title: control.ev.SW620.biorep1

description:
pLKO_Empty_Vector_SW620
Gene expression data from colorectal cancer cell lines used for knock-down experiments


title: hypocotyl_dark_rep2

status: Public on Dec 23 2013

type: RNA

city: New York

first: Huan

last: Wang

state: New York

address: 1230 York Avenue

country: USA

institute: The Rockefeller University

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

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x60k array slides.

data_processing: Raw data of processed signal intensities are obtained by analysis using Feature Extraction Software (Agilent) with default parameters. Standard QC analysis, background normalization and quantile normalization were performed using GeneSpring GX Software (Agilent) with default parameters.

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: hypocotyl, dark, replicate 2

label_protocol: We performed RNA labeling, hybridization and scaning using protocols according to the Agilent's instructions. Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent).

growth_protocol: Arabidopsis thaliana ecotype Col-0 plants were used in this study. For sampling etiolated and de-etiolated seedlings, seeds were surface-sterilized in a 70% ethanol briefly and placed directly into a 30% Clorox with 0.1% Triton X-100 for 10 min and rinsed five times with sterilized water. Seeds were resuspended in a sterilized 0.15% (w/v) agarose and then sown in rows onto Murashige and Skoog (MS; MB biomedical, LLC, 263324) medium with 1% sucrose, Myo-inositol (Sigma, I3011), MES (Sigma, M8250) and 0.8% Bactoagar.

extract_protocol: Total RNA was extracted and treated with DNase I using RNeasy Plant mini kit (Qiagen).

treatment_protocol: Seeds on plate were stratified at 4℃ for 3 days and exposed to white light (100 umol m-2 s-1) for 1h at 22℃ to initiate germination before being transferred to continuous darkness at 22℃ for 4 day. After sampling of etiolated seedlings in the dark, seedlings on plates were exposed to continuous white light (100 umol m-2 s-1) for 1 and 6h. Prior to sampling, de-etiolated seedlings were divided into cotyledons, hypocotyls and roots, and organ samples were harvested and frozen immediately in liquid nitrogen and stored at -80℃.

tag: organ

value: hypocotyl

tag: light treatment

value: dark


title: cotyledon_dark_rep1

source_name: cotyledon, dark, replicate 1

value: cotyledon


title: Cerebellum_rep3 En2KO

city: Trento

first: Erik

last: Dassi

state: TN

address: Via Sommarive, 9

department: CIBIO

country: Italy

institute: University of Trento

description: The original *En2* mutants (mixed 129Sv x C57BL/6 and outbred genetic background) were crossed at least five times into a C57BL/6 background.

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

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with FeatureExtractor  (protocol GE1_107_Sep09 and Grid: 014868_D_F_20120131) . Intensity values were then processed with Agi4x44PreProcess using default parameters to remove low-quality probes. Signals where then normalized by means of the quantile normalization method.

molecule: total RNA

organism: Mus musculus

source_name: entire cerebellum

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted from fresh tissue using RNAeasy miniki (Qiagen) following the manufacturer's recommendations.  The protocol includes on-column DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: tissue

value: Cerebellum

tag: genotype


title: hypocotyl_dark_rep1

source_name: hypocotyl, dark, replicate 1


title: Cerebellum_rep2 En2KO


title: control.ev.SW480.biorep1

city: Toronto

first: Benjamin

last: Haibe-Kains

state: Ontario

address: 610 University Avenue

department: Princess Margaret Research

country: Canada

institute: Princess Margaret Cancer Centre

description:
pLKO_Empty_Vector_SW480
Gene expression data from colorectal cancer cell lines used for knock-down experiments

hyb_protocol: standard Affymetrix procedure.

scan_protocol: standard Affymetrix procedure.

data_processing: The data were analyzed with frozen RMA (log2) normalized data using the frma function in the frma package in Biocinductor

label: biotin

organism: Homo sapiens

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

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

treatment_protocol: short hairpin RNA complexes with complemen- tary sequence to the mRNA sequence of 8 RAS pathway genes

tag: cell line

tag: genotype/variation


title: CDK5KD.SW620.biorep.6

description:
CDK5-A5-B2
Gene expression data from colorectal cancer cell lines used for knock-down experiments

value: CDK5 knockdown


title: root_1h_rep2

source_name: root, white light 1h, replicate 2

value: root

value: white light 1h


title: CDK5KD.SW620.biorep.5

description:
CDK5-A5-B1
Gene expression data from colorectal cancer cell lines used for knock-down experiments


title: CDK5KD.SW480.biorep.6


title: broiler, biological rep6

city: Knoxville

first: Bo

last: Ji

address: 2640 Morgan Circle Drive

department: Animal Science

institute: University of Tennessee

description: Gene expression data from adipose tissue of 3 week broiler

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Statistical analysis of the microarray data was performed using R 2.13.2 and routines contained in Bioconductor (bioconductor.org). GC robust multi-array average (GCRMA) was used to normalize and scale the raw data from CEL files.

organism: Gallus gallus

source_name: Broiler

label_protocol: standard Affymetrix protocol

extract_protocol: Total RNA was isolated from chicken adipose samples using the RNeasy Lipid kit and incorporating an on-column DNase treated with the RNase-free DNase Set according to the manufacturer's protocol.

treatment_protocol: At 3 week of age, male birds from three distinct genetic lines of chickens (Broiler, Fayoumi and Leghorn) were used.

value: adipose

tag: breed

value: Broiler

tag: age

value: 3 weeks

tag: gender

value: male


title: root_WT_3

source_name: root, WT, replicate 3

growth_protocol: Plants of Arabidopsis thaliana were grown in a greenhouse under long-day conditions (22°C, 16/8 h photoperiod cycles). Flowers buds were collected from 4-week-old wild-type (Col-0) plants. Root and leaf samples were collected from 30-d-old wild-type plants (Col-0) grown hydroponically in full-strength MGRL medium under long-day conditions.

treatment_protocol: No treatment

value: wild type


title: root_WT_1

source_name: root, WT, replicate 1


title: cotyledon_dark_rep2

source_name: cotyledon, dark, replicate 2


title: Cerebellum_rep3 En2WT


title: CDK5KD.SW480.biorep.5


title: Hippocampus_rep3 En2KO

source_name: entire hippocampus

value: Hippocampus


title: Cerebellum_rep1 En2WT


title: Cerebellum_rep1 En2KO


title: cotyledon_dark_rep3

source_name: cotyledon, dark, replicate 3


title: CDK5KD.SW620.biorep.4

description:
CDK5-A5-A2
Gene expression data from colorectal cancer cell lines used for knock-down experiments


title: Cerebellum_rep2 En2WT


title: Hippocampus_rep2 En2KO


title: root_WT_2

source_name: root, WT, replicate 2


title: leaf_WT_1

source_name: leaf, WT, replicate 1

value: leaf


title: CDK5KD.SW620.biorep.3

description:
CDK5-A5-A1
Gene expression data from colorectal cancer cell lines used for knock-down experiments


title: CDK5KD.SW480.biorep.3


title: leaf_WT_2

source_name: leaf, WT, replicate 2


title: leaf_WT_3

source_name: leaf, WT, replicate 3


title: CDK5KD.SW620.biorep2

description:
SW620 CDK5
Gene expression data from colorectal cancer cell lines used for knock-down experiments

source_name: SW620 CDK5


title: CDK5KD.SW480.biorep2

description:
SW480 CDK5
Gene expression data from colorectal cancer cell lines used for knock-down experiments

source_name: SW480 CDK5


title: Hippocampus_rep3 En2WT


title: inflorescence_WT_1

source_name: inflorescence, WT, replicate 1

value: inflorescence


title: Hippocampus_rep2 En2WT


title: CDK5KD.SW480.biorep1

description:
CDK5_A5_SW480
Gene expression data from colorectal cancer cell lines used for knock-down experiments


title: inflorescence_WT_2

source_name: inflorescence, WT, replicate 2


title: inflorescence_WT_3

source_name: inflorescence, WT, replicate 3


title: MB204

status: Public on Dec 22 2013

first: Ming

last: Tsao

department: Ontario Cancer Institute

institute: University of Toronto

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

data_processing: Microarray data for 181 samples was preprocessed using RMA implemented in R/Bioconductor ‘affy’ package (ref: PMID:12538238). Normalized data values were transformed in log2 space and used in subsequent analysis

source_name: Primary NSCLC

tag: Sex

value: F

tag: histology

value: adenocarcinoma

tag: t-stage

tag: n-stage

tag: m-stage

tag: Stage

tag: smoking

value: Ex-smoker

tag: survival time

tag: status

value: dead

tag: disease-free survival time

tag: recurrence

value: Y


title: Hippocampus_rep1 En2KO

tag: tissue

tag: genotype


title: MB205

value: M

value: Current

value: N


title: MB206

value: Never

value: alive


title: MB203

value: Unable to determine


title: MB208


title: broiler, biological rep3

value: adipose

value: Broiler

value: 3 weeks


title: MB200

value: squamous cell carcinoma


title: MB202


title: MB201

value: large cell carcinoma


title: MB199

value: U


title: MB197


title: MB207

value: F


title: MB193

value: squamous cell carcinoma X2


title: MB192

value: adenocarcinoma


title: MB195

value: dead


title: MB198

value: Y


title: MB194


title: Hippocampus_rep1 En2WT

value: Hippocampus


title: MB186


title: MB189

value: M

value: Ex-smoker


title: MB187

value: N


title: MB191


title: MB183


title: CDK5KD.SW480.biorep.4

tag: cell line

tag: genotype/variation

value: CDK5 knockdown


title: MB177

tag: age


title: MB181

value: Current

value: alive


title: MB178


title: MB184

value: Unable to determine


title: MB175


title: MB179


title: MB176


title: MB172


title: MB170


title: MB171


title: MB174


title: MB169


title: MB168


title: MB167


title: MB173


title: MB156


title: MB162

value: Never


title: MB165

value: squamous cell carcinoma


title: MB159


title: MB161


title: MB157


title: MB158


title: MB163


title: MB164


title: MB153


title: MB151


title: MB147


title: MB152


title: MB155


title: MB148


title: MB146


title: MB154


title: MB149


title: MB141


title: MB150

value: large cell carcinoma


title: MB137


title: MB135


title: MB140


title: MB134


title: MB138


title: MB130


title: MB139

value: U


title: MB129


title: MB127

value: F


title: MB131


title: MB136


title: MB124

value: NSCLC-favor adenocarcinoma


title: MB120

value: adenocarcinoma


title: MB128

value: dead


title: MB132


title: MB125


title: MB123


title: MB133

value: Y


title: MB116


title: MB122


title: MB118


title: MB112


title: MB119


title: MB114


title: MB117


title: MB111


title: MB109


title: MB115


title: MB108


title: MB106


title: MB110


title: MB113


title: MB102


title: MB105


title: MB101


title: MB107


title: MB100


title: MB095


title: MB098


title: MB090


title: MB104


title: MB097


title: MB092


title: MB094


title: MB093


title: MB099


title: MB088


title: MB096


title: MB091

value: adenosquamous carcinoma


title: MB086


title: MB089


title: MB085


title: MB081


title: MB083


title: MB145


title: MB078

value: M


title: MB072

value: Ex-smoker


title: MB077

value: N


title: MB084


title: MB074


title: MB087


title: MB073


title: MB079


title: MB076


title: MB082


title: MB071


title: MB066


title: MB070


title: MB063

value: NSClarge cell carcinoma-mixed


title: MB065


title: MB061


title: MB062


title: MB064

value: Current


title: MB055


title: MB068

value: alive


title: MB053


title: MB059


title: MB052


title: MB054


title: A2780-CPR70 replicate 1

city: Bethesda

first: Yuelin

middle: Jack

last: Zhu

state: MD

address: 9000 Rockville Pike

department: Genetics Branch, Center for Cancer Research

institute: NCI

hyb_protocol: Labelled cDNA was hybridized as described at http://research.nhgri.nih.gov/microarray/hybridization.shtml

scan_protocol: Slides were scanned in an Agilent  G2565AA microarray scanner.

data_processing: Data was extracted from the scans using Dearray software in IP Labs as described at http://research.nhgri.nih.gov/microarray/image_analysis.shtml

source_name: A2780-CPR70 ovarian cancer cell line

label_protocol: RNA was labeled with Cy3 or Cy5 by reverse transcription in the presence of dye-coupled dUTP.

growth_protocol: Normal growth conditions in RPMI1640 with 10% fetal calf serum.

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

tag: cisplatin reaction

value: cisplatin resistant

tag: cisplatin derivative

source_name: A2780-CPR00 ovarian cancer cell line

value: cisplatin sensitive


title: A2780-CPR55 replicate 2

source_name: A2780-CPR55 ovarian cancer cell line


title: MB047

tag: Sex

tag: histology


title: MB126

value: squamous cell carcinoma

tag: t-stage

tag: n-stage


title: A2780-CPR70 replicate 2


title: MB051

value: large cell carcinoma

tag: m-stage

tag: Stage


title: MB048

tag: smoking

tag: survival time


title: MB046

tag: status

tag: disease-free survival time


title: MB050

tag: recurrence


title: MB039

value: Never


title: MB045


title: MB040


title: MB041


title: MB042

value: F


title: Fetal_Kidney_04

city: Heidelberg

first: Sven

last: Diederichs

address: Im Neuenheimer Feld 280

department: RNA Biology & Cancer

country: Germany

institute: German Cancer Research Center (DKFZ)

data_processing: Data are presented as linear signal intensity values with a minimum signal (cut-off) of 32. Jun Lu et al., Nature 2005, PMID: 15944708

source_name: Fetal Kidney

extract_protocol: TRIzol (Invitrogen / LifeTechnologies)

tag: tissue

value: Fetal Kidney


title: Fetal_Kidney_05

hyb_protocol: Jun Lu et al., Nature 2005, PMID: 15944708


title: MB037

value: adenocarcinoma


title: Fetal_Kidney_03

scan_protocol: Jun Lu et al., Nature 2005, PMID: 15944708


title: Fetal_Kidney_02

label_protocol: Jun Lu et al., Nature 2005, PMID: 15944708


title: MB038

value: dead


title: A2780-CPR55 replicate 1

tag: cell line


title: A2780-CPR40 replicate 1

source_name: A2780-CPR40 ovarian cancer cell line


title: Adult_Kidney_03

source_name: Normal Adult Kidney

value: Normal Adult Kidney


title: A2780-CPR40 replicate 2


title: A2780-CPR20 replicate 2

source_name: A2780-CPR20 ovarian cancer cell line


title: MB035

value: Y


title: BMDCs MHCIIlo C

city: South San Francisco

first: Jason

middle: A

last: Hackney

state: CA

address: 1 DNA Way

department: Department of Bioinformatics and Computational Biology

institute: Genentech, Inc.

description: Biological replicate 2 of 4: MHC.II low BMDCs.

hyb_protocol: Agilent In Situ Hybridization Kit Plus was used where Cy-dye labeled control and test samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, the arrays were washed twice, dried and then scanned.

scan_protocol: Scanned on an Agilent scanner, images were processed using Agilent Feature Extraction software version 10.7.

data_processing: Raw intensity data were background subtracted using the normal + exponential method from the limma Bioconductor package. The test/reference ratio was log2 transformed and normalized using loess normalization for each array. Loess normalized log2 ratios were then subjected to quantiles normalization across all arrays in the dataset.

source_name: BMDCs, MHCIIlo

label_protocol: Total RNA was converted to double-stranded cDNA and then into Cy-dye labeled cRNA using Agilent's Quick Amp Labeling Kit. For all samples, 750 ng of the labeled cRNA was fragmented and hybridized against Cy3-labeled Universal mouse reference (Stratagene, La Jolla, CA).

growth_protocol: Hematopoietic bone marrow progenitors cultured in RPMI supplemented with GM-CSF and IL-4 for 5 days.

extract_protocol: RNA was extracted with RNeasy Plus kit (Qiagen) with removal of genomic DNA.

treatment_protocol: BMDCs cultured for 6 days were sorted by flow cytometry for MHC-IIhi (spontaneous activated) and MHC-IIlo (inactive) populations.

tag: strain/background

tag: genotype/variation

value: wild type

tag: cell type

value: bone marrow-derived dendritic cells

tag: mhc.ii subpopulation

value: MHC-IIlo

source_name: Universal mouse reference (UMR) from Stratagene

tag: sample type

value: pooled mouse reference RNA


title: MB032

tag: Sex

value: M

tag: histology

tag: age

value: Current

value: N


title: MB033

tag: t-stage

tag: n-stage

tag: m-stage


title: MB034

tag: Stage

tag: smoking

tag: survival time


title: BMDCs MHCIIlo A

description: Biological replicate 1 of 4: MHC.II low BMDCs.


title: MB031

value: Ex-smoker

tag: status

value: alive

tag: disease-free survival time

tag: recurrence


title: Adult_Kidney_02

tag: tissue


title: MB036

value: squamous cell carcinoma


title: BMDCs MHCIIhi C

description: Biological replicate 2 of 4: MHC.II high BMDCs.

source_name: BMDCs, MHCIIhi

tag: strain/background

tag: genotype/variation

value: MHC-IIhi


title: A2780-CPR20 replicate 1

tag: cisplatin reaction

value: cisplatin resistant

tag: cell line

tag: cisplatin derivative

value: cisplatin sensitive


title: BMDCs MHCIIhi D

description: Biological replicate 3 of 4: MHC.II high BMDCs.

tag: cell type

tag: mhc.ii subpopulation

tag: sample type


title: Wilms_Tumor_20

source_name: Wilms Tumor

value: Wilms Tumor


title: BMDCs MHCIIlo D

description: Biological replicate 3 of 4: MHC.II low BMDCs.


title: Adult_Kidney_01


title: MB030

tag: Sex

value: F

tag: histology

value: adenocarcinoma

tag: t-stage

tag: n-stage

tag: age


title: BMDCs MHCIIhi E

description: Biological replicate 4 of 4: MHC.II high BMDCs.


title: BMDCs MHCIIhi A

description: Biological replicate 1 of 4: MHC.II high BMDCs.


title: MB029

tag: m-stage

tag: Stage

tag: smoking

value: Never

tag: survival time

tag: status

value: Y


title: Wilms_Tumor_18

tag: tissue


title: MB027

value: dead

tag: disease-free survival time

tag: recurrence


title: BMDCs MHCIIlo E

description: Biological replicate 4 of 4: MHC.II low BMDCs.

tag: strain/background

tag: genotype/variation

value: wild type

value: bone marrow-derived dendritic cells

value: MHC-IIlo


title: CD11c-Cre BMDCs LPS 6 hrs D

description: Biological replicate 4 of 5: BMDCs treated with LPS for 6 hours.

source_name: CD11c-Cre BMDCs, LPS, 6 hrs

growth_protocol: Murine bone marrow-derived dendritic cells (BMDCs) were generated from CD11c-Cre mice (control) or CD11c-Cre IRF-4 flox/flox mice (KO).

extract_protocol: RNA was extracted with Qiagen RNeasy Plus kit with removal of genomic DNA.

treatment_protocol: BMDCs were left unstimulated or were stimulated with LPS for 6 or 24 hours. CD11c+ cells were then purified by selection with magnetic beads.

tag: cell type

tag: treatment

value: LPS 6hrs

value: pooled mouse reference RNA


title: Wilms_Tumor_17


title: CD11c-Cre BMDCs LPS 6 hrs B

description: Biological replicate 2 of 5: BMDCs treated with LPS for 6 hours.

tag: sample type


title: CD11c-Cre BMDCs LPS 6 hrs C

description: Biological replicate 3 of 5: BMDCs treated with LPS for 6 hours.


title: Wilms_Tumor_19


title: MB026

tag: Sex

tag: histology

value: N


title: CD11c-Cre BMDCs Unstimulated E

description: Biological replicate 5 of 5: unstimulated BMDCs.

source_name: CD11c-Cre BMDCs, unstimulated

value: unstimulated


title: Wilms_Tumor_16


title: MB024

tag: t-stage

tag: n-stage

value: Ex-smoker

value: alive


title: CD11c-Cre BMDCs Unstimulated D

description: Biological replicate 4 of 5: unstimulated BMDCs.


title: CD11c-Cre BMDCs LPS 6hrs A

description: Biological replicate 1 of 5: BMDCs treated with LPS for 6 hours.


title: CD11c-Cre BMDCs Unstimulated C

description: Biological replicate 3 of 5: unstimulated BMDCs.


title: Wilms_Tumor_15


title: MB023

tag: m-stage

tag: age


title: Wilms_Tumor_14


title: MB022

value: M

tag: Stage

tag: smoking


title: Wilms_Tumor_13


title: MB025

value: Current

tag: survival time

tag: status


title: Chordoma sample 1

description: Chordoma sample 1 used array platform GPL13376

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Common probes between GPL6104 and GPL13376 were normalised using quantile normalisation with the lumi package(v.2.4.0) in R (v.2.13.2)/Bioconductor.

source_name: Chordoma

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: tissue type

value: Primary tumor


title: Wilms_Tumor_12

tag: tissue

value: Wilms Tumor


title: 1021_delta_SMc03169, biological rep2

city: Lisboa

first: Leonilde

middle: Morais

last: Moreira

address: A. Rovisco Pais

department: Bioengineering

country: Portugal

institute: Instituto Superior Tecnico

description: delta SMc03169 mutant

hyb_protocol: Following fragmentation, 2 µg of end-labeled fragmented cDNA were used in a 200-µl hybridization cocktail containing added hybridization controls and hybridized on arrays for 16 hours at 48ºC. Modified post-hybridization wash and double-stain protocols (FLEX450_0005; GeneChip HWS kit, Affymetrix) were used on an Affymetrix GeneChip Fluidics Station 450.

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

data_processing: Scanned arrays were analyzed with Affymetrix Expression Console software. Subsequent analysis was carried out with DNA-Chip Analyzer 2008. First a digital mask was applied, leaving for analysis only the 8305 probe sets on the array representing Sinorhizobium meliloti 1021 transcripts. Then the 6 arrays were normalized to a baseline array with median CEL intensity by applying an Invariant Set Normalization Method. Normalized CEL intensities of the arrays were used to obtain model-based gene expression indices based on a Perfect Match (PM)-only model. Replicate data (triplicates) for each bacterial isolate was weighted gene-wise by using inverse squared standard error as weights. All genes compared were considered to be differentially expressed if the 90% lower confidence bound of the fold change between experiment and baseline was above 1.2.

organism: Sinorhizobium meliloti

source_name: 1021 delta_SMc03169 grown in GMS medium with luteolin for 4 hours

label_protocol: RNA was processed for use on Affymetrix Medicago/Sinorhizobium Genome Arrays, according to the manufacturer’s Prokaryotic Target Preparation Assay. Briefly, 10 ug of total RNA containing spiked in Poly-A RNA controls (GeneChip Expression GeneChip Eukaryotic Poly-A RNA Control Kit; Affymetrix, Santa Clara, CA) was used in a reverse transcription reaction with random primers (Invitrogen Life Technologies) to generate first-strand cDNA. After removal of RNA, 2 ug of cDNA were fragmented with DNase and end-labeled with biotin using terminal polynucleotidyl transferase (GeneChip WT Terminal Labeling Kit; Affymetrix). Size distribution of the fragmented and end-labeled cDNA, was assessed using an Agilent 2100 Bioanalyzer.

growth_protocol: Wild-type Sm1021 and delta SMc03169 mutant  were grown overnight in TY medium and inoculated into 50 ml GMS medium supplemented with 10 micromolar of luteolin (with OD600nm 0.1) contained into 100 ml Erlenmyer flasks at 30ºC, 180 r.p.m. for 4 h, followed by RNA extraction.

extract_protocol: Total RNA extraction was carried out using the RNeasy MiniKit (Qiagen) by following manufacturer’s recommendation

treatment_protocol: Bacterial cells were resuspended in RNAprotect bacteria reagent (Qiagen).


title: 1021_delta_SMc03169, biological rep3

description: delta SMc03169 mutant


title: Chordoma sample 3

description: Chordoma sample 3 used array platform GPL13376


title: CD11c-Cre BMDCs Unstimulated B

description: Biological replicate 2 of 5: unstimulated BMDCs.

tag: strain/background


title: MB021

value: adenocarcinoma

tag: disease-free survival time

tag: recurrence


title: 1021_delta_SMc03169, biological rep1

description: delta SMc03169 mutant

tag: genotype/variation


title: CD11c-Cre IRF4flox BMDCs LPS 24 hrs E

description: Biological replicate 5 of 5: Irf4 knockout BMDCs treated with LPS for 24 hours.

source_name: CD11c-Cre IRF4flox BMDCs, LPS, 24 hrs

value: CD11c-Cre IRF4flox

tag: cell type

tag: treatment

value: LPS 24hrs

tag: sample type


title: Chordoma sample 2

description: Chordoma sample 2 used array platform GPL13376


title: CD11c-Cre BMDCs Unstimulated A

description: Biological replicate 1 of 5: unstimulated BMDCs.


title: Wilms_Tumor_11


title: MB020

source_name: Primary NSCLC

tag: Sex

tag: histology

tag: t-stage

value: dead


title: Wilms_Tumor_10


title: Wilms_Tumor_09


title: Wilms_Tumor_08


title: 1021_WT, biological rep2

description: wild-type strain

source_name: 1021 wild-type grown in GMS medium with luteolin for 4 hours


title: 1021_WT, biological rep3

description: wild-type strain


title: MB019

tag: n-stage

tag: m-stage

tag: age


title: CD11c-Cre IRF4flox BMDCs LPS 24 hrs D

description: Biological replicate 4 of 5: Irf4 knockout BMDCs treated with LPS for 24 hours.


title: CD11c-Cre IRF4flox BMDCs LPS 24 hrs C

description: Biological replicate 3 of 5: Irf4 knockout BMDCs treated with LPS for 24 hours.


title: Wilms_Tumor_07


title: MB018

value: F

value: squamous cell carcinoma

tag: Stage

tag: smoking

tag: survival time


title: MB017

tag: status


title: 1021_WT, biological rep1

description: wild-type strain


title: MNV18

city: Dunedin

first: Christopher

middle: Michael

last: Brown

address: 710 Cumberland St

department: Biochemistry

country: New Zealand

institute: University of Otago

description: Mouse RAW cells mock transfected after 18 h

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430_2 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using an Affymtrix scanner

data_processing: The data were analyzed with GenePattern, using RMA and quantile normalisation using the ExpressionFileCreator in Genepattern (Reich et al., 2006), preprocessed using PreprocessDataset,  comparison was done using ComparativeMarkerSelection.

label: Biotin

growth_protocol: RAW264.7 cells were grown  at 37˚C + 5% CO2 in GIBCO DMEM with 4.5 g/L glucose + 2.5 mM HEPES + 5% fetal calf serum, in 6-well plates. Once cells were 70% confluent, infection was performed

extract_protocol: Qiagen RNeasy mini kit

treatment_protocol: RAW264.7 cells were infected with MNV-1 at a multiplicity of infection of 1, or mock infected, for 9 and 18 hours

value: Mouse RAW cells


title: Wilms_Tumor_06

tag: tissue


title: CD11c-Cre IRF4flox BMDCs LPS 24 hrs A

description: Biological replicate 1 of 5: Irf4 knockout BMDCs treated with LPS for 24 hours.

tag: strain/background

value: bone marrow-derived dendritic cells


title: MB014

tag: disease-free survival time

tag: recurrence


title: CD11c-Cre IRF4flox BMDCs LPS 6 hrs E

description: Biological replicate 5 of 5: Irf4 knockout BMDCs treated with LPS for 6 hours.

source_name: CD11c-Cre IRF4flox BMDCs, LPS, 6 hrs

tag: genotype/variation

tag: cell type

value: LPS 6hrs

value: pooled mouse reference RNA


title: Wilms_Tumor_05


title: MB013

value: N


title: CD11c-Cre IRF4flox BMDCs LPS 6 hrs D

description: Biological replicate 4 of 5: Irf4 knockout BMDCs treated with LPS for 6 hours.

tag: treatment

tag: sample type


title: CD11c-Cre IRF4flox BMDCs LPS 24 hrs B

description: Biological replicate 2 of 5: Irf4 knockout BMDCs treated with LPS for 24 hours.


title: MB016

tag: Sex

tag: histology

value: Ex-smoker


title: Wilms_Tumor_04


title: Wilms_Tumor_03


title: MOCK9


title: Wilms_Tumor_02


title: CD11c-Cre IRF4flox BMDCs LPS 6 hrs B

description: Biological replicate 2 of 5: Irf4 knockout BMDCs treated with LPS for 6 hours.


title: MNV9


title: CD11c-Cre IRF4flox BMDCs LPS 6 hrs C

description: Biological replicate 3 of 5: Irf4 knockout BMDCs treated with LPS for 6 hours.


title: MB011

tag: t-stage

tag: n-stage

value: Never

value: Y


title: MB012

value: M

tag: m-stage

tag: age

value: alive


title: Wilms_Tumor_01

value: Wilms Tumor


title: CD11c-Cre IRF4flox BMDCs LPS 6 hrs A

description: Biological replicate 1 of 5: Irf4 knockout BMDCs treated with LPS for 6 hours.


title: MB007

tag: Stage

tag: smoking


title: Uninfected Cells at D16, biological rep2

city: Edmonton

first: Allen

last: Herbst

state: AB

address: 114C BARB

institute: University of Alberta

description:
0R2
Gene expression data from C2C12 myotubes.

hyb_protocol: Following fragmentation, cRNA was hybridized on an Affymetrix MG430_2 mouse genome array. GeneChips were washed and stained in the Affymetrix GC450.

scan_protocol: GeneChips were scanned using an Affymetrix GC3000 7G Scanner.

data_processing: Data were processed using ArrayStar and Robust Multiarray Averaging.

source_name: C2C12 myotubes at day 16 uninfected with RML

label_protocol: Biotinylated cRNA were prepared using the MessageAMP Premier RNA amplification kit according to the manufacturer's instructions.

growth_protocol: Differentiated cells were grown in DMEM with 10% horse serum. Media was changed daily.

extract_protocol: RNA was isolated by using the Qiagen RNeasy cell protocol and QIAshredders.

treatment_protocol: Cells were infected or not by the addition of 100ul of a 10% brain homogenate derived from a mouse clinically affected with RML prions. The brain homogenate was mixed with 10mL of media and incubated on the cells for one day.

tag: cell line

value: myotube cell line

tag: time

value: 16 days


title: Uninfected Cells at D16, biological rep3

description:
0R3
Gene expression data from C2C12 myotubes.


title: Uninfected Cells at D16, biological rep1

description:
0R1
Gene expression data from C2C12 myotubes.


title: MOCK18


title: CD11c-Cre IRF4flox BMDCs Unstimulated D

description: Biological replicate 4 of 5: unstimulated Irf4 knockout BMDCs.

source_name: CD11c-Cre IRF4flox BMDCs, unstimulated

tag: strain/background

value: CD11c-Cre IRF4flox

value: unstimulated


title: CD11c-Cre IRF4flox BMDCs Unstimulated A

description: Biological replicate 1 of 5: unstimulated Irf4 knockout BMDCs.


title: MB006

value: Current

tag: survival time

tag: status

tag: disease-free survival time


title: Infected Cells at D16, biological rep1

description:
1R1
Gene expression data from C2C12 myotubes infected with RML prions.

source_name: C2C12 myotubes at day 16 infected with RML

tag: cell type

value: RML prions


title: MB009

value: F

value: adenocarcinoma

tag: recurrence


title: MB004


title: CD11c-Cre IRF4flox BMDCs Unstimulated B

description: Biological replicate 2 of 5: unstimulated Irf4 knockout BMDCs.

tag: genotype/variation

value: bone marrow-derived dendritic cells

tag: treatment

tag: sample type


title: Infected Cells at D16, biological rep2

description:
1R2
Gene expression data from C2C12 myotubes infected with RML prions.


title: MB008

tag: Sex

tag: histology

tag: t-stage

value: dead


title: CD11c-Cre IRF4flox BMDCs Unstimulated C

description: Biological replicate 3 of 5: unstimulated Irf4 knockout BMDCs.

value: pooled mouse reference RNA


title: MB003

tag: n-stage

tag: m-stage

tag: age

value: N


title: Infected Cells at D16, biological rep3

description:
1R3
Gene expression data from C2C12 myotubes infected with RML prions.

tag: cell line


title: MB005

tag: Stage

tag: smoking


title: CD11c-Cre IRF4flox BMDCs Unstimulated E

description: Biological replicate 5 of 5: unstimulated Irf4 knockout BMDCs.

tag: strain/background


title: MB001

value: adenosquamous carcinoma

tag: survival time

tag: status


title: C57BL/6JE18.5

city: Nashville

first: Jing

institute: Vanderbilt University

hyb_protocol: Standard Affymetrix protocols for hybridization to the Affymetrix Mouse Genome 430 2.0 GeneChip Expression Arrays (Santa Clara, CA) were used.

scan_protocol: GeneChip Scanner was used for scanning and generating the raw .CEL files.

data_processing: The normalization was performed using the 'affy' package (Version 1.22.1) in R (Version 2.9.2). The RMA algorithm was used for data normalization.

label_protocol: Standard Affymetrix protocols were used.

extract_protocol: Total RNA was first purified with trizol and then repurified by RNeasy kits with DNase I (Qiagen, Valencia, CA), following the manufacturer’s protocol.

tag: strain

value: inbred C57BL/6

tag: developmental stage

value: embryonic day E18.5


title: Chordoma xenograft sample 2

description: Chordoma xenograft sample 2 used array platform GPL6104

source_name: Chordoma xenograft

tag: host strain

value: NOD/SCID/IL-2R γ-null mice

tag: tissue type

value: xenograft


title: CD11c-Cre BMDCs LPS 24 hrs B

description: Biological replicate 2 of 5: BMDCs treated with LPS for 24 hours.

source_name: CD11c-Cre BMDCs, LPS, 24 hrs

tag: genotype/variation

tag: cell type

tag: treatment

value: LPS 24hrs

tag: sample type


title: Chordoma xenograft sample 1

description: Chordoma xenograft sample 1 used array platform GPL6104


title: C57BL/6JE16.5

value: embryonic day E16.5


title: CD11c-Cre BMDCs LPS 24 hrs E

description: Biological replicate 5 of 5: BMDCs treated with LPS for 24 hours.


title: C57BL/6JADULT COLON

value: adult (eight week post-natal)


title: CD11c-Cre BMDCs LPS 24 hrs D

description: Biological replicate 4 of 5: BMDCs treated with LPS for 24 hours.


title: Fetal_Kidney_01

source_name: Fetal Kidney

tag: tissue

value: Fetal Kidney


title: MB002

tag: Sex

tag: histology

tag: t-stage

tag: n-stage

tag: m-stage

value: Current

value: alive

tag: disease-free survival time

tag: recurrence


title: C57BL/6JE14.5

value: embryonic day E14.5


title: CD11c-Cre BMDCs LPS 24 hrs C

description: Biological replicate 3 of 5: BMDCs treated with LPS for 24 hours.

tag: strain/background

source_name: Universal mouse reference (UMR) from Stratagene


title: C57BL/6JE17.5

tag: strain

value: embryonic day E17.5


title: CD11c-Cre BMDCs LPS 24 hrs A

description: Biological replicate 1 of 5: BMDCs treated with LPS for 24 hours.

value: bone marrow-derived dendritic cells


title: CD11c-Cre BMDCs LPS 6 hrs E

description: Biological replicate 5 of 5: BMDCs treated with LPS for 6 hours.

value: LPS 6hrs


title: C57BL/6JE15.5

tag: developmental stage

value: embryonic day E15.5


title: Mreg_no IFN-γ_2

status: Public on Dec 21 2013

city: Bergisch-Gladbach

first: Stefan

last: Tomiuk

address: Friedrich-Ebert-Str. 68

department: Bioinformatics

institute: Miltenyi Biotec GmbH

description: M reg no IFN-g (Series 2)

hyb_protocol: The hybridization procedure was performed according to the the “One-Color Microarray-Based Gene Expression Analysis protocol (version 5.7, part number G4140-90040) using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 1.65 µg Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65C) to Agilent Whole Mouse Genome Oligo Microarrays 4x44K using Agilent's recommended hybridization chamber and oven. Following hybridization, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37 C) for 1 min. The last washing step was performed with acetonitrile.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies). The Agilent Feature Extraction Software (FES) 10.5.1.1 was used to read out and process the microarray image files.

data_processing: FES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system (Rosetta Biosoftware, Rosetta error model; Lee Weng et al 2006).

source_name: Mreg_no IFN-γ

label_protocol: Sample labeling was performed as detailed in the “One-Color Microarray-Based Gene Expression Analysis protocol (version 5.7, part number G4140-90040). Briefly, 0.5 µg of each total RNA samples was used for the amplification and labeling step using the Agilent Quick Amp Labeling Kit (Agilent Technologies). Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer (NanoDrop Technologies).

growth_protocol: Input cells for M reg generation were FACS-sorted CD11b+ Ly6C+ Ly6G- monocytes from bone-marrow. Cells were cultured for 7 days in 35 mm untreated petri dishes containing 2 ml of RPMI 1640 with 100 U/ml penicillin-streptomycin, 25 mM HEPES, 2 mM glutamine, 2 mM GlutaMAXTM (Invitrogen) supplemented with 10% FCS (Biochrom), 10% human AB serum (Lonza) and 5 ng/ml M-CSF (Sigma). On day 6, cultures were stimulated with 25 ng/ml IFN-γ (Chemicon). The other macrophages were cultured in the same medium supplemented with 10% FCS (Biochrom) and 20 ng/ml M-CSF (Sigma), and stimulated on day 6 as indicated (see characteristics). For culture of M2b MΦ, petri dishes were coated overnight with 1 mg/ml human immunoglobulin (Sandoglobulin, CSL Behring) in Na- Bicarbonate buffer at 4°C, and washed 3 times with PBS before use.

extract_protocol: RNA was isolated using the RNeasy Plus Mini Kit (Qiagen). RNA quality was determined using the Agilent 2100 Bioanalyzer platform and only RNAs with calculated RNA Integrity Numbers (RIN) higher than 6 were accepted.

tag: tissue origin

value: Bone marrow

tag: sample group/subtype

value: Mreg_no IFN-γ

tag: sample origin

value: FACS-sorted Ly6C+ Ly6G- CD11b+ monocytes

tag: culture media (6-day culture period) supplemented with

value: 10% HABS + 10% FCS + 5ng/ml M-CSF

tag: 24h stimulation


title: C57BL/6JE13.5

value: inbred C57BL/6

value: embryonic day E13.5


title: Mreg_unpurified_3

description: Unpurified M reg (Series 3)

value: Bone marrow, spleen, blood

value: Adherent mononuclear cells

value: 25ng/ml IFN-γ


title: Mreg_no IFN-γ_3

description: M reg no IFN-g (Series 3)


title: MΦ_M2b_2

description: M2b Mphi (Series 2)

value: 10% FCS + 20ng/ml M-CSF + complexed Ig

value: 25 ng/ml IFN-γ


title: MΦ_M2b_3

description: M2b Mphi (Series 3)


title: Mreg_+LPS_1

description: M reg + LPS (Series 1)

value: 25ng/ml IFN-γ + 100µg/ml LPS


title: Mreg_1

description: M reg (Series 1)

source_name: Mreg

value: Mreg


title: Mreg_unpurified_1

description: Unpurified M reg (Series 1)


title: MΦ_M2c_3

description: M2c Mphi (Series 3)

value: 10% FCS + 20ng/ml M-CSF

value: 10-7 M Dexamethasone


title: Mreg_+LPS_3

description: M reg + LPS (Series 3)


title: Mreg_2

description: M reg (Series 2)


title: MΦ_M2b_1

description: M2b Mphi (Series 1)


title: Mreg_unpurified_2

description: Unpurified M reg (Series 2)


title: MΦ_M2c_1

description: M2c Mphi (Series 1)


title: MΦ_M2c_2

description: M2c Mphi (Series 2)


title: Mreg_3

description: M reg (Series 3)


title: mouse, spleen and lymph nodes,Treg cells

city: Tokyo

first: Noriko

last: Komatsu

address: 7-3-1 Hongo, Bunkyo-ku

department: Immunology

country: Japan

institute: the Univ of Tokyo

description:
C57BL/6  8-10 week-old  diffetentiated T cells from spleen and lymph nodes
IL-17(GFP)-Foxp3(APC)+ cells were sorted after the culture
04_Treg

hyb_protocol: The cRNA was hybridized to oligonucleotide probes on the Mouse Genome 430 2.0 Array(GPL1261) for 16 hours at 45˚C according to the Affymetrix protocol. The hybridized probe array underwent an automated washing and staining in an Affymetrix GeneChip Fluidics Station 450 using the protocol EukGE-WS2v5.

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

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

source_name: IL-17-Foxp3+ T cells from Foxp3+CD4+T cells in the presence of IL-2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001,Affymetrix).

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

value: spleen and lymph nodes

tag: age

value: 8-10 week-old

tag: t-cell subset

value: Treg cells


title: MΦ_M2a_3

description: M2a Mphi (Series 3)

value: Bone marrow

value: 20ng/ml IL-4


title: mouse, spleen and lymph nodes, Th17 cells

description:
C57BL/6  8-10 week-old  diffetentiated T cells from spleen and lymph nodes
IL-17(GFP)+Foxp3(APC)- cells were sorted after the culture
02_Th17

source_name: IL-17+Foxp3- T cells from naïve CD4+T cells under Th17 conditions

tag: tissue

value: Th17 cells


title: Mreg_no IFN-γ_1

description: M reg no IFN-g (Series 1)

value: Mreg_no IFN-γ

value: FACS-sorted Ly6C+ Ly6G- CD11b+ monocytes

value: 10% HABS + 10% FCS + 5ng/ml M-CSF


title: Mreg_+LPS_2

description: M reg + LPS (Series 2)


title: mouse, spleen and lymph nodes, exFoxp3Th17 cells

description:
C57BL/6  8-10 week-old  diffetentiated T cells from spleen and lymph nodes
IL-17(GFP)+Foxp3(APC)- cells were sorted after the culture
03_exFoxp3Th17

source_name: IL-17+Foxp3- T cells from Foxp3+CD4+T cells under Th17 conditions

value: exFoxp3Th17 cells


title: MΦ_M2a_1

description: M2a Mphi (Series 1)


title: MΦ_M2a_2

description: M2a Mphi (Series 2)


title: mouse, spleen and lymph nodes, Th0 cells

description:
C57BL/6  8-10 week-old  diffetentiated T cells from spleen and lymph nodes
IL-17(GFP)-Foxp3(APC)- cells were sorted after the culture
01_Th0

source_name: IL-17-Foxp3- T cells from naïve CD4+T cells under Th0 conditions

value: Th0 cells


title: MΦ_M1_2

description: M1 Mphi (Series 2)


title: MΦ_M0_3

description: M0 Mphi (Series 3)


title: Vegetal-most halves_rep3

city: Washington

first: Sally

middle: A.

last: Moody

state: DC

address: 2300 I St. NW

department: Anatomy and Regenerative Biology

institute: The George Washington University School of Medicine and Health Sciences

description:
NIH-Moody-V3-Xen
Maternally deposited RNAs present at the vegetal cortex and vegetal most half of vegetal blastomeres.

hyb_protocol: The labeled cDNAs were purified with the Dye Ex kit (Qiagen), and shipped to the NINDS-NIMH Microarray Consortium at The Translational Genomics Research Institute (T-GEN, Tempe, AZ).

scan_protocol: The chips were washed and scanned as recommended by the Ovation Biotin RNA Amplification and Labeling System User Guide (version 1.0).

data_processing: GCOS software was used to determine signal intensities and detection calls for each gene.  Please note that the data was processed by a service facility, who no longer exists. Thus, the submitter is not sure about software version or algorithm used for processing.

organism: Xenopus laevis

source_name: Vegetal Blastomeres

label_protocol: Total RNAs were labeled and fragmented with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.) according to standard protocol.

growth_protocol: Embryos were collected after hormone-induced natural matings of 2-pairs of adult Xenopus laevis,

extract_protocol: RNA was extracted with the RNeasy mini kit (Qiagen) using manufacturer's instructions.

treatment_protocol: Jelly coat was removed by incubation at room temp. in 2% cysteine, pH 8.0 for 4 minutes, and fixed in 98% ethanol, 2% acetic acid for dissections.

value: 8-cell embryos

value: vegetal-most halves of vegetal blastomeres


title: Vegetal-most halves_rep1

description:
NIH-Moody-V1-Xen
Maternally deposited RNAs present at the vegetal cortex and vegetal most half of vegetal blastomeres.


title: MΦ_M1_3

description: M1 Mphi (Series 3)

value: 25ng/ml IFN-γ + 100µg/ml LPS


title: MΦ_M1_1

description: M1 Mphi (Series 1)


title: Vegetal-most halves_rep2

description:
NIH-Moody-V2-Xen
Maternally deposited RNAs present at the vegetal cortex and vegetal most half of vegetal blastomeres.


title: Animal-blastomeres_rep3

description:
NIH-Moody-A3-Xen
Maternally deposited RNAs present in animal blastomeres

source_name: Animal Blastomeres

value: animal blastomeres


title: MΦ_M0_2

description: M0 Mphi (Series 2)

value: 10% FCS + 20ng/ml M-CSF


title: MΦ_M0_1

description: M0 Mphi (Series 1)


title: MΦ_IFN-γ_3

description: IFN-g Mphi (Series 3)

value: 25 ng/ml IFN-γ


title: Animal-blastomeres_rep2

description:
NIH-Moody-A2-Xen
Maternally deposited RNAs present in animal blastomeres


title: Chordoma SNP array sample 1

type: genomic

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Genomic DNA extracted from chordoma tumors was genotyped using Infinium HumanCNV370v1 Genotyping BeadChips (Illumina).

label: C-Bio and A-DNP

molecule: genomic DNA

label_protocol: 750ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from fresh frozen tissue was performed using lysis and proteinase K treatment, phenol-chloroform extraction, and ethanol preciptitation.

tag: host strain

value: NOD/SCID/IL-2R γ-null mice

value: Chordoma xenograft


title: MΦ_IFN-γ_2

description: IFN-g Mphi (Series 2)


title: Animal-blastomeres_rep1

description:
NIH-Moody-A1-Xen
Maternally deposited RNAs present in animal blastomeres


title: Chordoma SNP array sample 2


title: ALL_Relapse_of_Patient_L405_Nsp_Array

city: Newcastle Upon Tyne

first: Vikki

last: Rand

state: Tyne and Wear

address: Paul O'Gorman Building, Newcastle University

department: Northern Institute for Cancer Research

country: United Kingdom

institute: Newcastle University

hyb_protocol: Labelled DNA was hybridised according to manufacturer’s protocol.

scan_protocol: Arrays were scanned according to manufacturer’s protocol.

data_processing: The microarray data was processed using Affymetrix Genotyping Console (GTC) v4.0 to determine data quality. Genotype data was checked using the Concordance Check function within GTC to ensure no sampling errors had occurred during array processing. Copy number alterations were determined for 10 patients using the paired remission sample and the Hapmap894 reference 5 set within Partek Genomics Suite v6.5 (Partek, USA) as the reference for the remaining sample (L625). Further analysis, visualization and identification of genomic gains and losses were performed using Partek Genomics Suite v6.5 (Partek, USA) and SNPView2 v2.6 (Ilixa, UK). Regions of aberration were mapped according to the human reference sequence GRCh37.

source_name: bone marrow

label_protocol: DNA was labelled according to the standard Affymetrix protocol for the Affymetrix GeneChip Human Mapping 500K Array Set.

extract_protocol: Genomic DNA was extracted from bone marrow aspirates using the Qiagen DNAeasy blood and tissue kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel eletrophoresis.

tag: disease stage

value: Relapse


title: ALL_Remission_of_Patient_L578_Nsp_Array

value: Remission


title: ALL_Presentation_of_Patient_L578_Nsp_Array

value: Presentation


title: Monocytes_3

description: Monocytes (Series 3)

source_name: Monocytes

value: Bone marrow

value: Monocytes


title: ALL_Presentation_of_Patient_L554_Nsp_Array


title: ALL_Presentation_of_Patient_L296_Nsp_Array


title: ALL_Relapse_of_Patient_L554_Nsp_Array


title: ALL_Remission_of_Patient_L296_Nsp_Array


title: ALL_Relapse_of_Patient_L296_Nsp_Array


title: ALL_Remission_of_Patient_L554_Nsp_Array


title: MΦ_IFN-γ_1

description: IFN-g Mphi (Series 1)

value: FACS-sorted Ly6C+ Ly6G- CD11b+ monocytes


title: Monocytes_2

description: Monocytes (Series 2)


title: ALL_Relapse_of_Patient_L578_Nsp_Array


title: ALL_Remission_of_Patient_L405_Nsp_Array


title: ALL_Presentation_of_Patient_L625_Nsp_Array


title: ALL_Relapse_of_Patient_L625_Nsp_Array


title: ALL_Presentation_of_Patient_L405_Nsp_Array


title: Monocytes_1

description: Monocytes (Series 1)


title: ALL_Remission_of_Patient_L173_Nsp_Array


title: ALL_Remission_of_Patient_L169_Nsp_Array


title: ALL_Relapse_of_Patient_L173_Nsp_Array


title: ALL_Presentation_of_Patient_L173_Nsp_Array


title: Mo-DC_2

description: Mo-DC (Series 2)

source_name: Mo-DC

value: Mo-DC

value: 10% FCS + 20ng/ml GM-CSF + 20ng/ml IL-4


title: Mo-DC_3

description: Mo-DC (Series 3)


title: ALL_Relapse_of_Patient_L625_Sty_Array


title: Mo-DC_1

description: Mo-DC (Series 1)


title: ALL_Relapse_of_Patient_L169_Nsp_Array


title: ALL_Relapse_of_Patient_L68_Nsp_Array


title: ALL_Presentation_of_Patient_L169_Nsp_Array


title: Sca-1+ PDC, replicate 4

description:
1+_0h_4
gene expression analysis of SuperAmplified™ polyA RNA

hyb_protocol: Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Mouse Genome Oligo Microarrays (8x60K) using Agilent’s recommended hybridization chamber and oven.Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C and a final wash step with acetonitrile for 30 sec at RT.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing:
The Agilent Feature Extraction Software (FES 10.7.3.1 ) was used to read out and process the microarray image files.
FES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system (Rosetta Biosoftware, Rosetta error model; Lee Weng et al 2006).

source_name: Sca-1+ PDC collected from in vitro culture of differentiated bone marrow precursor cells using mFlt3-L

label_protocol: 100 ng of each RNA was used as template to produce Cy3- labeled cRNA. The RNA samples were amplified and labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.

growth_protocol: Cells were directly isolated from indicated cell culture sources by magnetic and flow cytometric cell sorting.

extract_protocol: RNA was isolated using the NucleoSpin® RNA II kit (Macherey-Nagel) following manufacturer's instructions.

treatment_protocol: Cells were directly lysed in RA1 buffer (Macherey-Nagel).

value: BALB/c

tag: gender

value: female

tag: cell type

value: plasmacytoid dendritic cells (PDC)

tag: genotype/variation


title: ALL_Presentation_of_Patient_L68_Nsp_Array


title: Sca-1+ PDC, replicate 2

description:
1+_0h_2
gene expression analysis of SuperAmplified™ polyA RNA


title: Sca-1+ PDC, replicate 1

description:
1+_0h_1
gene expression analysis of SuperAmplified™ polyA RNA


title: Sca-1- PDC, replicate 4

description:
1-_0h_4
gene expression analysis of SuperAmplified™ polyA RNA

source_name: Sca-1- PDC collected from in vitro culture of differentiated bone marrow precursor cells using mFlt3-L


title: ALL_Remission_of_Patient_L68_Nsp_Array


title: Sca-1- PDC, replicate 2

description:
1-_0h_2
gene expression analysis of SuperAmplified™ polyA RNA


title: Sca-1- PDC, replicate 3

description:
1-_0h_3
gene expression analysis of SuperAmplified™ polyA RNA


title: Sca-1+ PDC, replicate 3

description:
1+_0h_3
gene expression analysis of SuperAmplified™ polyA RNA


title: ALL_Relapse_of_Patient_L64_Nsp_Array


title: ALL_Presentation_of_Patient_L625_Sty_Array


title: Sca-1- PDC, replicate 1

description:
1-_0h_1
gene expression analysis of SuperAmplified™ polyA RNA


title: ALL_Remission_of_Patient_L64_Nsp_Array


title: ALL_Remission_of_Patient_L578_Sty_Array


title: WT-t0_vs_WT-t60min+0.7M NaCl

city: Madison

first: Audrey

last: Gasch

state: WI

address: 3456 Biotechnology Center 425G Henry Mall

institute: University of Wisconsin-Madison

description: Denoted strain grow in SC 30C and exposed to 0.7M NaCl for 60 min

hyb_protocol: Hybridization on Maui hyb station according to Nimblegen and Maui protocols

scan_protocol: Axon GenePix scanner

data_processing:
Background-subtracted signal intentisties for all probes were normalized by quantile normalization, removing probes with missing signal, media signal within ORFs was compared for each channel, and log2(red/green) values were median-centered such that the average of all values = 0.
Values in the sample data table represent log2 fold-change in T30min or T60min vs T0min (unstressed) sample for each denoted strain;  Data have been converted so that positive log2 values correspond to gene induction (i.e. higher transcript abundance in T30 sample) and negative log2 values represent gene repression (i.e. higher transcript abundance in unstressed T0 sample).  Samples collected together are annotated by sets.

label: Oyster 550

organism: Saccharomyces cerevisiae

source_name: WT BY4742 his3kan treated with 0.7M NaCl for 60 min

label_protocol: Amino-allyl-dUTP incorporated into generated cDNA;  post-synthesis coupling to cyanine dyes (see Lee & Topper. 2011. Mol Sys Bio 7:514)

growth_protocol: S. cerevisiae strains grown in synthetic complete (SC) medium at 30C in batch-culture with shaking.

extract_protocol: Hot phenol lysis to isolate total RNA

treatment_protocol: Pre-warmed NaCl in SC added to each culture to a final concentration of 0.7M NaCl

value: WT his3kan

tag: treated with

value: 0.7M NaCl for 60 min

label: Oyster 650

source_name: WT BY4742 his3kan - unstressed t0 min

value: none (unstressed control)


title: ALL_Relapse_of_Patient_L554_Sty_Array


title: ALL_Presentation_of_Patient_L578_Sty_Array


title: ALL_Remission_of_Patient_L45_Nsp_Array


title: ALL_Relapse_of_Patient_L578_Sty_Array


title: ALL_Presentation_of_Patient_L64_Nsp_Array


title: ALL_Presentation_of_Patient_L45_Nsp_Array


title: ALL_Remission_of_Patient_L554_Sty_Array


title: ALL_Remission_of_Patient_L37_Nsp_Array


title: ALL_Relapse_of_Patient_L45_Nsp_Array


title: ALL_Presentation_of_Patient_L37_Nsp_Array


title: ALL_Presentation_of_Patient_L554_Sty_Array


title: KD d6 replicate 2

city: Barcelona

first: Luciano

last: Di Croce

address: Dr. Aiguader, 88

country: Spain

institute: Centre for Genomic Regulation

hyb_protocol: After fragmentation, 600 ng of labeled cRNA from each sample was hybridized in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ºC with Gene Expression Wash buffer 2 (Agilent).

scan_protocol: Scanned on an Agilent G2539A scanner at 5um resolution and 100%PMT The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing: Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples.

source_name: KD d6

label_protocol: 100 ng of total RNA from each sample were amplified by Oligo-dT-T7 reverse transcription and labeled by in vitro transcription with T7 RNA polymerase in the presence of Cy3-CTP using the LowInputQuick Amp Labeling kit (Agilent) and purified using RNAeasy columns (Qiagen, Hilden, Germany)

extract_protocol: Total RNAs were prepared with Qiagen Rneasy minikit according to manufacturer’s protocol

value: RGC-like NPC

tag: treatment

value: Zrf1 KD


title: KD d6 replicate 3


title: ALL_Relapse_of_Patient_L405_Sty_Array


title: KD d6 replicate 4


title: Control d6 replicate 4

source_name: Control d6

value: control


title: Δura3 Media M15 biological replicate 1

city: Seattle

first: Nicolas

last: Pinel

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

description: Normalized log10 intensity of X_INT/Y_INT (sample/reference) averaged over dye flip between sample and reference RNA.

hyb_protocol: Whole-genome tiling arrays were designed using e-Array (Agilent Technologies) for the H. salinarum NRC-1 main chromosome (NC_002607), and pNRC100 (NC_001869) and pNRC200 (NC_002608) plasmids using a 60k feature design of 60-mer strand-specific probes spaced at 24 bp. Arrays included manufacturer’s control probes and were printed by Agilent Technologies. Hybridization and washing was performed as described (Turkarslan et al 2011), with dye flip experiments performed for each sample. See http://www.chem.agilent.com/Scripts/PDS.asp?lPage=34519 for details.

scan_protocol: Arrays were scanned in ScanArray 5000 (Perkin Elmer) using Packard BioChip ScanArray software. See http://www.systemsbiology.org/Scientists_and_Research/Technology/ISB_Facilities/Microarray for microarray scanning details.

data_processing:
Spot finding was performed using Feature Extraction (Agilent Technologies). See http://www.systemsbiology.org/Scientists_and_Research/Technology/Data_Management/Microarray_Pipeline for more details.
Normalization and statistical analysis were performed as described before (Koide et al, 2009). Values are normalized log10 ratios representing test/reference. Interarray comparisons were normalized relative to a reference RNA sample generated from unperturbed H. salinarum NRC-1 batch culture in the standard complex medium to OD600 = 0.471.

organism: Halobacterium salinarum NRC-1

source_name: Δura3 Media M15 biological replicate 1

label_protocol: RNAs were direct labeled with Alexa547 and Alexa647 dyes (Kreatech). See Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35.

growth_protocol: The parental strain (delta-ura3) was grown from colony in standard complex media (CM; media M2), before passage into each of 10 media that vary in ion composition but not total salinity. During batch growth in the experimental media, samples for microarrays were taken at OD600 ~ 0.4-0.5, to capture mid-log phase and the range where growth rate approaches maximum. Cells were batch cultured in flasks at 37°C with constant shaking (~220 rpm). The standard complex media composition is as follows: 250 g/l NaCl, 20 g/l MgSO4, 2 g/l KCl, 3 g/l sodium citrate, 10 g/l Oxoid brand bacteriological peptone. Media were supplemented with 50mg/l uracil to compensate for the uracil deficiency caused by the delta-ura3 marker. All media were at total salinity of 4.388 M.  All contain the same levels of sodium citrate and peptone.  The levels of NaCl, MgSO4, and KCl varied as follows. M1: 4.28 M NaCl, 0.108 M MgSO4, 0 M KCl. M2: 4.28 M NaCl, 0.081 M MgSO4, 0.027 M KCl. M5: 4.28 M NaCl, 0 M MgSO4, 0.108 M KCl. M6: 3.42 M NaCl, 0.968 M MgSO4, 0 M KCl. M7: 3.42 M NaCl, 0.726 M MgSO4, 0.242 M KCl. M9: 3.42 M NaCl, 0.242 M MgSO4, 0.726 M KCl. M12: 2.57 M NaCl, 1.364 M MgSO4, 0.454 M KCl. M13: 2.57 M NaCl, 0.909 M MgSO4, 0.909 M KCl. M14: 2.57 M NaCl, 0.454 M MgSO4, 1.364 M KCl. M15: 2.57 M NaCl, 0 M MgSO4, 1.818 M KCl

extract_protocol: Total RNA was prepared from the cell pellets using the mirVANA RNA kit (Ambion, Austin, TX) according to manufacturer's instructions and then treated with RNase-free DNase (Promega).

treatment_protocol: Cells from 2 ml of culture were pelleted (16k x g, 60 s) and flash frozen.

tag: strain

tag: genotype

tag: temperature

tag: od

source_name: Halobacterium salinarum NRC-1 reference sample

value: wild type


title: KD d6 replicate 1


title: Control d6 replicate 3


title: Control d6 replicate 2


title: Δura3 Media M14 biological replicate 1

source_name: Δura3 Media M14 biological replicate 1


title: Δura3 Media M9 biological replicate 1

source_name: Δura3 Media M9 biological replicate 1


title: ALL_Presentation_of_Patient_L405_Sty_Array


title: ALL_Relapse_of_Patient_L37_Nsp_Array

value: Relapse


title: Δura3 Media M7 biological replicate 1

source_name: Δura3 Media M7 biological replicate 1


title: ALL_Remission_of_Patient_L405_Sty_Array

value: Remission


title: Δura3 Media M13 biological replicate 1

source_name: Δura3 Media M13 biological replicate 1


title: Control d6 replicate 1


title: ALL_Remission_of_Patient_L296_Sty_Array


title: WT-t0_vs_WT-t30min+0.7M NaCl

description: Denoted strain grow in SC 30C and exposed to 0.7M NaCl for 30 min

source_name: WT BY4742 his3kan treated with 0.7M NaCl for 30 min

value: 0.7M NaCl for 30 min

source_name: WT BY4742 his3kan - O25


title: Δura3 Media M5 biological replicate 1

source_name: Δura3 Media M5 biological replicate 1


title: ALL_Remission_of_Patient_L173_Sty_Array

source_name: bone marrow


title: final_differentiated_cells_PSA-NCAM-enriched_rep1

description:
Sample name: step 5 enriched 1
Agilent Feature Extraction file:
252665510972_S01_GE2_105_Jan09_1_4.txt

hyb_protocol: Hybridisation was performed as detailed in the “Two-Color Microarray-Based Gene Expression Analysis protocol” (Agilent). Briefly, 825 ng of the corresponding Cy3- and Cy5-labeled fragmented cRNA were combined and hybridized overnight (17 hours, 65 °C) to Agilent Whole mouse Genome Oligo Microarrays 4x44K Version 2 using Agilent’s recommended hybridization chamber and oven. Finally, the microarray was washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37 °C) for 1 min. The last washing step was performed with acetonitrile.

scan_protocol: The Agilent Feature Extraction Software (FES) version 10.7.3.1 was used to read out and process the microarray image files.

data_processing: FES derived output data files were further processed using the Rosetta Resolver® gene expression data analysis system (Rosetta Biosoftware).

source_name: [test] mESC derived neuronal cells after neuronal differentiation, PSA-NCAM enriched

label_protocol: Sample labeling was performed as detailed in the “Two-Color Microarray-Based Gene Expression Analysis protocol” (Agilent). For the linear T7-based amplification step, 100 ng of each total RNA sample was used. To produce Cy3- and Cy5-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol. Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer (NanoDrop Technologies).

growth_protocol: Actin-eGFP C57BL/6 mESCs were propagated on Mitomycin-C (Sigma-Aldrich-Aldrich)-treated mouse fibroblasts in DMEM (Miltenyi Biotec) supplemented with 1mM nonessential amino acids (PAA), 1x NaPyruvate (PAA), 2mM L-Glutamin (PAA) 0.1 mM β-Mercaptoethanol, 1% Penicillin Streptomycin (PAA), 10% FCS (PAA) and 0.01% LIF (Miltenyi Biotec) (step 1). Cells were split every two days and plated at a concentration of 25000/cm2. Before embryoid bodies (EBs) differentiation (step 2), cells were harvested with 0,05% Trypsin (Sigma), subjected to feeder depletion with Feeder Removal MicroBeads Kit (Miltenyi Biotec) and then plated on nonadherent bacterial dishes for four days in LIF free EB medium containing 5% of Knockout serum replacement (Invitrogen) 5% FCS (PAA). EBs were then plated onto adhesive tissue culture surface. After 24h in culture, selection of neural progenitors cells was initiated in serum-free 1x ITS liquid media supplements (Sigma-Aldrich) plus 5µg/ml Fn (Biopure) supplemented DMEM medium (ITSFn, step 3). After 6 days (6d) of selection, cells were harvested with AccuMax (PAA), plated on polyornithine (Sigma-Aldrich) and laminin (Sigma-Aldrich) coated 24 well plates and cultivated for 5d (step 4) in Macs Neuro Medium (Miltenyi) supplemented with 1x N2 supplement (PAA), 1mM nonessential amino acids, 2mM L-Glutamin, 1% Penicillin Streptomycin, 1 µg/ml laminin, 10 ng/ml bFGF (Miltenyi). For neuronal differentiation (step 5) bFGF was removed to induce differentiation, N2 supplement was substituted with 1x B27 (PAA) supplement and 200 µM Ascorbic Acid was added. Cells were cultivated in neuronal differentiation medium for 7d.

extract_protocol: 1x 106 cells were harvested, rapidly frozen in liquid nitrogen and stored at -70 °C.  RNA was isolated using standard RNA extraction protocols (Trizol). RNA quality and integrity were determined using the Agilent RNA 6000 Nano Kit on the Agilent 2100 Bioanalyzer (Agilent Technologies). RNA was quantified by measuring A260nm on the ND-1000 Spectrophotometer (NanoDrop Technologies).

treatment_protocol: Cell suspensions containing approximately 3x106 cells were first labeled with anti-PSA-NCAM antibody conjugated to APC fluorochrome (Miltenyi Biotec). Then magnetic MicroBeads coupled to anti-APC antibody were applied. Cells were re-suspended in mESC medium and the cell suspension was loaded onto an MS-column (Miltenyi Biotec), which was placed in the magnetic field of a MACS Separator. The column was rinsed three times with 0.5 ml of medium. Magnetically isolated PSA-NCAM positive cells were retained in the column and eluted as the positively selected cell fraction after removing the column from the magnet. Immunomagnetic removal of dead cells prior enrichment with anti-PSA-NCAM was performed using the Dead Cell Removal Kit (Miltenyi Biotec).  Isolated in vitro derived PSA-NCAM positive cells were seeded on polyornithine and laminin coated 24-well plates and further differentiated into neuronal lineage as describe above for in vitro analysis or were collected in medium at a concentration of 50000/ul and used for transplantation.

tag: enrichment

value: PSA-NCAM

tag: cultivation

value: step 5

source_name: [control] mESC


title: ALL_Relapse_of_Patient_L173_Sty_Array


title: Δura3 Media M1 biological replicate 1

source_name: Δura3 Media M1 biological replicate 1


title: final_differentiated_cells_PSA-NCAM-enriched_rep2

description:
Sample name: step 5 enriched 2
Agilent Feature Extraction file:
252665512019_S01_GE2_105_Jan09_1_4.txt


title: HP1 8-16h embryonic D.melanogaster ChIP Rep2

type: SRA

first: DCC

last: modENCODE

address: MaRS Centre, South Tower, 101 College Street, Suite 800

institute: Ontario Institute for Cancer Research

description: ChIP DNA; Antibody information listed below: official name: HP1 antibody (ab24726);target name: HP1;host: Rabbit;antigen: Recombinant full length protein (Fruit fly (Drosophila melanogaster)).;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab24726;short description: Rabbit polyclonal to HP1;input DNA

library_source: genomic

data_processing: Solexa_Alignment protocol. Raw image files were processed following the following Illumina-compatible pipeline:1.  The Raw images were first processed with the Casava 1.7.0.2.  Base-called sequences with confidence metrics were obtained using OLB-1.9.0.  All multiplexed samples were demultiplexed using Casava 1.7.0.3. Finally the BWA program was used to align the sequence reads to the Drosophila melanogaster (v5.32) genome, allowing up to 2 edit distance in the seed region and 3 in the full read length. Tags that aligned to more than one  location were excluded from our analysis for both ChIP sample and the corresponding control sample (input chromatin). Only properly aligned reads with mapping quality more than 30 were kept. MACS_Peak-calling protocol. Peak calls were determined by using Model-based Analysis of ChIP-Seq (MACS) software, version 2 (MACS2). MACS2 was supplied with the following parameters:tagSize = 50mfold = 2genomeSize = 120000000bandwidth = 100pvalue = 1e-5  Processed data are obtained using following parameters: genome version is flybase BDGPv5

organism: Drosophila melanogaster

source_name: HP1 8-16h embryo ChIP Rep.2

extract_protocol:
1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder.   2. For a 8-16 hours egg laying, new plates are added after a 2 hours pre-egglaying at 12 pm and flies are allowed to lay eggs for 8 hours.   3. Embryos are collected at 7.45 am using a filter mesh and a brush. They are rinsed with EWB and cross-linked at 8am in 1.8% formaldehyde at room temperature for 15 min.
Solutions and MaterialsLysis buffer: (see above)5mg/ml RNaseA (DNase free)PAS suspension: 100 mg of CL-4B (Amersham, 17-0780-01) PAS shoµld be resuspended in 1 ml of lysis buffer + protease inhibitors + 0.1 mg/ml BSA for 50 %v suspension. Wash in lysis buffer 2-3 times, overall equilibration time 1h. Store up to one week at 4 C.TE: 10 mM Tris-HCl pH 8.0, 1 mM EDTAElution buffer1: 10 mM EDTA, 1% SDS, 50 mM Tris-Cl pH 8.Elution buffer2: TE+0.67% SDS.LiCL 4M? Protocol 1. To an amount of chromatin corresponding to 150 mg of biological material, suspended in a final volume of chromatin extract of 1 ml (in lysis buffer + protease inhibitors), add 100 µl of PAS suspension for preincubation. Incubate several hours or overnight at 4°C, then remove PAS. Crosslinked chromatin at this stage can be stored several days at 4°C or frozen at ?70°C.2. [Optional : Check for amount of DNA. From the 1 ml solution above, take a 100 µl aliquot, Add proteinase K up to 100 ug/ml and SDS to 1%, incubate 6h at 60°C, then 20 min at 70°C, add RNAse to 50 ug/ml and incubate additional 2h at 37°C. Phenol-chlorophorm extract, ethanol precipitate. Run on an agarose gel to check amount and size of DNA.]3. Separate chromatin sample into 4x250 µl aliquots (one aliquot is enough for one IP but the amount may be decreased further). Immunoprecipitate chromatin by adding the antibody (Ab) of interest (amount of Ab shoµld be determined empirically, usually the same concentration than for a successfµl IF experiement). Keep a control sample without Ab IP, named "Mock".4. Incubate 4 h at 4°C on a head to head rotating wheel, then add 50 µl of PAS suspension and incubate 4 h or overnight. Spin down PAS and proceed to washes.5. Wash PAS 4x with lysis buffer, followed by 2x with TE (without protease inhibitors). Each wash is for 5 min at 4°C, using 1 ml of solution.6. Elution of precipitated material. Spin down PAS. Add 100 µl of elution buffer, mix and incubate 10 min at 65°C. Spin down PAS and transfer supernatant to new tube. Add 150 µl of elution buffer 2 to PAS, mix, centrifuge at fµll speed and transfer eluate to a tube together with the eluate from the first centrifugation. The combined material is the "chromatin precipitate" (approx. 250 µl).7. Incubate precipitate 6 h (or overnight) at 65 C to reverse cross-links. Add 250 µl of Proteinase K solution, incubate at 50°C 2-3 h.8. Add 55 µl of 4M LiCl and 500 µl of phenol-chlorophorm. Mix and microfuge at fµll speed at RT. Transfer aqueous phase to a new tube and precipitate with 1 ml of 100% ethanol. Wash with 750 µl of 70% ethanol. Spin down and dry precipitate.9. Dissolve in 25 µl of water. This is the chromatin immunoprecipitate or ?Native ChIP? sample.
DNA fragments recovered following chromatin IP prepared for Illumina sequencing using the Epicentre Nextera DNA Sample Prep Kit (Cat. # GA0911).  After a final gel purification step the DNA is loaded into a flow cell for multiplexed sequencing.

value: Y cn bw sp

tag: developmental stage

value: Embryo 8-16h


title: final_differentiated_cells_PSA-NCAM-enriched_rep3

description:
Sample name: step 5 enriched 3
Agilent Feature Extraction file:
252665510973_S01_GE2_105_Jan09_1_4.txt


title: Δura3 Media M2 biological replicate 1 technical replicate 2


title: Δura3 Media M6 biological replicate 1

source_name: Δura3 Media M6 biological replicate 1


title: ALL_Relapse_of_Patient_L169_Sty_Array


title: final_differentiated_cells_no-enrichment_rep3

description:
Sample name: step 5 control 3
Agilent Feature Extraction file:
252665510973_S01_GE2_105_Jan09_1_3.txt

source_name: [test] mESC derived neuronal cells after neuronal differentiation

value: no


title: ALL_Presentation_of_Patient_L173_Sty_Array

value: Presentation


title: Δura3 Media M15 biological replicate 2

source_name: Δura3 Media M15 biological replicate 2


title: final_differentiated_cells_no-enrichment_rep2

description:
Sample name: step 5 control 2
Agilent Feature Extraction file:
252665512019_S01_GE2_105_Jan09_1_3.txt


title: ALL_Presentation_of_Patient_L296_Sty_Array


title: Δura3 Media M2 biological replicate 1

source_name: Δura3 Media M2 biological replicate 1


title: Δura3 Media M14 biological replicate 2

source_name: Δura3 Media M14 biological replicate 2

source_name: Halobacterium salinarum NRC-1 reference sample


title: ALL_Relapse_of_Patient_L296_Sty_Array


title: neural-precursors_PSA-NCAM-enriched_rep2

description:
Sample name: step 4 enriched 2
Agilent Feature Extraction file:
252665512019_S01_GE2_105_Jan09_1_2.txt

source_name: [test] mESC derived neural precursors, PSA-NCAM enriched

value: step 4


title: final_differentiated_cells_no-enrichment_rep1

description:
Sample name: step 5 control 1
Agilent Feature Extraction file:
252665510972_S01_GE2_105_Jan09_1_3.txt


title: Δura3 Media M13 biological replicate 2

source_name: Δura3 Media M13 biological replicate 2


title: neural-precursors_PSA-NCAM-enriched_rep3

description:
Sample name: step 4 enriched 3
Agilent Feature Extraction file:
252665510973_S01_GE2_105_Jan09_1_2.txt


title: ALL_Remission_of_Patient_L169_Sty_Array


title: ALL_Presentation_of_Patient_L68_Sty_Array


title: ALL_Relapse_of_Patient_L68_Sty_Array


title: huvec_premir146a_rep3

city: Liege

first: Ingrid

last: Struman

address: Avenue de l'Hôpital, 1

department: BMGG

country: Belgium

institute: GIGA-R

description:
replicate 3
pre-miR146a-3

hyb_protocol: 750 ng of biotinylated aRNA probe was hybridized to the Human Ref-8 BeadChip array (Illumina). Wash and scan were performed according to the manufacturer's instructions.

scan_protocol: The arrays were scanned using a BeadArray reader (Illumina). The images were registered and extracted automatically during the scan according to the manufacturer's settings.

data_processing: Raw microarray intensity data were analysed with  BeadStudio software (version 1.1.0),  normalized using the quantile normalization method according to the manufacturer's recommendation. Differential analysis are performed for each group and the data were filtered on Differential Score. Probes are considered as expressed by filtering data on detection p-value lower than 0.01.

label_protocol: 250 ng total RNA was labeled using the Illumina TotalPrep RNA amplification kit (Ambion, TX) according the manufacturer's instructions.

growth_protocol: HUVEC were grown on gelatin-coated plates with EGM-2 bullet kit medium (Lonza, Belgium)+ 0.5% FBS

extract_protocol: total RNA was isolated using the miRNeasy kit (Qiagen). Purity and quality of extracted RNA was evaluated using the Experion RNA StdSens Analysis kit (Bio-Rad Laboratories CA). High quality RNA with RNA Quality Indicator (RQI) score ≥ 9.5 was used for hybridization.

treatment_protocol: HUVEC were transfected with 50 nM of pre-miR molecules using Dharmafect-4 reagent according to the manufacturer's instructions (Dharmacon, C0) for 24h.

value: Human vein umbilical endothelial cells (HUVEC)

tag: transfectant


title: ALL_Remission_of_Patient_L68_Sty_Array


title: ALL_Presentation_of_Patient_L169_Sty_Array


title: huvec_premir146a_rep2

description:
replicate 2
pre-miR146a-2


title: neural-precursors_no-enrichment_rep3

description:
Sample name: step 4 control 3
Agilent Feature Extraction file:
252665510973_S01_GE2_105_Jan09_1_1.txt

source_name: [test] mESC derived neural precursors


title: ALL_Relapse_of_Patient_L64_Sty_Array


title: neural-precursors_PSA-NCAM-enriched_rep1

description:
Sample name: step 4 enriched 1
Agilent Feature Extraction file:
252665510972_S01_GE2_105_Jan09_1_2.txt


title: Δura3 Media M12 biological replicate 2

source_name: Δura3 Media M12 biological replicate 2


title: neural-precursors_no-enrichment_rep2

description:
Sample name: step 4 control 2
Agilent Feature Extraction file:
252665512019_S01_GE2_105_Jan09_1_1.txt


title: huvec_premir146a_rep1

description:
replicate 1
pre-miR146a-1


title: Δura3 Media M7 biological replicate 2

source_name: Δura3 Media M7 biological replicate 2


title: huvec_premir_rep2

description:
replicate 2
pre-control-2

value: Pre-miR-control


title: neural-precursors_no-enrichment_rep1

description:
Sample name: step 4 control 1
Agilent Feature Extraction file:
252665510972_S01_GE2_105_Jan09_1_1.txt


title: Δura3 Media M9 biological replicate 2

source_name: Δura3 Media M9 biological replicate 2


title: ALL_Remission_of_Patient_L64_Sty_Array

source_name: bone marrow


title: Δura3 Media M5 biological replicate 2

source_name: Δura3 Media M5 biological replicate 2


title: NPC_Taurine(TAU)vsControl(CTR)_rep1-3

city: México DF

first: Reyna

last: Hernandez-Benitez

address: Circuito Exterior S/N Ciudad Universitaria

department: Neurociencias

country: Mexico

institute: Instituto de Fisiología Celular UNAM

description: Sample 2

hyb_protocol: For pre-hybridization the slides were re-hydrated with water vapor at 60°C, and fixed with two cycles of UV light (1200J). After boiling for two minutes at 92°C, slides were washed with 95% ethanol for one minute and prehybridzed in 5X SSC, 0.1% SDS and 1% BSA for one hour at 42°C. The slides were washed and dried for further hybridization.  Equal quantities of labeled cDNA were hybridized using hybridization solution UniHyb (TeleChem International INC), to the 22 thousand oligos mouse arrays for 14 h at 42°C.

scan_protocol: Acquisition and quantification of array images was performed in ScanArray 4000 with its accompanying software ScanArray 4000 from Packard BioChips. All images were captured using 65% PMT gain, 70 to 75% laser power and 10µm resolution at 50% scan rate. For each spot the Alexa555 and Alexa647 density mean value (Dty), background mean value (Bck) and Signal (Sig) cross channel loees normalization value (by subgrids) were calculated with software ArrayPro Analyzer from Media Cibernetics.

data_processing:
Microarray data analysis was performed with free software genArise, developed in the Computing Unit of Cellular Physiology Institute of UNAM. GenArise carry out a number of transformations: background correction, lowess normalization, intensity filter, replicates analysis and selecting differentially expressed genes. The goal of genArise is to identify which of the genes show good evidence of being differentially expressed. The software identifies differential expressed genes by calculating an intensity-dependent z-score. Using a sliding window algorithm to calculate the mean and standard deviation within a window surrounding each data point, and define a z-score where z measures the number of standard deviations a data point is from the mean. zi = (Ri – mean(R)) / sd(R) Where zi is the z-score for each element, Ri is the log-ratio for each element, and sd(R) is the standard deviation of the log-ratio. With this criterion, the elements with a z-score > 2 standard deviations would be the significantly differentially expressed genes.

Please note that the original raw data .xls file was modified to include the dye assignment in the file names and post-calculated log2ratios data (column X). Both the original and modified data files are provided.

source_name: taurine NPC culture

label_protocol: 10 µg of total RNA were used for cDNA synthesis incorporating dUTP-Alexa555 or dUTP-Alexa647 employing the Firs-Strand cDNA labeling kit (Invitrogen). Incorporation of fluorophore was analyzed by using the absorbance at 555 nm for Alexa555 and 650 nm for Alexa647.

growth_protocol: Neural precursor cells were obtained from the subventricular zone of adult mouse brains and cultured as neurospheres. Tissue from the subventricular zones of adult CD1 mice was mechanically dissociated to yield a cell suspension. The cells were incubated in medium containing DMEM/F12, glutamax 100×, 25 µg/mL insulin, 100 µg/mL transferrin, 20 nM progesterone, 60 µM putresine, 30 nM sodium selenite, 50 U/mL penicillin, 50 μg/mL streptomycin, and the growth factors EGF and FGF2 (20 ng/mL each) in sterile 6-well plates (30,000 cells/well). The cultures were maintained at 37°C in humidified 5% CO2 / 95% air atmosphere for 9 - 15 days. The neurospheres that had formed were mechanically disaggregated, and the cells were seeded as secondary cultures.

extract_protocol: The total RNA from the control and taurine NPC cultures was purified using the RNeasy mini kit (Qiagen, Hilden, Germany) according the instructions of manufacturer.

treatment_protocol: To obtain taurine (TAU) cultures, the medium was supplemented with 10 mM taurine (FlukaBioChemica, Sigma-Aldrich).

tag: strain background

value: brain

value: Neural precursor cells (NPC) from subventricular zone

source_name: control NPC culture

tag: strain backgroud

value: CD1 strain


title: Δura3 Media M6 biological replicate 2

source_name: Δura3 Media M6 biological replicate 2


title: huvec_premir_rep1

description:
replicate 1
pre-control-1


title: NPC_Control(CTR)vsTaurine(TAU)_rep1-3

description: Sample 1

tag: tissue


title: ALL_Relapse_of_Patient_L45_Sty_Array

tag: disease stage


title: ALL_Presentation_of_Patient_L45_Sty_Array


title: ALL_Remission_of_Patient_L45_Sty_Array


title: Δura3 Media M1 biological replicate 2

source_name: Δura3 Media M1 biological replicate 2


title: Δura3 Media M2 biological replicate 2

source_name: Δura3 Media M2 biological replicate 2


title: ripe_berry_stage2_night_rep3

status: Public on Dec 20 2013

city: Montpellier

first: markus

last: rienth

address: 2, Place Pierre Viala

country: France

institute: INRA Montpellier

hyb_protocol: Hybridization was performed on a NimbleGen microarray 090818 Vitis exp HX12 (Roche, NimbleGen Inc., Madison, WI), consisting of 29,549 predicted genes on the basis of the 12X grapevine V1 gene prediction version V1 http://srs.ebi.ac.uk/.

scan_protocol: Nimblegen protocol

data_processing: The Robust Multi-array Analysis (RMA) algorithm was used for background correction, normalization and expression levels. Differential expression analysis was performed with the bayes t-statistics from the linear models for microarray data (limma). P-values were corrected for multiple-testing using the Benjamini-Hochberg’s method.

organism: Vitis vinifera

source_name: ripening vitis vinifera berry night sampled

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

growth_protocol: Microvines grown under fully controlled environment in phytotrons

extract_protocol: Qiagen Rneasy kit adapted to berry tissue

treatment_protocol: Day/Night sampling on different berry development stages

value: DRCF mutant

value: ripe berry stage2

tag: sampling time

value: night

value: berry


title: ripe_berry_stage2_night_rep2


title: ripe_berry_stage2_night_rep1


title: ripe_berry_stage2_day_rep2

source_name: ripening vitis vinifera berry day sampled

value: day


title: ripe_berry_stage1_night_rep3

value: ripe berry stage1


title: ALL_Relapse_of_Patient_L37_Sty_Array

value: Relapse


title: ripe_berry_stage1_night_rep2


title: ALL_Remission_of_Patient_L37_Sty_Array

value: Remission


title: ripe_berry_stage1_day_rep3


title: green_berry_stage2_night_rep3

source_name: green vitis vinifera berry night sampled

value: green berry stage2


title: green_berry_stage2_day_rep3

source_name: green vitis vinifera berry day sampled


title: ripe_berry_stage2_day_rep1


title: green_berry_stage1_night_rep3

value: green berry stage1


title: ripe_berry_stage1_night_rep1


title: ripe_berry_stage1_day_rep2


title: green_berry_stage2_night_rep2


title: green_berry_stage2_day_rep2


title: ripe_berry_stage1_day_rep1


title: DobermPinscher-BI_20953

city: Cambridge

first: Hyun Ji

last: Noh

state: MA

address: 7 Cambridge Center

department: Genome Sequencing and Analysis

institute: Broad Institute

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The array image was acquired using Affymetrix GeneChip® Operating Software.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

organism: Canis lupus familiaris

source_name: blood

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from blood using the Puregene DNA purification Kit (Gentra Systems) protocol.

tag: phenotype

value: compulsive disorder


title: DobermPinscher-BI_20958

value: control


title: DobermPinscher-BI_20956


title: green_berry_stage1_day_rep3


title: DobermPinscher-BI_20955


title: green_berry_stage1_night_rep2


title: DobermPinscher-BI_20952_rep


title: DobermPinscher-BI_20952


title: DobermPinscher-BI_20951_rep


title: green_berry_stage2_night_rep1


title: DobermPinscher-BI_20951


title: DobermPinscher-BI_20950


title: green_berry_stage2_day_rep1


title: green_berry_stage1_day_rep2


title: green_berry_stage1_night_rep1


title: DobermPinscher-BI_20949


title: DobermPinscher-BI_20948


title: DobermPinscher-BI_20947


title: DobermPinscher-BI_20944_rep


title: DobermPinscher-BI_20946


title: ALL_Presentation_of_Patient_L37_Sty_Array

value: Presentation


title: DobermPinscher-BI_20944


title: control rep2

city: London

first: Ariana

middle: Pia

last: Gatt

address: London

institute: King's College London

description: Gene expression data from control CNS tissue

hyb_protocol: Hybridisations were performed using the Affymetrix Terminal Labelling kit on Drosophila Gene 1.0 ST Arrays (Affymetrix).

scan_protocol: Imaging of the arrays was performed using the Affymetrix GCS3000 microarray system.

data_processing: Data normalization was processed using a Robust Multichip Average (RMA) algorithm and analysed using the Omics Explorer package (Qlucore). A false discovery rate (FDR) of 0.2% was used.

source_name: CNS tissue from nsybGal4/+ control larvae

label_protocol: cRNA was prepared from 500ng of total RNA using the Ambion WT Expression kit  (Ambion).

growth_protocol: Larvae were grown on standard fly food at 25 degrees.

extract_protocol: For the microarray analysis the complete CNS from 10-15 wandering third instar larvae were dissected in PBS and placed into PBS on ice and then transferred into 100ul of lysis buffer from the Absolutely RNA Microprep kit (Stratagene) and vortexed for 5 seconds. Total RNA was then prepared using this kit. For each genotype RNA samples were prepared in triplicate and stored at -80oC.

treatment_protocol: One control and one experimental genotypes were used: Control (nsybGal4/+) and TFAM3M (nsybGal4>UAS-TFAM3M).

value: larvae

value: CNS

tag: genotype/variation

value: Control (nsybGal4/+)


title: DobermPinscher-BI_20943_rep


title: green_berry_stage1_day_rep1


title: TFAM OE rep3

description: Gene expression data from CNS tissue over-expressing TFAM in neurons

source_name: CNS tissue from nsybGal4/UAS-TFAM3M larvae

value: TFAM3M (nsybGal4>UAS-TFAM3M)


title: DobermPinscher-BI_20943


title: control rep3


title: DobermPinscher-BI_20942


title: ALL_Presentation_of_Patient_L64_Sty_Array


title: TFAM OE rep2


title: TFAM OE rep1


title: control rep1


title: DobermPinscher-BI_20945


title: DobermPinscher-BI_20941


title: DobermPinscher-BI_20940


title: DobermPinscher-BI_20939


title: DobermPinscher-BI_20938


title: DobermPinscher-BI_20937


title: DobermPinscher-BI_20935_rep


title: DobermPinscher-BI_20936


title: DobermPinscher-BI_20936_rep


title: DobermPinscher-BI_20935


title: p1617_Chronic_24hr_rep3

city: Menlo Park

first: J. Tyson

last: McDonald

address: 333 Ravenswood Avenue

institute: SRI International

description: SAMPLE 31

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Data files were opened with Illlumina's GenomeStudio software. Non-normalized, non-background corrected signal intensity values for each sample were normalized to the mean-of-means for seven housekeeping genes (TUBB2A, UBC, EEF1A1, TXN, GAPDH, ACTB, RPS9). Samples were uploaded to GenePattern, log2 transformed, quantile normalized and processed with the ComBat module to remove non-biological batch effects.

source_name: Primary prostate fibroblasts from patient p1617_Chronic_24hr

label_protocol: Biotinylated cRNA was prepared with the Ambion MessageAmp kit for Illumina arrays.

growth_protocol: Normal prostate tissue samples (~1cm3) were minced and collagenase digested overnight before plating.  Primary fibroblast cell cultures were grown using RPMI-1640 plus 10% fetal bovine serum (Lonza, Hopkinton, MA) and maintained in a humidified 37ºC incubator with 5% CO2.

extract_protocol: Total RNA was extracted after treatment using TRIzol (Life Technologies, Grand Island, NY) according to the manufacturer’s instructions. RNA quality and quantity was assessed using the Agilent 2100 Bioanalyzer.

treatment_protocol: Cells were irradiated acutely with 10cGy or 200cGy using a Cesium-137 (Cs-137) Mark I irradiator with a dose-rate of 0.48Gy per minute.  For each experimental replicate, in parallel with acute exposures, chronic low dose-rate exposure used a sealed flat uniform sheet of Cobalt-57 (Eckert & Ziegler Isotope Products, Valencia, CA) with a dose rate of 7 to 17µGy per minute resulting in a total dose of 1.0 to 2.45cGy.  Samples were in a dedicated incubator directly above the Cobalt-57 source while control and acutely irradiated samples were placed in an incubator with identical conditions without an irradiation source.

tag: patient id

tag: gender

value: male

tag: patient age

value: 66 years

value: prostate

tag: cell type

value: primary prostate fibroblasts


title: p1617_Chronic_24hr_rep2

description: SAMPLE 30


title: p1541_200cGy_24hr_rep4

description: SAMPLE 20

source_name: Primary prostate fibroblasts from patient p1541_200cGy_24hr

value: 54 years


title: p1617_200cGy_24hr_rep3

description: SAMPLE 23

source_name: Primary prostate fibroblasts from patient p1617_200cGy_24hr


title: p1617_Chronic_24hr_rep1

description: SAMPLE 29


title: p1617_200cGy_24hr_rep2

description: SAMPLE 22


title: p1541_Chronic_24hr_rep4

description: SAMPLE 28

source_name: Primary prostate fibroblasts from patient p1541_Chronic_24hr


title: p1617_Chronic_24hr_rep4

description: SAMPLE 32


title: p1541_Chronic_24hr_rep3

description: SAMPLE 27


title: p1541_Chronic_24hr_rep1

description: SAMPLE 25


title: p1541_Chronic_24hr_rep2

description: SAMPLE 26


title: p1617_200cGy_24hr_rep4

description: SAMPLE 24


title: p1541_200cGy_24hr_rep3

description: SAMPLE 19


title: p1617_200cGy_24hr_rep1

description: SAMPLE 21


title: DobermPinscher-BI_20931


title: DobermPinscher-BI_20934


title: DobermPinscher-BI_20932


title: DobermPinscher-BI_20930


title: ripe_berry_stage2_day_rep3

tag: genotype

value: DRCF mutant

value: ripe berry stage2

value: day

value: berry


title: DobermPinscher-BI_20933


title: DobermPinscher-BI_20929


title: p1617_10cGy_24hr_rep1

description: SAMPLE 13

source_name: Primary prostate fibroblasts from patient p1617_10cGy_24hr


title: p1541_200cGy_24hr_rep1

description: SAMPLE 17


title: DobermPinscher-BI_20928_rep


title: p1617_10cGy_24hr_rep3

description: SAMPLE 15


title: DobermPinscher-BI_20928


title: DobermPinscher-BI_20926


title: p1541_200cGy_24hr_rep2

description: SAMPLE 18


title: DobermPinscher-BI_20927


title: DobermPinscher-BI_20925


title: DobermPinscher-BI_20924


title: DobermPinscher-BI_20923


title: DobermPinscher-BI_20920_rep


title: DobermPinscher-BI_20927_rep


title: DobermPinscher-BI_20922


title: DobermPinscher-BI_20921


title: p1541_10cGy_24hr_rep3

description: SAMPLE 11

source_name: Primary prostate fibroblasts from patient p1541_10cGy_24hr


title: p1541_10cGy_24hr_rep1

description: SAMPLE 9


title: p1617_10cGy_24hr_rep4

description: SAMPLE 16


title: p1617_0cGy_24hr_rep1

description: SAMPLE 5

source_name: Primary prostate fibroblasts from patient p1617_0cGy_24hr


title: DobermPinscher-BI_20920


title: p1541_10cGy_24hr_rep4

description: SAMPLE 12


title: DobermPinscher-BI_20919_rep


title: p1617_10cGy_24hr_rep2

description: SAMPLE 14


title: p1617_0cGy_24hr_rep3

description: SAMPLE 7


title: p1617_0cGy_24hr_rep2

description: SAMPLE 6


title: p1617_0cGy_24hr_rep4

description: SAMPLE 8


title: p1541_0cGy_24hr_rep4

description: SAMPLE 4

source_name: Primary prostate fibroblasts from patient p1541_0cGy_24hr


title: DobermPinscher-BI_20919


title: p1541_0cGy_24hr_rep2

description: SAMPLE 2


title: p1541_0cGy_24hr_rep3

description: SAMPLE 3


title: p1541_10cGy_24hr_rep2

description: SAMPLE 10


title: DobermPinscher-BI_20918


title: 293T_Cul4Ash_rep2

city: Los Angeles

first: Kyunghwan

last: Kim

state: California

address: 1450 Biggy Street NRT6517

department: Biochemistry and Molecular Biology

institute: University of Southern California

description:
Cul4Ash-2
replicate 2

data_processing: The data were processed/normalized and analyzed by the Array Pipe software.

label_protocol: Biotinylated cRNA was prepared with the Ambion MessageAmp kit for Illumina array.

extract_protocol: Total RNA was isolated using the TRIzol reagent according to the manufacturer's instructinos.

tag: cell line

value: 293T embryonic kidney cells (derived from 293 cells but stably express the SV40 T antigen)

value: Cul4A depletion


title: 293T_PAF1sh_rep2

description:
PAF1sh-2
replicate 2

value: PAF1 depletion


title: p1541_0cGy_24hr_rep1

description: SAMPLE 1


title: DobermPinscher-BI_20914

value: compulsive disorder


title: DobermPinscher-BI_20915

value: control


title: DobermPinscher-BI_20917


title: DobermPinscher-BI_20916


title: 293T_PAF1sh_rep1

description:
PAF1sh-1
replicate 1


title: 293T_NCsh_rep2

description:
NCsh-2
replicate 2


title: DobermPinscher-BI_20913


title: DobermPinscher-BI_20912


title: DobermPinscher-BI_20912_rep


title: DobermPinscher-BI_20911


title: 293T_H1.2sh_rep1

description:
H1.2sh-1
replicate 1

value: H1.2 depletion


title: DobermPinscher-BI_20910


title: DobermPinscher-BI_20909