title: WG0093351-DNAC01_Brittany Spaniels

hyb_protocol: standard Illumina protocols were used and hybridization was performed by Illumina Inc. USA

scan_protocol: standard Illumina protocols were used and scanning was performed by Illumina Inc. USA

data_processing:
Illumina Inc. USA performed the intial data processing (http://res.illumina.com/documents/products/datasheets/datasheet_caninehd.pdf). The standard cluster file that was used as reference when Log R ratios and B allele frequencies were calculated was created with the samples herein by Illumina Inc. USA. Further processing was perfromed by the authors using GenomeStudio V2010.3, Genotyping Module 1.8.4 where the Log R Ratio was corrected for GC content and low quality SNPs and intensity-only SNPs were removed. Remaining number of SNPs used in the CNV calling were 172115.
ID REF, LRR_GCC are Log R ratio values after GC-correction and this was used in the subsequent CNV discovery, Score, Theta, R, Gtype, B Allele Freq, Log R Ratio

extract_protocol: genomic DNA was extracted from blood using standard procedures

value: blood


title: isolate1

status: Public on Mar 28 2014

type: genomic

city: Baltiomore

first: Christopher

last: Jacob

state: MD

address: 685 W. Baltimore St.

department: Center for Vaccine Development

country: USA

institute: University of Maryland School of Medicine

hyb_protocol: described in Jacob et al, 2014

scan_protocol: Arrays were scanned on a NimbleGen MS 200 scanner using autogain setting per manufacturer's protocol (www.NimbleGen.com)

data_processing: data were processed by both a previously published method (PMCID: PMC3218861), and by a custom algorithm (Jacob et al, 2014, Submitted) (attached)

molecule: genomic DNA

organism: Plasmodium falciparum

source_name: DNA from Southeast Asian Field Isolate

label_protocol: described in Jacob et al, 2014

extract_protocol: all samples were extracted using a Qiagen blood extraction mini prep (qiagen.com)

tag: origin

value: Field Isolate

tag: parasitemia (parasites/ul)

tag: leukocyte depletion status

value: Yes

tag: whole genome amplification status

value: No

tag: dna amount (qpcr determined) (ng)


title: MIR_99A_2

type: RNA

city: Frankfurt

first: Jan-Henning

last: Klusmann

address: Theodor-Stern-Kai 7

department: Pediatric Hematology and Oncology

country: Germany

institute: Goehte University Frankfurt

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 10.5 (Agilent) using default parameters  to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

molecule: total RNA

organism: Homo sapiens

source_name: CB-HSPCs, transduced with LeGO-miR-99a, grown 7 days in megakarycytic differentiation medium, exp 2

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

growth_protocol: CB-HSPCs cells were grown in StemSpan, supplemented with SCF (1ng/ml), TPO (30ng/ml), IL-9 (13.5ng/ml), IL-6 (7.5ng/ml).

extract_protocol: Direct-zol™ RNA MiniPrep Kit (Zymo Research)

treatment_protocol: CB-HSPCs were transduced with the indicated virus.

tag: cell line

value: cord blood CD34+-hematopoietic stem and progenitor cells (CB-HSPCs)

tag: genotype/variation (vector)

tag: exp


title: WG0093351-DNAB02_Brittany Spaniels

city: Uppsala

first: Anna-Maja

last: Molin

address: Gerda Nilssons väg 2

department: Department of Animal Breeding and Genetics

country: Sweden

institute: Swedish University of Agricultural Sciences

label: biotin

organism: Canis lupus familiaris

source_name: blood

label_protocol: standard Illumina protocols were used and labelling was performed by Illumina Inc. USA

tag: breed

value: Brittany Spaniels

tag: gender

value: Female

tag: tissue


title: MIR_SC_2

source_name: CB-HSPCs, transduced with LeGO-miR-SC, grown 7 days in megakarycytic differentiation medium, exp 2

value: LeGO-miR-SC


title: 3D7_17

source_name: DNA from 3D7 strain (MR4 repository provided)

value: Lab Isolate

tag: strain


title: 3D7_16


title: 3D7_18


title: WG0093351-DNAB01_Brittany Spaniels


title: MIR_99A-125B_1

source_name: CB-HSPCs, transduced with LeGO-miR-99a~125b-2, grown 7 days in megakarycytic differentiation medium, exp 1


title: LET_7C_1

source_name: CB-HSPCs, transduced with LeGO-let-7c, grown 7 days in megakarycytic differentiation medium, exp 1


title: 3D7_15


title: MIR_125B_1

source_name: CB-HSPCs, transduced with LeGO-miR-125b-2, grown 7 days in megakarycytic differentiation medium, exp 1


title: WG0093352-DNAH02_Border collies

value: Border collies

value: Male


title: 3D7_14


title: WG0093351-DNAA02_Brittany Spaniels


title: MIR_SC_1

source_name: CB-HSPCs, transduced with LeGO-miR-SC, grown 7 days in megakarycytic differentiation medium, exp 1


title: MIR_99A_1

source_name: CB-HSPCs, transduced with LeGO-miR-99a, grown 7 days in megakarycytic differentiation medium, exp 1


title: SCR_E_2

source_name: FL-HSPCs, transduced with LeGO-iG-shSC, grown 0 days in myeloid differentiation medium, duplicate 2

growth_protocol: FL-HSPCs cells were grown in RPMI, 20% FCS, 1% P/S, SCF (5ng/ml), GM-CSF (10ng/ml), G-SCF (10ng/ml), IL-3 (5ng/ml)

extract_protocol: RNeasy Mini Kit (Qiagen)

treatment_protocol: FL-HSPCs were transduced with the indicated virus.

value: wild-type CD34+-hematopoietic stem and progenitor cells

value: LeGO-iG-shSC

tag: days


title: WG0093352-DNAG02_Border collies


title: WG0093352-DNAF02_Border collies


title: 3D7_12


title: 3D7_11


title: 3D7_13


title: WG0093352-DNAE03_Border collies


title: WG0093352-DNAD02_Border collies


title: SCR_E_1

source_name: FL-HSPCs, transduced with LeGO-iG-shSC, grown 0 days in myeloid differentiation medium, duplicate 1


title: 3D7_9


title: SCR_1

source_name: FL-HSPCs, transduced with LeGO-iG-shSC, grown 4 days in myeloid differentiation medium, duplicate 1


title: WG0093352-DNAE02_Border collies


title: 3D7_8


title: SCR_2

source_name: FL-HSPCs, transduced with LeGO-iG-shSC, grown 4 days in myeloid differentiation medium, duplicate 2


title: 3D7_7


title: G1S_D14

source_name: FL-HSPCs, transduced with LeGO-iG-Gata1s/shG1, grown 14 days in myeloid differentiation medium, duplicate 1


title: WG0093352-DNAB03_Border collies


title: WG0093352-DNAC02_Border collies


title: WG0093351-DNAH02_Bernese Mountain Dogs

value: Bernese Mountain Dogs


title: WG0093351-DNAG03_Bernese Mountain Dogs


title: WG0093352-DNAA03_Border collies


title: WG0093351-DNAH03_Bernese Mountain Dogs


title: G1S_2

source_name: FL-HSPCs, transduced with LeGO-iG-Gata1s/shG1, grown 4 days in myeloid differentiation medium, duplicate 2


title: WG0093351-DNAF03_Bernese Mountain Dogs


title: NF54_12

source_name: DNA from NF54 strain (Sanaria Inc. provided)


title: G1S_1

source_name: FL-HSPCs, transduced with LeGO-iG-Gata1s/shG1, grown 4 days in myeloid differentiation medium, duplicate 1


title: 3D7_10


title: G1_2

source_name: FL-HSPCs, transduced with LeGO-iG-Gata1/shG1, grown 4 days in myeloid differentiation medium, duplicate 2


title: NF54_11


title: NF54_10


title: G1_1

source_name: FL-HSPCs, transduced with LeGO-iG-Gata1/shG1, grown 4 days in myeloid differentiation medium, duplicate 1


title: NF54_8


title: NF54_7


title: WG0093351-DNAD03_Bernese Mountain Dogs

source_name: blood


title: small_airway_bronch_NORMAL22

city: Vancouver

first: Wan

middle: L.

last: Lam

state: British Columbia

address: 675 West 10th Avenue

department: Integrative Oncology

country: Canada

institute: British Columbia Cancer Research Centre

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard

data_processing: Probeset summarization and generation of numerical gene expression levels were performed using the makecdfenv package and RMA normalization using the HuGene-1_0-st-v1.CDF file in R (v.2.12)

source_name: small airway epithelia

label_protocol: Standard Affymetrix labelling protocol

growth_protocol: collected during bronchoscopy, placed directly into RNALater (not expanded in vitro)

extract_protocol: cell pellets were lysed and total RNA was isolated using standard Trizol extraction

treatment_protocol: bronchial brush specimens were stored in RNALater at -80°C. Prior to processing, vials are thawed on ice, centirfuged and the pellet washed twice in PBS.

value: M

tag: age

tag: smoking status

value: Former Smoker

tag: yearsquitsmking

tag: packyears


title: WG0093351-DNAC03_Bernese Mountain Dogs


title: small_airway_bronch_NORMAL21

value: F


title: small_airway_bronch_NORMAL23


title: NF54_9

tag: origin


title: NF54_6

tag: parasitemia (parasites/ul)


title: small_airway_bronch_NORMAL8


title: WG0093351-DNAC04_Bernese Mountain Dogs

value: blood


title: small_airway_bronch_NORMAL19


title: NF54_4

tag: leukocyte depletion status


title: small_airway_bronch_NORMAL18


title: NF54_5

tag: whole genome amplification status


title: WG0093351-DNAA04_Bernese Mountain Dogs


title: NF54_3

tag: dna amount (qpcr determined) (ng)


title: small_airway_bronch_NORMAL16


title: WG0093351-DNAA03_Bernese Mountain Dogs


title: WG0093351-DNAB03_Bernese Mountain Dogs


title: small_airway_bronch_NORMAL17


title: small_airway_bronch_NORMAL15


title: NF54_1


title: NF54_2


title: WG0087816-DNAH07_Belgian Tervuren

value: Belgian Tervuren


title: WG0087816-DNAH06_Belgian Tervuren


title: Dd2_6

source_name: DNA from Dd2 strain (MR4 repository provided)


title: small_airway_bronch_NORMAL14


title: small_airway_bronch_NORMAL13


title: Dd2_5


title: WG0093351-DNAD01_Brittany Spaniels


title: WG0087816-DNAF08_Belgian Tervuren


title: WG0087816-DNAG07_Belgian Tervuren


title: small_airway_bronch_NORMAL12


title: Dd2_2


title: small_airway_bronch_NORMAL11


title: WG0087816-DNAG08_Belgian Tervuren


title: WG0093351-DNAE03_Bernese Mountain Dogs


title: Dd2_3


title: WG0087816-DNAE08_Belgian Tervuren


title: small_airway_bronch_NORMAL10


title: WG0087816-DNAF07_Belgian Tervuren


title: WG0087816-DNAD08_Belgian Tervuren


title: Dd2_1


title: small_airway_bronch_COPD8


title: small_airway_bronch_COPD5


title: 3D7_6

source_name: DNA from 3D7 strain (MR4 repository provided)


title: 3D7_5


title: Dd2_4


title: small_airway_bronch_COPD14


title: 3D7_3


title: WG0087816-DNAE07_Belgian Tervuren


title: WG0087816-DNAC07_Belgian Tervuren


title: 3D7_4


title: small_airway_bronch_COPD6


title: small_airway_bronch_COPD13


title: WG0087816-DNAD07_Belgian Tervuren


title: WG0087816-DNAC08_Belgian Tervuren


title: WG0087816-DNAB08_Belgian Tervuren


title: 3D7_2


title: small_airway_bronch_COPD1


title: WG0087816-DNAB07_Belgian Tervuren


title: WG0087816-DNAA08_Belgian Tervuren


title: small_airway_bronch_COPD11


title: WG0087816-DNAA07_Belgian Tervuren


title: small_airway_bronch_COPD12


title: 11

status: Public on Mar 27 2014

city: Geneva

first: Giorgio

last: Ramadori

address: Michel Servet 1

country: Switzerland

institute: University of Geneva

description: high calorie diet 6

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

organism: Mus musculus

source_name: dissected lung tumor

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

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

tag: genotype/variation

tag: diet

value: high calorie


title: primary tumor sample long-term OS 3448F

city: Leipzig

first: Edith

last: Willscher

address: Haertelstraße 16-18

institute: IZBI

description: Gene expression data from primary Glioblastoma

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

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

data_processing: Raw probe intensities were calibrated and summarized into one expression value per probe set using the hook method, and then quantile-normalised. The expression value of each gene was transformed into log10-scale and centered with respect to its mean value averaged over all samples investigated

source_name: Human Brain, primary Glioblastoma

label_protocol: Sample preparation was done with 2.5 μg total-RNA using the One Cycle Target Labelling and Controls kit (Affymetrix).

extract_protocol: DNA and RNA were extracted by ultracentrifugation.

treatment_protocol: Tumor samples were shock-frozen after resection and stored at -80 °C. Only specimens with a histologically estimated tumor cell content of 80% or more were used for molecular analyses.

tag: survival

value: long-term OS

value: Human Brain, primary Glioblastoma


title: primary tumor sample long-term OS 2610F


title: 9

description: high calorie diet 4


title: primary tumor sample long-term OS 21812F


title: primary tumor sample long-term OS 9151M


title: 10

description: high calorie diet 5


title: primary tumor sample long-term OS 9979H


title: BGL024_Beagle

tag: breed

value: Beagle


title: BGL031_Beagle

tag: gender

value: Female


title: 8

description: high calorie diet 3


title: BGL027_Beagle

tag: tissue


title: 6

description: high calorie diet 1


title: primary tumor sample long-term OS 2085H


title: 4

description: standard diet 4

value: standard


title: primary tumor sample long-term OS 1260E


title: primary tumor sample long-term OS 2027C


title: 7

description: high calorie diet 2


title: 3D7_1

value: Lab Isolate

tag: strain

value: No


title: 3

description: standard diet 3


title: 5

description: standard diet 5


title: primary tumor sample intermediate OS 2498A

value: intermediate OS


title: 2

description: standard diet 2


title: primary tumor sample long-term OS 3442E


title: primary tumor sample intermediate OS 1782H


title: BGL015_Beagle


title: 1

description: standard diet 1


title: BGL021_Beagle


title: primary tumor sample short-term OS 2550T

value: short-term OS


title: BGL023_Beagle

value: Male


title: ∆mazEFlexA3 10 μg/ml NA rep2

city: jerusalem

first: Hanna

last: Engelberg-Kulka

state: Israel

address: Ein Karem

department: Microbiology and Molecular Genetics

country: Israel

institute: The Hebrew University Hadassa Medical School

description: E. coli strain MC4100relA+ ∆mazEFlexA3 in mid log phase incubated at 37ºC for 4 hours with 10 μg/ml NA

hyb_protocol: Finally, labeled cDNA samples were hybridized to Affymetrix GeneChip E. coli arrays. Hybridized arrays were stained and washed using the Affymetrix ﬂuidic station 450.

scan_protocol: After staining, arrays were scanned with a GC3000 scanner. For CEL file generation, we used the software Affymetrix® GeneChip® Command Console® Software (AGCC).

data_processing:
RMA normalization was performed on CELL ﬁles using the Partek Genomic Suite 6.5. Additional statistical analysis was carried out using the Spotﬁre software package (Somerville, MA, USA) and custom Matlab (R2010B) routines.
Gene selection was done using the False Discovery Rate (FDR) correction procedure for adjusting genes with p-value smaller than 0.05 and Fold Change greater than 2.

organism: Escherichia coli

label_protocol: The RNA was subjected to cDNA synthesis, fragmentation, and end terminus biotin labeling according to the standard Affymetrix prokaryotic GeneChip expression protocol with the following modiﬁcations: cDNA synthesis was preformed with SuperScriptIII reverse transcriptase (Molecular Probes, Invitrogen (Carlsbad, CA, USA)), and cDNA reactions were incubated at 42°C overnight.

growth_protocol: We grew cells in 10 ml M9 minimal medium to OD600=0.5-0.6. Then, we divided each culture into 500µl aliquots to which we added the appropriate concentration of NA.

extract_protocol: We extracted RNA using RNAprotect Bacteria reagent (Qiagen) and RNeasy Mini Kit (Qiagen) combined with RNase-Free DNase Set (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: We incubated each aliquot at 37ºC for 4 hours with NA

tag: sample type

tag: genotype

tag: treatment

value: 10 μg/ml nalidixic acid


title: BGL014_Beagle


title: ∆mazEFlexA3 10 μg/ml NA rep1

source_name: E. coli strain MC4100relA+ ∆mazEFlexA3 in mid log phase incubated at 37ºC for 4 hours with 10 μg/ml NA


title: ∆mazEFlexA3 100 μg/ml NA rep1

description: E. coli strain MC4100relA+ ∆mazEFlexA3 in mid log phase incubated at 37ºC for 4 hours with 100 μg/ml NA

value: 100 μg/ml nalidixic acid


title: primary tumor sample long-term OS 8075F


title: ∆mazEFlexA3 100 μg/ml NA rep2

source_name: E. coli strain MC4100relA+ ∆mazEFlexA3 in mid log phase incubated at 37ºC for 4 hours with 100 μg/ml NA


title: ∆mazEF 10 μg/ml NA rep2

description: E. coli strain MC4100relA+ ∆mazEF in mid log phase incubated at 37ºC for 4 hours with 10 μg/ml NA

value: ∆mazEF


title: ∆mazEFlexA3 0 μg/ml NA rep1

description: E. coli strain MC4100relA+ ∆mazEFlexA3 in mid log phase incubated at 37ºC for 4 hours without treatment

value: 0 μg/ml nalidixic acid


title: primary tumor sample long-term OS 8067H


title: ∆mazEFlexA3 0 μg/ml NA rep2

source_name: E. coli strain MC4100relA+ ∆mazEFlexA3 in mid log phase incubated at 37ºC for 4 hours without treatment


title: BGL004_Beagle

value: blood


title: primary tumor sample long-term OS 8073T


title: primary tumor sample long-term OS 3081F


title: ∆mazEF 100 μg/ml NA rep3

description: E. coli strain MC4100relA+ ∆mazEF in mid log phase incubated at 37ºC for 4 hours with 100 μg/ml NA


title: ∆mazEF 10 μg/ml NA rep1

source_name: E. coli strain MC4100relA+ ∆mazEF in mid log phase incubated at 37ºC for 4 hours with 10 μg/ml NA


title: primary tumor sample long-term OS 3087H


title: primary tumor sample long-term OS 4276K


title: ∆mazEF 100 μg/ml NA rep1

source_name: E. coli strain MC4100relA+ ∆mazEF in mid log phase incubated at 37ºC for 4 hours with 100 μg/ml NA


title: primary tumor sample long-term OS 3001C


title: ∆mazEF 100 μg/ml NA rep2

value: E. coli strain MC4100relA+ ∆mazEF in mid log phase incubated at 37ºC for 4 hours with 100 μg/ml NA


title: primary tumor sample long-term OS 2646E


title: ∆mazEF 0 μg/ml NA rep2

description: E. coli strain MC4100relA+ ∆mazEF in mid log phase incubated at 37ºC for 4 hours without treatment


title: primary tumor sample long-term OS 3002F


title: ∆mazEF 0 μg/ml NA rep1

source_name: E. coli strain MC4100relA+ ∆mazEF in mid log phase incubated at 37ºC for 4 hours without treatment


title: primary tumor sample long-term OS 2259E


title: WT 10 μg/ml NA rep2

description: E. coli strain MC4100relA+ in mid log phase incubated at 37ºC for 4 hours with 10 μg/ml NA

value: WT


title: WT 10 μg/ml NA rep1

source_name: E. coli strain MC4100relA+ in mid log phase incubated at 37ºC for 4 hours with 10 μg/ml NA


title: WT 100 μg/ml NA rep1

description: E. coli strain MC4100relA+ in mid log phase incubated at 37ºC for 4 hours with 100 μg/ml NA


title: primary tumor sample long-term OS 21221M

value: long-term OS


title: primary tumor sample long-term OS 2607F

value: Human Brain, primary Glioblastoma


title: primary tumor sample long-term OS 21171L


title: WT 0 μg/ml NA rep2

description: E. coli strain MC4100relA+ in mid log phase incubated at 37ºC for 4 hours without treatment.


title: primary tumor sample intermediate OS 6366T


title: primary tumor sample long-term OS 21360A


title: primary tumor sample intermediate OS 6010C


title: WT 100 μg/ml NA rep2

source_name: E. coli strain MC4100relA+ in mid log phase incubated at 37ºC for 4 hours with 100 μg/ml NA


title: WT 0 μg/ml NA rep1

source_name: E. coli strain MC4100relA+ in mid log phase incubated at 37ºC for 4 hours without treatment.


title: primary tumor sample intermediate OS 8051A


title: BGL005_Beagle

value: Beagle


title: Jurkat Nemo deificent-MSCV K13-ER-TAM-treated with 4OHT

city: Los Angeles

first: Vasu

last: Punj

state: CA

address: Biggy Street

institute: USC

hyb_protocol: Following fragmentation, 15 µg of cRNA were hybridized for 16hr on Affymetrix GeneChip U133A 2.0 Array as recommended by manufacturer

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000A.

data_processing: The data were analyzed with Gene Spring GX 11.5.1.

label_protocol: Starting from 5 µg total RNA, labeled cRNA was prepared using the Roche Microarray cDNA Synthesis, Microarray RNA Target Synthesis (T7) and Microarray Target Purification Kit, according to the manufacturer's instructions.

growth_protocol: Jurkat cells were grown in RPMI medium containing 10% FBS (fetal bovine serum) .  Cells were stably transduced with either a MSCVneo vector or MSCVneo expressing a 4-Hydroxytamoxifen (4-OHT)-inducible K13-ER-TAM.

extract_protocol: RNA was extracted from the cells using  RNeasy mini kit (Qiagen Valenica, CA)

treatment_protocol: Cells were grown in presence or absence of 4OHT.

tag: cell line

value: Jurkat (BCBL1)

tag: cell type

value: Leukemia


title: primary tumor sample intermediate OS 4506T


title: primary tumor sample intermediate OS 4363C


title: primary tumor sample intermediate OS 4318M


title: primary tumor sample intermediate OS 4536N


title: primary tumor sample intermediate OS 4489E


title: primary tumor sample intermediate OS 3902H


title: Jurkat WT-MSCV K13-ER-TAM-treated with 4OHT


title: Jurkat Nemo deficent-MSCV-vector-untreated


title: primary tumor sample intermediate OS 4313N


title: Jurkat Nemo deificent-MSCV K13-ER-TAM-untreated


title: primary tumor sample intermediate OS 3626F


title: Jurkat WT-MSCV K13-ER-TAM-untreated

source_name: Jurkat WT-MSCV K13-ER-TAM-untreated


title: primary tumor sample intermediate OS 3421K


title: primary tumor sample intermediate OS 3400N


title: primary tumor sample intermediate OS 3384E


title: WT 100 μg/ml NA rep3

value: E. coli strain MC4100relA+ in mid log phase incubated at 37ºC for 4 hours with 100 μg/ml NA


title: primary tumor sample intermediate OS 3432T


title: Jurkat WT-MSCV-vector -treated with 4OHT


title: Jurkat WT-MSCV-vector-untreated

source_name: Jurkat WT-MSCV-vector-untreated


title: primary tumor sample intermediate OS 3149C


title: primary tumor sample intermediate OS 3360T


title: primary tumor sample intermediate OS 3170F


title: primary tumor sample intermediate OS 2231E


title: primary tumor sample intermediate OS 3176H


title: primary tumor sample intermediate OS 31126F


title: primary tumor sample intermediate OS 2447K


title: primary tumor sample intermediate OS 3051K


title: primary tumor sample intermediate OS 2312F


title: primary tumor sample intermediate OS 1298K


title: primary tumor sample intermediate OS 21372M


title: primary tumor sample intermediate OS 3155M


title: primary tumor sample intermediate OS 3172M


title: primary tumor sample short-term OS 3472A


title: primary tumor sample short-term OS 3777F


title: primary tumor sample short-term OS 3373N


title: primary tumor sample short-term OS 3461L


title: primary tumor sample intermediate OS 1257E


title: primary tumor sample short-term OS 8047P


title: primary tumor sample short-term OS 3715F


title: PMN cells donor 3

city: Stockholm

first: Karl

last: Ekwall

address: Alfred Nobels Alle 7

institute: Karolinska Inst

description: cells isolated from healthy bone marrow

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using Iscan Array scanner using standard recommended Illumina scanner setting

data_processing: GenomeStudio software v2011.1

label: Cy5 and Cy3

source_name: bone marrow

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted with Trizol.

value: Polymorphonuclear neutrophil

value: male


title: PMN cells donor 2

description: cells isolated from healthy bone marrow


title: primary tumor sample short-term OS 2249T

value: short-term OS


title: primary tumor sample short-term OS 3143A


title: primary tumor sample short-term OS 2562L


title: PMC cells donor 3

description: cells isolated from healthy bone marrow

value: peritoneal macrophages


title: primary tumor sample short-term OS 2350A


title: primary tumor sample short-term OS 21540H


title: primary tumor sample short-term OS 21363L


title: CSH50 E-minimal medium pH 4.5 90 min replicate 1

city: Dublin

first: Heather

middle: J

last: Quinn

address: College green

department: Microbiology

country: Ireland

institute: Trinity College Dublin

hyb_protocol: Samples were prepared for hybridisation as follows: 50 µl 2X Hi-RPM Hybridisation buffer (Agilent), 25 µl ChIP DNA, 5 µl input DNA, 10 µl 10X GE blocking Agent (Agilent) and 10 µl nuclease-free H2O. Samples were added to a microfuge tube, vortexed briefly and collected by short centrifugation spin. 100 µl was added to an array on the microarray slides. The arrays were sealed with the appropriate gasket slide and loaded into the Agilent Microarray Hybridisation Chamber Kit (G2534A). Microarrays were hybridised for 24 h at 65°C in a hybridization oven (Agilent). Slides were washed in wash buffer 1 followed by wash buffer 2 as described below. 200 ml of buffer was used for each wash step. Wash buffers were made up as 1 L solutions and filter sterilised using 0.22 µM pore membrane (Nalgene) as follows: Wash buffer 1: 1.4 L ddH2O, 0.6 L 20X SSC (Sigma), 1 ml 10% Triton. Wash buffer 2: 994.5 L ddH2O, 5 ml 20X SSC (Sigma), 500 µl 10% Triton. The slide was removed from the hybridisation oven and prised apart whilst submerged in wash buffer 1 that was pre-warmed to 60°C. The slide was then  washed in buffer 1 at 37°C for 10 min with stirring, followed by washing in wash buffer 1 at room temperature for 10 min. The slide was then washed in wash buffer 2 at room temperature for 5 min with stirring; this was followed by a second wash in fresh wash buffer 2 for 5 min.

scan_protocol: Slides were scanned on an Agilent G2565CA Microarray Scanner

data_processing: Agilent Feature Extraction Software version 10.5.1.1.

organism: Escherichia coli K-12

source_name: CSH50 E-minimal medium pH 4.5 90 min

label_protocol: The BioPrime Array CGH kit (Invitrogen) was used to fluorescently label DNA for ChIP microarray experiments. 100 µl volume IP labelling reactions were set up as follows: 40 µl 2.5X random primers, 40 µl of IP DNA, 6.5 µl nuclease-free H2O, this was heated to 100°C for 10 min and chilled on ice for 5 min. To this sample, 10 µl of 10X dNTP mix (1mM dCTP, 2mM dGTP, 2mM dTTP, 2 mM dATP), 1.5 µl of   Cy3/Cy5-dCTP (23 nmol GE Healthcare) and 2 µl exo-Klenow (40 U/µl) was added. Reactions were carried out at 37°C overnight in the dark. 15 µl of stop buffer was added to each sample to terminate the reaction. 200 ng of input DNA was labelled as described above. Samples were purified using Qiagen MinElute PCR purification kit as per manufacturer’s instructions.

growth_protocol: Strains were grown overnight in LB broth and then equalised to 0.15 optical density (OD600nm) units. Cells were collected and washed in EG minimal medium (pH 7.2). This wash step was repeated twice more with centrifugation to collect the cells. The final pellet was resuspended in 1 ml of 1X EG minimal (pH 7.2). Cells were grown to OD600 ~0.5-0.6 in a 40 ml volume in a 250 ml flask at 37°C and 200 rpm.

extract_protocol: OD600 15 units of cells were harvested for each ChIP procedure. Cells were harvested by centrifugation at 4,000 rpm for 8 min at room temperature and resuspended in 50 ml of pre-warmed PBS (37°C) in a 250 ml flask. DNA-protein and protein-protein interactions were cross-linked by adding 1,351 µl of formaldehyde drop-wise to a final concentration of 1%. Samples were cross-linked at room temperature with stirring for 30 min. Glycine was added to a final concentration of 0.125 M with stirring for 5 min at room temperature. Cells were centrifuged at 4,000 rpm for 8 min at 4°C and the supernatant removed. The pellet was re-suspended in 0.6 ml of lysis buffer containing 50 mM Tris-HCl, 10 mM EDTA, 1% SDS and incubated on ice for 10 min. 1.4 ml of IP dilution buffer (20 mM Tris-HCl pH 8.1, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.01% SDS, Roche protease inhibitor cocktail) was added and the chromatin was sonicated on ice in a 5ml tube to reduce the DNA length to an average size of approximately 500 bp using the Sanyo/MES Soniprep sonicator (8 bursts at an amplitude 10 microns for 30 seconds, with 1 minute cooling between bursts). This was transferred to a 2 ml microfuge tube and spun at 13,200 rpm for 10 min at 4°C. Supernatant was removed and 1 ml dilution buffer added.The chromatin material was precleared by adding 50 µl of normal rabbit immunoglobulin G (IgG, 1 mg/ml, Millipore). Samples were incubated for 1 h at 4°C on a rotating wheel. 100 µl of homogenous protein G-agarose (Roche) was added to the precleared chromatin and the samples were incubated for 3-5 h at 4°C on a rotating wheel. Samples were centrifuged at 4,000 rpm for 2 min at 4°C and this supernatant was used to set up immunoprecipitation reactions. 200 µl chromatin was removed and used as an input sample. Experimental immunoprecipitation were set up using 1,350 µl chromatin and 3.3 µg/µl of anti-FLAG antibody (Sigma). Mock immunoprecipitation 1,350 µl chromatin and 10 µg of normal mouse IgG (Millipore). Samples were incubated overnight on a rotating wheel at 4°C. Samples were centrifuged at 13,000 rpm for 5 min at 4°C and the supernatant was transferred to 2 ml microfuge tubes. 50 µl of protein G-agarose was added to each sample and incubated at 4°C for 3 h. The samples were centrifuged at 7,500 rpm for 2 min at 4°C to pellet the protein G-agarose beads. The supernatant was removed and the protein G-agarose beads were carefully washed. 91 For each wash, the wash buffer was added; the samples were vortexed briefly and were centrifuged at 7,500 rpm for 2 min at 4°C. The samples were left to stand on ice for 1 min before removing the supernatant. The washes were carried out in the following sequence: The beads were washed twice with 750 µl of cold IP wash buffer 1 containing 20 mM Tris-HCl (pH 8.1), 50 mM NaCl, 2mM EDTA, 1% Triton X-100, 0.1% SDS. The beads were transferred to a 1.5 ml microfuge tube after the first wash. The beads were washed once with 750 µl of cold IP wash buffer 2 containing 10 mM Tris-HCl (pH 8.1), 250 mM LiCl, 1 mM EDTA, 1% NP-40, 1% deoxycholic acid. The beads were washed twice with 750 µl of ice-cold TE buffer containing 10 mM Tris base (pH 8) and 1 mM EDTA. DNA-protein-antibody complexes were eluted from the protein G-agarose beads by adding 225 µl of IP elution buffer containing 100 mM NaHCO3 and 1% SDS. The beads were resuspended in IP elution buffer, briefly vortexed and centrifuged at 7,500 rpm for 2 min at room temperature. The supernatant was collected in fresh 1.5 ml microfuge tubes. The bead pellets in the original tubes were resuspended in 225 µl of IP elution buffer again and briefly vortexed and centrifuged at 7,500 rpm for 2 min. IP and input samples were thawed on ice. 0.1 µl of RNase A (10 mg/ml, ICN Biochemicals) and 16 µl of 5 M NaCl (to a final concentration of 0.3 M) was added to the input sample. Similarly, 0.2 µl of RNase A and 27 µl of 5 M NaCl (to a final concentration of 0.3 M) was added to each IP sample. All samples including the input DNA were incubated at 65°C for 6 h to reverse cross-links. 9 µl of Proteinase K (10 mg/ml, GibcoBRL) was added to each sample and incubated overnight at 45°C. 2 µl of yeast tRNA (5mg/ml, Invitrogen) was added to each sample followed by 250 µl of phenol (pH 8, Sigma) and 250 µl of chloroform. Samples were centrifuged at 13,000 rpm for 5 min at room temperature. The aqueous layer was collected in fresh 1.5 ml centrifuge tubes and 500 µl of chloroform was added. The samples were vortexed and centrifuged at 13,000 rpm for 5 min and room temperature. The aqueous layer was transferred to a 2 ml microfuge tube. 5 µg of glycogen (5 mg/ml, Roche), 1 µl of tRNA (5 mg/ml, Invitrogen) and 50 µl of 3 M NaAc (pH 5.2) was added to each sample and mixed well. The DNA was precipitated with 1,375 µl of 95% ethanol and incubated at -80°C for 1 h. The samples were centrifuged at 13,000 rpm for 20 min at 4°C. The DNA pellets were washed with 500 µl of ice-cold 70% ethanol and centrifuged at 13,000 rpm for 5 min at 4°C. The supernatant was removed and the samples were air-dried for 10-15 min. DNA pellets of IP samples were resuspended in 50 µl nuclease-free H2O. Input DNA samples were resuspended in 100 µl of nuclease-free H2O. Samples were incubated at 37°C for 1 h.

treatment_protocol: The culture was divided into two 20-ml volumes and the cells collected by centrifugation. The supernatant was removed and the two pellets were subjected to different treatments. One was resuspended in 1 ml of pre-warmed 1X EG-minimal medium pH 7.2. The second was resuspended in 1 ml of pre-warmed 1X EG-minimal medium pH 4.5. Each suspension was added to a final volume of 20 ml 1X EG minimal medium of the same pH in a 250 ml flask. Cells were grown at 37°C and 200 rpm shaking for 90 min before harvesting for analysis.

tag: chip antibody

value: Anti-FLAG (sigma-aldrich cat no F3165)

value: none, input


title: primary tumor sample short-term OS 2347A


title: CSH50 E-minimal medium pH 4.5 90 min replicate 3


title: PMC cells donor 2

description: cells isolated from healthy bone marrow


title: PMN cells donor 1

description: cells isolated from healthy bone marrow

value: female


title: PMC cells donor 1

description: cells isolated from healthy bone marrow


title: CSH50 E-minimal medium pH 7 90 min replicate 3

source_name: CSH50 E-minimal medium pH 7 90 min


title: GMP cells donor 2

description: cells isolated from healthy bone marrow

value: Granulocyte-macrophage progenitor


title: CSH50 E-minimal medium pH 7 90 min replicate 1


title: primary tumor sample short-term OS 21132M


title: GMP cells donor 1

description: cells isolated from healthy bone marrow


title: primary tumor sample short-term OS 1273A


title: CSH50 E-minimal medium pH 4.5 90 min replicate 2


title: CSH50 E-minimal medium pH 7 90 min replicate 2


title: Nr3_ctrl

city: Wuerzburg

first: Susanne

middle: Elma

last: Kneitz

address: Biozentrum, Am Hubland

department: Physiologigcal Chemistry

institute: University of Wuerzburg

description: Gene expression data from control miR transfected PC-3 cells

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on HG U 133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station_450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000

data_processing: The data were analyzed with Bioconductor packages (under R) and vsn as normalization method using perfect match only

source_name: PC-3 cell  control mir

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (GeneChip® Expression Analysis Manual, Affymetrix).

growth_protocol: PC-3 cells were purchased from the American Type Culture Collection (ATCC) and were grown in medium as indicated by ATCC instructions.

extract_protocol: RNA was isolated using the Rneasy Mini Kit from Qiagen (including Dnase digest)

treatment_protocol: Cells were transfected with human precursor mir-221 or negative control oligonucleotides using lipofectamin following the manufacturer’s instructions (Apllied Biosystems). The optimal miRNA oligonucleotide concentrations were titrated for optimal transfection results. In all experiments the final miRNA concentration was 10 nmol/L.

tag: transfection

value: control miR


title: GMP cells donor 3

description: cells isolated from healthy bone marrow


title: CSH50 control (mock igG) E-minimal medium replicate 2

source_name: CSH50 control E-minimal medium 90 min

value: normal rabbit IgG (Upstate Biotechnology, Cat. no. 12-370)


title: CSH50 control (mock igG) E-minimal medium replicate 1


title: CMP cells donor 3

description: cells isolated from healthy bone marrow

value: Common myeloid progenitor


title: Nr4_ctrl


title: Nr1_pre221

description: Gene expression data from pre-mir-221 transfected PC-3 cells

source_name: PC-3 cell  pre mir-221


title: CMP cells donor 2

description: cells isolated from healthy bone marrow


title: curdlan1

city: Eiheiji

first: Yukihiro

last: Kimura

state: Fukui

address: 23-3 Matsuoka-Shimoaizuki

country: Japan

institute: University of Fukui

hyb_protocol: Following fragmentation, 1.85 ug of cDNA were hybridized for 17 hr at 45C on GeneChip Rat Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix fluidics station 450

scan_protocol: GeneChips were scanned by GeneChip Scanner 3000 7G using Affymetrix GeneChip Command Console Software.

data_processing:
The data were imported into Subio platform version 1.16 (Subioinc, Kagoshima, Japan) for database management and quality control.
affymetrix-algorithm-name = rma-gene-default
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.1.2800.19935

organism: Rattus norvegicus

source_name: Curdlan-stimulated RBL-2H3 overexpressing Dectin-1 WT

label_protocol: Biotinylated cDNA were prepared from 5.5 ug of synthesized cDNA by using GeneChip WT Terminal labeling kit according to the manufacturer’s instructions

growth_protocol: RBL-2H3 cells were maintained as monolayer cultures in Dulbecco’s modified Eagle’s medium with 100 U/mL of penicillin and 10% (v/v) heat-inactivated fetal calf serum.

extract_protocol: Total RNA from RBL-2H3 cells was isolated by using High Pure RNA Isolation Kit (Roche) according to the manufacturer's instructions.

value: mast cells

value: overexpressing Dectin-1 WT

tag: stimulated with

value: Curdlan


title: Nr2_pre221


title: R4062

source_name: R406-pretreated and Curdlan-stimulated RBL-2H3 overexpressing Dectin-1 WT

tag: pretreated with

value: Syk inhibitor R406


title: control2

source_name: RBL-2H3 overexpressing Dectin-1 WT

value: none (control)


title: control1


title: Menin_WT_TH

city: Toon-shi

first: Makoto

last: Kuwahara

state: Ehime

address: Shitsukawa

department: Department of Immunology

institute: Graduate School of Medicine, Ehime University

description: gene expression in Menin WT TH cells

hyb_protocol: Hybridization and washing were done according to Agilent One-Color Gene Expression protocol

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2565CA) using one color scan setting

data_processing: Raw signal intensities were extracted with Agilent Feature Extraction Software v10.7 using default parameters (protocol GE1-107_Sep09). The dataset was normalized using the 75 percentile median shift method.

source_name: Primary CD4 T cell from spleen

label_protocol: 500 ng of total RNA was amplified and labeled using the One-Color Agilent Quick Amp Labeling kit

growth_protocol: Menin WT or Menin KO naïve CD4 T cells were prepared using a CD4+CD62L+ T cell isolation kit II (Miltenyi Biotec).  Naïve CD4 T cells were stimulated with immobilized anti-TCR-β mAb (3μg/ml, H57-597, BioLegend) and an anti-CD28 mAb (1μg/ml, 37.5, BioLegend) for two days in the presence of IL-2 (2.5 ng/ml).  Next, cells were transferred to a new plate and cultured for an additional 3 days in the presence of IL-2 (2.5 ng/ml).

extract_protocol: Total RNA was isolated with TRIZOL regent (invitrogen)

value: Menin WT

value: Primary CD4 T cell from spleen

value: spleen


title: R4061


title: curdlan2


title: Menin_KO_TH

description: gene expression in Menin KO TH cells

value: Menin KO


title: SL1344 LB  25ug/ml novobiocin 40 min replicate 2

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: SL1344 LB 25 ug/ml novobiocin 40 min

growth_protocol:
All novobiocin experiments were conducted on cells in steady-state exponential growth. To measure the effects of novobiocin on DNA supercoiling, a streak-isolated colony was suspended in 0.5 ml of LB (0% NaCl) and used to inoculate two parallel pre-warmed 250 ml ﬂasks containing 60 ml of LB (0% NaCl) and carbenicillin (100 μg/ml). Cells were grown exponentially for over 3 h (to OD600 0.1) before treatment with novobiocin (25μg/ml), and cells were harvested from treated and untreated cells 40 min after the addition of novobiocin. Flasks were shaken at 140 rpm to reduce aeration and incubated at 37°C.
Strains were grown overnight in LB broth and then equalised to 0.15 optical density (OD600nm) units. Cells were collected and washed in EG minimal medium (pH 7.2). This wash step was repeated twice more with centrifugation to collect the cells. The final pellet was resuspended in 1 ml of 1X EG minimal (pH 7.2). Cells were grown to OD600 ~0.5-0.6 in a 40 ml volume in a 250 ml flask at 37°C and 200 rpm.

extract_protocol: OD600 15 units of cells were harvested for each ChIP procedure. Cells were   harvested by centrifugation at 4,000 rpm for 8 min at room temperature and resuspended in 50 ml of pre-warmed PBS (37°C) in a 250 ml flask. DNA-protein and protein-protein interactions were cross-linked by adding 1,351 µl of formaldehyde drop-wise to a final concentration of 1%. Samples were cross-linked at room temperature with stirring for 30 min. Glycine was added to a final concentration of 0.125 M with stirring for 5 min at room temperature. Cells were centrifuged at 4,000 rpm for 8 min at 4°C and the supernatant removed. The pellet was re-suspended in 0.6 ml of lysis buffer containing 50 mM Tris-HCl, 10 mM EDTA, 1% SDS and incubated on ice for 10 min. 1.4 ml of IP dilution buffer (20 mM Tris-HCl pH 8.1, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.01% SDS, Roche protease inhibitor cocktail) was added and the chromatin was sonicated on ice in a 5ml tube to reduce the DNA length to an average size of approximately 500 bp using the Sanyo/MES Soniprep sonicator (8 bursts at an amplitude 10 microns for 30 seconds, with 1 minute cooling between bursts). This was transferred to a 2 ml microfuge tube and spun at 13,200 rpm for 10 min at 4°C. Supernatant was removed and 1 ml dilution buffer added.The chromatin material was precleared by adding 50 µl of normal rabbit immunoglobulin G (IgG, 1 mg/ml, Millipore). Samples were incubated for 1 h at 4°C on a rotating wheel. 100 µl of homogenous protein G-agarose (Roche) was added to the precleared chromatin and the samples were incubated for 3-5 h at 4°C on a rotating wheel. Samples were centrifuged at 4,000 rpm for 2 min at 4°C and this supernatant was used to set up immunoprecipitation reactions. 200 µl chromatin was removed and used as an input sample. Experimental immunoprecipitation were set up using 1,350 µl chromatin and 3.3 µg/µl of anti-FLAG antibody (Sigma). Mock immunoprecipitation 1,350 µl chromatin and 10 µg of normal mouse IgG (Millipore). Samples were incubated overnight on a rotating wheel at 4°C. Samples were centrifuged at 13,000 rpm for 5 min at 4°C and the supernatant was transferred to 2 ml microfuge tubes. 50 µl of protein G-agarose was added to each sample and incubated at 4°C for 3 h. The samples were centrifuged at 7,500 rpm for 2 min at 4°C to pellet the protein G-agarose beads. The supernatant was removed and the protein G-agarose beads were carefully washed. 91 For each wash, the wash buffer was added; the samples were vortexed briefly and were centrifuged at 7,500 rpm for 2 min at 4°C. The samples were left to stand on ice for 1 min before removing the supernatant. The washes were carried out in the following sequence: The beads were washed twice with 750 µl of cold IP wash buffer 1 containing 20 mM Tris-HCl (pH 8.1), 50 mM NaCl, 2mM EDTA, 1% Triton X-100, 0.1% SDS. The beads were transferred to a 1.5 ml microfuge tube after the first wash. The beads were washed once with 750 µl of cold IP wash buffer 2 containing 10 mM Tris-HCl (pH 8.1), 250 mM LiCl, 1 mM EDTA, 1% NP-40, 1% deoxycholic acid. The beads were washed twice with 750 µl of ice-cold TE buffer containing 10 mM Tris base (pH 8) and 1 mM EDTA. DNA-protein-antibody complexes were eluted from the protein G-agarose beads by adding 225 µl of IP elution buffer containing 100 mM NaHCO3 and 1% SDS. The beads were resuspended in IP elution buffer, briefly vortexed and centrifuged at 7,500 rpm for 2 min at room temperature. The supernatant was collected in fresh 1.5 ml microfuge tubes. The bead pellets in the original tubes were resuspended in 225 µl of IP elution buffer again and briefly vortexed and centrifuged at 7,500 rpm for 2 min. IP and input samples were thawed on ice. 0.1 µl of RNase A (10 mg/ml, ICN Biochemicals) and 16 µl of 5 M NaCl (to a final concentration of 0.3 M) was added to the input sample. Similarly, 0.2 µl of RNase A and 27 µl of 5 M NaCl (to a final concentration of 0.3 M) was added to each IP sample. All samples including the input DNA were incubated at 65°C for 6 h to reverse cross-links. 9 µl of Proteinase K (10 mg/ml, GibcoBRL) was added to each sample and incubated overnight at 45°C. 2 µl of yeast tRNA (5mg/ml, Invitrogen) was added to each sample followed by 250 µl of phenol (pH 8, Sigma) and 250 µl of chloroform. Samples were centrifuged at 13,000 rpm for 5 min at room temperature. The aqueous layer was collected in fresh 1.5 ml centrifuge tubes and 500 µl of chloroform was added. The samples were vortexed and centrifuged at 13,000 rpm for 5 min and room temperature. The aqueous layer was transferred to a 2 ml microfuge tube. 5 µg of glycogen (5 mg/ml, Roche), 1 µl of tRNA (5 mg/ml, Invitrogen) and 50 µl of 3 M NaAc (pH 5.2) was added to each sample and mixed well. The DNA was precipitated with 1,375 µl of 95% ethanol and incubated at -80°C for 1 h. The samples were centrifuged at 13,000 rpm for 20 min at 4°C. The DNA pellets were washed with 500 µl of ice-cold 70% ethanol and centrifuged at 13,000 rpm for 5 min at 4°C. The supernatant was removed and the samples were air-dried for 10-15 min. DNA pellets of IP samples were resuspended in 50 µl nuclease-free H2O. Input DNA samples were resuspended in 100 µl of nuclease-free H2O. Samples were incubated at 37°C for 1 h.


title: SL1344 control (mock igG) E-minimal medium replicate 2

source_name: SL1344 control E-minimal medium 90 min


title: SL1344 LB  25ug/ml novobiocin 40 min replicate 1


title: SL1344 E-minimal medium pH 4.5 90 min replicate 1

source_name: SL1344 E-minimal medium pH 4.5 90 min


title: SL1344 control (mock igG) E-minimal medium replicate 1


title: SL1344 control (mock igG) E-minimal medium replicate 3


title: SL1344 E-minimal medium pH 4.5 90 min replicate 3


title: SL1344 E-minimal medium pH 7 90 min replicate 2

source_name: SL1344 E-minimal medium pH 7 90 min


title: SL1344 LB  0 novobiocin 40 min replicate 1

source_name: SL1344 LB 0 novobiocin 40 min

growth_protocol:
All novobiocin experiments were conducted on cells in steady-state exponential growth. To measure the effects of novobiocin on DNA supercoiling, a streak-isolated colony was suspended in 0.5 ml of LB (0% NaCl) and used to inoculate two parallel pre-warmed 250 ml ﬂasks containing 60 ml of LB (0% NaCl). Cells were grown exponentially for over 3 h (to OD600 0.1) before treatment with novobiocin (25μg/ml). Cells were harvested from treated and untreated cultures 40 min after the addition of novobiocin. Flasks were shaken at 140 rpm to reduce aeration and incubated at 37°C.
Strains were grown overnight in LB broth and then equalised to 0.15 optical density (OD600nm) units. Cells were collected and washed in EG minimal medium (pH 7.2). This wash step was repeated twice more with centrifugation to collect the cells. The final pellet was resuspended in 1 ml of 1X EG minimal (pH 7.2). Cells were grown to OD600 ~0.5-0.6 in a 40 ml volume in a 250 ml flask at 37°C and 200 rpm.


title: Lung Replicate 2 [log ratio]

status: Public on Mar 26 2014

city: Jerusalem

first: Deborah

last: Nejman

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.

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.

growth_protocol: DNA was purchased from Biochain or Bioserve.

extract_protocol: Human (10µg) 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: Lung

value: Male

tag: age


title: SL1344 E-minimal medium pH 4.5 90 min replicate 2

value: Anti-FLAG (sigma-aldrich cat no F3165)

value: none, input


title: Colon Young Replicate 2 [log ratio]

source_name: Young Colon_INPUT

value: Young Colon

source_name: Young Colon_BOUND


title: SL1344 E-minimal medium pH 7 90 min replicate 1


title: SL1344 LB  0 novobiocin 40 min replicate 2


title: Colon Young Replicate 1 [log ratio]


title: Lung Replicate 1 [log ratio]


title: Whole cell extract #1

city: Montpellier

first: Philippe

last: Pasero

address: 141 rue de la Cardonille

country: France

institute: Institute of Human Genetics - CNRS

description:
n/a
Whole cell extract

hyb_protocol: DNA was hybridized to Affymetrix Genechip S. cerevisiae Tiling 1.0R Array (5 bpresolution, Affymetrix PN 900645) using the GeneChip Hybridization, Wash, and Stain Kit (Affymetrix, PN 900720).

scan_protocol: Tiling arrays were scanned with the GeneChip scanner 3000 7G

data_processing: Signals were normalized with TAS 1.1.02 (Affymetrix) using quantile normalisation. Analysis results were stored in log2 scale for signal intensity and in -10Log10 for p-values. Probe signals were analysed using perfect matches only with a bandwidth of 300. P-value intervals were generated using the following parameters: cutoff: 10-5, max gap: 80 and min run: 40.

label: Biotin

organism: Saccharomyces cerevisiae W303

source_name: Whole cell extract #1

label_protocol: 7 µg of amplified DNA was fragmented and labelled using the GeneChip WT Double-Stranded DNA Terminal Labelling kit (Affymetrix, PN 900812) following manufacturer's recommendations. 7 µg of amplified DNA was fragmented and labelled using the GeneChip WT Double-Stranded DNA Terminal Labelling kit (Affymetrix, PN 900812) following manufacturer recommendations.

growth_protocol: Cells were grown on YPD at 25°C and were arrested in G1 with alpha-factor. G1-synchronised cells were released into S phase in the presence of Hydroxyurea (200mM) and BrdU (400µg/ml) for the indicated time.

extract_protocol: For immunoprecipitation of BrdU-labelled DNA, 1.5x109 cells were lysed for 5 x 2 minutes in NIB buffer (17 % glycerol, 50 mM MOPS buffer, 150mM potassium acetate, 2 mM magnesium chloride, 500 µM spermidine and 150 µM spermine, pH7.2) with Zirconium beads on a Vibrax (VXR basic, Ika) at 4C. DNA was isolated using Qiagen Genomic DNA extraction kit and sonicated to reach an average DNA size of 300-600 bp. For each immunoprecipitation, 10 µl of mouse anti-BrdU IgG1 (BDBioscience 555627) was prebound to Dynabeads M-280 Sheep anti-mouse IgG (Invitrogen 112.02) and added to the denatured purified DNA. For immunoprecipitation of BrdU-labelled DNA, 1.5x109 cells were lysed for 5 x 2 minutes in NIB buffer (17 % glycerol, 50 mM MOPS buffer, 150mM potassium acetate, 2 mM magnesium chloride, 500 µM spermidine and 150 µM spermine, pH7.2) with Zirconium beads on a Vibrax (VXR basic, Ika) at 4C. DNA was isolated using Qiagen Genomic DNA extraction kit and sonicated to reach an average DNA size of 300-600 bp. For each immunoprecipitation, 10 µl of mouse anti-BrdU IgG1 (BDBioscience 555627) was prebound to Dynabeads M-280 Sheep anti-mouse IgG (Invitrogen 112.02) and added to the denatured purified DNA. For immunoprecipitation of BrdU-labelled DNA, 1.5x109 cells were lysed for 5 x 2 minutes in NIB buffer (17 % glycerol, 50 mM MOPS buffer, 150mM potassium acetate, 2 mM magnesium chloride, 500 µM spermidine and 150 µM spermine, pH7.2) with Zirconium beads on a Vibrax (VXR basic, Ika) at 4C. DNA was isolated using Qiagen Genomic DNA extraction kit and sonicated to reach an average DNA size of 300-600 bp. For each immunoprecipitation, 10 µl of mouse anti-BrdU IgG1 (BDBioscience 555627) was prebound to Dynabeads M-280 Sheep anti-mouse IgG (Invitrogen 112.02) and added to the denatured purified DNA. For immunoprecipitation of BrdU-labelled DNA, 1.5.109 cells were lysed for 5 x 2 min in NIB buffer (17% glycerol, 50 mM MOPS buffer, 150 mM potassium acetate, 2 mM magnesium chloride, 500 µM spermidine and 150 µM spermine, pH 7.2) with zirconium beads on a vibrax (VXR basic, IKA) at 4°C. DNA was isolated using Qiagen Genomic DNA extraction kit and sonicated to reach an average DNA size of 300-600 bp. For each immunoprecipitation, 10µl of mouse anti-BrdU IgG1 (BD Biosciences) was prebound to Dynabeads M-280 Sheep anti-mouse IgG (Invitrogen) and added to the denaturated purified DNA.

treatment_protocol: Samples were collected in early S phase +/- 200 mM HU (hydroxyurea).

tag: treatment(s)


title: Whole cell extract #2

description:
n/a
Whole cell extract

source_name: Whole cell extract #2


title: Brain Tumor Replicate 2 [log ratio]

source_name: Brain Tumor_INPUT

value: Brain Tumor

source_name: Brain Tumor_BOUND


title: Lung Cancer Replicate 2 [log ratio]

source_name: Lung Cancer_INPUT

value: Lung Cancer

source_name: Lung Cancer_BOUND


title: SL1344 E-minimal medium pH 7 90 min replicate 3


title: Primary Lung cancer, metastasized in Brain [log ratio]

source_name: Brain metastasis_INPUT

value: Brain metastasis

source_name: Brain metastasis_BOUND


title: sir2 high overexpression

description:
sir2_high_signal.bar
Effect of initiation factors

source_name: sir2 high overexpression

tag: antibody

value: anti-BrdU IgG1 (BD Biosciences)

value: HU


title: Primary Liver cancer, metastasized in Lung [log ratio]

source_name: Lung metastasis_INPUT

value: Lung metastasis

source_name: Lung metastasis_BOUND


title: Lung Cancer Replicate 1 [log ratio]


title: CMP cells donor 1

description: cells isolated from healthy bone marrow

source_name: bone marrow

value: Common myeloid progenitor

value: female


title: sir3

description:
sir3_signal.bar
HDAC mutants + HU


title: sir2 low overexpression

description:
sir2_low_signal.bar
Effect of initiation factors

source_name: sir2 low overexpression


title: wt no overexpression

description:
wt_no_signal.bar
Effect of initiation factors

source_name: wt no overexpression


title: rpd3 sir2 #2

description:
rpd3_sir2_signal.bar
HDAC mutants + HU

source_name: rpd3 sir2 #2


title: Colon Polyp Replicate 2 [log ratio]

value: Polyp


title: Jurkat Nemo deficent-MSCV-vector-treated with 4OHT

value: Jurkat (BCBL1)

value: Leukemia


title: Colon Polyp Replicate 1 [log ratio]


title: sir2 no overexpression

description:
sir2_no_signal.bar
Effect of initiation factors

source_name: sir2 no overexpression


title: sir2 fob1 20-copy rDNA

description:
sir2_fob1_20_copy_signal.bar
Effect of rDNA copy number

source_name: sir2 fob1 20-copy rDNA


title: wt low overexpression

description:
wt_low_signal.bar
Effect of initiation factors

source_name: wt low overexpression


title: wt high overexpression

description:
wt_high_signal.bar
Effect of initiation factors

source_name: wt high overexpression


title: Hepatocellular Carcinoma Replicate 2 [log ratio]

value: HCC


title: Lung Cancer Replicate 4 [log ratio]


title: Colon Fetal Replicate 2 [log ratio]

source_name: Fetal Colon_INPUT

value: Fetal Colon

value: 29 weeks

source_name: Fetal Colon_BOUND


title: Brain Tumor Replicate 1 [log ratio]

source_name: Brain Tumor_INPUT

value: Male

source_name: Brain Tumor_BOUND


title: sir2 fob1

description:
sir2_fob1_signal.bar
Effect of rDNA copy number

source_name: sir2 fob1


title: Lung Cancer Replicate 3 [log ratio]

source_name: Lung Cancer_INPUT

source_name: Lung Cancer_BOUND


title: sir2 S

description:
sir2_S_signal.bar
HDAC mutants - HU

source_name: sir2 S

value: w/o HU


title: Colon Fetal Replicate 1 [log ratio]

value: 26 weeks


title: fob1 20-copy rDNA

description:
fob1_20_copy_signal.bar
Effect of rDNA copy number

source_name: fob1 20-copy rDNA


title: rpd3 sir2 #1

description:
rpd3_sir2_signal.bar
HDAC mutants + HU

source_name: rpd3 sir2 #1


title: rpd3 S

description:
rpd3_S_signal.bar
HDAC mutants - HU

source_name: rpd3 S


title: wt #2

description:
wt_signal.bar
HDAC mutants + HU

source_name: wt #2


title: wt #3

description:
wt_signal.bar
HDAC mutants + HU

source_name: wt #3


title: rpd3 #2

description:
rpd3_signal.bar
HDAC mutants + HU

source_name: rpd3 #2


title: sir2 #2

description:
sir2_signal.bar
HDAC mutants + HU

source_name: sir2 #2


title: sum1 #1

description:
sum1_signal.bar
HDAC mutants + HU

source_name: sum1 #1


title: wt S

description:
wt_S_signal.bar
HDAC mutants - HU

source_name: wt S


title: sir2 #1

description:
sir2_signal.bar
HDAC mutants + HU

source_name: sir2 #1


title: hst3 hst4

description:
hst3_hst4_signal.bar
HDAC mutants + HU

source_name: hst3 hst4


title: rad53 #2

description:
rad53_signal.bar
HDAC mutants + HU


title: rpd3 #1

description:
rpd3_signal.bar
HDAC mutants + HU

source_name: rpd3 #1


title: sum1 #2

description:
sum1_signal.bar
HDAC mutants + HU

source_name: sum1 #2


title: wt #1

description:
wt_signal.bar
HDAC mutants + HU

source_name: wt #1


title: hst2

description:
hst2_signal.bar
HDAC mutants + HU


title: rad53 #1

description:
rad53_signal.bar
HDAC mutants + HU


title: hst1 #2

description:
hst1_signal.bar
HDAC mutants + HU

source_name: hst1 #2


title: hst1 #1

description:
hst1_signal.bar
HDAC mutants + HU

source_name: hst1 #1


title: hos3

description:
hos3_signal.bar
HDAC mutants + HU


title: hos1

description:
hos1_signal.bar
HDAC mutants + HU


title: hos2

description:
hos2_signal.bar
HDAC mutants + HU


title: hda1 #1

description:
hda1_signal.bar
HDAC mutants + HU

source_name: hda1 #1


title: hda1 #2

description:
hda1_signal.bar
HDAC mutants + HU

source_name: hda1 #2


title: Treg cells unstimulated rep3

city: Indianapolis

first: Mark

middle: H

last: Kaplan

state: IN

address: 635 Barnhill Dr. MS 420

department: Microbiology and Immunology

institute: Indiana University

description:
Gene expression in T cells cultured for 5d in Treg conditions
Treg_non-stim_3

hyb_protocol: The hybridization procedure ws performed accoridng to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit. Cy3-labeled and fragmented cRNA was hybridzed overnight (17 hours 65°C) to the Agilent Whole Mouse Genome Oligo Microarrays 4x44K as recommended in the protocol. Microarrays were washed with Agilent Gene Expression Wash Buffer 1 for 1 min at room temp followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 at 37°C for 1 min. A final wash was performed with acetonitrile.

scan_protocol: Fluorescence signals were detected using Agilent's Microarray Scanner System.

data_processing:
The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. For determination of differential gene expressionFES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system.
The .txt Supplementary files were generated with Resolver Software.

source_name: naïve CD4 T cell cultured under Treg conditions for 5 days

label_protocol: For the linear T7 based amplification step, 0.5 ug of total RNA was used to produce Cy3-labelled cRNA with amplification and labeling performed using the Agilent Quick Amp Labelling Kit. Incroporation rates were 12-17 fmol/ng.

growth_protocol: Naive CD4+CD62L+ T cells were purified from spleens and lymph nodes by magnetic selection (Miltenyi Biotec). Naive CD4+ T cells (1 x 106 cells/ml complete RPMI 1640 medium) were activated with plate-bound anti-CD3 (2 mg/ml; 145-2C11; BioXcell) and soluble anti-CD28 (1 mg/ml; 37.51; BD Biosciences) and cultured under Th9 conditions (IL-4 [20 ng/ ml; PeproTech], TGF-b [2 ng/ml; R&D Systems], and anti–IFN-g [10 mg/ ml; XMG; BioXcell]); Th2 conditions (IL-4 and anti–IFN-g); Th1 con- ditions (IL-12 [5 ng/ml; R&D Systems], IL-2 [50 U/ml; PeproTech], and anti–IL-4 [10 mg/ml; 11B11; BioXcell]); and Treg conditions (TGF-b and anti–IL-4). After 3 d, cultures were expanded with fresh complete RPMI 1640 medium with IL-4 and TGF-b added to the Th9 cells; half the dose of IL-1b, IL-23, and IL-6 added to the Th17 cells; and IL-2 added to Tregs. RNA was harvested after 5 days of culture

extract_protocol: performed by Miltenyi Biotec using standard RNA extraction protocols (NucleoSpin RNA II, Macherey-Nagel). Quality was assessed using electropherograms of agarose gels.

treatment_protocol: As described in growth protocol. For stimulated Th9 cultures, after five day sof culture, cells were stimulated with 1 ug/ml anti-CD3 for six hours.

value: Treg

tag: activation status

value: unstimulated


title: Th9 cells stimulated rep2

description:
Gene expression in T cells cultured for 5d in Th9 conditions and stimulated for 6h with anti-CD3
Th9_stim_2

source_name: naïve CD4 T cell cultured under Th9 conditions for 5 days and activated with anti-CD3

value: stimulated (with 1 ug/ml anti-CD3 for six hours)


title: Th9 cells stimulated rep3

description:
Gene expression in T cells cultured for 5d in Th9 conditions and stimulated for 6h with anti-CD3
Th9_stim_3


title: Treg cells unstimulated rep1

description:
Gene expression in T cells cultured for 5d in Treg conditions
Treg_non-stim_1


title: Th2 cells unstimulated rep1

description:
Gene expression in T cells cultured for 5d in Th2 conditions
Th2_non-stim_1

source_name: naïve CD4 T cell cultured under Th2 conditions for 5 days


title: Th9 cells unstimulated rep2

description:
Gene expression in T cells cultured for 5d in Th9 conditions
Th9_non-stim_2

source_name: naïve CD4 T cell cultured under Th9 conditions for 5 days


title: Treg cells unstimulated rep2

description:
Gene expression in T cells cultured for 5d in Treg conditions
Treg_non-stim_2


title: Th9 cells stimulated rep1

description:
Gene expression in T cells cultured for 5d in Th9 conditions and stimulated for 6h with anti-CD3
Th9_stim_1


title: Th2 cells unstimulated rep3

description:
Gene expression in T cells cultured for 5d in Th2 conditions
Th2_non-stim_3


title: Colorectal Cancer Replicate 3 [log ratio]

value: CRC


title: fob1

description:
fob1_signal.bar
Effect of rDNA copy number

value: anti-BrdU IgG1 (BD Biosciences)

value: HU


title: Th9 cells unstimulated rep3

description:
Gene expression in T cells cultured for 5d in Th9 conditions
Th9_non-stim_3


title: Th2 cells unstimulated rep2

description:
Gene expression in T cells cultured for 5d in Th2 conditions
Th2_non-stim_2


title: Liver Fetal Replicate 2 [log ratio]

source_name: Fetal Liver_INPUT

value: Fetal Liver

source_name: Fetal Liver_BOUND


title: Pancreas Replicate 2 [log ratio]

value: Pancreas


title: Th9 cells unstimulated rep1

description:
Gene expression in T cells cultured for 5d in Th9 conditions
Th9_non-stim_1


title: Muscle Fetal Replicate 3 [log ratio]

source_name: Fetal Skeletal Muscle_INPUT

value: Fetal Skeletal Muscle

value: 24 weeks

source_name: Fetal Skeletal Muscle_BOUND


title: Hepatocellular Carcinoma Replicate 1 [log ratio]


title: Primary colon cancer, metastasized in Liver [log ratio]

source_name: Liver metastasis_INPUT

value: Liver metastasis

source_name: Liver metastasis_BOUND


title: Liver Young Replicate 2 [log ratio]

source_name: Young Liver_INPUT

value: Young Liver

source_name: Young Liver_BOUND


title: Liver Fetal Replicate 3 [log ratio]


title: Liver Young Replicate 1 [log ratio]


title: Colorectal Cancer Replicate 1 [log ratio]


title: Muscle Fetal Replicate 2 [log ratio]


title: Liver Fetal Replicate 1 [log ratio]


title: Brain Fetal Replicate 1 [log ratio]

source_name: Fetal Brain_INPUT

value: Fetal Brain

value: Female

value: 28 weeks

source_name: Fetal Brain_BOUND


title: Colorectal Cancer Replicate 2 [log ratio]

value: Male


title: Muscle Fetal Replicate 1 [log ratio]

value: 29 weeks


title: Pancreas Replicate 1 [log ratio]


title: Brain Fetal Replicate 2 [log ratio]

value: 37 weeks


title: RDX 8.0 mg/L, rep1

city: Vicksburg

first: Kurt

middle: A

last: Gust

state: MS

address: 3909 Halls Ferry Rd.

department: Environmental Laboratory

institute: US Army ERDC

description:
RDX 8-1
Acropora formosa Consortium (coral and eukaryotic endosymbionts).

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the custom-designed Agilent test array 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), 1 minute with 37°C GE Wash buffer 2 (Agilent), 30 seconds with Acetonitrile, and dried with Agilent Stabilization and Drying Solution.

scan_protocol: Slides were scanned immediately after washing on a GenePix 4200AL scanner at PMT gain level 420 using default setting (Scan resolution 5um, One channel-Green, Laser power 100%).

data_processing: Data were extracted from microarray images using Agilent Feature Extraction software, version 9.5.1 (Agilent Technologies). Microarray data were normalized to the 50th percentile within each array and normalized to the median signal for each gene among arrays using GeneSpring Software version 7.3 (Agilent Technologies). GeneSpring was additionally used to conduct statistical analyses to identify DET among treatments using one-way ANOVA including Benjamini and Hochberg multiple testing corrections (Benjamini and Hochberg, 1995). A post-hoc test (volcano plot) including a parametric t-test (p = 0.05) and fold change cutoff of ≥ 1.5 was used to discern statistically significant differences in transcript expression for each RDX dose relative to the control. Given the sense-antisense architecture of the microarray, all differentially expressed microarray targets were examined to identify and eliminate microarray targets for which both the sense and antisense probes were differentially expressed.

organism: Acropora formosa

source_name: Coral soft tissue, RDX 8.0 mg/L

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.7 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: Fragments of the living branched coral Acropora formosa were obtained from Oceans, Reefs and Aquaria (http://www.orafarm.com). Ten gallon aquaria were used to expose 5 coral fragments per condition. All corals were allowed to acclimate to exposure chambers for 24 hours prior to experiment initiation. Exposures were conducted in reconstituted seawater where each aquarium was equipped with Coralife Protein Skimmers with Bio Balls (Central Garden & Pet Co. Walnut Creek, CA) placed in the outlet filtration box. Tanks were maintained at 27°C by water re-circulating REMCOR heating/cooling units (REMCOR Products Company, Glendale Heights, IL). Salinity was maintained at 30 psa and a 16:8 h light:dark photoperiod was applied where each aquarium was illuminated by four full spectrum fluorescent lights placed approximately 6 inches above each.

extract_protocol: At the termination of the 5d RDX dose-series experiment, all biological replicates dedicated to genomic inquiry were immediately fixed in RNA Later™ (Ambion, Austin, TX) following manufacturer's recommendations. Coral soft tissues for RNA extraction were scraped from the calcium carbonate skeleton. RNA was prepared using the RNeasy mini kit (QIAGEN, Valencia, CA) 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: Ten gallon aquaria were used to expose 5 coral fragments to control or RDX exposure conditions (0.49, 0.93, 1.77, 3.67 and 7.18 mg/L, measured concentrations). RDX was added to each tank carried in 4.6 L of artificial seawater to achieve target concentrations. RDX concentrations and water quality parameters including temperature, salinity, pH, dissolved water concentration, ammonia concentration, and nitrogen concentration were measured daily.

value: adult coral soft tissue

value: RDX 8.0 mg/L


title: RDX 0.5 mg/L, rep1

description:
RDX 0.5-1
Acropora formosa Consortium (coral and eukaryotic endosymbionts).

source_name: Coral soft tissue, RDX 0.5 mg/L

value: RDX 0.5 mg/L


title: Treated/untreated cell 1, replicate 1

city: Taipei

first: Jun-Yi

last: Leu

address: No. 128, Sec. 2, Academia Rd., Nangang Dist.

country: Taiwan

institute: Institute of Molecular Biology

description:
dox1-1
Biological replicate 1 of 2. Technical replicate 1 of 3. Dox-treated/untreated log-phase cells.

hyb_protocol: Hybridization protocol was adapted from Microarray Core Facility, Institute of Molecular Biology, Academia Sinica, TW (http://www.imb.sinica.edu.tw/mdarray/methods.html).

scan_protocol: Arrays were scanned for F635 and F532 fluorescence intensities using AXON 4000B (Molecular Device, Sunnyvale, CA).

data_processing: LOWESS normalized, background subtracted data obtained from signals. Agilent GeneSpring GX 7.3 was used.

label: Alexa Fluor 647

organism: Saccharomyces cerevisiae

source_name: dox-treated

label_protocol: Labeling protocol was adapted from Microarray Core Facility, Institute of Molecular Biology, Academia Sinica, TW (http://www.imb.sinica.edu.tw/mdarray/methods.html).

growth_protocol: Cells were grown to log phase in a modified synthetic complete (SC) medium which contains double the amount of amino acid supplements containing either 40 mg/L L-arginine and 60 mg/L L-lysine (light labeling) or 40 mg/L 13C6-arginine and 60 mg/L 13C6-lysine (heavy labeling).

extract_protocol: Total RNA was isolated using the Qiagen RNeasy Midi Kit (Qiagen, Valencia, CA).

treatment_protocol: For biological replicate 1, light-labeled cells were treated with 5 μg/mL dox for 11 hours until log phase. For biological replicate 2, heavy-labeled cells were treated, instead.

tag: strain/background

tag: genotype/variation

value: TETp-HSC82 hsp82Δ arg4Δ lys5Δ car2Δ::URA3

value: doxycycline

label: Alexa Fluor 555

source_name: untreated


title: Control, rep3

description:
RDX 0-3
Acropora formosa Consortium (coral and eukaryotic endosymbionts).

source_name: Coral soft tissue, untreated

tag: tissue


title: RDX 8.0 mg/L, rep3

description:
RDX 8-3
Acropora formosa Consortium (coral and eukaryotic endosymbionts).


title: Treated/untreated cell 2, replicate 1

description:
dox2-1
Biological replicate 2 of 2. Technical replicate 1 of 3. Dox-treated/untreated log-phase cells.


title: Control, rep2

description:
RDX 0-2
Acropora formosa Consortium (coral and eukaryotic endosymbionts).


title: RDX 8.0 mg/L, rep2

description:
RDX 8-2
Acropora formosa Consortium (coral and eukaryotic endosymbionts).


title: Treated/untreated cell 1, replicate 2

description:
dox1-2
Biological replicate 1 of 2. Technical replicate 2 of 3. Dox-treated/untreated log-phase cells.


title: RDX 2.0 mg/L, rep1

description:
RDX 2-1
Acropora formosa Consortium (coral and eukaryotic endosymbionts).

source_name: Coral soft tissue, RDX 2.0 mg/L

value: RDX 2.0 mg/L


title: Treated/untreated cell 1, replicate 3

description:
dox1-3
Biological replicate 1 of 2. Technical replicate 3 of 3. Dox-treated/untreated log-phase cells.


title: RDX 2.0 mg/L, rep3

description:
RDX 2-3
Acropora formosa Consortium (coral and eukaryotic endosymbionts).


title: Treated/untreated cell 2, replicate 2

description:
dox2-2
Biological replicate 2 of 2. Technical replicate 2 of 3. Dox-treated/untreated log-phase cells.


title: RDX 0.5 mg/L, rep2

description:
RDX 0.5-2
Acropora formosa Consortium (coral and eukaryotic endosymbionts).


title: Treated/untreated cell 2, replicate 3

description:
dox2-3
Biological replicate 2 of 2. Technical replicate 3 of 3. Dox-treated/untreated log-phase cells.


title: RDX 2.0 mg/L, rep2

description:
RDX 2-2
Acropora formosa Consortium (coral and eukaryotic endosymbionts).


title: RDX 0.5 mg/L, rep3

description:
RDX 0.5-3
Acropora formosa Consortium (coral and eukaryotic endosymbionts).


title: Irradiated Worm Pharynx Wound Plug 24 hrs Post Amputation Replicate 2

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

hyb_protocol: Custom Agilent 4x44k arrays with design id: 033226 were hybridized using oligoarray control targets and Agilent hybridization buffers according to the manufacturer protocols.

scan_protocol: Arrays were scanned using an Agilent G2505C scanner and quantified with Agilent Feature Extraction software version 10.5 using protocol GE2_105_Dec08.

data_processing: Data was analyzed in the R environment using the Limma library (Smyth, 2004) for loess normalization and calculation of p-values between treatments.

organism: Schmidtea mediterranea

source_name: Irradiated Worm Tissue Plug 24 hrs

label_protocol: Starting with 100 ng total RNA, amplification and labeling with Cy3 or Cy5 was performed using the Low Input Quick Amp Labeling Kit Two-Color from Agilent Technologies (#5190-2306).

growth_protocol: Schmidtea mediterranea asexual clonal line CIW4 was maintained and used as previously described (Newmark and Sánchez Alvarado, 2000).

extract_protocol: At specified times after amputation, plugs were extracted using 1mm microcapillary pipets (FHC, catalog # 30-30-0), and transferred directly into Trizol (Life Technologies) using a mouth pipet. For each replicate, 25 plugs were homogenized together, and then chloroform-extracted. The pellet was then precipitated with isopropanol, washed, and resuspended in water. RNA was then passed over an RNEasy column and DNasetreated.

treatment_protocol: Irradiated animals were exposed to 10,000 rads on a GammaCell 40 Exactor irradiator. Planarian water was replaced with 100mM sodium azide (diluted in Montjuïc water). After 5-7 minutes, the pharynx was visibly extended out of the body. Vigorous pipetting often dislodged the pharynx from the body; if necessary, fine serrated forceps were used to remove the pharynx, followed by several washes in Montjuïc.

tag: time

value: 24 hr

tag: radiation

value: 10k rad

tag: replicate

source_name: Irradiated Worm Tissue Plug 0 hrs

value: 0 hr


title: Irradiated Worm Pharynx Wound Plug 48 hrs Post Amputation Replicate 3

source_name: Irradiated Worm Tissue Plug 48 hrs

value: 48 hr


title: Irradiated Worm Pharynx Wound Plug 24 hrs Post Amputation Replicate 3


title: Irradiated Worm Pharynx Wound Plug 72 hrs Post Amputation Replicate 1

source_name: Irradiated Worm Tissue Plug 72 hrs

value: 72 hr


title: Irradiated Worm Pharynx Wound Plug 48 hrs Post Amputation Replicate 2


title: Irradiated Worm Pharynx Wound Plug 48 hrs Post Amputation Replicate 1


title: Irradiated Worm Pharynx Wound Plug 72 hrs Post Amputation Replicate 2


title: Irradiated Worm Pharynx Wound Plug 24 hrs Post Amputation Replicate 1


title: Irradiated Worm Pharynx Wound Plug 72 hrs Post Amputation Replicate 3


title: Irradiated Worm Pharynx Wound Plug 18 hrs Post Amputation Replicate 3

source_name: Irradiated Worm Tissue Plug 18 hrs

value: 18 hr


title: Control, rep1

description:
RDX 0-1
Acropora formosa Consortium (coral and eukaryotic endosymbionts).

tag: treatment


title: Control Worm Pharynx Wound Plug 72 hrs Post Amputation Replicate 1

source_name: Control Worm Tissue Plug 72 hrs

source_name: Control Worm Tissue Plug 0 hrs


title: Control Worm Pharynx Wound Plug 72 hrs Post Amputation Replicate 2


title: Irradiated Worm Pharynx Wound Plug 6 hrs Post Amputation Replicate 3

source_name: Irradiated Worm Tissue Plug 6 hrs

value: 6 hr


title: Irradiated Worm Pharynx Wound Plug 6 hrs Post Amputation Replicate 1


title: Irradiated Worm Pharynx Wound Plug 6 hrs Post Amputation Replicate 2


title: Irradiated Worm Pharynx Wound Plug 18 hrs Post Amputation Replicate 1


title: Control Worm Pharynx Wound Plug 48 hrs Post Amputation Replicate 2

source_name: Control Worm Tissue Plug 48 hrs


title: Irradiated Worm Pharynx Wound Plug 12 hrs Post Amputation Replicate 3

source_name: Irradiated Worm Tissue Plug 12 hrs

value: 12 hr


title: Irradiated Worm Pharynx Wound Plug 18 hrs Post Amputation Replicate 2


title: Control Worm Pharynx Wound Plug 24 hrs Post Amputation Replicate 3

source_name: Control Worm Tissue Plug 24 hrs


title: Control Worm Pharynx Wound Plug 48 hrs Post Amputation Replicate 3


title: Control Worm Pharynx Wound Plug 72 hrs Post Amputation Replicate 3


title: Control Worm Pharynx Wound Plug 48 hrs Post Amputation Replicate 1


title: Control Worm Pharynx Wound Plug 24 hrs Post Amputation Replicate 1


title: Control Worm Pharynx Wound Plug 24 hrs Post Amputation Replicate 2


title: Control Worm Pharynx Wound Plug 18 hrs Post Amputation Replicate 2

source_name: Control Worm Tissue Plug 18 hrs


title: Control Worm Pharynx Wound Plug 18 hrs Post Amputation Replicate 3


title: Control Worm Pharynx Wound Plug 12 hrs Post Amputation Replicate 3

source_name: Control Worm Tissue Plug 12 hrs


title: Control Worm Pharynx Wound Plug 12 hrs Post Amputation Replicate 2


title: Irradiated Worm Pharynx Wound Plug 12 hrs Post Amputation Replicate 1


title: Control Worm Pharynx Wound Plug 6 hrs Post Amputation Replicate 1

source_name: Control Worm Tissue Plug 6 hrs


title: Control Worm Pharynx Wound Plug 12 hrs Post Amputation Replicate 1


title: Control Worm Pharynx Wound Plug 6 hrs Post Amputation Replicate 2


title: Irradiated Worm Pharynx Wound Plug 12 hrs Post Amputation Replicate 2


title: Control Worm Pharynx Wound Plug 6 hrs Post Amputation Replicate 3


title: Control Worm Pharynx Wound Plug 18 hrs Post Amputation Replicate 1


title: Vegetative buds_40d chilling

city: Kyoto

first: Hisayo

last: Yamane

address: Sakyo-ku

department: Grad. Sch. of Agriculture

institute: Kyoto University

description:
40d
The branches collected in November were artificially defoliated, and transferred to a 12/6 degreeC (9h light/15h dark). After 40 days, vegetative buds were excised from the middle portions of the long branches.

hyb_protocol: The labeled samples were hybridized to the oligoarray slides using a Gene Expression Hybridization Kit (Agilent Technologies) at 65°C for 17 h in an oven-chamber.

scan_protocol: Following hybridization, arrays were washed with Gene Expression Wash Buffer (Agilent Technologies) according to the manufacturer’s instructions. The dried slides were scanned using an Agilent scanner. Raw data from scanning of the array were captured using Agilent Feature Extraction Ver. 9.5.1 (Agilent Technologies).

data_processing: Data sets for each array were normalized and analyzed using the Subio software platform (Subio Inc, Japan). First, probes with low hybridization signals were removed. Then, hybridization intensities were log2 transformed, and arrays were normalized by global normalization, quantile normalization, and centering. For the samples in dataset 1 (three different time points during chilling treatment), three technical replicates (60K × 3 per sample) with three biological replicates were averaged, whereas three technical replicates were averaged for the samples in dataset 2 (10 different seasonal time points).

organism: Prunus mume

source_name: Buds with 40d chilling

label_protocol: Labeling of mRNA was performed using the Low Input Quick Amp Labeling Kit, One-Color (Agilent Technologies) from total RNA (200 ng) according to the manufacturer’s instructions.

growth_protocol: Field-grown Japanese apricot ‘Nanko’ trees (11 years old, seed-grafted) grown at the Kyoto University Experimental Farm, Kyoto, Japan, were used in this study.

extract_protocol: Total RNA was isolated from the buds as described by Yamane et al. (2008). RNA concentration was measured by spectrophotometry (NanoDrop 1000, Thermo Fisher Scientific, USA) and integrity was assessed using a Bioanalyzer (Agilent Technologies, USA).

treatment_protocol: For the samples, 0d, 40d and 60d, collected branches were artificially defoliated, and transferred to a growth chamber under a 9-h light/15-h dark photoperiod cycle at temperature conditions of 12°C in the light, and 6°C in the dark, for 0d, 40d and 60d. The basal parts of these branch cuttings were placed in water. For all samples, vegetative buds were excised from the middle portions of the branches, immediately frozen in liquid nitrogen and stored at -80°C until required.

tag: timepoints

value: Chilled for 40d

tag: Stage

value: endo/ecodormant


title: Vegetative buds_middle of February

description:
Feb
Vegetative buds were excised from the middle portions of the long branches collected in the middle of February

source_name: Buds collected in February

value: February

value: ecodormant


title: Vegetative buds_middle of December

description:
Dec
Vegetative buds were excised from the middle portions of the long branches collected in the middle of December

source_name: Buds collected in December

value: December

value: endodormant


title: Vegetative buds_middle of June

description:
Jun
Vegetative buds were excised from the middle portions of the long branches collected in the middle of June

source_name: Buds collected in June

value: June

value: paradormant due to apical dominance


title: Vegetative buds_middle of November

description:
Nov
Vegetative buds were excised from the middle portions of the long branches collected in the middle of November

source_name: Buds collected in November

value: November


title: Vegetative buds_middle of March

description:
Mar
Vegetative buds were excised from the middle portions of the long branches collected in the middle of March

source_name: Buds collected in March

value: March


title: Vegetative buds_middle of January

description:
Jan
Vegetative buds were excised from the middle portions of the long branches collected in the middle of January

source_name: Buds collected in January

value: January


title: Vegetative buds_middle of October

description:
Oct
Vegetative buds were excised from the middle portions of the long branches collected in the middle of October

source_name: Buds collected in October

value: October


title: Recolonized flies, biological replicate 3

city: Lyon

first: François

last: Leulier

address: 46, allée d'Italie

institute: Institut of Functional Genomics Lyon

description: Gene expression data from flies at 7 days of age raised axenic and recolonized with a mix of commensal bacteria after emergence

hyb_protocol: Hybridization was conducted as recommended by Affymetrix using dedicated systems and protocol using 7.5 g biotinilated cRNA by chip

scan_protocol: Affymetrix microarrays were scanned using a GCS3000 scanner

data_processing: Raw data were processed using Affymetrix Command Console to generate CEL files

organism: Drosophila melanogaster

source_name: Flies at 7 days of age raised axenic and recolonized with a mix of commensal bacteria after emergence

label_protocol: One microgram of total RNA was amplified according Affymetrix protocol  (IVT), to generate a minimum of 90 g of biotinylated cRNA

extract_protocol: NucleoSpin RNA clean up from, Macherey Nagel, as described in details in the related article that will be published soon in PLoS One

value: whole flies

tag: genotype

value: yellow white


title: Blood female Saint Joseph Bay, FL SJB 2005_X13

city: Ferrara

first: Annalaura

last: Mancia

address: via L.Borsari, 46

department: Life Sciences and Biotechnology

country: Italy

institute: University of Ferrara

description: Gene expression wild dolphin blood

hyb_protocol: 500ng of Cy3-labelled 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 custom Tursiops truncatus Microarray (Agilent) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately with a wash in acetonitrile (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides (Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software A8.5.3 (Agilent) using default parameters (protocol GE1) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Tursiops truncatus

source_name: Peripheral Blood

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Amplification  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 and the Agilent 2100 Bioanalyzer.

extract_protocol: Total RNA from blood samples from wild dolphins was extracted using the RNAeasy Kit according to the manufacturer (Qiagen, Valencia, CA). RNA was quantified using a NanoDrop ND-1000 (Wilmington, DE), qualified on an Agilent 2100 Bioanalyzer (Foster City, CA) and stored at −80°C until needed for gene expression profiling.

treatment_protocol: Blood samples were collected from wild dolphins in PAXgene™ Blood tubes (Qiagen, Valencia, CA, USA), mixed immediately to stabilize the RNA, and stored according to the manufacturer’s instructions.

value: whole blood

tag: gender

value: female

tag: location

value: Saint Joseph Bay, FL


title: Blood female Saint Joseph Bay, FL SJB 2005_X07

description: Gene expression wild dolphin blood


title: Vegetative buds_60d chilling

description:
60d
The branches collected in November were artificially defoliated, and transferred to a 12/6 degreeC (9h light/15h dark). After 60 days, vegetative buds were excised from the middle portions of the long branches.

source_name: Buds with 60d chilling

value: Chilled for 60d


title: Blood male Saint Joseph Bay, FL SJB 2005_X06

description: Gene expression wild dolphin blood

value: male


title: Vegetative buds_middle of July

description:
Jul
Vegetative buds were excised from the middle portions of the long branches collected in the middle of July

source_name: Buds collected in July

value: July

value: facultative endodormant


title: ES

city: Tokyo

first: Tomohisa

last: Seki

address: 35 Shinanomachi, Shinjuku-ku

institute: Keio University School of Medicine

description: Kindly gifted from Dr. Nakatsuji.

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 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 (G2505CA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (GE1_1100_Jul11 and Grid: 026652_D_F_20120130) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: ES

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.4 ug RNA using the One-Color 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.

extract_protocol: RNA was prepared using the Trizol and RNeasy Kit following the manufacturer's manuals.  RNA was quantified using a NanoDrop-1000 Spectrophotometer.

treatment_protocol: TiPS cells and ES cells were collected by treatment of CTK solution. Activated T cells were collected by pipetting the dish and centrifugation.

tag: cell type

value: ES cell


title: Recolonized flies, biological replicate 1

value: raised axenic and recolonized with a mix of commensal bacteria after emergence


title: Vegetative buds_middle of September

description:
Sep
Vegetative buds were excised from the middle portions of the long branches collected in the middle of September

source_name: Buds collected in September

value: September

value: (facultative) endodormant


title: T cell

source_name: T cell

value: Activated T cell


title: Vegetative buds_0d chilling

description:
0d
Vegetative buds were excised from the middle portions of the long branches collected in the middle of November

source_name: Buds with 0d chilling

value: Chilled for 0d

value: endodormant


title: Vegetative buds_middle of August

description:
Aug
Vegetative buds were excised from the middle portions of the long branches collected in the middle of August

source_name: Buds collected in August

value: August


title: Axenic flies, biological replicate 3

description: Gene expression data from flies at 7 days of age raised and kept axenic after emergence

source_name: Flies at 7 days of age raised and kept axenic after emergence

value: whole flies

value: raised and kept axenic after emergence


title: TiPS1

value: Undifferentiated TiPS cell


title: Axenic flies, biological replicate 2

value: yellow white


title: Blood female Saint Joseph Bay, FL SJB 2005_X11

description: Gene expression wild dolphin blood

value: whole blood

value: female

value: Saint Joseph Bay, FL


title: TiPS2


title: Recolonized flies, biological replicate 2


title: Control, rep4

description:
RDX 0-4
Acropora formosa Consortium (coral and eukaryotic endosymbionts).

source_name: Coral soft tissue, untreated

value: adult coral soft tissue


title: Blood male Saint Joseph Bay, FL SJB 2005_X08

description: Gene expression wild dolphin blood

value: male


title: Axenic flies, biological replicate 1


title: Blood female Saint Joseph Bay, FL SJB 2005_X02

description: Gene expression wild dolphin blood


title: genomic DNA from healty normal breast controls [44_rp42]

city: Oslo

first: Ann Rita

last: Halvorsen

address: Montebello

country: Norway

institute: OUS- The Norwegian Radium Hospital

description: normal breast biopsy

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2 [data processing]

source_name: norma breast tissue

extract_protocol: genomic DNA was extracted and purified from tumor and normal samples using Maxwell 16 DNA Purification Kit according to standard instructions

value: Female

tag: irradiation status

value: Non-irradiated

tag: disease state

value: normal


title: genomic DNA from healty normal breast controls [47_rp71]

description: normal breast biopsy


title: Blood female Saint Joseph Bay, FL SJB 2005_X00_a

description: Gene expression wild dolphin blood


title: Blood male Sarasota, FL SAR 2005_232

description: Gene expression wild dolphin blood

value: Sarasota, FL


title: genomic DNA from healty normal breast controls [42_rp38]

description: normal breast biopsy


title: genomic DNA from healty normal breast controls [46_rp68]

description: normal breast biopsy


title: Blood female Saint Joseph Bay, FL SJB 2005_X03

description: Gene expression wild dolphin blood


title: genomic DNA from healty normal breast controls [43_rp40]

description: normal breast biopsy


title: SF BAY RNA + 500 nM AA

city: Livermore

first: Xavier

last: Mayali

address: 7000 East Ave

department: Chemical Science

institute: Lawrence Livermore National Laboratory

description:
SF Bay seawater; samples were from a mixed natural community which includes hundreds of different species.
isotopically labeled RNA
Isotope signal representing ribosomal RNA isotope labeling for treatment medium

hyb_protocol: 1X Nimblegen hub buffer, 18 hours, 42 degrees

scan_protocol: Genescan 4000B, PMT = 650 for fluorescence data; NanoSIMS 50 for isotopic data

data_processing: isotopic data were corrected for unhybridized probes

organism: marine metagenome

source_name: SF BAY RNA + 500 nM AA

label_protocol: Alexafluor 532 Ulysis labeling

growth_protocol: seawater collected at Berkeley pier and incubated in glass bottles in the dark with added 15N labeled mixed amino acids for 12 hours

extract_protocol: the cells are collected and the  RNA is extracted with Qiagen RNEasy kit from the total community

treatment_protocol: amino acids were added at 3 different concentrations (50 nM, 500 nM, 5 uM)

value: 15N labeled mixed amino acids, medium concentration


title: SF BAY RNA + 5 uM AA

description:
SF Bay seawater; samples were from a mixed natural community which includes hundreds of different species.
isotopically labeled RNA
Isotope signal representing ribosomal RNA isotope labeling for treatment high

source_name: SF BAY RNA + 5 uM AA

value: 15N labeled mixed amino acids, high concentration


title: Blood female Sarasota, FL SAR 2005_187

description: Gene expression wild dolphin blood


title: Blood male Saint Joseph Bay, FL SJB 2005_X01

description: Gene expression wild dolphin blood


title: Blood male Sarasota, FL SAR 2005_218

description: Gene expression wild dolphin blood


title: genomic DNA from healty normal breast controls [41_rp37]

description: normal breast biopsy


title: genomic DNA from healty normal breast controls [45_rp59]

description: normal breast biopsy


title: genomic DNA from breast tumor tissue [33_123af]

description: breast tumor biopsy

source_name: tumor tissue

value: Irradiated

value: breast cancer


title: Blood female Sarasota, FL SAR 2005_135

description: Gene expression wild dolphin blood


title: Blood male Sarasota, FL SAR 2005_220

description: Gene expression wild dolphin blood


title: SF BAY RNA + 50 nM AA

description:
SF Bay seawater; samples were from a mixed natural community which includes hundreds of different species.
isotopically labeled RNA
Isotope signal representing ribosomal RNA isotope labeling for treatment low

source_name: SF BAY RNA + 50 nM AA

value: 15N labeled mixed amino acids, low concentration


title: genomic DNA from healty normal breast controls [40_rp36]

description: normal breast biopsy