title: WTM1

description: Raw reads_Normalized_JKKIM

source_name: Wild type Male #1


title: MOLM-13, 6h stenodactylin, rep 3

status: Public on Mar 10 2020

type: RNA

city: Bologna

first: Daniele

last: Mercatelli

address: Via Irnerio 45

department: Pharmacy and Biotechnology

country: Italy

institute: University of Bologna

description: replicate 3

hyb_protocol: Biotin-labeled cRNA (750 ng) was hybridized to the The Illumina Sentrix BeadChip according to Manufacturer's instructions.

scan_protocol: Transcriptome analysis was performed using the Illumina iScan, which is based upon fluorescence detection of biotin-labeled cRNA following Manufacturer's instructions.

data_processing: Bead summary data was imported into GenomeStudio to remove control probes and to produce a text file containing the signal and detection p-values per probe for all samples. The text file was imported into J-Express Pro 2012 (http://jexpress.bioinfo.no), and signal intensity values were quantile normalized (Bolstad et al., 2003) and log2 transformed.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: MOLM-13 cell line

label_protocol: Using the Illumina TotalPrep RNA Amplification Kit (version 280508, Applied Biosystems/Ambion, USA), 300 ng of total RNA from each sample were reversely transcribed, amplified and Biotin-16-UTP–labeled.

growth_protocol: MOLM-13 cells were maintained in RPMI 1640 medium (Sigma-Aldrich Co., St Louis, MO, USA) containing 10% heat-inactivated fetal bovine serum (FBS), 2 mM L-glutamine, 100U/ml penicillin and 100 µg/ml streptomycin (Sigma-Aldrich), hereafter named complete medium. All the cultures were kept under standard incubation conditions (humidified atmosphere, 5 % CO2, 37 °C) and passed from two to three times a week to keep them in logarithmic growth phase.

extract_protocol: Total RNA was extracted using the RNeasy Plus Minikit (Qiagen, Germany), following manufacturer’s instructions

treatment_protocol: Cells were treated with stenodactylin 10-9M for 2, 4, and 6 hours.

tag: cell line

tag: treatment

value: treated with stenodactylin for 6 hours


title: validation - 9w - replicate 2

type: SRA

city: Huddinge

first: Simon

last: Joost

address: Blickagången 16

department: BioNut

country: Sweden

institute: Karolinska Institutet

library_source: transcriptomic

data_processing:
Main data: The 10x demux pipeline (now deprecated) was used to demultiplex the flowcells. Count data were subsequently generated using CellRanger(v1.1.0) pooling replicates from each time point. In particular, 5w replicates were pooled from lanes 1-3, while 9w replicates were pooled from lanes 4-6. Later during data analysis, it became apparent that data in 9w - replicate 3 (lane 6) was of low quality. Barcodes linked to this replicate were retroactively removed using the following file: assigned_barcodes.txt. Validation data: Count data was generated using CellRanger(v3.0.2)
Fastq files: Fastq files were demultiplexed using mkfastq included in CellRanger.
Genome_build: mm10
Supplementary_files_format_and_content: 'matrix_Xw.mtx':mtx file containing unnormalized count data; 'barcodes_Xw.tsv':list of single-cell barcodes corresponding to count matrix; 'genes_Xw.tsv':list of genes corresponding to count matrix. '10X_19_0XX_filtered_feature_bc_matrix.h5': h5 file containing gene x barcode count matrix (CellRanger filtered, unnormalised) of validation data.

organism: Mus musculus

source_name: Skin

extract_protocol:
After sacrifice, the back of the mice was shaved and the dorsal skin was isolated and floated on HBSS + 0.04% BSA. The skin was then cut into smaller pieces (around 1 mm in width) and incubated in 0.2% collagenase at 37°C for one hour. The partly digested skin was placed in a 70 µm cell strainer, smashed with a piston and rinsed three times with HBSS + 0.04% BSA. The flow-through was saved on ice, while the undigested tissue remaining in the cell strainer was incubated in 0.05% trypsin-EDTA for 15 minutes at 37°C. The trypsin-digested tissue was smashed once more and then passed through a 70 µm cell strainer. The flow-through of the collagenase digestion (containing mainly stromal cells) and the flow-through of the trypsin digestion (containing mainly epidermal cells) were pooled, spun down and subsequently filtered through a 40 µm cell strainer. The viability of the cell suspension was determined using trypan blue.
Single-cell cDNA libraries were prepared using the 10X Genomics Chromium Single Cell 3’ kit (main dataset: version1; validation dataset: version 3) according to the manufacturer’s instruction. The prepared libraries were sequenced on an Illumina HiSeq2500 (main dataset) or Illumina NovaSeq 6000 (validation dataset) respectively.

treatment_protocol: All experiments were performed on female C57BL/6 mice. The mice were fed ad libitum, and handled and housed under standard conditions in the animal facility of Karolinska University Hospital Huddinge. All mouse experiments were performed in accordance to Swedish legislation and approved by the Stockholm South Animal Ethics Committee. Mice were sacrificed by cervical dislocation either during second anagen at 5 weeks of age or during second telogen at 9 weeks of age. Single-cell transcriptomes from n = 3 anagen and n = 2 telogen mice were included in the final dataset (main dataset). In addition, a validation dataset from n = 3 anagen and n = 2 telogen mice was created.

tag: strain

tag: tissue

value: Skin

tag: time point

value: 9w - telogen


title: WTF4

city: Fayetteville

first: Jeong Hoon

last: Pan

state: Arkansas

address: 987 W. Maple St.

country: USA

institute: University of Arkansas

description: Raw reads_Normalized_JKKIM

data_processing:
Sequenced reads were performed quality assessment using FastQC.
Sequenced reads were then aligend to GRCm38.p5 reference genome using ArrayStar
Raw read counts then obtained from ArrayStar were then analyzed using JMP Genomics.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: Test files include raw read counts for each sample and a tab of raw read counts filtered for detected transcripts.

source_name: Wild type Female #4

extract_protocol:
Total RNA from liver tissues was isolated using the RNeasy Plus Mini Kit (Qiagen, Hilden, Germany) and then the quality of isolated RNA was first assessed using the conventional A260/280 ratio and A260/230 ratio measurement (SpectraMax i3x; Molecular Devices, Sunnyvale, CA, USA) which were all satisfactory. In addition, RNA Integrity Number (also known as RIN) was assessed using the RNA R6K assay for the Agilent 2200 TapeStation (Agilent Technology, Santa Clara, CA, USA) in which RINs ranged between 8.5 and 9.5 hence satisfactory.
Illumina TruSeq RNA Library Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.

value: Liver

tag: genotype

value: wild type

tag: Sex

value: Female


title: NoD_14569_30mM (SC.7)

city: Chicago

first: Michael

last: Grassi

state: IL

address: 1855 West Taylor Street

department: Department of Ophthalmology and Visual Sciences

institute: University of Illinois at Chicago

hyb_protocol: Hybridizationwas done to Illumina HT12v4 microarrays (Catalog number: 4393543)

scan_protocol: Scanned on an Illumina HiScan scanner

data_processing: Analysis of the gene expression data was performed as follows. For a given individual Si (i= 1,…,22) and gene Gk (k= 1,...,15591), we calculated ∆i,k= HGi,k - SGi,k, where ∆ is response to glucose RG, HG is gene expression in high glucose culture, and SG is gene expression in standard glucose culture. All replicate data was fit using a mixed model that accounted for the correlation between repeated measures within individuals. We built a design matrix using the model.matrix function, and accounted for correlation between biological triplicates using limma’s duplicatecorrelation function. A mixed linear model was then fit that incorporates this correlation and ∆i,k (where ∆ is response to glucose, RG = HGi,k - SGi,k) using the lmFit function. The analysis was performed using the R package limma

source_name: Lymphoblastoid cell line

label_protocol: Samples were processed using the Illumina™ TotalPrep™-96 RNA Amplification Kit (ThermoFisher 4393543)

growth_protocol: Lymphoblastoid cell lines were thawed and cultured in RPMI and 10% FBS until they reached over 85% cell viability. Cells were seeded in a T25 flask. Two replicates were performed per cell line. Cells were counted every day or every other day for five to ten days and recorded.

extract_protocol: Quality control from RNA extraction was performed using the Agilent bio-analyzer.

treatment_protocol: All lymphoblastoid cell lines were maintained in conventional lymphocyte cell culture conditions of RPMI 1640 with 10% FBS in a 25-cm2 cell culture flask. The cells were incubated at 370C in 5% CO2 and the media was changed twice each week. Prior to the experiments (below), lymphoblastoid cells following serum starvation were passaged for a minimum of one week in either standard (SG) RPMI 1640 (11mM glucose) or high glucose (HG) RPMI media (30mM glucose)

value: Lymphoblastoid cell line


title: validation - 5w - replicate 3

value: 5w - anagen


title: Input DNA

city: Rochester

first: jinlong

last: lu

state: NY

address: 213 Hutchinson Hall

institute: University of Rochester

library_source: genomic

data_processing:
Library strategy: ChIRP-Seq
Basecalls performed using CASAVA version
ChIRP retrived DNA-Seq reads were aligned to the mm9 genome assembly using Bowtie2 (version 2.2.2)  with the default parameters
Peaks of each sample were called using MACS v. 1.4.2
Genome_build: Genome_build: mm9
Supplementary_files_format_and_content: Supplementary_files_format_and_content: L1 RNA peaks called by MACS with default parameters; L1 and Malat1 ChIRP-seq signal

molecule: genomic DNA

source_name: E14 ES cells

growth_protocol: Cell culture: ESCs were maintained in strandard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1000 U/ml recombinant leukemia inhibitory factor (LIF, millipore).

extract_protocol:
ChIRP was done as described previously with the following modifications (Chu et al. 2011). First, 59 nt DNA probes were biotinylated through terminal transferase (New England Biolabs). Intensive crosslinking of cells was performed in the following sequence: two rounds of 3000J UV treatment on ice, 0.8% of formaldehyde (FMA) for 10 minutes, 2mM of DSP (Dithiobis [succinimidyl propionate]) for 30 minutes, and followed by 3.7% of FMA for 10 minutes at room temperature. Crosslinked cell pellets were lysed. Chromatin was fragmented into a range of 2 - 5 kb by sonication. Hybridization, washing and elution steps were performed as described previously, except that we included an additional stringent wash (0.1x SSC). After elution and reverse crosslinking, RNA was further extracted by TRIzol reagent (Life Technologies).
The library was constructed by library preparation modules (New England Biolabs) according to manufacturer's instructions. Briefly, ChIRP retrived RNA was fragmentated by NEBNext Magnesium RNA Fragmentation Module at 94 ℃ for 210 seconds. The fragementated RNA was reverse transcribed by SuperScript III First-Strand Synthesis System for RT-PCR kit (Life Technology), 2'nd strand was then synthesized by NEBNext mRNA Second Strand Synthesis Module , the end repair, dA-tailing and adaptor ligation were also following the instruments by respect module. the adaptor for the libary was sythersized from IDT with the first 7nt is "TCACGTT" as a barcode. After liagation, the DNA was amplified by primer 1.0 (AATGATACGGCGACCACCGAGATCTACAC, synthersized from IDT) and 2.0 (CAAGCAGAAGACGGCATACGAGAT, synthersized from IDT) for 15 cycles. After this, the product was further purified and size selected by Ampure XP beads (Beckman Coulter). The library was sequenced on the Genome Analyzer following the manufacturer's protocols.

value: E14 ES cells

tag: cell type

value: embryonic stem cells


title: MOLM-13, 6h stenodactylin, rep 1

description: replicate 1


title: Malat1 RNA ChIRP-seq


title: MOLM-13, 4h stenodactylin, rep 5

description: replicate 5

value: treated with stenodactylin for 4 hours


title: MOLM-13, 4h stenodactylin, rep 6

description: replicate 6


title: MOLM-13, 4h stenodactylin, rep 4

description: replicate 4


title: WTF1

description: Raw reads_Normalized_JKKIM

source_name: Wild type Female #1


title: KOF2

description: Raw reads_Normalized_JKKIM

source_name: Idh2-/- Female #2


title: P42_Retina_Ribo_rep2

city: Guangzhou

first: Hongwei

last: Wang

state: Guangdong

address: No 7 Jinsui Rd, Research Building, Rm 301

department: Zhongshan Ophthalmic Center

country: China

institute: Sun Yat-Sen University

description: ribosome protected RNA

data_processing:
Raw sequence reads were demultiplexed using CASAVA (version 1.8.2), and the 3'-end adapter was clipped using Cutadapt (version 1.8.1) (with the parameters '-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -match-read-wildcards -m 6').
Low-quality sequences were trimmed using Sickle (version 1.33) (with the parameters '-q 20').
The trimmed reads were filtered by length with the ranges [25, 34] for ribosome footprints and [20, 50] for mRNA.
The retained reads that mapped to reference mouse rRNA or tRNA were further removed. The remaining reads were then aligned to the mouse reference genome (download from GENCODE, Release M18: GRCm38.p6) using Tophat2 (version 2.0.14)] with the following command: ' tophat2 -g 20 -N 2 --transcriptome-index [index_file] -G [gtf_file] [fastq_file] -o [output_directory]'.
Only those uniquely mapped reads were extracted for gene expression determination. The total number of aligned count reads per gene was obtained using the Subread R package-featureCounts (version 1.6.2), and further converted to TPM value (Transcripts Per Kilobase Million).
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: Retina

extract_protocol:
Frozen tissue samples were lysed separately using 1 ml of mammalian lysis buffer (200 µl 5x Mammalian Polysome Buffer, 100 µl 10% Triton X-100, 10 µl DTT(100 mM), 10 µl DNase I (1U/µl), 2 µl Cycloheximide (50 mg/ml), 10 µl 10% NP-40 and 668 µl Nuclease-Free Water). After incubation for 20 min on ice, lysates were cleared by centrifugation at 10000 x g for 3 min at 4°C. Ribosomal RNA was depleted using the Ribo-Zero magnetic kit (Epicentre). Sequencing libraries of ribosome protected fragments were generated using ARTseqTM Ribosome Profiling Kit according to the manufacturer's instructions. Sequencing libraries of poly(A)+ RNA were generated using VAHTSTM mRNA-seq v2 Library Prep Kit for Illumina according to the manufacturer's instructions.
Sequencing libraries of ribosome protected fragments were generated using ARTseqTM Ribosome Profiling Kit (Epicentre, RPHMR12126) according to the manufacturer's instructions. And, sequencing libraries of poly(A)+ RNA were  generated using VAHTSTM mRNA-seq v2 Library Prep Kit for Illumina (Vazyme Biotech, NR601-01) according to the manufacturer's instructions.

value: Retina

tag: age

value: postnatal days 42


title: DwoC_25224_normal (SC.23)


title: P42_Lung_Ribo_rep1

description: ribosome protected RNA

source_name: Lung

value: Lung


title: P42_Liver_Ribo_rep2

description: ribosome protected RNA

source_name: Liver


title: P42_Liver_Ribo_rep1

description: ribosome protected RNA


title: validation - 5w - replicate 2


title: L1 RNA ChIRP-seq


title: P42_Kidney_Ribo_rep2

description: ribosome protected RNA

source_name: Kidney

value: Kidney


title: P42_Lung_Ribo_rep2

description: ribosome protected RNA


title: validation - 5w - replicate 1


title: MOLM-13, 2h stenodactylin, rep4

description: replicate 4

value: treated with stenodactylin for 2 hours


title: P42_Kidney_Ribo_rep1

description: ribosome protected RNA


title: MOLM-13, 4h stenodactylin, rep 1

description: replicate 1


title: MOLM-13, 2h stenodactylin, rep6

description: replicate 6


title: P42_Retina_mRNA_rep2

molecule: polyA RNA


title: P42_Brain_Ribo_rep1

description: ribosome protected RNA

source_name: Brain

value: Brain


title: P42_Heart_Ribo_rep1

description: ribosome protected RNA

source_name: Heart

value: Heart


title: P42_Lung_mRNA_rep2


title: P42_Retina_mRNA_rep1


title: P42_Brain_Ribo_rep2

description: ribosome protected RNA


title: MOLM-13, 4h stenodactylin, rep 2

description: replicate 2


title: P42_Lung_mRNA_rep1


title: P42_Retina_Ribo_rep1

description: ribosome protected RNA


title: P42_Kidney_mRNA_rep2


title: P42_Liver_mRNA_rep2


title: P42_Liver_mRNA_rep1


title: P42_Heart_mRNA_rep2


title: MOLM-13, 2h stenodactylin, rep5

description: replicate 5


title: MOLM-13, 2h stenodactylin, rep2

description: replicate 2


title: P42_Heart_mRNA_rep1


title: DwoC_25224_30mM (SC.17)


title: MOLM-13, Ctrl rep 5

description: replicate 5

value: untreated control


title: MOLM-13, 2h stenodactylin, rep1

description: replicate 1


title: P42_Brain_mRNA_rep1


title: MOLM-13, 2h stenodactylin, rep3

description: replicate 3


title: MOLM-13, Ctrl rep 4

description: replicate 4


title: pip5k1 pip5k2_Mock_7d_rep3

city: Wuhan

first: Qiang

last: Li

state: Saskatchewan

address: #1 Shizishan Street

institute: Huazhong Agricultural University

data_processing:
Trimming using Trimmomatics-0.32
Read mapping using STAR-2.4.0j
Alignment using StringTie-1.0.3
Raw counts using htseq-count-0.6.0
Differentially expression analysis using DESeq2 1.12.4
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited .csv files include normalized counts for each sample

organism: Arabidopsis thaliana

source_name: plant leaves

growth_protocol: Arabidopsis thaliana Col-0 wild type and pip5k1 pip5k2 plants were grown at 21 ℃ with a 16-h photoperiod of ~125 μE m-2s-1.

extract_protocol:
RNA samples were extracted using the Plant RNA Isolation Mini Kit (Agilent Technologies) according to the manufacturer’s protocol.
Thirty-six cDNA libraries were constructed using the TruSeq RNA Sample Preparation Kit v2 (Illumina) with three replicates for each sample.

treatment_protocol: Three to four week Arabidopsis Col-0 wild type and pip5k1 pip5k2 plants were inoculated with E. cichoracearum conidiospores. The leaves without or with Ec-inoculation at 2, 5 and 7 dpi were collected, flash frozen in liquid nitrogen, and stored at -80 ℃ until required.

value: leaves

tag: pathogen

value: 7 d

value: pip5k1 pip5k2 mutant


title: MOLM-13, Ctrl rep 6

description: replicate 6


title: MOLM-13, Ctrl rep 3

description: replicate 3


title: KO2

city: Chapel Hill

first: Jesse

last: Niehaus

state: NC

address: 116 Manning Drive, 7008B Mary Ellen Jones Building

department: Neuroscience Center

institute: University of North Carolina at Chapel Hill

data_processing:
We converted FASTQ files to BAM files,  barcode tagged,, quality-filtered, trimmed, polyA-trimmed, and converted back to FASTQ as previously described (Macosko et al, Cell, 2015; Loo et al, Nature Communications, 2019)
Reads were aligned to a mouse- (mm10)  human (hg19) hybrid genome using STAR before being exon-tagged as described previously (Macosko et al, Cell, 2015; Loo et al, Nature Communications 2019)
Bead synthesis errors were corrected as described previously (Shekhar et al, Cell, 2016; Loo et al. Nature Communications 2019).
UMIs were determine to be species specific if >90% of transcripts came from a single species. Resulting gene expression matricies for mouse-spsecific UMIs were combined for downstream analyses.
Genome_build: mm10
Supplementary_files_format_and_content: .txt files with rows pertaining to genes and columns pertaining to single cells.

source_name: Cortex from post-natal day 7

extract_protocol:
Single-cell suspensions were co-encapsulated in nanoliter sized droplets with barcoded beads via Dropseq.
cDNA was generated using Maxima H Minus reverse transcriptase and amplified (13 cycles) using KAPA HIFI master mix.
1ng of amplified libraries were multiplexed and tagged with illumina adapter sequences and further amplified using the Nextera XT library amplification kit.

value: Top1 f/f; NEX-cre +/-

value: Male


title: pip5k1 pip5k2_Mock_7d_rep2


title: KO1


title: Col_Mock_7d_rep2

value: Col-0 wild type


title: MOLM-13, Ctrl rep 1

description: replicate 1


title: Col_Mock_7d_rep3


title: Col_Mock_7d_rep1


title: WT2

value: Top1 f/f


title: P42_Kidney_mRNA_rep1

value: wild type


title: pip5k1 pip5k2_Mock_7d_rep1


title: WT1


title: pip5k1 pip5k2_Mock_5d_rep3

value: 5 d


title: P42_Brain_mRNA_rep2


title: pip5k1 pip5k2_Mock_5d_rep1


title: Col_Mock_5d_rep3


title: MOLM-13, Ctrl rep 2

description: replicate 2


title: Col_Mock_5d_rep2


title: pip5k1 pip5k2_Mock_2d_rep3

value: 2 d


title: pip5k1 pip5k2_Mock_2d_rep2


title: pip5k1 pip5k2_Mock_2d_rep1


title: Col_Mock_2d_rep3


title: P42_Heart_Ribo_rep2

description: ribosome protected RNA

value: postnatal days 42


title: Col_Mock_5d_rep1


title: pip5k1 pip5k2_Mock_5d_rep2


title: pip5k1 pip5k2_Ec_7dpi_rep3

value: Erysiphe cichoracearum

value: 7 dpi


title: Col_Ec_7dpi_rep2


title: Col_Mock_2d_rep1


title: pip5k1 pip5k2_Ec_7dpi_rep2


title: Col_Mock_2d_rep2


title: DEN_18wk_water_237

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

hyb_protocol: Refer to the Illumina System Manual

scan_protocol: Refer to the Illumina System Manual

data_processing: Raw scan data were normalized with the use of cubic spline algorithm implemented in Illumina Normalizer module of GenePattern software (www.broadinstitute.org/genepattern).

organism: Rattus norvegicus

label_protocol: Refer to the Illumina System Manual

extract_protocol: Using frozen non-tumor liver tissues, total RNA was extracted using TRIzol (Invitrogen).

treatment_protocol: Animals received humane care according to the criteria outlined in the “Guide for the Care and Use of Laboratory Animals” of the National Academy of Sciences. All animals were maintained in accordance with the institutional guidelines of the Massachusetts General Hospital Subcommittee on Research Animal Care. Male Wistar rats received weekly IP injections of diethylnitrosamine (DEN) at 50 mg/kg for 18 weeks. A subset of rats received either daily (5X a week) 0.02% EGCG in drinking water (n=3) or water (n=3) during weeks 13-18. Animals were sacrificed at 19 weeks after a one-week washout period to eliminate acute effects of DEN. At the time of sacrifice, the non-tumor liver tissues were collected in RNase-free tubes and snap-frozen in liquid nitrogen. Frozen tissues were stored at -80°C until RNA extraction.

value: Wistar

tag: tissue type

value: liver

value: water


title: CFT073 delta Fur delta RyhB RNA Replicate 3

city: Madison

first: Kevin

middle: S

last: Myers

state: WI

address: 5127 WEI, 1552 University Ave

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin - Madison

data_processing:
For RNA-seq analysis. The reads from NGS were mapped to the complete CFT073 genome (NC004431.1) with the bwa-mem program (version 0.7.12) using default settings. The mapped reads in SAM file format were converted to BAM file format using SAMtools. An average of 10% of reads from each dataset did not align to the CFT073 genome and were removed. For visualization purposes the aligned BAM files were converted to WIG files using QuEST (version 1.2) and viewed in the MochiView genome browser.  Differentially expressed genes were assigned to regulons using the regulatory information present in EcoCyc for E. coli K12 and ASAP. The transcript expression levels for all CFT073 genes were estimated using the software package RSEM (version 1.3.0) using the bowtie2 aligner to map reads against the set of all predicted CFT073 transcripts downloaded from the ASAP database. The expected read counts generated with RSEM for all 3 replicates were used as an input for the DEseq2 software package  using the default settings on the RNA-seq 2G server (http://52.90.192.24:3838/rnaseq2g) to obtain the relative fold change of mutant versus wild-type transcript levels and the statistical significance of the changes for each gene. Genes which showed greater than 2.0-fold change in expression with FDR < 0.05 were labeled as differentially expressed genes in our analysi.
Genome_build: NC_004431.1
Supplementary_files_format_and_content: RNA-seq processed data are normalized read counts.

organism: Escherichia coli CFT073

source_name: DFurDRyhB Replicate 3 Total RNA isolated from total cultures grown to OD600 of 0.25.

growth_protocol: Total RNA was isolated from CFT073∆fur∆ryhB (WAM5499) strain replicate 1 grown anaerobically in MOPS minimal media supplemented with 0.2% glucose sparged with a gas mix of 95% N2 and 5% CO2 until an OD600nm of 0.25.

extract_protocol:
RNA was extracted by adding 10 mL of cultures at OD 600nm=0.25  to 1.25 mL Stop Solution (5% water saturated phenol and 95% ethanol).Cells are spun at 9000 rpm for 5 min at 4°C, the liquid is removed and the pellet were resuspended in TE, lysozyme and 10% SDS and heated at 65°C for 2 minutes. Sodium acetate was added and the sample was added to an equal volume of phenol at 65°C and incubated for 6 min with agitation every 40 seconds. Samples were spun at 14,000 rpm at 4°C and the aqueous layer was transferred to equal volume of chloroform. Samples were spunat 14,000 rpm at 4°C and the aqueous layer was transferred to 1/10 volume sodium acetate and 2 volumes ethanol for ethanol precipitation. Dried pellets were resuspended in 200 μL DEPC treated H2O and incubated with DNAse I (2 U) at 37°C for 30 minutes. DNAse I was inactivated  with using equal volumes of phenol and/or chloroform in a phenol extraction, a phenol/chloroform extraction and two chloroform extractions, followed by ethanol precipitation. RNA was resuspended in 50 μL DEPC-treated H2O.
Strand–specific RNA-sequencing libraries were prepared using NEBNext Ultra RNA Library Prep Kit (NEB, Ipswich, MA, USA) as per manufacturer’s instruction. Briefly, enriched RNAs were fragmented for 15 minutes at 94°C. First and second strands of cDNA were sequentially synthesized, end repaired, adenylated at 3’ ends and universal adapters were ligated, followed by index addition and library enrichment with limited cycle PCR. Sequencing libraries were validated using the Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (Applied Biosystems, Carlsbad, CA, USA) using the adaptor sequences as primers. The sequencing libraries were multiplexed and clustered on one lane of a flow cell. After clustering, the flow cell was loaded on the Illumina HiSeq instrument as per manufacturer’s instructions. The samples were sequenced using a 2x150 Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq were converted into fastq.gz files and de-multiplexed using Illumina's bcl2fastq.gz 2.17 software. One mismatch was allowed for index sequence identification. Library generation and sequencing was conducted at Genewiz (NJ, USA).

treatment_protocol: Depletion of rRNA was performed using Ribozero rRNA removal kit (Bacteria probe) (Illumina, San Diego, CA, USA).

value: Bacterial Culture

tag: media

value: MOPS minimal media (pH 7.4) 0.2% glucose

tag: oxygen

value: Anaerobic


title: pip5k1 pip5k2_Ec_5dpi_rep3

value: leaves

value: 5 dpi

value: pip5k1 pip5k2 mutant


title: pip5k1 pip5k2_Ec_5dpi_rep1


title: DEN_18wk_water_224


title: pip5k1 pip5k2_Ec_5dpi_rep2


title: CFT073 delta Fur delta RyhB RNA Replicate 1

source_name: DFurDRyhB Replicate 1 Total RNA isolated from total cultures grown to OD600 of 0.25.


title: DEN_18wk_EGCG_236

value: EGCG


title: CFT073 delta RyhB RNA Replicate 3

source_name: DRyhB Replicate 3 Total RNA isolated from total cultures grown to OD600 of 0.25.

growth_protocol: Total RNA was isolated  CFT073 CFT073∆ryhB (WAM 5497)  strain replicate 3 grown anaerobically in MOPS minimal media supplemented with 0.2% glucose sparged with a gas mix of 95% N2 and 5% CO2 until an OD600nm of 0.25.


title: Col_Ec_5dpi_rep3

value: Col-0 wild type


title: DEN_18wk_EGCG_234


title: CFT073 delta Fur delta RyhB RNA Replicate 2

source_name: DFurDRyhB Replicate 2 Total RNA isolated from total cultures grown to OD600 of 0.25.


title: Col_Ec_5dpi_rep1


title: Col_Ec_5dpi_rep2


title: CFT073 delta RyhB RNA Replicate 2

source_name: DRyhB Replicate 2 Total RNA isolated from total cultures grown to OD600 of 0.25.

growth_protocol: Total RNA was isolated  CFT073 CFT073∆ryhB (WAM 5497)  strain replicate 2 grown anaerobically in MOPS minimal media supplemented with 0.2% glucose sparged with a gas mix of 95% N2 and 5% CO2 until an OD600nm of 0.25.


title: DEN_18wk_water_227


title: pip5k1 pip5k2_Ec_2dpi_rep2

value: 2 dpi


title: pip5k1 pip5k2_Ec_7dpi_rep1


title: Col_Ec_7dpi_rep3


title: pip5k1 pip5k2_Ec_2dpi_rep3


title: Col_Ec_7dpi_rep1


title: pip5k1 pip5k2_Ec_2dpi_rep1


title: Col_Ec_2dpi_rep2


title: Col_Ec_2dpi_rep3


title: Col_Ec_2dpi_rep1


title: CFT073 delta Fur RNA Replicate 3

source_name: DFur Replicate 3 Total RNA isolated from total cultures grown to OD600 of 0.25.

growth_protocol: Total RNA was isolated from CFT073 CFT073∆fur (WAM 5491)  strain replicate 3 grown anaerobically in MOPS minimal media supplemented with 0.2% glucose sparged with a gas mix of 95% N2 and 5% CO2 until an OD600nm of 0.25.


title: CFT073 WT RNA Replicate 3

source_name: WT Replicate 3 Total RNA isolated from total cultures grown to OD600 of 0.25.

growth_protocol: Total RNA was isolated from CFT073 wild-type (WAM 4505) strain replicate 3 grown anaerobically in MOPS minimal media supplemented with 0.2% glucose sparged with a gas mix of 95% N2 and 5% CO2 until an OD600nm of 0.25.


title: CFT073 WT RNA Replicate 2

source_name: WT Replicate 2 Total RNA isolated from total cultures grown to OD600 of 0.25.

growth_protocol: Total RNA was isolated from CFT073 wild-type (WAM 4505) strain replicate 2 grown anaerobically in MOPS minimal media supplemented with 0.2% glucose sparged with a gas mix of 95% N2 and 5% CO2 until an OD600nm of 0.25.


title: DEN_18wk_EGCG_228


title: CPT ActD time-course 2h rep2

city: San Francisco

first: Binyamin

last: Zuckerman

state: California

institute: UCSF

description: total RNA, poly(A) enriched

data_processing:
MARS-seq Raw data was processed using UTAP (Kohen et al. 2019) with default parameters.
Corrected counts of control samples were normalized by Renilla mRNA spike, which was counted using Bowtie2 (Langmead et al., 2009).
Corrected counts of CPT-treated samples were normalized by mouse PolyA+ enriched RNA, which was mapped to mouse genome using STAR (Dobin et al. 2013) not allowing mismatches. Percent of uniquely mapped reads per sample was used as normalization factor.
Biological replicates were averaged and means were used for fitting a nonlinear least-squares model assuming first-order decay kinetics, while corrected counts at t=0 were used as C0 and inverse of standard errors of the corrected count means were used as weights for fitting. Half lives of all genes were then calculated. Genes with mean corrected read count < 5 at t=0 were removed from subsequent analysis. Negative half life values and half lives > 24h were set to 24h.
RNA-seq analysis: Since mouse PolyA+ enriched RNA was used for normalization, reads were first mapped to mouse genome (mm9) using STAR and unmapped reads from this step were remapped to the human genome (hg19 assembly). For normalization, reads were mapped separately to the mouse genome not allowing mismatches and percent of uniquely mapped reads per sample was used as normalization factor. Gene expression levels were quantified using RSEM (Li and Dewey, 2011) and Bowtie2. GENCODE v26 annotations were used for this and all subsequent analysis, with all histone genes removed from annotation. TPM values were normalized by mouse normalization factors and filtered by a minimal value of 1 TPM. Means of the two replicates were used for subsequent analysis.
Genome_build: hg19; GENCODE v26 annotation was used for this analysis.
Supplementary_files_format_and_content: An Excel spreadsheet including calculated half-life values measured in hours (using MARS-seq data) and abundance measurements estimating transcription levels gene-level TPM values obtained by RSEM quantification of the data for each gene  (using RNA-seq data).

source_name: MCF7 cell line

growth_protocol: cells were grown in DMEM media (Gibco) supplemented with 10% bovine serum and 1% penicillin/streptomycin (Gibco) in 5%CO2-buffered incubators at 37 degrees.

extract_protocol: TRIZOL and Direct-zol RNA MiniPrep kit (Zymo research). Followed MARS-seq protocol: https://www.ncbi.nlm.nih.gov/pubmed/31101904

treatment_protocol: CPT 6uM, 24 hours

tag: protocol

value: MARS-seq (applied to bulk cells)


title: CPT ActD time-course 4h rep2

description: total RNA, poly(A) enriched


title: CFT073 delta Fur RNA Replicate 1

source_name: DFur Replicate 1 Total RNA isolated from total cultures grown to OD600 of 0.25.

growth_protocol: Total RNA was isolated from  CFT073 CFT073∆fur (WAM 5491)  strain replicate 1 grown anaerobically in MOPS minimal media supplemented with 0.2% glucose sparged with a gas mix of 95% N2 and 5% CO2 until an OD600nm of 0.25.


title: CPT ActD time-course 6h rep2

description: total RNA, poly(A) enriched


title: CPT ActD time-course 6h rep1

description: total RNA, poly(A) enriched


title: CPT ActD time-course 0h rep2

description: total RNA, poly(A) enriched


title: CPT ActD time-course 2h rep1

description: total RNA, poly(A) enriched


title: ActD time-course 6h rep3

description: total RNA, poly(A) enriched


title: CPT ActD time-course 4h rep1

description: total RNA, poly(A) enriched


title: ActD time-course 6h rep2

description: total RNA, poly(A) enriched


title: CPT ActD time-course 0h rep1

description: total RNA, poly(A) enriched


title: ActD time-course 6h rep1

description: total RNA, poly(A) enriched


title: CFT073 deltaFUR ChIP-seq INPUT Replicate 1

description: DFur Replicate 1 Input DNA isolated from total cultures grown to OD600 of 0.25 after formaldehyde crosslinking.

data_processing:
For ChIP-seq analysis.  ChIP-seq sequence reads of low quality were removed from each file using Trimmomatic (version 0.30) using standard settings. Furthermore, the first and last five bases from each read were trimmed to remove the locations with the lowest average quality scores. This removed between 0.1% and 2.6% of reads. Filtered sequence reads were aligned to the published E. coli CFT073 genome (NC_004431.1) using the software package Bowtie 2 (version 2.2.2), using default settings. Sequence reads that didn’t align to the CFT073 genome at all or were aligned to more than one location were eliminated (an average of 15% of reads were removed). Areas of Fur enrichment were identified using MOSAiCS (version 1.6.0) with peaks with an FDR < 0.05 being included as significant. For visualization, aligned BAM files were converted into WIG files using QuEST (version 1.2) using standard settings. All WIG files were visualized in MochiView. For identification of Fur ChIP-seq peaks in the promoters of genes, a cut-off of 19.5 was selected for peak summit height.
Genome_build: NC_004431.1
Supplementary_files_format_and_content: RNA-seq processed data are RPKM normalized read counts. ChIP-seq processed data are in WIG format.

source_name: Bacterial Culture

growth_protocol: CFT073 ∆fur (WAM 5491) strain replicate 1 was grown in a MOPS minimal medium (pH 7.4) supplemented with 0.2% glucose, which contains 10.0 μM FeSO4, an amount considered iron sufficient.  Anaerobic growthof cultures was achieved by sparging cells with a gas mix containing 95% N2 and 5% CO2. Optical density (OD600nm) was measured in a Perkin Elmer Lambda 25 UV/Vis spectrophotometer.

extract_protocol:
Cells were harvested at 7500 rpm for 10 min at 4°C followed by sonication using a water bath sonicator (Misonix) to shear the DNA to a fragment size of 150-400bp to facilitate library production. The cell lysate was incubated with antibody specific to Fur that was affinity purified over His6-Fur bound HiTrap N-hydroxy-succinimide (NHS)-activated high performance (HP) column (GE Healthcare) (72). DNA was reversed crosslinked and eluted from the DNA-protein complex using 50mM Tris pH 8.0, 10mM EDTA, 1% SDS.
Ten ng of purified input was used to construct DNA libraries as described in the Illumina TruSeq ChIP preparation kit (IP-202-1012), except the products of ligation reactions were purified using 2% size select agarose gel (Invitrogen). After library construction and amplification, quantity and quality were validated using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) and Agilent 2100 Bioanalyzer before submitting them to University of Wisconsin-Madison DNA Sequencing facility for Illumina sequencing (Illumina HiSeq 2500) for single end 1X50bp reads, as per manufacturer recommendations.

treatment_protocol: . Cellular DNA was crosslinked to proteins by addition of 1% formaldehyde


title: CFT073 delta RyhB RNA Replicate 1

source_name: DRyhB Replicate 1 Total RNA isolated from total cultures grown to OD600 of 0.25.

growth_protocol: Total RNA was isolated  CFT073 CFT073∆ryhB (WAM 5497)  strain replicate 1 grown anaerobically in MOPS minimal media supplemented with 0.2% glucose sparged with a gas mix of 95% N2 and 5% CO2 until an OD600nm of 0.25.


title: CFT073 WT ChIP-seq INPUT Replicate 2

description: WT Replicate 2 Input DNA isolated from total cultures grown to OD600 of 0.25 after formaldehyde crosslinking.

growth_protocol: CFT073 wild-type (WAM 4505) strain replicate 2 was grown in a MOPS minimal medium (pH 7.4) supplemented with 0.2% glucose, which contains 10.0 μM FeSO4, an amount considered iron sufficient.  Anaerobic growthof cultures was achieved by sparging cells with a gas mix containing 95% N2 and 5% CO2. Optical density (OD600nm) was measured in a Perkin Elmer Lambda 25 UV/Vis spectrophotometer.


title: CFT073 WT CHIP-seq INPUT Replicate 1

description: WT Replicate 1 Input DNA isolated from total cultures grown to OD600 of 0.25 after formaldehyde crosslinking.

growth_protocol: CFT073 wild-type (WAM 4505) strain replicate 1 was grown in a MOPS minimal medium (pH 7.4) supplemented with 0.2% glucose, which contains 10.0 μM FeSO4, an amount considered iron sufficient.  Anaerobic growthof cultures was achieved by sparging cells with a gas mix containing 95% N2 and 5% CO2. Optical density (OD600nm) was measured in a Perkin Elmer Lambda 25 UV/Vis spectrophotometer.


title: CFT073 delta Fur RNA Replicate 2

source_name: DFur Replicate 2 Total RNA isolated from total cultures grown to OD600 of 0.25.

growth_protocol: Total RNA was isolated from CFT073 CFT073∆fur (WAM 5491)  strain replicate 2 grown anaerobically in MOPS minimal media supplemented with 0.2% glucose sparged with a gas mix of 95% N2 and 5% CO2 until an OD600nm of 0.25.


title: ActD time-course 4h rep3

description: total RNA, poly(A) enriched


title: ActD time-course 4h rep1

description: total RNA, poly(A) enriched


title: ActD time-course 4h rep2

description: total RNA, poly(A) enriched


title: CFT073 deltaFUR ChIP-seq Replicate 2

description: DFur Replicate 2 ChIP DNA isolated from total cultures grown to OD600 of 0.25 after formaldehyde crosslinking.

growth_protocol: CFT073 ∆fur (WAM 5491) strain replicate 2 was grown in a MOPS minimal medium (pH 7.4) supplemented with 0.2% glucose, which contains 10.0 μM FeSO4, an amount considered iron sufficient.  Anaerobic growthof cultures was achieved by sparging cells with a gas mix containing 95% N2 and 5% CO2. Optical density (OD600nm) was measured in a Perkin Elmer Lambda 25 UV/Vis spectrophotometer.

extract_protocol:
Cells were harvested at 7500 rpm for 10 min at 4°C followed by sonication using a water bath sonicator (Misonix) to shear the DNA to a fragment size of 150-400bp to facilitate library production. The cell lysate was incubated with antibody specific to Fur that was affinity purified over His6-Fur bound HiTrap N-hydroxy-succinimide (NHS)-activated high performance (HP) column (GE Healthcare) (72). DNA was reversed crosslinked and eluted from the DNA-protein complex using 50mM Tris pH 8.0, 10mM EDTA, 1% SDS.
Ten ng of purified  IP DNA was used to construct DNA libraries as described in the Illumina TruSeq ChIP preparation kit (IP-202-1012), except the products of ligation reactions were purified using 2% size select agarose gel (Invitrogen). After library construction and amplification, quantity and quality were validated using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) and Agilent 2100 Bioanalyzer before submitting them to University of Wisconsin-Madison DNA Sequencing facility for Illumina sequencing (Illumina HiSeq 2500) for single end 1X50bp reads, as per manufacturer recommendations.


title: ActD time-course 2h rep3

description: total RNA, poly(A) enriched


title: ActD time-course 2h rep2

description: total RNA, poly(A) enriched


title: CFT073 deltaFUR ChIP-seq Replicate 1

description: DFur Replicate 1 ChIP DNA isolated from total cultures grown to OD600 of 0.25 after formaldehyde crosslinking.


title: ActD time-course 0h rep3

description: total RNA, poly(A) enriched


title: ActD time-course 0h rep2

description: total RNA, poly(A) enriched


title: CFT073 FUR ChIP-seq Replicate 2

description: WT Replicate 2 ChIP DNA isolated from total cultures grown to OD600 of 0.25 after formaldehyde crosslinking.


title: ActD time-course 0h rep1

description: total RNA, poly(A) enriched


title: MOLM-13, 4h stenodactylin, rep 3

description: replicate 3

source_name: MOLM-13 cell line

growth_protocol: MOLM-13 cells were maintained in RPMI 1640 medium (Sigma-Aldrich Co., St Louis, MO, USA) containing 10% heat-inactivated fetal bovine serum (FBS), 2 mM L-glutamine, 100U/ml penicillin and 100 µg/ml streptomycin (Sigma-Aldrich), hereafter named complete medium. All the cultures were kept under standard incubation conditions (humidified atmosphere, 5 % CO2, 37 °C) and passed from two to three times a week to keep them in logarithmic growth phase.

value: treated with stenodactylin for 4 hours


title: transcription 4sU labeling RNAseq 2

description: 4sU-labeled, rRNA-depleted total RNA

extract_protocol: TRIZOL and Direct-zol RNA MiniPrep kit (Zymo research).

value: Lexogen SENSE Total RNA-seq kit; single-end 100-bp library


title: transcription 4sU labeling RNAseq 1

description: 4sU-labeled, rRNA-depleted total RNA


title: CFT073 WT RNA Replicate 1

source_name: WT Replicate 1 Total RNA isolated from total cultures grown to OD600 of 0.25.

growth_protocol: Total RNA was isolated from CFT073 wild-type (WAM 4505) strain replicate 1 grown anaerobically in MOPS minimal media supplemented with 0.2% glucose sparged with a gas mix of 95% N2 and 5% CO2 until an OD600nm of 0.25.


title: CFT073 FUR ChIP-seq Replicate 1

description: WT Replicate 1 ChIP DNA isolated from total cultures grown to OD600 of 0.25 after formaldehyde crosslinking.


title: HD3-pl-2-Streck-EV-RNA

city: Hamburg

first: Harriet

last: Wikman

address: Martinistrasse 52

department: Department of Tumor Biology

country: Germany

institute: University Medical Center Hamburg-Eppendorf

data_processing:
1. Calibrate miRBAse Entries
2. Trim adapter and low quality bases
3. Identify insert sequences and Unique Molecular Index sequences
4. Align insert sequences
4.1.  Mature miRNA: modified miRBase V21 - mature miRNA (basically, all mature miRNAs lengthened to 25 bp [using the sequences in miRBase] to allow for optimal mapping and ragged ends)
4.2. Precursor miRNA: precursor database from miRBase
4.3. piRNA: piRNABank
4.4. rRNA: Ensembl, 1 mismatch allowed
4.5. tRNA: Genomic tRNA Database, 1 mismatch allowed
4.6. otherRNA: snoRNAs from snoRNABase, Ensembl for others. 1 mismatch allowed
4.7. mRNA: Ensembl, no mismatch allowed
4.8. Remap to mature miRNA: Allowing 2 mismatches, first and last 3 nucleotides are ignored
4.9. NotCharacterized_Mappable: Human Genome Reference Consortium GRCh38
5. Count reads and unique molecules for miRNAs and piRNAs
Genome_build: Human Genome Reference Consortium GRCh38
Supplementary_files_format_and_content: Excel file includes a Summary of Reads and UMI counts for each Sample and for each mapped category ...

source_name: Healthy Donor

growth_protocol: human plasma

extract_protocol:
miRNeasy Serum/Plasma Advanced Kit , Qiagen
Libraries were prepared according to QIAGEN's instructions accompanying the QIAseq miRNA Library Kit (Catalog #: 331505) and QIAseq miRNA NGS 48 Index IL (Catalog #: 331595) for Illumina instruments.

tag: disease state

value: Healthy

value: plasma

tag: preparation

value: Streck Tube

tag: molecule

value: Extra cellular vesicle miRNA


title: HD2-pl-2-Streck-EV-RNA


title: HD5-pl-2-EDTA-EV-RNA

value: EDTA Tube


title: HD4-pl-2-Streck-EV-RNA


title: HD5-pl-2-Streck-EV-RNA


title: HD4-pl-2-EDTA-EV-RNA


title: HD3-pl-2-EDTA-EV-RNA


title: ActD time-course 2h rep1

description: total RNA, poly(A) enriched

tag: cell line


title: HD1-pl-2-Streck-EV-RNA


title: HD2-pl-2-EDTA-EV-RNA


title: P10-Streck-EV-RNA

source_name: Melanoma Sample

value: Melanoma


title: P9-Streck-EV-RNA


title: HD1-pl-2-EDTA-EV-RNA


title: P10-EDTA-EV-RNA


title: P8-Streck-EV-RNA


title: P8-EDTA-EV-RNA


title: P7-Streck-EV-RNA


title: YW_control_biol_rep3_tech_rep1

city: Iowa City

first: David

middle: H

last: Price

state: IA

address: 500 Newton Road

department: Biochemistry and Molecular Biology

institute: University of Iowa

description: Control imaginal wing discs of 3rd instar larvae. First technical replicate of the third biological replicate

hyb_protocol: Hybridization was performed following their standard protocol. See www.roche.com.

scan_protocol: Scanning was performed following their standard protocol. See www.roche.com.

data_processing: Raw data (.pair files) were normalized in ArrayStar software version 12.0.0 (DNASTAR, Inc, Madison, WI). The robust multichip analysis (RMA) algorithm was used for background correction, quantile normalization, and median polish summarization. A Student’s t test corrected for multiple testing with the Benjamini and Hochberg false discovery rate (FDR) method was calculated for each experiment.

organism: Drosophila melanogaster

source_name: Wing discs of control 3rd instar larvae

label_protocol: Labeling was performed following their standard protocol. See www.roche.com.

growth_protocol: Flies were mantined at 25°C in malt-based media (Archon Scientific).

extract_protocol: RNA was extracted using TRIzol (Invitrogen) and purified with RNeasy Mini Kit (Qiagen). Double-stranded cDNA was generated using Double-Stranded cDNA Synthesis Kit with random hexamer (Invitrogen). RNA and cDNA quality were analyzed using Experion RNA and DNA analysis kits (Bio-Rad), respectively.

treatment_protocol: 3rd instar larvae were dissected in 1X PBS (pH 7.4)

value: Yellow white (yw^67)

tag: phenotype

value: Yellow body and white eyes

tag: gender

value: Male

tag: developmental stage

value: 3rd instar larvae

value: Imaginal wing disc


title: YW_control_biol_rep3_tech_rep2

description: Contrl imaginal wing discs of 3rd instar larvae. Second technical replicate of the third biological replicate

tag: tissue


title: P7-EDTA-EV-RNA


title: YW_control_biol_rep2_tech_rep2

description: Control imaginal wing discs of 3rd instar larvae. Second technical replicate of the second biological replicate

tag: genotype


title: YW_control_biol_rep2_tech_rep4

description: Control imaginal wing discs of 3rd instar larvae. Fourth technical replicate of the second biological replicate


title: YW_control_biol_rep2_tech_rep3

description: Control imaginal wing discs of 3rd instar larvae. Third technical replicate of the second biological replicate


title: YW_control_biol_rep2_tech_rep1

description: Control imaginal wing discs of 3rd instar larvae. First technical replicate of the second biological replicate


title: P5-EDTA-EV-RNA


title: YW_control_biol_rep1_tech_rep4

description: Control imaginal wing discs of 3rd instar larvae. Fourth technical replicate of the first biological replicate


title: P6-Streck-EV-RNA


title: P5-Streck-EV-RNA


title: P3-EDTA-EV-RNA


title: P4-Streck-EV-RNA


title: P2-Streck-EV-RNA


title: P6-EDTA-EV-RNA


title: HFD+LYC rep3_RNC

city: Nanning

first: Lei

last: Zhou

state: Guangxi

address: Daxuedong Road, Xixiangtang District

department: College of Animal Science and Technology

institute: Guangxi University

description: eight-week-old male mouse was fed high-fat diet plus lycopene for 8 weeks

data_processing:
Basecalls performed using bcl2fastq.
High quality reads that passed the Illumina quality filters were mapped to RefSeq mRNA reference sequence (mm10 25-Mar-2017) using the FANSe2 algorithm with the parameters –L80 –E5 –I0 –S14 –B1 –U0. Reads that mapped to alternative splice variants of one gene were merged.
The mRNA and RNC-mRNA in each sample were normalized using rpkM (reads per kilobase per million reads).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: RNC-Seq

extract_protocol:
Total RNA of a liver sample was extracted using the TRIzol reagent. RNC isolation was performed in accordance with a previously reported procedure with some modifications. Briefly, 90 mg liver tissue was treated with 200 μl lysis buffer (1% Triton X-100 in ribosome buffer [20 mM HEPES, 2 mM dithiothreitol, 15 mM MgCl2, 200 mM KCl and 100 µg/ml cycloheximide]) and was homogenized. An additional 700 μl lysis buffer was added to the samples, followed by incubation in an ice-bath for 30 min. After centrifuging at 16,200 x g for 20 min at 4°C, supernatants were added to the surface of 5 ml of sucrose buffer (30% sucrose in ribosome buffer), and the RNC complex was pelleted by ultra-centrifugation at 330,000 x g for 3 h at 4°C. RNC-RNA was extracted from the RNC complex using TRIzol.
RNA libraries were prepared according to the protocol of the VAHTS mRNA-seq v.3 Library Prep Kit for Illumina (Vazyme Biotech Co., Ltd, Nanjing, Jiangsu, China).

tag: strain

value: liver

value: 16 weeks

value: male

tag: diet

value: high-fat diet plus lycopene

value: wild type


title: P4-EDTA-EV-RNA


title: HFD+LYC rep2_RNC

tag: age


title: Myb_mutant_biol_rep3_tech_rep3

description: Myb mutant imaginal wing discs of 3rd instar larvae. Third technical replicate of the third biological replicate

source_name: Wing discs of Myb mutant 3rd instar larvae

value: Myb^MH107:mutation induced by P-element mobilization by Delta2-3 transposase

value: Lethal-early pupal stage


title: Myb_mutant_biol_rep3_tech_rep2

description: Myb mutant imaginal wing discs of 3rd instar larvae. Second technical replicate of the third biological replicate


title: P3-Streck-EV-RNA

value: plasma


title: YW_control_biol_rep1_tech_rep2

description: Control imaginal wing discs of 3rd instar larvae. Second technical replicate of the first biological replicate


title: YW_control_biol_rep1_tech_rep1

description: Control imaginal wing discs of 3rd instar larvae. First technical replicate of the first biological replicate


title: Myb_mutant_biol_rep3_tech_rep4

description: Myb mutant imaginal wing discs of 3rd instar larvae. Fourth technical replicate of the third biological replicate


title: P9-EDTA-EV-RNA


title: P2-EDTA-EV-RNA


title: P1-EDTA-EV-RNA


title: P1-Streck-EV-RNA

value: Streck Tube


title: HD5-pl-2-Streck-Plasma

value: Healthy

value: Plasma miRNA


title: YW_control_biol_rep1_tech_rep3

description: Control imaginal wing discs of 3rd instar larvae. Third technical replicate of the first biological replicate


title: HD2-pl-2-Streck-Plasma


title: YW_control_biol_rep3_tech_rep3

description: Control imaginal wing discs of 3rd instar larvae. Third technical replicate of the third biological replicate


title: HD5-pl-2-EDTA-Plasma

value: EDTA Tube


title: HD4-pl-2-Streck-Plasma


title: HD2-pl-2-EDTA-Plasma


title: HD4-pl-2-EDTA-Plasma


title: HFD+LYC rep1_RNC


title: HD1-pl-2-Streck-Plasma


title: HFD rep3_RNC

description: eight-week-old male mouse was fed high-fat diet for 8 weeks

value: high fat diet


title: Myb_mutant_biol_rep3_tech_rep1

description: Myb mutant imaginal wing discs of 3rd instar larvae. First technical replicate of the third biological replicate


title: HD1-pl-2-EDTA-Plasma


title: Myb_mutant_biol_rep2_tech_rep4

description: Myb mutant imaginal wing discs of 3rd instar larvae. Fourth technical replicate of the second biological replicate


title: HFD rep2_RNC


title: P10-EDTA-Plasma

value: Melanoma


title: HFD rep1_RNC


title: control rep2_RNC

description: eight-week-old male mouse was fed normal chow diet for 8 weeks

value: normal chow


title: control rep3_RNC


title: P9-EDTA-Plasma


title: P10-Streck-Plasma


title: control rep1_RNC


title: P9-Streck-Plasma


title: Myb_mutant_biol_rep2_tech_rep2

description: Myb mutant imaginal wing discs of 3rd instar larvae. Second technical replicate of the second biological replicate

value: Male

value: 3rd instar larvae


title: HFD+LYC rep3_mRNA

source_name: RNA-Seq

value: liver


title: Myb_mutant_biol_rep2_tech_rep3

description: Myb mutant imaginal wing discs of 3rd instar larvae. Third technical replicate of the second biological replicate

value: Imaginal wing disc


title: Myb_mutant_biol_rep1_tech_rep3

description: Myb mutant imaginal wing discs of 3rd instar larvae. Third technical replicate of the first biological replicate


title: Myb_mutant_biol_rep2_tech_rep1

description: Myb mutant imaginal wing discs of 3rd instar larvae. First technical replicate of the second biological replicate


title: P7-EDTA-Plasma


title: P8-Streck-Plasma


title: Myb_mutant_biol_rep1_tech_rep4

description: Myb mutant imaginal wing discs of 3rd instar larvae. Fourth technical replicate of the first biological replicate


title: P8-EDTA-Plasma


title: HFD+LYC rep1_mRNA

description: eight-week-old male mouse was fed high-fat diet plus lycopene for 8 weeks

value: 16 weeks

value: male


title: P4-Streck-Plasma


title: P6-EDTA-Plasma


title: Myb_mutant_biol_rep1_tech_rep2

description: Myb mutant imaginal wing discs of 3rd instar larvae. Second technical replicate of the first biological replicate


title: P5-EDTA-Plasma


title: P6-Streck-Plasma


title: HFD rep3_mRNA

value: wild type


title: P4-EDTA-Plasma


title: P5-Streck-Plasma


title: SAMPLE 155: MSA 40, BS

type: genomic

city: Odense

first: Rasmus

last: Rydbirk

address: Fioniavej 34

department: Functional Genomics and Biochemistry

country: Denmark

institute: University of Southern Danmark

hyb_protocol: BS or oxBS converted genomic DNA was hybridized to Illumina Infinium MethylationEPIC BeadChips according to the manufacturer's instructions.

scan_protocol: Arrays were scanned on an Illumina iScan instrument.

data_processing:
Data were analysed using ChAMP v. 2.13.5. Probes were filtered according to standard settings before imputation and BMIQ normalization.
Matrix table is BMIQ normalized beta

label: Cy5 and Cy3

source_name: Prefrontal cortex 77

label_protocol: Not provided

extract_protocol: Genomic DNA was extracted using the PCI method.

tag: sample type

value: Prefrontal cortex

tag: Sex

value: Female

tag: pmi (hours)

tag: condition

value: MSA

tag: brain bank

value: Bispebjerg Brain Bank

value: Brain

tag: conversion

value: BS


title: Myb_mutant_biol_rep1_tech_rep1

description: Myb mutant imaginal wing discs of 3rd instar larvae. First technical replicate of the first biological replicate

value: Myb^MH107:mutation induced by P-element mobilization by Delta2-3 transposase

value: Lethal-early pupal stage


title: SAMPLE 156: MSA 41, BS

source_name: Prefrontal cortex 78

value: MRC London Neurodegenerative Diseases Brain Bank

tag: identifier


title: SAMPLE 154: MSA 39, BS

source_name: Prefrontal cortex 76


title: HFD+LYC rep2_mRNA

value: high-fat diet plus lycopene


title: SAMPLE 153: MSA 38, BS

source_name: Prefrontal cortex 75


title: P3-Streck-Plasma

tag: disease state

value: Melanoma

value: plasma

tag: preparation

value: Streck Tube

tag: molecule

value: Plasma miRNA


title: HFD rep2_mRNA

value: liver

value: 16 weeks

tag: gender

value: high fat diet


title: P2-EDTA-Plasma

value: EDTA Tube


title: HFD rep1_mRNA

value: male

value: wild type


title: P3-EDTA-Plasma


title: P1-Streck-Plasma


title: SAMPLE 151: MSA 36, BS

source_name: Prefrontal cortex 73

value: Prefrontal cortex

value: Male

value: MSA


title: P2-Streck-Plasma


title: control rep3_mRNA

value: normal chow


title: control rep2_mRNA


title: Peripheral_blood_macrophage-M2_siGCN2_rep3

city: Braunschweig

first: Andreas

last: Kloetgen

state: NI

address: Inhoffenstr 7

department: Department for Computational Biology of Infection Research

institute: Helmholtz Centre for Infection Research

description:
processed data file:
RNAseq_FPKM_peripheral-blood-macrophages_M2.tsv

data_processing:
Read alignment: STAR aligner version 2.5.0c was used to map reads against the reference genome hg19 (human) or mm10 (mouse). Only uniquely mapping reads were kept (specific parameters: --trim5p=13, --outFilterMultimapNmax 1, --outFilterMismatchNoverLmax 0.05)
Read counting: STAR aligner version 2.5.0.c integrated read-counting was used on annotated genes from Ensembl V75 (human) or Ensembl V85 (mouse).
Normalization: edgeR version 3.14.0 was used to normalize read counts per sample and genes were filtered for counts-per-million > 1. CDS length from Ensembl Genes V75 (human) or Ensembl Genes V85 (mouse) was used to calculate FPKM values for filtered genes.
Genome_build: mm10 / hg19
Supplementary_files_format_and_content: tsv - FPKM

growth_protocol: Subcutaneously injected B16 F10 whole tumors were obtained from BL6 or GCN2 Lys M Cre mice and dissociated using Collagenase IV and Dnase 1. Tumor associated macrophages ("TAMs") and MDSCs were FACS sorted or whole tumors were used. For human peripheral blood macrophages, CD14+ monocytes were differentiated using m-CSF for 7 days resulting in M0 population. Resulting M0 macrophages were either treated with LPS and INFgamma overnight (M1) or IL-4 overnight (M2). Human melanoma tumor associated macrophages ("TAM") were obtained by FACS sorting.

extract_protocol:
Extraction of RNA was performed using Norgen Single Cell RNA extraction kit or Rneasy Plus  Mini extraction kit
SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech #634894) was used per manufacturer’s instructions for amplification of RNA and subsequent cDNA synthesis, All samples proceeded through NexteraXT DNA Library Preparation (Illumina FC-131-1096) using NexteraXT Index Kit V1 or V2 Set A (FC-131-1002 or FC-131-2001) followed by manufacturer’s instructions.

treatment_protocol: For knock-down experiments in human PB macrophages, M0, M1 or M2 macrophages were transfected with siRNAs using human macrophage nucleofector kit from Lonza. siRNAs were purchased from Ambion cat #AM16704 (siRNA #260008 for siGCN2; siRNA #122168 for siATF4) and TermoFisher Silencer Select Negative Control No. 1 (siRNA #4390843 for non-targeting siCTRL).

tag: subject status

value: Healthy donor

tag: cell type

tag: treatment

value: IL-4; siGCN2


title: SAMPLE 150: MSA 35, BS

source_name: Prefrontal cortex 72

value: MRC London Neurodegenerative Diseases Brain Bank

tag: tissue

value: Brain

value: BS


title: control rep1_mRNA

tag: strain

tag: diet

tag: genotype


title: Peripheral_blood_macrophage-M2_siGCN2_rep2


title: SAMPLE 149: MSA 34, BS

source_name: Prefrontal cortex 71

tag: sample type

tag: Sex

tag: age


title: Peripheral_blood_macrophage-M2_siGCN2_rep1


title: SAMPLE 148: MSA 33, BS

source_name: Prefrontal cortex 70

tag: pmi (hours)

tag: condition

tag: brain bank


title: SAMPLE 147: MSA 32, BS

source_name: Prefrontal cortex 69

value: Female

tag: identifier

tag: conversion


title: Peripheral_blood_macrophage-M2_siATF4_rep1

value: IL-4; siATF4


title: Peripheral_blood_macrophage-M2_siATF4_rep3


title: Peripheral_blood_macrophage-M2_siCTRL_rep3

value: IL-4; siCTRL


title: Peripheral_blood_macrophage-M2_siCTRL_rep2


title: Slide 494 Chamber 3

city: Maastricht

first: Rick

last: Kamps

address: P.O. Box 616

department: Genetics and Cell Biology

country: Netherlands

institute: Maastricht University

description: Dye flip of Slide 483 Chamber 2

hyb_protocol: For fragmentation, 825 ng labelled cRNA was used and the final volume was adjusted to 41.8 µl with RNase-free water, followed by the hybridization procedure, as described by the manufacturer (Ambion). Dye-swap hybridizations (2+2) were performed on microarray slides (4x44K zebrafish V3, Agilent) using gasket slides and a hybridization chamber and incubated for 17 h at 65ºC and 10 rpm in the hybridization oven (Agilent Technologies). Slides were washed with Triton X-102, freshly added to the Wash Buffers.

scan_protocol: Microarray slides were scanned using a DNA Microarray scanner with SureScan High-Resolution Technology (Model 2565CA, Agilent).

data_processing: The arrays contained 45,220 probes. Each probe identifier was transformed to Ensembl gene IDs (ENSDARG). This resulted in 36,156 probes containing a non-empty transcript ID of which 19,459 were unique transcripts and kept for the analysis. All transcripts were analysed using a multivariate Gaussian linear regression (MVN(mu,Sigma) where mu is the mean and Sigma is the covariance matrix) including slide differences (Slide), dye swap (Dye), background level (Bg), injection (Inj) and a random effect. The inference criterion used for comparing the models is their ability to predict the observed data, i.e. models are compared directly through their minimized minus log-likelihood. When the numbers of parameters in models differ, they are penalized by adding the number of estimated parameters, a form of the Akaike information criterion. For each transcript, a model containing the relevant covariates mentioned above (E(y) =Slide+Dye+Bg+Inj) was fitted in order to obtain a reference AIC. Then a model containing the treatment group (Trt) was fitted (E(y)=Slide+Dye+Bg+Inj+Inj:Trt). The transcript under consideration was found to be differentially expressed if the AIC of this second model decreased compared to the model not containing the treatment. These statistical analysis were performed using the freely available program R and the publicly available libraries 'rmutil' and ‘growth’. An unbiased Gene-ontology analysis and visualization of microarray data on biological pathways was performed using PANTHER (Protein Analysis THrough Evolutionary Relationships) with the Danio rerio (Dr_Derby_Ensembl_80) gene product/protein database. Differentially expressed genes (DEGs) were mapped to unique Entrez Gene IDs and to Gene Ontology (GO) classes, using the PANTHER Overrepresentation Test (Released 2018-02-03) enrichment method of PANTHER version 13.1.

organism: Danio rerio

label_protocol: After labelling, amplified cRNA samples were purified using the RNeasy Mini kit (Qiagen) and Cyanine 3 and Cyanine 5 dye concentration, RNA absorbance ratio (260/280nm) and cRNA concentration were quantified using the nanodrop 2000C (Thermoscientific). Only samples with a yield >0.825 µg and a specific dye activity >6.0 pmol/µg were used for fragmentation and hybridization.

growth_protocol: Zebrafish (Danio rerio) were housed and raised in the zebrafish facility of the University of Liège as described before. To retrieve eggs, wild-type adult male and female zebrafish were separated within the same breeding tank by a plastic divider the day before breeding. This separation was removed the next day after the light was turned on in order to allow natural mating and eggs were collected after spawning. Eggs were collected in Petri dishes containing 1x E3 medium for zebrafish at 28°C (580 mg/l NaCl, 27 mg/l KCl, 97 mg/l CaCl2·2H2O, 163 mg/l MgCl2·6H2O and 0.0001% methylene blue (Sigma-Aldrich), pH 7.2). Embryos were microscopically staged according to the embryonic development as described before. Unless stated otherwise, all reagents used in this study were obtained from Thermo Fisher Scientific.

extract_protocol: For gene expression studies, 12 embryos for the injected controls, 12 embryos for the injected TFAM, and 9 embryos for the non-injected control group were individually collected in sterile tubes. RNA from single embryos was isolated using the MagMax-96 for microarray kit (Ambion) and 200 ng RNA was labelled (Cyanine 3-CTP and Cyanine 5-CTP), fragmented and hybridized using the Low Input Quick Amp Labeling Kit, Two-colour (Ambion), according to manufacturer’s instructions.

treatment_protocol: Antisense morpholino oligonucleotides (MO) were purchased from Gene Tools and micro-injected into one or two-cell stage embryos. A splice modifying MO was used, targeting the boundary of exon 2 and intron 2-3 of the zebrafish tfam gene (Ensembl: ENSDART00000092009, tfam splice-MO: 5’- CGGCAGATGGAAATTTACCAGGATT-3’). For controlling the effect of the MO injection, an equal concentration of a standard control-morpholino (Ctrl-MO: 5'-CCTCTTACCTCAGTTACAATTTATA-3') was used in separate embryos of the same batch during each experiment. All MOs were dissolved in 1x Danieau buffer (58 mM NaCl, 0.7 mM KCl, 0.4 mM MgSO4, 0.6 mM Ca(NO3)2, and 5.0 mM HEPES pH 7.6) and 0.5% rhodamine dextran (Thermo Fisher) was added to the MO solution upon injection. At 1 hpf, 1 nl was injected into each embryo using microinjection. The next day, distribution of the rhodamine dextran dye was checked using fluorescence stereomicroscopy to verify proper injections. Only those embryos in which the rodamine dextran dye was visible were used for follow-up investigations.

tag: group

value: non-injected control

value: whole fish embryo

tag: developmental stage

value: 4 dpf

value: injected control


title: P1-EDTA-Plasma

tag: disease state

value: Melanoma

value: plasma

tag: preparation

value: EDTA Tube

tag: molecule

value: Plasma miRNA


title: Peripheral_blood_macrophage-M2_siCTRL_rep1

tag: subject status

tag: cell type

tag: treatment


title: Peripheral_blood_macrophage-M1_siGCN2_rep3

description:
processed data file:
RNAseq_FPKM_peripheral-blood-macrophages_M1.tsv

value: LPS + INFgamma; siGCN2


title: Peripheral_blood_macrophage-M1_siGCN2_rep2

value: Healthy donor


title: Slide 494 Chamber 2

description: Dye flip of Slide 483 Chamber 3

value: injected TFAM

tag: tissue


title: Slide 494 Chamber 1

description: Dye flip of Slide 483 Chamber 4


title: Slide 487 Chamber 4

description: Dye flip of Slide 482 Chamber 1


title: SAMPLE 145: MSA 30, BS

source_name: Prefrontal cortex 67

tag: sample type

value: Prefrontal cortex

value: MSA

value: MRC London Neurodegenerative Diseases Brain Bank


title: SAMPLE 143: MSA 28, BS

source_name: Prefrontal cortex 65

tag: Sex

value: Female

value: Bispebjerg Brain Bank

value: Brain

value: BS


title: Peripheral_blood_macrophage-M1_siATF4_rep1

value: LPS + INFgamma; siATF4


title: Slide 494 Chamber 4

description: Dye flip of Slide 483 Chamber 1

value: whole fish embryo

value: 4 dpf


title: Peripheral_blood_macrophage-M1_siATF4_rep3


title: Peripheral_blood_macrophage-M1_siCTRL_rep2

value: LPS + INFgamma; siCTRL


title: P7-Streck-Plasma

value: Melanoma

value: plasma

value: Streck Tube


title: SAMPLE 146: MSA 31, BS

source_name: Prefrontal cortex 68

tag: age


title: SAMPLE 141: MSA 26, BS

source_name: Prefrontal cortex 63

tag: pmi (hours)


title: Peripheral_blood_macrophage-M0_siGCN2_rep2

description:
processed data file:
RNAseq_FPKM_peripheral-blood-macrophages_M0.tsv


title: Peripheral_blood_macrophage-M1_siCTRL_rep3


title: Peripheral_blood_macrophage-M2_siATF4_rep2

value: IL-4; siATF4


title: SAMPLE 152: MSA 37, BS

source_name: Prefrontal cortex 74

tag: condition


title: Slide 487 Chamber 3

description: Dye flip of Slide 482 Chamber 2

value: non-injected control

value: injected control


title: Slide 487 Chamber 1

description: Dye flip of Slide 482 Chamber 4


title: Peripheral_blood_macrophage-M0_siGCN2_rep1

value: Healthy donor


title: Slide 486 Chamber 3

description: Dye flip of Slide 481 Chamber 2


title: Peripheral_blood_macrophage-M1_siATF4_rep2


title: Slide 487 Chamber 2

description: Dye flip of Slide 482 Chamber 3

value: injected TFAM


title: SAMPLE 142: MSA 27, BS

source_name: Prefrontal cortex 64

value: Prefrontal cortex

value: MSA

tag: brain bank

value: MRC London Neurodegenerative Diseases Brain Bank


title: Slide 486 Chamber 2

description: Dye flip of Slide 481 Chamber 3


title: Peripheral_blood_macrophage-M1_siCTRL_rep1


title: Peripheral_blood_macrophage-M0_siATF4_rep1


title: Peripheral_blood_macrophage-M0_siGCN2_rep3


title: Peripheral_blood_macrophage-M0_siCTRL_rep2

value: siCTRL


title: SAMPLE 140: MSA 25, BS

source_name: Prefrontal cortex 62

value: Male

tag: identifier

value: Brain

value: BS


title: Slide 486 Chamber 4

description: Dye flip of Slide 481 Chamber 1

value: whole fish embryo

value: 4 dpf


title: Peripheral_blood_macrophage-M0_siATF4_rep3


title: SAMPLE 138: MSA 23, BS

source_name: Prefrontal cortex 60

value: Bispebjerg Brain Bank

tag: conversion


title: Peripheral_blood_macrophage-M0_siCTRL_rep3


title: SAMPLE 139: MSA 24, BS

source_name: Prefrontal cortex 61


title: Slide 486 Chamber 1

description: Dye flip of Slide 481 Chamber 4

tag: group


title: Peripheral_blood_macrophage-M0_siATF4_rep2


title: SAMPLE 137: MSA 22, BS

source_name: Prefrontal cortex 59

value: Female


title: Peripheral_blood_macrophage_melanoma_donor2

description:
processed data file:
RNAseq_FPKM_peripheral-blood-macrophages_melanoma.tsv

value: Melanoma donor

value: TAM


title: Peripheral_blood_macrophage-M0_siCTRL_rep1


title: Peripheral_blood_macrophage_melanoma_donor3


title: Peripheral_blood_macrophage_melanoma_donor5


title: SAMPLE 135: MSA 20, BS

source_name: Prefrontal cortex 57


title: Slide 485 Chamber 4

description: Dye flip of Slide 480 Chamber 1

tag: developmental stage


title: Peripheral_blood_macrophage_melanoma_donor1


title: Peripheral_blood_macrophage_melanoma_donor4


title: Slide 485 Chamber 3

description: Dye flip of Slide 480 Chamber 2

value: non-injected control


title: SAMPLE 134: MSA 19, BS

source_name: Prefrontal cortex 56


title: Slide 485 Chamber 2

description: Dye flip of Slide 480 Chamber 3

value: injected control


title: Slide 485 Chamber 1

description: Dye flip of Slide 480 Chamber 4


title: SAMPLE 133: MSA 18, BS

source_name: Prefrontal cortex 55


title: Slide 484 Chamber 4

description: Dye flip of Slide 479 Chamber 1


title: Slide 484 Chamber 3

description: Dye flip of Slide 479 Chamber 2


title: HGSOC-4_RNA-seq

city: Los Angeles

first: Kate

last: Lawrenson

state: CA

address: 8700 Beverly Blvd

department: Women's Cancer Program

institute: Cedars-Sinai Medical Center

description:
counts.txt
processed data column header: KL13-NEBindex13_S13_R1_001

data_processing:
ChIP-seq data was processed using AQUAS v0.3.3
RNA-seq data was first aligned using STAR v2.5.1b to GRCh38.p10 (GENCODE 26)
then read counts for mapped reads were generated using featureCounts v1.5.0-p1
Genome_build: ChIP-seq: hg19, RNA-seq: hg38
Supplementary_files_format_and_content: narrowPeaks generated with AQUAS v0.3.3
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample ...

source_name: Epithelial ovarian cancer

extract_protocol:
Chromatin was incubated at 4°C overnight with 1 µg H3K27ac antibody (DiAGenode, C15410196, Denville, NJ) that had been coupled with protein A and protein G beads (Life Technologies, Carlsbad, CA)
ChIP-seq libraries were built using the ThruPLEX-FD Prep Kit (Rubicon Genomics, Ann Arbor, MI). RNA was extracted using the AllPrep kit (QIAgen, Hilden, Germany).

treatment_protocol: One flash frozen 3 mm core was biopsied from an epithelial-rich portion of the tumor. The tissue was pulverized in a pulverization bag (TT05) using the Covaris CryoPrep system (Covaris, Woburn, MA) twice at intensity 4. The tissue was then fixed using 1% formaldehyde (Thermo fisher, Waltham, MA) in Phosphate-buffered saline solution for 10 minutes at room temperature with rotation, and quenched with 125 mM glycine for 10 min at room temperature, also with rotation. One core was reserved for RNA-seq, this tissue was disrupted using an Omni Tissue Homogenizer.

value: High-grade serous ovarian cancer


title: MOC-5_RNA-seq

description:
counts.txt
processed data column header: KL19-NEBindex20_S19_R1_001

value: Mucinous ovarian cancer


title: MOC-1_RNA-seq

description:
counts.txt
processed data column header: KL15-NEBindex15_S15_R1_001


title: MOC-4_RNA-seq

description:
counts.txt
processed data column header: KL18-NEBindex19_S18_R1_001


title: MOC-2_RNA-seq

description:
counts.txt
processed data column header: KL16-NEBindex16_S16_R1_001


title: HGSOC-5_RNA-seq

description:
counts.txt
processed data column header: KL14-NEBindex14_S14_R1_001


title: MOC-3_RNA-seq

description:
counts.txt
processed data column header: KL17-NEBindex18_S17_R1_001


title: HGSOC-1_RNA-seq

description:
counts.txt
processed data column header: KL10-NEBindex10_S10_R1_001


title: SAMPLE 136: MSA 21, BS

source_name: Prefrontal cortex 58

value: Prefrontal cortex


title: SAMPLE 129: MSA 14, BS

source_name: Prefrontal cortex 51

value: MSA


title: EnOC-4_RNA-seq

description:
counts.txt
processed data column header: KL08-NEBindex8_S8_R1_001

value: Endometrioid ovarian cancer


title: HGSOC-2_RNA-seq

description:
counts.txt
processed data column header: KL11-NEBindex11_S11_R1_001


title: SAMPLE 130: MSA 15, BS

source_name: Prefrontal cortex 52


title: Slide 484 Chamber 2

description: Dye flip of Slide 479 Chamber 3

value: injected TFAM


title: SAMPLE 128: MSA 13, BS

source_name: Prefrontal cortex 50

value: MRC London Neurodegenerative Diseases Brain Bank


title: SAMPLE 131: MSA 16, BS

source_name: Prefrontal cortex 53

value: Male

value: Brain


title: Slide 484 Chamber 1

description: Dye flip of Slide 479 Chamber 4

value: whole fish embryo


title: EnOC-2_RNA-seq

description:
counts.txt
processed data column header: KL07-NEBindex7_S7_R1_001


title: HGSOC-3_RNA-seq

description:
counts.txt
processed data column header: KL12-NEBindex12_S12_R1_001


title: EnOC-5_RNA-seq

description:
counts.txt
processed data column header: KL09-NEBindex9_S9_R1_001


title: Slide 483 Chamber 3

description: Dye flip of Slide 494 Chamber 2

value: 4 dpf


title: Slide 483 Chamber 4

description: Dye flip of Slide 494 Chamber 1


title: SAMPLE 132: MSA 17, BS

source_name: Prefrontal cortex 54

value: BS


title: CCOC-4_RNA-seq

description:
counts.txt
processed data column header: KL04-NEBindex4_S4_R1_001

value: Clear cell ovarian cancer


title: SAMPLE 126: MSA 11, BS

source_name: Prefrontal cortex 48


title: CCOC-3_RNA-seq

description:
counts.txt
processed data column header: KL03-NEBindex3_S3_R1_001


title: MOC-5_Input_DNA


title: EnOC-1_RNA-seq

description:
counts.txt
processed data column header: KL06-NEBindex6_S6_R1_001


title: CCOC-5_RNA-seq

description:
counts.txt
processed data column header: KL05-NEBindex5_S5_R1_001


title: SAMPLE 127: MSA 12, BS

source_name: Prefrontal cortex 49

value: Female

value: Bispebjerg Brain Bank


title: Slide 483 Chamber 2

description: Dye flip of Slide 494 Chamber 3

value: non-injected control


title: CCOC-1_RNA-seq

description:
counts.txt
processed data column header: KL01-NEBindex1_S1_R1_001


title: CCOC-2_RNA-seq

description:
counts.txt
processed data column header: KL02-NEBindex2_S2_R1_001


title: SAMPLE 123: MSA 8, BS

source_name: Prefrontal cortex 45


title: Slide 482 Chamber 2

description: Dye flip of Slide 487 Chamber 3

value: injected control


title: HGSOC-5_Input_DNA

value: High-grade serous ovarian cancer


title: MOC-3_Input_DNA

value: Mucinous ovarian cancer


title: MOC-2_Input_DNA


title: SAMPLE 121: MSA 6, BS

source_name: Prefrontal cortex 43

value: Prefrontal cortex


title: Slide 482 Chamber 4

description: Dye flip of Slide 487 Chamber 1


title: SAMPLE 124: MSA 9, BS

source_name: Prefrontal cortex 46

value: MSA


title: MOC-4_Input_DNA


title: Slide 483 Chamber 1

description: Dye flip of Slide 494 Chamber 4


title: SAMPLE 122: MSA 7, BS

source_name: Prefrontal cortex 44


title: HGSOC-2_Input_DNA


title: MOC-1_Input_DNA


title: Slide 482 Chamber 3

description: Dye flip of Slide 487 Chamber 2


title: SAMPLE 125: MSA 10, BS

source_name: Prefrontal cortex 47


title: Slide 481 Chamber 4

description: Dye flip of Slide 486 Chamber 1


title: HGSOC-4_Input_DNA


title: SAMPLE 119: MSA 4, BS

source_name: Prefrontal cortex 41


title: FAK KO3

city: Cincinnati

first: Jun

middle: lin

last: Guan

state: Ohio

address: 3125 Eden Ave

department: Cancer Biology

institute: University of Cincinnati

data_processing:
To analyze differential gene expression, sequence reads were aligned to the genome using standard Illumina sequence analysis pipeline. Standard Differential expression analysis was performed using the R package DESeq2.
Probes were declared significantly differentially expressed if the FDR p-value was <0.01，
If the absolute log fold change was > 2 (<0.5), it was up-regulated (down-regulated).

source_name: Mammary tumor

growth_protocol: Cells were grown in DMEM/F12 medium supplemented with 10% FBS, 10ng/ml EGF, 20μg/ml insulin and 50units/ml penicillin-streptomycin

extract_protocol:
RNA from tumor cells were isolated using mirVana miRNA Isolation Kit (Thermo Scientific) according to manufacturer’s instructions for total RNA isolation.
Targeted RNA enrichment was achieved using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs) and PrepX mRNA Library kit (WaferGen) combined with Apollo 324 NGS automated library prep system was used for library preparation. Cluster generation and HiSeq sequencing were carried out using the cBot and HiSeq systems (Illumina) respectively.

tag: strain

value: FVB

tag: genotype

value: FAK-/-


title: SAMPLE 120: MSA 5, BS

source_name: Prefrontal cortex 42

value: MRC London Neurodegenerative Diseases Brain Bank


title: EnOC-4_Input_DNA

source_name: Epithelial ovarian cancer

value: Endometrioid ovarian cancer


title: Slide 482 Chamber 1

description: Dye flip of Slide 487 Chamber 4

value: injected TFAM


title: Slide 481 Chamber 2

description: Dye flip of Slide 486 Chamber 3

value: whole fish embryo


title: SAMPLE 118: MSA 3, BS

source_name: Prefrontal cortex 40

value: Male

value: Brain


title: EnOC-3_Input_DNA


title: HGSOC-1_Input_DNA


title: SAMPLE 144: MSA 29, BS

source_name: Prefrontal cortex 66

value: BS


title: SAMPLE 116: MSA 1, BS

source_name: Prefrontal cortex 38

value: Female


title: EnOC-5_Input_DNA


title: HGSOC-3_Input_DNA


title: Slide 481 Chamber 3

description: Dye flip of Slide 486 Chamber 2

value: 4 dpf


title: SAMPLE 117: MSA 2, BS

source_name: Prefrontal cortex 39

value: Bispebjerg Brain Bank


title: Slide 480 Chamber 4

description: Dye flip of Slide 485 Chamber 1

value: non-injected control

value: injected control


title: Slide 481 Chamber 1

description: Dye flip of Slide 486 Chamber 4


title: Slide 480 Chamber 2

description: Dye flip of Slide 485 Chamber 3


title: EnOC-2_Input_DNA


title: CCOC-4_Input_DNA

value: Clear cell ovarian cancer


title: Slide 480 Chamber 3

description: Dye flip of Slide 485 Chamber 2


title: EnOC-1_Input_DNA


title: FAK KO1


title: Ctrl2

value: FAK Wildtype


title: Slide 480 Chamber 1

description: Dye flip of Slide 485 Chamber 4


title: SAMPLE 113: Control 35, BS

source_name: Prefrontal cortex 35

value: Prefrontal cortex

value: CTRL


title: Ctrl3

value: FVB


title: SAMPLE 115: Control 37, BS

source_name: Prefrontal cortex 37

value: MRC London Neurodegenerative Diseases Brain Bank


title: Ctrl1


title: CCOC-5_Input_DNA


title: CCOC-3_Input_DNA


title: SAMPLE 112: Control 34, BS

source_name: Prefrontal cortex 34


title: Control + vit D rat 37

city: Copenhagen N

first: Jakob

middle: Lewin

last: Rukov

address: Ole Maaløes Vej 5

institute: University of Copenhagen

description:
index = GTTTCG
Effect of CKD on calcified aorta by RNAseq Processed data.xlsx

data_processing:
Adapter sequence was removed from sequencing reads using cutadapt (version 1.3), which required a read length of at least 25 nt after removal
three positions were trimmed off the 5=-end of all reads to remove possible untemplated products of the first-strand reaction using the FASTQ Trimmer tool
Reads with < 10% of positions having a quality score of < 25 were then discarded using the FASTQ Quality Filter
remaining reads were mapped to the rat genome (assembly rn5) using Tophat (version 2.0.10) with library type set to fr-secondstrand, segment length set to 20 nt, and allowed segment mismatches set to 1. Ref-Seq gene annotations (46) were used to guide mapping (-G parameter). Reads mapping to rRNA, tRNA, and chrM were discarded from the analysis.
Analysis of differential gene expression was performed using Cuffdiff as implemented in Cufflinks (version 2.1.1) (57) and Ref-Seq gene annotations. No effective length correction was performed, whereas a multiread correction was applied. The false discovery rate was set to 0.05, and P
Genome_build: rn5
Supplementary_files_format_and_content: Excel file with matrix of RPKM values for rat genes for the studied samples

source_name: Aorta

extract_protocol:
The rat aortas were dissected free from the level of the renal arteries and up to the heart, connective tissue and blood were removed by gentle manipulation and a rinse with sterile saline. The aorta was instantly snap frozen in liquid nitrogen. Total RNA from the aorta was extracted with TRIzol (Sigma-Aldrich, St. Louis, MO). Purified total RNA was treated with the Qiagen RNase-free DNase set followed by purification on miRNeasy columns (Qiagen, Germantown, MD). Two rounds of enrichment of polyadenylated RNA were then performed using the Poly(A)Purist MAG kit (Ambion, Fisher Scientific, MA) followed by RNA purification on RNAClean XP beads (Agencourt, Beckman Coulter).
The RNA sample was fragmented on ice by adding fragmentation buffer to a final concentration of 50 mM Tris·HCl (pH 8) and 5 mM MgCl2 followed by incubation at 95°C for 3 min and 20 s. The sample was then immediately placed back on ice, and EDTA was added at 10 nM to stabilize RNA. Fragmented RNA was purified on RNAClean XP beads (Agencourt) and eluted in 13 ul diethylpyrocarbonate-treated H2O. cDNA synthesis and ligation of an adapter to the 3=-end of the cDNA was performed (21). The first-strand synthesis and adapter ligation steps result in a cDNA pool containing adapters both at the 5=- and 3=-ends, which can be used for subsequent PCR and Illumina sequencing. Three microliters of PCR_forward (10 uM) primer (5=-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCT ACACGACGCT-3=), 10 ul Phusion 5 x HF buffer, 1 ul of 10 mM dNTPs, 26.5 ul H2O, 1 ul Phusion DNA polymerase, 2.5 ul indexing primer (10 uM, 5=-CAAGCAGAAGACGGCATACGAGATNNNNN- NGTGACTGGAGTTCAGACGTGTGCTCTTCCGA TCT-3=; with NNNNNN indicating the index sequence), and 6 ul purified linker ligated cDNA were mixed and run with the following PCR program: 98°C for 3 min, (98°C for 80 s, 64°C for 15 s, and 72°C for 30 s) x 4, (98°C for 80 s and 72°C for 45 s) x 10, 72°C for 5 min, and hold at 4°C. The resulting sequencing libraries were quantified on a Bioanalyzer 2100 (Agilent Technologies) using a DNA1000 chip (Agilent) for smear analysis and molarity calculation. Samples were mixed in equimolar amounts, and PCR amplicons in the 200- to 600-bp size range were extracted from a 2% E-Gel SizeSelect Agarose Gel in an E-Gel Electrophoresis System (Life Technologies, Paisley, UK). The eluate was purified using Agencourt Ampure XP beads (Beckman Coulter). The final sample was again run on a DNA1000 chip (Agilent) in a Bioanalyzer 2100 for smear analysis.

value: Dark Agouti

tag: gender

value: Control + vit D


title: Control + vit D rat 38

description:
index = ACTTGA
Effect of CKD on calcified aorta by RNAseq Processed data.xlsx


title: Slide 479 Chamber 4

description: Dye flip of Slide 484 Chamber 1

value: whole fish embryo


title: CCOC-2_Input_DNA


title: Control + vit D rat 36

description:
index = GTGGCC
Effect of CKD on calcified aorta by RNAseq Processed data.xlsx

value: Male


title: Peripheral_blood_macrophage-M1_siGCN2_rep1

description:
processed data file:
RNAseq_FPKM_peripheral-blood-macrophages_M1.tsv

tag: subject status

value: Healthy donor

value: LPS + INFgamma; siGCN2


title: SAMPLE 114: Control 36, BS

source_name: Prefrontal cortex 36

value: Female

value: Brain

value: BS


title: Control + vit D rat 39

description:
index = TAGCTT
Effect of CKD on calcified aorta by RNAseq Processed data.xlsx


title: SAMPLE 111: Control 33, BS

source_name: Prefrontal cortex 33


title: Slide 479 Chamber 3

description: Dye flip of Slide 484 Chamber 2

value: 4 dpf

value: injected TFAM


title: Slide 479 Chamber 1

description: Dye flip of Slide 484 Chamber 4

value: injected control


title: Slide 479 Chamber 2

description: Dye flip of Slide 484 Chamber 3

value: non-injected control


title: Uremic aorta rat 27

description:
index = TGACCA & CCGTCC (technical replicate)
Effect of CKD on calcified aorta by RNAseq Processed data.xlsx

value: Uremia was induced by 5/6 nephrectomy


title: SAMPLE 110: Control 32, BS

source_name: Prefrontal cortex 32

value: Prefrontal cortex

value: CTRL

value: Bispebjerg Brain Bank


title: Uremic aorta rat 28

description:
index = ACAGTG
Effect of CKD on calcified aorta by RNAseq Processed data.xlsx

value: Dark Agouti


title: MOC-4_H3K27ac_ChIP-seq

value: Mucinous ovarian cancer


title: MOC-3_H3K27ac_ChIP-seq


title: Slide 478 Chamber 4

description: Dye flip of Slide 477 Chamber 1

value: whole fish embryo


title: SAMPLE 106: Control 28, BS

source_name: Prefrontal cortex 28

value: MRC London Neurodegenerative Diseases Brain Bank


title: Uremic aorta rat 17

description:
index = GTAGAG
Effect of CKD on calcified aorta by RNAseq Processed data.xlsx

value: Male


title: FAK KO2

value: FVB

value: FAK-/-


title: Slide 478 Chamber 1

description: Dye flip of Slide 477 Chamber 4


title: SAMPLE 108: Control 30, BS

source_name: Prefrontal cortex 30

value: Brain


title: MOC-1_H3K27ac_ChIP-seq


title: SAMPLE 107: Control 29, BS

source_name: Prefrontal cortex 29

value: Female

value: BS


title: Slide 478 Chamber 3

description: Dye flip of Slide 477 Chamber 2

value: 4 dpf


title: Slide 478 Chamber 2

description: Dye flip of Slide 477 Chamber 3

value: injected TFAM

value: injected control


title: MOC-2_H3K27ac_ChIP-seq


title: SAMPLE 105: Control 27, BS

source_name: Prefrontal cortex 27


title: CCOC-1_Input_DNA

value: Clear cell ovarian cancer


title: Control aorta rat 46

description:
index = AGTCAA
Effect of CKD on calcified aorta by RNAseq Processed data.xlsx

value: control


title: HGSOC-5_H3K27ac_ChIP-seq

value: High-grade serous ovarian cancer


title: SAMPLE 109: Control 31, BS

source_name: Prefrontal cortex 31

value: Prefrontal cortex

value: CTRL


title: HGSOC-4_H3K27ac_ChIP-seq

source_name: Epithelial ovarian cancer


title: Uremic aorta rat 20

description:
index = GTCCGC
Effect of CKD on calcified aorta by RNAseq Processed data.xlsx

value: Dark Agouti

value: Uremia was induced by 5/6 nephrectomy


title: SAMPLE 103: Control 25, BS

source_name: Prefrontal cortex 25

value: Bispebjerg Brain Bank


title: HGSOC-3_H3K27ac_ChIP-seq


title: Slide 477 Chamber 4

description: Dye flip of Slide 478 Chamber 1

value: non-injected control

value: whole fish embryo


title: Uremic aorta rat 9

description:
index = CGATGT
Effect of CKD on calcified aorta by RNAseq Processed data.xlsx

value: Male


title: Control aorta rat 42

description:
index = GAGTGG
Effect of CKD on calcified aorta by RNAseq Processed data.xlsx


title: SAMPLE 101: Control 23, BS

source_name: Prefrontal cortex 23

value: MRC London Neurodegenerative Diseases Brain Bank

value: Brain


title: Control aorta rat 44

description:
index = CTTGTA
Effect of CKD on calcified aorta by RNAseq Processed data.xlsx


title: MOC-5_H3K27ac_ChIP-seq

value: Mucinous ovarian cancer


title: SAMPLE 104: Control 26, BS

source_name: Prefrontal cortex 26

value: Female

value: BS


title: EnOC-5_H3K27ac_ChIP-seq

value: Endometrioid ovarian cancer


title: Slide 477 Chamber 3

description: Dye flip of Slide 478 Chamber 2

value: injected control

value: 4 dpf

value: injected TFAM


title: Pro35SARR1 rep2

city: Qingdao

first: Zhenhua

last: Liu

address: Binhai Road 72

institute: Shandong University

data_processing:
Illumina Casava software used for basecalling.
DESeq and the Q value were used to identify differentially transcribed genes (DTGs).
Differential transcription was inferred by applying a false discovery rate threshold of 0.001 and the |log2 Ratio| ≥ 1.
Functional categorization was inferred from a BLAST search of the non-redundant GenBank (http://www.ncbi.nlm.nih.gov/genbank/), KEGG Pathway (http://www.genome.jp/kegg/pathway.html), and UniProt protein databases (http://www.uniprot.org/), and was further analyzed by the Gene Ontology (http://geneontology.org/) method.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
Supplementary_files_format_and_content: A: Processed data related with the manuscript: Differentially transcribed genes (DTGs) in arr1 vs. wild type and AOE vs. wild type.
Supplementary_files_format_and_content: B KEGG.xls: Processed data related with the manuscript: Pathway enrichment of DTGs in arr1 vs. wild type
Supplementary_files_format_and_content: C T01_T02_vs_T03_T04.DEG.final: Processed data related with the manuscript: Transcript profiling of DTGs related to auxin transport and signaling from arr1 vs. wild type.
Supplementary_files_format_and_content: AllSample.isoforms_expression: Complete processed data

source_name: root explants

growth_protocol: the explants were initially cultured for five days on CIM under continuous light at 22 ± 1°C. Calli were subsequently re-plated on SIM (MS medium supplemented with Gamborg’s B-5 vitamins plus 10 g/L sucrose, 0.5 g/L MES, 6 g/L agar, 1 mg/L N6-(2-isopentenyl) adenine (Sigma, USA), and 0.15 mg/L IAA (Sigma, USA), pH 5.8) under continuous light at 22 ± 1°C for 7 days.

extract_protocol:
Explants were flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: Pro35SARR1 rep1


title: SAMPLE 102: Control 24, BS

source_name: Prefrontal cortex 24

value: Prefrontal cortex


title: 1502_1502IRN_144h_3

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

data_processing:
Illumina Casava v1.8.2 software used for base-calling
All RNA-seq FastQ reads were aligned with the reference genome (UCSC human genome build hg19) using TopHat2 default settings. To remove RNA species from host (mouse RNA), a custom-designed algorithm was performed to align reads using TopHat2 to both host genome (mm9) and graft genome (hg19). We kept reads as human-specific or human/mouse-common based on number of mis-match bases, number of gaps and alignment QC scores. The human RNA sequence reads (unique to human + common human/mouse) were then re-aligned to graft genome hg19 using TopHat2, and the BAM files obtained after alignment were processed using HTSeq-count to obtain the counts per gene
gene count measurements were obtained using HTSeq-count
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

source_name: Ewing sarcoma

growth_protocol: C.B.17SC scid−/− (C.B-Igh-1b/IcrTac-Prkdcscid) female mice (Taconic Farms, Germantown NY) were used to propagate subcutaneously implanted tumors. All mice were maintained under barrier conditions and experiments were carried out using protocols and conditions approved by the institutional animal care and use committee of UTHSA.

extract_protocol:
Total RNA was extracted from snap-frozen xenografts chilled under liquid nitrogen to prevent thawing. RNA was extracted with TRIzol reagent and purified on an RNeasy mini column (Qiagen). On-column DNase digestion was performed with Qiagen RNase-free DNase kit.
RNA-seq library preparation by following the Illumina TruSeq stranded mRNA sample preparation guide

treatment_protocol: Mice were randomized into groups of 10, and treatment was started when tumors were 200-400 mm^3. Eribulin was dissolved in sterile water and administered days 1 and 8, and irinotecan was dissolved in saline and administered days 1-5, with the cycle repeated at day 21. Eribulin was dosed at 1 mg/kg and irinotecan at 2.5 mg/kg. Both drugs were administered by intraperitoneal injection.

value: Ewing sarcoma

tag: tumor

value: ES4 xenograft

value: eribulin (1mg/kg) + irinotecan (2.5 mg/kg)

tag: harvest time

value: 144 hour


title: HGSOC-2_H3K27ac_ChIP-seq

tag: tissue

value: High-grade serous ovarian cancer


title: Slide 477 Chamber 1

description: Dye flip of Slide 478 Chamber 4

value: whole fish embryo


title: Control aorta rat 41

description:
index = CGTACG
Effect of CKD on calcified aorta by RNAseq Processed data.xlsx

value: Dark Agouti

value: Male

tag: treatment

value: control


title: SAMPLE 98: Control 20, BS

source_name: Prefrontal cortex 20

tag: sample type

tag: Sex

value: CTRL

value: MRC London Neurodegenerative Diseases Brain Bank

value: Brain


title: Slide 477 Chamber 2

description: Dye flip of Slide 478 Chamber 3

value: non-injected control


title: HGSOC-1_H3K27ac_ChIP-seq


title: SAMPLE 100: Control 22, BS

source_name: Prefrontal cortex 22

tag: age

tag: pmi (hours)

value: BS


title: 1502_1502IRN_144h_1


title: SAMPLE 99: Control 21, BS

source_name: Prefrontal cortex 21

value: Female

tag: condition

tag: brain bank


title: EnOC-2_H3K27ac_ChIP-seq

value: Endometrioid ovarian cancer


title: Jul11_2016_15-18ss_etv2gfp

first: Saulius

last: Sumanas

address: 3333 Burnet Ave

department: Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

description:
single cell technology: Fluidigm C1
GFP positive cells sorted from vascular endothelial reporter line

data_processing:
Alignment with Kallisto/AltAnalyze
Iterative clustering and guide-gene selection (ICGS) with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects
Markerfinder to identify enriched genes in each group
Genome_build: Zv9 Ensembl release 72

source_name: Vascular Endothelial Cells

growth_protocol: Embryos grown in standard E3 medium at 28.5C

extract_protocol: Embryos were non-enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells

treatment_protocol: No treatment

tag: cell type

value: Vascular Endothelial Cells

tag: animal line

value: 15-18 somite stage


title: Aug1_2016_20ss_etv2gfp

tag: developmental stage

value: 20 somite stage


title: Control aorta rat 43

description:
index = GGTAGC
Effect of CKD on calcified aorta by RNAseq Processed data.xlsx

source_name: Aorta

tag: strain


title: 1502_1502IRN_24h_3

value: Ewing sarcoma

value: ES4 xenograft

value: eribulin (1mg/kg) + irinotecan (2.5 mg/kg)

value: 24 hour


title: EnOC-1_H3K27ac_ChIP-seq


title: WT rep1

tag: genotype

value: wild type


title: EnOC-4_H3K27ac_ChIP-seq


title: arr1 rep2


title: SAMPLE 94: Control 16, BS

source_name: Prefrontal cortex 16

value: Prefrontal cortex

tag: identifier

tag: conversion


title: EnOC-3_H3K27ac_ChIP-seq


title: SAMPLE 97: Control 19, BS

source_name: Prefrontal cortex 19

value: Male


title: arr1 rep1


title: 1502_1502IRN_144h_2

tag: tumor

value: 144 hour


title: SAMPLE 93: Control 15, BS

source_name: Prefrontal cortex 15

value: CTRL

value: MRC London Neurodegenerative Diseases Brain Bank


title: SAMPLE 96: Control 18, BS

source_name: Prefrontal cortex 18

value: Brain


title: SAMPLE 95: Control 17, BS

source_name: Prefrontal cortex 17

value: BS


title: WT.IP.rep1

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

country: Israel

institute: Tel Aviv University

description:
4264_7_WT-1_IP_GCCAAT_S15_L004
RNAPII WT. Rep1

data_processing:
library strategy: RIP-seq (m6A-seq)
MeRIP data was aligned to the genome (hg19) using Tophat2.
MACS2 was used to detect m6A peaks (at FDR=1%).
Genome_build: hg19
Supplementary_files_format_and_content: m6A peaks

growth_protocol: DMEM, 10%FCS, 37 degrees, 5% CO2

extract_protocol:
Trizol
MeRIP library was prepared using EpiMark® N6-Methyladenosine Enrichment Kit and Illumina Truseq RNA kit according to the manufacturer's manual. Briefly, RNA was fragmented and bound to m6A antibody-coupled protein G beads for 3h. Beads were then washed with reaction buffer, low salt buffer, and high salt buffer. Enriched RNA was eluted with buffer RLT and purified with Dynabeads MyOne silane. Input RNA and enriched RNA were then reverse-transcribed, end-repaired and dA-tailed, following ligation with sequencing adaptors. The library was PCR amplified, purified and analyzed on Bioanalyzer before sequencing.

treatment_protocol: Doxycyclin (1ug/ml) for for 24 hours, then Doxycyclin in parallel with alpha-amanitin 2.5ug/ml for 42 hours

tag: cell line

tag: genotype/variation


title: CCOC-3_H3K27ac_ChIP-seq

source_name: Epithelial ovarian cancer

tag: tissue

value: Clear cell ovarian cancer


title: 1502_1502IRN_24h_1

tag: treatment

tag: harvest time


title: CCOC-5_H3K27ac_ChIP-seq


title: SAMPLE 92: Control 14, BS

source_name: Prefrontal cortex 14

tag: sample type

tag: Sex

value: Female

tag: age


title: 1502_1502IRN_24h_2


title: 1502_IRN_144h_3

value: irinotecan, 2.5mg/kg


title: WT rep2


title: WT.IP.rep2

description:
4264_8_WT-2_IP_GTGAAA_S22_L004
RNAPII WT. Rep2


title: CCOC-1_H3K27ac_ChIP-seq


title: CCOC-2_H3K27ac_ChIP-seq


title: SAMPLE 90: Control 12, BS

source_name: Prefrontal cortex 12

tag: pmi (hours)

tag: condition

tag: brain bank


title: SAMPLE 91: Control 13, BS

source_name: Prefrontal cortex 13


title: 1502_IRN_24h_3


title: SAMPLE 89: Control 11, BS

source_name: Prefrontal cortex 11

value: Bispebjerg Brain Bank