol Reagent (Invitrogen) according to the manufacturer's instructions.

value: Polg+/+ mice

tag: gender

value: 13 months

value: gastrocnemius muscle


title: Polg_D257A_GN_13mo_2-30M

source_name: PolgD257A/D257A mice, gastrocnemius muscle

value: PolgD257A/D257A mice


title: scrambled siRNA 2, biological rep2

description: control RNA 44 hrs post transfection


title: scrambled siRNA 3, biological rep3

description: control RNA 44 hrs post transfection


title: Polg_WT_GN_13mo_2-3M


title: Polg_WT_GN_13mo_1-12M


title: Polg_D257A_GN_13mo_2-21M


title: Polg_WT_GN_13mo_2-32M


title: scrambled siRNA 1, biological rep1

description: control RNA 44 hrs post transfection


title: Polg_D257A_GN_13mo_2-25M


title: Polg_D257A_GN_13mo_2-27M


title: TgA, cerebellum, 26 month, male [E5R_054e02]

city: Tuebingen

first: Michael

last: Bonin

state: BW

address: CAlwerstr. 7

department: Medical Genetics

institute: University Tuebingen

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Complete data analysis, including GC-RMA normalization, was performed with Genespring 11.

source_name: TgA, cerebellum, 26 month, male

label_protocol: Standard Affymetrix protocol

extract_protocol: Standard RNA extraction protocol with qiagen products

value: TgA

value: cerebellum

value: 26 month


title: TgA, brainstem, 26 month, male [E5R_054e01]

source_name: TgA, brainstem, 26 month, male

value: brainstem

value: male


title: mrhl siRNA 2, biological rep2

description: silenced RNA 44 hrs post transfection


title: wt, cerebellum, 26 month, male [E5R_054f02]

source_name: wt, cerebellum, 26 month, male

value: wt


title: wt, brainstem, 28 month, female [E5R_054d01]

source_name: wt, brainstem, 28 month, female

value: 28 month


title: wt, cerebellum, 28 month, female [E5R_054d02]

source_name: wt, cerebellum, 28 month, female

value: female


title: wt, brainstem, 26 month, male [E5R_054f01]

source_name: wt, brainstem, 26 month, male


title: wt, striatum, 28 month, female [E5R_054d03]

source_name: wt, striatum, 28 month, female

value: striatum


title: wt, striatum, 26 month, male [E5R_054f03]

source_name: wt, striatum, 26 month, male


title: wt, striatum, 20 month, female+male [E5R_054b03]

source_name: wt, striatum, 20 month, female+male

value: 20 month

value: female+male


title: TgA, striatum, 26 month, male [E5R_054e03]

source_name: TgA, striatum, 26 month, male


title: TgA, cerebellum, 28 month, female [E5R_054c02]

source_name: TgA, cerebellum, 28 month, female


title: wt, cerebellum, 20 month, female+male [E5R_054b02]

source_name: wt, cerebellum, 20 month, female+male


title: Polg_WT_GN_13mo_3-18M


title: TgA, brainstem, 28 month, female [E5R_054c01]

source_name: TgA, brainstem, 28 month, female


title: TgB, cerebellum, 20 month, female+male [E5R_054a02]

source_name: TgB, cerebellum, 20 month, female+male

value: TgB


title: wt, brainstem, 20 month, female+male [E5R_054b01]

source_name: wt, brainstem, 20 month, female+male


title: TgB, striatum, 20 month, female+male [E5R_054a03]

source_name: TgB, striatum, 20 month, female+male


title: TgB, cerebellum, 22 month, female [E5R_031i02]

source_name: TgB, cerebellum, 22 month, female

value: 22 month


title: TgB, cerebellum, 22 month, female [E5R_031i01]


title: TgA, cerebellum, 21 month, female [E5R_031h01]

source_name: TgA, cerebellum, 21 month, female

value: 21 month


title: TgA, cerebellum, 21 month, female [E5R_031h02]


title: TgA, striatum, 28 month, female [E5R_054c03]

source_name: TgA, striatum, 28 month, female


title: TgB, cerebellum, 22 month, female [E5R_031i03]


title: wt, cerebellum, 22 month, female [E5R_031g02]

source_name: wt, cerebellum, 22 month, female


title: Polg_D257A_GN_13mo_2-17M

source_name: PolgD257A/D257A mice, gastrocnemius muscle

value: 13 months


title: TgA, brainstem, 21 month, female [E5R_031e02]

source_name: TgA, brainstem, 21 month, female


title: TgB, brainstem, 22 month, female [E5R_031f03]

source_name: TgB, brainstem, 22 month, female


title: wt, cerebellum, 22 month, female [E5R_031g03]


title: TgB, brainstem, 22 month, female [E5R_031f02]


title: wt, cerebellum, 22 month, female [E5R_031g01]


title: wt, brainstem, 22 month, female [E5R_031d02]

source_name: wt, brainstem, 22 month, female


title: TgA, cerebellum, 21 month, female [E5R_031h03]


title: TgA, brainstem, 21 month, female [E5R_031e01]


title: wt, striatum, 22 month, female [E5R_031a01]

source_name: wt, striatum, 22 month, female


title: wt, brainstem, 22 month, female [E5R_031d01]


title: wt, brainstem, 22 month, female [E5R_031d03]


title: TgB, striatum, 22 month, female [E5R_031c02]

source_name: TgB, striatum, 22 month, female


title: TgB, cerebellum, 6 month, female [E5R_011c05_b]

source_name: TgB, cerebellum, 6 month, female

value: 6 month


title: TgA, cerebellum, 6 month, male [E5R_011c04_b]

source_name: TgA, cerebellum, 6 month, male


title: wt, cerebellum, 6 month, male [E5R_011c02_b]

source_name: wt, cerebellum, 6 month, male


title: TgB, brainstem, 6 month, female [E5R_011b05_b]

source_name: TgB, brainstem, 6 month, female


title: TgA, brainstem, 6 month, male [E5R_011b04_b]

source_name: TgA, brainstem, 6 month, male


title: TgB, brainstem, 6 month, male [E5R_011b06_b]

source_name: TgB, brainstem, 6 month, male


title: wt, brainstem, 6 month, female [E5R_011b01_b]

source_name: wt, brainstem, 6 month, female


title: TgA, cerebellum, 6 month, female [E5R_011c03_b]

source_name: TgA, cerebellum, 6 month, female


title: TgB, cerebellum, 6 month, male [E5R_011c06_b]

source_name: TgB, cerebellum, 6 month, male


title: wt, cerebellum, 6 month, female [E5R_011c01_b]

source_name: wt, cerebellum, 6 month, female


title: TgA, brainstem, 6 month, female [E5R_011b03_b]

source_name: TgA, brainstem, 6 month, female


title: TgA, striatum, 6 month, male [E5R_011a04_b]

source_name: TgA, striatum, 6 month, male


title: wt, brainstem, 6 month, male [E5R_011b02_b]

source_name: wt, brainstem, 6 month, male


title: TgB, striatum, 6 month, male [E5R_011a06_b]

source_name: TgB, striatum, 6 month, male


title: TgB, striatum, 6 month, female [E5R_011a05_b]

source_name: TgB, striatum, 6 month, female


title: wt, striatum, 6 month, female [E5R_011a01_b]

source_name: wt, striatum, 6 month, female


title: wt, striatum, 6 month, male [E5R_011a02_b]

source_name: wt, striatum, 6 month, male


title: TgA, striatum, 6 month, female [E5R_011a03_b]

source_name: TgA, striatum, 6 month, female


title: Huh7 cells_Mock Infected 6 hours_ rep2

city: London

middle: J

last: McGarvey

address: Norfolk Place

country: United Kingdom

institute: Imperial College London

description: Gene expression data from Huh7 cells treated with mock media for 6 hours

hyb_protocol: Hybridisation of cRNA was performed using a hybridisation cocktail of 15ug cRNA, 50pM control oligonucleotide B2, Eukaryotic hybridisation controls (1.5pM bioB, 5pM bioC, 25pM bioD and 100pM cre), 0.1mg/ml Herring sperm DNA, 0.5mg/ml BSA, 1x hybridisation buffer and 10% DMSO. The hybridisation cocktail was heated to 99°C for 5 minutes followed by 45°C for 5 minutes. The array was filled with 1x hybridisation buffer and heated to 45°C for 10 minutes. Hybridisation buffer was removed from the array and the hybridisation cocktail was added and incubated for 16 hours at 45°C. Following hybridisation, arrays were washed using both non-stringent and stringent wash buffers. The array was then stained using 10ug/ml streptavidin phycoerythrin diluted in stain buffer with 2mg/ml BSA for 10 minutes, followed by incubation with goat anti-streptavidin biotinylated antibody diluted in stain buffer containing 2mg/ml BSA and 0.1mg/ml goat IgG stock for 10 minutes and a second round of staining with 10ug/ml streptavidin phycoerythrin diluted in stain buffer with 2mg/ml BSA for 10 minutes.The array was washed again with non-stringent wash buffer and was placed onto the scanner.

scan_protocol: The stained array chips were scanned using the Affymetrix genechip scanner 3000 which was operated using the Affymetrix GeneChip Operating System (GCOS).

data_processing: Raw microarray expression data was analyzed with Array Studio software (Omicsoft, USA) using MicroArray data default settings and RMA signal extraction method.  Two samples (Mock_6hrs_1 and JFH-1_6hrs_1) did not pass our data quality control measures and were excluded from the analysis.  Data was analyzed on the log2 scale, using analysis of variance (ANOVA), followed by pre-specified contrast statements.  Fold changes were obtained from the estimated least squares mean differences.  Host genes demonstrating at least a 2 fold change in expression, a significant differential expression at a raw p-value level of 0.05, and an intensity level above 32 (5 on the log2 scale) for at least one of the treatment means were selected for further investigation.

source_name: Huh7 cells, Mock Infected, 6 hours.

label_protocol: Total RNA was first reverse transcribed using a T7-Oligo(dT) Promoter Primer in the first-strand cDNA synthesis reaction. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA was purified and served as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction was carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling.The biotinylated cRNA targets were then cleaned up, fragmented, and hybridized to GeneChip expression arrays. Quality of labeled RNA was assessed using the Agilent Bioanalyser.

growth_protocol: Huh7 cells: Huh7 cells were grown in Dulbecco’s modified Eagles Medium (DMEM) supplemented with 10% foetal calf serum, 100U/ml penicillin and 100µg/ml streptomycin (Invitrogen) at 37°C, 5% CO2. HCV JFH-1 production: Full-length JFH-1 virus was produced using Huh7.5 cells transfected with RNA transcribed from the pJFH-1 plasmid.  Transfected cells were maintained for 21 days and growth medium containing infectious JFH-1 was serially passaged onto naive Huh7.5 cells every four days. Culture medium containing virus was harvested at each passage, clarified by centrifugation and 0.45µm filtration, and concentrated using Amicon Ultra-15 centrifugal filter units (Millipore).

extract_protocol: 3ml of TRIzol reagent (Invitrogen) was added to the cells in each T25 flask. RNA was extracted according to the manufacturer’s protocol.

treatment_protocol: 5x105 Huh7 cells were seeded in 25cm2 culture flasks and infected in triplicate either with the genotype 2a HCV clone, JFH-1 at a multiplicity of infection (MOI) of 3 or mock infected with an equal volume of concentrated conditioned growth medium

value: hepatoma cells


title: Huh7 cells_JFH-1 Infected 24 hours_ rep3

description: Gene expression data from Huh7 cells Infected with JFH-1 for 24 hours

source_name: Huh7 cells, JFH-1 Infected, 24 hours.


title: Huh7 cells_Mock Infected 18 hours_ rep1

description: Gene expression data from Huh7 cells treated with mock media for 18 hours

source_name: Huh7 cells, Mock Infected, 18 hours


title: Huh7 cells_Mock Infected 6 hours_ rep3


title: Huh7 cells_Mock Infected 48 hours_ rep3

description: Gene expression data from Huh7 cells treated with mock media for 48 hours

source_name: Huh7 cells, Mock Infected, 48 hours.


title: Huh7 cells_Mock Infected 18 hours_ rep2


title: Huh7 cells_Mock Infected 12 hours_ rep1

description: Gene expression data from Huh7 cells treated with mock media for 12 hours

source_name: Huh7 cells, Mock Infected, 12 hours.


title: Huh7 cells_Mock Infected 24 hours_ rep1

description: Gene expression data from Huh7 cells treated with mock media for 24 hours

source_name: Huh7 cells, Mock Infected, 24 hours


title: Huh7 cells_JFH-1 Infected 48 hours_ rep1

description: Gene expression data from Huh7 cells Infected with JFH-1 for 48 hours

source_name: Huh7 cells, JFH-1 Infected, 48 hours


title: Huh7 cells_JFH-1 Infected 18 hours_ rep1

description: Gene expression data from Huh7 cells Infected with JFH-1 for 18 hours

source_name: Huh7 cells, JFH-1 Infected, 18 hours.


title: TgB, brainstem, 20 month, female+male [E5R_054a01]

source_name: TgB, brainstem, 20 month, female+male


title: Huh7 cells_Mock Infected 24 hours_ rep2


title: Huh7 cells_Mock Infected 24 hours_ rep3


title: Huh7 cells_JFH-1 Infected 48 hours_ rep2


title: Huh7 cells_Mock Infected 48 hours_ rep1


title: Huh7 cells_JFH-1 Infected 18 hours_ rep3


title: Huh7 cells_Mock Infected 12 hours_ rep2


title: Huh7 cells_JFH-1 Infected 48 hours_ rep3


title: Huh7 cells_Mock Infected 18 hours_ rep3


title: Huh7 cells_Mock Infected 48 hours_ rep2


title: Huh7 cells_JFH-1 Infected 12 hours_ rep3

description: Gene expression data from Huh7 cells Infected with JFH-1 for 12 hours

source_name: Huh7 cells, JFH-1 Infected, 12 hours


title: Huh7 cells_JFH-1 Infected 18 hours_ rep2


title: Huh7 cells_JFH-1 Infected 12 hours_ rep2


title: Huh7 cells_JFH-1 Infected 24 hours_ rep1


title: Huh7 cells_JFH-1 Infected 6 hours_ rep3

description: Gene expression data from Huh7 cells Infected with JFH-1 for 6 hours

source_name: Huh7 cells, JFH-1 Infected, 6 hours.


title: Huh7 cells_JFH-1 Infected 6 hours_ rep2


title: Huh7 cells_JFH-1 Infected 12 hours_ rep1


title: Huh7 cells_JFH-1 Infected 24 hours_ rep2


title: Huh7 cells_Mock Infected 12 hours_ rep3


title: 4hr serum stimulation biological rep 2

first: Karen

last: Zeller

address: 720 Rutland Ave

institute: Johns Hopkins School of Medicine

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

source_name: 4hr serum stimulation biological rep 2

label_protocol: Affymetrix protocol

growth_protocol: Fibroblasts grown in DMEM 10% serum until start of experiment

extract_protocol: Qiagen total RNA extraction protocol

treatment_protocol: Cells treated 48 hrs with 0.1% serum and then stimulated with 10% serum.

value: primary fibroblasts

tag: time point

tag: biological replicate


title: 6hr serum stimulation biological rep 2

source_name: 6hr serum stimulation biological rep 2


title: 8hr serum stimulation biological rep 1

source_name: 8hr serum stimulation biological rep 1


title: ZMYM2/FGFR1 biological replicate 2

city: Lund

first: Helena

last: Ågerstam

address: Lund University Hospital

country: Sweden

institute: Lund University

description: Gene expression profile of human CD34+ cord blood cells expressing ZMYM2/FGFR1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Gene Chip Human Gene U133 plus 2.0 microarrays. GeneChips were washed and stained in the Affymetrix Fluidics station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner GSC3000.

data_processing: Normalization was performed using the RMA method in Gene Chip Operating Software and the obtained data matrix was imported into the TIGR Multi Experiment Viewer for further analysis.

source_name: Human CD34+ cord blood cells expressing ZMYM2/FGFR1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Gene Expression Analysis Technical Manual 701021 rev.5).

extract_protocol: RNA was isolated using the RNeasy isolation kit (Qiagen, Valencia, CA) according to the manufacturers’ instructions. RNA quality was assessed using a Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA).

tag: cell source

value: Human CD34+ cells isolated from umbilical cord blood

tag: agent


title: 2hr serum stimulation biological rep 1

source_name: 2hr serum stimulation biological rep 1


title: 2hr serum stimulation biological rep 2

source_name: 2hr serum stimulation biological rep 2


title: MIG control biological replicate 2

description: Gene expression profile of human CD34+ cord blood cells expressing the empty MIG control vector

source_name: Human CD34+ cord blood cells expressing the empty MIG control vector

value: MIG control


title: 4hr serum stimulation biological rep 1

source_name: 4hr serum stimulation biological rep 1


title: BCR/FGFR1 biological replicate 3

description: Gene expression profile of human CD34+ cord blood cells expressing BCR/FGFR1

source_name: Human CD34+ cord blood cells expressing BCR/FGFR1


title: HEK 293 cells, top 25 miRNAs inhibited, siRNA-transfected, replicate 1

status: Public on Apr 29 2010

city: New York

last: Hafner

state: NY

address: 1230 York Ave, Box 186

department: Laboratory of RNA Molecular Biology

institute: The Rockefeller University

description:
Gene expression data from HEK 293 cells transfected with a cocktail of 2'OMe oligoribonucleotides inhibiting the top 25 miRNAs.
miRNA inhibition repl 1

hyb_protocol: 3 µg cRNA was hybridized to HGU133 Plus 2.0 Arrays for 16 h at 45ºC.

scan_protocol: GeneChips were scanned on an Affymetrix GeneChip 3000 7G scanner.

data_processing: We imported the CEL files into the R software (http://www.R-project.org) using the BioConductor affy package (Gentleman et al., 2004). The transcript probe set intensities were background-corrected, adjusted for non-specific binding and quantile normalized with the GCRMA algorithm (Wu, 2006). Probe sets with more than 6 of the 11 probes mapping ambiguously to the genome were discarded, as were probe sets that mapped to multiple genes. We then collected all probe sets matching a given gene, and we selected for further analysis the RefSeq transcript with median 3'UTR length corresponding to that gene. In total, 16,063 transcripts were identified. The log-intensity of probe sets mapping to the gene were then averaged to obtain the expression level per RefSeq transcript. The changes of transcript abundances were computed as the logarithm of the ratio of transcript expression in the cocktails of siRNA-treated samples and mock-transfected cells. Detailed analysis procedures can be found in the Supplement to PMID 20371350.

source_name: HEK 293, miRNA siRNAs

label_protocol: 2 µg of purified total RNA was used in the One-Cycle Eukaryotic Target Labeling Assay (Affymetrix) according to manufacturer's protocol. Biotinylated cRNA targets were cleaned up, fragmented, and hybridized to Human Genome U133 Plus 2.0 Arrays (Affymetrix).

growth_protocol: HEK 293 T-REx Flp-In cells (Invitrogen) were grown in D-MEM high glucose with 10% (v/v) fetal bovine serum, 1% (v/v) 2 mM L-glutamine, 1% (v/v) 10,000 U/ml penicillin/10,000 µg/ml streptomycin, 100 µg/ml zeocin and 15 µg/ml blasticidin. Cell lines stably expressing FLAG/HA-tagged proteins were generated by co-transfection of pFRT/TO/FLAG/HA or pFRT/FLAG/HA constructs with pOG44 (Invitrogen). Cells were selected by exchanging zeocin with 100 µg/ml hygromycin. Expression of FLAG/HA-IGF2BP1, -2, -3 and TNRC6A, B and C was induced by addition of 250 ng/ml doxycycline 15 to 20 h before crosslinking. Detailed experimental procedures can be found in the Supplement to PMID 20371350.

treatment_protocol: siRNA, miRNA and 2'-O-methyl oligonucleotide transfections of HEK 293 T-REx Flp-In cells were performed in 6-well format using Lipofectamine RNAiMAX (Invitrogen) as described by the manufacturer. Detailed experimental procedures can be found in the Supplement to PMID 20371350.

value: HEK 293

tag: sirna

value: 25 miRNAs


title: 8hr serum stimulation biological rep 2

source_name: 8hr serum stimulation biological rep 2


title: 0hr serum stimulation biological rep 2

source_name: 0hr serum stimulation biological rep 2


title: 0hr serum stimulation biological rep 1

source_name: 0hr serum stimulation biological rep 1


title: ZMYM2/FGFR1 biological replicate 3


title: HESC HS181p50

city: Montpellier

first: John

last: De Vos

address: 80 av. Augustin Fliche

department: Institute for Research in Biotherapy

institute: University Hospital of Montpellier

description:
The hesc lines hs181 was derived at the Karolinska Institute of Stockholm, Sweden, and cultured on human foreskin fibroblast feeder cells (crl-2429; american type culture collection, manassas, va, http: //www. atcc.org). (Hovatta et al. 2003).
The transcriptome of this hESC was compared to the transcriptome of fully reprogrammed human induced pluripotent stem cells, the parental fibroblast cells and partially reprogrammed cells.

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45C on the GeneChip Human U133 plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data were analyzed with the GCOS 1.2 software (Affymetrix), using the default analysis settings and global scaling as normalization method, with a trimmed mean target intensity value (TGT) of each array arbitrarily set to 100.

source_name: Human embryonic stem cell line HS181 passage 50

label_protocol: Complementary RNA (cRNA) was prepared according to the manufacturer’s (Affymetrix) protocol ‘small sample protocol II’, starting from 100 ng total RNA.

growth_protocol: The culture medium used for hESCs culture consisted of 80% KO-DMEM, 20% knockout SR, 2 mM L-glutamine, 1% nonessential amino acids, 0.5 mM β-mercaptoethanol (all from Gibco Invitrogen, Cergy-Pontoise, France) and 10 ng/mL of bFGF (Abcys, Paris, France). All passaging were performed mechanically by cutting colonies using a #15 scalpel under the microscope. Human foreskin fibroblasts (HFF)( SCRC-1041; ATCC, Manassas, VA, USA), mitotically inactivated using irradiation (40 Gy), were used as feeder cells (Hovatta et al. 2003).

extract_protocol: Total RNA was isolated using RNeasy mini kits (Qiagen) according to the manufacturer's instructions and quantified using a NanoDrop spectrophotometer.

value: HS181, obtained from the Karolinska Institute of Stockholm, Sweden.

value: human embryonic stem cells


title: BCR/FGFR1 biological replicate 2


title: BCR/FGFR1 biological replicate 1


title: MIG control biological replicate 1


title: BCR/ABL1 biological replicate 1

description: Gene expression profile of human CD34+ cord blood cells expressing BCR/ABL1

source_name: Human CD34+ cord blood cells expressing BCR/ABL1


title: MIG control biological replicate 3


title: BCR/ABL1 biological replicate 2


title: ZMYM2/FGFR1 biological replicate 1


title: HEK 293 cells expressing FLAG/HA-tagged IGF2BP1, siRNA-transfected, replicate 2

description:
Gene expression data from HEK 293 cells inducibly expressing FLAG/HA-tagged IGF2BP1 after knockdown with IGF2BP1-3 siRNA.
IGF2BP siRNA 2

source_name: HEK 293, IGF2BP siRNA

value: IGF2BP1, IGF2BP2, IGF2BP3


title: HEK 293 cells, mock-transfected, replicate 2

description:
Gene expression data from HEK 293 cells.
Mock transfected 2

source_name: HEK 293, mock

value: mock


title: HEK 293 cells expressing FLAG/HA-tagged IGF2BP1, siRNA-transfected, replicate 1

description:
Gene expression data from HEK 293 cells inducibly expressing FLAG/HA-tagged IGF2BP1 after knockdown with IGF2BP1-3 siRNA.
IGF2BP siRNA 1


title: HEK 293 cells, mock-transfected, replicate 1

description:
Gene expression data from HEK 293 cells.
Mock transfected 1


title: HEK 293 cells expressing FLAG/HA-tagged QKI, siRNA set B transfected, replicate 2

description:
Gene expression data from HEK 293 cells inducibly expressing FLAG/HA-tagged QKI after knockdown with QKI siRNA ste B.
QKI siRNA B 2

source_name: HEK 293, QKI siRNA

value: QKI


title: HEK 293 cells expressing FLAG/HA-tagged IGF2BP1, mock-transfected, replicate 2

description:
Gene expression data from HEK 293 cells inducibly expressing FLAG/HA-tagged IGF2BP1.
IGF2BP Mock transfected 2


title: HEK 293 cells, top 25 miRNAs inhibited, siRNA-transfected, replicate 2

description:
Gene expression data from HEK 293 cells transfected with a cocktail of 2'OMe oligoribonucleotides inhibiting the top 25 miRNAs.
miRNA inhibition repl 2


title: HESC_HD90_p8

description:
This human embryonic stem cell line was derived on an irradiated human fibroblast feeder, in 20% KO-SR medium, from an embryo carrying a mutation in the VHL gene as evidence by preimplantation genetic diagnostic (PGD). RNA extraction was carried out at passage 8.
HD90 was compared to a compendium of 84 transcriptome covering a broad range of adult tissues and other human embryonic stem cell lines. Data can also be accessed at http://www.amazonia.transcriptome.eu.

source_name: Human embryonic stem cell line HD90/FE07-142-L1, carrying a point mutation in the VHL gene

growth_protocol: The culture medium used for hESCs derivation and culture consisted of 80% KO-DMEM, 20% knockout SR, 2 mM L-glutamine, 1% nonessential amino acids, 0.5 mM β-mercaptoethanol (all from Gibco Invitrogen, Cergy-Pontoise, France) and 10 ng/mL of bFGF (Abcys, Paris, France). All passaging were performed mechanically by cutting colonies using a #15 scalpel under the microscope. Human foreskin fibroblasts (HFF)( SCRC-1041; ATCC, Manassas, VA, USA), mitotically inactivated using irradiation (40 Gy), were used as feeder cells (Hovatta et al. 2003).

tag: embryo characteristic

value: mutation in VHL gene


title: HEK 293 cells expressing FLAG/HA-tagged QKI, siRNA set A transfected, replicate 2

description:
Gene expression data from HEK 293 cells inducibly expressing FLAG/HA-tagged QKI after knockdown with QKI siRNA ste A.
QKI siRNA A 2


title: HEK 293 cells expressing FLAG/HA-tagged QKI, siRNA set B transfected, replicate 1

description:
Gene expression data from HEK 293 cells inducibly expressing FLAG/HA-tagged QKI after knockdown with QKI siRNA ste B.
QKI siRNA B 1


title: HEK 293 cells expressing FLAG/HA-tagged IGF2BP1, mock-transfected, replicate 1

description:
Gene expression data from HEK 293 cells inducibly expressing FLAG/HA-tagged IGF2BP1.
IGF2BP Mock transfected 1


title: HEK 293 cells expressing FLAG/HA-tagged QKI, mock-transfected, replicate 2

description:
Gene expression data from HEK 293 cells inducibly expressing FLAG/HA-tagged QKI.
QKI Mock transfected 2


title: U87MGL3, biological rep2

city: Seoul

first: Woong Yang

last: Park

address: 28 Yongondong, Chongnogu

department: Biochemistry and Molecular Biology

country: South Korea

institute: Seoul National University

description: Gene expression data from glioma cell

hyb_protocol: Biotinylated cRNA was fragmented and hybridized to Affymetrix Human Genome U133 Plus 2.0 Array for 16 h at 45 ºC.

scan_protocol: Fluorescence intensity was processed and measured using a GeneChip scanner 3000.

data_processing: A multivariate permutation test was used to provide 95% confidence that the false discovery rate was <1%.  The false discovery rate is the proportion of the list of genes claimed to be differentially expressed but actually false positive.

source_name: non- invasive glioma cell line (U87MGL3)

label_protocol: 5 ug of total RNA were used to generate biotinylated cRNA.

growth_protocol: U87MG cells (which are purchased from ATCC) were maintained in Dulbecco’s modified Eagle’s medium (DMEM) enriched with 10% fetal bovine serum (Hyclone), 1% penicillin/streptomycin (GIBCO-BRL), and 2 mM L-glutamine (GIBCO-BRL).  For the neurosphere formation assay, cells were plated into 96-well plates at a density of one cell per well and maintained in neural stem cell culture conditions (NeurobasalTM A medium enriched with 20 ng/mL EGF, 20 ng/mL bFGF, 1× B27, N2, and 1% penicillin/streptomycin) for 10-14 days.

extract_protocol: Total RNA from glioma cell lines was isolated using TRIzol (Invitrogen) and an RNeasy mini kit (Qiagen).

treatment_protocol: Cultured cells were harvested with 0.25% trypsin/0.02% EDTA for 2 min, washed twice with Hank’s balanced salt solution (HBSS), and resuspended in Ca2+/Mg2+-free HBSS.  Cell viability was determined by trypan blue exclusion.  Only single-cell suspensions with >90% viability were used for in vivo studies.  Cells (2 × 105) in 5 μl HBSS were stereotactically injected into the left striata of nude mice (6-week-old BALB/c nu/nu; coordinates: anterior-posterior, +2.2; medial-lateral, +2.5; dorsal-ventral, –2.2 mm from Bregma).  When body weight had decreased more than 25%, mice were considered to have GBM.  Brains with tumors were mechanically and enzymatically dissociated into single cells, red blood cells were removed by differential centrifugation, and tumor cells were cultured in the conditions described above.  This procedure was repeated four times to enrich for non-migratory and migratory glioma cells.  All mouse experiments were performed in accordance with government and institutional guidelines and regulations.

value: glioma


title: day-7 testis, wild type-6

status: Public on Apr 27 2010

city: Pittsburgh

first: Aleksandar

last: Rajkovic

state: PA

address: 204 Craft Ave. Suite A230

department: Dept. of Obstetrics, Gynecology & Reproductive Sciences

institute: Magee-Womens Research Institute

description: Gene expression data of day-7 wild-type testis.

hyb_protocol: A hybridization cocktail containing Affymetrix spike-in controls and fragmented labeled cRNA was loaded onto a GeneChip® array.  The array was hybridized overnight at 45°C with rotation at 60 rpm and then washed and stained with a strepavidin, R-phycoerythrin conjugate stain.  Signal amplification was done using biotinylated antistreptavidin.

scan_protocol: The stained array was scanned on the Affymetrix GeneChip® Scanner 3000. The images were analyzed and quality control metrics recorded using Affymetrix GCOS software version 1.4.

data_processing: Data were scaled using Affymetrix MAS5.0/GCOS software.

source_name: day-7 testis, wild type

label_protocol: Sample quality checks were conducted using the Nanodrop ND-1000 spectrophotometer and Agilent Bioanalyer 2100.  The Affymetrix GenechipT microarray system was then used. Samples were labeled using the standard Affymetrix T7 oligo(dT) primer protocol.  Five µg of total RNA was reverse transcribed to produce double-stranded cDNA.  The cDNA product was used as a template for the vitro transcription reaction, producing biotin-labeled cRNA.  The labeled cRNA was quantified using the NanoDrop® ND-1000 spectrophotometer.  15.0 µg of the labeled cRNA was fragmented and re-checked for concentration.

extract_protocol: 3 testes (1 testis from each animal) were pooled per Affymetrix array. Total RNA was isolated using Qiagen Rneasy mini kits. On-column Dnase digestion step was performed. RNA was eluted in RNase-free water and frozen at -80 degrees Celsius until sample quality could be accessed with the Agilent Bioanalyzer system.

treatment_protocol: Testes were dissected from postnatal day 7 animals and placed in RNAlater (Ambion) for 24 hours at 4 degrees Celsius. After 24 hours, RNAlater solution was removed and testes were frozen and placed in a -80 degree freezer.

value: C57BL/6, 129S5, SvEvBrd hybrid background

tag: genotype

value: wild-type

value: testis

value: postnatal day 7


title: HEK 293 cells expressing FLAG/HA-tagged QKI, mock-transfected, replicate 1

first: Markus

description:
Gene expression data from HEK 293 cells inducibly expressing FLAG/HA-tagged QKI.
QKI Mock transfected 1


title: day-7 testis, wild type-5

tag: tissue


title: U87MGR3, biological rep2

description: Gene expression data from glioma cell

source_name: highly invasive glioma cell line (U87MGR3)

tag: cell type


title: day-7 testis, Sohlh2 KO-1

description: Gene expression data of day-7 Sohlh2-KO testis.

source_name: day-7 testis, Sohlh2 KO


title: U87MG, biological rep2

description: Gene expression data from glioma cell

source_name: parental U87MG glioma cells

tag: cell line


title: U87MGL2, biological rep1

description: Gene expression data from glioma cell

source_name: non- invasive glioma cell line (U87MGL2)


title: U87MG, biological rep1

description: Gene expression data from glioma cell


title: day-7 testis, Sohlh1 KO-3

description: Gene expression data of day-7 Sohlh1-KO testis.

source_name: day-7 testis, Sohlh1 KO


title: day-7 testis, Sohlh1 KO-2


title: day-7 testis, Sohlh2 KO-4


title: day-7 testis, Sohlh2 KO-3-1


title: day-7 testis, Sohlh1 KO-4


title: day-7 testis, wild type-4


title: HEK 293 cells expressing FLAG/HA-tagged QKI, siRNA set A transfected, replicate 1

description:
Gene expression data from HEK 293 cells inducibly expressing FLAG/HA-tagged QKI after knockdown with QKI siRNA ste A.
QKI siRNA A 1


title: day-7 testis, Sohlh2 KO-5


title: U87MGR2, biological rep1

description: Gene expression data from glioma cell

source_name: highly invasive glioma cell line (U87MGR2)


title: day-7 testis, wild type-3


title: day-7 testis, Sohlh1 KO-5


title: 6hr serum stimulation biological rep 1

source_name: 6hr serum stimulation biological rep 1


title: liver from Patient R6

status: Public on Apr 26 2010

city: Bethesda

first: Patrizia

last: Farci

address: 50 South Drive

department: National Institute of Allergy and Infectious Diseases

institute: National Institutes of Health

description: Gene expression data from liver

hyb_protocol: Following fragmentation, 10 to 18 µg (mean 12.8 µg) of cRNA was hybridized for 16 hr at 45°C on Affymetrics Human U133 Plus 2 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using GeneArray Scanner 3000_7Gplus

data_processing: Affymetrics probeset summaries were computed using MAS 5.0 algorithm.  Data were then imported to BRB-ArrayTools and subsequent data filtering, median normalization and statistical analyses were performed using this software.

source_name: specimen obtained from resected liver 6

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 50 ng total RNA (GeneChip Expression Analysis Technical Manual, 2005-2006, Affymetrix).

value: liver

tag: origin

value: resected normal liver


title: liver from Patient R3

description: Gene expression data from liver

source_name: specimen obtained from resected liver 3


title: liver from Patient R11

description: Gene expression data from liver

source_name: specimen obtained from resected liver 11


title: liver from Patient R4

description: Gene expression data from liver

source_name: specimen obtained from resected liver 4


title: liver from Patient R7

description: Gene expression data from liver

source_name: specimen obtained from resected liver 7


title: NT-3

city: Boston

first: Matthias

last: Stadtfeld

state: MA

address: 185 Cambridge Street

institute: MGH

hyb_protocol: Biotinylated cRNA was hybridized to Affymetrix Mouse Genome 430 2.0 arrays using the GeneChip Hybridization, Wash and Stain Kit (Affymetrix).

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Normalization of the array data was done using the "mean normalize" function in GeneSifter.

source_name: NT-ESC from Adeno-1, subclone 3

label_protocol: Biotinylated cRNA was prepared from total RNA using the GeneChip IVT Express Kit (Affymetrix).

growth_protocol: All cells were cultured in standard ESC media (15% FBS, LIF) on irradiated MEFs.

extract_protocol: Total RNA was extracted using the QIAGEN miRNeasy kit.

treatment_protocol: Cells were trypsinized and preplated for 45 minutes to remove MEFs.

value: cloned blastocyst

value: embryonic stem cell


title: liver from Patient R10

description: Gene expression data from liver

source_name: specimen obtained from resected liver 10


title: liver from Patient R2

description: Gene expression data from liver

source_name: specimen obtained from resected liver 2


title: liver from Patient R9 - 2

description: Gene expression data from liver

source_name: specimen obtained from resected liver 9


title: NT-1

source_name: NT-ESC from Adeno-1, subclone 1


title: liver from Patient R8

description: Gene expression data from liver

source_name: specimen obtained from resected liver 8


title: liver from Patient R5

description: Gene expression data from liver

source_name: specimen obtained from resected liver 5


title: liver from Patient R9 - 1

description: Gene expression data from liver


title: liver from Patient R1

description: Gene expression data from liver

source_name: specimen obtained from resected liver 1


title: NT-2

source_name: NT-ESC from Adeno-1, subclone 2


title: Adeno-1

source_name: Adeno-iPSC, clone 1

value: tail-tip fibroblasts (TTFs)

value: induced pluripotent stem cell


title: explanted liver Patient 1 (HBV-associated acute liver failure) - 1

description: Gene expression data from liver

source_name: specimen obtained from explanted liver Patient 1

value: HBV-associated acute liver failure


title: liver donor 20

description: Gene expression data from liver

source_name: specimen obtained from liver donor 20

value: liver donor


title: liver donor 60

description: Gene expression data from liver

source_name: specimen obtained from liver donor 60


title: liver donor 16

description: Gene expression data from liver

source_name: specimen obtained from liver donor 16


title: explanted liver Patient 1 (HBV-associated acute liver failure) - 4

description: Gene expression data from liver


title: explanted liver Patient 2 (HBV-associated acute liver failure) - 1

description: Gene expression data from liver

source_name: specimen obtained from explanted liver Patient 2


title: explanted liver Patient 1 (HBV-associated acute liver failure) - 3

description: Gene expression data from liver


title: liver donor 29

description: Gene expression data from liver

source_name: specimen obtained from liver donor 29


title: liver donor 37

description: Gene expression data from liver

source_name: specimen obtained from liver donor 37


title: liver donor 62

description: Gene expression data from liver

source_name: specimen obtained from liver donor 62


title: liver donor 18

description: Gene expression data from liver

source_name: specimen obtained from liver donor 18


title: explanted liver Patient 2 (HBV-associated acute liver failure) - 2

description: Gene expression data from liver


title: liver donor 8

description: Gene expression data from liver

source_name: specimen obtained from liver donor 8


title: explanted liver Patient 2 (HBV-associated acute liver failure) - 3

description: Gene expression data from liver


title: explanted liver Patient 2 (HBV-associated acute liver failure) - 4

description: Gene expression data from liver


title: Arabidopsis rosette_Light Control_Rep3

status: Public on Apr 22 2010

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: Arabidopsis rosette_Light Control_Rep3

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C and at 60 rounds/min.  The GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and 450.

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

data_processing: Normalised using GCRMA with default parameters

source_name: Arabidopsis rosette, no treatment, 60 min in light

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 microg total RNA.

growth_protocol: Surface-sterilised seeds were grown on half-strength Murashige and Skoog basal salt mixture, adjusted to pH 5.8 with 1 M KOH, with 1% sucrose and 0.6% plant cell tissue culture grade agar, in a controlled environment growth room following a 10/14 hour light/dark regime with PAR of 250 µmol m-2 s-1 and temperatures of 20 ± 2º C. Ten-day-old seedlings were subsequently transplanted to a sieved, pre-autoclaved compost and sand mixture (3:1) and plants grown in individual pots (Aracon system) in the same controlled environment growth room. Plants were watered daily by spraying.

extract_protocol: For each treatment, a single RNA extract was made from 15-17 pooled individuals. Frozen plant tissue was ground to a fine powder in a pre-cooled pestle and mortar with liquid nitrogen and acid-washed sand, and transferred to a 15 mL polypropylene centrifuge tube. 2 ml well mixed RNA extraction buffer (1:1 mix of phenol and 0.1 M LiCl, 0.1 M Tris.Cl pH 8.0, 10 mM EDTA and 1% SDS) at 95ºC was added per gram of fresh weight plant material and tubes vortexed until thoroughly mixed. Half a volume of chloroform/isoamyl alcohol (24:1) was added and mixed well by vortexing. After centrifugation in a bench top centrifuge at 3500 x g for 10 min at 4ºC, the upper aqueous phase was removed to a new 15 ml centrifuge tube and re-extracted with chloroform/isoamyl alcohol before centrifugation for a further 10 min as before. The aqueous phase was removed to a new centrifuge tube and mixed with an equal volume of 4 M LiCl and incubated overnight at 4ºC. Tubes were then centrifuged for 15 min at 3500 x g at 4ºC to pellet precipitated RNA. The supernatant was removed and the pellet drained and resuspended in 300 µl 0.3 M NaOAc pH 5.2, before being transferred to an Eppendorf tube. RNA was re-precipitated by the addition of 750 µl cold ethanol, followed by centrifugation in a microcentrifuge for 10 min at 14000 rpm. Pellets were drained and rinsed in 70% ethanol and left to dry on the bench, for ~ 30 min, under a 60 W lamp, after which pellets were resuspended in 50-100 µl ddH2O. 100 µg of RNA was purified using a Qiagen RNeasy kit, using the specified protocol (RNeasy® Mini Handbook, Fourth Edition, April 2006).

treatment_protocol: Control plants were left to acclimatise for 30 min in controlled environment growth cabinets at 22º C in the light (PAR - 250 µmol m-2 s-1) with relative humidity between 55-60%. Plants were then left under these conditions for a further 60 min, after which whole rosettes were cut off at the base of the stem and frozen in liquid nitrogen.

tag: Arabidopsis thaliana, ecotype Columbia (Col-0). Age = 4 weeks. Developmental stage = mid rosette growth. Tissue = rosette.


title: Arabidopsis rosette_Light Control_Rep2

description: Arabidopsis rosette_Light Control_Rep2


title: Arabidopsis rosette_Dark Control_Rep3

description: Arabidopsis rosette_Dark Control_Rep3

source_name: Arabidopsis rosette, unwounded leaves, 60 min in dark

treatment_protocol: Plants were left to acclimatise for 30 min in controlled environment growth cabinets at 22º C in the dark, with relative humidity between 55-60%. Plants were then left under these conditions for a further 60 min, after which whole rosettes were cut off at the base of the stem and frozen in liquid nitrogen.


title: Arabidopsis rosette_Light Wounded_Rep2

description: Arabidopsis rosette_Light Wounded_Rep2

source_name: Arabidopsis rosette, wounded leaves, 60 min in light

treatment_protocol: Plants were left to acclimatise for 30 min in controlled environment growth cabinets at 22º C in the light (PAR - 250 µmol m-2 s-1) with relative humidity between 55-60%. Subsequently, rosette leaves were mechanically wounded using a metal haemostat, once or twice dependent on size, so that a wound site is present at any point on the leaf within a 1cm radius. Leaves were wounded closest to the largest width of the leaf and perpendicular to the mid-vein. Wounded plants were returned to the same controlled environment for a further 60 min in the light, after which whole rosettes were cut off at the base of the stem and frozen in liquid nitrogen.


title: explanted liver Patient 1 (HBV-associated acute liver failure) - 2

description: Gene expression data from liver

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


title: Arabidopsis rosette_Dark Control_Rep2

description: Arabidopsis rosette_Dark Control_Rep2


title: Arabidopsis rosette_Light Wounded_Rep3

description: Arabidopsis rosette_Light Wounded_Rep3


title: Arabidopsis rosette_Light Wounded_Rep1

description: Arabidopsis rosette_Light Wounded_Rep1


title: Arabidopsis rosette_Dark Wounded_Rep1

description: Arabidopsis rosette_Dark Wounded_Rep1

source_name: Arabidopsis rosette, wounded leaves, 60 min in dark

treatment_protocol: Plants were left to acclimatise for 30 min in controlled environment growth cabinets at 22º C in the dark, with relative humidity between 55-60%. Plants were then wounded in the dark under a 15 watt Kodak safe light with a yellow 0B filter (PAR - 0 µmol m-2 s-1). Rosette leaves were mechanically wounded using a metal haemostat, once or twice dependent on size, so that a wound site is present at any point on the leaf within a 1cm radius. Leaves were wounded closest to the largest width of the leaf and perpendicular to the mid-vein. Wounded plants were returned to the same controlled environment for a further 60 min in the dark, after which whole rosettes were cut off at the base of the stem and frozen in liquid nitrogen.


title: Arabidopsis rosette_Dark Wounded_Rep2

description: Arabidopsis rosette_Dark Wounded_Rep2

treatment_protocol: DW


title: Arabidopsis rosette_Dark Wounded_Rep3

description: Arabidopsis rosette_Dark Wounded_Rep3


title: Arabidopsis rosette_Light Control_Rep1

description: Arabidopsis rosette_Light Control_Rep1


title: Arabidopsis rosette_Dark Control_Rep1

description: Arabidopsis rosette_Dark Control_Rep1


title: rosettes_wildtype_drought_rep1

status: Public on Apr 21 2010

city: Lincoln

first: Jean-Jack

middle: M.

last: Riethoven

state: NE

address: 1901 Vine Street

department: Beadle Center for Biotechnology

institute: University of Nebraska-Lincoln

description: Biological replicate 1 of 2.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C, refer to GeneChip Expression Analysis Technical Manual (www.affymetrix.com). GeneChips were washed and stained with streptavidin-phycoerythrin conjugate on an Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G; Pixel size: 1.56 um; Filter: 570 nm.

data_processing: The data was analysed using Affyminer. Arrays were normalised via RMA, and all treatments were compared to the control watered wildtype.  A p-value of 0.05 was taken as significance cutoff, and a 1.5 log2ratio cutoff was also applied.

source_name: vegetative rosettes, wildtype, water deficit

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (reaction at 37C for 16h) from 15 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

treatment_protocol: Soil water deficit stress was imposed on four week old plants by withholding water until plants reached a relative water content (RWC) of 65%.

tag: cultivar


title: rosettes_myoox_drought_rep2

description: Biological replicate 2 of 2.

source_name: vegetative rosettes, myoox, water deficit

tag: mutant

value: MYO-OX


title: rosettes_atx_drought_rep1

description: Biological replicate 1 of 2.

source_name: vegetative rosettes, atx, water deficit


title: rosettes_atx_drought_rep2

description: Biological replicate 2 of 2.


title: rosettes_myoox_watered_rep2

description: Biological replicate 2 of 2.

source_name: vegetative rosettes, myoox, watered

treatment_protocol: Four week old plants were continued to be watered.


title: rosettes_wildtype_drought_rep2

description: Biological replicate 2 of 2.


title: rosettes_atx_watered_rep2

description: Biological replicate 2 of 2.

source_name: vegetative rosettes, atx, watered


title: rosettes_myoox_watered_rep1

description: Biological replicate 1 of 2.


title: rosettes_wildtype_watered_rep2

description: Biological replicate 2 of 2.

source_name: vegetative rosettes, wildtype, watered


title: rosettes_wildtype_watered_rep1

description: Biological replicate 1 of 2.


title: rosettes_atx_watered_rep1

description: Biological replicate 1 of 2.


title: MDA-MB-231 breast cell line subpopulation expressing CXCR4 2

status: Public on Apr 20 2010

city: Indianapolis

first: Harikrishna

last: Nakshatri

state: IN

address: 980 W. Walnut St. R3C218C

department: General Surgery

institute: Indiana University School of Medicine

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 17 hr at 45C onto Human HGU133 plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanned using Affymetrix 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. The trimmed mean target intensity of each array was arbitrarily set to 1000.

source_name: MDA-MB-231 cell line

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix standard single cycle 3' IVT protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were maintained in Minimum Essentail Media with 10% fetal calf serum, penecilin/streptomycin, and 1 nM Insulin. Cells were cultured for three days after sorting.

extract_protocol: Qiagen Rneasy

treatment_protocol: Cells were treated with SDF-1alpha (400ng/ml) for 1 hour or were left untreated.

value: Breast cancer cell line

tag: cell population

value: CXCR4 positive

tag: treatment


title: BCR/ABL1 biological replicate 3

description: Gene expression profile of human CD34+ cord blood cells expressing BCR/ABL1

source_name: Human CD34+ cord blood cells expressing BCR/ABL1

value: Human CD34+ cells isolated from umbilical cord blood


title: MDA-MB-231 breast cell line subpopulation not expressing CXCR4 4

value: CXCR4 negative


title: MDA-MB-231 breast cell line subpopulation expressing CXCR4 treated with SDF-1alpha 4


title: MDA-MB-231 breast cell line subpopulation expressing CXCR4 4


title: MDA-MB-231 breast cell line subpopulation expressing CXCR4 1


title: MDA-MB-231 breast cell line subpopulation not expressing CXCR4 1


title: MDA-MB-231 breast cell line subpopulation not expressing CXCR4 3