title: 540nm-550nm_1

city: San Marcos

first: Yuan

last: Lu

state: TX

address: university drive

institute: Xiphophorus Genetic Stock Center

data_processing:
Illumina Hi-Seq 2000 was used to sequence all samples
raw reads were trimmed and filtered using a custom Perl script,The reads were truncated based on similarity to library adaptor sequences. Then, low-scoring sections of each read were removed, preserving the longest remaining fragment
Filtered reads are mapped to the Xiphophorus transcriptome using GSNAP
Gene expression were quantified using eXpress.
Genome_build: Xiphophorus maculatus Ensembl 80
Supplementary_files_format_and_content: Format: .csv; Content: gene expression profiles

organism: Xiphophorus maculatus

growth_protocol: Fish utilized were mature male X. maculatus Jp 163 B, 10 to 11 months of age, from the 105th generation of sibling inbreeding were used. All fish were housed in the Xiphophorus Genetic Stock Center following standard animal mainteince protocol.

extract_protocol:
RNA isolation was performed following the Qiagen RNeasy RNA isolation protocol (Qiagen, Valencia, CA, USA). Skin samples harvested from fish were first homogenized using a hand-held homogenizer in a 1.5 mL microcentrifuge tube while the sample remained frozen in TRI Reagent (Sigma Inc., St Louis, MO, USA). After homogenization, 300 μL of fresh 4°C TRI Reagent was added to the samples followed by incubation (rt) for 5 min. Chloroform extraction was performed by adding 120 μL chloroform and shaken for 15 sec. Samples were centrifuged (16,100 rcf for 5 min at 4°C) for phase partition. The aqueous layer was transferred to a new 1.5 mL microcentrifuge tube and a second chloroform extraction performed (300 μL TRI Reagent, 60 μL chloroform). After extraction, nucleic acids in the aqueous phase were precipitated with 500 μL 70% EtOH in diethylpyrocarbonate (DEPC) treated water. The sample was then transferred to a Qiagen RNeasy mini spin column and on-column DNase treatment was performed for 15 min at 25°C. RNA samples were then washed and eluted in 100 μL RNase free water. RNA concentration was measured with a Qubit 2.0 fluorometer (Life Technologies, Grand Island, NY, USA). To further assess the RNA quality, a RNA integrity (RIN) score was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). All samples processed for RNA sequencing had a RIN score above 8.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: FL exposure occurred in a specially designed wooden box (77 cm in length, 41 cm in height, and 36 cm in depth), with a hinged wooden lid capable of sealing the interior of the box from external light. On the bottom of each of the two sides (41 cm x 36 cm) were 15.5 cm diameter high-speed fans that maintained interior temperatures of the closed box at less than 24°C.  For FL exposure single fish were placed into UV transparent (UVT) plastic cuvettes (9 cm x 7.5 cm x 1.5 cm) in about 95 ml water and the cuvettes were suspended in a rack centered between and about 10 cm from the a bank of four FL bulbs (each side) inside the exposure chamber. FL sources were ‘‘cool white’’ Philips F 20T12/CW 20W, Alto (i.e., 4100K FL)) fluorescent lamps provided doses of 35 kJ/m2, that equated to an exposure time of about 40 min.   For waveband exposure of X. maculatus to 50 nm [300-350 (7.3 kJ/m2), 350-400 18.6 kJ/m2), 400-450 (21.6 kJ/m2), 450-500 (21.2 kJ/m2), 500-550 (17.4 kJ/m2), and 550-600 nm (13.8 kJ/m2)] or 10 nm wavebands of light [500-510nm, 510-520, 520-530, 530-540 ,and 540-550), we utilized a TLS-300X Series Tunable Light Source (Newport Corporation, Irvine, CA, USA) containing an Ushio 300 W Xenon Short Arc Lamp Model 6258. Exposures were as detailed previously. Briefly, light emitted from the source was passed through a Cornerstone 130 Monochromator (Newport Corporation, Irvine, CA, USA) to define specific wavelengths. The bulb was burned in 15 min prior to all exposure treatments. The specific wavelengths were divided by 2 fiber optic light cables, allowing the fish to be exposed on both sides simultaneously to the defined wavelengths of light. Spectral distributions were made to determine the power output of each light source at specific wavelengths using a Newport 1918-R power meter (Newport Corporation, Irvine, CA, USA).  The spectral distribution of the xenon light source was measured at full spectrum (0 nm) using an Ocean Optics STS 350-800 nm Microspectrometer (Ocean Optics Inc., Dundedin, FL, USA) and OceanView software v1.5 (http://oceanoptics.com/product/oceanview/). The microspectrometer was calibrated to a known standard using Ocean Optics Halogen Calibrated Light Source HL-3P-CAL (Ocean Optics Inc., Dundedin, FL, USA). To cover each wavelength in each 50 nm regions, the monochromator was set to scan and repeat (i.e. loop) using Asoftech Automation (http://www.asoftech.com/) through the wavelengths of each region (1 nm/sec for 50 sec) for the duration of the light exposure.   Each fish was then placed in a 4 cm length x 1 cm wide x 4.5 cm height quartz cuvette filled with 14 mL of filtered aquaria water. The cuvette was then centered between the 2 fiber optic light cables and covered by a cardboard box to eliminate ambient light. After exposure, the fish was removed from the cuvette, rinsed with filtered aquaria water, placed back into a 125 mL flask filled with 100 mL of filtered aquaria water, and in the dark for 6 hours to allow for gene expression prior to sacrifice and tissue dissection.

value: 10-11 month

value: Jp 163 B

tag: light treatment

value: skin


title: 540nm-550nm_2

status: Public on Apr 30 2018

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

tag: gender

value: male

tag: age

tag: strain

tag: tissue


title: H170-1

type: RNA

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

description:
Gene expression of secondgeneration  xenotransplant mouse  control sample
for internal reference only

hyb_protocol: The hybridizations were performed for 17 hours at 10 rpm and 65°C in the hybridization oven (Agilent). Washing and staining of the arrays were done according to the manufacturer's recommendation.

scan_protocol: Cy3 intensities were detected by one-color scanning using an Agilent DNA microarray scanner (G2505B) at 3 micron resolution. Scanned image files were visually inspected for artifacts and then analyzed.

data_processing: Intensity data were extracted using Agilent's Feature Extraction (FE) software (version 11.5.1.1) including a quality control based on internal controls using Agilent's protocol GE1_107_Sep09. All chips passed the quality control and were analyzed using the Limma packages of Bioconductor.

organism: Homo sapiens

source_name: HPV-negative hypopharyngeal squamous cell carcinoma

label_protocol: Microarrays were done using the Low RNA Input linear Amplification Kit Plus, One Color protocol (Cat. N°: 5188-5339, 2007; Agilent Technologies, Inc., Santa Clara, CA) and the Agilent RNA Spike-In Kit for One color (Agilent Technologies, Inc. 2007; Cat. N°: 5188-5282) following the manufacturer's standard protocol. Global gene expression analysis was applied using the SurePrint G3 Human Gene Expression 8x60K v2 Microarray Kit, Product number G4851B, (Agilent Microarray Design ID 039494). 200 ng of total RNA were used as a starting material to prepare cDNA. cDNA synthesis and in vitro transcription (IVT) were performed according to the manufacturer's recommendation. Quantity and efficiency of the labeled amplified cRNA were determined using the NanoDrop ND-1000 UV-VIS Spectrophotometer version 3.2.1.

growth_protocol: Tumor tissue was collected from primary tumor and metastasis during curative treatment in the operating theater. Parts of it were stored in RNAlater for subsequent gene expression profiling. Seperate parts were xenotransplanted subcutaneously into NMRI-nu mice. After euthanasia of the animals, tumor tissue was dissociated and a cell line was established. For  the enrichment of cancer stem cells, this cell line was kept in ultra-low-attachment wells under serum-free conditions.

extract_protocol: Total RNA was extracted from cells using TRIzol® (Invitrogen/Life Technologies). mRNA was reverse-transcribed using oligo-dT and random hexameric primers and was quantified via qRT-PCR analysis using SYBR Green (Invitrogen/Life Technologies).

tag: phenotype

value: second generation xenotransplant in NMRI-nu mouse

value: control


title: M-2

description: Gene expression of sample extracted from metastasis stage

value: HPV-negative hypopharyngeal squamous cell carcinoma

value: lymph node metastasis

value: metastasis

tag: biological replicate number


title: Stomach_Sham_rep1

city: Genoa

first: Alberto

last: Izzotti

address: Via A. Pastore 1

country: Italy

institute: University of Genoa

description:
DISSALMouse3Kv2.0_035
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray analyzes the expression of 1135 mouse miRNAs. The total RNA from each sample is labeled with Label IT® miRNA Labeling Kits, Version 2 (Mirus Bio, WI) following the standard protocol.  Total RNA (500 ng) was mixed with 10 µl 10x labeling buffer, 4 µl Label IT reagent (containing Cy 3 or Cy 5 fluorescent tracers), and water to 86 µl

hyb_protocol: The hybridization was performed in GlassArray Hybridization Cassettes (Invitrogen Ltd, Paisley, UK) in a water bath at 37°C for 16 h and then a wash sequence was performed.

scan_protocol: The array was dried by centrifugation and scanned by a laser scanner (ScanArray, PerkinElmer, Waltham, MA) to record fluorescent signals produced by each spotted probe effectively hybridized with the corresponding miRNA.

data_processing:
The microarray data were processed by GeneSpring software and their overall variability, as related to treatments, was examined by box-plot analysis, scatter-plot analysis (SPA), hierarchical cluster analysis (HCA),and principal component analysis (PCA). Due to the huge number of datasets to be analyzed, pooled analysis of microarray data was performed without taking into account intergender differences, a goal that was out of the scope of the present study and that had been evaluated in previous studies  (Izzotti et al., Oncotarget 2016).
Differences in body weight gain between MCS-exposed and sham-exposed mice was evaluated for statistical significance by ANOVA followed by Student’s t test for unpaired data.  miRNA microarray data, after local background subtraction, log transformation, and normalization were analyzed by GeneSpring software (Agilent, Santa Clara, CA).

organism: Mus musculus

source_name: Stomach,Sham

growth_protocol: Immediately after sacrifice, the BAL was performed by intubating the trachea and lavaging with 5 ml of PBS per mouse. The blood was collected by heart puncture and used for preparing serum.  The urines were collected for 8 h and pooled from the mice belonging to each experimental group by using metabolic cages during the day preceding euthanasia of mice.

extract_protocol: RNA was extracted individually from the 10 organs of mice belonging to all experimental groups, whereas the body fluids were pooled within each group, irrespective of gender due to the low amounts of samples available.  RNA was extracted from mouse organs (miRNeasy, Qiagen, Hilden, Germany) and body fluids (Exiqon’s miRCURY™ RNA Isolation Kit – Biofluids (Exiqon, Vedbaek, Denmark)

treatment_protocol: Ten organs, including lungs, liver, heart, kidney, spleen, urinary bladder, skeletal muscle (left gastrocnemius), colon, stomach, and brain, were collected.  Immediately after collection, each organ or fluid was immersed in RNAlater and kept at -80°C. The urines were centrifuged in order to remove the sediment.

value: Male

tag: treatment

value: Sham

tag: organs

value: Stomach


title: u45-2

description:
Gene expression of xenotransplant control sample
for internal reference only

value: xenotransplant in NMRI-nu mouse


title: u45-1


title: SphK-1

description: Gene expression of spheroid colony of cells extracted from primary tumor

value: spheroid colony of cell line derived from primary tumor

value: primary tumor


title: Spleen_Sham_rep2

description:
DISSALMouse3Kv2.0_039
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray

source_name: Spleen,Sham

label_protocol: The total RNA from each sample is labeled with Label IT® miRNA Labeling Kits, Version 2 (Mirus Bio, WI) following the standard protocol

value: Spleen


title: 530nm-540nm_2


title: T-3

description: Gene expression of sample extracted from primary tumor


title: NZK-3

value: cell line derived from primary tumor


title: NZK-2


title: M-1


title: T-2


title: M-3


title: u45-3


title: SphK-2

description: Gene expression of spheroid colony of cells  extracted from primary tumor


title: SphK-3


title: 530nm-540nm_1

value: 10-11 month


title: 520nm-530nm_2

value: Jp 163 B


title: NZK-1


title: T-1


title: 520nm-530nm_1

value: skin


title: 510nm-520nm_2

value: male


title: 510nm-520nm_1


title: Muscle_MCS_rep2

description:
DISSALMouse3Kv2.0_034
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray analyzes the expression of 1135 mouse miRNAs. The total RNA from each sample is labeled with Label IT® miRNA Labeling Kits, Version 2 (Mirus Bio, WI) following the standard protocol.  Total RNA (500 ng) was mixed with 10 µl 10x labeling buffer, 4 µl Label IT reagent (containing Cy 3 or Cy 5 fluorescent tracers), and water to 86 µl

source_name: Muscle,MCS

value: MCS

value: Muscle


title: Muscle_MCS_rep1

description:
DISSALMouse3Kv2.0_033
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray analyzes the expression of 1135 mouse miRNAs. The total RNA from each sample is labeled with Label IT® miRNA Labeling Kits, Version 2 (Mirus Bio, WI) following the standard protocol.  Total RNA (500 ng) was mixed with 10 µl 10x labeling buffer, 4 µl Label IT reagent (containing Cy 3 or Cy 5 fluorescent tracers), and water to 86 µl

value: Female


title: 500nm-510nm_2


title: 500nm-510nm_1


title: 10nm_control_2


title: 10nm_control_1


title: Muscle_Sham_rep2

description:
DISSALMouse3Kv2.0_032
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray analyzes the expression of 1135 mouse miRNAs. The total RNA from each sample is labeled with Label IT® miRNA Labeling Kits, Version 2 (Mirus Bio, WI) following the standard protocol.  Total RNA (500 ng) was mixed with 10 µl 10x labeling buffer, 4 µl Label IT reagent (containing Cy 3 or Cy 5 fluorescent tracers), and water to 86 µl

source_name: Muscle,Sham


title: Muscle_Sham_rep1

description:
DISSALMouse3Kv2.0_031
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray analyzes the expression of 1135 mouse miRNAs. The total RNA from each sample is labeled with Label IT® miRNA Labeling Kits, Version 2 (Mirus Bio, WI) following the standard protocol.  Total RNA (500 ng) was mixed with 10 µl 10x labeling buffer, 4 µl Label IT reagent (containing Cy 3 or Cy 5 fluorescent tracers), and water to 86 µl


title: FL_1

source_name: FL

value: FL


title: FL_2


title: 550nm-600nm_2


title: FL_control_1


title: FL_control_3


title: FL_control_2


title: FL_control_4


title: Liver_Sham_rep1

description:
DISSALMouse3Kv2.0_026
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray analyzes the expression of 1135 mouse miRNAs. The total RNA from each sample is labeled with Label IT® miRNA Labeling Kits, Version 2 (Mirus Bio, WI) following the standard protocol.  Total RNA (500 ng) was mixed with 10 µl 10x labeling buffer, 4 µl Label IT reagent (containing Cy 3 or Cy 5 fluorescent tracers), and water to 86 µl

source_name: Liver, MCS

value: Liver


title: Liver_MCS_rep1

description:
DISSALMouse3Kv2.0_028
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray analyzes the expression of 1135 mouse miRNAs. The total RNA from each sample is labeled with Label IT® miRNA Labeling Kits, Version 2 (Mirus Bio, WI) following the standard protocol.  Total RNA (500 ng) was mixed with 10 µl 10x labeling buffer, 4 µl Label IT reagent (containing Cy 3 or Cy 5 fluorescent tracers), and water to 86 µl


title: Liver_Sham_rep2

description:
DISSALMouse3Kv2.0_027
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray analyzes the expression of 1135 mouse miRNAs. The total RNA from each sample is labeled with Label IT® miRNA Labeling Kits, Version 2 (Mirus Bio, WI) following the standard protocol.  Total RNA (500 ng) was mixed with 10 µl 10x labeling buffer, 4 µl Label IT reagent (containing Cy 3 or Cy 5 fluorescent tracers), and water to 86 µl


title: 550nm-600nm_1


title: 500nm-550nm_2


title: 500nm-550nm_1


title: 450nm-500nm_1


title: 450nm-500nm_2


title: 400nm-450nm_1


title: Heart_MCS_rep2

description:
DISSALMouse3Kv2.0_025
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray analyzes the expression of 1135 mouse miRNAs. The total RNA from each sample is labeled with Label IT® miRNA Labeling Kits, Version 2 (Mirus Bio, WI) following the standard protocol.  Total RNA (500 ng) was mixed with 10 µl 10x labeling buffer, 4 µl Label IT reagent (containing Cy 3 or Cy 5 fluorescent tracers), and water to 86 µl

source_name: Heart, MCS

value: Heart


title: 400nm-450nm_2


title: 350nm-400nm_2


title: Heart_MCS_rep1

description:
DISSALMouse3Kv2.0_024
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray analyzes the expression of 1135 mouse miRNAs. The total RNA from each sample is labeled with Label IT® miRNA Labeling Kits, Version 2 (Mirus Bio, WI) following the standard protocol.  Total RNA (500 ng) was mixed with 10 µl 10x labeling buffer, 4 µl Label IT reagent (containing Cy 3 or Cy 5 fluorescent tracers), and water to 86 µl

value: Male


title: 350nm-400nm_1


title: Heart_Sham_rep2

description:
DISSALMouse3Kv2.0_023
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray analyzes the expression of 1135 mouse miRNAs. The total RNA from each sample is labeled with Label IT® miRNA Labeling Kits, Version 2 (Mirus Bio, WI) following the standard protocol.  Total RNA (500 ng) was mixed with 10 µl 10x labeling buffer, 4 µl Label IT reagent (containing Cy 3 or Cy 5 fluorescent tracers), and water to 86 µl

source_name: Heart, Sham

value: Sham


title: Liver_MCS_rep2

description:
DISSALMouse3Kv2.0_029
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray analyzes the expression of 1135 mouse miRNAs. The total RNA from each sample is labeled with Label IT® miRNA Labeling Kits, Version 2 (Mirus Bio, WI) following the standard protocol.  Total RNA (500 ng) was mixed with 10 µl 10x labeling buffer, 4 µl Label IT reagent (containing Cy 3 or Cy 5 fluorescent tracers), and water to 86 µl


title: 300nm-350nm_2


title: 300nm-350nm_1


title: 50nm_control_2


title: 50nm_control_1


title: Kidney_Sham_rep2

description:
DISSALMouse3Kv2.0_019
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray analyzes the expression of 1135 mouse miRNAs. The total RNA from each sample is labeled with Label IT® miRNA Labeling Kits, Version 2 (Mirus Bio, WI) following the standard protocol.  Total RNA (500 ng) was mixed with 10 µl 10x labeling buffer, 4 µl Label IT reagent (containing Cy 3 or Cy 5 fluorescent tracers), and water to 86 µl

source_name: kidney,Sham

value: Kidney


title: Kidney_MCS_rep2

description:
DISSALMouse3Kv2.0_021
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray analyzes the expression of 1135 mouse miRNAs. The total RNA from each sample is labeled with Label IT® miRNA Labeling Kits, Version 2 (Mirus Bio, WI) following the standard protocol.  Total RNA (500 ng) was mixed with 10 µl 10x labeling buffer, 4 µl Label IT reagent (containing Cy 3 or Cy 5 fluorescent tracers), and water to 86 µl

source_name: kidney,MCS


title: Heart_Sham_rep1

description:
DISSALMouse3Kv2.0_022
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray analyzes the expression of 1135 mouse miRNAs. The total RNA from each sample is labeled with Label IT® miRNA Labeling Kits, Version 2 (Mirus Bio, WI) following the standard protocol.  Total RNA (500 ng) was mixed with 10 µl 10x labeling buffer, 4 µl Label IT reagent (containing Cy 3 or Cy 5 fluorescent tracers), and water to 86 µl


title: Kidney_MCS_rep1

description:
DISSALMouse3Kv2.0_020
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray analyzes the expression of 1135 mouse miRNAs. The total RNA from each sample is labeled with Label IT® miRNA Labeling Kits, Version 2 (Mirus Bio, WI) following the standard protocol.  Total RNA (500 ng) was mixed with 10 µl 10x labeling buffer, 4 µl Label IT reagent (containing Cy 3 or Cy 5 fluorescent tracers), and water to 86 µl


title: flc2_2_F3_m1c

description: Agigas.count.table.csv

data_processing:
Color-space short sequencing reads in  format were mapped to Asian arowana cDNA reference sequences (GenBank: LGSG00000000.1) using Bowtie 1.
Mapped short sequencing reads were quantified as raw counts per transcript using custom perl scripts.
Genome_build: GenBank: LGSG00000000.1
Supplementary_files_format_and_content: csv/ gene expression profiles. A FASTA of the transcript sequences is available on the series record.

molecule: polyA RNA

organism: Arapaima gigas

source_name: brain

growth_protocol: The fish were sampled in a fish farm and they were in the reproductive period (animals with 4+ years old and 100-120 cm length total). Male A. gigas individuals were determined by the presence of intratesticular spermatozoa, and the female by the presence of primary oocytes in the ovaries.

extract_protocol:
Total RNA was isolated from gonads and brain tissue of six A. gigas individuals using the TRIzol Reagent (Applied Biosystems, USA) as per manufacturer’s protocol. Total RNA was treated for 10 min at 65 °C with RNAsecure reagent (Ambion, USA). To eliminate genomic DNA contamination, all RNA preparations were treated with RNase-free Turbo DNase (Ambion, USA) for 15 min at 37 °C. Total RNA was further purified using RNAeasy Mini RNA kit (Qiagen) as per manufacturer's protocol. For the creation of cDNA libraries, poly(A) mRNA was isolated by two consecutive purification cycles on oligo d(T) cellulose using a Micro-PolyA-Purist kit (Ambion, USA). RNA was quantified using NanoDrop® 2000 spectrophotometer (Thermo Scientific, USA) and the quality checked on an agarose gel (electrophoresis in 1.5% w/v) and Bioanalyzer 2100 (Agilent Inc., USA) using the RNA 6000 Nano Kit (Agilent Inc., USA). For quality control, two aliquots of RNA were taken per extraction, one was left at 37 °C for two hours, while the other was stored at 4 °C. Both aliquots were run on an Agilent RNA nano-chip (Agilent Inc., USA) and the resulting electropherograms inspected for signs of degradation. The samples of RNA total had an RNA Integrity Number (RIN) value between 8.0-8.5. Equal volumes of RNA from each sample of tissue were used for cDNA synthesis.
Approximately 500 ng of mRNA from each tissues sample was used to construct RNA-Seq libraries with the SOLiD™ Total RNA-Seq Kit for Whole Transcriptome Libraries (Applied Biosystems, USA) following the manufacturer’s instructions. Barcodes were used to identify each library individually. A total of 24 sequencing libraries were constructed. Each sample tissue of the gonads and brain (three male and three female) was sequenced individually as biological replicates. The libraries were deposited on six lanes of a slide and sequenced using a SOLiD 4 sequencer (Applied Biosystems, USA) to generate 50nt short sequencing read. Sequencing was performed in the “Laboratório de Ecofisiologia e Evolução do Instituto Nacional de Pesquisas da Amazônia”, Manaus, Brazil.

value: brain

value: 4+ years

tag: length


title: flc2_2_F3_m2c

description: Agigas.count.table.csv


title: flc2_2_F3_m2g

description: Agigas.count.table.csv

source_name: gonad

value: gonad


title: flc2_2_F3_f3g

description: Agigas.count.table.csv

value: female


title: flc2_2_F3_f3c

description: Agigas.count.table.csv


title: flc2_2_F3_f2g

description: Agigas.count.table.csv


title: Colon_MCS_rep2

description:
DISSALMouse3Kv2.0_017
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray analyzes the expression of 1135 mouse miRNAs. The total RNA from each sample is labeled with Label IT® miRNA Labeling Kits, Version 2 (Mirus Bio, WI) following the standard protocol.  Total RNA (500 ng) was mixed with 10 µl 10x labeling buffer, 4 µl Label IT reagent (containing Cy 3 or Cy 5 fluorescent tracers), and water to 86 µl

source_name: Colon, MCS

value: Colon


title: Kidney_Sham_rep1

description:
DISSALMouse3Kv2.0_018
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray analyzes the expression of 1135 mouse miRNAs. The total RNA from each sample is labeled with Label IT® miRNA Labeling Kits, Version 2 (Mirus Bio, WI) following the standard protocol.  Total RNA (500 ng) was mixed with 10 µl 10x labeling buffer, 4 µl Label IT reagent (containing Cy 3 or Cy 5 fluorescent tracers), and water to 86 µl


title: flc2_2_F3_f2c

description: Agigas.count.table.csv


title: flc2_2_F3_f1g

description: Agigas.count.table.csv


title: flc2_2_F3_m3g

description: Agigas.count.table.csv


title: flc2_2_F3_m3c

description: Agigas.count.table.csv


title: flc2_2_F3_f1c

description: Agigas.count.table.csv


title: Colon_Sham_rep2

description:
DISSALMouse3Kv2.0_015
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray analyzes the expression of 1135 mouse miRNAs. The total RNA from each sample is labeled with Label IT® miRNA Labeling Kits, Version 2 (Mirus Bio, WI) following the standard protocol.  Total RNA (500 ng) was mixed with 10 µl 10x labeling buffer, 4 µl Label IT reagent (containing Cy 3 or Cy 5 fluorescent tracers), and water to 86 µl

source_name: Colon, Sham


title: Colon_MCS_rep1

description:
DISSALMouse3Kv2.0_016
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray analyzes the expression of 1135 mouse miRNAs. The total RNA from each sample is labeled with Label IT® miRNA Labeling Kits, Version 2 (Mirus Bio, WI) following the standard protocol.  Total RNA (500 ng) was mixed with 10 µl 10x labeling buffer, 4 µl Label IT reagent (containing Cy 3 or Cy 5 fluorescent tracers), and water to 86 µl


title: flc2_2_F3_m1g

description: Agigas.count.table.csv


title: Colon_Sham_rep1

description:
DISSALMouse3Kv2.0_014
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray analyzes the expression of 1135 mouse miRNAs. The total RNA from each sample is labeled with Label IT® miRNA Labeling Kits, Version 2 (Mirus Bio, WI) following the standard protocol.  Total RNA (500 ng) was mixed with 10 µl 10x labeling buffer, 4 µl Label IT reagent (containing Cy 3 or Cy 5 fluorescent tracers), and water to 86 µl


title: flc1_2_F3_m3c

description: Agigas.count.table.csv


title: flc1_2_F3_m3g

description: Agigas.count.table.csv


title: flc1_2_F3_m2g

description: Agigas.count.table.csv


title: Brain_Sham_rep2

description:
DISSALMouse3Kv2.0_011
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray analyzes the expression of 1135 mouse miRNAs. The total RNA from each sample is labeled with Label IT® miRNA Labeling Kits, Version 2 (Mirus Bio, WI) following the standard protocol.  Total RNA (500 ng) was mixed with 10 µl 10x labeling buffer, 4 µl Label IT reagent (containing Cy 3 or Cy 5 fluorescent tracers), and water to 86 µl

source_name: Brain, Sham

value: Brain


title: Brain_MCS_rep2

description:
DISSALMouse3Kv2.0_013
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray analyzes the expression of 1135 mouse miRNAs. The total RNA from each sample is labeled with Label IT® miRNA Labeling Kits, Version 2 (Mirus Bio, WI) following the standard protocol.  Total RNA (500 ng) was mixed with 10 µl 10x labeling buffer, 4 µl Label IT reagent (containing Cy 3 or Cy 5 fluorescent tracers), and water to 86 µl

source_name: Brain, MCS


title: Case A1679-2 (fetal)

city: Guangzhou

first: Xiao-Peng

last: Tian

address: 651 Dong Feng RD East

department: Department of Medical Oncology

country: China

institute: Sun Yat-sen University Cancer Center

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

scan_protocol: Scanned in a InnoScan 710 Microarray Scanner (Innopsys,Carbonne, France).The microarray scanning images were digitized with GenPix Pro 6.0 program.

data_processing:
The raw signal data were extracted, computed the average and subtracted background.Then we normalized (Quantile normalization) using GPR analysis software (edited in-house).
The "400" values were calculated by our automatic software.  If the original normalized data is less than 400, it is deemed as no signal, and  assigned 400 value (the maximum background value), in order to eliminate nonspecific signal.

source_name: fetal thymus

label_protocol: 2.5 μg of total RNA of tissue was employed with 100 nmol/L of pCp-DY647 (Dharmacon, Lafayette, CO, USA) and 15 Units of T4 RNA ligase (Life Technologies, Carlsbad, CA, USA) in a total reaction volume of 20 µL at 16°C overnight

extract_protocol: Total RNA was extracted using an acid phenol/chloroform extraction method followed by ethanol precipitation.

value: <1 years

tag: Sex

value: fetal thymus


title: Brain_MCS_rep1

description:
DISSALMouse3Kv2.0_012
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray analyzes the expression of 1135 mouse miRNAs. The total RNA from each sample is labeled with Label IT® miRNA Labeling Kits, Version 2 (Mirus Bio, WI) following the standard protocol.  Total RNA (500 ng) was mixed with 10 µl 10x labeling buffer, 4 µl Label IT reagent (containing Cy 3 or Cy 5 fluorescent tracers), and water to 86 µl

value: MCS


title: Brain_Sham_rep1

description:
DISSALMouse3Kv2.0_010
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray analyzes the expression of 1135 mouse miRNAs. The total RNA from each sample is labeled with Label IT® miRNA Labeling Kits, Version 2 (Mirus Bio, WI) following the standard protocol.  Total RNA (500 ng) was mixed with 10 µl 10x labeling buffer, 4 µl Label IT reagent (containing Cy 3 or Cy 5 fluorescent tracers), and water to 86 µl


title: flc1_2_F3_m1g

description: Agigas.count.table.csv

value: male


title: flc1_2_F3_m2c

description: Agigas.count.table.csv


title: flc1_2_F3_m1c

description: Agigas.count.table.csv


title: flc1_2_F3_f3g

description: Agigas.count.table.csv


title: flc1_2_F3_f2g

description: Agigas.count.table.csv


title: flc1_2_F3_f3c

description: Agigas.count.table.csv


title: Bladder_MCS_rep1

description:
DISSALMouse3Kv2.0_008
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray analyzes the expression of 1135 mouse miRNAs. The total RNA from each sample is labeled with Label IT® miRNA Labeling Kits, Version 2 (Mirus Bio, WI) following the standard protocol.  Total RNA (500 ng) was mixed with 10 µl 10x labeling buffer, 4 µl Label IT reagent (containing Cy 3 or Cy 5 fluorescent tracers), and water to 86 µl

source_name: Bladder, MCS

value: Female

value: Bladder


title: Bladder_MCS_rep2

description:
DISSALMouse3Kv2.0_009
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray analyzes the expression of 1135 mouse miRNAs. The total RNA from each sample is labeled with Label IT® miRNA Labeling Kits, Version 2 (Mirus Bio, WI) following the standard protocol.  Total RNA (500 ng) was mixed with 10 µl 10x labeling buffer, 4 µl Label IT reagent (containing Cy 3 or Cy 5 fluorescent tracers), and water to 86 µl


title: leiomyoma C, Clariom D

city: Rostock

first: Carsten

last: Holzmann

address: Ernst-Heydemann-Str. 8

department: Institute of Medical Genetics

institute: University Rostock Medical Center

description:
transcriptome array data of a  morcellated leiomyoma specimen
7065-13C

hyb_protocol: Prior to hybridization samples were denatured at 95°C. The hybridization was carried out at 49°C (OncoScan) or 45°C (Clariom D) in the GeneChipR Hybridization Oven 645 (Affymetrix) over night. Staining and washing was done using a GeneChip Fluidics Station 450 (Affymetrix) following the manufacturer’s instructions.

scan_protocol: Arrays were scanned using the GeneChipR Scanner 3000.

data_processing: Clariom D probe level analysis with SST/RMA (signal space transformation/robust multichip average) and data visualization was done with TAC (Transcriptome Analysis Console 4.0; Applied Biosystems).

label: biotin

source_name: 50 year old woman, morcellated specimen of uterine fibroids after LASH

label_protocol: For OncoScan FFPE assay, labelling of 80 ng dsDNA was done following the manufacturer’s instructions (Affymetrix P/N 703175). For Clariom D assay, 45 ng whole RNA was used for  first strand cDNA synthesis is introducing by N6-‐ and Oligo-‐dT priming a T7 promoter sequence 5extended with an universal PCR primer site. To perform a preamplification (Pre-‐IVT Amplification) the primer site at the 5`ends of the first cDNA strand is countered by a second strand synthesis random primed (N6) with an adaptor attaching the reverse primer site to each end of the second strand fragments produced by Klenow polymerase. These templates were amplified exponentially for 6 cycles followed by a linear amplification step using the T7 promoter in an over night reaction (IVT, 14 h). Using 20 mg of each aRNA sample after purification as template in a reverse 3 transcription reaction a strand-‐identical single strand DNA was produced by adding random primers and dNTP`s. To enable an endpoint fragmentation reaction a certain fraction of dTTP is replaced by dUTP. After complete RNA removal (RNaseH) the enzymatic fragmentation is performed by uracil deglycosidase for removing uracil in combination with apurinic apyrimidinic endonuclease 1, which is breaking the free endonucleolytic phosphodiester bonds. Desoxynucleotidyl--‐transferase is adding Biotin--‐ 11--‐dXTP to the 3ends.

extract_protocol: Simultaneous extraction and purification of DNA and RNA from FFPE tissue samples using Covaris adaptive focused acoutics (AFATM) and truXTRACTM FFPE DNA and RNA kits: The emulsification of the paraffin was done applying 5 minutes focused acoustic waves of 75 watts to a 10 mm FFPE section using a Covaris M220 device (Woburn, Massachusetts, USA). A Proteinase K digestions was performed at 56° C for 15 minutes. The paraffin including the genomic DNA was sedimented at 16.000 g. For RNA isolation the supernatant was heated to 80° C to reverse the formaldehyde crosslink followed by a DNaseI digestion step and a spincolumn cleanup procedure. Accordingly the pellet was subjected to spincolumn cleanup of the genomic DNA after an additional Proteinase K digestion. Fluorometric quantification was performed with the QubitTM 2.0 fluorometer using the QubitTM dsDNA HS-‐ and RNA HS Assay Kit (Thermo Fisher Scientific).

treatment_protocol: Laparoscopic supracervical hysterectomy (LASH) due to multiple uterine fibroids. Further tumors were removed by laparotomy. For histologic examination tissues were fixed in paraformaldehyde (4% in PBS), and processed for paraffin embedding using standard techniques.

value: uterus

tag: histology

value: leiomyoma


title: leiomyoma D, Clariom D

description:
transcriptome array data of a  morcellated leiomyoma specimen
7065-13D


title: flc1_2_F3_f2c

description: Agigas.count.table.csv


title: leiomyosarcoma, Clariom D

description:
transcriptome array data of a  derivative leiomyosarcoma
12814-15

source_name: cystic adnexal mass of the same patient, removed by laparotomy 28 months after LASH

value: leiomyosarcoma


title: Lung_MCS_rep2

description:
DISSALMouse3Kv2.0_005
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray analyzes the expression of 1135 mouse miRNAs. The total RNA from each sample is labeled with Label IT® miRNA Labeling Kits, Version 2 (Mirus Bio, WI) following the standard protocol.  Total RNA (500 ng) was mixed with 10 µl 10x labeling buffer, 4 µl Label IT reagent (containing Cy 3 or Cy 5 fluorescent tracers), and water to 86 µl

source_name: Lung Tissue. MCS

value: Male

value: Lung


title: Bladder_Sham_rep1

description:
DISSALMouse3Kv2.0_006
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray analyzes the expression of 1135 mouse miRNAs. The total RNA from each sample is labeled with Label IT® miRNA Labeling Kits, Version 2 (Mirus Bio, WI) following the standard protocol.  Total RNA (500 ng) was mixed with 10 µl 10x labeling buffer, 4 µl Label IT reagent (containing Cy 3 or Cy 5 fluorescent tracers), and water to 86 µl

source_name: Bladder, Sham

value: Sham


title: Bladder_Sham_rep2

description:
DISSALMouse3Kv2.0_007
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray analyzes the expression of 1135 mouse miRNAs. The total RNA from each sample is labeled with Label IT® miRNA Labeling Kits, Version 2 (Mirus Bio, WI) following the standard protocol.  Total RNA (500 ng) was mixed with 10 µl 10x labeling buffer, 4 µl Label IT reagent (containing Cy 3 or Cy 5 fluorescent tracers), and water to 86 µl


title: Lung_Sham_rep3

description:
DISSALMouse3Kv2.0_004
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray analyzes the expression of 1135 mouse miRNAs. The total RNA from each sample is labeled with Label IT® miRNA Labeling Kits, Version 2 (Mirus Bio, WI) following the standard protocol.  Total RNA (500 ng) was mixed with 10 µl 10x labeling buffer, 4 µl Label IT reagent (containing Cy 3 or Cy 5 fluorescent tracers), and water to 86 µl

source_name: Lung Tissue, Sham


title: leiomyoma B, Clariom D

description:
transcriptome array data of a  morcellated leiomyoma specimen
7065-13B


title: flc1_2_F3_f1g

description: Agigas.count.table.csv

value: 4+ years


title: leiomyoma A, Clariom D

description:
transcriptome array data of a  morcellated leiomyoma specimen
7065-13 A2


title: flc1_2_F3_f1c

description: Agigas.count.table.csv

value: brain


title: Lung_MCS_rep1

description:
DISSALMouse3Kv2.0_001
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray analyzes the expression of 1135 mouse miRNAs. The total RNA from each sample is labeled with Label IT® miRNA Labeling Kits, Version 2 (Mirus Bio, WI) following the standard protocol.  Total RNA (500 ng) was mixed with 10 µl 10x labeling buffer, 4 µl Label IT reagent (containing Cy 3 or Cy 5 fluorescent tracers), and water to 86 µl

source_name: Lung Tissue, MCS


title: Lung_Sham_rep1

description:
DISSALMouse3Kv2.0_002
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray analyzes the expression of 1135 mouse miRNAs. The total RNA from each sample is labeled with Label IT® miRNA Labeling Kits, Version 2 (Mirus Bio, WI) following the standard protocol.  Total RNA (500 ng) was mixed with 10 µl 10x labeling buffer, 4 µl Label IT reagent (containing Cy 3 or Cy 5 fluorescent tracers), and water to 86 µl


title: Lung_Sham_rep2

description:
DISSALMouse3Kv2.0_003
For evaluating the expression of miRNAs, we used the 7th generation miRCURY LNATM microRNA Array (Exiqon), which contains 3100 capture probes covering human, mouse, and rat miRNAs.  In particular, this microarray analyzes the expression of 1135 mouse miRNAs. The total RNA from each sample is labeled with Label IT® miRNA Labeling Kits, Version 2 (Mirus Bio, WI) following the standard protocol.  Total RNA (500 ng) was mixed with 10 µl 10x labeling buffer, 4 µl Label IT reagent (containing Cy 3 or Cy 5 fluorescent tracers), and water to 86 µl


title: PNET_p53_Rb_rep3

status: Public on Apr 29 2018

city: London

first: Sebastian

last: Brandner

state: State...

address: Queen square house, UCL Institute of Neurology

department: Institute of Neurology

country: United Kingdom

institute: University College London

description: Sample name: PNET551

hyb_protocol: Pair-wise RNA samples labelled with Hy3 or Hy5 dye were hybridized to the miRCURY LNA microRNA Array 7 (Exiqon), which contains capture probes targeting all microRNAs for human, mouse or rat registered in the miRBASE 18.0. The hybridization was performed according to the miRCURY LNA™ microRNA Array Instruction manual using a Tecan HS4800 hybridization station (Tecan, Austria).

scan_protocol: Microarray slides were scanned using Agilent G2565BA Microarray Scanner System (Agilent Technologies, USA).

data_processing: Images were quantified using ImaGene 9 (Exiqon, Denmark). The quantified signals were background corrected (Normexp with offset value 10, see Ritchie et al. 2007) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm. The file normalized_data.txt contains the normalized log2 ratio (Hy3/Hy5) representing test/reference. The gal file "lot35016-35016_mmu-and-related-vira_from_mb200.gal" contains the miRNA IDs for each probe number.

source_name: AdCre-induced PNET, Rb/p53 background

label_protocol: MiRNAs from 600ng of total RNA were labelled with Hy3 or Hy5 fluorophores according to manufacturer’s protocol (miRCURY LNA microRNA Hi-Power Labelling kit, Exiqon) by Exiqon company

growth_protocol: The total RNA in this study is directly extracted from frozen tumour tissue. Tumours were directly dissected from fresh brain. Before RNA extraction, the samples were stored in -80°C.

extract_protocol: Total RNA used for microarray was extracted from frozen tumours using TRIzol method.

treatment_protocol: Combinations of the conditional konck-out  RbLoxP/LoxP, p53LoxP/LoxP,and PtenLoxP/LoxP,all in a ROSA26loxP/loxP background was achieved using adenovirus expressing Cre recombinase. The injection of adenovirus in relation to bregma was anterior 0mm; lateral 0.5mm and ventral 2.5mm. Injections were administered with a Hamilton syringe 1701RN and 26G needle.

value: PNET

tag: developmental stage

value: young adult mouse

tag: background strain

value: C57 BL/6 and FVB mixed background

tag: genotype

value: p53/Rb codeletion

source_name: Reference RNA

tag: sample type

value: a pool of RNA consisting of equal amounts of each individual sample in this study


title: Glioma_p53_Rb_rep2

description: Sample name: Glio1258

source_name: AdCre-induced glioma, Rb/p53 background

value: glioma


title: Glioma_p53_Rb_rep1

description: Sample name: Glio2670


title: PNET_p53_Rb_rep2

description: Sample name: PNET2893


title: slc6a2_JD1538_UB1

city: St Louis

first: Joseph

middle: D

last: Dougherty

state: Missouri

address: 4566 Scott Ave, box 8232

department: Genetics and Psychiatry

institute: Washington University

description: Total tissue RNA (unbound)

hyb_protocol: Standard Affymetrix protocol for mouse 430 2.0 platform

data_processing: Data were analyzed using the Bioconductor module within the statistical package R.  GCRMA was used to normalize within replicates, and to biotinylated spike in probes between conditions.  Fold change, Specificity Index (SI) and pSI (see PMID: 20308160) were calculated for all genes with expression above non-specific background, and >50 arbitrary fluorescent units, as described.  The threshold to identify genes expressed in the neurons above non-specific background was conservatively set at the mean plus 2 standard deviations of the fold change of negative control transcripts comparing the TRAP samples to hindbrain mRNA.  Genes with expression below this level may or may not be found in LC neurons.  To identify transcripts enriched in LC neurons compared to hindbrain RNA, we utilized the empirical Bayesian statistic with FDR correction within the Limma package. Hierarchical clustering was conducted in R utilizing the expression values from any genes with pSI <.01 in any cell type.

label: Biotin

source_name: unbound (total) RNA from JD1538 Slc6a2 line

label_protocol: Affymetrix two-cycle amplification kit

extract_protocol: Replicate pools of 5 mixed sex adult mice from each of the Slc6a2 lines were sacrificed and brains were removed and transferred to ice cold dissection buffer containing cycloheximide, and hindbrain, posterior to the pontine/hypothalamic junction was collected, discarding the cerebellum. TRAP was conducted as described (see PMID: 24810037).  Briefly, each pool was homogenized for 12 strokes in a glass teflon homogenizer on ice, in buffer (10 mM HEPES [pH 7.4], 150 mM KCl, 5 mM MgCl2, 0.5 mM dithiothreitol, 100 μg/ml cycloheximide, protease inhibitors, and recombinant RNase inhibitors).   Nuclei and debris were removed with centrifugation at 2000g for 10 min at 4C.  DHPC (Avanti, Alabastar, AL) and NP-40 (Ipgal-ca630, Sigma, St Louis, MO) were added to supernatant to final concentrations of 30mM and 1%, respectively.  After 5 min incubation of ice, supernatant was centrifuged for 15 minutes at 20,000g, and pellet was discarded.   Supernatant was mixed with protein G coated magnetic beads (Invitrogen/Life Technologies, Grand Island, NY), previously conjugated with a mix of two monoclonal anti-GFP antibodies,52 and incubated with rotation for 30 minutes at 4C.  Beads were washed three times with high salt wash buffer (10 mM HEPES [pH 7.4], 350 mM KCl, 5 mM MgCl2, 1% NP-40, 0.5 mM dithiothreitol, and 100 μg/ml cycloheximide) and RNA was purified from ribosomes using Trizol (Invitrogen), followed by DNAse treatment and further purification and concentration with Rneasy min-elute columns, all following manufacture’s protocol (Qiagen, Hilden, Germany).  RNA was also harvested in parallel from each unbound fraction of affinity purification as a measure of total hindbrain RNA. RNA concentration of all samples was measured with Nanodrop spectrophotometer and integrity was confirmed with PicoChips on the Agilent BioAnalyzer (RIN>8).

value: hindbrain, posterior to the pontine/hypothalamic junction; cerebellum removed

tag: rna type

value: unbound

value: both

value: adult (6-12 weeks)

tag: number of mice

tag: line


title: slc6a2_JD1537_IP1

description: RNA from immunoprecipitated ribsomes

scan_protocol: Standard Affymetrix protocol for mouse 430 2.0 platform

source_name: TRAP'd RNA from JD1537 Slc6a2 line

value: TRAP

tag: age


title: PNET_p53_Rb_rep1

description: Sample name: PNET2634


title: Glioma_p53_Pten_rep1

description: Sample name: Glio1565

source_name: AdCre-induced glioma, p53/Pten background

value: p53/Pten codeletion


title: Glioma_p53_Pten_rep3

description: Sample name: Glio2767


title: Glioma_p53_Rb_rep3

description: Sample name: Glio209


title: D26_anac057_D1

city: Daejeon

first: Ji-Hwan

last: Park

address: 125 Gwahak-ro, Yuseong-gu

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology (KRIBB)

description: Raw data: Matrix _raw_data_4

hyb_protocol: Hybridizations were carried out by combining each RNA sample with nCounter Reporter probes in hybridization buffer and nCounter Capture probes (for a total reaction volume of 15 μL) overnight at 65°C for 16-20 hrs. Excess probes were removed using two-step magnetic bead based purification on the nCounter Prep Station (Nanostring Technologies).

scan_protocol: Abundances of specific target molecules were quantified on the nCounter Digital Analyzer by counting the individual fluorescent barcodes and assessing the target molecules. For each assay, a high-density scan encompassing 280 fields of view was performed. The data was collected using the nCounter Digital Analyzer after taking images of the immobilized fluorescent reporters in the sample cartridge with a CCD camera.

data_processing: The count data of the samples were normalized by using the previously reported normalization method for Nanostring data (C. D. Brumbaugh et al., BMC bioinformatics, 2011), in which positive and negative correction and sample content normalization using housekeeping genes were performed sequentially.

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana leaf, 26 days

label_protocol:
nCounter capture and reporter probe mix from manufacturer
For 5 μL of each RNA sample, 8 μL of reporter probe and 2 μL of capture probe mix that was provided by NanoString Technologies for the custom codeset.

growth_protocol: Arabidopsis thaliana ecotype Columbia (Col) was the parent strain for all mutants used in this study. The T-DNA insertion lines of NAC genes were obtained from the SALK T-DNA insertion collection, SAIL collection, or GABI-KAT collection. Plants used for most of the experiments were grown in an environmentally controlled growth room under a 16-hr-light/8-hr-dark cycle (photon flux density 100 µmol m-2s-1) at 22°C.

extract_protocol: Total RNA was extracted using a eCube RNA Mini Kit for cultured cells (Philekorea Technology, Seoul, South Korea). RNA yield and purity were assessed using a DS 11 Spectrophotometer (Denovix Inc, DE, USA). According to Nanostring protocol, 100 ng of total RNA to be added to the sample preparation reaction in the availalbe 5 µL volumne. RNA quality was checked by Fragment Analyzer (Advanced Analytical Technologies, IA, USA).

tag: ecotype

value: Columbia (Col)

tag: Stage

value: 26 days

value: leaf


title: D26_anac086_D1

description: Raw data: Matrix _raw_data_4

tag: tissue


title: D26_anac084_D2

description: Raw data: Matrix _raw_data_4


title: D26_anac086_D2

description: Raw data: Matrix _raw_data_4


title: Glioma_p53_Pten_rep2

description: Sample name: Glio2458


title: D26_ntl9_D2

description: Raw data: Matrix _raw_data_4


title: D26_anac035_D1

description: Raw data: Matrix _raw_data_4


title: D26_anac101_C1

description: Raw data: Matrix _raw_data_4


title: D26_anac035_D2

description: Raw data: Matrix _raw_data_4


title: D26_anac101_C2

description: Raw data: Matrix _raw_data_4


title: D26_anac057_D2

description: Raw data: Matrix _raw_data_4


title: D26_anac084_D1

description: Raw data: Matrix _raw_data_4


title: D26_ntl9_D1

description: Raw data: Matrix _raw_data_4


title: D26_anac090_C2

description: Raw data: Matrix _raw_data_4


title: slc6a2_JD1537_UB1

description: Total tissue RNA (unbound)

source_name: unbound (total) RNA from JD1537 Slc6a2 line


title: D26_anac090_C1

description: Raw data: Matrix _raw_data_4


title: slc6a2_JD1538_IP1

description: RNA from immunoprecipitated ribsomes

source_name: TRAP'd RNA from JD1538 Slc6a2 line


title: D26_anac078_C2

description: Raw data: Matrix _raw_data_4


title: D26_anac081_C2

description: Raw data: Matrix _raw_data_4


title: D26_anac081_C1

description: Raw data: Matrix _raw_data_4


title: D26_anac078_C1

description: Raw data: Matrix _raw_data_4


title: D26_anac076_C1

description: Raw data: Matrix _raw_data_4


title: D26_anac076_C2

description: Raw data: Matrix _raw_data_4


title: D26_at3g12910_C2

description: Raw data: Matrix _raw_data_4


title: D26_at3g12910_C1

description: Raw data: Matrix _raw_data_4


title: D26_anac048_C1

description: Raw data: Matrix _raw_data_4


title: D26_anac048_C2

description: Raw data: Matrix _raw_data_4


title: D26_anac004_C2

description: Raw data: Matrix _raw_data_4


title: D26_anac104_B2

description: Raw data: Matrix _raw_data_4


title: D26_anac004_C1

description: Raw data: Matrix _raw_data_4


title: D26_anac056_B1

description: Raw data: Matrix _raw_data_4


title: D26_anac096_B2

description: Raw data: Matrix _raw_data_4


title: D26_anac102_B2

description: Raw data: Matrix _raw_data_4


title: D26_anac056_B2

description: Raw data: Matrix _raw_data_4


title: D26_anac102_B1

description: Raw data: Matrix _raw_data_4


title: D26_anac059_B2

description: Raw data: Matrix _raw_data_4


title: D26_anac059_B1

description: Raw data: Matrix _raw_data_4


title: D26_anac096_B1

description: Raw data: Matrix _raw_data_4


title: D26_anac046_B1

description: Raw data: Matrix _raw_data_4


title: D26_anac047_B2

description: Raw data: Matrix _raw_data_4


title: D26_anac052_B2

description: Raw data: Matrix _raw_data_4


title: D26_anac046_B2

description: Raw data: Matrix _raw_data_4


title: D26_anac047_B1

description: Raw data: Matrix _raw_data_4


title: D26_anac052_B1

description: Raw data: Matrix _raw_data_4


title: D26_anac045_B2

description: Raw data: Matrix _raw_data_4


title: D26_anac045_B1

description: Raw data: Matrix _raw_data_4


title: D26_anac042_B2

description: Raw data: Matrix _raw_data_4


title: D26_anac021_B2

description: Raw data: Matrix _raw_data_4


title: D26_anac028_B1

description: Raw data: Matrix _raw_data_4


title: D26_anac104_B1

description: Raw data: Matrix _raw_data_4


title: D26_anac021_B1

description: Raw data: Matrix _raw_data_4


title: D26_anac061_B1

description: Raw data: Matrix _raw_data_4


title: D26_anac061_B2

description: Raw data: Matrix _raw_data_4


title: D26_anac018_B1

description: Raw data: Matrix _raw_data_4


title: D26_anac014_B1

description: Raw data: Matrix _raw_data_4


title: D26_anac007_B2

description: Raw data: Matrix _raw_data_4


title: D26_anac042_B1

description: Raw data: Matrix _raw_data_4


title: D26_anac010_B1

description: Raw data: Matrix _raw_data_4


title: D26_anac007_B1

description: Raw data: Matrix _raw_data_4


title: D26_anac028_B2

description: Raw data: Matrix _raw_data_4


title: D26_anac100_A1

description: Raw data: Matrix _raw_data_4


title: D26_anac100_A2

description: Raw data: Matrix _raw_data_4


title: D26_anac001_B2

description: Raw data: Matrix _raw_data_4


title: D26_anac087_A2

description: Raw data: Matrix _raw_data_4


title: D26_anac087_A1

description: Raw data: Matrix _raw_data_4


title: D26_anac001_B1

description: Raw data: Matrix _raw_data_4


title: D26_anac082_A1

description: Raw data: Matrix _raw_data_4


title: D26_anac018_B2

description: Raw data: Matrix _raw_data_4


title: D26_anac083_A2

description: Raw data: Matrix _raw_data_4


title: D26_anac083_A1

description: Raw data: Matrix _raw_data_4


title: D26_anac014_B2

description: Raw data: Matrix _raw_data_4


title: D26_anac082_A2

description: Raw data: Matrix _raw_data_4


title: D26_anac055_A2

description: Raw data: Matrix _raw_data_4


title: D26_anac079_A1

description: Raw data: Matrix _raw_data_4


title: D26_anac072_A1

description: Raw data: Matrix _raw_data_4


title: D26_anac079_A2

description: Raw data: Matrix _raw_data_4


title: D26_anac053_A2

description: Raw data: Matrix _raw_data_4


title: D26_anac010_B2

description: Raw data: Matrix _raw_data_4


title: D26_anac050_A2

description: Raw data: Matrix _raw_data_4


title: D26_anac074_A1

description: Raw data: Matrix _raw_data_4


title: D26_anac074_A2

description: Raw data: Matrix _raw_data_4


title: D26_anac072_A2

description: Raw data: Matrix _raw_data_4


title: D26_anac055_A1

description: Raw data: Matrix _raw_data_4


title: D26_anac053_A1

description: Raw data: Matrix _raw_data_4


title: D26_anac050_A1

description: Raw data: Matrix _raw_data_4


title: D26_anac041_A1

description: Raw data: Matrix _raw_data_4


title: D26_anac041_A2

description: Raw data: Matrix _raw_data_4


title: D26_anac019_A1

description: Raw data: Matrix _raw_data_4


title: D26_anac032_A2

description: Raw data: Matrix _raw_data_4


title: D26_anac029_A1

description: Raw data: Matrix _raw_data_4


title: D26_anac016_A1

description: Raw data: Matrix _raw_data_4


title: D26_anac016_A2

description: Raw data: Matrix _raw_data_4


title: D26_anac019_A2

description: Raw data: Matrix _raw_data_4


title: D26_anac017_A2

description: Raw data: Matrix _raw_data_4


title: D26_anac017_A1

description: Raw data: Matrix _raw_data_4


title: D26_anac092_B2

description: Raw data: Matrix _raw_data_4


title: D26_anac092_A2

description: Raw data: Matrix _raw_data_4


title: D26_Col_D2

description: Raw data: Matrix _raw_data_4

value: Wild type


title: D26_anac092_A1

description: Raw data: Matrix _raw_data_4


title: D26_Col_B2

description: Raw data: Matrix _raw_data_4


title: D26_Col_B1

description: Raw data: Matrix _raw_data_4


title: D26_Col_C2

description: Raw data: Matrix _raw_data_4


title: D26_Col_C1

description: Raw data: Matrix _raw_data_4


title: D22_anac086_D1

description: Raw data: Matrix _raw_data_3

source_name: Arabidopsis thaliana leaf, 22 days

value: 22 days


title: D26_anac032_A1

description: Raw data: Matrix _raw_data_4


title: D26_Col_A2

description: Raw data: Matrix _raw_data_4


title: D22_anac084_D1

description: Raw data: Matrix _raw_data_3


title: D26_Col_D1

description: Raw data: Matrix _raw_data_4


title: D22_anac084_D2

description: Raw data: Matrix _raw_data_3


title: D26_anac029_A2

description: Raw data: Matrix _raw_data_4


title: D22_anac057_D1

description: Raw data: Matrix _raw_data_3


title: D26_anac002_A1

description: Raw data: Matrix _raw_data_4


title: D26_anac002_A2

description: Raw data: Matrix _raw_data_4


title: D26_anac092_B1

description: Raw data: Matrix _raw_data_4


title: D22_ntl9_D2

description: Raw data: Matrix _raw_data_3


title: D22_anac101_C2

description: Raw data: Matrix _raw_data_3


title: D22_anac035_D1

description: Raw data: Matrix _raw_data_3


title: D22_anac101_C1

description: Raw data: Matrix _raw_data_3


title: D22_ntl9_D1

description: Raw data: Matrix _raw_data_3


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description: Raw data: Matrix _raw_data_3


title: D22_anac090_C1

description: Raw data: Matrix _raw_data_3


title: D22_anac086_D2

description: Raw data: Matrix _raw_data_3


title: D26_Col_A1

description: Raw data: Matrix _raw_data_4


title: D22_anac078_C2

description: Raw data: Matrix _raw_data_3


title: D22_anac078_C1

description: Raw data: Matrix _raw_data_3


title: D22_anac076_C2

description: Raw data: Matrix _raw_data_3


title: D22_anac076_C1

description: Raw data: Matrix _raw_data_3


title: D22_at3g12910_C1

description: Raw data: Matrix _raw_data_3


title: D22_at3g12910_C2

description: Raw data: Matrix _raw_data_3


title: D22_anac057_D2

description: Raw data: Matrix _raw_data_3


title: D22_anac048_C2

description: Raw data: Matrix _raw_data_3


title: D22_anac035_D2

description: Raw data: Matrix _raw_data_3


title: D22_anac004_C1

description: Raw data: Matrix _raw_data_3


title: D22_anac102_B2

description: Raw data: Matrix _raw_data_3


title: D22_anac004_C2

description: Raw data: Matrix _raw_data_3


title: D22_anac104_B1

description: Raw data: Matrix _raw_data_3


title: D22_anac102_B1

description: Raw data: Matrix _raw_data_3


title: D22_anac096_B2

description: Raw data: Matrix _raw_data_3


title: D22_anac081_C1

description: Raw data: Matrix _raw_data_3


title: D22_anac081_C2

description: Raw data: Matrix _raw_data_3


title: D22_anac096_B1

description: Raw data: Matrix _raw_data_3


title: D22_anac059_B2

description: Raw data: Matrix _raw_data_3


title: D22_anac056_B2

description: Raw data: Matrix _raw_data_3


title: D22_anac061_B2

description: Raw data: Matrix _raw_data_3


title: D22_anac052_B2

description: Raw data: Matrix _raw_data_3


title: D22_anac047_B1

description: Raw data: Matrix _raw_data_3


title: D22_anac104_B2

description: Raw data: Matrix _raw_data_3


title: D22_anac047_B2

description: Raw data: Matrix _raw_data_3


title: D22_anac046_B1

description: Raw data: Matrix _raw_data_3


title: D22_anac045_B1

description: Raw data: Matrix _raw_data_3


title: D22_anac028_B2

description: Raw data: Matrix _raw_data_3


title: D22_anac042_B2

description: Raw data: Matrix _raw_data_3


title: D22_anac045_B2

description: Raw data: Matrix _raw_data_3


title: D22_anac021_B1

description: Raw data: Matrix _raw_data_3


title: D22_anac021_B2

description: Raw data: Matrix _raw_data_3


title: D22_anac061_B1

description: Raw data: Matrix _raw_data_3


title: D22_anac018_B2

description: Raw data: Matrix _raw_data_3


title: D22_anac014_B2

description: Raw data: Matrix _raw_data_3


title: D22_anac056_B1

description: Raw data: Matrix _raw_data_3


title: D22_anac018_B1

description: Raw data: Matrix _raw_data_3


title: D22_anac048_C1

description: Raw data: Matrix _raw_data_3


title: D22_anac052_B1

description: Raw data: Matrix _raw_data_3


title: D22_anac059_B1

description: Raw data: Matrix _raw_data_3


title: D22_anac010_B2

description: Raw data: Matrix _raw_data_3


title: D22_anac010_B1

description: Raw data: Matrix _raw_data_3


title: D22_anac007_B1

description: Raw data: Matrix _raw_data_3


title: D22_anac001_B1

description: Raw data: Matrix _raw_data_3


title: D22_anac001_B2

description: Raw data: Matrix _raw_data_3


title: D22_anac100_A2

description: Raw data: Matrix _raw_data_3


title: D22_anac007_B2

description: Raw data: Matrix _raw_data_3


title: D22_anac046_B2

description: Raw data: Matrix _raw_data_3


title: D22_anac042_B1

description: Raw data: Matrix _raw_data_3


title: D22_anac028_B1

description: Raw data: Matrix _raw_data_3


title: D22_anac087_A1

description: Raw data: Matrix _raw_data_3


title: D22_anac087_A2

description: Raw data: Matrix _raw_data_3


title: D22_anac082_A2

description: Raw data: Matrix _raw_data_3


title: D22_anac014_B1

description: Raw data: Matrix _raw_data_3


title: D22_anac083_A2

description: Raw data: Matrix _raw_data_3


title: D22_anac083_A1

description: Raw data: Matrix _raw_data_3


title: D22_anac074_A2

description: Raw data: Matrix _raw_data_3


title: D22_anac079_A1

description: Raw data: Matrix _raw_data_3


title: D22_anac074_A1

description: Raw data: Matrix _raw_data_3


title: D22_anac082_A1

description: Raw data: Matrix _raw_data_3


title: D22_anac079_A2

description: Raw data: Matrix _raw_data_3


title: D22_anac072_A2

description: Raw data: Matrix _raw_data_3


title: D22_anac055_A2

description: Raw data: Matrix _raw_data_3


title: D22_anac053_A1

description: Raw data: Matrix _raw_data_3


title: D22_anac072_A1

description: Raw data: Matrix _raw_data_3


title: D22_anac053_A2

description: Raw data: Matrix _raw_data_3


title: D22_anac100_A1

description: Raw data: Matrix _raw_data_3


title: D22_anac055_A1

description: Raw data: Matrix _raw_data_3


title: D22_anac050_A1

description: Raw data: Matrix _raw_data_3


title: D22_anac050_A2

description: Raw data: Matrix _raw_data_3


title: D22_anac041_A1

description: Raw data: Matrix _raw_data_3


title: D22_anac032_A2

description: Raw data: Matrix _raw_data_3


title: D22_anac029_A1

description: Raw data: Matrix _raw_data_3


title: D22_anac041_A2

description: Raw data: Matrix _raw_data_3


title: D22_anac019_A2

description: Raw data: Matrix _raw_data_3


title: D22_anac019_A1

description: Raw data: Matrix _raw_data_3


title: D22_anac017_A1

description: Raw data: Matrix _raw_data_3


title: D22_anac017_A2

description: Raw data: Matrix _raw_data_3


title: D22_anac016_A2

description: Raw data: Matrix _raw_data_3


title: D22_anac016_A1

description: Raw data: Matrix _raw_data_3


title: D22_anac092_B1

description: Raw data: Matrix _raw_data_3


title: D22_anac092_B2

description: Raw data: Matrix _raw_data_3


title: D22_anac092_A2

description: Raw data: Matrix _raw_data_3


title: D22_anac092_A1

description: Raw data: Matrix _raw_data_3


title: D22_anac002_A1

description: Raw data: Matrix _raw_data_3


title: D22_anac032_A1

description: Raw data: Matrix _raw_data_3


title: D22_Col_D2

description: Raw data: Matrix _raw_data_3


title: D22_Col_D1

description: Raw data: Matrix _raw_data_3


title: D22_Col_B1

description: Raw data: Matrix _raw_data_3


title: D22_Col_A2

description: Raw data: Matrix _raw_data_3


title: D22_Col_C1

description: Raw data: Matrix _raw_data_3


title: D22_Col_C2

description: Raw data: Matrix _raw_data_3


title: D22_anac029_A2

description: Raw data: Matrix _raw_data_3


title: D18_anac086_D1

description: Raw data: Matrix _raw_data_2

source_name: Arabidopsis thaliana leaf, 18 days

value: 18 days


title: D18_anac086_D2

description: Raw data: Matrix _raw_data_2


title: D18_anac084_D1

description: Raw data: Matrix _raw_data_2


title: D22_Col_A1

description: Raw data: Matrix _raw_data_3


title: D22_Col_B2

description: Raw data: Matrix _raw_data_3


title: D18_anac084_D2

description: Raw data: Matrix _raw_data_2


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description: Raw data: Matrix _raw_data_2


title: D18_anac057_D1

description: Raw data: Matrix _raw_data_2


title: D18_anac035_D2

description: Raw data: Matrix _raw_data_2


title: D22_anac002_A2

description: Raw data: Matrix _raw_data_3


title: D18_anac035_D1

description: Raw data: Matrix _raw_data_2


title: D18_ntl9_D1

description: Raw data: Matrix _raw_data_2


title: D18_ntl9_D2

description: Raw data: Matrix _raw_data_2


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description: Raw data: Matrix _raw_data_2


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description: Raw data: Matrix _raw_data_2


title: D18_anac101_C1

description: Raw data: Matrix _raw_data_2


title: D18_anac090_C1

description: Raw data: Matrix _raw_data_2


title: D18_anac078_C1

description: Raw data: Matrix _raw_data_2


title: D18_anac081_C1

description: Raw data: Matrix _raw_data_2


title: D18_anac081_C2

description: Raw data: Matrix _raw_data_2


title: D18_at3g12910_C2

description: Raw data: Matrix _raw_data_2


title: D18_anac076_C2

description: Raw data: Matrix _raw_data_2


title: D18_anac076_C1

description: Raw data: Matrix _raw_data_2


title: D18_anac078_C2

description: Raw data: Matrix _raw_data_2


title: D18_anac048_C2

description: Raw data: Matrix _raw_data_2


title: D18_at3g12910_C1

description: Raw data: Matrix _raw_data_2


title: D18_anac004_C1

description: Raw data: Matrix _raw_data_2


title: D18_anac048_C1

description: Raw data: Matrix _raw_data_2


title: D18_anac004_C2

description: Raw data: Matrix _raw_data_2


title: D18_anac104_B1

description: Raw data: Matrix _raw_data_2


title: D18_anac104_B2

description: Raw data: Matrix _raw_data_2


title: D18_anac102_B2

description: Raw data: Matrix _raw_data_2


title: D18_anac059_B2

description: Raw data: Matrix _raw_data_2


title: D18_anac061_B2

description: Raw data: Matrix _raw_data_2


title: D18_anac056_B2

description: Raw data: Matrix _raw_data_2


title: D18_anac061_B1

description: Raw data: Matrix _raw_data_2


title: D18_anac052_B2

description: Raw data: Matrix _raw_data_2


title: D18_anac056_B1

description: Raw data: Matrix _raw_data_2


title: D18_anac096_B1

description: Raw data: Matrix _raw_data_2


title: D18_anac059_B1

description: Raw data: Matrix _raw_data_2


title: D18_anac047_B2

description: Raw data: Matrix _raw_data_2


title: D18_anac047_B1

description: Raw data: Matrix _raw_data_2


title: D18_anac052_B1

description: Raw data: Matrix _raw_data_2


title: D18_anac102_B1

description: Raw data: Matrix _raw_data_2


title: D18_anac046_B2

description: Raw data: Matrix _raw_data_2


title: D18_anac045_B1

description: Raw data: Matrix _raw_data_2


title: D18_anac045_B2

description: Raw data: Matrix _raw_data_2


title: D18_anac042_B1

description: Raw data: Matrix _raw_data_2


title: D18_anac042_B2

description: Raw data: Matrix _raw_data_2


title: D18_anac028_B2

description: Raw data: Matrix _raw_data_2


title: D18_anac021_B2

description: Raw data: Matrix _raw_data_2


title: D18_anac046_B1

description: Raw data: Matrix _raw_data_2


title: D18_anac096_B2

description: Raw data: Matrix _raw_data_2


title: D18_anac028_B1

description: Raw data: Matrix _raw_data_2


title: D18_anac014_B2

description: Raw data: Matrix _raw_data_2


title: D18_anac021_B1

description: Raw data: Matrix _raw_data_2


title: D18_anac014_B1

description: Raw data: Matrix _raw_data_2


title: D18_anac018_B2

description: Raw data: Matrix _raw_data_2


title: D18_anac018_B1

description: Raw data: Matrix _raw_data_2


title: D18_anac010_B2

description: Raw data: Matrix _raw_data_2


title: D18_anac010_B1

description: Raw data: Matrix _raw_data_2


title: D18_anac001_B2

description: Raw data: Matrix _raw_data_2


title: D18_anac007_B1

description: Raw data: Matrix _raw_data_2


title: D18_anac007_B2

description: Raw data: Matrix _raw_data_2


title: D18_anac100_A1

description: Raw data: Matrix _raw_data_2


title: D18_anac087_A2

description: Raw data: Matrix _raw_data_2


title: D18_anac100_A2

description: Raw data: Matrix _raw_data_2


title: D18_anac001_B1

description: Raw data: Matrix _raw_data_2


title: D18_anac083_A2

description: Raw data: Matrix _raw_data_2


title: D18_anac087_A1

description: Raw data: Matrix _raw_data_2


title: D18_anac083_A1

description: Raw data: Matrix _raw_data_2


title: D18_anac079_A2

description: Raw data: Matrix _raw_data_2


title: D18_anac082_A1

description: Raw data: Matrix _raw_data_2


title: D18_anac082_A2

description: Raw data: Matrix _raw_data_2


title: D18_anac079_A1

description: Raw data: Matrix _raw_data_2


title: D18_anac072_A1

description: Raw data: Matrix _raw_data_2


title: D18_anac055_A2

description: Raw data: Matrix _raw_data_2


title: D18_anac074_A2

description: Raw data: Matrix _raw_data_2


title: D18_anac072_A2

description: Raw data: Matrix _raw_data_2


title: D18_anac074_A1

description: Raw data: Matrix _raw_data_2


title: D18_anac050_A1

description: Raw data: Matrix _raw_data_2


title: D18_anac053_A1

description: Raw data: Matrix _raw_data_2


title: D18_anac053_A2

description: Raw data: Matrix _raw_data_2


title: D18_anac041_A2

description: Raw data: Matrix _raw_data_2


title: D18_anac041_A1

description: Raw data: Matrix _raw_data_2


title: D18_anac029_A2

description: Raw data: Matrix _raw_data_2


title: D18_anac050_A2

description: Raw data: Matrix _raw_data_2


title: D18_anac029_A1

description: Raw data: Matrix _raw_data_2


title: D18_anac032_A2

description: Raw data: Matrix _raw_data_2


title: D18_anac032_A1

description: Raw data: Matrix _raw_data_2


title: D18_anac019_A2

description: Raw data: Matrix _raw_data_2


title: D18_anac019_A1

description: Raw data: Matrix _raw_data_2


title: D18_anac017_A2

description: Raw data: Matrix _raw_data_2


title: D18_anac017_A1

description: Raw data: Matrix _raw_data_2


title: D18_anac016_A2

description: Raw data: Matrix _raw_data_2


title: D18_anac002_A1

description: Raw data: Matrix _raw_data_2


title: D18_anac092_B1

description: Raw data: Matrix _raw_data_2


title: D18_anac055_A1

description: Raw data: Matrix _raw_data_2


title: D18_anac016_A1

description: Raw data: Matrix _raw_data_2


title: D18_Col_D2

description: Raw data: Matrix _raw_data_2


title: D18_anac002_A2

description: Raw data: Matrix _raw_data_2


title: D18_anac092_B2

description: Raw data: Matrix _raw_data_2


title: D18_anac092_A2

description: Raw data: Matrix _raw_data_2


title: D18_anac092_A1

description: Raw data: Matrix _raw_data_2


title: D18_Col_D1

description: Raw data: Matrix _raw_data_2


title: D18_Col_C1

description: Raw data: Matrix _raw_data_2


title: D18_Col_B1

description: Raw data: Matrix _raw_data_2


title: D18_Col_B2

description: Raw data: Matrix _raw_data_2


title: D18_Col_C2

description: Raw data: Matrix _raw_data_2


title: D18_Col_A2

description: Raw data: Matrix _raw_data_2


title: D14_anac086_D2

description: Raw data: Matrix _raw_data_1

source_name: Arabidopsis thaliana leaf, 14 days

value: 14 days


title: D14_anac086_D1

description: Raw data: Matrix _raw_data_1


title: D14_anac084_D1

description: Raw data: Matrix _raw_data_1


title: D14_anac084_D2

description: Raw data: Matrix _raw_data_1


title: D14_anac057_D1

description: Raw data: Matrix _raw_data_1


title: D18_Col_A1

description: Raw data: Matrix _raw_data_2


title: D14_anac035_D1

description: Raw data: Matrix _raw_data_1


title: D14_anac057_D2

description: Raw data: Matrix _raw_data_1


title: D14_ntl9_D1

description: Raw data: Matrix _raw_data_1


title: D14_anac035_D2

description: Raw data: Matrix _raw_data_1


title: D14_ntl9_D2

description: Raw data: Matrix _raw_data_1


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description: Raw data: Matrix _raw_data_1


title: D14_anac101_C1

description: Raw data: Matrix _raw_data_1


title: D14_anac090_C1

description: Raw data: Matrix _raw_data_1


title: D14_anac090_C2

description: Raw data: Matrix _raw_data_1


title: D14_anac081_C2

description: Raw data: Matrix _raw_data_1


title: D14_anac081_C1

description: Raw data: Matrix _raw_data_1


title: D14_anac078_C2

description: Raw data: Matrix _raw_data_1


title: D14_anac078_C1

description: Raw data: Matrix _raw_data_1


title: D14_anac076_C2

description: Raw data: Matrix _raw_data_1


title: D14_at3g12910_C2

description: Raw data: Matrix _raw_data_1


title: D14_anac076_C1

description: Raw data: Matrix _raw_data_1


title: D14_at3g12910_C1

description: Raw data: Matrix _raw_data_1


title: D14_anac004_C2

description: Raw data: Matrix _raw_data_1


title: D14_anac048_C1

description: Raw data: Matrix _raw_data_1


title: D14_anac102_B2

description: Raw data: Matrix _raw_data_1


title: D14_anac104_B2

description: Raw data: Matrix _raw_data_1


title: D14_anac048_C2

description: Raw data: Matrix _raw_data_1


title: D14_anac004_C1

description: Raw data: Matrix _raw_data_1


title: D14_anac102_B1

description: Raw data: Matrix _raw_data_1


title: D14_anac061_B2

description: Raw data: Matrix _raw_data_1


title: D14_anac061_B1

description: Raw data: Matrix _raw_data_1


title: D14_anac096_B2

description: Raw data: Matrix _raw_data_1


title: D14_anac059_B1

description: Raw data: Matrix _raw_data_1


title: D14_anac047_B1

description: Raw data: Matrix _raw_data_1


title: D14_anac052_B2

description: Raw data: Matrix _raw_data_1


title: D14_anac047_B2

description: Raw data: Matrix _raw_data_1


title: D14_anac059_B2

description: Raw data: Matrix _raw_data_1


title: D14_anac096_B1

description: Raw data: Matrix _raw_data_1


title: D14_anac046_B2

description: Raw data: Matrix _raw_data_1


title: D14_anac056_B2

description: Raw data: Matrix _raw_data_1


title: D14_anac045_B2

description: Raw data: Matrix _raw_data_1


title: D14_anac056_B1

description: Raw data: Matrix _raw_data_1


title: D14_anac045_B1

description: Raw data: Matrix _raw_data_1


title: D14_anac046_B1

description: Raw data: Matrix _raw_data_1


title: D14_anac104_B1

description: Raw data: Matrix _raw_data_1


title: D14_anac042_B2

description: Raw data: Matrix _raw_data_1


title: D14_anac028_B2

description: Raw data: Matrix _raw_data_1


title: D14_anac021_B2

description: Raw data: Matrix _raw_data_1


title: D14_anac042_B1

description: Raw data: Matrix _raw_data_1


title: D14_anac021_B1

description: Raw data: Matrix _raw_data_1


title: D14_anac018_B2

description: Raw data: Matrix _raw_data_1


title: D14_anac018_B1

description: Raw data: Matrix _raw_data_1


title: D14_anac010_B2

description: Raw data: Matrix _raw_data_1


title: D14_anac010_B1

description: Raw data: Matrix _raw_data_1


title: D14_anac052_B1

description: Raw data: Matrix _raw_data_1


title: D14_anac014_B1

description: Raw data: Matrix _raw_data_1


title: D14_anac007_B1

description: Raw data: Matrix _raw_data_1


title: D14_anac007_B2

description: Raw data: Matrix _raw_data_1


title: D14_anac001_B1

description: Raw data: Matrix _raw_data_1


title: D14_anac001_B2

description: Raw data: Matrix _raw_data_1


title: D14_anac100_A1

description: Raw data: Matrix _raw_data_1


title: D14_anac100_A2

description: Raw data: Matrix _raw_data_1


title: D14_anac087_A2

description: Raw data: Matrix _raw_data_1


title: D14_anac087_A1

description: Raw data: Matrix _raw_data_1


title: D14_anac083_A1

description: Raw data: Matrix _raw_data_1


title: D14_anac028_B1

description: Raw data: Matrix _raw_data_1


title: D14_anac082_A2

description: Raw data: Matrix _raw_data_1


title: D14_anac083_A2

description: Raw data: Matrix _raw_data_1


title: D14_anac072_A1

description: Raw data: Matrix _raw_data_1


title: D14_anac079_A2

description: Raw data: Matrix _raw_data_1


title: D14_anac082_A1

description: Raw data: Matrix _raw_data_1


title: D14_anac079_A1

description: Raw data: Matrix _raw_data_1


title: D14_anac014_B2

description: Raw data: Matrix _raw_data_1


title: D14_anac074_A1

description: Raw data: Matrix _raw_data_1


title: D14_anac055_A1

description: Raw data: Matrix _raw_data_1


title: D14_anac072_A2

description: Raw data: Matrix _raw_data_1


title: D14_anac074_A2

description: Raw data: Matrix _raw_data_1


title: D14_anac050_A2

description: Raw data: Matrix _raw_data_1


title: D14_anac053_A2

description: Raw data: Matrix _raw_data_1


title: D14_anac041_A2

description: Raw data: Matrix _raw_data_1


title: D14_anac053_A1

description: Raw data: Matrix _raw_data_1


title: D14_anac050_A1

description: Raw data: Matrix _raw_data_1


title: D14_anac032_A2

description: Raw data: Matrix _raw_data_1


title: D14_anac041_A1

description: Raw data: Matrix _raw_data_1


title: D14_anac032_A1

description: Raw data: Matrix _raw_data_1


title: D14_anac029_A2

description: Raw data: Matrix _raw_data_1


title: D14_anac019_A1

description: Raw data: Matrix _raw_data_1


title: D14_anac029_A1

description: Raw data: Matrix _raw_data_1


title: D14_anac019_A2

description: Raw data: Matrix _raw_data_1


title: D14_anac055_A2

description: Raw data: Matrix _raw_data_1


title: D14_anac017_A2

description: Raw data: Matrix _raw_data_1


title: D14_anac002_A2

description: Raw data: Matrix _raw_data_1


title: D14_anac002_A1

description: Raw data: Matrix _raw_data_1


title: D14_anac092_A2

description: Raw data: Matrix _raw_data_1


title: D14_Col_D2

description: Raw data: Matrix _raw_data_1


title: D14_Col_D1

description: Raw data: Matrix _raw_data_1


title: 12.2B

city: Boston

first: Sowmya

last: Iyer

state: MA

department: Pathology

institute: Massachusetts General Hospital

data_processing:
Demultiplexed reads were aligned using STAR(Dobin et al., 2013) to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCounts(Liao Y, Smyth GK and Shi W 2014).
Genome_build: GRCz10
Supplementary_files_format_and_content: count matrix provided as supplementary file

organism: Danio rerio

source_name: Leukemia cells

extract_protocol:
Leukemia cell pellets were mixed 350ul of QIAGEN RLT buffer containing 1% 2-mercaptoethanol, followed by RNA isolation using the RNAeasy Mini kit (QIAGEN). RNA samples were prepped and sequenced on the Illumina HiSeq 2000 platform as previously described in Tang et al. (PMID 28878000).
RNA from bulk tumors were reverse-transcribed and sequenced on the Illumina HiSeq 2000 platform.

tag: replicate number

tag: self-renewal capacity

value: low

tag: cell type

value: blood


title: 12.2A


title: D14_anac016_A2

description: Raw data: Matrix _raw_data_1


title: 10.2A


title: D14_anac017_A1

description: Raw data: Matrix _raw_data_1


title: 10.2B


title: 9.2B


title: 9.2A


title: D14_Col_C2

description: Raw data: Matrix _raw_data_1


title: 7.2.1B

value: high


title: D14_Col_C1

description: Raw data: Matrix _raw_data_1


title: D14_anac016_A1

description: Raw data: Matrix _raw_data_1


title: 7.2.1A


title: D14_Col_B2

description: Raw data: Matrix _raw_data_1


title: 15.2A


title: 15.2B


title: D14_anac092_B1

description: Raw data: Matrix _raw_data_1


title: D14_anac092_B2

description: Raw data: Matrix _raw_data_1


title: 2.1B


title: 2.1A


title: D14_anac092_A1

description: Raw data: Matrix _raw_data_1


title: 8.3B


title: 8.3A


title: D14_Col_A3

description: Raw data: Matrix _raw_data_1


title: D14_Col_A2

description: Raw data: Matrix _raw_data_1


title: 4.3.1B


title: 13.1.1B


title: 14.1.1.1


title: 4.3.1A


title: D14_Col_A1

description: Raw data: Matrix _raw_data_1


title: 13.1.1A


title: 8.4.1.1.1


title: 6555c3

status: Public on Apr 28 2018

city: New York

first: Jinyang

last: Li

state: New York

address: 1230 York Ave

institute: The Rockefeller University

library_source: genomic

data_processing:
Regions of accessible chromatin were identified using the Kundaje Lab's ATAC-seq pipeline (https://github.com/kundajelab/atac_dnase_pipelines)
Reads were counted for each region for each sample using featureCounts
The resulting count table was analyzed for regions with differential accessibility between groups of samples using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: text file including raw peak counts of each sample

molecule: genomic DNA

source_name: sorted T cell high tumor cells

growth_protocol: T cell low or high pancreatic tumor cells were subcutaneously implanted into C57BL/6 mice. Sorted tumor cell samples were prepared from tumors 3 weeks following implantation.

extract_protocol:
no extraction of DNA before the start of library construction protocol
ATAC-seq samples were prepared by sorting 50,000 tumor cells from subcutaneously implanted tumors derived from each tumor cell clones. The libraries were prepared as previously published (Pauken et al., Epigenetic stability of exhausted T cells limits durability of reinvigoration by PD-1 blockade. Science 354, 1160–1165.).

treatment_protocol: no treatment administrated

tag: strain

value: sorted tumor cells

tag: t cell phenotype


title: 6694c2

source_name: sorted T cell low tumor cells


title: 6556c3


title: 7160c2


title: D14_Col_B1

description: Raw data: Matrix _raw_data_1


title: 6499c3


title: 6422c5

source_name: sorted T cell intermediate tumor cells

value: intermediate


title: D14_Col_A4

description: Raw data: Matrix _raw_data_1


title: 6422c1


title: 6419c5


title: 6419c1


title: 7160c5


title: 6620c1


title: 2699c4


title: 6421c2


title: 6499c4


title: PARA10

city: Biella

first: Paola

last: Ostano

address: via Malta 3

institute: Fondazione Edo ed Elvo Tempia

hyb_protocol: Six hundred ng of labeled RNA were hybridized on SurePrint G3 Human Gene Expression 8x60K v2 glass arrays.

scan_protocol: Arrays were scanned and images analyzed by the Feature Extraction Software from Agilent Technologies (version 10.7)

data_processing: Raw data were then processed using the Bioconductor package Limma (Linear models for microarray analysis). Background correction was performed with the normexp method with an offset of 50, and quantile was used for the between-array normalization. The empirical Bayes method was used to compute a moderated t-statistics

source_name: paracentesys of intrahepatic cholangiocarcinoma

label_protocol: For GEP analysis, 100 ng of total RNA was amplified and labeled using Low Input Quick Amp Labeling Kit, one-color kit (Agilent Technologies).

extract_protocol: Tissues were homogenized by using TissueLyser LT (Qiagen s.r.l. Milano, Italy) and total RNA was extracted and purified by Absolutely RNA miRNA kit (Agilent Technologies), following manufacturer’s protocols.  Quantitative and qualitative evaluation of total RNA was performed by Nanodrop and BioAnalyzer, respectively.

tag: gender

value: M


title: PARA7

value: paracentesys of intrahepatic cholangiocarcinoma


title: PARA11


title: 2838c3


title: PARA4

value: F


title: CHC012


title: PARA9


title: CHC018

source_name: primary intrahepatic cholangiocarcinoma

value: primary intrahepatic cholangiocarcinoma


title: PARA5


title: CHC003


title: CHC010


title: CHC004


title: CHC001


title: CHC017


title: CHC009


title: PARA2


title: CHC024


title: CHC005


title: RS_Setd2KO_RNA-seq_rep1

city: Shanghai

first: Fei

last: Lan

address: No131 Dongan Road, Xuhui District.

institute: Institute of Biochemical Science

data_processing:
Basecalls performed using CASAVA.
RNA-seq datas were aligned to the mm9 genome assembly using Tophat2 with the following parameters:tophat2 -p 8 -o RNA-seq_thout mm9_assemblies RNA-seq.fq
Transcriptome is assemblied using cufflinks;differential expressed genes were identified by cuffdiff.
FPKM value of Refseq genes were calculated by FPKM_count in RseQC toolkit.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file include the FPKM values of Refseq genes in Mus musculus genome

source_name: round spermatids

growth_protocol: Testes from adults were collected in PBS and placed on ice. After removal of the tunica albuginea, the testes were first digested with PBS containing 120 U/ml of collagenase type I (Worthington), further digested with 0.25% trypsin (Gibco), and DNAse I (5mg/ml, Gibco), and then terminated by adding fetal bovine serum (FBS). The dissociated testicular cell suspension was collected and resuspended at a concentration of 1x106 cells/ml in DMEM (Hyclone). Spermatocytes and round spermatids were collected based on Ho33342/PI staining using fluorescence-activated cell sorting (FACS).

extract_protocol:
RNA samples were prepared by RNeasy minikit (Qiagen). mRNA pools were enriched from total RNA by poly A beads.
Barcoded RNA-seq libraries were constructed using NEBNext Ultra Directional RNA library prep kit for Illumina according to the manufacturer’s instructions (New England Biolabs).

treatment_protocol: Total RNAs were isolated from PD and RS cells with WT-Setd2 and Setd2 loss.

value: round spermatids


title: RS_WT_RNA-seq_rep2

value: WT


title: RS_Setd2KO_RNA-seq_rep2


title: CHC011


title: RS_WT_RNA-seq_rep1


title: PD_Setd2KO_RNA-seq_rep2

source_name: pachytene/diplotene spermatocytes

value: pachytene/diplotene spermatocytes


title: CHC006


title: Normal fibroblast, biological replicate 2

city: Tlalpan

first: Claudia

last: Rangel Escareño

state: Mexico City

address: Periferico Sur 4809

department: Computational Genomics

country: Mexico

institute: INMEGEN

description: MicroRNA profile data

hyb_protocol: The samples were hybridized on the miRNA 4.0 array(Affymetrix) with standard protocol given by the manufacturer.

scan_protocol: Standard Affymetrix protocol.

data_processing: The expression signals were corrected with robust multiarray averaging and normalized using quantile normalization using R (affy package).

organism: synthetic construct

source_name: Normal fibroblast

label_protocol: 150 ng of total RNA was prepared for labeling with a FlashTag Biotin HSR RNA Labeling Kit (Genisphere, Hatfield, PA, USA), according to the manufacturer´s protocol.

growth_protocol: F-CAFs, In-CAFs, and NFs were cultured in DMEM-S to 80% confluency. Then, the medium was changed to DMEM without FBS, and the cells were cultured for another 48 h. The CM was collected from the supernatant and centrifuged at 15,000 x g for 15 min to remove cell debris and stored at -80 °C until further use.

extract_protocol: Total RNA was isolated from early passages (passages 3 to 4) cultures of F-CAFs, InCAFs, and NFs using Trizol reagent (Invitrogen), according to the manufacture´s instructions.

value: Normal fibroblasts


title: Inner tumor CAF, biological replicate 2

description: MicroRNA profile data

source_name: Inner tumor CAF

value: Cancer-associated fibroblasts


title: Inner tumor CAF, biological replicate 4

description: MicroRNA profile data


title: Tumor front CAF, biological replicate 3

description: MicroRNA profile data

source_name: Tumor front CAF


title: CHC002


title: yfp_6499c3_no1

data_processing:
Alignment using STAR aligner with default settings
Raw counts calling using featureCounts
Genome_build: mm10
Supplementary_files_format_and_content: text file including raw counts of each gene for all samples

extract_protocol:
RNA was extracted using Qiagen Rneasy Micro Kit.
500 ng of total RNA was used for the preparation of sequencing libraries using NEB RNA-seq library preparation kit with standard protocol. RNA-seq libraries were sequenced on an Illumina Nextseq 550 high-throughput sequencer.


title: Tumor front CAF, biological replicate 4

description: MicroRNA profile data


title: Normal fibroblast, biological replicate 4

description: MicroRNA profile data


title: yfp_6422c5_no2


title: PD_WT_RNA-seq_rep2


title: Normal fibroblast, biological replicate 1

description: MicroRNA profile data


title: Inner tumor CAF, biological replicate 1

description: MicroRNA profile data


title: Tumor front CAF, biological replicate 2

description: MicroRNA profile data


title: Tumor front CAF, biological replicate 1

description: MicroRNA profile data


title: PD_WT_RNA-seq_rep1


title: yfp_6422c1_no1


title: yfp_6422c5_no1


title: PD_Setd2KO_RNA-seq_rep1


title: yfp_6421c2_no2


title: Inner tumor CAF, biological replicate 3

description: MicroRNA profile data


title: yfp_6421c2_no1


title: yfp_6419c5_no2


title: Normal fibroblast, biological replicate 3

description: MicroRNA profile data


title: yfp_6419c4_no3


title: yfp_2838c3_no4


title: yfp_6419c1_no1


title: yfp_6419c1_no2


title: yfp_2838c3_no2


title: yfp_2838c3_no1