title: CRI-G1-RS 02

description: Rotenone sensitive CRI-G1 cell line; biological sample #2

source_name: CRI-G1-RS 02


title: CRI-G1-RS 03

status: Public on Aug 31 2010

type: RNA

city: San Francisco

first: Natasha

last: Chandiramani

state: CA

address: 513 Parnassus Av

department: Pathology

country: USA

institute: University of California San Francisco

description: Rotenone sensitive CRI-G1 cell line; biological sample #3

hyb_protocol: Affymetrix Rat 230 2.0 Array; GeneChip Expression Analysis Technical Manual 701021 Rev. 3

data_processing: GCOS 1.4

label: BIOTIN

molecule: total RNA

organism: Rattus norvegicus

source_name: CRI-G1-RS 03

label_protocol: Biotinylated cRNA was prepared using Ambion MessageAmp II-Biotin Enhanced Kit according to the manufacturers's instructions, starting from 1 ug of tRNA/sample.

growth_protocol: Cells were grown in high glucose DMEM with Glutamax, supplemented with 10% FBS and antibotics; six different passages were collected in a paired fashion (one sample for each cell type) ~ 24 h after plating, pelleted and frozen at -80 C until tRNA extraction.

extract_protocol: tRNA was extracted using Quiagen RNeasy kit with on column DNAse digerstion according to the manufacturer's instructions.

treatment_protocol: No treatment.

tag: cell line

value: Rotenone sensitive CRI-G1


title: CRI-G1-RS 05

description: Rotenone sensitive CRI-G1 cell line; biological sample #5

source_name: CRI-G1-RS 05


title: CRI-G1-RS 01

description: Rotenone sensitive CRI-G1 cell line; biological sample #1

source_name: CRI-G1-RS 01


title: CRI-G1-RR 05

description: Rotenone resistant CRI-G1 cell line; biological sample #5

source_name: CRI-G1-RR 05

value: Rotenone resistant CRI-G1


title: HEP_HPFH_III-2

city: Rotterdam

first: Sjaak

last: Philipsen

address: Dr. Molewaterplein 50

department: Cell Biology

country: Netherlands

institute: Erasmus MC

description: Gene expression data from KLF1 p.K288X/wt HEPs

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. We used RMAExpress version 1.0 beta 9. 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.

label: biotin

organism: Homo sapiens

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: Human erythroid progenitor cells (HEPs) were cultured as described (Leberbauer, C. et al. Different steroids co-regulate long-term expansion versus terminal differentiation in primary human erythroid progenitors. Blood 105, 85-94 (2005).) in the presence of recombinant human Epo (1 unit/ml, kind gift of Ortho-Biotech, Tilburg, The Netherlands), recombinant human SCF (50 ng/ml, kind gift of Amgen, Breda, The Netherlands) and dexamethasone (5 × 10−7 M; Sigma, St. Louis, MO, USA).  Cells were counted with an electronic cell counter (CASY-1, Schärfe System, Reutlingen, Germany).

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

tag: tissue type

value: Cultured erythroid progenitors

tag: hpfh

value: HPFH

tag: klf1k288x mutation

value: KLF1 p.K288X/wt

tag: hbf level (%)


title: HEP_HPFH_II-5


title: HEP_wt_III-1

description: Gene expression data from wt/wt HEPs

value: No

value: wt/wt


title: CRI-G1-RR 02

description: Rotenone resistant CRI-G1 cell line; biological sample #2

source_name: CRI-G1-RR 02

growth_protocol: Cells were grown in high glucose DMEM with Glutamax, supplemented with 10% FBS and antibotics; six different passages were collected in a paired fashion

value: rotenone resistant CRI-G1


title: CRI-G1-RR 03

description: Rotenone resistant CRI-G1 cell line; biological sample #3

source_name: CRI-G1-RR 03


title: HEP_wt_III-14

description: Gene expression data from wt/wt HEPs


title: CRI-G1-RS 04

description: Rotenone sensitive CRI-G1 cell line; biological sample #4

source_name: CRI-G1-RS 04


title: CRI-G1-RR 06

description: Rotenone resistant CRI-G1 cell line; biological sample #6

source_name: CRI-G1-RR 06


title: CRI-G1-RR 01

description: Rotenone resistant CRI-G1 cell line

source_name: CRI-G1-RR 01


title: CRI-G1-RR 04

description: Rotenone resistant CRI-G1 cell line; biological sample #4

source_name: CRI-G1-RR 04


title: Gm_48_9C_17C3

status: Public on Sep 15 2010

city: Pacific Grove

first: Cheryl

middle: A

last: Logan

address: 120 Ocean View Blvd

institute: Stanford University

hyb_protocol: Hybridizations were conducted overnight at 65°C in Genetix (Boston, MA, USA) humid hybridization chambers. After hybridization, slides were washed by repeated vigorous immersion in 0.5x SSC and 0.01% SDS for 2 min to remove unbound dye. Slides were then washed in 0.6x SSC on a shaker for 15 min and dried by centrifugation.

scan_protocol: The slides were scanned on an AXON GenePix 4000B microarray scanner in GenePix 4.0 (Axon Instruments, Molecular Devices, Sunnyvale, CA, USA).

data_processing: Raw data for each gene (median pixel intensity of each spot with background correction) were imported from GenePix 4.0 into GeneSpring version 7.3 (Silicon Genetics, Redwood, CA, USA) for subsequent analysis. We normalized the data using intensity-dependent locally weighted linear regression (lowess) transformation to correct for spatial variation in the array due to inconsistencies in printing pins, slide surface variability, and differences in local hybridization conditions across a slide. We normalized and filtered our data in Genespring 7.3. To obtain a set of reliable genes from the normalized data, we discarded all probes that were flagged as irregular by Genepix 4.0 software or by hand (irregularities are generally due to specks of dust or scratches on slides) and genes that showed standard deviations of >1.4. All subsequent analyses were performed on this filtered list comprising 7,488 probes.

organism: Gillichthys mirabilis

source_name: Gillichthys mirabilis, gill tissues, 9C acclim, sampled at 17C

label_protocol: Single stranded cDNA was labeled with either Cy3 (reference samples) or Cy5 (heat shock samples) cyanine monoreactive dye (Amersham, Piscataway, NJ, USA), prepared in 80 µl of dimethylsulfoxide.

growth_protocol: Fish were acclimated to 9C, 19C or 28C for one month

extract_protocol: Total RNA was extracted from gill tissue using the Qiagen Tissuelyser for homogenization and the RNeasy Mini Kit (Qiagen, Valencia, CA, USA).  Total RNA was determined by A260 absorbance using a Nanodrop ND-1000 spectrophotometer (Nanodrop, Wilmington, DE, USA).  Samples were run on 1% agarose gels to confirm RNA integrity. 15 µg of total RNA from each sample were reverse transcribed with 3 µl of AffinityScript enzyme (Agilent Technologies, Santa Clara, CA, USA), 0.75 µl oligo(dT15) and 0.75 µl pdN9 random hexamer primers, and amino-allyl modified dNTPs. RNA templates were removed from the RT reactions by incubation at 65°C for 30 min in 0.2 mol l-1 NaOH and 0.1 mol l-1 EDTA. cDNA was precipitated at -80°C for 20 min in 4.5 µl 3M sodium acetate and 2.5 volumes on 100% ethanol. Samples were centrifuged at 10,000 rpm for 20 min at 4°C and resuspended in 8 µl of nuclease free water and 2 µl of fresh 0.5 M sodium bicarbonate.

treatment_protocol: Fish underwent an acute heat stress ramp (4C/hr) starting at their acclimation temperature. 2-3 fish were sampled at every hour during the heat ramp (or every 4C) until they reach their critical thermal maxima

tag: condition

value: 9C acclim, sampled at 17C

tag: tissue

value: Gill tissue

source_name: Gillichthys mirabilis, gill tissue, flow-through seawater tank (~13C), pooled total RNA for reference

tag: reference

value: pooled total RNA


title: NL_58

status: Public on Aug 30 2010

city: Aurora

first: Christopher

middle: D

last: Coldren

state: CO

address: 12700 East 17th Place

department: Medicine

institute: University of Colorado School of Medicine

description:
gene expression data
NL_58_6

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: Raw data was normalized using RMA and presented as non-log transformed signal intensity

source_name: PMBCs

label_protocol: Microarray targets were prepared from 5µg of total RNA using the Affymetrix (Santa Clara, CA) kit for reverse transcription and a single round of in vitro transcription.  HG-U133+2.0 were hybridized with 10µg of cRNA and processed per the manufacturer’s protocol.

extract_protocol:
Collection protocol: Whole blood was drawn from each subject via peripheral venipuncture into BD Vacutainer® CPT™ tubes with sodium citrate.
Isolation protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from whole blood by centrifugation, and cells were stored in RNALater (Qiagen Inc., Valencia, CA) at -80°C.
Total RNA was isolated from PBMCs using Trizol (Invitrogen, Corporation, Carlsbad, CA) extraction and isopropyl alcohol precipitation, followed by clean-up with a Qiagen RNeasy mini-kit (Qiagen).

tag: cell type

value: PMBCs

tag: disease state

value: Normal (no pulmonary hypertension)

tag: gender

value: Female


title: NL_24

description:
gene expression data
NL_24_4


title: NL_35

description:
gene expression data
NL_35_4


title: NL_18

description:
gene expression data
NL_18_2


title: NL_23

description:
gene expression data
NL_23_2


title: NL_53

description:
gene expression data
NL_53_4


title: IPAH_150

description:
gene expression data
IPAH_150_3

value: Idiopathic Pulmonary Arterial Hypertension


title: IPAH_69

description:
gene expression data
IPAH_69_2


title: HEP_HPFH_III-9


title: NL_171

description:
gene expression data
NL_171_3


title: IPAH_89

description:
gene expression data
IPAH_89_3


title: IPAH_64

description:
gene expression data
IPAH_64_2


title: IPAH_10

description:
gene expression data
IPAH_10_6


title: IPAH_12

description:
gene expression data
IPAH_12_1


title: SSc-PH_172

description:
gene expression data
CRP_172_3

value: Scleroderma with Pulmonary Hypertension


title: IPAH_17

description:
gene expression data
IPAH_17_1


title: SSc-PH_174

description:
gene expression data
CRP_174_3


title: SSc-PH_169

description:
gene expression data
CRP_169_4


title: SSc-PH_118

description:
gene expression data
CRP_118_2


title: SSc-PH_114

description:
gene expression data
CRP_114_3


title: NL_59

description:
gene expression data
NL_59_3


title: NL_7

description:
gene expression data
NL_7_1


title: IPAH_87

description:
gene expression data
IPAH_87_4


title: NL_2

description:
gene expression data
NL_2_1


title: SSc-PH_154

description:
gene expression data
CRP_154_2


title: SSc-PH_82

description:
gene expression data
CRP_82_4


title: SSc-PH_48

description:
gene expression data
CRP_48_1


title: SSc-PH_94

description:
gene expression data
CRP_94_1


title: SSc-PH_163

description:
gene expression data
CRP_163_6


title: SSc_158

description:
gene expression data
CRN_158_3

value: Scleroderma without Pulmonary Hypertension


title: BrdU50Rel

status: Public on Aug 28 2010

type: genomic

city: Milano

first: Andrea

last: Cocito

state: MI

address: Via Adamello 16

department: Molecular Medicine Program

country: Italy

institute: IFOM Institute FIRC  of Molecular Oncology

hyb_protocol: Labelled probes were hybridized to Affymetrix S.cerevisiae whole genome tiling R arrays

scan_protocol: Arrays were scanned on an Affymetrix Scanner

data_processing:
BAR files were produced with Tiling Array Suite 1.1 from the command line with these options: tilecore -analysis -bpmap Sc03b_MR_v04.bpmap -type 1 -n 1 -nt 1 -export 1 -output_type 0 -format_type 1 -band 150 -pval_scale 0 -sig_scale 2 -tail_type 1 -nscale 1 -tgt 500 [files]
TXT results were produced by GCOS using a custom CDF which summarizes probes into sets covering 50 basepairs ranges.
Submitter unable to obtain the CDF file.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: IP fraction of BrdU50Rel-BrdU sy2201 S-Rel Hu-Rel

label_protocol: Synthesis of cDNA, IVT amplification, and labeling were carried out following the Affymetrix GeneChip Expression Anaysis protocol

growth_protocol: Cells were grown in YPD.

extract_protocol: Extracton was performed as described in Katou et al., 2003.

treatment_protocol:
G1 synchronization was performed by α−factor treatment (2 μg/ml), S synchronization release from factor block in 200 mM HU, G1-G2 synchronization released from alpha factor block in nocodazole 10 μg/ml.
Glu: Strains were grown in YPD  (at 23 degree) containing 2% glucose as fermentable carbon source
Gal: Strains were grown in YP  plus 2% galactose as fermentable carbon source
HU: Strains were arrested in G1 and released in 0.2M HU in YPD.
HU-Rel: Strains were arrested in G1 and released in 0.2M HU for 90'.  Then cells HU was washed away and cells released in a new YPD medium.
37C: Strains were grown in YPD at 37 degree

tag: fraction

value: IP fraction

tag: chip antibody

value: anti-BrdU MI-11-3 (MBL)

tag: strain

tag: phase

value: S-Rel

tag: treatment

value: Hu-Rel

source_name: SUP of BrdU50Rel-BrdU sy2201 S-Rel Hu-Rel

value: supernatant fraction


title: BrdU1hHU

source_name: IP fraction of BrdU1hHU-BrdU sy2201 S-HU HU

value: S-HU

value: HU

source_name: SUP of BrdU1hHU-BrdU sy2201 S-HU HU


title: Rpc25

data_processing: BAR files were produced with Tiling Array Suite 1.1 from the command line with these options: tilecore -analysis -bpmap Sc03b_MR_v04.bpmap -type 1 -n 1 -nt 1 -export 1 -output_type 0 -format_type 1 -band 150 -pval_scale 0 -sig_scale 2 -tail_type 1 -nscale 1 -tgt 500 [files]

source_name: IP fraction of Rpc25-Flag cy8735 S-HU HU

value: Anti-Flag M2 (Sigma)

source_name: SUP of Rpc25-Flag cy8735 S-HU HU


title: BrdU90hHU

source_name: IP fraction of BrdU90hHU-BrdU sy2201 S-HU HU

source_name: SUP of BrdU90hHU-BrdU sy2201 S-HU HU


title: BrdU30Rel

source_name: IP fraction of BrdU30Rel-BrdU sy2201 S-Rel Hu-Rel

source_name: SUP of BrdU30Rel-BrdU sy2201 S-Rel Hu-Rel


title: SSc_133

description:
gene expression data
CRN_133_2


title: Top2-Noco

source_name: IP fraction of Top2-Noco-Flag cy8592 M Glu

value: M

value: Glu

source_name: SUP of Top2-Noco-Flag cy8592 M Glu


title: AhR-KO2 melanocytes

status: Public on Sep 05 2010

city: Dusseldorf

first: Charlotte

last: Esser

address: Auf´m Hennekamp 50

department: Molecular Immunology

country: Germany

institute: IUF

description: no additional information

hyb_protocol: RNA was hybridized to MOE430A 2.0 gene chips (Affymetrix).   Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: MAS5 calculated signal intensity

organism: Mus musculus

source_name: ex vivo cultivated melanocytes

label_protocol: RNA was biotinylated (Enzo Bio Array™HighYield™ RNA transcript labeling kit (Affymetrix, High Wycombe, UK)) and purified.

growth_protocol: Epidermal cell (eC) suspensions were prepared from tail skin of C57BL/6 and AhR-/- mice as described previously. EC were seeded 1.5x106 cells/ml in 6-well plates in serum free Melanocyte Growth Medium (Promocell, Heidelberg, Germany). Normal mouse melanocytes (NMM) were grown for 6-8 weeks, and passaged when confluent. All cells contained visible amounts of melanin at the end of the culture.

extract_protocol: Total RNA was isolated with Trizol™ (Invitrogen) according to the manufacturers’ instructions. For microarray analysis mRNA was amplified prior to chip-hybridization using the MessageAmp™ Kit of Ambion (Woodward St. Austin, USA).

tag: genotype/variation

value: AhR knockout

value: female

value: skin melanocytes


title: PHF8siRNA, 1

status: Public on Sep 01 2010

city: La Jolla

first: Michael

last: Rosenfeld

address: 9500 Gilman Drive

department: School of Medicine

institute: HHMI/UCSD

hyb_protocol: hybridization for 18hrs at 58 degree and stained with Streptavidin-Cy3

scan_protocol: Slides were scanned using the illumina BeadArray Reader scanner

data_processing: Raw data was extracted with the Illumina Beadstudio software. The data was processed according to Illumina protocols and normalized using the multi-loess method mloess.

source_name: HeLa cells

label_protocol: RNA was labeled with biotin using the Ambion Illumina TotalPrep RNA Amplification Kit

extract_protocol: Rneasy Mini Kit (QIAGEN)

tag: cell line

value: HeLa cells

tag: transfection


title: Top2b

source_name: IP fraction of Top2b-Flag cy8592 S Glu

value: S

source_name: SUP of Top2b-Flag cy8592 S Glu


title: SSc_138

description:
gene expression data
CRN_138_2

source_name: PMBCs

value: PMBCs

value: Female


title: SSc_123

description:
gene expression data
CRN_123_1

value: Scleroderma without Pulmonary Hypertension


title: SSc_155

description:
gene expression data
CRN_155_3


title: BrdU30-NT

source_name: IP fraction of BrdU30-NT-BrdU sy2201 S-NT Glu

value: IP fraction

value: anti-BrdU MI-11-3 (MBL)

value: S-NT

source_name: SUP of BrdU30-NT-BrdU sy2201 S-NT Glu


title: BrdU60-NT

source_name: IP fraction of BrdU60-NT-BrdU sy2201 S-NT Glu

source_name: SUP of BrdU60-NT-BrdU sy2201 S-NT Glu

value: supernatant fraction


title: BrdU50-NT

source_name: IP fraction of BrdU50-NT-BrdU sy2201 S-NT Glu

source_name: SUP of BrdU50-NT-BrdU sy2201 S-NT Glu


title: SSc_140

description:
gene expression data
CRN_140_4


title: BrdU40-NT

source_name: IP fraction of BrdU40-NT-BrdU sy2201 S-NT Glu

source_name: SUP of BrdU40-NT-BrdU sy2201 S-NT Glu


title: SSc_126

description:
gene expression data
CRN_126_4


title: SSc_157

description:
gene expression data
CRN_157_3


title: SSc_102

description:
gene expression data
CRN_102_1


title: SSc_139

description:
gene expression data
CRN_139_4


title: Brain (Dorsal Motor Nucleus of the Vagus)_Control_case5

status: Public on Aug 19 2010

city: new york

first: scott

last: small

state: NY

institute: Columbia University

description: Gene expression data from the dorsal motor nucleus of the vagus in a control subject.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133A 2.0 expression array.

scan_protocol: Affymetrix Human Genome U133A 2.0 array was scanned on Affymetrix’s GeneChip Scanner 3000 7G and reviewed for quality control.

data_processing: HG-U133A 2.0 microarray was analyzed with Affymetrix Microarray Suite v5.0 and GeneSpring v5.0.3 (Silicon Genetics) software.

source_name: Brain (Dorsal Motor Nucleus of the Vagus)_control subject_#5

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

extract_protocol: Total RNA was extracted using Invitrogen's TRIzol reagent and purified with RNeasy mini columns (Qiagen), following the manufactures protocols.

tag: sample

tag: subject

value: Control case #5

tag: brain

tag: age

tag: sex

value: Male

tag: region

value: Dorsal motor nucleus of the vagus


title: Brain (Inferior Olivary Nucleus)_Parkinson's disease_case6

description: Gene expression data from the Inferior olivary nucleus in a Parkinson's disease subject.

source_name: Brain (Inferior Olivary Nucleus)_Parkinson's disease subject_#6

value: PD case #6

value: Inferior olivary nucleus


title: Brain (Inferior Olivary Nucleus)_Parkinson's disease_case4

description: Gene expression data from the inferior olivary nucleus in a Parkinson's disease subject.

source_name: Brain (Inferior Olivary Nucleus)_Parkinson's disease subject_#4

value: PD case #1


title: Brain (Inferior Olivary Nucleus)_Parkinson's disease_case5

source_name: Brain (Inferior Olivary Nucleus)_Parkinson's disease subject_#5

value: PD case #5


title: Brain (Dorsal Motor Nucleus of the Vagus)_Parkinson's disease_case6

description: Gene expression data from the dorsal motor nucleus of the vagus in a Parkinson's disease subject.

source_name: Brain (Dorsal Motor Nucleus of the Vagus)_Parkinson's disease subject_#6


title: Brain (Inferior Olivary Nucleus)_Control_case5

description: Gene expression data from the inferior olivary nucleus in a control subject.

source_name: Brain (Inferior Olivary Nucleus)_control subject_#5


title: Brain (Inferior Olivary Nucleus)_Parkinson's disease_case2

description: Gene expression data from the inferior olivary nucleus in a parkinson's disease subject.

source_name: Brain (Inferior Olivary Nucleus)_Parkinson's disease subject_#2

value: PD case #2


title: Brain (Dorsal Motor Nucleus of the Vagus)_Parkinson's disease_case5

source_name: Brain (Dorsal Motor Nucleus of the Vagus)_Parkinson's disease subject_#5


title: Brain (Inferior Olivary Nucleus)_Control_case3

source_name: Brain (Inferior Olivary Nucleus)_control subject_#3

value: Control case #3


title: Brain (Inferior Olivary Nucleus)_Parkinson's disease_case3

source_name: Brain (Inferior Olivary Nucleus)_Parkinson's disease subject_#3

value: PD case #3


title: Brain (Inferior Olivary Nucleus)_Control_case4

source_name: Brain (Inferior Olivary Nucleus)_control subject_#4

value: Control case #4

value: Inferior Olivary Nucleus


title: Brain (Dorsal Motor Nucleus of the Vagus)_Control_case4

source_name: Brain (Dorsal Motor Nucleus of the Vagus)_control subject_#4

value: Female


title: Brain (Dorsal Motor Nucleus of the Vagus)_Parkinson's disease_case3

description: Gene expression data from the dorsal motor nucleus of the vagus in a parkinson's disease subject.

source_name: Brain (Dorsal Motor Nucleus of the Vagus)_Parkinson's disease subject_#3


title: Brain (Dorsal Motor Nucleus of the Vagus)_Control_case1

source_name: Brain (Dorsal Motor Nucleus of the Vagus)_control subject_#1

value: Control case #1


title: Brain (Dorsal Motor Nucleus of the Vagus)_Control_case3

source_name: Brain (Dorsal Motor Nucleus of the Vagus)_control subject_#3


title: Brain (Dorsal Motor Nucleus of the Vagus)_Parkinson's disease_case2

source_name: Brain (Dorsal Motor Nucleus of the Vagus)_Parkinson's disease subject_#2


title: Brain (Inferior Olivary Nucleus)_Control_case1

source_name: Brain (Inferior Olivary Nucleus)_control subject_#1


title: Brain (Dorsal Motor Nucleus of the Vagus)_Parkinson's disease_case4

source_name: Brain (Dorsal Motor Nucleus of the Vagus)_Parkinson's disease subject_#4

value: PD case #4


title: Brain (Dorsal Motor Nucleus of the Vagus)_Control_case2

source_name: Brain (Dorsal Motor Nucleus of the Vagus)_control subject_#2

value: Control case #2


title: Brain (Inferior Olivary Nucleus)_Control_case2

source_name: Brain (Inferior Olivary Nucleus)_control subject_#2


title: Brain (Dorsal Motor Nucleus of the Vagus)_Parkinson's disease_case1

source_name: Brain (Dorsal Motor Nucleus of the Vagus)_Parkinson's disease subject_#1


title: Capan-1 V2 control

status: Public on Aug 01 2010

city: Berlin

first: Wolfgang

last: Kemmner

address: Lindenberger Weg 80

institute: ECRC Berlin

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000. Images were processed using AGCC 2.01.

data_processing: CEL data files were imported in GeneSpring GX 10.0.2 software (Agilent Technologies, Santa Clara, USA) and pre-processed using the GC-RMA algorithm. Statistical analysis for differentially expressed genes was performed using Welch-test.

source_name: Capan-I cells allStar-transfected

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The human pancreatic carcinoma cell line Capan-1 (HTB 79; American Type Culture Collection) was grown in monolayer cultures in RPMI medium supplemented with 15% fetal calf serum, 2 mM glutamine, 0.25 mg/ml Amphotericin B in a humidified atmosphere containing 5% CO2 at 37°C.

extract_protocol: RNeasy (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Transfection of siRNA was performed with TransMessenger Transfection Reagent (Qiagen, Hilden, Germany) in 6-well plates. Briefly, 7x10^4 cells were transfected with siRNA (0.4 µg per 500 µl well) two times within an interval of 48 h according to manufacturer’s instructions. The transfection complex was replaced by RPMI with supplements after 7 h. Cells were harvested 72 h after the second transfection.

tag: cell type

value: pancreatic carcinoma cells

tag: gne mrna

value: unchanged


title: Capan-1 V2 siGNE

source_name: Capan-I cells siGNE-transfected

value: knock-down


title: Capan-1 V1 siGNE


title: Capan-1 V1 control


title: Capan-1 V3 siGNE


title: Capan-1 V3 control


title: Capan-1 V3 p16

source_name: Capan-1 cells p16-transfected

treatment_protocol: Briefly, for generation of p16-transfectants, full-length human p16INK4a cDNA was subcloned into the eukaryotic expression vector pRC/CMV, where p16INK4a is under the control of the CMV promoter and can be selected by neomycin resistance. Transfected cells were selected in the presence of 0.1 mg/ ml hygromycin and 1 mg/ml G418.

tag: p16 restoration

value: yes


title: UTA21_stat phase_rep1

city: Reno

first: Paul

last: Sumby

state: NV

address: 1554 N. Virginia St.

department: Microbiology & Immunology

institute: University of Nevada

hyb_protocol: Labeled cDNA was hybridized to our custom array for 16h at 40ºC.  GeneChips were washed and stained using  the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using a GeneArray Scanner G2500A.

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 50.

label: Biotin

organism: Bacillus anthracis

source_name: Stationary phase

label_protocol: RNA was converted to cDNA, the cDNA was fragmented, and the cDNA labeled with biotin

growth_protocol: Approximately 1x106  B. anthracis spores were inoculated into 25-ml of LB medium and cultures were incubated until mid-exponential (OD600 = 0.5-0.6) or early stationary (OD600 = 3.5-3.9) growth phase

extract_protocol: Total RNA was extracted using a standard hot phenol precipitation.

treatment_protocol: 6-ml samples were taken in exponential phase and 2-mls samples were collected in stationary phase of growth.   Cells were pelleted at 2,400 x g for 10 min at 4ºC and pellets were frozen at -80ºC.

tag: growth phase

value: Stationary phase


title: Ames_stat phase_rep2

value: Ames


title: Ames_stat phase_rep3


title: UTA21_expo phase_rep2

source_name: Exponential phase

value: Exponential phase


title: Ames_expo phase_rep2


title: UTA21_expo phase_rep1


title: Ames_expo phase_rep3


title: UTA21_expo phase_rep3


title: Ames_expo phase_rep1


title: UTA21_stat phase_rep3


title: Capan-1 V2 p16


title: Capan-1 V1 p16


title: Ames_stat phase_rep1


title: UTA21_stat phase_rep2


title: Capan-1 V1 mock

source_name: Capan-1 cells mock-transfected

value: no


title: Veg_rep1

city: Spokane

first: Lucia

last: Peixoto

state: WA

address: PO Box 1495

department: College of Medicine

institute: Washington State University, Spokane

description:
replicate 1
4418463312_A
Sentrix Barcode: 4418463312
Sample Section: A

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was average normalized, no background substraction, and differential expression determined using Illumina Bead Studio Gene expression module v 3.3 with uninfected HFF cells used as reference group. Normalization was performed across all samples. Non-compatible probes between platforms Human Ref8 V2 and V3 were automatically eliminated during normalization leaving only 15,555 human genes for analysis across all samples.

source_name: Human Foreskin fibroblasts, infected with different strains of Toxoplasma gondii

label_protocol: Biotinylated cRNA were prepared with the Ovation Aminoallyl RNA Amplification and Labeling System

growth_protocol: Veg, RH, RH-ROP21 and RH-ROP38 parasites were cultivated using standard methods (Roos, Donald et al. 1994) harvested by syringe passage and inoculated at a 20:1 multiplicity of infection (MOI) into HFF cells. 24hs incubation was allowed before harvest and RNA isolation.

extract_protocol: RNA was harvested from HFF cellsusing the RNeasy kit (Qiagen) according to the manufacturer’s instructions.  RNA quality was ascertained using a spectrophotometer (NanoDrop), and confirmed with an Agilent Bioanalyzer. Only samples with comparable ratios of parasite:host RNA (deter¬mined by Agilent Bioanalyzer) were used for hybridization.

tag: infection

value: Veg


title: Capan-1 V2 mock


title: Capan-1 V3 mock


title: Veg_rep2

description:
replicate 2
4418463312_B
Sentrix Barcode: 4418463312
Sample Section: B


title: RH_ROP38_rep4

description:
replicate 4
4418463143_F
Sentrix Barcode: 4418463143
Sample Section: F


title: Veg_rep3

description:
replicate 3
4418463312_C
Sentrix Barcode: 4418463312
Sample Section: C


title: RH_ROP38_rep2

description:
replicate 2
4418463143_D
Sentrix Barcode: 4418463143
Sample Section: D


title: RH_rep1

description:
replicate 1
4247668011_D
Sentrix Barcode: 4247668011
Sample Section: D

value: RH


title: HFF_rep4

description:
replicate 4
4418463143_C
Sentrix Barcode: 4418463143
Sample Section: C

source_name: Human Foreskin fibroblasts, uninfected (control)

value: uninfected


title: H3K9me3_10day

city: Providence

first: Sara

last: Hillenmeyer

state: RI

address: 60 Olive St

department: MCB

institute: Brown University

description: 10day, h3k9me3 ChIP Biological Rep 1-3

hyb_protocol: The entire labeled sample was used in the hybridization cocktail (200 ul final volume) and the entire sample was hybridized overnight to Drosophila 2.0 tiling arrays following Affymetrix standard protocol.

scan_protocol: Staining and washing was done on an Affymetrix FS450 Fluidics Station using protocol FS450_001 and array staining was visualized using and Affymetrix 3000 7G scanner.

data_processing: Background probes were used to calculate median background signal which was subtracted from the signal of each genomic probe based on GC content.  All non-unique probe sequences were removed from further analysis. The intensities were quantile normalized together, grouped by antibody. The Hodges-Lehman estimate of triplicate IP samples - triplicate input samples in a 500 bp window centered on the probe was calculated as signal.

organism: Drosophila melanogaster

source_name: ChIP DNA from 10day female heads

label_protocol: 7.5 ug dsDNA were fragemented for 60 min in standard PCR machine at 37 ºC with 15 U UDG and 225 U APE enzymes, followed by a 2 min incubation at  93 ºC. Successful fragmentation was analyzed on a RNA 6000 Bioanalyzer chip using the total RNA mode. The fragmented samples were labeled with for 60 min at 37 ºC with 1 ul TdT, followed by heat inactivation of the enzyme at 70 ºC for 10 min. Enzymes from fragmentation and labeling were from Affymetrix WT double stranded DNA terminal labeling Kit, (cat # 900812).

growth_protocol: Mixed sex Canton-S flies were grown in cages for 10 days or 40 days on standard food (6% yeast, 12% sucrose, 5% cornmeal), in a humidified (50%), incubator with 12 hour on/off light cycle at 25˚C, changing food every 2-3 days.

extract_protocol: Flies were kept at -80°C, then sexed, and heads removed by vortexing. 200 mg of heads were used to prepare chromatin (10),with sonication to an average size of 500 bp. 250 µl chromatin extract was immunoprecipitaed with one of the following antibodies: 4H8 (Abcam ab5408, 2 µl/IP), H3K4me3 (Abcam ab8580, 4 µl/IP), H3K9me3 (Millipore 07-442, 4 µl/IP), H3K36me3 (Abcam ab9050, 4 µl/IP), or HP1 (Developmental Studies Hybridoma Bank C1A9, 2 µl/IP). After elution, DNA was purified with the MinElute PCR cleanup kit (Qiagen) and amplified with the WGA2 kit (Sigma).

tag: tissue

value: head

tag: antibody

tag: antibody manufacturer

value: Millipore

tag: antibody catalog number

tag: strain

value: Canton-S

source_name: Input DNA from 10day female heads


title: H3K36_40day

description: 40day, h3k36 ChIP Biological Rep 1-3

source_name: ChIP DNA from 40day female heads

value: Abcam

source_name: Input DNA from 40day female heads


title: RH_rep3

description:
replicate 3
4247668011_F
Sentrix Barcode: 4247668011
Sample Section: F


title: H3K36_10day

description: 10day, H3k36 ChIP Biological Rep 1-3


title: H3K4_40day

description: 40day, h3k4 ChIP Biological Rep 1-3


title: 4h8_40day

description: 40day, 4h8 ChIP Biological Rep 1-3

value: RNA polymerase 4H8


title: RH_ROP38_rep3

description:
replicate 3
4418463143_E
Sentrix Barcode: 4418463143
Sample Section: E


title: RH_rep2

description:
replicate 2
4247668011_E
Sentrix Barcode: 4247668011
Sample Section: E


title: HFF_rep3

description:
replicate 3
4418463143_B
Sentrix Barcode: 4418463143
Sample Section: B


title: HFF_rep2

description:
replicate 2
4418463143_A
Sentrix Barcode: 4418463143
Sample Section: A


title: RH_ROP38_rep1

description:
replicate 1
4247668011_H
Sentrix Barcode: 4247668011
Sample Section: H


title: H3K9me3_40day

description: 40day, h3k9me3 ChIP Biological Rep 1-3


title: HP1_40dy

description: 40day, Hp1 ChIP Biological Rep 1-3

value: Developmental Studies Hybridoma Bank


title: RH_ROP21_rep2

description:
replicate 2
4247668011_B
Sentrix Barcode: 4247668011
Sample Section: B


title: 4h8_10day

description: 10day, 4h8 ChIP Biological Rep 1-3


title: HFF_rep1

description:
replicate 1
4247668011_G
Sentrix Barcode: 4247668011
Sample Section: G


title: H3K4_10day

description: 10day, H3k4 ChIP Biological Rep 1-3


title: RH_ROP21_rep3

description:
replicate 3
4247668011_C
Sentrix Barcode: 4247668011
Sample Section: C


title: RH_ROP21_rep1

description:
replicate 1
4247668011_A
Sentrix Barcode: 4247668011
Sample Section: A


title: 799 -L t120 cy5ctrl

city: Chicago

first: John

middle: Michael

last: Zaborske

state: IL

address: 929 E 57th St

department: Biochemistry and Molecular Biology

institute: University of Chicago

description: dye swap of sample 60

hyb_protocol: Hybridization was performed in a GeneMachines Hyb4 at 60°C overnight (16 hours) with 1 to 2.5µg each of Cy3- or Cy5-labeled total RNA as previously described. Slides were washed with 2X SSC / 0.1% SDS, 0.1X SSC / 0.1% SDS, and 0.1X SSC prior to drying and scanning.

scan_protocol: Arrays were scanned using a GenePix 4000b scanner and GenePix Pro 6.0 (Axon Instruments). For both Cy3 and Cy5 wavelengths, PMT gain was set at 600 and power at 100%.

data_processing: Image and data analysis were carried out using GenePix Pro 6.0 and Microsoft Excel. Median Cy5/Cy3 ratios were obtained from all spot replicates. To account for differences in labeling and hybridization efficiencies, the following normalization procedure was used. First, the median Cy5/Cy3 ratio for each probe was divided by the corresponding time 0 reference ratio. Second, the obtained value was divided by the averaged Cy5/Cy3 ratio value for the three tRNA standards added as controls (E. coli tRNALys, E. coli tRNATyr, and E. coli tRNAPhe).  Finally each timepoint was normalized to the median value.  These normalizations yield relative tRNA abundance values for the sample relative to the reference time. Values from dye-swapped data sets were averaged and converted to log2 ratios for visualization as TreeView images.

source_name: GCN2 knockout yeast

label_protocol: Cy3/Cy5 labeling: after deacylation, tRNA in the total RNA mixture was selectively labeled with either Cy3 or Cy5 fluorophore using an enzymatic ligation method. The ligation reaction relies on an 8-base pair RNA:DNA hybrid helix containing a Cy3 or Cy5 fluorophore pre-attached to the loop and an overhang complementary to the universally conserved 3'CCA nucleotides present in all tRNAs. The ligation reaction was carried out overnight (~16 hours) at 16°C with 1U/µL T4 DNA ligase (USB Corporation, 70042X) and 9µM labeling oligonucleotide.

growth_protocol: Cells were grown in filter sterilized synthetic complete (SC) media containing 2% dextrose, 0.5% ammonium sulfate, and the designated amino acids.

extract_protocol:
Yeast cells were cultured as described above and collected by centrifugation. Cell pellets were resuspended in lysis buffer solution (0.3 m NaOAc/HOAc (pH 4.5) and 10 mm EDTA) and then vortexed with acetate-saturated phenol/CHCl3 (pH 4.5) three times each for 30 s. Lysates were placed in an ice bath following each vortex mixing.  Following cold centrifugation at 18,600 relative centrifugal force, the aqueous layers were removed and subjected to another extraction with acetate-saturated phenol/CHCl3 (pH 4.5) solution.  RNA was ethanol precipitated twice and resuspended in a solution containing 10 mm NaOAc/HOAc (pH 4.5) and 1 mm  EDTA for subsequent microarray analyses.
Deacylation: 0.1µg/µl total RNA premixed with three tRNA standards (E. coli tRNALys, E. coli tRNATyr, and E. coli tRNAPhe) at 0.06µM each was incubated in 100mM Tris-HCl (pH 9.0) at 37°C for 30 minutes. The solution was neutralized by the addition of an equal volume of 100mM Na-acetate/acetic acid (pH 4.8) plus 100mM NaCl, followed by ethanol precipitation. Deacylated total RNA was dissolved in water, and its integrity verified by agarose gel electrophoresis.

treatment_protocol: Yeast cells were grown overnight at 30 °C in SC media. Cells were then diluted in SC to A600 ~0.1 and cultured to A600 between 0.4 and 0.5, collected by centrifugation, and inoculated into SC medium or SC medium devoid of the designated amino acids. Cells were cultured in theseconditions for 15 or 60 minutes.

tag: trna state

value: oxidized tRNA

tag: genotype

value: GCN2 knockout

tag: treatment

value: Leu depletion

value: total tRNA


title: 799 abundance 0cy3 60cy5

value: Utreated reference

value: Trp depletion


title: 799 -L t45 cy5ctrl

description: dye swap of sample 59


title: keratinocytes_proliferating_rep3

city: Lausanne

first: Magdalena

last: Obarzanek-Fojt

address: Beaumont 29

department: Dermatology

country: Switzerland

institute: CHUV

description: Proliferating keratinocytes, replicate 3

hyb_protocol: Affymetrix HG-U133A 2.0 arrays were hybridized with 11 microgramme of labeled, amplified cRNA , washed, stained and scanned according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol EukGeWS2v5_450)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 7G

data_processing: Normalized expression signals were calculated from Affymetrix CEL files in GeneSpring using RMA (Irizarry et al., 2003).

source_name: Primary human keratinocytes cultured in low calcium concentration medium, proliferating cells

label_protocol: 100ng of total RNA were amplified and labeled using the Message Amp II-biotin Enhanced reagents (Ambion; catalog #AM1791)

growth_protocol: Primary keratinocytes were cultured in defined serum-free keratinocytes medium (DKSFM, Invitrogen) with growth supplement and penicillin/streptomycin.

extract_protocol: Total RNA from NHK cultures was extracted using RNeasy Mini Kit (Qiagen) according to the manufacturer’s recommendations. Additional RNA precipitation (NaOAc:ethanol) was performed to improve RNA quality for microarray experiment. The analysis of RNA integrity was performed using Agilent RNA 6000 Nano Kit and Bioanalyzer (Agilent Technology).

treatment_protocol: Differentiation of keratinocytes was induced at 80% cell confluency by increasing the calcium concentration in DKSFM to 1.2 mM.

value: Normal human primary keratinocytes


title: keratinocytes_differentiating_rep4

description: Differentiating keratinocytes, replicate 4

source_name: Primary human keratinocytes cultured in high calcium concentration medium, cells differentiated for seven days


title: 799 abundance 60cy3 0cy5

value: Untreated reference


title: keratinocytes_differentiating_rep1

description: Differentiating keratinocytes, replicate 1


title: 799 abundance 0cy3 0cy5


title: keratinocytes_proliferating_rep2

description: Proliferating keratinocytes, replicate 2


title: keratinocytes_differentiating_rep2

description: Differentiating keratinocytes, replicate 2


title: keratinocytes_differentiating_rep5

description: Differentiating keratinocytes, replicate 5


title: keratinocytes_proliferating_rep5

description: Proliferating keratinocytes, replicate 5


title: 798 -L t120 cy5ctrl

description: dye swap of sample 56

source_name: WT yeast

value: WT


title: 798 -L t45 cy5ctrl

description: dye swap of sample 55


title: 798 -L t5 cy5ctrl

description: dye swap of sample 54


title: 799 t5 cy3ctrl

value: Reference


title: 799 -L t45 cy3ctrl


title: 798 -L t120 cy3ctrl


title: 799 t5 cy5ctrl

description: dye swap of sample 57


title: 799 -L t120 cy3ctrl


title: 798 -L t45 cy3ctrl


title: 799 -L t5 cy5ctrl

description: dye swap of sample 58


title: 798 t5 cy5ctrl

description: dye swap of sample 53


title: 799 -L t5 cy3ctrl


title: keratinocytes_differentiating_rep3

description: Differentiating keratinocytes, replicate 3


title: keratinocytes_proliferating_rep4

description: Proliferating keratinocytes, replicate 4


title: keratinocytes_proliferating_rep1

description: Proliferating keratinocytes, replicate 1


title: 798 t5 cy3ctrl


title: 799 -R+Orn t0 cy5ctrl

description: dye swap of sample 48


title: 799 -R+Orn t60 cy5ctrl

description: dye swap of sample 50

value: Arg depletion with Ornithine suplementation


title: 799 -R+Orn t0 cy3ctrl


title: 798 -R+Orn t60 cy3ctrl


title: 799 -R+Orn t15 cy3ctrl


title: 798 -R+Orn t15 cy3ctrl


title: 798 -R+Orn t0 cy3ctrl


title: 799 -WYF t60 cy3ctrl

value: WYF depletion


title: 799 -WYF t0 cy3ctrl


title: 799 -WYF t15 cy3ctrl


title: 798 -L t5 cy3ctrl


title: 799 -W t0 cy5ctrl


title: 798 -WYF t0 cy3ctrl


title: 799 -W t15 cy5ctrl


title: 799 -W t60 cy5ctrl


title: 798 -W t0 cy5ctrl


title: 798 -W t15 cy5ctrl


title: 799 -W t15 cy3ctrl


title: 799 -W t60 cy3ctrl


title: 799 -R+Orn t60 cy3ctrl


title: 798 -W t60 cy5ctrl


title: 799 -WYF t60 cy5ctrl

description: dye swap of sample 42


title: 799 -W t0 cy3ctrl


title: 799 -WYF t0 cy5ctrl

description: dye swap of sample 40


title: 798 -W t60 cy3ctrl


title: 798 -WYF t60 cy3ctrl


title: 798 -W t15 cy3ctrl


title: 798 -W t0 cy3ctrl


title: 798 -WYF t15 cy3ctrl


title: 799 -R t60 cy5ctrl

description: dye swap of sample 18

value: Arg depletion


title: 799 -R t15 cy5ctrl

description: dye swap of sample 17


title: 799 -R t0 cy5ctrl

description: dye swap of sample 16


title: 798 -R t60 cy5ctrl

description: dye swap of sample 15


title: 798 -R t0 cy5ctrl

description: dye swap of sample 13


title: Mtb H37Rv versus Mtb clinical isolate HN878 dosR1 haploid (GC_26)

city: Montreal

first: Pilar

last: Domenech

state: Quebec

address: 1001 Décarie Boulevard

department: IDIGH Program

country: Canada

institute: Research Institute of McGill University Health Centre

hyb_protocol: Microarray hybridization was carried out in Hybridization buffer (24% formamide, 0.5% SDS, 5X SSC) in the presence of 4 µg yeast tRNA and  1 µg salmon sperm DNA at 45°C for 16 hours.  Following hybridization, microarray slides were washed three times (15 mins/wash) with 0.5X SSC + 0.01% SDS, 0.06X SSC + 0.01% SDS and 0.06X SSC.

scan_protocol: Scanned on ScanArray Lite (Packard) Images were quantified using ScanArray Express software (Packard).

data_processing: Mean fluorescence values for each spot, minus the surrounding background were used in the analysis.  Spots flagged as misrepresentative or those with a negative value following background correction were subsequently excluded from further analysis.  The fluorescence intensity ratios (Cy3/Cy5 or Cy5/Cy3, representing test/reference) were calculated for each spot, log10 transformed and then normalized with respect to the mean value of all fluorescence ratios. A Z- score [Z = (log10 fluorescence ratio - mean)/standard deviation] was calculated for each spot.

organism: Mycobacterium tuberculosis

label_protocol: 2 µg of purified genomic DNA was labeled with either Cy3 or Cy5-NHS esters (GE Healthcare) via the aminoallyl indirect labeling method (Yu et al., 2002) in the presence  DNA polymerase I Klenow fragment (NEB).  Labeled  gDNA was subsequently purified using the QIAquick PCR Purification Kit (Qiagen) and samples to be co-hybridized on the same array were mixed and concentrated to 6µl in a Savant SpeedVac Concentrator.

extract_protocol: Bacteria were harvested by centrifugation (10 min, 3,000 rpm) at room temperature, resuspended in SET solution (25% Sucrose, 50mM EDTA, 50 mM Tris pH=8) containing 4 mg/ml of lysozyme. Cell lysates were treated with RNase, Proteinase K and after phenol-chloroform extraction, DNA was precipitated with isopropanol.

tag: properties

value: Derivative from clinical isolate of the Beijing lineage. 295 kb duplication, dosR1 gene is replaced with the hyg cassette

value: Laboratory strain

value: H37Rv ATCC27294


title: Mtb H37Rv versus Mtb clinical isolate HN878 dosR1 haploid (GC_25)


title: 798 -R t15 cy5ctrl

description: dye swap of sample 14


title: Mtb H37Rv versus Mtb clinical isolate HN878 dosR2 haploid (GC_24)

value: Derivative from clinical isolate of the Beijing lineage. 220 kb duplication, dosR2 gene is replaced with the hyg cassette


title: 799 -R t15 cy3ctrl

value: oxidized tRNA


title: 798 -R t60 cy3ctrl


title: 799 -R t0 cy3ctrl

value: GCN2 knockout


title: 798 -R t15 cy3ctrl


title: 798 -R t0 cy3ctrl


title: Mtb H37Rv versus Mtb clinical isolate HN878 dosR2 haploid (GC_23)


title: Mtb H37Rv versus Mtb clinical lisolate T28 (GC_16)

description: Mtb H37Rv versus Mtb clinical isolate T28

value: Clinical isolate of the Beijing lineage


title: Mtb H37Rv versus Mtb clinical lisolate HN878-wt-27 (GC_19)

description: Mtb H37Rv versus Mtb clinical isolate HN878-wt-27

value: Laboratory isolate derivative from clinical isolate HN878


title: Mtb H37Rv versus Mtb clinical lisolate W10 (GC_17)

description: Mtb H37Rv versus Mtb clinical isolate W10


title: Mtb H37Rv versus Mtb clinical lisolate W10 (GC_18)


title: 799 -H t15 cy5ctrl

description: dye swap of sample 5

value: His depletion

value: total tRNA


title: 799 -H t60 cy5ctrl

description: dye swap of sample 6


title: Mtb H37Rv versus Mtb clinical lisolate HN878-wt-27 (GC_20)


title: Mtb H37Rv versus Mtb clinical lisolate STR 049 (GC_15)

description: Mtb H37Rv versus Mtb clinical isolate STR 049

source_name: STR 049

value: STR 049


title: Mtb H37Rv versus Mtb clinical lisolate HN878-wt-45 (GC_21)

description: Mtb H37Rv versus Mtb clinical isolate HN878-wt-45


title: Mtb H37Rv versus Mtb clinical lisolate STR 049 (GC_14)


title: HP1_10day

description: 10day, HP1 ChIP Biological Rep 1-3

tag: age

value: head

value: Developmental Studies Hybridoma Bank

value: Canton-S


title: Mtb H37Rv versus Mtb clinical lisolate 98_1863 (GC_13)

description: Mtb H37Rv versus Mtb clinical isolate 98_1863


title: Mtb H37Rv versus Mtb clinical lisolate HN878-wt-45 (GC_22)


title: Mtb H37Rv versus Mtb clinical lisolate 59660 (GC_12)

description: Mtb H37Rv versus Mtb clinical isolate 59660


title: 799 -H t0 cy5ctrl

description: dye swap of sample 4

value: Reference


title: 798 -H t60 cy5ctrl

description: dye swap of sample 3

value: WT


title: 798 -H t15 cy5ctrl

description: dye swap of sample 2


title: Mtb H37Rv versus Mtb clinical lisolate 59660 (GC_11)


title: 799 -H t60 cy3ctrl


title: 798 -H t0 cy5ctrl

description: dye swap of sample 1


title: 799 -H t0 cy3ctrl


title: 799 -H t15 cy3ctrl


title: Mtb H37Rv versus Mtb clinical lisolate 00_4661 (GC_8)

description: Mtb H37Rv versus Mtb clinical isolate 00_4661


title: Mtb H37Rv versus Mtb clinical lisolate 97_1039 (GC_10)

description: Mtb H37Rv versus Mtb clinical isolate 97_1039


title: 798 -H t60 cy3ctrl


title: 798 -H t15 cy3ctrl


title: 799 -R t60 cy3ctrl

value: Arg depletion


title: 798 -H t0 cy3ctrl


title: Mtb H37Rv versus Mtb clinical lisolate HN878 (GC_6)

description: Mtb H37Rv versus Mtb clinical isolate HN878


title: Mtb H37Rv versus Mtb clinical lisolate 00_4661 (GC_7)


title: Mtb H37Rv versus Mtb clinical lisolate G4B1.2 (GC_3)

description: Mtb H37Rv versus Mtb clinical isolate G4B1.2


title: Mtb H37Rv versus Mtb clinical lisolate G4B1.2 (GC_2)


title: Mtb H37Rv versus Mtb clinical lisolate HN878 (GC_4)


title: Mtb H37Rv versus Mtb clinical lisolate HN878 (GC_5)


title: Mtb H37Rv versus Mtb clinical lisolate G4B1.2 (GC_1)


title: Mtb H37Rv versus Mtb clinical lisolate 97_1039 (GC_9)


title: ME49 tachyzoite, rep2

status: Public on Jul 31 2010

city: Philadelphia

middle: H

last: Davis

state: PA

address: 433 S. University Ave.

department: Biology

institute: University of Pennsylvania

hyb_protocol: Hybridization of arrays was performed using standard Affymetrix instrumentation and protocols for 11 micron, 169 format arrays.

scan_protocol: An Affymetrix GeneChip Scanner 3000 7G confocal scanner was used to collect fluorescence signal after excitation at 570 nm.   Affymetrix Command Console v2 software was used to determine raw intensities and generate CEL files. Default values provided by Affymetrix were applied to all analysis parameters. Border pixels were removed, and the average intensity of pixels within the 75th percentile was computed for each probe. The average of the lowest 2% of probe intensities occurring in each of 16 microarray sectors was set as background and subtracted from all features in that sector.

data_processing: RMAExpress 1.0.4 was used to compute gene expression summary values for Affymetrix data using the Robust Multichip Average expression summary.

organism: Toxoplasma gondii

source_name: tachyzoite-stage parasites from tissue culture, Type II Strain ME49

label_protocol: RNA was labeled using the NuGEN Ovation Amp kit according to manufacturer's instructions.

growth_protocol: Parasites were cultured in human foreskin fibroblast (HFF) cells as described in Roos, Donald et al. 1994.

extract_protocol: Prior to host cell rupture, monolayers were twice rinsed with cold 1x PBS, then infected human fibroblast cell monolayers were scraped from the flask, collected, and spun at 300g for 9 min. The resultant pellet was lysed with Buffer RLT from the Qiagen RNeasy Mini Kit (Valencia, CA) and RNA was extracted according to the manufacturer’s instructions.

treatment_protocol: HFF cells in flasks were grown to confluency in D10 media and infected with T. gondii freshly lysed parasites.  Parasites were isolated prior to host cell lysis.

tag: type

value: II

tag: developmental stage

value: tachyzoite


title: Prugniaud tachyzoite, rep4

source_name: tachyzoite-stage parasites from tissue culture, Type II Strain Prugniaud

value: Prugniaud


title: VEG tachyzoite, rep3

source_name: tachyzoite-stage parasites from tissue culture, Type III Strain VEG

value: III

value: VEG


title: ME49 tachyzoite, rep1


title: GT1 tachyzoite, rep1

source_name: tachyzoite-stage parasites from tissue culture, Type I Strain GT1

value: I


title: CTG tachyzoite, rep3

source_name: tachyzoite-stage parasites from tissue culture, Type III Strain CTG

value: CTG


title: CTG tachyzoite, rep4


title: RH tachyzoite, rep3

source_name: tachyzoite-stage parasites from tissue culture, Type I Strain RH

value: RH


title: Prugniaud tachyzoite, rep2


title: GT1 tachyzoite, rep3


title: VEG tachyzoite, rep2


title: GT1 tachyzoite, rep2


title: VEG tachyzoite, rep4


title: Prugniaud tachyzoite, rep1


title: GT1 tachyzoite, rep4


title: ME49 tachyzoite, rep3


title: RH tachyzoite, rep4


title: Prugniaud tachyzoite, rep3


title: CTG tachyzoite, rep2


title: VEG tachyzoite, rep1


title: CTG tachyzoite, rep1


title: Brain (Inferior Olivary Nucleus)_Parkinson's disease_case1

description: Gene expression data from the inferior olivary nucleus in a parkinson's disease subject.

source_name: Brain (Inferior Olivary Nucleus)_Parkinson's disease subject_#1

tag: sample

tag: subject

value: PD case #1

tag: brain

tag: sex

value: Female

tag: region

value: Inferior olivary nucleus


title: RH tachyzoite, rep1


title: RH tachyzoite, rep2


title: 28517102

status: Public on Jul 30 2010

city: Miami

first: Maria

middle: Eugenia

last: Figueroa

state: FL

address: 1501 NW 10th Ave, BRB 709A, Locator code C227

department: Human Genetics

institute: University of Miiami

hyb_protocol: Hybridizations were carried out for 18 hr at 42C in the NimbleGen Service Laboratory. See Roche NimbleGen website and PMID 16075461 (Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.) for details.

scan_protocol: Scanning was performed using a GenePix 4000B scanner (Axon Instruments) at 5-um resolution, and data were extracted from scanned images using NimbleScan 2.0 extraction software, as previously described in PMID 16075461 (Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.)

data_processing: Signal intensities at each HpaII-amplifiable fragment were calculated as a robust (25% trimmed) mean of their component probe-level signal intensities. Any fragments found within the level of background MspI signal intensity, measured as 2.5 mean-absolute-differences (MAD) above the median of random probe signals, were categorized as “failed.” These “failed” loci therefore represent the population of fragments that did not amplify by PCR, whatever the biological (e.g. genomic deletions and other sequence errors) or experimental cause. On the other hand, “Methylated” loci were so designated when the level of HpaII signal intensity was similarly indistinguishable from background. PCR-amplifying fragments (those not flagged as either “methylated” or “failed”) were normalized using an intra-array quantile approach wherein HpaII/MspI ratios are aligned across density-dependent sliding windows of fragment size-sorted data (described in detail in Thompson et al, Bioinformatics 2008;24:1161-1167). After normalization, background noise was calculated for each channel by determining a threshold of 2.5 median absolute deviations from the median of the random probes’ signal. Each normalized channel was subsequently centered by subtracting its noise threshold from the array’s signal. The HpaII/MspI (unmethylated/whole genome reference) ratio was then determined for each probe set on array.

source_name: Lymphoma tissue, Eu-myc, MspI

label_protocol: Random 9-mers pre-labeled with either Cy3 or Cy5.

extract_protocol: Representation of the genome generated by digestion with either MspI (methylation-insensitive) or HpaII (methylation-sensitive) and amplification by ligation-mediated PCR according to the HELP (HpaII tiny fragment Enrichment by Ligation-mediated PCR) protocol (See PMID 16809668: B. Khulan, et al. Genome Res. 2006 Aug;16(8):1046-55).

tag: tissue

value: lymphoma

value: Eu-myc

tag: gender

value: male

tag: cytogenetics

value: NN

tag: restriction enzyme

value: MspI

source_name: Lymphoma tissue, Eu-myc, HpaII

value: HpaII


title: 28485402

value: female


title: 28517202

source_name: Lymphoma tissue, hDNMT3B7/Eu-myc, MspI

source_name: Lymphoma tissue, hDNMT3B7/Eu-myc, HpaII


title: 28520902


title: 28485502


title: 28505902


title: L-UHO-1 siGATA-3  rep3

status: Public on Jul 24 2010

city: Frankfurt

first: Claudia

last: Döring

address: Theodor Stern Kai 7

department: Medical School, Institite of Pathology

institute: Johann Wolfgang-Goethe University Frankfurt a.M.

description: 25,000 GFP-positive cells

hyb_protocol: Human Gene 1.0 ST arrays (Affymetrix) were hybridized with 5.5 mg labelled cDNA.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Statistical analysis was done with the statistical computing environment R (version 2.8.1). Additional software packages (affy_1.20.2, vsn_3.8.0, geneplotter_1.20.0, multtest_1.23.3) were taken from the Bioconductor project.  Microarray preprocessing: Probe level normalization was conducted using the variance stabilization method (vsn) from Huber et al..
probe group file: Unsupported Human Gene 1.0 ST Array CDF Files
meta-probeset file: HuGene-1_0-st-v1 Probeset Annotations, CSV Format, Release 30 (11 MB 01/22/10)

source_name: siGATA-3 UHO-1

label_protocol: Samples were labelled with WT target labelling Kit (Affymetrix, Fremont, USA), washed and stained using the HWS Kit (Affymetrix).

growth_protocol: Cell lines were purchased from DSMZ (Braunschweig, Germany) and cultured in RPMI 1640 supplemented with 10% fetal calf serum (Biochrom; Berlin, Germany), 2 mM glutamine (Invitrogen; Groningen, The Netherlands) and 1% penicillin G/streptomycin sulfate (Invitrogen).UHO-1 cells were cultured as above but in IMDM.

extract_protocol: RNA from 25,000 GFP-positive cells was extracted using the RNeasy Micro Kit (Qiagen, Hilden, Germany). RNA was amplified with the WT expression Kit (Ambion, Austin, USA)

treatment_protocol: U-HO1 and L-1236 cells were transduced with shRNAs against GATA-3 or non-functional control shRNAs, cultured for three days, and sorted according to their GFP positivity.

tag: cell line

tag: sirna


title: L-UHO-1 siGATA-3  rep2

description: 25,000 GFP-positive cells


title: L-UHO-1 siSCR rep2

description: 25,000 GFP-positive cells

source_name: siSCR UHO-1

value: siSCR


title: L-UHO-1 siSCR rep3

description: 25,000 GFP-positive cells


title: L-1236 siGATA-3  rep2

description: 25,000 GFP-positive cells

source_name: siGATA-3 L-1236


title: L-1236 siGATA-3  rep3

description: 25,000 GFP-positive cells


title: L-1236 siGATA-3  rep1

description: 25,000 GFP-positive cells


title: L-UHO-1 siSCR rep1

description: 25,000 GFP-positive cells


title: L-1236 siSCR rep3

description: 25,000 GFP-positive cells

source_name: siSCR L-1236


title: L-UHO-1 siGATA-3  rep1

description: 25,000 GFP-positive cells


title: L-1236 siSCR rep1

description: 25,000 GFP-positive cells


title: L-1236 siSCR rep2

description: 25,000 GFP-positive cells


title: Syndecan-1 overexpressing cells 3

status: Public on Jul 20 2010

city: Stockholm

first: Fang

last: Zong

address: F46, Huddinge university hospital

department: LabMed

country: Sweden

institute: Karolinska

hyb_protocol: From non-degraded high-quality total RNA we prepared and hybridized biotinylated complementary RNA to Gene 1.0 ST Arrays, and then washed, stained and scanned slides using standardized protocols (Affymetrix Inc., Santa Clara, CA).

scan_protocol: We used standardized Affymetrix protocols (Affymetrix Inc., Santa Clara, CA).

data_processing: Subsequent data analyses were performed using the Affymetrix Expression Console (version 1.1). The processing methods were: Summarization: PLIER, Background Correction: PM-GCBG, Normalization: Global Median.

source_name: STAV-AB malignant mesothelioma cells

label_protocol: Total RNA were amplified and labeled using the Whole Transcript (WT) Sense Target Labeling Protocol.

growth_protocol: The STAV-AB malignant mesothelioma cells stably overexpressing full-length syndecan-1, or the EGFP vector were cultured for about 36 hours.

extract_protocol: Total RNA was isolated from sub-confluent cell cultures, using the High Pure RNA isolation Kit (Roche, Mannheim, Germany), with optional on-column DNase1 digestion, according to the supplied protocol.

tag: gene modulation status

value: syndecan-1 overexpressing


title: pEGFP vector control cells 1

value: vector control


title: Experimental_3

status: Public on Jul 15 2010

city: Toledo

first: Bina

last: Joe

state: OH

address: 3000 Arlington avenue

department: Physiology and Pharmacology

institute: University of toledo

description: Affymetrix Rat Genome 230 2.0 Array

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Rat Genome 230 2.0 Array.

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

data_processing: Sample data tables have MAS5 data. The data were further analyzed with R statistical package (version 2.8.1).

source_name: S.R(9)x3x2Bx1x8 Congenic Rat Kidney fed with High-salt (2%) diet

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: All rats born on the same day were selected and weaned at 30 days of age.

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

treatment_protocol: After weaning all rats were fed with High-salt (2%) diet (Harlan Teklad diet TD 7034; Harlan–Sprague-Dawley).

value: Kidney

tag: genotype

value: S.R(9)x3x2Bx1x8 Congenic rat with Dahl S background

value: 53 days old


title: Syndecan-1 overexpressing cells 2


title: pEGFP vector control cells 2


title: Syndecan-1 overexpressing cells 1


title: Experimental_1

description: Affymetrix Rat Genome 230 2.0 Array


title: control_2

description: Affymetrix Rat Genome 230 2.0 Array

source_name: Dahl S Rat fed with High-salt (2%) diet

value: Dahl salt sensitive rat


title: pEGFP vector control cells 3


title: control_3

description: Affymetrix Rat Genome 230 2.0 Array


title: control_1

description: Affymetrix Rat Genome 230 2.0 Array


title: CDEP biological rep 2

status: Public on Jul 10 2010

city: carrboro

first: Tina

last: Stevens

state: NC

address: 138 marlowe ct

institute: UNC

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on Mouse 430A gene chips. 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: Expression file creator in Gene Pattern was used to normalize cel files using the RMA method with quantile normalization, background correction, and median scaling

source_name: mouse lung, 18 hrs after 2nd CDEP intranasal exposure

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

extract_protocol: RNA from frozen lung tissue was isolated using Rneasy (Qiagen, Valencia,CA) following manufacture's protocol.

tag: strain

value: BALB/C

value: 8-10 weeks old

value: lung

tag: sensitized

value: no


title: CDEP biological rep 3

tag: age


title: ADEP biological rep 3

source_name: mouse lung, 18 hrs after 2nd ADEP intranasal exposure


title: T7p_rep1_a1

city: New York

first: Andrew

middle: J

last: Sharp

address: 1425 Madison Avenue

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

description: Turner syndrome with single paternally derived chromosome X

hyb_protocol: Roche Nimblegen hybridization protocol

scan_protocol: scanned on an G2565 Agilent scanner at 5 microm resolution.

data_processing:
Array images were analysed using NimbleScan v2.5 software (Roche NimbleGen, Madison WI, USA) with default parameters incorporating spatial correction. The probe log2 ratios were subsequently quantile normalized and potential outliers were replaced by the median probe intensity of four neighboring probes.
We have performed 2 analyses with 2 sets of samples, 12 and 11 samples each, but 6 samples are in common to both analyses. Since there is a step of quantile normalization, for these 6 samples we have 2 different highly correlated (rho=0.99) normalized values that have been used for the 2 different analyses.

label_protocol: immunoprecipitated DNA was labelled by random priming using Cy5-conjugated random nonamers (TriLink BioTechnologies, San Diego CA, USA)

extract_protocol: The DNAs were isolated by a custom salt/ethanol precipitation method from peripheral blood samples. Briefly, erythrocytes were lysed in a hypotonic buffer, and white cells pelleted by precipitation. The cell pellet was incubated with Proteinase K and SDS overnight to remove proteins, and DNA precipitated with salt and ethanol. The DNA pellet was washed and resuspended in TE buffer.

treatment_protocol: 15microg of DNA was sonicated to generate fragments 200-800bp in size (Branson 450D Sonifier, Danbury, CT, USA), incubated with 10microg of anti 5-methyl cytidine (Diagenode, Liege, Belgium), immunoprecipitated using Protein A sepharose beads (Life Technologies, Carlsbad CA, USA), and purified by phenol:chloroform extraction.

tag: fraction

value: meDIP

tag: cell type

value: peripheral blood

tag: disease state

label_protocol: input DNA was labelled by random priming using Cy3-conjugated random nonamers (TriLink BioTechnologies, San Diego CA, USA)

value: sonicated DNA


title: ADEP biological rep 2


title: T6p_rep2_a2

value: Turner syndrome with single paternally derived chromosome X

treatment_protocol: 15microg of DNA was sonicated to generate fragments 200-800bp in size (Branson 450D Sonifier, Danbury, CT, USA)


title: Experimental_2

description: Affymetrix Rat Genome 230 2.0 Array


title: T6p_rep2_a1


title: T7p_rep2_a1


title: T4m_rep1_a1

description: Turner syndrome with single maternally derived chromosome X


title: T4m_rep1_a2

value: Turner syndrome with single maternally derived chromosome X


title: FS3_rep1_a2

description: normal female

value: normal female


title: T6p_rep1_a1


title: T5p_rep1_a1


title: FS2_rep2_a2

description: normal female


title: T1m_rep2_a1


title: FS1_rep1_a2

description: normal female


title: T1m_rep2_a2


title: NDEP biological rep 2

source_name: mouse lung, 18 hrs after 2nd NDEP intranasal exposure

value: female


title: CDEP biological rep 1


title: NDEP biological rep 1


title: FS2_rep1_a2

description: normal female


title: FS1_rep2_a2

description: normal female


title: NDEP biological rep 3


title: Saline biological rep 2

source_name: mouse lung, 18 hrs after 2nd saline intranasal exposure


title: Saline biological rep 3


title: T1m_rep1_a2


title: T2m_rep2_a2


title: T7p_rep1_a2


title: CDEP/OVA biological rep 3

source_name: mouse lung, 18 hrs after 2nd CDEP/OVA intranasal exposure

value: yes


title: T1m_rep1_a1


title: CDEP/OVA biological rep 2


title: ADEP/OVA biological rep 3

source_name: mouse lung, 18 hrs after 2nd ADEP/OVA intranasal exposure


title: T2m_rep1_a1


title: T3m_rep2_a1


title: CDEP/OVA biological rep 1


title: NDEP/OVA biological rep 3

source_name: mouse lung, 18 hrs after 2nd NDEP/OVA intranasal exposure


title: ADEP/OVA biological rep 2


title: Saline biological rep 1


title: T3m_rep1_a1


title: NDEP/OVA biological rep 1


title: NDEP/OVA biological rep 2


title: Saline/OVA biological rep 3

source_name: mouse lung, 18 hrs after 2nd OVA intranasal exposure


title: ADEP/OVA biological rep 1


title: Saline/OVA biological rep 1


title: Saline/OVA biological rep 2


title: ADEP biological rep 1


title: RNA4_v_gDNA

status: Public on Jul 06 2010

type: mixed

city: Boston

first: Alex

middle: M

last: Tsankov

state: MA

address: 155 Bay State

institute: MIT

hyb_protocol: Standard Agilent protocols for Agilent Custom Oligo Microarray 8x15K G4427A

scan_protocol: Arrays were scanned using an Agilent scanner and analyzed with Agilent’s feature extraction software version 10.5.1.1.

data_processing: For each probe, the median signal intensities were background subtracted for both channels and combined by taking the log2 of the Cy3 to Cy5 channel ratio. To estimate the absolute expression values for each gene, we took the median of the log2 ratios across all probes. The experiments were highly reproducible; most biological replicates correlated at R = 0.99 and replicates with R < 0.95 were removed.

organism: Saccharomyces paradoxus

label_protocol: Indirect total RNA labeling

growth_protocol: Overnight cultures for each species were grown in 450ml of media at 220 RPM in a New Brunswick Scientific air-shaker at 30°C until reaching mid log-phase.

extract_protocol: Qiagen Yeast RNA extraction

treatment_protocol: 50 ml of the culture were transferred to a 50 ml conical and spun down immediately. The isolated cell pellets were then placed in liquid nitrogen, stored at -80°C, and were later archived in RNAlater for future RNA extraction.

label_protocol: Genomic DNA samples were labeled with Cy5 using a modification of the protocol developed by Joe Derisi (UCSF) and Rosetta Inpharmatics (Kirkland, WA) that can be obtained at www.microarrays.org.

extract_protocol: Genomic DNA was isolated using Genomic-tip 500/G (Qiagen) using the provided protocol for yeast.  DNA samples were sheared using Covaris sonicator to 500-1000 bp fragments, as verified using DNA 7500 and DNA 12000 kit for the Bioanalyzer 2100 (Agilent).


title: RNA1_v_gDNA

organism: Nakaseomyces glabratus

value: CLIB 138


title: RNA2_v_gDNA


title: RNA4_v_gDNA


title: RNA3_v_gDNA


title: RNA2_v_gDNA


title: T2m_rep2_a1


title: RNA1_v_gDNA


title: RNA4_v_gDNA

description: 252035410010_200812171227_S01_GE2-v5_10_Apr08_1_4

organism: Kluyveromyces lactis

treatment_protocol: 50 ml of the culture were transferred to a 50 ml conical and spun down immediately.  The isolated cell pellets were then placed in liquid nitrogen, stored at -80°C, and were later archived in RNAlater for future RNA extraction.

value: CLIB 209


title: RNA2_v_gDNA

description: 252035410010_200812171227_S01_GE2-v5_10_Apr08_1_2


title: RNA3_v_gDNA

description: 252035410010_200812171227_S01_GE2-v5_10_Apr08_1_3


title: RNA1_v_gDNA

description: 252035410010_200812171227_S01_GE2-v5_10_Apr08_1_1


title: RNA2_v_gDNA

description: 252035510011_200812171233_S01_GE2-v5_10_Apr08_1_2

organism: Candida albicans


title: RNA3_v_gDNA

description: 252035510011_200812171233_S01_GE2-v5_10_Apr08_1_3


title: RNA2_v_gDNA

description: 252047510008_200811251038_S01_GE2-v5_10_Apr08_2_2

organism: Saccharomyces bayanus


title: RNA4_v_gDNA

description: 252047510008_200811251038_S01_GE2-v5_10_Apr08_2_4


title: RNA4_v_gDNA

description: 252035510011_200812171233_S01_GE2-v5_10_Apr08_1_4


title: RNA3_v_gDNA

description: 252047510008_200811251038_S01_GE2-v5_10_Apr08_2_3


title: RNA1_v_gDNA

description: 252035510011_200812171233_S01_GE2-v5_10_Apr08_1_1


title: RNA4_v_gDNA

description: 252047410008_200902051036_S01_GE2-v5_10_Apr08_2_4

organism: Saccharomyces mikatae


title: RNA4_v_gDNA

organism: Lachancea kluyveri NRRL Y-12651


title: RNA1_v_gDNA


title: RNA3_v_gDNA


title: RNA3_v_gDNA

description: 252047410008_200902051036_S01_GE2-v5_10_Apr08_2_3


title: RNA1_v_gDNA

description: 252047510008_200811251038_S01_GE2-v5_10_Apr08_2_1


title: RNA2_v_gDNA


title: RNA2_v_gDNA

description: 252047410008_200902051036_S01_GE2-v5_10_Apr08_2_2


title: RNA1_v_gDNA

description: 252047410008_200902051036_S01_GE2-v5_10_Apr08_2_1


title: RNA4_v_gDNA

description: 252035310009_200812171241_S01_GE2-v5_10_Apr08_1_4

organism: Naumovozyma castellii


title: RNA3_v_gDNA

description: 252035310009_200812171241_S01_GE2-v5_10_Apr08_1_3


title: Nestin2

city: Bronx

last: Frenette

address: 1301 Morris Park Avenue

institute: Albert Einstein College of Medicine

hyb_protocol: Standard Affymetrix protocol using Affymetrix GeneChips Exon 1.0 ST Array for the mouse.

scan_protocol: Standard Affymetrix protocol using a GeneChip System (Affymetrix) including an Agilent Scanner.

data_processing: The raw data were first processed using the Affymetrix Expression Console V.1.1. Data were normalized using RMA and exported as text files. Following the normalization step, the probes were matched to genes IDs for each chip using the associated reference annotation files published on the Affymetrix website.

source_name: Nestin bone-marrow GFP+ cells

label_protocol: The cDNA was fragmented and labelled with the FL-Ovation cDNA Biotin Module V2 (NuGen Technologies).

growth_protocol: Freshly isolated bone marrow-derived GFP+ cells.

extract_protocol: RNA samples from FACS-sorted cells were obtained using the RNAdvance Cell kit (Agencourt), amplified with the WT-Ovation Pico RNA amplification system and converted to sense transcripts using the WT-Ovation Exon Module (NuGen Technologies).

value: bone marrow-derived GFP+

tag: genotype/variation

value: GFP expression is regulated under the nestin gene promoter


title: RNA4_v_gDNA

description: 252047310008_200902201341_S01_GE2-v5_10_Apr08_1_4

organism: Lachancea waltii

value: NCYC 2644


title: RNA3_v_gDNA

description: 252047310008_200902201341_S01_GE2-v5_10_Apr08_1_3


title: RNA5_v_gDNA

description: 251507210476_200902111217_S01_GE2-v5_10_Apr08_1_2

hyb_protocol: Standard Agilent protocols for Agilent-015072 Yeast Oligo Microarray 4x44K G2519F


title: RNA4_v_gDNA

description: 251507210476_200902111217_S01_GE2-v5_10_Apr08_1_1


title: RNA2_v_gDNA

description: 252035310009_200812171241_S01_GE2-v5_10_Apr08_1_2


title: RNA1_v_gDNA

description: 252035310009_200812171241_S01_GE2-v5_10_Apr08_1_1


title: RNA3_v_gDNA

description: 251507210457_200810221545_S01_GE2-v5_10_Apr08_1_2


title: Nestin3


title: RNA1_v_gDNA

description: 252047310008_200902201341_S01_GE2-v5_10_Apr08_1_1


title: RNA4_v_gDNA

organism: Yarrowia lipolytica

value: CLIB 89


title: RNA2_v_gDNA

description: 252047310008_200902201341_S01_GE2-v5_10_Apr08_1_2


title: RNA1_v_gDNA

organism: Debaryomyces hansenii

value: NCYC 2572


title: RNA4_v_gDNA


title: Nestin1


title: RNA2_v_gDNA


title: RNA1_v_gDNA

description: 251507210456_200810221545_S01_GE2-v5_10_Apr08_1_2

organism: Saccharomyces cerevisiae


title: RNA2_v_gDNA

description: 251507210457_200810221545_S01_GE2-v5_10_Apr08_1_1


title: RNA3_v_gDNA


title: RNA1_v_gDNA


title: RNA3_v_gDNA


title: shrna_series-GFP+shtop

status: Public on Jul 04 2010

city: Charlestown

first: Martin

last: Aryee

address: 149 13th Street

department: Pathology

institute: Massachusetts General Hospital

description: sh-TOP2B vector transfection and androgen deprivation.

hyb_protocol: Samples were hybridized to HG-U133 2.0 Plus whole genome gene expression microarrays (Affymetrix) according to the manufacturer’s protocols at the Johns Hopkins Microarray facility.

scan_protocol: HG-U133 2.0 Plus whole genome gene expression microarrays (Affymetrix) were scanned on the Affymetrix GeneChip Scanner 3000 7G at the Johns Hopkins Microarray facility

data_processing: Data from all microarrays were preprocessed in a single batch using RMA.

organism: Homo sapiens

source_name: LNCaP cells - GFP + TOPO2B shRNA

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

growth_protocol: LNCaP cells were propagated in RPMI medium supplemented with 10% fetal bovine serum ( = steady state). In order to deplete cells of basal androgens, all cells were washed with serum-free medium 3 times for 1 h and incubated in 5% charcoal-stripped FBS containing medium for 48 h prior to experiments.

extract_protocol: Total RNA was extracted from cell lines using a RNeasy RNA extraction kit (Qiagen, Valencia, CA).

treatment_protocol: For sh-RNA knockdown experiments LNCaP cells were transfected with GFP expression vectors encoding shRNA specific to TOP2Β (sh-TOP2Β) or sh-control, deprived of androgen and then treated with DHT (100 nM) or vehicle control for 16 h. GFP positive cells were collected by FACS sorting and subjected to microarray analysis. For inhibitor experiments LNCaP cells were androgen-deprived (control), subsequently stimulated with 100 nM DHT for 16 h (DHT), or pretreated with 100 μM etoposide (DHT+ET) or 100 μM merbarone (DHT+Mer) for 2 h prior to DHT stimulation.

value: LNCaP

tag: protocol

value: TOPO2B knockdown and androgen deprivation


title: shrna_series-GFP+shtop+DHT

description: sh-TOP2B vector transfection and androgen deprivation followed by DHT stimulation for 16 h.

source_name: LNCaP cells - GFP + DHT + TOPO2B shRNA

tag: agent

value: DHT


title: shrna_series-GFP+DHT

description: sh-control vector transfection and androgen deprivation followed by DHT stimulation for 16 h.

source_name: LNCaP cells - GFP + DHT

value: control transfection and androgen deprivation


title: RNA2_v_gDNA


title: inhibitor_series-DHT+ET

description: Androgen deprivation and etoposide 100 μM preterated (2 h) followed by DHT treatment (16 h).

source_name: LNCaP cells - DHT + Etoposide

value: androgen deprivation + Etoposide


title: inhibitor_series-DHT+MER

description: Androgen deprivation and merbarone 100 μM preterated (2 h) followed by DHT treatment (16 h).

source_name: LNCaP cells - DHT + Merbarone

value: androgen deprivation + Merbarone


title: inhibitor_series-control

description: Androgen deprivation.

source_name: LNCaP cells -  serum starved

value: androgen deprivation


title: leaf Col-0 rep2

status: Public on Jul 03 2010

city: Shanghai

first: Lin

last: XU

address: 300 Fenglin Road

department: Chinese Academy of Sciences

country: China

institute: Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences

description: Col refers to Col-0

hyb_protocol: Fragmentation of the labeled aRNA prepares the target for hybridization to GeneChip® 3’ expression arrays with GeneChip® hybridization oven 640.

scan_protocol: Wash and stain the arrays with GeneChip® fluidics station 450, Scan the arrays with the GeneArray scanner 3000 by the GeneChip® Operating  Software (GCOS) or Command Console® (AGCC) Software.

data_processing: RMA data were obtained by using Partek GS 6.4.

organism: Arabidopsis thaliana

label_protocol: In Vitro Transcription to Synthesize Biotin-Modified aRNA with IVT Labeling Master Mix generates multiple copies of biotin-modified aRNA from  the double-stranded cDNA templates; this is the amplification step.aRNA Purification removes unincorporated NTPs, salts, enzymes, and  inorganic phosphate to improve the stability of the biotin-modified aRNA.

growth_protocol: 16 h light, 8 h dark, 21°C

extract_protocol: Extract and purify the total RNA by the Qiagen RNeasy Mini Kit.Reverse Transcription to Synthesize First-Strand cDNA is primed with  T7 oligo(dT) primer to synthesize cDNA containing a T7 promoter sequence.Second-Strand cDNA Synthesis converts the single-stranded cDNA into  a double-stranded DNA (dsDNA) template for transcription. The reaction employs DNA polymerase and RNase H to simultaneously degrade the RNA  and synthesize second strand cDNA.

treatment_protocol: no treatment

tag: tissue

value: leaf

tag: genetic background

value: wild type


title: leaf Col-0 rep3

description: Col refers to Col-0


title: inhibitor_series-DHT

description: Androgen deprivation followed by DHT (100 nM) treatment for 16 h.

source_name: LNCaP cells - DHT treated


title: shrna_series-GFP

description: sh-control vector transfection and androgen deprivation.

source_name: LNCaP cells - GFP only


title: leaf rlt1-1rlt2-1 rep2

description: 3a3B refers to rlt1-1 rlt2-1

source_name: rlt1-1 rlt2-1

value: rlt1-1 rlt2-1


title: leaf rlt1-1rlt2-1 rep1

description: 3a3B refers to rlt1-1 rlt2-1


title: leaf rlt1-1rlt2-1 rep3

description: 3a3B refers to rlt1-1 rlt2-1


title: Mature crab testis Replicate 2

status: Public on Jul 01 2010

city: Xiamen

first: zou

last: zhihua

state: Fujian

address: NO.43 Yindou road

department: Fishry college

institute: Jimei University

description: Dye-swaps 2 of 2

hyb_protocol: The cyt3/cyt5 probe mixture was resuspended in a pre-warmed 68°C solution containing 8 µL of 1.5 mM EDTA and 32 µl of SlideHyb™ Glass Array Hybridization Buffer #2 by pipeting. This probe mixture was heated at 95 °C for 3 min then hybridized on an array prewarmed at 70 °C under a 22 • 40 mm2 coverslip (Corning Inc., Corning, NY) in a light protected and humidified hybridization chamber (Corning Inc.). Samples were hybridized for 18–24 h at 65 °C in a water bath. The hybridized array was washed once with 2 x SSC, 0.1% SDS; and once with 0.2 x SSC for 10 min at 37°C. Slides were then washed.

scan_protocol: Scanned at 635 nm (cyt5) and 535 nm (cyt3) on a ScanArray Lite (Packard BioChip Technologies, Billerica, MA, USA) Images were quantified using Scanarray Express3.0 (PerkinElmer Life Sciences).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Scanarray Express3.0 software was used.

organism: Scylla paramamosain

source_name: testis

label_protocol: 10μg of total RNA of each sample from mature testis and ovary was treated with DNase I to remove remaining trace amounts of DNA at room temperature for 15 min, after stopping the activity of DNase I by adding 2 μL of 15mM EDTA, mixed with 4 μL Random Hexamer primers (3mg/mL, Invitrogen) in RNase free water (final volume of 37 μL) and incubation at 70℃ for 2 min. The tubes were cooled on ice for 2 min and 6 L of 0.1 M DTT, 12 μL of 5X 1st strand buffer; 1.2 μL 50X aminoallyl-dNTP mix were added to each tube. The tubes were incubated at 42℃ for 2 min and 4 μL of Superscriptase II was added followed by further incubation at 42 ℃ for overnight. Labeling reactions were terminated and RNAs were degraded by adding 20 μL of 1 M NaOH and 20 μL of 0.5 M EDTA to each tube, which was then held at 65 ℃ for 15 min. The reaction mixtures were neutralized by adding 20 μL of 1 M HCl, prior to purification with Qiagen PCR purification kit (Qiagen Corp, Valencia, CA). For purification, the cDNA reaction was added with 600 μL (5X reaction volume) buffer PB and transferred to a QIAquick column. The column was placed in a 2 mL collection tube and centrifuged at ~13,000 rpm for 1 min followed by washed with 750 μL phosphate buffer. The wash and centrifugation step of the collection tube was repeated once. 30 μL of phosphate elution buffer was applied to the center of the column membrane. After incubation for 1 min. at room temperature, the probes were eluted by centrifugation at ~13,000 rpm for 1 min. 30 μL of phosphate elution buffer was added to elute labeling products again. The final elution volume was ~60 μL. The eluted solution was mixed by pipeting. The eluted aminoallyled cDNA was separate equally into two different tubes labeled as cyt3 and cyt5.  Samples were then dried in a speed vac. The dried aminoallyl-labeled cDNA was resuspended in 4.5 μL 0.1 M sodium carbonate buffer (Na2CO3) with a pH of 9.0. 4.5 μL of the NHS-ester cyt3 dye and cyt5 dye was added to the tubes labeled as cyt3 and cyt5 separately. The solution was incubated for 1 hour in the dark at room temperature (~20oC). To end the reaction, 35 μL of 100 mM NaOAc pH 5.2 and 250 μL (5X reaction volume) of Buffer PB (Qiagen) were added to the solution. The solution was then applied to a QIAquick spin column placed in a 2 mL collection tube (Qiagen). The column was centrifugated at ~13,000 for 1 min to bind labeled cDNA onto column. 0.75 mL of Buffer PE (Qiagen) was added to the column and centrifuge at ~13,000 for 1 min to wash the column. The column was transferred to a new collection tube and centrifuged for an additional 1 min at maximum speed. The washed column was then placed into a clean 1.5 mL microfuge tube. 30 μL of Buffer EB (Qiagen) was carefully added to the center of the column membrane. After incubation for 1 min at room temperature, the labeled cDNA was eluted by centrifugation at ~13,000 rpm for 1 min. In order to increase the yield, each column was eluted twice. The final elution volume of labeled cDNA was ~60 μL.

extract_protocol: Total RNA extracted using homemade RDP reagent following Trizol‘s manufacturer's instructions

tag: development stage

value: Mature

source_name: ovary


title: leaf Col-0 rep1

description: Col refers to Col-0


title: F11_FSK24h_rep1

city: Amsterdam

first: Harold

last: MacGillavry

address: De Boelelaan 1087

department: Center for neurogenomics and cognitive research

institute: Vrije Universiteit

description: gene expression data of regenerating dorsal root ganglion neurons

hyb_protocol: According to manufacturers instructions.

scan_protocol: Agilent scanner

data_processing: The data were analyzed with the R packages 'bioconductor' and 'limma'. Raw spot intensities were background corrected using Edwards method and loess normalized within arrays.

organism: Rattus norvegicus

source_name: F11 neuroblastoma cells

label_protocol: Agilent labeling kit, according to manufacturers instructions.

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

tag: reference

value: F11 cells, no forskolin

tag: time point

tag: replicate

value: 10µM forskolin


title: BRD7 shRNA 2 expressing BJ cells untreated vs control

first: Anna

middle: E

last: Burrows

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

hyb_protocol: Samples were hybridized using Agilent 10x blocking agent and 25x fragmentation buffer, and 2xGEx hybridization buffer according to the manufacturer's instructions (Agilent Two-Color Gene Expression Array) for 17 hours at 65C.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction

source_name: Primay middle passage human BJ fibroblasts stably expressing BRD7 shRNA from the MSCV-mir30 based expression vector

label_protocol: 1.5ug of total RNA were harvested and primed and labeled using the QuickAmp Labeling Kit (Agilent) according to the manufacturer's instructions, using T7 priming and MMLV-RT to generate cDNA. cRNA is then prepared using T7 RNA Polymerase according to the manufacturer's instructions, and labeled with either cyanine 3-CTP (Cy3) or cyanine-5-CTP (Cy5).

growth_protocol: BJ  fibroblasts were grown in DMEM media (invitrogen) with 15% FBS under low oxygen (3%) conditions. Mid-passage BJs (approximately PD 45) were infected with retroviruses expressing either FF2 control shRNA or BRD7 shRNAs from an MSCV-mir30 shRNA expression vector and were selected for 5 days with 1ug/ml puromycin (Clontech).

extract_protocol: Total RNA was harvested using an RNAeasy Mini Kit according to the manufacturer's instructions (Qiagen).

treatment_protocol: Cells were either untreated or treated with 8uM nutlin-3a (Cayman Chemicals) for 8 hours and then harvested.

value: human foreskin BJ fibroblasts

source_name: Primay middle passage human BJ fibroblasts stably expressing control FF2 shRNA from the MSCV-mir30 based expression vector


title: F11_FSK24h_rep2


title: F11_FSK48h_rep1


title: F11_FSK48h_rep2


title: BRD7 shRNA 1 expressing BJ cells untreated vs control


title: F11_FSK4h_rep3


title: F11_FSK48h_rep3


title: F11_FSK4h_rep1


title: F11_FSK24h_rep3


title: F11_FSK2h_rep3


title: BRD7 shRNA 2 expressing BJ cells treated with nutlin-3a for 8 hours vs control

source_name: Primay middle passage human BJ fibroblasts stably expressing BRD7 shRNA from the MSCV-mir30 based expression vector treated with 8uM nutlin-3a for 8 hours

source_name: Primay middle passage human BJ fibroblasts stably expressing control FF2 shRNA from the MSCV-mir30 based expression vector treated with 8uM nutlin-3a for 8 hours


title: inhibitor_series-steadystate

description: LNCaP cells grown in RPMI supplemented with 10% FBS.

source_name: LNCaP cells -  steady state

tag: cell line

value: steady state


title: F11_FSK4h_rep2


title: F11_FSK2h_rep1


title: F11_FSK2h_rep2


title: Mature crab testis Replicate 1

description: Dye-swaps 1 of 2


title: Mature crab ovary Replicate 2

description: Biological replicate 2 of 3.


title: Mature crab ovary Replicate 1

description: Biological replicate 1 of 3.


title: Mature crab ovary Replicate 3

description: Biological replicate 3 of 3.


title: SK-N-AS_24hrs_HZ4

city: Liverpool

first: Stuart

last: Gillies

address: Crown Street

department: Physiology

country: United Kingdom

institute: University Of Liverpool

hyb_protocol: 20 ug of fragmented, biotinylated cRNA were hybridized for 16hrs at 45OC on an Affymetrix GeneChip Human Genome U133 Plus 2.0 Array.  GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Arrays were scanned with an Affymetrix Scanner 3000

data_processing: The image data was analysed using Affymetrix GCOS software

source_name: 24hrs treatment of SK-N-AS cells with HZ4 expression construct

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3.3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: SK-N-AS cells cultures in DMEM's solution containing 10% FBS, 1% Pen/Strep, 1% NEAA, 1% 200mM L-Glutamine. Incubated at 37OC, with 5% CO2.

value: human neuroblastoma cells

value: SK-N-AS

tag: time

tag: expression

value: truncated NRSF


title: SK-N-AS_0hrs_UNTREATED

source_name: 0hrs untreated SK-N-AS cells


title: SK-N-AS_0hrs_HZ4

source_name: 0hrs baseline control treatment of SK-N-AS cells with HZ4 expression construct


title: SK-N-AS_24hrs_RE-EX1

source_name: 24hrs treatment of SK-N-AS cells with RE-EX1 expression construct

value: full length NRSF


title: SK-N-AS_24hrs_UNTREATED

source_name: 24hrs untreated SK-N-AS cells


title: SK-N-AS_48hrs_HZ4

source_name: 48hrs treatment of SK-N-AS cells with HZ4 expression construct


title: SK-N-AS_48hrs_UNTREATED

source_name: 48hrs untreated SK-N-AS cells


title: SK-N-AS_0hrs_RE-EX1

source_name: 0hrs baseline control treatment of SK-N-AS cells with RE-EX1 expression construct


title: SK-N-AS_48hrs_RE-EX1

source_name: 48hrs treatment of SK-N-AS cells with RE-EX1 expression construct


title: Double deletion reapply RPL12A, biological rep1

city: Taipei

first: yu-chen

last: Huang

address: Academia Sinica. 128 Sec. 2

country: Taiwan

institute: Institute of Molecular Biology

description: Gene expression data from 6EA1+RPL12A in early log phase

hyb_protocol: Following fragmentation, 11 ug of cRNA were hybridized for 16.5 hr at 45℃ with GeneChip (Yeast 2.0). Washing and staining were done in the Affymetrix GeneChip Fluidics Station-450.

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

data_processing: 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 500.

source_name: Total RNA from 6EA1+RPL12A

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (GeneChip Expression Analysis Technical Manual rev5, Affymetrix).

growth_protocol: Yeast cells were cultured in YNPD (0.67% yeast nitrogen base without amino acids and 2% glucose) medium supplemented with  appropriate nutritional requirements at 40mg/liter at 30℃ to 0.5-0.6 A600 unit.

extract_protocol: Total yeast RNAs were extracted from whole cells with phenol-chloroform according to Del Aguila et al. [BMC Mol Biol, 6, 9 (2005)].

tag: culture

value: early log phase (0.5~0.6 A600 unit)

tag: genotype

value: RPL12A  RPL12B double deletion and high copy RPL12A


title: Wildtype, biological rep1

description: Gene expression data from W303 in early log phase

source_name: Total RNA from W303


title: RPL12 double deletion, biological rep2

description: Gene expression data from 6EA1 in early log phase

source_name: Total RNA from 6EA1

value: RPL12A  RPL12B double deletion


title: Double deletion reapply RPL12B, biological rep1

description: Gene expression data from 6EA1+RPL12B in early log phase

source_name: Total RNA from 6EA1+RPL12B

value: RPL12A  RPL12B double deletion and high copy RPL12B


title: Double deletion reapply RPL12B, biological rep2


title: Wildtype, biological rep2


title: double knock-out_rep 2

city: Portland

first: Grover

middle: C

last: Bagby

state: OR

address: 3181 SW Sam Jackson Park Rd.

department: Dept. of Medicine

institute: Oregon Health & Science University

hyb_protocol: The arrays were hybridized in a GeneChip Hybridization Oven 640 (Affymetrix, Santa Clara, CA) for 16 hours at 45⁰C, followed by washing, staining with streptavidin-phycoerythrin (SAPE; Molecular Probes, Eugene, OR), signal amplification with biotinylated anti-streptavidin antibody (Vector Labs, Burlingame, CA), and a final staining with SAPE. The staining and washing were performed using GeneChip Fluidic Station 400s (Affymetrix, Santa Clara, CA) running standard Affymetrix fluidics script, EukGE_WSv5 450.

scan_protocol: The distribution of fluorescent material on the processed array was determined using the Affymetrix GeneChip Scanner 3000 with AutoLoader. The array image scan was processed using Affymetrix GeneChip Operating Software (GCOS) v. 1.2, which employs the Microarray Suite, version 5.0 (MAS 5.0) algorithm.  Image processing resulted in the generation of raw, probe level data in the CEL file format.

data_processing: The data were processed by GeneSifter (Seattle, WA) and Partek Genomic Suite (Partek, Inc, St. Louis, MO) software using Robust Multichip Analysis (RMA) that includes a background correction, quantile normalization, and median polish as summarization.

organism: Mus musculus

source_name: unfractionated bone marrow

label_protocol: Each total RNA sample was labeled and amplified following the recommended protocol in the Affymetrix GeneChip Expression Analysis Technical Manual, rev.3 (http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf). Using 2 µg of total RNA as input for all samples (with the exception of sample 09A-11H1H_FAGKO3_216GB.CEL, which used 0.91 µg of total RNA), messenger RNA was amplified and labeled in two steps. In the first step, mRNA was converted to double-stranded cDNA using Superscript Reverse Transcriptase (Invitrogen, Carlsbad, CA, USA) and an oligo-dT primer linked to a T7 RNA polymerase binding site sequence (IDT, Coralville, IA). Double-stranded cDNA was purified by phenol-chloroform-isoamyl alcohol extraction and a standard ethanol precipitation. In the second step, the cDNA was converted to labeled cRNA (the target) using T7 RNA polymerase in the presence of biotinylated UTP and CTP (Enzo, Farmingdale, NY). Unincorporated nucleotides were removed using the RNeasy Mini kit (Qiagen) and was followed by an ethanol precipitation of the labeled target. The target was fragmented to produce a uniform distribution of short cRNAs. 10µg each of fragmented target was combined with hybridization control oligomer (Affymetrix, Santa Clara, CA) and control cRNAs (1.5pM BioB, 5.0pM BioC, 25pM BioD, and 100pM Cre; Affymetrix, Santa Clara, CA), in hybridization buffer and applied to the array.

extract_protocol: Unfractionated bone marrow cells were flushed from the tibial and femoral cavities into phosphate buffered saline containing 0.1% bovine serum albumin. Total RNA was then extracted using the Rneasy Mini kit (Qiagen, Inc.)

value: Double Fancc-/-//Fancg-/-


title: Fancc-/-_rep 1

value: Fancc-/-


title: FGF-10, EB Day2

city: Tainan

first: Vivienne

middle: HJ

last: Lee

address: No.100, Daxue Rd., East Dist., Tainan City 701, Taiwan (R.O.C.)

department: Institute of Clinical Investigation

institute: National Cheng Kung University

description: Expression data-FGF-10-differentiation medium plus FGF-10 recombinant protein (100ng/ml)

hyb_protocol: 11ug labeled samples were hybridized to GeneChip* at 45℃ for 16.5 hours.

scan_protocol: The wash and staining were performed by Fluidic Station-450 and the the GeneChip* were scanned with Affymetrix GeneChip Scanner 7G.

data_processing: The data was first analyzed, globly normalized, and backup correction with MAS 5.0 provied by Affymetrix and the Scale Factor is 2.798.

source_name: Embryoid bodies formed from hanging drops

label_protocol: 10ug total RNA were used for cDNA synthesis, labeled by in vitro transcription followed by fragmentation following the manufactory’s suggestion (GeneChip Expression Analysis Technical Manual rev5, Affymetrix).

growth_protocol: ES cells were cultured without feeder cells in GMEM (Glasgow Minimum Essential Medium) supplemented with pyruvate, non-essential amino acids, 2-mercaptoethanol, 10% ES cell fetal bovine serum, and leukemia inhibitory factor (LIF)

extract_protocol: RNA was extracted from EBs on day 2 by using Trizol reagent (Invitrogen Carlsbad, CA) according to the manufacturer`s protocol.

treatment_protocol: Embryoid bodies were formed by hanging drops and then suspended in differentiation medium on day 2 with recombinant proteins (100 ng/ml)

value: CGR8 ES cells

tag: strain

value: 100 ng/ml FGF10


title: Fancc-/-_rep 3


title: double knock-out_rep 1


title: RPL12 double deletion, biological rep1


title: Fancg-/-_rep 1

value: Fancg-/-


title: Fancg-/-_rep 2


title: wild-type_rep 1

value: wild type


title: wild-type_rep 3


title: double knock-out_rep 3


title: Fancg-/-_rep 3


title: Fancc-/-_rep 2


title: Double deletion reapply RPL12A, biological rep2


title: wild-type_rep 2


title: Control, EB Day2

description: Expression data-control-differentiation medium only