title: Menopausal/diabetic 1 vs. diabetic 2

description: Menopausal/Diabetic mouse kidney cortex 1 vs. Diabetic mouse kidney cortex 2

source_name: Menopausal/diabetic

extract_protocol: total RNA was extracted from kidney cortex 6 weeks after STZ injection using Qiagen Rneasy mini columns according the the manufacturer's protocol

value: VCD and STZ

value: Menopausal/diabetic

source_name: Diabetic

value: STZ

value: Diabetic


title: Menopausal 3 vs. Menopausal 1

status: Public on Sep 14 2010

type: RNA

city: Tucson

first: Heddwen

middle: L

last: Brooks

state: AZ

address: PO Box 245218 1656 E Mabel

country: USA

institute: University of Arizona

description: Menopausal mouse kidney cortex 3 vs. Menopausal mouse kidney cortex 1

hyb_protocol: cDNA was  hybridized to slides in the presence of Cot-1 cDNA (Invitrogen, cat.#  18440-016) for 16-24 hours at 42°C in a hybridization buffer containing 8X SSC,  60% Formamide, and 0.2% SDS.  After completion, a  short wash was run after which the slide was removed and dipped in 0.05X SSC to remove any  residual nonhybridized cDNA.

scan_protocol: Fluorescent array images were collected for both Alexa Fluor 546 and Alexa Fluor 647 with an arrayWoRxe biochip reader and software.  Description

data_processing: After local background subtraction, data was linlog (base 2) transformed and LOWESS normalized.

label: Alexa Fluor 546

molecule: total RNA

organism: Mus musculus

source_name: Menopausal

label_protocol: Total RNA was amplified using the Message Amp aRNA kit from  Ambion (cat.# 1750), following the kit's protocols for First and Second-strand cDNA synthesis (Parts B and C), cDNA purification (Part E), and In Vitro  Transcription to Synthesize aRNA (Part F).   Amplified aRNA was converted to single-stranded cDNA with incorporation  of amino allyl dUTP using the Ambion EndoFree RT kit (cat.# 1740).  The cDNA was labeled with Alexa fluor via the  free amine modification.

extract_protocol: total RNA was extracted from kidney cortex using Qiagen Rneasy mini columns according the the manufacturer's protocol

tag: treatment

value: VCD

tag: disease state

value: Menopausal

label: Alexa Fluor 647


title: Control 1 vs. Menopausal 2

description: Control mouse kidney cortex 1 vs. Menopausal mouse kidney cortex 2

source_name: Control

value: Control


title: Menopausal/diabetic 3 vs. Menopausal/diabetic 1

description: Menopausal/Diabetic mouse kidney cortex 3 vs. Menopausal/Diabetic mouse kidney cortex 1


title: Diabetic 3 vs. diabetic 1

description: Diabetic mouse kidney cortex 3 vs. Diabetic mouse kidney cortex 1


title: Menopausal 2 vs. Menopausal 3

description: Menopausal mouse kidney cortex 2 vs. Menopausal mouse kidney cortex 3


title: Control 3 vs. Control 1

description: Control mouse kidney cortex 3 vs. Control mouse kidney cortex 1


title: Menopausal 2 vs. Control 3

description: Menopausal mouse kidney cortex 2 vs. Control mouse kidney cortex 3


title: breast tumor_7

city: Oslo

first: Simen

last: Myhre

address: Montebello

department: Dept of Genetics

country: Norway

institute: Oslo University Hospital

description:
HB009H3
7

hyb_protocol: 10ug labeled and fragmneted cRNA was hybridized onto single channel Applied Biosystems Human Genome Survey micro arrays v2.0 for 16 hours at 55ºC according to the manufacturer’s protocol.

scan_protocol: After hybridization, slides were manually washed and prepared according to manufacturers’ recommendation before image capturing using the AB1700 reader. Identification and quantification of gene expression signals, signal-to-noise ratios and flagging of failed spots were conducted using the Applied Biosystems Expression System software. Raw data files were exported for further analysis.

data_processing: First, flagged intensities and probes with signal to noise ratio below 3 were removed from the raw data. Next, the number of probes was further reduced to 17910, by removing those that had missing values in more that 80% of the samples. The quantile normalization procedure was applied using ABarray library in R and the missing values were imputed using the k-nearest neighbors algorithm of the smida library in R. After re-scaling the expression on each array so that they sum to 1 a log2 transformation was applied.

label: digoxigenin

organism: Homo sapiens

source_name: Mastectomy bulk primary tumor

label_protocol: For each sample, Digoxigenin-UTP labeled cRNA was generated from 500 ng total RNA according to the NanoAmp RT-IVT Labeling Kit Protocol.

extract_protocol: Approximately 40 mg of tissue was used for total RNA extraction using the Qiagen Midi kit Extraction column procedure (Qiagen) after homogenisation using the Mixer Mill (MM301, Retsch). RNA quality was assessed using the NanoDrop instrument (concentration and purity), and the Agilent Bioanalyser instrument (degradation). Samples showing a degradation factor > 20 % were excluded from further analyses: the remaining 218 RNA samples of good quality were stored at -80C

treatment_protocol: Primary breast tumors were collected after mastectomy. Fresh frozen and kept in storage at minus 80 degrees celcius.

tag: assayname

value: Mastectomy bulk primary tumor

tag: tumor epi %

tag: tumor-stroma %

tag: adipocyte cells%

tag: dm = 1 nodm = -1


title: Control 2 vs. Control 3

description: Control mouse kidney cortex 2 vs. Control mouse kidney cortex 3


title: Menopausal 1 vs. Control 2

description: Menopausal mouse kidney cortex 1 vs. Control mouse kidney cortex 2


title: Menopausal/diabetic 3 vs. diabetic 1

description: Menopausal/Diabetic mouse kidney cortex 3 vs. Diabetic mouse kidney cortex 1


title: Menopausal 1 vs. Menopausal 2

description: Menopausal mouse kidney cortex 1 vs. Menopausal mouse kidney cortex 2


title: breast tumor_10b

description:
HB009BO
10b


title: Diabetic 2 vs. diabetic 3

description: Diabetic mouse kidney cortex 2 vs. Diabetic mouse kidney cortex 3


title: Diabetic 1 vs. Menopausal/diabetic 2

description: Diabetic mouse kidney cortex 1 vs. Menopausal/Diabetic mouse kidney cortex 2


title: Menopausal/diabetic 2 vs. Menopausal/diabetic 3

description: Menopausal/Diabetic mouse kidney cortex 2 vs. Menopausal/Diabetic mouse kidney cortex 3


title: Diabetic 2 vs. Menopausal/diabetic 3

description: Diabetic mouse kidney cortex 2 vs. Menopausal/Diabetic mouse kidney cortex 3


title: Menopausal/diabetic 1 vs. Menopausal/diabetic 2

description: Menopausal/Diabetic mouse kidney cortex 1 vs. Menopausal/Diabetic mouse kidney cortex 2


title: Diabetic 1 vs. Diabetic 2

description: Diabetic mouse kidney cortex 1 vs. Diabetic mouse kidney cortex 2


title: Menopausal/diabetic 2 vs. diabetic 3

description: Menopausal/Diabetic mouse kidney cortex 2 vs. Diabetic mouse kidney cortex 3


title: Diabetic 3 vs. Menopausal/diabetic 1

description: Diabetic mouse kidney cortex 3 vs. Menopausal/Diabetic mouse kidney cortex 1


title: Liver_NPC1_rep3

city: Santiago

first: Leonardo

middle: Ignacio

last: Pavez

state: Santiago

address: Av Manuel Montt #948

country: Chile

institute: Universidad de Las Américas

hyb_protocol: 2 µg of each labeled probe were used for hybridization event. The two dye probes were mixed and concentrated to a volume of 30 µL in a solution containing 20% formamide, 5x SSC and SDS 0.1%. Hibridizations were performed according to microarray manufacturer’s instructions, incubating slides for 16 hours at 42 ºC. The hybridization was automatically performed using HybArray 12™ DNA hybridization system (Perkin Elmer) equipment

scan_protocol: the fluorescent derivatives detection we used ScanArray GX as laser reader Spot identification and quantification was performed with GenePix 5.1 software (Molecular Devices)

data_processing: Array data were analyzed using the R statistical language and environment (http://www.r-project.org), specifically with the microarray analysis tools available from the Bioconductor Project (http://www.bioconductor.org). Spots that showed qcom < 0.5 (Wang, 2001) were considered as low-quality spots and were removed. Data were background-subtracted and normalized using the LIMMA Bioconductor package (Smyth, 2004). Data obtained from biological replicates were averaged and then linear models were applied. Differentially expressed genes were determined by using empirical Bayesian methods and p<0.01 was considered statistically significant

source_name: liver, NPC-/-

label_protocol: 1 µg of total RNA was used to synthesize mRNA using the MessageAmp II mRNA amplification kit (Ambion, #1753). Mice from Mutant mice (NPC -/-) were dye-coupled with Cy5

extract_protocol: Total RNA was extracted from homogenized mice liver with TRI Reagent (Ambion) according to the manufacturer’s instructions

tag: strain

value: balb/c mice

tag: genotype/variation

value: carrying a heterozygous mutation in the npc1 gene were used to generate mutants (npc1 (-/-); mut)

tag: gender

value: male

tag: tissue

value: Liver

source_name: liver, NPC+/+

label_protocol: 1 µg of total RNA was used to synthesize mRNA using the MessageAmp II mRNA amplification kit (Ambion, #1753). 5 µg of a pooled mRNA of three wild type (NPC+/+) mice from WT mice were dye-coupled with Cy3

value: carrying a heterozygous mutation in the npc1 gene were used to generate controls (npc1 (+/+); wt)


title: Wild-type Treg cell pair2

status: Public on Sep 13 2010

city: New York

first: Weiming

last: Ouyang

state: NY

institute: MSKCC

description: Wild-type Treg cell pair2

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: MAS 5.0

label: Biotin

source_name: mouse spleen

label_protocol: Affymetrix protocol

extract_protocol: RNA was extracted by using miRNease kit from Qiagen

tag: genotype

value: wild-type


title: Liver_NPC1_rep1

hyb_protocol: 2 µg of each labeled probe were used for hybridization event. The two dye probes were mixed and concentrated to a volume of 30 µL in a solution containing 20% formamide, 5x SSC and SDS 0.1%. Hibridizations were performed according to microarray manufacturer’s instructions, incubating slides for 16 hours at 42 ºC. The hybridization was automatically performed using HybArray 12™ DNA hybridization system (Perkin Elmer) equipment.


title: -Sall4a -Sall4b, biological replicate 2

city: Boston

first: Sridhar

last: Rao

state: MA

address: 1 Blackfan Circle

department: Pediatric Oncology

institute: Dana Farber Cancer Institute and Children's Hospital, Boston

description:
ES cells infected with a lentivirus with an shRNA that targets both isoforms of Sall4.
WT+shRNA2

hyb_protocol: The biotinylated cDNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The chips are then transferred to a fluidics instrument that performs washes to remove cDNA that has not hybridized to its complementary oligonucleotide probe. The bound cDNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: Each cDNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.  GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: .gct and .res files were created by RMA normalization using GenePattern (https://www.broad.harvard.edu/cancer/software/genepattern/). These files (specifically the .gct) was used for downstream analysis by GSEA.

label: biotin

source_name: ES cells expressing neither Sall4a and Sall4b

label_protocol: The purified cDNA is fragmented through a chemical and enzymatic process.  The fragmented product is labeled via enzymatic attachment of a biotin-labeled nucleotide to the 3’-hydroxyl end of the fragmented cDNA.

growth_protocol: CJ7 cells were grown under standard conditions prior to infection.

extract_protocol: Cells were lysed with Trizol and total RNA collected. Total RNA was further purified by the Promega S40 total rna isolation system per manufacturer's protocol.  Total RNA was amplified by the Nugent process (http://chip.dfci.harvard.edu/index.php?option=com_content&task=view&id=14&Itemid=28#NuGen).

treatment_protocol: Adherent cells were infected with concentrated lentivirus for 24 hrs in the presence of polybrene 2.5 mcg/mL.  Media was then changed to ES cell media with LIF and puromycin (2 mcg/mL).  Cells were then cultured for 48hrs post infection.

tag: cell line

tag: cell type

value: embryonic stem (ES) cells

tag: sall4 isoform expression


title: -Sall4a +Sall4b, biological replicate 1

description:
ES cells infected with a lentivirus with an shRNA that targets both isoforms of Sall4 and also contain an immune version of Sall4b.
Sall4bIMM+shRNA1

source_name: ES cells expressing only Sall4b


title: Spleen_normal_3

city: Birmingham

first: Carl

middle: E

last: Bruder

state: AL

address: 2000 9th Ave South

department: Viral Biochemistry

institute: Southern Research Institute

description: platform: V1

hyb_protocol: One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol, V5.7

scan_protocol: The arrays were then scanned using a GenePix 4000B scanner (Molecular Devices, Sunnyvale, CA). Each slide was scanned at 5 um resolution with two different PMT settings (450 and 480 V). The 450V scans were used for all tissues except for blood.

data_processing: The image files were opened in Agilent's Feature Extraction software using the default Gene Expression protocol and the GE1_QCM_Feb07 quality control metric set. This software performed gridding, quality control and feature extraction. The individual tab delimited raw data files were then opened in MS Excel and the column containing the signal intensity (gProcessedSignal) was normalized by dividing all data points with the signal value of the 75th percentile of all of non-control probes (gPercentileIntensityProcessedSignal), as suggested by Agilent. The average gPercentileIntensityProcessedSignal for all experiemnts was then used to scale each indiviual array to allow for comparision. This is the procedure recomended by Agilent.

organism: Mustela putorius furo

extract_protocol: Trizol RNA extraction according to protocol supplied by InVitrogen for preparation of total RNA for brain, liver, spleen and lungs. PaxGene RNA system from total RNA extraction from blood, according to manufacturers protocol.

value: Spleen

value: Male


title: Wild-type Treg cell pair1

description: Wild-type Treg cell pair1


title: Foxo1/3-deficient Treg cell pair1

description: Foxo1/3-deficient Treg cell pair1


title: Liver_NPC1_rep2


title: WT cell, biological replicate 2

description:
ES cells infected with a lentivirus with no shRNA.
WT2

source_name: ES cells expressing both Sall4a and Sall4b

value: Sall4a, Sall4b


title: -Sall4a -Sall4b, biological replicate 1

description:
ES cells infected with a lentivirus with an shRNA that targets both isoforms of Sall4.
WT+shRNA1


title: Spleen_normal_2

description: platform: V1

label_protocol: One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol, V5.7


title: -Sall4a +Sall4b, biological replicate 2

description:
ES cells infected with a lentivirus with an shRNA that targets both isoforms of Sall4 and also contain an immune version of Sall4b.
Sall4bIMM+shRNA2


title: WT cell, biological replicate 1

description:
ES cells infected with a lentivirus with no shRNA.
WT1


title: +Sall4a -Sall4b, biological replicate 1

description:
ES cells infected with a lentivirus with an shRNA that targets both isoforms of Sall4 and also contain an immune version of Sall4a.
Sall4aIMM+shRNA1

source_name: ES cells expressing only Sall4a


title: +Sall4a -Sall4b, biological replicate 2

description:
ES cells infected with a lentivirus with an shRNA that targets both isoforms of Sall4 and also contain an immune version of Sall4a.
Sall4aIMM+shRNA2


title: DMSO_ 12 hours_replicate2

city: Taipei

first: Ning-Sun

last: Yang

state: Taiwan

address: No.128 Sec.2, Academia Rd.

department: Agricultural Biotechnology Research Center

country: Taiwan

institute: Academia Sinica

description:
DMSO-12 hours.
584

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

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 30007G.

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 500.

source_name: immature dendritic cells (BMDC) isolated from cultured mouse bone marrow, DMSO, 12h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10ug total RNA.

growth_protocol: Mouse bone marrow cells were isolated and cultured for 9 days in RPMI-1640 medium supplemented with 200 U/mL GM-CSF.

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

treatment_protocol: BMDC culture was treated with DMSO (0.1%)  or [BF/S+L/Ep], a chemically defined Echinacea purpurea extract,  at a final concentration of 75 µg/mL using DMSO as vehicle for 4 hours or 12 hours.

value: bone marrow

value: dendritic cells

value: DMSO

tag: treatment time

value: 12 hours


title: DMSO_ 12 hours_replicate1

description:
DMSO-12 hours.
583


title: BF/S+L/Ep_12 hours_replicate2

description:
BF/S+L/Ep-12 hours.
586

source_name: immature dendritic cells (BMDC) isolated from cultured mouse bone marrow, BF/S+L/Ep, 12h

value: BF/S+L/Ep


title: BF/S+L/Ep_4 hours_replicate2

description:
BF/S+L/Ep-4 hours.
582

source_name: immature dendritic cells (BMDC) isolated from cultured mouse bone marrow, BF/S+L/Ep, 4h

value: 4 hours


title: BF/S+L/Ep_12 hours_replicate1

description:
BF/S+L/Ep-12 hours.
585


title: Foxo1/3-deficient Treg cell pair2

description: Foxo1/3-deficient Treg cell pair2


title: Spleen_normal_1

description: platform: V1

value: Female


title: BF/S+L/Ep_4 hours_replicate1

description:
BF/S+L/Ep-4 hours.
581


title: Lung_normal_4_rep3

description: platform: V1

source_name: Ferret right caudal lung

value: Lung

tag: technical replicate


title: Lung_normal_3

description: platform: v2


title: Lung_normal_2

description: platform: v2


title: Lung_normal_4_rep1

description: platform: V1


title: Liver_normal_4

description: platform: V1

source_name: Ferret left caudal lobe of the liver


title: Liver_normal_5_rep2

description: platform: V1


title: Liver_normal_3

description: platform: v2


title: Brain_normal_5_rep2

description: platform: V1

source_name: Ferret whole brain

value: Brain


title: Liver_normal_5_rep1

description: platform: V1


title: Lung_normal_4_rep2

description: platform: V1


title: DMSO_4 hours_replicate1

description:
DMSO-4 hours.
579

source_name: immature dendritic cells (BMDC) isolated from cultured mouse bone marrow, DMSO, 4h

tag: treatment


title: Brain_normal_5_rep1

description: platform: V1


title: Liver_normal_2

description: platform: v2


title: Brain_normal_2

description: platform: v2


title: DMSO_4 hours_replicate2

description:
DMSO-4 hours.
580


title: Liver_normal_1

description: platform: v2


title: Col whole leaf, 4d SA, 4mM, biological rep 2

city: Berkeley

first: Mary

middle: C

last: Wildermuth

state: CA

address: 221 Koshland Hall MC3102

department: Plant and Microbial Biology

institute: University of California Berkeley

description: Gene expression data from wild type whole mature leaves at 4d after 4 mM salicylic acid treatment

hyb_protocol: Microarray hybridizations to Affymetrix Arabidopsis ATH1 GeneChips were performed according to the protocol given in the Affymetrix GeneChip Expression Analysis Technical Manual 701025 rev 1.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G at the Univeristy of California, Berkeley, Functional Genomics Lab.

data_processing: Log2 (expression values) were extracted using robust multi-array analysis (RMA) implemented in the function rma() in the Bioconductor software package affy. Background correction was performed by correcting PM (perfect match) only, to reduce noise from signal intensity. Quantile normalization was performed to make the distributions of signal intensities uniform across chips. Quality assessment was done using the weights outputted from the linear model fitting function fitPLM() in the R package AffyExtensions.

organism: Arabidopsis thaliana

source_name: Col whole leaf treated with 4mM salicylic acid 4d

label_protocol: Target labeling was performed according to the protocol given in the Affymetrix GeneChip Expression Analysis Technical Manual 701025 rev 1.

growth_protocol: Arabidopsis seeds were stratified in 0.1% agarose for 3-5 days and planted in boxes containing Metromix 200 soil. Seeds were equally distributed in each box using a template, with 12 plants per box.  The flats (6 boxes per flat) were covered with plastic trays for 1 week and then uncovered. Flats were watered from below and fertilized at 2-1/2 weeks. Plants were grown on growth carts with 12 h photoperiod with photosynthetically active radiation=100 µE m-2 s-1.

extract_protocol: Total RNA was extracted using the RNeasy mini kit from Qiagen according to the manufacturer's instructions from  whole leaf samples.  Samples were subject to on-column DNase digestion using  DNase I from Qiagen. RNA quality was determined by the A260/A280 ratio and by its profile on an Agilent 2100 Bioanalyzer.

treatment_protocol: At four weeks, a subset of boxes was treated with 4 mM of a neonicotinoid solution.  Samples were harvested at 4 d after treatment. An untreated 4 d sample was also collected.  For each sample, fully expanded mature leaves were excised, with 100 mg leaf tissue used to prepare each RNA sample.  Two independent experiments were performed and one sample from each experiment was processed.

value: wild type

tag: agent

value: 4mM salicylic acid

tag: age

value: 4 weeks old at time of treatment

value: whole leaf


title: Blood_normal_2

description: platform: v2

source_name: Ferret whole blood

value: Blood


title: Lung_normal_1

description: platform: v2


title: Col whole leaf, 4d SA, 4mM, biological rep 1


title: Brain_normal_3

description: platform: v2


title: Brain_normal_4

description: platform: V1


title: Blood_normal_1

description: platform: v2


title: Brain_normal_1

description: platform: v2


title: Blood_normal_3

description: platform: v2


title: Input DNA

type: genomic

description: Affymetrix Mouse Promoter 1.0R array

hyb_protocol: About 2-4 ug of labeled DNA were hybridized for 16 hr at 45C on tiling arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing:
Model Based Analysis of Tiling Arrays (MAT) was used to extract peaks based upon default parameters, using mm8 build
The three biological replicates were pooled for each type of sample (Input, Bir A ChIP, Sall4a ChIP, Sall4b ChIP) and then compared (BirA ChIP vs. Input= Bir A; Sall4a ChIP vs Input= Sall4a; Sall4b ChIP s Input= Sall4b) and .bed and .bar files generated by MAT with a p-value set for 10^-4.

molecule: genomic DNA

source_name: Input DNA

label_protocol: Fragmented DNA was labeled with biotin-N6-ddATP by terminal deoxynucleiotidyl transferase.

growth_protocol: ES cells were grown on gelatin adapted TC plates (in the absence of feeders) in the presence of LIF and standard ES cell media till confluent

extract_protocol: ChIP reactions were performed similar to (Kim J. et al, Cell, 2008).  Briefly, ES cells harboring either BirA alone,Sall4a, or Sall4b were crosslinked for 10 min in 1% formaldehyde which was terminated by the addition of 125mM glycine.  Cells were washed, collected, and then resuspended in ChIP dilution buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20 mM Tris-CL pH8.1, 150 mM NaCl and protease inhibitors).  Cells were fragmented by sonication and was confirmed to have an average size of approximately 0.5-1kb by agarose gel electrophoresis.  The samples were centrifuged at 40C for 10min and the supernant collected and pre-cleared with pre-washed protein A beads (Roche) at 40C for 60 min with rotation.  The beads were pelleted by centrifugation and the supernant was incubated overnight at 40C with prewashed Dynabead Ò MyOneä Streptavidin T1 beads (Invitrogen). A sample of the pre-cleared supernant was saved as genomic control from the J1 ES cells expressing BirA alone.  DNA absorbed beads were washed with Buffer I (2% SDS) twice, Buffer II (0.1% Deoxycholate, 1% Triton X-100, 1mM EDTA, 1mM HEPES pH7.5, 500 mM NaCl) once, Buffer III (250 mM LiCl, 0.5% NP-40, 0.5% Deoxycholate, 1 mM EDTA, 10 mM Tris-Cl pH 8.1) once, and TE (10 mM Tris pH8.1, 1 mM EDTA) twice.  All washes were 10 min at room temperature with agitation, and beads were pelleted using magnetic separation.  SDS elution buffer (1% SDS, 10 mM EDTA, 50 mM Tris, pH 8.1) was added and the DNA was eluted off and de-crosslinked overnight at 650C.  The samples was treated with RNase A and Proteinase K, extracted with phenol:chloroform:isoamyl alcohol and precipitated.  Samples were then used as either a substrate in qPCR or were amplified for hybridization to microarray. ChIP samples were amplified by LM-PCR as described in (Lupien et al., 2008) DNA was subsequently fragmented by DNase I treatment and biotin labeled per manufacturer?s instructions (www.affymetrix.com/support/downloads/manuals/chromatin_immun_ChIP.pdf).

treatment_protocol: No treatment

value: J1 derived ES cells

tag: experiment

value: input


title: Col whole leaf, 4d IMI, 4mM, biological rep 2

description: Gene expression data from wild type whole mature leaves at 4d after 4 mM imidacloprid treatment

source_name: Col whole leaf treated with 4mM imidacloprid 4d

value: 4mM imidacloprid


title: ChIP of bio-Sall4b cells

description: Affymetrix Mouse Promoter 1.0R array

source_name: ChIP of bio-Sall4b cells vs Input

value: ChIP with streptavidin


title: ChIP of bio-Sall4a cells

description: Affymetrix Mouse Promoter 1.0R array

source_name: ChIP of bio-Sall4a cells vs Input


title: ChIP of BirA cells

description: Affymetrix Mouse Promoter 1.0R array

source_name: ChIP of BirA cells vs Input


title: Liver harvested at 330 days replicate 3 [normal]

city: Bangor

first: Sharon

middle: E.

last: Hook

state: NSW

address: Private Mail Bag 7

department: Centre for Environmental Contaminants Research

country: Australia

institute: CSIRO

description: Biological replicate 1

hyb_protocol: Samples were mixed with 20 µg tRNA and 20 µg Herring Sperm DNA to prevent non specific hybridization, then mixed with 35 µl of modified “Genisphere” hybridization buffer (50% formamide, 40% 20x SSC, 9% Denhardt’s solution, 1% SDS).  This mixture was then applied to the arrays and allowed to hybridize overnight (16 hr) at 45 o C.  After hybridization, arrays were washed in SSC/SDS buffers with descending stringency to remove any unhybridized or weakly (nonspecifically) hybridized cDNA’s.

scan_protocol: Arrays were scanned using a Perkin Elmer ScanArray Express, with laser power and PMT gain varied to equalize fluorescence intensity between channels and to prevent over saturation of signal intensity.

data_processing:
Data were extracted using ScanArray Express software (Perkin Elmer).  The median fluorescence intensity with background subtracted was imported Genespring microarray analysis software for further analysis.  Data were LOWESS normalized and spots that did not meet a minimum signal intensity were removed.
Processed/normalized  data not provided for this record

label: Alexa Fluor 555

organism: Oncorhynchus mykiss

source_name: liver (control)

label_protocol: Labelled using I\nvitrogen’s Superscript cDNA Indirect Labeling kit and the manufacturer's protocol, and Alexa fluors.

extract_protocol: Trizol extraction following the manufacturer's protocol

treatment_protocol: Post Spawned Female Rainbow Trout over the course of a Normal photoperiod

tag: harvested on which day of the normal photoperiod

value: Day 0

source_name: liver (test)

value: Day 330


title: Col whole leaf, 4d IMI, 4mM, biological rep 1


title: pituitary harvested at 51 days replicate 3 [compressed]

description: Biological replicate 1

source_name: pituitary (control)

treatment_protocol: Post Spawned Female Rainbow Trout over the course of a compressed photoperiod

source_name: pituitary (test)

value: Day 51


title: Col whole leaf, 4d CLO, 4mM, biological rep 2

description: Gene expression data from wild type whole mature leaves at 4d after 4 mM clothianidin treatment

source_name: Col whole leaf treated with 4mM clothianidin 4d

value: 4mM clothianidin


title: Control 1 vs. Control 2

description: Control mouse kidney cortex 1 vs. Control mouse kidney cortex 2

source_name: Control

value: Control

tag: disease state


title: Col whole leaf, 4d untreated, biological rep 1

description: Gene expression data from 4d untreated wild type whole mature leaves

source_name: Col whole leaf untreated 4d


title: At_PR_OZ2_22

status: Public on Sep 12 2010

city: Durham

first: Miguel

middle: Angel

last: Moreno-Risueno

state: NC

address: 124 Science Dr

department: Biology

institute: Duke University

description: Gene expression data the OZ2 (upper half) under standard conditions for 5 days

hyb_protocol: see Affymetrix standard protocols

scan_protocol: see Affymetrix standard protocols

label_protocol: see Affymetrix standard protocols

extract_protocol: see Affymetrix standard protocols

tag: ecotype

value: Columbia

value: 5 days after germination

value: lower half of seedling root

tag: growth media

value: Standard media for 5 days

tag: periodic order


title: At_PR_OZ2_32


title: At_PR_OZ2_19


title: At_PR_OZ2_13


title: MrNodule_rep3

city: Kagohima

first: Ken-ichi

last: Kucho

address: Korimoto 1-21-35

country: Japan

institute: Kagoshima University

description:
This entry corresponds to data A (experiment A) in the paper.
4-plex format was applied.

hyb_protocol: Hybridization was performed by Nimblegen expression service laboratory (Reykjavik, Iceland and Tokyo, Japan), according to its standard protocol (NimbleGen Arrays User’s Guide: Gene Expression Analysis (Version 3.2), http://www.nimblegen.com/products/lit/exp_userguide_v3p2.pdf).

scan_protocol: Scanning was performed by Nimblegen expression service laboratory (Reykjavik, Iceland and Tokyo, Japan), according to its standard protocol (NimbleGen Arrays User’s Guide: Gene Expression Analysis (Version 3.2), http://www.nimblegen.com/products/lit/exp_userguide_v3p2.pdf).

data_processing: Normalization of the signal intensity was performed by Nimblegen expression service laboratory (Reykjavik, Iceland and Tokyo, Japan), according to its standard protocol (NimbleGen Arrays User’s Guide: Gene Expression Analysis (Version 3.2) using quantile normalization method (Bolstad et al., 2003, Bioinformatics 19: 185-193). Normalized gene expression values were generated using the robust multichip average (RMA) algorithm (Irizarry et al., 2003, Biostatistics 4: 249-264).

organism: Frankia alni ACN14a

source_name: Myrica rubra nodule

label_protocol: Synthesis and labelling of double-stranded cDNA were performed by Nimblegen expression service laboratory (Reykjavik, Iceland and Tokyo, Japan), according to its standard protocol (NimbleGen Arrays User’s Guide: Gene Expression Analysis (Version 3.2), http://www.nimblegen.com/products/lit/exp_userguide_v3p2.pdf), except that three times more nodule cDNA was used.

growth_protocol: Seeds of the plant were planted and grown for five to ten weeks in a soil/vermiculite substrate (1/1, v/v) in a glasshouse under fluorescent lamp with 16 h light/8 h dark regime at temperature 21-25°C. Seedlings were transferred to Broughton and Dilworth's solution (1971, Biochemistry Journal 125: 1075–1080) in plastic pots. They were grown for four to nine weeks with 0.5 g/L KNO3 and then for one week without KNO3. Frankia alni ACN14a cells derived from 75 mL of log-phase culture were inoculated to a pot. Root nodules (≤ 3 lobes) were harvested at 3-4 weeks post inoculation.

extract_protocol: RNA was purified using the cetyltrimethylammonium bromide (CTAB) method (Chang and Cairney, 1993, Plant Mol. Biol. Rep. 11:113-116) with the following modifications. Cells were ground by mortar and pestle with 2 x CTAB solution (2% CTAB, 0.1 M Tris-HCl [pH 9.5], 20 mM EDTA, 1.4 M NaCl, 1% β- mercaptoethanol) and liquid nitrogen. The lysate was transferred to microtubes and an equal volume of chloroform was added. The mixture was vortexed, centrifuged at 860 x g for 10 min, and the supernatant was transferred to new tubes. The RNA was precipitated with 2-propanol, and the pellet was dissolved in 2 M LiCl. The RNA was incubated on ice for more than 2 h and then precipitated by centrifugation at 21,500 x g for 10 min at 4°C. The RNA pellet was dissolved in RNase-free water, and contaminating protein was removed by phenol/chloroform (1 : 1) treatment. RNA was recovered by precipitation with 2-propanol and dissolved in RNase-free water. Contaminating DNA was removed by DNaseI (RT grade, Wako, Osaka, Japan). Purity, concentration and quality of RNA samples were checked using an ultrospec 3300 pro photospectrometer (Amersham Biosciences, Buckinghamshire, UK) and agarose gel electrophoresis.

value: Symbiotic cells in nodules formed on Myrica rubra


title: At_PR_OZ1_32

description: Gene expression data the OZ1 (lower half) under standard conditions for 5 days

value: upper half of seedling root


title: At_PR_OZ2_9


title: At_PR_OZ2_36


title: At_PR_OZ1_6


title: At_PR_OZ1_3


title: At_PR_OZ1_35


title: MrNodule_rep1


title: At_PR_OZ1_31


title: Col whole leaf, 4d CLO, 4mM, biological rep 1

value: wild type

tag: strain

value: 4 weeks old at time of treatment

value: whole leaf


title: At_PR_OZ2_35

tag: tissue


title: Col whole leaf, 4d untreated, biological rep 2

tag: genotype


title: At_PR_OZ2_20


title: At_PR_OZ1_10


title: MgNodule_rep3

source_name: Myrica gale nodule

value: Symbiotic cells in nodules formed on Myrica gale


title: MgNodule_rep2


title: At_PR_OZ1_16


title: MrNodule_rep2


title: At_PR_OZ1_15


title: Zic3 ChIP-on-chip in mouse ES cells

city: Singapore

first: Linda

middle: Shushan

last: Lim

address: 60 Biopolis Street, Genome building, #02-01

department: Stem Cell Biology

country: Singapore

institute: Genome Institute of Singapore

description: The transcription factor Zic3 is required for maintenance of embryonic stem (ES) cell pluripotency (Lim LS et al, Mol Biol Cell. 2007;18:1348-1358). By genome-wide chromatin immunoprecipitation (ChIP-chip) in ES cells, we have identified 379 direct Zic3 targets, many of which are functionally associated with pluripotency, cell cycle, proliferation, oncogenesis and early embryogenesis.

hyb_protocol: Labeled Cy3 and Cy5 DNA were hybridized to the Mouse Promoter ChIP-on-chip Microarray (G4490A, Agilent Technologies) for 40 hours at 65 degrees. The arrays were washed and processed as stated in the Agilent mammalian ChIP-on-chip protocol (Version 9.1, August 2006).

scan_protocol: Chips were washed and scanned using the Agilent G2505B Scanner as per manufacturer’s protocol - Agilent mammalian ChIP-on-chip protocol (Version 9.1, August 2006).

data_processing: Raw array data were processed with Agilent's ChIP Analytics software v1.3 as specified in the Agilent mammalian ChIP-on-chip protocol (Version 9.1, August 2006).

source_name: Mouse ESC ChIP-chip input sample (WCE; whole cell extract)

label_protocol: WCE DNA was labeled with Cy3 dye using Invitrogen’s CGH labeling kit as detailed in the Agilent mammalian ChIP-on-chip protocol (Version 9.1, August 2006).

extract_protocol: Zic3 ChIP-on-chip was performed with the Mouse Promoter ChIP-on-chip Microarray Set (G4490A, Agilent Technologies). Cross-linked and sheared gDNA from mouse ES cells were subjected to ChIP using a rabbit polyclonal Zic3 antibody as described (Lim LS et al, paper in review). Purified WCE (input) and Zic3-immunoprecipitated DNA were subjected to blunt ligation with linker oligos, linker mediated PCR (LM-PCR), dye labeling, hybridization and washing according to the Agilent mammalian ChIP-on-chip protocol (Version 9.1, August 2006).

tag: cell line

value: Mouse embryonic stem cells, E14

tag: antibody

source_name: Mouse ESC Zic3 ChIP-chip sample

label_protocol: Zic3-ChIP DNA was labeled with Cy5 dye using Invitrogen’s CGH labeling kit as detailed in the Agilent mammalian ChIP-on-chip protocol (Version 9.1, August 2006).


title: AnNodule_rep2

source_name: Alnus nepalensis nodule

tag: cell type

value: Symbiotic cells in nodules formed on Alnus nepalensis


title: AnNodule_rep3


title: MgNodule_rep1


title: AgNodule_experimentA_rep3

source_name: Alnus glutinosa nodule

value: Symbiotic cells in nodules formed on Alnus glutinosa


title: FreeLiving_experimentB_rep1

description: This entry corresponds to data B (experiment B) in the paper.

source_name: Free-living cells

label_protocol: Synthesis and labelling of double-stranded cDNA were performed by Nimblegen expression service laboratory (Reykjavik, Iceland and Tokyo, Japan), according to its standard protocol (NimbleGen Arrays User’s Guide: Gene Expression Analysis (Version 3.2), http://www.nimblegen.com/products/lit/exp_userguide_v3p2.pdf).

growth_protocol: Frankia alni ACN14a (Normand and Lalonde, 1982, Can. J. Microbiol. 28: 1133-1142) was grown according to Schwencke (1991, Plant Soil 137: 37-41), at 28°C under stirring at 200 rpm in defined basal medium with propionate (BAP) containing 5 mM ammonium chloride (Murry et al. 1984, Plant Soil. 78: 61-78) with some minor modifications: Fe-citrate, 10 mg/L was used instead of FeNa-EDTA; CoSO4.7H2O; 0.001 g/L was added in the micronutrient stock solution and biotin was replaced by the vitamin mixture described by Tjepkema et al (1981, Can. J. Microbiol. 27: 815-823). After 5 days of culture, stirring was stopped.

extract_protocol: RNA was purified using RNeasy Plant mini kit (QIAGEN) and on-column DNA digestion with the RNase-free DNase set (QIAGEN). In order to avoid any remaining DNA contaminations, a second DNAse treatment was performed with RQ1 RNase-free DNase (Promega, Charbonnières-les-Bains, France) followed by RNA cleanup using RNeasy mini kit. Purity, concentration and quality of RNA samples were checked using a NanoDrop 1000 spectrophotometer (Thermo Fischer Scientific, Courtaboeuf, France) and agarose gel electrophoresis

value: Free-living cells grown in nitrogen-replete medium


title: FreeLiving_experimentB_rep2


title: FreeLiving_experimentA_rep3


title: AgNodule_experimentB_rep2


title: AgNodule_experimentB_rep1


title: FreeLiving_experimentA_rep1


title: AgNodule_experimentA_rep2


title: AgNodule_experimentA_rep1


title: AgNodule_experimentB_rep3


title: FreeLiving_experimentA_rep2


title: P0997-02-D076-U133Plus-2

status: Public on Sep 11 2010

city: Shanghai

first: Leming

last: Shi

address: 2005 Songhu Road

department: School of Life Sciences

country: China

institute: Fudan University

description: MAQC-II multiple myeloma (MM) data set (endpoints F, G, H, and I)

hyb_protocol: As recommended by manufacturer

scan_protocol: As recommended by manufacturer

data_processing: All data used in these analyses were derived with the Affymetrix Microarray Suite GCOS1.1 software.

source_name: pre-treatment bone marrow

label_protocol: As recommended by manufacturer

extract_protocol: Total RNA was isolated with RNeasy Mini Kit (Qiagen, Valencia, CA).

value: Validation

tag: Sex

value: male

tag: randomly assigned class label

tag: efs milestone outcome (24 months)

value: 1=event occurred < 24 months, 0=no event in first 24 months:0

tag: os milestone outcome (24 months)

value: 1= deceased by 24 months, 0= alive at 24 months:0


title: FreeLiving_experimentB_rep3


title: P0995-02-D102-U133Plus-2

tag: age

value: female


title: P0990-02-C968-U133Plus-2


title: P0996-04-D062-U133Plus-2

value: 1=event occurred < 24 months, 0=no event in first 24 months:1


title: AnNodule_rep1


title: P0986-01-C780-U133Plus-2

value: Training

value: 1= deceased by 24 months, 0= alive at 24 months:1


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title: P0168-01-A602-U133Plus-2


title: P1645-01-F048-U133Plus-2


title: P1603-01-E929-U133Plus-2


title: P1635-01-E988-U133Plus-2


title: P0171-01-A617-U133Plus-2


title: P1646-01-F012-U133Plus-2


title: P0175-01-A638-U133Plus-2


title: P1622-01-E994-U133Plus-2


title: P1639-01-F130-U133Plus-2


title: P0165-01-A596-U133Plus-2


title: P0199-01-A780-U133Plus-2


title: P1602-01-E914-U133Plus-2


title: P1606-01-E950-U133Plus-2


title: P0170-01-A609-U133Plus-2


title: P1614-01-E995-U133Plus-2


title: P1604-01-E912-U133Plus-2


title: P1618-01-F008-U133Plus-2


title: P0163-01-A575-U133Plus-2


title: P1605-01-E926-U133Plus-2


title: P1600-01-E869-U133Plus-2


title: P1601-01-E893-U133Plus-2


title: P1598-01-E812-U133Plus-2


title: P1599-01-E877-U133Plus-2


title: P1596-01-E739-U133Plus-2


title: P1595-01-E769-U133Plus-2


title: P1581-01-E800-U133Plus-2


title: P0158-01-A554-U133Plus-2


title: P1569-01-E902-U133Plus-2


title: P1597-01-E810-U133Plus-2


title: P1593-01-E738-U133Plus-2


title: P1587-01-E921-U133Plus-2


title: P1590-01-E719-U133Plus-2


title: P1583-01-E853-U133Plus-2


title: P1591-01-E712-U133Plus-2


title: P1594-01-E747-U133Plus-2


title: P1579-01-E903-U133Plus-2


title: P0157-01-A547-U133Plus-2


title: P1562-01-E829-U133Plus-2


title: P1589-01-E584-U133Plus-2


title: P1580-01-E714-U133Plus-2


title: P1571-01-E644-U133Plus-2


title: P1592-01-E710-U133Plus-2


title: P1558-02-E821-U133Plus-2


title: P0155-01-A537-U133Plus-2


title: P1586-01-E742-U133Plus-2


title: P1465-01-E735-U133Plus-2


title: P1502-01-E768-U133Plus-2


title: P1507-01-E797-U133Plus-2


title: P1477-01-E681-U133Plus-2


title: P1456-01-E388-U133Plus-2


title: P1492-01-E680-U133Plus-2


title: P0154-01-A533-U133Plus-2


title: P1529-01-E818-U133Plus-2


title: P1550-01-E679-U133Plus-2


title: P1458-01-E488-U133Plus-2


title: P1463-01-E600-U133Plus-2


title: P1480-01-E701-U133Plus-2


title: P1453-01-E515-U133Plus-2


title: P1509-01-E814-U133Plus-2


title: P1445-01-E571-U133Plus-2


title: P1503-01-E387-U133Plus-2


title: P1454-01-E513-U133Plus-2


title: P1443-01-E544-U133Plus-2


title: P1455-01-E588-U133Plus-2


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title: P1444-01-E568-U133Plus-2


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title: P1451-01-E558-U133Plus-2


title: P0144-01-A488-U133Plus-2


title: P1403-01-E454-U133Plus-2


title: P1434-01-E537-U133Plus-2


title: P1400-01-E435-U133Plus-2


title: P1424-02-E484-U133Plus-2


title: P1402-01-E441-U133Plus-2


title: P1437-01-E510-U133Plus-2


title: P1412-01-E507-U133Plus-2


title: P1408-01-E461-U133Plus-2


title: P1439-01-E614-U133Plus-2


title: P1391-00-E358-U133Plus-2


title: P1407-01-E466-U133Plus-2


title: P1438-01-E539-U133Plus-2


title: P1405-01-E440-U133Plus-2


title: P0208-01-A823-U133Plus-2


title: P1390-00-E300-U133Plus-2


title: P1409-01-E433-U133Plus-2


title: P1374-01-E347-U133Plus-2


title: P1372-01-E294+299-U133Plus-2


title: P1375-01-E113-U133Plus-2


title: P1389-00-E033-U133Plus-2


title: P1432-01-E634-U133Plus-2


title: P1384-01-E385-U133Plus-2


title: P1401-01-E437-U133Plus-2


title: P1383-01-E337-U133Plus-2


title: P0138-01-A293-U133Plus-2


title: P1366-01-E227-U133Plus-2


title: P1371-01-E336-U133Plus-2


title: P1367-01-E264-U133Plus-2


title: P1350-01-E288-U133Plus-2


title: P1339-01-E247-U133Plus-2


title: P1338-01-E237-U133Plus-2


title: P1341-01-E149-U133Plus-2


title: P1368-01-E276-U133Plus-2


title: P1337-01-E200-U133Plus-2


title: P1362-01-E229-U133Plus-2


title: P1336-02-E158-U133Plus-2


title: P1321-00-E004-U133Plus-2


title: P1354-01-E286-U133Plus-2


title: P1323-01-E099-U133Plus-2


title: P1331-02-E169-U133Plus-2


title: P1313-02-D975-U133Plus-2


title: P1314-00-D963-U133Plus-2


title: P0131-01-A476-U133Plus-2


title: P1365-01-E165-U133Plus-2


title: P1309-01-E068-U133Plus-2


title: P1316-00-D934-U133Plus-2


title: P1307-01-E064-U133Plus-2


title: P1361-01-D981-U133Plus-2


title: P1359-01-E293-U133Plus-2


title: P1308-01-E066-U133Plus-2


title: P1363-01-E262-U133Plus-2


title: P1295-01-E043-U133Plus-2


title: P1320-01-E088-U133Plus-2


title: P1312-02-D995-U133Plus-2


title: P1296-00-D980-U133Plus-2


title: P1282-01-D962-U133Plus-2


title: P1364-01-E278-U133Plus-2


title: P1291-02-E002-U133Plus-2


title: P1305-01-E053-U133Plus-2


title: P0124-01-A314-U133Plus-2


title: P1263-01-D755-U133Plus-2


title: P1259-01-D865-U133Plus-2


title: P1239-01-D778A-U133Plus-2


title: P1235-01-D729-U133Plus-2


title: P1228-01-D816-U133Plus-2


title: P1283-01-D918-U133Plus-2


title: P1248-01-D777-U133Plus-2


title: P0127-01-A471-U133Plus-2


title: P1271-01-D891-U133Plus-2


title: P1232-01-D646-U133Plus-2


title: P1223-02-D452-U133Plus-2


title: P1225-01-D807-U133Plus-2


title: P1236-01-D742-U133Plus-2


title: P1231-01-D615-U133Plus-2


title: P0120-01-A284-U133Plus-2


title: P1191-01-D722-U133Plus-2


title: P0119-01-A196-U133Plus-2


title: P1195-01-D624-U133Plus-2


title: P1201-01-D769-U133Plus-2


title: P1189-01-D662-U133Plus-2


title: P1224-01-D803-U133Plus-2


title: P1196-01-D432-U133Plus-2


title: P1186-01-D612-U133Plus-2


title: P1187-01-D657-U133Plus-2


title: P0121-01-A289-U133Plus-2


title: P0122-01-A295-U133Plus-2


title: P1182-01-D617-U133Plus-2


title: P1188-01-D658-U133Plus-2


title: P1181-01-D629-U133Plus-2


title: P1183-01-D417-U133Plus-2


title: P1190-01-D723-U133Plus-2


title: P1176-01-D600-U133Plus-2


title: P1177-01-D639-U133Plus-2


title: P1166-01-D468-U133Plus-2


title: P1178-01-D566-U133Plus-2


title: P1173-01-D516-U133Plus-2


title: P1185-01-D588-U133Plus-2


title: P1184-01-D637-U133Plus-2


title: P0117-01-A315-U133Plus-2


title: P0118-01-A103-U133Plus-2


title: P1142-01-D343-U133Plus-2


title: P1146-01-D263-U133Plus-2


title: P1144-01-D361-U133Plus-2


title: P1165-01-D454-U133Plus-2


title: P1141-01-D334-U133Plus-2


title: P1167-01-D486-U133Plus-2


title: P1145-01-D422-U133Plus-2


title: P1164-01-D505-U133Plus-2


title: P1143-01-D215-U133Plus-2


title: P1139-01-D229-U133Plus-2


title: P1138-02-D405-U133Plus-2


title: P1122-00-D443-U133Plus-2


title: P1130-03-D440-U133Plus-2


title: P1117-00-D346-U133Plus-2


title: P1120-01-C865-U133Plus-2


title: P1119-01-D487-U133Plus-2


title: P1101-02-D459-U133Plus-2


title: P1132-03-D485-U133Plus-2


title: P1113-01-D323-U133Plus-2


title: P1112-01-D320-U133Plus-2


title: P1118-00-D465-U133Plus-2


title: P1121-01-D491-U133Plus-2


title: P1116-00-D453-U133Plus-2


title: P1100-01-D431-U133Plus-2


title: P1114-01-D342-U133Plus-2


title: P1081-02-D279-U133Plus-2


title: P1077-02-D264-U133Plus-2


title: P0107-01-A445-U133Plus-2


title: P1094-01-D451-U133Plus-2


title: P1088-01-D251-U133Plus-2


title: P1080-02-D300-U133Plus-2


title: P1070-01-D245-U133Plus-2


title: P1092-01-D262-U133Plus-2


title: P0111-01-A403-U133Plus-2


title: P1079-02-D278-U133Plus-2


title: P1093-01-D394-U133Plus-2


title: P1086-01-D205-U133Plus-2


title: P1068-01-D099-U133Plus-2


title: P1065-01-D005-U133Plus-2


title: P1066-01-D115-U133Plus-2


title: P1064-01-C986-U133Plus-2


title: P1063-01-C981-U133Plus-2


title: P1055-03-D246-U133Plus-2


title: P1023-01-D006-U133Plus-2


title: P0103-01-A401-U133Plus-2


title: P1049-01-D097-U133Plus-2


title: P0104-01-A366-U133Plus-2


title: P0096-01-A303-U133Plus-2


title: P1010-01-D039-U133Plus-2


title: P1052-01-D070-U133Plus-2


title: P1011-01-D025-U133Plus-2


title: P1067-01-D131-U133Plus-2


title: P1027-02-D051-U133Plus-2


title: SSEA1+ day 4 RA  Pten-/-  mESC, biological rep1

city: Los Angeles

first: Anne

last: Lindgren

address: 621 Charles E Young Dr S

department: MCDB

institute: UCLA

hyb_protocol: Affymetrix Mouse Genome 430 2.0 Array

scan_protocol: Chips were scanned using the Affymatrix 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.

source_name: SSEA1+ RA differentiated Pten-/- mouse ESC, biological rep1

label_protocol: FL-Ovation® cDNA Biotin Module V2

growth_protocol: Cells were grown in 6 well plates at a starting number of 50,000 for 4 days in mESC media without LIF with 10uM Ratinoic acid without media changes

extract_protocol: QIAGEN Rneasy Micro kit and Nu-GEN WT-Ovation® FFPE RNA Amplification System

treatment_protocol: Cells were differentiated for 4 days on mouse ES media without LIF and with 10uM Retinoic acid. Cells were stained and sorted for SSEA1 on a BD FACS ARIA.

value: differentiated cells

value: Pten-/-

value: wild type 129 background


title: P1013-01-D098-U133Plus-2


title: P0102-01-A388-U133Plus-2


title: P0101-01-A383-U133Plus-2


title: P1017-01-D092-U133Plus-2


title: P0099-01-A425-U133Plus-2


title: P1016-04-E483-U133Plus-2


title: P0098-01-A308-U133Plus-2


title: P0095-01-A355-U133Plus-2


title: P1003-02-D033-U133Plus-2


title: SSEA1+ day 4 RA  Pten-/-  mESC, biological rep2

source_name: SSEA1+ RA differentiated Pten-/- mouse ESC, biological rep2


title: P0092-01-A353-U133Plus-2


title: SSEA1+ day 4 RA  Pten-/-  mESC, biological rep3

source_name: SSEA1+ RA differentiated Pten-/- mouse ESC, biological rep3


title: SSEA1+ day 4 RA  wt mESC, biological rep3

source_name: SSEA1+ RA differentiated wild type mouse ESC, biological rep3

value: wild type


title: P1169-01-D553-U133Plus-2


title: SSEA1+ day 4 RA  wt mESC, biological rep2

source_name: SSEA1+ RA differentiated wild type mouse ESC, biological rep2


title: P0091-01-A326-U133Plus-2


title: P0061-01-A246-U133Plus-2


title: P0083-01-A389-U133Plus-2


title: P0084-01-A629-U133Plus-2


title: P0085-01-A396-U133Plus-2


title: P0065-01-A261-U133Plus-2


title: P0066-01-A264-U133Plus-2


title: P0063-01-A248-U133Plus-2


title: P0054-01-A194-U133Plus-2


title: SSEA1+ day 4 RA  wt mESC, biological rep1

source_name: SSEA1+ RA differentiated wild type mouse ESC, biological rep1


title: P0067-01-A274-U133Plus-2


title: P0077-01-A357-U133Plus-2


title: P0090-01-A427-U133Plus-2


title: P0048-01-A172-U133Plus-2


title: P0052-01-A180-U133Plus-2


title: P1140-01-D331-U133Plus-2


title: P0043-01-A153-U133Plus-2


title: P0051-01-A185-U133Plus-2


title: P0037-01-A111-U133Plus-2


title: P0055-01-A204-U133Plus-2


title: P0069-01-A296-U133Plus-2


title: P0057-01-A217-U133Plus-2


title: P0075-01-A332-U133Plus-2


title: P0053-01-A209-U133Plus-2


title: P0036-01-A120-U133Plus-2


title: ovarian epithelial cells T29A2 (with HMGA2)

city: Chicago

first: Jingjing

last: Wu

state: IL

address: 303 E. Chicago Avenue

department: pathology

institute: northwestern university

hyb_protocol: It was hybridized by using 1*Hybridization Buffer (Signosis) for 16h at 420C which was followed by washing two times.

scan_protocol: Mix equal amounts of ECL substrate A and B. Incubate the hybridized membrane in the substrate solution at room temperature for 5 min. Expose the membrane by using ECL film in the dark room. Use the schematic diagram to identify the spots on the array.

data_processing: We first obtained the ratio of RNU48 by dividing the densities of two samples, and normalized the densities of one of samples by multiplying or dividing the ratio. The microRNAs which have different expression with fold>2 were further analyzed.

label_protocol: Firstly, mix total RNA with provided oligos to form RNA/DNA hybrids. Then select the hybrids and remove free oligos. After that, amplify DNA with T7 transcription into RNA in the presence of biotin-UTP which are used for hybridization.

growth_protocol: Cells were maintained at 37oC in 5% CO2.

extract_protocol: Total RNA was isolated by miRNA isolation kit from Ambion according to manufacturer’s protocol.

value: immortalized ovarian epithelial cell lines


title: ovarian epithelial cells T29 (without HMGA2)


title: P0079-01-A351-U133Plus-2


title: P0016-01-A21-U133Plus-2


title: P0030-01-A72-U133Plus-2


title: P0015-01-A016-U133Plus-2


title: P0009-01-FAKE05-U133Plus-2


title: GPR86 WT M-2

status: Public on Sep 10 2010

city: Rahway

first: Oscar

last: Puig

state: NJ

address: 126 East Lincoln Ave

department: Molecular Profiling Research Informatics

institute: Merck Research Laboratories

description: GPR86 WT M-2

hyb_protocol: GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques.  Arrays are hybridized for 18 hours at 45C with vigorous mixing.  Unbound sample is removed and staining is accomplished through the binding of streptavidin-conjugated phycoerythrin to the hybridized target. Excess label is removed.  Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: Data were loaded into the Rosetta Resolver? system (Rosetta Biosoftware, Seattle, WA) and processed using the RMA algorithm (http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=12582260).  Intensities were calculated based on RMA, a Rosetta-developed error, and a MAS-5 p-value.  The Rosetta-developed error is used in the calculation of xdev for the ratio p-values as described in section 2.2 (http://bioinformatics.oxfordjournals.org/cgi/content/full/22/9/1111).

source_name: Liver, male, WT

label_protocol: The final in vitro transcription incorporates biotin moieties that are later labeled with streptavidin-conjugated phycoerythrin.  After amplification, samples are put through a controlled fragmentation to improve hybridization sensitivity and consistency.  The labeled molecules are biotinylated-cRNA.

extract_protocol: Samples are processed in parallel in 96-well plates to minimize potential variation.  Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.

value: liver

tag: gender

value: WT


title: P0025-01-A53-U133Plus-2


title: P0029-01-A70-U133Plus-2


title: P0018-01-A30-U133Plus-2


title: P0019-01-A40-U133Plus-2


title: GPR86 WT M-3

description: GPR86 WT M-3


title: GPR86 WT F-5

description: GPR86 WT F-5

source_name: Liver, female, WT


title: P1053-02-D082-U133Plus-2


title: GPR86 WT M-5

description: GPR86 WT M-5


title: GPR86 WT F-1

description: GPR86 WT F-1


title: GPR86 WT M-6

description: GPR86 WT M-6


title: P0002-01-FAKE03-U133Plus-2


title: GPR86 WT F-3

description: GPR86 WT F-3


title: GPR86 WT F-2

description: GPR86 WT F-2


title: GPR86 WT M-4

description: GPR86 WT M-4


title: GPR86 WT F-6

description: GPR86 WT F-6


title: P0010-01-FAKE06-U133Plus-2


title: GPR86 WT F-4

description: GPR86 WT F-4


title: GPR86 KO M-4

description: GPR86 KO M-4

source_name: Liver, male, GPR86 KO

value: GPR86 KO


title: GPR86 KO M-5

description: GPR86 KO M-5


title: P0034-01-A113-U133Plus-2


title: GPR86 KO M-3

description: GPR86 KO M-3


title: P0008-01-FAKE04-U133Plus-2


title: Leaf 2

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

country: United Kingdom

description: US94100321_251807310337_S01_GE1_105_Dec08_1_2.txt

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >12.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 30µL containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 30µL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Brassica 60-mer array (GPL8513) for 17 hours at 65°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 37°C GE Wash buffer 2 (Agilent), then air dried immediately, and stored under nitrogen until scanning.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using Gene Expression one color scan settings for 2x102k array slides (Scan Area 61x21.6 mm, Scan resolution 5µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 018073_D_F_20071106) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Brassica rapa

source_name: 23 day old semi-expanded leaves

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.6 ug RNA using the the QuickAmp Labelling kit (Agilent Technologies) according to the manufacturer's instructions and included 3 µL of Spike-Mix, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Plants grown in 13 cm pots containing a high nutrient, medium grade, peat based compost, pH; 5.3 - 5.7, N:P:K; 280:160: 350 g m-3. Grown under greenhouse conditions; 16hr photoperiod, 13.3 C - 22.3 C mean temperature range.

extract_protocol: RNA was isolated using a modified TRIzol protocol. To each sample, 1ml of TRIzol was added and total RNA extracted according to the manufactrer's instructions, with the following modifications: (i) after homogenisation the samples were centrfuged and supernatant transferred to a clean Eppendorf tube, and (ii) to aid precipitaion of RNA from the aqeous phase, 0.25ml of isopropanol and 0.25ml 1.2M NaCl solution containing 0.8M sodium citrate. Extracted total RNA was then purified using the 'RNA Cleanup' protocol for Qiagen RNeasy columns.

value: Leaf

tag: line

value: 23 days


title: Root 3

institute: Nottingham Arabidopsis Stock Centre (NASC)

description: US94100321_251807310339_S01_GE1_105_Dec08_1_2.txt

source_name: 11 day old roots

growth_protocol: Sterilised seeds (washed in 70% ethanol, rinsed in deionised water and surface-sterilised using NaOCl) were sown in large sqaure (20cm x 20 cm) Petri dish plates containing 250ml 0.8% agar with 1x Murashige & Skoog salts adjusted to pH 5.6. Plants were grown under 16 hour photoperiod at 24 C.

value: Root

value: 11 days


title: GPR86 KO F-4

description: GPR86 KO F-4

source_name: Liver, female, GPR86 KO


title: RT_93_13_215_IODO_Mus_Lung_Mouse430_2_RT_HON07_MusLung

description: MAQC_Distribution_Status: MAQC_V -- Validation

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

source_name: B6C3F1 Lung

label_protocol: standard Affymetrix protocol

extract_protocol: Extraction Method: Trizol; Additional Purification Method: Qiagen Rneasy

value: Lung

tag: compound

value: IODO

tag: hybdate

tag: dose

tag: endpointcode

value: A


title: GPR86 KO M-1

description: GPR86 KO M-1

value: male


title: RT_93_13_213_IODO_Mus_Lung_Mouse430_2_RT_HON07_MusLung

tag: strain


title: GPR86 KO F-2

description: GPR86 KO F-2

tag: tissue

value: female


title: Root 2

description: US94100321_251807310339_S01_GE1_105_Dec08_1_1.txt


title: RT_50000_13_289_TFEA_Mus_Lung_Mouse430_2_RT_HON07_MusLung

value: TFEA


title: RT_93_13_224_IODO_Mus_Lung_Mouse430_2_RT_HON07_MusLung


title: RT_60_13_162_TCPN-60_Lung_07008_Mouse430_2_RSTLRI000_2


title: RT_600_13_45_DCBZ-600_Lung_07008_Mouse430_2_RSTLRI000_2


title: GPR86 KO F-5

description: GPR86 KO F-5

tag: genotype


title: Leaf 1

description: US94100321_251807310337_S01_GE1_105_Dec08_1_1.txt


title: RT_50000_13_290_TFEA_Mus_Lung_Mouse430_2_RT_HON07_MusLung


title: Root 1

description: US94100321_251807310338_S01_GE1_105_Dec08_1_2.txt


title: GPR86 KO M-6

description: GPR86 KO M-6


title: RT_60_13_163_TCPN-60_Lung_07008_Mouse430_2_RSTLRI000_2


title: GPR86 KO F-6

description: GPR86 KO F-6


title: RT_600_13_41_DCBZ-600_Lung_07008_Mouse430_2_RSTLRI000_2


title: RT_60_13_165_TCPN-60_Lung_07008_Mouse430_2_RSTLRI000_2


title: RT_4000_13_217_MECL-4000_Lung_07008_Mouse430_2_RSTLRI000_2


title: RT_600_13_43_DCBZ-600_Lung_07008_Mouse430_2_RSTLRI000_2


title: RT_3925_13_203_TCFM_Mus_Lung_Mouse430_2_RT_HON07_MusLung

value: TCFM


title: RT_3925_13_209_TCFM_Mus_Lung_Mouse430_2_RT_HON07_MusLung


title: RT_30_13_284_NPTH-30_Lung_07008_Mouse430_2_RSTLRI000_2


title: RT_50000_13_292_TFEA_Mus_Lung_Mouse430_2_RT_HON07_MusLung


title: RT_4000_13_218_MECL-4000_Lung_07008_Mouse430_2_RSTLRI000_2


title: GPR86 KO F-1

description: GPR86 KO F-1


title: RT_30_13_285_NPTH-30_Lung_07008_Mouse430_2_RSTLRI000_2


title: RT_30_13_283_NPTH-30_Lung_07008_Mouse430_2_RSTLRI000_2


title: RT_60_13_164_TCPN-60_Lung_07008_Mouse430_2_RSTLRI000_2


title: RT_3925_13_210_TCFM_Mus_Lung_Mouse430_2_RT_HON07_MusLung


title: RT_1250_13_272_TFEL_Mus_Lung_Mouse430_2_RT_HON07_MusLung

value: TFEL


title: RT_1250_13_276_TFEL_Mus_Lung_Mouse430_2_RT_HON07_MusLung


title: RT_2_13_108_VANP-2_Lung_07008_Mouse430_2_RSTLRI000_2


title: RT_20000_13_243_ABDQ_Mus_Lung_Mouse430_2_RT_HON07_MusLung

value: ABDQ


title: RT_1200_13_99_PGBE-1200_Lung_07008_Mouse430_2_RSTLRI000_2


title: GPR86 KO F-3

description: GPR86 KO F-3


title: RT_20000_13_245_ABDQ_Mus_Lung_Mouse430_2_RT_HON07_MusLung


title: RT_2_13_109_VANP-2_Lung_07008_Mouse430_2_RSTLRI000_2


title: RT_4000_13_216_MECL-4000_Lung_07008_Mouse430_2_RSTLRI000_2


title: RT_20000_13_237_ABDQ_Mus_Lung_Mouse430_2_RT_HON07_MusLung


title: RT_1200_13_96_PGBE-1200_Lung_07008_Mouse430_2_RSTLRI000_2


title: RT_1000_13_256_TDPP_Mus_Lung_Mouse430_2_RT_HON07_MusLung

value: TDPP


title: RT_1250_13_267_TFEL_Mus_Lung_Mouse430_2_RT_HON07_MusLung


title: RT_2_13_106_VANP-2_Lung_07008_Mouse430_2_RSTLRI000_2


title: RT_93_13_221_IODO_Mus_Lung_Mouse430_2_RT_HON07_MusLung


title: Newly diagnosed, pediatric ALL, standard risk #6

city: St. Peter

first: Sanjive

last: Qazi

state: MN

address: 800 west College Av

institute: Gustavus Adolphus College

hyb_protocol: Human Atlas  cDNA Expression Arrays User Manual was used. After discarding prehybridization solution, arrays were hybridized overnight.

scan_protocol: Arrays were washed 4 times by using 2X SSC/1% SDS and 2 times by using 0.1X SSC/0.5% SDS.  Membranes were sealed and exposed to phosphoscreen (Molecular Dynamics).

data_processing: Density readings from the phosphor images were normalized to 5  housekeeping genes (glyceraldehyde-3-phosphate dehydrogenase (G3PDH; GADPH),  myosin I, ornithine decarboxylase (ODC), phospholipase A and hypoxantine-guanine  phosphoribosyltransferase (HPRT)).  The mean signal intensity within  each spot was subtracted from the sub-grid median of the background signal. For  thresholding, the intensities of the duplicate spots for each gene were averaged and  floored to a signal value of 2 units.

source_name: Human, with ALL

label_protocol: After DNAase treatment, total RNA was converted into radioactively labeled cDNA using [a-32P] dATP (Amersham) by reverse transcriptase (Clontech). Chroma Spin columns (Clontech) were used to purify labeled cDNA.

extract_protocol: total RNA was isolated using Tripure isolation reagent (Boehringer), a monophasic solution of phenol and guanidine thiocyanate

tag: sample type

value: Ficoll-Hypaque separated bone marrow mononuclear cells

value: bone marrow mononuclear cells

tag: disease state


title: Newly diagnosed, pediatric ALL, standard risk #7

tag: cell type


title: Newly diagnosed, pediatric ALL, standard risk #5


title: Newly diagnosed, pediatric ALL, standard risk #4


title: RT_20000_13_241_ABDQ_Mus_Lung_Mouse430_2_RT_HON07_MusLung


title: Newly diagnosed, pediatric ALL, high risk #20


title: Newly diagnosed, pediatric ALL, high risk #21


title: Newly diagnosed, pediatric ALL, high risk #22


title: Newly diagnosed, pediatric ALL, high risk #23


title: Newly diagnosed, pediatric ALL, standard risk #3


title: Newly diagnosed, pediatric ALL, standard risk #2


title: Newly diagnosed, pediatric ALL, standard risk #1


title: Newly diagnosed, pediatric ALL, high risk #19


title: Newly diagnosed, pediatric ALL, high risk #17


title: Newly diagnosed, pediatric ALL, high risk #15


title: Newly diagnosed, pediatric ALL, high risk #18


title: Newly diagnosed, pediatric ALL, high risk #16


title: RT_1000_13_248_TDPP_Mus_Lung_Mouse430_2_RT_HON07_MusLung


title: Newly diagnosed, pediatric ALL, high risk #13


title: Newly diagnosed, pediatric ALL, high risk #12


title: Newly diagnosed, pediatric ALL, high risk #14


title: Newly diagnosed, pediatric ALL, high risk #11


title: Newly diagnosed, pediatric ALL, high risk #10


title: RT_0_13_52r_CCO5_Lung_07008_Mouse430_2_RSTLRI000_2


title: RT_1000_13_250_TDPP_Mus_Lung_Mouse430_2_RT_HON07_MusLung


title: RT_1200_13_97_PGBE-1200_Lung_07008_Mouse430_2_RSTLRI000_2


title: RT_0_13_53r_CCO5_Lung_07008_Mouse430_2_RSTLRI000_2


title: Newly diagnosed, pediatric ALL, high risk #9


title: Newly diagnosed, pediatric ALL, high risk #8


title: RT_100_13_227_ETOX-100_Lung_07008_Mouse430_2_RSTLRI000_2


title: RT_0_13_54r_CCO5_Lung_07008_Mouse430_2_RSTLRI000_2


title: RT_0_13_291_ACO5_Lung_07008_Mouse430_2_RSTLRI000_2


title: RT_0_13_294_ACO5_Lung_07008_Mouse430_2_RSTLRI000_2


title: Newly diagnosed, pediatric ALL, high risk #6


title: Newly diagnosed, pediatric ALL, high risk #7


title: RT_100_13_228_ETOX-100_Lung_07008_Mouse430_2_RSTLRI000_2


title: RT_0_13_339_ACO1_Mus_Lung_Mouse430_2_RT_HON07_MusLung


title: Newly diagnosed, pediatric ALL, high risk #3


title: Newly diagnosed, pediatric ALL, high risk #5


title: Newly diagnosed, pediatric ALL, high risk #2


title: Newly diagnosed, pediatric ALL, high risk #4


title: RT_100_13_230_ETOX-100_Lung_07008_Mouse430_2_RSTLRI000_2


title: RT_0_13_295_ACO5_Lung_07008_Mouse430_2_RSTLRI000_2


title: RT_0_13_340_ACO1_Mus_Lung_Mouse430_2_RT_HON07_MusLung


title: RT_0_13_266_FCO1_Mus_Lung_Mouse430_2_RT_HON07_MusLung


title: RT_0_13_338_ACO1_Mus_Lung_Mouse430_2_RT_HON07_MusLung


title: Newly diagnosed infant ALL #31

value: infant ALL


title: Newly diagnosed, pediatric ALL, high risk #1


title: RT_0_13_258_FCO1_Mus_Lung_Mouse430_2_RT_HON07_MusLung


title: Newly diagnosed infant ALL #30


title: RT_0_13_260_FCO1_Mus_Lung_Mouse430_2_RT_HON07_MusLung


title: RT_4000_13_220_MECL-4000_Lung_07008_Mouse430_2_RSTLRI000_2


title: RT_0_13_238_ACO4_Lung_07008_Mouse430_2_RSTLRI000_2


title: P0056-01-A211-U133Plus-2

value: Training

tag: Sex

value: 1=event occurred < 24 months, 0=no event in first 24 months:0

value: 1= deceased by 24 months, 0= alive at 24 months:0


title: RT_0_13_292_ACO5_Lung_07008_Mouse430_2_RSTLRI000_2


title: RT_600_13_44_DCBZ-600_Lung_07008_Mouse430_2_RSTLRI000_2


title: RT_0_13_239_ACO4_Lung_07008_Mouse430_2_RSTLRI000_2


title: RT_30_13_282_NPTH-30_Lung_07008_Mouse430_2_RSTLRI000_2


title: RT_0_13_237_ACO4_Lung_07008_Mouse430_2_RSTLRI000_2


title: Newly diagnosed infant ALL #29


title: RT_0_13_235_CCO4_Mus_Lung_Mouse430_2_RT_HON07_MusLung


title: RT_0_13_337_ACO1_Mus_Lung_Mouse430_2_RT_HON07_MusLung


title: Newly diagnosed infant ALL #25


title: RT_100_13_229_ETOX-100_Lung_07008_Mouse430_2_RSTLRI000_2


title: RT_1250_13_269_TFEL_Mus_Lung_Mouse430_2_RT_HON07_MusLung


title: Newly diagnosed infant ALL #27


title: Newly diagnosed infant ALL #28


title: Newly diagnosed infant ALL #26


title: Newly diagnosed infant ALL #24


title: Newly diagnosed infant ALL #22


title: Newly diagnosed infant ALL #23


title: Newly diagnosed infant ALL #21


title: RT_0_13_232_CCO4_Mus_Lung_Mouse430_2_RT_HON07_MusLung


title: Newly diagnosed infant ALL #20


title: Newly diagnosed infant ALL #19


title: Newly diagnosed infant ALL #18


title: Newly diagnosed infant ALL #16


title: Newly diagnosed infant ALL #17


title: Newly diagnosed infant ALL #12


title: Newly diagnosed infant ALL #11


title: RT_0_13_227_CCO4_Mus_Lung_Mouse430_2_RT_HON07_MusLung


title: Newly diagnosed infant ALL #10


title: RT_0_13_175r_CCO6_Lung_07008_Mouse430_2_RSTLRI000_2


title: Newly diagnosed infant ALL #8


title: Newly diagnosed infant ALL #14


title: Newly diagnosed infant ALL #13


title: Newly diagnosed infant ALL #15


title: RT_0_13_116_ACO3_Lung_07008_Mouse430_2_RSTLRI000_2


title: Newly diagnosed infant ALL #9


title: RT_0_13_174_CCO6_Lung_07008_Mouse430_2_RSTLRI000_2


title: RT_0_13_172_CCO6_Lung_07008_Mouse430_2_RSTLRI000_2


title: RT_0_13_120_ACO3_Lung_07008_Mouse430_2_RSTLRI000_2


title: RT_0_13_263_FCO1_Mus_Lung_Mouse430_2_RT_HON07_MusLung


title: RT_0_13_225_CCO4_Mus_Lung_Mouse430_2_RT_HON07_MusLung


title: RT_0_13_51_CCO5_Lung_07008_Mouse430_2_RSTLRI000_2


title: RT_1200_13_98_PGBE-1200_Lung_07008_Mouse430_2_RSTLRI000_2


title: RT_50000_13_293_TFEA_Mus_Lung_Mouse430_2_RT_HON07_MusLung


title: Newly diagnosed infant ALL #7


title: RT_1000_13_252_TDPP_Mus_Lung_Mouse430_2_RT_HON07_MusLung


title: RT_3925_13_201_TCFM_Mus_Lung_Mouse430_2_RT_HON07_MusLung


title: RT_2_13_107_VANP-2_Lung_07008_Mouse430_2_RSTLRI000_2


title: Newly diagnosed infant ALL #3


title: Newly diagnosed infant ALL #6


title: RT_0_13_240_ACO4_Lung_07008_Mouse430_2_RSTLRI000_2


title: Newly diagnosed infant ALL #5


title: Newly diagnosed infant ALL #2


title: RT_0_13_55r_CCO5_Lung_07008_Mouse430_2_RSTLRI000_2


title: RT_0_13_119_ACO3_Lung_07008_Mouse430_2_RSTLRI000_2


title: RT_0_13_293_ACO5_Lung_07008_Mouse430_2_RSTLRI000_2


title: RT_0_13_173_CCO6_Lung_07008_Mouse430_2_RSTLRI000_2


title: RT_0_13_171r_CCO6_Lung_07008_Mouse430_2_RSTLRI000_2


title: BB12_XOS/Glucose

city: Cadorago

first: Martin

middle: Bastian

last: Pedersen

state: CO

address: Via Manzoni 29

department: R&D

country: Italy

institute: Sacco Srl

description: Comparison of the growth of BB12 on XOS relative to glucose.

hyb_protocol: According to the Amersham protocol the Cy3 and Cy5 labelled cDNA were combined and lyophilized. Hereafter they were resuspended in 3uL of nuclease free water and, 5uL of hybdridization buffer (4x), and 12uL of formamide was added. This 20uL solution was applied to the array under a 24x24mm LifterSlip (Erie Scientific Company, Portsmouth, NH) and put in an airtight box containing paper towels soaked with NaCl-saturated water. Arrays were hybridized for 16-20h at 42ºC, and then washed using the UltraGAPS protocol (Corning B.V.).

scan_protocol: Arrays were scanned using the GenePix 4100A Personal Scanner with GenePix Pro 6.0 software (Axon Instruments Inc., Union City, CA). The photo multiplier tube (PMT) sensitivity was set to "Auto-PMT" with a "saturation tolerance" of 0.1%.

data_processing:
A grid with 110um spots was laid over the array and was manually adjusted to fit small irregularities in spotting. Spots clearly covered by for example dust particles were flagged “Bad”. The intensity of all spots was then calculated using the “Analyze” function. Spots with very weak signals in both channels were also flagged “Bad”. These were spots where the signal-to-noise ratio [SNR] < 1 in both channels, or where [% > B + 2SD] < 20 in both channels. All other spots were considered “Found” and had a “Flag” value of >= 0. All data was exported from GenePix Pro in tab-delimited format.
In the further analysis the variables of feature (spot) intensity minus the background intensity around the spot was used, i.e. [F635 median – B635]=Cy5 and [F532 median – B532]=Cy3. The log2(ratio) of this was calculated as log2(Cy5/Cy3). Some spots may have a significant signal in one channel but no signal in the other channel. The latter may result in a negative value due to noise and thus and illegal log2(ratio). To avoid this a macro in Excel 2000 (Microsoft Corporation, Redmond, WA) was used to change [F635 median – B635] and [F532 median – B532] values of <10 to 10 for “Found” spots (the signal scale goes from 0, no signal, to 65535, saturated signal). For these spots the log2(ratio) was re-calculated. The corrected data was exported from Excel and imported into Acuity 4.0 (Axon) where they were ratio-normalized based on the “Found” spots.
In Acuity a dataset was created. For each array only genes were included where 1) at least 3 of the 4 replicate spots were “Found”, 2) the standard deviation was <0.5 among “Found” spots, and 3) <30% of the pixels in “Found” spots, in both channels, were saturated.

organism: Bifidobacterium animalis subsp. lactis

label_protocol: 10ug of total RNA was lyophilized in a speed-vac. The copying into cDNA and labeling with either Cy3 (reference) or Cy5 (test) was done using the CyScribe Post-Labelling Kit using manufacturer’s protocol (Amersham Biosciences, Hillerød, Denmark). 1uL of random nonamer was used for priming.

growth_protocol: BB12 grown at 37ºC in MRS medium made from its components (except carbon source) with 2% of glucose added and 0.05% CysHCl. Harvest was at OD600 ca.  1. There was no agitation, except gentle shaking at the times of OD measurements.

extract_protocol: At OD 1.0, samples of 0.67mL were collected in 1.33mL RNAprotect according to protocol (QIAGEN, Valencia, CA). Total RNA was isolated using the RNeasy Mini Kit (QIAGEN) except for the following: the 200uL TE buffer contained 15mg/mL of lysozyme, 15uL of proteinase K at 20mg/mL, and 2uL of mutanolysin at 25U/uL with vortexing every 10s at 37ºC for the 2min. The quality and concentration of RNA was determined using the RNA 6000 Nano Kit on the Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). Routinely, 20-50ug of total RNA was obtained. Only high quality total RNA, as indicated by two sharp rRNA peaks, was used.

tag: carbon source

value: glucose

growth_protocol: BB12 grown at 37ºC in MRS medium made from its components (except carbon source) with 2% of XOS added and 0.05% CysHCl. Harvest was at OD600 ca.  1. There was no agitation, except gentle shaking at the times of OD measurements.

value: xylo-oligosaccharide


title: Newly diagnosed infant ALL #1


title: BB12_Glucose/XOS

label_protocol: 10ug of total RNA was lyophilized in a speed-vac. The copying into cDNA and labeling with either Cy5 (reference) or Cy3 (test) was done using the CyScribe Post-Labelling Kit using manufacturer’s protocol (Amersham Biosciences, Hillerød, Denmark). 1uL of random nonamer was used for priming.


title: FVB_Control_spleen_3

hyb_protocol: Atlas  cDNA Expression Arrays User Manual, Section VII.B was used and all 68oC incubations were performed at 71oC instead. After discarding prehybridization solution, arrays were hybridized overnight.

source_name: splenocytes

tag: genetic background

value: FVB

value: splenocytes

value: wild type


title: Newly diagnosed infant ALL #4


title: RT_0_13_117_ACO3_Lung_07008_Mouse430_2_RSTLRI000_2

value: Lung

value: A


title: FVB_Control_spleen_1


title: CD22_Transg_spleen_E5827

value: CD22DE12 transgenic


title: CD22_Transg_spleen_E4232


title: FVB_Control_spleen_2


title: CD22_Transg_spleen_E5871


title: RT_0_13_236_ACO4_Lung_07008_Mouse430_2_RSTLRI000_2


title: p73_ME180_6

first: Kevin

last: Struhl

address: 240 Longwood Ave.

department: Dept. Of Biological Chemistry & Molecular Pharmacology

institute: Harvard Medical School

description: p73 ChIP Biological Rep 1-3, chip F

hyb_protocol: Biotinylated DNA was hybridized to the Affymetrix tiled, human whole genome arrays, washed, and stained according to manufacturer's instructions.

scan_protocol: The microarrays were scanned using a custom-built Affymetrix scanner with a laser spot size of 3.5 um and a resolution (pixel size) of 1.0 um.

data_processing: Normalization and two sample comparison analysis were performed using Tiling Analyais Software 1.1.02. Log2(signal) and -10log10(p-value) were reported in BAR files. Supplementary file GSE18650_p73_ME180_BindingSites_hg17.xls contains p73 binding sites at three different significance thresholds.

source_name: p73 ChIP DNA from ME180 cell line

label_protocol: Standard Affymetrix labeling protocol using biotin.

growth_protocol: Cells were grown in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% Fetal Bovine Serum.

extract_protocol:
1. Trypsinized cells were placed into fresh media and cross-linked by the addition of formaldehyde.
2. Cells were then spun down and the cell pellet was then resuspended in micrococcal nuclease (MNase) reaction buffer.
3. The chromatin was then sonicated, spun down and the supernatant was diluted with IP-dilution buffer.
4. Diluted chromatin was precleared with protein A/G sepharose beads, and a portion reserved for control, or 'input', DNA (i.e. omitting immunoprecipitation).
5. The remaining chromatin was incubated with AKp73 anti-p73 antibody-coupled protein A/G seppharose beads.
6. Input and eluted material was de-crosslinked and purified.
Amplified ChIP (or matching input) DNA was fragmented with DNase I, and then biotin-labeled using terminal transferase (TdT).

treatment_protocol: Cells were treated with ethanol (vehicle control) for 24-26 hrs before harvesting by trypsinization.

value: 66 yrs

value: cervical carcinoma

tag: antibody

value: anti-p73 monoclonal antibody (AKp73)

source_name: Input DNA from ME180 cell line


title: hES-T3 grown in hES medium (containing 4 ng/ml bFGF) supplemented with 5 ng/ml activin A, biological rep1

first: Sung-Liang

last: Yu

address: Jen Ai Road Section1

department: Clinical Laboratory Sciences and Medical Biotechnology

institute: National Taiwan University

description: The mRNA profilings of T3MF, T3CM and T3BA cells were analyzed using Affymetrix Human Genome U133 plus 2.0 GeneChip according to the Manufacturer¡¦s protocols (Santa Clara, CA, USA, http://www.affymetrix.com).

hyb_protocol: Following fragmentation, 10 micrograms of cRNA were hybridized for 16 hr at 45oC on Affymetrix Human Genome U133 plus 2.0 GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips from the hybridization experiments were read by the Affymetrix GeneChip scanner 3000.

data_processing: The data were processed by GeneSpring GX software version 7.3.1 GC-RMA preprocessor to use on the CEL files

source_name: hES-T3 cells grown in hES medium (containing 4 ng/ml bFGF) supplemented with 5 ng/ml activin A

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms purified cRNA (Expression Analysis Technical Manual, 2004, Affymetrix, http://www.affymetrix.com).

growth_protocol: The hES-T3 cells were grown on feeder-free Matrigel-coated dish in hES medium (containing 4 ng/ml bFGF) supplemented with 5 ng/ml activin A (human recombinant activin A expressed and derived in CHO cells, R&D systems), and these cells were designated as T3BA. Since activin A was previously reported to be necessary and sufficient for the maintenance of self-renewal and pluripotency of hES cells in long-term feeder- and serum-free culture [Xiao et al. 2006], the hES-T3 cells were also grown on feeder-free Matrigel in hES medium (without bFGF) supplemented with 5, 10 and 25 ng/ml activin A.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNAs extracted using TRIZOL reagent were quantified spectrophotometrically. The cDNA synthesis was carried out by using SUPERSCRIPTTM one-step RT-PCR kit (Invitrogen). For the reverse transcription step, the whole 5 ul of the resuspended RNAs were incubated for 60 min at 42oC, then 15 min at 72oC in 50 ul of reaction mixture containing 25 ul of 2x Reaction Mix (Invitrogen) and 1 ul of RT/PLANTINUM Taq Mix (Invitrogen). 28.5 ul of the cDNAs present in the 50 ul RT reaction mixture purified by Microarray Target Purification Kit (Roche Applied Science, Indianapolis, ID, USA, http://www.roche-applies-science.com) were used as templates to amplify cDNA by Microarray Target Amplification Kit. The amplified cDNAs were purified by Microarray Target Purification Kit, and complementary RNAs (cRNAs) were synthesized from 200 ng cDNA with Microarray RNA Target Synthesis Kit (Roche Applied Science).

treatment_protocol: Non

tag: growth conditions

value: female

tag: cell line


title: CD22_Transg_spleen_E5870


title: Leaf 3

description: US94100321_251807310338_S01_GE1_105_Dec08_1_1.txt

value: Leaf

tag: line

tag: age

value: 23 days


title: Human embryonic stem cells, hES-T3, grown on MEF feeder, biological rep2

source_name: hES-T3 cells grown on MEF feeder

growth_protocol: Human embryonic stem cell line hES-T3, which is one of the five hES cell lines derived with institutional review board approval from preimplantation embryos donated at IVF clinics in Taiwan, exhibits normal female karyotype (46, XX), and it has been continuously cultured on mitomycin C (10 ug/ml) mitotically inactivated MEF feeder in hES medium under 5% CO2 at 37oC and underwent freezing/thawing processes. The hES culture medium consisted of DMEM/F12 (1:1, GIBCO) supplemented with 20% KSR (Invitrogen), 1% non-essential amino acids, 1 mM L-glutamine, 0.1 mM £]-mercaptoethanol, and 4 ng/ml human basic fibroblast growth factor (bFGF; Life Technologies). Routine passages of hES-T3 cells every 5-7 days were done with collagenase ( type IV, 1 mg/ml, Invitrogen) treatment and mechanical scrape. The hES-T3 cells grown on MEF feeder were designated as T3MF.

value: hES-T3 cells grown on MEF feeder

tag: gender


title: CD22_Transg_spleen_E5869


title: CD22_Transg_spleen_E5129


title: GPR86 KO M-2

description: GPR86 KO M-2

value: liver

value: male

value: GPR86 KO


title: Human embryonic stem cells, hES-T3, grown on feeder-free Matrigel in MEF-conditioned medium, biological rep2

source_name: hES-T3 cells grown on feeder-free Matrigel in MEF-conditioned medium

growth_protocol: The MEF cells were cultured in MEF medium overnight, and the mitotically inactivated MEF were maintained in hES medium containing 4 ng/ml bFGF. After 24 h, the MEF-conditioned medium was collected and filtered through 0.2 um membrane (PN4612, Pall Life Sciences) as previously described [Xu et al., 2001]. The culture dish was coated with Matrigel diluted with DMEM/F12 (1:30) overnight at 4oC. The BD MartigelTM (Matrix 354234) is the manufacturer¡¦s Trademark for extracellular matrix extracted from the Engelbreth-Holm-Swarm tumor. The hES-T3 cells grown on feeder-free Martigel-coated dish in MEF-conditioned medium (with additional 4 ng/ml bFGF) were designated as T3CM.


title: Human embryonic stem cells, hES-T3, grown on feeder-free Matrigel in MEF-conditioned medium, biological rep1

value: hES-T3 cells grown on feeder-free Matrigel in MEF-conditioned medium


title: hES-T3 grown in hES medium (containing 4 ng/ml bFGF) supplemented with 5 ng/ml activin A, biological rep2

value: hES-T3 cells grown in hES medium (containing 4 ng/ml bFGF) supplemented with 5 ng/ml activin A


title: CcpA_L2vsWT_L2

city: Zürich

first: Marc

last: Stevens

address: Winterthurerstrasse 272

department: Vetsuisse

country: Switzerland

institute: University of Zurich

hyb_protocol: Two individual ,  differentially labeled ,  cDNAs were incubated at  , 95° C for 3' cooled down  , to 68° C and mixed ,  (final-volume 20 µl). To ,  these mixed cDNAs 180 µl  , of pre-heated (68° C) ,  Slidehyb#1 hybridization ,  buffer (Ambion Austin ,  USA) was added and the ,  resulting solution was ,  applied on a pre-heated ,  slide (68° C). Slides were ,  then hybridized at 44° C for  , 16 hours. Subsequently ,  slides were washed at ,  42°C once in 1 x ,  SSC/0.2% SDS and twice  , in 1 x SSC and dried by ,  centrifugation (1 x SSC is ,  0.15 M NaCl and 0.15 M ,  Sodium Citrate).

scan_protocol: Using the Scan Array ,  Express microarray ,  scanner. 1.Turn on the ,  scanner and the computer  , (in this order) 2.Login: ,  scanner 3.Double click the  , 'ScanArray Express' icon  , 4.Switch on lasers 1 and  3 , at least 15 minutes prior  to , scanning arrays 5.Click  the , 'File' button This is to  , prevent you from ,  accidentally turning off the  , laser after the 15 minutes  , warming-up phase  6.Insert , the slide with the  array-side , up and the  label towards , the outside.  On Agilent , slides the  array side is the , side with  the label that has , the  word  Agilent on it ,  7.Press 'Scan | Prescan' ,  8.Put resolution at 50 m ,  select both labels used ,  and set PMT values for ,  both channels 9.Press ,  'Start' 10.Press 'Palette ' ,  'Green' as soon as ,  projection of the image has  , started (first dye) select ,  the red colour as soon as ,  scanning of the second ,  layer (second dye) has ,  started 11.Adjust PMT ,  values to balance signals ,  obtained for both ,  channels. If necessary do ,  a few low-resolution scans  , to obtain a optimal  balance , 12.Click the  'Scan' button , again  13.Select frame for , high  resolution scan adjust ,  resolution (to 10 m) and ,  scan the array for both ,  dyes 14.Press 'File | Save'  , to save the files 'Save all'  , saves both dye layers ,  Create a new folder for ,  each array  'Save all' ,  saves the signals from  both , layers in individual  files , 15.Switch off the  lasers

data_processing: Lowess normalized log2 ratio (Cy3/Cy5). No interslide normalization

organism: Lactiplantibacillus plantarum

label_protocol: Annealing Mix  x µl RNA preparation  (=5µg) y µl  nuclease-free water 1 µl  Random Nonamers 11  µl TOTAL 1. mix  Annealing Mix in a 200  µl PCR tube gently by  pipetting up and down  2. incubate for 5’ 70°C  3. cool at room  temperature for 10’  (annealing) 4. spin down  the mixture to the  bottom of the tube 5.  place on ice Reverse  transcription Reverse  Transcription Mix 4 µl 5x  buffer 2 µl 0.1 M DTT 1  µl dNTP-mix 1 µl  AA-dUTP 1 µl TMIII  (keep only briefly  outside 20°C) 20 µl  TOTAL 1. Mix by very  gently by pipetting up  and down (vigorous  pipetting will denature  the enzyme!) 2.  Incubate for 3 hrs at  42°C (in PCR-machine)  3. Cool on ice for  immediate purification or  place at 20°C for  storage Degradation of  mRNA 1. Add 2 µl 2.5 M  NaOH 2. Mix (vortex)  and spin down 3.  Incubate for 15 min. at  37°C 4. Add 10 µl 2 M  HEPES free acid 5. Mix  (vortex) and spin down  6. Ready for purification  or store at 20°C  Labelling and  purification of cDNA  with cyanine dyes  Followed Ge Healthcare  kit Amersham CyDye  (Cy3/Cy5)Reactive Dye  Protocols for Post  Labelling  Aminoallyl-cDNA and  Aminoallyl-aRNA code  RPN5661 Labelling of  amino allyl-modified  cDNA with CyDye 1.  Add the amino allyl  modified cDNA (in 0.1 M  sodium bicarbonate)  directly into one aliquot  of CyDye NHS Ester.  Resuspend the ester  completely by pipetting  several times and  transfer the solution to  an amber 1.5 ml tube 2.  Incubate at room  temperature, in the dark  for 60 to 90 minutes 3.  Add 15 µl 4 M  Hydroxylamine to each  coupling reaction 4. Mix  by stirring and incubate  at room temperature, in  the dark, for 15 minutes  5. Proceed directly to  purification of  CyDye-labelled cDNA  Purification of CyDye  labelled cDNA Followed  Ge Healthcare kit  Amersham CyDye  (Cy3/Cy5)Reactive Dye  Protocols for Post  Labelling  Aminoallyl-cDNA

growth_protocol: Cultures were grown in batch fermentation on a chemically defined medium untill an optical density of 1.0 before being stressed with Na-L-lactate

extract_protocol: Collecting  cells Quenching Buffer  66.7 mM HEPES (pH  6.5) 60%Methanol  Extraction Mixture  (Prepared in a  screw-cap tube) -500 µll  phenol/Chloroform -30  µl10% SDS -30 µl3 M  NaAc (pH 5.2) -500 mg  glass-beads (75-150 µm)  -400 µlTE buffer 1.For  each sample prepare a  tube with Extraction  Mixture 2.Harvest cells  and quench them  immediately in  Quenching Buffer. Add  4 volumes of Quenching  Buffer ( 40°C) to 1  volume of cell culture  3.Mix and store the  sample at -40°C  4.Centrifuge cells at -20  C at 9000 rpm for 10  minutes (Centrifuge  RC5B) 5.Discard the  supernatant; keep the  cell pellet cooled and  work quickly to prevent  condensation of water.  Transfer the pellet with  a pre-cooled spatula to  a screw-crap tube with  Extraction Mixture 6.Mix  the cell pellet thoroughly  with Extraction Mixture  by shaking by hand  7.Freeze the tube  immediately in liquid  nitrogen 8.Break cells in  the Savant FastPrep  FP120. Three times 40  seconds at speed 4.0  (cool cells between  steps if necessary)  9.Centrifuge for 5  minutes at 4°C in an  Eppendorf centrifuge at  10.000 rpm 10.Transfer  500 µl of the  supernatant to a new  tube. Add 400 µl  chloroform (chloroform  should be cooled at  4°C) 11.Centrifuge for 2  minutes in an Eppendorf  centrifuge at full speed  (4°C) 5.Continue with  the High Pure RNA  Isolation Kit from  Roche (order # 1 828  665) 6.Incubate for 60  minutes with DnaseI,  elute with 50 µl elution  buffer 7.Store the RNA  in at least 2 aliquots,  one of 20 µl (for  concentration and  quality analysis and  labelling) and one  back-up of 30 µl at  -80°C.

treatment_protocol: Harvested cultures were quenced in extraction mix containing Phenol/Chloroform, SDS, Na-acetate, glass-beads and TE buffer.

value: WCFS1- wild type

tag: growth stage

value: mid log

tag: treatment

value: Na-L-lactate

value: CcpA K.O.


title: CcpA_L1vsWT_L1

value: early log


title: CcpA_L4vsCcpA_L1

value: early stationary