title: KB1_vs_ABC8 Targeted CGH

city: Seattle

first: Jeffrey

last: Kidd

state: WA

address: 1705 NE Pacific St

department: Department of Genome Sciences

institute: University of Washington

description: The results of this array-CGH experiment were used to conform predicted copy number differences between samples KB1 and NA18507.  This array targets regions of predicted copy number difference between KB1 and BA18507

hyb_protocol: Genomic DNA  was hybridized in the Eichler Lab, University of Washington following the NimbleGen suggested protocols.

scan_protocol: The array slide was scanned in the Eichler Lab, University of Washington following the NimbleGen suggested protocols.

data_processing: normalized log2 ratios calculated by NimbleGen software.  These log2 ratios were used for copy number analysis (available on Series record).

label_protocol: Genomic DNA labeled in Eichler Lab, University of Washington following the manufacturers (NimbleGen) protocols.

extract_protocol: Genomic DNA was extracted from whole blood using the Qiagen DNA mini extraction kit.

tag: sample

tag: cell type

value: whole blood

extract_protocol: Genomic DNA for sample NA18507 was obtained from a transformed lymphocyte cell line.  Extractions were performed by Coriell Institute for Medical Research (http://www.coriell.org/), from whom a DNA aliquot was obtained.

value: transformed lymphocyte cell line


title: Breast primary B8 T

status: Public on Feb 18 2010

type: genomic

city: Cambridge

first: Craig

last: Mermel

state: MA

address: 7 Cambridge Center

department: Cancer Program

country: USA

institute: Broad Institute

description: Hybridized to 250K_Sty

hyb_protocol: Each sample was genotyped using the Sty I chip of the 500K Human Mapping Array wet (Affymetrix), containing probes to 238,270 SNP loci, according to manufacturer’s instructions. In brief, 250 ng of genomic DNA was digested with the StyI restriction enzyme (New England Biolabs), ligated to an adaptor with T4 ligase (New England Biolabs), and PCR-amplified using a 9700 Thermal Cycler I (Applied Biosystems) and Titanium Taq (Clontech) to achieve fragments ranging from 200-1100 bp. These fragments were pooled, concentrated, processed through a clean-up step, and further fragmented with DNaseI (Affymetrix) before being labeled, denatured, and hybridized to arrays

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

data_processing: Probe-level signal intensities were normalized to a common reference array using quantile normalization and combined to form SNP-level signal intensities using the dChip model-based expression (PM/MM) method . Genome-wide copy number estimates were obtained using tangent normalization, in which tumor signal intensities are divided by signal intensities from the linear combination of all normal samples that is most similar to the tumor (as described in Beroukhim et al, In Press; and Getz et al., In Preparation). Cancer samples were normalized against a pool of 1,480 reference samples derived from multiple studies; the code and reference data necessary to replicate this analysis are available for download in GEO. Genotype Call (SNP call) are provided in .CHP.TXT files: AA, AB, BB, NC, and NoCall.

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: B8 T

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: DNA was obtained from cell line pellets or tumors frozen at the time of surgical dissection and maintained at -80C until use, with the exception of 11 gliomas from which sufficiently high-quality DNA could be obtained from paraffin-embedded samples. The majority of tumors were obtained at primary surgery, with the exceptions of 27 prostate tumors obtained through rapid autopsy programs at the Universities of Washington and Michigan

value: Breast primary

tag: cell line


title: NA18507_vs KB1 array CGH

middle: M


title: Control #1

city: Bronx

first: Reid

middle: F

last: Thompson

state: NY

address: 1301 Morris Park Avenue

department: Molecular Genetics

institute: Albert Einstein College of Medicine

hyb_protocol: See Roche NimbleGen website and R.R. Selzer et al., PMID: 16075461, for details.

scan_protocol: Scanned using a GenePix 4000B scanner (Axon Instruments) (See R.R. Selzer et al., PMID: 16075461).

data_processing: Signal intensities at each HpaII amplifiable fragment were calculated as a robust (25% trimmed) mean of their component probe-level signal intensities. Any fragments found within the level of background MspI signal intensity, measured as 2.5 mean-absolute-differences (MAD) above the median of random probe signals, were categorized as “failed.” These “failed” loci therefore represent the population of fragments that did not amplify by PCR, whatever the biological (e.g. genomic deletions and other sequence errors) or experimental cause. On the other hand, “Methylated” loci were so designated when the level of HpaII signal intensity was similarly indistinguishable from background. PCR-amplifying fragments (those not flagged as either “methylated” or “failed”) were normalized using an intra-array quantile approach wherein HpaII/MspI ratios are aligned across density-dependent sliding windows of fragment size-sorted data (See R.F. Thompson et al., PMID: 18353789, for more details).  Robust multichip average (RMA) was then applied to each group independently (See R.A. Irizarry et al., PMID: 12925520).

source_name: CD34+, control, MspI

label_protocol: Random 9-mers pre-labeled with Cy3 or Cy5, for MspI or HpaII, respectively.

extract_protocol: Representation of the genome generated by digestion with either HpaII or MspI and amplification by ligation-mediated PCR according to the revised HELP protocol (See M. Oda, et al., PMID:19386619).

tag: birth weight

tag: ponderal index

tag: gender

value: female

tag: gestational age

value: 41 weeks

tag: tissue

value: umbilical cord blood

value: CD34+ cells

tag: restriction enzyme

value: MspI

source_name: CD34+, control, HpaII

value: HpaII


title: leaf_gDNA_Tsu_rep6

status: Public on Feb 17 2010

city: Austin

first: Thomas

middle: E.

last: Juenger

state: TX

address: 1 University Station, C0930

department: Section of Integrative Biology

institute: University of Texas at Austin

description: gDNA hybridizations to explore sequence polymorphisms

hyb_protocol: standard Affymetrix protocol

scan_protocol: Affymetrix GeneChip Scanner 3000, GCOS v1.3

data_processing: Microarray Suite 5, data processed with JMP Genomics, R statistics

label: biotin

organism: Arabidopsis thaliana

label_protocol: Biotin labeling, Invitrogen Bioprime kit, following Borevitz 2005

growth_protocol: standard Arabidopsis growth conditions in a Percival growth chamber - 16L/8D, 21 degrees day, 18 degrees night

extract_protocol: Qiagen Dneasy Plant Mini prep

treatment_protocol: no treatment

tag: accession

value: rosette leaf

tag: batch

value: B


title: leaf_gDNA_Tsu_rep4


title: Wt HSC v. CML rep 3

type: RNA

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: Hematopoiesis, development
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/51319.gif

hyb_protocol: not provided

scan_protocol: GenePix 4000A

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

molecule: total RNA

organism: Mus musculus

source_name: CML

label_protocol: not provided

extract_protocol: not provided

tag: test

value: CML

source_name: wt

tag: reference

value: WT


title: Control #2

value: male

value: 40 weeks


title: leaf_gDNA_Tsu_rep3

value: A


title: Wt HSC v. Day2Mob dye swap of 4570

description:
Simple annotation: Hematopoiesis, Drug treatment
Image: http://smd.stanford.edu/MicroArray/gifs//50364.gif

source_name: D2 Cy/G BM HSC

value: D2 Cy/G BM HSC

source_name: WT BM HSC

value: WT BM HSC


title: Control #5


title: leaf_gDNA_Tsu_rep2


title: Control #3


title: leaf_gDNA_Kas_rep6


title: leaf_gDNA_Kas_rep5


title: Wt HSC v. Day2Mob dye swap of 0457

description:
Simple annotation: Hematopoiesis, development
Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55577.gif

source_name: WT


title: leaf_gDNA_Kas_rep4


title: leaf_gDNA_Kas_rep3


title: Wt HSC v. Day2Mob rep 1

description:
Simple annotation: Hematopoiesis, Drug treatment
Image: http://smd.stanford.edu/MicroArray/gifs//50363.gif


title: IUGR #4

source_name: CD34+, IUGR, MspI

value: 39.7 weeks

source_name: CD34+, IUGR, HpaII


title: IUGR #5


title: Wt HSC v. CML rep 1

description:
Simple annotation: Hematopoiesis, development
Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55574.gif

source_name: CtrlCMLHSC

source_name: CMLHSC

value: CML HSC


title: Control #4

value: female

value: 39.4 weeks


title: Wt HSC v. CML rep 2

description:
Simple annotation: Hematopoiesis, development
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58397.gif

source_name: 13k CML HSC

value: 13k CML HSC

source_name: 6.7k Ctrl HSC

value: 6.7k Ctrl HSC


title: leaf_gDNA_Kas_rep2


title: Wt HSC v. Day2Mob dye swap of 5355

description:
Simple annotation: Hematopoiesis, development
Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55351.gif


title: Wt HSC v. CML dye swap of 3116

description:
Simple annotation: Hematopoiesis, development
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/51320.gif


title: leaf_gDNA_Kas_rep1


title: Wt HSC v. Day2Mob rep 3

description:
Simple annotation: Hematopoiesis, development
Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55350.gif


title: leaf_gDNA_Col_rep6


title: leaf_gDNA_Col_rep5


title: Wt HSC v. Day2Mob rep 4

description:
Simple annotation: Hematopoiesis, Drug treatment
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50243.gif


title: Wt HSC v. Day2Mob rep 2

description:
Simple annotation: Hematopoiesis, development
Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55576.gif


title: leaf_gDNA_Col_rep4


title: IUGR #1

value: 39.9 weeks

value: umbilical cord blood

value: CD34+ cells

value: MspI


title: leaf_gDNA_Col_rep2

value: rosette leaf


title: Wt HSC v. CML dye swap of 0460

description:
Simple annotation: Hematopoiesis, development
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58398.gif

source_name: 13k CML  HSC


title: Wt HSC v. CML dye swap of 4564

description:
Simple annotation: Hematopoiesis, development
Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55575.gif

value: WT


title: leaf_gDNA_Col_rep1


title: leaf_gDNA_Tsu_rep5

value: B


title: IUGR #2

value: 40.1 weeks

value: HpaII


title: leaf_gDNA_Col_rep3

value: A


title: IUGR #3


title: leaf_gDNA_Tsu_rep1


title: leaf_tsu_wet_11

description: cRNA hybridizations to explore gene expression

hyb_protocol: standard Affymetrix protocol using Affymetrix Model 640 hybridization oven

label_protocol: biotin-labeled targets (cRNA) using a MessageAmp™ II-based protocol

growth_protocol: Arabidopsis accessions were grown in 6x6x5-cm plastic pots filled with ~150 ml Profile™ porous ceramic rooting media.  Plants were thinned to one per pot and were grown and treatments applied in a controlled environment chamber with 10-h photoperiod of 330 µmol m-2 s-1 photosynthetic photon flux density.  Daytime/nighttime temperatures were 23/18 C with 60% relative humidity.  During growth all plants were fertilized with the nutrient solution every two days and watered daily.

extract_protocol: Qiagen RNAasy Plant Mini prep, samples initially harvested in RNAlater

treatment_protocol: During the drydown treatment each pot was weighed daily at ‘pre-dawn’ (WTpot&soil) and distilled water was added by pipette at the base of the rosette to bring the percent water remaining (WatRem%) in each pot to the target level for that day (e.g. 90% on day one, 80% on day two, etc.) until a final drying treatment level of ~50% was reached by all pots on the fifth day.  A major goal of the slow drydown treatment was to allow the intact, growing plants to acclimate to the imposed soil moisture stress.  WatRem% was calculated as 100*(WTpot&soil-DWpot&soil)/( FCpot&soil- DWpot&soil).  Wet (control) pots were treated identically, except WatRem% was maintained near 90% for the entire drydown period.

tag: treatment

value: Wet


title: leaf_tsu_dry_3

value: Dry


title: leaf_tsu_dry_5


title: leaf_tsu_wet_9


title: leaf_kas_wet_7


title: leaf_tsu_wet_8


title: leaf_tsu_dry_2


title: leaf_tsu_wet_10


title: leaf_kas_dry_4


title: leaf_kas_wet_11


title: leaf_tsu_dry_4


title: leaf_tsu_dry_6


title: leaf_kas_wet_10


title: leaf_kas_wet_9


title: leaf_tsu_wet_7


title: leaf_tsu_wet_12


title: leaf_kas_wet_8


title: leaf_kas_dry_5


title: Renal_Cell_Carcinoma_A7

city: Nashville

first: Kimryn

last: Rathmell

state: TN

address: 2220 Pierce Ave

department: Medicine

institute: Vanderbilt

description: Gene expression data from Human RCC sample

hyb_protocol: Tumor sample RNA and reference RNA were hybridized on Agilent Whole Human Genome 4x44k arrays by UNC Lineberger Comprehensive Cancer Center Genomics Core

scan_protocol: Agilent gene chips were scanned on an Agilent model C scanner by UNC Lineberger Comprehensive Cancer Center Genomics Core

data_processing: Data was retrieved from the UNC Microarray Database as LOWESS normalized, log2 of processed Red/Green signal (median), filter for 70% good data (Exclude if spot is not found in either channel, spot or spot background is a non-uniform outlier, spot or spot background is a non-uniform outlier for the population, spot is not a positive and significant signal in either channel, or Ch1 and 2 lowess normalized net (median) <10). Missing data was imputed with KNN (k=10) in SAM. Data from three RNA preparation types was merged using Distance Weighted Discriminant. Each array was standard normalized (subtract the mean of the array and divide by the standard deviation).

source_name: Renal Clear Cell Carcinoma

label_protocol: Tumor sample RNA and reference RNA was labelled using the Agilent Two-Color Microarray-Based Gene Expression Analysis v 5.2 protocol by UNC Lineberger Comprehensive Cancer Center Genomics Core.

extract_protocol:
Frozen RCCs were obtained through University of North Carolina - Chapel Hill's Tissue Procurement Facility
RNA was extracted with a Qiagen RNeasy kit.
RNA quality was determined using an Agilent LabChip Bioanalyzer. H&E was performed on tumor tissue samples to confirm clear cell or normal histopathology

tag: identifier

value: kidney

tag: histology

value: Clear Cell

tag: disease state

value: Clear Cell Carcinoma

tag: biosourcetype

value: Frozen Sample

source_name: Perou lab reference RNA

value: Cancer cell lines

value: various cancer cell lines (reference)


title: leaf_kas_dry_6


title: leaf_kas_wet_12


title: leaf_kas_dry_3


title: leaf_tsu_dry_1


title: leaf_kas_dry_2


title: KB1 vs ABC8 (NA18507) on HD2

description: The results of this array-CGH experiment were used to conform predicted copy number differences between samples KB1 and NA18507.  This was a genome-wide array.

tag: sample

tag: cell type

value: whole blood

value: transformed lymphocyte cell line


title: leaf_kas_dry_1


title: Ball milled aspen repB 15341402_532

city: Madison

first: Dan

last: Cullen

state: WI

address: One Gifford Pinchot Dr

institute: UW/FPL

description: Ball milled aspen repB 15341402_532

hyb_protocol: Hybridization was carried out with 6ug of labeled cDNA suspended in NimbleGen hybridization solution for 17 hours at 42°C

scan_protocol: Arrays were scanned on the Axon4000B Scanner (Molecular Dynamics) and data was extracted from the scanned image using NimbleScan v2.4.

data_processing: Quantile normalization and robust multi-array averaging (RMA) applied

organism: Phanerodontia chrysosporium

source_name: mycelium

label_protocol: One ug of each cDNA sample was amplified and labeled with 1 unit per ul of Klenow Fragment (New England BioLabs) and 1 O.D unit of Cy3 fluorophore (TriLink Biotechnologies, Inc.) for 2 hours at 37°C

growth_protocol: 5 days growth in shake flasks at 37C

extract_protocol: RNA was converted to double-strand cDNA and labeled with the Cy3 fluorophore sample for hybridization to the array by Roche NimbleGen (Iceland).  In brief, 10ug of total RNA was incubated with 1X first strand buffer, 10 mM DTT, 0.5mM dNTPs, 100 pM oligo T7 d(T)24  primer, and 200 units of SuperScript II (Invitrogen) for 60 min at 42°C. Second strand cDNA was synthesized by incubation with 1X second strand buffer, 0.2mM dNTPs, 0.07 units per ul DNA ligase (Invitrogen), 0.27 units per ul DNA polymerase I (Invitrogen), 0.013 units per ul RNase H (Invitrogen), at 16°C for 2 hours.  Immediately following, 10 units T4 DNA polymerase (Invitrogen) was added for additional 5 minute incubation at 16°C.  Double-stranded cDNA was treated with 27ng/ul of RNase A (EpiCenter Technologies)  for 10 minutes at 37°C.  Treated cDNA was purified using an equal volume of phenol:chloroform:isoamyl alcohol (Ambion), ethanol precipitated, washed with 80% ethanol, and resuspended in 20ul water.

tag: condition

value: Ball milled aspen

tag: strain


title: Gene_level_control_24 hours_rep4

city: ORSAY

first: Martin

last: Dutertre

address: Rue Henri Becquerel

country: France

institute: INSERM

description: gene-level data

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

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using EASANA from GenoSplice technology. GC background correction were applied to probe intensities (core), gene and exon level expression were summarized from the corrected intensities and then quantile normalized.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: MCF7 cells

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

growth_protocol: MCF7 cells were maintained in DMEM with 10% fetal bovine serum in a CO2 humidified chamber at 37 °C, then grown for 3 days in phenol red-free medium supplemented with 2% charcoal-stripped serum before treatment.

extract_protocol: Total RNA was isolated using Trizol total RNA isolation reagent (Invitrogen) according to the manufacturer's protocol.

treatment_protocol: Cells were treated with 17β-estradiol (Sigma, 10 nM) or 0.1% ethanol as a control.

value: ER+ breast cancer

tag: cell line

tag: agent

value: 0.1% ethanol (control)

tag: time point

value: 24 hours


title: Gene_level_estradiol_24 hours_rep1

description: gene-level data

value: estradiol


title: Gene_level_estradiol_24 hours_rep4

description: gene-level data


title: Gene_level_control_24 hours_rep2

description: gene-level data


title: Ball milled aspen repC 15340902_532

description: Ball milled aspen repC 15340902_532


title: Gene_level_estradiol_24 hours_rep3

description: gene-level data


title: Gene_level_control_24 hours_rep3

description: gene-level data


title: Gene_level_estradiol_6 hours_rep4

description: gene-level data

value: 6 hours


title: Gene_level_control_24 hours_rep1

description: gene-level data


title: Gene_level_estradiol_24 hours_rep2

description: gene-level data


title: Ball milled aspen repA 15340402_532

description: Ball milled aspen repA 15340402_532


title: Gene_level_estradiol_6 hours_rep3

description: gene-level data


title: BLA_Control_rep 6

city: Cincinnati

first: Yvonne

last: Ulrich-Lai

state: OH

address: 2170 E. Galbraith Rd. ML0506

institute: University of Cincinnati

description: Control-BLA pooled from rats 18 and 24

hyb_protocol: cRNA was hybridized to Affymetrix microarray gene chips (Rat Genome 230 2.0 Array) according to the manufacturer's instructions.

scan_protocol: Genechips were visualized using R-phycoerythrin streptavidin (Invitrogen) and biotinylated anti-streptavidin antibody (Vector Laboratories) and scanned using Genechip operating software 1v4 on the Affymetrix GeneChip Scanner 3000.

data_processing:
The data were analyzed by Cincinnati Children's Hospital Medical Center Biomedical Informatics Core using GeneSpring software (Agilent Technologies; Foster City, CA) version 7.3 using RMA normalization, then normalized to the mean of control samples. Hybridization controls included comparison of 3' and 5' probe sets for internal control genes and prokaryotic spike controls.
Filters were applied to remove genes with little-to-no expression in the BLA (signal <100) and those that were not affected by treatment (fold change 0.8-1.2)
Functional cluster analysis was performed on the list of 145 significantly upregulated genes using Ingenuity Pathway Analysis (Ingenuity Systems, Redwood City, CA).  See supplementary file on Series GSE20344 record.

organism: Rattus norvegicus

source_name: BLA tissue after 14 days, 2x daily water control

label_protocol: Biotinylated cRNA was prepared using the TargetAmp 1-Round Aminoallyl-aRNA Amplification Kit (Epicentre Biotechnolgies) using TargetAmp t7-oligo(dT) primer A, Full Spectrum Multistart T7 IVT primers (SBI System Biosciences), and Biotin-X-X-NHS (Epicentre Biotechnologies).

growth_protocol: Housing protocol: Male, Long-Evans rats (225-250g) were single housed in shoebox cages and had free access to normal chow and water throughout the experiment

extract_protocol:
Qiagen's mRNeasy extraction of total RNA was performed according to the manufacturer's instructions. Right and left BLA tissue was pooled from two animals of the same treatment group to make each sample.
Total RNA quality was verified using RNA 6000 Nano Assay, Agilent Bioanalyzer 2100 (Hewlett-Packard Company).

treatment_protocol: Rats were given additional 2x daily access to 4mL of 30%sucrose for 14 days. The morning of day 15, rats were sacrificed by decapitation and the BLA was quickly dissected and placed in RNAlater (Ambion) and stored at -80°C until RNA extraction.

tag: treatment protocol

value: Control

tag: tissue

value: basolateral amygdala

value: Long-Evans

tag: gender

value: male

tag: age

value: 2-3 months


title: Exon_level_estradiol_24 hours_rep2

description: exon-level data


title: Exon_level_control_24 hours_rep3

description: exon-level data


title: BLA_Control_rep 5

description: Control-BLA pooled from rats 17 and 23


title: Exon_level_estradiol_6 hours_rep3

description: exon-level data


title: Exon_level_estradiol_24 hours_rep4

description: exon-level data


title: Gene_level_estradiol_6 hours_rep2

description: gene-level data


title: Exon_level_estradiol_6 hours_rep4

description: exon-level data


title: Exon_level_estradiol_24 hours_rep3

description: exon-level data


title: Exon_level_control_24 hours_rep4

description: exon-level data


title: Gene_level_estradiol_6 hours_rep1

description: gene-level data


title: BLA_Control_rep 3

description: Control-BLA pooled from rats 15 and 21


title: Exon_level_estradiol_6 hours_rep2

description: exon-level data


title: BLA_Control_rep 4

description: Control-BLA pooled from rats 16 and 22


title: Exon_level_control_24 hours_rep1

description: exon-level data


title: Exon_level_estradiol_6 hours_rep1

description: exon-level data


title: Exon_level_control_24 hours_rep2

description: exon-level data


title: BLA_Control_rep 2

description: Control-BLA pooled from rats 14 and 20


title: Exon_level_estradiol_24 hours_rep1

description: exon-level data


title: U-87MG miR-30e* Rep_1

city: Guangzhou

first: Mengfeng

last: Li

state: Guangdong

address: 74# zhongshan 2 Rd.

department: Zhongshan school of medicine

country: China

institute: Sun Yat-sen University

description: U-87MG miR-30e* transfection replicate 1, 36hr

hyb_protocol: Label, hybridization and scanning was performed in shanghai biochip corporation (http://www.shbiochip.com/) following standard Agilent protocol.

data_processing: Data normalization and transformation was performed on Genespring GX 11 (Agilent) in shanghai biochip corporation.

growth_protocol: The glioma cells were cultured in complete DMEM medium and supplied with 10% FBS.

extract_protocol: Total RNA was isolated using RNeasy RNA isolation kit (Qiagen) following supplier’s protocol.

treatment_protocol: Transfection was performed following standard protocol of Lipofectamine 2000 transfection.


title: Gene_level_control_6 hours_rep3

description: gene-level data


title: U-87MG miR-30e* Rep_2

description: U-87MG miR-30e* transfection replicate 2, 36hr

scan_protocol: Label, hybridization and scanning was performed in shanghai biochip corporation (http://www.shbiochip.com/) following standard Agilent protocol.


title: Gene_level_control_6 hours_rep2

description: gene-level data


title: PUN1 deleted, biological rep 3

city: Ann Arbor

first: Tao

last: Xu

state: MI

address: 210 Washtenaw Ave

department: Life Science Institute

institute: University of Michigan

description: PUN1 deleted 3

hyb_protocol: Affymetrix GeneChip Hybridization protocol, and GeneChip Fluidics Station 450 default protocol

scan_protocol: Affymetrix GeneChip Scanner 3000 default parameters

data_processing: Image analysis, scaling (TGT = 500), and probeset-level data analysis using default parameters in GCOS v1.1. GC-RMA data was generated using affy and limma packages of Bioconductor. Differentially expressed genes were identified by significance analysis of microarrays (SAM).

organism: Saccharomyces cerevisiae

source_name: PUN1 deletion mutant of Σ1278b background under low Nitrogen

label_protocol: Affymetrix One Cycle Target Labeling Kit

growth_protocol: A 50-ml yeast culture was grown at 30 to an OD600 of 0.6 in YPDmedium (1% yeast extract, 2%peptone, 2%glucose). Cells were harvested by centrifugation and washed twice before being transferred to SLAD medium (2% glucose, 50 mm ammonium sulfate, 0.17% yeast nitrogen base without amino acids, and ammonium sulfate, supplemented with essential amino acids for nutritional auxotrophies), cells were harvest after 6 hours.

extract_protocol: AmbionPoly(A) Purist kit

treatment_protocol: Cells grow under low nitrogen medium for 6 hours

value: PUN1 mutant of Σ1278b


title: BLA_Control_rep 1

description: Control-BLA pooled from rats 13 and 19


title: Exon_level_control_6 hours_rep4

description: exon-level data


title: Exon_level_control_6 hours_rep3

description: exon-level data


title: Exon_level_control_6 hours_rep2

description: exon-level data


title: Gene_level_control_6 hours_rep1

description: gene-level data


title: PUN1 deleted, biological rep 2

description: PUN1 deleted 2


title: Exon_level_control_6 hours_rep1

description: exon-level data


title: PUN1 deleted, biological rep 1

description: PUN1 deleted 1


title: U-87MG miRNA mimic negative control Rep_2

description: U-87MG miRNA mimic negative control transfection replicate 2, 36hr

label_protocol: Label, hybridization and scanning was performed in shanghai biochip corporation (http://www.shbiochip.com/) following standard Agilent protocol.


title: BLA_sucrose_rep 6

description: Sucrose-BLA pooled from rats 6 and 12

source_name: BLA tissue after 14 days, 2x daily limited sucrose

value: 30% sucrose snack treatment


title: Control, biological rep3

description: Control 3

source_name: wild-type diploid strain of Σ1278b background under low Nitrogen

value: Diploid wide-type filamentous Σ1278b


title: BLA_sucrose_rep 5

description: Sucrose-BLA pooled from rats 5 and 11


title: shS6K1_EB_d6_RA, biological rep1

first: Mario

last: Medvedovic

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

description: Mouse ES cell infected with S6K1 shRNA lentivirus (TRCN0000022904, Sigma-Aldrich)

hyb_protocol: Mouse Genome 430 2.0 Array GeneChips were hybridized with 15 ug of fragmented aRNA. The hybridization, staining, and washing were carried out using the Affymetrix GeneChip Hybridization Wash and Stain Kit (P/N 900720) following the manufacturer’s protocols. The arrays were hybridized for 16 hr at 45oC using an Affymetrix Hybridization Oven 640 (P/N 800139). FS450_0001 protocol was used for staining and washing the GeneChips using the Affymetrix Fluidics Station 450 (P/N 00-0079).

scan_protocol: The GeneChips were scanned with Affymetrix GeneChip Scanner 3000 7G using GCOS software and Affymetrix preset settings.

data_processing: Data was processed by performing background correction, quantile normalization, and calculation of expression set summaries using the Robust Multichip Average (RMA) protocol (Irizarry et al. (2003); Biostatistics 4: pages 249-264) as implemented in the affy packge from Bioconductor (http://www.bioconductor.org). Gene-specific probesets were constructed using the Entrez Gene – centric custom CDF, version 11 (Dai et al. (2005); Nucl Acids Res 33: e175).

label_protocol: Total RNA samples of 1 μg or greater were amplified one round, and the amplified RNA (aRNA) was biotinylated using Ambion Biotin-Enhanced Message Amp II kit (#1791, Ambion, Austin, Texas), following the manufacturer’s protocols.

growth_protocol: ES cells were maintained in DMEM supplemented with 15% ES FCS (GIBCO), 1x non-essential amino acids (Sigma-Aldrich), 50 µM β-mercaptoethanol (Sigma-Aldrich), 0.1% sodium bicarbonate (Sigma-Aldrich), 100 IU/ml penicillin, 100µg/ml streptomycin (Hyclone), and 1000 units/ml murine leukemia inhibitory factor (LIF) (ESGRO; Chemicon) (ES cell Medium).

extract_protocol: Total RNA was obtained by using RNeasy kit (invitrogen) according to the manufacturer's instructions.

treatment_protocol: ES cells were seeded in hanging drops on bacteriological plate lids (day 0) and allowed to form EBs for two days in ES cell medium without LIF. EBs were then transferred to plates and kept in suspension. After 24 hrs (day 3), the EBs were incubated with 1µM all-trans-retinoic acid (RA) (Sigma-Aldrich) for 3 days (till day6).

value: embryonic stem cells

tag: shrna treatment

value: S6K1 shRNA lentivirus


title: U-87MG miRNA mimic negative control Rep_1

description: U-87MG miRNA mimic negative control transfection replicate 1, 36hr


title: SNB-19 miR-30e* Rep_2

description: SNB-19 miR-30e* transfection replicate 2, 36hr


title: BLA_sucrose_rep 4

description: Sucrose-BLA pooled from rats 4 and 10


title: shNS_EB_d6_RA, biological rep2

description: Mouse ES cell infected with non-silencing shRNA lentivirus (SHC002V,Sigma-Aldrich)

value: non-silencing shRNA lentivirus


title: BLA_sucrose_rep 3

description: Sucrose-BLA pooled from rats 3 and 9


title: dcr1ΔC103-nls tiling array 1

status: Public on Feb 16 2010

city: Basel

first: Stephan

last: Emmerth

address: Maulbeerstrasse 66

country: Switzerland

institute: FMI

description: matches column SPB368.1 in the RMA file

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: RMA expressionSet created using R/Bioconductor packages affy and limma; script available upon request

organism: Schizosaccharomyces pombe

source_name: dcr1ΔC103-nls total RNA

label_protocol: Samples (200 ng of DNA) were enzymatically fragmented and labeled according to the GeneChip® Whole Transcript(WT) Double-Stranded Target Assay

growth_protocol: Cells were collected at OD600=0.5

extract_protocol: Total RNA was extracted using the hot phenol method (Leeds, 1991): resuspend cell pellet in 1.2 ml AE Buffer (50mM NaOAc pH 5.2, 10mM EDTA), add 80 ml 25 % SDS and 1.2 ml acidic phenol, incubate for 10 minutes at 65 °C and then put on ice for 5 minutes transfer to 15 ml phase lock Falcon tubes, add 1.3 ml chloroform, mix by inverting tube, spin 10 minutes 3000 rpm at room temperature, pour the supernatant into a 15 ml Falcon tube, add 3 ml glycogen, 4 ml 100 % ethanol and 160 ml 3M NaOAc pH 5.2-5.6, spin 30 minutes 12000 rpm at 4°C, wash 2 times with 70% ethanol, air dry pellet, resuspend in 500 ul water.


title: dcr1ΔC103-nls tiling array 2

description: matches column SPB368.2 in the RMA file


title: dcr1ΔC103-nls tiling array 3

description: matches column SPB368.3 in the RMA file


title: dcr1ΔC33inactive tiling array 2

description: matches column SPB311.2 in the RMA file

source_name: dcr1ΔC33inactive total RNA


title: dcr1ΔC103 tiling array 2

description: matches column SPB139.2 in the RMA file

source_name: dcr1ΔC103 total RNA


title: dcr1ΔC103 tiling array 1

description: matches column SPB139.1 in the RMA file


title: shNS_EB_d6_RA, biological rep1

source_name: Mouse ES cell infected with non-silencing shRNA lentivirus (SHC002V,Sigma-Aldrich)


title: shS6K1_EB_d6_RA, biological rep2

source_name: Mouse ES cell infected with S6K1 shRNA lentivirus (TRCN0000022904, Sigma-Aldrich)


title: Control, biological rep2

description: Control 2


title: dcr1ΔC33inactive tiling array 1

description: matches column SPB311.1 in the RMA file


title: BLA_sucrose_rep 2

description: Sucrose-BLA pooled from rats 2 and 8


title: SNB-19 miRNA mimic negative control Rep_1

description: SNB19 miRNA mimic negative control transfection replicate 1, 36hr


title: dcr1ΔC33 tiling array 6

description: matches column SPB287.6 in the RMA file

source_name: dcr1ΔC33 total RNA


title: dcr1ΔC33 tiling array 5

description: matches column SPB287.5 in the RMA file


title: SNB-19 miRNA mimic negative control Rep_2

description: SNB19 miRNA mimic negative control transfection replicate 2, 36hr


title: dcr1ΔC33 tiling array 3

description: matches column SPB287.3 in the RMA file


title: dcr1Δ tiilng array 3

description: matches column SPB81.3 in the RMA file

source_name: dcr1Δ total RNA


title: Control, biological rep1

description: Control 1


title: dcr1ΔC33 tiling array 1

description: matches column SPB287.1 in the RMA file


title: dcr1ΔC33 tiling array 2

description: matches column SPB287.2 in the RMA file


title: dcr1ΔC33 tiling array 4

description: matches column SPB287.4 in the RMA file


title: dcr1Δ tiilng array 5

description: matches column SPB81.5 in the RMA file


title: dcr1Δ tiilng array 4

description: matches column SPB81.4 in the RMA file


title: wt tiling array 6

description: matches column SPB80.6 in the RMA file

source_name: wt total RNA


title: wt tiling array 3

description: matches column SPB80.3 in the RMA file


title: dcr1Δ tiilng array 6

description: matches column SPB81.6 in the RMA file


title: wt tiling array 2

description: matches column SPB80.2 in the RMA file


title: dcr1Δ tiilng array 2

description: matches column SPB81.2 in the RMA file


title: wt tiling array 1

description: matches column SPB80.1 in the RMA file


title: dcr1Δ tiilng array 1

description: matches column SPB81.1 in the RMA file


title: BLA_sucrose_rep 1

description: Sucrose-BLA pooled from rats 1 and 7


title: LKS+ cells from Apcmin mouse rep3

first: Fatima

last: Al-Shahrour

department: Cancer program

institute: Broad Institute of MIT and Harvard

description: Gene expression data from Lin-, cKit high, Sca-1+ cells from Apcmin mouse

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: Signal normalization was performed by RMA method.

source_name: Lin-, cKit high, Sca-1+ cells

label_protocol: NuGen Ovation Biotin labeling system

growth_protocol: LKS+ cells were isolated from Apcmin or WT mice using high-speed multiparameter flow cytometry as described previously. At least 2x104 cells per mouse were isolated with confirmed purity in excess of 90%

extract_protocol:
The LKS+ cells were treated with RLT lysis buffer (Qiagen) containing beta-mercaptoethanol to stabilize RNA.
RNA was extracted using Qiagen RNeasy Micro Kit according to manufacturers instruction. The RNA was amplified using a linear amplification protocol (Nugen Ovation V2 amplification system)

tag: genotype/variation

value: APC min


title: wt tiling array 5

description: matches column SPB80.5 in the RMA file


title: SNB-19 miR-30e* Rep_1

description: SNB-19 miR-30e* transfection replicate 1, 36hr


title: wt tiling array 4

description: matches column SPB80.4 in the RMA file


title: LKS+ cells from Apcmin mouse rep2


title: P4_Ovary_NT3_biological rep3

city: Pullman

first: Michael

middle: K

last: Skinner

address: Abelson 507

department: SBS

institute: WSU

description: Gene expression data from rat P4 Ovary cultured for 48 hours with NT3

hyb_protocol: Following fragmentation, cRNA were hybridized  on Affymetrix GeneChip Rat Genome 230 2.0 Array according to standard Affymetrix protocol. Chips were washed and stained in the   Affymetrix Fluidics Station 4500.

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

data_processing: The data were analyzed with GeneSpring GX7 (Agilent Technologies, Santa Clara, CA) software using MAS5.0 algorithm for pre-processing  and global scaling as normalization method.  The trimmed mean target intensity of each array was set to 210.

source_name: P4 Ovary cultured for 48 hours with NT3

label_protocol: Biotin-labeled cRNA were prepared according to the standard Affymetrix protocol from at least 3 ug total RNA  (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Four-day old female Sprague-Dawley rats (Harlan Laboratories, Inc., USA) were euthanized according to Washington State University IACUC approved protocols and the ovaries removed and cultured whole as described previously

extract_protocol: RNA was isolated from whole rat ovaries (2-3 ovaries per each sample) after homogenization in 1 ml Trizol™ reagent (Sigma-Aldritch, USA), according to manufacturer’s instructions.

treatment_protocol: Ovaries dissected from 4-day old female rat pups were maintained in a whole organ culture system on floating filters (0.4 µm Millicell-CM; Millipore Corp., Billerica, MA, USA) in 0.5 ml DMEM-Ham's F-12 medium (1:1, vol/vol; Life Technologies, Inc.) containing 0.1% BSA (Sigma), 0.1% albumax (Life Technologies, Inc.), 0.05 mg/ml L-ascorbic acid (Sigma), and 27.5 µg/ml transferrin (Sigma) in a 4-well culture plate (Nunc plate; Applied Scientific, South San Francisco, CA, USA). Medium was supplemented with final concentration 5 µg/ml gentamicin, 3.25 µg/ml streptomycin, and 3.25 units/ml penicillin to prevent bacterial contamination. Ovaries were treated with no factor (control) or NT3 (rh NT3, 50 ng/ml; R&D Systems, Minneapolis, MN, USA).

value: Sprague-Dawley

value: Female

value: ovary

tag: developmental stage

value: day P4 cultured for 2 more days


title: P4_Ovary_NT3_biological rep1


title: P4_Ovary_NT3_biological rep2


title: LKS+ cells from wild type mouse rep1

description: Gene expression data from Lin-, cKit high, Sca-1+ cells from wild type mouse

value: Wild type


title: P4_Ovary_Control_biological rep3

description: Gene expression data from rat P4 Ovary cultured for 48 hours with no treatment


title: LKS+ cells from wild type mouse rep3


title: mouse embryonic fibroblasts (MEF) from WT, biological rep1

status: Public on Feb 15 2010

first: Jiangwen

last: Zhang

address: 7 Divinity Ave

department: FAS Center for Systems Biology

institute: Harvard University

description:
Gene expression data from mouse embryonic fibroblasts (MEF) from wt.
MEF_wt_batch1.CEL

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were were normalized by robust multi-chip analysis (RMA) (Bioconductor release 2.8) using PM-only models.

source_name: Primary MEFs derived from from wt embryos at 13.5 dpc

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

growth_protocol: To preserve a constant 129/C57BL/6 mixed genetic background, we have crossed Pten hy/+ mice with Pten +/- for more than seven generations prior to analysis.

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

treatment_protocol: MEFs were obtained by crossing Ptenhy/+ and Pten+/- animals, embryos were harvested at 13.5 dpc, and individual MEFs were produced and cultured.

tag: genetic background

value: 129/C57BL/6 mixed

tag: genotype

value: wt

value: mouse embryonic fibroblasts (MEF)


title: mouse embryonic fibroblasts (MEF) from PTENHy/+, biological rep1

description:
Gene expression data from mouse embryonic fibroblasts (MEF) from PTENHy/+.
MEF_PTENHy+_batch1.CEL

source_name: Primary MEFs derived from from PTENHy/+ embryos at 13.5 dpc

value: PTENHy/+


title: 50 mg/kg ANIT, 6 hr, hepatocyte, biological replicate 3

status: Public on Feb 24 2010

city: Research Triangle Park

first: Neal

last: Cariello

state: NC

address: 5 Moore Drive, Bldg 9, Rom 2011

department: Safety Assessment

institute: GlaxoSmithKline

description:
Gene expression data
183_50mg_6hr_Hep.CEL

hyb_protocol: Following fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on Rat RAE230A GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: First, a log2-transformed signal matrix with RMA and additional QC is generated using ArrayStudio 3.5. Differentially expressed probesets were identified using the integrated pipeline in Resolver RatioBuild which combines signal quantification and detection of differential expression in Rosetta Resolver Version 5.1 (Rosetta Biosoftware, Seattle , WA). Rosetta Resolver incorporates an error model that captures the variance-intensity for Affymetrix GeneChips which conservatively estimates intensity error and then utilizes this value to stabilize the variance estimation. (Weng et al., 2006) The performance of Resolver's error model for signal quantification and detection of differentially expressed genes was among the best of signal quantification and statistical methods evaluated by Vardhanabhuti et al. (Vardhanabhuti et al., 2006) In our study each treatment group was compared with the concurrent control group, with the output containing fold-changes relative to control and p-values for all probesets interrogated. These final processed ratio data are presented in supplementary files on the Series record.

source_name: Rat hepatocytes from animal 6 hr after dosing with ANIT in the vehicle

label_protocol: Total RNA was amplified and labeled using the NuGen Ovation RNA Amplification System V2 and FL-Ovation cDNA Biotin Module V2 kits from NuGen Technologies

growth_protocol: Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, 8 week old Sprague Dawley rats were used. Groups of 5 treated and 5 control rats were used.

extract_protocol: RNA isolation was performed using the Picopure RNA Isolation kit according to protocol from Molecular Devices Corp.

treatment_protocol: Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, rats were treated with ANIT prepared in corn oil at 50 mg/kg or corn oil alone.

value: Sprague Dawley

value: 8 weeks old

value: liver

value: hepatocyes

tag: isolation method

value: Laser Capture Microdissection


title: TM 86 treated with Dex at 1uM, rep A

city: Irvine

first: Alissar

last: Nehme

address: 2525 Dupont Drive

institute: Allergan Inc.

description: 2/8/08 TM 86 p5 Dex A  24 hr

hyb_protocol: An equal amount of Cy3-labeled cRNA (1.6 g) was hybridized to the Agilent Human Whole Genome Oligo Microarray (Agilent Technologies) for 17 hours, prior to washing and scanning.

scan_protocol: Data were extracted from scanned images using Agilent's Feature Extraction Software (Agilent Technologies) using default settings.

data_processing: Gene expression data were loaded into the Rosetta Resolver® Gene Expression Analysis System version 7.1.0.1.11. Data from three biological replicate hybridizations were combined using an error-weighted average and the following criteria was used to identify differentially expressed transcripts: a log ratio p-value < 0.001, and a log(10) intensity measurement > -1.8.

source_name: TM 86 treated with Dex at 1uM

label_protocol: 500 ng of total RNA from each RNA sample was amplified and labeled with a fluorescent dye (Cy3) using the Low RNA Input Linear Amplification Labeling kit (Agilent Technologies, Palo Alto, CA, USA) following the manufacturer's protocol.

growth_protocol: TM 86 and TM 93 cells were maintained in low glucose DMEM medium supplemented with 10% FBS and antibiotics.

extract_protocol: RNA was isolated from flash frozen cell culture plates using RNeasy Mini columns (Qiagen, Valencia, CA) according to the manufacturer's protocol. There were three biological replicates per treatment condition.

treatment_protocol: TM 86 and TM 93 cells were treated with Dex, FA, and TA at 1 uM or 0.1% DMSO v/v as vehicle control .

value: human trabecular meshwork cells

value: TM 86


title: mouse embryonic fibroblasts (MEF) from WT, biological rep2

description:
Gene expression data from mouse embryonic fibroblasts (MEF) from wt.
MEF_wt_batch2.CEL


title: P4_Ovary_Control_biological rep2

source_name: P4 Ovary cultured for 48 hours with no treatment


title: TM 93 treated with FA at 1uM, rep C

description: 2/15/08 TM 93 p4 FA   C  24 hr

source_name: TM 93 treated with FA at 1uM

value: TM 93


title: TM 93 treated with Dex at 1uM, rep A

description: 2/15/08 TM 93 p4 Dex A  24 hr

source_name: TM 93 treated with Dex at 1uM


title: TM 86 treated with Dex at 1uM, rep B

description: 2/8/08 TM 86 p5 Dex B  24 hr


title: TM 93 treated with FA at 1uM, rep A

description: 2/15/08 TM 93 p4 FA   A  24 hr


title: TM 93 treated with Dex at 1uM, rep B

description: 2/15/08 TM 93 p4 Dex B  24 hr


title: Gene_level_control_6 hours_rep4

description: gene-level data

source_name: MCF7 cells

tag: disease state

value: ER+ breast cancer

value: 0.1% ethanol (control)

value: 6 hours


title: P4_Ovary_Control_biological rep1

value: Sprague-Dawley

value: Female

value: ovary

value: day P4 cultured for 2 more days


title: mouse embryonic fibroblasts (MEF) from PTENHy/+, biological rep2

description:
Gene expression data from mouse embryonic fibroblasts (MEF) from PTENHy/+.
MEF_PTENHy+_batch2.CEL

value: 129/C57BL/6 mixed

tag: cell type

value: mouse embryonic fibroblasts (MEF)


title: LKS+ cells from wild type mouse rep2

value: Wild type


title: TM 93 treated with FA at 1uM, rep B

description: 2/15/08 TM 93 p4 FA   B  24 hr


title: TM 86 treated with Dex at 1uM, rep C

description: 2/8/08 TM 86 p5 Dex C  24 hr


title: TM 93 treated with Dex at 1uM, rep C

description: 2/15/08 TM 93 p4 Dex C  24 hr


title: TM 86 treated with 0.1% DMSO, rep C

description: 2/8/08 TM 86 p5 Control C  24 hr

source_name: TM 86 treated with 0.1% DMSO


title: LKS+ cells from Apcmin mouse rep1

value: APC min


title: TM 86 treated with FA at 1uM, rep B

description: 2/8/08 TM 86 p5 FA   B  24 hr

source_name: TM 86 treated with FA at 1uM


title: TM 86 treated with TA at 1uM, rep C

description: 2/8/08 TM 86 p5 TA  C  24 hr

source_name: TM 86 treated with TA at 1uM


title: TM 86 treated with FA at 1uM, rep C

description: 2/8/08 TM 86 p5 FA   C  24 hr


title: TM 86 treated with 0.1% DMSO, rep A

description: 2/8/08 TM 86 p5 Control A  24 hr


title: MCF 3A2 pulldown rep3

type: other

city: North Chicago

first: J

middle: Wade

last: Davis

state: IL

address: 1 N Waukegan Rd

institute: AbbVie

description: replicate 3

hyb_protocol: Biotin-labeled, amplified cDNA (1.5µg) was hybridized to a Sentrix® Human-6 v.2 Whole Genome Expession BeadChips. The chips were hybridized at 48°C for 20 hr in the hybridization buffer provided by the manufacturer. After hybridization, the chips were washed and stained with streptavidin-C3.

scan_protocol: The chips were scanned on the BeadArray Reader, as described by Illumina at http://www.illumina.com.

data_processing: The Illumina Beadstudio software was used to assess fluorescent hybridization signals. The data were background adjusted with lumi in R using the 'forcePositive' method, and then log base 2 transformed. The data were then normalized using quantile normalization with lumi in R.

source_name: MCF

label_protocol: The entire amount of recovered RNA per immunoprecipitation was amplified using the WT-Ovation™ Pico RNA Amplification System. Forty ng of total RNA was used as starting material to generate at least 6μg of cDNA. Amplified cDNA was purified and then incubated at 50°C for 30 minutes with 5μl of UNG buffer and 5μl UNG enzyme and 60 minutes with 5μl labeling buffer and 5μl ARP (biotin) solution as described in NuGen’s labeling protocol for the Illumina Beadarray platform. All samples were quantitated, and RNA quality and integrity were assessed on selected samples with the Experion™ automated electrophoresis system.

extract_protocol: HuR Immunoprecipitations (RIP-Chip): Cell lysates were prepared from exponentially growing MB-231 and MCF-7 cells. Equal amounts of protein lysates were used (100-300μg). HuR monoclonal antibody 3A2 or isotype control IgG1 were pre-coated onto protein A Sepharose beads (PAS) and extensively washed. Lysates from each cell line initially were pre-absorbed with 30 μg of IgG1 and then removed by addition of PAS beads. Individual pull downs were performed at 4°C for only 1-2 hr to minimize potential re-assortment of mRNAs.

tag: ip

tag: er status


title: TM 93 treated with TA at 1uM, rep A

description: 2/15/08 TM 93 p4 TA  A  24 hr

source_name: TM 93 treated with TA at 1uM

tag: cell line


title: TM 93 treated with 0.1% DMSO, rep A

description: 2/15/08 TM 93 p4 Control A  24 hr

source_name: TM 93 treated with 0.1% DMSO


title: TM 86 treated with 0.1% DMSO, rep B

description: 2/8/08 TM 86 p5 Control B  24 hr


title: TM 93 treated with 0.1% DMSO, rep C

description: 2/15/08 TM 93 p4 Control  C  24 hr


title: TM 93 treated with 0.1% DMSO, rep B

description: 2/15/08 TM 93 p4 Control B  24 hr


title: MCF IgG pulldown rep2

description: replicate 2

value: IgG


title: Mouse No Cldn16 B9 461

city: Berlin

first: Constanze

last: Will

address: Hessische Str. 3 - 4

department: CCR

country: Germany

institute: Charité

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with BeadStudio Software. Data were exported to Microsoft Excel for applying student´s t-test on analysis groups of Cldn16 -/- and Cldn16 +/+ animals. Data with a p-value of < 0.05 were considered as significant.

source_name: genotype Cldn16 -/-, renal tissue

label_protocol: Biotinylated cRNA was prepared with the AMIL1791 Illumina® TotalPrep™ RNA Amplification Kit.

growth_protocol: Animals were of the following genetic background: 129S7/SvEvBrd-Hprtb-m2, F2, 1 backross to C57BL/6N. Mice were weaned at the age of 4 weeks, and afterwards supplied with standard nutrition until sacrification.

extract_protocol:
Poles were removed from freshly dissected kidneys, followed by immediate snap-freezing.
Total RNA was extracted with Trizol reagent, followed by DNAse treatment and purification via RNEasy columns. RNA purity and concentration was assessed with a Bioanalyzer.

value: female

value: juvenile, 8 weeks (P58)

tag: strain

value: Sv129 / C57BL/6N mixed background

tag: tissue type

value: renal tissue


title: TM 86 treated with FA at 1uM, rep A

description: 2/8/08 TM 86 p5 FA   A  24 hr

value: human trabecular meshwork cells

value: TM 86


title: Mouse No Cldn16 B9 449


title: Mouse No Cldn16 B9 441

value: juvenile, 8 weeks (P59)


title: Mouse No Cldn16 B9 457

source_name: genotype Cldn16 +/-, renal tissue


title: MDA 3A2 pulldown rep2

description: replicate 2

source_name: MDA


title: MDA 3A2 pulldown rep3

description: replicate 3


title: Mouse No Cldn16 B9 458

source_name: genotype Cldn16 +/+, renal tissue


title: MDA IgG pulldown rep1

description: replicate 1


title: MCF IgG pulldown rep3

description: replicate 3


title: Mouse No Cldn16 B9 443


title: MDA IgG pulldown rep3

description: replicate 3


title: TM 86 treated with TA at 1uM, rep B

description: 2/8/08 TM 86 p5 TA  B  24 hr


title: Mouse No Cldn16 B9 451


title: MCF 3A2 pulldown rep2

description: replicate 2


title: MDA IgG pulldown rep2

description: replicate 2


title: MDA 3A2 pulldown rep1

description: replicate 1


title: MCF 3A2 pulldown rep1

description: replicate 1


title: Mouse No Cldn16 B9 452


title: TM 93 treated with TA at 1uM, rep C

description: 2/15/08 TM 93 p4 TA  C  24 hr

value: TM 93


title: MCF IgG pulldown rep1

description: replicate 1


title: Mouse No Cldn16 B9 442


title: Mouse No Cldn16 B9 450


title: E13-Cultured_Testis_Flutamide_biological rep2

status: Public on Feb 14 2010

description: Gene expression data from rat E13 embryo testis treated with Flutamid in vitro

hyb_protocol: Following fragmentation, cRNA were hybridized on Affymetrix GeneChip Rat Genome 230 2.0 array according to standard Affymetrix protocol. Chips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using Affymetrix Scanner 3000.

data_processing: The data were analyzed with GCOS using MAS5.0 algorithm with Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 107.

source_name: Rat E13 embryo testis cultured with Flutamide in ethanol for 3 days

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from at least 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Rats in early estrus were bred overnight and mating confirmed by sperm positive smears, denoted as day 0 of pregnancy.

extract_protocol: Trizol reagent (Sigma) extraction of total RNA from tetstis was performed according to the manufacturer's instructions.

treatment_protocol: Rat gonads from E13 embryos were dissected with mesonephros intact and cultured for 3 days with flutamide. Briefly, gonads were placed in drops of medium on Millicell CM filters (Millipore, Bedford, MA, USA) floating on 0.4 ml of CMRL 1066 medium (Gibco BRL) supplemented with penicillin–streptomycin, insulin (10 µg/ml), L-glutamine (350 µM), transferrin (10 µg/ml), and BSA (0.01%). Gonadal pairs were split with one gonad treated with 0.5 µM flutamide in ethanol and the contra-lateral gonad with ethanol only as a vehicle control. Media and treatments were changed daily and given fresh flutamide. Gonads were maintained in culture for 3 days at which time testis cords formed and testes were used for histological analysis or separated from mesonephros and used in RNA collections. Sex was determined by PCR using primers specific for Sry on genomic DNA isolated from embryo tails as previously described [Levine E, et al.,2000].

value: Sprague-Dawley

tag: sex

value: Male

value: Testis

value: day E13 embryo


title: Mouse No Cldn16 B9 439


title: E13-Cultured_Testis_Control_biological rep1

description: Gene expression data from rat E13 embrio testis treated with DMSO (vehicle) in vitro

data_processing: The data were analyzed with GCOS using MAS5.0 algorithm with Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 218.

source_name: Rat E13 embryo testis cultured with DMSO for 3 days

treatment_protocol: Rat gonads from E13 embryos were dissected with mesonephros intact and cultured for 3 days with Vinclozolin. Briefly, gonads were placed in drops of medium on Millicell CM filters (Millipore, Bedford, MA, USA) floating on 0.4 ml of CMRL 1066 medium (Gibco BRL) supplemented with penicillin–streptomycin, insulin (10 µg/ml), L-glutamine (350 µM), transferrin (10 µg/ml), and BSA (0.01%). Gonadal pairs were split with one gonad treated with 50µM vinclozolin in DMSO and the contra-lateral gonad with DMSO only as a vehicle control. Media and treatments were changed daily and given fresh vinclozolin. Gonads were maintained in culture for 3 days at which time testis cords formed and testes were used for histological analysis or separated from mesonephros and used in RNA collections. Sex was determined by PCR using primers specific for Sry on genomic DNA isolated from embryo tails as previously described [Levine E, et al.,2000].

tag: tissue


title: midguts fed BSA + Ecoli rep 1

status: Public on Feb 13 2010

city: Rockville

first: Alvaro

last: Molina-Cruz

state: MD

address: 12735 Twinbrook Parkway

department: NIAID

institute: NIH

description: Gene expression data from midguts 3hr after a artifitial protein meal containing heat killed E. coli.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 48 hr at 45C on GeneChip Plasmodium falciparum Anopheles gambiae Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix 7Gplus GeneChip scanner.

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.

organism: Anopheles gambiae

source_name: Anopheles gambiae midguts 3hr after a BSA + heat killed E. coli meal

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix GeneChip Expression 3'-Amplification, One-cycle target labeling assay from 5 ug total RNA.

growth_protocol: Anopheles gambiae mosquitoes strain G3 were reared at 27C and 80% humidity on a 12-hr light dark cycle.

extract_protocol: Total RNA was extracted with the RNeasy Mini kit (Qiagen) following manufacturers instructions.

treatment_protocol: Anopheles gambiae G3 mosquitoes 5-6 day-old  were fed BSA (20% in PBS with fresh 10 mM sodium bicarbonate) with or without heat killed E. coli (equivalent of  2.5 ml of 0.8 OD) .  Three pools of 10 mosquito midguts were dissected after 3h and processed for microarray analysis of gene expression.

value: midgut

value: G3 strain

value: 5 to 6 day-old mosquitoes


title: E13-Cultured_Testis_Control_biological rep2


title: midguts fed BSA + Ecoli rep 3


title: E14_Testis_Control_biological rep2

description: Gene expression data from rat embryo testis at day E14 treated with DMSO (vehicle) in utero

hyb_protocol: Following fragmentation, cRNA were hybridized on Affymetrix GeneChip Rat Genome 230 2.0 array according to standard Affymetrix protocol. Chips were washed and stained in the  Affymetrix Fluidics Station 400.

data_processing: The data were analyzed with R software and Bioconductor with MAS5.0 algorithm using global scaling as normalization method. Trimmed mean target intensity of each array was determined as 210. R was used for additional quality control and computing statistics with corrected variances.

source_name: Rat embryo testis at day E14 treted with DMSO (vehicle) in utero

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

treatment_protocol: Pregnant rats were injected with 100mg/kg/day of vinclozolin, or DMSO vehicle only, daily on days E8-E14 of pregnancy to expose pups in utero during this time. Animals were euthanized at E13, E14, or E16 of pregnancy, and embryonic gonads were collected for RNA isolation and hystology. Sex was determined by PCR using primers specific for Sry on genomic DNA isolated from embryo tails as previously described [Levine E, et al.,2000]. Therefore, in addition to the histological presence of testis cords in E14 and E16 the sex was confirmed with SRY PCR, in particular for the E13 testis.

value: day E14 embryo


title: E13-Cultured_Testis_Control_2_biological rep1

description: Gene expression data from rat E13 embryo testis treated with ethanol (vehicle) in vitro

source_name: Rat E13 embryo testis cultured with ethanol for 3 days


title: midguts fed BSA rep 1

description: Gene expression data from midguts 3hr after a artifitial protein meal.

source_name: Anopheles gambiae midguts 3hr after a BSA meal


title: E14_Testis_Vinclozolin_biological rep2

description: Gene expression data from rat embryo testis at day E14 treated with Vinclozolin in utero

source_name: Rat embryo testis at day E14 treted with Vinclozolin in DMSO in utero


title: E13-Cultured_Testis_Control_2_biological rep2


title: E13-Cultured_Testis_Vinclozolin_biological rep2

description: Gene expression data from rat E13 embrio testis treated with Vinclozolin in vitro

source_name: Rat E13 embryo testis cultured with Vinclozolin in DMSO for 3 days


title: E13-Cultured_Testis_Vinclozolin_biological rep1


title: E13_Testis_Vinclozolin_biological rep2

description: Gene expression data from rat embryo testis at day E13 treated with Vinclozolin in utero

source_name: Rat embryo testis at day E13 treted with Vinclozolin in DMSO in utero


title: E16_Testis_Vinclozolin_biological rep1

description: Gene expression data from rat embryo testis at day E16 treated with Vinclozolin in utero

source_name: Rat embryo testis at day E16 treted with Vinclozolin in DMSO in utero

value: day E16 embryo


title: E16_Testis_Vinclozolin_biological rep2


title: E13_Testis_Control_biological rep1

description: Gene expression data from rat embryo testis at day E13 treated with DMSO (vehicle) in utero

source_name: Rat embryo testis at day E13 treted with DMSO (vehicle) in utero


title: E14_Testis_Vinclozolin_biological rep1


title: E13_Testis_Vinclozolin_biological rep1


title: E14_Testis_Control_biological rep1


title: E16_Testis_Control_biological rep1

description: Gene expression data from rat embryo testis at day E16 treated with DMSO (vehicle) in utero

source_name: Rat embryo testis at day E16 treted with DMSO (vehicle) in utero


title: midguts fed BSA rep 3


title: E16_Testis_Control_biological rep2


title: E13_Testis_Control_biological rep2


title: midguts fed BSA rep 2


title: midguts fed BSA + Ecoli rep 2


title: Population DR Day D0 Replicate 3 Dye Cy5

city: Eugene

first: Kevin

middle: James

last: Emerson

state: OR

address: 5289 University of Oregon

department: Center for Ecology and Evolutionary Biology

institute: University of Oregon

description: Reference sample labelled CTL, other samples labelled as population.day

hyb_protocol: Vacuum dried labeling reactions were resuspended in 50% formamide, 3XSSC, 1%SDS, 5X Denhardts soluation and 0.6mg/mL poly(A), boiled for 2 minutes and added to arrays which were then covered with lifterslips and hybridized overnight at 42C

scan_protocol: Scanned and inintially analyzed by GenePix 6.1

data_processing: Normalized and analyzed using limma package for R - estimates of ratio were estimated by empirical bayes

organism: Wyeomyia smithii

label_protocol: For each array, 15ug of each of two samples (reference and treatment) was reverse transcribed and labeled with dUTP (Perkin Elmer) using the Superscript cDNA labelling system (invitrogen) according to manufacturer's protocol

growth_protocol: Mosquitos reared under short days to synchronize diapause, transferred to light:dark = 14.6:9.4 for experiment

extract_protocol: Total RNA was extracted (TRIzol, Invitrogen) from three replicates of 50 whole larvae for each sampling point within 20 minutes of 10 h after lights on.  A reference containing equimolar parts of all samples was created.

treatment_protocol: Two populations (DR and DB) at Light:Dark = 14.6:9.4 sampled at 10 h post-dawn after 0 (D0) or 6 (D6) days.

tag: population

value: DR

tag: time

value: day 0

source_name: CTL

tag: reference

value: contains equimolar parts of all samples was created


title: Population DB Day D6 Replicate 5 Dye Cy3

value: DB

value: day 6


title: Population DR Day D0 Replicate 4 Dye Cy3


title: TM 86 treated with TA at 1uM, rep A

description: 2/8/08 TM 86 p5 TA  A  24 hr

source_name: TM 86 treated with TA at 1uM

value: human trabecular meshwork cells

value: TM 86


title: Population DB Day D0 Replicate 2 Dye Cy3


title: Population DR Day D0 Replicate 5 Dye Cy5


title: Population DB Day D0 Replicate 2 Dye Cy5


title: Population DR Day D0 Replicate 4 Dye Cy5


title: Population DB Day D6 Replicate 1 Dye Cy3


title: Population DB Day D6 Replicate 4 Dye Cy5


title: Population DB Day D0 Replicate 3 Dye Cy5


title: Population DB Day D0 Replicate 3 Dye Cy3


title: Population DR Day D6 Replicate 3 Dye Cy5


title: Population DB Day D6 Replicate 4 Dye Cy3


title: Population DR Day D0 Replicate 3 Dye Cy3


title: Population DB Day D6 Replicate 1 Dye Cy5


title: PC12 1 hour NGF LY294002 rep1

city: Bunkyo-ku

first: Jaehoon

last: Chung

state: Tokyo

address: 7-3-1 Hongo

department: Department of Biophysics and Biochemistry

country: Japan

institute: Tokyo university

description: Gene expression of 3 hours after 1hr NGF stimulation in presence of LY294002

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60℃ for 30 minutes in a reaction volume of 55 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Rat Genome Oligo Microarrays (G4131F) for 17 hours at 65℃ 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 37℃ GE Wash buffer 2 (Agilent), then dried.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 014879_D_20070207) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: PC12, 1 hour NGF stimulation in presence of LY294002, 3 hr, replicate 1

label_protocol: Six hundred nanograms of total RNA was converted into labeled complementary RNA (cRNA) with nucleotides coupled to a fluorescent dye (Cy-3) by means of the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies). The quality and quantiy of the resulting labeled cRNA were assessed with an ND-1000 spectrophotometer and an Agilent 2100 Bioanalyzer.

growth_protocol: PC12 cells were maintained in Dulbecco’s modified Eagle’s medium containing 5% horse serum and 10% bovine calf serum （Nichirei） at 5% CO2, 37℃.

extract_protocol: Total RNA was extracted and purified with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions. The concentration of isolated RNA was determined by an ND-1000 spectrophotometer (Nanodrop), according to manual instructions. Integrity and quantity of isolated total RNA were assessed by the Agilent 2100 Bioanalyzer (Agilent), according to manual instructions.

treatment_protocol: For stimulants treatment, PC12 cells were plated on poly-l-lysine-coated dishes in complete medium for 24 hours and then switched to complete medium supplemented with the 50 ng/ml of NGF (R&D), 100 nM of PACAP (Sigma), 50 ng/ml of bFGF (Sigma), 50 ng/ml of EGF (Roche), 10 nM of insulin (Sigma) or 10 μM of forskolin (Sigma). For pharmacological inhibition of MEK1 and PI3K activity, cultures were pretreated with 50 μM U0126 (Promega) and 50 μM LY294002 (Sigma) respectively, for 20 minutes before addition of NGF. For washing of extension factors or inhibitors in compounds containing culture medium, the culture medium was replaced with an equal volume of complete medium four times.


title: PC12 1 hour NGF LY294002 rep2

source_name: PC12, 1 hour NGF stimulation in presence of LY294002, 3 hr, replicate 2


title: PC12 1 hour Insulin rep2

description: Gene expression of 3 hours after 1hr InsulinPACAP stimulation

source_name: PC12, 1 hr Insulin stimulation, 3 hr, replicate 2


title: Population DR Day D6 Replicate 1 Dye Cy3


title: PC12 1 hour PACAP rep2

description: Gene expression of 3 hours after 1hr PACAP stimulation

source_name: PC12, 1 hr PACAP stimulation, 3 hr, replicate 2


title: Population DB Day D0 Replicate 4 Dye Cy5


title: Population DB Day D0 Replicate 4 Dye Cy3


title: Population DR Day D6 Replicate 1 Dye Cy5


title: Population DR Day D6 Replicate 3 Dye Cy3


title: E13-Cultured_Testis_Flutamide_biological rep1

source_name: Rat E13 embryo testis cultured with Flutamide in ethanol for 3 days


title: PC12 1 hour NGF rep4

description: Gene expression of 3 hours after 1hr NGF stimulation

source_name: PC12, 1 hr NGF stimulation, 3 hr, replicate 4


title: PC12 control rep3

description: Gene expression of 3 hours after complete medium stimulation

source_name: PC12, Continuous complete medium stimulation, 3 hr, replicate 3


title: PC12 control rep4

source_name: PC12, Continuous complete medium stimulation, 3 hr, replicate 4


title: Population DR Day D6 Replicate 4 Dye Cy3


title: Population DB Day D6 Replicate 5 Dye Cy5


title: Population DR Day D6 Replicate 4 Dye Cy5


title: Population DR Day D0 Replicate 5 Dye Cy3


title: PC12 1 hour Insulin rep1

source_name: PC12, 1 hr Insulin stimulation, 3 hr, replicate 1


title: PC12 1 hour PACAP rep1

source_name: PC12, 1 hr PACAP stimulation, 3 hr, replicate 1


title: DC NCFM+Z9 Rep2

city: Kongens Lyngby

first: Simon

last: Rasmussen

address: Kemitorvet, Building 208

department: Department of Systems Biology

country: Denmark

institute: Technical University of Denmark

hyb_protocol: The aRNA was fragmented and hybridized to Affymetrix Gene Chip Mouse genome 430 2.0 arrays (Affymetrix, Santa Clara, CA, USA) according to manufacturers instructions.

scan_protocol: The arrays were scanned according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA, USA) using Affymetrix GeneChip Scanner 7G.

data_processing: The microarray data was analyzed using R and Bioconductor (Gentleman et al. 2004). Raw probe intensities were normalized using qspline and expression index calculations were performed using rma (Irizarry et al. 2003;Workman et al. 2002). For statistical testing Two-Way ANOVA was performed and statistical significance was assessed by estimating False Discovery Rate (FDR) by a Monte Carlo approach.

source_name: Bone-marrow derived dendritic cells, Lactobacillus acidophilus NCFM + Bifidobacterium bifido Z9 treated, 10h

label_protocol: 1 μg RNA per stimulation condition was converted into cDNA, and biotin-labeled aRNA was synthesized using the MessageAmpTM II-Biotin Enhanced Kit (Ambion, Austin, TX, USA) according to the manufacturers instructions.

growth_protocol: Bone marrow from three male C57BL/6 mice (Charles River Breeding Laboratories, Portage, MI, USA) was flushed out from the femur and tibia and washed. 3 x 105/ml bone marrow cells were seeded into 10 cm Petri dishes in 10 ml RPMI 1640 (Sigma-Aldrich, St. Louis, MO) containing 10% (v/v) heat-inactivated fetal calve serum supplemented with penicillin (100 U/ml), streptomycin (100 µg/ml), glutamine (4 mM), 50 µm 2-mercaptoethanol (all purchased from Cambrex Bio Whittaker) and 15 ng/ml murine GM-CSF (harvested from a GM-CSF transfected Ag8.653 myeloma cell line). The cells were incubated for 8 days at 37ºC in 5% CO2 humidified atmosphere. On day 3, 10ml of complete medium containing 15 ng/ml GM-CSF was added. On day 6, 10ml were removed and replaced by fresh medium. Nonadherent, immature DC were harvested on day 8.

extract_protocol: Murine DC were harvested after 10 h of stimulation, homogenised by QIAshredder (Qiagen, Ballerup, Denmark), and RNA was extracted using the RNeasy Plus Mini Kit (Qiagen). RNA quality was verified by Bioanalyzer (Agilent, Santa Clara, USA), and the concentration was determined by Nanodrop (Thermo, Wilmington, USA).

treatment_protocol: Immature DC (2 x 10^6 cells/ml) were resuspended in fresh medium supplemented with 10 ng/ml GM-CSF, and 500 µl/well were seeded in 48-well tissue culture plates (Nunc, Roskilde, Denmark). Lactobacillus acidophilus NCFM (final concentration 10 ng/ml) and Bifidobacterium bifidum Z9 (final concentration 40 ng/ml) were added both individually and in combination (100 µl/well). The cell cultures were incubated at 37 ºC in 5 % CO2. The cells were harvested after 10h of stimulation.

value: Bone-marrow derived dendritic cells

tag: treatment group

value: Lactobacillus acidophilus NCFM + Bifidobacterium bifidum Z9

tag: treatment time

value: 10 hours


title: DC NCFM+Z9 Rep3


title: PC12 control rep1

source_name: PC12, Continuous complete medium stimulation, 3 hr, replicate 1


title: PC12 1 hour NGF U0126 rep2

description: Gene expression of 3 hours after 1hr NGF stimulation in presence of U0126

source_name: PC12, 1 hr NGF stimulation in presence of U0126, 3 hr, replicate 2


title: DC Bifidobacterium Z9 Rep3

source_name: Bone-marrow derived dendritic cells, Bifidobacterium bifidum Z9 treated, 10h

value: Bifidobacterium bifidum Z9


title: DC Lactobacillus NCFM Rep2

source_name: Bone-marrow derived dendritic cells, Lactobacillus acidophilus NCFM treated, 10h

value: Lactobacillus acidophilus NCFM


title: PC12 Continuous NGF rep1

description: Gene expression of 3 hours after continuous NGF stimulation

source_name: PC12, Continuous NGF stimulation, 3 hr, replicate 1


title: DC Lactobacillus NCFM Rep3


title: DC control Rep3

source_name: Bone-marrow derived dendritic cells, saline control, 10h

value: Control


title: PC12 Continuous NGF rep2

source_name: PC12, Continuous NGF stimulation, 3 hr, replicate 2


title: DC Bifidobacterium Z9 Rep1


title: PC12 1 hour NGF rep1

source_name: PC12, 1 hr NGF stimulation, 3 hr, replicate 1


title: DC Lactobacillus NCFM Rep1


title: PC12 1 hour NGF rep2

source_name: PC12, 1 hr NGF stimulation, 3 hr, replicate 2


title: PC12 control rep2

source_name: PC12, Continuous complete medium stimulation, 3 hr, replicate 2


title: DC Bifidobacterium Z9 Rep2


title: DC NCFM+Z9 Rep1


title: PC12 1 hour NGF U0126 rep1

source_name: PC12, 1 hr NGF stimulation in presence of U0126, 3 hr, replicate 1


title: PC12 1 hour NGF rep3

source_name: PC12, 1 hr NGF stimulation, 3 hr, replicate 3


title: 4465171114_J

status: Public on Feb 12 2010

city: New York

first: Mariano

middle: Javier

last: Alvarez

address: 1130 St. Nicholas ave.

department: Systems Biology

institute: Columbia University

description: Lentiviral-mediated expression of STAT3 and CEBPb shRNA in SNB19 human glioma cells for 72h. 200 ng of total RNA were hybridized in Illumina HumanHT12v3 expression arrays.

hyb_protocol: According to Illumina whole-genome gene expression direct hybridization assay guide

scan_protocol: The arrays were scanned using an iScan (Illumina). Images were segmented and quantified by BeadStudio (Illumina).

data_processing: BeadStudio-based background subtraction; followed by variance stabilization transformation and robust spline normalization as implemented in lumi R package (Bioconductor)

source_name: SNB19 human glioma cell line transduced with STAT3 and CEBPb shRNA lentivirus-vectors for 72h

label_protocol: 200 ng total RNA were processed according to Illumina TotalPrep RNA amplification kit (Ambion)

extract_protocol: TRIZOL followed by MagMAX96 for microarrays total RNA isolation kit (Ambion)

tag: cell type/line

tag: transduction

value: STAT3 shRNA (Sigma TRCN0000020843) and CEBPb (Sigma TRCN0000007442)


title: 4465171114_K


title: 4465171114_L


title: DC control Rep2


title: 4465171114_F

description: Lentiviral-mediated expression of STAT3 shRNA in SNB19 human glioma cells for 72h. 200 ng of total RNA were hybridized in Illumina HumanHT12v3 expression arrays.

source_name: SNB19 human glioma cell line transduced with STAT3 shRNA lentivirus-vector for 72h

value: STAT3 shRNA (Sigma TRCN0000020843)


title: 4465171114_H

description: Lentiviral-mediated expression of CEBPb shRNA in SNB19 human glioma cells for 72h. 200 ng of total RNA were hybridized in Illumina HumanHT12v3 expression arrays.

source_name: SNB19 human glioma cell line transduced with CEBPb shRNA lentivirus-vector for 72h

value: CEBPb shRNA (Sigma TRCN0000007442)


title: 4465171114_G


title: DC control Rep1


title: 4465171114_C

description: Lentiviral-mediated expression of non-target control shRNA in SNB19 human glioma cells for 72h. 200 ng of total RNA were hybridized in Illumina HumanHT12v3 expression arrays.

source_name: SNB19 human glioma cell line transduced with NT control shRNA lentivirus-vector for 72h

value: non-target control shRNA (Sigma SHC002)


title: 4465171114_D


title: 4465171114_I


title: 4465171114_B


title: 4455416126_L

description: Lentiviral-mediated expression of STAT3 and CEBPb shRNA in BTIC cells for 72h. 200 ng of total RNA were hybridized in Illumina HumanHT12v3 expression arrays.

source_name: BTIC cells transduced with STAT3 and CEBPb shRNA lentivirus-vectors for 72h

value: BTIC


title: 4465171114_A


title: 4455416126_J

description: Lentiviral-mediated expression of STAT3 shRNA in BTIC cells for 72h. 200 ng of total RNA were hybridized in Illumina HumanHT12v3 expression arrays.

source_name: BTIC cells transduced with STAT3 shRNA lentivirus-vector for 72h


title: 4455416126_B


title: 4455416126_D


title: 4465171114_E


title: 4455416126_H


title: 4455416126_C

description: Lentiviral-mediated expression of CEBPb shRNA in BTIC cells for 72h. 200 ng of total RNA were hybridized in Illumina HumanHT12v3 expression arrays.

source_name: BTIC cells transduced with CEBPb shRNA lentivirus-vector for 72h


title: 4455416126_F


title: 4455416124_K


title: 4455416126_G


title: 4455416126_I

description: Lentiviral-mediated expression of non-target control shRNA in BTIC cells for 72h. 200 ng of total RNA were hybridized in Illumina HumanHT12v3 expression arrays.

source_name: BTIC cells transduced with NT control shRNA lentivirus-vector for 72h


title: 4455416124_J


title: 4455416124_D


title: 4455416124_I


title: 4455416126_E


title: 4455416126_A


title: 4455416124_G


title: 4455416124_E


title: 4455416126_K


title: 4455416124_L


title: 4455416124_H


title: 4433719048_K


title: 4455416124_B


title: 4433719048_L


title: 4455416124_A


title: 4455416124_C


title: 4455416124_F


title: 4433719048_J


title: 4433719048_F


title: 4433719048_G


title: 4433719048_D


title: 4433719048_A


title: 4433719048_E


title: 4433719042_E


title: 4481649093_B


title: 4433719048_C


title: 4433719048_H


title: 4433719042_F


title: 4433719048_B


title: 4433719042_A


title: 4433719042_C


title: Mtf2_RNAi_1_2days

status: Public on Feb 20 2010

city: Urbana

first: Dan

last: Xie

address: 3215 Digital Computer Lab, MC-278, 1304 W. Springfield Ave

department: Bioengineering

institute: University of Illinois at Urbana and Champaign

description: gene expression of cells transfected with plasmid pSuper-Mtf2-RNAi-1 and selected by Puromycin(1mg/ml) for 2 days

hyb_protocol: 825 ng of labeled RNA was fragmented and hybridized on the slide in a rotating hybridzation oven at 60C overnight. Slides were washed according to the manufactureres protocols using Agilent wash buffers.

scan_protocol: Slides were scanned in an Axon 4000B scanner using GenePix 6 software to generate gpr files.

data_processing: Data normalized with dChip.

source_name: Mtf2_RNAi_1, 2days

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the Quick-Amp One-Color  (Agilent) according to the manufactruers instructions. Total amount of cRNA and dye incorporation was measured using a nanodrop instrument.

extract_protocol: Extracted by Trizol  Reagent(Invitrogen 15596-018)

treatment_protocol: Plasmids were transfected into the E14 mESC cell lines by lipofectamine 2000 and selected by Puromycin (1 mg/ml) after 1 day of transfection. The sample of 2 days maintained in puromycin was harvested.

value: E14 mESC


title: 4433719048_I


title: 4481649093_E

description: Lentiviral-mediated expression of RunX1 shRNA in SNB19 human glioma cells for 72h. 200 ng of total RNA were hybridized in Illumina HumanHT12v3 expression arrays.

source_name: SNB19 human glioma cell line transduced with RunX1 shRNA lentivirus-vector for 72h

value: RunX1 shRNA (Sigma TRCN0000013660)


title: 4433719042_H


title: 4481649093_C


title: 4481649093_F


title: 4433719042_D


title: 4433719042_B


title: 4481649093_A


title: 4455416129_I

description: Lentiviral-mediated expression of BHLHB2 shRNA in SNB19 human glioma cells for 72h. 200 ng of total RNA were hybridized in Illumina HumanHT12v3 expression arrays.

source_name: SNB19 human glioma cell line transduced with BHLHB2 shRNA lentivirus-vector for 72h

value: BHLHB2 shRNA (Sigma TRCN0000013249)


title: 4455416129_J


title: 4455416129_L


title: 4481649093_D


title: 4433719042_G


title: 4455416129_K


title: in vitro derived DC subsets (pooled biological replicates 1-3)

city: Vienna

first: Jennifer

last: Jurkin

address: Lazarettgasse 19

department: Institut of Immunology

country: Austria

institute: Medical University of Vienna

description: miRNA profiling

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). Hybridization used 100 µL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.  After hybridization detection used fluorescence labeling using tag-specific Cy3 and Cy5 dyes

scan_protocol: Hybridization images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics)

data_processing: Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter10 (Locally-weighted Regression). The ratio of the two sets of detected signals (log2 transformed, balanced) and p-values of the t-test were calculated

source_name: intDCs

label_protocol: An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining; two different tags were used for the two RNA samples.

growth_protocol: CD34+ cells were grown in serum free media with GM-CSF, FL, SCF, TNFa and TGF-b1 for 7d (for LCs) or GM-CSF, FL, SCF, TNFa for 4 days and afterwards GM-CSF and IL-4 for 5 days (for intDCS). Cells were purifiedby FACS to obtain purities > 95%

extract_protocol: total RNA sample was size fractionated using a YM-100 Microcon centrifugal filter (from Millipore) and the small RNAs (< 300 nt) isolated were 3’-extended with a poly(A) tail using poly(A) polymerase.

treatment_protocol: no treatment

tag: sample

value: B

value: interstitial-type dendritic cells (intDCs)

tag: source of cell type

value: in vitro derived primary cells differentiated from human cord blood  CD34+ cells

source_name: LCs

value: A

value: Langernas cells (LCs)


title: 4455416129_F

description: Lentiviral-mediated expression of FosL2 shRNA in SNB19 human glioma cells for 72h. 200 ng of total RNA were hybridized in Illumina HumanHT12v3 expression arrays.

source_name: SNB19 human glioma cell line transduced with FosL2 shRNA lentivirus-vector for 72h

value: FosL2 shRNA (Sigma TRCN0000016142)


title: 4455416129_D


title: Bergmann glial cell at age P30, biological replicate 4

city: Boston

first: Gabriel

last: Corfas

address: 300 Longwood Avenue

department: Neurobiology Program

institute: Children's Hospital Boston

description: Gene expression data from single Bergmann glial cell from P30 mouse cerebellum

hyb_protocol: Following fragmentation, 10-15 ug of cDNA were hybridized on Mouse Gene 430 2.0 expression arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using a Affymetrix GC 3000 high density scanner

data_processing: Analyses of individual microarrays and comparisons between P6 and P30 were performed using GeneSpring GX 7.3 (Agilent).  Raw CEL files were processed using the RMA (Robust Multichip Average) normalization algorithm as implemented in GeneSpringGX 7.3. Normalization was performed using default settings, which included data transformation (RAW values of less than 0.01 were set to 0.01), per chip normalization to the median (each measurement was divided by the 50th percentile of all measurements in that sample), and per gene normalization (the raw expression level of each gene was divided by the median of its measurements in all samples).  Raw and normalized signal values as well as Present or Absent calls generated using GeneSpring are given in the Sample data table.

molecule: other

source_name: GFAP-GFP Mouse cerebellum, age P30

label_protocol: Biotinylated single-cell cDNA was prepared as described before (Tietjen et al, 2003, Neuron)

extract_protocol: Addition of lysis buffer directly to single cell, reverse transcription and PCR based amplification of single cell cDNA was performed as described in previous studies (Tietjen et al, 2003, Neuron; Dulac and Axel, 1995, Cell)

value: mid-sagittal portion of cerebellum

tag: genotype

value: GFAP-GFP reporter line

tag: age


title: Bergmann glial cell at age P30, biological replicate 3


title: 4455416129_B


title: TLD-30-rep2

city: Princeton

first: Dipen

last: Sangurdekar

state: NJ

address: 132 Carl Icahn laboratory, Princeton University

department: Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

description: Biological replicate 2

hyb_protocol: Labeling and hybing procedure according to Khodursky et al, Methods Mol Biol. 2003;224:61-78

scan_protocol: Scanned on Agilent GenePix scanner

data_processing: Lowess normalized data. Resultant data is log2 normalized.

organism: Escherichia coli

source_name: E. coli - 0 min before nutrient shift

growth_protocol: E. coli MG1655 thyA- cells grown in M9 minimal medium + 0.2% glucose and 20 ug/ml thymine

extract_protocol: Total RNA extracted using QIAGEN RNeasy kit according to manufacturer's instructions

treatment_protocol: Cells harvested at mid-exponential phase, spun, washed twice with M9 medium and shifted to limiting or no thymine medium. Samples taken at listed intervals.

value: MG1655 thyA-

source_name: E. coli - 30 min after shift to thymineless medium


title: 4457278023_C

description: CEBPB retrovirus transduction of murine NSCs. 200 ng of total RNA were hybridized in Illumina MouseWG-6v2 expression arrays.

source_name: Primary murine neural stem cells (NCS) isolated from E13.5 mouse telencephalon, transduced with CEBPB retroviral vector

value: NSC

value: CEBPB retroviral vector


title: TLD-60-rep2

description: Biological replicate 2

label_protocol: Labeling and hybing procedure according to Khodursky et al, Methods Mol Biol. 2003;224:61-78

source_name: E. coli - 60 min after shift to thymineless medium


title: TLD-45-rep2

description: Biological replicate 2

source_name: E. coli - 45 min after shift to thymineless medium


title: 4455416129_H


title: TLD-90-rep2

description: Biological replicate 2

source_name: E. coli - 90 min after shift to thymineless medium


title: Bergmann glial cell at age P30, biological replicate 5


title: 4455416129_E


title: 4457278023_D

description: STAT3C and CEBPB retrovirus transduction of murine NSCs. 200 ng of total RNA were hybridized in Illumina MouseWG-6v2 expression arrays.

source_name: Primary murine neural stem cells (NCS) isolated from E13.5 mouse telencephalon, transduced with STAT3 and CEBPB retroviral vectors.

value: STAT3C and CEBPB retroviral vectors


title: 4455416129_C

source_name: SNB19 human glioma cell line transduced with NT control shRNA lentivirus-vector for 72h

value: non-target control shRNA (Sigma SHC002)


title: 4457278013_F


title: Bergmann glial cell at age P30, biological replicate 2


title: 4457278023_B

description: STAT3C retrovirus transduction of murine NSCs. 200 ng of total RNA were hybridized in Illumina MouseWG-6v2 expression arrays.

source_name: Primary murine neural stem cells (NCS) isolated from E13.5 mouse telencephalon, transduced with STAT3C retroviral vector

value: STAT3C retroviral vector


title: 4457278013_E


title: 4455416129_A


title: 4457278023_E

description: Control pBabe retrovirus transduction of murine NSCs. 200 ng of total RNA were hybridized in Illumina MouseWG-6v2 expression arrays.

source_name: Primary murine neural stem cells (NCS) isolated from E13.5 mouse telencephalon, transduced with a control pBabe retroviral vector

value: control pBabe retroviral vector


title: Bergmann glial cell at age P30, biological replicate 1


title: Bergmann glial cell at age P6, biological replicate 5

description: Gene expression data from single Bergmann glial cell from P6 mouse cerebellum

source_name: GFAP-GFP Mouse cerebellum, age P6


title: 4457278023_F


title: 4457278013_C


title: 4457278023_A


title: 4457278013_D


title: TLD-15-rep2

description: Biological replicate 2

source_name: E. coli - 15 min after shift to thymineless medium


title: TLD-90-rep1

description: Biological replicate 1


title: Bergmann glial cell at age P6, biological replicate 4


title: 4457278013_A


title: 4457278013_B


title: Bergmann glial cell at age P6, biological replicate 1


title: 4457278014_F


title: 4427941023_F

description: STAT3C and CEBPB retrovirus transduction of C17.2 murine neural stem cells. 200 ng of total RNA were hybridized in Illumina MouseWG-6v2 expression arrays.

source_name: C17.2 murine neural stem cells transduced with a constitutively active mutant of STAT3 and CEBPB both cloned in retroviral vectors


title: TLD-60-rep1

description: Biological replicate 1


title: TLD-45-rep1

description: Biological replicate 1


title: TLM-90

description: Biological replicate 1

source_name: E. coli - 90 min after shift to limiting medium


title: 4457278014_D


title: TLD-30-rep1

description: Biological replicate 1


title: Bergmann glial cell at age P6, biological replicate 2


title: 4457278014_E


title: Bergmann glial cell at age P6, biological replicate 3


title: 4427941023_E


title: TLD-15-rep1

description: Biological replicate 1


title: 4427941023_B

description: CEBPB retrovirus transduction of C17.2 murine neural stem cells. 200 ng of total RNA were hybridized in Illumina MouseWG-6v2 expression arrays.

source_name: C17.2 murine neural stem cells transduced with CEBPB retroviral vector


title: 4427941023_C


title: 4457278014_C

source_name: Primary murine neural stem cells (NCS) isolated from E13.5 mouse telencephalon, transduced with a control pBabe retroviral vector.


title: 4427941023_D


title: 4457278014_A


title: 4457278014_B


title: 4427941023_A


title: TLM-60

description: Biological replicate 1

source_name: E. coli - 60 min after shift to limiting medium


title: TLM-45

description: Biological replicate 1

source_name: E. coli - 0 min before nutrient shift

source_name: E. coli - 45 min after shift to limiting medium


title: TLM-30

description: Biological replicate 1

source_name: E. coli - 30 min after shift to limiting medium


title: 4457278021_E


title: TLM-15

description: Biological replicate 1

source_name: E. coli - 15 min after shift to limiting medium


title: 4455416129_G

source_name: SNB19 human glioma cell line transduced with FosL2 shRNA lentivirus-vector for 72h


title: 4457278021_C

description: STAT3C retrovirus transduction of C17.2 murine neural stem cells. 200 ng of total RNA were hybridized in Illumina MouseWG-6v2 expression arrays.

source_name: C17.2 murine neural stem cells transduced with a constitutively active mutant of STAT3 cloned in a retroviral vector


title: 4457278021_D


title: 4457278021_B


title: UTX input_Foot_1of2

city: Stanford

first: Jordon

last: Wang

address: 269 Campus Dr.

department: Dermatology

institute: Stanford University

hyb_protocol: Standard Nimblegen hybridization kits and protocols were used

scan_protocol: Arrays were scanned with Axon scanner at 5 um resolution according to standard Nimblegen protocols

data_processing: Arrays were processed using Nimblegens standard protocol for Nimblescan 2.4 ChIP data extraction

source_name: Input

label_protocol: Standard Nimblegen ChIP labeling protocol (1 ug of Amplified ChIP DNA, direct incorporation of cy labeled primers with klenow extension

growth_protocol: Fibroblasts were grown in DMEM with 10% Fetal Bovine Serum until ~70% confluent

extract_protocol: ChIP was performed on 4x10^6 fibroblast cells and Farnham ChIP protocol was used to derive ChIP DNA and was amplified by sigma WGA2 kit for 1 round of amplification

tag: cell type

value: foot primary human fibroblasts


title: MC58_Iron-deplete_3

status: Public on Feb 11 2010

first: Ryan

middle: S

last: McClure

address: 650 Albany St.

department: Microbiology

institute: Boston University

description: One of three biological replicates of RNA isolated from wild-type MC58 under iron-deplete conditions

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: Nimblegen 4-plexTM microarrays are single-channel arrays meaning cDNA samples were labeled with only a single dye.  Intensity of bound sample for each probe was quantified using the NimbleScan2.3 software suite to determine an absolute probe intensity value.  Individual probe intensities were then background adjusted within each individual array and normalized between differing arrays using the method of quantile normalization as described by Bolstad et al.  Expression values for a given open reading frame were derived from a given set of corresponding probes using the method of robust multiarray average as described by Irizarry et al.  Subsequent to quantile normalization and RMA analysis, gene expression characteristics were further analyzed using the Arraystar 2.0 software suite (DNAStar Inc., Madison, WI).  Arraystar analysis enabled visualization of gene expression data using scatterplots and agglomerative hierarchical clustering as well as statistical analyses of expression data by the analysis of variance (ANOVA) method.  For each strain and condition three biological replicates were analyzed for a total of 18 arrays.

organism: Neisseria meningitidis MC58

source_name: Neisseria meningitidis MC58 wild-type

label_protocol: Total RNA (30 μg) for each sample was converted to double-stranded cDNA using the SuperScriptTM double-stranded cDNA conversion kit (Invitrogen, Carlsbad, CA).  Samples were labeled, hybridized according to Nimblegen’s protocols.

growth_protocol: For all growth experiments bacteria were plated from glycerol stocks onto GCB agar plates and grown overnight.  Cells were then inoculated into chemically defined media (CDM) or GCK media (GC broth supplemented 1:100 with Kellogg’s I supplement) to an OD600 of .06-.08 using a Genesys 20 spectrophotometer and cuvettes with a pathlength of 10mm.

extract_protocol: Total RNA was isolated using Trizol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions.  RNA was DNaseI treated and removal of DNA contamination was verified by PCR.

treatment_protocol: For experiments in which RNA was to be isolated, cells were grown to an OD600 of 0.4-0.5 before being divided and inoculated with either 100 μg/ml Ferric nitrate or 100 μg/ml of the iron chelator desferal to constitute iron-replete or iron-deplete conditions, respectively.  Cultures were grown an additional 30 min before RNA was harvested.

tag: genotype/variation

value: Wild-type

tag: treatment protocol

value: iron-deplete


title: Hfq- mutant_Iron-deplete_2

description: One of three biological replicates of RNA isolated from hfq- mutant MC58 under iron-deplete conditions

source_name: Neisseria meningitidis MC58 hfq- mutant

value: hfq-  knockout mutant (pleotropic growth defects, sRNA circuits are potentially misregulated)


title: 4457278015_F

description: Control retrovirus transduction of C17.2 murine neural stem cells. 200 ng of total RNA were hybridized in Illumina MouseWG-6v2 expression arrays.

source_name: C17.2 murine neural stem cells transduced with pBabe control retroviral vector


title: 4457278021_A


title: Complemented-Hfq-mutant_Iron-deplete_2

description: One of three biological replicates of RNA isolated from complemented hfq- mutant MC58 under iron-deplete conditions

source_name: Neisseria meningitidis MC58 complemented hfq- mutant

value: Complemented hfq-  knockout mutant


title: Complemented-Hfq-mutant_Iron-deplete_1


title: 4457278015_C


title: MC58_Iron-deplete_2


title: UTX chip_Foot_2of2

source_name: ChIP


title: 4457278021_F


title: Hfq- mutant_Iron-deplete_1


title: Complemented-Hfq-mutant_Iron-deplete_3


title: Complemented-Hfq-mutant_Iron-replete_2

description: One of three biological replicates of RNA isolated from complemented hfq- mutant MC58 under iron-replete conditions

value: iron-replete


title: Hfq- mutant_Iron-deplete_3


title: Complemented-Hfq-mutant_Iron-replete_3


title: 4457278015_D


title: 4457278015_E


title: Hfq- mutant_Iron-replete_3

description: One of three biological replicates of RNA isolated from hfq- mutant MC58 under iron-replete conditions


title: MC58_Iron-deplete_1


title: Complemented-Hfq-mutant_Iron-replete_1


title: Hfq- mutant_Iron-replete_2


title: Hfq- mutant_Iron-replete_1


title: UTX chip_Foot_1of2


title: MC58_Iron-replete_1

description: One of three biological replicates of RNA isolated from wild-type MC58 under iron-replete conditions


title: UTX input_Lung_2of2

value: lung primary human fibroblasts