title: Cattle2- day 3

status: Public on Oct 20 2017

city: Bengaluru

first: Suresh

last: Basagoudanavar

state: Karnataka

address: IVRI, Hebbal

department: FMD Research Laboratory

institute: Indian Veterinary Research Institute

description: Circulating miRNA in serum of cattle 72 h after contacting FMDV infection

hyb_protocol: The labeled cRNA samples were hybridized on to a Whole Genome Bos indicus 8x60k (AMADID: 072447). 200ng of Cyanine 3-pCp labeled miRNA sample were hybridized.  The hybridization was carried out at 55°C for 20 hours. After hybridization, the slides were washed using Gene Expression Wash Buffer1 (Agilent Technologies, Part Number 5188-5325) at room temperature for 5 minutes and Gene Expression Wash Buffer 2 (Agilent Technologies, Part Number 5188-5326) at 37°C for 5 minutes.

scan_protocol: Slides were scanned using the Agilent Microarray Scanner G2600D scanner at 3 micron resolution.

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the 90th percentile shift.

organism: Bos indicus

source_name: Serum Cattle 2- day 3

label_protocol: The samples for miRNA expression were labeled using Agilent complete miRNA labeling and Hybridization Kit Cat # 5190-0456. 200ng of total RNA was dephosphorylated using Calf Intestinal Alkaline Phosphatase (CIP) master mix (Agilent Technologies, Part Number: 5190-0456) by incubating at 37oC for 30 minutes. The dephosphorylated miRNA sample was denatured by adding Dimethyl Sulfoxide and heating at 100°C for 10 minutes and transferred to ice-water bath. The Ligation master mix (Agilent Technologies, Part Number: 5190-0456) containing Cyanine 3-pCp was added to the denatured miRNA sample and incubated at 16°C for 2 hours. The Cyanine 3-pCp labeled miRNA sample was dried completely in the vacuum concentrator (Eppendorf, Concentrator Plus, Catalog Number 5305000) at 45°C for 2 hour. The dried sample was resuspended in nuclease free water and mixed with Hybridization Mix containing blocking solution (Agilent Technologies, Part Number: 5190-0456) and Hi-RPM Hybridization Buffer (Agilent Technologies, Part Number: 5190-0456) and incubated at 100°C for 5 minutes followed by snap chill on ice for 5 minutes.

growth_protocol: Cattle were experimentally infected with FMDV serotype ‘O’ by contact challenge. Serum was collected at 0, 24, 48 and 72 hours post contact with infected cattle. MicroRNAs from the serum  were analysed for differential expression.

extract_protocol: Isolation of RNA from serum samples was carried out by using Qiamp Circulating Nucleic Acid Kit (Cat # 55114)    (Qiagen, Cat # 55114).

treatment_protocol: Experimental infection of 6-9 month-old Indian cattle (Bos Indicus) with FMDV serotype ‘O’ by contact exposure

tag: sample type

value: Cattle2- 72 h post contact

tag: source

value: serum


title: Cattle2- day 2

type: RNA

middle: H

country: India

description: Circulating miRNA in serum of cattle 48 h after contacting FMDV infection

molecule: total RNA

source_name: Serum Cattle 2- day 2

value: Cattle2- 48 h post contact


title: Cattle2- day 0

description: Circulating miRNA in serum of cattle before contacting FMDV infection

source_name: Serum Cattle 2- day 0

value: Cattle2- control


title: Cattle2- day 1

description: Circulating miRNA in serum of cattle 24 h after contacting FMDV infection

source_name: Serum Cattle 2- day 1

value: Cattle2- 24 h post contact


title: MC [NM08_ATH1]

status: Public on Oct 22 2017

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

description: Gene expression of mesophyll cells

hyb_protocol: according to the instruction manual, as described in the Affymetrix website

data_processing: RMA normalization, summarization by mean, all were done by Partek Genomics suite (version 6.6) Copyright © 2012).

label: biotin

organism: Arabidopsis thaliana

source_name: Protoplast

label_protocol: Labeled RNA was hybridized to Affymetrix GeneChip® Arabidopsis ATH1 Genome Array (ATH1-121501), at the Biological Services unit of the Weizmann Institute of Science, Israel. We used three biological replicates for each cell type (BSCs and MCs).

growth_protocol: Individual bundle sheath protoplasts (with a diameter of 25-30 µm) were identified by their GFP fluorescence and the mesophyll protoplasts (with a diameter of 40-45 µm) – by their lack of fluorescence. Single type leaf protoplasts  were collected manually with as little solution as possible using a home-made plastic suction pipette (with a tip aperture of 200 µm; transferred into a 1.5 ml Eppendorf tube and flash-frozen in liquid nitrogen. The frozen samples were kept at -80ºC until further analysis.

extract_protocol: Total RNA was extracted from a pool of 20 single-type protoplasts using ExpressArt LCM RNAready LCM RNA isolation kit (C#9001-A100, AmpTec, Germany) according to the manufacturer’s protocol, except no vortex was used at any stage of the extraction (to preserve RNA quality), and with the addition of a pooling procedure.

treatment_protocol: No treatment

tag: cell type

value: mesophyll cells (MC)


title: BS [NM05_ATH1]

description: Gene expression of bundle sheath

scan_protocol: according to the instruction manual, as described in the Affymetrix website

value: bundle sheath (BS)


title: MCF10A_wt_7d_1

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

country: Germany

institute: University of Lübeck

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: All arrays were normalized together using the quantile normalization algorithm without background subtraction using the R Bioconductor beadarray package

label: Biotin

organism: Homo sapiens

source_name: MCF10A untreated after 7 days, rep1

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

growth_protocol: MCF10A cells were purchased from ATCC. MCF10Atet cells, constitutively expressing a Tet-regulated transcriptional transactivator, were provided by  T. Brummer (IMMZ, Freiburg, Germany). Both wild-type and stably transfected cell lines were maintained in growth medium consisting of DMEM/F12 supplemented with 5% horse serum, 10 µg/ml insulin, 0.5 µg/ml hydrocortisone, 20 ng/ml EGF and 0.1 µg/ml cholera toxin. Stable cell lines inducible for Rho overexpression were generated via nucleofection (AMAXA®) with the AhdI-linearized pWHE636 vector containing wild-type cDNA of RhoA or RhoC along with GFP and promoter binding sites for the Tet-regulated transcriptional transactivator (cf. Herr et al., Cell Comm Signaling, 2011 and Danke et al., J Gene Med, 2010).

extract_protocol: Total RNA was isolated from isolated tumor cells using the RNeasy Plus Mini Kit (Qiagen, 74136)

treatment_protocol: Doxycycline for the induction of transgenic overexpression was purchased from Sigma and added at 2 ug/ml before harvesting the cells at 1 and 7 days. CNF toxins were purified as described previously and used at 2 nM for the indicated time periods of 1 and 7 days (Reipschläger et al., JBC 2012). Inhibitors, toxins and inducers were renewed every 2-3 days with every medium exchange.

tag: cell line

tag: replicate

value: Replicate 1

tag: stimulus duration

value: 7 Days

tag: transfection

value: untransfected

tag: stimulus

tag: array id


title: MCF10A_CNF1_1d_1

source_name: MCF10A CNF1 treated after 1 day, rep1

value: 1 Day


title: Cattle1- day 0

source_name: Serum Cattle 1- day 0

value: Cattle1- control


title: BS [NM07_ATH1]

description: Gene expression of bundle sheath


title: Cattle1- day 1

source_name: Serum Cattle 1- day 1

value: Cattle1- 24 h post contact


title: Cattle1- day 2

source_name: Serum Cattle 1- day 2

value: Cattle1- 48 h post contact


title: MCF10A_wt_1d_1

source_name: MCF10A untreated after 1 day, rep1


title: MCF10A_CNF1_7d_1

source_name: MCF10A CNF1 treated after 7 days, rep1


title: MC [NM04_ATH1]

description: Gene expression of mesophyll cells


title: Cattle1- day 3

source_name: Serum Cattle 1- day 3

value: Cattle1- 72 h post contact


title: MCF10A_CNF1_7d_2

source_name: MCF10A CNF1 treated after 7 days, rep2

value: Replicate 2


title: MC [NM06_ATH1]

description: Gene expression of mesophyll cells


title: MCF10A_CNF1_1d_2

source_name: MCF10A CNF1 treated after 1 day, rep2


title: BS [NM03_ATH1]

description: Gene expression of bundle sheath


title: MCF10A_wt_7d_2

source_name: MCF10A untreated after 7 days, rep2


title: MCF10A_wt_1d_2

source_name: MCF10A untreated after 1 day, rep2


title: LT_G12_35

city: King of Prussia

first: Guanghui

last: Hu

state: PA

address: 709 Swedeland Road

country: USA

institute: GlaxoSmithKline

description: Smoke - Group 1 12w

hyb_protocol: Hybridization cocktails were prepared in accordance with NuGEN protocols. Cocktails were then hybridized to mouse 430_2 whole genome Gene Chips in two batches, in accordance with Affymetrix protocols.

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

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.

organism: Mus musculus

source_name: Lung tissue frozen in RNA Later for TA

label_protocol: For each sample, 50ng of total RNA was converted to amplified antisense sscDNA using the NuGEN Ovation RNA Amplification System V2, following manufacturer's instructions. cDNAs were purified using the Agencourt AMPure Magnetic Bead Purification System. The amplified cDNA concentrations were determined by measurement on a Thermo Electron Varioskan spectral scanning multimode reader and quality was assessed by nano chips on an Agilent 2100 bioanalyser. 4.4ug of amplified cDNA was fragmented and biotin-labelled using the FL-Ovation cDNA Biotin Module V2 (NuGEN Technologies).

growth_protocol: Female C57BL/6 mice were purchased from Jackson Laboratory (Bar Harbor, ME)

extract_protocol: Mouse small lobe lung tissue was preserved in RNALater (Qiagen) and stored at -80C. Samples were randomized and total RNA was extracted using a Polytron type homogeniser (YellowLine DI 25 Basic ) and TriZol reagent (Invitrogen, Paisley, UK) in a ratio of 1ml of TriZol to 20mg of tissue. RNA was further purified using RNeasy 96 universal tissue version 1.0   protocol on a Qiagen Biorobot 8000, including on-column DNAse-1 step and elution in water. The quantity of extracted RNA was determined using a Thermo Electron Varioskan spectral scanning multimode reader and quality was assessed using nano and pico chips on an Agilent 2100 bioanalyser (South Plainfield, NJ, USA). RNA yields were in the range of  1.4-5.4ug (Av. 3.5ug). All samples were of good quality as ascertained on the bioanalyser.

treatment_protocol: Mice received nose-only exposure of 4% mainstream cigarette smoke or air (sham exposure) for 2 hours/day, 5 days/week for 2, 12 or 24 weeks.  Mice undergoing smoke cessation received cigarette smoke exposure for 12 weeks, and then sham exposure for 12 weeks.

tag: tissue

value: Mouse small lobe lung

tag: age

tag: group

value: smoke


title: LT_G1_79

description: Smoke - Group 1 12w


title: LT_I1_57

description: Forced Air - Group 1 24w

value: forced air


title: LT_D2_22

description: Smoke - Group 1 2w


title: LT_A11_77

description: Untreated - Group 1 0m

value: untreated


title: LT_D6_85

description: Smoke - Group 1 2w


title: LT_G11_72

description: Smoke - Group 1 12w


title: LT_J8_59

description: Smoke - Group 1 24w


title: LT_D4_71

description: Smoke - Group 1 2w


title: LT_I30_53

description: Forced Air - Group 1 24w


title: LT_K25_33

description: Smoke to Forced Air - Group 1 24w

value: smoke to forced air


title: LT_J12_52

description: Smoke - Group 1 24w


title: LT_L28_82

description: Smoke to Room Air - Group 1 24w

value: smoke to room air


title: LT_I29_32

description: Forced Air - Group 1 24w


title: LT_L9_4

description: Smoke to Room Air - Group 1 24w


title: LT_K12_64

description: Smoke to Forced Air - Group 1 24w


title: LT_A7_31

description: Untreated - Group 1 0m


title: LT_L27_42

description: Smoke to Room Air - Group 1 24w


title: LT_K29_60

description: Smoke to Forced Air - Group 1 24w


title: LT_L11_87

description: Smoke to Room Air - Group 1 24w


title: LT_L30_158

description: Smoke to Room Air - Group 1 24w


title: LT_J5_18

description: Smoke - Group 1 24w


title: LT_K7_91

description: Smoke to Forced Air - Group 1 24w


title: LT_F2_8

description: Forced Air - Group 1 12w


title: LT_I5_2

description: Forced Air - Group 1 24w


title: LT_I11_23

description: Forced Air - Group 1 24w


title: LT_K11_29

description: Smoke to Forced Air - Group 1 24w


title: LT_F8_54

description: Forced Air - Group 1 12w


title: LT_D10_5

description: Smoke - Group 1 2w


title: LT_D12_157

description: Smoke - Group 1 2w


title: LT_D5_122

description: Smoke - Group 1 2w


title: LT_F4_145

description: Forced Air - Group 1 12w


title: LT_C5_138

description: Forced Air - Group 1 2w


title: LT_L5_141

description: Smoke to Room Air - Group 1 24w


title: LT_G2_154

description: Smoke - Group 1 12w


title: LT_C3_137

description: Forced Air - Group 1 2w


title: LT_A3_144

description: Untreated - Group 1 0m


title: LT_C4_134

description: Forced Air - Group 1 2w


title: LT_C10_105

description: Forced Air - Group 1 2w


title: LT_F9_127

description: Forced Air - Group 1 12w


title: LT_C8_120

description: Forced Air - Group 1 2w


title: LT_g8_117

description: Smoke - Group 1 12w


title: LT_A8_139

description: Untreated - Group 1 0m


title: LT_C6_130

description: Forced Air - Group 1 2w


title: LT_J10_121

description: Smoke - Group 1 24w


title: LT_F1_124

description: Forced Air - Group 1 12w


title: LT_A5_112

description: Untreated - Group 1 0m


title: LT_J6_131

description: Smoke - Group 1 24w


title: LT_I4_115

description: Forced Air - Group 1 24w


title: siSFPQ_rep3

city: Nice

first: Silvia

last: Bottini

address: 299, chemin de la ginestiere

country: France

hyb_protocol: Agilent : 600.0 ng at 65 degree_C during 17 hours

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner

data_processing: Feature extraction data processing. Quantile normalization and differential analysis using Limma package in R / Bioconductor

source_name: P19 cells

label_protocol: RNA samples were labeled with Cy3 dye using the low RNA input QuickAmp kit (Agilent)

extract_protocol: RNA extraction was performed with miRNeasy columns (Qiagen), according to manufacturer's instructions

tag: condition

value: SFPQ knockdown


title: siSFPQ_rep4


title: LT_F5_100

description: Forced Air - Group 1 12w


title: LT_J29_114

description: Smoke - Group 1 24w


title: siSFPQ_rep2


title: let7+siSFPQ_rep3

value: let-7a overexpression and SFPQ knockdown


title: let7+siSFPQ_rep4


title: LT_K26_152

description: Smoke to Forced Air - Group 1 24w


title: LT_A9_101

description: Untreated - Group 1 0m


title: siSFPQ_rep1


title: let7_rep3

value: let-7a overexpression


title: let7+siSFPQ_rep1


title: let7_rep2


title: 347T_tumor

type: genomic

city: Vejle

first: Mariana

last: Bisarro dos Reis

address: Kabbeltoft 25

country: Denmark

institute: Vejle Hospital

hyb_protocol: Bisulphite modified DNA was amplified, fragmented and hybridized in the Illumina Hybridization Oven according the standard Illumina protocol.

scan_protocol: Arrays were imaged using the HiScan system (Illumina).

data_processing: Methylation data were analyzed as β values. Probes were also filtered, using WateRmelon package, for low bead count (<3) and low quality (p detection >0.05). Samples having 1% of sites with a detection p-value > 0.05 were also removed. Data was adjusted for color bias, inter-sample normalization and corrected using BMIQ normalization. The batch effects were corrected using sva package.

molecule: genomic DNA

source_name: tumor tissue

label_protocol: Standard Illumina Protocol

growth_protocol: Not applicable

extract_protocol: Tumor and non-neoplastic adjacent tissues were macro-dissected and genomic DNA extracted using a standard phenol/chloroform method.

treatment_protocol: Genomic DNA samples were bisulfite-modified using EZ DNA Methylation Gold kit D5006 (Zymo Research, Irvine, CA, USA) according to the Illumina recommendation.

tag: histology

value: papillary thyroid cancer

tag: gender

value: Female

tag: race

value: Caucasian

tag: variant

value: Follicular + oncocitic


title: ctrl_rep4

value: control


title: let7_rep1


title: ctrl_rep3


title: let7+siSFPQ_rep2


title: ctrl_rep2


title: YAPtg #1

status: Public on Oct 19 2017

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description:
HYP487
Primary isolated hepatocytes derived from YAP(S127A) transgenic mice. Livers showed hyperplasia. Biological replicate #1.

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner 3000.

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of mouse MoGene-2_0-type from Affymetrix. A Custom CDF Version 20 with Entrez Gene-based gene definitions was used to annotate the arrays. The raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Median polish Probeset Summary.

source_name: hepatocytes isolated from YAP(S127A) transgenic mice

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

growth_protocol: C57/Bl6N (10-12 weeks) and LapYAP_AlbJag1 (10 weeks after induction) were used for the isolation of primary hepatocytes. Following i.p. anaesthesia (ketamine and xylazine), portal veins were incised, cannulated and perfused with EGTA and Collagenase buffer (Sigma Aldrich). Forceps-based mechanical removement of the liver capsule allowed the release of the digested hepatocytes and low velocity centrifugation was used to remove non parenchymal cells. Hepatocytes were seeded on Collagen 1 coated cellware (Corning) and Williams E medium (Biochrom) supplemented with FCS, L-glutamine, insulin and dexamethasone. Medium was changed once 4 hours after isolation to remove non-adherent cells. RNA of primary hepatocytes was extracted after over-night cultivation and RNA integrity measured prior to expression profiling analysis (RIN >8).

extract_protocol: For isolation of total RNA, the NucleoSpin RNA II kit (Machery-Nagel, Düren, Germany) was used.

treatment_protocol: Cultured for 24 hours.

tag: genotype/variation

value: YAP(S127A) transgenic

tag: disease status

value: liver hyperplasia

value: hepatocytes


title: ctrl_rep1


title: N31+W20_rep1

city: Kyoto

first: Takashi

last: Ikeda

address: 53 Shogoin Kawahara-cho Sakyo-ku

country: Japan

institute: Kyoto Univ.

description: W20-expressing NPCs

hyb_protocol: 600 ng 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 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Microarray 4x44K G4122F for 17 hours at 65°C in a rotating 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 setting for 4x44K array slides.

data_processing: The array data were analyzed using GeneSpring software (Agilent). Gene expression values were normalized by excluding low-signal intensity data and percentile shifts.

source_name: mouse ESC-derived neural progenitor cells

label_protocol: Microarray experiments were performed according to the manufacturer’s instruction. Twenty hundred nanograms of total RNA was labelled with cyanine 3-CTP and hybridized in Whole Mouse Genome Microarray 4x44K G4122F (Agilent Technologies).

growth_protocol: Neural progenitor cells cells were maintained on a gelatin-coated culture plate in an NPC medium, RHB basal (StemCells, Inc) containing the epidermal growth factor (EGF) (Peprotech) at 10 ng/ml and the human basic fibroblast growth factor (bFGF) (Peprotech) at 10 ng/ml.

extract_protocol: Total RNA was extracted using the RNeasy Kit (QIAGEN) and was assessed by Agilent 2100 Bioanalyzer and the RNA 6000 LabChip Kit (Agilent Technologies).

tag: cell type

value: neural progenitor cells


title: let7_rep4


title: N31+EGFP_rep2

description: control NPC cells

tag: cell line


title: YAPtg #3

description:
HYP512
Primary isolated hepatocytes derived from YAP(S127A) transgenic mice. Livers showed hyperplasia. Biological replicate #3.


title: YAPtg #2

description:
HYP508
Primary isolated hepatocytes derived from YAP(S127A) transgenic mice. Livers showed hyperplasia. Biological replicate #2.


title: N31+W20_rep2

description: W20-expressing NPCs


title: N31+EGFP_rep1

description: control NPC cells


title: wt #3

description:
WT5
Primary isolated hepatocytes derived from wildtype as control. Biological replicate #3.

source_name: hepatocytes isolated from WT mice

tag: strain/background

value: WT

value: normal liver


title: LIFR KO mESCs

city: Shanghai

first: Naihe

last: Jing

state: Shanghai

address: 320 Yueyang road

country: China

institute: Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

hyb_protocol: Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242):

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (Agilent p/n G2565BA) using one color scan setting for GE_4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and High 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: LIFR KO mESCs

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1.65 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: mESCs were cultured under standard conditions

extract_protocol: Total RNA was extracted with Trizol reagents.

value: LIFR KO

value: mESCs


title: wt #1

description:
WT2
Primary isolated hepatocytes derived from wildtype as control. Biological replicate #1.


title: wildtype mESCs

source_name: wildtype mESCs

value: wildtype


title: wt #2

description:
WT3
Primary isolated hepatocytes derived from wildtype as control. Biological replicate #2.


title: gp130 KO mESCs

source_name: gp130 KO mESCs

value: gp130 KO


title: C08

status: Public on Oct 18 2017

city: Ilsan

first: Jinyeong

last: Lim

address: Ilsan

country: South Korea

institute: National Cancer Center

description: 200118400057_A _Grn

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina Expression BeadChip according to the protocols provided by the manufacturer.

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader Confocal Scanner.

data_processing:
Array data export processing and analysis was performed using Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0). Normalization was performed using background correction using negative control probes and quantile normalization using negative and positive control probes.
R 3.3.2-software were used for analysis.

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin,TX).

growth_protocol: GCTB stromal cells in DMEM medium supplemented with 10% fetal bovine serum (FBS) and 5ug/ml of Gentamycin at 37C in a 5% CO2 pressure.

extract_protocol: To extract total RNA, we collected the cultured GCTB cell with 0.25% EDTA-trypsin and crushed biopsy samples using the Beads. We used QIAGEN RNeasy mini kit followed the standard protocol. QIAshredder spin columns and DNase I digestion step was included.

value: GCTB primary cell line

value: male

tag: ethnicity

value: Asian

tag: disease

value: Giant cell tumor of the bone (GCTB)

tag: h3f3a status


title: C09

description: 200118400057_B _Grn

value: female


title: C10

description: 200118400057_C _Grn


title: GF2-7

value: GCTB biopsy tissue


title: GF1-16


title: 587N_benign

source_name: benign lesion

value: lymphocytic thyroiditis

value: Female

value: Caucasian


title: WF1-9


title: GF2-5


title: C05


title: WM1-6


title: WM2-6


title: dkfzC-AX


title: GM2-1


title: GF1-22


title: GM1-15


title: WF1-2


title: GM1-21


title: dkfzC-KM1234

value: mesenchymal stem cell line


title: aeccC-FOB

value: osteoblast cell line


title: GM1-17


title: dkfzC-AW


title: 538N_benign


title: dkfzC-AS


title: dkfzC-AU


title: 535N_benign


title: C06


title: dkfzC-AT


title: T47D-MUT mouse Oas2 [+DOX]-rep3

city: Sydney

first: Daniel

last: Roden

state: NSW

address: 384 Victoria Street

country: Australia

institute: Garvan Institute

hyb_protocol: cDNA was then labeled and hybridized to the Affymetrix Human Transcriptome Array 2.0 as per the manufacturer's instructions (Affymetrix, CA, USA) at Ramiaciotti Centre for Genomics (UNSW, Sydney Australia).

scan_protocol: Arrays were scanned at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales (UNSW, Sydney, NSW, Australia), following manufacturer's instructions.

data_processing: Data was RMA normalised using the Affymetrix Power Tools apt-probeset-summarize software (version 1.16.1) (using the -a rma option). The HTA-2_0.r1.gene.cdf file was used. No additional filtering was performed.

source_name: T47D cell line, MUT mouse Oas2, +DOX

label_protocol: Total RNA was converted to cDNA. The cDNA was fragmented, biotin labeled at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales (UNSW, Sydney, NSW, Australia), following manufacturer's instructions.

extract_protocol: Total RNA was isolated using Trizol reagent (Gibco/Invitrogen, Vic) and measured on the 2100 Bioanalyzer (Agilent).

tag: cell line type

value: luminal-like breast cancer

tag: mouse oas2 expression

value: mutant Oas2

tag: doxycycline

value: +DOX


title: dkfzC-AQ


title: dkfzC-AR


title: T47D-MUT mouse Oas2 [-DOX]-rep2

source_name: T47D cell line, MUT mouse Oas2, -DOX

value: -DOX


title: T47D-WT mouse Oas2 [+DOX]-rep2

source_name: T47D cell line, WT mouse Oas2, +DOX

value: WT


title: dkfzC-AO


title: T47D-WT mouse Oas2 [-DOX]-rep3

source_name: T47D cell line, WT mouse Oas2, -DOX


title: T47D-WT mouse Oas2 [+DOX]-rep3


title: T47D-MUT mouse Oas2 [+DOX]-rep1


title: T47D-WT mouse Oas2 [+DOX]-rep1


title: T47D-WT mouse Oas2 [-DOX]-rep1


title: dkfzC-AP


title: T47D-MUT mouse Oas2 [+DOX]-rep2


title: T47D-MUT mouse Oas2 [-DOX]-rep1


title: T47D-WT mouse Oas2 [-DOX]-rep2


title: mammary_gland-Oas2_MT_2dpc-rep2

hyb_protocol: cDNA was then labeled and hybridized to the Affymetrix Mouse Transcriptome Array 1.0 as per the manufacturer's instructions (Affymetrix, CA, USA) at Ramiaciotti Centre for Genomics (UNSW, Sydney Australia).

data_processing: Data was RMA normalised using the Affymetrix Power Tools apt-probeset-summarize software (version 1.16.1) (using the -a rma option).

source_name: Mammary gland, MUT Oas2, 18dpc

growth_protocol: wt/wt or mt/mt mice were time mated, and mammary glands were collected at day 18 of pregnancy or 2 days after parturition (2 dpp) and snap frozen in liquid N2.

value: C57BL/6 and CBA/CaJ

value: Oas2 mutant

tag: tissue

value: mammary gland

tag: time point


title: mammary_gland-Oas2_MT_2dpp-rep2

source_name: Mammary gland, MUT Oas2, 2dpp


title: mammary_gland-Oas2_WT_2dpp-rep2

source_name: Mammary gland, WT Oas2, 2dpp


title: mammary_gland-Oas2_WT_2dpp-rep1


title: mammary_gland-Oas2_WT_2dpp-rep3


title: mammary_gland-Oas2_MT_2dpc-rep3


title: mammary_gland-Oas2_WT_2dpc-rep3

source_name: Mammary gland, WT Oas2, 18dpc


title: mammary_gland-Oas2_MT_2dpp-rep1


title: mammary_gland-Oas2_MT_2dpp-rep3


title: mammary_gland-Oas2_MT_2dpc-rep1


title: TC32 cell line, treated for 6 hours with THZ_5_31_1 500nM, biological rep 2

city: Cambridge

first: Gabriela

last: Alexe

state: MA

address: 415 Main St.

department: Computational Biology and Bioinformatics

institute: Broad Institute

description: RNA was extracted from Ewing sarcoma cells using the RNeasy kit (Qiagen) according to manufacturer’s instruction.  ERCC RNA Spike-In Mix (Ambion) was added to total RNA as previously described in Cell. 2012 Oct 26; 151(3): 476–482. doi:  10.1016/j.cell.2012.10.012

hyb_protocol: FS450_0002 for the Human GeneChip PrimeView arrays

scan_protocol: Affymetrix GeneChip Scanner 7G

data_processing: Microarray Suite 5.0 with spike-in normalization and collapsed to RefSeq GRCh37/hg19 genes, as described in Cell. 2012 Oct 26; 151(3): 476–482. doi:  10.1016/j.cell.2012.10.012.

source_name: TC32 cell line, treated with THZ_5_31_1 500nM

label_protocol: biotin

growth_protocol: A673 and TC32 cells were maintained in DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin with glutamine

treatment_protocol: A673 and TC32 cells were treated in duplicate with either DMSO, THZ_5_31_1 100 nM  or  THZ_5_31_1 500 nM  for 6 hours

tag: treatment

tag: dose

tag: time

value: 6 hours


title: TC32 cell line, treated for 6 hours with THZ_5_31_1 500nM, biological rep 1

extract_protocol: RNA was extracted from Ewing sarcoma cells using the RNeasy kit (Qiagen) according to manufacturer’s instruction.  ERCC RNA Spike-In Mix (Ambion) was added to total RNA as previously described in Cell. 2012 Oct 26; 151(3): 476–482. doi:  10.1016/j.cell.2012.10.012


title: mammary_gland-Oas2_WT_2dpc-rep2

tag: gender


title: TC32 cell line, treated for 6 hours with DMSO, biological rep 2

source_name: TC32 cell line, treated with DMSO

value: DMSO


title: C07

value: GCTB primary cell line

value: female

value: Asian

value: Giant cell tumor of the bone (GCTB)


title: TC32 cell line, treated for 6 hours with THZ_5_31_1 100nM, biological rep 2

source_name: TC32 cell line, treated with THZ_5_31_1 100nM


title: TC32 cell line, treated for 6 hours with DMSO, biological rep 1


title: TC32 cell line, treated for 6 hours with THZ_5_31_1 100nM, biological rep 1


title: A673 cell line, treated for 6 hours with THZ_5_31_1 500nM, biological rep 1

source_name: A673 cell line, treated with THZ_5_31_1 500nM


title: A673 cell line, treated for 6 hours with DMSO, biological rep 2

source_name: A673 cell line, treated with DMSO


title: A673 cell line, treated for 6 hours with THZ_5_31_1 500nM, biological rep 2


title: A673 cell line, treated for 6 hours with THZ_5_31_1 100nM, biological rep 2

source_name: A673 cell line, treated with THZ_5_31_1 100nM


title: A673 cell line, treated for 6 hours with DMSO, biological rep 1


title: A673 cell line, treated for 6 hours with THZ_5_31_1 100nM, biological rep 1


title: Control 0hr II

status: Public on Oct 17 2017

city: London

first: ajay

last: Mishra

address: Great Maze Pond

department: Centre for Stem Cells and Regenerative Medicine

country: United Kingdom

institute: King's College London

description: replicate 2

data_processing: The data were normalised using quantile normalisation with MatLab

source_name: Primary adult human keratinocytes

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

tag: type

value: Primary cell (Human Keratinocyte)

value: Control

value: epidermis


title: TSA 4hr II

description: replicate 2

value: TSA for 4hrs


title: Control 0hr I

description: replicate 1

value: control


title: PKC 12hr I

description: replicate 1

value: PKC for 12hrs


title: Vehicle 8hr I

description: replicate 1

value: DMSO for 8hrs


title: TSA 8hr II

description: replicate 2

value: TSA for 8hrs


title: TSA 8hr III

description: replicate 3


title: TSA 12hr III

description: replicate 3

value: TSA for 12hrs


title: Vehicle 4hr II

description: replicate 2

value: DMSO for 4hrs


title: Vehicle 8hr III

description: replicate 3


title: PKC 12hr III

description: replicate 3


title: Vehicle 8hr II

description: replicate 2


title: TSA 12hr II

description: replicate 2


title: TSA 12hr I

description: replicate 1


title: CPC3_S

city: Suita

first: Chiara

last: Furusawa

state: Osaka

address: Furuedai

institute: RIKEN Quantitative Biology Center

description: Transcriptome data of CPC resistant strain 3 with CPC stress

hyb_protocol: After confirmation of yields (> 825 ng) and specific activities (> 15 pmol/μg) of the Cy3-labbeled cRNAs using NanoDrop ND-2000, 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x GE Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to custom designed the Agilent 8× 60K arrays for E. coli W3110, E.coli_K12_Expression_Ver.1, 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.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G4900DA) using one color scan setting for 8x60k array slides (AgilentG3_GX_1Color, Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: ExternalFullGEML_043017_D_F_20120907) to obtain background subtracted and spatially detrended Processed Signal intensities.
Log10 normalized expression of ORF. ORF level expression was calculated by median value of all probes corresponding to each ORF.

organism: Escherichia coli str. K-12 substr. MDS42

source_name: CPC resistant strain with CPC stress

label_protocol: One hundred ng of purified total RNAs was labeled using the Low Input Quick Amp WT Labeling Kit (Agilent Technologies) with Cyanine3 (Cy3) in accordance with the manufacturer’s instructions.

growth_protocol: The cells were precultured for 60 hours under the same condition with the laboratory with or without the corresponding stressors. Then, 5×10e7 cells in the exponential growth phase were used to transcriptome analysis.

extract_protocol: Total RNA was isolated and purified from cells using an RNeasy micro kit with on-column DNA digestion (Qiagen) in accordance with the manufacturer’s instructions. The quality of the purified RNA was evaluated using Agilent 2100 Bioanalyzer with an RNA 6000 Nano kit (Agilent Technologies). Only purified RNAs that had RIN (RNA integrity number) of 9.0 or more were utilized. The purified RNAs were stored at −80°C prior to transcriptome analysis.

treatment_protocol: Exponential cultures were withdrawn rapidly, and cells were killed immediately by the addition of an equal volume of ice-cold ethanol that contained 10% (w/v) phenol. The cells were collected by centrifugation at 20,000 × g at 4 °C for 5 min, and the pelleted cells were stored at −80 °C prior to RNA extraction.

tag: strain

value: CPC resistant strain

tag: stress

value: CPC


title: TSA 8hr I

description: replicate 1


title: TSA 4hr III

description: replicate 3


title: CPC2_S

description: Transcriptome data of CPC resistant strain 2 with CPC stress


title: PKC 12hr II

description: replicate 2


title: CPC5_S

description: Transcriptome data of CPC resistant strain 5 with CPC stress


title: CPC4_S

description: Transcriptome data of CPC resistant strain 4 with CPC stress


title: Vehicle 12hr I

description: replicate 1

value: DMSO for 12hrs


title: CPC1_S

description: Transcriptome data of CPC resistant strain 1 with CPC stress


title: TSA 4hr I

description: replicate 1


title: Vehicle 12hr III

description: replicate 3


title: BuOH5_S

description: Transcriptome data of BuOH resistant strain 5 with BuOH stress

source_name: BuOH resistant strain with BuOH stress

value: BuOH resistant strain

value: BuOH


title: Vehicle 12hr II

description: replicate 2


title: BuOH4_S

description: Transcriptome data of BuOH resistant strain 4 with BuOH stress


title: BuOH2_S

description: Transcriptome data of BuOH resistant strain 2 with BuOH stress


title: BuOH3_S

description: Transcriptome data of BuOH resistant strain 3 with BuOH stress


title: Control 0hr III

description: replicate 3


title: MG4_S

description: Transcriptome data of MG resistant strain 4 with MG stress

source_name: MG resistant strain with MG stress

value: MG resistant strain

value: MG


title: MG2_S

description: Transcriptome data of MG resistant strain 2 with MG stress


title: Vehicle 4hr I

description: replciate 1

value: Primary cell (Human Keratinocyte)


title: Vehicle 4hr III

description: replicate 3


title: MG3_S

description: Transcriptome data of MG resistant strain 3 with MG stress


title: mammary_gland-Oas2_WT_2dpc-rep1

value: C57BL/6 and CBA/CaJ

tag: genotype/variation

value: WT

value: female

value: mammary gland


title: MG5_S

description: Transcriptome data of MG resistant strain 5 with MG stress


title: BuOH1_S

description: Transcriptome data of BuOH resistant strain 1 with BuOH stress


title: Croton5_S

description: Transcriptome data of Croton resistant strain 5 with Croton stress

source_name: Croton resistant strain with Croton stress

value: Croton resistant strain

value: Croton


title: MG1_S

description: Transcriptome data of MG resistant strain 1 with MG stress


title: Croton4_S

description: Transcriptome data of Croton resistant strain 4 with Croton stress


title: Metha5_S

description: Transcriptome data of Metha resistant strain 5 with Metha stress

source_name: Metha resistant strain with Metha stress

value: Metha resistant strain

value: Metha


title: Croton2_S

description: Transcriptome data of Croton resistant strain 2 with Croton stress


title: Metha2_S

description: Transcriptome data of Metha resistant strain 2 with Metha stress


title: Croton3_S

description: Transcriptome data of Croton resistant strain 3 with Croton stress


title: Metha4_S

description: Transcriptome data of Metha resistant strain 4 with Metha stress


title: Metha3_S

description: Transcriptome data of Metha resistant strain 3 with Metha stress


title: Mal5_S

description: Transcriptome data of Mal resistant strain 5 with Mal stress

source_name: Mal resistant strain with Mal stress

value: Mal resistant strain

value: Mal


title: Mal4_S

description: Transcriptome data of Mal resistant strain 4 with Mal stress


title: Croton1_S

description: Transcriptome data of Croton resistant strain 1 with Croton stress


title: Mal3_S

description: Transcriptome data of Mal resistant strain 3 with Mal stress


title: Mal2_S

description: Transcriptome data of Mal resistant strain 2 with Mal stress


title: Lac4_S

description: Transcriptome data of Lac resistant strain 4 with Lac stress

source_name: Lac resistant strain with Lac stress

value: Lac resistant strain

value: Lac


title: Mal1_S

description: Transcriptome data of Mal resistant strain 1 with Mal stress


title: SoCar2_S

description: Transcriptome data of SoCar resistant strain 2 with SoCar stress

source_name: SoCar resistant strain with SoCar stress

value: SoCar resistant strain

value: SoCar


title: SoCar4_S

description: Transcriptome data of SoCar resistant strain 4 with SoCar stress


title: SoCar5_S

description: Transcriptome data of SoCar resistant strain 5 with SoCar stress


title: SoCar1_S

description: Transcriptome data of SoCar resistant strain 1 with SoCar stress


title: Lac3_S

description: Transcriptome data of Lac resistant strain 3 with Lac stress


title: Lac5_S

description: Transcriptome data of Lac resistant strain 5 with Lac stress


title: Lac2_S

description: Transcriptome data of Lac resistant strain 2 with Lac stress


title: Lac1_S

description: Transcriptome data of Lac resistant strain 1 with Lac stress


title: Co5_S

description: Transcriptome data of Co resistant strain 5 with Co stress

source_name: Co resistant strain with Co stress

value: Co resistant strain

value: Co


title: SoCar3_S

description: Transcriptome data of SoCar resistant strain 3 with SoCar stress


title: Co4_S

description: Transcriptome data of Co resistant strain 4 with Co stress


title: Metha1_S

description: Transcriptome data of Metha resistant strain 1 with Metha stress


title: Co3_S

description: Transcriptome data of Co resistant strain 3 with Co stress


title: Co1_S

description: Transcriptome data of Co resistant strain 1 with Co stress


title: Co2_S

description: Transcriptome data of Co resistant strain 2 with Co stress


title: KCl5_S

description: Transcriptome data of KCl resistant strain 5 with KCl stress

source_name: KCl resistant strain with KCl stress

value: KCl resistant strain

value: KCl


title: NaCl5_S

description: Transcriptome data of NaCl resistant strain 5 with NaCl stress

source_name: NaCl resistant strain with NaCl stress

value: NaCl resistant strain

value: NaCl


title: NaCl1_S

description: Transcriptome data of NaCl resistant strain 1 with NaCl stress


title: KCl1_S

description: Transcriptome data of KCl resistant strain 1 with KCl stress


title: NaCl2_S

description: Transcriptome data of NaCl resistant strain 2 with NaCl stress


title: KCl3_S

description: Transcriptome data of KCl resistant strain 3 with KCl stress


title: KCl4_S

description: Transcriptome data of KCl resistant strain 4 with KCl stress


title: NaCl4_S

description: Transcriptome data of NaCl resistant strain 4 with NaCl stress


title: CPC5_NS

description: Transcriptome data of CPC resistant strain 5 without stress

source_name: CPC resistant strain without stress

value: CPC resistant strain

value: without stress


title: BuOH1_NS

description: Transcriptome data of BuOH resistant strain 1 without stress

source_name: BuOH resistant strain without stress

value: BuOH resistant strain


title: BuOH3_NS

description: Transcriptome data of BuOH resistant strain 3 without stress


title: BuOH2_NS

description: Transcriptome data of BuOH resistant strain 2 without stress


title: MG5_NS

description: Transcriptome data of MG resistant strain 5 without stress

source_name: MG resistant strain without stress

value: MG resistant strain


title: MG2_NS

description: Transcriptome data of MG resistant strain 2 without stress


title: Cro5_NS

description: Transcriptome data of Cro resistant strain 5 without stress

source_name: Cro resistant strain without stress

value: Cro resistant strain


title: CPC4_NS

description: Transcriptome data of CPC resistant strain 4 without stress


title: NaCl3_S

description: Transcriptome data of NaCl resistant strain 3 with NaCl stress


title: MG1_NS

description: Transcriptome data of MG resistant strain 1 without stress


title: MG3_NS

description: Transcriptome data of MG resistant strain 3 without stress


title: MG4_NS

description: Transcriptome data of MG resistant strain 4 without stress


title: CPC3_NS

description: Transcriptome data of CPC resistant strain 3 without stress


title: BuOH5_NS

description: Transcriptome data of BuOH resistant strain 5 without stress


title: CPC2_NS

description: Transcriptome data of CPC resistant strain 2 without stress


title: CPC1_NS

description: Transcriptome data of CPC resistant strain 1 without stress


title: KCl2_S

description: Transcriptome data of KCl resistant strain 2 with KCl stress


title: BuOH4_NS

description: Transcriptome data of BuOH resistant strain 4 without stress


title: Cro4_NS

description: Transcriptome data of Cro resistant strain 4 without stress


title: Cro3_NS

description: Transcriptome data of Cro resistant strain 3 without stress


title: Cro1_NS

description: Transcriptome data of Cro resistant strain 1 without stress


title: Metha4_NS

description: Transcriptome data of Metha resistant strain 4 without stress

source_name: Metha resistant strain without stress

value: Metha resistant strain


title: Metha5_NS

description: Transcriptome data of Metha resistant strain 5 without stress


title: Metha3_NS

description: Transcriptome data of Metha resistant strain 3 without stress


title: Metha2_NS

description: Transcriptome data of Metha resistant strain 2 without stress


title: Mal4_NS

description: Transcriptome data of Mal resistant strain 4 without stress

source_name: Mal resistant strain without stress

value: Mal resistant strain


title: Metha1_NS

description: Transcriptome data of Metha resistant strain 1 without stress


title: Mal3_NS

description: Transcriptome data of Mal resistant strain 3 without stress


title: Cro2_NS

description: Transcriptome data of Cro resistant strain 2 without stress


title: Mal2_NS

description: Transcriptome data of Mal resistant strain 2 without stress


title: Lac5_NS

description: Transcriptome data of Lac resistant strain 5 without stress

source_name: Lac resistant strain without stress

value: Lac resistant strain


title: Lac1_NS

description: Transcriptome data of Lac resistant strain 1 without stress


title: Lac4_NS

description: Transcriptome data of Lac resistant strain 4 without stress


title: Lac3_NS

description: Transcriptome data of Lac resistant strain 3 without stress


title: Mal1_NS

description: Transcriptome data of Mal resistant strain 1 without stress


title: Mal5_NS

description: Transcriptome data of Mal resistant strain 5 without stress


title: SoCar5_NS

description: Transcriptome data of SoCar resistant strain 5 without stress

source_name: SoCar resistant strain without stress


title: SoCar4_NS

description: Transcriptome data of SoCar resistant strain 4 without stress


title: Co5_NS

description: Transcriptome data of Co resistant strain 5 without stress

source_name: Co resistant strain without stress


title: SoCar3_NS

description: Transcriptome data of SoCar resistant strain 3 without stress


title: SoCar1_NS

description: Transcriptome data of SoCar resistant strain 1 without stress


title: Lac2_NS

description: Transcriptome data of Lac resistant strain 2 without stress


title: Co4_NS

description: Transcriptome data of Co resistant strain 4 without stress


title: Co1_NS

description: Transcriptome data of Co resistant strain 1 without stress


title: Co3_NS

description: Transcriptome data of Co resistant strain 3 without stress


title: Co2_NS

description: Transcriptome data of Co resistant strain 2 without stress


title: KCl5_NS

description: Transcriptome data of KCl resistant strain 5 without stress

source_name: KCl resistant strain without stress


title: KCl4_NS

description: Transcriptome data of KCl resistant strain 4 without stress


title: KCl3_NS

description: Transcriptome data of KCl resistant strain 3 without stress


title: KCl1_NS

description: Transcriptome data of KCl resistant strain 1 without stress


title: KCl2_NS

description: Transcriptome data of KCl resistant strain 2 without stress


title: NaCl5_NS

description: Transcriptome data of NaCl resistant strain 5 without stress

source_name: NaCl resistant strain without stress


title: SoCar2_NS

description: Transcriptome data of SoCar resistant strain 2 without stress


title: direct_programming.Mnx1pos_intermediate

city: Boston

first: James

middle: Alexander

last: Briggs

state: Massachusetts

address: 200 Longwood Avenue, Harvard Medical School

department: Department of Systems Biology

institute: Harvard Medical School

description: These cells are transitioning into the terminal motor neuron state.

hyb_protocol: Amplified RNA was hybridized to Affymetrix GeneChip Mouse Transcriptome Arrays (MTA 1.0).

scan_protocol: GeneChips were scanned using standard settings for Affymetrix arrays.

data_processing: Results were processed by the Boston Children’s Hospital Microarray Core Facility, and were analyzed using Affrymetrix’s Transcriptome Analysis Console and Expression Console software.

source_name: ESC-derived motor neuron progenitor cells

label_protocol: RNA was amplified and labeled using standard Affymetrix sample preparation techniques.

growth_protocol: ESCs were cultured in standard media (DMEM with LIF + 15% fetal bovine serum) on 0.2% gelatin-coated dishes.

extract_protocol: RNeasy Plus Extraction Kit (Qiagen) was used according to manufacturer specifications to isolate total RNA.

treatment_protocol: Twenty-four hours before starting differentiation, ESCs containing an Mnx1:GFP reporter construct were trypsinized and seeded onto plates pre-coated with a mix of poly-d-lysine (100 ug/ml) and laminin (50 ug/ml) instead of gelatin for adherence. ESCs were counted by a Beckman Coulter Counter and seeded at a density of approximately 200,000 cells per well of a 6-well dish. At day 0 (ESCs), the media was switched from standard ES media to N2B27 media (Invitrogen). Doxycycline was also added at 3 ug/ml starting to induce expression of the NIL transcription factors. Media was changed daily. For the standard programming protocol, the steps described in Wu et al. were followed strictly. Mnx1 positive intermediate states were isolated from direct programming and standard protocol cultures on day 6 and day 9 respectively by FACS on a BD FACSaria II machine. RNA was extracted immediately following FACS.

tag: cell type

tag: differentiation protocol

value: direct programming

tag: purification

value: Mnx1:GFP positive


title: NaCl2_NS

description: Transcriptome data of NaCl resistant strain 2 without stress


title: NaCl3_NS

description: Transcriptome data of NaCl resistant strain 3 without stress


title: standard_protocol.Mnx1pos_intermediate

value: ESC-derived motor neuron progenitor cells

value: standard protocol


title: NaCl4_NS

description: Transcriptome data of NaCl resistant strain 4 without stress


title: Parent_replicate1

description: Transcriptome data of Parent without stress replicate1

source_name: Parent without stress

value: Parent


title: Parent_replicate3

description: Transcriptome data of Parent without stress replicate3


title: P-NaCl

description: Transcriptome data of Parent with NaCl stress

source_name: Parent with NaCl stress


title: Parent_replicate2

description: Transcriptome data of Parent without stress replicate2


title: P-Metha

description: Transcriptome data of Parent with Metha stress

source_name: Parent with Metha stress

value: Metha


title: P-KCl

description: Transcriptome data of Parent with KCl stress

source_name: Parent with KCl stress

value: KCl


title: P-Co

description: Transcriptome data of Parent with Co stress

source_name: Parent with Co stress

value: Co


title: P-Lac

description: Transcriptome data of Parent with Lac stress

source_name: Parent with Lac stress

value: Lac


title: NaCl1_NS

description: Transcriptome data of NaCl resistant strain 1 without stress

value: NaCl resistant strain


title: P-CPC

description: Transcriptome data of Parent with CPC stress

source_name: Parent with CPC stress

value: CPC


title: P-Croton

description: Transcriptome data of Parent with Croton stress

source_name: Parent with Croton stress

value: Croton


title: P-MG

description: Transcriptome data of Parent with MG stress

source_name: Parent with MG stress

value: MG


title: P-BuOH

description: Transcriptome data of Parent with BuOH stress

source_name: Parent with BuOH stress

value: BuOH


title: P-SoCar

description: Transcriptome data of Parent with SoCar stress

source_name: Parent with SoCar stress

value: SoCar


title: Surgical7

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

hyb_protocol: 10ug cRNA was used to make 250ul hyb cocktail, of which 200ul were injected into GeneChip X3P arrays and hybridized for 16 hours at 45C. Arrays were washed and stained using Affymetrix Fluidics Station 450 with user-prepared reagents.

scan_protocol: Microarrays were scanned using the GeneChip Scanner 3000 system from Affymetrix.

data_processing: Data were normalized using RMA and the Affymetrix Command Console module.

source_name: Surgical: Human Islets LCM

label_protocol: Simultaneous cRNA synthesis and biotin labeling via 3' IVT protocol

growth_protocol: LCM samples were obtained from selected beta cell rich autofluorescent areas of islets or from generalized non-selected areas LCM of islet tissue.

extract_protocol: PicoPure, Dnase treatment, RiboAmp HS RNA Amplification Kit

value: pancreas

value: Islets LCM

tag: age

value: F

tag: bmi


title: P-Mal

description: Transcriptome data of Parent with Mal stress

source_name: Parent with Mal stress

value: Mal


title: Cadaver7

source_name: Cadaver: Human Islets LCM


title: Cadaver4

value: M


title: Cadaver6


title: Surgical4


title: Surgical3


title: Cadaver3


title: TCx_NoDem_TBI_F_95to99_368

status: Public on Oct 16 2017

type: SRA

city: Seattle

first: Jeremy

last: Miller

state: WA

address: 615 Westlake Ave N

institute: Allen Institute for Brain Science

library_source: transcriptomic

data_processing:
RNA sequencing was done on Illumina HiSeq 2500 using v4 chemistry, producing a minimum of 30M 50bp paired-end clusters per sample.
Raw read (fastq) files were aligned to the GRCh38.p2 human genome (current as of 01/15/2016).
Illumina sequencing adapters were then clipped using the fastqMCF program (Aronesty, 2011), and then mapped to the transcriptome using RNA-Seq by Expectation-Maximization (RSEM) (Li et al., 2010) using default settings except for two mismatch parameters: bowtie-e (set to 500) and bowtie-m (set to 100).
Reads that did not map to the transcriptome were then aligned to the hg38 genome sequence using Bowtie with default settings (Langmead et al., 2009), after which remaining unmapped reads were mapped to ERCCs.
For analysis, the FPKM data matrix was first adjusted for the total transcript count using TbT normalization (Kadota et al., 2012), which scales each sample based on the summed expression of all genes that are not differentially expressed. The differential expression vector was defined as TRUE if a sample was from either temporal or parietal cortex, and FALSE otherwise. Sample data were then log-transformed and scaled such that the total log2(FPKM+1) across the entire data set remained unchanged after normalization. The result was that all expression levels for a particular sample were multiplied by a scalar close to 1 (in most cases between 0.9-1.2).  The output of this step is the file "TBT_normalized_FPKM.csv"
As brain region and RIN were identified as the largest sources of variability, log-normalized quantifications of each gene were corrected for RNA quality independently within each brain region.  This was done as follows: 1) exclude outliers (>3 standard deviations from the mean) and zero values, 2) determine whether expression data is best fit by one or two Gaussians using Mclust (Fraley and Raftery, 2002), 3) model RIN as a quadratic variable in each of the one or two groups, taking the sum of the residual and the mean as the normalized value, and then setting any negative values to 0.  The output of this step is the file "RIN_corrected_FKPM.csv"
Genome_build: GRCh38.p2
Supplementary_files_format_and_content: The two processed files are both csv files with FPKM values, with genes as rows and samples as columns.  Column 1 is reserved for gene symbols and row 1 is reserved for sample names.

source_name: TCx

extract_protocol:
Specific areas for macrodissection were identified by neuroanatomists using images of Nissl-stained tissue sections immediately adjacent to the sampled tissue, and were excised from the remaining tissue frozen tissue block using a scalpel.  Tissue was immediately transferred to prepared tubes where RNA was isolated using the RNeasy Lipid Tissue Mini Kit (Qiagen #78404) as per manufacturer’s instructions.  RNA was then quantified on a Nanodrop 8000 spectrophotometer (Thermo Scientific, Wilmington, DE) and normalized to 5ng/μl before RNA QC was performed using a Bioanalyzer (Agilent Technologies) and RNA Integrity Number (RIN) was recorded.
Total RNA (250ng) was used as input into the Illumina TruSeq Stranded Total RNA Sample Prep Kit (RS-122-2203), which uses random hexamer first strand cDNA synthesis and includes rRNA depletion (Ribo-Zero Gold rRNA depletion kit to remove both cytoplasmic and mitochondrial rRNA) and fragmentation. External RNA Controls Consortium (ERCCs) (Baker et al., 2005) at a 1:10,000 dilution were spiked into each sample

tag: brain region

value: TCx

tag: batch

tag: hemisphere

value: left

tag: Sex

value: No Dementia

tag: braak

tag: cerad

value: N

value: Y

value: 1-2 min

tag: rin


title: Surgical5

tag: tissue

tag: gender


title: TCx_Dem_NoTBI_F_82_376

value: right

value: Dementia

value: Unknown or N/A


title: TCx_Dem_NoTBI_M_90to94_367


title: TCx_Dem_TBI_F_90to94_373

value: < 10 sec


title: TCx_Dem_TBI_F_83_375


title: TCx_Dem_NoTBI_M_86_365


title: TCx_NoDem_NoTBI_F_90to94_374


title: TCx_NoDem_TBI_M_86_364


title: TCx_NoDem_NoTBI_F_90to94_371


title: TCx_NoDem_NoTBI_F_95to99_369


title: Cadaver5


title: Cadaver2


title: Surgical6


title: TCx_NoDem_TBI_M_84_362

value: 10 min - 1 hr


title: TCx_NoDem_NoTBI_M_84_363


title: TCx_NoDem_NoTBI_M_78_361


title: TCx_Dem_TBI_M_90to94_358

value: 10 sec - 1 min


title: TCx_Dem_TBI_M_77_360


title: TCx_NoDem_NoTBI_M_86_372


title: TCx_NoDem_TBI_F_90to94_370


title: TCx_Dem_NoTBI_F_100plus_356


title: Cadaver1

value: pancreas


title: TCx_Dem_TBI_F_100plus_355


title: Surgical1

value: Islets LCM


title: Surgical2


title: TCx_Dem_NoTBI_M_90to94_359


title: TCx_Dem_NoTBI_F_95to99_354

value: F


title: TCx_NoDem_TBI_M_81_352

value: 3-5 min


title: TCx_NoDem_NoTBI_F_78_346


title: TCx_NoDem_TBI_F_89_342


title: TCx_Dem_TBI_F_89_357


title: TCx_Dem_TBI_F_78_345


title: TCx_NoDem_TBI_M_95to99_350

value: M


title: TCx_NoDem_NoTBI_M_87_347

value: TCx


title: TCx_NoDem_NoTBI_M_95to99_340


title: TCx_NoDem_TBI_F_95to99_353


title: TCx_NoDem_TBI_M_95to99_339


title: TCx_Dem_NoTBI_M_90to94_335

value: left


title: TCx_Dem_TBI_M_85_337


title: TCx_Dem_TBI_F_89_341


title: TCx_Dem_TBI_F_82_343


title: TCx_NoDem_NoTBI_F_89_333

value: No Dementia


title: TCx_NoDem_NoTBI_F_82_344

value: N


title: TCx_Dem_NoTBI_M_95to99_351


title: TCx_Dem_TBI_M_90to94_334

value: Y


title: TCx_Dem_TBI_F_89_332


title: TCx_NoDem_TBI_M_87_348


title: TCx_NoDem_NoTBI_F_86_331


title: TCx_NoDem_TBI_M_88_328


title: TCx_Dem_NoTBI_F_100plus_327


title: TCx_NoDem_NoTBI_M_87_349


title: TCx_Dem_NoTBI_M_90to94_336


title: TCx_Dem_NoTBI_M_89_325


title: TCx_NoDem_NoTBI_F_90to94_323


title: TCx_NoDem_NoTBI_M_88_329


title: TCx_NoDem_TBI_M_89_324


title: TCx_NoDem_NoTBI_M_95to99_321


title: TCx_Dem_TBI_F_88_318


title: TCx_Dem_NoTBI_F_88_319


title: TCx_NoDem_NoTBI_M_95to99_317


title: TCx_Dem_TBI_F_87_314


title: TCx_NoDem_TBI_M_85_312


title: TCx_Dem_TBI_F_100plus_326


title: TCx_NoDem_TBI_M_95to99_316


title: TCx_NoDem_TBI_M_78_311


title: TCx_Dem_NoTBI_F_87_315


title: TCx_NoDem_TBI_F_90to94_322

value: 1-2 min


title: TCx_NoDem_TBI_M_95to99_320

value: right


title: TCx_Dem_TBI_M_88_309

value: Dementia


title: TCx_Dem_TBI_M_88_308


title: TCx_Dem_TBI_F_86_330

value: Unknown or N/A


title: TCx_Dem_TBI_F_90to94_306

value: < 10 sec


title: TCx_NoDem_NoTBI_F_90to94_307


title: TCx_NoDem_NoTBI_F_90to94_305


title: TCx_Dem_NoTBI_M_84_302


title: TCx_Dem_TBI_F_90to94_304


title: TCx_NoDem_NoTBI_M_78_303


title: TCx_Dem_TBI_M_84_301

value: 10 min - 1 hr


title: TCx_Dem_NoTBI_M_85_313


title: TCx_NoDem_TBI_M_78_310


title: TCx_NoDem_NoTBI_M_78_300


title: TCx_NoDem_NoTBI_F_95to99_296


title: TCx_Dem_NoTBI_M_88_298


title: TCx_Dem_TBI_M_88_297

value: > 1 hr


title: TCx_NoDem_TBI_M_78_299


title: TCx_NoDem_TBI_M_81_291


title: TCx_NoDem_TBI_F_95to99_295


title: TCx_NoDem_NoTBI_M_81_292


title: TCx_NoDem_NoTBI_M_90to94_290


title: TCx_Dem_NoTBI_F_86_288


title: TCx_Dem_TBI_M_100plus_286


title: TCx_Dem_TBI_M_90to94_289


title: TCx_Dem_NoTBI_M_100plus_287


title: TCx_Dem_NoTBI_M_90to94_285


title: TCx_NoDem_TBI_M_79_293


title: TCx_Dem_TBI_M_90to94_284


title: TCx_Dem_NoTBI_M_85_338


title: TCx_NoDem_NoTBI_F_90to94_283


title: TCx_NoDem_NoTBI_M_90to94_282


title: TCx_Dem_NoTBI_M_90to94_280


title: TCx_NoDem_TBI_M_90to94_281


title: TCx_NoDem_TBI_M_90to94_279


title: PCx_Dem_NoTBI_F_82_278

source_name: PCx

value: PCx


title: PCx_NoDem_NoTBI_F_90to94_276


title: PCx_Dem_TBI_F_83_277


title: PCx_Dem_TBI_F_90to94_275


title: TCx_Dem_TBI_M_79_294


title: PCx_NoDem_NoTBI_F_95to99_272


title: PCx_NoDem_NoTBI_F_90to94_274


title: PCx_NoDem_TBI_F_95to99_271


title: PCx_Dem_NoTBI_M_90to94_270


title: PCx_NoDem_TBI_F_90to94_273


title: PCx_Dem_NoTBI_M_86_268


title: PCx_NoDem_TBI_M_84_265


title: PCx_Dem_TBI_M_77_263


title: PCx_NoDem_TBI_M_86_267


title: PCx_Dem_TBI_M_90to94_261

value: 10 sec - 1 min


title: PCx_Dem_NoTBI_M_90to94_262


title: PCx_Dem_TBI_F_89_259

value: F


title: PCx_NoDem_NoTBI_M_78_264


title: PCx_Dem_NoTBI_M_95to99_254


title: PCx_Dem_NoTBI_F_95to99_256


title: PCx_NoDem_NoTBI_F_78_249


title: PCx_NoDem_TBI_M_87_251


title: PCx_NoDem_NoTBI_M_87_252


title: PCx_Dem_TBI_F_100plus_257


title: PCx_Dem_NoTBI_F_100plus_258


title: PCx_NoDem_NoTBI_F_89_260


title: PCx_Dem_TBI_F_78_248

value: 3-5 min


title: PCx_NoDem_TBI_M_95to99_253

value: M


title: PCx_NoDem_TBI_M_87_250


title: PCx_Dem_TBI_M_90to94_269


title: PCx_NoDem_NoTBI_F_82_247


title: PCx_Dem_TBI_F_82_246


title: PCx_NoDem_NoTBI_M_84_266


title: PCx_Dem_TBI_F_89_244


title: PCx_NoDem_TBI_F_89_245


title: PCx_NoDem_TBI_M_81_255


title: PCx_Dem_NoTBI_M_85_241


title: PCx_NoDem_TBI_M_95to99_242


title: PCx_NoDem_NoTBI_F_89_236


title: PCx_Dem_NoTBI_M_90to94_239


title: PCx_Dem_NoTBI_M_90to94_238


title: PCx_Dem_TBI_M_85_240


title: PCx_Dem_TBI_M_90to94_237


title: TCx_Dem_TBI_M_90to94_366

value: TCx


title: PCx_NoDem_TBI_M_88_231


title: PCx_NoDem_NoTBI_F_86_234


title: PCx_Dem_TBI_F_86_233


title: PCx_Dem_NoTBI_F_100plus_230


title: PCx_NoDem_NoTBI_M_95to99_224

value: left


title: PCx_Dem_TBI_F_89_235


title: PCx_NoDem_TBI_M_89_227

value: No Dementia


title: PCx_NoDem_NoTBI_M_88_232

value: N


title: PCx_NoDem_NoTBI_F_90to94_226


title: PCx_NoDem_TBI_F_90to94_225

value: Y


title: PCx_Dem_NoTBI_M_89_228


title: PCx_Dem_TBI_F_100plus_229


title: PCx_Dem_NoTBI_F_88_223


title: PCx_NoDem_NoTBI_M_95to99_243


title: PCx_NoDem_TBI_M_95to99_220


title: PCx_NoDem_NoTBI_M_95to99_221


title: PCx_Dem_TBI_F_88_222


title: PCx_Dem_NoTBI_F_95to99_218


title: PCx_Dem_TBI_F_87_219


title: PCx_NoDem_TBI_M_85_216


title: PCx_Dem_NoTBI_M_85_217


title: PCx_NoDem_TBI_M_78_215


title: PCx_NoDem_TBI_M_78_214


title: PCx_NoDem_NoTBI_F_90to94_209


title: PCx_Dem_TBI_M_88_212


title: PCx_Dem_TBI_F_90to94_210


title: PCx_NoDem_NoTBI_F_90to94_211


title: PCx_Dem_TBI_M_88_213


title: PCx_Dem_NoTBI_M_84_207


title: PCx_NoDem_NoTBI_M_78_208


title: PCx_NoDem_TBI_M_78_205


title: PCx_Dem_NoTBI_M_88_204


title: PCx_NoDem_NoTBI_M_78_206


title: PCx_NoDem_TBI_F_95to99_201


title: PCx_NoDem_TBI_M_81_197


title: PCx_Dem_TBI_M_79_200


title: PCx_Dem_TBI_M_88_203


title: PCx_NoDem_TBI_M_79_199


title: PCx_NoDem_NoTBI_M_81_198


title: PCx_NoDem_NoTBI_F_95to99_202


title: PCx_Dem_TBI_M_90to94_195


title: PCx_Dem_NoTBI_M_100plus_194


title: PCx_Dem_TBI_M_100plus_193


title: PCx_NoDem_NoTBI_F_90to94_191


title: PCx_NoDem_NoTBI_M_90to94_190


title: PCx_Dem_NoTBI_M_90to94_189


title: HIP_Dem_NoTBI_F_82_187

source_name: HIP

value: HIP


title: PCx_NoDem_TBI_M_90to94_188


title: HIP_Dem_TBI_F_83_186

value: right


title: HIP_NoDem_NoTBI_F_90to94_185


title: HIP_Dem_TBI_F_90to94_184

value: Dementia


title: HIP_NoDem_NoTBI_F_95to99_180

value: Unknown or N/A


title: HIP_NoDem_NoTBI_M_86_183


title: HIP_NoDem_NoTBI_F_90to94_182


title: HIP_NoDem_TBI_F_90to94_181

value: < 10 sec


title: HIP_NoDem_TBI_F_95to99_179

value: 1-2 min


title: HIP_Dem_TBI_M_90to94_177


title: PCx_NoDem_NoTBI_M_90to94_196


title: HIP_Dem_NoTBI_M_90to94_178


title: HIP_NoDem_NoTBI_M_84_176


title: HIP_NoDem_TBI_M_84_175

value: 10 min - 1 hr


title: HIP_NoDem_NoTBI_M_78_174


title: PCx_Dem_TBI_M_90to94_192

value: PCx

value: > 1 hr


title: HIP_Dem_NoTBI_M_90to94_172


title: HIP_NoDem_NoTBI_F_89_170

value: F


title: HIP_Dem_TBI_M_77_173


title: HIP_Dem_TBI_F_100plus_167


title: HIP_Dem_NoTBI_F_100plus_168


title: HIP_Dem_NoTBI_F_95to99_166


title: HIP_Dem_TBI_F_89_169


title: HIP_Dem_NoTBI_M_95to99_162


title: HIP_NoDem_TBI_M_81_163

value: 3-5 min


title: HIP_NoDem_NoTBI_M_81_164

value: M


title: HIP_NoDem_TBI_M_95to99_161


title: HIP_NoDem_NoTBI_M_87_160


title: HIP_NoDem_NoTBI_M_87_159


title: HIP_NoDem_NoTBI_F_78_158


title: HIP_Dem_TBI_F_78_157


title: HIP_NoDem_NoTBI_F_82_156


title: HIP_NoDem_TBI_M_95to99_152


title: HIP_Dem_NoTBI_M_85_151


title: HIP_NoDem_NoTBI_M_95to99_153


title: HIP_Dem_NoTBI_M_90to94_149


title: HIP_Dem_TBI_F_89_154


title: HIP_NoDem_TBI_M_90to94_148


title: HIP_Dem_TBI_M_90to94_171

value: 10 sec - 1 min


title: HIP_NoDem_TBI_F_95to99_165


title: HIP_Dem_TBI_M_90to94_146


title: HIP_NoDem_NoTBI_F_89_145


title: HIP_Dem_NoTBI_M_90to94_147

value: left


title: HIP_Dem_TBI_F_89_144


title: HIP_Dem_TBI_F_86_142


title: HIP_Dem_NoTBI_F_100plus_139


title: HIP_NoDem_TBI_M_88_140

value: No Dementia


title: HIP_Dem_NoTBI_M_89_137

value: N


title: HIP_NoDem_NoTBI_M_88_141


title: HIP_Dem_TBI_F_100plus_138

value: Y


title: HIP_NoDem_NoTBI_F_86_143

value: HIP


title: HIP_NoDem_NoTBI_F_90to94_135

value: right


title: HIP_Dem_TBI_F_88_130

value: Dementia


title: HIP_Dem_NoTBI_F_88_131

value: Unknown or N/A


title: HIP_NoDem_TBI_M_89_136

value: < 10 sec


title: HIP_NoDem_NoTBI_M_95to99_129


title: HIP_NoDem_TBI_M_95to99_132


title: HIP_NoDem_NoTBI_M_95to99_133


title: HIP_NoDem_TBI_F_90to94_134

value: 1-2 min


title: HIP_NoDem_TBI_F_89_155


title: HIP_Dem_TBI_M_85_150


title: HIP_Dem_NoTBI_F_95to99_126


title: HIP_Dem_NoTBI_F_87_127


title: HIP_NoDem_TBI_F_100plus_125

value: 6-9 min


title: HIP_NoDem_TBI_M_95to99_128


title: HIP_NoDem_TBI_M_78_124


title: HIP_Dem_TBI_M_88_122


title: HIP_NoDem_TBI_M_78_123

value: 10 min - 1 hr


title: HIP_Dem_TBI_M_88_121


title: HIP_NoDem_NoTBI_F_90to94_118


title: HIP_NoDem_NoTBI_M_78_116


title: HIP_NoDem_TBI_M_78_115

value: > 1 hr


title: HIP_NoDem_NoTBI_M_78_112


title: HIP_NoDem_NoTBI_F_90to94_120

value: F


title: HIP_NoDem_NoTBI_F_95to99_110


title: HIP_NoDem_TBI_F_95to99_109


title: HIP_Dem_TBI_F_90to94_119


title: HIP_NoDem_TBI_M_78_111


title: HIP_Dem_TBI_M_79_108

value: 3-5 min


title: HIP_NoDem_TBI_M_79_107

value: M


title: HIP_Dem_NoTBI_M_100plus_103


title: HIP_Dem_TBI_M_84_113


title: HIP_Dem_TBI_M_100plus_102


title: HIP_NoDem_NoTBI_M_90to94_105


title: HIP_NoDem_TBI_M_81_106


title: HIP_Dem_NoTBI_M_90to94_101


title: HIP_Dem_NoTBI_F_86_104


title: HIP_Dem_TBI_M_90to94_100


title: HIP_NoDem_NoTBI_F_90to94_99


title: HIP_Dem_NoTBI_M_90to94_95


title: HIP_Dem_TBI_F_90to94_98


title: HIP_NoDem_NoTBI_M_90to94_97


title: HIP_NoDem_TBI_M_90to94_94


title: FWM_NoDem_NoTBI_F_90to94_91

source_name: FWM

value: FWM


title: FWM_Dem_TBI_F_83_92


title: FWM_Dem_NoTBI_F_82_93


title: HIP_Dem_TBI_F_90to94_117

value: left


title: HIP_Dem_NoTBI_M_84_114


title: FWM_Dem_TBI_F_90to94_90


title: FWM_NoDem_NoTBI_F_90to94_89

value: No Dementia


title: FWM_NoDem_NoTBI_F_95to99_87

value: N


title: FWM_NoDem_TBI_F_95to99_86

value: Y


title: FWM_NoDem_TBI_F_90to94_88


title: FWM_NoDem_TBI_M_86_82


title: FWM_Dem_NoTBI_M_90to94_85


title: FWM_NoDem_TBI_M_84_80


title: FWM_NoDem_NoTBI_M_84_81


title: FWM_NoDem_NoTBI_F_89_75


title: FWM_Dem_NoTBI_M_90to94_77


title: FWM_Dem_TBI_M_77_78


title: FWM_Dem_NoTBI_F_100plus_73


title: FWM_Dem_TBI_F_100plus_72


title: FWM_Dem_TBI_F_89_74


title: FWM_Dem_TBI_M_90to94_76

value: 10 sec - 1 min


title: HIP_NoDem_TBI_M_90to94_96

value: HIP


title: FWM_Dem_NoTBI_M_95to99_69

value: Dementia


title: FWM_NoDem_TBI_M_81_70

value: right


title: FWM_Dem_NoTBI_F_95to99_71

value: Unknown or N/A


title: FWM_NoDem_NoTBI_M_87_67


title: FWM_NoDem_TBI_M_87_66

value: < 10 sec


title: FWM_NoDem_NoTBI_F_78_64


title: FWM_Dem_TBI_F_78_63


title: FWM_NoDem_NoTBI_F_82_62


title: FWM_Dem_TBI_M_90to94_84


title: FWM_Dem_NoTBI_M_86_83


title: FWM_Dem_TBI_F_82_61


title: FWM_NoDem_TBI_F_89_60


title: FWM_NoDem_NoTBI_M_78_79


title: FWM_Dem_TBI_F_89_59

value: 1-2 min


title: FWM_NoDem_NoTBI_M_95to99_58


title: FWM_Dem_NoTBI_M_85_56


title: FWM_Dem_NoTBI_M_90to94_54


title: FWM_Dem_NoTBI_M_90to94_53


title: FWM_Dem_TBI_M_90to94_52


title: FWM_NoDem_TBI_M_95to99_68


title: FWM_Dem_NoTBI_F_100plus_45


title: FWM_NoDem_TBI_M_88_46

value: 10 min - 1 hr


title: FWM_NoDem_NoTBI_M_88_47


title: FWM_Dem_TBI_F_86_48


title: FWM_NoDem_TBI_M_87_65


title: FWM_Dem_NoTBI_M_89_43


title: FWM_NoDem_NoTBI_F_90to94_41


title: FWM_NoDem_TBI_M_89_42


title: FWM_NoDem_TBI_M_95to99_38


title: FWM_NoDem_TBI_F_90to94_40


title: FWM_Dem_NoTBI_F_88_37


title: FWM_NoDem_TBI_M_95to99_57


title: FWM_Dem_TBI_F_88_36


title: FWM_NoDem_NoTBI_M_95to99_35


title: FWM_Dem_TBI_F_87_33


title: FWM_Dem_TBI_M_85_55


title: FWM_Dem_NoTBI_M_85_31


title: FWM_Dem_NoTBI_F_95to99_32


title: FWM_NoDem_NoTBI_F_89_51


title: FWM_NoDem_TBI_M_78_28


title: FWM_NoDem_TBI_M_85_30


title: FWM_Dem_TBI_M_88_27


title: FWM_NoDem_NoTBI_F_90to94_25


title: FWM_Dem_TBI_F_89_50


title: FWM_Dem_TBI_F_100plus_44


title: FWM_Dem_TBI_M_88_26


title: FWM_NoDem_NoTBI_F_86_49


title: FWM_Dem_TBI_F_90to94_24


title: FWM_NoDem_NoTBI_M_78_20


title: FWM_Dem_NoTBI_M_84_21


title: FWM_NoDem_TBI_M_78_19


title: FWM_NoDem_NoTBI_M_95to99_39


title: FWM_NoDem_NoTBI_M_78_22


title: FWM_NoDem_TBI_M_95to99_34


title: FWM_Dem_NoTBI_M_88_18


title: FWM_NoDem_TBI_M_79_13


title: FWM_NoDem_NoTBI_F_95to99_16


title: FWM_Dem_TBI_M_88_17

value: > 1 hr


title: FWM_Dem_TBI_M_79_14


title: FWM_NoDem_TBI_F_95to99_15

value: F


title: FWM_NoDem_TBI_M_78_29


title: FWM_NoDem_NoTBI_M_81_12


title: 7hr DO 750 µg/ml, 2

city: Ottawa

first: Julie

last: Buick

state: Ontario

address: 50 Colombine Driveway

department: Mechanistic Studies Division

country: Canada

institute: Health Canada

description:
Co-hybridized with negative vehicle control pool (DMSO +S9)
Sample 8

hyb_protocol: Labelled cRNA samples (325 ng of cyanine-3 labelled cRNA and 325 ng of cyanine-5 labelled cRNA) were hybridized to Agilent SurePrint G3 Human GE 8x60K oligonucleotide microarrays (Agilent Catalogue No: G4851A or B, Agilent Microarray Design ID: 028004 or 039494; Agilent Technologies, Mississauga, ON, Canada) at 65oC for 17 hours.

scan_protocol: Slides were washed according to the manufacturer’s specifications and scanned using an Agilent G2505C DNA Microarray Scanner at 3 μm resolution. Agilent Feature Extraction (version 11.0.1.1) was used for data extraction purposes from the generated image files and to generate QC reports for each array.

data_processing:
The log2 of the ratio using the median signal intensities were normalized using lowess using the transform.madata function in the maanova library in R.  After normalization the log2 ratios for the dye swap were averaged yielding a ratio representing the treatment relative to the vehicle control.
Sample represents the lowess normalized, dye swapped log2 ratio's of the treatment relative to the vehicle control.

source_name: TK6 lymphoblastoid cell line

label_protocol: Gene expression profiles were generated using a two-colour dye swap design [Kerr and Churchill, 2001]. Microarray analysis was conducted on the 7-8 hour time points from the definitive studies (n=3 per concentration and time point), along with the corresponding vehicle and positive controls. Agilent Low-Input Quick Amp Labelling kits were used to ultimately generate cyanine-3 and cyanine-5 labelled cRNA from 100 ng of total RNA, according to the manufacturer’s instructions (Agilent Technologies, Mississauga, ON, Canada).

growth_protocol: TK6 cells, a human lymphoblastoid cell line, were obtained from American Type Culture Collection (ATCC# CRL-8015; ATCC, Manassas, VA, USA). TK6 cells were maintained as described elsewhere [Ellinger-Ziegelbauer et al., 2009]. Briefly, cells were cultured and maintained in RPMI 1640 medium containing 10% heat inactivated horse serum, in addition to 0.1% pluronics, sodium pyruvate and antibiotics (penicillin at 20 units/ml and streptomycin at 20 µg/ml) at 37 ± 1oC and 6 ± 1% CO2 in air. Immediately prior to chemical exposure, cells were seeded at a density of 4 (± 0.5) x 105 cells/ml in twelve-well plates with a final volume of 3 ml per well. Given that TK6 cells are not metabolically competent cells and that compound requires metabolic activation to form reactive metabolites, all cellular exposures were conducted in the presence of 2% Aroclor 1254-induced rat liver S9 (Moltox, Boone, NC, USA) with NADPH generating system cofactors. The in vitro cellular exposures were performed by Integrated Laboratory Systems, Inc. (ILS; Research Triangle Park, NC, USA), in addition to the associated cytotoxicity and genotoxicity testing.

extract_protocol: Following chemical exposures, total RNA was isolated from treated and control TK6 cells between 7 and 8 hours post-exposure. An RNeasy Mini Kit (Qiagen, Toronto, ON, Canada) was used to isolate and purify total RNA using the spin technology protocol with an on-column DNase I digestion, following the manufacturer’s instructions. Total RNA was quantified and assessed for purity and integrity using a NanoDrop® ND-1000 spectrophotometer and an Agilent 2100 Bioanalyzer. Only high quality total RNA samples, with RNA Integrity Numbers (RINs) ranging from 8.0 to 10 and A260/280 absorbance ratios ≥2.0 were used for gene expression analysis.

treatment_protocol: TK6 cells were exposed to 3 concentrations of the test chemical as follows: 50, 500 and 750 µg/ml, in addition to vehicle and positive controls (DMSO (+S9), and BaP(+S9), respectively). Cells were co-exposed to each chemical (+S9) for four hours, then the media was replaced and cells were collected 3 to 4 hours later. All exposures were done in the presence of 2% aroclor-induced rat liver S9 with NADPH generating system cofactors to act as a metabolic activation system (MAS), as TK6 cells do not have inherent metabolic capacity. Exponentially growing cells were exposed to each chemical for 4 ± 0.5 hours. At the end of each 4h exposure, the exposed and control TK6 cells for each time point were removed by centrifugation and the cells were rinsed in PBS. The cells were then re-suspended in 3 ml of media and re-incubated for an additional 3 to 4 hours before being harvested for RNA extraction. Cells dedicated for the purposes of RNA extraction were collected from each well (4 ± 0.5 x 106 cells), pelleted by centrifugation and flash frozen in liquid nitrogen. Cells were stored at -80oC until RNA extraction was performed.

tag: time

tag: agent

value: disperse orange

tag: concentration

value: 750 microg/ml

tag: reference

value: DMSO (Pool)


title: FWM_NoDem_TBI_M_81_11

value: FWM

value: left

value: M


title: 7hr DO 50 µg/ml, 2

description:
Co-hybridized with negative vehicle control pool (DMSO +S9)
Sample 6

value: 50 microg/ml


title: FWM_NoDem_NoTBI_F_90to94_23

value: No Dementia

value: Y

value: N


title: 7hr Control (DMSO), 2

description:
Co-hybridized with negative vehicle control pool (DMSO +S9)
Sample 5


title: FWM_Dem_NoTBI_M_100plus_8

value: right

value: Dementia


title: 7hr Control (DMSO), 1

description:
Co-hybridized with negative vehicle control pool (DMSO +S9)
Sample 4


title: FWM_Dem_NoTBI_M_90to94_6

value: Unknown or N/A


title: FWM_Dem_TBI_M_90to94_9


title: 7hr DO 500 µg/ml, 1

description:
Co-hybridized with negative vehicle control pool (DMSO +S9)
Sample 2

value: 500 microg/ml


title: 7hr DO 750 µg/ml, 1

description:
Co-hybridized with negative vehicle control pool (DMSO +S9)
Sample 3


title: FWM_Dem_TBI_M_90to94_5


title: FWM_NoDem_NoTBI_M_90to94_3


title: FWM_Dem_TBI_M_100plus_7


title: 7hr DO 500 µg/ml, 2

description:
Co-hybridized with negative vehicle control pool (DMSO +S9)
Sample 7


title: 7hr DO 50 µg/ml, 1

description:
Co-hybridized with negative vehicle control pool (DMSO +S9)
Sample 1


title: FWM_Dem_NoTBI_M_90to94_2


title: FWM_NoDem_NoTBI_M_90to94_10


title: FWM_NoDem_NoTBI_F_90to94_4


title: 1 mg/L Tetracycline Fourth Generation Replicate 2

city: Gent

first: Jana

last: Asselman

address: Coupure Links 653 (Building F, 2nd floor)

country: Belgium

institute: Ghent University

hyb_protocol: The Cy3-labeled aRNAs were resuspended in 50 μl of hybridization solution (Agilent technologies, CA, USA). Afterwards, labeled aRNAs were loaded on Agilent SurePrint G3 Custom (D. magna) GE 8×60K array (Agilent technologies, CA, USA) and covered by a Gasket 8-plex slide (Agilent technologies, CA, USA). The slides were hybridized for 17hr at 65ºC oven.

scan_protocol: The slides were centrifuged at 3000 rpm for 20 sec to dry. The arrays were analyzed using an Agilent scanner with associated software. Gene expression levels were calculated with Feature Extraction v10.7.3.1 (Agilent technologies, CA). Relative signal intensities for each gene were generated using the Robust Multi-Array Average algorithm.

data_processing: The data analysis was conducted in R using the LIMMA package with specific functions for one channel Agilent array data. The data was background corrected using the normexp method (Edwards 2003). Additionally, data was normalized between arrays using a quantile normalization method and averaged first across probes and then across ESTs (expressed sequence tags), resulting in a single average expression value for each EST (Smyth and Speed 2003). Then a linear model was fitted to all the arrays (LIMMA analysis using lmFit).

organism: Daphnia magna

source_name: Whole body tissue

label_protocol: Each total RNA sample (200 ng) was labeled and amplified using Low Input Quick Amp labeling kit (Agilent technologies, CA, USA).

growth_protocol: Daphnids in each aquarium were fed daily with 5 ml of YCT and green algae per each test chamber. Tests were conducted in 5 L aquaria containing 3 L media at 22±1˚C. The culture medium for D. magna was reconstituted with hard water (i.e., CaSO4 120 mg L-1, NaHCO3 192 mg L-1, MgSO4 120 mg L-1, and KCl 8.0 mg L-1) and renewed three times each week. The culture was maintained at 22±1°C in a temperature controlled room, with a 16-h light:8-h dark photo-cycle

extract_protocol: Total RNA of D. magna (21-day old, 30 individuals/replicate) was extracted using the TRIzol method (Invitrogen, USA) according to the manufacturer’s protocol.

treatment_protocol: The experimental design consisted of four tetracycline concentrations (control, 0.1, 1.0, and 10.0 mg L-1), in which tetracycline was added to the medium, and for four exposure generations (F1, F2, F3, and F4). Four successive generations of D. magna were continuously cultured in medium tanks for the exposure tests. For each generation, 21-d life-cycle toxicity test was performed in a static renewal system. One hundred daphnids were in each aquarium continuously exposed to target compound for 21 days through four generations without any recovery period. The media solution containing target compound was renewed three times a week during the exposure test. For the second generation’s (F2) exposure, neonates from the prior generation after third brood were transferred and started to be exposed to the same concentration of tetracycline as in F1. The test continued until the fourth generation (F4), using the same test method as that for the parental generation. For each generation, life-cycle toxicity test in static renewal system was performed.

tag: exposure

value: 1 mg/L Tetracycline

tag: generation

value: fourth

tag: life stage

value: Adult (21 day old)


title: 1 mg/L Tetracycline Fourth Generation Replicate 3


title: 1 mg/L Tetracycline Third Generation Replicate 3

value: third


title: 1 mg/L Tetracycline Third Generation Replicate 2


title: 1 mg/L Tetracycline Fourth Generation Replicate 1


title: Control treatment Third Generation Replicate 1

value: control


title: Control treatment Third Generation Replicate 2


title: 1 mg/L Tetracycline Third Generation Replicate 1


title: CT26-shCDK8

city: Columbia

first: Mengqian

last: Chen

state: SC

address: CLS710, 715 Sumter Street

department: College of Pharmacy

institute: University of South Carolina

data_processing: The data were normalized using quantile normalization

source_name: CDK8 knockdown, CT26 transduced with pLKO.1-shCDK8

extract_protocol: RNA was isolated with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions. Quality control was performed with Agilent Bioanalyser.

tag: cell line

tag: genotype/variation

value: CDK8 knockdown


title: 1 mg/L Tetracycline Second Generation Replicate 1

value: second


title: 7hr BZ 20 µg/ml, 3

description: Co-hybridized with negative vehicle control pool (DMSO +S9)

data_processing: The log2 of the ratio using the median signal intensities were normalized using lowess using the transform.madata function in the maanova library in R.  After normalization the log2 ratios for the dye swap were averaged yielding a ratio representing the treatment relative to the vehicle control.

treatment_protocol: TK6 cells were exposed to 3 concentrations of the test chemical as follows: 15, 20 and 30 µg/ml, in addition to vehicle and positive controls (water (+S9), and BaP(+S9), respectively). Cells were co-exposed to each chemical (+S9) for four hours, then the media was replaced and cells were collected 3 to 4 hours later. All exposures were done in the presence of 2% aroclor-induced rat liver S9 with NADPH generating system cofactors to act as a metabolic activation system (MAS), as TK6 cells do not have inherent metabolic capacity. Exponentially growing cells were exposed to each chemical for 4 ± 0.5 hours. At the end of each 4h exposure, the exposed and control TK6 cells for each time point were removed by centrifugation and the cells were rinsed in PBS. The cells were then re-suspended in 3 ml of media and re-incubated for an additional 3 to 4 hours before being harvested for RNA extraction. Cells dedicated for the purposes of RNA extraction were collected from each well (4 ± 0.5 x 106 cells), pelleted by centrifugation and flash frozen in liquid nitrogen. Cells were stored at -80oC until RNA extraction was performed.

value: 20 microg/ml

value: DMSO (Pool)


title: Control treatment Fourth Generation Replicate 1


title: CT26-pLKO.1

source_name: Control, CT26 transduced with pLKO.1 empty vector


title: 1 mg/L Tetracycline Second Generation Replicate 2


title: 7hr BaP 10 µg/ml [BT]

value: benzo[a]pyrene

value: 10 microg/ml


title: 7hr Control (Water), 3


title: 7hr BZ 20 µg/ml, 2


title: Control treatment Second Generation Replicate 1


title: Control treatment Second Generation Replicate 2


title: 7hr BZ 15 µg/ml, 3

value: 15 microg/ml


title: 7hr BZ 30 µg/ml, 2

value: 30 microg/ml


title: 7hr BZ 30 µg/ml, 3


title: 7hr BZ 15 µg/ml, 2


title: 7hr Control (Water), 1


title: 7hr BZ 30 µg/ml, 1


title: 7hr BaP 10 µg/ml

description:
Co-hybridized with negative vehicle control pool (DMSO +S9)
Sample 13


title: 7hr DO 500 µg/ml, 3

description:
Co-hybridized with negative vehicle control pool (DMSO +S9)
Sample 12

value: disperse orange


title: FWM_NoDem_TBI_M_90to94_1

tag: brain region

value: FWM

tag: batch

value: left

value: M

value: No Dementia

value: N

value: Y

value: > 1 hr


title: 7hr DO 50 µg/ml, 3

description:
Co-hybridized with negative vehicle control pool (DMSO +S9)
Sample 11

value: 50 microg/ml


title: 10 mg/L Tetracycline First Generation Replicate 1

value: 10 mg/L Tetracycline

value: first

value: Adult (21 day old)


title: 7hr DO 750 µg/ml, 3

description:
Co-hybridized with negative vehicle control pool (DMSO +S9)
Sample 9

value: 750 microg/ml

value: DMSO (Pool)


title: 7hr Control (DMSO), 3

description:
Co-hybridized with negative vehicle control pool (DMSO +S9)
Sample 10


title: 10 mg/L Tetracycline First Generation Replicate 2


title: 0.1 mg/L Tetracycline First Generation Replicate 2

value: 0.1 mg/L Tetracycline


title: 0.1 mg/L Tetracycline First Generation Replicate 1


title: 1 mg/L Tetracycline First Generation Replicate 2

value: 1 mg/L Tetracycline


title: 1 mg/L Tetracycline First Generation Replicate 1


title: 7hr BZ 20 µg/ml, 1

value: 20 microg/ml


title: Control treatment First Generation Replicate 2

value: control


title: 7hr BZ 15 µg/ml, 1

value: 15 microg/ml


title: 7hr Control (Water), 2


title: Control treatment First Generation Replicate 1


title: C07 Post

status: Public on Oct 15 2017

city: Washington

first: Robert

last: Freishtat

state: DC

address: 111 Michigan Avenue NW

department: Center for Genetic Medicine

institute: Children's National Medical Center

description: FABP4+ exosomes (adipocyte-derived) were isolated, amplified, and profiled from serum taken pre bariatric surgery.

hyb_protocol: For hybridization, we followed Affymetrix Gene Chip miRNA Array Procedure for Affymetrix miRNA 4.0 arrays to hybridize biotin-labeled sample.

scan_protocol: We scanned the Affymetrix miRNA 4.0 arrays following the Affymetrix Command Console User Manual Instructions.

data_processing: We analyzed the resulting data in Expression Console using RMA+DMBG (Affymetrix) and then exported it to Partek Genomics Suite for analyses. We used three-factor ANCOVA (ID*group (lean vs. obese)*adipose depot; age covariate) to compare miRNA expression, using unadjusted p ≤ 0.05 and fold change ≥ |1.2| as filters. We generated main effects for group (obesity-state) and tissue depot along with their interaction term. As a part of the overall ANCOVA, we used specific within-group (depot effects within obese or lean) and within-tissue (obesity effects within depot) contrasts. No corrections were made for multiple testing, as the primary purpose of list generation was to power pathway analysis, which mitigates false positive discovery risks.

source_name: C07 Post Serum

label_protocol: We used Affymetrix FlashTag Biotin HSR RNA Labeling Kit to label 1000 ng of cRNA from each sample.

growth_protocol: Human bariatric patient pre and post surgery serum (500 uL) was used for isolation of FABP4+ exosomes.

extract_protocol: To isolate exosomes, we used the serum from the bariatric patients (pre and post surgery) and used ExoQuick-TC precipitation solution, according to ExoQuick-TC protocol. Total RNA was isolated following mirVana's total RNA Isolation kit. We also used StemCell Technologies Magnetic Isolation Technique to isolate FABP4+ specific exosomes.

treatment_protocol: No Treatment

tag: biological fluid

value: Serum

tag: bmi pre

tag: bmi post

tag: age

tag: race

value: AF

tag: Sex

value: Female


title: C07 Pre

description: FABP4+ exosomes (adipocyte-derived) were isolated, amplified, and profiled from serum taken post bariatric surgery.

source_name: C07 Pre Serum


title: C06 Pre

source_name: C06 Pre Serum


title: C08 Post

source_name: C08 Post Serum


title: C08 Pre

source_name: C08 Pre Serum


title: kai2-2, dehydrated 4h, replicate 1

city: Lubbock

first: chien

middle: Van

last: ha

state: TX

address: 1006 Carton Avenue, Box 43135

department: IGCAST

institute: texas tech university

description: Gene expression data from dehydrated kai2-2

hyb_protocol: 1.65 µg of Cy3-labelled cRNA were fragmented at 60°C for 30 minutes following the manufacturer's instructions. Agilent hybridization buffer was then added to the fragmentation mixture and hybridized to Agilent 021169 Arabidopsis Ver.4 Oligo Microarray 4x44K G2519F for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarray slides were washed and dried immediately by a brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with GeneSpring GX12.6.1 (Agilent). Percentile normalization (75 percentile) was performed for each chip.

source_name: kai2-2, dehydrated 4h, replicate 1

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

growth_protocol: Two-week-old WT and kai2-2 mutant plants were transferred from GM plates to soil and grown for 10 additional day (22ºC, 16-h-light/8-h-dark, 60 μmol m-2 sec-1 photon flux density).

extract_protocol: Total RNA was extracted from the rosette leaves using RNeasy Plant Mini Kit (Qiagen) according to the manufacturer’s instruction.

treatment_protocol: The aerial of 24-d-old plants were detached and exposed to dehydration on KimTowel papers for 0, 2 or 4h.

tag: genotype

tag: tissue

value: rosette leaves

value: 24 day-old

tag: hydration status

value: dehydrated


title: kai2-2, dehydrated 4h, replicate 2

source_name: kai2-2, dehydrated 4h, replicate 2


title: C05 Pre

source_name: C05 Pre Serum


title: kai2-2, dehydrated 2h, replicate 3

source_name: kai2-2, dehydrated 2h, replicate 3


title: kai2-2, dehydrated 4h, replicate 3

source_name: kai2-2, dehydrated 4h, replicate 3


title: kai2-2, well-watered (0h), replicate 3

description: Gene expression data from well-watered kai2-2

source_name: kai2-2, well-watered, replicate 3

value: well-watered


title: wildtype, dehydrated 4h, replicate 3

description: Gene expression data from dehydrated WT

source_name: WT, dehydrated 4h, replicate 3

value: wildtype


title: C05 Post

source_name: C05 Post Serum


title: kai2-2, well-watered (0h), replicate 1

source_name: kai2-2, well-watered, replicate 1


title: kai2-2, dehydrated 2h, replicate 1

source_name: kai2-2, dehydrated 2h, replicate 1


title: C06 Post

source_name: C06 Post Serum


title: C01 Pre

source_name: C01 Pre Serum


title: C02 Post

source_name: C02 Post


title: wildtype, dehydrated 4h, replicate 1

description: Gene expression data from dehydrated WT

source_name: WT, dehydrated 4h, replicate 1


title: C02 Pre

source_name: C02 Pre Serum


title: kai2-2, well-watered (0h), replicate 2

source_name: kai2-2, well-watered, replicate 2


title: wildtype, dehydrated 4h, replicate 2

description: Gene expression data from dehydrated WT

source_name: WT, dehydrated 4h, replicate 2


title: C01 Post

source_name: C01 Post Serum


title: kai2-2, dehydrated 2h, replicate 2

source_name: kai2-2, dehydrated 2h, replicate 2


title: wildtype, dehydrated 2h, replicate 1

description: Gene expression data from dehydrated WT

source_name: WT, dehydrated 2h, replicate 1


title: wildtype, dehydrated 2h, replicate 2

description: Gene expression data from dehydrated WT

source_name: WT, dehydrated 2h, replicate 2


title: wildtype, dehydrated 2h, replicate 3

description: Gene expression data from dehydrated WT

source_name: WT, dehydrated 2h, replicate 3


title: wildtype, well-watered (0h), replicate 1

description: Gene expression data from well-watered WT

source_name: WT, well-watered, replicate 1


title: wildtype, well-watered (0h), replicate 2

source_name: WT, well-watered, replicate 2


title: wildtype, well-watered (0h), replicate 3

source_name: WT, well-watered, replicate 3


title: RGC_Gpc4_12hrs_Rep1

city: La Jolla

first: Nicola

last: Allen

state: CA

address: 10010 North Torrey Pines Rd

institute: Salk Institute

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Data was processed using Affymetrix Expression Console.

organism: Rattus norvegicus

source_name: Retinal ganglion cell neuron

label_protocol: RNA was processed, hybridized and scanned  following manufacturer instructions for Affymetrix Rat Genome 230 2.0 array

growth_protocol: RGC neurons were grown in vitro for 12 days in full growth medium supplemented with BDNF and CNTF, maintained at 37C and 10% CO2 in a humidified incubator.

extract_protocol: Total RNA was isolated from RGCs in vitro using a Qiagen RNeasy mini kit, with on column DNA digestion.

treatment_protocol: RGCs were treated with specified proteins for 12 hours by addition of protein to the growth media

value: Postnatal day 6 neurons

tag: div

value: Cultured 12 days before treatment

tag: treatment

value: Glypican 4 protein, 12 hours treatment


title: RGC_TSP1_12hrs_Rep2

value: Thrombospondin 1 protein, 12 hours treatment


title: RGC_Untreated_Rep1


title: RGC_TSP1_12hrs_Rep1


title: RGC_Gpc4_12hrs_Rep2


title: RGC_Untreated_Rep2


title: hda5/14/15/18 NaCl stress rep. 2

city: Yokohama

first: Akihiro

last: Matsui

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Sustainable Resource Science

institute: RIKEN

hyb_protocol: 600 ng of cRNAs  were hybridized to the microarray (GPL19830) at 65 degree for 17 hours, using Gene Expression Hybridization kit. After hybridization, the microarray was washed with Gene Expression Wash Buffer 1 (Agilent) and Gene Expression Wash Buffer  (Agilent), and then dried immediately by brief centrifugation.

scan_protocol: The microarray was scanned by Agilent DNA Microarray Scanner G2505B and  raw data was extracted using Feature Extraction program ver 9.1.

data_processing: RMA normalization was performed for signals of microarray probes using limma package (Ritchie et al., 2015) on R 2.12.1 program.

source_name: hda5/14/15/18 NaCl-stress

label_protocol: Fluorescent-labeled (Cy3) cRNAs were prepared from 400 ng total RNA from each sample using a Quick Amp labeling kit (Agilent Technologies)

growth_protocol: Seeds of Arabidopsis thaliana (Venus-UBP1b-overexpressing and Venus control, Col-0 ecotype) were grown on liguid MS medium containing 0.1% pure Agar at 22°C under 16-h-light/8-h-dark for 5 days.

extract_protocol: RNA was extracted from at least three biological replicates with the RNeasy Plant Mini Kit (QIAGEN) according to the manufacturer’s instructions

treatment_protocol: The salt treatment was performed at 5 day after germination in 125 mM NaCl condition. Samples were collected at 2 h after the NaCl treatment.

tag: protocol

value: salt stress

tag: ecotype


title: Col-0 NaCl stress rep. 3

source_name: Col-0 NaCl-stress


title: hda5/14/15/18 NaCl stress rep. 3


title: hda5/14/15/18 non-stress rep. 3

source_name: hda5/14/15/18 non-stress

value: non-stress


title: hda5/14/15/18 non-stress rep. 2


title: Col-0 NaCl stress rep. 2


title: Col-0 non-stress rep. 1

source_name: Col-0 non-stress


title: hda5/14/15/18 NaCl stress rep. 1


title: Col-0 NaCl stress rep. 1


title: Col-0 non-stress rep. 3


title: Col-0 non-stress rep. 2


title: hda19 NaCl stress rep. 2

source_name: hda19 NaCl stress

value: hda19 mutant


title: hda19 NaCl stress rep. 3


title: hda5/14/15/18 non-stress rep. 1


title: hda19 non-stress rep. 3

source_name: hda19 non-stress


title: Tr1_A7602

status: Public on Oct 14 2017

city: Bethesda

first: Timothy

middle: G

last: Myers

state: MD

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

description:
Tr1 #2
_8924929001_F

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol with Illumina HiScan-SQ

data_processing: Signal data was extracted from the image files with the Gene Expression module (v. 1.9.0) of the GenomeStudio software (v. 2011.1) from Illumina, Inc. Signal intensities were converted to log 2 scale. Probes that didn't show detection p-value < 0.1 in at least 2 arrays were removed from the dataset.  After filtering probes, quantile normalization was applied across all arrays.

source_name: Spleen T-cells

label_protocol: Illumina TotalPrep RNA Amplification Kit (Ambion)

growth_protocol: Naïve CD4+T cells were isolated from spleen of C57BL/6 mice by MACS separation techniques.

extract_protocol: RNA was isolated with Trizol and Qiagen RNAeasy kit

treatment_protocol: Naive CD4+ T cells were stimulated by bone marrow derived-dendritic cells (BMDC) in the presence of anti-CD3 mAb (0.2 mg/ml) with or without Zymosan-Depleted (pure Dectin-1 ligand; Invivogen, 100 microg/ml). Three days later, these culture supernatants were collected and added into a culture where a new set of naïve CD4+ T cells were stimulated with plate-bound anti-CD3 mAb and soluble anti-CD28 mAb (without BMDCs). The cells were collected at day 5 and proceeded for RNA isolation using Tripure and RNeasy. For other helper T cell induction, navie CD4+ T cells were stimulated by plate bound-anti-CD3 mAb and soluble anti-CD28 mAb in the presence of recombinant-IL-4 (20 ng/ml) and anti-IFN-g mAb (10 mg/ml) for Th2 cells, and recombinant IL-27 (50 ng/ml) for Tr1 cells for 5 days and preceded for RNA isolation.

tag: strain

value: Spleen

tag: source cell type

value: Naïve CD4+T cells

tag: stimulation

value: plate bound-anti-CD3 mAb and soluble anti-CD28 mAb in presence of recombinant IL-27 (50 ng/ml)

tag: cell subtype

value: Tr1 T-cell