title: Menadione (5uM) rep 1

city: Newcastle

first: Alexander

middle: Peter

last: Sobinoff

address: University Drive

department: Science and IT

institute: University of Newcastle Australia

hyb_protocol: Samples that pass QC check are then prepared for hybridisation to the Mouse 430 version 2.0 GeneChip by preparing a probe cocktail (cRNA @ 0.05ug/ul) that includes 1x Hybridisation Buffer (100mM MES, 1m NaCl, 20mM EDTA, 0.01% Tween-20), 0.1mg/ml Herring Sperm DNA, 0.5mg/ml BSA, and 7% DMSO. A total hybridisation volume of 300ul is prepared for each sample and 200ul loaded into a Mouse 430 version 2.0 GeneChip.  The chip is hybridised at 45C for 16 hours in an oven with a rotating wheel at 60rpm.  After hybridisation the chip is washed using the appropriate fluidics script in the Affymetrix Fluidics Station 450.

scan_protocol: Upon completion of the washing, the chips are then scanned using the Affymetrix GeneChip Scanner 3000.  The scanner operating software, GCOS, converts the signal on the chip into a DAT file, which will then be used for generating subsequent CEL and CHP files for analysis.

data_processing: The data were analyzed with Partek software  (Partek Genomics Suite) and were normalised using the Robust Multichip Average method using the DMSO treatment as a control.

source_name: Neonatal mouse ovaries cultured in Menadione (5uM)

label_protocol: Mouse total RNA was quality ascertained using the Agilent Bioanalyser 2100 using the NanoChip protocol.  A total of 7ug was labelled using the Affymetrix One Cycle cDNA synthesis kit (Millenium Sciences cat no. 900431).  The subsequent cDNA was cleaned using the Affymetrix GeneChip Sample Cleanup kit (Millenium Sciences cat no. 900371).  Upon cleaning of the cDNA the next step was to incorporate biotin into the resultant cRNA using the Affymetrix IVT labelling kit (Millenium Sciences cat no. 900449).  After the IVT process the labelled cRNA was cleaned using the above GeneChip Sample Cleanup kit. The quantity of product was ascertained using the Agilent Bioanalyser 2100 using the NanoChip protocol.  A total of 20ug of labelled cRNA was then fragmented to the 50-200bp size range and quality control checked using the Bioanalyser 2100 using the NanoChip protocol.

growth_protocol: Swiss neonates were sacrificed by CO2 inhalation followed by decapitation. Ovaries were excised, trimmed of excess tissue and placed on culture plate inserts in 6-well tissue culture plate wells floating atop 1.5ml DMEM/F12 medium containing 5% (v/v) fetal calf serum, 1mg/ml bovine serum albumin, 50µg/ml ascorbic acid, 27.5μg/ml insulin–transferrin–selenium, 2.5 mM glutamine and 5U/ml penicillin/streptomycin. Media were supplemented with 40 ng/ml basic fibroblast growth factor, 50 ng/ml leukemia inhibitory factor, and 25 ng/ml stem cell factor. Using fine forceps a drop of medium was placed over the top of each ovary to prevent drying. Ovaries were cultured for 4 days at 37°C and 5% CO2 in air, with media changes every two days.

extract_protocol: Total RNA was isolated from ovaries using two rounds of a modified acid guanidinium thiocyanate–phenol–chloroform protocol: washed cells resuspended in lysis buffer (4 M guanidinium thiocyanate, 25 mM sodium citrate, 0.5% sarkosyl, 0.72% β-mercaptoethanol). RNA was isolated by phenol/chloroform extraction and isopropanol precipitated.

treatment_protocol: Ovaries were treated with vehicle control medium (0.1% DMSO), VCD (50µM), MXC (50µM), or MEN (5µM). Xenobiotic culture concentrations were determined by pilot studies performed in our laboratory with the intention of inducing overt toxicity.

value: Swiss

value: Ovary

tag: agent

value: Menadione (5uM)

tag: replicate

value: Post natal day 3-13


title: Menadione (5uM) rep 2

status: Public on Aug 21 2010

type: RNA

state: NSW

country: Australia

label: biotin

molecule: total RNA

organism: Mus musculus

tag: strain

tag: tissue

tag: age

value: Post natal day 3-14


title: OP_3factor_1

city: Shinjuku

first: Yumi

last: Matsuzaki

state: Tokyo

address: 35 Shinanomachi

department: Physiology

country: Japan

institute: Keio University, School of Medicine

hyb_protocol: Samples were hybridized to a mouse Oligo Microarray (agilent) according to the manufacturer's protocol.

scan_protocol: Arrays were scanned with a G2565BA Microarray Scanner System (Agilent).

data_processing: Data were analysed using GeneSprings GX software (Agilent).

source_name: Bone marrow, OP (Osteo progenitor cell), infected Oct3/4, Sox2, and Klf4

label_protocol: Total RNA from ES cells, PαS cells, OB cells, TTF cells and iPS cells were labelled with Cy3.

extract_protocol: Total RNA was purified with Trizol (invitrogen) and treated with Turbo DNA-free kit (Ambion) to remove genomic DNA contamination.

value: Bone marrow

tag: cell source

value: OP (Osteo progenitor cell)


title: OP_3factor_2


title: Treatment-337

type: protein

city: Stanford

first: William

last: Robinson

state: CA

address: 269 Campus Dr

country: USA

institute: Stanford University

description: 1:200 dilution in PBS with 3% Fetal Bovine Serum

hyb_protocol: Synovial antigen arrays were produced using a robotic microarrayer to print peptides and proteins on ArrayIt SuperEpoxy microscope slides (TeleChem International, Sunnyvale, CA). On each slide, antigens are printed at 0.2 mg/ml in four replicates. Slides were then blocked overnight (phosphate-buffered saline (PBS), 3% fetal bovine serum, 0.1% Tween 20) and incubated for 1h at 4°C with individual mouse serum diluted at 1:200 in PBS/3% fetal bovine serum.  Slides were washed with PBS, water-rinsed, and spun dry.

scan_protocol: Slides were scanned to determine pixel intensities for each antigen feature (Genepix 4000B; Molecular Devices, Sunnyvale, CA, USA). Genepix Pro 5.0 software (Axon Instruments) at 532 nm was used to detect IgG and IgM reactivity. Images were saved as tiff files.

data_processing: GenePix Pro 6.0 software (Axon Instruments) was used to determine the net median pixel intensities for each antigen feature (each value is background-corrected by removing the background around each spotted protein). The median intensities for each protein were centered around 300 and log-scaled. A level of 10 digital fluorescence intensity units was set as a threshold for significant reactivity. The formula for values below 10 is log(10/300,2), and for all other values it is log(median pixel intensity/300,2).  Data analysis was performed using Significance Analysis for Microarrays (SAM) software (http://www-stat.stanford.edu/~tibs/SAM) to identify antigen features with statistically significant differences in reactivities between the experimental groups. Cluster software was then used to hierarchically group the samples and antigen features on the basis of a pairwise similarity function, and TreeView software was used to display the data as a heat map (http://rana.lbl.gov/EisenSoftware.htm).

molecule: protein

source_name: serum, 50 mg/kg Cl-amidine treatment group

label_protocol: After washing with phosphate-buffered saline (PBS)/3% fetal bovine serum/0.1% Tween 20, reactive antibodies were detected using Cy3-conjugated goat-anti-mouse IgG/IgM secondary antibody (diluted 1:4,000 in PBS/3% fetal bovine serum; Jackson Immunoresearch). After incubating for 45 minutes with the secondary antibody, the slides were washed with washing solution (PBS/3 % fetal bovine serum/0.1% Tween 20

growth_protocol: Male DBA/1J mice were obtained from Jackson Laboratories and were between 6 and 8 weeks of age when experiments were initiated.

extract_protocol: At the end of the injection courses (day 35), the mice were bled for their plasma.

treatment_protocol: Mice were immunized intradermally with 100 µL of Incomplete Freund’s Adjuvant (IFA) containing 200 µg of bovine CII (Elastin Products) and 200 µg of inactivated Mycobacterium tuberculosis (H37Ra; Difco) on days 0 and 21. Each experimental group consisted of 8 mice that were treated daily throughout the entire experiment, i.e. day 0 of the first injection through sacrifice on day 35, with one of five interventions: no injection, PBS (vehicle control), 1 mg/kg Cl-amidine, 10 mg/kg Cl-amidine or 50 mg/kg Cl-amidine. All injections were given i.p. in a standard volume of 200 μL containing the appropriate concentration of Cl-amidine.  Doses were calculated for the average weight of the group (20 g). At day 35, all animals were sacrificed by anesthesia with 2,2,2-tribromoethanol and cervical dislocation.  One mouse in the 1 mg/kg treatment group died on day 8 of the experiment of causes unrelated to treatment.

value: DBA (Jackson Laboratories)

tag: gender

value: male


title: Treatment-338


title: Treatment-339


title: 4-Vinylcyclohexene Diepoxide (50uM) rep 3

source_name: Neonatal mouse ovaries cultured in4-Vinylcyclohexene Diepoxide (50uM)

value: 4-Vinylcyclohexene Diepoxide (50uM)

value: Post natal day 3-9


title: Control (0.1% DMSO) rep 3

source_name: Neonatal mouse ovaries cultured in DMSO (0.1%)

value: Control (0.1% DMSO)

value: Post natal day 3-6


title: 4-Vinylcyclohexene Diepoxide (50uM) rep 1

value: Post natal day 3-7


title: Treatment-340


title: Methoxychlor (50uM) rep 1

source_name: Neonatal mouse ovaries cultured in Methoxychlor (50uM)

value: Methoxychlor (50uM)

value: Post natal day 3-10


title: OP_4factor_4

source_name: Bone marrow, OP (Osteo progenitor cell), infected Oct3/4, Sox2, Klf4, and c-Myc


title: OP_4factor_5


title: OP_4factor_2


title: LNM35_1st_GF202

city: Nagoya

first: Takashi

last: Takahashi

state: Aichi

address: 1-1 Kanokoden, Chikusa-ku

institute: Aichi Cancer Center

description:
compare profiles from N15_1st
ATCC no. HTB-177

hyb_protocol: Prehybridized for 2 h at 51°C with 0.5 mg/ml of poly-dA (Invitrogen) and 0.5 mg/ml Cot-1 DNA (Invitrogen) in 10 ml of AlkPhos DIRECT hybridization buffer (Amersham Bioscience) and then hybridized for 17 h at 51°C with the denatured radio-labeled probe. Hybridization of the arrays was followed by two washings with a solution containing 2 M of urea, 0.1 % of SDS, 50 mM of Na phosphate buffer (pH 7.0), 150 mM of NaCl, 1 mM of MgCl2 and 0.2 % of AlkPhos DIRECT blocking reagent (Amersham Bioscience)

scan_protocol: BAS5000 phosphoimager (Fuji Photo Film)

data_processing: Raw data from N15 are used for standard and no normalization were done. 1) Caluculate total intesity of signals from all of spots in both LNM35 and N15. 2) Total intensity of signals of LNM35 was divided by that of N15 (= normalization factor). 3) Intensity of each signal of LNM35 was divided by normalization factor that was calculated at step 2)

organism: Homo sapiens

label_protocol: 5 mg of total RNA was reverse-transcribed using oligo-dT primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen) in the presence of 100 mCi of [33P]dCTP (Amersham Bioscience)

growth_protocol: RPMI supplemented with 10% FBS

extract_protocol: Total RNA  extracted with RNAeasy (Qiagen) following manufacturer's instructions

tag: cell line


title: 4-Vinylcyclohexene Diepoxide (50uM) rep 2

value: Post natal day 3-8


title: Methoxychlor (50uM) rep 2

value: Swiss

value: Post natal day 3-11


title: Treatment-336


title: OP_4factor_3


title: Control (0.1% DMSO) rep 2

value: Ovary

value: Post natal day 3-5


title: Treatment-335


title: Treatment-334


title: Menadione (5uM) rep 3

value: Menadione (5uM)

value: Post natal day 3-15


title: Treatment-333


title: Vehicle control-316

source_name: serum, PBS vehicle control


title: Methoxychlor (50uM) rep 3

value: Post natal day 3-12


title: OP_4factor_1

value: Bone marrow

value: OP (Osteo progenitor cell)


title: Control (0.1% DMSO) rep 1

value: Post natal day 3-4


title: PaS_4factor_5

source_name: Bone marrow PaS (MSC), infected Oct3/4, Sox2, Klf4, and c-Myc

value: PaS (MSC)


title: PaS_3factor_5

source_name: Bone marrow PaS (MSC), infected Oct3/4, Sox2, and Klf4


title: PaS_3factor_4


title: skin.KO.replicate17

city: Valencia

first: Paloma

last: Perez

address: Jaime Roig 11

country: Spain

institute: Instituto Biomedicina Valencia, Consejo Superior Investigaciones Científicas

description: Gene expression data from dorsal skin of GR-/- E18.5 embryos.

hyb_protocol: 15 mg of fragmented cRNA were used for each sample and hybridization performed as described on the webpage of the genomic platform at the Centro de Investigación del Cáncer de Salamanca (http://ubioinfo.cicancer.org).

scan_protocol: GeneChips were scanned using a GenePix 4000B scanner (Molecular Devices, Sunnyvale, CA).

data_processing: Probe set intensity values were summarized and normalized according to the RMA method using R and BioC.

source_name: dorsal skin from GR-/- E18.5 embryo

label_protocol: Starting from an average of 5 mg total RNA, cDNA was synthesized and purified (one cycle cDNA synthesis Affy). cRNA was then biotin-labeled and purified (IVT Affy kit). After quantitation of the biotinylated cRNA, it was fragmented to perform the hybridization step as described on the webpage of the genomic platform at the Centro de Investigación del Cáncer de Salamanca (http://ubioinfo.cicancer.org).

growth_protocol: Mice were housed in standard temperature and humidity conditions and animal experimentation was conducted with accepted standards of humane animal care in our animal facility (Instituto de Biomedicina de Valencia IBV-CSIC).

extract_protocol: Total RNA was obtained using the RNeasy RNA extraction kit (Qiagen, Valencia, CA).  RNA integrity was tested using the Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: GR-/- and GR+/+ embryo littermates were obtained by cesarean derivation at 18.5 days post-conception (the morning of the day that the vaginal plug was seen was considered as day 0.5).

value: dorsal skin

tag: genotype/variation


title: PaS_3factor_3


title: PaS_3factor_1


title: Vehicle control-310

value: DBA (Jackson Laboratories)

value: male


title: OP_3factor_5


title: Vehicle control-313


title: Vehicle control-312


title: PaS_3factor_2


title: skin.KO.replicate25


title: skin.KO.replicate5


title: skin.wt.replicate29

description: Gene expression data from dorsal skin of GR+/+ E18.5 embryos.

source_name: dorsal skin from GR+/+ E18.5 embryo


title: skin.KO.replicate26


title: PaS_4factor_4


title: PaS_4factor_2


title: Vehicle control-315


title: skin.wt.replicate6


title: skin.wt.replicate4


title: PaS_4factor_1


title: skin.wt.replicate28


title: PaS_4factor_3


title: IVDS2-P1

status: Public on Aug 20 2010

city: Taipei

first: Chun

middle: Ying

last: Yu

address: 128 Academia Road, Section 2

department: Genomic Research center

country: Taiwan

institute: Academia sinica

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

scan_protocol: Chips were scanned with Affymetrix GeneChip Scanner 7G

data_processing: Raw data were analyized by Genespring GX, normalized by RMA (Robust Multichip Average) and the weakly expressed signals (<20% of total samples) were excluded

organism: Macaca mulatta

source_name: In vitro differentiation stage2-peripheral

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: The monkey ESC (ORMES6)[42] were grown on MEF feeders (2 × 104 cells/cm2) in DMEM/F12 medium plus 20% Knockout Serum Replacement (Invitrogen) and bFGF (4 ng/ml, Sigma)

extract_protocol: Total RNA was isolated from cells with TRI Reagent (Molecular Research Center) and treated with DNase I according to manufacturer’s instruction

treatment_protocol: The primate ESC were co-cultured with hESdF to induce hepatic foci formation

tag: cell type

value: ESC


title: IVDS2-C1

source_name: In vitro differentiation stage2-central


title: IVDS2-P2


title: IVDS2-C2


title: IVDS2-1

source_name: In vitro differentiation stage2


title: IVDS3-2

source_name: In vitro differentiation stage3


title: IVDS2-2


title: IVDS3-1


title: ES-2


title: Skin Biopsy_subject 031_0.5h_NON

city: Odense

first: Mads

last: Thomassen

address: Soender Boulevard 9

department: Clinical Genetics (KKA)

country: Denmark

institute: Odense University Hospital

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: Model based expression in dCHIP omitting mismatch probes, normalization in R using VSN

source_name: Skin Biopsy_epidermis fraction_0.5h_NON

label_protocol: Ambion MessageAmp

extract_protocol: TissueLyser, RNeasy Micro Kit

value: epidermis


title: Skin Biopsy_subject 029_d11_NON

source_name: Skin Biopsy_epidermis fraction_NON


title: ES-1


title: Skin Biopsy_subject 025_4h_NON

source_name: Skin Biopsy_epidermis fraction_4h_NON


title: Skin Biopsy_subject 034_4h_NON


title: Skin Biopsy_subject 026_24h_NON

source_name: Skin Biopsy_epidermis fraction_24h_NON


title: Skin Biopsy_subject 026_05h_NON

source_name: Skin Biopsy_epidermis fraction_05h_NON


title: Skin Biopsy_subject 034_24h_NON


title: Skin Biopsy_subject 034_0h_NON

source_name: Skin Biopsy_epidermis fraction_0h_NON


title: Skin Biopsy_subject 029_0h_NON


title: Skin Biopsy_subject 026_0h_NON


title: Skin Biopsy_subject 029_4h_NON


title: Skin Biopsy_subject 031_0h_NON


title: Skin Biopsy_subject 023_d11_NON


title: Skin Biopsy_subject 025_05h_NON


title: Skin Biopsy_subject 023_05h_NON


title: Skin Biopsy_subject 025_0h_NON


title: Skin Biopsy_subject 022_0.5h_NON


title: Skin Biopsy_subject 022_0h_NON


title: Hypothyroid2

city: ottawa

first: hongyan

last: dong

address: 50 colombine Dr.

country: Canada

institute: health canada

hyb_protocol: Not applicable

scan_protocol: Not applicable

data_processing: Using the log2 of the delta Ct values differentially expressed miRNAs were identified using an F-test with U6 as a housekeeping miRNA. The critical value of the F-test statistic was determined by bootstrapping the residuals from the one way ANOVA model using the R software.  Residuals were re-sampled within each treatment condition to avoid making the common variance assumption.  Multiple comparison adjustment was applied to the final results using the FDR approach.

label: FAM dye

label_protocol: Not applicable

growth_protocol: C57BL/6 mice were purchased from Charles River (St. Constant, QC, Canada) and were housed in hanging polycarbonate cages under a 12:12 hr light-dark cycle at 23ºC with food (Purina rodent chow 5010; Ralston-Purina, St. Louis, MO, USA) and sugar water (1%) available ad libitum.  All cages contained shelters and nesting material. After a 10 day acclimation period breeding was initiated by transferring two sexually mature female mice (8 weeks post natal) into the home cage of a sexually mature (10 weeks) male. After 4 nights of co-housing each female was transferred to a separate cage. Dams were allowed to litter naturally and litter numbers were not adjusted.

extract_protocol: Four male mice from each of the control and treatment groups respectively were used to comprehensively analyze miRNA expression. Total RNA was extracted with mirVana miRNA Isolation Kit (Ambion, Inc., Applied Biosystems, Foster city, CA, USA) according to the manufacturer's instructions and 750 ng were used to perform reverse transcriptions with the Taqman miRNA Reverse Transcription kit and Megaplex RT Primers Rodent Pool A and B (Applied Biosystem). RT-PCR reactions were performed with TaqMan Rodent miRNA Array A and B (containing up to 600 rodent miRNAs) by the Institut de Recherche en Immunologie et en Cancérologie (IRIC), University de Montreal, with the 7900 HT system. http://www3.appliedbiosystems.com/cms/groups/mcb_support/documents/generaldocuments/cms_053965.pdf

treatment_protocol:
On post natal day (PND) 12, half of the dams with litters were provided with sugar water containing MMI (0.05%) and perchlorate (1%).   All animal care and handling was in accordance with Canadian Council for Animal Care Guidelines and was reviewed by the Health Canada Animal Care Committee prior to the start of the study.
On PND 15, a male pup from each litter was sacrificed by exsanguination under isofluorane anaesthesia. Serum, prepared using Serum Separator Tubes (BD Biosciences, Mississauga, ON, Canada) was retained for T4 analysis with RIA kits (MP Biomedicals, Medicorp, Montreal, QC, Canada). Liver was dissected as rapidly as possible, immediately frozen in liquid nitrogen and stored at -80ºC.

tag: group

value: hypothyroid

value: liver


title: Hypothyroid1


title: Skin Biopsy_subject 020_24h_NON


title: Skin Biopsy_subject 023_0h_NON


title: Skin Biopsy_subject 020_d11_NON


title: Hypothyroid4


title: Skin Biopsy_subject 017_d11_SLS

source_name: Skin Biopsy_epidermis fraction_SLS


title: Skin Biopsy_subject 019_0.5h_NON


title: Control4

value: control


title: Control3


title: Skin Biopsy_subject 019_0h_NON


title: Skin Biopsy_subject 020_0h_NON


title: Hypothyroid3


title: Control2


title: Skin Biopsy_subject 016_0h_SLS

source_name: Skin Biopsy_epidermis fraction_0h_SLS


title: wt_-ile_tp12

city: Norman

first: Tyrrell

last: Conway

state: OK

address: 101 David L. Boren Blvd.

department: Advanced Center for Genome Technology

institute: University of Oklahoma

hyb_protocol: Hybridization was at 60 degrees C for 16 h according to Affymetrix protocol ProkGE_WS2v2-450.

scan_protocol: Affymetrix GCOS scanner software and GeneChip Scanner 3000.

data_processing: RMA with quartile normalization according to method of Irizarry et al, 2003. The raw .cel files were processed in RMA using Bioconductor R package: affy Version:1.8.1 Date:2005-09-03, with the option Filter.genes corresponding to the MG1655 subset of probesets from the arrays, as reflected in the sample files. Replicates were averaged for ratio calculations. Ratio calculations are provided in the supplementary files on the Series record. For GPL3154, the probeset filter file was created by parsing Affymetrix  E_coli_2.na29.annot.csv  file (create_date=2009-06-30 PDT 20:45:08): 1. Selected all MG1655 locustags from Transcript ID(Array Design) (4070 locustags). 2. Selected all  IG intergenic regions from Transcript ID(Array Design) (1297 Igs). 3. Manually selected based on NC_000913 alignment value (250 locustags).

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E. coli wild-type, isoleucine starved

label_protocol: RNA converted to cDNA by random-hexamer primed first strand synthesis with Superscript II and biotinylated with Roche Enzo kit according to Affymetrix protocol.

growth_protocol: Cultures were grown in a fermentor with constant O2 saturation and pH was maintained at 7.4. Growth medium was MOPS+glucose+20 AAs (as described by Wanner 1977). Replete isoleucine was 400 um; isoleucine starvation was with 60 uM. The control was wildtype grown with replete ile from which total RNA was extracted in log phase (OD600 of ~0.4). For ile starved wt and mutants, total RNA was extracted ~40 min after growth arrest.

extract_protocol: Qiagen RNeasy kit extraction with optional DNase step

treatment_protocol: Cells were allowed to starve for isoleucine in medium containing 60 uM ile.

value: wild-type

tag: time point (post-inoculation)

value: 493 min


title: Skin Biopsy_subject 015_d11_SLS


title: Skin Biopsy_subject 016_24h_SLS

source_name: Skin Biopsy_epidermis fraction_24h_SLS


title: Skin Biopsy_subject 017_0h_SLS


title: Skin Biopsy_subject 015_0h_SLS


title: wt_-ile_tp10

value: 445 min


title: wt_-ile_tp11

value: 460 min


title: Control1


title: Skin Biopsy_subject 016_4h_SLS

source_name: Skin Biopsy_epidermis fraction_4h_SLS


title: Skin Biopsy_subject 013_0h_SLS


title: Skin Biopsy_subject 014_0h_SLS


title: Skin Biopsy_subject 014_05h_SLS

source_name: Skin Biopsy_epidermis fraction_05h_SLS


title: Skin Biopsy_subject 014_24h_SLS


title: wt_-ile_tp9

value: 430 min


title: wt_-ile_tp5

value: 395 min


title: wt_-ile_tp8

value: 420 min


title: wt_-ile_tp7

value: 410 min


title: wt_-ile_tp6

value: 400 min


title: wt_-ile_tp4

value: 390 min


title: wt_-ile_tp2

value: 370 min


title: wt_-ile_tp3

value: 380 min


title: WT_+ile_rep2

source_name: E. coli wild-type, replete isoleucine, control


title: Skin Biopsy_subject 009_d11_SLS


title: wt_-ile_tp1

value: 340 min


title: Anther2.0mm fs Rep4

first: John

middle: F

last: Fernandes

address: 385 Serra Mall

department: Bio Sci

description: ms8 fertile sibling Anther 2.0mm compared to biological replicate

hyb_protocol: 825 ng of each labeled target cRNA were hybridized for 17 h at 60C.

scan_protocol: Slides were scanned on an Agilent DNA microarray scanner as indicated in the manual.  Images were processed with the Agilent Feature Extraction software.

data_processing: After removal of spots flagged by Feature Extraction as below background or saturated or outliers, intensities for each channel from Feature Extraction were normalized using lowess.  Average intensities were then calculated for each sample type for comparison.

organism: Zea mays

label_protocol: Total RNA (500 ng) was amplified & labeled with Cy3 or Cy5 using Agilent Low RNA Input Linear Amplification Kit.

growth_protocol: Plants were grown and dissected at the Stanford field; tissues were collected and frozen in liquid nitrogen immediately.

extract_protocol: Total RNA was extracted from 30 - 60 mg of frozen tissues with TRIzol, digested with DNase I, and cleaned up with Qiagen RNeasy Mini kit.

value: ms8 fertile sibling

tag: anther stage


title: Skin Biopsy_subject 009_05h_SLS

value: epidermis


title: Anther2.0mm fs Rep2


title: Skin Biopsy_subject 013_0.5h_SLS

source_name: Skin Biopsy_epidermis fraction_0.5h_SLS


title: Skin Biopsy_subject 009_0h_e_SLS

source_name: Skin Biopsy_epidermis fraction_0h_e_SLS


title: Skin Biopsy_subject 008_0h_SLS


title: Skin Biopsy_subject 008_05h_SLS


title: WT_+ile_rep1


title: Anther1.0mm fs Rep4

description: ms8 fertile sibling Anther 1.0mm compared to biological replicate


title: Skin Biopsy_subject 007_4h_SLS


title: Anther1.5mm fs Rep4

description: ms8 fertile sibling Anther 1.5mm compared to biological replicate


title: Skin Biopsy_subject 007_0h_SLS


title: Skin Biopsy_subject 007_05h_SLS


title: Liver_GermFree_HFdiet_14

city: Lausanne

first: Frederic

last: Raymond

address: Campus EPFL - Quartier de l'Innovation

department: Functional Genomics

country: Switzerland

institute: Nestle Institute of Health Sciences

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data generated with Genome Studio software (Illumina). Quantile normalized together with 33 unknown samples (included in GSE19038_non-normalized.txt)

label: Biotin

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

extract_protocol: Agencourt RNAdvance tissue kit

treatment_protocol: High fat diet

value: Liver


title: Anther1.5mm fs Rep2


title: Anther1.0mm fs Rep2


title: Liver_GermFree_HFdiet_13


title: Skin Biopsy_subject 004_24h_SLS


title: Skin Biopsy_subject 004_4h_SLS


title: Liver_GermFree_HFdiet_12


title: Anther1.5mm ms8 Rep4

description: ms8 Anther 1.5mm compared to biological replicate

value: ms8 mutant


title: Anther2.0mm ms8 Rep4

description: ms8 Anther 2.0mm compared to biological replicate


title: Liver_GermFree_HFdiet_11


title: Anther1.5mm ms8 Rep2


title: Anther2.0mm ms8 Rep2


title: Skin Biopsy_subject 004_0h_SLS


title: Liver_GermFree_HFdiet_08


title: Liver_GermFree_HFdiet_10


title: Anther1.0mm ms8 Rep2

description: ms8 Anther 1.0mm compared to biological replicate


title: Liver_GermFree_HFdiet_05


title: Anther1.0mm ms8 Rep4


title: Anther2.0mm fs Rep1


title: Liver_GermFree_HFdiet_06


title: Liver_GermFree_HFdiet_09


title: Liver_GermFree_HFdiet_07


title: Anther1.5mm fs Rep3


title: Liver_GermFree_HFdiet_04


title: Anther1.5mm fs Rep1


title: CP1_3

city: Los Angeles

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

description:
1541554067_H
Choroid Plexus, timepoint 1h after LPS treatment, replicate 3

hyb_protocol: Illumina protocol

scan_protocol: Illumina protocol

data_processing: BeadStudio, quantile normalization

source_name: Time 1h

label_protocol: Biotin

extract_protocol: Trizol

treatment_protocol: Animals were injected intraperitoneally with LPS (5μg/g of body weight) or vehicle alone

tag: timepoint

tag: treatment

value: Experiment


title: Anther2.0mm fs Rep3


title: Liver_GermFree_HFdiet_02


title: Anther1.0mm fs Rep1


title: Liver_GermFree_HFdiet_01


title: Anther1.5mm ms8 Rep1


title: CP0_3

description:
1541554067_G
Choroid Plexus, timepoint 0, replicate 3

source_name: Time 0

value: Control


title: Anther1.5mm ms8 Rep3


title: Liver_Conventional_HFdiet_16


title: Anther1.0mm ms8 Rep3


title: Anther2.0mm ms8 Rep3


title: Liver_Conventional_HFdiet_14


title: Liver_Conventional_HFdiet_15


title: CP72_2

description:
1541554067_F
Choroid Plexus, timepoint 72h after LPS treatment, replicate 2

source_name: Time 72h


title: Anther1.0mm ms8 Rep1


title: Liver_Conventional_HFdiet_12


title: Skin Biopsy_subject 015_05h_SLS


title: Liver_Conventional_HFdiet_13


title: Anther1.0mm fs Rep3


title: Liver_GermFree_HFdiet_03


title: CP24_1

description:
1541554067_C
Choroid Plexus, timepoint 24h after LPS treatment, replicate 1

source_name: Time 24h


title: Liver_Conventional_HFdiet_11


title: CP24_2

description:
1541554067_D
Choroid Plexus, timepoint 24h after LPS treatment, replicate 2


title: Liver_Conventional_HFdiet_10


title: CP12_2

description:
1541554067_B
Choroid Plexus, timepoint 12h after LPS treatment, replicate 2

source_name: Time 12h


title: CP72_1

description:
1541554067_E
Choroid Plexus, timepoint 72h after LPS treatment, replicate 1


title: Ecoli rpoS -ile rep2

data_processing: RMA with quartile normalization according to method of Irizarry et al, 2003. The raw .cel files were processed in RMA using Bioconductor R package: affy Version:1.8.1 Date:2005-09-03, with the option Filter.genes corresponding to the MG1655 subset of probesets from the arrays, as reflected in the sample files. Replicates were averaged for ratio calculations. Ratio calculations are provided in the supplementary files on the Series record.

source_name: E. coli rpoS, isoleucine starved

value: rpoS


title: CP12_1

description:
1541554067_A
Choroid Plexus, timepoint 12h after LPS treatment, replicate 1


title: Ecoli rpoS -ile rep1


title: Ecoli lrp -ile rep2

source_name: E. coli lrp, isoleucine starved

value: lrp


title: Liver_Conventional_HFdiet_08


title: CP6_2

description:
1541554016_H
Choroid Plexus, timepoint 6h after LPS treatment, replicate 2

source_name: Time 6h


title: 626_hypothyroid

hyb_protocol: Agilent Whole Mouse Genome Microarrays (G4122F; containing over 41,000 genes and transcripts) were hybridized with 825 ng Cy5-labelled exposed (hypo, hyper or hypo+) RNA and 825 ng Cy3-labelled Universal Mouse Reference RNA (Stratagene, CA, USA), used as a common reference on all arrays.  Arrays were incubated for 17 hours at 65 ºC in Agilent hybridization solution and washed according to manufacturer’s instructions.

scan_protocol: Arrays were scanned using Agilent DNA Microarray Scanner (G2565CA) and data was acquired with Feature Extraction 10.1.1 (Agilent Technologies Canada Inc., Mississauga, ON, Canada).

data_processing:
The median signal intensity of each microarray sample was used. Technical replicates were not averaged.  Data for each probe was flagged (flag=1) if the median signal intensity for that probe was less than the mean of the negative controls ((-)3xSLv1) plus three standard deviations.
RawCy5 and RawCy3 are the median signal intensities for the Cy5 and Cy3 channels on each microarray. NormCy5 and NormCy3 are the loess normalized signal intensities for the Cy5 and Cy3 channels within each array; this is a within-array normalization performed separately for each array. Flag indicates whether the median signal intensity falls in the background, i.e below threshold calculated from the negative controls (mean plus three standard deviations of the negative controls.) Ratio is calculated as log2(NormCy5/NormCy3) (Relative Intensity, logged.)

label_protocol: Individual 200 ng aliquots of RNA from each samples were amplified and labelled using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent).

extract_protocol: RNA was isolated using the TRIzol reagent (Invitrogen Canada Inc., Burlington, ON, Canada), and further purified using RNeasy Mini Kits (Qiagen Inc., Mississauga, ON, Canada).  RNA was quantified using UV spectrophotometer and quality was confirmed using the Agilent 2100 Bioanalyzer and RNA 6000 NanoLab Chip Kit (Agilent Technologies Canada Inc., Mississauga, ON, Canada).

treatment_protocol: C57BL/6 mice were purchased from Charles River (St. Constant, QC, Canada) and were housed in hanging polycarbonate cages under a 12:12 hr light-dark cycle at 23ºC with food (Purina rodent chow 5010; Ralston-Purina, St. Louis, MO, USA) and sugar water (1%) available ad libitum.  All cages contained shelters and nesting material. After a 10 day acclimation period breeding was initiated by transferring two sexually mature female mice (8 weeks post natal) into the home cage of a sexually mature (10 weeks) male. After 4 nights of co-housing each female was transferred to a separate cage. Dams were allowed to litter naturally and litter numbers were not adjusted.  On post natal day (PND) 12, half of the dams with litters were provided with sugar water containing MMI (0.05%) and perchlorate (1%).   All animal care and handling was in accordance with Canadian Council for Animal Care Guidelines and was reviewed by the Health Canada Animal Care Committee prior to the start of the study.

value: hypothyroid

value: liver

source_name: universal mouse reference total RNA (Stratagene, Cedar Creek, TX, USA)

extract_protocol: Unknown: Material was purchased as total RNA (universal mouse reference total RNA (Stratagene, CA, USA))

tag: reference


title: CP6_1

description:
1541554016_G
Choroid Plexus, timepoint 6h after LPS treatment, replicate 1


title: 723_hypothyroid

value: universal mouse reference total RNA (Stratagene, Cedar Creek, TX, USA)


title: Liver_Conventional_HFdiet_09


title: 311_hypothyroid


title: Liver_Conventional_HFdiet_07


title: Liver_Conventional_HFdiet_06


title: 576_hypothyroid


title: CP3_1

description:
1541554016_E
Choroid Plexus, timepoint 3h after LPS treatment, replicate 1

source_name: Time 3h


title: CP3_2

description:
1541554016_F
Choroid Plexus, timepoint 3h after LPS treatment, replicate 2


title: Ecoli dksA -ile rep2

source_name: E. coli dksA, isoleucine starved

value: dksA


title: Liver_Conventional_HFdiet_05


title: 616_control

value: control


title: Ecoli lrp -ile rep1


title: Ecoli dksA -ile rep1


title: CP1_2

description:
1541554016_D
Choroid Plexus, timepoint 1h after LPS treatment, replicate 2


title: 891_hypothyroid


title: Ecoli crp -ile rep2

source_name: E. coli crp, isoleucine starved

value: crp


title: Liver_Conventional_HFdiet_03


title: CP1_1

description:
1541554016_C
Choroid Plexus, timepoint 1h after LPS treatment, replicate 1


title: Liver_Conventional_HFdiet_02


title: Ecoli crp -ile rep1


title: 522_control


title: Liver_Conventional_HFdiet_01


title: CP0_1

description:
1541554016_A
Choroid Plexus, timepoint 0, replicate 1


title: 391_control


title: 881_control


title: Liver_Conventional_HFdiet_04


title: CP0_2

description:
1541554016_B
Choroid Plexus, timepoint 0, replicate 2


title: 832_control


title: LM1_rep1

status: Public on Aug 19 2010

city: New York

first: Venkata

middle: J

last: Thodima

state: NY

department: Cell Biology

institute: Memorial Sloan-Kettering Cancer Center

description: miRNA expression in  first generation metastatic cell line LM1

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Scanner G2505C US83903565 using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 019118_D_20080214) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: LM1 cell line, rep1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by miRNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: miRNAs were extracted using Qiagen miRNeasy kit according to the manufacturer's instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: disease state

value: metastatic


title: LM2_rep2

description: miRNA expression in  second generation metastatic cell line LM2

source_name: LM2 cell line, rep2


title: SN12C_rep3

description: miRNA expression in non-metastatic cell line SN12C

source_name: SN12C cell line, rep3

value: non-metastatic


title: SN12C_rep2

source_name: SN12C cell line, rep2


title: SN12C_rep1

source_name: SN12C cell line, rep1


title: RNA IP with FLAG-RHA rep 3

city: Columbus

first: Kathleen

last: Boris-Lawrie

state: OH

address: 1925 Coffey Rd

department: Department of Veterinary Biosciences

institute: The Ohio State University

description: Biological replicate 3 of 4.

hyb_protocol: Arrays were hybridized for 17 hours at 65 degrees Celsius.

scan_protocol: Scanned with Agilent G2505C Microarray Scanner using the AgilentHD_GX_2Color protocol

data_processing:
The information about each probe on the array was extracted from the image data using Agilent Feature Extraction 10.9 (FE). This data is stored in the FE “.txt” files. The raw intensity values from these files is imported into the mathematical software package “R”, which is used for all data input, diagnostic plots, normalization and quality checking steps of the analysis process using scripts developed in-house by Peter White specifically for this analysis.
The median red (Cy5) and green (Cy3) intensities are used to calculate the ratio of expression for each element on the array, in terms of M (log2(Red/Green)) and A ((log2(Red) + log2(Green))/2)). The M values are then global loess normalized within each array using the LIMMA microarray processing package in “R” (Smyth, 2004). This intensity based normalization approach adjusts the red and green intensities relative to one another so that the red/green ratios are as far as possible an unbiased representation of relative expression.

molecule: cytoplasmic RNA

source_name: RNA IP with FLAG-RHA

label_protocol: Two-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling Version 6.5, May 2010

growth_protocol: Four replicate 150 mm plates seeded with 2 x 10e6 HEK 293 cells were transfected with pcDNA-FLAG-RHA. After 48 hours, the cells were harvested and a 200 ul cytoplasmic lysate was made.

extract_protocol: Lysates were processed with Qiagen RNA minElute kit according to manufacturer's protocol

treatment_protocol: The immunoprecipitation utilized anti-FLAG M2 monoclonal antibody-conjugated agarose beads (Sigma). Cytoplasmic lysates were incubated with the beads overnight at 4°C. RHA mRNP complexes were eluted with 2 ml 100 ng/ul of 3X FLAG peptide solution (Sigma) according to manufacturer’s instructions.

value: HEK 293

tag: fraction

value: Immunoprecipitated poly A RNA

source_name: RNA IP with FLAG


title: RNA IP with FLAG-RHA rep 2

description: Biological replicate 2 of 4.


title: RNA IP with FLAG-RHA rep 1

description: Biological replicate 1 of 4.


title: pph13 otd at 72hr APF Replicate 1

city: Bloomington

first: Andrew

last: Zelhof

state: IN

address: 1001 E Third Street

department: Department of Biology

institute: Indiana University

hyb_protocol: Using the Dendrimer Use and Hybridization Protocol by Lucy Cherbas, February 28, 2005 and Genisphere Array50 protocol (available as a supplementary file on the Series record).

scan_protocol: Scanned on GenePix Scanner 4200A

data_processing: LOWESS normalized data obtained from log2 of Red/Green signal using Bioconductor packages marray (v 1.26.0), limma (v 3.4.4), OLIN (v 1.26.0) in R v 2.5.1.

organism: Drosophila melanogaster

source_name: pph13 otd cn bw total head RNA

label_protocol: labeled using Array 50 dendrimer kit (Genisphere) with Cy3 and Cy5 dyes

extract_protocol: Total RNA extracted using TRIZOL

value: head

value: pph13 otd cn bw

tag: development stage

value: 72 hours after puparium formation

source_name: cn bw total head RNA

value: cn bw


title: pph13 otd at 72hr APF Replicate 4

tag: strain


title: pph13 otd at 72hr APF Replicate 2

tag: tissue


title: pph13 otd at 96hr APF Replicate 4

value: <1 day after puparium formation


title: LM1_rep2

source_name: LM1 cell line, rep2


title: pph13 otd at 72hr APF Replicate 3


title: pph13 otd at 96hr APF Replicate 3


title: LM2_rep1

source_name: LM2 cell line, rep1


title: pph13 otd at 96hr APF Replicate 2


title: Polysome Experiment Rep 3

description: Biological replicate 3 of 3.

organism: Chlorocebus aethiops

source_name: Heavy polysome mRNA from control cells

growth_protocol: Four 150 mm plates seeded with 2 x 106 cells were transfected with siRNAs targeting RHA or scrambled control siRNA. Incubation for 4 hours at 37°C in medium without serum was followed by a 24 hour incubation in 10% FBS medium. Cells were split and 24 hours later transfected again with siRNAs as above and incubated at 37°C for 24 hours.

extract_protocol: Cytoplasmic lysates were loaded on linear sucrose gradients (15%-45%) and the fractions corresponding to the heavy polysomes were pooled. RNA was ethanol precipitated and processed using the Qiagen RNA minElute kit according to manufacturer's protocol

treatment_protocol: For RHA downregulation , COS cells were transfected with siRNAs (Dharmacon) targeted to the coding region (nucleotides 2701-2721 and 2784-2803) of human RHA (NCBI accession code NM_001357), or scrambled RHA siRNAs to a final concentration of 0.5 nM.

value: Sc control COS7

source_name: Heavy polysome mRNA from RHA knock down cells

tag: test

value: RHA knock down in COS7


title: Polysome Experiment Rep 1

description: Biological replicate 1 of 3.


title: RNA IP with FLAG-RHA rep 4

description: Biological replicate 4 of 4.


title: pph13 otd at 96hr APF Replicate 1


title: Polysome Experiment Rep 2

description: Biological replicate 2 of 3.


title: pph13 at 72hr APF Replicate 4

source_name: pph13 cn bw total head RNA

value: pph13 cn bw


title: pph13 at 96hr APF Replicate 2


title: pph13 at 72hr APF Replicate 2


title: pph13 at 72hr APF Replicate 3


title: pph13 at 72hr APF Replicate 1


title: pph13 at 96hr APF Replicate 4


title: pph13 at 96hr APF Replicate 3


title: Anther2.0mm ms8 Rep1

description: ms8 Anther 2.0mm compared to biological replicate

value: ms8 mutant


title: Fibroblast cell line IMR90

first: Kathrin

last: Plath

address: 615 Charles E. Young Drive South

department: Biological Chemistry

description: Gene expression data from IMR90 fibroblasts

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on human expression arrays

scan_protocol: Gene chips were analyzed using GeneChip® Scanner 3000.

data_processing:
The raw data was processed using the RMA algorithm and was implemented using R (Bioconductor).
The data is presented as a summary of the highest confidence probesets for each given RefSeq identifier. (See Materials and Methods, Chin, et al. Cell Stem Cell, 2009)

source_name: IMR90 fibroblasts

growth_protocol: Cell lines were cultured in hESC cell media for hESC and hiPSC lines (Lowry, et al. PNAS, 2008) and DMEM for the fibroblast line.

extract_protocol: Total RNA was extracted using Stratagene's Lysis Buffer and extracted according to the manufacturer's instructions.

treatment_protocol: Reprogrammed Cell lines were treated as described in Lowry, et al. (PNAS, 2008)

value: Fibroblast cell line

tag: cell  line


title: Hopx-null heart, biological rep2

city: Philadelphia

first: Jonathan

middle: A

last: Epstein

state: PA

address: 421, Curie Blvd

department: Cell and Developmental Biology

institute: University of Pennsylvania, School of Medicine

description: Gene expression data from Hopx knockout E16.5 heart

hyb_protocol: The cRNA products were fragmented to 200 nucleotides or less, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Affimatrix MOE 430 2.0 microarrays. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A confocal scanner was used to collect fluorescence signal at 3um resolution after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray feature.

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

source_name: Hopx-null mouse embryonic ventricle at E16.5

label_protocol: Biotinylated cRNA were prepared according the Affymetrix GeneChip Expression Analysis Technical Manual. Briefly, total RNA was converted to first-strand cDNA using Superscript II reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 promoter. Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.

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

value: embryonic cardiac ventricle

value: Hopx knockout

tag: age

value: Embryonic day 16.5


title: Fibroblast cell line NHDF 17914

description: Gene expression data from NHDF 17914 fibroblasts

source_name: NHDF 17914 fibroblasts


title: Hdac2-Hopx double-null heart, biological rep2

description: Gene expression data from Hdac2-Hopx double knockout E16.5 heart

source_name: Hdac2-Hopx-null mouse embryonic ventricle at E16.5

value: Hdac2-Hopx knockout


title: Hdac2-null heart, biological rep3

description: Gene expression data from Hdac2 knockout E16.5 heart

source_name: Hdac2-null mouse embryonic ventricle at E16.5

value: Hdac2 knockout


title: Reprogrammed iPSC line  hiPSC line 2

description: Gene expression data from hiPSC line 2

source_name: hiPSC line 2 (p77)

value: hiPSC cell line

value: hiPSC line 2


title: Reprogrammed iPSC line  hiPSC line 18

description: Gene expression data from hiPSC line 18

source_name: hiPSC line 18 (p77)

value: hiPSC line 18


title: pph13 at 96hr APF Replicate 1

value: head


title: Hdac2-null heart, biological rep1


title: Hopx-null heart, biological rep3


title: Human ES cell line H9

description: Gene expression data from H9

value: Human embryonic stem cell line


title: Reprogrammed iPSC line 18 hiPSC pMIP3

description: Gene expression data from hiPSC pMIP line 3

source_name: hiPSC pMIP line 3 (p6)

value: hiPSC pMIP3


title: Wild-type heart, biological rep3

description: Gene expression data from wild-type E16.5 heart

source_name: Wild-type mouse embryonic ventricle at E16.5

value: Wild-type


title: Reprogrammed iPSC line  hiPSC pMIP2

description: Gene expression data from hiPSC pMIP line 2

source_name: hiPSC pMIP line 2 (p6)

value: hiPSC pMIP2


title: Reprogrammed iPSC line  hiPSC G

description: Gene expression data from hiPSC 17914 line G

source_name: hiPSC 17914 line G (p22)

value: hiPSC G


title: Reprogrammed iPSC line  hiPSC E

description: Gene expression data from hiPSC 17914 line E

source_name: hiPSC 17914 line E (p22)

value: hiPSC E


title: Hdac2-null heart, biological rep2


title: Reprogrammed iPSC line  hiPSC 3975

description: Gene expression data from hiPSC 3975

source_name: hiPSC 3975 line (p24)

value: hiPSC 3975


title: Reprogrammed iPSC line  hiPSC line 1

description: Gene expression data from hiPSC1 line 1

source_name: hiPSC line 1 (p82)

value: hiPSC line 1


title: Wild-type heart, biological rep2

value: embryonic cardiac ventricle


title: Wild-type heart, biological rep1


title: Human ES cell line HSF1

description: Gene expression data from HSF1


title: Human ES cell line H1

description: Gene expression data from H1


title: Hdac2-Hopx double-null heart, biological rep3


title: Hopx-null heart, biological rep1

value: Hopx knockout


title: DMSO

status: Public on Aug 18 2010

city: San Diego

middle: R

last: Walker

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

description: DMSO

hyb_protocol: Standard Affymetrix protocols were used to process Affymetrix rat genome 230_2 microarrays (Affymetrix).

scan_protocol: standard Affymetrix procedures

data_processing: CEL files were processed using the "full model" of GCRMA (Wu Z, Irizarry RA: Stochastic models inspired by hybridization theory for short oligonucleotide arrays. J Comput Biol 2005, 12(6):882-893.) and R version 2.6.2.  GCRMA and associated packages were downloaded from Bioconductor (www.bioconductor.org).  GCRMA output was unlogged.

organism: Rattus norvegicus

source_name: DMSO

label_protocol: GeneChip 3' IVT Express kits (Affymetrix) were used to amplify cRNA from 5 ug total RNA.

extract_protocol: RNeasy kits (Qiagen) were used to extract total RNA from DMSO- or compound-treated NPCs. The integrity and concentration of RNA were determined via microfluidic analysis on an Experion instrument (BioRad).

treatment_protocol: Rat NPCs were derived and cultured as described previously by others. After hippocampal cell isolation, the number of dissociated cells was determined and 5 × 105 cells were plated in 60-mm uncoated plates. After overnight incubation (37 °C, 5% CO2, and 95% humidity), the medium was changed and the cells were expanded and maintained in an undifferentiated state on polyornithine- (10 ug/mL in water; Sigma) and laminin-coated (5 ug/mL in PBS; Invitrogen) dishes in DMEM/F12 (Invitrogen) supplemented with N2 (Invitrogen) and basic fibroblast growth factor (bFGF, 20 ng/mL; Invitrogen). For KHS101 and shRNA-induction experiments, early passage cells (passaged no more than six times after hippocampal isolation) were trypsinized and plated at a density of 1,000 cells/cm2 into N2 medium (DMEM/F12 supplemented with N2) containing KHS analogs (e.g., KHS101, KHS92, and NP) at different concentrations (0.5-5 uM) or DMSO(0.1%), RA (1-2 uM), BDNF (100 ng/mL), and/or BMP4 (50-100 ng/mL) for 4 d.

value: Fisher 344

value: hippocampal progenitor cells

value: DMSO


title: Hdac2-Hopx double-null heart, biological rep1

value: Hdac2-Hopx knockout

value: Embryonic day 16.5


title: 1_uM_retinoic_acid_forskolin_


title: Chiloplacus sp. (isolate KS584)

type: genomic

city: Manhattan

first: Michael

last: Herman

state: KS

address: 266 Chalmers Hall

department: Division of Biology

institute: Kansas State University, Ecological Genomics Institute

description: CEL files contain raw intensity data, without scaling or smoothing

hyb_protocol: GeneChip Hybridization, Wash, and Stain kit, according to manufacturer's specifics, using GeneChip Fluidics station 400

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G

data_processing:
Data was extracted with GeneChip Operating Software (GCOS) and processed using Tiling Analysis Software (TAS).
Normalized intensity file is tab-delimited and contains probe-level normalized intensity for each species, as described in the manuscript.

molecule: genomic DNA

organism: Chiloplacus sp. MAH-2010

source_name: Genomic DNA from Chiloplacus sp. (isolate KS584)

label_protocol: GeneChip WT Double-Stranded DNA Terminal Labeling Kit, according to manufacturer's specifications

growth_protocol: Maintained on NGM growth media at 20 degrees C, seeded with E. coli OP50

extract_protocol: Whole individuals were washed off NGM plates with M9 buffer and genomic DNA was extracted with phenol-chloroform

tag: isolate

value: whole-body


title: 1.7_uM_KHS_101


title: Acrobeloides sp. (isolate KS586)

organism: Acrobeloides sp. MAH-2010

source_name: Genomic DNA from Acrobeloides sp. (isolate KS586)

treatment_protocol: Maintained on NGM growth media at 20 degrees C, seeded with E. coli OP50


title: Oscheius sp. FVV-2 (isolate KS555)

organism: Oscheius sp. FVV-2

source_name: Genomic DNA from Oscheius sp. FVV-2 (isolate KS555)


title: Oscheius tipulae (isolate KS585)

organism: Oscheius tipulae

source_name: Genomic DNA from Oscheius tipulae (isolate KS585)


title: HCT116_shBgal-rep3

city: Seattle

first: Mei

last: Xu

state: WA

address: 1100 Fairview Ave N

department: MCB

institute: Fred Hutchinson Cancer Research Center

hyb_protocol: The target preparation and hybridization were conducted as described in the Affymetrix technical manual.

scan_protocol: GeneChIP scanner 3000 7G, as described in the affymetrix technical manual

data_processing: The data were analyzed with dChIP using Affymetrix default analysis settings and global scaling as normalization method.

source_name: HCT116 with Bgal knockdown

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

growth_protocol: HCT116 cells were grown in Dulbecco’s modified Eagle’s medium (DME medium, GIBCO-BRL) + 10% FBS + penicillin-streptomycin

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNA was purified using an RNeasy kit from Qiagen.

treatment_protocol: HCT116 cells stably expressing NFX1-91 shRNA or control β-Galactosidase shRNA were delivered by lentiviral vector FUGW.

tag: cell line

value: HCT116 Human colon cancer

tag: shRNA expressing

value: B-Galactosidase


title: TAIL6_SPT

city: Fort Collins

first: Rachel

middle: Lockridge

last: Mueller

state: CO

address: 1878 Campus Delivery

department: Biology

institute: Colorado State University

description: Gene expression data from 21-somite stage tail tissue

hyb_protocol: Following standard Affymetrix protocols by the University of Chicago functional genomics core facility

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: Image acquisition and initial array quantification were performed using the Affymetrix Microarray Suite Version 5.0. Subsequent identification of differentially expressed genes between wild-type and mutant tissue was performed using dCHIP with invariant set normalization.

organism: Danio rerio

source_name: Zebrafish Tail Mesoderm 21-somite stage

label_protocol: Biotin following standard Affymetrix protocols by the University of Chicago functional genomics core facility

growth_protocol: Fish were grown and cared for following standard techniques (Westerfield M: The zebrafish book: a guide for the laboratory use of zebrafish (Danio rerio): University of Oregon Press Eugene, OR; 1995)

extract_protocol: RNA was extracted using the PicoPure isolation kit (Arcturus)

treatment_protocol: No treatments were given to the fish -- comparisons were made between wild-type and mutant individuals. Mutants harbored the b104 mutant allele of the transcription factor tbx16/spt.

tag: developmental stage

tag: genotype

value: spt/tbx16 mutant


title: Caenorhabditis elegans (isolate CB4856)

organism: Caenorhabditis elegans

source_name: Genomic DNA from Caenorhabditis elegans (isolate CB4856)


title: TAIL4_SPT


title: HCT116_shN91_rep3

source_name: HCT116 with NFX1-91 knockdown


title: TAIL3_WT

value: wild-type


title: TAIL2_WT


title: HCT116_shN91_rep1


title: TAIL1_WT


title: 5_uM_KHS_101

tag: cell type


title: IM5_SPT

description: Gene expression data from 4/5-somite stage intermediate mesoderm

source_name: Zebrafish Intermediate Mesoderm 4/5-somite stage

extract_protocol: total RNA (amplified using two rounds of RNA amplification carried out using the RiboAmp HS RNA Amplification Kit (Arcturus)). RNA was extracted using the PicoPure isolation kit (Arcturus)


title: HCT116_shBgal-rep1


title: Mesorhabditis sp. (isolate KS587)

organism: Mesorhabditis sp. MAH-2010

source_name: Genomic DNA from Mesorhabditis sp. (isolate KS587)


title: Caenorhabditis briggsae (isolate AF16)

organism: Caenorhabditis briggsae

source_name: Genomic DNA from Caenorhabditis briggsae (isolate AF16)


title: Caenorhabditis elegans (isolate N2)

source_name: Genomic DNA from Caenorhabditis elegans (isolate N2)


title: IM4_SPT


title: Delta smelt-Cu-Exposed-2

city: Davis

first: Richard

middle: Edward

last: Connon

address: One Shields Avenue

department: Anatomy, Physiology and Cell Biology

institute: University of California at Davis

hyb_protocol: Hybridization was carried out in an automated tecan HS4800 hybridization station (Tecan, San Jose, Ca, USA)

scan_protocol: Slides were scanned using a GenePix 4000B scanner instrument (Axon Instruments, Sunnyvale, Ca, USA) 317171_635PMT_600_532PMT_500_.gpr

data_processing:
Data analysis: All data analyses were performed using S-plus 2000® [http://spotfire.tibco.com/products/s-plus/statistical-analysis-software.aspx]. Print tip normalization was carried out within slides and sequential single slide data analysis was carried out as an alternative to between-slide normalization. An alpha-outlier-generating model was used to identify differentially expressed genes by applying the following decision rule for multiple-slide data analysis: a given gene was selected as a candidate if it was consistently detected as up- or downregulated in 3 of 3 replicates (raw p value = 0.0625 using exact binomial test and considering outcomes as Bernoulli trials). The approach did not use scale estimation for statistical inference and, therefore did not require between-slide normalization.
Filtration: Prefiltered, normalized, log2 ratios are presented in the Sample table below.  The software used microarray data from single-slide experiments as an input and generated tables with candidate differentially expressed cDNAs. Filtration was conducted using different types of the corresponding ratios, unadjusted p-values, adjusted p-values, and q-values. We applied an average false positive cutoff of 0.0625 to identify candidates for differential gene expression. Therefore only normalized, log2 ratios for features passing set criteria are presented in the Series GSE23238 supplementary file. Expression values for each sample were obtained by subtracting the mean control ratios (samples 4 to 6) from each of the three exposed samples (samples 1 to 3), where permisible. We used a higher than usual cut-off point of 0.0625, due to normal microarray normalization stringencies, as the purpose of this investigation was to identify genes that could be assessed as probable q-PCR based molecular biomarkers for future monitoring programs. Full analytical details are presented in Loguinov et al (2004) [Loguinov AV, Mian IS, Vulpe CD. 2004. Exploratory differential gene expression analysis in microarray experiments with no or limited replication. Genome biology 5:R18. http://genomebiology.com/mkt/6220/2004/5/3/R18].

label: Alexa Fluor 647

organism: Hypomesus transpacificus

source_name: Whole organism, test

label_protocol: Fifteen micrograms of total RNA was labeled with Alexa Fluor dyes using Superscript Plus Indirect cDNA Labeling System (Invitrogen, Carlsbad, Ca, USA)

growth_protocol: Juveniles obtained from the Fish Culture Conservation Facility (FCCL) at the University of California at Davis.

extract_protocol: Total RNA was extracted using Trizol Reagent (Invitrogen, Carlsbad, Ca, USA) as per manufacturer's protocol

treatment_protocol: 57d-old juveniles were exposed for 7 days to 42 ug/L dissolved copper

value: larva

value: 57-days old

tag: stress

value: copper

label: Alexa Fluor 555

source_name: Whole organism, reference

tag: reference composition

value: Pooled mixed age


title: delta smelt-Control-2

scan_protocol: Slides were scanned using a GenePix 4000B scanner instrument (Axon Instruments, Sunnyvale, Ca, USA) 317167_635PMT_600_532PMT_500_.gpr

value: control


title: delta smelt-Control-3

scan_protocol: Slides were scanned using a GenePix 4000B scanner instrument (Axon Instruments, Sunnyvale, Ca, USA) 317168_635PMT_600_532PMT_500_.gpr


title: Delta smelt-Cu-Exposed-3

scan_protocol: Slides were scanned using a GenePix 4000B scanner instrument (Axon Instruments, Sunnyvale, Ca, USA) 317172_635PMT_600_532PMT_500_.gpr


title: Delta smelt-Cu-Exposed-1

scan_protocol: Slides were scanned using a GenePix 4000B scanner instrument (Axon Instruments, Sunnyvale, Ca, USA) 233101_635PMT_600_532PMT_500_.gpr


title: IM3_SPT


title: IM1_WT


title: delta smelt-Control-1

scan_protocol: Slides were scanned using a GenePix 4000B scanner instrument (Axon Instruments, Sunnyvale, Ca, USA) 233125_635PMT_600_532PMT_500_.gpr


title: AD-2cardA/B

status: Public on Aug 17 2010

city: Rochester

first: Jie

last: Dong

state: MN

address: 200 1st SW

department: Thoracic Surgery

institute: Mayo Clinic

description:
micro expression data from different lung development stages
reverse_transcription_protocol: MiRNA was reverse transcibed to cDNA using the Megaplex TM RT Rodent Primers Pool and the TaqMan MicroRNA Reverse Transcription Kit
real-time_PCR: Quantitative 384 well TaqMan Low Density Array real-time PCR was run on the ABI PRISM 7900 System using the TaqMan Universal PCR Master Mix

hyb_protocol: not applicable

scan_protocol: Raw miRNA array data was analyzed by using RQ manager software on the ABI system

data_processing: Normalized CT (ΔCT) was calculated by comparing each miRNA value to that of small nuclear U6 RNA. The U6 RNA is a common internal control for each microRNA array card.

label: SYBR

organism: Mus musculus

source_name: lung

growth_protocol: ICR female mice were bred for timed pregnancies. The day of plug observation was considered day 0 of gestation.

extract_protocol: Total RNA was extracted using mir VanaTM miRNA Isolation Kit (Ambion) according to the manufacturer's instructions.

treatment_protocol: Lungs were isolated by manual dissection with the aid of a dissecting microscope where necessary. Lungs were washed twice with PBS before total RNA extraction

value: ICR

tag: gender

value: female

value: adult


title: P10-2cardA/B

value: postnatal day 10


title: AD-1cardA/B


title: IM2_WT


title: E16-2cardA/B

source_name: embryo lung

value: embryo day 16


title: E18-2cardA/B

value: embryo day 18


title: P2-1cardA/B

value: postnatal day 2


title: P2-2cardA/B


title: E18-1cardA/B


title: HCT116_shBgal-rep2

organism: Homo sapiens


title: E14-1cardA/B

value: embryo day 14


title: E14-2cardA/B


title: E12-2cardA/B

value: embryo day 12


title: E12-1cardA/B


title: patient 2

city: Houston

first: zhishuo

last: ou

state: TX

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of medicine

description: Chromosomal microarray analysis with BAC V5.1 array discovered chromosome 4p deletion and 11p gain of this patient

hyb_protocol: Labeled probes hybridized onto the arrays at 37°C for 24 hours.

scan_protocol: The slides were washed and fluorescent signals on the slides were scanned into image files using an Axon microarray scanner and ScanArray software (GenePix 4000B from Axon Instruments, Union City, CA).

data_processing: Individual microarray LogRatio values were normalized using lowess smoothing to correct for intensity and spatially structured variation in the logRatio values.  The logRatio values for replicate spots were then averaged within each array.  These within array averaged values were then scaled by array using the median absolute deviation (MAD) of the smoothed, averaged  logRatios.  The scale factor for each array is determined to make the post scaling MAD values equivalent in between arrays using the geometric mean method.  Finally, the dye-reversed pair of arrays are sign corrected and averaged to create a final statistic for determing segmental events and a final combined log-ratio value -- and this value is reported as the combined logRatio.

source_name: blood

label_protocol: Genomic DNAs from patient samples and controls were differentially labeled with cyanin-3 (Cy3) and Cy5 (Perkin Elmer,Boston, MA) using a Bioprime DNA direct labeling kit (Invitrogen, Carlsbad, CA)

extract_protocol: Genomic DNA was extracted  from peripheral blood  using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

value: Female

tag: patient

source_name: Blood

tag: reference

value: gender matched normal reference sample


title: patient 2, dye swap


title: P10-1cardA/B

tag: development stage


title: E16-1cardA/B

tag: strain


title: patient 5

description: Chromosomal microarray analysis with OLIGO V6.3 array discovered chromosome 8p deletion and 12p gain of this patient

hyb_protocol: The labeled samples were applied to an array, which was placed in a microarray hybridization chamber (Agilent Technologies), hybridized for more than 20 hours at 65°C in a rotating hybridization oven and washed according to the manufacturer’s protocol (Agilent Technologies).

scan_protocol: The slides were scanned into image files using a GenePix Model 4000B microarray  scanner (Molecular Devices, Sunnyvale, CA) or an Agilent Microarray Scanner (PN G2565BA).

data_processing: Microarray image files of oligo arrays were quantified using Agilent Feature Extraction software (v9.0) default setting, and text file outputs from the quantitation analysis were converted to BAC-level emulation data by combining oligo data corresponding to regions encompassed by BAC clones (“emulated BAC clone”) and then using our in-house analysis package for copy number analysis.

label_protocol: 1-2 μg of genomic DNA from experimental and gender matched reference samples were digested with AluI (10 units) and RsaI (10 units) (Promega, Madison, WI) at 37°C for 2 hours. The labeling reaction was performed using the Bioprime CGH Labeling Module (Invitrogen, Carlsbad, CA) at 37°C for 2 hours in the presence of cyanine 5-dCTP (for the experimental sample) or cyanine 3-dCTP (for the reference sample) (PerkinElmer, Boston, MA).


title: 6909

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

hyb_protocol: Dye incorporations of post-labeling products were measured by ND-1000 spectrophotometer (NanoDrop Technologies) and the parameters that predicted successful hybridization were a yield of 5-7 ug and an incorporation of 25-40 pmol/ug for Cy3 and an incorporation of 20-35 pmol/ug for Cy5. Fluorescent-labeled reference and disease DNAs were mixed with 50 ug of human Cot-1 DNA (Invitrogen Life Technologies) and were hybridized to Human Gdi-dupl-jvdw Custom CGH Microarray 4x44K (Agilent Technologies). Slides were hybridized using a Hybridization gasket slide (Agilent Technologies), placed in rotisserie (20 RPM rotation speed) in the hybridization oven at 65° C for 24 hrs (Agilent Technologies). After hybridization the slides were washed with Agilent washing solutions (including Stabilization and Drying solutions), according to Agilent Oligonucleotide array-based CGH for genomic DNA analysis protocol (version 6.0).

scan_protocol: After washing, the slides were scanned at 10 µm resolution by using a DNA microarray scanner (Agilent Technologies). Scan settings: * Scan region was set to Scan Area (61 × 21.6 mm),   * Green PMT was set to 100%,  * Red PMT was set to 100%. Images were processed with the Feature Extraction Software version 10.1 (Agilent Technologies).

data_processing: Prior to normalization, data from control and empty spots was removed. Due to the large number of probes on the X chromosome that are duplicated, the Loess based normalization as performed within the Agilent Feature extraction software (version 10.1.1.1) fails. Therefore, we fit the Loess regression line through a subset of the data, i.e., those probes that are not located in the region that is expected to be duplicated/deleted. We base ourselves on the uncorrected intensities obtained with the Agilent Feature extraction software (version 10.1.1.1) and we base our Loess fit on the subset of clones that map to the region 152,765,000 - 152,865,000 on the X chromosome. We omit data from unmapped clones and from spots that were not above background in both channels. The presented values are log-(Cy5/Cy3)-ratios. In case of multiple probes for the same Agilent ID, log-ratios were averaged.

label_protocol: 500 ng genomic DNA was digested with AluI/RsaI restriction enzyme mix (Promega, Madison, WI). Fragmented DNA was labeled by direct enzymatic incorporation of fluorescent tags. Genomic DNA was labeled with Cy5-dUTP using the Agilent Genomic DNA Labeling kit PLUS (Agilent Technologies). Briefly, 50 ul reaction mix was incubated with Exo-Klenow Fragment at 37°C for 2 hrs. Unincorporated nucleotides were removed on Microcon YM-30 filters (Millipore, Billerica, MA) according to the manufacturer protocol.

extract_protocol: Genomic DNA from patients as well as from healthy controls was isolated from peripheral blood using the Wizard Genomic DNA purification Kit (Promega, Madison, WI) and using manufacturer’s protocol.

tag: organism

value: Homo sapiens

value: Male

tag: tissue

value: White Blood Cells

source_name: Co1-XY (control)

label_protocol: 500 ng genomic DNA was digested with AluI/RsaI restriction enzyme mix (Promega, Madison, WI). Fragmented DNA was labeled by direct enzymatic incorporation of fluorescent tags. Genomic DNA was labeled with Cy3-dUTP using the Agilent Genomic DNA Labeling kit PLUS(Agilent Technologies). Briefly, 50 ul reaction mix was incubated with Exo-Klenow Fragment at 37°C for 2 hrs. Unincorporated nucleotides were removed on Microcon YM-30 filters (Millipore, Billerica, MA) according to the manufacturer protocol.


title: patient 6

description: Chromosomal microarray analysis with OLIGO V6.4 array discovered chromosome 8p deletion and 12p gain of this patient


title: Mouse lung-embryo day 14-rep1

description: Gene expression data from different lung development stages

hyb_protocol: The targets for Affymetrix DNA microarray analysis were prepared according to the manufacturer’s instructions. Biotin-labeled cRNA, produced by in vitro transcription, was fragmented and hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 Arrays at 45°C for 16 hr and then washed and stained using the GeneChip Fluidics.

scan_protocol: The arrays were scanned by a GeneArray Scanner and patterns of hybridization detected as light emitted from the fluorescent reporter groups incorporated into the target and hybridized to oligonucleotide probes.

data_processing: The data were analyzed with Partek Genomics Suite 6.4 using Affymetrix default analysis settings and GC-RMA as normalization method

label_protocol: Labeling was performed according to Affymetrix Gene Chip technical manual


title: Mouse lung-postnatal day 10-rep2


title: Mouse lung-embryo day 16-rep2


title: Mouse lung-postnatal day 2-rep1


title: 6911


title: Mouse lung-embryo day 18-rep2


title: Mouse lung-embryo day 18-rep1


title: 6912


title: TAIL5_SPT

value: spt/tbx16 mutant


title: Mouse lung-embryo day 12-rep1


title: Mouse lung-embryo day 12-rep2


title: 6910


title: Mouse lung-embryo day 16-rep1


title: Mouse lung-postnatal day 30-rep1


title: Mouse lung-embryo day 14-rep2


title: patient 3

description: Chromosomal microarray analysis with OLIGO V6.1 array discovered chromosome 4p deletion and 11p gain of this patient

scan_protocol: The slides were scanned into image files using a GenePix Model 4000B microarray scanner (Molecular Devices, Sunnyvale, CA) or an Agilent Microarray Scanner (PN G2565BA).


title: T00321814

first: Changkyu

last: Lee

address: 551 N 34th St

institute: Allen Institute for Brain Science

description: sample barcode: T00321814

hyb_protocol: Samples were applied to CodeLink Mouse Whole Genome Bioarrays (formerly supplied by GE Healthcare, Piscataway, NJ; now supplied by Applied Microarrays, Inc, Tempe, AZ) in hybridization buffer. Arrays were hybridized (37°C for 18 h) in a shaking incubator, washed in 0.75X Tris-buffered saline (pH 7.6) at 46°C for 1 h, and stained with Cy5-Streptavidin dye conjugate for 30 min.

scan_protocol: Rinsed and dried arrays were scanned with a GenePixTM 4000B scanner [Molecular Devices, (formerly Axon Instruments), Sunnyvale, CA] at 5 µm resolution.

data_processing: Codelink Expression Analysis software (Applied Microarrays, Inc, Tempe, AZ) was used for gridding and feature intensity extraction from the scanned array images. quantile normalization followed by COMBAT

label_protocol: Following the second round of reverse transcription, second-strand cDNA synthesis, and purification of double-stranded cDNA, in vitro transcription was performed using T7 RNA polymerase in the presence of Biotin-11-UTP. Purified cRNA (10 µg) was fragmented to uniform size (~0.1 kb).

extract_protocol: Laser microdissection using the Leica LMD6000 was carried out on tissue sections (10 um) lightly stained with cresyl violet. Tissue was isolated into RLT buffer (Qiagen) and purified using the RNeasy kit (Qiagen). Using 5 ng total RNA as starting material, a two-round RNA amplification (Ambion MessageAmp II kit) was used to produce sufficient cDNA for biotin-labeling and hybridization to microarrays.

tag: tissue region

value: TMN

tag: region name

value: Tuberomammillary Nucleus, ventral

tag: condition

value: W

tag: specimen

tag: time of day


title: T00333412

description: sample barcode: T00333412

tag: age


title: Mouse lung-postnatal day 30-rep2

value: ICR

value: female


title: Mouse lung-postnatal day 2-rep2


title: Mouse lung-postnatal day 10-rep1

value: postnatal day 10


title: T00333419

description: sample barcode: T00333419


title: T00321666

description: sample barcode: T00321666


title: T00333415

description: sample barcode: T00333415

value: SDC


title: T00333369

description: sample barcode: T00333369


title: T00321942

description: sample barcode: T00321942


title: T00333414

description: sample barcode: T00333414

value: SD


title: T00321662

description: sample barcode: T00321662


title: T00333368

description: sample barcode: T00333368


title: T00321813

description: sample barcode: T00321813

value: RSC


title: T00333371

description: sample barcode: T00333371

value: RS


title: T00320806

description: sample barcode: T00320806


title: T00321944

description: sample barcode: T00321944


title: T00320808

description: sample barcode: T00320808


title: T00321943

description: sample barcode: T00321943


title: T00333379

description: sample barcode: T00333379

value: SCh

value: Suprachiasmatic Nucleus


title: T00320807

description: sample barcode: T00320807


title: T00320809

description: sample barcode: T00320809


title: T00333413

description: sample barcode: T00333413


title: T00320666

description: sample barcode: T00320666


title: HCT116_shN91_rep2

tag: cell line

value: HCT116 Human colon cancer

tag: shRNA expressing


title: T00333421

description: sample barcode: T00333421


title: T00320680

description: sample barcode: T00320680


title: T00321820

description: sample barcode: T00321820


title: T00321665

description: sample barcode: T00321665


title: T00321799

description: sample barcode: T00321799


title: T00321650

description: sample barcode: T00321650


title: T00321819

description: sample barcode: T00321819


title: T00320679

description: sample barcode: T00320679


title: T00320683

description: sample barcode: T00320683


title: T00333422

description: sample barcode: T00333422


title: T00320664

description: sample barcode: T00320664


title: T00321649

description: sample barcode: T00321649


title: T00333423

description: sample barcode: T00333423


title: T00321663

description: sample barcode: T00321663


title: T00320665

description: sample barcode: T00320665


title: T00321800

description: sample barcode: T00321800


title: T00320681

description: sample barcode: T00320681


title: T00321648

description: sample barcode: T00321648


title: T00333418

description: sample barcode: T00333418

value: COApm

value: Cortical Amygdala, posteromedial


title: T00321647

description: sample barcode: T00321647


title: T00321801

description: sample barcode: T00321801


title: T00320812

description: sample barcode: T00320812


title: T00320768

description: sample barcode: T00320768


title: T00333417

description: sample barcode: T00333417


title: T00333380

description: sample barcode: T00333380


title: T00333409

description: sample barcode: T00333409


title: T00320624

description: sample barcode: T00320624

value: ORB

value: Orbital Cortex


title: T00320769

description: sample barcode: T00320769


title: T00320754

description: sample barcode: T00320754


title: T00319412

description: sample barcode: T00319412


title: T00320802

description: sample barcode: T00320802


title: T00320800

description: sample barcode: T00320800


title: T00321808

description: sample barcode: T00321808


title: T00320757

description: sample barcode: T00320757


title: T00320803

description: sample barcode: T00320803


title: T00321645

description: sample barcode: T00321645


title: T00321809

description: sample barcode: T00321809


title: T00320755

description: sample barcode: T00320755


title: T00333382

description: sample barcode: T00333382


title: T00319413

description: sample barcode: T00319413


title: T00320770

description: sample barcode: T00320770


title: T00320627

description: sample barcode: T00320627


title: T00320756

description: sample barcode: T00320756


title: T00320689

description: sample barcode: T00320689


title: T00320626

description: sample barcode: T00320626


title: T00333383

description: sample barcode: T00333383


title: T00320813

description: sample barcode: T00320813


title: T00321818

description: sample barcode: T00321818

value: ENT

value: Dorsal Entorhinal Cortex


title: T00333408

description: sample barcode: T00333408


title: T00320753

description: sample barcode: T00320753


title: T00320811

description: sample barcode: T00320811


title: placebo donor 505 left kidney

city: Vienna

first: Julia

last: Wilflingseder

address: Währinger Gürtel 18-20

department: Nephrology and Dialysis

country: Austria

institute: Medical University of Vienna

description: Two micrograms of isolated total RNA were amplified using the RiboAmp RNA amplification kit (Arcturus, Mountain View, California). The amplified RNA was inspected on an ethidium bromide stained 1% agarose gel and on the Agilent 2100 Bioanalyzer. For the 40 zero hour kidney biopsies the RNA was of sufficient quality to proceed with microarray analysis.

hyb_protocol: Samples were loaded onto arrays and incubated for 18 hours in a 65°C water bath. The arrays were washed three times before scanning. All protocols can be found at http://www.meduniwien.ac.at/nephrogene/

scan_protocol: The fluorescence images of the hybridized microarrays were examined using a GenePix 4100A scanner (Axon Instruments, Union City, California).

data_processing: The GenePix Pro 6.0 software was used to grid images and to calculate spot intensities. The arrays were numbered according to the anonymous organ donor ID, and were processed in random order. Image-, grid- and data-files were submitted to the Stanford Microarray Database (http://genome-www5.stanford.edu/MicroArray/SMD/)

source_name: kidney wedge biopsy

label_protocol: Using a type II experimental set-up, 1 µg of sample and standard Stratagene Universal human reference aRNA were labeled with CyScribe cDNA post labeling kit (Amersham Pharmacia Biotech, Buckinghamshire, UK) in a two-step procedure.

extract_protocol: Total RNA was isolated and purified using chloroform and trizol reagent (Invitrogen, Carlsbad, California). RNA yield and quality was checked with the Agilent 2100 Bioanalyzer and RNA6000 LabChipÒ kit (Agilent, Palo Alto, California). Stratagene Universal human reference RNA was used as reference (Stratagene, La Jolla, California).

treatment_protocol: After brain death was declared the deceased donor was randomized to receive 1000mg of methylprednisolone (corticosteroid) or blinded placebo (0.9% saline) at least three hours before organ harvesting.

tag: agent

value: placebo

source_name: Stratagene Universal reference RNA

tag: different cell lines


title: T00320678

description: sample barcode: T00320678

value: W


title: placebo donor 147 left kidney


title: T00319420

description: sample barcode: T00319420


title: T00319415

description: sample barcode: T00319415


title: T00320801

description: sample barcode: T00320801


title: T00321815

description: sample barcode: T00321815


title: T00320766

description: sample barcode: T00320766


title: T00321810

description: sample barcode: T00321810


title: T00320620

description: sample barcode: T00320620


title: T00333376

description: sample barcode: T00333376


title: placebo donor 143 right kidney


title: placebo donor 196 right kidney


title: T00320625

description: sample barcode: T00320625


title: T00319426

description: sample barcode: T00319426


title: T00319431

description: sample barcode: T00319431


title: placebo donor 327 left kidney


title: T00333420

description: sample barcode: T00333420


title: placebo donor 151 right kidney


title: T00320623

description: sample barcode: T00320623


title: placebo donor 505 right kidney


title: placebo donor 118 right kidney


title: T00333381

description: sample barcode: T00333381


title: placebo donor 118 left kidney


title: T00320672

description: sample barcode: T00320672


title: T00320676

description: sample barcode: T00320676


title: T00320616

description: sample barcode: T00320616


title: placebo donor 117 left kidney


title: placebo donor 503 right kidney


title: placebo donor 393 left kidney


title: T00321817

description: sample barcode: T00321817


title: T00333362

description: sample barcode: T00333362


title: placebo donor 355 left kidney


title: placebo donor 162 left kidney


title: placebo donor 138 left kidney


title: placebo donor 131 right kidney


title: placebo donor 180 right kidney


title: T00320810

description: sample barcode: T00320810


title: T00320673

description: sample barcode: T00320673


title: T00321816

description: sample barcode: T00321816


title: placebo donor 117 right kidney


title: T00320617

description: sample barcode: T00320617


title: corticosteroid donor 389 left kidney

value: corticosteroid


title: placebo donor 376 left kidney


title: T00333375

description: sample barcode: T00333375

value: LC

value: Locus Coeruleus


title: T00319429

description: sample barcode: T00319429


title: placebo donor 125 left kidney


title: T00319430

description: sample barcode: T00319430


title: corticosteroid donor 157 left kidney


title: T00320684

description: sample barcode: T00320684

value: SDC


title: T00320671

description: sample barcode: T00320671


title: T00319425

description: sample barcode: T00319425


title: corticosteroid donor 184 left kidney


title: corticosteroid donor 134 left kidney


title: T00320752

description: sample barcode: T00320752


title: corticosteroid donor 145 right kidney


title: corticosteroid donor 139 right kidney


title: corticosteroid donor 386 left kidney


title: T00320748

description: sample barcode: T00320748


title: corticosteroid donor 198 right kidney


title: T00320667

description: sample barcode: T00320667

value: SD


title: T00320668

description: sample barcode: T00320668


title: corticosteroid donor 501 right kidney


title: corticosteroid donor 139 left kidney


title: corticosteroid donor 124 left kidney


title: corticosteroid donor 198 left kidney


title: T00319422

description: sample barcode: T00319422


title: T00319421

description: sample barcode: T00319421


title: T00320747

description: sample barcode: T00320747


title: corticosteroid donor 124 right kidney


title: corticosteroid donor 195 right kidney


title: T00320688

description: sample barcode: T00320688

value: RSC


title: corticosteroid donor 168 right kidney


title: corticosteroid donor 106 right kidney


title: T00320749

description: sample barcode: T00320749

value: RS


title: T00319424

description: sample barcode: T00319424


title: corticosteroid donor 172 right kidney


title: T00333361

description: sample barcode: T00333361


title: CRX versus IgG ChIP of retinal tissue

city: Regensburg

first: Thomas

last: Langmann

address: Franz-Josef-Strauss-Allee 11

department: University of Regensburg

country: Germany

institute: Institute of Human Genetics

description: CRX ChIP vs IgG ChIP with Affymetrix Promoter 1.0 Arrays

hyb_protocol: DNA was hybridzed using the Affymetrix hybridization kit

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G

data_processing:
Affymetrix GCOS processed image files to generate CEL-Files. Genomatix ChipInspector was used to retrieve significant promoters (bed.files)
additional results files: CRX vs IgG Significant Transcripts.txt
results file descriptions: Transcripts of promoters bound by CRX

source_name: CRX ChIP from 2 month wt retinas

label_protocol: Samples were enzymatically fragmented and labeled using the WT Labeling Kit (Affymetrix) to add biotinylated compound to the ends of the fragments

extract_protocol: Chromatin was prepared as described in Corbo et al. 2010, Genome Research doi:10.1101/gr.109405.110

value: 2 months postnatal

value: retina

tag: antibody

tag: antibody manufacturer

value: Santa Cruz

tag: antibody catalog #

tag: genetic background

source_name: IgG ChIP from 2 month wt retinas

value: Normal rabbit IgG

value: Upstate


title: corticosteroid donor 101 right kidney


title: T00320669

description: sample barcode: T00320669

tag: strain


title: corticosteroid donor 113 left kidney


title: MLR-DC_IL10_3

city: Bergisch-Gladbach

first: Stefan

last: Tomiuk

address: Friedrich-Ebert-Str. 68

department: Bioinformatics

institute: Miltenyi Biotec GmbH

description: gene expression analysis of SuperAmplified™ polyA RNA

hyb_protocol: 1.25 μg Cy3 labeled and purified (CyScribe GFX Purification Kit, GE Healthcare) cDNAs in hybridization buffer were hybridized overnight (17 hours, 65°C) to 4x44K Agilent Whole Human Genome Oligo Microarrays using Agilent’s recommended hybridization chamber and oven. Following hybridization, the microarrays were washed once with Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated (37°C) Agilent Gene Expression Wash Buffer 2 containing 0.005% N-lauroylsarcosine for 1 min. The last washing step was performed with acetonitrile for 30 sec.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies). The Agilent Feature Extraction Software (FES, v.9.5.1.1.) was used to read out and process the microarray image files.

data_processing: For determination of differential gene expression FES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system (v.7.1.0.0., Rosetta Inpharmatics LLC). Ratios were computed for each sample/control pair and transformed to log2 scale. Additionally, p-values indicating the reliability of a observed difference between a sample and its corresponding control were calculated for each gene applying the universal error model implemented in the Rosetta Resolver software.

molecule: polyA RNA

source_name: mixed lymphocyte culture (responder: PBMC, stimulator: IL-10 treated dendritic cells)

label_protocol: 250 ng of the purified PCR product (NucleoSpin Extract II Kit, Macherey & Nagel) was labeled with Cy3-dCTP (GE Healthcare) in a Klenow Fragment reaction.

growth_protocol: CD14+ monocytes were isolated as the adherent fraction after an incubation of 1h in RPMI 1640 (Biowhittaker) with 5% pooled AB human serum (HS)  (BioWhittaker), 100 U/ml penicillin/streptomycin (Bristol-Myers Squibb), and 2mM L-glutamine (GIBCO BRL, Gaithersburg) (DC medium) at 37°C. After different washing steps, adherent monocytes were cultured in 10 ng/ml rhIL-4 (R&D Systems) and 100 ng/ml rhGM-CSF (R&D Systems) in DC medium alone or in the presence of 10 ng/ml of rhIL-10 (BD Bioscience, Mountain View, CA) for 5 days. After 5 days, DC differentiated in the absence of IL-10 were matured with lipopolysaccharide from E. coli (LPS) (1 µg/ml, Sigma Chemicals, St Louis, MO) for additional 2 days. At day 7, DC generated in the presence of IL-10 (DC-10), and mature DC (mDC) were collected, irradiated at 6000 Rads and used to stimulate T cells. The purity and maturation state of DC were checked by flow cytometry to determine expression of CD1a, CD14, CD83 and HLA-DR.

extract_protocol: Cell samples were lysed using SuperAmp™ Lysis Buffer following manufacturer’s instructions and stored at -80°C. DNA microarray analysis of gene expression was performed at Miltenyi Biotec´s Genomics Service facility (Bergisch Gladbach, Germany), using Agilent technology (Agilent Technologies, Inc.). SuperAmplification was performed according to manufacturer’s instruction. Briefly, cell samples were collected in 6.4 μl lysis buffer (including detergent, tRNA and Protease), the mRNA extracted using magnetic beads and transcribed into cDNA using tagged random and oligo(dT) primer. First strand cDNA was 5’ tagged using terminal deoxynucleotidyl transferase (Fermentas). Tagged cDNA was globally amplified (Expand Long Template PCR System DNA Pol Mix, Roche) using primers complementary to the tag sequence. Amplified cDNAs were quantified using ND-1000 Spectrophotometer (NanoDrop Technologies, Inc). Integrity of the cDNA was checked via the Agilent 2100 Bioanalyzer platform (Agilent Technologies, Inc.)

treatment_protocol: Human peripheral blood was obtained from healthy donors, haploidentical donors, and HLA-matched unrelated donors in accordance with local ethical committee approval. Peripheral blood mononuclear cells (PBMC) were separated by density gradient centrifugation over Lymphoprep (Nycomed Amersham, Uppsala, Sweden). Total PBMC were used as responder cells and CD3-depleted cells or DC as stimulators. When CD3-depleted cells were used as stimulators, responder cells were plated at 1:1 ratio: 5x105/well with the same number of stimulator cells in a final volume of 1 ml, in 24-well-plates (Costar, Cambridge, MA), or 1x105/well in a final 200ul in round bottomed 96-well-plates, in the presence or absence of rhIL-10 (10 ng/ml). When DC were used as stimulators, responder cells were plated at 10:1 ratio: 106/well PBMC with 105/well of DC (mDC or DC-10) in a final volume of 1 ml, in 24-well-plates (Costar), or 105/well PBMC with 104/well of DC in a final 200l in round bottomed 96-well-plates. To evaluate secondary responses, primary cultures were carried on in 24-well plates for 10 days, in the presence or absence of IL-10. At day 7 half of the medium, with or without cytokines, was replaced with fresh one. At day 10 cells were collected, washed and plated in 96-well plates with newly prepared stimulator cells (at 1:1 ratio for CD3-depleted cells or 10:1 ratio for mDC), without the addition of cytokines.

tag: cell type

value: mixed lymphocyte culture:PBMC + DC

tag: stimulator

tag: responder-to-stimulator ratio


title: T00321940

description: sample barcode: T00321940

tag: tissue region

value: Hcrt

tag: region name

value: Hypocretin area


title: T00319423

description: sample barcode: T00319423

tag: condition

tag: specimen


title: Polysomal RNA purified from MEFs derived from a EIF4E-KI mouse rep 2

type: other

city: Stockholm

first: Ola

last: Larsson

department: Department of oncology-pathology

country: Sweden

institute: Karolinska Institutet

hyb_protocol: Standard hybridization optimized by Illumina

scan_protocol: Standard scan protocoll optimized by Illumina

data_processing: Data was transformed using Variance Stabilizing Transformation  (VST) and normalized using Robust Spline Normalization (RSN) in the statistical environment R using the lumi package.

molecule: other

label_protocol: 250ng RNA (polysomal or total) was labelled using the single round Illumina protocol

growth_protocol: MEFs were isolated from 14.5d pregnant females as previously described (Le Bacquer et al. 2007 The Journal of Clinical Investigation). WT and KI MEFs (5 x106) immortalized by passage were grown in DMEM supplemented with 10% FBS.

extract_protocol: Polysomal and total cytoplasmic RNA was isolated as described (Larsson et al. 2007, Cancer Research). Fractions containing mRNAs bound to >3 ribosomes were pooled and designated heavy polysomal RNA. RNA isolation procedure was performed in two independent experiments from one pair of KI and WT MEFs.

tag: genotype


title: corticosteroid donor 113 right kidney


title: T00320686

description: sample barcode: T00320686

tag: age

tag: time of day


title: Total RNA purified from MEFs derived from a EIF4E-KI mouse rep 2


title: T00320629

description: sample barcode: T00320629


title: T00333378

description: sample barcode: T00333378


title: MLR-mDC_3

source_name: mixed lymphocyte culture (responder: PBMC, stimulator: mature dendritic cells)


title: Polysomal RNA purified from MEFs derived from a WT mouse rep 2

value: WT


title: T00321796

description: sample barcode: T00321796


title: T00320763

description: sample barcode: T00320763

value: W


title: T00320751

description: sample barcode: T00320751


title: MLR-DC_IL10_1


title: T00321668

description: sample barcode: T00321668


title: Total RNA purified from MEFs derived from a WT mouse rep 2


title: T00320759

description: sample barcode: T00320759


title: MLR-mDC_2


title: sorted tumor epithelium 838

city: Boston

first: Qiyuan

last: Li

state: MA

address: 44 Binney street

department: Medical Oncology

institute: Dana Farber Cancer Institute

description: Gene expression data from breast cancer epithelial cells prified from tumor tissue using BerEp4 antibody coated magnetic beads.

hyb_protocol: standard Affymetrix procedures.

scan_protocol: standard Affymetrix procedures.

data_processing: Raw gene expression values were obtained using Affymetrix GeneChip software and further analyzed using the DNA-Chip Analyzer (dChip).

source_name: sorted tumor epithelium

label_protocol: Approximately 1 microgram of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Isolation of RNA was performed using the Trizol method (Invitrogen) according to the manufacturers instructions and was purified using RNeasy mini-columns (Qiagen, Valencia, CA). The quality of the RNA obtained from each tumour sample was assessed based on the RNA profile generated by the bioanalyzer (Agilent Inc)olation of RNA was performed using the Trizol method (Invitrogen) according to the manufacturers instructions and was purified using RNeasy mini-columns (Qiagen, Valencia, CA). The quality of the RNA obtained from each tumour sample was assessed based on the RNA profile generated by the bioanalyzer (Agilent Inc).

treatment_protocol: Primary tumor samples were collagenase digested then sorted for epithelial cells using BerEp4 antibody coated magnetic beads

value: sorted breast tumor epithelium

value: Unknown

tag: invasive tumour type

value: Ductal

tag: invasive b-r grade

value: I

tag: er status

value: pos

tag: pr status

tag: her2 status

value: neg


title: Total RNA purified from MEFs derived from a WT mouse rep 1


title: MLR-DC_IL10_2


title: MLR-mDC_1


title: T00319434

description: sample barcode: T00319434

value: SDC


title: Polysomal RNA purified from MEFs derived from a WT mouse rep 1


title: sorted tumor epithelium 818

value: II


title: T00320618

description: sample barcode: T00320618

value: ENT

value: Dorsal Entorhinal Cortex

value: RSC


title: T00333372

description: sample barcode: T00333372

value: SD


title: MLR-MEC_IL10_2

source_name: mixed lymphocyte culture (responder: PBMC, stimulator: IL-10 treated CD3-depleted cells)

value: mixed lymphocyte culture:PBMC + MEC


title: T00320758

description: sample barcode: T00320758

value: Hcrt


title: Polysomal RNA purified from MEFs derived from a EIF4E-KI mouse rep 1


title: sorted tumor epithelium 795

value: III


title: MLR-MEC_IL10_3


title: Total RNA purified from MEFs derived from a EIF4E-KI mouse rep 1


title: sorted tumor epithelium 718


title: T00321795

description: sample barcode: T00321795

value: Hypocretin area


title: MLR-MEC_IL10_1


title: MLR-MEC_3

source_name: mixed lymphocyte culture (responder: PBMC, stimulator: CD3-depleted cells)


title: T00333377

description: sample barcode: T00333377


title: MLR-MEC_2


title: Breast cancer cell line HCC1402

description: Gene expression data from breast cancer tumor cell line

source_name: Cell line

value: Breast cancer cell line


title: sorted tumor epithelium 850

value: sorted breast tumor epithelium

value: M


title: Breast cancer cell line HCC1401

value: Ductal


title: T00320761

description: sample barcode: T00320761


title: T00333374

description: sample barcode: T00333374

value: LC

value: Locus Coeruleus


title: Breast cancer cell line HCC1399

value: wt

value: neg

value: pos


title: MLR-MEC_1


title: T00321939

description: sample barcode: T00321939


title: Breast cancer cell line HCC1398


title: T00319433

description: sample barcode: T00319433