title: HPMEC_4C library_1

hyb_protocol: Labeled samples were hybridized to 3x720K 16q24.1m arrays at 42°C for 24 hrs,followed by disassembling of slides from hybridization apparatus at 42° in the wash buffer containing DTT followed by three washes at room temperature in the same buffer for 2mins, 1min and 15secs respectively. The slides were dried in a microarray dryer for 1 min.

scan_protocol: 3x720K  microarrays were scanned on a Roche-NimbleGen MS 200 Microaarray scanner

data_processing: Scanned images were processed using NumbleScan v2.5(Roche Nimblegen) and analyzed using Signalmap v1.9 ( RocheNimbleGen)

source_name: 4C library from HPMEC

label_protocol: 0.5ug of gDNA from 4C template/ reference DNA was labeled using the NimbleGen Dual-color DNA labeling kit according to manufacturer's instructions

growth_protocol: HPMEC were cultured to confluence in EMS medium supplemented with 10% FBS, ECGS and 1% penicillin-streptomycin at 37°C with 5% CO2

extract_protocol: Genomic DNA was by phenol extraction and sodium acetate/ethanol precipitation to obtain the 3C library. The 4C library was further digested by TaqI, religated and redigested with HindIII.4C template was obtained by performing 16 amplification PCR ractions using the Expand Long Template PCR System ( Roche Applied Science). Pooled PCR products were purified using Qiagen PCR cleanup kit (Qiagen). To generate reference DNA, genomic DNA was isolated from uncrosslinked HPMEC or lymphoblasts with Puregene Blood core Kit A and digested overnight with EcoRI and TaqI.

treatment_protocol: 1x107 cells were crosslinked by incubating for 10 mins at room temperature with 37% formaldehyde followed by quenching with 2.5M glycine for 5 mins.The cells were then lysed in 1 ml of lysis buffer containing 0.1ml protease inhibitor cocktail, for 15 mins on ice. The crosslinked chromatin was sheared using a dounce homogenizer. The homogenized cells were then digested overnight using a rare cutter restriction enzyme EcoRIin presence of triton X-100 and SDS.This was followed by ligation with T4 DNA ligase for 2h at 16°C and overnight incubation with proteinase K at 65°C to reverse crosslinks.

value: Human pulmonary microvascular endothelial cells (HPMEC)

source_name: genomic DNA  from uncrosslinked HPMEC


title: KOVB2_98

status: Public on Jul 10 2012

type: RNA

city: Kyoto

first: Kaoru

last: Abiko

address: 54 Shogoin Kawaharacho, Sakyo-ku

department: Department of Gynecology and Obstetrics

country: Japan

institute: Kyoto University Graduate School of Medicine

hyb_protocol: Following fragmentation, 12.5ug of cRNA were hybridized for 16hr at 45C on Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were analyzed with Affymetrix microarray scanner using AGCC software.

data_processing: The data were analyzed with R.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: ovarian cancer, ascites1

label_protocol: Labeling was performed according to Affymetrix GeneChip 3' IVT Express Kit protocol.

extract_protocol: Total RNA was extracted using Qiagen RNA easy.

tag: tissue

value: ovarian cancer

value: positive

tag: Stage

tag: histology

value: endometrioid

tag: age


title: KOVB3_144

value: serous low grade


title: KOVB3_130

value: serous


title: KOVB4_4


title: KOVB4_22


title: KOVB4_33


title: KOVB3_128


title: KOVB3_131


title: KOVB3_121


title: KOVB2_95


title: KOVB2_92


title: KOVB3_115


title: lymphoblasts_4C library

status: Public on Jul 11 2012

type: genomic

city: Houston

first: Pawel

last: Stankiewicz

state: TX

address: One Baylor Plaza

department: Molecular Human Genetics

country: USA

institute: Baylor College of Medicine

molecule: genomic DNA

source_name: 4C library from lymphoblasts

growth_protocol: Lymphoblasts were cultured to confluence in DMEM medium supplemented with 10%FBS and 1% penicillin-streptimycin at 37°C with 10% CO2

tag: cell type

value: lymphoblasts

source_name: genomic DNA  from uncrosslinked lymphoblasts


title: KOVB2_89


title: Mtb infected-8wks-3

city: Newark

first: Selvakumar

last: Subbian

state: NJ

address: 225 Warren Street

department: Medicine

institute: Public Health Research Institute at UMDNJ

description:
Biological replicate
Mtb infected-8w-3

hyb_protocol: standard protocol used can be found at <http://www.cag.icph.org/downloads_page.htm#LabelingProtocols> from the center for applied genomics of the Public Health Research Institute of UMDNJ was used for all the experiments

scan_protocol: The rabbit microarray slides were scanned using Agilent scanner

data_processing:
Microarray data from the scanned images were extracted using feature extraction software from Agilent technologies and downstream analysis was performed using commercial software.
Lowess-error-normalised log2 ratio (Red vs Green Channel) for significant difference in fold change in gene expression was calculated and represented as Mtb infected at Tx/uninfected

organism: Oryctolagus cuniculus

source_name: Lung

label_protocol: cDNA was synthesised from total RNA using First strand synthesis kit (Invitrogen) and was labelled with either Cy3 or Cy5 using the kit from the manufacturer (Agilent Technologies)

growth_protocol: New Zealand White rabbits were infected aerogenically with MtbCDC1551 at 3.5log10 (on day 0).  Lung tissues from rabbits were isolated from uninfected and at Day 2,4, 8 and 12 weeks post infection and used for total RNA isolation.

extract_protocol: Total RNA from the rabbit lungs were isolated using TRIzol reagent (Invitrogen, CA, USA) according to the instructions of the manufacturers

treatment_protocol: Lung samples were snap frozen at -80oC before isolation of total RNA (using TRIzol method)

tag: infection

value: Uninfected

tag: time point

value: 8 wks post infection


title: HPMEC_4C library_2


title: KOVB2_85


title: KOVB4_32

source_name: ovarian cancer, ascites0

value: negative


title: KOVB2_106


title: KOVB4_29


title: KOVB4_23


title: KOVB3_143

value: clear


title: KOVB4_21


title: KOVB3_140


title: KOVB2_100


title: KOVB2_87


title: KOVB2_111


title: KOVB4_15


title: KOVB4_19


title: KOVB4_11


title: KOVB4_20


title: KOVB3_135


title: KOVB3_126

value: mucinous


title: KOVB3_142

value: carcinosarcoma


title: KOVB4_27


title: KOVB4_24


title: KOVB4_25


title: KOVB2_86


title: KOVB2_113


title: KOVB4_18


title: KOVB2_108


title: KOVB3_136


title: KOVB3_154


title: Bem1 Knockout Replicate 1

city: Pittsburgh

first: Anthony

last: Gitter

state: PA

address: 5000 Forbes Ave

department: Computer Science Department

institute: Carnegie Mellon University

description: WIS_251632210283_pmt10_GE2_107_Sep09_1_1.txt

hyb_protocol: The samples were hybridized to yeast dual color expression microarrays (8x15K, G2509F) using standard Agilent protocols, reagents, and instruments.

scan_protocol: The scanned images were analyzed using Agilent's Feature Extraction software.

data_processing: After background subtraction, probe location normalization based on a Gaussian image filtering technique was applied.  This was followed by quantile normalization. The software we used included Agilent Feature Extraction Software version 10.7.3.1 for scanning, the MATLAB Bioinformatics Toolbox version 3.4 (R2009b) for quantile normalization, and a custom script from a colleague for the probe location normalization.

organism: Saccharomyces cerevisiae

source_name: Bem1 Knockout Replicate 1

label_protocol: The samples were amplified, labeled, using standard Agilent protocols, reagents, and instruments.

growth_protocol: Cells were grown to logarithmic phase in SC medium (OD=0.5). The cells were harvested, pelleted and frozen for further analysis.

extract_protocol: Total RNA was extracted using MasterPure™ yeast RNA purification Kit (Epicentre).

treatment_protocol: Soribitol experiments were similarly performed by growing to logarithmic phase in SC medium and then washing and resuspending in SC medium with 1M sorbitol for 30 minutes.

tag: genotype/variation

value: Bem1 Knockout

tag: medium

value: sorbitol


title: ACD lung_gDNA3 (sample 60.4)

hyb_protocol: Labeled samples were hybridized to 4.2M whole genome arrays at 42°C for 60-72 hrs,followed by disassembling of slides from hybridization apparatus at 42° in the wash buffer containing DTT followed by three washes at room temperature in the same buffer for 2mins, 1min and 15secs respectively. The slides were dried in a microarray dryer for 1 min.

scan_protocol: 4.2M microarrays were scanned on a Roche-NimbleGen MS 200 Microaarray scanner

data_processing: Scanned images were processed using NumbleScan v2.5 (Roche Nimblegen) and analyzed using Signalmap v1.9 (rocheNimbleGen)

source_name: Genomic DNA from frozen/FFPE lung tissue of ACD/MPV patient

label_protocol: 0.5ug of genomic DNA was labeled using the NimbleGen Dual-color DNA labeling kit according to manufacturer's instructions.

extract_protocol: Peripheral blood DNA was extracted using Gentra Puregene Blood Kit (Qiagen), DNA from frozen lung tissues was extracted using Dneast Blood & Tissue kit(Qiagen), DNA from FFPE lung tissues was isolated following manufacturer's protocol ( Agilent technologies)

tag: diagnosis

value: Alveolar Capillary Dysplasia with Misalignment of Pulmonary Veins (ACD/MPV)

value: lung

source_name: Peripheral blood genomic DNA from normal control

value: healthy

value: peripheral blood


title: KOVB3_124

value: ovarian cancer


title: KOVB3_122


title: KOVB3_125 rehyb


title: KOVB2_105

value: undifferentiated


title: KOVB3_120


title: KOVB3_116


title: KOVB2_96


title: Memory_B_cell_1

city: Pamplona

first: Victor

last: Segura

state: Navarra

address: Avda. Pío XII, 55

department: Unit of Proteomics, Genomics and Bioinformatics

country: Spain

institute: FIMA

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized to the Affymetrix HG-U133_Plus2 chip according to the protocols provided by the manufacturer.

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

data_processing: RMA (R/Bioconductor processing)

source_name: Purified cells, tonsil, memory B cells

label_protocol: The cDNA was prepared from 5 microg total RNA using the One –Cycle cDNA Synthesis kit from Affymetrix. This cDNA was used for synthezising the cRNA using the IVT labeling kit (Affimetrix). The synthezised cRNA was purified with the GeneChip Sample Cleanup Module (Affimetrix).

growth_protocol: Frozen biopsies from previously untreated patients for lymphoma samples and purified populations from tonsil or peripheral blood for normal controls.

extract_protocol: The cells were harvested with TRIzol Reagent (Invitrogen) and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

value: tonsil

value: memory B cells

tag: disease status

value: healthy control


title: Peripheral blood_Marginal_B_cell_2

source_name: Purified cells, blood, IgM+IgD+CD27+

value: blood


title: Naïve_B_cell_1

source_name: Purified cells, tonsil, naive B cells

value: naive B cells


title: KOVB2_94

value: negative


title: KOVB3_123

value: clear


title: KOVB2_88

value: positive


title: KOVB2_107


title: KOVB2_112

value: endometrioid


title: Peripheral blood_Marginal_B_cell_1


title: KOVB2_102 rehyb


title: T_cell

source_name: Purified cells, tonsil, T cells

value: T cells


title: Memory_B_cell_2


title: Peripheral blood_CD19_activated_2

source_name: Purified cells, blood, CD19+, αIgM,αCD40,IL4, 24h

value: CD19+, αIgM,αCD40,IL4, 24h


title: Naïve_B_cell_2


title: KOVB2_91

value: serous/clear


title: KOVB2_104


title: Peripheral blood_CD19_activated_1


title: Peripheral blood_CD19_2

source_name: Purified cells, blood, CD19+


title: Splenic_Marginal_B_Cell_lymphoma_4

source_name: Frozen biopsy, SMZL

value: frozen biopsy

value: lymphoma

value: SMZL


title: Peripheral blood_CD19_1


title: Splenic_Marginal_B_Cell_lymphoma_6


title: Splenic_Marginal_B_Cell_lymphoma_9


title: Centroblast_1

source_name: Purified cells, tonsil, centroblats

value: centroblats


title: Splenic_Marginal_B_Cell_lymphoma_3


title: Splenic_Marginal_B_Cell_lymphoma_5


title: Splenic_Marginal_B_Cell_lymphoma_7


title: Follicular_B_Cell_lymphoma_8

source_name: Frozen biopsy, FCL

value: FCL


title: Follicular_B_Cell_lymphoma_7


title: Splenic_Marginal_B_Cell_lymphoma_8


title: Splenic_Marginal_B_Cell_lymphoma_1


title: Splenic_Marginal_B_Cell_lymphoma_10


title: Follicular_B_Cell_lymphoma_6


title: Splenic_Marginal_B_Cell_lymphoma_2


title: Follicular_B_Cell_lymphoma_15


title: Splenic_Marginal_B_Cell_lymphoma_12


title: Follicular_B_Cell_lymphoma_2


title: Splenic_Marginal_B_Cell_lymphoma_11


title: Follicular_B_Cell_lymphoma_3


title: Follicular_B_Cell_lymphoma_14


title: Follicular_B_Cell_lymphoma_5


title: Follicular_B_Cell_lymphoma_4


title: Follicular_B_Cell_lymphoma_13


title: Follicular_B_Cell_lymphoma_10


title: Follicular_B_Cell_lymphoma_11


title: Follicular_B_Cell_lymphoma_12


title: Follicular_B_Cell_lymphoma_9


title: Diffuse_Large_B_Cell_lymphoma_9

source_name: Frozen biopsy, DLBCL

value: DLBCL


title: Diffuse_Large_B_Cell_lymphoma_4


title: L. ruminis ATCC25644 (Cy5) vs L. ruminis ATCC27782 (Cy3) - non-motile growth phase

city: Cork

first: Paul

middle: W

last: O'Toole

address: Western Rd.

department: Microbiology

country: Ireland

institute: Univeristy College Cork

hyb_protocol: An Oligo aCGH/ChIP-on chip hybridization kit (Agilent) was used for hybridisation of the labelled cDNA to the microarrays. Probe hybridization took place at 65°C for 20 hrs with constant rotation (10 rpm).

scan_protocol: Microarrays were scanned using the Agilent Microarray Scanner System (G2505B) and the scanned files were converted to data files with Feature Extraction software (Agilent).

data_processing: Agilent feature extraction software (version 9.5) was used to generate data files from the scanned images.

organism: Ligilactobacillus ruminis ATCC 27782

source_name: L. ruminis ATCC27782

label_protocol: cDNA for microarray analysis was prepared by reverse transcription of 5 µg of total RNA using random nonomers (MWG-Biotech, Germany). 0.75 µg cDNA was labelled with Cy3 using the ULS cDNA synthesis and labeling kit, DSK-001 (Kreatech) according to the manufacturer's protocol.

growth_protocol: L. ruminis strains were inoculated into MRS broth (20ml), (1% inoculum), and were incubated anaerobically at 37°C for 16-20 hrs.

extract_protocol: 1ml of each culture was added to 2ml of RNAprotect Bacteria Reagent (Qiagen).  Total RNA was isolated according to the protocol for "enzymatic digestion and mechanical disruption of bacteria" outlined in the RNAprotect Bacteria Reagent (Qiagen) handbook. The RNeasy Mini kit (Qiagen) was used to complete the extraction procedure. Contaminating DNA was removed with the Turbo DNA-free kit (Ambion).

treatment_protocol: L. ruminis cultures were incubated anaerobically at 37°C.

tag: strain

value: L. ruminis ATCC 27782

tag: motility

value: Non-motile growth phase

tag: media

value: MRS broth

organism: Ligilactobacillus ruminis ATCC 25644

source_name: L. ruminis ATCC25644

label_protocol: cDNA for microarray analysis was prepared by reverse transcription of 5 µg of total RNA using random nonomers (MWG-Biotech, Germany). 0.75 µg cDNA was labelled with Cy5 using the ULS cDNA synthesis and labeling kit, DSK-001 (Kreatech) according to the manufacturer's protocol.

value: L. ruminis ATCC 25644

value: Not motile


title: Diffuse_Large_B_Cell_lymphoma_7


title: Diffuse_Large_B_Cell_lymphoma_8


title: Diffuse_Large_B_Cell_lymphoma_6


title: Diffuse_Large_B_Cell_lymphoma_25


title: Diffuse_Large_B_Cell_lymphoma_26


title: Diffuse_Large_B_Cell_lymphoma_24


title: Diffuse_Large_B_Cell_lymphoma_3


title: Diffuse_Large_B_Cell_lymphoma_23


title: L. ruminis ATCC25644 (Cy5) vs L. ruminis ATCC27782 (Cy3) - motile growth phase (biol rep 2)

label_protocol: cDNA for microarray analysis was prepared by reverse transcription of 10 µg of total RNA using random nonomers (MWG-Biotech, Germany). 1 µg cDNA was labelled with Cy3 using the ULS cDNA synthesis and labeling kit, DSK-001 (Kreatech) according to the manufacturer's protocol.

growth_protocol: L. ruminis strains were inoculated into MRS broth (20ml), (0.25% inoculum), and were incubated anaerobically at 37°C for 15 hrs.

extract_protocol: Each 20ml culture was centrifuged at room temperature to harvest the cells that were immediately resuspended in 500 µl of RNAprotect Bacteria Reagent (Qiagen). Total RNA was isolated according to the protocol for "enzymatic digestion and mechanical disruption of bacteria" outlined in the RNAprotect Bacteria Reagent (Qiagen) handbook, but with an extended proteinase K incubation (40 mins). The RNeasy Mini kit (Qiagen) was used to complete the extraction procedure. Contaminating DNA was removed with the Turbo DNA-free kit (Ambion).

value: Motile growth phase

label_protocol: cDNA for microarray analysis was prepared by reverse transcription of 10 µg of total RNA using random nonomers (MWG-Biotech, Germany). 1 µg cDNA was labelled with Cy5 using the ULS cDNA synthesis and labeling kit, DSK-001 (Kreatech) according to the manufacturer's protocol.


title: L. ruminis ATCC25644 (Cy5) vs L. ruminis ATCC27782 (Cy3) - motile growth phase (biol rep 1)

hyb_protocol: An Oligo aCGH/ChIP-on chip hybridization kit (Aglient) was used for hybridisation of the labelled cDNA to the microarrays.  Probe hybridization took place at 65°C for 20 hrs with constant rotation (10 rpm).

scan_protocol: Microarrays were scanned using the Agilent Microarray Scanner System (G2505B) and the scanned files were converted to data files with Feature Extraction software (Aglient, version 9.1).

label_protocol: cDNA for microarray analysis was prepared by reverse transcription of 10 µg of total RNA using random nonomers (MWG-Biotech, Germany).  1 µg cDNA was labelled with Cy3 using the ULS cDNA synthesis and labeling kit, DSK-001 (Kreatech) according to the manufacturer's protocol.

extract_protocol: Each 20ml culture was centrifuged at room temperature to harvest the cells that were immediately resuspended in 500 µl of RNAprotect Bacteria Reagent (Qiagen).  Total RNA was isolated according to the protocol for "enzymatic digestion and mechanical disruption of bacteria" outlined in the RNAprotect Bacteria Reagent (Qiagen) handbook, but with an extended proteinase K incubation (40 mins). The RNeasy Mini kit (Qiagen) was used to complete the extraction procedure. Contaminating DNA was removed with the Turbo DNA-free kit (Ambion).

label_protocol: cDNA for microarray analysis was prepared by reverse transcription of 10 µg of total RNA using random nonomers (MWG-Biotech, Germany).  1 µg cDNA was labelled with Cy5 using the ULS cDNA synthesis and labeling kit, DSK-001 (Kreatech) according to the manufacturer's protocol.


title: Diffuse_Large_B_Cell_lymphoma_21


title: L. ruminis ATCC25644 (Cy5) vs L. ruminis ATCC27782 (Cy3) - motile growth phase (biol rep 3)


title: Diffuse_Large_B_Cell_lymphoma_22


title: Diffuse_Large_B_Cell_lymphoma_5


title: Diffuse_Large_B_Cell_lymphoma_20


title: KOVB2_114

value: ovarian cancer

value: negative

value: serous


title: Pparg-null TSC, 4 day diff, w/ Rosi, bio rep 1

first: Yaacov

last: Barak

address: 204 Craft Ave

department: OBGYN and Reproductive Sciences

institute: Magee-Womens Research Institute/University of Pittsburgh

hyb_protocol: Standard Affymetrix protocol in Fluidic Station 450.

scan_protocol: GeneChip 3000 Laser Confocal Slide Scanner. Quantification using Gene-Chip Operating Software version 1.2 (Affymetrix).

data_processing: Expression values were summarized using the robust multichip average (RMA) function. P values for each set of 3 WT vs 2 null cell lines were assigned using analysis of variance (ANOVA) (Churchill, 2004), whereas the three Rosi-treated vs. untreated WT TSC lines were compared pair-wise using LIMMA (Smyth, 2004). q-values were assigned as described (Storey and Tibshirani, 2003), after first limiting the field only to genes that passed fold-change (FC) and q thresholds of 1.3x and 0.05, respectively, for WT vs. Pparg-null placentas.

label: Biotin

organism: Mus musculus

source_name: Pparg-null TSC, differentiated for 4 days in the presence of Rosi

label_protocol: cRNA biotinylation according to Affymetrix protocol

growth_protocol: TSC lines were plated on feederless plates in the presence of RPMI, 20% FBS, 70% MEF conditined medium, 25ng/ml FGF4 and 1ug/ml heparin. After 24 hours differentiation was initiated by replacing the medium with RPMI + 20% FBS, w/o the condition medium, FGF4 or heparin.

extract_protocol: Cells were extracted with Tri-Reagent according to manufacturer's protocol. Prior to labeling samples were treated with DNase I to remove any remainig genomic DNA.

treatment_protocol: Cell were differentiated for two or four days, as indicated, either as is (Untreated) or in the presence of 1uM Rosi for the entire duration of differentiation

value: TSC

value: Pparg-null

tag: time [duration of differentiation]

value: 4 days

tag: agent

value: PPARg agonist Rosiglitazone (Rosi), 1uM


title: Diffuse_Large_B_Cell_lymphoma_19

value: frozen biopsy

value: lymphoma


title: Diffuse_Large_B_Cell_lymphoma_18


title: WT TSC, 4 day diff, w/ Rosi, bio rep 3

source_name: WT TSC, differentiated for 4 days in the presence of Rosi

value: WT


title: Diffuse_Large_B_Cell_lymphoma_16

value: DLBCL


title: Diffuse_Large_B_Cell_lymphoma_2


title: Diffuse_Large_B_Cell_lymphoma_17


title: Pparg-null TSC, 4 day diff, w/ Rosi, bio rep 2


title: Diffuse_Large_B_Cell_lymphoma_15


title: WT TSC, 4 day diff, no Rosi, bio rep 3

source_name: WT TSC, differentiated for 4 days

value: Untreated


title: WT TSC, 4 day diff, no Rosi, bio rep 1


title: Diffuse_Large_B_Cell_lymphoma_14


title: Pparg-null TSC, 2 day diff, w/ Rosi, bio rep 2

source_name: Pparg-null TSC, differentiated for 2 days in the presence of Rosi

value: 2 days


title: Diffuse_Large_B_Cell_lymphoma_13


title: WT TSC, 4 day diff, w/ Rosi, bio rep 2


title: WT TSC, 2 day diff, w/ Rosi, bio rep 2

source_name: WT TSC, differentiated for 2 days in the presence of Rosi


title: WT TSC, 4 day diff, w/ Rosi, bio rep 1


title: WT TSC, 2 day diff, w/ Rosi, bio rep 3


title: Diffuse_Large_B_Cell_lymphoma_10


title: Pparg-null TSC, 2 day diff, w/ Rosi, bio rep 1


title: Diffuse_Large_B_Cell_lymphoma_11


title: Diffuse_Large_B_Cell_lymphoma_12


title: WT TSC, 2 day diff, no Rosi, bio rep 2

source_name: WT TSC, differentiated for 2 days


title: Follicular_B_Cell_lymphoma_1

value: FCL


title: WT TSC, 2 day diff, no Rosi, bio rep 3


title: Diffuse_Large_B_Cell_lymphoma_1


title: MALT_lymphoma_8

source_name: Frozen biopsy, MALT lymphoma

value: MALT lymphoma


title: MALT_lymphoma_9


title: WT TSC, 4 day diff, no Rosi, bio rep 2


title: Centroblast_2

value: tonsil

value: centroblats

value: healthy control


title: WT TSC, 2 day diff, w/ Rosi, bio rep 1


title: WT TSC, 2 day diff, no Rosi, bio rep 1


title: MALT_lymphoma_6


title: MALT_lymphoma_7


title: Ncoa6-null placenta, bio rep 1

description:
Ncoa6_Null_placenta_pool_1
Each pool of WT placentas is litter-matched to the similarly numbered Ncoa6-null pool

data_processing: Expression values were summarized using the robust multichip average (RMA) function. P values for each set of 3 WT vs 3 null pools were assigned using analysis of variance (ANOVA) (Churchill, 2004). q-values were assigned as described (Storey and Tibshirani, 2003), after first omitting all probe sets that were ‘Absent’ in all test samples according to MAS5.0.

source_name: pool of three Ncoa6-null placentas at E9.5

growth_protocol: Mouse pairs heterozygous for the respective null alleles were mated. Noon of copulation plug detection was considered E0.5. At E9.5 dams were euthanized and placentas were isolated individually from the conceptus sacs after careful removal of the decidua and remnants of the yolk sac and allantoic vessels.

extract_protocol: After genotyping pooled and extracted with Tri-Reagent according to manufacturer's protocol. Prior to labeling samples were treated with DNase I to remove any remainig genomic DNA.

treatment_protocol: Samples were stored in RNALater at 4°C for 1-3 weeks, until genotyping of enough samples was completed.

value: Placenta

tag: strain [background]

value: Ncoa6 Null


title: Ncoa6-null placenta, bio rep 2

description:
Ncoa6_Null_placenta_pool_2
Each pool of WT placentas is litter-matched to the similarly numbered Ncoa6-null pool

tag: tissue


title: Ncoa6+/+ placenta, bio rep 4

description:
Ncoa6_WT_placenta_pool_4
Each pool of WT placentas is litter-matched to the similarly numbered Ncoa6-null pool

source_name: pool of three Ncoa6+/+ placentas at E9.5

tag: Stage

value: Ncoa6 WT


title: Ncoa6-null placenta, bio rep 4

description:
Ncoa6_Null_placenta_pool_4
Each pool of WT placentas is litter-matched to the similarly numbered Ncoa6-null pool


title: MALT_lymphoma_4


title: MALT_lymphoma_31


title: MALT_lymphoma_30


title: Ncoa6+/+ placenta, bio rep 2

description:
Ncoa6_WT_placenta_pool_2
Each pool of WT placentas is litter-matched to the similarly numbered Ncoa6-null pool


title: Ncoa6+/+ placenta, bio rep 1

description:
Ncoa6_WT_placenta_pool_1
Each pool of WT placentas is litter-matched to the similarly numbered Ncoa6-null pool


title: MALT_lymphoma_28


title: MALT_lymphoma_29


title: MALT_lymphoma_26


title: Med1-null placenta, bio rep 1

description:
Med1_Null_placenta_pool_1
Each pool of WT placentas is litter-matched to the similarly numbered Med1-null pool

source_name: pool of three Med1-null placentas at E9.5

value: Med1 Null


title: MALT_lymphoma_25


title: Med1-null placenta, bio rep 3

description:
Med1_Null_placenta_pool_3
Each pool of WT placentas is litter-matched to the similarly numbered Med1-null pool


title: Rxra+/+ placenta, bio rep 4

description:
Rxra_WT_placenta_pool_4
Each pool of WT placentas is litter-matched to the similarly numbered Rxra-null pool

source_name: pool of three Rxra+/+ placentas at E9.5

value: B6;129 F2 outbred

value: Rxra WT


title: Rxra+/+ placenta, bio rep 2

description:
Rxra_WT_placenta_pool_2
Each pool of WT placentas is litter-matched to the similarly numbered Rxra-null pool


title: MALT_lymphoma_22

value: frozen biopsy


title: MALT_lymphoma_27

value: lymphoma


title: MALT_lymphoma_20


title: MALT_lymphoma_3


title: Med1+/+ placenta, bio rep 1

description:
Med1_WT_placenta_pool_1
Each pool of WT placentas is litter-matched to the similarly numbered Med1-null pool

source_name: pool of three Med1+/+ placentas at E9.5

value: Med1 WT


title: MALT_lymphoma_23


title: Rxra-null placenta, bio rep 4

description:
Rxra_Null_placenta_pool_4
Each pool of WT placentas is litter-matched to the similarly numbered Rxra-null pool

source_name: pool of three Rxra-null placentas at E9.5

value: Rxra Null


title: MALT_lymphoma_19


title: MALT_lymphoma_21


title: Med1-null placenta, bio rep 2

description:
Med1_Null_placenta_pool_2
Each pool of WT placentas is litter-matched to the similarly numbered Med1-null pool


title: Med1+/+ placenta, bio rep 3

description:
Med1_WT_placenta_pool_3
Each pool of WT placentas is litter-matched to the similarly numbered Med1-null pool


title: MALT_lymphoma_2


title: Med1+/+ placenta, bio rep 2

description:
Med1_WT_placenta_pool_2
Each pool of WT placentas is litter-matched to the similarly numbered Med1-null pool


title: Rxra+/+ placenta, bio rep 3

description:
Rxra_WT_placenta_pool_3
Each pool of WT placentas is litter-matched to the similarly numbered Rxra-null pool


title: Rxra-null placenta, bio rep 3

description:
Rxra_Null_placenta_pool_3
Each pool of WT placentas is litter-matched to the similarly numbered Rxra-null pool


title: MALT_lymphoma_24


title: Rxra-null placenta, bio rep 2

description:
Rxra_Null_placenta_pool_2
Each pool of WT placentas is litter-matched to the similarly numbered Rxra-null pool


title: MALT_lymphoma_17


title: Pparg-null placenta, bio rep 4

description:
Pparg_Null_placenta_pool_4
Each pool of WT placentas is litter-matched to the similarly numbered Pparg-null pool

source_name: pool of three Pparg-null placentas at E9.5

value: B6129 hybrid

value: Pparg Null


title: MALT_lymphoma_18


title: Pparg-null placenta, bio rep 3

description:
Pparg_Null_placenta_pool_3
Each pool of WT placentas is litter-matched to the similarly numbered Pparg-null pool


title: Pparg+/+ placenta, bio rep 4

description:
Pparg_WT_placenta_pool_4
Each pool of WT placentas is litter-matched to the similarly numbered Pparg-null pool

source_name: pool of three Pparg+/+ placentas at E9.5

value: Pparg WT


title: Pparg-null placenta, bio rep 1

description:
Pparg_Null_placenta_pool_1
Each pool of WT placentas is litter-matched to the similarly numbered Pparg-null pool


title: Pparg+/+ placenta, bio rep 3

description:
Pparg_WT_placenta_pool_3
Each pool of WT placentas is litter-matched to the similarly numbered Pparg-null pool


title: MALT_lymphoma_15

value: MALT lymphoma


title: MALT_lymphoma_16


title: WT TLR2L 4h-B

city: Charlestown

first: Jin Mo

last: Park

state: MA

address: 149 Thirteenth Street

department: Cutaneous Biology Research Center

institute: Massachusetts General Hospital

description: Gene expression data from WT DCs 4 h after TLR2 activation

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse Genome 430 2.0 Array. Arrays were washed and stained by streptavidin-phycoerythrin conjugate in the Affymetrix Fluidics Station 400.

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

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

source_name: LN DCs TLR2-stimulated, 4 h

label_protocol: GeneChip 3' IVT Express Labeling Kit was used to prepare biotinylated cRNA according to the standard Affymetrix protocol from 0.2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mouse primary dendritic cells were isolated from lymph nodes and cultured at 37C until treatment.

extract_protocol: Total RNA was extracted by using Trizol (Invitrogen) and then purified by using RNeasy MinElute Cleanup Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Pam3CSK4 (1 mg/ml) was added to DC culture. DCs were incubated at 37C for 0, 2, and 4 h after treatment.

value: wild type


title: WT TLR2L 2h-B

description: Gene expression data from WT DCs 2 h after TLR2 activation

source_name: LN DCs TLR2-stimulated, 2 h


title: MALT_lymphoma_10


title: KO TLR2L 4h-B

description: Gene expression data from p38a-KO DCs 4 h after TLR2 activation


title: WT TLR2L 4h-A


title: WT TLR2L 0h-B

description: Gene expression data from WT DCs without TLR2 activation

source_name: LN DCs unstimulated


title: Pparg+/+ placenta, bio rep 1

description:
Pparg_WT_placenta_pool_1
Each pool of WT placentas is litter-matched to the similarly numbered Pparg-null pool


title: WT TLR2L 0h-A


title: KO TLR2L 2h-B

description: Gene expression data from p38a-KO DCs 2 h after TLR2 activation


title: Blood IFNalpha Tx day 21 Animal ID FKN

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

description: Gene expression data from whole blood of SIV-infected sooty mangabey monkeys after injection of interferon alpha

hyb_protocol: Following fragmentation, 20 micrograms of cRNA were diluted into 300 microlitres of hybridization cocktail, with 200 microlitres hybridized for 16 hr at 45 C on GeneChip Rhesus Macaque Genome Array in Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data from .CEL files were uploaded to the RACE Bioconductor utility to perform RMA normalization. RACE normalized files were uploaded and analyzed using Partek Genomics Suite.

organism: Cercocebus atys

source_name: Blood IFNalpha Tx day 21

label_protocol: 0.5 micrograms of total RNA was labeled using a modified version of the Affymetrix IVT Express protocol, incorporating blocking PNA oligos specific for rhesus & mangabey hemoglobin into the initial reverse transcription step, as reported in Taaffe et al. 2009 J Med Primatol and Bosinger et al. J Clin Invest 2009.

extract_protocol: Whole blood was drawn into PAXgene tubes and stored at -80, samples were purified using standard Paxgene purification with QIAshredder columns and on-column DNAse digestion.

treatment_protocol: SIV+ Sooty mangabey monkeys were injected with 500,000 units subcutaneously with recombinant rhesus macaque IFNalpha2-IGFC fusion protein every week for 16 weeks.

value: peripheral whole blood

tag: infection status

value: SIV-positive

tag: treatment

value: IFNalpha

tag: time

value: day 21

tag: subject

value: Animal ID FKN


title: MALT_lymphoma_1

tag: cell type


title: Blood IFNalpha Tx day 84 Animal ID FKN

source_name: Blood IFNalpha Tx day 84

value: day 84


title: MALT_lymphoma_14


title: Blood IFNalpha Tx day 180 Animal ID FKN

source_name: Blood IFNalpha Tx day 180

value: day 180


title: KO TLR2L 4h-A

tag: genotype/variation


title: MALT_lymphoma_11


title: MALT_lymphoma_12


title: MALT_lymphoma_13


title: WT TLR2L 2h-A


title: Blood IFNalpha Tx day 7 Animal ID FKN

source_name: Blood IFNalpha Tx day 7

value: day 7


title: KO TLR2L 0h-B

description: Gene expression data from p38a-KO DCs without TLR2 activation


title: KO TLR2L 2h-A


title: Blood Baseline day -21 Animal ID FKN

description: Gene expression data from whole blood of SIV-infected sooty mangabey monkeys before injection of interferon alpha

source_name: Blood Baseline day -21

value: Baseline

value: day -21


title: KO TLR2L 0h-A


title: Blood IFNalpha Tx day 180 Animal ID FFQ

value: Animal ID FFQ


title: Blood IFNalpha Tx day 7 Animal ID FFQ


title: Blood IFNalpha Tx day 84 Animal ID FFQ


title: Blood IFNalpha Tx day 119 Animal ID FFQ

source_name: Blood IFNalpha Tx day 119

value: day 119


title: Blood IFNalpha Tx day 21 Animal ID FFQ


title: Blood IFNalpha Tx day 119 Animal ID FKN


title: Blood IFNalpha Tx day 180 Animal ID FQG

value: Animal ID FQG


title: Blood Baseline day -21 Animal ID FFQ


title: Sca1-MALT1_splenic lymphoma_3

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized to the Affymetrix Mouse_430_2 chip according to the protocols provided by the manufacturer.

source_name: frozen tissue, splenic lymphoma, Sca1-MALT1

growth_protocol: Frozen biopsies from spleen of WT or Sca1-MALT1 transgenic mice.

value: spleen

value: lymphoma


title: Sca1-MALT1_splenic lymphoma_5


title: Sca1-MALT1_splenic lymphoma_1


title: Blood IFNalpha Tx day 21 Animal ID FQG


title: WT_spleen_3

source_name: frozen tissue, spleen, WT

value: healthy control


title: Sca1-MALT1_splenic lymphoma_4


title: Blood IFNalpha Tx day 84 Animal ID FQG


title: Sca1-MALT1_splenic lymphoma_2


title: WT_spleen_4

value: wild type


title: WT_spleen_2


title: Sca1-MALT1_Sca1+Lin-_5

source_name: sorting purified, Sca1+Lin-, Sca1-MALT1

growth_protocol: Sorting purified Sca1+Lin- from bone marrow.

treatment_protocol: RNA lineal amplification using Megascript T7 in vitro transcription kit.

value: bone marrow


title: WT_spleen_1


title: MALT_lymphoma_5

source_name: Frozen biopsy, MALT lymphoma

value: frozen biopsy

value: MALT lymphoma


title: Blood IFNalpha Tx day 7 Animal ID FQG

value: peripheral whole blood

value: SIV-positive

value: IFNalpha


title: Blood IFNalpha Tx day 180 Animal ID FTR

value: day 180

value: Animal ID FTR


title: Blood IFNalpha Tx day 119 Animal ID FTR


title: Sca1-MALT1_Sca1+Lin-_4


title: Blood Baseline day -21 Animal ID FQG

value: Baseline


title: Blood IFNalpha Tx day 84 Animal ID FTR

value: day 84


title: Sca1-MALT1_Sca1+Lin-_3


title: WT_Sca1+Lin-_3

source_name: sorting purified, Sca1+Lin-, WT


title: Sca1-MALT1_Sca1+Lin-_2


title: WT_Sca1+Lin-_2


title: Blood IFNalpha Tx day 7 Animal ID FTR

value: day 7


title: Blood IFNalpha Tx day 21 Animal ID FTR

value: day 21


title: Sca1-MALT1_Sca1+Lin-_1


title: WT_Sca1+Lin-_1


title: Blood IFNalpha Tx day 180 Animal ID FBQ

value: Animal ID FBQ


title: Blood IFNalpha Tx day 84 Animal ID FBQ


title: Blood IFNalpha Tx day 7 Animal ID FBQ


title: Blood IFNalpha Tx day 119 Animal ID FBQ

value: day 119


title: Blood Baseline day -21 Animal ID FBQ

value: day -21


title: Blood IFNalpha Tx day 21 Animal ID FBQ


title: Blood Baseline day -21 Animal ID FTR


title: WT Tx vs. Mock 24hr 3

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

institute: University of Washington

hyb_protocol: Microarray slide hybridization was performed with Agilent human microarrays according to the manufacturer’s instructions. Each microarray experiment was done with four technical replicates by reverse dye hybridization for experimental and reference samples.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B).

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 8.1.1.1) and the GE2-v5_95_Feb07 extraction protocol.

source_name: A549 mock treated, 24hr

label_protocol: Cy3- and Cy5-labeled cRNA probes were generated by using an Agilent Low RNA Input Linear Amplification kit.

growth_protocol:
A549 cells were infected with human H1N1 influenza A/Texas/91 virus (Tx/91) or recombinant influenza Tx/91 NS1:1-126 virus. A549 cells were harvested at 12 and 24 hr post-infection. HTBE cells were harvested at 9.5 and 24 hrs post infection for microarray.
HTBE cells were homogenized in TRIzol reagent, and A549 cells were lysed in solution D (4 M guanidinium thiocyanate, 25 mM sodium citrate, 0.5 % sarcosyl, 0.1 M β-mercaptoethanol) and kept at -80 degrees C prior to RNA isolation.

extract_protocol: Lysates were were phase-separated, and RNA was isolated from the aqueous phase using Qiagen RNeasy columns and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.

tag: cell line

tag: infection

value: mock

source_name: A549 Tx/91 treated, 24hr

value: influenza Tx/91


title: NS1(1-126) vs. Mock 24hr 4

source_name: A549 Tx/91 NS1 : 1–126 treated, 24hr

value: influenza Tx/91 NS1

tag: dose

value: Tx/91 NS1 : 1–126 viruses per filter


title: WT Tx vs. Mock 12hr 3

source_name: A549 mock treated, 12hr

source_name: A549 Tx/91 treated, 12hr


title: NS1(1-126) vs. Mock 24hr 3


title: WT Tx vs. Mock 12hr 4


title: NS1(1-126) vs. Mock 12hr 4

source_name: A549 Tx/91 NS1 : 1–126 treated, 12hr


title: WT Tx vs. Mock 12hr 1


title: NS1(1-126) vs. Mock 12hr 2


title: WT Tx vs. Mock 24hr 4


title: Blood IFNalpha Tx day 84 Animal ID FAV

value: Animal ID FAV


title: Blood IFNalpha Tx day 21 Animal ID FAV

source_name: Blood IFNalpha Tx day 21

value: peripheral whole blood


title: Blood IFNalpha Tx day 180 Animal ID FFV

value: SIV-positive

value: Animal ID FFV


title: Blood IFNalpha Tx day 180 Animal ID FAV

value: IFNalpha

value: day 180


title: NS1(1-126) vs. Mock 12hr 1


title: NS1(1-126) vs. Mock 12hr 3


title: Blood IFNalpha Tx day 84 Animal ID FFV

source_name: Blood IFNalpha Tx day 84


title: WT Tx vs. Mock 12hr 2


title: Blood Baseline day -21 Animal ID FAV

value: Baseline


title: Blood IFNalpha Tx day 21 Animal ID FFV


title: Blood IFNalpha Tx day 119 Animal ID FAV


title: Blood IFNalpha Tx day 7 Animal ID FAV


title: NS1(1-126) vs. Mock 24hr 1


title: Mock 24h A549 pooled

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for all processing steps, including Cy3-cDNA probe preparation, hybridization and array washing.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505C).

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol.

source_name: A549 Cells

growth_protocol: A549 cells were treated with IFN-alpha, IFN-beta, IFN-gamma, or mock treated. Samples were harvested for microarray analysis at 12 and 24hr post-treatment.

extract_protocol: All TRIzol lysates were processed simultaneously: they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2 fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.

treatment_protocol: Cells were prepared as TRIzol homogenates for subsequent RNA extraction.

value: mock-no treatment


title: Blood Baseline day -21 Animal ID FFV


title: WT Tx  vs. Mock 24hr 1


title: NS1(1-126) vs. Mock 24hr 2


title: Blood IFNalpha Tx day 7 Animal ID FFV

source_name: Blood IFNalpha Tx day 7

value: day 7


title: Blood IFNalpha Tx day 180 Animal ID FYM

source_name: Blood IFNalpha Tx day 180

value: Animal ID FYM


title: Blood IFNalpha Tx day 119 Animal ID FFV

source_name: Blood IFNalpha Tx day 119


title: WT Tx vs. Mock 24hr 2


title: Blood IFNalpha Tx day 119 Animal ID FYM


title: IFN-γ 12h A549 pooled

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for all processing steps, including Cy3-cDNA probe preparation, hybridization and array washing.

value: IFN-gamma


title: plasma Control Individual19-Rep1

city: Toronto

first: Rene

last: Cortese

state: Ontario

address: 250 College St.

department: The Krembil Family Epigenetics Laboratory

country: Canada

institute: CAMH

description: Control group - Patient 19 Rep.1

hyb_protocol: Labelled samples were co-hybridized to the HCGI12k microarrays (UHN, Toronto, ON) containing 12,192 CpG rich clones, as previously described (Schumacher, A., et al. (2006). Microarray-based DNA methylation profiling: technology and applications. Nucleic acids research 34, 528-542.). For all patients and controls, two technical replicates were tested.

scan_protocol: Hybridized microarrays were scanned using the Axon 4000B scanner and signals were processed using the GenePix Pro software (v6.1.0.4).

data_processing: Microarray data was pre-processed using a modified version of the Variance Stabilizing Normalization (VSN) method, using the vsn package (v3.20.0) (Huber, W.,et al. (2002). Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics (Oxford, England) 18 Suppl 1, S96-104). Pre-processed data was then analyzed with spot-wise linear-model fitting followed by an empirical Bayes moderation of the standard error (Smyth, G.K. (2004). Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Statistical applications in genetics and molecular biology 3, Article3). A false-discovery rate (FDR) adjustment for multiple-testing was used and q-values (FDR-adjusted p-values) were assigned (Storey, J.D., and Tibshirani, R. (2003). Statistical significance for genomewide studies. Proceedings of the National Academy of Sciences of the United States of America 100, 9440-9445).

source_name: plasma cirDNA from Control individual.

label_protocol: 1.5 μg of purified enriched modified cirDNA was labelled using Cy3 (GE Healthcare, Baie d’Urfe, QC) and blood DNA reference pool was labelled using Cy5 (GE Healthcare, Baie d’Urfe, QC), according to the protocol detailed in Schumacher et al, 2006 (Schumacher, A., et al. (2006). Microarray-based DNA methylation profiling: technology and applications. Nucleic acids research 34, 528-542.)

extract_protocol: cirDNA was isolated from 1 mL of plasma using glass columns (sample set 1; Vivantis, Selangor, Malaysia) and QIAamp DNA Blood Mini Kit (sample set 2; Qiagen, Hilden, Germany), according to manufacturers’ instructions. DNA samples extracted from white blood cells (WBC) of 20 individuals unrelated to this project were pooled and used as reference. Isolated DNA was pooled and sheared by sonication to 200-500 bp fragments. 50 ng of cirDNA and sonicated DNA from pooled WBC genomic DNA (reference sample) were blunted using T4 DNA polymerase (NEB, Pickering, ON) and universal adaptors were ligated by overnight incubation at 4°C with T4 ligase (NEB, Pickering, ON). Blunt universal adaptors were prepared by annealing two oligonucleotides (oligo 1: GCGGTGACCCGGGAGATCTGAATTC and oligo 2: GAATTCAGATC). Next, adaptor-ligated DNA was digested using a cocktail of DNA modification-sensitive restriction enzymes (HpaII, HinP1I and HpyCH4IV) (NEB, Pickering, ON), which do not cut when the corresponding restriction sites contain modified nucleotides, 5-mC or 5-hmC. Therefore, the subsequent PCR, with primers complementary to the adaptors, amplifies only the fragments bearing such modifications. The digestion product was amplified in 25 µL final volume under the following conditions: 1x PCR buffer (Sigma-Aldrich, Oakville, ON) 2.875 mM MgCl2 (Sigma-Aldrich, Oakville, ON), 275 µM aminoallyl dNTP mix (Ambion, Austin, TX), 1.6 µM oligo 1 and 25 units Taq DNA polymerase (NEB, Pickering, ON). The PCR program started with an initial extension at 72°C for 5 min followed by 24 cycles of denaturation at 95°C for 1 minute, annealing at 94°C for 40 seconds and elongation at 72°C for 2.5 minutes, with a final extension step at 72°C for 5 minutes. Amplification was checked by electrophoresis in agarose gels. PCR products were purified using the MinElute kit (Qiagen, Mississauga, ON) and quantified using a Nanodrop 2000.

tag: disease state

value: Control (no prostatic disease)

tag: sample type

value: plasma circulating DNA

source_name: Blood reference pool

value: white blood cell

value: white blood cell genomic DNA

value: pool of 20 individuals

value: control


title: Mock 12h A549 pooled


title: plasma Control Individual18-Rep2

description: Control group - Patient 18 Rep.2


title: IFN-β 24h A549 pooled

value: IFN-beta


title: plasma Control Individual20-Rep2

description: Control group - Patient 20 Rep.2


title: plasma Control Individual19-Rep2

description: Control group - Patient 19 Rep.2


title: IFN-α 12h A549 pooled

value: IFN-alpha


title: IFN-γ 24h A549 pooled


title: IFN-α 24h A549 pooled


title: plasma Control Individual17-Rep2

description: Control group - Patient 17 Rep.2


title: Blood IFNalpha Tx day 7 Animal ID FYM

value: peripheral whole blood

value: SIV-positive


title: plasma Control Individual20-Rep1

description: Control group - Patient 20 Rep.1


title: Inedi_date_t_2

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

country: France

institute: INRA

description: Drought is the main cause or crop loss around the globe and it is expected to be more so in years to come. Helianthus genus comprises species that are able to grow in harsh environments suffering from severe water shortage. Cultivated H.annuus, i.e. sunflower, is a highly valuable oil crop due to, among other features, its ability to grow under low input conditions. The aim of our project is to unravel the transcriptional regulation underpinning drought tolerance in sunflower, with the ultimate goal of improving crop yield.

hyb_protocol: labelled extract quantity: 5.5ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

organism: Helianthus annuus

source_name: Inedi: water deprivation for fixed harvest, ftsw: time 6day

label_protocol: labelling Biotin indirect, amplification=yes, ssDNA 5.5 ug.

growth_protocol: caulin leaf - Plants were grown in the glasshouse between 29th May 2009 and 5th July 2009. Tissue collection was carried out between 29th May 2009 and 5th July 2009.

treatment_protocol: Name:water deprivation for fixed harvest - environmental treatment - abiotic stress,ftsw:time 6day . The factor value for each sample is in the note of the sample

tag: cultivar

value: Inedi

tag: age

value: 33 days


title: SF326_date_c_2

source_name: SF326: no treatment

treatment_protocol: no treatment


title: Blood IFNalpha Tx day 84 Animal ID FYM

value: IFNalpha

value: day 84


title: plasma Control Individual16-Rep1

description: Control group - Patient 16 Rep.1


title: SF326_date_t_2

source_name: SF326: water deprivation for fixed harvest, ftsw: time 6day


title: plasma Control Individual16-Rep2

description: Control group - Patient 16 Rep.2


title: plasma Control Individual15-Rep2

description: Control group - Patient 15 Rep.2


title: plasma Control Individual17-Rep1

description: Control group - Patient 17 Rep.1


title: SF107_date_c_2

source_name: SF107: no treatment


title: SF109_FTSW_c_5

source_name: SF109: no treatment

value: 35 days


title: SF028_FTSW_t_5

source_name: SF028: water deprivation for fixed water stress, ftsw: quantity -0.015

treatment_protocol: Name:water deprivation for fixed water stress - environmental treatment - abiotic stress,ftsw:quantity -0.015 . The time elapsed treatment for each sample is in the note of the sample

value: 37 days


title: SF028_FTSW_t_4


title: plasma Control Individual14-Rep2

description: Control group - Patient 14 Rep.2


title: plasma Control Individual13-Rep2

description: Control group - Patient 13 Rep.2


title: plasma Control Individual14-Rep1

description: Control group - Patient 14 Rep.1


title: plasma Control Individual15-Rep1

description: Control group - Patient 15 Rep.1


title: plasma Control Individual12-Rep2

description: Control group - Patient 12 Rep.2


title: Melody_FTSW_t_5

source_name: Melody: water deprivation for fixed water stress, ftsw: quantity -0.015

value: Melody

value: 34 days


title: plasma Control Individual13-Rep1

description: Control group - Patient 13 Rep.1

value: Control (no prostatic disease)

value: plasma circulating DNA


title: SF107_FTSW_t_5

source_name: SF107: water deprivation for fixed water stress, ftsw: quantity -0.015

value: 36 days


title: plasma Control Individual12-Rep1

description: Control group - Patient 12 Rep.1

value: white blood cell

value: white blood cell genomic DNA

value: pool of 20 individuals


title: SF326_FTSW_c_5


title: plasma Control Individual11-Rep1

description: Control group - Patient 11 Rep.1

value: control


title: SF193_FTSW_c_5

source_name: SF193: no treatment

value: 39 days


title: SF107_FTSW_c_4


title: Inedi_date_c_1

source_name: Inedi: no treatment


title: Inedi_date_c_2


title: plasma Control Individual10-Rep2

description: Control group - Patient 10 Rep.2


title: Tekny_date_c_2

source_name: Tekny: no treatment

value: Tekny


title: plasma Control Individual11-Rep2

description: Control group - Patient 11 Rep.2


title: plasma Control Individual10-Rep1

description: Control group - Patient 10 Rep.1


title: plasma Control Individual8-Rep2

description: Control group - Patient 8 Rep.2


title: SF193_FTSW_t_5

source_name: SF193: water deprivation for fixed water stress, ftsw: quantity -0.015


title: SF109_date_t_1

source_name: SF109: water deprivation for fixed harvest, ftsw: time 6day


title: plasma Control Individual9-Rep1

description: Control group - Patient 9 Rep.1


title: plasma Control Individual9-Rep2

description: Control group - Patient 9 Rep.2


title: SF109_FTSW_c_6


title: SF028_date_t_1

source_name: SF028: water deprivation for fixed harvest, ftsw: time 6day


title: plasma Control Individual8-Rep1

description: Control group - Patient 8 Rep.1


title: SF028_FTSW_c_6

source_name: SF028: no treatment


title: plasma Control Individual7-Rep2

description: Control group - Patient 7 Rep.2

source_name: plasma cirDNA from Control individual.


title: plasma Control Individual6-Rep2

description: Control group - Patient 6 Rep.2

source_name: Blood reference pool


title: plasma Control Individual7-Rep1

description: Control group - Patient 7 Rep.1


title: SF107_date_c_1


title: Tekny_FTSW_c_6


title: plasma Control Individual4-Rep2

description: Control group - Patient 4 Rep.2


title: plasma Control Individual4-Rep1

description: Control group - Patient 4 Rep.1


title: plasma Control Individual18-Rep1

description: Control group - Patient 18 Rep.1


title: plasma Control Individual5-Rep2

description: Control group - Patient 5 Rep.2


title: SF028_date_c_1


title: Melody_FTSW_t_6


title: plasma Control Individual6-Rep1

description: Control group - Patient 6 Rep.1


title: plasma Control Individual3-Rep1

description: Control group - Patient 3 Rep.1


title: Tekny_date_t_1

source_name: Tekny: water deprivation for fixed harvest, ftsw: time 6day


title: SF326_FTSW_c_6

source_name: SF326: no treatment


title: plasma Control Individual2-Rep2

description: Control group - Patient 2 Rep.2


title: plasma Control Individual3-Rep2

description: Control group - Patient 3 Rep.2


title: plasma Control Individual5-Rep1

description: Control group - Patient 5 Rep.1


title: Melody_FTSW_c_6

source_name: Melody: no treatment


title: SF109_date_t_2


title: SF326_date_t_1

source_name: SF326: water deprivation for fixed harvest, ftsw: time 6day


title: plasma Control Individual2-Rep1

description: Control group - Patient 2 Rep.1


title: IFN-β 12h A549 pooled

source_name: A549 Cells

value: IFN-beta


title: Inedi_FTSW_c_6

value: Inedi

value: 33 days


title: SF109_FTSW_t_6

source_name: SF109: water deprivation for fixed water stress, ftsw: quantity -0.015


title: Blood IFNalpha Tx day 21 Animal ID FYM

source_name: Blood IFNalpha Tx day 21

value: peripheral whole blood

value: SIV-positive

value: IFNalpha

value: day 21

value: Animal ID FYM


title: plasma Control Individual1-Rep1

description: Control group - Patient 1 Rep.1

value: Control (no prostatic disease)


title: plasma Control Individual1-Rep2

description: Control group - Patient 1 Rep.2

value: plasma circulating DNA


title: plasma Prostate Cancer Patient17-Rep2

description: Prostate Cancer group - Patient 17 Rep.2

source_name: plasma cirDNA from Prostate Cancer patient.

value: Prostate Cancer


title: Melody_date_t_1

source_name: Melody: water deprivation for fixed harvest, ftsw: time 6day

value: Melody


title: SF193_FTSW_t_6

value: 35 days


title: plasma Prostate Cancer Patient18-Rep2

description: Prostate Cancer group - Patient 18 Rep.2

value: white blood cell

value: white blood cell genomic DNA

value: pool of 20 individuals


title: plasma Prostate Cancer Patient19-Rep1

description: Prostate Cancer group - Patient 19 Rep.1

value: control


title: plasma Prostate Cancer Patient16-Rep2

description: Prostate Cancer group - Patient 16 Rep.2


title: plasma Prostate Cancer Patient18-Rep1

description: Prostate Cancer group - Patient 18 Rep.1


title: SF107_FTSW_t_6

source_name: SF107: water deprivation for fixed water stress, ftsw: quantity -0.015

value: 36 days


title: plasma Prostate Cancer Patient15-Rep2

description: Prostate Cancer group - Patient 15 Rep.2


title: Melody_date_c_3


title: plasma Prostate Cancer Patient16-Rep1

description: Prostate Cancer group - Patient 16 Rep.1


title: plasma Prostate Cancer Patient17-Rep1

description: Prostate Cancer group - Patient 17 Rep.1


title: plasma Prostate Cancer Patient15-Rep1

description: Prostate Cancer group - Patient 15 Rep.1


title: SF193_date_c_1

source_name: SF193: no treatment


title: Melody_date_c_2


title: SF326_date_c_3


title: Melody_date_c_1


title: SF107_date_t_3

source_name: SF107: water deprivation for fixed harvest, ftsw: time 6day


title: Inedi_date_t_1

source_name: Inedi: water deprivation for fixed harvest, ftsw: time 6day

value: Inedi


title: plasma Prostate Cancer Patient19-Rep2

description: Prostate Cancer group - Patient 19 Rep.2


title: SF109_date_c_2

source_name: SF109: no treatment

value: 33 days


title: SF326_FTSW_t_6

source_name: SF326: water deprivation for fixed water stress, ftsw: quantity -0.015


title: Inedi_date_t_3


title: SF326_date_t_3


title: plasma Prostate Cancer Patient14-Rep1

description: Prostate Cancer group - Patient 14 Rep.1


title: plasma Prostate Cancer Patient14-Rep2

description: Prostate Cancer group - Patient 14 Rep.2


title: plasma Prostate Cancer Patient13-Rep2

description: Prostate Cancer group - Patient 13 Rep.2


title: plasma Prostate Cancer Patient12-Rep2

description: Prostate Cancer group - Patient 12 Rep.2


title: Tekny_date_c_3

source_name: Tekny: no treatment

value: Tekny


title: SF109_date_c_1


title: Inedi_date_c_3

source_name: Inedi: no treatment


title: plasma Prostate Cancer Patient13-Rep1

description: Prostate Cancer group - Patient 13 Rep.1

source_name: Blood reference pool


title: plasma Prostate Cancer Patient11-Rep2

description: Prostate Cancer group - Patient 11 Rep.2


title: Inedi_FTSW_t_6

description: Drought is the main cause or crop loss around the globe and it is expected to be more so in years to come. Helianthus genus comprises species that are able to grow in harsh environments suffering from severe water shortage. Cultivated H.annuus, i.e. sunflower, is a highly valuable oil crop due to, among other features, its ability to grow under low input conditions. The aim of our project is to unravel the transcriptional regulation underpinning drought tolerance in sunflower, with the ultimate goal of improving crop yield.

source_name: Inedi: water deprivation for fixed water stress, ftsw: quantity -0.015


title: SF193_date_c_3


title: plasma Prostate Cancer Patient11-Rep1

description: Prostate Cancer group - Patient 11 Rep.1


title: plasma Prostate Cancer Patient10-Rep2

description: Prostate Cancer group - Patient 10 Rep.2


title: Tekny_FTSW_t_6

source_name: Tekny: water deprivation for fixed water stress, ftsw: quantity -0.015

value: 34 days


title: SF193_FTSW_c_6


title: plasma Prostate Cancer Patient8-Rep1

description: Prostate Cancer group - Patient 8 Rep.1


title: plasma Prostate Cancer Patient8-Rep2

description: Prostate Cancer group - Patient 8 Rep.2


title: Tekny_FTSW_c_4


title: SF193_date_c_2


title: plasma Prostate Cancer Patient9-Rep2

description: Prostate Cancer group - Patient 9 Rep.2


title: SF193_date_t_3

source_name: SF193: water deprivation for fixed harvest, ftsw: time 6day


title: plasma Prostate Cancer Patient10-Rep1

description: Prostate Cancer group - Patient 10 Rep.1


title: plasma Prostate Cancer Patient9-Rep1

description: Prostate Cancer group - Patient 9 Rep.1


title: Blood Baseline day -21 Animal ID FYM

description: Gene expression data from whole blood of SIV-infected sooty mangabey monkeys before injection of interferon alpha

source_name: Blood Baseline day -21

value: peripheral whole blood

value: SIV-positive

value: Baseline

value: day -21


title: plasma Prostate Cancer Patient12-Rep1

description: Prostate Cancer group - Patient 12 Rep.1

value: plasma circulating DNA


title: Melody_FTSW_c_5

source_name: Melody: no treatment


title: MRS vs CDM

city: Ede

first: Michiel

last: Wels

address: Kernhemseweg 2

country: Netherlands

institute: NIZO food research

hyb_protocol: Hybridization buffer (Agilent In Situ Hybridization Kit Plus) was added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers at 65 degrees Celcius for 17 h. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.7.5)

data_processing: scanned slides were Lowess normalised using Prep (van Hijum, Applied Bioinformatics 2003 2(4):241-244). Interslide scaling was performed using Postprep (van Hijum, Applied Bioinformatics 2003 2(4):241-244).

organism: Lactiplantibacillus plantarum

source_name: grown in MRS

label_protocol: Total RNA and enriched mRNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 3 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

growth_protocol: Cultures were grown in CDM and MRS at 37˚C without agitation.

extract_protocol: Cultures were lysed by beat-beating and total RNA was isolated by subsequent phenol-chloroform extraction, followed by RNA purification and mRNA enrichment

treatment_protocol: Harvested cultures were immediately pelleted at 4570xg and 4˚C

tag: strain

tag: rna subtype

value: total RNA

source_name: grown in CDM


title: SF028_FTSW_c_5

source_name: SF028: no treatment

value: 37 days


title: Inedi_FTSW_c_5


title: Tekny_date_c_1


title: plasma Prostate Cancer Patient6-Rep1

description: Prostate Cancer group - Patient 6 Rep.1

source_name: plasma cirDNA from Prostate Cancer patient.

value: Prostate Cancer


title: plasma Prostate Cancer Patient7-Rep2

description: Prostate Cancer group - Patient 7 Rep.2

value: white blood cell


title: MRSenriched vs MRS

value: enriched mRNA


title: CDM vs CDMenriched


title: Tekny_date_t_2

source_name: Tekny: water deprivation for fixed harvest, ftsw: time 6day


title: plasma Prostate Cancer Patient6-Rep2

description: Prostate Cancer group - Patient 6 Rep.2

value: white blood cell genomic DNA

value: pool of 20 individuals


title: Inedi_FTSW_t_5


title: plasma Prostate Cancer Patient7-Rep1

description: Prostate Cancer group - Patient 7 Rep.1

value: control


title: plasma Prostate Cancer Patient5-Rep1

description: Prostate Cancer group - Patient 5 Rep.1


title: Tekny_FTSW_t_5


title: SF107_FTSW_c_6

source_name: SF107: no treatment

value: 36 days


title: plasma Prostate Cancer Patient4-Rep2

description: Prostate Cancer group - Patient 4 Rep.2


title: plasma Prostate Cancer Patient5-Rep2

description: Prostate Cancer group - Patient 5 Rep.2


title: hiPS-HUVhiPS4F3 cells BMP4-treated, biological replicate 2

city: La Jolla

first: Sergio

last: Ruiz

state: CA

address: 10010 North Torrey Pine Rd

department: Gene Expression Laboratory

institute: Salk Institute for Biological Studies

description:
HUVhiPS4F3_BMP4-Day5_2
Gene expression data from BMP4-differentiated hiPSCs-hiPS-HUVhiPS4F3

hyb_protocol: 5.5ug single strand sense cDNA was fragmented and labelled with Affy terminal labeling kit, then were hybridized for 16 hr at 45C on GeneChip Human Gene 1.0 ST array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affmetrix GenChip scanner 3000 7G.

data_processing: The data were analyzed with R-Bioconductor using affy package. Background correction were using RMA method and furthernormalized using quantile as normalization method.

source_name: BMP4-differentiated hiPSCs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA

growth_protocol: Pluripotent cell lines were grown in matrigel with mTeSR media (feeder-free conditions)

extract_protocol: Total RNA was extracted from cells using Trizol using recomended protocol. RNA was purified using Rneasy MinElute Cleanup (Quiagen).

treatment_protocol: Cells were treated daily with mTeSR+ 100ng/ml of Activin or modified mTeSR + 50 ng/ml BMP4 as described in Xu et al, 2002

tag: treated with

value: 50 ng/ml BMP4 daily during 5 days


title: hiPS-HUVhiPS4F3 cells BMP4-treated, biological replicate 1

description:
HUVhiPS4F3_BMP4-Day5_1
Gene expression data from BMP4-differentiated hiPSCs-hiPS-HUVhiPS4F3


title: CDMenriched vs MRSenriched


title: Inedi_FTSW_c_4

value: Inedi

value: 33 days


title: WT.2.816

city: Kansas City

first: Ariel

last: Paulson

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

description: WT IP/Input, Array 1/2, Biological Replicate 2.

hyb_protocol: A mixture of Cy5-labeled IP DNA and Cy3-labeled input DNA (4.5 µg each for replicates 1, and 9 µg each for replicates 2) was hybridized at 65ºC for 40 hours to Drosophila Whole Genome ChIP-on-Chip Set 244K arrays using Agilent Technologies CGH protocol and reagents (Oligo aCGH Hybridization Kit; Cat. No.: 5188-5220 and Oligo aCGH Wash Buffer Kit; Cat. No.: 5188-5226).

scan_protocol: Slides were scanned with an Agilent High-Resolution DNA Microarray Scanner (G2505C), and image analysis was performed with Agilent Technologies Feature Extraction software (version 10.5.1.1).

data_processing: Arrays were median-normalized in R using the limma package.

organism: Drosophila melanogaster

source_name: WT whole embryos, ChIP

label_protocol: Immunoprecipitated (IP) samples and input samples (200 ng) were amplified by ligation-mediated PCR (LM-PCR ), and 2 µg each were differentially labeled by random-primed, Klenow-based extension as described in PMID 17406303.

growth_protocol: dKDM4A mutant with P element insertion (y1 w67c23; P{y+mDint2 wBR.E.BR=SUPor-P}Kdm4AKG04636) was obtained from Bloomington Stock Center at Indiana University (stock #13828). P element KG04636 was mobilized by crossing the mutant to y1w*; CyO, H{w[+mc]=PΔ2-3}Hop2.1/Bc1EgfrE1 flies. Males of KG04646 over the transposase gene PΔ2-3 were crossed to a CyO balanced stock. P element excision was screened by eye color and confirmed by PCR.  To generate the dKDM4A genomic rescue, a fragment containing the dKDM4A locus (incl. 1.6 KB upstream / 220 bp downstream) was amplified from genomic DNA of Oregon R flies. Double FLAG tags were added at dKDM4A C-terminus. V423A mutation was generated using Quick Change II XL Site-Directed Mutagenesis Kit (Stratagene); fragment was cloned into pCa4B vector [PMID:18311141]. Site-specific integration at attP40 landing site (2L 25C7) was carried out by Genetic Services. To rescue the mutant, the transgene (FLAG-dKDM4A or dKDM4A-V423A) on the second chromosome was recombined to the chromosome carrying KG04636 insertion.

extract_protocol: Genomic DNA was purified by phenol-chloroform extraction and ethanol precipitation.

treatment_protocol: ChIP was performed from staged 2-4 hours embryos collected in population cages as described in PMID 17406543 and PMID 17322397 with minor modifications. Briefly, embryos were cross-linked in 1.8% formaldehyde and homogenized in Buffer A1 (15 mM Hepes pH 7.5, 15 mM NaCl, 60 mM, KCl, 4 mM MgCl, 0.5% Triton X-100, 0.5 mM DTT and protease inhibitors). Nuclei were resuspended in A2 buffer (15 mM Hepes pH 7.5, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% sodium deoxycholate, 1% SDS, 0.5% N-lauroylsarcosine and protease inhibitors) and sonicated to obtain chromatin fragments with an average size of ~500 bp. For input controls, 50 μl of chromatin was used. About 700µg to 1mg of chromatin was incubated with 1.5µg anti-H3K36me3 antibody (abcam, ab9050) overnight at 4ºC. 30 µl of sheep anti-rabbit IgG Dynabeads was added to each chromatin/antibody solution and incubated for 2 hr, 4ºC, then beads were washed 5 times with RIPA Buffer (50 mM Hepes pH 7.5, 0.5 M LiCl, 1 mM EDTA, 1% NP-40, 0.7% sodium deoxycholate) and once with 50mM NaCl in TE. Bound complexes were eluted twice with 200 μl of elution buffer (50mM Tris pH 8.0, 10 mM EDTA, 1% SDS) at 65ºC for 30min. The eluate were treated with RNase A (0.2 μg/μl) for 1 hour at 37ºC followed by Proteinase K treatment (0.2 μg/μl) for 1 hour at 55ºC. Crosslinks were reversed by incubating samples at 65ºC overnight.

value: Bloomington Drosophila Stock Center No. 13828

value: wild type

tag: tissue

value: whole body

tag: developmental stage

value: 2-4 hour embryos

tag: chip antibody

tag: antibody vendor

value: abcam

tag: antibody catalog #

source_name: WT whole embryos, input


title: MU.2.816

description: KDM4A Mutant IP/Input, Array 1/2, Biological Replicate 2.

source_name: dKDM4A mutant whole embryos, ChIP

value: dKDM4A mutant

source_name: dKDM4A mutant whole embryos, input


title: plasma Prostate Cancer Patient3-Rep2

description: Prostate Cancer group - Patient 3 Rep.2

value: plasma circulating DNA

tag: subject

source_name: Blood reference pool

tag: cell type


title: SF326_FTSW_t_4

source_name: SF326: water deprivation for fixed water stress, ftsw: quantity -0.015


title: hiPS-HUVhiPS4F3 cells untreated, biological replicate 1

description:
HUVhiPS4F3_Day0_1
Gene expression data from Undifferentiated hiPSCs-hiPS-HUVhiPS4F3

source_name: Undifferentiated hiPSCs

tag: cell line


title: hiPS-HUVhiPS4F1 cells BMP4-treated, biological replicate 1

description:
HUVhiPS4F1_BMP4_Day5_1
Gene expression data from BMP4-differentiated hiPSCs-hiPS-HUVhiPS4F1


title: hiPS-HUVhiPS4F3 cells activin-treated, biological replicate 2

description:
HUVhiPS4F3_Activin-Day5_2
Gene expression data from Activin-differentiated hiPSCs-hiPS-HUVhiPS4F3

source_name: Activin-differentiated hiPSCs

value: 100 ng/ml of activin daily during 5 days


title: plasma Prostate Cancer Patient4-Rep1

description: Prostate Cancer group - Patient 4 Rep.1

value: Prostate Cancer

value: white blood cell


title: SF028_date_c_2


title: MU.1.816

description: KDM4A Mutant IP/Input, Array 1/2, Biological Replicate 1.

tag: genotype/variation


title: hiPS-HUVhiPS4F3 cells activin-treated, biological replicate 1

description:
HUVhiPS4F3_Activin-Day5_1
Gene expression data from Activin-differentiated hiPSCs-hiPS-HUVhiPS4F3


title: plasma Prostate Cancer Patient2-Rep2

description: Prostate Cancer group - Patient 2 Rep.2

value: white blood cell genomic DNA


title: SF326_FTSW_c_4

source_name: SF326: no treatment


title: SF326_FTSW_t_5

value: 35 days


title: Tekny_FTSW_t_4

source_name: Tekny: water deprivation for fixed water stress, ftsw: quantity -0.015

value: Tekny

value: 34 days


title: hiPS-HUVhiPS4F1 cells BMP4-treated, biological replicate 2

description:
HUVhiPS4F1_BMP4_Day5_2
Gene expression data from BMP4-differentiated hiPSCs-hiPS-HUVhiPS4F1

value: 50 ng/ml BMP4 daily during 5 days


title: WT.1.816

description: WT IP/Input, Array 1/2, Biological Replicate 1.


title: plasma Prostate Cancer Patient3-Rep1

description: Prostate Cancer group - Patient 3 Rep.1

value: pool of 20 individuals

value: control


title: SF193_FTSW_c_4

description: Drought is the main cause or crop loss around the globe and it is expected to be more so in years to come. Helianthus genus comprises species that are able to grow in harsh environments suffering from severe water shortage. Cultivated H.annuus, i.e. sunflower, is a highly valuable oil crop due to, among other features, its ability to grow under low input conditions. The aim of our project is to unravel the transcriptional regulation underpinning drought tolerance in sunflower, with the ultimate goal of improving crop yield.

source_name: SF193: no treatment


title: plasma Prostate Cancer Patient1-Rep2

description: Prostate Cancer group - Patient 1 Rep.2


title: plasma Prostate Cancer Patient2-Rep1

description: Prostate Cancer group - Patient 2 Rep.1


title: Melody_FTSW_t_4

source_name: Melody: water deprivation for fixed water stress, ftsw: quantity -0.015

value: Melody

value: 36 days


title: hiPS-HUVhiPS4F1 cells activin-treated, biological replicate 2

description:
HUVhiPS4F1_Activin_Day5_2
Gene expression data from Activin-differentiated hiPSCs-hiPS-HUVhiPS4F1


title: hES-H9 cells BMP4-treated, biological replicate 1

description:
H9_BMP4-Day5_1
Gene expression data from BMP4-differentiated hESCs-H9

source_name: BMP4-differentiated hESCs


title: hiPS-HUVhiPS4F1 cells activin-treated, biological replicate 1

description:
HUVhiPS4F1_Activin_Day5_1
Gene expression data from Activin-differentiated hiPSCs-hiPS-HUVhiPS4F1


title: plasma Prostate Cancer Patient1-Rep1

description: Prostate Cancer group - Patient 1 Rep.1

source_name: plasma cirDNA from Prostate Cancer patient.


title: Tekny_FTSW_c_5

source_name: Tekny: no treatment


title: hiPS-HUVhiPS4F1 cells untreated, biological replicate 2

description:
HUVhiPS4F1_Day0_2
Gene expression data from Undifferentiated hiPSCs-hiPS-HUVhiPS4F1


title: hES-H9 cells BMP4-treated, biological replicate 2

description:
H9_BMP4-Day5_2
Gene expression data from BMP4-differentiated hESCs-H9


title: plasma Benign Prostatic Hyperplasia Patient20-Rep2

description: BPH group - Patient 20 Rep.2

source_name: plasma cirDNA from Benign Prostatic Hyperplasia patient.

value: Benign Prostatic Hyperplasia


title: hiPS-HUVhiPS4F1 cells untreated, biological replicate 1

description:
HUVhiPS4F1_Day0_1
Gene expression data from Undifferentiated hiPSCs-hiPS-HUVhiPS4F1


title: hES-H9 cells activin-treated, biological replicate 1

description:
H9_Activin-Day5_1
Gene expression data from Activin-differentiated hESCs-H9

source_name: Activin-differentiated hESCs


title: hES-H9 cells untreated, biological replicate 2

description:
H9_Day0_2
Gene expression data from Undifferentiated hESCs-H9

source_name: Undifferentiated hESCs


title: SF107_FTSW_t_4

source_name: SF107: water deprivation for fixed water stress, ftsw: quantity -0.015


title: hES-H9 cells untreated, biological replicate 1

description:
H9_Day0_1
Gene expression data from Undifferentiated hESCs-H9


title: SF109_FTSW_c_4

source_name: SF109: no treatment


title: hES-H9 cells activin-treated, biological replicate 2

description:
H9_Activin-Day5_2
Gene expression data from Activin-differentiated hESCs-H9


title: plasma Benign Prostatic Hyperplasia Patient19-Rep2

description: BPH group - Patient 19 Rep.2


title: CaseF (AML) 0 min [BM]

city: Be'er Yacob

first: Yossi

last: Cohen

address: Zeriffin

department: Hematology

country: Israel

institute: Asaf Harofeh University Hospital

description: SAMPLE 14

hyb_protocol: Biotin-labeled cRNA was hybridized onto 1.0 ST Expression Bead Chips

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner.

data_processing: The data were analyzed Affymetrix gene expression console (GCOS5)

source_name: AML_bone-marrow_Immediate fixation

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

growth_protocol: Cultured bone marrow cells were grown in high cell density imposing cell-cell contact

extract_protocol: Frozen samples were lyzed by adding 300 µl lysis buffer to tubes. Samples stored in RNAlater were fractionated and lyzed by x10 volumes (v/v) lysis buffer. RNA was isolated by MagNA Pure LC RNA Isolation procedure using MagNA Pure instrument (Roche). Integrity of RNA was examined by Agilent 2100 Bioanalyzer.

value: whole bone marrow

value: Immediate fixation following aspiration


title: CaseC (AML) 0 min [culture]

description: SAMPLE 16

source_name: AML_WBC_Immediate fixation

value: culture (WBC)

value: Immediate fixation following spread from the bottom well


title: CaseF (AML) 300 min [WBC]

description: SAMPLE 15

source_name: AML_WBC_Delayed fixation

value: bone marrow (WBC)

value: Delayed fixation following aspiration (RBC depleted)


title: CaseD (myeloma) 120 min [culture]

description: SAMPLE 17

value: Delayed fixation following spread from the bottom well


title: plasma Benign Prostatic Hyperplasia Patient20-Rep1

description: BPH group - Patient 20 Rep.1

value: plasma circulating DNA

source_name: Blood reference pool

value: white blood cell

value: white blood cell genomic DNA


title: SF107_date_t_2

source_name: SF107: water deprivation for fixed harvest, ftsw: time 6day

value: 33 days


title: CaseE (AML) 20 min [BM]

description: SAMPLE 12

source_name: AML_bone-marrow_Delayed fixation

value: Delayed fixation following aspiration


title: plasma Benign Prostatic Hyperplasia Patient19-Rep1

description: BPH group - Patient 19 Rep.1

value: pool of 20 individuals


title: CaseE (AML) 120 min [BM]

description: SAMPLE 13


title: plasma Benign Prostatic Hyperplasia Patient18-Rep2

description: BPH group - Patient 18 Rep.2

value: control


title: hiPS-HUVhiPS4F3 cells untreated, biological replicate 2

description:
HUVhiPS4F3_Day0_2
Gene expression data from Undifferentiated hiPSCs-hiPS-HUVhiPS4F3

source_name: Undifferentiated hiPSCs


title: plasma Benign Prostatic Hyperplasia Patient18-Rep1

description: BPH group - Patient 18 Rep.1


title: CaseD (APL) 260 min [BM]

description: SAMPLE 10

source_name: APL_bone-marrow_Delayed fixation


title: SF109_FTSW_t_5

source_name: SF109: water deprivation for fixed water stress, ftsw: quantity -0.015

value: 35 days


title: SF028_date_t_2

source_name: SF028: water deprivation for fixed harvest, ftsw: time 6day


title: CaseE (AML) 0 min [BM]

description: SAMPLE 11


title: CaseD (APL) 0 min [BM]

description: SAMPLE 8

source_name: APL_bone-marrow_Immediate fixation


title: CaseC (APL) 310 min [BM]

description: SAMPLE 6


title: CaseC (APL) 0 min [PB]

description: SAMPLE 7

source_name: APL_peripheral-blood_Immediate fixation

value: whole blood

value: Immediate fixation following blood draw


title: SF109_FTSW_t_4

value: 34 days


title: SF028_FTSW_c_4

source_name: SF028: no treatment


title: Inedi_FTSW_t_4

source_name: Inedi: water deprivation for fixed water stress, ftsw: quantity -0.015

value: Inedi


title: CaseD (APL) 120 min [BM]

description: SAMPLE 9

value: whole bone marrow


title: plasma Benign Prostatic Hyperplasia Patient17-Rep1

description: BPH group - Patient 17 Rep.1

source_name: plasma cirDNA from Benign Prostatic Hyperplasia patient.

value: Benign Prostatic Hyperplasia


title: CaseB (APL) 0 min [BM]

description: SAMPLE 3

value: Immediate fixation following aspiration


title: SF193_date_t_2

source_name: SF193: water deprivation for fixed harvest, ftsw: time 6day


title: CaseC (APL) 0 min [BM]

description: SAMPLE 5


title: plasma Benign Prostatic Hyperplasia Patient16-Rep1

description: BPH group - Patient 16 Rep.1


title: plasma Benign Prostatic Hyperplasia Patient17-Rep2

description: BPH group - Patient 17 Rep.2


title: plasma Benign Prostatic Hyperplasia Patient16-Rep2

description: BPH group - Patient 16 Rep.2


title: SF193_FTSW_t_4

source_name: SF193: water deprivation for fixed water stress, ftsw: quantity -0.015


title: CaseA (DLBCL) 0 min [BM]

description: SAMPLE 1

source_name: DLBCL_bone-marrow_Immediate fixation


title: Tekny_date_t_3

source_name: Tekny: water deprivation for fixed harvest, ftsw: time 6day

value: Tekny


title: plasma Benign Prostatic Hyperplasia Patient15-Rep2

description: BPH group - Patient 15 Rep.2


title: Melody_FTSW_c_4

source_name: Melody: no treatment

value: Melody

value: 36 days


title: MALT_Patient_4

description:
Paciente_San1.CEL
Gene expression data from human BM CD34+ cells from patients with lymphoma

hyb_protocol: Labeled sense cDNA was hybridized to the Affymetrix HuGene-1_0-st chip according to the the manufacturer protocols and using GeneChip® Hybridization, Wash and Stain Kit.

scan_protocol: Genechips were scanned with the Affymetrix GeneChip® Scanner 3000.

data_processing: The data were normalized with Bioconductor software using RMA algorithm.

source_name: CD34+ cells from bone marrow of a MALT patient

label_protocol: The sense cDNA was prepared from 300 ng of total RNA using the Ambion® WT Expression Kit. The sense strand cDNA was then fragmented and biotinylated with the Affymetrix GeneChip® WT Terminal Labeling Kit (PN 900671).

growth_protocol: For isolation of human BM CD34+ cells from patients with lymphoma and healthy donors, CD34-positive cell isolation was carried out in the BM samples from five patients with MALT lymphoma and five healthy donors using the AutoMACs automated separation system using CD34 microBeads (Miltenyi-Biotec).

extract_protocol: The cells were harvested with TRIzol Reagent (Invitrogen)  and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

treatment_protocol: Final purity was checked by flow cytometry using a PE mouse anti-human CD34 antibody (BD Pharmigen), being >95% in all cases. The cells were subjected to RNA extraction and gene expression microarray analysis.

value: MALT patient

value: CD34+ cells from bone marrow


title: MALT_Patient_2

description:
Paciente_Bar27913.CEL
Gene expression data from human BM CD34+ cells from patients with lymphoma


title: plasma Benign Prostatic Hyperplasia Patient14-Rep2

description: BPH group - Patient 14 Rep.2

value: plasma circulating DNA

source_name: Blood reference pool

value: white blood cell

value: white blood cell genomic DNA


title: MALT_Patient_5

description:
Paciente_San3.CEL
Gene expression data from human BM CD34+ cells from patients with lymphoma


title: MALT_Patient_3

description:
Paciente_Bar27915.CEL
Gene expression data from human BM CD34+ cells from patients with lymphoma


title: plasma Benign Prostatic Hyperplasia Patient15-Rep1

description: BPH group - Patient 15 Rep.1

value: pool of 20 individuals

value: control


title: CaseB (APL) 180 min [BM]

description: SAMPLE 4

value: Delayed fixation following aspiration


title: plasma Benign Prostatic Hyperplasia Patient14-Rep1

description: BPH group - Patient 14 Rep.1


title: MALT_Patient_1

description:
Paciente_Bar27839.CEL
Gene expression data from human BM CD34+ cells from patients with lymphoma


title: CaseA (DLBCL) 83 min [BM]

description: SAMPLE 2

source_name: DLBCL_bone-marrow_Delayed fixation


title: SF107_FTSW_c_5

description: Drought is the main cause or crop loss around the globe and it is expected to be more so in years to come. Helianthus genus comprises species that are able to grow in harsh environments suffering from severe water shortage. Cultivated H.annuus, i.e. sunflower, is a highly valuable oil crop due to, among other features, its ability to grow under low input conditions. The aim of our project is to unravel the transcriptional regulation underpinning drought tolerance in sunflower, with the ultimate goal of improving crop yield.

source_name: SF107: no treatment


title: Healthy_donor_2

description:
Donante_MO_12.CEL
Gene expression data from human BM CD34+ cells from healthy donors

source_name: CD34+ cells from bone marrow of a healthy donor

value: healthy donor


title: Healthy_donor_5

description:
Donante_MO_17.CEL
Gene expression data from human BM CD34+ cells from healthy donors


title: Healthy_donor_1

description:
Donante_MO_11.CEL
Gene expression data from human BM CD34+ cells from healthy donors


title: SF107_date_c_3

value: 33 days


title: SF028_date_t_3


title: Healthy_donor_4

description:
Donante_MO_16.CEL
Gene expression data from human BM CD34+ cells from healthy donors


title: Healthy_donor_3

description:
Donante_MO_13.CEL
Gene expression data from human BM CD34+ cells from healthy donors


title: plasma Benign Prostatic Hyperplasia Patient13-Rep2

description: BPH group - Patient 13 Rep.2


title: Mock vs. WT Tx  9.5hr 3

source_name: HTBE mock treated, 9.5hr

value: Primary human tracheobronchial epithelial (HTBE) cells

tag: infection

value: mock

tag: time

source_name: HTBE Tx/91 treated, 9.5hr

value: influenza Tx/91


title: SF109_date_c_3

source_name: SF109: no treatment


title: Mock vs. WT Tx  9.5hr 4


title: Mock vs. WT Tx  9.5hr 2


title: plasma Benign Prostatic Hyperplasia Patient12-Rep2

description: BPH group - Patient 12 Rep.2

tag: disease state

value: Benign Prostatic Hyperplasia

tag: sample type


title: Mock vs. WT Tx  9.5hr 1


title: Mock vs. WT Tx  25hr 1

source_name: HTBE Tx/91 treated, 25hr

source_name: HTBE mock treated, 25hr


title: SF326_date_c_1

source_name: SF326: no treatment

tag: cultivar

tag: age


title: Mock vs. NS1(1-126)  9.5hr 3

source_name: HTBE Tx/91 NS1 : 1–126 treated, 9.5hr

value: influenza Tx/91 NS1

tag: dose

value: Tx/91 NS1 : 1–126 viruses per filter


title: Mock vs. WT Tx  25hr 3


title: plasma Benign Prostatic Hyperplasia Patient13-Rep1

description: BPH group - Patient 13 Rep.1

source_name: plasma cirDNA from Benign Prostatic Hyperplasia patient.


title: SF193_date_t_1

source_name: SF193: water deprivation for fixed harvest, ftsw: time 6day


title: Mock vs. NS1(1-126)  9.5hr 4


title: Mock vs. WT Tx  25hr 4


title: Melody_date_t_3

source_name: Melody: water deprivation for fixed harvest, ftsw: time 6day

value: Melody


title: SF028_date_c_3

source_name: SF028: no treatment


title: Mock vs. NS1(1-126)  9.5hr 1


title: Mock vs. WT Tx  25hr 2


title: plasma Benign Prostatic Hyperplasia Patient11-Rep2

description: BPH group - Patient 11 Rep.2


title: Mock vs. NS1(1-126)  25hr 1

source_name: HTBE Tx/91 NS1 : 1–126 treated, 25hr


title: plasma Benign Prostatic Hyperplasia Patient10-Rep1

description: BPH group - Patient 10 Rep.1


title: BCWM1-scr-48hr

city: Boston

first: Yong

last: Zhang

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: Gene expression data from BCWM.1 cells treated with LNA scramble control for 48 hours

hyb_protocol: The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The hybridization solution is then removed.

scan_protocol: The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE. Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.

data_processing: CHP files processed using ExpressionStat 5.0 Algorithm.  Data were further processed and analyzed using dChip  (DNA-Chip Analyzer), Build date: Nov 10 2010

label_protocol: RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out.  The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates.  The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using magnetic particles. The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. Those cRNA's that fall outside of an acceptable range will not routinely be carried forward in the analysis. Should this occur, investigators would be notified and asked how they would like to proceed. The purified cRNA is fragmented in order to facilitate the subsequent hybridization step.

growth_protocol: BCWM.1 cells were cultured at 37°C in RPMI 1640 containing 10% fetal bovine serum, 2 mM L-glutamine, 100 U/mL penicillin, and 100 µg/mL streptomycin.

extract_protocol: Qiazol extraction of total RNA was performed according to the manufacturer(Qiagen) 's instructions.

treatment_protocol: BCWM.1 cells were treated with 20µM LNA antimiR-155 or scramble control for 48 hours.

value: BCWM.1 cells


title: Mock vs. NS1(1-126)  9.5hr 2


title: plasma Benign Prostatic Hyperplasia Patient9-Rep2

description: BPH group - Patient 9 Rep.2


title: plasma Benign Prostatic Hyperplasia Patient10-Rep2

description: BPH group - Patient 10 Rep.2


title: Mock vs. NS1(1-126)  25hr 3


title: SF028_FTSW_t_6

source_name: SF028: water deprivation for fixed water stress, ftsw: quantity -0.015

value: 36 days


title: plasma Benign Prostatic Hyperplasia Patient12-Rep1

description: BPH group - Patient 12 Rep.1

value: plasma circulating DNA

source_name: Blood reference pool


title: Mock vs. NS1(1-126)  25hr 4


title: Tpk2 Knockout Replicate 2

description: SH_253218010002_S01_GE2_107_Sep09_1_4.txt

hyb_protocol: The samples were hybridized to yeast dual color expression microarrays using standard Agilent protocols, reagents, and instruments.

scan_protocol: The scanned images were analyzed using Agilent's Feature Extraction software.

data_processing: After background subtraction, probe distance normalization was applied by calculating the Lowess fit of the probe distance from the 3'UTR and probe expression and subtracting it from the expression level. This was followed by quantile normalization. The software used included Agilent Feature Extraction Software version 10.7.3.1 for scanning and the MATLAB  Bioinformatics Toolbox version 3.4 (R2009b) for Lowess and quantile normalization.

label_protocol: The samples were amplified and labeled using standard Agilent protocols, reagents, and instruments.

growth_protocol: Cells were grown to logarithmic phase in SC medium (OD=0.5). The cells were harvested, pelleted and frozen for further analysis.

extract_protocol: Total RNA was extracted using MasterPure™ yeast RNA purification Kit (Epicentre).

treatment_protocol: Soribitol experiments were performed by growing to logarithmic phase in SC medium and then washing and resuspending in SC medium with 1M sorbitol for 30 minutes.

value: Tpk2 Knockout

tag: medium

value: sorbitol


title: Melody_date_t_2


title: 59Q-TBP; third biological replicate; 60 hours post transfection

city: NEW DELHI

first: REEMA

last: ROSHAN

address: A-93/94, IGIB, NARAINA INDUSTRIAL AREA, NARAINA

department: FGU

country: India

institute: INSTITUTE OF GENOMICS AND INTEGRATIVE BIOLOGY

description: transfection using Amaxa nucleofection as per manufacturer's instructions

hyb_protocol: Manusfacturer's Instructions

scan_protocol: Manusfacturer's Instructions

data_processing: Quantile normalization was performed after removing spots which were flagged by the signal well above Background criteria in the scan output file. The Software used is Avadis (version - 3.1).

source_name: Neuro2A cells

label_protocol: Manusfacturer's Instructions

extract_protocol: Trizol

treatment_protocol: Amaxa transfection

tag: strain

value: A

tag: tranfection

tag: replicate

value: third biological replicate

tag: time point

value: 60 hours post transfection


title: plasma Benign Prostatic Hyperplasia Patient11-Rep1

description: BPH group - Patient 11 Rep.1

value: white blood cell

value: white blood cell genomic DNA

value: pool of 20 individuals

value: control


title: Mock vs. NS1(1-126)  25hr 2

value: Primary human tracheobronchial epithelial (HTBE) cells

value: mock


title: 59Q-TBP; first biological replicate; 60 hours post transfection

value: first biological replicate


title: 16Q-TBP; second biological replicate; 60 hours post transfection

value: second biological replicate


title: BCWM1-anti155-48hr

description: Gene expression data from BCWM.1 cells treated with LNA anti-miR-155 for 48 hours


title: Wild Type Sorbitol Replicate 5

description:
SH_253218010002_S01_GE2_107_Sep09_1_2.txt
Control

value: wild type


title: 16Q-TBP; first biological replicate; 60 hours post transfection


title: SF109_date_t_3

source_name: SF109: water deprivation for fixed harvest, ftsw: time 6day

value: 33 days


title: SF107_date_t_1

source_name: SF107: water deprivation for fixed harvest, ftsw: time 6day


title: 59Q-TBP; second biological replicate; 60 hours post transfection


title: plasma Benign Prostatic Hyperplasia Patient9-Rep1

description: BPH group - Patient 9 Rep.1

value: Benign Prostatic Hyperplasia


title: plasma Benign Prostatic Hyperplasia Patient8-Rep2

description: BPH group - Patient 8 Rep.2

value: plasma circulating DNA


title: mouseC-CTL, vs PDL1-depleted ID8

city: Kyoto

first: Kaoru

last: Abiko

address: 54 Shogoin Kawaharacho, Sakyo-ku

institute: Kyoto University Graduate School of Medicine

description: Gene expression data from CTLs co-incubated with PDL1-depleted ID8

hyb_protocol: Following fragmentaion, 10ug of cRNA were hybridized for 16hr at 45C on Mouse Genome 430A 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were analyzed with Affymetrix microarray scanner using AGCC software.

data_processing: The data were analyzed with R.

source_name: mouseC-CTL, vs PDL1-depleted ID8

label_protocol: Labeling was performed according to Affymetrix GeneChip 3' IVT Express Kit protocol.

extract_protocol: Total RNA was exracted using Qiagen RNA easy.

treatment_protocol: Activated OT-1-mouse CTLs were co-incubated with ID8 cells loaded with OVA peptide for 4 hours at an E/T ratio of 30. Then CTLs were collected by magnetic separation.

tag: tissue

value: CD8+ T lymphocytes

tag: treatment

value: co-incubated with PDL1-depleted ID8


title: plasma Benign Prostatic Hyperplasia Patient8-Rep1

description: BPH group - Patient 8 Rep.1

tag: subject

tag: cell type


title: Tpk2 Knockout Replicate 1

description: SH_253218010002_S01_GE2_107_Sep09_1_3.txt

tag: genotype/variation

value: Tpk2 Knockout

value: sorbitol


title: Wild Type Sorbitol Replicate 6

description:
SH_253218010002_S01_GE2_107_Sep09_2_1.txt
Control


title: mouseD-CTL, vs PDL1-overexpressed ID8

description: Gene expression data from CTLs co-incubated with PDL1-overexpresssed ID8

source_name: mouseD-CTL, vs PDL1-overexpressed ID8


title: 59Q-TBP; second biological replicate; 36 hours post transfection

value: A

tag: cell line

value: 36 hours post transfection


title: mouseD-CTL, vs PDL1-depleted ID8

source_name: mouseD-CTL, vs PDL1-depleted ID8


title: 59Q-TBP; third biological replicate; 36 hours post transfection

value: third biological replicate


title: Wild Type Synthetic Complete Replicate 2

description: SH_253218010002_S01_GE2_107_Sep09_2_2.txt

value: synthetic complete


title: 16Q-TBP; third biological replicate; 60 hours post transfection

value: 60 hours post transfection


title: plasma Benign Prostatic Hyperplasia Patient5-Rep1

description: BPH group - Patient 5 Rep.1

value: white blood cell

value: white blood cell genomic DNA

value: pool of 20 individuals

value: control


title: mouseB-CTL, vs PDL1-overexpressed ID8

source_name: mouseB-CTL, vs PDL1-overexpressed ID8

value: co-incubated with PDL1-overexpresssed ID8


title: Wild Type Synthetic Complete Replicate 1

description: SH_253218010002_S01_GE2_107_Sep09_1_1.txt

value: wild type


title: plasma Benign Prostatic Hyperplasia Patient6-Rep1

description: BPH group - Patient 6 Rep.1

value: Benign Prostatic Hyperplasia


title: plasma Benign Prostatic Hyperplasia Patient6-Rep2

description: BPH group - Patient 6 Rep.2

value: plasma circulating DNA


title: plasma Benign Prostatic Hyperplasia Patient5-Rep2

description: BPH group - Patient 5 Rep.2


title: plasma Benign Prostatic Hyperplasia Patient7-Rep1

description: BPH group - Patient 7 Rep.1


title: Ssk2-Ssk22-Ste11 Triple Knockout Replicate 1

description: SH_253218010002_S01_GE2_107_Sep09_1_2.txt

value: Ssk2-Ssk22-Ste11 triple knockout


title: mouseA-CTL, vs PDL1-depleted ID8

source_name: mouseA-CTL, vs PDL1-depleted ID8

value: CD8+ T lymphocytes

value: co-incubated with PDL1-depleted ID8


title: Ssk2-Ssk22-Sho1 Triple Knockout Replicate 2

value: Ssk2-Ssk22-Sho1 triple knockout

value: sorbitol


title: plasma Benign Prostatic Hyperplasia Patient4-Rep2

description: BPH group - Patient 4 Rep.2


title: mouseC-CTL, vs PDL1-overexpressed ID8

source_name: mouseC-CTL, vs PDL1-overexpressed ID8


title: 59Q-TBP; first biological replicate; 36 hours post transfection

value: A

value: first biological replicate

value: 36 hours post transfection


title: 16Q-TBP; second biological replicate; 36 hours post transfection

value: second biological replicate


title: Ssk2-Ssk22-Ste11 Triple Knockout Replicate 2

description: SH_253218010002_S01_GE2_107_Sep09_2_1.txt


title: plasma Benign Prostatic Hyperplasia Patient4-Rep1

description: BPH group - Patient 4 Rep.1

value: white blood cell


title: 16Q-TBP; third biological replicate; 36 hours post transfection

value: third biological replicate


title: Ssk2-Ssk22-Sho1 Triple Knockout Replicate 1


title: mouseB-CTL, vs PDL1-depleted ID8

source_name: mouseB-CTL, vs PDL1-depleted ID8


title: Hog1 Knockout Replicate 1

value: Hog1 knockout


title: mouseA-CTL, vs PDL1-overexpressed ID8

source_name: mouseA-CTL, vs PDL1-overexpressed ID8


title: Hog1 Knockout Replicate 2


title: plasma Benign Prostatic Hyperplasia Patient7-Rep2

description: BPH group - Patient 7 Rep.2

source_name: plasma cirDNA from Benign Prostatic Hyperplasia patient.

value: white blood cell genomic DNA

value: pool of 20 individuals

value: control


title: plasma Benign Prostatic Hyperplasia Patient3-Rep1

description: BPH group - Patient 3 Rep.1

value: Benign Prostatic Hyperplasia


title: 59Q-TBP; first biological replicate; 24 hours post transfection

value: 24 hours post transfection


title: 16Q-TBP; third biological replicate; 24 hours post transfection


title: 59Q-TBP; second biological replicate; 24 hours post transfection


title: 16Q-TBP; second biological replicate; 24 hours post transfection


title: plasma Benign Prostatic Hyperplasia Patient2-Rep2

description: BPH group - Patient 2 Rep.2

value: plasma circulating DNA


title: 59Q-TBP; third biological replicate; 24 hours post transfection


title: plasma Benign Prostatic Hyperplasia Patient1-Rep1

description: BPH group - Patient 1 Rep.1


title: 16Q-TBP; first biological replicate; 36 hours post transfection


title: plasma Benign Prostatic Hyperplasia Patient3-Rep2

description: BPH group - Patient 3 Rep.2


title: plasma Benign Prostatic Hyperplasia Patient1-Rep2

description: BPH group - Patient 1 Rep.2


title: plasma Benign Prostatic Hyperplasia Patient2-Rep1

description: BPH group - Patient 2 Rep.1


title: 16Q-TBP; first biological replicate; 24 hours post transfection


title: Human Whole blood RNA 233

status: Public on Jul 09 2012

city: Los Angeles

first: Simone

last: de Jong

state: California

address: 695 Charles E. Young Drive south

institute: UCLA

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were backgroundcorrected in Beadstudio (v. 3.2.3) and transformed (vst) and normalised (rsn) in Lumi (R package)

source_name: schizophrenia (SCZ)_whole blood

label_protocol: Standard Illumina TotalPrep kit amplification and labeling protocol

extract_protocol: Standard Qiagen PAXgene extraction (manual and Qiacube)

tag: gender

value: male

tag: status

value: schizophrenia (SCZ)

value: whole blood


title: Human Whole blood RNA 234


title: Human Whole blood RNA 237