title: Dam_only-7

city: Heidelberg

first: Ingrid

last: Lohmann

address: Im Neuenheimer Feld 230

institute: Universität Heidelberg, Centre for Organismal Studies

description: processed data file: PolII_Germline.bedGraph

hyb_protocol: Affymetrix Processing of DamID DNA to GeneChip Drosophila Tiling Array, was performed as in http://www.flychip.org.uk/protocols/chip/affy_chip.php .

data_processing:
CEL files were processed with R function 'BPMAPCelParser' from R package 'rMAT' using bmap file for Dm_tiling2_MR_v01. Probe intensities were quantile normalized with R function 'normalize.Probes' from R package 'Starr’. The ratio between fused Dam and Dam only was calculated with R function 'getRatio' from R package 'Starr’.
BedGraphs were created using R. The columns represent the ratio (4th column) between experiments (fused Dam and Dam only) and genomic position (chromosome = 1st column, start = 2nd column, end = 3rd column).

organism: Drosophila melanogaster

source_name: control DamID, expt 7

growth_protocol: Dam was fused to the N terminus of abdA and zfh-1 (isoform RB 3165bp) and transgenic flies were generated. As a control for nonspecific Dam activity, transgenic flies expressing the Dam alone were used (Choksi et al., 2006). To express the AbdA-Dam fusion protein, we first generated a pNDam-Myc-abdA construct by cloning abdA in the pNDam-Myc vector (van Steensel et al., 2001) and then subcloned the NDam-Myc-abdA fragment into the pUAST-attB. The large isoform of the abd-A cDNA (abdA-RB) was amplified using the following primers: 5’- CAC CAT GTC AAA ATT TGT TTT CGA TAG -3’ (forward) and 5’- TTA GGA GTT GAC TTT GCT GAC -3’ (reverse). To express the Zfh1-Dam fusion protein, we first generated a pNDam-Myc-zfh1 construct by cloning zfh1 in the pNDam-Myc vector (van Steensel et al., 2001) and then subcloned the NDam-Myc-zfh1 fragment into the pUAST-attB. The large isoform of the zfh-1 cDNA (zfh1-RB) was amplified using the following primers: 5’- CAC CAT GTT GTC CTG TCT GGC GCC -3’ (forward) and 5’- CTA TTC CCT GTA GGG CTT GCA ATA GGA ATA CCG -3’ (reverse). Generation of transgenic flies using the PhiC31-integrase system (Bischof et al., 2013) and balancing of the stock was done by BestGene Inc. (Chino Hills, CA, U.S.A.). Plasmid DNA (pUAST-Dam-Myc-abdA-attB and pUAST-Dam-Myc-zfh1-attB) was injected into embryos of strain attP40 (cytogenetic location of attP-landing site: 25C7) to create an NDam-abdA-RB and an NDam-zfh1-RB fusion. Transgenic flies were balanced over CyO.

extract_protocol:
Isolation of genomic DNA (gDNA) for DamID: Genomic DNA was extracted from L3 testes, expressing either the NDam-abdA or the NDam-Zfh1 fusion protein and the Dam protein alone using a specific protocol (Tolhuis et al., 2011) and van Steensel personal communication. Testes from NDam-Myc (control), NDam-Myc-abdA transgenic, NDam-Myc-zfh1 and wt flies were dissected in PBS and transferred to a glass well on ice containing ice-cold PBS. Around 200 testes were pooled in 100 μl of lysis (TENS) buffer. 2 μl of Proteinase K (20 μg ml-1) (Roche) were added and incubated for 7 hours at 65°C. Tubes were mixed every 60 min by gentle tapping. RNAs were degraded by RNase A treatment: 1 μl RNase A (100 μg ml-1) (Qiagen) were added and incubated for 30 min at 37°C. An equal volume (200 μl) of phenol: chloroform: isoamyl alcohol (25:24:1, v/v, Invitrogen) was added and mixed well by inversion until a homogenous solution was acquired. Mixture was then applied onto spin phase lock gel light 1.5 ml tube (5PRIME, Inc.) for efficient separation of the two phases. Tubes were prepared by centrifugation for 1 min at 14,000 (Eppendorf Centrifuge-5424). Spin phase lock gel light tubes containing homogenous mixture of aqueous and organic solution were then spun for 5 min at 14,000 rpm. The gel inside the spin phase lock gel light tube then separated the aqueous and organic solution and the upper aqueous solution containing gDNA was transferred to a clean 1.5 ml tube, followed by DNA precipitation. Absence of DNA degradation and of RNA was verified on a 1% agarose gel.
Digestion and PCR amplification of Dam-methylated DNA. DNA digestion and PCR amplification was done essentially as previous described (Papagiannouli et al., 2014). To cut methylated GATC sequences, gDNA (2.5 μg) from each genotype (NDam-Myc, NDam-Myc-abdA, NDam-Myc-zfh1 and wt) was digested with DpnI in a total volume of 10 μl (1x buffer 4, NEB) at 37°C o/n in a PCR machine with a heated lid to avoid evaporation and condensation. For PCR amplification of the DpnI cut DNA sequences, adaptors were ligated to those fragments. Double-stranded adaptors were generated by mixing equal volumes of oligo AdRt (100 μM) (5’-CTAATACGACTCACTATAGGGCAGCGTGGTCGCGGCCGAGGA-3’) and oligo AdRb (100 μM) (5’-TCCTCGGCCG-3’)(Vogel et al., 2007) and heating to 100°C for 1 min. Adaptors were then allowed to cool down in about 20 min at RT. 5 μl of DpnI digested DNA (1.25 μg) and 2 μM of adaptors and 5 units of T4 Ligase in a final volume of 20 μl (1x T4 ligase buffer, Fermentas) were incubated for 3 hours at 16°C in a PCR machine. The ligase was inactivated at 65 °C for 10 min. To avoid amplification of fragments between two neighboring methylated GATC, which was not bound by the fusion construct itself, ligated fragments were cut at unmethylated GATC sites using DpnII. 20 μl of ligation product (1.25 μg) were mixed with 5 units of DpnII enzyme in a final volume of 80 μl (1x DpnII buffer, NEB) and incubated for 2 hours at 37°C in a PCR machine with heated lid to avoid evaporation and condensation. The enzyme was not inactivated and digested DNA was directly used for PCR reaction or stored at -20°C. DpnII digested DNA was amplified using following PCR program. The primer (5’-GGTCGCGGCCGAGGATC-3’) was designed to fit to the adaptor(Vogel et al., 2007). Reaction mix contained approximately 313 ng DNA, 0.2 mM dATP, dCTP, dGTP, 0.16 mM dTTP, 0.04 mM dUTP (needed for fragmentation of the DNA when Affymetrix microarrays are used), 1 μM primer and 1.6 μl of Advantage cDNA Polymerase Mix in a total volume of 80 μl (1x Advantage Polymerase Mix Buffer, Clontech). The PCR product was purified using the QIAquick PCR Purification Kit according to manufacturer’s instruction and eluted in 50μl ddH2O. Successful amplification was verified by running a small aliquot on a 1% agarose gel containing a final concentration of 0.5μg/ml ethidium bromide. Targeted DamID (TaDa) in Drosophila 3rd instar testes cyst and germline cells.
Cell-type specific DamID was performed in cyst cells (CySCs and SCCs) and early germline of 3rd instar larval testes for profiling RNA Pol II occupancy in these cells by crossing UAS-LT3-Dam-Pol II and UAS-LT3-Dam control flies to c587-GAL4 (somatic lineage) or Nanos-GAL4 (early germline) drivers. The protocol used for TaDa in L3 testes cyst cells was based on the protocol described above by integrating the modifications suggested by Tony Southall (Southall et al., 2013).

treatment_protocol: For identifying abd-A and Zfh1 binding regions in the Drosophila testis the fusion protein was expressed from the uninduced minimal Hsp70 promoter of the UAS vector pUAST.

value: testis

tag: gender

value: male

value: Dam only


title: Dam_PolII-4

status: Public on Jul 30 2018

type: genomic

country: Germany

scan_protocol: Affymetrix Processing of DamID DNA to GeneChip Drosophila Tiling Array, was performed as in http://www.flychip.org.uk/protocols/chip/affy_chip.php .

label: biotin

molecule: genomic DNA

source_name: Germline PolII, expt 2

tag: tissue

tag: treatment

value: Dam fused


title: Dam_only-3

description: processed data file: Zfh1.bedGraph

source_name: control DamID, expt 3

label_protocol: Affymetrix Processing of DamID DNA to GeneChip Drosophila Tiling Array, was performed as in http://www.flychip.org.uk/protocols/chip/affy_chip.php .


title: Dam_PolII-1

description: processed data file: PolII_Soma.bedGraph

source_name: Soma PolII DamID, expt 1


title: Dam_Zfh1-2

description: processed data file: Zfh1.bedGraph

source_name: Zfh1 DamID, expt 2


title: Dam_only-5

source_name: control DamID, expt 5


title: Dam_Zfh1-1

description: processed data file: Zfh1.bedGraph

source_name: Zfh1 DamID, expt 1


title: Dam_only-4

description: processed data file: Zfh1.bedGraph

source_name: control DamID, expt 4


title: Dam_only-6

source_name: control DamID, expt 6


title: Dam_AbdA-1

description: processed data file: AbdA.bedGraph

source_name: AbdA DamID, expt 1


title: Dam_PolII-2

source_name: Soma PolII DamID, expt 2


title: Dam_AbdA-2

description: processed data file: AbdA.bedGraph

source_name: AbdA DamID, expt 2


title: Dam_only-2

description: processed data file: AbdA.bedGraph

source_name: control DamID, expt 2


title: DCM_11

type: SRA

city: Tokyo

first: Seitaro

last: Nomura

state: Select a State or Province

address: 7-3-1, Hongo, Bunkyo-ku

department: Department of Cardiovascular Medicine

country: Japan

institute: The University of Tokyo

library_source: transcriptomic

data_processing:
For human single-cardiomyocyte RNA-seq, reads were mapped to the human genome (hg19) using Bowtie (version 1.1.1) with the parameters “-S -m 1 -l 36 -n 2 hg19”.
RPKM was calculated with reads mapped to the nuclear genome using DEGseq (version 1.8.0).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files including RPKM values for each sample

molecule: polyA RNA

organism: Homo sapiens

source_name: Cardiomyocytes

extract_protocol:
All experiments were approved by the ethics committee of the University of Tokyo. All procedures were conducted according to the Declaration of Helsinki, and all patients gave written informed consent before taking part in the study. Heart samples from normal subjects and patients with DCM (n = 10) were used. Heart tissues were obtained immediately after death due to non-cardiac causes (normal cardiac function) or during left ventricular assist device (LVAD) surgery, respectively. Immediately after the collection of the heart tissue, rod-shaped live cardiomyocytes were isolated, as previously described previously, and then incubated in lysis buffer.
Single-cell cDNA libraries were generated using the Smart-seq2 protocol.

tag: cell type

value: Cardiomyocytes

tag: disease

value: patients with dilated cardiomyopathy

tag: single cell or bulk

value: single cell


title: Dam_only-1

description: processed data file: AbdA.bedGraph

source_name: control DamID, expt 1


title: Dam_PolII-3

source_name: Germline PolII, expt 1


title: Dam_only-8

source_name: control DamID, expt 8


title: p300_Differentiating-24h_ChIP-seq

city: Ottawa

first: Qiao

last: Li

state: Ontario

address: 451 smyth road

department: Cellular and Molecular Medicine

country: Canada

institute: University of Ottawa

library_source: genomic

data_processing:
Sequencing reads were mapped to the mouse genome build mm9 using BWA-MEM, marking shorter split hits as secondary. Picard was used to filter out replicated reads and BAM files were converted into BED files after which aligned reads were extended by 125 bp at their 3’ end, and converted to bigwig format using the bedtools2 package.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files were generated with the bedtools2 package for ChIP-seq datasets and represent an indexed binary format allowing visualization of coverage with an appropriate genome browser.

organism: Mus musculus

source_name: C2C12 myoblasts

growth_protocol: Cells of the murine myoblasts cell line C2C12 (ATCC) were maintained in growth medium (GM), Dulbecco’s Modified Eagle Medium (D-MEM) supplemented with 10% Fetal Bovine Serum, at 37ºC with 5% CO2. Cells were induced to differentiate for up to 24 hours, by changing the medium of 80% confluent cell cultures to differentiation medium (DM), D-MEM supplemented with 2% horse serum.

extract_protocol:
Cells were crosslinked in formaldehyde and sonicated with a Covaris S220 Ultra-Sonicator system. DNA was precipitated with the appropriate antibody and sent for sequencing to the McGill University Genome Quebec Innovation Centre using Illumina HiSeq 2000 platform.
Genomic DNA libraries were prepared for sequencing by McGill University Genome Quebec Innovation Centre using standard Illumina protocols.

tag: strain

tag: chip antibody

value: p300 (Santa Cruz_sc-584)

tag: cell line

value: differentiated myoblast


title: GFP-positive rep 1 (Casz1 cKO)

first: Pierre

last: Mattar

state: ON

address: CCW6109, Box 511, 501 Smyth Rd.

institute: OHRI

data_processing:
Quality control was performed using FastQC
Reads were aligned to the mm10 genome using TopHat
Raw alignment counts were obtained using htseq-count
Differential expression analysis was performed using DESeq
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized read counts for each sample

molecule: total RNA

source_name: Flow sorted 4N retinal cells

growth_protocol: Cells were harvested from freshly dissected retinas, and cultured for 30 minutes in serum free medium described in Cayouette et al., Neuron 40(5):897

extract_protocol:
RNeasy mini columns (Qiagen)
RNA amplification was performed using Truseq PE Cluster kit v3 PE50 (Illumina)

value: retina

tag: age

value: post natal day 2

tag: genotype

value: Casz1 cKO


title: GFP-negative rep 2 (wild-type)

value: wild type


title: GFP-negative rep 1 (wild-type)


title: Input_ChIP-seq


title: p300_Proliferating_ChIP-seq

value: proliferating myoblasts


title: GFP-positive rep 2 (Casz1 cKO)


title: High fat diet 2

type: RNA

city: Monroe

first: Matthew

middle: Edward

last: Talbert

state: LA

address: 700 University Avenue

department: Biology

country: USA

institute: University of Louisiana at Monroe

description:
Gene expression from whole head tissue of mated female flies of genotype w1118 exposed to a high fat diet.
Mated female, w1118, head tissue.

hyb_protocol: Affymetrix Genome 2.0 Array manufacturer's protocols on biotinylated cRNA performed by the UT Southwestern Microarray Core Facility.

scan_protocol: Manufacturer's Affymetrix Scanning Protocol was followed on a Affymetrix GeneArray Scanner or the GeneChip Scanner 3000.

data_processing: Expression Console was utilized to generate CHP files (1.3.1.187). The data was analyzed by the UT Southwestern Microarray Core Facility using default analysis settings in GeneSpring GX with Tukey's Biweight normalization (Agilent). Significant results were filtered by a fold change of >1.5 and a P-value of less than .05.

source_name: Head tissue, high fat diet, 7 days

label_protocol: Biotinylated cRNA was generated per standard Affymetrix protocols using at least 1 ug of total RNA. RNA Integrity was verified prior in a 2100 Bioanalyzer (Agilent Technologies). Generated by the UT Southwestern Microarray Core Facility.

growth_protocol: All stocks were maintained on a Normal Diet (ND) in an incubator at 25°C and 30–50% humidity. Adult virgin female w1118 flies were collected at 0–3 days and transferred to separate vials of ND media at approximately equal population density. Virgin females were then mated synchronously with isogenic males for 48 hours.

extract_protocol: Total RNA from 25-50 snap-frozen and vibration-decapitated Drosophila head tissue extracted with RNeasy Mini Kit (Qiagen) using manufacturer's protocol.

treatment_protocol: Mated females were placed on respective experimental media (normal and high fat diets) and incubated for 7 days at 23°C in most cases, unless otherwise noted. Normal diet consisted of 10% lyophilized yeast, 10% sucrose, 5.2% cornmeal, 1.2% agar, 3.3% tegosept (dissolved in 70% ethanol) and 0.3% propionic acid (w/v). High fat diet consisted of the same but included 20% w/v coconut oil.

value: female

value: whole head

value: High-fat diet

tag: treatment duration

value: 7 days


title: High fat diet 1


title: Normal diet 3

description:
Gene expression from whole head tissue of mated female flies of genotype w1118 exposed to a normal and non-fat diet.
Mated female, w1118, head tissue.

source_name: Head tissue, normal diet, 7 days

value: Normal diet


title: Neocortex_WT_replicate_1

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

hyb_protocol: The standard hybridization protocol was used as recommended by Affymetrix

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000 through the University of Washington Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health (http://depts.washington.edu/ceeh/ServiceCores/FC1/FC1.html).

data_processing: RMA normalization at the transcript level, log2 transformed, using the oligo package of Bioconductor

label: Cy3 fluorescent label

source_name: mouse embryonic neocortex

label_protocol: For microarray hybridization, RNA was processed for hybridization to Affymetrix Mouse 1.0 ST Array through a core facility in the Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health at the University of Washington according to the manufacturer's instructions.

extract_protocol: RNA was extracted from tissue samples using the Qiagen RNeasy kit, following the manufacturer's recommendations. Quality and quantity were assessed using an Agilent 2100 Bioanalyzer, and NanoDrop 8000 spectrophotometer, respectively.

value: embryonic cortex

tag: developmental stage

value: Wild type


title: Neocortex_Tbr1_KO.Tbr2_cKO_replicate_2

value: Tbr1 knockout/Tbr2 conditional knockout


title: Neocortex_WT_replicate_2


title: High fat diet 3


title: Normal diet 1


title: Neocortex_WT_replicate_3


title: Neocortex_Tbr1_KO_replicate_4

value: Tbr1 knockout


title: Neocortex_Tbr1_KO.Tbr2_cKO_replicate_3


title: Neocortex_Tbr1_KO_replicate_2


title: Normal diet 2


title: Neocortex_Tbr1_KO_replicate_3


title: Neocortex_Tbr1_KO.Tbr2_cKO_replicate_1


title: H1

city: Ribeirão Preto

first: Ana

middle: Lucia

last: Fachin

state: SP

address: Av. Costabile Romano, 2201

department: Biotechonology  Unit

country: Brazil

institute: Unaerp

description:
HaCat cell line - control, replicate I
geneCounts_hg19_H.txt
DESeq_hg19_CO_vs_H.csv

data_processing:
FastQC v0.11.2 was used to visualize the libraries quality before and after trimming.
FASTX-Tookit (fastq_quality_filter) was used to remove poor quality sequences, such that remaining sequences had a minimum quality score of 20 with a minimum of 50% of bases within a read meeting this quality score requirement.
Filtered reads were mapped onto the T. rubrum genome using the Bowtie2 v2.1.0.
Reads were assigned to annotated genes and counted using the "summarizeOverlaps" function from the GenomicRanges Bioconductor package.
The data were analyzed using the R package DESeq version 1.28.0. The samples were normalized, and the dispersions were estimated using the default DESeq settings. DESeq was then used to identify differentially expressed genes for each pairwise comparison of interest. Genes with an adjusted P value of < 0.05 and a log2(foldchange) > 1.0 (upregulation) or < -1.0 (downregulation) were called as differentially expressed.
Genome_build: Broad T. rubrum strain CBS118892 genome
Supplementary_files_format_and_content: tab-delimited text files include reads count values for each sample and DESeq output in CSV format containing mean expression, fold changes and p value.

source_name: HaCat cell line - control

growth_protocol: The Trichophyton rubrum strain CBS 118892 was cultured on Sabouraud dextrose agar  for 15 days at 28ºC. Keratinocytes were cultured in RPMI medium)supplemented with 10% fetal bovine serum (FBS) at 37ºC in a humidified atmosphere containing 5% CO2.

extract_protocol:
RNA extraction of T. rubrum and HaCat cell were performed using an Illustra RNAspin Mini RNA Isolation according to GE Healthcare guidelines.
RNA libraries were prepared for sequencing according to Illumina guidelines.

treatment_protocol: Pre-cultured conidia of T. rubrum were added to HaCat cell line and the co-culture was incubated for 24 h  at 37ºC in a humidified atmosphere containing 5% CO2.

tag: culture

value: HaCat cell line - control


title: root_Fe- and S-deficient_1

city: Verona

first: Anita

last: Zamboni

address: Strada Le Grazie, 15

department: Biotechnology

country: Italy

institute: University of Verona

hyb_protocol: 1.65 µg of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the custom Array 4x44K (GPL13627) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent G2565CA Mycroarray Scanner System (Agilent) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 3 µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (GE1_105_Dec08 and Grid: 022297_D_20160201) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Triticum turgidum subsp. durum

source_name: 5-day-old wheat seedlings grown for 14 additional days in Fe- and S-deficiency

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

growth_protocol: Durum wheat seeds (Triticum durum L. cv. Svevo) were germinated for five days in darkness at 20°C on paper towels soaked with distilled water. After germination, uniform seedlings were transferred to plastic pots (12 seedlings per pot) filled with 2.2 l of continuously aerated nutrient solutions. Nutrient solution was changed every 3 days. Plants were grown at 26°C for 14 h of light at 200 µmol m-2 s-1 PAR at leaf level and at 20°C for 10 h in dark (relative humidity 80%). Wheat roots were collected two weeks after the transfer to the NS.

extract_protocol: Total RNA was isolated using the SpectrumTM Plant Total RNA kit (Sigma-Aldrich).

treatment_protocol: Five-day-old wheat seedlings grown for 14 additional days in four different nutritional conditions (control, C, 1.2 mM sulfate and 80 µM FeIII-EDTA; Fe deficiency, Fe, 1.2 mM sulfate and 0 µM FeIII-EDTA; S deficiency, S, 0 mM sulfate and 80 µM FeIII-EDTA; dual deficiency, D, 0 mM sulfate and 0 µM FeIII-EDTA).

tag: cultivar

value: Durum wheat (Triticum durum L. cv. Svevo)

tag: developemental stage

value: 5-day-old wheat seedlings

tag: nutritional condition

value: Fe- and S-deficiency for 14 additional days

value: root


title: root_S-deficient_2

source_name: 5-day-old wheat seedlings grown for 14 additional days in S-deficiency

value: S-deficiency for 14 additional days


title: N+WEHS_8h_rep2

description: Roots of plants treated with NO3- and WEHS for 8h. It is the first of NO3-- and WEHS- treated biological replicates (8h) used in this experiment.

hyb_protocol: Hybridization and washing procedures were performed according to the NimbleGen Arrays User’s Guide (V 3.2).

scan_protocol: Each microarray was scanned using a Axon GenePix 4400 A at 532 nm (Cy-3 absorption peak) and GenePix Pro7 software (Molecular Devices, Sunnyvale, CA, USA) according to the manufacturers' instructions.

data_processing: Images were analyzed using NimbleScan v2.5 software (Roche), background correction and standard RMA normalization were selected.

organism: Zea mays

source_name: 5-day-old-plants treated with NO3- and WEHS for 8 h

label_protocol: cDNA synthesis and labeling reactions were performed according to the NimbleGen Arrays User’s Guide (V 3.2).

growth_protocol:
Maize seed (Zea mays L., cv. PR33T56, Pioneer Hybrid Italia S.p.A.) were germinated over aerated 0.5 mM CaSO4 solution in a dark growth chamber at 25°C. After 3 days, the seedlings were transferred into an aerated hydroponic system under controlled climatic conditions: day/night photoperiod, 16/8 h;
light intensity, 220 µE m-2 s-1; temperature (day/night) 25/20°C; RH 70 to 80 %. 5-day-old plants were transferred to a nutrient solution containing (µM): KCl 5; CaSO4 500; MgSO4 100; KH2PO4 175; NaFe-EDTA 20; H3BO3 2.5; MnSO4 0.2; ZnSO4 0.2; CuSO4 0.05; Na2MoO4 0.05.
Nitrogen was supplied in form of: 0.5 mM calcium nitrate (NO3- treatment) and 0.5 mM calcium nitrate and 5 mg Corg L-1 WEHS WEHS (NO3-+WEHS treatment). As control, plants were exposed to a nitrogen-free nutrient solution (Ctr treatment). For WEHS treatment plants was treated with 5 mg Corg L-1 WEHS (WEHS treatment).The pH of solution was adjusted to pH 6.0 with KOH.
After 4 hours six plants from each treatment were pooled together and root samples were frozen in liquid nitrogen and stored at -80°C until further processing. For NO3-+WEHS treatemnt plants were also sampled after 8 hours.

extract_protocol: Total RNA was isolated using the Invisorb Spin Plant RNA kit (Stratec Molecular, Berlin, Germany)

treatment_protocol:
Roots of 5-d-old maize plants were exposed for 4 and 8 hours to nutrient solution containing nitrogen in form of: 0.5 mM Ca(NO3)2 (NO3- treatment), 5 mg Corg L-1 WEHS (WEHS treatment) and  0.5 mM Ca(NO3)2 and  5 mg Corg L-1 WEHS (NO3-+WEHS treatment). As control plants were exposed to a nitrogen-free nutrient solution (Ctr).
Roots of six plants were pooled at the end of the experiment.

value: 5 day-old


title: N+WEHS_8h_rep3


title: root_Fe- and S-deficient_2


title: root_S-deficient_3


title: N+WEHS_4h_rep2

description: Roots of plants treated with NO3- and WEHS for 4h. It is the first of NO3-- and WEHS- treated biological replicates (4h) used in this experiment.

source_name: 5-day-old-plants treated with NO3- and WEHS for 4 h


title: root_Fe- and S-deficient_3


title: Neocortex_Tbr1_KO_replicate_1


title: N+WEHS_4h_rep1


title: WEHS_4h_rep3

description: Roots of plants treated with WEHS for 4h. It is the first of WEHS3- treated biological replicates (4h) used in this experiment.

source_name: 5-day-old-plants treated with WEHS for 4h


title: N+WEHS_8h_rep1


title: root_S-deficient_1


title: root_Fe-deficient_2

source_name: 5-day-old wheat seedlings grown for 14 additional days in Fe-deficiency

value: Fe-deficiency  for 14 additional days


title: Neocortex_Tbr2_cKO_replicate_1

value: Tbr2 conditional knockout


title: WEHS_4h_rep2


title: root_Fe-deficient_3


title: root_control_3

source_name: 5-day-old wheat seedlings grown for 14 additional days in a complete nutrient solution

value: complete nutrient solution for 14 additional days


title: root_control_2


title: root_Fe-deficient_1


title: Nitrate_4h_rep3

description: Roots of plants treated with NO3- for 4h. It is the first of  NO3- treated biological replicates (4h) used in this experiment.

source_name: 5-day-old-plants treated with NO3- for 4h


title: WEHS_4h_rep1


title: root_control_1


title: 786-0, drug treated and infected_DMF

first: Mohammed

last: Selman

address: 501 Smyth Road

department: Cancer Center

institute: Ottawa Hospital

description: Gene expression data from treated 786-0 cells

hyb_protocol: cRNA  was Hybridized for 16 hr at 45°C to Affymetrix Human PrimeView Array. Performed by The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Canada.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: Microarray data was processed using Transcriptome Analysis Console (TAC) 3.0 under default parameters of Gene Level Differential Expression Analysis.  The value definition was carried out with the Affymetrix Expression Console Software.

source_name: 786-0 cells 24 hour after Dimethyl fumarate treatment and  infection with VSVd51

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

growth_protocol: 786-0 cells were grown in in HyQ high-glucose Dulbecco’s modified Eagle’s medium supplemented with 10 % fetal calf serum and incubated at 37 °C in a 5% CO2 humidified incubator.

extract_protocol: Twenty-four hours post infection, RNA was collected using an RNA-easy kit (Qiagen, Valencia, CA, USA).

treatment_protocol: Cells were pretreated for 4hours with DEM, DEF, DMM, DMF or the vehicle. Following pre-treatment, the cells were infected with VSVΔ51 at an MOI of 0.01 or left uninfected.

value: kidney

value: renal cell adenocarcinoma


title: CO1

description:
Co-culture, replicate I
geneCounts_Trub_CO.txt
geneCounts_hg19_CO.txt
DESeq_Trub_CO_vs_CBS.csv
DESeq_hg19_CO_vs_H.csv

organism: Trichophyton rubrum

source_name: Co-culture

value: T. rubrum co-cultured with HaCat cells


title: Nitrate_4h_rep2


title: Control_4h_rep2

description: Roots of control plants (4h). It is the third of control biological replicates used in this experiment.


title: Nitrate_4h_rep1


title: Control_4h_rep3


title: CBS1

description:
CBS 118892 - control, replicate I
geneCounts_Trub_CBS.txt
DESeq_Trub_CO_vs_CBS.csv

source_name: CBS 118892 - control

value: CBS 118892 - control


title: clnR control - repl 2

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Reads were mapped to the Clostridium difficile Strain: 630Derm GCA_000953275.1 assembly genomic reference with the STAR aligner (v2.5.2b) with default alignment parameters.
Abundance estimation was performed with htseq-count (v 0.9.1)
Normalized expression (normalized read counts) was performed with DESeq2 (v1.10.1)
Genome_build: Clostridium difficile (Clostridioides difficile) Strain: 630Derm, (GCA_000953275.1_CD630DERM_genomic.fna, GCA_000953275.1_CD630DERM_genomic.gff)
Supplementary_files_format_and_content: tab delimited text file containing normalized read counts for each sample (in columns) and each annotated transcript (in rows).

organism: Clostridioides difficile

source_name: bacterial culture

growth_protocol: Active cultures of bacteria were diluted to an OD600 of approximately 0.05 in BHIS medium in an anaerobic chamber at 37˚C with or without the addition of 2 µg/ml LL-37. Samples were harvested for RNA extraction at OD600 = 0.50 during mid-logarithmic growth.

extract_protocol:
RNA was extracted using the Qiagen RNeasy kit and treated with DNase I.
Ribosomal transcripts were depleted from 2 ug of total RNA, and libraries were generated following Illumina's Scripseq V2 Complete- Bacterial library prep kits. (Epicentre, Madison, WI, USA)

treatment_protocol: Samples for RNA extraction were stored in 1:1 ethanol:acetone at -80˚C.

value: clnR


title: 630∆erm LL - repl 2

value: 2 ug/ml


title: clnR LL - repl 2


title: CO3

description:
Co-culture, replicate III
geneCounts_Trub_CO.txt
geneCounts_hg19_CO.txt
DESeq_Trub_CO_vs_CBS.csv
DESeq_hg19_CO_vs_H.csv


title: clnR LL - repl 1


title: clnR control - repl 1


title: CO2

description:
Co-culture, replicate II
geneCounts_Trub_CO.txt
geneCounts_hg19_CO.txt
DESeq_Trub_CO_vs_CBS.csv
DESeq_hg19_CO_vs_H.csv


title: 630∆erm control - repl 2


title: 786-0, drug treated and infected_DMM

source_name: 786-0 cells 24 hour after Dimethyl maleate treatment and  infection with VSVd51


title: 630∆erm control - repl 1


title: liver_STZ-O_ rep1

city: Chongqing

first: XINYU

last: LI

address: 1 YOUYI ROAD

country: China

institute: The First Affiliated Hospital of Chongqing Medical University

description:
D1_(RTA-1_0)
Gene expression data from offspring liver of male rats with high glucose level and then bred with normal female; high glucose level was caused by intraperitoneally injected streptozotocin

hyb_protocol: For instructions on how to fragment and label the single-stranded cDNA, refer to   the Affymetrix GeneChip® WT Terminal Labeling and Hybridization User Manual (PN 702880).

scan_protocol: After washing and staining, the arrays were scanned by the Affymetrix Scanner 3000(Affymetrix).

data_processing: Array signal intensities were analyzed with Expression Console software (version 1.4.1, Affymetrix). Briefly, raw data probes were normalized using robust multiarray analysis (RMA) for the background correction and quantile algorithm.

organism: Rattus norvegicus

source_name: liver of adult offspring from hyperglycemia father

label_protocol: The Affymetrix GeneChip WT Terminal Labeling Kit (PN 900671 or equivalent) is used for the fragmentation and labeling of the cDNA. Because the 2nd-cycle   (sense-strand) cDNA contains dUTP, the kit uses uracil-DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE1) to recognize and fragment the   cDNA at the unnatural dUTP residues. DNA is then labeled by terminal  deoxynucleotidyl transferase (TdT) using the Affymetrix proprietary DNA Labeling Reagent.

growth_protocol: All animals (both males and females) were maintained on a regular chow diet and had free access to water throughout the study. At the end of the experiment, animals were sacrificed in a fed condition by CO2 inhalation. One rat per litter (no differentiation in gender was made) was used for each test.

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

treatment_protocol: Following dissection, tissues were snap-frozen in liquid nitrogen. Prior to extraction and to facilitate multiple extractions from the same tissue, samples were pulverized in liquid nitrogen and were never allowed to thaw.

value: Sprague Dawley

tag: paternal status

value: hyperglycemia father

tag: tlssue

value: liver


title: 786-0, drug treated and infected_DEF

source_name: 786-0 cells 24 hour after Diethyl fumarate treatment and  infection with VSVd51

tag: tissue


title: 786-0, drug treated_DMM

source_name: 786-0 cells 24 hour after  Dimethyl maleate treatment

tag: cell type


title: liver_STZ-O_ rep2

description:
E1_(RTA-1_0)
Gene expression data from offspring liver of male rats with high glucose level and then bred with normal female; high glucose level was caused by intraperitoneally injected streptozotocin


title: 786-0, untreated, rep2

description: Gene expression data from 786-0 cells

source_name: 786-0 cells 24 hour after mock treatment


title: liver_CB-O_ rep1

description:
G1_(RTA-1_0)
Gene expression data from offspring liver of male rats with normal glucose level and then bred with normal female;male rats were intraperitoneally injected with citrate buffer.

source_name: liver of adult offspring from father with normal blood sugar level

value: father with normal blood sugar level


title: liver_STZ-O_ rep3

description:
F1_(RTA-1_0)
Gene expression data from offspring liver of male rats with high glucose level and then bred with normal female; high glucose level was caused by intraperitoneally injected streptozotocin


title: 786-0, infected, rep1

source_name: 786-0 cells 24 hour after infection with VSVd51


title: 786-0, drug treated_DEM

source_name: 786-0 cells 24 hour after  Diethyl maleate treatment


title: 786-0, drug treated_DMF

source_name: 786-0 cells 24 hour after  Dimethyl fumarate treatment


title: 786-0, infected, rep2


title: CBS2

description:
CBS 118892 - control, replicate II
geneCounts_Trub_CBS.txt
DESeq_Trub_CO_vs_CBS.csv


title: liver_CB-O_ rep2

description:
H1_(RTA-1_0)
Gene expression data from offspring liver of male rats with normal glucose level and then bred with normal female;male rats were intraperitoneally injected with citrate buffer.


title: N+WEHS_4h_rep3

source_name: 5-day-old-plants treated with NO3- and WEHS for 4 h


title: 786-0, drug treated and infected_DEM

source_name: 786-0 cells 24 hour after Diethyl maleate treatment and  infection with VSVd51


title: liver_CB-O_ rep3

description:
A2_(RTA-1_0)
Gene expression data from offspring liver of male rats with normal glucose level and then bred with normal female;male rats were intraperitoneally injected with citrate buffer.


title: 786-0, drug treated_DEF

source_name: 786-0 cells 24 hour after  Diethyl fumarate treatment


title: Control_4h_rep1


title: 630∆erm LL - repl 1


title: CBS3

description:
CBS 118892 - control, replicate III
geneCounts_Trub_CBS.txt
DESeq_Trub_CO_vs_CBS.csv


title: colon cancer cells of patient #5_rep1

status: Public on Jul 29 2018

city: Callaghan

first: Lei

last: Jin

state: NSW

address: University Drive

country: Australia

institute: The University of Newcastle

description: lncRNA expression profile in colon cancer cells of patient #5

hyb_protocol: The labeled samples were hybridized with Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242) in Agilent’s SureHyb Hybridization Chambers according to the manufacturer’s standard protocols (Agilent Technologies).

scan_protocol: The arrays were scanned by the Agilent Microarray Scanner (Agilent p/n G2565BA).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies).

source_name: laser capture micro-dissected (LCM) colon cancer cells of patient #5,replicate1

label_protocol: The toatl RNA were labled with the Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) according to the manufacturer's instruction.

value: colon cancer cells

tag: gender

value: Male

tag: age at diagnosis

tag: tnm stage

value: II


title: normal colon epithelial cells of patient #4_rep1

description: lncRNA expression profile in normal colon epithelial cells of patient #4

source_name: laser capture micro-dissected (LCM) normal colon epithelial cells of patient #4,replicate1

value: normal colon epithelial cells

value: Female


title: CD14 IL4_I

city: Vienna

first: Maximilian

last: Kauer

address: Zimmermannplatz 10

department: Molecular Biology

country: Austria

institute: CCRI, St.Anna Children Cancer Research Institute

hyb_protocol: Resulting double-stranded cDNA was used as a template to generate biotin-targeted cRNA following manufacturer’s specifications. Fifteen micrograms of the biotin labeled cRNA was fragmented to strands between 35 and 200 bases in length, 10 micrograms of which was hybridised onto the GeneChip® Human Genome U133 Plus 2.0 Array overnight in the GeneChip® Hybridisation oven 6400 using standard procedures. The arrays were washed and then stained in a GeneChip® Fluidics Station 45.

scan_protocol: Scanning was carried out with the GeneChip® Scanner 3000 and image analysis was performed using GeneChip® Operating Software

data_processing: The data was analyzed in R statistical environment using Bioconductor packages. Normalization was done using the frma algorithm

label: Biotin

source_name: peripheral blood- isolated CD14 monocytes

label_protocol: The preparation of labeled cRNA was performed according to the the GeneChip® Expression 3′-Amplification Reagents Two-cycle cDNA synthesis kit instructions (Affymetrix Inc, Santa Clara, CA, USA) to produce double-stranded cDNA

extract_protocol: RNA was extrated using the Qiagen RNeasy extraction kit according to the manufacturer's instructions.

value: sorted CD1a+CD207+ cells

tag: treatment


title: normal colon epithelial cells of patient #5_rep1

description: lncRNA expression profile in normal colon epithelial cells of patient #5

source_name: laser capture micro-dissected (LCM) normal colon epithelial cells of patient #5,replicate1


title: CD14 IL4_K


title: CD14 JAG2_Q

source_name: peripheral blood- sorted myeloid dendritic cell (CD1c DC)


title: colon cancer cells of patient #4_rep1

description: lncRNA expression profile in colon cancer cells of patient #4

source_name: laser capture micro-dissected (LCM) colon cancer cells of patient #4,replicate1


title: 786-0, untreated, rep1

description: Gene expression data from 786-0 cells

tag: cell line


title: CD1c JAG2_M


title: CD14 JAG2_I


title: normal colon epithelial cells of patient #3_rep1

description: lncRNA expression profile in normal colon epithelial cells of patient #3

source_name: laser capture micro-dissected (LCM) normal colon epithelial cells of patient #3,replicate1

value: III


title: Embryonic eye (e13.5)_Ftx KO_female_11-1

city: Bunkyo-ku

first: Yusuke

last: Hosoi

address: 1-5-45 Yushima

institute: Tokyo Medical and Dental University

description:
Gene expression of embryonic eye (e13.5)
KO F-11-1

hyb_protocol: Cy3-labeled RNA probes were hybridized to a whole mouse genome DNA oligo microarray (8 × 60K, Agilent) for 16 hours at 65°C according to the manufacturer’s instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner at a 5 um resolution.

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent).

source_name: Ftx KO_female_11-replicate1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated using RNAeasy column (QIAGEN).

treatment_protocol: Eyes of which the pigmented epithelium layer was surgically removed were collected.

value: Ftx KO

value: eye

value: female

value: Embryonic day 13.5


title: CD14 JAG2_K


title: CD1c IgG_N

value: human IgG


title: normal colon epithelial cells of patient #1_rep1

description: lncRNA expression profile in normal colon epithelial cells of patient #1

source_name: laser capture micro-dissected (LCM) normal colon epithelial cells of patient #1,replicate1


title: Embryonic eye (e13.5)_Ftx KO_female_10-1

description:
Gene expression of embryonic eye (e13.5)
KO F-10-1

source_name: Ftx KO_female_10-replicate1


title: CD14 IL4_Q


title: CD1c JAG2_N


title: Embryonic eye (e13.5)_Ftx KO_female_11-2

description:
Gene expression of embryonic eye (e13.5)
KO F-11-2

source_name: Ftx KO_female_11-replicate2


title: colon cancer cells of patient #3_rep1

description: lncRNA expression profile in colon cancer cells of patient #3

source_name: laser capture micro-dissected (LCM) colon cancer cells of patient #3,replicate1


title: colon cancer cells of patient #1_rep1

description: lncRNA expression profile in colon cancer cells of patient #1

source_name: laser capture micro-dissected (LCM) colon cancer cells of patient #1,replicate1


title: normal colon epithelial cells of patient #2_rep1

description: lncRNA expression profile in normal colon epithelial cells of patient #2

source_name: laser capture micro-dissected (LCM) normal colon epithelial cells of patient #2,replicate1


title: Embryonic eye (e13.5)_Ftx KO_female_9-2

description:
Gene expression of embryonic eye (e13.5)
KO F-9-2

source_name: Ftx KO_female_9-replicate2


title: CD1c JAG2_O


title: CD1c IgG_P


title: Embryonic eye (e13.5)_Ftx KO_female_10-2

description:
Gene expression of embryonic eye (e13.5)
KO F-10-2

source_name: Ftx KO_female_10-replicate2


title: Neocortex_Tbr2_cKO_replicate_2

source_name: mouse embryonic neocortex

value: embryonic cortex

value: Tbr2 conditional knockout


title: CD1c JAG2_P


title: colon cancer cells of patient #2_rep1

description: lncRNA expression profile in colon cancer cells of patient #2

source_name: laser capture micro-dissected (LCM) colon cancer cells of patient #2,replicate1


title: CD1c JAG2_L


title: Embryonic eye (e13.5)_Ftx KO_female_9-1

description:
Gene expression of embryonic eye (e13.5)
KO F-9-1

source_name: Ftx KO_female_9-replicate1


title: Embryonic eye (e13.5)_Ftx KO_female_6-2

description:
Gene expression of embryonic eye (e13.5)
KO F-6-2

source_name: Ftx KO_female_6-replicate2


title: CD1c_L

value: peripheral blood- isolated CD1c+ DCs

value: untreated


title: Embryonic eye (e13.5)_Ftx KO_female_8-2

description:
Gene expression of embryonic eye (e13.5)
KO F-8-2

source_name: Ftx KO_female_8-replicate2


title: CD14 JAG2_L

source_name: peripheral blood- isolated CD14 monocytes


title: CD14 JAG2_M


title: Embryonic eye (e13.5)_Ftx KO_female_5-2

description:
Gene expression of embryonic eye (e13.5)
KO F-5-2

source_name: Ftx KO_female_5-replicate2


title: Embryonic eye (e13.5)_Ftx KO_female_5-1

description:
Gene expression of embryonic eye (e13.5)
KO F-5-1

source_name: Ftx KO_female_5-replicate1


title: Embryonic eye (e13.5)_Ftx KO_female_6-1

description:
Gene expression of embryonic eye (e13.5)
KO F-6-1

source_name: Ftx KO_female_6-replicate1


title: Embryonic eye (e13.5)_Ftx KO_female_7-1

description:
Gene expression of embryonic eye (e13.5)
KO F-7-1

source_name: Ftx KO_female_7-replicate1


title: CD14_Q

value: peripheral blood- isolated CD14 monocytes


title: Embryonic eye (e13.5)_Ftx KO_female_4-2

description:
Gene expression of embryonic eye (e13.5)
KO F-4-2

source_name: Ftx KO_female_4-replicate2


title: CD14_L


title: CD14_N


title: Embryonic eye (e13.5)_Ftx KO_female_3-2

description:
Gene expression of embryonic eye (e13.5)
KO F-3-2

source_name: Ftx KO_female_3-replicate2


title: Embryonic eye (e13.5)_Ftx KO_female_8-1

description:
Gene expression of embryonic eye (e13.5)
KO F-8-1

source_name: Ftx KO_female_8-replicate1


title: Embryonic eye (e13.5)_Ftx KO_female_7-2

description:
Gene expression of embryonic eye (e13.5)
KO F-7-2

source_name: Ftx KO_female_7-replicate2


title: CD1c_O

source_name: peripheral blood- sorted myeloid dendritic cell (CD1c DC)


title: CD1c_M


title: Embryonic eye (e13.5)_Ftx KO_female_3-1

description:
Gene expression of embryonic eye (e13.5)
KO F-3-1

source_name: Ftx KO_female_3-replicate1


title: CD14_M


title: Embryonic eye (e13.5)_Ftx KO_female_4-1

description:
Gene expression of embryonic eye (e13.5)
KO F-4-1

source_name: Ftx KO_female_4-replicate1


title: CD14 JAG2_N


title: Embryonic eye (e13.5)_Ftx KO_female_1-1

description:
Gene expression of embryonic eye (e13.5)
KO F-1-1

source_name: Ftx KO_female_1-replicate1


title: CD14_I


title: CD14_K


title: Embryonic eye (e13.5)_Ftx KO_female_2-1

description:
Gene expression of embryonic eye (e13.5)
KO F-2-1

source_name: Ftx KO_female_2-replicate1


title: CD1c_P


title: Embryonic eye (e13.5)_Ftx KO_female_2-2

description:
Gene expression of embryonic eye (e13.5)
KO F-2-2

source_name: Ftx KO_female_2-replicate2


title: sRNA  Setaria viridis spikelet, stage 4 (completely out of leaf sheath) spik_stage4_r1_sRNA

status: Public on Jul 28 2018

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

data_processing:
Small RNA-seq: the adapter sequences were trimmed from raw sequence reads, and then the small RNA sequences were trimmed to the lengths between 18 and 34 nucleotides. small RNA reads were mapped to the maize genome (version  JGI version1 genome).
Genome_build: Setaria Genome (version JGI version1)
Supplementary_files_format_and_content: Tag count file
Supplementary_files_format_and_content: Text containing distinct smallRNAs with their raw abundance after removing the adapter sequences

organism: Setaria viridis

source_name: spikelet

extract_protocol: sRNA library constructed from leaf, whole panicle, and spikelet of Setaria. The small RNA libraries were generated as described by Lu et al. (Methods 2007, 43:110), followed by  Illumina TruSeq sample preparation followed by sequencing with Illumina's HiSeq 2000 instrument. The adapter sequences were removed, and the abundance of each distinct small RNA was determined.


title: sRNA  Setaria viridis spikelet, stage 3 (coming out of leaf sheath) spik_stage3_r1_sRNA


title: sRNA  Setaria viridis whole panicle, stage 5 (completely out of leaf sheath, after polination) wp_stage5_r2_sRNA

source_name: whole panicle


title: sRNA  Setaria viridis spikelet, stage 2 (inside leaf sheath) spik_stage2_r1_sRNA

value: spikelet, stage 2 (inside leaf sheath)


title: sRNA  Setaria viridis spikelet, stage 2 (inside leaf sheath) spik_stage2_r2_sRNA


title: sRNA  Setaria viridis spikelet, stage 3 (coming out of leaf sheath) spik_stage3_r2_sRNA


title: sRNA  Setaria viridis whole panicle, stage 5 (completely out of leaf sheath, after polination) wp_stage5_r1_sRNA


title: Embryonic eye (e13.5)_Ftx KO_male_3

description:
Gene expression of embryonic eye (e13.5)
KO M-3

source_name: Ftx KO_male_3

value: male


title: Embryonic eye (e13.5)_Ftx KO_female_1-2

description:
Gene expression of embryonic eye (e13.5)
KO F-1-2

source_name: Ftx KO_female_1-replicate2


title: Embryonic eye (e13.5)_Ftx KO_male_1

description:
Gene expression of embryonic eye (e13.5)
KO M-1

source_name: Ftx KO_male_1


title: Embryonic eye (e13.5)_WT_male_1

description:
Gene expression of embryonic eye (e13.5)
WT M-1

value: WT


title: Embryonic eye (e13.5)_WT_female_4

description:
Gene expression of embryonic eye (e13.5)
WT F-4


title: sRNA  Setaria viridis whole panicle, stage 3 (coming out of leaf sheath) wp_stage3_r2_sRNA


title: sRNA  Setaria viridis whole panicle, stage 2 (inside leaf sheath) wp_stage2_r2_sRNA


title: sRNA  Setaria viridis whole panicle, stage 3 (coming out of leaf sheath) wp_stage3_r1_sRNA


title: sRNA  Setaria viridis whole panicle, stage 1 (1.5 cm, inside leaf sheath) wp_stage1_r1_sRNA


title: sRNA  Setaria viridis leaf  leaf_Sv_r2_sRNA

source_name: leaf

value: leaf


title: Embryonic eye (e13.5)_Ftx KO_male_2

description:
Gene expression of embryonic eye (e13.5)
KO M-2

source_name: Ftx KO_male_2


title: Embryonic eye (e13.5)_WT_female_2

description:
Gene expression of embryonic eye (e13.5)
WT F-2


title: Embryonic eye (e13.5)_WT_male_2

description:
Gene expression of embryonic eye (e13.5)
WT M-2


title: sRNA  Setaria viridis leaf  leaf_Sv_r1_sRNA


title: sRNA  Setaria viridis whole panicle, stage 1 (1.5 cm, inside leaf sheath) wp_stage1_r2_sRNA


title: Embryonic eye (e13.5)_WT_female_1

description:
Gene expression of embryonic eye (e13.5)
WT F-1


title: sRNA  Setaria viridis whole panicle, stage 4 (completely out of leaf sheath) wp_stage4_r1_sRNA


title: sRNA  Setaria viridis spikelet, stage 4 (completely out of leaf sheath) spik_stage4_r2_sRNA


title: Embryonic eye (e13.5)_WT_male_3

description:
Gene expression of embryonic eye (e13.5)
WT M-3


title: sRNA  Setaria viridis whole panicle, stage 4 (completely out of leaf sheath)  wp_stage4_r2_sRNA


title: sRNA  Setaria viridis whole panicle, stage 2 (inside leaf sheath) wp_stage2_r1_sRNA


title: tissue-dexamethasone-rep4

city: Krakow

first: Marcin

last: Piechota

address: Smetna 12

department: Molecular Neuropharmacology

country: Poland

institute: Institute of Pharmacology PAS

hyb_protocol: High-quality cRNA was then hybridized using Illumina’s direct hybridization array kit (Illumina). Each cRNA sample (1.5μg) was hybridized overnight to MouseWG-6 v2 BeadChip arrays (Illumina) in a multiple-step procedure according to the manufacturer’s instructions.

scan_protocol: The chips were washed, dried and scanned on a BeadArray Reader (Illumina). Raw microarray data were generated using BeadStudio v3.0 (Illumina).

data_processing:
The data were normalized using quantile normalization and then log2-transformed.
BeadArray R package v2.14.1 computed signal intensity.

source_name: mouse tissue, dexamethasone

label_protocol: A starting amount of 200 ng of high-quality total RNA (samples from individual mice were hybridized to separate microarrays) was used to generate cDNA and cRNA with an Illumina Total Prep RNA Amplification Kit (Illumina Inc., San Diego, CA, USA). The procedure consisted of reverse transcription using an oligo (dT) primer bearing a T7 promoter with an Array-Script. The obtained cDNA became a template for in vitro transcription with T7 RNA polymerase and biotin UTP, which generated multiple copies of biotinylated cRNA. The purity and concentration of the cRNA were checked using an ND- 1000 Spectrometer.

extract_protocol: RNA was isolated following the manufacturer's protocol and further purified using the RNeasy Mini Kit (Qiagen Inc.). The total RNA concentration was measured using a NanoDrop ND-1000 Spectrometer (NanoDrop Technologies Inc., Montchanin, DE, USA).

value: NAc

tag: agent

value: dexamethasone

tag: strain

tag: replicate


title: neuron-saline-rep5

source_name: mouse neuron, saline

value: neuron

value: saline


title: astrocyte-dexamethasone-rep4

source_name: mouse astrocyte, dexamethasone

value: astrocyte


title: neuron-dexamethasone-rep2

source_name: mouse neuron, dexamethasone


title: tissue-dexamethasone-rep2


title: astrocyte-saline-rep4

source_name: mouse astrocyte, saline


title: neuron-dexamethasone-rep3


title: neuron-dexamethasone-rep5


title: tissue-saline-rep4

source_name: mouse tissue, saline


title: astrocyte-saline-rep3


title: astrocyte-dexamethasone-rep2


title: astrocyte-saline-rep5


title: tissue-saline-rep2


title: astrocyte-dexamethasone-rep1


title: neuron-saline-rep3


title: astrocyte-dexamethasone-rep5


title: astrocyte-saline-rep2


title: tissue-saline-rep5


title: neuron-dexamethasone-rep4


title: tissue-dexamethasone-rep5


title: tissue-saline-rep1


title: tissue-dexamethasone-rep3


title: neuron-saline-rep1


title: astrocyte-dexamethasone-rep3


title: tissue-dexamethasone-rep1


title: neuron-saline-rep4


title: tissue-saline-rep3


title: neuron-saline-rep2


title: astrocyte-saline-rep1


title: V467_C6K5PANXX_GTGGCC_L007: Donor V467 white blood cells

city: Parkville

first: CSL

last: Research

state: VIC

address: 30 Flemington Rd

institute: CSL Limited / bio21 Institute

description: Donor V467 white blood cells

data_processing:
Reads were mapped to Homo sapiens GRCh37.p10 genome, using TopHat (TopHat v2.1.0, bowtie v2.2.5; Trapnell et al.,2009).
Mapped reads were summaried on a gene level using Ensembl ID gene annotation (Ensembl Release 70 based on GRCh37.p10 genome build) and featureCounts (Rsubread package v1.23.2; Yang et al., 2014) software.
Summarised read counts in this submission were NOT normalised nor filtered. We recommend using Bioconductor edgeR package functions: i) calcNormFactors (TMM method) to normalise between samples based on library sizes,  and ii) rpkm function to normalise between genes within a sample based on gene lengths.
Genome_build: GRCh37.p10
Supplementary_files_format_and_content: All processed data files are in a tab delimited file format. They contain raw read counts summarised on a gene level according to Ensembl Release 70 annotation.

source_name: RNA from white blood cells

extract_protocol:
RNA was extracted using RNeasy Mini Kit (QIAGEN, Germany)
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Peripheral blood was collected in EDTA vacutainers and red blood cells (RBC) lysed in ammonium chloride lysing solution. The remaining white blood cells (WBC) were stored in RNAprotect (QIAGEN, Germany) for later use

value: Blood

value: White blood cells

tag: donor

value: F

tag: age

tag: ancestry

tag: phenotype

value: Healthy

tag: das score

tag: disease activity

tag: arthropathymeds

tag: nsaids

tag: steroids

tag: biologics

tag: plaquenil

tag: leflumide

tag: sulfasalazine

tag: rituximab

tag: othermeds


title: V76_C6K5PANXX_GTGGCC_L005: Donor V76 white blood cells

description: Donor V76 white blood cells

tag: tissue

tag: cell type

tag: gender


title: V436_C6K5PANXX_CCGTCC_L003: Donor V436 white blood cells

description: Donor V436 white blood cells

tag: donor

tag: age


title: V405_C6K5PANXX_GTTTCG_L008: Donor V405 white blood cells

description: Donor V405 white blood cells

tag: ancestry

tag: phenotype


title: V3_C6K5PANXX_GTTTCG_L005: Donor V3 white blood cells

description: Donor V3 white blood cells

tag: das score

tag: disease activity


title: V448_C6K5PANXX_TGACCA_L002: Donor V448 white blood cells

description: Donor V448 white blood cells

value: M

tag: arthropathymeds

tag: nsaids


title: V58_C6K5PANXX_GGCTAC_L004: Donor V58 white blood cells

description: Donor V58 white blood cells

tag: steroids

tag: biologics


title: V391_C6K5PANXX_GTGAAA_L002: Donor V391 white blood cells

description: Donor V391 white blood cells

tag: plaquenil

tag: leflumide


title: V382_C6K5PANXX_ACTGAT_L002: Donor V382 white blood cells

description: Donor V382 white blood cells

tag: sulfasalazine

tag: rituximab


title: V447_C6K5PANXX_AGTTCC_L005: Donor V447 white blood cells

description: Donor V447 white blood cells

tag: tissue

tag: othermeds


title: V444_C6K5PANXX_ATGTCA_L003: Donor V444 white blood cells

description: Donor V444 white blood cells

tag: cell type

tag: gender


title: V418_C6K5PANXX_ACTTGA_L007: Donor V418 white blood cells

description: Donor V418 white blood cells

tag: donor

tag: age


title: V433_C6K5PANXX_CGATGT_L005: Donor V433 white blood cells

description: Donor V433 white blood cells

tag: ancestry

tag: phenotype


title: V268_C6K5PANXX_GCCAAT_L006: Donor V268 white blood cells

description: Donor V268 white blood cells

tag: das score

tag: disease activity


title: V269_C6K5PANXX_CGATGT_L008: Donor V269 white blood cells

description: Donor V269 white blood cells

tag: arthropathymeds

tag: nsaids


title: V279_C6K5PANXX_GTCCGC_L005: Donor V279 white blood cells

description: Donor V279 white blood cells

tag: steroids

tag: biologics


title: V311_C6K5PANXX_TAGCTT_L007: Donor V311 white blood cells

description: Donor V311 white blood cells

tag: plaquenil

tag: leflumide


title: V264_C6K5PANXX_ATGTCA_L001: Donor V264 white blood cells

description: Donor V264 white blood cells

tag: sulfasalazine

tag: rituximab


title: V250_C6K5PANXX_GAGTGG_L005: Donor V250 white blood cells

description: Donor V250 white blood cells

tag: tissue

tag: othermeds


title: V303_C6K5PANXX_GTGAAA_L008: Donor V303 white blood cells

description: Donor V303 white blood cells

tag: cell type

tag: gender


title: V183_C6K5PANXX_ATCACG_L008: Donor V183 white blood cells

description: Donor V183 white blood cells

tag: donor

tag: age


title: V305_C6K5PANXX_TGACCA_L004: Donor V305 white blood cells

description: Donor V305 white blood cells

tag: ancestry

tag: phenotype


title: V157_C6K5PANXX_AGTCAA_L001: Donor V157 white blood cells

description: Donor V157 white blood cells

tag: das score

tag: disease activity


title: V141_C6K5PANXX_TTAGGC_L001: Donor V141 white blood cells

description: Donor V141 white blood cells

tag: arthropathymeds

tag: nsaids


title: SN628_C6K5PANXX_ACTTGA_L001: Donor SN628 white blood cells

description: Donor SN628 white blood cells

value: Caucasian

value: Psoriatic arthritis

value: Methotrexate

tag: steroids

tag: biologics

value: Golimumab

value: Leflumide


title: V400_C6K5PANXX_GTTTCG_L007: Donor V400 white blood cells

description: Donor V400 white blood cells

tag: plaquenil

tag: leflumide


title: SN620_C6K5PANXX_ACTGAT_L007: Donor SN620 white blood cells

description: Donor SN620 white blood cells

value: Ankylosing spondylitis

value: Infliximab

tag: sulfasalazine

value: Sulfasalazine

tag: rituximab

value: Ibuprofen  digesic  PPI  Anti-hypertensive  zolendronic acid


title: V182_C6K5PANXX_CAGATC_L006: Donor V182 white blood cells

description: Donor V182 white blood cells

tag: tissue

tag: othermeds


title: neuron-dexamethasone-rep1

tag: cell type

value: neuron

tag: agent

value: dexamethasone

tag: strain

tag: replicate


title: SN615_C6K5PANXX_GAGTGG_L004: Donor SN615 white blood cells

description: Donor SN615 white blood cells

tag: donor

tag: gender

tag: age

tag: ancestry

tag: phenotype

value: Rheumatoid arthritis

value: Rituximab


title: SN605_C6K5PANXX_CAGATC_L003: Donor SN605 white blood cells

description: Donor SN605 white blood cells

value: Blood

value: White blood cells

tag: das score

tag: disease activity

value: Low

tag: arthropathymeds

tag: nsaids

tag: steroids

value: Prednisolone 10mg/day

value: Adalimumab

value: Leflumide 20mg/day


title: SN602_C6K5PANXX_CTTGTA_L003: Donor SN602 white blood cells

description: Donor SN602 white blood cells

value: F

value: Caucasian

value: Moderate

value: Prednisolone 5mg/day

tag: biologics

tag: plaquenil

value: Plaquenil

tag: leflumide

tag: sulfasalazine

tag: rituximab

value: Metformin


title: SN618_C6K5PANXX_TAGCTT_L001: Donor SN618 white blood cells

description: Donor SN618 white blood cells

tag: tissue

tag: cell type

value: M

value: Rheumatoid or Psoriatic arthritis

value: remission

value: Etanercept

tag: othermeds


title: SN589_C6K5PANXX_CGATGT_L001: Donor SN589 white blood cells

description: Donor SN589 white blood cells

tag: donor

tag: gender

value: Rheumatoid arthritis

value: Methotrexate

value: Rituximab

value: Allopurinol


title: SN619_C6K5PANXX_GCCAAT_L002: Donor SN619 white blood cells

description: Donor SN619 white blood cells

value: Blood

value: White blood cells

tag: age

tag: ancestry

value: Ankylosing spondylitis

value: Maybe Celebrex


title: SN612_C6K5PANXX_ATTCCT_L008: Donor SN612 white blood cells

description: Donor SN612 white blood cells

value: F

value: Caucasian

tag: phenotype

value: Psoriatic arthritis

tag: das score

value: Adalimumab


title: SN583_C6K5PANXX_ACTTGA_L006: Donor SN583 white blood cells

description: Donor SN583 white blood cells

value: Somalian

tag: disease activity

tag: arthropathymeds

value: Plaquenil

value: Leflumide 20mg/day

value: Insulin


title: SN525_C6K5PANXX_ATGTCA_L005: Donor SN525 white blood cells

description: Donor SN525 white blood cells

value: M

tag: nsaids

tag: steroids


title: SN569_C6K5PANXX_GCCAAT_L004: Donor SN569 white blood cells

description: Donor SN569 white blood cells

value: Rheumatoid arthritis

value: remission

value: Methotrexate 20mg/wk

tag: biologics

value: Tocilizumab

tag: plaquenil


title: SN575_C6K5PANXX_CAGATC_L007: Donor SN575 white blood cells

description: Donor SN575 white blood cells

value: Blood

tag: leflumide

tag: sulfasalazine


title: SN570_C6K5PANXX_CTTGTA_L007: Donor SN570 white blood cells

description: Donor SN570 white blood cells

tag: tissue

value: White blood cells

value: Prednisolone 5mg/day

tag: rituximab

value: Maybe Epilim  nortriptylline  oxycodone  panedein forte


title: SN591_C6K5PANXX_TAGCTT_L004: Donor SN591 white blood cells

description: Donor SN591 white blood cells

tag: cell type

value: Low

tag: othermeds

value: Quetiapine  Venlafaxine


title: SN599_C6K5PANXX_AGTTCC_L007: Donor SN599 white blood cells

description: Donor SN599 white blood cells

tag: donor

tag: gender

value: F

value: Caucasian

value: Methotrexate

value: Prednisolone 3mg/day

value: Infliximab

value: Irbesartan


title: SN606_C6K5PANXX_GTCCGC_L002: Donor SN606 white blood cells

description: Donor SN606 white blood cells

tag: age

tag: ancestry

value: Moderate

value: Prednisolone 10mg/day

value: Plaquenil

value: Sulfasalazine


title: SN588_C6K5PANXX_ATTCCT_L007: Donor SN588 white blood cells

description: Donor SN588 white blood cells

tag: phenotype

value: Rheumatoid arthritis

tag: das score

value: remission

value: prosyn

value: Tocilizumab


title: V160_C6K5PANXX_TTAGGC_L002: Donor V160 white blood cells

description: Donor V160 white blood cells

value: Blood

value: White blood cells

value: Healthy

tag: disease activity

tag: arthropathymeds


title: SN596_C6K5PANXX_GTGGCC_L008: Donor SN596 white blood cells

description: Donor SN596 white blood cells

value: F

value: Methotrexate 20mg/wk

tag: nsaids

value: Meloxicam

tag: steroids

value: Prednisolone 1mg/day

value: Esomeprazole  padol osteo


title: SN597_C6K5PANXX_GAGTGG_L007: Donor SN597 white blood cells

description: Donor SN597 white blood cells

value: Caucasian

value: Prednisolone 5mg/day

tag: biologics

tag: plaquenil


title: SN581_C6K5PANXX_GATCAG_L003: Donor SN581 white blood cells

description: Donor SN581 white blood cells

tag: leflumide

tag: sulfasalazine


title: SN568_C6K5PANXX_CCGTCC_L008: Donor SN568 white blood cells

description: Donor SN568 white blood cells

tag: tissue

value: Adalimumab

tag: rituximab


title: SN586_C6K5PANXX_ATTCCT_L002: Donor SN586 white blood cells

description: Donor SN586 white blood cells

tag: cell type

value: M

value: Golimumab

tag: othermeds

value: Candesartan


title: SN552_C6K5PANXX_ATCACG_L005: Donor SN552 white blood cells

description: Donor SN552 white blood cells

tag: donor

tag: gender

value: Psoriatic arthritis


title: SN523_C6K5PANXX_GTGGCC_L003: Donor SN523 white blood cells

description: Donor SN523 white blood cells

tag: age

tag: ancestry

value: Rheumatoid arthritis

value: remission

value: Plaquenil


title: SN522_C6K5PANXX_GTGAAA_L006: Donor SN522 white blood cells

description: Donor SN522 white blood cells

value: Blood

value: White blood cells

tag: phenotype

tag: das score

value: Methotrexate 10mg/wk

value: Leflumide 10mg/day


title: SN520_C6K5PANXX_TGACCA_L001: Donor SN520 white blood cells

description: Donor SN520 white blood cells

value: F

tag: disease activity

tag: arthropathymeds


title: SN518_C6K5PANXX_ATCACG_L001: Donor SN518 white blood cells

description: Donor SN518 white blood cells

value: Ankylosing spondylitis

tag: nsaids

tag: steroids

value: Infliximab


title: SN519_C6K5PANXX_GATCAG_L004: Donor SN519 white blood cells

description: Donor SN519 white blood cells

value: Caucasian

value: Moderate

value: Meloxicam

value: Kecort 40mg x2 on day of bloods

tag: biologics

tag: plaquenil


title: SN514_C6K5PANXX_GATCAG_L006: Donor SN514 white blood cells

description: Donor SN514 white blood cells

value: M

value: Methotrexate 15mg/wk

value: Adalimumab

tag: leflumide

tag: sulfasalazine

value: Targin  paracetamol


title: SN512_C6K5PANXX_TTAGGC_L005: Donor SN512 white blood cells

description: Donor SN512 white blood cells

tag: tissue

value: Etanercept

tag: rituximab

value: Padol  fexofedine


title: SN507_C6K5PANXX_TTAGGC_L004: Donor SN507 white blood cells

description: Donor SN507 white blood cells

value: Blood

tag: cell type

value: Golimumab

tag: othermeds

value: Esomeprazole


title: SN511_C6K5PANXX_TAGCTT_L003: Donor SN511 white blood cells

description: Donor SN511 white blood cells

value: White blood cells

tag: donor

tag: gender

value: Methotrexate

value: OCP


title: SN490_C6K5PANXX_CGTACG_L005: Donor SN490 white blood cells

description: Donor SN490 white blood cells

tag: age

tag: ancestry

value: Psoriatic arthritis

value: Prednisolone 5mg/day

value: aspirin  atenolol  amlodipine  perindopril  atorvastatin  fosamax


title: SN498_C6K5PANXX_ATCACG_L002: Donor SN498 white blood cells

description: Donor SN498 white blood cells

value: F

value: Caucasian

tag: phenotype

tag: das score

value: Infliximab

value: Calcium  Vit D  HRT


title: SN509_C6K5PANXX_ATCACG_L004: Donor SN509 white blood cells

description: Donor SN509 white blood cells

tag: disease activity

tag: arthropathymeds

value: prosyn

value: Gabapentin


title: SN487_C6K5PANXX_ACTGAT_L005: Donor SN487 white blood cells

description: Donor SN487 white blood cells

value: Rheumatoid arthritis

value: High

tag: nsaids

tag: steroids

value: Prednisolone


title: SN451_C6K5PANXX_TTAGGC_L008: Donor SN451 white blood cells

description: Donor SN451 white blood cells

value: Blood

value: M

value: remission

tag: biologics

value: Etanercept

tag: plaquenil

value: Telmisartan  atenolol. Atorvastatin  alendronic acid


title: SN506_C6K5PANXX_CCGTCC_L002: Donor SN506 white blood cells

description: Donor SN506 white blood cells

value: White blood cells

value: Filipino

value: Psoriatic arthritis

tag: leflumide

value: Leflumide

tag: sulfasalazine

value: Alendronic acid  atorvastatin


title: SN448_C6K5PANXX_CAGATC_L004: Donor SN448 white blood cells

description: Donor SN448 white blood cells

tag: tissue

value: Caucasian

value: Plaquenil

tag: rituximab

value: Digoxin  Warfarin


title: SN486_C6K5PANXX_CTTGTA_L004: Donor SN486 white blood cells

description: Donor SN486 white blood cells

tag: cell type

value: Moderate

value: Methotrexate

value: Abatacept

tag: othermeds

value: Maybe Metformin  metoprolol  perinopril  lecanidipine


title: SN479_C6K5PANXX_ACTGAT_L008: Donor SN479 white blood cells

description: Donor SN479 white blood cells

value: Blood

tag: donor

tag: gender

value: F

value: Rheumatoid arthritis

value: Methotrexate 20mg/wk

value: Prednisolone 7.5mg/day

value: Infliximab


title: SN481_C6K5PANXX_ATTCCT_L005: Donor SN481 white blood cells

description: Donor SN481 white blood cells

value: White blood cells

tag: age

tag: ancestry

value: Ankylosing spondylitis

value: Celebrex

value: Prednisolone

value: Golimumab

value: Sulfasalazine

value: Escitalopram


title: SN461_C6K5PANXX_GTGGCC_L002: Donor SN461 white blood cells

description: Donor SN461 white blood cells

value: Chinese

tag: phenotype

tag: das score

value: remission

value: Plaquenil


title: SN444_C6K5PANXX_GCCAAT_L001: Donor SN444 white blood cells

description: Donor SN444 white blood cells

value: Caucasian

tag: disease activity

value: High

tag: arthropathymeds


title: SN454_C6K5PANXX_TAGCTT_L006: Donor SN454 white blood cells

description: Donor SN454 white blood cells

value: Blood

value: F

value: Low

tag: nsaids

tag: steroids


title: SN445_C6K5PANXX_CGTACG_L008: Donor SN445 white blood cells

description: Donor SN445 white blood cells

value: Rheumatoid arthritis

value: Moderate

value: Methotrexate 20mg/wk

value: Prednisolone 5mg/day

tag: biologics

value: Adalimumab

tag: plaquenil

value: Plaquenil 200mg/day


title: SN517_C6K5PANXX_AGTTCC_L001: Donor SN517 white blood cells

description: Donor SN517 white blood cells

value: White blood cells

value: M

value: Ankylosing spondylitis

value: MethotrexateMaybe

value: Infliximab

tag: leflumide

tag: sulfasalazine


title: SN443_C6K5PANXX_CTTGTA_L001: Donor SN443 white blood cells

description: Donor SN443 white blood cells

tag: tissue

value: remission

value: Prednisolone 4mg/day

value: Etanercept

tag: rituximab


title: SN437_C6K5PANXX_GTCCGC_L008: Donor SN437 white blood cells

description: Donor SN437 white blood cells

value: Blood

tag: cell type

value: Pakistani

value: Methotrexate

tag: othermeds


title: S11 MCF7 ribo removed

city: Frederick

first: Bruce

last: Shapiro

state: Maryland

address: Building 560/Room 11-83

institute: National Cancer Institute

description: ribo removed

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and de-multiplexing reads for artificial PCR amplification
Reads were quality-filtered using the program sickle (version 1.33)
Reads were mapped to transcriptome using program salmon (version 0.9.1). Options: salmon quant -i INDEXFILE -l SF -r FASTQFILE -p 1 -o OUTPUTFILE
Transcripts listed in the quantification files generated by the salmon program were annotated with an RNA type classification.
Genome_build: hg38
Supplementary_files_format_and_content: transcript quantification files are in comma-separated-value (csv) format. Columns are: Name: Name of transcript; Length: Length of transcript; EffectiveLength: effective length; TPM: relative expression (transcripts per million); NumReads: number of mapped reads; RelNumReads: relative number of reads; Type: annotated type of RNA

source_name: cell line

growth_protocol: Cell culture

extract_protocol:
RNA was extracted from cell lines using Trizol
Sequencing libraries were prepared using standard protocols with homemade adaptors

tag: passage


title: SN435_C6K5PANXX_AGTTCC_L006: Donor SN435 white blood cells

description: Donor SN435 white blood cells

tag: donor

tag: gender

value: F

tag: age

value: Indian

value: Rheumatoid arthritis

value: Celebrex


title: S13 U2OS ribo removed

description: ribo removed


title: S14 293T rRNA band

description: rRNA band


title: S12 U2OS native

description: native


title: Sample 10_BJAB_NaB/TPA

city: Pittsburgh

first: Tuna

last: Toptan

state: PA

address: 5117 Centre Ave, Research Pav. Suite 1.8

department: Cancer Virology Program

institute: Hillman Cancer Center

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with trim galore, then mapped to Hg19 or KSHV/EBV genomes
FASTA formatted reference sequence and a SAM alignment generated by the BWA-MEM algorithm
Backspliced splice junctions were identified and mapped using CIRI2 prediction algorithm
Genome_build: Hg19 and EBV (Mutu strain KC207814), KSHV (BCBL1 strain HQ404500.1) reference genome files
Supplementary_files_format_and_content: ciri2 outfile (txt)

extract_protocol:
Trizol reagent (Invitrogen) was used to extract total RNA, according to the manufacturer’s instructions and treated with DnaseI (Ambion) to remove geomic DNA.
For RNA qulity control and circRNA library preparation, a total amount of 6 μg RNA per sample was used as input material. Ribosomal RNA was removed by rRNA probe andlinear RNA was removed by Rnase R (Lucigen). The CircRNA was interrupted randomly in adding fragmentation buffer
Using the fragmented CircRNA as a template, the first strand was synthesized with a random hexamers of six bases, followed by the addition of buffer, dNTPs, RNase H and DNA polymerase I to synthesize the second strand of the cDNA, then the CircRNA was purified by AMPure XP beads. The cohesive ends of the DNA were repaired to blunt ends using T4 DNA polymerase and Klenow DNA polymerase, 3'-end plus A-tail and ligated to the sequencing adapter followed by selection of the size of the fragment with AMPure XP beads, afterwards, the second strand of cDNA containing U was degraded with USER enzyme. CircRNA library was amplified by PCR

treatment_protocol: Samples 5, 7, and 9 were treated with DMSO for 48 hours and harvested for RNA extraction. Samples 6, 8, and 10 were treated with 20ng/ml TPA and 3mM NaB for 48 hours and harvested for RNA extraction.

tag: cell line

value: BJAB

tag: tissue/cell type

value: Burkitt-like lymphoma cell line

tag: dmso vs nab/tpa

value: NaB/TPA treated for 48h

tag: molecule subtype

value: RnaseR+, ribosome depleted RNA


title: SN483_C6K5PANXX_AGTCAA_L003: Donor SN483 white blood cells

description: Donor SN483 white blood cells

value: White blood cells

value: M

tag: ancestry

value: Caucasian

tag: phenotype

tag: das score

tag: disease activity

tag: arthropathymeds

tag: nsaids

tag: steroids

value: Sulfasalazine


title: SN484_C6K5PANXX_ACAGTG_L004: Donor SN484 white blood cells

description: Donor SN484 white blood cells

tag: tissue

tag: cell type

value: Psoriatic arthritis

tag: biologics

value: Infliximab

tag: plaquenil

tag: leflumide

tag: sulfasalazine

tag: rituximab


title: S10 MCF7 native

description: native

tag: passage


title: S9 HeLa ribo removed

description: ribo removed

value: HeLa


title: SN433_C6K5PANXX_AGTCAA_L006: Donor SN433 white blood cells

description: Donor SN433 white blood cells

value: Blood

tag: donor

tag: gender

tag: age

value: Chinese

value: High

tag: othermeds


title: SN446_C6K5PANXX_CGATGT_L002: Donor SN446 white blood cells

description: Donor SN446 white blood cells

tag: ancestry

tag: phenotype

tag: das score

value: remission

value: Prednisolone 6mg/day

value: Etanercept


title: S7 293T ribo removed

description: ribo removed


title: S8 HeLa native

description: native


title: Sample 9_BJAB_UNT

tag: cell line

value: BJAB

tag: tissue/cell type

tag: dmso vs nab/tpa

value: DMSO treated

tag: molecule subtype


title: S15 HeLa rRNA band

description: rRNA band

tag: cell type


title: SN431_C6K5PANXX_GATCAG_L001: Donor SN431 white blood cells

description: Donor SN431 white blood cells

tag: tissue

value: Rheumatoid arthritis

tag: disease activity

value: Moderate

tag: arthropathymeds

tag: nsaids

tag: steroids

tag: biologics

tag: plaquenil


title: Sample 8_BCBL1_NaB/TPA

value: B cell lymphoma cell line

value: NaB/TPA treated for 48h

value: RnaseR+, ribosome depleted RNA


title: S4 HeLa native

description: native

tag: passage


title: Sample 7_BCBL1_UNT


title: SN425_C6K5PANXX_CGATGT_L004: Donor SN425 white blood cells

description: Donor SN425 white blood cells

value: White blood cells

tag: donor

tag: gender

value: M

tag: age

tag: leflumide

tag: sulfasalazine

tag: rituximab

tag: othermeds


title: SN426_C6K5PANXX_GGCTAC_L001: Donor SN426 white blood cells

description: Donor SN426 white blood cells

value: F

tag: ancestry

value: Caucasian

tag: phenotype

tag: das score


title: S5 HeLa-protein removed

description: protein removed

tag: cell type

value: HeLa


title: Sample 6_BC1_NaB/TPA

tag: cell line

tag: tissue/cell type

value: lymphoma cell line

tag: dmso vs nab/tpa

tag: molecule subtype


title: S2 293T native

description: native


title: SN424_C6K5PANXX_GTGAAA_L003: Donor SN424 white blood cells

description: Donor SN424 white blood cells

tag: tissue

value: Blood

tag: disease activity

tag: arthropathymeds

value: Methotrexate

tag: nsaids

tag: steroids

value: Prednisolone

tag: biologics

value: Adalimumab

tag: plaquenil

value: Plaquenil

value: Sulfasalazine


title: S3 293T protein removed

description: protein removed

tag: passage


title: Sample 5_BC1_UNT

value: DMSO treated


title: SN423_C6K5PANXX_CCGTCC_L005: Donor SN423 white blood cells

description: Donor SN423 white blood cells

tag: donor

tag: gender

tag: age

value: Rheumatoid arthritis

value: remission

value: Etanercept

tag: leflumide

tag: sulfasalazine

tag: rituximab

tag: othermeds


title: S1 293T native with added control duplex

description: native with added control duplex

tag: cell type


title: Sample 4_PTLD9

source_name: tissue

tag: tissue/cell type

value: post-transplant lymphoproliferative disease (PTLD)

tag: ebv status with eber

value: EBER staining positive

tag: molecule subtype

value: RnaseR+, ribosome depleted RNA


title: Sample 3_PTLD6


title: S6 293T native

description: native


title: SN422_C6K5PANXX_GAGTGG_L002: Donor SN422 white blood cells

description: Donor SN422 white blood cells

tag: tissue

value: White blood cells

value: F

tag: ancestry

tag: phenotype

tag: das score

tag: disease activity

value: High

tag: arthropathymeds

value: Prednisolone 15mg/day for 1 week


title: Sample 2_PTLD5

value: EBER staining negative


title: SN420_C6K5PANXX_AGTCAA_L005: Donor SN420 white blood cells

description: Donor SN420 white blood cells

value: Blood

tag: donor

value: Caucasian

tag: nsaids

tag: steroids

tag: biologics

tag: plaquenil

value: Plaquenil 400mg/day

value: Propranolol


title: Sample 1_PTLD4


title: SN401_C6K5PANXX_CCGTCC_L006: Donor SN401 white blood cells

description: Donor SN401 white blood cells

tag: gender

tag: age

value: Adalimumab

tag: leflumide

tag: sulfasalazine

tag: rituximab


title: SN399_C6K5PANXX_ACTTGA_L003: Donor SN399 white blood cells

description: Donor SN399 white blood cells

tag: cell type

value: Methotrexate 20mg/wk

value: Prednisolone 7.5mg/day

tag: othermeds


title: SN421_C6K5PANXX_AGTTCC_L003: Donor SN421 white blood cells

description: Donor SN421 white blood cells

tag: tissue

tag: ancestry

value: Rheumatoid arthritis

value: Moderate


title: SN393_C6K5PANXX_GAGTGG_L008: Donor SN393 white blood cells

description: Donor SN393 white blood cells

tag: phenotype

tag: das score


title: SN392_C6K5PANXX_ACAGTG_L002: Donor SN392 white blood cells

description: Donor SN392 white blood cells

tag: disease activity

value: remission

tag: arthropathymeds

value: prosyn

value: Prednisolone 3mg/day

value: Sulfasalazine 20mg/day

value: Ca  Vit D  irbesartan


title: SN419_C6K5PANXX_GTGAAA_L005: Donor SN419 white blood cells

description: Donor SN419 white blood cells

value: White blood cells

tag: donor

value: M

tag: nsaids


title: SN293_C6K5PANXX_ACAGTG_L006: Donor SN293 white blood cells

description: Donor SN293 white blood cells

value: F

value: Meloxicam

tag: steroids

value: Prednisolone

tag: biologics


title: SN258_C6K5PANXX_CTTGTA_L006: Donor SN258 white blood cells

description: Donor SN258 white blood cells

value: Blood

tag: gender

value: Caucasian

value: Methotrexate 25mg/wk

value: Prednisolone 15mg/day

value: Tocilizumab

tag: plaquenil

value: Plaquenil 400mg/day

value: Leflumide 20mg/day


title: 415-CM

city: Ann Arbor

first: Simpa

middle: S

last: Salami

state: MI

address: 1500 E Medical Center Dr

department: Urology

institute: University of Michigan

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data processing, quality control and differential gene expression analysis were performed in R (version 3.4.4). BeadArray-specific variance stabilization, normalization, and gene annotation were performed using the lumi package. Data from all three batches were combined prior to quantile normalization using the normalizeBetweenArrays function from the limma package

source_name: cerebral milaria

label_protocol: Total RNA was purified from PAXgene-stabilized whole blood and depleted of globin mRNA transcripts using GLOBINclear Kits. RNA quality was assessed with either an Agilent 2100 Bioanalyzer or a Perkin Elmer LabChip GX and quantity was assessed with a NanoDrop 1000A Spectrophotometer. After RNA purification and quality assessment, 20 samples from each group were randomly selected for transcriptome analyses based on sufficient RNA yield and RNA integrity numbers (>6.1). Approximately 300 ng of total RNA was used in Illumina TotalPrep RNA Amplification Kits to produce cRNA. Whole genome expression analyses were performed using HumanHT-12 v4 Expression BeadChips and an Illumina BeadArray Reader.

extract_protocol: Peripheral blood was collected by venipuncture on hospital admission (CM and SMA) or as an outpatient (CC) for thin and thick smears, hematological testing, plasma, and filter paper blood spots. Whole blood was collected for RNA using the PAXgene Blood RNA System (PreAnalytiX GmbH; Hombrechtikon, Switzerland). Plasma and PAXgene whole-blood samples were stored at -80°C until further processing and analysis.

tag: diagnosis

value: cerebral milaria

tag: processing batch

tag: age

tag: Sex

value: Male

tag: parasite density on admission

tag: plasma pfhrp2

tag: hemoglobin

tag: hb genotype

value: AA

tag: hiv screen

tag: platelet

tag: plasma epo ria

tag: ifn-gamma

tag: tnf

tag: plasma ho-1

tag: total bilirubin


title: 585-CC

source_name: community children without Plasmodium falciparum infection

value: no Plasmodium falciparum infection


title: 463-CC

value: Female

value: AS


title: A498 DGAT1/2 shRNA cells, doxycycline treatment, hypoxia, biol repl 2

city: Philadelphia

first: Daniel

last: Ackerman

address: 421 Curie Blvd, BRB II/III, Rm 646

institute: University of Pennsylvania

hyb_protocol: Five and a half micrograms of labeled cDNA were added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Human Transcriptome 2.0 ST GeneChips (Affymetrix Inc., Santa Clara CA) using the GeneChip Hybridization oven 645. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A GeneChip 3000 7G scanner was used to collect fluorescence signal.

data_processing: RMA-sst was applied using Affymetroix Transcriptome Analysis Console (TAC) with default settings

source_name: A498 expressing induced DGAT1/2 shRNA construct grown under serum deprivation and hypoxia

label_protocol: 250ng of total RNA was converted to biotinylated cDNA using standard protocols used by the Molecular Profiling Core at the University of Pennsylvania

growth_protocol: Low serum growth conditions. Vehicle/Doxycycline treatment was applied for 5 days and normoxic/hypoxic treatment was applied for 2 days before RNA extraction

extract_protocol: total RNA extraction was performed with RNEasy columns according to the manufacturer's instructions

tag: treatment

value: doxycycline

tag: cell line

tag: cell type

value: Clear cell renal cell carcinoma (ccRCC)

tag: genotype/variation

value: DGAT1/2 knockdown

tag: oxygen levels

value: hypoxia


title: 382-CC

tag: diagnosis

tag: processing batch

tag: age

tag: Sex


title: 352-SMA

source_name: severe malaral anemia

value: severe malaral anemia

tag: parasite density on admission

tag: plasma pfhrp2

tag: hemoglobin

tag: hb genotype


title: 344-CM

tag: hiv screen

tag: platelet

tag: plasma epo ria

tag: ifn-gamma


title: 357-CM

tag: tnf

tag: plasma ho-1

tag: total bilirubin


title: A498 DGAT1/2 shRNA cells, doxycycline treatment, normoxia, biol repl 4

source_name: A498 expressing induced DGAT1/2 shRNA construct grown under serum deprivation and normoxia

treatment_protocol: Vehicle/Doxycycline treatment was applied for 5 days and normoxic/hypoxic treatment was applied for 2 days before RNA extraction

tag: treatment

tag: cell line

tag: cell type

tag: genotype/variation

value: normoxia


title: A498 DGAT1/2 shRNA cells, doxycycline treatment, hypoxia, biol repl 4

tag: oxygen levels


title: 335-SMA

tag: diagnosis

tag: processing batch

tag: age

tag: Sex


title: 320-CC

tag: parasite density on admission

tag: plasma pfhrp2

tag: hemoglobin

tag: hb genotype


title: 408-CM

tag: hiv screen

tag: platelet

tag: plasma epo ria

tag: ifn-gamma


title: 358-CC

tag: tnf

tag: plasma ho-1

tag: total bilirubin


title: 370-CC


title: 416-CM


title: 570-CM


title: 346-CM


title: 338-CC


title: 356-SMA


title: A498 DGAT1/2 shRNA cells, doxycycline treatment, hypoxia, biol repl 1

tag: treatment

tag: cell line

tag: cell type

tag: genotype/variation


title: A498 DGAT1/2 shRNA cells, doxycycline treatment, hypoxia, biol repl 3

tag: oxygen levels


title: A498 DGAT1/2 shRNA cells, doxycycline treatment, normoxia, biol repl 3


title: 556-CC

tag: diagnosis

tag: processing batch

tag: age

tag: Sex


title: 345-SMA

tag: parasite density on admission

tag: plasma pfhrp2

tag: hemoglobin

tag: hb genotype


title: 291-CM

tag: hiv screen

tag: platelet

tag: plasma epo ria

tag: ifn-gamma


title: C84_C6K5PANXX_CGTACG_L002: Donor C84 white blood cells

description: Donor C84 white blood cells

tag: tissue

value: Blood

value: White blood cells

tag: donor

tag: gender

value: F

tag: ancestry

tag: phenotype

value: Healthy

tag: das score

tag: disease activity

tag: arthropathymeds

tag: nsaids

tag: steroids

tag: biologics

tag: plaquenil

tag: leflumide

tag: sulfasalazine

tag: rituximab

tag: othermeds


title: C82_C6K5PANXX_CAGATC_L001: Donor C82 white blood cells

description: Donor C82 white blood cells

tag: cell type

value: M

tag: age


title: 398-CC

tag: diagnosis

tag: processing batch

tag: Sex

tag: parasite density on admission

tag: plasma pfhrp2

tag: hemoglobin

tag: hb genotype

tag: hiv screen

tag: platelet

tag: plasma epo ria

tag: ifn-gamma

tag: tnf

tag: plasma ho-1

tag: total bilirubin


title: A498 DGAT1/2 shRNA cells, doxycycline treatment, normoxia, biol repl 2

tag: treatment

tag: cell line

tag: genotype/variation

tag: oxygen levels


title: 330-CM

tag: diagnosis

value: cerebral milaria

tag: processing batch

tag: age


title: 321-SMA

tag: Sex

value: Male

tag: parasite density on admission

tag: plasma pfhrp2

value: SS


title: C72_C6K5PANXX_ATGTCA_L006: Donor C72 white blood cells

description: Donor C72 white blood cells

tag: tissue

tag: cell type

tag: donor

tag: gender

tag: ancestry

tag: phenotype

tag: das score

tag: disease activity

tag: arthropathymeds

tag: nsaids

tag: steroids

tag: biologics

tag: plaquenil

tag: leflumide

tag: sulfasalazine

tag: rituximab

tag: othermeds


title: C56_C6K5PANXX_GTCCGC_L003: Donor C56 white blood cells

description: Donor C56 white blood cells

tag: tissue

tag: age


title: C478_C6K5PANXX_GGCTAC_L006: Donor C478 white blood cells

description: Donor C478 white blood cells

tag: cell type

tag: donor


title: 287-SMA

tag: diagnosis

tag: processing batch

tag: Sex

tag: parasite density on admission

tag: plasma pfhrp2

tag: hemoglobin

tag: hb genotype

value: AA

tag: hiv screen

tag: platelet

tag: plasma epo ria

tag: ifn-gamma

tag: tnf

tag: plasma ho-1

tag: total bilirubin


title: 248-CM

tag: age


title: C473_C6K5PANXX_TGACCA_L006: Donor C473 white blood cells

description: Donor C473 white blood cells

tag: tissue

tag: cell type

tag: gender

tag: ancestry

tag: phenotype

tag: das score

tag: disease activity

tag: arthropathymeds

tag: nsaids

tag: steroids

tag: biologics

tag: plaquenil

tag: leflumide

tag: sulfasalazine

tag: rituximab

tag: othermeds


title: 264-CM

tag: diagnosis

tag: processing batch

tag: age

tag: Sex

value: Female

tag: parasite density on admission

tag: plasma pfhrp2

tag: hemoglobin

tag: hb genotype

tag: hiv screen

tag: platelet

tag: plasma epo ria

tag: ifn-gamma

tag: tnf

tag: plasma ho-1

tag: total bilirubin


title: C473_C6K5PANXX_CGTACG_L003: Donor C473 white blood cells

description: Donor C473 white blood cells

tag: tissue

tag: cell type

tag: donor

tag: gender

tag: ancestry

tag: phenotype

tag: das score

tag: disease activity

tag: arthropathymeds

tag: nsaids

tag: steroids

tag: biologics

tag: plaquenil

tag: leflumide

tag: sulfasalazine

tag: rituximab


title: 230-CM

tag: diagnosis

tag: processing batch

tag: age

tag: Sex

tag: parasite density on admission

tag: plasma pfhrp2

tag: hemoglobin

tag: hb genotype

tag: hiv screen

tag: platelet

tag: plasma epo ria

tag: ifn-gamma

tag: tnf

tag: plasma ho-1

tag: total bilirubin


title: 226-CM


title: C470_C6K5PANXX_GATCAG_L007: Donor C470 white blood cells

description: Donor C470 white blood cells

tag: tissue

tag: cell type

tag: donor

tag: gender

tag: ancestry

tag: phenotype

tag: das score

tag: disease activity

tag: arthropathymeds

tag: nsaids

tag: steroids

tag: biologics

tag: plaquenil

tag: leflumide

tag: sulfasalazine

tag: othermeds


title: 227-CM

tag: diagnosis

tag: processing batch

tag: age

tag: Sex

tag: parasite density on admission

tag: plasma pfhrp2

tag: hemoglobin

tag: hb genotype

tag: hiv screen

tag: platelet

tag: plasma epo ria

tag: ifn-gamma

tag: tnf

tag: plasma ho-1

tag: total bilirubin


title: 203-CM


title: 224-CC

value: no Plasmodium falciparum infection


title: 216-CC


title: A498 DGAT1/2 shRNA cells, doxycycline treatment, normoxia, biol repl 1

tag: treatment

value: doxycycline

tag: cell line

tag: cell type

tag: genotype/variation

tag: oxygen levels


title: C480_C6K5PANXX_ATTCCT_L004: Donor C480 white blood cells

description: Donor C480 white blood cells

tag: tissue

tag: donor

tag: gender

tag: age

tag: ancestry

tag: phenotype

tag: das score

tag: disease activity

tag: arthropathymeds

tag: nsaids

tag: steroids

tag: biologics

tag: plaquenil

tag: leflumide

tag: sulfasalazine

tag: rituximab

tag: othermeds


title: A498 DGAT1/2 shRNA cells, vehicle treatment, hypoxia, biol repl 3

source_name: A498 expressing non-induced DGAT1/2 shRNA construct grown under serum deprivation and hypoxia

tag: treatment

value: vehicle

tag: cell line

tag: cell type

value: Clear cell renal cell carcinoma (ccRCC)

tag: genotype/variation

value: wildtype

tag: oxygen levels


title: A498 DGAT1/2 shRNA cells, vehicle treatment, hypoxia, biol repl 2

value: hypoxia


title: A498 DGAT1/2 shRNA cells, vehicle treatment, normoxia, biol repl 4

source_name: A498 expressing non-induced DGAT1/2 shRNA construct grown under serum deprivation and normoxia

value: normoxia


title: A498 DGAT1/2 shRNA cells, vehicle treatment, hypoxia, biol repl 1


title: 100-SMA

tag: diagnosis

value: severe malaral anemia

tag: processing batch

tag: age

tag: Sex

tag: parasite density on admission

tag: plasma pfhrp2

tag: hemoglobin

tag: hb genotype

tag: hiv screen

tag: platelet

tag: plasma epo ria

tag: ifn-gamma

tag: tnf

tag: plasma ho-1

tag: total bilirubin


title: 189-SMA


title: 187-SMA


title: A498 DGAT1/2 shRNA cells, vehicle treatment, hypoxia, biol repl 4

tag: treatment

tag: cell line

tag: cell type

tag: genotype/variation


title: 180-SMA

tag: diagnosis

tag: processing batch

tag: age


title: A498 DGAT1/2 shRNA cells, vehicle treatment, normoxia, biol repl 3

tag: oxygen levels


title: 106-CM

tag: Sex

tag: parasite density on admission

tag: plasma pfhrp2

tag: hemoglobin


title: 184-SMA

tag: hb genotype

tag: hiv screen

tag: platelet

tag: plasma epo ria


title: 186-SMA

tag: ifn-gamma

tag: tnf

tag: plasma ho-1

tag: total bilirubin


title: A498 DGAT1/2 shRNA cells, vehicle treatment, normoxia, biol repl 2

tag: treatment

tag: cell line

tag: cell type

tag: genotype/variation


title: 99-CM

tag: diagnosis

tag: processing batch

tag: age


title: C451_C6K5PANXX_GCCAAT_L008: Donor C451 white blood cells

description: Donor C451 white blood cells

tag: tissue

value: Blood

value: White blood cells

tag: donor

tag: gender

tag: ancestry

tag: phenotype

tag: das score

tag: disease activity

tag: arthropathymeds

tag: nsaids

tag: steroids

tag: biologics

tag: plaquenil

tag: leflumide

tag: sulfasalazine

tag: rituximab

tag: othermeds


title: 86-SMA

tag: diagnosis

tag: processing batch

tag: age

tag: Sex

tag: parasite density on admission

tag: plasma pfhrp2

tag: hemoglobin

tag: hb genotype

tag: hiv screen

tag: platelet

tag: plasma epo ria

tag: ifn-gamma

tag: tnf

tag: plasma ho-1

tag: total bilirubin


title: C454_C6K5PANXX_GTTTCG_L002: Donor C454 white blood cells

description: Donor C454 white blood cells

tag: tissue

tag: cell type

tag: donor

tag: gender

tag: ancestry

tag: phenotype

value: Healthy

tag: das score

tag: disease activity

tag: arthropathymeds

tag: nsaids

tag: steroids

tag: biologics

tag: plaquenil

tag: leflumide

tag: sulfasalazine

tag: rituximab


title: C468_C6K5PANXX_ACAGTG_L008: Donor C468 white blood cells

description: Donor C468 white blood cells

value: M

tag: age

tag: othermeds


title: C450_C6K5PANXX_GTTTCG_L003: Donor C450 white blood cells

description: Donor C450 white blood cells

tag: tissue

tag: cell type


title: A498 DGAT1/2 shRNA xenograft, 200mg/kg doxycycline chow, 5 days, biol repl 4

description: Gene expression data from A498 cells following DGAT knockdown

source_name: A498 DGAT1/2 shRNA tumor from mouse treated with 200mg/kg doxycycline chow

growth_protocol: After subcutaneous injection of 5e6 A498 cells in NIH-III mice, tumors were allowed to grow to 300mm3 and were then randomly assigned to the two treatment groups

treatment_protocol: Mice were fed either control or doxycycline chow for 5 days ad lititum

value: A498 xenograft tumor

tag: treatment

tag: genotype/variation

value: DGAT1/2 knockdown


title: C455_C6K5PANXX_ATGTCA_L007: Donor C455 white blood cells

description: Donor C455 white blood cells

tag: donor

tag: gender

tag: ancestry

tag: phenotype


title: A498 DGAT1/2 shRNA cells, vehicle treatment, normoxia, biol repl 1

tag: cell line

tag: oxygen levels


title: C39_C6K5PANXX_GTCCGC_L006: Donor C39 white blood cells

description: Donor C39 white blood cells

value: F

tag: das score

tag: disease activity

tag: arthropathymeds

tag: nsaids

tag: steroids

tag: biologics


title: 77-SMA

tag: diagnosis

tag: processing batch

tag: age

tag: Sex

tag: parasite density on admission

tag: plasma pfhrp2

tag: hemoglobin

tag: hb genotype

value: AA

tag: hiv screen

tag: platelet

tag: plasma epo ria

tag: ifn-gamma

tag: tnf

tag: plasma ho-1

tag: total bilirubin


title: C392_C6K5PANXX_TGACCA_L008: Donor C392 white blood cells

description: Donor C392 white blood cells

tag: tissue

tag: cell type

tag: donor

tag: gender

tag: ancestry

tag: phenotype

tag: das score

tag: disease activity

tag: arthropathymeds

tag: nsaids

tag: steroids

tag: plaquenil

tag: leflumide

tag: sulfasalazine

tag: rituximab

tag: othermeds


title: C383_C6K5PANXX_ACAGTG_L001: Donor C383 white blood cells

description: Donor C383 white blood cells

tag: age

tag: biologics


title: 76-SMA

tag: diagnosis

tag: processing batch

tag: Sex

value: Male

tag: parasite density on admission

tag: plasma pfhrp2

tag: hemoglobin

tag: hb genotype

value: SS

tag: hiv screen

tag: platelet

tag: plasma epo ria

tag: ifn-gamma

tag: tnf

tag: plasma ho-1

tag: total bilirubin


title: C43_C6K5PANXX_GGCTAC_L007: Donor C43 white blood cells

description: Donor C43 white blood cells

tag: tissue

tag: cell type

tag: donor

tag: gender

tag: ancestry

tag: phenotype

tag: das score

tag: disease activity

tag: arthropathymeds

tag: nsaids

tag: steroids

tag: plaquenil

tag: leflumide

tag: sulfasalazine

tag: rituximab

tag: othermeds


title: A498 DGAT1/2 shRNA xenograft, 200mg/kg doxycycline chow, 5 days, biol repl 3

tag: treatment

value: doxycycline

tag: genotype/variation


title: C391_C6K5PANXX_GGCTAC_L003: Donor C391 white blood cells

description: Donor C391 white blood cells

tag: tissue

tag: cell type

tag: age

tag: biologics