title: OM+N+G-R3

status: Public on Apr 30 2013

type: RNA

city: Lund

first: Tomas

last: Johansson

address: Sölvegatan 37

department: Biology

country: Sweden

institute: Lund University

description: Treat OM+N+G; Replicate 3 (subarray 12)

hyb_protocol: Hybridization was performed using the NimbleGen Hybridization kit (#05 583 683 001) according to their Gene Expression v5.0 protocol (www.nimblegen.com).

scan_protocol: Scanning was performed at single-label (Cy3) wavelength (532nm) on an Agilent High-Resolution Microarray Scanner set at 2 um resolution and 20% PMT.

data_processing: The bursted and gridded tif-files (.tif file) were directly subjected data extraction, background reduction and quantile normalization using the RMA (Robust Multi-Chip Average) algoritm as implemented by the NimbleScan software package, version 2.5.26 (Roche NimbleGen, Inc.)(www.nimblegen.com).

molecule: total RNA

organism: Paxillus involutus ATCC 200175

source_name: mycelium patch

label_protocol: Single-color labeling was performed using the Roche/NimbleGen One-Color DNA Labeling kit (# 05 223 55 001) following their Gene Expression v5.0 protocol (www.nimblegen.com).

growth_protocol: Paxillus involutus (Batsch) Fr. (ATCC 200175) was grown axenically in Petri dishes on a layer of glass beads immersed in extracts of indicated organic matter. The fungus was first grown for 9 days on a Minimum Melin Norkrans (MMN) medium and then starved for N during 24 h.

extract_protocol: Total RNA was extracted using the Plant RNeasy Mini kit (www.qiagen.com) and concentrated using RNA MinElute kit (www.qiagen.com). RNA quality/integrity and concentration was assessed by analysis on a RNA 6000 Nano chip using the 2100 Bioanalyzer (Agilent). From total RNA, cDNA was produced using the SuperScript double-stranded cDNA Synthesis kit (Invitrogen, #11917-0xx) according to the NimbleGen Gene Expression v5.0 protocol (www.nimblegen.com).

treatment_protocol: Organic matter was extracted from maize compost material using hot water (MH). Particles were removed by sequentially filtering (0.2 um) and low molecular weight compounds by ultrafiltration (cut-off 10 kDa). The organic matter extracts were added and the cultures were incubated for an additional 7 days.

tag: treatment

value: OM+N+G


title: OM+N+G-R2

description: Treat OM+N+G; Replicate 2 (subarray 11)


title: OM-R1

description: Treat OM; Replicate 1 (subarray 01)

value: OM


title: OM-R3

description: Treat OM; Replicate 3 (subarray 03)


title: OM-R2

description: Treat OM; Replicate 2 (subarray 02)


title: OM+G-R2

description: Treat OM+G; Replicate 2 (subarray 08)

value: OM+G


title: OM+N-R1

description: Treat OM+N; Replicate 1 (subarray 04)

value: OM+N


title: OM+G-R3

description: Treat OM+G; Replicate 3 (subarray 09)


title: OM+G-R1

description: Treat OM+G; Replicate 1 (subarray 07)


title: OM+N-R2

description: Treat OM+N; Replicate 2 (subarray 05)


title: OM+N+G-R1

description: Treat OM+N+G; Replicate 1 (subarray 10)


title: OM+N-R3

description: Treat OM+N; Replicate 3 (subarray 06)


title: trophoblast_0h_replicate_2

city: Houston

first: Scott

middle: Andrew

last: Ochsner

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

country: USA

institute: Baylor College of Medicine

description: Human trophoblast primary culture prior to siRNA transfection.

hyb_protocol: RNA was labeled and hybridized to an Illumina HumanHT-12 v4 BeadChip, according to the manufacturer’s protocol.

scan_protocol: The BeadChip was scanned using an Illumina HiScan.

data_processing: The data were normalised using quantile normalisation with BeadStudio.

label: biotin

organism: Homo sapiens

source_name: trophoblast cells

growth_protocol: Midtrimester human placental tissues (16–24 wk gestation) were obtained from Advanced Bioscience Resources (Alameda, CA) in accordance with the Donors Anatomical Gift Act of the State of Texas. Protocols were approved by the Institutional Review Board of the University of Texas Southwestern Medical Center. The placental tissues were washed with Hank’s balanced salt solution, pH 7.4 (Life Technologies, Inc., Gaithersburg, MD), and then finely minced and digested with 0.125% trypsin in Hank’s balanced salt solution at 37°C for 20 min. This procedure was repeated three times. At the end of each digestion step, the supernatant was collected, layered over 10 ml of serum, and then briefly centrifuged. The pellet was suspended in DMEM (Life Technologies, Inc.), filtered and layered over a Percoll gradient (70–5%). The gradients were centrifuged at 1200×g for 20 min at room temperature, and cells in the middle layer (density, 1.045–1.062 g/ml) were collected, washed, and counted.

extract_protocol: RNA from three independent experiments using placental tissues from three abortuses was extracted by miRNeasy® Mini Kit (Qiagen, Maryland, USA).

treatment_protocol: Lentiviral vectors containing shRNA targeting ERRγ in pGIPZ vectors were obtained from a lentivirus shRNA library (Open Biosystems, Huntsville, AL). Two different shRNA vectors were used for silencing of ERRγ: Open Biosystems catalog no. RHS4430–98514497 and catalog no. RHS4430-98912788. Lentiviral supernatants were produced in human embryonic kidney 293T cells by Lipofectamine 2000 (Invitrogen, Carlsbad, CA) mediated transfection of plasmids, pMD2.G, psPAX2, and human GIPZ lentiviral shRNA for ERRγ. Lentiviral supernatants were collected after 24, 48, and 72 h of culture. The viral particles were concentrated by ultracentrifugation, and the titers of the viral stocks, expressed as multiplicity of infection (moi), were determined according to the protocol recommended by Open Biosystems. For control experiments, cells were infected with nonsilencing GIPZ lentiviral shRNA control.  The collected placental cells were then resuspended in DMEM supplemented with 10% fetal bovine serum (FBS) and 1.2% antibiotic/antimycotic solution (Life Technologies, Inc.), plated at a density of 2×106 cells per 35-mm culture dish and transfected with recombinant lentiviruses expressing ERRγ shRNA, or a control, nonsilencing shRNA. The cells were cultured overnight, after which the medium was changed to DMEM containing 2% FBS.

tag: cell type

value: trophoblast cells

tag: transfection


title: trophoblast_0h_replicate_3

label_protocol: RNA was labeled and hybridized to an Illumina HumanHT-12 v4 BeadChip, according to the manufacturer’s protocol.


title: trophoblast_72h_control siRNA_replicate_2

description: Human trophoblast primary culture 72h after control, non-silencing shRNA transfection.

value: control siRNA


title: trophoblast_72h_control siRNA_replicate_3


title: trophoblast_72h_ERRG siRNA_replicate_3

description: Human trophoblast primary culture 72h after ERRG shRNA transfection.

value: ERRG siRNA


title: trophoblast_72h_ERRG siRNA_replicate_2


title: trophoblast_72h_ERRG siRNA_replicate_1


title: trophoblast_72h_control siRNA_replicate_1


title: trophoblast_0h_replicate_1

description: Human trophoblast primary culture prior to shRNA transfection.


title: normal skin 6

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

hyb_protocol: Affymetrix protocol

scan_protocol: Hewlett-Packard GeneArray Scanner G25Time: 0Time: 0A.

data_processing: GCRMA (using gcrma package from R/Bioconductor)

source_name: normal skin epidermal cells

label_protocol: Affymetrix double amplification protocol

extract_protocol: QIAGEN Rneasy Kit

tag: subject

value: healthy volunteer 6

tag: condition

value: normal epidermis

tag: amplification

value: Double

tag: material

value: sliced section


title: normal skin 9

value: healthy volunteer 9


title: normal skin 8

value: healthy volunteer 8


title: normal skin 7

value: healthy volunteer 7


title: normal skin 5

value: healthy volunteer 5


title: normal skin 3

value: healthy volunteer 3


title: normal skin 10

value: healthy volunteer 10


title: SCC 070809 TM

source_name: SCC_tumor_in situ

value: patient 2

value: in situ squamous cell carcinoma


title: SCC 070909-1 TM

value: patient 1

value: invasive squamous cell carcinoma


title: normal skin 4

value: healthy volunteer 4


title: SCC 062209 TM/D

value: patient 3


title: SCC 062209 TM/E


title: SCC #4 TM

value: patient 8


title: normal skin 2

value: healthy volunteer 2


title: normal skin 1

value: healthy volunteer 1

value: normal epidermis


title: SCC 072209 TM/E

value: patient 4

value: Double

value: sliced section


title: BCC#5 AK

value: patient 9

value: actinic keratosis


title: SCC 070809 AK


title: SCC 062209 AK


title: SCC 061809 TM

value: patient 6


title: AK 052109

value: patient 10


title: SCC 072209 TM/D


title: SCC #4 AK


title: SCC #2 TM

value: patient 7


title: SCC 070909-2 TM

value: patient 5

value: in situ squamous cell carcinoma


title: negative control transfected cells rep2

city: San Francisco

first: Kevin

last: Blansit

state: Ca

address: UCSF Helen Diller Family Comprehensive Cancer Center

institute: UCSF

hyb_protocol: Standar hybridization cocktail, hybed 17 hours at 45C.

scan_protocol: Standard wash and stain controlled by GCOS

data_processing: Cel Files generated by GCOS, imported into Partek (ver. 6.2) and RMA signals were generated for only the core probe sets (28,869).   RMA signals were generated for the core probe sets using the RMA background correction, quantile normalization and summarization by Median Polish.  Summarized signals for each probe set were log2 transformed.

source_name: SKOv3_negative control

label_protocol: Standard Affymetrix WT labeling and control kit.

extract_protocol: Trizol protocol

treatment_protocol: transfected with either has-miR-378 mimic or negative control

tag: cell line

value: ovarian carcinoma cells

tag: transfected with

value: negative control


title: miR-378 transfected cells rep2

value: has-miR-378 mimic


title: miR-378 transfected cells rep1


title: negative control transfected cells rep4


title: miR-378 transfected cells rep3


title: negative control transfected cells rep1


title: miR-378 transfected cells rep4


title: negative control transfected cells rep3


title: Athlete7-WBC-T4

city: Moscow

first: Maxim

last: Shkurnikov

address: 2 bld. 85, Ugreshkaya st.

country: Russia

institute: SRC Bioclinicum

description: Gene expression before exercise (1 week later)

hyb_protocol: Fragmented target DNA was hybridized on GeneChip Human Gene 1.0 ST Arrays (Affymetrix, USA) in a Hybridization Oven 640 (Affymetrix, USA) at 45ºC for 16h. Arrays were washed free of nonspecifically bound fragments and stained on Fluidics Station 450 (Affymetrix, USA) using the FS450_0007 protocol.

scan_protocol: Scanning was done on the GeneChip Scanner 3000 7G system (Affymetrix, USA) using GSOC v1.4 software.

data_processing: Microarray data was processed using bioconductor xps package implementation of RMA.

source_name: White blood cells, baseline for MT

label_protocol: Briefly, double-strand cDNA was synthesized with random hexamers tagged with a T7 promoter sequence from 2µg of total RNA. The cDNA was subsequently used as a template and amplified by T7 RNA polymerase, producing many copies of antisense cRNA. In the second cycle of cDNA synthesis, random hexamers were used to prime reverse transcription of the cRNA from the first cycle to produce single-stranded DNA in the sense orientation. The resulting sense strand DNA was fragmented to an average strand length of 100 bases and labeled with biotin.

extract_protocol: Blood for total RNA extraction was drawn in PAXgene blood RNA tubes (Qiagen, Germany). Total RNA was extracted as recommended by the manufacturer. RNA quality was checked using the Agilent Bioanalyzer 2100 System. For all samples, RIN was greater than 8.

tag: gender

value: male

tag: age

tag: exercise stage

value: before exercise (1 week later)

tag: body mass

tag: bmi


title: Athlete7-WBC-T7

description: Gene expression after 60 min of recovery period (MT)

source_name: White blood cells, 60 min recovery after MT

value: after 60 min of recovery period (MT)


title: Athlete8-WBC-T7


title: Athlete8-WBC-T6

description: Gene expression after 30 min of recovery period (MT)

source_name: White blood cells, 30 min recovery after MT

value: after 30 min of recovery period (MT)


title: Athlete8-WBC-T4


title: Athlete4-WBC-T7


title: Athlete7-WBC-T1

description: Gene expression before exercise

source_name: White blood cells, baseline for RTE

value: before exercise


title: Athlete7-WBC-T6


title: Athlete4-WBC-T5

description: Gene expression after running at 80% VO2 peak for 30 min on a treadmill

source_name: White blood cells, MT


title: Athlete7-WBC-T5

value: after running at 80% VO2 peak for 30 min on a treadmill


title: Athlete7-WBC-T2

description: Gene expression after ramp test to exaustion

source_name: White blood cells, RTE

value: after ramp test to exaustion


title: Athlete8-WBC-T3

description: Gene expression after 30 min of recovery period (RTE)

source_name: White blood cells, 30 min recovery after RTE

value: after 30 min of recovery period (RTE)


title: Athlete8-WBC-T1

description: Gene expression before exercise


title: Athlete7-WBC-T3


title: Athlete4-WBC-T6


title: Athlete4-WBC-T4


title: Athlete8-WBC-T5


title: Athlete8-WBC-T2


title: RAL820_8hr_drug

city: Ithaca

first: Clement

middle: Y

last: Chow

address: 227 Biotech Bldg

institute: Cornell University

description: gene expression after 8 hr on tunicamycin

hyb_protocol: Hybridized overnight at 60 C

scan_protocol: Microarrays were scanned on an Axon 4000B scanner

data_processing: Agilent Feature Extraction and GenePix Pro-6.0 software

organism: Drosophila melanogaster

label_protocol: Samples were labelled following the Ambion amino allyl messageAMP II aRNA Kit

extract_protocol: RNA was extracted by standard phenol/chloroform protocol

treatment_protocol: Flies were placed on Tunicamycin or control food for 8 or 20 hours. Food: 1% sucrose, 1.3% low melting agarose, water. Tunicamycin concentration: 12uM

tag: tissue

value: whole fly

tag: Sex

value: 3-6 days

tag: line

tag: time

value: 8 hr

value: tunicamycin


title: RAL890_8hr_control

description: gene expression after 8 hr on control treatment

tag: treatment

value: control


title: RAL820_8hr_control


title: RAL820_20hr_drug

description: gene expression after 20 hr on tunicamycin

value: 20 hr


title: RAL890_8hr_drug


title: RAL801_8hr_control


title: Athlete4-WBC-T3


title: Athlete4-WBC-T1

description: Gene expression before exercise


title: RAL801_8hr_drug


title: RAL820_20hr_control

description: gene expression after 20 hr on control treatment


title: RAL783_8hr_drug


title: RAL783_8hr_control


title: Athlete6-WBC-T3


title: Athlete4-WBC-T2


title: Athlete6-WBC-T4


title: Athlete6-WBC-T2


title: Athlete5-WBC-T7


title: Athlete6-WBC-T6


title: RAL712_20hr_drug


title: Athlete5-WBC-T5


title: RAL721_8hr_control


title: RAL721_8hr_drug


title: Athlete6-WBC-T5


title: RAL486_8hr_control


title: RAL716_8hr_control


title: Athlete3-WBC-T7


title: Athlete3-WBC-T5


title: Athlete5-WBC-T3


title: Athlete3-WBC-T6


title: Athlete5-WBC-T4


title: Athlete5-WBC-T6


title: RAL563_8hr_control


title: RAL563_8hr_drug


title: RAL712_8hr_drug


title: Athlete5-WBC-T1

description: Gene expression before exercise


title: RAL712_8hr_control


title: RAL486_8hr_drug


title: RAL716_8hr_drug


title: RAL440_8hr_drug


title: RAL712_20hr_control


title: Athlete6-WBC-T1

description: Gene expression before exercise


title: RAL440_8hr_control


title: Athlete5-WBC-T2


title: Athlete3-WBC-T3


title: Athlete3-WBC-T1

description: Gene expression before exercise


title: Athlete3-WBC-T4


title: RAL379_8hr_drug


title: RAL379_20hr_control


title: Athlete2-WBC-T4


title: Athlete2-WBC-T7


title: RAL375_8hr_drug


title: RAL375_20hr_drug


title: RAL379_20hr_drug


title: Athlete2-WBC-T6


title: Athlete2-WBC-T5


title: RAL370_8hr_drug


title: Athlete3-WBC-T2


title: Athlete2-WBC-T3


title: RAL375_8hr_control


title: RAL358_20hr_drug


title: Athlete1-WBC-T5


title: Athlete1-WBC-T6


title: RAL375_20hr_control


title: Athlete1-WBC-T7


title: RAL370_8hr_control


title: RAL379_8hr_control


title: Athlete2-WBC-T1

description: Gene expression before exercise


title: RAL358_8hr_control


title: Athlete1-WBC-T4


title: RAL358_8hr_drug


title: Athlete6-WBC-T7


title: RAL318_8hr_drug


title: Athlete2-WBC-T2


title: Athlete1-WBC-T1

description: Gene expression before exercise


title: Athlete1-WBC-T2


title: RAL335_8hr_control


title: RAL318_8hr_control


title: RAL318_20hr_drug


title: RAL358_20hr_control


title: RAL335_8hr_drug


title: RAL318_20hr_control


title: O2ACH iPS-2

city: Cambridge

first: Jose

last: Silva

state: Cambridgeshire

address: Tennis Court Road

department: Biochemistry

country: United Kingdom

institute: Wellcome Trust Centre for Stem Cell Research

hyb_protocol: Performed according to the Whole Genome Gene Expression Direct Hybridization Guide on the MouseWG-6 v2.0 Expression BeadChip (Illumina).

data_processing: The raw data were filtered to remove any non expressed genes from the set. The data were then transformed using VST (Variance Stabilizing Transform) and normalised by quantile normalisation. To obtain the normalized data, the raw data have been filtered to remove any non-expressed genes, then transformed using VST (close to a log2 transformation) and finally normalised. In two of our samples (O2ACH iPS and Cl25) Pou5f1 gene is represented by a long fusion transcript. This influences the hybridization efficiency of the transcript and makes gene expression signal incomparable to Pou5f1 in ESC sample.

organism: Mus musculus

source_name: PB-Oct4.2A.cherry iPS-/- cells

label_protocol: Amplification and labeling of RNA were performed according to the TotalPrep-96 RNA Amplification Kit for the Illumina platform (Ambion).

growth_protocol: iPS and ES cells were cultured in knockout serum replacement-containing medium supplemented with LIF and 2i inhibitors (Ying et al., 2008), CHIR99021 (3μM) and PD0325901 (1μM).

extract_protocol: Total RNA was extracted using RNeasy kit (Qiagen)

tag: background strain

tag: cell type

value: PB-Oct4.2A.cherry iPS-/-


title: CL25-2

scan_protocol: Performed according to the Whole Genome Gene Expression Direct Hybridization Guide on the MouseWG-6 v2.0 Expression BeadChip (Illumina).

source_name: PB-Oct4.2A.cherry (low) cl2.5 iPS-/- cells

value: PB-Oct4.2A.cherry (low) cl2.5 iPS-/-


title: ESC-2

source_name: ES cells

value: embryonic stem (ES)


title: RAL301_8hr_control

value: male


title: RAL301_20hr_control


title: O2ACH iPS-1


title: Athlete1-WBC-T3


title: CL25-1


title: RAL301_20hr_drug


title: RAL301_8hr_drug


title: Cells with no CSF1 treatment

city: new haven

first: chen

last: yao

address: 300 cedar street

institute: yale

description: Gene expression data from macrophages without CSF1 treatment

hyb_protocol: Standard Affymetrix protocols for Mouse Genome 430 2.0 Array

data_processing: The data were analyzed with Gene spring 6.2 software using default parameters

source_name: Cells with no CSF1 treatment

growth_protocol: Wild type C57/BL6 mice were treated with 0.2 ml 10 % thioglycolate medium (FTG) / mouse by intra-peritoneal injection. Mice were sacrificed one week after injection followed by intra-peritoneal lavage with 15ml PBS. Macrophages were plated at a density of 1.5×10^6/well in 6-well plates and cultured in α-MEM supplemented with 10% FBS.

extract_protocol: RNeasy kit (Qiagen, Gaithersburg, MD) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: At 80% confluence, cells were treated with 100ng/ml CSF1 or without treatment for 12 hours and RNA extracted.

value: Mouse peritoneal macrophages

tag: strain

value: 8 weeks


title: ESC-1


title: RAL208_8hr_drug


title: Cells with 12hrs CSF1 treatment

description: Gene expression data from macrophages with 12hr CSF1 treatment

scan_protocol: Standard Affymetrix protocols for Mouse Genome 430 2.0 Array

source_name: Cells with 12hrs CSF1 treatment


title: SB15_flag leaf_rep2_6-8DAA

city: Brisbane

first: Gang-Ping

last: Xue

state: Qld

address: 306 Carmody Rd., St Lucia

department: Plant Industry

country: Australia

institute: CSIRO

hyb_protocol: Refer to the AGRF website http://www.agrf.org.au for details of the protocol used.

data_processing: The raw GeneChip data (CEL files) were normalized using GeneChip robust multiarray average (GC-RMA), a log scale measurement of expression developed by Wu et al. (2004), using the default settings for the Affymetrix package within Bioconductor, running within the R statistical programming environment (http://www.r-project.org/).

organism: Triticum aestivum

source_name: The flag leaf of SB15 line at 6-8 days after anthesis, field replicate 2

growth_protocol: Plants were grown with two field replicates of each line under irrigated conditions in 2007 at the CSIRO Cooper Laboratory at Gatton, Queensland, Australia (latitude 27o  34΄ S, longitude 152o 17΄ E).  The site was on a deep fertile prairie loam soil developed on alluvium with a plant available water holding capacity of about 250 mm to a depth of 1.5 m.  Plot size in each field trial was 6 m  1.76 m (8 rows) with an inter-row spacing of 22 cm.

extract_protocol: Total RNA was isolated from samples using Plant RNA Reagent (Invitrogen, California, USA), according to the manufacturer’s instruction. RNA was further purified through a Qiagen RNeasy column (Qiagen, Australia) after pre-treatment with RNase-free DNase I

tag: developmental stage

value: 6-8 days after anthesis

tag: organ

value: flag leaves

tag: field replicate


title: DC-activated CD8+ OT-I derived Teff Sample 16 (analysis 2)

city: Bonn

first: Joachim

middle: L

last: Schultze

address: Carl-Troll-Str. 31

department: LIMES Institute

country: Germany

institute: University of Bonn

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation using R Statistical language and packages from the Bioconductor project

source_name: coculture with splenic  DC

label_protocol: Biotinylated cRNA was prepared with the TargetAmp Nano-g Biotin aRNA Labeling Kit (Biozym Scientific GmbH, Hessisch Oldendorf, Germany).

extract_protocol: RNA was extracted with QIAzol Lysis Reagent using the miRNeasy Mini Kit  according to the manufacturer´s protocol (Qiagen, Hilden, Germany). Quality control was performed with denaturing gel electrophoresis and UV measurement.

value: C57Bl/6 background

value: 2-6 months

tag: sample type

value: isolated lymphocytes

value: CD8+ Teff


title: DC-activated CD8+ OT-I derived Teff Sample 17 (analysis 2)


title: RAL208_8hr_control

value: whole fly

value: 3-6 days


title: SB189_flag leaf_rep2_6-8DAA

scan_protocol: Refer to the AGRF website http://www.agrf.org.au for details of the protocol used.

source_name: The flag leaf of SB189 line at 6-8 days after anthesis, field replicate 2


title: SB15_flag leaf_rep1_6-8DAA

source_name: The flag leaf of SB15 line at 6-8 days after anthesis, field replicate 1

label_protocol: Refer to the AGRF website http://www.agrf.org.au for details of the protocol used.


title: RAL208_20hr_control


title: RAL049_8hr_drug

value: 8 hr

value: tunicamycin


title: OT-I derived CD8+ LSEC-primed T cells Sample 15 (analysis 2)

source_name: coculture with  LSEC

value: CD8+ Tpm


title: naive CD8+ OT-I T cells Sample 13 (analysis 2)

source_name: spleen

value: naive CD8+ T cells


title: SB53_flag leaf_rep2_6-8DAA

source_name: The flag leaf of SB53 line at 6-8 days after anthesis, field replicate 2


title: DC-activated CD8+ OT-I derived Teff Sample 10 (analysis 2)


title: SB138_flag leaf_rep1_6-8DAA

source_name: The flag leaf of SB138 line at 6-8 days after anthesis, field replicate 1


title: SB165_flag leaf_rep2_6-8DAA

source_name: The flag leaf of SB165 line at 6-8 days after anthesis, field replicate 2


title: SB80_flag leaf_rep2_6-8DAA

source_name: The flag leaf of SB80 line at 6-8 days after anthesis, field replicate 2


title: RAL045_8hr_drug


title: SB189_flag leaf_rep1_6-8DAA

source_name: The flag leaf of SB189 line at 6-8 days after anthesis, field replicate 1


title: RAL045_8hr_control

value: control


title: RAL049_8hr_control


title: OT-I derived CD8+ LSEC-primed T cells Sample 14 (analysis 2)


title: SB146_flag leaf_rep2_6-8DAA

source_name: The flag leaf of SB146 line at 6-8 days after anthesis, field replicate 2


title: naive CD8+ OT-I T cells Sample 11 (analysis 2)


title: DC-activated CD8+ OT-I derived Teff Sample 8 (analysis 2)


title: SB80_flag leaf_rep1_6-8DAA

source_name: The flag leaf of SB80 line at 6-8 days after anthesis, field replicate 1


title: SB146_flag leaf_rep1_6-8DAA

source_name: The flag leaf of SB146 line at 6-8 days after anthesis, field replicate 1


title: DC-activated CD8+ OT-I derived Teff Sample 6 (analysis 2)


title: RAL208_20hr_drug

value: 20 hr


title: SB165_flag leaf_rep1_6-8DAA

source_name: The flag leaf of SB165 line at 6-8 days after anthesis, field replicate 1.


title: memory CD8+ OT-I T cells  three months after Listeria monocytogenes OVA infection Sample 9 (analysis 2)

value: memory CD8+ T cells


title: naive CD8+ OT-I T cells Sample 12 (analysis 2)


title: Day3_Ctrl_3

city: Boston

first: Michelle

last: Arya

address: 15 Kneeland Street

institute: MCRI

data_processing: Robust spline normalization and base calling performed using R and analysis package lumi

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

growth_protocol: C2C12 cells grown in DMEM-HG media with 20% FBS

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

treatment_protocol: At 70% confluence growth medium was replaced with DMEM-HG and 2% Horse Serum +/- 100mM Ethanol. Daily medium changes.

value: C2C12 myoblast cells


title: Day3_EtOH_2


title: SB138_flag leaf_rep2_6-8DAA

source_name: The flag leaf of SB138 line at 6-8 days after anthesis, field replicate 2


title: SB53_flag leaf_rep1_6-8DAA

source_name: The flag leaf of SB53 line at 6-8 days after anthesis, field replicate 1


title: SB33_flag leaf_rep1_6-8DAA

source_name: The flag leaf of SB33 line at 6-8 days after anthesis, field replicate 1


title: Day3_EtOH_3


title: Day3_EtOH_1


title: Day3_Ctrl_2


title: memory CD8+ OT-I T cells  three months after Listeria monocytogenes OVA infection Sample 5 (analysis 2)


title: OT-I derived CD8+ LSEC-primed T cells Sample 4 (analysis 2)

value: CD8+ LSEC-primed T cells


title: DC-activated CD8+ OT-I derived Teff Sample 17 (analysis 1)

source_name: coculture with splenic  DC


title: OT-I derived CD8+ LSEC-primed T cells Sample 7 (analysis 2)


title: OT-I derived CD8+ LSEC-primed T cells Sample 15 (analysis 1)


title: memory CD8+ OT-I T cells  three months after Listeria monocytogenes OVA infection Sample 3 (analysis 2)


title: naive CD8+ OT-I T cells Sample 2 (analysis 2)


title: Day2_EtOH_3


title: naive CD8+ OT-I T cells Sample 1 (analysis 2)


title: Day3_Ctrl_1


title: Day2_Ctrl_2


title: Day2_Ctrl_3


title: Day2_EtOH_2


title: PAR-2_2

city: Taipei

first: Che-Ming

last: Teng

address: No.1, Jen-Ai Road

department: Pharmacology

country: Taiwan

institute: National Taiwan University

hyb_protocol: Fluorescent targets were hybridized to the Human Whole Genome OneArrayR (HOA5.1) with Phalanx hybridization buffer using Phalanx Hybridization System. After 16 hrs hybridization at 50 ℃, non-speciﬁc binding targets were washed away by three different washing steps (WashⅠ 42 ℃ 5 mins；Wash Ⅱ 42 ℃, 5 mins, 25 ℃ 5 mins; Wash Ⅲ rinse 20 times).

scan_protocol: The arrays were scanned by Axon GenePix 4000B scanner (635nm power 100 PMT 550~570 ; 532nm power 10, PMT 460) and quantify the fluoresence intensity.

data_processing:
The signal intensity of each spot was loaded into Rosetta Resolver SystemR (Rosetta Biosoftware) to process data analysis. Normalized spot intensities were transformed to gene expression log2 ratios between the control and treatment groups under Rosetta Resolver error model adjustment.
The spots with log2 ratio ≥ 0.5 or log2 ratio ≤ -0.5 and P-value < 0.05 are tested for further analysis.

source_name: BxPC-3 cells with PAR-2 AP-2

label_protocol: Fluorescent aRNA targets were prepared from 2.5 μg total RNA samples using OneArrayR Amino Allyl aRNA Amplification Kit (Phalanx Biotech Group, Taiwan) and Cy5 dyes (Amersham Pharmacia, Piscataway, NJ, USA).

growth_protocol: Human pancreatic cancer cell line BxPC-3 were cultured in RPMI-1640 with 10% FBS (v/v) and were maintained in a humidified incubator at 37℃ in 5% CO2/95% air..

extract_protocol: Total RNA were harvested by Trizol reagent, followed by purification using RNeasy Mini kit (Qiagen, Valencia, CA). RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧8).

treatment_protocol: Human pancreatic cancer cell line BxPC-3 were treated with or without PAR-2 AP for 4 hours.

value: PAR-2 AP

value: human pancreatic adenocarcinoma

tag: cell line


title: Day2_Ctrl_1


title: OT-I derived CD8+ LSEC primed T cells Sample 14 (analysis 1)

value: C57Bl/6 background

tag: age


title: Day2_EtOH_1


title: Control_1

source_name: BxPC-3 cells with vehicle-1


title: Day1_EtOH_4


title: DC-activated CD8+ OT-I derived Teff Sample 16 (analysis 1)

value: 2-6 months


title: PAR-2_1

source_name: BxPC-3 cells with PAR-2 AP-1


title: Control_2

source_name: BxPC-3 cells with vehicle-2


title: Day1_EtOH_2


title: Day1_Ctrl_4


title: G. metallireducens_acetate_rep3

city: Amherst

first: Tian

last: Zhang

state: MA

address: 639 North Pleasant St.

department: Microbiology

institute: University of Massachusetts

description: This sample is of Geobacter metallireducens DSM 7210. It is the third of three biological replicates grown on acetate used in this experiment, each from separate cultures.

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: Geobacter metallireducens

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

growth_protocol: Geobacter metallireducens DSM 7210 was grown in strict anaerobic conditions (80:20 N2/CO2) in medium previously described (Lovley and Phillips, Appl. Environ. Microbiol. 1988, 54(6): 1472-1480) with 10 mM acetate as electron donor and 56 mM ferric citrate as electron acceptor. Cultures were incubated at 30 °C in the dark.

extract_protocol: 1L cultures were divided into 500 ml centrifuge bottles, and cells were pelleted with centrifugation at 10,000 X g for 10 minutes. Pellets were then immediately frozen in liquid nitrogen and stored at -80 °C. Total RNA was extracted according to the HG protocol described in Holmes et al., ISME Journal, 2011.

tag: electron donor

value: Acetate

tag: electron donor type

value: fatty acid


title: G. metallireducens_acetate_rep1

description: This sample is of Geobacter metallireducens DSM 7210. It is the first of three biological replicates grown on acetate used in this experiment, each from separate cultures.

source_name: 10 mM acetate as electron donor and 56 mM ferric citrate as electron acceptor


title: Day1_EtOH_1


title: G. metallireducens_acetate_rep2

description: This sample is of Geobacter metallireducens DSM 7210. It is the second of three biological replicates grown on acetate used in this experiment, each from separate cultures.


title: SB33_flag leaf_rep2_6-8DAA

source_name: The flag leaf of SB33 line at 6-8 days after anthesis, field replicate 2

value: 6-8 days after anthesis

value: flag leaves


title: Day1_EtOH_3


title: naive CD8+ OT-I T cells Sample 13 (analysis 1)

source_name: spleen

value: isolated lymphocytes


title: Day1_Ctrl_3


title: naive CD8+ OT-I T cells Sample 11 (analysis 1)


title: Normal Sample 2, CD133-

city: Stanford

first: Hadi

last: Zarkoob

state: California

address: 450 Serra Mall  Stanford

institute: Stanford University

description: Gene expression data from normal fetal neural cells, marked negative when sorted for CD133 cell surface protein

hyb_protocol: Following fragmentation, 12.5 µg of fragmented and labeled aRNA was hybridized for 16h at 450C on Human Genome U133 Plus 2.0 arrays and GeneChip fluidic station P450 with protocol EuKGE_WS2v4_450.

scan_protocol: Gene Chips were scanned using Affymetrix GeneChip Scanner 7G.

data_processing: We used MATLAB software to obtain log2 based gene expression values from the .CEL files. The resulting gene expression values were background adjusted, normalized, and summarized using the Robust Multi-array Average (RMA) procedure.

source_name: Sorted Normal Sample 2, CD133-

label_protocol: Biotinylated cRNA was prepared from 1 µg of total RNA using  Affymetrix GeneChip 3’ Express kit according to manufacturer’s instructions.

growth_protocol: Cells isolated from human primary Glioblastoma (GBM) tumours and fetal neural tissue were grown as neurospheres in neural stem cell media with growth factors : LIF (10ng/mL), FGF (20ng/mL)and EGF (20ng/mL). Cultures were maintained at 37°C and 5% CO2 .

extract_protocol: Total RNA from CD133+ and CD133- cells was isolated using the RNeasy Micro kit (Qiagen) as per manufacturer’s instructions.

treatment_protocol: Single cell suspension isolated from dissociated neurospheres was labeled with CD133/1 (Miltenyi) and CD133+ cells were purified using magnetic bead cell sorting (MACS; STEMCELL Technologies) as per manufacturer’s instructions.

value: Normal fetal neural cells


title: G. metallireducens_toluene_rep2

description: This sample is of Geobacter metallireducens DSM 7210. It is the second of three biological replicates grown on toluene used in this experiment, each from separate cultures.

growth_protocol: Geobacter metallireducens DSM 7210 was grown in strict anaerobic conditions (80:20 N2/CO2) in medium previously described (Lovley and Phillips, Appl. Environ. Microbiol. 1988, 54(6): 1472-1480) with 500 µM toluene as electron donor and 56 mM ferric citrate as electron acceptor. Cultures were incubated at 30 °C in the dark.

value: Toluene

value: aromatic


title: G. metallireducens_toluene_rep3

description: This sample is of Geobacter metallireducens DSM 7210. It is the third of three biological replicates grown on toluene used in this experiment, each from separate cultures.

source_name: 500 µM toluene as electron donor and 56 mM ferric citrate as electron acceptor


title: G. metallireducens_toluene_rep1

description: This sample is of Geobacter metallireducens DSM 7210. It is the first of three biological replicates grown on toluene used in this experiment, each from separate cultures.


title: naive CD8+ OT-I T cells Sample 12 (analysis 1)

value: naive CD8+ T cells


title: DC-activated CD8+ OT-I derived Teff Sample 8 (analysis 1)

value: CD8+ Teff


title: G. metallireducens_benzoate_rep3

description: This sample is of Geobacter metallireducens DSM 7210. It is the third of three biological replicates grown on benzoate used in this experiment, each from separate cultures.

growth_protocol: Geobacter metallireducens DSM 7210 was grown in strict anaerobic conditions (80:20 N2/CO2) in medium previously described (Lovley and Phillips, Appl. Environ. Microbiol. 1988, 54(6): 1472-1480) with 1 mM benzoate as electron donor and 56 mM ferric citrate as electron acceptor. Cultures were incubated at 30 °C in the dark.

value: Benzoate


title: DC-activated CD8+ OT-I derived Teff Sample 10 (analysis 1)


title: OT-I derived CD8+ LSEC-primed T cells Sample 7 (analysis 1)

source_name: coculture with  LSEC

value: CD8+ Tpm


title: memory CD8+ OT-I T cells  three months after Listeria monocytogenes OVA infection Sample 9 (analysis 1)

value: memory CD8+ T cells


title: RefDay0_3

value: C2C12 myoblast cells


title: G. metallireducens_phenol_rep2

description: This sample is of Geobacter metallireducens DSM 7210. It is the second of three biological replicates grown on phenol used in this experiment, each from separate cultures.

growth_protocol: Geobacter metallireducens DSM 7210 was grown in strict anaerobic conditions (80:20 N2/CO2) in medium previously described (Lovley and Phillips, Appl. Environ. Microbiol. 1988, 54(6): 1472-1480) with 500 µM phenol as electron donor and 56 mM ferric citrate as electron acceptor. Cultures were incubated at 30 °C in the dark.

value: Phenol


title: Wild type retina 3

city: Bellaterra

first: Miquel

last: Garcia

state: -- Please Select (only U.S. / Can / Aus)

address: Campus UAB Edifici H

country: Spain

institute: UAB

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

source_name: retina WT3

label_protocol: standard Affymetrix protocol

extract_protocol: To prepare total RNA for microarray analysis, we used retinas from 4 month-old Wt and TgIGF-I mice. We used the recommended Affymetrix protocol for RNA extraction (Expression Analysis Technical Manual; http://www.affymetrix.com). Briefly, each pair of retinas were homogenised with Trizol (Invitrogen) before precipitation and column purification (Qiagen). On-column DNase I digestion was carried out (Qiagen). (Parameters: Extracted product = total RNA, Amplification = none)

value: retina

tag: biosource type

value: frozen sample

value: male

tag: genotype

value: wild type


title: RefDay0_2


title: G. metallireducens_benzoate_rep2

description: This sample is of Geobacter metallireducens DSM 7210. It is the second of three biological replicates grown on benzoate used in this experiment, each from separate cultures.

source_name: 1 mM benzoate as electron donor and 56 mM ferric citrate as electron acceptor


title: memory CD8+ OT-I T cells  three months after Listeria monocytogenes OVA infection Sample 5 (analysis 1)

value: C57Bl/6 background

value: 2-6 months


title: G. metallireducens_phenol_rep3

description: This sample is of Geobacter metallireducens DSM 7210. It is the third of three biological replicates grown on phenol used in this experiment, each from separate cultures.

source_name: 500 µM phenol as electron donor and 56 mM ferric citrate as electron acceptor


title: Normal Sample 2, CD133+

description: Gene expression data from normal fetal neural cells, marked positive when sorted for CD133 cell surface protein

source_name: Sorted Normal Sample 2, CD133+

tag: tissue


title: GBM Sample 1, CD133-

description: Gene expression data from GBM cells, marked negative when sorted for by CD133 cell surface protein

source_name: Sorted GBM Sample 1, CD133-

value: Brain tumor, GBM


title: DC-activated CD8+ OT-I derived Teff Sample 6 (analysis 1)

value: isolated lymphocytes


title: GBM Sample 2, CD133-

description: Gene expression data from GBM cells, marked negative when sorted for CD133 cell surface protein

source_name: Sorted GBM Sample 2, CD133-


title: GBM Sample 1, CD133+

description: Gene expression data from GBM cells, marked positive when sorted for CD133 cell surface protein

source_name: Sorted GBM Sample 1, CD133+


title: RefDay0_1


title: Normal Sample 1, CD133+

source_name: Sorted Normal Sample 1, CD133+

value: Normal fetal neural cells


title: Day1_Ctrl_1


title: Wild type retina 2

source_name: retina WT2

tag: Sex


title: RefDay0_4


title: OT-I derived CD8+ LSEC-primed T cells Sample 4 (analysis 1)


title: G. metallireducens_benzoate_rep1

description: This sample is of Geobacter metallireducens DSM 7210. It is the first of three biological replicates grown on benzoate used in this experiment, each from separate cultures.

value: aromatic


title: GBM Sample 2, CD133+

source_name: Sorted GBM Sample 2, CD133+


title: Normal Sample 1, CD133-

source_name: Sorted Normal Sample 1, CD133-


title: G. metallireducens_phenol_rep1

description: This sample is of Geobacter metallireducens DSM 7210. It is the first of three biological replicates grown on phenol used in this experiment, each from separate cultures.


title: Day1_Ctrl_2


title: Transgenic retina 3

source_name: retina Tg3

tag: genetic modification

value: Tg


title: memory CD8+ OT-I T cells  three months after Listeria monocytogenes OVA infection Sample 3 (analysis 1)


title: naive CD8+ OT-I T cells Sample 2 (analysis 1)

value: naive CD8+ T cells


title: Transgenic retina 2

source_name: retina Tg2


title: Transgenic retina 1

source_name: retina Tg1


title: Wild type retina 1

source_name: retina WT1


title: Cow 7264 -30d relative to parturition

city: Corvallis

first: Massimo

last: Bionaz

state: OR

address: 316A Withycombe Hall

department: Animal and Rangeland Sciences

institute: Oregon State University

description: The cDNA from Mac-T cells was pooled before hybridization and used as a reference

hyb_protocol: Labelled cDNA from all Mac-T cells samples was pooled before hybridization. The hybridisation was performed using 80 μL of the hybridization buffer #1 (Ambion).  Slides placed in humidified slide chambers (Corning) in water bath for 40 h at 42 °C. Prior scanning the microarray were washed for 5 min by agitation 3 times with wash buffers in the following order: 1×SSC and 0.2% SDS solution preheated at 45°C, 0.1×SSC and 0.2% SDS solution, and 0.1×SSC solution. Lastly, slides were inserted into a 50 mL tube, spin-dried and gassed with Argon to preserve dye from bleaching.

scan_protocol: Arrays were scanned with a ScanArray 4000 (GSI-Lumonics) dual-laser confocal scanner and images were processed and edited using GenePix 6.0 (Axon Instruments).

data_processing: Array quality was assessed using an in-house parser written in Perl language. Spots that received a -100 flag by GenePix 6.0 were removed from further analysis and background intensity was subtracted from the foreground intensity. Spots on the slide were considered “good” if the median intensity was ≥3 standard deviation above median background for each channel (i.e., dye). Spots were flagged “present” when both dyes passed the criteria, “marginal” if only one dye passed the criteria, or “absent” when both dyes failed to pass the criteria. Statistical analysis was conducted on oligos that were flagged as “present” and “marginal”. Data from a total of 120 microarrays were normalized for dye and array effects (i.e., Loess normalization and array centering and scaling) before statistical analysis.

organism: Bos taurus

source_name: Mammary biopsy of cow at -30 day relative to parturition

label_protocol: Labelled with Cy3 and Cy5 during cDNA synthesis from total RNA using Superscript III Kit (Invitrogen) as manufacturers instructions.

growth_protocol: Cows were maintain in a normal farm management/ Mac-T cells were growth in 6 well plates in a basal Minimum Essential Medium/Earles Balanced Salts HyQ with insulin (5 mg/L), hydrocortisone (1 mg/L), transferrin (5 mg/L), ascorbic acid (5 μM/L), sodium acetate (5 mM/L), penicillin/streptomycin (10 mL/L), 10% fetal bovine serum, and growth-promoting factors (1 mg/L of progesterone, 0.05% lactalbumin, 0.05% α-lactose).

extract_protocol: Mammary tissue was obtained by percutaneous biopsy. After biopsy tissue was weighted (~0.5-1.0 g) and immediately immerged in ice-cold TRIZol. Mac-T cells were harvested by addition of 1 mL TRIZol and immediately frozen at -80C. After RNA extraction genomic DNA was removed from RNA with DNAse (Qiagen) using RNeasy Mini Kit columns (Qiagen).

treatment_protocol: 36 h before harvesting (approximately 90% confluence), Mac-T cells were cultured in 6 well plates in high-glucose Dulbecco’s modified Eagle’s medium devoid of fetal bovine serum and supplemented with BSA (1 g/L) and prolactin (2.5 mg/L)

tag: breed

value: Holstein dairy cow

value: Mammary biopsy

source_name: Mac-T cells induced to lactation for 24h

value: Holstein dairy cows

value: Mac-T cells


title: naive CD8+ OT-I T cells Sample 1 (analysis 1)

source_name: spleen


title: G. metallireducens_benzene_rep3

description: This sample is of Geobacter metallireducens DSM 7210. It is the third of three biological replicates grown on benzene used in this experiment, each from separate cultures.

growth_protocol: Geobacter metallireducens DSM 7210 was grown in strict anaerobic conditions (80:20 N2/CO2) in medium previously described (Lovley and Phillips, Appl. Environ. Microbiol. 1988, 54(6): 1472-1480) with 250 µM benzene as electron donor and 56 mM ferric citrate as electron acceptor. Cultures were incubated at 30 °C in the dark.

value: Benzene


title: Cow 7264 60d relative to parturition

source_name: Mammary biopsy of cow at 60 day relative to parturition


title: Cow 7257 -30d relative to parturition


title: Bacteria were cultured in TSB S2308_2

city: Shanghai

first: Mingxing

last: Tian

address: NO.518, Ziyue Road, Minhang District

country: China

institute: Shanghai Veterinary Research Institute

description: Bacteria were cultured in TSB

hyb_protocol: Each labeled cRNA sample (1 µg) was fragmented by adding 11 μL of 10 × Agilent blocking agent and 2.2 μL of 25 × fragmentation buffer, heated at 60°C for 30 min, and then combined with 55 μL of 2 × gene expression hybridization buffer to dilute the labeled cRNA. Next, hybridization solution (100 μL) was dispensed into the gasket slide, which was then assembled to the gene expression microarray slide. The slides were incubated for 17 h at 65°C in a hybridization oven (Agilent Technologies, Inc.).

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505B)

data_processing: Agilent Feature Extraction software (version 10.7.3.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies).

organism: Brucella abortus str. 2308 A

source_name: microorganism

label_protocol: 1 μg of total RNA from each sample was linearly amplified and fluorescently labeled with Cy3-deoxycytidine triphosphate. The labeled cRNAs were purified using the RNAeasy Mini Kit (Qiagen)

growth_protocol: The intracellular Brucella abortus were isolated from infected RAW264.7 macrophages at 24h post-infection.  In vitro, Brucella abortus strains were cultured in Tryptic Soy Broth at 37oC with 5% CO2  for 24h.

extract_protocol: Total RNA was extracted from bacteria (1×108 CFU) using TRIzol® RNA Isolation Reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol. Genomic DNA contamination was removed using the TURBO DNA-free kit (Ambion, Inc., Austin, TX, USA)

tag: host


title: Bacteria were cultured in TSB S2308_3

description: Bacteria were cultured in TSB


title: Bacteria were cultured in TSB S2308_1

description: Bacteria were cultured in TSB


title: naïve spleen LTi_rep4

city: Philadelphia

first: Laurel

middle: A

last: Monticelli

state: PA

address: 344 BRB II/III, 421 Curie Blvd

institute: University of Pennsylvania

hyb_protocol: cDNA was amplified with NuGen WT Ovation Pico kit and hybridized to Affymetrix GeneChip Mouse Gene 1.0 ST microarrays at the University of Pennsylvania’s Microarray facility.

scan_protocol: A confocal scanner was used to collect fluorescence signal at 3um resolution after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray feature.

data_processing: Affymetrix Power Tools were used to process and quantile normalize fluorescent hybridization signals using Robust Multichip Averaging. Transcript values were log2 normalized.

source_name: naïve spleen

label_protocol: Microarrays were washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain

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

value: naïve spleen

value: wild-type C57Bl/6 female


title: Cow 7251 60d relative to parturition

tag: cell type


title: Cow 7257 60d relative to parturition


title: Cow 7251 -30d relative to parturition


title: naïve spleen LTi_rep2


title: naïve spleen LTi_rep1


title: naïve lung ILC_rep4

source_name: naïve lung

value: naïve lung


title: G. metallireducens_benzene_rep1

description: This sample is of Geobacter metallireducens DSM 7210. It is the first of three biological replicates grown on benzene used in this experiment, each from separate cultures.

source_name: 250 µM benzene as electron donor and 56 mM ferric citrate as electron acceptor

tag: strain


title: G. metallireducens_benzene_rep2

description: This sample is of Geobacter metallireducens DSM 7210. It is the second of three biological replicates grown on benzene used in this experiment, each from separate cultures.


title: Bacteria isolated from RAW264.7 macrophages C2308_1

description: Bacteria isolated from RAW264.7 microphages


title: Bacteria isolated from RAW264.7 macrophages C2308_2


title: naïve spleen LTi_rep3


title: naïve lung ILC_rep2


title: Bacteria isolated from RAW264.7 macrophages C2308_3


title: Th2 SH-2251 4hr stimulation

city: Toon

first: Junpei

last: Suzuki

address: Shitukawa

department: Graduate School of Medicine

country: Japan

institute: Ehime University

description: gene expression after 4 hours in immunobilized anti-TCR-b-stimulated SH-2251-treated Th2 cells

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

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

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

source_name: Primary CD4 T cell from spleen

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

growth_protocol: Splenic CD4 T cells were prepared using a magnetic cell sorter (AutoMACS; Miltenyi Biotec). The cells were stimulated for 2 days with immobilized anti-TCR-β mAb (3μg/ml; H57-597; BioLegend), plus an anti-CD28 mAb (1μg/ml; 37.5; BioLegend) in the presence of IL-2 (2.5 ng/ml) and IL-4 (10 ng/ml; PeproTech) with or without SH-2251 (1 μM; Ishihara Sangyo Kaisha). Then cells were transferred new plate, and cultured for an additional 3 days in the presence of  IL-2 (2.5 ng/ml) and IL-4 (10 ng/ml) with or withoutSH-2251 (1 mM).

extract_protocol: Total RNA was isolated with Trizol regent (GIBCO)

treatment_protocol: SH-2251-treated and untreated Th2 cells were stimulated or unstimulated for 4 hours with immobilized anti-TCR-β mAb.

tag: treatment

value: SH-2251 + anti-TCR-β mAb

value: CD4 Th2

tag: gender

value: female

value: spleen


title: naïve lung ILC_rep1


title: naïve lung ILC_rep3


title: Th2 Control 4hr stimulation

description: gene expression after 4 hours in immunobilized anti-TCR-b-stimulated Th2 cells

value: anti-TCR-β mAb


title: Th2  SH-2251 unstimulation

description: gene expression in SH-2251-treated Th2 cells


title: Th2 Control unstimulation

description: gene expression in Th2 cells

value: control


title: primary HSCs, day 3, vehicle rep1

status: Public on Apr 29 2013

city: La Jolla

first: Ruth

middle: T

last: Yu

state: CA

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

data_processing: The data were normalized using cubic spline in Illumina GenomeStudio (v.2011.1) and also using the VAMPIRE Bayesian model with a 2-sided Bonferroni-corrected threshold of 0.05.

organism: Rattus norvegicus

source_name: primary HSCs_day 3_vehicle

value: Wistar rat

value: male

value: 10 weeks

value: primary rat hepatic stellate cells

tag: treated with

value: vehicle


title: primary HSCs, day 3, 1,25(OF)2-D3 treated rep1

source_name: primary HSCs_day 3_1,25(OF)2-D3 treated


title: primary HSCs, day 3, vehicle rep2


title: Human Esophageal Squamous Cell Carcinoma Replicate 57

type: genomic

city: Beijing

first: Ming-Rong

last: Wang

address: 17 Panjiayuan Nanli, Chaoyang District, Beijing, China

institute: Cancer Institute (Hospital), Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China

description: Biological replicate 57 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue

hyb_protocol: Reference DNA probes and dysplasia/carcinoma DNA probes was combined and Human Cot-1 DNA (Invitrogen), 10 Blocking Agent and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, then samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential.

scan_protocol: Scanned on an Agilent G2505B Scanner Images were quantified using Agilent Feature Extraction Software (version 9.1.3.1).

data_processing: Agilent Feature Extraction Software (version 9.1.3.1) was used for background subtraction and Linear normalization. Agilent Genomic Workbench Lite Edition 6.5 used centralization algorithm to normalize the data of arrays and used ADM-2 algorithm to analyze the aberration data.

molecule: genomic DNA

source_name: [TEST] Human Esophageal Squamous Cell Carcinoma Surgical Tissue

label_protocol: 500 ng the reference commercial genomic DNA (promega) and the same amount of carcinoma DNA (or 400 ng the reference commercial genomic DNA and the same amount of dysplasia DNA ) were digested with Alu I (promega) and RSA I (promega) following Agilent's instructions. The digested DNA fragments were labeled with cyanine-3 dUTP or cyanine-5 dUTP using Agilent Genomic DNA Enzymatic Labeling Kit (Agilent p/n 5190-0449). Then Microcon YM-30 (Millipore) was used to clear up the labeled probes.

growth_protocol: Biopsy tissue and surgical tissue were stored at -80 ℃ before DNA extraction.

extract_protocol: Genomic DNA was extracted using Qiagen DNeasy Blood & Tissue Kit following manufacturer's instructions.

value: Carcinoma

value: Male

tag: location

value: Esophagus

tag: lymph node metastasis

tag: distant metastasis at diagnosis

tag: Stage

value: IIA

tag: grade

source_name: [REF] Commercial Human Genomic DNA: Male

tag: reference

value: Commercial Human Genomic DNA

tag: company (vendor)

value: Promega

tag: catalog#


title: Human Esophageal Squamous Cell Carcinoma Replicate 58

description: Biological replicate 58 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue

tag: tissue

tag: age

tag: Sex

value: III


title: Human Esophageal Squamous Cell Carcinoma Replicate 56

description: Biological replicate 56 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue


title: Human Esophageal Squamous Cell Carcinoma Replicate 59

description: Biological replicate 59 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue

value: Female

source_name: [REF] Commercial Human Genomic DNA: Female


title: freshly isolated HSCs

source_name: freshly isolated HSCs


title: Human Esophageal Squamous Cell Carcinoma Replicate 55

description: Biological replicate 55 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue


title: Human Esophageal Squamous Cell Carcinoma Replicate 54

description: Biological replicate 54 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue


title: Human Esophageal Squamous Cell Carcinoma Replicate 53

description: Biological replicate 53 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue


title: FFPE urothelial carcinoma 43

first: Markus

last: Riester

address: 3 Blackfan Circle

department: Biostatistics & Computational Biology

institute: Dana-Farber Cancer Institute

description:
X0005036_A08
AT_array: a520683-00-811017-122311-4124355-81540.CEL
CG_array: a520683-00-811022-122411-4124510-84144.CEL

hyb_protocol: Hybridization was performed by Affymetrix according to the platform protocol

scan_protocol: Scanning was performed by Affymetrix

data_processing:
Data processing was performed by Affymetrix using the NEXUS software (v.6). Tables contain the following columns as provided by Affymetrix.
CopyNumber: The measured copy number value summed over both alleles of the SNP.
Copy_A:The data in this column corresponds to the measured number of copies of the Major_Allele. Values of -1 or -0.5 are an indication of untrustworthy data. -0.5 is used as a minimum value for allelic copy values and -1 is an indication of erroneous data.
Copy_B: The measured number of copies of the Minor_Allele.
AlleleRatio: The allele ratio for the two alleles of the SNP. This ratio corresponds to copy_B/copy_A (minor /major) with the caveat that it is flipped to be copy_A/copy_B (major / minor) in cases where copy_B is significantly larger than copy_A (for the given sample). This flipping (mostly) constrains the allele ratio to the range 0 to 1, so that allele ratios can be smoothed over neighboring SNPs (after excluding homozygous cases). For example, for diploid samples the heterozygous SNPs will smooth to an allele ratio value of 1.0. Or consider another example where a sample has 3 total copies in a given region. This will produce unflipped allele ratios of approximately 0/3, 1/2, 2/1, 3/0. After flipping these values will be normalized to two cases: 0/3 & 1/2. If we then exclude the 0/3 (homozygous) cases and smooth the data across the region the allele ratio will average out to 1/2. A negative allele ratio is due to negative allele copy number. Small negative allele ratios should be treated as zero, while large negative allele ratios are clearly outliers and should be disregarded.
AllelicDifference: The Allelic Difference calculation is based on the formula: (Copy A - Copy B)/(Copy A + Copy B).

label: Biotin

source_name: FFPE urothelial carcinoma

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: As per manufacturer (Affymetrix)

tag: procedure

value: TURBT

tag: site

value: bladder


title: Human Esophageal Squamous Cell Carcinoma Replicate 52

description: Biological replicate 52 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue

value: IIB


title: FFPE urothelial carcinoma 33

description:
X0005035_D08
AT_array: a520683-00-805859-103011-4119206-21273.CEL
CG_array: a520683-00-805884-110111-4119208-28318.CEL


title: FFPE urothelial carcinoma 34

description:
X0005035_D09
AT_array: a520683-00-805859-103011-4119206-21310.CEL
CG_array: a520683-00-805884-110111-4119208-28333.CEL


title: Human Esophageal Squamous Cell Carcinoma Replicate 51

description: Biological replicate 51 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue


title: FFPE urothelial carcinoma 36

description:
X0005036_A02
AT_array: a520683-00-811017-122311-4124355-81543.CEL
CG_array: a520683-00-811022-122411-4124510-84151.CEL


title: FFPE urothelial carcinoma 35

description:
X0005036_A01
AT_array: a520683-00-811017-122311-4124355-81573.CEL
CG_array: a520683-00-811022-122411-4124510-84094.CEL

value: female


title: FFPE urothelial carcinoma 37

description:
X0005036_A03
AT_array: a520683-00-811017-122311-4124355-81577.CEL
CG_array: a520683-00-811022-122411-4124510-84097.CEL


title: FFPE urothelial carcinoma 41

description:
X0005036_A06
AT_array: a520683-00-811017-122311-4124355-81570.CEL
CG_array: a520683-00-811023-122411-4124510-84221.CEL


title: FFPE urothelial carcinoma 32

description:
X0005035_D07
AT_array: a520683-00-805859-103011-4119206-21269.CEL
CG_array: a520683-00-805884-110111-4119208-28332.CEL


title: FFPE urothelial carcinoma 30

description:
X0005035_D05
AT_array: a520683-00-805859-103011-4119206-21284.CEL
CG_array: a520683-00-805884-110111-4119208-28320.CEL


title: FFPE urothelial carcinoma 40

description:
X0005036_A05
AT_array: a520683-00-811023-122411-4124510-84197.CEL
CG_array: a520683-00-811022-122411-4124510-84098.CEL


title: Human Esophageal Squamous Cell Carcinoma Replicate 49

description: Biological replicate 49 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue


title: primary HSCs, day 3, 1,25(OF)2-D3 treated rep2

tag: strain

value: Wistar rat

tag: cell type


title: Human Esophageal Squamous Cell Carcinoma Replicate 50

description: Biological replicate 50 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue

tag: gender


title: Human Esophageal Squamous Cell Carcinoma Replicate 48

description: Biological replicate 48 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue


title: Human Esophageal Squamous Cell Carcinoma Replicate 47

description: Biological replicate 47 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue


title: FFPE urothelial carcinoma 26

description:
X0005035_D01
AT_array: a520683-00-805859-103011-4119206-21311.CEL
CG_array: a520683-00-805884-110111-4119208-28326.CEL

value: male


title: FFPE urothelial carcinoma 39

description:
X0005036_A04
AT_array: a520683-00-811017-122311-4124355-81545.CEL
CG_array: a520683-00-811017-122311-4124355-81520.CEL


title: FFPE urothelial carcinoma 27

description:
X0005035_D02
AT_array: a520683-00-805859-103011-4119206-21328.CEL
CG_array: a520683-00-805884-110111-4119208-28323.CEL


title: FFPE urothelial carcinoma 29

description:
X0005035_D04
AT_array: a520683-00-805859-103011-4119206-21337.CEL
CG_array: a520683-00-805884-110111-4119208-28306.CEL


title: FFPE urothelial carcinoma 25

description:
X0005035_C11
AT_array: a520683-00-805859-103011-4119206-21296.CEL
CG_array: a520683-00-805884-110111-4119208-28303.CEL


title: FFPE urothelial carcinoma 28

description:
X0005035_D03
AT_array: a520683-00-805859-103011-4119206-21312.CEL
CG_array: a520683-00-805884-110111-4119208-28324.CEL


title: Human Esophageal Squamous Cell Carcinoma Replicate 46

description: Biological replicate 46 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue


title: FFPE urothelial carcinoma 42

description:
X0005036_A07
AT_array: a520683-00-811017-122311-4124355-81550.CEL
CG_array: a520683-00-811023-122411-4124510-84280.CEL


title: FFPE urothelial carcinoma 24

description:
X0005035_C10
AT_array: a520683-00-805859-103011-4119206-21295.CEL
CG_array: a520683-00-805884-110111-4119208-28322.CEL


title: Human Esophageal Squamous Cell Carcinoma Replicate 44

description: Biological replicate 44 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue


title: Polyploid TGCs day E9.5_aCGH_Replicate 2

first: Jessica

last: Von Stetina

address: 9 Cambridge Center

institute: Whitehead Institute

description: Biological replicate 2 of 2; hand-dissected E9.5 polyploid TGCs.

hyb_protocol: Samples were co-hybridized to a 1-million probe custom tiling array designed for C57BL/6J (Agilent-027414).

scan_protocol: Slides were washed and scanned using an Agilent microarray scanner.

data_processing: Using the Ringo package in R, probes were median-normalized and smoothened by running medians prior to calling under-replicated or amplified regions, defined by at least 5 adjacent probes with a fold change (copy number vs. overall ploidy) greater than 1.3.   Microarrays were also converted into Nimblegen format and processed by MA2C software.

source_name: murine E9.5 polyploid TGCs

label_protocol: Genomic DNA samples were differentially labeled with Invitrogen’s BioPrime Total for Agilent aCGH labeling kit.

extract_protocol: Embryonic cells and purified TGCs from 14 implantation sites (replicate 2) were lysed in CHIP buffer (50mM HEPES pH. 7.5; 140mM NaCl; 1mM EDTA; 1% Triton-X100; 0.1% Na deoxycholate), sonicated, and treated with proteinase K and RNAse. DNA was isolated following standard phenol:chloroform extraction.

tag: cell population

value: polyploid TGCs

tag: developmental stage

source_name: murine E9.5 embryonic cells

value: embryonic cells


title: Human Esophageal Squamous Cell Carcinoma Replicate 42

description: Biological replicate 42 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue

tag: location

tag: lymph node metastasis


title: Human Esophageal Squamous Cell Carcinoma Replicate 40

description: Biological replicate 40 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue

tag: distant metastasis at diagnosis

tag: Stage


title: Polyploid TGCs day E9.5_aCGH_Replicate 1

description: Biological replicate 1 of 2; hand-dissected E9.5 polyploid TGCs.

extract_protocol: Embryonic cells and purified TGCs from 29 implantation sites (replicate 1)  were lysed in CHIP buffer (50mM HEPES pH. 7.5; 140mM NaCl; 1mM EDTA; 1% Triton-X100; 0.1% Na deoxycholate), sonicated, and treated with proteinase K and RNAse. DNA was isolated following standard phenol:chloroform extraction.


title: Polyploid (16C-128C) MKs_aCGH_Replicate 1

description: Replicate 1: bone marrow cells were differentiated into MKs after culturing with thrombopoietin for 4 days.

source_name: C57Bl/6J bone marrow cells

growth_protocol: Bone marrow cells from twenty-four 6-8-week old C57B6/J mice were culture with IMDM media (Invitrogen) containing 10% fetal bovine serum, 1% penicillin-streptomycin, 4mM L-glutamine, and 25ng/ml human thrombopoietin for 4 days.

extract_protocol: Polyploid and diploid MKs were lysed in CHIP buffer (50mM HEPES pH. 7.5; 140mM NaCl; 1mM EDTA; 1% Triton-X100; 0.1% Na deoxycholate), sonicated, and treated with proteinase K and RNAse. DNA was isolated following standard phenol:chloroform extraction.

treatment_protocol: MKs were treated with 25ng/ml human thrombopoietin for 4 days to induce differentiation and polyploidization.

value: Polyploid MKs

value: Diploid MKs


title: FFPE urothelial carcinoma 23

description:
X0005035_C09
AT_array: a520683-00-805884-110111-4119208-28262.CEL
CG_array: a520683-00-805884-110111-4119208-28340.CEL

tag: grade


title: Human Esophageal Squamous Cell Carcinoma Replicate 39

description: Biological replicate 39 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue

value: Carcinoma

value: Male

tag: reference

tag: company (vendor)


title: FFPE urothelial carcinoma 21

description:
X0005035_C08
AT_array: a520683-00-805864-103111-4119207-24284.CEL
CG_array: a520683-00-805884-110111-4119208-28341.CEL


title: Human Esophageal Squamous Cell Carcinoma Replicate 41

description: Biological replicate 41 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue

tag: tissue

value: Esophagus

value: IIA

tag: catalog#


title: Human Esophageal Squamous Cell Carcinoma Replicate 35

description: Biological replicate 35 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue

tag: age

tag: Sex

value: Commercial Human Genomic DNA

value: Promega


title: Human Esophageal Squamous Cell Carcinoma Replicate 38

description: Biological replicate 38 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue


title: Human Esophageal Squamous Cell Carcinoma Replicate 37

description: Biological replicate 37 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue

value: III


title: Human Esophageal Squamous Cell Carcinoma Replicate 36

description: Biological replicate 36 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue


title: FFPE urothelial carcinoma 14

description:
X0005035_C02
AT_array: a520683-00-805864-103111-4119207-24335.CEL
CG_array: a520683-00-805859-103011-4119206-21360.CEL

tag: procedure

value: TURBT

tag: site


title: FFPE urothelial carcinoma 20

description:
X0005035_C07
AT_array: a520683-00-805864-103111-4119207-24300.CEL
CG_array: a520683-00-805884-110111-4119208-28339.CEL

value: bladder


title: Human Esophageal Squamous Cell Carcinoma Replicate 45

description: Biological replicate 45 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue

value: Female

value: IIB


title: FFPE urothelial carcinoma 19

description:
X0005035_C06
AT_array: a520683-00-805884-110111-4119208-28279.CEL
CG_array: a520683-00-805884-110111-4119208-28321.CEL


title: Human Esophageal Squamous Cell Carcinoma Replicate 34

description: Biological replicate 34 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue


title: FFPE urothelial carcinoma 12

description:
X0005035_C01
AT_array: a520683-00-805884-110111-4119208-28281.CEL
CG_array: a520683-00-805859-103011-4119206-21344.CEL


title: FFPE urothelial carcinoma 11

description:
X0005035_B11
AT_array: a520683-00-805859-103011-4119206-21317.CEL
CG_array: a520683-00-805859-103011-4119206-21338.CEL

value: female


title: Human Esophageal Squamous Cell Carcinoma Replicate 32

description: Biological replicate 32 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue


title: FFPE urothelial carcinoma 18

description:
X0005035_C05
AT_array: a520683-00-805859-103011-4119206-21313.CEL
CG_array: a520683-00-805884-110111-4119208-28314.CEL

value: male


title: Human Esophageal Squamous Cell Carcinoma Replicate 33

description: Biological replicate 33 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue


title: FFPE urothelial carcinoma 17

description:
X0005035_C04
AT_array: a520683-00-805864-103111-4119207-24277.CEL
CG_array: a520683-00-805884-110111-4119208-28313.CEL


title: Human Esophageal Squamous Cell Carcinoma Replicate 29

description: Biological replicate 29 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue


title: FFPE urothelial carcinoma 10

description:
X0005035_B10
AT_array: a520683-00-805864-103111-4119207-24334.CEL
CG_array: a520683-00-805859-103011-4119206-21342.CEL


title: Human Esophageal Squamous Cell Carcinoma Replicate 43

description: Biological replicate 43 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue


title: FFPE urothelial carcinoma 16

description:
X0005035_C03
AT_array: a520683-00-805859-103011-4119206-21272.CEL
CG_array: a520683-00-805884-110111-4119208-28294.CEL


title: FFPE urothelial carcinoma 9

description:
X0005035_B09
AT_array: a520683-00-805859-103011-4119206-21293.CEL
CG_array: a520683-00-805859-103011-4119206-21308.CEL


title: Human Esophageal Squamous Cell Carcinoma Replicate 30

description: Biological replicate 30 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue


title: Human Esophageal Squamous Cell Carcinoma Replicate 28

description: Biological replicate 28 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue


title: FFPE urothelial carcinoma 8

description:
X0005035_B08
AT_array: a520683-00-805862-103011-4119206-21771.CEL
CG_array: a520683-00-805859-103011-4119206-21336.CEL


title: Human Esophageal Squamous Cell Carcinoma Replicate 26

description: Biological replicate 26 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue


title: Human Esophageal Dysplasia Replicate 16

description: Biological replicate 16 of 16 Human Esophageal Dysplasia Biopsy Tissue

source_name: [TEST] Human Esophageal Dysplasia Biopsy Tissue

value: Dysplasia


title: Human Esophageal Dysplasia Replicate 15

description: Biological replicate 15 of 16 Human Esophageal Dysplasia Biopsy Tissue


title: FFPE urothelial carcinoma 4

description:
X0005035_B04
AT_array: a520683-00-805859-103011-4119206-21271.CEL
CG_array: a520683-00-805884-110111-4119208-28301.CEL


title: FFPE urothelial carcinoma 7

description:
X0005035_B07
AT_array: a520683-00-805862-103011-4119206-21802.CEL
CG_array: a520683-00-805859-103011-4119206-21333.CEL


title: FFPE urothelial carcinoma 5

description:
X0005035_B05
AT_array: a520683-00-805865-103111-4119207-24476.CEL
CG_array: a520683-00-805859-103011-4119206-21335.CEL


title: FFPE urothelial carcinoma K418 B T

description:
X0005035_A06
AT_array: a520683-00-805859-103011-4119206-21285.CEL
CG_array: a520683-00-805884-110111-4119208-28293.CEL

value: nephroureterectomy

value: renal pelvis


title: Human Esophageal Squamous Cell Carcinoma Replicate 23

description: Biological replicate 23 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue


title: FFPE urothelial carcinoma 6

description:
X0005035_B06
AT_array: a520683-00-805865-103111-4119207-24475.CEL
CG_array: a520683-00-805859-103011-4119206-21352.CEL


title: Human Esophageal Squamous Cell Carcinoma Replicate 31

description: Biological replicate 31 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue


title: Human Esophageal Dysplasia Replicate 13

description: Biological replicate 13 of 16 Human Esophageal Dysplasia Biopsy Tissue


title: Human Esophageal Squamous Cell Carcinoma Replicate 25

description: Biological replicate 25 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue


title: Human Esophageal Squamous Cell Carcinoma Replicate 22

description: Biological replicate 22 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue


title: FFPE urothelial carcinoma 161B T

description:
X0005035_A01
AT_array: a520683-00-805859-103011-4119206-21315.CEL
CG_array: a520683-00-805859-103011-4119206-21364.CEL

value: cystectomy


title: FFPE urothelial carcinoma 2

description:
X0005035_B02
AT_array: a520683-00-805864-103111-4119207-24279.CEL
CG_array: a520683-00-805884-110111-4119208-28330.CEL


title: Human Esophageal Dysplasia Replicate 12

description: Biological replicate 12 of 16 Human Esophageal Dysplasia Biopsy Tissue


title: FFPE urothelial carcinoma 1

description:
X0005035_B01
AT_array: a520683-00-805859-103011-4119206-21266.CEL
CG_array: a520683-00-805859-103011-4119206-21347.CEL


title: Human Esophageal Squamous Cell Carcinoma Replicate 20

description: Biological replicate 20 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue

value: Carcinoma

value: I


title: FFPE urothelial carcinoma 169B T

description:
X0005035_A04
AT_array: a520683-00-805859-103011-4119206-21278.CEL
CG_array: a520683-00-805884-110111-4119208-28311.CEL


title: FFPE urothelial carcinoma K411B T

description:
X0005035_A05
AT_array: a520683-00-805859-103011-4119206-21287.CEL
CG_array: a520683-00-805859-103011-4119206-21298.CEL


title: Human Esophageal Squamous Cell Carcinoma Replicate 21

description: Biological replicate 21 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue

value: Esophagus


title: FFPE urothelial carcinoma 3

description:
X0005035_B03
AT_array: a520683-00-805859-103011-4119206-21290.CEL
CG_array: a520683-00-805859-103011-4119206-21345.CEL


title: Human Esophageal Squamous Cell Carcinoma Replicate 16

description: Biological replicate 16 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue

value: Male


title: Human Esophageal Squamous Cell Carcinoma Replicate 17

description: Biological replicate 17 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue

value: Commercial Human Genomic DNA


title: Human Esophageal Squamous Cell Carcinoma Replicate 27

description: Biological replicate 27 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue

value: Promega


title: Human Esophageal Squamous Cell Carcinoma Replicate 15

description: Biological replicate 15 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue


title: Human Esophageal Squamous Cell Carcinoma Replicate 18

description: Biological replicate 18 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue

value: IIA


title: Human Esophageal Dysplasia Replicate 11

description: Biological replicate 11 of 16 Human Esophageal Dysplasia Biopsy Tissue


title: Human Esophageal Dysplasia Replicate 10

description: Biological replicate 10 of 16 Human Esophageal Dysplasia Biopsy Tissue


title: Human Esophageal Dysplasia Replicate 14

description: Biological replicate 14 of 16 Human Esophageal Dysplasia Biopsy Tissue


title: Human Esophageal Squamous Cell Carcinoma Replicate 14

description: Biological replicate 14 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue


title: FFPE urothelial carcinoma 31

description:
X0005035_D06
AT_array: a520683-00-805859-103011-4119206-21283.CEL
CG_array: a520683-00-805884-110111-4119208-28315.CEL

value: TURBT


title: Human Esophageal Dysplasia Replicate 9

description: Biological replicate 9 of 16 Human Esophageal Dysplasia Biopsy Tissue


title: FFPE urothelial carcinoma 158B T

description:
X0005034_D08
AT_array: a520683-00-805865-103111-4119207-24453.CEL
CG_array: a520683-00-805865-103111-4119207-24409.CEL

value: bladder


title: FFPE urothelial carcinoma 159B T

description:
X0005034_D09
AT_array: a520683-00-805866-103111-4119207-24613.CEL
CG_array: a520683-00-805865-103111-4119207-24441.CEL


title: Human Esophageal Squamous Cell Carcinoma Replicate 19

description: Biological replicate 19 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue


title: Human Esophageal Dysplasia Replicate 8

description: Biological replicate 8 of 16 Human Esophageal Dysplasia Biopsy Tissue

value: Female


title: Human Esophageal Squamous Cell Carcinoma Replicate 12

description: Biological replicate 12 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue


title: Human Esophageal Squamous Cell Carcinoma Replicate 9

description: Biological replicate 9 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue


title: FFPE urothelial carcinoma 156B T

description:
X0005034_D06
AT_array: a520683-00-805865-103111-4119207-24455.CEL
CG_array: a520683-00-805865-103111-4119207-24428.CEL


title: Human Esophageal Dysplasia Replicate 6

description: Biological replicate 6 of 16 Human Esophageal Dysplasia Biopsy Tissue


title: Human Esophageal Squamous Cell Carcinoma Replicate 8

description: Biological replicate 8 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue

value: IIB


title: Human Esophageal Squamous Cell Carcinoma Replicate 13

description: Biological replicate 13 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue


title: Human Esophageal Squamous Cell Carcinoma Replicate 6

description: Biological replicate 6 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue


title: Human Esophageal Squamous Cell Carcinoma Replicate 7

description: Biological replicate 7 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue


title: Human Esophageal Squamous Cell Carcinoma Replicate 11

description: Biological replicate 11 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue


title: Human Esophageal Dysplasia Replicate 5

description: Biological replicate 5 of 16 Human Esophageal Dysplasia Biopsy Tissue


title: FFPE urothelial carcinoma 157B T

description:
X0005034_D07
AT_array: a520683-00-805861-103011-4119206-21669.CEL
CG_array: a520683-00-805866-103111-4119207-24518.CEL


title: Human Esophageal Squamous Cell Carcinoma Replicate 10

description: Biological replicate 10 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue


title: Human Esophageal Squamous Cell Carcinoma Replicate 5

description: Biological replicate 5 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue


title: Human Esophageal Dysplasia Replicate 7

description: Biological replicate 7 of 16 Human Esophageal Dysplasia Biopsy Tissue


title: FFPE urothelial carcinoma 155B T

description:
X0005034_D05
AT_array: a520683-00-805861-103011-4119206-21653.CEL
CG_array: a520683-00-805865-103111-4119207-24419.CEL


title: Human Esophageal Squamous Cell Carcinoma Replicate 4

description: Biological replicate 4 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue


title: Human Esophageal Dysplasia Replicate 3

description: Biological replicate 3 of 16 Human Esophageal Dysplasia Biopsy Tissue


title: FFPE urothelial carcinoma 153B T

description:
X0005034_D04
AT_array: a520683-00-805862-103011-4119206-21766.CEL
CG_array: a520683-00-805865-103111-4119207-24406.CEL


title: FFPE urothelial carcinoma 166B T

description:
X0005035_A03
AT_array: a520683-00-805864-103111-4119207-24302.CEL
CG_array: a520683-00-805884-110111-4119208-28337.CEL


title: Human Esophageal Dysplasia Replicate 2

description: Biological replicate 2 of 16 Human Esophageal Dysplasia Biopsy Tissue


title: Human Esophageal Dysplasia Replicate 1

description: Biological replicate 1 of 16 Human Esophageal Dysplasia Biopsy Tissue


title: Human Esophageal Squamous Cell Carcinoma Replicate 24

description: Biological replicate 24 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue

value: III


title: Human Esophageal Squamous Cell Carcinoma Replicate 2

description: Biological replicate 2 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue


title: Human Esophageal Dysplasia Replicate 4

description: Biological replicate 4 of 16 Human Esophageal Dysplasia Biopsy Tissue


title: FFPE urothelial carcinoma 162B T

description:
X0005035_A02
AT_array: a520683-00-805864-103111-4119207-24304.CEL
CG_array: a520683-00-805884-110111-4119208-28307.CEL

value: male


title: Human Esophageal Squamous Cell Carcinoma Replicate 1

description: Biological replicate 1 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue


title: FFPE urothelial carcinoma 150B T

description:
X0005034_D02
AT_array: a520683-00-805860-103011-4119206-21514.CEL
CG_array: a520683-00-805865-103111-4119207-24405.CEL

value: female


title: FFPE urothelial carcinoma 151B T

description:
X0005034_D03
AT_array: a520683-00-805862-103011-4119206-21804.CEL
CG_array: a520683-00-805865-103111-4119207-24415.CEL


title: FFPE urothelial carcinoma 142B T

description:
X0005034_D01
AT_array: a520683-00-805862-103011-4119206-21791.CEL
CG_array: a520683-00-805865-103111-4119207-24393.CEL


title: EMFR35_w 15mM furfural

city: Gainesville

first: Ryan

last: Geddes

state: Florida

address: Building 981 Museum Road

department: Microbiology and Cell Science

institute: University of Florida

description:
E. coli W derivative
The strain EMFR35 was derived from LY180 during a growth based adaption in the presence of furfural.
15 mM furfural addition

organism: Escherichia coli W

source_name: E. coli EMFR35 15 mM furfural added

label_protocol: Conversion of RNA to cDNA and labeling with Cy3 was performed by Roche NimbleGen following their standard operating protocol. See www.nimblegen.com.

growth_protocol:
Cultures were grown in small fermentors. Furfural (5mM or 15 mM) was added and incubation continued for 15 min prior to harvesting.
Strains were grown in AM1 medium with 14% xylose to OD 550 = 1.5 (0.66 g dcw/liter). 4 replicate 350 ml fermentors per strain.

extract_protocol: Cells were chilled in dry ice/ethanol, centrifuged, and the pellet resuspended in RNA Later (Qiagen) before storing at –80 C. Total RNA was extracted using the RNeasy Mini kit (Qiagen), and DNA was removed by digestion with RNase-Free DNase I. RNA quality and concentration was checked with an Agilent bioanalyzer at the University of Florida Gene Expression core before submitting the RNA to Roche Nimblegen in Iceland for analysis.

tag: strain

tag: genotype

value: furfural resistant mutant of LY180

tag: phenotype

value: ethanologenic, furfural tolerant

tag: adapted for

value: xylose fermentation in the presence of furfural

tag: agent

value: 15 mM furfural


title: FFPE urothelial carcinoma 138B T

description:
X0005034_C10
AT_array: a520683-00-805862-103011-4119206-21767.CEL
CG_array: a520683-00-805865-103111-4119207-24435.CEL

tag: gender

value: cystectomy


title: Human Esophageal Squamous Cell Carcinoma Replicate 3

description: Biological replicate 3 of 59 Human Esophageal Squamous Cell Carcinoma Surgical Tissue

value: Carcinoma

tag: location

value: Esophagus

tag: lymph node metastasis

tag: distant metastasis at diagnosis


title: EMFR35

description:
E. coli W derivative
The strain EMFR35 was derived from LY180 during a growth based adaption in the presence of furfural.
No furfural

source_name: E. coli EMFR35 no furfural added

value: No furfural


title: FFPE urothelial carcinoma 141B T

description:
X0005034_C11
AT_array: a520683-00-805862-103011-4119206-21792.CEL
CG_array: a520683-00-805865-103111-4119207-24403.CEL

tag: Stage

tag: grade


title: EPI_E3

status: Public on Apr 28 2013

city: Hannover

first: Helge

last: Küster

address: Herrenhäuser Str. 2

department: Institut für Pflanzengenetik

institute: Leibniz Universität Hannover

description: Epidermal cells from mycorrhizal roots biological replicate 3

hyb_protocol: The fragmented aRNA was added to a 300 µl hybridization cocktail also containing hybridization controls. 200 µl of the mixture were hybridized to GeneChips for 16 h at 45°C. Standard post-hybridization wash and double-stain protocols (FS450_0001; GeneChip HWS hit; Affymetrix, Santa Clara, California, USA) were used on an Affymetrix GeneChip fluidics station 450.

scan_protocol: GeneChips were scanned on an Affymetrix GeneChip scanner 3000 7G.

data_processing: Cel files obtained from Medicago GeneChip hybridizations were analysed using the Robin software (http://mapman.gabipd.org/web/guest/robin). Normalization was performed across all GeneChips using the Robust Multichip Average (RMA) algorithm. Intensity values calculated for each probe set were log2-transformed and averaged across all three biological replicates. Log2 differences between the conditions studied were evaluated statistically by a Student's t-test implemented in Robin.

organism: Medicago truncatula

source_name: Epidermal cells from mycorrhizal roots

label_protocol: Biotinylated aRNA obtained for each sample was fragmented as recommend (GeneChip 3'IVT express kit, Affymetrix, Santa Clara, California, USA). The size distribution of the fragmented aRNA was assessed via an Agilent bioanalyzer (Agilent Technologies, Böblingen, Germany) using an RNA 6000 assay.

growth_protocol: Medicago truncatula Gaertn cv Jemalong genotype A17 seeds were surface-sterilized and scarified. Plants were grown in the climate chamber (humidity: 70 %; photosynthetic photon flux: 150 μmol m-2 s-1) at a 16 h light (23 °C) and 8 h dark (18 °C) regime.

extract_protocol: Roots were embedded using the Steedman`s wax protocol as described in Hogekamp et al. (Plant Physiol 157(4):2023-43, 2011). For the collection of ARB, CMR, and EPI cell pools, the whole root system of mycorrhizal plants was cut into approximately 1 cm pieces and embedded. Longitudinal sections of 12 µm on glass slides were obtained using a P.A.L.M. microbeam system with a Capmover (Zeiss, München, Germany). Total RNA was isolated from laser-microdissected cells using the RNeasy Micro kit (Qiagen, Hilden, Germany). 350 µl of RLT buffer containing β-mercaptoethanol were added to each sample followed by a 30-min incubation at room temperature. The lysate was spun down for 5 min at 13400 g, mixed 1:1 with ethanol absolute, and transferred to the clean-up column. On-column DNAse I digestion was performed according to the manufacturer’s instructions. RNA was amplified using the TargetAmp 2-round Biotin aRNA amplification kit (Epicentre Biotechnologies, Madison, USA). For each sample, several rounds of amplification were carried out and pooled subsequently. Quantity and quality of total RNA as well as T7-amplified biotinylated aRNA was checked via capillary electrophoresis in RNA 6000 pico and nano assays, respectively, using an Agilent 2100 bioanalyzer (Agilent Technologies, Böblingen, Germany).

treatment_protocol: Plants were mycorrhized with Glomus intraradices under conditions of phosphate limitation (20 µM phosphate).

tag: tissue

value: Epidermal cells from mycorrhizal roots

value: Jemalong A17

value: 21 days


title: FFPE urothelial carcinoma 137B T

description:
X0005034_C09
AT_array: a520683-00-805862-103011-4119206-21800.CEL
CG_array: a520683-00-805862-103011-4119206-21811.CEL

value: bladder


title: FFPE urothelial carcinoma 132B T

description:
X0005034_C06
AT_array: a520683-00-805860-103011-4119206-21520.CEL
CG_array: a520683-00-805862-103011-4119206-21824.CEL


title: EPI_E1

description: Epidermal cells from mycorrhizal roots biological replicate 1


title: EPI_E2

description: Epidermal cells from mycorrhizal roots biological replicate 2


title: FFPE urothelial carcinoma 126B T

description:
X0005034_C01
AT_array: a520683-00-805862-103011-4119206-21794.CEL
CG_array: a520683-00-805862-103011-4119206-21825.CEL


title: FFPE urothelial carcinoma 130B T

description:
X0005034_C05
AT_array: a520683-00-805860-103011-4119206-21535.CEL
CG_array: a520683-00-805866-103111-4119207-24541.CEL


title: CMR_K1

description: Cortical cells from mycorrhizal roots biological replicate 1

source_name: Cortical cells from mycorrhizal roots

value: Cortical cells from mycorrhizal roots


title: FFPE urothelial carcinoma 123B T

description:
X0005034_B10
AT_array: a520683-00-805860-103011-4119206-21525.CEL
CG_array: a520683-00-805865-103111-4119207-24420.CEL

value: nephroureterectomy

value: renal pelvis


title: ARB_A5

description: Arbuscule-containing cells from mycorrhizal roots biological replicate 5


title: FFPE urothelial carcinoma 128B T

description:
X0005034_C03
AT_array: a520683-00-805860-103011-4119206-21534.CEL
CG_array: a520683-00-805862-103011-4119206-21786.CEL

value: male


title: CMR_K4

description: Cortical cells from mycorrhizal roots biological replicate 4


title: FFPE urothelial carcinoma 135B T

description:
X0005034_C08
AT_array: a520683-00-805860-103011-4119206-21526.CEL
CG_array: a520683-00-805862-103011-4119206-21818.CEL

value: cystoprostatectomy


title: FFPE urothelial carcinoma 118B T

description:
X0005034_B07
AT_array: a520683-00-805860-103011-4119206-21567.CEL
CG_array: a520683-00-805865-103111-4119207-24442.CEL


title: FFPE urothelial carcinoma 129B T

description:
X0005034_C04
AT_array: a520683-00-805860-103011-4119206-21527.CEL
CG_array: a520683-00-805866-103111-4119207-24539.CEL


title: FFPE urothelial carcinoma 127B T

description:
X0005034_C02
AT_array: a520683-00-805860-103011-4119206-21529.CEL
CG_array: a520683-00-805862-103011-4119206-21828.CEL


title: FFPE urothelial carcinoma 122B T

description:
X0005034_B09
AT_array: a520683-00-805862-103011-4119206-21797.CEL
CG_array: a520683-00-805865-103111-4119207-24436.CEL


title: CMR_K5

description: Cortical cells from mycorrhizal roots biological replicate 5


title: ARB_A1

description: Arbuscule-containing cells from mycorrhizal roots biological replicate 1


title: FFPE urothelial carcinoma 125B T

description:
X0005034_B11
AT_array: a520683-00-805860-103011-4119206-21509.CEL
CG_array: a520683-00-805865-103111-4119207-24427.CEL

value: female


title: FFPE urothelial carcinoma 120B T

description:
X0005034_B08
AT_array: a520683-00-805863-103111-4119207-24036.CEL
CG_array: a520683-00-805865-103111-4119207-24421.CEL

value: Ta


title: FFPE urothelial carcinoma 110B T

description:
X0005034_B02
AT_array: a520683-00-805860-103011-4119206-21518.CEL
CG_array: a520683-00-787804-110211-4119209-30559.CEL

value: ureterocystectomy

value: ureter


title: FFPE urothelial carcinoma 133B T

description:
X0005034_C07
AT_array: a520683-00-805860-103011-4119206-21530.CEL
CG_array: a520683-00-805862-103011-4119206-21783.CEL

value: cystectomy


title: NAP_C3

description: Non-appressorial areas from mycorrhizal roots biological replicate 3

source_name: Non-appressoria-containing areas from mycorrhizal roots

extract_protocol: Roots were embedded using the Steedman`s wax protocol as described in Hogekamp et al. (Plant Physiol 157(4):2023-43, 2011). Root segments with extraradical hyphae were embedded for APP samples, while distant root segments with no visible fungal structures were embedded for NAP samples. Longitudinal sections of 12 µm on glass slides were obtained using a P.A.L.M. microbeam system with a Capmover (Zeiss, München, Germany). Total RNA was isolated from laser-microdissected cells using the RNeasy Micro kit (Qiagen, Hilden, Germany). 350 µl of RLT buffer containing β-mercaptoethanol were added to each sample followed by a 30-min incubation at room temperature. The lysate was spun down for 5 min at 13400 g, mixed 1:1 with ethanol absolute, and transferred to the clean-up column. On-column DNAse I digestion was performed according to the manufacturer’s instructions. RNA was amplified using the TargetAmp 2-round Biotin aRNA amplification kit (Epicentre Biotechnologies, Madison, USA). For each sample, several rounds of amplification were carried out and pooled subsequently. Quantity and quality of total RNA as well as T7-amplified biotinylated aRNA was checked via capillary electrophoresis in RNA 6000 pico and nano assays, respectively, using an Agilent 2100 bioanalyzer (Agilent Technologies, Böblingen, Germany).

value: 5-6 days


title: NAP_C2

description: Non-appressorial areas from mycorrhizal roots biological replicate 2

value: Non-appressoria-containing areas from mycorrhizal roots


title: FFPE urothelial carcinoma 111B T

description:
X0005034_B03
AT_array: a520683-00-805863-103111-4119207-24063.CEL
CG_array: a520683-00-805866-103111-4119207-24557.CEL


title: ARB_A3

description: Arbuscule-containing cells from mycorrhizal roots biological replicate 3


title: FFPE urothelial carcinoma 109B T

description:
X0005034_B01
AT_array: a520683-00-805863-103111-4119207-24066.CEL
CG_array: a520683-00-787804-110211-4119209-30585.CEL


title: FFPE urothelial carcinoma 115B T

description:
X0005034_B06
AT_array: a520683-00-805860-103011-4119206-21568.CEL
CG_array: a520683-00-805866-103111-4119207-24564.CEL


title: FFPE urothelial carcinoma 112B T

description:
X0005034_B04
AT_array: a520683-00-805863-103111-4119207-24048.CEL
CG_array: a520683-00-805862-103011-4119206-21830.CEL


title: FFPE urothelial carcinoma 102B T

description:
X0005034_A08
AT_array: a520683-00-805863-103111-4119207-24084.CEL
CG_array: a520683-00-787804-110211-4119209-30571.CEL


title: APP_P1

description: Appressoria-containing areas from mycorrhizal roots biological replicate 1


title: FFPE urothelial carcinoma 104B T

description:
X0005034_A09
AT_array: a520683-00-805863-103111-4119207-24097.CEL
CG_array: a520683-00-787804-110211-4119209-30579.CEL


title: APP_P3

description: Appressoria-containing cells from mycorrhizal roots biological replicate 3

source_name: Appressoria-containing areas from mycorrhizal roots


title: SS_A3_Comp.2

status: Public on Apr 27 2013

city: Worcester

first: Scarlet

last: Shell

address: 60 Prescott St

department: Biology and Biotechnology

institute: Worcester Polytechnic Institute

description: Gene expression data from a complemented M. tuberculosis methyltransferase deletion mutant

hyb_protocol: Affymetrix protocol recommended for Pseudomonas aeruginosa

scan_protocol: Microarrays were scanned using Affymetrix GeneArray Scanner 3000 7G Plus according to the manufacturer's protocol.

data_processing: Gene expression estimates were derived from the probe-level hybridization intensities using the RMA algorithm through the Expression Console software package (Affymetrix) using library files obtained from the array manufacturer (Affymetrix).

organism: Mycobacterium tuberculosis H37Rv

source_name: Complemented Rv3263 deletion mutant replicate 2

label_protocol: Standard Affymetrix protocol for prokaryotic microarrays

growth_protocol: Cultures were grown to OD 0.8-0.9 in 7H9 supplemented with OADC, 0.05% Tween-80, and 0.2% glycerol in roller bottles

extract_protocol: Cultures were inactivated with RNAlater, disrupted with bead-beating in the presence of Trizol, and total RNA was extracted according to the manufacturer's instructions. RNA was then treated with Dnase and re-purified with RNeasy.

value: deltaRv3263 complemented


title: FFPE urothelial carcinoma 107B T

description:
X0005034_A11
AT_array: a520683-00-805863-103111-4119207-24053.CEL
CG_array: a520683-00-787804-110211-4119209-30572.CEL


title: SS_A1_RV.3

description: Gene expression data from wildtype M. tuberculosis

source_name: Wildtype H37Rv replicate 3

value: Wildtype


title: SS_A3_Comp.3

source_name: Complemented Rv3263 deletion mutant replicate 3


title: FFPE urothelial carcinoma 105B T

description:
X0005034_A10
AT_array: a520683-00-805863-103111-4119207-24056.CEL
CG_array: a520683-00-787804-110211-4119209-30577.CEL


title: SS_A2_d3263.2

description: Gene expression data from an M. tuberculosis methyltransferase deletion mutant

source_name: Rv3263 deletion mutant replicate 2


title: NAP_C1

description: Non-appressorial areas from mycorrhizal roots biological replicate 1

value: Jemalong A17


title: APP_P2

description: Appressoria-containing cells from mycorrhizal roots biological replicate 2

value: Appressoria-containing areas from mycorrhizal roots


title: SS_A2_d3263.3

source_name: Rv3263 deletion mutant replicate 3


title: FFPE urothelial carcinoma 114B T

description:
X0005034_B05
AT_array: a520683-00-805863-103111-4119207-24087.CEL
CG_array: a520683-00-805862-103011-4119206-21787.CEL


title: SS_A1_RV.2

source_name: Wildtype H37Rv replicate 2


title: SS_A2_d3263.1

source_name: Rv3263 deletion mutant replicate 1


title: WT_DCs pool 2

city: Berlin

first: Marie

last: Gebhardt

address: Robert-Rössle-Str. 10

department: Cancer

institute: Max-Delbrück-Center for Molecular Medicine

description: Gene expression of wildtype splenic DCs

hyb_protocol: Hybridization was performed according to the standard Affymetrix protocols by Kompetenzzentrum Fluoreszente Bioanalytik (Regensburg, Germany)

scan_protocol: Scanning was performed according to the standard Affymetrix protocols by Kompetenzzentrum Fluoreszente Bioanalytik (Regensburg, Germany)

data_processing: Primary analysis was performed with the Affymetrix GeneChip® Software (AGCC) and Expression Console Software. The data were analyzed using R/Bioconductor and the RMA normalization method.

source_name: splenic DCs - CD3e-CD19-CD11c+

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocols by Kompetenzzentrum Fluoreszente Bioanalytik (Regensburg, Germany)

growth_protocol: Mice of 6-10 weeks of aged were used in this experiment

extract_protocol: Total RNA extraction was performed by Rneasy mini or Rneasy micro kit (Qiagen) according to manufacturers recommendations

treatment_protocol: BM cells from long bones as well as splenice were extracted, RBC lysis was performed, cells were stained with fluorescently labelled antibdies targeted against cell-population specific surface antigens and separated by flow cytometry directly into RNA extraction cell lysis buffer

value: spleen

tag: cell type

value: dendritic cells - CD3e-CD19-CD11c+

tag: genotype/variation

value: wild-type