title: 254706910069_b1 - col_mock_5mM_1 vs col_Ea_5mM_1

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

description: Effect of N nutrition of Arabidopsis response to Erwinia infection

hyb_protocol: col_Ea_5mM_1 Cy5 / col_mock_5mM_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 50%, Cy5:635nm,pmt voltage 700V,laser power 45%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: aerial,rosette - Unfertilized Jiffy plugs were satutared (100% plug water capacity) with nutritive solution containing 0.5 mM KNO3. Seeds were sowed after stratification and after 7 days in short days (8h light 150 microE/m2), one plant was kept. Weight of the plugs were adjusted with watering every day (with nutritive solution at 5 or 0.5 mM KNO3) so that humidity was lowered by 10%/day until 60%. Then plugs were weighted and watered evry day to maintain 60% of total water caapcity (humidity) with the two nutritive solution (5mM KNO3, ample nitrate, 0.5 mM limiting nitrate). After 4 weeks plugs were watered with full capacity with the two nutritive solutions.

treatment_protocol: Name:Nitrogen_Erwinia_5mM - environmental treatment -  ,nitrogen concentration + pathogen infection,kno3 + erwinia:quantity 5mM time 6hour . Note : Unfertilized Jiffy plugs were satutared (100% plug water capacity) with nutritive solution containing 0.5 mM KNO3. Seeds were sowed after stratification and after 7 days in short days (8h light 150 microE/m2), one plant was kept. Weight of the plugs were adjusted with watering every day (with nutritive solution at 5 or 0.5 mM KNO3) so that humidity was lowered by 10%/day until 60%. Then plugs were weighted and watered evry day to maintain 60% of total water caapcity (humidity) with the two nutritive solution (5mM KNO3, ample nitrate, 0.5 mM limiting nitrate). After 4 weeks plugs were watered with full capacity with the two nutritive solutions.

tag: ecotype

value: columbia

value: boyes et al. plant cell 2001

tag: harvest date

treatment_protocol: Name:Mock_5mM - environmental treatment - mock,mock:quantity 5mM time 6hour . Note : Unfertilized Jiffy plugs were satutared (100% plug water capacity) with nutritive solution containing 0.5 mM KNO3. Seeds were sowed after stratification and after 7 days in short days (8h light 150 microE/m2), one plant was kept. Weight of the plugs were adjusted with watering every day (with nutritive solution at 5 or 0.5 mM KNO3) so that humidity was lowered by 10%/day until 60%. Then plugs were weighted and watered evry day to maintain 60% of total water caapcity (humidity) with the two nutritive solution (5mM KNO3, ample nitrate, 0.5 mM limiting nitrate). After 4 weeks plugs were watered with full capacity with the two nutritive solutions.


title: 254706910069_b2 - col_Ea_5mM_1 vs col_mock_5mM_1

status: Public on Apr 12 2017

type: RNA

hyb_protocol: col_mock_5mM_1 Cy5 / col_Ea_5mM_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

molecule: total RNA


title: 254706910073_b4 - col_Ea_5mM_2 vs col_mock_5mM_2

hyb_protocol: col_mock_5mM_2 Cy5 / col_Ea_5mM_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: NEG3

city: Irvine

first: Bogi

last: Andersen

state: CA

address: 839 Health Sciences Dr.

department: Medicine

country: USA

institute: University of California, Irvine

description: 253452510007_201107280954_S01 [2_3]

hyb_protocol: The labeled cRNA is fragmented and placed on the human 8x15K microarray and hybridized at 65oC for ~17 hours.

scan_protocol: The arrays are washed and scanned at 5 μM resolution on an Agilent G2565CA High Resolution Scanner.

data_processing: Data was processed through Agilent’s Feature Extraction software version 10.7.31.

organism: Homo sapiens

source_name: neonatal human epidermal keratintocyes

label_protocol: One-color labeling reactions were prepared using the Agilent One-Color Protocol (Version 5.7) with 300 ng total RNA input. RNA with the appropriate concentration of RNA spike-in controls is converted into double stranded cDNA using an olido (dT) primer linked to the T7 promoter sequence and MMLV-RT. The double stranded cDNA is then in vitro transcribed by T7 RNA polymerase, which simultaneously amplifies and incorporates cyanine 3-labeled CTP into the resulting cRNA. Labeled cRNA is then purified using Qiagen RNeasy columns and the labeling efficiency determined by the NanoDrop spectrophotometer.

growth_protocol: Normal Human Epidermal Keratinocytes (NHEK) were purchased from LifeLine Technologies and grown according to the manufacturer’s instructions in DermaLife medium (LifeLine Tech) supplemented with DermaLife growth factors (LifeLine Tech). Cells were induced to differentiate by addition of high calcium medium (1.8mM Ca2+).

extract_protocol: Cells were collected and lysed in Trizol, followed purification with Zymo RNA extraction kit.  RNA concentration and quality were quantified on a NanoDrop.

treatment_protocol: Lipofectamine RNAi Max (Life Technologies) in OptiMEM medium was used for siRNA transfections. Pooled siRNA for each factor (Dharmacon) were used for knockdown in NHEK. 24 hours after knockdown, cells were induced to differentiate by the addition of high calcium media, and collected 24 hours later.

tag: transcription factor


title: XBP1

description: 253452510006_201107281010_S01 [2_4]


title: TCF4

description: 253452510007_201107280954_S01 [1_3]


title: SOX6

description: 253452510006_201107281010_S01 [1_4]


title: STAT3

description: 253452510005_201107281002_S01 [2_4]


title: SMAD4

description: 253452510006_201107281010_S01 [2_2]


title: 254706910068_b4 - col_Ea_0.5mM_2 vs col_mock_0.5mM_2

hyb_protocol: col_mock_0.5mM_2 Cy5 / col_Ea_0.5mM_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

treatment_protocol: Name:Mock_0.5mM - environmental treatment - mock,mock:quantity 0.5mM time 6hour . Note : Unfertilized Jiffy plugs were satutared (100% plug water capacity) with nutritive solution containing 0.5 mM KNO3. Seeds were sowed after stratification and after 7 days in short days (8h light 150 microE/m2), one plant was kept. Weight of the plugs were adjusted with watering every day (with nutritive solution at 5 or 0.5 mM KNO3) so that humidity was lowered by 10%/day until 60%. Then plugs were weighted and watered evry day to maintain 60% of total water caapcity (humidity) with the two nutritive solution (5mM KNO3, ample nitrate, 0.5 mM limiting nitrate). After 4 weeks plugs were watered with full capacity with the two nutritive solutions.


title: 254706910068_b1 - col_mock_0.5mM_1 vs col_Ea_0.5mM_1

hyb_protocol: col_Ea_0.5mM_1 Cy5 / col_mock_0.5mM_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Ebola-Day 7-replicate 1

city: Seattle

first: kathie

last: walters

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

description: Gene expression profilign of peripheral blood from Ebola infected patient

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

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

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Ebola-Day 7

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.3 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated from approximately 2.5 mls of peripheral blood in Paxgene tubes according to manufacturer's protocol under BSL4 conditions.  RNA quality was assessed using Agilent Bioanalyzer.

treatment_protocol: Peripheral blood was collected from either a patient infected with Ebola virus or healthy volunteers and stored in Paxgene tubes (Qiagen) according to manufacturer's instructions.

tag: tissue

value: Peripheral blood

tag: virus strain

value: Ebola


title: NEG2

description: 253452510007_201107280954_S01 [2_2]


title: SP1

description: 253452510006_201107281010_S01 [1_3]


title: PRDM1

description: 253452510005_201107281002_S01 [2_2]


title: STAT1

description: 253452510006_201107281010_S01 [1_1]


title: RUNX2

description: 253452510006_201107281010_S01 [2_3]


title: RARG

description: 253452510005_201107281002_S01 [2_1]

value: RARG


title: SP3

description: 253452510006_201107281010_S01 [1_2]


title: 254706910073_b3 - col_mock_5mM_2 vs col_Ea_5mM_2

hyb_protocol: col_Ea_5mM_2 Cy5 / col_mock_5mM_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910068_b3 - col_mock_0.5mM_2 vs col_Ea_0.5mM_2

hyb_protocol: col_Ea_0.5mM_2 Cy5 / col_mock_0.5mM_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: RBL1

description: 253452510005_201107281002_S01 [1_4]


title: PBX2

description: 253452510005_201107281002_S01 [2_3]


title: SOX11

description: 253452510006_201107281010_S01 [2_1]


title: 254706910068_b2 - col_Ea_0.5mM_1 vs col_mock_0.5mM_1

hyb_protocol: col_mock_0.5mM_1 Cy5 / col_Ea_0.5mM_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: NR3C1

description: 253452510008_201108230945_S01 [2_4]


title: RORA

description: 253452510005_201107281002_S01 [1_2]

value: RORA


title: RUNX1

description: 253452510005_201107281002_S01 [1_1]


title: JUN

description: 253452510003_201108120906_S01 [2_4]

value: JUN


title: RELB

description: 253452510005_201107281002_S01 [1_3]

value: RELB


title: PBX1

description: 253452510008_201108230945_S01 [2_1]


title: OVOL1

description: 253452510008_201108230945_S01 [2_2]


title: OVOL2

description: 253452510008_201108230945_S01 [2_3]


title: KLF4

description: 253452510008_201108230945_S01 [1_3]


title: JUND

description: 253452510008_201108230945_S01 [1_2]

value: JUND


title: JUNB

description: 253452510008_201108230945_S01 [1_1]

value: JUNB


title: GRHL2

description: 253452510003_201108120906_S01 [2_2]


title: LRRFLP1

description: 253452510008_201108230945_S01 [1_4]


title: GRHL1

description: 253452510003_201108120906_S01 [2_1]


title: GRHL3

description: 253452510003_201108120906_S01 [2_3]


title: GABP1

description: 253452510003_201108120906_S01 [1_1]


title: FOXN2

description: 253452510003_201108120906_S01 [1_3]


title: FOXN1

description: 253452510003_201108120906_S01 [1_2]


title: FOXP1

description: 253452510003_201108120906_S01 [1_4]


title: FOXD1

description: 253452510002_201108110904_S01 [2_4]


title: FOSL2

description: 253452510002_201108110904_S01 [2_3]


title: A6L_CTRL

type: genomic

city: LONDON

first: Sladana

last: Zagorac

address: Charterhouse square

country: United Kingdom

institute: Barts Cancer Institute

description:
Control
genomic DNA from sample 13

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol

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

data_processing: R environment using the Bioconductor minfi package 3

label: Cy5 and Cy3

molecule: genomic DNA

source_name: PDAC cancer cells_Control

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted using standard phenol-chloroform extraction

value: PDAC cancer cells

tag: disease state

value: pancreatic ductal adenocarcinoma (PDAC)


title: FOSL1

description: 253452510002_201108110904_S01 [2_2]


title: TUDCA-Sham 6 (TS6)

city: Gwangju

first: Dohan

last: Kim

state: Gwangju

address: oryong dong buk gu, cheomdan

department: Dept. of Life science

country: South Korea

institute: gwangju institute of science and technology

description: biological replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Array probes that have detection p-value ≥ 0.05 (similar to signal to noise) in over 50% samples were filtered out. Selected gene signal value was transformed by logarithm and normalized by quantile method.

label: biotin

organism: Mus musculus

source_name: mouse heart

label_protocol: Total RNA was amplified and purified using the Ambion Illumina RNA amplification kit (Ambion, Austin, USA) to yield biotinylated cRNA according to the manufacturer’s instructions.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent 2100 Bioanalyser.

tag: strain

tag: age

value: 8-10 weeks

value: heart


title: TUDCA-TAC 2 (TT2)

description: biological replicate 1


title: 185_SCD2S+_FLO-

description:
non CSC 3
genomic DNA from sample 5

source_name: PDAC cancer cells_non CSC 3


title: A6L_23-2-10_FLO+

description:
CSC 6
genomic DNA from sample 12

source_name: PDAC cancer cells_CSC 6


title: TUDCA-Sham 4 (TS4)

description: biological replicate 2


title: ETS1

description: 253452510002_201108110904_S01 [1_3]


title: TUDCA-Sham 1 (TS1)

description: biological replicate 1


title: TUDCA-TAC 4 (TT4)

description: biological replicate 3


title: FOS

description: 253452510002_201108110904_S01 [1_4]

value: FOS


title: Veh-TAC 9 (T9)

description: biological replicate 3


title: IVD

description:
IVD 1
genomic DNA from sample 16

source_name: IVD control 1

value: none (IVD control 1)


title: 185_SCD1S+_FLO-

description:
non CSC 2
genomic DNA from sample 3

source_name: PDAC cancer cells_non CSC 2


title: TUDCA-TAC 3 (TT3)

description: biological replicate 2


title: A6L_ZEB

description:
Zebularine 1
genomic DNA from sample 14

source_name: PDAC cancer cells_Zebularine 1


title: CREB5

description: 253452510002_201108110904_S01 [1_1]


title: A6L_8-1-10_FLO-

description:
non CSC 5
genomic DNA from sample 9

source_name: PDAC cancer cells_non CSC 5


title: 185_ZEB

description:
Zebularine 2
genomic DNA from sample 15

source_name: PDAC cancer cells_Zebularine 2


title: CEBPG

description: 253452510004_201108230953_S01 [2_4]

value: CEBPG


title: 185_4/12_FLO+

description:
CSC 4
genomic DNA from sample 8

source_name: PDAC cancer cells_CSC 4


title: TUDCA-TAC 1 (TT1)

description: biological replicate 4


title: E2F1

description: 253452510002_201108110904_S01 [1_2]


title: 185_8-6-11_FLO+

description:
CSC 1
genomic DNA from sample 2

source_name: PDAC cancer cells_CSC 1


title: 185_4/12_FLO-

description:
non CSC 4
genomic DNA from sample 7

source_name: PDAC cancer cells_non CSC 4


title: 185_SCD1S+_FLO+

description:
CSC 2
genomic DNA from sample 4

source_name: PDAC cancer cells_CSC 2


title: 185_SCD2S+_FLO+

description:
CSC 3
genomic DNA from sample 6

source_name: PDAC cancer cells_CSC 3


title: A6L_23-2-10_FLO-

description:
non CSC 6
genomic DNA from sample 11

source_name: PDAC cancer cells_non CSC 6


title: IVD_2

description:
IVD 2
genomic DNA from sample 17

source_name: IVD control 2

value: none (IVD control 2)


title: FOSB

description: 253452510002_201108110904_S01 [2_1]

source_name: neonatal human epidermal keratintocyes

value: FOSB


title: A6L_8-1-10_FLO+

description:
CSC 5
genomic DNA from sample 10

source_name: PDAC cancer cells_CSC 5


title: 185_8-6-11_FLO-

description:
non CSC 1
genomic DNA from sample 1

source_name: PDAC cancer cells_non CSC 1


title: Veh-TAC 3 (T3)

description: biological replicate 1

source_name: mouse heart


title: BRIP1

description: 253452510004_201108230953_S01 [2_2]


title: NOTCH3

description: 253452510004_201108230953_S01 [2_3]


title: ATF4

description: 253452510004_201108230953_S01 [1_3]


title: ATF5

description: 253452510004_201108230953_S01 [1_4]


title: Veh-Sham 4 (S4)

description: biological replicate 2


title: Veh-Sham 6 (S6)

description: biological replicate 3


title: ATF7

description: 253452510004_201108230953_S01 [2_1]


title: ATF3

description: 253452510004_201108230953_S01 [1_2]


title: ATF2

description: 253452510004_201108230953_S01 [1_1]


title: HCCLM3_cultured_rep3

city: Tianjin

first: Yongmei

last: Li

address: No.22, Qixiangtai Road, Heping District

country: China

institute: Tianjin Medical University

description:
Biological replicate 3 of 3. HCCLM3 cell line.
LM3_29_3_NS

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3‐labeled cRNA using Gene Expression Hybridization Kit (Cat#5188‐5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188‐5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One‐Color (Cat#5190‐2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: All the cells were cultured in DMEM with 10% FBS

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596‐018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase‐Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

tag: cell line

tag: cell type

value: HCC cell line


title: Huh7_cultured_rep2

description:
Biological replicate 2 of 3. Huh_7 cell line.
Huh_7_4_4_NS


title: HCCLM3_cultured_rep2

description:
Biological replicate 2 of 3. HCCLM3 cell line.
LM3_1_4_NS


title: HCCLM3_cultured_rep1

description:
Biological replicate 1 of 3. HCCLM3 cell line.
LM3_16_3_NS


title: MHCC97L_cultured_rep3

description:
Biological replicate 3 of 3. MHCC97L cell line.
97L_23_4B_NS


title: Veh-Sham 3 (S3)

description: biological replicate 1


title: Huh7_cultured_rep1

description:
Biological replicate 1 of 3. Huh_7 cell line.
Huh_7_22_3_NS


title: Impaired HIVE 10133

status: Public on Apr 11 2017

city: Edmonton

first: William

middle: George

last: Branton

state: Alberta

address: 611 HMRC University of Alberta

country: Canada

institute: University of Alberta

description: miRNA expression data from post mortem human neocortex

hyb_protocol: labeled samples were hybridized to Affymetrix miRNA 3.0 GeneChip array at 48 °C for 16 h

scan_protocol: Arrays were stained and washed on Affymetrix GeneChip Fluidics 450 following manufacturer's protocol and scanned with Affymetrix GeneChip Scanner 3000 7G System

data_processing: GeneSpring (version 12.6, Agilent Technologies) were used to normalize the data  based on the Robust Multiarray Average algorithm, in which data are background-corrected, log 2 transformed and quartile normalized

label: Biotin

source_name: post mortem human neocortex

label_protocol: 8 µg total RNA labelled with Affymetrix FlashTag Biotin HSR kit as per manufacturer's instructions

growth_protocol: Archived post mortem human neocortex

extract_protocol: Qiagen miRNeasy serum/plasma kit extraction as per manufacturer's instructions

tag: Sex

value: female


title: Impaired HIVE 7100616568


title: Impaired HIVE 2035


title: Impaired HIVE 6800127569


title: Impaired HIVE 7100107766


title: Impaired HIVE 10129


title: MHCC97L_cultured_rep1

description:
Biological replicate 1 of 3. MHCC97L cell line.
97L_18_4_NS


title: Impaired HIVE 10065


title: Huh7_cultured_rep3

description:
Biological replicate 3 of 3. Huh_7 cell line.
Huh_7_8_4_NS


title: Impaired HIVE 10026


title: MHCC97L_cultured_rep2

description:
Biological replicate 2 of 3. MHCC97L cell line.
97L_23_4A_NS


title: Veh-TAC 8 (T8)

description: biological replicate 2


title: HIV+ Impaired 7100658283


title: Impaired HIVE 7102458266

value: male


title: Impaired HIVE 2066


title: HIV+ Impaired 7200186777


title: HSC-2 Adhesion restricted condition_4

city: Chiyoda-ku

first: Shogo

last: Okazaki

state: Tokyo

address: 1-8-13 Kanda-Surugadai

department: School of Dentistry

country: Japan

institute: Nihon University

description: Gene expression data from HSC-2 cells cultured attachment restricted condition

hyb_protocol: The Agilent array were hybridized and washed using the manufacturer's protocol.

scan_protocol: Agilent arrays were scanned using the Agilent Technologies Scanner G2505C.

data_processing: The data were normalized with 75 Percentile method

source_name: Adhesion restriction_4

label_protocol: Cy3 labeled cRNA were prepared according to the standard Agilent protocol.

growth_protocol: HSC-2 cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% FBS in 5% CO2.

extract_protocol: RNA was extracted using Trizol reagent (Invitrogen) according to the manufacturer’s instructions.

value: oral squamous cell carcinoma

tag: culture condition

value: Adhesion restricted


title: HSC-2 Adhesion restricted condition_3

source_name: Adhesion restriction_3


title: HSC-2 Adhesion restricted condition_1

source_name: Adhesion restriction_1


title: HIV+ Impaired 6800207680


title: HSC-2 Normal condition_4

description: Gene expression data from HSC-2 cells cultured normal condition

value: Normal


title: HSC-2 Adhesion restricted condition_2

source_name: Adhesion restriction_2


title: HSC-2 Normal condition_2


title: HIV+ Impaired 6032


title: Xylose_Fermentation_9hr_run3

city: Kobe

first: Akihiko

last: Kondo

address: 1-1 Rokkodai, Nada

department: Chemical Science and Engineering

institute: Kobe University

description: 50 g/L xylose

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Yeast Microarrays for 17 hours at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with Wash Buffer 1 (Agilent) and 1 minute with 37°C Wash Buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides (Scan Region 61x21.6 mm, Scan resolution 5um, R PMT is set to 100% and G PMT is set to 100%, XDR=0.10).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.1.1.1 (Agilent) using default parameters (protocol GE1-v5_10 Apr08) and Grid: 015072_D_20060913) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Saccharomyces cerevisiae

source_name: YeastCell, 9hr, Xylsoe, replicate3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ug RNA using the One-Color Low-input QuickAmp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer, and its quality checked by Agilent 2100 Bioanalyzer.

extract_protocol: Total RNA was obtained by following the protocol provided for the Total RNA Isolation Mini Kit (Agilent Technologies, Palo Alto, CA, USA). RNA concentration and quality were measured using a NanoDrop ND-1000 spectrophotometer (NanoDrop, Delaware, USA) and an Agilent 2100 Bioanalyzer (Agilent Technologies), respectively.

tag: carbon source

value: Xylose

tag: time point

value: 9 h


title: Glucose_Fermentation_3hr_run1

description: 50 g/L glucose

source_name: YeastCell, 9hr, Glucose, replicate1

value: Glucose

value: 3 h


title: Glucose_Fermentation_3hr_run2

description: 50 g/L glucose

source_name: YeastCell, 9hr, Glucose, replicate2


title: HSC-2 Normal condition_3


title: Xylose_Fermentation_9hr_run2

description: 50 g/L xylose

source_name: YeastCell, 9hr, Xylsoe, replicate2


title: HIV+ Impaired 20013


title: HIV+ NOT IMPAIRED 7101236568


title: HIV+ Impaired 10119


title: HIV+ Impaired 6037


title: Glucose_Fermentation_3hr_run3

description: 50 g/L glucose

source_name: YeastCell, 9hr, Glucose, replicate3


title: HIV+ Impaired 10045


title: HIV+ NOT IMPAIRED 7200848468


title: HSC-2 Normal condition_1


title: HIV+ Impaired 7200116866


title: Xylose_Fermentation_9hr_run1

description: 50 g/L xylose

source_name: YeastCell, 9hr, Xylsoe, replicate1


title: HIV+ NOT IMPAIRED 7200597771


title: HIV+ Impaired 7200537480


title: HIV+ NOT IMPAIRED 7101328666


title: HIV+ NOT IMPAIRED 6800907480


title: HIV+ NOT IMPAIRED 20033


title: HIV+ NOT IMPAIRED 7200267172


title: HIV+ NOT IMPAIRED 7102027465


title: HIV+ NOT IMPAIRED CA186


title: Lymphoma BCR-negative (ID # 2676) - CHIR99021 treated

city: Milan

first: Federica

last: Zanardi

address: via Adamello 16

country: Italy

institute: IFOM, the FIRC Institute of Molecular Oncology

hyb_protocol: Array hybridization, washing and scanning were performed on a GeneAtlas Instrument according to the manufacturer’s recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneAtlas Imaging Station instrument

data_processing:
Raw data were normalized by the robust multichip average (RMA) method using the Affymetrix Power Tools (APT) Software Package.
MoGene-1_1-st-v1.r4.pgf
MoGene-1_1-st-v1.r4.mps

source_name: BCR-negative lymphoma B cells purified from a BCR+/BCR- mixed lymphoma cell culture grown for four days in the presence of CHIR99021

label_protocol: The Ambion WT Expression Kit (P/N 4411974) and Affymetrix GeneChip WT Teminal Labeling Kit (P/N 900670) were used for the preparation of labelled cDNA from 150ng of total RNA without rRNA reduction.

growth_protocol: Primary in vitro cultures of B lymphoma cells isolated from l-MYC;B1-8f mice. BCR-independent lymphomas were derived after prolonged in vitro culture of BCR-negative tumors.

extract_protocol: BCR-positive and BCR-negative lymphoma cells from mixed cultures were purified by FACS-assisted cell sorting, centirfuged and subjected to Rneasy Mini kit (Qiagen) total RNA extraction protocol.

treatment_protocol: Lymphoma cultures were TAT-Cre transduced to ablate the BCR and exposed in some experiments to CHIR99021 to inhibit GSK3b activity. Mixed cultures with BCR-independent lymphomas were estabslished mixing BCR-positive malignant cells to clones of BCR-independent lymphoma cells of the same tumor.

value: C57BL/6J x BALB/c


title: Lymphoma BCR-positive (ID # 2676) - Untreated (2)

source_name: BCR-positive lymphoma B cells purified from a BCR+/BCR- mixed lymphoma cell culture grown for four days


title: HIV+ NOT IMPAIRED 7100246771


title: Lymphoma BCR-independent  (ID # 2646, clone 7) - Untreated

source_name: BCR-independent lymphoma B cells purified from a BCR+/BCR-independent mixed lymphoma cell culture grown for four days


title: Lymphoma BCR-negative (ID # 2646) - CHIR99021 treated


title: Lymphoma BCR-independent  (ID # 2567, clone 8) - Untreated


title: Lymphoma BCR-negative  (ID # 2676) - Untreated (2)

source_name: BCR-negative lymphoma B cells purified from a BCR+/BCR- mixed lymphoma cell culture grown for four days


title: Lymphoma BCR-negative (ID # 2567) - CHIR99021 treated


title: Lymphoma BCR-positive (ID # 2646) - Untreated (2)


title: Lymphoma BCR-independent  (ID # 2676, clone 1) - Untreated


title: Lymphoma BCR-positive (ID # 2676) - CHIR99021 treated

source_name: BCR-positive lymphoma B cells purified from a BCR+/BCR- mixed lymphoma cell culture grown for four days in the presence of CHIR99021

growth_protocol: Primary in vitro cultures of B lymphoma cells isolated from l-MYC;B1-8f mice

treatment_protocol: Lymphoma cultures were TAT-Cre transduced to ablate the BCR and exposed in some experiments to CHIR99021 to inhibit GSK3b activity


title: Lymphoma BCR-negative  (ID # 2676) - Untreated


title: Lymphoma BCR-negative  (ID # 2646) - Untreated (2)


title: Lymphoma BCR-negative (ID # 2676)  - CHIR99021 treated


title: Lymphoma BCR-positive (ID # 2567) - Untreated


title: Lymphoma BCR-positive (ID # 2646) - CHIR99021 treated


title: Lymphoma BCR-negative  (ID # 2646) - CHIR99021 treated


title: Lymphoma BCR-positive (ID # 2646) - Untreated


title: Lymphoma BCR-negative  (ID # 2567) - Untreated


title: Lymphoma BCR-positive (ID # 2564) - CHIR99021 treated


title: Lymphoma BCR-positive (ID # 2676) - Untreated


title: Lymphoma BCR-negative (ID # 2564) - CHIR99021 treated


title: Lymphoma BCR-positive (ID # 2564) - Untreated


title: E2P4_3

city: Cambridge

first: Margherita

last: Turco

address: Department of Pathology, Tennis Court Road

department: Department of Pathology

institute: University of Cambridge

description: organoid cultures of human endometrium

data_processing: The data were normalised using the function lumiN from lumi R package, selecting the default quantile normalization method

source_name: E2P4-treated endometrial organoid culture

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

growth_protocol: ExM culture conditions

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.  On column DNase I treatment was done following the manufacturer's instructions.

treatment_protocol: ExM supplemented with E2+P4+cAMP

value: human endometrial organoids

tag: stimulated with

value: estrogen (E2) + progesterone (P4) + cAMP


title: Lymphoma BCR-negative  (ID # 2564) - Untreated


title: E2_1

description: organoid cultures of human endometrium

source_name: E2-treated endometrial organoid culture

treatment_protocol: ExM supplemented with E2

value: estrogen (E2)


title: Control_3

description: organoid cultures of human endometrium

source_name: Control endometrial organoid culture

treatment_protocol: ExM

value: none (control)


title: E2P4_2

description: organoid cultures of human endometrium


title: E2P4_1

description: organoid cultures of human endometrium


title: Lymphoma BCR-negative  (ID # 2646) - Untreated


title: E2_2

description: organoid cultures of human endometrium


title: Organoids_9

source_name: Decidual organoids

tag: sample id

value: Donor 9

value: Decidual organoids


title: E2_3

description: organoid cultures of human endometrium


title: Organoids_12

value: Donor 12


title: Control_1

description: organoid cultures of human endometrium


title: Glands_7

source_name: Endometrial glands

value: Donor 7

value: Endometrial glands


title: Organoids_8

value: Donor 8


title: Organoids_7

source_name: Endometrial organoids

value: Endometrial organoids


title: Stroma_7

source_name: Endometrial stroma

value: Endometrial stroma


title: Control_2

description: organoid cultures of human endometrium


title: Organoids_13

value: Donor 13


title: Glands_6

value: Donor 6


title: Glands_5

value: Donor 5


title: Organoids_6


title: Organoids_10

value: Donor 10


title: Organoids_11

value: Donor 11


title: Stroma_6


title: Stroma_4

value: Donor 4


title: Glands_4


title: Organoids_4


title: Stroma_5


title: Organoids_5


title: Stroma_3

value: Donor 3


title: PF-KT_PF_without_cation_1

city: Tokyo

first: Hideaki

last: Nojiri

address: 1-1-1 Yayoi, Bunkyo-ku

department: Biotechnology Research Center

institute: The University of Tokyo

description: This is an Affymetrix custom-commercial tiling array that covers thePseudomonas fluorescens Pf0-1 chromosome (RefSeq: NC_007492) at 11-bp density.  BPMAP files are provided as supplementary files. PFO1b520543F-3-FWD.bpmap represents  the forward strand of Pf0-1 chromosome, and PFO1b520543F-3-REV.bpmap represents the reverse strand of Pf0-1 chromosome.

hyb_protocol: The labelled samples were hybridized individually with each chip using a GeneChip Hybridization Oven 640 (Affymetrix) at 60 rpm and 50°C for 16 h. The chips were then washed and stained using a Hybridization, Wash and Stain Kit (Affymetrix) according to a modified version of the FleX450-0005 protocol of the GeneChip Fluidics station 450 (Affymetrix)

scan_protocol: Signals were detected using a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The CEL files were generated using Affymetrix GCOS. Data was quantile normalized and analyzed with Affymetrix Tiling Analysis Software v1.1, which uses non-parametric quantile normalization and a Hodges-Lehmann estimator for fold enrichment.The intensities were linearly scaled so that the median was 100. Each CEL file was converted into the BAR files using PFO1b520543F-3-FWD.bpmap for the forward strand and PFO1b520543F-3-REV.bpmap for the reverse strand; the BAR files with F indicate the forward strand and with R indicate the reverse strand of Pf0-1 chromosome. Bandwidth: 30, Threshold: 0, MaxGap: 30, MinRun, 30.

organism:
Pseudomonas putida KT2440
Pseudomonas fluorescens Pf0-1

source_name: cDNA prepared from Pf0-1(pCAR1) and KT2440 incubated in CF buffer without cation

label_protocol: Labelling of the cDNA was achieved using a GeneChip WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix, Santa Clara, CA).

growth_protocol: Donor (Pseudomonas fluorescens Pf0-1) and recipient (Pseudomonas putida KT2440) were grown overnight in 1/2LB. The cells were harvested by centrifugation and washed five times by CF buffer.

extract_protocol: The cells were treated with RNA Protect Bacteria reagent (Qiagen, CA, USA). Total RNA was extracted using NucleoSpin RNA II (Macherey-Nagel, Düren, Germany) and RNeasy Midi kit (Qiagen). The eluted RNA was treated with RQ1 RNase-free DNase (Promega, Madison, WI). After inactivation of DNase by the addition of the provided stop reagent and subsequent incubation, total RNA was repurified using NucleoSpin RNA Clean-up (Macherey-Nagel). cDNA was synthesized using SuperScript II (Invitrogen, Carlsbad, CA) in the presence of actinomycin D (Sigma, St.Louis, MO) to prevent generation of spurious second-strand cDNA.

treatment_protocol: The cells were suspended in 4 mL CF buffer and the turbidity of donor and the recipient was adjusted to 2.0 at 600 nm. As for the mixture samples of donor and recipient, each 4 mL suspension was mixed in the 50 mL tube. For the donor and recipient samples, the 4 mL of each culture was mixed with another 4 mL CF buffer in 50 mL tube. The concentration of the cations was set to 0 μM or 400 μM (CaCl2 and MgSO4), respectively. The mating duration was 24 h.


title: PF-KT_PF_without_cation_2


title: PF-KT_PF_with_cation_1

source_name: cDNA prepared from Pf0-1(pCAR1) and KT2440 incubated in CF buffer with cation


title: PF_PF_without_cation_1

organism: Pseudomonas fluorescens Pf0-1

source_name: cDNA prepared from Pf0-1(pCAR1) incubated in CF buffer without cation


title: PF_PF_without_cation_2


title: PF_PF_with_cation_2

source_name: cDNA prepared from Pf0-1(pCAR1) incubated in CF buffer with cation


title: PF_PF_with_cation_1


title: PF-KT_PF_with_cation_2


title: Organoids_3


title: Stroma_1

value: Donor 1


title: Glands_1


title: Organoids_1


title: Stroma_2

value: Donor 2


title: Glands_3


title: Glands_2


title: TH17(beta)_WT_rep2

city: Onna-son,Kunigami-gun

first: Hiroki

last: Ishikawa

address: 1919-1 Tancha

institute: Okinawa Institute of Science and Technology Graduate University

hyb_protocol: Frangmented and labeled ss-cDNA  were hybridized for 16 hr at 45°C on GeneChip Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G from Affymetrix using AGCC scan control software ver 2.0.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label_protocol: Labled ss-cDNA was prepared using GeneChIP WT Plus reagent kit and GeneChip Hybridization, wash and stain kit (Affymetrix)., according to the instructions.

growth_protocol: CD4+ T cells from single cell suspensions of murine spleens and lymph nodes were enriched using a MACS magnetic cell sorting system with anti-CD4 microbeads (Miltenyi). Then naive CD4+ T cells (CD4+CD25-CD62LhiCD44lo) were sorted by FACS AriaII or AriaIII (BD). Cells were activated with plate bound anti-CD3 antibody (Biolegend) and soluble anti-CD28 antibody (Biolegend) in IMDM media (Invitrogen) supplemented with 10% Fetal calf serum (FCS) (Invitrogen) containing the following cytokines and antibodies:  IL-2 (20 ng/mL), anti-IFNγ (1  μg/mL) and anti-IL-4 (1 μg/mL) for TH0; IL-6 (20 ng/mL) and TGF-β (3 ng/mL) for TH17(β); IL-6 (20 ng/mL), IL-1β (20 ng/mL) and IL-23 (40 ng/mL) for TH17(23) differentiation.

extract_protocol: Total RNA was isolated from cells using an RNeasy Mini Plus kit (Qiagen).

tag: genotype/variation


title: TH17(23)_KO_rep2


title: TH17(23)_WT_rep2


title: TH17(23)_WT_rep1


title: TH0_KO_rep2


title: TH17(23)_KO_rep1


title: TH17(beta)_KO_rep1


title: TH0_KO_rep1


title: TH17(beta)_WT_rep1


title: SS-Group-2 SGEC line S4

city: ATHENS

first: Menelaos

middle: N.

last: Manoussakis

address: 75 MIKRAS ASIAS STR

department: Pathophysiology

country: Greece

institute: National and Kapodistrian University of Athens

description: SS-Group-2 SGEC line S4

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HuGene-1_0-st-v1. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: RMA normalization was performed with R/Bioconductor

source_name: Minor salivary gland biopsy  with heavy mononuclear infiltrations (focus score ≥2)

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

growth_protocol: Non-neoplastic secondary SGEC lines were established from minor salivary gland tissues by the explant outgrowth technique. Cell were maintained in serum-free keratinocyte basal medium supplemented with EGF, as previously described (Dimitriou et al, Eur J Oral Sci, 2002, 110:21-30).

extract_protocol: Total RNA was extracted with the RNeasy mini kit (Qiagen)

treatment_protocol: All SGEC lines studied were untreated.

tag: disease

value: Patient with primary Sjögren’s syndrome

tag: gender

value: Female

value: Long-term cultured non-neoplastic secondary salivary gland epithelial cell (SGEC) line of ductal type


title: TH17(beta)_KO_rep2


title: TH0_WT_rep1


title: 10µM_Nimodipine_treated_N9_cells

city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

country: Germany

institute: University Hospital Würzburg

hyb_protocol: 130µl hybridization mix prepared from labeled ssDNA was hybridized for 17h at 45°C to GeneChip Mouse Gene 2.0 ST arrays. Microarrays were washed and stained in the Affymetrix Fluidics Station 450 using script FS450_002.

scan_protocol: Microarrays were scanned using a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Data were preprocessed with the Expression Console v1.2.1.20 software (Affymetrix); background correction, nomalization and gene-level probeset summary were performed with the RMA sketch workflow using default parameter settings.

source_name: micoglial cell line N9

label_protocol: 100ng total RNA from each sample was processed with the WT PLUS reagent kit (Affymetrix, Santa Clara, CA) following the manufacturer's protocol.

growth_protocol: DMEM medium containing 10% FBS,), penicillin (100 IU/ml) streptomycin (100 mg/ml); maintained at 37 °C and 3.5% CO2

extract_protocol: Total RNA was isolated from homogenized murine tissue or murine N9 cell pellets by the use of TRIzol (15596018 Invitrogen Life Technologies) for 5 min. Afterwards chlorophorm was added to the lysate and centrifuged at 13.000 g at 4°C for 15 min. The supernatant was precipitated by isopropanol at room temperature for 10 min. Subsequently, ethanol was added to the RNA pellet, mixed well and centrifuged at 7500 g and 4 °C for 5 min. The pellet was dried and resuspended in DEPC water, stored at -80 °C for at least 1 h and quantified. The concentration of each RNA extract was determined by spectrophotometric measurement using a Nanodrop 2000c spectrophotometer (Thermo Fisher Scientific).

treatment_protocol: treatment with either 10µM nimodipine or 20µM nimodipine and respective veicle solution

tag: group

value: treated

tag: treatment

value: 10µM Nimodipine


title: TH0_WT_rep2


title: SS-Group-2 SGEC line S2

description: SS-Group-2 SGEC line S2


title: SS-Group-2 SGEC line S3

description: SS-Group-2 SGEC line S3


title: 20µM_Nimodipine_treated_N9_cells

value: 20µM Nimodipine


title: SS-Group-2 SGEC line S5

description: SS-Group-2 SGEC line S5


title: SS-Group-2 SGEC line S6

description: SS-Group-2 SGEC line S6


title: SS-Group-2 SGEC line S1

description: SS-Group-2 SGEC line S1


title: Organoids_2

tag: tissue

value: Endometrial organoids


title: vehicle_treated_N9_cells_1

value: control

value: vehicle


title: Non-SS Control-SGEC line C3

description: Non-SS Control-SGEC line C3

source_name: Minor salivary gland biopsy without mononuclear infiltrates

value: Sicca patient without clinical or laboratory evidence of Sjögren’s syndrome


title: SS-Group-1 SGEC line M1

description: SS-Group-1 SGEC line M1

source_name: Minor salivary gland biopsy with moderate lymphocytic infiltrations (focus score>1 and <2)


title: Non-SS Control-SGEC line C2

description: Non-SS Control-SGEC line C2


title: Non-SS Control-SGEC line C1

description: Non-SS Control-SGEC line C1


title: vehicle_treated_N9_cells_2


title: SS-Group-1 SGEC line M3

description: SS-Group-1 SGEC line M3


title: SS-Group-1 SGEC line M2

description: SS-Group-1 SGEC line M2


title: CML progenitor cells at 48hrs without IM, biological rep5

city: Mexico City

first: Sócrates

last: Avilés-Vázquez

state: México City

address: Av, Cuauhtemoc 330 Col Doctores Oncology Hospital 3rd Floor

country: Mexico

institute: IMSS

description: gene expression data of chronic myeloid leukemia progenitor cells isolated by flow cytometry using CD34 and CD38 markers after 48 hrs of culture without imatinib

hyb_protocol: Hybridization was performed at 60 rpm for 16 h at 45°C. Wash and stain processes were performed with the Genechip Expression Wash and Stain Kit in the GeneChip Fluidics Station 450 (Affymetrix, Santa Clara CA, USA).

scan_protocol: The arrays were scanned using the GeneChip Scanner 3000 7G and Affymetrix GeneChip Command Console Software (AGCC) (Affymetrix, Santa Clara CA, USA)

data_processing: Affymetrix Expression Console was used to process the original .CEL files. The .chp files were generated using the RMA-sketch workflow after signal summarization (Median polish) and data normalization (Sketch-Quantile method). Gene level analysis was further conducted with Affymetrix Transcriptome Analysis Console software.

source_name: chronic myeloid leukemia progenitor cells CD34+CD38+lin- at 48hrs cultured without IM

label_protocol: Fifteen μg of cRNA were input into the second cycle cDNA reaction. 5.5 μg of ss-cDNA were input for fragmentation. Each DNA fragment was end labeled with biotin using terminal deoxynucleotidyl transferase before being hybridized to the arrays.

growth_protocol: Mononuclear cells were isolated from bone marrow samples using Ficoll Paque Plus (GE Healthcare Life Sciences)-based gradients. CD34+lin- cells were enriched using the StemSep Human Hematopoietic Progenitor Cell Enrichment Kit (Stem Cell Technologies, Vancouver, Canada), according to the manufacturer’s instructions. The enriched cells were collected in StemSpan medium, stained with CD34-FITC and CD38-APC antibodies (eBioscience, San Diego, CA, USA), and sorted using a BD FACSAria (BD Biosciences, San Jose. CA, USA) into hematopoietic progenitor (CD34+CD38+Lin-; HPCs) and stem (CD34+CD38-Lin-; HSCs) cells

extract_protocol: Total RNA was extracted with Trizol (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions

treatment_protocol: Progenitor cells were cultured for 48 hrs in StemSpan Serum-Free Expansion Media (Stem Cell Technologies, Vancouver, Canada) supplemented with the following cytokines: Erythropoietin (EPO); Thrombopoietin (TPO); Flt-3-ligand (Flt-3L); Stem Cell Factor (SCF); Interleukin-6 (IL6); IL3; Granulocyte Colony-stimulating Factor (G-CSF); and Granulocyte-Macrophage CSF (GM-CSF) with or without 2.5 µM IM (Gleevec, Novartis Pharmaceuticals).

value: chronic myeloid leukemia bone marrow in chronic phase


title: NBM progenitor cells at T0, biological rep3

description: gene expression data of normal bone marrow progenitor cells at T0 isolated by flow cytometry using CD34 and CD38 markers

source_name: normal bone marrow progenitor cells CD34+CD38+lin- at T0

value: normal bone marrow from hip sugery of healthy subjects


title: NBM progenitor cells at 48hrs without IM, biological rep2

description: gene expression data of normal bone marrow progenitor cells isolated by flow cytometry using CD34 and CD38 markers after 48 hrs of culture without imatinib

source_name: normal bone marrow progenitor cells CD34+CD38+lin- at 48hrs cultured without IM


title: NBM progenitor cells at 48hrs without IM, biological rep5


title: CML progenitor cells at 48hrs without IM, biological rep3


title: NBM progenitor cells at 48hrs with IM, biological rep2

description: gene expression data of normal bone marrow progenitor cells isolated by flow cytometry using CD34 and CD38 markers after 48 hrs of culture with imatinib

source_name: normal bone marrow progenitor cells CD34+CD38+lin- at 48hrs cultured with IM


title: NBM progenitor cells at 48hrs with IM, biological rep4


title: NBM progenitor cells at T0, biological rep4


title: NBM progenitor cells at 48hrs with IM, biological rep5


title: CML progenitor cells at 48hrs with IM, biological rep1

description: gene expression data of chronic myeloid leukemia progenitor cells isolated by flow cytometry using CD34 and CD38 markers after 48 hrs of culture with imatinib

source_name: chronic myeloid leukemia progenitor cells CD34+CD38+lin- at 48hrs cultured with IM


title: NBM progenitor cells at 48hrs with IM, biological rep3


title: NBM progenitor cells at 48hrs without IM, biological rep1


title: CML progenitor cells at 48hrs with IM, biological rep3


title: CML progenitor cells at 48hrs without IM, biological rep4


title: CML progenitor cells at 48hrs with IM, biological rep2


title: CML progenitor cells at 48hrs without IM, biological rep2


title: CML progenitor cells at 48hrs with IM, biological rep4


title: NBM progenitor cells at 48hrs without IM, biological rep4


title: NBM progenitor cells at 48hrs with IM, biological rep1


title: CML progenitor cells at 48hrs without IM, biological rep1


title: NBM progenitor cells at 48hrs without IM, biological rep3


title: CML progenitor cells at 48hrs with IM, biological rep5


title: NBM progenitor cells at T0, biological rep5


title: NBM progenitor cells at T0, biological rep2


title: NBM progenitor cells at T0, biological rep1


title: CML progenitor cells at T0, biological rep3

description: gene expression data of chronic myeloid leukemia progenitor cells at T0 isolated by flow cytometry using CD34 and CD38 markers

source_name: chronic myeloid leukemia progenitor cells CD34+CD38+lin- at T0


title: CML progenitor cells at T0, biological rep4


title: CML progenitor cells at T0, biological rep5


title: CML progenitor cells at T0, biological rep1


title: CML progenitor cells at T0, biological rep2


title: NBM stem cells at T0, biological rep3

description: gene expression data of normal bone marrow stem cells at T0 isolated by flow cytometry using CD34 and CD38 markers

source_name: normal bone marrow stem cells CD34+CD38-lin- at T0


title: NBM stem cells at T0, biological rep5


title: CML stem cells at T0, biological rep1

description: gene expression data of chronic myeloid leukemia stem cells at T0 isolated by flow cytometry using CD34 and CD38 markers

source_name: chronic myeloid leukemia stem cells CD34+CD38-lin- at T0


title: CD14 MM17

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

institute: IRCCS Istituto Nazionale dei Tumori

description: Gene expression profiling data of CD14+ cells from bone marrow of MM patient 17

hyb_protocol: Following fragmentation, 15 micrograms of cRNA were hybridized for 16 hr  at 45°C on GeneChip HG-U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: HG-U133 2.0 Plus arrays were scanned using the Scanner G3000 7G (Affymetrix).

data_processing: The probe-level signals were converted to expression values using the Bioconductor function for Robust Multi-array Analysis (RMA), in which perfect match intensities are background adjusted, normalized by means of quantile-quantile normalization and log2-transformed.

source_name: Bone marrow CD14+ cells from MM patient 17

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

growth_protocol: CD14+ cells from bone marrow of 8 MGUS, 11 SMM and 16 MM patients. The CD14+ cell fraction was obtained by immunomagnetic cells sorting using anti-CD14 monoclonal antibody-coated microbeads (MACS, Miltenyi Biotec., Bergish-Gladbach, Germany). Samples with a purity of more than 90%, tested via flow-cytometry (BD biosciences, San Josè, CA) were analyzed. These samples were evaluated immediately after purification.

extract_protocol: Total RNA was extracted from CD14+ cells with Rneasy Mini Kit (Qiagen, Valencia, CA)

treatment_protocol: No treatment was applied to CD14+ cells.

value: bone marrow

value: 84 years


title: CD14 MM18

description: Gene expression profiling data of CD14+ cells from bone marrow of MM patient 18

source_name: Bone marrow CD14+ cells from MM patient 18

value: 86 years


title: NBM stem cells at T0, biological rep4


title: CD14 MM19

description: Gene expression profiling data of CD14+ cells from bone marrow of MM patient 19

source_name: Bone marrow CD14+ cells from MM patient 19

value: 73 years


title: CML stem cells at T0, biological rep5


title: CML stem cells at T0, biological rep2


title: CD14 SMM12

description: Gene expression profiling data of CD14+ cells from bone marrow of SMM patient 12

source_name: Bone marrow CD14+ cells from SMM patient 12

value: 83 years


title: CD14 MGUS9

description: Gene expression profiling data of CD14+ cells from bone marrow of MGUS patient 9

source_name: Bone marrow CD14+ cells from MGUS patient 9

value: 50 years


title: CD14 MM20

description: Gene expression profiling data of CD14+ cells from bone marrow of MM patient 20

source_name: Bone marrow CD14+ cells from MM patient 20

value: 56 years


title: CD14 MM22

description: Gene expression profiling data of CD14+ cells from bone marrow of MM patient 22

source_name: Bone marrow CD14+ cells from MM patient 22

value: 75 years


title: CD14 MM21

description: Gene expression profiling data of CD14+ cells from bone marrow of MM patient 21

source_name: Bone marrow CD14+ cells from MM patient 21


title: CML stem cells at T0, biological rep3


title: CML stem cells at T0, biological rep4


title: CD14 MM23

description: Gene expression profiling data of CD14+ cells from bone marrow of MM patient 23

source_name: Bone marrow CD14+ cells from MM patient 23

value: 77 years


title: CD14 SMM13

description: Gene expression profiling data of CD14+ cells from bone marrow of SMM patient 13

source_name: Bone marrow CD14+ cells from SMM patient 13

value: 47 years


title: CD14 SMM14

description: Gene expression profiling data of CD14+ cells from bone marrow of SMM patient 14

source_name: Bone marrow CD14+ cells from SMM patient 14

value: 41 years


title: CD14 SMM15

description: Gene expression profiling data of CD14+ cells from bone marrow of SMM patient 15

source_name: Bone marrow CD14+ cells from SMM patient 15

value: 65 years


title: White Pupa Centralbrain_DIP2 knockdown_rep2

city: Asahimachidori, Chuo-ku, Niigata-shi

first: Yohei

last: Nitta

state: Niigata

address: 757, Ichibancho,

institute: Niigata University

description: Gene expression profiles of DIP2 knockdown at 24hrs APF

hyb_protocol: 1.65 µg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 ml containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ml of 2x GE Hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Drosophila Gene Expression Microarrays (G2519F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with Agilent Gene Expression Wash Buffer 1 (Agilent) and 1 minute with 37°C Agilent Gene Expression Wash Buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: The arrays were scanned using an Agilent G2565CA Microarray scanner (Agilent Technologies).

data_processing: Images were quantified using Feature Extraction 10.5.1.1 (Agilent Technologies). To identify candidate genes (p<0.05) whose expression levels were altered in the DIP2 RNAi brains, the data were analyzed using R statistical software (R core team).

organism: Drosophila melanogaster

source_name: OK107-Gal4/UAS-dicer2;DIP2-IR, DIP2 knockdown, white pupa, replicate 2

label_protocol: First strand synthesis and amplification of Cy3-labeled RNA were performed using an Agilent Low-Input QuickAmp Labeling Kit (Agilent Technologies), followed by RNeasy mini kit purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Experimental flies were raised at 29 °C

extract_protocol: The total RNA was extracted from the central brains using an RNeasy Purification Kit (QIAGEN). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Experion (BIO-RAD).

value: central brain

value: female

tag: Stage

value: white pupa


title: White Pupa Centralbrain_Control_rep1

description: Gene expression profiles of control at 24hrs APF

source_name: OK107-Gal4/UAS-dicer2, control, white pupa, replicate 1


title: White Pupa Centralbrain_Control_rep3

source_name: OK107-Gal4/UAS-dicer2, control, white pupa, replicate 3


title: CD14 MM16

description: Gene expression profiling data of CD14+ cells from bone marrow of MM patient 16

source_name: Bone marrow CD14+ cells from MM patient 16

value: 70 years


title: White Pupa Centralbrain_DIP2 knockdown_rep3

source_name: OK107-Gal4/UAS-dicer2;DIP2-IR, DIP2 knockdown, white pupa, replicate 3


title: White Pupa Centralbrain_DIP2 knockdown_rep1

source_name: OK107-Gal4/UAS-dicer2;DIP2-IR, DIP2 knockdown, white pupa, replicate 1


title: CD14 MM15

description: Gene expression profiling data of CD14+ cells from bone marrow of MM patient 15

source_name: Bone marrow CD14+ cells from MM patient 15


title: White Pupa Centralbrain_Control_rep2

source_name: OK107-Gal4/UAS-dicer2, control, white pupa, replicate 2


title: PF-KT_pCAR1_with_cation_2

description: This is an Affymetrix custom-commercial tiling array that covers the IncP-7 carbazole-degradative plasmid pCAR1  (RefSeq: NC_004444) at 9-bp density. BPMAP files are provided as supplementary files. pCAR1_8b520435FR-3.bpmap represents  the forward strand of pCAR1, and pCAR1_8b520435FF-3.bpmap represents the reverse strand of pCAR1.

hyb_protocol: The labelled samples were hybridized individually with each chip using a GeneChip Hybridization Oven 640 (Affymetrix) at 60 rpm and 45°C for 16 h. The chips were then washed and stained using a Hybridization, Wash and Stain Kit (Affymetrix) according to the FlexFS450-0002 protocol of the GeneChip Fluidics station 450 (Affymetrix)

data_processing: The CEL files were generated using Affymetrix GCOS. Data was quantile normalized and analyzed with Affymetrix Tiling Analysis Software v1.1, which uses non-parametric quantile normalization and a Hodges-Lehmann estimator for fold enrichment.The intensities were linearly scaled so that the median was 100. Each CEL file was converted into the BAR files using pCAR1_8b520435FR-3.bpmap for the forward strand and pCAR1_8b520435FF-3.bpmap for the reverse strand; the BAR files with F indicate the forward strand and with R indicate the reverse strand of pCAR1. Bandwidth: 30, Threshold: 0, MaxGap: 30, MinRun, 30.

source_name: cDNA prepared from Pf0-1(pCAR1) and KT2440 incubated in CF buffer with cation

tag: strain


title: PF-KT_pCAR1_with_cation_1


title: PF-KT_pCAR1_without_cation_2

source_name: cDNA prepared from Pf0-1(pCAR1) and KT2440 incubated in CF buffer without cation


title: CD14 MM8

description: Gene expression profiling data of CD14+ cells from bone marrow of MM patient 8

source_name: Bone marrow CD14+ cells from MM patient 8

tag: age

value: 79 years


title: 29 deg C Centralbrain_DIP2 knockdown_rep2

growth_protocol: Experimental flies were raised at 29°C

value: 24hrs APF


title: 29 deg C Centralbrain_Control_rep2


title: CD14 MM14

description: Gene expression profiling data of CD14+ cells from bone marrow of MM patient 14

source_name: Bone marrow CD14+ cells from MM patient 14

value: bone marrow

value: 74 years


title: CD14 MM9

description: Gene expression profiling data of CD14+ cells from bone marrow of MM patient 9

source_name: Bone marrow CD14+ cells from MM patient 9

value: 57 years


title: 25 deg C Centralbrain_DIP2 knockdown_rep3

data_processing: Images were quantified using Feature Extraction 10.5.1.1 (Agilent Technologies). To identify candidate genes (p<0.05) whose expression levels were altered in the DIP2 RNAi brains, the data were analyzed using R statistical software (R core team)

growth_protocol: Experimental flies were raised at 25°C


title: 29 deg C Centralbrain_Control_rep1


title: CD14 MM7

description: Gene expression profiling data of CD14+ cells from bone marrow of MM patient 7

source_name: Bone marrow CD14+ cells from MM patient 7

value: 69 years


title: CD14 MM10

description: Gene expression profiling data of CD14+ cells from bone marrow of MM patient 10

source_name: Bone marrow CD14+ cells from MM patient 10

value: 71 years


title: CD14 MM11

description: Gene expression profiling data of CD14+ cells from bone marrow of MM patient 11

source_name: Bone marrow CD14+ cells from MM patient 11

value: 60 years


title: CD14 MM1

description: Gene expression profiling data of CD14+ cells from bone marrow of MM patient 1

source_name: Bone marrow CD14+ cells from MM patient 1

value: 83 years


title: CD14 MM13

description: Gene expression profiling data of CD14+ cells from bone marrow of MM patient 13

source_name: Bone marrow CD14+ cells from MM patient 13

value: 73 years


title: CD14 MM4

description: Gene expression profiling data of CD14+ cells from bone marrow of MM patient 4

source_name: Bone marrow CD14+ cells from MM patient 4

value: 80 years


title: CD14 MM6

description: Gene expression profiling data of CD14+ cells from bone marrow of MM patient 6

source_name: Bone marrow CD14+ cells from MM patient 6


title: CD14 MM2

description: Gene expression profiling data of CD14+ cells from bone marrow of MM patient 2

source_name: Bone marrow CD14+ cells from MM patient 2

value: 75 years


title: CD14 MM12

description: Gene expression profiling data of CD14+ cells from bone marrow of MM patient 12

source_name: Bone marrow CD14+ cells from MM patient 12

value: 78 years


title: CD14 MM3

description: Gene expression profiling data of CD14+ cells from bone marrow of MM patient 3

source_name: Bone marrow CD14+ cells from MM patient 3

value: 59 years


title: 25 deg C Centralbrain_Control_rep2

description: Gene expression profiles of control at 24hrs APF

value: central brain

value: female


title: CD14 MM5

description: Gene expression profiling data of CD14+ cells from bone marrow of MM patient 5

source_name: Bone marrow CD14+ cells from MM patient 5

value: 76 years


title: 25 deg C Centralbrain_Control_rep3

source_name: OK107-Gal4/UAS-dicer2, control, white pupa, replicate 3


title: 25 deg C Centralbrain_Control_rep1

source_name: OK107-Gal4/UAS-dicer2, control, white pupa, replicate 1


title: 25 deg C Centralbrain_DIP2 knockdown_rep2

description: Gene expression profiles of DIP2 knockdown at 24hrs APF

source_name: OK107-Gal4/UAS-dicer2;DIP2-IR, DIP2 knockdown, white pupa, replicate 2


title: 25 deg C Centralbrain_DIP2 knockdown_rep1

source_name: OK107-Gal4/UAS-dicer2;DIP2-IR, DIP2 knockdown, white pupa, replicate 1


title: 29 deg C Centralbrain_DIP2 knockdown_rep1


title: PF-KT_pCAR1_without_cation_1

description: This is an Affymetrix custom-commercial tiling array that covers the IncP-7 carbazole-degradative plasmid pCAR1  (RefSeq: NC_004444) at 9-bp density. BPMAP files are provided as supplementary files. pCAR1_8b520435FR-3.bpmap represents  the forward strand of pCAR1, and pCAR1_8b520435FF-3.bpmap represents the reverse strand of pCAR1.

source_name: cDNA prepared from Pf0-1(pCAR1) and KT2440 incubated in CF buffer without cation


title: PF_pCAR1_without_cation_2

source_name: cDNA prepared from Pf0-1(pCAR1) incubated in CF buffer without cation


title: PF_pCAR1_without_cation_1


title: PF_pCAR1_with_cation_1

source_name: cDNA prepared from Pf0-1(pCAR1) incubated in CF buffer with cation


title: PF_pCAR1_with_cation_2


title: PF-KT_KT_without_cation_2

description: This is an Affymetrix custom-commercial tiling array that covers the Pseudomonas putida KT2440 chromosome (RefSeq: NC_002947) at 11-bp density.  BPMAP files are provided as supplementary files. KT2440b520511FR-3.bpmap represents  the forward strand of KT2440 chromosome, and KT2440b520511FF-3.bpmap represents the reverse strand of KT2440 chromosome.

data_processing: The CEL files were generated using Affymetrix GCOS. Data was quantile normalized and analyzed with Affymetrix Tiling Analysis Software v1.1, which uses non-parametric quantile normalization and a Hodges-Lehmann estimator for fold enrichment.The intensities were linearly scaled so that the median was 100. Each CEL file was converted into the BAR files using KT2440b520511FR-3.bpmap for the forward strand and KT2440b520511FF-3.bpmap for the reverse strand; the BAR files with F indicate the forward strand and with R indicate the reverse strand of KT2440 chromosome. Bandwidth: 30, Threshold: 0, MaxGap: 30, MinRun, 30.


title: CD14 SMM11

description: Gene expression profiling data of CD14+ cells from bone marrow of SMM patient 11

source_name: Bone marrow CD14+ cells from SMM patient 11


title: PF-KT_KT_with_cation_2

source_name: cDNA prepared from Pf0-1(pCAR1) and KT2440 incubated in CF buffer with cation


title: CD14 SMM9

description: Gene expression profiling data of CD14+ cells from bone marrow of SMM patient 9

source_name: Bone marrow CD14+ cells from SMM patient 9

value: 70 years


title: PF-KT_KT_without_cation_1


title: CD14 SMM8

description: Gene expression profiling data of CD14+ cells from bone marrow of SMM patient 8

source_name: Bone marrow CD14+ cells from SMM patient 8

value: 56 years


title: PF-KT_KT_with_cation_1


title: CD14 SMM10

description: Gene expression profiling data of CD14+ cells from bone marrow of SMM patient 10

source_name: Bone marrow CD14+ cells from SMM patient 10

value: bone marrow

value: 67 years


title: KT_KT_without_cation_2

organism: Pseudomonas putida KT2440

source_name: cDNA prepared from KT2440 incubated in CF buffer without cation


title: CD14 SMM6

description: Gene expression profiling data of CD14+ cells from bone marrow of SMM patient 6

source_name: Bone marrow CD14+ cells from SMM patient 6

value: 51 years


title: KT_KT_with_cation_1

source_name: cDNA prepared from KT2440 incubated in CF buffer with cation


title: CD14 MGUS7

description: Gene expression profiling data of CD14+ cells from bone marrow of MGUS patient 7

source_name: Bone marrow CD14+ cells from MGUS patient 7

value: 43 years


title: CD14 SMM5

description: Gene expression profiling data of CD14+ cells from bone marrow of SMM patient 5

source_name: Bone marrow CD14+ cells from SMM patient 5

value: 64 years


title: CD14 MGUS8

description: Gene expression profiling data of CD14+ cells from bone marrow of MGUS patient 8

source_name: Bone marrow CD14+ cells from MGUS patient 8

value: 91 years


title: CD14 SMM1

description: Gene expression profiling data of CD14+ cells from bone marrow of SMM patient 1

source_name: Bone marrow CD14+ cells from SMM patient 1


title: CD14 SMM3

description: Gene expression profiling data of CD14+ cells from bone marrow of SMM patient 3

source_name: Bone marrow CD14+ cells from SMM patient 3

value: 58 years


title: CD14 MGUS6

description: Gene expression profiling data of CD14+ cells from bone marrow of MGUS patient 6

source_name: Bone marrow CD14+ cells from MGUS patient 6


title: CD14 SMM2

description: Gene expression profiling data of CD14+ cells from bone marrow of SMM patient 2

source_name: Bone marrow CD14+ cells from SMM patient 2

value: 72 years


title: CD14 SMM7

description: Gene expression profiling data of CD14+ cells from bone marrow of SMM patient 7

source_name: Bone marrow CD14+ cells from SMM patient 7

value: 55 years


title: CD14 MGUS3

description: Gene expression profiling data of CD14+ cells from bone marrow of MGUS patient 3

source_name: Bone marrow CD14+ cells from MGUS patient 3

value: 42 years


title: KT_KT_without_cation_1


title: CD14 MGUS4

description: Gene expression profiling data of CD14+ cells from bone marrow of MGUS patient 4

source_name: Bone marrow CD14+ cells from MGUS patient 4

value: 78 years


title: KT_KT_with_cation_2


title: CD14 SMM4

description: Gene expression profiling data of CD14+ cells from bone marrow of SMM patient 4

source_name: Bone marrow CD14+ cells from SMM patient 4


title: CD14 MGUS2

description: Gene expression profiling data of CD14+ cells from bone marrow of MGUS patient 2

source_name: Bone marrow CD14+ cells from MGUS patient 2

value: 52 years


title: CD14 MGUS5

description: Gene expression profiling data of CD14+ cells from bone marrow of MGUS patient 5

source_name: Bone marrow CD14+ cells from MGUS patient 5

value: 54 years


title: Wild Type_189

city: Chapel Hill

first: Scott

last: Bultman

state: NC

department: Department of Pathology and Laboratory Medicine; Department of Genetics

institute: University of North Carolina at Chapel Hill

hyb_protocol: Agilent's Hybridization Oven set at 65C, Add Cy3 labeled cRNA, gene expression blocking agent and fragmentation buffer. Incubate. Add HI-RPM Hybridization buffer to stop reaction. Use hybridization chamber , slides with barcodes,. Load samples and hybridize rotating in chamber 17 hrs. Wash in 2 buffers, and then Milli Q water wash

scan_protocol: Agilent C Microarray Scanner, Feature Extraction software 10.7.1 or later, Agilent Scan Control software.

data_processing: Agilent feature extraction software.

source_name: heart NTg + Tamoxifen

label_protocol: Agilent Low Input Quick Amp Labeling Protocol for Cy3 labeling. In tube add RNA, spike mix and T7 primer. Denature. Add cDNA master mix including Affinity Script RNAse Block Mix. Incubate. Add Transcription master mix including T7 RNA Polymerase blend and incubate, then purify labeled/amplified RNA & quantify.

extract_protocol: Norgen #25700 Animal Tissue RNA Purification Kit following manufacturers specifications.

value: Wild Type

value: adult

value: female

value: cardiomyocytes


title: Mutant_188

source_name: heart Tg + Tamoxifen

value: Brg1 and Brm knockout


title: Wild Type_176


title: Mutant_175


title: Mutant_182


title: Wild Type_183


title: Mutant_187


title: Wild Type_181


title: CD14 MGUS1

description: Gene expression profiling data of CD14+ cells from bone marrow of MGUS patient 1

source_name: Bone marrow CD14+ cells from MGUS patient 1

value: bone marrow


title: NBM stem cells at T0, biological rep2

description: gene expression data of normal bone marrow stem cells at T0 isolated by flow cytometry using CD34 and CD38 markers

source_name: normal bone marrow stem cells CD34+CD38-lin- at T0

value: normal bone marrow from hip sugery of healthy subjects


title: NBM stem cells at T0, biological rep1


title: AML Patient A253_T Diagnostic

status: Public on Apr 10 2017

city: Philadelphia, PA

first: Richard

last: Aplenc

state: PA

address: 3501 Civic Center Blvd

department: Division of Oncology

institute: Children's Hospital of Philadelphia

description: hybridized to Genome-Wide Human SNP 6.0 Array

hyb_protocol: Samples were hybridized for 16-18 hr and washed and stained on the GeneChip fluidics station 450 using the appropriate fluidics protocol.

scan_protocol: The arrays were inserted into the Affymetrix autoloader carousel and scanned using the GeneChip Scanner 3000 7G.

data_processing: Genotyping Console 3.02 was used for data processing and GeneChip quality control. Data quality control and data analysis was performed using Partek GS 6.4.  SNP calls were made using Birdseed V-2.  Copy number calls of SNP 6.0  data were determined using R package ASCAT (van Loo et al, PNAS 2010).

source_name: AML Patient A253 Diagnostic

label_protocol: Samples were end labeled using terminal deoxynucleotidyl transferase according to the Affymetrix protocol.

extract_protocol: Genomic DNA was isolated with phenol extraction according to the standard protocol (Sambrook, J., Fritsch, E. F. & Maniatis, T. Molecular cloning; a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 1989).

tag: disease state

value: AML

tag: individual

value: Patient A253

value: Bone Marrow

tag: patient status

value: Diagnostic


title: AML Patient A254_N Remission

source_name: AML Patient A254 Remission

value: Patient A254

value: Remission


title: AML Patient A247_T Diagnostic

source_name: AML Patient A247 Diagnostic

value: Patient A247


title: AML Patient A251_T Diagnostic

source_name: AML Patient A251 Diagnostic

value: Patient A251


title: AML Patient A253_N Remission

source_name: AML Patient A253 Remission


title: AML Patient A248_T Diagnostic

source_name: AML Patient A248 Diagnostic

value: Patient A248


title: AML Patient A243_T Diagnostic

source_name: AML Patient A243 Diagnostic

value: Patient A243


title: AML Patient A249_T Diagnostic

source_name: AML Patient A249 Diagnostic

value: Patient A249


title: AML Patient A249_N Remission

source_name: AML Patient A249 Remission


title: AML Patient A254_T Diagnostic

source_name: AML Patient A254 Diagnostic


title: AML Patient A244_T Diagnostic

source_name: AML Patient A244 Diagnostic

value: Patient A244


title: AML Patient A245_N Remission

source_name: AML Patient A245 Remission

value: Patient A245


title: AML Patient A246_N Remission

source_name: AML Patient A246 Remission

value: Patient A246


title: AML Patient A244_N Remission

source_name: AML Patient A244 Remission


title: AML Patient A243_N Remission

source_name: AML Patient A243 Remission


title: AML Patient A240_T Diagnostic

source_name: AML Patient A240 Diagnostic

value: Patient A240


title: AML Patient A242_N Remission

source_name: AML Patient A242 Remission

value: Patient A242


title: AML Patient A250_N Remission

source_name: AML Patient A250 Remission

value: Patient A250


title: AML Patient A245_T Diagnostic

source_name: AML Patient A245 Diagnostic

value: AML


title: AML Patient A241_T Diagnostic

source_name: AML Patient A241 Diagnostic

value: Patient A241


title: AML Patient A252_T Diagnostic

source_name: AML Patient A252 Diagnostic

value: Patient A252

value: Bone Marrow


title: AML Patient A247_N Remission

source_name: AML Patient A247 Remission


title: AML Patient A242_T Diagnostic

source_name: AML Patient A242 Diagnostic

value: Diagnostic


title: AML Patient A246_T Diagnostic

source_name: AML Patient A246 Diagnostic


title: AML Patient A250_T Diagnostic

source_name: AML Patient A250 Diagnostic


title: AML Patient A252_N Remission

source_name: AML Patient A252 Remission

value: Remission


title: AML Patient A251_N Remission

source_name: AML Patient A251 Remission


title: AML Patient A240_N Remission

source_name: AML Patient A240 Remission


title: AML Patient A248_N Remission

source_name: AML Patient A248 Remission


title: AML Patient A241_N Remission

source_name: AML Patient A241 Remission


title: AML Patient A239_N Remission

source_name: AML Patient A239 Remission

value: Patient A239


title: AML Patient A237_N Remission

source_name: AML Patient A237 Remission

value: Patient A237


title: AML Patient A238_T Diagnostic

source_name: AML Patient A238 Diagnostic

value: Patient A238


title: AML Patient A239_T Diagnostic

source_name: AML Patient A239 Diagnostic


title: AML Patient A238_N Remission

source_name: AML Patient A238 Remission


title: AML Patient A236_T Diagnostic

source_name: AML Patient A236 Diagnostic

value: Patient A236


title: AML Patient A234_N Remission

source_name: AML Patient A234 Remission

value: Patient A234


title: AML Patient A226_N Remission

source_name: AML Patient A226 Remission

value: Patient A226


title: AML Patient A235_T Diagnostic

source_name: AML Patient A235 Diagnostic

value: Patient A235


title: AML Patient A233_N Remission

source_name: AML Patient A233 Remission

value: Patient A233


title: AML Patient A234_T Diagnostic

source_name: AML Patient A234 Diagnostic


title: AML Patient A231_T Diagnostic

source_name: AML Patient A231 Diagnostic

value: Patient A231


title: AML Patient A235_N Remission

source_name: AML Patient A235 Remission


title: AML Patient A237_T Diagnostic

source_name: AML Patient A237 Diagnostic


title: AML Patient A230_N Remission

source_name: AML Patient A230 Remission

value: Patient A230


title: AML Patient A227_T Diagnostic

source_name: AML Patient A227 Diagnostic

value: Patient A227


title: AML Patient A228_T Diagnostic

source_name: AML Patient A228 Diagnostic

value: AML

value: Patient A228


title: AML Patient A228_N Remission

source_name: AML Patient A228 Remission


title: AML Patient A231_N Remission

source_name: AML Patient A231 Remission


title: AML Patient A229_T Diagnostic

source_name: AML Patient A229 Diagnostic

value: Patient A229


title: AML Patient A230_T Diagnostic

source_name: AML Patient A230 Diagnostic

value: Bone Marrow


title: AML Patient A227_N Remission

source_name: AML Patient A227 Remission


title: AML Patient A232_N Remission

source_name: AML Patient A232 Remission

value: Patient A232


title: AML Patient A229_N Remission

source_name: AML Patient A229 Remission

value: Remission


title: AML Patient A226_T Diagnostic

source_name: AML Patient A226 Diagnostic

value: Diagnostic


title: AML Patient A232_T Diagnostic

source_name: AML Patient A232 Diagnostic


title: AML Patient A225_N Remission

source_name: AML Patient A225 Remission

value: Patient A225


title: AML Patient A233_T Diagnostic

source_name: AML Patient A233 Diagnostic


title: AML Patient A236_N Remission

source_name: AML Patient A236 Remission


title: AML Patient A225_T Diagnostic

source_name: AML Patient A225 Diagnostic


title: AML Patient A224_T Diagnostic

source_name: AML Patient A224 Diagnostic

value: Patient A224


title: AML Patient A224_N Remission

source_name: AML Patient A224 Remission


title: AML Patient A223_N Remission

source_name: AML Patient A223 Remission

value: Patient A223


title: AML Patient A220_T Diagnostic

source_name: AML Patient A220 Diagnostic

value: Patient A220


title: AML Patient A222_T Diagnostic

source_name: AML Patient A222 Diagnostic

value: Patient A222


title: AML Patient A222_N Remission

source_name: AML Patient A222 Remission


title: AML Patient A220_N Remission

source_name: AML Patient A220 Remission


title: AML Patient A219_N Remission

source_name: AML Patient A219 Remission

value: Patient A219


title: AML Patient A215_T Diagnostic

source_name: AML Patient A215 Diagnostic

value: Patient A215


title: AML Patient A221_N Remission

source_name: AML Patient A221 Remission

value: Patient A221


title: AML Patient A212_T Diagnostic

source_name: AML Patient A212 Diagnostic

value: Patient A212


title: AML Patient A213_T Diagnostic

source_name: AML Patient A213 Diagnostic

value: Patient A213


title: AML Patient A218_N Remission

source_name: AML Patient A218 Remission

value: AML

value: Patient A218


title: AML Patient A210_T Diagnostic

source_name: AML Patient A210 Diagnostic

value: Patient A210


title: AML Patient A217_N Remission

source_name: AML Patient A217 Remission

value: Patient A217

value: Bone Marrow


title: AML Patient A215_N Remission

source_name: AML Patient A215 Remission

value: Remission


title: AML Patient A213_N Remission

source_name: AML Patient A213 Remission


title: AML Patient A221_T Diagnostic

source_name: AML Patient A221 Diagnostic

value: Diagnostic


title: AML Patient A223_T Diagnostic

source_name: AML Patient A223 Diagnostic


title: AML Patient A211_T Diagnostic

source_name: AML Patient A211 Diagnostic

value: Patient A211


title: AML Patient A219_T Diagnostic

source_name: AML Patient A219 Diagnostic


title: AML Patient A210_N Remission

source_name: AML Patient A210 Remission


title: AML Patient A211_N Remission

source_name: AML Patient A211 Remission


title: AML Patient A214_N Remission

source_name: AML Patient A214 Remission

value: Patient A214


title: AML Patient A217_T Diagnostic

source_name: AML Patient A217 Diagnostic


title: AML Patient A218_T Diagnostic

source_name: AML Patient A218 Diagnostic


title: AML Patient A214_T Diagnostic

source_name: AML Patient A214 Diagnostic


title: AML Patient A216_N Remission

source_name: AML Patient A216 Remission

value: Patient A216


title: AML Patient A209_T Diagnostic

source_name: AML Patient A209 Diagnostic

value: Patient A209


title: AML Patient A209_N Remission

source_name: AML Patient A209 Remission


title: AML Patient A216_T Diagnostic

source_name: AML Patient A216 Diagnostic


title: AML Patient A208_T Diagnostic

source_name: AML Patient A208 Diagnostic

value: Patient A208


title: AML Patient A207_N Remission

source_name: AML Patient A207 Remission

value: Patient A207


title: AML Patient A212_N Remission

source_name: AML Patient A212 Remission


title: AML Patient A207_T Diagnostic

source_name: AML Patient A207 Diagnostic


title: AML Patient A206_T Diagnostic

source_name: AML Patient A206 Diagnostic

value: Patient A206


title: AML Patient A200_T Diagnostic

source_name: AML Patient A200 Diagnostic

value: Patient A200


title: AML Patient A206_N Remission

source_name: AML Patient A206 Remission


title: AML Patient A203_N Remission

source_name: AML Patient A203 Remission

value: Patient A203


title: AML Patient A203_T Diagnostic

source_name: AML Patient A203 Diagnostic


title: AML Patient A204_T Diagnostic

source_name: AML Patient A204 Diagnostic

value: Patient A204


title: AML Patient A200_N Remission

source_name: AML Patient A200 Remission

value: AML


title: AML Patient A208_N Remission

source_name: AML Patient A208 Remission


title: AML Patient A201_N Remission

source_name: AML Patient A201 Remission

value: Patient A201


title: AML Patient A205_T Diagnostic

source_name: AML Patient A205 Diagnostic

value: Patient A205


title: AML Patient A202_N Remission

source_name: AML Patient A202 Remission

value: Patient A202


title: AML Patient A202_T Diagnostic

source_name: AML Patient A202 Diagnostic

value: Bone Marrow


title: AML Patient A204_N Remission

source_name: AML Patient A204 Remission

value: Remission


title: AML Patient A199_N Remission

source_name: AML Patient A199 Remission

value: Patient A199


title: AML Patient A198_T Diagnostic

source_name: AML Patient A198 Diagnostic

value: Patient A198

value: Diagnostic


title: AML Patient A199_T Diagnostic

source_name: AML Patient A199 Diagnostic


title: AML Patient A201_T Diagnostic

source_name: AML Patient A201 Diagnostic


title: AML Patient A195_N Remission

source_name: AML Patient A195 Remission

value: Patient A195


title: AML Patient A196_T Diagnostic

source_name: AML Patient A196 Diagnostic

value: Patient A196


title: AML Patient A205_N Remission

source_name: AML Patient A205 Remission


title: AML Patient A195_T Diagnostic

source_name: AML Patient A195 Diagnostic


title: AML Patient A196_N Remission

source_name: AML Patient A196 Remission


title: AML Patient A194_N Remission

source_name: AML Patient A194 Remission

value: Patient A194


title: AML Patient A198_N Remission

source_name: AML Patient A198 Remission


title: AML Patient A197_N Remission

source_name: AML Patient A197 Remission

value: Patient A197


title: AML Patient A197_T Diagnostic

source_name: AML Patient A197 Diagnostic


title: AML Patient A192_T Diagnostic

source_name: AML Patient A192 Diagnostic

value: Patient A192


title: AML Patient A193_N Remission

source_name: AML Patient A193 Remission

value: Patient A193


title: AML Patient A193_T Diagnostic

source_name: AML Patient A193 Diagnostic


title: AML Patient A192_N Remission

source_name: AML Patient A192 Remission


title: AML Patient A194_T Diagnostic

source_name: AML Patient A194 Diagnostic


title: AML Patient A189_T Diagnostic

source_name: AML Patient A189 Diagnostic

value: Patient A189


title: AML Patient A183_T Diagnostic

source_name: AML Patient A183 Diagnostic

value: Patient A183


title: AML Patient A190_N Remission

source_name: AML Patient A190 Remission

value: AML

value: Patient A190


title: AML Patient A191_N Remission

source_name: AML Patient A191 Remission

value: Patient A191


title: AML Patient A189_N Remission

source_name: AML Patient A189 Remission


title: AML Patient A188_T Diagnostic

source_name: AML Patient A188 Diagnostic

value: Patient A188


title: AML Patient A190_T Diagnostic

source_name: AML Patient A190 Diagnostic

value: Bone Marrow


title: AML Patient A182_N Remission

source_name: AML Patient A182 Remission

value: Patient A182

value: Remission


title: AML Patient A184_N Remission

source_name: AML Patient A184 Remission

value: Patient A184


title: AML Patient A187_N Remission

source_name: AML Patient A187 Remission

value: Patient A187


title: AML Patient A187_T Diagnostic

source_name: AML Patient A187 Diagnostic

value: Diagnostic


title: AML Patient A186_N Remission

source_name: AML Patient A186 Remission

value: Patient A186


title: AML Patient A191_T Diagnostic

source_name: AML Patient A191 Diagnostic


title: AML Patient A180_T Diagnostic

source_name: AML Patient A180 Diagnostic

value: Patient A180


title: AML Patient A185_N Remission

source_name: AML Patient A185 Remission

value: Patient A185


title: AML Patient A183_N Remission

source_name: AML Patient A183 Remission


title: AML Patient A188_N Remission

source_name: AML Patient A188 Remission


title: AML Patient A185_T Diagnostic

source_name: AML Patient A185 Diagnostic


title: AML Patient A186_T Diagnostic

source_name: AML Patient A186 Diagnostic


title: AML Patient A179_T Diagnostic

source_name: AML Patient A179 Diagnostic

value: Patient A179


title: AML Patient A182_T Diagnostic

source_name: AML Patient A182 Diagnostic


title: AML Patient A180_N Remission

source_name: AML Patient A180 Remission


title: AML Patient A184_T Diagnostic

source_name: AML Patient A184 Diagnostic


title: AML Patient A178_N Remission

source_name: AML Patient A178 Remission

value: Patient A178


title: AML Patient A179_N Remission

source_name: AML Patient A179 Remission


title: AML Patient A178_T Diagnostic

source_name: AML Patient A178 Diagnostic


title: AML Patient A177_T Diagnostic

source_name: AML Patient A177 Diagnostic

value: Patient A177


title: AML Patient A174_T Diagnostic

source_name: AML Patient A174 Diagnostic

value: Patient A174


title: AML Patient A175_T Diagnostic

source_name: AML Patient A175 Diagnostic

value: AML

value: Patient A175


title: AML Patient A181_N Remission

source_name: AML Patient A181 Remission

value: Patient A181


title: AML Patient A176_T Diagnostic

source_name: AML Patient A176 Diagnostic

value: Patient A176


title: AML Patient A174_N Remission

source_name: AML Patient A174 Remission

value: Bone Marrow


title: AML Patient A171_T Diagnostic

source_name: AML Patient A171 Diagnostic

value: Patient A171


title: AML Patient A172_T Diagnostic

source_name: AML Patient A172 Diagnostic

value: Patient A172


title: AML Patient A173_N Remission

source_name: AML Patient A173 Remission

value: Patient A173

value: Remission


title: AML Patient A176_N Remission

source_name: AML Patient A176 Remission


title: AML Patient A168_T Diagnostic

source_name: AML Patient A168 Diagnostic

value: Patient A168

value: Diagnostic


title: AML Patient A170_N Remission

source_name: AML Patient A170 Remission

value: Patient A170


title: AML Patient A171_N Remission

source_name: AML Patient A171 Remission


title: AML Patient A167_T Diagnostic

source_name: AML Patient A167 Diagnostic

value: Patient A167


title: AML Patient A175_N Remission

source_name: AML Patient A175 Remission


title: AML Patient A169_T Diagnostic

source_name: AML Patient A169 Diagnostic

value: Patient A169


title: AML Patient A172_N Remission

source_name: AML Patient A172 Remission


title: AML Patient A169_N Remission

source_name: AML Patient A169 Remission


title: AML Patient A173_T Diagnostic

source_name: AML Patient A173 Diagnostic


title: AML Patient A166_T Diagnostic

source_name: AML Patient A166 Diagnostic

value: Patient A166


title: AML Patient A167_N Remission

source_name: AML Patient A167 Remission


title: AML Patient A177_N Remission

source_name: AML Patient A177 Remission

value: Patient A177


title: AML Patient A165_N Remission

source_name: AML Patient A165 Remission

value: Patient A165


title: AML Patient A163_T Diagnostic

source_name: AML Patient A163 Diagnostic

value: AML

value: Patient A163


title: AML Patient A166_N Remission

source_name: AML Patient A166 Remission


title: AML Patient A164_N Remission

source_name: AML Patient A164 Remission

value: Patient A164


title: AML Patient A163_N Remission

source_name: AML Patient A163 Remission


title: AML Patient A162_T Diagnostic

source_name: AML Patient A162 Diagnostic

value: Patient A162


title: AML Patient A161_T Diagnostic

source_name: AML Patient A161 Diagnostic

value: Patient A161

value: Bone Marrow


title: AML Patient A162_N Remission

source_name: AML Patient A162 Remission


title: AML Patient A164_T Diagnostic

source_name: AML Patient A164 Diagnostic


title: AML Patient A181_T Diagnostic

source_name: AML Patient A181 Diagnostic

value: Patient A181


title: AML Patient A157_T Diagnostic

source_name: AML Patient A157 Diagnostic

value: Patient A157


title: AML Patient A170_T Diagnostic

source_name: AML Patient A170 Diagnostic