title: T3AQBC06092008A_3401_CY3_STERNE_CY5_13824576_B

description: T3AQBC06092008A_3401_CY3_STERNE_CY5_13824576_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3AQBC06092008A_3407_CY3_STERNE_CY5_13843677_B

status: Public on Nov 25 2009

type: genomic

city: Rockville

first: Chun-Hua

last: Wan

state: MD

address: 9704 Medical Center Dr

department: Pathogen Functional Genomics Resources Center (PFGRC)

country: USA

institute: The J. Craig Venter Institute

description: T3AQBC06092008A_3407_CY3_STERNE_CY5_13843677_anno_sub_95th_MDS.mev.refIsMEDB.out

hyb_protocol: Aminosaline coated slides were prehybridized in 5x SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate) (Invitrogen), 0.1% sodium dodecyl sulfate, and 1% bovine serum albumin at 42 degree Celcius for 45 min. The slides then were washed at room temperature with distilled water, dipped in isopropanol, and spun dry. Equal concentrations of DNA probe from the appropriate Cy3 and Cy5 labeled probes were combined, dried and then resuspended in a solution of 35% formamide, 5x SSC, and 0.1% sodium dodecyl sulfate. Resuspended probes were denatured at 95 degree Celcius prior to hybridization. The probe mixture then was added to the microarray slide and allowed to hybridize overnight at 42 degree Celcius. Hybridized slides were washed sequentially in solutions of 1x SSC-0.2% SDS, 0.1x SSC-0.2% SDS, and 0.1x SSC at room temperature.

scan_protocol: Scanned on Axon GenePix 4000 scanner. PMT values were optimized during scanning to balance channel intensities.

data_processing:
Procedures to calculate the value of log2 ratio:
1. Use software suite TM4 (www.tm4.org) to analyze spotted arrays.
2. Use Spotfinder with background correction to compute the spot intensities of the hybridized arrays.
3. Perform the following filtering steps:
All PFGRC arrays used in this study have 3 types of spots.
(1). Species spot: oligos designed for the species under investigation.
(2). Reserved spot or control spot: oligos designed from Arabidopsis genes as controls.
(3). Empty spots: no oligos or any DNA.
Step 1: Identify the replicates.
Sort the .mev file from Spotfinder by oligo_id.
Step 2: Identify the outliers within each set of replicates for each channel.
Outliers are identified using the Sprents method (The Handbook of Parametric and Nonparametric Statistical Procedures, Third Edition by David J. Sheskin, PP 400-402).
|Xi - M|/MAD > Max
Xi = Each intensity value from the set of replicates.
M = Median intensity value from the set of replicates.
MAD = Median absolute deviation.
Max = the critical value that the result of the inequality must exceed in order to conclude that the Xi value is an outlier. The value of 5 was used for Max.
Step 3: Replace the outliers.
Replace the outliers by the value closest to them from the tail that they occur. For example, if the outlier identified is the highest value in channel A, that value will be replaced by the next highest value of its replicate set in channel A.
Step 4: Subtract the 95th percentile of the reserved spots.
Calculate the 95th percentile of all the reserved spots and subtract that value from all the species spots and reserved spots.
Step 5: Replace zero (0) by one (1).
After subtracting the 95th percentile of the reserved spots, if one of the channel intensities is less than zero (0), replace that value by one (1); If both channels become less than zero (0), set both channels to zero (0).
Step 6. Output the filtered .mev file.
4. Use Midas X for CGH normalization:
1). Plot the histogram of the Log2 ratio data (Reference/Query) from the filtered .mev file, and identify the central peak containing oligos predicted to be shared by both the reference and query strains.
2). Fit a Gaussian curve to the central peak by 'tweaking' the log ratio mean and by shrinking or stretching the standard deviation of the curve to find the smallest least sum of squares difference.
3). Perform Log Mode Centering normalization on the channel that contains the query sample only (Either Cy3 or Cy5).
4). Output the normalized *.mev file.
5. Calculate the value of log2 ratio (Reference/Query) from the normalized .mev file:
1). If both channels (QUERY_MEDIAN_INTENSITY and REF_MEDIAN_INTENSITY) are zero, assign the value "null".
2). If one channel is zero and the other is not zero, substitute the zero with one (1) and then, assign the log2 ratio of QUERY_MEDIAN_INTENSITY/REF_MEDIAN_INTENSITY to VALUE
3). If neither channel is zero, assign the log2 ratio of QUERY_MEDIAN_INTENSITY/REF_MEDIAN_INTENSITY to VALUE.

molecule: genomic DNA

organism: Bacillus cereus

label_protocol: 4ug of genomic DNA was labeled at 37 degree Celcius overnight using DNA polymerase I Klenow fragment (New England Biolabs), a 25X 2:1 amino allyl dUTP (Ambion) dNTP mix, and random hexamers (Invitrogen). Labeled DNA was purified with the Qiaquick PCR purification kit (QIAGEN). The purified labelled DNA was then dye coupled with the appropriate cyanine dye (Cy3/Cy5).

growth_protocol: Cells grown in Lysogeny broth (LB) at 37 degrees Celcius overnight.

extract_protocol: Epicentre MasterPure DNA Extraction Kit.

treatment_protocol: None.

tag: strain

organism: Bacillus anthracis str. Sterne

source_name: Sterne reference

value: Sterne


title: T3AQBC06092008A_3400_CY3_STERNE_CY5_13839222_B

description: T3AQBC06092008A_3400_CY3_STERNE_CY5_13839222_anno_sub_95th_MDS.mev.refIsMEDB.out


title: Ductal Breast Carcinoma A10

city: PARIS

first: Gaelle

last: PIERRON

address: 26, rue d'ULM

country: France

institute: INSTITUT CURIE

description: the same reference sample is used for all experiments

hyb_protocol: The aCGH slide was previously preblocked with a buffer containing 2.6mg succinic anhydride/118ml N-methyl-2-pyrrolidinone/32ml sodium tetraborate decahydrate, pH 8.0 (Sigma-Aldrich, Lyon, France).

scan_protocol: After washing, arrays were scanned using a 4000B scan (Axon, Union City, CA). Image analysis was performed first with Genepix software (Axon) (firstly with version 5.1 and then with the 6.0.1.27 when it was available)  and ratios of Cy5/Cy3 signals were determined.

data_processing: Background subtracted data obtained from log2 of processed Red signal/processed Green signa values generated by the MANOR algorithm  (Neuvial P. et al, 2006), and missing data were interpolated within each array.

organism: Homo sapiens

source_name: Tumoral DNA

label_protocol: After digestion with DPNII (Ozyme, Saint Quentin en Yvelines, France) and column purification (Qiaquick PCR purification kit; Qiagen, Courtaboeuf, France), tumor DNAs were labeled by the random priming method (Bioprime DNA labelling system; Invitrogen, Cergy-Pontoise, France) with cyanine-5 (Perkin-Elmer, Wellesley, MA). Using the same procedure, we labeled control DNAs with cyanine-3. After ethanol-coprecipitation with 210g of Human Cot-1 DNA (Invitrogen, Cergy-Pontoise, France), resuspension in hybridization buffer (50% formamide), denaturation at 95°C for 10 minutes and prehybridization at 37°C for 90 minutes, probes were cohybridized on aCGH.

extract_protocol: DNAs were extracted from frozen tumors using either the cesium chloride protocol (Chirgwin JM. Et al. 1979, Coombs LM. et al 1990) (for Samples A01 to A62 and B01 to B28) or a standard phenol-chlorofom procedure with separation of the aqueous and organic phases on Phase Lock GelTM following manufacturer’s instructions (for samples V01 to V91).

treatment_protocol: Samples of of primary infiltrating ductal breast carcinomas were flash frozen and stored at –80°C. All tumor samples contained >50% cancer cells

tag: gender

value: female

tag: age

tag: pn

value: I

value: P

value: N

value: no

tag: adjuvant hormonotherapy

tag: adjuvant chemotherapy

value: No event

tag: tumor cellularity

tag: set

value: training

tag: group

value: A

value: LR

source_name: Normal reference DNA

value: male


title: Ductal Breast Carcinoma A08


title: Ductal Breast Carcinoma A09


title: AR6_Rep2

type: RNA

city: Hangzhou

first: youying

last: mao

address: Yuhangtang Road,NO.388

country: China

institute: Zhejiang University

description: PBMC samples from renal transplants of stable renal function recipients, acute rejection, borderline change and acute tubule necrosis.

hyb_protocol: The hybridizations were performed overnight at 50C in a hybridization oven (Hybaid, Middlesex, UK). Subsequently, the nylon membranes were washed twice at 48C in 2xSSC and 0.1% SDS for 20 min.

scan_protocol: The signals of the array were absorbed by storage phosphor screen (Kodak, Rochester, New York, USA) for three days, and signal intensities were measured by scanning the storage phosphor screen with the Typhoon 9200 scanner (Amersham Pharmacia Biotech, Piscataway, NJ, USA).

data_processing: The signal intensity of each microarray spot on the array was quantified using the software ArrayVision6.0 (Imaging Research, Ontario, Canada). The normalization was performed by dividing a spot's signal intensity by the average signal intensity of the whole image (global normalization). Two individual hybridization experiments were performed for each probe, resulting in six replicated spots for each gene per sample.

molecule: total RNA

source_name: kidney

label_protocol: The RNA samples were labeled with 33P-dCTP during the first-strand reverse transcription reactions.

extract_protocol: Total RNA was isolated by TRIZol according to manufacturer's instruction. Contaminating genomic DNA was removed by treatment with RNase-free DNase (Promega, Madison, WI, USA). RNA quality was confirmed by electropherogram. RNA was further purified using Rneasy mini kit (Qiagen).

tag: tissue type

value: kidney

tag: state

value: acute rejection


title: AR7_Rep1


title: Ductal Breast Carcinoma A07

value: II


title: Ductal Breast Carcinoma A13

value: yes


title: Ductal Breast Carcinoma A06


title: AR6_Rep1


title: T3AQBC06092008A_3390_CY3_STERNE_CY5_13839179_B

description: T3AQBC06092008A_3390_CY3_STERNE_CY5_13839179_anno_sub_95th_MDS.mev.refIsMEDB.out


title: AR4_Rep2


title: AR5_Rep1


title: T3AQBC06092008A_3396_CY3_STERNE_CY5_13839173_B

description: T3AQBC06092008A_3396_CY3_STERNE_CY5_13839173_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3AQBC06092008A_3383_CY3_STERNE_CY5_13839171_B

description: T3AQBC06092008A_3383_CY3_STERNE_CY5_13839171_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3AQBC06092008A_3358_CY3_STERNE_CY5_13843678_B

description: T3AQBC06092008A_3358_CY3_STERNE_CY5_13843678_anno_sub_95th_MDS.mev.refIsMEDB.out


title: AR5_Rep2


title: Ductal Breast Carcinoma A05

value: HR


title: Ductal Breast Carcinoma A04


title: AR3_Rep2


title: AR4_Rep1


title: T3AQBC06092008A_3384_CY3_STERNE_CY5_13839172_B

description: T3AQBC06092008A_3384_CY3_STERNE_CY5_13839172_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3AQBC06092008A_3248_CY3_STERNE_CY5_13839185_B

description: T3AQBC06092008A_3248_CY3_STERNE_CY5_13839185_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3AQBC06092008A_3293_CY3_STERNE_CY5_13824596_B

description: T3AQBC06092008A_3293_CY3_STERNE_CY5_13824596_anno_sub_95th_MDS.mev.refIsMEDB.out


title: Ductal Breast Carcinoma A03


title: Ductal Breast Carcinoma A01

value: III


title: T3AQBC06092008A_3242_CY3_STERNE_CY5_13839184_B

description: T3AQBC06092008A_3242_CY3_STERNE_CY5_13839184_anno_sub_95th_MDS.mev.refIsMEDB.out

value: Sterne


title: AR3_Rep1


title: AR2_Rep2


title: T3AQBC06092008A_3159_CY3_STERNE_CY5_13839183_B

description: T3AQBC06092008A_3159_CY3_STERNE_CY5_13839183_anno_sub_95th_MDS.mev.refIsMEDB.out


title: Human macrophages, LPS vs N/T

status: Public on Nov 24 2009

type: other

city: Jerusalem

first: Hermona

last: Soreq

address: Safra Campus, Givat Ram

department: Department of Biological Chemistry

country: Israel

institute: The Hebrew University of Jerusalem

description: Dye-swapping tests served to exclude dye-specific labeling differences.

hyb_protocol: Labeled miRNA were added to the hybridization solution (3 SSC, 0.1% SDS, 10 μg  polyA, 20 μg  tRNA), heated at 95C for 4 min for eliminating secondary structures and applied to the slides in hybridization chambers (Corning, NY,USA) for 15h at 64C. Hybridized slides were successively washed in: 1XSSC, 0.1% SDS (5 min); 0.1XSSC, 0.1% SDS (5 min) and 0.1xSSC (3x1.5 min) and dried by centrifugation (~1000g).

scan_protocol: Affymetrix 428 Array Scanner was used  at the maximum  gain setting, at the wavelengths of 532nm and 650nm. Scans were controlled by the “Jaguar” software (Affymetrix, CA, USA), saved as TIFF files and exported to the “Imagene” program (Biodiscovery Inc, CA, USA)

data_processing: Analysis was performed using the Normalize Suite for Windows, V. 2.6 Beta, (c) Ben Beheshti 2001-2006; NORMALISATION TYPE: Simple, LOCAL (Sub arrays)

molecule: other

source_name: LPS

label_protocol: Labeling used the CyDye reactive dye pack (Amersham, NSW, Australia), as instructed.

extract_protocol: Total RNA containing a population of RNAs that are 200 bases and smaller was extracted from cells or tissue samples using the mirVana miRNA isolation kit (Ambion, Austin, TX). Short RNAs isolated by electrophoresis.

tag: cell type

value: macrophage

source_name: non-treated control


title: AR1_Rep1


title: Human macrophages, GpG vs N/T (dye swap)

description: Dye-swapping tests served to exclude dye-specific labeling differences. This slide is a dye-swap, the wavelengths in the processed data are reversed.

hyb_protocol: Labeled miRNA were added to the hybridization solution (3 SSC, 0.1% SDS, 10 μg polyA, 20 μg tRNA), heated at 95C for 4 min for eliminating secondary structures and applied to the slides in hybridization chambers (Corning, NY,USA) for 15h at 64C. Hybridized slides were successively washed in: 1XSSC, 0.1% SDS (5 min); 0.1XSSC, 0.1% SDS (5 min) and 0.1xSSC (3x1.5 min) and dried by centrifugation (~1000g).

scan_protocol: Affymetrix 428 Array Scanner was used at the maximum gain setting, at the wavelengths of 532nm and 650nm. Scans were controlled by the “Jaguar” software (Affymetrix, CA, USA), saved as TIFF files and exported to the “Imagene” program (Biodiscovery Inc, CA, USA)

source_name: CpG


title: AR1_Rep2


title: Human macrophages, LPS vs N/T (dye swap)

scan_protocol: Affymetrix 428 Array Scanner was used  at the maximum  gain setting, at the wavelengths of 532nm and 635nm. Scans were controlled by the “Jaguar” software (Affymetrix, CA, USA), saved as TIFF files and exported to the “Imagene” program (Biodiscovery Inc, CA, USA)


title: AR2_Rep1


title: Human macrophages, GpG vs N/T


title: T3AQBC06092008A_3390_CY5_STERNE_CY3_13824590_A

description: T3AQBC06092008A_3390_CY5_STERNE_CY3_13824590_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3AQBC06092008A_3248_CY5_STERNE_CY3_13824589_A

description: T3AQBC06092008A_3248_CY5_STERNE_CY3_13824589_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3AQBC06092008A_3161_CY3_STERNE_CY5_13839187_B

description: T3AQBC06092008A_3161_CY3_STERNE_CY5_13839187_anno_sub_95th_MDS.mev.refIsMEDB.out


title: nrpe1_rep3

city: Beaucouzé

first: Etienne

last: Bucher

address: 42 rue Georges Morel

institute: IRHS

description: nrpe1 mutant Arabidopsis RNA chip 3

hyb_protocol: Approximately 7.5 μg of fragmented cDNA was hybridized for 16 hours at 60 rpm

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

data_processing: Data was processed in R as described in Naouar et al. Quantitative RNA expression analysis with Affymetrix Tiling 1.0R arrays identifies new E2F target genes. Plant J (2009) vol. 57 (1) pp. 184-94.  Briefly, RMA was used for normalization, and the 'limma' and 'QValue' packages from Bioconductor were used for statistical analysis.

label: biotin

organism: Arabidopsis thaliana

source_name: Rosette leaves RNA

label_protocol: RNA (5-μg aliquots) was reverse transcribed using T7 oligo dT (Ambion) and Superscript II (Invitrogen) and the second strand synthesised using DNA polymerase I. cDNA was then amplified using IVT (Affymetrix). The resulting cRNA was purified with the GeneChip Sample Cleanup Module (Affymetrix). cRNA (7-μg aliquots) was then reverse transcribed and made double-stranded in the presence of dUTP. Following cleanup (Qiagen kit), the cDNA was fragmented and labeled using the Affymetrix kit 900812 GeneChip® WT Double Stranded DNA Terminal Labeling Kit.

growth_protocol: Plants were grown under standard growth condition with 16 hours of light (long day).

extract_protocol: RNA was extracted using the Ambion miRVANA RNA isolation kit.

value: 17 days

tag: tissue

value: rosette leaves

tag: genome/variation

value: nrpe1 mutant


title: T3AQBC06092008A_3293_CY5_STERNE_CY3_13824588_A

description: T3AQBC06092008A_3293_CY5_STERNE_CY3_13824588_anno_sub_95th_MDS.mev.refIsMEDA.out


title: mom1_nrpe1_rep2

description: mom1 nrpe1 double mutant Arabidopsis RNA chip 2

value: mom/nrpe1 double mutant


title: mom1_nrpe1_rep1

description: mom1 nrpe1 double mutant Arabidopsis RNA chip 1


title: mom1_rep3

description: mom1 mutant Arabidopsis RNA chip 3

value: mom1 mutant


title: nrpe1_rep1

description: nrpe1 mutant Arabidopsis RNA chip 1


title: mom1_nrpe1_rep3

description: mom1 nrpe1 double mutant Arabidopsis RNA chip 3


title: nrpe1_rep2

description: nrpe1 mutant Arabidopsis RNA chip 2


title: mom1_rep2

description: mom1 mutant Arabidopsis RNA chip 2


title: mom1_rep1

description: mom1 mutant Arabidopsis RNA chip 1


title: MLL Interphase

city: Cold Spring Harbor

first: Christopher

last: Vakoc

state: NY

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

description: MLL Interphase

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.

source_name: anti MLL ChIP from HeLa cells arrested in Interphase

label_protocol: 1 µg ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers (ChIP DNA isolated from normal rabbit IgG-immunoprecipitated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: Cells grown in DMEM 10% FBS

extract_protocol: Cells were crosslinked on tissue culture plates following replacement of growth medium with 1X PBS (25 mls for 15 cm plate). For suspension cells, cells were centrifuged (500g) and resuspended in 1X PBS. Formaldehyde was added to a final concentration of 1% and incubated for 10 min at room temperature with mixing. Crosslinking was quenched by adding glycine to a final concentration of 0.125 M. Crosslinked cells were centrifuged (900g), resuspended in 1 ml 1X PBS, and transferred to 1.6 ml eppendorf tube and centrifuged. Cells were then resuspended in 1 ml cell lysis buffer (10 mM Tris pH 8.0, 10 mM NaCl, 0.2% NP-40) and incubated on ice for 15 minutes. Cells were centrifuged (900g) and resuspended in 1 ml nuclear lysis buffer (50 mM Tris pH 8.1, 10 mM EDTA, 1% SDS). 0.6 ml of IP dilution buffer (20 mM Tris pH 8.1, 2 mM EDTA, 150 mM NaCl, 1% Triton X-100, 0.01% SDS) was added and the chromatin sample was transferred to a 14 ml polypropylene round-bottom tube (Falcon). Sonication was performed on ice with a Misonix 3000: 3 minutes total time, 1 second ON, 1 second OFF, Output level setting 3.0. Sonicated chromatin was transferred to 1.6 ml eppendorf tube centrifuged (16,000g) and supernatant was transferred to 3.4 mls IP dilution buffer. Chromatin samples were pre-cleared for 2 hours with 50 ul Protein G beads (50:50 mixture) with 50 microgram control IgG. During this time, IP antibodies (5 micrograms) were pre-bound to 35 ul Protein G beads in 1 ml 1X PBS for 2 hours. Pre-bound antibodies were centrifuged (5000g) and supernatant discarded. Pre-cleared chromatin was centrifuged (5000g) and supernatant transferred to a new tube. 180 ul of input material (3.6%) was set aside. 1.25 ml of chromatin was then transferred to pre-bound antibodies (corresponding to chromatin from 5x106 cells) and incubated 2 hours or overnight. Beads were then washed once with 1 ml IP wash 1 (20 mM Tris pH 8.1, 2 mM EDTA, 50 mM NaCl, 1% Triton X-100, 0.1% SDS), twice with high salt wash buffer (20 mM Tris pH 8.1, 2 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.01% SDS), once  with IP wash 2 (10 mM Tris pH 8.1, 1 mM EDTA, 0.25M LiCl, 1% NP-40, 1% deoxycholic acid), and twice with TE. Chromatin was then eluted twice with 100 ul elution buffer (100 mM sodium bicarbonate, 1% SDS). 2 ug of RNase A and 12 ul of 5 M NaCl were added to the 200 ul elution and also to input sample, mixed, and incubated overnight at 65 degrees to reverse crosslinks. The next day, 60 micrograms of Proteinase K were added and incubated at 42 degrees for 2 hours. Samples were then diluted with TE to a final volume of 400 microliters. Samples were phenol:chloroform:IAA extracted (twice for input) then chloroform extracted. 10 micrograms of glycogen were then added followed ethanol precipitation. Pellets were then washed with 70% ethanol, dried on 70 degree heat block, then resuspended in deionized water (60 microliters for IP, 120 microliters for input).

treatment_protocol: Double thymidine block

tag: cell stage

tag: chip antibody

value: anti MLL

source_name: IP DNA from Interphase-arrest HeLa

tag: reference

value: input, HeLa_Interphase


title: Pol2 Mitosis

description: Pol2 Mitosis

source_name: anti Pol2 ChIP from HeLa cells arrested in Mitosis

treatment_protocol: thymidine-nocodazole block

value: anti pol2

source_name: IP DNA from Mitosis arrest HeLa

value: input, HeLa_Mitosis


title: miRNA profiling from frozen livers, T60 minutes

city: Heidelberg

first: Mirco

last: Castoldi

address: Im Neuenheimer Feld 156

department: Department of Pediatric Oncology, Hematology and Immunology

country: Germany

institute: University of Heidelberg

description: Evaluation of the effect of RNA degradation on miRNA expression profiling

hyb_protocol: For each sample a microarray chamber with a microarray gasket slide (Agilent technologies, cat. G2534-60005) was prepared and labeled samples are sandwiched between the microarray gasket slide and the printed arrays. The secured holders were placed into the hybridization oven (Agilent technologies, cat. G2545A), and hybridization is carried out for at least 16 h with a rotating speed of four using a hybridization temperature of 54 °C. After hybridization, arrays were washed. Microarray chambers are removed one by one from the hybridization oven. Microarray chambers are opened and the gasket slide-array sandwiches are submerged in washing buffer 1 (W1; 2 x SSC, 0.1%SDS, at room temperature), and separated using forceps. Subsequently, hybridized arrays were stored in W1 (room temperature) until all arrays have been removed from the oven and separated from the microarray gasket slides. Successively, arrays were transferred into fresh W1 (room temperature) and washed on a rocking shaker for 10 min. Then, arrays were washed once in washing buffer 2 (W2, 0.2 x SSC, at room temperature) and washing buffer 3 (W3, 0.1 x SSC, at room temperature), each time for 10 min, and once in W3 for 5 min (all washes are performed at room temperature on a shaker). Finally, arrays are rinsed in double-distilled water (room temperature) and dried by centrifugation at 1500 rpm for 2 min at room temperature.

scan_protocol: Slides were scanned using a GenePix 4200AL microarray scanner (Axon instruments). Microarray images are analyzed using Genepix Pro 6.0 software (Axon instruments).

data_processing: Array images were generated by using the Genepix 4200AL laser scanner (Auto Loader, Axon Instruments). For this purpose, miChip arrays are scanned in batches using the Genepix auto PMT (Photo Multiplayer) algorithm, with pixel saturation tolerance set to 1% following the supplier’s protocol. The tiff images generated by the Genepix 4200AL scanner were loaded into Genepix 6 microarray analysis software. Artifact-associated spots were removed by both software- and visual-guided flags. Genepix measures signal intensities according to the local background subtraction method as a function of the median of foreground pixels minus median of background pixels. miChip data analysis was performed by one of the following options: (A) using Genespring GX software (Agilent Technologies)for both data normalization and clustering or (B) using Bioconductor running the miCHIP library (v 0.5.3) for data normalization in combination with the TMeV tool for data clustering.

organism: Mus musculus

source_name: Livers from C57Bl/6 mice, T60 minutes

label_protocol:
Labeling of total RNA for miChip v8.0 (Mouse) hybridizations has been described in detail before (Castoldi M et al., Nature Protocol, miChip: an array-based method for microRNA expression profiling using locked nucleic acid capture probes, 2008)
1 µg of total RNA was aliquoted in a volume of 10 µl of RNase free water and placed on ice. To minimize variability a labeling master mix was prepared that contains 1 x T4 RNA ligase buffer (Ambion), ATP (1.3 mM, final concentration), RNase inhibitors (20 U, final amount), RNA ligase (10 U, final amount), Cy3 labeled RNA linker (5´-p-rUrUrUrU-Cy3-3´, Biospring; 6.67 µM, final concentration) and PEG (15.5%, final concentration) per reaction. 20 µl of the labeling master mix was added to the 5 µg of total RNA to yield a final volume of 30 µl. The reaction mix was then incubated for 12–16 h at 4°C. T4 RNA ligase and RNase inhibitor were heat denatured for 5 min at 95 °C and the reaction is briefly spun to collect the condensate at the bottom of the tube. Samples were stored on ice until further use. 70 µl of precipitation master mix containing sodium acetate (300 mM, final concentration) and linear acrylamide (2.5 µg, final amount) per reaction was added to each sample. To precipitate the RNA, 300 µl of 100% ethanol were added to each sample and then samples are incubated for at least one hour at -80 °C. Samples are spun for 30 min at 20,000g, 4 °C. The supernatant was discarded and pellets were washed with 1 ml of 75% ethanol and centrifuged for 5 min at 13,000 rpm at room temperature. Pellets are then briefly air-dried at room temperature. Subsequently, pellets were dissolved in 440 µl of hybridization buffer [5 x SSC, 0.1% SDS, 25% formamide and 100 µg/ml of herring sperm DNA (Promega, D181B)], denatured for 5 min at 95 °C, and centrifuged for 5 min at 13,000 rpm at room temperature.

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen, Paisley, Scotland) according to the manufacturer´s instructions. RNA quality was controlled using the RNA 6000 Pico LabChip kit (Agilent, Waldbronn, Germany) and quantified with a NanoDrop ND-1000 Spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).

treatment_protocol: Wild type female mice of the C57BL/6J genetic background were used for this experiment. Mice were housed in the EMBL animal facility under a constant light-dark cycle, maintained on a standard mouse diet, and allowed ad libitum access to food and water. Mice were euthanized by CO2 inhalation and livers were immediately harvested, snap-frozen in liquid nitrogen and stored in the -80˚C for more than 12 months. In order to obtain RNA of different quality frozen tissues were cut in five fragments of similar size, placed into individual eppendorf tubes and stored in dry ice. At time point, zero (T0) samples were moved into ice and at different time points 1 ml of Trizol (Invitrogen) was added to the sample (time 0 to time 240). Tissues were immediately disrupted by using mechanical shearing (Tissuelyzer, Quiagen) and RNA was extracted following vendor instruction.

value: liver

tag: strain


title: miRNA profiling from frozen livers, T240 minutes

source_name: Livers from C57Bl/6 mice, T240 minutes


title: MLL Mitosis

description: MLL Mitosis

source_name: anti MLL ChIP from HeLa cells arrested in Mitosis


title: miRNA profiling from frozen livers, T120 minutes

source_name: Livers from C57Bl/6 mice, T120 minutes


title: miRNA profiling from frozen livers, T30 minutes

source_name: Livers from C57Bl/6 mice,  T30 minutes


title: miRNA profiling from frozen livers, T0 replica B

source_name: Livers from C57Bl/6 mice, T0 replica B


title: wt_rep1

description: wt Arabidopsis RNA chip 1

growth_protocol: Plants were grown under standard growth condition with 16 hours of light (long day)..

value: wild type


title: wt_rep2

description: wt Arabidopsis RNA chip 2


title: wt_rep3

description: wt Arabidopsis RNA chip 3


title: miRNA profiling from frozen livers, T0, replica A

source_name: Livers from C57Bl/6 mice, T0 replica A


title: miRNA profiling from frozen duodenums, T240 minutes

source_name: Duodenum from C57Bl/6 mice,  T240 minutes

treatment_protocol: Wild type female mice of the C57BL/6J genetic background were used for this experiment. Mice were housed in the EMBL animal facility under a constant light-dark cycle, maintained on a standard mouse diet, and allowed ad libitum access to food and water. Mice were euthanized by CO2 inhalation, duodenums were immediately harvested, snap-frozen in liquid nitrogen and stored in the -80˚C for more than 12 months. In order to obtain RNA of different quality frozen tissues were cut in five fragments of similar size, placed into individual eppendorf tubes and stored in dry ice. At time point, zero (T0) samples were moved into ice and at different time points 1 ml of Trizol (Invitrogen) was added to the sample (time 0 to time 240). Tissues were immediately disrupted by using mechanical shearing (Tissuelyzer, Quiagen) and RNA was extracted following vendor instruction.

value: duodenum


title: Hela_siZNF263_2

city: Davis

first: Seth

middle: Eric

last: Frietze

state: CA

address: 451 Health Sciences Dr. GBSF 4617A

department: Genome Center

institute: UC Davis

description:
experiment replicate 2
4763734020_B

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Beadstudio

source_name: HelaS3 cells

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

growth_protocol: HelaS3 cells were grown in a 150 mm dish containing DMEM + 5% calf serum to a confluency of ~70%.

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.

treatment_protocol: Cells were transfected with 20nM siRNA duplex using lipofectamine2000.

tag: sirna treatment


title: Hela_siCONTROL_3

description:
control replicate 3
4763734020_F

value: CONTROL


title: Hela_siCONTROL_1

description:
control replicate 1
4763734020_D


title: Hela_siZNF263_3

description:
experiment replicate 3
4763734020_C


title: Pol2 Interphase

description: Pol2 Interphase

source_name: anti Pol2 ChIP from HeLa cells arrested in Interphase


title: Hela_siZNF263_1

description:
experiment replicate 1
4763734020_A


title: miRNA profiling from frozen duodenums, T120 minutes

source_name: Duodenum from C57Bl/6 mice, T120 minutes


title: Hela_siCONTROL_2

description:
control replicate 2
4763734020_E


title: Lung_infected_necrotic-area_Animal-25

city: Tjele

first: Jakob

last: Hedegaard

address: PO-box 50

department: Department of Genetics and Biotechnology

country: Denmark

institute: Aarhus University, Faculty of Agricultural Sciences

description: Expression profiles of porcine lung tissues were studied to inditify genes beeing significantly affected at various sites in bacterially infected porcine lungs as opposed to not infected porcine lungs. Samples was taken from three different sites of the lung in pigs experimentally infected with A. pleuropneumoniae, serotype 5b, these were; 1. Necrotic area, samples were taken from within the pulmonary lesion, 2. Demarcation zone, samples were taken from the suburb area of the pulmonary lesion, and, 3. Visually unaffected area, samples were taken either from the visually unaffected lung lobules, if there is one, or as far away from the pulmonary lesion in an affected lung. Samples of lung tissue were furthermore sampled from healthy non-inoculated control pigs from the same heard. Samples were investigated for changes in gene expression by means of quantitative real-time PCR and global cDNA microarrays.

hyb_protocol: The slides were hybridized in a Discovery XT hybridization station (Ventana Discovery Systems, Tucson, AZ, USA). Transfer Chip Prep-2 from 4 ºC to room temperature 1 hour before use. Prepare ChipSpread by mixing equal volumes of ChipSpread A (20 mg/mL BSA, 4x SSC, 0.5 mg/mL sodium azide) and B (formamide; 2 mg/mL SDS) and incubate at room temperature for 1 hour before use. A total of 2.5 mL is needed per slide. Print labels, trim them and place them on the slides. Mix the Chip Map reagents (Chip Prep-1, -2 and - 3) by inversion, remove the cap and place the reagents in the Discovery. Place the slides in the machine and initiate the run. Cover slide with 2.5 mL ChipSpread when the message appears (after few minutes). The machine now runs for app. 1.5 hours to pre-hybridize the slides. Heat a waterbath to 90°C or use a PCR machine. Mix the Chiphybe80, add 200 µL to the sample (<20 µL) and mix carefully. Heat the sample mixture at 90°C for 3 minutes and mix carefully by pipetting. Press the button on the machine which then prepares the slides for hybridization. When the message appears apply the samples onto the slides and press the button and the machine hybridizes at 48 ºC for 6 hours. Wipe oil from backside of slides using a clean-room napkin and place slides in the slide-holder from the High Throughput Wash Station (Telechem, cat.no. HTW) placed in a mTub filled with RiboWash. If processing more than 20 slides, place equal number of slides in two slide-holders and continue in parallel. Transfer the slide-holder to a HTW filled with RiboWash and wash for 2 min with magnetic stirring at 700 rpm. Refill the HTW with RiboWash and repeat the wash. Dip the slide-holder in 2x SSC filled in a mTub (200 mL 20x SSC, Elga H2O + 1800 mL water). Transfer the slide-holder to a HTW filled with 2x SSC and wash for 2 min with magnetic stirring at 700 rpm. Refill the HTW with 2x SSC and repeat the wash. Dip the slide-holder 10 times in 0.1x SSC filled in a mTub (5 mL 20x SSC, Elga H2O + 995 mL water) and leave the holder submerged in 0.1x SSC. Transfer the slides to a mBox slide holder placed in a mTub filled with Elga H2O. Dry arrays by centrifugation (at 300 x g for 4 min placed in a mBox).

scan_protocol: Scanner: ScanArray Express HT system (Perkin Elmer), 5 µm resolution, 100 % laser power and PMT adjusted individually for each channel. Image analysis software: GenePix Pro (version 6.0.1.27, Molecular Devices) using FeatureType = Irregular Filled and MorphologicalClosingFollowedByOpening as background measurement.

data_processing: Statistical analysis was carried out in the R computing environment (version 2.6.1 for Windows) using the package Linear Models for Microarray Analysis (Limma, version 2.12.0) which is part of the Bioconductor project. Control spots and spots with more than 50 % of saturated pixels were weighted 0 before the log2-transformed ratios of Alexa-555 to Alexa-647 (not background corrected) were normalized within-slide using global-loess with default parameters as implemented in Limma. The set of normalized log-ratios were analyzed in Limma to identify genes being significantly differentially expressed between lungs of uninfected control animals and the three different regions sampled from lungs of infected animals (unaffected areas, the demarcation zone, and necrotic areas). The false discovery rate was controlled using the method of Benjamini and Hochberg as implemented in Limma and a corrected P-value below 0.01 was considered significant.

organism: Sus scrofa

extract_protocol: RNeasy Midi Kit with DNase treatment following the enclosed protocol (Qiagen)

treatment_protocol: Pigs assigned as healthy non-inoculated control animals were killed and sampled prior to inoculation of the infected group. Samples of approximately 500 mg tissue were taken from the lungs, snap frozen in liquid nitrogen and stored at minus 80 degrees until further use. Pigs assigned as infected animals, were inoculated with Actinobacillus pleuropneumoniae 5b (strain L20) by dripping 1 ml bacterial suspension, (McFarland 0.5, mixed 1:1 with Brain Heart Infusion + 0.1 % NAD) containing approximately 0.7 x107 CFU, in each nostril during inhalation. Culture of bacteria as well as inoculation procedures has previously been described by (Kristensen et al., Vet. Microbiol. 98, 243-249, 2004). Animals were killed 14 – 18 hours post inoculation by means of captive bolt pistol followed by pitching and exsanguinations. All animal procedures were approved by the Danish Animal Experiments Inspectorate. Immediately after killing, lungs were inspected for sizes and numbers of pulmonary lesions. To verify the infection, samples from lung, liver, tonsil and spleen were cultivated on PPLO agar (BD, Brøndby, Denmark) to re-isolate the inoculation strain, which hereafter was serotyped using latex agglutination (Giese et al., Acta. Vet. Scand. 34, 223-225, 1993). From the lungs of infected animals, samples of approximately 500 mg tissue were taken from three different sites, 1. necrotic area, within the pulmonary lesion, 2. demarcation zone, surrounding area to the pulmonary lesion, and 3. visually unaffected area, as far away from the pulmonary lesions as possible. Samples were snap frozen in liquid nitrogen and stored at minus 80 degrees until further use.

tag: Breed

value: Danish Landrace/Yorkshire/Duroc cross, Herd:high health free from A. pleuropneumoniae, Gender:castrated males, Age:8-10 weeks, Treatment:AP serotype 5b infected, Sample:Lung_infected_necrotic-area, Animal:25

source_name: Reference, pool of equal amount of total-RNA from all samples

label_protocol: 20 µg total RNA was labelled by using the Superscript Direct cDNA Labeling System (Invitrogen) following the enclosed protocols. Spike-in RNA from the Lucidea Universal ScoreCard (Amersham Biosciences) was added to the labelling reactions. Green spike-in RNA was added to the common reference samples and red spike-in RNA was added to the samples. The fluorescently labelled cDNA was purified using the NucleoSpin 96 Extract II PCR Clean-up kit (Macherey-Nagel, Düren, Germany). The labelled reference samples were mixed and divided into aliquots before combining it with a labelled sample.

value: Danish Landrace/Yorkshire/Duroc cross, Herd:high health free from A. pleuropneumoniae, Gender:castrated males, Age:8-10 weeks, Reference, pool of equal amount of total-RNA from all lung samples in experiment


title: miRNA profiling from frozen duodenums, T30 minutes

source_name: Duodenum from C57Bl/6 mice, T30 minutes


title: miRNA profiling from frozen duodenums, T60 minutes

source_name: Duodenum from C57Bl/6 mice, T60 minutes


title: miRNA profiling from frozen duodenums, Time 0 replica A

description: Evaluation of the effect of RNA degradation on miRNA expression profiling.

source_name: Duodenum from C57Bl/6 mice, T0 replica A


title: Lung_infected_demarcation-zone_Animal-34

label_protocol: 20 µg total RNA was labelled by using the Superscript Direct cDNA Labeling System (Invitrogen) following the enclosed protocols. Spike-in RNA from the Lucidea Universal ScoreCard (Amersham Biosciences) was added to the labelling reactions. Green spike-in RNA was added to the common reference samples and red spike-in RNA was added to the samples. The fluorescently labelled cDNA was purified using the NucleoSpin 96 Extract II PCR Clean-up kit (Macherey-Nagel, Düren, Germany).

value: Danish Landrace/Yorkshire/Duroc cross, Herd:high health free from A. pleuropneumoniae, Gender:castrated males, Age:8-10 weeks, Treatment:AP serotype 5b infected, Sample:Lung_infected_demarcation-zone, Animal:34


title: miRNA profiling from frozen duodenums, Time 0 replica B

source_name: Duodenum from C57Bl/6 mice, T0 replica B


title: Lung_infected_necrotic-area_Animal-31

value: Danish Landrace/Yorkshire/Duroc cross, Herd:high health free from A. pleuropneumoniae, Gender:castrated males, Age:8-10 weeks, Treatment:AP serotype 5b infected, Sample:Lung_infected_necrotic-area, Animal:31


title: Lung_infected_visually-unaffected-area_Animal-31

value: Danish Landrace/Yorkshire/Duroc cross, Herd:high health free from A. pleuropneumoniae, Gender:castrated males, Age:8-10 weeks, Treatment:AP serotype 5b infected, Sample:Lung_infected_visually-unaffected-area, Animal:31


title: Lung_infected_visually-unaffected-area_Animal-34

value: Danish Landrace/Yorkshire/Duroc cross, Herd:high health free from A. pleuropneumoniae, Gender:castrated males, Age:8-10 weeks, Treatment:AP serotype 5b infected, Sample:Lung_infected_visually-unaffected-area, Animal:34


title: Lung_infected_demarcation-zone_Animal-25

value: Danish Landrace/Yorkshire/Duroc cross, Herd:high health free from A. pleuropneumoniae, Gender:castrated males, Age:8-10 weeks, Treatment:AP serotype 5b infected, Sample:Lung_infected_demarcation-zone, Animal:25


title: Lung_infected_visually-unaffected-area_Animal-26

value: Danish Landrace/Yorkshire/Duroc cross, Herd:high health free from A. pleuropneumoniae, Gender:castrated males, Age:8-10 weeks, Treatment:AP serotype 5b infected, Sample:Lung_infected_visually-unaffected-area, Animal:26


title: Lung_infected_necrotic-area_Animal-30

value: Danish Landrace/Yorkshire/Duroc cross, Herd:high health free from A. pleuropneumoniae, Gender:castrated males, Age:8-10 weeks, Treatment:AP serotype 5b infected, Sample:Lung_infected_necrotic-area, Animal:30


title: Lung_infected_necrotic-area_Animal-36

value: Danish Landrace/Yorkshire/Duroc cross, Herd:high health free from A. pleuropneumoniae, Gender:castrated males, Age:8-10 weeks, Treatment:AP serotype 5b infected, Sample:Lung_infected_necrotic-area, Animal:36


title: Lung_infected_visually-unaffected-area_Animal-28

value: Danish Landrace/Yorkshire/Duroc cross, Herd:high health free from A. pleuropneumoniae, Gender:castrated males, Age:8-10 weeks, Treatment:AP serotype 5b infected, Sample:Lung_infected_visually-unaffected-area, Animal:28


title: Lung_healthy_control_Animal-22

value: Danish Landrace/Yorkshire/Duroc cross, Herd:high health free from A. pleuropneumoniae, Gender:castrated males, Age:8-10 weeks, Treatment:healthy control, Sample:Lung_healthy_control, Animal:22


title: Lung_infected_demarcation-zone_Animal-32

value: Danish Landrace/Yorkshire/Duroc cross, Herd:high health free from A. pleuropneumoniae, Gender:castrated males, Age:8-10 weeks, Treatment:AP serotype 5b infected, Sample:Lung_infected_demarcation-zone, Animal:32


title: Lung_infected_demarcation-zone_Animal-27

value: Danish Landrace/Yorkshire/Duroc cross, Herd:high health free from A. pleuropneumoniae, Gender:castrated males, Age:8-10 weeks, Treatment:AP serotype 5b infected, Sample:Lung_infected_demarcation-zone, Animal:27


title: Lung_infected_necrotic-area_Animal-34

value: Danish Landrace/Yorkshire/Duroc cross, Herd:high health free from A. pleuropneumoniae, Gender:castrated males, Age:8-10 weeks, Treatment:AP serotype 5b infected, Sample:Lung_infected_necrotic-area, Animal:34


title: Lung_infected_visually-unaffected-area_Animal-30

value: Danish Landrace/Yorkshire/Duroc cross, Herd:high health free from A. pleuropneumoniae, Gender:castrated males, Age:8-10 weeks, Treatment:AP serotype 5b infected, Sample:Lung_infected_visually-unaffected-area, Animal:30


title: Lung_infected_demarcation-zone_Animal-33

value: Danish Landrace/Yorkshire/Duroc cross, Herd:high health free from A. pleuropneumoniae, Gender:castrated males, Age:8-10 weeks, Treatment:AP serotype 5b infected, Sample:Lung_infected_demarcation-zone, Animal:33


title: Lung_infected_demarcation-zone_Animal-31

value: Danish Landrace/Yorkshire/Duroc cross, Herd:high health free from A. pleuropneumoniae, Gender:castrated males, Age:8-10 weeks, Treatment:AP serotype 5b infected, Sample:Lung_infected_demarcation-zone, Animal:31


title: Lung_infected_necrotic-area_Animal-27

value: Danish Landrace/Yorkshire/Duroc cross, Herd:high health free from A. pleuropneumoniae, Gender:castrated males, Age:8-10 weeks, Treatment:AP serotype 5b infected, Sample:Lung_infected_necrotic-area, Animal:27

value: Danish Landrace/Yorkshire/Duroc cross, Herd:high health free from A. pleuropneumoniae, Gender:castrated males, Age:8-10 weeks, Reference, pool of equal amount of total-RNA from all lung samples in experiment


title: Lung_infected_visually-unaffected-area_Animal-25

value: Danish Landrace/Yorkshire/Duroc cross, Herd:high health free from A. pleuropneumoniae, Gender:castrated males, Age:8-10 weeks, Treatment:AP serotype 5b infected, Sample:Lung_infected_visually-unaffected-area, Animal:25


title: Lung_healthy_control_Animal-24

value: Danish Landrace/Yorkshire/Duroc cross, Herd:high health free from A. pleuropneumoniae, Gender:castrated males, Age:8-10 weeks, Treatment:healthy control, Sample:Lung_healthy_control, Animal:24


title: Lung_infected_necrotic-area_Animal-33

value: Danish Landrace/Yorkshire/Duroc cross, Herd:high health free from A. pleuropneumoniae, Gender:castrated males, Age:8-10 weeks, Treatment:AP serotype 5b infected, Sample:Lung_infected_necrotic-area, Animal:33


title: Lung_infected_demarcation-zone_Animal-28

value: Danish Landrace/Yorkshire/Duroc cross, Herd:high health free from A. pleuropneumoniae, Gender:castrated males, Age:8-10 weeks, Treatment:AP serotype 5b infected, Sample:Lung_infected_demarcation-zone, Animal:28


title: Lung_healthy_control_Animal-21

value: Danish Landrace/Yorkshire/Duroc cross, Herd:high health free from A. pleuropneumoniae, Gender:castrated males, Age:8-10 weeks, Treatment:healthy control, Sample:Lung_healthy_control, Animal:21


title: Lung_infected_visually-unaffected-area_Animal-32

value: Danish Landrace/Yorkshire/Duroc cross, Herd:high health free from A. pleuropneumoniae, Gender:castrated males, Age:8-10 weeks, Treatment:AP serotype 5b infected, Sample:Lung_infected_visually-unaffected-area, Animal:32


title: Lung_infected_visually-unaffected-area_Animal-27

value: Danish Landrace/Yorkshire/Duroc cross, Herd:high health free from A. pleuropneumoniae, Gender:castrated males, Age:8-10 weeks, Treatment:AP serotype 5b infected, Sample:Lung_infected_visually-unaffected-area, Animal:27


title: Lung_infected_necrotic-area_Animal-26

value: Danish Landrace/Yorkshire/Duroc cross, Herd:high health free from A. pleuropneumoniae, Gender:castrated males, Age:8-10 weeks, Treatment:AP serotype 5b infected, Sample:Lung_infected_necrotic-area, Animal:26


title: Lung_infected_demarcation-zone_Animal-26

value: Danish Landrace/Yorkshire/Duroc cross, Herd:high health free from A. pleuropneumoniae, Gender:castrated males, Age:8-10 weeks, Treatment:AP serotype 5b infected, Sample:Lung_infected_demarcation-zone, Animal:26


title: Lung_infected_necrotic-area_Animal-28

value: Danish Landrace/Yorkshire/Duroc cross, Herd:high health free from A. pleuropneumoniae, Gender:castrated males, Age:8-10 weeks, Treatment:AP serotype 5b infected, Sample:Lung_infected_necrotic-area, Animal:28


title: Lung_infected_visually-unaffected-area_Animal-33

value: Danish Landrace/Yorkshire/Duroc cross, Herd:high health free from A. pleuropneumoniae, Gender:castrated males, Age:8-10 weeks, Treatment:AP serotype 5b infected, Sample:Lung_infected_visually-unaffected-area, Animal:33


title: Lung_infected_demarcation-zone_Animal-36

value: Danish Landrace/Yorkshire/Duroc cross, Herd:high health free from A. pleuropneumoniae, Gender:castrated males, Age:8-10 weeks, Treatment:AP serotype 5b infected, Sample:Lung_infected_demarcation-zone, Animal:36


title: Lung_infected_necrotic-area_Animal-32

value: Danish Landrace/Yorkshire/Duroc cross, Herd:high health free from A. pleuropneumoniae, Gender:castrated males, Age:8-10 weeks, Treatment:AP serotype 5b infected, Sample:Lung_infected_necrotic-area, Animal:32


title: Lung_healthy_control_Animal-20

value: Danish Landrace/Yorkshire/Duroc cross, Herd:high health free from A. pleuropneumoniae, Gender:castrated males, Age:8-10 weeks, Treatment:healthy control, Sample:Lung_healthy_control, Animal:20


title: TG1/pMMB206-TOM-Green/pBS(Kan)-EchA F108L/I219L/C248I, cis-DCE

city: College Station

first: Jintae

last: Lee

state: TX

department: Chemical Engineering

institute: Texas A&M University

hyb_protocol: The biotin-labeled target was hybridized to the Affymetrix GeneChip E. coli array at 45C for 16 hour at 60 rpm using the Hybridization Oven 640 (Affymetrix), then a three-step fluorescent staining was conducted using the Fluidics Station 450 (Affymetrix) during the washing and staining procedure.

scan_protocol: The microarray was scanned at 570 nm to get an image file by the GeneChip Scanner 3000 (Affymetrix).  Using GeneChip® Operating Software, total cell intensity was scaled automatically in the software to an average value of 500.

data_processing: MAS 5.0 Expression Analysis Default Setting

organism: Escherichia coli

label_protocol: The total RNA samples were first converted into cDNA through a reverse transcription reaction with poly-A RNA controls spiked into the same reaction mixture to monitor the entire target labeling process.  The cDNA was then digested with DNase I (Amersham Biosciences) to produce 50-200 bp fragments, which was checked by running the fragmented cDNA on a 2% agarose gel.  The fragmented cDNA was labeled at the 3’ termini by the Enzo BioArray Terminal Labeling Kit with Biotin-ddUTP (Affymetrix, P/N 900181).

extract_protocol: To lyse the cells, 1.0 mL RLT buffer (Qiagen, Inc., Valencia, CA) and 0.2 mL 0.1 mm zirconia/silica beads (Biospec) were added to the frozen bead beater tubes containing the cell pellets. The tubes were closed tightly and beat for 50 seconds at the maximum speed in a mini bead beater (cat. no. 3110BX, Biospec). The total RNA was isolated by following the protocol of the RNeasy Mini Kit (Qiagen) including an on-column DNase digestion with RNase-free DNase I (Qiagen).

tag: RNA extracted from cells of TG1/pMMB206-TOM-Green/pBS(Kan)-EchA F108L/I219L/C248I after contacting for 2 h with cis-DCE (1 mM) in Tris-HNO3 buffer with succinate (5 mM), IPTG (0.5 mM) at 37oC


title: Lung_healthy_control_Animal-23

value: Danish Landrace/Yorkshire/Duroc cross, Herd:high health free from A. pleuropneumoniae, Gender:castrated males, Age:8-10 weeks, Treatment:healthy control, Sample:Lung_healthy_control, Animal:23


title: Lung_infected_demarcation-zone_Animal-30

value: Danish Landrace/Yorkshire/Duroc cross, Herd:high health free from A. pleuropneumoniae, Gender:castrated males, Age:8-10 weeks, Treatment:AP serotype 5b infected, Sample:Lung_infected_demarcation-zone, Animal:30


title: WT3

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

description: wildtype , larval stage L4, independent replicate 3

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip C. elegans Genome 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: C. elegans GeneChip arrays were analyzed by using affymetrix power tools (command line arguments apt-probeset-summarize -a rma-sketch -a plier-mm-sketch -d Celegans.CDF)

organism: Caenorhabditis elegans

source_name: wildtype , larval stage L4

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from ~5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Synchronized worms were cultured at 25C on standard agar plates seeded with OP50 bacterial food

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

treatment_protocol: WT and alg-1(-) worms were compared at the larval stage L4

value: whole worm

tag: developmental stage

value: larval stage L4

tag: genotype

value: wildtype


title: TG1/ pMMB206-TOM-Green/pBS(Kan), cis-DCE

tag: RNA extracted from cells of TG1/ pMMB206-TOM-Green/pBS(Kan) after contacting for 2 h with cis-DCE (1 mM) in Tris-HNO3 buffer with succinate (5 mM), IPTG (0.5 mM) at 37oC.


title: WT1

description: wildtype , larval stage L4, independent replicate 1


title: WT2

description: wildtype , larval stage L4, independent replicate 2


title: ALG-1(-) 2

description: alg-1(-) mutant, larval stage L4, independent replicate 2

source_name: alg1(-) mutant, larval stage L4


title: ALG-1(-) 1

description: alg-1(-) mutant, larval stage L4, independent replicate 1


title: ALG-1(-) 3

description: alg-1(-) mutant, larval stage L4, independent replicate 3


title: GIST Pre Treatment Biopsy 56

city: Baltimore

first: Michael

middle: F

last: Ochs

address: 550 North Broadway, Ste 1103

department: Oncology Biostatistics

institute: Johns Hopkins University

description: Ovation Aminoallyl RNA amplification and labeling system (NuGEN)

hyb_protocol: Labeled sample and reference were combined and hybridized on 44K Whole Human Genome Oliho Microarray (Agilent) at 60 degrees for 17hrs.

scan_protocol: Arrays were scanned with an Agilent GMS 428 scanner.

data_processing: The data matrix was generated using a two-color Agilent microarray with tumor or biopsy samples in channel 1 and human reference RNA in channel 2.

label: Alexa Fluor 647 dye

source_name: GIST Tumor

label_protocol: 50ng of RNA from tissue samples and universal human reference RNA were amplified using Ovation Aminoallyl RNA amplification and labeling system.  Sample aminoallyl cDNA was labeled with AlexaFluor 647 dye (Invitrogen) and reference aminoallyl cDNA was labeled with AlexaFluor 555 (Invitrogen) dye.

growth_protocol: Tumor and biopsy samples, no growth protocols.

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

treatment_protocol: All  patients received IM at 600mg daily by mouth for 8-12 weeks.

tag: initial tumor increase/(-)decrease

tag: kit mutation

value: unknown

value: GIST Tumor

label: Alexa Fluor 555 dye

source_name: Universal Human Reference RNA

tag: sample type

value: Universal Human Reference RNA (Stratagene)


title: GIST Post Treatment Sample 48


title: GIST Post Treatment Sample 47

value: exon 11


title: GIST Pre Treatment Biopsy 47


title: GIST Pre Treatment Biopsy 43


title: GIST Pre Treatment Biopsy 39


title: GIST Post Treatment Sample 50


title: GIST Pre Treatment Biopsy 45


title: GIST Pre Treatment Biopsy 50


title: GIST Pre Treatment Biopsy 37


title: GIST Post Treatment Sample 54


title: GIST Post Treatment Sample 41


title: GIST Pre Treatment Biopsy 36


title: GIST Post Treatment Sample 38


title: Lung_infected_visually-unaffected-area_Animal-36

value: Danish Landrace/Yorkshire/Duroc cross, Herd:high health free from A. pleuropneumoniae, Gender:castrated males, Age:8-10 weeks, Treatment:AP serotype 5b infected, Sample:Lung_infected_visually-unaffected-area, Animal:36

value: Danish Landrace/Yorkshire/Duroc cross, Herd:high health free from A. pleuropneumoniae, Gender:castrated males, Age:8-10 weeks, Reference, pool of equal amount of total-RNA from all lung samples in experiment


title: CLP_RAGlow, biological rep1

city: Toronto

first: Sasan

last: Zandi

state: Ontario

address: 101 college St

country: Canada

institute: UHN

description: Gene expression data from CLPGFPlow sorted from bone marrow of adult 8- to 12-week-old mice.

hyb_protocol: RNA was hybridized to MOE430_2 chips according to the manufacturer's manual.

scan_protocol: GeneChips were scanned using the GeneChipTM Scanner 3000.

data_processing: Probe level expression values and normalization were calculated using RMAExpress and further analysis was done using dChip.

source_name: Mouse bone marrow, CLP_RAGlow

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2,000 cells.

extract_protocol: Total RNA extraction was performed with the Qiagen microRNeasy kit according to the manufacturer's instructions.

tag: age

value: 8-12 weeks

value: bone marrow

value: common lymphoid progenitor (CLP)

tag: cell subpopulation


title: GIST Post Treatment Sample 34

tag: tissue


title: GIST Post Treatment Sample 32


title: BW25113 ychH, H2O2

description: BW25113 ychH, H2O2

source_name: BW25113 ychH, H2O2

tag: RNA extracted from cells of BW25113 ychH at OD 1.0 after contacting for 10 min with 2 mM H2O2 in LB at 37oC.


title: TG1/pBS(Kan)/pMMB277 2nd

description:
Ten RNA samples for five sets of microarray experiments were prepared: (i) cells of the TG1 with TOM-Green/IsoILR1/GSHI* vs. no cloned genes contacted for 2 h with 1 mM cis-DCE to determine the effect of expressing eight genes (TOM-Green/IsoILR1/GSHI*) on cis-DCE mineralization, (ii) cells of TG1 with TOM-Green/EchA F108L/I219L/C248I vs. TOM-Green contacted for 2 h with 1 mM cis-DCE to determine the effect of the evolved epoxide hydrolase on cis-DCE mineralization, (iii) cells of BW25113 with 2 mM H2O2 vs. no H2O2 contacted for 10 min with shaking to determine gene expression in response to H2O2, (iv) cells of the BW25113 ygiW strain with 2 mM H2O2 vs. no H2O2 contacted for 10 min to determine gene expression in response to H2O2 in the absence of YgiW, and (v) cells of the BW25113 ychH strain with 2 mM H2O2 vs. no H2O2 contacted for 10 min to determine gene expression in response to H2O2 in the absence of YchH.
	For the cis-DCE degradation system, the exponentially-grown TG1 cells (Table 1) were contacted with 1 mM cis-DCE together with 0.5 mM IPTG and 5 mM succinate (as a carbon/energy source during the cis-DCE degradation) in 60 mL vials for 2 hr as performed previously in the proteomics study J. Proteome Res. 5: 1388 - 1397 (2006). After 2 hr contact with cis-DCE, samples were centrifuged, and the cell pellets were frozen immediately with dry ice and stored at -80°C.  For the H2O2 stress system, overnight cultures of BW25113, BW25113 ygiW, and BW25113 ychH were re-grown to mid-log phase in LB (turbidity at 600 nm of 1), then the cultures were split into two cultures and 2 mM H2O2 and water (negative control) were added.   After contacting for 10 min, samples were centrifuged and the cell pellets frozen immediately with dry ice and stored at -80°C. RNA was isolated from the biofilm cells as described previously using sonication and a bead beater Appl. Microbiol. Biotechnol. 64: 515-524 (2004)..
For DNA microarray analysis, the E. coli Genechip antisense genome array (Affymetrix, P/N 900381, Santa Clara, CA) and the E. coli GeneChip Genome 2.0 Array (Affymetrix, P/N 900551) were used to study the differential gene expression profile of the K12 cells; the E. coli Genechip antisense genome array contains probe sets for all 4290 open reading frames (ORF), rRNA, tRNA, and 1350 intergenic regions, and the E. coli GeneChip Genome 2.0 Array contains 10,208 probe sets for open reading frames, rRNA, tRNA, and intergenic regions for four E. coli strains: MG1655, CFT073, O157:H7-Sakai, and O157:H7-EDL933. The same type of microarray was used for each binary comparison.  cDNA synthesis, fragmentation, and hybridizations were as described previously J. Bacteriol. 188: 587-598 (2006). Hybridization was performed for 16 h, and the total cell intensity was scaled to an average value of 500. The probe array images were inspected for any image artifact.  Background values, noise values, and scaling factors of both arrays were examined and were comparable. The intensities of polyadenosine RNA control were used to monitor the labeling process. For each binary microarray comparison of differential genes expression, if the gene with the larger transcription rate did not have a consistent transcription rate based on the 11-15 probe pairs (p-value less than 0.05), these genes were discarded.
Extract protocol: To lyse the cells, 1.0 mL RLT buffer (Qiagen, Inc., Valencia, CA) and 0.2 mL 0.1 mm zirconia/silica beads (Biospec) were added to the frozen bead beater tubes containing the cell pellets. The tubes were closed tightly and beat for 50 seconds at the maximum speed in a mini bead beater (cat. no. 3110BX, Biospec). The total RNA was isolated by following the protocol of the RNeasy Mini Kit (Qiagen) including an on-column DNase digestion with RNase-free DNase I (Qiagen).

hyb_protocol: The biotin-labeled target was hybridized to the Affymetrix GeneChip E. coli array at 45C for 16 hour at 60 rpm using the Hybridization Oven 640 (Affymetrix), then a three-step fluorescent staining was conducted using the Fluidics Station 450 (Affymetrix) during the washing and staining procedure.

source_name: Channel 1

tag: RNA extracted from cells of TG1/pBS(Kan)/pMMB277 after contacting for 2 h with cis-DCE (1 mM) in Tris-HNO3 buffer with succinate (5 mM), IPTG (0.5 mM) at 37oC


title: BW25113 ygiW, H2O2

description: BW25113 ygiW, H2O2

source_name: BW25113 ygiW, H2O2

tag: RNA extracted from cells of BW25113 ygiW at OD 1.0 after contacting for 10 min with 2 mM H2O2 in LB at 37oC.


title: BW25113 ygiW, water (negative control)

description: BW25113 ygiW, water (negative control)

source_name: BW25113 ygiW, water (negative control)

tag: RNA extracted from cells of BW25113 ygiW at OD 1.0 after contacting for 10 min with water (negative control) in LB at 37oC.


title: GIST Pre Treatment Biopsy 29


title: BW25113 ychH, water (negative control)

description: BW25113 ychH, water (negative control)

source_name: BW25113 ychH, water (negative control)

tag: RNA extracted from cells of BW25113 ychH at OD 1.0 after contacting for 10 min with water (negative control) in LB at 37oC.


title: GIST Post Treatment Sample 29


title: TG1/pBS(Kan)-TOM-Green/pMMB277-IsoILR1-GSHI 2nd

tag: RNA extracted from cells of TG1/pBS(Kan)-TOM-Green/pMMB277-IsoILR1-GSHI after contacting for 2 h with cis-DCE (1 mM) in Tris-HNO3 buffer with succinate (5 mM), IPTG (0.5 mM) at 37oC


title: CLP_RAGhigh, biological rep2

description: Gene expression data from CLPGFPhigh sorted from bone marrow of adult 8- to 12-week-old mice.

source_name: Mouse bone marrow, CLP_RAGhigh

tag: strain

tag: cell type


title: GIST Pre Treatment Biopsy 30


title: CLP_RAGlow, biological rep2


title: GIST Pre Treatment Biopsy 31


title: CLP_RAGhigh, biological rep1


title: GIST Post Treatment Sample 28


title: GIST Pre Treatment Biopsy 32


title: BW25113, H2O2

description: BW25113, H2O2

tag: RNA extracted from cells of BW25113 at OD 1.0 after contacting for 10 min with 2 mM H2O2 in LB at 37oC.


title: TG1/pBS(Kan)/pMMB277, cis-DCE

description: TG1/pBS(Kan)/pMMB277, cis-DCE

source_name: TG1/pBS(Kan)/pMMB277, cis-DCE


title: GIST Pre Treatment Biopsy 28


title: GIST Post Treatment Sample 27

value: exon 9


title: GIST Pre Treatment Biopsy 27


title: TG1/pBS(Kan)-TOM-Green/pMMB277-IsoILR1-GSHI, cis-DCE


title: BW25113, water (negative control)

description: BW25113, water (negative control)

source_name: BW25113, water (negative control)

tag: RNA extracted from cells of BW25113 at OD 1.0 after contacting for 10 min with water (negative control) in LB at 37oC.


title: GIST Pre Treatment Biopsy 22


title: GIST Post Treatment Sample 19


title: GIST Post Treatment Sample 23


title: GIST Pre Treatment Biopsy 23


title: GIST Post Treatment Sample 22


title: GIST Pre Treatment Biopsy 16


title: GIST Pre Treatment Biopsy 19


title: GIST Pre Treatment Biopsy 18


title: GIST Post Treatment Sample 15


title: T-DNA-insertion mutant of LBD37 seedling in FN, biological rep1

city: Potsdam

first: Grit

last: Rubin

address: Am Mühlenberg 1

department: Stitt

institute: MPI-MP

description: grown in sterile liquid culture (Scheible et al., 2004) for nine days in N-replete conditions (FN, 4 mM KNO3)

hyb_protocol: All procedures including (i) quality control of RNA, (ii) biotin labeling of the cRNA target, (iii) hybridization, washing, staining, and scanning procedures, and (iv) processing of Affymetrix raw data (CEL files) were performed as outlined previously (Scheible et al., 2004).

data_processing: The data were analyzed with Robin and RMA-normalized

label: Biotin

source_name: T-DNA-insertion mutant of LBD37 (KO37) seedling in full nutrition (FN)

growth_protocol: Arabidopsis seedlings were grown in sterile liquid culture (Scheible et al., 2004) either for nine days in N-replete conditions (FN, 4 mM KNO3), or first during 7 days in FN and then for 2 days in N-deprivation conditions (no N added; noN).

extract_protocol: Total RNA was prepared using Quiagen RNeasy plant mini kit

treatment_protocol: Seedlings were pre-grown in 24 h light (150-180 µE, 20°C) on sterile 0.5% (w/v) agar plates (Falcon IntegridTM 100 mm square) containing 27 ml FN medium, and after 7 days seedlings were transferred individually to 24-well culture plates (Greiner Bio-one Cellstar #662160) containing 1 ml medium per well

tag: ecotype

value: whole seedling

value: 9 days

tag: treatment

value: full nutrition


title: GIST Post Treatment Sample 13

tag: initial tumor increase/(-)decrease

tag: kit mutation


title: GIST Pre Treatment Biopsy 15

tag: sample type


title: GIST Pre Treatment Biopsy 13


title: A non-tumourigenic human breast epithelial cell line MCF10, biological rep3

city: London

first: Danny

middle: Asher

last: Bitton

address: Darwin Building, Gower Street

department: Department of Genetics, Evolution & Environment

country: United Kingdom

institute: University College London

description: probe_group_file:  HuEx-1_0-st-v2.pgf

hyb_protocol: Exon 1.0 ST Hybridisation v1.0 protocol, Exon 1.0 ST Hybridisation v1.0 (hybridisation cocktail)

scan_protocol: Affymetrix GeneChip scanner 3000 7G

data_processing: Exon array analysis was performed using the Bioconductor package Exonmap. Data were summarised using RMA (affy package in Bioconductor)

label_protocol: WT sense target prep (1.5ug) v 1.0

extract_protocol: Rneasy Midi (QIAGEN)

tag: cell line


title: A non-tumourigenic human breast epithelial cell line MCF10, biological rep1

description: probe_group_file:  HuEx-1_0-st-v2.pgf


title: Human breast cancer cell line MCF7, biological rep2

description: probe_group_file:  HuEx-1_0-st-v2.pgf


title: Human breast cancer cell line MCF7, biological rep3

description: probe_group_file:  HuEx-1_0-st-v2.pgf


title: Human breast cancer cell line MCF7, biological rep1

description: probe_group_file:  HuEx-1_0-st-v2.pgf


title: GIST Pre Treatment Biopsy 12

tag: tissue


title: cicb FCS

first: Gady

last: Cojocaru

address: Kiryat Hadassah

department: Pathology

institute: hadassah medical center

description: Gene expression data fron LAPC4

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133A  Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: 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: LAPC4 cell infected with β-TrCP shRNA and treated with full fetal calf serum

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

growth_protocol: LAPC4 cells were grown in RPMI 1640 containig either 10% fetal calf serum supplimented with 100pM Methyltrienolone or with 10% charcoal stripped serum. Cells were incubated at 37°C 5% CO2.

treatment_protocol: Cell were treated for 72 hours.

value: Prostate cancer cell line LAPC4

tag: transfection

value: β-TrCP shRNA

tag: growth protocol

value: full fetal calf serum


title: GIST Pre Treatment Biopsy 10


title: GIST Post Treatment Sample 11

value: wildtype


title: GIST Pre Treatment Biopsy 04


title: GIST Pre Treatment Biopsy 09


title: GIST Post Treatment Sample 10


title: GIST Post Treatment Sample 08


title: GIST Pre Treatment Biopsy 11


title: GFP CSS

description: Gene expression data fron LAPC4

source_name: LAPC4 cell infected with GFP and treated with charcoal stripped serum

value: GFP

value: charcoal stripped serum


title: GIST Pre Treatment Biopsy 08

value: GIST Tumor

value: Universal Human Reference RNA (Stratagene)


title: GIST Pre Treatment Biopsy 03

value: exon 11


title: GIST Post Treatment Sample 12


title: GIST Post Treatment Sample 09


title: cicb CSS

description: Gene expression data fron LAPC4

source_name: LAPC4 cell infected with β-TrCP shRNA and treated with charcoal stripped serum


title: GIST Post Treatment Sample 06


title: GFP FCS

description: Gene expression data fron LAPC4

source_name: LAPC4 cell infected with GFP and treated with full fetal calf serum


title: GIST Post Treatment Sample 03


title: GIST Post Treatment Sample 01


title: GIST Post Treatment Sample 02


title: GIST Pre Treatment Biopsy 02


title: SCAN96

status: Public on Nov 23 2009

city: Uppsala

first: Anders

last: Isaksson

address: Akademiska sjukhuset ing61 3tr

country: Sweden

institute: Uppsala University

description: Array experiments were performed according to the standard protocols for Affymetrix GeneChip Mapping 250K arrays (Gene Chip Mapping 500K Assay Manual (P/N 701930 Rev2.), Affymetrix Inc., Santa Clara, CA).

hyb_protocol: Hybridized probes were captured by streptavidin-phycoerythrin conjugates using Fluidics Station 450

scan_protocol: GeneChip Scanner 3000 7G (Affymetrix Inc., Santa Clara, CA)

data_processing: QC, genotype calling and log2 ratios were produced in Affymetric Genotyping Console 3.0.1. The Dynamic Model (DM) algorithm was used to perform single sample QC. The QC specification for 250K is a Call Rate > 93

label: Total genomic DNA was digested with a restriction enzyme (Nsp1), ligated to an appropriate adapter for the enzyme, and subjected to PCR amplification using a single primer

source_name: Blood

label_protocol: After digestion with DNase I, the PCR products were labeled with a biotinylated nucleotide analogue using terminal deoxynucleotidyl transferase and hybridized to the microarray

extract_protocol: Extraction of genomic DNA was performed using QIAamp DNA Mini kit (Qiagen) according to the manufacturer's instructions.

value: Blood

tag: phenotype

value: CLL sample


title: SCAN97


title: SCAN94


title: SCAN80


title: SCAN95


title: SCAN93


title: SCAN81


title: SCAN70


title: SCAN7


title: SCAN83


title: SCAN78


title: SCAN90


title: SCAN72


title: SCAN77


title: SCAN89


title: SCAN69


title: SCAN79


title: SCAN75


title: A non-tumourigenic human breast epithelial cell line MCF10, biological rep2

description: probe_group_file:  HuEx-1_0-st-v2.pgf


title: SCAN74


title: SCAN68


title: SCAN63


title: SCAN60


title: SCAN64


title: SCAN6


title: SCAN62


title: SCAN59


title: SCAN51


title: SCAN52


title: SCAN67


title: SCAN55


title: SCAN46


title: SCAN47


title: SCAN48


title: SCAN407


title: SCAN410


title: SCAN5


title: SCAN411


title: SCAN54


title: SCAN403


title: SCAN405


title: SCAN404


title: SCAN45


title: SCAN44


title: SCAN61


title: SCAN401


title: SCAN406


title: SCAN408


title: SCAN396


title: SCAN4


title: SCAN398


title: SCAN393


title: SCAN394


title: SCAN384_1


title: SCAN39


title: SCAN392


title: SCAN373


title: SCAN372


title: SCAN377


title: SCAN379


title: SCAN368


title: SCAN362


title: SCAN36


title: SCAN365


title: SCAN35


title: SCAN355


title: SCAN354


title: SCAN356


title: SCAN360


title: SCAN347


title: SCAN389


title: SCAN352


title: SCAN380


title: SCAN345


title: SCAN382


title: SCAN346


title: SCAN339


title: SCAN340_1


title: SCAN33


title: SCAN344


title: SCAN343


title: SCAN353


title: SCAN341


title: SCAN34


title: SCAN312


title: SCAN311


title: SCAN298


title: SCAN301


title: SCAN308


title: SCAN309


title: SCAN30


title: SCAN295


title: SCAN306


title: SCAN304


title: SCAN305


title: SCAN290


title: SCAN294


title: SCAN296


title: SCAN292


title: SCAN3


title: SCAN289


title: SCAN291


title: SCAN299


title: SCAN29


title: SCAN303


title: SCAN288


title: SCAN284


title: SCAN31


title: SCAN28


title: SCAN279


title: SCAN32


title: SCAN272


title: SCAN260


title: SCAN22


title: SCAN21


title: SCAN211


title: SCAN256


title: SCAN214


title: SCAN23


title: SCAN278


title: SCAN252


title: SCAN196


title: SCAN274


title: SCAN212


title: SCAN247


title: SCAN24


title: SCAN251


title: SCAN194


title: SCAN206


title: SCAN2


title: SCAN204


title: SCAN255


title: SCAN265


title: SCAN262


title: SCAN193


title: SCAN192


title: SCAN191


title: Mammary pregnant microGravity control vivarium VIVB

city: Grand Rapids

first: Karl

last: Dykema

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

description: Gene expression data from three tissue types within rats in lactation/pregnancy and micro/standard/hyper gravity.

hyb_protocol: 2.2ug of biotin labeled, fragmented cDNA hybridized to Rat 230 2.0 Affy GeneChips.

scan_protocol: Affymetrix Genearray scanner 3000, with 7G upgrade

data_processing: Data analyzed with RMA and MAANOVA.

label: R-Phycoerythrin Streptavidin (SAPE), from Molecular Probes, 1 mg/ml  ( we use 6 ul per reaction )

organism: Rattus norvegicus

source_name: Rattus norvegicus

label_protocol: 25ng total RNA for cDNA synthesis, amplification and biotin labeling with NuGEN Ovation Biotin System.

extract_protocol: Total RNA was isolated with TRIzol (Invitrogen) for mammary and liver; RNeasy Lipid (QIAGEN) for adipose.

tag: subtype


title: SCAN258


title: SCAN19


title: Mammary pregnant microGravity FLTD


title: Mammary pregnant microGravity control vivarium VIVC


title: SCAN189


title: SCAN187


title: Mammary pregnant microGravity control flight FDSA


title: SCAN243


title: Mammary pregnant microGravity control flight FDSB


title: Mammary pregnant microGravity control vivarium VIVD


title: Mammary pregnant microGravity FLTA


title: SCAN182


title: Mammary pregnant microGravity control flight FDSC


title: SCAN181


title: SCAN185


title: SCAN186


title: SCAN180


title: SCAN18


title: SCAN178


title: Mammary pregnant microGravity FLTB


title: SCAN175


title: cell line SEMK2 with zebularine

city: Rotterdam

first: Dominique

last: Stumpel

address: Dr. Molewaterplein 50-room Ee15-14

department: Pediatric Oncology/ Hematology

country: Netherlands

institute: Erasmus MC _ Sophia Children's Hospital

description:
pre-B

Please refer to Differential Methylation Hybridization (DMH) protocol by Dr. Tim H. Huang and coworkers. (PMID 18987809: Yan PS, Potter D, Deatherage DE, Huang TH, Lin S., Differential methylation hybridization: profiling DNA methylation with a high-density CpG island microarray.Methods Mol Biol. 2009;507:89-106.)

hyb_protocol: Oligoarray control targets and hybridization buffer (the Oligo aCGH/ChIP-on-Chip Hybridization Kit) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially according to the Agilent protocol.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing:
Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).
Agilent Feature Extraction Software (v 8.5.1.1) was used for data extraction. The R and Bioconductor statistical environment (version 2.7) were used for quality control and LOESS normalization (limma package). No background correction was performed.

source_name: SEMK2 with zebularine

label_protocol: Using the BioPrime Array-CGH Genomic Labeling kit (Invitrogen, Carlsbad, USA), amino-allyl dUTPs were incorporated into 500ng of the methylated amplicons (generated by DMH) , allowing the amplicons to be labeled with the fluorescent dyes Cy5 (patient samples) and Cy3 (common reference samples).

growth_protocol: All cell lines were maintained as suspension cultures in RPMI 1640 with L-Alanyl-L-Glutamine (Invitrogen) supplemented with 10% FCS (Integro), 100 IU/ml  penicillin, 100 μg/ml streptomycin, and 0.125 μg/ml fungizone (Invitrogen) at 37°C in humidified air containing 5% CO2.

extract_protocol: Total DNA extracted using Trizol following manufacturer's instructions.

treatment_protocol: Only applicable for the cell lines: treated with 100nM of zebularine for 10 days.

tag: cell line derivation

value: bone marrow

tag: gender

value: female

tag: genotype

source_name: peripheral blood, healthy

value: peripheral blood

tag: sample description

value: mix from 5 healthy males and 5 healthy females

value: reference


title: cell line SEMK2


title: SCAN174


title: SCAN173


title: SCAN188


title: SCAN176


title: SCAN172


title: SCAN171


title: Mammary pregnant microGravity control vivarium VIVA


title: Mammary pregnant microGravity FLTC


title: Mammary pregnant microGravity control flight FDSD


title: SCAN17


title: cell line RS4;11 with zebularine

source_name: RS4;11 with zebularine


title: SCAN170


title: Normal bone marrow, 629

description: Please refer to Differential Methylation Hybridization (DMH) protocol by Dr. Tim H. Huang and coworkers. (PMID 18987809: Yan PS, Potter D, Deatherage DE, Huang TH, Lin S., Differential methylation hybridization: profiling DNA methylation with a high-density CpG island microarray.Methods Mol Biol. 2009;507:89-106.)

source_name: bone marrow, normal

value: normal


title: cell line RS4;11


title: SCAN166


title: SCAN165


title: Normal bone marrow, 624

value: male


title: SCAN184


title: Mammary pregnant standardG M48S


title: SCAN160


title: SCAN161


title: Adipose lactating standardG A202S


title: SCAN157


title: SCAN169


title: SCAN162


title: Liver lactating standardG L202S


title: Normal bone marrow, 585


title: Mammary lactating standardG M202S


title: SCAN156


title: SCAN16


title: Adipose pregnant standardG A48S


title: SCAN154


title: SCAN151


title: Normal bone marrow, 584


title: SCAN153


title: Liver pregnant standardG L48S


title: SCAN150


title: SCAN15


title: SCAN147


title: Normal bone marrow, 576


title: Normal bone marrow, 577


title: SCAN149


title: Normal bone marrow, 656


title: SCAN146


title: Mammary lactating hyperG M206H


title: Liver lactating hyperG L206H


title: Adipose lactating hyperG A206H


title: Untranslocated infant ALL, 450

source_name: bone marrow, untranslocated

value: untranslocated


title: Adipose lactating standardG A214S


title: SCAN142


title: SCAN144


title: SCAN133


title: Untranslocated infant ALL, 587


title: Untranslocated infant ALL, 593

description:
common B

Please refer to Differential Methylation Hybridization (DMH) protocol by Dr. Tim H. Huang and coworkers. (PMID 18987809: Yan PS, Potter D, Deatherage DE, Huang TH, Lin S., Differential methylation hybridization: profiling DNA methylation with a high-density CpG island microarray.Methods Mol Biol. 2009;507:89-106.)


title: Liver lactating standardG L214S


title: SCAN143


title: SCAN14


title: SCAN126


title: Adipose lactating hyperG A217H


title: Mammary lactating standardG M214S


title: SCAN141


title: Untranslocated infant ALL, 626

source_name: peripheral blood, untranslocated


title: Untranslocated infant ALL, 683


title: SCAN132


title: Liver lactating hyperG L217H


title: Untranslocated infant ALL, 586


title: SCAN124


title: SCAN135


title: Mammary lactating hyperG M217H


title: SCAN125


title: Untranslocated infant ALL, 625


title: SCAN123


title: Untranslocated infant ALL, 543


title: Adipose pregnant hyperG A60H


title: SCAN119


title: SCAN140


title: SCAN115


title: SCAN117


title: SCAN12


title: Untranslocated infant ALL, 633


title: Untranslocated infant ALL, 449

description:
unspecified B

Please refer to Differential Methylation Hybridization (DMH) protocol by Dr. Tim H. Huang and coworkers. (PMID 18987809: Yan PS, Potter D, Deatherage DE, Huang TH, Lin S., Differential methylation hybridization: profiling DNA methylation with a high-density CpG island microarray.Methods Mol Biol. 2009;507:89-106.)


title: Liver pregnant hyperG L60H


title: SCAN113


title: Mammary pregnant hyperG M60H


title: SCAN118


title: SCAN109


title: Liver lactating standardG L219S


title: SCAN11


title: Untranslocated infant ALL, 634


title: SCAN112


title: lung_16 week old, treated with inhaled LPS, then mechanical ventilation for 2 hr_rep3

city: Seattle

first: Lincoln

middle: S

last: Smith

state: WA

address: 1660 S. Columbian Wy, 151L

department: Pediatrics

institute: University of WA

description: no additional information

hyb_protocol: Standard Affymetrix overnight 3' IVT hybridization

scan_protocol: Standard Affymetrix 3' IVT scanning protocol, Affymetrix microarray scanner 3000-7G

data_processing: Normalization factor of 1 with scaling to target 250. Intensity units as output by MAS 5.0 algorithm.

source_name: whole lung, treated with inhaled LPS followed by MV

label_protocol: Standard Affymetrix 3' IVT array labeling

extract_protocol: At the end of the study period, the lungs were immediately removed and placed into RNAlater (Ambion, Austin, TX) for at least 24 hr.  Total lung mRNA was purified using the Stratgene Absolutely RNA kit (Ambion).  The RNA was concentrated using potassium acetate precipitation and reconstituted in RNase free water.   The quality of the RNA was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc, Santa Clara, CA), and samples with an RNA integrity index of greater than 7.0 were reverse transcribed, labeled and hybridized on the Affymetrix mouse 430 2.0 expression array chip

treatment_protocol: Animals were untreated, spontaneous breathing controls; treated with mechanical ventilation VT=15 mL/kg, PEEP = 2 cmH2O, 30% O2 for 2 hr; aerosolized LPS (20 mL of 0.1 mg/mL) for 30 min. in a sealed aerosol chamber and then allowed to breathe spontaneously with free access to food and water for 2 hr; aerosolized LPS followed immediately by mechanical ventilation for 2 hr.

tag: strain

tag: age

value: 16 week

tag: stress


title: SCAN110


title: Adipose lactating standardG A219S


title: lung_16 week old, treated with inhaled LPS, then mechanical ventilation for 2 hr_rep4

description: no additional information


title: SCAN107


title: MLL-AF9 infant ALL, 541

source_name: bone marrow, t(9;11)


title: lung_16 week old, treated with inhaled LPS, then mechanical ventilation for 2 hr_rep2

description: no additional information


title: SCAN106


title: SCAN104


title: Mammary lactating standardG M219S


title: lung_16 week old, treated with inhaled LPS, then mechanical ventilation for 2 hr_rep1

description: no additional information


title: lung_16 week old, treated with inhaled LPS, then spontaneous breathing for 2 hr_rep3

description: no additional information

source_name: whole lung, treated with inhaled LPS

value: inhaled LPS


title: MLL-AF9 infant ALL, 582

description:
pro-B

Please refer to Differential Methylation Hybridization (DMH) protocol by Dr. Tim H. Huang and coworkers. (PMID 18987809: Yan PS, Potter D, Deatherage DE, Huang TH, Lin S., Differential methylation hybridization: profiling DNA methylation with a high-density CpG island microarray.Methods Mol Biol. 2009;507:89-106.)


title: Adipose pregnant standardG A57S


title: lung_16 week old, treated with inhaled LPS, then spontaneous breathing for 2 hr_rep4

description: no additional information


title: MLL-AF9 infant ALL, 588


title: SCAN108


title: Untranslocated infant ALL, 682


title: MLL-AF9 infant ALL, 574

source_name: peripheral blood, t(9;11)


title: SCAN102


title: lung_16 week old, treated with inhaled LPS, then spontaneous breathing for 2 hr_rep2

description: no additional information


title: lung_16 week old, treated with mechanical ventilation for 2 hr_rep4

description: no additional information

source_name: whole lung, treated with MV (15mL/kg)

value: mechanical ventilation


title: Liver pregnant standardG L57S


title: MLL-AF9 infant ALL, 476


title: lung_16 week old, treated with mechanical ventilation for 2 hr_rep1

description: no additional information


title: Adipose lactating hyperG A212H


title: Liver lactating hyperG L212H


title: lung_16 week old, treated with mechanical ventilation for 2 hr_rep2

description: no additional information


title: lung_16 week old, treated with mechanical ventilation for 2 hr_rep3

description: no additional information


title: lung_16 week old, untreated, spontaneously breathing control_rep1

description: no additional information

source_name: whole lung, untreated, spontaneously breathing

value: control


title: lung_16 week old, treated with inhaled LPS, then spontaneous breathing for 2 hr_rep1

description: no additional information


title: lung_16 week old, untreated, spontaneously breathing control_rep4

description: no additional information


title: MLL-AF9 infant ALL, 649


title: Mammary lactating hyperG M212H


title: lung_16 week old, untreated, spontaneously breathing control_rep2

description: no additional information


title: lung_21 day old, treated with inhaled LPS, then mechanical ventilation for 2 hr_rep3

description: no additional information

value: 21 days


title: lung_16 week old, untreated, spontaneously breathing control_rep3

description: no additional information


title: Adipose pregnant hyperG A56H


title: Mammary pregnant standardG M57S


title: lung_21 day old, treated with inhaled LPS, then mechanical ventilation for 2 hr_rep1

description: no additional information


title: lung_21 day old, treated with inhaled LPS, then mechanical ventilation for 2 hr_rep2

description: no additional information


title: MLL-ENL infant ALL, 475

source_name: bone marrow, t(11;19)


title: MLL-ENL infant ALL, 632

source_name: peripheral blood, t(11;19)


title: MLL-ENL infant ALL, 573


title: MLL-ENL infant ALL, 680


title: Liver pregnant hyperG L56H


title: Mammary pregnant hyperG M56H


title: Adipose lactating hyperG A203H


title: lung_21 day old, treated with mechanical ventilation for 2 hr_rep3

description: no additional information


title: Mammary lactating hyperG M203H


title: lung_21 day old, treated with inhaled LPS, then spontaneous breathing for 2 hr_rep3

description: no additional information


title: lung_21 day old, treated with inhaled LPS, then spontaneous breathing for 2 hr_rep2

description: no additional information


title: lung_21 day old, treated with mechanical ventilation for 2 hr_rep2

description: no additional information


title: lung_21 day old, treated with inhaled LPS, then spontaneous breathing for 2 hr_rep4

description: no additional information


title: lung_21 day old, untreated, spontaneously breathing control_rep3

description: no additional information


title: lung_21 day old, treated with mechanical ventilation for 2 hr_rep1

description: no additional information


title: lung_21 day old, treated with inhaled LPS, then spontaneous breathing for 2 hr_rep1

description: no additional information


title: Adipose pregnant hyperG A50H


title: lung_21 day old, untreated, spontaneously breathing control_rep4

description: no additional information


title: MLL-ENL infant ALL, 540


title: Liver pregnant hyperG L50H


title: MLL-ENL infant ALL, 447


title: MLL-ENL infant ALL, 583


title: Liver lactating hyperG L203H


title: MLL-ENL infant ALL, 650


title: Mammary pregnant hyperG M50H


title: Adipose lactating standardG A201S


title: lung_21 day old, untreated, spontaneously breathing control_rep2

description: no additional information


title: C10 cell line with an inducible form of C/EBPa, treated with beta estradiol for 24 hours sample 1

city: Barcelona

first: Thomas

last: GRAF

address: Dr.Aiguader, 88

country: Spain

institute: Center for Genomic Regulation (CRG)

hyb_protocol: Hybridized according to Affymetrix Hybridization protocol

scan_protocol: Scanned according to Affymetrix scanning protocol

data_processing: Processed using the Affymetrix Gene Chip Operating System

label_protocol: Biotynilated according to Affymetrix labeling protocol

extract_protocol: Trizol reagent


title: C10 cell line with an inducible form of C/EBPa, treated with beta estradiol for 24 hours sample 2


title: MLL-ENL infant ALL, 539


title: C10 cell line with an inducible form of C/EBPa, treated with beta estradiol for 48 hours sample 1


title: lung_21 day old, untreated, spontaneously breathing control_rep1

description: no additional information


title: MLL-ENL infant ALL, 609


title: C10 cell line with an inducible form of C/EBPa, treated with beta estradiol for 48 hours sample 2


title: MLL-ENL infant ALL, 681


title: C10 cell line with an inducible form of C/EBPa, treated with beta estradiol for 3 hours sample 2


title: C10 cell line with an inducible form of C/EBPa, treated with beta estradiol for 3 hours sample 1


title: C10 cell line with an inducible form of C/EBPa, treated with beta estradiol for 12 hours sample 2


title: Liver lactating standardG L201S


title: MLL-ENL infant ALL, 608


title: MLL-ENL infant ALL, 642


title: C10 cell line with an inducible form of C/EBPa, treated with beta estradiol for 12 hours sample 1


title: C10 cell line with an inducible form of C/EBPa, treated with ethanol sample 2

source_name: C10 cell line with an inducible form of C/EBPa, treated with ethanol.


title: C10 cell line with an inducible form of C/EBPa, treated with ethanol sample 1


title: Mammary lactating standardG M201S


title: HAFTL cell line treated with beta estradiol sample 1

source_name: fetal liver derived, Ha-ras oncogene transformed mouse cell line (Alessandrini et al., 1987)

value: HAFTL


title: HAFTL cell line treated with beta estradiol sample 2

source_name: fetal liver derived, Ha-ras oncogene transformed mouse cell line (Alessandrini et al., 1987).


title: Mammary pregnant standardG M44S

source_name: Rattus norvegicus


title: Adipose pregnant standardG A44S


title: mSMC-TNF-LTBR-24h-2

city: Munich

first: Andreas

middle: Johann Richard

last: Habenicht

state: Bavaria

address: Pettenkoferstraße 9a

department: Medicine

institute: Ludwig Maximilians Universität München

description: Staining with Fluidic Station 450 Protocol: EukGe-WS2v4

hyb_protocol: 60rpm, 18h, 45°C in Affymetrix Hybridization Buffer

scan_protocol: Affymetrix Scanner 3000, single scan

data_processing: GCOS 1.4, scaled to 500

label: Biotin/SAPE with Anti Streptavidin signal amplification

source_name: Aortic Smooth Muscle Cells

label_protocol: ENZO T7 High Yield Transcript Labelling Kit, 16h IVT

growth_protocol: Maintained in DMEM/F12, 10% FCS, feed every 48h

extract_protocol: Qiagen RNEasy Lipid Tissue Mini Kit, Standard protocol

treatment_protocol: Cells were feed 24h prior to stimulation, stimuli were added in PBS, Cells were stimulated with 1ng/ml TNFalpha + 10µg/ml alpha-LTBR

value: C57BL/6J, Gender:male, Age:10-12 weeks, Tissue:aorta


title: mSMC-TNF-LTBR-24h-1


title: MLL-ENL infant ALL, 500

source_name: peripheral blood, healthy


title: Liver pregnant hyperG L55H


title: mSMC-TNF-LTBR-24h-3


title: mSMC-TNF-24h-2

treatment_protocol: Cells were feed 24h prior to stimulation, stimuli were added in PBS, Cells were stimulated with 1ng/ml TNFalpha


title: mSMC-TNF-24h-1


title: mSMC-TNF-6h-0


title: Mammary pregnant hyperG M55H


title: MLL-AF4 infant ALL, 495

source_name: bone marrow, t(4;11)


title: mSMC-LTBR-24h-3

treatment_protocol: Cells were feed 24h prior to stimulation, stimuli were added in PBS, Cells were stimulated with  10µg/ml alpha-LTBR


title: MLL-AF4 infant ALL, 473


title: Adipose pregnant hyperG A55H


title: mSMC-TNF-24h-0


title: mSMC-TNF-24h-3


title: MLL-ENL infant ALL, 474


title: MLL-AF4 infant ALL, 679

source_name: peripheral blood, t(4;11)


title: MLL-AF4 infant ALL, 606


title: MLL-AF4 infant ALL, 604


title: mSMC-LTBR-24h-2


title: mSMC-LTBR-24h-0


title: Adipose pregnant standardG A42S


title: MLL-AF4 infant ALL, 472


title: Mammary pregnant standardG M42S


title: mSMC-LTBR-24h-1


title: Adipose pregnant hyperG A59H


title: mSMC-Control-24h-3

treatment_protocol: Cells were feed 24h prior to stimulation, stimuli were added in PBS, Cells were supplemented with PBS only


title: mSMC-LTBR-2h-0


title: mSMC-LTBR-6h-0


title: A57F48

status: Public on Dec 01 2009

city: Raleigh

first: Youssef

last: Idaghdour

state: NC

address: South Gardner Hall

department: Genetics

institute: NCSU

hyb_protocol: Illumina's BeadArray protocol

scan_protocol: Illumina's BeadArray protocol and BeadStudio (Gene expression Module)

data_processing: Raw data was log2 transformed and median-centered using JMP Genomics (SAS, Cary NC).

source_name: Leukocytes, Agadir, Urban

label_protocol: cDNA and cRNA labeling and amplification were all performed using a single kit: Ambion's Illumina TotalPrep RNA Amplification kit.

extract_protocol: Total RNA was extrated from leukocyte samples using Ambion's Leukolocks kit. Quality control was performed using Agilent's Bioanalyzer.

tag: geographic location

value: Agadir

tag: lifestyle

value: urban

tag: cell type

value: leukocytes


title: Liver pregnant standardG L42S


title: mSMC-Control-24h-1


title: mSMC-Control-24h-0


title: mSMC-Control-24h-2


title: Liver pregnant hyperG L59H


title: MLL-AF4 infant ALL, 546

value: bone marrow

value: female

tag: sample type


title: Adipose pregnant standardG A52S


title: MLL-AF4 infant ALL, 640

value: peripheral blood

value: mix from 5 healthy males and 5 healthy females


title: mSMC-Control-6h-0


title: Mammary pregnant hyperG M59H


title: Liver pregnant standardG L52S


title: Liver lactating hyperG L210H


title: MLL-AF4 infant ALL, 592

value: reference


title: mSMC-Control-2h-0


title: Liver pregnant standardG L44S


title: MLL-AF4 infant ALL, 641

value: male


title: MLL-AF4 infant ALL, 591