title: Pleural_LTH_24hr_G9_rep8

city: River Forest

first: Robert

middle: J

last: Calin-Jageman

state: IL

address: 7900 West Division

department: Psychology

institute: Dominican University

description:
Group 9: S767, C762
US83800207_254938410007_S01_GE2_1105_Oct12_2_4

hyb_protocol: Samples were hybridized to the microarray slide at 65C and 10rpm for 17 hours.  All labeling and post-labeling processing was carried out in an ozone regulated environment, monitored at < 5ppb.

scan_protocol: Slides were scanned on an Agilent C scanner at 3um resolution.  Data was extracted using Agilent Feature Extraction software, v. 11.5.

data_processing: Microarray data was analyzed using limma  (G. Smyth, 2005) from the Bioconductor suite of tools (Gentleman et al., 2004) for R (Team, 2013).  Our processing script is posted on the Open Science Framework.   Median expression values were analyzed (Zahurak et al., 2007).  These were corrected for background using the normexp+offset algorithm recommended for Agilent microarrays by Ritchie et al. (2007).  An offset of 30 was selected based on inspection of MAPlots and based on maximizing correlations with qPCR measurements from the same material (a set of measurements for 10 transcripts).  Expression was normalized within each array using the loess function (G. K. Smyth & Speed, 2003).  Where multiple probes were used to measure the same EST or mRNA, these were then averaged.  Finally, trained and untrained expression were compared using an empirical Bayes-moderated t-test (G. K. Smyth, 2004).  Statistical significance was calculated using Benjamini-Hochberg correction for multiple comparisons to maintain a 5% overall false-discovery rate (Benjamini & Hochberg, 1995).  Rather than test for significant regulation and then use a fold-change threshold to evaluate practical significance, we used the treat function from limma (McCarthy & Smyth, 2009) to test not only against a null hypotheses of no change (Ho: |Mean Fold Change| > 1) but also changes of 1.1, 1.25, and 1.5 fold (e.g. Ho: |Mean Fold Change| > 1.5).

organism: Aplysia californica

source_name: trained

label_protocol: A two-color approach was used with each array hybridized to a trained (Cy5) or untrained (Cy3) sample.  Sample integrity was determined by Bioanalyzer RNA 6000, Pico total RNA protocol.  300ng of total RNA was amplified and labeled with Cy3 or Cy5 using the Agilent Quick Amp Two-Color Labeling Kit. Dye incorporation and yield was determined by Nanodrop.

growth_protocol: Animals (75-125g) were obtained from the RSMAS National Resource for Aplysia (Miami, FL) and maintained at 16o C in one of two 90-gallon aquariums with continuously circulating artificial sea water (Instant Ocean, Aquarium Systems Inc.).  Animals were separately housed in rectangular colanders (11.5cm wide, 16.5cm long, 7.3cm deep), fed dried seaweed twice a week, and maintained on a 12 hr light-dark cycle.  2 days prior to any experimental testing, animals were fed to satiation and then food deprived for the remained of the experiment (Levenson, Byrne, & Eskin, 1999; Wainwright, Zhang, Byrne, & Cleary, 2002).  To control for batch/shipment effects, animals from at least 2 different shipments were used for each experiment.

extract_protocol: Animals were harvested 24 hours after training.   To analyze transcription, pleural ganglia RNA was isolated.  These ganglia were selected because they contain the cell bodies of the VC nociceptors (Illich & Walters, 1997; Walters, Byrne, Carew, & Kandel, 1983) which produce both IPSPs and action potentials to the brush stimulus used to train animals.  Briefly, animals were anesthetized with an injection of isotonic MgCl2 (50% of body weight), and an incision was then made along the ventral midline to expose the CNS.  As dissection can alter gene expression (Alberini et al., 1994) cit_af ref_bf(Alberini, C. M. 1994 ref_num764)ref_af, we extracted ganglia rapidly (< 5 minutes per animal) and transferred them immediately to RNAlater (Ambion, Austin, TX)on ice.  Tissue was homogenized and RNA extracted using Trizol (Invitrogen, Carlsbad CA) and Direct-Zol Mini RNA Kit (Zymo, Irvine, CA). Samples were homogenized using the Bullet Blender (NextAdvance, Averill Park, NY). Quantity and quality of RNA was assessed using the NanoDrop 1000 (Thermo Scientific, Wilmington, DE).  RNA was reverse transcribed using oligo(dT) primes and RevertAid First Strand cDNA Synthesis Kit (Fermentas, Glen Burnie MD).

treatment_protocol: Based on pilot testing we developed a standard “spaced” habituation protocol consisting of 10 sessions of brushing a day, with each session consisting of 15 minutes of stimulation at a 10s ISI followed by a 15 minute rest (Figure 2A).  Thus, each day’s training lasted 285 minutes and contained 900 back-then-forth brush stimuli.  We applied this training protocol for 3 or 4 consecutive days.  This protocol involves significantly more stimulation than in previous studies of long-term habituation in Aplysia (e.g. 20 stimuli for each of 5 days; Castellucci et al. 1978).  The intention for our procedure, however, was to produce the strongest and most reliable behavioral impact possible.    Massed training consisted of a single session lasting 285 minutes at an ISI of 6.33s with no rest periods (Figure 3A).  This yielded 2,700 stimulations in a single session, the same cumulative number of stimuli delivered over 3 days of spaced training, but compressed into the same amount of time required for one day’s spaced training.  This massed protocol confounds changes in ISI (10s vs. 6.33s) with pattern of training (breaks vs. no breaks).  The goal, however, was to provide a no-memory control exposed to the same total amount of stimulation.  Control animals were placed in a holding rack but without a brushing apparatus.  Thus, they experienced the same colander handling and the same exposure to the surface of the tank as trained animals.    To monitor the effectiveness of LTH training, siphon-, tail-, and head-elicited SWR responses were measured before (pre-test) and after the end of training (1, 2, or 7 days).  To monitor the progress in acquiring LTH, the siphon-elicited SWR was also measured 1 hour before and 1 hour after each training session.  Measurements taken 1 hour after training provide a measure of short-term retention (labeled ST in figures).  Measures taken 1 hour before training provide a measure of long-term retention from the previous day’s training (approximately 14 hours from the end of the prior day’s training; labeled LT in figures).  Once all training was completed, long-term measures were timed to be precisely 24h, 48h, or 7 days from the end of training.    To maintain blinding, different researchers were responsible for SWR measurement and training.    Protocols (including SWR measures before and after training) were always begun early in the light cycle of the animals (within 2 hours of light onset).  Based on pilot testing we developed a standard “spaced” habituation protocol consisting of 10 sessions of brushing a day, with each session consisting of 15 minutes of stimulation at a 10s ISI followed by a 15 minute rest (Figure 2A).  Thus, each day’s training lasted 285 minutes and contained 900 back-then-forth brush stimuli.  We applied this training protocol for 3 or 4 consecutive days.  This protocol involves significantly more stimulation than in previous studies of long-term habituation in Aplysia (e.g. 20 stimuli for each of 5 days; Castellucci et al. 1978).  The intention for our procedure, however, was to produce the strongest and most reliable behavioral impact possible.    Control animals were placed in a holding rack but without a brushing apparatus.  Thus, they experienced the same colander handling and the same exposure to the surface of the tank as trained animals.    To monitor the effectiveness of LTH training, siphon-, tail-, and head-elicited SWR responses were measured before (pre-test) and after the end of training (24 hours post).  To monitor the progress in acquiring LTH, the siphon-elicited SWR was also measured 1 hour after the first training session.    To maintain blinding, different researchers were responsible for SWR measurement and training.    Protocols (including SWR measures before and after training) were always begun early in the light cycle of the animals (within 2 hours of light onset).

value: pleural ganglia

source_name: control


title: Pleural_LTH_24hr_G6_rep5

status: Public on Jul 16 2014

type: RNA

country: USA

description:
Group 6: S788, C789
US83800207_254938410007_S01_GE2_1105_Oct12_2_1

molecule: total RNA

tag: tissue


title: 0N_CTL_Cy5_vs_24hN_EXP_Cy3

city: Fayetteville

first: Nilda

last: Burgos

address: 1366 W Altheimer Dr

institute: University of Arkansas

hyb_protocol: The 60-mer oligonucleotide rice microarray manufactured by the University of California-Davis-NSF Rice Oligonucleotide Array Project contained 43,312 oligos corresponding to 44,974 TIGR V3 rice gene models (Jung et al. 2008). Microarray slides were hybridized for 14 h in humidified chambers maintained at 42°C. Hybridization for each treatment comparison was performed twice. After hybridization, slides were washed twice with 2x SSC + 0.1% SDS for 10 min, twice with 0.1x SSC + 0.1% SDS for 10 min, and twice with 0.1x SSC for 10 min.

scan_protocol: Slides were scanned with a GenePix Pro 4200 scanner (Axon Instruments, Union City, CA) which measured fluorescence of each spot at two separate laser channels for 532 nm (Cy3) and 635 nm (Cy5) emissions.

data_processing:
Image analysis and signal quantification were performed using GenePix Pro 5.1 (Axon Instruments, Union City, CA) scanner, which measured transcript regulation as intensities of green and red fluorescent dyes for each spot. Background subtraction intensity (BSI) of each dye in each spot was used in subsequent analysis. Quality control to eliminate bad features/spots was done in two stages: at probe and gene level. At probe level, weak signals were detected and flagged -2; and large background intensities were flagged -3 after detecting features with foreground/mean background<1. At gene level, poorly hybridized features with median background-adjusted spot signal <50 were flagged -5 and excluded.
After low-quality features were excluded, 7,287 features remained and were normalized within arrays. Log ratios were transformed to fold-change values. Up- or down regulation was defined as a fold-increase or decrease in N deficiency stress relative to control (0N versus full N) or N stress recovery relative to N deficiency (24- or 48-h N supplementation versus 0 N).   Features detected at two out of three treatment comparisons, numbering 2,367 in all, were combined in a Microsoft Excel spreadsheet. Gene annotation was updated with gene ontology (GO) terms and pathway assignments as queried from the Gramene and RiceCyc databases (http://pathway.gramene.org/RICE/class-tree?object=Pathways). These annotated genes were used in subsequent analyses.

organism: Oryza sativa

source_name: Leaf tissue, from plants grown in 0 N

label_protocol: Four independent biological replicates were performed for three treatment comparisons: T1(control) versus T2 (stress treatment) = Condition I; T2 (control) versus T3  (early recovery treatment) = Condition II; T2 (control) versus T4   (late recovery treatment) = Condition III. Equal amounts of total RNA (20 μg) from control and treatment tissues of Stf-3 rice were amplified using the MessageAmpTM II antisense RNA (aRNA) amplification kit (Ambion, Austin, TX) and labeled with Cy3 (treatment sample) and Cy5 (control sample) dyes using the CyScribe post-cDNA synthesis labeling kit (Amersham-GE Healthcare, Piscataway, NJ) following manufacturer protocols. Labelled aRNA from control and treatment samples for each treatment comparison (Condition I, II, or III) were mixed and applied onto a microarray slide.

growth_protocol: Weedy red rice (WRR) accession Stf-3 was grown in aerated nutrient solution in a greenhouse set to a day:night length of 14:10 h. Stf-3 is a strawhull weedy red rice representative of the most prevalent ecotype in the state. Nutrient solution pH, temperature and relative humidity were monitored daily.

extract_protocol: Total RNA was isolated from the youngest fully expanded leaves of both Stf-3 and Wells, using TRIzol (Invitrogen, Grand Island, NY) following the manufacturer’s protocol.

treatment_protocol: Plants were subjected to four treatments: T1 – Full N; T2 – NH4NO3starvation until NSI <95%; T3 - 24-h NH4NO3 readdition post-starvation; and T4 – 48-h NH4NO3 readdition post-starvation.

value: leaf tissue

tag: treatment

value: 0 N

source_name: Leaf tissue, from plants grown in 24-h N supplementation

value: 24-h N supplementation


title: Patient 3 BC

type: protein

city: Daejeon

first: Myung-Shin

last: Lee

address: Yongdu-dong, Jung-gu

department: Microbiology and Immunology

country: South Korea

institute: Eulji University School of Medicine

description: 3pairs of BC/normal mucosa were analyzed by antibody arrary with 656 antibodies

hyb_protocol: Biotin labeled extract was hybridized with antibody-spotted slide for 2hr at room temperature. After hybridization, slide was washed with 1X wash buffer (Fullmoon Bio) and de-ionized water. Detection Buffer including Cy3-Streptavidin (fullmoon Bio) was treated for 20min at room temperature. And slide was washed with 1X wash buffer (Fullmoon Bio) and de-ionized water.

scan_protocol: Scanned on an Axon 4000B scanner.

data_processing: GenePix Software (v 6.1) was used for data extraction and Genowiz software (v 4.0.5.6) was used for global normalization.

label: biotin

molecule: protein

organism: Homo sapiens

source_name: primary bladder cancer

label_protocol: 50ug of Tissue extract was labeled with Biotin and label buffer (Fullmoon Bio).

extract_protocol: 10~40mg of tissues were washed with cold 1X PBS. And tissue samples were homogenized with Extracting buffer (Fullmoon Bio). Debris was removed from tissue extract with centrifuge.

treatment_protocol: Primary high grade non-muscle invasive bladder cancer tissues were obtained from TURBT. Adjacent normal mucosa tissues were used as controls

tag: gender

value: Male

value: bladder

tag: cell type

value: bladder cancer


title: Pleural_LTH_24hr_G8_rep7

description:
Group 8: S779, C780
US83800207_254938410007_S01_GE2_1105_Oct12_2_3


title: 0N_CTL_Cy5_vs_48hN_EXP_Cy3

source_name: Leaf tissue, from plants grown in 48-h N supplementation

value: 48-h N supplementation


title: Pleural_LTH_24hr_G7_rep6

description:
Group 7: C769, S768
US83800207_254938410007_S01_GE2_1105_Oct12_2_2


title: Pleural_LTH_24hr_G3_rep3

description:
Group 3: C796, S777
US83800207_254938410007_S01_GE2_1105_Oct12_1_3


title: KBD PBMCs Replicate 13

city: Xi'an

first: Xi

last: Wang

address: No.76 Yanta West Road

country: China

institute: Xi‘an Jiaotong University Health Science Center

description: Biological replicate 13 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.

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

scan_protocol: The microarray slides were scanned using Gene-Pix 4000B (Axon Instruments Inc., Foster City, California, USA), which used a 532nm laser for Cy3 measurement and a 635nm laser for Cy5 measurement.

data_processing: Sixteen-bit TIFF images produced by the Axon scanner were analyzed using the GenePixPro 3.0 software package (Axon Instruments Inc.). Data were normalized using the Global normalization method.

source_name: KBD PBMCs

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-labe

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

value: peripheral blood mononuclear cells (PBMCs)

tag: age

tag: Sex

value: Female

tag: Stage

value: Ⅱ


title: KBD PBMCs Replicate 12

description: Biological replicate 15 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: Pleural_LTH_24hr_G5_rep4

description:
Group 5: C770, S773
US83800207_254938410007_S01_GE2_1105_Oct12_1_4


title: KBD PBMCs Replicate 7

description: Biological replicate 7 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.

value: Ⅰ


title: KBD PBMCs Replicate 6

description: Biological replicate 6 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: Pleural_LTH_24hr_G2_rep2

description:
Group 2: S785, C787
US83800207_254938410007_S01_GE2_1105_Oct12_1_2


title: KBD PBMCs Replicate 10

description: Biological replicate 10 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 9

description: Biological replicate 9 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 8

description: Biological replicate 8 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 5

description: Biological replicate 5 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 3

description: Biological replicate 3 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 2

description: Biological replicate 2 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 11

description: Biological replicate 11 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: FullN_CTL_Cy5_vs_0N_EXP_Cy3

source_name: Leaf tissue, from plants grown in full N

value: full N


title: KBD PBMCs Replicate 1

description: Biological replicate 1 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: 12814

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: Strain: Sarcophaga crassipalpis Maquart

hyb_protocol: A mixture of purified and labeled cRNA (Cy3 label: 300ng; Cy5 label: 300ng) was hybridised on the custom Agilent array followed by (manual) washing, according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, arrays were scanned using the Agilent DNA MicroArray Scanner with surescan High-Resolution Technology and probe signals were quantified using Agilent’s Feature Extraction software (version 10.7.3.1).

data_processing: The dataset contains the Agilent processed signal values (i.e., feature rProcessedSignal/gProcessedSignal from Agilent Feature Extraction v 10.7.3.1). Base 2 log-transformed log-ratios (Cy5/Cy3) were averaged over the replicate probes.

organism: Sarcophaga crassipalpis

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with 10 viral polyA transcript controls (Agilent) was converted to double stranded cDNA in a reverse transcription reaction. Subsequently the sample was converted to antisense cRNA, amplified and labeled with Cyanine 5-CTP (Cy5) in an in vitro transcription reaction according to the manufacturer’s protocol (Agilent).

extract_protocol: RNA was extracted using the RNeasy Lipid Tissue Mini Kit (Qiagen). Due to the hard puparium, the Tissue Rupter was used after adding one stainless steel bead (5mm mean diameter) and ¼ of a PCR tube of zirconia/silica beads to one individual pupa. An on-column DNase I treatment with the RNase-free DNase set (Qiagen) was performed. RNA was eluted twice – first with 30 µl RNase free water, then with 20 µl RNase free water – and stored at -80°C.

value: 5 days old pupae

tag: condition

value: Control

tag: replicate

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with 10 viral polyA transcript controls (Agilent) was converted to double stranded cDNA in a reverse transcription reaction. Subsequently the sample was converted to antisense cRNA, amplified and labeled with Cyanine 3-CTP (Cy3) in an in vitro transcription reaction according to the manufacturer’s protocol (Agilent).


title: KBD PBMCs Replicate 4

description: Biological replicate 4 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: 12815

description: Strain: Sarcophaga crassipalpis Maquart

value: 25 hours after parasitization by Nasonia vitripennis


title: 12809

description: Strain: Sarcophaga crassipalpis Maquart

value: 3 hours after parasitization by Nasonia vitripennis


title: Control PBMCs Replicate 99

description: Biological replicate 99 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.

source_name: Control  PBMCs

value: Healthy


title: Control PBMCs Replicate 100

description: Biological replicate 100 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Pleural_LTH_24hr_G1_rep1

description:
Group1: C778, S789
US83800207_254938410007_S01_GE2_1105_Oct12_1_1

value: pleural ganglia


title: 12808

description: Strain: Sarcophaga crassipalpis Maquart


title: Control PBMCs Replicate 98

description: Biological replicate 98 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 97

description: Biological replicate 97 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: 12817

description: Strain: Sarcophaga crassipalpis Maquart


title: Control PBMCs Replicate 96

description: Biological replicate 96 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 95

description: Biological replicate 95 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: 12806

description: Strain: Sarcophaga crassipalpis Maquart


title: 12813

description: Strain: Sarcophaga crassipalpis Maquart


title: 12816

description: Strain: Sarcophaga crassipalpis Maquart


title: 12810

description: Strain: Sarcophaga crassipalpis Maquart


title: Control PBMCs Replicate 94

description: Biological replicate 94 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 93

description: Biological replicate 93 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: 12812

description: Strain: Sarcophaga crassipalpis Maquart


title: 12811

description: Strain: Sarcophaga crassipalpis Maquart


title: 12807

description: Strain: Sarcophaga crassipalpis Maquart


title: 12802

description: Strain: Sarcophaga crassipalpis Maquart


title: 12805

description: Strain: Sarcophaga crassipalpis Maquart


title: Control PBMCs Replicate 92

description: Biological replicate 92 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: 12803

description: Strain: Sarcophaga crassipalpis Maquart


title: 12804

description: Strain: Sarcophaga crassipalpis Maquart


title: Control PBMCs Replicate 89

description: Biological replicate 89 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 90

description: Biological replicate 90 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 91

description: Biological replicate 91 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 88

description: Biological replicate 88 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 86

description: Biological replicate 86 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 87

description: Biological replicate 87 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 85

description: Biological replicate 85 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 84

description: Biological replicate 84 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 81

description: Biological replicate 81 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 78

description: Biological replicate 78 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 80

description: Biological replicate 80 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 82

description: Biological replicate 82 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 83

description: Biological replicate 83 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 77

description: Biological replicate 77 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 79

description: Biological replicate 79 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 76

description: Biological replicate 76 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: WIN1 6i/L/A

city: Cambridge

first: Rudolf

last: Jaenisch

state: MA

address: 9 Cambridge Center

department: Biology

institute: MIT/Whitehead Institute

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized at 45C for 16 hr at 60RPM on GeneChip Arrays (PrimeView). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manurfacturer's instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Expression Console. A CDF containing the ERCC probes was provided by Affymetrix.

data_processing: A CDF provided by Affymetrix, which contained the ERCC probes (PrimeView_withERCC_binary.cdf) was used instead of the standard PrimeView cdf. The data were analyzed with Bioconductor using the MAS5 normalization method. Then, these data were renormalized to the external spike-ins. See manuscript for additional details.

source_name: Embryonic stem cells

label_protocol: Biotinylated aRNA was prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip 3' IVT Express Kit User Manual, 2009, Affymetrix).

growth_protocol: Conventional (primed) human ESCs were cultured on mitomycin C inactivated mouse embryonic ﬁbroblast (MEF) feeder layers and passaged mechanically using a drawn Pasteur pipette or enzymatically by treatment for 20 minutes with 1 mg/mL Collagenase Type IV (Gibco) followed by sequential sedimentation steps in human ESC medium to remove single cells. Naive human ESCs were cultured on mitomycin C-inactivated MEF feeder cells, and were passaged every 5-7 days by a brief PBS wash followed by single-cell dissociation using 3-5 minute treatment with Accutase (Gibco) and centrifugation in fibroblast medium. See the manuscript for composition of primed hESM and naive 5i/L/A and 6i/L/A culture media.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. External spike-in RNAs (ERCC ExFold RNA Spike-In kit, Ambion, 4456739) were added based on cell number. See manuscript for details.

treatment_protocol: All samples were briefly washed in PBS, dissociated to single cells using trypsin, and 1 million naive or primed human ESCs were purified from GFP-labeled MEFs using the FACSAria (Beckton-Dickinson) prior to lysis and RNA extraction.

value: Naive WIN1 ESCs derived from human blastocysts in 5i/L/FA and maintained in the absence of FGF and presence of a JNK inhibitor for 2 passages (P10)


title: Control PBMCs Replicate 75

description: Biological replicate 75 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 74

description: Biological replicate 74 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: WIBR2 6i/L/A, biological rep2

value: Naive WIBR2 human ESCs converted from the primed state in 5i/L/A and supplemented with a JNK inhibitor (P14)


title: WIBR2 6i/L/A, biological rep1

value: Naive WIBR2 human ESCs converted from the primed state in 5i/L/A and supplemented with a JNK inhibitor (P12)


title: Control PBMCs Replicate 73

description: Biological replicate 73 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.

value: Male


title: WIN1 5i/L/A

value: Naive WIN1 ESCs derived from human blastocysts in 5i/L/FA and maintained in the absence of FGF (P10)


title: WIBR3 6i/L/A

value: Naive WIBR3 human ESCs converted from the primed state in 5i/L/A and supplemented with a JNK inhibitor (P9)


title: Control PBMCs Replicate 72

description: Biological replicate 72 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.

value: peripheral blood mononuclear cells (PBMCs)


title: WIBR2 hESM

value: Primed WIBR2 human ESCs cultured in hESM


title: Control PBMCs Replicate 71

description: Biological replicate 71 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.

value: Female


title: WIBR3 hESM

value: Primed WIBR3 human ESCs cultured in hESM


title: Control PBMCs Replicate 69

description: Biological replicate 69 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 67

description: Biological replicate 67 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 68

description: Biological replicate 68 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 64

description: Biological replicate 64 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 65

description: Biological replicate 65 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 66

description: Biological replicate 66 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: miR396b overexpressor B

city: Rosario

first: Juan

middle: Manuel

last: Debernardi

state: Santa Fe

address: Ocampo y Esmeralda

country: Argentina

institute: IBR

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The data were analyzed with Robina software (version_1.2.4), analysis strategy: Limma normalization, method: gcrma

organism: Arabidopsis thaliana

source_name: Apices from 35S:miR396b plants

label_protocol: standard Affymetrix protocol

growth_protocol: Plants were grown on soil medium in short photoperiods (8 h light/16 h dark) at 23 °C.

extract_protocol: Total RNA was extracted from dissected vegetative apices  using the RNeasy plant mini kit (QIAGEN).

treatment_protocol: Vegetative apices together with the leaf primordia were dissected from plants of 20 days.

tag: ecotype background

tag: genotype/variation

value: 35S:miR396b; miR396b overexpressor

value: 20 day-old plants grown in shortdays

value: vegetative apices together with the leaf primordia


title: Control PBMCs Replicate 63

description: Biological replicate 63 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 62

description: Biological replicate 62 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: miR396b overexpressor A


title: Control PBMCs Replicate 70

description: Biological replicate 70 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 61

description: Biological replicate 61 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 59

description: Biological replicate 59 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 60

description: Biological replicate 60 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 58

description: Biological replicate 58 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: ST-01012998_S-001146754_8450989151_C

city: New Haven

first: Jen-hwa

last: Chu

state: CT

department: Pulmonary, Critical Care and Sleep Medicine

institute: Yale University School of Medicine

hyb_protocol: The samples were then blinded, randomized to chip position and hybridized to the Illumina MouseRef-8 v2.0 Expression BeadChips. All chips had one array dedicated as an RNA control.

scan_protocol: The chips were read using standard illumina protocols using an Illumina iScan reader.

data_processing: VSN normalized, background corrected

organism: Mus musculus

source_name: Mouse lung tissue

label_protocol: RNA from all biological samples was labeled at once using the Ambion TotalPrep-96 RNA Amplification Kit according to the manufacturer's instructions.

extract_protocol: For mRNA isolation lung tissue was immersed in RNAlater (Qiagen) and total RNA was then extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions. RNA quality (RIN>=7) was confirmed using an Agilent 2100 Bioanalyzer.

value: LPS

tag: time collected


title: ST-01013014_S-001146798_8450989151_D

value: untreated


title: ST-01013017_S-001146806_8450989151_F


title: ST-01012999_S-001146757_8450989151_E


title: Control PBMCs Replicate 57

description: Biological replicate 57 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.

value: Healthy


title: ST-01013009_S-001146781_8450989151_A


title: ST-01013002_S-001146763_8450989134_G


title: ST-01013018_S-001146808_8450989151_B


title: ST-01013002_S-001146765_8450989151_H


title: ST-01012992_S-001146739_8450989134_C


title: ST-01012997_S-001146753_8450989134_E


title: Control PBMCs Replicate 56

description: Biological replicate 56 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 52

description: Biological replicate 52 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 53

description: Biological replicate 53 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 51

description: Biological replicate 51 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 54

description: Biological replicate 54 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: ST-01012998_S-001146755_8450989132_G


title: Control PBMCs Replicate 50

description: Biological replicate 50 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: ST-01012990_S-001146731_8450989134_F


title: ST-00003825_S-000434102_8450989134_B


title: ST-01013006_S-001146774_8450989134_H


title: ST-01013005_S-001146770_8450989134_A


title: ST-01012994_S-001146745_8450989134_D


title: Control PBMCs Replicate 49

description: Biological replicate 49 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 47

description: Biological replicate 47 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 46

description: Biological replicate 46 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: ST-01013019_S-001146812_8450989132_A


title: ST-01013001_S-001146762_8450989132_E


title: ST-01012991_S-001146736_8450989132_F


title: ST-01012988_S-001146725_8450989132_D


title: ST-01012990_S-001146732_8450989132_H


title: ST-00003825_S-000434102_8450989132_B


title: ST-01013004_S-001146766_8450989132_C


title: ST-01013015_S-001146799_8450989120_H


title: Control PBMCs Replicate 44

description: Biological replicate 44 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 45

description: Biological replicate 45 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 43

description: Biological replicate 43 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 48

description: Biological replicate 48 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: ST-01013011_S-001146787_8450989120_G


title: Control PBMCs Replicate 42

description: Biological replicate 42 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 41

description: Biological replicate 41 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: ST-01012987_S-001146720_8450989120_E


title: ST-01013010_S-001146786_8450989120_F


title: Control PBMCs Replicate 40

description: Biological replicate 40 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 39

description: Biological replicate 39 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: ST-01013007_S-001146776_8450989120_C


title: Control PBMCs Replicate 38

description: Biological replicate 38 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 37

description: Biological replicate 37 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 36

description: Biological replicate 36 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: ST-01013006_S-001146772_8450989120_D


title: Control PBMCs Replicate 33

description: Biological replicate 33 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 34

description: Biological replicate 34 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 32

description: Biological replicate 32 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 35

description: Biological replicate 35 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 30

description: Biological replicate 30 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 31

description: Biological replicate 31 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 29

description: Biological replicate 29 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 28

description: Biological replicate 28 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 27

description: Biological replicate 27 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: ST-01012993_S-001146743_8450989120_B


title: ST-01013019_S-001146811_8450989113_G


title: ST-01013017_S-001146805_8450989113_H


title: ST-01012989_S-001146729_8450989113_E


title: ST-00003825_S-000434102_8450989120_A


title: ST-01012999_S-001146758_8450989113_C


title: ST-01013015_S-001146800_8450989113_A


title: ST-01012996_S-001146749_8450989113_D


title: ST-00003825_S-000434102_8450989113_F


title: ST-01013005_S-001146769_8450989072_H


title: ST-00003825_S-000434102_8450989072_G


title: Control PBMCs Replicate 24

description: Biological replicate 24 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: ST-01012991_S-001146734_8450989072_C


title: ST-00003825_S-000434102_8450989151_G


title: ST-01012987_S-001146721_8450989113_B


title: Control PBMCs Replicate 22

description: Biological replicate 22 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: ST-01013016_S-001146802_8450989072_A


title: ST-01013002_S-001146764_8450989072_E


title: ST-01012989_S-001146728_8450989072_F


title: ST-01012993_S-001146744_8450989072_D


title: ST-01013012_S-001146790_8450989072_B


title: ST-01012998_S-001146756_8450989010_H


title: Control PBMCs Replicate 26

description: Biological replicate 26 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 25

description: Biological replicate 25 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 19

description: Biological replicate 19 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 23

description: Biological replicate 23 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 20

description: Biological replicate 20 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 18

description: Biological replicate 18 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 21

description: Biological replicate 21 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 17

description: Biological replicate 17 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 55

description: Biological replicate 55 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 16

description: Biological replicate 16 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 15

description: Biological replicate 15 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: ST-00003825_S-000434102_8450989010_E


title: ST-01013018_S-001146810_8450989010_G


title: Control PBMCs Replicate 13

description: Biological replicate 13 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 12

description: Biological replicate 12 of 100.Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 14

description: Biological replicate 14 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 11

description: Biological replicate 11 of 100.Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 10

description: Biological replicate 10 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.

tag: status after 5 years

value: Alive


title: Control PBMCs Replicate 9

description: Biological replicate 9 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 8

description: Biological replicate 8 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.

value: Dead


title: ST-01012986_S-001146719_8450989010_D


title: Control PBMCs Replicate 7

description: Biological replicate 7 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: Control PBMCs Replicate 6

description: Biological replicate 6 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: ST-01012996_S-001146748_8450989010_C


title: ST-01013010_S-001146785_8450989010_A


title: Control PBMCs Replicate 5

description: Biological replicate 5 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: ST-01012994_S-001146747_8450989010_F


title: Control PBMCs Replicate 4

description: Biological replicate 4 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: ST-01012986_S-001146718_8450989135_G


title: ST-01012996_S-001146750_8450989135_E


title: ST-01012989_S-001146727_8450989135_C


title: ST-01013005_S-001146771_8450989010_B


title: ST-01013012_S-001146792_8450989133_G


title: ST-01012992_S-001146740_8450989135_H


title: ST-01012987_S-001146722_8450989135_F


title: Control PBMCs Replicate 2

description: Biological replicate 2 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: ST-01013011_S-001146789_8450989133_E


title: ST-01013018_S-001146809_8450989135_A


title: ST-01013008_S-001146778_8450989133_C


title: Control PBMCs Replicate 3

description: Biological replicate 3 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.


title: ST-01013001_S-001146760_8450989135_B


title: ST-01012999_S-001146759_8450989133_A


title: ST-00003825_S-000434102_8450989129_E


title: ST-01012999_S-001146757_8450989129_G


title: ST-00003825_S-000434102_8450989135_D


title: ST-00003825_S-000434102_8450989133_H


title: ST-01012992_S-001146738_8450989133_F


title: ST-01013001_S-001146761_8450989129_C


title: ST-01012997_S-001146751_8450989129_A


title: ST-01013004_S-001146768_8450989133_D


title: HO1519 cells expressing Hhex rep1

city: Valencia

first: Roque

last: Bort

address: Campanar 21

department: Unidad Hepatologia Experimental

country: Spain

institute: IIS La Fe

description: H0159 H1

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45ºC on Affymetrix Rat Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the Affymetrix-recommended protocol.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Data (.CEL files) were normalized using the robust multiarray algorithm (RMA).

organism: Rattus norvegicus

source_name: HO15.19 expressing Hhex. Biological replicate 1

label_protocol: Total RNA (300 ng per sample) was labeled using the Affymetrix GeneChip WT cDNA Synthesis and Amplification kit according to the Affymetrix-recommended protocol.

growth_protocol: Dulbecco´s Modified Eagle´s Medium (DMEM), 10% fetal bovine serum, 1x penicillin/streptomycin (Life-Technologies)

extract_protocol: Sorted cells were collected in Trizol. Following Trizol protocol we obtained an aqueous solution of RNA that was subsequently purified using RNeasy columns (Qiagen). This RNA was measured and quality viability-analized with Agilent 2100 bioanalyzer. Samples had a RIN >9

tag: cell line

tag: expression

value: Hhex-IRES-GFP


title: TGR-1 cells expressing Hhex rep3

description: TGR HEX3

source_name: TGR-1 expressing Hhex. Biological replicate 3


title: TGR-1 cells expressing GFP rep1

description: TGR V1

source_name: TGR-1 expressing GFP. Biological replicate 1

value: IRES-GFP (control)


title: HO1519 cells expressing Hhex rep3

description: H0159 H3

source_name: HO15.19 expressing Hhex. Biological replicate 3


title: HO1519 cells expressing Hhex rep2

description: H0159 H2

source_name: HO15.19 expressing Hhex. Biological replicate 2


title: TGR-1 cells expressing GFP rep3

description: TGR V3

source_name: TGR-1 expressing GFP. Biological replicate 3


title: ST-01013013_S-001146795_8450989133_B


title: ST-01012993_S-001146742_8450989129_H


title: ST-01013016_S-001146803_8450989122_G


title: ST-01013006_S-001146773_8450989129_F


title: TGR-1 cells expressing GFP rep2

description: TGR V2

source_name: TGR-1 expressing GFP. Biological replicate 2


title: Control PBMCs Replicate 1

description: Biological replicate 1 of 100. Control peripheral blood mononuclear cells, untreated, harvested after several passages.

value: Male


title: TGR-1 cells expressing Hhex rep1

description: TGR HEX1

source_name: TGR-1 expressing Hhex. Biological replicate 1


title: TGR-1 cells expressing Hhex rep2

description: TGR HEX2

source_name: TGR-1 expressing Hhex. Biological replicate 2


title: ST-01012990_S-001146733_8450989129_D


title: ST-01013004_S-001146767_8450989129_B


title: ST-01012991_S-001146737_8450989122_H


title: HO1519 cells expressing GFP rep3

description: H0159 V2

source_name: HO15.19 expressing GFP. Biological replicate 3


title: ST-01013008_S-001146780_8450989122_E


title: ST-00003825_S-000434102_8450989122_F


title: HO1519 cells expressing GFP rep2

description: H0159 V1

source_name: HO15.19 expressing GFP. Biological replicate 2


title: ST-01013009_S-001146782_8450989122_D


title: Control (siControl-2)_MDA-LM2-shDicer

city: San Francisco

first: Hani

last: Goodarzi

state: CA

department: Biochemistry and Biophysics

institute: UCSF

description: replicate 2

hyb_protocol: Per manufacturer's instruction

scan_protocol: Per manufacturer's instruction

data_processing:
Data were quantile-normalized and processed using the Lumi package.
Non-normalized values indicate the average probe hybridization signal.
Normalized values are quantile-normalized.
Final processed values are logFC of average normalized signals in siTARBP2 relative to siControl.

source_name: MDA-LM2 shDicer

label_protocol: Samples were biotin-labeled using the TargetAmp-Nano Labeling Kit for Ilumina Expression BeadChip

growth_protocol: Cells were grown in DMEM-based media supplemented with 10% FBS, 1% L-glutamine, 1% Sodium Pyruvate, and 1% Pen/Strep

extract_protocol: 48hr post-transfection, total RNA was extracted and on-column Dnase treated using Norgen Biotek total RNA extraction kit (per manufacturer instructions).

treatment_protocol: Cells were transfected with siTARBP2 and siControl using Lipofectamin 2000 per manufacturer guidelines.

value: MDA-LM2-shDicer cells

tag: transfection


title: ST-01013015_S-001146801_8450989122_C


title: ST-01012986_S-001146717_8450989122_B


title: TARBP2 knock-down (siTARBP2-2)_MDA-LM2-shDicer

description: replicate 2


title: Control (pCMV-GFP-2)_MDA-231

description: replicate 2

data_processing:
Data were quantile-normalized and processed using the Lumi package.
Non-normalized values indicate the average probe hybridization signal.
Normalized values are quantile-normalized.
Final processed values are logFC of average normalized signals in pCMV-TARBP2 relative to pCMV-GFP.

source_name: MDA-231 cells

treatment_protocol: Cells were transfected with pCMV-TARBP2 and pCMV-GFP using TransIT regaent (Mirus) per manufacturer guidelines.

value: pCMV-GFP


title: Control (siControl-1)_MDA-LM2-shDicer

description: replicate 1


title: ST-00003825_S-000434102_8450989118_C


title: ST-01013010_S-001146784_8450989118_G


title: Control (pCMV-GFP-1)_MDA-231

description: replicate 1


title: HO1519 cells expressing GFP rep1

description: H0159 V

source_name: HO15.19 expressing GFP. Biological replicate 1


title: ST-01012991_S-001146735_8450989118_D


title: ST-01012994_S-001146746_8450989118_E


title: TARBP2 over-expression (pCMV-TARBP2-1)_MDA-231

description: replicate 1


title: ST-01013016_S-001146804_8450989118_H


title: ST-01013017_S-001146807_8450989122_A


title: TARBP2 knock-down (siTARBP2-1)_CN-LM1a

description:
siRNA
replicate 1

data_processing:
Data were quantile-normalized and processed using the Lumi package.
Non-normalized values indicate the average probe hybridization signal.
Normalized values are quantile-normalized.
Final processed values are log2FC of average normalized signals in siTARBP2 relative to siControl.

source_name: CN-LM1a cells


title: ST-01013013_S-001146794_8450989118_F


title: Control (siControl-1)_CN-LM1a

description:
siControl
replicate 1


title: ST-01012987_S-001146723_8450989087_G


title: TARBP2 knock-down (siTARBP2-1)_MDA-LM2-shDicer

description: replicate 1


title: ST-01012993_S-001146741_8450989087_E


title: ST-01013007_S-001146775_8450989087_H


title: ST-01013014_S-001146797_8450989118_A


title: ST-01012988_S-001146726_8450989118_B


title: Control (siControl-2)_CN-LM1a

description:
siControl
replicate 2


title: TARBP2 over-expression (pCMV-TARBP2-2)_MDA-231

description: replicate 2


title: Control (siControl)_293T

description: replicate 1

data_processing:
Data were quantile-normalized and processed using the Lumi package.
Non-normalized values indicate the average probe hybridization signal.
Normalized values are quantile-normalized.
Final processed values are logFC of siTARBP2 relative to siControl.

source_name: 293T cells

tag: tranfection

value: siControl


title: TARBP2 knock-down (siTARBP2-2)_CN-LM1a

description:
siRNA
replicate 2


title: ST-00003825_S-000434102_8450989087_A

source_name: Mouse lung tissue


title: ST-01012997_S-001146752_8450989087_C


title: ST-01013009_S-001146783_8450989018_C


title: TARBP2 knock-down (siTARBP2-1)_293T

description: replicate 1


title: ST-01013012_S-001146791_8450989018_E


title: ST-01013014_S-001146796_8450989018_G


title: ST-01012986_S-001146717_8450989018_A


title: Control (shControl-3)

description: replicate 3

data_processing:
Data were quantile-normalized and processed using the Lumi package.
Non-normalized values indicate the average probe hybridization signal (supplementary file linked to Series record).
Normalized values are quantile-normalized.
Final processed values are logFC of average normalized signals in shZNF395 relative to siControl (supplementary file linked to Series record).

treatment_protocol: MDA-LM2-shTARBP2 cells were transduced with shZNF395 and shControl lentiviral particles and selected for short-hairpin expression.

value: shControl


title: Control (siControl-2)_18hrs

description:
replicate 2
siControl-2 (18 hr)

data_processing:
Data were quantile-normalized and processed using the Lumi package.
Non-normalized values indicate the average probe hybridization signal (supplementary file linked to Series record).
Normalized values are quantile-normalized.
Final processed values are logFC of average stability measurements in siTARBP2 relative to siControl. The stability measurements are calculated as the 18 hr to 0 hr processed signal ratio, further corrected based on the amount of input total and labeled RNA for each sample (supplementary file linked to Series record).

source_name: MDA-LM2 cells

extract_protocol: Total RNA was extracted and on-column Dnase treated using Norgen Biotek total RNA extraction kit (per manufacturer instructions).

treatment_protocol: Cells were transfected with siTARBP2 and siControl using Lipofectamin 2000 per manufacturer guidelines. 48 hr post-transfection, cells were treated with alpha-amanitine at 10uM for 0 and 18 hours.

value: control

tag: agent

value: alpha-amanitine at 10uM

tag: time-point

value: 18 hr


title: Control (shControl-1)

description: replicate 1


title: ZNF395 knock-down (shZNF395-1)

description: replicate 1


title: Control (shControl-2)

description: replicate 2


title: Control (siControl-1)_18hrs

description:
replicate 1
siControl-1 (18 hr)


title: TARBP2 knock-down (siTARBP2-2)_18hrs

description:
replicate 2
siTARBP2-2 (18 hr)

value: TARBP2 knock-down


title: Control (siControl-2)_0hrs

description:
replicate 2
siControl-2 (0 hr)

value: 0 hr


title: ZNF395 knock-down (shZNF395-4)

description: replicate 4


title: Control (siControl-1)_0hrs

description:
replicate 1
siControl-1 (0 hr)


title: ST-01012989_S-001146730_8450989018_B

tag: treatment

value: LPS


title: Control (shControl-4)

description: replicate 4


title: ST-01013007_S-001146777_8450989018_D

value: untreated


title: TARBP2 knock-down (siTARBP2-2)_293T

description: replicate 2


title: ZNF395 knock-down (shZNF395-3)

description: replicate 3


title: ST-01012988_S-001146724_8450989087_F


title: RNACtrl_CHP10

tag: experiment time

tag: circadian time

tag: light regimen ld vs dd

tag: health state


title: T40L2DD

value: DD

value: Basal


title: ST-01013008_S-001146779_8450989087_B


title: ST-01013011_S-001146788_8450989087_D


title: ZNF395 knock-down (shZNF395-2)

description: replicate 2


title: TARBP2 knock-down (siTARBP2-1)

description:
replicate 1
siRNA

data_processing:
Data were quantile-normalized and processed using the Lumi package.
Non-normalized values indicate the average probe hybridization signal (supplementary file linked to Series record).
Normalized values are quantile-normalized.
Final processed values are logFC siTARBP2 relative to siControl. (supplementary file linked to Series record).


title: Control (siControl-2)

description:
replicate 2
siControl

value: Control


title: T32L2DD


title: ST-01013013_S-001146793_8450989018_H


title: sRSE decoy 2 (#T8)

description: replicate 2

data_processing:
Data were quantile-normalized and processed using the Lumi package.
Non-normalized values indicate the average probe hybrydization signal. Normalized values are quantile-normalized. Final processed values are logFC of decoy values relative to scrambled controls.

treatment_protocol: Cells were transfected with capped and poly-adenylated RNA molecules (either sRSE decoy or scrambled) using Lipofectamin 2000 per manufacturer guidelines.

value: sRSE decoy


title: ST-00003825_S-000434102_8450989018_F


title: T20L2MR

value: LD


title: TARBP2 knock-down (siTARBP2-2)

description:
replicate 2
siRNA


title: T32L2MR


title: TARBP2 knock-down (siTARBP2-2)_0hrs

description:
replicate 2
siTARBP2-2 (0 hr)


title: T4L2DD


title: Control (siControl-1)

description:
replicate 1
siControl


title: T44L4MR


title: T4L1MR


title: TARBP2 knock-down (siTARBP2-1)_18hrs

description:
replicate 1
siTARBP2-1 (18 hr)


title: T8L3DD


title: T0L2DD


title: TARBP2 knock-down (siTARBP2-1)_0hrs

description:
replicate 1
siTARBP2-1 (0 hr)


title: Scrambled 2 (#T6)

description: replicate 2

value: Scrambled control


title: T36L5MR


title: Scrambled 1 (#T2)

description: replicate 1


title: RNACtrl_CHP9


title: T16L3DD


title: T40L3DD


title: T0L3DD


title: RNACtrl_CHP8


title: T16L4MR


title: T24L2MR


title: sRSE decoy 1 (#T4)

description: replicate 1


title: T40L4MR


title: T4L2MR


title: T0L2MR


title: T24L1DD


title: T28L2MR


title: T28L1DD


title: T28L5MR


title: T0L1MR


title: RNACtrl_CHP7


title: T20L3DD


title: RNACtrl_CHP6


title: T24L3DD


title: T4L3DD


title: T12L3DD


title: T16L2DD


title: T24L3MR


title: T44L3MR


title: T32L1DD


title: T24L2DD


title: T32L5MR


title: RNACtrl_CHP5


title: T16L1DD


title: doxycycline and 4u8c treated, rep1

city: Toronto

first: Allen

last: Volchuk

address: 101 College st

country: Canada

institute: University of Toronto

description: Dox (4ug/mL) and 4u8c (5uM)

hyb_protocol: 15.0 ug of aRNA for each samples was fragmented and hybridized to Rat Genome 230 2.0 arrays for 18hrs at 45oC at 60 RPM. Arrays were washed using GeneChip Fluidics Station P450 fluidic station

scan_protocol: Rat Genome 230 2.0 arrrays were scanned with Affymetrix GeneChip Scanner 7G

data_processing: Data was analyzed using the Genespring (agilent) v 12.0 software package.  Raw cel files obtained from Affymetrix scans were imported for analysis using the RMA summarization algorithm. Furthermore, each gene was normalized additionally to the median value across all samples.

source_name: (C96Y-Ins2) INS1 insulinoma cell line, doxycycline and 4u8c treated, rep1

label_protocol: 200 ng of total RNA for each sample was used as input material in 3’IVT Express protocol

growth_protocol: Cells were maintained in RPMI 1640 (11.1 mM glucose, 1 mM sodium pyruvate, 10 mM HEPES) supplemented with 10% fetal bovine serum, 2 mM L-glutamine, 55 μM β-mercaptoethanol with antibiotics (100 units/ml penicillin and 100 μg/ml streptomycin) and selection drugs (200 μg/ml G418 and 50 μg/ml hygromycin).

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen) followed by isolation using an RNeasy mini kit (QIAGEN).

treatment_protocol: Cells were treated with indicated small molecule for 48 hours prior to collection.

tag: cell type

value: insulinoma


title: T8L2MR


title: T44L1DD


title: doxycycline treated, rep1

description: Dox (4ug/mL)

source_name: (C96Y-Ins2) INS1 insulinoma cell line, doxycycline treated, rep1


title: untreated, rep1

source_name: (C96Y-Ins2) INS1 insulinoma cell line, untreated, rep1


title: doxycycline and 4u8c treated, rep2

description: Dox (4ug/mL) and 4u8c (5uM)

source_name: (C96Y-Ins2) INS1 insulinoma cell line, doxycycline and 4u8c treated, rep2


title: untreated, rep2

source_name: (C96Y-Ins2) INS1 insulinoma cell line, untreated, rep2


title: T8L3MR


title: T4L5MR


title: RNACtrl_CHP4


title: T36L2MR


title: T12L2MR


title: T4L1DD


title: doxycycline treated, rep2

description: Dox (4ug/mL)

source_name: (C96Y-Ins2) INS1 insulinoma cell line, doxycycline treated, rep2


title: T20L1DD


title: T8L2DD


title: T36L2DD


title: T44L2MR


title: T16L5MR


title: T0L1DD


title: T16L1MR


title: T28L2DD


title: Ang II + TT, biol rep5

city: Nashville

first: Annet

last: Kirabo

address: 2220 Pierce Avenue

institute: Vanderbilt

description: Ang II-treated dendritic cells from WT mice co-treated with a combination of hydralazine and hydrochlorothiazide, biological replicate 5

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix mouse Gene 1.0 ST arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using an Affymetrix high resolution GenePix 4000B scanner

data_processing: The data were analyzed with Partek Genomics Suite 6.6 software using gene expression analysis default analysis settings and RMA (Robust Multi-chip Average) as the normalization method.

source_name: Spleen

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Primary dendritic cells were obtained from C57BL6/J wild type and NOX2 knockout mice

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

treatment_protocol: Ang II with or without 2-HOBA or a combination of hydralazine and hydrochlorothiazide

tag: tissue

value: primary dendritic cells

tag: genotype

value: C57BL6/J wild-type

tag: age

value: 3 mo old


title: T12L3MR


title: Ang II + TT, biol rep6

description: Ang II-treated dendritic cells from WT mice co-treated with a combination of hydralazine and hydrochlorothiazide, biological replicate 6


title: T28L3DD


title: RNACtrl_CHP3


title: T36L3MR


title: T36L3DD


title: Ang II + TT, biol rep2

description: Ang II-treated dendritic cells from WT mice co-treated with a combination of hydralazine and hydrochlorothiazide, biological replicate 2


title: vessel at T0, biological rep1

city: beijing

first: zhang

middle: yun

last: long

state: beijing

address: No.10 Xitoutiao, You An Men

department: Department of Physiology and Pathophysiology,

institute: School of Basic Medical Sciences, Capital Medical University

description: Gene expression data from mouse vessel with no Angiotensin II  treatmeant

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip Mouse Genome 430 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Genechips were scanned by GeneChip® Scanner 3000.

data_processing: The data were analyzed with Expression Console™, Version 1.3.1.

source_name: Mouse vessel with no Angiotensin II  treatmeant

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-8 ug total RNA

growth_protocol: Eight to ten-week-old C57BL/6 male mice were kept at least 1 wk at 22°C and 55% relative humidity in a 12-h day/night lighting environment with free access to food and water.

extract_protocol: All mice were euthanized by an overdose of pentobarbital on days 1, 3 and 7 of Ang II treatment. Total RNA was isolated with TRIzol (Invitrogen) from brains, hearts, kidneys and vessels at each time point according to manufacturer's instructions.

treatment_protocol: Mice were implanted with osmotic pumps (Alzet Model 1007D; Cupertino, CA,USA) and infused with Angiotensin II at 1500ng/kg/min in Ringer's solution (0.01mmol/L acetic acid in saline) for 1, 3, and 7 days . Systolic blood pressure was measured by the tail-cuff method before starting treatment and again every day after Angiotensin II infusion.

tag: strain

tag: gender

value: male

value: vessel


title: vessel at T3, biological rep1

description: Gene expression data from mouse vessel Angiotensin II treated for 3days

source_name: Mouse vessel Angiotensin II treated for 3days


title: Ang II + TT, biol rep3

description: Ang II-treated dendritic cells from WT mice co-treated with a combination of hydralazine and hydrochlorothiazide, biological replicate 3


title: Ang II + TT, biol rep1

description: Ang II-treated dendritic cells from WT mice co-treated with a combination of hydralazine and hydrochlorothiazide, biological replicate 1


title: T20L4MR


title: WT Ang II THOBA, biol rep3

description: Ang II-treated dendritic cells from WT mice co-treated with 2-HOBA, biological replicate 3


title: Kidney at T7, biological rep1

description: Gene expression data from mouse kidney Angiotensin II treated for 7days

source_name: Mouse kidney Angiotensin II treated for 7days

value: Kidney


title: T12L1DD


title: Kidney at T3, biological rep2

description: Gene expression data from mouse kidney Angiotensin II treated for 3days

source_name: Mouse kidney Angiotensin II treated for 3days


title: T28L3MR


title: vessel at T1, biological rep1

description: Gene expression data from mouse vessel Angiotensin II treated for 1days

source_name: Mouse vessel Angiotensin II treated for 1days


title: vessel at T7, biological rep1

description: Gene expression data from mouse vessel Angiotensin II treated for 7days

source_name: Mouse vessel Angiotensin II treated for 7days


title: mCherry+/- organoids

city: Bunkyo-ku

first: Kiichiro

last: Tsuchiya

address: 1-5-45 Yushima

country: Japan

institute: Tokyo Medical and Dental University

hyb_protocol: Hybridization was performed using the Gene Expression Hybridization Kit (Agilent Technologies). cRNA samples (1.65 μg) were subjected to fragmentation (30 min at 60°C) and then hybridized on an Superprint G3 Mouse GE microarray Kit 8×60K (G4852A, Agilent Technologies) in a rotary oven (10 rpm at 65°C for 17 h).

scan_protocol: Slides were washed in Agilent Gene Expression Wash Buffers 1 and 2 (Agilent Technologies) and scanned with an Agilent DNA Microarray Scanner (Agilent Technologies).

data_processing: Gene expression values measured with the microarrays were normalized with GeneSpring software (Agilent Technologies) using the 75th percentile value.

source_name: mCherry-positive organoids

label_protocol: RNA samples were labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies). Labeling of 50 ng of total RNA was performed using cyanine 3-CTP or 5-CTP.

growth_protocol: For conventional culture, 30 μl of Matrigel® was seeded on 24-well plates. For live imaging experiments, 60 μl of Matrigel® was placed on 40-mm coverslips placed in 60-mm culture dishes. After the Matrigel® solidified, advanced DMEM/F12 medium (Invitrogen) containing 20 ng/ml EGF (Peprotech), 100 ng/ml Noggin, 500 ng/ml R-spondin1 (R&D systems), 2 mM L-glutamine (GIBCO) and penicillin/streptomycin was overlaid.

extract_protocol: Total RNA was extracted using RNeasy® reagent (Qiagen)

tag: tissue source

value: small intestine

value: organoids

source_name: mCherry-negative organoids


title: WT Ang II THOBA, biol rep2

description: Ang II-treated dendritic cells from WT mice co-treated with 2-HOBA, biological replicate 2


title: Kidney at T3, biological rep1


title: Kidney at T7, biological rep2


title: T40L1MR

source_name: Mouse lung tissue


title: Kidney at T1, biological rep2

description: Gene expression data from mouse kidney Angiotensin II treated for 1days

source_name: Mouse kidney Angiotensin II treated for 1days


title: T44L3DD


title: Kidney at T0, biological rep2

description: Gene expression data from mouse kidney with no Angiotensin II  treatmeant

source_name: Mouse kidney with no Angiotensin II  treatmeant


title: Kidney at T1, biological rep1


title: WT Ang II THOBA, biol rep4

description: Ang II-treated dendritic cells from WT mice co-treated with 2-HOBA, biological replicate 4


title: Heart at T7, biological rep2

description: Gene expression data from mouse heart Angiotensin II treated for 7days

source_name: Mouse heart Angiotensin II treated for 7days

value: Heart


title: T12L2DD


title: Heart at T3, biological rep3

description: Gene expression data from mouse heart Angiotensin II treated for 3days

source_name: Mouse heart Angiotensin II treated for 3days


title: T32L3MR


title: Kidney at T0, biological rep1


title: T20L3MR


title: WT Ang II THOBA, biol rep1

description: Ang II-treated dendritic cells from WT mice co-treated with 2-HOBA, biological replicate 1


title: WT Ang II, biol rep1

description: Ang II-treated dendritic cells from WT mice, biological replicate 1


title: WT Ang II, biol rep2

description: Ang II-treated dendritic cells from WT mice, biological replicate 2


title: WT Ang II, biol rep4

description: Ang II-treated dendritic cells from WT mice, biological replicate 4


title: WT Ang II, biol rep3

description: Ang II-treated dendritic cells from WT mice, biological replicate 3


title: Heart at T3, biological rep1


title: Heart at T7, biological rep1


title: Heart at T7, biological rep3


title: T0L5MR


title: T32L3DD


title: Heart at T1, biological rep1

description: Gene expression data from mouse heart Angiotensin II treated for 1days

source_name: Mouse heart Angiotensin II treated for 1days


title: WT Sham, biol rep6

description: Vehicle-treated dendritic cells from WT mice, biological rep6


title: WT Sham, biol rep7

description: Vehicle-treated dendritic cells from WT mice, biological rep7


title: Heart at T1, biological rep2


title: T40L1DD


title: LMNB1 transfected DLD-1 cells with vector V2LHS_62675. Clone number 12. Biological replicate 3

city: Barcelona

first: Jordi

last: Camps

state: Catalonia

address: c/Rosselló 149-153 4th floor, Center Esther Koplowitz

department: Gastroenterology

institute: IDIBAPS / Hospital Clinic

description: DLD-1 cells transfected with shRNA against lamin B1. Cells derived from sibgle cell clone number 2, replicate 3.

hyb_protocol: The hybridization cocktail containing the fragmented and biotin-labeled cDNAs were hybridized to the Affymetrix GeneChip Human Exon 1.0 ST Array. The chips were washed and stained by the Affymetrix Fluidics Station.

scan_protocol: Affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays.

data_processing:
Data processing cel files were normalized with 'rma' function of the Bioconductor package (v2.10) 'affy' in R.2.15.1
probe group file: HuEx-1_0-st-v2
meta-probeset file: HuEx-1_0-st-v2

source_name: LMNB1 knockdown

label_protocol: RNA was then reverse transcribed in the presence of dT7N6 primers to generate cDNA. An in vitro transcription was then performed, and the resulting cRNA was purified. A first-strand cDNA was generated form the cRNA in the presence of dUTPs. After RNA hydrolysis, the single-stranded cDNA was fragmented and end-labeled with biotin.

growth_protocol: Cells were grown in RPMI supplemented with 10% FBS and using standard cell culture conditions.

extract_protocol: Total RNA was extracted using Trizol. See protocol details at http://www.riedlab.nci.nih.gov/index.php/protocols. The total RNA was first subjected to a ribosomal RNA reduction using the Invitrogen RiboMinus Transcriptome Isolation Kit.

treatment_protocol: All cell cultures, except for wild-type, were maintained with puromycin (2mg/ml)

tag: knockdown

value: LMNB1 knockdown

tag: cell line

value: shRNA against lamin B1. Cells derived from single cell clone number 2


title: WT Sham, biol rep5

description: Vehicle-treated dendritic cells from WT mice, biological rep5


title: Heart at T0, biological rep3

description: Gene expression data from mouse heart with no Angiotensin II  treatmeant

source_name: Mouse heart with no Angiotensin II  treatmeant


title: Heart at T1, biological rep3


title: T44L2DD

value: DD

value: Basal


title: Heart at T0, biological rep2


title: LMNB1 transfected DLD-1 cells with vector V2LHS_62673. Clone number 12

description: DLD-1 cells transfected with shRNA against lamin B1. Cells derived from sibgle cell clone number 12.

tag: transfection

value: shRNA against lamin B1. Cells derived from single cell clone number 12.


title: Heart at T0, biological rep1


title: T12L5MR

value: LD


title: T8L1DD


title: T40L5MR


title: LMNB1 transfected DLD-1 cells with vector V2LHS_62673. Clone number 9

description: DLD-1 cells transfected with shRNA against lamin B1. Cells derived from sibgle cell clone number 9.

value: shRNA against lamin B1. Cells derived from single cell clone number 9.


title: LMNB1 transfected DLD-1 cells with vector V2LHS_62673. Clone number 8

description: DLD-1 cells transfected with shRNA against lamin B1. Cells derived from sibgle cell clone number 8.

value: shRNA against lamin B1. Cells derived from single cell clone number 8.


title: Brain at T7, biological rep2

description: Gene expression data from mouse brian Angiotensin II treated for 7days

source_name: Mouse brain Angiotensin II treated for 7days

value: Brain


title: Brain at T3, biological rep1

description: Gene expression data from mouse brian Angiotensin II treated for 3days

source_name: Mouse brain Angiotensin II treated for 3days


title: T36L1DD


title: T8L4MR


title: Ang II + TT, biol rep4

description: Ang II-treated dendritic cells from WT mice co-treated with a combination of hydralazine and hydrochlorothiazide, biological replicate 4

source_name: Spleen

value: primary dendritic cells

value: C57BL6/J wild-type


title: Empty vector control transfected DLD-1 cells. Biological replicate 2

description: DLD-1 cells transfected with an empty vector control

source_name: Empty vector

value: Negative control

value: empty vector control


title: Brain at T3, biological rep2

value: male


title: Brain at T7, biological rep1


title: LMNB1 transfected DLD-1 cells with vector V2LHS_62675. Clone number 12. Biological replicate 2

description: DLD-1 cells transfected with shRNA against lamin B1. Cells derived from sibgle cell clone number 2, replicate 2.


title: Empty vector control transfected DLD-1 cells. Biological replicate 3


title: LMNB1 transfected DLD-1 cells with vector V2LHS_62675. Clone number 12. Biological replicate 1

description: DLD-1 cells transfected with shRNA against lamin B1. Cells derived from sibgle cell clone number 2, replicate 1.


title: WT Sham, biol rep3

description: Vehicle-treated dendritic cells from WT mice, biological rep3

value: 3 mo old


title: WT Sham, biol rep2

description: Vehicle-treated dendritic cells from WT mice, biological rep2


title: GP91 Phox Ang I, biol rep3

description: Ang II-treated dendritic cells from NOX2 KO mice, biological rep3

value: GP91 Phox knockout


title: WT Sham, biol rep4

description: Vehicle-treated dendritic cells from WT mice, biological rep4


title: Brain at T0, biological rep2

description: Gene expression data from mouse brian with no Angiotensin II  treatmeant

source_name: Mouse brain with no Angiotensin II  treatmeant


title: WT Sham, biol rep1

description: Vehicle-treated dendritic cells from WT mice, biological rep1


title: T20L2DD


title: T24L1MR


title: GP91 Phox Ang I, biol rep4

description: Ang II-treated dendritic cells from NOX2 KO mice, biological rep4


title: Empty vector control transfected DLD-1 cells. Biological replicate 1


title: GP91 Phox Ang I, biol rep2

description: Ang II-treated dendritic cells from NOX2 KO mice, biological rep2


title: Control (siControl-3)_DICER-null MEF

description: replicate 3

source_name: DICER-null MEFs

value: DICER-null MEFs


title: Control (siControl-2)_DICER-null MEF

description: replicate 2


title: Brain at T0, biological rep1


title: Wild type DLD-1 cells

description: DLD-1 cells wild type

source_name: Wild type


title: Control (siControl-1)_DICER-null MEF

description: replicate 1


title: GP91 Phox Sham, biol rep3

description: Vehicle-treated dendritic cells from NOX2 KO mice, biological rep3


title: GP91 Phox Ang I, biol rep1

description: Ang II-treated dendritic cells from NOX2 KO mice, biological rep1


title: TARBP2 knock-down (siTARBP2-1)_DICER-null MEF

description: replicate 1


title: TARBP2 knock-down (siTARBP2-2)_DICER-null MEF

description: replicate 2


title: KMS11_shLuc_48h_Rep1

city: Singapore

first: Zhigang

last: Xie

address: 14 Medical Drive, CeLS Building #02-07

department: CSI Singapore

country: Singapore

institute: National University of Singapore

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

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

data_processing: The data were analyzed with Genespring GX12 (Agilent Technologies) using MAS5 algorithm

source_name: KMS11 cells, shLuc, 48 h

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (GeneChip 3' IVT Express Kit Manual, 2009, Affymetrix).

growth_protocol: Human t(4;14) MM cell line KMS11 was maintained in RPMI 1640, supplemented with 10% fetal calf serum (FCS), 100 U/mL penicillin and 100 μg/mL streptomycin. Cells were grown at 37 C in a humidified atmosphere with 5% CO2.

extract_protocol: Total RNA was extracted by using the Qiagen RNeasy Mini kit (Germany).

treatment_protocol: Cells were infected with lentiviruses in the presence of 8 µg/mL polybrene (Sigma-Aldrich). Twenty four hours after infection, infection mixtures were replaced with normal growth medium. Cells were incubated at 37C in a humidified, 5% CO2 atmosphere for 24 h and subsequently collected for RNA extraction.

value: Multiple Myeloma Cell Line


title: KMS11_shMMSET#4_48h_Rep1

source_name: KMS11 cells, shMMSET#4, 48 h


title: Heart at T3, biological rep2

description: Gene expression data from mouse heart Angiotensin II treated for 3days

value: Heart


title: GP91 Phox Sham, biol rep2

description: Vehicle-treated dendritic cells from NOX2 KO mice, biological rep2


title: KMS11_shMMSET#2_48h_Rep1

source_name: KMS11 cells, shMMSET#2, 48 h


title: GP91 Phox Sham, biol rep1

description: Vehicle-treated dendritic cells from NOX2 KO mice, biological rep1


title: KH004-100-24h-313034

status: Public on Jul 15 2014

first: Sachel

last: Mok

address: 60 Nanyang Drive

institute: Nanyang Technological University

description: Reference sample is laboratory strain 3D7.

hyb_protocol: Equal amounts of labelled sample and reference cDNA were hybridized on the microarray chip using the Agilent hybridization system. Hybridizations were performed for 20 hours at 65°C in a rotating hybridization oven at 10rpm.

scan_protocol: Microarray scanning was done using PowerScanner (Tecan, Austria) at 10uM resolution and with autogain PMT adjustments for both channels. Data was acquired using GenePix Pro v6.0 software (Axon Instruments, USA) as described in Mok, S., M. Imwong et al (2011) Artemisinin resistance in Plasmodium falciparum is associated with an altered temporal pattern of transcription. BMC Genomics 12: 391.

data_processing: Features with flag>0 and with median foreground intensity greater than 1.5 fold median background intensity for either channel passed quality control and were accepted. Local background correction using normexp, followed by lowess normalization across all features were carried out to generate the normalized Log2 gene expression ratios.

organism: Plasmodium falciparum

source_name: P. falciparum field isolate (ex-vivo), Pailin Cambodia, KH004-100

label_protocol: Synthesis of aminoallyl-coupled cDNA by reverse transcription and labeling of samples with Cy fluorophore were carried out as described in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211.

extract_protocol: Total RNA was extracted using Trizol following manufacturer's instructions and as described in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211.

tag: culture

value: ex vivo

tag: Stage

value: blood

tag: timepoint

value: 24h post-sampling from patient

tag: patient sample id

tag: geographic origin

value: Pailin, Cambodia

tag: barcode

tag: parasite clearance halflife upon artemisinin treatment in patient

source_name: P. falciparum 3D7 RNA reference pool

tag: strain/background

value: in vitro

value: asexual blood

tag: composition

value: mixture of equal amounts of RNA harvested every 6 hours over the 48-hour parasite's intraerythrocytic life cycle

tag: sample type

value: reference


title: KH004-098-16h-313027

source_name: P. falciparum field isolate (ex-vivo), Pailin Cambodia, KH004-098

value: 16h post-sampling from patient


title: KH004-098-24h-313028


title: KH004-098-40h-313030

value: 40h post-sampling from patient


title: KH004-100-8h-313032

value: 8h post-sampling from patient


title: KH004-100-16h-313033


title: KH004-100-0h-313031

value: 0h post-sampling from patient


title: KH004-094-8h-313008

source_name: P. falciparum field isolate (ex-vivo), Pailin Cambodia, KH004-094


title: KH004-098-8h-313026


title: KH004-096-32h-313023

source_name: P. falciparum field isolate (ex-vivo), Pailin Cambodia, KH004-096

value: 32h post-sampling from patient


title: KH004-098-32h-313029


title: KH004-096-16h-313021


title: KH004-098-0h-313025


title: KH004-094-32h-313011


title: KH004-096-24h-313022


title: KH004-094-40h-313012


title: KH004-094-24h-313010


title: KH004-096-8h-313020


title: KH004-094-16h-313009


title: KH004-100-32h-313035


title: KH004-096-40h-313024


title: KH004-100-40h-313036


title: KH004-093-32h-313005

source_name: P. falciparum field isolate (ex-vivo), Pailin Cambodia, KH004-093


title: KH004-094-0h-313007


title: KH004-093-24h-313004


title: KH004-093-16h-313003


title: KH004-093-0h-313001


title: KH004-093-40h-313006


title: KH004-090-8h-312996

source_name: P. falciparum field isolate (ex-vivo), Pailin Cambodia, KH004-090


title: KH004-090-24h-312998


title: KH004-093-8h-313002


title: KH004-089-32h-312993

source_name: P. falciparum field isolate (ex-vivo), Pailin Cambodia, KH004-089


title: KH004-089-40h-312994


title: KH004-090-32h-312999


title: KH004-090-0h-312995


title: KH004-089-8h-312990


title: KH004-090-16h-312997


title: KH004-089-24h-312992


title: KH004-089-16h-312991


title: KH004-086-24h-312987

source_name: P. falciparum field isolate (ex-vivo), Pailin Cambodia, KH004-086


title: KH004-086-40h-312988


title: KH004-086-8h-312985


title: KH004-089-0h-312989


title: KH004-080-32h-312976

source_name: P. falciparum field isolate (ex-vivo), Pailin Cambodia, KH004-080


title: KH004-086-16h-312986


title: KH004-080-40h-312977


title: KH004-082-16h-312980

source_name: P. falciparum field isolate (ex-vivo), Pailin Cambodia, KH004-082


title: KH004-086-0h-312984


title: KH004-082-0h-312978


title: KH004-080-8h-312973


title: KH004-082-8h-312979


title: KH004-082-32h-312982


title: KH004-082-40h-312983


title: KH004-082-24h-312981


title: KH004-080-24h-312975


title: KH004-077-32h-312970

source_name: P. falciparum field isolate (ex-vivo), Pailin Cambodia, KH004-077


title: KH004-077-40h-312971


title: KH004-077-8h-312967


title: KH004-076-24h-312963

source_name: P. falciparum field isolate (ex-vivo), Pailin Cambodia, KH004-076


title: KH004-076-16h-312962


title: KH004-080-0h-312972


title: KH004-080-16h-312974


title: KH004-076-0h-312960


title: KH004-075-24h-312957

source_name: P. falciparum field isolate (ex-vivo), Pailin Cambodia, KH004-075


title: KH004-075-40h-312959


title: KH004-077-16h-312968


title: KH004-075-32h-312958


title: KH004-077-24h-312969


title: KH004-075-0h-312954


title: KH004-076-8h-312961


title: KH004-075-8h-312955


title: KH004-074-16h-312950

source_name: P. falciparum field isolate (ex-vivo), Pailin Cambodia, KH004-074


title: KH004-074-24h-312951


title: KH004-073-40h-312947

source_name: P. falciparum field isolate (ex-vivo), Pailin Cambodia, KH004-073


title: KH004-074-8h-312949


title: KH004-073-8h-312943


title: KH004-074-40h-312953


title: KH004-074-32h-312952


title: KH004-076-40h-312965


title: KH004-074-0h-312948


title: KH004-076-32h-312964


title: KH004-077-0h-312966


title: KH004-075-16h-312956


title: KH004-073-16h-312944


title: KH004-073-24h-312945


title: KH004-073-0h-312942


title: KH004-073-32h-312946


title: KH004-072-32h-312940

source_name: P. falciparum field isolate (ex-vivo), Pailin Cambodia, KH004-072


title: KH004-072-16h-312938


title: KH004-072-24h-312939


title: KH004-072-8h-312937


title: KH004-072-40h-312941


title: KH004-071-8h-312931

source_name: P. falciparum field isolate (ex-vivo), Pailin Cambodia, KH004-071


title: KH004-071-40h-312935

source_name: P. falciparum 3D7 RNA reference pool


title: KH004-072-0h-312936


title: KH004-070-40h-312929

source_name: P. falciparum field isolate (ex-vivo), Pailin Cambodia, KH004-070


title: KH004-071-24h-312933


title: KH004-071-16h-312932


title: KH004-070-32h-312928


title: KH004-070-8h-312925


title: KH004-071-0h-312930


title: KH004-068-24h-312921

source_name: P. falciparum field isolate (ex-vivo), Pailin Cambodia, KH004-068


title: KH004-068-16h-312920


title: KH004-070-16h-312926


title: KH004-070-0h-312924


title: KH004-068-40h-312923


title: KH004-068-8h-312919


title: VN001-120-218647

description:
VN001-120-218647
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-120

value: in vivo

value: Binh Phuoc, Vietnam

value: prior to artemisinin combination therapy (ACT)

tag: parasite clearance halflife upon artemisinin treatment (h)

value: In vitro


title: VN001-119-218643

description:
VN001-119-218643
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-119


title: KH004-068-0h-312918

value: ex vivo


title: KH004-068-32h-312922

value: blood


title: VN001-117-218635

description:
VN001-117-218635
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-117


title: VN001-112-218346

description:
VN001-112-218346
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-112


title: VN001-116-218631

description:
VN001-116-218631
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-116


title: VN001-118-218639

description:
VN001-118-218639
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-118


title: VN001-109-218334

description:
VN001-109-218334
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-109


title: VN001-115-218627

description:
VN001-115-218627
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-115


title: VN001-108-218330

description:
VN001-108-218330
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-108


title: VN001-113-218350

description:
VN001-113-218350
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-113


title: VN001-101-227153

description:
VN001-101-227153
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-101


title: VN001-102-227154

description:
VN001-102-227154
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-102


title: VN001-114-218354

description:
VN001-114-218354
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-114


title: VN001-110-218338

description:
VN001-110-218338
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-110


title: VN001-103-227155

description:
VN001-103-227155
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-103

source_name: P. falciparum 3D7 RNA reference pool


title: VN001-111-218342

description:
VN001-111-218342
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-111


title: VN001-107-218326

description:
VN001-107-218326
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-107


title: VN001-097-218285

description:
VN001-097-218285
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-097


title: VN001-099-218294

description:
VN001-099-218294
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-099


title: VN001-104-218314

description:
VN001-104-218314
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-104


title: KH004-071-32h-312934

description: Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate (ex-vivo), Pailin Cambodia, KH004-071


title: VN001-100-218298

description:
VN001-100-218298
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-100


title: VN001-105-218318

description:
VN001-105-218318
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-105


title: VN001-094-218274

description:
VN001-094-218274
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-094


title: VN001-106-218322

description:
VN001-106-218322
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-106


title: VN001-092-218266

description:
VN001-092-218266
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-092


title: VN001-093-218270

description:
VN001-093-218270
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-093


title: VN001-088-214822

description:
VN001-088-214822
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-088


title: VN001-089-214828

description:
VN001-089-214828
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-089


title: VN001-087-214818

description:
VN001-087-214818
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-087


title: VN001-086-214814

description:
VN001-086-214814
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-086


title: VN001-096-218282

description:
VN001-096-218282
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-096

source_name: P. falciparum 3D7 RNA reference pool


title: VN001-098-218290

description:
VN001-098-218290
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-098


title: VN001-079-214786

description:
VN001-079-214786
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-079


title: VN001-078-214782

description:
VN001-078-214782
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-078


title: VN001-077-214778

description:
VN001-077-214778
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-077


title: VN001-070-204129

description:
VN001-070-204129
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-070


title: VN001-082-214798

description:
VN001-082-214798
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-082


title: VN001-067-204117

description:
VN001-067-204117
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-067


title: VN001-084-214806

description:
VN001-084-214806
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-084


title: VN001-068-204121

description:
VN001-068-204121
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-068


title: VN001-072-204057

description:
VN001-072-204057
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-072


title: VN001-080-214790

description:
VN001-080-214790
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-080


title: VN001-073-214762

description:
VN001-073-214762
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-073


title: VN001-085-214810

description:
VN001-085-214810
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-085


title: VN001-069-204125

description:
VN001-069-204125
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-069


title: VN001-074-214766

description:
VN001-074-214766
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-074


title: VN001-064-204105

description:
VN001-064-204105
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-064


title: VN001-081-214794

description:
VN001-081-214794
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-081

source_name: P. falciparum 3D7 RNA reference pool


title: VN001-075-214770

description:
VN001-075-214770
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-075


title: VN001-076-214774

description:
VN001-076-214774
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-076


title: VN001-062-204092

description:
VN001-062-204092
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-062


title: VN001-063-204101

description:
VN001-063-204101
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-063


title: VN001-066-204113

description:
VN001-066-204113
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-066


title: VN001-091-218262

description:
VN001-091-218262
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-091


title: VN001-059-204081

description:
VN001-059-204081
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-059


title: VN001-060-204085

description:
VN001-060-204085
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-060


title: VN001-057-204073

description:
VN001-057-204073
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Binh Phuoc Vietnam, VN001-057