title: bric-16-cyt-ground-h-f3

city: Mountain View

first: NASA

last: GeneLab

address: Mail Stop N211

institute: NASA Ames Research Center

hyb_protocol: Hybridization to the microarray gene chip was conducted following the standard protocol outlined in the technical manual for Affymetrix GeneChip Expression Analysis (Affymetrix, Santa Clara, CA).

scan_protocol: Raw data from microarray studies was processed using Microarray Suite Version 5 software (Affymetrix, Santa Clara, CA) to convert the intensity information to quantitative values.

data_processing: All samples, ground and flight, each processed using PLIER, MAS5, and RMA.

organism: Arabidopsis thaliana

label_protocol: RNA amplification and purification of BRIC-16-Cyt were conducted by the ICBR using the Ovation Pico WTA system for biotin target labeling. Chemical and enzymatic fragmentation of cRNA was completed in a thermal cycler at 37°C for 60 min, and 70°C for 10 min, with a final holding at 4° C until sample removal. A Nano Drop spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE) was used to assess the yield of the labeled cRNA.

growth_protocol: Arabidopsis thaliana seedlings were grown in darkness using the Biological Research in Canisters-Petri Dish Fixation Unit (BRIC-PDFU) hardware flown on the space shuttle. Samples were removed from the hardware and placed in microcentrifuge tubes with fresh RNAlater. They were transported to the University of Florida, Gainesville, where they were stored at -80°C until the RNA was extracted.

extract_protocol: RNA was extracted using the RNeasy Mini Plant RNA extraction kit.

tag: ecotype

value: Landsberg (LER-0) ecotype

tag: factor value [microgravity]

value: Ground Control

value: Shoots of seedlings


title: bric-16-cyt-ground-h-f2

status: Public on Nov 01 2017

type: RNA

country: USA

label: biotin

molecule: total RNA

tag: tissue


title: Zgalactanivorans_agar_rep1

city: Roscoff

first: Francois

last: Thomas

address: Place George Teissier

department: UMR8227, CNRS-UPMC

country: France

institute: Station Biologique de Roscoff

description:
Zobellia galactanivorans grown with agar as sole carbon source
This sample is of Z.galactanivorans grown with agar as a sole carbon source. It is the first of three biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed by PartnerChip, Evry, France, following the Nimblegen standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by PartnerChip, Evry, France, following the Nimblegen standard operating protocol. See www.nimblegen.com.

data_processing: Gene expression was summarized from probe sets and normalized using the Analysis of NimbleGen Arrays Interface (Simon and Biot, 2010 Bioinformatics 26 (19): 2468-2469)

organism: Zobellia galactanivorans

label_protocol: Labeling was performed by PartnerChip, Evry, France, following the Nimblegen standard operating protocol. See www.nimblegen.com.

growth_protocol: Zobellia galactanivorans DsijT was grown to late log-phase in marine mineral medium (Thomas et al. 2011, Journal of Microbiological Methods 84: 61-66) containing a single carbon source, aerobically at 20°C, 180 rpm.

extract_protocol: Samples were directly transferred from -80°C to a 65°C water bath for 15 min to lyse to cells and mixed with 50 µl chloroform for 5 min at room temperature. The aqueous phase was recovered after centrifugation for 15 min at 13000g, 4°C. Total RNA was purified using RNeasy Mini Kit (Qiagen) with on-column DNase I treatment

treatment_protocol: Cells were pelleted by centrifugation (10 min, 4000g), resuspended in Trizol and frozen in liquid nitrogen

tag: genotype/strain

value: wild-type DsijT


title: ML-2

city: Seattle

first: Serdar

last: Turkarslan

state: WA

address: 401 Terry Ave

institute: Institute for Systems Biology

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

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

data_processing:
All microarray data were analyzed using DNAStar ArrayStar software
Data reported in Microarray Raw Data file are Fluorescent Intensities. Data reported in Log2 ratio data file are normalized expression values (averages of all probes for each individual gene) for all 1795 protein-coding genes. Data were exported from ArrayStar, log 2 transformed, and averaged among biological replicates.

organism: Nitrosopumilus maritimus SCM1

source_name: Mid-Log Phase Cell Replicate 2

label_protocol: Three biological replicate hybridizations were done for the mid-log and 24-hour ammonia-starved conditions and two replicates for recovery from ammonia starvation.

growth_protocol: Nitrosopumilus maritimus cells were cultured in synthetic seawater medium at 30°C in the dark.

extract_protocol: Total RNA was extracted with the hot phenol extraction method and purified with DNA-free kit

treatment_protocol: The mid-log control treatment was comprised of mid-exponential phase cells after ~0.5 mM ammonia consumption. For the ammonia starvation treatment, the mid-log phase cells were harvested by filtration, resuspended in ammonia free media, and incubated for 24 hours. Ammonia-starved cells were then exposed to 1 mM NH 4 Cl and incubated for 24 hours to investigate gene expression during recovery

tag: strain

tag: treatment

value: Mid-Log growth


title: AS24_1

source_name: After Starvation 24 hours Replicate 1

value: After starvation


title: ML-3

source_name: Mid-Log Phase Cell Replicate 3


title: ML-1

source_name: Mid-Log Phase Cell Replicate 1


title: AS24_2

source_name: After Starvation 24 hours Replicate 2


title: AR24_1

source_name: After Recovery 24 hours Replicate 1

value: After recovery


title: AR24_2

source_name: After Recovery 24 hours Replicate 2


title: AS24_3

source_name: After Starvation 24 hours Replicate 3


title: bric-16-cyt-flight-f-f4

value: Spaceflight


title: bric-16-cyt-flight-f-f2


title: bric-16-cyt-ground-h-f4


title: miR-21_WT1_Ipsi_(Mouse430_2)

city: London

first: David

last: Chambers

state: London

address: Guy's Campus

department: Wolfson CARD

country: United Kingdom

institute: King's College Londonn

description: Gene expression data

hyb_protocol: Following fragmentation, 8 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 230 v2 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and analyzsed in Affymetrix Transcript Analysis Console

label: Biotin

organism: Mus musculus

source_name: F4/80+ CD11b+ macrophages

label_protocol: Biotinylated cRNA were prepared according to the standard WT Pico KIt Affymetrix protocol from  <1ng total RNA

extract_protocol: Agilent total RNA microprep kit

treatment_protocol: FACS F4/80+ CD11b+ macrophages (population P5) isolated from a pool of ipsilateral L4/L5 DRG directly into lysis buffer

tag: cell type

tag: genotype/variation

value: wild type WT


title: WT_zeocin_2h_rep2

city: Ikoma

first: Nobuo

last: Ogita

state: Nara

address: 8916-5 Takayama-cho

department: Graduate School of Biological Sciences

country: Japan

institute: Nara Institute of Science and Technology

hyb_protocol: 600 ng of cRNAs were hybridized to an Arabidopsis Agilent custom microarrays at 65oC for 17 h, using Gene Expression Hybridization kit. After hybridization, the microarrays were washed with Gene Expression Wash Buffer 1 (Agilent) and Gene Expression Wash Buffer (Agilent), then dried immediately by brief centrifugation.

scan_protocol: The microarrays were scanned by Agilent DNA Microarray Scanner (G2539A ver.C).

data_processing:
When Agilent feature extraction software outputted raw data, the software omitted rows associated with spots where DNA proves were not spotted (8198 negative spots).
RMA normalization was performed for signals of microarray probes using limma package (Ritchie et al., 2015) on R (ver. 3.4.2) (R Core Team, 2013).

source_name: Col-0, whole plants, 15 µM zeocin, 2h

label_protocol: 200 ng of total RNA was used to prepare for Cy3-labeled cRNA, using Low Input Quick Amp Labeling Kit (Agilent).

growth_protocol: Arabidopsis plants were grown in liquid Murashige and Skoog (MS) medium [0.5 x MS salts, 0.5 g/l 2-(N-morpholino)ethanesulfonic acid (MES), 1% sucrose, and 1 x vitamin (pH 6.3)] with gentle shaking (70 rpm) under continuous light at 22 ˚C.

extract_protocol: Total RNA was extracted from two biological replicates with Plant Total RNA Mini Kit (FAVORGEN) according to the manufacturer’s instructions.

treatment_protocol: Two-week-old WT and sog1-1 plants were transferred to liquid MS medium with or without 15 µM zeocin and treated for 2 h.

value: whole plants

tag: genotype

value: WT

value: 15 µM zeocin


title: sog1-1_zeocin_2h_rep2

source_name: sog1-1, whole plants,15 µM zeocin, 2h


title: bric-16-cyt-flight-f-f3


title: WT_zeocin_2h_rep1


title: sog1-1_zeocin_2h_rep1


title: WT_mock_rep2

source_name: Col-0, whole plants, mock

value: mock


title: sog1-1_mock_rep1

source_name: sog1-1, whole plants, mock


title: embryo_Zic2 +/+_rep3

status: Public on Oct 31 2017

city: liverpool

first: Iain

middle: M

last: Dykes

state: Select...

address: James Parson Bl, Byrom Street,

department: Pharmacy & Biomolecular science

institute: Liverpool John Moores University

description:
WT3
Replicate 3

hyb_protocol: Standard Illumina hybridization protocol. MouseWG-6_V2_0_R0_11278593_A

scan_protocol: Standard Illumina protocol

data_processing:
Raw signal intensities were background corrected using array-specific measures of background intensity based on negative control probes
variance-stabilizing transformation and normalization with the ‘vsn’ package

source_name: E8.5 whole embryo_wild-type

label_protocol: Standard Illumina protocol

growth_protocol: Zic2 iso/+ parents were interbred and whole embryos harvested at embryonic day E8.0-E8.5. Approximately 25% of embryos were iso/iso and 25% +/+. Pools of 8 stage-matched embryos were used for each replicate.

extract_protocol: Embryos were snap-frozen in liquid nitrogen. RNA was prepared using the RNeasy Plus Micro kit (Qiagen) following the manufacturer's instructions. Quality control was performed using an Agilent Bioanalyzer.

tag: developmental stage

value: Whole embryo

value: wild-type


title: sog1-1_mock_rep2


title: embryo_Zic2 +/+_rep1

description:
WT1
Replicate 1


title: embryo_Zic2 iso/iso_rep2

description:
KO2
Replicate 2

source_name: E8.5 whole embryo_Zic2 iso/iso

value: mutant Zic2 iso/iso


title: embryo_Zic2 +/+_rep2

description:
WT2
Replicate 2


title: embryo_Zic2 iso/iso_rep3

description:
KO3
Replicate 3


title: embryo_Zic2 iso/iso_rep1

description:
KO1
Replicate 1


title: p53 KO immortal replicate 3

city: Clayton

first: Jason

last: Cain

address: 27-31 Wright St

country: Australia

institute: Hudson Institute of Medical Research

description:
replicate 3
SAMPLE 9

hyb_protocol: Standard Illumina hybrisation protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Non-normalized values exported from GenomeStudio - Normalised values processed with neqc function limma's (default paramenters, offset = 16)

source_name: 9703881019_D: p53KO immortal MEFs

label_protocol: standard Illumina protocol

growth_protocol: All cells were maintained in DMEM + 10%FCS prior to extraxction

extract_protocol: RNA and DNase I treatment was performed using the QIAGEN Rneasy Mini Kit Trizol reagent, in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.


title: WT_mock_rep1


title: Hic1 KO preimmortal replicate 1

description:
replicate 1
SAMPLE 8

source_name: 7911798045_C: Hic1KO preimmortal MEFs

growth_protocol: All cells were maintained in DMEM + 10%FCS prior to extraction


title: Hic1 KO preimmortal replicate 4

description:
replicate 4
SAMPLE 11

source_name: 7911798045_F: Hic1KO preimmortal MEFs


title: Control no TAM reanalysis replicate 4

description:
replicate 4
SAMPLE 3

source_name: 7911801036_D: Control MEFs


title: Hic1 KO preimmortal replicate 3

description:
replicate 3
SAMPLE 10

source_name: 7911798045_E: Hic1KO preimmortal MEFs


title: Hic1 KO immortal replicate 1

description:
replicate 1
SAMPLE 4

source_name: 9703559003_A: Hic1 KO immortal MEFs


title: Control no TAM replicate 4

description:
replicate 4
SAMPLE 3

source_name: 7911801036_D: Control preimmortal MEFs


title: p53 KO immortal replicate 1

description:
replicate 1
SAMPLE 7

source_name: 9703881019_B: p53KO immortal MEFs


title: Control no TAM reanalysis replicate 2

description:
replicate 2
SAMPLE 2

source_name: 7911801036_B: Control MEFs


title: Hic1 KO immortal replicate 2

description:
replicate 2
SAMPLE 5

source_name: 9703559003_C: Hic1 KO immortal MEFs


title: p53 KO immortal replicate 2

description:
replicate 2
SAMPLE 8

source_name: 9703881019_C: p53KO immortal MEFs


title: Control TAM replicate 4

description:
replicate 4
SAMPLE 7

source_name: 7911798045_B: Control preimmortal MEFs


title: Control TAM replicate 3

description:
replicate 3
SAMPLE 6

source_name: 7911798045_A: Control preimmortal MEFs


title: Control no TAM reanalysis replicate 1

description:
replicate 1
SAMPLE 1

source_name: 7911801036_A: Control MEFs


title: Hic1 KO immortal replicate 4

description:
replicate 4
SAMPLE 6

source_name: 9703881019_F: Hic1 KO immortal MEFs


title: Hic1 KO preimmortal replicate 2

description:
replicate 2
SAMPLE 9

source_name: 7911798045_D: Hic1KO preimmortal MEFs


title: Control TAM replicate 1

description:
replicate 1
SAMPLE 4

source_name: 7911801036_E: Control preimmortal MEFs


title: Control-rep2

city: Kyotanabe

first: Tsuyoshi

last: Waku

address: 1-3 Tatara Miyakodani

institute: Doshisha University

description: Gene expression data from DLD1 cells transfected with control siRNA

hyb_protocol: Following fragmentation, 2 ug of cDNA were hybridized for 17 hr at 45C on GeneChip Human Gene 1.0ST array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Expression console  (Build 1.4.1.46) using Affymetrix default analysis settings and RMA scaling as normalization method.

organism: Homo sapiens

label_protocol: Biotinated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Ambion WT expression kit and Gene Chip WT Terminal Labeling and Hybridization Kit Manual, Affymetrix).

growth_protocol: DLD-1 cells were cultured in DMEM supplemented with 10% FBS, 40 μg/ml streptomycin, and 40 units/ml penicillin.

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

treatment_protocol: DLD-1 cells were cultured for 16 hr in medium without antibiotics. The cells were then transfected with siRNA . At 48 hr after transfection, the cells were utilized for RNA extraction.

tag: cell line

value: Human colon adenocarcinoma Derived from human colorectal adenocarcinoma

tag: sirna

value: control siRNA


title: Control TAM replicate 2

description:
replicate 2
SAMPLE 5

source_name: 7911801036_F: Control preimmortal MEFs


title: Control no TAM replicate 2

description:
replicate 2
SAMPLE 2

source_name: 7911801036_B: Control preimmortal MEFs


title: NRF3KD-rep2

description: Gene expression data from DLD1 cells transfected with NRF3 siRNA

source_name: DLD1 cells transfected with NRF3 siRNA

value: NRF3 knockdown


title: Control no TAM replicate 1

description:
replicate 1
SAMPLE 1

source_name: 7911801036_A: Control preimmortal MEFs


title: NRF3KD-rep1


title: TLR7 WT - 3

first: Michael

middle: Paul

last: Gantier

state: VIC

address: Hudson Institute of Medical Research

department: Centre for Innate Immunity and Infectious Diseases

description:
SAMPLE 6
Mouse C57B/6

hyb_protocol: 600ng of Cy3 labeled cRNA (specific activity > 6 pmol Cy3/ug cRNA) was fragmented at 60C for 30 minutes in a reaction volume of 25ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion, 25 μl of 2x Agilent gene expression hybridisation buffer was added and 43 μl of sample hybridised for 17 hours at 67°C in a rotating Agilent hybridisation oven.

scan_protocol: After hybridisation, microarrays were sequentially washed 1 minute with room temperature GE wash buffer 1 (Agilent) and 1 minute with 37°C GE wash buffer 2 (Agilent). Slides were scanned on the Agilent C, DNA microarray scanner using one-color scan settings for 8x60k array slides. Scan area 61x21.6mm, scan resolution 3um, dye channel is set to Green and 20 bit Tiff.

data_processing:
The scanned images were analysed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1-1100_Jul11 and Grid: 028005_D_F_20120201) to obtain background subtracted and spatially detrended Processed Signal intensities.
The probes that were not “Detected” in any of the samples were removed. Log2 transformation and quantile normalization of the data were conducted. Array weights were computed using the “arrayWeights” function in the limma package. Correlated samples from 2 separate experiments were handled by random effect model through the R function “duplicateCorrelation” and were accommodated in the following linear model. We fitted the normalized data to a linear model using “lmFit”, while taking into account the array weights and batch sample correlation.

source_name: Primary bone marrow-derived macrophages from mouse 3 WT, infected 24 h with STM

label_protocol: Cy3 labelled cRNA was prepared from 0.1 μg total RNA using the One-Color Low input Quick Amp labelling Kit (Agilent, v6.6 September 2012), followed by RNeasy column purification (Qiagen). 600 ng of Cy3 labeled cRNA was fragmented at 60°C for 30 minutes in 1x Agilent fragmentation buffer and 2x Agilent blocking agent. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Femurs were flushed with DMEM complemented with 1x antibiotic/antimycotic and 10% fetal bovine serum (FBS) and cells were plated in complete DMEM supplemented with 20% L-929 cell-conditioned medium in T75 flasks for 6 days at 37°C (with one change of medium on day 3). Cells were collected on day 6 and plated overnight in 20% L-cell medium.

extract_protocol: Total RNA containing small RNAs was purified from BMMs using the ISOLATE II RNA Mini Kit (BIOLINE).

treatment_protocol: Thirty minutes before infection, cells were washed twice with pure DMEM and incubated for 30 minutes before addition of a suspension of 1x10^7 CFU/ml S. Typhimurium (MOI of 5). Infected cells were incubated for 45 minutes and rinsed with complete DMEM containing 100 μg/ml gentamicin for 10 minutes to remove extracellular bacteria. Cells were then incubated in complete DMEM containing 10 μg/ml gentamicin up to 24 h post infection.

tag: strain/background

value: Primary bone marrow-derived macrophages

value: Salmonella enterica serovar Typhimurium (STM) Infection

tag: time post infection

tag: experiment


title: TLR7 KO - 2

description:
SAMPLE 4
Mouse Congenic

source_name: Primary bone marrow-derived macrophages from mouse 2 KO, infected 24 h with STM

value: TLR7 KO


title: TLR7 KO - 4

description:
SAMPLE 7
Mouse Congenic

source_name: Primary bone marrow-derived macrophages from mouse 4 KO, infected 24 h with STM


title: TLR7 KO - 1

description:
SAMPLE 2
Mouse Congenic

source_name: Primary bone marrow-derived macrophages from mouse 1 KO, infected 24 h with STM


title: TLR7 KO - 3

description:
SAMPLE 5
Mouse Congenic

source_name: Primary bone marrow-derived macrophages from mouse 3 KO, infected 24 h with STM


title: TLR7 WT - 1

description:
SAMPLE 1
Mouse C57B/6

source_name: Primary bone marrow-derived macrophages from mouse 1 WT, infected 24 h with STM


title: TLR7 WT - 2

description:
SAMPLE 3
Mouse C57B/6

source_name: Primary bone marrow-derived macrophages from mouse 2 WT, infected 24 h with STM


title: A-type fibroblasts 2

city: Hamamatsu city

first: Toshihide

last: Iwashita

state: Shizuoka

address: 1-20-1 Handayama, Higashi-ku

department: Department of Regenerative and Infectious Pathology

institute: Hamamatsu University School of Medicine

description: Gene expression of A-type fibroblasts

hyb_protocol: Gene Expression Hybridization Kit (5188-5242) (Agilent) was used for hybridization. 1.4 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse Gene Expression 8X60K Microarray Kit (G4852) (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven (G2545A, G2530-60029) (Agilent).  After hybridization, Gene Expression Wash Buffer Kit (5188-5327) (Agilent) was used for washing of the slides. Microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2539A) (Agilent) and Scan Control (version A.8.5.1) (Agilent) using one color scan setting (Scan Area 61x21.6 mm, Scan resolution 3um, TIFF file dynamic range 20bit, Dye channel is set to Green and Green PMT is set to 100%, XDR ration No XDR).

data_processing: The scanned images were analyzed with Feature Extraction Software (version 10.10.1.1) (Agilent) using default parameters (Grit template 028005_D_F_20140728, FE protocol GE1_1010_Sep10, QC metric GE1_QCMT_Sep10) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: A-type fibroblasts

label_protocol: 10 ng RNA was amplified using Ovation PicoSL WTA System V2 (NuGen, San Carlos, CA, USA). Cyanine-3 (Cy3) labeled cDNA was prepared from 2.0 ug DNA using the Sure tag Complete DNA Labeling Kit (5190-4240) (Agilent) according to the manufacturer's instructions, followed by column purification.  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer (version 3.5.2) and Agilent 2100 Bioanalyzer (G2939A) (Agilent).

growth_protocol: Adult mouse lungs.

extract_protocol: Total RNA was extracted from two independently prepared samples of 50,000 A-, B-, and C-type fibroblasts and pulmonary single cells freshly isolated from adult (12–16-week-old) female C57BL/6 mice using RNeasy Mini Kit (Qiagen, Hilden, Germany). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Three fibroblast subpopulations and pulmonary single cells were freshly isolated from adult mouse lungs.

tag: age

value: 12-16 weeks

value: adult

tag: gender

value: female

value: lung

value: A-type fibroblasts


title: C-type fibroblasts 1

description: Gene expression of C-type fibroblasts

source_name: C-type fibroblasts

value: C-type fibroblasts


title: MSK1_KO-14

city: Columbus

first: Diego

middle: Fernando

last: Alzate Correa

state: OH

address: 333 W 10th Avenue

department: Neuroscience

institute: The Ohio State University

description: Invariant Set Normalization method derived from the dChip software; gene-level analysis

hyb_protocol: Biotinylated cRNA was hybridized with GeneChip 430A 2.0 Mouse Genome Array. Microarray hybridization and profiling was performed at The Ohio State University Microarray Core Facility.

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

data_processing: Raw data (cel files) were processed using dChip software (http://www.hsph.harvard.edu/cli/complab/dchip/) . Data were filtered to identify genes that were significantly altered by the deletion of MSK1.  Data were considered significantly altered if they were up- or down-regulated by at least 1.25-fold with a p-value less than 0.05.

source_name: MSK1 null Hippocampus

label_protocol: RNA was prepared for array profiling using the GeneChip one-cycle target labeling kit (Affymetrix) usign the manufacturer's protocol.

growth_protocol: Hippocampal tissue (bilateral) was collected from adult (6 week old) WT and MSK1-/- mice

extract_protocol: Total RNA was isolated using TRIZOL reagent (Invitrogen) using the manufacturer’s protocol. RNA quantity and quality was assayed using an Agilent 2100 Bioanalyzer (Agilent Technologies)

value: Hippocampus


title: MSK1_KO-15


title: B-type fibroblasts 2

description: Gene expression of B-type fibroblasts

source_name: B-type fibroblasts

value: B-type fibroblasts


title: Control-rep1

source_name: DLD1 cells transfected with control siRNA


title: B-type fibroblasts 1

description: Gene expression of B-type fibroblasts


title: WT-1

source_name: Wild type Hippocampus


title: Pulmonary single cells 1

description: Gene expression of Pulmonary single cells

source_name: Pulmonary single cells

value: Pulmonary single cells


title: MSK1_KO-9


title: WT-2


title: Pulmonary single cells 2


title: A-type fibroblasts 1

description: Gene expression of A-type fibroblasts


title: WT-7


title: 3286 Med LN 32hr

city: Silver Spring

first: Aarti

last: Gautam

state: MD

address: 503 Robert Grant Avenue

department: Medical Readiness Systems Biology

institute: WRAIR

description: Medistenial lymph node 32hr

hyb_protocol: cRNA was hybridized to a whole mouse genome microarray (Agilent Technologies) following manufacturer's instructions

scan_protocol: Scanned on a Agilent Technologies Scanner G2505C Images were quantified using Agilent Feature Extraction Software

data_processing: Agilent Feature Extraction Software (v 10.7) was used for background subtraction and GeneSpring v.10.1 (Agilent Technologies, Inc., CA) software was used to conduct the preliminary data filtration and statistical analysis. Filtered data available on Series record supplementary file.

organism: Chlorocebus aethiops

source_name: Medistenial lymph node 32hr post-infection

label_protocol: Total RNA (200-2000ng) was used as starting material, which was amplified using the Quick Amp Two-Color Kit (Agilent Technologies).The labelled cDNA was purified using an RNeasy Mini Kit (Qiagen, Hilden, Germany), and eluted, labelled cRNA was quantified using a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific Inc, Waltham, MA, USA).

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

value: Male

value: Lymph Nodes

organism:
Macaca fascicularis
Macaca mulatta

source_name: Monkey Universal RNA

value: several major organs


title: 5507 Med LN 42hr

description: Medistenial lymph node 42hr

source_name: Medistenial lymph node 42hr post-infection


title: 6472 Med LN 24hr

description: Medistenial lymph node 24hr

source_name: Medistenial lymph node 24hr post-infection


title: 6645 Med LN 24hr

description: Medistenial lymph node 24hr


title: C-type fibroblasts 2

description: Gene expression of C-type fibroblasts


title: 5096 Med LN 42hr

description: Medistenial lymph node 42hr


title: 6606 Med LN 32hr

description: Medistenial lymph node 32hr


title: 6528 Med LN 24hr

description: Medistenial lymph node 24hr


title: 6607 Med LN 12hr

description: Medistenial lymph node 12hr

source_name: Medistenial lymph node 12hr post-infection


title: 3274 Med LN 12hr

description: Medistenial lymph node 12hr


title: 6513 Med LN 42hr

description: Medistenial lymph node 42hr


title: I035 Med LN- control

description: Control-Medistenial lymph node

source_name: Medistenial lymph node 9hr post-infection


title: 6560 Med LN 12hr

description: Medistenial lymph node 12hr


title: 6606 lung 32hr

description: Lung 32hr

source_name: Lung 32hr post-infection

value: Lung


title: 5507-lung 42hr

description: Lung 42hr

source_name: Lung 42hr post-infection


title: 6513 lung 42hr

description: Lung 42hr


title: 6409 Med LN 9hr

description: Medistenial lymph node 9hr


title: T855 Med LN- control

description: Control-Medistenial lymph node


title: 6436 Med LN 9hr

description: Medistenial lymph node 9hr


title: 5021 Med LN 9hr

description: Medistenial lymph node 9hr


title: 6573 lung 32hr

description: Lung 32hr


title: 6645 lung 24hr

description: Lung 24hr

source_name: Lung 24hr post-infection


title: 6614 Med LN 12hr

description: Medistenial lymph node 12hr


title: 5096-lung 42hr

description: Lung 42hr


title: 3286-lung 32hr

description: Lung 32hr


title: 6472 lung 24hr

description: Lung 24hr


title: I079 Med LN- control

description: Control-Medistenial lymph node


title: 6560-lung 12hr

description: Lung 12hr

source_name: Lung 12hr post-infection


title: 6628 lung 24hr

description: Lung 24hr


title: 5096 Sub LN 42hr

description: Submandibular lymph node 42hr

source_name: Submandibular lymph node 42hr post-infection


title: 6528 lung 24hr

description: Lung 24hr


title: 3274-lung 12hr

description: Lung 12hr


title: IO35-lung- control

description: Control- Lung

source_name: Lung 9hr post-infection


title: 5021 lung 9hr

description: Lung 9hr


title: 6607-lung 12hr

description: Lung 12hr


title: 6436 lung 9hr

description: Lung 9hr


title: T855-lung- control

description: Control- Lung


title: 6614-lung 12hr

description: Lung 12hr


title: 6606 Sub LN 32hr

description: Submandibular lymph node 32hr

source_name: Submandibular lymph node 32hr post-infection


title: 6645 Sub LN 24hr

description: Submandibular lymph node 24hr

source_name: Submandibular lymph node 24hr post-infection


title: 3274 Sub LN 12hr

description: Submandibular lymph node 12hr

source_name: Submandibular lymph node 12hr post-infection


title: 6436 Sub LN 9hr

description: Submandibular lymph node 9hr

source_name: Submandibular lymph node 9hr post-infection


title: 3286 Sub LN 32hr

description: Submandibular lymph node 32hr


title: 6513 Sub LN 42hr

description: Submandibular lymph node 42hr


title: IO79-lung- control

description: Control- Lung


title: 6409 Sub LN 9hr

description: Submandibular lymph node 9hr


title: 14d_SN_1

city: Nantong

first: Lili

last: Zhao

address: 19 Qixiu

country: China

institute: Nantong university

description: miRNA expression in sciatic nerve at 14d after injury

hyb_protocol: The Cy3-labelled cRNA was first blocked with 10X×GE Blocking Agent following the manufacturers instructions. Total 45 ul system contain sample and 2×Hi-RPM Hybridization Buffer were add on to the Agilent  rat miRNA Microarray for 20 hours at 55°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent) and 5 minute with 37°C GE Wash buffer 2 (Agilent), then dried with bibulous paper for microarray scanning.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Agilent Feature Extraction (FE) software version 9.5.3 using default parameters ( miRNA-v1_95_May07) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Rattus norvegicus

source_name: proximal stumps of sciatic nerve, 14d after injury, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA  using the Agilent’s miRNA Complete Labeling and Hyb Kit (p/n 5190-0456) according to the manufacturer's recommendations.

extract_protocol: RNA was prepared using the mirVana™ RNA Isolation Kit (Applied Biosystem p/n AM1556) following the manufacturer's recommendations.

treatment_protocol: Crush model of sciatic nerve in rats was first carried out. Then the damage sections about 0.5mm of sciatic nerve were took out for RNA extract at 1d, 4d, 7d, 14d after crush successively. 0d present the normal sciatic nerve without crush.

value: injury site of sciatic nerve

value: male

tag: timepoint

value: 14d after injury


title: 14d_SN_3

source_name: proximal stumps of sciatic nerve, 14d after injury, replicate 3


title: 6409 lung 9hr

description: Lung 9hr

source_name: Monkey Universal RNA


title: 6528 Sub LN 24hr

description: Submandibular lymph node 24hr


title: 5507 Sub LN 42hr

description: Submandibular lymph node 42hr


title: 5021 Sub LN 9hr

description: Submandibular lymph node 9hr


title: 7d_SN_3

description: miRNA expression in sciatic nerve at 7d after injury

source_name: proximal stumps of sciatic nerve, 7d after injury, replicate 3

value: 7d after injury


title: GIC7, GPR56 knockout, rep 4

city: Barcelona

first: Nuria

last: de la Iglesia

address: Rossello 153

country: Spain

institute: IDIBAPS

description: gene expession of GPR56 knockout glioma initiating cells in serum-free neural stem cell medium

hyb_protocol: 1.5 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K Microarray (Agilent-072363) for 17 hours at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565C) using one color (Cy3) scan setting for expression array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (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. Data normalization was carried out using GeneSpring GX version 11.5 (Agilent Technologies).

source_name: glioma stem-like cell, GPR56 knockout (KO5)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Patient-derived GICs were cultured under adherent conditions on laminin in serum-free neural stem cell medium (in the presence of bFGF and EGF) at 37°C, 5% CO2 and 5% oxygen.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen). RNA was quantified using a NanoDrop-1000 spectrophotometer and RNA quality control was monitored in a 2100 Bioanalyzer (Agilent Technologies). In all cases, the RNA integrity number was >9.

treatment_protocol: Parental- and GPR56 knockout-GICs were obtained by CRISPR/Cas9-mediated gene editing followed by clonal selection. Clone #5 (KO5) was used for the microarray analysis.

value: GPR56 knockout (KO5)

tag: tumor type

value: Glioblastoma

value: glioma stem-like initiating cell


title: 6472 Sub LN 24hr

description: Submandibular lymph node 24hr

tag: tissue


title: 14d_SN_2

source_name: proximal stumps of sciatic nerve, 14d after injury, replicate 2

value: adult


title: 6573 Sub LN 32hr

description: Submandibular lymph node 32hr


title: GIC7, parental-control, rep 4

description: gene expession of parental-control glioma initiating cells in serum-free neural stem cell medium

source_name: glioma stem-like cell, parental-control

value: parental-control


title: T855 Sub LN  control

description: Control-Submandibular lymph node


title: GIC7, GPR56 knockout, rep 3


title: 7d_SN_1

source_name: proximal stumps of sciatic nerve, 7d after injury, replicate 1


title: 1d_SN_1

description: miRNA expression in sciatic nerve at 1d after injury

source_name: proximal stumps of sciatic nerve, 1d after injury, replicate 1

value: 1d after injury


title: 1d_SN_2

source_name: proximal stumps of sciatic nerve, 1d after injury, replicate 2


title: 4d_SN_2

description: miRNA expression in sciatic nerve at 4d after injury

source_name: proximal stumps of sciatic nerve, 4d after injury, replicate 2

value: 4d after injury


title: 7d_SN_2

source_name: proximal stumps of sciatic nerve, 7d after injury, replicate 2


title: 4d_SN_1

source_name: proximal stumps of sciatic nerve, 4d after injury, replicate 1


title: 4d_SN_3

source_name: proximal stumps of sciatic nerve, 4d after injury, replicate 3


title: 1d_SN_3

source_name: proximal stumps of sciatic nerve, 1d after injury, replicate 3


title: 0h_SN_1

description: miRNA expression in sciatic nerve at 0h after injury

source_name: proximal stumps of sciatic nerve, 0h after injury, replicate 1

value: 0h after injury


title: GIC7, parental-control, rep 3


title: 0h_SN_2

source_name: proximal stumps of sciatic nerve, 0h after injury, replicate 2


title: GIC7, GPR56 knockout, rep 1


title: 0h_SN_3

source_name: proximal stumps of sciatic nerve, 0h after injury, replicate 3


title: GIC7, parental-control, rep 2


title: JL17_44

city: Stockholm

first: Jurga

last: Laurencikiene

address: Hälsovägen 7

country: Sweden

institute: Karolinska Institutet

hyb_protocol: Fragmented cRNA were hybridized for 16 hr at 45C to Affymetrix Clariom D human arrays according to standard protocol. Washing and staing were performed using Affymetrix Fluidics Station 450.

scan_protocol: The arrays were scannned using an Affymetrix Gene Chip Scanner 3000.

data_processing: Generated CEL files were analyzed in Affymetrix Expression Console v. 1.4 using the SST-RMA method.

source_name: FACS sorted hWAT SVF

label_protocol: 10 ng of total RNA were amplified in 4 cycles to prepare biotinylated ss-cDNA according to the Affymetrix WT Pico protocol

growth_protocol: fresh samples

extract_protocol: collagenase purification of adipocytes and SVF has been described previously in

treatment_protocol: no treatments

value: Progenitor

tag: experimental group

value: overweight/obese


title: GIC7, GPR56 knockout, rep 2


title: JL32_87

source_name: Collagenase purified from hWAT

value: Mature adipocytes


title: I035 Sub LN  control

description: Control-Submandibular lymph node

source_name: Submandibular lymph node 9hr post-infection

value: Male

value: Lymph Nodes

source_name: Monkey Universal RNA

value: several major organs


title: I079 Sub LN  control

description: Control-Submandibular lymph node


title: JL22_56

value: Total T-cells


title: JL26_64

value: CD8+ T-cells


title: JL23_57

value: CD4+ T-cells


title: GIC7, parental-control, rep 1


title: JL31_86


title: JL18_45


title: 6560 Sub LN 12hr

description: Submandibular lymph node 12hr

source_name: Submandibular lymph node 12hr post-infection


title: JL29_78

value: M2 Macrophage


title: JL21_55


title: JL20_51

value: CD14+ Myeloid


title: JL14_33

value: lean


title: JL25_62


title: JL24_58


title: JL30_79


title: JL16_85


title: JL28_70

value: M1 Macrophage


title: JL27_69


title: JL15_84


title: JL19_48


title: JL13_32


title: JL12_29


title: 4°C_2

city: Vienna

first: Abhishek

last: Srivastava

address: Althanstrasse 14

country: Austria

institute: University of Vienna

hyb_protocol: 0.625 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Agilent P. necessarius 8x15K Microarrays (G48102) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by using Acetonitrile.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x15K array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software (version 10.5.1.1) (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 048102_D_F_20130312) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Polynucleobacter asymbioticus

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Quick Amp Labeling (Agilent) and the Full Spectrum Multistart Primer (BioCat GmbH, Heidelberg, Germany) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Hilden, Germany).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Polynucleobacter asymbioticus strain QLW-P1DMWA-1T was cultured in nutritionally rich liquid R2A media. Incubation was performed at 26ºC, in UV permeable polyethylene bags (~35% permeability). Rotation of the incubator was set at 200 rpm. Bacteria was allowed to grow until they reached an O.D. (260nm) of 0.1. Afterwards, they were subjected to three experimental treatments. Three treatments were (a). 26ºC, (b). 26ºC with UV irradiation, and (c). 4ºC incubation.

extract_protocol: Whole RNA extraction was performed with the NucleoSpin® RNA kit (Macherey-Nagel GmbH & Co. KG; Düren, Germany) according to the RNA isolation protocol provided by the company.

treatment_protocol: Once the bacterial samples reached OD = 0.1, they were subjected to three experimental scenarios. One batch continued rotating at 26ºC. Second batch was transferred to 4ºC incubator, set at 200 rpm. Third batch (already growing at 26ºC) was periodically treated with 30 min. of UV irradiation (two times a day). Entire experiment was run for three days. Cells were harvested after 72 hrs. (OD ~ 0.25) by treating with RNAlaterTM stabilization solution. Cell pellets were transferred to -80ºC freezer till whole RNA extraction.

tag: strain


title: 4°C_1

source_name: Polynucleobacter asymbioticus strain QLW-P1DMWA-1T


title: JL06_18


title: JL09_23


title: UV_1


title: JL11_28


title: JL08_20


title: JL10_26


title: UV_2


title: JL04_13


title: JL07_22


title: JL01_03


title: 26°C_3


title: JL02_04


title: 26°C_2


title: JL05_17


title: P12-130 Healthy individuals non-contactants of leprosy patients

city: Belo Horizonte

first: Alex

middle: FIORINI

last: Carvalho

state: MG

address: Avenida Antonio Carlos 6627

department: DMVP

country: Brazil

institute: UFMG

description: leprosy patients had never taken any specific leprosy treatment (MDT) or were under any other medication at the time of diagnosis and did not present other diseases

hyb_protocol: Labeled miRNAs were hybridized to the Agilent Human miRNA microarray (G4872A-031181 – 8  60K) GPL15018 using the G4851A SurePrint G3 Human GE 8x60k Microarray Kit (Agilent, Santa Clara, USA). Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent  Array slides were scanned immediately after washing on the Agilent DNA Microarray G2565BA scanner using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and R/G PMT is set to XDR.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0. (Agilent) using default parameters (miRNA_1010_Sep10 and Grid: 031181_D_F_20101116).

source_name: healthy individuals

label_protocol: The quantity and efficiency of the labeled Cy3 miRNA were determined with a NanoDrop™ ND-1000 (Thermo Scientific, Wilmington, Delaware, USA).

extract_protocol: Skin biopsy samples (stored in RNAlater) were individually fragmented using a 194 scalpel and transferred to a ceramic bead tube (CK28-Bertin Technologies). QIAzol 195 reagent (700 µL; Qiagen) was added and the samples were processed (homogenization 196 and lysis) in a Precellys 24 homogenizer (Bertin Technologies) with three cycles of 10-s 197 pulses, and further incubated at 4 °C for 5 min. Total RNA (including miRNA) was 198 extracted using the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s 199 instructions in a QIAcube apparatus (Qiagen). The RNA was recovered in 30 µL of 200 RNase-free water. RNA quantification was performed using a Nanodrop 2000 201 (ThermoScientific), and integrity was evaluated using a Bioanalyzer 2100 202 electrophoresis system (GE Healthcare Bio-Sciences). Samples with low quality or 203 insufficient RNA for analysis were excluded.

value: Skin biopsy

tag: disease state


title: P12-131 Healthy individuals non-contactants of leprosy patients


title: MT2645 Type 2 Reaction - R2

source_name: leprosy patients

value: Type 2 Reaction - R2


title: P12-132 Healthy individuals non-contactants of leprosy patients


title: O: MHL-3 vs. LLH-2

first: Isidoro

last: Metón

state: Barcelona

address: Joan XIII 27-31

department: Bioquímica i Fisiologia

institute: Universitat de Barcelona

hyb_protocol: For each labelled sample, 2.5 μg were hybridized to the oligo-microarray at 65 ºC for 17 h following Gene Expression Hybridization Kit instructions (Agilent Technologies).

scan_protocol: Scanning was performed using an Agilent Microarray Scanner G2565BA.

data_processing: Outlier spots and spot intensity were extracted with Agilent Feature Extraction software version 10.7. Loess and Aquantile normalization for within-and inter-array normalization, respectively, was applied using the R-Bioconductor package.

organism: Sparus aurata

source_name: Muscle from fish fed MHL

label_protocol: 200 ng of total RNA was labeled with Cy3 or Cy5 using Low Input Quick Amp Labeling Kit (Agilent Technologies).

extract_protocol: Total RNA was extracted from liver and white skeletal muscle using the RNeasy tissue and RNeasy fibrous tissue, respectively, mini kits (Qiagen).

treatment_protocol: Sparus aurata juveniles were maintained in 260 L aquaria in our research facilities at the University of Barcelona. Three groups of fish were fed at a ration of 25 g/kg body weight once a day (10 a.m.) for 23 days with diets HLL, MHL, and LLH. First, second and third letters indicate the levels (H: high; M: medium; L: low) of protein, lipids and carbohydrates, respectively. A fourth group of fish was starved during the same period of time.

value: Skeletal muscle

value: Juveniles

source_name: Muscle from fish fed LLH


title: JL03_12

tag: cell type


title: UV_3


title: P12-134 Healthy individuals non-contactants of leprosy patients


title: P12-127 Healthy individuals non-contactants of leprosy patients


title: 26°C_1


title: P12-140 Healthy individuals non-contactants of leprosy patients


title: M: Starved-3 vs. HLL-3

source_name: Muscle from starved fish

source_name: Muscle from fish fed HLL


title: P: LLH-3 vs. Starved-2


title: RO235 Lepromatous leprosy form - LL

value: Lepromatous leprosy form - LL


title: RO186 Lepromatous leprosy form - LL


title: K: Starved-1 vs. LLH-4


title: J: LLH-1 vs. MHL-4


title: P12-ENH Type 2 Reaction - R2


title: P12-136 Healthy individuals non-contactants of leprosy patients


title: RO234 Borderline Lepromatous leprosy form - BL


title: N: HLL-2 vs. MHL-2


title: BMSCs co-cultured with HCT116, biological rep 2

city: Beijing

first: XIN

last: FU

address: 33 Ba-Da-Chu Road

department: Research Center

institute: Plastic Surgery Hospital (Institute), Peking Union Medical College & Chinese Academy of Medical Sciences

description: Gene expression data from human BMSCs co-cultured with HCT116 for 5 days

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: Human BMSCs co-cultured with HCT116 for 5 days

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Human BMSCs were isolated from the iliac crest bone marrow of the patient following their bone defect reconstruction using gradient centrifugation with Ficoll-PaqueTM Plus solution. BMSCs were cultured in MSC Medium (ScienCell) and were incubated at 37°C in a humidified atmosphere containing 5% CO2.

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

treatment_protocol: The BMSCs at passage three (P3) were seeded on transwell chamber with density at 1´10E5/ transwell and cultured alone or co-cultured with HT29 or HCT116 at a ratio at 2:1 for 5 days in high glucose DMEM supplemented with 10% FBS

value: male


title: H: LLH-3 vs. Starved-3

source_name: Liver from fish fed LLH

value: Liver

source_name: Liver from starved fish


title: BMSCs co-cultured with HT29,  biological rep 3

description: Gene expression data from human BMSCs co-cultured with HT29 for 5 days

source_name: Human BMSCs co-cultured with HT29 for 5 days


title: 37B Type 1 Reaction - R1

description: reactional patients under specific leprosy treatment (MDT)

value: Type 1 Reaction - R1


title: BMSCs co-cultured with HCT116, biological rep 3


title: BMSCs co-cultured with HT29,  biological rep 2


title: BMSCs co-cultured with HCT116, biological rep 1


title: F: HLL-3 vs. MHL-3

source_name: Liver from fish fed HLL

source_name: Liver from fish fed MHL


title: L: HLL-4 vs. Starved-4


title: C2 Healthy individuals non-contactants of leprosy patients


title: I: MHL-1 vs. HLL-1


title: 41B Type 1 Reaction - R1


title: BMSCs cultured alone,  biological rep 3

description: Gene expression data from human BMSCs cultured alone for 5 days

source_name: Human BMSCs cultured alone for 5 days


title: C: Starved-4 vs. LLH-4


title: 5P Borderline Borderline leprosy form - BB

value: Borderline Borderline leprosy form - BB


title: BMSCs co-cultured with HT29,  biological rep 1


title: C1 Healthy individuals non-contactants of leprosy patients


title: BMSCs cultured alone,  biological rep 2


title: E: Starved-2 vs. HLL-2


title: B: LLH-1 vs. MHL-1


title: 17R Borderline Borderline leprosy form - BB


title: G: MHL-2 vs. LLH-2


title: RO178 Borderline Lepromatous leprosy form - BL


title: 29B Type 1 Reaction - R1


title: 13R Type 1 Reaction - R1


title: 6P Tuberculoid leprosy form - TT

value: Tuberculoid leprosy form - TT


title: BMSCs cultured alone,  biological rep 1


title: A: MHL-4 vs. HLL-4


title: D: HLL-1 vs. Starved-1


title: 31B Type 1 Reaction - R1


title: 101R Borderline Borderline leprosy form - BB


title: 3P Tuberculoid leprosy form - TT


title: 112R Tuberculoid leprosy form - TT


title: 13P Borderline-Tuberculoid leprosy form - BT


title: 98R Borderline Borderline leprosy form - BB


title: 44B Type 2 Reaction - R2


title: 19B Type 1 Reaction - R1


title: 11P Borderline-Tuberculoid leprosy form - BT


title: RO118 Borderline Lepromatous leprosy form - BL


title: 50R Type 1 Reaction - R1


title: 19P Type 1 Reaction - R1


title: 37R Tuberculoid leprosy form - TT


title: 115R Borderline-Tuberculoid leprosy form - BT


title: RO143 Borderline Lepromatous leprosy form - BL


title: 12P Borderline-Tuberculoid leprosy form - BT


title: 45B Type 1 Reaction - R1


title: 43B Type 2 Reaction - R2


title: 36B Type 2 Reaction - R2


title: 01R Borderline Borderline leprosy form - BB


title: 107R Borderline Borderline leprosy form - BB


title: 16P Borderline Lepromatous leprosy form - BL


title: 32B Type 1 Reaction - R1


title: 42B Borderline Borderline leprosy form - BB


title: 2B Type 2 Reaction - R2


title: 39R Borderline-Tuberculoid leprosy form - BT


title: 29R Tuberculoid leprosy form - TT


title: 17P Borderline Lepromatous leprosy form - BL


title: 59B Borderline-Tuberculoid leprosy form - BT


title: 52R Tuberculoid leprosy form - TT


title: 09R Borderline Borderline leprosy form - BB


title: 111R Lepromatous leprosy form - LL


title: 68B Type 2 Reaction - R2


title: 16B Tuberculoid leprosy form - TT


title: 47B Type 2 Reaction - R2


title: 40B Type 1 Reaction - R1


title: 14P Borderline Borderline leprosy form - BB


title: 56B Type 1 Reaction - R1


title: 15P Borderline Lepromatous leprosy form - BL


title: 33B Type 2 Reaction - R2


title: 10B Type 1 Reaction - R1


title: 97R Borderline Lepromatous leprosy form - BL


title: 123R Lepromatous leprosy form - LL


title: 41R Borderline-Tuberculoid leprosy form - BT


title: 99R Borderline Lepromatous leprosy form - BL


title: 12B Tuberculoid leprosy form - TT


title: 44R Borderline-Tuberculoid leprosy form - BT


title: 11B Type 2 Reaction - R2


title: 32R Type 1 Reaction - R1


title: 66B Borderline Lepromatous leprosy form - BL


title: 36R Tuberculoid leprosy form - TT


title: 94R Borderline Borderline leprosy form - BB


title: WT2-T24-BCG

status: Public on Oct 30 2017

city: Doha

first: Nico

last: Marr

address: OPC Al-Luqta Street

department: Systems Biology

country: Qatar

institute: Sidra Medical and Research Center

hyb_protocol: Following fragmentation, 3,6 ug of cDNA were hybridized for 17 hr at 45C on GeneChip HumanGene2.0ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GC3000 Scanner.

data_processing: Data were normalized using RMA.

source_name: PBMC

label_protocol: Biotinylated cDNA were prepared according to the standard Nugen Ovation PicoV2 protocol from 600 pg total RNA.

growth_protocol: PBMCs were used to seed culture plates at a density of 2x10^5 cells/well (96 well plate) and then cultured in RPMI + 10% SVF for 24h.

extract_protocol: RNA was extracted using the ZR RNA MicroPrepZymo kit (Zymo Research) according to the manufacturer's instructions

treatment_protocol: The cells were either left unstimulated or stimulated for 24 hours with BCG (MOI 20) or Tw (MOI 1)

tag: irf4 genotype

value: WT homozygous

tag: clinical phenotype

value: healthy

tag: tw serology results

value: Neg.

tag: tw culture results

value: Neg. (saliva and feces)

tag: relation to individuals with wd

value: related

tag: subject label

tag: group label

value: Wild Type

tag: time point

tag: treatment

value: BCG


title: 45R Tuberculoid leprosy form - TT

value: Skin biopsy


title: 114R Borderline-Tuberculoid leprosy form - BT


title: WT3-T24-TW

tag: age

value: Pos. (weak)

value: Tropheryma Whipplei


title: WT4-T24-TW


title: WT1-T24-TW


title: WT2-T24-TW


title: 8P Borderline-Tuberculoid leprosy form - BT


title: WT4-T24-BCG


title: WT4-T24-NS

value: Non-Stimulated


title: WT3-T24-NS


title: WT2-T24-NS


title: WT3-T24-BCG


title: P1-T24-BCG

value: heterozygous

tag: variant

value: WD

value: Pos.

value: Neg. (saliva and feces); Pos. (joint fluid)

value: Patient 1

value: Patient


title: WT1-T24-NS

value: WT homozygous


title: P2-T24-NS

value: Pos. (saliva and feces)

value: Patient 2


title: P3-T24-NS

value: Neg.

value: Pos. then Neg. (feces); Neg. (saliva)

value: Patient 3


title: P3-T24-TW

value: related


title: P3-T24-BCG

value: BCG


title: HET2-T24-TW

value: healthy

value: Pos. (feces); Neg. (saliva)

value: Heterozygous 2

value: Heterozygous


title: HET3-T24-BCG

value: heterozygous

value: Heterozygous 3


title: P2-T24-TW

value: WD

value: Pos. (weak)

value: Tropheryma Whipplei


title: HET3-T24-TW

value: Pos.


title: WT1-T24-BCG

value: WT homozygous

value: Neg. (saliva and feces)

value: Wild Type


title: P1-T24-NS

value: Neg. (saliva and feces); Pos. (joint fluid)

value: Patient 1

value: Patient

value: Non-Stimulated


title: HET2-T24-BCG

value: healthy

value: related

value: BCG


title: P2-T24-BCG

value: Pos. (saliva and feces)

value: Patient 2


title: P1-T24-TW

value: heterozygous


title: C2-T24-TW

value: unrelated

value: Control 2

value: Control


title: C1-T24-TW

value: Control 1

value: Tropheryma Whipplei


title: HET3-T24-NS

value: Pos.

value: Pos. (feces); Neg. (saliva)

value: Heterozygous 3

value: Heterozygous


title: C1-T24-BCG

value: WT homozygous


title: C2-T24-NS

value: Non-Stimulated


title: HET1-T24-BCG

value: healthy

value: Neg.

value: Heterozygous 1


title: C1-T24-NS


title: HET1-T24-TW

value: Pos. (saliva and feces)

value: related


title: HET2-T24-NS

value: heterozygous

value: Heterozygous 2


title: snf6 Grace+tet+FBS vs snf6 grace-tet+FBS (replica 3)

status: Public on Oct 28 2017

city: Québec

first: Faiza

last: Tebbji

address: 2705 Boulevard Laurier

country: Canada

institute: CHU Québec

description: Arrays are organized in 48 sub-arrays spotted with 6459 70-mer oligonucleotides.

hyb_protocol: The microarray slides were pre-hybridized for1 hours at 42°C with DIGeasy hybridization buffer (Roche) containing 0.5 ug/ul of yeast tRNA (Roche) and 0.5 ug/ul of salmon sperm DNA (Invitrogen) and subsequently washed with 0.1X SSC and air dried. The slides were then hybridized with labeled cDNAs overnight at 42°C in DIGeasy hybridization buffer with yeast tRNA and salmon sperm DNA. The slides were washed twice for 10 min at 42°C with 1× SSC, 0.1% SDS, twice for 10 min at 37°C with 0.1× SSC, 0.1% SDS, and finally, with quick consecutive washes in three 0.1× SSC baths. Slides were air-dried.

scan_protocol: Slides were scanned with a ScanArray 5000 scanner (Perkin Elmer) at 10-µm resolution.

data_processing: Expression array data were normalized as following : Signal intensity was quantified with QuantArray software (Perkin Elmer) and final Lowess normalization and inspection of the data was done with the GeneSpring package GX v.7.3 (Agilent Technologies).

organism: Candida albicans

source_name: Snf6 grace mutant - tet (YPD 37oC)

label_protocol: Indirect labeling with Cy3 and Cy5 was performed as described by Lavoie et al. BMC Genomics 2008, 9:578. The labeled DNA was purified with QIAquick PCR Purification Kit (Qiagen). For expression profiling experiment, 20 µg of total RNA was reverse transcribed using oligo(dT)21 in the presence of either Cy3-dCTP or Cy5-dCTP (Perkin-Elmer-Cetus/NEN) and Superscript III reverse transcriptase (Invitrogen). Thereafter, template RNA was degraded by adding 2.5 units of RNase H (USB) and 1 ug of RNase A (Pharmacia) followed by incubation for 15 min at 37°C. The labeled cDNAs were purified with QIAquick PCR Purification Kit (Qiagen).

extract_protocol: ChIP-chip experiment was performed as described by Lavoie et al. BMC Genomics 2008, 9:578. chromatin was sonicated to an average 300 bp, and 700 μl of whole-cell extract (WCE) were incubated with IgG-Sepharose 6 beads Fast Flow (GE Healthcare, catalog number 17-0969-01beads). RNAs were extracted as described by Sellam et al. (2009) Eukaryotic Cell 8 (8), 1174–1183, using RNeasy Mini kit (Qiagen).

treatment_protocol: For ChIP-chip analysis, an overnight cultures in YPD were diluted to OD600nm =0.2 and grown to OD600nm=2 in 40 ml YPD at 30oC. For gene expression profiling under yeast-promoting conditions, cells were collected directly from agar plates with or without doxycycline (40µg/ml) after growing for 48h at 30°C. For the hyphae form, cells were harvested from agar plate with 10 % FBS with or without doxycycline after 48h at 37°C. Harvested cells were rapidly frozen in liquid nitrogen and immediately processed for RNA extraction.

tag: strains

source_name: Snf6 grace mutant + tet (YPD 37oC)


title: snf6 Grace+tet+FBS vs snf6 grace-tet+FBS (replica 1)


title: snf6 Grace+tet+FBS vs snf6 grace-tet+FBS (replica 2)


title: C2-T24-BCG

value: unrelated

value: Control 2

value: BCG


title: HET1-T24-NS


title: GST for TBP IP, biological rep1

city: Illkirch Graffenstaden

first: Ivanka

last: Kamenova

state: Alsace

address: 1 Rue Laurent Fries

institute: IGBMC

description:
HeLa polysome RNA, cells treated with 100ug/ml cycloheximide for 15min before harvest
mock for TBP IP

hyb_protocol: Following fragmentation and end-labeling, 3 μg of cDNAs were hybridized for 16 hours at 45oC on GeneChip® Human Gene 2.0 ST arrays (Affymetrix). The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix).

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

data_processing: Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 4.1. CEL files were further processed with Affymetrix Expression Console software version 1.4.1 to calculate probe set signal intensities using Robust Multi-array Average (RMA) algorithms with default settings.

molecule: cytoplasmic RNA

source_name: mock for TBP IP

label_protocol: Biotinylated single strand cDNA targets were prepared, starting from 100 to 200 ng of total RNA, using the Ambion WT Expression Kit (Cat # 4411974) and the Affymetrix GeneChip® WT Terminal Labeling Kit (Cat # 900671) according to Affymetrix recommendations. Reference manuals: The Ambion® WT Expression Kit Protocol P/N 4425209 Rev.B 05/2009  GeneChip® WT Terminal Labeling and Hybridization User Manual, for use with Ambion WT Expression Kit, Affymetrix, P/N 702808 Rev.1

growth_protocol: adherent cells were grown on 15cm plates in DMEM 1g/L glucose supplemented with 5% FCS and 40ug/ul gentamycin until ~80-90% confluency in a humidified 5% CO2 incubator at 37deg Celsius

extract_protocol: Macherey-Nagel total RNA extraction kit was used according to manufacturer's instructions

treatment_protocol: cells were treated with 100ug/ml Cycloheximide for 15 min at 37deg before harvesting; plates were placed on ice, washed twice with cold PBS and scraped in 2ml lysis buffer (20 mM HEPES KOH pH 7.5, 150 mM KCl, 10 mM MgCl2 and 0.5% (vol/vol) NP-40) supplemented with protease inhibitors, 0.5mM DTT, 100 ug/ml cycloheximide, and 40 u/ml RNasin; cells were lysed with 10 strokes of a B-type dounce, clarified and either a fraction was saved as input (frozen in Macherey-Nagel Total RNA Lysis buffer RA1) or they were used for IP; after IP, beads were washed and eluted in Macherey-Nagel Total RNA Lysis buffer RA1

tag: cell line

value: HeLa WS


title: TBP IP, biological rep3

description:
HeLa polysome RNA, cells treated with 100ug/ml cycloheximide for 15min before harvest
TBP IP

source_name: TBP IP


title: Snf6 Grace+tet vs Snf6 grace-tet (replica 2)

source_name: Snf6 grace mutant - tet (YPD 30oC)

source_name: Snf6 grace mutant + tet (YPD 30oC)


title: TBP IP, biological rep1


title: GST IP for TAF10, biological rep3

description:
HeLa polysome RNA, cells treated with 100ug/ml cycloheximide for 15min before harvest
mock for TAF10 IP

source_name: mock for TAF10 IP


title: TAF10 IP, biological rep1

description:
HeLa polysome RNA, cells treated with 100ug/ml cycloheximide for 15min before harvest
TAF10 IP

source_name: TAF10 IP


title: GST IP for TAF10, biological rep2


title: GST for TBP IP, biological rep2


title: Snf6 Grace+tet vs Snf6 grace-tet (replica 1)


title: TBP IP, biological rep2


title: input for TBP, biological rep1

description:
HeLa polysome RNA, cells treated with 100ug/ml cycloheximide for 15min before harvest
input for TBP IP

source_name: input for TBP IP


title: input for TBP, biological rep2


title: input for TAF10, biological rep1

description:
HeLa polysome RNA, cells treated with 100ug/ml cycloheximide for 15min before harvest
input for TAF10 IP

source_name: input for TAF10 IP


title: input for TAF10, biological rep2


title: Genome-wide occupancy of Snf6p in hyphae condition [R2]

type: genomic

description: Starting from sequences from the C. albicans Genome Assembly 21, we extracted a continuous series of 242,860 60-bp oligonucleotides each overlapping by 1 bp. We then eliminated 2062 probes containing stretches of 13 or more A or T nucleotides. The remaining 240,798 sequences were then used to produce an antisense (Crick) whole genome tiling array using the Agilent Technologies eArray service (https://earray.chem.agilent.com/earray/).

data_processing: ChIP-Chip data was normalized as described by Lavoie et al. (2010) PLoS Biol 8(3): e1000329.

molecule: genomic DNA

source_name: WT under yeast conditions (YPD 37oC)- Input sample

source_name: Snf6p-TAP under yeast conditions (YPD 37oC)-ChIP sample


title: GST for TBP IP, biological rep3


title: TAF10 IP, biological rep2


title: input for TAF10, biological rep3


title: input for TBP, biological rep3


title: GST IP for TAF10, biological rep1


title: Genome-wide occupancy of Snf6p in hyphae condition [R1]


title: TAF10 IP, biological rep3


title: Genome-wide occupancy of Snf6p in yeast condition [R1]

source_name: WT under yeast conditions (YPD 30oC)- Input sample

source_name: Snf6p-TAP under yeast conditions (YPD 30oC)-ChIP sample


title: M127012016_WB_Input

status: Public on Oct 27 2017

type: SRA

city: Lausanne

last: Cortez

address: Rue de Lausanne

country: Switzerland

institute: Univerity of Lausanne - CIG

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8.
ChIP-Seq reads were aligned to the AnoCar2.0 genome assembly using BWA v0.7.15 with default parameters.
PCR duplicates and reads mapping to multiple genome positions were filtered out from the alignments.
In order to allow comparisons between different samples and across genomic features, the data were: i) normalized by library size; ii) all samples were input normalized by dividing the read counts of ChIPed samples by the read counts in the corresponding input over a window size of 50bp; these analyses were performed using the deepTools (v2.4.0).
Genome_build: AnoCar2.0
Supplementary_files_format_and_content: BigWig files were produced using deepTools v2.4.0.

organism: Anolis carolinensis

source_name: Brain, Male, Input

extract_protocol:
The DNA was purified using QIAquick PCR Purification columns (Qiagen) according to manufacturer’s instructions.
5 ng of input and ChIPed DNA were used to prepare sequencing libraries using NEBNext Ultra II Library Prep kit as described by the manufacturer (New England Biolab, E7645S).

tag: Sex

value: Male

tag: tissue

value: Brain

tag: developmental stage

value: Adult

tag: marker

value: Input

tag: chip antibody


title: M127012016_Lv1_Input

source_name: Liver, Male, Input

value: Liver


title: M11060514_WB_H4K16ac

source_name: Brain, Male, H4K16ac ChIP


title: F127012016_Lv2_Inp

source_name: Liver, Female, Input

value: Female


title: F127012016_WB_Input

source_name: Brain, Female, Input


title: F1040_WB_H4K16ac

source_name: Brain, Female, H4K16ac ChIP


title: F127012016_WB_H4K16ac


title: M127012016_Lv1_H4K16ac

source_name: Liver, Male, H4K16ac ChIP


title: M11060514_Lv_H4K16ac


title: F1040_Lv_H4K16ac

source_name: Liver, Female, H4K16ac ChIP


title: Genome-wide occupancy of Snf6p in yeast condition [R2]


title: ossified ligament flava tissuess, biological rep2

city: Tianjin

first: Kun

last: Zhang

address: Qixiangtai Road NO.22

department: Department of Histology and Embryology

institute: Tianjin medical university

description: Gene expression in human ossified ligament flava tissues

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images for raw data extraction, quantile normalization of raw data and subsequent data processing were performed using the R software limma package.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the One-Color Quick Amp Labeling Kit (Agilent p/n 5190-0442) according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen p/n 74104).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the TRIzol® Reagent (Invitrogen life technologies) following the manufacturer's recommendations. The concentrations of the RNA samples were determined by OD260 using a NanoDrop ND-1000 instrument. The integrity of RNA were assessed by electrophoresis on a denaturing agarose gel and Agilent 2100 Bioanalyzer.

treatment_protocol: Freshly ossified and normal ligament flavums tissues from patients during surgery were collected. The organizations were stored in a refrigerator at -80 ° C.

value: ossified ligament


title: chondrocyte-like cells (ChiPS), biological rep3

city: Poznan

first: Marcin

last: Rucinski

address: Swiecicki 6

department: Histology and Embriology

country: Poland

institute: Poznan University of Medical Science

description:
Gene expression data from chondrocyte-like cells (ChiPS)
taxonomic name: chondrocyte-like cells differentiated from hiPSCs; procedure obtaining: chondrogenic differentiation in vitro via monolayer culture; phenotypic or genetic characteristics: expression of genes and proteins chracteristic for chondrocytes; phenotypic and genetic stability: likelihood of dedifferentiation process

hyb_protocol: Biotin-labeled fragments of cDNA (5.5 μg) were hybridized by the Affymetrix Human Gene 2.1 ST ArrayStrip (20 h, 48°C).

scan_protocol: Microarrays were washed and stained according to the technical protocol, using AffymetrixGeneAtlasFuidics Station. The array strips were scanned employing Imaging Station of GeneAtlas System.

data_processing: Obtained CEL files were subjected for background correction and normalization using RobustMultiarrayAveraging (RMA) algorithm implemented in affy package of BioConductor.

source_name: hiPSCs differentiated towards chondrocytes

label_protocol: The entire procedure for preparing RNA for hybridization was performed using the GeneChip WT PLUS Reagent Kit (Affymetrix, Santa Clara, CA, USA). One-hundred ng of RNA was subjected to a two-step cDNA synthesis reaction using random primers extended by the T7 RNA polymerase promoter sequence. Synthesis of cRNA was performed using in vitro transcription (16 h, 40°C). cRNA was purified and re-transcribed into cDNA, which was biotin labeled and fragmented using the Affymetrix GeneChip WT Terminal Labeling and Hybridization kit (Affymetrix, Santa Clara, CA, USA).

growth_protocol: GPCCi001-A were cultured on mouse embryonic fibroblasts (MEFs) feeder layer in standard hiPSC growth medium containing the following: Dulbecco's modified Eagle's medium (DMEM) F12 with L-glutamine; 20% KnockOut Serum Replacement; 1% non-essential amino acid solution; 0.1 mM β-mercaptoethanol; and 0.5% penicillin-streptomycin. Prior to use, the medium was supplemented with fibroblast growth factor 2 (10 ng/ml). ChiPS were cultured Dulbecco's modified Eagle's medium (DMEM) F12 with L-glutamine; 10% FBS and  0.5% penicillin-streptomycin.

extract_protocol: Total RNA isolation was carried out using the modified Chomczynski method with TRI Reagent (Sigma, St Louis, MO, USA) and RNeasy Mini Elute cleanup Kit (Qiagen, Hilden, Germany), according to the manufacturer's guidelines. The concentration of the total RNA was determined spectrophotometrically by measuring absorbance at 260 nm. The purity of the isolated RNA was determined by using the 260/280 nm absorption ratio, which was > 1.8, as assumed. (NanoDrop spectrophotometer, Thermo Scientific, MA, USA). The quality and integrity of RNA was also checked in a Bioanalyzer 2100 (Agilent Technologies, Inc., Santa Clara, CA, USA). The resulting RNA integrity numbers (RINs) ranged from 8.5 to 10, with a mean of 9.2 (Agilent Technologies, Inc., Santa Clara, CA, USA).

treatment_protocol: GPCCi001-A were cultured for 1 week in a pro-mesodermal medium consisting of the following: DMEM F12 with L-Glutamine, 10% FBS supplemented with FGF-2 (10 ng/ml); BMP-4 (10 ng/ml); and PDGF-BB (10 ng/ml). Then, the medium was replaced with a standard chondrogenic medium  supplemented with TGF-β3 (10 ng/ml) for another week. After that, the medium was replaced with a chondrogenic medium supplemented with TGF-β3 (10 ng/ml) and IGF-1 (10 ng/ml)  for one final week of enhanced chondrogenesis in vitro. We used a standard chondrogenic medium, as follows: DMEM F12 with L-Glutamine; 10% FBS; 50 μM L-proline; 50 μM ascorbic acid; 1 mM sodium pyruvate; 1% ITS + Premix; 1% P/S and 10−7 M dexamethasone.

tag: cell type


title: ossified ligament flava tissuess, biological rep3

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G2530-60029) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

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

data_processing: The scanned images were analyzed with Feature Extraction (FE) Software (Agilent), check the Extraction Set Configuration, save the FE Project (.fep) by selecting File > Save As and browse for desired location, select Project > Start Extracting and export data to txt.

extract_protocol: RNA was prepared using the TRIzol® Reagent (Invitrogen life technologies) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer.


title: ossified ligament flava tissues, biological rep1


title: normal ligament flava tissues, biological rep4

description: Gene expression in human normal ligament flava tissues

value: normal ligament


title: chondrocyte-like cells (ChiPS), biological rep2

value: chondrocyte-like cells differentiated from hiPSCs


title: CEBPB_5mC_rep2

status: Public on Oct 26 2017

type: protein

city: Bethesda

first: Desiree

last: Tillo

address: 41 Center Dr, Room D310

institute: NIH/NCI

description: CEBPB PBM experiment, 5mC

hyb_protocol: The double-stranded arrays were blocked with 4% milk for 1 hour and washed with 0.1% Tween-20 in 1x PBS.  Freshly synthesized protein (25 µL) was mixed with 125 µL of protein binding reaction mixture consisting of 4% milk in 1x PBS, 50 ng of salmon testes DNA and 0.2 µg/µL bovine serum albumin and added to double-stranded array.  The protein binding reactions were carried out in hydration chamber for 1 hour followed by one wash with 0.5% Tween-20 in 1xPBS.  The protein bound array was incubated with Alexa Fluor 647 conjugated Anti-GST antibody for 1 hour, followed by three washes with 0.05 % Tween-20.  Finally array slides were washed and dried in 1x PBS and scanned using an Agilent Sure Scan II scanner.

scan_protocol: The array was imaged using an Agilent microarray scanner at 2 micron resolution. Images were scanned at two power settings: 100% photomultiplier tube (PMT) voltage (high), and 10% PMT (low). The two resulting grid images were then manually examined, and the scan with the fewest number of saturated spots was used. Image spot intensities were quantified using ImaGene software (BioDiscovery).

data_processing: For all possible 65,536 8-mers, a transformed 8-mer median intensity (Z-score) was calculated from the median signal intensity across array probes containing each 8-mer.  8-mer Z-scores of the modified strand (the reverse complement of the array probe sequence) were used for downstream analyses.

molecule: protein

source_name: CEBPB, HK design

label_protocol: 180 ng of plasmid containing DNA binding domains of Zta or CEBPB or cJun|cFos were used to express proteins using PureExpress in-vitro transcription translation kit (NEB) in 25 µL reaction volume as per manufacturer’s instructions.

extract_protocol: DNA binding domain (DBD) sequences along with 15 amino acid residues on either side of cJun or CEBPB were cloned as NcoI-SacI fragments into a T7-driven C-terminal GST expression vector (Sharrocks 1994, Gene:138, 105-108).  Zta was cloned into a modified pDEST15 MAGIC (N-terminal GST)  vector.  The DBD of cFOS was cloned into NdeI and HindIII sites in a pT5 expression plasmid.

treatment_protocol: The single-stranded oligonucleotide microarrays were double-stranded by primer extension as described in Badis et al. Science (2009).   Arrays were double-stranded using either cytosine, 5-methylcytosine (5mC, NEB) or 5-hydroxymethylcytosine (5hmC, Zymo Research). The resulting double-stranded DNA on the array thus contained probes with either cytosine on both strands or modified cytosine (5mC/5hmC) on one strand and cytosine on the second strand. This results in a hemi-methylated or hemi-hydroxymethylated state.

tag: dbd

value: BZIP

tag: protein

value: CEBPB

tag: double-stranding treatment


title: CEBPB_5hmC_rep2

description: CEBPB PBM experiment, 5hmC


title: CEBPB_5mC_rep4

description: CEBPB PBM experiment, 5mC


title: CEBPB_5mC_rep5

description: CEBPB PBM experiment, 5mC


title: CEBPB_5hmC_rep3

description: CEBPB PBM experiment, 5hmC


title: normal ligament flava tissues, biological rep3


title: human induced pluripotent stem cells (GPCCi001-A), biological rep1

description:
Gene expression data from human induced pluripotent stem cells (GPCCi001-A)
taxonomic name: human induced pluripotent stem cells; procedure obtaining: genetic modification with lentiviral policistronic vector coding  transcription factors: POU5F1, KLF4, SOX2 and C-myc; phenotypic or genetic characteristics: expression of transcription factors responsible for self-renewal and capacity to differentiate into derivatives of three primary germ layers; phenotypic and genetic stability: normal karyotype

source_name: hiPSC cell line reprogrammed from fibroblasts; cultured in feeder-dependent defined conditions

value: hiPSCs


title: human induced pluripotent stem cells (GPCCi001-A), biological rep3


title: human induced pluripotent stem cells (GPCCi001-A), biological rep2


title: CEBPB_5mC_rep3

description: CEBPB PBM experiment, 5mC


source_name: ossified ligament flava tissues, biological rep1


title: CEBPB_5mC_rep1

description: CEBPB PBM experiment, 5mC


title: normal ligament flava tissues, biological rep1


title: normal ligament flava tissues, biological rep2


title: CEBPB_5hmC_rep1

description: CEBPB PBM experiment, 5hmC


title: chondrocyte-like cells (ChiPS), biological rep1


title: ossified ligament flava tissuess, biological rep4


title: CEBPB_C_rep4

description: CEBPB PBM experiment, cytosine

value: cytosine


source_name: ossified ligament flava tissuess, biological rep3


title: CEBPB_C_rep5

description: CEBPB PBM experiment, cytosine


source_name: ossified ligament flava tissuess, biological rep4


source_name: normal ligament flava tissues, biological rep3


source_name: ossified ligament flava tissuess, biological rep2


source_name: normal ligament flava tissues, biological rep1


source_name: normal ligament flava tissues, biological rep2


title: CEBPB_C_rep1

description: CEBPB PBM experiment, cytosine


title: CEBPB_C_rep3

description: CEBPB PBM experiment, cytosine


source_name: normal ligament flava tissues, biological rep4


title: Zta_5hmC_rep4

description: Zta PBM experiment, 5hmC

organism: human gammaherpesvirus 4

source_name: Zta, HK design

value: Zta


title: cJun_cFos_5hmC

description: cJun|cFos PBM experiment, 5hmC

source_name: cJun|cFos, HK design

value: cJun|cFos


title: Zta_5hmC_rep3

description: Zta PBM experiment, 5hmC


title: cJun-cFos_5mC_rep2

description: cJun|cFos PBM experiment, 5mC


title: Zta_5mC_rep3

description: Zta PBM experiment, 5mC


title: Zta_5mC_rep2

description: Zta PBM experiment, 5mC


title: Zta_5hmC_rep2

description: Zta PBM experiment, 5hmC


title: Zta_5hmC_rep1

description: Zta PBM experiment, 5hmC


title: Zta_5mC_rep5

description: Zta PBM experiment, 5mC


title: Zta_5mC_rep4

description: Zta PBM experiment, 5mC


title: cJun-cFos_C

description: cJun|cFos PBM experiment, cytosine


title: cJun-cFos_5mC_rep1

description: cJun|cFos PBM experiment, 5mC


title: CEBPB_C_rep2

description: CEBPB PBM experiment, cytosine


title: Zta_C_rep5

description: Zta PBM experiment, cytosine


title: Zta_5mC_rep1

description: Zta PBM experiment, 5mC


title: Zta_C_rep4

description: Zta PBM experiment, cytosine


title: Zta_C_rep3

description: Zta PBM experiment, cytosine


title: Zta_C_rep1

description: Zta PBM experiment, cytosine


title: Zta_C_rep2

description: Zta PBM experiment, cytosine


title: CEBPB_5mCG_rep2

description: CEBPB  PBM  experiment, methylated

data_processing: For all 32,896 8-bp long DNA sequences (8-mers), a transformed median intensity (Z-score) was calculated from the median signal intensity across array probes containing each 8-mer.

label_protocol: 180 ng of plasmid containing DNA binding domains of Zta or CREB1 or CEBPB were used to express proteins using PureExpress in-vitro transcription translation kit (NEB) in 25 µL reaction volume as per manufacturer’s instructions.

extract_protocol: DNA binding domain (DBD) sequences along with 15 amino acid residues on either side of CREB1 or CEBPB were cloned as NcoI-SacI fragments into a T7-driven C-terminal GST expression vector (Sharrocks 1994, Gene:138, 105-108).  Zta was cloned into a modified pDEST15 MAGIC (N-terminal GST)  vector.

treatment_protocol: The double stranded arrays were either methylated (5mCG) or unmethylated (C). The methylation of the double stranded microarray were performed using 10 μl of M.SssI (New England Biolabs)in a total volume of 150μl at 37 °C for 3 hrs. The arrays were washed three times with PBS/0.5% Tween-20 and once with PBS.

tag: probe state

value: methylated


title: CEBPB_5mCG_rep3

description: CEBPB  PBM  experiment, methylated


title: CEBPB_5mCG_rep1

description: CEBPB  PBM  experiment, methylated


title: CREB1_5mCG

description: CREB1  PBM  experiment, methylated

source_name: CREB1, HK design


title: CEBPB_C_rep4

description: CEBPB  PBM  experiment, unmethylated

value: unmethylated


title: CEBPB_C_rep3

description: CEBPB  PBM  experiment, unmethylated


title: CEBPB_C_rep2

description: CEBPB  PBM  experiment, unmethylated


title: CEBPB_C_rep5

description: CEBPB  PBM  experiment, unmethylated


title: Zta_5mCG_rep1

description: Zta  PBM  experiment, methylated


title: CEBPB_C_rep1

description: CEBPB  PBM  experiment, unmethylated


title: Zta_C_rep5

description: Zta  PBM  experiment, unmethylated


title: Zta_C_rep4

description: Zta  PBM  experiment, unmethylated


title: Zta_C_rep2

description: Zta  PBM  experiment, unmethylated


title: Zta_C_rep3

description: Zta  PBM  experiment, unmethylated


title: Zta_5mCG_rep2

description: Zta  PBM  experiment, methylated


title: Zta_C_rep1

description: Zta  PBM  experiment, unmethylated


title: 2361 CNEO 15.5 5

city: Dallas

first: Thomas

middle: Joseph

last: Carroll

state: Texas

address: 5323 Harry Hines Blvd

department: Internal Medicine and Molecular Biology

institute: UTSW Med Ctr.

hyb_protocol: After fragmentation, 15ug cRNA was hybridilzed to the Affy GeneChip Mouse Genome 430 2.0 Array at 45 degrees for 15 hours by the UTSW Genomics and Microarray Core. 5 chips were stained with mutant cRNA and 5 with wildtype cRNA.

scan_protocol: Gene chips were washed and stained using the Affy microfluidics station. Chiips were scanned on the GeneArray Scanner or the GeneChip Scanner 3000.

data_processing: Data was analyzed using GeneSpring GX and the Gene Set Analysis Tool kite (Webgestalt). Genes showing a 2 fold change in expression were further analyzed.

source_name: E15.5 urogenital system

label_protocol: Biotinylated cRNA were prepared from 1ug total RNA from 1-2 UGS according to the Ambion  MessageAmp II-biotin Enhanced kie (#AM1791). cRNA synthesis was repeated for 5 distinct pools of RNA for wildtype and mutant.

extract_protocol: Trizol according to manufacturers instructions.

treatment_protocol: E15.5 UGS was dissected away from the embryo and samples were placed in Trizol

value: E15.5 urogenital system

tag: Stage

tag: genotype


title: 2361 WT 15.5 4


title: 2361 WT 15.5 2


title: 2361 CNEO 15.5 4.CHP


title: 2361 CNEO 15.5 1.CHP


title: Wnt 9b Wt E11.5 Mesenchyme

source_name: Isolated Metanephric mesenchyme from Wnt9b+/+ littermate

label_protocol: Biotinylated cRNA were prepared from 1ug total RNA from 25-30 isolated mesenchymes according to the Ambion  MessageAmp II-biotin Enhanced kie (#AM1791). cRNA synthesis was repeated for 5 distinct pools of RNA for wildtype and mutant.

treatment_protocol: E11.5 metanephroi were treated with trypsin/pancreatin and the metanephric mesenchyme was isolated away from the ureteric bud. RNA was extracted only from the mesenchyme.

value: Metanephric mesenchyme


title: Wnt 9b- - MM

source_name: Isolated Metanephric mesenchyme from Wnt9b mutant


title: 2361 CNEO 15.5 3.CHP


title: 2361 WT 2361 WT 15.5 1


title: Wnt 9b Wt E11.5 MM


title: Wnt9B ko MM


title: 2361 WT 15.5 5


title: Wnt9B wt MM


title: podocytes treated with thapsigargin + forskolin, biological rep2

city: Boston

first: Abbe

middle: Rose

last: Clark

state: Massachusetts

address: 4 Blackfan Circle, HIM 534

institute: Harvard, Brigham and Women's Hospital

description:
podocytes cultured in vitro
thapsi_forskolin_E2

hyb_protocol: As performed by UTSW core facility

scan_protocol: As performed by UTSW core facility

data_processing: Data were processed using ‘affy’ package in R. Background correction, normalization and expression calculation was performed with the rma function using default parameters.

source_name: podocytes cultured in vitro

label_protocol: As performed by UTSW core facility

growth_protocol: Podocytes were differentiated at 37 C for 11 days prior to treatment

extract_protocol: Total RNA extraction performed as in Sieber et al., 2013

treatment_protocol: 2.5µM thapsigargin in the presence or absence of 10µM forskolin for 16 hours

value: podocyte


title: Wnt9b Mutant E11.5 mesenchyme


title: 2361 WT 15.5 3


title: Wnt 9b Mutant E11.5MM_2


title: Wnt 9b Wt E11.5 MM2


title: podocytes treated with thapsigargin + forskolin, biological rep1

description:
podocytes cultured in vitro
thapsi_forskolin_E1


title: podocytes treated with thapsigargin + forskolin, biological rep3

description:
podocytes cultured in vitro
thapsi_forskolin_E3


title: podocytes treated with thapsigargin, biological rep2

description:
podocytes cultured in vitro
thapsi_D2


title: podocytes treated with thapsigargin, biological rep1

description:
podocytes cultured in vitro
thapsi_D1


title: Wnt 9b Mutant E11.5 MM2


title: podocytes treated with DMSO as control, biological rep1

description:
podocytes cultured in vitro
control_A1


title: 2361 CNEO 15.5 2.CHP


title: Wnt 9b Wild type MM

source_name: Isolated Metanephric mesenchyme from Isolated Metanephric mesenchyme from Wnt9b+/+ littermate


title: CRHR-Cre;AAV-flex (CA)CRHR 4

city: Houston

first: Benjamin

middle: R

last: Arenkiel

address: 1250 Moursund St, 11th floor, Ste 1150.01

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description: Gene expression in mouse olfactory bulbs with CRHR1+ olfactory granule cells expressing a Cre-dependent constitutively active variant of CRHR1.

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 600 ng Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 ¡C) to Agilent Whole Mouse Genome Oligo Microarrays 8x60K using Agilent's recommended hybridization chamber and oven. Finally, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37 °C) for 1 min.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent's Microarray Scanner System (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software v.9.1was used to read out and process the microarray image files. The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences.

source_name: Olfactory bulb

label_protocol: For the linear T7-based amplification step, 100 ng of each total RNA sample was used. To produce Cyanine-3 (Cy3)-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer's protocol. Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer (NanoDrop Technologies).

extract_protocol: Total bulb RNA was isolated by TRIzol reagent (Ambion, Invitrogen) according to manufacturer's protocol and treated with DNaseI (Promega).

treatment_protocol: The three animal groups in this experiment were CRHR1-/- mice injected with control AAV-flex-EGFP (CRHR1-/-;AAV-flex-EGFP = low CRH signaling group), CRHR1-Cre;AAV-flex-GFP (pseudo-wild type CRH signaling group), and CRHR1-Cre;AAV-flex-(CA)CRHR1 (high CRH signaling group) (n = 5 per group). All animals were males aged 6-8 weeks old. Animals were injected with 500 nL of virus (titer  5x10^10 particles/l) and sacrificed for total bulb RNA extraction 2 weeks post-injection.

tag: strain

value: 6-8 week old

tag: gender

value: Male

value: Olfactory bulb infected with AAV-FLEX-(CA)CRHR1


title: podocytes treated with thapsigargin, biological rep3

description:
podocytes cultured in vitro
thapsi_D3


title: CRHR1-/- KO;AAV-flex GFP 1

description: Gene expression in mouse olfactory bulbs with CRHR1 knocked out of mouse genome, including olfactory granule cells.

tag: age

value: Olfactory bulb infected with AAV-FLEX-GFP


title: CRHR-Cre;AAV-flex GFP 4

description: Gene expression in mouse olfactory bulbs with CRHR1+ olfactory granule cells expressing a control, Cre-dependent EGFP.


title: CRHR-Cre;AAV-flex (CA)CRHR 3


title: CRHR-Cre;AAV-flex GFP 5


title: CRHR-Cre;AAV-flex (CA)CRHR 5


title: podocytes treated with DMSO as control, biological rep2

description:
podocytes cultured in vitro
control_A2


title: CRHR-Cre;AAV-flex GFP 1


title: CRHR1-/- KO;AAV-flex GFP 3


title: CRHR-Cre;AAV-flex (CA)CRHR 2


title: CRHR-Cre;AAV-flex GFP 2


title: PCC6803_pVZ325-Ptacefe_rep1

city: Freiburg

first: Stephan

last: Klähn

state: Baden-Würtemberg

address: Schänzlestrasse 1

department: Institute of Biology III

country: Germany

institute: University of Freiburg

hyb_protocol: The labelled RNA was fragmented and hybridized as described by the manufacturer's instructions for Agilent one color microarrays with 1.65 µg of labeled RNA

scan_protocol: Arrays were scanned on the Agilent Technologies Scanner G2505B, using Agilent Feature Extraction Software 10.7.3.1 and the protocols GE1_107_Sep09  for Cy3 labelled arrays

data_processing: Raw data were processed with the R package Limma. After background correction the median signal intensity was cyclic loess normalized.

organism: Synechocystis sp. PCC 6803

source_name: cells from liquid culture grown 4h in presence of 1mM IPTG

label_protocol: The RNA was labeled directly, without cDNA synthesis in 2 µg aliquots with the Kreatech “ULS labeling kit for Agilent gene expression arrays” with Cy3 according to the manufacturers protocol.

growth_protocol: Wild-type and ethylene producing strains were grown in BG11 medium (Rippka et al., 1979; J Gen Microbiol 111: 1–61) in Erlenmeyer flasks and supplemented with 10 mM NaHCO3 and 10 mM N-tris(hydroxymethyl)methyl-2-aminoethanesulfonic acid (TES)-KOH at pH 8.0. For selection and maintenance of the ethylene producing strain streptomycin (10 μg ml-1) and gentamycin (5 μg ml-1) were added to the medium.

extract_protocol: Cells were lysed in 1 ml PGTX, with the following composition: 39.6% (w/v) phenol, 7% (v/v) glycerol, 7 mM 8-hydroxyquinoline, 20 mM EDTA, 97.5 mM sodium acetate, 0.8 M guanidine-thiocyanate, and 0.48 M guanidine hydrochloride (Pinto et al., 2009; BMC Mol Biol 10: 79). Phenol was extracted twice with chloroform:isoamyl alcohol (24:1) and RNA was precipitated with isopropanol at -20°C, followed by centrifugation at 4°C. The RNA pellet was washed with 70% ethanol and resuspended in RNase-free A. dest.

treatment_protocol: To induce EFE expression 1 mM IPTG was added to the cultures. RNA was extracted 4 h after treatment.

value: ethylene producing strain


title: PCC6803_pVZ325-Ptacefe_rep2


title: CRHR-Cre;AAV-flex (CA)CRHR 1


title: Pcan1H3

city: Göttingen

first: Victor

last: Chano

address: Buesgenweg 2

department: Forest Genetics and Forest Tree Breeding

institute: University of Göttingen

description: Pc6 CH2 (Cy3) vs Pc6 H2 (Cy5)

hyb_protocol: Probes were mixed and hybridized to a 60K custom microarray (Agilent Technologies) for 17 hours at 65ºC in Gex Hybridization Buffer HI-RPM in a hybridization oven. Arrays were washed according to the manufacturer’s instructions, dried by centrifugation.

scan_protocol: Arrays were scanned at 3 mm resolution on Agilent DNA Microarrays Scanner (G2565BA, Agilent Technologies) and the images were analyzed with Feature Extraction software (Agilent Technologies).

data_processing: For local background correction and normalization, the methods normexp and loess in LIMMA were used, respectively (Smyth and Speed 2003).

organism: Pinus canariensis

source_name: Traumatic xylem formed in wound margins

label_protocol: The Low Input Quick Amp Labeling Kit, Two-Color generates fluorescent cRNA (complimentary RNA) with 200 ng of total RNA  for two-color processing. The method uses T7 RNA Polymerase Blend (red cap), which simultaneously amplifies target material and incorporates Cyanine 3-CTP or Cyanine 5-CTP.

growth_protocol: Pines were grown in greenhouse, using 650 ml conical containers with 3:1 (v/v) peat:vermiculite. After the first year, trees were transferred to soil in experimental garden at UPM facilities, and grown under environmental conditions. At the moment of the beginning of this experiment, trees were 5 years old, approximately 2 m high and 7-10 cm diameter at the base.

extract_protocol: Total RNA was isolated from differentiating xylem samples stored at -80ºC, using the CTAB-LiCl precipitation method (Chang et al. 1993), and purified with the RNeasy Plant Mini Kit (Qiagen, CA, USA). Quantity of total RNA for each sample was measured with Nanodrop model ND-1000 (Thermo Scientific, MA, USA), and RNA quality was checked using the Experion Bioanalyzer (Bio-Rad, CA, USA).

value: Traumatic xylem

source_name: Cambial cells differentiating to xylem in remote parts of the plant

value: Xylem (control)


title: Pcan2H3

description: Pc14 CH2 (Cy5) vs Pc14 H2 (Cy3)


title: Pcan3H3

description: Pc5 CH2 (Cy5) vs Pc5 H2 (Cy3)


title: CRHR1-/- KO;AAV-flex GFP 4


title: PCC6803_Wildtype_rep1

value: WT


title: Pcan2H2

description: Pc15 CH1 (Cy5) vs Pc15 H1 (Cy3)


title: Pcan1H2

description: Pc4 CH1 (Cy3) vs Pc4 H1 (Cy5)


title: Pcan3H2

description: Pc2 CH1(Cy5) vs Pc2 H1 (Cy3)


title: CRHR1-/- KO;AAV-flex GFP 2


title: Pcan2H1

description: Pc3 CH0 (Cy5) vs Pc3 H0 (Cy3)


title: PCC6803_Wildtype_rep2