title: Human Peripheral Blood T cells [Sample_27]


title: Human Peripheral Blood T cells [Sample_23]

status: Public on Feb 10 2016

type: RNA

city: New Haven

first: Rakesh

last: Verma

state: CT

address: 333 Cedar St.

department: Yale Cancer Center

country: USA

institute: Yale University

hyb_protocol: Samples were hybridized with GeneChip® Human Transcriptome Array 2.0 (Affymetrix) and scanned at the Yale Center for Genome Anlaysis (YCGA) Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Data on coding genes were analyzed using Genespring GX 12.5 platform. Data were imported via exon expression workflow employing RMA16 or PLIER16 (normalization) for analyzing the coding genes using the specific annotation support file for human transcriptome array 2.0 (as provided by Genespring GX).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Human Peripheral Blood T cells

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Not Applicable

extract_protocol: RNA was isolated from sorted peripheral blood T cells using RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

tag: gender

value: M

tag: tissue

value: Peripheral Blood T cells

tag: agent

tag: time point

value: pre


title: Human Peripheral Blood T cells [Sample_38]

value: F

value: post


title: Human Peripheral Blood T cells [Sample_22]


title: Human Peripheral Blood T cells [Sample_26]


title: Human Peripheral Blood T cells [Sample_20]


title: Human Peripheral Blood T cells [Sample_21]


title: Human Peripheral Blood T cells [Sample_16]


title: Human Peripheral Blood T cells [Sample_19]


title: Human Peripheral Blood T cells [Sample_15]


title: Human Peripheral Blood T cells [Sample_17]


title: Human Peripheral Blood T cells [Sample_14]


title: Human Peripheral Blood T cells [Sample_9]


title: Human Peripheral Blood T cells [Sample_8]


title: Human Peripheral Blood T cells [Sample_13]


title: Human Peripheral Blood T cells [Sample_11]


title: Human Peripheral Blood T cells [Sample_10]


title: Human Peripheral Blood T cells [Sample_6]


title: Human Peripheral Blood T cells [Sample_5]


title: Human Peripheral Blood T cells [Sample_12]


title: Human Peripheral Blood T cells [Sample_7]


title: Human Peripheral Blood T cells [Sample_4]


title: 147T_NOD-_ER-_PR-_HER-

city: Bangalore

first: Neeraj

last: KUMAR

address: Indian Institute of Science Bangalore

department: MRDG

country: India

institute: Indian Institute of Science Bangalore

hyb_protocol: 750 ng of labelled cRNA each from normal and Tumor were mixed with blocking agent and fragmentation buffer followd by incubation at 65 °C for 30 min. This is followed by addition of 55 ul of 2x GEx Hybridization Buffer HI-RPM to stop the fragmentation reaction. Later 100 ul of the above mix were added to each array.

scan_protocol: Agilent Feature Extraction Software (10.5.1.1) was used for background subtraction and LOWESS normalization.

data_processing: normalized log10 ratio (Cy5/Cy3) tumor/normal

source_name: breast tissue

label_protocol: 200 ng of RNA each from normal and tumor samples were used. Labeling of the probes was done using the Low RNA Input Linear Amplification Kit (Agilent Technologies, USA). Briefly 200 ng of RNA were reverse transcribed using T7promoter attached Oligo-dT primers at 40 °C for 2 hrs followed by 65 °C for 15 min. This cDNA were transcribed using T7 polymerase with respective labelled nucleotides at 40 °C for 2hrs. This synthesized labelled cRNA were purified using RNeasy mini column.

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

value: normal breast tissues

value: tumor breast tissue

tag: patient id

tag: nod status

value: NOD-

tag: er status

value: ER-

tag: pr status

value: PR-

tag: her status

value: HER-

tag: er

tag: pr

tag: her

tag: age

tag: size

tag: diag.

value: IDC-III with infiltrating margins, wide areas of necrosis

tag: skin

value: Free

tag: dsm

tag: nodal status

tag: last follow-up

tag: last follow-up notes

value: NAD

tag: other relevant investigations

tag: follow-up period


title: Human Peripheral Blood T cells [Sample_3]

tag: gender

tag: tissue

tag: agent

tag: time point


title: Human Peripheral Blood T cells [Sample_2]


title: control_cold_2

city: Durham

first: Rana

middle: K

last: Gupta

state: North Carolina

address: Carmichael Building, 300 North Duke St.

department: Duke Molecular Physiology Institute

institute: Duke University

hyb_protocol: Samples were hybridized with GeneChip Mouse Transcriptome Arrays (Affymetrix) and scanned at the UTSW Microarray Core Facility.

data_processing: Raw data were processed with Affymetrix Expression console software for background correction and normalization.

organism: Mus musculus

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT plus reagent kit. (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Control and adipocyte Zfp423 knockout animals were raised at room temperature till 8 weeks of age before doxycycline administration

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

treatment_protocol: Global gene expression profiles (microarray analysis) were obtained using total RNA extracted from iWAT of:  Cohort 1 (RT): Control mice maintained at room temperature on dox-containing chow diet for 28 days.   Cohort 2 (KO): Age-matched Zfp423-iAKO mice maintained at room temperature on dox-containing chow diet for 28 days.   Cohort 3 (CE):  Control mice maintained on dox-containing chow diet for 28 days, with the last 14 days at 6°C to induce the formation of beige adipocytes.

tag: genotype/variation

value: control; Adiponectin-rtTA; TRE-Cre; Zfp423+/+

tag: temperature

value: cold exposure

value: Inguinal white adipose tissue


title: Human Peripheral Blood T cells [Sample_18]


title: Zfp423_knockout_room temp_3

source_name: Zfp423_knockout_room temp

value: doxycycline-inducible adipocyte Zfp423 knockout; Adiponectin-rtTA; Tre-CRE; Zfp423loxP/loxP

value: room temperature


title: control_cold_1


title: Zfp423_knockout_room temp_1


title: control_room temp_1

source_name: control_room temp


title: Human Peripheral Blood T cells [Sample_1]

value: M

value: Peripheral Blood T cells

value: pre


title: control_cold_3


title: ATRA-2

city: Torino

first: Francesco

last: Neri

state: Italy

address: Via Nizza 52

country: Italy

institute: University of Torino

description:
PolyA RNA
Replicate 2

hyb_protocol: Direct Hybridization of RNA library was performed using Standard Operating Procedures in Whole-Genome Gene Expression Direct Hybridization Assay Guide (Illumina).

scan_protocol: Chips were scanned using Illumina HiScan software.

data_processing: Data were normalized using quantile normalization and background subtraction by default parameters in GenomeStudio (Illumina).

source_name: Embryonic stem cells, ATRA

label_protocol: RNA library were performed using Illumina Total Prep RNA Amplification Kit following the manufacturer's protocol.

growth_protocol: Embryonic stem cells were cultured in DMEM high glucose medium (Invitrogen) supplemented with 15% FBS (Millipore), 0.1mM nonessential amino acids (Invitrogen), 1mM sodium pyruvate (Invitrogen), 0.1mM 2-mercaptoethanol, 1500U/ml LIF (Millipore), 25 U of penicillin/ml, and 25 µg of streptomycin/ml.

extract_protocol: RNA was extracted using TRIzol reagent from Invitrogen.

treatment_protocol: Cells were induced with DMSO (vehicle) or all-trans retinoic acid (ATRA) for 2 hours.

tag: cell line

tag: cell type

value: embryonic stem cells

tag: treatment

value: all-trans retinoic acid (ATRA) for 2hr


title: Zfp423_knockout_room temp_2


title: control_room temp_2


title: control_room temp_3


title: Coxiella grown in Vero cells, time 21D, replicate 1

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description:
5102_KMS_2_Cb3_58_Vero-21-r1-855_01_8703
Gene expression data from Coxiella grown in Vero cells, time 21D replicate 1.

hyb_protocol: All cRNAs were hybridized to a custom Affymetrix GeneChip.

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

data_processing: The data were analyzed with GCOS 1.4 using Affymetrix default analysis with a scale filter for Ft genes setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Coxiella burnetii

source_name: Coxiella grown in Vero cells, time 21D, late SCV

label_protocol: Biotin-labeled cRNA was then in vitro transcribed using cDNA as a template. Ten ug of labeled cRNA was fragmented using Ambion 10X fragmentation buffer (Invitrogen) and incubation at 75°C for 15 min.

growth_protocol: C. burnetii was grown in Vero cells for the time specified.

extract_protocol: Trizol extraction followed by a MicrobEnrich kit (Applied Biosystems) was used to increase the relative level of C. burnetii RNA. Enriched RNA (~1 μg) was amplified using a MessageAmp II Bacteria kit (Applied Biosystems).

treatment_protocol: C. burnetii was profiled at day 3, day 5, day 7, day 14 and day 21 post-infection of Vero cells.

tag: strain/background

value: bacterial cells

tag: infected

value: Vero epithelial cells

tag: time point (post-infection)

value: 21 days

tag: developmental stage

value: late SCV


title: Coxiella grown in Vero cells, time 21D, replicate 3

description:
5104_KMS_2_Cb3_60_Vero-21-r3-857_01_8756
Gene expression data from Coxiella grown in Vero cells, time 21D replicate 3.


title: Coxiella grown in Vero cells, time 7D, replicate 1

description:
5094_KMS_2_Cb3_50_Vero-7-r1-835_01_8726
Gene expression data from Coxiella grown in Vero cells, time 7D replicate 1.

source_name: Coxiella grown in Vero cells, time 7D, intermediate LCV/SCV forms

value: 7 days

value: intermediate LCV/SCV forms


title: Coxiella grown in Vero cells, time 14D, replicate 4

description:
5101_KMS_2_Cb3_57_Vero-14-r4-850_01_8757
Gene expression data from Coxiella grown in Vero cells, time 14D replicate 4.

source_name: Coxiella grown in Vero cells, time 14D, early SCV

value: 14 days

value: early SCV


title: Coxiella grown in Vero cells, time 21D, replicate 4

description:
5105_KMS_2_Cb3_61_Vero-21-r4-858_01_8743
Gene expression data from Coxiella grown in Vero cells, time 21D replicate 4.


title: wt-1

description:
PolyA RNA
Replicate 1

source_name: Embryonic stem cells, untreated

value: DMSO vehicle for 2hr


title: Coxiella grown in Vero cells, time 3D, replicate 2

description:
5087_KMS_2_Cb3_43_Vero-3-r2-812_01_8693
Gene expression data from Coxiella grown in Vero cells, time 3D replicate 2.

source_name: Coxiella grown in Vero cells, time 3D, early LCV

value: 3 days

value: early LCV


title: ATRA-1

description:
PolyA RNA
Replicate 1


title: Coxiella grown in Vero cells, time 5D, replicate 2

description:
5091_KMS_2_Cb3_47_Vero-5-r2-824_01_8676
Gene expression data from Coxiella grown in Vero cells, time 5D replicate 2.

source_name: Coxiella grown in Vero cells, time 5D, late LCV

value: 5 days

value: late LCV


title: Coxiella grown in Vero cells, time 5D, replicate 3

description:
5092_KMS_2_Cb3_48_Vero-5-r3-825_01_8742
Gene expression data from Coxiella grown in Vero cells, time 5D replicate 3.


title: Coxiella grown in Vero cells, time 14D, replicate 1

description:
5098_KMS_2_Cb3_54_Vero-14-r1-847_01_8685
Gene expression data from Coxiella grown in Vero cells, time 14D replicate 1.


title: Coxiella grown in Vero cells, time 5D, replicate 4

description:
5093_KMS_2_Cb3_49_Vero-5-r4-826_01_8704
Gene expression data from Coxiella grown in Vero cells, time 5D replicate 4.


title: Coxiella grown in Vero cells, time 7D, replicate 3

description:
5096_KMS_2_Cb3_52_Vero-7-r3-837_01_8700
Gene expression data from Coxiella grown in Vero cells, time 7D replicate 3.


title: Coxiella grown in Vero cells, time 7D, replicate 2

description:
5095_KMS_2_Cb3_51_Vero-7-r2-836_01_8701
Gene expression data from Coxiella grown in Vero cells, time 7D replicate 2.


title: Coxiella grown in Vero cells, time 21D, replicate 2

description:
5103_KMS_2_Cb3_59_Vero-21-r2-856_01_8677
Gene expression data from Coxiella grown in Vero cells, time 21D replicate 2.


title: Coxiella grown in Vero cells, time 3D, replicate 4

description:
5089_KMS_2_Cb3_45_Vero-3-r4-814_01_8744
Gene expression data from Coxiella grown in Vero cells, time 3D replicate 4.


title: wt-2

description:
PolyA RNA
Replicate 2


title: Coxiella grown in Vero cells, time 7D, replicate 4

description:
5097_KMS_2_Cb3_53_Vero-7-r4-838_01_8674
Gene expression data from Coxiella grown in Vero cells, time 7D replicate 4.


title: Coxiella grown in Vero cells, time 14D, replicate 3

description:
5100_KMS_2_Cb3_56_Vero-14-r3-849_01_8686
Gene expression data from Coxiella grown in Vero cells, time 14D replicate 3.


title: Coxiella grown in Vero cells, time 5D, replicate 1

description:
5090_KMS_2_Cb3_46_Vero-5-r1-823_01_8764
Gene expression data from Coxiella grown in Vero cells, time 5D replicate 1.


title: Coxiella grown in Vero cells, time 3D, replicate 3

description:
5088_KMS_2_Cb3_44_Vero-3-r3-813_01_8750
Gene expression data from Coxiella grown in Vero cells, time 3D replicate 3.


title: Coxiella grown in Vero cells, time 3D, replicate 1

description:
5086_KMS_2_Cb3_42_Vero-3-r1-811_01_8662
Gene expression data from Coxiella grown in Vero cells, time 3D replicate 1.


title: control 6

city: Prague 2

first: Monika

last: Belickova

address: U nemocnice 1

country: Czech Republic

institute: Institute of Hematology and Blood Transfusion

hyb_protocol: Standard Illumina hybridzation protocol. Illumina Human HT-12 v. 4 microarrays.

scan_protocol: Standard Illumina scanning protocol on BeadStation 500.

data_processing: Raw data was extracted using BeadStudio Software. Dopsat

source_name: bone marrow CD34+ cells

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification kit.

extract_protocol: Total RNA was extracted using the acid guanidine-thiocyanate-phenol-chloroform method. Samples were incubated with DNase I (Qiagen) and RNA quality was evaluated on Agilent Bioanalyzer 2100 (Agilent Technologies).

tag: diagnosis

value: healthy control


title: control 9


title: control 10


title: Coxiella grown in Vero cells, time 14D, replicate 2

description:
5099_KMS_2_Cb3_55_Vero-14-r2-848_01_8665
Gene expression data from Coxiella grown in Vero cells, time 14D replicate 2.


title: control 4


title: control 2


title: treatment_response_12

value: female

tag: age

value: AML with MRC


title: control 1


title: treatment_response_13


title: treatment_response_5

value: male


title: treatment_response_6


title: treatment_response_9


title: control 3


title: treatment_response_1

value: CMML


title: treatment_response_7


title: treatment_response_8


title: treatment_response_4


title: stable_disease_6


title: control 5


title: stable_disease_9


title: stable_disease_7


title: stable_disease_10


title: stable_disease_8


title: treatment_response_10


title: treatment_response_2


title: treatment_response_11

value: RCMD


title: HG003_DpitA_8h_rep2

type: mixed

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

country: Switzerland

institute: Genomic Research Laboratory

description: Staphylococcus aureus strain HG003 DpitA versus Staphylococcus aureus gDNA pool

hyb_protocol: A mixture of RNA from HG003 or its pitA mutant and gDNA pool was diluted in 50 µl Agilent hybridization buffer, and hybridized at a temperature of 60°C for 17 hours in a dedicated hybridization oven

scan_protocol: 100% PMT using Agilent scanner

data_processing: Fluorescence intensities were quantified using Feature Extraction software (Agilent, version 8). Green and red feature data were extracted, processed, and imported in GeneSpring. Data were normalized to baseline using red channel data as a control and mean to estimate the baseline

organism: Staphylococcus aureus

source_name: S. aureus HG003 DpitA

label_protocol: Incorporation during reverse transcription

growth_protocol: 6 or 8 hours of growth in TSB in static conditions at 37°C in medium

extract_protocol: After a rapid centrifugation of cell suspensions, pellets were stabilized in Trizol. Batches of 3 µg of total S. aureus RNA were labeled by Cy3-dCTP using SuperScript II. Labeled products were then purified onto QiaQuick columns.

treatment_protocol: No treatment

tag: strain

tag: genotype

value: DpitA mutant

tag: growth time

molecule: genomic DNA

source_name: Staphylococcus aureus gDNA pool

tag: reference

value: Staphylococcus aureus gDNA pool


title: stable_disease_4

tag: gender


title: HG003_DpitA_6h_rep2


title: HG003_DpitA_8h_rep1


title: control 8


title: genomic DNA hybridization of bambara groundnut DNA with Soybean chip

type: genomic

city: Nottingham

first: Venkata Suresh

last: Bonthala

address: Wollaton Road

department: School of Computer Science

country: United Kingdom

institute: University of Nottingham

description: this data were used to filter RNA expression data

hyb_protocol: Following fragmentation of genomic DNA of bambara groundnut, 10 μg of genomic DNA were hybridized with Soybean’s GeneChip (Affymetrix) for 16 hours at 45°C using standard hybridization protocol (Affymetrix). Purified cRNA (15 μg) were heat-treated and then hybridized to Soybean’s GeneChip (Affymetrix) for 16 hours at 45°C using standard hybridization protocol (Affymetrix).

scan_protocol: GeneChip were scanned using GeneChip® Scanner 3000

data_processing: The data were analysed and normalized using RMA (Robust Multichip Average) algorithm present in “affy” R-package

label: Biotin

organism: Vigna subterranea

source_name: Genomic DNA from leaflet of Bambara groundnut

label_protocol: Total RNA (5 μg) from bambara groundnut of optimal, sub-optimal and very sub-optimal temperature stresses was reverse-transcribed to synthesize double stranded cDNA using standard protocol and then the resulting samples were in-vitro transcribed to generate complementary RNAs (cRNAs) using biotinylated nucleotides by T7 DNA polymerase. Genomic DNA from bambara groundnut’s leaf tissue was labelled with the Bioprime DNA labelling system kit.

growth_protocol: Three plants of Bambara groundnut landrac S19-3 were grown in controlled environment growth rooms at Sutton Bonington Campus, University of Nottingham under a 12 hour photoperiod and at a constant temperature of 27°C. A single, fully-expanded leaflet was sampled from each of the three plants growing at 27°C, snap frozen in liquid nitrogen and stored at -80°C. Plants were given a further 3 days at 27°C to recover from sampling before being moved to a controlled environment room at 23°C. On the fifth day at 23°C a single fully-expanded leaflet was sampled and stored, as described above. After 3 further days plants were moved to 18°C, and then five days later were sampled again.

extract_protocol: Extraction of genomic DNA was carried using 100 mg ground leaf tissue, using a DNeasy Plant Mini Kit (Qiagen), according to manufacturer’s directions. For extraction of total RNA, 100 mg ground leaf tissue was processed, as per manufacturer’s instructions, using a RNeasy Plant Mini Kit (Qiagen).

tag: tissue

value: Leaflet

value: Fully-expanded leaflet


title: HG003_DpitA_6h_rep1


title: stable_disease_2


title: HG003_wt_8h_rep2

description: Staphylococcus aureus wt strain HG003 versus Staphylococcus aureus gDNA pool

source_name: S. aureus HG003 wt

value: wild type


title: treatment_response_3


title: stable_disease_1


title: stable_disease_3


title: HG003_wt_8h_rep1


title: HG003_wt_6h_rep2


title: stable_disease_5


title: HG003_wt_6h_rep1


title: progressed _disease_ 8


title: Crypt region_Zfp148gt/+APCMin/+ (892)

city: Gothenburg

first: Per

last: Lindahl

address: Sahlgrenska University Hospital, Bruna Straket 16

department: Institute of Medicine

country: Sweden

institute: University of Gothenburg

hyb_protocol: GeneChip ST Arrays ( GeneChip® MoGene-2_0-st Array) were hybridized for 16 hours in a 45°C incubator, rotated at 60 rpm. According to the GeneChip® Expression Wash, Stain and Scan Manual (PN 702731 Rev 3, Affymetrix Inc., Santa Clara, CA) the arrays were then washed and stained using the Fluidics Station 450 and finally scanned using the GeneChip® Scanner 3000 7G.

data_processing: The raw data was normalized in the free software Expression Console provided by Affymetrix (http://www.affymetrix.com) using the robust (RMA) method first suggested by Li and Wong in 2001. Subsequent analysis of the gene expression data was carried out in the freely available statistical computing language R (http://www.r-project.org) using packages available from the Bioconductor project (www.bioconductor.org).

source_name: Crypt-enriched tissue from proximal small intestine of Zfp148gt/+APCMin/+ mice

label_protocol: 250 nanograms of total RNA from each sample were used to generate amplified and biotinylated sense-strand cDNA from the entire expressed genome according to the GeneChip® WT PLUS Reagent Kit User Manual ( P/N 703174 Rev 1 Affymetrix Inc., Santa Clara, CA).

growth_protocol: Zfp148gt/+APCMin/+ and Zfp148+/+APCMin/+ mice were kept under standard conditions

extract_protocol: Total RNA was extracted from crypt-enriched tissues that were isolated by laser microdissection (PALM) from 10mm thick cryosections of OCT-embedded and snap frozen Swiss roll preparations of small intestines (proximal). Total RNA was extracted with the QIAGEN RNeasy Micro Kit.

tag: genotype/variation

value: small intestine crypts


title: Crypt region_Zfp148gt/+APCMin/+ (911)

scan_protocol: According to the GeneChip® Expression Wash, Stain and Scan Manual (PN 702731 Rev 3, Affymetrix Inc., Santa Clara, CA) the arrays were then washed and stained using the Fluidics Station 450 and finally scanned using the GeneChip® Scanner 3000 7G.


title: Plant at 18°C, biological rep 3

description: Gene expression data from fully expanded single leaflet under 18°C

source_name: Bambara groundnut leaves at 18°C after 3 days


title: progressed _disease_ 7


title: progressed _disease_ 6


title: Plant at 18°C, biological rep 2


title: progressed _disease_ 9


title: Plant at 18°C, biological rep 1


title: Crypt region_Zfp148gt/+APCMin/+ (897)


title: Crypt region_Zfp148gt/+APCMin/+ (783)


title: Plant at 23°C, biological rep 2

description: Gene expression data from fully expanded single leaflet under 23°C

source_name: Bambara groundnut leaves at 23°C after 3 days


title: control 7


title: progressed _disease_ 5


title: Crypt region_Zfp148+/+APCMin/+ (899)

source_name: Crypt-enriched tissue from proximal small intestine of Zfp148+/+APCMin/+ mice


title: Crypt region_Zfp148gt/+APCMin/+ (893)


title: progressed _disease_ 4


title: Crypt region_Zfp148+/+APCMin/+ (895)


title: Plant at 23°C, biological rep 1


title: Plant at 23°C, biological rep 3


title: progressed _disease_ 3


title: Crypt region_Zfp148+/+APCMin/+ (885)


title: Crypt region_Zfp148+/+APCMin/+ (888)


title: progressed _disease_ 2


title: Crypt region_Zfp148+/+APCMin/+ (889)


title: progressed _disease_ 1


title: BAT_ChR2-AgRP_replicate_3

city: Cologne

first: Peter

last: Frommolt

address: Joseph-Stelzmannstr. 26

country: Germany

institute: CECAD

description:
Gene expression data in BAT following acute somatic activation of AgRP neurons
BAT2

hyb_protocol: Probes were hybridized to the Affymetrix GeneChip Mouse Gene 2.0 ST Array according to the manufacturer’s instructions.

scan_protocol: Chips were scanned with a GeneChip 3000 7G scanner.

data_processing: Raw data (CEL files) were processed using the robust multi-array average (RMA) algorithm and quantile normalization with the Affymetrix Power Tools, version 1.12.0, and platformspecific library files. Differential gene expression was analyzed using descriptive statistics (fold change) and Student’s T-Test method for pairwise comparisons. Genes were prioritized by statistical evidence. In order to create candidate lists for differential gene expression between conditions, we used all genes regulated at least 1.5-fold where differential expression was significant at level 0.05. Type I error inflation was ignored because the p-values were used to prioritize the list rather than being interpreted in a confirmatory sense.

source_name: BAT from a ChR2-AgRP mouse somatically light-stimulated

label_protocol: cDNA probes were labelled with Encore Biotin Module (NuGen Technologies, Inc.)

growth_protocol: Mice were on a mixed B6:129 background. All experiments were conducted according to the Bezirksregierung Köln. Mice were housed according to standardized conditions at the Max Planck Institute for Metabolism animal facility.

extract_protocol: Total RNA from BAT was isolated using a commercially available kit (mirVana miRNA Isolation Kit, Ambion), and RNA quality was assessed on the Agilent 4200 TapeStation system.

treatment_protocol: Mice implanted with optical fibers targeting the arcuate nucleus were optogenetically stimulated for one hour in the absence of food.

value: mixed B6:129 background

tag: Sex

value: blue light-stimulation of arcuate nucleus

value: whole interscapular BAT


title: Crypt region_Zfp148+/+APCMin/+ (782)


title: BAT_Ctrl_replicate_4

description:
Gene expression data in BAT from a ChR2 wild-type littermate
BAT4

source_name: BAT from a ChR2-fl/wt mouse somatically light-stimulated

value: control


title: BAT_Ctrl_replicate_3

description:
Gene expression data in BAT from a ChR2 wild-type littermate
BAT3


title: BAT_ChR2-AgRP_replicate_4

description:
Gene expression data in BAT following acute somatic activation of AgRP neurons
BAT6


title: Crypt region_Zfp148gt/+APCMin/+ (891)


title: Plant at 27°C, biological rep 3

description: Gene expression data from fully expanded single leaflet under 27°C

source_name: Bambara groundnut leaflet at 27°C after 3 days


title: BAT_ChR2-AgRP_replicate_2

description:
Gene expression data in BAT following acute somatic activation of AgRP neurons
BAT12


title: Plant at 27°C, biological rep 2


title: WM266-4 transfected with miR-7-5p 3

city: Nedlands

first: Patrick

middle: Aaron

last: Candy

state: Western Australia

address: 6 Verdun St

department: Cancer Medicine

country: Australia

institute: Perkins Institute

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: WM266-4 melanoma cells

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

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

value: WM266-4 melanoma cells

tag: transfection


title: Crz1 Overexpression pREP1 Replicate 2

city: Calgary

first: Gordon

last: Chua

state: Alberta

address: 2500 University Drive NW

department: Biological Sciences

country: Canada

institute: University of Calgary

description:
CRZ1 OE pREP1-rep2
Untreated strains.

hyb_protocol: Hybridization was performed according to the manufacturer's instruction (Agilent Technology). Microarray was washed in 6X SSPE/0.005% sodium N-lauroylsarcosine at room temperature for 5 min, followed by a second wash in pre-heated 42°C 0.6X SSPE for 2 min.

scan_protocol: Microarrays were scanned on a GenePix 4200A instrument with GenePix 3.0 software.

data_processing: The raw data was lowess normalized and the average log2 ratios with the corresponding t-test p values from the dye-swap experiments were obtained using the R Bioconductor Limma package.

organism: Schizosaccharomyces pombe

source_name: empty vector pREP1 auxotrophic strain, untreated

label_protocol: 2 ug of mRNA were converted into cDNA using 140 nmol of Oligo-dT(25) anchored primer (Sigma), 20 nmol of aminoallyl dUTP dNTP (Sigma) mixture, and 200 units of SuperScript II reverse transcriptase (Invitrogen). 1 ug of cDNA each from overexpression or deletion strain and empty vector control strain was labeled with Cy3 or Cy5 (GE Healthcare) and were combined for QIAquick purification (QIAGEN).

growth_protocol: S. pombe yeast cells were inoculated in EMM+AU minimal media with no thiamine and cultured for 18-22hr.

extract_protocol: Total RNA was extracted using hot phenol-chloroform method, followed by mRNA isolation using gravity-flow Oligo-dT cellulose beads.

value: empty vector pREP1

source_name: Crz1 OE pREP1 auxotrophic strain, untreated

value: Crz1 OE pREP1


title: Crz1 Overexpression pREP41 Replicate 2

description:
CRZ1 OE pREP41-rep2
Untreated strains.

source_name: empty vector pREP41 auxotrophic strain, untreated

value: empty vector pREP41

source_name: Crz1 OE pREP41 auxotrophic strain, untreated

value: Crz1 OE pREP41


title: WM266-4 transfected with miR-NC 1

description: replicate 1

tag: cell type

value: miR-NC


title: BAT_Ctrl_replicate_2

description:
Gene expression data in BAT from a ChR2 wild-type littermate
BAT13

value: female

tag: treatment


title: Crz1 Overexpression pREP41 Replicate 1

description:
CRZ1 OE pREP41-rep1
Untreated strains.

tag: strain/background


title: Plant at 27°C, biological rep 1


title: prz1 Overexpression Replicate 2

description:
prz1 OE-rep2
Untreated strains.

source_name: prz1 OE pREP1 auxotrophic strain, untreated

value: prz1 OE pREP1


title: BAT_ChR2-AgRP_replicate_1

description:
Gene expression data in BAT following acute somatic activation of AgRP neurons
BAT10

value: male


title: WM266-4 transfected with miR-7-5p 1

description: replicate 1


title: BAT_Ctrl_replicate_1

description:
Gene expression data in BAT from a ChR2 wild-type littermate
BAT1


title: WM266-4 transfected with miR-NC 3

description: replicate 3


title: WM266-4 transfected with miR-7-5p 2

description: replicate 2


title: WM266-4 transfected with miR-NC 2

description: replicate 2


title: prz1 Overexpression Replicate 1

description:
prz1 OE-rep1
Untreated strains.


title: LNANT3

city: Miami

first: Kerry

last: Burnstein

state: Fl

department: Molecular and Cellular Pharmacology

institute: University of Miami

description: replicate 3

data_processing: Illumina Inc. GenomeStudio version 1.9.0

source_name: LNCaP AntagomiR-23b and -27b

growth_protocol: Low passage PC3-ML and LNCaP cells were grown in RPMI media according to standard cell culture procedures. Transfection/transduction of miR-23b/-27b or antagomiRs were carried out as described in manuscript (Rice, Ishteiwy et al.)

extract_protocol: RNA was isolated using Trizol reagent according to manufacturers protocol

treatment_protocol: PC3-MLCells were transduced with miR-23b/-27b or Scrambled Control for two consecutive nights, then allowed 48 hours to recover. Cells were tested for efficiency using flow cytometry. LNCaP cells were transfected with antagomiRs to miR-23b and miR-27b or a control antagomiR 48 hours prior to cell harvest.

tag: cell line

value: LNCaP

value: prostate cancer


title: LNANT2

description: replicate 2


title: HCT116 cells, shH2AX RNA, rep 4

city: Bethesda

first: Urbain

middle: S

last: Weyemi

state: MD

address: 9000 Rockville Pike

department: National Cancer Institute

institute: National Institutes of Health

hyb_protocol: Three replicates of each group were prepared, labeled, and hybridized to Affymetrix Human Gene 2.0 ST arrays

scan_protocol: GeneChips were scanned on Affymetrix GeneChip scanner 3000

data_processing: Affymetrix Expression Console (EC) was used to generate CHP files from CEL files.Then, the CEL files were loaded into Partek Genomics Suite software, version 6.6 for normalization and differential expression analysis.

label_protocol: Amplified, biotinylated and reverse-transcribed single-stranded DNA targets were prepared from 100ng total RNA, according to the standard Affymetrix protocols (GeneChip WT PLUS Reagent Kit User Manual, 2013, Affymetrix).

growth_protocol: HCT116 expressing control shRNA (shCTRL) or shRNA targeting H2AFX (shH2A.X) were cultured in DMEM supplemented with 10% FBS for 72 hours.

extract_protocol: Total RNAs from HCT116 cells infected with scrambled shRNAs (shCTRL) or with shRNAs targeting H2A.X (shH2A.X) were extracted using RNeasy Mini Kit (Qiagen, Valencia, CA, USA) following manufacturer’s instructions.

treatment_protocol: Cells were infected with shRNA targeting H2AFX gene or with control shRNA.

tag: shRNA


title: prz1 Deletion vs. pmr1 Deletion Replicate 1

description:
prz1 del vs. pmr1 del-rep1
Untreated strains.

source_name: pmr1 deletion auxotrophic strain, untreated

growth_protocol: S. pombe yeast cells were inoculated in YES+ALU media and cultured for 16-20hr.

value: pmr1 deletion

source_name: prz1 deletion auxotrophic strain, untreated

value: prz1 deletion


title: prz1 Deletion vs. pmr1 Deletion Replicate 2

description:
prz1 del vs. pmr1 del-rep2
Untreated strains.


title: LNANT1

description: replicate 1


title: HCT116 cells, shH2AX RNA, rep 5


title: HCT116 cells, shH2AX RNA, rep 2


title: Crz1 Overexpression pREP1 Replicate 1

description:
CRZ1 OE pREP1-rep1
Untreated strains.


title: LNNEG3

description: replicate 3

source_name: LNCaP Control AntagomiR


title: LNNEG2

description: replicate 2


title: prz1 Deletion vs. Wild Type + Calcium Replicate 2

description:
prz1 del vs. wt + calcium-rep2
Treated with 0.5 M calcium.

source_name: prz1 deletion auxotrophic strain, calcium

growth_protocol: S. pombe yeast cells were inoculated in YES+ALU media and cultured for 16-20hr. The ch1 and ch2 samples were exposed to 0.15 M calcium for the last 30 minutes.

value: calcium

source_name: wild type auxotrophic strain, calcium

value: wild type


title: HCT116 cells, shH2AX RNA, rep 1


title: PCSCR3

description: replicate 3

source_name: PC3-ML Scrambled


title: HCT116 cells, shH2AX RNA, rep 3


title: prz1 Deletion vs. Wild Type + Tunicamycin Replicate 2

description:
prz1 del vs. wt + tunicamycin-rep2
Treated with 2.5 µg/mL tunicamycin.

source_name: prz1 deletion strain, tunicamycin

growth_protocol: S. pombe yeast cells were inoculated in YES+ALU media and cultured for 16-20hr. The ch1 and ch2 samples were exposed to 2.5 µg/mL tunicamycin for the last 1.5 hours.

value: tunicamycin

source_name: wild type strain, tunicamycin


title: prz1 Deletion vs. Wild Type + Tunicamycin Replicate 1

description:
prz1 del vs. wt + tunicamycin-rep1
Treated with 2.5 µg/mL tunicamycin.


title: PCMIR2

description: replicate 2

source_name: PC3-ML MiR-23b/-27b


title: PCMIR3

description: replicate 3


title: HCT116 cells, scrambled RNA, rep 4

value: shCTRL


title: PCSCR1

description: replicate 1


title: LNNEG1

description: replicate 1


title: HCT116 cells, scrambled RNA, rep 3


title: prz1 Deletion Replicate 2

description:
prz1 del-rep2
Untreated strains.

source_name: wild type auxotrophic strain, untreated


title: PCMIR1

description: replicate 1


title: PCSCR2

description: replicate 2


title: HCT116 cells, scrambled RNA, rep 2


title: HCT116 cells, scrambled RNA, rep 1


title: prz1 Deletion vs. Wild Type + Calcium Replicate 1

description:
prz1 del vs. wt + calcium-rep1
Treated with 0.5 M calcium.


title: prz1 Deletion Replicate 1

description:
prz1 del-rep1
Untreated strains.


title: EB_51_Rep1

status: Public on Feb 09 2016

city: Chicago

first: Courtney

last: Burrows

state: Illinois

address: 920 E. 58th St. CLSC

department: Human Genetics

institute: University of Chicago

data_processing: The data were normalised using quantile normalization with the lumi package in R. For final expression data, replicates were averaged.

source_name: Endometrial Biopsy

label_protocol: Standard Illumina labeling protocol

growth_protocol: Endometrial biopsies were performed during the mid-secretory phase (9-11 days after endogenous luteinizing hormone [LH] surge, detected by each woman testing her daily urine) and immediately frozen on dry ice

extract_protocol: Samples were stored at -80oC until RNA was extracted. RNA was extracted from the endometrial biopsies using a phenol-chloroform phase separation with TRIzol® per the manufacturer’s directions (Life Technologies Corp., Carlsbad, CA, USA) and RNeasy RNA extraction kit (Qiagen, Venlo, Netherlands; per manufacturer’s directions). RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The samples were not treated

value: Female

tag: ethnicity

value: Caucasian


title: EB_52_Rep1


title: EB_52_Rep2


title: EB_50_Rep2


title: EB_53_Rep1


title: EB_53_Rep2


title: EB_51_Rep2


title: EB_50_Rep1


title: EB_48_Rep2


title: EB_49_Rep1


title: EB_48_Rep1


title: Pig Muscle 10, lysine excess

city: Mississipi State

first: Shengfa

last: Liao

state: MS

address: 4021 Wise Center, 240 Wise Center Drive

department: Animal & Dairy Sciences

institute: Mississippi State University

description:
Lysine concentration was fomulated referring to NRC swine requirement
M10

hyb_protocol: Samples were hybridized with Porcine Gene 1.0 ST Array (Affymetrix) at University of Mississippi Medical Center Molecular and Genomics Core Facility (Jackson, MS).

scan_protocol: The reaction image and signals were read with a GeneChip Scanner (GCS 3000, 7G).

data_processing: Data were collected using the GeneChip Operating Software (GCOS, version 1.2). The raw gene expression intensity values from the software (i.e., the *.cel files) were imported into Partek Genomics Suite (PGS) software (version 6.6; Partek Inc., St. Louis, MO) for analysis. For background correction, the algorithm of Robust Multichip Averaging adjusted with probe sequence and GC oligo contents was implemented. The background-corrected data were further converted into expression values using quantile normalization across all the chips and median polish summarization of multiple probes for each probe set.

organism: Sus scrofa

source_name: lysine excess, longissimus dorsi

label_protocol: Ambion WT Expression Kit (Affymetrix) was used to generate amplified sense-strand cDNA ready for fragmentation and labeling using the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix)

growth_protocol: At the end of the 5 weeks, pigs were slaughtered and muscle samples were collected from the middle portion of longissimus dorsi (between the 10th and 12th ribs).

extract_protocol: For each muscle sample, total RNA was extracted from approximately 50 mg of frozen muscle tissue using TRIzol Reagent (Invitrogen Corporation, Carlsbad, CA) following the manufacturer’s instructions.

treatment_protocol: not applicable

value: Male

tag: diet

value: lysine excess

value: longissimus dorsi (between 10th and 12th ribs)


title: EB_49_Rep2


title: EB_50_Rep3


title: EB_47_Rep1


title: EB_44_Rep1


title: EB_45_Rep1


title: EB_45_Rep2


title: EB_41_Rep2


title: Pig Muscle 11, lysine excess

description:
Lysine concentration was fomulated referring to NRC swine requirement
M11


title: EB_43


title: Pig Muscle 9, lysine excess

description:
Lysine concentration was fomulated referring to NRC swine requirement
M9


title: EB_47_Rep2


title: EB_42


title: EB_46_Rep2


title: Pig Muscle 7, lysine adequate

description:
Lysine concentration was fomulated referring to NRC swine requirement
M7

source_name: lysine adequate, longissimus dorsi

value: lysine adequate


title: EB_41_Rep1


title: EB_40_Rep2


title: EB_44_Rep2


title: EB_46_Rep1


title: EB_40_Rep1


title: Pig Muscle 6, lysine adequate

description:
Lysine concentration was fomulated referring to NRC swine requirement
M6


title: Pig Muscle 5, lysine adequate

description:
Lysine concentration was fomulated referring to NRC swine requirement
M5


title: EB_39_Rep1

value: Asian


title: Pig Muscle 3, lysine deficiency

description:
Lysine concentration was fomulated referring to NRC swine requirement
M3

source_name: lysine deficiency, longissimus dorsi

value: lysine deficiency


title: Pig Muscle 2, lysine deficiency

description:
Lysine concentration was fomulated referring to NRC swine requirement
M2


title: EB_39_Rep3


title: EB_38_Rep2


title: EB_39_Rep2


title: Pig Muscle 1, lysine deficiency

description:
Lysine concentration was fomulated referring to NRC swine requirement
M1


title: EB_37_Rep2


title: EB_35_Rep2


title: EB_34_Rep2


title: EB_35_Rep1


title: EB_38_Rep1


title: EB_34_Rep1


title: EB_36


title: EB_37_Rep1


title: EB_32_Rep1


title: EB_33_Rep2


title: EB_33_Rep1


title: EB_26_Rep2


title: EB_28


title: EB_27


title: EB_25


title: strain 104 control vs pulse replicate 1

city: Leicester

first: Eran

last: Tauber

address: University Road

department: Genetics

institute: University of Leicester

description: Biologicial replicate 1 out of 2, RIL104 strong light response

hyb_protocol: The purified Alexa 555 and Alexa 647 labelled cDNA were hybridised to Drosophila Oligo 14Kv1 array (Canadian Drosophila Microarray Centre) according to University Health Network (UHN)

scan_protocol: The array slides were scanned on Molecular Devices' GENEPIX 4000 microarray scanner.

data_processing: The R limma package was used. Background correction by subtraction (default), Print-tip Lowes normalization, using default values of the normalizeWithinArrays function.

label: Alexa 555

organism: Drosophila melanogaster

source_name: heads, Zt16.5 no pulse

label_protocol: Invitrogen superscript plus indirect cDNA kit was used to generate fluorescently labelled cDNA from 35 μg total RNA according to the manufacturer’s protocol (Invitrogen).

growth_protocol: Adult Drosophila maintained at 25 deg. LD 12:12, for 5 days at standrd sugar media

treatment_protocol: Flies were presented with a 30 min 1500 lux light pulse at ZT 15 on the last dark phase of the LD cycle, and collected at Zt. 16.5

value: male

value: control

tag: collection time

value: head

label: Alexa 647

source_name: heads, 1 hr after light pulse

value: light pulse


title: B177-1_Naive

city: Aalborg

first: Julie

middle: Støve

last: Bødker

address: Sdr. Skovvej 15

department: Department of Heamatology

country: Denmark

institute: Aalborg University Hospital

hyb_protocol: As described in the user guide, appendix A, of the The Encore™Biotin Module  (NuGEN)

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G. CEL-files generated using AGCC

data_processing: RMA normalized using R (v3.1.2), the affy-package (v1.44.0) from Bioconductor, and probe set data extracted from custom CDF [Brainarray, huex10sthsensgcdf_18.0.0].

source_name: Naive cells from fresh tonsils using FACS

label_protocol: The following two kits from NuGEN were used following manufactures guide lines: The WT-Ovation™ Exon Module Version 1.0 and The Encore™Biotin Module

extract_protocol: mRNA was isolated using the μMACS™ technology (Miltenyi Biotech, Bergisch-Gladbach, Germany), using μ Columns and elution with pure water. Amplification was performed using WT Ovation Pico RNA Amplificatio System (NuGEN Technologies, Inc., San Carlos, CA) following manufactures protocol.

treatment_protocol: Tonsils from homo sapiens were collected from six patients during routine tonsillectomy. Mononuclear cells were isolated from tonsils and prepared for multiparametric flow cytometry using an optimized and validated protocol. B-cell subsets of naive, centroblasts, centrocytes, menory and plasmablast cells were isolated.

tag: patient id

value: Tonsils

value: mononuclear cells

tag: b-cell subset

value: Naive cells


title: EB_24


title: EB_29


title: EB_30


title: B177-4_Memory

source_name: Memory cells from fresh tonsils using FACS

value: Memory cells


title: EB_31

value: African American


title: EB_32_Rep2

value: Female


title: EB_26_Rep1

value: Caucasian


title: strain 104 control vs pulse replicate 2

description: Biologicial replicate 2 out of 2, RIL104 srong light resonse

tag: strain


title: B177-2_Centroblast

source_name: Centroblast cells from fresh tonsils using FACS

value: Centroblast cells


title: strain 58 control vs pulse replicate 2

description: Biologicial replicate 1 out of 2, RIL58 weak light response


title: B177-3_Centrocyte

source_name: Centrocyte cells from fresh tonsils using FACS

value: Centrocyte cells


title: EB_23_Rep2


title: EB_21


title: EB_23_Rep1


title: strain 58 control vs pulse replicate 1

description: Biologicial replicate 2 out of 2, RIL58 weak light response


title: EB_19


title: B176-5_Plasmablast

source_name: Plasmablast cells from fresh tonsils using FACS

value: Plasmablast cells


title: B176-1_Naive


title: EB_20_Rep2


title: EB_22


title: B176-3_Centrocyte


title: EB_20_Rep1


title: B170-2_Centroblast


title: B176-2_Centroblast


title: B170-5_Plasmablast


title: B170-4_Memory


title: B176-4_Memory


title: EB_17


title: EB_14


title: EB_15_Rep2


title: B170-1_Naive


title: B169-5_Plasmablast


title: EB_18_Rep2


title: EB_15_Rep1


title: EB_16


title: EB_18_Rep1


title: B170-3_Centrocyte


title: B169-4_Memory


title: B169-3_Centrocyte


title: B169-1_Naive


title: B177-5_Plasmablast


title: B169-2_Centroblast


title: EB_12


title: EB_13


title: EB_11_Rep2


title: B164-2_Centroblast


title: B164-5_Plasmablast


title: EB_11_Rep1


title: EB_9_Rep2


title: B164-4_Memory


title: EB_10


title: B163-5_Plasmablast


title: EB_9_Rep1


title: B164-1_Naive


title: B164-3_Centrocyte


title: B163-2_Centroblast


title: EB_8


title: B163-3_Centrocyte


title: B163-4_Memory


title: EB_7_Rep1


title: EB_7_Rep2


title: EB_5_Rep1


title: EB_6


title: B163-1_Naive

source_name: Naive-cells from fresh tonsils using FACS

value: Naive-cells


title: EB_4_Rep2


title: BB168-4_Naive

source_name: Naive-cells from sternal bonemarrow using FACS

treatment_protocol: Bone marrow tissue was obtained by physical scraping of the medulla from seven patients undergoing cardiac surgery. Mononuclear cells were isolated from bone marrow and prepared for multiparametric flow cytometry using an optimized and validated protocol. B-cell subsets of PreBI, PreBII, Immature, Naive, Memory and Plasma cells were isolated.

value: Sternal bone marrow


title: EB_5_Rep2


title: BB168-6_Plasma

source_name: Plasma-cells from sternal bonemarrow using FACS

value: Plasma-cells


title: BB168-5_Memory

source_name: Memory-cells from sternal bonemarrow using FACS

value: Memory-cells


title: BB168-3_Immature

source_name: Immature-cells from sternal bonemarrow using FACS

value: Immature-cells


title: BB104-6_Plasma


title: EB_4_Rep1


title: BB168-2_preBII

source_name: PreBII-cells from sternal bonemarrow using FACS

value: PreBII-cells


title: BB104-4_Naive


title: EB_3_Rep2

source_name: Endometrial Biopsy


title: EB_3_Rep3


title: EB_2_Rep1


title: BB104-5_Memory


title: EB_2_Rep2


title: BB104-3_Immature


title: BB168-1_preBI

source_name: PreBI-cells from sternal bonemarrow using FACS

value: PreBI-cells


title: BB104-2_preBII


title: EB_1_Rep1


title: MK144 LRRK2 G2019S  iPSc clone 7 [gene expression]

city: Oxford

first: Sally

middle: A

last: Cowley

address: South Parks Road

department: Sir William Dunn School of Pathology

institute: University of Oxford

data_processing: Quality control results were within expected range. The data were normalised using cubic spline normalisation with background subtraction in GenomeStudio v2011.1 Gene Expression module 1.9.0. Missing values were imputed by the software. Manifest file used was HumanHT-12_V4_R2_15002873_B

source_name: iPSC derived from dermal fibroblasts, Parkinson's Disease patient LRRK2 G2019S MK144, clone 7

label_protocol: Biotinylated cRNA were prepared as standard  for Illumina arrays, by Wellcome Trust Centre for Human Genomics, Oxford

extract_protocol: RNA was extracted using QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit and with on-column Dnase treatment. Quality control was performed with Agilent Bioanalyser and was RIN 10 for each sample.

treatment_protocol: untreated cell samples, all grown in mTeSR-1 medium + ES-qualified matrigel prior to harvest

tag: subject status

value: female

value: induced pluripotent stem (iPSC) cell line derived from dermal fibroblasts

tag: culture conditions

value: mTeSR-1 + matrigel


title: MK002 LRRK2 G2019S  iPSc clone 4 [gene expression]

source_name: iPSC derived from dermal fibroblasts, Parkinson's Disease patient LRRK2 G2019S MK002, clone 4

tag: gender


title: BB104-1_preBI

tag: tissue

value: mononuclear cells


title: AH016 control iPSc clone 3 [gene expression]

source_name: iPSC  derived from dermal fibroblasts, control donor AH016, clone 3

value: control donor

value: male


title: JR036 LRRK2 G2019S  iPSc clone 1 [gene expression]

source_name: iPSC derived from dermal fibroblasts, Parkinson's Disease patient LRRK2 G2019S JR036, clone 1


title: BB96-3_Naive


title: EB_3_Rep1

value: Female

value: Caucasian


title: BB96-1_preBII


title: CD44hiCD133lo 1

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

hyb_protocol: 10 ug of cDNA was hybridized for 16 hr to the Affymetrix array as described in the Expression Analysis Technical Manual. GeneChips were washed and stained in the Affymetrix Fluidics Station FS450.

scan_protocol: Affymetrix GeneArray scanner 7G

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

source_name: CD44hiCd133lo 1  (Xenograft and FACS derived)

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

growth_protocol: Xenograft of tumorigenic MCF7 cells which were previously labeled with GFP.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA extraction plus kit was used to isolate RNA, and cDNA was made with invitrogen superscriptase.

treatment_protocol: Cancer cells were isolated from primary tumor and metastases following 7-9 month of mammary fat pad growth of GFP-labeled MCF7 cells.

value: CD44hiCd133lo cancer cells

tag: cancer cells isolated from

value: primary tumor and metastases following 7-9 month of mammary fat pad growth of MCF7 xenograft


title: CD133hiCD44lo 2

source_name: CD133hiCD44lo 2  (Xenograft and FACS derived)

value: CD133hiCD44lo cancer cells


title: CD133hiCD44lo 1

source_name: CD133hiCD44lo 1  (Xenograft and FACS derived)


title: BB96-4_Memory

value: Sternal bone marrow


title: Oxidated LDL-24hour-rep1

city: México City

first: Juan

middle: Pablo

last: Reyes-Grajeda

state: DF

address: Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan. México,

department: Proteomics and transciptomics

country: Mexico

institute: National Instiutute of Genomic Medicine

description: Gene expression data from VSMC cells with 24 hour endocytosis treatment using oxidized LDLs

hyb_protocol: The cRNA products were  used as templates for a second cycle cDNA syhthesis where dUTPs will be incorporated to the new strand. The cDNA will then be fragmented using uracil-DNA glycosilase and apurin apirymidin endonuclease. The fragments  ( 40-70mers ) where then  labeled by means of a  biotin-labeled deoxynucleotide terminal addition reaction. The labeled cDNA product  was  heated to 95°C and hybridized to the Human Gene 1.0 ST microarray (Affymetrix Inc.) for 17 + 1 hr at 45°C.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G (Affymetrix, Inc)

data_processing: The data were analyzed with Partek Genomic Suite  version 6.4 using Affymetrix default analysis settings and global scaling as normalization method.

source_name: oxidized LDL endocytosis, 24 hour

label_protocol: 200 ng of the pooled RNA was converted to first-strand cDNA using Superscript II reverse transcriptase primed by a poly(T) oligomer. Second strand cDNA synthesis was followed by an in vitro transcription to generate cRNA.

growth_protocol: VSMC were maintained in F12K medium containing 0.05 mg/ml ascorbic acid; 0.01 mg/ml insulin; 0.01 mg/ml transferrin; 10 ng/ml sodium selenite; 0.03 mg/ml Endothelial Cell Growth Supplement (ECGS); 10% fetal bovine serum, 10 mM HEPES, 10 mM TES, 100 U/mL penicillin, 100 U/mL streptomycin and 0.01% amphotericin B. Cells were incubated in a humidified environment at 370C in an atmosphere of 95% air and 5% CO2.

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

treatment_protocol: After 1, 5 or 24 hours of treatment with native or oxidized LDL, the cell were harvested

value: VSMC cell culture

tag: genotype

value: This is a normal human cell line with a 46,XX karyotype

tag: age

value: 11 months


title: Oxidated LDL-24hour-rep3

tag: cell type


title: Oxidated LDL-5hour-rep3

description: Gene expression data from VSMC cells with 5 hour endocytosis treatment using oxidized LDLs

source_name: oxidized LDL endocytosis, 5 hour


title: Oxidated LDL-24hour-rep2


title: BB81-6_Plasma

value: Plasma-cells


title: BB81-3_Immature

value: Immature-cells


title: BB96-5_Plasma


title: CD133loCD44lo 1

source_name: CD133loCD44lo 1 (Xenograft and FACS derived)

value: CD133loCD44lo cancer cells


title: CD44hiCD133lo 2

source_name: CD44hiCD133lo 2  (Xenograft and FACS derived)

value: CD44hiCD133lo cancer cells


title: BB81-4_Naive

source_name: Naive-cells from sternal bonemarrow using FACS

value: Naive-cells


title: BB81-1_preBI

value: mononuclear cells

value: PreBI-cells


title: BB81-5_Memory

source_name: Memory-cells from sternal bonemarrow using FACS

value: Memory-cells


title: CD133loCD44lo 2

source_name: CD133loCD44lo 2  (Xenograft and FACS derived)


title: EB_1_Rep2

value: Female


title: BB68-4_Naive


title: BB68-6_Plasma

source_name: Plasma-cells from sternal bonemarrow using FACS


title: Oxidated LDL-5hour-rep2

value: Caucasian

value: female


title: BB68-5_Memory


title: BB81-2_preBII

source_name: PreBII-cells from sternal bonemarrow using FACS

value: PreBII-cells


title: Oxidated LDL-1hour-rep3

description: Gene expression data from VSMC cells with 1 hour endocytosis treatment using oxidized LDLs

source_name: oxidized LDL endocytosis, 1 hour


title: Oxidated LDL-5hour-rep1


title: BB66-6_Plasma


title: BB66-5_Memory


title: BB68-1_preBI

source_name: PreBI-cells from sternal bonemarrow using FACS


title: Retinal Progenitor Cells_E17.5

city: Mexico city

first: Monica

last: Lamas

state: Distrito Federal

address: Calzada de los Tenorios 235

department: Pharmacobiology

institute: CINVESTAV

description: Gene expression data from Retinal Progenitor Cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hours at 48°C and 60 rpm on Affymetrix GeneChip miRNA Arrays. GeneChips were washed and stained in the Fluidics Station 450: Fluidics Script, FS450_0003

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Scanned images of microarray chips were analyzed using Expression Console (Affymetrix) with the default settings. Raw data were processed using different algorithms. Detected Above Background algorithm (DABG) and RMA Background Adjustment algorithm were performed in order to remove the background value.

source_name: Retinal Progenitor Cells, E-17.5 mouse embryos

label_protocol: 1 ug of total RNA was prepared using Flashtag according to the standard Affymetrix protocol.

growth_protocol: For CD73-positive Rods we dissected retinas from PN5 day mice and then we used a PE-conjugated antibody against CD73 to perform fluorecence activated cell sorting (FACS).  For Müller glia primary cultures, enucleated eyes from PN8 mice were maintained in Optimem/SFB4% ovenight, then the retinas were isolated, enzymatically digested and plated in cell culture flasks; the next day the medium was replaced to eliminate non-adherent cells and cellular debris. For Retinal Progenitor Cells, we enucleated eyes from mouse embryos E17.5, then, neural retinas were isolated and enzymatically digested, the resultant solution was filtered through a mesh strainer and centrifugated, finally, the cells were resuspended in neurosphere forming medium and plated.

extract_protocol: miRNeasy extraction kit following manufacturer's instructions

value: Retina

value: wild type

tag: developmental stage

value: E17.5 mouse embryos


title: Oxidated LDL-1hour-rep1

value: VSMC cell culture

value: This is a normal human cell line with a 46,XX karyotype


title: Oxidated LDL-1hour-rep2

value: 11 months


title: BB66-3_Immature

source_name: Immature-cells from sternal bonemarrow using FACS

value: Sternal bone marrow

value: Immature-cells


title: Native LDL - 24hour-rep1

description: Gene expression data from VSMC cells with 24 hour endocytosis treatment using native LDLs

source_name: native LDL endocytosis, 24 hour


title: Müller glia_Primary culture

description: Gene expression data from Müller glia primary cultures

source_name: Primary Müller glia cultures, postnatal day 8 mice

value: Postnatal day 8


title: BB66-1_preBI


title: BB64-4_Naive

value: Naive-cells


title: BB66-2_preBII

value: mononuclear cells


title: Native LDL - 24hour-rep2


title: Native LDL - 24hour-rep3


title: BB66-4_Naive


title: BB64-6_Plasma

value: Plasma-cells


title: Native LDL - 5hour-rep1

description: Gene expression data from VSMC cells with 5 hour endocytosis treatment using native LDLs

source_name: native LDL endocytosis, 5 hour


title: Native LDL - 5hour-rep3


title: BB64-3_Immature


title: Native LDL - 5hour-rep2


title: BB64-5_Memory

value: Memory-cells


title: Native LDL - 1hour-rep3

description: Gene expression data from VSMC cells with 1 hour endocytosis treatment using native LDLs

source_name: native LDL endocytosis, 1 hour


title: Rods_CD73-positive

description: Gene expression data from CD73-positive RODS

source_name: FACS isolated CD73-positive Rods, postnatal day 5 mice

value: Postnatal day 5


title: BB64-2_preBII


title: BB64-1_preBI

value: PreBI-cells


title: Native LDL - 1hour-rep1

value: Caucasian

value: female


title: Native LDL - 1hour-rep2


title: VSMC-control, tech-rep3

description: Gene expression data from VSMC cells without endocytosis treatment

source_name: VSMC control


title: control-C5

first: Zarema

middle: H

last: Arbieva

state: IL

address: 835 S. Wolcott A301

department: RRC

institute: UIC

hyb_protocol: The GeneChip® Hybridization, Wash, and Stain Kit was used as per manufacturer’s protocols. The GeneChip® Fluidics Station 450 was used for washing and staining using fluidics script FS450_0002.

scan_protocol: Microarray chips were read on the GeneChip® Scanner 3000 7G with AGCC version 4.0.0.1567.

data_processing: RMA in Partek

source_name: hepatic tissue

label_protocol: Samples were labeled using the Affymetrix GeneChip® WT PLUS Kit as per manufacturer's protocols.

growth_protocol: Homozygous ARSB-null mice were bred and housed under similar conditions as control C57BL/6J mice

extract_protocol: hepatic tissue was excised and frozen when 12-week old ARSB-deficient and control mice were euthanized following ketamine/xylazine and cervical dislocation

treatment_protocol: no treatment was administered

tag: background strain

value: male

value: 12 weeks


title: VSMC-control, tech-rep2


title: VSMC-control, tech-rep1


title: control-C6


title: colon tissue-CD1

city: Guangzhou

first: Shenghong

last: Zhang

address: NO.58 Zhongshan Road 2

country: China

institute: Sun Yat-sen University

description: Gene expression in colon tissue of Crohn's disease patient

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

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner ( (Agilent p/n G2565BA)) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

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

source_name: colon tissue-CD1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1ug  RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared form colon tissues of colonscopy specimems using the RNasey Mini Kit(Qiagen p/n 74104) following the manufacturer's recommendations.  The protocol includes  homogenization using the Mini-Bead-Beater-16 and an on-column DNase digestion. RNA was quantified and qualitified by NanoDrop ND-1000.RNA Integrity and gDNA contamination test were done by denaturing agarose gel electrophoresis.

treatment_protocol: Fresh specimens of colon tissues form Crohn's patients and normal controls were washed with RNAase free water and put into RNAlater(Qiagen) immediately and frozen in -80℃.

value: colon biopsies from endoscopy


title: colon tissue-NC1

description: Gene expression in colon tissue of normal control

source_name: colon tissue-NC1


title: colon tissue-CD3

source_name: colon tissue-CD3


title: colon tissue-NC2

source_name: colon tissue-NC2


title: control-C4


title: ARSB-null A4


title: ARSB-null A6


title: colon tissue-NC3

source_name: colon tissue-NC3


title: Left ventricle ILPD rep3

city: Berlin

first: Georgios

last: Kararigas

address: Hessische Str. 3-4

institute: Charite University Hospital

description: Left ventricle ILPD rep3

hyb_protocol: Biotinylated cRNA was prepared and hybridized according to the standard Affymetrix processing protocol.

scan_protocol: The array was scanned in a GeneChip Scanner 3000.

data_processing: The data were normalized and transformed using R version 2.14.2, the Bioconductor package 'vsn' and the vsnrma algorithm with all defualt values, i.e. library('vsn') vsnrmadata = vsnrma(object = data).

organism: Rattus norvegicus

source_name: Left ventricle ILPD rep3

growth_protocol: The rats were kept on a 12-hour light, 12-hour dark cycle in temperature-controlled rooms with water ad libitum.

extract_protocol: Total RNA was isolated using the RNeasy Fibrous Tissue Mini kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: Left ventricles were snap frozen in liquid nitrogen and stored at -80°C until further analysis.

tag: intervention

value: I/R

tag: treatment

value: ILPD

value: left ventricle


title: Left ventricle ILPD rep5

description: Left ventricle ILPD rep5

source_name: Left ventricle ILPD rep5

label_protocol: Biotinylated cRNA was prepared and hybridized according to the standard Affymetrix processing protocol.


title: colon tissue-CD2

source_name: colon tissue-CD2


title: ARSB-null A5


title: Left ventricle ILPD rep2

description: Left ventricle ILPD rep2

source_name: Left ventricle ILPD rep2


title: Left ventricle plac rep2

description: Left ventricle plac rep2

source_name: Left ventricle plac rep2

value: Plac


title: JR036 LRRK2 G2019S  iPSc clone 1

hyb_protocol: Standard Illumina hybridisation protocol

scan_protocol: Standard Illumina scanning protocol for BeadChip Arrays

data_processing: The scanned data files were processed by GenomeStudio Genotyping module v1.9, using the cluster file HumanCytoSNP-12v2-1_H.egt provided by Illumina. Raw data was also uploaded to KaryoStudio (Illumina) for generation of karyotype reports (see publication).

label: Biotin (C, G), Dinitrophenyl (A, T)

source_name: iPSC derived from dermal fibroblasts, Parkinson's Disease patient LRRK2 G2019S JR036, clone 1

label_protocol: Standard Illumina labelling protocol

extract_protocol: genomic DNA was extracted using QIAGEN DNeasy blood and tissue kit

treatment_protocol: untreated cell samples; Fibroblasts grown in ADMEM + 10% FCS; iPSc lines all grown in mTeSR-1 medium + ES-qualified matrigel prior to harvest

value: induced pluripotent stem (iPSC) cell line derived from dermal fibroblasts

value: mTeSR-1 + matrigel


title: Left ventricle ILPD rep1

description: Left ventricle ILPD rep1

source_name: Left ventricle ILPD rep1


title: 4tu-EV fraction, biological  rep3

status: Public on Feb 08 2016

first: joan

last: doidy

address: 12 Waverly place

department: Biology

institute: NYU

description: 4tu pull down RNA

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 18 hr at 45°C on GeneChip Arabidopsis Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner (Affymetrix)

data_processing: The raw probe intensities were normalized using the GC-robust multiarray averaging (GCRMA) package

organism: Arabidopsis thaliana

source_name: root protoplast 4tu-EV

label_protocol: 4tuU pull down RNA fractions were amplified and labeled with Ovation Pico WTA System V2 (NuGEN) and Encore Biotin Module (NuGEN) according to the manufacturer's instructions.

growth_protocol: Wild-type Arabidopsis thaliana seeds were grown on vertical agar plates containing 2.2g/L MS salts without N or C, 1% (w/v) sucrose, 0.5g/L MES sodium salt, 1mM KNO3 and 2% (w/v) agar under a 50umol/m2s and 16h light/8h dark regime at 22 deg C.

extract_protocol: RNA extraction was performed using an RNeasy Micro Kit with RNase-free DNaseI Set (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: Protoplast supsensions treated sequentially with 20mM KNO3 and NH4NO3 for 1h40min, 35uM cycloheximide for 20m, 10uM dexamethasone for 5h, 1.5mM 4tU and 0.2mM uracil for 20min.

value: Columbia Col-0

value: root cell protoplast

tag: transfection

value: Empty vector (EV=pJD385_35S::GR)


title: 4tu-EV fraction, biological  rep4

description: 4tu pull down RNA


title: MK144 LRRK2 G2019S  iPSc clone 7

source_name: iPSC derived from dermal fibroblasts, Parkinson's Disease patient LRRK2 G2019S MK144, clone 7


title: 4tu-EV fraction, biological  rep5

description: 4tu pull down RNA


title: MK002 LRRK2 G2019S  iPSc clone 4

source_name: iPSC derived from dermal fibroblasts, Parkinson's Disease patient LRRK2 G2019S MK002, clone 4


title: JR036 LRRK2 G2019S fibroblasts

description: HDF JR036

source_name: dermal fibroblasts, Parkinson's Disease patient LRRK2 G2019S JR036

value: dermal fibroblasts

value: ADMEM + 10% FCS


title: 4tu-bZIP1 fraction, biological  rep3

description: 4tu pull down RNA

source_name: root protoplast 4tu-bZIP1


title: Left ventricle ILPD rep4

description: Left ventricle ILPD rep4

source_name: Left ventricle ILPD rep4


title: 4tu-bZIP1 fraction, biological  rep4

description: 4tu pull down RNA


title: 4tu-bZIP1 fraction, biological  rep6

description: 4tu pull down RNA


title: Mvt-1 Ndn 50C over-expressing clone #9

first: Nigel

last: Crawford

address: 50 South Drive, Room 5154

institute: Human Genome Research Institute

hyb_protocol: The hybridization cocktail containing the fragmented and labeled cDNAs were hybridized to The Affymetrix Mouse GeneChip® 1.0 ST chips. The chips were washed and stained by the Affymetrix Fluidics Station using the standard format and protocols as described by Affymetrix.

scan_protocol: An Affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays.

data_processing: Data was processed via Partek and normalized using RMA.

label_protocol: Labeling performed using GeneChip® WT Terminal Labeling and Controls Kit according to manufacturer's protocol.

growth_protocol: Mvt-1 cells were incubated in 5% CO2 at 37 °C.

extract_protocol: Total RNA was isolated from cells using QIAGEN RNeasy Mini Kit with on-column DNaseI digestion.

tag: cell line

tag: variation

value: 50C over-expression of allelic variants of Ndn


title: AH016 control iPSc clone 3

source_name: iPSC derived from dermal fibroblasts, control donor AH016, clone 3

value: control donor


title: AH016 control fibroblasts

description: HDF AH016

source_name: dermal fibroblasts, control donor AH016


title: Left ventricle plac rep1

description: Left ventricle plac rep1

source_name: Left ventricle plac rep1


title: MK144 LRRK2 G2019S fibroblasts

description: HDF MK144

source_name: dermal fibroblasts, Parkinson's Disease patient LRRK2 G2019S MK144

value: female


title: Mvt-1 Ndn 50C over-expressing clone #5


title: MK002 LRRK2 G2019S fibroblasts

description: HDF MK002

source_name: dermal fibroblasts, Parkinson's Disease patient LRRK2 G2019S MK002


title: Mvt-1 Ndn 50T over-expressing clone #7

value: 50T over-expression of allelic variants of Ndn


title: jaz7-1D leaves, MeJA treatment, replicate 4

city: Floreat

first: Louise

middle: Faye

last: Thatcher

state: WA

address: 147 Underwood Ave

department: Agriculture and Food

institute: CSIRO

description: Expression data from jaz7-1D leaves harvested 6 hours after the MeJA treatment.

hyb_protocol: The RNA was labelled, hybridized, washed and scanned by the AGRF (Australian Genome Research Facility - http://www.agrf.org.au) according to Affymetrix requirements.

data_processing: The data was analyzed using GenespringGX 7.3.1. The raw CEL files were pre-processed using the RMA algorithm and the resulting expression values were normalized per chip to the median across all chips.

source_name: Leaf tissue from 4 week old Arabidopsis thaliana plants

growth_protocol: Plants were grown under short day conditions (8hrs light, 24C and 21C day night cycle) in plastic trays (30 cells 5cmx5cm) with two plants per cell for 4 weeks before treatment.

extract_protocol: Total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen) according to the manfacturer's instructions.

treatment_protocol: Treatment involved enclosing trays of plants under clear plastic covers with a cotton ball treated with Mock (ethanol) or MeJA and attached to the inside of the cover. Each tray and cover was sealed by two layers of opaque plastic bags and secured with masking tape. Samples were harvested after 6 hours.

tag: genotype/variation

value: leaves

value: MeJA

tag: ecotype


title: Mvt-1 Ndn 50T over-expressing clone #6


title: jaz7-1D leaves, MeJA treatment, replicate 3

scan_protocol: The RNA was labelled, hybridized, washed and scanned by the AGRF (Australian Genome Research Facility - http://www.agrf.org.au) according to Affymetrix requirements.


title: jaz7-1D leaves, MeJA treatment, replicate 2

label_protocol: The RNA was labelled, hybridized, washed and scanned by the AGRF (Australian Genome Research Facility - http://www.agrf.org.au) according to Affymetrix requirements.


title: 4tu-bZIP1 fraction, biological  rep2

description: 4tu pull down RNA


title: Left ventricle plac rep3

description: Left ventricle plac rep3

source_name: Left ventricle plac rep3

value: I/R


title: 4tu-EV fraction, biological  rep1

description: 4tu pull down RNA


title: 4tu-bZIP1 fraction, biological  rep1

description: 4tu pull down RNA


title: Mvt-1 Ndn 50C over-expressing clone #11


title: Mvt-1 Ndn 50T over-expressing clone #1


title: 4tu-EV fraction, biological  rep2

description: 4tu pull down RNA


title: jaz7-1D leaves, MeJA treatment, replicate 1


title: Mvt-1 control clone #2

value: stable over-expression of allelic variants of Ndn


title: Col-0 leaves, MeJA treatment, replicate 4

description: Expression data from Col-0 leaves harvested 6 hours after the MeJA treatment.

value: wildtype


title: Mvt-1 control clone #3


title: jaz7-1D leaves, Mock treatment, replicate 4

description: Expression data from jaz7-1D leaves harvested 6 hours after the Mock treatment.

value: Mock solution (100% ethanol)


title: Col-0 leaves, MeJA treatment, replicate 3


title: jaz7-1D leaves, Mock treatment, replicate 1


title: jaz7-1D leaves, Mock treatment, replicate 2


title: Col-0 leaves, MeJA treatment, replicate 2


title: Col-0 leaves, Mock treatment, replicate 4

description: Expression data from Col-0 leaves harvested 6 hours after the Mock treatment.


title: Failing heart, biological rep 4

city: Ann Arbor

first: Margaret

middle: V

last: Westfall

state: MI

address: 2800 Plymouth Road

department: Cardiac Surgery

institute: University of Michigan

description: Gene expression data from explanted heart

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

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

data_processing: Data was analyzed using the limma and affy Bioconductor packages implemented in the R-statistical environment. RMA was used to normalize the data and fit log2 transformed expression values.

source_name: Failing adult human heart

label_protocol: Biotinylated aRNA were prepared according to the Ambion Premier kit protocol from 500 ng total RNA (MessageAmp Premier RNA Amplification Kit Instruction Manual, 2008, Ambion).

extract_protocol: Tissue samples were homogenized in lysis buffer and RNA isolated using the Rneasy kit.  Purified RNA was diluted to >100 ng/ml in Rnase-free dH2O and RNA quality verified with an Agilent 2100 Bioanalyzer (RIN scores >9.0).

treatment_protocol: Each heart was flushed with ice-cold cardioplegia prior to explant and then small samples from the left ventricle were rapidly flash frozen in liquid N2 and then stored at -80oC until tissue was processed for gene expression.

value: Left ventricle


title: Col-0 leaves, MeJA treatment, replicate 1


title: Col-0 leaves, Mock treatment, replicate 3


title: Control vs Biofilm_Rep 1_dyeflip

city: Chandigarh

first: Ashwani

last: Kumar

state: Chandigarh

address: Sec 39A

department: Molecular Microbiology

institute: CSIR-Institute of Microbial Tech

description:
Control vs Biofilm_DTT treated_Rep 1_dyeflip
Comp4_C3(cy5) vs B2(cy3)

hyb_protocol: II. Prehybridization  1. Prepare Prehybridization Solution (Fresh Each Time) **this volume is based on a glass dish with a base measurement of 11x8cm. This dish allows for a pre-hyb of 1-4 slides. Adjust volume accordingly based on size of dish and/or number of slides. 106.0ml dH2O 3.0g BSA 1.2ml 10%SDS  2. Add Prehybridization solution to a glass slide-staining dish and place post-processed slides array side up into solution. Make sure there are no bubbles on the surfaces of the slides.  3. Place the staining jar containing the Prehybridization solution and slides into a waterbath and hybridize for 1 hour at 42oC.  4. Take the prehybridized slides out of the Prehybridization solution and place into a slide holder submerged in a slide-washing tray containing nuclease-free water. Wash slides for 2 minutes with constant shaking up and down.  5. Transfer slide rack to a slide washing tray containing isopropanol and wash for 2 minutes with constant shaking up and down.  6. Take the slides in the isopropanol bath to the centrifuge to keep the slides wet until you can dry them rapidly. Spin at 600 RPM in a 50ml conical for 3 minutes to dry. **Complete this step within one hour of hybridization  III. Hybridization  1. Add the following to the 5µl labeled sample. 0.5µl 10 mg/ml tRNA 1.0µl 20X SSC 2.5ul Formamide 1.0µl 1% SDS  2. Heat to 98 oC for 2 minutes. Spin in centrifuge for 1 min at 12,000 Xg. Let cool for 5 min.  3. Pipette cooled 10µl hybridization solution on microarray. Apply 22 x 22 coverslip to cover array (if bubbles appear under the cover slip, they will slowly migrate to the edges provided that the volume is accurate).  4. OPTIONAL: Apply thin wall of rubber cement around the 4 corners of the coverslip to avoid movement. This step is recommended if your waterbath is not perfectly level. 5. Hybridize in standard hyb. chambers with ~40µl water under each slide (20ul under both ends of each slide) overnight in 50oC water bath **Bubbles (esp. large ones) can be troublesome for your arrays since they can cause areas of non-hybridization. To avoid bubbles, do not use the blowout feature of the pipette when adding the probe to the slide. Also, clean your coverslips with alcohol and lint-free wipes before placing over probe.  IV. Post Hyb washes (next day)  1. Remove cover slip while array is submerged in first wash solution (2XSSC + 0.1% SDS), transfer to submerged microscope slide staining racks and rinse for 1 min in 1X SSC+0.05% SDS with agitation/shaking.  2. Rinse in 0.06X SSC with shaking. Transfer to another submerged staining rack and wash 2 min in fresh 0.06X SSC with shaking.  3. Centrifuge 3 min at 1000 rpm in a 50ml conical (array edge up) to dry. Scan immediately.

scan_protocol: After washing, the arrays were scanned with a GenePix4200AL scanner (Molecular Devices, Sunnyvale, CA).   The images were processed using GenePix Pro and the resulting text files were exported to Microsoft Excel.

data_processing: The chips were normalized by the print-tip Lowess method (Dudoit, 2000).

organism: Mycobacterium tuberculosis H37Rv

source_name: control

label_protocol: I. Synthesis and Labeling of cDNA  1. Bring 1.5µg of RNA to a volume of 11µl (in a PCR tube) with nucleotide-free water and add 2.2µl (2mg/ml) random primers (pulse spin to collect contents).  2. Heat 2 min at 98oC, snap cool on ice.  3. (Keep on ice) and add 11.1µl of the following reaction mix: 5.0µl 5X First-Strand buffer 2.5µl 100 mM DTT 2.3µl low dTdNTP mix (5mM A,G,C and 0.2mM T stock) 1.5ul Cy3 or Cy5 Then add 1.2ul Superscript, vortex to mix and spin to collect contents  4. Incubate 10 min at 25oC followed by 90 min at 42oC in PCR machine. **Can freeze or leave at 4oC overnight if necessary  5. Prime a microcon10 column (YM10 from Millipore) with 400µl TE and spin for 10 min at 10,000 Xg. Empty flow-through in collection tube and return primed column. Add both reactions (cy3 and cy5) to column and centrifuge at 10,000 Xg until ~25µl remaining (~20-30 min). Wash with 200µl TE and spin until almost dry (<5µl).  6. Recover cDNA by inverting microcon into new collection 1.5 ml tube and centrifuge at half max speed 1 min.  7. Bring sample to 5µl with TE.  The detailed labeling and hybridization protocol can be obtained at http://www.cag.icph.org/downloads_page.htm#LabelingProtocols.

growth_protocol: M.tb H37Rv culture was grown up to log phase

extract_protocol: Trizol method was used for RNA isolation as per manufacturer protocol

treatment_protocol: To the test sample added 6 mM DTT (reduced) for 29 hrs

value: Control (no treatment)

tag: rna source

value: log phase culture

source_name: DTT-treated

value: DTT

value: Biofilm


title: Control vs Biofilm_Rep 2_dyeflip

description:
Control vs Biofilm_DTT treated_Rep 2_dyeflip
Comp5_C4(cy5) vs B3(cy3)


title: Control vs Biofilm_Rep 2

description:
Control vs Biofilm_DTT treated_Rep 2
Comp2_C4(cy3) vs B3(cy5)


title: Control vs Biofilm_Rep 3

description:
Control vs Biofilm_DTT treated_Rep 3
Comp3_C5(cy3) vs B4(cy5)


title: Col-0 leaves, Mock treatment, replicate 2


title: Control vs Biofilm_Rep 3_dyeflip

description:
Control vs Biofilm_DTT treated_Rep 3_dyeflip
Comp6_C5(cy5) vs B4(cy3)


title: Mvt-1 control clone #1


title: jaz7-1D leaves, Mock treatment, replicate 3


title: Col-0 leaves, Mock treatment, replicate 1


title: Failing heart, biological rep 2


title: Failing heart, biological rep 3


title: Non-failing heart, biological rep 1

source_name: Non-failing adult human heart


title: Non-failing heart, biological rep 3


title: Control vs Biofilm_Rep 1

description:
Control vs Biofilm_DTT treated_Rep 1
Comp1_C3(cy3) vs B2(cy5)


title: Non-failing heart, biological rep 2


title: Q835.MUC1.0Gy.24hr

status: Public on Feb 07 2016

city: Herston

first: Rebecca

last: Johnston

state: QLD

address: Building 71/918, Royal Brisbane & Women's Hospital Campus

department: Molecular and Cellular Pathology

institute: University of Queensland Centre for Clinical Research

description:
Fluorescence-activated cell sorted normal breast epithelial cells
9236415017_H_Grn

hyb_protocol: Array hybridization was performed using the Expression BeadChip Kit (Illumina)

scan_protocol: Scanning was performed using an Illumina BeadArray Reader.

data_processing: Array data were processed using the R package limma. Data were background corrected using the normal and exponential convolution model method (normexp), quantile normalized, and log2 transformed. Only probes with an Illumina Detection Score of > 0.95 in > 50% of the samples were kept for further analyses.

source_name: Reduction mammoplasty

label_protocol: Biotin labelled cRNA was prepared with the Ambion TotalPrep RNA Amplification Kit.

extract_protocol: RNA was extracted using the QIAGEN AllPrep DNA/RNA Mini Kit as per the manufacturer’s protocol. RNA yield was measured using the NanoDrop 2000 (Thermo Scientific), and RNA integrity was confirmed using the Agilent Bioanalyzer 2100 (Agilent Technologies).

value: primary mammary epithelial cell culture

tag: patient id

tag: flow-sorted cell type

tag: ir dose

tag: collection time post-ir


title: Failing heart, biological rep 1

tag: tissue


title: Q835.MUC1.5Gy.2hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
9236415017_K_Grn


title: Q835.MUC1.2Gy.2hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
9236415017_I_Grn


title: Q835.CD10.2Gy.24hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
9236415017_D_Grn


title: Q835.CD10.0Gy.24hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
9236415017_B_Grn


title: Q835.MUC1.5Gy.24hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
9236415017_L_Grn


title: Q835.CD10.0Gy.2hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
9236415017_A_Grn


title: Q835.CD10.2Gy.2hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
9236415017_C_Grn


title: Non-failing heart, biological rep 4


title: Q835.MUC1.2Gy.24hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
9236415017_J_Grn


title: Q835.MUC1.0Gy.2hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
9236415017_G_Grn


title: Q835.CD10.5Gy.24hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
9236415017_F_Grn


title: Q835.CD10.5Gy.2hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
9236415017_E_Grn


title: Q827.MUC1.0Gy.2hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
9236415018_G_Grn


title: Q827.MUC1.2Gy.24hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
9236415018_J_Grn


title: Q827.MUC1.5Gy.2hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
9236415018_K_Grn


title: Q827.CD10.5Gy.24hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
9236415018_F_Grn


title: Q827.CD10.2Gy.24hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
9236415018_D_Grn


title: 4tu-bZIP1 fraction, biological  rep5

description: 4tu pull down RNA

tag: genotype

value: Columbia Col-0

value: root cell protoplast


title: Q827.CD10.5Gy.2hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
9236415018_E_Grn

tag: cell type


title: Q827.MUC1.5Gy.24hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
9236415018_L_Grn


title: Q827.MUC1.2Gy.2hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
9236415018_I_Grn


title: Q827.MUC1.0Gy.24hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
9236415018_H_Grn


title: Q706.MUC1.5Gy.24hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
8962917085_L_Grn


title: Q827.CD10.0Gy.24hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
9236415018_B_Grn


title: Q706.MUC1.2Gy.24hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
8962917085_K_Grn


title: Q827.CD10.2Gy.2hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
9236415018_C_Grn


title: Q706.MUC1.0Gy.24hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
8962917085_J_Grn


title: Q695.MUC1.5Gy.24hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
9236415012_L_Grn


title: Q827.CD10.0Gy.2hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
9236415018_A_Grn


title: Q695.MUC1.0Gy.24hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
9236415012_J_Grn


title: Q695.MUC1.2Gy.2hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
9236415012_H_Grn


title: Q706.CD10.0Gy.24hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
8962917085_D_Grn


title: Q706.MUC1.0Gy.2hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
8962917085_G_Grn


title: Q706.CD10.5Gy.24hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
8962917085_F_Grn


title: Q706.CD10.2Gy.24hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
8962917085_E_Grn


title: Q695.CD10.2Gy.24hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
9236415012_E_Grn


title: Q706.MUC1.5Gy.2hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
8962917085_I_Grn


title: Q706.CD10.2Gy.2hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
8962917085_B_Grn


title: Q695.MUC1.2Gy.24hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
9236415012_K_Grn


title: Q706.CD10.5Gy.2hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
8962917085_C_Grn


title: Q695.CD10.5Gy.2hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
9236415012_C_Grn


title: Q695.CD10.0Gy.24hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
9236415012_D_Grn


title: Q695.MUC1.5Gy.2hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
9236415012_I_Grn


title: Q695.CD10.0Gy.2hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
9236415012_A_Grn


title: Q706.CD10.0Gy.2hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
8962917085_A_Grn


title: Q695.MUC1.0Gy.2hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
9236415012_G_Grn


title: Q626.MUC1.2Gy.2hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
8967304015_I_Grn


title: Q626.MUC1.0Gy.2hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
8967304015_G_Grn


title: Q695.CD10.2Gy.2hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
9236415012_B_Grn


title: Q626.MUC1.5Gy.24hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
8967304015_L_Grn


title: Q695.CD10.5Gy.24hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
9236415012_F_Grn


title: Q626.MUC1.0Gy.24hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
8967304015_H_Grn


title: Q626.CD10.5Gy.2hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
8967304015_E_Grn


title: 2 week DM-cultured SaOS-2 cells, day14-2

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description:
day14-2
SaOS-2 cells cultured in differentiation medium and extracted at 2 week.

hyb_protocol: Before hybridization, 600 ng labeled cRNA of each product was fragmented and mixed with control targets and hybridization buffer according to the manufacturer's protocol (Agilent Technologies). Hybridizations were done for approximately 17h at 65°C. The slides were washed according to the manufacturer's manual, and scanning of microarrays was performed with 3µm resolution using a DNA microarray laser scanner (Agilent Technologies).

scan_protocol: The array was scanned using Agilent G2505C DNA microarray scanner. Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: The Subio Platform and Subio Basic Plug-in (v1.15; Subio Inc., Aichi, Japan) was then used to calculate the between-sample fold change.

source_name: SaOS-2 cells cultured in DM and extracted at 2 weeks

label_protocol: 200 ng of total RNAs were reverse-transcribed using oligo-dT primers containing the T7 RNA polymerase promoter sequence to generate cDNAs and AffinityScript, RTase, which were then subjected to in vitro transcription using T7 RNA polymerase to label the cRNAs with Cy3-CTP (Amersham) using a Low input Quick-Amp Labeling Kit (Agilent).

growth_protocol: SaOS-2 cells were plated in 6-well plates at a density of 3 x 10^4 cells per cm2 and cultured in maintenance medium or differentiation medium. MM consisted of alpha MEM (Wako, Japan) and 10% fetal bovine serum. Differentiation medium consisted of maintenance medium, 100 nM dexamethasone (Wako, Japan), 50 μM L-ascorbic acid (Sigma-Aldrich, USA) and 10 mM β-glycerophosphate (Sigma-Aldrich, USA) to the maintenance medium.

extract_protocol: Total RNA was extracted from cells using an miRNeasy Mini kit according to the manufacturer’s instructions (Qiagen).

treatment_protocol: RNA samples cultured in differentiation medium were extracted at 2 weeks and 3 weeks, whereas samples in maintenance medium were extracted at 1 week.

value: sarcoma cell line

tag: medium

value: differentiation medium

tag: time point

value: 2 weeks


title: Q626.MUC1.2Gy.24hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
8967304015_J_Grn


title: 2 week DM-cultured SaOS-2 cells, day14-1

description:
day14-1
SaOS-2 cells cultured in differentiation medium and extracted at 2 week.


title: 1 week MM-cultured SaOS-2 cells, UnD-3

description:
UnD-3
SaOS-2 cells cultured in maintenance medium and extracted at 1 week.

source_name: SaOS-2 cells cultured in MM and extracted at 1 week

value: maintenance medium

value: 1 week


title: Q626.CD10.2Gy.24hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
8967304015_D_Grn


title: Q626.MUC1.5Gy.2hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
8967304015_K_Grn


title: 3 week DM-cultured SaOS-2 cells, day21-2

description:
day21-2
SaOS-2 cells cultured in differentiation medium and extracted at 3 week.

source_name: SaOS-2 cells cultured in DM and extracted at 3 weeks

value: 3 weeks


title: Q626.CD10.2Gy.2hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
8967304015_C_Grn


title: 3 week DM-cultured SaOS-2 cells, day21-1

description:
day21-1
SaOS-2 cells cultured in differentiation medium and extracted at 3 week.


title: Q706.MUC1.2Gy.2hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
8962917085_H_Grn


title: Q626.CD10.0Gy.2hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
8967304015_A_Grn


title: Q626.CD10.0Gy.24hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
8967304015_B_Grn


title: peripheral blood T-cells remission4

status: Public on Feb 06 2016

city: Little Rock

first: Intawat

last: Nookaew

address: 4301 W Markham St

department: Department of Biomedical Informatics

institute: University of Arkansas for Medical Sciences

description: gene expression data from subcutaneous adipose tissue

hyb_protocol: Following fragmentation,15 ug of cRNA were hybridized for 16 hr at 45C on Human U133 Plus 2.0 arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: After hybridisation (according to the Minimum Information About a Microarray Experiment guideline, the arrays were scanned using an Affymetrix confocal laser scanner (Affymetrix, GeneArray scanner GCS3000) and visualised using GeneChip Operating Software (GCOS, Affymetrix).

data_processing: The raw expression signals were preprocessed following the method of Probe Logarithmic Intensity Error (PLIER) based on perfect match only (pm-only) calculation (Affymetrix).The robust quantile method was applied to get normalized expression values

source_name: peripheral blood T-cell

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was prepared using the RNeasy Lipid Tissue Kit (Qiagen)

treatment_protocol: Tissues were snap frozen in liquid nitrogen

tag: group

value: Remission ITP


title: 1 week MM-cultured SaOS-2 cells, UnD-2

description:
UnD-2
SaOS-2 cells cultured in maintenance medium and extracted at 1 week.


title: Q626.CD10.5Gy.24hr

description:
Fluorescence-activated cell sorted normal breast epithelial cells
8967304015_F_Grn


title: 1 week MM-cultured SaOS-2 cells, UnD-1

description:
UnD-1
SaOS-2 cells cultured in maintenance medium and extracted at 1 week.


title: peripheral blood T-cells remission3


title: peripheral blood T-cells remission6


title: peripheral blood T-cells remission5


title: 3 week DM-cultured SaOS-2 cells, day21-3

description:
day21-3
SaOS-2 cells cultured in differentiation medium and extracted at 3 week.


title: peripheral blood T-cells remission1


title: peripheral blood T-cells remission2


title: peripheral blood T-cells newly diagnosed ITP5

value: New ITP


title: Heliothis virescens  Rest of body-G032-3

city: Jena

first: Heiko

last: Vogel

address: Hans-Knoell-Strasse 8

department: Dpt. of Entomology

institute: Max Planck Institute for Chemical Ecology

description: pooled from 5 individuals

hyb_protocol: The Cy3 labeled cRNA was hybridized to H. virescens (4x 180 K) microarray slides for 17 h at 65 °C in a hybridization oven. The microarray slides were washed in GE Wash Buffers according to the manufacturer´s instructions (Agilent Technologies). Slides were treated in Stabilization and Drying Solution and scanned.

scan_protocol: As per manufacturers instruction, using an Agilent Microarray Scanner

data_processing: Data was extracted from TIFF images with Agilent Feature Extraction software version 9.1. Feature extracted data were analyzed using GeneSpring GX version 12.5 (Agilent Technologies) software. The data points were normalized between arrays to the median intensity and log base 2-transformation of the normalized data was performed.

organism: Heliothis virescens

source_name: Heliothis virescens  Rest of body-G032-3

label_protocol: Agilent Technologies spike-in RNA was added to 100 ng of total RNA and labeled following the One-color Microarray-Based Gene Expression Analyisis (Low Input Quick Amp Labeling kit) protocol (Agilent Technologies). Labeled amplified cRNA samples were purified using Qiagen RNeasy Minikit columns and analyzed on a Nanodrop ND-1000 spectrophotometer using the microarray function. Amplified cRNA samples were used for microarray hybridisation only if the yield was >1600 ng and the specific activity >6.0 pmol Cy3 per ug cRNA.

growth_protocol: H. virescens larvae were provided by North Carolina State University and had been originally collected in Clayton, North Carolina, USA, in 1988 (JEN strain). H. virescens larvae were reared on pinto bean diet (Joyner and Gould, 1985) under laboratory conditions (26 °C, 55% relative humidity, 16:8 h light:dark photoperiod) in Jena, Germany. For feeding assays pinto bean diet was used.  Newly molted 5th instar H. virescens  larvae were reared for 3 days on artificial control diet and diet supplemented with gossypol, respectively, with following concentrations: 0.32% (w/v) and  0% (w/v) of gossypol. Larvae were kept at 27 °C during treatment. After weighing, larvae were anesthetized on ice and dissected into gut and rest of the body. Tissues were pooled according to their biological replicates (5 larvae and 5 guts, respectively, are one replicate, four biological replicates were prepared), snap frozen in liquid nitrogen and stored at -80 °C until RNA isolation.

extract_protocol: For RNA isolation, tissues were ground to fine powder under liquid nitrogen. Total RNA was extracted by using the innuPREP RNA Mini Kit (Analytik Jena). RNA quality and integrity was assessed using RNA Nano chips on an Agilent 2100 Bioanalyzer (Agilent Technologies). The RNA quantity was determined using the NanoDrop ND-1000 spectrophotometer (Peqlab).

value: rest of body

tag: treatment


title: Heliothis virescens  Rest of body-G032-4

description: pooled from 5 individuals

source_name: Heliothis virescens  Rest of body-G032-4


title: Heliothis virescens  Rest of body-G032-1

description: pooled from 5 individuals

source_name: Heliothis virescens  Rest of body-G032-1