title: SARS_Mu_MA15e_young_48h_13

value: BALB/c

tag: gender

value: lung

tag: sample collection time post infection

tag: infected with

value: SARS mouse adapted variants

tag: variant type

value: MA15 epsilon


title: POB_125_rep3

status: Public on Jun 02 2014

type: RNA

city: Madison

first: Mark

middle: B

last: Meyer

state: WI

address: 1415 Linden Dr.

department: Nutritional Sciences

country: USA

institute: University of Wisconsin-Madison

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

molecule: total RNA

organism: Mus musculus

source_name: MC3T3-E1 cells

label_protocol: Labeling was performed using the NimbleGen Systems Inc., Madison, WI USA, standard operating protocol. See www.nimblegen.com.

growth_protocol: MC3T3-E1 cells were cultured in alpha MEM with 10% heat-inactivated fetal bovine serum from Hyclone (Logan, UT) and 1% penicillin-streptomycin.  Differentiated cells were cultured in complete media plus 10mM glycerol-2-phosphate and 50ug/mL ascorbic acid for 15 days, changing media every 2-3 days.

extract_protocol: RNA was isolated using the TRI-Reagent protocol (MRC, Cincinnati, OH) and amplification methods according Roche NimbleGen protocols.

treatment_protocol: Cells were treated with 100nM 1,25(OH)2D3 or ethanol vehicle for 24 hours.

tag: passage

tag: cell line

value: MC3T3-E1 cells

tag: treatment


title: hUtSMC_CON_72h_X1

city: Galway

first: Michael

last: Cairns

address: University Road

department: NCBES

country: Ireland

institute: NUI Galway

hyb_protocol: All hybridizations were carried out using the OpArray (Operon) hybridization and wash solutions as recommended by the manufacturer.

scan_protocol: Slides were scanned at 543 nm (Cy3) with a ScanArray Express HT scanner (Perkin Elmer). PMT settings were optimal at 70 %. Resolution was 10 micrometeres.

data_processing: Images were processes using GenePix Pro 6.1.0.4. gpr files were imported into GeneSpring GX 12.0 (Agilent Technologies). Data was log transformed and normalised by the Percentile Shift Method using the 75th percentile. Subsequently all normalised data was baseline transformed to the median of all samples. Three control samples (C1_0h, C2_0h, C3_0h) have been included as raw data (as they were included in the normalised experiment) but these were not part of the analysis (control vs treated).

organism: Homo sapiens

source_name: normal, non-pregnant female, 72h Control

label_protocol: All samples were prepared for microarray hybridization using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion) according to the manufacturer’s recommendations. Probes were hybridized against the Operon Human Genome Array-Ready Oligo Set Microarrays™ ((AROS) Version 4.0).

growth_protocol: hUtSMCs (Lonza) were cultured in complete Dulbecco’s modified essential medium (DMEM), supplemented with 10 % (v/v) fetal bovine serum (FBS), 100 units/ml penicillin and 0.1 mg/ml streptomycin (Sigma-Aldrich) until cells reached 90 % confluence.

extract_protocol: Total RNA was isolated from the cells using a combination of Trizol (Ambion) and Qiagen RNeasy Mini Kit (Qiagen). Cells were lysed in Trizol reagent (1 ml Trizol per 1x107 cells) and 0.2ml chloroform (Sigma-Aldrich) per millilitre of Trizol reagent was added, vortexed for 2 min and incubated at room temperature for 10 min. The mixture was centrifuged (13,000 rpm for 15 min at 4 °C), the upper phase mixed with an equal volume of 70% ethanol and loaded onto the RNeasy column (Qiagen). Total RNA was subsequently isolated using the RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol. RNA was quantified using a NanoDrop ND-1000 spectrophotomer (Thermo Scientific) and quality checked using the Agilent 2100 Bioanalyzer. All RNA yielded RNA integrity numbers (RIN) of greater than 9.0 (average 9.8)

treatment_protocol: At 90% confluence cells were preconditioned overnight with Phenol Red Free DMEM (PRF-DMEM), supplemented with 10% double charcoal-stripped fetal bovine serum (CS-FBS) (Biosera) and containing antibiotics. Cells were starved of endogenous steroids in ‘starvation media’ - PRF-DMEM supplemented with 2% CS-FBS and antibiotics until the cells attained 100% confluence. Subsequently, cells in ‘starvation media’ were supplemented with 10 nM 17β-estradiol (E2) (Sigma Aldrich). Control cells were grown in ‘starvation media’ in the absence of E2 until harvest. Cells were harvested after 6 h, 24 h and 72 h of E2 treatment along with corresponding controls and total RNA was isolated. The complete experiment was replicated three times

value: passage 5-8

tag: tissue

value: normal, non-pregnant female

tag: cell type

value: myometrial smooth muscle cell

tag: smooth muscle markers

value: calponin, smoothelin positive (RT-PCR)

tag: other markers

value: oxytocin receptor and ER-alpha positive (RT-PCR)

tag: estrogen response

value: monitored by CD38 and CX43 gene and protein levels


title: Voluntary Termination of Pregnancy (patient 6)

city: Valencia

first: Juan

middle: M

last: Moreno-Moya

address: Catedrático Agustín Escardino

country: Spain

institute: FIVI

description: each sample was previous tested for miRNAs using Small RNA Labchip in an agilent bioanalyzer

hyb_protocol: After H2O resuspended, samples were mixed with another Spike, mixed with blocking agent and Hi-RPM hybridization buffer and heated at 100ºC for 5' and cooled at 4ºC. Then samples were loaded onto gaskets slides and microarrays slides were put on them. Finally Samples were hybridized for 20h at 55ºC.

scan_protocol: Microarrays slides were washed and scanned in Genepix Personal 4100A Scanner and scanned in Genepix Pro Software with a spot resolution of 5um in the green channel

data_processing: Median intensity value of each spot data was normalized and log2 transformed using R software and libraries from bioconductor database. Next, replicated probes were merged by mean using GEPAS.

source_name: Trophoblast tissue

label_protocol: 100ng of total RNA were mixed with spike and treated with phosphatase for 30' at 37º then cooled at 4ºC. Next DMSO was added and heated at 100ºC for 7.5' then cooled at 4ºC. Next mixed with Cy3-pCp and T4 RNA Ligase for 2 hours at 16ºC and cooled at 4ºC. Samples were dried in a vacuum for 3h at 45ºC. Then H2O added.

growth_protocol: Endometrial fluid aspiration samples were immediately fast frozen at -80ºC until day of RNA extraction.

extract_protocol: To ensure that miRNA fraction will be recovered we performed RNA extraction using the miRNeasy Kit (Qiagen, Valencia, CA, USA). RNA extracted was quantified using a NanoDrop (Thermo Fisher Scientific Inc, MA, USA) spectrophotometer and the proportion of miRNAs was evaluated using the Small RNA LabChip BioAnalyzer 2100,  (Agilent Technologies Inc, DE, USA)

tag: type

value: tissue

tag: age

tag: week of gestation

tag: status

value: voluntary termination of pregnancy


title: hUtSMC_CON_72h_X2


title: POB_125_rep1


title: Voluntary Termination of Pregnancy (patient 5)


title: Control MEFs, biological rep 3, frac 1-4

city: Indianapolis

first: Ronald

middle: C

last: Wek

state: Indiana

address: 6238 Brokenhurst Road

department: Biochemistry & Molecular Biology

institute: Indiana University School of Medicine

description:
RW03M010.CEL
Gene expression data from RNA lysate subjected to sucrose ultracentrifugation for translational regulation

hyb_protocol: Labeled cRNA was hybridized for 17 hours to the Affymetrix Mouse Genome 430 2.0 Array.

scan_protocol: Arrays were scanned using GCOS.

data_processing:
MAS5 data was generated using Affymetrix GeneChip Operating Software (GCOS) and scaling = 1 so that no scaling was done. Arrays were scaled using the 3' and M poly-A bacterial spike-in probe set values as stated in Sampth, et al.: PMID 18462695.
Please note that the treatment plus fractionation based on association with different numbers of ribosomes did yield different populations of mRNAs, which resulted in considerable variation in normalized data across the samples.

label: biotin

source_name: RNA from polysome fractions

label_protocol: RNA preparations were labeled using the standard Affymetrix protocol for 3'-IVT arrays (Affymetrix, Santa Clara, CA) using 2ug of RNA for all samples. The poly A spike-in was omitted because they were spiked into the riobosomal fractions before RNA extraction to be used for normalization later.

growth_protocol: Mouse embryonic fibroblast (MEF) cells were grown in DMEM media supplemented with mM non-essential amino acids, 10% fetal bovine serum, 100 units/mL penicillin, and 100 ug/mL streptomycin at 37C.

extract_protocol: Cell lysates were subjected to sucrose gradient centrifugation and polysome fractionation.  A total of 14 fractions were collected from the top of the gradients into cold  microfuge tubes and immediately placed on ice. Each fraction was adjusted to 0.5% SDS, and fractions were combined to form three pools as follows: fractions 1-4, 5-8, 9-14  were combined as pools 1, 2, and 3, respectively. In parallel, total RNA was isolated from unfractionated lysates for analysis of total gene transcript levels. Synthetic Poly(A)  luciferase RNA (10ng/mL) (Promega), along with a bacterial spike-in control RNA (Affymetrix), were added to each gradient fraction pool. RNA was precipitated at -70C with 2.5  volumes 100% ethanol and purified using QIAGEN RNeasy midi-columns.

treatment_protocol: MEF cells were treated with 1 uM thapsigargin for 6 hours, or without treatment, and rinsed twice with chilled PBS before Trizol extraction. For polysome analysis, both treatment groups were also subjected to a 10 minute (50 ug/mL) cyclohexidime treatment prior to sucrose gradient ultracentrifugation and RNA extraction.

tag: strain

value: Mouse Embryonic Fibroblast (MEF) cells

tag: treated with

value: none (control)

tag: rna fraction

value: free mRNA (sucrose gradient fractions 1-4)

tag: molecule subtype

value: RNA from polysome fractions

tag: replicate


title: BalbC_SARS_MA15e_Aged_24h_B

city: Seattle

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. Two hundred fifty ng of each RNA sample was hybridized to one Agilent 4X44K human HG (Design ID 014850) array.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505C) using the XDR setting.

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol. All arrays were required to pass Agilent QC flags. Extracted raw data were background corrected using the norm-exp method and quantile normalized using Agi4x44PreProcess and RMA Bioconductor packages.

label_protocol: cRNA probes were generated from each sample by the use of an Agilent one-color Quick-Amp labeling kit. The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation.

growth_protocol: Young (8 weeks old) and aged (1 year old) female BALB/c mice were  intranasally infected with 10^5 PFU of either MA15, MA15 gamma, MA15 epsilon, or phosphate buffer solution (PBS; mock-infection). Lungs from aged mice were harvested at 12, 24, and 48 hours post-infection. Lungs from young mice were harvested at 12, 24, 48, and 96 hours post-infection.

extract_protocol: All TRIzol lysates were processed simultaneously: they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2 fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.

treatment_protocol: Lung samples for microarray analysis were stored as TRIzol homogenates at -80 degrees C prior to RNA extraction.

value: BALB/c

tag: gender

value: female

value: 1 yr (aged)

tag: sample collection time post infection

tag: infected with

tag: variant type

tag: biological replicate

value: B


title: BalbC_SARS_MA15e_Aged_12h_B_2

tag: tissue

value: lung

value: SARS mouse adapted variants

value: MA15 epsilon


title: hUtSMC_E2_24h_X3

source_name: normal, non-pregnant female, 24h 17beta estradiol treatment

tag: passage

value: passage 5-8

value: normal, non-pregnant female

tag: cell type

value: myometrial smooth muscle cell

tag: smooth muscle markers

tag: other markers


title: Voluntary Termination of Pregnancy (patient 4)

tag: type

tag: age

tag: week of gestation


title: Control MEFs, biological rep 2, frac 9-14

description:
RW03M008(2).CEL
Gene expression data from RNA lysate subjected to sucrose ultracentrifugation for translational regulation

tag: strain

tag: treated with

value: polysomal (≥ 4 ribosomes per mRNA, sucrose gradient fractions 9-14)


title: hUtSMC_E2_24h_X1

value: calponin, smoothelin positive (RT-PCR)

value: oxytocin receptor and ER-alpha positive (RT-PCR)

tag: estrogen response

value: monitored by CD38 and CX43 gene and protein levels


title: BalbC_SARS_MA15e_Aged_48h_C

value: C


title: hUtSMC_E2_24h_X2


title: Voluntary Termination of Pregnancy (patient 3)

value: tissue

tag: status

value: voluntary termination of pregnancy


title: Control MEFs, biological rep 2

description:
RW03M005.CEL
Gene expression data from whole MEF cell lysate for transcriptional regulation

source_name: Total RNA from MEF cells

value: Mouse Embryonic Fibroblast (MEF) cells

value: none (control)

tag: rna fraction

value: total RNA (no fractionation)

tag: molecule subtype

value: Total RNA

tag: replicate


title: hUtSMC_Con_24h_X3

source_name: normal, non-pregnant female, 24h Control


title: BalbC_SARS_MA15e_Aged_24h_C

value: BALB/c

tag: gender

value: female

value: 1 yr (aged)

value: lung

tag: sample collection time post infection

tag: infected with

tag: variant type


title: Voluntary Termination of Pregnancy (patient 1)


title: BalbC_SARS_MA15e_Aged_24h_A_2

tag: tissue

value: SARS mouse adapted variants

value: MA15 epsilon

tag: biological replicate

value: A


title: Control MEFs, biological rep 2, frac 1-4

description:
RW03M006(2).CEL
Gene expression data from RNA lysate subjected to sucrose ultracentrifugation for translational regulation

value: free mRNA (sucrose gradient fractions 1-4)

value: RNA from polysome fractions


title: Voluntary Termination of Pregnancy (patient 2)


title: hUtSMC_Con_24h_X4

tag: passage

value: passage 5-8

value: normal, non-pregnant female

tag: cell type

value: myometrial smooth muscle cell

tag: smooth muscle markers

value: calponin, smoothelin positive (RT-PCR)

tag: other markers

value: oxytocin receptor and ER-alpha positive (RT-PCR)

value: monitored by CD38 and CX43 gene and protein levels


title: Ectopic Pregnancy (patient 8)

tag: type

value: tissue

tag: age

tag: week of gestation

value: ectopic pregnancy


title: BalbC_SARS_MA15e_Aged_48h_A

tag: strain

value: BALB/c


title: hUtSMC_Con_24h_X5

tag: estrogen response


title: Control MEFs, biological rep 3

description:
RW03M009.CEL
Gene expression data from whole MEF cell lysate for transcriptional regulation

value: Mouse Embryonic Fibroblast (MEF) cells

tag: treated with

value: none (control)

tag: rna fraction

value: total RNA (no fractionation)

tag: molecule subtype

value: Total RNA


title: Control MEFs, biological rep 1, frac 9-14

description:
RW03M004(2).CEL
Gene expression data from RNA lysate subjected to sucrose ultracentrifugation for translational regulation

value: polysomal (≥ 4 ribosomes per mRNA, sucrose gradient fractions 9-14)

tag: replicate


title: Control MEFs, biological rep 2, frac 5-8

description:
RW03M007(2).CEL
Gene expression data from RNA lysate subjected to sucrose ultracentrifugation for translational regulation

value: 1_to_3 ribosomes per mRNA (sucrose gradient fractions 5-8)


title: Control MEFs, biological rep 1, frac 5-8

description:
RW03M003(2).CEL
Gene expression data from RNA lysate subjected to sucrose ultracentrifugation for translational regulation


title: BalbC_SARS_MA15e_Aged_48h_B

tag: gender

value: female

value: 1 yr (aged)

value: lung

tag: sample collection time post infection

tag: infected with

value: SARS mouse adapted variants

value: MA15 epsilon

value: B


title: Ectopic Pregnancy (patient 7)

tag: status


title: hUtSMC_Con_24h_X2

tag: passage

value: passage 5-8

tag: tissue

value: normal, non-pregnant female

value: myometrial smooth muscle cell

value: calponin, smoothelin positive (RT-PCR)

value: oxytocin receptor and ER-alpha positive (RT-PCR)


title: Control MEFs, biological rep 1, frac 1-4

description:
RW03M002(2).CEL
Gene expression data from RNA lysate subjected to sucrose ultracentrifugation for translational regulation

value: Mouse Embryonic Fibroblast (MEF) cells

value: free mRNA (sucrose gradient fractions 1-4)

value: RNA from polysome fractions


title: Ectopic Pregnancy (patient 5)

value: tissue

value: ectopic pregnancy


title: hUtSMC_Con_24h_X1

tag: cell type

tag: smooth muscle markers

value: monitored by CD38 and CX43 gene and protein levels


title: BalbC_SARS_MA15e_Aged_12h_A

value: BALB/c

value: female

tag: variant type

tag: biological replicate

value: A


title: Ectopic Pregnancy (patient 6)

tag: type

tag: age

tag: week of gestation


title: Ectopic Pregnancy (patient 3)


title: SARS_Mu_MA15_young_12h_50

tag: strain

value: 8 wks old (young)

value: lung

value: SARS mouse adapted variants


title: Steady-state potassium phosphate limited biological rep 3 of 3

city: Athens

first: Leong-Keat

last: Chan

state: GA

address: 325 Sanford Drive

department: Marine Sciences

institute: University of Georgia

description: Biological replicate 3 of 3 from the potassium phosphate limited growth regime

hyb_protocol: Labeled and purified mRNA samples were hybridized to custom microarray slides manufactured by Combimatrix (Mukilteo, WA, USA; GEO platform ID GPL4067) and imaged according to the procedures described in the manufacturer's protocol. Hybridized slides were stripped according to Combimatrix's protocol and re-used up to three times.

scan_protocol: Axon GenePix 4000B microarray scanner (Molecular Devices Corporation, Sunnyvale, CA, USA) at 5 µm resolution (450-550 PMT).

data_processing:
The procedures were modified from Bürgmann et al., 2007, Environmental Microbiology, 9: 2742-2755. Each gene was represented by up to two probes and each probe was spotted up to three times on the array (Bürgmann et al., 2007; see platform ID GPL4067 for the array design). Each hybridized spot was manually examined in GenePix Pro 6.0 Software (Molecular Devices, Sunnyvale, CA, USA) for quality. The median fluorescence value (F635 Median; see raw data files in the Supplement) for each hybridized spot was subtracted from the median fluorescence value of the five closest empty spots (B635 Median; see raw data files in the Supplement), resulted in the values specified in the PRE_VALUE columns in the Data Tables. Spots were flagged as bad with Acuity 4.0 (Molecular Devices) when they were unevenly hybridized (determined manually by checking the hybridization circularity), when the detected fluorescence minus the background fluorescence was less than two standard deviations of the background fluorescence (F635 Median-B635 Median <2 SD(B635); see raw data files in the Supplement), or when the signal to noise ratio (SNR635; see raw data files in the Supplement) was <3. Flagged spots are indicated by 'null' in the Data Tables. For the remaining spots with good hybridization signals, those targeting 5S rRNA, 16S rRNA, 23S rRNA, mismatch probes, and manufacturer's control probes (see platform ID GPL4067 for the array design) were removed. Then, fluorescence values from all spots (up to three) targeting a same probe were averaged and combined and used for normalization. The six arrays described in this accession were analyzed together with seven arrays previously deposited: GEO Series GSE27032 (platform GPL4067), samples GSM665914-GSM665917 (NH4Cl-limited, 0.26 mM; KH2PO4 excess, 0.50 mM; three biological replicates and one technical replicate) and samples GSM665918-GSM665920 (NH4Cl excess, 2.8 mM; KH2PO4-limited, 9.20 uM; three biological replicates); these seven samples were obtained from steady-state R. pomeroyi DSS-3 cells cultured using identical protocols and medium, but with different ammonium and phosphorus compounds and concentrations. Quality controls of the microarray hybridizations for these seven samples were performed with procedures identical to the six arrays described here. After quality controls, fluorescence values of probes from the two ammonium-limited, KH2PO4 excess technical replicates (samples GSM665914 and GSM665915) were averaged and combined. In total, the analysis resulted in 12 samples from four treatment regimes. Probes were removed across all 12 arrays if flagged spots were present in all triplicate samples within a treatment regime. This filtering step resulted in 5,650 probes for all 12 arrays and their fluorescence values (originated from everaging and combining the PRE_VALUEs from spots representing the same probes) were used for quantile normalization (Bolstad et al., 2003, Bioinformatics 19:185-193), resulted in the normalized fluorescence values (VALUE) in Data Tables. Some consecutively listed spots (each spot is represented by a unique ID_REF) in Data Tables are indicated with 'null' becuase these are spots that either did not pass quality controls or spots that passed quality controls but their normalized fluorescence values are listed with their corresponding set of probes in the rows immediately above.
ID_REF- Each ID_REF represents a spot on the array (as specified in column 1 in the platform GPL4067). ID_REFs targeting 5S rRNA, 16S rRNA, 23S rRNA, mismatch probes, and manufacturer's control probes were removed. Each probe was spotted up to three times on the array; thus, a probe_ID can have up to three different ID_REFs.
probe_ID- Each probe_ID represents a probe (as specified in column 2 in the platform GPL4067). Each probe was spotted up to three times on the array.
PRE_VALUE- F635 Median minus B635 Median fluorescence values (not normalized). 'Null' indicates spots that did not pass quality controls. In the ammonium-limited, potassium phosphate excess biological replicate 1 of 3 sample, values for both technical replicate microarray hybridizations (PRE_VALUE_1, originated from IPErep1_1.gpr, and PRE_VALUE_2, originated from IPErep1_2.gpr) are shown.
VALUE- Quantile-normalized fluorescence values. Fluorescence values of probes from 12 arrays originated from four treatment regimes were used for normalization (see procedures described in Data processing). Prior to normalization, good quality fluorescence values from all spots (up to three) targeting the same probes were averaged and combined. Fields for some consecutively listed ID_REFs (each ID_REF represents a spot on the array) are indicated with 'null' becuase these are spots that either did not pass quality controls or spots that passed quality controls but their normalized values are listed with their corresponding set of probes in the rows immediately above.

label: AlexaFluor dye 647 (red emission)

organism: Ruegeria pomeroyi DSS-3

source_name: R. pomeroyi, potassium phosphate limited, ammonium in excess

label_protocol: Amplified mRNA was labeled with AlexaFluor 647 dye (Invitrogen, Carlsbad, CA, USA; red emmision) according to manufacturer's recommended procedures. Amplified and labeled mRNA was purified with the MEGAclear kit (Applied Biosystems/Ambion, Austin, TX, USA) and concentrated by ethanol precipitation.

growth_protocol: Ruegeria pomeroyi strain DSS-3 was grown in 320 ml custom-made chemostats with a culture volume of 200 ml. Steady-state biomass was limited by ammonium (NH4Cl, 0.26 mM) or potassium phosphate (KH2PO4, 9.2 μM). Cell cultures limited by ammonium were supplied with an excess of D-ribose-5-phosphate (C5H9Na2O8P*2H2O, 0.5 mM), methyphosphonic acid (CH5PO3, 0.5 mM), or potassium phosphate (KH2PO4, 0.5 mM); those limited by potassium phosphate were supplied with an excess of ammonium (NH4Cl, 2.8 mM). Other non-limiting nutrients were provided in identical amounts for all cultures. The culture medium was buffered with 10 mM 1,3-bis(tris(hydroxymethyl)methylamino)propane and added with vitamins and trace metals (see Table A1 in the Appendix in Chan et al., 2012, Frontiers in Microbiology, 3:159. doi: 10.3389/fmicb.2012.00159 for components of cell culture medium). The feed medium was added to each chemostat culture at a constant rate (8.4 ml per hour), and spent medium and cells were removed at the same rate. During the incubation, cell cultures were mixed by constant stirring. Growth temperature was maintained at 30 degree celsius using a circulating water bath. Salinity was constant at 25. Oxygen was bubbled into the culture at a flow rate of 2 ml per minute through an aquarium air pump, controlled by a flow meter. The pH ranged from 6.6 to 7.0 during all growth regimes. Cell cultures were considered to be at steady-state when the change in OD600 was less than or equal to 10% between two successive measurements. All cultures reached steady-state after three volume exchanges. Cells were harvested after five volume exchanges. At steady-state, R. pomeroyi DSS3-3 has a doubling time of 16.5 hours.

extract_protocol: Total RNA from thawed steady-state cell culture previously fixed with phenol-ethanol solution was purified using the RNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s procedures. DNA was depleted by TURBO DNase treatment (Applied Biosystems/Ambion, Austin, TX, USA). Ribosomal RNA was depleted with MicrobeExpress (Applied Biosystems/Ambion), according to manufacturer's recommendations. Purified mRNA was amplified with MessageAmp II-Bacteria Kit (Applied Biosystems/Ambion) with procedures as described in the manufacturer's manual.

treatment_protocol: Steady-state cell culture from each replicate chemostat (45 ml) was rapidly fixed with 5 ml of phenol–ethanol solution (5% vol/vol). Cells were collected by centrifugation at 4,500 × g and the supernatant was removed. Loose cell pellets were frozen at −70 degree celcius.

tag: bacterial culture conditions, steady-state cell doubling time, limited nutrient, excess nutrient

value: Chemostat, 16.5 hours, ammonium (NH4Cl, 2.8 mM), potassium phosphate (KH2PO4,9.2 μM)


title: Ectopic Pregnancy (patient 4)


title: hUtSMC_E2_6h_X2

source_name: normal, non-pregnant female, 6h 17beta estradiol treatment

value: passage 5-8

value: normal, non-pregnant female

tag: other markers

tag: estrogen response


title: hUtSMC_E2_6h_X1

value: myometrial smooth muscle cell

value: calponin, smoothelin positive (RT-PCR)


title: hUtSMC_E2_6h_X3

value: oxytocin receptor and ER-alpha positive (RT-PCR)


title: BalbC_SARS_MA15e_Aged_12h_C

tag: gender

value: 1 yr (aged)

value: MA15 epsilon

value: C


title: Ectopic Pregnancy (patient 2)

value: tissue

value: ectopic pregnancy


title: SARS_Mu_MA15_young_24h_36

value: BALB/c

tag: sample collection time post infection


title: Control MEFs, biological rep 1

description:
RW03M001.CEL
Gene expression data from whole MEF cell lysate for transcriptional regulation

value: Mouse Embryonic Fibroblast (MEF) cells

tag: treated with

value: none (control)

tag: rna fraction

value: total RNA (no fractionation)

tag: molecule subtype

value: Total RNA

tag: replicate


title: Steady-state potassium phosphate excess biological rep 3 of 3

description: Biological replicate 3 of 3 from the potassium phosphate excess growth regime

source_name: R. pomeroyi, ammonium limited, potassium phosphate in excess

value: Chemostat, 16.5 hours, ammonium (NH4Cl, 0.26 mM), potassium phosphate (KH2PO4, 0.5 mM)


title: Steady-state potassium phosphate limited biological rep 1 of 3

description: Biological replicate 1 of 3 from the potassium phosphate limited growth regime

value: Chemostat, 16.5 hours, ammonium (NH4Cl, 2.8 mM), potassium phosphate (KH2PO4,9.2 μM)


title: SARS_Mu_MA15_young_24h_38

value: female

value: 8 wks old (young)

tag: tissue

value: lung

tag: infected with

value: SARS mouse adapted variants


title: hUtSMC_Con_6h_X2

source_name: normal, non-pregnant female, 6h Control

tag: passage

value: passage 5-8

value: normal, non-pregnant female

tag: cell type

value: myometrial smooth muscle cell

tag: smooth muscle markers

value: calponin, smoothelin positive (RT-PCR)

value: oxytocin receptor and ER-alpha positive (RT-PCR)

value: monitored by CD38 and CX43 gene and protein levels


title: SARS_Mu_MA15_young_12h_52

value: BALB/c

tag: age

tag: variant type

tag: biological replicate


title: Ectopic Pregnancy (patient 1)

tag: type

value: tissue

tag: week of gestation

tag: status

value: ectopic pregnancy


title: hUtSMC_Con_6h_X1

tag: other markers

tag: estrogen response


title: Steady-state potassium phosphate excess biological rep 2 of 3

description: Biological replicate 2 of 3 from the potassium phosphate excess growth regime

tag: bacterial culture conditions, steady-state cell doubling time, limited nutrient, excess nutrient


title: Steady-state potassium phosphate excess biological rep 1 of 3

description: Biological replicate 1 of 3 from the potassium phosphate excess growth regime (technical replicates 1 and 2 combined)


title: Late Secretory (patient 4)

source_name: endometrial fluid

tag: fluid

value: endometrial fluid

tag: day of menstrual cycle

tag: phase

value: late secretory


title: SARS_Mu_MA15_young_12h_53

tag: strain

tag: gender

tag: tissue

tag: sample collection time post infection


title: hUtSMC_Con_6h_X3

tag: passage

tag: cell type

tag: smooth muscle markers


title: SARS_Mu_MA15_young_24h_37

tag: age

tag: infected with

tag: variant type

tag: biological replicate


title: Late Secretory (patient 3)


title: SARS_Mu_MA15_young_96h_24


title: Late Secretory (patient 2)


title: Late Secretory (patient 1)


title: Steady-state methylphosphonate excess biological rep 3 of 3

description: Biological replicate 1 of 3 from the methylphosphonate excess growth regime

source_name: R. pomeroyi, ammonium limited, methylphosphonate in excess

value: Chemostat, 16.5 hours, ammonium (NH4Cl, 0.26 mM), methylphosphonate (CH5PO3, 0.5 mM)


title: Window Of Implantation (patient 3)

description: each sample was previous tested for miRNAs using Small RNA Labchip in an agilent bioanalyzer

value: window of implantation


title: Window Of Implantation (patient 4)


title: Steady-state ribose phosphate excess biological rep 1 of 3

description: Biological replicate 1 of 3 from the ribose phosphate excess growth regime

source_name: R. pomeroyi, ammonium limited, ribose phosphate in excess

value: Chemostat, 16.5 hours, ammonium (NH4Cl, 0.26 mM), ribose phosphate (C5H9Na2O8P*2H2O, 0.5 mM)


title: SARS_Mu_MA15_young_48h_8

value: female

value: 8 wks old (young)


title: Steady-state ribose phosphate excess biological rep 3 of 3


title: Steady-state methylphosphonate excess biological rep 1 of 3


title: SARS_Mu_MA15_young_48h_7

value: lung

value: SARS mouse adapted variants


title: Steady-state potassium phosphate limited biological rep 2 of 3

description: Biological replicate 2 of 3 from the potassium phosphate limited growth regime

value: Chemostat, 16.5 hours, ammonium (NH4Cl, 2.8 mM), potassium phosphate (KH2PO4,9.2 μM)


title: Steady-state methylphosphonate excess biological rep 2 of 3


title: Steady-state ribose phosphate excess biological rep 2 of 3


title: Window Of Implantation (patient 2)


title: SARS_Mu_MA15_young_12h_51


title: 48 hours after LTH seedling under normal temperature (26℃) replicate 1

city: Guangzhou

first: Junliang

last: Zhao

address: 29 Jinying Road, Tianhe District

country: China

institute: Guangdong Academy of Agricultural Science

description:
Biological replicate 1 of 3. normal temperature treated LTH 3 leaf seedling as control, harvest after 48 hours treatment.
CK 48h rep1

hyb_protocol: Microarray slides were hybridized with hybridization buffer containing two paired labeled samples in a final concentration of 5×Denhardt, 3×SSC and 0.2% SDS for 16 h at 65 ℃. After hybridization, the slides were subjected to four-step stringency washes (2×SSC + 0.2% SDS, twice at 42 ℃ for 4 min; 0.2×SSC, twice at 42 ℃ for 4 min).

scan_protocol: The slides were scanned using Axon 4000B scanner and analyzed by Genepix Pro 6.0 (Axon Instruments, USA).

data_processing:
Genepix Pro 6.0 was used for feature extraction and background subtraction. Acurity 4.0 was use for LOWESS normalization.
Filtering details: If the flouresent intensity of both channels is lower than 800 in the microarray, we concider this feature as non-expressed.

organism: Oryza sativa

source_name: LTH seedling under normal temperautre

label_protocol: 5µg RNA were primed with 6-mer random primer,then reversed transcribed into cDNA by MMLV reversed transcripase and then double-strand cDNA were synthetised. Double-strand cDNA were then transcripted into cRNA by T7 polymerase. cRNA were reversed transcribed into cDNA by MMLV reversed transcripase. cDNA were lable with Cy5/Cy3 by klenlow flagment.

growth_protocol: After incubation at 49 ℃ for 96 h to break dormancy, seeds were soaked in water for 36 h and then incubated at 30 ℃ for 48 h. The germinated seeds were sown in plastic trays (41 x 26.5 x 7.5 cm) filled with fine field soil. Materials were planted in 13 rows in a tray with 11 plants per row. The seedlings were allowed to grow for 14 days at 26 ℃ until the three-leaf stage.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Three-leaf stage seedlings were placed in a Conviron PGV36 growth chamber (Controlled Environments Ltd., Winnipeg) maintained at a constant temperature of 8 ℃, with a 13-h day length of 126 μmol m-2 s-1 light intensity and a relative humidity of 80 ± 5%. Control seedlings were grown under the same conditions, except the temperature was 26 ℃.

tag: cultivar

value: Lijiangxintuanheigu (LTH)

value: Leaf

tag: developmental stage

value: 3 leaf seedling

tag: stress

value: control

tag: time

value: 48 hours

source_name: Pool the normal temperature treated LTH seedling

tag: sample type

value: normal temperature treated LTH seedlings, pooled


title: 48 hours after LTH seedling under normal temperature (26℃) replicate 2

description:
Biological replicate 2 of 3. normal temperature treated LTH 3 leaf seedling as control, harvest after 48 hours treatment.
CK 48h rep2


title: SARS_Mu_MA15_young_96h_21

value: BALB/c


title: SARS_Mu_MA15_young_96h_22


title: SARS_Mu_MA15_young_48h_5


title: 48 hours after LTH seedling under normal temperature (26℃) replicate 13

description:
Biological replicate 3 of 3. normal temperature treated LTH 3 leaf seedling as control, harvest after 48 hours treatment.
CK 48h rep3


title: Primed for 4 days with M-CSF and 1 day M-CSF + RANKL

city: Amsterdam

first: Teun

middle: J.

last: de Vries

address: Gustav Mahlerlaan 3004

department: Periodontology

country: Netherlands

institute: Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and VU University

description:
Biological replicate 1: OCP1; boneCy3 plasticCy5; raw data file: US22502676_251486816096_S01_GE2_105_Dec08_1_1.txt
Biological replicate 2: OCP2; boneCy3 plasticCy5; raw data file: US22502676_251486816096_S01_GE2_105_Dec08_1_2.txt
Biological replicate 3: OCP3; boneCy5 plasticCy3; raw data file: US22502676_251486816096_S01_GE2_105_Dec08_1_3.txt
Biological replicate 4: OCP4; boneCy5 plasticCy3; raw data file: US22502676_251486816096_S01_GE2_105_Dec08_1_4.txt

hyb_protocol: Standard Agilent protocol

scan_protocol: Arrays were scanned using the Agilent GeneArray Scanner (Agilent, G25 05B) with default settings for two-color hybridization

data_processing: Intensities were preprocessed and normalized using Limma. The pre-processing consisted of a filtering step which removed probes with missing or low intensities in both channels, which was the case for 30% of the samples. In addition, Edwards’ background correction with an offset of 30 on the intensity level was performed. Within array and between array normalization was done by using ‘loess’ and ‘Aquantile’, respectively. Intensities were normalized and processed to yield an MA-object to be used in the Limma package of the statistical programming language R. Limma was used to determine the fold change of every probe with respect to the value for that probe on plastic and to assess whether this change was significant. Briefly, this analysis fits a linear model and shrink adjusts the standard deviation of a probe towards the overall standard deviation of all probes. The first is done to determine differential expression, the latter to robustify the estimate of the standard deviation. In addition, the Benjamini-Hochberg false discovery rate (FDR) correction method was applied to adjust the raw p-values resulting from limma.

label: Cy3, Cy5

source_name: Mouse myeloid blasts

label_protocol: Standard Agilent protocol

growth_protocol: Isolated myeloid blasts were cultured for 4 days with M-CSF and for 1 day with M-CSF and RANKL.

extract_protocol: Qiagen kit

treatment_protocol: Growth surface: plastic bottom of a 96 wells plate or a cortical bovine bone slice

tag: primary cell culture

value: Primary bone marrow cell isolate

value: Myeloid blasts

tag: growth condition

value: Bone

value: Plastic


title: S. cerevisiae_CG-1521_1h_rep2

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol on 3000G scanner

data_processing: Expression console software used to generate CHP files with RMA normalization.

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae, CG-1521, 1h

label_protocol: Biotin labeling using NuGEN Applause protocol

growth_protocol: Yeast cells were grown in YPD at 30°C while shaking.

extract_protocol: RNA was extracted using the mRNeasy mini kit (Qiagen) after enzymatic lysis using zymolyase.

treatment_protocol: Exponentially growing yeast cells were treated with 50 μM CG-1521 or vehicle control for 1h.

tag: strain


title: Early Secretory (patient 2)

tag: fluid

value: endometrial fluid

tag: day of menstrual cycle

tag: phase

value: early secretory


title: Early Secretory (patient 3)


title: Late Proliferative (patient 4)

value: late proliferative


title: Window Of Implantation (patient 1)

value: window of implantation


title: 48 hours after LTH seedling under cold (8℃) stress replicate 3

description:
Biological replicate 3 of 3. Cold treated LTH 3 leaf seedling, harvest after 48 hours treatment.
Cold 48h rep3

source_name: LTH seedling after cold stress

tag: tissue

value: cold


title: BalbC_SARS_MA15_Aged_12h_A

tag: gender

value: female

value: 1 yr (aged)

value: lung

tag: sample collection time post infection

value: SARS mouse adapted variants

value: A


title: 48 hours after LTH seedling under cold (8℃) stress replicate 1

description:
Biological replicate 1 of 3. Cold treated LTH 3 leaf seedling, harvest after 48 hours treatment.
Cold 48h rep1

value: Lijiangxintuanheigu (LTH)

value: Leaf

value: 3 leaf seedling

value: 48 hours

value: control


title: Early Secretory (patient 4)

tag: age


title: Late Proliferative (patient 3)


title: Late Proliferative (patient 2)


title: S. cerevisiae_control_1h_rep2

source_name: S. cerevisiae, control, 1h


title: Early Secretory (patient 1)


title: S. cerevisiae_CG-1521_1h_rep1


title: BalbC_SARS_MA15_Aged_48h_C

value: BALB/c

tag: infected with

tag: variant type

value: C


title: 24 hours after LTH seedling under normal temperature (26℃) replicate 13

description:
Biological replicate 3 of 3. normal temperature treated LTH 3 leaf seedling as control, harvest after 24 hours treatment.
CK 24h rep3

tag: cultivar

value: 24 hours

value: normal temperature treated LTH seedlings, pooled


title: 48 hours after LTH seedling under cold (8℃) stress replicate 2

description:
Biological replicate 2 of 3. Cold treated LTH 3 leaf seedling, harvest after 48 hours treatment.
Cold 48h rep2

tag: developmental stage


title: SARS_Mu_MA15_young_48h_6

value: 8 wks old (young)

tag: biological replicate


title: 24 hours after LTH seedling under normal temperature (26℃) replicate 2

description:
Biological replicate 2 of 3. normal temperature treated LTH 3 leaf seedling as control, harvest after 24 hours treatment.
CK 24h rep2

tag: stress

tag: time


title: Late Proliferative (patient 1)

value: endometrial fluid

value: late proliferative


title: S. cerevisiae_control_1h_rep1


title: 24 hours after LTH seedling under normal temperature (26℃) replicate 1

description:
Biological replicate 1 of 3. normal temperature treated LTH 3 leaf seedling as control, harvest after 24 hours treatment.
CK 24h rep1

tag: sample type


title: 24 hours after LTH seedling under cold (8℃) stress replicate 3

description:
Biological replicate 3 of 3. Cold treated LTH 3 leaf seedling, harvest after 24 hours treatment.
Cold 24h rep3

value: cold


title: Early Proliferative (patient 4)

value: early proliferative


title: BalbC_SARS_MA15_Aged_48h_A_2

value: female

value: 1 yr (aged)

value: lung


title: 12 hours after LTH seedling under normal temperature (26℃) replicate 13

description:
Biological replicate 3 of 3. normal temperature treated LTH 3 leaf seedling as control, harvest after 12 hours treatment.
CK 12h rep3

value: Lijiangxintuanheigu (LTH)

value: 12 hours


title: Extra-embryonic tissue sample mice 3

description: each sample was previous tested for total RNA quality using total pico RNA Labchip in an agilent bioanalyzer and with RIN above 9.0

hyb_protocol: 1.65 ug of cRNA was used to be fragmented in presence of blocking agent and fragmentation buffer for 30º at 60ºC and cooled. Then sample was mixed with hybridization buffer.

scan_protocol: Microarrays slides were washed and scanned in Genepix Personal 4100A Scanner and scanned in Genepix Pro Software with a spot resolution of 5um in the green channel.

data_processing: Median intensity value of each spot data was log2 transformed and normalized using R software and libraries from bioconductor database. Next, replicated probes were merged by mean using GEPAS.

source_name: Day 6.5 post-coitum murine implanted embryos

label_protocol: Total RNA was obtained from uterine and trophoblast tissues and analyzed as previously described [17]. Briefly, total RNA was extracted using Trizol reagent (Life Technologies, Paisley, UK) and treated with DNase I (Promega, Southampton, UK) for 30 min at 37°C and then reextracted with Trizol. RNA quality was assessed with an A2100 bioanalyzer (Agilent Technologies, Santa Clara, CA). Only those samples with a RNA integrity number (RIN)7.5 were included for microarray analysis. One microgram of each RNA sample were labeled and hybridized to the One-Color Agilent Whole Mouse Genome Microarray 44K.  For each group, 3 samples were analyzed in duplicate.

extract_protocol: To ensure that total RNA was recovered we performed RNA extraction using the Arcturus PicoPure RNA Isolation Kit (Life Technologies S.A. Madrid, Spain). RNA extracted was quantified using a NanoDrop (Thermo Fisher Scientific Inc, MA, USA) spectrophotometer and the RNA quality was evaluated using the total eukariote Pico RNA LabChip in the BioAnalyzer 2100,  (Agilent Technologies Inc, DE, USA)

value: B6CBA F1/J

value: ectoplacental cone


title: 12 hours after LTH seedling under normal temperature (26℃) replicate 2

description:
Biological replicate 2 of 3. normal temperature treated LTH 3 leaf seedling as control, harvest after 12 hours treatment.
CK 12h rep2

value: Leaf

value: 3 leaf seedling

value: control


title: Inter-implantation decidua sample mice 1

source_name: Day 6.5 post-coitum murine uterus

value: inter-implantation decidua


title: BalbC_SARS_MA15_Aged_12h_B

value: BALB/c

value: SARS mouse adapted variants

value: B


title: BalbC_SARS_MA15_Aged_24h_A

value: A


title: 24 hours after LTH seedling under cold (8℃) stress replicate 2

description:
Biological replicate 2 of 3. Cold treated LTH 3 leaf seedling, harvest after 24 hours treatment.
Cold 24h rep2

value: cold

value: 24 hours

value: normal temperature treated LTH seedlings, pooled


title: 24 hours after LTH seedling under cold (8℃) stress replicate 1

description:
Biological replicate 1 of 3. Cold treated LTH 3 leaf seedling, harvest after 24 hours treatment.
Cold 24h rep1


title: BalbC_SARS_MA15_Aged_48h_B

value: female

value: 1 yr (aged)


title: Inter-implantation decidua sample mice 3


title: Extra-embryonic tissue sample mice 2


title: BalbC_SARS_MA15_Aged_24h_B

value: lung


title: Surrounding decidua sample mice 2

value: surrounding decidua


title: Inter-implantation decidua sample mice 2

value: B6CBA F1/J


title: BalbC_SARS_MA15_Aged_12h_C

value: C


title: Extra-embryonic tissue sample mice 1

value: ectoplacental cone


title: Surrounding decidua sample mice 3


title: Early Proliferative (patient 3)

description: each sample was previous tested for miRNAs using Small RNA Labchip in an agilent bioanalyzer

value: endometrial fluid

value: early proliferative


title: Early Proliferative (patient 1)


title: BalbC_SARS_MA15_Aged_24h_C


title: Early Proliferative (patient 2)


title: 12 hours after LTH seedling under normal temperature (26℃) replicate 1

description:
Biological replicate 1 of 3. normal temperature treated LTH 3 leaf seedling as control, harvest after 12 hours treatment.
CK 12h rep1

value: Lijiangxintuanheigu (LTH)

value: Leaf

value: 3 leaf seedling

value: control

value: 12 hours


title: 6 hours after LTH seedling under normal temperature (26℃) replicate 13

description:
Biological replicate 3 of 3. normal temperature treated LTH 3 leaf seedling as control, harvest after 6 hours treatment.
CK 6h rep3

value: 6 hours


title: 12 hours after LTH seedling under cold (8℃) stress replicate 1

description:
Biological replicate 1 of 3. Cold treated LTH 3 leaf seedling, harvest after 12 hours treatment.
Cold 12h rep1

value: cold


title: Mimic 30d treated embryos biological replicate 3

source_name: Day 5 murine blastocyst embryos

label_protocol: 50ng of total RNA were mixed with spike and mixed with T7 promoter primer for 10' at 65º then cooled at 4ºC. Next to cDNA synthesis, First strand buffer, DTT, dNTP and RNAse block mix were added and incubated for 2 hours at 40ºC followed by 15' at 70ºC. Next for cRNA synthesis, transcription buffer, DTT, NTP, T7 RNA polymerase and Cy3-CTP were added and incubated for 2 hours at 40ºC and cooled for 5'. Then cRNA was purified according to Qiagen RNEasy kit protocol specifications. Yield and [cRNA] stimated. Then 1.65 ug de cRNA was used to be fragmented in presence of blocking agent and fragmentation buffer for 30º at 60ºC and cooled. Then sample was mixed with hybridization buffer.

growth_protocol: After embryos are four times washed in fresh CCM they were extracted immediately.

tag: sample

value: whole blastocyst

tag: treatment

value: 400nM of mir-30d MIMIC for 72 hours


title: 12 hours after LTH seedling under cold (8℃) stress replicate 3

description:
Biological replicate 3 of 3. Cold treated LTH 3 leaf seedling, harvest after 12 hours treatment.
Cold 12h rep3

value: normal temperature treated LTH seedlings, pooled


title: 12 hours after LTH seedling under cold (8℃) stress replicate 2

description:
Biological replicate 2 of 3. Cold treated LTH 3 leaf seedling, harvest after 12 hours treatment.
Cold 12h rep2


title: 6 hours after LTH seedling under cold (8℃) stress replicate 2

description:
Biological replicate 2 of 3. Cold treated LTH 3 leaf seedling, harvest after 6 hours treatment.
Cold 6h rep2


title: 6 hours after LTH seedling under cold (8℃) stress replicate 1

description:
Biological replicate 1 of 3. Cold treated LTH 3 leaf seedling, harvest after 6 hours treatment.
Cold 6h rep1


title: Scramble treated embryos biological replicate 2

tag: strain

value: 400nM of Scramble-Alexa 488 for 72 hours


title: Surrounding decidua sample mice 1

value: surrounding decidua


title: Mimic 30d treated embryos biological replicate 1


title: 6 hours after LTH seedling under cold (8℃) stress replicate 3

description:
Biological replicate 3 of 3. Cold treated LTH 3 leaf seedling, harvest after 6 hours treatment.
Cold 6h rep3


title: MCAM analysis of GC2

type: genomic

city: Augusta

first: Huidong

last: Shi

department: Georgia Cancer Center

institute: Augusta University

description:
DNA, PCR amplicon
Co-hybrdized to a custom 105K agilent oligonuclleotide array

hyb_protocol: Five micrograms of each labeled DNA were co-hybridized to Agilent 105K custom oligonucleotide microarrays for 48 hours and slides were washed three times according Agilent protocols.

scan_protocol: The microarray slides were scanned on a GenePix 4200A scanner (Molecular Devices, Sunnydale, CA, USA) according to Agilent protocols.

data_processing: Background model adjustment was carried out using the minimum normalization algorithm. Systematic differences between arrays were normalized using the quantile method as described by Bolstad et al. (Bioinformatics 19, 185-193 (2003).

label: Alexafluor 647

molecule: genomic DNA

source_name: Gastric cancer (GC) sample #2

label_protocol: Following purification of amplicons using Zymo clean and concentrator columns, 2μg each of GC and SM was labeled with Alexafluor647 or 555 using the Bioprime Plus Array CGH Indirect Genomic Labeling kit (Invitrogen) according to the manufacturers’ instructions.

extract_protocol: 5μg DNA were digested consecutively with SmaI and XmaI which cut unmethylated and methylated CCCGGG sites, respectively. SmaI digestion results in blunt ends and XmaI digestion produces sticky ends which can be ligated to linkers. Digested DNA was purified using Zymo clean and concentrator columns (Zymo Research, Orange, CA, USA) and 500ng was ligated to annealed RMCA12 and RMCA24 adapters then PCR amplified.

value: Stomach

tag: tissue type

value: gastric cancer (GC)

tag: gc status

value: Non-Metastatic GCs

label: Alexafluor 555

source_name: Surgical margin (SM) sample #2

value: Normal tissue (Surgical margin)


title: Scramble treated embryos biological replicate 1


title: 6 hours after LTH seedling under normal temperature (26℃) replicate 2

description:
Biological replicate 2 of 3. normal temperature treated LTH 3 leaf seedling as control, harvest after 6 hours treatment.
CK 6h rep2

tag: tissue


title: MCAM analysis of GC5

source_name: Gastric cancer (GC) sample #5

source_name: Surgical margin (SM) sample #5


title: 6 hours after LTH seedling under normal temperature (26℃) replicate 1

description:
Biological replicate 1 of 3. normal temperature treated LTH 3 leaf seedling as control, harvest after 6 hours treatment.
CK 6h rep1


title: MCAM analysis of GC4

source_name: Gastric cancer (GC) sample #4

source_name: Surgical margin (SM) sample #4


title: Scramble treated embryos biological replicate 3


title: MCAM analysis of GC3

source_name: Gastric cancer (GC) sample #3

value: Metastatic GCs

source_name: Surgical margin (SM) sample #3


title: MCAM analysis of GC1

source_name: Gastric cancer (GC) sample #1

source_name: Surgical margin (SM) sample #1


title: MCAM analysis of GC6

source_name: Gastric cancer (GC) sample #6

source_name: Surgical margin (SM) sample #6


title: MCAM analysis of GC7

source_name: Gastric cancer (GC) sample #7

source_name: Surgical margin (SM) sample #7


title: Mimic 30d treated embryos biological replicate 2


title: MCAM analysis of GC8

source_name: Gastric cancer (GC) sample #8

source_name: Surgical margin (SM) sample #8


title: NCCIT - EC cell line

status: Public on Jun 01 2014

city: Rotterdam

first: Martin

middle: Anne

last: Rijlaarsdam

address: Wytemaweg 80

department: Pathology

institute: Erasmus MC

hyb_protocol: The bisulfite converted DNA was processed and hybridized to the HumanMethylation450 BeadChip (Illumina, Inc.), according to the manufacturer's instructions.

scan_protocol: The BeadChip images were scanned on the iScan system and the data was extracted into GenomeStudio software v2011.1, using default analysis settings.

data_processing: Further processing was carried out in R using the LUMI package [1] following the optimized “lumi: QN+BMIQ” pipeline [2] This includes exclusion of poorly performing probes (p<0.01), color adjustment, quantile normalization and correction for probe type bias (Infinium I vs II) using the BMIQ algorithm [3].  1. Du, P., W.A. Kibbe, and S.M. Lin, lumi: a pipeline for processing Illumina microarray. Bioinformatics, 2008. 24(13): p. 1547-8.  2. Marabita, F., et al., An evaluation of analysis pipelines for DNA methylation profiling using the Illumina HumanMethylation450 BeadChip platform. Epigenetics, 2013. 8(3): p. 333-46.  3. Teschendorff, A.E., et al., A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data. Bioinformatics, 2013. 29(2): p. 189-96.

source_name: mediastinal germ cell tumor (embryonal carcinoma) (Teshima et al. 1988)

label_protocol: Bisulfite conversion was performed using 500 ng genomic DNA input using the EZ DNA Methylation Gold Kit (Zymo Research).

growth_protocol: Cells (wild type) were cultured in DMEM medium (Life Technologies, #31966-021) containing 10% fetal calf serum (FCS, Hyclone) in T75 cm2 flasks to 75-90% confluence.

extract_protocol: DNA was isolated using the DNeasy kit according to manufacturer’s instructions (QIAGEN, cat nr. 69504).

tag: histological_subtype_primary tumor

value: non-seminoma including an embryonal carcinoma component

tag: anatomical localisation

value: mediastinum

tag: cell line

value: NCCIT


title: TCam-2 - SE cell line

source_name: testicular seminoma (Mizuno et al, 1993, de Jong et al,2008)

value: seminoma

value: testis


title: 7878191070_R05C01 (batch2)

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing:
BeadStudio software
Raw data was processed using the Illumina GenomeStudio software (version 2010.3). Background correction and color normalization were performed using the R package minfi version 1.2.0 and normalization using Subset-quantile Within Array Normalization (SWAN). Probes were excluded from further analysis if >95% samples had detection p-value >0.01.
Raw data (Unmethylated and methylated signal intensities) linked as supplementary files on Series record.

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified with standard methods

tag: diagnosis

value: Control

tag: gender

value: FEMALE

tag: race

value: Caucasian

tag: age

tag: batch

value: Peripheral Blood


title: 7878191070_R06C02 (batch2)

value: UNKNOWN

value: Chinese


title: 7878191070_R05C02 (batch2)


title: 7970376110_R06C01 (batch2)

value: White


title: 7878191070_R04C01 (batch2)

value: FTD

value: Other Asian


title: 7878191070_R06C01 (batch2)


title: 7878191070_R04C02 (batch2)


title: 7878191070_R02C01 (batch2)


title: 7878191070_R02C02 (batch2)

value: MALE


title: 6229050017_R05C02 (batch2)


title: 6229050017_R05C01 (batch2)

value: AD


title: 7970376110_R06C02 (batch2)


title: 7970376110_R03C01 (batch2)


title: 6229050017_R06C02 (batch2)


title: 7970376110_R05C02 (batch2)


title: 7878191070_R03C01 (batch2)


title: 7878191070_R01C01 (batch2)


title: 7970376110_R01C01 (batch2)


title: 7970376110_R04C01 (batch2)


title: 7970376110_R02C02 (batch2)


title: 6229050017_R06C01 (batch2)


title: 7878191070_R03C02 (batch2)


title: 7970376110_R03C02 (batch2)


title: 7878191070_R01C02 (batch2)


title: 7970376110_R05C01 (batch2)

value: CBD


title: 6229050017_R04C02 (batch2)


title: 7970376110_R04C02 (batch2)


title: 7970376110_R02C01 (batch2)


title: 7970376110_R01C02 (batch2)


title: 6229050017_R04C01 (batch2)


title: 6229050017_R03C02 (batch2)


title: 6229050017_R02C01 (batch2)


title: 6229050017_R01C02 (batch2)


title: 6229050017_R02C02 (batch2)


title: 6229050017_R03C01 (batch2)


title: 7668610098_R05C02 (batch2)


title: 7668610098_R02C02 (batch2)


title: 6229050017_R01C01 (batch2)


title: 7668610127_R04C01 (batch2)


title: 7668610098_R04C01 (batch2)


title: 7668610127_R06C02 (batch2)


title: 7668610098_R01C01 (batch2)


title: 7668610098_R04C02 (batch2)


title: 7668610098_R06C02 (batch2)

value: White (Hispanic)


title: 7668610127_R03C01 (batch2)


title: 7668610098_R06C01 (batch2)

value: Unknown


title: 7668610127_R05C01 (batch2)

value: FTD/MND


title: 7668610127_R03C02 (batch2)


title: 7668610127_R02C02 (batch2)


title: 7668610127_R05C02 (batch2)


title: 7668610098_R03C02 (batch2)

value: Other Race


title: 7668610098_R05C01 (batch2)


title: 7668610127_R01C02 (batch2)


title: 7668610127_R04C02 (batch2)


title: 7668610127_R02C01 (batch2)


title: 7970376099_R06C01 (batch2)


title: 7668610098_R03C01 (batch2)


title: 7970376099_R06C02 (batch2)


title: 7970376099_R05C02 (batch2)


title: 7668610127_R01C01 (batch2)


title: 7970376099_R04C01 (batch2)


title: 7970376099_R03C02 (batch2)


title: 7668610098_R02C01 (batch2)


title: 7970376099_R04C02 (batch2)


title: 7970376099_R01C02 (batch2)


title: 7970376111_R05C01 (batch2)


title: 7668610127_R06C01 (batch2)


title: 7970376111_R03C02 (batch2)


title: 7970376099_R03C01 (batch2)


title: 7970376099_R02C02 (batch2)


title: 7970376099_R01C01 (batch2)


title: 7970376111_R05C02 (batch2)


title: 7970376111_R02C01 (batch2)


title: 7970376102_R05C01 (batch2)


title: 7970376099_R02C01 (batch2)


title: 7970376111_R03C01 (batch2)

value: Korean


title: 7970376111_R06C01 (batch2)


title: 7970376111_R01C02 (batch2)

value: Control


title: 7970376111_R01C01 (batch2)

value: FEMALE


title: 7970376111_R06C02 (batch2)


title: 7970376111_R02C02 (batch2)


title: 7970376102_R06C02 (batch2)


title: 7668610098_R01C02 (batch2)


title: 7970376099_R05C01 (batch2)


title: 7970376111_R04C02 (batch2)


title: 7970376102_R03C01 (batch2)


title: 7970376102_R02C02 (batch2)


title: 7970376102_R04C02 (batch2)


title: 7970376102_R02C01 (batch2)

value: PSP


title: 7970376111_R04C01 (batch2)

value: Peripheral Blood


title: 7970376102_R01C02 (batch2)


title: 7970376102_R05C02 (batch2)


title: 7973201133_R05C02 (batch2)

value: UNKNOWN


title: 7973201133_R06C01 (batch2)


title: 7973201133_R04C02 (batch2)


title: 7973201133_R04C01 (batch2)


title: 7970368004_R06C02 (batch2)


title: 7973201133_R03C01 (batch2)


title: 7970376102_R06C01 (batch2)


title: 7970376102_R03C02 (batch2)


title: 7970376102_R04C01 (batch2)


title: 7973201133_R05C01 (batch2)


title: 7973201133_R03C02 (batch2)


title: 7973201133_R02C01 (batch2)


title: 7973201133_R02C02 (batch2)


title: 7970368004_R05C02 (batch2)


title: M270

city: Singapore

first: Chong-Lei

last: Bi

address: #12-02, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive

country: Singapore

institute: Cancer Science Institute Singapore

description: miRNA expression profiling

hyb_protocol: The labeled samples were hybridized to Agilent human microRNA microarray V2 slide for 20hrs at 55°C, 20RPM as per manufacturer's instruction.

scan_protocol: Slides were scanned after washing on the Agilent DNA Microarray Scanner (G2565CA)

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: human ALL samples

label_protocol: For each sample, 100ng of total RNA was dephosphorylated, denatured and labeled with Cy3 according to Agilent miRNA system protocol v2.0 (Agilent Technologies, Santa Clara, CA)

extract_protocol: Trizol

tag: cell type

value: Bone Marrow Mononuclear Cells

tag: clinical state

value: NORMAL


title: M233

description: miRNA expression profiling


title: 7970368004_R05C01 (batch2)

value: FTD

value: White


title: 7973201133_R06C02 (batch2)


title: 7970376102_R01C01 (batch2)

value: Filipino


title: M271

description: miRNA expression profiling


title: 7970368004_R03C02 (batch2)


title: M218

description: miRNA expression profiling


title: M205

description: miRNA expression profiling


title: 7970368004_R04C01 (batch2)


title: 7973201133_R01C01 (batch2)

value: MALE


title: M209

description: miRNA expression profiling


title: KL535

description: miRNA expression profiling


title: 7970368004_R04C02 (batch2)


title: 7970368004_R01C01 (batch2)

value: Chinese


title: R369

description: miRNA expression profiling


title: KL64

description: miRNA expression profiling


title: 7970368004_R02C01 (batch2)


title: 7970368004_R03C01 (batch2)


title: R289

description: miRNA expression profiling


title: 7973201133_R01C02 (batch2)


title: 7973201148_R06C02 (batch2)


title: 7970368004_R02C02 (batch2)


title: M269

description: miRNA expression profiling


title: 7973201148_R06C01 (batch2)

value: AD


title: KL576PB

description: miRNA expression profiling


title: KL582

description: miRNA expression profiling

value: HIGHMRD


title: KL417PB

description: miRNA expression profiling


title: 7973201148_R05C01 (batch2)

value: Asian Indian


title: 7973201148_R05C02 (batch2)


title: 7970368004_R01C02 (batch2)


title: KL450PB

description: miRNA expression profiling


title: 7970368004_R06C01 (batch2)


title: KKH13

description: miRNA expression profiling

value: NOT DETECTED


title: 7973201148_R04C02 (batch2)


title: 7973201148_R02C02 (batch2)


title: KL322

description: miRNA expression profiling


title: 7973201148_R01C01 (batch2)


title: R203

description: miRNA expression profiling


title: 7973201148_R02C01 (batch2)


title: 7973201148_R01C02 (batch2)


title: R282

description: miRNA expression profiling


title: 7970368095_R04C02 (batch2)


title: wild type, replicate 5

city: Vicksburg

first: Natalia

last: Vinas

state: MS

address: 3909 Halls Ferry Rd

institute: Mississippi State University

hyb_protocol: 500 ng of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the custom-designed Agilent test array for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), 30 seconds with Acetonitrile, and dried with Agilent Stabilization and Drying Solution.

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

data_processing: The scanned images were analyzed withFeature extraction (Agilent) using default parameters and Agilient-provided GEML grid file 036574_D_F_20110917.xml to obtain signal intensities. GeneSpring GX (Agilent Technologies) was used to normalize data by quantile normalizaton and baseline transformation to the median of all samples. Statistical analysis was also performed in GeneSpring utilizing data from all microarray probes and consisted of one-way ANOVA to test for significant differential expression of microarray targets.

organism: Pimephales promelas

source_name: cell culture

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.4 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Replicate confluent monolayers of fathead minnow (Pimephales promelas) cells grown on 35 mm dishes

extract_protocol: Qiagen Rneasy

treatment_protocol: Cells were mock-infected or infected with wt- or ∆18K-FV3 at a MOI of 10 PFU/cell.

tag: cell line (p. promelas)

value: epithelial cell line FHM

tag: infection (frog virus 3)

value: wild type FV3


title: R205

description: miRNA expression profiling


title: 7973201148_R04C01 (batch2)


title: 7970368095_R06C02 (batch2)

value: Control


title: R259

description: miRNA expression profiling

value: HYPERDIPLOID


title: 7973201148_R03C02 (batch2)

value: FEMALE

value: Peripheral Blood


title: 7970368095_R01C01 (batch2)


title: 7970368095_R02C02 (batch2)


title: R494

description: miRNA expression profiling

value: Bone Marrow Mononuclear Cells


title: wild type, replicate 3


title: 7970368095_R04C01 (batch2)

value: UNKNOWN


title: 7970368095_R02C01 (batch2)

value: FTD


title: 7973201148_R03C01 (batch2)

value: White


title: 7970368095_R05C01 (batch2)


title: wild type, replicate 4


title: 7970368095_R06C01 (batch2)


title: 7970368095_R03C02 (batch2)


title: 7970368095_R03C01 (batch2)


title: 7970368095_R01C02 (batch2)


title: 7973201121_R06C02 (batch2)


title: wild type, replicate 2


title: 7973201121_R05C01 (batch2)


title: 7973201121_R04C02 (batch2)


title: R211

description: miRNA expression profiling


title: R245

description: miRNA expression profiling


title: wild type, replicate 1


title: R310

description: miRNA expression profiling


title: mock control, replicate 6

value: mock control


title: R252

description: miRNA expression profiling


title: R431

description: miRNA expression profiling


title: 7973201121_R06C01 (batch2)

value: MALE


title: 7970368095_R05C02 (batch2)


title: 7973201121_R04C01 (batch2)


title: 7973201121_R05C02 (batch2)

value: Chinese


title: R313

description: miRNA expression profiling


title: 7973201121_R03C02 (batch2)


title: mock control, replicate 4


title: R283

description: miRNA expression profiling


title: 7973201121_R02C02 (batch2)


title: mock control, replicate 3


title: 7973201121_R01C02 (batch2)


title: mock control, replicate 1


title: mock control, replicate 5


title: R314

description: miRNA expression profiling


title: 18K mutant, replicate 5

value: 18K knockout mutant FV3


title: mock control, replicate 2


title: R332

description: miRNA expression profiling


title: 7973201121_R03C01 (batch2)


title: R337

description: miRNA expression profiling


title: 7973201121_R01C01 (batch2)


title: 6229050009_R05C02 (batch2)


title: 7973201121_R02C01 (batch2)


title: 18K mutant, replicate 3


title: 6229050009_R04C02 (batch2)


title: 18K mutant, replicate 4


title: KKH18

description: miRNA expression profiling


title: KKH20

description: miRNA expression profiling


title: KKH27

description: miRNA expression profiling


title: 6229050009_R03C01 (batch2)

value: FTD/MND


title: 6229050009_R06C02 (batch2)

value: Filipino


title: 6229050009_R03C02 (batch2)


title: 6229050009_R04C01 (batch2)


title: 6229050009_R01C01 (batch2)


title: 18K mutant, replicate 1


title: 6229050018_R06C02 (batch2)


title: 6229050009_R01C02 (batch2)


title: 6229050009_R06C01 (batch2)

value: AD


title: 6229050018_R05C01 (batch2)


title: 6229050009_R02C01 (batch2)


title: 6229050009_R02C02 (batch2)


title: 6229050009_R05C01 (batch2)


title: 18K mutant, replicate 2

value: epithelial cell line FHM


title: KKH21

description: miRNA expression profiling


title: KKH28

description: miRNA expression profiling


title: 6229050018_R04C02 (batch2)


title: 6229050018_R05C02 (batch2)


title: KKH19

description: miRNA expression profiling


title: KL299

description: miRNA expression profiling


title: 6229050018_R06C01 (batch2)


title: KL262

description: miRNA expression profiling


title: 6229050018_R02C01 (batch2)


title: 6229050018_R03C01 (batch2)


title: 6229050018_R04C01 (batch2)


title: R240

description: miRNA expression profiling

value: HIGHMRD


title: KL441

description: miRNA expression profiling


title: KL596

description: miRNA expression profiling


title: 6229050018_R03C02 (batch2)

value: Control


title: 6229050033_R05C01 (batch2)


title: 6229050018_R01C01 (batch2)

value: Hispanic


title: 6229050018_R01C02 (batch2)


title: KL585

description: miRNA expression profiling


title: GHP7/7_H3K4me2

city: Paris

first: Celine

last: Morey

address: 35 rue Hélène Brion

department: University Paris 7

country: France

institute: UMR7216-Epigenetics and stem cell

description: Sample 12

hyb_protocol: Hybridisation was performed by NimbleGen (http://www.nimblegen.com/products/chip/)

scan_protocol: Scanning was performed by NimbleGen (http://www.nimblegen.com/products/chip/)

data_processing: Reproducibility and quality control of the data were assessed using the “R” software combined with an algorithm especially developed for ChIP-on-Chip data analysis of histone modifications (http://www.epigenome-noe.net/WWW/researchtools/protocol.php?protid=43). Briefly, the global hybridisation patterns across each array were controlled by MA-plotting of all the probe signals on the array and by calculating the Pearson correlation coefficients between pairs of replicates (all the coefficients were > 0.8). The two replicates showing the highest Pearson correlation coefficient were used for further analysis. We applied a Lowess normalisation to each dataset and the 'SAM' algorithms to determined statistically enriched probe (Tusher et al., PNAS, 2001). A VSN (variance stabilization) normalisation of each array was also performed independently, then a SAM algorithm and a lfdr > 0,2 (local false discovery rate probability test) to determine the significance of enrichment of each probel were applied (data not included in this submission but available upon request).

label_protocol: Labelling was performed by NimbleGen using 4 ug of ChIP DNA and 4 ug of Input DNA (http://www.nimblegen.com/products/chip/tutorial.html)

extract_protocol: Chromatin was fixed in 1% formaldehyde for 10 min, sheared to 200-700 bp using a Bioruptor (Diagenode). It was immunoprecipitated using the indicated antibody. Genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input by phenol extraction and ethanol precipitation. The ChIP material was amplified using whole genome amplification (WGA-2, SIGMA). For detailed protocol see (Navarro et al., Genes Dev, 2005).

treatment_protocol: No treatment

tag: genotype/variation

value: XWT/Y

value: male

value: Extra-embryonic endoderm Stem cells isolated from E3.5 blastocysts

tag: chip antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #

source_name: input DNA from wildtype male XEN cells H3K4me2 ChIP DNA

value: none, input DNA


title: 6229050033_R05C02 (batch2)

tag: tissue

value: Peripheral Blood


title: 6229050033_R01C02 (batch2)

value: FEMALE

value: White


title: 6229050033_R02C01 (batch2)

value: FTD

value: MALE


title: 6229050033_R04C02 (batch2)

value: UNKNOWN


title: 6229050033_R06C01 (batch2)


title: GHP7/9_H3K4me2_rep1

description: Sample 13

tag: strain

value: XHprt-/XWT

value: female

source_name: input DNA from wildtype female XEN cells H3K4me2 ChIP DNA


title: 6229050033_R03C02 (batch2)


title: 6229050033_R03C01 (batch2)


title: GHP7/9_H3K4me2_rep2

description: Sample 14

source_name: wildtype female XEN cells H3K4me2 ChIP DNA


title: 6229050033_R02C02 (batch2)

value: Mexican


title: F3_H3K4me2_rep1

description: Sample 10

source_name: wildtype male TS cells H3K4me2 ChIP DNA

value: Trophoblast Stem cells isolated from E3.5 blastocysts

source_name: input DNA from wildtype male TS cells H3K4me2 ChIP DNA


title: 6229050018_R02C02 (batch2)

value: Control


title: KKH38

description: miRNA expression profiling

value: Bone Marrow Mononuclear Cells

value: HIGHMRD


title: KL541

description: miRNA expression profiling

value: HYPERDIPLOID


title: F3_H3K4me2_rep2

description: Sample 11

source_name: input DNA from wildtype female TS cells H3K4me2 ChIP DNA


title: 6229050033_R04C01 (batch2)


title: 7512560139_R05C02 (batch1)


title: 6229050033_R01C01 (batch2)

value: Japanese


title: 7512560139_R06C01 (batch1)

value: Hispanic


title: 7512560139_R06C02 (batch1)


title: KL520

description: miRNA expression profiling


title: KL544

description: miRNA expression profiling


title: 7512560139_R05C01 (batch1)

value: Chinese


title: KL218

description: miRNA expression profiling


title: F2_H3K4me2

description: Sample 9

value: XHprt-/Y

value: male

value: Abcam

value: none, input DNA


title: R410

description: miRNA expression profiling


title: 7512560139_R03C02 (batch1)

value: MALE

value: White

value: Peripheral Blood


title: 7512560139_R04C02 (batch1)

value: FEMALE


title: GHP7/7_H3K27me3_rep2

description: Sample 6

value: XWT/Y

value: Extra-embryonic endoderm Stem cells isolated from E3.5 blastocysts

value: Millipore

source_name: input DNA from wildtype male XEN cells H3K27me3 ChIP DNA


title: GHP7/9_H3K27me3_rep2

description: Sample 8

value: XWT/XHprt-

value: female

source_name: input DNA from wildtype female XEN cells H3K27me3 ChIP DNA


title: 7512560139_R01C02 (batch1)

value: Control


title: 7512560139_R03C01 (batch1)


title: 7512560139_R02C01 (batch1)

value: FTD


title: GHP7/9_H3K27me3_rep1

description: Sample 7

source_name: wildtype female XEN cells H3K27me3 ChIP DNA


title: R391

description: miRNA expression profiling

value: Bone Marrow Mononuclear Cells

value: NORMAL


title: M231

description: miRNA expression profiling


title: 20Ent6-081008-a647vsb555

city: Nouzilly

first: Olivier

last: Grépinet

address: Centre de Tours

department: Tours

institute: INRA

description: Enterocytes purified from cecal tissue, 3 weeks post-infection

hyb_protocol: For hybridization, equal amounts of Alexa Fluor 555- and Alexa Fluor 647-labeled probes (120 pmol each) were mixed, dried using a speed-vacuum concentrator, and resuspended in 60 microliters Pronto! Long Oligo/cDNA Hybridization Solution (Corning, Lowell, MA). Probes were then boiled for 5 min and pipetted onto the prehybridized array slide. Hybridization was carried out at 42°C for 16 h in the SlideBooster (Advalytix, Munich, Germany), a hybridization station with an integrated surface acoustic wave microagitation. The slides were then washed according to the Pronto! Universal Hybridization Kit protocol (Corning) and dried by centrifugation.

scan_protocol: The slides were scanned at 532 and 635 nm with a GenePix 4000 B scanner (Axon Instruments) keeping a constant PMT gain for each channel. The GenePix Pro 6.0 software was used to acquire the fluorescent image, align the spots, quantify their intensity and finally export the GenePix report (GPR) files containing spot intensity raw data.

data_processing: All statistical analyses were performed with the R package Limma on the two datasets of twenty slides each. We used a filter so that any spot with a flag value less than -50 did not contribute to the step of normalization. The expression was corrected by the normexp function with an adaptative function of the background correction recommanded in the case of correlation between signal expression and signal background. The expression ratio transformed in log2 was normalized using a print-tip loess regression. For each dataset, we obtained the estimate of fold changes by fitting a linear model taking account biological repetition and dye-swap design. We defined the contrast of interest infected - control and performed the hypothesis tests based on the moderated t-statistic and adjusted the pvalues for multiple testing using the Benjamini and Hochberg's method to control the false discovery rate. Genes were declared differentially expressed if the adjusted pvalues were below a the threshold fixed at 0.1 and the fold change were above +/- 1.5. (i) the main reason for this relatively high variance is the variability between animals (ii) the data have not been normalized across samples as what is done in one-color experiments. The normalization was performed slide by slide (see previous paragraph). (iii) the variance decreases significantly if we use only the flagged data (the table of normalized data contains all the spots of the slides).

label: Alexa Fluor 647

organism: Gallus gallus

label_protocol: Two micrograms of amplified cDNA were fluorescently labeled using the BioPrime Plus Array CGH Indirect Genomic Labeling System (Invitrogen, Carlsbad, CA) according to the manufacturer's instructions.

extract_protocol: Total RNA was isolated from samples stored at -80°C in RLT Plus lysis buffer using RNeasy Plus Mini Kit (Qiagen) which allows removal of genomic DNA contamination using a specially designed column. Approximately 1 to 2 micrograms RNA were obtained for each sample. Amplification was then performed with the QuantiTect Whole Transcriptome Kit (Qiagen), providing 15 to 20 micrograms cDNA from 60 ng RNA.

treatment_protocol: Caeca and caecal tonsils were removed aseptically for quantification of bacterial load and purification of intestinal cells. Briefly, cells were scrapped from the mucosa and dissociated with collagenase H. After several steps of washing and filtration to remove any debris, cell sorting of purified mucosal cells was performed at 4°C using a MoFlo (Beckmann Coulter, Fort Collins, Co, USA) high-speed cell sorter. Enterocytes cells were sorted according to their side scatter and their native green fluorescence analyzed with a 530/40 nm band pass filter. Immediately after cell sorting, cells were centrifuged at 800 g for 10 min at 4°C, resuspended in 350 microliters RLT Plus lysis buffer (Qiagen, Hilden, Germany) and stored at -80°C until use.

tag: chicken line

tag: sample

value: infected

tag: cellular type

value: enterocyte

tag: time pi (weeks)

tag: caeca colonization (logcfu/g)

tag: weight inoculation (g)

tag: weight autopsy (g)

tag: family (father/mother)

label: Alexa Fluor 555

value: control


title: 7512560139_R02C02 (batch1)

tag: diagnosis

tag: gender

tag: race

value: Chinese

tag: age

tag: batch


title: M230

description: miRNA expression profiling

tag: cell type

tag: clinical state


title: 7512560129_R06C02 (batch1)

tag: tissue


title: 7512560139_R01C01 (batch1)

value: FTD/MND

value: MALE


title: 20Ent6-171209-a555vsb647


title: 19Ent6-011008-a555vsb647


title: M148

description: miRNA expression profiling


title: 18Ent6-171209-a555vsb647


title: GHP7/7_H3K27me3_rep1

description: Sample 5

source_name: wildtype male XEN cells H3K27me3 ChIP DNA

tag: strain

tag: genotype/variation

value: male

tag: chip antibody

tag: chip antibody vendor

tag: chip antibody cat. #

value: none, input DNA


title: 7512560129_R02C02 (batch1)

value: White

value: Peripheral Blood


title: KL481

description: miRNA expression profiling

value: HYPERDIPLOID


title: 7512560129_R03C02 (batch1)


title: KL269

description: miRNA expression profiling


title: 18Ent6-011008-a647vsb555

tag: chicken line

tag: sample

tag: cellular type

tag: time pi (weeks)

tag: caeca colonization (logcfu/g)


title: 7512560129_R04C02 (batch1)

tag: diagnosis

tag: gender

value: FEMALE


title: 7512560129_R05C01 (batch1)

tag: race

tag: age


title: 7512560129_R02C01 (batch1)

tag: batch


title: 7512560129_R04C01 (batch1)


title: 17Ent6-171209-a555vsb647

tag: weight inoculation (g)

tag: weight autopsy (g)

tag: family (father/mother)


title: 19Ent6-171209-a647vsb555


title: KL419

description: miRNA expression profiling

tag: cell type

tag: clinical state


title: 7512560129_R06C01 (batch1)

tag: tissue


title: 7512560129_R03C01 (batch1)


title: 7512560129_R01C02 (batch1)


title: 7512560139_R04C01 (batch1)


title: 7512560126_R06C01 (batch1)


title: 17Ent6-011008-a647vsb555


title: KL507

description: miRNA expression profiling


title: 16Ent6-260908-a555vsb647


title: KL84

description: miRNA expression profiling


title: 7512560126_R05C01 (batch1)


title: 7512560129_R05C02 (batch1)


title: KL503

description: miRNA expression profiling


title: 7512560126_R05C02 (batch1)


title: 05Ent6-161209-a647vsb555


title: 16Ent6-161209-a647vsb555


title: 6229050033_R06C02 (batch2)

value: UNKNOWN


title: 7512560126_R06C02 (batch1)

value: Control


title: 7512560126_R04C02 (batch1)

value: FTD


title: KL536

description: miRNA expression profiling

value: Bone Marrow Mononuclear Cells


title: 7512560126_R02C02 (batch1)


title: KL412

description: miRNA expression profiling

value: NOT DETECTED


title: 05Ent6-260908-a555vsb647

value: infected


title: M149

description: miRNA expression profiling

value: NORMAL


title: 04Ent6-260908-a647vsb555

value: enterocyte

value: control


title: 7512560126_R02C01 (batch1)

value: Japanese


title: KL493

description: miRNA expression profiling


title: 04Ent6-161209-a555vsb647


title: 7512560126_R03C01 (batch1)


title: 7512560129_R01C01 (batch1)

value: MALE


title: 7512560126_R04C01 (batch1)


title: 03Ent6-250908-a647vsb555


title: KL543

description: miRNA expression profiling


title: 7512560113_R05C01 (batch1)


title: KL461

description: miRNA expression profiling


title: KL401

description: miRNA expression profiling


title: 7512560126_R01C02 (batch1)


title: KL201

description: miRNA expression profiling

value: UNCERTAIN


title: 7512560113_R05C02 (batch1)


title: 7512560113_R06C02 (batch1)


title: 02Ent6-250908-a555vsb647


title: 7512560126_R01C01 (batch1)


title: 7512560126_R03C02 (batch1)


title: 02Ent6-151209-a647vsb555


title: KL317

description: miRNA expression profiling


title: 01Ent6-151209-a647vsb555


title: 7512560113_R04C01 (batch1)


title: KL439

description: miRNA expression profiling


title: 01Ent6-250908-a555vsb647


title: 7512560113_R01C01 (batch1)

value: Chinese


title: 03Ent6-151209-a555vsb647


title: 7512560113_R04C02 (batch1)

value: White


title: KL444

description: miRNA expression profiling


title: 20EntN-060509-a555vsb647

value: N


title: 7512560113_R03C01 (batch1)

value: Peripheral Blood


title: 7512560113_R02C01 (batch1)

value: FEMALE


title: 7512560113_R01C02 (batch1)


title: 7512560113_R06C01 (batch1)


title: 7512560098_R06C01 (batch1)


title: 19EntN-060509-a647vsb555


title: 20EntN-160708-a647vsb555


title: 7512560098_R05C02 (batch1)


title: 7512560098_R06C02 (batch1)


title: 7512560098_R05C01 (batch1)


title: 7512560113_R03C02 (batch1)


title: KL373

description: miRNA expression profiling


title: 7512560098_R04C02 (batch1)


title: 7512560113_R02C02 (batch1)


title: 7512560098_R03C02 (batch1)


title: 7512560098_R03C01 (batch1)


title: KL339

description: miRNA expression profiling


title: 7512560098_R04C01 (batch1)


title: KL375

description: miRNA expression profiling


title: KL250

description: miRNA expression profiling


title: KL366

description: miRNA expression profiling


title: 17EntN-060509-a555vsb647


title: 7512560098_R01C02 (batch1)


title: 17EntN-040708-a647vsb555


title: 7512560096_R06C01 (batch1)


title: 7512560098_R02C01 (batch1)


title: 19EntN-050908-a555vsb647


title: 7512560096_R06C02 (batch1)

value: FTD/MND


title: KL504

description: miRNA expression profiling


title: 7512560096_R05C02 (batch1)


title: 16EntN-290409-a555vsb647


title: 16EntN-160708-a647vsb555


title: 18EntN-060509-a555vsb647


title: KL485

description: miRNA expression profiling


title: 24 hpf zebrafish embryos: WT vs MO-Bad injected Replicate 2

city: Taipei

first: gen

middle: hwa

last: lin

state: Nankang

address: 128,section2,academia road

department: Institute of Cellular and Organismic Biology

country: Taiwan

institute: Academia Sinica

description: Biological replicate 2 of 2

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent Gene Expression Hybridization Kit) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction (FE) Software (version10.5.1.1).

data_processing: Agilent Feature Extraction Software (v10.5.1.1) was used for background subtraction and LOWESS normalization.

organism: Danio rerio

source_name: MO-Bad

label_protocol: Agilent's Quick Amp Labeling Kit denerates fluorescent cRNA with a sample input RNA 1 μg of total RNA for two-color processing.The method uses T7 RNA polymerase,which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP.

growth_protocol: The zebrafish were maintained at our own facility in a controlled environment with a 14/10-h light-dark cycle at 28 °C.  The fertilized eggs were collected at the 1-cell stage.

treatment_protocol: An injection volume from 2-3 nl of MOs was injected into 1-cell-stage embryos.

tag: sample type

value: zebrafish 24hpf morphant

tag: treatment

value: Bad deficiency

value: 24 hpf

value: embryo

source_name: WT

value: zebrafish 24 hpf embryo


title: 7512560096_R03C02 (batch1)

value: Control

value: UNKNOWN


title: 7512560096_R02C01 (batch1)


title: 7512560096_R04C01 (batch1)

value: FTD


title: 7512560096_R03C01 (batch1)


title: 7512560098_R01C01 (batch1)


title: 7512560096_R05C01 (batch1)


title: 7512560096_R04C02 (batch1)


title: 18EntN-040708-a647vsb555

tag: chicken line

tag: sample

value: infected

value: enterocyte

value: control


title: 7512560098_R02C02 (batch1)

value: Chinese


title: 05EntN-290409-a555vsb647

tag: cellular type

tag: time pi (weeks)


title: 24 hpf zebrafish embryos: WT vs MO-Bad injected Replicate 1

description: Biological replicate 1 of 2

value: zebrafish 24 hpf morphant


title: 12 hpf zebrafish embryos: WT vs MO-Bad injected Replicate 2

description: Biological replicate 2 of 2

value: zebrafish 12 hpf morphant

value: 12 hpf

value: zebrafish 12 hpf embryo


title: 12 hpf zebrafish embryos: WT vs MO-Bad injected Replicate 1

description: Biological replicate 1 of 2

value: zebrafish12 hpf embryo


title: 05EntN-040708-a647vsb555

value: N

tag: caeca colonization (logcfu/g)


title: FloraNero-2

city: Montpellier cedex1

first: Jean-Luc

last: Legras

address: 2, place Viala

department: UMR1083, Science pour l'Oenologie

description: analyzed strain (flor)

hyb_protocol: Winzeler2003 Genetics

scan_protocol: Affymetrix scanner

data_processing:
Background substraction with RMA and quantile normalisation and perfect match probe extraction with "apt-1-12-0" (241710 probes)
Then probes are filtered for having coordinates on S288C genome sequence  (Schizosacchaomyces pombe probes are removed), probes are scaled across all arrays.  Probes with signal values below 5 for one of S288C array or aberant values over 10000 3 probes on the whole dataset) are removed. 38864 probes are left.
From the filtered data, for each probe, after averaging the signal  from replicates , the log ratios  otained on are calculated using S288C as a reference . NA values are repalced by -2 hybridization on S288C genome and negative or null for other srains mean no hybridization of the probe)
The average of log ratios are calculated  for three adjacent positions in order to group them three by three in order to  reduce the number of probes (too many probes lead to a crash of DNAcopy). Log ratios are then centered  by substracting the median value.
Discontinuities in hybridization signal are detected with DNAcopy R package.
results file descriptions: RMA-bg quantile intensity file (RMAbackground quantile normalisation-probe intensity file)
results file descriptions: RMA-bgquantil+Saccerecoordinates (RMAbackground quantile normalisation-probe intensity file of Saccharomyces cerevisiae probes + coordinates)
results file descriptions: Log ratios for each probe (chromosome numbering changed from Sace A to 1 as requested by DNAcopy)
results file descriptions: Log ratios after averaging per three probes and centered
results file descriptions: Eg8segments (segments of hybridization found with DNAcopy for Eg8_
results file descriptions: CECT11758segments (segments of hybridization found with DNAcopy for CECT11758)
results file descriptions: Eg25segments (segments of hybridization found with DNAcopy for Eg25)
results file descriptions: FloraNerosegments (segments of hybridization found with DNAcopy for Flora Nero)
results file descriptions: LRJurasegments (segments of hybridization found with DNAcopy for LR Jura)
results file descriptions: MY138segments (segments of hybridization found with DNAcopy for My138)
results file descriptions: P3segments (segments of hybridization found with DNAcopy for P3)
results file descriptions: TA12CUBsegments (segments of hybridization found with DNAcopy for TA12CUB)
results file descriptions: U13segments (segments of hybridization found with DNAcopy for U13)
results file descriptions: V5segments (segments of hybridization found with DNAcopy for V5)

source_name: flor isolate, Sardinia, Italy

growth_protocol: overnight YPD shaken culture 28°

extract_protocol: DNA extraction according to legras et al. 2003 FEMS microbiol letters.

treatment_protocol: no treatment (CGH)

tag: strain

value: FloraNero


title: FloraNero-1

description: analyzed strain (flor)


title: TA12CUB-2

description: analyzed strain (flor)

source_name: flor isolate, Hungary


title: 04EntN-290409-a647vsb555


title: 7512560096_R02C02 (batch1)

tag: diagnosis

tag: gender

value: MALE

tag: race

value: White

value: Peripheral Blood


title: 7512560086_R06C01 (batch1)

tag: age

tag: batch


title: 04EntN-030708-a555vsb647

tag: weight inoculation (g)

tag: weight autopsy (g)

tag: family (father/mother)


title: TA12CUB-1

description: analyzed strain (flor)


title: 7512560096_R01C02 (batch1)

tag: tissue


title: 7512560086_R05C02 (batch1)

value: Control


title: P3-1

description: analyzed strain (flor)

source_name: flor isolate, Jura, France


title: 7512560086_R06C02 (batch1)

value: FEMALE


title: 03EntN-280409-a647vsb555


title: 7512560086_R02C02 (batch1)

value: FTD


title: P3-3

description: analyzed strain (flor)


title: 7512560096_R01C01 (batch1)


title: 01EntN-280409-a647vsb555

value: infected


title: 02EntN-280409-a647vsb555

value: enterocyte


title: 02EntN-030708-a555vsb647

value: control


title: 01EntN-030708-a555vsb647


title: 7512560086_R02C01 (batch1)


title: MY138-3

description: analyzed strain (flor)

source_name: flor isolate, Spain


title: MY138-2

description: analyzed strain (flor)


title: 03EntN-030708-a555vsb647


title: 7512560086_R04C01 (batch1)

value: Chinese


title: S. mutans UA159 parent strain pH5 maltose replicate 3

city: Rochester

first: Roberta

last: Faustoferri

address: 601 Elmwood Ave. Box 611

department: Center for Oral Biology

institute: University of Rochester Medical Center

hyb_protocol: The slides were hybridized in a mixture containing equal amounts of labeled test and reference cDNA as described by the protocol from the Pathogen Functional Genomics Research Center (PFGRC) for 16 h at 42°C in a MAUI hybridization chamber (BioMicro Systems, Salt Lake City, UT).  Hybridized slides were washed and scanned using a GenePix 4000b scanner (Molecular Devices, Inc., Sunnyvale, CA).

scan_protocol: Hybridized slides were washed using the method described by the Pathogen Functional Genomics Research Center (PFGRC) and scanned using a GenePix 4000b scanner (Molecular Devices, Inc., Sunnyvale, CA).

data_processing: Data were analyzed using software available at the J. Craig Venter Institute PFGRC website.  Single-channel images of the slides were loaded into Spotfinder and overlaid.  MIDAS software was used to normalize the spot intensity data using LOWESS and iterative log mean centering with default setting, followed by in-slide replicate analysis.  Statistical analysis was carried out with BRB array tools (http://linus.nci.nih.gov/BRB-ArrayTools.html) with a cutoff P-value of 0.01 and a ≥2-fold change of expression.

organism: Streptococcus mutans UA159

source_name: RNA from parent strain, steady-state pH5, maltose

label_protocol: Once RNA was purified as described above, cDNA was generated from 2µg RNA per sample as described by the protocol available from the Pathogen Functional Genomics Research Center (PFGRC) using Invitrogen Superscript III Reverse Transcriptase (Life Technologies, Carlsbad, CA) to increase cDNA yields.  Purified cDNAs were coupled to Cy3 (experimental samples) or Cy5 (reference cDNA).

growth_protocol: S. mutans UA159 was grown in continuous culture to steady-state pH values of 7and 5 with either glucose or maltose  in a BioFlo2000 fermentor at a dilution rate of 0.144h-1 in non-limiting sugar concentrations.

extract_protocol: RNA was isolated from homogenized S. mutans cells grown in continuous culture in TY + 1% glucose or maltose medium to steady-state pH value of 7 or 5, by repeated hot acid-phenol: chloroform extractions, and the nucleic acid was precipitated with 1 volume ice-cold isopropanol and one-tenth volume 3M sodium acetate (pH 5) at –20°C overnight.  RNA pellets were resuspended in 80 mL nuclease-free H2O, and treated with DNase I (Ambion) at 37°C for 30 minutes.  RNA concentrations were determined using a Nanodrop ND-1000 Spectrophotometer (Thermo Fisher Scientific, Waltham, MA), and 1 µL samples were run on an agarose gel to verify RNA integrity.  The RNA was purified again using the RNeasy mini kit (Qiagen), including a second on-column DNase treatment that was performed as recommended by the supplier.  Final RNA concentrations were determined spectrophotometrically.

tag: genotype

value: parental

tag: ph

tag: sugar

value: maltose

source_name: RNA from parent strain, mid-log

tag: growth phase

value: mid-log


title: S. mutans UA159 parent strain pH5 maltose replicate 2


title: S. mutans UA159 parent strain pH5 maltose replicate 4


title: S. mutans UA159 parent strain pH5 maltose replicate 1


title: synergid cells

city: Glarus

first: Marc

middle: William

last: Schmid

address: Hauptstrasse 34

country: Switzerland

institute: MWSchmid GmbH

description:
RNA amplification with Ambion Message AmpII Kit
synergid_cells1

scan_protocol: GCOS

data_processing:
BgPANP algorith with R/Bioconductor
presence absence p-values with BgPANP

organism: Boechera gunnisoniana

source_name: pool of synergid cells isolated by laser assisted microdissection

label_protocol: During the second round of amplification with the Message AmpII Kit (Ambion), biotin-11-UTP (ambion) was incorporated in th amplified aRNA for microarray analysis.

growth_protocol: Seeds were surface sterilized and grown on MS plates for 10-14 days before transfer to a mixture of soil (ED73, Universalerde, Germany) and sand (5:1) fertilized with Plantomaag (Syngenta, Switzerland) and Osmocote (Scotts, Marysville, USA). Plants were grown in a greenhouse chamber with 60% humidity and 16 h light/ 8 h darkness at 20 °C and 16 °C, respectively.

extract_protocol: For total RNA isolation from cells or tissues isolated by laser assisted microdissection, caps were covered with 10 ul extraction buffer from the PicoPure RNA isolation kit (Arcturus Engineering, Mountain View, USA), incubated at 42°C for 30 min before isolation according to manufacturers instructions. The DNAse treatment was performed on-column using the RNAse-free DNase set (QIAGEN, Hilden, Germany).

treatment_protocol: no treatment

value: female reproductive tissues, germline

tag: cell type

value: synergid cells


title: 7512560086_R05C01 (batch1)


title: 7512560086_R03C01 (batch1)


title: 7512560086_R01C01 (batch1)


title: 7512560086_R03C02 (batch1)


title: LRJura-2

description: analyzed strain (flor)

value: LRJura


title: S. mutans UA159 parent strain pH7 maltose replicate 4

source_name: RNA from parent strain, steady-state pH7, maltose


title: MY138-1

description: analyzed strain (flor)


title: central cell

description:
RNA amplification with Ambion Message AmpII Kit
central_cell1

source_name: pool of central cells isolated by laser assisted microdissection

value: central cell


title: 7512560086_R01C02 (batch1)

value: MALE


title: P3-2

description: analyzed strain (flor)


title: S. mutans UA159 parent strain pH7 maltose replicate 3


title: 7512560082_R06C02 (batch1)


title: egg cell

description:
RNA amplification with Ambion Message AmpII Kit
egg_cell1

source_name: pool of egg cells isolated by laser assisted microdissection

value: egg cell


title: LRJura-1

description: analyzed strain (flor)


title: 7512560082_R06C01 (batch1)

value: White

value: Peripheral Blood


title: S. mutans UA159 parent strain pH7 maltose replicate 2


title: S288C-3  (reanalysis of GSM786822)

source_name: reference strain


title: 7512560082_R05C01 (batch1)


title: sporophytic nucellus tissues 2

description:
RNA amplification with Ambion Message AmpII Kit
sporo_nucellus2

source_name: pool of sporophytic nucellus tissues isolated by laser assisted microdissection

value: sporophytic nucellus


title: 7512560082_R04C01 (batch1)

value: FTD


title: 7512560082_R04C02 (batch1)

value: Control


title: S288C-2  (reanalysis of GSM786821)


title: S. mutans UA159 parent strain pH7 maltose replicate 1


title: S288C-1  (reanalysis of GSM786820)


title: S. mutans UA159 parent strain pH5 glucose replicate 4

source_name: RNA from parent strain, steady-state pH5, glucose

value: glucose


title: sporophytic nucellus tissues 1

description:
RNA amplification with Ambion Message AmpII Kit
sporo_nucellus1


title: CECT11758-2

description: analyzed strain (flor)