title: 11N

description:
Gene expression in colorectal tissue
AR1033_37

value: normal tissue


status: Public on Sep 08 2017

type: RNA

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

country: USA

institute: NIH

description:
5776_EM_3_HuGene-2_0-st_04_P-Ba-HIV-N-HC-Y-M-64CM015_01_8647
Gene expression data from paired blood biopsy PRE treatment pair and rep 4.
Paired blood biopsy PRE treatment pair and rep 4-PAIRED WITH Paired blood biopsy POST treatment pair and rep 4.

hyb_protocol: Samples were hybridized onto Affymetrix GeneChip Human Gene 2.0 ST arrays according to manufacturer's recommendations.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7GPlus.

data_processing: The data were analyzed with EC 1.4 using RMA analysis.

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: Labeling was performed using the Ovation Pico WTA system (NuGEN, Inc., San Carlos, CA).

growth_protocol: This phase 2a, open-label, single center exploratory study assessed the safety, tolerability and potential efficacy of simtuzumab in HCV- and/or HIV-infected adults (NCT01707472).

extract_protocol: RNA was extracted using the RNeasy 96 kit according to manufacturer's recommendations.

treatment_protocol: Study participants received 700 mg of simtuzumab (Gilead Sciences, Inc., CA) intravenously over 30 minutes every 2 weeks for 22 weeks (12 infusions).

tag: age

value: adult

tag: disease state

value: advanced liver fibrosis

tag: tissue

value: blood

tag: treatment

tag: time point

value: pre-treatment

tag: participant


title: SCD patient 1_UC

city: Chicago

first: Zhengdeng

last: Lei

state: IL

address: 1853 W Polk St

department: Research Resources Center

institute: University of Illinois at Chicago

description: PBMC of SCD patient

hyb_protocol: GeneChip hybridization wash and stain kit was procured from Affymetrix and used according the manufacturers protocol.

scan_protocol: Affymetrix GeneChip Scanner

data_processing: Data were processed using Affymetrix Power Tools. The batch effect is corrected by ComBat

source_name: peripheral blood mononuclear cells

label_protocol: GeneChip WT Terminal labelling and controls kit was procured from Affymetrix and used according the manufacturers protocol.

extract_protocol: RNA was was extracted from PBMC accoding to standard protocol.

value: peripheral blood

tag: cell type

value: mononuclear cells

tag: disease

value: sickle cell disease


title: 9N

city: Tsuruoka

first: Kiyotoshi

last: Satoh

state: Yamagata

address: Mizukami 246-2, Kakuganji

department: Institute for Advanced Biosciences

country: Japan

institute: Keio University

description:
Gene expression in colorectal tissue
AR1033_33

hyb_protocol: Cy3-labelled cRNA (0.6 ug) was fragmented at 60ºC for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver2.0 (Agilent) for 17 hours at 65ºC 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 37ºC GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: colorectal cancer patient #9

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug total RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (Qiagen, Venlo, Netherlands) according to the manufacturer's protocol, including on-column DNase I incubation for 15 min at room temperature to reduce genomic DNA contamination. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: CRC

tag: individual

value: colorectal cancer patient #9

value: rectum

tag: tissue type

tag: gender

value: male


description:
5774_EM_3_HuGene-2_0-st_02_P-Ba-HIV-N-HC-Y-M-60CM017_01_8459
Gene expression data from paired blood biopsy PRE treatment pair and rep 2.
Paired blood biopsy PRE treatment pair and rep 2-PAIRED WITH Paired blood biopsy POST treatment pair and rep 2.


title: SCD patient 36_HU

description: PBMC of SCD patient


title: 3T

description:
Gene expression in colorectal tissue
AR1033_30

source_name: colorectal cancer patient #3

value: colorectal cancer patient #3

value: tumor tissue

tag: Stage

value: adenoma

value: female


title: SCD patient 37_HU

description: PBMC of SCD patient


title: SCD patient 38_HU

description: PBMC of SCD patient


title: 3N

description:
Gene expression in colorectal tissue
AR1033_29


title: 2T

description:
Gene expression in colorectal tissue
AR1033_28

source_name: colorectal cancer patient #2

value: colorectal cancer patient #2

value: cecum


title: SCD patient 35_HU

description: PBMC of SCD patient


title: SCD patient 34_HU

description: PBMC of SCD patient


description:
5773_EM_3_HuGene-2_0-st_01_P-Ba-HIV-N-HC-Y-M-57CM013_01_8457
Gene expression data from paired blood biopsy PRE treatment pair and rep 1.
Paired blood biopsy PRE treatment pair and rep 1-PAIRED WITH Paired blood biopsy POST treatment pair and rep 1.

value: adult


title: 2N

description:
Gene expression in colorectal tissue
AR1033_27

value: normal tissue


description:
5775_EM_3_HuGene-2_0-st_03_P-Ba-HIV-N-HC-Y-F-59CM009_01_8596
Gene expression data from paired blood biopsy PRE treatment pair and rep 3.
Paired blood biopsy PRE treatment pair and rep 3-PAIRED WITH Paired blood biopsy POST treatment pair and rep 3.

value: advanced liver fibrosis

value: blood


title: SCD patient 40_HU

description: PBMC of SCD patient

value: peripheral blood


title: 6T

description:
Gene expression in colorectal tissue
AR1033_24

source_name: colorectal cancer patient #6

value: colorectal cancer patient #6

value: sigmoid colon

value: stage 0


title: 8N

description:
Gene expression in colorectal tissue
AR1033_31

source_name: colorectal cancer patient #8

value: CRC

value: colorectal cancer patient #8

value: ascending colon


title: 1T

description:
Gene expression in colorectal tissue
AR1033_26

source_name: colorectal cancer patient #1

value: colorectal cancer patient #1

value: transverse colon


title: SCD patient 31_HU

description: PBMC of SCD patient

value: mononuclear cells

value: sickle cell disease


title: SCD patient 33_HU

description: PBMC of SCD patient


title: SCD patient 28_HU

description: PBMC of SCD patient


title: SCD patient 29_HU

description: PBMC of SCD patient


title: 1N

description:
Gene expression in colorectal tissue
AR1033_25

value: female


title: SCD patient 27_HU

description: PBMC of SCD patient


title: SCD patient 24_HU

description: PBMC of SCD patient


title: SCD patient 26_HU

description: PBMC of SCD patient


title: SCD patient 25_HU

description: PBMC of SCD patient


title: SCD patient 32_HU

description: PBMC of SCD patient


title: SCD patient 39_HU

description: PBMC of SCD patient


title: 6N

description:
Gene expression in colorectal tissue
AR1033_23


title: SCD patient 23_HU

description: PBMC of SCD patient


title: SCD patient 15_HU

description: PBMC of SCD patient


title: SCD patient 20_HU

description: PBMC of SCD patient


title: SCD patient 14_HU

description: PBMC of SCD patient


title: SCD patient 18_HU

description: PBMC of SCD patient


title: SCD patient 11_HU

description: PBMC of SCD patient


title: SCD patient 13_HU

description: PBMC of SCD patient


title: SCD patient 17_HU

description: PBMC of SCD patient


title: SCD patient 21_HU

description: PBMC of SCD patient


title: SCD patient 30_HU

description: PBMC of SCD patient


title: SCD patient 10_HU

description: PBMC of SCD patient


title: SCD patient 12_HU

description: PBMC of SCD patient


title: SCD patient 8_HU

description: PBMC of SCD patient


title: SCD patient 9_HU

description: PBMC of SCD patient


title: SCD patient 19_HU

description: PBMC of SCD patient


title: SCD patient 7_HU

description: PBMC of SCD patient


title: SCD patient 6_HU

description: PBMC of SCD patient


title: SCD patient 2_HU

description: PBMC of SCD patient


title: SCD patient 5_HU

description: PBMC of SCD patient


title: SCD patient 3_HU

description: PBMC of SCD patient


title: SCD patient 22_HU

description: PBMC of SCD patient


title: SCD patient 16_HU

description: PBMC of SCD patient


title: SCD patient 4_HU

description: PBMC of SCD patient


title: blood_patient19_t0

city: Illkirch/Strasbourg

first: Wolfgang

last: Raffelsberger

address: 1 rue Laurent Fries

department: DBGS

country: France

institute: IGBMC

description: blood sample

hyb_protocol: Following fragmentation, cRNA was hybridized on Human GeneChip HG-U133 Plus 2.0 kit (Affymetrix, Santa Clara, CA) and the arrays were washed and stained in the Affymetrix Fluidics Station 450 according to the standard Affymetrix protocol (Expression Analysis Technical Manual Rev. 2, 2005-2007, Affymetrix).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 3000 7G scanner

data_processing: RMA; quality control was performed using RReportGenerator (Raffelsberger et al, 2008, PMID:18037684)

source_name: blood sample

label_protocol: Biotinylated cRNA was prepared from the total RNA according to the Affymetrix protocol (Expression Analysis Technical Manual Rev. 2, 2005-2008, Affymetrix)

extract_protocol: Blood samples were taken from patients. Total RNA used for microarray studies was isolated using a PAXgene Blood RNA kit (Quiagen, Valencia, CA).

tag: infection

value: pneumonia

tag: survival

value: positive

tag: Sex

value: M

tag: time-point

value: early


title: blood_patient20_t1

description: blood sample

value: blood

value: late


title: SCD patient 1_HU

description: PBMC of SCD patient

value: peripheral blood


title: blood_patient20_t0

description: blood sample


title: blood_patient15_t0

description: blood sample


title: blood_patient12_t0

description: blood sample

value: negative

value: F


title: blood_patient17_t1

description: blood sample


title: blood_patient17_t0

description: blood sample


title: blood_patient12_t1

description: blood sample


title: blood_patient11_t1

description: blood sample


title: blood_patient10_t1

description: blood sample

value: activated protein C


title: blood_patient15_t1

description: blood sample


title: blood_patient09_t1

description: blood sample


title: blood_patient11_t0

description: blood sample


title: blood_patient10_t0

description: blood sample


title: blood_patient18_t1

description: blood sample


title: blood_patient14_t0

description: blood sample


title: blood_patient14_t1

description: blood sample


title: blood_patient13_t1

description: blood sample


title: blood_patient13_t0

description: blood sample


title: blood_patient18_t0

description: blood sample


title: blood_patient07_t0

description: blood sample


title: blood_patient16_t1

description: blood sample


title: blood_patient16_t0

description: blood sample


title: blood_patient09_t0

description: blood sample


title: blood_patient07_t1

description: blood sample


title: blood_patient06_t1

description: blood sample


title: blood_patient19_t1

description: blood sample


title: blood_patient08_t1

description: blood sample


title: blood_patient06_t0

description: blood sample


title: Apc+/-, colorectal polyps 110CP2

description:
Gene expression in colorectal tissue
110CP2

hyb_protocol: Cy3-labelled cRNA was fragmented at 60ºC for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Mouse GE 4x44K Microarray v2 (Agilent) for 17 hours at 65ºC 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 37ºC GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2505C) using one color scan setting for 4x44K array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green PMT is set to 100%).

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

organism: Mus musculus

growth_protocol: Mice were kept under a 12 hour light-dark cycle at 22C and fed ad libitum with CLEA CE-2 chow diet.

treatment_protocol: Construction of ApcΔ716 mice has been described previously (Proc Natl Acad Sci USA 92, 4482-4486 (1995)).

tag: strain

tag: genotype/variation

value: colorectum

value: polyps

value: 14 week


title: Apc+/-, normal colorectal tissue 103CN2

description:
Gene expression in colorectal tissue
103CN2

value: normal tissue

tag: age


title: Apc+/-, normal colorectal tissue 107CN2

description:
Gene expression in colorectal tissue
107CN2

tag: tissue


title: blood_patient05_t1

description: blood sample

tag: treatment


title: blood_patient04_t1

description: blood sample


title: Apc+/-, colorectal polyps 103CP2

description:
Gene expression in colorectal tissue
103CP2


title: blood_patient02_t1

description: blood sample


title: blood_patient08_t0

description: blood sample


title: blood_patient03_t1

description: blood sample


title: blood_patient02_t0

description: blood sample


title: Apc+/-, normal colorectal tissue 106CN2

description:
Gene expression in colorectal tissue
106CN2


title: blood_patient05_t0

description: blood sample


title: blood_patient04_t0

description: blood sample


title: blood_patient03_t0

description: blood sample


title: blood_patient01_t1

description: blood sample


title: Apc+/-, colorectal polyps 106CP2

description:
Gene expression in colorectal tissue
106CP2


title: Apc+/-, normal colorectal tissue 110CN2

description:
Gene expression in colorectal tissue
110CN2


title: wild-type, normal colorectal tissue 108CN2

description:
Gene expression in colorectal tissue
108CN2

source_name: wild-type

value: wild-type


title: wild-type, normal colorectal tissue 104CN2

description:
Gene expression in colorectal tissue
104CN2


title: wild-type, normal colorectal tissue 102CN2

description:
Gene expression in colorectal tissue
102CN2


title: wild-type, normal colorectal tissue 105CN2

description:
Gene expression in colorectal tissue
105CN2


title: blood_patient01_t0

description: blood sample


title: patient19_t0

description: blood sample


title: patient17_t0

description: blood sample


title: patient20_t0

description: blood sample


title: patient18_t0

description: blood sample


title: patient15_t0

description: blood sample


title: patient12_t0

description: blood sample


title: patient10_t0

description: blood sample


title: patient14_t0

description: blood sample


title: patient09_t0

description: blood sample


title: patient13_t0

description: blood sample


title: patient08_t0

description: blood sample


title: patient16_t0

description: blood sample


title: patient11_t0

description: blood sample


title: patient05_t0

description: blood sample


title: patient07_t0

description: blood sample


title: patient06_t0

description: blood sample


title: patient03_t0

description: blood sample


title: patient04_t0

description: blood sample


title: patient02_t0

description: blood sample


title: Apc+/-, colorectal polyps 107CP2

description:
Gene expression in colorectal tissue
107CP2


title: patient01_t0

description: blood sample


title: 755NL

city: Shanghai

first: Hongbin

last: Ji

address: YueYang Rd

country: China

institute: SIBCB

hyb_protocol: Affymetrix standard procedures

scan_protocol: Affymetrix standard procedures

data_processing: RMA-sketch

source_name: SCC adjacent normal

label_protocol: Affymetrix standard procedures

extract_protocol: Trizol extraction of total RNA

treatment_protocol: frozen

value: lung SCC adjacent normal


title: 467NL


title: 757NL


title: 433

source_name: SCC

value: lung squamous cell carcinomas


title: 444


title: 699-2


title: 611NL


title: 520


title: 731


title: 482


title: 428


title: 523


title: 159


title: 467


title: 538


title: 416


title: 281


title: 348


title: 400


title: 196


title: 554


title: 134


title: 321


title: 416NL


title: 700


title: 234


title: 408


title: 553


title: 503


title: 313


title: 144


title: 303


title: 301


title: 299


title: 94


title: 375


title: 207


title: 127


title: 755


title: 537


title: 171


title: 504


title: 343


title: 623


title: 160


title: 451


title: 545


title: 225


title: 310


title: 298


title: 417


title: 192


title: 656


title: 611


title: 170


title: PC-3

status: Public on Sep 07 2017

city: Singapore

first: Tze Hau

last: Lam

address: 70 Biopolis Street

country: Singapore

institute: Procter and Gamble

hyb_protocol: Samples were hybridized to Affymetrix Human Transcriptome 2.0 array for 16 hours at 45 °C with rotation at 60 rpm. Arrays were then washed and stained using the FS450_0001 fluidics protocol

scan_protocol: Affymetrix 3000 7G scanner

data_processing:
Data was processed and normalized using the Affymetrix® Expression Console™ Software (version 1.3.1.187)
HTA-2_0.r1.pgf
HTA-2_0.r1.Psrs.mps

source_name: cell line

label_protocol: Samples were fragmented and biotinylated using the Affymetrix GeneChip WT PLUS Reagent kit

growth_protocol: Cells were cultured according to recommendations by ATCC, maintained in humid 37 degree incubator with 5% CO2

extract_protocol: Total RNA was harvested using the Nucleospin RNA II Kit (Machery-Nagel) according to manufacturer's instructions.

treatment_protocol: Cells were seeded in 10cm dishes and harvested at 30h later when confluency reaches 50%.

tag: cell line

value: Prostate

tag: hbv status

value: Negative


title: 341

tag: cell type


title: COLO316

value: Ovary


title: 5637

value: Bladder


title: T24


title: 137


title: 438


title: 757


title: 185


title: Saos-2

value: Bone


title: A549

value: Lung


title: AGS

value: AGS

value: Stomach


title: Hep3B

value: liver

value: Positive


title: HepG2


title: PLC/PRF/5


title: 257


title: GLMT1 tumor cell excised from TNKO mouse, biological rep3

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

institute: Hirosaki University

hyb_protocol: Following fragmentation, 12.5 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: CEL files were quantified with the distribution free weighted method (DFW), using the statistical language R (R-2.7.2) and Bioconductor 2.2.

source_name: GLMT1 tumor cell grown in TNKO mouse

label_protocol: biotinylated aRNA was obtained from 100 ng of purified total RNA using a GeneChip 3’ IVT Express Kit (Affymetrix, Santa Clara, CA, USA).

growth_protocol: GLMT1 (GRS/A Lung Metastasis Tumor 1) cell was washed twice with phosphate buffered saline (PBS(-); Nissui, Tokyo, Japan), and then trypsinized with 0.05% trypsin-EDTA (Gibco BRL) once the cell line reached 90% confluence. The cell suspension was then centrifuged at 1,500 rpm for 5 min at 4°C, after inactivation of tryptic activity by adding 10% FBS-containing medium. Cells were re-suspended in the serum-free medium to adjust the cell density to 1 × 10^7 cells/ml. One hundred microliters of the cell suspension was then inoculated underneath the back skin of both WT and TNKO mice.

extract_protocol: Total RNA was isolated from the tissues and cells with RNeasy Lipid Tissue Mini Kit (Qiagen, Hilden, Germany), in accordance with the manufacturer’s instructions.

treatment_protocol: Excised tumor cells were immediately homogenized in solution D (4 M guanidine thiocyanate (Wako Pure Chemical, Osaka, Japan) solution containing 1% of 2-mercaptoethanol (Wako Pure Chemical)).

value: Male

tag: host strain background

value: GRS/A

tag: host genotype/variation

value: tenascin-C-deficient

tag: host age

value: 10 weeks

value: subcutaneously inoculated GLMT1 tumor cells


title: GLMT1 tumor cell excised from TNKO mouse, biological rep2

tag: gender


title: FS-04

value: Skin


title: 371

value: lung squamous cell carcinomas


title: Regenerating liver 3

city: Sendai

first: Yoshihiro

last: Sato

state: Miyagi

address: 2-1 Seiryo-machi, Aobaku

department: Biochemistry

institute: Tohoku University

hyb_protocol: 600 ng of Cy3-labelled 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, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (Agilent-028005) 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 using one color scan setting for 8x60k array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_107_Sep9 and Grid: 028005_D_F_20101029) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: PVBL, 3days, replicate 3

label_protocol: Total RNA was labeled with Cyanine 3-CTP by the use of Low Input Quick Amp Labeling Kit, One-Color (Agilent Technology)

extract_protocol: Total RNA was isolated using RNeasy Mini Kit (Qiagen) according to the manufacturer's protocol.

treatment_protocol: Mice underwent the operation were sacrificed at 3 days after operation, and right lobes were collected. Separated liver tissues were snap frozen in liquid nitrogen and kept under -80ºC.

value: Liver


title: Regenerating liver 2

source_name: PVBL, 3days, replicate 2


title: 756


title: Huh7

value: Negative


title: GLMT1 tumor cell excised from WT mouse, biological rep2

source_name: GLMT1 tumor cell grown in WT mouse

value: wild type


title: GLMT1 tumor cell excised from WT mouse, biological rep1


title: Caco-2

value: Colon


title: Sham liver 2

source_name: Sham, 3days, replicate 2


title: Sham liver 3

source_name: Sham, 3days, replicate 3


title: M4359 green PS

city: Hannover

first: Verena

last: Kopfnagel

address: Carl-Neuberg-Straße 1

department: Dermatology

country: Germany

institute: Hannover Medical School

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out exactly as recommended in the ‘Two-Color Microarray-Based Gene Expression Analysis Protocol V5.7’ (Agilent).

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 5 µm, bit depth 20).

data_processing: Data extraction and processing of raw fluorescence intensity values were performed with the ‘Feature Extraction Software V10.7.3.1’ by using the recommended default extraction protocol file: GE2_107_Sep09.xml.  For inter-array normalization, processed intensity values as generated in the Feature Extraction process, ‘gProcessedSignal’ (gPS) and ‘rProcessedSignal’ (rPS), were further transformed as follows: All PS values (gPS and rPS) of one particular microarray (‘Array I’ in the formula shown below) were multiplied with a microarray-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the gPS values calculated by the Feature Extraction software for that microarray. Accordingly, normalized PS values for all samples (microarray data sets) were calculated by the following formula:   normalized PSArray i = PSArray i  x (1500 / 75th Percentile gPSArray i)  Finally, a lower intensity threshold was defined as 1% of the reference 75th Percentile value (= 15). All of those normalized PS values that fell below this intensity border, were substituted by the respective surrogate value of 15.

source_name: donor 2 (1197) - pDC+RNAse7 10µg/ml

label_protocol: Total RNA was used to prepare C3- or C5-labeled cRNA (Quick Amp Labeling kit, two color, #5190-0444, Agilent Technologies) as directed by the company. Prior to the reverse transcription reaction, 1µl of a 1:6400 dilution of Agilent’s Two-Color spike-in mixes A (for Cy3-labeled samples) or B (for Cy5-labeled samples) (#5188-5282, Agilent Technologies) were added to 500ng of total RNA of each analyzed sample.

growth_protocol: Plasmacytoid dendritic cells (pDC) were isolated using the human Plasmacytoid Dendritic Cell Isolation Kit II (Miltenyi Biotech, Bergisch Gladbach, Germany).

extract_protocol: RNA was isolated by using the High Pure RNA Isolation Kit (Roche). mRNA was subjected to mRNA microarray analysis

treatment_protocol: Human pDCs from 2 different donors were stimulated with RNase 7 for 6h

tag: donor

value: human plasmacytoid dendritic cells


title: M4358 red PS

source_name: donor 1 (1191) - pDC+RNAse7 10µg/ml


title: M4359 red PS

source_name: donor 2 (1196) - pDC


title: M4358 green PS

source_name: donor 1 (1190) - pDC


title: h1RPE7 d14, biological rep5

city: Setagaya

first: Takuya

last: Kuroda

state: Tokyo

address: 1-18-1 Kamiyoga

department: Division of cell-based therapeutic products

institute: National Institute of Health and Sciences

hyb_protocol: Following fragmentation, 15 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.

data_processing:
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The TGT value is 500.
affymetrix-algorithm-name = ExpressionStat
affymetrix-algorithm-version = 5.0
affymetrix-array-type = HG-U133_Plus_2
affymetrix-progid = GeneChip.CallGEBaseCall.1
program-name = Expression Console
program-id = 1.2.0.20

source_name: h1RPE7 d14

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA.

extract_protocol: Extraction of total RNA was performed according to the manufacturer's instructions (RNeasy  Mini Kit, Qiagen)

value: immortalized retinal pigment epithelium (RPE)


title: 474


title: 601


title: h1RPE7 d14, biological rep4


title: 145


title: ARPE-19/HPV-16 d14, biological rep4


title: h1RPE7 d14, biological rep3


title: h1RPE7 d14, biological rep2


title: ARPE-19/HPV-16 d14, biological rep3


title: 209


title: 534


title: 214


title: Sham liver 1

source_name: Sham, 3days, replicate 1


title: ARPE-19/HPV-16 d14, biological rep1


title: pRPE-C d14, biological rep5

source_name: pRPE-C d14

value: primary retinal pigment epithelium (RPE)


title: ARPE-19 d14, biological rep3

source_name: ARPE-19 d14


title: ARPE-19/HPV-16 d14, biological rep2


title: ARPE-19 d14, biological rep5


title: 315


title: Regenerating liver 1

source_name: PVBL, 3days, replicate 1


title: GLMT1 tumor cell excised from TNKO mouse, biological rep1


title: pRPE-C d14, biological rep3


title: ARPE-19 d14, biological rep2


title: ARPE-19 d14, biological rep1


title: h1RPE7 d14, biological rep1


title: ARPE-19 d14, biological rep4


title: pRPE-C d14, biological rep2


title: ARPE-19/HPV-16 d14, biological rep5


title: GLMT1 tumor cell excised from WT mouse, biological rep3


title: pRPE-B d14, biological rep1

source_name: pRPE-B d14

value: pRPE-B (Lot. 0F3237)


title: pRPE-C d14, biological rep4


title: pRPE-B d14, biological rep2


title: pRPE-B d14, biological rep4


title: Kato III

description: Kato III

source_name: cell line

value: Kato III

value: Stomach


title: pRPE-A d14, biological rep5

source_name: pRPE-A d14

value: pRPE-A (Lot. 0F3292)


title: pRPE-B d14, biological rep3


title: pRPE-C d14, biological rep1


title: pRPE-A d14, biological rep3


title: pRPE-A d14, biological rep4


title: pRPE-A d14, biological rep1


title: Control 8

city: Athens

first: George

middle: I

last: Lambrou

state: Attiki

address: Thivon & Levadeias

department: First Department of Pediatrics

country: Greece

institute: National and Kapodistrian University of Athens

description: Raw_Data_Slide_3.txt, Block5

hyb_protocol: Slides were hybridized using the manufacturers protocol (APPLIED MICROARRAYS miRLinkTM v16 Bioarray Protocol).

scan_protocol: Images were scanned using an Agilent Microarray Scanner (G2565CA).

data_processing: Microarray raw data were extracted, as previously described, using the Imagene 6.0 software (Biodiscovery Inc., USA). The MATLAB® simulation environment (The Mathworks, Inc, Natick, MA) was applied for multi-parameter analyses. Normalization was performed using the quantile normalization algorithm. The two tailed student t-test was used to assess the mean differences between the two groups. Relative expression was estimated as the log2-transformed ratio of the individual miRNA expression levels over the mean expression level of all control samples for the respective miRNA under investigation. Final miRNA values have been calculated as the mean of each specific miRNA replicates on each array. Continuous variables were expressed as median ± standard deviation, unless differently indicated. MiRNAs were considered significant if they had a p-value<0.05 and False Discovery Ratedetection  Rate (FDR) ≤ 0.05.

source_name: Control, placenta

label_protocol: Labeling and hybridization were performed using the LabelIT miRNA labeling kit (Mirus Bio LLC, USA) according to the manufacturer’s instructions. Samples were hybridized to an Applied MicroArrays (miRlink Bioarray 300054-3PK) platform containing 1211 human miRNAs (Applied Biosystems, Foster City, CA).

growth_protocol: For the purpose of the study, two pieces of placental tissue approximately 1×1×1cm in size were randomly obtained from the central part of the placenta maternal phase, as previously described. Tissues were washed with isotonic saline solution to remove excess of blood cells and immediately stored at -80 °Co until further processing.

extract_protocol: For total RNA extraction, 100mg of placental tissue were mechanically homogenized in TRIzol (Life Technologies, Foster City, CA), treated with DNase I (Ambion, Austin, USA) and enriched for small RNAs (siRNAs, miRNAs) using the mirVana microRNA Isolation kit (Ambion, Austin, USA). RNA quantity and purity were measured using a Nanodrop spectrophotometer (ND-1000, NanoDrop Technologies, Houston, TX, USA).

value: FEMALE

tag: diagnosis

value: CONTROL

tag: onset

tag: iugr

value: NO

tag: hypertension

tag: proteinuria

value: Placenta


title: Control 7

description: Raw_Data_Slide_3.txt, Block4


title: Control 6

description: Raw_Data_Slide_2.txt, Block6


title: Control 5

description: Raw_Data_Slide_2.txt, Block5


title: HepG2 siLinc00176 / HepG2 control

first: Doan Duy Hai

last: Tran

state: Niedersachsen

address: Carl-Neubergsstr. 1

department: Institut of physiological Chemistry

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out exactly as recommended in the ‘Two-Color Microarray-Based Gene Expression Analysis Protocol V5.7’ (Agilent), except that 1000 ng of each labelled cRNA population (Cy3 and Cy5) were combined and cohybridized onto one Microarray.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20).

data_processing: Data extraction and processing of raw fluorescence intensity values were performed with the ‘Feature Extraction Software V10.7.3.1’ using the extraction protocol file ‘GE2_107_Sep09.xml’, except that ‘Multiplicative detrending’ algorithm was inactivated.  Measurements of on-chip replicates (quintuplicates) were averaged using the geometric mean of ‘ProcessedSignal’ values to retrieve one resulting value per unique non-control probe. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lie outside the interval of ‘1.42 x interquartile range‘ regarding the normalized gPS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5. Finally, a lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed to 15. All of those normalized PS values that fell below this intensity border were substituted by the respective surrogate value of 15.

source_name: HepG2 control

label_protocol: Synthesis of labeled cRNA was performed with the ‘Quick Amp Labeling kit, two color’ (#5190-0444, Agilent Technologies), except that NTP-mix and fluorescently-labeled CTP (to be used in the T7 reaction) were exchanged by a mix containing 15 mM of each ATP, CTP, GTP, 13.75 mM of UTP, and 1.25 mM of aaUTP (final concentration of each nucleotide was 1.875 mM). The labeling of aaUTP-cRNA was performed by use of the Amino Allyl MessageAmp™ II Kit (#AM1753; Life Technologies) and Alexa Fluor 555 and 647 Reactive Dyes (#A32756, #A32757; LifeTechnologies).

growth_protocol: Cells were grown in DMEM supplemented with 10% FCS.

extract_protocol: RNA was isolated  with the High Pure RNA Isolation kit (Roche Diagnostics) according to the manufacturer´s instructions.

treatment_protocol: control siRNA and siLinc00176 were  transfected using Lipofectamine 2000 (Gibco Life technology, ). After 24 hours, total RNAs were isolated.

tag: genotype/variation

value: control

source_name: HepG2 siLinc00176


title: Control 4

description: Raw_Data_Slide_2.txt, Block4


title: Control 3

description: Raw_Data_Slide_1.txt, Block6


title: Pre-eclampsia 16

description: Raw_Data_Slide_3.txt, Block8

source_name: Pre-eclampsia, placenta

value: PRE-ECLAMPSIA

value: EARLY

value: YES


title: Human_pulmonary_cultured_normal sample C

city: Philadelphia

first: Michael

last: Beers

state: PA

address: 3450 Hamilton Walk

institute: University of Pennsylvania

hyb_protocol: Hybridization of Reference with all samples were carried out by the Duke Institute for Genomic Sciences and Policy.

scan_protocol: Scans were carried out by the Duke Institute for Genomic Sciences and Policy using an Axon Genepix Scanner (Genepix 4000B) according to protocols for that scanner.

data_processing: Raw genepix data files (.GPR) derived from the HO36K human chip (Operon Human Oligo set V4) were downloaded from the Duke Website. All further analysis was carried out LIMMA, a BioConductor package that applies linear model on gene expression microarray data analysis with good statistic performance on experiments with small numbers of arrays.  Normalization and analysis were done using LIMMA in R.  A matrix of spot weights was computed for each comparison, spot with a Flags-value less than -50 was giving zero weight.  Samples with distinct overall density were removed (Total density picture).  Expression data was then normalized by robust spline for within array normalization, and quantile for between arrays normalization to ensure that intensities have the same empirical distribution across arrays and across channels. Fold changes and standard errors were estimated by fitting a linear model, and empirical Bayes smoothing was applied to the standard errors.  Lists of significant were generated by setting the threshold of Benjamini–Hochberg false discovery rate (FDR) to 0.01, and log fold change to 1.3.

source_name: cultured normal fibroblasts (P3)

label_protocol: Starting with about 1 micro gram total RNA at a concentration of about 100 ng/microliter, RNA was reverse transcriebed using the MessageAmp II™ aRNA Kit (Ambion Catalog # 1751).  Second strand cDNA synthesis and cDNA purification were also carried out using the same kit.  Using the same kit, in vitro transcription step was used to amino-allylate RNA with a reacion mixture that included: 3 uL (50 mM) aaUTP, 4 uL (75 mM) T7 ATP solution, 4 uL (75 mM) T7 CTP solution, 4 uL (75 mM) T7 GTP, 2 uL (75 mM) T7 UTP solution, 4 uL T7 10X Reaction Buffer, 4 uL T7 Enzyme mix (total 25 uL per sample). Samples were incubated at 37 C for 14 hours and then maintained at 4 C prior to purification of amino-allylated amplified RNA using the same Message Amp II Kit in 100 uL of nuclease free water. Yield was verified by Nano-drop.  10 micrograms of amino-allylated amplified RNA were then coupled with Cy5 for experiemental and control samples, and Cy3 for Stratagene Human reference aaaRNA by incubation in dark for 1 hour after addition of 1 ul of 1M sodium bicarbonate pH9.0  according to the TIGR protocol used by Duke Institute for Genomic Science and Policy. MEGAclear Kit (Cat#1908) was used to remove unincorporated Cy Dye

extract_protocol: Lung obtained in the operating room within 1 minute of explantation and briefly dissected into 4 regions representing the upper and lower regions of the lung and within these both the peripheral regions and the central regions were dissected apart.  Lung tissue was kept in ice cold (4 C) PBS for transportation to the lab.  In the lab, tissue was briefly and rapidly dissected into 1 mm cubed pieces and placed in 4% collagenase P (Roche) in DMEM media with 20% FBS, 2X Penicillin, Streptomycin, Amphotericin B in 37 C humidified incubator with a magnetic stir bar oscillating at a medium rate to dissociate the tissues for 2 hours.  Tissue was strained through sterile strainer and centrifuged for 5 minutes at 1,000 RPM.  The supernatant was removed, and the cell pellet was plated on standard cell culture dish for 45 minutes with DMEM, 20% FBS, 1%P/S/F.  After 45 minutes the plates were vigorously washed with 1X PBS to remove unattached cells.  The attached cells (fibroblasts) were flash frozen, and the total RNA extracted using Qiagen RNeasy Kit and QIAShredder columns to remove DNA contaminants.  Fibroblast identity confirmed using immunocytochemistry on cells isolated onto microscope slides.  Cells stained for alpha smooth muscle actin (ACTA2) and the absence of von willebrand's factor (endothelial cell marker), cytokeratin 18 (epithelial cell marker) and cd11b (macrophage/monocyte cell marker).  RNA QA/QC done on Agilent bio-analyzer to confirm purity and integrity.  RNA quantitated on Thermo-Fisher Nano drop.

value: cultured normal fibroblasts (P3)

source_name: Stratagene Human Reference RNA

tag: reference

value: Stratagene Human Reference RNA


title: Human_pulmonary_cultured_normal sample B


title: Pre-eclampsia 15

description: Raw_Data_Slide_3.txt, Block7

tag: tissue


title: Pre-eclampsia 14

description: Raw_Data_Slide_3.txt, Block6


title: Control 2

description: Raw_Data_Slide_1.txt, Block5


title: Control 1

description: Raw_Data_Slide_1.txt, Block4


title: Pre-eclampsia 13

description: Raw_Data_Slide_3.txt, Block3


title: Human_pulmonary_cultured_normal sample D


title: Human_pulmonary_non-cultured_normal sample A

source_name: non-cultured normal fibroblasts (P0)

value: non-cultured normal fibroblasts (P0)


title: Human_pulmonary_non-cultured_normal sample B


title: 7721_NC_48h

city: jinan

first: Yanli

last: Ren

state: shandong

address: huaiyin street

institute: SDCH

description: male,epithelial,liver,hepatocellular carcinoma

hyb_protocol: HOA 6.2 arrays were pre-heat at 60℃ for 10 mins, rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, 5 µg Cy5-labeled aRNA was hybridize on HOA in the presentation of the Phalanx OneArray hybridization buffer in duplication.

scan_protocol: The arrays were scanned by Agilent Scanner G2505C 0.1 XDR protocol and quantify the fluoresence intensity.

data_processing: Data processing was performed and calculated by Rosetta Resolver® (Rosetta Biosoftware). The probes that ﬂag <0 in all samples were filtered out, then normalized by median scaling method between technical replicates. Pair-wise comparisons between samples were calculated by Rosetta error model and presented by log2 ratio and p-value.

source_name: ATCC

label_protocol: 1 µg of total RNA was reverse-transcribed and amplified using MessageAmpTM aRNA Amplification Kit (Ambion).  Indirect labeling the aa-UTP whereon by NHS-CyDye (Cy5, Amershan).

growth_protocol: Volumes used in this protocol are for 25 cm2 flask; proportionally reduce or increase amount of dissociation medium for culture vessels of other sizes.  Remove and discard culture medium.  Briefly rinse the cell layer with 0.25% (w/v) Trypsin- 0.53 mM EDTA solution to remove all traces of serum that contains trypsin inhibitor.  Add 1.0 mL of Trypsin-EDTA solution to flask and observe cells under an inverted microscope until cell layer is dispersed (usually within 1 minutes).  Note: To avoid clumping do not agitate the cells by hitting or shaking the flask while waiting for the cells to detach. Cells that are difficult to detach may be placed at 37°C to facilitate dispersal.  Add 3.0 to 4.0 mL of complete growth medium and aspirate cells by gently pipetting.  Add appropriate aliquots of the cell suspension to new culture vessels.  Cultures can be established between 2 x 103 and 1 x 104 viable cells/cm2. Do not exceed 7 x 104 cels/cm2.  Incubate cultures at 37°C.  Interval: Maintain cultures at a cell concentration between 6 X 103 and 6 X 104 cell/cm2.  Subcultivation Ratio: A subcultivation ratio of 1:3 to 1:8 is recommended  Medium Renewal: 2 to 3 times per week

extract_protocol: RNA extraction by Trizol Reagent (). RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).

treatment_protocol: Twenty nanomolar siRNA or miRNA was used for transfection in serum free medium. Total RNA were prepared after transfection 48h.

value: hepatocellular carcinoma


title: Human_pulmonary_non-cultured_normal sample C


title: Human_pulmonary_cultured_fibroblast_idiopathic pulmonary fibrosis patient H

source_name: cultured IPF fibroblasts (P3)

value: cultured IPF fibroblasts (P3)


title: Human_pulmonary_non-cultured_normal sample D


title: pRPE-A d14, biological rep2

value: primary retinal pigment epithelium (RPE)


title: 7721_miR-215_48h


title: Pre-eclampsia 12

description: Raw_Data_Slide_3.txt, Block2


title: Pre-eclampsia 9

description: Raw_Data_Slide_2.txt, Block7

value: LATE


title: 7721_siPCAT1_48h


title: Human_pulmonary_cultured_fibroblast_idiopathic pulmonary fibrosis patient F


title: Human_pulmonary_cultured_fibroblast_idiopathic pulmonary fibrosis patient E


title: Human_pulmonary_cultured_fibroblast_idiopathic pulmonary fibrosis patient D


title: Pre-eclampsia 8

description: Raw_Data_Slide_2.txt, Block3


title: Pre-eclampsia 7

description: Raw_Data_Slide_2.txt, Block2


title: Pre-eclampsia 6

description: Raw_Data_Slide_2.txt, Block1


title: Human_pulmonary_cultured_fibroblast_idiopathic pulmonary fibrosis patient G


title: Pre-eclampsia 4

description: Raw_Data_Slide_1.txt, Block7


title: Pre-eclampsia 10

description: Raw_Data_Slide_2.txt, Block8


title: Pre-eclampsia 5

description: Raw_Data_Slide_1.txt, Block8


title: Pre-eclampsia 2

description: Raw_Data_Slide_1.txt, Block2


title: Human_pulmonary_non-cultured_fibroblast_idiopathic pulmonary fibrosis patient F

source_name: non-cultured IPF fibroblasts (P0)

value: non-cultured IPF fibroblasts (P0)


title: Pre-eclampsia 3

description: Raw_Data_Slide_1.txt, Block3


title: Human_pulmonary_non-cultured_fibroblast_idiopathic pulmonary fibrosis patient H


title: Human_pulmonary_cultured_fibroblast_idiopathic pulmonary fibrosis patient B


title: Pre-eclampsia 1

description: Raw_Data_Slide_1.txt, Block1


title: Human_pulmonary_cultured_fibroblast_idiopathic pulmonary fibrosis patient C


title: Human_pulmonary_cultured_fibroblast_idiopathic pulmonary fibrosis patient A


title: Human_pulmonary_non-cultured_fibroblast_idiopathic pulmonary fibrosis patient G


title: Human_pulmonary_cultured_normal sample A


title: Human_pulmonary_non-cultured_fibroblast_idiopathic pulmonary fibrosis patient B


title: Human_pulmonary_non-cultured_fibroblast_idiopathic pulmonary fibrosis patient C


title: Human_pulmonary_non-cultured_fibroblast_idiopathic pulmonary fibrosis patient A


title: Human_pulmonary_non-cultured_fibroblast_idiopathic pulmonary fibrosis patient D


title: Human_pulmonary_non-cultured_fibroblast_idiopathic pulmonary fibrosis patient E


title: Busulphan treated mice_ Sertoli cells

status: Public on Sep 06 2017

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: Gene expression of isolated Sertoli cells 1 month after busulphan treatment from adult male Swiss mice

hyb_protocol: 600 ng of labeled cRNA sample were fragmented at 60°C and hybridized on to a Agilent designed Mouse Gene expression Microarray 8x15K (AMADID No: 016270) arrays. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65° C for 16 hours.

scan_protocol: Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Images were quantified using the Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the quantile normalization method .

source_name: Testis_Busulphan treated

label_protocol: Samples for Gene expression were labeled using the Agilent Quick-Amp labeling Kit (p/n5190-0442). 500 ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasyMini kit columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

extract_protocol: RNA extraction from the samples was performed by Trizol RNA extraction . The concentration and purity of the RNA extracted were evaluated using the Nanodrop Spectrophotometer (Thermo Scientific; 1000).

treatment_protocol: For isolation of Sertoli cells, the testes were decapsulated, washed with PBS and incubated with 30ml of enzyme solution I (0.5mg/ml Collagenase IV) for 20 min, 37C, water bath. Dissociated tubules were then washed with PBS twice and transferred to enzyme solution II ( 0.5mg/ml Collagenase IV and 0.5mg/ml Hyaluronidase) and pipetted vigourously, incubated for 20 min, 37C, water bath. Reaction was stopped with Fetal bovine serum and centrifuged for 10 mins at 1000rpm. Pellet was washed twice and resuspended in 5 ml DMEM F12. Suspension was filtered through 100um cell strainer followed by 40um cell strainer. Sertoli cells get retained on the 40um strainer, and were collected (were not subjected to in vitro culture), centrifuged and resuspended in Trizol RNA extraction.

tag: strain

value: Swiss mice

tag: age

value: Adult; 3 months

value: Male

tag: treated with

value: 25mg/Kg body weight of busulphan

value: testis

value: Isolated Sertoli cells


title: SB2-V4

city: Clayton

first: Sam

last: Greenall

state: VIC

address: 27-31 Wright Street

department: Centre for Cancer Research

country: Australia

institute: Hudson Institute of Medical Research

hyb_protocol: 600ng of Cy3 labeled cRNA (specific activity > 6 pmol Cy3/ug cRNA) was fragmented at 60oC for 30 minutes in a reaction volume of 25ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the 67oC in a rotating Agilent hybridisation oven. After hybridisation, microarrays were washed 1 minute at room temperature with GE wash buffer 1(Agilent) and 1 minute with 37oC GE wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent C, DNA microarray scanner using one color scan settings for 8x60k array slides; scan area 61x21.6mm, scan resolution 3um, dye channel is set to Green and 20 bit Tiff.

data_processing: The scanned images were analysed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1-1100_Jul11 and Grid:039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Primary GBM neurosphere culture

label_protocol: Cyanine-3 (Cy3) labelled cRNA was prepared from 0.2ug total RNA using the One-Color Low input Quick Amp labelling Kit (Agilent, v6.6 September 2012) according to the manufacturer’s instructions, followed by RNeasy column purification (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: GBM neurospheres grown in NSC SFM medium throughout the experiment

extract_protocol: Cells were extracted and spun down at 300 x g for 3 min. Supernatants were discarded and tubes were drained on paper towel to remove excess liquid. Total RNA was harvested using an RNAeasy kit from Qiagen with on-column Dnase digest.

treatment_protocol: Either DMSO or 200 nM of THZ1 added directly to flasks and mixed. Incubated at 37 degrees C for 24 hours.

tag: cell line name

tag: treatment

value: DMSO vehicle 24 hours


title: SB2-V2


title: Control mice_Sertoli cells

description: Gene expression of isolated Sertoli cells from adult male Swiss mice

value: none (control)

tag: cell type


title: SB2-V1


title: GBM6-T4

value: CDK7 inhibitor THZ1 200 nM 24 hours


title: GBM6-V4


title: GBM6-T1


title: GBM6-T3


title: SB2-T1


title: GBM6-V3


title: SB2-T2


title: GBM6-V1


title: GBM6-V2


title: SB2-T3


title: pRPE-B d14, biological rep5

tag: cell line

value: pRPE-B (Lot. 0F3237)


title: SB2-V3


title: GBM6-T2


title: SB2-T4


title: Pre-eclampsia 11

description: Raw_Data_Slide_3.txt, Block1

tag: gender

value: FEMALE

value: PRE-ECLAMPSIA

value: EARLY

value: NO

value: YES

value: Placenta


title: DU145_Adh_17_OTX 4h

city: Bellinzona

first: Carlo

last: Catapano

address: Via Vela 6

department: Experimental therapeutics

country: Switzerland

institute: IOR

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol. Probes were extracted with GenomeStudio

data_processing: Values were set to null for detection calls lower then 0.06. Data were quantile normalized with BRB array tools

label_protocol: Biotinylated cRNA were marked with Illumina total prep 96 RNA amplification kit (Ambion)

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

treatment_protocol: Adherent and tumor-sphere DU145 cells were treated with 0.1% DMSO (control) for 0, 4 and 24 h or OTX015 (500 nM) for 0, 4 and 24 h in three independent replicates

value: Prostate cancer cell line

tag: growth conformation

value: adh

value: OTX 4h


title: DU145_PS_2_Control 4h

value: ps

value: Control 4h (DMSO)


title: DU145_PS_3_OTX 4h


title: DU145_Adh_16_Control 4h


title: DU145_PS_1_Time 0h

value: Time 0h


title: DU145_Adh_15_Time 0h


title: DU145_Adh_20_Control 24h

value: Control 24h (DMSO)


title: DU145_Adh_21_OTX 24h

value: OTX 24h


title: 9344730156_R02C01

type: genomic

city: Leiden

first: Roderick

last: Slieker

address: PO Box 9600

department: Medical Oncology

country: Netherlands

institute: Leiden University Medical Center

hyb_protocol: Isolated genomic DNA (500 ng) was treated with sodium bisulphite using the EZ-96 DNA methylation kit (Shallow) (Zymo Research, Irvine, CA, USA). Hybridization was performed following manufacturer’s instructions. DNA methylation of CpGs was measured by the Illumina HumanMethylation450K BeadChip using the manufacturer’s protocol (Illumina, Inc., San Diego, CA, USA).

scan_protocol: According to Illumina protocol.

data_processing: All data pre-processing and statistical analyses were performed in R software version 3.2.2 and Bioconductor version 3.1. We checked performance of built-in internal quality controls in the Control Dashboard using the methylation module of GenomeStudio (Illumina Inc., San Diego, USA). It included a sample call rate check, colour balance check and control dashboard checks. Probes targeting a CpG with documented single-nucleotide polymorphisms in the C or G nucleotides were removed (n=17,196) (Minor allele frequency > 0.05, European population, 1000 Genomes Project). Probes directed at the sex chromosomes (n=11,648) and with a detection P value >0.01 in more than 1% of samples (n=2,773) were also excluded. Out of all 485,512 probes, a total of 454,892 were left for further analysis. Normalisation was performed for all samples together by the Dasen method, which consists of background adjustment and between-array normalization, applied to Type I and Type II probes separately, by use of our duplicate samples that were included for each tissue (Bioconductor package watermelon version 1.80).

molecule: genomic DNA

source_name: UC-WBC, Early-onset preeclampsia

label_protocol: According to Illumina protocol.

extract_protocol: Thawed WBC pellets were subjected to erythrocyte lysis by use of an Erythrocyte Lysis Buffer (Qiagen, Hilden, Germany), following manufacturer’s protocols. Thirty mg frozen placental tissue was grinded manually on dry ice using a tissue grinder. The powder was immediately added to a cell lysis buffer and stored at -80 °C until further processing. Subsequently, genomic DNA was extracted from all tissues using the Allprep DNA/RNA isolation mini kit (Qiagen, Hilden, Germany), according to manufacturer’s instructions.

value: UC-WBC

tag: group

value: Early-onset preeclampsia


title: 9344730105_R03C01


title: 9344730091_R06C02

source_name: UC-WBC, Late-onset preeclampsia

value: Late-onset preeclampsia


title: 9344730121_R04C01


title: 9323071001_R05C02


title: DU145_Adh_14_OTX 24h


title: 9344730069_R03C01


title: 9323071001_R02C02


title: 9323071043_R04C02


title: 9344730115_R04C01


title: 9323071043_R01C01


title: 9344730105_R03C02


title: 9344730097_R03C01


title: 9344730092_R06C02


title: 9344730089_R06C02


title: 9323071007_R03C02


title: 9344715134_R02C02


title: 9344730069_R03C02


title: 9344730069_R01C01


title: 9344730091_R05C02


title: DU145_Adh_10_OTX 4h


title: 9344730159_R03C02


title: 9344730064_R04C02


title: DU145_Adh_6_Control 24h


title: 9344730092_R03C01


title: 9344730089_R01C02


title: 9344715134_R05C01

source_name: UC-WBC, Normotensive fetal growth restricted

value: Normotensive fetal growth restricted


title: 9344730097_R04C02


title: 9344730121_R05C01


title: DU145_Adh_9_Control 4h


title: 9344730089_R04C02


title: DU145_Adh_13_Control 24h


title: DU145_Adh_8_Time 0h


title: DU145_PS_9_Control 4h


title: DU145_Adh_7_OTX 24h


title: DU145_Adh_1_Time 0h


title: DU145_Adh_2_Control 4h


title: DU145_PS_15_Time 0h


title: DU145_Adh_3_OTX 4h


title: 9344730013_R05C02


title: DU145_PS_13_Control 24h


title: DU145_PS_8_Time 0h


title: DU145_PS_7_OTX 24h


title: DU145_PS_14_OTX 24h


title: 9344730123_R04C02


title: DU145_PS_10_OTX 4h


title: DU145_PS_20_Control 24h


title: DU145_PS_21_OTX 24h


title: 9344730123_R06C02


title: DU145_PS_16_Control 4h


title: DU145_PS_6_Control 24h


title: 9323071001_R02C01


title: 9323071007_R02C02


title: 9344730013_R05C01


title: stromal derived_mesenchymal stem cell_p2_rep8

city: Heidelberg

first: Laura

last: Milde

state: Baden-Württemberg

address: Im Neuenheimer Feld 280

department: Vascular Oncology and Metastasis

institute: German Cancer Research Center

description:
Sample 48
replicate MSC 3

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

source_name: stromal-derived mesenchmymal stem cell

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

growth_protocol: Cells were cultured and passaged in the correspondingly recommended medium of the corresponding company (lung, muscle and pancreas pericytes were cultured as brain and placents pericytes)

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

treatment_protocol: no treatment

tag: name on chip

value: mesenchymal stem cell

value: bone marrow

tag: passage

tag: source of cells

value: BioEngineering, #500048744 (without collagen cell carrier)


title: DU145_PS_17_OTX 4h


title: stromal derived_mesenchymal stem cell_p2_rep7

description:
Sample 47
replicate MSC 2

value: BioEngineering, #500048744 (with collagen cell carrier)


title: stromal derived_mesenchymal stem cell_p2_rep6

description:
Sample 46
replicate MSC 1


title: 9323071043_R06C02


title: 9344730013_R03C02


title: dermal_fibroblast_p8_rep7

description:
Sample 45
replicate fibroblast 7

source_name: dermal fibroblast

value: fibroblast

value: dermis


title: 9344730121_R01C02


title: 9344730092_R04C01


title: 9344730064_R02C01


title: 9344730064_R06C02


title: 9344730080_R03C02


title: dermal_fibroblast_p4_rep4

description:
Sample 42
replicate fibroblast 4


title: dermal_fibroblast_p4_rep5

description:
Sample 43
replicate fibroblast 5


title: dermal_fibroblast_p4_rep3

description:
Sample 41
replicate fibroblast 3

value: skin

value: PromoCell, #C-12300


title: 9344730064_R02C02


title: dermal_fibroblast_p2_rep1

description:
Sample 39
replicate fibroblast 1


title: 9344730069_R05C01


title: 9344730105_R02C01

source_name: UC-WBC, Normotensive preterm birth

value: Normotensive preterm birth


title: 9323071014_R01C01


title: 9344730058_R03C02


title: stromal derived_mesenchymal stem cell_p4_rep5

description:
Sample 38
replicate MSC 5


title: dermal_fibroblast_p2_rep2

description:
Sample 40
replicate fibroblast 2


title: stromal derived_mesenchymal stem cell_p2_rep4

description:
Sample 37
replicate MSC 4


title: stromal derived_mesenchymal stem cell_p2_rep3

description:
Sample 36
replicate MSC 3


title: stromal derived_mesenchymal stem cell_p2_rep2

description:
Sample 35
replicate MSC 2


title: 9344730064_R03C01


title: 9344730105_R04C02


title: 9344730089_R05C01


title: dermal_fibroblast_p8_rep6

description:
Sample 44
replicate fibroblast 6


title: 9344730092_R05C01


title: saphenous vein_endothelial cell_p2_rep1

description:
Sample 32
replicate HSaVEC 1

source_name: saphenous vein endothelial cell

value: endothelial cell

value: saphenous vein

value: PromoCell, #C-12231


title: saphenous vein_endothelial cell_p4_rep2

description:
Sample 33
replicate HSaVEC 2


title: 9344730064_R04C01


title: adipocyte_p8_rep3

description:
Sample 31
replicate adipocyte 3

source_name: subcutaneuos adipocyte

value: adipocyte

value: subcutaneous adipose tissue

value: PromoCell, #C-12730


title: 9344730091_R05C01

value: UC-WBC


title: 9323071001_R01C01

value: Normotensive fetal growth restricted


title: 9344730013_R04C01


title: adipocyte_p2_rep1

description:
Sample 29
replicate adipocyte 1


title: 9344730123_R04C01


title: 9323071014_R01C02


title: umbilical vein_endothelial cell_p4_rep2

description:
Sample 25
replicate HUVEC 2

source_name: umbilical vein endothelial cell

value: umbilical vein

value: PromoCell, #C-12203


title: stromal derived_mesenchymal stem cell_p2_rep1

description:
Sample 34
replicate MSC 1

value: mesenchymal stem cell

value: bone marrow

value: BioEngineering, #500048744 (without collagen cell carrier)


title: adipocyte_p4_rep2

description:
Sample 30
replicate adipocyte 2


title: umbilical artery_endothelial cell_p8_rep3

description:
Sample 26
replicate HUAEC 3

source_name: umbilical artery endothelial cell

value: umbilical artery

value: PromoCell, #C-12202


title: umbilical vein_endothelial cell_p8_rep3

description:
Sample 27
replicate HUVEC 3


title: placenta_pericyte_p2_rep4

description:
Sample 23
replicate placenta pericyte 4

source_name: placenta pericyte

value: pericyte

value: placenta

value: PromoCell, #C-12980


title: umbilical artery_endothelial cell_p9_rep4

description:
Sample 28
replicate HUAEC 4

value: endothelial cell


title: 9323071007_R05C01

value: Normotensive preterm birth


title: 9344730163_R04C02


title: placenta_pericyte_p4_rep3

description:
Sample 22
replicate placenta pericyte 3


title: lung_pericyte_p4_rep4

description:
Sample 24
replicate lung pericyte 4

source_name: lung pericyte

value: lung

value: kindly provided by Dr. Bruno Peault (Univ. of Edinburgh, UK)


title: 9344730121_R02C01


title: 9344730069_R06C01


title: 9344730064_R01C01


title: 9344730058_R04C01


title: 9323071014_R03C01


title: 9344730163_R05C01

source_name: UC-WBC, Uncomplicated control

value: Uncomplicated control


title: lung_pericyte_p4_rep3

description:
Sample 20
replicate lung pericyte 3


title: 9323071060_R04C01

value: UC-WBC


title: 9344730080_R04C01


title: muscle_pericyte_p4_rep5

description:
Sample 21
replicate muscle pericyte 5

source_name: muscle pericyte

value: muscle


title: 9344730080_R01C02


title: brain_pericyte_p4_rep3

description:
Sample 18
replicate brain pericyte 3

source_name: brain pericyte

value: brain

value: ScienCell, #1200


title: 9344730069_R04C01


title: pancreas_pericyte_p4_rep5

description:
Sample 19
replicate pancreas pericyte 5

source_name: pancreas pericyte

value: pancreas


title: 9344730058_R04C02


title: 9344730089_R03C01


title: pancreas_pericyte_p2_rep4

description:
Sample 16
replicate pancreas pericyte 4


title: 9344730115_R02C01


title: lung_pericyte_p2_rep2

description:
Sample 14
replicate lung pericyte 2


title: 9323071060_R03C02


title: 9344730105_R01C01


title: placenta_pericyte_p0_rep2

description:
Sample 15
replicate placenta pericyte 2


title: 9323071043_R02C02


title: umbilical artery_endothelial cell_p5_rep2

description:
Sample 12
replicate HUAEC 2


title: muscle_pericyte_p2_rep4

description:
Sample 13
replicate muscle pericyte 4


title: 9323071007_R05C02


title: muscle_pericyte_p8_rep3

description:
Sample 11
replicate muscle pericyte 3


title: brain_pericyte_p2_rep2

description:
Sample 17
replicate brain pericyte 2


title: umbilical vein_endothelial cell_p2_rep1

description:
Sample 10
replicate HUVEC 1

value: umbilical vein

value: PromoCell, #C-12203


title: umbilical artery_endothelial cell_p3_rep1

description:
Sample 9
replicate HUAEC 1

value: umbilical artery


title: pancreas_pericyte_p8_rep3

description:
Sample 8
replicate pancreas pericyte 3


title: 9344730159_R02C02


title: placenta_pericyte_p7_rep1

description:
Sample 6
replicate placenta pericyte 1


title: muscle_pericyte_p2_rep2

description:
Sample 7
replicate muscle pericyte 2


title: lung_pericyte_p8_rep1

description:
Sample 4
replicate lung pericyte 1


title: muscle_pericyte_p8_rep1

description:
Sample 5
replicate muscle pericyte 1


title: 9344730013_R06C01


title: 9323071001_R04C01


title: 9344730105_R01C02


title: 9344730115_R06C01


title: 9323071043_R03C02


title: pancreas_pericyte_p8_rep2

description:
Sample 3
replicate pancreas pericyte 2


title: 9344730159_R06C01


title: 9323071001_R03C01


title: fetal_liver_2

city: Düsseldorf

first: Wasco

last: Wruck

address: Moorenstr. 5

institute: Universitätsklinikum Düsseldorf

description: SAMPLE 10

data_processing: The data were normalised using rank invariant normalisation with BeadStudio version 3 (Illumina)

source_name: fetal liver

label_protocol: Illumina Gene Expression protocols contain a first- and second-strand  reverse transcription step, followed by a single in vitro transcription  (IVT) amplification that incorporates biotin-labeled nucleotides.  Subsequent steps include array hybridization, washing, blocking, and  streptavadin-Cy3 staining. Fluorescence emission by Cy3 is quantitatively  detected for downstream analysis.

growth_protocol: iPSCs were cultured on Matrigel-coated plates and conditioned medium (CM), prepared by culturing mitomycin C inactivated mouse embryonic fibroblast (MEFs) in Knockout DMEM (including 10% serum replacement, 0.1 mM glutamin, 0.1 mM non-essential amino acids and 0.5% penicillin and streptomycin; Invitrogen).

extract_protocol: The RNA was isolated using Direct-zol™ RNA MiniPrep Kit (Zymo Research; #R2050).

treatment_protocol: Differentiation was done as described by Sullivan et al. 2010 with slide modifications. In the last step of differentiation instead of hydrocortisone dexamethasone (25ng/ml) was used.

value: fetal liver


title: 9344730163_R03C02


title: fetal_liver_1

description: SAMPLE 9


title: PHH_1

description: SAMPLE 11

source_name: primary hepatocytes

value: primary hepatocytes


title: brain_pericyte_p8_rep1

description:
Sample 2
replicate brain pericyte 1

value: pericyte


title: 9323071014_R04C02


title: HLCs_1

description: SAMPLE 7

source_name: hepatocyte-like cells from IPSCs

value: hepatocyte-like cells


title: PHH_2

description: SAMPLE 12


title: HLCs_2

description: SAMPLE 8


title: 9344730105_R04C01

source_name: HUVEC, Late-onset preeclampsia

value: HUVEC

value: Late-onset preeclampsia


title: 9344715134_R04C02


title: 9344730105_R02C02


title: 9344730121_R01C01


title: 9344730097_R02C02


title: 9344730123_R01C01


title: 9323071014_R02C02


title: HE_2

description: SAMPLE 6

source_name: hepatic endoderm from IPSCs

value: hepatic endoderm


title: pancreas_pericyte_p4_rep1

description:
Sample 1
replicate pancreas pericyte 1

value: kindly provided by Dr. Bruno Peault (Univ. of Edinburgh, UK)


title: 9344730123_R03C02

source_name: HUVEC, Early-onset preeclampsia

value: Early-onset preeclampsia


title: 9344730115_R01C01


title: HE_1

description: SAMPLE 5


title: 9344730091_R02C01


title: DE_2

description: SAMPLE 4

source_name: definite endoderm from IPSCs

value: definite endoderm


title: iPSCs_2

description: SAMPLE 2

source_name: induced pluripotent stem cells from HFF

value: induced pluripotent stem cells


title: 9323071043_R06C01


title: 9344730097_R05C02


title: iPSCs_1

description: SAMPLE 1


title: 9323071007_R01C02


title: 9344730123_R05C02

value: UC-WBC

value: Uncomplicated control


title: 9323071001_R01C02


title: 9323071001_R06C01


title: 9344730069_R01C02


title: DE_1

description: SAMPLE 3


title: 9344730121_R04C02


title: 9344730156_R02C02


title: 9344730159_R01C01


title: 9344730163_R04C01


title: 9323071060_R04C02

source_name: HUVEC, Normotensive fetal growth restricted

value: Normotensive fetal growth restricted


title: 9344730105_R05C02


title: 9344730089_R04C01


title: 9344715134_R01C01


title: 9323071060_R03C01


title: 9344730089_R05C02


title: 9323071043_R02C01


title: 9344730089_R03C02


title: 9344730013_R06C02


title: 9344730159_R05C01


title: 9344730080_R01C01


title: 9344715134_R03C02


title: 9344730163_R03C01

source_name: HUVEC, Normotensive preterm birth

value: Normotensive preterm birth


title: 9344715134_R06C01


title: 9344730080_R03C01


title: NULL-infected vs. VP16-infected cultures (G)

city: Bellaterra

first: Luis

last: Pardo

state: Barcelona

address: Campus UAB Edificio M

country: Spain

institute: Universitat Autónoma de Barcelona

description:
NULL_B vs VP16_B
Normalized signal intensities in each channel ratio. Data in M-values.

hyb_protocol: The samples were hybridized in the Agilent-028279 SurePrint G3 Microarray slides according to the manufacturer's protocol. We used a direct comparison for infected samples and a loop design for treated samples.

scan_protocol: The microarray slides were scanned using the Agilent microarray scanner (G2565CA), and the resulting images were extracted with Agilent Feature Extraction Software (version 10.7).

data_processing: Background correction was performed using the normexp method (offset = 10) implemented in the Bioconductor LIMMA package to adjust local median (M) background estimates. Background-corrected intensity data were normalized using the loess method to remove the bias within each array. A-values quantile normalization (Aquantile) was used to remove the bias between arrays and make them comparable. Finally, the statistical linear model in LIMMA was applied to the resulting data to determine the target genes differentially expressed between the experimental groups.

organism: Rattus norvegicus

source_name: Cortical astrocytes, infected with Null virus

label_protocol: The samples were labeled with Cy5 or Cy3 using the Low Input Quick Amp Labeling kit (Agilent).

growth_protocol: Astrocytes were extracted from cortices of 24 h post-natal rat pups and cultured in DMEM 10% FBS with antibiotics. The culture medium was changed two hours after seeding and then every 7 days. Cells were maintained in a humidified atmosphere of 95% air-5% CO2 until confluence was reached.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen). The concentration was determined with the NanoDrop 1000 spectrophotometer (Thermo Scientific), and the RNA quality with the Agilent 2100 Bioanalyzer.

treatment_protocol: Treatments with 1 µM FSK and 10 µM NE were performed during 6 hours in confluent cultures by directly adding the agents to the culture medium, control samples were treated with vehicle. The over-expression of VP16-CREB was carried out by infection with the adenovirus Ad2/5-CMV-VP16-CREB in pre-confluent cultures using DMEM with 1% FBS and without antibiotics, control samples were infected with adenoviruses Ad2/5-CMV-Null. The medium was changed after 3 hours and cells were processed 18 h post-infection.

tag: strain/background

value: Sprague Dawley

value: cortical astrocytes

value: Ad2/5-CMV-Null infection

source_name: Cortical astrocytes, infected with VP16-CREB virus

value: Ad2/5-CMV-VP16-CREB infection


title: VP16-infected vs. NULL-infected cultures (H)

description:
VP16_C vs NULL_C
Normalized signal intensities in each channel ratio. Data in M-values.


title: 9344730013_R01C02


title: 9344730115_R03C02


title: 9344730121_R02C02


title: 9344730092_R04C02


title: 9323071060_R06C02


title: VP16-infected vs. NULL-infected cultures (F)

description:
VP16_A vs NULL_A
Normalized signal intensities in each channel ratio. Data in M-values.


title: 9344730080_R02C01


title: 9344715134_R05C02


title: 9344730121_R03C01


title: 9344730163_R02C02


title: Untreated cultures vs. FSK-treated (D)

description:
CT_A vs FSK_B
Normalized signal intensities in each channel ratio. Data in M-values.

source_name: Cortical astrocytes, control

value: vehicle control

source_name: Cortical astrocytes, treated with FSK

value: forskolin (FSK)


title: 9323071007_R06C01

value: HUVEC


title: FSK-treated vs. NE-treated cultures (E)

description:
FSK_C vs NE_C
Normalized signal intensities in each channel ratio. Data in M-values.

source_name: Cortical astrocytes, treated with NE

value: noradrenaline (NE)


title: 9344730091_R02C02


title: 9344730064_R01C02


title: NE-treated vs. untreated cultures (A)

description:
NE_A vs CT_A
Normalized signal intensities in each channel ratio. Data in M-values.


title: NE-treated vs. untreated cultures (C)

description:
NE_B vs CT_C
Normalized signal intensities in each channel ratio. Data in M-values.


title: siGalNT6-3

city: Taipei

first: Min-Chuan

last: Huang

address: No. 1, Sec. 1, Ren-Ai RD, Taipei, Taiwan, R.O.C.

department: Graduate Institute of Anatomy and Cell Biology

country: Taiwan

institute: National Taiwan University

description: Gene expression after 72 hours transfection

hyb_protocol: Agilent Gene Expression Hybridization Kits was used for hybridization according to the manufacturer’s instruction. Briefly, 16 ul of dye labeled cDNA in water was fragmented at 98°C for 3 mins in a reaction volume of 40 ul containing 4 ul Agilent 10x blocking agenr and 20 ul of Agilent 2xGExHybridization Buffer HI-RPM and hybridized to Agilent SurePrint G3 Human Gene Expression 8x60K v2 Microarray (G4851B) at 65°C and rotated at 10 rpm for 17 hours. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°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 (US9230696) using one color scan setting for 8x60k array slides (Scan Area 61x21.6mm, Scan resolution 2um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid:072363_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: ES-2 cells siGalNT6-3

label_protocol: cDNA prepared from 10μg of total RNA were labeled with aa-dUTP using Invitrogen SuperScriptTM Plus Indirect cDNA Labeling System according to the manufacturer's protocol, followed by aa-cDNA column purification (QIAGEN, Valencia, CA).  Alexa/CyDye was incorporated to aa-cDNA followed by column purification with Alexa/CyDye-cDNA cRNA purification (Qiagen).

growth_protocol: In 10% FBS/DMEM

extract_protocol: RNA was prepared using the Genejet RNA Purification kit (Thermo Scientific) 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).

value: ES-2 cells

tag: transfection


title: FSK-treated vs. untreated cultures (B)

description:
FSK_A vs CT_B
Normalized signal intensities in each channel ratio. Data in M-values.


title: 9323071043_R04C01


title: siGalNT6-2

source_name: ES-2 cells siGalNT6-2


title: 9344730080_R04C02


title: siGalNT6-1

source_name: ES-2 cells siGalNT6-1


title: 9344730159_R01C02

source_name: HUVEC, Uncomplicated control


title: 9344730156_R01C02


title: siControl-3

source_name: ES-2 cells siControl-3


title: siControl-2

source_name: ES-2 cells siControl-2


title: 9344730115_R01C02


title: 9344730069_R05C02


title: NMN_Fusarium_replication 2

city: Kanazawa

first: Takumi

last: Nishiuchi

address: 13-1 Takaramachi

institute: Kanazawa University

description: Gene expression of inoculated leaves with F. graminearum at 3 dpi after NMN pretreatment

hyb_protocol: 1.65 ug 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 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 Rat Genome Microarray 4x44K (G4131F) 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 (G2565BA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green. Scan mode is eXtended Dynamic range Scan mode and PMT is set to 10% and 100%).

data_processing: The images were analyzed using Feature Extraction Software (Ver. 10.7.3.1; Agilent Technologies). These data were analyzed further with GeneSpring GX12.5 software (Agilent Technologies).  Normalization was performed as follows: 1, intensity-dependent Lowess normalization; 2, data transformation, with measurements less than 0.01 set to 0.01; 3, per-chip normalization, in which the 75th percentile method was used to normalize each array

organism: Arabidopsis thaliana

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the Low RNA Input  Quick Amp 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: Arabidopsis plants  (ecotype Columbia-0) were grown in soil at 22ºC under long day conditions (16 h light/8 h dark) for about 4 weeks.

extract_protocol: Leaves were ground in liquid nitrogen. Total RNA was prepared using a Agilent Plant RNA Isolation Mini Kit.

treatment_protocol: The 0.3 mM NMN or water plus 0.001% silwetL-77 was sprayed onto Arabidopsis leaves. Then, these sprayed leaves were inoculated with F. graminearum 6 h after treatment. A conidial suspension of F. graminearum (1×105 conidia/ml) was injected into the abaxial side of the leaves using a needleless syringe. Inoculated plants were incubated in a chamber under approximately 100% relative humidity, at 22 °C for 3 days

value: mature rosette leaves

tag: genotype

value: wild type

tag: ecotype


title: siControl-1

source_name: ES-2 cells siControl-1


title: 9344715134_R02C01

tag: tissue


title: Water_Fusarium_replication 2

description: Gene expression of inoculated leaves with F. graminearum at 3 dpi after water pretreatment


title: 9344730121_R06C01


title: Water_replication 2

description: Gene expression of leaves at 6 h after spraying with water

source_name: leaves at 6 h after spraying with water


title: NMN_replication 2

description: Gene expression of leaves at 6 h after spraying with NMN

source_name: leaves at 6 h after spraying with NMN


title: 9344730115_R04C02


title: 9323071060_R02C01


title: 9344730069_R02C02


title: NMN_Fusarium_replication 1

source_name: inoculated leaves with F. graminearum at 3 dpi after NMN pretreatment


title: 9344730163_R06C01


title: Water_Fusarium_replication 1

source_name: inoculated leaves with F. graminearum at 3 dpi after water pretreatment


title: NMN_replication 1


title: 9344730097_R06C02


title: Lung_Bleomycin_EXT9 6

city: Lund

first: Anna

last: Löfdahl

address: Klinikgatan 30

department: Experimental Medical Science

country: Sweden

institute: Lund University, BMC

scan_protocol: Standard Illumina iScan N240 scanning protocol

data_processing: The data were normalised using quantile normalisation with BASE

source_name: distal lung tissue

label_protocol: Illumina®Totalprep-96RNA Amplification kit 4397949 RevD, (Modification of Amplification kit v 2.2)

extract_protocol: RNA was extracted with RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions, and the amount of total RNA was measured with a Nanophotometer. Samples were processed with Agilent RNA Nano 6000kit and Agilent 2100 Bioanalyzer (Agilent technologies)

treatment_protocol: C57BL/6 mice were treated subcutaneously with bleomycin (50IE/dose) 3 times/week for 2 weeks, with daily per oral treatment with EXT5 (30mg/kg), EXT9 (30mg/kg) or vehicle (Tween80 2.5%, w/v). Healthy controls were instead treated subcutaneously with physiological saline solution in combination with daily per oral vehicle treatment.

value: female

tag: strain

tag: age

value: 12.5 weeks

value: bleomycin (50IE/dose) with EXT9 (30mg/kg)


title: 9344730115_R05C02

value: Uncomplicated control


title: 9323071001_R05C01


title: Water_replication 1


title: Lung_Bleomycin_EXT9 4


title: Lung_Bleomycin_EXT9 5


title: 9344730097_R01C02


title: Lung_Bleomycin_EXT9 3


title: 9344730097_R01C01


title: Lung_Bleomycin_EXT9 1


title: 9344730097_R05C01


title: Lung_Bleomycin_EXT9 2


title: 9344730058_R01C01


title: 9323071014_R02C01


title: 9323071043_R01C02


title: DLD1-ShCRNDE_rep3

city: Guangzhou

first: wang

middle: yi

last: qing

institute: South Medical University

description: Gene expression after knockdown CRNDE in DLD1 cell

hyb_protocol: 1.65 ug 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 2.2ul containing 25X Fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55ul of 2x GEx Hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Hybridization oven rotator for Agilent Microarray Hybridization Chambers (Agilent p/n G2530-60029) for 17 hours at 65Â°C . After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (Agilent p/n G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

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

source_name: DLD1-ShCRNDE Cell, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The human CRC cell lines DLD-1 are obtained from a cell bank at the Chinese Academy of Sciences (Shanghai, China).Short-hairpin RNA (shRNA) sequences specially targeting CRNDE were designed and synthesized (supplementary information), and cloned into pGU6/GFP/Neo-shRNA vector (GenePharme, Shanghai, China). A scrambled shRNA oligo, namely pGU6/GFP/control, was used as a control.Stable cell lines of reduced CRNDE expression were constructed in DLD1

extract_protocol: RNA was prepared using RNasey Mini Kit(Qiagen p/n 74104) following the manufacturer's recommendations.  The protocol includes lysis of cells, and an on-column DNase digestion.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Cells are cultured with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum.   The cultures were incubated  at 37 ºC in a humidified incubator with 5% CO2.


title: DLD1-ShCRNDE_rep2

source_name: DLD1-ShCRNDE Cell, replicate 2


title: 9344730058_R06C02


title: 9344730013_R02C01


title: Lung_Bleomycin_EXT5 4

value: bleomycin (50IE/dose) with EXT5 (30mg/kg)


title: Lung_Bleomycin_EXT5 3


title: 9323071007_R01C01


title: Lung_Bleomycin_EXT5 2


title: DLD1-ShCRNDE_rep1

source_name: DLD1-ShCRNDE Cell, replicate 1


title: Lung_Bleomycin_EXT5 5


title: DLD1-NC_rep3

description: Gene expression  of CRNDE in control DLD1 cell

source_name: DLD1-NC Cell, replicate 3


title: Lung_Bleomycin_EXT5 1


title: 9344730058_R02C01


title: 9344715134_R01C02


title: 9323071014_R04C01


title: Lung_Bleomycin_Vehicle 6

value: bleomycin (50IE/dose) with Tween80 2.5%, w/v


title: 9344730091_R06C01


title: 9344730092_R03C02


title: DLD1-NC_rep2

description: Gene expression  of CRNDEin control DLD1 cell

source_name: DLD1-NC Cell, replicate 2


title: Lung_Bleomycin_Vehicle 4


title: Lung_Bleomycin_Vehicle 5


title: 9323071007_R04C02

source_name: Placenta, Late-onset preeclampsia

value: Placenta

value: Late-onset preeclampsia


title: Lung_Bleomycin_Vehicle 1


title: Lung_Saline_Vehicle 6


title: Lung_Bleomycin_EXT5 6


title: 9323071007_R06C02


title: Lung_Bleomycin_Vehicle 3


title: DLD1-NC_rep1

description: Gene expression of CRNDE in control DLD1 cell

source_name: DLD1-NC Cell, replicate 1


title: Lung_Bleomycin_Vehicle 2


title: 9344730159_R06C02


title: Lung_Saline_Vehicle 5


title: 9344730156_R06C01


title: 9344730105_R06C01


title: 9344730092_R02C02

source_name: Placenta, Early-onset preeclampsia

value: Early-onset preeclampsia


title: Lung_Saline_Vehicle 3


title: Lung_Saline_Vehicle 4


title: 9344730159_R04C02


title: 9344730156_R01C01


title: T1D  24

city: Miami

first: Marta

last: Garcia-Contreras

state: FL

address: 1450 NW 10 th Ave

department: Diabetes Research Insitute

institute: University of Miami

hyb_protocol: ligation of 100 ng of miRNA and hybridization to probes at 65°C for 18 hours following the manufacturer’s protocol.

scan_protocol: The hybridized probes were purified and counted on nCounter Prep Station and Digital Analyzer.

data_processing: Data was analyzed by  Nanosight NTA 2.3 Analytical Software. Using  5 miRNAs for normalization having % CV less than 15. The normalized data set with all control probes is available on the series record. The sample table does not include the control probes.

label: biotin label and molecular barcode

source_name: Plasma

label_protocol: not provided

extract_protocol: Exosomes were isolated from plasma by ultracentrifugation  for the extraction of total RNA.

value: Plasma

tag: tissue compartment

value: exosome

tag: diagnosis

value: Type 1 Diabetes

tag: Sex

value: Male


title: T1D  23


title: T1D  22

value: Female


title: 9344730064_R05C01


title: T1D  20


title: Lung_Saline_Vehicle 1

tag: treatment


title: 9323071007_R02C01


title: 9344730097_R02C01


title: T1D  19


title: Lung_Saline_Vehicle 2

tag: gender


title: 9323071060_R05C02


title: 9323071014_R05C02


title: 9344730058_R05C02


title: 9344715134_R03C01


title: 9344730159_R03C01


title: T1D  18


title: T1D  17


title: 9344730080_R05C01


title: T1D  16


title: 9344730091_R04C01


title: T1D  21


title: T1D  15


title: 9344730092_R06C01

source_name: Placenta, Normotensive fetal growth restricted

value: Normotensive fetal growth restricted


title: 9344730058_R06C01


title: 9323071014_R06C02


title: 9344730013_R02C02


title: 9344715134_R06C02


title: 9323071007_R04C01


title: Control 12

value: Control


title: 9344730064_R06C01


title: Control 10


title: T1D  13


title: 9344730156_R03C01


title: Control 8


title: Control 9


title: 9344730159_R04C01


title: 9344730091_R01C02


title: 9344730156_R04C01


title: Control 11


title: Control 6


title: 9344730080_R06C02


title: 9323071007_R03C01


title: 9323071043_R05C02


title: Control 5


title: 9344730097_R03C02


title: Control 4


title: Control 3


title: Control 7


title: 9344730069_R04C02


title: 9323071001_R06C02


title: 9344730163_R02C01


title: Control 2


title: Control 1


title: 9344730156_R05C02


title: T1D  14


title: 9344730089_R01C01


title: 9323071043_R03C01


title: 9344730156_R03C02


title: 9344730123_R03C01

source_name: Placenta, Normotensive preterm birth

value: Normotensive preterm birth


title: 9344730089_R06C01


title: 9323071001_R04C02


title: 9344730115_R03C01


title: 9344730091_R03C02


title: 9344730069_R02C01


title: 9344730123_R06C01


title: 9323071043_R05C01


title: 9344730089_R02C02


title: 9344730097_R04C01


title: 9344730091_R01C01


title: 9344730123_R02C01


title: 9344730069_R06C02


title: 9344730115_R05C01


title: 9344730156_R04C02

source_name: Placenta, Uncomplicated control


title: 9344730092_R02C01


title: 9344730064_R03C02


title: 9344730121_R06C02


title: 9323071014_R06C01


title: 9344730092_R01C02


title: 9344730092_R05C02


title: 9344730163_R05C02


title: 9344730123_R01C02


title: 9344730058_R01C02


title: 9344730013_R01C01


title: 9344730121_R03C02


title: 9344730058_R03C01


title: 9344730156_R05C01


title: Sample_535

status: Public on Sep 05 2017

type: SRA

city: Boston

first: Margaret

last: Parker

state: MA

address: 181 Longwood Ave

department: Medicine

institute: Brigham and Women's Hospital

library_source: transcriptomic

data_processing:
reads trimmed of adapters using Skewer with default parameters
alignment to grch28 reference genome with STAR v2.4.0h
gene/exon level counts generated using Rsubreads, ensembl v81 annotation
counts were normalized for library size using the TMM method implemented in the calcNormFactors function in the edgeR package
Genome_build: grch38
Supplementary_files_format_and_content: tab-delimited text files including normalized counts for each sample

source_name: Whole blood

extract_protocol:
PAXgene using Qiagen PreAnalytiX PAXgene
RNA libraries were prepared for sequencing using standard Illumina TruSeq Stranded Total RNAprotocols

treatment_protocol: Globin reduction with Ribo-Zero Globin kit

tag: race

value: NHW

value: female

tag: packyrs

tag: smoke


title: 9344730064_R05C02

tag: group


title: Samd7 KO retina at P12

city: Suita

first: Takahisa

last: Furukawa

state: Osaka

address: 6-2-4 Furuedai

department: Developmental Biology

institute: Osaka Bioscience Institute

description: Gene expression in Samd7 KO retina at P12

hyb_protocol: The labeled cDNA samples were hybridized using Gene Expression Hybridization Kit to the SurePrint G3 Mouse Gene Expression 8x60K microarray (Agilent Technology).

scan_protocol: Hybridized arrays were scanned using an Agilent DNA Microarray Scanner (G2565CA).

data_processing: Microarray analysis was performed by Takara Bio. The data analyses were performed using Feature Extraction software (Agilent Technology).

source_name: Samd7 KO retina at P12

label_protocol: The isolated total RNA was amplified and labeled with Cy3 using a Low Input Quick Amp Labeling Kit, One-Color (Agilent Technologies).

extract_protocol: Total RNA was purified using QIAzol reagent (Invitrogen).

treatment_protocol: Mouse retinas at P12 were dissected using fine forceps.

tag: Stage

value: retina

tag: genotype/variation

value: Samd7 KO


title: Sample_529


title: Sample_528

value: male


title: Sample_530


title: 9344730013_R03C01


title: 9344730163_R06C02

value: Uncomplicated control


title: Sample_522

value: AA


title: Sample_521


title: 9344730123_R05C01

value: Placenta


title: Sample_520


title: 9344730105_R06C02


title: Sample_519


title: Sample_536


title: Sample_533


title: 9344730159_R02C01


title: Sample_532


title: Sample_518


title: Sample_523


title: Sample_526


title: Samd7 WT retina at P12

description: Gene expression in Samd7 WT retina at P12

source_name: Samd7 WT retina at P12

value: wild type


title: Sample_525


title: 9344730080_R05C02


title: 9344730058_R02C02


title: Sample_516


title: 9344730080_R02C02


title: Sample_513


title: Sample_514


title: Sample_527


title: 9344730163_R01C02


title: Sample_511


title: Sample_524


title: Sample_510


title: Sample_531


title: Sample_509


title: 9323071060_R06C01


title: Sample_512


title: Sample_508


title: Sample_507


title: Sample_506


title: Sample_505


title: 9344730091_R04C02


title: Sample_504


title: Sample_503


title: Sample_502


title: Sample_501


title: Sample_499


title: Sample_500


title: Sample_498


title: Sample_497


title: Sample_515


title: 9344730091_R03C01


title: Sample_495


title: Sample_494


title: Sample_493


title: 9344730115_R06C02


title: 9344730105_R05C01


title: 9344730080_R06C01


title: Sample_490


title: Sample_492


title: Sample_491


title: Sample_496


title: Sample_489


title: Sample_487


title: Sample_483


title: Sample_480


title: Sample_482


title: Sample_481


title: Sample_484


title: Sample_485


title: Sample_486


title: Sample_479


title: Sample_517


title: Sample_478


title: Sample_476


title: Sample_475


title: Sample_474


title: Sample_477


title: Sample_534


title: Sample_471


title: Sample_469


title: Sample_472


title: Sample_467


title: Sample_470


title: Sample_473


title: Sample_466


title: Sample_463


title: Sample_465


title: Sample_461


title: Sample_462


title: Sample_459


title: Sample_458


title: Sample_455


title: Sample_456


title: Sample_448


title: Sample_449


title: Sample_451


title: Sample_447


title: Sample_446


title: Sample_454


title: Sample_445


title: Sample_443


title: Sample_468


title: Sample_442


title: Sample_441


title: Sample_440


title: Sample_444


title: Sample_438


title: Sample_437


title: Sample_436


title: Sample_434


title: Sample_435


title: Sample_439


title: Sample_432


title: Sample_433


title: Sample_431


title: Sample_457


title: Sample_429


title: Sample_428


title: Sample_453


title: Sample_427


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