title: Hi-C library mutant rep 2

city: Seattle

first: Alessandro

last: Bertero

state: WA

address: 850 Republican St

department: Institute for Stem Cell and Regenerative Medicine

institute: University of Washington

data_processing:
Reads were mapped with BWA-MEM version 0.7.13 to hg38 using default parameters. Secondary mappings were filtered out with samtools.
Primary mappings were processed using HIC-PRO version 2.7.6, excluding pairs less than 1KB apart and excluding MAPQ scores <30, to generate validPairs files and ICED normalized counts, outputed as a bed file of bins and a three column file of bins and contact counts.
validPair files were used as input for HOMER version 4.7 at 500KB resolution to generate PC1 values (A/B compartment calls).
Genome_build: hg38
Supplementary_files_format_and_content: allValidPairs file is processed output from HiC-Pro and contains read name and mapping location for the two reads after passing distance and quality threshold
Supplementary_files_format_and_content: iced.matrix file is the 3 column counts matrix (Bin1, Bin2, counts) corresponding to the bins.bed file at 500KB resolution, output from HiC-Pro.
Supplementary_files_format_and_content: PC1.bedGraph files are the ouput from HOMER on the processed Hi-C data, representing the A/B compartment calls, in bedGraph format (coordinates and score)

source_name: Hi-C library mutant

growth_protocol: Human induced pluripotent stem cells (hiPSCs) were cultured and differentiated into cardiomyocytes (hiPSC-CM) with minor modifications of previously described methods (Burridge et al., 2014; Fields et al., 2017). hiPSCs were cultured on plates pre-coated with 0.5 µg/cm2 recombinant human Laminin-521 matrix (rhLaminin521; Biolamina) with daily changes of antibiotic-free Essential 8 (E8) media (ThermoFisher). Cells were passaged as small clumps with Versene (ThermoFisher), and 10 µM Y-27632 (Tocris) was added for the first 16 hr. For hiPSC-CM generation, cells were passaged as single cells with Versene, and seeded at a density of 2.5 x 105 per well of a 12-well plate pre-coated with 2 µg/cm2 rhLaminin521 (denoted day -2). After 24 hr media was changed to E8 with 1 µM CHIR-99021 (Cayman), denoted day -1. On day 0 media was changed to RBA media (RPMI 1640 with glutamine, ThermoFisher, supplemented with 500 µg/ml BSA and 213 µg/ml ascorbic acid, both from Sigma-Aldrich) supplemented with 4 µM CHIR-99021. At day 2, media was changed to RBA with 2 µM WNT-C59 (Selleckchem). On day 4, media was changed to RBA. On day 6, media was changed to RPMI-B27 media (RPMI with 1x B-27 supplement, both from Thermo Fisher), with further media changes every other day. Beating was first observed between day 7 and day 9, and cells were cultured until day 14 before collection.

extract_protocol:
Cells were lysed using 10 mM Tris-HCl, pH 8.0, 10 mM NaCl, 0.2% Igepal CA-630, 1x Protease Inhibitor in ddH2O
Library prep was carried out using the in situ DNase Hi-C protocols (V. Ramani et al. Nat Protoc. 2016). Samples were barcoded during final library PCR and samples were demultiplexed prior to downstream analysis. Each library was sequenced two independent times, and the results were merged during downstream analysis.

treatment_protocol: Cells were fixed using 2% formaldehyde for 10 minutes.

tag: cell type

value: human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM)

value: R225X LMNA mutant hiPSCs

tag: time point

value: Day 14 of cardiac differentiation


title: UT241 peptide3

status: Public on Feb 13 2019

type: SRA

city: Minneapolis

first: Sathi

last: Wijeyesinghe

state: MN

country: USA

institute: University of Minnesota

description:
Ex vivo culture human tumor - peptide
Human 2 Unnormalized Counts.csv

library_source: transcriptomic

data_processing:
Quality control of FastQ files - FastQC
Low quality segments and adapters trimmed - Trimmomatic
Aligned to relevant reference genome - HiSat2
Differentially expressed genes were quantified - DESeq2
Genome_build: GRCm38; GRCh38
Supplementary_files_format_and_content: .csv files with normalized and unnormalized abundance measurements

molecule: total RNA

organism: Homo sapiens

source_name: endometrial tumor

extract_protocol:
RNA was isolated using TRIZOL and further purified using the QIAGEN RNA Cleanup Kit
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq Stranded mRNA Library Prep Kit)

tag: peptide

value: Relevant viral peptide

tag: peptide therapy

value: Ex vivo peptide culture w/ tumor slice


title: Hi-C library corrected 2 rep 2

library_source: genomic

molecule: genomic DNA

source_name: Hi-C library corrected 2

tag: cell line

value: R225R LMNA corrected 2 hiPSCs


title: UT241 peptide1


title: Hi-C library corrected 2 rep 1


title: Hi-C library mutant rep 1


title: 1771017037_E11

city: Freiburg

first: Ori

last: Staszewski

address: Breisacher Str. 64

department: Institute of Neuropathology

country: Germany

institute: University Medical Center Freiburg

data_processing:
Read processing was performed as described (Islam et al., Nat Methods. 2014 Feb;11(2):163-6), except that any RNA molecule (i.e. Unique Molecular Identifier) supported only by a single read were removed.
The first 6 bases of each read represent the random Unique Molecular Identifier used for molecule counting. After follows three or more Gs, stemming from the template switching at the mRNA 5' end during first strand cDNA synthesis. In some reads, one of the three Gs has been replaced by an A by the Illumina HiSeq software, representing failed base calling at that position. Cells were rejected if the showed less than 2000 mRNA molecules, more than 26,000 mRNA molecules (putative doublets) as well as cells that formed a separate cluster with no specific gene expression (putative damaged or dead cells). Genes that were detected at less than 4 molecules in the whole datasets were eliminated.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: comma separated file containing gene counts per sample

organism: Mus musculus

source_name: corpus callosum

extract_protocol:
The tissue pieces were dissociated using the Papain dissociation system (Worthington) following manufacturers recommendations, adjusting incubation time based on tissue piece size to 25-45 mins. Using glass pipettes of increasingly smaller tip diameter, the cell suspension was then filtered with 20um filter (Partec) and cells kept in N2 media, and cells loaded into C1 chips for cell capture.
Fluidigm C1 Autoprep System  Cells medium (10-17 micrometer) microfluidic was used to capture the cells. 14 microlitre of cell suspension (approx. 800 cells/microlitre in N2 culturing medium with DNaseI) was mixed with 7 microlitre C1 Suspension Reagent after filtering. Single-cells were then captured for 30 min at 4°C using the тАЬCell Load (1772x/1773x) script. The protocol for Lysis, RT and PCR was performed as previously described  (Islam et al., Nat Methods. 2014 Feb;11(2):163-6). Amplified cDNA was harvested with 13 microlitre Harvest Reagent and cDNA library quality was measured on an Agilent BioAnalyzer. Cell barcoding and fragmentation was performed in a single step using Tn5 DNA transposase as described previously. 1 microlitre Dynabeads MyOne Streptavidin C1 beads (Invitrogen) were resuspended in 20 microlitre Binding and Blocking buffer (10mM Tris, 250mM NaCl, 5mM EDTA, 0.5% SDS) and added to each well. After 15 min incubation at room temperature, all wells were pooled, the beads washed once with 100 microlitre Washing buffer (10mM Tris-150mM NaCl, 0.02% Tween), once in 100 microlitre Qiagen Qiaquick PB and then twice using 100 microlitre Washing buffer. Restriction was performed to cleave 3тАЩ fragments: the beads were incubated in 100 microlitre restriction mix (1x NEB CutSmart, 0.4 U/microlitre PvuI-HF enzyme) for 1h at 37°C. Finally, the beads were washed three times with Washing buffer, then resuspended in 30 µl ddH2O and incubated for 10 min at 70°C to elute the DNA. AMPure beads XP (Beckman Coulter) were used at 1.8x volume and eluted in 30 microlitre to remove short fragments.

tag: age


title: Hi-C library corrected 1 rep 2

source_name: Hi-C library corrected 1

value: R225R LMNA corrected 1 hiPSCs


title: COL237 peptide3

source_name: colon tumor


title: 1771017035_A01

source_name: cortex S1


title: 1771017034_E11


title: RNA-seq library mutant rep 3

description:
sample name in processed data file:
R225X_3_0

data_processing:
Reads were mapped to hg38 using STAR (version 2.5.2b) with default parameters and then quantified and processed through the Cufflinks suite (version 2.2.1), using cuffquant (CXB file), cuffnorm (fpkm and counts tables) and cuffdiff (differentiall expression).
Genome_build: hg38
Supplementary_files_format_and_content: gene_exp.diff is the differential expression between samples, applicable to all samples, from cuffdiff output.
Supplementary_files_format_and_content: genes.fpkm_table is the fpkm applicable to all samples, from cuffnorm output.

source_name: RNA-seq library mutant

extract_protocol:
Samples for RNA were collected in RLT and lysed with a Qiashredder (Qiagen) and then RNA was purified with a Qiagen RNeasy kit.
RNA-seq libraries were prepared from total RNA using the TruSeq Stranded Total RNA Ribo-Zero H/M/R kit (Illumina RS-122-2201). Samples were barcoded together for sequencing. RNA-seq libraries were sequenced on the NEXTSEQ.


title: Hi-C library corrected 1 rep 1


title: RNA-seq library mutant rep 2

description:
sample name in processed data file:
R225X_2_0


title: 1771017033_G06


title: RNA-seq library mutant rep 1

description:
sample name in processed data file:
R225X_1_0


title: COL237 control2

description:
Ex vivo culture human tumor - control
Human 2 Unnormalized Counts.csv

value: Irrelevant control peptide


title: COL237 control1


title: UT1424 peptide3

description:
Ex vivo culture human tumor - peptide
Human 1 Unnormalized Counts.csv


title: RNA-seq library corrected 2 rep 3

description:
sample name in processed data file:
R225R_38_3_0

source_name: RNA-seq library corrected 2


title: 1771017033_G02


title: UT1424 peptide2


title: 1771017032_H11


title: 1771017033_H02


title: RNA-seq library corrected 2 rep 2

description:
sample name in processed data file:
R225R_38_2_0


title: 1771017032_D10


title: UT1424 control3

description:
Ex vivo culture human tumor - control
Human 1 Unnormalized Counts.csv


title: UT241 control1


title: 1771017032_C11


title: RNA-seq library corrected 2 rep 1

description:
sample name in processed data file:
R225R_38_1_0


title: RNA-seq library corrected 1 rep 3

description:
sample name in processed data file:
R225R_15_3_0

source_name: RNA-seq library corrected 1


title: RNA-seq library corrected 1 rep 2

description:
sample name in processed data file:
R225R_15_2_0


title: COL237 peptide1


title: 1771017032_C08


title: RNA-seq library corrected 1 rep 1

description:
sample name in processed data file:
R225R_15_1_0


title: 1771013111_D04

source_name: ventral midbrain


title: 24h Mock

city: Cologne

first: Till

middle: David

last: Sauerwein

address: Gleueler Str. 60

department: Data Science and Services

institute: ZB MED - Information Centre for Life Sciences

description: Neisseria meningitidis + iPS-derived brain endothelial cells

data_processing:
Demultiplexing using bcl2fastq (v2.20.0.422)
Fastq quality trimming with Phred qualitiy score cut-off of 20 using cutadapt (v1.17)
Adapter removal using cutadapt (v1.17)
Poly(A)-trimming from the 3’ end (READemption 0.4.3, Förstner et al., 2014)
Size filtering: discarding reads shorter than 20 nt (READemption 0.4.3, Förstner et al., 2014)
Read mapping using segemehl version 0.2.0 (READemption 0.4.3, Förstner et al., 2014)
Coverage calculation (coverage-raw, READemption  0.4.3, Förstner et al., 2014)
Genome_build: Human: GENCODE release 28: GRCh38.p12,  Neisseria meningitidis MC58 (NCBI RefSeq accession number: NC_003112.2)
Supplementary_files_format_and_content: strand-specific wiggle

source_name: Bacterial cells + iPS-derived brain endothelial cells

growth_protocol: N. meningitidis MC58 strain was grown to mid-exponential phase in proteose-peptone medium (PPM) plus 1% Kellogg’s supplement I and II. Infection with a MOI of 10 was carried our for 24h.

extract_protocol:
RNA was precipitated through the TRIzol method followed by DNase treatment. Total RNA was precipitated by phenol-chloroform extraction followed by ethanol precipitation.
The libraries were generated by Vertis Biotechnologie AG (Munich, Germany). The samples were poly(A)-tailed by using poly(A) polymerase.  First-strand cDNA synthesis was performed with an oligo(dT)25 primer. The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and was analyzed by capillary electrophoresis. The primers used for PCR amplification were designed for TruSeq sequencing according to the instructions of Illumina.

treatment_protocol: Cells were detached through accutase treatment, and fixed with RNAlater. Sorting was based on size and GFP expression.

tag: infection

value: mock


title: HFD+DfCS-Ib_liver

city: Hangzhou

first: Shan

last: Li

state: 浙江省

address: 866 Yuhangtang Road

country: China

institute: Zhejiang University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Tophat2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
A |log2FoldChange|>1 and Q-value<0.001 were used to determine significance. Gene Ontology (GO) enrichment analysis of differentially expressed transcripts was implemented by the GOSeq R package, in which gene length bias was corrected. Kyoto Encyclopedia of Genes and Genomes (KEGG) biochemical pathways analysis was also performed by the web tool KEGG.
Genome_build: mm10, Ensembl v73
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: liver

growth_protocol: C57BL/6J mice, male, weighting from 24 ± 2 g, were purchased from the m Shanghai Slaccas Laboratory Animal Company (Certiﬁcate Number SCXK (hu) 2007-0005, Shanghai, China). The animals were housed in stainless steel cages at room temperature (25 ± 2 ℃) and 12 h light cycle. The animals were fed with a commercial chow for a week to acclimatize to animal facilities. The animals were then weighed and randomly divided into five groups of 8 mice. One group were fed regular chow (normal control) and the other two groups was fed on a HFD. All animal maintenance and use procedures were in accordance with the guidelines of the Laboratory Animal Centre at Zhejiang University.

extract_protocol:
Total RNA was isolated using a total tissue TRIzol® Plus RNA Purification Kit (Invitrogen, America). Equal amounts of total RNA were used to synthesize cDNA with the Quant II fast RT kit (Tools, Taiwan).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: One group receiving HFD served as a negative control; meanwhile anther group receiving HFD was given DfCS-Ib in a dose of 40 mg/kg as treatment. DfCS-Ib were dissolved in 0.3ml distilled water and administered orally by metallic gavage needle. The mice were allowed free access to food and water during the experimental period.

tag: strain

tag: Sex

value: male

value: 14 weeks

tag: sample group

value: HFD + 40 mg/kg  DfCS-Ib

tag: tissue

value: liver


title: Control_liver

value: regular chow (normal control)


title: HFD_liver

value: high-fat diet (HFD)


title: AG1478_384wPlateC

city: Nijmegen

first: Jan

middle: Patrick

last: Gerlach

address: Geert Grooteplein Zuid 28

department: Molecular Developmental Biology

country: Netherlands

institute: Radboud Institute for Molecular Life Sciences

data_processing:
Read1 and Read2 where swapped to allow compatibility with CELseq2 pipeline
Reads were assigned to individual cells using the demultiplexing function of the CELseq2 pipeline
Transcripts were Mapped and UMI corrected using standard settings of the CELseq2 pipeline - Reads were trimmed to 50 bases before mapping to UCSChg38 and hereafter matched to the gencode.v25.basic.annotation transcriptome
A count table from all six samples was generated (Transcripts_RAWcounts.tab.gz) where ControlA, ControlB, ControlC represent the untreated cells and AG1478A, AG1478B, AG1478C represent the treated cells
Antibody-RNA barcode UMIs were counted using an adapted version of the IDseq pipeline (van Buggenum et al) and a count table was generated (RAID_ARC_Rawcounts.csv)
For normalization of the transcriptome measurements, 4500 UMI counts were subsampled from the transcriptomes of all cells and cells with fewer counts were discarded. (mRNA_counts_SUB4500.csv.gz) is the count table with the sampled counts from the cells that passed this threshold. Note that cells that did not pass the threshold of 400 UMI counts for antibody measurements were also removed.
For normalization of the antibody measurements, 400 UMI counts were subsampled from the raw data of all cells and cells with fewer counts were discarded. (antibody_counts_SUB400.csv) is the count table with the sampled counts from the cells that passed this threshold.Note that cells that did not pass the threshold of 4500 UMI counts for mRNA were also removed.
Genome_build: UCSChg38
Supplementary_files_format_and_content: The .csv file (RAID_ARC_Rawcounts.csv) contains Antibody RNA-Barcode UMI counts for the indicated antibodies for all cells - without normalization
Supplementary_files_format_and_content: The tab.gz file (Transcripts_RAWcounts.tab.gz) contains transcript UMI counts of EGFR and ITGA6 for all cells - without normalization
Supplementary_files_format_and_content: The .csv file (antibody_counts_SUB400.csv) contains 400 sampled UMI counts for the Antibody RNA-Barcode measurements - for the cells that passed the quality threshold of 4500 transcript counts and 400 antibody-barcode counts
Supplementary_files_format_and_content: The .csv.gz file (mRNA_counts_SUB4500.csv.gz) contains 4500 sampled transcript UMI counts - for the cells that passed the quality threshold of 4500 transcript counts and 400 antibody-barcode counts

molecule: polyA RNA

source_name: Foreskin keratinocytes

extract_protocol:
Reverse Transcription from detergent and heat based lysates
RAID library prep

value: Foreskin keratinocytes

tag: treatment

value: Treated for 48 hours with 10 uM AG1478

tag: growth conditions

value: Keratinocyte Serum Free Medium


title: AG1478_384wPlateB


title: MCW SS HS_DT_RNA-seq Replicate 3 [862]

city: Milwaukee

first: Pengyuan

last: Liu

state: Wisconsin

address: 8701 Watertown Plank Road

department: Physiology

institute: Medical College of Wisconsin

data_processing:
Data QC and trim with trim_galore version 0.2.5
Read alignment with TopHap version 2.1.1
Transcript quantification and normalization with cufflinks version 2.2.1
Differential expression analysis with cufflinks version 2.2.1
Genome_build: rn5
Supplementary_files_format_and_content: transcript/gene abundance

organism: Rattus norvegicus

source_name: MCW SS HS_DT

extract_protocol:
Renal outer medulla tissues were collected, and RNA were extracted from these tissues using using Trizol reagent.
Libraries for RNA-Seq were prepared using a NeoPrep System from Illumina, following the vendor's instructions.

treatment_protocol: HS_SCR rats were treated with intra-renal administration of a scrambled GapmeR (4 mg/kg) and fed the 4% NaCl diet for 7 days. HS_DT rats were treated with intra-renal administration of GapmeR’s targeting Dnmt3a and Tet3 (2 mg/kg each) and fed the 4% NaCl diet for 7. “0.4% salt” rats were surgically prepared in the same way as the groups of HS_SCR and HS_DT, but used for tissue collection just prior to when we would initiate the GapmeR treatment and high salt diet.

value: MCW SS

tag: diet

value: high salt, 4.0%, NaCl

value: GapmeR's targetting Dnmt3 and Tet3

value: renal outer medulla


title: MCW SS HS_DT_RNA-seq Replicate 2 [782]


title: AG1478_384wPlateA


title: MV4;11 70 mg/kg CBL0137 treated replicate 1

city: Randwick

first: Michelle

last: Haber

state: NSW

address: Lowy Cancer Research Centre, PO BOX 81

country: Australia

institute: Children's Cancer Institute

description:
RNA sequencing data of MV4;11 CBL0137 treated replicate 1
MV701

data_processing:
Illumina paired-end RNA sequencing data was aligned using STAR to the human genome assembly hg19 and mouse genome assembly mm10
BAM files were sorted and index using SAMtools
Gene expression and isoform expression counts were calculated using RSEM
Genome_build: hg19 and mm10
Supplementary_files_format_and_content: txt file contains the TPM counts for each gene in each of the samples

organism:
Homo sapiens
Mus musculus

extract_protocol:
RNA was isolated with Trizol
RNA-seq libraries were generated using Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold prep kit using 1 μg of RNA input

treatment_protocol: > 1 million MV4;11 cells were inoculated subcutaneously in the flank of NOD/SCID (NOD/SCID NOD.CB17-Prkdcscid/SzJ) mice. When tumors measured around 100 mm3, mice were treated with CBL0137 (70 mg/kg CBL0137 intravenously) on day 0 and day 8. Tumors were harvested 24h post last injection on day 8. Tumors were also harvested from untreated mice. Tumors were flash frozen in liquid nitrogen and RNA was isolated.

value: Subcutaneous MV4;11 tumor

value: treated with curaxin CBL0137


title: MV4;11 70 mg/kg CBL0137 treated replicate 2

description:
RNA sequencing data of MV4;11 CBL0137 treated replicate 2
MV702

source_name: MV4;11 cells were inoculated subcutaneously in the flank of NOD/SCID (NOD/SCID NOD.CB17-Prkdcscid/SzJ) mice.


title: Untreated_384wPlateC

value: Untreated


title: UT1424 control2

value: Irrelevant control peptide

value: Ex vivo peptide culture w/ tumor slice


title: MCW SS HS_DT_RNA-seq Replicate 1 [781]


title: Untreated_384wPlateB


title: MCW SS HS_SCR_RNA-seq Replicate 3 [871]

source_name: MCW SS HS_SCR


title: UT1424 peptide1

value: Relevant viral peptide


title: Untreated_384wPlateA


title: MV4;11 untreated replicate 1

description:
RNA sequencing data of MV4;11 untreated replicate 1
MVcontr1

value: untreated


title: UT1424 control1


title: MCW SS HS_SCR_RNA-seq Replicate 2 [785]


title: MCW SS HS_SCR_RNA-seq Replicate 1 [784]


title: AS2

city: Beijing

first: Ruicai

last: Long

address: No. 2 Yuanmingyuan west road, Haidian, Beijing

institute: Institute of Animal Sciences, Chinese Academy fo Agricultral Sciences

data_processing:
Reads with 18-30nt were selected as clean reads.
Clean reads were aligned to Silva, GtRNAdb, Rfam databases with Bowtie to remove rRNA, tRNA, snRNA, snoRNA and other non-coding RNA.
The rest of the sRNA were aligned to Medicago truncatula genome (Version Mt4.0) with miRDeep2 which could identify and annotate conserved miRNA genes to obtain mapped reads, and the parameters were changed to fit for the plant miRNAs identification . The remaining reads were used to detect known miRNA and novel miRNA predicted by comparing with known miRNAs from miRBase. RNAfold and randfold were used in novel miRNA secondary structure prediction.
The miRNA expression fold changes between treatment and control groups were computed with using the DESeq R package (1.10.1) provide statistical routines for determining differential expression in digital miRNA expression data using a model based on the negative binomial distribution.
Genome_build: Medicago truncatula genome (Version Mt4.0)

organism: Medicago truncatula

source_name: plant seedling

growth_protocol: Seeds of Medicago truncatula genotype R108 were immersed in sulphuric acid for 2 minutes to remove the hard shell and sterilized with 75% ethanol for 10min, then rinsed with sterile water and cultivated with a single sheet of Whatman ﬁlter paper in three Petri dishes for germination.

extract_protocol:
The total RNA of each sample, three biological replicates were prepared, was isolated using Trizol Reagent (Invitrogen, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Ten milliliter water was applied to one dish as control and the other two dishes were applied with treatment solutions of NaCl + Na2SO4 (20 mM) or Na2CO3 + NaHCO3 (5 mM). The dishes were incubated in a growth chamber maintained at 25°C day and 20 °C night temperatures, 16h/8h light/dark photoperiod, and 60% relative humidity. After 72 h cultivation the entire seedlings in three different treatments were harvested.

tag: Stage

value: 3 day-old seedling

value: alkali

value: plant seedling


title: AS1


title: AS3


title: MCW SS 0.4% salt_RNA-seq Replicate 3 [861]

source_name: MCW SS 0.4% salt

value: Low salt, 0.4% NaCl


title: Pat5_2_2.coutt.csv

first: Sagar

address: Hugstetter Straße 55

department: Department of Internal Medicine II

description: library of 192 cells

data_processing:
For image aquisition, intensity extraction and basecalling HiSeq Control Software  2.0.2, RTA 2.4.11 / Recipe Fragment 2.0.0.2 was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57,207 isoforms derived from 57,207 gene loci with 57,114 isoforms mapping to fully annotated chromosomes (1 to 19, X, Y, M). All isoforms of the same gene were merged to a single gene locus. Furthermore, gene loci overlapping by >75% were merged to larger gene groups. This procedure resulted in 34,111 gene groups.
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a poly(T) stretch. The left read was not used for quantification. For each cell barcode, the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs was converted into transcript counts (Gruen et al., 2014).
Genome_build: ENCODE VM9
Supplementary_files_format_and_content: CSV files, columns represent each cell barcode (total barcodes used = 192), rows represent the geneid and the values in the file are the quantified number of transcripts.

source_name: Healthy brain parenchyma

extract_protocol:
Isolated myeloid cells were stained with antibodies for surface markers (CD45, CD3, CD19, CD20). All CD45+ cells were FACS-sorted in 384-well plates.
As described in mCEL-Seq2 protocol (Hashimshony et al. 2016 and Herman et al. 2018)
Adapted from TruSeq Small RNA Library Preparation Protocol

treatment_protocol: All subjects underwent brain surgery, the healthy samples were located at least 2 cm from the lesion the patients underwent surgery for; the MS samples were taken from the center of an active lesion

value: Temporal lobe


title: YAP2_HepG2#3

type: RNA

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description: HepG2 cells transfected with YAP2 specific siRNA

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of human Hugene-2_0-type from Affymetrix. A Custom CDF Version 19 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

label: biotin

source_name: liver cancer cell line

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

growth_protocol: HepG2 cells were cultured in RPMI medium supplemented with 10% FCS and 1% penicillin/streptomycin.

extract_protocol: For isolation of total RNA, the NucleoSpin RNA II kit was used according to the manufacturer's instructions (Machery-Nagel, Düren, Germany).

treatment_protocol: For siRNA inhibition assays cells were seeded one day before transfection. Untreated and nonsense siRNA-treated cells served as controls. SiRNAs (final concentration 20 nM) and the transfection reagent Oligofectamine (Life Technologies, Darmstadt, Germany) were diluted in Opti-MEM (Gibco/Life Technologies), mixed and incubated at room temperature, before being distributed onto the cells, which were covered with Opti-MEM. Four hours later fresh medium was added and 24 hours later the medium was replaced.

value: liver cancer cell line

tag: vector


title: YAP2_HepG2#1


title: AS7#: model_rep1

city: Shanghai

first: Xiaolan

last: Yu

address: 800 Dongchuan RD, Minhang District

institute: Shanghai JiaoTong Univerisity

description: Gene expression of progression of atherosclerosis

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, GeneSpring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Oryctolagus cuniculus

source_name: abdominal aorta, AS 30 day, replicate 1

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

growth_protocol: caged feeding,  temperature 20-26 °C, humidity 40%-70%

extract_protocol: Total RNA was extracted using TRIZOL reagent following the manufacturer’s instructions and checked for an RNA Integrity Number (RIN) to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA (RIN ≥ 7) was further purified by RNeasy micro kit (QIAGEN, GmBH, Germany) and RNase-Free DNase Set (QIAGEN, GmBH, Germany).

treatment_protocol: The rabbit model of progression and regression of atherosclerosis(AS) was established through balloon injury and high-cholesterol diet for 4 weeks and return to normal diet for 4 weeks.Blood was collected at each point at 0, 2, 4 and 8 weeks for lipid measurement, respectively. At the end of 4th and 8th weeks, we used intravascular ultrasound imaging to confirm the formation and regression of lesion. Control group is the 0 day of AS,  model group is the 30 day of AS,  recovery  group is the 60 day of AS.At the indicated time points, after IVUS analysis, rabbits were sacrificed and the abdominal aortas from the diaphragm to the iliofemoral artery were excised. The aortas were washed in phosphate buffered saline (PBS) and immediately fixed in RNA Later and stored at -80°C for mRNA extraction.

value: abdominal aorta

value: male


title: YAP2_HepG2#2


title: MCW SS 0.4% salt_RNA-seq Replicate 1 [859]

value: MCW SS


title: MV4;11 untreated replicate 2

description:
RNA sequencing data of MV4;11 untreated replicate 2
MVcontr2


title: MCW SS 0.4% salt_RNA-seq Replicate 2 [860]

value: renal outer medulla


title: SS3

value: salt


title: Pat5_1_1.coutt.csv

description: library of 192 cells


title: MCW SS HS_DT, Replicate 4 [783]

description:
RRBS_LOM783_TTAGGC_L008
processed data file: RRBS.dataset2.processed.txt.gz

data_processing:
Data QC and trim with trim_galore version 0.2.5
Read alignment with methylcoder version 2012-07-27
CpGs calling with methylcoder version 2012-07-27
Genome_build: rn5
Supplementary_files_format_and_content: read counts of methylated and unmethylated cyttosines at CpG sites

extract_protocol:
Renal outer medulla tissues were collected, and genomic DNA was extracted using PureLink genomic DNA mini kit
Libraries for RRBS were prepared and sequenced largely following the protocols described by Gu, et al (Nat Protoc. 2011;6(4):468-81)

treatment_protocol: MCW SS LS rats were maintained on a purified diet, AIN-76A, containing 0.4% NaCl until 8 weeks old. CRL SS LS rats were maintained a non-purified diet, 5L2F, containing 0.75% NaCl until 8 weeks old. MCW SS HS and CRL SS HS rats were maintained on AIN-76A diet containing 4% NaCl for 14 days starting at 6 weeks of age.  HS_SCR rats were treated with intra-renal administration of a scrambled GapmeR (4 mg/kg) and fed the 4% NaCl diet for 7 days. HS_DT rats were treated with intra-renal administration of GapmeR’s targeting Dnmt3a and Tet3 (2 mg/kg each) and fed the 4% NaCl diet for 7. “0.4% salt” rats were surgically prepared in the same way as the groups of HS_SCR and HS_DT, but used for tissue collection just prior to when we would initiate the GapmeR treatment and high salt diet.

value: high salt, 4.0%, NaCl

value: GapmeR's targetting Dnmt3 and Tet3


title: SS1


title: SS2


title: control_HepG2#3

description: HepG2 cells transfected with Nonsense/Scrambled siRNA

value: allstar


title: YAP1_HepG2#3

description: HepG2 cells transfected with YAP1 specific siRNA


title: YAP1_HepG2#1


title: Untreated_384wPlate1

data_processing:
Read1 and Read2 where swapped to allow compatibility with CELseq2 pipeline
Reads were assigned to individual cells using the demultiplexing function of the CELseq2 pipeline
Transcripts were Mapped and UMI corrected using standard settings of the CELseq2 pipeline - Reads were trimmed to 50 bases before mapping to UCSChg38 and hereafter matched to the gencode.v25.basic.annotation transcriptome
A count table from all samples was generated (Transcripts_RAWcounts.tab.gz)  where ControlA, ControlB represent the untreated cells and AG1478A, AG1478B represent the treated cell
Antibody-RNA barcode UMIs were counted using an adapted version of the IDseq pipeline (van Buggenum et al) and a count table was generated (ARC_Rawcounts_EGFR_ITGA6.csv)
For normalization of the transcriptome measurements, 10000 UMI counts were subsampled from the transcriptomes of all cells and cells with fewer counts were discarded. (mRNA_counts_SUB10K_genenames_JPGIII170.csv.gz) is the count table with the sampled counts from the cells that passed this threshold
Genome_build: UCSChg38
Supplementary_files_format_and_content: The .csv file (ARC_Rawcounts_EGFR_ITGA6.csv) contains Antibody RNA-Barcode UMI counts of EGFR and ITGA6 for all cells - without normalization
Supplementary_files_format_and_content: The tab.gz file (Transcripts_RAWcounts.tab.gz) contains transcript UMI counts for all cells - without normalization
Supplementary_files_format_and_content: The csv.gz file (mRNA_counts_SUB10K_genenames_JPGIII170.csv.gz) contains the subsampled transcript UMI counts - for the cells that passed the quality threshold of 10000 transcript counts and 2750 antibody-barcode counts

value: Foreskin keratinocytes

value: Untreated

value: Keratinocyte Serum Free Medium


title: AS8#: recovery_rep1

description: Gene expression of regression of atherosclerosis

source_name: abdominal aorta, AS 60 day, replicate 1


title: AG1478_384wPlate2

value: Treated for 48 hours with 10 uM AG1478


title: control_HepG2#2


title: control_HepG2#1


title: YAP1_HepG2#2


title: Untreated_384wPlate2


title: RAID_SetC

data_processing:
Read1 and Read2 where swapped to allow compatibility with CELseq2 pipeline
Reads were matched to individual cells using the demultiplexing function of the CELseq2 pipeline
Transcripts were Mapped and UMI corrected using standard settings of the CELseq2 pipeline - Reads were trimmed to 50 bases before mapping to UCSChg38 and hereafter matched to the gencode.v25.basic.annotation transcriptome
A count tables from all six samples was generated (UMI_Count_Table_JPGII170.tab.gz) where UnfixedA, UnfixedB, UnfixedC represent the unfixed cells and RAID-A, RAID-B, RAID-C represent the cells that were fixed and mock-stained according to the RAID procedure
For normalization, 40000 UMI counts were subsampled from all cells and cells with fewer counts were discarded. JPGII170_40K_SUB_GEO.csv.gz is the count table with the sampled counts
Genome_build: UCSChg38
Supplementary_files_format_and_content: The .csv.gz file contains 40000 sampled transcipt UMI counts for the cells from all 6 samples - samples are indicated in cell name
Supplementary_files_format_and_content: The tab.gz file contains contains raw transcipt UMI counts, as obtained from the CELseq2 pipeline, for the cells from all 6 samples - samples are indicated in cell name

extract_protocol:
Reverse Transcription from detergent and heat based lysates, according to the SORT-seq/CELseq2 protocol
CELseq2 library prep

tag: condition

value: RAID - Mock staining


title: RAID_SetB

tag: cell type


title: Pat4_Pl2_1_8.coutt.csv

description: library of 192 cells


title: AG1478_384wPlate1


title: DW3

value: 3 day-old seedling

value: control

value: plant seedling


title: MCW SS HS_DT, Replicate 3 [862]

description:
RRBS_LOM862_TAGCTT_L008
processed data file: RRBS.dataset2.processed.txt.gz


title: RAID_SetA


title: Pat4_Pl2_1_7.coutt.csv

description: library of 192 cells

value: Temporal lobe


title: MCW SS HS_DT, Replicate 2 [782]

description:
RRBS_LOM782_CGATGT_L008
processed data file: RRBS.dataset2.processed.txt.gz


title: MCW SS HS_DT, Replicate 1 [781]

description:
RRBS_LOM781_ATCACG_L008
processed data file: RRBS.dataset2.processed.txt.gz


title: DW1


title: DW2


title: Pat4_Pl1_1_5.coutt.csv

description: library of 192 cells


title: Pat4_Pl1_2_6.coutt.csv

description: library of 192 cells


title: PBS: control_rep1

description: Gene expression for control

source_name: abdominal aorta, AS 0 day, replicate 1

value: abdominal aorta


title: Unfixed_SetB

value: Unfixed cell


title: Pat3_GM_2_6.coutt.csv

description: library of 192 cells


title: 24h MC58 GFP +

organism:
Homo sapiens
Neisseria meningitidis MC58

value: Neisseria meningitidis MC58


title: Unfixed_SetA


title: MCW SS HS_SCR, Replicate 1 [784]

description:
RRBS_LOM784_TGACCA_L008
processed data file: RRBS.dataset2.processed.txt.gz

value: MCW SS

value: renal outer medulla


title: MCW SS HS_SCR, Replicate 3 [871]

description:
RRBS_LOM871_CTTGTA_L008
processed data file: RRBS.dataset2.processed.txt.gz

value: high salt, 4.0%, NaCl


title: Pat3_WM_2_8.coutt.csv

description: library of 192 cells


title: Pat2_WM_2_4.coutt.csv

description: library of 192 cells


title: Unfixed_SetC


title: MCW SS 0.4% salt, Replicate 4 [858]

description:
RRBS_LOM858_GCCAAT_L008
processed data file: RRBS.dataset2.processed.txt.gz

value: Low salt, 0.4% NaCl


title: MCW SS 0.4% salt, Replicate 3 [861]

description:
RRBS_LOM861_GATCAG_L008
processed data file: RRBS.dataset2.processed.txt.gz


title: Pat2_WM_1_3.coutt.csv

description: library of 192 cells


title: MCW SS HS_SCR, Replicate 4 [870]

description:
RRBS_LOM870_GGCTAC_L008
processed data file: RRBS.dataset2.processed.txt.gz


title: Pat3_GM_1_5.coutt.csv

description: library of 192 cells


title: Pat2_GM_2_2.coutt.csv

description: library of 192 cells


title: MCW SS HS_SCR, Replicate 2 [785]

description:
RRBS_LOM785_ACAGTG_L008
processed data file: RRBS.dataset2.processed.txt.gz


title: CRL SS HS Replicate 4 [1281]

description:
1281_ATGTCA_L006
processed data file: RRBS.dataset1.processed.txt.gz

source_name: CRL SS HS

value: CRL, SS


title: MCW SS 0.4% salt, Replicate 1 [859]

description:
RRBS_LOM859_CAGATC_L008
processed data file: RRBS.dataset2.processed.txt.gz


title: Pat1_WM_1_11.coutt.csv

description: library of 192 cells


title: CRL SS HS Replicate 2 [1279]

description:
1279_AGTCAA_L006
processed data file: RRBS.dataset1.processed.txt.gz


title: MCW SS 0.4% salt, Replicate 2 [860]

description:
RRBS_LOM860_ACTTGA_L008
processed data file: RRBS.dataset2.processed.txt.gz


title: CRL SS HS Replicate 3 [1280]

description:
1280_AGTTCC_L006
processed data file: RRBS.dataset1.processed.txt.gz


title: T0 (not depurated) pop4

city: Roscoff

first: Arnaud

last: TANGUY

address: Place Georges Teissier

department: Station Biologique

country: France

institute: Sorbonne University

description:
T0 (not depurated)
Biological replicate 4 of T0 (not depurated)

hyb_protocol: Slide hydridization in Appligen chambers at 65°C for 17h, slide washing with buffer 1a nd 2 (Agilent technologies, IncWilnington, USA)

scan_protocol: Feature extraction software (version 9.5.3.1, Agilent Technologies, Inc)

data_processing:
The background correction of the probe intensity was carried out using the normexp method using R Studio (www.rstudio.com) and BioConductor and Limma library. Technical artefacts were removed using quantile normalization while intra- and inter-slide loess normalizations were applied to remove Cy3 and Cy5 intensity dependent trends. Only probes showing signal intensity three times superior to the background signal – and this, in more than 20% of the samples – were kept for the analysis. Intensities’ data were then log2-transformed and replicated values of each gene were averaged. The expression ratio of each gene was then calculated by substracting the log2 signal intensity of the gene for one given sample by the average log2signal intensity of the gene from all samples (we obtain a deltalog2 value) in order to normalize gene expression.
Fold change are then calculated using the formula Power (2; deltalog2) to obtain a RQ index and when RQ is comprised between 1 and infinite, RQ corresponds to positive values of Fold Change and when RQ is comprised between 0 and 1, RQ is changed by the formula -1/RQ that corresponds to negative Fold Change values

organism: Bathymodiolus azoricus

label_protocol: Agilent Low Input Quick Amp Labelling Kit

extract_protocol: Total RNA extrcated using trizol following manufacturer's instructions

treatment_protocol: Mussels exposed in cages

value: Gill

value: Adult


title: 27_P4r

city: RTP

first: Leah

middle: M.

last: Norona

state: NC

address: 6 Davis Drive

department: Institute for Drug Safety Sciences

institute: University of North Carolina at Chapel Hill

hyb_protocol: Labeled cRNA (15 μg) was fragmented and prepared for hybridization

scan_protocol: The Affymetrix Clariom S Human 96 peg arrays were used with the Affymetrix Gene Titan system. Gene Titan robotic instrumentation was used to perform the hybridization, washing, and scanning of the peg arrays.

data_processing: Affymetrix CEL files were normalized using Robust Multi-array Average (RMA) method with a log base 2 (log2) transformation (Irizarry et al., 2003). Principal component analysis (PCA) was used to evaluate the overall performance of the arrays and identify outliers. Samples > 3 SD away from the mean suggest these samples may be aberrant and were therefore omitted from analysis (3_P3, 1_P3, 20_P1 and 14_P3). A filtering step was performed to remove control probe sets and the mean + 1 SD of the antigenomic probe sets was used to filter low expression probe sets. Gene expression differences were identified using ANOVA models with linear contrasts.

source_name: human bioprinted liver RNA

label_protocol: Double-stranded cDNA was synthesized from 50-150 ng (dependent on RNA yield) of total RNA, then transcribed to biotin-labeled cRNA using the 3’ Express IVT kit (Affymetrix) according to manufacturer’s instructions.

growth_protocol: 3D bioprinted tissues were manufactured using previously described methods (Norona et al., 2016). Tissues were allowed to mature for 6 days post-manufacture before initiating studies.

extract_protocol: Tissue lysates were prepared for each treatment group by homogenization in TRIzol® Reagent (ThermoFisher Scientific, Waltham, MA) using PreCellys RNase-free microfuge tubes and the Precellys 24 homogenizing instrument (Bertin Corp., Rockville, MD). Total RNA was isolated using the Direct-Zol™ RNA MiniPrep kit per the manufacturer’s instructions (Zymo Research, Irvine, CA).

treatment_protocol: Treatment was initiated on Day 7 post-manufacture. Dosing medium was replaced every 24hrs. Two treatment regimens were used for each tissue composition in which tissues were continuously exposed for either 14 or 28 days.

value: TGF

tag: concentration

tag: -/+ kcs

value: Yes

tag: time

tag: print

value: Print 4r


title: 28_P4r


title: Pat1_GM_1_5.coutt.csv

description: library of 192 cells


title: T0 (not depurated) pop3

description:
T0 (not depurated)
Biological replicate 3 of T0 (not depurated)


title: BasaltT3 (depurated) BasaltT3b

description:
BasaltT3 (depurated)
Biological replicate  2 of BasaltT3 (depurated)


title: 26_P4r


title: 21_P2

value: Print 2


title: Pat1_GM_2_6.coutt.csv

description: library of 192 cells


title: MS_case5_18_Plate2_2.coutt.csv

description: library of 192 cells

source_name: Active MS lesion

value: Patietal lobe


title: 21_P1

value: No

value: Print 1


title: T0 (not depurated) pop2

description:
T0 (not depurated)
Biological replicate 2 of T0 (not depurated)


title: Pat1_WM_1_12.coutt.csv

description: library of 192 cells

value: Temporal lobe


title: BasaltT1 (partially depurated) BasaltT1a

description:
BasaltT1 (partially depurated)
Biological replicate 1  of BasaltT1 (partially depurated)


title: T0 (not depurated) pop1

description:
T0 (not depurated)
Biological replicate 1 of T0 (not depurated)


title: BasaltT1 (partially depurated) BasaltT1b

description:
BasaltT1 (partially depurated)
Biological replicate  2 of BasaltT1 (partially depurated)


title: CRL SS LS Replicate 4 [1278]

description:
1278_CTTGTA_L006
processed data file: RRBS.dataset1.processed.txt.gz

source_name: CRL SS LS

value: Low salt, 0.75% NaCl


title: 21_P3

value: Print 3


title: Treated MGO800, biological rep3

description: Gene expression data from TNF-α stimulated HUVECs exposed to 800mM methylglyoxal (and 20mM carnosine)

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of human Hugene-2_0-type from Affymetrix. A Custom CDF Version 20 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

source_name: Human umbilical vein endothelial cells, 12,5 ng/ml TNF-α, 800mM MGO, 20mM carnosine, 24 hours

growth_protocol: Cells were cultured on 1% gelatin coated flasks (Fluka, Neu-Ulm, Germany) in endothelial growth cell growth medium (Provitro, Berlin, Germany) supplemented with essential growth factors and 5% fetal bovine serum (Gibco, Carlsbad, USA). Cultures were maintained at 37°C, 95% relative humidity and 5% CO2. Confluent monolayers were passaged by trypsin 0.025%/ EDTA 0.01% and experiments were conducted on cells in passage 2-6 at approximately 90-100% confluence.

extract_protocol: Total RNA was prepared using Trizol reagent (Ambion, Carlsbad, USA) according to the manufacturer's instructions. RNA quality was confirmed by capillary electrophoresis on an Agilent 2100 bioanalyzer.

treatment_protocol: HUVECs were treated with different substances as indicated: 12,5 ng/ml TNF-α (PeproTech, Hamburg, Germany), 400 – 800 µM MGO (Sigma-Aldrich, St. Louis, USA) and 20 mM L-carnosine (Sigma-Aldrich).

tag: donor

value: C

tag: methylglyoxal [um]

tag: carnosine [mm]


title: 20_P2


title: Treated MGO400, biological rep3

description: Gene expression data from TNF-α stimulated HUVECs exposed to 400mM methylglyoxal (and 20mM carnosine)

source_name: Human umbilical vein endothelial cells, 12,5 ng/ml TNF-α, 400mM MGO, 20mM carnosine, 24 hours


title: CRL SS HS Replicate 1 [1282]

description:
1282_CCGTCC_L006
processed data file: RRBS.dataset1.processed.txt.gz

tag: strain

value: renal outer medulla


title: CRL SS LS Replicate 3 [1277_RP]

description:
1277_RP_TTAGGC_L006
processed data file: RRBS.dataset1.processed.txt.gz


title: MS_case5_18_Plate1_2.coutt.csv

description: library of 192 cells


title: MS_case5_18_Plate2_1.coutt.csv

description: library of 192 cells


title: CRL SS LS Replicate 2 [1276]

description:
1276_TAGCTT_L006
processed data file: RRBS.dataset1.processed.txt.gz


title: CRL SS LS Replicate 1 [1275]

description:
1275_GATCAG_L006
processed data file: RRBS.dataset1.processed.txt.gz


title: BasaltT3 (depurated) BasaltT3a

description:
BasaltT3 (depurated)
Biological replicate 1  of BasaltT3 (partially depurated)


title: MS_case4_18_Plate2_2.coutt.csv

description: library of 192 cells


title: MS_case4_18_Plate2_1.coutt.csv

description: library of 192 cells


title: MS_case4_18_Plate1_2.coutt.csv

description: library of 192 cells


title: MCW SS HS Replicate 4 [1249]

description:
1249_ACTTGA_L006
processed data file: RRBS.dataset1.processed.txt.gz

source_name: MCW SS HS

value: MCW SS

value: high salt, 4.0%, NaCl


title: MS_case2_Plate2_2_8.coutt.csv

description: library of 192 cells

value: Frontal lobe


title: Treated Control, biological rep3

description: Gene expression data from TNF-α stimulated HUVECs exposed to 0mM methylglyoxal (and 20mM carnosine)

source_name: Human umbilical vein endothelial cells, 12,5 ng/ml TNF-α, 0mM MGO, 20mM carnosine, 24 hours


title: 19_P3


title: MS_case2_Plate2_1_7.coutt.csv

description: library of 192 cells


title: 20_P3


title: MCW SS HS Replicate 3 [1246]

description:
1246_GCCAAT_L006
processed data file: RRBS.dataset1.processed.txt.gz


title: 19_P2


title: 16_P4r

value: VEH


title: MCW SS HS Replicate 2 [1184]

description:
1184_TGACCA_L006
processed data file: RRBS.dataset1.processed.txt.gz


title: MS_case2_Plate1_1_3.coutt.csv

description: library of 192 cells


title: 19_P1


title: Untreated Control, biological rep3

description: Gene expression data from TNF-α stimulated HUVECs exposed to 0mM methylglyoxal (w/o carnosine)

source_name: Human umbilical vein endothelial cells, 12,5 ng/ml TNF-α, 0mM MGO, 0mM carnosine, 24 hours


title: Untreated MGO400, biological rep3

description: Gene expression data from TNF-α stimulated HUVECs exposed to 400mM methylglyoxal (w/o carnosine)

source_name: Human umbilical vein endothelial cells, 12,5 ng/ml TNF-α, 400mM MGO, 0mM carnosine, 24 hours


title: MCW SS HS Replicate 1 [1183]

description:
1183_TTAGGC_L006
processed data file: RRBS.dataset1.processed.txt.gz


title: MCW SS LS Replicate 3 [1245]

description:
1245_ACAGTG_L006
processed data file: RRBS.dataset1.processed.txt.gz

source_name: MCW SS LS

value: Low salt, 0.4% NaCl


title: MS_case1_Pl2_2_10.coutt.csv

description: library of 192 cells


title: MCW SS LS Replicate 2 [1156]

description:
1156_RP_ATCACG_L006
processed data file: RRBS.dataset1.processed.txt.gz


title: 14_P4r


title: Treated MGO800, biological rep2

value: B


title: Untreated MGO800, biological rep3

description: Gene expression data from TNF-α stimulated HUVECs exposed to 800mM methylglyoxal (w/o carnosine)

source_name: Human umbilical vein endothelial cells, 12,5 ng/ml TNF-α, 800mM MGO, 0mM carnosine, 24 hours


title: 13_P4r

value: Yes


title: 12_P3


title: 12_P1


title: Untreated MGO800, biological rep2


title: 12_P2


title: Treated MGO400, biological rep2


title: Untreated MGO400, biological rep2


title: Untreated Control, biological rep2


title: Treated Control, biological rep2


title: MCW SS LS Replicate 1 [1155_RP]

description:
1155_ATCACG_L006
processed data file: RRBS.dataset1.processed.txt.gz


title: MS_case1_Pl1_2_10.coutt.csv

description: library of 192 cells


title: Treated MGO800, biological rep1

description: Gene expression data from TNF-α stimulated HUVECs exposed to 800mM methylglyoxal (and 20mM carnosine)

value: A


title: 11_P2

value: Print 2


title: Treated MGO400, biological rep1

description: Gene expression data from TNF-α stimulated HUVECs exposed to 400mM methylglyoxal (and 20mM carnosine)


title: MS_case1_Pl1_1_9.coutt.csv

description: library of 192 cells

value: Patietal lobe


title: 11_P1

value: No


title: MS_case1_4.coutt.csv

description: library of 192 cells


title: MS_case2_Plate1_2_4.coutt.csv

description: library of 192 cells


title: MS_case1_3.coutt.csv

description: library of 192 cells


title: 11_P3


title: Treated Control, biological rep1


title: Ppsal-WW-3

city: Córdoba

first: Alfonso

last: Olaya Abril

state: Córdoba

address: Campus de Rabanales, edificio c6, primera planta, ala norte

department: Biochemistry and molecular biology

country: Spain

institute: University of Córdoba

data_processing:
Raw reads were trimmed using cutadapt 1.14. with the following parameters: ambiguous limit, 2 nucleotides; quality limit, 0.01 (error probability); remove from 5’ and 3’, 4 bp. Then, Rockhopper was used to predict unannotated RNA in the Pseudomonas pseudoalcaligenes CECT5344 (HG916826.1) reference genome by applying the following parameters: strand specific, yes; seed length, 0.33; allowed mismatches, 0.15; and minimum expression of UTR and ncRNAs, 0.8. Reads aligned to unannotated regions (higher than 30% in all samples) were selected. Raw (fastaq files), processed data (wig files) and mapping (bam files) will be available on the GEO database.
High quality sequencing reads were mapped against the genome using as parameters: length fraction, 0.95; similarity fraction, 0.95. Resulting data were used to determine the expression levels of the unannotated RNAs predicted by Rockhopper based on the transcripts per million (TPM). After, a generalized linear model approach influenced by the multi-factorial EdgeR was used to carry out a differential expression analysis. The genes expressed differentially were filtered according to previous stablished parameters and considering a fold change ≥ 2 or ≤-2 and a FDR p-value ≤ 0.05. The putative sRNAs were classified as intergenic (encoded in intergenic regions) or antisense (encoded in the reverse direction of the putative ORFs).
Only sRNAs differentially expressed when compared ammonia growth conditions to cyanide-dependent growth (sodium cyanide or jewelry wastewater) were curated manually and considered for further analyses. Thus, the genetic environment of each sRNA was analyzed manually and the nearest Rho-independent terminator to each sRNA was identified using the FindTerm and ARNold softwares. Bacterial promoters in intergenic regions were predicted by using Prokaryotic Promoter Predictor and BDGP. The presence of predicted promoter regions and stop codons was applied as selecting criteria. Mfold was used to predict sRNA secondary structures. Potential sRNAs targets were identified by using the TargetRNA2 software. To identify bacterial sRNA homologues the sofwares GLASSgo, the bacterial sRNA Database (BSRD) database and BLASTn were used.
Genome_build: HG916826.1
Supplementary_files_format_and_content: Wig and tab-delimited text files include RPKM values for each Sample

organism: Ectopseudomonas oleovorans

source_name: Cells growth in jewelry wastewater_replicate 3

growth_protocol: To isolate P. pseudoalcaligenes CECT5344 RNA, cells were cultured in 100 mL Erlenmeyer flasks filled to 20% with the phosphate-containing minimal medium M9 at pH adjusted to 9.5. 50 mM sodium acetate and 2 mM ammonium chloride were used as carbon and nitrogen sources, respectively. After 24 h, when ammonium was consumed the specific nitrogen source was added (2 mM concentration in the media) sodium cyanide, cyanide from the jewelry wastewater or ammonium chloride. Three independent biological replicates were carried out for each nitrogen source used.  Cultures were kept at 30 ºC and continuous agitation at 220 rpm on a shaker. When cultures reached an absorbance at 600 nm ⁓ 0.3 and the remaining nitrogen source in the media was about 30-50% as previously described, 10 mL-aliquots were harvested by centrifugation at 4,000  g for 15 min. Pellets were kept at -80 ºC until use.

extract_protocol:
P. pseudoalcaligenes CECT5344 cells were suspended in 500 µl TRIsureTM (Bioline) and total RNA was isolated using the Direct-zolTM RNA Miniprep kit (Zymo Research) according to the instruction of the manufacturer. DNase incubation was carried out in the column with RNase-free DNase set and, when required, an additional post-column treatment was applied with DNase I (Ambion). Quality and quantity of the total RNAs were checked with Bioanalyzer (Agilent) and ND1000 spectrophotometer (Nanodrop 1000, Agilent Technologies-Wilmington, DE, USA). All samples showed an integrity number (RIN) higher than 6.9.
Library preparation and sequencing were performed by STABvida, Portugal. After the integrity number (RIN) and concentration of RNAs were analyzed to ensure it is of sufficient integrity and quantity (>10 μg and 6.9, respectiely), cDNA was synthetized by using the Small RNA Library Preparation Kit (Bio Scientific). The resulting DNA library was sequenced in the Ilumina Hiseq 2500 platform using 100pb single-end sequencing reads. The corresponding FASTQ files were obtained as result.

treatment_protocol: Growth in different nitrogen sources

tag: growth source

value: jewelry wastewater


title: Ppsal-WW-2

source_name: Cells growth in jewelry wastewater_replicate 2


title: Ppsal-WW-1

source_name: Cells growth in jewelry wastewater_replicate 1


title: MS_case1_Pl2_1_9.coutt.csv

description: library of 192 cells

tag: tissue


title: 10_P2

tag: treatment


title: 10_P1

value: Print 1


title: 10_P3


title: Ppsal-CN-3

source_name: Cells growth in cyanide_replicate 3

value: cyanide


title: Untreated Control, biological rep1


title: 3_P4r

value: MTX

value: Print 4r


title: 4_P4r


title: WT_ipsilateralhemisphere_#3

description:
60 min MCAo+48 h reperfusion, w/o bulbi+cerebrellum
ipsiW_11

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 7, from SAS. Gene expression profiling was performed using arrays of mouse Mogene-2_0-type from Affymetrix. A Custom CDF Version 20 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

source_name: WT, ischemic hemisphere

growth_protocol: Male mice were used at the age of 7-9 weeks. Mice were maintained from the day before the treatment at an animal housing room in the institute.

extract_protocol: TRIreagent extraction of total RNA was performed according to the manufacturer's instructions. Extracted RNA was treated with DNAse and extracted again.

treatment_protocol: Mice were subjected to transient middle cererbal arrtery occlusion (MCAo): Mice were anesthetized for induction and maintenance by inhalation of a mixture containing 2.5-3.0% and 1.5% isoflurane, respectively, 70% N2O and remainder O2 using a vaporizer. Body temperature was maintained at 37°C with a feedback-controlled heating pad. A midline neck incision was made and the left common carotid artery as well as its bifurcation internal carotid artery (ICA) were isolated and dissected from surrounding tissue. Then, a 7-0 silicon rubber-coated monofilament (Doccol Corporation) was induced into the left CCA and pushed through the ICA towards the middle cerebral artery. The incision was closed, and the intraluminal suture was left for 60 minutes. Animals were anesthetized, and the filament was withdrawn to allow reperfusion. For sham surgery, the filament was inserted and withdrawn immediately. During MCAo and 30 min after start of reperfusion, mice were kept under observation under a heating lamp at 30°C. Then, mice were placed in a heating cabinet at 30°C until the next day. Then, mice were placed in a normal cabinet. Mice received softened food pellets and easily accessible drinking bottles. After 48 h of reperfusion. mice were anesthetized again. Thorax cavity was opened and a perfusion cannula (21G) was inserted into the left ventricle. The right atrium was incised and mice were perfused with PBS (RT) at a rate of 2 mL/min with a total volume of 10 mL. Subsequently, brains were carefully removed from the skull. Olfactory bulbs and cerebellum were removed, hemispheres were separated, quickly frozen in liquid nitrogen, and stored at -80°C until further usage.

tag: genotype

value: WT

value: brain

tag: tissue region

value: ipsilateral (ischemic) hemisphere


title: WT_contralateralhemisphere_#3

description:
60 min MCAo+48 h reperfusion, w/o bulbi+cerebrellum
contraW_12

source_name: WT, normoxic hemisphere

value: contralateral (normoxic) hemisphere


title: KO_ipsilateralhemisphere_#3

description:
60 min MCAo+48 h reperfusion, w/o bulbi+cerebrellum
ipsiE_9

source_name: Ephb2-KO, ischemic hemisphere


title: Untreated MGO400, biological rep1


title: Untreated MGO800, biological rep1


title: Ppsal-CN-2

source_name: Cells growth in cyanide_replicate 2


title: 3_P2

source_name: human bioprinted liver RNA


title: Ppsal-CN-1

source_name: Cells growth in cyanide_replicate 1


title: Ppsal-NH4-3

source_name: Cells growth in ammonium_replicate 3

value: ammonium


title: 2_P3

value: Print 3


title: KO_contralateralhemisphere_#3

description:
60 min MCAo+48 h reperfusion, w/o bulbi+cerebrellum
contraE_10

source_name: Ephb2-KO, normoxic hemisphere


title: KO_ipsilateralhemisphere_#2

description:
60 min MCAo+48 h reperfusion, w/o bulbi+cerebrellum
ipsiE_7


title: Ppsal-NH4-2

source_name: Cells growth in ammonium_replicate 2


title: KO_contralateralhemisphere_#2

description:
60 min MCAo+48 h reperfusion, w/o bulbi+cerebrellum
contraE_8


title: Ppsal-NH4-1

source_name: Cells growth in ammonium_replicate 1


title: WT_ipsilateralhemisphere_#2

description:
60 min MCAo+48 h reperfusion, w/o bulbi+cerebrellum
ipsiW_5


title: 2_P4r


title: 3_P1


title: iaa32iaa34-3

status: Public on Feb 12 2019

first: Renyi

state: Shanghai

address: 3888 Chenhua Road

department: Bioinformatics

institute: Shanghai Center for Plant Stress Biology

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads were first subject to 3’ adapter removal and quality filtering (Q > 17 and length >= 25 bp). Clean reads were mapped to the Arabidopsis thaliana genome sequence (http://mtweb.cs.ucl.ac.uk/mus/www/19genomes/fasta/MASKED/ler_0.v7.PR_in_lowercase.fas) using HISAT. Read counts of each gene were summarized by the HTSeq-count. Lowly expressed genes were removed and only genes with an expression level of at least 1 CPM (counts per million) in at least two samples were kept for further analysis.
Genome_build: v2i
Supplementary_files_format_and_content: Tab-delimited text file include RPM(Reads per Million) values for 9 Samples .

organism: Arabidopsis thaliana

source_name: apical hook

growth_protocol: Arabidopsis is grown in growth chamber at 22C under dark condition

extract_protocol:
The hook shaped structure without cotyledons (~2mm) were cut from the seedlings by blades. Total RNA was isolated from ~50 hooks per sample by using TRIzol™ Reagent (Invitrogen)
Total RNA (1μg) was used for performing the library preparation with NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs, E7420L) according to the manufacturer’s instructions with 9 different barcodes (triplicate biological samples)

tag: age

value: 45hours old plant

value: apical hook


title: iaa32iaa34-2


title: iaa32iaa34-1


title: WT_contralateralhemisphere_#1

description:
60 min MCAo+48 h reperfusion, w/o bulbi+cerebrellum
contraW_4


title: tmk1-3


title: tmk1-1


title: tmk1-2


title: WT-3


title: WT-2


title: 2_P1


title: WT-1


title: WT_ipsilateralhemisphere_#1

description:
60 min MCAo+48 h reperfusion, w/o bulbi+cerebrellum
ipsiW_3


title: KO_ipsilateralhemisphere_#1

description:
60 min MCAo+48 h reperfusion, w/o bulbi+cerebrellum
ipsiE_1


title: 20170924-H11-NA19160

city: Chicago

first: John

middle: D

last: Blischak

state: IL

address: 920 E. 58th Street, CLSC 317

department: Human Genetics

institute: University of Chicago

description:
eset-raw.rds
fucci-counts.txt.gz
fucci-annotation.txt
fucci-annotation-description.txt
eset-final.rds

data_processing:
We used `umi_tools extract` (UMI-tools 0.5.3) to extract the 6 base pair unique molecular identifier (UMI) from the 5’ end of each read.
We used `subjunc` (Subread 1.5.3) to map reads to the human genome (Ensembl GRCh37.75; chromosomes 1-22, X, Y, MT), ERCC spike-ins (http://tools.invitrogen.com/downloads/ERCC92.fa), and the mCherry and EGFP open reading frames from the FUCCI plasmid.
We used `featureCounts` (Subread 1.5.3) to count the number of reads for all protein-coding genes (Ensembl GRCh37 release 75) and the ERCC spike-in genes. We performed strand-specific counting (flag -s 1) because the UMI protocol preserves sequence strand information.
We used `umi_tools dedup` (UMI-tools 0.5.3) to deduplicate reads with the same UMI and start position to molecules.
We used `verifyBamID` (1.1.3) to identify the individual of origin for each sample based on the overlap of the RNA-seq reads with the known genotypes.
Genome_build: GRCh37
Supplementary_files_format_and_content: The file eset-raw.rds is a serialized R object of the Bioconductor class ExpressionSet. It can be imported into R with `readRDS(“eset-raw.rds”)`. It contains the gene counts, sample metadata, and feature metadata for 20,421 genes (H. sapiens, ERCC, EGFP, mCherry) and 1,536 single cells. The file fucci-counts.txt.gz is a gzipped tab-delimited plain text file that contains the counts for 20,421 genes for 1,536 single cells. The file fucci-annotation.txt is a tab-delimited plain text file that contains 43 metadata columns for the 1,536 single cells. The file fucci-annotation-description.txt is a tab-delimited plain text file that contains descriptions of the 43 metadata columns in fucci-annotation.txt. The file eset-final.rds is a serialized R object of the Bioconductor class ExpressionSet that contains the final data used to produce the results. It can be imported into R with `readRDS(“eset-final.rds”)`. It contains the gene counts, sample metadata, and feature metadata for the 11,093 genes (H. sapiens, ERCC, EGFP, mCherry) and 888 single cells that remained after applying filters for lowly expressed genes and low quality single cells.

source_name: LCL-derived iPSC

growth_protocol: We cultured Yoruba iPSCs (Banovich et al., 2018) in feeder-free conditions for at least ten passages in E8 medium (Life Technologies) (Chen et al., 2011).

extract_protocol:
We collected cells using the C1 Single-Cell Auto Prep IFC microfluidic chip (Fluidigm).
We performed single cell capture and library preparation as previously described using 6 bp Unique Molecular Identifiers (Tung et al., 2017). We pooled the 96 samples on each C1 chip and sequenced them on an Illumina HiSeq 2500 using the TruSeq SBS Kit v3-HS (FC-401-3002).

value: LCL-derived iPSC

tag: experiment

tag: well

tag: individual


title: 20170924-H09-NA19160

tag: cell type


title: 20170924-H10-NA18870


title: 1_P2

tag: concentration

tag: -/+ kcs

value: Yes

value: Print 2


title: 20170924-H07-NA18870


title: 1_P1

value: No

tag: time

tag: print


title: 20170924-H05-NA18870


title: WT_contralateralhemisphere_#2

description:
60 min MCAo+48 h reperfusion, w/o bulbi+cerebrellum
contraW_6


title: KO_contralateralhemisphere_#1

description:
60 min MCAo+48 h reperfusion, w/o bulbi+cerebrellum
contraE_2


title: 20170924-H02-NA19160


title: 20170924-H04-NA18870


title: 20170924-H06-NA19160


title: 20170924-H08-NA19160


title: 20170924-H01-NA19160


title: 20170924-H12-NA19160


title: 20170924-G09-NA18870


title: 20170924-G10-NA18870


title: 20170924-G12-NA18870


title: 20170924-G11-NA18870


title: 20170924-G08-NA19160


title: 20170924-G05-NA18870


title: 20170924-G06-NA18870


title: 20170924-G07-NA18870


title: 20170924-G03-NA19160


title: 20170924-G02-NA18870


title: 20170924-G04-NA18870


title: 20170924-G01-NA18870


title: 20170924-H03-NA18870


title: 20170924-F10-NA18870


title: 20170924-F08-NA19160


title: 20170924-F07-NA18870


title: 20170924-F09-NA18870


title: 20170924-F11-NA19160


title: 20170924-F12-NA19160


title: 20170924-F03-NA18870


title: 20170924-F04-NA19160


title: 20170924-F05-NA18870


title: 20170924-F01-NA19160


title: 20170924-F02-NA19160


title: 20170924-E11-NA18870


title: 20170924-E12-NA18870


title: 2_P2


title: 20170924-E09-NA19160


title: 20170924-E05-NA18870


title: 20170924-E01-NA19160


title: 20170924-E08-NA19160


title: 20170924-E07-NA18870


title: 20170924-E02-NA19160


title: 20170924-E03-NA19160


title: 20170924-E06-NA19160


title: 20170924-D11-NA19160


title: 20170924-D12-NA19160


title: 20170924-D10-NA19160


title: 20170924-E04-NA19160


title: 20170924-F06-NA19160


title: 20170924-D09-NA19160


title: 20170924-D08-NA19160


title: 20170924-D06-NA18870


title: 20170924-D07-NA19160


title: 20170924-D02-NA19160


title: 20170924-D03-NA19160


title: 20170924-D04-NA19160


title: 20170924-E10-NA18870


title: 20170924-D05-NA19160


title: 20170924-C11-NA19160


title: 20170924-C12-NA19160


title: 20170924-C10-NA18870


title: 20170924-C07-NA19160


title: 20170924-C06-NA19160


title: 20170924-C08-NA19160


title: 20170924-C05-NA18870


title: 20170924-D01-NA19160


title: 20170924-C09-NA19160


title: 20170924-C01-NA19160


title: 20170924-C03-NA18870


title: 20170924-B10-NA18870


title: 20170924-B11-NA19160


title: 20170924-B09-NA19160


title: 20170924-B05-NA19160


title: 20170924-B06-NA18870


title: 20170924-B08-NA18870


title: 20170924-B04-NA18870


title: 20170924-B02-NA19160


title: 20170924-B03-NA18870


title: 20170924-A12-NA19160


title: 20170924-A11-NA18870


title: 20170924-A09-NA19160


title: 20170924-A08-NA18870


title: 20170924-B01-NA19160


title: 20170924-A06-NA18870


title: 20170924-A07-NA19160


title: 20170924-C04-NA19160


title: 20170924-C02-NA18870


title: 20170924-A01-NA18870


title: 20170924-B07-NA18870


title: 20170922-H12-NA18870


title: 20170924-A02-NA19160


title: 20170924-B12-NA18870


title: 20170924-A03-NA19160


title: 20170922-H11-NA18511


title: 20170924-A04-NA18870


title: 20170922-H09-NA18870


title: 20170922-H08-NA18870


title: 20170922-H10-NA18511


title: 20170922-H04-NA18511


title: 20170922-H05-NA18870


title: 20170922-H03-NA18511


title: 20170922-H07-NA18511


title: 20170922-H06-NA18511


title: 20170922-H01-NA18511


title: 20170924-A10-NA18870


title: 20170922-H02-NA18511


title: 20170924-A05-NA19160


title: 20170922-G09-NA18870


title: 20170922-G08-NA18870


title: 20170922-G06-NA18870


title: 20170922-G12-NA18870


title: 20170922-G07-NA18511


title: 20170922-G10-NA18511


title: 20170922-F09-NA18511


title: 20170922-G02-NA18511


title: 20170922-G03-NA18870


title: 20170922-G04-NA18511


title: 20170922-F10-NA18511


title: 20170922-F08-NA18870


title: 20170922-F12-NA18511


title: 20170922-G01-NA18870


title: 20170922-F11-NA18511


title: 20170922-F07-NA18511


title: 20170922-F04-NA18511


title: 20170922-F06-NA18870


title: 20170922-F01-NA18511


title: 20170922-F02-NA18511


title: 20170922-E11-NA18870


title: 20170922-E12-NA18511


title: 20170922-G11-NA18511


title: 20170922-E07-NA18870


title: 20170922-E08-NA18511


title: 20170922-G05-NA18870


title: 20170922-E09-NA18511


title: 20170922-E04-NA18870


title: 20170922-E01-NA18511


title: 20170922-E02-NA18870


title: 20170922-E03-NA18511


title: 20170922-E06-NA18870


title: 20170922-D11-NA18511


title: 20170922-D10-NA18870


title: 20170922-D08-NA18870


title: 20170922-D12-NA18870


title: 20170922-F03-NA18511


title: 20170922-D03-NA18870


title: 20170922-D09-NA18511


title: 20170922-D02-NA18870


title: 20170922-D05-NA18511


title: 20170922-C11-NA18870


title: 20170922-E10-NA18511


title: 20170922-E05-NA18511


title: 20170922-C07-NA18511


title: 20170922-C06-NA18511


title: 20170922-C05-NA18511


title: 20170922-C08-NA18511


title: 20170922-C01-NA18870


title: 20170922-F05-NA18870


title: 20170922-D06-NA18511


title: 20170922-D07-NA18870


title: 20170922-C04-NA18511


title: 20170922-C03-NA18511


title: 20170922-B11-NA18870


title: 20170922-C12-NA18511


title: 20170922-D04-NA18511


title: 20170922-B10-NA18511


title: 20170922-B06-NA18511


title: 20170922-D01-NA18511


title: 20170922-B08-NA18870


title: 20170922-B09-NA18511


title: 20170922-B07-NA18870


title: 20170922-B02-NA18870


title: 20170922-C10-NA18870


title: 20170922-A12-NA18511


title: 20170922-A08-NA18870


title: 20170922-B04-NA18511


title: 20170922-A11-NA18511


title: 20170922-C09-NA18511


title: 20170922-B05-NA18511


title: 20170922-A06-NA18870


title: 20170922-A10-NA18511


title: 20170922-A02-NA18870


title: 20170922-A01-NA18511


title: 20170922-A05-NA18511


title: 20170922-A04-NA18870


title: 20170922-A03-NA18511


title: 20170921-H12-NA18870


title: 20170921-H11-NA18870


title: 20170921-H09-NA18870


title: 20170922-B12-NA18511


title: 20170921-H10-NA18870


title: 20170921-H06-NA18870


title: 20170921-H08-NA18870


title: 20170921-H04-NA18870


title: 20170921-H07-NA19160


title: 20170921-H05-NA18870


title: 20170921-H03-NA19160


title: 20170921-H01-NA19160


title: 20170921-G12-NA18870


title: 20170922-A09-NA18870


title: 20170921-G11-NA18870


title: 20170921-G09-NA18870


title: 20170922-C02-NA18511


title: 20170921-G08-NA19160


title: 20170922-A07-NA18511


title: 20170921-G06-NA19160


title: 20170921-F12-NA18870


title: 20170921-G02-NA18870


title: 20170921-G05-NA19160


title: 20170921-G10-NA18870


title: 20170921-G03-NA19160


title: 20170921-F11-NA18870


title: 20170921-F09-NA18870


title: 20170921-F08-NA19160


title: 20170921-F10-NA19160


title: 20170921-F06-NA18870


title: 20170921-F07-NA19160


title: 20170921-F04-NA19160


title: 20170921-F02-NA18870


title: 20170921-F03-NA18870


title: 20170921-E11-NA18870


title: 20170921-H02-NA19160


title: 20170921-E12-NA19160


title: 20170921-F01-NA19160


title: 20170921-G07-NA18870


title: 20170921-E10-NA18870


title: 20170921-E09-NA19160


title: 20170921-E06-NA19160


title: 20170921-E07-NA18870


title: 20170921-G01-NA18870


title: 20170921-G04-NA18870


title: 20170921-E05-NA18870


title: 20170921-E04-NA18870


title: 20170921-E03-NA18870


title: 20170921-E08-NA19160


title: 20170921-F05-NA18870


title: 20170921-E01-NA18870


title: 20170921-D09-NA18870


title: 20170921-D12-NA18870


title: 20170921-D11-NA18870


title: 20170921-D06-NA18870


title: 20170921-D08-NA18870


title: 20170921-D04-NA19160


title: 20170921-D05-NA18870


title: 20170921-E02-NA18870


title: 20170921-D01-NA19160


title: 20170921-D07-NA18870


title: 20170921-C12-NA18870


title: 20170921-D10-NA18870


title: 20170921-D03-NA18870


title: 20170921-C10-NA18870


title: 20170921-D02-NA19160


title: 20170921-C06-NA18870


title: 20170921-C11-NA18870


title: 20170921-C08-NA19160


title: 20170921-C04-NA19160


title: 20170921-C02-NA18870


title: 20170921-C09-NA18870


title: 20170921-C03-NA18870


title: 20170921-C07-NA18870


title: 20170921-C01-NA19160


title: 20170921-C05-NA18870


title: 20170921-B11-NA18870


title: 20170921-B12-NA19160


title: 20170921-B10-NA18870


title: 20170921-B04-NA19160


title: 20170921-B03-NA19160


title: 20170921-B07-NA19160


title: 20170921-B05-NA18870


title: 20170921-A08-NA18870


title: 20170921-A10-NA18870


title: 20170921-B06-NA18870


title: 20170921-B01-NA18870


title: 20170921-A11-NA18870


title: 20170921-B02-NA19160


title: 20170921-A05-NA18870


title: 20170921-A12-NA19160


title: 20170921-A09-NA19160


title: 20170921-A06-NA19160


title: 20170921-A04-NA18870


title: 20170921-A03-NA18870


title: 20170921-B09-NA19160


title: 20170921-A02-NA19160


title: 20170920-H11-NA19160


title: 20170920-H10-NA18511


title: 20170921-B08-NA18870


title: 20170920-H09-NA18511


title: 20170921-A01-NA18870


title: 20170921-A07-NA18870


title: 20170920-H08-NA19160


title: 20170920-H12-NA18511


title: 20170920-H06-NA18511


title: 20170920-H05-NA18511


title: 20170920-H04-NA18511


title: 20170920-H03-NA18511


title: 20170920-G10-NA18511


title: 20170920-G08-NA19160


title: 20170920-G11-NA18511


title: 20170920-G12-NA18511


title: 20170920-H01-NA19160


title: 20170920-G07-NA19160


title: 20170920-G05-NA18511


title: 20170920-G01-NA18511


title: 20170920-G04-NA18511


title: 20170920-G06-NA19160


title: 20170920-G03-NA19160


title: 20170920-F10-NA18511


title: 20170920-F12-NA18511


title: 20170920-G09-NA19160


title: 20170920-F11-NA19160


title: 20170920-F09-NA18511


title: 20170920-G02-NA18511


title: 20170920-F07-NA18511


title: 20170920-F06-NA18511


title: 20170920-H07-NA19160


title: 20170920-F08-NA18511


title: 20170920-F05-NA18511


title: 20170920-F04-NA19160


title: 20170920-F02-NA18511


title: 20170920-H02-NA18511


title: 20170920-F03-NA18511


title: 20170920-F01-NA19160


title: 20170920-E12-NA18511


title: 20170920-E11-NA18511


title: 20170920-E10-NA19160


title: 20170920-E07-NA18511


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