title: bladder_normal_rep25

status: Public on Feb 28 2014

type: RNA

city: Sheffield

first: Stefan

last: Peter

address: Beech Hill Road

department: Oncology

country: United Kingdom

institute: The University of Sheffield

description: RNA expression in healthy bladder tissue

hyb_protocol: 1.65 µg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 125 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 125 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the NCode microarrays for 17 hours at 65°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 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner platform (High Resolution Microarray Scanner C) using one color scan setting for 2x105k array slides (Scan Area 61x21.6 mm, Scan resolution 5µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (GE1-107_Sep09).
Raw intensity values for each microarray probe were used to calculate RNA expression. The NCode microarrays include multiple probes for each target RNA. We excluded RNAs whose targeting probes were not concordant (defined as signal ratio less than 0.5 or greater than 2.0) in all the arrays. Normalisation was achieved according to the 1-color default normalisation of Agilent’s Gene Spring software (version 7), by dividing each raw intensity value by the median of the chip and the median expression of that RNA in all samples.

molecule: total RNA

organism: Homo sapiens

source_name: Bladder tissue, healthy control, replicate 25

label_protocol: Each sample was prepared according to Agilent’s one-color microarray protocol. Briefly, 200ng RNA samples were mixed with spike in control RNA (Agilent) and labelled with cyanine 3-CTP (Low Input Quick Amp Labeling Kit, one-color, Agilent). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: From each tissue sample, 10 x 10µm thick sections were microdissected to extract normal and malignant urothelial cells (>90% content). Total RNA was extracted using the mirVanaTM kit (Ambion, TX) according to manufacturer’s protocol.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent, Cheshire, UK).

tag: Sex

tag: age [years]


title: bladder_normal_rep19

source_name: Bladder tissue, healthy control, replicate 19


title: bladder_normal_rep21

source_name: Bladder tissue, healthy control, replicate 21


title: bladder_normal_rep24

source_name: Bladder tissue, healthy control, replicate 24


title: bladder_normal_rep22

source_name: Bladder tissue, healthy control, replicate 22


title: bladder_normal_rep20

source_name: Bladder tissue, healthy control, replicate 20


title: bladder_normal_rep18

source_name: Bladder tissue, healthy control, replicate 18


title: bladder_normal_rep14

source_name: Bladder tissue, healthy control, replicate 14

value: male


title: bladder_normal_rep17

source_name: Bladder tissue, healthy control, replicate 17


title: bladder_normal_rep23

source_name: Bladder tissue, healthy control, replicate 23


title: bladder_normal_rep26

source_name: Bladder tissue, healthy control, replicate 26


title: bladder_normal_rep15

source_name: Bladder tissue, healthy control, replicate 15


title: bladder_normal_rep13

source_name: Bladder tissue, healthy control, replicate 13


title: bladder_normal_rep11

source_name: Bladder tissue, healthy control, replicate 11


title: bladder_normal_rep4

source_name: Bladder tissue, healthy control, replicate 4


title: bladder_normal_rep16

source_name: Bladder tissue, healthy control, replicate 16


title: bladder_normal_rep9

source_name: Bladder tissue, healthy control, replicate 9


title: bladdertumour_invasive_rep20

description: RNA expression in invasive bladder cancer

source_name: Bladder tissue, invasive tumour, replicate 20


title: bladder_normal_rep12

source_name: Bladder tissue, healthy control, replicate 12


title: bladder_normal_rep5

source_name: Bladder tissue, healthy control, replicate 5

value: female


title: bladder_normal_rep8

source_name: Bladder tissue, healthy control, replicate 8


title: bladdertumour_invasive_rep19

source_name: Bladder tissue, invasive tumour, replicate 19


title: bladdertumour_invasive_rep18

source_name: Bladder tissue, invasive tumour, replicate 18


title: bladder_normal_rep2

source_name: Bladder tissue, healthy control, replicate 2


title: bladder_normal_rep6

source_name: Bladder tissue, healthy control, replicate 6


title: bladder_normal_rep7

source_name: Bladder tissue, healthy control, replicate 7


title: bladder_normal_rep1

source_name: Bladder tissue, healthy control, replicate 1


title: bladder_normal_rep3

source_name: Bladder tissue, healthy control, replicate 3


title: bladdertumour_invasive_rep16

source_name: Bladder tissue, invasive tumour, replicate 16


title: bladder_normal_rep10

source_name: Bladder tissue, healthy control, replicate 10


title: bladdertumour_invasive_rep15

source_name: Bladder tissue, invasive tumour, replicate 15


title: bladdertumour_invasive_rep12

source_name: Bladder tissue, invasive tumour, replicate 12


title: bladdertumour_invasive_rep17

source_name: Bladder tissue, invasive tumour, replicate 17


title: bladdertumour_invasive_rep9

source_name: Bladder tissue, invasive tumour, replicate 9


title: bladdertumour_invasive_rep8

source_name: Bladder tissue, invasive tumour, replicate 8


title: bladdertumour_invasive_rep10

source_name: Bladder tissue, invasive tumour, replicate 10


title: bladdertumour_invasive_rep14

source_name: Bladder tissue, invasive tumour, replicate 14


title: bladdertumour_invasive_rep7

source_name: Bladder tissue, invasive tumour, replicate 7


title: bladdertumour_invasive_rep6

source_name: Bladder tissue, invasive tumour, replicate 6


title: bladdertumour_invasive_rep11

source_name: Bladder tissue, invasive tumour, replicate 11


title: bladdertumour_invasive_rep2

source_name: Bladder tissue, invasive tumour, replicate 2


title: bladdertumour_invasive_rep5

source_name: Bladder tissue, invasive tumour, replicate 5


title: bladdertumour_invasive_rep4

source_name: Bladder tissue, invasive tumour, replicate 4


title: bladdertumour_highgrade_rep14

description: RNA expression in high-grade bladder cancer

source_name: Bladder tissue, high grade NMI tumour, replicate 14


title: bladdertumour_highgrade_rep11

source_name: Bladder tissue, high grade NMI tumour, replicate 11


title: bladdertumour_highgrade_rep8

source_name: Bladder tissue, high grade NMI tumour, replicate 8


title: bladdertumour_highgrade_rep9

source_name: Bladder tissue, high grade NMI tumour, replicate 9


title: bladdertumour_highgrade_rep10

source_name: Bladder tissue, high grade NMI tumour, replicate 10


title: bladdertumour_invasive_rep1

source_name: Bladder tissue, invasive tumour, replicate 1


title: bladdertumour_highgrade_rep2

source_name: Bladder tissue, high grade NMI tumour, replicate 2


title: bladdertumour_highgrade_rep5

source_name: Bladder tissue, high grade NMI tumour, replicate 5


title: bladdertumour_highgrade_rep3

source_name: Bladder tissue, high grade NMI tumour, replicate 3


title: bladdertumour_highgrade_rep12

source_name: Bladder tissue, high grade NMI tumour, replicate 12


title: bladdertumour_invasive_rep3

source_name: Bladder tissue, invasive tumour, replicate 3


title: bladdertumour_highgrade_rep4

source_name: Bladder tissue, high grade NMI tumour, replicate 4


title: bladdertumour_highgrade_rep6

source_name: Bladder tissue, high grade NMI tumour, replicate 6


title: bladdertumour_lowgrade_rep18

description: RNA expression in low-grade bladder cancer

source_name: Bladder tissue, low grade NMI tumour, replicate 18


title: bladdertumour_invasive_rep13

source_name: Bladder tissue, invasive tumour, replicate 13


title: bladdertumour_highgrade_rep1

source_name: Bladder tissue, high grade NMI tumour, replicate 1


title: bladdertumour_lowgrade_rep17

source_name: Bladder tissue, low grade NMI tumour, replicate 17


title: bladdertumour_lowgrade_rep16

source_name: Bladder tissue, low grade NMI tumour, replicate 16


title: bladdertumour_lowgrade_rep21

source_name: Bladder tissue, low grade NMI tumour, replicate 21


title: bladdertumour_lowgrade_rep10

source_name: Bladder tissue, low grade NMI tumour, replicate 10


title: bladdertumour_lowgrade_rep23

source_name: Bladder tissue, low grade NMI tumour, replicate 23


title: bladdertumour_lowgrade_rep22

source_name: Bladder tissue, low grade NMI tumour, replicate 22


title: bladdertumour_lowgrade_rep12

source_name: Bladder tissue, low grade NMI tumour, replicate 12


title: bladdertumour_lowgrade_rep13

source_name: Bladder tissue, low grade NMI tumour, replicate 13


title: bladdertumour_lowgrade_rep20

source_name: Bladder tissue, low grade NMI tumour, replicate 20


title: bladdertumour_lowgrade_rep19

source_name: Bladder tissue, low grade NMI tumour, replicate 19


title: bladdertumour_highgrade_rep13

source_name: Bladder tissue, high grade NMI tumour, replicate 13


title: bladdertumour_lowgrade_rep15

source_name: Bladder tissue, low grade NMI tumour, replicate 15


title: bladdertumour_lowgrade_rep7

source_name: Bladder tissue, low grade NMI tumour, replicate 7


title: bladdertumour_lowgrade_rep6

source_name: Bladder tissue, low grade NMI tumour, replicate 6


title: bladdertumour_lowgrade_rep5

source_name: Bladder tissue, low grade NMI tumour, replicate 5


title: bladdertumour_lowgrade_rep1

source_name: Bladder tissue, low grade NMI tumour, replicate 1


title: MD_MB_199

type: genomic

city: Heidelberg

first: Peter

last: Lichter

address: Im Neuenheimer Feld 580

department: Molecular Genetics

country: Germany

institute: German Cancer Research Center

hyb_protocol: According to the manufacturer’s instructions

scan_protocol: Illumina iScan System, according to the manufacturer’s instructions

data_processing: Array processing was performed using Illumina GenomeStudio V2011.1 (Methylation Module version 1.9.0). The 'MB-450k_GEOupload_Raw.txt' contains unmethylated and methylated signal intensities. Signal intensities were obtained without background subtraction and normalized to internal controls. The 'MB-450k_GEOupload_Beta.txt' contains 'Beta-values'.

label: biotin/DNP

molecule: genomic DNA

source_name: Primary medulloblastoma tumor tissue

extract_protocol: Extraction of high molecular weight DNA from frozen tumor samples was carried out using a Qiagen Allprep DNA/RNA/Protein Mini Kit.

tag: gender

value: F

tag: age (yrs)

tag: tissue

value: Primary medulloblastoma tumor tissue

tag: molecular subgroup

value: Group 3

tag: sample type

value: formalin-fixed paraffin-embedded (FFPE)


title: MD_MB_202

label_protocol: According to the manufacturer’s instructions

value: Group 4


title: F4

source_name: Normal foetal cerebellum

value: M

value: Normal foetal cerebellum

value: fresh-frozen


title: MD_MB_200


title: A2

source_name: Normal adult cerebellum

value: Normal adult cerebellum


title: MD_MB_203


title: F1


title: A3


title: MD_MB_201


title: A4


title: A1


title: F2


title: F3


title: bladdertumour_lowgrade_rep3

source_name: Bladder tissue, low grade NMI tumour, replicate 3


title: bladdertumour_lowgrade_rep11

source_name: Bladder tissue, low grade NMI tumour, replicate 11


title: bladdertumour_lowgrade_rep14

source_name: Bladder tissue, low grade NMI tumour, replicate 14


title: bladdertumour_lowgrade_rep8

source_name: Bladder tissue, low grade NMI tumour, replicate 8


title: bladdertumour_lowgrade_rep2

source_name: Bladder tissue, low grade NMI tumour, replicate 2


title: MD_MB_197


title: MD_MB_198

value: WNT


title: MD_MB_196


title: bladdertumour_lowgrade_rep4

source_name: Bladder tissue, low grade NMI tumour, replicate 4


title: MD_MB_195


title: MD_MB_194


title: MD_MB_192


title: MD_MB_193

value: SHH


title: MD_MB_190


title: MD_MB_189


title: MD_MB_183


title: MD_MB_174


title: MD_MB_185


title: MD_MB_184


title: MD_MB_188


title: MD_MB_186


title: MD_MB_175


title: MD_MB_179


title: MD_MB_166


title: MD_MB_172


title: MD_MB_165


title: MD_MB_173


title: MD_MB_170


title: MD_MB_180


title: MD_MB_168


title: MD_MB_169


title: MD_MB_167


title: MD_MB_171


title: MD_MB_164


title: MD_MB_163


title: MD_MB_162


title: MD_MB_160


title: MD_MB_159


title: MD_MB_158


title: MD_MB_157


title: MD_MB_182


title: MD_MB_177


title: MD_MB_156


title: MD_MB_154


title: MD_MB_152


title: MD_MB_150


title: MD_MB_141


title: MD_MB_153


title: MD_MB_151


title: MD_MB_146


title: MD_MB_148


title: MD_MB_149


title: MD_MB_138


title: MD_MB_137


title: MD_MB_143


title: MD_MB_145


title: MD_MB_144


title: MD_MB_155


title: MD_MB_142


title: MD_MB_139


title: MD_MB_136


title: MD_MB_147


title: MD_MB_140


title: MD_MB_134


title: MD_MB_135


title: MD_MB_133


title: MD_MB_131


title: MD_MB_129


title: MD_MB_132


title: MD_MB_128


title: MD_MB_127


title: MD_MB_126


title: MD_MB_124


title: MD_MB_115


title: MD_MB_122


title: MD_MB_107


title: MD_MB_123


title: MD_MB_110


title: MD_MB_117


title: MD_MB_113


title: MD_MB_111


title: MD_MB_116


title: MD_MB_106


title: MD_MB_125


title: MD_MB_105


title: MD_MB_112


title: MD_MB_108


title: MD_MB_121


title: MD_MB_104


title: MD_MB_114


title: MD_MB_102


title: MD_MB_109


title: MD_MB_101


title: MD_MB_100


title: MD_MB_099


title: MD_MB_096


title: MD_MB_098


title: MD_MB_094


title: MD_MB_095


title: MD_MB_093


title: MD_MB_090


title: MD_MB_091


title: MDA-MB-231 cell clone 6 days + dox rep2

first: Martin

middle: R

last: Berger

address: INF 581

institute: DKFZ

description: replicate 3

hyb_protocol: Standard Illumina Hybridisation Protocol (Part # 11322355 Rev. A (Whole-Genome Gene Expression Direct Hybridisation Assay Guide))

scan_protocol: Standard Illumina Scanning Protocol (Part # 11322355 Rev. A (Whole-Genome Gene Expression Direct Hybridisation Assay Guide))

data_processing: The data were normalised using quantile normalisation. As test for significance the student’s t-test was used on the bead expression values of the two groups of interest (+dox and -dox). The average expression value was calculated as mean of the measured expressions of beads together with the standard deviation of the beads.

label: biotin

source_name: Mammary breast epithelial cell line

label_protocol: Illumina TotalPrep-RNA Amplification (P/N IL1791M Revision C)

growth_protocol: The established cell clone was cultivated in appropriate media with or without doxycycline for 3 or 6 days.

extract_protocol: The RNA was isolated by RNeasy mini-kit (Qiagen) in accordance with the prescribed protocol provided with the kit. The quality control of the total RNA was performed with Agilent Bioanalyser.

treatment_protocol: Upon activation of Tet-Off system, the miRNA mediated treament was stimulated for 3 and 6 days in the third, fourth and seventh, eight samples, respectively.

tag: treatment

value: control

tag: time (mirna expression)

value: 6 days off

tag: cell line


title: bladdertumour_highgrade_rep7

source_name: Bladder tissue, high grade NMI tumour, replicate 7


title: MD_MB_089


title: MDA-MB-231 cell clone 6 days - dox rep1

description: replicate 4

value: BSP knockdown

value: 6 days on


title: MDA-MB-231 cell clone 6 days - dox rep2

description: replicate 4


title: MD_MB_088


title: bladdertumour_lowgrade_rep9

source_name: Bladder tissue, low grade NMI tumour, replicate 9


title: MDA-MB-231 cell clone 6 days + dox rep1

description: replicate 3


title: MDA-MB-231 cell clone 3 days - dox rep1

description: replicate 2

value: 3 days on


title: MD_MB_097


title: MDA-MB-231 cell clone 3 days + dox rep1

description: replicate 1

value: 3 days off


title: MD_MB_087


title: MDA-MB-231 cell clone 3 days - dox rep2

description: replicate 2


title: MD_MB_086

value: F


title: 293T amiR-175 rep 3

city: Seattle

first: Jason

last: Arroyo

state: WA

address: 1100 Fairview Ave N

department: Human Biology

country: USA

institute: Fred Hutchinson Cancer Research Center

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with GenomeStudio. No background subtraction was performed.

label_protocol: Biotinylated cRNA were prepared with the llumina TotalPrep RNA Amplification Kit according to the manufacturer's protocol.

growth_protocol: 293T cells were grown in RPMI with 10% fetal bovine serum

extract_protocol: Total RNA was extracted using the Qiagen miRNeasy Kit according to the manufacturer’s protocol. RNA was quality checked using an Agilent Bioanalyzer.

treatment_protocol: Cells were transiently transfected with either an artificial miRNA or the non-targeting control (Allstars siRNA, Qiagen)

tag: cell type

value: human embryonic kidney


title: 293T amiR-268 rep 3


title: 293T amiR-268 rep 2


title: 293T amiR-175 rep 2


title: 293T amiR-143 rep 3


title: MDA-MB-231 cell clone 3 days + dox rep2

description: replicate 1


title: MD_MB_085

value: Primary medulloblastoma tumor tissue

value: Group 3


title: MD_MB_084

value: formalin-fixed paraffin-embedded (FFPE)


title: 293T amiR-268 rep 1


title: 293T amiR-143 rep 2


title: MD_MB_079

value: M


title: MD_MB_077


title: 293T amiR-143 rep 1


title: MD_MB_078


title: 293T amiR-175 rep 1


title: MD_MB_072

value: Group 4


title: MD_MB_076


title: MD_MB_073


title: MD_MB_074


title: 293T amiR-104 rep 3


title: 293T amiR-104 rep 2


title: MD_MB_071


title: MD_MB_075


title: 293T amiR-104 rep 1


title: MD_MB_081


title: MD_MB_068


title: MD_MB_065


title: MD_MB_064


title: MD_MB_062


title: MD_MB_063


title: MD_MB_066


title: 293T non-targeting control rep 1

source_name: 293T non-targeting control


title: 293T non-targeting control rep 2


title: MD_MB_067


title: MD_MB_056


title: MD_MB_059


title: 293T non-targeting control rep 3


title: MD_MB_054


title: MD_MB_053


title: MD_MB_052


title: MD_MB_051


title: MD_MB_047


title: MD_MB_050


title: MD_MB_045


title: MD_MB_046


title: MD_MB_044


title: MD_MB_042


title: MD_MB_043


title: MD_MB_041


title: MD_MB_040


title: MD_MB_039


title: MD_MB_038


title: VDC-Meso_4

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression from VDC induced mesotheliomas

hyb_protocol: 12.5 μg of amplified biotin-aRNAs were fragmented and 10 μg were hybridized to each array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: Data was obtained using the GeneChip® Command Console Software (AGCC; Version 1.1) using the MAS5 algorithm to generate .CHP files.

organism: Rattus norvegicus

source_name: VDC induced mesothelioma

label_protocol: One hundred ng of total RNA was amplified as directed in the Affymetrix 3' IVT Express kit protocol.

growth_protocol: RNA samples were obtained through a generous gift from Y. Kim, North Carolina State University. Tumors were collected from vehicle control and VDC-exposed F344/N rats from 2-year National Toxicology Program bioassays.

extract_protocol: RNA extraction was performed using the Invitrogen PureLink Mini kit (Invitrogen cat# 12183-018A). Frozen tissue samples were lysed and homogenized in TRIzol reagent using a rotor-stator homogenizer. RNA isolation was performed according to the mini kit protocol. On column DNase treatment was performed using the Invitrogen PureLink DNase kit (Invitrogen cat# 12185-010) to purify the RNA samples.   RNA concentration and 260/280 ratio were measured on a bioanalyzer (Agilent Technologies). RNA quality was checked on Embi Tec Precast RNA gels (Embec cat# GE-6010). Samples were aliquoted and stored at -80C.

tag: strain

value: VDC induced mesotheliomas


title: VDC-Meso_8


title: MD_MB_037


title: VDC-Meso_6


title: VDC-Meso_9


title: MD_MB_035


title: VDC-Meso_2


title: VDC-Meso_1


title: MD_MB_034


title: MD_MB_033


title: MD_MB_070


title: Regenerating liver at 168h after PH_technical rep3

city: Xinxiang

first: Cunshuan

last: Xu

address: No. 46, Construction East Road

country: China

institute: Henan Normal University

description:
PH168-3
Gene expression data from hepatocyte at termination phase of liver regeneration after partial hepatectomy.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45℃ on Rat Genome 230 2.0 array. GeneChips were washed and stained in the Affymetrix GeneChip® Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 (Affymetrix Inc., Santa Clara, CA, USA).

data_processing:
The data were analyzed with Affymetrix GCOS 2.0 software using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
When P value is < 0.05, it means that the gene is present (P), when < 0.065, means marginal (M), and when > 0.065, means marked absent (A). On the other hand, the normalized signal values in PH to that in control were used to calculate the relative value, that is, ratio value of gene expression abundance. When ratio value is ≥ 3, it means that gene expression change was significantly up-regulated, when ≤ 0.33, means significantly down-regulated, and when 0.33-2.99, means biologically insignificant. To minimize the technical errors from microarray analysis, each sample was tested at least three times using Rat Genome 230 2.0 microarray, and the average value was considered as a reliable value (Wang and Xu, 2010).

source_name: Regenerating liver at 168h after partial hepatectomy

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (GeneChip In Vitro Transcript Labeling Kit, ENZO Biochemical, New York, USA).

extract_protocol: Total RNA was extracted according to the manual of Trizol reagent (Invitrogen Corporation, Carlsbad, California, USA) and purified following the RNeasy mini protocol (Qiagen, Inc, Valencia, CA, USA).

treatment_protocol: After the operations were done, the rats at corresponding recovery time points were anaesthetized, and the intrahepatic blood was removed by hepatic portal vein infusion firstly, then the liver tissues from the middle part of the right lobe of the liver were collected in RNase-free tubes and stored at﹣80℃ until use.

value: Sprague-Dawley (SD)

value: Liver

value: hepatocyte

tag: genotype

value: yellow white and Oregon R parents

tag: age

value: PH

tag: time


title: VDC-Meso_3


title: Regenerating liver at 168h after PH_technical rep2

description:
PH168-2
Gene expression data from hepatocyte at termination phase of liver regeneration after partial hepatectomy.


title: Regenerating liver at 168h after PH_technical rep1

description:
PH168-1
Gene expression data from hepatocyte at termination phase of liver regeneration after partial hepatectomy.


title: Liver at 168h after sham operation_technical rep2

description:
S168-2
Gene expression data from hepatocyte at termination phase after sham operation

source_name: Liver at 168h after sham operation

value: sham operation


title: Regenerating liver at  120h after PH_technical rep1

description:
PH120-1
Gene expression data from hepatocyte at termination phase of liver regeneration after partial hepatectomy.

source_name: Regenerating liver at 120h after partial hepatectomy


title: Regenerating liver at  120h after PH_technical rep2

description:
PH120-2
Gene expression data from hepatocyte at termination phase of liver regeneration after partial hepatectomy.


title: Liver at 168h after sham operation_technical rep3

description:
S168-3
Gene expression data from hepatocyte at termination phase after sham operation


title: Liver at  120h after sham operation_technical rep3

description:
S120-3
Gene expression data from hepatocyte at termination phase after sham operation

source_name: Liver at 120h after sham operation


title: MD_MB_032

source_name: Primary medulloblastoma tumor tissue

value: SHH


title: MD_MB_031


title: MD_MB_029


title: VDC-Meso_7


title: MD_MB_025


title: Liver at  120h after sham operation_technical rep2

description:
S120-2
Gene expression data from hepatocyte at termination phase after sham operation


title: MD_MB_023


title: Regenerating liver at 72h after PH_technical rep2

description:
PH72-2
Gene expression data from hepatocyte at termination phase of liver regeneration after partial hepatectomy.

source_name: Regenerating liver at 72h after partial hepatectomy


title: Regenerating liver at 72h after PH_technical rep1

description:
PH72-1
Gene expression data from hepatocyte at termination phase of liver regeneration after partial hepatectomy.


title: Regenerating liver at  120h after PH_technical rep3

description:
PH120-3
Gene expression data from hepatocyte at termination phase of liver regeneration after partial hepatectomy.


title: Liver at 168h after sham operation_technical rep1

description:
S168-1
Gene expression data from hepatocyte at termination phase after sham operation


title: A173DPI_6 with array type Medicago from Affymetrix

city: evry

first: stephanie

last: huguet

address: 2 rue gaston cremieux

country: France

institute: inra

description:
LYR3 encodes a lysin motif-receptor-like kinase (LysM-RLK) that consists of an extracellular ligand-binding domain composed of three LysM domains, a single transmembrane domain and a cytoplasmic serine/threonine kinase domain. A reverse genetic approach was undertaken to study the role of this gene in the pathosystem Medicago truncatula – Aphanomyces euteiches (Ae). Results suggest that lyr3-1 and lyr3-2 mutants are more susceptible to the root pathogen Aphanomyces euteiches than the A17 wild type (WT) line.  In this study, we want to compare the early plant responses, 3 days post inoculation (dpi), between WT and the lyr3-1 and lyr3-2 mutants, in order to identify LYR3-dependent gene networks during infection.
medicago truncatula (a17)  - harvest date: 14-05-12

hyb_protocol: labelled extract quantity: 15ug

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

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

label: Biotin

organism: Medicago truncatula

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

growth_protocol: roots - - In vitro conditions on M medium - 16h light 8h dark 22°C

treatment_protocol: Name:A_EUTEICHES_3DPI* - inoculation with a. euteiches,environmental treatment - pathogen infection,ae 3dpi:time 3day . Factor value: 3 dpi Reference protocol or description Sample treatment protocol: Djebali et al, MPMI, 2009.

tag: genotype/variation

value: WT

tag: infection

value: A. euteiches zoospores

tag: harvest date


title: MD_MB_026


title: A17LYR3_1NI_7 with array type Medicago from Affymetrix

description:
LYR3 encodes a lysin motif-receptor-like kinase (LysM-RLK) that consists of an extracellular ligand-binding domain composed of three LysM domains, a single transmembrane domain and a cytoplasmic serine/threonine kinase domain. A reverse genetic approach was undertaken to study the role of this gene in the pathosystem Medicago truncatula – Aphanomyces euteiches (Ae). Results suggest that lyr3-1 and lyr3-2 mutants are more susceptible to the root pathogen Aphanomyces euteiches than the A17 wild type (WT) line.  In this study, we want to compare the early plant responses, 3 days post inoculation (dpi), between WT and the lyr3-1 and lyr3-2 mutants, in order to identify LYR3-dependent gene networks during infection.
medicago truncatula (a17)  mutant (lyr3-1) - harvest date: 27-04-12

growth_protocol: roots - In vitro condition on M medium 16h light 8h dark 22°C AGENT EMS

treatment_protocol: Name:no treatment  - non mentionne  - non mentionne ,control 3d:time 3day . Reference protocol or description Sample treatment protocol: Djebali et al, MPMI, 2009.

value: lyr3-1 mutant

value: NI


title: A173DPI_4 with array type Medicago from Affymetrix

description:
LYR3 encodes a lysin motif-receptor-like kinase (LysM-RLK) that consists of an extracellular ligand-binding domain composed of three LysM domains, a single transmembrane domain and a cytoplasmic serine/threonine kinase domain. A reverse genetic approach was undertaken to study the role of this gene in the pathosystem Medicago truncatula – Aphanomyces euteiches (Ae). Results suggest that lyr3-1 and lyr3-2 mutants are more susceptible to the root pathogen Aphanomyces euteiches than the A17 wild type (WT) line.  In this study, we want to compare the early plant responses, 3 days post inoculation (dpi), between WT and the lyr3-1 and lyr3-2 mutants, in order to identify LYR3-dependent gene networks during infection.
medicago truncatula (a17)  - harvest date: 27-04-12


title: A17LYR3_23DPI_17 with array type Medicago from Affymetrix

description:
LYR3 encodes a lysin motif-receptor-like kinase (LysM-RLK) that consists of an extracellular ligand-binding domain composed of three LysM domains, a single transmembrane domain and a cytoplasmic serine/threonine kinase domain. A reverse genetic approach was undertaken to study the role of this gene in the pathosystem Medicago truncatula – Aphanomyces euteiches (Ae). Results suggest that lyr3-1 and lyr3-2 mutants are more susceptible to the root pathogen Aphanomyces euteiches than the A17 wild type (WT) line.  In this study, we want to compare the early plant responses, 3 days post inoculation (dpi), between WT and the lyr3-1 and lyr3-2 mutants, in order to identify LYR3-dependent gene networks during infection.
medicago truncatula (a17)  mutant (lyr3_2) - harvest date: 07-05-12

growth_protocol: roots - - In vitro conditions on M medium - 16h light 8h dark 22°C AGENT EMS

value: lyr3-2 mutant


title: Regenerating liver at 72h after PH_technical rep3

description:
PH72-3
Gene expression data from hepatocyte at termination phase of liver regeneration after partial hepatectomy.


title: Liver at 72h after sham operation_technical rep3

description:
S72-3
Gene expression data from hepatocyte at termination phase after sham operation

source_name: Liver at 72h after sham operation


title: A17NI_3 with array type Medicago from Affymetrix


title: Liver at 72h after sham operation_technical rep2

description:
S72-2
Gene expression data from hepatocyte at termination phase after sham operation


title: MD_MB_024

value: F

value: Primary medulloblastoma tumor tissue

value: WNT


title: MD_MB_022

value: M

value: Group 4

value: formalin-fixed paraffin-embedded (FFPE)


title: A17NI_2 with array type Medicago from Affymetrix

description:
LYR3 encodes a lysin motif-receptor-like kinase (LysM-RLK) that consists of an extracellular ligand-binding domain composed of three LysM domains, a single transmembrane domain and a cytoplasmic serine/threonine kinase domain. A reverse genetic approach was undertaken to study the role of this gene in the pathosystem Medicago truncatula – Aphanomyces euteiches (Ae). Results suggest that lyr3-1 and lyr3-2 mutants are more susceptible to the root pathogen Aphanomyces euteiches than the A17 wild type (WT) line.  In this study, we want to compare the early plant responses, 3 days post inoculation (dpi), between WT and the lyr3-1 and lyr3-2 mutants, in order to identify LYR3-dependent gene networks during infection.
medicago truncatula (41528 population)  - harvest date: 07-05-12

growth_protocol: roots - In vitro condition on M medium -16h light 8h dark 22°C


title: A17LYR3_23NI_15 with array type Medicago from Affymetrix

description:
LYR3 encodes a lysin motif-receptor-like kinase (LysM-RLK) that consists of an extracellular ligand-binding domain composed of three LysM domains, a single transmembrane domain and a cytoplasmic serine/threonine kinase domain. A reverse genetic approach was undertaken to study the role of this gene in the pathosystem Medicago truncatula – Aphanomyces euteiches (Ae). Results suggest that lyr3-1 and lyr3-2 mutants are more susceptible to the root pathogen Aphanomyces euteiches than the A17 wild type (WT) line.  In this study, we want to compare the early plant responses, 3 days post inoculation (dpi), between WT and the lyr3-1 and lyr3-2 mutants, in order to identify LYR3-dependent gene networks during infection.
medicago truncatula (41528 population)  mutant (lyr2_2) - harvest date: 14-05-12


title: A173DPI_5 with array type Medicago from Affymetrix


title: A17LYR3_23DPI_16 with array type Medicago from Affymetrix

description:
LYR3 encodes a lysin motif-receptor-like kinase (LysM-RLK) that consists of an extracellular ligand-binding domain composed of three LysM domains, a single transmembrane domain and a cytoplasmic serine/threonine kinase domain. A reverse genetic approach was undertaken to study the role of this gene in the pathosystem Medicago truncatula – Aphanomyces euteiches (Ae). Results suggest that lyr3-1 and lyr3-2 mutants are more susceptible to the root pathogen Aphanomyces euteiches than the A17 wild type (WT) line.  In this study, we want to compare the early plant responses, 3 days post inoculation (dpi), between WT and the lyr3-1 and lyr3-2 mutants, in order to identify LYR3-dependent gene networks during infection.
medicago truncatula (a17)  mutant (lyr3_2) - harvest date: 27-04-12


title: MD_MB_021


title: MD_MB_019


title: Liver at 120h after sham operation_technical rep1

description:
S120-1
Gene expression data from hepatocyte at termination phase after sham operation

value: Sprague-Dawley (SD)

value: Liver


title: Liver at 72h after sham operation_technical rep1

description:
S72-1
Gene expression data from hepatocyte at termination phase after sham operation

value: hepatocyte

value: yellow white and Oregon R parents


title: MD_MB_018


title: MD_MB_017


title: A17LYR3_13DPI_12 with array type Medicago from Affymetrix

description:
LYR3 encodes a lysin motif-receptor-like kinase (LysM-RLK) that consists of an extracellular ligand-binding domain composed of three LysM domains, a single transmembrane domain and a cytoplasmic serine/threonine kinase domain. A reverse genetic approach was undertaken to study the role of this gene in the pathosystem Medicago truncatula – Aphanomyces euteiches (Ae). Results suggest that lyr3-1 and lyr3-2 mutants are more susceptible to the root pathogen Aphanomyces euteiches than the A17 wild type (WT) line.  In this study, we want to compare the early plant responses, 3 days post inoculation (dpi), between WT and the lyr3-1 and lyr3-2 mutants, in order to identify LYR3-dependent gene networks during infection.
medicago truncatula (a17)  mutant (lyr3_1) - harvest date: 14-05-12


title: A17LYR3_23NI_13 with array type Medicago from Affymetrix


title: A17LYR3_13DPI_11 with array type Medicago from Affymetrix


title: A17NI_1 with array type Medicago from Affymetrix


title: A17LYR3_13DPI_10 with array type Medicago from Affymetrix


title: Regenerating liver at 36h after PH_technical rep3

description:
PH36-3
Gene expression data from hepatocyte at proliferation phase of liver regeneration after partial hepatectomy.

source_name: Regenerating liver at 36h after partial hepatectomy

value: PH


title: A17LYR3_23NI_14 with array type Medicago from Affymetrix


title: MD_MB_016


title: MD_MB_008


title: MD_MB_013

value: SHH


title: MD_MB_010


title: MD_MB_007


title: A17LYR3_1NI_9 with array type Medicago from Affymetrix


title: Liver at 36h after sham operation_technical rep2

description:
S36-2
Gene expression data from hepatocyte at priming phase after sham operation

source_name: Liver at 36h after sham operation

value: sham operation


title: Liver at 36h after sham operation_technical rep1

description:
S36-1
Gene expression data from hepatocyte at priming phase after sham operation


title: Liver at 36h after sham operation_technical rep3

description:
S36-3
Gene expression data from hepatocyte at priming phase after sham operation


title: Regenerating liver at 30h after PH_technical rep2

description:
PH30-2
Gene expression data from hepatocyte at proliferation phase of liver regeneration after partial hepatectomy.

source_name: Regenerating liver at 30h after partial hepatectomy


title: MD_MB_014

value: Group 3


title: Regenerating liver at 30h after PH_technical rep3

description:
PH30-3
Gene expression data from hepatocyte at proliferation phase of liver regeneration after partial hepatectomy.


title: Regenerating liver at 30h after PH_technical rep1

description:
PH30-1
Gene expression data from hepatocyte at proliferation phase of liver regeneration after partial hepatectomy.


title: A17LYR3_1NI_8 with array type Medicago from Affymetrix

description:
LYR3 encodes a lysin motif-receptor-like kinase (LysM-RLK) that consists of an extracellular ligand-binding domain composed of three LysM domains, a single transmembrane domain and a cytoplasmic serine/threonine kinase domain. A reverse genetic approach was undertaken to study the role of this gene in the pathosystem Medicago truncatula – Aphanomyces euteiches (Ae). Results suggest that lyr3-1 and lyr3-2 mutants are more susceptible to the root pathogen Aphanomyces euteiches than the A17 wild type (WT) line.  In this study, we want to compare the early plant responses, 3 days post inoculation (dpi), between WT and the lyr3-1 and lyr3-2 mutants, in order to identify LYR3-dependent gene networks during infection.
medicago truncatula (a17)  mutant (lyr3-1) - harvest date: 27-04-12

value: lyr3-1 mutant


title: Regenerating liver at 36h after PH_technical rep1

description:
PH36-1
Gene expression data from hepatocyte at proliferation phase of liver regeneration after partial hepatectomy.


title: MD_MB_004


title: MD_MB_003


title: Regenerating liver at 36h after PH_technical rep2

description:
PH36-2
Gene expression data from hepatocyte at proliferation phase of liver regeneration after partial hepatectomy.


title: A17LYR3_23DPI_18 with array type Medicago from Affymetrix

value: A. euteiches zoospores


title: 5M17

value: fresh-frozen


title: Liver at 30h after sham operation_technical rep2

description:
S30-2
Gene expression data from hepatocyte at priming phase after sham operation

source_name: Liver at 30h after sham operation


title: Liver at 30h after sham operation_technical rep3

description:
S30-3
Gene expression data from hepatocyte at priming phase after sham operation


title: 5M7

value: F


title: Regenerating liver at 24h after PH_technical rep3

description:
PH24-3
Gene expression data from hepatocyte at proliferation phase of liver regeneration after partial hepatectomy.

source_name: Regenerating liver at 24h after partial hepatectomy


title: 5M6

value: Primary medulloblastoma tumor tissue


title: Regenerating liver at 24h after PH_technical rep1

description:
PH24-1
Gene expression data from hepatocyte at proliferation phase of liver regeneration after partial hepatectomy.


title: Regenerating liver at 24h after PH_technical rep2

description:
PH24-2
Gene expression data from hepatocyte at proliferation phase of liver regeneration after partial hepatectomy.


title: 4M58


title: Liver at 30h after sham operation_technical rep1

description:
S30-1
Gene expression data from hepatocyte at priming phase after sham operation


title: Tris and Retinoic Acid biological rep1

city: Vancouver

first: Joy

last: Richman

state: BC

address: 2350 Health Sciences Mall

department: Oral Health Sciences

country: Canada

institute: University of British Columbia

description: Gene expression data from stage 18 maxillary prominences, 16h post treatment

hyb_protocol: Hybridization was performed as described in the GeneChip Expression Analysis Technical Manual by the London Regional Genomics Centre, London, Ontario, Canada

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip scanner 3000

data_processing: The data were analyzed with GCOS1.4  using Affymetrix default analysis settings and Scaling within 3 fold of each other as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

organism: Gallus gallus

source_name: Stage 18 chicken embryos

label_protocol: Biotinylated cRNA were prepared according to two-cycle Affymetrix protocol from 500 ng total RNA (GeneChip Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Embryos were incubated at 38 degrees C until they reached Hamburger Hamilton Stage 15 or 25 somites. Beads were implanted and then embryos were reincubated for another 16h until they reached stage 18. Maxillary tissues were dissected from 12-15 embryos and pooled together to form one biological replicate.

extract_protocol: Qiagen RNAeasy kit was used.

treatment_protocol: Four different treatments were done each consisting of two beads placed into the side of the head between the eye and mandibular arch. Beads were soaked in 1 mg/ml Noggin protein (Affigel blue beads, 200 microns in diameter) or 1 mg/ml all-trans-retinoic acid (AG1X2, Formate form, 100 microns) for a minimum of 1 hour prior to implantation. Control beads were soaked in Tris (buffer for Noggin) or dimethylsulfoxide (solvent for retinoic acid). The following combinations were implanted, Noggin+ RA, Tris+RA, Noggin+DMSO, Tris+DMSO. All animals had bead implants.

value: Mesenchyme plus epithelium, maxillary

value: Tris and Retinoic Acid

value: Hamburger Hamilton stage 18


title: Tris and DMSO biological rep3

value: Tris and DMSO


title: Tris and Retinoic Acid biological rep3


title: Tris and Retinoic Acid biological rep2


title: Liver at 24h after sham operation_technical rep2

description:
S24-2
Gene expression data from hepatocyte at priming phase after sham operation

source_name: Liver at 24h after sham operation

value: Sprague-Dawley (SD)


title: Tris and DMSO biological rep1


title: Tris and DMSO biological rep2


title: Regenerating liver at 12h after PH_technical rep3

description:
PH12-3
Gene expression data from hepatocyte at proliferation phase of liver regeneration after partial hepatectomy.

source_name: Regenerating liver at 12h after partial hepatectomy

value: Liver


title: 4M21


title: Regenerating liver at 12h after PH_technical rep2

description:
PH12-2
Gene expression data from hepatocyte at proliferation phase of liver regeneration after partial hepatectomy.

value: hepatocyte


title: Liver at 24h after sham operation_technical rep1

description:
S24-1
Gene expression data from hepatocyte at priming phase after sham operation

value: yellow white and Oregon R parents


title: Noggin and Retinoic acid biological rep2

value: Noggin and Retinoic acid


title: Noggin DMSO biological rep1

value: Noggin DMSO


title: Noggin and Retinoic acid biological rep1


title: Noggin DMSO biological rep3


title: Noggin DMSO biological rep2


title: Noggin and Retinoic acid biological rep3


title: 2M21

value: SHH


title: Liver at 24h after sham operation_technical rep3

description:
S24-3
Gene expression data from hepatocyte at priming phase after sham operation

value: sham operation


title: 2M16


title: Liver at 12h after sham operation_technical rep3

description:
S12-3
Gene expression data from hepatocyte at priming phase after sham operation

source_name: Liver at 12h after sham operation


title: 2M9

value: M


title: 2M20


title: 2M14

value: Group 3


title: 4M28

value: WNT

value: fresh-frozen


title: Liver at 12h after sham operation_technical rep2

description:
S12-2
Gene expression data from hepatocyte at priming phase after sham operation


title: 4M8

value: Primary medulloblastoma tumor tissue


title: Liver at 12h after sham operation_technical rep1

description:
S12-1
Gene expression data from hepatocyte at priming phase after sham operation


title: Regenerating liver at 6h after PH_technical rep3

description:
PH6-3
Gene expression data from hepatocyte at proliferation phase of liver regeneration after partial hepatectomy.

source_name: Regenerating liver at 6h after partial hepatectomy

value: PH


title: 1M32


title: Regenerating liver at 12h after PH_technical rep1

description:
PH12-1
Gene expression data from hepatocyte at proliferation phase of liver regeneration after partial hepatectomy.


title: 1M24

value: Group 4


title: Liver at 6h after sham operation_technical rep2

description:
S6-2
Gene expression data from hepatocyte at priming phase after sham operation

source_name: Liver at 6h after sham operation


title: 2M7


title: 1M22


title: 1M21


title: Liver at 6h after sham operation_technical rep3

description:
S6-3
Gene expression data from hepatocyte at priming phase after sham operation


title: Regenerating liver at 6h after PH_technical rep1

description:
PH6-1
Gene expression data from hepatocyte at proliferation phase of liver regeneration after partial hepatectomy.


title: Liver at 6h after sham operation_technical rep1

description:
S6-1
Gene expression data from hepatocyte at priming phase after sham operation


title: HRASG12V 6

city: Glasgow

middle: D.

last: Adams

address: Switchback Rd, Bearsden

institute: University of Glasgow, Beatson Institute for Cancer Research

description: Gene expression data from Control and HRAS V12 infected cells

hyb_protocol: Subsequent labelling and hybrisation to HG_U133 Plus 2.0 arrays (Affymetrix, Santa Clara, CA) using the FL-Ovation cDNA Biotin Module v2.

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

data_processing: The data were analyzed with GCRMA (Bioconductor) using Affymetrix default analysis settings and quantile normalisation was used as the normalisation method.

molecule: polyA RNA

source_name: IMR90 cells

label_protocol: RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN, San Carlos, CA).

growth_protocol: Cells were cultured under standard conditions at low (3%) oxygen and RNA harvested when plates were 80% confluent.

extract_protocol: RNA was extracted using the RNA Easy Mini Kit (Qiagen, cat 74104).

treatment_protocol: Control cells were infected with empty vector virus (pBABE-puro). HRASG12V (senescent) cells were infected with H-RASG12V expressing virus (pBABE-puro-HRASG12V). Cells were puromycin-selected, cultured in parallel and harvested once the HRAS infected cells were confirmed senescent.

tag: vector


title: Regenerating liver at 2h after PH_technical rep3

description:
PH2-3
Gene expression data from hepatocyte at priming phase of liver regeneration after partial hepatectomy.

source_name: Regenerating liver at 2h after partial hepatectomy


title: HRASG12V 4


title: Regenerating liver at 2h after PH_technical rep2

description:
PH2-2
Gene expression data from hepatocyte at priming phase of liver regeneration after partial hepatectomy.


title: HRASG12V 3


title: 1M19

tag: gender

value: F


title: Regenerating liver at 6h after PH_technical rep2

description:
PH6-2
Gene expression data from hepatocyte at proliferation phase of liver regeneration after partial hepatectomy.


title: HRASG12V 2


title: HRASG12V 1


title: Liver at 2h after sham operation_technical rep3

description:
S2-3
Gene expression data from hepatocyte at priming phase after sham operation

source_name: Liver at 2h after sham operation


title: Liver at 2h after sham operation_technical rep2

description:
S2-2
Gene expression data from hepatocyte at priming phase after sham operation


title: Control 3

value: (pBABE-puro)


title: 1M17

source_name: Primary medulloblastoma tumor tissue

tag: age (yrs)


title: 1M20

tag: tissue


title: Regenerating liver at 2h after PH_technical rep1

description:
PH2-1
Gene expression data from hepatocyte at priming phase of liver regeneration after partial hepatectomy.

value: Sprague-Dawley (SD)


title: Control 4


title: 1M16

tag: molecular subgroup


title: Liver at 2h after sham operation_technical rep1

description:
S2-1
Gene expression data from hepatocyte at priming phase after sham operation

value: Liver


title: HRASG12V 5


title: Control 2


title: 1M15

tag: sample type


title: Regenerating liver at 0h after PH_technical rep3

description:
S0-3
Gene expression data from normal hepatocyte.

source_name: Regenerating liver at 0h after partial hepatectomy

value: hepatocyte

tag: treatment

value: control


title: Regenerating liver at 0h after PH_technical rep2

description:
S0-2
Gene expression data from normal hepatocyte.

value: yellow white and Oregon R parents


title: Control 1


title: 1M14


title: 1M5


title: 1M13


title: 1M3


title: 1M4


title: 1M2


title: 1M28


title: Regenerating liver at 0h after PH_technical rep1

description:
S0-1
Gene expression data from normal hepatocyte.


title: RHE 3 + IL22 200 ng/ml

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

description: Type: Vivo

hyb_protocol: RNA was hybridized to HGU133 Plus 2.0 chips to measure relative gene expression.

scan_protocol: Hewlett-Packard GeneArray Scanner

data_processing: GCRMA (using gcrma package from R/Bioconductor)

source_name: Reconstructed Human Epidermis

label_protocol: GeneChip Affymetrix protocol

extract_protocol: Total RNA was extracted using miRNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol with on-column DNase digestion


title: LFS_MB4


title: RHE 3 + IL17 200 ng/ml

description: Type: Vivo


title: RHE 3- No treatment

description: Type: Vivo

value: C


title: RHE 3 + IFNg 20 ng/ml

description: Type: Vivo

value: IFNg


title: RHE 2 + IL22 200 ng/ml

description: Type: Vivo


title: MD_MB_009

value: formalin-fixed paraffin-embedded (FFPE)


title: anti H3K4me3 ChIP in set1D

city: Montpellier

first: Marta

last: Radman-Livaja

address: 1919 route de Mende

department: IGMM

institute: CNRS

description: set1D H3K4me3

hyb_protocol: Labeled probes (a mixture of Cy5 labeled input and Cy3 labeled ChIPed material) were hybridized onto an Agilent yeast 4x44 whole genome array. The arrays were scanned at 5 micron resolution with the Agilent array scanner. Image analysis and data normalization were performed as previously described [1].

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent High Resolution C fluorescent scanner at 5 micron resolution and image intensity data were extracted and analyzed with GenePix Pro 5.1 analysis software.

data_processing: After background correction and removal of flagged values, data was block normalized by dilation and log base 2 ratios (Cy3/Cy5) were calculated to produce the values given in the data table.

organism: Saccharomyces cerevisiae

label_protocol: DNA samples were amplified, with a starting amount of up to 75 ng for ChIP samples, using the DNA linear amplification method described previously [Liu, C.L., S.L. Schreiber, and B.E. Bernstein, BMC Genomics, 2003. 4(1): p. 19.]. 2.5 micrograms of aRNA produced from the linear amplification were labeled via the amino-allyl method as described on www.microarrays.org.

growth_protocol: WT and mutant cells were grown to log phase in YPD media at 30°C

extract_protocol: SET1 (wt), set1Δ500, set1Δ700, and set1Δ cells were grown to log phase and fixed with 1% formaldehyde. Cell pellets (from 100 ml cells) were resuspended in 8.8 ml Buffer Z (1 M sorbitol, 50 mM Tris-Cl pH 7.4), with addition 6.5 μl of β- ME (14.3 M, final conc. 10 mM) and 350 μl of zymolyase solution (10 mg/ml in Buffer Z;Seikagaku America), and the cells were incubated at 30°C, shaking at 220 rpm. After spinning at 4000 G, 10 min, 4°C, spheroplast pellets were resuspended in 600 μl NP-S buffer (0.5 mM spermidine, 1 mM β -ME, 0.075% NP-40, 50 mM NaCl, 10 mM Tris pH 7.4, 5 mM MgCl2, 1mM CaCl2) per 100 ml cell culture equivalent. 25-40 units (depending on yeast strain and celldensity) of micrococcal nuclease (Worthington Biochemical) were added and spheroplasts were incubated at 37°C for 20 minutes. The digestion was stopped by shifting the reactions to 4°C and adding 0.5 M EDTA to a final concentration of 10 mM. All steps were done at 4°C unless otherwise indicated. For each aliquot, Buffer L (50 mM Hepes-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate) components were added from concentrated stocks (10-20X) for a total volume of 0.8 ml per aliquot. Each aliquot was rotated for 1 hour with 100 μl 50% Sepharose Protein A Fast-Flow bead slurry (Sigma) previously equilibrated in Buffer L. The beads were pelleted at 3000 G for 30sec, and approximately 100 μl of the supernatant was set aside for the inputsample. With the remainder, antibodies were added to each aliquot (equivalent to 100 ml of cell culture): 6μl of anti-H3K4me3 or anti-H3K4me2. Immunoprecipitation, washing, protein degradation, and DNA isolation were performed as previously described (Liu et al., 2003).

treatment_protocol: Cells were fixed in 1% formaldehyde.

tag: chip antibody

value: Anti-trimethyl-Histone H3 (Lys4) [Millipore(Upstate) - 07-473]

tag: antibody

value: none (input)


title: anti H3K4me3 ChIP in wt

description: wt H3K4me3

value: wt


title: anti H3K4me3 ChIP in set1D700

description: set1D700 H3K4me3

value: set1D700- 700bp N-treminal truncation of set1


title: anti H3K4me2 ChIP in wt

description: wt H3K4me2

value: Anti-dimethyl-Histone H3 (Lys4) [Millipore(Upstate)- 07-030]


title: anti H3K4me2 ChIP in set1D

description: set1D H3K4me2


title: anti H3K4me2 ChIP in set1D700

description: set1D700 H3K4me2


title: RHE 2 + IL17 200 ng/ml

description: Type: Vivo


title: anti H3K4me3 ChIP in set1D500

description: set1D500 H3K4me3

value: set1D500- 500bp N-treminal truncation of set1


title: RHE 1 + IL17 200 ng/ml

description: Type: Vivo


title: RHE 2- No treatment

description: Type: Vivo


title: 1M10

value: Primary medulloblastoma tumor tissue

value: Group 3

value: fresh-frozen


title: RHE 2 + IFNg 20 ng/ml

description: Type: Vivo


title: RHE 1 + IL22 200 ng/ml

description: Type: Vivo


title: LFS_MB1

value: F

value: SHH


title: ICGC_MB142

value: M


title: ICGC_MB139


title: anti H3K4me2 ChIP in set1D500

description: set1D500 H3K4me2


title: ICGC_MB141


title: ICGC_MB138

value: Group 4


title: ICGC_MB137


title: ICGC_MB134


title: ICGC_MB133


title: ICGC_MB132


title: ICGC_MB131


title: ICGC_MB130

value: WNT


title: Peripheral blood, normal control [N75]

city: Rochester

first: XING

last: LI

state: MN

address: 200 1st street SW

department: Health Sciences Research

institute: Mayo Clinic

description: normal control group

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array (HG-U133_Plus_2). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with R/Bioconductor using RMA.

source_name: Peripheral blood, normal control

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

growth_protocol: The study samples consisted of whole blood collected from first-time AMI patients within 48-hours post-MI and controls with a normal echocardiogram.

extract_protocol: Qiagen RNeasy kit.

treatment_protocol: Blood samples were collected in EDTA tubes within 48-hours of acute myocardial infarction or following recruitment into the study. Nucleated cells were fractionated from 5 mL of heparinized blood.

value: Peripheral blood

tag: disease status

value: normal control


title: Sox3 null Sample 4

city: Adelaide

first: Nicholas

middle: Alan

last: Rogers

state: South Australia

address: MLS building Gate 8 Victoria Drive

department: Biochemistry

country: Australia

institute: University of Adelaide

description: Differentiation batch 2

hyb_protocol: Samples hybridised using a GeneChip 450 fluidics station at the Adelaide Microarray Centre

scan_protocol: Samples scaned using the Affymetrics GeneChip scanner 3000 7Gplus at the Adelaide Microarray Centre

data_processing: Performed by the Adelaide Microarray Centre using the Partek Genomics Suite

organism: Mus musculus

source_name: Fourth day of N2B27 differentiation

label_protocol: Samples labeled using a GeneChip 450 fluidics station at the Adelaide Microarray Centre

growth_protocol: R1 ES cells (Both Conditional and Sox3 null) were mantained on gelatine coated plates in standard ES media before differentiation.

extract_protocol: RNA extractions at day 4 of N2B27 differentiation were performed using a QIAGEN Rneasy mini kit

treatment_protocol: Differentiation of ES cells into Neural progenitors was performed as previously described in Ying et al 2003. Independent samples 1 and 2 (both conditional and Sox3 null) are from an independent differentiation series to that of samples 3 and 4 (both conditional and Sox3 null).

value: Sox3 null

tag: cell line

tag: cell type

value: Embryonic stem cells differentiated into neural progenitor cells


title: Sox3 null Sample 3

description: Differentiation batch 2

tag: genotype


title: Conditional Sample 3

description: Differentiation batch 2

value: Sox3 positive


title: RHE1-No treatment

description: Type: Vitro

value: C


title: RHE 1 + IFNg 20 ng/ml

description: Type: Vivo

value: IFNg


title: Conditional Sample 2

description: Differentiation batch 1


title: Peripheral blood, patient without recurrent events [N74]

description: patient group

value: patient without recurrent events


title: ICGC_MB129


title: MD_MB_002

value: formalin-fixed paraffin-embedded (FFPE)


title: Conditional Sample 1

description: Differentiation batch 1


title: Conditional Sample 4

description: Differentiation batch 2


title: Sox3 null Sample 1

description: Differentiation batch 1


title: Peripheral blood, normal control [N70]

description: normal control group


title: Peripheral blood, normal control [N73]

description: normal control group


title: Peripheral blood, normal control [N68]

description: normal control group


title: Peripheral blood, normal control [N71]

description: normal control group


title: ICGC_MB124

value: Primary medulloblastoma tumor tissue


title: Sox3 null Sample 2

description: Differentiation batch 1


title: Peripheral blood, normal control [N69]

description: normal control group


title: ICGC_MB122


title: ICGC_MB121


title: Peripheral blood, normal control [N66]

description: normal control group


title: Peripheral blood, normal control [N67]

description: normal control group


title: Tumor_18w_vechicle_DEN_134

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

hyb_protocol: Standard Illumina protocol, refer to the Illumina beadarray Assay System Manual

data_processing: For each probe, replicated mesurements (beads) were averaged after removing outliers. Data were were then normalized using the cubic spline algorithm.

source_name: rat, hepatocellular carcinoma (DEN 50mg), treated with vehicle (week 18)

extract_protocol: Using frozen non-tumor liver tissues, total RNA was extracted using TRIzol (Invitrogen).

treatment_protocol: Animals received humane care according to the criteria outlined in the “Guide for the Care and Use of Laboratory Animals” of the National Academy of Sciences. All animals were maintained in accordance with the institutional guidelines of the Massachusetts General Hospital Subcommittee on Research Animal Care. Male Wistar rats received weekly IP injections of diethylnitrosamine (DEN) at 50 mg/kg or vehicle control (PBS) for 18 weeks. A subset of rats received either daily (5X a week) IP injections of 2 mg/kg erlotinib or vehicle control during weeks 13 - 18. Animals were sacrificed at 9, 13 and 19 weeks after a one-week washout period to eliminate acute effects of DEN. At the time of sacrifice, the non-tumor liver tissues were collected in RNase-free tubes and snap-frozen in liquid nitrogen. Frozen tissues were stored at -80°C until RNA extraction.

value: hepatocellular carcinoma tumor

value: vehicle

tag: strain

value: Wistar


title: ICGC_MB119

value: F

value: fresh-frozen


title: Peripheral blood, normal control [N65]

description: normal control group


title: Tumor_18w_erlotinib2_DEN_138

scan_protocol: Standard Illumina protocol, refer to the Illumina beadarray Assay System Manual

source_name: rat, hepatocellular carcinoma (DEN 50mg), treated with erlotinib 2mg (week 18)

value: erlotinib 2mg


title: ICGC_MB118

value: M

value: Group 4


title: Tumor_18w_vechicle_DEN_129

label_protocol: Standard Illumina protocol, refer to the Illumina beadarray Assay System Manual


title: Tumor_18w_vechicle_DEN_123


title: Peripheral blood, normal control [N64]

description: normal control group

value: Peripheral blood

value: normal control


title: ICGC_MB115


title: ICGC_MB114


title: 1M25


title: ICGC_MB113

value: WNT


title: Peripheral blood, normal control [N61]

description: normal control group


title: Peripheral blood, normal control [N63]

description: normal control group


title: Peripheral blood, normal control [N62]

description: normal control group


title: Tumor_18w_erlotinib2_DEN_127


title: wk18_DEN50_Erlotinib2_DEN_31

hyb_protocol: Refer to the Illumina beadarray Assay System Manual

data_processing: For each probe, replicate mesurements were averaged after removing outliers. Data were were then normalized using the cubic spline algorithm using GenePattern IlluminaNormalizer module.

source_name: rat liver, cirrhosis (DEN 50mg), treated with erlotinib 2mg (week 18)

treatment_protocol: Animals received humane care according to the criteria outlined in the “Guide for the Care and Use of Laboratory Animals” of the National Academy of Sciences. All animals were maintained in accordance with the institutional guidelines of the Massachusetts General Hospital Subcommittee on Research Animal Care. Male Wistar rats received weekly IP injections of diethylnitrosamine (DEN) at 50 mg/kg, 100mg/kg, or vehicle control (PBS) for 18 weeks. A subset of rats received either daily (5X a week) IP injections of 2 mg/kg erlotinib or vehicle control during weeks 13 - 18. In a separate study, the erlotinib dose was lowered to 0.5 mg/kg. The vehicle groups from the two studies were not significantly different so they were combined together for analysis. Rats were weighed at the end of each week. Animals were sacrificed at 9, 13 and 19 weeks after a one-week washout period to eliminate acute effects of DEN. At the time of sacrifice, the non-tumor liver tissues were collected in RNase-free tubes and snap-frozen in liquid nitrogen. Frozen tissues were stored at -80°C until RNA extraction.

tag: sex

value: male

value: liver

value: cirrhosis

tag: treatment group

value: treated with erlotinib 2mg


title: ICGC_MB112


title: Peripheral blood, normal control [N58]

description: normal control group


title: Peripheral blood, normal control [N57]

description: normal control group


title: ICGC_MB111

value: Group 3


title: Peripheral blood, normal control [N56]

description: normal control group


title: ICGC_MB110

value: Primary medulloblastoma tumor tissue


title: wk18_DEN50_Erlotinib05_DEN_74

scan_protocol: Refer to the Illumina beadarray Assay System Manual

source_name: rat liver, cirrhosis (DEN 50mg), treated with erlotinib 0.5mg (week 18)

value: treated with erlotinib 0.5mg


title: wk18_DEN50_Erlotinib05_DEN_73

label_protocol: Refer to the Illumina beadarray Assay System Manual


title: wk18_DEN50_Erlotinib2_DEN_29


title: ICGC_MB108


title: Peripheral blood, normal control [N59]

description: normal control group


title: wk18_DEN50_Erlotinib2_DEN_27


title: ICGC_MB107


title: wk18_DEN50_Erlotinib05_DEN_79


title: ICGC_MB106


title: ICGC_MB99


title: wk18_DEN50_Vehicle_DEN_59

source_name: rat liver, cirrhosis (DEN 50mg), treated with vehicle (week 18)

value: treated with vehicle


title: wk18_DEN50_Vehicle_DEN_69

value: Wistar


title: ICGC_MB98


title: Peripheral blood, normal control [N55]

description: normal control group


title: Tumor_18w_erlotinib2_DEN_126

value: hepatocellular carcinoma tumor


title: wk18_PBS_None_PBS_18

source_name: rat liver, control (PBS, week 18)

value: control


title: ICGC_MB96

value: fresh-frozen


title: Peripheral blood, normal control [N53]

description: normal control group


title: Peripheral blood, patient without recurrent events [N50]

description: patient group

value: patient without recurrent events


title: Peripheral blood, normal control [N54]

description: normal control group


title: wk18_PBS_None_PBS_8


title: Peripheral blood, normal control [N52]

description: normal control group


title: Peripheral blood, patient without recurrent events [N51]

description: patient group


title: ICGC_MB95

value: M


title: wk18_PBS_None_PBS_9


title: ICGC_MB94

value: F

value: Group 4


title: wk18_DEN50_Vehicle_DEN_24


title: wk12_DEN100__DEN_113

source_name: rat liver, cirrhosis (DEN 100mg, week 12)


title: ICGC_MB92


title: ICGC_MB91


title: Peripheral blood, patient without recurrent events [N49]

description: patient group

value: Peripheral blood


title: ICGC_MB90


title: Peripheral blood, patient without recurrent events [N48]

description: patient group


title: wk12_DEN50__DEN_14

source_name: rat liver, cirrhosis (DEN 50mg, week 12)

value: male


title: ICGC_MB89


title: Peripheral blood, patient with recurrent events [N47]

description: patient group

value: patient with recurrent events


title: ICGC_MB88

value: SHH


title: Peripheral blood, patient without recurrent events [N45]

description: patient group


title: ICGC_MB85


title: ICGC_MB86


title: Peripheral blood, patient without recurrent events [N44]

description: patient group


title: Peripheral blood, patient without recurrent events [N43]

description: patient group


title: wk12_DEN50__DEN_11

value: liver

value: cirrhosis


title: ICGC_MB83

value: Primary medulloblastoma tumor tissue


title: wk12_DEN100__DEN_111


title: wk12_DEN100__DEN_112


title: Peripheral blood, patient without recurrent events [N46]

description: patient group


title: wk12_PBS__PBS_110

source_name: rat liver, control (PBS, week 12)


title: Peripheral blood, patient without recurrent events [N42]

description: patient group


title: wk12_PBS__PBS_7


title: ICGC_MB84


title: ICGC_MB64


title: wk12_PBS__PBS_108


title: ICGC_MB65


title: Peripheral blood, patient without recurrent events [N41]

description: patient group


title: ICGC_MB51


title: ICGC_MB50

value: Group 3


title: Peripheral blood, patient without recurrent events [N40]

description: patient group


title: ICGC_MB49


title: Peripheral blood, patient without recurrent events [N39]

description: patient group


title: ICGC_MB46

value: WNT


title: ICGC_MB45


title: Peripheral blood, patient without recurrent events [N37]

description: patient group


title: ICGC_MB40


title: ICGC_MB39


title: Peripheral blood, patient without recurrent events [N35]

description: patient group


title: ICGC_MB38


title: ICGC_MB37


title: ICGC_MB36


title: Peripheral blood, patient with recurrent events [N38]

description: patient group


title: Peripheral blood, patient without recurrent events [N36]

description: patient group


title: ICGC_MB35


title: Peripheral blood, patient with recurrent events [N31]

description: patient group


title: Peripheral blood, patient without recurrent events [N33]

description: patient group


title: ICGC_MB34


title: Peripheral blood, patient without recurrent events [N27]

description: patient group


title: ICGC_MB32


title: Peripheral blood, patient without recurrent events [N30]

description: patient group


title: wk12_DEN50__DEN_51

value: Wistar


title: Peripheral blood, patient with recurrent events [N28]

description: patient group


title: ICGC_MB28


title: Peripheral blood, patient without recurrent events [N34]

description: patient group


title: Peripheral blood, patient without recurrent events [N26]

description: patient group


title: Peripheral blood, patient without recurrent events [N29]

description: patient group


title: Peripheral blood, patient without recurrent events [N25]

description: patient group


title: ICGC_MB27


title: Peripheral blood, patient without recurrent events [N24]

description: patient group


title: Peripheral blood, patient without recurrent events [N32]

description: patient group


title: ICGC_MB26


title: ICGC_MB24


title: ICGC_MB21


title: ICGC_MB19


title: ICGC_MB117


title: ICGC_MB18


title: ICGC_MB16


title: ICGC_MB15


title: ICGC_MB7


title: ICGC_MB9


title: ICGC_MB6


title: small_airway_bronch_Normal18

first: Wan

middle: L.

last: Lam

state: British Columbia

address: 675 West 10th Avenue

department: Integrative Oncology

institute: British Columbia Cancer Research Centre

description:
NORMAL18
Epithelial cell DNA from small airways (<2mm) retrieved by bronchial brush

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol.

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

data_processing:
Infinium HM27 methylation sentrix array files (.sdf) and .idat image files were loaded into Ilumina GenomeStudio. Raw data were exported and read into R: A Language and Environment for Statistical Computing version 2.12, and corrected for red green color channel bias and batch effect between multiple methylation experiments, using the Bioconductor package lumi, which applies a color correction and SSN normalization algorithm (Du et al. Lumi: A pipeline for processing illumina microarray. Bioinformatics 2008;24:1547-1548).
M-values exported from the Lumi pipeline were converted to β values by the formula: β values = 2^ M value/ (2^ M value +1), as described in BMC bioinformatics 2010;11:587.

label: Cy5 and Cy3

source_name: small airway epithelia collected during bronchoscopy

label_protocol: Standard Illumina Protocol

extract_protocol: cell pellets are lysed, using standard phenol chloroform extraction followed by ethanol precipitation

treatment_protocol: bronchial brush specimens were stored in Cytolyt at -80°C. Prior to processing, vials are thawed on ice, centirfuged and the pellet washed twice in PBS.

tag: age

value: small airway epithelial cell

tag: disease state

tag: smoking status

value: Former Smoker

tag: yearsquitsmking

tag: packyears


title: ICGC_MB8

tag: gender

tag: age (yrs)

tag: tissue

tag: molecular subgroup

value: fresh-frozen


title: Peripheral blood, patient with recurrent events [N21]

description: patient group


title: small_airway_bronch_Normal19

description:
NORMAL19
Epithelial cell DNA from small airways (<2mm) retrieved by bronchial brush


title: Peripheral blood, patient without recurrent events [N23]

description: patient group

value: patient without recurrent events


title: small_airway_bronch_Normal10

description:
NORMAL10
Epithelial cell DNA from small airways (<2mm) retrieved by bronchial brush


title: small_airway_bronch_Normal9

description:
NORMAL9
Epithelial cell DNA from small airways (<2mm) retrieved by bronchial brush

value: M


title: small_airway_bronch_Normal13

description:
NORMAL13
Epithelial cell DNA from small airways (<2mm) retrieved by bronchial brush


title: small_airway_bronch_Normal20

description:
NORMAL20
Epithelial cell DNA from small airways (<2mm) retrieved by bronchial brush

value: F


title: small_airway_bronch_Normal16

description:
NORMAL16
Epithelial cell DNA from small airways (<2mm) retrieved by bronchial brush


title: small_airway_bronch_Normal22

description:
NORMAL22
Epithelial cell DNA from small airways (<2mm) retrieved by bronchial brush


title: small_airway_bronch_Normal15

description:
NORMAL15
Epithelial cell DNA from small airways (<2mm) retrieved by bronchial brush


title: small_airway_bronch_Normal23

description:
NORMAL23
Epithelial cell DNA from small airways (<2mm) retrieved by bronchial brush


title: ICGC_MB17

tag: sample type


title: small_airway_bronch_Normal17

description:
NORMAL17
Epithelial cell DNA from small airways (<2mm) retrieved by bronchial brush


title: small_airway_bronch_Normal14

description:
NORMAL14
Epithelial cell DNA from small airways (<2mm) retrieved by bronchial brush


title: small_airway_bronch_Normal21

description:
NORMAL21
Epithelial cell DNA from small airways (<2mm) retrieved by bronchial brush


title: ICGC_MB3


title: small_airway_bronch_Normal12

description:
NORMAL12
Epithelial cell DNA from small airways (<2mm) retrieved by bronchial brush


title: ICGC_MB2

value: Group 4


title: ICGC_MB5


title: ICGC_MB1


title: small_airway_bronch_Normal7

description:
NORMAL7
Epithelial cell DNA from small airways (<2mm) retrieved by bronchial brush


title: small_airway_bronch_Normal11

description:
NORMAL11
Epithelial cell DNA from small airways (<2mm) retrieved by bronchial brush


title: small_airway_bronch_Normal6

description:
NORMAL6
Epithelial cell DNA from small airways (<2mm) retrieved by bronchial brush


title: CMS_PFC

city: Nichinomiya

first: Kyosuke

last: Yamanishi

state: Hyogo

address: 1-1, Mukogawa

department: Neuropsychiatry

country: Japan

institute: Hyogo College of Medicine

description: Gene expression with CMS treatment

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE 8x60K for 17 hours at 65°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 37°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 (G2565CA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: prefrontal cortex, with CMS treatment

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug Total RNA using the Low input Quick Amp Labeling Kit (Agilent) according to the manufacture’s instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Total RNA was purified from prefrontal cortex using a Sepasol-RNA I Super (Nacalai Tesque, Kyoto, Japan) according to the manufacturer’s instructions, and treated with five units of RNase free DNase I at 37°C for 30 min to remove genomic DNA contamination. After phenol/chloroform extraction and ethanol precipitation, total RNA was dissolved in de-ionized distilled water. RNA concentrations determined by spectrophotometry.

value: C57Bl/6 N sea

value: prefrontal cortex

tag: treatment

value: chronic mild stress


title: small_airway_bronch_Normal5

description:
NORMAL5
Epithelial cell DNA from small airways (<2mm) retrieved by bronchial brush


title: stat phase ΔscsA3 + 1µM cortisol (minimal medium)

type: mixed

city: Norwich

first: Arthur

last: Thompson

address: Colney Lane

institute: Institute of Food Research

description: Biologica replicate 3 of 3

hyb_protocol: Hybridisation according to Erikkson et al., 2006 Inf & Imm., 74:1243 and http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols

scan_protocol: GenePix 4000A at 10µm resolution

data_processing: Intensity ratios of channel 1 (cDNA) divided by channel 2 (reference gDNA) signals are calculated usiong BlueFuse 3.01 (BlueGnome, Cambridge, UK). Data centering was subsequently performed using the block median

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: S. Typhimurium ΔscsA + cort. Biol. Rep. 3

label_protocol: Labelling according to Erikkson et al., 2006 Inf & Imm., 74:1243 and http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols

growth_protocol: Grown aerobically at 370C with shaking at 250rpm in minimal medium MM5.8 (Erikkson et al., 2006 Inf & Imm., 74:1243) to stationary phase overnight

extract_protocol: RNA extracted according to Erikkson et al., 2006 Inf & Imm., 74:1243 and http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols

treatment_protocol: Where appropriate 1µm cortisol added.

value: 1µM cortisol

source_name: S. Typhimurium 112910a


title: Control_PFC

description: Gene expression with no treatment

source_name: prefrontal cortex, with no treatment

value: male

value: control


title: stat phase ΔscsA3 (minimal medium)

description: Biologica replicate 3 of 3

source_name: S. Typhimurium ΔscsA. Biol. Rep. 3


title: stat phase ΔscsA2 + 1µM cortisol (minimal medium)

description: Biologica replicate 2 of 3

source_name: S. Typhimurium ΔscsA + cort. Biol. Rep. 2


title: small_airway_bronch_Normal8

description:
NORMAL8
Epithelial cell DNA from small airways (<2mm) retrieved by bronchial brush


title: ICGC_MB14

hyb_protocol: According to the manufacturer’s instructions

scan_protocol: Illumina iScan System, according to the manufacturer’s instructions

data_processing: Array processing was performed using Illumina GenomeStudio V2011.1 (Methylation Module version 1.9.0). The 'MB-450k_GEOupload_Raw.txt' contains unmethylated and methylated signal intensities. Signal intensities were obtained without background subtraction and normalized to internal controls. The 'MB-450k_GEOupload_Beta.txt' contains 'Beta-values'.

source_name: Primary medulloblastoma tumor tissue

value: Primary medulloblastoma tumor tissue


title: stat phase ΔscsA1 + 1µM cortisol (minimal medium)

description: Biologica replicate 1 of 3

source_name: S. Typhimurium ΔscsA + cort. Biol. Rep. 1


title: small_airway_bronch_Normal4

description:
NORMAL4
Epithelial cell DNA from small airways (<2mm) retrieved by bronchial brush


title: liver_hypothyroid-orquiectomized rats_E2-GH_rep2

city: Las Palmas de Gran Canaria

first: Leandro

last: Fernandez-Perez

state: Las Palmas

address: Campus of San Cristóbal

department: Clinical Sciences

country: Spain

institute: University of Las Palmas de Gran Canaria

description: Biological replicate 2 of 4: hypothyroid-orquiectomized rats treated with E2 plus GH

hyb_protocol: Hybridized following the manufacturer’s protocol (ProntoTM Plus System, Promega). After 16 h of hybridization, the slides were washed and scanned.

scan_protocol: Scanned on a GenePix Microarray Scanner (Axon Instruments, CA) Images were quantified using the GenePix Pro 6.0 software (Axon Instruments, Union City, CA).

data_processing:
The LOWESS normalized, background subtracted data obtained from log2 of processed red signal/processed green signal. GenePix software was used.
If the measured probe sets were not present in at least 3 of the 4 chips, they were assumed to contain no information and therefore were eliminated to reduce data complexity. Differentially expressed genes were identified by using the SAM (Significance Analysis for Microarrays) statistical technique.

source_name: TXOX rats_liver_E2_GH

label_protocol: 5 µg of high-quality total RNA from the liver were reversed-transcribed, labeled, and hybridized following the manufacturer’s protocol (ProntoTM Plus System, Promega).

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

treatment_protocol: E2 benzoate plus GH to TXOX rats

value: Sprague-Dawley rats

tag: genotype/variation

value: hypothyroid-orchiectomized (TXOX)

tag: treated with

value: E2 plus GH (TXOXE2GH)

value: liver

value: 3 months

value: vehicle (TXOX)


title: liver_hypothyroid-orquiectomized rats_E2-GH_rep4

description: Biological replicate 4 of 4: hypothyroid-orquiectomized rats treated with E2 plus GH


title: stat phase ΔscsA2 (minimal medium)

description: Biologica replicate 2 of 3

source_name: S. Typhimurium ΔscsA. Biol. Rep. 2

tag: genotype


title: stat phase ΔscsA1 (minimal medium)

description: Biologica replicate 1 of 3

source_name: S. Typhimurium ΔscsA. Biol. Rep. 1

tag: strain


title: liver_hypothyroid-orquiectomized rats_E2-GH_rep1

description: Biological replicate 1 of 4: hypothyroid-orquiectomized rats treated with E2 plus GH


title: liver_hypothyroid-orquiectomized rats_E2-GH_rep3

description: Biological replicate 3 of 4: hypothyroid-orquiectomized rats treated with E2 plus GH


title: erlot5_CT36

source_name: mouse, liver (CCl4), treated with erlotinib 5mg (week 18)

treatment_protocol: Animals received humane care according to the criteria outlined in the “Guide for the Care and Use of Laboratory Animals” of the National Academy of Sciences. All animals were maintained in accordance with the institutional guidelines of the Massachusetts General Hospital Subcommittee on Research Animal Care. Strain A/J male mice (Jackson Laboratory, Bar Harbor, ME) were treated three times a week for 18 weeks with either 0.1cc of a 40 percent solution of CCl4 (Sigma) in olive oil or with vehicle control by oral gavage.  Mice were sacrificed at 19 weeks after a one-week washout to eliminate acute effects of CCl4.  The liver was sectioned and fixed in phosphate-buffered 10% formaldehyde for histological analysis.  The remaining portions of the liver were collected in RNase-free tubes and snap-frozen in liquid nitrogen.  Frozen tissues were stored at -80°C until use.

value: CCl4 and erlotinib 5 mg

value: A/J


title: erlot5_CT37


title: small_airway_bronch_COPD15

description:
COPD15
Epithelial cell DNA from small airways (<2mm) retrieved by bronchial brush

value: F

tag: cell type

value: small airway epithelial cell

value: Chronic Obstructive Pulmonary Disease

value: Former Smoker


title: small_airway_bronch_Normal1

description:
NORMAL1
Epithelial cell DNA from small airways (<2mm) retrieved by bronchial brush

value: M


title: small_airway_bronch_COPD14

description:
COPD14
Epithelial cell DNA from small airways (<2mm) retrieved by bronchial brush


title: small_airway_bronch_Normal2

description:
NORMAL2
Epithelial cell DNA from small airways (<2mm) retrieved by bronchial brush


title: liver_hypothyroid-orquiectomized rats_GH_rep4

description: Biological replicate 4 of 4: hypothyroid-orquiectomized rats treated with GH

source_name: TXOX rats_liver_GH

treatment_protocol: GH (0.3 mg/kg/day; sb;  two injections carried out at 08.00 h and 20.00 h) to TXOX rats x 7 days.

value: vehicle plus GH (TXOXGH)


title: small_airway_bronch_Normal3

description:
NORMAL3
Epithelial cell DNA from small airways (<2mm) retrieved by bronchial brush


title: erlot2_CT41

source_name: mouse, liver (CCl4), treated with erlotinib 2mg (week 18)

value: CCl4 and erlotinib 2mg


title: stat phase wt2 + 1µM cortisol (minimal medium)

description: Biologica replicate 2 of 3

source_name: S. Typhimurium wt + cort. Biol. Rep. 2

value: 1µM cortisol

value: wt


title: cont_OO12

source_name: mouse, liver (control) (week 18)

value: vehicle


title: stat phase wt1 + 1µM cortisol (minimal medium)

description: Biologica replicate 1 of 3

source_name: S. Typhimurium wt + cort. Biol. Rep. 1


title: stat phase wt3 + 1µM cortisol (minimal medium)

description: Biologica replicate 3 of 3

source_name: S. Typhimurium wt + cort. Biol. Rep. 3


title: erlot2_CT42


title: stat phase wt3 (minimal medium)

description: Biologica replicate 3 of 3

source_name: S. Typhimurium wt. Biol. Rep. 3


title: small_airway_bronch_COPD12

description:
COPD12
Epithelial cell DNA from small airways (<2mm) retrieved by bronchial brush

source_name: small airway epithelia collected during bronchoscopy


title: cont_OO11


title: small_airway_bronch_COPD11

description:
COPD11
Epithelial cell DNA from small airways (<2mm) retrieved by bronchial brush


title: small_airway_bronch_COPD13

description:
COPD13
Epithelial cell DNA from small airways (<2mm) retrieved by bronchial brush


title: small_airway_bronch_COPD10

description:
COPD10
Epithelial cell DNA from small airways (<2mm) retrieved by bronchial brush


title: liver_hypothyroid-orquiectomized rats_GH_rep2

description: Biological replicate 2 of 4: hypothyroid-orquiectomized rats treated with GH

value: Sprague-Dawley rats

value: hypothyroid-orchiectomized (TXOX)

value: male


title: stat phase wt1 (minimal medium)

description: Biologica replicate 1 of 3

source_name: S. Typhimurium wt. Biol. Rep. 1

source_name: S. Typhimurium 112910a


title: liver_hypothyroid-orquiectomized rats_GH_rep3

description: Biological replicate 3 of 4: hypothyroid-orquiectomized rats treated with GH

value: liver

value: 3 months


title: liver_hypothyroid-orquiectomized rats_E2_rep4

description: Biological replicate 4 of 4: hypothyroid-orquiectomized rats treated with E2

source_name: TXOX rats_liver_E2

treatment_protocol: E2 benzoate (50 ug/kg; sb; 5 days/week) to TXOX rats x 27 days

value: E2 benzoate (TXOXE2)

value: vehicle (TXOX)


title: liver_hypothyroid-orquiectomized rats_GH_rep1

description: Biological replicate 1 of 4: hypothyroid-orquiectomized rats treated with GH


title: CCl4_CT20

source_name: mouse, liver (CCl4) (week 18)

value: A/J


title: small_airway_bronch_COPD9

description:
COPD9
Epithelial cell DNA from small airways (<2mm) retrieved by bronchial brush

value: F

value: small airway epithelial cell


title: CCl4_CT19


title: CCF-004 replicate 3

city: Chicago

first: Guofei

last: Zhou

state: IL

address: 840 S Wood St, ste 1206, MC856

department: Pediatrics

institute: University of Illinois at Chicago

description: test

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://pcrdataanalysis.sabiosciences.com/pcr/arrayanalysis.php
For the normalization it uses the average of four housekeeping miRNA genes: has-SNORD48, has-SNORD47, has-SNORD44, has-U6. Each plate also contains 2 RNA quality (miRTC), and 2 PCR-positive controls (PPC).
Target miRNA gene signals normalized to housekeeping miRNA genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change worksheet reports test/control (i.e., PAH hPASMC/Normal hPASMC) ratios.

label: SYBR Green

source_name: PAH patient with Scleroderma

label_protocol: miRNAs were reversely transcribed using a RT2 miRNA First Strand Kit (SABiosciences).

growth_protocol: hPASMC are cultured with SmBM-2 medium containing 5% fetal bovine serum and growth factors (SmGM-2 BulletKit, purchased from Lonza) and 1% penicillin-streptomycin.

extract_protocol: hPASMC total RNA was isolated by miRNeasy Mini Kit (Qiagen) followed by Dnase I treatment (Rnase-Free Dnase Set (Qiagen)).

tag: diagnosis

value: PAH with Scleroderma Syndrome

tag: tissue type

value: lung

value: human pulmonary artery smooth muscle cells (HPASMC)


title: liver_hypothyroid-orquiectomized rats_E2_rep3

description: Biological replicate 3 of 4: hypothyroid-orquiectomized rats treated with E2

tag: age


title: small_airway_bronch_COPD6

description:
COPD6
Epithelial cell DNA from small airways (<2mm) retrieved by bronchial brush

tag: disease state

value: Chronic Obstructive Pulmonary Disease

tag: smoking status

value: Former Smoker


title: liver_hypothyroid-orquiectomized rats_E2_rep2

description: Biological replicate 2 of 4: hypothyroid-orquiectomized rats treated with E2


title: liver_hypothyroid-orquiectomized rats_E2_rep1

description: Biological replicate 1 of 4: hypothyroid-orquiectomized rats treated with E2


title: CD8 continuous 5 days, rep2

city: Neuherberg

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum München GmbH

description:
Sample 27
Gene expression data of CD8+ OT1-TCR transgenic cells stimulated with anti-CD3 and anti-CD28 for 2 days of culture and additional 3 days in antigen-expressing host.

hyb_protocol: Biotin-labled cRNA was hybridized on Affymetrix Mouse Genome 430.2 arrays in a GeneChip Hybridization oven 645, washed and stain3d with a GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000.

data_processing: Primary CEL files were normalized with the ExpressionFileCreator module implementing RMA and redundant probe sets collapsed with the CollapseDataset module.

source_name: day 5, CD8, continuously stimulated

label_protocol: Amplified aRNA (10µg) was processed using the Message Amp II-Biotin Enhanced Kit (Ambion).

growth_protocol: 1-2x10^5 TCR transgenic CD4+ or CD8+ T cells were cultured for 2 days in 96-well untreated round bottom plates or plates precoated with 10 µg/ml anti-CD3 and anti-CD28 mAbs in RPMI supplemented with 10% FCS, 2 mM glutamine, 50µM 2-ME, antibiotics and 5 ng/ml IL7.

extract_protocol: RNAs from AND and OT1 cells sorted from spleen and subcutaneous lymph nodes were isolated as described (Obst et al,. 2007, Proc Natl Acad Sci USA 104, 15460-15465).

treatment_protocol: For samples 13-28, T cells were adoptively transferred into antigen-free or -expressing (dtg-O or -M) hosts.

tag: strain/background

value: CD8+ OT1-TCR transgenic T lymphocytes

value: stimulated with anti-CD3 and anti-CD28 mAbs in culture

tag: host

value: antigen-expressing


title: CCF-004 replicate 2

description: test


title: CCF-004 replicate 1

description: test


title: CC-008 replicate 2

description: test

source_name: PAH patient with Eisenmenger’s syndrome

value: PAH with Eisenmenger's Syndrome


title: small_airway_bronch_COPD8

description:
COPD8
Epithelial cell DNA from small airways (<2mm) retrieved by bronchial brush

tag: gender

tag: yearsquitsmking

tag: packyears


title: B157 replicate 3

description: test

source_name: IPAH patient

value: IPAH


title: CD8 continuous 5 days, rep1

description:
Sample 26
Gene expression data of CD8+ OT1-TCR transgenic cells stimulated with anti-CD3 and anti-CD28 for 2 days of culture and additional 3 days in antigen-expressing host.


title: small_airway_bronch_COPD4

description:
COPD4
Epithelial cell DNA from small airways (<2mm) retrieved by bronchial brush

value: M


title: CD8 transient 5 days, rep2

description:
Sample 24
Gene expression data of CD8+ OT1-TCR transgenic cells stimulated with anti-CD3 and anti-CD28 for 2 days of culture and additional 3 days in antigen-free host.

source_name: day 5, CD8, transiently stimulated

value: antigen-free


title: small_airway_bronch_COPD7

description:
COPD7
Epithelial cell DNA from small airways (<2mm) retrieved by bronchial brush


title: small_airway_bronch_COPD5

description:
COPD5
Epithelial cell DNA from small airways (<2mm) retrieved by bronchial brush


title: CD8 continuous 5 days, rep3

description:
Sample 28
Gene expression data of CD8+ OT1-TCR transgenic cells stimulated with anti-CD3 and anti-CD28 for 2 days of culture and additional 3 days in antigen-expressing host.


title: CD8 transient 5 days, rep3

description:
Sample 25
Gene expression data of CD8+ OT1-TCR transgenic cells stimulated with anti-CD3 and anti-CD28 for 2 days of culture and additional 3 days in antigen-free host.


title: small_airway_bronch_COPD1

description:
COPD1
Epithelial cell DNA from small airways (<2mm) retrieved by bronchial brush


title: CC-008 replicate 3

description: test


title: B157 replicate 1

description: test


title: CD8 unstimulated 5 days, rep3

description:
Sample 22
Gene expression data of unstimulated CD8+ OT1-TCR transgenic cells following 2 days of culture and 3 days in an antigen-free host.

source_name: day 5, CD8, unstimulated

value: unstimulated in culture


title: LPS-24h

city: Birmingham

first: Gang

last: Liu

state: Alabama

address: 901 19TH ST S

department: Medicine

institute: University of Alabama at Birmingham

description: 1_Exiqon*.txt' and '0_Exiqon*.txt' represent the raw data for Hy3 and Hy5, respectively

hyb_protocol: The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY™ LNA Array version 10.0 (Exiqon, Denmark). The hybridization was performed according to the miRCURY™ LNA array manual using a Tecan hybridization station (Tecan, Austria).

scan_protocol: After hybridization, arrays are scanned with highly sensitive equipment in ozone free environment to reduce day-to-day variation to a minimum. Image Analysis is then performed to quantify the signals on the arrays.

data_processing: The quantified signals were background corrected (Normexp with offset value 10 – Ritchie et al., 2007) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.

source_name: Mouse peritoneal macrophages

label_protocol: RNA was labelled using the miRCURY™ Hy3™/Hy5™ power labelling kit (Exiqon, Denmark) following the procedure described by the manufacturer.

growth_protocol: DMEM containing 10% FBS, 37 degree and 5% CO2.

extract_protocol: Total RNA was extracted using Qiagen RNAeasy kit following manufacturer's instructions.

treatment_protocol: After overnight culture in complete medium, cells were treat with 100 ng/ml LPS for 0, 4, 12 and 24h, respectively.

tag: cell line

value: Peritoneal macrophages

value: 100 ng/ml LPS for 24 hrs


title: LPS-12h

tag: treatment

value: 100 ng/ml LPS for 12 hrs


title: LPS-4h

value: 100 ng/ml LPS for 4 hrs


title: CD8 unstimulated 5 days, rep1

first: Martin

description:
Sample 20
Gene expression data of unstimulated CD8+ OT1-TCR transgenic cells following 2 days of culture and 3 days in an antigen-free host.


title: small_airway_bronch_COPD2

description:
COPD2
Epithelial cell DNA from small airways (<2mm) retrieved by bronchial brush

value: small airway epithelial cell


title: small_airway_bronch_COPD3

description:
COPD3
Epithelial cell DNA from small airways (<2mm) retrieved by bronchial brush


title: B157 replicate 2

description: test

value: lung


title: CC-008 replicate 1

description: test

value: human pulmonary artery smooth muscle cells (HPASMC)


title: CD4 continuous 5 days, rep3

description:
Sample 19
Gene expression data of CD4+ AND-TCR transgenic cells stimulated with anti-CD3 and anti-CD28 for 2 days of culture and additional 3 days in antigen-expressing host.

source_name: day 5, CD4, continuously stimulated

value: CD4+ AND-TCR transgenic T lymphocytes


title: LPS-0h


title: CD8 unstimulated 5 days, rep2

description:
Sample 21
Gene expression data of unstimulated CD8+ OT1-TCR transgenic cells following 2 days of culture and 3 days in an antigen-free host.


title: C128 replicate 3

description: control

source_name: normal donor

value: Normal


title: CD4 continuous 5 days, rep2

description:
Sample 18
Gene expression data of CD4+ AND-TCR transgenic cells stimulated with anti-CD3 and anti-CD28 for 2 days of culture and additional 3 days in antigen-expressing host.


title: CD8 transient 5 days, rep1

description:
Sample 23
Gene expression data of CD8+ OT1-TCR transgenic cells stimulated with anti-CD3 and anti-CD28 for 2 days of culture and additional 3 days in antigen-free host.

value: CD8+ OT1-TCR transgenic T lymphocytes


title: CD4 continuous 5 days, rep1

description:
Sample 17
Gene expression data of CD4+ AND-TCR transgenic cells stimulated with anti-CD3 and anti-CD28 for 2 days of culture and additional 3 days in antigen-expressing host.

value: stimulated with anti-CD3 and anti-CD28 mAbs in culture


title: C128 replicate 2

description: control


title: C128 replicate 1

description: control


title: Control F

city: Boston

first: Vijay

middle: G

last: Sankaran

state: MA

address: 300 Longwood Avenue

institute: Boston Children's Hospital

description: Control F

hyb_protocol: Standard Affymetrix HG-U133A arrays were hybridized with purified RNA samples.

scan_protocol: Signal amplication on Affymetrix Fluidics station 400

data_processing: Microarray data were processed with RMA from the affy package in Bioconductor using custom probeset definitions for NCBI Entrez Genes derived from the method of Dai M et al (PMID: 16284200): HG-U133A Version 16 Custom CDF.

source_name: Control F

label_protocol: Standard Affymetrix label protocol

growth_protocol: Primary patient samples that did not involve cell culture.

extract_protocol: Qiagen RNA purification

treatment_protocol: Primary CD34+/CD71(high)/CD45- mononuclear cells of the bone marrow of DBA patients (with RPS19 mutations) and controls were harvested and sorted.

tag: tissue

value: bone marrow

tag: disease status

value: healthy control


title: Control E

description: Control E

source_name: Control E


title: CD4 transient 5 days, rep1

description:
Sample 15
Gene expression data of CD4+ AND-TCR transgenic cells stimulated with anti-CD3 and anti-CD28 for 2 days of culture and additional 3 days in antigen-free host.

source_name: day 5, CD4, transiently stimulated


title: CD4 unstimulated 5 days, rep2

description:
Sample 14
Gene expression data of unstimulated CD4+ AND-TCR transgenic cells following 2 days of culture and 3 days in an antigen-free host.

source_name: day 5, CD4, unstimulated


title: Control D

description: Control D

source_name: Control D


title: Control C

description: Control C

source_name: Control C


title: DBA patient A

description: DBA patient A

source_name: DBA patient A

value: Diamond-Blackfan anemia (due to RPS19 mutations)


title: DBA patient B

description: DBA patient B

source_name: DBA patient B