title: Testis_HybZoneMale_indFP043

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP043


title: Testis_HybZoneMale_indFP170

status: Public on Dec 04 2014

type: RNA

city: Ploen

first: Leslie

middle: M

last: Turner

address: August-Thienemann Str 2

department: Evolutionary Genetics

country: Germany

institute: Max Planck Institute for Evolutionary Biology

description: testis

hyb_protocol: Hybridization was performed following the One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol from Agilent.

scan_protocol: Arrays were scanned using a High Resolution Microarray Scanner (Agilent) and raw images processed using Feature Extraction Software (Agilent). Raw images and the distribution of non-uniformity outliers were visually inspected for large spatial artifacts (e.g. caused by buffer leakage or dust particles). We used quality control metrics from Feature Extraction protocol GE1_QCMT_Dec08.

data_processing: We mapped the 41,174 non-control probe sequences from the Whole Mouse Genome Microarray to the mouse reference genome (NCBI37, downloaded March 2011) using BLAT (minScore = 55, default settings for all other options).  We excluded probes with multiple perfect matches, more than nine matches, matches to non-coding/intergenic regions only, and matches to more than one gene. A total of 36,323 probes (covering 19,742 Entrez Genes) were retained. Preprocessing of microarray data was performed using the BioConductor package Agi4x44PreProcess. We used the “half” setting, which sets intensities below 0.5 to 0.5 following background subtraction, and an offset value of 50. The background signal was computed in Feature Extraction. During preprocessing, we filtered probes based on flags from Feature Extraction. Probes with signal above background in at least 10% of samples were retained (settings: wellaboveBG=TRUE, isfound=TRUE, wellaboveNEG=TRUE). We used default settings for quality-control flags. Following preprocessing, we removed probes for which the 98th percentile was <2-fold greater than background. The final data set includes 24,218 probes.

molecule: total RNA

organism: Mus musculus musculus x M. m. domesticus

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP170

label_protocol: We used single-color Quick-Amp Labeling Kits (Agilent) to amplify and label RNA. The yield (>2 μg) and specific activity (>9.0 pmol Cy3/μg cRNA) of labeling reactions was verified using a NanoDrop ND-1000 UV-VIS Spectrophotometer (NanoDrop, Wilmington, DE, USA).

growth_protocol: Pups were weaned at 28 days, and males were separated into individual cages. Males were killed for phenotyping at 62-86 days of age using carbon dioxide.

extract_protocol: We extracted RNA from testis using RNeasy kits (Qiagen, Hilden, Germany). RNA quality (RIN > 8) was verified using RNA 6000 Nano kits (Agilent) on a 2100 Bioanalyzer (Agilent).

treatment_protocol: Freshly dissected right testes were stored in RNAlater (Qiagen) at 4° overnight, then transferred to -20° until processed.

tag: tissue

value: testis


title: Testis_HybZoneMale_indFP079

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP079


title: Testis_HybZoneMale_indFP018

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP018


title: 191.242

city: Philadelphia

first: Hongzhe

last: Li

state: Pennsylvania

address: 415  Curie Blvd

department: Biostatistics and Epidemiology

country: USA

institute: University of Pennsylvania

hyb_protocol: RNA were reverse transcribed into cDNAs followed by fragmentation

scan_protocol: After hybridization to the GeneChip Human Gene 1.0 ST Arrays, the chips were labeled with a WT Terminal Labeling Kit (Affymetrix, Santa Clara, CA) and scanned on a GeneChip Scanner 3000 7G (Affymetrix, Santa Clara, CA).

data_processing: Data were normalized using the Robust Multi-Chip Average (RMA) method and Log2 transformed using Partek Genomics Suite 6.4 (Partek Inc., St. Louis, MO).

label: biotin

organism: Homo sapiens

source_name: ovary

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA

extract_protocol: Qiagen miRNeasy Mini kit

value: ovary

tag: tumor stage

value: III-IV


title: Testis_HybZoneMale_indFP092

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP092


title: Testis_HybZoneMale_indFP074

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP074


title: Testis_HybZoneMale_indFP070

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP070


title: Testis_HybZoneMale_indFP008

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP008


title: Testis_HybZoneMale_indFP187

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP187


title: Testis_HybZoneMale_indFP197

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP197


title: Testis_HybZoneMale_indFP030

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP030


title: Testis_HybZoneMale_indFP153

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP153


title: Testis_HybZoneMale_indFP152

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP152


title: Testis_HybZoneMale_indFP025

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP025


title: Testis_HybZoneMale_indFP146

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP146


title: Testis_HybZoneMale_indFP117

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP117


title: Testis_HybZoneMale_indFP058

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP058


title: Testis_HybZoneMale_indFP052

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP052


title: Testis_HybZoneMale_indFP062

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP062


title: Testis_HybZoneMale_indFP147

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP147


title: Testis_HybZoneMale_indFP151

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP151


title: Testis_HybZoneMale_indFP160

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP160


title: Testis_HybZoneMale_indFP120

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP120


title: Testis_HybZoneMale_indFP181

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP181


title: Testis_HybZoneMale_indFP106

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP106


title: Testis_HybZoneMale_indFP064

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP064


title: Testis_HybZoneMale_indFP133

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP133


title: Testis_HybZoneMale_indFP081

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP081


title: Testis_HybZoneMale_indFP116

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP116


title: Testis_HybZoneMale_indFP137

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP137


title: Testis_HybZoneMale_indFP101

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP101


title: Testis_HybZoneMale_indFP132

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP132


title: Testis_HybZoneMale_indFP176

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP176


title: Testis_HybZoneMale_indFP136

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP136


title: Testis_HybZoneMale_indFP068

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP068


title: Testis_HybZoneMale_indFP190

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP190


title: Testis_HybZoneMale_indFP139

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP139


title: Testis_HybZoneMale_indFP088

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP088


title: Testis_HybZoneMale_indFP173

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP173


title: Testis_HybZoneMale_indFP124

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP124


title: Testis_HybZoneMale_indFP069

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP069


title: Testis_HybZoneMale_indFP180

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP180


title: Testis_HybZoneMale_indFP192

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP192


title: Testis_HybZoneMale_indFP099

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP099


title: Testis_HybZoneMale_indFP156

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP156


title: Testis_HybZoneMale_indFP166

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP166


title: Testis_HybZoneMale_indFP046

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP046


title: Testis_HybZoneMale_indFP164

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP164


title: Testis_HybZoneMale_indFP150

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP150


title: Testis_HybZoneMale_indFP029

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP029


title: Testis_HybZoneMale_indFP189

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP189


title: Testis_HybZoneMale_indFP131

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP131


title: Testis_HybZoneMale_indFP179

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP179


title: Testis_HybZoneMale_indFP080

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP080


title: Testis_HybZoneMale_indFP110

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP110


title: Testis_HybZoneMale_indFP077

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP077


title: Testis_HybZoneMale_indFP048

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP048


title: Testis_HybZoneMale_indFP040

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP040


title: Testis_HybZoneMale_indFP014

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP014


title: Testis_HybZoneMale_indFP127

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP127


title: Testis_HybZoneMale_indFP035

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP035


title: Testis_HybZoneMale_indFP009

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP009


title: elt-2RNAi, P. aeruginosa_colonized, hand picked

city: Berkeley

first: Michael

last: Shapira

state: CA

address: 3060 Valley Life Sciences Bldg room 5163

department: Integrative Biology

institute: UC Berkeley

description:
Sample name: elt-2 colonized HP_05.09
Amplified polyA RNA
Single Biological sample

hyb_protocol: 2 ug of fragmented aRNA in a volume of 13 ul was combined with 13ul of kreablock(Kreatech) and 26 ul of 2X formamide based hybridization buffer (Genisphere). Static hybridizations under M-series Lifterslips from Erie Scientific were done at 43C (16-20hrs). Chambers were humidified with 4X SSC. Arrays were washed according to the Genisphere protocol.

scan_protocol: Scanned on a GenePix 4000B scanner, Images quantified using Genepix Pro 6

data_processing: Median intensity values were used, Signal to Noise (background checking) threshold of 2.5 used, LOWESS normalized, using MIDAS software

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: C.elegans_elt-2 RNAi then P. aeruginosa and colonized

label_protocol: RNA labeled using the ULS™ aRNA Labeling Kit (Kreatech)

growth_protocol: Grown at 25oC

extract_protocol: Total RNA extracted using Trizol (Invitrogen), and polyA RNA amplified using the MessageAmp™ II aRNA Amplification Kit (Ambion)

treatment_protocol: Animals treated with control or elt-2 RNAi from L4 to D2 of adulthood then exposed to E.coli or P. aeruginosa for ~18h (control RNAi) or ~12h (elt-2 RNAi)

tag: strain

tag: age

value: Day 2 old adult

tag: treatment

value: elt-2 RNAi

tag: exposure

value: P. aeruginosa

tag: colonization status

value: colonized

tag: sorting

value: hand picked

source_name: Mixed stage C.elegans fed E.coli strain OP50

growth_protocol: Animals grown at 25oC

tag: sample type

value: reference RNA sample from mixed stage C.elegans cultures


title: SMA-SMT

city: Notre Dame

first: Jacqueline

last: Lopez

state: Indiana

address: 019 Galvin Life Science Center

department: Biology

institute: University of Notre Dame

description:
Total RNA primed with Oligo-dT (Promega) and converted to ds cDNA using Double-stranded cDNA Synthesis Kit (Invitrogen). RNA degraded with RNaseA. ds cDNA purified with ChargeSwitch PCR Clean Up Kit (Invitrogen).
Nanodrop ND-1000 (ThermoScientific) used to determine Total RNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine Total RNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine ds cDNA concentration. Bioanalyzer 2100 (Agilent Technologies) and DNA7500 Kit (Agilent Technologies) used to determine ds cDNA integrity.

hyb_protocol: Hybridization and post-hybridization washing using Hybridization Systems Kit (Roche NimbleGen) and Wash Buffer Kit (Roche NimbleGen) per manufacturer's recommendations. http://www.nimblegen.com

scan_protocol: Image acquisition with Axon GenePix 4200A Professional scanner, 5 micron resolution.

data_processing: Raw signal intensities extracted with NimbleScan 2.6 Software (Roche NimbleGen) as PAIR files.

organism: Onthophagus taurus

source_name: SMA

label_protocol: ds cDNA labeled using NimbleGen Dual Color Labeling Kit (Roche NimbleGen) per manufacturer's recommendations. http://www.nimblegen.com

extract_protocol: Trizol

tag: nutritional condition

value: SUBOPTIMAL

tag: gender

value: MALE

tag: body region

value: ABDOMEN

source_name: SMT

value: THORAX


title: Testis_HybZoneMale_indFP059

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP059


title: elt-2RNAi, P. aeruginosa_non-colonized, hand picked, rep 1

description:
Sample name: elt-2 non-colonized HP_05.09
Amplified polyA RNA
Biological replicate 1 of 2

source_name: C.elegans_elt-2 RNAi then P. aeruginosa and not colonized

value: not colonized


title: elt-2RNAi, E.coli, hand picked, rep 1

description:
Sample name: elt-2 OP50 HP_05.09
Amplified polyA RNA
Biological replicate 1 of 2

source_name: C.elegans_elt-2 RNAi then E. coli OP50 E.coli


title: elt-2RNAi, E.coli, wormsorter, rep 2

description:
Sample name: elt-2 OP50 WS_04.23
Amplified polyA RNA
Biological replicate 2 of 2

value: wormsorter


title: SMH-SMA

source_name: SMH

value: HEAD


title: elt-2RNAi, P. aeruginosa_non-colonized, worm sorter, rep 2

description:
Sample name: elt-2 non-colonized WS_04.23
Amplified polyA RNA
Biological replicate 2 of 2


title: SMA-SML

source_name: SML

value: LEG


title: LML-LMH

source_name: LML

value: OPTIMAL

source_name: LMH


title: controlRNAi, P. aeruginosa_colonized, worm sorter, rep 2

description:
Sample name: control_colonized_WS_05.09
Amplified polyA RNA
Biological replicate 2 of 3

source_name: C.elegans control RNAi then P. aeruginosa and fully colonized

value: control RNAi

value: fully colonized


title: LMA-LMH

source_name: LMA


title: SFL-SFH

source_name: SFL

value: FEMALE

source_name: SFH


title: SMH-SML


title: controlRNAi, P. aeruginosa_colonized, hand picked, rep 1

description:
Sample name: control_colonized_HP_05.09
Amplified polyA RNA
Biological replicate 1 of 3

value: Day 2 old adult


title: LML-LMT

source_name: LMT


title: LMT-LMH


title: controlRNAi, P. aeruginosa_colonized, worm sorter, rep 3

description:
Sample name: control_colonized_WS_04.23
Amplified polyA RNA
Biological replicate 3 of 3

value: P. aeruginosa


title: LMT-LMA


title: controlRNAi, P. aeruginosa_non-colonized, worm sorter, rep 2

description:
Sample name: control_non-colonized_WS_05.09
Amplified polyA RNA
Biological replicate 2 of 3

source_name: C.elegans control RNAi then P. aeruginosa and not colonized


title: SMH-SMT


title: SMT-SML


title: SFA-SFL

source_name: SFA


title: controlRNAi, E.coli, worm sorter, rep 2

description:
Sample name: control_OP50_WS_05.09
Amplified polyA RNA
Biological replicate 2 of 3

source_name: C.elegans control RNAi then E.coli OP50 E.coli

source_name: Mixed stage C.elegans fed E.coli strain OP50


title: controlRNAi, P. aeruginosa_non-colonized, worm sorter, rep 3

description:
Sample name: control_non-colonized_WS_04.23
Amplified polyA RNA
Biological replicate 3 of 3


title: controlRNAi, E.coli, hand picked, rep 1

description:
Sample name: control_OP50_HP_05.09
Amplified polyA RNA
Biological replicate 1 of 3


title: controlRNAi, P. aeruginosa_non-colonized, hand picked, rep 1

description:
Sample name: control_non-colonized_HP_05.09
Amplified polyA RNA
Biological replicate 1 of 3


title: controlRNAi, E.coli, worm sorter, rep 3

description:
Sample name: control_OP50_WS_04.23
Amplified polyA RNA
Biological replicate 3 of 3


title: SFH-LFH

source_name: LFH


title: SMH-LMH


title: rpoS mutant strain probe replicate 6

type: mixed

city: St-Anne-de-Bellevue

first: Sebastien

last: Faucher

state: QC

address: 21,111 Lakeshore

department: Natural Resource Sciences

country: Canada

institute: McGill University

description:
rpoS probe_rep6
raw data file: rpoS_DFM_raw.txt

hyb_protocol: Hybridization was performed as previously described (Hovel-Miner, G 2009. JB, 191:2461).

scan_protocol: Scanning and image acquisition was performed on a InnoScan 710 using the mapix software. Spot intensity an local background was measured.

data_processing: Data were processed with the mapix software. Values from each channel were background subtracted and the ratio Ch2/Ch1 was calculated. We used gDNA for data normalization, as described in Talaat, 2002, NAR.

label: Alexa Fluor 546

molecule: genomic DNA

organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1

source_name: genomic DNA, reference channel

label_protocol: RNA: 15 ug of Total RNA was labeled with amino-allyl dUTP during reverse transcriptase and subsequently coupled with the succinimidyl ester fluorescent dye AlexaFluor 647 as previously described (Hovel-Miner, G 2009. JB, 191:2461). Genomic DNA: 5 ug of genomic DNA was labeled with amino-allyl dUTP with klenow fragment and random hexamer as previously described (Porwollik, S. 2001. Mutat Res 483:1). Subsequently, the resulting DNA was coupled to the succinimidyl ester fluorescent dye AlexaFluor 546.

extract_protocol: RNA: TRIzol reagent, reverse-transcribed into cDNA. Genomic DNA: QIAamp kit.

tag: genotype/variation

value: wild-type

tag: media

value: AYE broth, 37°C shaking

label: Alexa Fluor 647

source_name: rpoS mutant

value: rpoS mutant

value: DFM, 24h


title: rpoS mutant strain probe replicate 4

description:
rpoS probe_rep4
raw data file: rpoS_DFM_raw.txt


title: rpoS mutant strain probe replicate 3

description:
rpoS probe_rep3
raw data file: rpoS_DFM_raw.txt


title: p21 Transfection 3

city: Iowa City

first: Daniel

last: Fox

state: IA

address: 4400 PBDB, 500 Newton Rd.

department: Internal Medicine

institute: University of Iowa

description: skeletal muscle RNA

hyb_protocol: Amplified and labeled cRNA was quantified (Ribogreen assay) and hybridized to Mouse Ref-8 version 2.0 BeadChip Arrays (Illumina) overnight at 58°C. Following hybridization, arrays were washed, blocked, stained, and dried (Little Dipper Processor).

scan_protocol: Arrays were scanned with an iScan reader, and data were extracted and analyzed with BeadStudio Software (Illumina).

data_processing: Data was processed using Bioconductor Software with VST transformation and RSN normalization.

organism: Mus musculus

source_name: tibialis anterior

label_protocol: RNA was then amplified and labeled (Ambion TotalPrep Kit), and cDNA was synthesized using robotic-assisted magnetic capture. Using the cDNA template, biotinylated cRNA was produced via an in vitro transcription reaction.

growth_protocol: Not applicable

extract_protocol: Skeletal muscle RNA was extracted using TRIzol solution (Invitrogen) and then purified using the RNeasy kit and RNase Free DNase Set (Qiagen).

treatment_protocol: Bilateral tibialis anterior muscles of C57BL/6 mice were harvested seven days after transfection with p21 or control plasmid.

value: tibialis anterior

value: 8 weeks

tag: Sex

value: male


title: rpoS mutant strain probe replicate 5

description:
rpoS probe_rep5
raw data file: rpoS_DFM_raw.txt


title: p21 Transfection 4

description: skeletal muscle RNA


title: rpoS mutant strain probe replicate 2

description:
rpoS probe_rep2
raw data file: rpoS_DFM_raw.txt


title: SMT-LMT

description:
Total RNA primed with Oligo-dT (Promega) and converted to ds cDNA using Double-stranded cDNA Synthesis Kit (Invitrogen). RNA degraded with RNaseA. ds cDNA purified with ChargeSwitch PCR Clean Up Kit (Invitrogen).
Nanodrop ND-1000 (ThermoScientific) used to determine Total RNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine Total RNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine ds cDNA concentration. Bioanalyzer 2100 (Agilent Technologies) and DNA7500 Kit (Agilent Technologies) used to determine ds cDNA integrity.

source_name: SMT

value: SUBOPTIMAL

value: MALE

value: THORAX


title: SFT-LFT

source_name: SFT

source_name: LFT


title: SMA-LMA

source_name: SMA

value: ABDOMEN


title: SMT-SFT


title: p21 Transfection 2

description: skeletal muscle RNA


title: rpoS mutant strain probe replicate 1

description:
rpoS probe_rep1
raw data file: rpoS_DFM_raw.txt


title: p21 Transfection 1

description: skeletal muscle RNA


title: SMA-SFA


title: SFA-LFA

source_name: LFA

value: OPTIMAL


title: wild-type strain probe replicate 6

description:
WT probe_rep6
raw data file: WT_DFM_raw.txt

source_name: wild-type


title: SML-SFL

source_name: SML

value: LEG

source_name: SFL


title: wild-type strain probe replicate 5

description:
WT probe_rep5
raw data file: WT_DFM_raw.txt


title: LFH-LFT

value: HEAD


title: SFL-SFT

value: FEMALE


title: SMH-SFH

source_name: SMH

source_name: SFH


title: Control Transfection (p21) 3

description: skeletal muscle RNA

value: control


title: Control Transfection (p21) 2

description: skeletal muscle RNA


title: Control Transfection (p21) 1

description: skeletal muscle RNA


title: wild-type strain probe replicate 3

description:
WT probe_rep3
raw data file: WT_DFM_raw.txt


title: Control Transfection (p21) 4

description: skeletal muscle RNA


title: wild-type strain probe replicate 1

description:
WT probe_rep1
raw data file: WT_DFM_raw.txt


title: wild-type strain probe replicate 2

description:
WT probe_rep2
raw data file: WT_DFM_raw.txt


title: LFT-LFL

source_name: LFL


title: LFA-LFT


title: Spermine Oxidase Transfection 4

description: skeletal muscle RNA

treatment_protocol: Bilateral tibialis anterior muscles of C57BL/6 mice were harvested seven days after transfection with spermine oxidase or control plasmid.

value: spermine oxidase


title: LMH-LMT

source_name: LMH

source_name: LMT


title: Spermine Oxidase Transfection 2

description: skeletal muscle RNA


title: LMH-LMA

source_name: LMA


title: Spermine Oxidase Transfection 1

description: skeletal muscle RNA


title: Spermine Oxidase Transfection 3

description: skeletal muscle RNA


title: LFH-LFL

source_name: LFH


title: LMA-LML

source_name: LML


title: Control Transfection (spermine oxidase) 4

description: skeletal muscle RNA

source_name: tibialis anterior


title: Control Transfection (spermine oxidase) 3

description: skeletal muscle RNA


title: LFH-LFA


title: Control Transfection (spermine oxidase) 1

description: skeletal muscle RNA


title: Control Transfection (spermine oxidase) 2

description: skeletal muscle RNA


title: SFH-SFT


title: LMH-LML


title: Lung tissue from control mice at 6 months of age, biological replicate 3

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

description: Gene expression data from lung tissue from control mice at 6 months of age, biological replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data including background subtraction (GenomeStudioV2011.1 software, gene expression module version 1.9.0), removal of negative values by introducing an offset, quantile normalisation

label: Biotin

source_name: Lung tissue

label_protocol: Illumina TotalPrep RNA Amplification kit (Ambion)

growth_protocol: Animals housed under spf conditions

extract_protocol: RNeasy Mini Kit (Qiagen) including DNase treatment

treatment_protocol: Exposure to cigarette smoke as described in the paper

value: female

value: lung

value: 6 m


title: Lung tissue from control mice at 6 months of age, biological replicate 2

description: Gene expression data from lung tissue from control mice at 6 months of age, biological replicate 2


title: Pf_juvenile stage_rep3

city: Peking

first: Jun

last: Liu

address: school of lifer science

country: China

institute: Tsinghua University

description: gene expression during development

hyb_protocol: Each Slide was hybridized with 1.65 g Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer's instructions

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5 m, PMT 100%, 10%, 16bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

data_processing: To determine the significantly differentially expressed genes between developmental stages, expression profile comparisons were performed with Significance Analysis of Microarrays (SAM) software. Only the genes whose changes were consistent (p-value<5%, Fold-Change (FC)≥2) were selected as differentially expressed genes, then further analyzed.

organism: Pinctada fucata

source_name: juvenile

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer's instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany)

growth_protocol: The sperms and oocytes were differentially collected from the male and female oyster adults, then mixed and fertilized with ammonia sea water stimulation. The larvae were raised in a small aquarium for 2 days and followed by a 20-L tank, juveniles adhering to the board were then raised in the pools. The larvae were feed by golden alga at the earlier stage and green alga at the lateral stage. All the fertilization and growth processes were strictly following the course and carried out in the Marine Biology Research Station at Leizhou Bay, Guangdong Ocean University, Zhanjiang, China.

extract_protocol: For microarray analysis, total RNA of larvae samples from pools of the different developmental stages were extracted using TRIZOL Reagent (Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions.

treatment_protocol: Normal larval culture without special treatment

value: 35 days

tag: developmental stage

value: juvenile


title: LFA-LFL


title: Pf_juvenile stage_rep1

description: gene expression during development


title: Pf_umbonal stage_rep3

description: gene expression during development

source_name: umbonal stage larvae

value: 14 days

value: umbonal stage larvae


title: Pf_umbonal stage_rep2

description: gene expression during development


title: LML-LFL


title: LMH-SMH

value: SUBOPTIMAL


title: LMT-LFT

value: MALE

source_name: LFT


title: LFH-SFH


title: Pf_D-shaped stage_rep3

description: gene expression during development

source_name: D-shaped stage larvae

value: 48 hours

value: D-shaped stage larvae


title: LMT-LML

value: OPTIMAL

value: THORAX


title: Pf_umbonal stage_rep1

description: gene expression during development


title: Lung tissue from cigarette smoke-treated mice at 6 months of age, biological replicate 2

description: Gene expression data from lung tissue from cigarette smoke-treated mice at 6 months of age, biological replicate 2

value: cigarette smoke-treated


title: Donor2, Osteoclast

status: Public on Dec 03 2014

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

country: Spain

institute: Josep Carreras Research Institute (IJC)

description:
Monocytes stimulated with RANKL/MCSF for 21 days
D2 OC

data_processing: Interplate calibrator assigned value 1 on the Roche LC480 qPCR machine software. Normalized by hsa-miR-103

label: Sybr Green

source_name: In vitro differentiated osteoclasts

label_protocol: cDNA was generated using the miRCURY LNA microRNA PCR, Polyadenylation and cDNA synthesis kit II (ref: 203301) from Exiqon. MicroRNA expression profling was performed using the Ready-to-use microRNA PCR Human Panel I V2.R from Exiqon (Reference 203608) following the instructions manual (Exiqon, Vedbeak, Denmark).

growth_protocol: Human primary CD14+ monocytes grown in alpha mem

extract_protocol: Total RNA with Tripure

treatment_protocol: RANKL 50ng/ml  and MCSF 25ng/ml

tag: cell type

value: In vitro differentiated osteoclasts


title: LMT-SMT

source_name: SMT


title: Lung tissue from control mice at 4 months of age, biological replicate 2

description: Gene expression data from lung tissue from control mice at 4 months of age, biological replicate 2

tag: tissue

value: control

value: 4 m


title: LML-SML

value: LEG

source_name: SML


title: Lung tissue from cigarette smoke-treated mice at 6 months of age, biological replicate 3

description: Gene expression data from lung tissue from cigarette smoke-treated mice at 6 months of age, biological replicate 3

value: female

value: lung


title: Pf_trochophore stage_rep3

description: gene expression during development

source_name: trochophore stage larvae

value: 17 hours

value: trochophore stage larvae


title: Lung tissue from control mice at 4 months of age, biological replicate 3

description: Gene expression data from lung tissue from control mice at 4 months of age, biological replicate 3


title: Pf_trochophore stage_rep2

description: gene expression during development


title: Donor3, Osteoclast

description:
Monocytes stimulated with RANKL/MCSF for 21 days
D3 OC


title: Lung tissue from control mice at 4 months of age, biological replicate 1

description: Gene expression data from lung tissue from control mice at 4 months of age, biological replicate 1


title: Lung tissue from cigarette smoke-treated mice at 4 months of age, biological replicate 2

description: Gene expression data from lung tissue from cigarette smoke-treated mice at 4 months of age, biological replicate 2


title: Pf_D-shaped stage_rep1

description: gene expression during development


title: Lung tissue from cigarette smoke-treated mice at 6 months of age, biological replicate 1

description: Gene expression data from lung tissue from cigarette smoke-treated mice at 6 months of age, biological replicate 1

value: 6 m


title: Pf_D-shaped stage_rep2

description: gene expression during development


title: Lung tissue from cigarette smoke-treated mice at 4 months of age, biological replicate 3

description: Gene expression data from lung tissue from cigarette smoke-treated mice at 4 months of age, biological replicate 3


title: SFH-SFA

description:
Total RNA primed with Oligo-dT (Promega) and converted to ds cDNA using Double-stranded cDNA Synthesis Kit (Invitrogen). RNA degraded with RNaseA. ds cDNA purified with ChargeSwitch PCR Clean Up Kit (Invitrogen).
Nanodrop ND-1000 (ThermoScientific) used to determine Total RNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine Total RNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine ds cDNA concentration. Bioanalyzer 2100 (Agilent Technologies) and DNA7500 Kit (Agilent Technologies) used to determine ds cDNA integrity.

source_name: SFH

value: FEMALE

value: HEAD

source_name: SFA

value: ABDOMEN


title: LFT-SFT

source_name: SFT

value: SUBOPTIMAL


title: SFT-SFA


title: Lung tissue from cigarette smoke-treated mice at 4 months of age, biological replicate 1

description: Gene expression data from lung tissue from cigarette smoke-treated mice at 4 months of age, biological replicate 1


title: Pf_fertilized eggs_rep1

description: gene expression during development

source_name: fertilized eggs

value: 0 hours

value: fertilized eggs


title: Pf_fertilized eggs_rep3

description: gene expression during development


title: LMH-LFH

source_name: LMH

value: OPTIMAL

value: MALE


title: Pf_juvenile stage_rep2

description: gene expression during development

value: 35 days

value: juvenile


title: Donor3, Osteoclast 48h

description:
Monocytes stimulated with RANKL/MCSF for 2 days
D3 48H

value: In vitro differentiated osteoclasts


title: Pf_fertilized eggs_rep2

description: gene expression during development


title: LFL-SFL

source_name: LFL

value: LEG

source_name: SFL


title: LMA-LFA

source_name: LMA

source_name: LFA


title: Pf_trochophore stage_rep1

description: gene expression during development


title: wild-type strain probe replicate 4

description:
WT probe_rep4
raw data file: WT_DFM_raw.txt

source_name: genomic DNA, reference channel

value: wild-type

value: AYE broth, 37°C shaking

source_name: wild-type

value: DFM, 24h


title: Donor1, Osteoclast

description:
Monocytes stimulated with RANKL/MCSF for 21 days
D1 OC


title: Donor2, Osteoclast 48h

description:
Monocytes stimulated with RANKL/MCSF for 2 days
D2 48H


title: Donor1, Osteoclast 48h

description:
Monocytes stimulated with RANKL/MCSF for 2 days
D1 48H


title: Donor1, CD14+ Monocytes

description:
CD14+ Monocytes
D1 CD14

source_name: Circulating monocytes

value: Circulating monocytes


title: Donor3, CD14+ Monocytes

description:
CD14+ Monocytes
D3 CD14


title: Donor2, CD14+ Monocytes

description:
CD14+ Monocytes
D2 CD14


title: n2a-Pou3f3-kd-3

city: Oxford

first: Vladislava

last: Chalei

address: Sherrington building, Parks road

department: MRC FUnctional Genomics Unit, Department of Physiology, Anatomy and Genetics

country: United Kingdom

institute: University of Oxford

hyb_protocol: Fragmented ssDNA was then labelled and hybridized to the Affymetrix GeneChip Mouse Gene 1.0 ST Array (Affymetrix). Chips were processed on an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Chips were scanned on an Affymetrix Scanner 3000.

data_processing: Affymetrix CEL files were analysed using the Limma, oligo, and genefilter R Bioconductor packages. Arrays were RMA background corrected, quantile normalised and summary expression values calculated for Refseq and full length mRNAs. Before differential expression analysis, genes changing upon Pou3f3 knockdown were filtered to remove genes showing little variation in expression (variance cut off of 0.2).

source_name: N2A cells_Pou3f3 knockdown construct

label_protocol: 200 ng RNA was used to generate labelled sense single stranded DNA (ssDNA) for hybridization with the Ambion WT Expression Kit, the Affymetrix WT Terminal Labelling and Controls Kit and the Affymetrix Hybridization, Wash, and Stain Kit as described by the manufacturer.  Sense ssDNA was fragmented and the distribution of fragment lengths was measured on a BioAnalyzer.

growth_protocol: N2A mouse neuroblastoma cells were grown in DMEM supplemented with 10% fetal bovine serum.

extract_protocol: Total RNA was isolated using the Qiagen Mini RNeasy kit following the manufacturer’s instructions and RNA integrity assessed on a BioAnalyzer (Agilent Technologies).

treatment_protocol: Approximately 2x105 cells were plated per well in a 6 well plate. 16-24 hrs later cells were transfected with 1.5 ug shRNA expression construct using FuGENE 6 (Promega) according to the manufacturer’s instructions. Total RNA was extracted from the cells 2.5 days later.

tag: cell line

value: neuro 2A (N2A)

value: neuroblastoma cell line

value: transiently transfected with Pou3f3 knockdown construct


title: flesh of pummelo, 30 DAH,rep 1

city: Wuhan

first: Ding

last: Yuduan

address: No.1,Shizishan Street · Hongshan District · Wuhan · Hubei Province · 430070 · P.R.China

institute: Huazhong Agricultural University

description: Gene expression data from flesh of pummelo, 30 day after harvest

hyb_protocol: not provided

scan_protocol: not provided

data_processing: Quality control and MAS5 present/absent call values (P/M) were obtained using the XPS package and the expression values were obtained by RMA method using the Affy package.

organism: Citrus maxima

source_name: flesh of pummelo, 30 day after harvest

label_protocol: not provided

extract_protocol: RNA samples were independently isolated according to the method described by Tao (Tao et al., 2004) and were hybridized respectively with the commercial genechip® Citrus Genome Arrays (Affymetrix®; Santa Clara, CA, USA)

treatment_protocol: Fruits were collected in Yichang, Hubei Provence, China, in 2008 at harvest season. Randomly selected healthy fruits with uniform color and size were stored at ambient temperature (16 -20°C, relative humidity 85 -90%).

value: flesh

tag: time


title: flesh of pummelo, 40 DAH,rep 1

description: Gene expression data from flesh of pummelo, 40 day after harvest

source_name: flesh of pummelo, 40 day after harvest


title: Lung tissue from control mice at 6 months of age, biological replicate 1

description: Gene expression data from lung tissue from control mice at 6 months of age, biological replicate 1

source_name: Lung tissue

tag: strain

value: female

value: lung

value: control

tag: age

value: 6 m


title: flesh of pummelo, 10 DAH,rep 2

description: Gene expression data from flesh of pummelo, 10 day after harvest

source_name: flesh of pummelo, 10 day after harvest


title: flesh of pummelo, 20 DAH,rep 2

description: Gene expression data from flesh of pummelo, 20 day after harvest

source_name: flesh of pummelo, 20 day after harvest


title: n2a-Pou3f3-cont-2

source_name: N2A cells_non-targeting vector

value: transiently transfected with non-targeting vector


title: flesh of pummelo, 40 DAH,rep 2


title: flesh of pummelo, 50 DAH,rep 1

description: Gene expression data from flesh of pummelo, 50 day after harvest

source_name: flesh of pummelo, 50 day after harvest


title: n2a-dali_knockdownRA-R1

description:
dalikdRA1
dalikdRA1

data_processing: Affymetrix CEL files were analysed using the Limma, oligo, and genefilter R Bioconductor packages. Arrays were RMA background corrected, quantile normalised and summary expression values calculated for Refseq and full length mRNAs. Before differential expression analysis, genes changing upon Dali knockdown and/or RA treatment were filtered to remove genes showing little variation in expression (variance cut off of 0.5).

treatment_protocol: Approximately 2x105 cells were plated per well in a 6 well plate. 16-24 hrs later cells were co-transfected with the pBSU6-shRNA expression vector and pTK-Hyg (Clontech) at a 5:1 ratio using FuGENE 6 (Promega) according to the manufacturer’s instructions. 72 hours post-transfection 200 μg/ml Hygromycin B was added to the cells to select individual drug resistant clones that were later isolated and expanded under selective conditions. For RA differentiation, control or stable Dali KD N2A cells were plated at a density 1.5 x 105 cells/well in a 6-well plate to allow for neurite outgrowth. After 24 h, growth medium was replaced with differentiation medium containing 2% FBS and 20 μM all-trans retinoic acid. Cells were differentiated for 72 h. Total RNA was extracted from proliferating or RA differentiated control and Dali KD cells.

value: stably transfected with Dali knockdown construct and differentiated with RA


title: flesh of pummelo, 20 DAH,rep 1


title: flesh of pummelo, 30 DAH,rep 2


title: flesh of pummelo, 0 DAH,rep 1

description: Gene expression data from flesh of pummelo, first day after harvest


title: n2a-Pou3f3-kd-2


title: n2a-Pou3f3-cont-1


title: n2a-dali_knockdownRA-R3

description:
dalikdRA3
dalikdRA3


title: rind of pummelo, 40 DAH,rep 2

description: Gene expression data from rind of pummelo, 40 day after harvest

source_name: rind of pummelo, 40 day after harvest

value: rind


title: n2a-Pou3f3-kd-1


title: n2a-dali_knockdown-R2

description:
dalikd2
dalikd2

value: stably transfected with Dali knockdown construct


title: n2a-Pou3f3-cont-3


title: rind of pummelo,50 DAH,rep 2

description: Gene expression data from rind of pummelo, 50 day after harvest

source_name: rind of pummelo, 50 day after harvest


title: n2a-dali_knockdown-R3

description:
dalikd3
dalikd3


title: flesh of pummelo, 10 DAH,rep 1


title: n2a-dali_knockdownRA-R2

description:
dalikdRA2
dalikdRA2


title: flesh of pummelo, 50 DAH,rep 2


title: flesh of pummelo, 0 DAH,rep 2

source_name: flesh of pummelo, first day after harvest


title: n2a-dali_knockdown-R1

description:
dalikd1
dalikd1


title: rind of pummelo, 40 DAH,rep 1


title: rind of pummelo, 50 DAH,rep 1


title: rind of pummelo, 30 DAH,rep 1

description: Gene expression data from rind of pummelo, 30 day after harvest

source_name: rind of pummelo, 30 day after harvest


title: rind of pummelo, 30 DAH,rep 2


title: n2a-dali_scrambledRA-R2

description:
controlRA2
controlRA2

value: stably transfected with non-targeting vector and differentiated with RA


title: n2a-dali_scrambledRA-R1

description:
controlRA1
controlRA1


title: rind of pummelo, 10 DAH,rep 2

description: Gene expression data from rind of pummelo, 10 day after harvest

source_name: rind of pummelo, 10 day after harvest


title: rind of pummelo, 10 DAH,rep 1


title: n2a-dali_scrambledRA-R3

description:
controlRA3
controlRA3


title: flesh of satsuma, 50 DAH,rep 2

description: Gene expression data from flesh of satsuma, 50 day after harvest

organism: Citrus unshiu

source_name: flesh of satsuma, 50 day after harvest


title: rind of pummelo, 20 DAH,rep 2

description: Gene expression data from rind of pummelo, 20 day after harvest

source_name: rind of pummelo, 20 day after harvest


title: rind of pummelo, 0 DAH ,rep 1

description: Gene expression data from rind of pummelo, first day after harvest


title: n2a-dalikd-control-R3

data_processing: Affymetrix CEL files were analysed using the Limma, oligo, and genefilter R Bioconductor packages. Arrays were RMA background corrected, quantile normalised and summary expression values calculated for Refseq and full length mRNAs. Before differential expression analysis, genes changing upon Dali knockdown were filtered to remove genes showing little variation in expression (variance cut off of 0.5).

treatment_protocol: Approximately 2x10^5 cells were plated per well in a 6 well plate. 16-24 hrs later cells were transfected with 1.5 ug shRNA expression construct using FuGENE 6 (Promega) according to the manufacturer’s instructions. Total RNA was extracted from the cells 2.5 days later.

tag: transfected with

value: non-targeting vector


title: n2a-dali_scrambled-R2

description:
control2
control2

value: stably transfected with non-targeting vector


title: flesh of satsuma, 50 DAH,rep 1


title: rind of pummelo, 20 DAH,rep 1


title: n2a-dalikd-knockdown-R1

value: Dali knockdown construct


title: n2a-dali_scrambled-R3

description:
control3
control3


title: n2a-dali_scrambled-R1

description:
control1
control1


title: rind of pummelo, 0 DAH,rep 2

source_name: rind of pummelo, first day after harvest


title: n2a-dalikd-knockdown-R3


title: flesh of satsuma, 30 DAH,rep 1

description: Gene expression data from flesh of satsuma, 30 day after harvest

source_name: flesh of satsuma, 30 day after harvest


title: n2a-dalikd-control-R2


title: flesh of satsuma, 30 DAH,rep 2


title: flesh of satsuma, 20 DAH,rep 2

description: Gene expression data from flesh of satsuma, 20 day after harvest

source_name: flesh of satsuma, 20 day after harvest


title: flesh of satsuma, 40 DAH,rep 1

description: Gene expression data from flesh of satsuma, 40 day after harvest

source_name: flesh of satsuma, 40 day after harvest


title: flesh of satsuma, 40 DAH,rep 2


title: flesh of satsuma, 10 DAH,rep 1

description: Gene expression data from flesh of satsuma, 10 day after harvest

source_name: flesh of satsuma, 10 day after harvest


title: flesh of satsuma, 0 DAH,rep 2

description: Gene expression data from flesh of satsuma, first day after harvest


title: n2a-dalikd-control-R1


title: flesh of satsuma, 10 DAH,rep 2


title: flesh of satsuma, 20 DAH,rep 1


title: n2a-dalikd-knockdown-R2


title: rind of satsuma,50 DAH,rep 2

description: Gene expression data from rind of satsuma, 50 day after harvest

source_name: rind of satsuma, 50 day after harvest


title: rind of satsuma, 50 DAH,rep 1


title: rind of satsuma, 0 DAH ,rep 1

description: Gene expression data from rind of satsuma, first day after harvest


title: WT-t0_vs_WT-t30min+0.7M NaCl_Replicate12

city: madison

first: Audrey

last: Gasch

state: wi

address: 425G Henry mall

department: genetics

institute: university of wisconsin, madison

description: Denoted strain grow in YPD 30C and exposed to 0.7M NaCl for 30 min

hyb_protocol: Hybridization on Maui hyb station according to Nimblegen and Maui protocols

scan_protocol: Axon GenePix scanner

data_processing: Background-subtracted signal intentisties for all probes were normalized by quantile normalization, removing probes with missing signal, media signal within ORFs was compared for each channel, and log2(red/green) values were median-centered such that the average of all values = 0.Values in the matrix represent log2 fold-change in T30min vs T0min (unstressed) sample for each denoted strain; Data have been converted so that positive log2 values correspond to gene induction (i.e. higher transcript abundance in T30 sample) and negative log2 values represent gene repression (i.e. higher transcript abundance in unstressed T0 sample). Samples collected together are annotated by sets.

label: Oyster 550

organism: Saccharomyces cerevisiae

source_name: SetE_WT BY4741 mutant treated with 0.7M NaCl for 30 min

label_protocol: Amino-allyl-dUTP incorporated into generated cDNA;  post-synthesis coupling to cyanine dyes (see Lee & Topper. 2011. Mol Sys Bio 7:514)

growth_protocol: S. cerevisiae strains grown in rich YPD medium at 30C in batch-culture with shaking.

extract_protocol: Hot phenol lysis to isolate total RNA

treatment_protocol: Pre-warmed NaCl in YPD added to each culture to a final concentration of 0.7M NaCl

tag: treatment

value: treated with 0.7M NaCl for 30 min

value: WT BY4741

label: Oyster 650

source_name: SetE_WT BY4741 mutant - unstressed t0 min

value: unstressed t0 min


title: arf3-t0_vs_arf3-t30min+0.7M NaCl_Replicate1

source_name: SetE_arf3 mutant treated with 0.7M NaCl for 30 min

source_name: SetE_arf3 mutant - unstressed t0 min


title: flesh of ponkan, 10 DAH,rep 2

description: Gene expression data from flesh of ponkan, 10 day after harvest

organism: Citrus reticulata

source_name: flesh of ponkan, 10 day after harvest


title: flesh of ponkan, 20 DAH,rep 2

description: Gene expression data from flesh of ponkan, 20 day after harvest

source_name: flesh of ponkan, 20 day after harvest


title: flesh of satsuma, 0 DAH,rep 1

source_name: flesh of satsuma, first day after harvest


title: rind of satsuma, 40 DAH,rep 2

description: Gene expression data from rind of satsuma, 40 day after harvest

source_name: rind of satsuma, 40 day after harvest


title: rind of satsuma, 30 DAH,rep 2

description: Gene expression data from rind of satsuma, 30 day after harvest

source_name: rind of satsuma, 30 day after harvest


title: scd6-t0_vs_scd6-t30min+0.7M NaCl_Replicate1

source_name: SetE_scd6 mutant treated with 0.7M NaCl for 30 min

source_name: SetE_scd6 mutant - unstressed t0 min


title: rind of satsuma, 40 DAH,rep 1


title: flesh of ponkan, 40 DAH,rep 2

description: Gene expression data from flesh of ponkan, 40 day after harvest

source_name: flesh of ponkan, 40 day after harvest


title: rind of satsuma, 0 DAH,rep 2

description: Gene expression data from rind of satsuma, firs tday after harvest


title: flesh of ponkan, 50 DAH,rep 1

description: Gene expression data from flesh of ponkan, 50 day after harvest

source_name: flesh of ponkan, 50 day after harvest


title: flesh of ponkan, 40 DAH,rep 1


title: rind of satsuma, 10 DAH,rep 1

description: Gene expression data from rind of satsuma, 10 day after harvest

source_name: rind of satsuma, 10 day after harvest


title: pho85-t0_vs_pho85-t30min+0.7M NaCl_Replicate1

source_name: SetD_pho85 mutant treated with 0.7M NaCl for 30 min

source_name: SetD_pho85 mutant - unstressed t0 min


title: rind of satsuma, 30 DAH,rep 1


title: rind of satsuma, 20 DAH,rep 1

description: Gene expression data from rind of satsuma, 20 day after harvest

source_name: rind of satsuma, 20 day after harvest


title: flesh of ponkan, 30 DAH,rep 1

description: Gene expression data from flesh of ponkan, 30 day after harvest

source_name: flesh of ponkan, 30 day after harvest


title: flesh of ponkan, 30 DAH,rep 2


title: kin2-t0_vs_kin2-t30min+0.7M NaCl_Replicate1

source_name: SetD_kin2 mutant treated with 0.7M NaCl for 30 min

source_name: SetD_kin2 mutant - unstressed t0 min


title: rind of satsuma, 20 DAH,rep 2


title: WT-t0_vs_WT-t30min+0.7M NaCl_Replicate11

source_name: SetD_WT BY4741 treated with 0.7M NaCl for 30 min

source_name: SetD_WT BY4741 - unstressed t0 min


title: yak1-t0_vs_yak1-t30min+0.7M NaCl_Replicate1

source_name: SetC_yak1 mutant treated with 0.7M NaCl for 30 min

source_name: SetC_yak1 mutant - unstressed t0 min


title: rind of satsuma, 10 DAH,rep 2


title: flesh of ponkan, 20 DAH,rep 1

source_name: flesh of ponkan, 20 day after harvest


title: arf3-t0_vs_arf3-t30min+0.7M NaCl_Replicate2

source_name: arf3 mutant treated with 0.7M NaCl for 30 min

source_name: arf3 mutant - unstressed t0 min


title: flesh of ponkan, 10 DAH,rep 1

source_name: flesh of ponkan, 10 day after harvest


title: ckb12-t0_vs_ckb12-t30min+0.7M NaCl_Replicate2

source_name: SetB_ckb1ckb2 mutant treated with 0.7M NaCl for 30 min

source_name: SetB_ckb1ckb2 mutant - unstressed t0 min


title: cka2-t0_vs_cka2-t30min+0.7M NaCl_Replicate2

source_name: SetB_cka2 mutant treated with 0.7M NaCl for 30 min

source_name: SetB_cka2 mutant - unstressed t0 min


title: WT-t0_vs_WT-t30min+0.7M NaCl_Replicate9

source_name: SetB_WT BY4741 treated with 0.7M NaCl for 30 min

source_name: SetB_WT BY4741 - unstressed t0 min


title: cka1-t0_vs_cka1-t30min+0.7M NaCl_Replicate2

source_name: SetB_cka1 mutant treated with 0.7M NaCl for 30 min

source_name: SetB_cka1 mutant - unstressed t0 min


title: flesh of ponkan, 50 DAH,rep 2

source_name: flesh of ponkan, 50 day after harvest


title: nnk1-t0_vs_nnk1-t30min+0.7M NaCl_Replicate1

source_name: SetC_nnk1 mutant treated with 0.7M NaCl for 30 min

source_name: SetC_nnk1 mutant - unstressed t0 min


title: bck1-t0_vs_bck1-t30min+0.7M NaCl_Replicate1

source_name: SetC_bck1 mutant treated with 0.7M NaCl for 30 min

source_name: SetC_bck1 mutant - unstressed t0 min


title: WT-t0_vs_WT-t30min+0.7M NaCl_Replicate10

source_name: SetC_WT BY4741 treated with 0.7M NaCl for 30 min

source_name: SetC_WT BY4741 - unstressed t0 min


title: rind of ponkan,50 DAH,rep 2

description: Gene expression data from rind of ponkan, 50 day after harvest

source_name: rind of ponkan, 50 day after harvest


title: WT-t0_vs_WT-t30min+0.7M NaCl_Replicate8

source_name: SetA_WT BY4741 treated with 0.7M NaCl for 30 min

source_name: SetA_WT BY4741 - unstressed t0 min


title: flesh of ponkan, 0 DAH,rep 2

description: Gene expression data from flesh of ponkan, first day after harvest


title: ckb12-t0_vs_ckb12-t30min+0.7M NaCl_Replicate1

source_name: SetA_ckb1ckb2 mutant treated with 0.7M NaCl for 30 min

source_name: SetA_ckb1ckb2 mutant - unstressed t0 min


title: cka2-t0_vs_cka2-t30min+0.7M NaCl_Replicate1

source_name: SetA_cka2 mutant treated with 0.7M NaCl for 30 min

source_name: SetA_cka2 mutant - unstressed t0 min


title: W303 cdc14-3_90 min at 35C_vs_+0.7M NaCl at 5C_Replicate 2

source_name: W303 cdc14-3 grown at 25C then shifted to 35C for 90 min then + 0.7M NaCl for 30 min at 35C


title: rind of ponkan, 40 DAH,rep 1

description: Gene expression data from rind of ponkan, 40 day after harvest

source_name: rind of ponkan, 40 day after harvest


title: W303 cdc14-3_90 min at 35C_vs_+0.7M NaCl at 5C_Replicate 3

source_name: W303 cdc14-3 grown at 25C then shifted to 35C for 90 min

value: grown at 25C then shifted to 35C for 90 min then + 0.7M NaCl for 30 min at 35C


title: flesh of ponkan, 0 DAH,rep 1

source_name: flesh of ponkan, first day after harvest

value: flesh


title: WT W303_90 min at 35C_vs_+0.7M NaCl at 5C_Replicate 3

value: WT W303

source_name: WT W303 grown at 25C then shifted to 35C for 90 min then + 0.7M NaCl for 30 min at 35C


title: rind of ponkan, 40 DAH,rep 2


title: W303 cdc14-3_90 min at 35C_vs_+0.7M NaCl at 5C_Replicate 1

value: grown at 25C then shifted to 35C for 90 min


title: WT W303_90 min at 35C_vs_+0.7M NaCl at 5C_Replicate 2

source_name: WT W303 grown at 25C then shifted to 35C for 90 min


title: WT W303_90 min at 35C_vs_+0.7M NaCl at 5C_Replicate 1


title: cka1-t0_vs_cka1-t30min+0.7M NaCl_Replicate1

source_name: SetA_cka1 mutant treated with 0.7M NaCl for 30 min

source_name: SetA_cka1 mutant - unstressed t0 min


title: tpk1-t0_vs_tpk1-t30min+0.7M NaCl_Replicate1

source_name: tpk1 mutant treated with 0.7M NaCl for 30 min

source_name: tpk1 mutant - unstressed t0 min


title: sub1-t0_vs_sub1-t30min+0.7M NaCl_Replicate3

source_name: sub1 mutant treated with 0.7M NaCl for 30 min

source_name: sub1 mutant - unstressed t0 min


title: sub1-t0_vs_sub1-t30min+0.7M NaCl_Replicate1


title: pph3-t0_vs_pph3-t30min+0.7M NaCl_Replicate1

source_name: pph3 mutant treated with 0.7M NaCl for 30 min

source_name: pph3 mutant - unstressed t0 min


title: pph3-t0_vs_pph3-t30min+0.7M NaCl_Replicate2


title: ygr122w-t0_vs_ygr122w-t30min+0.7M NaCl_Replicate3

source_name: ygr122w mutant treated with 0.7M NaCl for 30 min

source_name: ygr122w mutant - unstressed t0 min


title: tpk1-t0_vs_tpk1-t30min+0.7M NaCl_Replicate2


title: ygr122w-t0_vs_ygr122w-t30min+0.7M NaCl_Replicate2


title: rind of ponkan, 30 DAH,rep 1

description: Gene expression data from rind of ponkan, 30 day after harvest

source_name: rind of ponkan, 30 day after harvest


title: rind of ponkan, 30 DAH,rep 2


title: rind of ponkan, 50 DAH,rep 1

source_name: rind of ponkan, 50 day after harvest


title: whi2-t0_vs_whi2-t30min+0.7M NaCl_Replicate1

source_name: whi2 mutant treated with 0.7M NaCl for 30 min

source_name: whi2 mutant - unstressed t0 min


title: whi2-t0_vs_whi2-t30min+0.7M NaCl_Replicate2


title: npr2-t0_vs_npr2-t30min+0.7M NaCl_Replicate1

source_name: npr2 mutant treated with 0.7M NaCl for 30 min

source_name: npr2 mutant - unstressed t0 min


title: npr2-t0_vs_npr2-t30min+0.7M NaCl_Replicate2


title: rind of ponkan, 20 DAH,rep 1

description: Gene expression data from rind of ponkan, 20 day after harvest

source_name: rind of ponkan, 20 day after harvest


title: rind of ponkan, 20 DAH,rep 2


title: rind of ponkan, 0 DAH,rep 2

description: Gene expression data from rind of ponkan, first day after harvest

source_name: rind of ponkan, first day after harvest


title: rind of ponkan, 10 DAH,rep 1

description: Gene expression data from rind of ponkan, 10 day after harvest

source_name: rind of ponkan, 10 day after harvest


title: rind of ponkan, 10 DAH,rep 2


title: flesh of orange, 50 DAH,rep 1

description: Gene expression data from flesh of orange, 50 day after harvest

organism: Citrus sinensis

source_name: flesh of orange, 50 day after harvest


title: swc3-t0_vs_swc3-t30min+0.7M NaCl_Replicate1

description: Denoted strain grow in YPD 30C and exposed to 0.7M NaCl for 30 min

source_name: swc3 mutant treated with 0.7M NaCl for 30 min

source_name: swc3 mutant - unstressed t0 min


title: swc5-t0_vs_swc5-t30min+0.7M NaCl_Replicate1

source_name: swc5 mutant treated with 0.7M NaCl for 30 min

source_name: swc5 mutant - unstressed t0 min


title: swc5-t0_vs_swc5-t30min+0.7M NaCl_Replicate2


title: swc3-t0_vs_swc3-t30min+0.7M NaCl_Replicate2


title: flesh of orange, 50 DAH,rep 2


title: rind of ponkan, 0 DAH ,rep 1


title: flesh of orange, 40 DAH,rep 2

description: Gene expression data from flesh of orange, 40 day after harvest

source_name: flesh of orange, 40 day after harvest


title: gpb2-t0_vs_gpb2-t30min+0.7M NaCl_Replicate2

source_name: gpb2 mutant treated with 0.7M NaCl for 30 min

source_name: gpb2 mutant - unstressed t0 min


title: gpb2-t0_vs_gpb2-t30min+0.7M NaCl_Replicate1


title: npr3-t0_vs_npr3-t30min+0.7M NaCl_Replicate1

source_name: npr3 mutant treated with 0.7M NaCl for 30 min

source_name: npr3 mutant - unstressed t0 min


title: flesh of orange, 40 DAH,rep 1


title: rim15-t0_vs_rim15-t30min+0.7M NaCl_Replicate2

source_name: rim15 mutant treated with 0.7M NaCl for 30 min

source_name: rim15 mutant - unstressed t0 min


title: rim15-t0_vs_rim15-t30min+0.7M NaCl_Replicate1


title: npr3-t0_vs_npr3-t30min+0.7M NaCl_Replicate2


title: pde2-t0_vs_pde2-t30min+0.7M NaCl_Replicate3

source_name: pde2 mutant treated with 0.7M NaCl for 30 min

source_name: pde2 mutant - unstressed t0 min


title: pde2-t0_vs_pde2-t30min+0.7M NaCl_Replicate2


title: pde2-t0_vs_pde2-t30min+0.7M NaCl_Replicate1


title: rim101-t0_vs_rim101-t30min+0.7M NaCl_Replicate3

source_name: rim101 mutant treated with 0.7M NaCl for 30 min

source_name: rim101 mutant - unstressed t0 min


title: rim101-t0_vs_rim101-t30min+0.7M NaCl_Replicate2


title: mck1-t0_vs_mck1-t30min+0.7M NaCl_Replicate2

source_name: mck1 mutant treated with 0.7M NaCl for 30 min

source_name: mck1 mutant - unstressed t0 min


title: mck1-t0_vs_mck1-t30min+0.7M NaCl_Replicate3


title: rim101-t0_vs_rim101-t30min+0.7M NaCl_Replicate1


title: msn2-t0_vs_msn2-t30min+0.7M NaCl_Replicate1

source_name: msn2 mutant treated with 0.7M NaCl for 30 min

source_name: msn2 mutant - unstressed t0 min


title: msn2-t0_vs_msn2-t30min+0.7M NaCl_Replicate2


title: msn2-t0_vs_msn2-t30min+0.7M NaCl_Replicate3


title: mck1-t0_vs_mck1-t30min+0.7M NaCl_Replicate1


title: hog1-t0_vs_hog1-t30min+0.7M NaCl_Replicate2

source_name: hog1 mutant treated with 0.7M NaCl for 30 min

source_name: hog1 mutant - unstressed t0 min


title: flesh of orange, 30 DAH,rep 1

description: Gene expression data from flesh of orange, 30 day after harvest

source_name: flesh of orange, 30 day after harvest


title: flesh of orange, 20 DAH,rep 1

description: Gene expression data from flesh of orange, 20 day after harvest

source_name: flesh of orange, 20 day after harvest


title: WT-t0_vs_WT-t30min+0.7M NaCl_Replicate5

source_name: WT BY4741 treated with 0.7M NaCl for 30 min

source_name: WT BY4741 - unstressed t0 min


title: WT-t0_vs_WT-t30min+0.7M NaCl_Replicate4


title: hog1-t0_vs_hog1-t30min+0.7M NaCl_Replicate1


title: flesh of orange, 10 DAH,rep 2

description: Gene expression data from flesh of orange, 10 day after harvest

source_name: flesh of orange, 10 day after harvest


title: flesh of orange, 0 DAH,rep 2

description: Gene expression data from flesh of orange, first day after harvest


title: WT-t0_vs_WT-t30min+0.7M NaCl_Replicate2


title: flesh of orange, 20 DAH,rep 2


title: hog1-t0_vs_hog1-t30min+0.7M NaCl_Replicate3


title: flesh of orange, 10 DAH,rep 1


title: WT-t0_vs_WT-t30min+0.7M NaCl_Replicate1


title: rind of orange, 50 DAH,rep 1

description: Gene expression data from rind of orange, 50 day after harvest

source_name: rind of orange, 50 day after harvest


title: flesh of orange, 30 DAH,rep 2


title: rind of orange,50 DAH,rep 2


title: WT-t0_vs_WT-t30min+0.7M NaCl_Replicate3


title: rind of orange, 40 DAH,rep 1

description: Gene expression data from rind of orange, 40 day after harvest

source_name: rind of orange, 40 day after harvest


title: rind of orange, 20 DAH,rep 2

description: Gene expression data from rind of orange, 20 day after harvest

source_name: rind of orange, 20 day after harvest


title: rind of orange, 30 DAH,rep 2

description: Gene expression data from rind of orange, 30 day after harvest

source_name: rind of orange, 30 day after harvest


title: ExVivo_TCD4+_HTLV1positive_6

city: Lyon

first: Céline

last: Vernin

address: 46 allée d'Italie

country: France

institute: ENS

description: monoclonal T-Cell clone

hyb_protocol: Dry sample with vacuum concentrator, approximately 1 hour, at 45°C to 55°C. The dried sample was resuspended in 17 µL of nuclease-free water and 28 µL of hybridization mix.The sample was incubated at 100°C for 5 minutes and immediately transfered to an ice water bath for 5 minutes.The samples were hybridized 20 hours, at 55°C, to 20 rpm.  After hybridization, microarrays were washed 5 minute at room temperature with Wash Buffer 1 (Agilent) and 5 minute at 37°C with Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Then data were normalized using labelling spike in GeneSpring 7.3 software.

source_name: ExVivo_TCD4+_HTLV1positive clone were obtained by limiting dilution culture of PBMC of HTLV-1 carriers

label_protocol: Cyanine-3 (Cy3) labeled miRNA was prepared from 100 ng RNA  according to the manufacturer's instructions (Agilent).

extract_protocol: RNA was extracted using Trizol/Glycogen reagent. RNA was quantified using a NanoDrop spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer.

tag: infection


title: flesh of orange, 0 DAH,rep 1

source_name: flesh of orange, first day after harvest


title: rind of orange, 30 DAH,rep 1


title: rind of orange, 10 DAH,rep 1

description: Gene expression data from rind of orange, 10 day after harvest

source_name: rind of orange, 10 day after harvest


title: rind of orange, 20 DAH,rep 1


title: rind of orange, 40 DAH,rep 2


title: ExVivo_TCD4+_HTLV1positive_5

description: monoclonal T-Cell clone


title: ExVivo_TCD4+_HTLV1positive_4

description: monoclonal T-Cell clone


title: ExVivo_TCD4+_HTLV1positive_1

description: monoclonal T-Cell clone


title: ExVivo_TCD4+_HTLV1positive_2

description: monoclonal T-Cell clone


title: rind of orange, 0 DAH,rep 2

description: Gene expression data from rind of orange, first day after harvest

source_name: rind of orange, first day after harvest


title: ExVivo_TCD8+_HTLV1negative_4

description: monoclonal T-Cell clone

source_name: ExVivo_TCD8+_HTLV1negative clone were obtained by limiting dilution culture of PBMC of HTLV-1 carriers


title: ExVivo_TCD8+_HTLV1negative_6

description: monoclonal T-Cell clone


title: ExVivo_TCD8+_HTLV1negative_5

description: monoclonal T-Cell clone


title: ExVivo_TCD8+_HTLV1negative_3

description: monoclonal T-Cell clone


title: ExVivo_TCD8+_HTLV1negative_2

description: monoclonal T-Cell clone


title: ExVivo_TCD8+_HTLV1positive_6

description: monoclonal T-Cell clone

source_name: ExVivo_TCD8+_HTLV1positive clone were obtained by limiting dilution culture of PBMC of HTLV-1 carriers


title: ExVivo_TCD8+_HTLV1positive_5

description: monoclonal T-Cell clone


title: ExVivo_TCD8+_HTLV1positive_4

description: monoclonal T-Cell clone


title: rind of orange, 10 DAH,rep 2


title: ExVivo_TCD4+_HTLV1positive_3

description: monoclonal T-Cell clone


title: ExVivo_TCD8+_HTLV1positive_3

description: monoclonal T-Cell clone


title: ExVivo_TCD8+_HTLV1positive_2

description: monoclonal T-Cell clone


title: ExVivo_TCD4+_HTLV1negative_2

description: monoclonal T-Cell clone

source_name: ExVivo_TCD4+_HTLV1negative clone were obtained by limiting dilution culture of PBMC of HTLV-1 carriers


title: ExVivo_TCD4+_HTLV1negative_3

description: monoclonal T-Cell clone


title: ExVivo_TCD4+_HTLV1negative_5

description: monoclonal T-Cell clone


title: ExVivo_TCD4+_HTLV1negative_4

description: monoclonal T-Cell clone


title: ExVivo_TCD4+_HTLV1negative_6

description: monoclonal T-Cell clone


title: ExVivo_TCD4+_HTLV1negative_1

description: monoclonal T-Cell clone


title: ExVivo_TCD8+_HTLV1negative_1

description: monoclonal T-Cell clone


title: rind of orange, 0 DAH,rep 1


title: TiO2_Final_01

first: Yvette

last: Piceno

address: 1 Cyclotron Rd., MS 70A-3317

department: Ecology

institute: LBNL

hyb_protocol: Arrays were hybridized overnight at 48degC and 60 rpm and then washed and stained using standard Affymetrix buffers/reagents.

scan_protocol: Images were captured on an Affymetrix GeneChip Scanner 3000 7G.

data_processing:
CEL files were converted to CELa files and then processed using proprietary software (PhyCA).
For the binary data, a value of one indicates a positive call for an OTU in a sample and a zero value indicates a negative call using the criteria stated in Section 6.   For the intensity data, the values on the first tab of the Excel file for each sample are trimmed mean (mean without the highest and lowest values) of the probe intensities for the perfectly-matched probes used to define each OTU. These values were scaled to an internal spike mix to account for array-to-array differences in intensity.  On the second tab, species binary calls (referred to as 'taxa' in the manuscript because many species or higher taxonomic classifications were 'unclassified') are presented.

organism: mixed sample

source_name: Activated sludge enrichment

label_protocol: TDT enzyme (Promega; Madison, WI) and GeneChip Labeling Reagent (Affymetrix; Santa Clara, CA) were used to label fragmented amplicons.

extract_protocol: DNA was extracted using the MoBio PowerSoil DNA Isolation Kit

tag: replicate

value: Sodium acetate

tag: c


title: Post-Starvation_03

value: PHB-enriched community, post-starvation

value: Not Determined

value: N:Not Determined


title: TiO2_Final_02


title: TiO2_Final_03


title: 5A_t20min+0.7N NaCl rep2

type: genomic

description: ChIP-chip of Rpb3 in 5A t20 sample

scan_protocol: Axon GenePix Scanner

data_processing:
ChIP-chip immunoprecipitated data was mean-scaled against its respective 'input' sample data, and then the ratio of scaled immunoprecipitation to the input was log2-transformed
scaled, log2 (ChIP/Input) ratio

source_name: Input DNA from 5A strain after 20min 0.7N NaCl treatment

label_protocol: Input and IP DNA were labeld with Cy5-dUTP and Cy3-dUTP, respectively via LM-PCR.

growth_protocol: Strains were grown to OD of 0.6~0.8 in YPD, then treated with 0.7N NaCl for 20mins

extract_protocol: Cells were grown overnight at 30°C then subcultured to 100 ml.  At an OD600 of 0.6~0.8, 50ml of culture were collected and crosslinked with 1% formaldehyde for 20 min.  The rest 50ml culture was treated with 0.7 M NaCl for 20 min then crosslinked as above.  The reaction was quenched with 2.75 ml of 2.5 M glycine. Cells were pelletted at 3000 rpm for 2 min and washed twice with 20 ml of cold TBS (200 mM Tris-HCl pH 7.5, 150 mM NaCl).  Pellets were then resuspended in 1 ml of TBS and transferred to 1.5 ml Eppendorf tubes and pelletted with 1 min spin at 13K rpm at room temperature.  All residual liquid was manually removed and cell pellets were snap frozen in liquid nitrogen and stored at -80°C.  The cell pellets were thawed on ice and resuspended in 700 μL of lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-Deoxycholate, 10 μg/ml aprotinin, 1 μg/ml leupeptin, 0.1 M PMSF, 0.1 M benzamidine, 1 μg/ml pepstatin).   300 μl volume of 425-600μm glass beads was added to each sample and vortexed at 4°C for 35 min. The samples were allowed to sit for 10 min, and then another round of vortexing was performed for 35 min. The tubes were pierced with a 22G 1½” needle and the tubes were placed in 1.5 ml Eppendorf tubes.  Centrifugation was performed at 7000 rpm for 1 min to transfer the pellet and whole cell extract, and the pellet and cell debris were resuspended.  Samples were sonicated (Misonix 4000, microplat horn) for 10 sec for 16 min with 10 sec rest in between then centrifuged at max speed (13-14K rpm) at 4°C for 5 min.  Supernatants were transferred to fresh 1.5 ml tubes and pellets were discarded.  500 μl of the whole cell extract (WCE) was transferred to a new 1.5 ml tube and 3 μl RPB3 antibody (Neoclone, Madison, WI) was added and rotated at 4°C overnight. The immunoprecipitation was performed for 1 hour with 50 μl of a 50/50 slurry of streptavidin protein G Dynabeads (Life Technologies, Carlsbad, CA) in lysis buffer.  The beads were then pelletted on magnetic rack.  The supernatant was manually removed and a series of washes were performed: 2 washes with 1 ml lysis buffer, 2 washes with 1 ml lysis buffer with 500 mM NaCl, 2 washes with 1 ml wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% NP40, 1% Na-Deoxycholate, 1 mM EDTA), and one wash with 1 ml TE (10 mM Tris-HCl pH 8, 1 mM EDTA).  Elution was performed using 95 μl elution buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, 0.5% SDS, 5 mM CaCl2) at 65°C for 30 min, resuspended briefly every 10 min.  Beads were pelletted on a magnetic rack, and the supernatant was transferred to a new 1.5ml tube.  85 μl elution buffer was added to 10 μl of WCE as input samples.  Crosslinks were reversed overnight by adding 5μL 2 mg/ml proteinase K (50 mM Tris-HCl pH 8, 10 mM CaCl2) and incubating at 65°C for 16-20 hours.  Samples were purified using the Qiangen PCR Purification Kit (QIAGEN Inc., Valencia, California, United States; Cat. No. 28106).

tag: antibody

value: Cells were treated with 0.7N NACl

source_name: Rpb3 ChIP DNA from 5A strain after 20min 0.7N NaCl treatment


title: 5A_t20min+0.7N NaCl rep1

description: ChIP-chip of Rpb3 in 5A t20 sample


title: 5A_t0 rep2

description: ChIP-chip of Rpb3 in 5A t0 sample

source_name: Input DNA from 5A strain before stress

growth_protocol: Strains were grown to OD of 0.6~0.8 in YPD

source_name: Rpb3 ChIP DNA from 5A strain before stress


title: 5A_t0 rep1

description: ChIP-chip of Rpb3 in 5A t0 sample


title: Post-Starvation_02


title: ExVivo_TCD8+_HTLV1positive_1

description: monoclonal T-Cell clone


title: Initial_03

source_name: Activated sludge

value: Activated sludge


title: Post-Starvation_01


title: CTD14_t0 rep2

description: ChIP-chip of Rpb3 in CTD14 t0 sample

source_name: Input DNA from CTD14 strain before stress

source_name: Rpb3 ChIP DNA from CTD14 strain before stress


title: CTD14_t20min+0.7N NaCl rep1

description: ChIP-chip of Rpb3 in CTD14 t20 sample

source_name: Input DNA from CTD14 strain after 20min 0.7N NaCl treatment

source_name: Rpb3 ChIP DNA from CTD14 strain after 20min 0.7N NaCl treatment


title: CTD14_t20min+0.7N NaCl rep2

description: ChIP-chip of Rpb3 in CTD14 t20 sample


title: CTD14_t0 rep1

description: ChIP-chip of Rpb3 in CTD14 t0 sample


title: Initial_02


title: AgNPs_Final_02


title: LNCaP shRB+IR(10Gy) 1

city: PHILADELPHIA

first: Adam

last: Ertel

state: PA

address: 233 S 10TH ST

department: Cancer Biology

institute: Thomas Jefferson University

description: gene expression profile of RB-knockdown LNCaP cells following IR exposure

hyb_protocol: Affymetrix GeneChip Human Gene 2.0 ST arrays (Affymetrix, Santa Clara, CA), were hybridized with fragmented and biotin-labeled target (2.5 ug) in 110 ul of hybridization cocktail. Target denaturation was performed at 99°C for 2 min. and then 45°C for 5 min, followed by hybridization for 18 h.

scan_protocol: Chips were scanned on an Affymetrix Gene Chip Scanner 3000, using Command Console Software.

data_processing: Background correction and normalization were done using Iterative Plier 16 with GeneSpring V12.0 software (Agilent, Palo Alto, CA, USA). 2-fold (p-value<0.05) differentially expressed gene list was generated. The differentially expressed gene list was loaded into Ingenuity Pathway Analysis (IPA) 8.0 software (http://www.ingenuity.com) to perform biological network and functional analyses.

source_name: Prostate cancer cell line

label_protocol: 2.5 ug ST-cDNAs were fragmented and chemically labeled with biotin to generate biotinylated ST-cDNA using FL-Ovation cDNA biotin module V2 (NuGen Technologies, Inc.).

growth_protocol: Cells were grown under 5% FBS and

extract_protocol: After 24 hours post IR, RNA was isolated by Trizol method

treatment_protocol: Cells were treated with RB shRNA (shRB), to achieve RB knockdown, and control scrambled shRNA (shControl) retro virus under puromysin selection. The shControl and shRB cells were exposed to 10 Gy Radiation and Microparray was performed after 24 hours post radiation.

value: LNCaP

tag: shRNA

value: shRB

tag: ir exposure

value: +IR 10gy


title: LNCaP shRB+IR(10Gy) 2


title: Control_Final_03

value: Control


title: AgNPs_Final_03


title: Initial_01


title: Control_Final_02


title: Control_Final_01


title: AgNPs_Final_01


title: AgNO3_Final_03


title: LNCaP shControl +IR 10gy 2

description: gene expression profile of RB-proficient LNCaP cells following IR exposure

value: shControl


title: LNCaP shControl +IR 10gy 1


title: AgNO3_Final_01


title: LNCaP shRB+IR(10Gy) 3


title: HCC2279_miRNA

city: Houston

first: Amin

middle: A

last: mOMIN

state: TX

address: 6767 Bertner Ave

department: Clinical cancer prevention

institute: MD anderson cancer center

data_processing:
Analysis was performed on Viia™7 software (V1.0)  (Applied Biosystems)
The miR that are below the limit of detection as labeled as null in files before and after normalization.

label: SYBR Green

source_name: Lung cancer cell line

label_protocol: 13 ul of each sample was used for reverse transcription with the miRCURY LNA Universal RT microRNA PCR kit (Exiqon).  Reverse transcription reaction products were combined with SYBR Green master mix (Exiqon), and loaded into Human panel I and II as directed.

growth_protocol: All cell lines were grown in 10% FBS + RPMI 1640 at 37 C at 5% CO2

extract_protocol: RNA was isolated using the miRNeasy RNA isolation kit (Qiagen)

value: Lung cancer cell line HCC2279

tag: histology

value: adenocarcinoma

value: female

tag: tumor origin

value: unknown

tag: emt state

value: Hybrid


title: HCC827_miRNA

value: Lung cancer cell line HCC827

tag: Sex

value: primary


title: HCC4011_miRNA

value: Lung cancer cell line HCC4011

value: male


title: HCC2935_miRNA

value: Lung cancer cell line HCC2935

value: Epithelial


title: PC-9_miRNA

value: Lung cancer cell line PC-9


title: HCC4019_miRNA

value: Lung cancer cell line HCC4019


title: HCC4017_miRNA

value: Lung cancer cell line HCC4017


title: H969_miRNA

value: Lung cancer cell line H969

value: metastatic


title: CTD5A-t0_vs_CTD5A-t30min+0.7M NaCl Rep2

description: CTD5A grow in YPD 30C and exposed to 0.7M NaCl for 30 min

data_processing: Background-subtracted signal intentisties for all probes were normalized by quantile normalization, removing probes with missing signal, media signal within ORFs was compared for each channel, and log2(red/green) values were median-centered such that the average of all values = 0. Values in the matrix represent log2 fold-change in t30min vs t0min (unstressed) sample for each denoted strain; Data have been converted so that positive log2 values correspond to gene induction (i.e. higher transcript abundance in T30 sample) and negative log2 values represent gene repression (i.e. higher transcript abundance in unstressed T0 sample).

source_name: CTD5A treated with 0.7M NaCl for 30 min

label_protocol: Amino-allyl-dUTP incorporated into generated cDNA;  post-synthesis coupling to cyanine dyes

growth_protocol: S. cerevisiae strains grown in rich YPD mediumin batch-culture with shaking at 30C

value: 0.7M NaCl for 30 min

source_name: CTD5A - unstressed t0 min

value: unstressed t0 min


title: CTD5A-t0_vs_CTD5A-t30min+0.7M NaCl Rep3


title: AgNO3_Final_02

value: Sodium acetate


title: H838_miRNA

value: Lung cancer cell line H838

value: adenocarcinoma

value: Mesenchymal


title: HCC4006_miRNA

value: Lung cancer cell line HCC4006

value: Hybrid


title: H820_miRNA

value: Lung cancer cell line H820


title: CTD2A-t0_vs_CTD2A-t30min+0.7M NaCl Rep3

description: CTD2A grow in YPD 30C and exposed to 0.7M NaCl for 30 min

source_name: CTD2A treated with 0.7M NaCl for 30 min

source_name: CTD2A - unstressed t0 min


title: H647_miRNA

value: Lung cancer cell line H647

value: male


title: CTD5A-t0_vs_CTD5A-t30min+0.7M NaCl Rep1


title: H522_miRNA

value: Lung cancer cell line H522

value: primary


title: H3255_miRNA

value: Lung cancer cell line H3255

value: female

value: unknown

value: Epithelial


title: CTD2A-t0_vs_CTD2A-t30min+0.7M NaCl Rep2

value: 0.7M NaCl for 30 min


title: CTD2A-t0_vs_CTD2A-t30min+0.7M NaCl Rep1

value: unstressed t0 min


title: H2405_miRNA

value: Lung cancer cell line H2405

value: metastatic


title: H650_miRNA

value: Lung cancer cell line H650

value: adenocarcinoma


title: H23_miRNA

value: Lung cancer cell line H23

value: Mesenchymal


title: CTD14-t0_vs_CTD14-t30min+0.7M NaCl Rep2

description: CTD14 grow in YPD 30C and exposed to 0.7M NaCl for 30 min

source_name: CTD14 treated with 0.7M NaCl for 30 min

source_name: CTD14 - unstressed t0 min


title: CTD14-t0_vs_CTD14-t30min+0.7M NaCl Rep3


title: CTD14-t0_vs_CTD14-t30min+0.7M NaCl Rep1


title: W303_cdc14-3_snf1_2hr at 35C_vs_+0.7M NaCl at 35C_Replicate3

description: W303_cdc14-3_snf1grown at 25C then shifted to 35C for 2hr then + 0.7M NaCl for 30 min at 35C

data_processing: Background-subtracted signal intentisties for all probes were normalized by quantile normalization, removing probes with missing signal, media signal within ORFs was compared for each channel, and log2(red/green) values were median-centered such that the average of all values = 0.

source_name: W303_cdc14-3_snf1 grown at 25C then shifted to 35C for 2hr, then treated with 0.7N NaCl for 30min-t30

label_protocol: Amino-allyl-dUTP incorporated into generated cDNA;  post-synthesis coupling to Oyster dyes

growth_protocol: S. cerevisiae strains grown in rich YPD medium at 25C in batch-culture with shaking, then heat shock to 35C with indicated time in ch1:source name.

tag: genotype/variation

source_name: W303_cdc14-3_snf1 grown at 25C then shifted to 35C for 2hr-unstressed t0 min


title: H2122_miRNA

tag: cell line

value: Lung cancer cell line H2122

value: Hybrid


title: EDT(early during treatment) BRAFi sample 1 Treated with dabrafenib

city: Westmead

first: Gulietta

last: Pupo

state: NSW

address: Darcy Road

country: Australia

institute: University of Sydney

data_processing: The data were normalised using with cubic spline using the Illumina GenomeStudio v2011.1

source_name: Melanoma tumour

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

value: BRAF V600K

tag: tissue

value: Melanoma- subcutaneous


title: W303_cdc14-3_snf1_2hr at 35C_vs_+0.7M NaCl at 35C_Replicate2


title: W303_cdc14-3_snf1_90 min at 35C_vs_+0.7M NaCl at 35C_Replicate1

description: W303_cdc14-3_snf1grown at 25C then shifted to 35C for 90 min then + 0.7M NaCl for 30 min at 35C

source_name: W303_cdc14-3_snf1 grown at 25C then shifted to 35C for 90 min, then treated with 0.7N NaCl for 30min-t30

source_name: W303_cdc14-3_snf1 grown at 25C then shifted to 35C for90minr-unstressed t0 min


title: Patient 10 Prog Treated with dabrafenib + trametinib

value: Melanoma- omentum


title: Patient 10 Pre Untreated

description: Patient 10 Pre untreated


title: Patient 9 Pre Untreated

description: Patient 9 Pre untreated

value: BRAF V600E


title: Patient 9 Prog Treated with dabrafenib + trametinib


title: H2228_miRNA

value: Lung cancer cell line H2228

tag: age

value: female

value: primary


title: Patient 7 Prog Treated with dabrafenib + trametinib (replicate)

value: Melanoma- peritoneal


title: H2009_miRNA

value: Lung cancer cell line H2009


title: H2030_miRNA

value: Lung cancer cell line H2030

value: male


title: EDT (early during treatment) BRAFi sample 2 Treated with dabrafenib


title: H1993_miRNA

value: Lung cancer cell line H1993

value: metastatic


title: Patient 10 Pre Untreated (replicate)

description: Patient 10 Pre untreated (replicate)


title: H1944_miRNA

value: Lung cancer cell line H1944

value: adenocarcinoma


title: H1975_miRNA

value: Lung cancer cell line H1975


title: W303_cdc14-3_2hr at 35C_vs_+0.7M NaCl at 35C_Replicate3

description: W303_cdc14-3grown at 25C then shifted to 35C for 2hr then + 0.7M NaCl for 30 min at 35C

source_name: W303_cdc14-3 grown at 25C then shifted to 35C for 2hr, then treated with 0.7N NaCl for 30min-t30

source_name: W303_cdc14-3 grown at 25C then shifted to 35C for 2hr-unstressed t0 min


title: H1693_miRNA

value: Lung cancer cell line H1693

value: Hybrid


title: W303_snf1_2hr at 35C_vs_+0.7M NaCl at 35C_Replicate2

description: W303_snf1grown at 25C then shifted to 35C for 2hr then + 0.7M NaCl for 30 min at 35C

source_name: W303_snf1 grown at 25C then shifted to 35C for 2hr, then treated with 0.7N NaCl for 30min-t30

source_name: W303_snf1 grown at 25C then shifted to 35C for 2hr-unstressed t0 min


title: H1650_miRNA

value: Lung cancer cell line H1650


title: H1792_miRNA

value: Lung cancer cell line H1792


title: W303_snf1_90 min at 35C_vs_+0.7M NaCl at 35C_Replicate1

description: W303_snf1grown at 25C then shifted to 35C for 90 min then + 0.7M NaCl for 30 min at 35C

source_name: W303_snf1 grown at 25C then shifted to 35C for 90 min, then treated with 0.7N NaCl for 30min-t30

source_name: W303_snf1 grown at 25C then shifted to 35C for 90min-unstressed t0 min


title: H1573_miRNA

source_name: Lung cancer cell line

value: Lung cancer cell line H1573

value: Epithelial


title: W303_cdc14-3_2hr at 35C_vs_+0.7M NaCl at 35C_Replicate2


title: Patient 7 Prog Treated with dabrafenib + trametinib

value: BRAF V600E


title: ExVivo_TCD4+_HTLV1negative_5

city: lyon

first: franck

last: mortreux

address: 46 allee d'Italie

institute: oncovirology and Biotherapies, UMR5239, LBMC

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: The Arrays were scanned using the Gene Chip Scanner 3000. Then CEL files were generated using the Affymetrix GeneChip Command Console software (AGCC) 3.0

data_processing:
Raw data were normalized using Partek Genomic Suite v.6.5 (Partek Incorporated, St. Louis, Missouri 63005) summarising probeset values to genes by median method: The normalization was performed using quantile method including RMA background correction and probe sequence adjustment.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: ExVivo_TCD4+_HTLV1negative clone obtained by limiting dilution culture of PBMC of HTLV-1 carriers

label_protocol: As per manufacturer (Affymetrix)

value: monoclonal T-Cell clone

tag: cell type


title: W303_snf1_2hr at 35C_vs_+0.7M NaCl at 35C_Replicate3


title: H1568_miRNA

value: Lung cancer cell line H1568

value: female


title: Patient 6 Pre Untreated

description: Patient 6 Pre untreated

value: BRAF V600K

value: Melanoma- subcutaneous


title: Patient 5 Pre Untreated

description: Patient 5 Pre untreated


title: Patient 5 Prog Treated with dabrafenib + trametinib


title: Patient 6 Prog Treated with dabrafenib + trametinib


title: Patient 7 Pre Untreated

description: Patient 7 Pre untreated

value: Melanoma- lymph node


title: H1395_miRNA

value: Lung cancer cell line H1395

value: primary


title: H1385_miRNA

value: Lung cancer cell line H1385

value: adenocarcinoma

value: metastatic


title: NSCLC_cell line_genomic DNA_HCC827

city: Freiburg

first: Gabriele

last: Greve

address: Hugstetter Str 55

department: Department of Internal Medicine 1

institute: University of Freiburg Medical Center

hyb_protocol: according to manufacturer (Affymetrix)

scan_protocol: according to manufacturer (Affymetrix)

data_processing: Data was analyzed with the Genotyping Console Software (Affymetrix) based on the reference genome hg19.

source_name: NSCLC cell line HCC827

label_protocol: according to manufacturer (Affymetrix)

growth_protocol: Cells were cultured in RPMI 1640 supplemented with 1% penicillin/streptamycin and 10% fetal calf serum.

extract_protocol: Genomic DNA was extracted from fresh frozen cell pellets obtained from NSCLC cell line cells using the Qiagen DNA Blood and Tissue Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer.

treatment_protocol: Cells were untreated prior to DNA extraction.

value: Non-Small-Cell Lung Cancer (NSCLC)

value: adenocarcinoma of the lung


title: H1437_miRNA

value: Lung cancer cell line H1437

value: male


title: H1373_miRNA

value: Lung cancer cell line H1373

value: unknown

value: Hybrid


title: DFCI024_miRNA

value: Lung cancer cell line DFC1024

value: Mesenchymal


title: DFCI032_miRNA

value: Lung cancer cell line DFC1032

value: female


title: H1355_miRNA

value: Lung cancer cell line H1355


title: ExVivo_TCD4+_HTLV1positive_3

source_name: ExVivo_TCD4+_HTLV1positive clone obtained by limiting dilution culture of PBMC of HTLV-1 carriers

value: monoclonal T-Cell clone


title: ExVivo_TCD4+_HTLV1negative_6


title: NSCLC_cell line_genomic DNA_A549

source_name: NSCLC cell line A549


title: NSCLC_cell line_genomic DNA_H460

source_name: NSCLC cell line NCI-H460

value: large cell carcinoma of the lung


title: ExVivo_TCD4+_HTLV1positive_2


title: Patient 3 Prog Treated with dabrafenib + trametinib

value: BRAF V600E

value: Melanoma- bowel


title: Patient 1 Pre (replicate)

description: Patient 1 Pre (replicate)

value: Melanoma- subcutaneous


title: ExVivo_TCD4+_HTLV1positive_5


title: ExVivo_TCD4+_HTLV1negative_2


title: Patient 3 Pre Untreated

description: Patient 3 Pre untreated


title: ExVivo_TCD4+_HTLV1positive_6


title: ExVivo_TCD4+_HTLV1positive_4


title: Patient 2 Prog2 Treated with dabrafenib + trametinib

value: BRAF V600K


title: Patient 1 Prog Treated with dabrafenib + trametinib


title: Patient 1 EDT (early during treatment treated) with dabrafenib + trametinib


title: Patient 2 Prog1 Treated with dabrafenib + trametinib


title: Patient 3 Pre (replicate)

description: Patient 3 Pre (replicate)


title: ExVivo_TCD4+_HTLV1negative_3


title: Patient 1 Pre Untreated

description: Patient 1 Pre untreated


title: Patient 2 Pre Untreated

description: Patient 2 Pre untreated

value: Melanoma- lymph node


title: Subject 11 - 24h post-meal

status: Public on Dec 02 2014

city: Leiden

first: Bruno

last: Guigas

address: P.O.Box 9600, Postzone L40-Q

department: Parasitology

country: Netherlands

institute: Leiden University Medical Center

scan_protocol: Standard Illumina scanning protocol using Illumina’s Genomestudio v.2011.1

data_processing: The data were normalised using quantile normalisation with the lumi package version 2.4.0 in R

source_name: Human skeletal muscle

label_protocol: Biotinylated cRNA were prepared using the Illumina TotalPrep-96 RNA Amplification kit

extract_protocol: Total RNA was isolated from skeletal muscle biopsies (~25-30 mg) using the phenol-chloroform extraction method (Tripure RNA Isolation reagent, Roche, Germany), treated with the TurboDNAse kit according to manufacturer protocol (TurboDNAse, Life Technologies, The Netherlands) and quantified by NanoDrop (ND1000, Thermo Scientific, The Netherlands). The quality and integrity of RNA was tested using 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany) and all the samples had a RIN score >8.

value: Skeletal muscle (musculus vastus lateralis)

tag: gender

value: Male

tag: post-meal time

tag: individual

value: Subject 11


title: Subject 12 - 10h post-meal

value: Subject 12


title: Subject 12 - 4h post-meal


title: Subject 12 - 1,5h post-meal


title: Subject 10 - 10h post-meal

value: Subject 10


title: Subject 11 - 4h post-meal


title: Subject 11 - 10h post-meal


title: Subject 10 - 24h post-meal


title: ExVivo_TCD4+_HTLV1negative_1

tag: infection


title: Patient 4 Pre Untreated

description: Patient 4 Pre untreated


title: Subject 9 - 24h post-meal

value: Subject 9


title: Subject 12 - 24h post-meal


title: Patient 4 Prog Treated with dabrafenib + trametinib


title: Subject 11 - 1,5h post-meal


title: ExVivo_TCD4+_HTLV1positive_1


title: Subject 9 - 1,5h post-meal


title: Subject 10 - 4h post-meal


title: ExVivo_TCD4+_HTLV1negative_4


title: Subject 9 - 10h post-meal


title: Subject 8 - 4h post-meal

value: Subject 8


title: Subject 10 - 1,5h post-meal


title: Subject 8 - 24h post-meal


title: Subject 8 - 1,5h post-meal


title: Subject 9 - 4h post-meal


title: Subject 8 - 10h post-meal


title: Subject 7 - 10h post-meal

value: Subject 7


title: Subject 7 - 24h post-meal


title: Subject 6 - 10h post-meal

value: Subject 6


title: Subject 6 - 4h post-meal


title: Subject 7 - 1,5h post-meal


title: Subject 5 - 24h post-meal

value: Subject 5


title: Subject 5 - 1,5h post-meal


title: Subject 4 - 24h post-meal

value: Subject 4


title: Subject 4 - 4h post-meal


title: Subject 6 - 24h post-meal


title: Subject 3 - 10h post-meal

value: Subject 3


title: Subject 4 - 1,5h post-meal


title: Subject 5 - 10h post-meal


title: Subject 3 - 4h post-meal


title: Subject 2 - 24h post-meal

value: Subject 2


title: Subject 2 - 1,5h post-meal


title: Subject 5 - 4h post-meal


title: Subject 4 - 10h post-meal


title: Subject 1 - 4h post-meal

value: Subject 1


title: Subject 3 - 24h post-meal


title: Subject 1 - 1,5h post-meal


title: Subject 2 - 10h post-meal


title: Subject 1 - 24h post-meal


title: Subject 3 - 1,5h post-meal


title: HR+ 3 day pregnant 2

city: Singapore

first: Alexandra

last: Pietersen

address: 11 Hospital Drive

country: Singapore

institute: National Cancer Centre Singapore

description: SAMPLE 5

hyb_protocol: 1.5 μg of biotinylated cRNA from each sample was hybridized at 58°C overnight using the Illumina Whole-Genome Gene Expression Direct Hybridization Assay system with the Illumina Mouse WG-6 v2.0 (six-sample BeadChip) platfor.

scan_protocol: The signal was developed using streptavidin-Cy3 and the BeadChips were scanned with an Illumina BeadArray Reader

data_processing: Raw signals were logarithmically transformed (to base 2) and quantile normalized.

source_name: Luminal HR+ mammary epithelial cells, 3-day pregnant 2

label_protocol: The amplified RNA was labelled with Biotin using the TargetAmp™ 2-Round Biotin-aRNA Amplification Kit 3.0 (epicentre #TAB2R710) as per the manufacturers protocol.

growth_protocol: Mammary glands were obtained from 9-11 week old female FVB mice.

extract_protocol: Mammary epithelial cells were processed to single cells and after exclusion of dead cells, CD45+ lymphocytes and stromal cells according to DOI 10.1186/bcr3593. Luminal cells were identified based on expression of CD24-FITC and CD49f-PEcy5, and  HR+ cells based on Sca1-PECy7 and CD49b-PE. One thousand HR+ cells from each animal were sorted into lysis buffer (20 IU RNase inhibitor (Invitrogen), 2mM DTT, 0.15% Tween-20 (Biorad) in 8µL of nuclease-free water) in PCR tubes, resulting in an end volume of approximately 12µL.  RNA  from 2µL of lysed cells (equivalent to 167 cells) was amplified using the TargetAmp™ 2-Round Biotin-aRNA Amplification Kit 3.0 (epicentre #TAB2R710) as per the manufacturers protocol. The concentration cRNA was determined by using a NanoDrop spectrophotometer (Thermo Scientific-NanoDrop  2000).

treatment_protocol: Virgin mice were in metestrus (determined by vaginal smear), 3-day and 7-day pregnant mice were determined by timed-matings, plug identification and at day 7 visual confirmation of embryos in the uterus. All animals received an i.p. injection with EdU (2mg/g) 24 hours before harvest.

tag: strain

value: FVB

tag: reproductive state

value: 3 day pregnant


title: HR+ 7 day pregnant 3

description: SAMPLE 9

source_name: Luminal HR+ mammary epithelial cells,7-day pregnant 3

value: 7 day pregnant


title: HR+ 7 day pregnant 2

description: SAMPLE 8

source_name: Luminal HR+ mammary epithelial cells,7-day pregnant 2


title: Subject 6 - 1,5h post-meal

value: Skeletal muscle (musculus vastus lateralis)


title: HR+ 7 day pregnant 1

description: SAMPLE 7

source_name: Luminal HR+ mammary epithelial cells,7-day pregnant 1


title: Subject 2 - 4h post-meal

value: Male


title: HR+ 3 day pregnant 1

description: SAMPLE 4

source_name: Luminal HR+ mammary epithelial cells, 3-day pregnant 1


title: HR+ Virgin 1

description: SAMPLE 1

source_name: Luminal HR+ mammary epithelial cells, virgin 1

value: Virgin Control


title: HR+ Virgin 3

description: SAMPLE 3

source_name: Luminal HR+ mammary epithelial cells, virgin 3


title: HR+ Virgin 2

description: SAMPLE 2

source_name: Luminal HR+ mammary epithelial cells, virgin 2


title: HR+ 3 day pregnant 3

description: SAMPLE 6

source_name: Luminal HR+ mammary epithelial cells, 3-day pregnant 3


title: Subject 1 - 10h post-meal


title: uninfected_2_rep

first: jinmiao

last: chen

address: 8A Biomedical Grove, #04-06 Immunos

institute: Singapore Immunology Network

hyb_protocol: 750ng of labelled cRNAs were hybridized to the Illumina mouse arrays for 16 hours at 58°C and the arrays were washed and stained according to the Illumina Wash Protocol

scan_protocol: The mouse chips were scanned using BeadArray Scanner 500GX and the images were analyzed using GenomeStudio Gene Expression v 1.9.0

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

source_name: uninfected

label_protocol: Biotinylated cRNA was prepared according to the Epicentre TargetAmp Nano-g Biotin-aRNA Labelling kit for Illumina system.

extract_protocol: RNA extraction was performed according to the miRVana miRNA isolation kit. Total RNA integrity was assessed by Agilent Bioanalyzer.

treatment_protocol: Mycobacterium tuberculosis infected mouse were treated with 500 mg/Kg of metformin starting day 7 post-infection for 30 days.

value: lung


title: uninfected_3


title: uninfected_4


title: day 30, infected + metformin treated_5

source_name: day 30, infected + metformin treated

value: Mycobacterium tuberculosis


title: day 30, infected + metformin treated_4


title: day 30, infected + metformin treated_3