title: Glycans rep 1

first: Katharina

last: Ribbeck

state: Massachusetts

address: 21 Ames St

department: Biological Engineering

institute: Massachusetts Institute of Technology

description: Planktonic bacterial cultures

data_processing:
Illumina genome analyzer modules Firecrest and Bustard were used for image analysis and base-calling, respectively.
Sequence reads were mapped onto the P. aeruginosa PAO1 reference genome, which is available for download from the Pseudomonas Genome Database (http://www.pseudomonas.com) using the Burrows Wheeler algorithm on the Galaxy server.
Read counts were quantified in R thes files are provided as processed data)
Gene expression values were normalized based on library size and differentially expressed genes were identified using a negative binomial test with a false discovery rate (FDR) less than 0.05.
Genome_build: Pseudomonas aeruginosa PAO1
Supplementary_files_format_and_content: comma-delimited text files with raw read counts

organism: Pseudomonas aeruginosa

source_name: Planktonic bacterial cultures

growth_protocol: Batch cultivation of Pseudomonas aeruginosa was carried out shaking at 37 °C in LB. Overnight cultures were diluted to an OD600 of 0.01 medium with or without (0.5%) MUC5AC, (0.5%) MUC5B, or (0.01%) MUC5AC-glycans and grown for 5 h at 37 °C in a static 96-well microtiter plate.

extract_protocol:
Total RNA was extracted using the MasterPure RNA Purification kit (Lucigen) and residual DNA was removed using the Turbo DNA-free kit (Ambion). The integrity of the total RNA was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies). 16S, 23S, and 5S rRNA were removed using the Ribo-Zero Magnetic Kit (Bacteria) (Epicentre).
Gene expression analysis was conducted via Illumina RNA sequencing (RNA-seq). Libraries were produced using the KAPA RNA HyperPrep kit (Kapa Biosystems). Libraries were sequenced using the Illumina HiSeq platform with a single-end protocol and read lengths of 40 nt or 52 nt.

tag: growth medium

value: ABTGC defined medium

tag: growth time

value: 5 h


title: Human donor AF treated 3

status: Public on Oct 20 2019

type: SRA

city: Princeton

first: Alexander

last: Ploss

state: NJ

address: Washington Road

department: Molecular Biology

country: USA

institute: Princeton University

description: Cells transfected in triplicate in a 6 well format for 24 h with 0.5 ug poly(I:C) (~0.05 ug/cm2) per well

library_source: transcriptomic

data_processing:
Samples sequenced on SN387 with HiSeq Rapid SBS Kit v2. Image analysis and base-calling was performed with RTA version 1.18.64.0.
Barcode splitting performed in Galaxy with 1 mismatch allowed unless otherwise stated in the Samples, column Special notes. Short reads were aligned to the human or the originating species’ genomes using RNA STAR  (Galaxy version 2.6.0b-1) with default parameters. Counts were generated using featureCounts with default settings (Galaxy version 1.6.3+galaxy2), downloaded, and read into R version 3.5.2 (2018-12-20) using scripts run in RStudio version 1.1.463.
htseq-count Gene counts analyzed further with DESeq2 (version 1.22.2) (Love MI, Huber W and Anders S (2014) “Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.” Genome Biology, 15, pp. 550. doi: 10.1186/s13059-014-0550-8) in RStudio (R version 3.3.3.), using two factors (donor + treatment)  as the experimental design.
genome build
Each species was aligned to human and its specific reference genome except for human (which was only aligned to the human genome) and mouse (which was only aligned to the mouse genome).
Species
Orangutan: ppyg2 (Ensembl 93)
Gorilla:  gorGor4 (Ensembl 95)
Pigtailed macaque : Mnem_1.0 (Ensembl 95)
Rhesus macaque: Mmul_8_0_1 (Ensembl 95)
Bonobo: panpan1.1 (Ensembl 95)
Chimpanzee: Pan_tro_3.0 (Ensembl 95)
Olive baboon: papAnu2 (Ensembl 95)
Squirrel monkey: SaiBol1.0 (Ensembl 95)
Human: GRCh38 (Ensembl 96)
Mouse: GRCm38 (Ensembl 85)
processed data files format and content: all tab-delimited text files of htseq-count "Gene counts" :

molecule: total RNA

organism: Homo sapiens

source_name: Dermal fibroblasts

growth_protocol: All cells were grown under standard conditions in Dulbecco’s modified Eagle medium containing 10% fetal bovine serum (FBS) and 1% v/v penicillin/streptomycin.

extract_protocol:
Total RNA extracted using Qiagen Rneasy Mini Kit per manufacturer's directions.
The integrity of total RNA from the primate samples were assessed on Bioanalyzer 2100 using RNA 6000 Nano chip (Agilent Technologies, CA), only samples with RNA Integrity Number (RIN) greater than 9.0 were used for RNA-seq.  One microgram of total RNA from each sample was subject to poly-A containing RNA enrichment by oligo-dT bead and converted to cDNA then sequencing library using PrepX RNA-seq library kit on the automated Apollo 324TM NGS Library Prep System (Wafergen Biosystems, CA) according to the manufacturer's protocol.  Different DNA barcodes were added to each library.  The libraries were examined on Agilent Bioanalyzer DNA High Sensitivity chips for size distribution, quantified by Qubit fluorometer (Invitrogen, CA).  The RNA-seq libraries were pooled at equal molar amount and sequenced on Illumina HiSeq 2500 Rapid flowcells as single-end 75nt reads following the standard protocol.  Raw sequencing reads were filtered by Illumina HiSeq Control Software and only the Pass-Filter (PF) reads were used for further analysis.

treatment_protocol: Cells were seeded the night before transfection with 200,000 cells/well in a 6 well format so that at the time of transfection they were at least 80% confluent. Each well received 0.5 ug high molecular weight poly(I:C) using using X-tremegene HP DNA transfection reagent in Opti-MEM.

tag: cell type

value: primary dermal fibroblasts

tag: treatment

value: 24 h transfection 0.05 ug/cm2 poly(I:C)

tag: passage


title: MUC5B rep 2

city: Cambridge

description: Planktonic bacterial cultures

tag: strain


title: human donor SR treated 1


title: Human donor AF treated 2


title: Human donor AF treated 1


title: MUC5B rep 3

description: Planktonic bacterial cultures


title: Human donor AF mock 3

description: Cells mock transfected in triplicate in a 6 well format for 24 h

value: 24 h mock transfected


title: MUC5B rep 1

description: Planktonic bacterial cultures


title: Human donor AF mock 2


title: unmatched reads from pigtailed macaque donor PR0058

description: Unmatched reads from multiple samples either mock transfected or transfected in triplicate in a 6 well format for 24 h with 0.5 ug poly(I:C) (~0.05 ug/cm2) per well

organism: Macaca nemestrina

value: 24 h transfection 0.05 ug/cm2 poly(I:C) and 24 h mock transfected


title: Glycans rep 2

description: Planktonic bacterial cultures


title: unmatched reads from pigtailed macaque donors  AG07923 and AG08490


title: Glycans rep 3

description: Planktonic bacterial cultures


title: human donor NHDF mock B


title: MUC5AC rep 3

description: Planktonic bacterial cultures


title: Human donor AF mock 1


title: MUC5AC rep 2

description: Planktonic bacterial cultures


title: unmatched reads from orangutan donors  AG06105 and PR00054

organism: Pongo abelii


title: Pigtailed macaque donor PR0058 mock 1


title: Pigtailed macaque donor PR0058 mock 2


title: Pigtailed macaque donor PR0058 mock 3


title: MUC5AC rep 1

description: Planktonic bacterial cultures


title: CBL Y371S rep3 [S12_L001]

city: Glasgow

first: Syed

middle: Feroj

last: Ahmed

state: Bearsden

address: Garscube Estate, Switchback Road

department: Structural Biology

country: United Kingdom

institute: Beatson Institute for Cancer Research

data_processing:
Quality checks on the raw RNASeq data files were done using fastqc version 0.10.1 and fastq_screen version 0.4.2
RNASeq paired-end reads were aligned to the GRCm38 version of the mouse genome using tophat2 version 2.0.13 with Bowtie version 2.2.4.0.
Expression levels were determined and statistically analised by a combination of HTSeq version 0.9.1, the R environment, version 3.1.1, utilizing packages from the Bioconductor data analysis suite and differential gene expression analysis based on the negative binomial distribution using the DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: xlsx files include FC and padj values for each sample (WT CBL, CBL 70Z and CBL Y371S) adjusted against EV

organism: Mus musculus

source_name: NIH-3T3_CBL Y371S

growth_protocol: NIH-3T3 cells were stably transfected with EV, WT CBL, CBL 70Z and CBL Y371S and cultured in DMEM in monolayer at 37 °C in 5% CO2, supplemented with 10% DBS, 20 mM L-glutamine, 6 mg/l gentamycin reagent solution, 0.1 mg/ml streptomycin and 100 units/ml penicillin (Invitrogen, USA).

extract_protocol:
RNA was extracted using TRIzol method and the quality of extracted RNA was checked using RNA screentape on Agilent 2200 Tapestation.
An adapted method from Fisher et al (Genome Biology, 2011) was followed to prepare libraries for cluster generation and DNA sequencing, using Illumina TruSeq RNA Library Preparation Kit v2.

tag: strain background

value: NIH/Swiss

tag: cell line

value: fibroblast

tag: passages

tag: genotype/variation

value: stably expressing mutant CBL Y371S


title: ABTGC rep6

description: Planktonic bacterial cultures


title: Pigtailed macaque donor PR0058 treated 3


title: CBL Y371S rep2 [S11_L001]


title: Orangutan donor PR00054 mock C


title: Pigtailed macaque donor AG08490 mock 2


title: ABTGC rep5

description: Planktonic bacterial cultures


title: Orangutan donor PR00054 treated B


title: Pigtailed macaque donor PR0058 treated 2


title: ABTGC rep3

description: Planktonic bacterial cultures


title: Orangutan donor PR00054 mock A


title: Orangutan donor PR00054 treated C


title: ABTGC rep4

description: Planktonic bacterial cultures


title: CBL 70Z rep1 [S7_L001]

source_name: NIH-3T3_CBL 70Z

value: stably expressing mutant CBL 70Z


title: Pigtailed macaque donor AG08490 mock 3


title: Orangutan donor PR00054 treated A


title: CBL 70Z rep2 [S8_L001]


title: Pigtailed macaque donor AG08490 mock 1


title: ABTGC rep2

description: Planktonic bacterial cultures


title: ABTGC rep1

description: Planktonic bacterial cultures


title: Orangutan donor AG06105 mock C


title: Pigtailed macaque donor AG08490 treated 3


title: diploid grass (DV92) embryo sample taken at two cell stage DV-1

status: Public on Oct 21 2019

city: Ottawa

first: Ziying

last: Liu

state: ON

address: 1200 Montreal Road

country: Canada

institute: National Research Council, Canada

data_processing:
RNA-seq reads were preprocessed by trimming the adaptor sequences, filtering low-quality reads (Phred Score <=20 [Phred]) and eliminating short reads (length <= 20 bps) using software package FASTX-toolkit [http://hannonlab.cshl.edu/fastx_toolkit/].
RAN-seq reads were aligned to the pan-genome of Chinese Spring (IWGSC RefSeq v1.0) from the IWGSC sequence repository hosted by URGI-INRA (https://wheat-urgi.versailles.inra.fr/) and Fusarium graminearum reference genome (Fusarium graminearum str. PH-1) from EnsemblFungi (http://fungi.ensembl.org/, Release 35) using STAR v2.5.3a
R package DESeq2 was used for data normalization and to generate differentially expressed gene (DEG)
Genome_build: IWGSC RefSeq v1.0
Supplementary_files_format_and_content: In excel file format, including raw read counts of each species

organism: Triticum monococcum

source_name: two cell

growth_protocol: Polyploidy wheats, AC Barrie, Strong Field and diploid wheat grass (DV92) plants were grown in growth chambers under long-day conditions of 16 h light, 22°C and 8 h dark, 20 °C; light intensity: 100 to 120 μmol m−2 s−1 for whole life cycle. TA2780 and TA101132 were initially grown in a growth chamber at 22°C under long days (16h day/8h night), at the fifth-leaf stage, plants were moved into a cold room with 4°C and the long day photoperiod for one month (vernalization treatment), then move back to 16 h light, 22°C and 8 h dark, 20 °C; light intensity: 100 to 120 μmol m−2 s−1 again to complete its life cycle

extract_protocol:
Total RNA was extracted from embryo, endosperm and seed coat of wheat speciesat different development stages following the protocol of RNAqueous-Micro kit (Ambion, Catalog# 1927), two replicates for each development stage. The quantity of RNA isolated from early stage was insufficient for preparation of libraries for the RNA-seq experiments. Therefore the mRNA of all stages was amplified and the aRNA were used for RNA-seq analysis. The mRNA amplification was conducted according to the protocol provided in the MessageAmp aRNA kit (Ambion, Catalog# 1750). For RNA-seq profile analysis, we prepared Illumina mRNA-seq libraries using the TruSeq RNA kit (version 1, rev A), the libraries were prepared by using aRNA according to manufacturer's instruction. For HiSeq 2500 sequencing, 4 libraries were pooled per sequencing lane
Libraries were prepared according to Illumina's instructions, using the TruSeq RNA v2 LT kit and sequenced on the Genome Analyzer following the manufacturer's protocols (https://www.illumina.com/documents/products/datasheets/datasheet_hiseq2500.pdf).

tag: genotype

value: diploid grass (DV92, A genome)

tag: tissue

value: embryo

tag: development stages

value: two cell


title: TLR4ΔIEC_9

city: Baltimore

first: David

middle: J.

last: Hackam

state: MD

address: Room 7323, 1800 Orleans Street

department: Surgery

institute: The Johns Hopkins University

description:
SM3
Barcode: BC09
SM3_avg_covrg.txtTx.txt

data_processing:
Read files were mapped using Tophat v. 2.0.10 in conjunction with Bowtie2 v2.1.0.
The resulting .bam files were used for compiling Quality Control Statistics and analyzed using RNASeqnator v0.8 to determine Transcript-level and Exon-level average coverage values.
To remove small RNA transcripts, transcript length distributions per sample were plotted, and transcripts with L < 223 were excluded.
The coverage values were analyzed using caGEDA for data normalization and G-Thresholding was used find differentially expressed genes.
J5 values were calculated on normalized data for deferentially expressed genes at transcript level.
Genome_build: Mouse Genome (mm10)
Supplementary_files_format_and_content: Text files including average coverage value

source_name: TLR4ΔIEC, Ileum

extract_protocol:
Ileum was removed and snap frozen in liquid nitrogen. Total RNA was extracted using Rneasy mini kit. The quality of the RNA samples was analyzed by Agilent Bioanalyzer 2100, and only RNA samples with an RNA integrity number greater than 7 were used for further analysis.
Whole Transcriptome library preparation requires rRNA depletion of total RNA using the GeneRead rRNA Depletion Kit (Qiagen).  EERC spike-in RNA controls are added to 500ng of the product before fragmentation with RNAse III. Fragmented RNA is purified and the concentration is assessed via florometric assay and size distribution verified on the Agilent 2100 Bioanalyzer Pico Chip. Using buffers and ligation enzymes supplied with the Ion Total RNA-Seq kit v2 for Whole Transcriptomes (Life Technologies), partial adapters are ligated to the prepared RNA and strand specific reverse transcription is performed with SuperScript® III Enzyme Mix followed by magnetic bead clean-up of the cDNA. The cDNA is amplified with a high fidelity polymerase that has proof reading activity (Platinum® PCR SuperMix High Fidelity) for a total of 16 cycles, using primers that complete the adapter sequence and add barcode sequences to each sample, followed by a further round of magnetic bead purification.  Yield and size distribution are assessed by florometric assay and Bioanalyzer High Sensitivity DNA Chip. Barcoded libraries are pooled and diluted for emulsion amplification on Ion Sphere™ Particiles (ISPs) using the Ion One Touch 2 System (Life Technologies). For emulsion PCR and sequencing, the Ion One Touch 2 System performs automated emulsion PCR of the prepared libraries and templated Ion Sphere™ Particle (ISP) enrichment.  Enriched ISP particles are prepared for sequencing by heat denaturing the template cDNA and annealing the sequencing primer.  An on-instrument chip QC is performed to ensure chip integrity prior to the addition of polymerase to the primed ISP templates. QC reagents are removed from the chip and the ISPs are loaded, mixed and centrifuged for even ISP distribution into the wells of the high density array.  Incorporation of nucleotides by polymerase during sequencing by synthesis releases a hydrogen ion, which is detected by an ion sensitive layer and ion sensors below the wells as a change in pH.  Nucleotides are sequentially flooded onto the chip. On incorporation a pH change is detected and the base is recorded digitally but if the nucleotide is not complementary to the template it is not incorporated, a H+ ion is not released and no base is called.  If more than one base is incorporated multiple H+ ions are released, the pH change is greater and multiple bases are recorded. Semiconductor sequencing can accurately read homopolymers up to eleven bases. Data can be aligned to a suitable reference sequence on-instrument and are exported as .bam, .bai and fastq files.

tag: age

value: 24 weeks

value: Ileum


title: WT CBL rep2 [S5_L001]

source_name: NIH-3T3_WT CBL

value: stably expressing WT CBL


title: CBL 70Z rep3 [S9_L001]


title: CBL Y371S rep1 [S10_L001]


title: Orangutan donor AG06105 mock B


title: Pigtailed macaque donor PR0058 treated 1


title: Pigtailed macaque donor AG08490 treated 2


title: TLR4ΔIEC_8

description:
SM3
Barcode: BC08
SM3_avg_covrg.txtTx.txt


title: Orangutan donor PR00054 mock B


title: WT CBL rep1 [S4_L001]


title: EV rep3 [S3_L001]

value: stably expressing empty vector


title: EV rep2 [S2_L001]


title: Pigtailed macaque donor AG07923 mock 3


title: Wild type_3

description:
SM1
Barcode: BC03
SM1_avg_covrg.txtTx.txt

source_name: Wild type, Ileum

value: Wild type


title: TLR4ΔIEC_7

description:
SM3
Barcode: BC07
SM3_avg_covrg.txtTx.txt


title: Pigtailed macaque donor AG08490 treated 1


title: Pigtailed macaque donor AG07923 mock 2


title: Orangutan donor AG06105 mock A


title: Orangutan donor AG06105 treated C


title: Wild type_1

description:
SM1
Barcode: BC01
SM1_avg_covrg.txtTx.txt


title: Orangutan donor AG06105 treated A


title: Orangutan donor AG06105 treated B


title: EV rep1 [S1_L001]


title: Pigtailed macaque donor AG07923 mock 1


title: WT CBL rep3 [S6_L001]


title: Wild type_2

description:
SM1
Barcode: BC02
SM1_avg_covrg.txtTx.txt


title: unmatched reads from mouse donors  C57A and C57B


title: U15

city: Philadelphia

first: Vinay

last: Parikh

state: PA

address: 1701 N. 13th Street, Weiss Hall

department: Psychology

institute: Temple University

data_processing:
Adaptor quality checked using Trimmomatic
Sequence data from FASTQ files were aligned to the Rnor 6.0 genome using Bowtie2 and TopHat2
HTSeq was used to generate gene-level count, using Rnor_6.0.87.gtf for annotation
Read counts derived from two lanes per sample were added together, and the Bioconductor package DESeq2 was used for count normalization and analysis.
Genome_build: Rnor 6.0
Supplementary_files_format_and_content: .txt file reports normalized counts for all samples

organism: Rattus norvegicus

source_name: prefrontal cortex

extract_protocol:
RNA was extracted using RNeasy Kit (Qiagen)
TruSeq stranded mRNA library. 1000ng total RNA from each sample was used to prepare the cDNA library
RNA-Seq (Illumina). Libraries were purified using AmPure beads, had a quality check on bioanalyzer (Agilent) and quantified with Qubit (Invitrogen). Sample libraries were subsequently pooled and loaded to the sequencer.

treatment_protocol: Young (3 months) and aged (22 months) rats were trained and tested for attentional capacities in an operant task. Non-performing age-matched controls were given the same contextual experience as the performing animals but were never engaged in any cognitive activity. Brains were removed and medial prefrontal cortex was isolated for transcriptomic analysis.

value: Wistar

tag: cognitive performance

value: nonperforming

value: aged

value: Prefrontal Cortex


title: Pigtailed macaque donor AG07923 treated 3

value: primary dermal fibroblasts

value: 24 h transfection 0.05 ug/cm2 poly(I:C)


title: U14

value: performing


title: Pigtailed macaque donor AG07923 treated 2


title: Orangutan donor PR01109 mock A

value: 24 h mock transfected


title: Pigtailed macaque donor AG07923 treated 1


title: Mouse donor C57C mock 1


title: U13


title: Orangutan donor PR01109 treated C


title: U12


title: Mouse donor C57C mock 3


title: Mouse donor C57C treated 3


title: Orangutan donor PR01109 treated B


title: U11


title: Rhesus macaque donor AG08312 mock 3

organism: Macaca mulatta


title: unmatched reads from rhesus macaque donors  AG08308 and AG08312

value: 24 h transfection 0.05 ug/cm2 poly(I:C) and 24 h mock transfected


title: U10


title: unmatched reads from gorilla donors PR00573 and PR0230

organism: Gorilla gorilla


title: Mouse donor C57B mock 3


title: Mouse donor C57C treated 1


title: Mouse donor C57C treated 2


title: Rhesus macaque donor AG08312 mock 2


title: Rhesus macaque donor AG08312 mock 1


title: Orangutan donor PR01109 mock C


title: U9

value: young


title: Rhesus macaque donor AG08312 treated 3


title: U8


title: Gorilla donor PR0230 mock 3


title: Orangutan donor PR01109 mock B


title: Mouse donor C57C mock 2


title: Gorilla donor PR0230 mock 2


title: Mouse donor C57B mock 2


title: U7


title: Rhesus macaque donor AG08312 treated 2


title: Mouse donor C57B mock 1


title: Gorilla donor PR0230 mock 1


title: Orangutan donor PR01109 treated A


title: Gorilla donor PR0230 treated 3


title: U6


title: Rhesus macaque donor AG08312 treated 1


title: Mouse donor C57B treated 2


title: Mouse donor C57B treated 3


title: VP-2


title: Gorilla donor PR0230 treated 2


title: Rhesus macaque donor AG08308 mock 3


title: Gorilla donor PR0230 treated 1


title: Mouse donor C57B treated 1


title: Mouse donor C57A mock 3


title: Rhesus macaque donor AG08308 mock 2


title: Rhesus macaque donor AG08308 mock 1


title: Mouse donor C57A mock 2


title: Rhesus macaque donor AG08308 treated 3


title: VP-1


title: unmatched reads from chimpanzee donor S3611

organism: Pan troglodytes


title: Chimpanzee donor S3611 mock 3


title: unmatched reads from chimpanzee donors  S4933 and S3649


title: Mouse donor C57A mock 1


title: Rhesus macaque donor AG08308 treated 2


title: Gorilla donor PR00573 mock 2


title: Gorilla donor PR00573 mock 3


title: Mouse donor C57A treated 3


title: Gorilla donor PR00573 mock 1


title: Rhesus macaque donor AG08308 treated 1


title: Chimpanzee donor S3611 mock 2


title: Chimpanzee donor S3611 mock 1


title: Mouse donor C57A treated 2


title: Gorilla donor PR00573 treated 2


title: Rhesus macaque donor AG08305 mock 3


title: Gorilla donor PR00573 treated 1


title: Chimpanzee donor S3611 treated 2


title: NG3

city: Guangzhou

first: Shineng

last: Zhang

state: Guangdong

address: No.107 Yanjiang West Road

country: China

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

data_processing:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol.
RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies). The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis. The libraries were constructed using TruSeq Stranded Total RNA with Ribo-Zero Gold (Illumina) and Ribonuclease R according to the manufacturer’s instructions.
CircRNA libraries were sequenced on the Illumina sequencing platform (HiSeq X Ten) and 150 bp/125bp paired-end reads were generated
Genome_build: H19
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each sample

source_name: pancreatic ductal adenocarcinoma

growth_protocol: 5 × 106 MIA PaCa-2 cells were seeded and cultured in 10 cm dish overnight. After 24 h incubation, cells were reincubated in none glucose DMEM medium with 10% fetal bovine serum (FBS) in the experiment group. Meanwhile, cells were reincubated in high glucose DMEM medium with 10% FBS in the control group. After 3 h incubation, cells were harvested for further high throughput sequencing. Three independent experiments were performed in each group.

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: MIA PaCa-2

value: pancreatic ductal adenocarcinoma

tag: culture condition

value: none glucose


title: Rhesus macaque donor AG08305 mock 1


title: Gorilla donor PR00107 mock 3


title: Rhesus macaque donor AG08305 treated 3


title: NG2


title: Rhesus macaque donor AG08305 treated 2


title: Gorilla donor PR00107 mock 2


title: NG1


title: Rhesus macaque donor AG08305 treated 1


title: Gorilla donor PR00107 mock 1


title: HG3

value: high glucose


title: Rhesus macaque donor AG08305 mock 2


title: Chimpanzee donor S3649 mock 2


title: unmatched reads from human donor NHDF samples mock C and treated C; all samples of PR00033

description:
Homo sapiens and Papio anubis
Unmatched reads from multiple samples either mock transfected or transfected in triplicate in a 6 well format for 24 h with 0.5 ug poly(I:C) (~0.05 ug/cm2) per well

organism:
Papio anubis
Homo sapiens


title: HG2


title: unmatched reads from human donor NHDF samples mock B and treated B; all samples of PR00039


title: Gorilla donor PR00107 treated 3


title: Chimpanzee donor S3649 mock 1


title: Gorilla donor PR00573 treated 3


title: Chimpanzee donor S3611 treated 3


title: Gorilla donor PR00107 treated 1


title: Mouse donor C57A treated 1


title: Gorilla donor PR00107 treated 2


title: HG1


title: unmatched reads from human donor NHDF samples mock A and treated A; all samples of PR00036


title: Chimpanzee donor S3611 treated 1


title: Chimpanzee donor S3649 treated 3


title: unmatched reads from squirrel monkey donors  SQMA and SQMB

organism: Saimiri sciureus

value: SQMA (p5), SQMB (p8)


title: unmatched reads from bonobo donors  PR235 and PR111

organism: Pan paniscus


title: Chimpanzee donor S3649 mock 3


title: Chimpanzee donor S4933 mock 3


title: Oive baboon donor PR00039 mock A

organism: Papio anubis


title: Squirrel monkey donor AG05311 mock 3


title: Bonobo donor PR00248 mock 3


title: Squirrel monkey donor AG05311 mock 2


title: Chimpanzee donor S3649 treated 2


title: Bonobo donor PR00248 mock 1


title: Oive baboon donor PR00039 treated B


title: Oive baboon donor PR00039 treated C


title: Squirrel monkey donor AG05311 treated 2


title: Chimpanzee donor S4933 mock 1


title: Squirrel monkey donor AG05311 mock 1


title: Oive baboon donor PR00039 treated A


title: Squirrel monkey donor AG05311 treated 3


title: Chimpanzee donor S4933 treated 3


title: Chimpanzee donor S4933 mock 2


title: Bonobo donor PR00248 treated 1


title: Chimpanzee donor S4933 treated 2


title: Squirrel monkey donor AG05311 treated 1


title: Bonobo donor PR00248 treated 3


title: olive baboon donor PR00033 mock B


title: Chimpanzee donor S3649 treated 1


title: Chimpanzee donor S4933 treated 1


title: Oive baboon donor PR00039 mock B


title: Oive baboon donor PR00039 mock C


title: olive baboon donor PR00033 mock C


title: Bonobo donor PR111 mock C


title: Squirrel monkey donor SQMB mock 3


title: Bonobo donor PR00248 mock 2


title: olive baboon donor PR00033 mock A


title: GFP

city: Nanjing

first: Jie

last: Huang

state: Jiangsu

address: NO.1 Weigang

department: Plant Pathology

institute: Nanjing Agricultural University

data_processing:
The raw RNA-seq reads generated from Illumina sequence platform were filtered using the ht2-filter from HTQC package (1.92.1) with the default parameters to remove low-quality reads. Then filtered reads were aligned to the soybean genome using tophat-2.0.11 with anchor length more than 8nt for spliced alignments.
Genome_build: Gmax_275_v2.0 (https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Gmax)
Supplementary_files_format_and_content: bigWig

organism: Glycine max

extract_protocol:
The total RNA was extracted using TRIZOL reagent (Invitrogen Cat#15596026).
Strand-specific RNA-Seq libraries generated from samples above were constructed using dUTP method (Parkhomchuk et al., 2009) and sequenced on Illumina Hiseq 2500.

treatment_protocol: No treatment

tag: cultivars

value: williams

value: GFP (control)

value: hairy roots


title: GmSRKP1-rep2

value: GFP-GmSRKP1 over-expression line


title: Bonobo donor PR00248 treated 2


title: Bonobo donor PR111 mock A


title: olive baboon donor PR00033 treated C


title: Squirrel monkey donor SQMB mock 1


title: Bonobo donor PR111 mock B


title: GmSRKP1-rep1


title: Bonobo donor PR111 treated 3


title: Squirrel monkey donor SQMB treated 3


title: Bonobo donor PR111 treated 2


title: Squirrel monkey donor SQMB treated 2


title: olive baboon donor PR00033 treated A


title: Bonobo donor PR235 mock 3


title: Squirrel monkey donor SQMB mock 2


title: Squirrel monkey donor SQMB treated 1


title: olive baboon donor PR00036 mock A


title: Squirrel monkey donor SQMA mock 3


title: olive baboon donor PR00036 mock B


title: Bonobo donor PR111 treated 1


title: Squirrel monkey donor SQMA mock 2


title: Bonobo donor PR235 mock 2


title: olive baboon donor PR00036 mock C


title: olive baboon donor PR00036 treated C


title: olive baboon donor PR00033 treated B


title: Squirrel monkey donor SQMA mock 1


title: Bonobo donor PR235 treated 3


title: olive baboon donor PR00036 treated B


title: WM3211-INV

type: RNA

city: Debrecen

first: Viktoria

last: Koroknai

address: 26/B Kassai str.

department: Department of Public Health and Epidemiology

country: Hungary

institute: University of Debrecen

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Affymetrix Expression Console was used for primary analysis, RMA algorithm with default settings.

label: biotin

source_name: melanoma cell line

label_protocol: Labeling, hybridization and image scan were performed according to the recent laboratory protocol of UD-GenoMed Medical Genomic Technologies Ltd.

growth_protocol: Human melanoma cell lines were maintained in RPMI 1640 medium supplemented with 10% foetal bovine serum, 300 mg/l L-glutamine and antibiotics.

extract_protocol: Total RNA was isolated using Qiagen Rneasy Plus Mini kit.

treatment_protocol: To select the invasive subpopulations, the invading cells in the lower layer chamber of Matrigel Invasion Assay were treated with a 0.5% trypsin/0.2% EDTA solution for recovery from the membrane and cultured using standard protocols until the RNA isolation.

tag: origin

value: selected from WM3211 cell line


title: olive baboon donor PR00036 treated A


title: Squirrel monkey donor SQMA treated 3


title: WM1366-INV

value: selected from WM1366 cell line


title: Squirrel monkey donor SQMA treated 2

value: primary dermal fibroblasts


title: Bonobo donor PR235 treated 2

value: 24 h transfection 0.05 ug/cm2 poly(I:C)


title: WM3211

value: primary melanoma tumor

tag: growth phase

value: RGP/VGP

tag: histologic type

value: SSM

tag: braf mutation status

value: wt


title: unmatched reads from mouse donor  C57C and rhesus macaque donor AG08305

description:
Mus musculus (C57/BL6) and Macaca mulatta
Unmatched reads from multiple samples either mock transfected or transfected in triplicate in a 6 well format for 24 h with 0.5 ug poly(I:C) (~0.05 ug/cm2) per well

organism:
Macaca mulatta
Mus musculus

tag: cell type

tag: treatment

value: 24 h transfection 0.05 ug/cm2 poly(I:C) and 24 h mock transfected

tag: passage


title: WM983A-INV

value: selected from WM983A cell line

tag: cell line


title: unmatched reads from bonobo donor  PR00248 and squirrel monkey donor AG05311

description:
Pan paniscus and Saimiri sciureus
Unmatched reads from multiple samples either mock transfected or transfected in triplicate in a 6 well format for 24 h with 0.5 ug poly(I:C) (~0.05 ug/cm2) per well

organism:
Saimiri sciureus
Pan paniscus


title: WM793B-INV

value: selected from 7WM793B cell line


title: WM1366

value: VGP


title: Bonobo donor PR235 treated 1


title: unmatched reads from orangutan donor PR01109 and gorilla donor PR00107

description:
Pongo abelii  and Gorilla gorilla
Unmatched reads from multiple samples either mock transfected or transfected in triplicate in a 6 well format for 24 h with 0.5 ug poly(I:C) (~0.05 ug/cm2) per well

organism:
Gorilla gorilla
Pongo abelii


title: WM793B

organism: Homo sapiens


title: Squirrel monkey donor SQMA treated 1


title: UA159 Minus Iron; Minus Manganese 2

status: Public on Oct 19 2019

city: Gainesville

first: Jessica

middle: K

last: Kajfasz

state: FL

address: 1395 Center Drive

department: Oral Biology

institute: University of Florida

description:
S. mutans UA159 grown to OD600 = 0.4 in FMC depleted of iron and manganese Replicate 2
UA159_FMC_Complete_vs_FeMn.csv

data_processing:
Read mapping was performed on a Galalxy server hosted by the University of Florida Research Computer
Map with Bowtie for Illumina was used to map the reads to the S. mutans UA159 genome (NC_004350.2)
htseq-count was used to tabulate the reads per open reading frame
Degust was used to make final comparisons in counts between cells grown in the complete versus the metal-depleted media.
Genome_build: NC_004350.2
Supplementary_files_format_and_content: The processed .csv data files contain counts for individual samples and comparisons of the pooled data (three replicates for each sample type) between two samples, represented as the log2 fold change of expression of each coding region (SMU).

organism: Streptococcus mutans

source_name: Laboratory stock

growth_protocol: Cells were grown to OD600 of 0.4, then harvested by centrifugation.  Pellets were treated with RNA protect reagent, harvested by centrifugation, and stored at -80°C until use

extract_protocol:
Harvested cells were resuspended in 1mL of RNA Protect Bacteria Reagent (Qiagen). Total RNA was isolated from homogenized S. mutans cell lysates by acid-phenol:chloroform extractions.  The nucleic acid was subjected to DNase I digestion (Ambion).   The RNA was then purified using the Qiagen RNeasy colum purification kit, including an additional on-column DNase digest.  Total RNA was subjected to two rounds of mRNA enrichment using the MICROBExpress Bacterial mRNA Purification kit (ThermoFisher).
cDNA libraries with unique barcoes were generated from 100ng enriched mRNA using the NEB Next UltraII Directional RNA Library Prep kit for Illumina (New England Biolabs).
Pooled libraries were subjected to RNA deep sequencing at the University of Florida Interdisciplinary Center for Biotechnology Research using the Illumina NextSeq500 platform.

treatment_protocol: Cells were grown in FMC complete medium, or FMC medium depleted of iron, manganese, or of both metals.

tag: strain

value: wild type

tag: growth medium

value: FMC Minus Iron; Minus Manganese


title: UA159 Minus Manganese 3

description:
S. mutans UA159 grown to OD600 = 0.4 in FMC depleted of manganese Replicate 3
UA159_FMC_Complete_vs_Mn.csv

tag: genotype

value: FMC Minus Manganese


title: UA159 Minus Iron; Minus Manganese 1

description:
S. mutans UA159 grown to OD600 = 0.4 in FMC depleted of iron and manganese Replicate 1
UA159_FMC_Complete_vs_FeMn.csv


title: UA159 Minus Manganese 2

description:
S. mutans UA159 grown to OD600 = 0.4 in FMC depleted of manganese Replicate 2
UA159_FMC_Complete_vs_Mn.csv


title: UA159 Minus Iron 3

description:
S. mutans UA159 grown to OD600 = 0.4 in FMC depleted of iron Replicate 3
UA159_FMC_Complete_vs_Fe.csv

value: FMC Minus Iron


title: UA159 Minus Iron 1

description:
S. mutans UA159 grown to OD600 = 0.4 in FMC depleted of iron Replicate 1
UA159_FMC_Complete_vs_Fe.csv


title: UA159 Complete 3

description:
S. mutans UA159 grown to OD600 = 0.4 in FMC complete Replicate 3
UA159_FMC_Complete_vs_Fe.csv

value: FMC Complete


title: UA159 Minus Manganese 1

description:
S. mutans UA159 grown to OD600 = 0.4 in FMC depleted of manganese Replicate 1
UA159_FMC_Complete_vs_Mn.csv


title: UA159 Minus Iron 2

description:
S. mutans UA159 grown to OD600 = 0.4 in FMC depleted of iron Replicate 2
UA159_FMC_Complete_vs_Fe.csv


title: UA159 Minus Iron; Minus Manganese 3

description:
S. mutans UA159 grown to OD600 = 0.4 in FMC depleted of iron and manganese Replicate 3
UA159_FMC_Complete_vs_FeMn.csv


title: Bonobo donor PR235 mock 1

description: Cells mock transfected in triplicate in a 6 well format for 24 h

value: 24 h mock transfected


title: UA159 Complete 2

description:
S. mutans UA159 grown to OD600 = 0.4 in FMC complete Replicate 2
UA159_FMC_Complete_vs_Fe.csv


title: UA159 Complete 1

description:
S. mutans UA159 grown to OD600 = 0.4 in FMC complete Replicate 1
UA159_FMC_Complete_vs_Fe.csv


title: Non-cancer control XB0850

city: Kanagawa

first: Satoko

last: Takizawa

address: kamakurashi

country: Japan

institute: Toray industries inc

description: Non-cancer control

hyb_protocol: Hybridized for 16 h at 32 ºC with rotary shaker (250 rpm). Hybridization buffer and washing protocol was attached in the 3D-Gene® miRNA oligo chip kit.

scan_protocol: 3D-Gene® Scanner (Toray Industries, Inc.) was used for scanning. Images were quantified using Extraction version 2.0.0.6 (Toray Industries, Inc.).

data_processing: The presence of miRNA was determined based on a corresponding microarray signal of greater than [the mean + 2 × standard deviation] of the negative controls signal, of which the top and bottom ranked ones by signal intensity were removed. Once a miRNA was considered present, the mean signal of the negative controls of which the top and bottom 5% ranked by signal intensity were removed was subtracted from the miRNA signal. When the signal value was negative (or undetEsophageal Cancerted) after background subtraction, the value was replaced by 0.1 on a base 2 logarithm scale.

source_name: Serum

label_protocol: miRNA was labeled using 3D-Gene® miRNA Labeling kit in accordance with the manufacturer's instructions.

extract_protocol: Total RNA was extracted each from 300uL serum samples using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.).

tag: Sex

value: Male


title: Non-cancer control XB0837

description: Non-cancer control


title: Non-cancer control XB0922

description: Non-cancer control


title: Non-cancer control XB0956

description: Non-cancer control


title: Non-cancer control XB0725

description: Non-cancer control


title: Non-cancer control XB0747

description: Non-cancer control


title: Non-cancer control XB0718

description: Non-cancer control


title: Non-cancer control XB0931

description: Non-cancer control


title: Non-cancer control XB0769

description: Non-cancer control


title: Non-cancer control XB0595

description: Non-cancer control


title: Non-cancer control XB0709

description: Non-cancer control


title: Non-cancer control XB0629

description: Non-cancer control


title: Non-cancer control XB0607

description: Non-cancer control


title: Non-cancer control XB0578

description: Non-cancer control


title: Non-cancer control XB0612

description: Non-cancer control


title: Non-cancer control XB0562

description: Non-cancer control


title: Non-cancer control XB0548

description: Non-cancer control


title: Non-cancer control XB0565

description: Non-cancer control


title: Non-cancer control XB0503

description: Non-cancer control


title: Non-cancer control XB0518

description: Non-cancer control


title: Non-cancer control XB0502

description: Non-cancer control


title: Non-cancer control XB0531

description: Non-cancer control


title: Non-cancer control XB0495

description: Non-cancer control


title: Non-cancer control XB0729

description: Non-cancer control


title: Non-cancer control XB0473

description: Non-cancer control


title: Non-cancer control XB0489

description: Non-cancer control


title: Non-cancer control XB0478

description: Non-cancer control


title: Non-cancer control XB0462

description: Non-cancer control


title: Non-cancer control XB0609

description: Non-cancer control


title: Non-cancer control XB0798

description: Non-cancer control


title: Non-cancer control XB0391

description: Non-cancer control


title: Non-cancer control XB0412

description: Non-cancer control


title: Non-cancer control XB0369

description: Non-cancer control


title: Non-cancer control XB0343

description: Non-cancer control


title: Non-cancer control XB0422

description: Non-cancer control


title: Non-cancer control XB0317

description: Non-cancer control


title: Non-cancer control XB0318

description: Non-cancer control


title: Non-cancer control XB0342

description: Non-cancer control


title: Non-cancer control XB0361

description: Non-cancer control


title: Non-cancer control XB0218

description: Non-cancer control


title: Non-cancer control XB0219

description: Non-cancer control


title: Non-cancer control XB0180

description: Non-cancer control


title: Non-cancer control XB0283

description: Non-cancer control


title: Non-cancer control XB0175

description: Non-cancer control


title: Non-cancer control XB0126

description: Non-cancer control


title: Non-cancer control XB0176

description: Non-cancer control


title: Non-cancer control XB0106

description: Non-cancer control


title: Non-cancer control XB0134

description: Non-cancer control


title: Non-cancer control XB0107

description: Non-cancer control


title: Non-cancer control XB0145

description: Non-cancer control


title: Non-cancer control XB0141

description: Non-cancer control


title: Non-cancer control XB0101

description: Non-cancer control


title: Non-cancer control XB0105

description: Non-cancer control


title: Non-cancer control XB0100

description: Non-cancer control


title: Non-cancer control XB0098

description: Non-cancer control


title: Non-cancer control XB0093

description: Non-cancer control


title: Non-cancer control XB0138

description: Non-cancer control


title: Non-cancer control XB0193

description: Non-cancer control


title: Non-cancer control XB0269

description: Non-cancer control


title: Non-cancer control XB0080

description: Non-cancer control


title: Non-cancer control XB0082

description: Non-cancer control


title: Non-cancer control XB0075

description: Non-cancer control


title: Non-cancer control XB0072

description: Non-cancer control


title: Non-cancer control XB0063

description: Non-cancer control


title: Non-cancer control XB0062

description: Non-cancer control


title: Non-cancer control XB0064

description: Non-cancer control


title: Non-cancer control XB0032

description: Non-cancer control


title: Non-cancer control XB0005

description: Non-cancer control


title: Non-cancer control XB0038

description: Non-cancer control


title: Non-cancer control XB0053

description: Non-cancer control


title: Non-cancer control XB0013

description: Non-cancer control


title: Non-cancer control XB0018

description: Non-cancer control


title: Non-cancer control XA0992

description: Non-cancer control

value: Female


title: Non-cancer control XB0028

description: Non-cancer control


title: Non-cancer control XA0981

description: Non-cancer control


title: Non-cancer control XA0930

description: Non-cancer control


title: Non-cancer control XB0029

description: Non-cancer control


title: Non-cancer control XA0929

description: Non-cancer control


title: Non-cancer control XA0892

description: Non-cancer control


title: Non-cancer control XA0871

description: Non-cancer control


title: Non-cancer control XA0903

description: Non-cancer control


title: Non-cancer control XB0014

description: Non-cancer control


title: Non-cancer control XA0880

description: Non-cancer control


title: Non-cancer control XA0847

description: Non-cancer control


title: Non-cancer control XA0852

description: Non-cancer control


title: Non-cancer control XA0836

description: Non-cancer control


title: Non-cancer control XA0833

description: Non-cancer control


title: Non-cancer control XA0799

description: Non-cancer control


title: Non-cancer control XA0789

description: Non-cancer control


title: Non-cancer control XA0780

description: Non-cancer control


title: Non-cancer control XA0787

description: Non-cancer control


title: Non-cancer control XA0777

description: Non-cancer control


title: Non-cancer control XA0748

description: Non-cancer control


title: Non-cancer control XA0713

description: Non-cancer control


title: Non-cancer control XA0685

description: Non-cancer control


title: Non-cancer control XA0744

description: Non-cancer control


title: Non-cancer control XA0614

description: Non-cancer control


title: Non-cancer control XA0730

description: Non-cancer control


title: Non-cancer control XA0659

description: Non-cancer control


title: Non-cancer control XA0668

description: Non-cancer control


title: Non-cancer control XA0638

description: Non-cancer control


title: Non-cancer control XA0643

description: Non-cancer control


title: Non-cancer control XA0536

description: Non-cancer control


title: Non-cancer control XA0541

description: Non-cancer control


title: Non-cancer control XA0553

description: Non-cancer control


title: Non-cancer control XA0529

description: Non-cancer control


title: Non-cancer control XA0608

description: Non-cancer control


title: Non-cancer control XA0598

description: Non-cancer control


title: Non-cancer control XA0758

description: Non-cancer control


title: Non-cancer control XA0589

description: Non-cancer control


title: Non-cancer control XA0511

description: Non-cancer control


title: Non-cancer control XA0507

description: Non-cancer control


title: Non-cancer control XA0572

description: Non-cancer control


title: Non-cancer control XA0746

description: Non-cancer control


title: Non-cancer control XA0644

description: Non-cancer control


title: Non-cancer control XA0504

description: Non-cancer control


title: Non-cancer control XA0544

description: Non-cancer control


title: Non-cancer control XA0680

description: Non-cancer control


title: Non-cancer control XA0500

description: Non-cancer control


title: Non-cancer control XA0485

description: Non-cancer control


title: Non-cancer control XA0483

description: Non-cancer control


title: Non-cancer control XA0405

description: Non-cancer control


title: Non-cancer control XA0506

description: Non-cancer control


title: Non-cancer control XA0468

description: Non-cancer control


title: Non-cancer control XA0451

description: Non-cancer control


title: Non-cancer control XA0426

description: Non-cancer control


title: Non-cancer control XA0318

description: Non-cancer control


title: Non-cancer control XA0325

description: Non-cancer control


title: Non-cancer control XA0252

description: Non-cancer control


title: Non-cancer control XA0311

description: Non-cancer control


title: Non-cancer control XA0240

description: Non-cancer control


title: Non-cancer control XA0232

description: Non-cancer control


title: Non-cancer control XA0214

description: Non-cancer control


title: Non-cancer control XA0181

description: Non-cancer control


title: Non-cancer control XA0173

description: Non-cancer control


title: Non-cancer control XA0257

description: Non-cancer control


title: Non-cancer control XA0293

description: Non-cancer control


title: Non-cancer control XA0296

description: Non-cancer control


title: Non-cancer control XA0298

description: Non-cancer control


title: Non-cancer control XA0281

description: Non-cancer control


title: Non-cancer control XA0419

description: Non-cancer control


title: Non-cancer control XA0172

description: Non-cancer control


title: Non-cancer control XA0163

description: Non-cancer control


title: Non-cancer control XA0385

description: Non-cancer control


title: Non-cancer control XA0132

description: Non-cancer control


title: Non-cancer control XA0140

description: Non-cancer control


title: Non-cancer control XA0115

description: Non-cancer control


title: Non-cancer control XA0110

description: Non-cancer control


title: Non-cancer control XA0120

description: Non-cancer control


title: Non-cancer control XA0104

description: Non-cancer control


title: Non-cancer control XA0147

description: Non-cancer control


title: Benign bone and soft tissue disease SA0830

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0821

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0837

description: Benign bone and soft tissue disease


title: Non-cancer control XA0103

description: Non-cancer control


title: Non-cancer control XA0081

description: Non-cancer control


title: Benign bone and soft tissue disease SA0841

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0843

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0825

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0798

description: Benign bone and soft tissue disease


title: Non-cancer control XA0026

description: Non-cancer control


title: Benign bone and soft tissue disease SA0814

description: Benign bone and soft tissue disease


title: Non-cancer control XA0004

description: Non-cancer control


title: Benign bone and soft tissue disease SA0854

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0909

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0797

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0895

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0824

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0858

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0916

description: Benign bone and soft tissue disease


title: Non-cancer control XA0019

description: Non-cancer control


title: Benign bone and soft tissue disease SA0852

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0927

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0791

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0792

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0753

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0775

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0767

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0785

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0751

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0720

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0722

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0688

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0687

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0703

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0700

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0747

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0707

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0678

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0727

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0721

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0723

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0714

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0717

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0671

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0667

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0719

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0745

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0677

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0665

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0664

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0642

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0653

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0656

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0636

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0630

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0627

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0626

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0618

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0608

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0595

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0563

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0560

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0612

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0611

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0570

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0593

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0599

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0574

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0552

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0589

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0629

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0547

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0533

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0587

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0538

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0539

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0621

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0522

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0578

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0590

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0572

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0615

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0520

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0518

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0512

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0531

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0515

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0525

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0503

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0505

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0502

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0511

description: Benign bone and soft tissue disease


title: Non-cancer control XB0120

description: Non-cancer control


title: Benign bone and soft tissue disease SA0500

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0494

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0528

description: Benign bone and soft tissue disease


title: Benign prostate disease PR1259

description: Benign prostate disease


title: Benign prostate disease PR1228

description: Benign prostate disease


title: Benign bone and soft tissue disease SA0472

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0508

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0482

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0491

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0486

description: Benign bone and soft tissue disease


title: Benign prostate disease PR1225

description: Benign prostate disease


title: Benign bone and soft tissue disease SA0506

description: Benign bone and soft tissue disease


title: Benign bone and soft tissue disease SA0514

description: Benign bone and soft tissue disease


title: Benign prostate disease PR1195

description: Benign prostate disease


title: Benign prostate disease PR1198

description: Benign prostate disease


title: Benign prostate disease PR1240

description: Benign prostate disease


title: Benign prostate disease PR1219

description: Benign prostate disease


title: Benign prostate disease PR1231

description: Benign prostate disease


title: Benign prostate disease PR1182

description: Benign prostate disease


title: Benign prostate disease PR1147

description: Benign prostate disease


title: Benign prostate disease PR1152

description: Benign prostate disease


title: Benign prostate disease PR1153

description: Benign prostate disease


title: Benign prostate disease PR1179

description: Benign prostate disease


title: Benign prostate disease PR1144

description: Benign prostate disease


title: Benign prostate disease PR1171

description: Benign prostate disease


title: Benign prostate disease PR1183

description: Benign prostate disease


title: Benign prostate disease PR1151

description: Benign prostate disease


title: Benign prostate disease PR1256

description: Benign prostate disease


title: Benign prostate disease PR1107

description: Benign prostate disease


title: Benign prostate disease PR1139

description: Benign prostate disease


title: Benign prostate disease PR1094

description: Benign prostate disease


title: Benign prostate disease PR1114

description: Benign prostate disease


title: Benign prostate disease PR1129

description: Benign prostate disease


title: Benign prostate disease PR1121

description: Benign prostate disease


title: Benign prostate disease PR1093

description: Benign prostate disease


title: Benign prostate disease PR1103

description: Benign prostate disease


title: Benign prostate disease PR1138

description: Benign prostate disease


title: Benign prostate disease PR1135

description: Benign prostate disease


title: Benign prostate disease PR1130

description: Benign prostate disease


title: Benign prostate disease PR1098

description: Benign prostate disease


title: Benign prostate disease PR1085

description: Benign prostate disease


title: Benign prostate disease PR1091

description: Benign prostate disease


title: Benign prostate disease PR1084

description: Benign prostate disease


title: Benign prostate disease PR1099

description: Benign prostate disease


title: Benign prostate disease PR1145

description: Benign prostate disease


title: Benign prostate disease PR1054

description: Benign prostate disease


title: Benign prostate disease PR1083

description: Benign prostate disease


title: Benign ovarian disease OV0352

description: Benign ovarian disease


title: Benign ovarian disease OV0421

description: Benign ovarian disease


title: Benign prostate disease PR1064

description: Benign prostate disease


title: Benign bone and soft tissue disease SA0485

description: Benign bone and soft tissue disease


title: Benign ovarian disease OV0341

description: Benign ovarian disease


title: Benign ovarian disease OV0358

description: Benign ovarian disease


title: Benign ovarian disease OV0306

description: Benign ovarian disease


title: Benign ovarian disease OV0303

description: Benign ovarian disease


title: Benign prostate disease PR1046

description: Benign prostate disease


title: Benign ovarian disease OV0267

description: Benign ovarian disease


title: Benign ovarian disease OV0286

description: Benign ovarian disease


title: Benign ovarian disease OV0263

description: Benign ovarian disease


title: Benign ovarian disease OV0289

description: Benign ovarian disease


title: No Glioma (Schwannnoma) GL0300

description: No Glioma (Schwannnoma)


title: Brain meta GL0295

description: Brain meta


title: Brain meta GL0286

description: Brain meta


title: Brain meta GL0292

description: Brain meta


title: Glioma GL0287

description: Glioma


title: Brain meta GL0294

description: Brain meta


title: Glioma GL0293

description: Glioma


title: PCNSL GL0296

description: PCNSL


title: Glioma GL0299

description: Glioma


title: Glioma GL0290

description: Glioma


title: Brain meta GL0288

description: Brain meta


title: No Glioma (infarction) GL0297

description: No Glioma (infarction)


title: Glioma GL0291

description: Glioma


title: Glioma GL0285

description: Glioma


title: Benign ovarian disease OV0302

description: Benign ovarian disease


title: Glioma GL0279

description: Glioma


title: Brain meta GL0278

description: Brain meta


title: Brain meta GL0282

description: Brain meta


title: Brain meta GL0277

description: Brain meta


title: Glioma GL0283

description: Glioma


title: Brain meta GL0281

description: Brain meta


title: Glioma GL0280

description: Glioma


title: Brain meta GL0276

description: Brain meta


title: Brain meta GL0284

description: Brain meta


title: No Glioma (Hemangiopericytoma) GL0272

description: No Glioma (Hemangiopericytoma)


title: No Glioma (Schwannnoma) GL0273

description: No Glioma (Schwannnoma)


title: Glioma GL0275

description: Glioma


title: Glioma GL0268

description: Glioma


title: Glioma GL0269

description: Glioma


title: Glioma GL0266

description: Glioma


title: Brain meta GL0265

description: Brain meta


title: Glioma GL0260

description: Glioma


title: Glioma GL0259

description: Glioma


title: No Glioma (Meningioma) GL0254

description: No Glioma (Meningioma)


title: PCNSL GL0258

description: PCNSL


title: Brain meta GL0264

description: Brain meta


title: PCNSL GL0253

description: PCNSL


title: Brain meta GL0248

description: Brain meta


title: Brain meta GL0263

description: Brain meta


title: Glioma GL0247

description: Glioma


title: Brain meta GL0252

description: Brain meta


title: No Glioma (Meningioma) GL0271

description: No Glioma (Meningioma)


title: Brain meta GL0250

description: Brain meta


title: No Glioma (Schwannnoma) GL0274

description: No Glioma (Schwannnoma)


title: No Glioma (Trauma) GL0242

description: No Glioma (Trauma)


title: Brain meta GL0245

description: Brain meta


title: PCNSL GL0243

description: PCNSL


title: Glioma GL0238

description: Glioma


title: No Glioma (Hemangiopericytoma) GL0241

description: No Glioma (Hemangiopericytoma)


title: Brain meta GL0246

description: Brain meta


title: Brain meta GL0236

description: Brain meta


title: PCNSL GL0232

description: PCNSL


title: Brain meta GL0234

description: Brain meta


title: Brain meta GL0233

description: Brain meta


title: Glioma GL0235

description: Glioma


title: Glioma GL0227

description: Glioma


title: Brain meta GL0228

description: Brain meta


title: PCNSL GL0229

description: PCNSL


title: PCNSL GL0237

description: PCNSL


title: Brain meta GL0224

description: Brain meta


title: Brain meta GL0222

description: Brain meta


title: Brain meta GL0223

description: Brain meta


title: Glioma GL0221

description: Glioma


title: Meningioma GL0217

description: Meningioma


title: Brain meta GL0220

description: Brain meta


title: Meningioma GL0214

description: Meningioma


title: Meningioma GL0212

description: Meningioma


title: Meningioma GL0209

description: Meningioma


title: Meningioma GL0216

description: Meningioma


title: Meningioma GL0219

description: Meningioma


title: Meningioma GL0210

description: Meningioma


title: Meningioma GL0211

description: Meningioma


title: Meningioma GL0206

description: Meningioma


title: Meningioma GL0207

description: Meningioma


title: Meningioma GL0205

description: Meningioma


title: Meningioma GL0208

description: Meningioma


title: Brain meta GL0226

description: Brain meta


title: Meningioma GL0204

description: Meningioma


title: Meningioma GL0202

description: Meningioma


title: Meningioma GL0203

description: Meningioma


title: Meningioma GL0200

description: Meningioma


title: Glioma GL0196

description: Glioma


title: Glioma GL0198

description: Glioma


title: Meningioma GL0199

description: Meningioma


title: Glioma GL0195

description: Glioma


title: Glioma GL0191

description: Glioma


title: Glioma GL0193

description: Glioma


title: Glioma GL0192

description: Glioma


title: Glioma GL0188

description: Glioma


title: PCNSL GL0187

description: PCNSL


title: Glioma GL0189

description: Glioma


title: PCNSL GL0186

description: PCNSL


title: Glioma GL0185

description: Glioma


title: Glioma GL0183

description: Glioma


title: Glioma GL0180

description: Glioma


title: Glioma GL0184

description: Glioma


title: Glioma GL0182

description: Glioma


title: Glioma GL0181

description: Glioma


title: Glioma GL0194

description: Glioma


title: Glioma GL0178

description: Glioma


title: Glioma GL0179

description: Glioma


title: PCNSL GL0177

description: PCNSL


title: PCNSL GL0175

description: PCNSL


title: PCNSL GL0174

description: PCNSL


title: Glioma GL0173

description: Glioma


title: PCNSL GL0171

description: PCNSL


title: Glioma GL0172

description: Glioma


title: Glioma GL0167

description: Glioma


title: Glioma GL0169

description: Glioma


title: Glioma GL0166

description: Glioma


title: Glioma GL0163

description: Glioma


title: Glioma GL0176

description: Glioma


title: Glioma GL0162

description: Glioma


title: Glioma GL0159

description: Glioma


title: Glioma GL0160

description: Glioma


title: Glioma GL0170

description: Glioma


title: Glioma GL0157

description: Glioma


title: Glioma GL0156

description: Glioma


title: Glioma GL0158

description: Glioma


title: PCNSL GL0155

description: PCNSL


title: Glioma GL0152

description: Glioma


title: Glioma GL0151

description: Glioma


title: Glioma GL0153

description: Glioma


title: Glioma GL0154

description: Glioma


title: Glioma GL0150

description: Glioma


title: Glioma GL0165

description: Glioma


title: Glioma GL0147

description: Glioma


title: Glioma GL0146

description: Glioma


title: Glioma GL0161

description: Glioma


title: PCNSL GL0148

description: PCNSL


title: Glioma GL0149

description: Glioma


title: Glioma GL0144

description: Glioma


title: Glioma GL0140

description: Glioma


title: Glioma GL0141

description: Glioma


title: Glioma GL0142

description: Glioma


title: PCNSL GL0168

description: PCNSL


title: Glioma GL0139

description: Glioma


title: Glioma GL0138

description: Glioma


title: Glioma GL0136

description: Glioma


title: Glioma GL0137

description: Glioma


title: Glioma GL0135

description: Glioma


title: Glioma GL0134

description: Glioma


title: Glioma GL0143

description: Glioma


title: PCNSL GL0132

description: PCNSL


title: PCNSL GL0129

description: PCNSL


title: PCNSL GL0127

description: PCNSL


title: Glioma GL0130

description: Glioma


title: Glioma GL0128

description: Glioma


title: Glioma GL0125

description: Glioma


title: PCNSL GL0122

description: PCNSL


title: Glioma GL0120

description: Glioma


title: Glioma GL0126

description: Glioma


title: Glioma GL0124

description: Glioma


title: Glioma GL0121

description: Glioma


title: Glioma GL0133

description: Glioma


title: Glioma GL0113

description: Glioma


title: Glioma GL0114

description: Glioma


title: Glioma GL0119

description: Glioma


title: PCNSL GL0123

description: PCNSL


title: PCNSL GL0116

description: PCNSL


title: Glioma GL0115

description: Glioma


title: Glioma GL0131

description: Glioma


title: Glioma GL0112

description: Glioma


title: Glioma GL0110

description: Glioma


title: Glioma GL0117

description: Glioma


title: Glioma GL0109

description: Glioma


title: Glioma GL0108

description: Glioma


title: Glioma GL0256

description: Glioma


title: Glioma GL0106

description: Glioma


title: Glioma GL0107

description: Glioma


title: Glioma GL0118

description: Glioma


title: Glioma GL0105

description: Glioma


title: Glioma GL0249

description: Glioma


title: Glioma GL0104

description: Glioma


title: PCNSL GL0102

description: PCNSL


title: Glioma GL0103

description: Glioma


title: Glioma GL0101

description: Glioma


title: PCNSL GL0098

description: PCNSL


title: Glioma GL0087

description: Glioma


title: PCNSL GL0096

description: PCNSL


title: Glioma GL0085

description: Glioma


title: Glioma GL0089

description: Glioma


title: Glioma GL0092

description: Glioma


title: Glioma GL0097

description: Glioma


title: Glioma GL0088

description: Glioma


title: PCNSL GL0083

description: PCNSL


title: Glioma GL0086

description: Glioma


title: Glioma GL0100

description: Glioma


title: Glioma GL0094

description: Glioma


title: Glioma GL0082

description: Glioma


title: PCNSL GL0095

description: PCNSL


title: Glioma GL0091

description: Glioma


title: PCNSL GL0099

description: PCNSL


title: Glioma GL0084

description: Glioma


title: Glioma GL0081

description: Glioma


title: Glioma GL0079

description: Glioma


title: Glioma GL0078

description: Glioma


title: PCNSL GL0080

description: PCNSL


title: PCNSL GL0077

description: PCNSL


title: Glioma GL0076

description: Glioma


title: Glioma GL0090

description: Glioma


title: Glioma GL0145

description: Glioma


title: Glioma GL0073

description: Glioma


title: Glioma GL0074

description: Glioma


title: Glioma GL0070

description: Glioma


title: Glioma GL0071

description: Glioma


title: Glioma GL0072

description: Glioma


title: PCNSL GL0058

description: PCNSL


title: PCNSL GL0064

description: PCNSL


title: Glioma GL0062

description: Glioma


title: Glioma GL0068

description: Glioma


title: Glioma GL0054

description: Glioma


title: Glioma GL0055

description: Glioma


title: Glioma GL0059

description: Glioma


title: Glioma GL0069

description: Glioma


title: Glioma GL0061

description: Glioma


title: Glioma GL0060

description: Glioma


title: Glioma GL0075

description: Glioma


title: Glioma GL0066

description: Glioma


title: Glioma GL0057

description: Glioma


title: Glioma GL0052

description: Glioma


title: Glioma GL0056

description: Glioma


title: Glioma GL0065

description: Glioma


title: Glioma GL0053

description: Glioma


title: Glioma GL0048

description: Glioma


title: Glioma GL0049

description: Glioma


title: Glioma GL0047

description: Glioma


title: Glioma GL0067

description: Glioma


title: PCNSL GL0063

description: PCNSL


title: Glioma GL0046

description: Glioma


title: Glioma GL0051

description: Glioma


title: Glioma GL0038

description: Glioma


title: Glioma GL0042

description: Glioma


title: Glioma GL0037

description: Glioma


title: Glioma GL0040

description: Glioma


title: Glioma GL0039

description: Glioma


title: Glioma GL0036

description: Glioma


title: Glioma GL0044

description: Glioma


title: PCNSL GL0035

description: PCNSL


title: Glioma GL0033

description: Glioma


title: PCNSL GL0027

description: PCNSL


title: Glioma GL0026

description: Glioma


title: Glioma GL0030

description: Glioma


title: Glioma GL0029

description: Glioma


title: PCNSL GL0025

description: PCNSL


title: Glioma GL0022

description: Glioma


title: Glioma GL0019

description: Glioma


title: Glioma GL0015

description: Glioma


title: PCNSL GL0017

description: PCNSL


title: PCNSL GL0018

description: PCNSL


title: Glioma GL0014

description: Glioma


title: Glioma GL0013

description: Glioma


title: Glioma GL0031

description: Glioma


title: PCNSL GL0032

description: PCNSL


title: Glioma GL0012

description: Glioma


title: Glioma GL0023

description: Glioma


title: Glioma GL0011

description: Glioma


title: Glioma GL0009

description: Glioma


title: Glioma GL0034

description: Glioma


title: Benign breast disease BC1509

description: Benign breast disease


title: Glioma GL0003

description: Glioma


title: Glioma GL0004

description: Glioma


title: Glioma GL0005

description: Glioma


title: Glioma GL0020

description: Glioma


title: PCNSL GL0006

description: PCNSL


title: Benign breast disease BC1453

description: Benign breast disease


title: Benign breast disease BC1621

description: Benign breast disease


title: Benign breast disease BC1461

description: Benign breast disease


title: Benign breast disease BC1445

description: Benign breast disease


title: Benign breast disease BC1269

description: Benign breast disease


title: Benign breast disease BC1111

description: Benign breast disease


title: MMNK-1 control3

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

description: Total RNA was isolated from MMNK-1 cells and analyzed miRNA expression by microarray.

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: MMNK-1 control

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray, Kamakura, Japan)

growth_protocol: HuccT1 and MMNK-1 cells were obtained and cultured as recommended by the supplier.

extract_protocol: RNA samples were extracted from cells using miRNeasy mini kit (Qigen).

tag: disease state

value: non-malignant human cholangiocyte


title: PCNSL GL0008

description: PCNSL

tag: age


title: MMNK-1 control1


title: Benign breast disease BC0973

description: Benign breast disease


title: MMNK-1 control2


title: PCNSL GL0001

description: PCNSL


title: Y2: Yellow leaf

city: Yangzhou

first: Li

last: Wang

address: Wenhui east road no. 48

institute: Yangzhou University

data_processing:
Illumina Casava 1.8+ software used for basecalling.
Clean reads were obtained by removing contaminating reads, adapter sequences, poly-A tails and other artifacts.
Clean reads were mapped to the Ginkgo biloba genome database downloaded from GigaDB (http://gigadb.org/dataset/100209) using HISAT v2.0.4 software with default parameters.
The read counts for each gene was calculated by HTSeq v0.6.1.
Supplementary_files_format_and_content: The tab-delimited text file include gene ID and readcount for each sample (.txt)

organism: Ginkgo biloba

source_name: Yellow leaf

growth_protocol: Three Healthy adult G. biloba trees used in this study were grown under natural conditions at Dahongqiao, Guangling District, Yangzhou, China. In these trees, the leaves from three developmental stages (September 12, October 26, November 8) were sampled.

extract_protocol:
G. biloba leaves grown at three different stages (September 12; October 26; November 8), with significantly changed leaf coloration, were extracted using the MiniBEST Plant RNA Extraction Kit according to the protocol of the manufacturer.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: development stage

value: Senescence stage (November 8)

tag: tissue

value: leaves


title: VEC_pos_1

city: Uppsala

first: Elisabetta

last: Dejana

address: Dag Hammarskjolds väg 20

department: Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala University

description: ECs derived from murine embryonic stem cells with homozygous null mutation of the VEC gene, but with wild type form VEC  introduced by using retrovirus-mediated Transfer

data_processing:
Trim Galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was used for quality/adapter trimming of the raw reads. In addition, 5 nucleotides from both 5’ and 3’ end of the reads were clipped to remove unwanted bias.
Trimmed reads were mapped to the mm10 mouse genome with > 70% overall mapping rate using TopHat v2.1.1
Differential gene expression (DEG) analysis was performed using R package DESeq2 v1.14
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes DESeq2 normalized gene expression values from each sample

organism: Mus musculus

source_name: Endothelial cells

growth_protocol: cells were cultured at 37°C in a humidified atmosphere with 5% CO2

extract_protocol: SMARTer Stranded Total RNA Sample Prep kit - High input Mammalian kit (Clontech),

treatment_protocol: The wild type form of VEC was introduced in VEC-null cells using retrovirus-mediated transfer to generate VEC-positive cells

value: VEC-positive


title: VEC_null_1

description: ECs derived from murine embryonic stem cells with homozygous null mutation of the VEC gene

value: VEC-null


title: VEC_pos_3

value: ECs derived from murine embryonic stem cells


title: VEC_pos_2


title: Y1: Yellow leaf


title: VEC_null_3


title: Scid.adh.2c2_sgBcl11b_RNA-rep2

city: Isehara

first: Hiroyuki

last: Hosokawa

address: 143 Shimokasuya

department: Department of Immunology

institute: Tokai University School of Medicine

data_processing:
ChIP-seq data were mapped to the mouse genome build NCBI37/mm9 using Bowtie (v1.1.1; http://bowtie-bio.sourceforge.net/index.shtml) with “-v 3 -k 11 -m 10 -t --best –strata” settings and HOMER tagdirectories were created with makeTagDirectory and visualized in the UCSC-genome browser (http://genome.ucsc.edu) (Speir et al., 2016).  ChIP peaks were identified with findPeaks.pl against a matched control sample using the settings “-P .1 -LP .1 -poisson .1 -style factor”.  Peak reproducibility was determined by a HOMER adaptation of the IDR (Irreproducibility Discovery Rate) package according to ENCODE guidelines (https://sites.google.com/site/anshulkundaje/projects/idr).  Only reproducible high quality peaks, with a normalized peak score ≥ 15, were considered for further analysis.    RNA-sequenced reads were trimmed with Trimmomatic (v.033; http://www.usadellab.org/cms/?page=trimmomatic) (Bolger et al., 2014) for removal of adapter –and low quality sequences (settings: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36).  Resulting reads were then mapped onto the mouse genome build NCBI37/mm9 with STAR (v2.4.0) (Dobin et al., 2013) and post-processed with RSEM (v1.2.25; http://deweylab.github.io/RSEM/) (Li and Dewey, 2011) according to the settings in the ENCODE long-rna-seq-pipeline (https://github.com/ENCODE-DCC/long-rna-seq-pipeline/blob/master/DAC/STAR_RSEM.sh) with the minor modifications that settings “--output-genome-bam --sampling-for-bam” was added to rsem-calculate-expression. STAR and RSEM reference libraries were created from genome build NCBI37/mm9 together with the Ensembl gene model file Mus_musculus.NCBIM37.66.gtf.  The resulting bam-files were used to create HOMER (Heinz et al., 2010) tag directories (makeTagDirectory with –keepAll setting).  For analysis of statistical significance among differentially expressed genes the raw gene counts were derived from each tag directory with analyzeRepeats.pl with the –noadj -condenseGenes options followed by the getDiffExpression.pl command using EdgeR (v3.6.8; http://bioconductor.org/packages/release/bioc/html/edgeR.html) (Robinson et al., 2010).
Genome_build: mm9
Supplementary_files_format_and_content: Processed files include BED-files  All genomic coordinates are relative to mm9 mouse assembly.

source_name: Scid.adh.2c2 cells

growth_protocol: Scid.adh.2c2 cells (Dionne et al., 2005) were cultured in RPMI1640 with 10% fetal bovine serum (FBS, Sigma-Aldrich), sodium pyruvate (Gibco), non-essential amino acids (Gibco), Pen-Strep-Glutamine (Gibco) and 50 mM b-mercaptoethanol (Sigma-Aldrich).   An ILC2 cell line, ILC2/b6 (Zhang et al., 2017) was cultured in OP9 medium (a-MEM, 20% FBS, 50 mM b-mercaptoethanol, Pen-Step-Glutamine) supplemented with 10 ng/ml of IL-2, IL-7 and IL-33 (Pepro Tech Inc.).

extract_protocol:
ChIP-seq; Ten million of ILC2/b6 or Schd.adh.2c2 cells were fixed with 1 mg/ml DSG (Thermo Scientific) in PBS for 30 min at RT followed by additional 10 min with addition of formaldehyde up to 1%.  The reaction was quenched by addition of 1/10 volume of 0.125M glycine and the cells were washed with HBSS (Gibco).  Pelleted nucleus were dissolved in lysis buffer (0.5% SDS, 10 mM EDTA, 0.5 mM EGTA, 50 mM Tris-HCl (pH 8) and PIC) and sonicated on a Bioruptor (Diagenode) for 18 cycles of 30sec sonication followed by 30sec rest, with max power.  Five μg per 107 cells of anti-Bcl11b Abs (a mixture of A300-383A (Bethyl), A300-385A (Bethyl), ab18465 (Abcam) and 12120 (CST)), anti-Runx3 (kindly provided from Dr. Ditsa Levanon and Dr. Yoram Groner, Weizmann Institute of Science), anti-GATA3 (a mixture of sc-268, Santa Cruz and MAB26051, R&D) or anti-Runx1 (ab23980, Abcam) were hybridized to Dynabeads anti-Rabbit, Dynabeads anti-Mouse or Dynabeads Protein A/G (Invitrogen) and added to the diluted chromatin complex.  They were incubated over night at 4°C, then washed and eluted for 6hr at 65°C in ChIP elution buffer (20 mM Tris-HCl, pH 7.5, 5 mM EDTA 50 mM NaCl, 1% SDS, and 50 μg/ml proteinase K).  Precipitated chromatin fragments were cleaned up using Zymo ChIP DNA Clean & Concentrator.  ChIP-seq libraries were constructed using NEBNext ChIP-Seq Library Preparation Kit (E6240, NEB) and sequenced on Illumina HiSeq2500 in single read mode with the read length of 50 nt.
RNA-seq; Total RNA was isolated from 300,000 cells using an RNAeasy MicroKit (Qiagen).  Libraries were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina (E7530, NEB) from ~1 μg of total RNA following manufacturer’s instructions.  Libraries were sequenced on Illumina HiSeq2500 in single read mode with the read length of 50 nt.

value: Transduced with sgBcl11b-CFP


title: B6_gamma_delta_17_1

city: Paris

first: Marc

last: Delord

address: Hopital Saint-Louis, 1 avenue Claude Vellefaux

department: Recherche clinique

country: France

institute: Centre hospitalier de Versailles

description: Not relevant

hyb_protocol: Incubeted with rotation at 60 RPM for 16 hours at 45C

scan_protocol: Scanned with the Affymetrix® GeneChip Scanner 3000 7G using the Command Console software (Affymetrix®)

data_processing: Data summarized and normalized using the rma implemented in the oligo R package

label: Biotin

source_name: Gamma-delta cells

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix manual target preparation for genechip ®  whole transcript expression array.

growth_protocol: Not relevant

extract_protocol: Total RNA was extracted from frozen tissue samples using the RNeasy Mini Kit Plus protocol

treatment_protocol: Not relevant

tag: cell phenotype


title: Y3: Yellow leaf


title: M2: Turning stage leaf

source_name: Turning stage leaf

value: Turning stage (October 26)


title: M3: Turning stage leaf


title: Scid.adh.2c2_sgCont_RNA-rep2

value: Transduced with sgControl-CFP


title: B6_ROR_minus_1

description: Not relevant

source_name: ROR- cells


title: BALBC_iNKT_17_3

description: Not relevant

source_name: INKT-17 cells

value: BALBC


title: B6_iNKT_17_2

description: Not relevant


title: BALBC_iNKT_17_2

description: Not relevant


title: BALBC_ROR_minus_3

description: Not relevant


title: Glioma GL0111

description: Glioma


title: B6_iNKT_17_1

description: Not relevant


title: VEC_null_2


title: B6_gamma_delta_17_2

description: Not relevant


title: Scid.adh.2c2_sgCont_RNA-rep1


title: BALBC_ROR_minus_1

description: Not relevant


title: G3: Green leaf

source_name: Green leaf

value: Mature stage (September 12)


title: B6_ROR_minus_2

description: Not relevant


title: BALBC_ROR_minus_2

description: Not relevant


title: BALBC_iNKT_17_1

description: Not relevant


title: ILC2_sgCont_RNA-rep2

source_name: ILC2/b6 cells


title: ILC2_sgBcl11b_RNA-rep2


title: G1: Green leaf


title: BDE-47 treatment group

city: Yantai

first: Yan

last: Fang

state: Shandong

address: No. 186 Hongqizhong Road

department: agriculture college

institute: Ludong university

data_processing:
The original image data was transferred into sequence data by base calling(using CASAVA version 1.5+), (defined as ‘raw reads’) and saved as fastq files that include the detailed reads sequences and the reads quality information.
To obtain clean reads, it is necessary to remove the dirty raw reads prior to data analysis. This process encompasses the following procedures: (1) remove reads with adaptors; (2) remove reads in which unknown bases are greater than 10%; (3) remove low-quality reads (the percentage of the low quality bases of quality value ≤ 5 is more than 50% in a read).
De novo assembly of the transcriptome was carried out using Trinity (release-20120608), a short reads assembling program. Blastx was employed to give annotations of the obtained unigenes in NR, NT, Swiss-Prot, KEGG and COG databases. The sequence orientation of unigenes was determined on the best results. If the results from different databases conflicted, the priority order was NR, NT, Swiss-Prot, KEGG, and COG. The software tool ESTScan was used to determine sequence directionality as the unigene aligned to none of the above databases.
Unigene expression was calculated and normalized by FPKM method. The differentially expressed unigenes between control group and BDE-47 treatment group were analyzed by modified Audic’s method. Differently expressed genes were identified with False Discovery Rate (FDR)≤0.001 and absolute value of log2Ratio≥1.

organism: Mactra quadrangularis

source_name: digestive gland_BDE-47 treated

extract_protocol:
TRIzol reagent (Invitrogen, Carlsbad, CA, USA) was used to extract the total RNA of control and treatment samples following the manufacturer's protocol.
After RNase-free DNase treatment (Takara Biotechnology, China), the purity of total RNA was determined using an ultraviolet spectrophotometry, Thermo Scientific NanoDrop 8000. RNA concentration was measured using Qubit®RNA Assay Kit in Qubit®2.0Flurometer (Life Technologies, CA, USA). RNA integrity was checked using the RNA Nano 6000 Assay Kit of the Agilent 2100 Bioanalyzer (Agilent Technologies,CA, USA). cDNA library construction was performed at Beijing Genomics Institute (BGI, Shenzhen, China) using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA). Briefly, mRNA was separated from the total RNA using poly-T oligo-attached magnetic beads and then interrupted into small pieces. The short mRNA was reverse transcribed into first-strand cDNA using reverse transcriptase and random hexamer primers. Followed by adding dNTPs, Rnase H, and DNA polymerase I, second strand cDNA was synthesized with first-strand cDNA as the template. Then, the double stranded cDNA was purified with QiaQuick PCR extraction kit (Qiagen, Hilden, Germany), repaired the cohesive, and ligated with sequencing adaptors. After screening the target fragment with agarose gel electrophoresis, PCR amplification was performed using the recovered fragments as the template. The quality and output of cDNA library were tested by Agilent 2100 Bioanalyzer and ABI StepOnePlus Real-time PCR System. Afterwards, library sequencing was performed on an Illumina Hiseq 2000 platform.

tag: exposed to

value: BDE-47 for 3 days

value: digestive gland


title: Scid.adh.2c2_sgBcl11b_RNA-rep1


title: ILC2_sgCont_RNA-rep1


title: G2: Green leaf


title: ILC2_sgBcl11b_RNA-rep1


title: M1: Turning stage leaf


title: Control group

source_name: digestive gland_control

value: DMSO (control)


title: ILC2_DSG_1%input-rep2

library_source: genomic

molecule: genomic DNA

tag: chip (antibody)


title: ILC2_DSG_1%input-rep1


title: Scid.adh.2c2_DSG_1%input-rep2


title: etv2_homo_24h-2

city: Tampa

first: Saulius

last: Sumanas

address: 560 Channelside Dr

department: Department of Pathology and Cell Biology

institute: University of South Florida

data_processing:
Sequencing was performed at 20M PE-150 read depth by Novogene Inc
Alignment to the zebrafish genome was performed using Strand 3.0 software using default parameters.
Genome_build: Zv9
Supplementary_files_format_and_content: Excel files include triplicate samples from heterozygous or homozygous embryos at each stage. DESeq-normalized log-scaled RPKM values are provided

organism: Danio rerio

source_name: Whole embryos

growth_protocol: etv2^ci32Gt heterozygous and homozygous embryos were obtained from the incross of etv2^ci32Gt+/-; UAS:GFP carriers. Embryos were incubated at 28 C for 24 hpf stage and at 24 C for 15-somite stage.

extract_protocol:
Bulk RNA was purified using RNA-quous 4-PCR kit (ThermoFisher).
Library synthesis was performed using NEB Next Ultra RNA library Prep Kit by Novogene, Inc

treatment_protocol: 3 batches of heterozygous and homozygous embryos 15-20 embryos each were sorted based on GFP expression pattern and frozen on dry ice.

value: Whole embryos

tag: line allele

value: Homozygous

tag: embryo stage

value: 24 hpf


title: etv2_homo_24h-1


title: Scid.adh.2c2_DSG_1%input-rep1

tag: cell type


title: etv2_homo_24h-3


title: ILC2_aRunx3_ChIP-rep2

value: anti-Runx3 Ab (kindly provided from Dr. Ditsa Levanon and Dr. Yoram Groner, Weizmann Institute of Science)


title: ILC2_aRunx3_ChIP-rep1


title: etv2_het_24h-2

value: Heterozygous


title: 92Q_29wk_3mice_L2363

city: La Jolla

first: Theresa

last: Gaasterland

state: CA

address: 9600 Gilman Drive MS 0202

department: Scripps Institution of Oceanography

institute: University of California San Diego

description: SCA7 repeat length, 92 CAG (Q)

data_processing:
RNAseq: For each condition, combine 3 fastq files; reducing 12 files to 4 files (Unix "cat" command)
POOLED RNAseq: alignment to reference mm10 mouse genome (mm10 downloaded 8/21/2014; mapped with bowtie v0.12.7, up to 3 mismatches, 1 match site allowed)
POOLED RNAseq: sam output files converted to bam format (samtools view, sort, index commands; samtools 0.1.12a)
POOLED RNAseq: generated readcounts per sample, normalized by millions-of-reads-per-sample (cuffdiff v1.3.0)
POOLED RNAseq: extracted normalized readcounts for each sample into one table (boutique scripts)
POOLED RNAseq: set aside ncRNA, miRNA, rRNA genes, zero signal, low signal (boutique scripts)
POOLED RNAseq: calculated log2 ratios for pairwise comparisons: 12wk WTQ vs 92Q; 29wk WTQ vs 92Q (boutique scripts)
POOLED RNAseq: identified differential patterns, WTQ vs 98Q, across 2 time points (boutique scripts)
Genome_build: mm10 (downloaded 8/21/2014)
Supplementary_files_format_and_content: format: tab-separated txt; content: columns: geneID, normalized readcounts per pooled sample

source_name: cerebellum

growth_protocol: Standard mouse colony conditions

extract_protocol:
Total RNA from the cerebellum of fxSCA7 92Q mice and wild-type littermates aged 12 and 29 weeks (n=3 per group) was isolated using TRIzol (Life Technologies) and purified using an RNeasy kit (Qiagen).  Samples were then sent to BGI Americas for deep sequencing on the Illumina HiSeqTM 2000 system (50SE).
Illumina TruSeq for RNA

tag: genotype/variation

value: fxSCA7 92Q

tag: timepoint

value: 29 weeks

tag: pool

value: 3 mice


title: 92Q_29wk_3mice_L2361

description: SCA7 repeat length, 92 CAG (Q)


title: 92Q_29wk_3mice_L2312

description: SCA7 repeat length, 92 CAG (Q)


title: Scid.adh.2c2_aRunx3_ChIP-rep2


title: ILC2_aRunx1_ChIP-rep2

value: anti-Runx1 Ab (ab23980, Abcam)


title: 92Q_12wk_3mice_L2416

description: SCA7 repeat length, 92 CAG (Q)

value: 12 weeks


title: ILC2_aRunx1_ChIP-rep1


title: Scid.adh.2c2_aRunx1_ChIP-rep2


title: etv2_homo_15som-3

value: 15 somite


title: Scid.adh.2c2_aRunx3_ChIP-rep1


title: Scid.adh.2c2_aRunx1_ChIP-rep1


title: ILC2_aBcl11b_ChIP-rep2

value: anti-Bcl11b Ab (a mixture of A300-383A (Bethyl), A300-385A (Bethyl), ab18465 (Abcam) and 12120 (CST))


title: ILC2_aBcl11b_ChIP-rep1


title: etv2_het_24h-3


title: etv2_homo_15som-1


title: etv2_het_15som-3


title: ILC2_FA_1%input-rep2


title: etv2_het_15som-2


title: WTQ_29wk_3mice_L2362

description: SCA7 repeat length, normal

value: wild type


title: Scid.adh.2c2_aBcl11b_ChIP-rep1


title: Scid.adh.2c2_aBcl11b_ChIP-rep2


title: 92Q_12wk_3mice_L2413

description: SCA7 repeat length, 92 CAG (Q)


title: Scid.adh.2c2_FA_1%input-rep2


title: WTQ_29wk_3mice_L2359

description: SCA7 repeat length, normal


title: etv2_het_24h-1


title: ILC2_aGATA3_ChIP-rep2

value: anti-GATA3 Ab (a mixture of sc-268, Santa Cruz Biotechnology and MAB26051, R&D Systems)


title: ILC2_FA_1%input-rep1


title: WTQ_29wk_3mice_L2358

description: SCA7 repeat length, normal


title: ILC2_aGATA3_ChIP-rep1


title: etv2_homo_15som-2


title: Scid.adh.2c2_aGATA3_ChIP-rep2


title: SCNT_KDM5B_8C_replicate 3

city: Yangling

first: Chuan

last: Zhou

state: Shaanxi

address: 3 Taicheng Road

department: College of Veterinary Medicine

institute: Northwest A&F University

data_processing:
bcl2fastq2 Conversion software (v2.16) was used for basecalling with the parameters bcl2fastq2-v2.16/bin/bcl2fastq --input-dir <runfolder-dir>/Data/Intensities/BaseCalls/ --output-dir <output-dir> --use-bases-mask Y*,Y*,Y*,Y*
Noise reads were removed in raw reads followed as: 1) Remove reads with adaptors; 2) Remove reads in which unknown bases(N) are more than 10%; 3) Remove low quality reads (we define the low quality read as the percentage of base which quality is lesser than 20 is greater than 50% in a read).
The filtered reads were stored in FASTQ format and mapped with HISAT (v0.1.6-beta) to the bovine UMD3.1.1 reference genome with the parameters: --phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000.
We used StringTie (v1.0.4) to reconstruct transcripts, and used CuffCompare (v2.2.1) to compare reconstructed transcripts to reference annotation. We then selected  'u','i','o','j' class code types as novel transcripts, and used CPC (v0.9-r2) to predict coding potential of novel transcripts. Complete reference consisted of coding novel   transcripts and reference transcripts.
Clean reads were mapped to the complete reference using Bowtie2 (v2.2.5). Expression level of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments) using RSEM (v1.2.12).
Genome_build: UMD 3.1.1
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each transcript in different samples.

organism: Bos taurus

source_name: SCNT KDM5B eight-cell embryos

extract_protocol:
BFFs were digested with trypsin and washed three times with PBS. After centrifugation, the supernatant was discarded and the cell precifitate was stored at -80°C. Pools of 8 eight-cell embryos were washed in RNase-free PBS, then transferred into the lysis buffer immediately on ice. Samples were then centrifuged at 10000 rpm for 30 s at 4°C, and stored at -80°C.
Embryos for each sample were directly lysed and used for cDNA synthesis using SuperScript III (Thermo Fisher Scientific). cDNAs were amplified and fragmented with the NEBNext Ultra DNA Library Prep Kit (E7370, New England Biolabs) to construct  cDNA library. RNA sequencing was performed on the HiSeq4000 (Illumina) platform.

tag: breed

value: Holstein

tag: sample group

value: SCNT embryos

value: KDM5B overexpression

tag: tissue/cell type

value: eight-cell embryos


title: WTQ_12wk_3mice_L2415

description: SCA7 repeat length, normal


title: SCNT_KDM5B_8C_replicate 2


title: WTQ_12wk_3mice_L2410

description: SCA7 repeat length, normal


title: 92Q_12wk_3mice_L2412

description: SCA7 repeat length, 92 CAG (Q)