title: Lisala_Bono

description: Sample name: Lisala_Bono


title: Cannabis Control T1, Sample60

status: Public on Feb 06 2014

type: RNA

city: Ottawa

first: Andrew

last: Williams

state: ON

address: 50 Columbine

country: Canada

institute: Health Canada

hyb_protocol: 825 ng of sample and reference cRNA were mixed and fragmented. cRNA was hybridized to whole mouse genome (4x44K) microarray slides (Agilent Technologies, Inc.) in stainless steel chambers. A block design was used with three samples and one control placed on each slide. Hybridization was carried out in a rotating hybridization oven in the dark at 65ºC and 10 rpm for 17 h. The slides were then washed for 1 min in each of Agilent's Gene Expression Wash Buffers 1 and 2.

scan_protocol: Arrays were scanned on an Agilent DNA Microarray Scanner using Agilent Scan Control software. Data were extracted using Agilent Feature Extraction 9.5 (protocol GE2-v5_95_Feb07).

data_processing: The median signal intensity of each microarray sample was used. Data was normalized using the Lowess approach using the R software. Technical replicates were averaged using the median.

molecule: total RNA

organism: Mus musculus

source_name: Pulmonary epithelial cell line from Muta™Mouse, cannabis, control, 6hr + 4hr recovery

label_protocol: Fluorescently labelled cRNA was generated according to Agilent's Two-Color Microarray-Based Gene Expression Analysis protocol. 200 ng of sample RNA was labelled with Cy5 and 200ng of Universal Mouse Reference RNA was labelled with Cy3 using Agilent Low RNA Input Linear Amplification Kits.

growth_protocol: Cells (passage 12) were seeded at a density of 2-5 x 10e4 cells per 150mm plate, and cultured in DMEM F-12 supplemented with 2% v/v fetal bovine serum, 1% v/v penicillin/streptomycin, and 0.02% v/v murine epidermal growth factor. Cells were incubated at 37ºC in a 5% CO2 atmosphere for 2 days.

extract_protocol: RNA was extracted from the cells using TRIzol (Invitrogen), and cleaned-up using an RNeasy Mini Kit (Qiagen, Mississauga, ON, Canada) according to manufacturer's instructions. RNA quantity and quality were measured using a NanoDrop ND-1000 spectrophotometer.

treatment_protocol: Hand-rolled marijuana and tobacco cigarettes were smoked according to an ISO smoking regime with a puff volume of 35 mL, a puff duration of 2 seconds and a puff interval of 60 seconds. Particulate matter from mainstream smoke was collected on a 92mm glass fibre filter disc and subsequently dissolved in dimethyl sulfoxide. Murine epithelial lung cells were exposed to the tobacco smoke condensates (0, 25, 50, 90 μg/ml) or marijuana smoke condensates (0, 2.5, 5, 10 μg/ml) in serum-free medium for a six hour period. Following the six hour exposure, cells were either harvested immediately, or washed with phosphate-buffered saline and incubated in fresh serum-free medium for a four hour recovery period.

tag: cell line

value: FEI

tag: cell type

value: pulmonary epithelial cells

tag: treatment

value: cannabis exposure

tag: treatment dosage

value: control

tag: time point

value: post exposure T1 = 6hr + 4hr recovery

source_name: Universal Mouse Reference Total RNA

extract_protocol: Universal Mouse Reference RNA (Agilent Technologies Canada, Inc., Mississauga, ON, CAN, catalogue #740100).

tag: sample type

value: reference


title: control_rep3

city: Nashville

first: Harold

middle: L

last: Moses

state: TN

address: 2220 Pierece Ave

department: Cancer Biology

country: USA

institute: Vanderbilt Univerisity

description: 3D culture D6

hyb_protocol: Following fragmentation, 10.5 ug of cRNA were hybridized for 16 hr at 40C.

scan_protocol: Scanned with Affymetrix using AGCC v. 3.2.4

data_processing: Analyzed in R 3.0.1 using the oligo package. Samples were normalized with the RMA algorithm, genes were annotated with the pd.hugene.1.0.st.v1 package, and differential gene expression analysis was conducted using the limma package.

organism: Homo sapiens

source_name: SUM159 3D culture, control

label_protocol: cRNA was prepared according to the standard Affymetrix protocol from 130 ug total RNA

growth_protocol: SUM159 grown in matrigel 3D cultures

extract_protocol: Aurum total RNA kit was used for RNA extraction

value: SUM159 breast cancer cell line

tag: genotype/variation


title: Cannabis Mid T2, Sample58

source_name: Pulmonary epithelial cell line from Muta™Mouse, cannabis, medium dose, 6hr

value: medium dose D2 (5 ug/ml)

value: post exposure T2 = 6hr


title: r03063H

type: genomic

city: Atlanta

first: Pankaj

last: Chopra

state: GA

address: 615 Michael St. NE, Ste. 375

department: Human Genetics

institute: Emory University

description: Sample name: r03063H

hyb_protocol: Contained within the Illumina Infinium HumanMethylation450 BeadChips protocol

scan_protocol: Using an Illumina HiScan

data_processing:
raw signal intensities were quantile normalized separately and imputed values calculated for missing values. The beta value was calculated as: (signal b)/(signal a + signal b + 100)
Unmethylated and methylated signal intensities (see supplementary file linked to Series record)

label: Cy3, Cy5

molecule: genomic DNA

organism: Macaca mulatta

source_name: Macaca mulatta, Fetal Heart

extract_protocol: Standard DNA extraction protocol

tag: tissue

value: Fetal Heart

tag: methylation type


title: r03063L

description: Sample name: r03063L

source_name: Macaca mulatta, Fetal Liver

label_protocol: Contained within the Illumina Infinium HumanMethylation450 BeadChips protocol

value: Fetal Liver


title: Knocking down control_2

city: Stockholm

first: Chunyan

last: Zhao

address: Hälsovägen 7-9

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

description:
72 hours of siRNA treatment
Cells were derived from a 69-year-old female.

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

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

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

source_name: MCF-7 cell line, total RNA, knocking down control

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

growth_protocol: cells were cultured in DMEM red medium with 10% FBS

extract_protocol: RNA was prepared using the Versagene RNA Purification kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Control group and siRNF31 group were treated with 100uM siControl or 100uM siRNF31, respectively

value: epithelial cancer cells

tag: sirna

value: siControl


title: WC_Chimp

description: Sample name: WC_Chimp

organism: Pan troglodytes

source_name: Pan troglodytes, Blood

value: Blood


title: Rhesus_2

description: Sample name: MK_5

source_name: Macaca mulatta, Skin

value: Skin


title: Rhesus_2_2

description: Sample name: MK_5_2


title: control_rep2

description: 3D culture D6


title: control_rep1

description: 3D culture D6


title: Cannabis Low T2, Sample57

source_name: Pulmonary epithelial cell line from Muta™Mouse, cannabis, low dose, 6hr

value: low dose D1 (2.5 ug/ml)


title: Cannabis Low T1, Sample54

source_name: Pulmonary epithelial cell line from Muta™Mouse, cannabis, low dose, 6hr + 4hr recovery


title: TGFBR3KD_rep1

description: 3D culture D6

source_name: SUM159 3D culture, TGFBR3KD


title: Rhesus_1_2

description: Sample name: MK_4_2


title: Rhesus_1

description: Sample name: MK_4


title: Cannabis Control T1, Sample55


title: TGFBR3KD_rep2

description: 3D culture D6


title: Rhesus_2_3

description: Sample name: MK_5_3


title: Cannabis High T2, Sample56

source_name: Pulmonary epithelial cell line from Muta™Mouse, cannabis, high dose, 6hr

value: high dose D3 (10 ug/ml)


title: Cannabis High T2, Sample52

value: FEI


title: Cannabis Mid T2, Sample50

value: pulmonary epithelial cells


title: Cannabis Control T2, Sample49

source_name: Pulmonary epithelial cell line from Muta™Mouse, cannabis, control, 6hr

value: cannabis exposure


title: Min6-t72h-rep2

city: Rehovot

first: Jean

last: Hausser

address: Herzl St.

country: Israel

institute: Weizmann Institute of Science

hyb_protocol: The labelled RNA is hybridized to the bead on the BeadChip overnight, washed and blocked the next day (using the blocking buffers supplied by the manufacturer) and later analytical probes are bound to the beadchip for signal detection.

scan_protocol: The BeadChips are scanned using the illumina iScan system using the GenomeStudio Integrated Informatics Platform according to the manufacturer's protocols.

data_processing: Raw data from the Illumina scanner were loaded into R using the lumi package. Mappings to gene names and gene IDs were provided by the lumiMouseID Mapping package. Light intensities were quantile-normalized using the lumiN function of the lumi package. The analysis focused on probes for which the detection p-value smaller than 0.05 either in the TC control or at any of the time-points of the experiment. For subsequent analyses, we focused on these probes, discarding all others. Mappings of probes to Entrez gene IDs were obtained from the lumiMouseAll.db package.

label: Biotin

source_name: MIN6_Dox-induced miR-184 for 72h

label_protocol: 500ng of total RNA was directly labeled using the Illumina TotalPrep RNA Amplification kit according to the manufacturer's protocol. The key steps included Reverse Transcription, cDNA purification, In vitro transcription to synthesize cRNA, and finally cRNA purification.

growth_protocol: MIN6 cells were grown in 6 well plates and transfected with the respective doxycycline responsive plasmids consisting of rtTA and tetO-184 plasmids overnight using lipofectamine. The untransfected control cells were treated with no vectors but with lipofectamine.

extract_protocol: After doxycycline induction, the cells were harvested for total RNA using Trizol reagent following the manufacturer's protocol.

treatment_protocol: The untransfected and transfected cells were treated with 1µg/ml doxycycline, except for the transfected control (uninduced control) for the respective time points such as 16, 24, 48, and 72 hours.

value: Pancreatic ß-cells

tag: transfectedwith

value: Dox-inducible miR-184 vector

tag: induced with

value: 1µg/ml doxycycline for 72hr


title: IDTC 1

city: Graz

first: Karin

last: Wagner

state: Styria

address: Stiftingtalstrasse 24

department: Molecular Biology

country: Austria

institute: Medical University Graz

description:
cDNA, from amplified total RNA
BRAF mutated

hyb_protocol: Affymetrix Human Gene 1.0 ST Array (Cat No. 901085); GeneChip® HT hybridization, Wash and Stain Kit (Cat No. 900720); Affymetrix Genechip®  fluidics station 450: protocol FS450_0007 for Cartridge Arrays

scan_protocol: Affymetrix Scanner: GCS3000; AGCC (Command Console Software  AGCC_3_1_1.)

data_processing:
Geneexpression Console v.1.1, Affymetrix (Expression Console  EC_1_1_2) using Affymetrix default analysis settings for generation of CEL-files.
Data Pre-Processing and Filtering (Partek Software, v.6.6): RMA  (background correction, quantile normalization across all chips in the experiment, log2 transformation, median polish summarization); Anova

source_name: WM164 Melanoma cell Line

label_protocol: The Ambion® WT Expression Kit; For Affymetrix® GeneChip® Whole Transcript (WT) Expression Arrays, 09/2009 Rev C (Cat No. 4411973 ), Affymetrix WT Terminal Labeling Kit 30rxn (Cat No. 900671)

growth_protocol: Cells were grown RPMI media supplimented with 5% FCS, 2mM L –Glutamine and 2x Penstrep .

extract_protocol: mRNA was  extracted  using RNeasy mini kit Qiagen

treatment_protocol: Cells were treated with 500nM PLX4032 for 16 days period with media containing inhibitor being changed every 3 days

value: Melanoma Lymph node Metastasis

value: 500nM PLX4032 for 16 days


title: Min6-t48h-rep2

source_name: MIN6_Dox-induced miR-184 for 48h

value: 1µg/ml doxycycline for 48hr


title: Cannabis High T2, Sample47

value: post exposure T2 = 6hr

value: reference


title: Cannabis Low T1, Sample46

value: post exposure T1 = 6hr + 4hr recovery


title: IDTC 3


title: Min6-t24h-rep2

source_name: MIN6_Dox-induced miR-184 for 24h

value: 1µg/ml doxycycline for 24hr


title: Rhesus_1_3

description: Sample name: MK_4_3


title: Cannabis Low T2, Sample48

source_name: Universal Mouse Reference Total RNA


title: Cannabis Low T2, Sample53


title: Cannabis Mid T2, Sample51

value: medium dose D2 (5 ug/ml)


title: IDTC 2


title: Min6-t16h-rep2

source_name: MIN6_Dox-induced miR-184 for 16h

value: 1µg/ml doxycycline for 16hr


title: Min6-TC-rep2

source_name: MIN6_non-induced Dox-inducible miR-184 vector

value: none (uninduced control)


title: Min6-CTR-rep2

value: none (untransfected control)

value: 1µg/ml doxycycline


title: Min6-t72h-rep1


title: Min6-t24h-rep1


title: Cannabis Control T1, Sample43

source_name: Pulmonary epithelial cell line from Muta™Mouse, cannabis, control, 6hr + 4hr recovery

value: FEI

value: pulmonary epithelial cells

value: control


title: Min6-t16h-rep1

value: Pancreatic ß-cells

value: Dox-inducible miR-184 vector


title: Cannabis High T1, Sample41

source_name: Pulmonary epithelial cell line from Muta™Mouse, cannabis, high dose, 6hr + 4hr recovery

value: cannabis exposure

value: high dose D3 (10 ug/ml)


title: Cannabis Mid T1, Sample39

source_name: Pulmonary epithelial cell line from Muta™Mouse, cannabis, medium dose, 6hr + 4hr recovery


title: Cannabis Control T2, Sample40


title: Cannabis Low T1, Sample42

value: low dose D1 (2.5 ug/ml)


title: Cannabis High T1, Sample45


title: Cannabis Control T2, Sample59

value: post exposure T2 = 6hr


title: Cannabis Mid T1, Sample44

value: reference


title: CD11b Gr1 hi A 1

city: Manchester

first: Dominic

middle: Graham

last: Rothwell

state: Manchester

address: Wilmslow Road

department: CEP

country: United Kingdom

institute: University of Manchester

description: MDSC Gr1 high

data_processing:
The real-time PCR data was analysed using SDS2.4 software according to the manufacturers protocol with automatic baseline and threshold calling
Relative expression data was genrated by comparing each amplicon to the GEOMEAN of the samples. Amplicons with no signal for any sample were removed.
Relative expression data (log2) was transferred to MeV software and used to generate heatmaps and hierarchical clustering.

label: FAM

source_name: Splenocytes-Myeloid Derived Suppressor Cells

label_protocol: cDNA was generated from 1 microgram of RNA using the Life Technologies RNA-cDNA kit (manufacturers protocol). Real-time PCR was performed on a 7900HT machine using the standard TLDA protcol.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit

treatment_protocol: Flow cytometric Cell Sorting from dissociated murine spleens

tag: gender

value: Female

tag: strain

value: Balb/c

value: Spleen

tag: sorted cells

value: CD11b Gr1 hi


title: Cannabis High T2, Sample38


title: Tobacco and Cannabis Control T2, Sample35

description: This sample was used in both the tobacco and cannabis analyses.

source_name: Pulmonary epithelial cell line from Muta™Mouse, tobacco, control, 6hr

value: tobacco exposure


title: post_Sample5

city: Houston

first: Min

last: Zhang

state: Texas

address: 7455 Fannin Street

institute: MD Anderson Cancer Center

description: SAMPLE 10

hyb_protocol: As per Illumina instructions, with detection by Streptavidin-Cy3 conjugate.

scan_protocol: As per instructions for Illumina BeadArray Reader.

data_processing: The non-normalized data were generated by GenomeStudio with background correction. The normalized data were generated from bead-level data by methods previously described (PMID: 20805315). In brief, bead-level values were adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, quantile-normalized, and then averaged to give a single probe-level value.

label: biotin

source_name: PAXgene blood samples

label_protocol: 300 ng of globin-cleared total RNA was amplified and biotin-labeled through an Eberwine procedure using  Illumina TotalPrep RNA Amplification kits (Ambion).

growth_protocol: Not applicable

extract_protocol: Total RNA was isolated with the PAXgene Blood RNA Kit (PreAnalytiX, CAT#: 762164). RNA quality was assessed by an Agilent 2100 Bioanalyzer. 1500 ng of RNA was treated with the GLOBINclear-Human Globin mRNA Removal Kit (Ambion, CAT#:AM1980).

treatment_protocol: Lenalidomide was given orally at 20 mg/day on days 1-21 of all 28-day cycles. Rituximab was given at 375 mg/m2 body-surface area on day 1 of each cycle.

tag: cancer type

value: Follicular lymphoma

value: lenalidomide plus rituximab, cycle 2, Day 15

value: peripheral blood


title: pre_Sample4

description: SAMPLE 7

value: Baseline sample


title: post_Sample6

description: SAMPLE 12


title: Tobacco Control T2, Sample32

value: FEI

value: pulmonary epithelial cells

value: control


title: pre_Sample7

description: SAMPLE 13


title: Cannabis Mid T2, Sample36

source_name: Pulmonary epithelial cell line from Muta™Mouse, cannabis, medium dose, 6hr

value: cannabis exposure

value: medium dose D2 (5 ug/ml)


title: WT control [MH02M002]

city: Indianapolis

first: Maureen

last: Harrington

address: 635 Barnhill Dr

department: Biochemistry & Mol Bio

institute: Indiana University

hyb_protocol: Standard Affymetrix hybridization protocol, hybridization for 17 hours.

scan_protocol: Arrays were scanned by Affymetrix 3000-7G scanner controlled by Affymetrix Genechip Command Console.

data_processing: CEL files were imported into Partek Genomics Suite (Partek, Inc., St. Louis, Mo). RMA signals were generated for the core probe sets using the RMA background correction, Quantile normalization and summarization by Median Polish.

source_name: embryonic fibroblast

label_protocol: Samples were labeled using Ambion WT expression kit followed by the Affymetrix WT terminal labeling kit.

growth_protocol: proliferating mouse embryonic fibroblasts

extract_protocol: manufacturer's conditions [Qiagen RNeasy® Mini Kit]

treatment_protocol: untreated or treated with recombinant human tumor necrosis factor-alpha (10 ng/ml) for 45 minutes

tag: genotype

value: WT


title: CD11b Gr1 hi A 2

description: MDSC Gr1 high


title: CD11b Gr1 lo A 1

description: MDSC Gr1 low

value: CD11b Gr1 lo


title: CD11b Gr1 lo A 2

description: MDSC Gr1 low


title: post_Sample4

description: SAMPLE 8


title: Tobacco High T2, Sample33

source_name: Pulmonary epithelial cell line from Muta™Mouse, tobacco, high dose, 6hr

tag: cell line

value: high dose D3 (90 ug/ml)

value: post exposure T2 = 6hr

value: reference


title: CD4+CD34+ B

description: CAR+ T-cells

source_name: Splenocytes- CAR T-cells

value: Female

value: Balb/c

value: Spleen


title: Neg A

source_name: Splenocytes- non CAR T-cells and MDSCs

value: negative fraction


title: Neg B


title: post_Sample7

description: SAMPLE 14

value: Follicular lymphoma

value: lenalidomide plus rituximab, cycle 2, Day 15


title: pre_Sample3

description: SAMPLE 5

value: Baseline sample

value: peripheral blood


title: pre_Sample5

description: SAMPLE 9


title: Cannabis Control T2, Sample37

source_name: Pulmonary epithelial cell line from Muta™Mouse, cannabis, control, 6hr

value: FEI

tag: cell type

value: pulmonary epithelial cells


title: Tobacco High T1, Sample27

source_name: Pulmonary epithelial cell line from Muta™Mouse, tobacco, high dose, 6hr + 4hr recovery

tag: treatment

value: tobacco exposure

value: post exposure T1 = 6hr + 4hr recovery


title: Tobacco Mid T2, Sample34

source_name: Pulmonary epithelial cell line from Muta™Mouse, tobacco, medium dose, 6hr

tag: treatment dosage

value: medium dose D2 (50 ug/ml)


title: Tobacco Mid T2, Sample31

tag: time point

source_name: Universal Mouse Reference Total RNA


title: Tobacco Low T2, Sample30

source_name: Pulmonary epithelial cell line from Muta™Mouse, tobacco, low dose, 6hr

value: low dose D1 (25 ug/ml)

tag: sample type


title: Tobacco Mid T1, Sample28

source_name: Pulmonary epithelial cell line from Muta™Mouse, tobacco, medium dose, 6hr + 4hr recovery


title: Tobacco Control T1, Sample29

source_name: Pulmonary epithelial cell line from Muta™Mouse, tobacco, control, 6hr + 4hr recovery

value: control


title: pre_Sample6

description: SAMPLE 11


title: post_Sample3

description: SAMPLE 6


title: CD4+CD34+ A

description: CAR+ T-cells


title: Min6-CTR-rep1

value: Pancreatic ß-cells

value: none (untransfected control)

value: 1µg/ml doxycycline


title: Tobacco Low T1, Sample26

source_name: Pulmonary epithelial cell line from Muta™Mouse, tobacco, low dose, 6hr + 4hr recovery

value: reference


title: pre_Sample1

description: SAMPLE 1


title: Min6-t48h-rep1

source_name: MIN6_Dox-induced miR-184 for 48h

value: Dox-inducible miR-184 vector

value: 1µg/ml doxycycline for 48hr


title: post_Sample2

description: SAMPLE 4

value: Follicular lymphoma


title: post_Sample1

description: SAMPLE 2

value: lenalidomide plus rituximab, cycle 2, Day 15


title: Tobacco Mid T1, Sample25


title: Tobacco High T1, Sample24

value: high dose D3 (90 ug/ml)


title: Tobacco High T1, Sample21


title: Tobacco High T1, Sample22


title: PulmonaryEndothelialCells_monocrotaline_rep4

city: Baltimore

first: Molong

last: Li

state: MD

address: 733 N. Broadway

department: School of Medicine

institute: Johns Hopkins University

description:
gene expression of primary pulmonary endothelial cells directly after isolation from rat 5 days after 60mg/kg monocrotaline injection
SAMPLE 8

hyb_protocol: Purified with Qiagen´s RNeasy mini spin columns, then 600ng fragmented cDNA hybridized for 17 hours at 65°C with blocking agent and hybridization buffer.

scan_protocol: Scanned with Agilent Technologies Scanner G2505C US23502401 and images processed with Agilent Feature Extraction Software v10.7 with GE1_107_Sep09 protocol.

data_processing: Agilent Feature Extraction Software provided background correction and detrending. Processed signal was then log2 transformed and quantile normalized with the Bioconductor limma package (v.3.6.9).

organism: Rattus norvegicus

source_name: primary pulmonary endothelial cells_monocrotaline

label_protocol: 10ng of RNA was primed using oligo-dT (T7) promoter primers and converted to cDNA with AffinityScript RNase Block. Primed cDNA was amplified and labeled using fluorescently labeled dNTP-nucleotides (Cy3) and T7 RNA polymerase.

growth_protocol: Sprague-Dawley rats aged 8-10 weeks

extract_protocol: Rat endothelial cells were isolated from collagenase digested whole lung tissue using CD31 antibody coated Dynabeads. RNA isolation was done using manufacturer´s instructions and straight from the magnetic beads without any cell culture conditions.

treatment_protocol: Rats were treated with subcutaneous injections of either 60mg/kg of monocrotaline or saline as control. Whole lungs were isolated 5 days after treatment.

value: Sprague-Dawley

tag: age

value: 8-10 weeks

tag: injected with

value: monocrotaline (60mg/kg)

value: lung

value: primary pulmonary endothelial cells


title: Tobacco Control T2, Sample23

source_name: Pulmonary epithelial cell line from Muta™Mouse, tobacco, control, 6hr

value: FEI

value: pulmonary epithelial cells

value: tobacco exposure

value: post exposure T2 = 6hr


title: pre_Sample2

description: SAMPLE 3

source_name: PAXgene blood samples

value: Baseline sample

tag: tissue

value: peripheral blood


title: LN RANKL2

city: LA

first: Sungyong

last: You

state: CA

address: Beverly Blvd 8400

department: Surgery

institute: Cedars-Sinai Medical Center

description: LNCaP cell expressing flag-tagged RANKL.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: The acquisition of array images was undertaken using the Affymetrix GeneChip Command Console 1.1 (AGCC).

data_processing: Data were normalized by GCRMA. GCRMA data was generated by using R packages including affy and gcrma.

source_name: LNCaP cell expressing flag-tagged RANKL

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2002, Affymetrix).

growth_protocol: LNCaP cell colonies expressing flag-tagged RANKL or neo plasmid were picked and the cells were amplified from a 48-well plate to a 10 cm dish in the presence of G418.  Stable clones were maintained in 200 ug/ml of G418 and routinely checked for flag-RANKL expression by Western blot analysis.

extract_protocol: Total RNA was extracted using RNA-Bee as per manufacturer's instructions and further cleaned up with Qiagen RNeasy Mini kit following the manufacturer's instructions.

treatment_protocol: For stable transfection, LNCaP cells were first transfected with either p3xFlag-tagged RANKL or neo-control-plasmid (p3×FLAG- myc-CMV-25) cDNA (Sigma–Aldrich, St. Louis, MO) in a 6-well plate for 48h, and the cells were trypsinized and seeded into a 15 cm dish. The cells containing the transfected vectors were selected in 400 ug/ml of G418 until individual colonies containing the transfected construct were confirmed.

value: LNCaP

value: prostate cancer cell line

tag: stable transfection

value: flag-tagged RANKL


title: Tobacco Low T1, Sample20

value: low dose D1 (25 ug/ml)

value: post exposure T1 = 6hr + 4hr recovery

value: reference


title: LN RANKL1


title: LN Neo2

description: LNCaP cell expressing flag-tagged neo plasmid.

value: flag-tagged neo plasmid


title: LN Neo1

source_name: LNCaP cell expressing flag-tagged neo plasmid


title: Tobacco Control T1, Sample19

value: control


title: PulmonaryEndothelialCells_monocrotaline_rep2

description:
gene expression of primary pulmonary endothelial cells directly after isolation from rat 5 days after 60mg/kg monocrotaline injection
SAMPLE 6

value: Sprague-Dawley

value: 8-10 weeks

value: monocrotaline (60mg/kg)


title: Min6-TC-rep1

source_name: MIN6_non-induced Dox-inducible miR-184 vector

value: Pancreatic ß-cells

tag: transfectedwith

value: Dox-inducible miR-184 vector

value: none (uninduced control)


title: PulmonaryEndothelialCells_monocrotaline_rep1

description:
gene expression of primary pulmonary endothelial cells directly after isolation from rat 5 days after 60mg/kg monocrotaline injection
SAMPLE 5

value: lung

value: primary pulmonary endothelial cells


title: PulmonaryEndothelialCells_monocrotaline_rep3

description:
gene expression of primary pulmonary endothelial cells directly after isolation from rat 5 days after 60mg/kg monocrotaline injection
SAMPLE 7


title: Sotos 9 cultured in the presence of Retinoic Acid

city: Leiden

first: Remco

last: Visser

address: Albinusdreef 2

department: Department of Pediatrics, J6-S

country: Netherlands

institute: Leiden University Medical Center

description: Gene expression data from fibroblasts in presence of retinoic acid from a Sotos syndrome patient

hyb_protocol: Hybridization was performed by the Leiden Genome Technology Center following manufacturer’s protocols (Affymetrix, Santa Clara, CA, USA)

scan_protocol: Scanning was performed by the Leiden Genome Technology Center ollowing manufacturer’s protocols (Affymetrix, Santa Clara, CA, USA)

data_processing: Analyses of the microarray expression data were made in R (version 2.7.0; www.r-project.org). Probe level data was preprocessed with the Robust Multi-array Average (RMA) algorithm in the Bioconductor (www.bioconductor.org) affy package (version 1.18.2).

source_name: Human dermal fibroblasts

label_protocol: Generation of cDNA, cRNA, and biotin-labeling were performed by ServiceXS Leiden according to manufacturer’s guidelines (Affymetrix, Santa Clara, CA, USA).

growth_protocol: Skin fibroblasts were cultured in Dulbecco’s modified Eagle’s Medium supplemented with glutamax and containing 10% fetal calf serum, 50IU/ml penicillin and 50μg/ml streptomycin. Medium was changed twice a week and cells were split at a ratio of 1:6 upon reaching monolayer confluence. The cell cultures were maintained at 37oC in a humidified atmosphere of 5% CO2 and 95% O2. In all experiments cell passages were between 2 and 10.

extract_protocol: Total RNA extraction was performed with the Nucleospin RNA II kit (Macherey-Nagel, Dϋren, Germany).

treatment_protocol: At reaching 80-90% monolayer confluency cells were stimulated with retinoic acid at a final concentration of 10-6M for 48h. Because of the light-sensitivity of RA, cell cultures were kept in the dark.

value: dermal fibroblasts

value: retinoic acid

tag: disease state

value: Sotos syndrome with NSD1 abnormality


title: Sotos 8

description: Gene expression data from fibroblasts from a Sotos syndrome patient

value: untreated


title: Sotos 7 cultured in the presence of Retinoic Acid


title: Sotos 9


title: Sotos 8 cultured in the presence of Retinoic Acid


title: Tobacco Mid T2, Sample18

value: FEI

value: pulmonary epithelial cells

value: tobacco exposure

value: medium dose D2 (50 ug/ml)

value: post exposure T2 = 6hr


title: Tobacco Low T1, Sample15

value: low dose D1 (25 ug/ml)

value: post exposure T1 = 6hr + 4hr recovery

value: reference


title: PulmonaryEndothelialCells_control_rep4

description:
gene expression of primary pulmonary endothelial cells directly after isolation from rat 5 days after saline injection
SAMPLE 4

source_name: primary pulmonary endothelial cells_saline

value: Sprague-Dawley

value: 8-10 weeks

value: saline (control)


title: Tobacco Mid T1, Sample16


title: Tobacco Low T2, Sample17


title: Sotos 6


title: PulmonaryEndothelialCells_control_rep3

description:
gene expression of primary pulmonary endothelial cells directly after isolation from rat 5 days after saline injection
SAMPLE 3

value: lung


title: Tobacco High T1, Sample14

value: high dose D3 (90 ug/ml)


title: Sotos 7

value: dermal fibroblasts


title: Sotos 6 cultured in the presence of Retinoic Acid

value: retinoic acid


title: PulmonaryEndothelialCells_control_rep1

description:
gene expression of primary pulmonary endothelial cells directly after isolation from rat 5 days after saline injection
SAMPLE 1

value: primary pulmonary endothelial cells


title: hela_mho_2weeks_rep3

city: Duesseldorf

first: Karl

last: Koehrer

address: Universitaetsstr. 1

department: BMFZ

country: Germany

institute: University of Duesseldorf

hyb_protocol: After fragmentation, labelled cRNA was hybridized to Agilent SurePrint G3 Human GE 8×60k Microarrays (Agilent Technologies, Boeblingen, Germany) for 17 h at 65 °C and scanned as described in the manufactureŕs protocol.

scan_protocol: Samples were scanned as described in the manufacturers protocol (Scanner G2505C, Agilent Technologies).

data_processing: Signal intensities on 20 bit tiff images were calculated by Feature Extraction software (FE, Vers. 10.7.1.1; Agilent Technologies) using scan protocol GE1_107_Sep09 / grid 028004_D_F_20100430. Data analyses were conducted with GeneSpring GX (Vers. 11.5; Agilent Technologies). Probe signal intensities were quantile normalized across all samples to reduce inter-array variability. Input data pre-processing was concluded by baseline transformation to the median of all samples.

source_name: cell co-culture

label_protocol: Synthesis of cDNA and subsequent fluorescent labelling of cRNA was performed on four replicates of each experimental condition according to the manufactureŕs protocol (One-Color Microarray-Based Gene Expression Analysis / Low Input Quick Amp Labeling; Agilent Technologies). Briefly, 100 ng of total RNA was converted to cDNA, followed by in vitro transcription and incorporation of Cy3-CTP into the nascent cRNA.

growth_protocol: The human cervical carcinoma cell line HeLa S3 (ATCC CCL2.2) was cultivated in DMEM medium supplemented with 10% (v/v) horse serum and 0.01% (w/v) penicillin/streptomycin in a humidified 10% CO2-enriched atmosphere at 37°C. Cells were harvested by trypsinisation, suspended in 10 ml buffered saline (PBS) and pelleted by subsequent low speed centrifugation (1,100×g, 10 min). The proportion of damaged cells was ascertained using trypan blue staining. The HeLa cell line chronically infected with M. hominis was cultivated in the same culture medium. M. hominis strain FBG was grown in arginine-medium.

extract_protocol: At 0 h, 4 h, 24 h and 48 h post infection, M. hominis-infected HeLa cells were subjected to RNA purification. Nucleic acids were prepared from each 75 cm2 cell culture flask after twice washing the adherent HeLa cells with 10 ml PBS and subsequent lysis in 650 µl RLT Buffer (RNeasy Kit; Qiagen GmbH, Hilden, Germany). 600µl lysate/RTL Buffer was used for total RNA preparation according to the instructions of the manufacturer. All RNA samples that were analysed by RT-PCR were pretreated with DNaseI to digest contaminating traces of DNA. RNA integrity was checked using an Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany). All samples in this study had high quality RNA integrity numbers (RIN 9.7–10). RNA was quantified photometrically using a Nanodrop ND1000 (Thermo Fisher Scientific GmbH, Dreieich, Germany).

treatment_protocol: Two days pre-infection 30 ml of a mid-logarithmic-phase broth culture of M. hominis was suspended in 300 ml DMEM-medium supplemented with 10% (v/v) horse serum, 0.01% (w/v) penicillin/streptomycin and 75 ml arginine-medium and cultivated for 48 h at 37°C. After sedimentation of the mycoplasma cells (4,000×g, 30 min) the sediment was washed with PBS, suspended in 300 ml DMEM/10% (v/v) horse serum/0.01% (w/v) penicillin/ streptomycin; and 10 ml M. hominis cell suspension was added to 1×10e7 HeLa cells that had been seeded 20 h pre-infection in 75 cm2 cell culture flasks. The multiplicity of infection (MOI) was controlled by measurement of the number of colour changing units (CCU) of M. hominis. In general, the procedure described above resulted in an MOI of 100. Recovery rates of M. hominis and HeLa cells at each time point of infection were estimated by TaqMan based quantification of HeLa (hgap) and M. hominis (hitA) genome equivalents, enabling the calculation of cell counts and the respective cell ratios.

value: HeLa S3 (ATCC CCL2.2)

tag: infection status

value: M.hominis infected


title: Tobacco Mid T2, Sample11

value: FEI

value: pulmonary epithelial cells


title: Tobacco Low T2, Sample12

value: tobacco exposure


title: PulmonaryEndothelialCells_control_rep2

description:
gene expression of primary pulmonary endothelial cells directly after isolation from rat 5 days after saline injection
SAMPLE 2

tag: strain


title: Tobacco Control T2, Sample13

value: control

value: post exposure T2 = 6hr


title: Sotos 5

value: untreated

value: Sotos syndrome with NSD1 abnormality


title: hela_mho_2weeks_rep4


title: Sotos 5 cultured in the presence of Retinoic Acid


title: hela_mho_2weeks_rep2


title: Sotos 4 cultured in the presence of Retinoic Acid


title: hela_mho_2weeks_rep1


title: Tobacco Low T2, Sample8

value: low dose D1 (25 ug/ml)

value: reference


title: Tobacco High T2, Sample10

source_name: Pulmonary epithelial cell line from Muta™Mouse, tobacco, high dose, 6hr


title: Tobacco Control T2, Sample9


title: Sotos 3


title: Sotos 3 cultured in the presence of Retinoic Acid


title: Sotos 4


title: hela_mho_48h_rep4


title: Tobacco High T2, Sample7


title: hela_mho_48h_rep3


title: Sotos 2 cultured in the presence of Retinoic Acid


title: Tobacco Mid T1, Sample5

value: medium dose D2 (50 ug/ml)

value: post exposure T1 = 6hr + 4hr recovery


title: Tobacco Control T1, Sample6


title: hela_mho_48h_rep1


title: Sotos 2


title: Tobacco Mid T2, Sample2

source_name: Pulmonary epithelial cell line from Muta™Mouse, tobacco, medium dose, 6hr


title: hela_mho_4h_rep3


title: hela_mho_48h_rep2


title: Tobacco Low T1, Sample4

source_name: Universal Mouse Reference Total RNA


title: hela_mho_4h_rep2


title: Tobacco Control T2, Sample3


title: Control 8 cultured in the presence of Retinoic Acid

description: Gene expression data from fibroblasts in presence of retinoic acid from a control individual


title: Nr4a1 kidney at week24, biological rep2

city: Jackson

first: Michael

middle: R

last: Garrett

state: MS

address: 2500 North State Street

department: Pharmacology

institute: University of Mississippi Medical Center

description: Gene expression data from Nr4a1-/- kidney at 24 weeks of age

hyb_protocol: Following fragmentation, cRNA were hybridized to Rat GeneChip 1.0ST Arrays. GeneChips were automatically washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G system

data_processing:
Analysis of microarray data was performed using software provided by Affymetrix (Affymetrix® Expression Console™ Software) and commercially available GeneSifter™ software platform. Microarrays were normalized using RMA alogrithm.
affymetrix-algorithm-name = rma-gene-default
affymetrix-algorithm-version = 1.0
affymetrix-array-type = RaGene-1_0-st-v1
program-name = Expression Console
program-version = 1.1.2800.28061
program-company = Affymetrix
affymetrix-algorithm-param-apt-engine = ProbesetSummarizeEngine
affymetrix-algorithm-param-apt-prog = Expression Console

source_name: Kidney isolated from Nr4a1-/- at week 24

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol for Rat GeneChip 1.0ST Arrays

growth_protocol: FHH and Nr4a1-/- rats were grown to 8, 16, and 24 weeks of age and kidney tissue was harvested.

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

treatment_protocol: Whole genome transcript analysis was performed using Affymetrix platform on  kidney tissue collected from FHH and Nr4a1-/- at week 8 (n=3 per group), 16 (n=3), and 24(n=3).

value: kidney

value: point mutation in exon 1 of Nr4a1 gene

value: 24 weeks of age


title: hela_mho_0h_rep4


title: Sotos 1 cultured in the presence of Retinoic Acid

value: dermal fibroblasts

value: retinoic acid


title: hela_mho_4h_rep1

value: HeLa S3 (ATCC CCL2.2)

value: M.hominis infected


title: hela_mho_4h_rep4


title: Sotos 1


title: Nr4a1 kidney at week24, biological rep3


title: Control 9

description: Gene expression data from fibroblasts from a control individual


title: Control 8


title: Tobacco High T2, Sample1

value: FEI

value: pulmonary epithelial cells

value: high dose D3 (90 ug/ml)


title: Control 9 cultured in the presence of Retinoic Acid

value: control


title: Control 7 cultured in the presence of Retinoic Acid


title: hela_mho_0h_rep2


title: Nr4a1 kidney at week24, biological rep1


title: hela_mho_0h_rep3


title: hela_mho_0h_rep1


title: hela_48h_rep4

source_name: cell culture

value: not infected


title: Control 7

value: untreated


title: FHH kidney at week24, biological rep2

description: Gene expression data from FHH kidney at 24 weeks of age

source_name: Kidney isolated from FHH at week 24

value: wild-type FHH


title: hela_48h_rep2


title: hela_48h_rep1


title: Control 6 cultured in the presence of Retinoic Acid


title: Control 5


title: Nr4a1 kidney at week16, biological rep3

description: Gene expression data from Nr4a1-/- kidney at 16 weeks of age

source_name: Kidney isolated from Nr4a1-/- at week 16

value: 16 weeks of age


title: Control 5 cultured in the presence of Retinoic Acid


title: Nr4a1 kidney at week16, biological rep2


title: FHH kidney at week24, biological rep3


title: FHH kidney at week16, biological rep2

description: Gene expression data from FHH kidney at 16 weeks of age

source_name: Kidney isolated from FHH at week 16


title: hela_48h_rep3


title: FHH kidney at week16, biological rep3


title: Control 4 cultured in the presence of Retinoic Acid


title: hela_4h_rep2


title: FHH kidney at week24, biological rep1


title: FHH kidney at week16, biological rep1


title: hela_4h_rep4


title: Control 4


title: Control 3 cultured in the presence of Retinoic Acid


title: C_ust1_14_25_48h

city: ATHENS

first: Scott

middle: E

last: Gold

address: 950 COLLEGE STATION RD

department: Toxicology and Mycotoxin Research

institute: USDA ARS

hyb_protocol: Arrays were hybridized using standardized Nimblegen protocol (please see http://www.nimblegen.com/index.html)

scan_protocol: Arrays were scanned using standardized Nimblegen protocol (please see http://www.nimblegen.com/index.html)

data_processing:
Data Processing was performed using Standardized Nimblegen protocol (please see http://www.nimblegen.com/index.html)
signal calculated by Nimblegen software. The values in the matrix table are expression avarages of 10 probes per gene per block. There were four blocks on 4-plex Nimblegen chip each containing different sample.

organism: Mycosarcoma maydis

source_name: RNA from mutant (ust1) fungal cells 48h in culture

label_protocol: Samles were labeled using standardized Nimblegen protocol (please see http://www.nimblegen.com/index.html)

growth_protocol: 48 hour in culture media

extract_protocol: Wild-type and ∆ust1 strains were grown in potato dextrose broth (PDB) for 48 h at 30 C. To allow effective comparison with other array data generated by U. maydis researchers, cells were then transferred to liquid array medium (6.25% Holiday salt solution, 30mM L-glutamine, 1% glucose, pH7.0, filter sterilized) at 30 C. Total RNA samples from WT 1/2  and ∆ust1 mutant strains grown in array medium for 24 h (mutant’s filamentous phase), and 48 h (mutant’s spore-like structure formation phase) were extracted and purified (Sigma Spectrum Plant Total RNA Kit, Cat.No.STRN50).

treatment_protocol: 30 C shaker (250 rpm)

tag: genotype/variation

value: ust1 mutant (14/25)

tag: culture time

value: 48 hour


title: Nr4a1 kidney at week8, biological rep3

description: Gene expression data from Nr4a1-/- kidney at 8 weeks of age

source_name: Kidney isolated from Nr4a1-/- at week 8

value: kidney

tag: genotype

value: 8 weeks of age


title: Control 2 cultured in the presence of Retinoic Acid


title: Control 6


title: hela_0h_rep4


title: C_ust1_14_25_24h

source_name: RNA from mutant (ust1) fungal cells 24h in culture

growth_protocol: 24 hour in culture media

value: 24 hour


title: hela_0h_rep2


title: hela_4h_rep3


title: Nr4a1 kidney at week16, biological rep1

value: point mutation in exon 1 of Nr4a1 gene


title: Control 2

value: dermal fibroblasts


title: Nr4a1 kidney at week8, biological rep2


title: C_WT_1_2_48h

source_name: RNA from wild type (WT) fungal cells 48h in culture


title: Control 1 cultured in the presence of Retinoic Acid

value: retinoic acid


title: hela_0h_rep1

value: HeLa S3 (ATCC CCL2.2)


title: hela_0h_rep3


title: C_WT_1_2_24h

source_name: RNA from wild type (WT) fungal cells 24h in culture


title: Nr4a1 kidney at week8, biological rep1


title: FHH kidney at week8, biological rep1

description: Gene expression data from FHH kidney at 8 weeks of age

source_name: Kidney isolated from FHH at week 8


title: STAT3 knockdown_1

status: Public on Feb 05 2014

city: Linköping

first: Sören

last: Bruhn

address: Ryddalsgatan 8a

institute: Linköping University

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a total volume of 25ul 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 Human Genome Oligo Microarrays (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x60k array slides.

data_processing:
The scanned images were analyzed with Feature Extraction Software (Agilent). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
The raw data was extracted and quantile normalized using GeneSpring GX software.

source_name: STAT3 knockdown

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 75ng total RNA using a Low Input QuickAmp Labeling Kit (Agilent Technologies, Palo Alto, Calif, USA) 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: Human CD4+ T cells (hBP CD4+ T cells, 2W-200, Lonza, Vallensbak Strand, Denkmark) were nucleofected either with nucleofection buffer, 1 µM human on target plus SMART pool siRNA against ELK1, GATA3, NFATC3, MAF, NFKB1, JUN, STAT3 (Dharmacon, Lafayette, CO) or non-targeting siRNA using the AMAXA nucleofection program U-014. Six hours after then nucleofection cells were washed, activated and polarized towards Th2. The CD4+ cells were activated with plate bound anti-CD3 (500ng / ml for coating of the plate), with soluble anti-CD28 (500ng / ml) and with IL-2 (17ng /ml, all purchased from R&D). Th2 polarization was induced with anti-IL-12 (5µg/ml) and IL-4 (10ng / ml). For RT-PCR and microarray analyisis the cells were harvested 12 hours of polarization and total RNA was extracted.

extract_protocol: Total RNA was extracted using the miRneasy Mini Kit (Qiagen, Valencia,CA, USA).

value: whole blood

value: CD4+ T cells

tag: sirna


title: STAT3 knockdown_4

tag: cell type


title: NFATC3 knockdown_3

source_name: NFATC3 knockdown


title: NFKB1 knockdown_2

source_name: NFKB1 knockdown


title: Control 1

source_name: Human dermal fibroblasts

tag: treatment


title: STAT3 knockdown_2


title: NFKB1 knockdown_3


title: NFATC3 knockdown_4


title: NFKB1 knockdown_1


title: MAF knockdown_4

source_name: MAF knockdown

value: MAF


title: MAF knockdown_2


title: MAF knockdown_1


title: NFKB1 knockdown_4


title: FHH kidney at week8, biological rep3


title: NFATC3 knockdown_1


title: STAT3 knockdown_3


title: FHH kidney at week8, biological rep2


title: MAF knockdown_3


title: NFATC3 knockdown_2


title: JUN Knockdown_2

source_name: JUN knockdown

value: JUN


title: JUN Knockdown_3


title: JUN Knockdown_1


title: JUN Knockdown_4


title: GATA3 Knockdown_2

source_name: GATA3 knockdown


title: GATA3 Knockdown_3


title: GATA3 Knockdown_1


title: GATA3 Knockdown_4


title: hela_4h_rep1

source_name: cell culture

value: not infected


title: Control 3

value: untreated

value: control


title: Control_replicate_4

source_name: scramble siRNA

value: scramble


title: ELK1 knockdown_4

source_name: ELK1 knockdown


title: Control_replicate_3


title: Control_replicate_6


title: ELK1 knockdown_1


title: ELK1 knockdown_3


title: Control_replicate_2


title: ELK1 knockdown_2


title: GM19238_Kd_IRF8_2

city: Tucson

first: Darren

middle: A.

last: Cusanovich

state: AZ

address: 1230 N Cherry Avenue, BSRL 421

department: Cellular and Molecular Medicine

institute: University of Arizona

hyb_protocol: Standard protocol

scan_protocol: Standard protocol

data_processing: First, probes overlapping SNPs were filtered out and the 3'-most probe for each gene was chosen. Then probes not meeting the detection threshold in at least one individual were filtered out. Intensity values were then log-transformed and quantile normalized using the 'lumi' package in R. Finally, the samples were corrected using the RUV-2 method.

source_name: LCL GM19238, Kd IRF8, 72hrs

label_protocol: Standard protocol

growth_protocol: Cells were grown at 37°C with 5% CO2 in RPMI-1640 (containing L-glutamine) supplemented with 15% FBS, 100 IU/ml penicilin and 100 µg/ml streptomycin.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy Plus 96 extraction kit. RNA quality was assessed with Agilent Bioanalyzer.

treatment_protocol: Cells were transfected with Lonza 96-well Nucleofector system, using solution SF and program DN-100.  For each knockdown, 1 million cells were transfected with 50pmol of siRNA and total RNA was extracted 72 hours later.

tag: chip number

tag: transfection plate

tag: target gene

tag: kd level

tag: rin

tag: transfection date


title: GM19238_Kd_CREBBP_3

source_name: LCL GM19238, Kd CREBBP, 72hrs

value: CREBBP


title: GM19238_Kd_STAT6_1

source_name: LCL GM19238, Kd STAT6, 72hrs


title: GM19238_Kd_TCF12_3

source_name: LCL GM19238, Kd TCF12, 72hrs


title: GM19238_Kd_NS2_24

source_name: LCL GM19238, Kd NS, 72hrs

value: NS


title: Control_replicate_5

tag: tissue


title: GM19238_Kd_RXRA_2

source_name: LCL GM19238, Kd RXRA, 72hrs

value: RXRA


title: GM19238_Kd_GTF2B_2

source_name: LCL GM19238, Kd GTF2B, 72hrs


title: GM19238_Kd_RELB_1

source_name: LCL GM19238, Kd RELB, 72hrs

value: RELB


title: GM19238_Kd_IKZF3_2

source_name: LCL GM19238, Kd IKZF3, 72hrs


title: GM19238_Kd_ZBTB38_2

source_name: LCL GM19238, Kd ZBTB38, 72hrs


title: GM19238_Kd_POU2F1_3

source_name: LCL GM19238, Kd POU2F1, 72hrs


title: GM19238_Kd_NS_P1_22


title: GM19238_Kd_JUND_1

source_name: LCL GM19238, Kd JUND, 72hrs

value: JUND


title: GM19238_Kd_IRF8_3


title: GM19238_Kd_PAX5_1

source_name: LCL GM19238, Kd PAX5, 72hrs


title: GM19238_Kd_HCST_2

source_name: LCL GM19238, Kd HCST, 72hrs

value: HCST


title: GM19238_Kd_ZHX2_2

source_name: LCL GM19238, Kd ZHX2, 72hrs


title: GM19238_Kd_IRF5_1_rep

source_name: LCL GM19238, Kd IRF5, 72hrs


title: GM19238_Kd_USF1_2

source_name: LCL GM19238, Kd USF1, 72hrs


title: Control_replicate_7

source_name: scramble siRNA


title: Control_replicate_8


title: GM19238_Kd_NFYC_2

source_name: LCL GM19238, Kd NFYC, 72hrs

value: NFYC


title: GM19238_Kd_E2F6_1

source_name: LCL GM19238, Kd E2F6, 72hrs


title: GM19238_Kd_STAT2_3

source_name: LCL GM19238, Kd STAT2, 72hrs


title: GM19238_Kd_NS1_21A

source_name: LCL GM19238, Kd NS, 72hrs


title: GM19238_Kd_RAD21_3

source_name: LCL GM19238, Kd RAD21, 72hrs


title: GM19238_Kd_NFE2L1_2

source_name: LCL GM19238, Kd NFE2L1, 72hrs


title: GM19238_Kd_RELA_1

source_name: LCL GM19238, Kd RELA, 72hrs

value: RELA


title: GM19238_Kd_WHSC1_1

source_name: LCL GM19238, Kd WHSC1, 72hrs


title: GM19238_Kd_NS_P1_21B


title: GM19238_Kd_NR3C1_1

source_name: LCL GM19238, Kd NR3C1, 72hrs


title: GM19238_Kd_BATF_2

source_name: LCL GM19238, Kd BATF, 72hrs

value: BATF


title: GM19238_Kd_IRF3_1

source_name: LCL GM19238, Kd IRF3, 72hrs


title: GM19238_Kd_TAF1_2

source_name: LCL GM19238, Kd TAF1, 72hrs


title: GM19238_Kd_SP1_2

source_name: LCL GM19238, Kd SP1, 72hrs


title: GM19238_Kd_BCL3_2

source_name: LCL GM19238, Kd BCL3, 72hrs


title: GM19238_Kd_YY1_3

source_name: LCL GM19238, Kd YY1, 72hrs


title: GM19238_Kd_SREBF2_1

source_name: LCL GM19238, Kd SREBF2, 72hrs


title: GM19238_Kd_ESRRA_1

source_name: LCL GM19238, Kd ESRRA, 72hrs

value: ESRRA


title: GM19238_Kd_RDBP_2

source_name: LCL GM19238, Kd RDBP, 72hrs

value: RDBP


title: GM19238_Kd_NFKB2_3

source_name: LCL GM19238, Kd NFKB2, 72hrs


title: GM19238_Kd_DIP2B_2

source_name: LCL GM19238, Kd DIP2B, 72hrs


title: GM19238_Kd_TCF12_1

source_name: LCL GM19238, Kd TCF12, 72hrs


title: GM19238_Kd_USF1_3

source_name: LCL GM19238, Kd USF1, 72hrs


title: GM19238_Kd_NS_P2_23

source_name: LCL GM19238, Kd NS, 72hrs


title: GM19238_Kd_RELB_3

source_name: LCL GM19238, Kd RELB, 72hrs


title: GM19238_Kd_KLF13_1

source_name: LCL GM19238, Kd KLF13, 72hrs


title: GM19238_Kd_IRF9_3

source_name: LCL GM19238, Kd IRF9, 72hrs


title: GM19238_Kd_JUND_3

source_name: LCL GM19238, Kd JUND, 72hrs


title: GM19238_Kd_IRF7_1

source_name: LCL GM19238, Kd IRF7, 72hrs


title: GM19238_Kd_EP300_3

source_name: LCL GM19238, Kd EP300, 72hrs


title: GM19238_Kd_TFE3_3

source_name: LCL GM19238, Kd TFE3, 72hrs


title: GM19238_Kd_TFE3_1


title: GM19238_Kd_TFDP1_3

source_name: LCL GM19238, Kd TFDP1, 72hrs


title: GM19238_Kd_POU2F2_3

source_name: LCL GM19238, Kd POU2F2, 72hrs


title: GM19238_Kd_TFE3_2


title: GM19238_Kd_POU2F2_2


title: GM19238_Kd_TFDP2_1

source_name: LCL GM19238, Kd TFDP2, 72hrs


title: GM19238_Kd_SP1_2_rep

source_name: LCL GM19238, Kd SP1, 72hrs


title: GM19238_Kd_TFDP1_2


title: GM19238_Kd_SP1_3_rep


title: GM19238_Kd_SP1_1_rep


title: GM19238_Kd_NS1_11


title: GM19238_Kd_SKIL_2

source_name: LCL GM19238, Kd SKIL, 72hrs

value: SKIL


title: GM19238_Kd_POU2F2_1


title: GM19238_Kd_TFDP1_1


title: GM19238_Kd_NR2F6_2

source_name: LCL GM19238, Kd NR2F6, 72hrs


title: GM19238_Kd_TFDP2_2


title: GM19238_Kd_NR2F6_3


title: GM19238_Kd_NS3_12


title: GM19238_Kd_SKIL_1


title: GM19238_Kd_SKIL_3


title: GM19238_Kd_NS_P6_12


title: GM19238_Kd_TFDP2_3


title: GM19238_Kd_NS_P3_11


title: GM19238_Kd_NS2_11


title: GM19238_Kd_NR1D2_2

source_name: LCL GM19238, Kd NR1D2, 72hrs


title: GM19238_Kd_NR1D2_1


title: GM19238_Kd_NFX1_1

source_name: LCL GM19238, Kd NFX1, 72hrs


title: GM19238_Kd_NR2F6_1


title: GM19238_Kd_NFX1_2


title: GM19238_Kd_NR1D2_3


title: GM19238_Kd_LCORL_1

source_name: LCL GM19238, Kd LCORL, 72hrs

value: LCORL


title: GM19238_Kd_LCORL_2


title: GM19238_Kd_LCORL_3


title: GM19238_Kd_HOXB7_3

source_name: LCL GM19238, Kd HOXB7, 72hrs


title: GM19238_Kd_IRF4_3

source_name: LCL GM19238, Kd IRF4, 72hrs


title: GM19238_Kd_IRF4_2


title: GM19238_Kd_IRF5_1

source_name: LCL GM19238, Kd IRF5, 72hrs


title: GM19238_Kd_IRF4_1


title: GM19238_Kd_IRF5_3


title: GM19238_Kd_IRF5_2


title: GM19238_Kd_HOXB7_1


title: GM19238_Kd_FOXA3_3

source_name: LCL GM19238, Kd FOXA3, 72hrs


title: GM19238_Kd_FOXA3_2


title: GM19238_Kd_FOXA3_1


title: Control_replicate_1

source_name: scramble siRNA

value: whole blood

value: CD4+ T cells


title: GM19238_Kd_EZH2_3

source_name: LCL GM19238, Kd EZH2, 72hrs


title: GM19238_Kd_E2F4_3

source_name: LCL GM19238, Kd E2F4, 72hrs


title: GM19238_Kd_E2F4_2


title: GM19238_Kd_HOXB7_2


title: GM19238_Kd_E2F1_2

source_name: LCL GM19238, Kd E2F1, 72hrs


title: GM19238_Kd_E2F1_3


title: GM19238_Kd_E2F1_1


title: GM19238_Kd_CLOCK_1

source_name: LCL GM19238, Kd CLOCK, 72hrs

value: CLOCK


title: GM19238_Kd_CLOCK_2


title: GM19238_Kd_EZH2_2


title: GM19238_Kd_E2F4_1


title: GM19238_Kd_ARNTL2_1

source_name: LCL GM19238, Kd ARNTL2, 72hrs


title: GM19238_Kd_ARNTL2_2


title: GM19238_Kd_EZH2_1


title: GM19238_Kd_CEBPG_3

source_name: LCL GM19238, Kd CEBPG, 72hrs

value: CEBPG


title: GM19238_Kd_CEBPG_1


title: GM19238_Kd_SP3_3

source_name: LCL GM19238, Kd SP3, 72hrs


title: GM19238_Kd_CEBPZ_2

source_name: LCL GM19238, Kd CEBPZ, 72hrs

value: CEBPZ


title: GM19238_Kd_TAF1_3

source_name: LCL GM19238, Kd TAF1, 72hrs


title: GM19238_Kd_TCF12_2

source_name: LCL GM19238, Kd TCF12, 72hrs


title: GM19238_Kd_CLOCK_3


title: GM19238_Kd_CEBPZ_3


title: GM19238_Kd_ARNTL2_3


title: GM19238_Kd_RAD21_1

source_name: LCL GM19238, Kd RAD21, 72hrs


title: GM19238_Kd_CREBBP_1

source_name: LCL GM19238, Kd CREBBP, 72hrs

value: CREBBP


title: GM19238_Kd_RDBP_1

source_name: LCL GM19238, Kd RDBP, 72hrs


title: GM19238_Kd_KLF13_2

source_name: LCL GM19238, Kd KLF13, 72hrs


title: GM19238_Kd_GTF2B_1

source_name: LCL GM19238, Kd GTF2B, 72hrs


title: GM19238_Kd_CEBPG_2


title: GM19238_Kd_CEBPZ_1


title: GM19238_Kd_POU2F1_2

source_name: LCL GM19238, Kd POU2F1, 72hrs


title: GM19238_Kd_NFE2L1_3

source_name: LCL GM19238, Kd NFE2L1, 72hrs


title: GM19238_Kd_YY1_2

source_name: LCL GM19238, Kd YY1, 72hrs


title: GM19238_Kd_STAT6_2

source_name: LCL GM19238, Kd STAT6, 72hrs


title: GM19238_Kd_IRF5_2_rep

source_name: LCL GM19238, Kd IRF5, 72hrs


title: GM19238_Kd_NFKB2_2

source_name: LCL GM19238, Kd NFKB2, 72hrs


title: GM19238_Kd_NS4_21B

source_name: LCL GM19238, Kd NS, 72hrs

value: NS


title: GM19238_Kd_STAT2_2

source_name: LCL GM19238, Kd STAT2, 72hrs


title: GM19238_Kd_NR3C1_2

source_name: LCL GM19238, Kd NR3C1, 72hrs


title: GM19238_Kd_IRF9_1

source_name: LCL GM19238, Kd IRF9, 72hrs


title: GM19238_Kd_BATF_1

source_name: LCL GM19238, Kd BATF, 72hrs


title: GM19238_Kd_BCL3_1

source_name: LCL GM19238, Kd BCL3, 72hrs


title: GM19238_Kd_E2F6_2

source_name: LCL GM19238, Kd E2F6, 72hrs


title: GM19238_Kd_JUND_2

source_name: LCL GM19238, Kd JUND, 72hrs


title: GM19238_Kd_WHSC1_3

source_name: LCL GM19238, Kd WHSC1, 72hrs


title: GM19238_Kd_IRF7_2

source_name: LCL GM19238, Kd IRF7, 72hrs


title: GM19238_Kd_HCST_1

source_name: LCL GM19238, Kd HCST, 72hrs


title: GM19238_Kd_NS4_12


title: GM19238_Kd_RXRA_3

source_name: LCL GM19238, Kd RXRA, 72hrs

value: RXRA


title: GM19238_Kd_NFE2L1_1

source_name: LCL GM19238, Kd NFE2L1, 72hrs


title: GM19238_Kd_EP300_1

source_name: LCL GM19238, Kd EP300, 72hrs


title: GM19238_Kd_RAD21_2

source_name: LCL GM19238, Kd RAD21, 72hrs


title: GM19238_Kd_IKZF3_3

source_name: LCL GM19238, Kd IKZF3, 72hrs


title: GM19238_Kd_ZHX2_3

source_name: LCL GM19238, Kd ZHX2, 72hrs


title: GM19238_Kd_RELA_3

source_name: LCL GM19238, Kd RELA, 72hrs


title: GM19238_Kd_NS3_21A

source_name: LCL GM19238, Kd NS, 72hrs


title: GM19238_Kd_NS2_23


title: GM19238_Kd_STAT6_3

source_name: LCL GM19238, Kd STAT6, 72hrs


title: GM19238_Kd_IRF9_2

source_name: LCL GM19238, Kd IRF9, 72hrs


title: GM19238_Kd_NS3_23


title: GM19238_Kd_RELA_2


title: GM19238_Kd_E2F6_3


title: GM19238_Kd_ESRRA_3

source_name: LCL GM19238, Kd ESRRA, 72hrs


title: GM19238_Kd_SP1_3

source_name: LCL GM19238, Kd SP1, 72hrs


title: GM19238_Kd_IRF3_2

source_name: LCL GM19238, Kd IRF3, 72hrs


title: GM19238_Kd_POU2F1_1

source_name: LCL GM19238, Kd POU2F1, 72hrs


title: GM19238_Kd_RDBP_3

source_name: LCL GM19238, Kd RDBP, 72hrs


title: GM19238_Kd_BCL3_3

source_name: LCL GM19238, Kd BCL3, 72hrs


title: GM19238_Kd_IRF7_3

source_name: LCL GM19238, Kd IRF7, 72hrs


title: GM19238_Kd_YY1_1

source_name: LCL GM19238, Kd YY1, 72hrs


title: GM19238_Kd_ESRRA_2


title: GM19238_Kd_DIP2B_3

source_name: LCL GM19238, Kd DIP2B, 72hrs


title: GM19238_Kd_ZBTB38_3

source_name: LCL GM19238, Kd ZBTB38, 72hrs


title: GM19238_Kd_NFKB2_1

source_name: LCL GM19238, Kd NFKB2, 72hrs


title: GM19238_Kd_GTF2B_3

source_name: LCL GM19238, Kd GTF2B, 72hrs


title: GM19238_Kd_NFYC_1

source_name: LCL GM19238, Kd NFYC, 72hrs


title: GM19238_Kd_STAT2_1

source_name: LCL GM19238, Kd STAT2, 72hrs


title: GM19238_Kd_SREBF2_3

source_name: LCL GM19238, Kd SREBF2, 72hrs


title: GM19238_Kd_DIP2B_1


title: GM19238_Kd_SP3_2

source_name: LCL GM19238, Kd SP3, 72hrs


title: GM19238_Kd_NFX1_3

source_name: LCL GM19238, Kd NFX1, 72hrs


title: GM19238_Kd_SP1_1


title: GM19238_Kd_SREBF2_2


title: GM19238_Kd_NR3C1_3

source_name: LCL GM19238, Kd NR3C1, 72hrs


title: GM19238_Kd_RELB_2

source_name: LCL GM19238, Kd RELB, 72hrs

value: RELB


title: GM19238_Kd_IRF8_1

source_name: LCL GM19238, Kd IRF8, 72hrs


title: GM19238_Kd_NS_P2_24

source_name: LCL GM19238, Kd NS, 72hrs


title: GM19238_Kd_WHSC1_2

source_name: LCL GM19238, Kd WHSC1, 72hrs


title: GM19238_Kd_PAX5_3

source_name: LCL GM19238, Kd PAX5, 72hrs


title: GM19238_Kd_EP300_2

source_name: LCL GM19238, Kd EP300, 72hrs


title: GM19238_Kd_USF1_1

source_name: LCL GM19238, Kd USF1, 72hrs


title: GM19238_Kd_HCST_3

source_name: LCL GM19238, Kd HCST, 72hrs

value: HCST


title: GM19238_Kd_NS1_22


title: GM19238_Kd_KLF13_3

source_name: LCL GM19238, Kd KLF13, 72hrs


title: GM19238_Kd_ZBTB38_1

source_name: LCL GM19238, Kd ZBTB38, 72hrs


title: GM19238_Kd_IKZF3_1

source_name: LCL GM19238, Kd IKZF3, 72hrs


title: GM19238_Kd_TAF1_1

source_name: LCL GM19238, Kd TAF1, 72hrs


title: GM19238_Kd_RXRA_1

source_name: LCL GM19238, Kd RXRA, 72hrs


title: GM19238_Kd_NFYC_3

source_name: LCL GM19238, Kd NFYC, 72hrs

value: NFYC


title: GM19238_Kd_IRF5_3_rep

source_name: LCL GM19238, Kd IRF5, 72hrs


title: GM19238_Kd_SP3_1

source_name: LCL GM19238, Kd SP3, 72hrs


title: GM19238_Kd_CREBBP_2

source_name: LCL GM19238, Kd CREBBP, 72hrs


title: GM19238_Kd_ZHX2_1

source_name: LCL GM19238, Kd ZHX2, 72hrs


title: Zfp706 reverted gene trap clone 1

city: Vienna

first: Martin

last: Leeb

address: Dr.-Bohr-Gasse 9/3

department: Max Perutz Labs

institute: University of Vienna

description:
diploidised post screen
Zfp706 REV 1

hyb_protocol: Hybridisation was performed following the illumina direct hybridisation protocol

scan_protocol: bead array reader (Illumina)

data_processing:
Raw data was loaded into R using the lumi package from bioconductor. Any non-expressed probes were filtered out using the detection p-value from Illumina: if for a given probe all the detection p-value for the samples are above 0.01 it was removed from the analysis as it is considered not expressed (not detected in all samples). After filtering data are transformed using the Variance Stabilization Transformation (VST) from lumi which is related to log2 transformation but without bias at low and high intensity.Thereafter data was normalized by quantile normalisation to remove technical variation between arrays.
Please note that the 'normalized_full.txt' contains normalized data with additional annotations.

source_name: Zfp706 reverted gene trap

label_protocol: samples were submitted to the Cambridge Genomic Services (CGS) for processing and primary data analysis. Amplification was performed according to the manufacturer's protocol using an Illumina Total prep 96 RNA Amplification kit (Ambion). Total RNA was first reverse transcribed followed by in vitro transcription to generate biotin- labelled RNA.

growth_protocol: 2i medium

extract_protocol: Quiagen Rneasy mini plus

treatment_protocol: untreated

tag: strain background

value: Zfp706 reverted gene trap

value: haploid ES cell


title: Zfp706 gene trap replicate 2

description:
diploidised post screen
Zfp706GT-VI13

source_name: Zfp706 gene trap

value: Zfp706 gene trap


title: Zfp706 reverted gene trap clone 3

description:
diploidised post screen
Zfp706 REV 6


title: Tg_nD_I_3

city: New Haven

first: Hailong

last: Meng

state: CT

address: 300 George Str

institute: Yale University

hyb_protocol: Hybridization buffer from the BeadChip kit (Illumina) was mixed with 1500 ng of biotin-labeled cRNA, heated to 65°C for 5 minutes, and then loaded onto the BeadChip. The BeadChips were sealed in a hybridization chamber and placed in an oven at 58°C with a rocker for 16-20 hours. After the hybridization, the BeadChips were washed and stained in a series of washes and stains as outlined in the Illumina protocol.

scan_protocol: The BeadChips were scanned on the Illumina Iscan.

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

source_name: Spleen

label_protocol: Preparation of cDNA, cRNA, and labeling were carried out by the Yale Center for Genomic Analysis using the standard Illumina protocols.

extract_protocol: RNA and DNA were isolated with Trizol from whole spleen frozen at -80 oC using a Qiagen AllPrep kit (80204) according to the manufacture’s instructions

value: Cyclin D1 Transgenic Mice

value: stimulated with SRBC with irradiation

tag: disease state

value: did not develop disease


title: Zfp706 gene trap replicate 3

description:
diploidised post screen
Zfp706GT-VI31b


title: Zfp706 gene trap replicate 1

description:
diploidised post screen
Zfp706GT-VI31


title: Zfp706 reverted gene trap clone 2

description:
diploidised post screen
Zfp706 REV 3


title: Tg_nD_I_1


title: Tg_nD_P_1

value: stimulated with SRBC with pristane


title: Tg_nD_A_3

value: stimulated with SRBC alone


title: Tg_nD_A_1


title: Tg_nD_I_2


title: Tg_nD_P_2


title: Tg_KO_nD_I_2

value: with Bim-deficient B-cells stimulated with SRBC with irradiation


title: Tg_nD_A_2


title: GM19238_Kd_IRF3_3

source_name: LCL GM19238, Kd IRF3, 72hrs


title: BM MSC3_late_TGF_12h

city: Aachen

first: Wolfgang

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

institute: RWTH Aachen University

hyb_protocol: standard Affy protocol

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: CEL files were processed using the Affymetrix Power Tools (APT) Software Package. Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003).

source_name: BM MSC3_late_TGF_12h

label_protocol: Standard Affymetrix procedures

growth_protocol: Bone marrow fragments from tibia plateau of patients undergoing surgery were flushed with PBS. Cell suspension was filtered through a 100 µm cell strainer and centrifuged for 7 min at 400xg. Cells were seeded into 75 cm2 tissue culture flasks with DMEM-LG (PAA) with 10% FCS (PAA), 2 mM L-glutamine (Sigma-Aldrich) and 100 U/mL penicilline/streptomycine (Lonza). The first medium exchange was performed after 48 hours to remove erythrocytes and other non-adherent cells. Thereafter, media was exchanged twice per week, and MSC were isolated by their plastic adherence. When reaching 80% confluence, cells were trypsinized, counted in a Neubauer counting chamber (Brand, Wertheim, Germany) and replated at 13,333 cells/cm2. When the cells were attached after 24 h 1ng/mL recombinant TGF-β1 (R&D Systems) was added to the culture media for different time points (1h, 4h, or 12h).

extract_protocol: RNeasy kit (Quiagen)

value: Bone marrow derived mesenchymal stromal cells (MSC)

tag: donor

tag: passage

value: 1ng/ml TGF-B1 at timepoint 12h


title: Tg_KO_nD_P_2

tag: genotype/variation

value: with Bim-deficient B-cells stimulated with SRBC with pristane


title: Tg_KO_D_P_1

value: developed MCL


title: Tg_KO_nD_I_3


title: GM19238_Kd_NS4_22

source_name: LCL GM19238, Kd NS, 72hrs

value: NS


title: Tg_KO_nD_P_1


title: GM19238_Kd_BATF_3

source_name: LCL GM19238, Kd BATF, 72hrs

value: BATF


title: Tg_KO_nD_A_1

value: with Bim-deficient B-cells stimulated with SRBC alone


title: Tg_KO_D_A_3


title: Tg_KO_nD_I_1


title: Tg_KO_nD_A_2


title: Tg_KO_D_I_3


title: Tg_KO_D_A_1


title: BM MSC3_late_TGF_1h

source_name: BM MSC3_late_TGF_1h

value: 1ng/ml TGF-B1 at timepoint 1h


title: Tg_KO_D_I_1


title: BM MSC3_early_TGF_12h

source_name: BM MSC3_early_TGF_12h


title: Tg_KO_D_I_2


title: BM MSC3_early_TGF_4h

source_name: BM MSC3_early_TGF_4h

value: 1ng/ml TGF-B1 at timepoint 4h


title: Tg_KO_D_A_2


title: BM MSC3_late_TGF_4h

source_name: BM MSC3_late_TGF_4h


title: GM19238_Kd_PAX5_2

source_name: LCL GM19238, Kd PAX5, 72hrs


title: BM MSC2_late_TGF_12h

source_name: BM MSC2_late_TGF_12h


title: BM MSC1_early_TGF_12h

source_name: BM MSC1_early_TGF_12h


title: BM MSC2_early_TGF_12h

source_name: BM MSC2_early_TGF_12h


title: BM MSC1_late_TGF_12h

source_name: BM MSC1_late_TGF_12h


title: BM MSC1_early_TGF_1h

source_name: BM MSC1_early_TGF_1h


title: BM MSC2_late_TGF_4h

source_name: BM MSC2_late_TGF_4h


title: BM MSC2_early_TGF_1h

source_name: BM MSC2_early_TGF_1h


title: BM MSC2_late_TGF_1h

source_name: BM MSC2_late_TGF_1h


title: BM MSC3_early_TGF_1h

source_name: BM MSC3_early_TGF_1h


title: BM MSC1_late_TGF_4h

source_name: BM MSC1_late_TGF_4h


title: BM MSC1_early_TGF_4h

source_name: BM MSC1_early_TGF_4h


title: BM MSC1_late_TGF_1h

source_name: BM MSC1_late_TGF_1h


title: BM MSC2_early_TGF_4h

source_name: BM MSC2_early_TGF_4h


title: flag leaf of Minghui 63, biological rep3

city: wuhan

first: wang

last: Jia

address: shizhishan

country: China

institute: hzau

description: expression variations in rice flag leaf at heading date

hyb_protocol: Microarray hybridization were conducted by the CapitalBio Corporation (Beijing, China) according to the Affymetrix standard protocols (Affymetrix GeneChip Expression Analysis Technical Manual)

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000.

data_processing: The probe intensity files (.cel files) for expression variations were read into R. Background correction, quantile normalization and summarization were performed using the RMA method in Bioconductor affy package.

organism: Oryza sativa

source_name: flag leaf at heading date, MH3

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

growth_protocol: The population used in the study contained 210 RILs derived by single-seed descent from a cross between Zhenshan 97 and Minghui 63. The RILs and two parents were planted in a seed bed and transplanted to the experimental farm of Huazhong Agricultural University in the rice growing seasons in Wuhan, China. The whole set of materials were sown in batches at 45 days apart for biological replicates. Two replicates were planted for each of the RILs and three replicated for each of the parents. A flag leaf from each of three random plants per replicate was collected at the heading stage (the day of the panicle emergence, Figure S6) between 8:00 and 9:30 am.

extract_protocol: Total RNA extraction was performed using Trizol, according to the manufacturer's instructions.

treatment_protocol: Untreated.

tag: subspecies

value: indica

tag: variety

value: Minghui 63


title: EA 127 amplified flight 8hr

city: Fort Detrick

first: Meskerem

last: Jibitu

address: 568 Doughten Drive

department: Integrative Systems Biology

institute: US Army Center for Environmental Health Research

hyb_protocol: Samples were hybridized to Agilent-014850 4x44K slides and incubated for 16 h at 55o C. A protocol with a series of washes was carried out.

scan_protocol: The slides were scanned using Agilent Technologies Scanner G2505C US09493743 and feature extracted (software v. 10.7, Agilent, Inc, CA).

data_processing: We processed the microarray mRNA data set by heuristic statistical manipulations accompanied by a systematic selection and rejection scheme. We performed pair-wise moderated t-test (p < 0.01), a recommended routine for small sample size enabling to deliver maximum confidence in the analyses.

source_name: Stratagene Universal Human Reference RNA

label_protocol: We labeled 12.5 ng amplified RNA and the same amount of reference RNA with Cy-5 and Cy-3 dyes, respectively.

growth_protocol: Human dermal microvascular endothelial cells (HMVEC-dBL) (Lonza, VA) were maintained in EGM-2MV growth medium (Lonza, VA) containing growth factors, antimicrobials, cytokines and 5% FBS (all purchased from Lonza, VA) at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol: We extracted mRNA and miRNA from the RLT solution using the AllPrep DNA/RNA extraction kit (Qiagen, MD) and from the TrizolTM portion following the manufacturer's protocols.

treatment_protocol: Exposures of 100 μg/ml LPS for 4 hr and 8 hr.

tag: sample type

value: reference

source_name: Human dermal microvascular endothelial cell line amplified, LPS, 8hr

tag: cell line

value: HMVEC-dBL

value: LPS

tag: treatment duration


title: EA 165 amplified ground 8hr

tag: cell type

value: dermal microvascular endothelial cell line

tag: treatment


title: EA 155 amplified flight 4hr

source_name: Human dermal microvascular endothelial cell line amplified, LPS, 4hr


title: EA 45 amplified flight 4hr


title: EA 125 amplified ground control

source_name: Human dermal microvascular endothelial cell line amplified, control

value: control


title: flag leaf of Minghui 63, biological rep1

source_name: flag leaf at heading date, MH1


title: EA 126 amplified flight 8hr


title: EA 79 amplified flight control


title: flag leaf of Minghui 63, biological rep2

source_name: flag leaf at heading date, MH2


title: EA 33 amplified ground control


title: EA 123 amplified ground 8hr


title: flag leaf of Zhenshan 97, biological rep3

source_name: flag leaf at heading date, ZS5

value: Zhenshan 97


title: EA 41 amplified ground 4hr


title: EA 39 amplified flight control


title: flag leaf of Zhenshan 97, biological rep1

source_name: flag leaf at heading date, ZS1


title: EA 47 amplified ground 4hr


title: flag leaf of Zhenshan 97, biological rep2

source_name: flag leaf at heading date, ZS3


title: flag leaf of R237

source_name: flag leaf at heading date, R237

value: Minghui 63/Zhenshan 97 RILs


title: flag leaf of R241

source_name: flag leaf at heading date, R241


title: flag leaf of R239

source_name: flag leaf at heading date, R239


title: flag leaf of R236

source_name: flag leaf at heading date, R236


title: flag leaf of R231

source_name: flag leaf at heading date, R231


title: flag leaf of R230

source_name: flag leaf at heading date, R230


title: flag leaf of R233

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title: P113S3L24H7: AggressiveGeneralizedControl

city: New York

first: Paolo

last: Guarnieri

state: NY

address: 1130 St. Nicholas Avenue

department: Systems Biology

institute: Columbia University

hyb_protocol: Labeled RNA hybridized with microarrays carrying probes for 1,205 human and 144 human viral miRNAs (SurePrint G3 Human v16 miRNA 8x60K Microarray Kit).

scan_protocol: Array images were scanned with Agilent Technologies Scanner G2505C US83000178 using grid 031181_D_F_20110707 and protocol miRNA_105_Dec08.

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using  031181_D_F_20110707.xml as design file to obtain background subtracted and Processed Signal intensities. Subsequent data analysis and normalization was performed within R/Bioconductor. Data was normalized and background corrected using rmaMicroRna function with background and normalize set to TRUE. Filtering was performed according to the recommended AgiMicroRna documentation having the following filterMicroRna parameters:
control = TRUE,
IsGeneDetected = TRUE,
wellaboveNEG = FALSE,
limIsGeneDetected = 75,
limNEG = 25

label: cyanine 3-pCp

source_name: periodontal tissue

label_protocol: miRNA profiling was carried out using the Agilent platform (Agilent Technologies). Total RNA (100 ng/specimen) was labeled to generate fluorescent miRNA by ligation of cyanine 3-pCp to the 3’end

extract_protocol: Tissue samples were stored in liquid RNA stabilization reagent (RNAlater, Austin, TX) overnight at 4°C, snap-frozen and stored in liquid nitrogen. Specimens were homogenized in Trizol (Invitrogen Life Technologies, Carlsbad, CA), incubated with chloroform and centrifuged at 12,000g. RNA collected in the upper aqueous phase was precipitated by mixing with 75% isopropyl-alcohol and additional centrifugation and washings, and was quantified spectrophotometrically. RNA quality was assessed by determining the RNA Integrity Number (RIN).

treatment_protocol: Gingival tissue samples comprising pocket/sulcus epithelium and the underlying connective tissue were obtained from patients with chronic or aggressive periodontitis in conjunction with periodontal surgery

tag: patient

tag: specimen

tag: biopsyid

tag: diagnosis

value: Aggressive

tag: extent

value: Generalized

tag: condition

value: Control

tag: labelbatch

tag: hybridizebatch


title: flag leaf of R013

source_name: flag leaf at heading date, R013


title: flag leaf of R004

source_name: flag leaf at heading date, R004


title: P113S1L25H8: AggressiveGeneralizedAffected

value: Affected


title: Cebpa_fl/fl_Mx1Cre_b

city: Copenhagen N

first: Marie

middle: S

last: Hasemann

address: Ole Maaløes Vej 5

department: Finsen Laboratory

country: Denmark

institute: Rigshospitalet

description: Murine Cebpafl/fl;Mx1Cre (deleted) LSKCD150- sample

hyb_protocol: Affymetrix EukGE-WS2v4_450 Hybridization protocol, according to manufacturers specifications

scan_protocol: Cell intesity files (CEL files) were generated in the Genechip Command Console Software (AGCC), (Affymetrix, Santa Clara, CA, USA)

data_processing: The Robust Multichip Average (RMA) algorithm as implemented in the Affymetrix Expression Console (version 1.1.2) was applied to generate normalized intensity values.

source_name: Sorted LSKCD150- from bone marrow samples, 18 days post conditional gene knock out

label_protocol: 2.5ug of amplified cDNA was fragmentated and labeled using Encore Biotin Module V2 according to manufactures instructions. www.nugeninc.com/nugen/index.cfm/products/pl/target-preparation/encore-biotin-module/

growth_protocol: Murine bone marrow cells were enriched for cKit+ and LSKCD150- cells were sorted by FACS.

extract_protocol: Total RNA from sorted cells were isolated with RNeasy Micro Kit (Qiagen). Samples were prepared in triplicates for each genotype. 20 ng of total RNA was amplified using Ovation Pico WTA system V2 (Nugene)according to manufactures instructions. www.nugeninc.com/nugen/index.cfm/products/cs/microarrays-and-qpcr/ovation-pico-wta-system-v2/manufacturers instructions.

treatment_protocol: Female mice were injected with pIpC, at day 18 they were sacrifized and bones were dissected, bone marrow cells were isolated by crushing and LSKCD150- cells were sorted by FACS.


title: Cebpa_fl/fl_c

description: Murine Cebpafl/fl (wild-type) LSKCD150- sample

value: Cebpafl/fl


title: Cebpa_fl/fl_Mx1Cre_c


title: P111S2L25H8: AggressiveGeneralizedAffected


title: Cebpa_fl/fl_Mx1Cre_a


title: Cebpa_fl/fl_a


title: flag leaf of R023

source_name: flag leaf at heading date, R023


title: flag leaf of R002

source_name: flag leaf at heading date, R002


title: Cebpa_fl/fl_b


title: P110S2L19H5: AggressiveGeneralizedAffected


title: P111S1L19H5: AggressiveGeneralizedAffected


title: flag leaf of R003

source_name: flag leaf at heading date, R003


title: P110S1L19H5: AggressiveGeneralizedAffected


title: P109S1L19H5: AggressiveGeneralizedAffected


title: flag leaf of R001

source_name: flag leaf at heading date, R001


title: P108S2L19H5: AggressiveGeneralizedAffected


title: P108S1L19H5: AggressiveGeneralizedAffected


title: P107S2L19H5: AggressiveGeneralizedAffected


title: P106S1L18H5: ChronicGeneralizedAffected

value: Chronic


title: P104S2L18H5: AggressiveGeneralizedAffected


title: P105S2L18H5: AggressiveGeneralizedAffected


title: P104S1L18H5: AggressiveGeneralizedAffected


title: P102S3L14H4: AggressiveGeneralizedControl


title: P102S1L17H5: AggressiveGeneralizedAffected


title: P109S2L19H5: AggressiveGeneralizedAffected


title: P102S2L18H5: AggressiveGeneralizedAffected


title: flag leaf of R021

source_name: flag leaf at heading date, R021


title: P106S2L18H5: ChronicGeneralizedAffected


title: flag leaf of R007

source_name: flag leaf at heading date, R007


title: P99S2L17H5: AggressiveLocalizedAffected

value: Localized


title: P101S3L17H5: AggressiveLocalizedAffected


title: P107S1L18H5: AggressiveGeneralizedAffected


title: P98S2L17H5: AggressiveGeneralizedAffected


title: P101S2L17H5: AggressiveLocalizedAffected


title: P99S1L17H5: AggressiveLocalizedAffected


title: P94S2L16H7: AggressiveGeneralizedAffected


title: P94S1L16H7: AggressiveGeneralizedAffected


title: P95S1L17H5: AggressiveGeneralizedAffected


title: P92S3L24H7: AggressiveLocalizedControl


title: P92S2L25H8: AggressiveLocalizedAffected


title: P105S1L18H5: AggressiveGeneralizedAffected


title: P92S1L16H7: AggressiveLocalizedAffected


title: P91S1L16H7: ChronicGeneralizedAffected


title: P91S3L16H7: ChronicGeneralizedControl


title: P91S2L16H7: ChronicGeneralizedAffected


title: P90S2L25H8: ChronicLocalizedAffected


title: P89S2L15H7: ChronicGeneralizedAffected


title: P98S1L17H5: AggressiveGeneralizedAffected


title: P84S2L15H7: ChronicGeneralizedAffected


title: P84S1L15H7: ChronicGeneralizedAffected


title: P93S1L25H8: ChronicGeneralizedAffected


title: P83S2L15H7: ChronicLocalizedAffected


title: P78S1L14H4: AggressiveGeneralizedAffected


title: P81S2L14H4: ChronicGeneralizedAffected


title: P77S3L14H4: ChronicLocalizedControl


title: P82S3L15H7: ChronicGeneralizedControl


title: P83S1L15H7: ChronicLocalizedAffected


title: P77S2L14H4: ChronicLocalizedAffected


title: P90S3L25H8: ChronicLocalizedControl


title: P89S1L15H7: ChronicGeneralizedAffected


title: P83S3L15H7: ChronicLocalizedControl


title: P77S1L14H4: ChronicLocalizedAffected


title: P75S2L13H4: ChronicLocalizedAffected


title: P76S2L14H4: AggressiveGeneralizedAffected


title: P75S1L13H4: ChronicLocalizedAffected


title: P74S1L13H4: ChronicGeneralizedAffected


title: P74S3L13H4: ChronicGeneralizedControl


title: P81S1L14H4: ChronicGeneralizedAffected


title: P74S2L13H4: ChronicGeneralizedAffected


title: P72S3L13H4: AggressiveLocalizedControl


title: P73S1L13H4: AggressiveGeneralizedAffected


title: P73S2L13H4: AggressiveGeneralizedAffected


title: P72S1L12H4: AggressiveLocalizedAffected


title: P72S2L12H4: AggressiveLocalizedAffected


title: P71S1L12H4: ChronicGeneralizedAffected


title: P70S1L12H4: ChronicGeneralizedAffected


title: P69S3L12H4: AggressiveLocalizedControl


title: P70S2L12H4: ChronicGeneralizedAffected


title: P67S2L20H6: ChronicLocalizedAffected


title: P68S2L20H6: ChronicLocalizedAffected


title: P68S3L20H6: ChronicLocalizedControl


title: P69S1L20H6: AggressiveLocalizedAffected


title: P71S2L12H4: ChronicGeneralizedAffected


title: P69S2L12H4: AggressiveLocalizedAffected


title: P67S1L20H6: ChronicLocalizedAffected


title: P66S2L20H6: ChronicLocalizedAffected


title: P66S3L20H6: ChronicLocalizedControl


title: P65S4L11H3: ChronicGeneralizedControl


title: P66S1L11H3: ChronicLocalizedAffected


title: P65S2L11H3: ChronicGeneralizedAffected


title: P64S3L11H3: ChronicGeneralizedControl


title: P68S1L25H8: ChronicLocalizedAffected


title: P64S1L11H3: ChronicGeneralizedAffected


title: P63S3L11H3: AggressiveGeneralizedControl


title: P64S2L11H3: ChronicGeneralizedAffected


title: P63S2L11H3: AggressiveGeneralizedAffected


title: P63S1L10H3: AggressiveGeneralizedAffected


title: teratoma D3 Replicate 1

city: Jerusalem

first: guy

last: ludwig

address: Ein Kerem

institute: Hebrew University

hyb_protocol: The labeled Input and Bound DNAs were combined and hybridized for 60 h at 67°C in 15% deionized formamide to a CpG island microarray using the Agilent aCGH hybridization buffer and protocol.

scan_protocol: Arrays were washed according to the Agilent aCGH protocol, immediately scanned on an Agilent microarray scanner and processed using Agilent Feature extraction software version 9.5.

data_processing: Probe log ratio signals were Loess normalized and transformed into Z-scores according to their Tm using Agilent Feature extraction software version 9.5.

label_protocol: The Input and Bound DNAs were labeled using the Agilent Technologies Genomic Labeling kit Plus according to the manufacturer’s instructions. Briefly, 300ng of each sample was labeled with Cyanine-3 or Cyanine-5 dUTP and purified using microcon YM 30 columns.

extract_protocol: mouse (40µg) DNA was sonicated to an average fragment size of 300–1000 bp, precipitated with  400 mM NaCl, 2 volumes of ethanol and 1 µl glycogen. 1.5 µg were set aside as the Input fraction. DNA was denatured and anti-5-methylcytidine  monoclonal antibody (10 µl for 5 µg) was added and incubated on a rotator at 4°C overnight. 40 µl Dynabeads (Sheep anti-Mouse IgG) were prewashed  with 0.1% BSA/PBS and added to the DNA. The DNA was then washed 3 times and Ab-bound DNA resuspended and extracted with proteinase K,  phenol-chloroform and ethanol precipitation.

value: teratoma D3


title: teratoma D3 Replicate 2


title: Placenta 19.5 Replicate 1

tag: strain background

tag: gender

value: Female

tag: age

tag: tissue

value: Placenta


title: Placenta 19.5 Replicate 2


title: teratoma C4 Replicate 2

value: teratoma C4


title: P61S4L10H3: ChronicLocalizedControl