title: A2P3-7141-E10_a2p3

description: Single MEP cell


title: A2P3-7141-E2_a2p3

status: Public on Apr 02 2016

type: RNA

city: Oxford

first: Adam

last: Mead

address: John Radcliffe Hospital

department: Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description: Single MEP cell

data_processing: Data were processed using a custom pipeline in R. Normalisation was performed by subtracting the mean of B2M and GAPDH expression

label: FAM

molecule: total RNA

organism: Homo sapiens

source_name: healthy donor apheresis

label_protocol: Cells were isolated by index-FACS into each well of 96-well PCR plates containing 5 μl lysis buffer (CellsDirect One-Step qRT-PCR kit [Invitrogen], SUPERASE-In RNase inhibitor [Ambion], TE buffer) and 0.2x Taqman assay mastermix. Plates were sealed, vortexed, briefly centrifuged and then cDNA synthesis and sequence-specific pre-amplification performed (reverse transcriptase – 50 oC, 15 min; Inactivation at 95 oC, 2 min; Specific target amplification 95 oC 15 sec then 60 oC 4 min, 22 cycles). Plates were stored at -20  oC until analysis. Preamplified products were diluted 4-fold prior to analysis. Samples were analyzed using Universal PCR Master Mix (Applied Biosystems) and individual Taqman gene expression assays (Life Technologies, Suppl. Table 1), on the Biomark System (Fluidigm) using the 96.96 Dynamic Arrays as per manufacturers protocol.

extract_protocol: Target cells isolated by immunomagnetic CD34-cell enrichment and then single cell FACS sorting in to 96-well PCR plates. Total RNA isolated using CellsDirect One-Step PCR Kit (Invitrogen) as per product protocol.

tag: tissue

value: Mobilized peripheral blood mononuclear cells

tag: cell type

value: megakaryocyte-erythroid progenitor


title: A2P3-7141-D9_a2p3

description: Single MEP cell


title: A2P3-7141-E1_a2p3

description: Single MEP cell


title: A2P3-7141-D8_a2p3

description: Single MEP cell


title: A2P3-7141-F7_a2p3

description: Single MEP cell


title: A2P3-7141-D5_a2p3

description: Single MEP cell


title: A2P3-7141-D6_a2p3

description: Single MEP cell


title: A2P3MEP-F12_a2p3

description: Single MEP cell


title: A2P3-7141-D7_a2p3

description: Single MEP cell


title: A2P3-7141-D4_a2p3

description: Single MEP cell


title: A2P3-7141-D2_a2p3

description: Single MEP cell


title: A2P3-7141-D12_a2p3

description: Single MEP cell


title: A2P3-7141-D3_a2p3

description: Single MEP cell


title: A2P3-7141-D1_a2p3

description: Single MEP cell


title: A2P3-7141-D11_a2p3

description: Single MEP cell


title: A2P3-7141-C5_a2p3

description: Single MEP cell


title: A2P3-7141-C4_a2p3

description: Single MEP cell


title: A2P3-7141-C9_a2p3

description: Single MEP cell


title: A2P3-7141-C6_a2p3

description: Single MEP cell


title: A2P3-7141-C3_a2p3

description: Single MEP cell


title: A2P3-7141-C12_a2p3

description: Single MEP cell


title: A2P3-7141-C2_a2p3

description: Single MEP cell


title: A2P3-7141-C7_a2p3

description: Single MEP cell


title: A2P3-7141-C10_a2p3

description: Single MEP cell


title: A2P3-7141-C1_a2p3

description: Single MEP cell


title: A2P3-7141-B7_a2p3

description: Single MEP cell


title: A2P3-7141-B8_a2p3

description: Single MEP cell


title: A2P3-7141-B3_a2p3

description: Single MEP cell


title: A2P3-7141-C8_a2p3

description: Single MEP cell


title: A2P3-7141-B2_a2p3

description: Single MEP cell


title: A2P3-7141-B12_a2p3

description: Single MEP cell


title: A2P3-7141-B4_a2p3

description: Single MEP cell


title: A2P3-7141-B11_a2p3

description: Single MEP cell


title: A2P3-7141-B5_a2p3

description: Single MEP cell


title: A2P3-7141-B1_a2p3

description: Single MEP cell


title: FFPE liver RNA - Control Group - rep7

city: Newcastle

first: Laura

last: Jardine

address: Framlington Place

department: Faculty of Medical Sciences

institute: Newcastle University

description: RNA was extracted using an AllPrep kit (Qiagen) as per manufacturer's specifications.

hyb_protocol: Hybridisation of the NanoString CodeSet occurred over 16 hours at 65 degrees Celsius as per manufacturer specifications.

scan_protocol: The sample cartridge was scanned by an nCounter Digital Analyse (NanoString Technologies) at 555 fields of view.

data_processing: The raw data were re-scaled to account for the differences in raw code counts. This was performed using nSolver Analysis Software (NanoString Technologies), incorporating positive, negative and 'normalisation' gene target counts.

label: NanoStrings

source_name: Liver RNA from FFPE material

label_protocol: Capture probes and reporter probes (NanoString Technologies) were added to the extracted 150ng of mRNA according to manufacturer guidelines.

extract_protocol: 10um-thick FFPE curls were prepared for the extraction of total RNA from FFPE blocks after discarding the outer 40um.

value: Liver

tag: sample type

value: Control


title: FFPE tissue in good prognosis patient-1

city: Shanghai

first: Chunxian

last: Zhou

address: 138 Yi Xue Yuan Road

country: China

institute: Fudan University

description: miRNA expression in human CRC tissue in good prognosis patient

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)in hybridization Oven(Cat#G2545A, Agilent technologies, Santa Clara, CA, US)at 55℃，20rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner(Cat#G2565BA，Agilent technologies, Santa Clara, CA, US).

data_processing: The scanned images were analyzed with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US)with default settings. Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0(Agilent technologies, Santa Clara, CA, US).

source_name: colon cancer tissue

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions, labeling section.

extract_protocol: Total RNA was extracted and purified using RecoverAllTM  Total Nucleic Acid Isolation (Cat#AM1975, Ambion, Austin, TX, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100(Agilent technologies, Santa Clara, CA, US)

tag: tumor stage

value: Dukes' A

value: FFPE tissue

tag: gender

value: male

tag: age


title: FFPE tissue in good prognosis patient-2

value: Dukes' B


title: FFPE tissue in good prognosis patient-3

value: female


title: FFPE liver RNA - Control Group - rep6


title: FFPE tissue in poor prognosis patient-4

description: miRNA expression in human CRC tissue in poor prognosis patient


title: FFPE tissue in poor prognosis patient-3


title: A2P3-7141-A7_a2p3

description: Single MEP cell


title: FFPE liver RNA - Control Group - rep8


title: A2P3-7141-A6_a2p3

description: Single MEP cell


title: A2P3-7141-A5_a2p3

description: Single MEP cell


title: FFPE liver RNA - Control Group - rep5


title: A2P3-7141-B6_a2p3

description: Single MEP cell


title: A2P3-7141-A4_a2p3

description: Single MEP cell


title: FFPE liver RNA - Control Group - rep4


title: A2P3-7141-A1_a2p3

description: Single MEP cell


title: A2P3-7141-A3_a2p3

description: Single MEP cell


title: FFPE liver RNA - Control Group - rep3


title: FFPE liver RNA - Control Group - rep2


title: FFPE tissue in poor prognosis patient-1


title: A2P3-7141-B10_a2p3

description: Single MEP cell


title: A2P2MEP-A2_a2p3

description: Single MEP cell


title: FFPE tissue in good prognosis patient-4


title: FFPE liver RNA - Control Group - rep1


title: FFPE liver RNA - High Risk Group - rep9

value: High Risk


title: A2P1MEP-D12_a2p3

description: Single MEP cell


title: FFPE liver RNA - High Risk Group - rep7


title: A2P2MEP-H9_a2p2

description: Single MEP cell


title: A2P1MEP-E12_a2p3

description: Single MEP cell


title: A2P2MEP-A1_a2p3

description: Single MEP cell


title: FFPE tissue in poor prognosis patient-2


title: FFPE liver RNA - High Risk Group - rep5


title: FFPE liver RNA - High Risk Group - rep4


title: A2P2MEP-H7_a2p2

description: Single MEP cell


title: A2P2MEP-H6_a2p2

description: Single MEP cell


title: FFPE liver RNA - High Risk Group - rep3


title: FFPE liver RNA - High Risk Group - rep2


title: A2P2MEP-H4_a2p2

description: Single MEP cell


title: A2P2MEP-H5_a2p2

description: Single MEP cell


title: Sanhe cattle-3

city: Beijing

first: Qing

last: Xu

address: Institute of Life Science and Biotechnology, Beijing Jiaotong University

institute: Beijing Jiaotong University

description: Gene expression data from cattle blood after cold exposure

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Affymetrix Bovine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed using GeneChip operating software (GCOS) and normalized according to the procedure of Robust Multi-array Average (RMA) algorithm using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: biotin

organism: Bos taurus

source_name: Blood 3 after cold exposure

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

growth_protocol: The cattle were semi-housed in the same cowshed and fed a total mixed ration

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

treatment_protocol: In order to induce cold stress, the cattle were transferred outdoor and were exposed to a temperature of -32°C for 3 hours followed by housing in cowshed at 5°C for 15 hours.

tag: breed

value: Sanhe

value: white blood cells

tag: developmental stage

value: heifer

tag: Sex


title: A2P2MEP-H3_a2p2

description: Single MEP cell


title: FFPE liver RNA - High Risk Group - rep8


title: FFPE liver RNA - High Risk Group - rep6


title: Sanhe cattle-4

description: Gene expression data from cattle blood before cold exposur

source_name: Blood 4 before cold exposure


title: Sanhe cattle-6

source_name: Blood 6 before cold exposure


title: A2P2MEP-H8_a2p2

description: Single MEP cell


title: Sanhe cattle-2

source_name: Blood 2 after cold exposure


title: Sanhe cattle-5

source_name: Blood 5 before cold exposure


title: A2P2MEP-H2_a2p2

description: Single MEP cell


title: A2P2MEP-H12_a2p2

description: Single MEP cell


title: A2P2MEP-H11_a2p2

description: Single MEP cell


title: A2P2MEP-H10_a2p2

description: Single MEP cell


title: A2P2MEP-H1_a2p2

description: Single MEP cell


title: FFPE liver RNA - Low Risk Group - rep5

value: Low Risk


title: Sanhe cattle-1

source_name: Blood 1 after cold exposure


title: A2P2MEP-G9_a2p2

description: Single MEP cell


title: FFPE liver RNA - Low Risk Group - rep6


title: FFPE liver RNA - Low Risk Group - rep3


title: FFPE liver RNA - Low Risk Group - rep4


title: FFPE liver RNA - Low Risk Group - rep2


title: FFPE liver RNA - Low Risk Group - rep7


title: FFPE liver RNA - High Risk Group - rep1


title: FFPE liver RNA - Low Risk Group - rep1


title: cell line control10

status: Public on Apr 01 2016

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

description:
control-10
Sample19

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

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray, Kamakura, Japan)

growth_protocol: Cells were grown in RPM I 1640(sample1～10) or DMEM (sample11～20) supplemented with 10% fetal bovine serum in a humidified atmosphere of 5% CO2 at 37°C.

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Quiagen).

treatment_protocol: CCC cells were treated with 0.1μg/ml gemcitabine or without gemcitabine for 48 h.

value: human cholangiocellular carcinoma


title: cell line gemcitabine10

description:
gem-10
Sample20


title: cell line gemcitabine9

description:
gem-9
Sample18


title: cell line gemcitabine6

description:
gem-6
Sample12


title: cell line gemcitabine5

description:
gem-5
Sample10


title: cell line control9

description:
control-9
Sample17


title: cell line control5

description:
control-5
Sample9


title: cell line gemcitabine7

description:
gem-7
Sample14


title: cell line gemcitabine8

description:
gem-8
Sample16


title: cell line control7

description:
control-7
Sample13


title: cell line control8

description:
control-8
Sample15


title: cell line control2

description:
control-2
Sample3


title: cell line gemcitabine2

description:
gem-2
Sample4


title: cell line control4

description:
control-4
Sample7


title: cell line gemcitabine3

description:
gem-3
Sample6


title: Organoid P7

source_name: Cholangiocarcinoma

growth_protocol: Cholangiocarcinoma xenograft tissues were subjected to organoid culture with a serum-free medium containing R-spondin 1.

extract_protocol: Total RNAs including small RNAs were extracted using mirVana isolation kit.

treatment_protocol: Total RNAs were extracted from cholangiocarcinoma xenografts and organoids (passage 7).

value: Organoid Passage 7

value: Cholangiocarcinoma


title: cell line control3

description:
control-3
Sample5


title: Xenograft

value: Xenograft


title: cell line control6

description:
control-6
Sample11


title: cell line gemcitabine1

description:
gem-1
Sample2


title: cell line control1

description:
control-1
Sample1


title: cell line gemcitabine4

description:
gem-4
Sample8


title: SM

city: Kyoto

first: Yuichi

last: Mitobe

address: Shogoin Kawaharatyo

institute: Kyoto University

description: Gene expression data from murine CD4+ T cell expressing SM

hyb_protocol: following manufacturer's instructions (Agilent Low Input Quick Amp WT Labeling Kit)

scan_protocol: Scaned using microarray scanner G2565CA

data_processing: The data was normalized using percentile shift algorithm (value=50, Genespring GX 12.5), and baseline-corrected (Baseline to median of all samples). Probesets were filtered by expression Lower cut off=15-20 and by Flags (default).

organism: Mus musculus

source_name: CD4 positive murine T cell expressing SM

growth_protocol: sRPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) and IL-2, and 2-mercaptethanol, antibiotics at 37°C under a 5% CO2 atmosphere.

extract_protocol: RNA were extracted with Rneasy mini kit (Qiagen), following manufacturer's instructions

value: CD4+ T cell

tag: strain


title: Polysome-associated RNA from MCF7 cells (Ins+Torin1) replicate 4

city: Stockholm

first: Ola

last: Larsson

department: Department of oncology-pathology

country: Sweden

institute: Karolinska Institutet

description: MCF7 under  Ins+Torin1 condition, Polysome-associated RNA rep4

hyb_protocol: The resulting labeled samples were hybridized to the Human Gene 1.1 ST Array. Array from Affymetrix according the instructions of the manufacturer

scan_protocol: Arrays were scanned using the GeneArray Scanner 3000 according to the instructions from the manufacturer.

data_processing: The oligo package version 1.30.0 was used to summarize and normalize expression data using robust multiarray average (rma) in R version 3.1.1 (www.r-project.org) and bioconductor version 3.0.

label_protocol: The Affymetrix kit for the Human Gene 1.1 ST Array  using conditions recommended by the manufacturer.

growth_protocol: MCF7 cells were obtained from ATCC and maintained inRPMI-1640, supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin and 1% L-Glutamine (all from Wisent Bio Products).

extract_protocol: Total RNA was extracted using Trizol.

treatment_protocol: MCF7 cells were seeded in a 15 cm Petri dish, serum starved for 16 hours  (“control”) and then treated with 4.2 nM of recombinant human insulin (Sigma-Aldrich) for 4 hours alone (“insulin”) or in combination with 250 nM torin1 (“insulin+torin1”).  Cells were harvested at 80% confluency and lysed in hypotonic lysis buffer [5 mM Tris HCl pH (7.5), 2.5 mM MgCl2, 1.5 mM KCl, 100 μg/ml cycloheximide, 2 mM DTT, 0.5% Triton, 0.5% Sodium Deoxycholate). 10% of the lysates was saved to isolate cytoplasmic mRNA. The amount of RNA in each lysate was measured at 254 nm and 12 ODs were loaded on 5%-50% sucrose gradients generated using Gradient Master (Biocomp) and subjected to ultracentrifugation (SW41 rotor; Beckman 36,000, 2h and 4oC). Sucrose gradients were fractionated by displacement by 60% sucrose/0.01% bromphenol blue using ISCO Foxy fraction collector (35 seconds for each fraction=750 μl/fraction) equipped with a UV-lamp for continuous absorbance monitoring. Fractions were flash frozen immediately after fractionation and stored at -80oC. RNA was isolated with Trizol according to manufacturer’s instruction. For microarray analysis fractions corresponding to polysome-associated RNA (more than 3 ribsomes) were pooled.

tag: cell line

tag: condition

tag: rna source

value: Polysome-associated

tag: replicate


title: Polysome-associated RNA from MCF7 cells (Ins+Torin1) replicate 3

description: MCF7 under  Ins+Torin1 condition, Polysome-associated RNA rep3


title: Cytoplasmic RNA from MCF7 cells (Ins+Torin1) replicate 2

description: MCF7 under  Ins+Torin1 condition, Cytoplasmic RNA rep2

value: Cytoplasmic


title: HBZ

description: Gene expression data from murine CD4+ T cell expressing HBZ

source_name: CD4 positive murine T cell expressing HBZ

label_protocol: following manufacturer's instructions (Agilent Low Input Quick Amp WT Labeling Kit)


title: TTG

description: Gene expression data from murine CD4+ T cell expressing TTG

source_name: CD4 positive murine T cell expressing TTG


title: Cytoplasmic RNA from MCF7 cells (Ins+Torin1) replicate 3

description: MCF7 under  Ins+Torin1 condition, Cytoplasmic RNA rep3


title: Control

description: Gene expression data from murine CD4+ T cell expressing control vector

source_name: CD4 positive murine T cell expressing control vector


title: Polysome-associated RNA from MCF7 cells (Ins+Torin1) replicate 1

description: MCF7 under  Ins+Torin1 condition, Polysome-associated RNA rep1


title: Polysome-associated RNA from MCF7 cells (Ins+Torin1) replicate 2

description: MCF7 under  Ins+Torin1 condition, Polysome-associated RNA rep2


title: Cytoplasmic RNA from MCF7 cells (Ins+Torin1) replicate 4

description: MCF7 under  Ins+Torin1 condition, Cytoplasmic RNA rep4


title: Cytoplasmic RNA from MCF7 cells (Control) replicate 2

description: MCF7 under  Control condition, Cytoplasmic RNA rep2

value: Control


title: Polysome-associated RNA from MCF7 cells (Ins) replicate 2

description: MCF7 under  Ins condition, Polysome-associated RNA rep2

value: Ins


title: Polysome-associated RNA from MCF7 cells (Control) replicate 3

description: MCF7 under  Control condition, Polysome-associated RNA rep3


title: Cytoplasmic RNA from MCF7 cells (Control) replicate 1

description: MCF7 under  Control condition, Cytoplasmic RNA rep1


title: Polysome-associated RNA from MCF7 cells (Ins) replicate 3

description: MCF7 under  Ins condition, Polysome-associated RNA rep3


title: Cytoplasmic RNA from MCF7 cells (Control) replicate 3

description: MCF7 under  Control condition, Cytoplasmic RNA rep3


title: Polysome-associated RNA from MCF7 cells (Control) replicate 1

description: MCF7 under  Control condition, Polysome-associated RNA rep1


title: Cytoplasmic RNA from MCF7 cells (Ins) replicate 4

description: MCF7 under  Ins condition, Cytoplasmic RNA rep4


title: Polysome-associated RNA from MCF7 cells (Ins) replicate 4

description: MCF7 under  Ins condition, Polysome-associated RNA rep4


title: Polysome-associated RNA from MCF7 cells (Control) replicate 2

description: MCF7 under  Control condition, Polysome-associated RNA rep2


title: Cytoplasmic RNA from MCF7 cells (Ins+Torin1) replicate 1

description: MCF7 under  Ins+Torin1 condition, Cytoplasmic RNA rep1


title: Cytoplasmic RNA from MCF7 cells (Ins) replicate 2

description: MCF7 under  Ins condition, Cytoplasmic RNA rep2


title: Cytoplasmic RNA from MCF7 cells (Control) replicate 4

description: MCF7 under  Control condition, Cytoplasmic RNA rep4


title: Polysome-associated RNA from MCF7 cells (Control) replicate 4

description: MCF7 under  Control condition, Polysome-associated RNA rep4


title: Adjacent normal colonic mucosa_6

city: PROVIDENCE

first: Alexander

last: Brodsky

state: RI

address: 593 Eddy St.

department: MCB

country: USA

institute: Rhode Island Hospital/Brown University

description: Gene Expression Data

hyb_protocol: 6 ug double stranded cDNA were hybridized to HTA2.0 arrays at 47 C, for 17 h, at 60 rpm,   Fluidics Station  FS450 was used for washing and staining.

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

data_processing: RMA was performed in Affymetrix Gene Expression Console

label: Biotin

source_name: Adjacent normal colonic mucosa

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (SensationPlus™ FFPE Amplification and WT Labeling Kit P/N 703089 Rev. 3 (2014))

extract_protocol: Total RNA was extracted using the RecoverAll Total Nucleic Acid Extraction Kit for FFPE tissues with Dnase incubation. RNA was purified with Rneasy FFPE kit (Qiagen).

treatment_protocol: Tissue sections of 10 uM were cut for manual microdissection. Sections were de-paraffinized, statined, dehydrated through graded alcohols using Paradise FFPE reagent system (Life Technologies) for UV laser capture microdissection.

value: colon

tag: disease state

value: Normal tissue


title: Cytoplasmic RNA from MCF7 cells (Ins) replicate 3

description: MCF7 under  Ins condition, Cytoplasmic RNA rep3


title: Adjacent normal colonic mucosa_5

description: Gene Expression Data


title: Cytoplasmic RNA from MCF7 cells (Ins) replicate 1

description: MCF7 under  Ins condition, Cytoplasmic RNA rep1


title: Adjacent normal colonic mucosa_1

description: Gene Expression Data


title: Polysome-associated RNA from MCF7 cells (Ins) replicate 1

description: MCF7 under  Ins condition, Polysome-associated RNA rep1


title: Adjacent normal colonic mucosa_4

description: Gene Expression Data


title: Adjacent normal colonic mucosa_2

description: Gene Expression Data


title: Medullary carcinoma_6

description: Gene Expression Data

source_name: Medullary carcinoma

value: Colon Cancer


title: Adjacent normal colonic mucosa_3

description: Gene Expression Data


title: Medullary carcinoma_5

description: Gene Expression Data


title: Medullary carcinoma_1

description: Gene Expression Data


title: O27

type: genomic

first: Man

last: Cai

address: No.5 Yiheyuan Road, Haidian District

institute: Peking University

description: GeoChip data for crude oil sample collected  from oil stratum with 35.5 °C

hyb_protocol: Then DNA was dried in a SpeedVac (ThermoSavant, Milford, MA, USA) at 45°C for 45 minutes. The hybridization was carried out at 42°C for 16 hours on a MAUI hybridization station (BioMicro, Salt Lake City, UT, USA).

scan_protocol: After purification, GeoChip microarrays were scanned by a NimbleGen MS200 scanner (Roche, Madison, WI, USA) at 633 nm using a laser power and photomultiplier tube (PMT) gain of 100% and 75%, respectively.

data_processing: Signal intensities were quantified and processed using the data analysis pipeline as previously described (He et al 2010). Then processed GeoChip data were analyzed using the following steps: (i) remove the poor quality spots, which were flagged as 1 or 3 by ImaGene or with a signal to noise ratio (SNR) of less than 2.0; (ii) normalize the signal intensity of each spot by dividing the signal intensity by the total intensity of the microarray followed by multiplying by a constant; (iii) transform the data to the natural logarithmic form; and (iv) remove genes detected in only one out of three samples from the same elevation.

molecule: genomic DNA

organism: uncultured bacterium

source_name: Crude oil microbes in Qinghai Oilfield

label_protocol: As previously described (Yang et al 2013), DNA samples were labeled with the fluorescent dye Cy-5 using a random priming method and purified using the QIA quick purification kit (Qiagen, Valencia, CA, USA).

growth_protocol: The production mixtures and injected water were sampled from the wellheads and stored in sterile cans. The cans were filled completely, sealed with screw caps, and sent to the laboratory at a temperature of approximately 5 °C.  In the laboratory, the production mixtures were pre-treated with overnight settlement to separate the floating oil and water phases. Subsequently, the water solutions (W813, W516, W48, and W27) and floating crude oil samples (O813, O516, O48, and O27) samples were preserved at -80°C before DNA extraction. Similar analyses were performed on the injected water solution (W517).

extract_protocol: After separation, the four water phase samples from the production mixtures and the injected water sample were filtered through 0.22-µm cellulose ester membranes to collect the cells. In contrast, the cells in the four separated oil-phase samples were collected, as described previously (Yoshida et al., 2005; Yamane et al., 2008) with modifications in the method. Briefly, 15 mL floating oil was mixed with 15 mL isooctane (2,2,4-trimethylpentane) and incubated overnight at 4°C. It was then vortexed for 5 min, and centrifuged at 5000 × g  for 1 h at 4°C. The precipitates were suspended in 20 mL isooctane, and centrifuged at 5000 × g for 30 min at 4°C thrice, and then lyophilized. Microbial genomic DNA was extracted from cells collected from the water and crude oil samples as described previously (Zhou et al., 1996).

tag: phase

value: crude oil

tag: bottom hole temperature of deriving production wells

tag: organism description

value: Petroleum microbes


title: Medullary carcinoma_2

description: Gene Expression Data

tag: tissue


title: Medullary carcinoma_4

description: Gene Expression Data


title: Medullary carcinoma_3

description: Gene Expression Data


title: O48

description: GeoChip data for crude oil sample collected  from oil stratum with 41.4 °C


title: O516

description: GeoChip data for crude oil sample collected  from oil stratum with 49.5 °C


title: GCT56

city: Chuo-ku

first: Shintaro

last: Fukushima

address: 5-1-1 Tsukiji

institute: National Cancer Center Research Institute

description: Germ cell tumor tisssues obtained by surgical procedure

hyb_protocol: The labeled paired DNA with 2 μg Cot-1 DNA (Agilent Technologies) were hybridized at 65 °C for 24 h to SurePrint G3 Human CGH 8 × 60 K Oligo Microarrays G4450A (Agilent Technologies).

scan_protocol: Arrays were scanned on a Microarray Scanner G2505C (Agilent Technologies).

data_processing: Data were quantified using the Feature Extraction software v10.7.3 (Agilent Technologies).

source_name: Germinoma

label_protocol: Genomic DNA was labeled by random priming with Cy5 or Cy3-dUTP after digestion with both restriction enzymes AluI and RsaI according to the Agilent instructions.

extract_protocol: Genomic DNA was extracted using a DNeasy Blood & Tissue Kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol.

value: Germinoma

value: Male

tag: site

value: Central nervous system

source_name: Sex-matched reference DNA (Promega, Madison, WI)


title: GCT58

source_name: Mature teratoma, Germinoma

value: Mature teratoma, Germinoma


title: GCT60

source_name: Germinoma, Embryonal carcinoma

value: Germinoma, Embryonal carcinoma


title: W516

description: GeoChip data for  oil production water sample collected from oil stratum with 49.5 °C

source_name: Oil production water microbes in Qinghai Oilfield

value: water


title: GCT54


title: GCT47


title: GCT50


title: W813

description: GeoChip data for oil production water sample collected from oil stratum with 69.0 °C


title: GCT49


title: GCT63

source_name: Mature teratoma

value: Mature teratoma


title: GCT61


title: GCT65

source_name: Yolk sac tumor

value: Yolk sac tumor


title: W517

description: GeoChip data for oilfield injection water sample

source_name: Injection water microbes in Qinghai Oilfield

value: injection water

value: enviromental temperature


title: W27

description: GeoChip data for  oil production water sample collected from oil stratum with 35.5 °C


title: O813

description: GeoChip data for crude oil sample collected  from oil stratum with 69.0 °C


title: GCT52


title: GCT59

source_name: Immature teratoma, Germinoma

value: Immature teratoma, Germinoma


title: GCT53


title: GCT45


title: GCT46


title: GCT62

value: Female


title: GCT44


title: GCT48


title: W48

description: GeoChip data for  oil production water sample collected from oil stratum with 41.4 °C


title: GCT57

source_name: Mature teratoma, Yolk sac tumor, Embryonal carcinoma, Germinoma


title: GCT41

source_name: Yolk sac tumor, Germinoma

value: Yolk sac tumor, Germinoma


title: GCT42

source_name: Embryonal carcinoma

value: Embryonal carcinoma


title: GCT55


title: GCT43

source_name: Germinoma, Immature teratoma, Choriocarcinoma, Embryonal carcinoma


title: GCT51

source_name: Immature teratoma, Germinoma, polyembryoma, Yolk sac tumor


title: GCT40


title: GCT39


title: GCT35


title: GCT30


title: GCT38


title: GCT36

source_name: Immature teratoma

value: Immature teratoma


title: GCT33


title: GCT31


title: GCT18


title: GCT32


title: GCT29


title: GCT17


title: GCT28


title: GCT37


title: GCT10


title: GCT14


title: GCT34


title: GCT19


title: GCT11


title: GCT23


title: GCT22


title: GCT13


title: GCT24


title: GCT27


title: GCT25


title: GCT21


title: GCT16


title: GCT26


title: GCT20


title: GCT15


title: GCT8


title: GCT9


title: GCT7


title: GCT5


title: GCT100


title: GCT4

source_name: Yolk sac tumor, Embryonal carcinoma, Immature teratoma, Germinoma


title: GCT6


title: GCT113

source_name: Embryonal carcinoma, Germinoma

value: Embryonal carcinoma, Germinoma


title: GCT2

source_name: Germinoma


title: GCT71

source_name: Teratoma with somatic type malignancy (rhabdomyosarcoma)

source_name: Sex-matched reference DNA (Promega, Madison, WI)


title: GCT96


title: GCT84


title: tGCT13

source_name: Seminoma

value: Seminoma

value: Testis


title: GCT85

value: Germinoma

value: Male


title: GCT1

value: Central nervous system


title: GCT94


title: GCT77

source_name: Germinoma, Yolk sac tumor

value: Germinoma, Yolk sac tumor


title: GCT68

source_name: Mature teratoma,

value: Mature teratoma,


title: ExVivo_TG_Spleen_1

city: Kodaira, Ogawahigashi

first: Atsushi

last: Kadowaki

state: Tokyo

department: Immunology

institute: National Institute of Neuroscience, National Center of Neurology and Psychiatry

description: Gene expression ex vivo

hyb_protocol: 600ng of Cy3-labelled cRNA was fragmented and hybridized over 1 Sureprint G3 Mouse GE microarray (60Kx8) kit.

scan_protocol: Agilent scanner

data_processing:
Raw fluorescence data was extracted using Genespring sofware GX 12.0
Normalization Method
- Threshold raw signal to 1.0
- Normalization algorithm : Percentile Shift
- Shift to percentile:75

source_name: 2D2 mouse Spleen CD4+ T cells

label_protocol: 15ng total RNA was amplfied and labeled with Cy3 using Low input Quick Amp labeling Kit (Agilent technologies) according to manufacture's instructions.

extract_protocol: Samples were sorted in QIAzol Lysis Reagent (QIAGEN) and total RNA was obtained using a miRNeasy Micro kit.

tag: genotype/variation

value: 2D2 -TCR transgenic mouse

value: Spleen


title: ExVivo_TG_Spleen_2

description: Gene expression ex vivo


title: ExVivo_TG_Spleen_3

description: Gene expression ex vivo


title: GCT95

tag: gender


title: tGCT2


title: tGCT7


title: GCT70

source_name: Mature teratoma, Germinoma, hemangioma

value: Mature teratoma, Germinoma, hemangioma


title: GCT86

source_name: Mature teratoma, Germinoma, Yolk sac tumor, Embryonal carcinoma


title: GCT66


title: GCT73

source_name: Choriocarcinoma, Germinoma, Immature teratoma


title: GCT67

source_name: Mature teratoma, Germinoma

value: Mature teratoma, Germinoma


title: ExVivo_WT_Spleen_1

description: Gene expression ex vivo

source_name: Wild type B6 mouse Spleen CD4+ T cells

value: Wild type

value: Gut


title: ExVivo_TG_Gut_3

description: Gene expression ex vivo

source_name: 2D2 mouse Gut CD4+ T cells


title: ExVivo_WT_Gut_2

description: Gene expression ex vivo

source_name: Wild type B6 mouse Gut CD4+ T cells


title: PHD2/3f/f_Cre+/-_rep03

city: Chapel Hill

first: Jonathan

middle: C

last: Schisler

state: NC

address: MBRB, Rm 2340C

department: McAllister Heart Institute

institute: The University of North Carolina at Chapel Hill

description:
Biological replicate 3 of 3
KO_64

hyb_protocol: Samples were hybridized following the manufacturer's protocol (Agilent) using a GeneTAC HybStation (Genomic Solutions/Perkin Elmer).

scan_protocol: Slides were scanned immediately on a GeneTAC UC-4 scanner (Genomic Solutions/Perkin Elmer).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (Protocol: GE1_1100_Jul11 and Grid: 028005_D_F_20110614) to obtain background subtracted and spatially detrended processed signal intensities. The intensities were imported into Genespring v13.0 (Agilent) using the technology Agilent.SingleColor.28005. Intesitites were thresholded to 1, logbase 2 transformed, upper quartile normalized, and each intensty were median value transformed across all samples. Non-uniform, population outliers, and saturated flags were excluded. Probes were only considered if they had detectable values in at least 67% of the samples. Missing values were imputed using KNN (n = 10) implemented by Significance Analysis of Microarrays (SAM, v4.0) using R v3.1.3.

source_name: mouse heart, PHD2/3 KO, replicate 03

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared using Amino-allyl (total RNA) labeling.

extract_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Total RNA was prepared from mouse hearts using Rneasy columns (Qiagen).

value: Heart

tag: genotype

value: PHD2/3f/f; Cre+/-

tag: age

value: 8 weeks


title: time point 60C exp2

city: Gothenburg

first: Zsolt

last: Szilagyi

address: Medicinaregatan 9A

institute: University of Gothenburg

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: RMA normalization

organism: Schizosaccharomyces pombe

source_name: time point 60C

label_protocol: Standard Affymetrix protocol.

extract_protocol: Hot phenol RNA extraction

tag: protocol

value: cycling

tag: time

value: 60 min


title: GCT69

source_name: Immature teratoma, Germinoma

value: Immature teratoma, Germinoma


title: ExVivo_WT_Spleen_2

description: Gene expression ex vivo

tag: strain


title: time point 60A exp1

source_name: time point 60A

value: arrested


title: time point 60C exp1


title: ExVivo_WT_Gut_1

description: Gene expression ex vivo


title: ExVivo_TG_Gut_1

description: Gene expression ex vivo


title: ExVivo_WT_Gut_3

description: Gene expression ex vivo


title: ExVivo_WT_Spleen_3

description: Gene expression ex vivo


title: PHD2/3f/f_Cre-/-_rep03

description:
Biological replicate 3 of 3
WT_60

source_name: mouse heart, WT, replicate 03

value: PHD2/3f/f; Cre-/-


title: time point 20C exp1

source_name: time poont 20C

value: 20 min


title: PHD2/3f/f_Cre-/-_rep02

description:
Biological replicate 2 of 3
WT_59

source_name: mouse heart, WT, replicate 02


title: ExVivo_TG_Gut_2

description: Gene expression ex vivo


title: PHD2/3f/f_Cre-/-_rep01

description:
Biological replicate 1 of 3
WT_58

source_name: mouse heart, WT, replicate 01


title: PHD2/3f/f_Cre+/-_rep02

description:
Biological replicate 2 of 3
KO_63

source_name: mouse heart, PHD2/3 KO, replicate 02


title: time point 20C exp2


title: time point 60A exp2


title: time point 20A exp2

source_name: time point 20A


title: shRNA-mediated LY75 knockdown clone sh-S6 vs control (mock-transfected) SKOV3 clone

city: Quebec

first: Dimcho

last: Bachvarov

state: Quebec

address: 9, rue McMahon

country: Canada

institute: CHU-Q, Centre de recherche-HDQ

description: Cy3 label sample being the reference

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

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: control (mock-transfected) SKOV3 clone

label_protocol: Fluorescently labeled cRNA targets were generated from 0.5 µg of total RNA in each reaction using the Fluorescent Linear Amplification Kit (Agilent) and 10.0 mM Cyanine 3- or 5-labeled CTP (PerkinElmer, Boston, MA), following the user’s manual. Labeled cRNAs were purified using the RNeasy Mini Kit (Qiagen) and applied to the Agilent Whole Human Genome microarrays, containing ~ 44,000 genes.

growth_protocol: SKOV3 cells were maintained in Roswell Park Memorial Institute (RPMI) 1640 (HyClone Europe Ltd, Cramlington, UK) supplemented with 10% heat-inactivated fetal calf serum, 2 mM l-glutamine, 1 mM sodium pyruvate, 100 units/ml penicillin and 100 μg/ml streptomycin (all reagents were from HyClone Europe). Cells were grown as adherent cells in a humidified atmosphere at 37°C in 5% CO2.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions. The quality of all RNA samples was examined by capillary electrophoresis using the Agilent 2100 Bioanalyzer.

treatment_protocol: Two LY75 shRNAs cloned into the pLKO.1-puro vector (targeting the LY75 mRNA sequences 5’-GCCCUAAUACUCAACCUCCAA-3’ and 5’-UCCCGTCUUACAUAUUCAUCAA-3’)  were retrieved from the Sigma Mission TRC human 1.5 shRNA library (clone numbers TRCN0000057363 and TRCN0000057364). Viral supernatants were generated by transfecting 293T cells with the shRNA constructs and the packaging vectors psPAX2 and pMD2.G (Addgene, Cambridge, MA). The high-titer lentiviral supernatants in the presence of 8 mg/ml polybrene were used to infect SKOV3 cells. Two days later, infected cells were treated with puromycin (0,5 mg/ml) for the selection of stably-transduced clones. The pLKO.1-puro vector encoding a scramble sequence not matching any mammalian sequence was used for the generation of mock-transduced (control) clones. Stable clones with inhibited LY75 expression were evaluated and validated by quantitative RT-PCR and Western blot.

tag: cell type

value: ovarian adenocarcinoma cell line

tag: cell line

tag: transfection

value: mock

source_name: shRNA-LY75 knockdown SKOV3 clone sh-S6

value: shRNA-LY75 knockdown


title: time point 20A exp1


title: shRNA-mediated LY75 knockdown clone sh-S3 vs control (mock-transfected) SKOV3 clone - dye-swap replica

description: Cy5 label sample being the reference

source_name: shRNA-LY75 knockdown SKOV3 clone sh-S3


title: Ets1 deleted replicate 2

city: Chicago

first: Barbara

middle: L

last: Kee

state: Illinois

address: 924 E57th st

department: Pathology

institute: The University of Chicago

hyb_protocol: Following fragmentation, 10 microg of cRNA was hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Chips were scanned using an Affymetrix GeneChip Scanner 3000. Chip target intensity was arbitrarily scaled to 100 before rendering CHP files.

data_processing: Expression values were calculated by RMA express (http://rmaexpress.bmbolstad.com/) using background adjustment and quantile normalization.

source_name: ICOS+ ILC2 cells cultued 2 week on OP9-DL1

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix; Small Sample Labelling Protocol v.2, with the exception that the second round of in vitro transcription (IVT) was performed using Affymetrix GeneChip Expression 3 amplification kit.

extract_protocol: Cells were directly sorted into buffer RLT and RNA prepared using RNeasy Micro (Qiagen) according to manufacturer's instructions.

value: ILC2 cells


title: shRNA-mediated LY75 knockdown clone sh-S6 vs control (mock-transfected) SKOV3 clone - dye-swap replica

description: Cy5 label sample being the reference


title: PHD2/3f/f_Cre+/-_rep01

description:
Biological replicate 1 of 3
KO_62

source_name: mouse heart, PHD2/3 KO, replicate 01


title: Ets1 deleted replicate 1


title: CRC29

city: sendai

first: Hidekazu

last: Takahashi

address: Seiryo-machi 4-1, Aoba-ku

department: Department of clinical oncology

institute: Institute of Development, Aging and Cancer, Tohoku University

hyb_protocol: DNase/RNase free water, 10x Gene Expression Blocking Agent and 2x Hi-RPM hybridization Buffer were added to the dried Cy3-labelled microRNA and hybridized to SurePrint G3 Human miRNA Rel. 16.0 microarray for 20 hours at 55°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 5 minute at room temperature with Wash Buffer 1 (Agilent) and 5 minute with 37°C  Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol miRNA_107_Sep09) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: FFPE

label_protocol: Cyanine-3 (Cy3) labeled miRNA was prepared from 100 ng RNA using the miRNA Complete Labeling and Hyb kit (Agilent) according to the manufacturer's instructions, followed by MicroBioSpin6 purification (BioRad, Hercules, CA, USA).

extract_protocol: RNA was prepared using the Ambion RecoverAll Total Nucleic Acid Isolation Kit (Life Technologies Corporation, Carlsbad, CA, USA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.

value: BRAF wild


title: CRC30


title: CRC28


title: shRNA-mediated LY75 knockdown clone sh-S3 vs control (mock-transfected) SKOV3 clone

description: Cy3 label sample being the reference


title: CRC27


title: CRC26

value: BRAF mutant


title: CRC23


title: LMC replicate 2

value: control


title: CRC22


title: CRC24


title: CRC21


title: CRC20


title: CRC19


title: CRC18


title: CRC17


title: CRC16


title: LMC replicate 1


title: CRC25


title: WT2 EL4 cells 2

city: Spokane

first: Kathryn

middle: E

last: Meier

state: WA

address: PO Box 1495

department: Pharmaceutical Sciences

institute: Washington State University

hyb_protocol: Following fragmentation, 15ug of biotinylated cRNA were hybridized to the Mouse 430 2.0 Genome Array for 16 hr ar at 45C, rotating at 50RPM in the GeneChip Hybridization over 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000

data_processing: The data were analyzed with Microarray Suite version 5.0(MAS5.0) using Affymetrix default setting and global scaling as normalization method. The trimmed mean target intensity level was arbitrarily set at 125. Further data analysis was performed using GeneSifter software (Perkin Elmer).

source_name: EL4 clonal cell line WT2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol starting from 10ug of Total RNA (Expression Analysis Technical Manual,2000, P/N 700236Rev3, Affymetrix)

growth_protocol: Actively growing cells were rinsed and resuspended in serum-free RPMI medium and grown overnight.

extract_protocol: RNeasy Mini kit (Qiagen), as per manufacturer's instructions Genomic DNA was removed by treatment with DNase 1 (Invitrogen)

treatment_protocol: No treatment except for serum removal. Duplicate aliquots of cells were analyzed in parallel, numbered "1" and "2".

tag: parental cell line

value: lymphoma

tag: pma sensitivity

value: sensitive

tag: tumor formation

value: non-metastatic

tag: adhesion to plastic

value: non-adherent


title: C5 EL4 cells 2

source_name: EL4 clonal cell line C5

value: resistant

value: highly metastatic

value: adherent


title: V7 EL4 cells 1

source_name: EL4 clonal cell line V7

value: metastatic


title: V7 EL4 cells 2


title: C5 EL4 cells 1


title: CRC13


title: CRC12


title: CRC15


title: CRC14


title: WT2 EL4 cells 1


title: CRC10


title: CRC11


title: CRC9


title: CRC7


title: CRC6


title: CRC8


title: CRC5


title: CRC4


title: CRC3


title: CRC2


title: CRC1


title: 128_SQ_OP_M_V_R-4

city: Las Vegas

first: Allen

middle: G.

last: Gibbs

state: Nevada

address: 4505 S Maryland Parkway

department: School of Life Sciences

institute: University of Nevada

description: This sample is of wild-type Drosophila mojavensis nonmated male originated from San Quintin, Baja California . These males were raised on fermenting cultures of Organ pipe cactus, Stenocereus thurberi.

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: Drosophila mojavensis

source_name: Drosophila mojavensis SQ08

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

growth_protocol: See methods in Etges, W. J.  1992.  Premating isolation is determined by larval rearing substrates in cactophilic Drosophila mojavensis. Evolution 46:1945-1950.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Harvard-Partners Center for Genetics and Genomics (Harvard Medical School, Cambridge, MA USA).

value: Wild-type

tag: Sex

value: male

tag: mating status

value: nonmated

tag: location

value: San Quintin, Baja California

tag: diet

value: Organ pipe cactus, Stenocereus thurberi

tag: phenotype

value: normal

tag: accession


title: 125_SQ_OP_M_V_R-2

tag: genotype


title: 126_SQ_OP_M_V_R-3


title: 124_SQ_OP_M_V_R-1


title: 123_SQ_OP_M_M_R-3

description: This sample is of wild-type Drosophila mojavensis mated male originated from San Quintin, Baja California . These males were raised on fermenting cultures of Organ pipe cactus, Stenocereus thurberi.

value: mated


title: 127_SQ_OP_M_V_R-3


title: 122_SQ_OP_M_M_R-2


title: 118_SQ_OP_F_V_R-3A

description: This sample is of wild-type Drosophila mojavensis nonmated female originated from San Quintin, Baja California . These females were raised on fermenting cultures of Organ pipe cactus, Stenocereus thurberi.

value: female


title: 112_SQ_OP_F_M_R-2

description: This sample is of wild-type Drosophila mojavensis mated female originated from San Quintin, Baja California . These females were raised on fermenting cultures of Organ pipe cactus, Stenocereus thurberi.


title: 120_SQ_OP_M_M_R-1


title: 110_SQ_AG_M_V_R-4

description: This sample is of wild-type Drosophila mojavensis nonmated male originated from San Quintin, Baja California . These males were raised on fermenting cultures of pitaya agria cactus, Stenocereus gummosus.


title: 106_SQ_AG_M_M_R-4

description: This sample is of wild-type Drosophila mojavensis mated male originated from San Quintin, Baja California . These males were raised on fermenting cultures of pitaya agria cactus, Stenocereus gummosus.


title: 107_SQ_AG_M_V_R-1

value: pitaya agria cactus, Stenocereus gummosus


title: 116_SQ_OP_F_V_R-2


title: 117_SQ_OP_F_V_R-2


title: 121_SQ_OP_M_M_R-1


title: 119_SQ_OP_F_V_R-4A


title: 115_SQ_OP_F_V_R-1


title: 109_SQ_AG_M_V_R-3


title: 108_SQ_AG_M_V_R-2


title: 111_SQ_OP_F_M_R-1


title: 105_SQ_AG_M_M_R-3


title: 103_SQ_AG_F_V_R-4

description: This sample is of wild-type Drosophila mojavensis non-mated female originated from San Quintin, Baja California . These females were raised on fermenting cultures of pitaya agria cactus, Stenocereus gummosus.


title: 102_SQ_AG_F_V_R-3

description: This sample is of wild-type Drosophila mojavensis nonmated female originated from San Quintin, Baja California . These females were raised on fermenting cultures of pitaya agria cactus, Stenocereus gummosus.


title: 114_SQ_OP_F_V_R-1

description: This sample is of wild-type Drosophila mojavensis non-mated female originated from San Quintin, Baja California . These females were raised on fermenting cultures of Organ pipe cactus, Stenocereus thurberi.


title: 101_SQ_AG_F_V_R-2


title: 113_SQ_OP_F_M_R-3


title: 104_SQ_AG_M_M_R-1


title: 99_SQ_AG_F_M_R-4

description: This sample is of wild-type Drosophila mojavensis mated female originated from San Quintin, Baja California . These females were raised on fermenting cultures of pitaya agria cactus, Stenocereus gummosus.


title: 100_SQ_AG_F_V_R-1


title: 97_SQ_AG_F_M_R-2


title: 98_SQ_AG_F_M_R-3


title: 96_SQ_AG_F_M_R-1


title: 88_PP_OP_M_M_R-1

description: This sample is of wild-type Drosophila mojavensis mated male originated from Punta Prieta, Baja California . These males were raised on fermenting cultures of organ pipe cactus, Stenocereus thurberi.

source_name: Drosophila mojavensis PP08

value: Punta Prieta, Baja California

value: organ pipe cactus, Stenocereus thurberi


title: 91_PP_OP_M_M_R-4


title: 84_PP_OP_F_V_R-1

description: This sample is of wild-type Drosophila mojavensis nonmated-mated female originated from Punta Prieta, Baja California . These females were raised on fermenting cultures of organ pipe cactus, Stenocereus thurberi.


title: 86_PP_OP_F_V_R-3

description: This sample is of wild-type Drosophila mojavensis nonmated female originated from Punta Prieta, Baja California . These females were raised on fermenting cultures of organ pipe cactus, Stenocereus thurberi.


title: 94_PP_OP_M_V_R-3

description: This sample is of wild-type Drosophila mojavensis nonmated male originated from Punta Prieta, Baja California . These males were raised on fermenting cultures of organ pipe cactus, Stenocereus thurberi.


title: 83_PP_OP_F_M_R-4

description: This sample is of wild-type Drosophila mojavensis mated female originated from Punta Prieta, Baja California . These females were raised on fermenting cultures of organ pipe cactus, Stenocereus thurberi.


title: 89_PP_OP_M_M_R-2


title: 78_PP_AG_M_V_R-3

description: This sample is of wild-type Drosophila mojavensis nonmated male originated from Punta Prieta, Baja California . These males were raised on fermenting cultures of pitaya agria cactus, Stenocereus gummosus.


title: 79_PP_AG_M_V_R-4


title: 90_PP_OP_M_M_R-3


title: 80_PP_OP_F_M_R-1


title: 76_PP_AG_M_V_R-1


title: 85_PP_OP_F_V_R-2


title: 75_PP_AG_M_M_R-4

description: This sample is of wild-type Drosophila mojavensis mated male originated from Punta Prieta, Baja California . These males were raised on fermenting cultures of pitaya agria cactus, Stenocereus gummosus.


title: 95_PP_OP_M_V_R-4


title: 81_PP_OP_F_M_R-2


title: 68_PP_AG_F_M_R-4

description: This sample is of wild-type Drosophila mojavensis mated female originated from Punta Prieta, Baja California . These females were raised on fermenting cultures of pitaya agria cactus, Stenocereus gummosus.


title: 69_PP_AG_F_V_R-1

description: This sample is of wild-type Drosophila mojavensis nonmated female originated from Punta Prieta, Baja California . These females were raised on fermenting cultures of pitaya agria cactus, Stenocereus gummosus.


title: 73_PP_AG_M_M_R-2


title: 71_PP_AG_F_V_R-3


title: 70_PP_AG_F_V_R-2


title: 74_PP_AG_M_M_R-3


title: 72_PP_AG_F_V_R-4


title: 92_PP_OP_M_V_R-1


title: 77_PP_AG_M_V_R-2


title: 66_PP_AG_F_M_R-2


title: 93_PP_OP_M_V_R-2


title: 65_PP_AG_F_M_R-1

description: This sample is of wild-type Drosophila mojavensis mated female originated from Punta Prieta, Baja California . These males fewere raised on fermenting cultures of pitaya agria cactus, Stenocereus gummosus.


title: 59_OPNM_OP_M_M_R-3

description: This sample is of wild-type Drosophila mojavensis mated male originated from Organ Pipe National Monument, Arizona . These males were raised on fermenting cultures of organ pipe cactus, Stenocereus thurberi.

source_name: Drosophila mojavensis OPNM08

value: Organ Pipe National Monument, Arizona


title: 57_OPNM_OP_M_M_R-1


title: 64-OPNM_OP_M_V_R-4

description: This sample is of wild-type Drosophila mojavensis nonmated male originated from Organ Pipe National Monument, Arizona . These males were raised on fermenting cultures of organ pipe cactus, Stenocereus thurberi.


title: 60_OPNM_OP_M_M_R-4


title: 54_OPNM_OP_F_V_R-2

description: This sample is of wild-type Drosophila mojavensis nonmated female originated from Organ Pipe National Monument, Arizona . These females were raised on fermenting cultures of organ pipe cactus, Stenocereus thurberi.


title: 61_OPNM_OP_M_V_R-1


title: 58_OPNM_OP_M_M_R-2


title: 56_OPNM_OP_F_V_R-4


title: 67_PP_AG_F_M_R-3


title: 62_OPNM_OP_M_V_R-2


title: 50_OPNM_OP_F_M_R-2

description: This sample is of wild-type Drosophila mojavensis mated female originated from Organ Pipe National Monument, Arizona . These females were raised on fermenting cultures of organ pipe cactus, Stenocereus thurberi.


title: 48_OPNM_AG_M_V_R-4

description: This sample is of wild-type Drosophila mojavensis nonmated male originated from Organ Pipe National Monument, Arizona . These males were raised on fermenting cultures of pitaya agria cactus, Stenocereus gummosus.


title: 49_OPNM_OP_F_M_R-1


title: 47_OPNM_AG_M_V_R-3


title: 41_OPNM_AG_M_M_R-1

description: This sample is of wild-type Drosophila mojavensis mated male originated from Organ Pipe National Monument, Arizona . These males were raised on fermenting cultures of pitaya agria cactus, Stenocereus gummosus.


title: 55_OPNM_OP_F_V_R-3


title: 53_OPNM_OP_F_V_R-1


title: 42_OPNM_AG_M_M_R-2


title: 43_OPNM_AG_M_M_R-3


title: 39_OPNM_AG_F_V_R-3

description: This sample is of wild-type Drosophila mojavensis nonmated female originated from Organ Pipe National Monument, Arizona . These females were raised on fermenting cultures of pitaya agria cactus, Stenocereus gummosus.


title: 40_OPNM_AG_F_V_R-4


title: 38_OPNM_AG_F_V_R-2


title: 46_OPNM_AG_M_V_R-2


title: 45_OPNM_AG_M_V_R-1


title: 37_OPNM_AG_F_V_R-1


title: 63_OPNM_OP_M_V_R-3


title: 52_OPNM_OP_F_M_R-4


title: 51_OPNM_OP_F_M_R-3


title: 44_OPNM_AG_M_M_R-4


title: 36_OPNM_AG_F_M_R-4

description: This sample is of wild-type Drosophila mojavensis mated female originated from Organ Pipe National Monument, Arizona . These females were raised on fermenting cultures of pitaya agria cactus, Stenocereus gummosus.


title: 28_PO_OP_F_M_R-4

description: This sample is of wild-type Drosophila mojavensis mated female originated from Punta Onah, Sonora . These females were raised on fermenting cultures of organ pipe cactus, Stenocereus thurberi.

source_name: Drosophila mojavensis PO07

value: Punta Onah, Sonora


title: 34_OPNM_AG_F_M_R-2


title: 30_PO_OP_F_V_R-2

description: This sample is of wild-type Drosophila mojavensis nonmated female originated from Punta Onah, Sonora . These males were raised on fermenting cultures of organ pipe cactus, Stenocereus thurberi.


title: 35_OPNM_AG_F_M_R-3


title: 33_OPNM_AG_F_M_R-1


title: 31_PO_OP_F_V_R-3


title: 21_PO_AG_F_V_R-1

description: This sample is of wild-type Drosophila mojavensis nonmated female originated from Punta Onah, Sonora . These females were raised on fermenting cultures of pitaya agria cactus, Stenocereus gummosus.


title: 29_PO_OP_F_V_R-1


title: 17_PO_AG_F_M_R-1

description: This sample is of wild-type Drosophila mojavensis mated female originated from Punta Onah, Sonora . These females were raised on fermenting cultures of pitaya agria cactus, Stenocereus gummosus.


title: 26_PO_OP_F_M_R-2


title: 13_PO_OP_M_V_R-1

description: This sample is of wild-type Drosophila mojavensis nonmated male originated from Punta Onah, Sonora . These males were raised on fermenting cultures of organ pipe cactus, Stenocereus thurberi.


title: 11_PO_OP_M_M_R-3

description: This sample is of wild-type Drosophila mojavensis mated male originated from Punta Onah, Sonora . These males were raised on fermenting cultures of organ pipe cactus, Stenocereus thurberi.


title: 20_PO_AG_F_M_R-4


title: 16_PO_OP_M_V_R-4


title: 10_PO_OP_M_M_R-2


title: 18_PO_AG_F_M_R-2


title: 14_PO_OP_M_V_R-2


title: 24_PO_AG_F_V_R-4


title: 9_PO_OP_M_M_R-1


title: 27_PO_OP_F_M_R-3


title: 23_PO_AG_F_V_R-3


title: 19_PO_AG_F_M_R-3


title: 32_PO_OP_F_V_R-4


title: 22_PO_AG_F_V_R-2

description: This sample is of wild-type Drosophila mojavensis nonmatedfemale originated from Punta Onah, Sonora . These females were raised on fermenting cultures of pitaya agria cactus, Stenocereus gummosus.


title: 25_PO_OP_F_M_R-1


title: 15_PO_OP_M_V_R-3


title: 8_PO_AG_M_V_R-4

description: This sample is of wild-type Drosophila mojavensis nonmated male originated from Punta Onah, Sonora . These males were raised on fermenting cultures of pitaya agria cactus, Stenocereus gummosus.


title: 7_PO_AG_M_V_R-3


title: 12_PO_OP_M_M_R-4


title: 6_PO_AG_M_V_R-2

description: This sample is of wild-type Drosophila mojavensis nonmated-male originated from Punta Onah, Sonora . These males were raised on fermenting cultures of pitaya agria cactus, Stenocereus gummosus.


title: 1_PO_AG_M_M_R-1

description: This sample is of wild-type Drosophila mojavensis mated male originated from Punta Onah, Sonora . These males were raised on fermenting cultures of pitaya agria cactus, Stenocereus gummosus.


title: 3_PO_AG_M_M_R-3


title: 5_PO_AG_M_V_R-1


title: 4_PO_AG_M_M_R-4


title: MCF10A_24hour

city: Monterrey

first: Sean-Patrick

last: Scott

state: Neuvo Leon

address: Morones Prieto 3000 Pte

department: Cellular Therapy

country: Mexico

institute: Tecnológico de Monterrey

description:
Red.Cy5.24
raw data: cy5 of 0041.gpr

hyb_protocol: Arrays were pre-coated with bovine serum albumin at 50°C for 2 hours. Arrays were washed and centrifuge-dried and incubated overnight for 16 hours at 60°C with 50μL of cDNA Hybridization Mix, which was prepared with 25μL of 2X SDS-Based Hybridization Buffer, 10μL of concentrated cDNA, 2μL of Locked Nucleic Acid dT Blocker, 1μg of InvitrogenTM Cot-1 Human DNA®, and enough nuclease-free water. After this time, the cDNA hybridized arrays were washed, centrifuge-dried and incubated for second time for 4 hours at 65°C with 50μL of 3DNA Hybridization Mix, which contains 2.5μL of Cy3 3DNA Capture Reagent, 2.5μL of Cy5 3DNA Capture Reagent, 25μL of 2X SDS-Based Hybridization Buffer, 0.25μL of anti-fade reagent and enough nuclease-free water. The fluorescent 3DNA Capture Reagent contains a capture sequence that is complementary to a sequence on the 5’ end of the RT primer. Then, the fluorescent hybridized arrays were washed, centrifuge-dried and dipped for 10 seconds into the fluorescent signal preserver DyeSaver2TM (Genisphere). Excess of DyeSaver2TM was partially polished from the microarray by dipping the array into toluene/acetone solution (3:1, v/v) until the layers of DyeSaver2TM were removed. The arrays were dried and stored in the dark until scanned.

scan_protocol: Arrays were scanned on a GenePix® 4000B Microarray Scanner (Molecular Devices, Downingtown, PA, USA) using GenePix® Pro 6.0.1.25 Acquisition and Analysis Software (Molecular Devices). GenePix® results (GPR) files were imported into R software version 2.15.3 [http://www.R-project.org]. Spot intensities were background-subtracted and normalized using the Linear Models for Microarray Data package (Limma, version 3.20.5) (Ritchie et al., 2007; Smyth & Speed, 2003). Limma is part of the Bioconductor project [http://www.bioconductor.org].

data_processing:
The normexp method implemented in the backgroundCorrect function of the Limma package was used to correct the overall measure of the intensity of the spots. For two colors microarray data, normalization is usually applied to the log-ratios of the G channel signal and R channel signal, which are defined as M and A: M = log2(R) – log2(G), and A = ½ (log2(R) + log2(G)).  The mean background-corrected intensities were normalized using the print-tip loess method, implemented in the normalizeWithinArrays function, which corrects the M-values for both sub-array spatial variation and intensity-based trends in each array separately. Print-tip loess normalization does not affect the A-values. Quantile normalization method, implemented in the normalizeBetweenArrays function, applied to the A-values makes the distributions essentially the same across arrays as well as channels.
The normalized log-ratios were split into their single channel composition using the following approximations: R = A + M/2, and G = A – M/2.

source_name: MCF-10A_24 hr time point

label_protocol: Two samples separated by 16 hours were hybridized in the same array. RNA samples for microarrays were purified using ethanol precipitation. One μg total RNA was retrotranscribed into cDNA using Invitrogen® SuperScript II enzyme (Life Technologies) and 1pmole of either Cy3 or Cy5 primers at 42°C for 2 hours. The cDNA reaction was stopped using 3.5μL of 0.5M NaOH/50mM EDTA (Amresco Inc., Solon, OH, USA), and incubated at 65°C for 15 minutes to denature the DNA/RNA hybrids and degrade the RNA. cDNA was concentrated at 60°C for 30 to 45 minutes in Vacufuge® 5301 Centrifugal Vacuum Concentrator from Eppendorf (Eppendorf Inc., Hamburg, Germany) to a final volume of 10μL.

growth_protocol: Noncancerous breast MCF-10A cells were grown in Mammary Epithelial Basal Medium (MEBM®, Lonza, Walkersville, MD, USA) supplemented with SingleQuots® (MEGM® BulletKit®, Lonza).

extract_protocol: Total RNA was isolated using the Ambion® RiboPure™ Kit (Life Technologies) according to the manufacturer’s instructions. Briefly, cell lysis was performed directly on the culture 6-well plates by adding 400μL of TRI Reagent® and incubated for 5 minutes. The homogenized sample was centrifuged at 13,000xg for 10 min at 4°C to remove insoluble material from homogenates and the supernatant was mixed with 40μL of bromo-chloro-propane (Aldrich-Sigma), mixed by vortex and incubated for 5 minutes at room temperature. Sample was centrifuged at 13,000xg for 5 min at 4°C, which produced fractionation phases. The upper aqueous phase was combined with molecular biology grade ethanol (Sigma-Aldrich). The RNA was isolated from the aqueous phase by binding to a glass-fiber filter by centrifugation at 13,000xg for 1 minute at room temperature. The filtrate was then rinsed twice with 500μL of the desalting Wash Solution by centrifugation at 13,000xg for 1 minute at room temperature. The purified RNA was then eluted off the filter using 100μL of Elution Buffer by centrifugation at 13,000xg for 1 minute at room temperature. RNA concentration and purity were determinated by spectrophotometry using BioTek’s Take3™ Multi-Volume Plate (BioTek Instruments, Inc., Vermont, USA) on the Synergy HT microplate reader (BioTek Instruments, Inc.). The quality of the RNA samples was also assessed by electrophoresis on a denaturing agarose gel. 500 ng of total RNA were reverse transcribed into cDNA using QuantiTect Reverse Transcription Kit (Qiagen, Valencia, CA, USA) according to the manufacturer‘s instructions. Briefly, RNA was first incubated with gDNA Wipeout Buffer to remove DNA contamination, then retrotranscribed with random primers in a PX2 thermal cycler (Thermo Electron Corporation, USA).

treatment_protocol: Cells seeded in 6-well plates were allowed to grow to full confluency and were entrained using the serum shock procedure previously described (Rossetti et al., 2012). Briefly, culture medium was removed and the cells were washed with 1X phosphate buffered saline (PBS, Gibco, Life Technologies). Confluent cells were starved overnight with FBS-free basal medium. For MCF-10A, ZR-75-30, and HCC-1954, the basal medium was RPMI-1640, and for MCF-7 and MDA-MB-231, D-MEM/F-12 was used as basal medium. Culture basal medium was removed and cells were then serum shocked with their respective growth basal medium supplemented with 50% horse serum (Biowest, France) and incubated for 2 hours. Following this, the cells were washed with PBS and basal culture medium was placed back into the culture dishes. The first time point was taken after the serum shock (t = 0) and then the cells were harvested every 4 hours for a period of 48 hours.

value: breast cancer epitheleal cell line

tag: time point

value: 24 hr


title: MCF10A_28hour

description:
Red.Cy5.28
raw data: cy5 of 0220.gpr

source_name: MCF-10A_28 hr time point

value: 28 hr


title: 2_PO_AG_M_M_R-2


title: MCF10A_20hour

description:
Red.Cy5.20
raw data: cy5 of 0219.gpr

source_name: MCF-10A_20 hr time point

value: 20 hr


title: MCF10A_4hour

description:
Green.Cy3.4
raw data: cy3 of 0219.gpr

source_name: MCF-10A_4 hr time point

value: 4 hr


title: MCF7_24hour

description:
Red.Cy5.24
raw data: cy5 of s034.gpr

data_processing:
The normexp method implemented in the backgroundCorrect function of the Limma package was used to correct the overall measure of the intensity of the spots. For two colors microarray data, normalization is usually applied to the log-ratios of the G channel signal and R channel signal, which are defined as M and A: M = log2(R) – log2(G), and A = ½ (log2(R) + log2(G)). The mean background-corrected intensities were normalized using the print-tip loess method, implemented in the normalizeWithinArrays function, which corrects the M-values for both sub-array spatial variation and intensity-based trends in each array separately. Print-tip loess normalization does not affect the A-values. Quantile normalization method, implemented in the normalizeBetweenArrays function, applied to the A-values makes the distributions essentially the same across arrays as well as channels.
The normalized log-ratios were split into their single channel composition using the following approximations: R = A + M/2, and G = A – M/2.

source_name: MCF-7_24 hr time point

growth_protocol: MCF-7 breast cancer cells were grown in Gibco® Dulbecco’s modified eagle medium: nutrient mixture F-12 (D-MEM/F-12, Life Technologies) supplemented with 10% heat-inactivated FBS. All culture medium were supplemented with Gibco® Penicillin-Streptomycin (Life Technologies) antibiotics. All cell cultures were propagated in an incubator at 37°C under an atmosphere of 5.0% CO2 and 95.0% air.


title: MCF10A_8hour

description:
Green.Cy3.8
raw data: cy3 of 0041.gpr

source_name: MCF-10A_8 hr time point

value: 8 hr


title: Colletotricum_whi2_dw rep1

city: Kanazawa

first: Takumi

last: Nishiuchi

address: 13-1 Takaramachi

institute: Kanazawa University

description:
Gene expression of the Co whi2Δ mutant without rapamycin treatment at 4 hpi on cucumber cotyledons
Co whi2ΔDW_rep1

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Rat Genome Colletotrichum orbiculare Microarray 8x60K for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried by raise it slowly from buffer 2.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 2um, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1.3.1 (Agilent) and GeneSpring GX12.1 using default parameters.

organism: Colletotrichum orbiculare

source_name: Co whi2Δ in distilled water replication1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the Low RNA Input Fluorescent Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Each strain was cultured in potato dextrose agar at 24 ℃. Conidia were harvested from 7 day old mycelia.

extract_protocol: RNA was prepared using the Agilent Plant RNA Isolation Mini kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2200 Tapestation (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Conidial suspensions (1.0×106 conidia/ml) of each strain in distilled water or 100nM rapamycin were placed the abaxial surface of cucumber cotyledons (1 week age) and incubated at 24℃ for 4h. Then, the epidermal cells of inoculation site was cut off by forceps

tag: preparation of conidia

value: water

tag: tissue

value: germinating conidia on host cucumber leaf surfaces

tag: time

value: 4 hpi


title: Colletotricum_whi2 rep3

description:
Gene expression of the Co whi2Δ mutant at 4 hpi on cucumber cotyledons
Co whi2Δ_rep3

source_name: Co whi2Δ replication3


title: 82_PP_OP_F_M_R-3

description: This sample is of wild-type Drosophila mojavensis mated female originated from Punta Prieta, Baja California . These females were raised on fermenting cultures of organ pipe cactus, Stenocereus thurberi.

value: Wild-type

value: normal


title: MCF7_8hour

description:
Green.Cy3.8
raw data: cy3 of s034.gpr

source_name: MCF-7_8 hr time point

tag: cell line

tag: cell type


title: Colletotricum_whi2_rapamycin rep2

description:
Gene expression of the Co whi2Δ mutant treated with rapamycin at 4 hpi on cucumber cotyledons
Co whi2ΔRAP_rep2

source_name: Co whi2Δ treated with rapamycin replication2

value: 100nM rapamycin


title: MCF7_12hour

description:
Green.Cy3.12
raw data: cy3 of s035.gpr

source_name: MCF-7_12 hr time point

value: 12 hr


title: MCF10A_0hour

description:
Green.Cy3.0
raw data: cy3 of 0042.gpr

source_name: MCF-10A_0 hr time point

value: 0 hr


title: MCF7_4hour

description:
Green.Cy3.4
raw data: cy3 of s033.gpr

source_name: MCF-7_4 hr time point


title: MCF7_0hour

description:
Green.Cy3.0
raw data: cy3 of s032.gpr

source_name: MCF-7_0 hr time point


title: Colletotricum_whi2_dw rep3

description:
Gene expression of the Co whi2Δ mutant without rapamycin treatment at 4 hpi on cucumber cotyledons
Co whi2ΔDW_rep3

source_name: Co whi2Δ in distilled water replication3


title: Colletotricum_whi2_rapamycin rep1

description:
Gene expression of the Co whi2Δ mutant treated with rapamycin at 4 hpi on cucumber cotyledons
Co whi2ΔRAP_rep1

source_name: Co whi2Δ treated with rapamycin replication1


title: MCF7_20hour

description:
Red.Cy5.20
raw data: cy5 of s033.gpr

source_name: MCF-7_20 hr time point


title: MCF7_28hour

description:
Red.Cy5.28
raw data: cy5 of s035.gpr

source_name: MCF-7_28 hr time point


title: Colletotricum_whi2 rep2

description:
Gene expression of the Co whi2Δ mutant at 4 hpi on cucumber cotyledons
Co whi2Δ_rep2

source_name: Co whi2Δ replication2


title: MCF10A_16hour

description:
Red.Cy5.16
raw data: cy5 of 0042.gpr

source_name: MCF-10A_16 hr time point

value: 16 hr


title: Colletotricum_whi2_rapamycin rep3

description:
Gene expression of the Co whi2Δ mutant treated with rapamycin at 4 hpi on cucumber cotyledons
Co whi2ΔRAP_rep3

source_name: Co whi2Δ treated with rapamycinreplication3


title: Colletotricum_whi2_dw rep2

description:
Gene expression of the Co whi2Δ mutant without rapamycin treatment at 4 hpi on cucumber cotyledons
Co whi2ΔDW_rep2

source_name: Co whi2Δ in distilled water replication2


title: Colletotricum_WT rep3

description:
Gene expression of the wild-type at 4hpi on cucumber cotyledons
WT_rep3

source_name: Wild-type replication3

value: wt


title: MCF10A_12hour

description:
Green.Cy3.12
raw data: cy3 of 0220.gpr

source_name: MCF-10A_12 hr time point


title: Colletotricum_whi2 rep1

description:
Gene expression of the Co whi2Δ mutant at 4 hpi on cucumber cotyledons
Co whi2Δ_rep1

source_name: Co whi2Δ replication1


title: MCF7_16hour

description:
Red.Cy5.16
raw data: cy5 of s032.gpr

source_name: MCF-7_16 hr time point


title: KU216 grown at 60˚C, replicate 2

city: Sanda

first: Ryota

last: Hidese

state: Hyogo

address: Gakuen 2-1

department: School of Science and Technology

institute: Kwansei-Gakuin University

description: Technical replicate 2 of 2. KU216 grown at 60°C

hyb_protocol: The labeled cDNA was dissolved in hybridization buffer (30 µl) containing 6×SSC (1×SSC is 0.1 M NaCl, 0.015 M sodium citrate), 0.2% Sodium lauryl sulfate, 5×Denhard's solution (Sigma-Aldrich), and 0.1 mg/ml denatured salmon sperm DNA. Hybridization was perfomed under a coverslip (Spaced cover glass XL, Takara bio) in a humidity chamber at 65˚C for 15 h. After hybridiztion, the microarray plates were washed four times with 2×SSC and 0.2% SDS at 55˚C for 5 min, rinsed in 0.05×SSC, and dried by centrifugation.

scan_protocol: The intensities of the Cy3 and Cy5 dyes were measured by using an Affymetrix 428 array scanner (Affymetrix)

data_processing: The microarray image analysis was processed by ImaGene 5.5 software (Biodiscovery) using a local background correction. For normalization of data, global intensity normalization was performed.

organism: Thermococcus kodakarensis

source_name: KU216 at 60°C

label_protocol: 10 µg of total RNA was annealed with random hexamers, and reverse transcription was performed in solutions containing CyDye-labeled dUTP (GE Healthcare). RNA was subsequently degraded with RNase H, and the labeled cDNA was purified by using a QiaQuick PCR purification kit (Qiagen).

growth_protocol: KU216 strain was individually cultivated at 85°C and 60°C in the rich media supplemented with elemental sulfur. Cells were harvested in the mid-logarithmic phase.

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

treatment_protocol: The grown cells were freezed at -80°C prior to RNA extraction.

value: ∆pyrF

tag: growth condition

value: The cells were grown in ASW-YT media supplemented with elemental sulfur at 60˚C for mid-logarithmic phase

source_name: KU216 at 85°C

value: The cells were grown in ASW-YT media supplemented with elemental sulfur at 85°C for mid-logarithmic phase


title: Colletotricum_WT rep2

description:
Gene expression of the wild-type at 4hpi on cucumber cotyledons
WT_rep2

source_name: Wild-type replication2


title: KU216 grown at 60˚C, replicate 1

description: Technical replicate 1 of 2. KU216 grown at 60°C


title: Colletotricum_WT rep1

description:
Gene expression of the wild-type at 4hpi on cucumber cotyledons
WT_rep1

source_name: Wild-type replication1


title: Unchallenged, Biological replicate 1

city: Edinburgh

first: Senthil

last: Gandi

address: 49 Little France Crescent

department: Division of Infection and Pathway Medicine

institute: University of Edinburgh

description: Gene expression data from bacteria grown in human whole blood for 30 hours

hyb_protocol: The hybridisation protocol was done as per suggestion in Affymetrix GeneChip® Expression Analysis Technical Manual, using GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: Processed arrays were scanned with GeneChip® Scanner 3000.

data_processing: Data analysis was carried out using the Partek Genomics Suite. Robust Multi-array Average (RMA) normalization performed using of signal intensity spot data which obtained by scanning process and it is indicated as a scatter plot data. Distribution of all genes which obtained result of the experiment is indicated as a histogram. Accuracy of the results of the experiment was determined through comparison of the histogram with the scatter plot data.

organism: Escherichia coli CFT073

source_name: bacteria that were grown in human whole blood for 30 hours

label_protocol: The labelling protocol was done as per suggestion in Affymetrix GeneChip® Expression Analysis Technical Manual, using GeneChip® DNA Labeling Reagent (Affymetrix, P/N 900542).

growth_protocol: E.coli CFT073 were grown in 15ml sterile tubes with 3ml of human whole blood at 37 degress celcius shaking at 200rpm for 24 hours, a subset of cultures were then treated with ciprofloxacin challenge at 0.008 mg/L and another subset was not treated.Growth was then continued for another 6 hours (total of 30 hours of growth). At this point, the bacterial total RNA was extracted from the cultures.

extract_protocol: The red blood sample in each sample were initially lysed with a strong base and Triton X-100, followed by the total RNA were stabilised using Qiagen RNA protect, following manufacturer's protocol. The total RNA were then extracted using Qiagen RNeasy Mini Kit. These samples were then treated with Ambion Turbo-DNA free DNase to remove any genomic DNA. The RNA samples were then checked for their quality and quantity using Nanodrop ND-1000 and an on-chip capillary electrophoresis method, Agilent 2100 Bioanalyzer.

treatment_protocol: The treatment in this study was the ciprofloxacin challenge at mid log phase. The effects of the treatment was compared to regulation of an organism without the treatment.

tag: growth phase

value: bacteria grown in whole blood until shortly after mid-log phase


title: Challenged, Biological replicate 4

description: Gene expression data from bacteria grown in human whole blood for 30 hours with ciprofloxacin challenge at 24 hours

source_name: bacteria that were grown in human whole blood, then challenged with ciprofloxacin after 24 hours from onset of growth, then left to grow for another 6 hours

value: bacteria grown in whole blood until shortly after mid-log phase in the presence of ciprofloxacin challenge


title: Unchallenged, Biological replicate 2


title: Unchallenged, Biological replicate 3


title: Challenged, Biological replicate 3


title: Unchallenged, Biological replicate 5


title: Challenged, Biological replicate 5


title: Challenged, Biological replicate 2


title: EDL, WT, mouse 90

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

country: Italy

institute: Eurac Researc

description: 2178_032_N3_90_EDL_mG1_AK_131114_(MoGene-1_0-st-v1).CEL.gz

hyb_protocol: Target samples were hybridized to Human Gene 1.0 ST v1 microarrays according to the manufacturer's protocols in a Affymetrix hybridization oven.

scan_protocol: Microarrays were scanned in an Affymetrix 3000 scanner.

data_processing: Raw microarray data was pre-processed using the generalgcrma package and our custom transcript-level CEL definition file (CDF) that defines probe sets for each transcript of all genes in the Ensembl database version 75. After GCRMA pre-processing a representative transcript probe set was selected for each gene based on a combination of its average expression and variance of expression across all EDL or Soleus samples.

label_protocol: Biotinylated hybridization targets were generated using the Affymetrix GeneChip WT Expression kit and the Affymetrix GeneChip WT Terminal Labeling kit.

extract_protocol: RNA was extracted using RNeasy® Fibrous Tissue Mini kit (Qiagen, Cat. No.74704, Venlo, NL).

tag: strain background

tag: mouse id

value: mouse 90

tag: genotype/variation

value: wild type

tag: sibling

tag: age

value: 6 months

tag: gender

value: female

value: extensor digitorum longus (EDL) muscle fibres


title: EDL, KO, mouse 69

description: 2177_032_N2_69_EDL_mG1_AK_131114_(MoGene-1_0-st-v1).CEL.gz

value: mouse 69

value: CaV1.1 delta E29 knockout


title: EDL, KO, mouse 83

description: 2175_032_N1_83_EDL_mG1_AK_131114_(MoGene-1_0-st-v1).CEL.gz

value: mouse 83


title: Challenged, Biological replicate 1


title: IST Unchallenged, Biological replicate 3

description: Gene expression data from bacteria grown in human IST for 12 hours

source_name: bacteria that were grown in human IST

growth_protocol: E.coli CFT073 were grown in 15ml sterile tubes with either 3ml of human serum or IST medium at 37 degress celcius shaking at 200rpm for 6 hours in IST medium and 36 hours in human serum, added ciprofloxacin challenge at 0.004 mg/L, then continued growth for 6 hours in IST medium and 36 hours for human serum. At this time points, the organism was at the end of log phase, the culture were then used to extract bacteria RNA.

extract_protocol: The cultures were stabilised using Qiagen RNA protect, following manufacturer's protocol. The total RNA were then extracted using Qiagen RNeasy Mini Kit. These samples were then treated with Ambion Turbo-DNA free DNase to remove any genomic DNA. The RNA samples were then checked for their quality and quantity using Nanodrop ND-1000 and an on-chip capillary electrophoresis method, Agilent 2100 Bioanalyzer.

value: bacteria grown in human serum until the end of log phase


title: EDL, KO, mouse 71

description: 2179_032_N3_71_EDL_mG1_AK_131114_(MoGene-1_0-st-v1).CEL.gz

value: mouse 71


title: IST Unchallenged, Biological replicate 4


title: Soleus, KO, mouse 71

description: 2173_032_N3_71_SOLEUS_mG1_AK_061114_(MoGene-1_0-st-v1).CEL.gz

value: Soleus


title: EDL, WT, mouse 88

description: 2174_032_N1_88_EDL_mG1_AK_131114_(MoGene-1_0-st-v1).CEL.gz

value: mouse 88


title: Soleus, WT, mouse 90

description: 2172_032_N3_90_SOLEUS_mG1_AK_061114_(MoGene-1_0-st-v1).CEL.gz


title: EDL, WT, mouse 91

description: 2176_032_N2_91_EDL_mG1_AK_131114_(MoGene-1_0-st-v1).CEL.gz

value: mouse 91


title: Soleus, WT, mouse 88

description: 2168_032_N1_88_SOLEUS_mG1_AK_061114_(MoGene-1_0-st-v1).CEL.gz


title: Soleus, KO, mouse 83

description: 2169a_032_N1_83_SOLEUS_mG1_AK_061114_(MoGene-1_0-st-v1).CEL.gz


title: Unchallenged, Biological replicate 4


title: IST Unchallenged, Biological replicate 1


title: Serum Unchallenged, Biological replicate 4

description: Gene expression data from bacteria grown in human serum for 72 hours

source_name: bacteria that were grown in human serum


title: IST challenged, Biological replicate 2

description: Gene expression data from bacteria grown in human IST for 12 hours with ciprofloxacin challenge at 6 hours

source_name: bacteria that were grown in human IST, then challenged with ciprofloxacin


title: IST challenged, Biological replicate 3


title: Serum Unchallenged, Biological replicate 3


title: IST challenged, Biological replicate 5


title: IST challenged, Biological replicate 1


title: Serum challenged, Biological replicate 1

description: Gene expression data from bacteria grown in human serum for 72 hours with ciprofloxacin challenge at 36 hours

source_name: bacteria that were grown in human serum, then challenged with ciprofloxacin


title: IST challenged, Biological replicate 4


title: IST Unchallenged, Biological replicate 2


title: Serum challenged, Biological replicate 5


title: Serum challenged, Biological replicate 4


title: Soleus, KO, mouse 69

description: 2171a_032_N2_69_SOLEUS_mG1_AK_061114_(MoGene-1_0-st-v1).CEL.gz


title: Soleus, WT, mouse 91

description: 2170_032_N2_91_SOLEUS_mG1_AK_061114_(MoGene-1_0-st-v1).CEL.gz


title: Serum challenged, Biological replicate 2


title: Device sample, Biological replicate 1

description: Gene expression data from bacteria grown in whole blood until mid-log phase, then the bacteria were passed through a microfluidic device

source_name: bacteria that were processed using microfluidic device

growth_protocol: E.coli CFT073 were grown in 15ml sterile tubes with 3ml of human whole blood at 37 degress celsius shaking at 200rpm for 24 hours, this ensured the organism was at mid-log phase of growth.

treatment_protocol: The treatment in this study was the microfluidic processing of the bacteria, the bacteria that were passed through the device were compared to the bacteria that were not passed through the device.

value: mid-log phase

tag: device

value: yes


title: Serum challenged, Biological replicate 3


title: Device sample, Biological replicate 3


title: Device sample, Biological replicate 4


title: Device sample, Biological replicate 2


title: Benchtop sample, Biological replicate 5

description: Gene expression data from bacteria grown in whole blood until mid-log phase

source_name: bacteria that were not processed using microfluidic device

value: no


title: Benchtop sample, Biological replicate 3


title: Benchtop sample, Biological replicate 1


title: Benchtop sample, Biological replicate 4


title: memory CD8 T cells_anti-CD3/CD28_24hr (2)

city: Shanghai

first: Cheng

last: Yang

address: 227 Chongqing South Road, Luwan District

institute: Shanghai Jiaotong University School of Medicine

description:
Gene expression in memory CD8 T cells stimulated with anti-CD3/CD28 for 24 hr
M_24h_2
M24h_8_NS

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

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

source_name: FACS-sorted memory CD8 T cell cultured ex vivo, with anti-CD3/CD28 stimulation for 24 hours

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

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit（Cat#217004, QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: Freshly sorted naive and memory CD8 T cells were cultured in R10 medium (RPMI 1640 + 10% fetal bovine serum + 100 U/mL Penicillin/Streptomycin) (GIBCO) at a cell concentration of 2×106 /mL in 96-U-bottom plates, and stimulated with anti-CD3 and anti-CD28 mAbs coupled magnetic beads (Invitrogen) at a cell-bead ratio of 1:1 for 4 hr, 24 hr or left unstimulated.

value: Peripheral Blood

value: memory CD8 T cells

tag: cell surface markers

tag: treatment

value: stimulation with anti-CD3/CD28 mAbs


title: Benchtop sample, Biological replicate 2


title: Serum Unchallenged, Biological replicate 2


title: Serum Unchallenged, Biological replicate 1


title: Device sample, Biological replicate 5


title: memory CD8 T cells_anti-CD3/CD28_4hr (2)

description:
Gene expression in memory CD8 T cells stimulated with anti-CD3/CD28 for 4 hr
M_4h_2
M4h_7_NS

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: FACS-sorted memory CD8 T cell cultured ex vivo, with anti-CD3/CD28 stimulation for 4 hours


title: resting memory CD8 T cells_0hr (2)

description:
Gene expression in resting memory CD8 T cells
M_0h_2
M0h_7_NS

source_name: FACS-sorted memory CD8 T cell cultured ex vivo, without anti-CD3/CD28 stimulation

value: control


title: naïve CD8 T cells_anti-CD3/CD28_24hr (2)

description:
Gene expression in naïve CD8 T cells stimulated with anti-CD3/CD28 for 24 hr
N_24h_2
N24h_8_NS

source_name: FACS-sorted naïve CD8 T cell cultured ex vivo, with anti-CD3/CD28 stimulation for 24 hours

value: naïve CD8 T cells


title: resting naïve CD8 T cells_0hr (1)

description:
Gene expression in resting naïve CD8 T cells
N_0h_1
N0h_12_NS

source_name: FACS-sorted naïve CD8 T cell cultured ex vivo, without anti-CD3/CD28 stimulation


title: memory CD8 T cells_anti-CD3/CD28_24hr (1)

description:
Gene expression in memory CD8 T cells stimulated with anti-CD3/CD28 for 24 hr
M_24h_1
M24h_12_NS


title: memory CD8 T cells_anti-CD3/CD28_4hr (1)

description:
Gene expression in memory CD8 T cells stimulated with anti-CD3/CD28 for 4 hr
M_4h_1
M4h_12_NS


title: resting naïve CD8 T cells_0hr (2)

description:
Gene expression in resting naïve CD8 T cells
N_0h_2
N0h_7_NS


title: resting memory CD8 T cells_0hr (1)

description:
Gene expression in resting memory CD8 T cells
M_0h_1
M0h_12_NS


title: naïve CD8 T cells_anti-CD3/CD28_4hr (2)

description:
Gene expression in naïve CD8 T cells stimulated with anti-CD3/CD28 for 4 hr
N_4h_2
N4h_7_NS

source_name: FACS-sorted naïve CD8 T cell cultured ex vivo, with anti-CD3/CD28 stimulation for 4 hours


title: Xenograft

city: Kamakura

first: Satoshi

last: Kondo

address: Tebiro 6-10-1

institute: Toray Industries,Inc.

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

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: Cholangiocarcinoma

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

extract_protocol: Total RNAs were extracted using mirVana isolation kit.

treatment_protocol: Total RNAs were extracted from cholangiocarcinoma xenografts and organoids (passage 7 and 32).

value: Xenograft

value: Cholangiocarcinoma


title: naïve CD8 T cells_anti-CD3/CD28_24hr (1)

description:
Gene expression in naïve CD8 T cells stimulated with anti-CD3/CD28 for 24 hr
N_24h_1
N24h_12_NS


title: TGF(+)48h_2

city: Kobe

first: MITSUGU

last: OMATA

address: 6-4-3, Minatojima-MInamimachi, Chuo-ku

institute: ASUBIO PHARMA CO., LTD.

description: Gene expression of hRPTEC incubated with TGF-b for 48h (replicate2)

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Microarray 4x44K (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 014850_D_F_20060807) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: hRPTEC

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the Low Input Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNAeasy column purification (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Cells were harvested with TRIzol (Invitrogen, Carlsbad, CA) and proceeded to RNA purification.

value: hRPTEC


title: naïve CD8 T cells_anti-CD3/CD28_4hr (1)

description:
Gene expression in naïve CD8 T cells stimulated with anti-CD3/CD28 for 4 hr
N_4h_1
N4h_12_NS


title: Organoid P7

value: Organoid Passage 7


title: TGF(+)48h+TGF(-)24h

description: Gene expression of hRPTEC incubated with TGF-b for 48h followed by the additional incubation without TGF-b for 24h.


title: Organoid P32

value: Organoid Passage 32


title: TGF(+)48h+TGF(+)24h

description: Gene expression of hRPTEC incubated with TGF-b for 48h followed by the additional incubation with TGF-b for 24h.


title: TGF(+)48h_1

description: Gene expression of hRPTEC incubated with TGF-b for 48h (replicate1)


title: FSHD8340_19_Cy3

city: Iowa City

first: Rolf

last: Turk

state: IA

address: 285 Newton Road, 4283CBRB

department: Molecular Physiology and Biophysics

institute: University of Iowa

hyb_protocol: Hybmix: 50% Formamide, 5x SSC, 0.5%SDS

scan_protocol: GenePix 4000B

data_processing: Hybridizations were performed in a dye-swap fashion. Microarrays were analyzed by GenePix Pro 6 (Axon). Local background corrected, median spot intensities were normalized using VSN in R. Oligonucleotides were considered expressed when at least 36 out of 48 replicates per array showed intensity higher than the background. Fold-changes were calculated on a linear scale by subtraction of averaged normalized intensities of control samples from FSHD samples, followed by returning e raised to the power of the difference.

source_name: Differentiated myoblast from FSHD83340

label_protocol: Small transcripts were isolated and amplified from 1 µg of total RNA using the Global MiRNA Amplification Kit (SBI System Biosciences, RA400A-1). The transcripts contain a T7 promotor sequence which was used for a second round of amplification using the T7 MEGAscript kit according to the manufacturer’s protocol (Ambion, AM1333). Aminoallyl-UTP (Ambion, AM8436) was incorporated during the in vitro transcription. Run-off transcripts were chemically labeled with either Cy3 or Cy5.

growth_protocol: Primary myoblasts were cultured in DMEM (Gibco) supplemented with 2mM L-Glutamine (Gibco), 1% Pen Strep (Gibco) and 20% Fetal Bovine Serum (HyClone). Primary myoblasts were forced into differentiation by switching to differentiation media, which contains DMEM (Gibco), 2mM L-Glutamine (Gibco), 1% Pen Strep (Gibco) and 2% Fetal Bovine Serum (HyClone).

extract_protocol: Total RNA was isolated according to the manufacturer’s protocol (TRIzol, Invitrogen).

treatment_protocol: The samples were not treated.

tag: Differentiated myoblast from FSHD83340


title: FSHD8340_20_Cy5

source_name: Differentiated myoblast from FSHD8340

tag: Differentiated myoblast from FSHD8340


title: CTRL8879_22_Cy3

source_name: Differentiated myoblast from CTRL8879

tag: Differentiated myoblast from CTRL8879