title: 3C_GCC

status: Public on Dec 25 2017

city: Auckland

first: Justin

middle: M.

last: O'Sullivan

address: 85 Park Road, Grafton

department: Liggins Institute

country: New Zealand

institute: University of Auckland

description: Genome conformation capture

library_source: genomic

data_processing:
Library strategy: GCC
To identify interacting DNA fragments from the paired-end sequence reads, network assembly was performed using the Topography suite v1.19 (Rodley et al. 2012). GCC networks were constructed from 100 bp paired-end Illumina Genome Analyser sequence reads. Except where indicated, bioinformatics and statistical analyses were performed on interactions identified by sequence reads that were uniquely mapped onto the reference genome and were above the cut-off value derived from the ligation control interactions . All bioinformatics analysis was performed using in house Perl and Python scripts . Statistical analyses were performed in R.
Bioinformatics and statistical analyses were performed on interactions identified by sequence reads that were uniquely mapped onto the reference genome and were above the FDR cut-off value derived from the ligation control interactions. All bioinformatics analysis was performed using in house Perl scripts, as previously described (Cagliero, C., Grand, R. S., Jones, M. B., Jin, D. J. & O’Sullivan, J. M. Genome conformation capture reveals that the Escherichia coli chromosome is organized by replication and transcription. Nucleic Acids Res. 41, 6058–6071 (2013)).
During the preparation of the GCC samples, random ligation events can occur during: 1) the ligation of the cross-linked fragments, and 2) the sequencing preparation step (i.e. the addition of linkers during sequencing library preparation). Two methods were employed for the identification of significant interactions: 1) a statistical method that calculates a false detection rate (FDR) cut off; and 2) external controls were added during the GCC library preparation to obtain estimates of the rates of inter-molecular ligation events. Two inter-molecular ligations events were detected which was the same frequency as the calculated significance cut-off value. Therefore, the cut-off for filtering out random ligations was set to 3 interactions; only fragment pairs that occurred 3 or more times were considered for analysis.
Genome_build: Escherichia coli MG1655 reference genome (NC_00091313-Feb-2011
Supplementary_file: unique interaction file: *.dat.txt
Supplementary_file: all interactions file: *.datcomb.txt
Supplementary_file: multiple interactions file: *.datmult.txt

Supplementary_file: The original raw data with quality scores was not available for this sample. The linked FASTA file (below) is provided as an alternative.

organism: Escherichia coli

source_name: Dividing t=2 hours

growth_protocol: Synchronization was achieved by passaging cells through one round of stationary phase according to Cutler and Evans 1966. Briefly: Individual colonies (LB plate, 37°C, 24 h) were inoculated into M9 media and grown O/N (37°C, 200 rpm). M9 media was inoculated to a final OD600 = 0.25 (early-logarithmic phase). Cultures were grown (37°C, 200 rpm) and maintained in stationary phase (OD600 1.8) for approximately 2 hours. An appropriate amount of each culture was used to inoculate pre-warmed (37°C) M9 media to a final OD600 = 0.25 (approximate 7-fold dilution).

extract_protocol:
E. coli chromatin was prepared according to Cagliero et al. 2013 with the following modifications. For each successive time point (T0, T60, T120), 100 mL of culture was cross-linked with formaldehyde (1% final v/v, 20 min, RT) and then quenched with glycine (125 mM final concentration, 10 min); 30 mL of culture was used for RNA extraction (see below); 2 x 1 mL samples were harvested for FACS and fluorescence microscopy. Following cross-linking and quenching, cells were collected in a 50 mL falcon tube by two successive rounds of centrifugation (4000 rpm, 15 min, 4°C). Pelleted cells were washed twice with 5 mL of 1% PBS, 1% Triton X-100, and then sedimented (4000 rpm, 15 min, 4°C). To break cells open, the cell pellets for each time point were suspended in 800 µL B1 lysis buffer (10 mM Tris pH 8.0, 50mM NaCl, 10mM EDTA, 20% (w/v) sucrose, 1mg/ml lysozyme) and transferred to 2 ml tubes. Each tube was incubated for 30 min at 37°C. 800 µL of B2 lysis buffer (200 mM Tris pH 8.0, 600 mM NaCL, 4 % TritonX-100, with 1 protease inhibitor tablet [Roche] per 10 ml of buffer added just prior to use) was gently added to each 2 mL tube, mixed by inversion 3-4 times, and incubated (30 min, 37°C). Cell lysates were centrifuged (21,500 g, 20 min, 4°C) and the supernatant removed. Chromatin pellets were washed once with 1 ml FA-lysis buffer (5 mM HEPES-potassium hydroxide pH 7.5, 14 mM NaCl, 100 µm EDTA pH 8.0, 9% of 11% Triton-x-100 (v/v), 1% of 10% deoxychlolic acid (v/v), with 1 protease inhibitor tablet [Roche] per 10 mL of buffer added just prior to use) by inversion (3-4 times) before centrifugation (21,500 g, 20 min, 4°C). The supernatant was decanted and the chromatin pellet suspended in 500 µL chromatin digestion buffer (10 mM Tris-HCL pH 8.0, 5 mM MgCL2, 0.1% TritonX-100). At this point samples were stored at -80°C until further use.   5 µL of 10% SDS was added to each tube and incubated for 10 min at 37°C. 45 µL of 11% TritonX-100 was added to make a final concentration of 1%. Each chromatin sample was aliquoted into 5 sets of 2 ml tubes (~5*108 cells per 55 µL aliquot) in order to carry out restriction enzyme digestion. A ligation control was added to the un-digested chromatin (either pRS426 or Lambda phage – see below). Samples were digested (37°C) with 5 µL HhaI (100U, New England Biolabs) for 2 hr with inversion every 20 min. 10% SDS (10 µL) was added to each tube and incubated for 20 min (65°C) to inactivate the restriction enzyme.  Following restriction enzyme digestion, samples were diluted ~20 fold and ligated (2 hr at 16°C) with 20 µL T4 DNA ligase (20 U, Invitrogen). Ligation reactions were inactivated by adding: 20 µL 0.5 M EDTA (pH 8.0), 12 µL 5 M NaCl, 1.2 µL 1 M Tris-HCL (pH 7.5). Cross-links were removed by incubation O/N at 65°C in the presence of proteinase K (0.45 U, Fermentas). RNA was removed by the addition of 2 µL of RNAseA (10 mg/ml) to each tube and incubation for 15 min at 37°C. 2 µL of 13.7 ng/mL pUC19 plasmid was added to each 2 mL tube (a concentration that was equivalent to one plasmid per E. coli genome) to act as a sequencing control. Three extractions were carried out with equal volumes of phenol:chloroform (1:1) in large Oakridge tubes. DNA was column purified (Zymo, DNA clean and concentratorTM-5 kit) according to the manufacturer’s instructions. Each of the 12 columns was eluted using 11 µL of 65°C mQ H2O into 4 tubes, giving a final volume of 33 µL in each tube. Approximately 10 µg of purified DNA for each sample was sent for paired-end sequencing (100 bp) at the BGI Hong Kong sequencing facility.
Production of external ligation controls for GCC library preparation  Two sets of primers were designed to obtain two PCR products (of approximately the same length between 150-200 bp) to act as ligation controls from the pRS426 and Lambda phage genome templates (Table S2). Both sets of primers were designed to include HhaI site at one end of the final product. Putative sequences of the ligation controls were aligned against the E. coli MG1655 genome using BLAST software to check for regions of homology. External ligation controls were produced by PCR amplification of short regions of the Lambda phase genome and the pRS426 plasmid using the two sets of primers. PCR amplification (95oC, 2min; [95oC, 30 s; 58oC, 20s;; 72oC, 20s] x35; 72oC, 2min) was performed on a GeneAmp® PCR System 9700. PCR products were analyzed following electrophoresis through a 2.0 % (w/v) agarose and subsequently viewed under ultraviolet illumination. PCR products were then gel purified using QIAquick Gel Extraction Kit (Quiagen), following the manufacturer’s instructions. Purified PCR products were digested with 4 U of HhaI and incubated for 2 hr at 37°C. Purified, digested PCR products were introduced into the GCC samples at a 1:1 ratio with the number of genomes prior to the restriction digestion step during GCC preparation. The Lambda ligation control was added to all time points of biological replicate one, and pRS426 ligation control was added to all time points of biological replicate two.   Except where indicated, bioinformatics and statistical analyses were performed on interactions identified by sequence reads that were uniquely mapped onto the reference genome and were above the FDR cut-off value derived from the ligation control interactions (see below). All bioinformatics analysis was performed using in house Perl scripts, as previously described22.

treatment_protocol: Released cultures were grown (37°C, 200 rpm) and harvested (time = 0, 1 hr, or 2 hr) for GCC and RNA isolation.

tag: time post release

value: E. coli cells 2 hour following release from Stationary phase (t=2)

tag: biological replicate

value: Replicate 1


title: FGK2_tcells

status: Public on Dec 27 2017

type: SRA

city: New Haven

first: Curtis

middle: J

last: Perry

address: 1 Gilbert st.

country: USA

institute: Yale University

description:
Sample 7
CD40

library_source: transcriptomic

data_processing:
aligned using STAR to the GRCm38 (mm10) reference genome
mappable data were counted using HTSeq
imported into R for differential expression analysis using the DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited txt file including normalized read counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: melanoma

growth_protocol: BrafCA; Tyr::CreER; Ptenlox4-5  mice have been previously described(Dankort et al., 2009b). Local tumor induction was performed as previously described(Ho et al., 2014). Age-matched mice that were housed in the same room of the same facility were used for each experiment. Mice were randomized to mouse size and litter, and treated mice were co-housed with controls whenever possible. The investigators were not blinded to mouse allocation. Group size was chosen based on constraints of age-matched litters.

extract_protocol:
Tumors for flow cytometry and RNAseq were minced in Hank’s Balanced Salt Solution with 0.5mg/ml collagenase IV and 200 mg/L DNase, digested in a 37C incubator for 30 minutes and filtered to remove debris. Tumors for Single Cell Barcode Chip or intracellular cytokine stain were minced in complete RPMI with 5% serum, 0.5mg/ml collagenase IV and 200 mg/L DNase, digested in a 37C incubator for 30 minutes and filtered to remove debris. The filtrate was incubated with ACK lysis buffer (Invitrogen) for 4 minutes, washed and re-suspended in complete RPMI. For RNAseq, single-cell suspension was purified of dead cells with Lymphoprep (Stem Cell) per protocol. For RNAseq, at least three tumors were pooled for each sample collected in triplicate, with further characterization of phenotype by flow cytometry of each independent tumor. Total RNA was purified with the use of QIAzol and RNeasy Mini kit (QIAGEN), in which an on-column DNase treatment was included. Purified RNA was submitted to the Yale Center for Genomic Analysis where it was subjected to mRNA isolation and library preparation.
Non-strand specific libraries were generated from 50ng total RNA using the SMARTer Ultra Low Input RNA for Illumina Sequencing kit.  Libraries were pooled, six samples per lane, and sequenced on an Illumina HiSeq 2500 (75-bp paired end reads), and aligned using STAR to the GRCm38 (mm10) reference genome. A count-based differential expression protocol was adapted for this analysis(Anders et al., 2013); mappable data were counted using HTSeq, and imported into R for differential expression analysis using the DESeq2.To find differentially regulated sets of genes for signature generation, a 1.5-Log2 fold-change difference between samples and p-adjusted (Holm-Sidak) ≤ 0.01 was used.

treatment_protocol: 30 days after tumor induction, when tumors were measurable but total volume less than 100 mm3, BrafCA; Tyr::CreER; Ptenlox4-5  mice received normal or CSF1Ri PLX6134 chow (600mg PLX6134/kg, generously provided by Plexxikon) for 30 days or until tumors reached endpoint ( 2 cm3 as pre-specified in each experiment). In various experiments, mice also received either control vehicle (PBS) or CD40 agonistic antibody (FGK4.5 10mg/kg every three days i.p.)  for a total of ten treatments or until pre-specified tumor endpoint,

tag: strain

value: BrafCA; Tyr::CreER; Ptenlox4-5

tag: tissue

value: tumor associated macrophages

tag: genotype

value: wild type


title: tumor cell line 1 _A2B1_replicate 1

status: Public on Dec 26 2017

type: RNA

city: Hannover

first: Astrid

last: Rohrbeck

state: Niedersachsen

address: Carl-Neuberg-Straße 1

department: Department of Toxicology

country: Germany

institute: Medizinische Hochschule Hannover

description:
tumor cell line 1
Isolation of control and tumor cells: Alveolar epithelial type II cells and tumor cells were isolated as originally described by Richards et al. (1987) [129], with the following modifications: Briefly, 8-month-old transgenic mice were anesthetized by intraperitoneal injection of Ketamin® (100 mg/kg) and Rompun® (10 mg/kg). After tracheotomy the trachea was cannulated with a bulb head cannula. Following midline incision and removal of the rib cage, a Luer cannula was inserted via the vena cava cranialis into the right atrium. The pulmonary circulation was perfused with ice cold PBS using a peristaltic pump at a flow rate of 4 ml/min. The perfusate was removed by incision of the left atrium, and perfusion with the buffer was continued for 2–3 min until the lungs were completely free of blood. The lungs were explanted, placed in a 50 ml Falcon tube containing 30 ml ice cold PBS and transferred to a sterile flow cabinet. The lungs were then lavaged four times with 6 ml PBS, and subsequently 6 ml Trypsin–EDTA solution (0.25%) was instilled into the trachea. The lungs were incubated with trypsin at 37 °C for a total of 45 min. Every 15 min, 4 ml trypsin solution was pumped via the tracheal cannula.The trachea and main bronchi were removed, and the parenchymal lung tissue was dissected into 1- to 2-mm pieces in a petri dish containing 10 ml ice cold PBS with Ca2+. The lung tissue suspension was incubated for 10 min with 10 ml DNase solution at a concentration of 250 μg/ml DNase and then filtered through a nylon mesh (100 and 60 μm pore size). The alveolar type II pneumocytes were prepared by discontinuous percoll gradient centrifugation (heavy density 1.089 and low density 1.040). Following centrifugation for 30 min at 250g and 4 °C, the cell fraction at the interface between the heavy and low-density gradient was removed and mixed with DNase solution containing 50 μg/ml DNase. The cell suspension was again centrifuged at 140g at 4 °C for 6 min. The resulting cell pellet was then resuspended in DMEM supplemented with 10% FCS or 5% rat serum and incubated in a 25 cm2 tissue culture flask at 37 °C for 60 min. The non-adherent cells were removed and plated on collagen-coated 12-well plates. Approximately 2 × 106 cells were seeded per cm2 in 1 ml culture medium.

hyb_protocol: Following fragmentation, labeled cRNA of each sample was hybridized to Affymetrix GeneChip® Mouse Genome -U74v2 Arrays covering approximately 12,000 full-length mouse gene transcripts and stained according to the manufacturer's instructions.

scan_protocol: The arrays were scanned using the GeneChip® Scanner 3000.

data_processing: Array data was normalized using scaling or per-chip normalization to adjust the total or average intensity of each array to be approximately the same. Microarray chips were analyzed by the GCOS (GeneChip Operating Software) from Affymetrix with the default settings except that the target signal was set to 250 and used to generate a microarray quality control and data report. First, we have evaluated and compared multiple data from each tumor cell line using statistical analysis with the Affymetrix Data Mining Tool (DMT). Since significant differences observed between the tumor cell lines we prepared additionally two replicates from tumor cell lines with most differences such as A2C12, cRaf_cMyc, A2B1, B3, gammaA7 and gammaB8 and conducted further data analysis. CEL files exported from GCOS were uploaded into ArrayTrack software (National Center for Toxicological Research, U.S. FDA, Jefferson, AR, USA (NCTR/FDA)).

label: biotin

source_name: mouse lung carcinoma cell line was isolated from lung tumors of double c-myc and c-raf transgenic mice

label_protocol: Total RNA (5µg) was used to generate biotin-labeled cRNA (10 µg) by means of GeneChip® One-Cycle cDNA Synthesis Kit and GeneChip® IVT Labeling Kit (Affymetrix). Sample processing was performed exactly as described by the microarray manufacturer (Affymetrix). Quality control of cRNA was performed using a Bioanalyzer (Agilent 2001 Biosizing, Agilent Technologies).

growth_protocol: Each cell line was passaged weekly and maintained in culture for up to 50 passages.  Eleven transformed mouse cell lines from lung tumor of double c-Myc and c-Raf transgenic mice were used for this project (A2B1, A2C12, B3, βD5, βD10, c-Myc_c-Raf, γA3, γA7, γB8, γD1, γD12).  The tumor cell lines were cultured in Dulbecco's Modified Eagle Medium (DMEM, PAA, Pashing, Austria) supplemented with 10% fetal calf serum (FCS, FHG, Pashing, Austria), 2mM L-Glutamin, 100units/ml streptomycin and 100µg/ml penicillin in a humidified atmosphere at 37ºC containing 5% CO2 to maintain the medium pH at a value of 7,4.  Alveolar epithelial cells (AECs) were used as control.

extract_protocol: RNA-extraction was performed with the RNeasy Mini Kit (RNeasy MidiKit Qiagen, Santa Clarita, CA, USA) according to the manufacturer’s instruction. A standard quality control of the total RNA was performed using the Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, USA).

tag: cell line

value: tumor cell line 1 (A2B1)

tag: disease state

value: lung cancer


title: control _AT2

description:
control
Isolation of control and tumor cells: Alveolar epithelial type II cells and tumor cells were isolated as originally described by Richards et al. (1987) [129], with the following modifications: Briefly, 8-month-old transgenic mice were anesthetized by intraperitoneal injection of Ketamin® (100 mg/kg) and Rompun® (10 mg/kg). After tracheotomy the trachea was cannulated with a bulb head cannula. Following midline incision and removal of the rib cage, a Luer cannula was inserted via the vena cava cranialis into the right atrium. The pulmonary circulation was perfused with ice cold PBS using a peristaltic pump at a flow rate of 4 ml/min. The perfusate was removed by incision of the left atrium, and perfusion with the buffer was continued for 2–3 min until the lungs were completely free of blood. The lungs were explanted, placed in a 50 ml Falcon tube containing 30 ml ice cold PBS and transferred to a sterile flow cabinet. The lungs were then lavaged four times with 6 ml PBS, and subsequently 6 ml Trypsin–EDTA solution (0.25%) was instilled into the trachea. The lungs were incubated with trypsin at 37 °C for a total of 45 min. Every 15 min, 4 ml trypsin solution was pumped via the tracheal cannula.The trachea and main bronchi were removed, and the parenchymal lung tissue was dissected into 1- to 2-mm pieces in a petri dish containing 10 ml ice cold PBS with Ca2+. The lung tissue suspension was incubated for 10 min with 10 ml DNase solution at a concentration of 250 μg/ml DNase and then filtered through a nylon mesh (100 and 60 μm pore size). The alveolar type II pneumocytes were prepared by discontinuous percoll gradient centrifugation (heavy density 1.089 and low density 1.040). Following centrifugation for 30 min at 250g and 4 °C, the cell fraction at the interface between the heavy and low-density gradient was removed and mixed with DNase solution containing 50 μg/ml DNase. The cell suspension was again centrifuged at 140g at 4 °C for 6 min. The resulting cell pellet was then resuspended in DMEM supplemented with 10% FCS or 5% rat serum and incubated in a 25 cm2 tissue culture flask at 37 °C for 60 min. The non-adherent cells were removed and plated on collagen-coated 12-well plates. Approximately 2 × 106 cells were seeded per cm2 in 1 ml culture medium.

source_name: isolated Alveolar epithelial type II cells isolated from healthy animals

value: control


title: TS73 rep3

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

country: United Kingdom

institute: Centre for Immunity, Infection and Evolution

description: Kp 342 (NC011283) containing pACRamR

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

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

data_processing: After QC assessment to identify substandard arrays, raw data were subjected to quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.31 (Roche NimbleGen, Inc.). Probe level data were summarised to yield gene level data and differential expression analysis was carried out using Limma (Smyth Stat Appl Genet Mol Biol 3 article 3)

organism: Klebsiella pneumoniae

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

growth_protocol: LB Broth RNA extracted at mid-log phase

extract_protocol: Total RNA was extracted using RNAeasy Miniprep Kit (Qiagen) . Double-stranded cDNA was synthesised using the double stranded cDNA synthesis kit (invitrogen)


title: tumor cell line 2 _A2C12_replicate 1

description:
tumor cell line 2
Isolation of control and tumor cells: Alveolar epithelial type II cells and tumor cells were isolated as originally described by Richards et al. (1987) [129], with the following modifications: Briefly, 8-month-old transgenic mice were anesthetized by intraperitoneal injection of Ketamin® (100 mg/kg) and Rompun® (10 mg/kg). After tracheotomy the trachea was cannulated with a bulb head cannula. Following midline incision and removal of the rib cage, a Luer cannula was inserted via the vena cava cranialis into the right atrium. The pulmonary circulation was perfused with ice cold PBS using a peristaltic pump at a flow rate of 4 ml/min. The perfusate was removed by incision of the left atrium, and perfusion with the buffer was continued for 2–3 min until the lungs were completely free of blood. The lungs were explanted, placed in a 50 ml Falcon tube containing 30 ml ice cold PBS and transferred to a sterile flow cabinet. The lungs were then lavaged four times with 6 ml PBS, and subsequently 6 ml Trypsin–EDTA solution (0.25%) was instilled into the trachea. The lungs were incubated with trypsin at 37 °C for a total of 45 min. Every 15 min, 4 ml trypsin solution was pumped via the tracheal cannula.The trachea and main bronchi were removed, and the parenchymal lung tissue was dissected into 1- to 2-mm pieces in a petri dish containing 10 ml ice cold PBS with Ca2+. The lung tissue suspension was incubated for 10 min with 10 ml DNase solution at a concentration of 250 μg/ml DNase and then filtered through a nylon mesh (100 and 60 μm pore size). The alveolar type II pneumocytes were prepared by discontinuous percoll gradient centrifugation (heavy density 1.089 and low density 1.040). Following centrifugation for 30 min at 250g and 4 °C, the cell fraction at the interface between the heavy and low-density gradient was removed and mixed with DNase solution containing 50 μg/ml DNase. The cell suspension was again centrifuged at 140g at 4 °C for 6 min. The resulting cell pellet was then resuspended in DMEM supplemented with 10% FCS or 5% rat serum and incubated in a 25 cm2 tissue culture flask at 37 °C for 60 min. The non-adherent cells were removed and plated on collagen-coated 12-well plates. Approximately 2 × 106 cells were seeded per cm2 in 1 ml culture medium.

value: tumor cell line 2 (A2C12)


title: control _AT


title: tumor cell line 2 _A2C12


title: MGH78758 rep3

description: Multidrug resistant sequenced strain isolated from Massachusetts General (NC009648)


title: TS68 rep1

description: markerless ramR deletion strain derived from Ecl8, ramA overexpresser


title: TS73 rep1

description: Kp 342 (NC011283) containing pACRamR


title: TS67 rep3

description: markerless ramA deletion strain derived from Ecl8


title: Kp342 rep2

description: Kp342 (NC011283)


title: Kp342 rep1

description: Kp342 (NC011283)


title: TS215 rep3

description: Multidrug resistant Clinical Isolate of Klebsiella pneumoniae  from Chile


title: TS67 rep1


title: TS68 rep2


title: TS73 rep2

description: Kp 342 (NC011283) containing pACRamR


title: VP gene expression profile in gastric cancer cells [VP_2_AGS]

city: Seoul

first: YUNYONG

last: PARK

address: 84 Heukseok-ro

country: South Korea

institute: ChuangAng University

description: VP treatment in gastric cancer cell

hyb_protocol: Hyb was done at 58 degree for 18 hrs

scan_protocol: HighScan was used

data_processing: GenomeStudio was used for data processing and quantile normalization method was used.

organism: Homo sapiens

source_name: gastric cancer cell

label_protocol: Extracted RNA was amplified and labeled with Amplification kit (AMIL1791; Ambion)

growth_protocol: The cells were grown in RPMI1640 media.

extract_protocol: miRvana kit was used for RNA extraction

treatment_protocol: Cells were treated with DMSO or VP for 36 hrs.

value: AGS

tag: agent

value: Verteporfin


title: TS67 rep2


title: TS75 rep1

description: Kp 342 (NC011283) containing pACYC177


title: TS215 rep2


title: TS75 rep2

description: Kp 342 (NC011283) containing pACYC177


title: VP gene expression profile in gastric cancer cells [DMSO_2_AGS]

description: control

value: DMSO


title: Ecl8Mdr1 rep3

description: Multidrug resistant mutant derived from Ecl8 George et al (1995) Microbiology 141 ( Pt 8):1909-20


title: Ecl8 rep3

description: Antibiotic sensitive clinical strain as described in George et al (1995) Microbiology 141 ( Pt 8):1909-20


title: S7 rep3

description: Multidrug Resistant Clinical strain of Klebsiella pneumoniae from Singapore, ramA overexpresser


title: tumor cell line 2 _A2C12_replicate 2


title: tumor cell line 1 _A2B1


title: TS215 rep1


title: S8 rep3

description: Antibiotic sensitive clinical strain from Singapore


title: VP gene expression profile in gastric cancer cells [DMSO_3_AGS]

description: control


title: Ecl8Mdr1 rep2


title: S7 rep2


title: MGH78758 rep2


title: Ecl8 rep2


title: S8 rep2


title: VP gene expression profile in gastric cancer cells [DMSO_1_AGS]

description: control


title: MGH78758 rep1


title: S7 rep1


title: S8 rep1


title: Ecl8 rep1


title: Ecl8Mdr1 rep1


title: HIV_s389

status: Public on Dec 23 2017

city: Berkeley

first: Michael

middle: B

last: Cole

state: CA

address: 378 Stanley Hall

institute: UC Berkeley

description:
norm_tpm.csv
s389

data_processing:
[Single-Cell RNA-Seq Expression Quantification] RNA-seq reads were aligned to the RefSeq hg38 transcriptome (GRCh38.2) using Bowtie2 (Langmead et al., 2012). The resulting transcriptome alignments were processed by RSEM to estimate the abundance (expected counts and TPM) of RefSeq transcripts (Li et al., 2011).
[Single-Cell Filtering and Gene Filtering] For each single-cell library we computed transcriptome alignment metrics using FastQC, Picard tools, and in-house scripts. Computed metrics included: (1) number of reads, (2) number of aligned reads, (3) percentage of aligned reads, (4) number of duplicate reads, (5) primer sequence contamination, (6) average insert size (7) variance of insert size, (8) sequence complexity, (9) percentage of unique reads (10) ribosomal read fraction, (11) coding read fraction, (12) UTR read fraction, (13) intronic read fraction, (14) intergenic read fraction, (15) mRNA read fraction, (16) coefficient of variation of coverage, (17) mean 5’ coverage bias, (18) mean 3’ coverage bias, and (19) mean 5’ to 3’ coverage bias.
We excluded from further analysis libraries with poor values for number of aligned reads (< 28,840), the percentage of aligned reads (< 15%), or the percentage of detected transcripts (< 33% of protein-coding genes expressed at >100 TPM in at least 10% of samples). Out of 2489 initial samples, only 393 samples passed.
Following cell filtering, genes were retained for downstream analysis if they were annotated as protein-coding, and expressed at levels greater than 100 TPM in at least 5 high-quality cells.
[Single-Cell Data Normalization] In order to normalize TPM data, we applied full-quantile normalization method, restoring original zero values to zero following normalization.
Genome_build: GRCh38.2
Supplementary_files_format_and_content: TPMs

source_name: Single dendritic cell

extract_protocol:
Single cells lysates were put directly into SPRI
[Trombetta et al CPMB 2014]
[Single cell Whole Transcriptome Amplification]: Following sorting, 96-well plates of single cells were whole transcriptome amplified as described in Trombetta et al. Lysed cell samples were cleaned with 2.2x volume AMPure XP SPRI beads (Beckman Coulter). Reverse transcription and PCR were then performed on the samples.  For population samples total RNA was isolated using a column (RNeasy plus Micro RNA kit; Qiagen) following manufacturer’s instructions. Two μL of extracted RNA were added to 8 μL of water and cleaned with 2.2x volume beads. While transcriptome amplification wa performed on these samples analogous to the amplification of the single cell samples.
[Preparation of cDNA Libraries  for RNAseq]: WTA products were diluted to a concentration of 0.1 to 0.4 ng/μL and tagmented and amplified using Nextera XT DNA Sample preparation reagents (Illumina). Tagmentation was performed according to manufacturer’s instructions, modified to use ¼ the recommended volume of reagents, extended tagmentation time to 10 minutes and extended PCR time to 60s. PCR primers were ordered form Integrated DNA Technologies. Nextera products were then cleaned twice with at 0.9x volume of SPRI beads and eluted in water. The library was quantified using Qubit and analyzed using a high sensitivity DNA chip. The library was diluted to 2.2 pM and sequenced on a NextSeq 500 (Illumina)
Indexing length: 8bp

tag: cell type

value: DC

tag: exposure

value: HIV

tag: exposuretime

tag: donor

tag: platebatch

tag: viabilitysortbatch

value: no


title: HIV_s390

description:
norm_tpm.csv
s390


title: HIV_s387

description:
norm_tpm.csv
s387


title: HIV_s388

description:
norm_tpm.csv
s388


title: HIV_s385

description:
norm_tpm.csv
s385


title: HIV_s391

description:
norm_tpm.csv
s391


title: HIV_s393

description:
norm_tpm.csv
s393


title: HIV_s384

description:
norm_tpm.csv
s384


title: HIV_s383

description:
norm_tpm.csv
s383


title: HIV_s381

description:
norm_tpm.csv
s381


title: HIV_s386

description:
norm_tpm.csv
s386


title: HIV_s392

description:
norm_tpm.csv
s392


title: HIV_s382

description:
norm_tpm.csv
s382


title: HIV_s378

description:
norm_tpm.csv
s378


title: HIV_s379

description:
norm_tpm.csv
s379


title: HIV_s377

description:
norm_tpm.csv
s377


title: HIV_s375

description:
norm_tpm.csv
s375


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description:
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s373


title: HIV_s371

description:
norm_tpm.csv
s371


title: HIV_s369

description:
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s369


title: HIV_s374

description:
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s374


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description:
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s365


title: HIV_s372

description:
norm_tpm.csv
s372


title: HIV_s368

description:
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s368


title: HIV_s376

description:
norm_tpm.csv
s376


title: HIV_s356

description:
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s356


title: HIV_s352

description:
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s352


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description:
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s366


title: HIV_s370

description:
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s370


title: HIV_s363

description:
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s363


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description:
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s355


title: HIV_s367

description:
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s367


title: HIV_s359

description:
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s359


title: HIV_s362

description:
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s362


title: HIV_s354

description:
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s354


title: HIV_s361

description:
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s361


title: HIV_s351

description:
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s351


title: HIV_s357

description:
norm_tpm.csv
s357


title: HIV_s360

description:
norm_tpm.csv
s360


title: HIV_s345

description:
norm_tpm.csv
s345


title: HIV_s380

description:
norm_tpm.csv
s380


title: HIV_s348

description:
norm_tpm.csv
s348


title: HIV_s342

description:
norm_tpm.csv
s342


title: HIV_s349

description:
norm_tpm.csv
s349


title: HIV_s364

description:
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s364


title: HIV_s353

description:
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s353


title: HIV_s347

description:
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s347


title: HIV_s350

description:
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s350


title: MED_s339

description:
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s339

value: MED

value: yes


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description:
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s346


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description:
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s330


title: MED_s340

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s340


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s344


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description:
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s338


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s331


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description:
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s343


title: MED_s335

description:
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s335


title: MED_s333

description:
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s333


title: MED_s334

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s334


title: MED_s328

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s328


title: MED_s325

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s325


title: MED_s324

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s324


title: MED_s341

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s341


title: MED_s323

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s323


title: MED_s337

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s337


title: MED_s336

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title: MED_s329

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s161


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s157


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s155


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s148


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s143


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s138


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s139


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s136


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s135


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s149


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s129


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s142


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s100


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s105


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s98


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s96


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description:
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s95


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description:
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s99


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description:
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s92


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description:
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s89


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s93


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s86


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s83


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description:
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s81


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description:
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description:
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s78


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description:
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s85


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description:
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s77


title: MED_s75

description:
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s75


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description:
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s76


title: NA19160_ATAC_LCL

city: Chicago

first: Nicholas

middle: E

last: Banovich

state: IL

address: 920 E. 58th Street, CLSC 317

department: Human Genetics

institute: University of Chicago

data_processing:
Paired end ATAC-seq reads were mapped using bowtie2 allowing for two mismatches per read. After mitochondrial reads were removed, we once again re-mapped all nuclear reads using the WASP to remove reads that map with allelic bias. We then removed all duplicate fragments (duplicates of both read pairs) and reads with a mapping quality (MAPQ) less than 10.
Genome_build: hg19
Supplementary_files_format_and_content: Each column represnets and individual and each row represnets an accibility window. Counts are raw counts of transposition events.

molecule: genomic DNA

source_name: Lymphoblastoid Cell Line

growth_protocol: Cell lines were grown in RPMI with 15% FBS

extract_protocol: Libraries were prepared using the ATAC-seq protocol

value: Lymphoblastoid Cell Line


title: NA19116_ATAC_LCL


title: NA19128_ATAC_LCL


title: HIV_s71

description:
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s71


title: NA19102_ATAC_LCL


title: MED_s94

description:
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s94


title: HIV_s73

description:
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s73


title: NA19257_ATAC_LCL


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description:
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s70


title: MED_s68

description:
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s68


title: HIV_s72

description:
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s72


title: NA19101_ATAC_LCL


title: NA19108_ATAC_LCL


title: HIV_s65

description:
norm_tpm.csv
s65


title: NA19098_ATAC_LCL


title: HIV_s69

description:
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s69


title: NA18912_ATAC_LCL


title: NA18870_ATAC_LCL


title: HIV_s63

description:
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s63


title: NA18855_ATAC_LCL


title: MED_s66

description:
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s66


title: HIV_s67

description:
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s67


title: MED_s61

description:
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s61


title: NA18511_ATAC_LCL


title: HIV_s64

description:
norm_tpm.csv
s64


title: NA18852_ATAC_LCL


title: NA18520_ATAC_LCL


title: HIV_s60

description:
norm_tpm.csv
s60


title: MED_s59

description:
norm_tpm.csv
s59


title: HIV_s62

description:
norm_tpm.csv
s62


title: NA18504_ATAC_LCL


title: NA18522_ATAC_LCL


title: NA18519_ATAC_LCL


title: HIV_s57

description:
norm_tpm.csv
s57


title: MED_s56

description:
norm_tpm.csv
s56


title: NA19128_ATAC_iPSC-CM

data_processing:
Paired end ATAC-seq reads were mapped using bowtie2 allowing for two mismatches per read. After mitochondrial reads were removed, we once again re-mapped all nuclear reads using the WASP to remove reads that map with allelic bias. We then removed all duplicate fragments (duplicates of both read pairs) and reads with a mapping quality (MAPQ) less than 10.
Genome_build: hg19
Supplementary_files_format_and_content: Each column represents and individual and each row represents an accessibility window. Counts are raw counts of transposition events.

source_name: Induced pluripotent stem cell derived cardiomyocyte

growth_protocol: iPSC cultures were grown using 0.01mg/cm2 (1:100) hESC-grade Matrigel and Essential 8 (E8) media. Cardiomyocotes were generated according to establsihed protocols.

tag: derived from cell line


title: NA19160_ATAC_iPSC-CM

value: Induced pluripotent stem cell derived cardiomyocyte


title: NA19116_ATAC_iPSC-CM


title: NA18501_ATAC_LCL


title: HIV_s54

description:
norm_tpm.csv
s54


title: MED_s58

description:
norm_tpm.csv
s58


title: NA19101_ATAC_iPSC-CM


title: HIV_s55

description:
norm_tpm.csv
s55


title: HIV_s51

description:
norm_tpm.csv
s51


title: NA18505_ATAC_LCL


title: HIV_s50

description:
norm_tpm.csv
s50


title: NA19098_ATAC_iPSC-CM


title: NA19108_ATAC_iPSC-CM


title: MED_s49

description:
norm_tpm.csv
s49


title: HIV_s53

description:
norm_tpm.csv
s53


title: MED_s47

description:
norm_tpm.csv
s47


title: HIV_s48

description:
norm_tpm.csv
s48


title: MED_s45

description:
norm_tpm.csv
s45


title: NA18502_ATAC_LCL


title: NA18520_ATAC_iPSC-CM


title: NA18852_ATAC_iPSC-CM


title: HIV_s52

description:
norm_tpm.csv
s52


title: NA18855_ATAC_iPSC-CM


title: MED_s46

description:
norm_tpm.csv
s46


title: NA18505_ATAC_iPSC-CM


title: NA18912_ATAC_iPSC-CM


title: NA18870_ATAC_iPSC-CM


title: NA18511_ATAC_iPSC-CM


title: HIV_s42

description:
norm_tpm.csv
s42


title: HIV_s43

description:
norm_tpm.csv
s43


title: HIV_s44

description:
norm_tpm.csv
s44


title: NA18499_ATAC_iPSC-CM


title: NA19257_ATAC_iPSC

data_processing:
Paired end ATAC-seq reads were mapped using bowtie2 allowing for two mismatches per read. After mitochondrial reads were removed, we once again re-mapped all nuclear reads using the WASP to remove reads that map with allelic bias. We then removed all duplicate fragments (duplicates of both read pairs) and reads with a mapping quality (MAPQ) less than 10.
Genome_build: hg19
Supplementary_files_format_and_content: Each column represents an individual and each row represents an accessibility window. Counts are raw counts of transposition events.

source_name: Induced pluripotent stem cell

growth_protocol: iPSC cultures were grown using 0.01mg/cm2 (1:100) hESC-grade Matrigel and Essential 8 (E8) media.

value: Induced pluripotent stem cell


title: HIV_s40

description:
norm_tpm.csv
s40


title: NA19225_ATAC_iPSC


title: NA19239_ATAC_iPSC


title: HIV_s41

description:
norm_tpm.csv
s41


title: NA19210_ATAC_iPSC


title: HIV_s38

description:
norm_tpm.csv
s38


title: HIV_s39

description:
norm_tpm.csv
s39


title: NA19206_ATAC_iPSC


title: NA19209_ATAC_iPSC


title: HIV_s37

description:
norm_tpm.csv
s37


title: HIV_s35

description:
norm_tpm.csv
s35


title: NA19204_ATAC_iPSC


title: NA19193_ATAC_iPSC


title: MED_s32

description:
norm_tpm.csv
s32


title: NA19192_ATAC_iPSC


title: MED_s34

description:
norm_tpm.csv
s34


title: NA19171_ATAC_iPSC


title: HIV_s36

description:
norm_tpm.csv
s36


title: HIV_s33

description:
norm_tpm.csv
s33


title: MED_s31

description:
norm_tpm.csv
s31


title: NA19190_ATAC_iPSC


title: HIV_s30

description:
norm_tpm.csv
s30


title: NA19160_ATAC_iPSC


title: NA19153_ATAC_iPSC


title: NA19159_ATAC_iPSC


title: NA19144_ATAC_iPSC


title: MED_s26

description:
norm_tpm.csv
s26


title: HIV_s28

description:
norm_tpm.csv
s28


title: HIV_s29

description:
norm_tpm.csv
s29


title: HIV_s25

description:
norm_tpm.csv
s25


title: NA19143_ATAC_iPSC


title: NA19138_ATAC_iPSC


title: NA19140_ATAC_iPSC


title: HIV_s21

description:
norm_tpm.csv
s21


title: NA19152_ATAC_iPSC


title: HIV_s20

description:
norm_tpm.csv
s20


title: HIV_s19

description:
norm_tpm.csv
s19


title: NA19119_ATAC_iPSC


title: HIV_s18

description:
norm_tpm.csv
s18


title: NA19116_ATAC_iPSC


title: NA19098_ATAC_iPSC


title: MED_s14

description:
norm_tpm.csv
s14


title: MED_s17

description:
norm_tpm.csv
s17


title: NA19128_ATAC_iPSC


title: HIV_s22

description:
norm_tpm.csv
s22


title: HIV_s24

description:
norm_tpm.csv
s24


title: NA19099_ATAC_iPSC


title: NA19127_ATAC_iPSC


title: NA19114_ATAC_iPSC


title: NA19108_ATAC_iPSC


title: NA19130_ATAC_iPSC


title: NA18913_ATAC_iPSC


title: HIV_s23

description:
norm_tpm.csv
s23


title: HIV_s16

description:
norm_tpm.csv
s16


title: NA19093_ATAC_iPSC


title: NA19102_ATAC_iPSC


title: NA18912_ATAC_iPSC


title: HIV_s13

description:
norm_tpm.csv
s13


title: MED_s10

description:
norm_tpm.csv
s10


title: NA18907_ATAC_iPSC


title: HIV_s8

description:
norm_tpm.csv
s8


title: NA18870_ATAC_iPSC


title: HIV_s27

description:
norm_tpm.csv
s27


title: MED_s12

description:
norm_tpm.csv
s12


title: NA19092_ATAC_iPSC


title: NA18855_ATAC_iPSC


title: MED_s2

description:
norm_tpm.csv
s2


title: NA18852_ATAC_iPSC


title: NA18520_ATAC_iPSC


title: NA18862_ATAC_iPSC


title: MED_s15

description:
norm_tpm.csv
s15


title: HIV_s5

description:
norm_tpm.csv
s5


title: HIV_s11

description:
norm_tpm.csv
s11


title: MED_s9

description:
norm_tpm.csv
s9


title: tlr_46hr_b3

data_processing:
[RNA-Seq Expression Quantification] RNA-seq reads were aligned to the RefSeq hg38 transcriptome (GRCh38.2) using Bowtie2 (Langmead et al., 2012). The resulting transcriptome alignments were processed by RSEM to estimate the abundance (expected counts and TPM) of RefSeq transcripts (Li et al., 2011), aggregating by gene symbol.
[Filtering] For each single-cell library we computed transcriptome alignment metrics using FastQC, Picard tools, and in-house scripts. Computed metrics included: (1) number of reads, (2) number of aligned reads, (3) percentage of aligned reads, (4) number of duplicate reads, (5) primer sequence contamination, (6) average insert size (7) variance of insert size, (8) sequence complexity, (9) percentage of unique reads (10) ribosomal read fraction, (11) coding read fraction, (12) UTR read fraction, (13) intronic read fraction, (14) intergenic read fraction, (15) mRNA read fraction, (16) coefficient of variation of coverage, (17) mean 5’ coverage bias, (18) mean 3’ coverage bias, and (19) mean 5’ to 3’ coverage bias.
We excluded from further analysis libraries with poor values for number of aligned reads (< 741,309), the percentage of aligned reads (< 76.4%), or the percentage of detected transcripts (< 99% of top genes by mean TPM). 8 samples passed.
Following cell filtering, genes were retained for downstream analysis if they were expressed in any sample.
[Data Normalization] In order to normalize TPM data for residual compositional bias, we applied the DESeq normalization method.

source_name: dendritic cell

extract_protocol:
Total RNA was isolated using a RNeasy plus Micro RNA kit (Qiagen, Hilden, Germany)
[Trombetta et al CPMB 2014]
[Whole Transcriptome Amplification]: Two μL of extracted RNA were added to 8 μL of water and cleaned with 2.2x volume beads. 1 μL of this cleaned RNA was used in a WTA reaction. Whole transcriptome amplification was performed on these samples analogous to the amplification of the single cell samples.
[Preparation of cDNA Libraries  for RNAseq]: WTA products were diluted to a concentration of 0.1 to 0.4 ng/μL and tagmented and amplified using Nextera XT DNA Sample preparation reagents (Illumina). Tagmentation was performed according to manufacturer’s instructions, modified to use ¼ the recommended volume of reagents, extended tagmentation time to 10 minutes and extended PCR time to 60s. PCR primers were ordered form Integrated DNA Technologies. Nextera products were then cleaned twice with at 0.9x volume of SPRI beads and eluted in water. The library was quantified using Qubit and analyzed using a high sensitivity DNA chip. The library was diluted to 2.2 pM and sequenced on a NextSeq 500 (Illumina)

treatment_protocol: Bulk cDCs incubated for 46 hours with or without various TLR ligands (TLRL: TLR2L, PGNA; TLR3L, Poly I:C; TLR4L, LPS; TLR8L, CL097)

tag: time point

tag: cell number


title: NA18859_ATAC_iPSC


title: HIV_s7

description:
norm_tpm.csv
s7


title: HIV_s4

description:
norm_tpm.csv
s4


title: tlr_46hr_b2


title: HIV_s3

description:
norm_tpm.csv
s3


title: tlr_46hr_b5


title: NA18522_ATAC_iPSC


title: NA18858_ATAC_iPSC


title: HIV_s1

description:
norm_tpm.csv
s1


title: tlr_46hr_b6


title: NA18861_ATAC_iPSC


title: NA18853_ATAC_iPSC


title: NA18505_ATAC_iPSC


title: NA18510_ATAC_iPSC


title: tlr_46hr_b7


title: tlr_46hr_b4


title: NA18856_ATAC_iPSC


title: NA18511_ATAC_iPSC


title: tlr_46hr_b8


title: HIV_s6

description:
norm_tpm.csv
s6


title: NA18519_ATAC_iPSC


title: NA18501_ATAC_iPSC


title: NA18517_ATAC_iPSC


title: NA18499_ATAC_iPSC


title: NA18498_ATAC_iPSC


title: tlr_46hr_b1


title: NA18502_ATAC_iPSC


title: NA18486_ATAC_iPSC


title: NA18489_ATAC_iPSC


title: NA18508_ATAC_iPSC


title: MDA231 soft biological replica D

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

description: Gene expression data from MDA-MB-231 human breast cancer cells, cultured on a soft substrate

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Standard Affymetrix scanning procedures on a GCS3000 7G Affymetrix scanner.

data_processing: RMA of .CEL files using affy Bioconductor library. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization

source_name: MDA-MB-231 human breast cancer cells

label_protocol: Biotinylated cRNA were prepared using the BioArrayTM HighYieldTM RNA Transcript Labeling Kit (ENZO Biochem, New York, NY) according to manufacturer's intructions.

growth_protocol: MDA-MB-231 cells were cultured in MDA-MB-231 medium (DMEM/F12 supplemented with 10% FBS, glutamine and antibiotics).

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

treatment_protocol: MDA-MB-231 cells were cultured either on a stiff substrate or on a soft substrate in MDA-MB-231 medium.

tag: substrate quality

value: soft


title: MDA231 stiff, biological replica D

description: Gene expression data from MDA-MB-231 human breast cancer cells, cultured on a stiff substrate

value: stiff


title: MDA231 soft biological replica C


title: MDA231 stiff, biological replica C


title: MDA231 soft biological replica A


title: Melanoma cell line #9  -3  (Cy5) /   Melanocytes Pool I -3 (Cy3)

status: Public on Dec 22 2017

city: barcelona

first: BELEN

last: MINANA

state: barcelona

address: dr aiguader 88

department: GENE REGULATION, STEM CELLS AND CANCER

country: Spain

institute: Center for genomic regulation

hyb_protocol: Slides were hybridized by Agilent in situ Hybridization Kit Plus following manufacturer protocol, with the exception that we hybridized 6 micrograms of each amplified cRNA sample and the Agilent hybridization oven was set to 60ºC.

scan_protocol: Fluorescent images were obtained using the G2565BA Microarray Scanner System (Agilent) with 100% laser power and 100% PMT settings and 16-bit TIFF images, one for each channel, were quantified using GenePix Pro 6.0 microarray analysis software (Molecular Devices, www.moleculardevices.com).

data_processing: Raw data were processed using SAPO (http://bioinfo.ciberehd.org/SAP.ang.htm) and CGEM (http://bioinfo.ciberehd.org/CGEM.ang.html) alternative splicing analysis tools, obtaining lowess normalized log2ratios. Mean foreground and background intensities were extracted from the red (Cy5) and green (Cy3) channels for every spot on the microarray. The background intensities are used to correct the foreground intensities for local variation on the array surface, resulting in corrected red and green intensities.

source_name: human melanoma cell line SK-Mel-103

label_protocol: Sample was labeled using the Quick-Amp labeling kit, no dye (Agilent 5190-0447) and cyanine 5-CTP and cyanine 3-CTP (Perkin-Elmer NEL580, NEL581). Purified using Quiagen RNeasy mini kit. Quality control assessed by Agilent Bioanalyzer 2100.

growth_protocol: The melanoma cell lines SK-Mel-103 (#9) and SK-Mel-19 (#3) were grown in DMEM medium supplemented with 10% fetal bovine serum, 1% penicillin and streptomycin (Gibco), and maintained at 37°C in humidified 5% CO2 atmosphere. Primary human melanocytes were cultured in Medium 254 supplemented with 1% melanocyte growth factors (HMGS, Cascade Biologics), 0.2 mM CaCl2 and 100 μg/mL Penicillin/Spreptomycin.

extract_protocol: Total RNA was purified using RNeasy Mini kit (Qiagen) and digested with DNase (Qiagen).

treatment_protocol: Melanoma cell lines SK-Mel-103 (#9) and SK-Mel-19 (#3) were harvested by trypsination at a confluency of approx. 70% and the pellets were stored at -80ºC. Melanocytes were harvested by trypsination at a confluency of approx. 70% confluency. Melanocytes derived from three different donors were pooled and the pellets stored at -80ºC.

value: melanoma cell line SK-Mel-103

source_name: human melanocyte pool I

value: melanocyte


title: Melanoma cell line #9  -2  (Cy3) /   Melanocytes Pool I -2 (Cy5)


title: Melanoma cell line #9  -3  (Cy3) /   Melanocytes Pool I -3 (Cy5)


title: MDA231 soft biological replica B


title: MDA231 stiff, biological replica A


title: MDA231 stiff, biological replica B


title: Melanoma cell line #9  -2  (Cy5) /   Melanocytes Pool I -2 (Cy3)


title: Melanoma cell line #3  -3  (Cy5) /   Melanocytes Pool I -3 (Cy3)

source_name: human melanoma cell line SK-Mel-19

value: melanoma cell line SK-Mel-19


title: Melanoma cell line #9  -1  (Cy3) /   Melanocytes Pool I -1 (Cy5)


title: gastrocnemius muscle_PN28

city: Portland

first: Zheng

last: Xia

state: Oregon

address: 3181 SW Sam Jackson Park Rd

department: Department of Biomedical Engineering

institute: Oregon Health & Science University

data_processing:
TopHat 2.0.5 is used to align reads to reference genome. RSEM is used to count reads and calculate Fragments Per Kilobase per Megabase of library size (FPKM).
UCSC mm9 gtf gene model is used for counting reads.
Genome_build: mm9
Supplementary_files_format_and_content: .txt file report Counts and FPKMs

molecule: polyA RNA

source_name: gastrocnemius muscle

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: FVB

value: wild type

tag: age

tag: gender

value: male

value: gastrocnemius muscle


title: gastrocnemius muscle_22wks

tag: strain

value: 22 wks

tag: tissue


title: Melanoma cell line #3  -2  (Cy5) /   Melanocytes Pool I -2 (Cy3)

tag: cell line


title: gastrocnemius muscle_PN14 rep2

tag: genotype


title: Melanoma cell line #3  -2  (Cy3) /   Melanocytes Pool I -2 (Cy5)


title: Melanoma cell line #3  -1  (Cy5) /   Melanocytes Pool I -1 (Cy3)


title: gastrocnemius muscle_PN14 rep1


title: Melanoma cell line #9  -1  (Cy5) /   Melanocytes Pool I -1 (Cy3)


title: Melanoma cell line #3  -3  (Cy3) /   Melanocytes Pool I -3 (Cy5)


title: gastrocnemius muscle_E18.5

value: pooled male and female


title: Melanoma cell line #3  -1  (Cy3) /   Melanocytes Pool I -1 (Cy5)


title: 010 (3994-071_p.12)

city: London

first: Georgios

last: Vlachogiannis

address: 15 Cotswold Road

institute: The Institute of Cancer Research

data_processing:
Image analysis and base calling were performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8).
Sequence quality was examined using the FastQC software.
The trimmed reads (trimmed 5’,3’-adaptor bases using Cutadapt) were aligned to reference genome using Hisat2 software (v2.0.4).
The transcript abundances for each sample was estimated with StringTie (v1.2.3).
The FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0).
Genome_build: Hg19
Supplementary_files_format_and_content: FPKM values generted; supplied in an xlsx file.

source_name: Patient-derived organoids

growth_protocol: PDOs were cultured in Advanced DMEM/F12, containing: EGF (50 ng/ml), Noggin (100 ng/ml), R-spondin 1 (500 ng/ml), Gastrin (10 nM), FGF-10 (10 ng/ml), FGF-basic (10 ng/ml), Wnt-3A (100 ng/ml), Prostaglandin E2 (1 uM), Y-27632 (10 uM), Nicotinamide (4mM), A83-01 (0.5 uM), SB202190 (5 uM).

extract_protocol:
AllPrep DNA/RMA/miRNA universal kit (Qiagen).
RNA sequencing and data analysis were outsourced to Arraystar (USA). In brief, 1-2 µg of total RNA were enriched by oligo(dT) magnetic beads (rRNA removal), and sequencing libraries were prepared using the KAPA Stranded RNA-Seq library prep kit (Illumina) which incorporates dUTP into the second cDNA strand and renders the RNA-seq library strand-specific. The completed libraries were qualified with Agilent 2100 Bioanalyzer and quantified by absolute quantification qPCR method. To sequence the libraries on the Illumina HiSeq 4000 instrument, the barcoded libraries were mixed, denatured to single stranded DNA in NaOH, captured on Illumina flow cell, amplified in situ, and subsequently sequenced for 150 cycles for both ends on Illumina HiSeq instrument.

tag: sample type

value: RNA from 3994-071 PDOs

tag: passage #

value: passage 12


title: 016 (4164-1010_p.07)

value: RNA from 4164-1010 PDOs

value: passage 07


title: 009 (3994-071_p.05)

value: passage 05


title: 026 (3994-055_p.10)

value: RNA from 3994-055 PDOs

value: passage 10


title: 013 (4164-1001_p.10)

value: RNA from 4164-1001 PDOs


title: Tumor, Splenic Diffuse Red Pulp Lymphoma, case 7

type: genomic

city: Barcelona

first: Alba

last: Navarro

address: Villaroel, 170

department: Pathology

institute: IDIBAPS - Hospital Clínic

description: Tumor  vs normal

hyb_protocol: The protocol Oligonucleotide Array-Based CGH for Genomic DNA Analysis (ULS labeling for Blood, Cells, Tissues or FFPE) was used.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Raw data were generated from scanned images using Agilent Feature Extraction Software (10.10.1.1). Log2ratios of background corrected values for tumour over normal DNA were calculated. Normalization was carried out on Agilent's CGH Analytics, integrated on the Agilent Genomic Workbench Standard Edition 6.5.0.58, using data from the internal set of control probes included in the microarray. Detection of Copy Number Alterations (CNAs) was performed using the ADM-2 algorithm, also implemented within the Agilent's genomics suite Genomic Workbench v5.0, with a threshold of 6.5 and a minimum of 5 consecutive probes and Nexus 6.0 Discovery Edition (Biodiscovery, El segundo, CA).

label_protocol: Following manufacturer instructions (Agilent)

extract_protocol: Genomic DNA was extracted form formalin fixed paraffin embedded (FFPE) tissues by phenol chloroform method. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, and agarose gel electrophoresis.

tag: cell type

value: splenic diffuse red pulp lymphoma

value: female

source_name: pool normal DNA

value: F


title: 004 (3770-1032_p.07)

value: RNA from 3770-1032 PDOs


title: 003 (3770-1032_p.04)

value: passage 04


title: lactis-marxianus mRNA isolate 3

city: San Francisco

first: Trevor

last: Sorrells

department: Biochemistry and Biophysics

institute: University of California, San Francisco

data_processing:
Quality analysis was performed using FastQC
Files were indexed and aligned to hybrid Kluyveromyces coding regions using bowtie2
Multimapping reads were removed, and then number of mapping reads were counted for each gene
mRNA reads were normalized to gDNA reads and the ratio of the lactis ortholog to the second species's ortholog was calculated
allele-specific expression values are reported as log2(lactis/second species allele)
Genome_build: The Kl. lactis genome was obtained from YGOB on 5/2/2014, the Kl. wickerhamii genome was obtained from Baker et. al. PNAS 2011, and the Kl. marxianus genome was obtained from Suzuki et. al. Genome Announc 2014. The wickerhamii and marxianus genomes were annotated using the online YGAP tool.
Supplementary_files_format_and_content: Tab-delimited text file containing the ortholog names for S. cerevisiae and the Kluyveromyces species along with the log2(allele-specific expression) value for each isolate

organism: Kluyveromyces lactis x Kluyveromyces marxianus

source_name: yeast in log phase

growth_protocol: cells were grown overnight to stationary phase (gDNA samples) and then diluted to OD600=0.2 and grown to OD600=0.7-1.0 (mRNA samples)

extract_protocol:
Cells were lysed with glass beads and DNA isolated with standard phenol chloroform. RNA was extracted using the RiboPure kit AM1926 (Applied Biosystems) and polyadenylated RNA was selected twice with Oligotex mRNA Kit 70022 (Qiagen)
Libraries were constructed with the NEBNext Ultra DNA Prep Kit E7370 and Ultra Directional RNA Library Prep Kit E7420 (NEB).

tag: media condition

value: grown in YEPD to OD=0.7-1.0


title: lactis-wickerhamii mRNA isolate 9

organism: Kluyveromyces lactis x Kluyveromyces wickerhamii


title: lactis-wickerhamii mRNA isolate 8


title: Tumor, Splenic Diffuse Red Pulp Lymphoma, case 8

description: Tumor  vs normal

value: male

value: M


title: Tumor, Splenic Diffuse Red Pulp Lymphoma, case 14

description: Tumor  vs normal


title: lactis-wickerhamii mRNA isolate 7


title: Tumor, Splenic Diffuse Red Pulp Lymphoma, case 18

description: Tumor  vs normal


title: gastrocnemius muscle_PN2

value: FVB

value: wild type

value: gastrocnemius muscle


title: Tumor, Splenic Diffuse Red Pulp Lymphoma, case 3

description: Tumor  vs normal


title: Tumor, Splenic Diffuse Red Pulp Lymphoma, case 17

description: Tumor  vs normal


title: lactis-marxianus mRNA isolate 2


title: lactis-wickerhamii mRNA isolate 6


title: Tumor, Splenic Diffuse Red Pulp Lymphoma, case 4

description: Tumor  vs normal


title: lactis-marxianus mRNA isolate 1


title: lactis-wickerhamii mRNA isolate 5


title: lactis-wickerhamii mRNA isolate 4


title: lactis-marxianus gDNA isolate 3

source_name: yeast in stationary phase

value: overnight YEPD culture


title: Tumor, Splenic Diffuse Red Pulp Lymphoma, case 6

description: Tumor  vs normal


title: lactis-marxianus gDNA isolate 2


title: lactis-wickerhamii mRNA isolate 2


title: 2-2SD2

city: College Park

first: Cecile

last: Parmentier-Line

address: Baltimore avenue

institute: University of MD

description:
UMCPLin-Poplar46_11-2S2.CEL
2-2 SD replicate 2

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 17 hr at 45C on GeneChip Poplar Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000.

data_processing: The data were analyzed using Genespring software

organism: Populus tremula x Populus alba

source_name: FD transgenic_shoot tips_SD

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip 3' IVT expression kit mannual).

growth_protocol: Plants were grown in growth chambers

extract_protocol: Extraction of total RNA was performed using Qiagen RNeasy plant mini kit and Qiacube with modifications

treatment_protocol: LD = Long day photoperiod (16h light/8h dark) or SD = 3 weeks under short day photoperiod (8h light/16h dark)

value: transgenic FD overexpressing

value: shoot tip

tag: collected after

value: 3 wks under short day photoperiod (8h light/16h dark)


title: Tumor, Splenic Diffuse Red Pulp Lymphoma, case 19

description: Tumor  vs normal


title: lactis-marxianus gDNA isolate 1


title: 017 (4164-1010_p.09)

value: RNA from 4164-1010 PDOs

value: passage 09


title: lactis-wickerhamii mRNA isolate 3


title: Tumor, Splenic Diffuse Red Pulp Lymphoma, case 10

description: Tumor  vs normal

value: splenic diffuse red pulp lymphoma


title: 025 (3994-055_p.05)

value: RNA from 3994-055 PDOs

value: passage 05


title: 2-2SD3

description:
UMCPLin-Poplar46_12-2S3.CEL
2-2 SD replicate 3


title: Tumor, Splenic Diffuse Red Pulp Lymphoma, case 11

description: Tumor  vs normal

value: female

value: F


title: 012 (4164-1001_p.06)

value: RNA from 4164-1001 PDOs

value: passage 06


title: 2-2SD1

description:
UMCPLin-Poplar46_10-2S1.CEL
2-2 SD replicate 1


title: Kl. wickerhamii parental gDNA isolate 3

organism: Kluyveromyces wickerhamii


title: 717SD3

description:
UMCPLin-Poplar46_9-7S3.CEL
717 SD replicate 3

source_name: WT_shoot tips_SD


title: 717SD2

description:
UMCPLin-Poplar46_8-7S2.CEL
717 SD replicate 2


title: Kl. wickerhamii parental gDNA isolate 2


title: Tumor, Splenic Diffuse Red Pulp Lymphoma, case 16

description: Tumor  vs normal


title: lactis-wickerhamii gDNA isolate 1


title: lactis-wickerhamii gDNA isolate 2


title: 717SD1

description:
UMCPLin-Poplar46_7-7S1.CEL
717 SD replicate 1


title: Kl. marxianus parental gDNA

organism: Kluyveromyces marxianus


title: lactis-wickerhamii mRNA isolate 1

value: grown in YEPD to OD=0.7-1.0


title: Kl. lactis parental gDNA isolate 2

organism: Kluyveromyces lactis


title: Kl. wickerhamii parental gDNA isolate 1


title: Kl. lactis parental gDNA isolate 1


title: 2-2LD3

description:
UMCPLin-Poplar46_6-2L3.CEL
2-2 LD replicate 2

source_name: FD transgenic_shoot tips_LD

value: Long day (LD) photoperiod (16h light/8h dark)


title: lactis-wickerhamii gDNA isolate 3


title: 2-2LD2

description:
UMCPLin-Poplar46_5-2L2.CEL
2-2 LD replicate 2


title: Tumor, Splenic Diffuse Red Pulp Lymphoma, case 12

description: Hybridized to SNP 6.0

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: Image data were analysed with Genotyping Console 4.0 to obtain the CEL data files, which were also exported to the Nexus Biodiscovery Edition for data analysis and visualization. Quality controls assessed by Genotyping Console included Contrast Quality Control (CQC>0.4) produced by Birdseed and Median of the Absolute values of all Pairwise Differences (MAPD<0.35). Tumour and normal DNA samples were analysed individually with the Nexus Biodiscovery Edition using the SNP-FASST2 segmentation algorithm and using segment reporting tool filters: minimum of 100 Kb minimum genomic size of a segment, as well as by visual inspection.

label: Biotin

source_name: Peripheral Blood

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from peripheral blood or spleen samples using the Qiagen DNA Blood Mini/Midi Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

value: peripheral blood

value: male


title: WB_OW_M2 WD2_123

status: Public on Dec 21 2017

first: Yinan

last: Zheng

state: Illinois

address: 680 N Lake Shore Drive, Suite 1400

department: Department of Preventive Medicine

institute: Northwestern University

description: WB_OW_M2 WD2_123 WD2_123

hyb_protocol: The samples were prepared for nCounter miRNA expression profiling according to the manufacturer’s recommendations (NanoString, Seattle, WA, USA)

data_processing: Raw data were log2 transformed, normalized using the mean of six positive controls – which were used  to calculated a scaling factor in each column (lane/sample) as suggest by the manufacturer guidelines – background corrected by subtracting the mean of six negative controls, and finally quantile normalized. PCA analysis was done on processed data to identify possible outlier samples. Finally, MiRNAs with non-detectable values in more than 10% of observations were removed.

extract_protocol: Peripheral blood form each participant on both examination days was collected in PAXgene Blood RNA tubes. All Samples were frozen at -80 degree and sent to laboratory. Total RNA was extraction from whole blood according to manufacturer’s protocols (Qiagen Chatsworth, CA, USA).

value: blood

tag: Sex

value: Male

tag: bmi


title: WB_TD_M1 WD1_125

description: WB_TD_M1 WD1_125 WD1_125

scan_protocol: The samples were prepared for nCounter miRNA expression profiling according to the manufacturer’s recommendations (NanoString, Seattle, WA, USA)

value: Female


title: WB_TD_M2 WD2_125

description: WB_TD_M2 WD2_125 WD2_125

label_protocol: The samples were prepared for nCounter miRNA expression profiling according to the manufacturer’s recommendations (NanoString, Seattle, WA, USA)


title: WB_OW_M2 WD2_120

description: WB_OW_M2 WD2_120 WD2_120


title: WB_OW_M1 WD1_121

description: WB_OW_M1 WD1_121 WD1_121


title: 2-2LD1

description:
UMCPLin-Poplar46_4-2L1.CEL
2-2 LD replicate 1

value: transgenic FD overexpressing

value: shoot tip


title: WB_OW_M2 WD2_121

description: WB_OW_M2 WD2_121 WD2_121


title: WB_OW_M1 WD1_122

description: WB_OW_M1 WD1_122 WD1_122


title: WB_OW_M2 WD2_122

description: WB_OW_M2 WD2_122 WD2_122


title: Tumor, Splenic Diffuse Red Pulp Lymphoma, case 1

description:
Hybridized to SNP 6.0
GSM1586429 and GSM1586430 are from the same patient and have the same CNCHP files.


title: Tumor, Splenic Diffuse Red Pulp Lymphoma, case 13

description: Tumor  vs normal

value: M


title: 717LD1

description:
UMCPLin-Poplar46_1-7L1.CEL
717 LD replicate 1

source_name: WT_shoot tips_LD

value: wild type


title: WB_OW_M2 WD2_119

description: WB_OW_M2 WD2_119 WD2_119


title: Tumor, Splenic Diffuse Red Pulp Lymphoma, case 9

description: Hybridized to SNP 6.0

value: splenic diffuse red pulp lymphoma


title: WB_OW_M1 WD1_118

description: WB_OW_M1 WD1_118 WD1_118


title: WB_OW_M2 WD2_118

description: WB_OW_M2 WD2_118 WD2_118


title: WB_OW_M2 WD2_117

description: WB_OW_M2 WD2_117 WD2_117


title: 717LD3

description:
UMCPLin-Poplar46_3-7L3.CEL
717 LD replicate 2


title: WB_OW_M2 WD2_115

description: WB_OW_M2 WD2_115 WD2_115


title: WB_OW_M2 WD2_116

description: WB_OW_M2 WD2_116 WD2_116


title: Tumor, Splenic Diffuse Red Pulp Lymphoma, case 1_SPLEEN

source_name: Spleen

value: spleen


description: Hybridized to SNP 6.0


title: WB_OW_M1 WD1_119

description: WB_OW_M1 WD1_119 WD1_119


title: WB_TD_M2 WD2_114

description: WB_TD_M2 WD2_114 WD2_114


title: WB_OW_M1 WD1_123

description: WB_OW_M1 WD1_123 WD1_123


title: WB_TD_M2 WD2_113

description: WB_TD_M2 WD2_113 WD2_113


title: WB_OW_M1 WD1_117

description: WB_OW_M1 WD1_117 WD1_117


title: WB_OW_M1 WD1_120

description: WB_OW_M1 WD1_120 WD1_120


title: WB_TD_M2 WD2_110

description: WB_TD_M2 WD2_110 WD2_110


title: WB_TD_M1 WD1_110

description: WB_TD_M1 WD1_110 WD1_110


title: WB_TD_M1 WD1_114

description: WB_TD_M1 WD1_114 WD1_114


title: WB_TD_M2 WD2_111

description: WB_TD_M2 WD2_111 WD2_111


title: WB_TD_M2 WD2_109

description: WB_TD_M2 WD2_109 WD2_109


title: WB_TD_M1 WD1_113

description: WB_TD_M1 WD1_113 WD1_113


title: WB_TD_M1 WD1_109

description: WB_TD_M1 WD1_109 WD1_109


title: WB_OW_M2 WD2_107

description: WB_OW_M2 WD2_107 WD2_107


title: WB_OW_M1 WD1_106

description: WB_OW_M1 WD1_106 WD1_106


title: WB_OW_M2 WD2_108

description: WB_OW_M2 WD2_108 WD2_108


title: WB_OW_M1 WD1_108

description: WB_OW_M1 WD1_108 WD1_108


title: WB_OW_M2 WD2_106

description: WB_OW_M2 WD2_106 WD2_106


title: WB_TD_M2 WD2_104

description: WB_TD_M2 WD2_104 WD2_104


title: WB_OW_M1 WD1_105

description: WB_OW_M1 WD1_105 WD1_105


title: WB_OW_M2 WD2_105

description: WB_OW_M2 WD2_105 WD2_105


title: WB_OW_M2 WD2_103

description: WB_OW_M2 WD2_103 WD2_103


title: WB_TD_M1 WD1_111

description: WB_TD_M1 WD1_111 WD1_111


title: WB_OW_M1 WD1_103

description: WB_OW_M1 WD1_103 WD1_103


title: WB_TD_M1 WD1_100

description: WB_TD_M1 WD1_100 WD1_100


title: WB_TD_M1 WD1_104

description: WB_TD_M1 WD1_104 WD1_104


title: WB_TD_M2 WD2_100

description: WB_TD_M2 WD2_100 WD2_100


title: WB_TD_M1 WD1_99

description: WB_TD_M1 WD1_99 WD1_99


title: WB_TD_M2 WD2_102

description: WB_TD_M2 WD2_102 WD2_102


title: WB_TD_M1 WD1_102

description: WB_TD_M1 WD1_102 WD1_102


title: WB_TD_M1 WD1_98

description: WB_TD_M1 WD1_98 WD1_98


title: WB_OW_M1 WD1_107

description: WB_OW_M1 WD1_107 WD1_107


title: WB_OW_M2 WD2_101

description: WB_OW_M2 WD2_101 WD2_101


title: WB_TD_M2 WD2_95

description: WB_TD_M2 WD2_95 WD2_95


title: WB_TD_M2 WD2_99

description: WB_TD_M2 WD2_99 WD2_99


title: WB_OW_M1 WD1_97

description: WB_OW_M1 WD1_97 WD1_97


title: WB_OW_M1 WD1_101

description: WB_OW_M1 WD1_101 WD1_101


title: WB_OW_M2 WD2_97

description: WB_OW_M2 WD2_97 WD2_97


title: WB_TD_M1 WD1_96

description: WB_TD_M1 WD1_96 WD1_96


title: WB_TD_M2 WD2_98

description: WB_TD_M2 WD2_98 WD2_98


title: WB_TD_M2 WD2_96

description: WB_TD_M2 WD2_96 WD2_96


title: WB_TD_M1 WD1_94

description: WB_TD_M1 WD1_94 WD1_94


title: WB_OW_M2 WD2_91

description: WB_OW_M2 WD2_91 WD2_91


title: WB_OW_M2 WD2_92

description: WB_OW_M2 WD2_92 WD2_92


title: WB_TD_M1 WD1_95

description: WB_TD_M1 WD1_95 WD1_95


title: WB_OW_M1 WD1_92

description: WB_OW_M1 WD1_92 WD1_92


title: WB_TD_M1 WD1_93

description: WB_TD_M1 WD1_93 WD1_93


title: 717LD2

description:
UMCPLin-Poplar46_2-7L2.CEL
717 LD replicate 2


title: WB_TD_M2 WD2_94

description: WB_TD_M2 WD2_94 WD2_94


title: WB_OW_M1 WD1_91

description: WB_OW_M1 WD1_91 WD1_91


title: WB_OW_M1 WD1_88

description: WB_OW_M1 WD1_88 WD1_88


title: WB_TD_M2 WD2_93

description: WB_TD_M2 WD2_93 WD2_93


title: WB_OW_M2 WD2_87

description: WB_OW_M2 WD2_87 WD2_87


title: WB_OW_M2 WD2_90

description: WB_OW_M2 WD2_90 WD2_90


title: WB_OW_M1 WD1_87

description: WB_OW_M1 WD1_87 WD1_87


title: WB_TD_M2 WD2_86

description: WB_TD_M2 WD2_86 WD2_86


title: WB_TD_M1 WD1_85

description: WB_TD_M1 WD1_85 WD1_85


title: WB_OW_M1 WD1_90

description: WB_OW_M1 WD1_90 WD1_90


title: WB_TD_M2 WD2_83

description: WB_TD_M2 WD2_83 WD2_83


title: WB_TD_M1 WD1_83

description: WB_TD_M1 WD1_83 WD1_83


title: WB_OW_M2 WD2_82

description: WB_OW_M2 WD2_82 WD2_82


title: WB_OW_M1 WD1_89

description: WB_OW_M1 WD1_89 WD1_89


title: WB_OW_M2 WD2_81

description: WB_OW_M2 WD2_81 WD2_81


title: WB_TD_M2 WD2_80

description: WB_TD_M2 WD2_80 WD2_80


title: WB_OW_M1 WD1_81

description: WB_OW_M1 WD1_81 WD1_81


title: WB_OW_M2 WD2_84

description: WB_OW_M2 WD2_84 WD2_84


title: WB_OW_M2 WD2_89

description: WB_OW_M2 WD2_89 WD2_89


title: WB_OW_M2 WD2_88

description: WB_OW_M2 WD2_88 WD2_88


title: WB_OW_M1 WD1_84

description: WB_OW_M1 WD1_84 WD1_84


title: WB_TD_M1 WD1_86

description: WB_TD_M1 WD1_86 WD1_86


title: WB_TD_M2 WD2_85

description: WB_TD_M2 WD2_85 WD2_85


title: WB_OW_M1 WD1_82

description: WB_OW_M1 WD1_82 WD1_82


title: WB_OW_M1 WD1_78

description: WB_OW_M1 WD1_78 WD1_78


title: WB_TD_M2 WD2_79

description: WB_TD_M2 WD2_79 WD2_79


title: WB_TD_M1 WD1_79

description: WB_TD_M1 WD1_79 WD1_79


title: WB_TD_M1 WD1_80

description: WB_TD_M1 WD1_80 WD1_80


title: WB_OW_M2 WD2_78

description: WB_OW_M2 WD2_78 WD2_78


title: WB_OW_M2 WD2_77

description: WB_OW_M2 WD2_77 WD2_77


title: WB_OW_M2 WD2_76

description: WB_OW_M2 WD2_76 WD2_76


title: WB_OW_M1 WD1_77

description: WB_OW_M1 WD1_77 WD1_77


title: WB_OW_M1 WD1_76

description: WB_OW_M1 WD1_76 WD1_76


title: WB_TD_M2 WD2_74

description: WB_TD_M2 WD2_74 WD2_74


title: WB_TD_M2 WD2_69

description: WB_TD_M2 WD2_69 WD2_69


title: WB_TD_M2 WD2_72

description: WB_TD_M2 WD2_72 WD2_72


title: WB_TD_M1 WD1_71

description: WB_TD_M1 WD1_71 WD1_71


title: WB_OW_M1 WD1_75

description: WB_OW_M1 WD1_75 WD1_75


title: WB_TD_M2 WD2_73

description: WB_TD_M2 WD2_73 WD2_73


title: WB_TD_M1 WD1_72

description: WB_TD_M1 WD1_72 WD1_72


title: WB_TD_M1 WD1_69

description: WB_TD_M1 WD1_69 WD1_69


title: WB_TD_M1 WD1_74

description: WB_TD_M1 WD1_74 WD1_74


title: WB_TD_M1 WD1_73

description: WB_TD_M1 WD1_73 WD1_73


title: WB_TD_M2 WD2_70

description: WB_TD_M2 WD2_70 WD2_70


title: WB_OW_M2 WD2_68

description: WB_OW_M2 WD2_68 WD2_68


title: WB_OW_M1 WD1_68

description: WB_OW_M1 WD1_68 WD1_68


title: WB_OW_M2 WD2_67

description: WB_OW_M2 WD2_67 WD2_67


title: WB_OW_M2 WD2_66

description: WB_OW_M2 WD2_66 WD2_66


title: WB_TD_M1 WD1_70

description: WB_TD_M1 WD1_70 WD1_70


title: WB_OW_M1 WD1_65

description: WB_OW_M1 WD1_65 WD1_65


title: WB_TD_M2 WD2_64

description: WB_TD_M2 WD2_64 WD2_64


title: WB_OW_M1 WD1_66

description: WB_OW_M1 WD1_66 WD1_66


title: WB_OW_M2 WD2_65

description: WB_OW_M2 WD2_65 WD2_65


title: WB_OW_M1 WD1_67

description: WB_OW_M1 WD1_67 WD1_67


title: WB_OW_M2 WD2_75

description: WB_OW_M2 WD2_75 WD2_75


title: WB_OW_M1 WD1_115

description: WB_OW_M1 WD1_115 WD1_115


title: WB_TD_M2 WD2_63

description: WB_TD_M2 WD2_63 WD2_63


title: WB_TD_M1 WD1_64

description: WB_TD_M1 WD1_64 WD1_64


title: WB_TD_M2 WD2_71

description: WB_TD_M2 WD2_71 WD2_71


title: WB_OW_M1 WD1_116

description: WB_OW_M1 WD1_116 WD1_116


title: WB_TD_M1 WD1_63

description: WB_TD_M1 WD1_63 WD1_63


title: WB_TD_M2 WD2_62

description: WB_TD_M2 WD2_62 WD2_62


title: WB_TD_M2 WD2_60

description: WB_TD_M2 WD2_60 WD2_60


title: WB_TD_M1 WD1_60

description: WB_TD_M1 WD1_60 WD1_60


title: WB_TD_M2 WD2_52

description: WB_TD_M2 WD2_52 WD2_52


title: WB_TD_M1 WD1_61

description: WB_TD_M1 WD1_61 WD1_61


title: WB_TD_M2 WD2_50

description: WB_TD_M2 WD2_50 WD2_50


title: WB_TD_M1 WD1_57

description: WB_TD_M1 WD1_57 WD1_57


title: WB_OW_M1 WD1_54

description: WB_OW_M1 WD1_54 WD1_54


title: WB_OW_M1 WD1_53

description: WB_OW_M1 WD1_53 WD1_53


title: WB_TD_M2 WD2_58

description: WB_TD_M2 WD2_58 WD2_58


title: WB_OW_M2 WD2_54

description: WB_OW_M2 WD2_54 WD2_54


title: WB_TD_M2 WD2_61

description: WB_TD_M2 WD2_61 WD2_61


title: WB_TD_M1 WD1_50

description: WB_TD_M1 WD1_50 WD1_50


title: WB_OW_M2 WD2_53

description: WB_OW_M2 WD2_53 WD2_53


title: WB_TD_M1 WD1_52

description: WB_TD_M1 WD1_52 WD1_52


title: WB_OW_M2 WD2_55

description: WB_OW_M2 WD2_55 WD2_55


title: WB_TD_M1 WD1_51

description: WB_TD_M1 WD1_51 WD1_51


title: WB_TD_M1 WD1_49

description: WB_TD_M1 WD1_49 WD1_49


title: WB_TD_M2 WD2_59

description: WB_TD_M2 WD2_59 WD2_59


title: WB_TD_M1 WD1_58

description: WB_TD_M1 WD1_58 WD1_58


title: WB_TD_M2 WD2_51

description: WB_TD_M2 WD2_51 WD2_51


title: WB_TD_M2 WD2_57

description: WB_TD_M2 WD2_57 WD2_57


title: WB_TD_M1 WD1_59

description: WB_TD_M1 WD1_59 WD1_59


title: WB_OW_M1 WD1_46

description: WB_OW_M1 WD1_46 WD1_46


title: WB_TD_M1 WD1_62

description: WB_TD_M1 WD1_62 WD1_62


title: WB_OW_M2 WD2_47

description: WB_OW_M2 WD2_47 WD2_47


title: WB_OW_M1 WD1_47

description: WB_OW_M1 WD1_47 WD1_47


title: WB_OW_M1 WD1_48

description: WB_OW_M1 WD1_48 WD1_48


title: WB_OW_M1 WD1_55

description: WB_OW_M1 WD1_55 WD1_55


title: WB_TD_M2 WD2_43

description: WB_TD_M2 WD2_43 WD2_43


title: WB_TD_M2 WD2_49

description: WB_TD_M2 WD2_49 WD2_49


title: WB_TD_M1 WD1_42

description: WB_TD_M1 WD1_42 WD1_42


title: WB_TD_M2 WD2_41

description: WB_TD_M2 WD2_41 WD2_41


title: WB_OW_M2 WD2_45

description: WB_OW_M2 WD2_45 WD2_45


title: WB_OW_M2 WD2_46

description: WB_OW_M2 WD2_46 WD2_46


title: WB_OW_M2 WD2_48

description: WB_OW_M2 WD2_48 WD2_48


title: WB_OW_M1 WD1_45

description: WB_OW_M1 WD1_45 WD1_45


title: WB_TD_M1 WD1_44

description: WB_TD_M1 WD1_44 WD1_44


title: WB_TD_M2 WD2_42

description: WB_TD_M2 WD2_42 WD2_42


title: Neonate_Unstim_0h_subj5 [pDC]

city: Vancouver

first: Edgardo

last: Fortuno III

state: BC

department: Paediatrics

country: Canada

institute: Child & Family Research Institute - University of British Columbia

description: Neonate subject 5

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with no background subtraction using Illumina's BeadStudio software version 3.1.3.0

source_name: Cord blood

label_protocol: Biotinylated cRNA were prepared with the Ambion's Illumina TotalPrep RNA Amplification Kit

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit with in-column DNAseI treatment in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

tag: subject

tag: age group

value: Neonate

value: Cord blood

value: pDC

tag: agent

value: Unstim

tag: time


title: WB_TD_M2 WD2_44

description: WB_TD_M2 WD2_44 WD2_44

tag: age


title: Neonate_3M003_6h_subj5 [pDC]

description: Neonate subject 5

tag: gender


title: Adult_3M003_6h_subj6 [pDC]

description: Adult subject 6

source_name: Peripheral blood

value: Adult

value: Peripheral blood


title: Neonate_Unstim_0h_subj6 [pDC]

description: Neonate subject 6


title: Neonate_3M003_1h_subj4 [pDC]

description: Neonate subject 4


title: Adult_3M003_1h_subj6 [pDC]

description: Adult subject 6


title: WB_OW_M2 WD2_39

description: WB_OW_M2 WD2_39 WD2_39


title: Adult_Unstim_0h_subj6 [pDC]

description: Adult subject 6


title: WB_TD_M1 WD1_43

description: WB_TD_M1 WD1_43 WD1_43


title: WB_TD_M1 WD1_41

description: WB_TD_M1 WD1_41 WD1_41


title: WB_OW_M2 WD2_38

description: WB_OW_M2 WD2_38 WD2_38


title: WB_OW_M1 WD1_40

description: WB_OW_M1 WD1_40 WD1_40


title: WB_OW_M2 WD2_40

description: WB_OW_M2 WD2_40 WD2_40


title: WB_OW_M1 WD1_39

description: WB_OW_M1 WD1_39 WD1_39


title: Neonate_3M003_6h_subj4 [pDC]

description: Neonate subject 4


title: Neonate_3M003_6h_subj6 [pDC]

description: Neonate subject 6


title: Neonate_3M003_1h_subj6 [pDC]

description: Neonate subject 6


title: WB_OW_M2 WD2_37

description: WB_OW_M2 WD2_37 WD2_37


title: WB_OW_M1 WD1_38

description: WB_OW_M1 WD1_38 WD1_38


title: WB_TD_M2 WD2_34

description: WB_TD_M2 WD2_34 WD2_34


title: WB_TD_M2 WD2_35

description: WB_TD_M2 WD2_35 WD2_35


title: WB_OW_M1 WD1_37

description: WB_OW_M1 WD1_37 WD1_37


title: WB_TD_M2 WD2_36

description: WB_TD_M2 WD2_36 WD2_36


title: WB_TD_M1 WD1_36

description: WB_TD_M1 WD1_36 WD1_36


title: WB_TD_M1 WD1_35

description: WB_TD_M1 WD1_35 WD1_35


title: WB_TD_M1 WD1_34

description: WB_TD_M1 WD1_34 WD1_34


title: WB_TD_M2 WD2_33

description: WB_TD_M2 WD2_33 WD2_33


title: Adult_3M003_6h_subj4 [pDC]

description: Adult subject 4


title: WB_OW_M2 WD2_32

description: WB_OW_M2 WD2_32 WD2_32


title: WB_TD_M1 WD1_33

description: WB_TD_M1 WD1_33 WD1_33


title: Adult_3M003_1h_subj5 [pDC]

description: Adult subject 5


title: Neonate_Unstim_0h_subj4 [pDC]

description: Neonate subject 4


title: Neonate_3M003_1h_subj5 [pDC]

description: Neonate subject 5


title: Adult_3M003_1h_subj4 [pDC]

description: Adult subject 4


title: Neonate_Unstim_0h_subj3 [pDC]

description: Neonate subject 3


title: Adult_3M003_6h_subj5 [pDC]

description: Adult subject 5


title: Adult_Unstim_0h_subj4 [pDC]

description: Adult subject 4


title: WB_OW_M2 WD2_30

description: WB_OW_M2 WD2_30 WD2_30


title: Neonate_3M003_1h_subj2 [pDC]

description: Neonate subject 2


title: Neonate_3M003_1h_subj3 [pDC]

description: Neonate subject 3


title: Adult_Unstim_0h_subj5 [pDC]

description: Adult subject 5


title: Adult_3M003_1h_subj3 [pDC]

description: Adult subject 3


title: Neonate_3M003_6h_subj3 [pDC]

description: Neonate subject 3


title: Neonate_Unstim_0h_subj2 [pDC]

description: Neonate subject 2


title: Adult_3M003_6h_subj3 [pDC]

description: Adult subject 3


title: WB_OW_M2 WD2_29

description: WB_OW_M2 WD2_29 WD2_29


title: Neonate_3M003_6h_subj2 [pDC]

description: Neonate subject 2


title: WB_OW_M2 WD2_31

description: WB_OW_M2 WD2_31 WD2_31


title: WB_TD_M2 WD2_27

description: WB_TD_M2 WD2_27 WD2_27


title: WB_TD_M2 WD2_26

description: WB_TD_M2 WD2_26 WD2_26


title: Adult_3M003_6h_subj2 [pDC]

description: Adult subject 2


title: Adult_Unstim_0h_subj3 [pDC]

description: Adult subject 3


title: Adult_Unstim_0h_subj2 [pDC]

description: Adult subject 2


title: WB_TD_M2 WD2_25

description: WB_TD_M2 WD2_25 WD2_25


title: WB_OW_M2 WD2_24

description: WB_OW_M2 WD2_24 WD2_24


title: WB_OW_M2 WD2_23

description: WB_OW_M2 WD2_23 WD2_23


title: WB_OW_M2 WD2_22

description: WB_OW_M2 WD2_22 WD2_22


title: WB_OW_M2 WD2_21

description: WB_OW_M2 WD2_21 WD2_21


title: WB_TD_M2 WD2_20

description: WB_TD_M2 WD2_20 WD2_20


title: Adult_3M003_1h_subj2 [pDC]

description: Adult subject 2


title: Neonate_Unstim_0h_subj1 [pDC]

description: Neonate subject 1


title: Neonate_3M003_6h_subj1 [pDC]

description: Neonate subject 1


title: Neonate_3M003_1h_subj1 [pDC]

description: Neonate subject 1


title: Adult_3M003_1h_subj1 [pDC]

description: Adult subject 1


title: WB_TD_M2 WD2_19

description: WB_TD_M2 WD2_19 WD2_19


title: WB_TD_M2 WD2_18

description: WB_TD_M2 WD2_18 WD2_18


title: WB_TD_M1 WD1_19

description: WB_TD_M1 WD1_19 WD1_19


title: Adult_3M003_6h_subj1 [pDC]

description: Adult subject 1


title: Adult_Unstim_0h_subj1 [pDC]

description: Adult subject 1


title: WB_TD_M1 WD1_18

description: WB_TD_M1 WD1_18 WD1_18


title: WB_TD_M2 WD2_17

description: WB_TD_M2 WD2_17 WD2_17


title: WB_OW_M2 WD2_16

description: WB_OW_M2 WD2_16 WD2_16


title: WB_OW_M1 WD1_16

description: WB_OW_M1 WD1_16 WD1_16


title: WB_TD_M1 WD1_17

description: WB_TD_M1 WD1_17 WD1_17


title: WB_OW_M2 WD2_15

description: WB_OW_M2 WD2_15 WD2_15


title: WB_OW_M2 WD2_14

description: WB_OW_M2 WD2_14 WD2_14


title: WB_OW_M1 WD1_15

description: WB_OW_M1 WD1_15 WD1_15


title: WB_OW_M1 WD1_14

description: WB_OW_M1 WD1_14 WD1_14


title: WB_OW_M1 WD1_13

description: WB_OW_M1 WD1_13 WD1_13


title: WB_OW_M2 WD2_13

description: WB_OW_M2 WD2_13 WD2_13


title: WB_TD_M1 WD1_12

description: WB_TD_M1 WD1_12 WD1_12


title: WB_TD_M1 WD1_11

description: WB_TD_M1 WD1_11 WD1_11


title: Adult_Unstim_0h_subj6 [mDC]

description: Adult subject 6

value: mDC


title: Adult_3M003_1h_subj6 [mDC]

description: Adult subject 6


title: Adult_3M003_6h_subj5 [mDC]

description: Adult subject 5


title: WB_TD_M2 WD2_12

description: WB_TD_M2 WD2_12 WD2_12


title: Adult_3M003_1h_subj4 [mDC]

description: Adult subject 4


title: Adult_Unstim_0h_subj5 [mDC]

description: Adult subject 5


title: Adult_3M003_6h_subj6 [mDC]

description: Adult subject 6


title: WB_TD_M2 WD2_9

description: WB_TD_M2 WD2_9 WD2_9


title: Adult_3M003_1h_subj5 [mDC]

description: Adult subject 5


title: WB_TD_M2 WD2_11

description: WB_TD_M2 WD2_11 WD2_11


title: Adult_3M003_6h_subj3 [mDC]

description: Adult subject 3


title: WB_TD_M1 WD1_9

description: WB_TD_M1 WD1_9 WD1_9


title: Adult_Unstim_0h_subj3 [mDC]

description: Adult subject 3


title: Adult_3M003_6h_subj4 [mDC]

description: Adult subject 4


title: WB_OW_M2 WD2_8

description: WB_OW_M2 WD2_8 WD2_8


title: Adult_Unstim_0h_subj4 [mDC]

description: Adult subject 4


title: Neonate_3M003_1h_subj6 [mDC]

description: Neonate subject 6


title: WB_OW_M1 WD1_8

description: WB_OW_M1 WD1_8 WD1_8


title: Adult_3M003_1h_subj3 [mDC]

description: Adult subject 3


title: Neonate_3M003_6h_subj5 [mDC]

description: Neonate subject 5


title: WB_OW_M2 WD2_7

description: WB_OW_M2 WD2_7 WD2_7


title: WB_OW_M1 WD1_7

description: WB_OW_M1 WD1_7 WD1_7


title: WB_OW_M2 WD2_6

description: WB_OW_M2 WD2_6 WD2_6


title: Neonate_Unstim_0h_subj5 [mDC]

description: Neonate subject 5


title: WB_OW_M1 WD1_6

description: WB_OW_M1 WD1_6 WD1_6


title: WB_OW_M2 WD2_5

description: WB_OW_M2 WD2_5 WD2_5


title: Neonate_3M003_6h_subj6 [mDC]

description: Neonate subject 6


title: Neonate_Unstim_0h_subj6 [mDC]

description: Neonate subject 6


title: Neonate_3M003_1h_subj4 [mDC]

description: Neonate subject 4


title: WB_OW_M1 WD1_5

description: WB_OW_M1 WD1_5 WD1_5


title: Adult_3M003_6h_subj2 [mDC]

description: Adult subject 2


title: WB_TD_M2 WD2_4

description: WB_TD_M2 WD2_4 WD2_4


title: Neonate_3M003_1h_subj5 [mDC]

description: Neonate subject 5


title: Neonate_3M003_6h_subj4 [mDC]

description: Neonate subject 4


title: Neonate_Unstim_0h_subj4 [mDC]

description: Neonate subject 4


title: WB_TD_M1 WD1_4

description: WB_TD_M1 WD1_4 WD1_4


title: WB_TD_M1 WD1_3

description: WB_TD_M1 WD1_3 WD1_3


title: WB_TD_M2 WD2_1

description: WB_TD_M2 WD2_1 WD2_1


title: WB_TD_M2 WD2_2

description: WB_TD_M2 WD2_2 WD2_2


title: WB_TD_M2 WD2_3

description: WB_TD_M2 WD2_3 WD2_3


title: WB_TD_M1 WD1_1

description: WB_TD_M1 WD1_1 WD1_1


title: Adult_3M003_6h_subj1 [mDC]

description: Adult subject 1


title: Adult_3M003_1h_subj2 [mDC]

description: Adult subject 2


title: WB_TD_M1 WD1_2

description: WB_TD_M1 WD1_2 WD1_2


title: Adult_Unstim_0h_subj2 [mDC]

description: Adult subject 2


title: Adult_3M003_1h_subj1 [mDC]

description: Adult subject 1