title: Patient 1_LUL_24 months

source_name: Bronchial brushing from patient 1, Left Upper Lobe, 24 months


title: 47,XY,+8 6 gene expression

status: Public on Dec 01 2012

type: RNA

city: Lund

first: Josef

last: Davidsson

address: BMC B13

department: Clinical Genetics

country: Sweden

institute: Lund University

description: Expression array

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Affymetrix gene expression console and Pearson signal correlation testing

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Fibroblast

label_protocol: standard Affymetrix protocol

growth_protocol: cells were maintained and passaged in RPMI 1640 medium (Invitrogen) containing 10% FBS (Sigma-Aldrich) in 250 ml cell culture flasks (BD Falcon) for 8 weeks.

extract_protocol: mirVana

treatment_protocol: Single-cell cloned and reference fibroblasts

tag: genotype

tag: cell type

value: fibroblast


title: MSC 15d_rep1

city: Yokohama

first: Ryota

last: Hasegawa

state: Kanagawa

address: 1-7-22 Suehiro-cho Tsurumi-ku

department: Omics science center

country: Japan

institute: RIKEN Yokohama

hyb_protocol: Standard Illumina hybridyzation protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with lumi in R

source_name: MSC 15d

label_protocol: Biotinylated cRNA were prepared with TotalPrep™ RNA Amplification Kit for Illumina arrays

growth_protocol: Human bone marrow derived mesenchymal stem cells (MSC) were maintained in Mesenchymal stem cell basal medium (MSCBM) supplemented with 10% fetal bovine serum (FBS), 10ml of L-Glutamine and 0.5 ul of antibiotics (Takara Inc). They were cultured at 37oC, 5% CO2. Medium was changed every 2 or 3 days.

extract_protocol: RNA was extracted with QIAGEN RNeasy kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Adipocyte differentiation was induced by incubating 100% confluent MSCs in Adipogenic induction medium (Takara Inc) containing 2ml of human-insulin, 1ml of dexamethasone, and 0.4ml of indomethacin and 0.2ml of IBMX. Three days post induction cells were maintained with the maintenance medium (Takara Inc) containing 2ml of h-insulin for 1day. Both induction and maintenance medium were supplemented with 10% fetal bovine serum (FBS) 4ml of L-Glutamine and 0.2 ul of antibiotics (Takara Inc). Total four cycles of induction medium (3d) and maintenance medium (1d) was performed to differentiate into adipocyte.

value: mesenchymal stem cells (MSC)

tag: time after induction


title: 46,XX 1lt gene expression

description: Expression array


title: 46,XX 7 gene expression

description: Expression array


title: MSC 12d_rep1

source_name: MSC 12d


title: MSC 15d_rep2


title: MSC 9d_rep2

source_name: MSC 9d


title: 47,XY,+8 4 gene expression

description: Expression array


title: MSC 9d_rep1


title: 46,XY 3 gene expression

description: Expression array


title: MSC 6d_rep2

source_name: MSC 6d


title: MSC 9d_rep3


title: Patient 3_RUL_36 months

city: Houston

first: Humam

last: Kadara

state: TX

address: 2130 W. Holcombe Blvd

country: USA

institute: University of Texas MD Anderson Cancer Center

hyb_protocol: Fragmented and labeled cDNA (2.5 micrograms) were hybridized onto Human Gene 1.0 ST arrays according to the manufacturer’s instructions (Affymetrix). Hybridization cocktails containing samples, control oligonucleotide and eukaryotic hybridization controls in addition to hybridization mixes, DMSO and nuclease-free water were heat denatured at 99oC for 5 minutes, cooled to 45oC for 5 minutes, and finally centrifuged at maximum speed for 1 minute.   After injecting 80 mL of the hybridization cocktails, arrays were incubated for 17 hours in a hybridization oven set to a temperature of 45oC with 60 rpm rotation.   Arrays were washed, stained and processed using Affymetrix GeneChip Fluidics Station 450 systems

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G for subsequent generation of raw data (*CEL files).

data_processing: Raw data were quantified using Robust Multichip Array (RMA) background correction, quantile normalization and RMA probe-level models (RmaPlm) summarization methods using the R language environment. After data preprocessing and normalization, a log base 2 transformation was applied.

label: Biotin

source_name: Bronchial brushing from patient 3, Right Upper Lobe, 36 months

label_protocol: Fragmented and biotin-labeled cDNA was then generated using the EncoreTM Biotin Module (NuGEN Technologies) according to the manufacturer's instructions using 5 micrograms of amplified cDNA

extract_protocol: Total RNA was isolated using the Rneasy Mini kit from Qiagen according to the manufacturer's instructions

tag: tissue

value: Bronchial brushing, normal airway epithelial cells

tag: patient id

tag: tumor location

value: RUL

tag: airway site

value: Adjacent

tag: time point


title: MSC 6d_rep3


title: 46,XY 8 gene expression

description: Expression array


title: MSC 4d_rep3

source_name: MSC 4d


title: 47,XY,+8 5 gene expression

description: Expression array


title: MSC 6d_rep1


title: MSC 4d_rep2


title: 46,XY 2 gene expression

description: Expression array


title: MSC 4d_rep1


title: human ileum, sample 199

city: Toronto

first: Boyko

last: Kabakchiev

state: Ontario

address: 60 Murray Street, Room L3-004

department: Samuel Lunenfeld Research Institute

country: Canada

institute: Mount Sinai Hospital

description:
sample_id: 217
Ileal tissue biopsies from human, post IPAA subjects

hyb_protocol: GeneChip Hybridization, Wash, and Stain Kit (Affymetrix)

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing:
Summarized probe cell intensity data were generated with an Affymetrix GeneChip Command Console. Probe-level summarization files were produced and the data were background-adjusted, normalized and log-transformed with a robust multiarray average (RMA) algorithm in Affymetrix Expression Console. The empirical Bayes (EB) method described by Johnson, W.E. et al. (2007) was applied to the normalized data to correct for batch effects which may have resulted from a non-linear sample extraction and microarray processing schedule. Lastly, duplicate and ambiguous Affymetrix probesets (Release 32) as well as those which no longer mapped to a gene in the current human genome build (GRCh37.p5) were removed from further analysis.
probe_group_file: HuGene-1_0-st-v1.r4.pgf
meta-probeset_file: HuGene-1_0-st-v1.r4.mps

source_name: ileum

label_protocol: GeneChip WT Terminal Labeling and Controls Kit (Affymetrix)

extract_protocol: miRNeasy Mini Kit (QIAGEN)

tag: batch

tag: gender

value: F

value: yes

tag: diagnosis

value: UC


title: 46,XY 1 gene expression

description: Expression array


title: MSC 2d_rep3

source_name: MSC 2d


title: MSC 2d_rep2


title: human ileum, sample 197

description:
sample_id: 141
Ileal tissue biopsies from human, post IPAA subjects

value: M


title: MSC 24hr_rep3

source_name: MSC 24hr


title: human ileum, sample 188

description:
sample_id: 333
Ileal tissue biopsies from human, post IPAA subjects

value: FAP


title: RNAPII-HA_vs_noTag--WT_#2

type: genomic

city: Montréal

first: François

last: Robert

state: Québec

address: 110, avenue des Pins Ouest

department: Chromatin and Genomic Expression

institute: Institut de recherches cliniques de Montréal (IRCM)

description: Biological replicate 2 of 2.

hyb_protocol: Resuspend colored pellet in 110uL hybridization buffer (100uL DIGEasy Buffer, 5uL 5mg/mL Salmon Sperm DNA, 20uL 8mg/mL yeast tRNA). Put at 95C for 3 minutes. Put at 65C while waiting for hybridization. Follow standard Agilent chamber hybridization protocols. Incubate 16-20h at 40C in hybridization oven at 20RPM rotation speed. Post-Hybridization Washes: Separate coverslip and slide in Wash buffer #1. Wash slides in Wash buffer #1 for 5 minutes at room temperature on an orbital shaker (cover the dish to avoid light on the slides). Wash in 31C Wash buffer #2 for 5 minutes on an orbital shaker. Take slides out of the buffer slowly to dry them, and allow them to air dry for 1 minute. Wash Buffer #1: 6x SSPE, 0.005% N-lauroylsarcosine. Wash Buffer #2: 0.06x SSPE.    Stripping is done in 500 ml of 5 mM Potassium phosphate buffer pH 6.6. 1. Use a 2L beaker, which can fit a slide rack. Pour the stripping buffer, submerge the rack with slides (from 1 to 10) and heat it up slowly while stirring with a stir bar until the liquid boils with big bubbles. It usually takes 15 to 20 minutes. Do not overboil it. 2. Remove the rack and briefly rinse in a container with water. Slowly remove the rack from the liquid. Cy5 channel will be stripped much better than Cy3, but this does not affect the performance of subsequent hybridizations. Stock solution of 1M Potassium phosphate buffer, pH 6.6: Mix 3.81 ml of 1M K2HPO4 + 6.19 ml of 1M KH2PO4. Dilute 2.5 ml of this 1M solution in 500 ml Milli-Q water to obtain 5mM Potassium phosphate buffer, pH 6.6.

scan_protocol: Axon GenePix 4000B scanner and the GenePix Pro extraction software were used. Scan at 100% laser power for both channels. Set the Pixel Size to 5um / pixel. Set the Lines to average to 1. Set the Focus Position to 0um. Adjust PMTs so that approximately 1-2% spots are saturated. This is done to ensure full dynamic range utilization. Adjust PMTs so that the intensity ratio is 0.9 - 1.1 when looking at intensity values greater than or equal to 3000 on the Intensity / Frequence histogram. Images were quantified using Axon GenePix (version 6.1.0.4).

data_processing: The raw data were corrected (foreground-background) then normalized using the limma's loess function (Yang et al.,2002) in BioConductor (from the ArrayPipe Analysis Pipeline (Hokamp et al., 2004)) and replicates were combined using a weighted average method as described previously (Pokholok et al., 2005).

molecule: genomic DNA

organism: Schizosaccharomyces pombe

label_protocol: Blunting: Do everything on ice! Add 70uL of the blunting solution (11uL NEB Buffer #2, 0.5uL BSA 10mg/mL, 0.5uL 20mM dNTPs, 0.2uL T4 DNA Polymerase 3U/uL, 57.8uL ddH2O) to 40uL of the resuspended DNA obtained at the end of the cleanup step. For WCEs, use 2uL + 38uL ddH2O instead of 40uL. Incubate 20 minutes at 12C. Add 11.5uL 3M NaOAc, pH 5.2, and 0.5uL Glycogen 20mg/mL and vortex briefly. Extract with 120uL Phenol/Chloroform/Isoamyl alcohol (25:24:1). Transfer 110uL to a new tube, and add 230uL -20C 100% EtOH. Put at -80C for 30min, then spin 20 minutes at 4C. Wash the pellet with 500uL -20C 70% EtOH and spin 15 minutes at 4C. Resuspend the pellet in 25uL ddH2O and place on ice.    Ligation: Thaw everything on ice, and do all manipulations on ice. Add 25uL of ligase mix (10uL 5x T4 Ligase Buffer, 6.7uL 15uM unidirectional linkers, 0.5uL T4 DNA Ligase, High Concentration, 8uL ddH2O) to the resuspended pellet from the blunting step. Incubate overnight at 16C. Add 6uL 3M NaOAc, pH 5.2, and vortex. Add 130uL -20C 100% EtOH and centrifuge 20 minutes at 4C. Wash the pellet (should be a smear on the side of the tube) with 500uL -20C 70% EtOH. Spin 15 minutes at 4C. Dry the pellet and resuspend in 25uL ddH2O.     Labeling: Add 15uL of PCR Labeling mix (4uL 10x ThermoPol Buffer, 2uL 5mM aa-dUTP mix, 1.25uL Oligo FR1, 7.75uL ddH2O) to the pellet from the ligation step. Start the PCR program, and during the first step (4 minutes at 55C), add 10uL of the polymerase mix (1uL 10x ThermoPol buffer, 1uL Taq Polymerase 5U/uL, 0.01uL Pfu Polymerase Turbo 2.5U/uL, 8uL ddH2O). PCR cycling conditions: 1) 5:00 at 55C 2) 5:00 at 72C 3) 2:00 at 95C 4) 0:30 at 95C 5) 0:30 at 55C 6) 1:00 at 72C 7) Repeat steps 4-6 31 more times. 8) 4:00 at 72C 9) Forever at 4C Purify PCR reactions with Qiagen PCR Cleanup kits, following their protocol BUT use a phosphate wash buffer and a phosphate elution buffer instead of their buffers PE and EB, respectively. Also, wash the columns only once, and elute twice with 30uL elution buffer. Speed-vac the eluate to dryness. Resuspend the pellets with fresh 4.5uL 0.1M Sodium Carbonate Buffer, pH 9.0. Add 4.5uL of the appropriate NHS-ester Cy-dye. Fresh tubes of NHS-ester Cy-dye should be resuspended in 73uL DMSO. Mix well, and incubate at room temperature in the dark for one hour. Add 35uL 0.1M NaOAc, pH 5.2. Purify using the Qiagen PCR Cleanup protocol using all their buffers, but wash only once and elute twice in 30uL. It is a good idea to elute both samples of a pair (Cy5 and Cy3) in the same tube to avoid DNA loss upon later resuspension. Speed-vac until 10-20uL are left, or to drynes+B33s. Phosphate Wash Buffer (100mL): 0.5mL 1M KPO4, pH 8.5 15.25mL ddH2O 84.25mL 95% EtOH Solution will be cloudy upon mixing. Phosphate Elution Buffer (10mL): 0.04mL 1M KPO4, pH 8.5 9.96mL ddH2O 1M KPO4, pH 8.5 (10mL): 9.5mL 1M K2HPO4 0.5mL 1M KH2PO4 1M Sodium Carbonate Buffer, pH 9.0 (100mL): 10.8g Na2CO3 80mL ddH2O pH to 9.0 with concentrated HCl Adjust volume to 100mL with ddH2O DILUTE 1:10 WHEN USING! Solution will change composition over time. Use only if less than a month old. Reference: Drouin S., Robert F. Methods (in press).

growth_protocol: 50 mL of YES were inoculated with 0.4 ml of over-night culture and incubated at 30C to OD600 0.4-0.6. The cells were then crosslinked by adding formaldehyde to a final concentration of 1 % and incubating at room temperature for 15 minutes.

extract_protocol: Crosslinked cells are washed twice with 50mL ice cold TBS and quickly frozen on dry ice. Subsequently, they are thawed on ice, resuspended in 400 uL lysis buffer (50mM HEPES-KOH, pH 7.5 140mM NaCl 1mM EDTA 1% Triton X-100 0.1% Na-deoxycholate 1mM PMSF, Roche protease inhibitor cocktail) and 500uL of acid-washed glass beads are added to the mixture. Then, cells are lysed using bead-beater (3x30 sec, with 5min breaks on ice). The whole cell extract is mixed with 500ul of lysis buffer.  The resulting extract is sonicated (6X30sec) using a Diagenode waterbath sonicator and subsequently centrifuged at 14000rpm for 5 minutes. The supernatant containing the sonicated chromatin is transferred to a new tube.    For the immunoprecipitation, antibody was added to 200 uL of chromatin solution and incubated overnight at 4C on a rocking platform. Subsequently 15 ul of protein A/G sepharose beads (Pierce #20421) are added and the incubation is continued for 1-2 hours. The beads are then washed with 0.5 mL FA-lysis Buffer (4 minutes rocking at room temp), then with 0.5 mL FA-lysis Buffer (500mM NaCl), then with ChIP wash buffer (10mM Tris-HCl, pH 8.0 250mM LiCl 0.5% NP40 0.5% Na-deoxycholate 1mM EDTA) and once with TE. The bound proteins are eluted by incubating the beads at 65?C for 20 minutes in 100ul of TE-SDS1%. The eluates were transferred to new tubes.  The beads were washed with 150 uL TE/0.67% SDS and the washes were combined with the eluates.  For WCEs 100 uL of chromatin solution was added to 150 uL TE/0.67% SDS.  To reverse the crosslinks the eluted material and WCEs were incubated overnight at 65C. The anti-HA antibody (Millipore 05-904) was used with 1 ul per immunoprecipitation. The anti-H3 C-terminal antibody (gift from A. Verrault, University of Montreal) was used with 1 ul per immunoprecipitation. The anti-acetylated H3 antibody (Millipore 06-599) was used with 1 uL per IP. The anti-trimethyl H3 antibody (Abcam ab8580) was used with 1 uL per IP. The anti-trimethyl H3K36 antibody (Abcam ab9050) was used with 1 uL per IP.    To clean-up the DNA, the protein are digested by adding 250ul of TE, 1ul of glycogen (20mg/ml) and 1 ul of RNase A (10 mg/mL).  Incubation was for 1 hour, 37 degrees.  50 ug of Proteinase K (10mg/ml) was then added and incubation continued for 2.5 hours at 37 degrees. 55 uL of 4 M LiCl was added to each sample.  The samples are then extracted with 500uL phenol/chloroform/isoamyl alcohol (25:24:1), and then 500 uL chloroform. The DNA is then precipitated with 1 ml of 100% ethanol. After incubation for one hour at -20C, the samples are centrifuged at maximum velocity for 20 minutes at 4C. The supernatant is discarded and the pellet is resuspended in 50ul of water.

tag: strain

tag: chip antibody

value: HA (Millipore 05-904)


title: MSC 12hr_rep2

source_name: MSC 12hr


title: MSC 1hr_rep3

source_name: MSC 1hr


title: human ileum, sample 198

description:
sample_id: 96
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 195

description:
sample_id: 194
Ileal tissue biopsies from human, post IPAA subjects

value: no


title: human ileum, sample 189

description:
sample_id: 184
Ileal tissue biopsies from human, post IPAA subjects


title: MSC 24hr_rep2


title: human ileum, sample 196

description:
sample_id: 115
Ileal tissue biopsies from human, post IPAA subjects


title: RNAPII-HA_vs_noTag--K119R_#2

description: Biological replicate 2 of 2.


title: human ileum, sample 190

description:
sample_id: 95
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 191

description:
sample_id: 70
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 193

description:
sample_id: 312
Ileal tissue biopsies from human, post IPAA subjects


title: MSC 12hr_rep3


title: RNAPII-HA_vs_noTag--WT_#1

description: Biological replicate 1 of 2.


title: MSC 12hr_rep1


title: MSC 2d_rep1


title: MSC 1hr_rep1


title: RNAPII-HA_vs_noTag--K119R_#1

description: Biological replicate 1 of 2.


title: MSC 1hr_rep2


title: human ileum, sample 194

description:
sample_id: 144
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 192

description:
sample_id: 126
Ileal tissue biopsies from human, post IPAA subjects


title: MSC 0hr_rep3

source_name: MSC 0hr


title: H3K4me3_vs_H3--WT_#1

description: Biological replicate 1 of 2.

value: H3K4me3 (Abcam ab8580)

value: H3 (provided by A. Verrault, University of Montreal)


title: H3K4me3_vs_H3--WT_#2

description: Biological replicate 2 of 2.


title: H3K36me3_vs_H3--WT_#1

description: Biological replicate 1 of 2.


title: human ileum, sample 187

description:
sample_id: 372
Ileal tissue biopsies from human, post IPAA subjects


title: MSC 0hr_rep1


title: H3K36me3_vs_H3--WT_#2

description: Biological replicate 2 of 2.


title: human ileum, sample 184

description:
sample_id: 190
Ileal tissue biopsies from human, post IPAA subjects


title: H3ac_vs_H3--WT_#1

description: Biological replicate 1 of 2.

value: H3ac (Millipore 06-599)


title: H3ac_vs_H3--K119R_#2

description: Biological replicate 2 of 2.


title: H3ac_vs_H3--set1D_#2

description: Biological replicate 2 of 2.


title: H3ac_vs_H3--WT_#2

description: Biological replicate 2 of 2.


title: H3ac_vs_H3--set1D_#1

description: Biological replicate 1 of 2.


title: H3ac_vs_H3--set2D_#2

description: Biological replicate 2 of 2.


title: MSC 0hr_rep2


title: human ileum, sample 185

description:
sample_id: 88
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 186

description:
sample_id: 33
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 182

description:
sample_id: 408
Ileal tissue biopsies from human, post IPAA subjects


title: H3ac_vs_H3--set2D_#1

description: Biological replicate 1 of 2.


title: human ileum, sample 181

description:
sample_id: 3
Ileal tissue biopsies from human, post IPAA subjects


title: H3ac_vs_H3--K119R_#1

description: Biological replicate 1 of 2.


title: H3_vs_WCE--set2D_#2

description: Biological replicate 2 of 2.


title: H3_vs_WCE--WT_#1

description: Biological replicate 1 of 2.


title: H3_vs_WCE--set2D_#1

description: Biological replicate 1 of 2.


title: human ileum, sample 183

description:
sample_id: 60
Ileal tissue biopsies from human, post IPAA subjects


title: H3_vs_WCE--set1D_#1

description: Biological replicate 1 of 2.


title: H3_vs_WCE--set1D_#2

description: Biological replicate 2 of 2.


title: H3_vs_WCE--WT_#2

description: Biological replicate 2 of 2.


title: H3_vs_WCE--K119R_#2

description: Biological replicate 2 of 2.


title: human ileum, sample 179

description:
sample_id: 668
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 178

description:
sample_id: 208
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 180

description:
sample_id: 62
Ileal tissue biopsies from human, post IPAA subjects


title: MSC 24hr_rep1


title: H3_vs_WCE--K119R_#1

description: Biological replicate 1 of 2.


title: human ileum, sample 177

description:
sample_id: 322
Ileal tissue biopsies from human, post IPAA subjects


title: H2AZ-HA_vs_noTag--WT_#2

description: Biological replicate 2 of 2.


title: 8WG16_vs_WCE--WT_#2

description: Biological replicate 2 of 2. RNAPII occupancy measured by the IP/Input ratio in WT cells.

extract_protocol: Crosslinked cells are washed twice with 50mL ice cold TBS and quickly frozen on dry ice. Subsequently, they are thawed on ice, resuspended in 400 uL lysis buffer (50mM HEPES-KOH, pH 7.5 140mM NaCl 1mM EDTA 1% Triton X-100 0.1% Na-deoxycholate 1mM PMSF, Roche protease inhibitor cocktail) and 500uL of acid-washed glass beads are added to the mixture. Then, cells are lysed using bead-beater (3x30 sec, with 5min breaks on ice). The whole cell extract is mixed with 500ul of lysis buffer.  The resulting extract is sonicated (6X30sec) using a Diagenode waterbath sonicator and subsequently centrifuged at 14000rpm for 5 minutes. The supernatant containing the sonicated chromatin is transferred to a new tube.    For the immunoprecipitation, antibody was added to 200 uL of chromatin solution and incubated overnight at 4C on a rocking platform. Subsequently 15 ul of protein A/G sepharose beads (Pierce #20421) are added and the incubation is continued for 1-2 hours. The beads are then washed with 0.5 mL FA-lysis Buffer (4 minutes rocking at room temp), then with 0.5 mL FA-lysis Buffer (500mM NaCl), then with ChIP wash buffer (10mM Tris-HCl, pH 8.0 250mM LiCl 0.5% NP40 0.5% Na-deoxycholate 1mM EDTA) and once with TE. The bound proteins are eluted by incubating the beads at 65?C for 20 minutes in 100ul of TE-SDS1%. The eluates were transferred to new tubes.  The beads were washed with 150 uL TE/0.67% SDS and the washes were combined with the eluates.  For WCEs 100 uL of chromatin solution was added to 150 uL TE/0.67% SDS.  To reverse the crosslinks the eluted material and WCEs were incubated overnight at 65C. The anti-H2Bub1 antibody (provided by M. Oren, Weizmann Institute, Israel) was used with 5 ul per immunoprecipitation. The anti-FLAG antibody (Sigma F1804) was used with 1 ul per immunoprecipitation. The 8WG16 anti-CTD of Rpb1 antibody (Covance MMS-126R) was used with 1 ul per immunoprecipitation.    To clean-up the DNA, the protein are digested by adding 250ul of TE, 1ul of glycogen (20mg/ml) and 1 ul of RNase A (10 mg/mL).  Incubation was for 1 hour, 37 degrees.  50 ug of Proteinase K (10mg/ml) was then added and incubation continued for 2.5 hours at 37 degrees. 55 uL of 4 M LiCl was added to each sample.  The samples are then extracted with 500uL phenol/chloroform/isoamyl alcohol (25:24:1), and then 500 uL chloroform. The DNA is then precipitated with 1 ml of 100% ethanol. After incubation for one hour at -20C, the samples are centrifuged at maximum velocity for 20 minutes at 4C. The supernatant is discarded and the pellet is resuspended in 50ul of water.

value: 8WG16 (Covance MMS-126R)


title: human ileum, sample 175

description:
sample_id: 35
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 174

description:
sample_id: 154
Ileal tissue biopsies from human, post IPAA subjects


title: 8WG16_vs_WCE--K119R_#1

description: Biological replicate 1 of 2. RNAPII occupancy measured by the IP/Input ratio in H2B-K119R cells.


title: H2AZ-HA_vs_noTag--WT_#1

description: Biological replicate 1 of 2.


title: human ileum, sample 176

description:
sample_id: 389
Ileal tissue biopsies from human, post IPAA subjects


title: H2Bub_vs_H2B--WT_#2

description: Biological replicate 2 of 2. H2Bub1 occupancy measured by the H2Bub1/H2B-Flag ratio in WT cells.

value: H2Bub1 (provided by M. Oren, Weizmann Institute)

value: Flag (Sigma F1804)


title: 8WG16_vs_WCE--K119R_#2

description: Biological replicate 2 of 2. RNAPII occupancy measured by the IP/Input ratio in H2B-K119R cells.


title: H2Bub_vs_H2B--WT_#1

description: Biological replicate 1 of 2. H2Bub1 occupancy measured by the H2Bub1/H2B-Flag ratio in WT cells.


title: human ileum, sample 173

description:
sample_id: 430
Ileal tissue biopsies from human, post IPAA subjects


title: 8WG16_vs_WCE--WT_#1

description: Biological replicate 1 of 2. RNAPII occupancy measured by the IP/Input ratio in WT cells.


title: human ileum, sample 172

description:
sample_id: 235
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 171

description:
sample_id: 621
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 169

description:
sample_id: 374
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 170

description:
sample_id: 425
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 167

description:
sample_id: 47
Ileal tissue biopsies from human, post IPAA subjects


title: Control replicate 3

city: Villeurbanne

first: Yvan

last: Rahbé

address: INSA-Lyon, 20 ave. A.-Einstein

department: SPE

country: France

institute: INRA

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 2.4.27 (Roche NimbleGen, Inc.).

organism: Dickeya dadantii 3937

source_name: Dickeya dadantii culture in AP3 medium

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

growth_protocol: For Control, Dickeya dadantii 3937 was grown 24h (O.D.600nm > 2)  at 28°C in AP3 medium (Rahbé and Febvay, 1993. Entomol. Exp. Appl.. 67). For Assay, Dickeya dadantii was grown inside aphid Acyrthosiphon pisum after inoculation by ingestion (Grenier et al. 2006. Appl. Environ. Microbiol. 72)

extract_protocol: Total RNA was extracted using the TRIzol® reagent (Invitrogen) and the RNAprotect Bacterial reagent (Qiagen). DNA was removed by with DNase I of the TURBO DNAfree™ kit (Ambion). RNA quality was determined on agarose gel electrophoresis and concentration was determined at 260 nm using an ND 100 Nanodrop spectrophotometer (Thermo Fisher Scientific).

treatment_protocol: For Control, bacterial cells were harvested by centrifugation before RNA extraction. For Assay, bacterial cells were separated from aphid cells fragments by centrifugation (10000g, 10 min, 4°C)  on a discontinuous sucrose gradient (10% to 50%) before RNA extraction.

tag: growth protocol

value: culture in AP3 medium


title: human ileum, sample 164

description:
sample_id: 529
Ileal tissue biopsies from human, post IPAA subjects


title: Assay replicate 1

source_name: Dickeya dadantii infecting Acyrthosiphon pisum

value: grown inside aphid after inoculation by ingestion


title: human ileum, sample 165

description:
sample_id: 650
Ileal tissue biopsies from human, post IPAA subjects


title: Assay replicate 2


title: human ileum, sample 168

description:
sample_id: 380
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 166

description:
sample_id: 503
Ileal tissue biopsies from human, post IPAA subjects


title: Control replicate 2


title: Control_Cardiomyocytes_Rep 2

city: Stanford

first: Leng

last: Han

state: CA

address: 265 Campus Dr

institute: Stanford University

description: Gene expression data from CPCs

hyb_protocol: Labeled cDNA was hybridized at 42°C overnight using an SC chamber on the MAUI® Hybridization System (BioMicro®) with 1X OneArray® Hybridization Buffer (Phalanx Biotech), 0.01 mg/ml sheared salmon sperm DNA (Promega), at a concentration of 0.025 mg/ml labeled target. After hybridization, the arrays were washed according to the OneArray® protocol. cDNA microarray analysis was performed using the OneArray® Mouse Whole Genome Array (Phalanx Biotech, Belmont, CA).

scan_protocol: Molecular Dynamics™ Axon 4100A scanner, measured using GenePixPro™ Software, and stored in GPR format. Although the chip is two color, we only used Cy5 as the data channel.

data_processing: The raw intensities were normalized with center median scaling by Phanlax

organism: Mus musculus

source_name: Cardiomyocytes isolated by centrifugation at 100 rpm for 1 min.

label_protocol: Amplified cDNA was labeled with Cy5™ NHS ester (GEH Lifesciences)

growth_protocol: Matrigel coated culture dishes and mTeSR

extract_protocol: Total RNA was extracted using Qiagen microkit; small RNAs preserved by using buffer from miRNAeasy kit; cDNA was synthesised and amplified using a WT-Ovation™ Pico RNA Amplification System

value: Cardiomyocytes cells

value: Normal


title: Cardiac progenitor Sca1 cells_Rep 3

description: Gene expression data from CPCs

source_name: Flow cytomtery based sorting of Sca1+CD45-CD31- cells from heart

value: Cardiac progenitor Sca1 cells


title: Control_Cardiomyocytes_Rep 1

description: Gene expression data from CPCs


title: Cardiac SP cells_Rep 1

description: Gene expression data from CPCs

source_name: Cardiac SP cells; Hoechst 33342 efflux assay

value: Cardiac SP cells


title: Cardiac progenitor Sca1 cells_Rep 1

description: Gene expression data from CPCs


title: Assay replicate 3


title: Cardiac progenitor c-kit cells_Rep 3

description: Gene expression data from CPCs

source_name: Flow cytomtery based sorting of ckit+ cells from heart

value: Cardiac progenitor c-kit cells


title: human ileum, sample 163

description:
sample_id: 107
Ileal tissue biopsies from human, post IPAA subjects

value: M

value: yes

value: UC


title: Cardiac SP cells_Rep 2

description: Gene expression data from CPCs


title: GBM 30617

city: Tampere

first: Matti

last: Annala

address: Korkeakoulunkatu 1

country: Finland

institute: Tampere University of Technology

hyb_protocol: As detailed in Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis ULS Labeling v3.

scan_protocol: Arrays were scanned with Agilent's dual-laser-based scanner (version G2505B).

data_processing: Feature extraction was performed using Agilent Feature Extraction software version 9.5.3.1.

source_name: Glioblastoma

value: Glioblastoma tumor

value: FGFR3-TACC3 negative

source_name: Commercial pooled reference DNA

tag: sample type

value: Commercial pooled reference DNA


title: Tianjin 1071

label_protocol: As detailed in Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis ULS Labeling v3.

value: FGFR3-TACC3 positive


title: Control replicate 1


title: human ileum, sample 162

description:
sample_id: 53
Ileal tissue biopsies from human, post IPAA subjects

value: F


title: Cardiac progenitor Sca1 cells_Rep 2

description: Gene expression data from CPCs


title: GBM 28340

extract_protocol: As detailed in Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis ULS Labeling v3.


title: Cardiac progenitor c-kit cells_Rep 2

description: Gene expression data from CPCs


title: GBM 45255


title: Bone Marrow MSC cells_Rep 1

description: Gene expression data from CPCs

source_name: Mesenchymal stem cells isolated from bone marrow; harvested after 5 passges

value: Bone Marrow MSC cells


title: Tianjin 342


title: Tianjin 19644A1


title: Cardiac progenitor c-kit cells_Rep 1

description: Gene expression data from CPCs


title: human ileum, sample 160

description:
sample_id: 222
Ileal tissue biopsies from human, post IPAA subjects


title: Bone Marrow MSC cells_Rep 2

description: Gene expression data from CPCs


title: Bone Marrow c-kit cells_Rep 3

description: Gene expression data from CPCs

source_name: Flow cytomtery based sorting of ckit+ cells from bone marrow

value: Bone Marrow c-kit cells


title: Bone Marrow MSC cells_Rep 3

description: Gene expression data from CPCs


title: Tianjin 360


title: Bone Marrow c-kit cells_Rep 2

description: Gene expression data from CPCs


title: A. pleuropneumoniae__serotype6_24h__rep3 [46-3]

city: Copenhagen

first: Kirstine

last: Klitgaard

address: Bulowsvej 27

country: Denmark

institute: National Veterinary Institute, Technical University of Denmark

description: This sample is of A. pleuropneumoniae strain 7712640. It is the third of three biological replicates for pig no. 46, each isolated from separate lung lesions.

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 Robust Multichip Average (RMA)function was applied for normalization of the microarray data (Irizarry et al. Biostatistics 4(2):249). For RMA normalization we have used RGui version 2.9.2 (2009-08-24) (http://cran.r-project.org/bin/windows/base/), using the package Oligo.

organism: Actinobacillus pleuropneumoniae

source_name: Actinobacillus pleuropneumoniae 7712640 from pig lung 24h

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

growth_protocol: Immediately post mortem, infected lung tissue was isolated, cut into pieces smaller than 0.5×0.5 cm and preserved in RNAlater stabilization reagent (Ambion, Cambridgeshire, United Kingdom) at -20°C.

extract_protocol: Total RNA was extracted using the RNeasy Lipid kit (QIAGEN, Hilden, Germany). Genomic DNA was eliminated by RNase-free DNase I treatment during the isolation procedure. After RNA extraction, the material was further treated by TURBO™ DNase, according to the protocol provided by the manufacturer (Ambion). The RNA concentration and quality were measured by NanoDrop (Thermo Scientific, Wilmington, DE, USA) and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA), respectively. For each sample, 30 µg of total RNA was enriched for bacterial RNA applying the MicrobEnrich Kit according to the supplied protocol (Ambion). Subsequently, one µg of the enriched RNA was amplified using a MessageAmp II-Bacteria kit (Ambion) according to the manufacturer's instructions.

treatment_protocol: Prior to RNA extraction, 100 to 300 mg lung tissue with visual lesions was finely chopped by scalpel, transferred to 5 ml Phenol:Guanidinthiocyanat lysis buffer (provided in the Qiagen kit) in which it was divided further by a Tissue shearer  for 2 min.

tag: serotype


title: human ileum, sample 158

description:
sample_id: 427
Ileal tissue biopsies from human, post IPAA subjects

source_name: ileum


title: human ileum, sample 157

description:
sample_id: 513
Ileal tissue biopsies from human, post IPAA subjects


title: A. pleuropneumoniae__serotype6_24h__rep1 [46-1]

description: This sample is of A. pleuropneumoniae strain 7712640. It is the first of three biological replicates for pig no. 46, each isolated from separate lung lesions.


title: A. pleuropneumoniae__serotype6_24h__rep3 [48-3]

description: This sample is of A. pleuropneumoniae strain 7712640. It is the third of three biological replicates for pig no. 48, each isolated from separate lung lesions.


title: A. pleuropneumoniae__serotype6_12h__rep3 [38-3]

description: This sample is of A. pleuropneumoniae strain 7712640. It is the third of three biological replicates for pig no. 38, each isolated from separate lung lesions.

source_name: Actinobacillus pleuropneumoniae 7712640 from pig lung 12h


title: A. pleuropneumoniae__serotype6_12h__rep1 [40-1]

description: This sample is of A. pleuropneumoniae strain 7712640. It is the first of three biological replicates for pig no. 40, each isolated from separate lung lesions.


title: A. pleuropneumoniae__serotype6_24h__rep2 [46-2]

description: This sample is of A. pleuropneumoniae strain 7712640. It is the second of three biological replicates for pig no. 46, each isolated from separate lung lesions.


title: A. pleuropneumoniae__serotype6_12h__rep2 [40-2]

description: This sample is of A. pleuropneumoniae strain 7712640. It is the second of three biological replicates for pig no. 40, each isolated from separate lung lesions.


title: human ileum, sample 156

description:
sample_id: 306
Ileal tissue biopsies from human, post IPAA subjects


title: A. pleuropneumoniae__serotype6_12h__rep3 [40-3]

description: This sample is of A. pleuropneumoniae strain 7712640. It is the third of three biological replicates for pig no. 40, each isolated from separate lung lesions.


title: A. pleuropneumoniae__serotype6_12h__rep2 [38-2]

description: This sample is of A. pleuropneumoniae strain 7712640. It is the second of three biological replicates for pig no. 38, each isolated from separate lung lesions.


title: human ileum, sample 155

description:
sample_id: 341
Ileal tissue biopsies from human, post IPAA subjects


title: A. pleuropneumoniae__serotype6_24h__rep2 [48-2]

description: This sample is of A. pleuropneumoniae strain 7712640. It is the second of three biological replicates for pig no. 48, each isolated from separate lung lesions.


title: A. pleuropneumoniae__serotype6_6h__rep3 [33-3]

description: This sample is of A. pleuropneumoniae strain 7712640. It is the third of three biological replicates for pig no. 33, each isolated from separate lung lesions.

source_name: Actinobacillus pleuropneumoniae 7712640 from pig lung 6h


title: A. pleuropneumoniae__serotype6_6h__rep1 [36-1]

description: This sample is of A. pleuropneumoniae strain 7712640. It is the first of three biological replicates for pig no. 36, each isolated from separate lung lesions.


title: A. pleuropneumoniae__serotype6_24h__rep1 [48-1]

description: This sample is of A. pleuropneumoniae strain 7712640. It is the first of three biological replicates for pig no. 48, each isolated from separate lung lesions.


title: human ileum, sample 154

description:
sample_id: 505
Ileal tissue biopsies from human, post IPAA subjects


title: A. pleuropneumoniae__serotype6_6h__rep3 [36-3]

description: This sample is of A. pleuropneumoniae strain 7712640. It is the third of three biological replicates for pig no. 36, each isolated from separate lung lesions.


title: Bone Marrow c-kit cells_Rep 1

description: Gene expression data from CPCs


title: A. pleuropneumoniae__serotype6_6h__rep2 [33-2]

description: This sample is of A. pleuropneumoniae strain 7712640. It is the second of three biological replicates for pig no. 33, each isolated from separate lung lesions.


title: human ileum, sample 153

description:
sample_id: 450
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 152

description:
sample_id: 637
Ileal tissue biopsies from human, post IPAA subjects


title: A. pleuropneumoniae__serotype6_12h__rep1 [38-1]

description: This sample is of A. pleuropneumoniae strain 7712640. It is the first of three biological replicates for pig no. 38, each isolated from separate lung lesions.


title: human ileum, sample 151

description:
sample_id: 687
Ileal tissue biopsies from human, post IPAA subjects


title: A. pleuropneumoniae__serotype6_6h__rep1 [33-1]

description: This sample is of A. pleuropneumoniae strain 7712640. It is the first of three biological replicates for pig no. 33, each isolated from separate lung lesions.


title: A. pleuropneumoniae__serotype6_6h__rep2 [36-2]

description: This sample is of A. pleuropneumoniae strain 7712640. It is the second of three biological replicates for pig no. 36, each isolated from separate lung lesions.


title: human ileum, sample 150

description:
sample_id: 2
Ileal tissue biopsies from human, post IPAA subjects


title: A. pleuropneumoniae__serotype2_48h__rep2 [78-2]

description: This sample is of A. pleuropneumoniae strain 4226. It is the second of three biological replicates for pig no. 78, each isolated from separate lung lesions.

source_name: Actinobacillus pleuropneumoniae 4226 from pig lung 48h


title: A. pleuropneumoniae__serotype2_48h__rep1 [78-1]

description: This sample is of A. pleuropneumoniae strain 4226. It is the first of three biological replicates for pig no. 78, each isolated from separate lung lesions.


title: A. pleuropneumoniae__serotype2_48h__rep3 [78-3]

description: This sample is of A. pleuropneumoniae strain 4226. It is the third of three biological replicates for pig no. 78, each isolated from separate lung lesions.


title: A. pleuropneumoniae__serotype2_48h__rep1 [76-1]

description: This sample is of A. pleuropneumoniae strain 4226. It is the first of three biological replicates for pig no. 76, each isolated from separate lung lesions.


title: A. pleuropneumoniae__serotype2_48h__rep3 [76-3]

description: This sample is of A. pleuropneumoniae strain 4226. It is the third of three biological replicates for pig no. 76, each isolated from separate lung lesions.


title: A. pleuropneumoniae__serotype2_48h__rep2 [76-2]

description: This sample is of A. pleuropneumoniae strain 4226. It is the second of three biological replicates for pig no. 76, each isolated from separate lung lesions.


title: A. pleuropneumoniae__serotype2_48h__rep3 [75-3]

description: This sample is of A. pleuropneumoniae strain 4226. It is the third of three biological replicates for pig no. 75, each isolated from separate lung lesions.


title: A. pleuropneumoniae__serotype2_48h__rep2 [75-2]

description: This sample is of A. pleuropneumoniae strain 4226. It is the second of three biological replicates for pig no. 75, each isolated from separate lung lesions.


title: human ileum, sample 147

description:
sample_id: 613
Ileal tissue biopsies from human, post IPAA subjects

value: no


title: A. pleuropneumoniae__serotype2_48h__rep2 [73-2]

description: This sample is of A. pleuropneumoniae strain 4226. It is the second of three biological replicates for pig no. 73, each isolated from separate lung lesions.


title: A. pleuropneumoniae__serotype2_48h__rep3 [73-3]

description: This sample is of A. pleuropneumoniae strain 4226. It is the third of three biological replicates for pig no. 73, each isolated from separate lung lesions.


title: A. pleuropneumoniae__serotype2_48h__rep1 [75-1]

description: This sample is of A. pleuropneumoniae strain 4226. It is the first of three biological replicates for pig no. 75, each isolated from separate lung lesions.


title: human ileum, sample 149

description:
sample_id: 398
Ileal tissue biopsies from human, post IPAA subjects


title: A. pleuropneumoniae__serotype2_48h__rep1 [73-1]

description: This sample is of A. pleuropneumoniae strain 4226. It is the first of three biological replicates for pig no. 73, each isolated from separate lung lesions.


title: human ileum, sample 161

description:
sample_id: 120
Ileal tissue biopsies from human, post IPAA subjects

value: FAP


title: human ileum, sample 148

description:
sample_id: 229
Ileal tissue biopsies from human, post IPAA subjects


title: A. pleuropneumoniae__serotype2_24h__rep2 [70-2]

description: This sample is of A. pleuropneumoniae strain 4226. It is the second of three biological replicates for pig no. 70, each isolated from separate lung lesions.

source_name: Actinobacillus pleuropneumoniae 4226 from pig lung 24h


title: human ileum, sample 146

description:
sample_id: 591
Ileal tissue biopsies from human, post IPAA subjects


title: A. pleuropneumoniae__serotype2_24h__rep2 [71-2]

description: This sample is of A. pleuropneumoniae strain 4226. It is the second of three biological replicates for pig no. 71, each isolated from separate lung lesions.


title: A. pleuropneumoniae__serotype2_24h__rep3 [71-3]

description: This sample is of A. pleuropneumoniae strain 4226. It is the third of three biological replicates for pig no. 71, each isolated from separate lung lesions.


title: A. pleuropneumoniae__serotype2_24h__rep3 [70-3]

description: This sample is of A. pleuropneumoniae strain 4226. It is the third of three biological replicates for pig no. 70, each isolated from separate lung lesions.


title: A. pleuropneumoniae__serotype2_24h__rep1 [71-1]

description: This sample is of A. pleuropneumoniae strain 4226. It is the first of three biological replicates for pig no. 71, each isolated from separate lung lesions.


title: A. pleuropneumoniae__serotype2_24h__rep1 [70-1]

description: This sample is of A. pleuropneumoniae strain 4226. It is the first of three biological replicates for pig no. 70, each isolated from separate lung lesions.


title: human ileum, sample 144

description:
sample_id: 204
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 142

description:
sample_id: 172
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 143

description:
sample_id: 628
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 145

description:
sample_id: 681
Ileal tissue biopsies from human, post IPAA subjects


title: A. pleuropneumoniae__serotype2_24h__rep2 [69-2]

description: This sample is of A. pleuropneumoniae strain 4226. It is the second of three biological replicates for pig no. 69, each isolated from separate lung lesions.


title: A. pleuropneumoniae__serotype2_24h__rep3 [69-3]

description: This sample is of A. pleuropneumoniae strain 4226. It is the third of three biological replicates for pig no. 69, each isolated from separate lung lesions.


title: human ileum, sample 141

description:
sample_id: 452
Ileal tissue biopsies from human, post IPAA subjects


title: A. pleuropneumoniae__serotype2_24h__rep1 [69-1]

description: This sample is of A. pleuropneumoniae strain 4226. It is the first of three biological replicates for pig no. 69, each isolated from separate lung lesions.


title: human ileum, sample 140

description:
sample_id: 98
Ileal tissue biopsies from human, post IPAA subjects


title: A. pleuropneumoniae__serotype2_24h__rep3 [67-3]

description: This sample is of A. pleuropneumoniae strain 4226. It is the third of three biological replicates for pig no. 67, each isolated from separate lung lesions.


title: A. pleuropneumoniae__serotype2_24h__rep2 [67-2]

description: This sample is of A. pleuropneumoniae strain 4226. It is the second of three biological replicates for pig no. 67, each isolated from separate lung lesions.


title: A. pleuropneumoniae__serotype2_12h__rep1 [62-1]

description: This sample is of A. pleuropneumoniae strain 4226. It is the first of three biological replicates for pig no. 62, each isolated from separate lung lesions.

source_name: Actinobacillus pleuropneumoniae 4226 from pig lung 12h


title: A. pleuropneumoniae__serotype2_12h__rep3 [62-3]

description: This sample is of A. pleuropneumoniae strain 4226. It is the third of three biological replicates for pig no. 62, each isolated from separate lung lesions.


title: A. pleuropneumoniae__serotype2_12h__rep2 [66-2]

description: This sample is of A. pleuropneumoniae strain 4226. It is the second of three biological replicates for pig no. 66, each isolated from separate lung lesions.


title: A. pleuropneumoniae__serotype2_12h__rep3 [60-3]

description: This sample is of A. pleuropneumoniae strain 4226. It is the third of three biological replicates for pig no. 60, each isolated from separate lung lesions.


title: A. pleuropneumoniae__serotype2_12h__rep1 [66-1]

description: This sample is of A. pleuropneumoniae strain 4226. It is the first of three biological replicates for pig no. 66, each isolated from separate lung lesions.


title: A. pleuropneumoniae__serotype2_12h__rep3 [66-3]

description: This sample is of A. pleuropneumoniae strain 4226. It is the third of three biological replicates for pig no. 66, each isolated from separate lung lesions.


title: A. pleuropneumoniae__serotype2_12h__rep2 [62-2]

description: This sample is of A. pleuropneumoniae strain 4226. It is the second of three biological replicates for pig no. 62, each isolated from separate lung lesions.


title: human ileum, sample 139

description:
sample_id: 5
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 138

description:
sample_id: 314
Ileal tissue biopsies from human, post IPAA subjects


title: A. pleuropneumoniae__serotype2_12h__rep2 [60-2]

description: This sample is of A. pleuropneumoniae strain 4226. It is the second of three biological replicates for pig no. 60, each isolated from separate lung lesions.


title: human ileum, sample 135

description:
sample_id: 349
Ileal tissue biopsies from human, post IPAA subjects


title: A. pleuropneumoniae__serotype2_24h__rep1 [67-1]

description: This sample is of A. pleuropneumoniae strain 4226. It is the first of three biological replicates for pig no. 67, each isolated from separate lung lesions.


title: human ileum, sample 137

description:
sample_id: 366
Ileal tissue biopsies from human, post IPAA subjects


title: A. pleuropneumoniae__serotype2_6h__rep3 [58-3]

description: This sample is of A. pleuropneumoniae strain 4226. It is the third of three biological replicates for pig no. 58, each isolated from separate lung lesions.

source_name: Actinobacillus pleuropneumoniae 4226 from pig lung 6h


title: A. pleuropneumoniae__serotype2_12h__rep1 [60-1]

description: This sample is of A. pleuropneumoniae strain 4226. It is the first of three biological replicates for pig no. 60, each isolated from separate lung lesions.


title: A. pleuropneumoniae__serotype2_6h__rep1 [59-1]

description: This sample is of A. pleuropneumoniae strain 4226. It is the first of three biological replicates for pig no. 59, each isolated from separate lung lesions.


title: human ileum, sample 136

description:
sample_id: 49
Ileal tissue biopsies from human, post IPAA subjects


title: A. pleuropneumoniae__serotype2_6h__rep2 [58-2]

description: This sample is of A. pleuropneumoniae strain 4226. It is the second of three biological replicates for pig no. 58, each isolated from separate lung lesions.


title: A. pleuropneumoniae__serotype2_6h__rep3 [59-3]

description: This sample is of A. pleuropneumoniae strain 4226. It is the third of three biological replicates for pig no. 59, each isolated from separate lung lesions.


title: A. pleuropneumoniae__serotype2_6h__rep1 [58-1]

description: This sample is of A. pleuropneumoniae strain 4226. It is the first of three biological replicates for pig no. 58, each isolated from separate lung lesions.


title: A. pleuropneumoniae__serotype2_6h__rep3 [57-3]

description: This sample is of A. pleuropneumoniae strain 4226. It is the third of three biological replicates for pig no. 57, each isolated from separate lung lesions.


title: human ileum, sample 132

description:
sample_id: 37
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 133

description:
sample_id: 210
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 131

description:
sample_id: 39
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 130

description:
sample_id: 202
Ileal tissue biopsies from human, post IPAA subjects


title: A. pleuropneumoniae__serotype2_6h__rep2 [57-2]

description: This sample is of A. pleuropneumoniae strain 4226. It is the second of three biological replicates for pig no. 57, each isolated from separate lung lesions.


title: A. pleuropneumoniae__serotype2_6h__rep1 [57-1]

description: This sample is of A. pleuropneumoniae strain 4226. It is the first of three biological replicates for pig no. 57, each isolated from separate lung lesions.


title: human ileum, sample 134

description:
sample_id: 25
Ileal tissue biopsies from human, post IPAA subjects


title: A. pleuropneumoniae__serotype2_6h__rep2 [59-2]

description: This sample is of A. pleuropneumoniae strain 4226. It is the second of three biological replicates for pig no. 59, each isolated from separate lung lesions.


title: A. pleuropneumoniae__serotype2_6h__rep3 [56-3]

description: This sample is of A. pleuropneumoniae strain 4226. It is the third of three biological replicates for pig no. 56, each isolated from separate lung lesions.


title: A. pleuropneumoniae__serotype2_6h__rep2 [56-2]

description: This sample is of A. pleuropneumoniae strain 4226. It is the second of three biological replicates for pig no. 56, each isolated from separate lung lesions.


title: A. pleuropneumoniae__serotype2_6h__rep3 [55-3]

description: This sample is of A. pleuropneumoniae strain 4226. It is the third of three biological replicates for pig no. 55, each isolated from separate lung lesions.


title: A. pleuropneumoniae__serotype2_6h__rep1 [56-1]

description: This sample is of A. pleuropneumoniae strain 4226. It is the first of three biological replicates for pig no. 56, each isolated from separate lung lesions.


title: A. pleuropneumoniae__serotype2_6h__rep2 [55-2]

description: This sample is of A. pleuropneumoniae strain 4226. It is the second of three biological replicates for pig no. 55, each isolated from separate lung lesions.


title: A. pleuropneumoniae__serotype2_6h__rep1 [55-1]

description: This sample is of A. pleuropneumoniae strain 4226. It is the first of three biological replicates for pig no. 55, each isolated from separate lung lesions.


title: Tobacco CPxMPT42W,rep 2

city: Buenos Aires

first: Gabriela

last: Conti

address: N. repetto y Los Reseros

country: Argentina

institute: INTA

description: Gene expression data from MPxCPT42W

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

scan_protocol: GeneChips were scanned using the  Gene Chip Scanner 3000 7G

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

organism: Nicotiana tabacum

source_name: tobacco plants expressing MP and CPT42W from TMV

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Gene Chip Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: Tobacco plants were grown in greenhouse  with 16-8hs photoperiod, temperature ranging from 25-22°C.

extract_protocol: Total RNA was extracted with RNeasy™ Plant Mini kit (Qiagen), according to manufacturer's instructions.

treatment_protocol: Stable transgenic isogenic lines. The first line co-expresses movement protein and a variant of coat protein from Tobacco mosaic virus (TMV) and the second line has sponatneously silenced both transgenes

tag: transgene

value: expressing MP and CPT42W from TMV

value: leaf

tag: cultivar

value: xanthi

tag: age

value: 6 wk


title: Tobacco CPxMPT42W,rep 3

description: Gene expression data from MPxCPT42W


title: human ileum, sample 128

description:
sample_id: 645
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 129

description:
sample_id: 66
Ileal tissue biopsies from human, post IPAA subjects


title: A. pleuropneumoniae__serotype6_48h__rep3 [54-3]

description: This sample is of A. pleuropneumoniae strain 7712640. It is the third of three biological replicates for pig no. 54, each isolated from separate lung lesions.

source_name: Actinobacillus pleuropneumoniae 7712640 from pig lung 48h


title: human ileum, sample 125

description:
sample_id: 105
Ileal tissue biopsies from human, post IPAA subjects


title: Tobacco cpxmpT42W*,rep 3

description: Gene expression data from mpxcpT42W*

source_name: tobacco isogenic plants with silenced MP and CPT42W from TMV

value: silenced MP and CPT42W from TMV


title: Tobacco CPxMPT42W,rep 1

description: Gene expression data from MPxCPT42W


title: A. pleuropneumoniae__serotype6_48h__rep2 [54-2]

description: This sample is of A. pleuropneumoniae strain 7712640. It is the second of three biological replicates for pig no. 54, each isolated from separate lung lesions.


title: Tobacco cpxmpT42W*,rep 2

description: Gene expression data from mpxcpT42W*


title: human ileum, sample 126

description:
sample_id: 633
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 127

description:
sample_id: 652
Ileal tissue biopsies from human, post IPAA subjects


title: A. pleuropneumoniae__serotype6_48h__rep1 [54-1]

description: This sample is of A. pleuropneumoniae strain 7712640. It is the first of three biological replicates for pig no. 54, each isolated from separate lung lesions.


title: human ileum, sample 123

description:
sample_id: 330
Ileal tissue biopsies from human, post IPAA subjects

value: M


title: Tobacco cpxmpT42W*,rep 1

description: Gene expression data from mpxcpT42W*


title: A. pleuropneumoniae__serotype6_48h__rep3 [51-3]

description: This sample is of A. pleuropneumoniae strain 7712640. It is the third of three biological replicates for pig no. 51, each isolated from separate lung lesions.


title: human ileum, sample 124

description:
sample_id: 113
Ileal tissue biopsies from human, post IPAA subjects

value: yes


title: human ileum, sample 159

description:
sample_id: 335
Ileal tissue biopsies from human, post IPAA subjects

value: UC


title: human ileum, sample 120

description:
sample_id: 423
Ileal tissue biopsies from human, post IPAA subjects


title: A. pleuropneumoniae__serotype6_48h__rep2 [51-2]

description: This sample is of A. pleuropneumoniae strain 7712640. It is the second of three biological replicates for pig no. 51, each isolated from separate lung lesions.


title: human ileum, sample 122

description:
sample_id: 440
Ileal tissue biopsies from human, post IPAA subjects


title: A. pleuropneumoniae__serotype6_48h__rep1 [51-1]

description: This sample is of A. pleuropneumoniae strain 7712640. It is the first of three biological replicates for pig no. 51, each isolated from separate lung lesions.


title: A. pleuropneumoniae__serotype6_48h__rep3 [50-3]

description: This sample is of A. pleuropneumoniae strain 7712640. It is the third of three biological replicates for pig no. 50, each isolated from separate lung lesions.


title: A. pleuropneumoniae__serotype6_48h__rep2 [50-2]

description: This sample is of A. pleuropneumoniae strain 7712640. It is the second of three biological replicates for pig no. 50, each isolated from separate lung lesions.


title: A. pleuropneumoniae__serotype6_48h__rep1 [50-1]

description: This sample is of A. pleuropneumoniae strain 7712640. It is the first of three biological replicates for pig no. 50, each isolated from separate lung lesions.


title: 15hTR3

city: Beaverton

first: Cecily

middle: Vauna

last: Bishop

state: OR

address: 505 NW 185th Ave

department: Division of Reproductive & Developmental Sciences

institute: Oregon National Primate Research Center

description:
410RS_2_045A-21H1_15hTR3
dissected isolated luteal tissue

label: biotin-CTP

organism: Macaca mulatta

source_name: D15 CL + hCG  + TRL + R5020_Rep3

extract_protocol: TRIzol® (Invitrogen) according to manufacturer's protocols

treatment_protocol: Adult female cycling rhesus macaques were treated as described by Duffy and Stouffer Biol Reprod. 1997 Dec;57(6):1451-60 (PMID: 9408254)

tag: tissue type

value: Corpus Luteum

tag: Sex

value: Adult Female

tag: tissue stage

value: Mid-late/Late Luteal Phase

tag: tissue treatment

value: hCG (Simulated Early Pregnancy) luteal day 15+TRL+R5020


title: 15hTR5

description:
410RS_3_055A-11H1_15hTR5
dissected isolated luteal tissue

source_name: D15 CL + hCG  + TRL + R5020_Rep4


title: human ileum, sample 119

description:
sample_id: 679
Ileal tissue biopsies from human, post IPAA subjects

value: F


title: human ileum, sample 117

description:
sample_id: 9
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 121

description:
sample_id: 103
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 115

description:
sample_id: 80
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 118

description:
sample_id: 490
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 116

description:
sample_id: 78
Ileal tissue biopsies from human, post IPAA subjects


title: 15hT1

description:
410RS_2_038A-21H1_15hT1
dissected isolated luteal tissue

source_name: D15 CL + hCG  + TRL_Rep1

value: hCG (Simulated Early Pregnancy) Luteal day 15+TRL


title: 15hTR1

description:
410RS_2_043A-21H1_15hTR1
dissected isolated luteal tissue

source_name: D15 CL + hCG  + TRL + R5020_Rep1


title: 15hTR2

description:
410RS_2_050A-21H1_15hTR2
dissected isolated luteal tissue

source_name: D15 CL + hCG  + TRL + R5020_Rep2


title: human ileum, sample 113

description:
sample_id: 339
Ileal tissue biopsies from human, post IPAA subjects


title: 15hT4

description:
410RS_2_046A-21H1_15hT4
dissected isolated luteal tissue

source_name: D15 CL + hCG  + TRL_Rep3


title: 15hT5

description:
410RS_3_056A-11H1_15hT5
dissected isolated luteal tissue

source_name: D15 CL + hCG  + TRL_Rep4


title: human ileum, sample 114

description:
sample_id: 639
Ileal tissue biopsies from human, post IPAA subjects

source_name: ileum


title: D15h5

description:
410RS_1_024A-11H1_D15h3
dissected isolated luteal tissue

source_name: D15 CL + hCG_Rep5

value: hCG (Simulated Early Pregnancy) luteal day 15


title: human ileum, sample 110

description:
sample_id: 84
Ileal tissue biopsies from human, post IPAA subjects

value: no


title: 15hT3

description:
410RS_2_048A-21H1_15hT3
dissected isolated luteal tissue

source_name: D15 CL + hCG  + TRL_Rep2


title: human ileum, sample 112

description:
sample_id: 135
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 109

description:
sample_id: 396
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 111

description:
sample_id: 498
Ileal tissue biopsies from human, post IPAA subjects


title: D15h4_reanalysis

description:
GSM623436
410RS_1_034A-11H1_D15h4 {2}
dissected isolated luteal tissue

source_name: D15 CL + hCG_Rep4


title: D15h2_reanalysis

description:
GSM623434
410RS_1_033A-11H1_D15h2 {2}
dissected isolated luteal tissue

source_name: D15 CL + hCG_Rep2


title: D15h3_reanalysis

description:
GSM623435
410RS_3_054A-11H1_15h3
dissected isolated luteal tissue

source_name: D15 CL + hCG_Rep3


title: human ileum, sample 108

description:
sample_id: 64
Ileal tissue biopsies from human, post IPAA subjects


title: D15h1_reanalysis

description:
GSM623433
410RS_1_010B-11H1_D15h1
dissected isolated luteal tissue

source_name: D15 CL + hCG_Rep1


title: human ileum, sample 107

description:
sample_id: 139
Ileal tissue biopsies from human, post IPAA subjects


title: 10hTR4

description:
410RS_2_039A-21H1_10hTR4
dissected isolated luteal tissue

source_name: D10 CL + hCG  + TRL + R5020_Rep4

value: hCG (Simulated Early Pregnancy) luteal day 10+TRL+R5020


title: 10hTR3

description:
410RS_2_049A-21H2_10hTR3
dissected isolated luteal tissue

source_name: D10 CL + hCG  + TRL + R5020_Rep3


title: 10hTR2

description:
410RS_2_053A-21H1_10hTR2
dissected isolated luteal tissue

source_name: D10 CL + hCG  + TRL + R5020_Rep2


title: human ileum, sample 105

description:
sample_id: 90
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 106

description:
sample_id: 318
Ileal tissue biopsies from human, post IPAA subjects

value: MC


title: human ileum, sample 104

description:
sample_id: 683
Ileal tissue biopsies from human, post IPAA subjects

value: FAP


title: human ileum, sample 103

description:
sample_id: 400
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 102

description:
sample_id: 672
Ileal tissue biopsies from human, post IPAA subjects


title: D10hT4

description:
410RS_1_004B-11H1_D10hT4
dissected isolated luteal tissue

source_name: D10 CL + hCG  + TRL_Rep4

value: hCG (Simulated Early Pregnancy) Luteal day 10+TRL


title: human ileum, sample 101

description:
sample_id: 21
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 97

description:
sample_id: 231
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 98

description:
sample_id: 444
Ileal tissue biopsies from human, post IPAA subjects


title: D10hT1

description:
410RS_1_027A-11H1_D10hT1 {2}
dissected isolated luteal tissue

source_name: D10 CL + hCG  + TRL_Rep1


title: human ileum, sample 94

description:
sample_id: 685
Ileal tissue biopsies from human, post IPAA subjects


title: D10h3_reanalysis

description:
GSM623427
410RS_1_023A-11H1_D10h3 {2}
dissected isolated luteal tissue

source_name: D10 CL + hCG_Rep3

value: hCG (Simulated Early Pregnancy) luteal day 10


title: human ileum, sample 99

description:
sample_id: 463
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 92

description:
sample_id: 376
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 95

description:
sample_id: 174
Ileal tissue biopsies from human, post IPAA subjects


title: D109

description:
410RS_2_044A-21H1_D109
dissected isolated luteal tissue

source_name: D10 Control corpora lutea_Rep9

value: Control luteal day 10


title: 10hTR1

description:
410RS_2_052A-21H1_10hTR1
dissected isolated luteal tissue

source_name: D10 CL + hCG  + TRL + R5020_Rep1


title: D10 4_reanalysis

description:
GSM623424
410RS_1_035A-11H1_D10 4 {3}
dissected isolated luteal tissue

source_name: D10 Control corpora lutea_Rep4


title: D108

description:
410RS_2_042A-21H1_D108
dissected isolated luteal tissue

source_name: D10 Control corpora lutea_Rep8


title: D10hT2

description:
410RS_1_017A-11H1_D10hT2 {2}
dissected isolated luteal tissue

source_name: D10 CL + hCG  + TRL_Rep2


title: D10h2_reanalysis

description:
GSM623426
410RS_1_026A-11H1_D10h2 {2}
dissected isolated luteal tissue

source_name: D10 CL + hCG_Rep2


title: D106

description:
410RS_2_041A-21H1_D106
dissected isolated luteal tissue

source_name: D10 Control corpora lutea_Rep6


title: human ileum, sample 96

description:
sample_id: 167
Ileal tissue biopsies from human, post IPAA subjects

source_name: ileum


title: human ileum, sample 100

description:
sample_id: 302
Ileal tissue biopsies from human, post IPAA subjects

value: M


title: D107

description:
410RS_2_040A-21H1_D107
dissected isolated luteal tissue

source_name: D10 Control corpora lutea_Rep7


title: D10h1_reanalysis

description:
GSM623425
410RS_1_018A-11H1_D10h1
dissected isolated luteal tissue

source_name: D10 CL + hCG_Rep1


title: D10h4_reanalysis

description:
GSM623428
410RS_1_011B-11H1_D10h4
dissected isolated luteal tissue

source_name: D10 CL + hCG_Rep4


title: human ileum, sample 93

description:
sample_id: 198
Ileal tissue biopsies from human, post IPAA subjects

value: yes


title: D10hT3

description:
410RS_1_036A-11H1_D10hT3 {4}
dissected isolated luteal tissue

source_name: D10 CL + hCG  + TRL_Rep3


title: WoundSkin_0D_rep4

city: Chicago

first: Wei

last: Xu

state: IL

address: 303 E Chicago Ave, Tarry 4-714

department: Surgery

institute: Northwestern University, Feinberg School of Medicine

hyb_protocol: For each array, 1650 ng of Cy3 labeled was fragmented and hybridized with rotation at 65°C for 17 hours. Samples were hybridized to rabbit custom design 4X44k arrays (Agilent Technologies, Inc).

scan_protocol: The arrays were washed according to the manufacturer’s protocol and then scanned on an Agilent G2505B scanner. Data were extracted using Feature Extraction 10.1.1.1 software (Agilent Technologies, Inc.).

data_processing: Using Limma software package in R environment (R386 2.15.2), the background of extracted microarray data was corrected by ‘normexp’ with offset 50. After normalized within and between arrays, the data was fit in a linear model with the empirical Bayes to moderate the standard errors. The p values of output data were adjusted with Benjamini and Hochberg's method to control the false discovery rate.

organism: Oryctolagus cuniculus

source_name: Wounded skin_untreated_day 0

label_protocol: RNA concentration was determined on a NanoDrop Spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE) and sample quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA). cDNA was synthesized from 400 ng of total RNA using the Quick-Amp labeling Kit (Agilent Technologies, Inc.) according the manufacturer’s protocol. Briefly, the cDNA was used as a template for in vitro transcription (IVT) in the presence of T7 RNA Polymerase and cyanine labeled CTP’s.  The amplified, labeled mRNA was purified using the RNeasy Mini Kit (Qiagen).

growth_protocol: One half of the each harvested wound was incubated with 0.5M ammonium thiocyanate at room temperature for 30 min. The epidermis of the wounding area was separated from the dermis and rinsed with PBS solution.

extract_protocol: The epidermis was immediately put into Tri Reagent® for RNA isolation (Sigma-Aldrich, St. Louis, MO) following the manufacture instruction. The TurboTM DNase (Life Technologies, Carlsberg, CA) was used to remove the genomic DNA from the total RNA followed by a RNA clean-up step with RNeasy® Mini Kit (Qiagen, Valencia, CA).

treatment_protocol: The superficial incisional grids on rabbit ear were created by using a double blade scalpel with 1 mm space between the two blades (Fig.1A and 1B). A single layer of Tegaderm was used to cover the wounding areas on both right and left ears until the wounding areas were fully re-epithelialized (two days post wounding, POE0). Thereafter, the Tegaderm on right ear was completely removed (NOW) while four more layers of Tegaderms were applied on left ear wounds (FOW). Rabbit ear samples were harvested at POE0, POE3 and POE5.

tag: breed

value: New Zealand White rabbit

value: female

tag: tissue

value: wounded skin epithelium

tag: samples harvested on

value: day 0 post epithelialization


title: D10 2_reanalysis

description:
GSM623422
410RS_1_015A-11H1_D10 2
dissected isolated luteal tissue

source_name: D10 Control corpora lutea_Rep2

value: Corpus Luteum

value: Adult Female

value: Mid-late/Late Luteal Phase


title: human ileum, sample 87

description:
sample_id: 666
Ileal tissue biopsies from human, post IPAA subjects

tag: batch

tag: gender

value: F

value: UC


title: human ileum, sample 90

description:
sample_id: 293
Ileal tissue biopsies from human, post IPAA subjects

tag: diagnosis


title: FXNPXY-1

city: Cambridge

first: Patrycja

last: Kozik

address: Hills Road

department: Cambridge Institute for Medical Research

country: United Kingdom

institute: University of Cambridge

description:
SAMPLE 3
replicate 1

hyb_protocol: Standard Illumina scanning protocol

scan_protocol: Illumina BeadStation 500 platform

data_processing: The data were transformed using variance stabilization transformation. Non-expressed genes were removed (where a detection p-value was above 0.01 for all four samples). Robust spline normalization algorithm was used for data normalization.

source_name: transfected HeLa-M tissue culture cells

label_protocol: Standard Illumina hybridization protocol

growth_protocol: The HeLa-M cells were grown at 37°C with 5% CO2 in Dulbeccoʼs Modified Eagleʼs medium supplemented with 10% fetal bovine serum, 2 mM L-glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin.

extract_protocol: RNA was isolated from 10^6 CD8-YXXΦ or CD8-FXNPXY cells (harvested by trypsinization) using the Purescript RNA Purification Kit (Life Sciences Germany)

treatment_protocol: Untreated

tag: cell line

value: HeLa-FXNPXY

tag: genotype/variation

value: stably expressing pIRESneo2-CD8-FXNPXY plasmid construct


title: WoundSkin_0D_rep5


title: WoundSkin_0D_rep3


title: human ileum, sample 91

description:
sample_id: 601
Ileal tissue biopsies from human, post IPAA subjects

value: IC


title: D10 3_reanalysis

description:
GSM623423
410RS_1_002B-11H1_D10 3
dissected isolated luteal tissue

source_name: D10 Control corpora lutea_Rep3


title: YXXF-1

description:
SAMPLE 1
replicate 1

value: HeLa-YXXΦ

value: stably expressing pIRESneo2-CD8-YXXΦ plasmid construct


title: YXXF-2

description:
SAMPLE 2
replicate 2


title: NormalSkin_rep2

source_name: Normal skin epithelium

value: normal skin epithelium


title: human ileum, sample 89

description:
sample_id: 363
Ileal tissue biopsies from human, post IPAA subjects

value: M


title: human ileum, sample 85

description:
sample_id: 664
Ileal tissue biopsies from human, post IPAA subjects

value: no


title: human ileum, sample 86

description:
sample_id: 320
Ileal tissue biopsies from human, post IPAA subjects

value: yes


title: NormalSkin_rep1

value: New Zealand White rabbit

value: female


title: human ileum, sample 83

description:
sample_id: 629
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 78

description:
sample_id: 642
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 84

description:
sample_id: 357
Ileal tissue biopsies from human, post IPAA subjects


title: WoundSkin_0D_rep2

value: wounded skin epithelium

value: day 0 post epithelialization


title: 8958.Webster.7

city: La Jolla

first: Nick

last: Webster

address: 9500 Gilman Drive

department: Medicine

institute: UCSD

description: plier normalized core exons

hyb_protocol: Hybridized using standard Affymetrix procedure

scan_protocol: Scanned using Standard Affymetric procedure

data_processing:
Data normalized by PLIER, core exons used.
affymetrix-algorithm-version: 2.0
program-name: Expression Console

source_name: Mouse liver

label_protocol: Labeled using standard Affymetrix procedure by the VA/VMRF GeneChip Core

growth_protocol: Livers harvested from one month old mice

extract_protocol: Total RNA from liver tissues of the three SRSF3HKO mice and age-matched WT controls was isolated using an RNeasy Kit (QIAGEN).  RNA quality was assessed by using the Agilent Model 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: no treatment

tag: genotype


title: 8940.Webster.6

description: plier normalized core exons


title: 8939.Webster.5

description: plier normalized core exons


title: human ileum, sample 82

description:
sample_id: 337
Ileal tissue biopsies from human, post IPAA subjects


title: 8935.Webster.1

description: plier normalized core exons

data_processing:
Data normalized by PLIER, core exons used
affymetrix-algorithm-version: 2.0
program-name: Expression Console

value: WT


title: human ileum, sample 80

description:
sample_id: 137
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 79

description:
sample_id: 542
Ileal tissue biopsies from human, post IPAA subjects


title: WoundSkin_0D_rep1


title: 8936.Webster.2

description: plier normalized core exons


title: human ileum, sample 76

description:
sample_id: 72
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 81

description:
sample_id: 186
Ileal tissue biopsies from human, post IPAA subjects


title: D10 1_reanalysis

description:
GSM623421
410RS_1_006B-11H1_D10 1
dissected isolated luteal tissue

source_name: D10 Control corpora lutea_Rep1

value: Corpus Luteum

value: Adult Female

value: Mid-late/Late Luteal Phase

value: Control luteal day 10


title: FXNPXY-2

description:
SAMPLE 4
replicate 2

value: HeLa-FXNPXY

value: stably expressing pIRESneo2-CD8-FXNPXY plasmid construct


title: 8937.Webster.3

description: plier normalized core exons


title: NT2shDNMT3B+aza-rep2

city: Urbana

first: Michael

last: Spinella

address: 2001 South Lincoln Ave

department: Comparative Biosciences

institute: University of Illinois

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol with Illumina BeadArray Reader

data_processing: The data were normalized using quantile normalization in Genome Studio

source_name: NT2/D1-R1 shDNMT3B cells +aza (10 nM, 3 days)

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

growth_protocol: Cells maintained with DMEM 10% FBS, 37oC, 5% CO2

extract_protocol: RNA was extracted with Trizol reagent. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cells were untreated or treated with 10 nm 5-aza deoxycytidine for 3 days.   5-aza was added fresh each day

tag: cell type

value: human ebryonal carcinoma


title: human ileum, sample 75

description:
sample_id: 57
Ileal tissue biopsies from human, post IPAA subjects

value: UC


title: human ileum, sample 74

description:
sample_id: 188
Ileal tissue biopsies from human, post IPAA subjects


title: NT2shDNMT3B-rep3

description: replicate 3

source_name: NT2/D1-R1 shDNMT3B cells


title: NT2shDNMT3B-rep1

description: replicate 1


title: human ileum, sample 70

description:
sample_id: 92
Ileal tissue biopsies from human, post IPAA subjects

value: F


title: human ileum, sample 71

description:
sample_id: 19
Ileal tissue biopsies from human, post IPAA subjects

value: M


title: IST408, genomic

city: Lisboa

first: Leonilde

middle: Morais

last: Moreira

address: A. Rovisco Pais

department: Bioengineering

country: Portugal

institute: Instituto Superior Tecnico

description:
Mucoid wild-type clinical strain.

The CEL file for this Sample was analyzed in Xspecies DNA hyb CDF batchmaker v3.2 to generate Bcc1sa520656F_Xspecies.CEL80.cdf. This Sample does not have processed data.

hyb_protocol: Following fragmentation, 5 µg of end-labeled fragmented DNA were used in a 200-µl hybridization cocktail containing added hybridization controls and hybridized on arrays for 16 hours at 50ºC. Modified post-hybridization wash and double-stain protocols (FLEX450_0005; GeneChip HWS kit, Affymetrix) were used on an Affymetrix GeneChip Fluidics Station 450.

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

data_processing: DNA-based probe-selection was performed using Xspecies DNA hyb CDF batchmaker v3.2, available here: http://affymetrix.arabidopsis.info/xspecies/. An optimal signal cutoff of 80 and minimum number of probes per probe set of 7 were determined empirically, resulting in the masking of 24223 of the original 226576 probes on the array and the exclusion of 156 probe sets. The new cdf file created (Bcc1sa520656F_Xspecies.CEL80.cdf) was used in DNA-Chip Analyzer 2008 for the subsequent gene expression analyses.

organism: Burkholderia cepacia

source_name: IST408 wild-type grown in S medium overnight

label_protocol: For DNA analysis, a total of 1.5 ug of genomic DNA from B. cepacia IST408 was labeled using the Bioprime DNA labelling System (Invitrogen,Paisley, UK) following a strategy for genomic DNA hybridization to GeneChips developed by Hammond and co-authors (2005). Cleanup was performed using the MinElute PCR Purification Kit (Qiagen, Hilden), and quality was checked on an Agilent 2100 Bioanalyzer using a DNA 1000 assay.

growth_protocol: Bacteria were grown in S medium overnight.

extract_protocol: Total DNA was extracted from bacterial cells using the DNeasy blood and tissue kit (Qiagen) following the manufacturer's instructions.

treatment_protocol: Bacterial cells were resuspended in RNAprotect Bacteria Reagent (Qiagen).

tag: isolate

value: wild-type


title: NT2shcontrol+aza-rep2

description: replicate 2

source_name: NT2/D1-R1 control cells +aza (10 nM, 3 days)


title: human ileum, sample 73

description:
sample_id: 486
Ileal tissue biopsies from human, post IPAA subjects

value: no


title: NT2shDNMT3B+aza-rep1

description: replicate 1


title: NT2shDNMT3B-rep2

description: replicate 2


title: human ileum, sample 69

description:
sample_id: 7
Ileal tissue biopsies from human, post IPAA subjects

value: yes


title: human ileum, sample 72

description:
sample_id: 394
Ileal tissue biopsies from human, post IPAA subjects


title: NT2shDNMT3B+aza-rep3

description: replicate 3


title: NT2shcontrol+aza-rep3

description: replicate 3


title: NT2shcontrol-rep3

description: replicate 3

source_name: NT2/D1-R1 control cells


title: NT2shcontrol-rep2

description: replicate 2


title: human ileum, sample 77

description:
sample_id: 609
Ileal tissue biopsies from human, post IPAA subjects

source_name: ileum


title: human ileum, sample 68

description:
sample_id: 102
Ileal tissue biopsies from human, post IPAA subjects


title: IST408_bceF::Tp, biological rep2

description:
IST408_bceF_2
Mutation in the bceF gene.

hyb_protocol: Following fragmentation, 2 µg of end-labeled fragmented cDNA were used in a 200-µl hybridization cocktail containing added hybridization controls and hybridized on arrays for 16 hours at 50ºC. Modified post-hybridization wash and double-stain protocols (FLEX450_0005; GeneChip HWS kit, Affymetrix) were used on an Affymetrix GeneChip Fluidics Station 450.

data_processing:
DNA-based probe-selection was performed using Xspecies DNA hyb CDF batchmaker v3.2, available here: http://affymetrix.arabidopsis.info/xspecies/. An optimal signal cutoff of 80 and minimum number of probes per probe set of 7 were determined empirically, resulting in the masking of 24223 of the original 226576 probes on the array and the exclusion of 156 probe sets. The new cdf file created (Bcc1sa520656F_Xspecies.CEL80.cdf) was used in DNA-Chip Analyzer 2008 for the subsequent gene expression analyses.

The 9 arrays were normalized to a baseline array with median CEL intensity by applying an Invariant Set Normalization Method. Normalized CEL intensities of the arrays were used to obtain model-based gene expression indices based on a Perfect Match (PM)-only model. Replicate data (triplicates) for each bacterial isolate was weighted gene-wise by using inverse squared standard error as weights. All genes compared were considered to be differentially expressed if the 90% lower confidence bound of the fold change (LCB) between experiment and baseline was above 1.2 when the bceF::Tp mutant was compared with the wild-type IST408 and 1.6 for the comparison between the bceE::Tp mutant and IST408.

source_name: IST408 bceF::Tp with 12h growth in S medium

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

growth_protocol: Bacterial strains were grown in 100 ml S medium in 250 ml Erlenmeyer flasks at 30ºC, 250 r.p.m. for 12 h.

extract_protocol: Total RNA extraction was carried out using the RNeasy MiniKit (Qiagen) by following the manufacturer's recommendations.

value: IST408 bceF::Tp

value: bceF mutation


title: human ileum, sample 67

description:
sample_id: 654
Ileal tissue biopsies from human, post IPAA subjects


title: NT2shcontrol+aza-rep1

description: replicate 1


title: human ileum, sample 66

description:
sample_id: 196
Ileal tissue biopsies from human, post IPAA subjects


title: IST408_bceF::Tp, biological rep1

description:
IST408_bceF_1
Mutation in the bceF gene.


title: IST408_bceE::Tp, biological rep2

description:
IST408_bceE_2
Mutation in the bceE gene.

source_name: IST408 bceE::Tp with 12h growth in S medium

value: IST408 bceE::Tp

value: bceE mutation


title: human ileum, sample 63

description:
sample_id: 404
Ileal tissue biopsies from human, post IPAA subjects


title: SW48_control

city: Dallas

first: Masanobu

last: Takahashi

address: 3500 Gaston Avenue, suite H-250

institute: Baylor University Medical Center

hyb_protocol: Standard Illumina hybridization protocol (type of tips; HT12v3)

scan_protocol: BAR: Bead Array Reader

data_processing: The data were normalised using average normalisation with IlluminaGUI in R

source_name: SW48, non-treated

label_protocol: Cy3-labelled cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: The SW48 cells were cultured in Iscove's Modified Dulbecco's Medium with 10% fetal bovine serum.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit (Qiagen).

treatment_protocol: The cells were treated with 0.1% DMSO (vehicle controls) or AKBA (Sigma Chemical Co.), at a dose range of 20 μM for 6 days.

value: colorectal cancer


title: human ileum, sample 64

description:
sample_id: 421
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 65

description:
sample_id: 657
Ileal tissue biopsies from human, post IPAA subjects


title: SW48_AKBA

source_name: SW48, AKBA treated, 6 d


title: IST408_bceE::Tp, biological rep1

description:
IST408_bceE_1
Mutation in the bceE gene.


title: IST408, biological rep2

description:
B. cepacia_IST408_2
Mucoid wild-type clinical strain.

source_name: IST408 wild-type with 12h growth in S medium


title: IST408_bceF::Tp, biological rep3

description:
IST408_bceF_3
Mutation in the bceF gene.


title: H3255 ControlsiRNA rep2

city: Bethesda

first: William

middle: Wallace

last: Lockwood

state: MD

address: 50 South Drive

institute: National Human Genome Research Institute

data_processing: The data were normalised using quantile normalization with Partek Genomics Suite

source_name: H3255 ControlsiRNA rep2

growth_protocol: 400,000 cells were seeded in antibiotic-free RPMI-1640 media supplemented with 10% FBS, in 6-well culture plates

extract_protocol: 72-hours post-transfection, RNA was harvested using Trizol (Invitrogen)

treatment_protocol: Cells were transfected at a final concentration of 100nM siRNA using 6ul DharmaFECT 1 (Dharmacon) according to the manufacturer's instructions. ON-TARGETplus SMARTpool small interfering RNAs (siRNAs) targeting TITF1 along with a negative control (ON-TARGETplus siCONTROL nontargeting siRNA pool) were obtained from Dharmacon

tag: tumor type

value: Lung Adenocarcinoma


title: IST408, biological rep3

description:
B. cepacia_IST408_3
Mucoid wild-type clinical strain.


title: NT2shcontrol-rep1

description: replicate 1


title: H3255 TITF1siRNA rep2

source_name: H3255 TITF1siRNA rep2


title: human ileum, sample 61

description:
sample_id: 165
Ileal tissue biopsies from human, post IPAA subjects

extract_protocol: miRNeasy Mini Kit (QIAGEN)


title: WoundSkin_0D_rep6

source_name: Wounded skin_untreated_day 0

value: New Zealand White rabbit

value: female

value: wounded skin epithelium

value: day 0 post epithelialization


title: IST408_bceE::Tp, biological rep3

description:
IST408_bceE_3
Mutation in the bceE gene.


title: human ileum, sample 59

description:
sample_id: 593
Ileal tissue biopsies from human, post IPAA subjects


title: H3255 ControlsiRNA rep1

source_name: H3255 ControlsiRNA rep1


title: H3255 TITF1siRNA rep1

source_name: H3255 TITF1siRNA rep1


title: IST408, biological rep1

description:
B. cepacia_IST408_1
Mucoid wild-type clinical strain.


title: HCC4019 ControlsiRNA rep2

source_name: HCC4019 ControlsiRNA rep2


title: HCC4019 ControlsiRNA rep1

source_name: HCC4019 ControlsiRNA rep1


title: human ileum, sample 60

description:
sample_id: 87
Ileal tissue biopsies from human, post IPAA subjects


title: BC00035

first: Ravand

last: Samaeekia

department: Ben May Department of Cancer Research

institute: University of Chicago

description: Total RNA was submitted to exiqon for 757 miRNA expression detection and normalized based on pooled samples.

hyb_protocol: Using Tecan hybridization stations the hybridization and washing steps were fully automated for higher reproducibility.

scan_protocol: Arrays were scanned with highly sensitive equipment in ozone free environment to reduce day-to-day variation to a minimum. Image Analysis was then performed to quantify the signals on the arrays.

data_processing: First, a technical quality assessment was performed based on results from spike in controls, flagging of spots, background intensity levels and signal intensity distribution.The data obtained was normalized using methods applicable to the performed experiment. Customized data analysis can also be provided (including heat map/Unsupervised Hierarchical Clustering, PCA-plots etc based on TTests or ANOVA).

source_name: Breast Tumor

label_protocol: Exiqon commercial miRCURY™ LNA Array Power labeling kit for labeling. This method allowed highly efficient and uniform labeling of microRNAs with minimal sequence bias.

extract_protocol: The Qiagen miRNA easy kit with total RNA extraction.

value: Breast Tumor

tag: OS time

tag: race

value: Black

tag: er

value: pos

tag: pr

value: neg

tag: tumor subtype ihc

value: LUM A

source_name: Common Reference Pool

tag: sample type

value: referene pool


title: BC00034

tag: tissue

tag: pathological stage_t

tag: tumor size

tag: tnm

value: Pos

value: LumB


title: BC00041

tag: grade

value: U

value: Basal


title: BC00024

value: Neg

value: BASAL


title: human ileum, sample 58

description:
sample_id: 17
Ileal tissue biopsies from human, post IPAA subjects

data_processing:
Summarized probe cell intensity data were generated with an Affymetrix GeneChip Command Console. Probe-level summarization files were produced and the data were background-adjusted, normalized and log-transformed with a robust multiarray average (RMA) algorithm in Affymetrix Expression Console. The empirical Bayes (EB) method described by Johnson, W.E. et al. (2007) was applied to the normalized data to correct for batch effects which may have resulted from a non-linear sample extraction and microarray processing schedule. Lastly, duplicate and ambiguous Affymetrix probesets (Release 32) as well as those which no longer mapped to a gene in the current human genome build (GRCh37.p5) were removed from further analysis.
probe_group_file: HuGene-1_0-st-v1.r4.pgf
meta-probeset_file: HuGene-1_0-st-v1.r4.mps

tag: batch

tag: gender

value: M

value: yes

tag: diagnosis

value: UC


title: human ileum, sample 88

description:
sample_id: 124
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 57

description:
sample_id: 458
Ileal tissue biopsies from human, post IPAA subjects

value: F


title: 7045913

value: Unclassified

value: LumA


title: HCC4019 TITF1siRNA rep2

source_name: HCC4019 TITF1siRNA rep2

value: Lung Adenocarcinoma


title: 7045272

value: Breast Tumor

value: Black

value: pos


title: human ileum, sample 56

description:
sample_id: 150
Ileal tissue biopsies from human, post IPAA subjects

value: no


title: HCC4019 TITF1siRNA rep1

source_name: HCC4019 TITF1siRNA rep1


title: human ileum, sample 55

description:
sample_id: 472
Ileal tissue biopsies from human, post IPAA subjects

source_name: ileum


title: human ileum, sample 53

description:
sample_id: 675
Ileal tissue biopsies from human, post IPAA subjects


title: NT2shDNMT3B+aza-rep1

description: replicate 1

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: GenomeStudio software

label: Cy5 and Cy3

source_name: NT2/D1-R1 shDNMT3B cells +aza (10 nM, 3 days)

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from cell line samples using Qiagen DNeasy Kit according to standard instructions

tag: cell line

tag: cell type

value: human ebryonal carcinoma


title: NT2shDNMT3B+aza-rep3

description: replicate 3


title: human ileum, sample 54

description:
sample_id: 206
Ileal tissue biopsies from human, post IPAA subjects


title: NT2shDNMT3B-rep3

description: replicate 3

source_name: NT2/D1-R1 shDNMT3B cells


title: BC00014

value: Pos

value: neg

value: LUM A

value: referene pool


title: NT2shDNMT3B+aza-rep2

description: replicate 2


title: 7027919

value: U


title: AF6FR0002E7B8

source_name: Normal

value: Normal


title: human ileum, sample 51

description:
sample_id: 55
Ileal tissue biopsies from human, post IPAA subjects

value: M

value: yes


title: NT2shcontrol+aza-rep3

description: replicate 3

source_name: NT2/D1-R1 control cells +aza (10 nM, 3 days)


title: human ileum, sample 52

description:
sample_id: 82
Ileal tissue biopsies from human, post IPAA subjects

value: F

value: UC


title: human ileum, sample 50

description:
sample_id: 296
Ileal tissue biopsies from human, post IPAA subjects


title: 7016941

value: LumA


title: 6006062


title: 6005697

value: LumB


title: 6004586

value: Breast Tumor

value: Basal


title: 6002353

value: Black


title: 6004768

value: Tis

value: pos


title: 6003933

value: Unclassified


title: 64628

value: White


title: NT2shcontrol+aza-rep2

description: replicate 2

value: human ebryonal carcinoma


title: NT2shDNMT3B-rep1

description: replicate 1


title: 64574

value: neg

value: referene pool


title: NT2shcontrol-rep3

description: replicate 3

source_name: NT2/D1-R1 control cells


title: NT2shcontrol-rep2

description: replicate 2


title: NT2shDNMT3B-rep2

description: replicate 2


title: human ileum, sample 49

description:
sample_id: 169
Ileal tissue biopsies from human, post IPAA subjects

value: no


title: human ileum, sample 45

description:
sample_id: 76
Ileal tissue biopsies from human, post IPAA subjects

value: M


title: human ileum, sample 47

description:
sample_id: 281
Ileal tissue biopsies from human, post IPAA subjects

value: yes


title: human ileum, sample 48

description:
sample_id: 615
Ileal tissue biopsies from human, post IPAA subjects


title: 64559


title: human ileum, sample 43

description:
sample_id: 361
Ileal tissue biopsies from human, post IPAA subjects

value: IC


title: ARCaP-M 5-aza 3D

city: Atlanta

first: Khanjan

last: Gandhi

state: Georgia

address: 1365-B Clifton Rd NE, Room 4107

institute: Winship Cancer Institute, Emory University.

description: SAMPLE 22

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: BeadChips were scanned using the Illumina BeadArray Scanner.

data_processing: Average beta values were calculated using Genome Studio Software v2010.3.

source_name: ARCaP-M prostate cancer cells, 5-aza-deoxycytidine

label_protocol: PCR product was prepared with the standard Illumina protocol for arrays.

growth_protocol: ARCaP-E and ARCaP-M cells were purchased from Novicure Biotechnology and propagated in MCaP-Medium (Novicure Biotechnology, Inc, Birmingham, AL), supplemented with 5% FBS, 200mM L-glutamine, and pen-strep. Additionally, PREC cells (Lonza, Basel, Switzerland) were used as a normal human prostate cell line control.  Total DNA was submitted to the Emory Winship Cancer Institute Cancer Genomics Shared Resource for analysis with Illumina 27K CpG Methylation Arrays that interrogate 27,578 CpG loci > 14,000 genes using the Illumina Beadstation 500 instrument.

extract_protocol: DNA was isolated from the cells.

treatment_protocol: ARCaP-E and ARCaP-M cells were treated with DMSO control, 20 µM genistein, or 1 µM 5-aza for six days, and PrEC cells were untreated. Fresh drugs and media were changed every other day.

value: ARCaP-M

value: prostate cancer cells

tag: treatment


title: human ileum, sample 46

first: Boyko

last: Kabakchiev

institute: Mount Sinai Hospital

description:
sample_id: 359
Ileal tissue biopsies from human, post IPAA subjects

hyb_protocol: GeneChip Hybridization, Wash, and Stain Kit (Affymetrix)

label_protocol: GeneChip WT Terminal Labeling and Controls Kit (Affymetrix)

value: UC


title: BC00097

description: Total RNA was submitted to exiqon for 757 miRNA expression detection and normalized based on pooled samples.

value: Breast Tumor

tag: OS time

value: U


title: human ileum, sample 44

description:
sample_id: 152
Ileal tissue biopsies from human, post IPAA subjects


title: ARCaP-M 5-aza 2D

description: SAMPLE 21


title: NT2shcontrol+aza-rep1

description: replicate 1


title: PREC 3

description: SAMPLE 23

source_name: PREC normal prostate cells, untreated

value: PREC

value: normal prostate cells


title: NT2shcontrol-rep1

description: replicate 1


title: PREC 4

description: SAMPLE 24


title: human ileum, sample 42

description:
sample_id: 308
Ileal tissue biopsies from human, post IPAA subjects

value: F


title: BC00094

tag: race

value: Black

value: Unclassified


title: BC00071

value: White

tag: er

value: pos


title: ARCaP-E 5-aza 2D

description: SAMPLE 20

source_name: ARCaP-E prostate cancer cells, 5-aza-deoxycytidine

value: ARCaP-E


title: BC00063 N

value: Normal

value: referene pool


title: ARCaP-E 5-aza 1D

description: SAMPLE 19


title: BC00063 T

value: neg

tag: pr


title: ARCaP-M GEN 1D

description: SAMPLE 18

source_name: ARCaP-M prostate cancer cells, genistein

value: genistein


title: human ileum, sample 40

description:
sample_id: 661
Ileal tissue biopsies from human, post IPAA subjects

value: M

value: no


title: human ileum, sample 39

description:
sample_id: 520
Ileal tissue biopsies from human, post IPAA subjects

value: yes

value: UC


title: BC00061

value: Breast Tumor

value: U

tag: tumor subtype ihc

value: LumA

value: LumB


title: human ileum, sample 41

description:
sample_id: 478
Ileal tissue biopsies from human, post IPAA subjects

value: F


title: human ileum, sample 38

description:
sample_id: 611
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 36

description:
sample_id: 132
Ileal tissue biopsies from human, post IPAA subjects


title: BC00055

value: Black

value: Unclassified

tag: sample type


title: ARCaP-E GEN 3D

description: SAMPLE 16

source_name: ARCaP-E prostate cancer cells, genistein

value: prostate cancer cells


title: BC00057

tag: tissue

value: pos


title: ARCaP-M DMSO 3D

description: SAMPLE 17

source_name: ARCaP-M prostate cancer cells, DMSO

value: ARCaP-M

value: DMSO


title: ARCaP-E GEN 2D

description: SAMPLE 15

value: ARCaP-E