title: LRPPRC knockdown2, biological replicate 1

description:
Gene expression data from LRPPRC knockdown 2 cell line, with only 33% expression of LRPPRC compared to control.
2.1


title: Ishikawa Hcells, dosed with egf, harvested at 12 hr, rep1

status: Public on Mar 13 2010

type: RNA

city: Albuquerque

first: Gavin

last: Pickett

state: NM

address: 2325 Camino de Salud NE

department: Genomics

country: USA

institute: UNM

description: Gene expression data from human endometrial adenocarcinoma cell line 12 hr dosed with EGF

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human HGU133 2.0+ Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: type I endometrial adenocarcinoma cell line 12 hr dosed with EGF

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Affymetrix One-Cycle Target Labeling Kit).

growth_protocol: Hec50co cells and Ishikawa Hcells were cultured in DMEM containing 10% FBS substitute and 2mM L-Glutamine and 1x antibiotic-antimycotic solution.

extract_protocol: Qiagen RNeasy used for total RNA extraction and was performed according to manufacture's instructions.

treatment_protocol: The two different tissue culture cell lines were dosed with 0.1% DMSO (vehicle=undosed) or with 1uM gefitinib, or with 30ng/ml EGF for 12 or 24 hours then the cells were harvested and total RNA extracted and purified.

tag: tissue type

value: Type I endometrial adenocarcinoma

tag: cell line

value: Ishikawa H


title: HUVEC_Pre-17_24h_rep2

city: Frankfurt am Main

first: Carmen

last: Doebele

address: Theodor-Stern-Kai 7

country: Germany

institute: Goethe University

description: Transfection of HUVEC with 10 nM Pre-miR-17 (Ambion) with Lipofectamine RNAiMax (Invitrogen)

hyb_protocol: Fifteen micrograms fragmented, biotinylated cRNA was hybridized to an HG-U133plus 2.0 microarray (Affymetrix) according to the Affymetrix protocol.

scan_protocol: After hybridization, the microarray was washed and stained on an Affymetrix fluidics station and was scanned with an Fluorescence intensity normalized to the average fluorescence for the entire microarray.

data_processing: GeneChip image analysis was performed using GCOS Version 1.3 (Affymetrix). We used Gene Spring Version 4.2 and the rma normalization method for data analysis (Agilent Technologies, Santa Clara, CA).

source_name: HUVEC, Pre-17 transfected, 24h

label_protocol: To assay 10µg of total RNA, the standard Affymetrix target amplification protocol was used for in vitro transcription for synthesis of the biotinylated cRNA.

growth_protocol: Pooled human umbilical vein endothelial cells (HUVECs) were purchased from Lonza and cultured in endothelial basal medium (EBM; Lonza) supplemented with hydrocortisone, bovine brain extract, epidermal growth factor, gentamycin sulphate, amphotericin-B, and 10% fetal calf serum (FCS; Invitrogen) until the third passage. One day before transfection 3.5x105 cells were seeded in 6 cm cell culture dishes.

extract_protocol: Total RNA was isolated using TRI reagent (Sigma) according to the manufacturer´s protocol.

treatment_protocol: HUVECs were transfected at 40-60% confluence using Lipofectamine RNAiMax (Invitrogen) according to the manufacturer´s protocol. For overexpression of the individual miRs 10 nM of miR-17 precursor molecules (Pre-17) or control pre-miR (Pre-Co, Ambion) were used.

tag: cell type

value: pooled human umbilical vein endothelial cells (HUVEC; Lonza)

tag: transfection


title: HUVEC_Pre-17_24h_rep3


title: MDS patient 177

city: Oxford

first: Andrea

last: Pellagatti

address: John Radcliffe Hospital

department: NDCLS, RDM

country: United Kingdom

institute: University of Oxford

description: Gene expression data from bone marrow CD34+ cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Affymetrix CEL files were pre-processed using Robust MultiChip Analysis (RMA) using GeneSpring 7.3.1.

label: Biotin

source_name: Bone marrow CD34+ cells

label_protocol: 50 ng of total RNA were amplified and biotin-labelled with the Two-Cycle cDNA Synthesis and the Two-Cycle Target Labelling and Control Reagent packages according to the standard Affymetrix protocol.

extract_protocol: Total RNA was extracted using TRIZOL following the manufacturer’s protocol

treatment_protocol: Mononuclear cells were separated using Histopaque density gradient centrifugation, labelled with CD34 MicroBeads, and then CD34+ cells were isolated using MACS magnetic cell separation columns according to the manufacturer’s recommendations.

value: bone marrow

value: CD34+ hematopoietic stem cells (HSC)

tag: disease status

value: myelodysplastic syndromes (MDS)

tag: disease subtype

value: refractory anemia with excess blasts 1 (RAEB1)

tag: genome/variation

value: other


title: HUVEC_Pre-Co_24h_rep1

description: Transfection of HUVEC with 10 nM Pre-miR-Co (Ambion) with Lipofectamine RNAiMax (Invitrogen)

source_name: HUVEC, Pre-Co transfected, 24h

value: Pre-miR-Co


title: HUVEC_Pre-17_24h_rep1


title: MDS patient 175

value: refractory anemia with excess blasts 2 (RAEB2)

value: normal


title: MDS patient 154

value: refractory anemia (RA)


title: MDS patient 112


title: HUVEC_Pre-Co_24h_rep2


title: MDS patient 122


title: MDS patient 109


title: MDS patient 111

value: del5q plus monosomy7/del7q plus other


title: MDS patient 83


title: MDS patient 105


title: MDS patient 100


title: MDS patient 110


title: MDS patient 145

value: refractory anemia with ringed sideroblasts (RARS)


title: HUVEC_Pre-Co_24h_rep3


title: MDS patient 93


title: MDS patient 137


title: MDS patient 78


title: MDS patient 182


title: MDS patient 95


title: MDS patient 86


title: MDS patient 119

value: del5q plus monosomy7/del7q plus trisomy8 plus other


title: MDS patient 77


title: MDS patient 73


title: MDS patient 126

value: del5q plus other


title: MDS patient 56


title: MDS patient 65


title: MDS patient 70


title: MDS patient 60


title: MDS patient 49


title: MDS patient 64


title: MDS patient 51


title: MDS patient 47


title: MDS patient 44


title: Hec50co cells, dosed with iressa, harvested at 12 hr, rep1

description: Gene expression data from human endometrial adenocarcinoma cell line 12 hr dosed with Iressa

source_name: type II endometrial adenocarcinoma cell line 12 hr dosed with Iressa

value: Type II endometrial adenocarcinoma


title: MDS patient 48


title: MDS patient 45


title: MDS patient 41


title: MDS patient 39


title: MDS patient 35


title: MDS patient 28


title: MDS patient 46


title: MDS patient 24


title: MDS patient 42


title: MDS patient 19


title: MDS patient 21


title: MDS patient 38


title: MDS patient 31


title: MDS patient 36


title: MDS patient 40


title: MDS patient 16


title: MDS patient 30


title: MDS patient 23


title: MDS patient 34


title: MDS patient 32


title: MDS patient 17


title: MDS patient 20


title: MDS patient 7


title: MDS patient 6


title: MDS patient 22


title: MDS patient 18


title: MDS patient 37


title: MDS patient 8


title: MDS patient 13


title: MDS patient 2


title: MDS patient 26


status: Public on Mar 12 2010

type: genomic

city: Toronto

first: DCC

last: modENCODE

state: Ontario

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

country: Canada

institute: Ontario Institute for Cancer Research

description: channel ch1 is input DNA;

hyb_protocol: 1. Prehybridize array for 1 hr in 200ml of 1xMES-Triton at 450C with 45 rpm rotation.   2. Incubate hybridization cocktail for 10min at 1000C then 10min at 450C. Spin at max speed for 3 min at RT. Transfer the supernatant to new tube. Spin for 3 more minutes use 200ml of resulted supernatant for hybridization.   3. Hybridize 18hr at 450C with 45 rpm rotation.   4. Use fluidics station EukGE-WS2v4 protocol (Affymetrix) for washing and staining.

scan_protocol: Standard Affymetrix Array Scanning Protocol was used

data_processing: M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Cell Line ML-DmBG3-c2;Antibody H3K4me3 (ab8580 lot1) extraction2_array1 channel_1

extract_protocol:
1. Grow cell cultures in large T-flasks (175-225cm2) to a density of~5x106 cells/ml. Combine the content of 2-3 flasks in one. Immediately proceed with the following steps.   2. Add 37% formaldehyde (Sigma) to final concentration 1.8% directly to the culture incubate for 10min at 250C on a rotating or rocking platform.   3. Stop reaction by adding 1.25M glycine pH 7.0 to each culture to the final concentration of 125mM. Mix well, within next 5 min aliquot cell suspension into 50ml falcon tubes and accumulate them on ice.   4. Pellet fixed cells by spinning for 2' at 1500g, +40C. Use swinging bucket rotor.   5. Resuspend each pellet in 5ml of sterile 1xPBS, pool suspensions together.   6. Pellet the cells by spinning for 2' at 1500g, +40C.   7. Resuspend the cells in 10ml of ChIP wash A solution. Transfer suspension to a new 15ml Falcon tube. Wash fixed cells for 10min at +40C using rotating wheel. Pellet as above.   8. Thoroughly resuspend fixed cells in 10ml of  ChIP wash B solution, wash for 10min at +40C. Use rotating wheel.
After treatment with formaldehyde, Drosophila tissue culture cells were lysed with SDS and sonication (on ice) in the presence of protease inhibitors.  The resulting chromatin was treated with non-ionic detergents at physiological concentrations of monovalent cations.  Ribonucleic acid was removed by RNAse A, and the DNA was purified using SDS, proteinase K, and organic extraction, followed by ethanol precipitation.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called 'Input DNA' or simply 'Input') following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: 'Isolation of ChIP Input DNA' protocol).

tag: tissue

value: CNS-derived cell-line

tag: developmental stage

value: third instar larval stage

tag: genotype

value: y v f mal

tag: sex

value: Unknown


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody H3K4me2 extraction2_array1 channel_1

label_protocol: 1. Prehybridize array for 1 hr in 200ml of 1xMES-Triton at 450C with 45 rpm rotation.   2. Incubate hybridization cocktail for 10min at 1000C then 10min at 450C. Spin at max speed for 3 min at RT. Transfer the supernatant to new tube. Spin for 3 more minutes use 200ml of resulted supernatant for hybridization.   3. Hybridize 18hr at 450C with 45 rpm rotation.   4. Use fluidics station EukGE-WS2v4 protocol (Affymetrix) for washing and staining.

value: embryo-derived cell-line

value: late embryonic stage

value: Male


title: MDS patient 4

value: bone marrow

value: CD34+ hematopoietic stem cells (HSC)

value: myelodysplastic syndromes (MDS)

value: refractory anemia with excess blasts 1 (RAEB1)


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody WDS Q2691 extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody H3K79Me1 extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line CME-W1-Cl.8+;Antibody H3K9ac extraction4_array1 channel_1

value: dorsal mesothoracic disc


description: channel ch1 is input DNA;

source_name: Cell Line ML-DmBG3-c2;Antibody H3K4me3 (ab8580 lot1) extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody H3K4me2 extraction4_array1 channel_1


title: MDS patient 3

value: normal


description: channel ch1 is input DNA;

source_name: Cell Line CME-W1-Cl.8+;Antibody H3K9ac extraction2_array1 channel_1


title: MDS patient 5

value: refractory anemia (RA)


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody H3K79Me1 extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody WDS Q2691 extraction2_array1 channel_1


title: MCF-10A cells, wild-type full-length Notch1, biological rep3

city: Boston

first: Joan

middle: S.

last: Brugge

state: MA

address: 240 Longwood Avenue

department: Department of Cell Biology

institute: Harvard Medical School

hyb_protocol: Following fragmentation, 10 ug cRNA were hybridized to the Affymetrix GeneChip Human Genome U133 Plus 2.0 Array for 16 hrs.  GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneArray Chip Scanner, HP/Affymetrix Inc.

data_processing: Background correction and normalization of microarray data was performed using the Robust Multichip Average method implemented in the rma function of R/BioConductor. The differential expression was assessed using the empirical Bayes method implemented in BioConductor Limma package. The criteria for selecting differentially expressed genes was a false discovery rate (FDR)-corrected p-value of less than 0.05 and a fold change greater than 1.5.

label_protocol: Biotinylated cRNAs were prepared according to the Affymetrix standard labeling protocol.

growth_protocol: Standard MCF10A growth conditions

extract_protocol: RNeasy miniprep columns (Qiagen) were used according to the manufacturer's instructions.

treatment_protocol: Retroviral infection for 48 hours


title: MCF-10A cells, NICD, biological rep2

description: NICDgfp-B

source_name: MCF-10A cells, NICD


title: MCF-10A cells, Notch1 L1601P+∆P, biological rep2

description: DoubleM-B

source_name: MCF-10A cells, Notch1 L1601P+∆P


description: channel ch1 is input DNA;

source_name: Cell Line ML-DmBG3-c2;Antibody Su(var)3-9 extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line ML-DmBG3-c2;Antibody SU(HW)-HB extraction4_array1 channel_1


title: MCF-10A cells, Notch1 L1601P+∆P, biological rep3

description: DoubleM-C


description: channel ch1 is input DNA;

source_name: Cell Line ML-DmBG3-c2;Antibody SU(HW)-HB extraction2_array1 channel_1


title: MCF-10A cells, Notch1 L1601P+∆P, biological rep1

description: DoubleM-A


title: MCF-10A cells, NICD, biological rep3

description: NICDgfp-C


title: MCF-10A cells, NICD, biological rep1

description: NICDgfp-A


title: MCF-10A cells, vector control, biological rep1

description: Control-A

source_name: MCF-10A cells, vector control


title: MCF-10A cells, wild-type full-length Notch1, biological rep2


title: MCF-10A cells, vector control, biological rep3

description: Control-C


description: channel ch1 is input DNA;

source_name: Cell Line ML-DmBG3-c2;Antibody RNA pol II (ALG) extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line ML-DmBG3-c2;Antibody Su(var)3-9 extraction4_array1 channel_1


title: MCF-10A cells, wild-type full-length Notch1, biological rep1


description: channel ch1 is input DNA;

source_name: Cell Line ML-DmBG3-c2;Antibody PCL Q3412 extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line Kc167;Antibody PIWI-Q2569 extraction4_array1 channel_1

value: se/e

value: Female


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody JIL1 Q3433 extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody MBD-R2 Q2567 extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line ML-DmBG3-c2;Antibody PCL Q3412 extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line ML-DmBG3-c2;Antibody RNA pol II (ALG) extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody NURF301 Q2602 extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody MBD-R2 Q2567 extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody NURF301 Q2602 extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line Kc167;Antibody PIWI-Q2569 extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody HP2 (Ab2-90) extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody JIL1 Q3433 extraction2_array1 channel_1


title: MCF-10A cells, vector control, biological rep2

description: Control-B


title: MDS patient 1

source_name: Bone marrow CD34+ cells

value: refractory anemia with ringed sideroblasts (RARS)


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody HP1c (MO 462) extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line ML-DmBG3-c2;Antibody HP1c (MO 462) extraction4_array1 channel_1

value: CNS-derived cell-line


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody HP1c (MO 462) extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody HP1b (Henikoff) extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line ML-DmBG3-c2;Antibody HP1c (MO 462) extraction2_array1 channel_1

value: third instar larval stage


description: channel ch1 is input DNA;

source_name: Cell Line CME-W1-Cl.8+;Antibody H3K9me3 (new lot) extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody HP2 (Ab2-90) extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody HP1b (Henikoff) extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line Kc167;Antibody H3K9me2-Ab2 (new lot) extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line CME-W1-Cl.8+;Antibody H3K9me2-Ab2 (new lot) extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line CME-W1-Cl.8+;Antibody H3K9me3 (new lot) extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line CME-W1-Cl.8+;Antibody H3K9me2-Ab2 (new lot) extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line CME-W1-Cl.8+;Antibody H3K18Ac (new lot) extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody dRING Q3200 extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line ML-DmBG3-c2;Antibody CP190-HB extraction4_array1 channel_1

value: y v f mal


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody CP190-HB extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line ML-DmBG3-c2;Antibody dRING Q3200 extraction2_array1 channel_1

value: Unknown


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody dMi-2 Q2626 extraction2_array1 channel_1

value: embryo-derived cell-line


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody BEAF-70 extraction4_array1 channel_1

value: late embryonic stage


description: channel ch1 is input DNA;

source_name: Cell Line ML-DmBG3-c2;Antibody BEAF-70 extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line ML-DmBG3-c2;Antibody BEAF-70 extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody dRING Q3200 extraction4_array1 channel_1

value: Male


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody BEAF-70 extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line Kc167;Antibody H3K9me2-Ab2 (new lot) extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody dMi-2 Q2626 extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line ML-DmBG3-c2;Antibody CP190-HB extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line ML-DmBG3-c2;Antibody dRING Q3200 extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody CP190-HB extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody Su(Hw)-VC extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody RNA pol II (ALG) extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody SU(HW)-HB extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line CME-W1-Cl.8+;Antibody H3K18Ac (new lot) extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line Kc167;Antibody RNA pol II (ALG) extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody RNA pol II (ALG) extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line CME-W1-Cl.8+;Antibody RNA pol II (ALG) extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line Kc167;Antibody RNA pol II (ALG) extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody SU(HW)-HB extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody Pc extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody Pc extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line ML-DmBG3-c2;Antibody Pc extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line ML-DmBG3-c2;Antibody mod2.2-VC extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line ML-DmBG3-c2;Antibody Pc extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody H4K8ac extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody H4K5ac extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line ML-DmBG3-c2;Antibody mod2.2-VC extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody H4K8ac extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody H4K5ac extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line ML-DmBG3-c2;Antibody H4K16ac(L) extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line Kc167;Antibody H4K16ac(L) extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody H3K9me3 extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody H4K16ac(M) extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody H4K16ac(L) extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line ML-DmBG3-c2;Antibody H4K16ac(L) extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody H3K9me3 extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody H4K16ac(M) extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line CME-W1-Cl.8+;Antibody H4K16ac(L) extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line ML-DmBG3-c2;Antibody H3K9me3 (new lot) extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody H4K16ac(L) extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody H3K9me2 antibody2 extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line ML-DmBG3-c2;Antibody H3K9me2-Ab2 (new lot) extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody H3K9me2 antibody2 extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line CME-W1-Cl.8+;Antibody RNA pol II (ALG) extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody H3K9ac extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line CME-W1-Cl.8+;Antibody H4K16ac(L) extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line ML-DmBG3-c2;Antibody H3K9me2-Ab2 (new lot) extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody H3K79Me2 extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line ML-DmBG3-c2;Antibody H3K79Me2 extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line ML-DmBG3-c2;Antibody H3K79Me2 extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody H3K79Me2 extraction4_array1 channel_1


title: Antibody H3K4Me3(LP) extraction4_array1

description: channel ch1 is input DNA;

source_name: Antibody H3K4Me3(LP) extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody H3K36me3 extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody H3K9ac extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line Kc167;Antibody H3K36me3 extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody H3K4me1 extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line ML-DmBG3-c2;Antibody H3K36me1 extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line ML-DmBG3-c2;Antibody H3K36me3 extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody H3K36me3 extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody H3K4me1 extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line ML-DmBG3-c2;Antibody H3K9me3 (new lot) extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody H3K4me1 extraction6_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line Kc167;Antibody H3K36me3 extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody H3K27Me3 (Abcam2) extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody H3K27Me3 (Abcam2) extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line ML-DmBG3-c2;Antibody H3K36me1 extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody H3K27Ac extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line ML-DmBG3-c2;Antibody H3K27Me3 (Abcam2) extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line ML-DmBG3-c2;Antibody H3K27Ac extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line ML-DmBG3-c2;Antibody H3K27Me3 (Abcam2) extraction2_array1 channel_1


title: Antibody H3K4Me3(LP) extraction6_array1

description: channel ch1 is input DNA;

source_name: Antibody H3K4Me3(LP) extraction6_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody H3K27Ac extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line ML-DmBG3-c2;Antibody H3K23ac extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line ML-DmBG3-c2;Antibody H3K23ac extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line ML-DmBG3-c2;Antibody H3K27Ac extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody H3K23ac extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody H3K23ac extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody H3K18ac extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody H3K18ac extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody GAF extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line Kc167;Antibody H2B-ubiq (NRO3) extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line ML-DmBG3-c2;Antibody H3K18ac extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody H2B-ubiq (NRO3) extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line ML-DmBG3-c2;Antibody H2B-ubiq (NRO3) extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody H2B-ubiq (NRO3) extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line Kc167;Antibody H2B-ubiq (NRO3) extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line ML-DmBG3-c2;Antibody H2B-ubiq (NRO3) extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody Ez extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody Ez extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody Ez extraction6_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody CTCF-VC extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody CTCF-VC extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody CP190-VC extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line ML-DmBG3-c2;Antibody CTCF-VC extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line ML-DmBG3-c2;Antibody CTCF-VC extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line ML-DmBG3-c2;Antibody H3K18ac extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody GAF extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody Chro(Chriz)WR extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody CP190-VC extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody Chro(Chriz)BR extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody Chro(Chriz)WR extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody Chro(Chriz)BR extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line CME-W1-Cl.8+;Antibody Chro(Chriz)BR extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line ML-DmBG3-c2;Antibody Chro(Chriz)BR extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line Kc167;Antibody Chro(Chriz)BR extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line Kc167;Antibody Chro(Chriz)BR extraction4_array1 channel_1


title: Standard condition, Col-0 plant #3; sir1-1 plant#3, dye swap

city: Heidelberg

first: Markus

last: Wirtz

address: Im Neuenheimer Feld 360

department: Molecular Biology of Plants

institute: University of Heidelberg

description: Biological replicate 3 (Col-0 plant#3 versus sir1-1 plant#3) technical replicate 2 with dye switch

hyb_protocol: Labeled cDNA was concentrated in a vacuum concentrator to a final volume of 20 µL. The resulting sample was immediately denatured by the addition of 20 µL of prewarmed hybridization buffer H (5xSSC, 0.1% [v/v] SDS, 0.06% [w/v] fish sperm DNA and 40% [v/v] formamide) followed by incubation at 100°C for 5 min. The microarray was prehybridized with buffer P (53 SSC, 0.2% SDS, and 0.5% bovine serumalbumin) for 45 min and washed three times with 250 mL of double-distilled water, before the denatured sample was applied and incubated for 20 h at 50°C in a Slide Booster (Advalytix).

scan_protocol: Slides were scanned using the ScanArray5000 confocal laser scanner (Packard BioChip Technologies)

data_processing: Signals were quantified with the GenePix Pro 4.1 analysis software (Axon Instruments). The microarray datasets were analyzed with the M-CHiPS software set described in Fellenberg, K. et al (2001). In M-CHiPS, differentially expressed genes were identified using the linear models of the limma package according to Smyth, G.K. (2004). Regression coefficients, moderated t-statistic, and p-values were calculated using Empirical Bayesian statistics, accounting for a complete pair-wise comparisons contrast matrix (across all samples). P-values computed for the F-statistic were adjusted for multiple testing by Benjamini and Hochberg's algorithm, to control the False Discovery Rate (FDR) at 5%.  Genes were selected that show intensity levels of more than 1000 in at least one of the conditions and at the same time show adjusted p-values smaller 0.05.

organism: Arabidopsis thaliana

source_name: soil grown plants under short day conditions

label_protocol: 10µg of total RNA was transcribed with SuperscriptIII Reverse Transcriptase (Invitrogen) with Random hexamer primers (Invitrogen) and labeled with Cy3 or Cy5 at 42°C for 12h, according to the manufacturer's instructions, labeled cDNA was purified with the QiaQuick™ PCR Purification Kit (Quiagen)

growth_protocol: Arabidopsis thaliana plants were grown for 7 weeks on soil under short day conditions (humidity 50%, day: 8.5 hours light, 100µE, 22°C; night: 18°C), 150mg of rossette leaves were harvested from independent plants

extract_protocol: Leaf material (150mg fresh weight) was harvested and grinded in liquid nitrogen; total RNA was extracted with Rneasy Plant Mini Kit (Qiagen) and RNase free DNASe Kit (Qiagen), according to the manufacturer's protocols

tag: strain

tag: genotype/variation

value: wildtype


title: Antibody H3K4Me3(LP) extraction2_array1

description: channel ch1 is input DNA;

source_name: Antibody H3K4Me3(LP) extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line ML-DmBG3-c2;Antibody H3K36me3 extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody BEAF-HB extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody BEAF-HB extraction2_array1 channel_1


title: Standard condition, Col-0 plant #3; sir1-1 plant#3

description: Biological replicate 3 (Col-0 plant#3 versus sir1-1 plant#3) technical replicate 1


title: Standard condition, Col-0 plant #1; sir1-1 plant#1

description: Biological replicate 1 (Col-0 plant#1 versus sir1-1 plant#1) technical replicate 1


title: Standard condition, Col-0 plant #2; sir1-1 plant#2

description: Biological replicate 2 (Col-0 plant#2 versus sir1-1 plant#2) technical replicate 1


title: Standard condition, Col-0 plant #2; sir1-1 plant#2, dye swap

description: Biological replicate 2 (Col-0 plant#2 versus sir1-1 plant#2) technical replicate 2 with switched dyes


description: channel ch1 is input DNA;

source_name: Cell Line CME-W1-Cl.8+;Antibody Chro(Chriz)BR extraction4_array1 channel_1


title: Standard condition, Col-0 plant #1; sir1-1 plant#1, dye swap

description: Biological replicate 1 (Col-0 plant#1 versus sir1-1 plant#1) technical replicate 2 with switched dyes


description: channel ch1 is input DNA;

source_name: Cell Line ML-DmBG3-c2;Antibody Chro(Chriz)BR extraction4_array1 channel_1


title: MCF-10A cells, overexpression TAp63γ, biological rep3

hyb_protocol: Following fragmentation, 10 ug cRNA were hybridized to the Affymetrix GeneChip Human Genome U133Av2 for 16 hrs.  GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: Background correction and normalization of microarray data was performed using the Robust Multichip Average method implemented in the rma function of R/BioConductor.

source_name: MCF-10A cells, overexpression TAp63γ

treatment_protocol: Retroviral or adenoviral infection for 48 hours


title: MCF-10A cells, overexpression ΔNp63α, biological rep3

source_name: MCF-10A cells, overexpression ΔNp63α


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody H4AcTetra extraction4_array1 channel_1


title: rice wild-type panicle Rep1

city: Beijing

first: Wenying

last: Xu

address: Datun Road, Chaoyang District

country: China

institute: Institute of Genetics and Developmental Biology of the Chinese Academy of Sciences

description: Gene expression data from rice wild-type panicle

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45 degree on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChip was scanned using the Affymetrix GeneChip Scanner

data_processing: The data were analyzed with GCOS software (Microarray Suite version 5.0, MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Oryza sativa

source_name: rice wild-type panicle Rep1

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: plants were grown in the field in May to October in Fuzhou, China

extract_protocol:
the panicle (2-10mm) was collected directly
total RNA was isolated by  TRIZOL and  purified by Qiagen RNeasy kit.

value: Gui-630 (indica) X Taiwanjing (Japonica)

value: rice panicle (2-10mm)


title: rice mutant  lemmata panicle rep 3

description: Gene expression data from rice mutant lemmata panicle

source_name: rice mutant lemmata panicle Rep3

value: Oryza sativa L. ssp. Indica, mutant lemmata


title: rice mutant  lemmata panicle rep 2

source_name: rice mutant lemmata panicle Rep2


title: rice mutant lemmata panicle rep 1

source_name: rice mutant lemmata panicle Rep1


title: rice wild-type panicle Rep2

source_name: rice wild-type panicle Rep2


title: MCF-10A cells, overexpression vector control, biological rep1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody H4AcTetra extraction2_array1 channel_1


title: MCF-10A cells, overexpression vector control, biological rep3


title: JF14b

city: London

first: James

last: Flanagan

address: Du Cane Rd

department: Dept of Oncology

institute: Imperial College London

description: meDIP of breast cancer

hyb_protocol: The arrays were hybridized using Affymetrix hybridization reagents, using an Affymetrix hybridization oven, and stained/washed using the Fluidics Station 450 (Affymetrix, High Wycombe, UK)

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000 7G with autoloader.

data_processing: Raw data were extracted using GeneChip Operating System (GCOS) software from Affymetrix. Raw data were analyzed using the MAT algorithm which models the baseline probe behavior and standardizes the probe value through the probe model {Johnson et al PNAS 2006}. The MAT output t-values (MeDIP minus input) was then calculated for each probe. For each gene an average (+/- 250 bp) was used.

source_name: MeDIP Breast Tumor DNA

label_protocol: Samples (6μg of DNA) were enzymatically fragmented (APE/UDG) and labeled using the WT Labeling Kit (Affymetrix) to add biotinylated compound to the ends of the fragments

extract_protocol: MeDIP was performed using the Diagenode MeDIP kit and the manufacturer’s protocol (Diagenode, Leige, Belgium). We performed triplicate MeDIP reactions for each tumor and amplified using whole-genome amplification with Genomiphi V2 and the manufacturer’s protocol (GE Healthcare). The triplicates were then pooled for one MeDIP array and one input array per sample.

tag: mutation

source_name: Input DNA


title: JF2b1

description: meDIP of breast cancer


title: MCF-10A cells, shRNA targetting p63 TA, biological rep2

source_name: MCF-10A cells, shRNA targetting p63 TA


title: MCF-10A cells, overexpression vector control, biological rep2


title: MCF-10A cells, overexpression TAp63γ, biological rep2


title: MCF-10A cells, overexpression TAp63γ, biological rep1


title: JF37b

description: meDIP of breast cancer


title: JF8b

description: meDIP of breast cancer

value: BRCAx


description: channel ch1 is input DNA;

source_name: Cell Line Kc167;Antibody H4K16ac(L) extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: Cell Line S2-DRSC;Antibody Su(Hw)-VC extraction4_array1 channel_1


title: JF13b

description: meDIP of breast cancer


title: MCF-10A cells, shRNA vector control, biological rep2

source_name: MCF-10A cells, shRNA vector control


title: MCF-10A cells, shRNA targetting p63 DBD, biological rep2

source_name: MCF-10A cells, shRNA targetting p63 DBD


title: JF25b

description: meDIP of breast cancer


title: MCF-10A cells, overexpression ΔNp63α, biological rep2


title: JF2b

description: meDIP of breast cancer


title: JF38b

description: meDIP of breast cancer


title: MCF-10A cells, shRNA vector control, biological rep1


title: JF41b

description: meDIP of breast cancer


title: MCF-10A cells, shRNA targetting p63 TA, biological rep1


title: MCF-10A cells, shRNA targetting p63 DBD, biological rep1


title: JF5b

description: meDIP of breast cancer


title: JF20b

description: meDIP of breast cancer


title: MCF-10A cells, overexpression ΔNp63α, biological rep1


title: JF15b

description: meDIP of breast cancer


title: rice wild-type panicle Rep3

source_name: rice wild-type panicle Rep3


title: JF9b

description: meDIP of breast cancer


title: JF31b

description: meDIP of breast cancer


title: JF6b1

description: meDIP of breast cancer


title: JF18b

description: meDIP of breast cancer


title: JF3b

description: meDIP of breast cancer


title: JF27b

description: meDIP of breast cancer


title: JF1b1

description: meDIP of breast cancer


title: JF16b

description: meDIP of breast cancer


title: JF7b

description: meDIP of breast cancer


title: JF24b

description: meDIP of breast cancer


title: JF26b

description: meDIP of breast cancer


title: JF4b

description: meDIP of breast cancer


title: JF39b

description: meDIP of breast cancer


title: JF29b

description: meDIP of breast cancer


title: JF40b

description: meDIP of breast cancer


title: JF36b

description: meDIP of breast cancer


title: JF4b1

description: meDIP of breast cancer


title: JF17b

description: meDIP of breast cancer


title: JF6b

description: meDIP of breast cancer


title: JF3b1

description: meDIP of breast cancer


title: JF5b1

description: meDIP of breast cancer


title: Normal_8

status: Public on Mar 11 2010

city: Providence

first: Graham

middle: M

last: Poage

state: RI

address: 70 Ship St

institute: Brown University

hyb_protocol: Illumina GoldenGate® methylation bead arrays interrogated 1505 CpG loci associated with 803 cancer-related genes processed at the UCSF Institute for Human Genetics, Genomics Core Facility as described in Bibikova et al. High-throughput DNA methylation profiling using universal bead arrays. Genome research 2006;16:383-93.

data_processing: Illumina BeadStudio Methylation software was used for dataset assembly. Fluorescent signals for methylated (Cy5) and unmethylated (Cy3) alleles give methylation level: beta =(max(Cy5 , 0))/(|Cy3| + |Cy5| + 100) with ~30 replicate bead measurements per locus. Detection P-values determined poor performing samples (n=2) and CpG loci (n=8), which were removed from analysis. X chromosome loci were also removed, leaving 1413 CpG loci associated with 773 genes. Raw average beta values were used and not subjected to normalization as per manufacturer's recommendations

source_name: head&neck normal_59167U

label_protocol: sodium bisulfite modified using the EZ DNA Methylation Kit (Zymo Research, Orange, CA).

extract_protocol: DNA from fresh frozen tissue was isolated with QIAamp DNA mini kit (Qiagen, Valencia, CA)

tag: tumor site

tag: state

value: methylated

value: unmethylated


title: Normal_7

scan_protocol: Bibikova et al. High-throughput DNA methylation profiling using universal bead arrays. Genome research 2006;16:383-93.

source_name: head&neck normal_59167T


title: Normal_9

source_name: head&neck normal_59240L


title: Normal_6

source_name: head&neck normal_59167L


title: Normal_11

source_name: head&neck normal_59375U


title: fibroblasts_mock transfected_rep2

city: New York

first: Thomas

last: Templin

state: NY

address: 630 West 168th Street

institute: Columbia University Medical Center

description:
Gene expression after transfection with empty transfection complexes.
xcont_3_24_2

hyb_protocol: Following the manufacturer’s recommendations, 1.5 µg labeled cRNA (>9 pmol Cy3 per µg cRNA) was fragmented and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) using the Gene Expression Hybridization Kit.

scan_protocol: Microarrays with labeled cRNA were scanned at 5 µm resolution with an Agilent DNA Microarray Scanner (G2505B).

data_processing: Default parameters of Feature Extraction v. 10.5 software (Agilent) were used for image analysis, data extraction, background correction, and flagging of non-uniform features. Background-corrected intensities were log2-transformed and median-normalized using BRB-ArrayTools v. 3.8.0. Non-uniform outliers or features not significantly above background intensity in 25% or more of the hybridizations were removed, leaving a set of 5800 features that were used for subsequent analyses.

source_name: AG01522 normal human fibroblasts, mock-transfected

label_protocol: For array analysis, 0.3 µg RNA was used to produce Cyanine-3 (Cy3)-labeled cRNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent).

growth_protocol: Human fibroblasts (AG01522) were received as cell cultures from Coriell at passage (PDL) 16 and expanded until PDL 20 by culturing in EEMEM (Invitrogen) supplemented with 15% FBS (ATCC).

extract_protocol: Total RNA was isolated using the Ribopure kit (Applied Biosystems), following the manufacturer's instructions.

treatment_protocol: Typically, for a 60 mm plate, 500 µl of optiMEM (Invitrogen) was mixed with 2.5 µl of TransIT-siQUEST (Mirus) and incubated for 10 min. The small RNA fraction (800 ng in ~15 µl) was added to this mixture and incubated for 10 more min. This mixture was placed on the bottom of a 60 mm plate and immediately 500,000 cells in 3.5 ml of complete media were added followed by incubation of the cells for 38 h. The media was changed after 24 h. Control cells were mock-transfected using the same conditions without the addition of RNA.

value: cultured fibroblasts

tag: supplier

value: Coriell

tag: passage

value: mock


title: fibroblasts_miRNA transfected_rep4

description:
Gene expression after transfection with endogenous small RNA fraction.
mir_5_72_1

source_name: AG01522 normal human fibroblasts, miRNA-transfected

tag: cell line

value: miRNA


title: fibroblasts_mock transfected_rep3

description:
Gene expression after transfection with empty transfection complexes.
xcont_4_71_1

tag: cell type


title: fibroblasts_mock transfected_rep5

description:
Gene expression after transfection with empty transfection complexes.
xcont_6_71_3

tag: transfection


title: Normal_4

source_name: head&neck normal_58926U


title: Normal_5

source_name: head&neck normal_59036T


title: Normal_10

source_name: head&neck normal_59303U


title: Normal_2

source_name: head&neck normal_58926L


title: fibroblasts_mock transfected_rep4

description:
Gene expression after transfection with empty transfection complexes.
xcont_5_71_2


title: Normal_3

source_name: head&neck normal_58926T


title: Normal_1

source_name: head&neck normal_58862L


title: fibroblasts_miRNA transfected_rep1

description:
Gene expression after transfection with endogenous small RNA fraction.
mir_2_24_4


title: fibroblasts_miRNA transfected_rep3

description:
Gene expression after transfection with endogenous small RNA fraction.
mir_4_71_4


title: fibroblasts_mock transfected_rep1

description:
Gene expression after transfection with empty transfection complexes.
xcont_2_24_1


title: fibroblasts_miRNA transfected_rep2

description:
Gene expression after transfection with endogenous small RNA fraction.
mir_3_14_1


title: fibroblasts_miRNA transfected_rep5

description:
Gene expression after transfection with endogenous small RNA fraction.
mir_6_72_2


title: 001926_WT

city: Raleigh

first: David

middle: Ryan

last: Georgianna

state: NC

address: 851 Main Campus Dr

department: Plant Pathology

institute: North Carolina State University

description: Investigators: Jiujang Yu, Sigal Horowitz, Nancy Keller. 10E5 conidia were inoculated into liquid GMM + 2% sorbitol in a 60 x 15 mm Petri plate. Plates were incubated at 29°C under continuous dark for 6 d.  RNA was isolated using a trizol prep according to manufacturer's instructions

hyb_protocol: Purdue Genomics Core Facility, Standard Affymetrix protocols were followed for hybridization of single-stranded cRNA to the single-stranded DNA oligonucleotides on the Affymetrix GeneChip® and to generate .DAT and .CEL files (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).

data_processing: RMA background correction, log2 transformation, quantile normalization, median polish probe summary, using JMP Genomics v3.0

organism: Aspergillus flavus

source_name: WT sclerotia

growth_protocol: see description column

extract_protocol: see description column: For total RNA extraction the Qiagen RNeasy kit RNA cleanup protocol was typically used, for most samples a phenol chloroform extraction protocol preceeded use of the RNeasy kit. For some samples phenol chloroform extractions and LiCl precipitation was used to purify RNA, this protocol is available from http://www.aspergillusflavus.org/protocols/.

treatment_protocol: see description column

value: WT


title: 001864_WT_7

scan_protocol: Purdue Genomics Core Facility, Standard Affymetrix protocols were followed for hybridization of single-stranded cRNA to the single-stranded DNA oligonucleotides on the Affymetrix GeneChip® and to generate .DAT and .CEL files (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).


title: 001928_OE_laeA

source_name: OE sclerotia

label_protocol: Purdue Genomics Core Facility, Standard Affymetrix protocols were followed for hybridization of single-stranded cRNA to the single-stranded DNA oligonucleotides on the Affymetrix GeneChip® and to generate .DAT and .CEL files (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).

value: laeA OE


title: 001873_WT_4


title: 001576_37_rep4

description: Investigator: Gary Payne. Inbred Line B73 was grown in the field at Clayton, NC.  Ears containing kernels at the late milk to early dough stage of development (Ritchie et al. 1997) were harvested, placed on ice, and taken to the laboratory. Once in the laboratory, intact kernels were plucked from each ear.  Only sound, intact kernels with no visible injury were chosen.  Kernels were surface disinfested using the following protocol: kernels were dipped in 95% ethanol, transferred to a 10% bleach solution containing 0.1% Tween and soaked for 4 minutes, transferred to autoclaved diH2O and soaked for 4 minutes, and transferred again to autoclaved diH2O and soaked for 4 minutes.  The kernels were then placed on sterile paper towels in a laminar flow hood and allowed to dry for 10-15 minutes.  Conidia from the wild-type A. flavus strain NRRL 3357, obtained from the National Center for Agricultural Utilization Research in Peoria, IL, were collected with 0.05% Triton-X100 from PDA plates incubated at 28ºC for 10 days.  Conidia were counted using a hemacytometer and a diluted conidial suspension of 1x106/ml was created using 0.05% TritonX-100.  A sterilized stainless steel pin was dipped into the conidial suspension and inserted once through the top of each kernel to a depth of approximately 5 mm.  Eight inoculated kernels from a single ear were placed in a scintillation vial.  The lids of each vial were tightened and then loosened by rotating the cap lid 360º.  This procedure provided uniform air exchange in the vials.  The vials were incubated at 37ºC in the dark for 4 days.  Each day, the vials were briefly shaken to prevent moisture from collecting on the bottom of the vials.  After 4 days, half of the vials were moved to a 28ºC incubator.  The vials were incubated for one additional day (24 hours) at the respective temperatures.  After 5 days of incubation, the kernels were flash frozen in liquid nitrogen and stored at -80ºC until RNA extraction.

source_name: Detached B73 kernels


title: 001875_OE_laeA_9


title: 001784_B73_Af_Rep3_72hrs

description: Investigator: Gary Payne. Inbred line B73 was planted at the Central Crops Research Station at Clayton, NC during the 2006, 2007, and 2008 growing season. The field was laid out in a randomized block design. Each block represented a biological rep; all experiments had a total of three replicates. Corn was hand pollinated to ensure all experimental ears were at the same stage of development. Ear selection for inoculation was based on date of pollination. Ears identified at the blister, milk, dough, and dent stages were used for each treatment. Ears within +/- 1 day of pollination were husked such that the husk remained attached. The exposed pin-bar needles were dipped into either a 1x106 spores/mL conidial suspension. The needles were then inserted into a row of kernels, introducing approximately 11-13 conidia into each kernel. Five rows were inoculated per ear. Using a rubber band, the husk was repositioned around the ear and a pollinating bag placed over the ear. At the late milk-early dough stage of development, kernels were inoculated with A.flavus. Harvesting took place 48, 60, 72, and 96 hours after inoculation. Only two replicates were used in the analysis due to the lack of infection in one of the replicates.

source_name: 72 h maize B73 infection


title: 001575_37_rep3


title: 001866_OE__laeA_9


title: 001774_B73_Af_Rep2_60hrs

source_name: 60 h maize B73 infection


title: 001778_B73_Af_Rep3_96hrs

source_name: 96 h maize B73 infection


title: 001927_delta_laeA

source_name: delta laeA sclerotia

value: delta laeA


title: 001776_B73_Af_Rep2_96hrs


title: 001574_28_rep5


title: 001573_28_rep4


title: 001775_B73_Af_Rep2_72hrs


title: 001862_delta_laeA_5


title: 001577_37_rep5


title: WK3_Day5P

description: Investigator: Charles Woloshuk. Whole kernels (WK), endosperm (ENDO) and germs of B73 were autoclaved, placed in vials, inoculated with 1 X 105 conidia, and incubated at 29 C (+/- 1 C) for 5 days.

source_name: Autoclaved B73 maize whole kernel


title: 000831_28C

description: Investigator: Gary Payne. One replication only.  A 1x108 condial suspension of A. flavus 3357 was added to 100ml  of modified A&M medium (320ug/ml arginine added) in 500 ml flask.  The cultures were incubated as shake cultures (200 rpm) for 24 hrs at either 28 or 37C.

source_name: A&M shake culture


title: 001783_B73_Af_Rep3_60hrs


title: MilkRep2_Aflavus

description: Investigator: Gary Payne. Inbred line B73 was planted at the Central Crops Research Station at Clayton, NC during the 2006, 2007, and 2008 growing season. The field was laid out in a randomized block design. Each block represented a biological rep; all experiments had a total of three replicates. Corn was hand pollinated to ensure all experimental ears were at the same stage of development. Ear selection for inoculation was based on date of pollination. Ears identified at the blister, milk, dough, and dent stages were used for each treatment. Ears within +/- 1 day of pollination were husked such that the husk remained attached. The exposed pin-bar needles were dipped into either a 1x106 spores/mL conidial suspension. The needles were then inserted into a row of kernels, introducing approximately 11-13 conidia into each kernel. Five rows were inoculated per ear. Using a rubber band, the husk was repositioned around the ear and a pollinating bag placed over the ear for approximately 4 days.

source_name: Maize B73 Milk


title: 001572_28_rep3


title: 001865_delta_laeA_8


title: 000830_37C


title: 001782_B73_Af_Rep3_48hrs

source_name: 48 h maize B73 infection


title: WKRep1


title: Milk_Aflavus_Rep3


title: Milk_aflavus_Rep1


title: 001773_B73_Af_Rep2_48hrs


title: 02398_G3

source_name: Autoclaved B73 maize germ


title: WKRep2


title: 02394_E2

source_name: Autoclaved B73 maize endosperm


title: 02393_E1


title: 02395_E3


title: Dough_aflavus_Rep2

source_name: Maize B73 Dough


title: 02396_G1


title: Dough_Af_Rep1


title: DentRep2_Aflavus

source_name: Maize B73 Dent


title: Dent_aflavus_Rep1


title: 02397_G2


title: Dent_Aflavus_Rep3


title: Blister_aflavus_Rep1

source_name: Maize B73 Blister


title: 001134_OE_2_6h

description: Investigator:  Nancy Keller.  Gene expression in three strains of A. flavus; Wild type (WT), leaA deletion (delta_leaA); and over expression (OE). Cultures were sampled at 6 and 24 hr.

source_name: laeA OE_2_6h


title: 001136_OE_1_24h

source_name: laeA OE_1_24h


title: 001135_OE_3_6h

source_name: laeA OE_3_6h


title: Blister_Aflavus_Rep3


title: 001137_OE_2_24h

source_name: laeA OE_2_24h


title: BlisterRep2_Aflavus


title: Porcine 7 liver tissue

city: Ya'an

first: Jun

last: He

address: Xinkang Road

institute: Sichuan Agricultural University

description: Gene expression after diet treatment for 21 d

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

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

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 020109_D_F_20090417) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. The quantile normalization method was used in our microarray analysis.

organism: Sus scrofa

source_name: Liver tissue

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

extract_protocol: Total RNA was isolated from liver using Trizol reagent (Invitrogen, Carlsbad, CA, USA) and further purified by Qiagen RNeasy Mini kit (Qiagen, Valencia, CA, USA).

treatment_protocol: Pigs were housed individually in metabolism cages (0.7×1.5m) with woven wire flooring in an environmentally controlled room (22 to 24℃) and were given ad libitum access to water through a water nipple. All Pigs were fed their assigned diet (either wheat or cassava starch) for 21 d.

tag: diet

value: Cassava starch diet


title: Porcine 2 liver tissue

value: Wheat starch diet


title: 001138_OE_3_24h

source_name: laeA OE_3_24h


title: Porcine 6 liver tissue


title: ILTV Infected chicken embryo lung cells at 7 dpi Replicate 3

city: Fayetteville

first: Byung-whi

last: Kong

state: AR

address: 1260 W. Maple, POSC, L-426

department: Poultry Science

institute: University of Arkansas

description: Biological replicate 3 of 3. ILTV infected chicken embryo lung cells, harvested at 7dpi.

hyb_protocol: An equal amount (825 ng) of Cy3 and Cy5 labeled cRNA probes were mixed with gene expression hybridization kit (Agilent, part No. 5188-5242) and hybridized on a 4X44K Agilent custom chicken oligo microarray (array ID: 017698). The hybridized slides were washed using a commercial kit package (Agilent).

scan_protocol: Scanned on an Genepix 4000B scanner (Molecular Devices Corporation)

data_processing: Gene Pix Pro (v 6.1) with Accuity software (v 4.0). Background-corrected red and green intensities for each spot were used in the subsequent analysis. Global normalization based on local polynomial regression (loess) was applied to the intensities for removing effects which arise from undesirable systematic variations in microarray experiment.

organism: Gallus gallus

source_name: Embryo lung cells

label_protocol: 2 µg of total RNA were used for this experiment, and all procedures were followed to manufacturer's instructions.

growth_protocol: Cells were grown in a 1:1 ratio of mammary epithelial growth media (MEGM; Lonza, Rockland, ME, USA) and Dulbecco’s Modified Eagle’s Medium (DMEM, 0.45% glucose) plus 2% fetal bovine serum (FBS), 100 units/ml penicillin, 100 µg/ml streptomycin, and 2 mM L-glutamine in 10 cm tissue culture plates (Sarstedt Inc., Newton, NC, USA) pretreated with 0.5 % gelatin in PBS to improve cell adhesion.

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

tag: infection

value: embryo lung cells

treatment_protocol: ILTV was infected the chicken embryonic lung cells at a multiplicity of infection (m.o.i.) of 0.1.

value: infectious laryngotracheitis virus (ILTV)

tag: time point

value: 7 dpi

tag: replicate


title: Porcine 11 liver tissue


title: Porcine 14 liver tissue


title: 001131_delta_laeA2_24h


title: 001132_delta_laeA3_24h


title: ILTV Infected chicken embryo lung cells at 5 dpi Replicate 3

description: Biological replicate 3 of 3. ILTV infected chicken embryo lung cells, harvested at 5dpi.

value: 5 dpi


title: 001133_OE_1_6h

source_name: laeA OE_1_6h


title: Porcine 10 liver tissue


title: Porcine 15 liver tissue


title: Porcine 3 liver tissue


title: 001127_delta_laeA1_6h


title: ILTV Infected chicken embryo lung cells at 3 dpi Replicate 3

description: Biological replicate 3 of 3. ILTV infected chicken embryo lung cells, harvested at 3dpi.

value: 3 dpi


title: 001129_delta_laeA3_6h


title: 001130_delta_laeA1_24h


title: 001128_delta_laeA2_6h


title: ILTV Infected chicken embryo lung cells at 1 dpi Replicate 3

description: Biological replicate 3 of 3. ILTV infected chicken embryo lung cells, harvested at 1dpi.

value: 1 dpi


title: ILTV Infected chicken embryo lung cells at 7 dpi Replicate 2

description: Biological replicate 2 of 3. ILTV infected chicken embryo lung cells, harvested at 7dpi.


title: 001125_WT_2_24h


title: 001126_WT_3_24h


title: 002197_RIB40_Koji_2d_3

description: Investigator: Gary Payne. A comaprison of gene expression between A. flavus NRRL3357 and A. oryzae RIB40 on wheat bran and field inoculated maize line B73. Wheat bran koji is commonly used for propagation of A. oryzae prior to fermentations. Opportunistic maize infection is part of the A. flavus lifestyle as a pathogen.

organism: Aspergillus oryzae

source_name: 2 day wheat bran koji


title: 001121_WT_1_6h


title: ILTV Infected chicken embryo lung cells at 7 dpi Replicate 1

description: Biological replicate 1 of 3. ILTV infected chicken embryo lung cells, harvested at 7dpi.


title: ILTV Infected chicken embryo lung cells at 5 dpi Replicate 2

description: Biological replicate 2 of 3. ILTV infected chicken embryo lung cells, harvested at 5dpi.


title: 001122_WT_2_6h


title: 002195_RIB40_Koji_2d_1


title: 002194_3357_Koji_2d_3


title: 001124_WT_1_24h


title: ILTV Infected chicken embryo lung cells at 3 dpi Replicate 2

description: Biological replicate 2 of 3. ILTV infected chicken embryo lung cells, harvested at 3dpi.


title: 002196_RIB40_Koji_2d_2


title: ILTV Infected chicken embryo lung cells at 5 dpi Replicate 1

description: Biological replicate 1 of 3. ILTV infected chicken embryo lung cells, harvested at 5dpi.


title: ILTV Infected chicken embryo lung cells at 1 dpi Replicate 2

description: Biological replicate 2 of 3. ILTV infected chicken embryo lung cells, harvested at 1dpi.


title: ILTV Infected chicken embryo lung cells at 3 dpi Replicate 1

description: Biological replicate 1 of 3. ILTV infected chicken embryo lung cells, harvested at 3dpi.


title: ILTV Infected chicken embryo lung cells at 1 dpi Replicate 1

description: Biological replicate 1 of 3. ILTV infected chicken embryo lung cells, harvested at 1dpi.


title: 002192_3357_Koji_2d_1


title: 002193_3357_Koji_2d_2


title: Transcriptome analysis_PknB_chip26_1

city: Wuerzburg

first: Stefanie

last: Donat

address: Roentgenring 11

department: Institute for Molecular Infection Biology

institute: University of Wuerzburg

description:
Staphylococcus aureus subsp. aureus strain NCTC 8325 wild type. This strain was originally used as a propagating strain for bacteriophage 47 of the international typing set of bacteriophages. This strain is generally considered to be the prototypical strain for most genetic research on S. aureus. Source DNA is available from www.narsa.net
S. aureus NCTC 8325 possesses 11-bp deletion in rsbU.

hyb_protocol: Microarray transcriptional profiling by competitive hybridization of fluorescence-labeled cDNA was performed using the custom PCR product full-genome chip sciTracer (Scienion, Berlin, Germany) containing 2666 unique open reading frames representing 90% of the S. aureus N315 genome (NC_002745). Additional information on the microarray platform is described elsewhere. To increase reproducibility, each experiment was performed 5 times including a dye swap resulting in five chips per competitive comparison. All hybridizations were done with equal amounts of fluorescence-labeled cDNA probes or picomols of dye. Fluorescence-labeled cDNA probes were mixed in hybridization buffer (Scienion) in a total volume of 55 µl and denatured at 95°C for 2 min and subsequently applied to the microarray slide following incubation at 42°C for 72 hours under humidified conditions according to the manufacturer’s instructions. Hybridized microarrays were washed at room temperature in SSC buffer with decreasing salt concentrations (1 x SSC/0.3% SDS for 5 min, 0.2 x SSC for 5 min, 0.06 x SSC for 30s).

scan_protocol: The intensity of fluorescence of the microarray was scanned with a GenePix 4000B scanner (Axon Instruments/Distribution by Biozyme Scientific GmbH, Hessisch Oldendorf, Germany). TIFF images were captured and analysed with GenePixPro4.1 software (Axon Instruments). The actual signal intensity was calculated by substracting the mean value of the local background intensity from the mean value of the signal intensity of the individual spot.

data_processing: The data sets were then normalized by using Acuity 4.0 software (Axon Instruments) and by applying the LOWESS algorithm. Significant changes of gene expression were determined by implementing SAM (significance analysis of microarrays; http://www-stat.stanford.edu/~tibs/SAM/; (Tusher, V. G., R. Tibshirani, and G. Chu. 2001. Significance analysis of microarrays applied to the ionizing radiation response. Proc.Natl.Acad.Sci.U.S.A 98:5116-5121.)) using the one class response and a false discovery rate of < 1.5% with a medium number of falsely called significant genes of <1.5.

organism: Staphylococcus aureus subsp. aureus NCTC 8325

source_name: Staphylococcus aureus NCTC 8325

label_protocol: Fluorescence-labeled single-stranded cDNA was obtained by reverse transcription of total RNA. The RNA was isolated from cultures in the exponential growth phase at an OD600 of 1.0 at 37°C. 10 µg of total RNA from S. aureus NCTC 8325 wild type was used for reverse transcription with random primers and Superscript ІІІ reverse transcriptase (Invitrogen). The integrity of RNA was analysed with a Bioanalyzer (Agilent Technologies). The fluorescent labelling was performed during the RT reaction by incorporating the dye Cy3 according to the manufacture`s instruction (Scienion Berlin, Germany). Four different biological experiments were made, and a reverse labelling (dye switch) experiment was performed to minimize bias due to differential dye bleaching or incorporation of Cy3 and Cy5 dyes during the RT reaction.

extract_protocol: Total RNA was isolated from S. aureus cultures in exponential growth phase (OD600 of 1.0). Bacteria were harvested with addition of RNA Protect (QIAGEN, Hilden, Germany) according to the manufacturer`s instruction. The cells were centrifuged for 10 min at 5,000 x g, and the bacterial pellet was resuspended in 1 ml RLT-buffer and mechanically disrupted with glass beads in a Fast Prep shaker (Qbiogene, Heidelberg, Germany) two times for 45 s at a speed of 6.5 units. The cell lysate was centrifuged for 30 s at 13,000 x g, and the supernatant was used for RNA isolation. RNA was isolated using an RNeasy Mini kit (QIAGEN) according to the standard QIAGEN RNeasy protocol. The isolated RNA was treated with RNase-free DNase І (Roche, Penzberg, Germany), to remove DNA template. The integrity of RNA was monitored by analysis with a Bioanalyzer (Agilent Technologies). Only probes with a RNA integrity number (RIN) >9 were used in further experiments.

treatment_protocol: S. aureus wild type NCTC 8325 cultures for RNA preparations were diluted to an OD600 of 0.05 from LB overnight cultures into fresh LB-medium and further incubated until they reached an OD600 ~1.0.

value: NCTC 8325

value: wildtype

source_name: Staphylococcus aureus NCTC 8325 ΔpknB

label_protocol: Fluorescence-labeled single-stranded cDNA was obtained by reverse transcription of total RNA. The RNA was isolated from cultures in the exponential growth phase at an OD600 of 1.0 at 37°C. 10 µg of total RNA from S. aureus NCTC 8325 ΔpknB was used for reverse transcription with random primers and Superscript ІІІ reverse transcriptase (Invitrogen). The integrity of RNA was analysed with a Bioanalyzer (Agilent Technologies). The fluorescent labelling was performed during the RT reaction by incorporating the dye Cy5 according to the manufacture`s instruction (Scienion Berlin, Germany). Four different biological experiments were made, and a reverse labelling (dye switch) experiment was performed to minimize bias due to differential dye bleaching or incorporation of Cy3 and Cy5 dyes during the RT reaction.

treatment_protocol: S. aureus NCTC 8325 ΔpknB cultures for RNA preparations were diluted to an OD600 of 0.05 from LB overnight cultures into fresh LB-medium and further incubated until they reached an OD600 ~1.0.

value: ΔpknB


title: 001123_WT_3_6h


title: 002097_3357_3_Corn

source_name: 5 day field inoculated maize


title: 002095_3357_1_Corn


title: 002094_RIB40_3_Corn


title: Transcriptome analysis_PknB_chip26

hyb_protocol: Microarray transcriptional profiling by competitive hybridization of fluorescence-labeled cDNA was performed using the custom PCR product full-genome chip sciTracer (Scienion, Berlin, Germany) containing 2666 unique open reading frames representing 90% of the S. aureus N315 genome (NC_002745). Additional information on the microarray platform is described elsewhere. To increase reproducibility, each experiment was performed 5 times including a dye swap resulting in fiver chips per competitive comparison. All hybridizations were done with equal amounts of fluorescence-labeled cDNA probes or picomols of dye. Fluorescence-labeled cDNA probes were mixed in hybridization buffer (Scienion) in a total volume of 55 µl and denatured at 95°C for 2 min and subsequently applied to the microarray slide following incubation at 42°C for 72 hours under humidified conditions according to the manufacturer’s instructions. Hybridized microarrays were washed at room temperature in SSC buffer with decreasing salt concentrations (1 x SSC/0.3% SDS for 5 min, 0.2 x SSC for 5 min, 0.06 x SSC for 30s).


title: Transcriptome analysis_PknB_chip24


title: 002096_3357_2_Corn


title: Transcriptome analysis_PknB_chip25


title: 002093_RIB40_2_Corn


title: Transcriptome analysis_PknB_chip21_1


title: 002092_RIB40_1_Corn


title: Patient_5864_relapse

status: Public on Mar 10 2010

city: Wageningen

first: Dick

middle: de

last: de Ridder

address: Droevendaalsesteeg 1

department: Plant Sciences

country: Netherlands

institute: Wageningen University

hyb_protocol: Affymetrix standard 16 hours at 45 C Hybridization Oven 640

scan_protocol: GeneChip® Scanner 3000; GCOSv1

data_processing: Data were quantile normalized and RMA was used for probeset summarization; when subsets were analysed, these were individually normalized and summarized. Differential expression was assessed using SAM (Significance Analysis of Microarrays). All analyses were performed in Matlab; the code is available upon request.

source_name: leukemic cells, purified using CD19 beads on autoMACS

label_protocol: Afymetrix one cycle labeling kit

extract_protocol: Qiagen RNAesy plus shredder

value: leukemic lymphoblasts

tag: disease status

value: Acute Lymphoblastic Leukemia (ALL)

tag: all type

value: Precursor-B-ALL

tag: all subtype

value: Common ALL

tag: gender

value: female

tag: relapse type

value: isolated bone marrow

tag: months to relapse

tag: conclusions ig/tcr

value: stable

tag: selected

value: yes


title: Patient_6309_relapse

value: male

value: some clonal evolution

value: no


title: Patient_7304_relapse

value: unstable


title: Patient_6190_relapse


title: Patient_7170_relapse


title: DLBCL_CH1_TSA

city: Grenoble

first: Mary

middle: Bridgid

last: Callanan

address: Rond point de la Chantourne, La Tronche

department: Cell differentiation and transformation

country: France

institute: INSERM-UJF U823, Institut Albert Bonniot

description:
The formation of aberrant heterochromatic foci, coupled to abnormal enrichment of adjacent 2p sequences in repressive heterochromatin marks (H4K20me3, H3K9me3 and HP1), delayed replication and repositioning of the rearranged chromosome 2 to the nuclear periphery, could be associated to altered gene expression of at least those genes brought into close proximity to heterochromatin. To assess this question, global gene expression profiling was performed in the lymphoma B cells presenting the aberrant heterochromatin foci (CH1), treated or not with the histone deacetylase inhibitor, trichostatin A.
This TSA-treated DLBCL_CH1 sample was compared to a non-treated sample.

hyb_protocol: Hybridization and washing was carried out on a GeneChip (Affymetrix) station, washing according to the manufacturer’s protocol.

scan_protocol: Scann carried out on a GeneChip (Affymetrix) station (7G Scanner) according to the manufacturer’s protocol.

data_processing: Data were analyzed with the GCOS 1.2 software (Affymetrix), using the default analysis settings and global scaling as normalization method, with a trimmed mean target intensity value (TGT) of each array arbitrarily set to 100.

source_name: Diffuse large B-cell lymphoma line CH1, Trichostatin A-treated

label_protocol: Biotinylated cRNA was amplified with double in vitro transcription and hybridized to the Affymetrix HG U133 Plus 2.0 microarrays, according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA, USA).

growth_protocol: The diffuse large B-cell lymphoma line CH1was cultivated at 37°C in a humidified 5% CO2 atmosphere, in RPMI 1640 medium supplemented with 10% human AB+ serum, 100 µg/ml penicillin-streptomycin, 1.4 mM sodium pyruvate and 1.4 mM non-essential amino acids (Life Technologies, Grand Island, NY, USA). Six hours before lysing the cells, trichostatin A was added to the culture medium at a concentration of 50 ng/mL.

extract_protocol: RNA was extracted using the TRIzol reagent (Invitrogen Life Technologies), quality controlled by using the Agilent Bioanalyzer system and quantified, prior to labelling, by NanoDrop (Thermo Scientific).

treatment_protocol: Trichostatin A-treated: 50 ng/mL during 6 hours

value: B-cell lymphoma CH1


title: Patient_6285_relapse

value: Pre-B-ALL


title: Patient_6558_relapse


title: Patient_8237_relapse


title: Patient_6557_relapse


title: Patient_8237_diagnosis


title: Patient_6145_relapse

value: combined


title: Patient_6892_relapse


title: Patient_6991_relapse

value: Pro-B-ALL


title: Patient_5449_relapse


title: Patient_5500_relapse


title: Patient_7304_diagnosis


title: Patient_6475_relapse


title: DLBCL_CH1_Ctrl

description:
The formation of aberrant heterochromatic foci, coupled to abnormal enrichment of adjacent 2p sequences in repressive heterochromatin marks (H4K20me3, H3K9me3 and HP1), delayed replication and repositioning of the rearranged chromosome 2 to the nuclear periphery, could be associated to altered gene expression of at least those genes brought into close proximity to heterochromatin. To assess this question, global gene expression profiling was performed in the lymphoma B cells presenting the aberrant heterochromatin foci (CH1), treated or not with the histone deacetylase inhibitor, trichostatin A.
This control DLBCL_CH1 sample was compared to a Trichostatin A treated sample.

source_name: Diffuse large B-cell lymphoma line CH1, non-treated

growth_protocol: The diffuse large B-cell lymphoma line CH1was cultivated at 37°C in a humidified 5% CO2 atmosphere, in RPMI 1640 medium supplemented with 10% human AB+ serum, 100 µg/ml penicillin-streptomycin, 1.4 mM sodium pyruvate and 1.4 mM non-essential amino acids (Life Technologies, Grand Island, NY, USA).

treatment_protocol: No  treatment


title: Patient_6557_diagnosis


title: Patient_5513_relapse


title: Patient_5189_relapse


title: Patient_5361_relapse


title: Patient_6991_diagnosis


title: Patient_6449_relapse


title: Patient_6475_diagnosis


title: Patient_5260_relapse


title: Patient_6309_diagnosis


title: Patient_6449_diagnosis


title: Patient_5864_diagnosis


title: Patient_5513_diagnosis


title: Patient_5361_diagnosis


title: Patient_5449_diagnosis


title: Patient_6285_diagnosis


title: Patient_5189_diagnosis


title: Patient_5500_diagnosis


title: Patient_5260_diagnosis


title: Patient_6190_diagnosis


title: mRNA Jurkat not exposed rep3

city: seoul

first: jinhee

last: choi

address: 90 Jeonnong-dong, Dongdaemun-gu

department: College of Urban Science

country: South Korea

institute: University of Seoul

description: replicate 3

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina HumanHT-12 Expression Beadchip according to the protocols provided by the manufacturer.

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader  Confocal  Scanner

data_processing: Array data export processing and analysis was performed using Illumina BeadStudio v3.1.3  (Gene Expression Module v3.3.8). The data were normalised using quantile normalisation with ArrayAssist® 5.5.1 (Stratagene, La Jolla, USA) and R statistical language v. 2.4.1

source_name: mRNA isolated from Jurkat cells

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin,TX).

growth_protocol: Human leukemia Jurkat cells were were maintained in RPMI 1640 (GIBCO BRL Life Technologies, Rockville, MD, USA) and supplemented with 10% (v/v) fetal bovine serum, at 37 ◦C in a humidified atmosphere of air and 5% CO2.

extract_protocol: The total RNA prepared from the exposed and control cells according to the standard protocol of the RNeasy Mini kit (Qiagen, Hilden, Germany).

treatment_protocol: From stock solutions, experimental concentration(0.2mg/L) of AgNPs and Ag ions was prepared in medium. For toxicity tests, cells were incubated for 24 hr at 37 ◦C in a humidified atmosphere of air and 5% CO2.

value: Human leukemia Jurkat cells


title: mRNA Jurkat 24hr AgNPs exposure rep3

description: replicate 3


title: mRNA Jurkat 24hr Ag ions exposure rep3

description: replicate 3


title: SAE 13972466 GEO D3’ – cy3 vs S3’ – cy5

city: Cologne

first: Ludwig

last: Eichinger

address: Joseph-Stelzmann-Strasse 52

institute: Institute for Biochemistry 1

description: DNA microarrays cotainining 5,423 non-redundant ESTs from the D. discoideum cDNA project (Urushihara et al., 2004), partial sequences of 450 selected genes, probes of the SpotReport-10 Array Validation System (Stratagene, La Jolla, USA) and appropriate positive and negative controls were produced in-house using standard protocols (see also: http://www.uni-koeln.de/medfak/biochemie/transcriptomics/ production.e.shtml). Briefly, probes were amplified by two 100µl PCR reactions in 96-well microtiter plates using standard primers (M13F2: 5’-GTAAAACGACGGCCAGTG-3’, M13R2: 5’-C6-Aminolink-ACCATGATTACGCCAAGC-3’) for the cloned ESTs and gene-specific primers for the selected genes and the positive controls. After analysis by agarose gel electrophoresis (10µl of each reaction) the two reactions were combined, precipitated, solubilised in 11µl 25% DMSO, 1µl separated again by agarose gel electrophoresis and evaluated (Farbrother et al., 2002). Probes were transferred with the proteineer dp pipetting robot (Bruker, Germany) into 384-well microarray plates with cylindrical wells (Abgene, Hamburg, Germany) and printed onto UltraGaps slides (Corning, New York, USA) at 18°C and 45% humidity with a BioRobotics MicroGrid 600 microarray robot (Genomic Solutions, Huntingdon, UK) using MicroSpot 2500 microarraying pins. Each probe was spotted in duplicate, positive and negative controls were spotted 6, 24, 192 or 286 times and the SpotReport controls 96 times. The microarray is composed of three grids with 16 subarrays each and 14,620 spots in total. The complete microarray dataset is available at GEO, http://www.ncbi.nlm.nih.gov/geo; accession number GPL1972.

hyb_protocol: Cy3 and Cy5 labelled targets were mixed, ethanol precipitated and dissolved in 65 µl of hybridisation buffer (Noegel et al., 1985) with 500 µg/ml Fish sperm DNA (Roche, Mannheim, Germany) and 2 µM Oligo dA 18-mer. The hybridisation mix was heated to 80 °C for 10 min, applied to the microarray under a cover-slip and incubated in a hybridisation chamber (Corning, New York, USA) for 15 hours at 37°C. Post-hybridisation washes were performed twice with 2x SSC, 0.1% SDS and once with 0.1x SSC, 0.1% SDS for 5 min each, five times with 0.1x SSC and once with with 0.01x SSC for 5 sec each and dried by centrifugation at 235xg for 5 min. See also Farbrother et al., Cell. Microbiol., 3:438-456, 2006.

scan_protocol: Signal detection was performed with the ScanArray 4000XL confocal laser scanner (PerkinElmer Life Sciences, Wellesley, USA). Images for Cy3 and Cy5 were obtained, spots were detected and quantified with ScanArray Express v2.2 (PerkinElmer Life Sciences), then manually inspected and if necessary corrected. See also Farbrother et al., Cell. Microbiol., 3:438-456, 2006.

data_processing:
For each individual comparison four microarrays were hybridised and analysed. Two imagepairs were produced per microarray slide, one with high laser intensity so that signals for most probes and also some saturated signals were obtained and a second one with lower laser intensity so that none of the signals was saturated. This way the dynamic range of the measurement was expanded. To handle the import and export of microarray data to different analysis programs an Excel Add-In, Array tools (http://www.uni-koeln.de/med-fak/biochemie/ transcriptomics/tools-array.e.shtml), was programmed in Visual Basic. Upon import of two data files of the same microarray scanned with different laser powers the saturated spots of the high laser power scan were replaced by non-saturated spots from the low laser power scan. In addition the import also performed data filtering by flagging SpotReport controls, negative controls, empty spots, spots where only spotting solution was printed and spots whose intensities were below or equal to zero as "Bad". Fluorescence ratios were normalised by LOWESS-norma-lisation using R1.6.2 (BioConductor, http://www.bioconductor.org/). The normalized M values (M = log2 (Intensityexperiment/Intensitycontrol) were transferred into a new worksheet for significance analysis of microarrays (SAM) analysis (Tusher et al., 2001). At the transfer all probes spotted in higher replicates were reduced to double spots by averaging. Furthermore all probes that were flagged "Found" in less than half of the spots, were excluded from SAM analysis. Differentially regulated genes were identified using the one-class SAM method calculating 1000 permutations. The SAM program not only identifies the differentially regulated genes, but also predicts the number of false positives. These are the genes that are falsely reported as differentially expressed. This feature was used in all microarray experiments to set the significance level such, that the 90th percentile of the false discovery rate (FDR) was minimal.
See also Farbrother et al., Cell. Microbiol., 3:438-456, 2006.

organism: Dictyostelium discoideum

source_name: D3’ – cy3

label_protocol: Fairplay indirect labelling kit (Stratagene)

extract_protocol: RNA was isolated using TRIzol

tag: sample type

value: AX2 cells in Soerensen phosphate buffer as control. Total RNA isolated at 3h time point.

tag: strain

source_name: S3’ – cy5

value: AX2 cells treated with S. typhimurium. Total RNA isolated at 3h time point.


title: mRNA Jurkat not exposed rep1

description: replicate 1

tag: cell line


title: SAE 13972467 GEO D3’ – cy5 vs S3’ – cy3

source_name: S3’ – cy3

source_name: D3’ – cy5


title: SAE 13972542 GEO D3’ – cy5 vs S3’ – cy3


title: mRNA Jurkat 24hr Ag ions exposure rep1

description: replicate 1


title: SAE 13727645 GEO D3 – cy3 vs S3 – cy5

source_name: D3 – cy3

source_name: S3 – cy5


title: mRNA Jurkat 24hr Ag ions exposure rep2

description: replicate 2


title: mRNA Jurkat 24hr AgNPs exposure rep1

description: replicate 1


title: mRNA Jurkat 24hr AgNPs exposure rep2

description: replicate 2


title: mRNA Jurkat not exposed rep2

description: replicate 2


title: SAE 13972527 GEO D3 – cy5 vs S3 – cy3

source_name: S3 – cy3

source_name: D3 – cy5


title: SAE 13972526 GEO D3 – cy3 vs S3 – cy5


title: SAE 13972552 GEO D6’ – cy5 vs S6’ – cy3

source_name: S6’ – cy3

value: AX2 cells treated with S. typhimurium. Total RNA isolated at 6h time point.

source_name: D6’ – cy5

value: AX2 cells in Soerensen phosphate buffer as control. Total RNA isolated at 6h time point.


title: SAE 13972528 GEO D3’ – cy3 vs S3’ – cy5


title: SAE 13972544 GEO D6 – cy5 vs S6 – cy3

source_name: S6 – cy3

source_name: D6 – cy5


title: SAE 13727484 GEO E3 t3 - cy3 vs S3 t3 - cy5

source_name: E3 t3 - cy3

tag: AX2 cells treated with E. Coli B/r as control. Total RNA isolated at 3h time point.

source_name: S3 t3 - cy5

tag: AX2 cells treated with S. typhimurium. Total RNA isolated at 3h time point.


title: SAE 13727485 GEO E3 t3 - cy5 vs S3 t3 - cy3

source_name: S3 t3 - cy3

source_name: E3 t3 - cy5


title: SAE 13731053 GEO E1' t3 - cy5 vs S2' t3 - cy3


title: SAE 13972543 GEO D6 – cy3 vs S6 – cy5

source_name: D6 – cy3

source_name: S6 – cy5


title: SAE 13972509 GEO D6’ – cy3 vs S6’ – cy5

source_name: D6’ – cy3

source_name: S6’ – cy5


title: SAE 13720998 GEO E1' t3 - cy3 vs S2' t3 - cy5


title: SAE 13727478 GEO E3' t3 - cy3 vs S3' t3 - cy5


title: SAE 13972510 GEO D6’ – cy5 vs S6’ – cy3


title: SAE 13513953 GEO E2 t3 - cy5 vs S2 t3 - cy3

source_name: S2 t3 - cy3

source_name: E2 t3 - cy5


title: SAE 13972551 GEO D6’ – cy3 vs S6’ – cy5


title: MCF-7 P-65

city: Arlington

first: Li

middle: Lily

last: Chen

state: VA

address: 4300 Wilson Blvd., Suite 750

department: The Bradley Department of Electrical and Computer Engineering

institute: Virginia Tech

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Protocol for Affymetrix GeneChip Scanner 3000

data_processing: PLIER

source_name: Epithelial cells derived from metastatic adenocarcinoma

label_protocol: Standard one-cycle Affymetrix protocol

growth_protocol: Cells were grown in complete IMEM media supplemented with 5% Fetal Bovine Serum.  Both Control and Treated cells were kept in a 37C incubator with 5% C02 and regulated humidity.

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

treatment_protocol: Stripped cells were grown over 96 hours (4 successive days) in phenol-red free IMEM media supplemented with 5% Charcoal-Stripped Calf Serum.  Every 24 hours the media was removed and replaced with fresh phenol-red free IMEM media supplemented with 5% Charcoal-Stripped Calf Serum (3 times total).

value: Female

tag: age

value: 69 years

tag: race

value: Caucasian


title: SAE 13727479 GEO E3' t3 - cy5 vs S3' t3 - cy3


title: MCF-7 P-62


title: SAE 13731042 GEO E1' t2 - cy5 vs S1' t2 - cy3

value: AX2 cells treated with S. typhimurium. Total RNA isolated at 2h time point.

value: AX2 cells treated with E. Coli B/r as control. Total RNA isolated at 2h time point.


title: MCF-7 P-67 (STRIPPED)

description: estrogen-deprived MCF-7 human breast cancer cells


title: MCF-7 P-63


title: MCF-7 P-64 (STRIPPED)


title: SAE 13727628 GEO E2' t2 - cy3 vs S3' t2 - cy5


title: BHI_Typhimurium_chlorine_390ppm_rep1

city: SUMMIT

first: SIYUN

last: WANG

state: IL

address: 6502 S ARCHER ROAD

institute: ILLINOIS INSTITUTE OF TECHNOLOGY

description: This sample is of Salmonella enterica Typhimurium in BHI broth w/ 390ppm chlorine treatment for 10 minutes . It is the first of three biological replicates used in this experiment, each from separate cultures.

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

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

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.5 (Roche NimbleGen, Inc.).

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

source_name: Salmonella enterica Typhimurium, chlorine, 390ppm 10min

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

growth_protocol: Salmonella Enteritidis and Typhimurium were grown to early-log phase at 37°C in BHI broth

extract_protocol: Total RNA was extracted using the RNeasy Midi kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer.

treatment_protocol: Cells were washed and resuspended in (1) BHI broth, 30 min (2) chlorinated BHI broth, 130 ppm, 30 min (3) chlorinated BHI broth, 390 ppm, 10 min

tag: genotype

value: Wild-type

tag: accession


title: SAE 13513951 GEO E2 t3 - cy3 vs S2 t3 - cy5

source_name: E2 t3 - cy3

source_name: S2 t3 - cy5


title: SAE 13727668 GEO E2' t2 - cy5 vs S3' t2 - cy3


title: BHI_Typhimurium_chlorine_390ppm_rep3

description: This sample is of Salmonella enterica Typhimurium in BHI broth w/ 390ppm chlorine treatment for 10 minutes . It is the third of three biological replicates used in this experiment, each from separate cultures.


title: BHI_Typhimurium_chlorine_390ppm_rep2

description: This sample is of Salmonella enterica Typhimurium in BHI broth w/ 390ppm chlorine treatment for 10 minutes . It is the second of three biological replicates used in this experiment, each from separate cultures.


title: SAE 13727461 GEO E3 t2 - cy3 vs S3 t2 - cy5

source_name: E3 t2 - cy3

source_name: S3 t2 - cy5


title: SAE 13731046 GEO E1' t2 - cy3 vs S1' t2 - cy5


title: SAE 13727462 GEO E3 t2 - cy5 vs S3 t2 - cy3

source_name: S3 t2 - cy3

source_name: E3 t2 - cy5


title: MCF-7 P-65 (STRIPPED)


title: BHI_Typhimurium_chlorine_130ppm_rep2

description: This sample is of Salmonella enterica Typhimurium in BHI broth w/ 130ppm chlorine treatment for 30 minutes . It is the second of three biological replicates used in this experiment, each from separate cultures.

source_name: Salmonella enterica Typhimurium, chlorine, 130ppm 30min


title: BHI_Typhimurium_chlorine_130ppm_rep3

description: This sample is of Salmonella enterica Typhimurium in BHI broth w/ 130ppm chlorine treatment for 30 minutes . It is the third of three biological replicates used in this experiment, each from separate cultures.


title: BHI_Typhimurium_chlorine_control_rep3

description: This sample is of Salmonella enterica Typhimurium in BHI broth. It is the third of three biological replicates used in this experiment, each from separate cultures.

source_name: Salmonella enterica Typhimurium, control


title: BHI_Typhimurium_chlorine_control_rep2

description: This sample is of Salmonella enterica Typhimurium in BHI broth. It is the second of three biological replicates used in this experiment, each from separate cultures.


title: SAE 13513774 GEO E1 t2 - cy3 vs S1 t2 - cy5

source_name: E1 t2 - cy3

source_name: S1 t2 - cy5


title: BHI_Typhimurium_chlorine_control_rep1

description: This sample is of Salmonella enterica Typhimurium in BHI broth. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: SAE 13513775 GEO E1 t2 - cy5 vs S1 t2 - cy3

source_name: S1 t2 - cy3

source_name: E1 t2 - cy5


title: SAE 13720994 GEO E2' t1 - cy3 vs S3' t1 - cy5

value: AX2 cells treated with E. Coli B/r as control. Total RNA isolated at 1h time point.

value: AX2 cells treated with S. typhimurium. Total RNA isolated at 1h time point.


title: BHI_Enteritidis_chlorine_390ppm_rep3

description: This sample is of Salmonella enterica Enteritidis in BHI broth w/ 390ppm chlorine treatment for 10 minutes . It is the third of three biological replicates used in this experiment, each from separate cultures.

organism: Salmonella enterica subsp. enterica serovar Enteritidis

source_name: Salmonella enterica Enteritidis, chlorine, 390ppm 10min


title: BHI_Enteritidis_chlorine_390ppm_rep2

description: This sample is of Salmonella enterica Enteritidis in BHI broth w/ 390ppm chlorine treatment for 10 minutes . It is the second of three biological replicates used in this experiment, each from separate cultures.


title: SAE 13720997 GEO E2' t1 - cy5 vs S3' t1 - cy3