title: Patient 04 - 0867_post

description:
Microarray analysis of human samples. The same FFPE samples were also used for RNA extraction in a subset of the human tumors (n=9 patients, 18 paired samples) using the RNeasy FFPE kit from Qiagen (catalog # 73504). The SensationPlus 3' IVT A&L FFPE kit was used for the labeling and amplification of the RNA (Affymetrix, Inc. catalog # 902028). The Almac Xcel™ Array was used for profiling of the FFPE samples (Affymetrix, Inc. catalog # 902016). The Xcel™arrays provide a 3’ gene expression array designed and optimized for use with FFPE tissues with probe sets for over 97,000 transcripts. The RNA Gene expression estimates were obtained using the Robust Multi-array Average (RMA) algorithm. Next, gene filtering was performed to select the top 10% of the probe sets with the highest coefficient of variation across all 18 samples. Paired samples t-tests were performed using the Bioconductor limma package (13) to identify differentially expressed probe sets caused by radiation. Probe sets with q-values less than 5% were selected as differentially expressed.
Formalin fixed and paraffin-embedded (FFPE) samples were obtained at the time of diagnosis. Patients then received a single large dose of radiation to the intact tumor and proceeded to surgical resection within 10 days of treatment. A second post-radiation sample was obtained at the time of surgical excision.
867


title: Patient 08 - 3484_pre

status: Public on Jan 01 2018

type: RNA

city: Durham

first: Wei

last: Chen

state: NC

address: 101 Science Drive

department: Center for Genomic and Computational Biology

country: USA

institute: Duke University

description:
Microarray analysis of human samples. The same FFPE samples were also used for RNA extraction in a subset of the human tumors (n=9 patients, 18 paired samples) using the RNeasy FFPE kit from Qiagen (catalog # 73504). The SensationPlus 3' IVT A&L FFPE kit was used for the labeling and amplification of the RNA (Affymetrix, Inc. catalog # 902028). The Almac Xcel™ Array was used for profiling of the FFPE samples (Affymetrix, Inc. catalog # 902016). The Xcel™arrays provide a 3’ gene expression array designed and optimized for use with FFPE tissues with probe sets for over 97,000 transcripts. The RNA Gene expression estimates were obtained using the Robust Multi-array Average (RMA) algorithm. Next, gene filtering was performed to select the top 10% of the probe sets with the highest coefficient of variation across all 18 samples. Paired samples t-tests were performed using the Bioconductor limma package (13) to identify differentially expressed probe sets caused by radiation. Probe sets with q-values less than 5% were selected as differentially expressed.
Formalin fixed and paraffin-embedded (FFPE) samples were obtained at the time of diagnosis. Patients then received a single large dose of radiation to the intact tumor and proceeded to surgical resection within 10 days of treatment. A second post-radiation sample was obtained at the time of surgical excision.
3484

hyb_protocol: Hybridization of samples to Affymetrix GeneChip arrays was performed according to Affymetrix manual instructions .

scan_protocol: Scanning of Affymetrix GeneChip arrays was performed according to the Affmetrix manual instructions.

data_processing: The Almac Xcel™ Array was used for profiling of the FFPE samples (Affymetrix, Inc. catalog # 902016). The Xcel™arrays provide a 3’ gene expression array designed and optimized for use with FFPE tissues with probe sets for over 97,000 transcripts.   The RNA Gene expression estimates were obtained using the Robust Multi-array Average (RMA) algorithm. Next, gene filtering was performed to select the top 10% of the probe sets with the highest coefficient of variation across all 18 samples. Paired samples t-tests were performed using the Bioconductor limma package  to identify differentially expressed probe sets caused by radiation. Probe sets with q-values less than 5% were selected as differentially expressed.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Patients with biologically favorable early stage breast cancer participating in an IRB approved phase I dose-escalation preoperative radiotherapy protocol at Duke University Medical Center.

label_protocol: Affymetrix  SensationPlus 3' IVT A&L FFPE  for the human FFPE samples (for the Xcel™ Array ).

extract_protocol: Microarray analysis of human samples: The same FFPE samples were also used for RNA extraction in a subset of the human tumors (n=9 patients, 18 paired samples) using the RNeasy FFPE kit from Qiagen (catalog # 73504). The SensationPlus 3' IVT A&L FFPE kit was used for the labeling and amplification of the RNA (Affymetrix, Inc. catalog # 902028).

tag: tissue

value: breast

tag: cell type

value: breast cancer


title: Human colon cancer cell line HCT116 was transfected with a control non-targeting siRNA to cells for 36 hours 3

city: Changsha

first: Jian

last: Ma

state: Hunan

address: 110  Xiangya  Road

department: Cancer  Research Institute

country: China

institute: Central South University

description: Expression data for human colon cancer cell line HCT116 transfected with siRNA targeting YAP1.

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

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000.

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 500.

label: biotin

source_name: colon cancer

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 μg total RNA.

growth_protocol: The human colon cancer cell lines HCT116 were cultured in both DMEM medium supplemented with 10% fetal bovine serum, 100 units/m of penicillin and streptomycin. Cultures were incubated at 37°C in a humidified incubator at 5% CO2.

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

treatment_protocol: Cells were grown in DMEM medium (with 2% serum), and was transfected with a control non-targeting siRNA to cells or transfected with siRNA targeting YAP1 for 36 hours.

tag: agent

value: control siRNA(100nM)


title: Patient 03 - 1866_post

description:
Microarray analysis of human samples. The same FFPE samples were also used for RNA extraction in a subset of the human tumors (n=9 patients, 18 paired samples) using the RNeasy FFPE kit from Qiagen (catalog # 73504). The SensationPlus 3' IVT A&L FFPE kit was used for the labeling and amplification of the RNA (Affymetrix, Inc. catalog # 902028). The Almac Xcel™ Array was used for profiling of the FFPE samples (Affymetrix, Inc. catalog # 902016). The Xcel™arrays provide a 3’ gene expression array designed and optimized for use with FFPE tissues with probe sets for over 97,000 transcripts. The RNA Gene expression estimates were obtained using the Robust Multi-array Average (RMA) algorithm. Next, gene filtering was performed to select the top 10% of the probe sets with the highest coefficient of variation across all 18 samples. Paired samples t-tests were performed using the Bioconductor limma package (13) to identify differentially expressed probe sets caused by radiation. Probe sets with q-values less than 5% were selected as differentially expressed.
Formalin fixed and paraffin-embedded (FFPE) samples were obtained at the time of diagnosis. Patients then received a single large dose of radiation to the intact tumor and proceeded to surgical resection within 10 days of treatment. A second post-radiation sample was obtained at the time of surgical excision.
1866


title: Human colon cancer cell line HCT116 was transfected with YAP1 siRNA to cells for 36 hours 2

value: YAP1 siRNA(100nM)


title: Human colon cancer cell line HCT116 was transfected with YAP1 siRNA to cells for 36 hours 1


title: Patient 08 - 13597_post

description:
Microarray analysis of human samples. The same FFPE samples were also used for RNA extraction in a subset of the human tumors (n=9 patients, 18 paired samples) using the RNeasy FFPE kit from Qiagen (catalog # 73504). The SensationPlus 3' IVT A&L FFPE kit was used for the labeling and amplification of the RNA (Affymetrix, Inc. catalog # 902028). The Almac Xcel™ Array was used for profiling of the FFPE samples (Affymetrix, Inc. catalog # 902016). The Xcel™arrays provide a 3’ gene expression array designed and optimized for use with FFPE tissues with probe sets for over 97,000 transcripts. The RNA Gene expression estimates were obtained using the Robust Multi-array Average (RMA) algorithm. Next, gene filtering was performed to select the top 10% of the probe sets with the highest coefficient of variation across all 18 samples. Paired samples t-tests were performed using the Bioconductor limma package (13) to identify differentially expressed probe sets caused by radiation. Probe sets with q-values less than 5% were selected as differentially expressed.
Formalin fixed and paraffin-embedded (FFPE) samples were obtained at the time of diagnosis. Patients then received a single large dose of radiation to the intact tumor and proceeded to surgical resection within 10 days of treatment. A second post-radiation sample was obtained at the time of surgical excision.
13597


title: Human colon cancer cell line HCT116 was transfected with a control non-targeting siRNA to cells for 36 hours 2


title: Patient 01 - 4077_post

description:
Microarray analysis of human samples. The same FFPE samples were also used for RNA extraction in a subset of the human tumors (n=9 patients, 18 paired samples) using the RNeasy FFPE kit from Qiagen (catalog # 73504). The SensationPlus 3' IVT A&L FFPE kit was used for the labeling and amplification of the RNA (Affymetrix, Inc. catalog # 902028). The Almac Xcel™ Array was used for profiling of the FFPE samples (Affymetrix, Inc. catalog # 902016). The Xcel™arrays provide a 3’ gene expression array designed and optimized for use with FFPE tissues with probe sets for over 97,000 transcripts. The RNA Gene expression estimates were obtained using the Robust Multi-array Average (RMA) algorithm. Next, gene filtering was performed to select the top 10% of the probe sets with the highest coefficient of variation across all 18 samples. Paired samples t-tests were performed using the Bioconductor limma package (13) to identify differentially expressed probe sets caused by radiation. Probe sets with q-values less than 5% were selected as differentially expressed.
Formalin fixed and paraffin-embedded (FFPE) samples were obtained at the time of diagnosis. Patients then received a single large dose of radiation to the intact tumor and proceeded to surgical resection within 10 days of treatment. A second post-radiation sample was obtained at the time of surgical excision.
4077


title: Patient 02 - 4971_post

description:
Microarray analysis of human samples. The same FFPE samples were also used for RNA extraction in a subset of the human tumors (n=9 patients, 18 paired samples) using the RNeasy FFPE kit from Qiagen (catalog # 73504). The SensationPlus 3' IVT A&L FFPE kit was used for the labeling and amplification of the RNA (Affymetrix, Inc. catalog # 902028). The Almac Xcel™ Array was used for profiling of the FFPE samples (Affymetrix, Inc. catalog # 902016). The Xcel™arrays provide a 3’ gene expression array designed and optimized for use with FFPE tissues with probe sets for over 97,000 transcripts. The RNA Gene expression estimates were obtained using the Robust Multi-array Average (RMA) algorithm. Next, gene filtering was performed to select the top 10% of the probe sets with the highest coefficient of variation across all 18 samples. Paired samples t-tests were performed using the Bioconductor limma package (13) to identify differentially expressed probe sets caused by radiation. Probe sets with q-values less than 5% were selected as differentially expressed.
Formalin fixed and paraffin-embedded (FFPE) samples were obtained at the time of diagnosis. Patients then received a single large dose of radiation to the intact tumor and proceeded to surgical resection within 10 days of treatment. A second post-radiation sample was obtained at the time of surgical excision.
4971


title: Patient 04 - 4930_pre

description:
Microarray analysis of human samples. The same FFPE samples were also used for RNA extraction in a subset of the human tumors (n=9 patients, 18 paired samples) using the RNeasy FFPE kit from Qiagen (catalog # 73504). The SensationPlus 3' IVT A&L FFPE kit was used for the labeling and amplification of the RNA (Affymetrix, Inc. catalog # 902028). The Almac Xcel™ Array was used for profiling of the FFPE samples (Affymetrix, Inc. catalog # 902016). The Xcel™arrays provide a 3’ gene expression array designed and optimized for use with FFPE tissues with probe sets for over 97,000 transcripts. The RNA Gene expression estimates were obtained using the Robust Multi-array Average (RMA) algorithm. Next, gene filtering was performed to select the top 10% of the probe sets with the highest coefficient of variation across all 18 samples. Paired samples t-tests were performed using the Bioconductor limma package (13) to identify differentially expressed probe sets caused by radiation. Probe sets with q-values less than 5% were selected as differentially expressed.
Formalin fixed and paraffin-embedded (FFPE) samples were obtained at the time of diagnosis. Patients then received a single large dose of radiation to the intact tumor and proceeded to surgical resection within 10 days of treatment. A second post-radiation sample was obtained at the time of surgical excision.
4930


title: Patient 09 - 31675_post

description:
Microarray analysis of human samples. The same FFPE samples were also used for RNA extraction in a subset of the human tumors (n=9 patients, 18 paired samples) using the RNeasy FFPE kit from Qiagen (catalog # 73504). The SensationPlus 3' IVT A&L FFPE kit was used for the labeling and amplification of the RNA (Affymetrix, Inc. catalog # 902028). The Almac Xcel™ Array was used for profiling of the FFPE samples (Affymetrix, Inc. catalog # 902016). The Xcel™arrays provide a 3’ gene expression array designed and optimized for use with FFPE tissues with probe sets for over 97,000 transcripts. The RNA Gene expression estimates were obtained using the Robust Multi-array Average (RMA) algorithm. Next, gene filtering was performed to select the top 10% of the probe sets with the highest coefficient of variation across all 18 samples. Paired samples t-tests were performed using the Bioconductor limma package (13) to identify differentially expressed probe sets caused by radiation. Probe sets with q-values less than 5% were selected as differentially expressed.
Formalin fixed and paraffin-embedded (FFPE) samples were obtained at the time of diagnosis. Patients then received a single large dose of radiation to the intact tumor and proceeded to surgical resection within 10 days of treatment. A second post-radiation sample was obtained at the time of surgical excision.
31675


title: Patient 01 - 5785_pre

description:
Microarray analysis of human samples. The same FFPE samples were also used for RNA extraction in a subset of the human tumors (n=9 patients, 18 paired samples) using the RNeasy FFPE kit from Qiagen (catalog # 73504). The SensationPlus 3' IVT A&L FFPE kit was used for the labeling and amplification of the RNA (Affymetrix, Inc. catalog # 902028). The Almac Xcel™ Array was used for profiling of the FFPE samples (Affymetrix, Inc. catalog # 902016). The Xcel™arrays provide a 3’ gene expression array designed and optimized for use with FFPE tissues with probe sets for over 97,000 transcripts. The RNA Gene expression estimates were obtained using the Robust Multi-array Average (RMA) algorithm. Next, gene filtering was performed to select the top 10% of the probe sets with the highest coefficient of variation across all 18 samples. Paired samples t-tests were performed using the Bioconductor limma package (13) to identify differentially expressed probe sets caused by radiation. Probe sets with q-values less than 5% were selected as differentially expressed.
Formalin fixed and paraffin-embedded (FFPE) samples were obtained at the time of diagnosis. Patients then received a single large dose of radiation to the intact tumor and proceeded to surgical resection within 10 days of treatment. A second post-radiation sample was obtained at the time of surgical excision.
5785


title: Human colon cancer cell line HCT116 was transfected with YAP1 siRNA to cells for 36 hours 3


title: Keratinocytes WT, biological rep1_MoGene-2

city: Dallas

first: Richard

middle: C

last: Wang

state: TX

address: 5323 Harry Hines Blvd

department: Dermatology

institute: UT Southwestern

description: Gene expression data of primary keratinocytes from 1 week old mice

hyb_protocol: Following fragmentation, 15ug cRNA of each sample was hybridized for 16 hours at 45C on the GeneChip Mouse 2.0 ST Arrays (Affymetrix).

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

data_processing: Raw data were processed with the Expression Console (Affymetrix) for RMA summarization and Quantile normalization.

organism: Mus musculus

source_name: WT_Primary cultured mouse keratinocytes

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

growth_protocol: Primary keratinocytes were cultured in KFSM medium (Invitrogen, 37010022) supplemented with 0.05mM CaCl2, 0.05ug/ml Hydrocortisone, 5ng/ml EGF, 7.5ug/ml Bovine Pitutary Exract, 0.5ug/ml insulin, 100 U/mL penicillin, and 100ug/mL streptomycin

extract_protocol: WT (1.5 x 106 cells each) and KO (1.0 x 106 cells each) samples were lysed in TRIzol  (1ml) using 20 strokes of a 20G 1.5 needle and then further processed using the standard protocol with QIAGEN’s RNeasy Lipid Tissue Mini Kit which included an on-filter DNAse digestion.  Final elution volume was 40 ul.

treatment_protocol: Cells were seeded at the same number in collagen coated plates, cultured overnight. Two plate of cells of the same genotype were harvested in trizol, then were combined together as one sample.

tag: strain

tag: age

value: 1 week

tag: genotype/variation

value: wild type

value: primary keratinocytes


title: Patient 10 - 37598_post

description:
Microarray analysis of human samples. The same FFPE samples were also used for RNA extraction in a subset of the human tumors (n=9 patients, 18 paired samples) using the RNeasy FFPE kit from Qiagen (catalog # 73504). The SensationPlus 3' IVT A&L FFPE kit was used for the labeling and amplification of the RNA (Affymetrix, Inc. catalog # 902028). The Almac Xcel™ Array was used for profiling of the FFPE samples (Affymetrix, Inc. catalog # 902016). The Xcel™arrays provide a 3’ gene expression array designed and optimized for use with FFPE tissues with probe sets for over 97,000 transcripts. The RNA Gene expression estimates were obtained using the Robust Multi-array Average (RMA) algorithm. Next, gene filtering was performed to select the top 10% of the probe sets with the highest coefficient of variation across all 18 samples. Paired samples t-tests were performed using the Bioconductor limma package (13) to identify differentially expressed probe sets caused by radiation. Probe sets with q-values less than 5% were selected as differentially expressed.
Formalin fixed and paraffin-embedded (FFPE) samples were obtained at the time of diagnosis. Patients then received a single large dose of radiation to the intact tumor and proceeded to surgical resection within 10 days of treatment. A second post-radiation sample was obtained at the time of surgical excision.
37598

source_name: Patients with biologically favorable early stage breast cancer participating in an IRB approved phase I dose-escalation preoperative radiotherapy protocol.


title: Keratinocytes WT, biological rep2_MoGene-2


title: Cardiac CD11b+ DC rep 2

city: Toronto

first: Slava

last: Epelman

state: Ontario

address: 101 College St

department: Medicine

country: Canada

institute: University of Toronto

hyb_protocol: Following fragmentation, 5.5 ug of cRNA were hybridized for 16 hr at 45C on Mouse Gene 2.0 ST Array. GeneChips were washed and stained in the GeneChip Fluidics Stations 450.

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

data_processing: The data were analyzed using Partek Genomics Suite.

label: Biotin Allonamide Triphosphate

source_name: Cardiac dendritic cells at steady state

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 600 pg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Approximately 10- to 12-week-old C57BL/6J mice were housed in a clean facility at the Princess Margaret Cancer Research Tower.

extract_protocol: RNA from sorted cardiac cDCs and MFs was extracted using the Qiagen micro-kit (Qiagen). cDNA was prepared using pre-IVT Amplification Master Mix (Affymetrix). A total of 600 pg of RNA per subset was amplified using GeneChip WT Pico Reagent Kit (Affymetrix).

treatment_protocol: Male and female mice were sacrificed and cardiac tissue was minced, digested, and turned into single-cell suspension. Cells were stained with cell-surface antibodies and sorted for CD103+ and CD11b+ classical dendritic cells and MHC-IIhi macrophages. We gated live cells using DAPI exclusion and excluded doublets using SSC-H/SSC-A and FSC-H/FSC/A gates. We then gated CD45+, CD64-, CD11c+, MHC-II+ and either CD103+ or CD11b+ dendritic cells. We gated MHC-IIhi macrophages as CD45+, CD11b+, CD64+ and MHC-II+.

tag: strain/background

tag: gender

value: pooled male and female

value: Cardiac CD11b+ dendritic cells


title: 01_control

city: Kobe

first: Takehiko

last: Ueyama

state: Hyogo

address: Rokkodai-cho 1-1, Nada-ku

department: Biosignal Research Center

country: Japan

institute: Kobe university

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

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

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

source_name: U87-control si

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA from U87 cells was extracted using NucleoSpin RNA (MACHEREY-NAGEL GmbH & Co. KG).

value: Glioblastoma

value: U87MG astrocytic cells


title: Cardiac MHC-IIhi MF rep 3

source_name: Cardiac macrophages at steady state

value: Cardiac MHC-II hi macrophages


title: Human colon cancer cell line HCT116 was transfected with a control non-targeting siRNA to cells for 36 hours 1


title: Cardiac CD11b+ DC rep 1


title: Keratinocytes KO, biological rep2_MoGene-2

source_name: KO_Primary cultured mouse keratinocytes


title: Cardiac CD103+ DC rep 2

value: Cardiac CD103+ dendritic cells


title: Cardiac MHC-IIhi MF rep 1


title: Cardiac MHC-IIhi MF rep 2


title: HEC1A-Ctrl 1

city: LA

first: Madhuri

last: Wadehra

state: CA

address: 675 Charles Young Dr. South/ 4726 MRL

department: Pathology and Lab Medicine

institute: UCLA

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials

scan_protocol: Standard Affymetrix protocol. GeneChip Scanner 3000 7G Scanner type: M10 Hardware version: 1.0 Software version: 4.0.0.16

data_processing: Data were analyzed with Partek genomics Suite 6.6

source_name: control vector

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: McCoys + 10% FBS

extract_protocol: Qiagen total RNA purification

treatment_protocol: untreated

tag: cell line

value: control


title: Cardiac CD11b+ DC rep 3


title: Cardiac CD103+ DC rep 3


title: 4 PUVA 7D 1189

city: Graz

first: Karin

last: Wagner

state: Styria

address: Stiftingtalstrasse 24

department: Molecular Biology

country: Austria

institute: Medical University Graz

hyb_protocol: Affymetrix Mouse Gene 2.0 ST Array (Cat No. 902118); Affymetrix GeneChip® HT hybridization, Wash and Stain Kit (Cat No. 900720); Affymetrix Genechip® fluidics station 450: protocol FS450_0002 for Cartridge Arrays

scan_protocol: Affymetrix Scanner: GCS3000; AGCC (Command Console Software AGCC 4.0.0)

data_processing: Affymetrix Genexpression Console (1.3.1) using Affymetrix default analysis settings for generation of CEL-files.

organism: Mus

source_name: Group VI

label_protocol: 500ng for Affymetrix WT PLUS Reagent Kit P/N 703147 Rev5, (Cat No. 902280)

growth_protocol: BALB/c mice were purchased from Charles-River and housed in the animal facility of the Centre for Medical Research, Medical University of Graz, Austria. All procedures to which the mice were subjected were approved by the Austrian Government, Federal Ministry for Science and Research, through protocol no. BMWF-66-010/0032-11/3b/2013

extract_protocol: miRNeasy Mini Kit inclusive DNase digest (Qiagen; Hilden, Germany; Cat No. 217004)

treatment_protocol: Mouse skin was pretreated with topical psoralen and 0.25 J/cm2 UVA or 0.2 J/cm2 UVB twice a week for 2 weeks followed by IMQ after a gap of 3 or 7 days vs no gap for controls.

value: BALBc

tag: Sex

value: Female

value: 7-8 weeks

value: skin


title: 4 PUVA 7D 1187


title: Cardiac CD103+ DC rep 1


title: Keratinocytes KO, biological rep1_MoGene-2


title: 02_CDC42/RAC1-DKD

source_name: U87-CDC42/RAC1 si


title: 4 PUVA 7D 1188


title: 4 PUVA 3D 1177

source_name: Group V


title: 4 PUVA 3D 1178


title: 4 PUVA 7D 1185


title: 4 PUVA 3D 1176


title: 4 PUVA 3D 1175


title: HEC1A-EMP2 upregulation

source_name: upregulation of EMP2

value: EMP2 overexpression


title: Hs181 cells grown in Matrigel + Y-27632

city: Barcelona

first: Gerardo

last: García-Díaz Barriga

state: Barcelona

address: Casanova 143

department: Biomedicine

country: Spain

institute: University of Barcelona

description: Hs181 cells grown in Matrigel + Y-27632

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

scan_protocol: GeneChips were scanned using the Agilent Bioanalyzer 2100

data_processing: Microarray data was normalized using the R environment with Bioconductor using robust multiarray normalization (RMA package), and subjected to quality metrics assessment (Qarray package)

source_name: hESCs_matrigel + Y-27632

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (PrimeScriptTM RT reagent Kit (Perfect Real Time; Takara Bio Co. Ltd).

growth_protocol: hESC-medium used was KO-DMEM (Gibco), 20% KO-SR, 1x NEEA, 1x Glutamax, 50 μM beta-Mercaptoethanol, 50 U/ml Penicilin/Streptomycin (all from Invitrogen), 10 ng/ml bFGF (Peprotech)

treatment_protocol: For Feeder cultures human fibroblasts γ-irradiated and plated on gelatin-coated 6 well plates (Corning Inc.) in HEF-media IMDM (Gibco) supplemented with 10% FBS (Invitrogen) and Penicilin/Streptomycin (50U/ml; Invitrogen)

value: Human Embrionic Stem Cells (hESC)

tag: growth condition

value: matrigel

tag: treated with


title: THP-1 control, biological replicate 3

hyb_protocol: Affymetrix Human Gene 2.0 ST Array (Cat No. 902112); Affymetrix GeneChip® HT hybridization, Wash and Stain Kit (Cat No. 900720);  Affymetrix Genechip®  fluidics station 450: protocol FS450_0002 for Cartridge Arrays

source_name: THP-1 cells

label_protocol: 250ng total RNA for Affymetrix WT PLUS Reagent Kit  P/N 703147 Rev5, (Cat No. 902280);

growth_protocol: Cells were maintained at 37°C/5% CO2 in RPMI-1640, enriched with 10% heat-inactivated FCS and 1X Antibiotic-Antimycotic (Thermo Fischer Scientific, including 100U/mL penicillin, 100 mg/mL streptomycin and 0.25 mg/mL amphotericin B).

extract_protocol: miRNeasy Mini Kit including DNase digest (Qiagen; Hilden, Germany; Cat No. 217004)

treatment_protocol: Cells were transduced with either RKIP shRNA or empty control (both psi-LVRU6GP; Genecopeia), and were selected and maintained with 1.5 µg/mL puromycin.

value: acute myeloid leukemia cell line

tag: transduction


title: Hs293 cells grown in Matrigel + Y-27632

description: Hs293 cells grown in Matrigel + Y-27632


title: THP-1 RKIP shRNA, biological replicate 2

value: RKIP shRNA


title: Hs293 cells grown in Feeders

description: Hs293 cells grown in Feeders

value: feeders


title: THP-1 RKIP shRNA, biological replicate 1


title: Hs293 cells grown in Matrigel

description: Hs293 cells grown in Matrigel


title: THP-1 control, biological replicate 2


title: THP-1 control, biological replicate 1


title: THP-1 RKIP shRNA, biological replicate 3


title: cont 1370

source_name: Group VIII


title: cont 1158


title: Hs420 cells grown in Matrigel + Y-27632

description: Hs420 cells grown in Matrigel + Y-27632


title: Hs420 cells grown in Matrigel

description: Hs420 cells grown in Matrigel


title: Hs181 cells grown in Matrigel

description: Hs181 cells grown in Matrigel


title: Hs420 cells grown in Feeders

description: Hs420 cells grown in Feeders


title: Hs181 cells grown in Feeders

description: Hs181 cells grown in Feeders


title: liver_control_WIK_male_3

city: Portland

first: Kim

middle: H

last: Brown

state: OR

address: 1719 SW 10th Ave

department: Department of Biology

institute: Portland State University

description: Baseline gene expression of WIK male

hyb_protocol: Samples with total cRNA yields greater than 1.65 µg and specific activity greater than 6 pmol Cy3/µg were fragmented, hybridized to array slides at 65°C for 17 hours, washed briefly, and scanned on an Agilent SureScan array scanner.

scan_protocol: Data were extracted from raw TIFF files using Agilent FeatureExtraction software with grid file 026437_D_F_20140627 and scan protcol AgilentHD_GX_1Color.

data_processing: Data were cleaned by subtracting background fluorescence, normalizing across arrays, and averaging duplicate probes within the limma package (Ritchie et al. 2015). Principle component analysis illustrated a clear separation between male and female samples, so all downstream analysis was performed with male and female datasets separated. Within limma, empirical Bayes fitting of a linear model and pairwise contrasts were applied to AB, TU, and WIK strains separately to test for differences between males and females per strain. These results will be referred to as “sex differences”. Similarly, a linear model and pairwise contrasts were applied to males and females separately to test for differences between AB, TU, and WIK per sex. These results will be referred to as “strain differences”.

organism: Danio rerio

source_name: naïve liver, WIK, male, individual 3

label_protocol: Commercially available 4x44K zebrafish mRNA expression arrays, RNA spike-in kit, and Low Input Quick Amp one-color labeling kit (Agilent) were used following manufacturer’s protocols. In brief, cDNA was synthesized from RNA and transcribed into cRNA using Cyanine-3 fluorescent dCTP. Labeled cRNA was purified using a Qiagen RNeasy mini kit per the manufacturer’s protocol and quantified on a NanoDrop spectrophotometer.

extract_protocol: Liver tissue was disrupted with a mortar and pestle prior to homogenization by passing the samples through a nuclease-free syringe and needle in beta-mercaptoethanol lysis buffer. Total RNA was extracted on Qiagen RNeasy columns per the manufacturer's protocol. Nucleic acid concentrations were determined on a Nanodrop Spectrophotometer 2000 and exhibited high 260/280 ratios of 2.10 ± 0.03, respectively (average ± SD).

treatment_protocol: All samples were collected from naïve adult zebrafish housed within the Brown lab zebrafish facility for 2 generations. AB, Tuebingen, and WIK zebrafish were originally sourced from ZIRC (Eugene, OR) as batches of 100 embryos. Livers were extracted from naive adults aged 12-18 months within 30 minutes of ice water euthanasia and immediately frozen in liquid nitrogen. Individuals were sexed via visual identification of eggs or testes at the time of dissection.

value: WIK

value: male

tag: treatment

value: control/naïve

tag: developmental stage

value: adult

value: liver


title: liver_control_WIK_female_1

description: Baseline gene expression of WIK female

source_name: naïve liver, WIK, female, individual 1

value: female


title: Control HeLa cells biological rep 3

city: Heidelberg

first: Julien

last: Béthune

address: Im Neuenheimerfeld 328

country: Germany

institute: Heidelberg University Biochemistry Center

description: Gene expression data from control cells

hyb_protocol: Following fragmentation, cDNA were hybridized for 16 hr at 45°C to Affymetrix Human Gene 2.0 arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC) Software (version 4.0) using Affymetrix default analysis settings.

source_name: HeLa cells 24h post transfection

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500ng ug total RNA (Ambion WT Expression kit, catalog number 4411974 and Affymetrix GeneChip® WT Terminal Labeling and Controls Kit, catalogue number 901524).

growth_protocol: HeLa cells were grown in DMEM medium containing 10% FBS

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

treatment_protocol: Cells were transfected with PEI 24h before RNA extraction

value: HeLa

tag: transfection

value: control plasmid


title: liver_control_WIK_female_3

description: Baseline gene expression of WIK female

source_name: naïve liver, WIK, female, individual 3


title: Control GIGY2-overexpressing  HeLa cells biological rep 3

description: Gene expression data from GIGYF2-overexpressing cells

value: plasmid coding for GIGYF2 under a CMV promoter


title: Control GIGY2-overexpressing  HeLa cells biological rep 2


title: liver_control_WIK_female_2

description: Baseline gene expression of WIK female

source_name: naïve liver, WIK, female, individual 2


title: liver_control_Tuebingen_female_3

description: Baseline gene expression of Tuebingen female

source_name: naïve liver, Tuebingen, female, individual 3

value: Tuebingen


title: Control HeLa cells biological rep 2

description: Gene expression data from control cells


title: liver_control_Tuebingen_female_2

source_name: naïve liver, Tuebingen, female, individual 2


title: liver_control_Tuebingen_male_1

description: Baseline gene expression of Tuebingen male

source_name: naïve liver, Tuebingen, male, individual 1


title: liver_control_WIK_male_1

description: Baseline gene expression of WIK male

source_name: naïve liver, WIK, male, individual 1


title: liver_control_WIK_male_2

description: Baseline gene expression of WIK male

source_name: naïve liver, WIK, male, individual 2


title: liver_control_Tuebingen_male_2

source_name: naïve liver, Tuebingen, male, individual 2


title: Control GIGY2-overexpressing  HeLa cells biological rep 1


title: liver_control_Tuebingen_male_3

source_name: naïve liver, Tuebingen, male, individual 3


title: Control HeLa cells biological rep 1

description: Gene expression data from control cells


title: liver_control_Tuebingen_female_1

source_name: naïve liver, Tuebingen, female, individual 1


title: liver_control_AB_female_3

description: Baseline gene expression of AB female

source_name: naïve liver, AB, female, individual 3

value: AB


title: liver_control_AB_female_2

description: Baseline gene expression of AB female

source_name: naïve liver, AB, female, individual 2


title: Larvae_effluent_0.5x_rep3

city: Singapore

first: Siew Hong

last: Lam

address: #02-01, T-Lab Building, 5A Engineering Drive 1

country: Singapore

institute: National University of Singapore

description: Gene expression after 5 days in half concentration of secondary effluent from a wastewater treatment plant

hyb_protocol: An equal amount of Cy3-labelled cRNA (1.65 µg) was hybridized to G2519F Agilent Zebrafish Whole Genome Oligo Microarray Ver3.0, 4x44K  at 65 °C for 17 h.  The hybridized microarray slides were then washed according to manufacturer’s protocol.

scan_protocol: Slides were scanned using an Agilent G2565BA scanner (Agilent, CA, USA) at 5-µm resolution with green dye channel and a scan region of 61 mm x 21.6 mm.

data_processing: Signal intensity data were then extracted from the scanned Tiff image (20 bit) by Agilent Feature Extraction software version 10.7. Batch normalization of signal intensity was performed using Agilent GeneSpring software version 7.3.1.

source_name: larvae, 5dpf, half concentration of effluent, replicate 3

label_protocol: For each replicate, 200 ng total RNA was diluted using Agilent One-Color RNA Spike-In Kit, followed by amplification and labelling with the Cy3 using Agilent Low Input Quick Amp Labeling Kit  according to the manufacturer’s protocol. The Cy3 labelled cRNA samples were then purified using RNeasy Mini Kit.

growth_protocol: Embryos of wild type AB strain zebrafish were collected and maintained at 28 ± 0.5 °C in E3 medium [5 mM NaCl, 0.17 mM KCl, 0.33 mM CaCl2·2H2O, 0.33 mM MgSO4·7H2O, 0.0001% Methylene blue in Milli-Q water, buffered with 1 normal NaOH to pH 7.1–7.2].

extract_protocol: Total RNA of wild-type larvae was extracted TRIzol® Reagentand treated with DNase I, Amplification Grade 100UN according to respective manufacturer’s protocols. Samples with RNA Integrity Number above eight as determined by Agilent 2100 Bioanalyzer were used for further experiments.

treatment_protocol: A total of 25-30 embryos aged 3 h post-fertilisation (hpf) were randomly placed into each well of a 6-well plate containing 4 mL of original (1x) or half (0.5x) effluent which was reconsituted in E3 medium with a maximum of 0.05% DMSO. The control group contained 0.05% (v/v) DMSO in E3 medium only. All media were renewed every 24 h. At 5 dpf, larvae were collected, snap-frozen in liquid nitrogen and stored at -80 °C until RNA extraction.

value: whole larvae

value: AB strain

value: wild type

value: 5 days


title: Larvae_effluent_0.5x_rep4

source_name: larvae, 5dpf, half concentration of effluent, replicate 4


title: liver_control_AB_male_3

description: Baseline gene expression of AB male

source_name: naïve liver, AB, male, individual 3


title: liver_control_AB_male_1

description: Baseline gene expression of AB male

source_name: naïve liver, AB, male, individual 1


title: liver_control_AB_male_2

description: Baseline gene expression of AB male

source_name: naïve liver, AB, male, individual 2


title: Larvae_effluent_1x_rep5

description: Gene expression after 5 days in original concentration of secondary effluent from a wastewater treatment plant

source_name: larvae, 5dpf,original concentration of effluent, replicate 5


title: Larvae_DMSO Control_rep4

description: Gene expression after 5 days in 0.05% DMSO

source_name: larvae, 5dpf, 0.05%DMSO, replicate 4


title: liver_control_AB_female_1

description: Baseline gene expression of AB female

source_name: naïve liver, AB, female, individual 1


title: Larvae_effluent_0.5x_rep1

source_name: larvae, 5dpf, half concentration of effluent, replicate 1


title: Larvae_effluent_1x_rep1

source_name: larvae, 5dpf,original concentration of effluent, replicate 1


title: Larvae_DMSO Control_rep2

source_name: larvae, 5dpf, 0.05%DMSO, replicate 2


title: Larvae_effluent_1x_rep2

source_name: larvae, 5dpf,original concentration of effluent, replicate 2


title: Larvae_effluent_0.5x_rep5

source_name: larvae, 5dpf, half concentration of effluent, replicate 5


title: Larvae_effluent_0.5x_rep2

source_name: larvae, 5dpf, half concentration of effluent, replicate 2


title: Larvae_effluent_1x_rep4

source_name: larvae, 5dpf,original concentration of effluent, replicate 4


title: Larvae_effluent_1x_rep3

source_name: larvae, 5dpf,original concentration of effluent, replicate 3


title: Larvae_DMSO Control_rep3

source_name: larvae, 5dpf, 0.05%DMSO, replicate 3


title: Primary Tumour [genotype]

type: genomic

city: Herston

first: Fares

last: Al-Ejeh

state: QLD

address: 300 Herston Road

department: Cancer

country: Australia

institute: QIMR Berghofer

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: Regions of copy number aberrations (CNAs) were identified using the genoCN software, which simultaneously describes copy number states and genotype calls whilst controlling for tissue contamination.

label: cy3, cy5

molecule: genomic DNA

source_name: Fresh Tissue

label_protocol: Whole genome amplification was performed using the Infinium II assay protocol (Illumina).

growth_protocol: P7731 cells were maintained in RPMI1640 + 10% FBS.

extract_protocol: DNA from the primary tumour and cell line were extracted using the salting-out method followed by a phenol-chloroform extraction.

tag: sample type

value: Primary Tumour


title: P7731 [genotype]

description: Cell Line_430274362_B

label: cy3, cy6

source_name: Cell line

value: Cell line derived from metastasis


title: PBS Liver 1

city: Brisbane

first: Katharine

last: Irvine

address: Translational Research Institute

institute: Mater Research Institute UQ

description: liver from PBS-treated rat (daily injection of newborn rat for 5 days, harvest on day 6)

hyb_protocol: per Affymetrix instructions

scan_protocol: per Affymetrix instructions

data_processing: The data were analyzed with Expression Console using Affymetrix default analysis

organism: Rattus norvegicus

source_name: PBS Liver

label_protocol: per Affymetrix instructions

extract_protocol: Trizol

value: Sprague Dawley

value: PBS-treated rat

tag: tissue


title: BMDM 1

description: rat bone marrow derived macrophages generated by culture of bone marrow cells in CSF1 for 7 days

source_name: BMDM

value: Dark Agouti

value: bone marrow cells cultured in CSF1

tag: cell type

value: BMDM


title: CSF1 Liver 2

description: liver from CSF1-treated rat (daily injection of newborn rat for 5 days, harvest on day 6)

source_name: CSF1 Liver

value: CSF1-treated rat

value: liver


title: BMDM 3


title: CSF1 Liver 4


title: PBS Liver 2


title: CSF1 Liver 1


title: WT primary astrocyte

source_name: WT primary astrocyte

extract_protocol: Total RNA from primary astrocytes was extracted using NucleoSpin RNA (MACHEREY-NAGEL GmbH & Co. KG).

value: postnatal day 1

value: primary astrocyte


title: BMDM 2


title: EVT-PP8

city: Maplewood

first: Nick

last: Illsley

state: NJ

address: Richmond Ave

institute: Placental Research Group LLC

description: Control

data_processing:
Normalization was performed using the geometric mean of one or more housekeeping genes selected from ACTB, B2M, GAPDH, HPRT1 and RPLP0 (no significant difference between control & test, p < 0.05, t test)
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_HKG − Ct_Target)]
Fold change calculations performed using 2^deltadeltaCt.
The fold_change.txt reports test/control ratios

label: SYBR Green

source_name: EVT from placenta previa

label_protocol: Samples were analyzed using the Epithelial-Mesenchymal Transition (EMT) RT2 Profile PCR Array (Cat. #PAHS-090Z, Qiagen) using an ABI 7900 HT Fast Real-Time PCR System (Applied Biosystems, Foster City, CA) under cycling conditions recommended for the PCR Array

growth_protocol: Placental tissue (basal plate) obtained immediately after cesarean section. Uteroplacental tissue (percreta; leading edge of invasion) obtained immediatley after cesarean/hysterectomy. Percreta confirmed by histopathology.

extract_protocol: RNA was extracted using the Invitrogen RNeasy Mini Kit (Life Technologies) according to the manufacturer's instructions. cDNA was transcribed from 400 ng of RNA using an RT2 First Starnad Kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions, using the RT2 PreAmp Pathway Primer Mix specific for the Epithelial-Mesenchymal Transition (EMT) RT2 Profile PCR Array (Cat. #PBH-090Z, Qiagen).

treatment_protocol: Cytotrophoblast and extravillous trophoblast obtained via trypsin/dispase digestion, Percoll step gradient separation and immunomagnetic bead purification using anti-integrin beta 4 (cytotrophoblast) or anti-HLA-G (extravillous trophoblast)

tag: gestational age @ delivery (weeks)

tag: clinical group

value: Previa

value: Extravillous trophoblast cells (EVT)


title: Larvae_DMSO Control_rep1

source_name: larvae, 5dpf, 0.05%DMSO, replicate 1

value: whole larvae

tag: strain

tag: age


title: MC4R_WD CD11c-positive 3

city: Tokyo

first: Michiko

last: Itoh

address: 1-5-45 Yushima, Bunkyo-ku

institute: Tokyo Medical and Dental University

description: Gene expression of hepatic resident macrophages

hyb_protocol: 0.6 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 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of Agilent 2x GE Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse Gene Expression (G4852A) 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 (G2539A) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Data were obtained in quintuplicate. The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09  and Grid: 028005_D_F_20110614) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Data were normalized to the median of wildtype macrophages using GeneSpring software version 14.5 (Agilent Technologies).

source_name: CD11c-positive resident macrophage from NASH liver

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop 2000c Spectrophotometer.

extract_protocol: Total RNAs were extracted from pooled macrophages of 7 to 9 mice using PureLink RNA Micro Kit (Invitrogen).

treatment_protocol: Eight-week old male MC4R-KO mice were fed Western diet for 20 weeks, and wildtype mice were kept under standard diet. The livers were digested with collagenases, and F4/80 highly expressed macrophages were sorted based on the expression levels of CD11c.

value: macrophage

tag: cd11c status

value: male

tag: genotype

tag: diet

value: Western diet

tag: disease state

value: NASH


title: EVT-AIP7

description: Test

source_name: EVT from abnormally invasive placenta

value: Previa, percreta


title: EVT-PP7

description: Control


title: CSF1 Liver 3

value: Sprague Dawley


title: EVT-AIP8

description: Test


title: MC4R_WD CD11c-positive 4

tag: gender


title: EVT-AIP2

description: Test


title: EVT-AIP4

description: Test


title: EVT-AIP1

description: Test


title: EVT-AIP5

description: Test


title: EVT-AIP6

description: Test


title: EVT-AIP3

description: Test


title: MC4R_WD CD11c-positive 5


title: MC4R_WD CD11c-positive 2


title: MC4R_WD CD11c-positive 1


title: EVT-PP6

description: Control


title: MC4R_WD CD11c-negative 5

source_name: CD11c-negative resident macrophage from NASH liver


title: EVT-PP4

description: Control


title: EVT-PP1

description: Control


title: EVT-PP2

description: Control


title: EVT-NT4

description: Test

source_name: EVT from normal thrd trimester placenta

value: Normal, term


title: EVT-NT8

description: Test


title: EVT-NT7

description: Test


title: EVT-NT5

description: Test


title: EVT-NT3

description: Test


title: EVT-PP5

description: Control


title: EVT-NT6

description: Test


title: EVT-NT2

description: Test


title: CTB-PP3

description: Control

source_name: CTB from placenta previa

value: Cytotrophoblast cells (CTB)


title: CTB-PP2

description: Control


title: CTB-AIP3

description: Test

source_name: CTB from abnormally invasive placenta


title: EVT-NT1

description: Test


title: CTB-AIP1

description: Test


title: MC4R_WD CD11c-negative 1


title: WT_SD 5

source_name: resident macrophage from normal liver

value: wildtype

value: standard diet

value: normal


title: MC4R_WD CD11c-negative 3

value: liver


title: WT_SD 4


title: EVT-PP3

description: Control


title: MC4R_WD CD11c-negative 2


title: CTB-PP1

description: Control


title: CTB-AIP2

description: Test


title: WT_SD 3


title: CTB-NT3

description: Control

source_name: CTB from normal thrd trimester placenta


title: CTB-NT4

description: Control


title: WT_SD 1


title: CTB-NT2

description: Control


title: Peripheral T-cell lymphoma 26

city: Madrid

first: Rebeca

last: Manso

state: Madrid

address: Av. Reyes Católicos, 2

department: Pathology

institute: Fundación Jiménez Díaz

description:
Non-coding RNA profiling by array
SAMPLE 30

hyb_protocol: Hybridization settings: 20 hours, at 55ºC, at 20rpm. Blocking agent, hybridization and washing buffers was performed according to agilent recomandation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565AA).

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. Data are normalized to the median of the series (between arrays) by R program version 2.4, (available at http://www.r-project.org/). For normalization was used the "Processed Signal" of the feature extraction files (already includes background subtraction) was used. Average of miRs replicates was then applied using the following web page: http://prep.bioinfo.cnio.es/. Significance Analysis of Microarray excel macro (SAM) was used.

source_name: Peripheral T-cell lymphoma 26

label_protocol: 100ng of total RNA were dephosphorilated, desnaturalizated, treated with ligase  T4 and labelled with Cy3 for 2 hours at 16ºC.

growth_protocol: Samples were frozen to preserve the RNA properties.

extract_protocol: Total RNA was extracted by Trizol reagent (Invitrogen, Carlsbad, CA, USA)

value: lymph node

tag: disease status

value: peripheral T cell lymphoma (PTCL)


title: Reactive lymph node 2

description:
Non-coding RNA profiling by array
SAMPLE 2

source_name: Reactive lymph node 2

value: non-lymphoma


title: Reactive lymph node 1

description:
Non-coding RNA profiling by array
SAMPLE 1

source_name: Reactive lymph node 1


title: Peripheral T-cell lymphoma 25

description:
Non-coding RNA profiling by array
SAMPLE 29

source_name: Peripheral T-cell lymphoma 25


title: CTB-NT1

description: Control


title: exosome_24hr_0ug/ml_ome

city: Tianjin

first: Xu-wen

last: Guan

state: Tianjin

address: Huanhuxi Road, Tiyuanbei, Hexi District

institute: Tianjin Medical University

description: miRNA expression in exosomes from medium of SGC-7901 cells after 24hr in 0ug/ml omeprazole treatment

hyb_protocol: Cy3 labeled RNA re-suspended in hybridization buffer and hybridized to the array platform overnight (20 hours) at 55 °C in a rotating Agilent hybridization oven using Agilent's recommended hybridization chamber.

scan_protocol: Fluorescence signals after hybridization were detected with a DNA microarray scanner G2505C (Agilent Technologies) using one color scan setting for 8 × 60 K array slides (Scan Area 61 × 21.6 mm, Scan resolution 2 μm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: In order to obtain background subtracted and outlier rejected signal intensities, the scanned microarray images were analyzed and processed with the Agilent feature extraction software (v10.7.3.1) using default parameters (Grid: 046064_D_20121223).

source_name: exosome, 24hr, 0ug/ml_ome

label_protocol: Equal amount of  small RNA (defined by Agilent bioanalyzer pico assay) was labeled with Cyanine3 (Cy3) according to the manufacturer's instructions.

growth_protocol: SGC-7901 cells were cultured in RPMI-1640 medium (Gibco, USA) supplemented with 10% fetal calf serum (Gibco, USA) at 37˚C in a humidified atmosphere containing 5% CO2.

extract_protocol: The medium of SGC-7901 cells were collected and the exosomes were isolated by ExoQuick-TC exosome precipitation solution (System Bioscience, USA)  according to the manufacturer's instructions. Then the miRNA involved in exosomes was isolated by the total RNA purification Kit (Norgen, USA) according to the manufacturer's instructions.

treatment_protocol: SGC-7901 cells were treated with PBS or 80ug/ml omeprazole and cultured in RPMI-1640 medium (Gibco, USA) supplemented with 10% exosome-free FBS (Gibco, USA) and then incubated with for 24 hours at 37 ºC in a humidified incubator with 5% CO2.

tag: source

value: medium of SGC-7901 cells

tag: drug intervention


title: kidney organoid immediately after reconstruction rep3

city: Kumamoto

first: Atsuhiro

last: Taguchi

state: Kumamoto

department: IMEG

institute: Kumamoto Univ.

hyb_protocol: Agilent one-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocolGE1_107_Sep09 and Grid: 028005_D_F_20100804) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Agilent one-color Low RNA Input Linear Amplification Kit labeling protocol

growth_protocol: E11.5 or reconstructed kidney organoids were cultured on the transwell mounted by 50% Matrigel plus DMEM/F12 containing 10% FBS.  DMEM/F12 containing 10% FBS were used for the culture media.

extract_protocol: Each specimens were mechanically homogenized and total RNA was extracted using Rneasy Plus Micro Kit purchased from QIAGEN following manufacture's protocol.

tag: developmental stage

value: embryo

tag: strain/genotype

value: ICR, wild type plus mESC, with B6 and 129SV background

value: kidney organoid


title: Peripheral T-cell lymphoma 23

description:
Non-coding RNA profiling by array
SAMPLE 27

source_name: Peripheral T-cell lymphoma 23


title: Keratinocytes WT, biological rep1_MTA-1_0

description: 013378_(MTA-1_0)_WT1.sst-rma-gene-full-Signal

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 RMA normalization.

source_name: WT_primary cultured mouse keratinocytes

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).

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

treatment_protocol: 2000000 Cells were seeded at the same number in collagen coated plates, cultured overnight, then quickly harvest the cells in Trizol solution (Sigma) on ice.Two plate of cells of the same genotype were harvested in trizol, then were combined together as one sample. there were two samples for WT and Glut1 deficient keratinocytes separatedly.

tag: strain background

value: 1 week

tag: genotype/variation

value: wild type

value: primary keratinocytes


title: E11.5 embryonic kidney

source_name: E11.5 whole embryonic kidney without ureter

value: embryo E11.5

value: ICR, wild type

tag: tissue

value: kidney


title: WT_SD 2

tag: cell type

value: macrophage

value: male

value: wildtype


title: 7-days cultured E11.5 embryonic kidney

source_name: 7-days cultured E11.5 embryonic kidney

value: 7-days cultured E11.5 embryonic kidney


title: kidney organoid immediately after reconstruction rep2


title: Keratinocytes KO, biological rep1_MTA-1_0

description: 013378_(MTA-1_0)_KO1.sst-rma-gene-full-Signal

source_name: KO_primary cultured mouse keratinocytes


title: 7-days cultured kidney organoid rep2

source_name: 7-days cultured kidney organoid rep2


title: 7-days cultured kidney organoid rep3

source_name: 7-days cultured kidney organoid rep3


title: Reactive lymph node 4

description:
Non-coding RNA profiling by array
SAMPLE 4

source_name: Reactive lymph node 4

value: lymph node


title: Reactive lymph node 3

description:
Non-coding RNA profiling by array
SAMPLE 3

source_name: Reactive lymph node 3


title: E13.5 embryonic kidney

source_name: E13.5 whole embryonic kidney without ureter

value: embryo E13.5


title: 7-days cultured kidney organoid rep1

source_name: 7-days cultured kidney organoid rep1


title: P0 embryonic kidney

source_name: P0 whole embryonic kidney without ureter

value: embryo P0


title: Keratinocytes WT, biological rep2_MTA-1_0

description: 013378_(MTA-1_0)_WT2.sst-rma-gene-full-Signal


title: kidney organoid immediately after reconstruction rep1


title: Keratinocytes KO, biological rep2_MTA-1_0

description: 013378_(MTA-1_0)_KO2.sst-rma-gene-full-Signal


title: E15.5 embryonic kidney

source_name: E15.5 whole embryonic kidney without ureter

value: embryo E15.5


title: Peripheral T-cell lymphoma 13

description:
Non-coding RNA profiling by array
SAMPLE 17

source_name: Peripheral T-cell lymphoma 13

value: peripheral T cell lymphoma (PTCL)


title: Peripheral T-cell lymphoma 12

description:
Non-coding RNA profiling by array
SAMPLE 16

source_name: Peripheral T-cell lymphoma 12


title: Peripheral T-cell lymphoma 24

description:
Non-coding RNA profiling by array
SAMPLE 28

source_name: Peripheral T-cell lymphoma 24


title: Peripheral T-cell lymphoma 10

description:
Non-coding RNA profiling by array
SAMPLE 14

source_name: Peripheral T-cell lymphoma 10


title: Peripheral T-cell lymphoma 7

description:
Non-coding RNA profiling by array
SAMPLE 11

source_name: Peripheral T-cell lymphoma 7


title: Peripheral T-cell lymphoma 20

description:
Non-coding RNA profiling by array
SAMPLE 24

source_name: Peripheral T-cell lymphoma 20


title: Peripheral T-cell lymphoma 18

description:
Non-coding RNA profiling by array
SAMPLE 22

source_name: Peripheral T-cell lymphoma 18


title: Peripheral T-cell lymphoma 21

description:
Non-coding RNA profiling by array
SAMPLE 25

source_name: Peripheral T-cell lymphoma 21


title: exosome_24hr_80ug/ml_ome

description: miRNA expression in exosomes from medium of SGC-7901 cells after 24hr in 80ug/ml omeprazole treatment

source_name: exosome, 24hr, 80ug/ml_ome

value: medium of SGC-7901 cells

value: Omeprazole


title: MC4R_WD CD11c-negative 4

description: Gene expression of hepatic resident macrophages

source_name: CD11c-negative resident macrophage from NASH liver

value: liver

value: Western diet

value: NASH


title: Peripheral T-cell lymphoma 22

description:
Non-coding RNA profiling by array
SAMPLE 26

source_name: Peripheral T-cell lymphoma 22


title: Peripheral T-cell lymphoma 19

description:
Non-coding RNA profiling by array
SAMPLE 23

source_name: Peripheral T-cell lymphoma 19


title: Peripheral T-cell lymphoma 5

description:
Non-coding RNA profiling by array
SAMPLE 9

source_name: Peripheral T-cell lymphoma 5


title: Peripheral T-cell lymphoma 3

description:
Non-coding RNA profiling by array
SAMPLE 7

source_name: Peripheral T-cell lymphoma 3


title: Peripheral T-cell lymphoma 16

description:
Non-coding RNA profiling by array
SAMPLE 20

source_name: Peripheral T-cell lymphoma 16


title: Peripheral T-cell lymphoma 11

description:
Non-coding RNA profiling by array
SAMPLE 15

source_name: Peripheral T-cell lymphoma 11


title: Peripheral T-cell lymphoma 17

description:
Non-coding RNA profiling by array
SAMPLE 21

source_name: Peripheral T-cell lymphoma 17


title: Peripheral T-cell lymphoma 14

description:
Non-coding RNA profiling by array
SAMPLE 18

source_name: Peripheral T-cell lymphoma 14


title: E17.5 embryonic kidney

source_name: E17.5 whole embryonic kidney without ureter

value: embryo E17.5


title: Peripheral T-cell lymphoma 9

description:
Non-coding RNA profiling by array
SAMPLE 13

source_name: Peripheral T-cell lymphoma 9


title: Peripheral T-cell lymphoma 1

description:
Non-coding RNA profiling by array
SAMPLE 5

source_name: Peripheral T-cell lymphoma 1


title: Peripheral T-cell lymphoma 6

description:
Non-coding RNA profiling by array
SAMPLE 10

source_name: Peripheral T-cell lymphoma 6


title: Peripheral T-cell lymphoma 2

description:
Non-coding RNA profiling by array
SAMPLE 6

source_name: Peripheral T-cell lymphoma 2


title: Peripheral T-cell lymphoma 15

description:
Non-coding RNA profiling by array
SAMPLE 19

source_name: Peripheral T-cell lymphoma 15


title: Peripheral T-cell lymphoma 4

description:
Non-coding RNA profiling by array
SAMPLE 8

source_name: Peripheral T-cell lymphoma 4


title: sham-injured [7_10s-sham]

city: Jackson

first: Michael

middle: R

last: Garrett

state: MS

address: 2500 North State Street

department: Pharmacology

institute: University of Mississippi Medical Center

description: placed on HFD after 4 weeks surgical recovery

hyb_protocol: Following fragmentation, cRNA were hybridized to Rat GeneChip 2.0ST Arrays. GeneChips were automatically washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G

data_processing: Analysis of microarray data was performed using software provided by Affymetrix (Affymetrix® Expression Console™ Software) and commercially available GeneSifter™ software platform using RMA

source_name: fresh spinal cord excised after conscious decapitation

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol for Rat GeneChip 2.0ST Arrays

growth_protocol: Male, Long Evans rats (400g) (Harlan, Indianapolis, IN) (N=10) werewere maintained on standard chow (#8640, Envigo, 3.0 kCal/g; 17% fat, 54% carbohydrate, 29% protein). Rats were assigned to either sham-laminectomy (Sham) or thoracic spinal cord injury (tSCI) group in a counterbalanced fashion based on body weight on the day prior to the start of surgery. Surgery was performed and animals were allowed to recover for 4 weeks following surgery. Rats were switched to a palatable, high-fat diet (HFD) (#D03082706, Research Diets, New Brunswick, NJ, 4.54 kCal/g; 40% fat, 46% carbohydrate, 15% protein) for the remainder of the study totaling 8 weeks.

extract_protocol: RNA was isolated using TRIzol® and Invitrogen PureLink Kit (Life Technologies) and evaluated for quality and integrity (Bio-Rad Experion™ System)

treatment_protocol: Whole genome transcript analysis was performed using Affymetrix platform on  T11-12 spinal cord tissue isolated from two groups of animals- sham (n=4) and spinal cord injured (SCI, n=4))

value: T10-11 spinal cord tissue

tag: protocol

value: sham-injured

tag: Sex

value: Long Evans

value: approximately 175 days old


title: thoracic spinal cord injury [1_4s-sci]

value: thoracic spinal cord injury

value: male

tag: strain

tag: age


title: Peripheral T-cell lymphoma 8

description:
Non-coding RNA profiling by array
SAMPLE 12

source_name: Peripheral T-cell lymphoma 8

value: lymph node


title: thoracic spinal cord injury [3_7s-sci]


title: sham-injured [6_9s-sham]


title: Subject 7 with high HbF,HbF_007

city: Nanning

first: Ketong

last: Lai

address: Shuangyong Road

department: Department of Pediatrics

institute: the First Affiliated Hospital of Guangxi Medical University

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 56℃ on miRCURY LNA Array (v.18.0) (Exiqon) . GeneChips were washed several times using Wash buffer kit (Exiqon).

scan_protocol: GeneChips were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization.

source_name: peripheral blood

label_protocol: Hy3™-labeled cRNA were prepared according to the standard Exiqon's manual from 1 ug total RNA (Exiqon, Vedbaek, Denmark).

growth_protocol: 2 mL peripheral blood anticoagulated by ethylene diamine tetraacetic acid (EDTA) was collected from every subject and stored at 4 ℃.

treatment_protocol: Each sample was depleted of CD45+ cells to remove leukocytes and then enriched for CD71+ erythroid cells by Miltenyi magnetic microbeads (Miltenyi Biotec), and placed on ice in the Trizol solution(invitrogen).

tag: cell

value: circulating CD71+ erythroid progenitors

value: 38 years

value: Female

tag: sample type

value: b-thalssemia minor with high HbF


title: Subject 8 with normal HbF,HbF_008

description: Each sample was depleted of CD45+ cells to remove leukocytes and then enriched for CD71+ erythroid cells

value: 32 years

value: control


title: thoracic spinal cord injury [4_8s-sci]


title: Subject 11 with normal HbF,HbF_011

value: 31 years


title: Subject 13 with normal HbF,HbF_013

value: 30 years

value: Male


title: Subject 14 with normal HbF,HbF_014

value: 39 years


title: thoracic spinal cord injury [2_6s-sci]

value: T10-11 spinal cord tissue


title: Subject 12 with normal HbF,HbF_012

value: 28 years


title: Subject 5 with high HbF,HbF_005


title: Subject 9 with normal HbF,HbF_009

value: 41 years


title: 8W_old_rosette_leaves_non_acclimated_replicate_1 [Tuva_NA_R1]

city: Potsdam

first: Ellen

last: Zuther

address: Am Muehlenberg 1

department: Transcript Profiling

institute: MPI of Molecular Plant Physiology

description: Gene expression for non acclimated Tuva rosette leaves. RNA was hybridized on custom made Agilent Thellungiella salsuginea expression array

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ml of 2x 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to a custom Gene Expression Agilent Microarray  (G2514F; DesignID 031554) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for AgilentHD_GX for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5µm, Dye channel is set to Green and Green PMT is set to 100%, Tiff 20bit).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 031554_D_F_20101207) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Eutrema salsugineum

source_name: 8-week-old rosette leaves, non-acclimated

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling (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.

growth_protocol: Seeds of Arabidopsis thaliana accessions were stratified at 4°C for 1 week and grown on soil at 20°C for 3 weeks under 8 hrs light/16 hrs dark cycle at growth chamber. Seedlings plants were continued grown at 20°C for 2 weeks under 16 hrs light/8 hrs dark cycle at greenhouse. Tuva and Yukon seeds were stratified at 4°C for 1 week and grown on soil at 20°C for 8 weeks under 16 hrs light/8 hrs dark cycle at greenhouse.

extract_protocol: Total RNA was isolated and on-column DNA digestion was performed with the RNeasy Plant mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol.

treatment_protocol: For cold acclimation, soil grown 6-week-old Arabidopsis plants were cold acclimated at 4°C for 2 weeks. Soil grown 8-week-old Tuva plants were cold acclimated at 4°C for 2 weeks.

tag: accession

value: Tuva

value: rosette leaves


title: 8W_old_rosette_leaves_non_acclimated_replicate_3 [Tuva_NA_R3]


title: 8W_old_rosette_leaves_non_acclimated_replicate_2 [Tuva_NA_R2]


title: sham-injured [5_5s-sham]

value: sham-injured

value: male

value: Long Evans

value: approximately 175 days old


title: sham-injured [8_11s-sham]


title: 8W_old_rosette_leaves_2W_cold_acclimated_replicate_3 [Tuva_ACC_R3]

description: Gene expression for 2 weeks cold acclimated Tuva rosette leaves at 4 °C. RNA was hybridized on custom made Agilent Thellungiella salsuginea expression array

source_name: 8-week-old rosette leaves, 2-week cold-acclimated


title: Subject 2 with high HbF,HbF_002

value: circulating CD71+ erythroid progenitors

value: 27 years

value: Female


title: 8W_old_rosette_leaves_2W_cold_acclimated_replicate_1 [Tuva_ACC_R1]


title: 8W_old_rosette_leaves_2W_cold_acclimated_replicate_2 [Tuva_ACC_R2]


title: Subject 3 with high HbF,HbF_003

value: b-thalssemia minor with high HbF


title: Subject 10 with normal HbF,HbF_010

value: 34 years

value: control


title: Subject 4 with high HbF,HbF_004

value: 33 years


title: Subject 1 with high HbF,HbF_001


title: Subject 6 with high HbF,HbF_006

value: 32 years

value: Male


title: microRNA profile of case T96

city: Guangzhou

first: jingye

last: hu

address: 651 Dongfeng East Road

institute: Sun Yat-sen University Cancer Center

hyb_protocol: The labeled RNAs from breast cancer and noncancerous breast were hybridized to the array with a 1×hybridization solution (5× Denhart’s solution, 0.5% SDS, 5× SSC) in a Hybridization Chamber (Corning Inc, Corning, NY, USA) at 46°C for 12 to 16 hours.

scan_protocol: Scanned in a LuxScanTM -10K Scanner (capitalBio Inc.,Beijing, China).

data_processing: Quantile normalization across multiple arrays, log 2 transformation of expression levels, BRB ArrayTools v.3.8.0 was used.

source_name: breast cancer

label_protocol: 2.5 μg of total RNA was employed with 100 nmol/L of pCp-DY647 (Dharmacon, Lafayette, CO, USA) and 15 Units of T4 RNA ligase (USB, Cleveland, Oh, USA) in a total reaction volume of 20 µL at 16°C overnight

extract_protocol: Total RNA was extracted from the paraffin-embedded breast cancer and noncancerous breast samples, using a modification of the phenol/chloroform extraction method after processing by dimethylbenzene.

tag: survival

value: breast cancer


title: microRNA profile of case T98


title: KGN/shPWRN2-3

city: Shanghai

first: Xin

last: Huang

state: Shanghai

address: No.2699 Gaoke east road

department: Reproductive Medicine Centre

institute: Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine

description: Gene expression of KGN cell lines treated with lentivirus shRNA for PWRN2

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 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan.

data_processing: The lncRNA+mRNA array data were analyzed for data summarization, normalization and quality control by using the GeneSpring software V11.5 (Agilent). The data were normalized by percentile 75 normalization. To select the differentially expressed genes, we used threshold values of ≥2.0 and ≤-2.0 -fold change and a Benjamini-Hochberg corrected p value of 0.05.

source_name: KGN cell lines

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: the KGN cells were cultured in 1:1 Dulbecco’s modified Eagle’s medium and Ham’s F-12 medium (DMEM/ F12; Nissui Pharmaceutical, Tokyo, Japan) supplemented with 10% foetal bovine serum (FBS) and antibiotics (100 IU/mL penicillin and 100 μg mL streptomycin). On the day before the Lentivirus transfection, the KGN cells were placed into the medium without serum and incubated overnight.

extract_protocol: Total RNA isolation was performed using the Qiagen RNeasy Mini Kit (Qiagen, Hilder, Germany) according to the manufacturer’s instructions.

treatment_protocol: We selected three target sequences to construct the lentiviral shRNAs (LV-PWRN2-homo-502, LV-PWRN2-homo-1574, LV-PWRN2-homo-1261) including the negative control (LV-NC). The target sequences were used to design two complementary oligonucleotides, which were synthesized and cloned into pGLV3/H1/GFP+Puro Vector (GenePharma, China). The positive purified lentiviral shRNA-expressing plasmids were transfected with the packaging plasmids into 293T cells for lentivirus generation (Genepharma, China). Then, the vectors described above were used to infect KGN cells. Stable KGN cell lines were selected using 3ug/mL bulk puromycin-resistance culturing (puromycin, Sigma, St Louis, MO, USA) for 5 days. After that, the cells were examined microscopically for lentiviral GFP expression and analyzed by real-time PCR.

tag: cell line

value: KGN

tag: treatment

value: treated with LV-PWRN2-homo-1261 to interfere the PWRN2 expression


title: microRNA profile of case T97


title: microRNA profile of case T95


title: microRNA profile of case T92


title: microRNA profile of case T90


title: microRNA profile of case T91


title: microRNA profile of case T9


title: microRNA profile of case T94


title: microRNA profile of case TR10


title: microRNA profile of case T99


title: microRNA profile of case TR2


title: microRNA profile of case T89


title: microRNA profile of case T93


title: microRNA profile of case T88


title: KGN/shPWRN2-1

value: treated with LV-PWRN2-homo-502 to interfere the PWRN2 expression


title: NC-3

description: Gene expression of KGN cell lines treated with negative control lentivirus vector

value: treated with LV-negative control


title: activated NSC, replicate 4

city: Fontenay-aux-Roses

first: Marc-André

last: MOUTHON

address: Route du Panorama

department: IRCM

country: France

institute: CEA

description: Gene expression data from activated neural stem cells of adult mouse subventricular zone

hyb_protocol: Following fragmentation, 5 µg of cDNA were hybridized for 16 hr at 45°C on GeneChip MOE 430 2.0. GeneChips were washed and stained.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000.

data_processing: The .CEL files were generated using Affymetrix software and the data were analyzed using GeneSpring GX12. Sample 3 and Sample 12 did not pass QC.

source_name: Adult mouse brain

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

growth_protocol: Neural stem cells were freshly sorted from adult mouse brain

extract_protocol: Total RNA were extracted using Qiagen then transcribed into cDNA and 5 µg of cDNA were amplified using NuGEN Ovation Pico WTA System

value: subventricular zone

tag: gender

value: male

tag: state

value: activated neural stem cells


title: NC-2


title: NC-1


title: KGN/shPWRN2-2

value: treated with LV-PWRN2-homo-1574 to interfere the PWRN2 expression


title: microRNA profile of case T82


title: microRNA profile of case T80


title: microRNA profile of case T87


title: activated NSC, replicate 2


title: microRNA profile of case T83


title: activated NSC, replicate 3


title: activated NSC, replicate 1


title: microRNA profile of case T81


title: quiescent NSC 48h after irradiation, replicate 4

description: Gene expression data from quiescent neural stem cells during the recovery phase 48h after radiation exposure


title: quiescent NSC 48h after irradiation, replicate 3

value: quiescent neural stem cells during the recovery phase 48h after radiation exposure


title: quiescent NSC 48h after irradiation, replicate 2


title: microRNA profile of case T8


title: quiescent NSC, replicate 3

description: Gene expression data from quiescent neural stem cells of adult mouse subventricular zone

value: quiescent neural stem cells


title: microRNA profile of case T79


title: Starvation Metformin treated C

city: Bern

first: Christa

middle: E.

last: Flück

address: Freiburgstrasse 15 / C845

department: Pediatric Endocrinology and Diabetology of the Department of Pediatrics and Department of Clinical Research

country: Switzerland

institute: University of Children's Hospital, Bern

description:
time points: 48h
Cells were treated with metformin drug in serum starvation condition

hyb_protocol: Affymetrix Human Gene 1.0 ST arrays, were hybridized with 2.7ug of biotinylated target, at  45°C for 17 hours washed and stained according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol FS450_0007).

scan_protocol: The arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix).

data_processing: All statistical analysis were performed using the free high-level interpreted statistical language R and various Bioconductor packages. Hybridization quality was assessed using the Expression Console software (Affymetrix). Normalized expression signals were calculated from Affymetrix CEL files using the RMA normalization method. Differential hybridized features were identified using Bioconductor package “limma” that implements linear models for microarray data. P values were adjusted for multiple testing with Benjamini and Hochberg’s method to control for false discovery rate (FDR).

source_name: Human adrenal H295R cells

label_protocol: Samples were enzymatically fragmented and biotinylated using the GeneChip WT Terminal Labeling Kit (Affymetrix).

growth_protocol: H295R cells were grown under normal growth, serum starvation and metformin treated conditions for 48h.

extract_protocol: After 48h of condition, cells were washed with PBS and total RNA was isolated and purified with an RNeasy Micro kit (Qiagen GmbH, Hilden, Germany).

treatment_protocol: H295R cells were first grown in normal growth medium for 24 h. Cells were incubated after 24h either with normal growth media or in serum-free medium or treated with 10mM metformin in serum-free medium for 48 h


title: Serum Starvation condition C

description:
time points: 48h
Cells grown in serum starvation (hyperandrogenic) condtion


title: Serum Starvation condition A


title: Serum Starvation condition B


title: quiescent NSC, replicate 4


title: quiescent NSC 48h after irradiation, replicate 1


title: Starvation Metformin treated B


title: Starvation Metformin treated A


title: Normal Growth condition C

description:
time points: 48h
Cells grown in normal condition


title: quiescent NSC, replicate 2


title: Normal Growth condition B


title: microRNA profile of case T78


title: microRNA profile of case T77


title: microRNA profile of case T75


title: microRNA profile of case T74


title: Normal Growth condition A


title: Ductal breast cancer 43

city: Baltimore

first: leslie

last: cope

state: MD

address: 550 N. Broadway

institute: leslie cope

description: Sample 43

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: Ductal breast cancer

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

extract_protocol: Using manufacturer's protocols, mRNA was isolated from formalin-fixed, paraffin-embedded tissue and analyzed using the Illumina whole-genome cDNA-mediated annealing, selection, extension, and ligation (DASL) array assay.

value: primary breast tumor tissue

tag: age at diagnosis

tag: tnm

tag: Stage

value: IIB

tag: histologic type

value: Ductal

tag: size(cm)

tag: tubule formation

tag: nuclear pleomorhism score

tag: mitotic count

tag: histologic grade (nottingham)

tag: geographic necrosis

value: N

tag: tumor border

value: Infiltrating

tag: stromal lymphocytosis

tag: vimentin

tag: egfr

tag: death by last follow-up (y/n)

tag: disease-free interval (months)

tag: overall survival (months)

tag: disease state

value: triple negative breast cancer


title: Ductal breast cancer 114

description: Sample 114

tag: tissue

tag: age at diagnosis

tag: tnm

value: I


title: quiescent NSC, replicate 1

tag: gender

tag: strain

tag: state


title: Ductal breast cancer 25

description: Sample 25

tag: Stage

tag: histologic type

tag: size(cm)

tag: tubule formation

tag: nuclear pleomorhism score

tag: mitotic count

value: Y

value: Expansile


title: Ductal breast cancer 146

description: Sample 146

value: IIA

tag: histologic grade (nottingham)

tag: geographic necrosis

tag: tumor border

tag: stromal lymphocytosis

tag: vimentin

tag: egfr


title: Ductal breast cancer 46

description: Sample 46

tag: tissue

tag: age at diagnosis

tag: death by last follow-up (y/n)

tag: disease-free interval (months)

tag: overall survival (months)

tag: disease state


title: D4-6

city: Innsbruck

first: Daniel

last: Bindreither

state: Tirol

address: Innrain 82

department: Division of Molecular Pathophysiology

institute: Medical University Innsbruck

hyb_protocol: Resulting targets (i.e. fragmented and labeled RNA) were hybridized to the Affymetrix Yeast Genome 2.0 Arrays in an Affymetrix fluidic station 450

scan_protocol: GeneChips were scanned using the Affymetrix scanner 3000

data_processing: Quality assessment and preprocessing of the microarrays was done in R by utilizing the Bioconductor packages (v.2.20.0) affyPLM and GCRMA respectively

organism: Saccharomyces cerevisiae

source_name: mRNA extracts from a VPS4 knock out yeast strain

label_protocol: Biotinylated hybridization targets for each sample were generated using the Affymetrix GeneChip 3′ IVT Express kit and the Affymetrix GeneChip hybridization, wash, and stain kit

growth_protocol: Cells were grown in YNB synthetic medium supplemented with required amino acids at 26°C.

extract_protocol: Total RNA of midlog phase yeast cells was isolated via RNeasy Kit (Qiagen Pty. Ltd., Hilden, Germany)

tag: genotype/variation

value: Delta VPS4

tag: culture stage

value: midlog phase yeast cells


title: microRNA profile of case T72

tag: survival

value: breast cancer


title: D4-5


title: D4-4


title: cord blood 7 buffy

city: Ann Arbor

first: Kelly

last: Bakulski

state: MI

address: 1415 Washington Heights

department: Department of Epidemiology

institute: University of Michigan

hyb_protocol: DNA was bisulfite treated and cleaned using the EZ DNA methylation kit (Zymo Research), then hybridized on the Infinium MethylationEPIC BeadChip (Illumina)

scan_protocol: Methylation NXT scan setting with Illumina iScan

data_processing: Raw image array files were processed in R statistical software (version 3.3) using the minfi package (version 1.20.2). Data were processed with noob background correction. Probes that failed detection p > 0.01 in 1 or more samples were dropped (n = 2,699). An additional 43,096 probes annotated as cross reactive were also removed.

label: biotin and dinitrophenyl

source_name: cord blood

label_protocol: Illumina HD Methylation protocol

extract_protocol: DNA was extracted using the DNeasy Blood kit (Qiagen) per manufacturer instructions

tag: individual

tag: sample type

value: BuffyDNA

tag: slide id

tag: Sex

value: M

tag: race

value: White

tag: gestational age (weeks)


title: cord blood 5 buffy


title: cord blood 8 whole

value: WholeBloodDNA


title: cord blood 6 whole

value: F


title: cord blood 7 whole


title: microRNA profile of case T7


title: cord blood 5 whole


title: Ductal breast cancer 53

description: Sample 53

value: primary breast tumor tissue

tag: tnm

tag: Stage

value: IIIC

tag: histologic type

tag: size(cm)

tag: tubule formation

tag: nuclear pleomorhism score

tag: mitotic count

tag: histologic grade (nottingham)

tag: geographic necrosis

tag: tumor border

tag: stromal lymphocytosis

tag: vimentin


title: Ductal breast cancer 28

description: Sample 28

tag: tissue

tag: age at diagnosis

value: IIB

value: Ductal

value: N

tag: egfr

tag: death by last follow-up (y/n)

tag: disease-free interval (months)

tag: overall survival (months)

tag: disease state


title: cord blood 2 whole

tag: individual

tag: sample type

tag: slide id

tag: Sex

tag: race

tag: gestational age (weeks)


title: Ductal breast cancer 61.2

description: Sample 61.2

tag: tnm

tag: Stage

tag: histologic type

tag: size(cm)

tag: tubule formation

tag: nuclear pleomorhism score

tag: mitotic count

tag: histologic grade (nottingham)

tag: geographic necrosis

value: Infiltrating

value: triple negative breast cancer


title: cord blood 8 buffy


title: Ductal breast cancer 87

description: Sample 87

tag: tissue

tag: age at diagnosis

tag: tumor border

tag: stromal lymphocytosis

value: Y

tag: vimentin

tag: egfr

tag: death by last follow-up (y/n)

tag: disease-free interval (months)

tag: overall survival (months)


title: cord blood 4 whole

tag: individual

tag: sample type

tag: slide id

tag: Sex

tag: race

value: Asian Indian

tag: gestational age (weeks)


title: microRNA profile of case T71

tag: survival


title: microRNA profile of case T69


title: WT-6

source_name: mRNA extracts from a wild type yeast strain

tag: genotype/variation

value: Wild type

tag: culture stage


title: cord blood 2 buffy


title: cord blood 4 buffy


title: Ductal breast cancer 107

description: Sample 107

tag: tissue

tag: age at diagnosis

tag: tnm

tag: Stage

value: IIA

tag: histologic type

tag: size(cm)

tag: tubule formation

tag: nuclear pleomorhism score

tag: mitotic count

tag: histologic grade (nottingham)

tag: geographic necrosis

tag: disease state


title: cord blood 3 whole

tag: individual

tag: sample type

tag: slide id

tag: Sex

tag: race

value: More than one


title: WT-3

tag: genotype/variation

tag: culture stage

value: midlog phase yeast cells


title: Ductal breast cancer 16

description: Sample 16

tag: tissue

tag: age at diagnosis

tag: tnm

value: I

tag: tumor border

value: Expansile

tag: stromal lymphocytosis

tag: vimentin

tag: egfr

tag: death by last follow-up (y/n)

tag: disease-free interval (months)

tag: overall survival (months)


title: Ductal breast cancer 23

description: Sample 23

tag: Stage

tag: histologic type

tag: size(cm)

tag: tubule formation

tag: nuclear pleomorhism score

tag: mitotic count

tag: histologic grade (nottingham)

tag: geographic necrosis

tag: disease state


title: cord blood 6 buffy

tag: individual

tag: sample type

value: BuffyDNA

tag: slide id

tag: Sex

tag: race

value: White

tag: gestational age (weeks)


title: cord blood 1 whole

value: WholeBloodDNA

value: M


title: microRNA profile of case T66

tag: survival

tag: tissue

value: breast cancer


title: microRNA profile of case T67


title: microRNA profile of case T65


title: microRNA profile of case T64


title: WT-4

tag: genotype/variation

tag: culture stage


title: microRNA profile of case T63


title: Ductal breast cancer 62

description: Sample 62

value: primary breast tumor tissue

tag: age at diagnosis

tag: tnm

tag: Stage

tag: histologic type

value: Ductal

tag: size(cm)

tag: tumor border

tag: stromal lymphocytosis

tag: vimentin

tag: egfr

tag: death by last follow-up (y/n)

tag: disease-free interval (months)

tag: overall survival (months)


title: microRNA profile of case T62


title: cord blood 3 buffy

tag: individual

tag: sample type

tag: slide id

tag: Sex

value: F

tag: race

tag: gestational age (weeks)


title: Ductal breast cancer 15

description: Sample 15

tag: tissue

tag: age at diagnosis

tag: tnm

tag: tubule formation

tag: nuclear pleomorhism score

tag: mitotic count

tag: histologic grade (nottingham)

tag: geographic necrosis

value: N

value: Infiltrating

tag: disease state

value: triple negative breast cancer


title: Ductal breast cancer 59

description: Sample 59

tag: Stage

tag: histologic type

tag: size(cm)

tag: tumor border

tag: stromal lymphocytosis

tag: vimentin

tag: egfr

tag: death by last follow-up (y/n)

tag: disease-free interval (months)


title: cord blood 1 buffy

tag: individual

tag: sample type

tag: slide id

tag: Sex

tag: race

tag: gestational age (weeks)


title: Ductal breast cancer 60

description: Sample 60

tag: tissue

tag: age at diagnosis

tag: tnm

tag: tubule formation

tag: nuclear pleomorhism score

tag: mitotic count

tag: histologic grade (nottingham)

tag: geographic necrosis

tag: overall survival (months)


title: microRNA profile of case T60

tag: survival


title: Micropapillary breast cancer 66

description: Sample 66

source_name: Micropapillary breast cancer

tag: Stage

value: IIIC

tag: histologic type

value: Micropapillary

tag: size(cm)

tag: tumor border

tag: stromal lymphocytosis

value: Y

tag: vimentin

tag: egfr

tag: death by last follow-up (y/n)

tag: disease-free interval (months)

tag: disease state


title: Ductal breast cancer 81.2

description: Sample 81.2

tag: tissue

tag: age at diagnosis

tag: tnm

value: IIA

tag: tubule formation


title: Ductal breast cancer 113

description: Sample 113

tag: nuclear pleomorhism score

tag: mitotic count

tag: histologic grade (nottingham)

tag: geographic necrosis


title: microRNA profile of case T6

tag: survival


title: Ductal breast cancer 136

description: Sample 136

tag: Stage

tag: histologic type

tag: size(cm)

tag: overall survival (months)


title: Medullary breast cancer 120

description: Sample 120

source_name: Medullary breast cancer

value: Medullary

tag: tumor border

tag: stromal lymphocytosis

tag: vimentin

tag: egfr


title: microRNA profile of case T58

tag: tissue


title: Ductal breast cancer 21

description: Sample 21

tag: age at diagnosis

value: Expansile

tag: death by last follow-up (y/n)

tag: disease-free interval (months)

tag: disease state


title: Ductal breast cancer 61.1

description: Sample 61.1

tag: tnm

tag: tubule formation

tag: nuclear pleomorhism score

tag: mitotic count


title: Ductal breast cancer 81.1

description: Sample 81.1

tag: Stage

tag: histologic grade (nottingham)

tag: geographic necrosis


title: microRNA profile of case T57

tag: survival


title: Ductal breast cancer 142

description: Sample 142

value: I

tag: histologic type

tag: size(cm)

tag: tumor border

tag: overall survival (months)


title: Medullary breast cancer 117

description: Sample 117

tag: tissue

value: IIB

tag: stromal lymphocytosis

tag: vimentin

tag: egfr


title: Ductal breast cancer 103

description: Sample 103

tag: age at diagnosis

tag: death by last follow-up (y/n)

tag: disease-free interval (months)

tag: disease state


title: microRNA profile of case T55


title: microRNA profile of case T56


title: 6W_old_rosette_leaves_non_acclimated_replicate_3 [Sah-0_NA_R3]

description: Gene expression for non acclimated Sah-0 rosette leaves. RNA was hybridized on Agilent Arabidopsis expression array

organism: Arabidopsis thaliana

source_name: 6-week-old rosette leaves, non-acclimated

tag: accession

value: rosette leaves


title: Macrophage cell, D6 Male, LPS 24 h, 7 Prednisolone

city: Midlothian

first: Tim

last: Regan

address: Easter Bush Campus

department: Genetics and genomics

country: United Kingdom

institute: The Roslin Institute, University of Edinburgh

hyb_protocol: Labeled cDNA (3.5 ug) was then hybridized to the GeneChip Human Gene 2.1 ST array (Affymetrix, Inc.) using the Affymetrix GeneTitan® MC Instrument with the   GeneTitan® Hybridization, Wash, and Stain Kit for WT Array Plates.

scan_protocol: Scanning was performed on the Affymetrix GeneTitan® MC Instrument

data_processing: CEL files were assessed for quality using arrayQualityMetrics (AQM), a Bioconductor R package. Samples which failed 2 or more tests were discounted from the dataset. The matrix was then subject to RMA normalisation and probesets were reduced to a single gene. Statistical analysis was performed using lme4, another Bioconductor R package. Each donor was set as a random effect while drug or inflammatory treatments were set as fixed effects for each analysis.

source_name: human monocyte derived macrophage

label_protocol: Total RNA (500 ng) was reverse transcribed and the single stranded cDNA was amplified using the Ambion WT Expression Kit (Life Technologies, Inc.). The purified cDNA (5.5 μg) was subsequently fragmented and labeled using the GeneChip WT Terminal Labeling Kit (Affymetrix Inc., Santa Clara, CA, U.S.A.)

growth_protocol: Freshly isolated CD14+ monocytes were seeded at a density of 4x10E5/well on 12-well NUNC coated plates in RPMI with 10% FCS 1% pen/Strep and rh-CSF-1 for 1 week until they had transformed into macrophage-like cells.

extract_protocol: Following tretment, supernatant was removed and 350 µl of Rneasy buffer RLT (Qiagen, Skelton House, Manchester, UK) was added to each well and plates were frozen at -80C. RNA extraction was performed using the Rneasy column extraction kit with on column DNase digestion according to the manufacturers protocol.

treatment_protocol: For each treatment, cells were supplemented with the inflammatory stimuli +/- drugs at the same time for 7 or 24 h. Cells were subject to inflammatory stimulus with LPS (10 ng/ml) or IFNα (50 U/ml) for 7 or 24 h or incubated for 24 h with no inflammatory stimulus. In each of these 5 conditions, cells were treated for the same amount of time with either vehicle control (DMSO), escitalopram (1 µM, SSRI antidepressant), nortriptyline (100 nM, tricyclic antidepressant), anti-TNFα (5 µg/ml, neutralising antibody anti-inflammatory), indomethacin (100 µM, non-steroidal anti-inflammatory), prednisolone (1 µM, steroidal anti-inflammatory) or left untreated.

value: blood

tag: cell type

value: monocyte derived macrophage

tag: donor

tag: Sex

value: M

tag: inflammatory stimulus

value: LPS 24 h

tag: drug treatment

value: 7 Prednisolone


title: Ductal breast cancer 95

description: Sample 95

value: primary breast tumor tissue

tag: tnm

tag: Stage

tag: histologic type

value: Ductal

tag: size(cm)

tag: tubule formation

tag: nuclear pleomorhism score

tag: mitotic count

tag: histologic grade (nottingham)

tag: geographic necrosis

value: N


title: 6W_old_rosette_leaves_2W_cold_acclimated_replicate_3 [Sah-0_ACC_R3]

description: Gene expression for 2 weeks cold acclimated Sah-0 rosette leaves at 4 °C. RNA was hybridized on Agilent Arabidopsis expression array

source_name: 6-week-old rosette leaves, 2-week cold-acclimated

tag: tissue


title: 6W_old_rosette_leaves_non_acclimated_replicate_2 [Sah-0_NA_R2]


title: 6W_old_rosette_leaves_2W_cold_acclimated_replicate_2 [Sah-0_ACC_R2]


title: microRNA profile of case T54

tag: survival

value: breast cancer


title: Macrophage cell, D6 Male, LPS 24 h, 6 Indomethacin

value: 6 Indomethacin


title: Macrophage cell, D6 Male, LPS 24 h, 5 Anti-TNFa

value: 5 Anti-TNFa


title: Macrophage cell, D6 Male, LPS 24 h, 1 Untreated

value: 1 UNT


title: 6W_old_rosette_leaves_non_acclimated_replicate_3 [N13_NA_R3]

description: Gene expression for non acclimated N13 rosette leaves. RNA was hybridized on Agilent Arabidopsis expression array

tag: accession