title: Pupae at RPM (0g) constrained (ΔT), biological rep1

description:
DmPupae_70A.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis

value: suboptimal


title: Pupae outside RPM (1g) without constrains, biological rep3

status: Public on Jun 26 2013

type: RNA

city: Madrid

first: Raúl

last: Herranz

state: Madrid

address: Ramiro de Maeztu 9

department: Plant Cell Nucleolus, proliferation and microgravity

country: Spain

institute: Centro Investigaciones Biológicas

description:
DmPupae_81C.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis

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

scan_protocol: GeneChips were scanned using GeneChip® Scanner 3000 7G System

data_processing: Analysis was performed using FIESTA viewer (bioinfogp.cnb.csic.es/tools/FIESTA). Robust Multi-array Analysis (RMA) algorithm was used for background correction, normalization and expression levels summarization (Irizarry et al., 2003). Next, differential expression analysis was performed with the Bayes t-statistics from the linear models for Microarray data (limma). P-values were corrected for multiple-testing using the Benjamini-Hochberg’s method (False Discovery Rate) (Benjamini and Hochberg, 1995; Reiner et al., 2003).

label: biotin

molecule: total RNA

organism: Drosophila melanogaster

source_name: Drosophila pupae before imagoes hatch

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: OreR late larvae were developed at 24C during 3.5 days into different gravitational and environmental conditions

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

treatment_protocol: Early pupae were exposed to a cold step (ΔT) previous to the gravitational treatment or not. During the gravitational treatment pupae have a limite amount of oxigen (↓O2) in a closed container or not. Flies were exposed to different altered gravity simulators (RPM, Magnetic levitator, centrifgue) and inmediately after the treatment were placed on ice in the Trizol solution (GibcoBRL).

tag: developmental stage

value: late pupae

tag: strain

value: Oregon R

tag: age

value: late pupae just before eclosion

tag: g level

tag: environment (Δt)

value: normal

tag: environment (↓o2)

tag: magnetic field (*)

value: No


title: colon_NMS_M_2

city: Perugia

first: Stefano

last: Fiorucci

address: Via E dal Pozzo

department: Dipartimento di Medicina Clinica e Sperimentale

country: Italy

institute: Universita di Perugia

hyb_protocol: Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to Agilent Whole Rat Genome Oligo Microarrays 8x60K using Agilent’s recommended hybridization chamber and oven. Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C and a final wash step with acetonitrile for 30 sec at RT.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: FES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system (Rosetta Biosoftware, Rosetta error model; Lee Weng et al 2006). Cotrol probes were not included in the processing.

organism: Rattus norvegicus

label_protocol: 100 ng of each RNA was used as template to produce Cy3- labeled cRNA. The RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.

growth_protocol: Male, Wistar rats  (200-250 g, Charles River, Monza, Italy) were housed in plastic cages and maintained under controlled conditions. All experimental procedures were approved by our institutional animal research committees and were in accordance with nationally approved guidelines for the treatment of laboratory animals. All experiments were conducted in blind manner in that the observers  were not aware of the identity of drugs administered to each animal. Pups in the NMS group were separated from their mothers and placed into individual cages in another room for 180 min daily from postnatal day 2 to day 14, whereas normally-handled (NH) pups were maintained in their home cage with the dam. All rats were treated daily by gavage with placebo or VSL#3 at the dose of 18 billions in 100 μL saline according to the experimental design. Microarray studies were conducted on in Group 2 (healthy, CRD, Group C), Group 4 (NMS, CRD, Group M) and Group 5 (NMS, VSL#3 administered from day 3 to day 60, CRD, Group D).  At the end of the studies (postnatal day 60), animals were sacrificed and the colon collected.

extract_protocol: The RNA was isolated by using standard RNA extraction protocols (Trizol, Sigma-Aldrich) and the RNA quality checked via the Agilent 2100 Bioanalyzer platform (Agilent Technologies). Only RNAs with calculated RNA Integrity Numbers (RIN) higher than 6 were accepted.

value: Wistar rats

tag: gener

value: male

tag: weight

tag: tissue

value: colon

tag: neonatal maternal separation (nms)

value: yes

tag: treatment

value: daily by gavage with placebo (100 ul saline)

tag: treatment period

value: day 3 to day 60


title: 016514

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description:
Mela-TBD35 vs. Amela-514
Date:2006/09/01

hyb_protocol: CGH-Agilent-4rpm : 750.0 ng at 62 degree_C during 17 hours

scan_protocol: Scanned on a GenePix 4000B fluorescent scanner. Image intensity data were extracted with GenePix Pro 6.0 analysis software.

data_processing: Interslide normalization: scale, Intraslide normalization: printtiploess, Background normalization: Kooperberg, Software used: rscript. VALUE data obtained from log of processed Red signal/processed Green signal.

organism: Mus musculus

label_protocol: Ambion

extract_protocol: Roche

value: TiRP Ink4a/ArfF/F B10.D2

tag: sample

value: pigmented melanotic melanoma

value: nonpigmented amelanotic melanoma


title: 032865

description:
Amela cell line 288 vs. Amela-288
Date:2007/04/04

hyb_protocol: Agilent : 750.0 ng at 62 degree_C during 16 hours

data_processing: Interslide normalization: quantile, Intraslide normalization: printtiploess, Background normalization: Kooperberg, Software used: rscript. VALUE data obtained from log of processed Red signal/processed Green signal.

source_name: Amela cell line 288

extract_protocol: Other

value: Amela cell line 288

tag: cell line

value: Amela 288

tag: cell type

value: nonpigmented amelanotic melanoma cells


title: 016650

description:
CTRL vs. Mela-442
Date:2006/09/05

source_name: CTRL

value: CTRL

value: healthy tail skin


title: Pupae outside RPM (1g) without constrains, biological rep2

description:
DmPupae_81B.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis

value: late pupae

value: Oregon R

value: late pupae just before eclosion


title: Hakas9_162

type: genomic

city: Tartu

first: Mait

last: Metspalu

address: Riia 23

country: Estonia

institute: Estonian Biocentre

description: Genomic DNA extracted from blood was genotyped using Human660W-Quad v1.0 Genotyping BeadChips (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48°C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol, dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Image data was analyzed using Genomestudio v2011.1 with GT module 1.9.4 (Illumina).

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: blood

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37°C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from blood was performed using standard extraction protocols.

value: blood

tag: gender

value: Male

tag: population

value: Khakases

tag: region

value: South Siberia


title: colon_NMS_M_1

tag: strain

value: Wistar rats

value: male

value: colon

value: yes

value: daily by gavage with placebo (100 ul saline)


title: 032927

description:
Amela cell line 429 vs. Amela-353
Date:2007/04/04

source_name: Amela cell line 429

value: TiRP Ink4a/ArfF/F B10.D2

value: Amela cell line 429

value: Amela 429

value: nonpigmented amelanotic melanoma


title: Pupae outside RPM (1g) without constrains, biological rep1

description:
DmPupae_81A.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis

tag: developmental stage

tag: age

tag: g level

value: normal

value: No


title: 017539

description:
CTRL vs. Amela-514
Date:2006/09/05

value: CTRL

value: healthy tail skin


title: colon_healthy_C_4

value: no (NH; normally handled)

value: day 3 to day 60


title: SR-TK_rep2

city: Ghent

first: Wannes

last: Dermauw

address: Coupure Links 653

department: Crop Protection

country: Belgium

institute: University Ghent

description: Biological replicate 2 of 2, SR-TK vs. LS-VL

hyb_protocol: Cy3 and Cy5 labeled cRNAs were pooled and hybridized using the Gene Expression Hybridization Kit (Agilent Technologies) for 17h in a rotating hybridization oven at 20 r.p.m. and 65°C; Slides were washed using the Gene Expression Wash Buffer Kit (Agilent Technologies)

scan_protocol: Hybridized arrays were scanned using an Agilent Microarray High Resolution Scanner.

data_processing: Data were extracted and normalized using Agilent Feature Extraction Software 10.5 with default parameter settings for gene expression two-color microarrays (protocol GE2_105_Dec08). Further processed 'fold change' data are generated using Genespring.

organism: Tetranychus urticae

source_name: SR-TK

label_protocol: 100 ng of total RNA (+ RNA-spike in control) was used to generate Cy3 or Cy5 labeled cRNAs, using the Agilent Low Input Quick Amp Labeling Kit (version 6.5 Agilent Technologies)

growth_protocol:
T. urticae  strains, LS-VL, SR-VP and SR-TK, were grown on potted kidney bean (Phaseolus vulgaris cv. "Prelude") plants at 26+-0.5°C, 60% RH and a 16/8h light/dark period. In addition, SR-VP and SR-TK were maintained under selection pressure using 5000 mg/L and 1000 mg/L spirodiclofen, respectively.
For microarray experiments, 3 x 250 adult females of each strain were permitted to lay eggs, for approximately 6 hours, on a bean leaf on wet cotton wool (250 females/strain/bean leaf) after which they were removed.
Bean leaves were then placed in a climatically controlled room at 26°, 60% RH and 16/8h L/D photoperiod. Egss hatched and once developed to the deutonymph stage, mites of each strain were collected for total RNA extraction.

extract_protocol: Total RNA was extracted from about 200 deutonymph female spider mites using RNEasy Mini Kit (Qiagen) following manufacturer's instructions.

value: deutonymph

value: female

source_name: LS-VL


title: Pupae at RPM (0g) without constrains, biological rep3

description:
DmPupae_80C.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis

value: late pupae

value: Oregon R

value: late pupae just before eclosion

tag: environment (Δt)

tag: environment (↓o2)

tag: magnetic field (*)


title: colon_healthy_C_3

value: Wistar rats

tag: gener

value: male

tag: weight

tag: tissue

value: colon


title: 016482

description:
Amela-353 vs. Mela-281
Date:2006/09/07

value: TiRP Ink4a/ArfF/F B10.D2

value: pigmented melanotic melanoma


title: Pupae at RPM (0g) without constrains, biological rep2

description:
DmPupae_80B.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: colon_NMS_M_3

tag: neonatal maternal separation (nms)

value: yes

tag: treatment

value: daily by gavage with placebo (100 ul saline)

tag: treatment period


title: colon_healthy_C_2


title: Hakas8_238

value: blood

value: Male

value: Khakases

value: South Siberia


title: 016532

description:
Mela-281 vs. CTRL
Date:2006/09/08

tag: sample

value: CTRL

value: healthy tail skin


title: colon_healthy_C_1

value: no (NH; normally handled)

value: day 3 to day 60


title: Pupae at RPM (0g) without constrains, biological rep1

description:
DmPupae_80A.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis

value: late pupae

value: Oregon R

value: normal

value: No


title: 016508

description:
Amela-396 vs. Mela-442
Date:2006/09/01

value: nonpigmented amelanotic melanoma


title: SR-VP_rep3

description: Biological replicate 3 of 3, SR-VP vs. LS-VL

source_name: SR-VP

value: deutonymph

tag: gender

value: female


title: Hakas6

tag: population


title: 016668

description:
Mela-TBD35 vs. CTRL
Date:2006/09/05

value: TiRP Ink4a/ArfF/F B10.D2

value: pigmented melanotic melanoma


title: Healthy T5N_Gene1.0_2

status: Public on Jun 25 2013

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

institute: IRCCS Istituto Nazionale dei Tumori

description: Gene expression profiling data from human healthy donor T5N

hyb_protocol: The fragmented labeled single-stranded DNA target was hybridized for 16 hours and 30 minutes at 45°C on GeneChip® Gene 1.0 ST array according to the standard Affymetrix protocol.

scan_protocol: Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450 and GeneChip Scanner 7G).

data_processing: The raw intensity expression values were processed by Robust Multi-array Average (RMA) complete procedure with the re-mapped Chip Definition Files (CDF) from BrainArray libraries version 15.0.0 available at http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/15.0.0/entrezg.asp.

source_name: Human tonsillar plasma cells from healthy donor T5N

label_protocol: 5.5 micrograms of single-stranded DNA target obtained from 100 ng of purified total RNA was fragmented and then labeled using the WT Terminal Labeling Kit according to the standard Affymetrix protocol (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (Gibco BRL). RNA was purified using the Rneasy Mini Kit according to the manufacturer's instruction (Qiagen).

treatment_protocol: Plasma cells were purified from bone marrow samples using CD138 immunomagnetic microbeads according to the manufacturer's instructions (MidiMACS system, Miltenyi Biotec); the purity of the positively selected PCs was assessed by morphology and flow cytometry and was > 90% in all cases.

tag: cell type

value: Human tonsillar plasma cells

tag: disease state

value: healthy

tag: genetic variation

value: normal sample


title: SR-TK_rep1

description: Biological replicate 1 of 2, SR-TK vs. LS-VL

tag: age


title: Healthy T6N_Gene1.0_2

description: Gene expression profiling data from human healthy donor T6N

source_name: Human tonsillar plasma cells from healthy donor T6N


title: Hakas58

value: blood

value: Male

value: Khakases

tag: region

value: South Siberia


title: Healthy T4N_Gene1.0_2

description: Gene expression profiling data from human healthy donor T4N

source_name: Human tonsillar plasma cells from healthy donor T4N


title: Plasma cell leukemia PCL-031_Gene1.0_2

description: Gene expression profiling data from human primary plasma cell leukemia patient PCL-031

source_name: Human bone marrow plasma cells from primary plasma cell leukemia patient PCL-031

value: Human bone marrow plasma cells

value: primary plasma cell leukemia


title: Plasma cell leukemia PCL-033_Gene1.0_2

description: Gene expression profiling data from human primary plasma cell leukemia patient PCL-033

source_name: Human bone marrow plasma cells from primary plasma cell leukemia patient PCL-033

value: del(13) +; del(17p)-; 1q gain n.d.; HD n.d.; no IgH traslocation


title: Hakas57_114


title: Plasma cell leukemia PCL-013_Gene1.0_2

description: Gene expression profiling data from human primary plasma cell leukemia patient PCL-013

source_name: Human bone marrow plasma cells from primary plasma cell leukemia patient PCL-013


title: SR-VP_rep2

description: Biological replicate 2 of 3, SR-VP vs. LS-VL


title: Hakas72


title: SR-VP_rep1

description: Biological replicate 1 of 3, SR-VP vs. LS-VL


title: Plasma cell leukemia PCL-009_Gene1.0_2

description: Gene expression profiling data from human primary plasma cell leukemia patient PCL-009

source_name: Human bone marrow plasma cells from primary plasma cell leukemia patient PCL-009


title: Plasma cell leukemia PCL-011_Gene1.0_2

description: Gene expression profiling data from human primary plasma cell leukemia patient PCL-011

source_name: Human bone marrow plasma cells from primary plasma cell leukemia patient PCL-011


title: Healthy PC7_Gene1.0_2

description: Gene expression profiling data from human healthy donor PC7

source_name: Human tonsillar plasma cells from healthy donor PC7


title: Plasma cell leukemia PCL-005_Gene1.0_2

description: Gene expression profiling data from human primary plasma cell leukemia patient PCL-005

source_name: Human bone marrow plasma cells from primary plasma cell leukemia patient PCL-005


title: Plasma cell leukemia PCL-006_Gene1.0_2

description: Gene expression profiling data from human primary plasma cell leukemia patient PCL-006

source_name: Human bone marrow plasma cells from primary plasma cell leukemia patient PCL-006


title: Multiple Myeloma MM-335_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-335

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-335

value: multiple myeloma


title: Multiple Myeloma MM-239_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-239

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-239

value: del(13) +; del(17p)-; 1q gain-; HD+; no IgH traslocation


title: Multiple Myeloma MM-229_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-229

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-229

value: del(13) -; del(17p)-; 1q gain-; HD-; no IgH traslocation


title: Multiple Myeloma MM-195_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-195

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-195


title: Multiple Myeloma MM-208_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-208

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-208


title: Multiple Myeloma MM-179_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-179

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-179


title: Multiple Myeloma MM-224_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-224

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-224


title: Multiple Myeloma MM-246_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-246

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-246


title: Multiple Myeloma MM-253_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-253

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-253

value: del(13) +; del(17p)-; 1q gain+; HD+; no IgH traslocation


title: Hakas5_123

description: Genomic DNA extracted from blood was genotyped using Human660W-Quad v1.0 Genotyping BeadChips (Illumina).

source_name: blood


title: Multiple Myeloma MM-177_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-177

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-177

value: del(13) +; del(17p)-; 1q gain+; HD-; no IgH traslocation


title: Multiple Myeloma MM-243_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-243

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-243

value: del(13) -; del(17p)-; 1q gain n.d.; HD n.d.; no IgH traslocation


title: Multiple Myeloma MM-206_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-206

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-206


title: Multiple Myeloma MM-212_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-212

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-212


title: Multiple Myeloma MM-154_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-154

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-154


title: Multiple Myeloma MM-140_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-140

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-140


title: Multiple Myeloma MM-151_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-151

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-151

value: del(13) -; del(17p)-; 1q gain-; HD+; no IgH traslocation


title: Multiple Myeloma MM-295_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-295

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-295


title: Hakas35_386


title: Hakas4


title: Multiple Myeloma MM-143_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-143

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-143


title: Multiple Myeloma MM-126_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-126

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-126


title: Multiple Myeloma MM-079_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-079

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-079


title: Multiple Myeloma MM-094_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-094

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-094


title: Multiple Myeloma MM-115_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-115

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-115


title: Multiple Myeloma MM-087_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-087

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-087


title: Multiple Myeloma MM-233_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-233

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-233


title: Multiple Myeloma MM-074_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-074

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-074


title: Multiple Myeloma MM-083_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-083

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-083


title: Multiple Myeloma MM-104_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-104

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-104


title: Multiple Myeloma MM-069_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-069

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-069


title: Plasma cell leukemia PCL-007_Gene1.0_2

description: Gene expression profiling data from human primary plasma cell leukemia patient PCL-007

source_name: Human bone marrow plasma cells from primary plasma cell leukemia patient PCL-007


title: Multiple Myeloma MM-111_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-111

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-111


title: Multiple Myeloma MM-056_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-056

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-056


title: Hakas2

description: Genomic DNA extracted from blood was genotyped using Human660W-Quad v1.0 Genotyping BeadChips (Illumina).

source_name: blood


title: Hakas17_306


title: Hakas13


title: Hakas16_101


title: Hakas3

value: Female


title: Hakas29_394


title: Multiple Myeloma MM-066_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-066

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-066


title: Multiple Myeloma MM-043_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-043

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-043

value: del(13) -; del(17p)-; 1q gain+; HD+; no IgH traslocation


title: Multiple Myeloma MM-031_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-031

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-031


title: Multiple Myeloma MM-038_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-038

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-038


title: Multiple Myeloma MM-042_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-042

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-042


title: Multiple Myeloma MM-034_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-034

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-034


title: Multiple Myeloma MM-049_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-049

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-049


title: Multiple Myeloma MM-039_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-039

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-039


title: Multiple Myeloma MM-050_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-050

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-050


title: Multiple Myeloma MM-040_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-040

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-040


title: Multiple Myeloma MM-123_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-123

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-123


title: Multiple Myeloma MM-055_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-055

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-055


title: Multiple Myeloma MM-021_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-021

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-021


title: Multiple Myeloma MM-036_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-036

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-036


title: Multiple Myeloma MM-016_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-016

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-016


title: Multiple Myeloma MM-004_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-004

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-004


title: Multiple Myeloma MM-015_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-015

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-015


title: Input_Gr1dim_Lsd1_KO_helicos

type: SRA

city: Boston

first: Marc

middle: A.

last: Kerenyi

state: Massachusetts

address: 1 Blackfan Street - Karp Research Building

department: Hematology / Oncology

country: USA

institute: Boston Children's Hospital and Dana Farber Cancer Institute

description: FACS-purified primary Gr1dim Mac1+ bone marrow granulocyte progenitor cells

library_source: genomic

data_processing:
Basecalls performed using Solexa pipeline for data generated by HiSeq 2000 or Helicos pipeline for data generated by Helicos Heliscope.
Sequencing reads were aligned to mouse genome assembly mm9 using Illumina software pipeline (data generated by HiSeq 2000) or Helisphere (data generated by Helicos).
Only ChIP-seq reads that aligned to exactly one location in the reference mouse genome (mm9) were retained for downstream data analysis.
Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/).
The wig files were generated by a moving window of size 200bp. The tag count in the windown was further normalized in unit RPKM (# read per kb per million total reads) for ChIP-seq data generated by HiSeq 2000.
Genome_build: mm9
Supplementary_files_format_and_content: Mapped read bed file, wig file, and peak bed file

growth_protocol: Freshly isolated primary bone marrow cells, the cells have NOT been cultured in vitro.

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody or no antibody for Input samples.  ChIP DNA was quantified by Qubit assay HS kit. For ChIP-Seq analysis using the HeliScope™ Single Molecule Sequencer, ChIP DNA was processed for 3’ polyA tailing, followed by 3’ ddATP-blocking as described previously (Hart et al., 2010; Thompson and Steinmann, 2010). Processing samples by ligation, amplification and size selection are not required by Helicos sequencing. Briefly, 6-10 ng of ChIP DNA or input DNA was used in the 3’ polyA tailing reaction in 14.8 μl containing 2 μl of 2.5 mM CoCl2, 2 μl of 10 x terminal transferase buffer and nuclease-free water. The reaction mixture was denatured in 95oC for 5 min, followed by rapid cooling in ice water slurry. Then 1 U of terminal transferase, 4 μl of 50 μM dATP and 0.2 μl of NEB BSA were added to the mixture. Samples were incubated in a thermocycler at 37°C for 1 h, 70°C 10 min, followed by denaturing at 95°C for 5 min and rapid cooling in ice water slurry. For 3’ ddATP-blocking, 0.5 μl of 200 μM ddATP, 1 μl of 10 x terminal transferase, 1 μl of 2.5 mM CoCl2, 1 U of terminal transferase, and 6.5 μl of nuclear-free water were added to the above reaction. Samples were incubated in a thermocycler at 37°C for 1 h and 70°C for 20 min. Then 2 picomoles of carrier oligonucleotide were added to the reaction, and samples (=H3K4me2-ChIP and H3K4me3-ChIP from wild type and Lsd1 knockout Gr1dim Mac1+ cells + matching input control) were hybridized to the HelicosTM flow cells for sequencing at the Dana-Farber Cancer Institute (DFCI) Molecular Biology Core Facility. Sequencing reads were aligned to mouse genome assembly mm9 (NCBI Build 37) using Helisphere software with default parameters. Only the reads that were uniquely aligned to reference genome with read alignment score higher than 4.5 were retained for further analysis.

treatment_protocol: Both, Lsd1fl/fl and Lsd1fl/fl Mx1Cre mice were injected with three doses of high molecular weight p(I:C) (Invivogen, San Diego, USA) at a concentration of 12.5µg/g body weight. Forty million Gr1dim Mac1+ were cross-linked with 1% formaldehyde for 10 min at room temperature. Crosslinking was stopped with 125mM glycine for 5 minutes and cells were rinsed twice with 1X PBS. Cells were resuspended, lysed in lysis buffer, and sonicated to solubilize and shear cross-linked DNA. The samples were sonicated using a Heat Systems Ultrasonic Processor with a micro tip (settings: duty cycle 60%, output 4.5, 1 sec pulse, 30 sec. 6-10 times with at least 60 second pause between pulse sets) while suspended in a sonication buffer containing 10mM Tris-HCl pH7.4, 300mM NaCl, 1mM EDTA, 0.1% SDS, 1% Triton X-100, 0.1% NaDOC.  Samples were kept on an ethanol ice bath at all times. The resulting whole cell extract was split into chromatin aliquots equivalent to 10x106 of input cells and incubated overnight at 4°C with approximately 5 µg of the appropriate antibody. Protein A Dynabeads (Invitrogen) were used for collection of chromatin. Beads were washed 2X with 10mM Tris-HCl pH 7.4, 1mM EDTA, 0.1% SDS, 1% Triton X-100, 0.1% NaDOC; 2X with 10mM Tris-HCl pH 7.4, 300mM NaCl, 1mM EDTA, 0.1% SDS, 1% Triton X-100, 0.1% NaDOC; 2x with 10mM Tris-HCl pH 8.0, 250mM LiCl, 2mM EDTA, 0.5% NP40, 0.5% NaDOC and 2X with TE. Bound complexes were eluted from the beads (50 mM Tris-Hcl, pH 8.0, 10 mM EDTA and 1% SDS) by heating at 65°C for 1 hour with occasional vortexing. Crosslinking was reversed by overnight incubation at 65°C. Ten percent of input DNA was also treated for crosslink reversal.

value: Bone marrow derived Gr1dim Mac1+ granulocytic progenitor cells

tag: strain

tag: genotype/variation

value: Lsd1fl/fl Mx1Cre (knockout)

tag: chip antibody


title: Input_Gr1dim_WT_helicos

source_name: Gr1dim Mac1+ granulocytic progenitor cells

value: Lsd1fl/fl (wild type)


title: Multiple Myeloma MM-027_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-027

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-027


title: H3K4me3_Gr1dim_Lsd1_KO

tag: antibody vendor/catalog/lot#


title: Multiple Myeloma MM-030_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-030

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-030


title: Multiple Myeloma MM-025_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-025

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-025


title: Multiple Myeloma MM-052_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-052

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-052


title: Hakas15_223

description: Genomic DNA extracted from blood was genotyped using Human660W-Quad v1.0 Genotyping BeadChips (Illumina).

source_name: blood

value: blood

value: Male

value: Khakases


title: H3K4me3_Gr1dim_WT


title: Hakas7

value: South Siberia


title: H3K4me2_Gr1dim_Lsd1_KO


title: Multiple Myeloma MM-026_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-026

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-026

value: Human bone marrow plasma cells


title: H3K4me2_Gr1dim_WT


title: Multiple Myeloma MM-035_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-035

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-035

value: multiple myeloma

value: del(13) -; del(17p)-; 1q gain-; HD n.d.; no IgH traslocation


title: Multiple Myeloma MM-131_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-131

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-131


title: Multiple Myeloma MM-081_Gene1.0_2

description: Gene expression profiling data from human multiple myeloma patient MM-081

source_name: Human bone marrow plasma cells from multiple myeloma patient MM-081

value: del(13)  n.d.; del(17p)n.d.; 1q gain n.d.; HD n.d.; no IgH traslocation


title: 3h p.i. Control

city: Berlin

first: Soroush

last: Sharbati

address: Oertzenweg 19b

department: Institute of Veterinary Biochemistry

country: Germany

institute: Freie Universitaet Berlin

description: 3h p.i. C [mRNA]

hyb_protocol: Fully automated hybridisation and washings were carried out in the aHyb™ Hybridization Station (Miltenyi Biotec). Firts, slides were pre-hybridised at 45°C for 5 min in pre-hybridisation buffer (5xSSC, 0.1%SDS, 1%BSA). Hybridisation was performed for 16h at 50°C with a pump rate of 1 ml/min. Finally the slides were washed in wash buffers with increased stringency. At first for 1 min at 50°C in wash buffer 1 (2xSSC, 0.5%SDS), followed by wash buffer 2 (0.5$SSC, 0.5%SDS), and wash buffer 3 (0.1%SSC, 0.2%SDS) each 1 min at 25°C. Afterwards, dipped in bi-distilled water dried by brief centrifugation.

scan_protocol: The microarrays were scanned at 10 µm resolution using a GenePix 4000B scanner (Molecular Devices).

data_processing: Microarray image analysis and ratio-based normalisation of the microarray data was conducted using the software package GenePix Pro 6.1 (Molecular Devices). Data was filtered according following criteria: [SNR 635] < 3 AND [SNR 532] < 3 AND [% > B532 + 2 SD] < 70 OR [% > B 635 + 2 SD] < 70 OR [F 532 Median – B 532] < 500 AND [F 635 Median – B 635] < 500.

organism: Sus scrofa

source_name: non-infected control

label_protocol: Total RNA was converted into cDNA and fluorescently labelled using the SuperScript Plus Indirect cDNA Labelling System (Life technologies) and the Alexa Fluor Dyes according to the manufacturor's protocol.

extract_protocol: ntestinal samples (~ 2 cm circle segments) were taken at time points 3h, 3d and 28d post infection from ileum of ten S.typhimurium infected piglets (S), ten S.typhimurium infected piglets and additional treated with E.faecium (SP) and five healthy control piglets(C) (EUROC x Pietrain). The piglets were weaned at the age of 28 days and infected with S. typhimurium. Samples were quick-frozen in liquid nitrogen and stored at -80 °C. In order to obtain representative measurements in each intestinal locus, three cross sections of approximately 2 mm out of the 2 cm segment of frozen intestine were examined. These 3 sections were pooled and total RNA was isolated from samples using an automated homogenizer (FastPrep Instrument, MP Biomedicals, Heidelberg, Germany) and the mirVana miRNA Isolation Kit (Applied Biosystems, Darmstadt, Germany), according to the manufacturer’s protocol. The RNA quality and quantity of all samples were proven using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano Kits (Agilent, Waldbronn, Germany) and the Nanodrop 1000 Spectrophotometer (Thermo Scientific, MA, USA).

treatment_protocol: piglets in S and SP group were infected with S.typhimurium DT104 at day 28 postpartum directly after weaning; piglets in SP group had free access to feed supplemented with the probiotic strain E.faecium NCIMB 10415

value: ileum

tag: infection

value: non infected control

value: no treatment

tag: time

source_name: common reference

tag: composition

value: equal amounts of total RNA of each ileum pool and additional total RNA from ascending colon


title: 3h p.i. Salmonella + E.faecium

description: 3h p.i. SP [mRNA]

source_name: S.typhimurium infected + Enterococcus faecium treatment

tag: tissue

tag: treatment


title: 3h p.i. Salmonella

description: 3h p.i. S [mRNA]

source_name: S.typhimurium infected


title: 3d p.i. Control

description: 3d p.i. C [mRNA]


title: 28d p.i. Control

description: 28d p.i. C [mRNA]


title: 3d p.i. Salmonella

description: 3d p.i. S [mRNA]


title: 3d p.i. Salmonella + E.faecium

description: 3d p.i. SP [mRNA]


title: 28d p.i. Salmonella + E.Faecium

description: 28d p.i. SP [mRNA]


title: NPC tissue 1

city: shanghai

first: shu

last: yang

address: State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science

country: China

institute: Fudan University

description: NPC tissue

hyb_protocol: Refer to the Illumina Gene Expression System Manual

data_processing: Cubic spline normalization using Illumina BeadStudio Version BSGX Version3.2.3

source_name: human nasopharyngeal carcinoma tissue

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

extract_protocol: Total RNA was extracted from 8 NPC and 4 nasopharyngeal tissues using Trizol (Invitrogen) reagent according to the manufacture’s instructions.

value: nasopharyngeal carcinoma tissue

value: female

tag: tumor stage

value: II


title: NPC tissue 2

description: NPC tissue

scan_protocol: Refer to the Illumina Gene Expression System Manual

tag: gender

value: male


title: nasopharyngeal tissue 1

description: nasopharyngeal tissue

source_name: human nasopharyngeal tissue

value: nasopharyngeal tissue


title: nasopharyngeal tissue 3

description: nasopharyngeal tissue


title: nasopharyngeal tissue 2

description: nasopharyngeal tissue


title: nasopharyngeal tissue 4

description: nasopharyngeal tissue


title: NPC tissue 5

description: NPC tissue

value: III


title: NPC tissue 4

description: NPC tissue

value: IV


title: NPC tissue 3

description: NPC tissue


title: NPC tissue 8

description: NPC tissue


title: NPC tissue 7

description: NPC tissue


title: NPC tissue 6

description: NPC tissue


title: 28d p.i. Salmonella

description: 28d p.i. S [mRNA]


title: fibroblast-S1

city: Shanghai

first: Min

last: Li

address: 50 Chifeng Rd., Yangpu District

department: Life Sciences and Technology

institute: Tongji University

description: Gene expression of human fibroblast cells

hyb_protocol: 100μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505B).

data_processing: Agilent Feature Extraction software (version 10.7.3.1) was used to analyze the acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 4 out of 12 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes were identified through volcano plot filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 11.5.1). GO analysis and Pathway analysis were performed in the standard enrichment computation method

source_name: fbroblast-S 1

label_protocol: 1 μg of total RNA from each sample was linearly amplified and labeled with Cy3-dCTP. The Labeled cRNAs were purified by RNAeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60 °C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA

growth_protocol: Human umbilical vein endothelial cells and human dermal fibroblasts cells were were cultured in DMEM/F12 medium supplemented with 10% FBS.Adipose tissues obtained from the patients should be washed 3 times by PBS with 1% penicillin/streptomycin and then carefully minced by sterile operation scissors. The minced tissues were then enzymatically dissociated for 45 minutes at 37 °C by 0.15% collagenase type I (GIBCO). Then the suspension was then neutralized with isometric culture medium and centrifuged at 500g for 5 minutes. The cell pellet was resuspended in DMEM/F12 medium (GIBCO) supplemented with 10% FBS (GIBCO) or 10% KSR (Invitrogen)at a density of 2x106 cell/mL.  Cell cultures were maintained at 37 °C in a humidified incubator supplemented with 5% CO2. Passage 3 cells were used for whole human genome microarray.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and RNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis

value: fibroblast cells


title: liposuction 1-4

description: Gene expression of human adipose derived stem cells

scan_protocol: scanned with using the Agilent DNA Microarray Scanner (part number G2505B).

value: adipose derived stem cells

value: 32 years


title: endothelial cell-H1

description: Gene expression of human endothelial cells

source_name: endothelial cell-H1

value: endothelial cells


title: liposuction 1-5

value: 29 years


title: liposuction 1-6

value: 37 years


title: Combination CLL3

city: Cardiff

first: Chris

last: Pepper

address: Heath Park

country: United Kingdom

institute: Cardiff University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45oC on Affymetrix U133 2.0 Gene Chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with MADRAS bespoke software using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Primary CLL cells (treated with 0.1uM CDKI-73 and 10 μM fludarabine for 4h)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.

growth_protocol: Primary CLL cells were cultured in RPMI supplemented with 10% fetal bovine serum (FBS), penicillin (50 U/ml), streptomycin (50 µg/ml) and recombinant human IL-4 (R and D Systems, Abingdon, UK) (5 ng/ml).

treatment_protocol: 5x106 CLL cells were treated with 0.1 μM CDKI-73, 10 μM fludarabine or the two drugs in combination for 4h.

value: CLL B-cells


title: Combination CLL1

value: 0.1uM CDKI-73 and 10 μM fludarabine for 4h


title: Combination CLL2


title: Control subject 95_biological replicate 1

city: New York

first: Catherine

last: Clelland

state: NY

address: 630 West 168th Street, P&S 12-461A

institute: Columbia University Medical Center

hyb_protocol: Following fragmentation, 10 ug of cRNA was hybridized to an Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400, using standard procedures.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 with Autoloader

data_processing: The data were analyzed using  BRB-Array Tools versions: 3.8.1 (as described in the manuscript) and 4.2.1 (the processed matrix GEO data).  Cell files were imported into the BRBArray Tools package, and converted to normalized intensity values using the Almost RMA (aRMA) algorithm.  A total of 199 cel files were imported into the project, including expression data obtained from patients with other psychiatric disorders.  Normalized intensity values reflect the a-RMA parameters employed across the entire sample dataset.   Analyses were performed on the sub-set of samples relevent to the study hypothesis.  Cel files and processed matrix data for those samples are uploaded here.

source_name: Control subject

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was extracted from leukocytes using the QIAamp RNA Blood Mini Kit (Qiagen), with an off-collumn Dnase (Qiagen) treatment followed by  purification using an RNeasy MinElute column (Qiagen). All procedures were performed according to the manufacturer's instructions (Qiagen).

value: leukocytes from whole blood

tag: genotype

value: control subject


title: BP patient 92_biological replicate 2

source_name: medicated bipolar patient

value: bipolar patient


title: Control subject 95_biological replicate 2


title: BP patient 98_biological replicate 1


title: After treatment (week 2) RAB44

city: Debrecen

first: Bertalan

last: Mesko

address: Egyetem tér 1.

department: Department of Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen

hyb_protocol: Samples were hybridized at 45 degrees Celsius for 16 hours and then standard washing protocol was performed using GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned on GeneChip Scanner 7G (Affymetrix).

data_processing: Gene Spring GX 10 was used for data analysis,  CEL files were imported using RMA algorithm and median normalization was performed. CHP files were generated using Affymetrix Expression Control.

source_name: PBMC

label_protocol: Ambion WT Expression Kit (Applied Biosystems) and GeneChip WT Terminal Labeling and Control Kit (Affymetrix) were used for amplifying and labeling 250 ng of RNA samples.

extract_protocol: Peripheral blood momonuclear cells were separated by Ficoll gradient centrifugation.

treatment_protocol: Treatment was infliximab infusion at week 0 and at week 2.

tag: cell type

value: PBMC

tag: subject

value: Patient 15

tag: response

value: R - responder

value: infliximab

value: week 2

value: Rheumatoid arthritis


title: Untreated CLL3

source_name: Primary CLL cells (untreated)

value: untreated


title: liposuction 1-3

value: adipose derived stem cells

tag: age

value: 35 years

value: female


title: BP patient 92_biological replicate 1

value: male


title: Fludara CLL3

source_name: Primary CLL cells (treated with 10 μM fludarabine for 4h)

value: 10 μM fludarabine for 4h


title: liposuction 1-2

value: 31 years


title: After treatment (week 2) RAB38

value: Patient 14

tag: disease state


title: After treatment (week 2) RAB68

value: Patient 19


title: CDKI-73 CLL2

source_name: Primary CLL cells (treated with 0.1 μM CDKI-73 for 4h)

value: 0.1 μM CDKI-73 for 4h

value: CLL B-cells


title: Untreated CLL2


title: Fludara CLL1


title: liposuction 1-1

value: 39 years


title: After treatment (week 2) RAB102

value: PBMC

value: Patient 13

value: NR - non-responder


title: BP patient 96_biological replicate 1

value: leukocytes from whole blood

value: bipolar patient


title: After treatment (week 2) RAB59

value: Patient 17

value: R - responder

value: infliximab

value: week 2

value: Rheumatoid arthritis


title: After treatment (week 2) RAB52

value: Patient 16


title: After treatment (week 2) RAB62

value: Patient 18


title: Fludara CLL2

value: 10 μM fludarabine for 4h


title: After treatment (week 2) RAB100

value: Patient 12


title: CDKI-73 CLL1

value: 0.1 μM CDKI-73 for 4h


title: CDKI-73 CLL3

value: CLL B-cells


title: Untreated CLL1

value: untreated


title: BP patient 96_biological replicate 2

value: male


title: Control subject 97_biological replicate 1

value: control subject


title: BP patient 91_biological replicate 2


title: Control subject 97_biological replicate 2


title: BP patient 91_biological replicate 1


title: After treatment (week 2) RAB96

value: PBMC

value: Patient 11

value: NR - non-responder


title: After treatment (week 2) RAB87

value: Patient 9


title: BP patient 79_biological replicate 2

value: leukocytes from whole blood

value: bipolar patient


title: After treatment (week 2) RAB66

value: Patient 7

value: infliximab

value: week 2


title: first-episode BP patient 77_biological replicate 2

source_name: first-episode bipolar patient


title: After treatment (week 2) RAB75

value: Patient 8

value: Rheumatoid arthritis


title: BP patient 81_biological replicate 1


title: After treatment (week 2) RAB43

value: Patient 5


title: After treatment (week 2) RAB50

value: Patient 6


title: BP patient 75_biological replicate 2


title: first-episode BP patient 77_biological replicate 1


title: BP patient 75_biological replicate 1


title: BP patient 81_biological replicate 2


title: BP patient 88_biological replicate 1


title: BP patient 78_biological replicate 1


title: Control subject 87_biological replicate 1


title: BP patient 79_biological replicate 1


title: BP patient 88_biological replicate 2


title: BP patient 83_biological replicate 1


title: After treatment (week 2) RAB107

value: Patient 4


title: BP patient 57_biological replicate 1


title: BP patient 60_biological replicate 1


title: After treatment (week 2) RAB106

value: Patient 3


title: first-episode BP patient 74_biological replicate 2

value: male


title: first-episode BP patient 74_biological replicate 1


title: After treatment (week 2) RAB94

value: Patient 10


title: BP patient 56_biological replicate 2


title: BP patient 56_biological replicate 1


title: BP patient 60_biological replicate 2


title: After treatment (week 2) RAB17

value: PBMC

value: Patient 1


title: BP patient 54_biological replicate 2


title: After treatment (week 2) RAB105

value: Patient 2

value: NR - non-responder


title: BP patient 55_biological replicate 1

value: leukocytes from whole blood


title: BP patient 55_biological replicate 2

value: bipolar patient


title: BP patient 54_biological replicate 1


title: Before treatment (week 0) RAB56

value: Patient 18

value: R - responder

value: Before treatment

value: week 0


title: BP patient 53_biological replicate 2


title: BP patient 52_biological replicate 1


title: BP patient 53_biological replicate 1


title: Before treatment (week 0) RAB60

value: Patient 19

value: Rheumatoid arthritis


title: Before treatment (week 0) RAB35

value: Patient 15


title: Before treatment (week 0) RAB42

value: Patient 16


title: BP patient 48_biological replicate 2


title: BP patient 48_biological replicate 1


title: BP patient 51_biological replicate 2


title: BP patient 49_biological replicate 1


title: BP patient 51_biological replicate 1


title: BP patient 50_biological replicate 1


title: Before treatment (week 0) RAB53

value: Patient 17


title: Before treatment (week 0) RAB28

value: Patient 14


title: Control subject 45_biological replicate 1

value: control subject

value: male


title: Control subject 46_biological replicate 1


title: Before treatment (week 0) RAB98

value: PBMC

value: Patient 13


title: Control subject 47_biological replicate 1


title: Before treatment (week 0) RAB97

value: Patient 12

value: NR - non-responder


title: Control subject 40_biological replicate 2

value: leukocytes from whole blood


title: Control subject 44_biological replicate 1


title: Control subject 41_biological replicate 1


title: Control subject 40_biological replicate 1


title: Control subject 42_biological replicate 2


title: Before treatment (week 0) RAB72

value: Patient 8


title: Before treatment (week 0) RAB90

value: Patient 10


title: Control subject 43_biological replicate 1


title: Control subject 39_biological replicate 2


title: Before treatment (week 0) RAB93

value: Patient 11

value: Before treatment


title: Control subject 34_biological replicate 1


title: Before treatment (week 0) RAB41

value: Patient 6

value: week 0


title: Control subject 42_biological replicate 1


title: Control subject 32_biological replicate 2


title: Control subject 29_biological replicate 2


title: Before treatment (week 0) RAB31

value: Patient 5

value: Rheumatoid arthritis


title: Before treatment (week 0) RAB83

value: Patient 9


title: Control subject 33_biological replicate 1


title: Control subject 34_biological replicate 2


title: Before treatment (week 0) RAB63

value: Patient 7


title: Control subject 26_biological replicate 1

value: control subject


title: Control subject 24_biological replicate 1

value: male


title: Control subject 33_biological replicate 2


title: Control subject 29_biological replicate 1


title: Control subject 32_biological replicate 1


title: Control subject 39_biological replicate 1


title: Control subject 25_biological replicate 1


title: Control subject 23_biological replicate 1


title: Before treatment (week 0) RAB101

value: PBMC

value: Patient 2


title: Before treatment (week 0) RAB07

value: Patient 1


title: first-episode BP patient 120_biological replicate 2

value: bipolar patient


title: Control subject 117_biological replicate 2

value: leukocytes from whole blood


title: After treatment (week 2) IBDB02

value: Patient 20

value: NR - non-responder

value: infliximab

value: week 2

value: Crohn's disease


title: Control subject 116_biological replicate 2


title: Before treatment (week 0) RAB103

value: Patient 3

value: Before treatment

value: week 0


title: Control subject 117_biological replicate 1


title: Before treatment (week 0) RAB104

value: Patient 4

value: Rheumatoid arthritis


title: first-episode BP patient 120_biological replicate 1


title: After treatment (week 2) IBDB05

value: Patient 19

value: R - responder


title: Control subject 116_biological replicate 1

value: control subject

value: male


title: After treatment (week 2) IBDB15

value: PBMC

value: Patient 17


title: After treatment (week 2) IBDB25

value: Patient 16


title: After treatment (week 2) IBDB45

value: Patient 14


title: BP patient 111_biological replicate 1

value: leukocytes from whole blood

value: bipolar patient


title: Control subject 106_biological replicate 1


title: BP patient 110_biological replicate 2


title: BP patient 104_biological replicate 2


title: Control subject 107_biological replicate 1


title: Control subject 23_biological replicate 2


title: After treatment (week 2) IBDB11

value: Patient 18

value: infliximab

value: week 2


title: Control subject 107_biological replicate 2


title: After treatment (week 2) IBDB47

value: Patient 13

value: Crohn's disease


title: BP patient 111_biological replicate 2


title: BP patient 110_biological replicate 1


title: After treatment (week 2) IBDB31

value: Patient 15


title: After treatment (week 2) IBDB49

value: Patient 12

value: NR - non-responder


title: After treatment (week 2) IBDB46

value: Patient 11

value: R - responder


title: BP patient 104_biological replicate 1

value: male


title: Control subject 102_biological replicate 2

value: control subject


title: Lacrimal glands at 20 weeks, biological rep4

city: Gainesville

first: Ammon

middle: B

last: Peck

state: FL

address: 1945 SW 16th Avenue

department: Department of Infectious Diseases & Pathology

institute: University of Florida

description: Gene expression profiles within the Lacrimal glands of C57BL/6.NOD-Aec1Aec2 mice at 20 weeks of age (representing the early onset of clinical SjS-like disease characterized by secretory dysfunction).

hyb_protocol: Fragmented cRNA was hybridized for 16 h at 45°C to the array chips (Affymetrix). Genechips were washed ans stained in the Affymetrix Fluidics Station 400.

data_processing: Microarray data were normalized using the “robust multi-array average” (GCRMA) algorithm.

extract_protocol: Total RNA was isolated using the RNeasy Mini-Kit (Qiagen, Valencia, CA), as per the manufacturer’s protocol.

value: Lacrimal glands

value: 20 week

value: Male


title: Lacrimal glands at 20 weeks, biological rep1

source_name: Lacrimal glands of C57BL/6.NOD-Aec1Aec2 mice at 20 weeks of age


title: Lacrimal glands at 20 weeks, biological rep2


title: Lacrimal glands at 20 weeks, biological rep3


title: Lacrimal glands at 20 weeks, biological rep5


title: Control subject 102_biological replicate 1

value: leukocytes from whole blood


title: BP patient 101_biological replicate 2

value: bipolar patient


title: Lacrimal glands at 16 weeks, biological rep5

description: Gene expression profiles within the Lacrimal glands of C57BL/6.NOD-Aec1Aec2 mice at 16 weeks of age (representing the early clinical phase of autoimmunity).

value: 16 week


title: BP patient 101_biological replicate 1


title: After treatment (week 2) IBDB36

value: PBMC

value: Patient 8

value: infliximab


title: After treatment (week 2) IBDB35

value: Patient 7

value: week 2

value: Crohn's disease


title: Lacrimal glands at 16 weeks, biological rep3

source_name: Lacrimal glands of C57BL/6.NOD-Aec1Aec2 mice at 16 weeks of age


title: Lacrimal glands at 16 weeks, biological rep2


title: MCL_IGHV_MUT (R1970)

city: Barcelona

first: Pedro

last: Jares

state: Barcelona

address: c/ Villarroel 170

department: Genomics Unit

institute: IDIBAPS

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HU133plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: The data were analyzed with the Expression Console applilcation from Affymetrix. We performed RMA to summarize the data.

source_name: B cell lymphocytes from MCL patient

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol using the 3' IVT Express kit from Affymetrix

extract_protocol: Total RNA was extracted from mononuclear cell preparations of leukemic B cells obtained fromp peripheral blood prior to treatment using TRIZOL. RNA quality and quantity was assessed using the bionalyzer 2100 and nanodrop spectrophotometer

value: Mantle Cell Lymphoma

value: B cell lymphocyte

tag: ighv status

value: MUT


title: Lacrimal glands at 16 weeks, biological rep4


title: After treatment (week 2) IBDB38

value: Patient 9

value: R - responder


title: After treatment (week 2) IBDB30

value: Patient 6


title: MCL_IGHV_MUT (R1941)


title: MCL_IGHV_UNMUT (R1897)

value: UNMUT


title: MCL_IGHV_UNMUT (R1388)


title: Lacrimal glands at 12 weeks, biological rep6

description: Gene expression profiles within the Lacrimal glands of C57BL/6.NOD-Aec1Aec2 mice at 12 weeks of age (representing the initial influx of leukocytes into the Lacrimal glands).

value: Lacrimal glands

value: 12 week

value: Male


title: After treatment (week 2) IBDB29

value: Patient 5

value: NR - non-responder


title: Lacrimal glands at 16 weeks, biological rep1

value: 16 week


title: Lacrimal glands at 12 weeks, biological rep5

source_name: Lacrimal glands of C57BL/6.NOD-Aec1Aec2 mice at 12 weeks of age


title: After treatment (week 2) IBDB24

value: PBMC

value: Patient 4

value: infliximab


title: MCL_IGHV_MUT (R1940)


title: MCL_IGHV_MUT (R1938)


title: After treatment (week 2) IBDB21

value: Patient 3

value: week 2

value: Crohn's disease


title: Lacrimal glands at 12 weeks, biological rep4


title: MCL_IGHV_MUT (R1942)

value: Mantle Cell Lymphoma

value: B cell lymphocyte

value: MUT


title: MCL_IGHV_UNMUT (R1338)


title: After treatment (week 2) IBDB16

value: Patient 1

value: R - responder


title: Lacrimal glands at 12 weeks, biological rep3

value: Lacrimal glands


title: Lacrimal glands at 12 weeks, biological rep1

value: 12 week


title: After treatment (week 2) IBDB19

value: Patient 2


title: Lacrimal glands at 12 weeks, biological rep2

value: Male


title: MCL_IGHV_UNMUT (R1762)

value: UNMUT


title: MCL_IGHV_MUT (R1301)


title: Before treatment (week 0) IBDB13

value: Patient 17

value: NR - non-responder

value: Before treatment

value: week 0


title: Before treatment (week 0) IBDB01

value: PBMC

value: Patient 20


title: MCL_IGHV_MUT (R1339)


title: MCL_IGHV_MUT (R1610)


title: Before treatment (week 0) IBDB23

value: Patient 16

value: Crohn's disease


title: Lacrimal glands at 8 weeks, biological rep5

description: Gene expression profiles within the Lacrimal glands of C57BL/6.NOD-Aec1Aec2 mice at 8 weeks of age (representing the early pre-clinical stage).

value: 08 week


title: Lacrimal glands at 8 weeks, biological rep6

source_name: Lacrimal glands of C57BL/6.NOD-Aec1Aec2 mice at 8 weeks of age


title: MCL_IGHV_MUT (02_201)

value: Mantle Cell Lymphoma

value: B cell lymphocyte

value: MUT


title: Lacrimal glands at 8 weeks, biological rep2

value: Lacrimal glands


title: MCL_IGHV_UNMUT (R1595)


title: MCL_IGHV_MUT (R1640)


title: Before treatment (week 0) IBDB08

value: Patient 18

value: R - responder


title: Before treatment (week 0) IBDB41

value: Patient 14


title: Lacrimal glands at 8 weeks, biological rep4

value: Male


title: Before treatment (week 0) IBDB42

value: Patient 13


title: MCL_IGHV_MUT (R1626)


title: Lacrimal glands at 8 weeks, biological rep1


title: Lacrimal glands at 8 weeks, biological rep3


title: Before treatment (week 0) IBDB03

value: Patient 19


title: Before treatment (week 0) IBDB39

value: Patient 11

value: Before treatment


title: Lacrimal glands at 4 weeks, biological rep3

description: Gene expression profiles within the Lacrimal glands of C57BL/6.NOD-Aec1Aec2 mice at 4 weeks of age (representing the pre-disease stage).

value: 04 week


title: Before treatment (week 0) IBDB26

value: PBMC

value: Patient 15

value: week 0


title: MCL_IGHV_MUT (R1585)


title: MCL_IGHV_MUT (R1589)


title: Lacrimal glands at 4 weeks, biological rep4

source_name: Lacrimal glands of C57BL/6.NOD-Aec1Aec2 mice at 4 weeks of age


title: Before treatment (week 0) IBDB37

value: Patient 9

value: Crohn's disease


title: MCL_IGHV_MUT (R1341)

value: Mantle Cell Lymphoma

value: B cell lymphocyte


title: MCL_IGHV_MUT (R1629)

value: MUT


title: Before treatment (week 0) IBDB44

value: Patient 12

value: NR - non-responder


title: MCL_IGHV_MUT (R1333)


title: Lacrimal glands at 4 weeks, biological rep1

value: Lacrimal glands


title: Before treatment (week 0) IBDB40

value: Patient 10

value: R - responder


title: MCL_IGHV_MUT (R1304)


title: Lacrimal glands at 4 weeks, biological rep2

value: Male


title: Before treatment (week 0) IBDB33

value: Patient 7


title: MCL_IGHV_MUT (R1302)


title: Before treatment (week 0) IBDB34

value: Patient 8

value: Before treatment


title: Lsd1fl/fl Mx1Cre biological replicate #3 [LT-HSC]

description: FACS-purified primary CD150+ CD48- lin- c-Kit+ Sca-1+ LT-HSCs

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: We RMA-normalized the arrays using the expression file creator package from GenePattern (Broad Institute, Boston, USA). The RMA-normalized *.gct files were then analyzed by the comparative marker selection package from GenePattern (Broad Institute, Boston, USA).

source_name: CD150+ CD48- lin- c-Kit+ Sca-1+ LT-HSCs

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

extract_protocol: Total RNA was extracted with the RNeasy Micro Kit (QIAGEN), treated with DNaseI, reverse transcribed. RNA extracted from CD150+ CD48- lin- c-Kit+ Sca-1+ cells was amplified with the Ovation Pico WTA RNA Amplification System 2 (NuGEN Technologies). Single-stranded cDNA amplification products were purified using QIAquick PCR Purification Kit (QIAGEN) and labeled with the FL-Ovation cDNA Biotin Module V2 (NuGEN).

treatment_protocol: Both, Lsd1fl/fl and Lsd1fl/fl Mx1Cre mice were injected with three doses of high molecular weight p(I:C) (Invivogen, San Diego, USA) at a concentration of 12.5µg/g body weight.

tag: strain

value: adult bone marrow

value: male

tag: genotype/variation

value: Lsd1fl/fl Mx1Cre


title: MCL_IGHV_MUT (R1591)


title: Before treatment (week 0) IBDB28

value: PBMC

value: Patient 6

value: week 0


title: Before treatment (week 0) IBDB27

value: Patient 5

value: Crohn's disease


title: Lsd1fl/fl Mx1Cre biological replicate #2 [LT-HSC]


title: Lsd1fl/fl biological replicate #2 [LT-HSC]


title: Lsd1fl/fl Mx1Cre biological replicate #1 [LT-HSC]


title: MCL_IGHV_MUT (R1305)

value: Mantle Cell Lymphoma

value: B cell lymphocyte

value: MUT


title: liposuction 1-6 [miRNA]

description:
microRNA expression of human adipose derived stem cells
SAMPLE 6

hyb_protocol: the Hy3TM-labeled samples were hybridized on the miRCURYTM LNA 5th generation Array (Exiqon) according to array manual. The total 25 μL mixture from Hy3TM-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min and then hybridized to the microarray for 16 – 20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA), which provides an active mixing action and constant incubation temperature to improve hybridization uniformity and enhance signal. Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon), and finally dried by centrifugation for 5 min at 400 rpm.

scan_protocol: Scanning is performed with the Axon GenePix 4000B microarray scanner.  GenePix pro V6.0 is used to read the raw intensity of the image.

data_processing: The intensity of green signal is calculated after background subtraction and four Replicated spots of each probe on the same slide have been averaged. We use Median Normalization Method to obtain 'Normalized Data', Normalized Data= (Foreground-Background)/median, the median is 50 percent quantile of microRNA intensity which is larger than 50 in all samples after background correction. After normalization, the statistical significance of differentially expressed miRNA was analyzed by T-test.

label_protocol: The miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling. One microgram of each sample was 3'-end-labeled with Hy3TM fluorescent label, using T4 RNA ligase by the following procedure: RNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C, and was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture. The labeling reaction was incubated for 1 h at 16°C, and terminated by incubation for 15 min at 65°C.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis

value: adipose derived stem cells

value: 37 years

value: female


title: Lsd1fl/fl biological replicate #1 [LT-HSC]


title: MCL_IGHV_UNMUT (043-01-4TR)

value: UNMUT


title: liposuction 1-5 [miRNA]

description:
microRNA expression of human adipose derived stem cells
SAMPLE 5

value: 29 years


title: liposuction 1-4 [miRNA]

description:
microRNA expression of human adipose derived stem cells
SAMPLE 4

value: 32 years


title: After treatment (week 2) IBDB43

value: Patient 10

value: R - responder

value: infliximab

value: week 2


title: liposuction 1-3 [miRNA]

description:
microRNA expression of human adipose derived stem cells
SAMPLE 3

value: 35 years


title: Lsd1fl/fl Mx1Cre biological replicate #2 [Gr1dim Mac1]

description: FACS-purified primary Gr1dim Mac1+ bone marrow granulocyte progenitor cells

source_name: Gr1dim Mac1+ granulocytic progenitor cells

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

value: adult bone marrow

value: male

value: Lsd1fl/fl Mx1Cre


title: Before treatment (week 0) IBDB14

value: PBMC

value: Patient 1

value: Before treatment

value: week 0

value: Crohn's disease


title: MCL_IGHV_MUT (R1628)

value: Mantle Cell Lymphoma

value: B cell lymphocyte

value: MUT


title: Lsd1fl/fl Mx1Cre biological replicate #3 [Gr1dim Mac1]


title: MCL_IGHV_UNMUT (268-01-5TR)

value: UNMUT


title: Before treatment (week 0) IBDB18

value: Patient 3


title: liposuction 1-2 [miRNA]

description:
microRNA expression of human adipose derived stem cells
SAMPLE 2

value: adipose derived stem cells

value: 31 years

value: female


title: Lsd1fl/fl biological replicate #3 [LT-HSC]


title: MCL_IGHV_MUT (269-01-5TR)


title: Before treatment (week 0) IBDB17

value: Patient 2

value: R - responder


title: Lsd1fl/fl biological replicate #3 [Gr1dim Mac1]

value: adult bone marrow

value: male


title: Lsd1fl/fl Mx1Cre biological replicate #1 [Gr1dim Mac1]

value: Lsd1fl/fl Mx1Cre


title: liposuction 1-1 [miRNA]

description:
microRNA expression of human adipose derived stem cells
SAMPLE 1

value: 39 years


title: MCL_IGHV_UNMUT (R1587)


title: Lsd1fl/fl biological replicate #2 [Gr1dim Mac1]


title: endothelial cell-H1 [miRNA]

description:
microRNA expression of human endothelial cells
SAMPLE 8

source_name: endothelial cell-H1

value: endothelial cells


title: fibroblast-S1 [miRNA]

description:
microRNA expression of human fibroblast cells
SAMPLE 7

value: fibroblast cells


title: common reference (CR)

description: CR [miRNA]

hyb_protocol: Hybridization for 16 hours at 42°C has been carried out overnight according to manufacturs instructions. Then, the biochip was washed automatically and a program for signal enhancement was processed with the Geniom Real Time Analyzer

scan_protocol: The resulting detection pictures were evaluated using the Geniom Wizard Software.

data_processing:
For each array, the median signal intensity was extracted from the raw data file such that for each miRNA seven intensity values have been calculated corresponding to each replicate copy of miRBase on the array. Following background subtraction replicate intensity values of each miRNA were summarized by their median value. To normalize the data across different arrays, quantile normalization was applied using febit proprietary software packages. Only miRNAs with a value above 6 were used for further analysis.
Log 2 ratio was calculated (sample/CR) and is provided as a supplementary file on the Series record.

source_name: common reference

label_protocol: Sample labeling with biotin has been carried out either by using the miRVANA™ miRNA Labeling Kit (Applied Biosystems Inc, Foster City, California USA) or by microfluidic-based enzymatic on-chip labeling of miRNAs (MPEA)

extract_protocol: Intestinal samples (~ 2 cm circle segments) were taken at time points 3h, 3d and 28d post infection from ileum of ten S.typhimurium infected piglets (S), ten S.typhimurium infected piglets and additional treated with E.faecium (SP) and five healthy control piglets(C) (EUROC x Pietrain). The piglets were weaned at the age of 28 days and infected with S. typhimurium. Samples were quick-frozen in liquid nitrogen and stored at -80 °C. In order to obtain representative measurements in each intestinal locus, three cross sections of approximately 2 mm out of the 2 cm segment of frozen intestine were examined. These 3 sections were pooled and total RNA was isolated from samples using an automated homogenizer (FastPrep Instrument, MP Biomedicals, Heidelberg, Germany) and the mirVana miRNA Isolation Kit (Applied Biosystems, Darmstadt, Germany), according to the manufacturer’s protocol. The RNA quality and quantity of all samples were proven using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano Kits (Agilent, Waldbronn, Germany) and the Nanodrop 1000 Spectrophotometer (Thermo Scientific, MA, USA).

value: equal amounts of total RNA of each ileum pool and additional total RNA from ascending colon


title: Before treatment (week 0) IBDB22

value: PBMC

value: Patient 4

value: NR - non-responder

value: Before treatment

value: week 0

value: Crohn's disease


title: MCL_IGHV_MUT (R1400)

value: Mantle Cell Lymphoma

value: B cell lymphocyte

value: MUT


title: HIV-1 Tat (T2) [miRNA]

city: Philadelphia

first: Bassel

middle: E

last: Sawaya

state: PA

address: 3307 N. Broad Street

department: Neurology

institute: Temple University

description: YL-03212013-miRNA3_0-T24b_Temple.rma-dabg-Signal

hyb_protocol: RNA was labeled using the miRCURY LNATM miRNA, Hy5 Power Labeling Kit (Exiqon) as per manufacturer’s recommendations using Maui SC Hybridization Chambers (BioMicro Systems, Salt Lake City, UT).

scan_protocol: Array chips were scanned using Axon GenePix Scanner (Molecular Devices, Downingtown, PA) and Genepix 4000 image capture software (Molecular Devices, Downingtown, PA).

data_processing: Quantile normalization was used using JMP Genomics (JMP, Cary, NC) at Harvard Catalyst - Laboratory for Innovative Translational Technology (HC-LITT) and differentially regulated miRNAs were determined. Untreated cells were used as control. Sample data table includes only human miRNA (i.e. all other probes related to other species were excluded).

label: Hy5 Power labeling

source_name: SH-SY5Y_HIV-1 Tat

growth_protocol: Human neuronal cell line SH-SY5Y (5 x 10^5)  were grown in DMEM + 10% FBS on MatTek glass bottom plates treated with collagen (MatTek, Ashland, MA).

extract_protocol: Total RNA was isolated using Trizol (Invitrogen, Carlsbad, CA). 750 ng of total RNA was used for miRNA array analysis using miRCURY LNATM microRNA Array, v. 11.0 (Exiqon, Woburn, MA).

treatment_protocol: Cells were treated with Tat (10 ng/ml) kindly received from NIH (AIDS reagnets Bank) for 24 hours.

tag: cell line

value: human fetal neuronal cells

tag: treated with

value: 10ng of HIV-1 Tat protein


title: 28d p.i. Salmonella

description: 28d p.i. S [miRNA]

source_name: S.typhimurium infected

value: ileum

tag: infection

value: no treatment

tag: time


title: HIV-1 Tat (T1) [miRNA]

description: YL-03212013-miRNA3_0-T24a_Temple.rma-dabg-Signal

label_protocol: RNA was labeled using the miRCURY LNATM miRNA, Hy5 Power Labeling Kit (Exiqon) as per manufacturer’s recommendations using Maui SC Hybridization Chambers (BioMicro Systems, Salt Lake City, UT).


title: 28d p.i. Salmonella + E.Faecium

description: 29d p.i. SP [miRNA]

source_name: S.typhimurium infected + Enterococcus faecium treatment

tag: tissue


title: 28d p.i. Control

description: 28d p.i. C [miRNA]

source_name: non-infected control

value: non infected control

tag: treatment


title: Control M1 [miRNA]

description: YL-03212013-miRNA3_0-M24a_Temple.rma-dabg-Signal

value: none (control)


title: Control M2 [miRNA]

description: YL-03212013-miRNA3_0-M24b_Temple.rma-dabg-Signal


title: 3d p.i. Salmonella

description: 3d p.i. S [miRNA]


title: MCL_IGHV_UNMUT (R1329)

value: UNMUT


title: MCL_IGHV_UNMUT (R1332)


title: MCL_IGHV_UNMUT (R1328)


title: 3d p.i. Control

description: 3d p.i. C [miRNA]


title: MCL_IGHV_UNMUT (R1306)


title: 3d p.i. Salmonella + E.faecium

description: 3d p.i. SP [miRNA]


title: MCL_IGHV_MUT (R1399_M)


title: Lsd1fl/fl EpoRCre biological replicate #2 [CD71/c-Kit]

description: FACS-purified primary CD71_high / c-Kit_high fetal liver pro-erythroblasts

source_name: CD71_high c-Kit_high pro-erythroblasts

growth_protocol: Freshly isolated primary fetal liver cells, the cells have NOT been cultured in vitro.

tag: developmental stage

value: fetal liver

value: Lsd1fl/fl EpoRCre


title: WT-Act_1

city: Madison

first: Melba

middle: Marie

last: Tejera

state: WI

address: 2015 Linden Drive

department: Pathobiological Sciences

institute: UW-Madison

description: Gene expression in purified CD8 D54 PI LCMV-Arm

hyb_protocol: Cy3 labeled cDNAs were hybridized overnight (17 hours, 65°C) to an Agielent Whole Mouse Genome Oligo Microarray (8 x 60K) using Agilent's recommended bybridization chamber and oven. Microarrays were washed once with Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature. Followed by a second wash with preheated Agilent Gene Expression Was Buffer 2 (37°C) for 1 min. The last washing step was perfomed with acetonitrile.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent's Microarray Scanner System (Agilent Techonologies) using one color scan settings for 8x60k array slides.

data_processing: Agilent Feature Extraction Software was used to read out and process the microarray image files.

source_name: D54 PI

label_protocol: 250ng of each of the cDNAs were used as template for Cy3 labeling which was perfomed according to Miltenyi Biotec's undisclosed protocol.

extract_protocol: Total RNA was extracted from the sorted cells by TRIzol Reagent (per manufacturer's protocol recommendations).  SuperAmp RNA amplification was performed according to Miltenyi Biotec's undisclosed procedure. Briefly, though, he amplification is based on a global PCR protocol using mRNA-derived cDNA. MRNA was isolated via magnetic bead technology and amplified cDNA samples were quantified using the ND-1000 Spetrophotometer.

treatment_protocol: 6 to 8 week old WT and FoxO1-/- mice were infected intraperitoneally with 2 x 10^5 PFU Armstrong strain of LCMV to induce acute infection. At day 54 post infection spleens were harvested and CD8 T cells were purfied.

value: Spleen

value: wild type

tag: cell population

value: CD8 CD44 high 1

value: purified CD8

value: 6-8 weeks-old


title: KO_Tet_1

tag: genotype

value: CD8 CD44 high Tetramer positive 1


title: 3h p.i. Salmonella

description: 3h p.i. S [miRNA]


title: KO_N_2

value: CD8 CD44 low 2

tag: cell type


title: KO-Act_2

value: CD8 CD44 high 2


title: 3h p.i. Control

description: 3h p.i. C [miRNA]


title: MCL_IGHV_UNMUT (R1680)

value: Mantle Cell Lymphoma

value: B cell lymphocyte


title: Lsd1fl/fl biological replicate #1 [Gr1dim Mac1]

value: adult bone marrow

tag: gender

value: male


title: MCL_IGHV_UNMUT (R1394)


title: Lsd1fl/fl EpoRCre biological replicate #1 [CD71/c-Kit]


title: 3h p.i. Salmonella + E.faecium

description: 3h p.i. SP [miRNA]

value: ileum


title: KO_Tet_2

value: CD8 CD44 high Tetramer positive 2


title: Lsd1fl/fl biological replicate #1 [CD71/c-Kit]


title: WT_N_2


title: WT_Act_2


title: WT_Tet_2


title: Lsd1fl/fl biological replicate #2 [CD71/c-Kit]


title: TCD4_10H_D0005Gy_Ind4

status: Public on Jun 24 2013

city: Fontenay aux Roses Cedex

first: Gaetan

last: GRUEL

address: BP 17

department: Service de RadioBiologie et d'Epidemiologie

institute: Institut de Radioprotection et de Surete Nucleaire

description: Gene expression in Lymphocyte TCD4 600min post-exposure to 5mGy of human whole blood:IMDM (1:10)

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4845A) 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 DNA Microarray Scanner (G2565AA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um double pass, 16 bit Dye channel is set to Green and Green PMT is set to 100%, XDR set to 0.1).

data_processing: The scanned images were analyzed with Feature Extraction Software 7.5 (Agilent) using default parameters (protocol GE1-107_sep08 and Grid: 026652_D_F_20101031) to obtain raw signal intensities. Microarray raw data were analyzed, normalized and filtered with R software, limma and Agi4x44PreProcess package of the Bioconductor repository. Briefly, the mean signal intensity for each spot was used and a log base 2 transformation was performed. The normalization step was performed using the quantile method of the normalizeBetweenArrays function of the limma package. Agilent Feature Extraction Software flagged undetected spot and bad features allowing excluding them from the analysis. The filtering criteria consisted of removing a probe when it was undetected in at least 75% of the replicates. A total of 19,246 probes were selected after filtering step.

source_name: Lymphocyte TCD4, 600min, 5mGy, Individual4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug total RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from lymphocyte T CD4+ using RNeasy Mini columns from the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer.

treatment_protocol: Human whole blood samples from 5 healthy donors were diluted in IMDM medium (1:10) and exposed to 500, 100, 50, 25, 10 and 5 mGy of Cobalt 60 gamma-rays. Gene expression alterations were measured 150, 300, 450 and 600 min post exposure after negative cell sorting of lymphocytes TCD4+ cells.

value: Lymphocyte TCD4


title: DKOG4_ES_DexPlus_24h_rep1

city: Kobe

first: Yuichi

last: Kumaki

address: 2-2-3 Minatojima-minamimachi, Chuo-ku

department: Center for Developmental Biology

country: Japan

institute: RIKEN

description: Gene expression data from Dnmt3a-/-Dnmt3b-/- Gata4GR ES cells diffentiating to primitive endoderm cells with 24hr-culture in the presence of dexamethasone to activate Gata4GR transgene

hyb_protocol: 600 ng of Cy3-labeled cRNA was hybridized in Agilent hybridization chambers for 17 hours at 65 degrees C and 10 rpm according to the manufacturer's instructions (G4140-90040 One-Color Microarray-Based Gene Expression Analysis Protocol Version 6.5).

scan_protocol: Slide scanning was performed using the Agilent DNA Microarray Scanner G2505C with 3 um resolution and 20-bit dynamic range.

data_processing: The scanned images were processed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid 028005_D_F_20110406) to generate background subtracted and spatially detrended green Processed Signal intensities. Normalize signal intensities were obtained by a) removal of data of control probes, b) log2 transformation, and c) quantile normalization, which was performed using the normalizeQuantiles function of the limma package of the R.

source_name: mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, +Dex, 24hr, replicate 1

label_protocol: Amplification and Cy3 labeling of RNA was prepared from 50 ng of RNA using the Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions (G4140-90040 One-Color Microarray-Based Gene Expression Analysis Protocol Version 6.5). Purification of Cy3-labeled cRNA was performed using the RNeasy Mini Kit (Qiagen). Quantity, quality and dye incorporation of Cy3-labeled cRNA were checked using the NanoDrop ND-1000 Spectrophotometer (Thermo) and the 2100 Bioanalyzer (Agilent).

growth_protocol: ES cells were cultured in Glasgow Minimum Essential Medium (GMEM, Sigma) supplemented with 10% fetal calf serum (FCS), 0.1 mM nonessential amino acids (Invitrogen), 1 mM sodium pyruvate, 0.1 mM 2-mercaptoethanol, and 2000 U/ml leukemia inhibitory factor (LIF) on gelatinized culture dishes without feeder cells.

extract_protocol: Total RNA was isolated by using the QIAshredder and the RNeasy Plus Micro Kit with gDNA Eliminator column (Qiagen) according to the manufacturer's protocols. RNA was quantified and quality controlled using the NanoDrop ND-1000 Spectrophotometer (Thermo) and the 2100 Bioanalyzer (Agilent).

treatment_protocol: 100 nM dexamethasone (Dex) was added to ES cells stably expressing Gata4GR. The cells were recovered by trypsinization after 24 hours after addition of Dex, and used for RNA preparation.

value: Line 16G4.3

value: Dnmt3a-/-Dnmt3b-/-, stably expressing Gata4-glucocorticoid receptor ligand binding domain fusion gene

value: embryonic stem (ES) cells differentiating to primitive endoderm cells

tag: dexamethasone

value: yes


title: TCD4_10H_D0005Gy_Ind5

source_name: Lymphocyte TCD4, 600min, 5mGy, Individual5


title: DKOG4_ES_DexPlus_12h_rep2

description: Gene expression data from Dnmt3a-/-Dnmt3b-/- Gata4GR ES cells diffentiating to primitive endoderm cells with 12hr-culture in the presence of dexamethasone to activate Gata4GR transgene

source_name: mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, +Dex, 12hr, replicate 2

treatment_protocol: 100 nM dexamethasone (Dex) was added to ES cells stably expressing Gata4GR. The cells were recovered by trypsinization after 12 hours after addition of Dex, and used for RNA preparation.


title: DKOG4_ES_DexPlus_72h_rep1

description: Gene expression data from Dnmt3a-/-Dnmt3b-/- Gata4GR ES cells diffentiating to primitive endoderm cells with 72hr-culture in the presence of dexamethasone to activate Gata4GR transgene

source_name: mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, +Dex, 72hr, replicate 1

treatment_protocol: 100 nM dexamethasone (Dex) was added to ES cells stably expressing Gata4GR. The cells were recovered by trypsinization after 72 hours after addition of Dex, and used for RNA preparation.


title: DKOG4_ES_DexPlus_12h_rep1

source_name: mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, +Dex, 12hr, replicate 1


title: DKOG4_ES_DexPlus_48h_rep2

description: Gene expression data from Dnmt3a-/-Dnmt3b-/- Gata4GR ES cells diffentiating to primitive endoderm cells with 48hr-culture in the presence of dexamethasone to activate Gata4GR transgene

source_name: mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, +Dex, 48hr, replicate 2

treatment_protocol: 100 nM dexamethasone (Dex) was added to ES cells stably expressing Gata4GR. The cells were recovered by trypsinization after 48 hours after addition of Dex, and used for RNA preparation.


title: DKOG4_ES_0h_rep1

description: Gene expression data from Dnmt3a-/-Dnmt3b-/- Gata4GR ES cells

source_name: mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, replicate 1

treatment_protocol: The cells were recovered by trypsinization and used for RNA preparation.

value: embryonic stem (ES) cells


title: DKOG4_ES_DexPlus_72h_rep2

source_name: mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, +Dex, 72hr, replicate 2


title: DKOG4_ES_DexPlus_48h_rep1

source_name: mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, +Dex, 48hr, replicate 1


title: DKOG4_ES_DexPlus_3h_rep2

description: Gene expression data from Dnmt3a-/-Dnmt3b-/- Gata4GR ES cells diffentiating to primitive endoderm cells with 3hr-culture in the presence of dexamethasone to activate Gata4GR transgene

source_name: mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, +Dex, 3hr, replicate 2

treatment_protocol: 100 nM dexamethasone (Dex) was added to ES cells stably expressing Gata4GR. The cells were recovered by trypsinization after 3 hours after addition of Dex, and used for RNA preparation.


title: TCD4_7H30_D0005Gy_Ind5

description: Gene expression in Lymphocyte TCD4 450min post-exposure to 5mGy of human whole blood:IMDM (1:10)

source_name: Lymphocyte TCD4, 450min, 5mGy, Individual5


title: TCD4_10H_D0005Gy_Ind1

source_name: Lymphocyte TCD4, 600min, 5mGy, Individual1


title: WTG4_ES_DexPlus_48h_rep2

description: Gene expression data from wild-type Gata4GR ES cells diffentiating to primitive endoderm cells with 48hr-culture in the presence of dexamethasone to activate Gata4GR transgene

source_name: mouse wild-type Gata4GR (WTG4) ES cells, +Dex, 48hr, replicate 2

value: Line J1G4.211

value: wild-type, stably expressing Gata4-glucocorticoid receptor ligand binding domain fusion gene


title: WTG4_ES_DexPlus_72h_rep2

description: Gene expression data from wild-type Gata4GR ES cells diffentiating to primitive endoderm cells with 72hr-culture in the presence of dexamethasone to activate Gata4GR transgene

source_name: mouse wild-type Gata4GR (WTG4) ES cells, +Dex, 72hr, replicate 2


title: DKOG4_ES_DexPlus_6h_rep1

description: Gene expression data from Dnmt3a-/-Dnmt3b-/- Gata4GR ES cells diffentiating to primitive endoderm cells with 6hr-culture in the presence of dexamethasone to activate Gata4GR transgene

source_name: mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, +Dex, 6hr, replicate 1

treatment_protocol: 100 nM dexamethasone (Dex) was added to ES cells stably expressing Gata4GR. The cells were recovered by trypsinization after 6 hours after addition of Dex, and used for RNA preparation.


title: DKOG4_ES_DexPlus_6h_rep2

source_name: mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, +Dex, 6hr, replicate 2


title: DKOG4_ES_0h_rep2

source_name: mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, replicate 2


title: WTG4_ES_DexPlus_72h_rep1

source_name: mouse wild-type Gata4GR (WTG4) ES cells, +Dex, 72hr, replicate 1


title: TCD4_7H30_D0005Gy_Ind4

source_name: Lymphocyte TCD4, 450min, 5mGy, Individual4


title: TCD4_7H30_D0005Gy_Ind3

source_name: Lymphocyte TCD4, 450min, 5mGy, Individual3


title: TCD4_7H30_D0005Gy_Ind2

source_name: Lymphocyte TCD4, 450min, 5mGy, Individual2


title: DKOG4_ES_DexPlus_24h_rep2

source_name: mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, +Dex, 24hr, replicate 2


title: DKOG4_ES_DexPlus_3h_rep1

source_name: mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, +Dex, 3hr, replicate 1


title: WTG4_ES_DexPlus_24h_rep2

description: Gene expression data from wild-type Gata4GR ES cells diffentiating to primitive endoderm cells with 24hr-culture in the presence of dexamethasone to activate Gata4GR transgene

source_name: mouse wild-type Gata4GR (WTG4) ES cells, +Dex, 24hr, replicate 2


title: WTG4_ES_DexPlus_24h_rep1

source_name: mouse wild-type Gata4GR (WTG4) ES cells, +Dex, 24hr, replicate 1


title: WTG4_ES_DexPlus_48h_rep1

source_name: mouse wild-type Gata4GR (WTG4) ES cells, +Dex, 48hr, replicate 1


title: TCD4_5H_D0005Gy_Ind5

description: Gene expression in Lymphocyte TCD4 300min post-exposure to 5mGy of human whole blood:IMDM (1:10)

source_name: Lymphocyte TCD4, 300min, 5mGy, Individual5


title: WTG4_ES_DexPlus_12h_rep2

description: Gene expression data from wild-type Gata4GR ES cells diffentiating to primitive endoderm cells with 12hr-culture in the presence of dexamethasone to activate Gata4GR transgene

source_name: mouse wild-type Gata4GR (WTG4) ES cells, +Dex, 12hr, replicate 2


title: TCD4_5H_D0005Gy_Ind4

source_name: Lymphocyte TCD4, 300min, 5mGy, Individual4


title: TCD4_5H_D0005Gy_Ind2

source_name: Lymphocyte TCD4, 300min, 5mGy, Individual2


title: TCD4_10H_D001Gy_Ind4

description: Gene expression in Lymphocyte TCD4 600min post-exposure to 10mGy of human whole blood:IMDM (1:10)

source_name: Lymphocyte TCD4, 600min, 10mGy, Individual4


title: TCD4_10H_D001Gy_Ind5

source_name: Lymphocyte TCD4, 600min, 10mGy, Individual5


title: WTG4_ES_DexPlus_12h_rep1

source_name: mouse wild-type Gata4GR (WTG4) ES cells, +Dex, 12hr, replicate 1


title: WTG4_ES_DexPlus_3h_rep2

description: Gene expression data from wild-type Gata4GR ES cells diffentiating to primitive endoderm cells with 3hr-culture in the presence of dexamethasone to activate Gata4GR transgene

source_name: mouse wild-type Gata4GR (WTG4) ES cells, +Dex, 3hr, replicate 2


title: TCD4_5H_D0005Gy_Ind1

source_name: Lymphocyte TCD4, 300min, 5mGy, Individual1


title: TCD4_2H30_D0005Gy_Ind2

description: Gene expression in Lymphocyte TCD4 150min post-exposure to 5mGy of human whole blood:IMDM (1:10)

source_name: Lymphocyte TCD4, 150min, 5mGy, Individual2


title: WTG4_ES_0h_rep2

description: Gene expression data from wild-type Gata4GR ES cells

source_name: mouse wild-type Gata4GR (WTG4) ES cells, replicate 2


title: WTG4_ES_DexPlus_3h_rep1

source_name: mouse wild-type Gata4GR (WTG4) ES cells, +Dex, 3hr, replicate 1


title: WTG4_ES_DexPlus_6h_rep1

description: Gene expression data from wild-type Gata4GR ES cells diffentiating to primitive endoderm cells with 6hr-culture in the presence of dexamethasone to activate Gata4GR transgene

source_name: mouse wild-type Gata4GR (WTG4) ES cells, +Dex, 6hr, replicate 1


title: DKOG4_Flk1_long_DexPlus_72h_rep1

description:
Gene expression data from Flk1+/Ecad- mesoderm cells derived from Dnmt3a-/-Dnmt3b-/- Gata4GR ES cells, with further 72hr-culture in the presence of dexamethasone to activate Gata4GR transgene
'short' sample represents short time course experiment (0-3h). In this experiment, dexamethasone was added before FACS sorting.
'long' sample represents long time course experiment (0-72h). In this experiment, dexamethasone was added after FACS sorting.

source_name: Flk1+/Ecad- mesoderm cells derived from mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, +Dex, 72hr, replicate 1

growth_protocol: ES cells were plated onto a 10-cm dish with confluent OP9 stromal cells in the differentiation medium (alpha-MEM supplemented with 10% FCS and 50 uM 2-mercaptoethanol) for 4 days.

treatment_protocol: The cells were collected using 0.25% trypsin-EDTA, and single cell suspensions were stained using APC-conjugated anti-Flk1, biotinylated anti-E-cadherin (Eccd2, Takara Bio or DECMA-1, eBioscience) antibodies, and PE-conjugated streptavidin. Flk1 positive/E-cadherin negative cells were sorted by FACS-Aria (BD Biosciences). The cells were further cultured on type IV collagen-coated dishes in the differentiation medium  (alpha-MEM supplemented with 10% FCS and 50 uM 2-mercaptoethanol) for 72 hours in the presence of 100 nM dexamethasone.

value: Flk1+/Ecad- mesoderm cells derived from embryonic stem (ES) cells, with further culture


title: TCD4_2H30_D0005Gy_Ind4

source_name: Lymphocyte TCD4, 150min, 5mGy, Individual4


title: TCD4_2H30_D0005Gy_Ind1

source_name: Lymphocyte TCD4, 150min, 5mGy, Individual1


title: TCD4_2H30_D0005Gy_Ind5

source_name: Lymphocyte TCD4, 150min, 5mGy, Individual5


title: WTG4_ES_0h_rep1

source_name: mouse wild-type Gata4GR (WTG4) ES cells, replicate 1


title: WTG4_ES_DexPlus_6h_rep2

source_name: mouse wild-type Gata4GR (WTG4) ES cells, +Dex, 6hr, replicate 2


title: DKOG4_Flk1_long_DexPlus_72h_rep2

source_name: Flk1+/Ecad- mesoderm cells derived from mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, +Dex, 72hr, replicate 2