title: AR55

status: Public on Oct 31 2016

type: RNA

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

hyb_protocol: Standard Agilent hybridization protocol

scan_protocol: Standard Agilent scanning protocol; raw data were generated using the Feature Extraction Software v10.7.3.1 (Agilent Technologies)

data_processing: The data were processed and quantile normalised  using AgiMicroRna R package (Lopez-Romero P  BMC Genomics. 2011;12:64)

molecule: total RNA

organism: Homo sapiens

source_name: ovarian cancer

label_protocol: Total RNA from each sample was labeled according to the manufacturers recommendations.

extract_protocol: RNA was extracted with QIAGEN FFPE RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

tag: tissue

value: primary ovarian tumor

tag: age

tag: histology

tag: Stage

value: III

tag: grading

tag: dekulking

value: GRD


title: AR53

value: mRD


title: AR56

value: IV


title: AR58


title: AQ55

value: NO


title: AR57


title: AR48


title: AR54


title: AR51


title: AR50


title: AR49

value: NED


title: AR47

value: I


title: AR52


title: AQ68


title: AR44

value: II


title: AQ64


title: AR43


title: AR41


title: AR42


title: AR39


title: AQ31


title: AR37


title: AR35


title: AR32


title: AR34


title: AR30

value: undiff


title: AR33


title: AQ34


title: AR29


title: AQ99


title: AR31


title: AR27


title: AQ46


title: AQ63


title: AR20


title: AQ96


title: AR19


title: AR16


title: AR24


title: AR22


title: AR18


title: AR17


title: AP35


title: AP39


title: AP43


title: AP45


title: AR14


title: AP41


title: AP33


title: AR15


title: AR21


title: AP47


title: AR12


title: AR13


title: AR09


title: AR10


title: AR00


title: AR04


title: AR06


title: AR03


title: AR05


title: AQ33


title: AR07


title: AR01


title: AR08


title: AR11


title: AQ65


title: AR28


title: AQ91


title: AQ90


title: AQ92


title: AQ94


title: AQ93


title: AQ71


title: AR23


title: AQ97


title: AQ87


title: AQ57


title: AQ58


title: AQ78


title: AQ81


title: AQ79


title: AQ88


title: AQ77


title: AQ80


title: AQ76


title: AQ84


title: AQ82


title: AQ74


title: AQ75


title: AQ70


title: AQ72


title: AQ73


title: AQ95


title: AQ69


title: AQ83


title: AQ59


title: AR45


title: AR46


title: AQ98


title: AQ62


title: AQ89


title: Exhausted CD8 T cells from anti-PD-L1 mice after 2 weeks,biological rep4

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

state: PA

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

country: USA

institute: University of Pennsylvania

description:
Expression data from CD8 T cells from anti-PD-L1 treated mice infected with LCMV Cl13 infection
a-PD-L1_4

hyb_protocol: RNA was processed, amplified, labeled, and hybridized to Affymetrix GeneChip  MoGene 2.0 ST microarrays at the University of Pennsylvania Microarray Facility

scan_protocol: Arrays were scanned following manufacturers instructions, by the University of Pennsylvania Microarray Facility

data_processing:
Microarray CEL files were imported and normalized using rma function from bioconductor package oligo
Background adjusted,quantile normalized and summarized signal value by rma,combat

label: biotin

organism: Mus musculus

source_name: Clone13 LCMV infected mice treated with anti-PD-L1

label_protocol: RNA was labeled using the Affymetrix IVT Express kit

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: For LCMV-Cl13 infections,CD4 Tcells were depleted by intraperitoneal injection of 200 ug of anti-CD4 (clone GK1.5, Bio X Cell) on days -1 and +1 post infection with LCMV clone 13. Anti-PD-L1 (clone 10F.9G2, Bio X Cell) or a control (Rat IgG2b, Bio X Cell or PBS) was administered i.p. starting between day 22-25 p.i., 200 ug/injection for five injections every third day for 5 total treatments.

tag: infection

value: Spleen

tag: strain

value: 6-8 weeks

tag: treatment

tag: cell type

value: CD8 T cells


title: AR26


title: AQ85


title: AQ66


title: AQ67


title: Exhausted CD8 T cells from anti-PD-L1 mice after 2 weeks,biological rep2

description:
Expression data from CD8 T cells from anti-PD-L1 treated mice infected with LCMV Cl13 infection
a-PD-L1_2


title: AQ61


title: AQ54


title: Exhausted CD8 T cells from anti-PD-L1 mice after 2 weeks,biological rep1

description:
Expression data from CD8 T cells from anti-PD-L1 treated mice infected with LCMV Cl13 infection
a-PD-L1_1


title: AP37


title: AQ60


title: Exhausted CD8 T cells from control mice after 2 weeks,biological rep2

description:
Expression data from CD8 T cells from control mice infected with LCMV Cl13 infection
Control2

source_name: Clone13 LCMV infected mice with control treatment

value: control


title: Exhausted CD8 T cells from control mice after 2 weeks,biological rep4

description:
Expression data from CD8 T cells from control mice infected with LCMV Cl13 infection
Control4


title: AQ56


title: Exhausted CD8 T cells from control mice after 2 weeks,biological rep3

description:
Expression data from CD8 T cells from control mice infected with LCMV Cl13 infection
Control3


title: AQ25


title: AQ49


title: AQ53


title: AQ50


title: AR59


title: AQ51


title: AQ47


title: AQ86


title: AQ42


title: AQ41


title: AR25


title: AQ37


title: AQ38


title: AQ23


title: AQ39


title: AQ27


title: AQ36


title: TM263

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were processed and normalised using quantile normalisation with BeadStudio software v3.8

label_protocol: RNA from each sample was labeled according to the manufacturers recommendations (Illumina MicroRNA Expression Profiling Assay Guide).

extract_protocol: Tissues were mechanically disrupted and simultaneously homogenized in the presence of TRIzol Lysis reagent and using a dismembrator (Braun Biotech International, Melsungen, Germany). RNA was extracted using the miRNeasy Mini kit (Qiagen) according to manufacturer’s instructions.

tag: debulking


title: AR38


title: TM262


title: AQ43


title: AQ30


title: AQ32


title: Exhausted CD8 T cells from anti-PD-L1 mice after 2 weeks,biological rep3

description:
Expression data from CD8 T cells from anti-PD-L1 treated mice infected with LCMV Cl13 infection
a-PD-L1_3


title: TM261


title: AQ29


title: AR36


title: TM260


title: AQ28


title: AQ35


title: NPC_E12.5_pheno_rep2

city: Toyohashi

first: Toshio

last: Kojima

address: 1-1 Hibarigaoka Tenpaku-cho

department: Health Care Center

country: Japan

institute: Toyohashi University of Technology

hyb_protocol: The labeled cRNAs were purified, fragmented, and hybridized to microarrays in a rotating hybridization oven at 10 rpm for 17 h at 65 °C.

scan_protocol: After hybridization, the microarrays were washed according to the manufacturer’s protocol and scanned on an Agilent DNA Microarray Scanner G2505C with the Scan Control software (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028005_D_F_20110614) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Neural progenitor cells, E12.5, phenobarbital exposed

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low Input Quick Amp Labeling 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.

extract_protocol: Total RNA was isolated from cultured cells using the RNeasy mini kit (Qiagen, Hilden, Germany) with homogenization by the QIAshredder spin column (Qiagen), and On-Column digestion using RNase-free DNase (Qiagen). The purified total RNA was re-purified and concentrated using the RNeasy micro kit (Qiagen).

treatment_protocol: Timed-pregnant C57BL/6N mice (SLC Japan) received two i.p. injections of either saline (control) or 8 mg/mL phenobarbital in saline (80 mg/kg ) twice a day, 6 h apart at E10-11. Cortical tissues of the E12 embryos were mechanically dissociated and plated on 6-well culture plate coated with both 0.0015% (w/v) poly-L-ornithine and 2µg/mL Fibronectin (Wako). The NPCs were maintained at 37°C, 5% (v/v) CO2 and 100% humidity. 4 h after plating, total RNA was isolated and purified from the NPCs.

value: phenobarbital injection

value: cerebral neocortex

value: NPC


title: AR02

value: primary ovarian tumor


title: Exhausted CD8 T cells from control mice after 2 weeks,biological rep1

description:
Expression data from CD8 T cells from control mice infected with LCMV Cl13 infection
Control1


title: NPC_E12.5_cont_rep1

source_name: Neural progenitor cells, E12.5, control


title: NPC_E12.5_pheno_rep3


title: NPC_E12.5_cont_rep3


title: NPC_E12.5_cont_rep2


title: TM257

value: III


title: NPC_E12.5_pheno_rep1


title: TM255

value: GRD


title: TM256


title: AQ40


title: AQ45


title: AQ26


title: AQ21


title: AQ17


title: TM258

value: BL


title: AQ13


title: AQ19

value: IV


title: AQ24


title: AQ15

value: mRD


title: TM259

value: NED


title: AQ11


title: TM251


title: TM250


title: TM252


title: AQ09


title: TM248


title: AQ07


title: TM249


title: TM247


title: AQ03


title: TM245

value: I


title: AQ01


title: TM246


title: AP99


title: TM243


title: AP97


title: TM240


title: AP93


title: TM242


title: TM241


title: TM239


title: AP95


title: AP91


title: TM244


title: TM237


title: AQ05


title: TM236


title: AP81


title: TM235


title: AP77


title: AP79


title: TM234


title: AP89


title: TM238


title: AP75


title: AP85


title: AP71


title: AP73


title: TM233


title: AP83

value: II


title: AP69


title: AP67


title: TM232


title: AP65


title: TM231


title: AP87


title: AP63


title: AP59


title: TM230


title: AP55


title: AP53


title: TM228


title: AP51


title: TM227


title: TM229


title: AP49


title: AP61


title: TM226


title: TM253


title: LLC4_2cPE

city: udine

first: raffaella

last: picco

address: piazzale kolbe 4

department: department of medical and biological sciences

institute: university of Udine

description: Human Chronic lymphocytic leukemia cells  treated with 2cPE

hyb_protocol: Labeled cRNA was hybridized on Affymetrix Human Genome U219 Array.

scan_protocol: The HG-U219 Array Strips (Affymetrix; Santa Clara, CA) hybridization, staining, and scanning were performed by using the GeneAtlas Platform.

data_processing: Data processing was performed with BioConductor packages (http://www.bioconductor.org/), using Brainarray HGU219_Hs_ENTREZG version 18 custom chip definition file. Robust Multi-Array Average (RMA) normalization was applied.Normalized intensity values for all probes on the Affymetrix chip are presented in the Matrix table. Data analysis was performed using the paired t-test as implemented in the R statistical package.  P values were adjusted for multiple testing using the False Discovery Rate method. Differentially expressed genes (DEGs) were selected based on fold change >1.5 and <-1.5 fold and P values <0.05.

source_name: CLL cells - treated with 2cPE, patient LLC4

label_protocol: cDNA synthesis and biotin-labeled target synthesis were performed using the GeneAtlas 3´ IVT Express Kit according to the protocol supplied by Affymetrix.

growth_protocol: Purified peripheral blood cells were cultured in RPMI-1640 medium supplemented with 10% heated inactivated fetal calf serum. Mediums were supplied with penicillin (100 U/mL), glutamine (2 mmol/L), and streptomycin (100 μg/mL).

extract_protocol: Total RNA was isolated using RNeasy Mini kit (Qiagen). RNA samples concentration and purity (assessed as 260/280 nm and 260/230 nm ratios) were evaluated by NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies; Wilmington, DE), while RNA integrity was assessed by using the Agilent 2100 Bioanalyzer (Agilent Technologies; Waldbrunn, Germany).

treatment_protocol: Leukemia CD19+ B-cells from 10 different patients were treated or not for 6 hours with 6nM of bortezomib or with 4µM of 2cPE

tag: patient id

value: chronic lymphocytic leukemia (CLL)


title: LLC43_BORTEZOMIB

description: Human Chronic lymphocytic leukemia cells  treated with Bortezomib

source_name: CLL cells - treated with Bortezomib, patient LLC43


title: TM225


title: LLC43_NT

description: Human Chronic lymphocytic leukemia cells  untreated

source_name: CLL cells - untreated, patient LLC43


title: TM224


title: USCF525 Genomic DNA Control

type: genomic

city: Darlington

first: Tracy

last: Chew

state: NSW

address: Merewether Building (H04) City Rd & Butlin Ave

department: Sydney Informatics Hub

country: Australia

institute: University of Sydney

description: Parent of USCF516 and USCF519

hyb_protocol: According to the service provider GeneSeek, NE, http://genomics.neogen.com/en/beadchips

data_processing: The processed and raw data files were provided as a service by GeneSeek (Lincoln, NE, USA). The matrix was generated using GSGT Version 1.9.4 using standard protocols.

label: Cy3 and Cy5

molecule: genomic DNA

organism: Canis lupus familiaris

source_name: Whole blood, healthy

extract_protocol: The illustra Nucleon BACC2 kit (GE Healthcare) was used to isolate genomic DNA from EDTA stabilized whole blood

tag: disease state

value: healthy

tag: gender

value: Male


title: USCF526 Genomic DNA Control

scan_protocol: According to the service provider GeneSeek, NE, http://genomics.neogen.com/en/beadchips

value: Female


title: LLC37_NT

source_name: CLL cells - untreated, patient LLC37


title: LLC37_BORTEZOMIB

source_name: CLL cells - treated with Bortezomib, patient LLC37


title: LLC4_NT

source_name: CLL cells - untreated, patient LLC4


title: USCF524 Genomic DNA Control

description: Parent of USCF519

label_protocol: According to the service provider GeneSeek, NE, http://genomics.neogen.com/en/beadchips


title: AP57


title: USCF532 Genomic DNA Control


title: AQ44


title: TM223


title: TM254


title: USCF522 Genomic DNA Control


title: USCF523 Genomic DNA Control


title: TM222


title: TM221


title: LLC37_2cPE

source_name: CLL cells - treated with 2cPE, patient LLC37


title: LLC366_NT

source_name: CLL cells - untreated, patient LLC366


title: USCF518 Genomic DNA Control


title: LLC351_NT

source_name: CLL cells - untreated, patient LLC351


title: USCF521 Genomic DNA Control


title: TM220


title: USCF517 Genomic DNA Control


title: LLC366_2cPE

source_name: CLL cells - treated with 2cPE, patient LLC366


title: LLC366_BORTEZOMIB

source_name: CLL cells - treated with Bortezomib, patient LLC366


title: QGP1_OE1

city: Kurume

first: Yu

last: Ikezono

state: Fukuoka

address: 67 Asahimachi

department: Department of Medicine

institute: Kurume University School of Medicine

description: SAMPLE 2

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v3; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

source_name: QGP1_DCLK1 overexpressed

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: Total RNA was isolated from tissues using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)

treatment_protocol: A DCLK1-expression plasmid was constructed by Myc-DDK-tagged clone of Homo sapiens doublecortin-like kinase, transcript variant 1. (RC217050) And control plasmid was EMX1 (Myc-DDK-tagged)-Human empty spiracles homeobox 1. (RC208006)  The DCLK1-expression plasmid and control  (empty vector) plasmid were transfected into QGP1 cells with Lipofectamine 2000 (Invitrogen) according to the manufacturer’s instruction. And we established QGP1_OE cells stably express DCLK1 and QGP1_NT cells transfected empty vector plasmid, were selected by G418 (400 µg/mL) (Nacalai Tesque).

value: Pancreas

tag: cell line

value: pancreatic neuroendocrine tumor (PNET) cells

tag: transfected with

value: DCLK1 cDNA


title: LLC351_2cPE

source_name: CLL cells - treated with 2cPE, patient LLC351


title: LLC305_NT

source_name: CLL cells - untreated, patient LLC305


title: TM218

source_name: ovarian cancer


title: QGP1_NT1

description: SAMPLE 1

source_name: QGP1_empty vector

value: empty vector


title: LLC270_NT

description: Human Chronic lymphocytic leukemia cells untreated

source_name: CLL cells - untreated, patient LLC270


title: LLC300_NT

source_name: CLL cells - untreated, patient LLC300


title: LLC305_2cPE

source_name: CLL cells - treated with 2cPE, patient LLC305


title: USCF519 Genomic DNA Case

description: PRA, obesity

source_name: Whole blood, affected

value: affected


title: TM217

value: primary ovarian tumor

value: III

value: undiff


title: USCF350 Genomic DNA Control

source_name: Whole blood, healthy


title: USCF520 Genomic DNA Control


title: TM219


title: TM216


title: TM215


title: TM214


title: TM212


title: TM213


title: TM211


title: TM210


title: TM209


title: TM208


title: USCF516 Genomic DNA Case

description: PRA, obesity


title: USCF347 Genomic DNA Control

description: Parent of USCF516


title: LLC122_2cPE

source_name: CLL cells - treated with 2cPE, patient LLC122


title: LLC270_2cPE

source_name: CLL cells - treated with 2cPE, patient LLC270


title: LLC195_2cPE

source_name: CLL cells - treated with 2cPE, patient LLC195


title: LLC122_NT

source_name: CLL cells - untreated, patient LLC122


title: LLC195_BORTEZOMIB

source_name: CLL cells - treated with Bortezomib, patient LLC195


title: LLC43_2cPE

source_name: CLL cells - treated with 2cPE, patient LLC43


title: TM207


title: LLC195_NT

source_name: CLL cells - untreated, patient LLC195


title: CR41_532

city: Jeonju

first: Chang-Kug

last: Kim

address: 370, Nongsaengmyeong-ro

department: Genomics Division

country: South Korea

institute: National Institute of Agricultural Sciences (NAS)

description: expression analysis of chinese cabbage (B.rapa ssp. pekinensis), Man-Su : cold stress conditions 120 minutes

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.).

organism: Brassica rapa subsp. pekinensis

source_name: Total RNAs of Man-Su_120minutes

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

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen).

tag: genotype

value: Man-Su

value: cold stress 120 min


title: LLC270_BORTEZOMIB

source_name: CLL cells - treated with Bortezomib, patient LLC270


title: CR31_532

description: expression analysis of chinese cabbage (B.rapa ssp. pekinensis), Man-Su : cold stress conditions 60 minutes

source_name: Total RNAs of Man-Su_60minutes

value: cold stress 60 min


title: CR11_532

description: expression analysis of chinese cabbage (B.rapa ssp. pekinensis), Man-Su : cold stress conditions 15 minutes

source_name: Total RNAs of Man-Su_15minutes

value: cold stress 15 min


title: CR21_532

description: expression analysis of chinese cabbage (B.rapa ssp. pekinensis), Man-Su : cold stress conditions 30 minutes

source_name: Total RNAs of Man-Su_30minutes

value: cold stress 30 min


title: CC31_532

description: expression analysis of chinese cabbage (B.rapa ssp. pekinensis), Shin-Hong : cold stress conditions 60 minutes

source_name: Total RNAs of Shin-Hong_60minutes

value: Shin-Hong


title: CC21_532

description: expression analysis of chinese cabbage (B.rapa ssp. pekinensis), Shin-Hong : cold stress conditions 30 minutes

source_name: Total RNAs of Shin-Hong_30minutes


title: 3 pooled mutant PSM E9.5 biological rep3

city: Illkirch

first: Stephane

middle: D

last: VINCENT

address: 1 rue Laurent Fries

department: Development and Stem Cells

country: France

institute: IGBMC

description: gene expression data from E9.5 PSM

hyb_protocol: Following fragmentation and end-labeling, 1.9 μg of cDNAs were hybridized for 16 hours at 45oC on GeneChip® Mouse Gene 1.0 ST arrays (Affymetrix). The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix)

scan_protocol: Microarrays were scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 0.7 µm.

data_processing: Normalization was performed with Bioconductor (RMA background correction, quantile normalization and median polish summarization). Data were then  filtrated based on 3 times the 100th lowest value as threshold and finally by removing manually all the pseudogenes and expressed sequences (after filtration, 18064 out of 34760 probesets (51.9%) remained).Statistical analysis was performed using the FCROS package  version 1.1 (Dembele and Kastner, BMC Bioinformatics, 2014, 15:14)

source_name: microdissected presomitic mesoderm from E9.5 embryo

label_protocol: Biotinylated single strand cDNA targets were prepared, starting from 150 ng of total RNA, using the Ambion WT Expression Kit (Cat # 4411974) and the Affymetrix GeneChip® WT Terminal Labeling Kit (Cat # 900671) according to Affymetrix recommendations.

growth_protocol: embryos were dissected at E9.5

extract_protocol: Total RNA was prepared with TRIzol (Invitrogen).

treatment_protocol: PSM were microdissected with pancreatin and tungsten needles and individually lysed in 200µl TRIzol and yolk sac was used for genotyping

tag: tissue

value: presomitic mesoderm

value: mutant (TCre/+;Taf10flox/flox)


title: CC41_532

description: expression analysis of chinese cabbage (B.rapa ssp. pekinensis), Shin-Hong : cold stress conditions 120 minutes

source_name: Total RNAs of Shin-Hong_120minutes


title: TM206

source_name: ovarian cancer

tag: age

value: GRD


title: 3 pooled mutant PSM E9.5 biological rep1

description: gene expression data from E9.5 PSM


title: TM205

tag: histology


title: CC11_532

description: expression analysis of chinese cabbage (B.rapa ssp. pekinensis), Shin-Hong : cold stress conditions 15 minutes

source_name: Total RNAs of Shin-Hong_15minutes


title: 3 pooled mutant PSM E9.5 biological rep2

description: gene expression data from E9.5 PSM


title: 3 pooled control PSM E9.5 biological rep1

description: gene expression data from E9.5 PSM

value: WT (Taf10Flox/+ or Taf10flox/flox)


title: 3 pooled control PSM E9.5 biological rep3

description: gene expression data from E9.5 PSM


title: TM203

tag: Stage

value: NED


title: 3 pooled control PSM E9.5 biological rep2

description: gene expression data from E9.5 PSM


title: AR1_1_532

description: expression analysis of chinese cabbage (B.rapa ssp. pekinensis), Shin-Hong Wild type: cold stress conditions

source_name: Total RNAs of Shin-Hong

value: normal


title: TM202

tag: grading


title: TM201


title: TM204

value: mRD


title: TM200


title: Aspergillus fumigatus 4hr vs 6hr biological replicate 2

city: Higashihiroshima

first: Ken

last: Oda

state: Hiroshima

address: 3-7-1 Kagamiyama

department: Fundamental research division

institute: National research institute of brewing

description:
Analysis used isotropically expanding cell's RNA as control samples for comparison to the experimental samples taken at 6 and 8hr.
Sample 11

hyb_protocol: The resulting labeled cDNA was hybridized to an A. fumigatus glass slide microarray spotted with 70-mers representing all predicted open frames (PFGRC/TIGR A. fumigatus microarray, version 3; a full description and annotation are available at Gene Expression Omnibus [accession no. GPL5346; http://www.ncbi.nlm.nih.gov/geo/ ] according to the standard J.C.V.I. protocol (SOP M0008).

scan_protocol: The slides were scanned at 10um resolution and 85% laser power using a Perkin-Elmer ScanArray microarray scanner.

data_processing: The resulting tagged-image format file images were imported into TIGR Spotfinder (version 3.1.1). Raw intensities were calculated for each detectable spot using the Otsu method, and quality control filtering was used to eliminate values from spots with poor morphology or low signal-to-noise ratios. The resulting intensities were then imported into TIGR MIDAS (version 2.20), and spots with values of <10,000 were removed from the data set by using the low intensity filter. Normalization was done using the LOWESS (Locifit) algorithm (global mode; 0.33 smoothing parameter), and print tip bias was addressed by using standard deviation regularization. The dye swap consistency filter was used to remove data for genes with inconsistent expression levels between dye swap replicates. Finally, the in-slide replicate function was used to average the normalized intensity values representing replicate spots on the array.

organism: Aspergillus fumigatus

source_name: 4hr isotropically expanding cells

label_protocol: cDNA synthesis and indirect Cy dye incorporation were performed using the standard J. Craig Venter Institute (J.C.V.I.) protocol (standard operating procedure [SOP] M007) with the following modifications: Six micrograms of total RNA was used in the first-strand cDNA reaction with a 3:1 aminoallyl-dUTP to dTTP ratio. Dried aminoallyl labeled cDNA was resuspened in 9 ml of 50 mM sodium carbonate (pH9.0) and added directly to the appropriate dye vial from the Amersham CyDye postlabeling reactive dye pack (RPN5661).

growth_protocol: Flasks containing 150 ml complete medium were inoculated with conidia to a final concentration of 3.0 x10^6 / ml and incubated for 0, 1, 2, 4, 6, and 8hr at 37°C with constant shaking (220 rpm). Following incubation, cells were harvested using a Steritop filter (Millipore), frozen, ground with liquid nitrogen.

extract_protocol: RNA was purified with TRIzol (Invitrogen) and the RNeasy MiniElute Clean up kit (Qiagen) according to the manufacturers’ instructions.

treatment_protocol: The strain was cultured on CM agar (0.6% NaNO3, 0.052% KCl, 0.052% MgSO4・7H2O, 0.152% KH2PO4, 0.1% Glucose, 0.2% Peptone, 0.1% Yeast Extract, 0.1% Casamino acid, 0.0001% Biotin, 0.0001% Pyridoxine, 0.0001% Thiamine, 0.0001% Riboflavin, 0.0001% ƿ-aminobenzoic acid, 0.0001% Nicotinic acid and trace elements).

source_name: 6hr polarity extending cells


title: Aspergillus fumigatus 4hr vs 6hr biological replicate 1

description:
Analysis used isotropically expanding cell's RNA as control samples for comparison to the experimental samples taken at 6 and 8hr.
Sample 10


title: TM199


title: Control sample #1 vs SMB-overexpression #1

city: Ikoma

first: Keiji

last: Nakajima

state: Nara

address: 8916-5 Takayama

department: Graduate School of Biological Sciences

institute: Nara Institute of Science and Technology

hyb_protocol: Labelled cRNA targets were hybridized with the microarrays at 65C for 17 hours with agitation.

scan_protocol: Scanned on an Agilent G2505C scanner at 5 micro m resolution.

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and Lowess normalization.

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana roots

label_protocol: Labeling was carried out with Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions.

growth_protocol: Sterilized Arabidopsis seeds were plated on nutrient agar medium and grown at 23 ˚C with 16h-light/8h-dark cycle. Plants were grown for 2 days after germination. For comparison between the SMB-overexpressing root and the control roots, plants were treated for the Dexamethason (DEX) inducer for 17 hours.

extract_protocol: Root tips of about 1 cm long were harvested and used to extract total RNAs by the RNeasy Plant Minikit (Invitrogen).

treatment_protocol: For comparison of the transcriptomes between the SMB-overexpresser and the control plants, seedlings were grown under normal conditions for 2 days after germination and then transferred to the medium containing the dexamethasone (DEX) inducer and grown for 17 hours.

tag: genotype/variation

value: Control (35S-GVG)

tag: ecotype

value: Root tip

value: SMB-overexpresser (UAS-SMB 35S-GVG)


title: Aspergillus fumigatus 0hr vs 4hr biological replicate 2

description:
Analysis used domant conidia RNA as control samples for comparison to the experimental samples taken at 1, 2, and 4hr.
Sample 8

source_name: 0hr dormant cells

tag: strain


title: SMB-over expression #2 vs Control sample #2


title: AC1_1_532

description: expression analysis of chinese cabbage (B.rapa ssp. pekinensis), Man-Su Wild type : cold stress conditions

source_name: Total RNAs of Man-Su

tag: treatment


title: Aspergillus fumigatus 0hr vs 4hr biological replicate 1

description:
Analysis used domant conidia RNA as control samples for comparison to the experimental samples taken at 1, 2, and 4hr.
Sample 7


title: C_S_CD8_9371989071_F.mean

city: Heidelberg

first: Markus

last: Feuerer

state: Baden-Württemberg

address: Im Neuenheimer Feld 280

department: Tumor Immunology

country: Germany

institute: DKFZ

description:
SAMPLE 18
9371989071

hyb_protocol: 1.5 µg of cDNA were hybridized for 17hrs at 55.4 °C on Illumina Mouse WG-6-Microarray

scan_protocol: Illumina iSCAN-Scanner according to Std Illumina Scanning Protocol Part # 11322355 (Whole-Genome Gene Expression Direct Hybridization Assay Guide). Microarray scanning was done using an iScan array scanner

data_processing: Microarray scanning was done using an iScan array scanner. Data extraction was done for all beads individually, and outliers are removed when the absolute difference to the median is greater than 2.5 times MAD(2.5 Hampelís method). All remaining bead level data points are than quantile normalized [1]. As test for significance the studentís t-test is used on the bead expression values of the two groups of interest. In the case of significance of expression against background we tested for greater than all negative beads for this sample and in the case of comparing separate groups we tested for inequality of the means of the groups. In both cases Benjamini-Hochberg correction [2] was applied to the complete set of p-values of all 48107 ProbeIDs on the chip. The average expression value is calculated as mean of the measured expressions of beads together with the standard deviation of the beads. [1] Probe Level Quantile Normalization of High Density Oligonucleotide Array Data, Ben Bolstad, Division of Biostatistics, University of California, Berkeley December 2001. [2] Y. Benjamini and Y. Hochberg (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society B, Vol. 57, 289ñ300.

label_protocol: The NuGEN Ovation Pico WTA System (linear isothermal DNA amplification process) was used to generate single-stranded cDNA from small input amounts of 2.5 ng RNA. Labeled cRNA was prepared according to Nugene Encore BiotinIL Module.

extract_protocol: Tumors and spleen were harvested when tumor size were about 10mm diameter

treatment_protocol: Mice were injected s.c. with 50,000 B16F10 melanoma cells

value: female

value: spleen

tag: cell type

value: CD8+ CD4- CD11b- T cells

tag: replicate


title: C_S_CD4_9371989071_E.mean

description:
SAMPLE 17
9371989071

value: CD4+Foxp3- CD8- CD11b- Tconv


title: TM198

value: primary ovarian tumor

value: III

value: undiff

tag: debulking


title: scramble rep2

city: Bangkok

first: Pattarin

last: TANGTANATAKUL

state: กรุงเทพมหานคร

address: Thoethai Road

country: Thailand

institute: Chulalongkorn University

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

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

data_processing: Array data export processing and analysis was performed using Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0)

source_name: Human mesangial cells

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

growth_protocol: Human mesangial cells were purchased from available company.  The cells (P5-P8) were thaw and culture for 1 passage.  Then the cells (2x105) were trypsinized and culture in transfection medium overnight before start the transfection.

extract_protocol: Total RNAs were extracted using mirVana® microRNA extraction kit.  There are two fractions including small RNA and large RNA which size larger than 200 nt.  The RNA concentration, purity and quality were determined by using Agilent Bioanalyzer and NanoDrop 1000.

treatment_protocol: The miR-10a inhibitor (10 nM) were transfected into primary human mesangial cells (2x105) by Lipofectamine®  RNAiMax reagents for 24 hours.  Then total cells were harvested by trypsinized and washed 2 times in one milliliter DPBS.  The cells were pelleted by 500xg 5 minutes.

value: primary mesangial cells


title: scramble rep3

state: กรุงเทพมหานคร


title: C_S_Treg_9371989071_D.mean

description:
SAMPLE 16
9371989071

value: CD4+CD25+Foxp3+ CD8- CD11b- Treg


title: Triple mutant sample #2 vs Col-0 sample #2

value: smb brn1 brn2 triple mutant

value: Wild-type Col-0


title: Col-0 sample #1  vs  triple mutant sample #1

value: Wild-type


title: TM197


title: genomic DNA from CD3+ blood cell donor T-cell 16

type: SRA

city: Uppsala

first: Jessica

last: Nordlund

address: Box 1432, BMC

department: Department of Medical Sciences

country: Sweden

institute: Uppsala University

library_source: genomic

data_processing:
Bisulfite converted reads were aligned to reference hg19 as in Johnson MD, Mueller M, Game L, Aitman TJ: Single Nucleotide Analysis of Cytosine Methylation by Whole-Genome Shotgun Bisulfite Sequencing. In Current Protocols in Molecular Biology. John Wiley & Sons, Inc.; 2001
BisSNP was used for DNA methylation calling (Liu Y, Siegmund KD, Laird PW, Berman BP: Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data. Genome Biology 2012, 13:R61)
The R-package bsseq (Hansen KD, Langmead B, Irizarry RA: BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions.) was used to smoothen methylation calls from WGBS data, segment data and call differentially methylated regions between sample pairs. To call a segment as a differentially methylated region (DMR) ? 3 consecutive CpG sites and an average difference > 0.3 in the DNA methylation levels between an ALL sample and the control were required. DMRs with an average mapability score (wgEncodeCrgMapabilityAlign100mer, download from UCSC table browser) of < 0.5 across segments and DMRs where the average coverage in any of the compared pair of samples was less than 3 or larger than 50 (except in pooled samples), were removed to ensure that potential mapping errors did not inflate DMR detection.
RNA-seq reads were mapped to the reference genome (human_g1k_v37) using Tophat2 (version 2.0.4) with default settings.
The number of fragments per transcript was calculated from Tophat bam files using the function featureCounts in Rsubread R-package and fragments per transcript per kilobase per million (FPKM) was computed by the function rpkm in the package edgeR. Transcript fragment counts were normalized to log2 counts using the voom function in the limma R-package
Genome_build: hg19
Supplementary_files_format_and_content: cpg site methylation level bedgraph: 4th column is methylation level (0-100) over a CpG dinucleotide
Supplementary_files_format_and_content: cpg site read coverage bedgraph: 4th column is read coverage over a CpG di nucleotide
Supplementary_files_format_and_content: expression bed: name column is ensemble gene id, score column is expression in fpkm
Supplementary_files_format_and_content: normalized expression bed: name column is ensemble gene id, score column is voom normalized expression.
Supplementary_files_format_and_content: [Table_S2_dmrs.txt] list of differentially methylated regions (tab delimited text). Columns are: comparison: samples compared, chr: chromosome, start: start of region, end: end of region, avgdiff(smoothed_meth): average difference in smoothed methylation in region, nCpGsites: number of CpG sites considered in region, rawdiff: average difference in non-smoothed methylation in region.

source_name: Peripheral blood

extract_protocol:
DNA was extracted using the AllPrep DNA/RNA Mini Kit (QIAGEN)
Whole-genome bisulfite sequencing libraries were prepared using the Illumina TruSeq DNA Library preparation kit starting with 1 µg of DNA. End-repair, A-tailing and ligation of adaptors was performed according to the Illumina TruSeq protocol. Subsequent bisulfite conversion of the sequencing libraries was performed using reagents from the EpiTect Bisulfite kit (Qiagen). Bisulfite converted adaptor-ligated fragments were amplified by PCR using Pfu TurboCx Hot-start DNA polymerase (Stratagen).

tag: disease state

value: normal CD3+ cells

tag: immunophenotype

tag: subtype

value: normal


title: LLC300_2cPE

description: Human Chronic lymphocytic leukemia cells  treated with 2cPE

source_name: CLL cells - treated with 2cPE, patient LLC300

tag: patient id

value: chronic lymphocytic leukemia (CLL)


title: C_B16_CD8_9371989071_C.mean

description:
SAMPLE 15
9371989071

tag: gender

value: B16 melanoma


title: genomic DNA from CD3+ blood cell donor T-cell 14


title: TM196

tag: tissue

value: GRD


title: genomic DNA from CD3+ blood cell donor T-cell 15


title: C_B16_Treg_9371989071_A.mean

description:
SAMPLE 13
9371989071

value: female


title: scramble rep1

state: กรุงเทพมหานคร


title: miR10a knockdown rep3

state: กรุงเทพมหานคร


title: genomic DNA from CD3+ blood cell donor T-cell 17


title: miR10a knockdown rep1

state: กรุงเทพมหานคร


title: TM195

tag: age

value: mRD


title: genomic DNA from CD3+ blood cell donor T-cell 12


title: genomic DNA from CD3+ blood cell donor T-cell 13


title: B_S_CD8_9371989058_F.mean

description:
SAMPLE 12
9371989058

value: spleen

value: CD8+ CD4- CD11b- T cells


title: genomic DNA from CD3+ blood cell donor T-cell 11


title: miR10a knockdown rep2

state: กรุงเทพมหานคร


title: C_B16_CD4_9371989071_B.mean

description:
SAMPLE 14
9371989071

value: CD4+Foxp3- CD8- CD11b- Tconv


title: genomic DNA from CD3+ blood cell donor T-cell 10


title: TM194

value: primary ovarian tumor

tag: histology

value: III

value: NED


title: genomic DNA from CD3+ blood cell donor T-cell 8


title: TM193

tag: Stage


title: B_S_CD4_9371989058_E.mean

description:
SAMPLE 11
9371989058


title: LLC122_BORTEZOMIB

description: Human Chronic lymphocytic leukemia cells  treated with Bortezomib

source_name: CLL cells - treated with Bortezomib, patient LLC122


title: genomic DNA from CD3+ blood cell donor T-cell 9


title: B_S_Treg_9371989058_D.mean

description:
SAMPLE 10
9371989058

value: CD4+CD25+Foxp3+ CD8- CD11b- Treg


title: TM192

tag: grading


title: B_B16_CD8_9371989058_C.mean

description:
SAMPLE 9
9371989058

tag: genotype/variation


title: genomic DNA from CD3+ blood cell donor T-cell 7


title: B_B16_CD4_9371989058_B.mean

description:
SAMPLE 8
9371989058


title: genomic DNA from CD3+ blood cell donor T-cell 3


title: genomic DNA from CD3+ blood cell donor T-cell 4


title: B_B16_Treg_9371989058_A.mean

description:
SAMPLE 7
9371989058


title: TM191

value: undiff


title: TM190


title: genomic DNA from CD19+ blood cell donor B-cell 7

value: normal CD19+ cells


title: genomic DNA from CD3+ blood cell donor T-cell 1


title: genomic DNA from CD19+ blood cell donor B-cell 8


title: TM189


title: TM188


title: genomic DNA from CD19+ blood cell donor B-cell 5


title: genomic DNA from CD3+ blood cell donor T-cell 6


title: genomic DNA from CD3+ blood cell donor T-cell 2


title: A_S_CD8_9371989055_F.mean

description:
SAMPLE 6
9371989055


title: genomic DNA from CD19+ blood cell donor B-cell 4


title: A_S_CD4_9371989055_E.mean

description:
SAMPLE 5
9371989055


title: TM187


title: A_B16_CD8_9371989055_C.mean

description:
SAMPLE 3
9371989055


title: TM186

value: I

value: BL


title: genomic DNA from CD19+ blood cell donor B-cell 3

value: normal


title: genomic DNA from CD19+ blood cell donor B-cell 2


title: A_B16_CD4_9371989055_B.mean

description:
SAMPLE 2
9371989055


title: genomic DNA from CD19+ blood cell donor B-cell 6


title: TM184


title: A_S_Treg_9371989055_D.mean

description:
SAMPLE 4
9371989055


title: TM183


title: total RNA from CD3+ blood cell donor 899_T

library_source: transcriptomic

extract_protocol:
RNA was extracted using the AllPrep DNA/RNA Mini Kit (QIAGEN)
Ribosomal RNA was depleted from 1 μg total RNA using Ribozero and strand-specific RNA-seq libraries were constructed with the ScriptSeq V2 Kit (Epicentre).

value: normal CD3+ cells


title: TM185


title: genomic DNA from CD19+ blood cell donor B-cell 1


title: total RNA from CD3+ blood cell donor 867_T


title: SIOD FSGS, biological replicate 3

city: Vancouver

first: Cornelius

middle: F.

last: Boerkoel

state: British Columbia

address: 950 West 28th Avenue

department: Medical Genetics

country: Canada

institute: University of British Columbia

hyb_protocol: Following fragmentation, cRNA was hybridized for on a GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in an Affymetrix GeneChip Fluidics Station according to standard protocols.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with GeneSpring version 13.0 using default analysis settings and RMA (summarziation method) for the normalization method.

label: Biotin

source_name: Cultured renal proximal tubular cells established from kidney biopsy of a patient with SIOD-associated FSGS

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

growth_protocol: Primary renal proximal tubular cells were cultured in DMEM/F-12 supplemented with sodium bicarbonate, 5 μg/ml insulin, 5 μg/ml transferrin, 5 ng/ml selenium, 10 ng/ml epidermal growth factor, 50 nM hydrocortisone, 5 pM triiodothyronine, 50 μM prostaglandin E1, 100 U/ml penicillin, and 100 μg/ml streptomycin at 37°C and 5% carbon dioxide.

extract_protocol: RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer's specifications.

treatment_protocol: Not applicable.

tag: siod disease status

value: SIOD

tag: Sex

value: Female

tag: age at biopsy

value: 4.75 years


title: TM182

value: II


title: A_B16_Treg_9371989055_A.mean

description:
SAMPLE 1
9371989055

tag: strain

value: female

value: B16 melanoma

tag: cell type


title: total RNA from CD3+ blood cell donor 858_T


title: SIOD FSGS, biological replicate 1


title: Non-SIOD FSGS control, biological replicate 2

source_name: Cultured renal proximal tubular cells established from kidney biopsy of a patient with non-SIOD-associated FSGS

value: Unaffected

value: < 10 years


title: TM181

value: primary ovarian tumor

value: III

tag: debulking

value: mRD


title: TM180

value: NED


title: TM179


title: total RNA from CD3+ blood cell donor 845_T

tag: disease state


title: total RNA from CD19+ blood cell donor 899_B

value: normal CD19+ cells

tag: immunophenotype


title: SIOD FSGS, biological replicate 2


title: total RNA from CD3+ blood cell donor 817_T

tag: subtype


title: total RNA from CD19+ blood cell donor 867_B


title: total RNA from CD19+ blood cell donor 858_B


title: TM176


title: total RNA from CD19+ blood cell donor 817_B


title: total RNA from CD19+ blood cell donor 845_B


title: TM175


title: TM174

value: I

value: undiff


title: 48hpf_TCS_rep2

city: Corvallis

first: Robert

middle: L

last: Tanguay

state: OR

department: EMT

institute: Oregon State University

description: Gene expression after 48 hpf exposure to TCS

hyb_protocol: Samples were hybridized to OakLabs ArrayXS Zebrafish microarrays using the Gene Experssion Hybridization Kit (Agilent)

scan_protocol: Slides were scanned after hybridization using the SureScan Microarray Scanner (Agilent)

data_processing: Scanned images were read and processed using Agilent Feature Extraction software (ver 11) and analzed using limma in R. Data were background corrected using the MLE method and then quantile normalized. Prior to linear modeling and differential expression calculation, control probes and any probe that was less than 10% brighter than the negative control probes on at least four of the arrays were excluded from the analysis

organism: Danio rerio

source_name: Whole embryo, 48 hpf, TCS treated, replicate 2

label_protocol: 0.5 ug of Cy3-labeled cRNA was generated using the Low Input Quick Amp WT Labeling Kit (Agilent Technologies, Santa Clara, CA)

extract_protocol: Total RNA was exctracted using the Quick-RNA MiniPrep kit (Zymo Research, Irvine, CA) according to manufacturer's protocols with the optional Dnase I digestion. Whole embryos were homogenized in 300 uL lysis buffer with 0.5 mm zirconium oxide beads using a bullet blender (Next Advance, Averill Park, NY) for 3 min at speed 8.

treatment_protocol: Dechorionated embryos were nominally exposed to statis aqueous concentrations of 7.37 or 0 uM TCS (0.64% DMSO) from 6-48 hpf. Embryos were maintained at 28 °C throughout exposure

value: whole embryo

tag: treatment

value: TCS


title: 48hpf_TCS_rep3

source_name: Whole embryo, 48 hpf, TCS treated, replicate 3


title: Non-SIOD FSGS control, biological replicate 1


title: 48hpf_DMSO_rep1

source_name: Whole embryo, 48 hpf, DMSO control, replicate 1

value: DMSO


title: 48hpf_DMSO_rep4

source_name: Whole embryo, 48 hpf, DMSO control, replicate 4


title: genomic DNA at diagnosis from BCP-ALL patient C2

source_name: Bone Marrow

value: ALL diagnosis

value: BCP-ALL

value: primary acute lymphoblastic leukemia cells


title: genomic DNA at diagnosis from BCP-ALL patient C3


title: TM178

source_name: ovarian cancer


title: TM172

value: II


title: 48hpf_DMSO_rep3

source_name: Whole embryo, 48 hpf, DMSO control, replicate 3


title: TM173


title: TM171


title: genomic DNA at diagnosis from BCP-ALL patient C1


title: TM177


title: total RNA at diagnosis from T-ALL patient P4 replicate 1

value: T-ALL


title: total RNA at diagnosis from BCP-ALL patient P3

value: non-recurrent


title: TM169


title: total RNA at diagnosis from T-ALL patient P4 replicate 2


title: TM168


title: WholeFish 50ng/L  repD5

city: Davis

last: Jeffries

state: CA

address: One Shields Avenue

institute: UC Davis

hyb_protocol: Prior to hybridization, 1.65 µg of dye labeled complementary RNA for each sample was combined with 2.2 µl of 25x fragmentation buffer, 11 µl of 10X Gene Expression Blocking Agent and nuclease-free water to bring the final volume to 55 µl. The fragmentation mix was incubated at 60°C for 30 min, cooled on ice for 1 min, and the fragmentation was stopped by adding 55 µl of 2X Hi-RPM Hybridization Buffer. Samples were centrifuged for 1 min, placed on ice and 100 µl of the mix was loaded onto arrays and each microarray slide was placed in a single hybridization chamber. Individuals from each treatment were randomized between slides and array position on the slide. All samples were hybridized to the arrays (custom designed Agilent 4x44K oligonucleotide microarrays) for 17 h at 65°C, followed by a wash with Gene Expression Wash Buffer 1 (Agilent) at room temperature and a wash with Gene Expression Wash Buffer 2 (Agilent) heated to 37ºC. Slides were scanned immediately after washing.

scan_protocol: Fluorescent images were scanned using an Axon GenePix 4000B Scanner and the analysis software GenePix Pro (Molecular Devices, LLC, Sunnyvale, CA). The images were quantified using Feature Extraction 11.5.1.1 (Agilent Technologies).

data_processing: Normalization of the microarray data was performed in Genespring v12.6 (Agilent Technologies). Probes that had a raw signal less than 80 (~2 times the intensity of the background) were filtered out of the statistical analysis to eliminate sources of background noise, but still retain probes with low intensity. Data was quantile normalized and Log2 transformed prior to statistical analysis, which was performed using TIGR MultiExperiment Viewer.

organism: Menidia beryllina

source_name: WholeFish, 50ng/L bifenthrin exposure

label_protocol: Two hundred ng of total RNA was amplified and labeled with Cy3 using the Low Input Quick Amp Labeling kit (Agilent Technologies). To minimize technical artefacts, labeling reactions were performed simultaneously.  Dye incorporation and cRNA yield were assessed with a NanoDrop Spectrophotometer.

growth_protocol: Menidia beryllina were allowed to acclimatize to holding conditions at the Aquatic Toxicology Laboratory at the University of California Davis.

extract_protocol: At the termination of the 14 d exposure period, fish were sacrificed by a lethal dose of MS-222 and whole fish were immediately frozen in liquid nitrogen and stored at -80°C until RNA extraction. Whole fish from the 14 d exposures were homogenized and RNA was extracted using RNeasy Plus Mini Kits (Qiagen) following manufacturer’s protocols. Concentration and purity (260/280, 260/230) were assessed using a Nanodrop spectrophotometer (Thermo Scientific) and RNA integrity was determined through electrophoresis.

treatment_protocol: Menidia beryllina were exposed for 14 d to nominal concentrations of 0.5, 5 and 50 ng/L of bifenthrin, along with a solvent (methanol) control group handled identically to the other treatments.

value: 50ng/L bifenthrin exposure


title: 48hpf_TCS_rep4

source_name: Whole embryo, 48 hpf, TCS treated, replicate 4


title: TM170

value: primary ovarian tumor


title: 48hpf_DMSO_rep2

source_name: Whole embryo, 48 hpf, DMSO control, replicate 2


title: total RNA at diagnosis from BCP-ALL patient P2 replicate 1

value: undefined


title: TM165

value: III


title: TM164

value: NED


title: genomic DNA at diagnosis from T-ALL patient P4


title: WholeFish 50ng/L  repB1


title: TM162


title: total RNA at diagnosis from BCP-ALL patient P2 replicate 2


title: WholeFish 50ng/L  repA1


title: genomic DNA at diagnosis from BCP-ALL patient P3


title: TM167

value: mRD


title: 48hpf_TCS_rep1

source_name: Whole embryo, 48 hpf, TCS treated, replicate 1


title: WholeFish 50ng/L  repB5


title: TM166


title: TM161

value: I


title: genomic DNA at diagnosis from BCP-ALL patient P2


title: total RNA at diagnosis from BCP-ALL patient P1 replicate 1


title: TM163

value: GRD


title: genomic DNA at diagnosis from BCP-ALL patient P1


title: WholeFish 5ng/L  repC2

source_name: WholeFish, 5ng/L bifenthrin exposure

value: 5ng/L bifenthrin exposure


title: WholeFish 5ng/L  repB3


title: WholeFish 50ng/L  repA2


title: TM160


title: TM159


title: WholeFish 5ng/L  repC4


title: WholeFish 50ng/L  repD1


title: WholeFish 5ng/L  repA8


title: WholeFish 5ng/L  repA6


title: TM156


title: WholeFish 0.5ng/L  repB4

source_name: WholeFish, 0.5ng/L bifenthrin exposure

value: 0.5ng/L bifenthrin exposure


title: TM155


title: TM154


title: TM153


title: TM152


title: WholeFish 0.5ng/L  repD4


title: genomic DNA from CD3+ blood cell donor T-cell 5

source_name: Peripheral blood

value: normal CD3+ cells

value: normal


title: TM157


title: WholeFish 0.5ng/L  repD6


title: WholeFish 0.5ng/L  repA7


title: WholeFish Control repC7

source_name: WholeFish, Control

value: Control


title: WholeFish Control repD2


title: TM158


title: WholeFish Control repC3


title: WholeFish Control repB1


title: WholeFish Control repB6


title: TM148


title: WholeFish Control repA2


title: WholeFish Control repD3


title: TM149


title: TM147


title: TM151


title: TM146


title: TM145


title: TM150


title: TM143


title: TM144


title: TM141


title: LD_3 [miRNA]

city: Göteborg

first: Cecilia

last: Lässer

address: Box 424

department: Krefting Research Centre

institute: University of Gothenburg

description: Sample 10 - LD 3

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner (Toray Industries Inc., Tokyo, Japan) was used for scanning, with auto gain, auto focus, and auto analysis settings.

data_processing: RNA expression in each dataset was normalized by quantile normalization 50 with MATLAB (version 2010a). Fold changes (log2-ratio) were also calculated by MATLAB (version 2010a).

source_name: Low density fractions of a sucrose gradient of extracellular RNA released by HMC-1 cells

label_protocol: Extracted total RNA was labeled with Hy5 using the miRCURY LNA microRNA Array Power Labeling kit  (Exiqon, Vedbaek, Denmark).

growth_protocol: Cells were cultured in a 37°C humidified incubator with 5% CO2

extract_protocol: RNA was extracted with the miRCURY™ RNA Isolation Kit - Cell and Plant (Exiqon A/S, Vedbaek, Denmark) according to the manufacturer's protocol (with 1% 2-mercaptoethanol in the lysis buffer).

tag: cell line

value: human mast cell line

tag: molecule subtype

value: Extracellular RNA

tag: fraction


title: LD_2 [miRNA]

description: Sample 7 - LD 2

value: Low density fractions of a sucrose gradient of extracellular RNA


title: LD_1 [miRNA]

description: Sample 4 - LD 1


title: TM140

city: Milan

last: De Cecco

institute: IRCSS Istituto Nazionale Tumori

extract_protocol: Tissues were mechanically disrupted and simultaneously homogenized in the presence of TRIzol Lysis reagent and using a dismembrator (Braun Biotech International, Melsungen, Germany). RNA was extracted using the miRNeasy Mini kit (Qiagen) according to manufacturer’s instructions.

tag: tissue

tag: age

tag: histology


title: TM139

tag: Stage

tag: grading


title: HD_3 [miRNA]

description: Sample 9 - HD 3

source_name: High density fractions of a sucrose gradient of extracellular RNA released by HMC-1 cells


title: HD_2 [miRNA]

description: Sample 6 - HD 2

value: High density fractions of a sucrose gradient of extracellular RNA


title: Cell_1 [miRNA]

description: Sample 2 - Cell 1

source_name: Human mast cell line HMC-1

value: Cellular RNA


title: Cell_3 [miRNA]

description: Sample 8 - Cell 3


title: Cell_2 [miRNA]

description: Sample 5 - Cell 2


title: TM142

value: primary ovarian tumor


title: HD_1 [miRNA]

description: Sample 3 - HD 1


title: TM136

value: undiff


title: TM134

value: III


title: TM133


title: TM135


title: TM132

value: IV

value: NED


title: TM131


title: TM138

value: II


title: Aspergillus fumigatus 4hr vs 8hr biological replicate 3

description:
Analysis used isotropically expanding cell's RNA as control samples for comparison to the experimental samples taken at 6 and 8hr.
Sample 15

source_name: 4hr isotropically expanding cells

source_name: 8hr germ tube


title: TM137

value: I


title: Aspergillus fumigatus 4hr vs 8hr biological replicate 1

description:
Analysis used isotropically expanding cell's RNA as control samples for comparison to the experimental samples taken at 6 and 8hr.
Sample 13


title: Aspergillus fumigatus 0hr vs 4hr biological replicate 3

description:
Analysis used isotropically expanding cell's RNA as control samples for comparison to the experimental samples taken at 6 and 8hr.
Sample 9

source_name: 0hr dormant cells


title: Aspergillus fumigatus 4hr vs 6hr biological replicate 3

description:
Analysis used isotropically expanding cell's RNA as control samples for comparison to the experimental samples taken at 6 and 8hr.
Sample 12

source_name: 6hr polarity extending cells


title: Aspergillus fumigatus 4hr vs 8hr biological replicate 2

description:
Analysis used isotropically expanding cell's RNA as control samples for comparison to the experimental samples taken at 6 and 8hr.
Sample 14


title: Aspergillus fumigatus 0hr vs 2hr biological replicate 3

description:
Analysis used domant conidia RNA as control samples for comparison to the experimental samples taken at 1, 2, and 4hr.
Sample 6

source_name: 2hr isotropically expanding cells


title: Aspergillus fumigatus 0hr vs 1hr biological replicate 2

description:
Analysis used domant conidia RNA as control samples for comparison to the experimental samples taken at 1, 2, and 4hr.
Sample 2

source_name: 1hr isotropically expanding cells


title: Aspergillus fumigatus 0hr vs 1hr biological replicate 1

description:
Analysis used domant conidia RNA as control samples for comparison to the experimental samples taken at 1, 2, and 4hr.
Sample 1


title: Aspergillus fumigatus 0hr vs 1hr biological replicate 3

description:
Analysis used domant conidia RNA as control samples for comparison to the experimental samples taken at 1, 2, and 4hr.
Sample 3


title: Aspergillus fumigatus 0hr vs 2hr biological replicate 1

description:
Analysis used domant conidia RNA as control samples for comparison to the experimental samples taken at 1, 2, and 4hr.
Sample 4


title: U266_3

city: Belfast

first: Lisa

last: Crawford

address: 97 Lisburn Road

department: CCRCB

country: United Kingdom

institute: Queen's University Belfast

description: Biological replicate 2 of 3

hyb_protocol: Fluorescently labelled samples were hybridized overnight to topic-defined PIQOR Ubiquitin-PS Microarrays Human Antisense according the PIQOR user manual.

scan_protocol: Fluorescent signals were detected using the Axon GenePix 4400A Microarray Scanner (MDS analytical technologies) and associated GenePix Pro 7.0 acquisition and data-extraction software.

data_processing: Gpr files were generated using the GenePic Pro 7.0 software and were further processed using R/ Bioconductor (package limma) by background correction (normexp), wihtin-array normalization by LOWESS method, and between-array normalization my quantile normalization. Median values per probeset were calculated and provided as log2-ratios of each test sample relative to the co-hybridized reference sample.

source_name: U266 cell line

label_protocol: Cy3/Cy5 labelled first-strand cDNA was generated according to the PIQOR user manual (Miltenyi Biotech, Germany).

extract_protocol: Total RNA was extracted from cells, followed by poly(A)+ RNA isolation and amplification using the μMACS One-step T7 Template Kit according to the manufacterer's instructions (Miltenyi Biotech, Germany).

value: U266 cell line

source_name: pooled reference

tag: reference

value: pooled reference RNA


title: Aspergillus fumigatus 0hr vs 2hr biological replicate 2

description:
Analysis used domant conidia RNA as control samples for comparison to the experimental samples taken at 1, 2, and 4hr.
Sample 5


title: U266_2

description: Biological replicate 1 of 3


title: Non-targeting siRNA vs. Knockdown of SUB1 by siRNA 1 in PC3

city: Birmingham

first: Sooryanarayana

last: Varambally

state: Alabama

address: 1824 6th Avenue S

department: Pathology

institute: University of Alabama

description: PC3_Non-T siRNA Vs SUB1 siRNA1

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

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Data from the two channel experiment arrays were lowess normalized usinf 'agilp' bioconductor package. Then, differential expression is measured by log2(reference/test).

source_name: Non-targeting siRNA

label_protocol: 1 µg of total RNA were primed with 2 µl of 100 µM T7-oligo-dT DNA primer at 65°C for 10 min, then reversed transcribed at 40°C for 2 h in the presence of 400 U MMLV RTase (Agilent), and labeled with T7 polymerase with 100 µM each of dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy5-label or Cy3-label.

growth_protocol: Cells were cultured in ATCC recommended media supplemented with 10% FBS.

extract_protocol: Total RNA was isolated using miRNeasy Kit (Qiagen USA) following the manufacturer's instructions.

treatment_protocol: Small interfering RNA (siRNA) duplexes used to inhibit SUB1 expression and non-targeting siRNA were purchased from Qiagen, USA. For RNA inference, we seeded PC3 at 1 × 105 cells per well in a 6-well plate and twelve hours later the cells were transfected either with siRNA duplexes using  Lipofectamine RNAImax reagent (Life Technologies, NY). A second identical transfection was performed 24 hours later. Seventy-two hours after the first transfection, cells were harvested for RNA isolation.

value: prostate cancer cell line

tag: sirna

value: Non-targeting

source_name: SUB1 siRNA 1  PC3 cells


title: Non-targeting siRNA vs. Knockdown of SUB1 by siRNA 2 in PC3

description: PC3_Non-T siRNA Vs SUB1 siRNA2

source_name: SUB1 siRNA 2  PC3 cells


title: U266_4

description: Biological replicate 3 of 3


title: OPM_4

description: Biological replicate 4 of 4

source_name: OPM-2 cell line

value: OPM-2 cell line


title: OPM_3

description: Biological replicate 3 of 4


title: Adult CMP CD27- biological rep. 1

city: Stevenage

first: Nikolai

middle: Nikolaevich

last: Belyaev

address: Gunnels Wood Road

department: Refractory Respiratory Inflammation

institute: GlaxoSmithKline

description: Gene expression data from CD27- common myelo-erythroid progeniotrs from bone marrow

hyb_protocol: The biotinylated cRNA was cleaned up by the Sample Cleanup Modules (Affymetrix), fragmented by metal-induced hydrolysis and hybridised to the Mouse 430A_2.0 GeneChip for 16hours at 45oC and 60rpm.

scan_protocol: GeneChips were scanned by the Affymetrix GeneChip Scanner.

data_processing: Data was normalised by the GC-RMA algorithm and analysed by the GeneSpringGX 11.0 software (Agilent).

source_name: Lin neg. CD117+, Sca-1-, CD34+, CD16/32-, CD27- bone marrow progenitor cells

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

extract_protocol: Total RNA from 80 x 10^3 cells from each population was extracted with Trizol according to manufacturer's protocol. Subsequently, RNA was cleaned up using the Qiagen RNeasy Micro Kit following the Clean Up protocol.

tag: strain

tag: gender

value: Female

value: 4-6 weeks


title: Adult CMP CD27+ biological rep. 1

description: Gene expression data from CD27+ common myelo-erythroid progeniotrs from bone marrow

source_name: Lin neg. CD117+, Sca-1-, CD34+, CD16/32-, CD27+ bone marrow progenitor cells


title: Adult GMP biological rep. 1

description: Gene expression data from committed granulocyte-monocyte progeniotrs from bone marrow

source_name: Lin neg. CD117+, Sca-1-, CD34+, CD16/32+, CD27+ bone marrow progenitor cells


title: Adult GMP biological rep. 3


title: Adult CMP CD27+ biological rep. 2


title: OPM_1

description: Biological replicate 1 of 4


title: Adult GMP biological rep. 2


title: OPM_2

description: Biological replicate 2 of 4


title: Adult CMP CD27+ biological rep. 3


title: NBM_D

description: Biological replicate 4 of 5

source_name: Normal bone marrow

value: Normal bone marrow


title: NBM_E

description: Biological replicate 5 of 5


title: NBM_C

description: Biological replicate 3 of 5


title: Adult CMP CD27- biological rep. 2


title: Adult CMP CD27- biological rep. 3


title: NBM_B

description: Biological replicate 2 of 5


title: Adult MEP biological rep. 2

description: Gene expression data from committed megakaryocyte-erythrocyte progeniotrs from bone marrow

source_name: Lin neg. CD117+, Sca-1-, CD34-, CD16/32-, CD27- bone marrow progenitor cells


title: NBM_A

description: Biological replicate 1 of 5


title: total RNA at diagnosis from BCP-ALL patient P1 replicate 2

source_name: Bone Marrow

value: ALL diagnosis

value: BCP-ALL

tag: cell type

value: primary acute lymphoblastic leukemia cells


title: Adult MEP biological rep. 3


title: WholeFish 50ng/L  repC3

source_name: WholeFish, 50ng/L bifenthrin exposure

value: 50ng/L bifenthrin exposure


title: Adult MEP biological rep. 1


title: LD_3

description: Sample 10 - LD 3

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. with auto gain, auto focus and auto analysis settings on 6 samples. For 4 of the samples focus had to be set to zero.

source_name: Low density fractions of a sucrose gradient of extracellular RNA released by HMC-1 cells

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Cat No. AM1753, Life Technologies). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

value: human mast cell line

value: Extracellular RNA


title: LD_2

description: Sample 7 - LD 2

value: Low density fractions of a sucrose gradient of extracellular RNA


title: MCF10A_B3-overexpressing_rep2

city: quebec

first: Francine

last: Durocher

state: quebec

address: 2705, Laurier Blvd

department: Molecular Medicine

institute: CHU de Quebec Research Centre

hyb_protocol: Standard illumina protocol

scan_protocol: Standard illumina protocol

data_processing: The GenomeStudio® software version 2011.1 (Illumina Inc.) and the  Methylation Module were used. Beta values were estimated and data  correction (background subtraction and normalization) was applied using  internal control probe pairs. CpG sites with a detection p-value > 0.05 were  removed from analysis.

source_name: MCF10A, DNMT3B2-transfected

label_protocol: Standard illumina protocol

growth_protocol: The human breast cancer cell lines MCF7, CAMA-1, ZR-75-1, T-47D, MDA-MB-231, BT549 as well as the human MCF10A cell line are all routinely cultured in our laboratory, and the conditions have been optimized as recommended by the American Type Culture Collection (ATCC, Manassas, VA).

extract_protocol: Genomic DNA was isolated using the QIAamp DNA mini kit (QIAGEN Inc., Mississauga, ON) as described by the manufacturer.   kit, as recommended by the manufacturer

treatment_protocol: MCF7, T-47D, ZR-75-1 and CAMA-1 cell lines were untreated (negative control), either transduced with scramble shRNA/transfected with empty pcDNA3 vector (B2-overexpressing), transduced with DNMT3B2 shRNA or transduced with DNMT3B2 shRNA/transfected with DNMT3B3 pcDNA3 vector. MDA-MB-231, BT-549 and MCF10A cell lines were untreated, transfected with empty pcDNA3 vector (B3-overexpressing) or transfected with DNMT3B2 pcDNA3 vector (B2-overexpressing).  MDA-MB-231, BT-549 and MCF10A cell lines were untreated, transfected with empty pcDNA3 vector (B3-overexpressing) or transfected with DNMT3B2 pcDNA3 vector (B2-overexpressing)


title: MCF10A_nt_rep3

source_name: MCF10A, untreated


title: MCF10A_B3-overexpressing_rep1


title: MCF10A_nt_rep2


title: MCF10A_B3-overexpressing_rep3


title: MCF10A_B2-overexpressing_rep1

source_name: MCF10A, empty pcDNA3 vector-transfected


title: MCF10A_B2-overexpressing_rep2


title: MDA231_B3-overexpressing_rep3

source_name: MDA-MB-231, DNMT3B2-transfected


title: HD_3

description: Sample 9 - HD 3

source_name: High density fractions of a sucrose gradient of extracellular RNA released by HMC-1 cells


title: MDA231_B3-overexpressing_rep1


title: MDA231_B3-overexpressing_rep2


title: MDA231_B2-overexpressing_rep2

source_name: MDA-MB-231, empty pcDNA3 vector-transfected


title: LD_1

description: Sample 4 - LD 1


title: HD_1

description: Sample 3 - HD 1

value: High density fractions of a sucrose gradient of extracellular RNA


title: HD_4

description: Sample 1 - HD 4


title: BT549_B2-overexpressing_rep2

source_name: BT549, empty pcDNA3 vector-transfected


title: MDA231_B2-overexpressing_rep1


title: MDA231_B2-overexpressing_rep3


title: MDA231_nt_rep2

source_name: MDA-MB-231, untreated


title: BT549_B3-overexpressing_rep2

source_name: BT549, DNMT3B2-transfected


title: BT549_B3-overexpressing_rep1


title: MDA231_nt_rep1


title: MCF10A_B2-overexpressing_rep3


title: MDA231_nt_rep3


title: MCF10A_nt_rep1


title: BT549_B2-overexpressing_rep3


title: BT549_B2-overexpressing_rep1


title: BT549_B3-overexpressing_rep3


title: BT549_nt_rep3

source_name: BT549, untreated


title: Cell_3

description: Sample 8 - Cell 3

source_name: Human mast cell line HMC-1

value: Cellular RNA


title: Cell_2

description: Sample 5 - Cell 2


title: Cell_1

description: Sample 2 - Cell 1


title: BT549_nt_rep2


title: V. campbellii, WT with 100 mM indole, biological rep5

city: Washington

first: Baochuan

last: Lin

state: DC

address: 4555 Overlook Avenue, S. W.

department: Center for Bio/Molecular Science & Engineering

institute: US Naval Research Laboratory

description: Gene expression data from wild type V. campbellii with 100 mM indole at 24 hours

hyb_protocol: The cocktail was hybridized onto the Custom design Vharveyi520694 arrays (Affymetrix). Hybridization was carried out for 16 h at 49 °C with rotation at 60 rpm. The microarrays were then washed and stained using the Affymetrix GeneChip Fluidics Station 450 and scanned using the GeneChip 7G Scanner.

scan_protocol: The microarrays were then washed and stained using the Affymetrix GeneChip Fluidics Station 450 and scanned using the GeneChip Scanner 3000. GeneChip® Operating Software 1.2 (GCOS 1.2) (Affymetrix) was used to acquire and process array images, determine the quantity and presence or absence of a transcript using the Microarray Suite 5.0 (MAS5) algorithm, and generated the Report files summarizing the quality of target detection for each microarray.

data_processing: CEL files were processed using the Bioconductor affy package.

organism: Vibrio campbellii

source_name: ATCC® BAA-1116

label_protocol: Target Preparation and Hybridization to Arrays: 600ng of mRNA contained PolyA RNA controls (Affymetrix, Santa Clara, CA) with known concentrations to monitor the quality of the procedures. The labeling reaction is carried out in 30 uL reaction volume using KREATECH’s aRNA Labeling Kit (KREATECH Biotechnology, Amsterdam, the Netherlands) according to the manufacture’s recommended protocol. Labeled mRNAs were purified and fragmented using fragmentation buffer from Ambion (Austin, TX). Fragmentation from reaction was carried out in a reaction volume of 33 uL containing 1x fragmentation buffer (Ambion), labeled mRNA, and incubated at 70oC for 15 minutes. After incubation, the reaction is stopped by adding 1 uL stop solution.

growth_protocol: Replicates of V. campbellii were grown in 5 mL of fresh LB35 broth, with and without 100 μM indole at 28°C and 100 rpm for 24h.

extract_protocol: Total RNA was extracted with the SV Total RNA Isolation System (Promega, Leiden, The Netherlands) according to the manufacturer’s instructions. The quality and quantity of RNA samples were determined using RNA 6000 Nano kit with 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA) and NanoDrop ND2000 (Thermo Scientific Inc., Waltham, MA) spectrophotometer. The RNA samples were accepted for mRNA enrichment if the A260/A280 ratios were between 1.9-2.1, the ratio of intensities of the 23S and 16S rRNA were 1.5-2.5:1 and the RNA integrity no. was between 7 and 10. mRNA enrichment were performed with 10 ug total RNA using using the MICROBExpress kit (Ambion) according to the manufacturer’s protocol. The quantity of mRNA samples were determined by NanoDrop ND2000 (Thermo Scientific Inc., Waltham, MA) spectrophotometer.

treatment_protocol: No treatment difference

tag: growth phase

value: Stationary phase


title: V. campbellii, WT with 100 mM indole, biological rep3


title: T47D_shB2_rep2

source_name: T47D, B2 shRNA-transduced


title: T47D_shB2_rep3


title: V. campbellii, WT with 100 mM indole, biological rep4


title: BT549_nt_rep1


title: V. campbellii, WT with 100 mM indole, biological rep2


title: T47D_shB2_rep1


title: V. campbellii, WT, biological rep4

description: Gene expression data from wild type V. campbellii at 24 hours


title: V. campbellii, WT, biological rep2 (2)


title: V. campbellii, WT, biological rep1 (2)


title: V. campbellii, WT with 100 mM indole, biological rep1


title: V. campbellii, WT, biological rep5


city: Campinas

first: Camila

middle: Pinto da

last: Cunha

state: Sao Paulo

address: Rua Monteiro Lobato, 255, bloco H

country: Brazil

institute: UNICAMP

description:
Sample 24
Technical replicate 2 of 2. Control (mock) at 5 DAA versus AVG at 5 DAA (upper internode) Replicate 2

hyb_protocol: Gene Expression Hybridization kit and the Gene Expression Wash Buffer kit (Agilent Technologies, Santa Clara, USA).

scan_protocol: GenePix 4000B scanner (Molecular Devices, Sunnyvale, USA) using Agilent (C or B) Scanner Settings.

data_processing: Scan data was extracted for gene expression measurement using Feature Extraction software version 9.5.3.1 (Agilent Technologies, Santa Clara, USA) using the protocol GE2-v5_95_Feb07. After a background signal correction, the data was normalized by a linear method followed by the LOWESS method [YANG, Y. H. et al. Nucleic Acids Res., v. 30, n. 4, p. e15, 2002.] to correct intensity-dependent dye biases. Outlier genes were identified by a modified HTself method [VÊNCIO, R. Z. N.; KOIDE, T. DNA Research, v. 12, p. 211-214, 2005.] with 90% confidence for reference dataset, using the following parameters to define significant differentially expressed (DE) genes in each experimental samples: minimum of 70% of all spots showing a similar pattern; and positively flagged in the two technical replicates. Finally, the log2 ratio was calculated.

organism: Saccharum sp.

source_name: Control (mock)_5 DAA

label_protocol: Two-Color Microarray-Based Gene Expression Analysis protocol. Quick Amp Labeling kit, two-color (Agilent Technologies, Santa Clara, USA).

growth_protocol: Greenhouse (open-sided and plastic roofed with a 4 m-height arch structure) at the Santa Elisa Farm, Agronomic Institute of Campinas (IAC), Campinas, SP, Brazil. Sugarcane plantlets were grown in concrete tanks with 1.54 m3 of soil.

extract_protocol: Total RNA extraction from leaves and internodes were performed using the protocol described by  LOGEMANN, J. et al. Analytical Biochemistry, v. 163, p. 16-20, 1987. The RNA samples were treated with DNase in solution and puriﬁed on-column using the RNase-Free DNase Set (Qiagen, Hilden, Germany), according to the manufacturer.

treatment_protocol: Ethephon (Ethrel 240, Bayer CropScience, Charleston, USA; 519 µM of active ingredient); AVG (Retain, Valent BioScience, Libertyville, USA; 46 µM a. i.); and mock (distilled water plus surfactant, Haiten, ArystaLifescience, Salto de Pirapora, Brazil; 1 mL/mL of spray mixture) applied with sugarcane plants with 10 months. Products were applied with a spray boom with three hollow cone nozzles (TP8002VK, maximum nominal pressure of 20 bar, TeeJet, Springﬁeld, USA), coupled with an electrical backpack sprayer (model 16 L Jett, Sanmaq, Braganc¸a Paulista, Brazil) at the maximum ﬂow rate (0.8 L min−1) and with a total volume of 16 L.

tag: cultivar

tag: chemical

value: mock, water plus surfactant

tag: days after chemical application (daa)

value: upper internode (pith)

source_name: AVG_5 DAA

value: AVG


title: V. campbellii, WT, biological rep3 (2)


title: T47D_B3-overexpressing_rep4

source_name: T47D, scramble shRNA-transduced+B3 transfected

tag: cell line


title: T47D_B3-overexpressing_rep2


description:
Sample 23
Technical replicate 1 of 2. Control (mock) at 5 DAA versus AVG at 5 DAA (upper internode) Replicate 1


title: T47D_B3-overexpressing_rep3


title: T47D_B2-overexpressing_rep3

source_name: T47D, scramble shRNA-transduced


title: T47D_B2-overexpressing_rep2


description:
Sample 22
Technical replicate 2 of 2. Control (mock) at 5 DAA versus Ethephon at 5 DAA (upper internode) Replicate 2

source_name: Ethephon_5 DAA

value: Ethephon


description:
Sample 20
Technical replicate 2 of 2. Control (mock) at 1 DAA versus AVG at 5 DAA (upper internode) Replicate 2

source_name: Control (mock)_1 DAA


description:
Sample 19
Technical replicate 1 of 2. Control (mock) at 1 DAA versus AVG at 5 DAA (upper internode) Replicate 1


description:
Sample 18
Technical replicate 2 of 2. Control (mock) at 1 DAA versus Ethephon at 5 DAA (upper internode) Replicate 2


title: T47D_B3-overexpressing_rep1


description:
Sample 17
Technical replicate 1 of 2. Control (mock) at 1 DAA versus Ethephon at 5 DAA (upper internode) Replicate 1


description:
Sample 21
Technical replicate 1 of 2. Control (mock) at 5 DAA versus Ethephon at 5 DAA (upper internode) Replicate 1


description:
Sample 16
Technical replicate 2 of 2. Control (mock) at 1 DAA versus AVG at 1 DAA (upper internode) Replicate 2

source_name: AVG_1 DAA


title: HD_2

description: Sample 6 - HD 2

tag: molecule subtype


description:
Sample 15
Technical replicate 1 of 2. Control (mock) at 1 DAA versus AVG at 1 DAA (upper internode) Replicate 1


description:
Sample 14
Technical replicate 2 of 2. Control (mock) at 1 DAA versus Ethephon at 1 DAA (upper internode) Replicate 2

source_name: Ethephon_1 DAA


title: Non-celiac/non-inflamed patient_15

city: Leioa

first: Jose Ramon

last: Bilbao

state: Outside the US or Canada

address: Bº Sarriena

department: Genetics, Physical Anthropology and Animal Physiology

country: Spain

institute: University of the Basque Country (UPV/EHU)

description:
Sample name = 211101
Taqman Gene Expression assays.

data_processing:
Housekeeping gene RPLPO was simultaneously quantified and used as an endogenous control of input RNA (Life Technologies).
Relative expression in each sample was calculated using the accurate Ct method and normalized to the average expression value of the control samples.
Fold_Change worksheet reports Active CD/CONTROL, Treated CD/CONTROL and Active CD/Treated CD ratios.

label: FAM

source_name: Duodenum, control

label_protocol:
RNA was normalized to 8 ng/ul and converted to cDNA using the AffinityScript cDNA Synthesis kit (Agilent Technologies) following manufacturer's protocol.
Specific Target Amplification (STA) was performed.
Gene expression analyses were performed using Fluidigm Biomark 96.96 dynamic arrays and commercially available TaqMan Gene Expression assays.

growth_protocol: Samples stored in liquid nitrogen until RNA extraction.

extract_protocol: NucleoSpin microRNA kit following manufacturer's instructions for total RNA.

tag: disease status

value: Non-celiac disease

value: Duodenum, non-inflamed mucosa

tag: sample type

value: Control


description:
Sample 13
Technical replicate 1 of 2. Control (mock) at 1 DAA versus Ethephon at 1 DAA (upper internode) Replicate 1

tag: tissue


title: T47D_nt_rep2

source_name: T47D, untreated


title: Non-celiac/non-inflamed patient_14

description:
Sample name = 211096
Taqman Gene Expression assays.


title: ZR751_B3-overexpressing_rep6

source_name: ZR751, scramble shRNA-transduced+B3 transfected


title: T47D_nt_rep3


title: T47D_B2-overexpressing_rep1


title: T47D_nt_rep1


title: Non-celiac/non-inflamed patient_13

description:
Sample name = 211091
Taqman Gene Expression assays.


title: ZR751_shB2_rep3

source_name: ZR751, B2 shRNA-transduced


description:
Sample 12
Technical replicate 2 of 2. Control (mock) at 5 DAA versus AVG at 5 DAA (leaf) Replicate 2

value: leaf +1


title: ZR751_shB2_rep1


title: T47D_B3-overexpressing_rep5


title: ZR751_shB2_rep2


title: ZR751_B3-overexpressing_rep5


title: Non-celiac/non-inflamed patient_11

description:
Sample name = 211084
Taqman Gene Expression assays.


title: Non-celiac/non-inflamed patient_10

description:
Sample name = 211078
Taqman Gene Expression assays.


description:
Sample 9
Technical replicate 1 of 2. Control (mock) at 5 DAA versus Ethephon at 5 DAA (leaf) Replicate 1


description:
Sample 10
Technical replicate 2 of 2. Control (mock) at 5 DAA versus Ethephon at 5 DAA (leaf) Replicate 2


title: Non-celiac/non-inflamed patient_9

description:
Sample name = 211075
Taqman Gene Expression assays.


title: ZR751_B2-overexpressing_rep2

source_name: ZR751, scramble shRNA-transduced


title: ZR751_B3-overexpressing_rep3


title: ZR751_B2-overexpressing_rep3


description:
Sample 7
Technical replicate 1 of 2. Control (mock) at 1 DAA versus AVG at 5 DAA (leaf) Replicate 1


description:
Sample 8
Technical replicate 2 of 2. Control (mock) at 1 DAA versus AVG at 5 DAA (leaf) Replicate 2


title: CAMA_shB2_rep3

source_name: CAMA, B2 shRNA-transduced

value: CAMA


title: Non-celiac/non-inflamed patient_8

description:
Sample name = 211074
Taqman Gene Expression assays.


title: ZR751_B3-overexpressing_rep2


title: ZR751_B2-overexpressing_rep1


title: ZR751_nt_rep3

source_name: ZR751, untreated


title: ZR751_nt_rep2


description:
Sample 6
Technical replicate 2 of 2. Control (mock) at 1 DAA versus Ethephon at 5 DAA (leaf) Replicate 2


title: ZR751_B3-overexpressing_rep1


title: ZR751_B3-overexpressing_rep4


description:
Sample 11
Technical replicate 1 of 2. Control (mock) at 5 DAA versus AVG at 5 DAA (leaf) Replicate 1


title: Non-celiac/non-inflamed patient_12

description:
Sample name = 211090
Taqman Gene Expression assays.


title: Non-celiac/non-inflamed patient_7

description:
Sample name = 211073
Taqman Gene Expression assays.


description:
Sample 5
Technical replicate 1 of 2. Control (mock) at 1 DAA versus Ethephon at 5 DAA (leaf) Replicate 1


title: Non-celiac/non-inflamed patient_4

description:
Sample name = 210006
Taqman Gene Expression assays.


title: CAMA_shB2_rep2


title: ZR751_nt_rep1


description:
Sample 4
Technical replicate 2 of 2. Control (mock) at 1 DAA versus AVG at 1 DAA (leaf) Replicate 2


title: Non-celiac/non-inflamed patient_5

description:
Sample name = 210007
Taqman Gene Expression assays.


title: CAMA_shB2_rep1

source_name: CAMA, scramble shRNA-transduced+B3 transfected


description:
Sample 3
Technical replicate 1 of 2. Control (mock) at 1 DAA versus AVG at 1 DAA (leaf) Replicate 1


description:
Sample 2
Technical replicate 2 of 2. Control (mock) at 1 DAA versus Ethephon at 1 DAA (leaf) Replicate 2


description:
Sample 1
Technical replicate 1 of 2. Control (mock) at 1 DAA versus Ethephon at 1 DAA (leaf) Replicate 1


title: Non-celiac/non-inflamed patient_1

description:
Sample name = 24012
Taqman Gene Expression assays.


title: Non-celiac/non-inflamed patient_2

description:
Sample name = 21013
Taqman Gene Expression assays.


title: Non-celiac/non-inflamed patient_3

description:
Sample name = 29129
Taqman Gene Expression assays.


title: CAMA_B3-overexpressing_rep5


title: Treated celiac patient_15

description:
Sample name = 26060
Taqman Gene Expression assays.

source_name: Duodenum, treated CD

value: Treated celiac disease (CD)

tag: patient identifier


title: CAMA_B3-overexpressing_rep4


title: CAMA_B3-overexpressing_rep3


title: Treated celiac patient_14

description:
Sample name = 27035
Taqman Gene Expression assays.


title: Treated celiac patient_13

description:
Sample name = 27057
Taqman Gene Expression assays.


title: Treated celiac patient_11

description:
Sample name = 29109
Taqman Gene Expression assays.


title: CAMA_B3-overexpressing_rep2


title: Treated celiac patient_9

description:
Sample name = 25087
Taqman Gene Expression assays.


title: Treated celiac patient_10

description:
Sample name = 29091
Taqman Gene Expression assays.


title: Treated celiac patient_12

description:
Sample name = 210051
Taqman Gene Expression assays.


title: Non-celiac/non-inflamed patient_6

description:
Sample name = 210008
Taqman Gene Expression assays.


title: Treated celiac patient_8

description:
Sample name = 25085
Taqman Gene Expression assays.


title: Treated celiac patient_7

description:
Sample name = 25080
Taqman Gene Expression assays.


title: CAMA_B2-overexpressing_rep2

source_name: CAMA, scramble shRNA-transduced


title: Treated celiac patient_6

description:
Sample name = 27023
Taqman Gene Expression assays.


title: CAMA_B2-overexpressing_rep3


title: Treated celiac patient_5

description:
Sample name = 27005
Taqman Gene Expression assays.


title: CAMA_nt_rep3

source_name: CAMA, untreated


title: Treated celiac patient_4

description:
Sample name = 28050
Taqman Gene Expression assays.


title: Treated celiac patient_2

description:
Sample name = 25040
Taqman Gene Expression assays.


title: Active celiac patient_15

description:
Sample name = 24052
Taqman Gene Expression assays.

source_name: Duodenum, active CD

value: Active celiac disease (CD)

value: Duodenum, inflamed mucosa


title: Treated celiac patient_3

description:
Sample name = 27031
Taqman Gene Expression assays.


title: CAMA_nt_rep1


title: CAMA_B2-overexpressing_rep1


title: Treated celiac patient_1

description:
Sample name = 25052
Taqman Gene Expression assays.


title: MCF7_shB2_rep3

source_name: MCF7, B2 shRNA-transduced


title: CAMA_B3-overexpressing_rep1


title: Active celiac patient_14

description:
Sample name = 25037
Taqman Gene Expression assays.


title: Active celiac patient_13

description:
Sample name = 25061
Taqman Gene Expression assays.


title: WT 5

city: Paris

first: Fiona

last: Francis

address: 17 rue du Fer à Moulin

department: Inserm UMRS-839

institute: Institut du Fer à Moulin

description:
CA3 layer
UPMC P3S Paris

hyb_protocol: The Whole-genome Gene Expression Direct Hybridization Assay (Illumina) according to manufacturers’ instructions. cRNA samples were hybridized to the Illumina Mouse-Ref-8 expression beadchip arrays in the appropriate buffer overnight at 58 °C. After hybridization and washes, fluorescent tagging was achieved by incubation with streptavidin-Cy3.

scan_protocol: Standard Illumina scanning protocol. Each array contains approximately 25,600 well-annotated RefSeq transcripts, represented as oligonucleotides attached to beads (average of 30 beads/per transcript), corresponding to over 19,100 unique genes.

data_processing:
Intra-sample normalization: In order to compare gene expression intensities between samples, expression values within samples were first normalised to account e.g. for differences in mRNA library preparation. To this end, each log-transformed expression value was corrected by subtracting the median of the distribution of log-transformed expression values and dividing by the standard deviation of this distribution. Inter-sample normalization: Samples were distributed on two different slides, requiring a correction for potential experimental or technical differences between slides. A principal component analysis of the expression values of the 15 samples showed that the principal eigenvector (Z[1]) can separate the samples according to their slide of origin. To normalize, we averaged the expression values of each gene across the four SPI and the four SPE samples of slide 1 respectively. We subtracted this average value from the value of the single SPI and SPE samples on slide 2. When data points are close to zero on both axes, this indicates that slides 1 and 2 show the same expression values. While this appears to be true for many genes, we also observed a distribution of points along a slope. For genes lying on this diagonal, this indicates a bias of the same magnitude for both SPI and SPE samples. We first performed a gene-wise correction of the SPI samples on slide 1 to be compatible with corresponding samples on slide 2. The corrected value for each gene j is obtained as the sum of the original value and an estimate of the bias error. The estimate of the bias is based on the bias of SPE (since we assume this to be independent of the sample, i.e. affecting intensities in the same way on the two slides) weighted with a constant wI. Similarly, the SPE samples were corrected on slide 1 with the bias estimated from SPI and thus all samples were aligned to the samples as found on slide 2. After corrections, principal component analysis showed that SPI and SPE samples from slide 2 respectively cluster with the SPI and SPE samples from slide 1.Finally the linear model fit of the LIMMA package was applied on these bias-corrected expression values in order to detect the differentially expressed genes pertaining to the three conditions, using a t-test. The Benjamini-Hochberg false discovery rate control (with P = 0.05) was applied to correct for multiple testing. Results are presented as ratios between the conditions.
Mean absolute and relative expression values from probe intensities.

source_name: Mouse hippocampus

label_protocol: 15 samples, corresponding to n=5 samples for each condition were processed using the Illumina TotalPrep RNA Amplification Kit (Ambion, Life Technologies) and the Whole-genome Gene Expression Direct Hybridization Assay (Illumina) according to manufacturers’ instructions. Briefly, 150-200 ng total RNA was used to prepare double-stranded cDNA using a T7 oligo (dT) primer (Illumina protocol). Reverse transcription was followed by in vitro transcription in the presence of biotinylated nucleotides.

extract_protocol: Total RNA was isolated from pooled microdissected material using an RNA isolation kit (Arcturus picopure) according to manufacturer instructions. RNA for each brain was eluted in 13 µl of the elution buffer provided in the kit. RNA quantity was measured using a nanodrop spectrophotometer. RNA quality was checked using an Agilent 2100 Bioanalyzer with the RNA 6000 Pico LabChip Kit (5065-4473, Agilent Technologies, Palo Alto).

tag: genotype

value: Wild type

value: Brain, Hippocampus, CA3

tag: age


title: MCF7_shB2_rep1


title: WT 4

description:
CA3 layer
UPMC P3S Paris


title: MCF7_shB2_rep2


title: Active celiac patient_12

description:
Sample name = 28049
Taqman Gene Expression assays.


title: MCF7_B3-overexpressing_rep5

source_name: MCF7, scramble shRNA-transduced+B3 transfected


title: CAMA_nt_rep2


title: MCF7_B3-overexpressing_rep6


title: Active celiac patient_11

description:
Sample name = 27056
Taqman Gene Expression assays.


title: MCF7_B3-overexpressing_rep4


title: WT 3

description:
CA3 layer
UPMC P3S Paris


title: Active celiac patient_10

description:
Sample name = 27050
Taqman Gene Expression assays.


title: Active celiac patient_9

description:
Sample name = 23068
Taqman Gene Expression assays.


title: WT 2

description:
CA3 layer
UPMC P3S Paris


title: Outer 5 Dcx KO

description:
External CA3 layer
UPMC P3S Paris

value: Mutant


title: Active celiac patient_8

description:
Sample name = 23057
Taqman Gene Expression assays.


title: Outer 3 Dcx KO

description:
External CA3 layer
UPMC P3S Paris


title: WT 1

description:
CA3 layer
UPMC P3S Paris


title: Outer 4 Dcx KO

description:
External CA3 layer
UPMC P3S Paris


title: MCF7_B3-overexpressing_rep3


title: Active celiac patient_6

description:
Sample name = 25022
Taqman Gene Expression assays.


title: MCF7_B3-overexpressing_rep2


title: MCF7_nt_rep3

source_name: MCF7, untreated


title: Active celiac patient_4

description:
Sample name = 26047
Taqman Gene Expression assays.


title: Active celiac patient_3

description:
Sample name = 24051
Taqman Gene Expression assays.


title: Active celiac patient_5

description:
Sample name = 25016
Taqman Gene Expression assays.


title: Active celiac patient_7

description:
Sample name = 23040
Taqman Gene Expression assays.


title: MCF7_B2-overexpressing_rep3

source_name: MCF7, scramble shRNA-transduced


title: MCF7_B3-overexpressing_rep1


title: Outer 2 Dcx KO

description:
External CA3 layer
UPMC P3S Paris


title: Active celiac patient_2

description:
Sample name = 23014
Taqman Gene Expression assays.


title: MCF7_nt_rep2


title: Outer 1 Dcx KO

description:
External CA3 layer
UPMC P3S Paris


title: Inner 4 Dcx KO

description:
Internal CA3 layer
UPMC P3S Paris


title: Active celiac patient_1

description:
Sample name = 23017
Taqman Gene Expression assays.


title: Inner 2 Dcx KO

description:
Internal CA3 layer
UPMC P3S Paris


title: Inner 3 Dcx KO

description:
Internal CA3 layer
UPMC P3S Paris


title: Inner 5 Dcx KO

description:
Internal CA3 layer
UPMC P3S Paris


title: MCF7_nt_rep1


title: MCF7_B2-overexpressing_rep1


title: MCF7_B2-overexpressing_rep2


title: Arabidopsis rglg1/2 leaves biological rep2

status: Public on Oct 30 2016

city: Taichung

first: I-Chun

last: Pan

address: Kuo-Kuang

department: Horticulture

country: Taiwan

institute: Chung Hsing University

description: L rglg-2

hyb_protocol: 11 ug labeled samples were hybridized to GeneChip at 45℃ for 16.5 hours.

scan_protocol: the GeneChip were scanned with Affymetrix GeneChip Scanner 7G.

data_processing:
The data were analyzed with GeneSpring  5.0 (version 11.5, Agilent, Santa Clara, USA) using RMA method.
Data was Filter by expression, the lower and upper cut-off values are 20.0 and 19195.738 respectively.Entities where at least 100 percent of samples in any 1 out of 8 conditions have values within cut-off.

source_name: 10 days plants treated with iron sufficient mediem for 3 days

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol(Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Arabidopsis plants grown in a growth chamber with 21C under continuous illumination

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Ten days old plants were treated with iron-suficient(40 uM FeEDTA) or iron-deficiency (100 µM 3-(2-pyridyl)-5,6-diphenyl-1,2,4-triazine sulfonate) mediem for 3 days.

tag: ecotype

value: Col

tag: genotype/variation

value: rglg1 rglg2 double mutant

value: Leaves

value: 13 days

tag: treated with

value: iron sufficient medium for 3 days


title: Arabidopsis rglg1/2-Fe leaves biological rep2

description: L rglg-Fe-2

source_name: 10 days plants treated with iron deficiency mediem for 3 days

value: iron deficiency medium for 3 days


title: Arabidopsis rglg1/2 leaves biological rep3

description: L rglg-3


title: Arabidopsis rglg1/2-Fe leaves biological rep3

description: L rglg-Fe-3


title: Arabidopsis rglg1/2 leaves biological rep1

description: L rglg-1


title: Arabidopsis Col-Fe leaves biological rep3

description: L Col-Fe-3

value: wild type


title: Inner 1 Dcx KO

description:
Internal CA3 layer
UPMC P3S Paris


title: Arabidopsis rglg1/2-Fe leaves biological rep1

description: L rglg-Fe-1


title: Arabidopsis Col leaves biological rep1

description: L Col-1


title: Arabidopsis rglg1/2-Fe root biological rep1

description: R rglg-Fe-1

value: Roots


title: Arabidopsis rglg1/2-Fe root biological rep3

description: R rglg-Fe-3


title: Arabidopsis rglg1/2-Fe root biological rep2

description: R rglg-Fe-2


title: Arabidopsis Col-Fe leaves biological rep1

description: L Col-Fe-1


title: Arabidopsis Col-Fe leaves biological rep2

description: L Col-Fe-2


title: Arabidopsis Col leaves biological rep3

description: L Col-3


title: Arabidopsis Col leaves biological rep2

description: L Col-2


title: Arabidopsis Col-Fe root biological rep3

description: R Col-Fe-3


title: Arabidopsis rglg1/2 root biological rep2

description: R rglg-2


title: Arabidopsis rglg1/2 root biological rep3

description: R rglg-3


title: Arabidopsis rglg1/2 root biological rep1

description: R rglg-1


title: Arabidopsis Col root biological rep3

description: R Col-3


title: Arabidopsis Col root biological rep2

description: R Col-2


title: Arabidopsis Col root biological rep1

description: R Col-1


title: Arabidopsis Col-Fe root biological rep1

description: R Col-Fe-1