title: B.longum ATCC15697 and B.adolescentis 22L supplemented to mice vs only B.longum ATCC15697 supplemented to mice

description: Sample name: ATCC15697_22L_vs ATCC15697

organism:
Bifidobacterium adolescentis
Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088

source_name: B.longum subsp. infantis ATCC 15697 awas supplemented to BALB/c mice. B. adolescentis 22L was supplemented to BALB/c mice.

growth_protocol:
B.longum subsp. infantis ATCC 15697 was supplemented to five 3 months old female BALB/c mice. Bacterial colonization will be established by five consecutive daily administrations whereby each animal received 20 µl of 10E9 cells using a micropipette tip placed immediately behind the incisors.
B. adolescentis 22L was supplemented to five 3 months old female BALB/c mice. Bacterial colonization will be established by five consecutive daily administrations whereby each animal received 20 µl of 10E9 cells using a micropipette tip placed immediately behind the incisors.

source_name: B.longum subsp. infantis ATCC15697 was supplemented to BALB/c mice.

growth_protocol: B.longum subsp.infantis ATCC 15697 was supplemented to five 3 months old female BALB/c mice. Bacterial colonization will be established by five consecutive daily administrations whereby each animal received 20 µl of 10E9 cells using a micropipette tip placed immediately behind the incisors.


title: B.bifidum PRL2010 and B.longum ATCC15697 supplemented to mice vs only B.longum ATCC15697 supplemented to mice

status: Public on Aug 23 2017

type: RNA

city: Parma

first: Marco

last: Ventura

address: Viale delle Scienze 11/A

department: Dept. Life Sciences

country: Italy

institute: University of Parma

description: Sample name: PRL_ATCC15697_vs ATCC15697

hyb_protocol: Labelled cDNA was hybridized using the Agilent Gene Transcription hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Transcription Analysis v4.0 manual (G4140-90050). Following hybridization, microarrays were washed in accordance with Agilent's standard procedures.

scan_protocol: Scanning was performed on InnoScan 700 (Innopsys) scanner.

data_processing: Signal intensities for each spot and data extraction were carried out using Mapix 5.5 software (Innopsys, Carbonne, France). The normalization of data was performed using Linear Normalization Correction Method by Agilent Feature Extraction 10.10 software. Data processing was performed using Limma package for R software.

molecule: total RNA

organism:
Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088
Bifidobacterium bifidum PRL2010

source_name: B.bifidum PRL2010 was supplemented to BALB/c mice. B.longum subsp. infantis ATCC 15697 was supplemented to BALB/c mice.

label_protocol: Reverse transcription and amplification of 500 ng of total RNA was performed with ImProm-IITM Reverse Transcriptase (Promega, Madison, USA) according to the manufacturer’s instructions. Five µg of cDNA was then labeled with ULS Labeling kit with Cy5 or Cy3 (Kreatech, The Netherlands).

growth_protocol:
B.bifidum PRL2010 was supplemented to five 3 months old female BALB/c mice. Bacterial colonization will be established by five consecutive daily administrations whereby each animal received 20 µl of 10E9 cells using a micropipette tip placed immediately behind the incisors.
B.longum subsp. infantis ATCC 15697 was supplemented to five 3 months old female BALB/c mice. Bacterial colonization will be established by five consecutive daily administrations whereby each animal received 20 µl of 10E9 cells using a micropipette tip placed immediately behind the incisors.

extract_protocol: Total RNA was isolated using a previously described method (Turroni et al., 2013, PNAS). Briefly, tissue materials were resuspended in 1 ml of QUIAZOL (Qiagen, UK) and placed in a tube containing 0.8 g of glass beads (diameter, 106 μm; Sigma). The cells were lysed by shaking the mix on a BioSpec homogenizer at 4°C for 2 min (maximum setting). The mixture was then centrifuged at 12,000 rpm for 15 min, and the upper phase containing the RNA-containing sample was recovered. The RNA sample was further purified by phenol extraction and ethanol precipitation according to an established method (Sambrook et al., 1989). The quality of the RNA was checked by analysing the integrity of rRNA molecules by Experion (BioRad).

tag: strain


title: Cortex-0hr-Rep3

city: Coventry

first: Miriam

last: Gifford

address: Gibbet Hill Road

department: School of Life Sciences

country: United Kingdom

institute: University of Warwick

description: NimbleGen gene expression array data for custom-design array based on the TAIR10 release of the Arabidopsis thaliana genome

hyb_protocol: Following fragmentation, 4 ug of cRNA was hybridized for 16 hr at 42oC on a NimbleGen.

scan_protocol: Slides were scanned using an MS 200 microarray scanner and associated NimbleGen software using only the 480 nm laser with gain calculated using the autogain feature of NimbleScan, based on a representative region of the slide (an area covering around half an array found to have average intensity based on a prescan at lower resolution), as per manufacturer’s instructions. Grids were aligned automatically to each microarray image and manually veriﬁed, ensuring reference spots in each corner and in the centre of the array were aligned to the grid and the alignment score minimised.

data_processing: Data were obtained using NimbleScan and normalised by robust multichip averaging (RMA) (quantile normalisation, taking into account outlier probes per gene) and summarised to gene level by median polish.

organism: Arabidopsis thaliana

source_name: 12 day old Arabidopsis Col0 root cortex cells,

label_protocol: RNA samples were amplified using Ovation Pico WTA System V2 kit (NuGEN Technologies Inc., San Carlos, CA, USA) as per the manufacturer’s ‘quick’ protocol. Post-ampliﬁcation puriﬁcation of cDNA was performed using the QIAquick PCR Puriﬁcation Kit (Qiagen) as manufacturer’s guidelines. RNA was labelled with the Cy3 dye according to NimbleGen protocols.

growth_protocol: Plants were grown for 9 days in long day (16hr light/8hr dark) 22 oC conditions in a Sanyo growth chamber (MLR251).  Plants were grown vertically on plates on basal MS containing no nitrogen, supplemented with 0.1mM KNO3 and 30mM sucrose.

extract_protocol: FACS samples were collected in RLT lysis buffer (Qiagen) with 1 % (v:v) β-mercaptoethanol, then total RNA extracted using the Qiagen plant RNeasy kit.

treatment_protocol: At dawn on the 9th day plants were either transferred to 5mM KNO3-containing plates (High N), treated with a 0.8 OD600 of Sinorhizobium meliloti culture (rhizobium treatment), or moved to fresh 0.1mM KNO3 (Low N) plates. Whole roots were harvested then prototplast generation and Fluorescence-Activated Cell Sorting (FACS) used to isolate pericycle or cortical cells (following methods in Gifford et al 2008 PNAS).

tag: ecotype

tag: tissue

value: root

tag: cell type

value: cortex cells


title: Bbifidum PRL2010 and Blongum subsp infantis ATCC15697 supplemented to mice vs only Bbifidum PRL2010 supplemented to mice

description: Sample name: PRL_ATCC15697_vs PRL

source_name: B.bifidum PRL2010 was supplemented to BALB/c mice. B. longum subsp. infantis ATCC15697 was supplemented to BALB/c mice.

growth_protocol:
B.bifidum PRL2010 was supplemented to five 3 months old female BALB/c mice. Bacterial colonization will be established by five consecutive daily administrations whereby each animal received 20 µl of 10E9 cells using a micropipette tip placed immediately behind the incisors.
B. longum subsp. infantis ATCC15697 was supplemented to five 3 months old female BALB/c mice. Bacterial colonization will be established by five consecutive daily administrations whereby each animal received 20 µl of 10E9 cells using a micropipette tip placed immediately behind the incisors.

organism: Bifidobacterium bifidum PRL2010


title: Cortex-Standard-10hr-Rep2


title: Cortex-Standard-1hr-Rep3


title: all 4 bifidobacteria species supplemented to mice vs only B.longum subsp infantis ATCC15697 supplemented to mice

description: Sample name: ALL_ATCC15697

organism:
Bifidobacterium adolescentis
Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088
Bifidobacterium bifidum PRL2010
Bifidobacterium breve 12L

growth_protocol: All 4 bifidobacterial species were supplemented to mice. Five animals of 3 months old female BALB/c mice were orally inoculated with all 4 bifidobacterial species. Bacterial colonization will be established by five consecutive daily administrations whereby each animal received 20 µl of 10E9 cells using a micropipette tip placed immediately behind the incisors.

value: 22L (Bifidobacterium adolescentis 22L)

growth_protocol: Five animals of 3 months old female BALB/c mice were orally inoculated with B. longum subsp. infantis ATCC 15697. Bacterial colonization will be established by five consecutive daily administrations whereby each animal received 20 µl of 10E9 cells using a micropipette tip placed immediately behind the incisors.


title: B.breve 12L and B.longum subsp. infantis ATCC15697 supplemented to mice vs only B.longum ATCC15697 supplemented to mice

description: Sample name: 12L_ATCC15697_vs ATCC15697

organism:
Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088
Bifidobacterium breve 12L

source_name: B.breve 12L was supplemented to BALB/c mice. B.longum subsp. infantis ATCC 15697 was supplemented to BALB/c mice.

growth_protocol:
B.breve 12L was supplemented to five 3 months old female BALB/c mice. Bacterial colonization will be established by five consecutive daily administrations whereby each animal received 20 µl of 10E9 cells using a micropipette tip placed immediately behind the incisors.
B.longum subsp. infantis ATCC 15697 was supplemented to five 3 months old female BALB/c mice. Bacterial colonization will be established by five consecutive daily administrations whereby each animal received 20 µl of 10E9 cells using a micropipette tip placed immediately behind the incisors.


title: Cortex-0hr-Rep2


title: B.adolescentis 22L and B.breve 12L supplemented to mice vs only B.adolescentis 22L supplemented to mice

description: Sample name: 22L_12L_vs 22L

organism:
Bifidobacterium adolescentis
Bifidobacterium breve 12L

source_name: B.adolescentis 22L and B.breve 12L were supplemented to BALB/c mice.

growth_protocol:
B.adolescentis 22L was supplemented to five 3 months old female BALB/c mice. Bacterial colonization will be established by five consecutive daily administrations whereby each animal received 20 µl of 10E9 cells using a micropipette tip placed immediately behind the incisors.
B.breve 12L was supplemented to five 3 months old female BALB/c mice. Bacterial colonization will be established by five consecutive daily administrations whereby each animal received 20 µl of 10E9 cells using a micropipette tip placed immediately behind the incisors.

organism: Bifidobacterium adolescentis

source_name: B.adolescentis 22L was supplemented to BALB/c mice.


title: B.longum subsp infantis ATCC15697 supplemented to mice vs B.longum ATCC15697 growth in mice food

description: Sample name: ATCC15697_mono

organism: Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088

source_name: B.longum subsp. infantis ATCC 15697 supplemented to mice.

source_name: B.longum subsp. infantis ATCC 15697 growth in mice food.

growth_protocol: B. longum susb. infantis ATCC 15697 was grown anaerobically in mice food medium supplemented with 0.05% (w/v) L-cysteine hydrochloride and incubated at 37°C.


title: B.bifidum PRL2010 and B. adolescentis 22L supplemented to mice vs only B.adolescentis 22L supplemented to mice

description: Sample name: PRL_22L_vs 22L

organism:
Bifidobacterium adolescentis
Bifidobacterium bifidum PRL2010

source_name: B.bifidum PRL2010 was supplemented to BALB/c mice. B. adolescentis 22L was supplemented to BALB/c mice.

growth_protocol:
B.bifidum PRL2010 was supplemented to five 3 months old female BALB/c mice. Bacterial colonization will be established by five consecutive daily administrations whereby each animal received 20 µl of 10E9 cells using a micropipette tip placed immediately behind the incisors.
B. adolescentis 22L was supplemented to five 3 months old female BALB/c mice. Bacterial colonization will be established by five consecutive daily administrations whereby each animal received 20 µl of 10E9 cells using a micropipette tip placed immediately behind the incisors.

growth_protocol: B.adolescentis 22L was supplemented to five 3 months old female BALB/c mice. Bacterial colonization will be established by five consecutive daily administrations whereby each animal received 20 µl of 10E9 cells using a micropipette tip placed immediately behind the incisors.


title: all 4 bifidobacteria species supplemented to mice vs only B.adolescentis 22L supplemented to mice

description: Sample name: ALL_22L

source_name: All 4 bifidobacterial species supplemented to mice. Five animals of 3 months old female BALB/c mice were orally inoculated with all 4 bifidobacterial species.


title: B.adolescentis 22L supplemented to mice vs B.adolescentis 22L growth in mice food

description: Sample name: 22L_mono

source_name: B.adolescentis 22L supplemented to mice.

growth_protocol: Five animals of 3 months old female BALB/c mice were orally inoculated with B. adolescentis 22L. Bacterial colonization will be established by five consecutive daily administrations whereby each animal received 20 µl of 10E9 cells using a micropipette tip placed immediately behind the incisors.

source_name: B.adolescentis 22L growth in mice food.

growth_protocol: B. adolescentis 22L was grown anaerobically in mice food medium supplemented with 0.05% (w/v) L-cysteine hydrochloride and incubated at 37°C.


title: B.bifidum PRL2010 and B.breve 12L supplemented to mice vs only B.breve 12L supplemented to mice

description: Sample name: PRL_12L_vs 12L

organism:
Bifidobacterium bifidum PRL2010
Bifidobacterium breve 12L

source_name: B.bifidum PRL2010 was supplemented to BALB/c mice. B.breve 12L was supplemented to BALB/c mice.

growth_protocol:
B.bifidum PRL2010 was supplemented to five 3 months old female BALB/c mice. Bacterial colonization will be established by five consecutive daily administrations whereby each animal received 20 µl of 10E9 cells using a micropipette tip placed immediately behind the incisors.
B.breve 12L was supplemented to five 3 months old female BALB/c mice. Bacterial colonization will be established by five consecutive daily administrations whereby each animal received 20 µl of 10E9 cells using a micropipette tip placed immediately behind the incisors.

organism: Bifidobacterium breve 12L


title: B.breve 12L and B.longum subsp. infantis ATCC15697 supplemented to mice vs only B.breve 12L supplemented to mice

description: Sample name: 12L_ATCC15697_vs 12L

source_name: B.breve 12L was supplemented to BALB/c mice. B.longum subsp. Infantis ATCC 15697 was supplemented to BALB/c mice.

growth_protocol: B.breve 12L was supplemented to five 3 months old female BALB/c mice. Bacterial colonization will be established by five consecutive daily administrations whereby each animal received 20 µl of 10E9 cells using a micropipette tip placed immediately behind the incisors.


title: B.adolescentis 22L and B.breve 12L supplemented to mice vs only B.breve 12L supplemented to mice

description: Sample name: 22L_12L_vs 12L

source_name: B.adolescentis 22L was supplemented to BALB/c mice. B.breve 12L was supplemented to BALB/c mice.


title: all 4 bifidobacteria species supplemented to mice vs only B.breve 12L supplemented to mice

description: Sample name: ALL_12L

source_name: B.breve 12L was supplemented to BALB/c mice.

growth_protocol: Five animals of 3 months old female BALB/c mice were orally inoculated with B. breve 12L. Bacterial colonization will be established by five consecutive daily administrations whereby each animal received 20 µl of 10E9 cells using a micropipette tip placed immediately behind the incisors.


title: B.breve 12L supplemented to mice vs B.breve 12L growth in mice food

description: Sample name: 12L_mono

source_name: B.breve 12L supplemented to mice.

source_name: B.breve 12L growth in mice food.

growth_protocol: B. breve 12L was grown anaerobically in mice food medium supplemented with 0.05% (w/v) L-cysteine hydrochloride and incubated at 37°C.


title: Cortex-0hr-Rep1

source_name: 12 day old Arabidopsis Col0 root cortex cells,


title: Cortex-Standard-4hr-Rep2


title: WT 7 Tcf ++

city: Lausanne

first: Paolo

last: Angelino

address: Quartier Sorge, Bâtiment Génopode

department: BCF

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

description: Tcf ++

hyb_protocol: AffAffymetrix GeneChip Mouse Gene 1.0 ST arrays (Affymetrix, Santa Clara , CA, USA) were hybridized according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual

scan_protocol: The arrays were scanned with the GeneChip® Scanner 3000 7G (Affymetrix).

data_processing: Normalized expression signals were calculated from Affymetrix CEL files by the Robust Multi-array Average algorithm (RMA), using the Affymetrix Expression Console Software (version 1.1.2800.28061)

label: biotin

organism: Mus musculus

source_name: Bone marrow mNK cells, Tcf7+/+

label_protocol: Affymetrix protocol

growth_protocol: BM mNK cells (CD3- CD19- CD122+ NK1.1+ DX5+) from Tcf7+/+ (WT) and Tcf7-/- (KO) mice were isolated by flow sorting

extract_protocol: Trizol (Invitrogen) extraction of total RNA and RNA clean up using Rneasy mini kit (Qiagen) were performed according to the manufacturers instructions.

treatment_protocol: Macs sorting (positive selection) Facs sorting

value: Bone marrow mNK cells

tag: genotype


title: KO 2 Tcf –

description: Tcf –

source_name: Bone marrow mNK cells, Tcf7-/-

value: B6.129 Tcf7Tm1Cle


title: KO 4 Tcf –

description: Tcf –


title: OSCC primary tumor tissue 327

first: Nicoletta

last: Bertani

state: Parma

address: Parco Area delle Scienze, 11/A

department: Life Science

hyb_protocol: Labeled-amplified RNA samples were mixed with Agilent hybridization buffer and were applied onto 4X44K Whole Human genome DNA microarray slides (Agilent). After hybridization, slides were washed sequential.

scan_protocol: We used the Agilent Technologies Scanner G2505B US45102976 to scan the microarray slides. Data from .tif images were extracted using the Feature Extraction (FE) software version 9.5.1.1 with a grid template 014850_D_F_20060807 and the GE2-v5_95_Feb07 Gene Expression protocol.

data_processing:
Agilent Feature Extraction Software (v 9.5.1.1) was used to obtain numerical values which are proportional to the fluorescent signal intensity.
Loess normalization with R package limma was used for background subtraction and normalization of microarray data.

organism: Homo sapiens

source_name: OSCC primary tumor tissue

label_protocol: 200 ng of total RNA were reversed transcribed then labeled with fluorescent dye (Cyanine 3 or Cyanine 5) and simultaneously amplified following the Two-Color Microarry-Based Gene Expression Analysis (Quick Amp Labeling) Protocol (Agilent Technologies).

growth_protocol: OSSC surgical specimen were collected and stored in RNA later solution at -80°C. CAL 27 cells were kept in a complete growth medium (DMEM with 10% FBS).

extract_protocol: Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) following manufacturer's instructions.

tag: gender

value: f

tag: age

tag: pstagetnm

value: IV

tag: pnstage

tag: recurrence

tag: suvival

source_name: Tongue squamous cell carcinoma cells

tag: cell line

value: CAL 27 cell line (ATCC CRL-2095)


title: WT 1 Tcf ++

description: Tcf ++


title: KO 8 Tcf –

description: Tcf –


title: OSCC primary tumor tissue 326

value: m

value: I


title: OSCC primary tumor tissue 329

value: II


title: OSCC primary tumor tissue 325


title: OSCC primary tumor tissue 328


title: OSCC primary tumor tissue 293


title: OSCC primary tumor tissue 303


title: OSCC primary tumor tissue 305


title: OSCC primary tumor tissue 309


title: OSCC primary tumor tissue 261

value: III


title: OSCC primary tumor tissue 260


title: OSCC primary tumor tissue 306


title: OSCC primary tumor tissue 308


title: OSCC primary tumor tissue 264


title: OSCC primary tumor tissue 256


title: OSCC primary tumor tissue 304


title: OSCC primary tumor tissue 330


title: OSCC primary tumor tissue 253


title: OSCC primary tumor tissue 255


title: OSCC primary tumor tissue 258


title: OSCC primary tumor tissue 252


title: OSCC primary tumor tissue 307


title: WT 3 Tcf ++

description: Tcf ++


title: OSCC primary tumor tissue 257


title: OSCC primary tumor tissue 250


title: OSCC primary tumor tissue 233


title: OSCC primary tumor tissue 247


title: OSCC primary tumor tissue 245


title: OSCC primary tumor tissue 232


title: OSCC primary tumor tissue 223


title: OSCC primary tumor tissue 216


title: OSCC primary tumor tissue 251


title: OSCC primary tumor tissue 229


title: OSCC primary tumor tissue 248


title: OSCC primary tumor tissue 227


title: OSCC primary tumor tissue 215


title: OSCC primary tumor tissue 244


title: OSCC primary tumor tissue 219


title: OSCC primary tumor tissue 217


title: OSCC primary tumor tissue 254


title: OSCC primary tumor tissue 210


title: OSCC primary tumor tissue 214


title: OSCC primary tumor tissue 211


title: OSCC primary tumor tissue 212


title: OSCC primary tumor tissue 209


title: OSCC primary tumor tissue 208


title: OSCC primary tumor tissue 206


title: OSCC primary tumor tissue 226


title: OSCC primary tumor tissue 207


title: OSCC primary tumor tissue 193


title: OSCC primary tumor tissue 222


title: OSCC primary tumor tissue 199


title: OSCC primary tumor tissue 246


title: OSCC primary tumor tissue 181


title: OSCC primary tumor tissue 182


title: OSCC primary tumor tissue 175


title: OSCC primary tumor tissue 180


title: OSCC primary tumor tissue 178


title: OSCC primary tumor tissue 184


title: OSCC primary tumor tissue 170


title: OSCC primary tumor tissue 174


title: OSCC primary tumor tissue 179


title: OSCC primary tumor tissue 163


title: OSCC primary tumor tissue 171


title: OSCC primary tumor tissue 164


title: B.longum infantis ATCC15697 and B. adolescentis 22L supplemented to mice vs only B.adolescentis 22L supplemented to mice

description: Sample name: ATCC15697_22L_vs 22L

source_name: B.longum subsp. Infantis ATCC 15697 was supplemented to BALB/c mice. B. adolescentis 22L was supplemented to BALB/c mice.

growth_protocol:
B.longum subsp. infantis ATCC 15697 was supplemented to five 3 months old female BALB/c mice. Bacterial colonization will be established by five consecutive daily administrations whereby each animal received 20 µl of 10E9 cells using a micropipette tip placed immediately behind the incisors.
B. adolescentis 22L was supplemented to five 3 months old female BALB/c mice. Bacterial colonization will be established by five consecutive daily administrations whereby each animal received 20 µl of 10E9 cells using a micropipette tip placed immediately behind the incisors.

source_name: B.adolescentis 22L was supplemented to BALB/c mice.


title: OSCC primary tumor tissue 169


title: OSCC primary tumor tissue 168


title: OSCC primary tumor tissue 160


title: OSCC primary tumor tissue 167


title: OSCC primary tumor tissue 159


title: OSCC primary tumor tissue 158


title: OSCC primary tumor tissue 155


title: OSCC primary tumor tissue 156


title: OSCC primary tumor tissue 151


title: OSCC primary tumor tissue 148


title: OSCC primary tumor tissue 147


title: OSCC primary tumor tissue 142


title: OSCC primary tumor tissue 134


title: OSCC primary tumor tissue 154


title: OSCC primary tumor tissue 146


title: OSCC primary tumor tissue 152


title: OSCC primary tumor tissue 157


title: OSCC primary tumor tissue 150


title: OSCC primary tumor tissue 145


title: OSCC primary tumor tissue 144


title: OSCC primary tumor tissue 140


title: OSCC primary tumor tissue 149


title: OSCC primary tumor tissue 106


title: OSCC primary tumor tissue 103


title: OSCC primary tumor tissue 100


title: OSCC primary tumor tissue 98


title: OSCC primary tumor tissue 102


title: OSCC primary tumor tissue 101


title: OSCC primary tumor tissue 96


title: OSCC primary tumor tissue 104


title: OSCC primary tumor tissue 94


title: OSCC primary tumor tissue 93


title: OSCC primary tumor tissue 95


title: SEVERE_ASTHMA_33

city: South San Francisco

first: Mark

last: McCreary

state: California

address: 1 DNA Way, MS 93

department: Bioinformatics

country: USA

institute: Genentech

description: Severe Asthma endobronchial biopsy sample 33 - ICS - BOBCAT

hyb_protocol: Labeled cRNA (750 ng) was fragmented and hybridized to Agilent Whole Human Genome 4×44k arrays. All samples were labeled with Cy5 and were hybridized against a Cy3-labeled universal human reference (Stratagene).

scan_protocol: Agilent Feature Extraction software version 11.5 was used to analyze the acquired array images.

data_processing: All statistical calculations were performed with the R Project software package, version 3.1.1 (http://www.R-project.org). Array quality control was assessed with the arrayQualityMetrics package for R. Microarrays were normalized and probe intensities transformed with the vsn package of Bioconductor. Independent filtering of microarray data was performed with the genefilter package to increase statistical power to detect true positives while maintaining type I error control. Because array features that were invariant or did not correspond to an Entrez gene transcript were uninformative for differential gene expression analysis, filtering on the basis of annotation and expression variability was performed.

source_name: SEVERE_ASTHMA (BOBCAT)

label_protocol: Total RNA was converted to double-stranded cDNA and then to Cy-labeled cRNA with an Agilent Quick Amp Labeling kit. The labeled cRNA was purified with an RNeasy mini kit (Qiagen). The yield of cRNA and the extent of incorporation of the Cy dye were determined with an ND-1000 spectrophotometer (Thermo Scientific).

extract_protocol: Total RNA was extracted from endobronchial biopsies with the Qiagen RNeasy Kit. The quantity and quality of the total RNA samples were determined with the Bioanalyzer 2100 (Agilent Technologies).

tag: primary tissue

value: LUNG:ENDOBRONCHIAL BIOPSY

tag: tissue diagnosis

value: ASTHMA

tag: test article

value: ICS

source_name: Universal human reference (Stratagene)

tag: sample type

value: reference


title: SEVERE_ASTHMA_34

description: Severe Asthma endobronchial biopsy sample 34 - ICS - BOBCAT


title: SEVERE_ASTHMA_31

description: Severe Asthma endobronchial biopsy sample 31 - ICS - BOBCAT


title: SEVERE_ASTHMA_32

description: Severe Asthma endobronchial biopsy sample 32 - ICS - BOBCAT


title: OSCC primary tumor tissue 92


title: SEVERE_ASTHMA_26

description: Severe Asthma endobronchial biopsy sample 26 - ICS - BOBCAT


title: SEVERE_ASTHMA_35

description: Severe Asthma endobronchial biopsy sample 35 - ICS - BOBCAT


title: SEVERE_ASTHMA_25

description: Severe Asthma endobronchial biopsy sample 25 - ICS - BOBCAT


title: SEVERE_ASTHMA_22

description: Severe Asthma endobronchial biopsy sample 22 - ICS - BOBCAT


title: SEVERE_ASTHMA_21

description: Severe Asthma endobronchial biopsy sample 21 - ICS - BOBCAT


title: SEVERE_ASTHMA_28

description: Severe Asthma endobronchial biopsy sample 28 - ICS - BOBCAT


title: SEVERE_ASTHMA_29

description: Severe Asthma endobronchial biopsy sample 29 - ICS - BOBCAT


title: SEVERE_ASTHMA_27

description: Severe Asthma endobronchial biopsy sample 27 - ICS - BOBCAT


title: SEVERE_ASTHMA_20

description: Severe Asthma endobronchial biopsy sample 20 - ICS - BOBCAT


title: SEVERE_ASTHMA_14

description: Severe Asthma endobronchial biopsy sample 14 - ICS - BOBCAT


title: SEVERE_ASTHMA_15

description: Severe Asthma endobronchial biopsy sample 15 - ICS - BOBCAT


title: SEVERE_ASTHMA_12

description: Severe Asthma endobronchial biopsy sample 12 - ICS - BOBCAT


title: SEVERE_ASTHMA_23

description: Severe Asthma endobronchial biopsy sample 23 - ICS - BOBCAT


title: SEVERE_ASTHMA_19

description: Severe Asthma endobronchial biopsy sample 19 - ICS - BOBCAT


title: SEVERE_ASTHMA_16

description: Severe Asthma endobronchial biopsy sample 16 - ICS - BOBCAT


title: SEVERE_ASTHMA_18

description: Severe Asthma endobronchial biopsy sample 18 - ICS - BOBCAT


title: SEVERE_ASTHMA_17

description: Severe Asthma endobronchial biopsy sample 17 - ICS - BOBCAT


title: SEVERE_ASTHMA_11

description: Severe Asthma endobronchial biopsy sample 11 - ICS - BOBCAT


title: SEVERE_ASTHMA_24

description: Severe Asthma endobronchial biopsy sample 24 - ICS - BOBCAT


title: SEVERE_ASTHMA_30

description: Severe Asthma endobronchial biopsy sample 30 - ICS - BOBCAT


title: SEVERE_ASTHMA_13

description: Severe Asthma endobronchial biopsy sample 13 - ICS - BOBCAT


title: SEVERE_ASTHMA_10

description: Severe Asthma endobronchial biopsy sample 10 - ICS - BOBCAT


title: SEVERE_ASTHMA_8

description: Severe Asthma endobronchial biopsy sample 8 - ICS - BOBCAT


title: SEVERE_ASTHMA_7

description: Severe Asthma endobronchial biopsy sample 7 - ICS - BOBCAT


title: SEVERE_ASTHMA_4

description: Severe Asthma endobronchial biopsy sample 4 - ICS - BOBCAT


title: SEVERE_ASTHMA_5

description: Severe Asthma endobronchial biopsy sample 5 - ICS - BOBCAT


title: SEVERE_ASTHMA_2

description: Severe Asthma endobronchial biopsy sample 2 - ICS - BOBCAT


title: SEVERE_ASTHMA_1

description: Severe Asthma endobronchial biopsy sample 1 - ICS - BOBCAT


title: SEVERE_ASTHMA_3

description: Severe Asthma endobronchial biopsy sample 3 - ICS - BOBCAT


title: plus_parental_40

city: Cleveland

first: Vladimir

last: Makarov

state: OH

address: 9500 Euclid Ave

department: LRI

institute: Cleveland Clinic

hyb_protocol: Hybridization was done according to the standard Affymetrix protocol.

scan_protocol: Affymetrix chips were scanned as per manufacturer's instructions.

data_processing: Normalization was performed with the AffyPLM package in BioConductor (v3.3), using RMA background correction, quantile normalization, and the Tukey biweight summary method

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

growth_protocol: Stable immortalized astrocytes were grown in DMEM + 10% FBS. Inducible astrocytes were grown in DMEM + Tetracycline-free FBS (10%) and IDH1 R132H expression was induced with the addition of 1 ug/ml of doxycycline. Tumorspheres were grown in NeuroCult NS-A Proliferation media (STEMCELL Technologies) with EGF and FGF.

extract_protocol: RNA was extracted using Qiagen's RNAeasy plus mini kit according to manufacturer's instructions

value: immortalized human astrocytes

tag: genotype/variation

value: empty vector

tag: dox

value: plus

tag: passage

value: 40 passages after baseline


title: minus_parental_20

value: minus

value: 20 passages after baseline


title: minus_mutant_20

value: IDH1 R132H


title: plus_mutant_10

value: 10 passages after baseline


title: off_parental_20

value: withdrawn


title: off_mutant_40


title: minus_parental_40


title: plus_mutant_20


title: off_mutant_20


title: CD24_pos rep1

source_name: immortalized human astrocytes_CD24_pos

value: plus, sorted cells, CD24 pos population


title: plus_parental_20


title: plus_mutant_40


title: minus_mutant_10


title: CD24_pos rep2


title: minus_mutant_40


title: off_mutant_10


title: off_parental_40


title: off_parental_10


title: CD24_neg rep1

source_name: immortalized human astrocytes_CD24_neg

value: plus, sorted cells, CD24 neg population


title: plus_parental_10


title: CD24_neg rep2


title: minus_parental_10


title: plus_mutant_5

value: 5 passages after baseline


title: off_mutant_5


title: minus_mutant_5


title: plus_parental_5


title: off_parental_5


title: minus_parental_5


title: off_mutant_1

value: 1 passage after baseline


title: plus_parental_1

value: baseline (30)


title: plus_mutant_1


title: minus_mutant_1


title: off_parental_1


title: IPAH_Lung_explant_rep3

city: Baltimore

first: Li

last: Gao

state: MD

address: 5501 Hopkins Bayview Circle, Rm. 3B.65B

department: Clinical Immunology

institute: Johns Hopkins University School of Medicine

description: whole lung tissue miRNA profiling from IPAH patient

hyb_protocol: Hybridization was 20hr at 55°C with 20 RPM rotation in an Agilent G2545A microRNA hybridization oven.

scan_protocol: Scanning used an Agilent G2505-C scanner controlled by Agilent Scan Control 7.0 software.

data_processing: GeneView signal intensity files from Agilent Feature Extraction 9.5.3.1 software for miRNA were imported into Partek GS v6.6. The gTotalGeneSignal values were quantile normalized and transformed to log2 notation after negative values were set to 0.001.

source_name: Lung Tissue, explant, IPAH, replicate 3

label_protocol: Total RNA (100 ng) was dephosphorylated with 15 units of calf intestine alkaline phosphatase at 37℃ for 30min then end-labeled with pCp-Cy3 (Agilent Technologies) and T4 RNA ligase (Agilent Technologies) at 16°C for 2h.

growth_protocol: Lung tissue from IPAH patients and failed donor control subjects was obtained during lung transplantation

extract_protocol: Total RNA was isolated with RNeasy and miRNeasy Mini kits (Qiagen) according to the manufacturer’s protocol. RNA concentration, purity and RNA integrity number (RIN) of microarray assay were determined on a Bioanalyzer (Agilent). Only samples with RIN>=7.0 were acceptable for microarray analysis.

treatment_protocol: Lung tissue from IPAH patients and failed donor control subjects was preserved in RNAlater before RNA isolation

tag: group

value: IPAH

value: Female

tag: race

value: White


title: IPAH_Lung_explant_rep4

source_name: Lung Tissue, explant, IPAH, replicate 4

value: Male


title: IPAH_Lung_explant_rep5

source_name: Lung Tissue, explant, IPAH, replicate 5


title: IPAH_Lung_explant_rep6

source_name: Lung Tissue, explant, IPAH, replicate 6

value: Black or African American


title: IPAH_Lung_explant_rep2

source_name: Lung Tissue, explant, IPAH, replicate 2


title: IPAH_Lung_explant_rep7

source_name: Lung Tissue, explant, IPAH, replicate 7


title: IPAH_Lung_explant_rep1

source_name: Lung Tissue, explant, IPAH, replicate 1


title: SEVERE_ASTHMA_9

description: Severe Asthma endobronchial biopsy sample 9 - ICS - BOBCAT

value: LUNG:ENDOBRONCHIAL BIOPSY

value: ASTHMA

value: ICS

value: reference


title: minus_parental_1

tag: cell type

value: immortalized human astrocytes

value: empty vector

value: minus


title: control 3 6hr

city: London

first: Paul

last: Lavender

address: 5th Floor, Tower Wing, Great Maze Pond

department: School of Immunology and Microbial Sciences

institute: King's College London

description:
9703801127_I_Grn.idat
control IgG treated
Sample name: 9703801127_I

hyb_protocol: Illumina HT12.v4 arrays were hybridized using standard Illumina protocols at 48 C

scan_protocol: Standard Illumina scanning

data_processing: data was quantile normalized within Illumina Genome Studio

source_name: control IgG treated_and_LPS

label_protocol: cDNA was labelled  usin NuGen Encore Biotin IL kits

growth_protocol: Human peripheral blood monocytes were isolated from healthy donors  using magnetic CD14  microbeads respectively (Miltenyi Biotec). MPO-ANCA (n=3, from 3 different patients) and control IgG (n=3, from 3 different donors) were protein G purified from patients with ANCA vasculitis or healthy controls respectively.

extract_protocol: Genomic DNA and RNA was isolated using Qiagen Allprep. 5pg total RNA was amplified using  NuGen Ovation Pico WTA System V2

treatment_protocol: 5X10^5 monocytes were incubated with 100ng/ml LPS (From Escherichia coli, O55:B5, L6529, Sigma Aldrich,) and MPO-ANCA or control IgG (250μg/ml) for 6 hours

tag: tissue

value: blood

value: monocytes

tag: treatment duration

value: 6 hr


title: patient 1 1hr

description:
9703801127_D_Grn.idat
MPO-ANCA treated
Sample name: 9703801127_D

source_name: MPO-ANCA treated_and_LPS

value: 1 hr


title: control 2 1hr

description:
9703801127_B_Grn.idat
control IgG treated
Sample name: 9703801127_B


title: patient 3 6hr

description:
9703801127_L_Grn.idat
MPO-ANCA treated
Sample name: 9703801127_L


title: control 2 6hr

description:
9703801127_H_Grn.idat
control IgG treated
Sample name: 9703801127_H


title: patient 2 6hr

description:
9703801127_K_Grn.idat
MPO-ANCA treated
Sample name: 9703801127_K


title: Ctl_Lung_explant_rep8

description: whole lung tissue miRNA profiling from Failed Donor control

source_name: Lung Tissue, explant, FD, replicate 8

value: control

tag: gender

tag: age


title: control 1 6hr

description:
9703801127_G_Grn.idat
control IgG treated
Sample name: 9703801127_G


title: Ctl_Lung_explant_rep7

source_name: Lung Tissue, explant, FD, replicate 7


title: control 3 1hr

description:
9703801127_C_Grn.idat
control IgG treated
Sample name: 9703801127_C


title: patient 3 1hr

description:
9703801127_F_Grn.idat
MPO-ANCA treated
Sample name: 9703801127_F


title: patient 1 6hr

description:
9703801127_J_Grn.idat
MPO-ANCA treated
Sample name: 9703801127_J


title: patient 2 1hr

description:
9703801127_E_Grn.idat
MPO-ANCA treated
Sample name: 9703801127_E


title: Ctl_Lung_explant_rep5

source_name: Lung Tissue, explant, FD, replicate 5


title: control 1 1hr

description:
9703801127_A_Grn.idat
control IgG treated
Sample name: 9703801127_A


title: OSCC primary tumor tissue 90

source_name: OSCC primary tumor tissue

value: f

tag: pstagetnm

value: III

tag: pnstage

tag: recurrence

source_name: Tongue squamous cell carcinoma cells

value: CAL 27 cell line (ATCC CRL-2095)


title: Ctl_Lung_explant_rep6

source_name: Lung Tissue, explant, FD, replicate 6

value: Male

value: White


title: Ctl_Lung_explant_rep3

source_name: Lung Tissue, explant, FD, replicate 3


title: Ctl_Lung_explant_rep2

source_name: Lung Tissue, explant, FD, replicate 2

value: Female


title: Ctl_Lung_explant_rep1

source_name: Lung Tissue, explant, FD, replicate 1


title: Ctl_Lung_explant_rep4

source_name: Lung Tissue, explant, FD, replicate 4


title: SEVERE_ASTHMA_6

description: Severe Asthma endobronchial biopsy sample 6 - ICS - BOBCAT

source_name: SEVERE_ASTHMA (BOBCAT)

tag: primary tissue

value: LUNG:ENDOBRONCHIAL BIOPSY

value: ASTHMA

source_name: Universal human reference (Stratagene)


title: MES008

type: genomic

first: Jie

last: Wang

state: Maryland

address: 400 N Broadway

institute: Johns Hopkins University

description:
7668610083_R03C02_Grn.idat
7668610083_R03C02_Red.idat

hyb_protocol: Performed at Center for Inherited Disease Research (CIDR;  Johns Hopkins University

data_processing: We processed the Illumina 450K data using the minfi Bioconductor. We then performed a modified version of quantile normalization (preprocessQuantile in the minfi package) to normalize across samples, which, briefly, forces the distribution of type I and type II probes on the Illumina 450K microarray to be the same across samples.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Fresh postmortem eye

label_protocol: DNA samples (1.3 mg) were processed for the Illumina Infinium  HumanMethylation450 Bead Array platform at the Center for Inherited Disease Research (CIDR;  Johns Hopkins University) as per the manufacturers  protocols.

extract_protocol: DNA was isolated from the tissue using AllPrep DNA/RNA Mini Kit (Qiagen, Germantown, Maryland)

value: retina

tag: Sex

value: F

tag: disease

value: AMD/glaucoma


title: TS603 [TS603_2]

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450K Beadchip using manufacturer's protocol

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

data_processing: Normalized (using ChAMP package in R with BMIQ normalization method) Average Beta. Data is not corrected for batch effects.

source_name: glioma tumorsphere_TS603

label_protocol: Standard Illumina Protocol

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

value: glioma tumorsphere

tag: genotype

value: IDH1 R132H

value: endogenous


title: Parental plus dox [SV20_P20plus]

source_name: immortalized human astrocytes_Parental plus dox

value: immortalized human astrocytes

value: empty vector

value: plus

value: 20 passages after baseline


title: CD24minus [7]

source_name: immortalized human astrocytes_CD24minus

value: 30 passages after baseline


title: Parental no dox [SV13_P10minus]

source_name: immortalized human astrocytes_Parental no dox

value: minus

value: 10 passages after baseline


title: CD24plus [8]

source_name: immortalized human astrocytes_CD24plus


title: MES013

description:
7668610082_R01C02_Grn.idat
7668610082_R01C02_Red.idat

scan_protocol: Performed at Center for Inherited Disease Research (CIDR;  Johns Hopkins University

value: M

value: LCM control


title: MES027

description:
8667045014_R01C01_Grn.idat
8667045014_R01C01_Red.idat

value: Control


title: TS603 [TS603_1]


title: Parental with dox [SV14_P10plus]

source_name: immortalized human astrocytes_Parental with dox


title: Parental minus dox [SV19_P20minus]

source_name: immortalized human astrocytes_Parental minus dox


title: MES019

description:
7512551063_R05C02_Grn.idat
7512551063_R05C02_Red.idat


title: Parental off dox [SV15_P10off]

source_name: immortalized human astrocytes_Parental off dox

value: withdrawn


title: MES005

description:
7497398107_R05C01_Grn.idat
7497398107_R05C01_Red.idat

value: retina

value: control


title: MES032

description:
8655677109_R06C02_Grn.idat
8655677109_R06C02_Red.idat

value: F

value: AMD


title: MES024

description:
8655677109_R02C02_Grn.idat
8655677109_R02C02_Red.idat


title: Parental with dox [SV8_P5plus]

value: 5 passages after baseline


title: Parental off dox [SV21_P20off]


title: MES022

description:
8667045022_R01C02_Grn.idat
8667045022_R01C02_Red.idat


title: MES029

description:
8655677109_R04C02_Grn.idat
8655677109_R04C02_Red.idat


title: Parental off dox [SV9_P5off]


title: MES009

description:
7497398047_R03C01_Grn.idat
7497398047_R03C01_Red.idat


title: MES004

description:
7497398075_R06C02_Grn.idat
7497398075_R06C02_Red.idat

value: AMD/glaucoma


title: MES028

description:
8655685202_R01C01_Grn.idat
8655685202_R01C01_Red.idat


title: MES010

description:
7539308143_R05C01_Grn.idat
7539308143_R05C01_Red.idat


title: MES003

description:
7497398096_R05C01_Grn.idat
7497398096_R05C01_Red.idat


title: MES016

description:
7539308166_R03C02_Grn.idat
7539308166_R03C02_Red.idat


title: MES012

description:
7539308136_R03C02_Grn.idat
7539308136_R03C02_Red.idat


title: MES011

description:
7497398084_R04C02_Grn.idat
7497398084_R04C02_Red.idat


title: MES030

description:
8655677145_R03C01_Grn.idat
8655677145_R03C01_Red.idat


title: C8-1_WholeBlood_Control_Male_Age31

city: Itabashi

first: Junji

last: OHNISHI

state: Tokyo

department: Department of Food and Nutrition

country: Japan

institute: Tokyo Kasei University

hyb_protocol: Agilent one-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution.

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. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: WholeBlood, Control, Male, Age31

label_protocol: Agilent one-color Low Input Quick Amp Labeling Kit labeling protocol

extract_protocol: RNA was prepared using the PAXgene Blood miRNA Kit (QIAGEN) according to the manufacture’s instructions.

treatment_protocol: Peripheral blood samples were freshly drawn from recruited priests and healthy volunteers at 11:00 before taking lunch.

value: Whole Blood

value: Male


title: C10-1_WholeBlood_Control_Male_Age34

source_name: WholeBlood, Control, Male, Age34


title: C9-1_WholeBlood_Control_Male_Age31


title: C7-1_WholeBlood_Control_Male_Age40

source_name: WholeBlood, Control, Male, Age40


title: C6-1_WholeBlood_Control_Male_Age32

source_name: WholeBlood, Control, Male, Age32


title: C4-1_WholeBlood_Control_Male_Age52

source_name: WholeBlood, Control, Male, Age52


title: Parental no dox [SV7_P5minus]

value: immortalized human astrocytes

value: empty vector


title: C3-1_WholeBlood_Control_Male_Age29

source_name: WholeBlood, Control, Male, Age29


title: C5-1_WholeBlood_Control_Male_Age34


title: Parental with dox [P70+]

value: plus

value: 40 passages after baseline


title: Parental with dox [SV2_P1plus]

value: baseline (30)


title: C1-1_WholeBlood_Control_Male_Age50

source_name: WholeBlood, Control, Male, Age50


title: Parental no dox [SV1_P1minus]

value: minus


title: Mutant off dox [SV18_M10off]

source_name: immortalized human astrocytes_Mutant off dox

value: IDH1 R132H

value: 10 passages after baseline


title: Mutant plus dox [SV17_M10plus]

source_name: immortalized human astrocytes_Mutant plus dox


title: Mutant off dox [SV24_M20off]

value: withdrawn

value: 20 passages after baseline


title: C2-1_WholeBlood_Control_Male_Age33

source_name: WholeBlood, Control, Male, Age33

value: Control


title: Parental off dox [P70 off 40]


title: B6-1_WholeBlood_Priest_Male_Age38

source_name: WholeBlood, Priest, Male, Age38

value: Priest


title: Mutant minus dox [SV22_M20minus]

source_name: immortalized human astrocytes_Mutant minus dox


title: Parental no dox [P70-]

source_name: immortalized human astrocytes_Parental no dox


title: Mutant with dox [SV11_M5plus]

source_name: immortalized human astrocytes_Mutant with dox


title: Mutant with dox [M70 +]


title: Mutant off dox [M70 off 40]


title: Mutant plus dox [SV23_M20plus]


title: Mutant with dox [SV5_M1plus]


title: Mutant off dox [SV12_M5off]


title: B7-1_WholeBlood_Priest_Male_Age46

source_name: WholeBlood, Priest, Male, Age46


title: Mutant no dox [M70-]

source_name: immortalized human astrocytes_Mutant no dox


title: B8-1_WholeBlood_Priest_Male_Age30

source_name: WholeBlood, Priest, Male, Age30


title: Mutant no dox [SV10_M5minus]


title: Mutant minus dox [SV16_M10minus]


title: Mutant no dox [SV4_M1minus]


title: Mutant dox off [SV6_M1off]

source_name: immortalized human astrocytes_Mutant dox off

value: 1 passage after baseline


title: A1-1_WholeBlood_Priest_Male_Age50

source_name: WholeBlood, Priest, Male, Age50


title: injured_PHi_3hrs_R35

city: Collegeville

first: Johannes

middle: M

last: Freudenberg

state: Pennsylvania

address: 1250 S Collegeville Rd

department: Human Genetics

institute: GlaxoSmithKline

description: Gene expression data from injured, PHi treated gastrocnemius muscle tissue collected after 3 hrs

hyb_protocol: RNA samples were amplified, labeled, hybridized to Affymetrix HG-U133 plus 2.0 GeneChip® microarrays, and scanned using standard protocols (Q2 Solutions, Inc., Durham, North Carolina, U.S.A.) to generate raw data files (CEL files).

data_processing: Raw data files (CEL files) were analyzed using a battery of data quality checks and samples failing these checks were removed from subsequent analyses.  Raw data was then pre-processed using the RMA (Robust Multi-chip Average) pipeline  in combination with the most current re-annotated probeset definitions.

source_name: gastrocnemius muscle

extract_protocol: Mouse gastrocnemius samples were collected and flash frozen in liquid nitrogen then stored at -80oC. For RNA isolation, ~100mg samples were used in 1ml Trizol and isolation was done according to the manufacturers protocol (Ambion Cat #15596-068). Purified RNA went through Qiagen RNA clean up kit (Cat #74204) and eluted in 50ul elution buffer.

treatment_protocol: Normal C57Bl6/NJ mice were housed individually (12hr:12hr day:night cycle) in a temperature- and humidity-controlled environment and fed standard chow and water ad libitum. Right hind limbs were injured while left hind limbs were used as control.  Animals were treated either with PHI or vehicle.

value: gastrocnemius

tag: drug

value: PHi

tag: injury

value: yes

tag: time

tag: animal

tag: limb

value: right

tag: strain


title: B10-1_WholeBlood_Priest_Male_Age40

source_name: WholeBlood, Priest, Male, Age40

tag: tissue

value: Whole Blood

tag: group

value: Male


title: B9-1_WholeBlood_Priest_Male_Age29

source_name: WholeBlood, Priest, Male, Age29

tag: gender


title: injured_PHi_3hrs_R34

scan_protocol: RNA samples were amplified, labeled, hybridized to Affymetrix HG-U133 plus 2.0 GeneChip® microarrays, and scanned using standard protocols (Q2 Solutions, Inc., Durham, North Carolina, U.S.A.) to generate raw data files (CEL files).


title: injured_vehicle_3hrs_R32

description: Gene expression data from injured, vehicle treated gastrocnemius muscle tissue collected after 3 hrs

label_protocol: RNA samples were amplified, labeled, hybridized to Affymetrix HG-U133 plus 2.0 GeneChip® microarrays, and scanned using standard protocols (Q2 Solutions, Inc., Durham, North Carolina, U.S.A.) to generate raw data files (CEL files).

value: vehicle


title: injured_vehicle_3hrs_R28


title: injured_PHi_3hrs_R27


title: injured_vehicle_6hrs_R24

description: Gene expression data from injured, vehicle treated gastrocnemius muscle tissue collected after 6 hrs


title: injured_vehicle_3hrs_R33


title: B4-1_WholeBlood_Priest_Male_Age52

source_name: WholeBlood, Priest, Male, Age52

tag: age


title: injured_vehicle_3hrs_R36


title: injured_vehicle_3hrs_R29


title: injured_PHi_3hrs_R30


title: B5-1_WholeBlood_Priest_Male_Age36

source_name: WholeBlood, Priest, Male, Age36


title: injured_PHi_3hrs_R26


title: injured_PHi_6hrs_R22

description: Gene expression data from injured, PHi treated gastrocnemius muscle tissue collected after 6 hrs


title: injured_vehicle_3hrs_R25


title: injured_PHi_3hrs_R31


title: injured_PHi_6hrs_R23


title: injured_vehicle_6hrs_R17


title: injured_vehicle_6hrs_R21


title: injured_vehicle_6hrs_R20


title: injured_PHi_6hrs_R14


title: injured_PHi_6hrs_R19


title: injured_PHi_6hrs_R15


title: injured_vehicle_6hrs_R16


title: injured_PHi_6hrs_R18


title: injured_PHi_9hrs_R10

description: Gene expression data from injured, PHi treated gastrocnemius muscle tissue collected after 9 hrs


title: B1-1_WholeBlood_Priest_Male_Age39

source_name: WholeBlood, Priest, Male, Age39


title: injured_vehicle_9hrs_R9

description: Gene expression data from injured, vehicle treated gastrocnemius muscle tissue collected after 9 hrs


title: injured_PHi_9hrs_R11


title: injured_vehicle_6hrs_R13


title: injured_PHi_9hrs_R7


title: injured_PHi_9hrs_R6


title: injured_vehicle_9hrs_R12


title: injured_vehicle_9hrs_R5


title: injured_PHi_9hrs_R3


title: Skin Biopsy R11_12

city: Iowa City

first: Ali

last: Jabbari

state: IA

address: 200 Hawkins Dr, 40025 PFP

institute: University of Iowa

hyb_protocol: Following fragmentation, 3.75 ug of cDNA was hybridized for 16 hr at 45 deg C on GeneChip Human Genome U133 Plus 2.0.  GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 7G3000

data_processing: The data were analyzed with Bioconductor/R and were GCRMA normalized.

source_name: skin biopsy

label_protocol: NuGen Encore Biotin Protocol using 3.75 ug cDNA from NuGen Ovation RNA Amplification V2 system

extract_protocol: PreAnalytiX- PAX Tissue miRNA kit

treatment_protocol: Scalp biopsy specimens were fixed using PAXgene tissue container kits

tag: patientid

tag: week

tag: rnabatch

value: F

tag: agebaseline

tag: ethnicity

value: Asian

tag: episodeduration

tag: aatype

tag: response

value: R


title: mammary_gland_13wks_rep2

city: Burlington

first: Jonathan

middle: AR

last: Gordon

state: VT

address: 89 Beaumont Ave Given E209

department: Biochemistry

institute: University of Vermont

description: miRNA expression data from mammary gland of MMTV-PyMT mouse with late-stage breast cancer

hyb_protocol: Biotinylated samples were hybridized onto the Affymetrix GeneChip miRNA 3.0 Array and processed according to Affymetrix technical protocols.

scan_protocol: Scanned images of individual microarray chips were analyzed by Affymetrix GCOS software.

data_processing: The data were analyzed with Partek Genomic Suites, version 6.6 (Copyright 2009, Partek Inc., St. Louis, MO, USA).

label: Biotin

source_name: Mammary gland tissue; Multiple large tumor lesions present; late stage disease

label_protocol: The Affymetrix® FlashTag™ Biotin HSR RNA Labeling Kit was used according to the manufacturer's instructions.

growth_protocol: Female FVB/NJ mice were crossed with male FVB mice that were transgenic (+/-) for PyMT antigen under control of the MMTV promoter. Female wildtype mice from this cross were saved and sacrificed at 4, 8, and 13 weeks of age for analysis.

extract_protocol: Total RNA was isolated from mouse mammary gland tissue specimens using Trizol (Life Technologies) and purified with the Zymo RNA purification kit (Zymo), both according to the manufacturer’s instructions.

treatment_protocol: Whole mammary glands were excised before promptly being snap frozen in liquid nitrogen for total RNA extraction using Trizol reagent.

tag: genotype

value: MMTV-PyMT +/- (Wildtype)

value: 13 weeks

tag: disease state

value: late (13 weeks) stage breast cancer

value: Mammary Gland


title: injured_vehicle_9hrs_R4

tag: drug

tag: injury

tag: time

tag: animal


title: mammary_gland_13wks_rep1

tag: strain

tag: tissue


title: mammary_gland_13wks_rep3

tag: age


title: Skin Biopsy R10_12

tag: patientid

tag: gender

value: White

value: totalis


title: injured_vehicle_9hrs_R8

tag: limb


title: mammary_gland_8wks_rep1

description: miRNA expression data from mammary gland of MMTV-PyMT mouse with mid-stage breast cancer

source_name: Mammary gland tissue; Multiple small tumor lesions present; Mid stage disease

value: 8 weeks

value: mid (8 weeks) stage breast cancer


title: injured_PHi_9hrs_R2

value: gastrocnemius

value: PHi


title: Skin Biopsy R08_12

tag: week

tag: rnabatch

tag: agebaseline


title: Skin Biopsy R02_24

tag: ethnicity

tag: episodeduration

tag: aatype


title: injured_vehicle_9hrs_R1

value: yes

value: right


title: uninjured_PHi_3hrs_L35

description: Gene expression data from uninjured, PHi treated gastrocnemius muscle tissue collected after 3 hrs

value: no

value: left


title: B2-1_WholeBlood_Priest_Male_Age30

value: Whole Blood

tag: group

value: Priest

value: Male


title: Skin Biopsy R09_12

value: M

tag: response

value: R


title: mammary_gland_4wks_rep3

description: miRNA expression data from mammary gland of MMTV-PyMT mouse with early-stage breast cancer

source_name: Mammary gland tissue; hyperplasia present; early stage disease

tag: genotype

value: MMTV-PyMT +/- (Wildtype)

value: 4 weeks

tag: disease state

value: early (4 weeks) stage breast cancer


title: Skin Biopsy R06_12

value: F

value: Hispanic

value: NR


title: uninjured_PHi_3hrs_L34

value: gastrocnemius

tag: drug

tag: injury

tag: time

tag: animal


title: mammary_gland_4wks_rep2

tag: strain

tag: age

tag: tissue

value: Mammary Gland


title: uninjured_vehicle_3hrs_L36

description: Gene expression data from uninjured, vehicle treated gastrocnemius muscle tissue collected after 3 hrs

value: vehicle

tag: limb


title: mammary_gland_8wks_rep3

value: 8 weeks

value: mid (8 weeks) stage breast cancer


title: mammary_gland_4wks_rep1


title: uninjured_PHi_3hrs_L31

value: PHi

value: no

value: left


title: Skin Biopsy R02_12

tag: patientid

tag: week

tag: rnabatch

tag: gender

value: White


title: uninjured_vehicle_3hrs_L32


title: mammary_gland_8wks_rep2


title: Skin Biopsy R04_8

value: M

tag: agebaseline

tag: ethnicity

tag: episodeduration

tag: aatype


title: Skin Biopsy R07_4

tag: response


title: Skin Biopsy R03_12

value: R


title: Skin Biopsy R08_4_1


title: Skin Biopsy R04_12


title: Skin Biopsy R01_12


title: uninjured_vehicle_3hrs_L33

tag: drug


title: uninjured_vehicle_3hrs_L29

tag: injury


title: uninjured_PHi_3hrs_L27

tag: time


title: Skin Biopsy R06_4


title: uninjured_vehicle_3hrs_L28

tag: animal


title: Skin Biopsy R11_0

value: Asian


title: Skin Biopsy R12_0

value: Black

value: universalis


title: Skin Biopsy R09_0


title: Skin Biopsy R10_0

value: F

value: totalis


title: Skin Biopsy R10_2


title: uninjured_vehicle_6hrs_L24

description: Gene expression data from uninjured, vehicle treated gastrocnemius muscle tissue collected after 6 hrs

tag: strain


title: uninjured_PHi_3hrs_L26


title: uninjured_vehicle_3hrs_L25


title: uninjured_PHi_6hrs_L22

description: Gene expression data from uninjured, PHi treated gastrocnemius muscle tissue collected after 6 hrs


title: Skin Biopsy R03_8


title: uninjured_PHi_6hrs_L23


title: uninjured_PHi_6hrs_L15


title: uninjured_vehicle_6hrs_L17


title: Skin Biopsy R08_0


title: uninjured_vehicle_6hrs_L16


title: Skin Biopsy R04_0


title: uninjured_PHi_6hrs_L14


title: uninjured_PHi_6hrs_L19


title: uninjured_vehicle_6hrs_L20


title: uninjured_vehicle_6hrs_L21


title: Skin Biopsy R05_0

value: Hispanic

value: NR


title: Skin Biopsy R01_0


title: Skin Biopsy R03_0


title: Skin Biopsy R06_0


title: Skin Biopsy R07_0


title: uninjured_PHi_6hrs_L18

value: gastrocnemius


title: Skin Biopsy NC108

value: N

value: NC


title: Skin Biopsy R02_0


title: Skin Biopsy NC098


title: Tbx4 neg Lung fibroblasts

city: Los Angeles

first: ting

last: Xie

state: CA

address: 127 San Vicente Blvd

department: Pulmonary

institute: Cedars-Sinai Medical Center

description: Gene expression data from Tbx4-TdTomato- cultured lung fibroblasts

hyb_protocol: Hybridization targets were prepared with the Ovation Pico WT Amp V2 kit (NuGen, San Carlos, CA) and the Encore Biotin Module (NuGen, San Carlos, CA) from total RNA, hybridized to GeneChip® mouse 430.2 arrays in Affymetrix GeneChip® hybridization oven 645, washed in Affymetrix GeneChip® Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® Command Console Scan Control 3.2.3.1515

data_processing: GeneSpring GX

source_name: mouse lung

label_protocol: cDNA were amplyfied by Ovation Pico WT Amp V2 kit and labeling were done by the Encore Biotin Module (NuGen, San Carlos, CA)

growth_protocol: Lung fibroblasts were cultured from Tbx4-Cre;RosaTm mice. Tomato positive and negative cells were sorted at passage 3.

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

tag: cell type

value: lung fibroblasts

tag: cell population


title: Tbx4 pos Lung fibroblasts

description: Gene expression data from Tbx4-TdTomato+ cultured lung fibroblasts


title: uninjured_vehicle_9hrs_L12

description: Gene expression data from uninjured, vehicle treated gastrocnemius muscle tissue collected after 9 hrs

tag: tissue

value: vehicle

tag: limb


title: uninjured_vehicle_9hrs_L9

value: no


title: uninjured_PHi_3hrs_L30

value: PHi

value: left


title: uninjured_PHi_9hrs_L11

description: Gene expression data from uninjured, PHi treated gastrocnemius muscle tissue collected after 9 hrs


title: Skin Biopsy NC084

tag: patientid

tag: week

value: M

value: White


title: uninjured_vehicle_6hrs_L13


title: uninjured_PHi_9hrs_L10


title: uninjured_PHi_9hrs_L6


title: uninjured_PHi_9hrs_L7


title: uninjured_vehicle_9hrs_L8


title: uninjured_vehicle_9hrs_L5


title: uninjured_vehicle_9hrs_L4


title: uninjured_PHi_9hrs_L3


title: uninjured_vehicle_9hrs_L1


title: microRNA profile of case 787T

status: Public on Aug 22 2017

city: Guangzhou

first: Heng-Ying

last: Pu

address: 651, Dongfeng East Road

country: China

institute: Cancer Centre, Sun Yat-sen University

hyb_protocol: The labeled RNAs from NSCLC and NC were hybridized to the array with a 1×hybridization solution (5× Denhart’s solution, 0.5% SDS, 5× SSC) in a Hybridization Chamber (Corning Inc, Corning, NY, USA) at 46°C for 12 to 16 hours.

scan_protocol: Scanned in a LuxScanTM -10K Scanner (capitalBio Inc.,Beijing, China).

data_processing: Quantile normalization across multiple arrays, log 2 transformation of expression levels, BRB ArrayTools v.3.8.0 was used.

source_name: non-small-cell lung cancer

label_protocol: 2.5 μg of total RNA was employed with 100 nmol/L of pCp-DY547 (Dharmacon, Lafayette, CO, USA) and 15 Units of T4 RNA ligase (USB, Cleveland, Oh, USA) in a total reaction volume of 20 µL at 16°C overnight

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

tag: survival


title: microRNA profile of case 400N

source_name: Matched noncancerous lung tissue of NSCLC


title: microRNA profile of case 401N


title: microRNA profile of case 793T


title: microRNA profile of case 786T


title: microRNA profile of case 402N


title: microRNA profile of case 403N


title: microRNA profile of case 789T


title: microRNA profile of case 406N


title: microRNA profile of case 409N


title: microRNA profile of case 781T


title: mNSC_E14.5_GFP_sample_8

city: Durham

first: Hai

last: Yan

state: NC

address: 199B-MSRB, Research Drive

department: Pathology

institute: Duke University

description: M

hyb_protocol: Product generated from the label protocol was hybridized onto the Affymetrix GeneChip Mouse Gene 2.0 ST array in Affymetrix GeneChip® hybridization oven 645, washed in Affymetrix GeneChip®  Fluidics Station 450 according to standard Affymetrix GeneChip® Hybridization, Wash, and Stain protocols. (Affymetrix, Santa Clara,CA).

scan_protocol: Arrays were scanned with Affymetrix GeneChip® Scanner 7G according to Affymetrix GeneChip protocols.

data_processing: Affymetrix Expression Console was used for data processing and normalization. RMA normailzation was applied

source_name: embyronic day 14.5 cortex

label_protocol: Total RNA were assessed for quality with Agilent 2100 Bioanalyzer G2939A (Agilent Technologies,Santa Clara, CA)) and Nanodrop 8000 spectrophotometer (Thermo Scientific/Nanodrop, Wilmington, DE). Hybridization targets were prepared with Ambion WT Expression Kit Life Technologies/Ambion (Grand Island, NY) and Affymetrix GeneChip WT Terminal Labeling Kit from total RNA.

growth_protocol: mNSCs were cultured following the NeuroCult protocol In vitro proliferation and differentiation of mouse neural stem and progenitor cells using NeuroCult.

extract_protocol: RNA was isolated from cells following the Qiagen Rneasy mini kit.

treatment_protocol: mNSCs were treated with adenoviral-GFP or adenoviral-Cre-recombinase available from VectorBiolabs.100MOI was used for infection.  24 hours post-infection, cells were washed and cultured in complete media.

tag: age

value: neural stem cell

tag: transduction

value: adenoviral-GFP


title: microRNA profile of case 782T


title: microRNA profile of case 778T


title: microRNA profile of case 780T


title: microRNA profile of case 779T


title: microRNA profile of case 785T


title: mNSC_E14.5_Cre_sample_7

value: adenoviral-Cre recombinase


title: microRNA profile of case 776T


title: microRNA profile of case 791T


title: mNSC_E14.5_Cre_sample_2

description: M


title: mNSC_E14.5_GFP_sample_7

description: WT


title: mNSC_E14.5_GFP_sample_2


title: mNSC_E14.5_Cre_sample_8

description: WT


title: microRNA profile of case 772T


title: microRNA profile of case 768T


title: microRNA profile of case 770T


title: microRNA profile of case 764T


title: microRNA profile of case 762T


title: microRNA profile of case 760T


title: microRNA profile of case 763T


title: microRNA profile of case 767T


title: microRNA profile of case 758T


title: microRNA profile of case 766T


title: microRNA profile of case 784T


title: microRNA profile of case 765T


title: microRNA profile of case 771T


title: microRNA profile of case 759T


title: microRNA profile of case 757T


title: microRNA profile of case 752T


title: microRNA profile of case 753T


title: microRNA profile of case 749T


title: microRNA profile of case 741T


title: microRNA profile of case 745T


title: microRNA profile of case 739T


title: microRNA profile of case 747T


title: microRNA profile of case 738T


title: microRNA profile of case 734T


title: microRNA profile of case 735T


title: microRNA profile of case 736T


title: microRNA profile of case 729T


title: microRNA profile of case 733T


title: microRNA profile of case 732T


title: microRNA profile of case 756T


title: uninjured_PHi_9hrs_L2


title: microRNA profile of case 728T


title: microRNA profile of case 726T


title: microRNA profile of case 725T


title: microRNA profile of case 724T


title: microRNA profile of case 721T


title: microRNA profile of case 720T


title: microRNA profile of case 719T


title: microRNA profile of case 717T


title: microRNA profile of case 711T


title: microRNA profile of case 714T


title: microRNA profile of case 718T


title: microRNA profile of case 710T


title: microRNA profile of case 709T


title: microRNA profile of case 705T


title: microRNA profile of case 697T


title: microRNA profile of case 703T


title: microRNA profile of case 698T


title: microRNA profile of case 704T


title: microRNA profile of case 722T


title: microRNA profile of case 699T


title: microRNA profile of case 700T


title: microRNA profile of case 701T


title: microRNA profile of case 696T


title: microRNA profile of case 694T


title: microRNA profile of case 690T


title: microRNA profile of case 692T


title: microRNA profile of case 689T


title: microRNA profile of case 686T


title: microRNA profile of case 685T


title: microRNA profile of case 687T


title: microRNA profile of case 706T


title: microRNA profile of case 683T


title: microRNA profile of case 680T


title: microRNA profile of case 684T


title: microRNA profile of case 678T


title: microRNA profile of case 677T


title: microRNA profile of case 679T


title: microRNA profile of case 693T


title: microRNA profile of case 676T


title: microRNA profile of case 675T


title: microRNA profile of case 674T


title: WM793-NME1-P96S_4

city: Lexington

first: Joseph

middle: Robert

last: McCorkle

state: KY

address: 760 Press Ave.

institute: University of Kentucky

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned at the University of Kentucky Microarray Core Facility

scan_protocol: Array scanning was performed according to the manufacturer's instructions (Affymetrix)

data_processing: Arrays were normalized by the Robust Multi-Array Average (RMA) method implemented using the 'aroma.affymetrix' R package. Differential expression analysis was performed with Linear Models of Microarrays (LIMMA) R package. A linear model was first fitted to expression data for each gene, and the empirical Bayes method was then used to assess differential expression between wild-type NME1 cells and metastasis suppressor deficient cell lines (parent WM793, E5A or K12Q NME1 mutant lines)

source_name: vertical growth phase melanoma (cell line)

label_protocol: RNA integrity is assessed using an Agilent 2100 Bioanalyzer, then biotin-labeled cRNA probes are prepared for hybridization using the standard protocol in the Affymetrix GeneChip Expression Analysis Manual

growth_protocol: Cells were grown for 3 days to 70-80% confluence in Tu2% growth media.

extract_protocol: Total cellular RNA was harvested using the RNEasy Extraction Kit (Qiagen) according to the manufacturer's instructions and diluted to concentrations of ~1 mg/mL with RNAse-free deionized water

tag: cell line

tag: genotype/variation


title: WM793-NME1-P96S_3


title: microRNA profile of case 681T


title: microRNA profile of case 667T


title: microRNA profile of case 668T


title: microRNA profile of case 666T


title: microRNA profile of case 672T


title: microRNA profile of case 665T


title: microRNA profile of case 669T


title: microRNA profile of case 662T


title: microRNA profile of case 661T


title: microRNA profile of case 664T


title: WM793-NME1-P96S_1


title: WM793-NME1-E5A_4


title: WM793-NME1-K12Q_4


title: WM793-NME1-K12Q_2


title: WM793-NME1-E5A_2


title: WM793-NME1-K12Q_1


title: microRNA profile of case 657T


title: microRNA profile of case 659T


title: WM793-NME1-P96S_2


title: microRNA profile of case 660T


title: microRNA profile of case 654T


title: microRNA profile of case 646T


title: microRNA profile of case 653T


title: WM793-NME1-E5A_3


title: WM793-NME1-K12Q_3


title: microRNA profile of case 642T


title: microRNA profile of case 644T


title: microRNA profile of case 647T


title: microRNA profile of case 641T


title: microRNA profile of case 652T


title: microRNA profile of case 645T


title: microRNA profile of case 650T


title: WM793-NME1-wild-type_2


title: microRNA profile of case 640T


title: microRNA profile of case 636T


title: WM793-NME1-wild-type_3


title: microRNA profile of case 635T


title: WM793-Parent_4

value: Parent


title: WM793-Parent_3


title: WM793-Parent_2


title: WM793-Parent_1


title: WM793-NME1-wild-type_1


title: WM793-NME1-E5A_1


title: Crosssectional CAN9

city: San Francisco

first: Minnie

last: Sarwal

address: 500 Parnassus Ave

institute: UCSF

hyb_protocol: The cDNA fragments of all 161 protocol biopsies were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays comprising more than 54,000 probe sets, covering more than 47,000 transcripts and variants, including 38,500 well-characterized human genes (Affymetrix Inc., Santa Clara, CA, USA), according to the Manufacterer's guidelines

scan_protocol: The microarrays were scanned using GeneChip Scanner 3000 (Affymetrix Inc., Santa Clara, CA, USA).

data_processing: For processing and normalization of the scanned images, dChip 2006 software was used, with perfect match [PM]/mismatch [MM] difference modeling and invariant set normalization.

source_name: Presence of chronic allograft nephropathy

label_protocol: RNA was amplified to cDNA and biotin labeled using the OvationTM Biotin System (NuGEN Technologies, San Carlos, CA, USA).

extract_protocol: Total RNA was extracted from each biopsy using TRIzol Reagent (Invitrogen, Carlsbad, CA, USA). RNA integrity was ensured using the RNA 6000 Nano LabChip® Kit (Agilent Technologies, Waldbronn, Germany) on a 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany).

value: kidney

tag: condition

tag: genotype

value: normal

value: pediatrics/young adult


title: Crosssectional CAN7

value: Presence of chronic allograft nephropathy


title: microRNA profile of case 633T


title: Crosssectional CAN11


title: WM793-NME1-wild-type_4


title: Crosssectional CAN6


title: Crosssectional CAN12


title: Crosssectional CAN8


title: Crosssectional CAN10


title: microRNA profile of case 632T


title: microRNA profile of case 631T


title: Crosssectional CAN5


title: microRNA profile of case 630T


title: microRNA profile of case 629T


title: microRNA profile of case 628T


title: microRNA profile of case 627T


title: Crosssectional CAN2


title: Crosssectional CAN4


title: Crosssectional noCAN9

source_name: Absence of chronic allograft nephropathy


title: microRNA profile of case 625T


title: microRNA profile of case 624T


title: microRNA profile of case 623T


title: Crosssectional CAN3


title: Crosssectional CAN1


title: microRNA profile of case 626T


title: microRNA profile of case 618T


title: Crosssectional noCAN8

value: Absence of chronic allograft nephropathy


title: microRNA profile of case 619T


title: microRNA profile of case 620T


title: Crosssectional noCAN4


title: microRNA profile of case 617T


title: microRNA profile of case 616T


title: Crosssectional noCAN12


title: Crosssectional noCAN10


title: Crosssectional noCAN11


title: Crosssectional noCAN7


title: microRNA profile of case 622T


title: Crosssectional BKVN12

source_name: BKVN biopsy

value: BKVN


title: Crosssectional BKVN14


title: microRNA profile of case 615T


title: microRNA profile of case 613T


title: Crosssectional BKVN15


title: Crosssectional BKVN13


title: Crosssectional BKVN8


title: microRNA profile of case 655T


title: Crosssectional BKVN10


title: Crosssectional BKVN11


title: microRNA profile of case 608T


title: microRNA profile of case 614T


title: microRNA profile of case 611T


title: microRNA profile of case 612T


title: Crosssectional BKVN9


title: microRNA profile of case 607T


title: microRNA profile of case 606T


title: microRNA profile of case 605T


title: microRNA profile of case 603T


title: Crosssectional BKVN5


title: Crosssectional BKVN3


title: microRNA profile of case 599T


title: microRNA profile of case 600T


title: microRNA profile of case 601T


title: Crosssectional BKVN4


title: Crosssectional BKVN7


title: Crosssectional BKVN1


title: microRNA profile of case 598T


title: microRNA profile of case 594T


title: microRNA profile of case 595T


title: microRNA profile of case 597T


title: Crosssectional BKVN6


title: microRNA profile of case 592T


title: Crosssectional AR12

source_name: Acute rejection biopsy

value: Acute rejection


title: Crosssectional AR14


title: microRNA profile of case 593T


title: Crosssectional BKVN2


title: Crosssectional AR13


title: microRNA profile of case 591T


title: microRNA profile of case 590T


title: Crosssectional AR15


title: Crosssectional AR11


title: microRNA profile of case 586T


title: microRNA profile of case 589T


title: microRNA profile of case 588T


title: microRNA profile of case 584T


title: microRNA profile of case 582T


title: microRNA profile of case 583T


title: Crosssectional AR10


title: Crosssectional AR8


title: Crosssectional AR9


title: Crosssectional AR6


title: Crosssectional AR7


title: microRNA profile of case 579T


title: microRNA profile of case 575T


title: Crosssectional AR3


title: Crosssectional AR5


title: Crosssectional AR4


title: Crosssectional AR1


title: Crosssectional STA29

source_name: Stable graft

value: Stable graft


title: Crosssectional STA26


title: microRNA profile of case 574T


title: Crosssectional STA28


title: Crosssectional AR2


title: Crosssectional STA30


title: microRNA profile of case 573T


title: Crosssectional STA27


title: Crosssectional STA25


title: Crosssectional STA24


title: microRNA profile of case 570T


title: microRNA profile of case 569T


title: microRNA profile of case 571T


title: microRNA profile of case 567T


title: microRNA profile of case 568T


title: microRNA profile of case 566T


title: Crosssectional STA23


title: microRNA profile of case 557T


title: microRNA profile of case 558T


title: microRNA profile of case 565T


title: microRNA profile of case 562T


title: microRNA profile of case 561T


title: microRNA profile of case 559T


title: Crosssectional STA21


title: microRNA profile of case 555T


title: Crosssectional STA19


title: Crosssectional STA17


title: Crosssectional STA15


title: microRNA profile of case 553T


title: Crosssectional STA13


title: Crosssectional STA20


title: Crosssectional STA22


title: Crosssectional STA11


title: Crosssectional STA18


title: microRNA profile of case 556T


title: Crosssectional STA16


title: Crosssectional STA14


title: Crosssectional STA12


title: microRNA profile of case 552T


title: microRNA profile of case 550T


title: Crosssectional STA7


title: microRNA profile of case 545T


title: microRNA profile of case 547T


title: microRNA profile of case 541T


title: microRNA profile of case 542T


title: microRNA profile of case 549T


title: microRNA profile of case 539T


title: microRNA profile of case 540T


title: Crosssectional STA8


title: Crosssectional STA10


title: microRNA profile of case 538T


title: Crosssectional STA9


title: Crosssectional STA6


title: microRNA profile of case 537T


title: Crosssectional STA1


title: Crosssectional STA2


title: Crosssectional STA4


title: microRNA profile of case 548T


title: Crosssectional STA5


title: microRNA profile of case 536T


title: microRNA profile of case 543T


title: microRNA profile of case 535T


title: microRNA profile of case 532T


title: microRNA profile of case 534T


title: microRNA profile of case 533T


title: microRNA profile of case 528T


title: microRNA profile of case 523T


title: microRNA profile of case 530T


title: Crosssectional STA3


title: microRNA profile of case 520T


title: microRNA profile of case 516T


title: microRNA profile of case 517T


title: microRNA profile of case 511T


title: microRNA profile of case 513T


title: microRNA profile of case 512T


title: microRNA profile of case 508T


title: microRNA profile of case 509T


title: microRNA profile of case 505T


title: microRNA profile of case 510T


title: microRNA profile of case 506T


title: microRNA profile of case 501T


title: microRNA profile of case 503T


title: microRNA profile of case 498T


title: microRNA profile of case 502T


title: microRNA profile of case 496T


title: microRNA profile of case 494T


title: microRNA profile of case 488T


title: microRNA profile of case 489T


title: microRNA profile of case 493T


title: microRNA profile of case 492T


title: microRNA profile of case 491T


title: microRNA profile of case 485T


title: microRNA profile of case 484T


title: microRNA profile of case 487T


title: microRNA profile of case 480T


title: microRNA profile of case 481T


title: microRNA profile of case 479T


title: microRNA profile of case 482T


title: microRNA profile of case 483T


title: microRNA profile of case 478T


title: microRNA profile of case 475T


title: microRNA profile of case 468T


title: microRNA profile of case 469T


title: microRNA profile of case 470T


title: microRNA profile of case 471T


title: microRNA profile of case 473T


title: microRNA profile of case 466T


title: microRNA profile of case 465T


title: microRNA profile of case 467T


title: microRNA profile of case 461T


title: microRNA profile of case 464T


title: microRNA profile of case 460T


title: microRNA profile of case 462T


title: microRNA profile of case 463T


title: microRNA profile of case 459T


title: microRNA profile of case 458T


title: microRNA profile of case 456T


title: microRNA profile of case 457T


title: microRNA profile of case 472T


title: microRNA profile of case 474T


title: microRNA profile of case 449T


title: microRNA profile of case 447T


title: microRNA profile of case 452T


title: microRNA profile of case 454T


title: microRNA profile of case 455T


title: microRNA profile of case 504T


title: microRNA profile of case 453T


title: microRNA profile of case 446T


title: microRNA profile of case 441T


title: microRNA profile of case 439T


title: microRNA profile of case 436T


title: microRNA profile of case 434T


title: microRNA profile of case 433T


title: microRNA profile of case 448T


title: microRNA profile of case 451T


title: microRNA profile of case 431T


title: microRNA profile of case 426T


title: microRNA profile of case 425T


title: microRNA profile of case 438T


title: microRNA profile of case 428T


title: microRNA profile of case 421T


title: microRNA profile of case 424T


title: microRNA profile of case 423T


title: microRNA profile of case 445T


title: microRNA profile of case 419T


title: microRNA profile of case 420T


title: microRNA profile of case 417T


title: microRNA profile of case 422T


title: microRNA profile of case 416T


title: microRNA profile of case 418T


title: microRNA profile of case 414T


title: microRNA profile of case 415T


title: microRNA profile of case 411T


title: microRNA profile of case 413T


title: microRNA profile of case 429T


title: microRNA profile of case 430T


title: microRNA profile of case 410T


title: microRNA profile of case 409T


title: microRNA profile of case 406T


title: microRNA profile of case 427T


title: microRNA profile of case 398T


title: microRNA profile of case 402T


title: microRNA profile of case 399T


title: microRNA profile of case 401T


title: microRNA profile of case 400T


title: microRNA profile of case 396T


title: microRNA profile of case 397T


title: microRNA profile of case 395T


title: microRNA profile of case 394T


title: microRNA profile of case 390T


title: microRNA profile of case 391T


title: microRNA profile of case 392T


title: microRNA profile of case 393T


title: microRNA profile of case 389T


title: microRNA profile of case 384T


title: microRNA profile of case 387T


title: microRNA profile of case 388T


title: microRNA profile of case 383T


title: microRNA profile of case 380T


title: microRNA profile of case 403T


title: microRNA profile of case 381T


title: microRNA profile of case 378T


title: microRNA profile of case 385T


title: microRNA profile of case 379T


title: microRNA profile of case 376T


title: microRNA profile of case 374T


title: microRNA profile of case 373T


title: microRNA profile of case 370T


title: microRNA profile of case 369T


title: microRNA profile of case 367T


title: microRNA profile of case 363T


title: microRNA profile of case 364T


title: microRNA profile of case 366T


title: microRNA profile of case 359T


title: microRNA profile of case 358T


title: microRNA profile of case 382T


title: microRNA profile of case 355T


title: microRNA profile of case 357T


title: microRNA profile of case 351T


title: microRNA profile of case 347T


title: microRNA profile of case 343T


title: microRNA profile of case 342T


title: microRNA profile of case 338T


title: microRNA profile of case 339T


title: microRNA profile of case 345T


title: microRNA profile of case 337T


title: microRNA profile of case 329T


title: microRNA profile of case 335T


title: microRNA profile of case 330T


title: microRNA profile of case 328T


title: microRNA profile of case 327T


title: microRNA profile of case 325T


title: microRNA profile of case 322T


title: microRNA profile of case 326T


title: microRNA profile of case 319T


title: microRNA profile of case 323T


title: microRNA profile of case 317T


title: microRNA profile of case 315T


title: microRNA profile of case 311T


title: microRNA profile of case 307T


title: microRNA profile of case 309T


title: microRNA profile of case 306T


title: microRNA profile of case 304T


title: microRNA profile of case 305T


title: microRNA profile of case 301T


title: microRNA profile of case 302T


title: microRNA profile of case 300T


title: microRNA profile of case 298T


title: microRNA profile of case 321T


title: microRNA profile of case 292T


title: microRNA profile of case 296T


title: microRNA profile of case 294T


title: microRNA profile of case 295T


title: microRNA profile of case 291T


title: microRNA profile of case 290T


title: microRNA profile of case 286T


title: microRNA profile of case 287T


title: microRNA profile of case 283T


title: microRNA profile of case 280T


title: microRNA profile of case 299T


title: microRNA profile of case 275T


title: microRNA profile of case 279T


title: microRNA profile of case 266T


title: microRNA profile of case 297T


title: 1c_GFP_min

city: New York

first: Timothy

middle: Cragin

state: NY

address: 1130 St. Nicholas Ave

department: Medicine- Liver and Digestive Diseases

institute: Columbia University Medical Center

description: Gene expression of bone marrow derived cells from HdcGFP mice sorted for HdcGFP-/loCD11b+Gr1+ .

hyb_protocol: Hybridization was performed on Mouse Genome 430. 2.0 GeneChips (Affymetrix). All samples were prepared with the standard protocol recommended by the manufacturer.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000-7G scanner with GCOS software. Scanning was peformed according to the protocol described in the Affymetrix GeneChip® Expression Analysis Technical Manual, November 2004 Edition.

data_processing: Data was normalized using the GCRMA algorithm

source_name: Bone marrow from the femur and tibia bones.

label_protocol: 100 ng of total RNA was labeled with 3' IVT Express Kit (Affymetrix)

growth_protocol: Mice were maintained at all times on a 12-hour light-dark cycle in a specific pathogen-free environment with free access to rodent chow and water.

extract_protocol: Extraction of total RNA was performed using Rneasy Micro Kit (Qiagen) according to the manufacturer's instructions.

tag: gender

value: female

value: HdcGFP mice (C57/BL6 background).

value: bone marrow

tag: sorted cell


title: 2b_GFP_plus

description: Gene expression of bone marrow derived cells from HdcGFP mice sorted for HdcGFP+/hiCD11b+Gr1+ .

source_name: Bone marrow from the femur and tibia bones

value: HdcGFP mice (C57BL/6 background)


title: microRNA profile of case 268T


title: microRNA profile of case 269T


title: 2a_GFP_plus


title: microRNA profile of case 249T


title: microRNA profile of case 285T


title: microRNA profile of case 237T


title: 1a_GFP_min

description: Gene expression of bone marrow derived cells from HdvGFP mice sorted for HdcGFP-/loCD11b+Gr1+ .

hyb_protocol: Hybridization was performed oon Mouse Genome 430. 2.0 GeneChips (Affymetrix). All samples were prepared with the standard protocol recommended by the manufacturer.


title: 2c_GFP_plus


title: microRNA profile of case 236T


title: microRNA profile of case 238T


title: microRNA profile of case 231T


title: microRNA profile of case 216T


title: microRNA profile of case 193T


title: microRNA profile of case 265T


title: microRNA profile of case 185T


title: 1b_GFP_min

description: Gene expression of bone marrow derived cells from HdcGFP mice sorted for HdcGFP-/loCD11b+Gr1- .

value: HdcGFP mice (C57/BL6 background)


title: microRNA profile of case 270T


title: microRNA profile of case 240T


title: Ly49G2_A+_NK

city: Sacramento

first: Clifford

middle: G.

last: Tepper

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

description: Affymetrix microarray gene expression profiling data

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the Affymetrix GeneChip Mouse Gene 2.0 Sense Target (ST) Arrays using Affymetrix hybridization kit materials. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using protocol FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using GeneSpring GX 12.0 software. Microarray probe intensity values (CEL files) were background-corrected, summarized, and normalized using the Robust Multi-array Average (RMA16) algorithm (Irizarry et al., 2003) and filtered by raw signal intensity values (upper cut-off 100th and lower cut-off 20th percentile). Comparison analysis were performed to identify genes that were differentially expressed using a cut-off of ≥1.5-fold between groups.  Data were processed using GeneSpring GX 12.0 software.

source_name: Unlicensed NK cells: FACS-sorted for CD3-CD122+Ly49G2+Ly49A+Ly49C/I- cells

label_protocol: Biotinylated sense strand DNA targets were prepared from 100 ng total RNA using the Ambion WT Expression and Affymetrix GeneChip WT Terminal Labeling Kits according to the standard manufacturer's protocols

extract_protocol: Total RNA was isolated from NK cell subsets (obtained  by FACS sorting of primary murine splenocytes) using the using the Qiagen RNeasy kit (Qiagen, Valencia, CA).

value: Unlicensed NK cells:FACS-sorted for CD3-CD122+Ly49G2+Ly49A+Ly49C/I- cells


title: microRNA profile of case 169T


title: Ly49C_I+_NK

source_name: Licensed NK cells: FACS-sorted for CD3-CD122+Ly49G2-A-Ly49C/I+ cells

value: Licensed NK cells:FACS-sorted for CD3-CD122+Ly49G2-A-Ly49C/I+ cells


title: microRNA profile of case 170T


title: Ly49_negative

source_name: Unlicensed NK cells: FACS-sorted for CD3-CD122+Ly49G2 A Ly49C/I- cells

value: Unlicensed NK cells:FACS-sorted for CD3-CD122+Ly49G2 A Ly49C/I- cells


title: microRNA profile of case 168T


title: microRNA profile of case 163T


title: microRNA profile of case 149T


title: microRNA profile of case 230T


title: microRNA profile of case 147T


title: microRNA profile of case 791N


title: microRNA profile of case 789N


title: microRNA profile of case 793N


title: microRNA profile of case 786N


title: microRNA profile of case 784N


title: microRNA profile of case 785N


title: microRNA profile of case 143T


title: microRNA profile of case 781N


title: microRNA profile of case 780N


title: microRNA profile of case 782N


title: microRNA profile of case 779N


title: microRNA profile of case 159T


title: Placenta_Hypoxia_MitoQNP_08_rep1

city: Cardiff

first: Hannah

last: Scott

address: Hadyn Ellis Building, Maindy Road

department: UK Dementia Research Institute

institute: Cardiff University

description: Placenta_NS08_v_HM08.txt; Placenta_HS08_v_HM08.txt

hyb_protocol: Samples were hybridised using the NanoString nCounter rat miRNA Expression Assay kit. See nCounter miRNA Expression Assay User Manual for protocol.

scan_protocol: Samples were analysed using the NanoString nCounter Analysis System (Gen2). See Gen2 Prep Station User Manual.

data_processing:
Raw output files were converted into lists of counts. To compare two groups, the respective raw counts were passed into RUVSeq for normalisation and removal of unwanted variation. Adjusted counts were then analysed for differential expression analysis using edgeR.
Normalised counts can be found in attached text files, instead of in the matrix table, as specified in the 'Description' column under the 'Samples' heading. Values are Reporter Probe signal intensities captured with the nCounter Analysis System and normalised using RUVSeq.

organism: Rattus norvegicus

source_name: placenta conditioned medium, maternal hypoxia_ maternal MitoQ-nanoparticle injection, exposure to 8% oxygen in vitro

label_protocol: Samples were labelled using the NanoString nCounter rat miRNA Expression Assay kit. See nCounter miRNA Expression Assay User Manual for protocol.

growth_protocol: Three-month-old female Sprague-Dawley rats were maintained on ad libitum standard rat chow and tap water in a 10:14-h light-dark cycle and acclimatised before breeding. All protocols were approved by the University of Alberta Health Sciences Animal Policy and Welfare Committee, in accordance with the Canadian Council on Animal Care guidelines.

extract_protocol: Foetal blood was collected into EDTA-containing tubes, pooled per litter, and plasma was extracted. Placentae were isolated, placed into cell culture medium and incubated at 2, 8 or 21% oxygen for 24 h. Total RNA was extracted from 100 μl foetal plasma using the Qiagen miRNeasy Serum/Plasma Kit or from 200 μl conditioned media using the Qiagen miRNeasy Mini Kit.

treatment_protocol: On gestational day 15 of pregnancy the rats were injected ntravenously with saline or 125 μM MitoQ-nanoparticles and exposed for the next 6 days to 21% or 11% oxygen.

tag: foetal age

value: Pacenta

tag: maternal oxygen status

value: Hypoxia

tag: maternal injections

value: MitoQ-nanoparticles

tag: in vitro oxygen condition


title: Placenta_Hypoxia_MitoQNP_08_rep2

tag: tissue


title: microRNA profile of case 778N


title: Placenta_Normoxia_MitoQNP_08_rep1

source_name: placenta conditioned medium, maternal normoxia, maternal MitoQ-nanoparticle injection, exposure to 8% oxygen in vitro

value: Normoxia


title: Placenta_Normoxia_MitoQNP_08_rep3


title: Placenta_Normoxia_MitoQNP_08_rep2


title: microRNA profile of case 776N


title: microRNA profile of case 772N


title: Placenta_Hypoxia_Saline_08_rep3

description: Placenta_NS08_v_HS08.txt; Placenta_HS08_v_HM08.txt

source_name: placenta conditioned medium, maternal hypoxia, maternal saline injection, exposure to 8% oxygen in vitro

value: Saline


title: microRNA profile of case 770N


title: microRNA profile of case 768N


title: Placenta_Hypoxia_Saline_08_rep1


title: Placenta_Hypoxia_MitoQNP_08_rep3


title: Placenta_Hypoxia_Saline_08_rep2


title: Placenta_Normoxia_Saline_08_rep2

description: Placenta_NS08_v_HS08.txt; Placenta_NS08_v_NM08.txt; Placenta_NS08_v_HM08.txt

source_name: placenta conditioned medium, maternal normoxia, maternal saline injection, exposure to 8% oxygen in vitro


title: Placenta_Normoxia_Saline_08_rep3


title: microRNA profile of case 148T

source_name: non-small-cell lung cancer


title: microRNA profile of case 767N

source_name: Matched noncancerous lung tissue of NSCLC


title: Placenta_Normoxia_Saline_08_rep1


title: microRNA profile of case 766N


title: Placenta_Hypoxia_MitoQNP_02_rep4

description: Placenta_NS21_v_HM02.txt; Placenta_HS02_v_HM02.txt

source_name: placenta conditioned medium, maternal hypoxia, maternal MitoQ-nanoparticle injection, exposure to 2% oxygen in vitro


title: microRNA profile of case 764N


title: microRNA profile of case 763N


title: microRNA profile of case 771N


title: microRNA profile of case 765N


title: Placenta_Hypoxia_MitoQNP_02_rep2


title: Placenta_Hypoxia_MitoQNP_02_rep3


title: microRNA profile of case 762N


title: microRNA profile of case 758N


title: microRNA profile of case 759N


title: Placenta_Hypoxia_MitoQNP_21_rep4

description: Placenta_NS21_v_HM21.txt; Placenta_HS21_v_HM21.txt

source_name: placenta conditioned medium, maternal hypoxia, maternal MitoQ-nanoparticle injection, exposure to 21% oxygen in vitro


title: Placenta_Hypoxia_MitoQNP_02_rep1


title: Placenta_Hypoxia_MitoQNP_21_rep3


title: Placenta_Hypoxia_MitoQNP_21_rep1


title: Placenta_Hypoxia_MitoQNP_21_rep2


title: microRNA profile of case 757N


title: microRNA profile of case 760N


title: microRNA profile of case 753N


title: Placenta_Normoxia_MitoQNP_21_rep4

source_name: placenta conditioned medium, maternal normoxia, maternal MitoQ-nanoparticle injection, exposure to 21% oxygen in vitro


title: Psc3-GFP ChIP in wild-type

city: Bethesda

first: Shiv

last: Grewal

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

hyb_protocol: Equal amounts of Cy5-labeled ChIP DNA and Cy3-labeled whole-cell extract DNA were mixed and combined with human Cot1 DNA, Agilent Blocking Agent and Agilent Hybridization buffer, and hybridized to high-density microarrays in Agilent SureHyb hybridization chamber for 24 hours at 65˚C, 10 rpm. After hybridization, slides were washed according to Agilent protocol.

scan_protocol: Scanned on an Agilent G2600D scanner.

data_processing: Data were extracted using Agilent Feature Extraction Software. Signal was normalized by combined rank consistency filtering with LOWES intensity normalization.

organism: Schizosaccharomyces pombe

source_name: WT, Psc3-GFP ChIP DNA

label_protocol: ChIP and whole-cell extract DNA were amplified by random-primed PCR and conjugated with Cy5 (ChIP DNA) or Cy3 (whole-cell extract DNA).

growth_protocol: WT and sap1-1 cells were initially cultured in rich media (YEA) at 26°C and then shifted to 33°C for 6 hours. Hydroxyurea (HU) was used to arrest wild type and sap1-1 cells at S-phase.

extract_protocol: Fixed cells were lysed with glass-beads, DNA sheared by sonication to 500-1000bp fragments and immunoprecipitated with GFP antibody (Abcam, ab290), Sap1 antibody (antibody was kindly provided by B. Arcangioli) or with Mcm6 antibody (antibody was kindly provided by H. Masukata). Immunoprecipitated DNA was recovered by incubation with protein A slurry and reversed-crosslinked at 65˚C.

treatment_protocol: Exponentially growing cells were fixed in 3% paraformaldehyde at room temperature. Cells were further crosslinked with DMA for 45 min at room temperature.

tag: strain/background

value: Wild type

tag: chip antibody

value: GFP

source_name: WT, whole-cell extract DNA

tag: fraction

value: whole-cell extract


title: Sap1 ChIP in sap1-1

source_name: sap1-1, Sap1 ChIP DNA

source_name: sap1-1, whole-cell extract DNA


title: Taz1-GFP ChIP in wild-type

source_name: WT, Taz1-GFP ChIP DNA


title: microRNA profile of case 756N

tag: survival


title: microRNA profile of case 752N


title: Psc3-GFP ChIP in sap1-1

source_name: sap1-1, Psc3-GFP ChIP DNA


title: Sap1 ChIP in wild-type

source_name: WT, Sap1 ChIP DNA


title: GFP-Bqt3 ChIP in sap1-1

source_name: sap1-1, GFP-Bqt3 ChIP DNA


title: Placenta_Normoxia_MitoQNP_21_rep3


title: Mcm6 ChIP in sap1-1

source_name: sap1-1, Mcm6 ChIP DNA


title: Placenta_Normoxia_MitoQNP_21_rep2


title: GFP-Bqt3 ChIP in wild-type

source_name: WT, GFP-Bqt3 ChIP DNA


title: microRNA profile of case 173T


title: microRNA profile of case 745N


title: Placenta_Normoxia_MitoQNP_21_rep1


title: CGH_Revertant_1

hyb_protocol: Equal amounts of Cy5-labeled DNA and Cy3-labeled DNA were mixed and combined with human Cot1 DNA, Agilent Blocking Agent and Agilent Hybridization buffer, and hybridized to high-density microarrays in Agilent SureHyb hybridization chamber for 24 hours at 65˚C, 10 rpm. After hybridization, slides were washed according to Agilent protocol.

data_processing:
Data were extracted using Agilent Feature Extraction Software. Signal was normalized by combined rank consistency filtering with LOWES intensity normalization.
Relative copy number values were calculated as a log 2 ratio of Cy5 processed signal/ Cy3 processed signal.

source_name: sap1-1 revertant

label_protocol: Genomic DNA from wild type or sap1-1 revertant was digested with AluI and RsaI. Digested DNA was used as template for a genomic DNA labelling reaction using the BioPrime® Array CGH Genomic Labeling kit (Invitrogen) according to the manufacturer's protocol.

extract_protocol: Grow 20 ml cells to OD595 of 1.0. After cell wall digestion using Zymolyase 100T, cells were resuspended in 0.55 ml TE, 1% SDS, 100ug of proteinase K and incubated at 65°C for 30 min. Add 175 µl 5M potassium acetate. Keep on ice for 5 minutes. Lysate was centrifuged for 15 min at maximum speed for removing the cell debris. Genomic DNA was precipitated with isopropanol. After RNaseA treatment, genomic DNA was purified by phenol/chloroform/isoamyl alcohol (PCI) extraction twice and precipitated with ethanol.

source_name: wild-type

value: wild-type


title: Mcm6 ChIP in wild-type

source_name: WT, Mcm6 ChIP DNA


title: Placenta_Hypoxia_Saline_02_rep4

description: Placenta_NS21_v_HS02.txt; Placenta_HS02_v_HM02.txt

source_name: placenta conditioned medium, maternal hypoxia, maternal saline injection, exposure to 2% oxygen in vitro