title: BrUseqRep2_WT15m_SSPE_TagDir

data_processing:
ChIP-seq, BrU-seq and ATAC-seq data analyses: For RNAPII-Ser2 ChIP-seq, low-quality sequence reads and adapters were filtered out by Trimmomatic (v3.36) (A. M. Bolger et al, 2014). The trimmed reads were aligned to the human reference genome (GRC h37/hg19) with the Burrows-Wheeler Aligner (BWA-v0.7.12-r1039) (H. Li et al, 2013). Biobambam2 (v2.0.72) (G. Tischler et al, 2014) was used to remove duplicate reads from the aligned reads. Sequence reads were locally realigned and base-quality scores were recalibrated with the IndelRealigner and BaseRecalibrator programs in Genome Analysis Toolkit (GATK-v3.5) (McKenna et al, 2010).
For pan-RNAPII ChIP-seq, BrU-seq and ATAC-seq, reads were aligned to the Human Genome 38 (Hg38) using bwa-mem tools (BWA (Version 0.7.16a) or STAR (Version 2.5.3a)) (H. Li et al, 2013; Dobin et al, 2013). Only high-quality reads (> q30) were included in the analyses and duplicates were removed using Samtools (Version 1.6) with fixmate -m and markdup -r settings (Table S7). Bam files were converted into stranded TagDirectories and UCSC genome tracks using HOMER tools (Version 4.8.2) (S. Heinz et al, 2010). A list of 49,948 genes was obtained from the UCSC genome database (https://genome.ucsc.edu/cgi-bin/hgTables) selecting the knownCanonical table containing the canonical transcription start sites per gene. To prevent contamination of binding profiles, genes should be non-overlapping with at least 2 kb between genes. Subsequent selection of sets of genes is described per analysis.
For ChIP-seq, binding profiles within selected areas of individual genes (e.g. around TSS or TTS), were defined using the AnnotatePeaks.pl tool of HOMER using the default normalization to 10mln reads. Metagene profiles were defined using the makeMetaGeneProfile.pl tool of HOMER, using default settings. Read densities in input samples were subtracted from individual ChIP-seq datasets to background-correct our data in which negative values were converted to 0, to prevent the use of impossible negative read densities in further calculations. Individual datasets were subsequently processed into heatmaps or binding profiles using R (Version 3.5.3) (R. Core Team, R, 2019). ChIP-seq binding and metagene profiles were averaged per set of genes and profiles were normalized to area under the curve to allow proper comparison of the profiles without effects of overall differences in read density.
ATAC-seq and BrU-seq heatmaps were generated as described for ChIP-seq analyses, except for the input subtraction and removal of negative values. BrU-seq aggregated profiles, were defined using the AnnotatePeaks.pl tool or makeMetaGeneProfile.pl tool of HOMER using the default normalization to 10mln reads, as for ChIP-sequencing. Genes were selected on size and strongest binding of RNAPII at the TSS in undamaged condition, as for ChIP-sequencing. Averaged binding profiles were subsequently normalized to nascent transcript levels, as quantified by 5-EU labelling, relative to the control in their specific cell type. For example, WT cells 3 h after UV irradiation showed 35% RNA relative to WT control cells, so we multiplied the expression of the bins by 0.35.  RNA-seq analyses: Obtained sequencing reads were cleaned by 5'-end quality trimming and Illumina-adapter clipping by Trimmomatic (A. M. Bolger et al, 2014). Pre-alignment quality control of the cleaned sequencing reads was done with FastQC. The alignment to reference genome hg19 of trimmed sequencing reads was done with Hisat2, guided by gene annotation in the refGene UCSC table (D. Kim et al, 2015). The generated SAM files were converted to the binary counterpart BAM, followed by BAM sorting and indexing with SAMtools (H. Li et al, 2009).  Counting reads to the UCSC's genomic features hg19 was performed by Subread/featureCounts (Y. Liao et al, 2014). Differential expression analysis was carried out, using edgeR (M. D. Robinson et al, 2010). Only genes indicating at least 2 counts per million in at least 20% of samples were included in the analysis. Data were normalized for sample specific effects by the trimmed mean of M-values. This was followed by estimating the dispersion and determining the differentially expressed genes using the general linear model (GLM). FDR-adjusted p-values < 0.05 were considered significant.
Genome_build: hg19 or hg38 as indicated per sample
Supplementary_files_format_and_content: excel tables providing stranded metagene profiles for the top 3000 genes for each individual sample, and the BrU-seq counts versus distance from the TSS for genes of 25-50Kb, 50-100Kb and >100Kb

tag: uv-c dose

value: not applicable

value: 1h pretreatment with DRB, followed by 15 min labeling with 2mM BrU


title: Athaliana_ataf2-2-2 (replicate 2)

status: Public on Apr 20 2021

type: SRA

city: Pullman

first: Hao

last: Peng

state: WA

department: Crop and Soil Sciences

country: USA

institute: Washington State University

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Hisat2/2.1.0 was used to build reference from Arabdopsis genome Athaliana_447_TAIR10.fa and map the RNASeq reads with parameters --dta -x -q
The sam files generated were conveted to bam files by Samtools/1.9.
Athaliana_447_Araport11.gene.gtf was used for transcript assembly and quantification with StringTie/2.1.4.
Differential expression analysis was performed using Ballgown.
Genome_build: Athaliana_447_TAIR10.fa
Supplementary_files_format_and_content: gtf files with transcript assembly and quantification information.
Athaliana_stringtie_merged.gtf (Merged)

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Four-day old seedlings

growth_protocol: Arabidopsis seeds were plated on half-strength MS media, put in the dark cold room for four days (stratification), and grew on 10uE white light for four days.

extract_protocol:
Total RNA was extracted using the RNeasy Plant Kit (Qiagen). The DNase I Digestion Set (Sigma) was used for on-column elimination of genomic DNA contamination.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatment

tag: Stage

value: Seedling

tag: age

value: Four days

tag: tissue

value: Whole plant

tag: genotype

value: ATAF2 knockout line


title: RNA sequencing Mouse-Liver biological replicate 1

city: Chengdu

first: jin

last: long

address: Hui ming

country: China

institute: Sichuan Agricultural University

description:
Mouse-Liver
mouse_exp.txt

data_processing:
Gene-level expression was estimated as transcripts per million (TPM) using the high-speed transcript quantification tool Kallisto (version 0.43.0).
Genome_build: Felis_catus_6.2, Gallus_gallus-5.0, CanFam3.1, Cavpor3.0, Mmul_8.0.1, GRCm38.p5, OryCun2.0, Rnor_6.0, Oar_v3.1
Supplementary_files_format_and_content: genes expression level (TPM) text file

organism: Mus musculus

source_name: Liver

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen).
We used an rRNA depletion protocol (Ribo-Zero kit, Epicentre) coupled with the Illumina TruSeq stranded RNA-Seq library protocol to construct the RNA-Seq libraries. All libraries were quantified using the Qubit dsDNA High Sensitivity Assay Kit (Invitrogen) and sequenced on HiSeq X Ten (Illumina) platform to produce average ~ 49 million 150-bp paired-end raw reads and ~ 48 million high-quality reads for each library.

tag: breed

value: Liver

value: Adult

tag: Sex

value: female


title: RNA-seq data of Human replicate 1 sequenced by HiSeq X-ten

data_processing:
Gene-level expression was estimated as transcripts per million (TPM) using the high-speed transcript quantification tool Kallisto (version 0.43.0).
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: genes expression level (TPM) text file

organism: Homo sapiens

source_name: Adipose tissue

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen).
We used an rRNA depletion protocol (Ribo-Zero kit, Epicentre) coupled with the Illumina TruSeq stranded RNA-Seq library protocol to construct the RNA-Seq libraries. All libraries were quantified using the Qubit dsDNA High Sensitivity Assay Kit (Invitrogen) and sequenced on HiSeq X Ten (Illumina) platform.

tag: ethinicity

value: Asian

value: Abdominal subcutaneous adipose

tag: developmental stage

value: male


title: Athaliana_Col-0-3 (replicate 3)

value: Wild-type


title: ATACseq_ELOFKOMock_Rep1_TagDir

city: Leiden

first: Martijn

middle: S.

last: Luijsterburg

state: zuid-holland

address: Einthovenweg 20

department: Human Genetics

country: Netherlands

institute: LUMC

description:
genomic DNA (ATAC-seq)
genome used for mapping:
Hg38

library_source: genomic

molecule: genomic DNA

source_name: RPE1-iCas9 ELOF1-KO

growth_protocol: DMEM GlutaMAX +10% Fetal Calf Serum + antibiotics

extract_protocol:
ATAC-seq: For each experimental condition 50.000 cells were harvested and washed with cold PBS containing protease inhibitors (Roche). The cells were resuspended in 50  l Transposase mixture, containing 1x Tagment DNA buffer Illumina Kit, #20034197), 0.5  l Tagment DNA enzyme (Illumina Kit, #20034197) and 0,2  g/ l Digitonin (Promega, #G9441), and incubated at 37  C for 30 min. Fragmented DNA was purified using a Qiagen MinElute kit (#28204).  BrU-seq: For BrU(DRB)-seq, cells were pre-treated with 100  M DRB for 1-3hrs (as indicated per sample) after which cells were washed with PBS and immdeidately, or 30 min later, incubated with 2 mM bromouridine (Bru) at 37 C for 15 or 30 min. For regular BrU-seq, cells were either mock-treated or irradiated with UV-C light (9 J/m2). Cells were then incubated in conditioned media for different periods of time before being incubated with 2 mM bromouridine (Bru) at 37 C for a 30 min. The cells were then lysed in TRIzol reagent (Invitrogen) and Bru-containing RNA isolated as previously described (Andrade-Lima et al., 2015). ChIP-seq: Cells were mock treated or UV-irradiated with 9 J/m2 and incubated in conditioned media for different periods of time (1, 4, 8, 16 h). Cells were crosslinked with 0.5 mg/mL disuccinimidyl glutarate (DSG; Thermo Fisher) in PBS for 45 min at room temperature. Cells were washed with PBS and crosslinked with 1% PFA for 20 min at room temperature. Fixation was stopped by adding 1.25 M Glycin in PBS to a final concentration of 0.1 M for 3 minutes at room temperature. Cells were washed with cold PBS and lysed and collected in a buffer containing 0.25% Triton X-100, 10 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0) and 20 mM Hepes (pH 7.6). Chromatin was pelleted in 5 min at 400 g and incubated in a buffer containing 150 mM NaCl, 1 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0) and 50 mM Hepes (pH 7.6) for 10 minutes at 4 C. Chromatin was again pelleted for 5 min at 400 g and resuspended in ChIP-buffer (0.15 % SDS, 1 % Triton X-100, 150 mM NaCl, 1 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0) and 20 mM Hepes (pH 7.6)) to a final concentration of 15x106 cells/ml. Chromatin was sonicated to approximately 1 nucleosome using a Bioruptor waterbath sonicator (Diagenode). Chromatin of ~5x106 cells was incubated with 3  g antibody (Antibodies are listed in Table S3) overnight at 4 C, followed by a 1.5 h protein-chromatin pull-down with a 1:1 mix of protein A and protein G Dynabeads (Thermo Fisher; 10001D and 10003D). ChIP samples were washed extensively, followed by decrosslinking for 4 h at 65 C in the presence of proteinase K. DNA was purified using a Qiagen MinElute kit.  RNA-seq: Cells were UV-irradiated (254 nm, 9 J/m2) or mock-treated and harvested 24 h later. Total RNA was isolated using the RNeasy mini kit (Qiagen) according to the manufacturer's protocol. Up to 5   106 cells per sample were lysed in RLT buffer. For quantification purposes, 24 ng of the eight ArrayControl(tm) RNA Spikes (Thermo Fisher Scientific) were added to each sample (3 ng/spike).
ATAC-seq: Libraries were prepared by PCR using NEBNext High-Fidelity 2x PCR Master Mix (New England Labs, #M0541) and Nextera XT index Kit v2 (Illumina). Samples were sequenced on an Illumina HiSeq X system (Macrogen), resulting in 150 bp paired-end reads. BrU-seq: cDNA libraries were made from the Bru-labeled RNA using the Illumina TruSeq library kit and paired-end 151 bp sequenced using the Illumina NovaSeq platform at the University of Michigan Advanced Genomics Core. Indicated is whether single-end or paired-end sequencing data was used for downstream analyses ChIP-seq: For RNAPII-Ser2 ChIP-seq sample libraries were prepared from 1 ng ChIPed DNA using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S) and index primer sets (NEB, E7335S). Strand-biased library amplification was performed using high-fidelity KAPA HiFi Enzyme (Roche, KK2102). The prepared libraries were sequenced on an Illumina HiSeq 2500 system (Illumina), resulting in 150 bp paired-end reads. For the remaining ChIP-seq samples, libraries were prepared using kapa hyper prep kit (Roche) and A-T mediated ligation of full Y-shaped IDT adapters. Samples were sequenced on an Illumina HiSeq X system (Macrogen), resulting in 150 bp paired-end reads. RNA-seq: Samples were purified using the KAPA mRNA Hyperprep kit (Roche) and prepared for sequencing using the TruSeq RNA Library Prep Kit v2 (Illumina) according to the manufacturer's instructions, and sequenced in a single lane on an Illumina HiSeq4000.

treatment_protocol: DNA damage was induced by irradiating cells with varying doses of UV-C as indicated per sample; samples were assayed at different time-periods after UV treatment as indicated per sample.

tag: cell line

value: mock

tag: time after uv-c

tag: chip-antibody


title: ATACseq_ELOFKOMock_Rep2_TagDir


title: RNA sequencing Mouse-Kidney biological replicate 1

description:
Mouse-Kidney
mouse_exp.txt

source_name: Kidney

value: Kidney


title: Athaliana_ataf2-2-3 (replicate 3)


title: Athaliana_Col-0-2 (replicate 2)


title: ATACseq_WTMock_Rep2_TagDir

source_name: RPE1-iCas9 WT

value: WT


title: RNA sequencing Mouse-skeletal-muscle biological replicate 1

description:
Mouse-skeletal-muscle
mouse_exp.txt

source_name: skeletal muscle

value: skeletal muscle


title: RNA sequencing Mouse-Heart biological replicate 1

description:
Mouse-Heart
mouse_exp.txt

source_name: Heart

value: Heart


title: RNA sequencing Mouse-Adipose biological replicate 1

description:
Mouse-Adipose
mouse_exp.txt

source_name: Adipose

value: Adipose


title: ATACseq_WTMock_Rep1_TagDir

value: not applicable


title: Athaliana_Col-0-1 (replicate 1)

value: Seedling

value: Four days


title: RNA sequencing Mouse-Lung biological replicate 1

description:
Mouse-Lung
mouse_exp.txt

source_name: Lung

value: Lung


title: E17_deletion_RNA-seq_rep2

status: Public on Apr 19 2021

city: Bangalore

first: Bharath

last: Saravanan

state: Karnataka

address: Bellary Road

department: Genetics and Development

country: India

institute: National centre for Biological Sciences

data_processing:
Basecalls performed using standard illumina pipeline
RNA-seq reads were aligned to the genome assembly using Hisat2 version 2.1.0 with default configurations
htseq-count was used to obtain raw feature counts using reverse option
Raw feature counts from the different datasets were provided as input to DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: raw feature counts

source_name: HeLa

growth_protocol: HeLa cell grown as per ATCC protocol.

extract_protocol:
Total RNA was isolaed from WT and enhancer deleted cells. The RNA was subjeced to ribo minus library preparation protocol
Libraries were prepared NEB kits for total RNA-seq (Ribo minus)

value: HeLa


title: E17_deletion_RNA-seq_rep1


title: E12_deletion_RNA-seq_rep1


title: mouse HSPCs wildtype FUS-HOXA9 rep1

city: Chapel Hill

first: Gang

middle: Greg

last: Wang

state: NC

address: 450 West Drive

department: Dept of Biochemistry and Biophysics

institute: UNC Lineberger Comprehensive Cancer Center

data_processing:
All reads were mapped to the human genome (hg19) or mouse genome (mm10) using the BWA alignment software. Unique reads mapped to a single best-matching location with no more than two mismatches were kept using Samtools. We filter out reads with a mapping quality score < 20 for downstream analysis
Then the quantification was done by salmon (ver 0.14.1). Different expression analysis was done using DESeq2.
Genome_build: GRCh37/hg19 or GRCm38/mm10
processed data files format and content: Excel spread sheet of DEseq2 result

source_name: primary murine hematopoietic stem/progenitor cells (HSPCs)

growth_protocol: HEK 293 cells were grown in DMEM plus 10% FBS and 1% antibiotics. mouse HSPC cells were grown in Opti-medium plus 10% FBS, 2% mSCF, 1% FLT3L, 1% antibiotics and 0.1% beta-mercaptoethanol

extract_protocol:
Total RNAs were purified using RNeasy Plus kit (Qiagen, #74136) and further processed with Turbo DNA-free kit (Thermo Fisher, #AM1907) to ensure the purity of RNA sample.
For RNA-seq, the RNA samples were either sent to Novogene or processed using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, #E7490) and NEBNext Ultra II RNA library Prep kit (NEB, #E7770) following the instructions of the manufacture’s product manual.

treatment_protocol: HEK293 cells and mouse HSPCs were first infected with virus produced with either MSCV empty vector or that with 3XHA-3XFLAG-tagged NUP98-HOXA9 or FUS-HOXA9, and subject to drug selection and examination by western blotting for chimera expression. Stable HEK293 cells with comparable expression levels of IDR-WT and IDR-mutated fusion were maintained in the above DMEM medium. The mouse HSPCs were collected for RNA isolation 7 days after infection and drug selection in the OptiMEM medium supplemented with the HSPC-supporting cytokines.

tag: cell type

tag: expression

value: wildtype FUS-HOXA9


title: mouse HSPCs wildtype FUS-HOXA9 rep2

value: primary murine hematopoietic stem/progenitor cells (HSPCs)


title: mouse HSPCs FS mutant NUP98-HOXA9 rep1

value: FS mutant NUP98-HOXA9


title: E8_deletion_RNA-seq_rep1


title: E8_deletion_RNA-seq_rep2


title: mouse HSPCs FS mutant NUP98-HOXA9 rep2


title: mouse HSPCs MSCV empty vector rep2

value: MSCV empty vector


title: mouse HSPCs wildtype NUP98-HOXA9 rep2

value: wildtype NUP98-HOXA9


title: E12_deletion_RNA-seq_rep2


title: mouse HSPCs wildtype NUP98-HOXA9 rep1


title: WT_RNA-seq_rep_1


title: O3-6_No

city: Seoul

first: Young-Joon

last: Kim

address: Yonsei-ro 50

country: South Korea

institute: Yonsei university

description: mRNA samples from human cell line

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequence reads were mapped by TopHat with paramters-p 8 -G genes.gtf genome read1.fastq read2.fastq.
Mapped reads were assembled by Cufflinks and FPKM value was calculated by Cufflnorm.
Genome_build: mm10

source_name: Peripheral blood

growth_protocol: Human HT-1080 cells were cultured in Dulbecco’s modified Eagle medium (DMEM; ThermoFisher Scientific) supplemented with 10% fetal bovine serum (FBS; Gibco/ThermoFisher Scientific), 50 U/ml penicillin, and 50 mg/ml streptomycin. Human monocytic THP-1 cells were maintained in culture in Roswell Park Memorial Institute culture medium (RPMI 1640; Invitrogen/ThermoFisher Scientific) containing 10% FBS, 50 U/ml penicillin, and 50 mg/ml streptomycin. THP-1 monocytes were differentiated into macrophages by 48 h incubation with 50 nM phorbol 12-myristate 13-acetate (PMA, Sigma, P8139).

extract_protocol:
RNAs from cell lysates or polysome fractions were purified with RNeasy mini kit (Qiagen), including a DNase digestion, and were converted to cDNA libraries according to the Illumina TruSeq RNA SamplePrep Guide.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were transfected with 1 μg/ml poly(I:C) (Invivogen) using Lipofectamine 2000 (Life Technologies/ThermoFisher Scientific) according to the manufacturer’s protocol.

value: Monocyte

value: OAS3 knock out


title: O3-18_IC6

description: mRNA samples from human cell line


title: O3-6_IC6

description: mRNA samples from human cell line


title: O3-18_No

description: mRNA samples from human cell line


title: O1-4_IC6

description: mRNA samples from human cell line

value: OAS1 knock out


title: O1-4_No

description: mRNA samples from human cell line


title: O1-1_No

description: mRNA samples from human cell line


title: O1-1_IC6

description: mRNA samples from human cell line


title: THP1_IC6

description: mRNA samples from human cell line

value: wild type


title: mouse HSPCs MSCV empty vector rep1


title: WT_RNA-seq_rep_2

value: WT


title: S52A 6h polysomes-Rep1

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

data_processing:
Raw reads, in FASTQ format, were quality checked with FASTQC
Paired-end reads were aligned against Schizosaccharomyces pombe genome and sorted by coordinate position with STAR. Alignment files (BAM) were indexed with samtools
Aligned reads were assigned to Schizosaccharomyces pombe genes with function QC from QoRTs software package using default parameters for paired-end and strand-specific sequences
Normalization of read counts and differential expression was estimated with bioconductor package DESeq2 with default parameters
Genome_build: ASM294v2 Ensembl fungi release 35
Supplementary_files_format_and_content: Raw and normalized counts are placed in two separated sheets of an Excel file. Gene names and descriptions are also included.

organism: Schizosaccharomyces pombe

source_name: S52A 6h polysomes

growth_protocol: Fission yeast cells were cultivated in YES medium at 30ºC until the reach OD550=0.5 (time 0 hours). They were cultivated for 6 additional hours (time 6 hours), time which coincides with early entry in stationary phase.

extract_protocol:
Total RNA and polysomal RNA were extracted as described in Swaminathan et al. 2006
TruSeq Stranded mRNA Sample Preparation Guide, Part #15031047 Rev. E

value: substitution of serine 52 of eIF2alpha by alanine

tag: timepoint

value: at the early entry into stationary phase (6 hours)

tag: molecule subtype

value: mRNA extracted from polysomes


title: WT 6h polysomes-Rep2

source_name: WT 6h polysomes

value: wild type 972


title: A2780-pGIPZ-nc#1

city: jinan

first: Shourong

address: 44 Wenhua Xi Road

institute: Shandong University

data_processing:
Sequenced reads were generated by base calling using the Illumina standard pipeline
Raw reads were filtered to obtain clean reads after removal of reads containing adapter and at low quality
High-quality reads were mapped to the human reference genome hg19 using HISAT2 software
Alignment was independently performed for reads from each sample, and reads mapping to more than three genomic sites were discarded
Based on the value of reads per kilobase per million mapped reads, gene expression levels were determined using Cufflinks software
Genome_build: hg19
Supplementary_files_format_and_content: abundance measurements

extract_protocol:
Total RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: serous ovarian cancer cell line

tag: transfection

value: pGIPZ-NC

tag: transfection method

value: lenti-virus


title: S52A 0h polysomes-Rep1

source_name: S52A 0h polysomes

value: at exponential phase (0 hours)


title: S52A 0h polysomes-Rep2


title: S52A 6h total-Rep2

source_name: S52A 6h total

value: Total RNA


title: WT 6h total-Rep1

source_name: WT 6h total


title: WT 6h polysomes-Rep1


title: S52A 6h total-Rep1


title: S52A 0h total-Rep1

source_name: S52A 0h total


title: WT 0h polysomes-Rep1

source_name: WT 0h polysomes


title: S52A 6h polysomes-Rep2


title: WT 0h total-Rep2

source_name: WT 0h total


title: WT 6h total-Rep2


title: WT 0h polysomes-Rep2


title: WT 0h total-Rep1


title: S52A 0h total-Rep2


title: Chor+Pnhd7

city: New York

first: Keiji

last: Itoh

state: NY

address: One Gustave L Levy Place, Box 1020, ANBG 25-40

department: Cell, Developmental and Regenerative Biology

institute: Icahn School of Medicine at Mount Sinai

description:
Chor+Pnhd7-1
Chor_Pnhd7-2

data_processing:
Illumina HiSeq2000 analyzers used for basecalling
The raw reads were filtered to remove reads containing adaptors or read of low quality
The sequences were mapped to the Xenopus genome version XL-9.1_v1.8.3.2 available at http://www.xenbase.org/other/static/ftpDatafiles.jsp using the software hisat2
Supplementary_files_format_and_content: Excel file with raw gene counts for every gene and every sample

organism: Xenopus laevis

source_name: ectodermal explants

growth_protocol: culture in 0.6 x MMR solution

extract_protocol:
RNeasy kit
paired-end 150 bp sequencing

treatment_protocol: ectoderm explant isolation

value: ectodermal explants

tag: group

value: Pinhd and chordin expressing explants (Chor-Pinh)

value: early neurula stage


title: FPinh6

description:
FPinh6-1
FPinh6-2

value: Flag-Pnhd expressing explants (Fpinh)


title: Chor4

description:
Chor4-1
Chor4-2

value: Chordin expressing explants (Chor)


title: Chor3

description:
Chor3-1
Chor3-2


title: FPinh5

description:
FPinh5-1
FPinh5-2


title: Chor+Pnhd8

description:
Chor+Pnhd8-1
Chor_Pnhd8-2


title: co2

description:
co2-1
co2-2

value: control ectodermal explants


title: co_st15_1

description:
co_st15_1-1
co_st15_1-2

value: wild type


title: THP1_No

description: mRNA samples from human cell line

value: Monocyte


title: Colon_SeqScope_2nd

city: Ann Arbor

first: Jun Hee

last: Lee

state: MI

address: 109 Zina Pitcher Pl

institute: University of Michigan

description: SeqScope 2nd-Seq library

data_processing:
Library strategy: Seq-Scope
Sequencing by Illumina HiSeqX, HiSeq4000 and NovaSeq platforms .
Tissue Boundary Detection: The HiSeq data were joined into MiSeq data according to their HDMI sequence. For each of HiSeq data whose HDMI is found from MiSeq, tile number and XY coordinates were assigned.  A density plot was generated to visualize the density of HiSeq reads in a given XY space of each tile. The density plots were manually assigned to the corresponding H&E images. The process is done with customized codes written in Python 3.7.1.
Alignment: From MiSeq data, HDMI sequences of clusters located on the bottom tile were extracted and used as a “whitelist” for the cell (HDMI) barcode. First 9 basepairs of HiSeq data Read 2 were copied to Read 1 and used as the unique molecular identifier (UMI). Read 2 was trimmed at the 3’end to remove polyA tails of length 10 or greater, then aligned to mouse genome (mm10) using GeneFull and Velocyto option with no length threshold and no cell filtering using Star/StarSolo 2.7.5c
Data Binning and Collapsing: The digital expression matrix generated by STARsolo with GeneFull option were combined with spatial information, and further the imaging space were divided into into 100 μm2 (10 μm-sided) square grids and collapsing all HDMI-UMI information into one barcode per grid. Alternatively, data binning was also performed with square 25 μm2 (5 μm-sided) square grids. After data binning, gene types were filtered to only contain protein_coding genes, lncRNA genes, or immunoglobulin/T cell receptor genes, to contain only the first-appearing splicing isoform, and to exclude hypothetical gene models (genes designated as Gm-number).
Clustering: The binned and processed DGE matrix was analyzed in the Seurat v4 package. Feature number threshold was applied to remove the grids that corresponded to the area that was not overlaid by the tissue or was extensively damaged through scratches. Data were normalized using regularized negative binomial regression implemented in Seurat’s SCTransform function. Clustering was performed using the shared nearest neighbor modularity optimization implemented in Seurat’s FindClusters function
Subcellular analysis: Genes from digital expression matrix generated by STARsolo Velocyto option were devided into three groups , and three groups of spliced and unspliced read counts were obtained and then independent images were produced. By plotting spliced and unspliced read counts in each group were compared with each other.
Genome_build: mm10

source_name: Mouse colon

growth_protocol: Standard Mouse rearing condition

extract_protocol: Seq-Scope experiment is divided into two consecutive sequencing steps: 1st-Seq and 2nd-Seq. 1st-Seq of Seq-Scope starts with the solid-phase amplification of a single-stranded synthetic oligonucleotide library using an Illumina sequencing-by-synthesis (SBS) platform. 2nd-Seq of Seq-scope begins with overlaying the tissue section slice onto the HDMI-array.

value: OCT-frozen colon

tag: condition

value: 8 weeks old male mouse


title: WT 3h LPS rep 3

city: Amsterdam

first: Menno

last: de Winther

address: Meibergdreef 9

department: Medical Biochemistry

institute: Academic Medical Center University of Amsterdam

data_processing:
Bases were called using Illumina CASAVA 1.8.2
Reads were aligned to the mouse genome mm10 by STAR 2.5.2b
BAM files were indexed and filitered on MAPQ > 15 with SAM Tools 1.3.1
Raw tag counts per gene were counted using HOMER2’s analyzeRepeats.pl script
Genome_build: mm10
Supplementary_files_format_and_content: matrix of read counts per gene

source_name: Bone marrow-derived macrophages

extract_protocol:
RNA was extracted uisng the Qiagen RNAeasy mini kit
Libraries were constructed using the KAPA HyperPrep mRNA kit

value: WT

tag: treatment

value: LPS 3h


title: WT 3h LPS rep 2

tag: genotype


title: WT 3h LPS rep 1


title: WT 24h LPS rep 4

value: LPS 24h


title: WT 24h LPS rep 3


title: KO 24h LPS rep 3

value: KO


title: WT 24h LPS rep 2


title: KO 3h LPS rep 1


title: KO 3h LPS rep 2


title: WT 24h LPS rep 1


title: KO 3h LPS rep 3


title: KO 24h LPS rep 2


title: KO 24h LPS rep 1


title: 10879T

first: Rork

last: Kuick

address: University of Michigan, SPH II, 1415 Washington Heights, Room M2533

data_processing:
fastq generated using bcl2fastq v2.20.0.422.
Reads were trimmed for quality and adapter contamination using Trimmomatic v0.36 and the following parameters: ILLUMINACLIP: TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 MINLEN: 25 SLIDINGWINDOW:4:15.
Read pairs surviving the trimming step were aligned to the mm10 (GRCm38) reference genome with STAR v2.5.2a via RSEM v1.2.31 using the default parameters for STAR.
Gene and isoform level expression values were calculated using RSEM (v.1.2.31).
Insert sizes for paired-end reads were estimated for each fastq file pair using BBMerge v38.49 (BBTools Suite, https://jgi.doe.gov/data-and-tools/bbtools/).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: See 'Readme_GEOsupplements_s0.txt' file.

molecule: polyA RNA

source_name: oviductal tumor

extract_protocol:
RNA was extracted with the miRNeasy Mini Kit (Qiagen).
Libraries were prepared using Illumina TruSeq Stranded reagents and polyA selection.

treatment_protocol: For those mice treated with tamoxifen, they received intraperitoneal injections of TAM (T5648; Sigma‐Aldrich, Indianapolis, IN, USA) at 100 mg/kg body weight on three consecutive days when mice were 6-8 weeks old.

tag: normal or tumor source

value: tumor

tag: primary, organoid, or organoid cultured in monolayer

value: primary

tag: tumor type

value: Endometrioid Carcinoma (EC)

tag: used in our analysis

value: yes

tag: pooling information

value: no pooling

tag: strain

value: mixed background

tag: tamoxifen treatment

tag: brca1 germline genotype

value: wt/wt

tag: trp53 germline genotype

tag: rb1 germline genotype

tag: nf1 germline genotype

tag: apc germline genotype

value: fl/fl

tag: pten germline genotype

tag: age (months)


title: 10868T


title: 10870T


title: 10847T


title: 2519T

value: Malignant Mixed Mullerian Tumor (MMMT)


title: 13576T

value: High Grade Serous Carcinoma (HGSC)

value: fl/wt


title: 14474T

value: fl/del


title: 13085T


title: 14399T


title: 14397T


title: 2163T


title: 2285T


title: 14433T


title: 3807T


title: 13179T


title: 14526T


title: 14174T


title: 14104T


title: 14109T

value: no:suspected medullary thyroid metastasis, neural gene expression


title: 10875T


title: 14085T


title: 10830T


title: 14576T


title: 14396T


title: 2942T

value: no:low RIN, lowest effective library size.


title: Od4

source_name: oviduct

value: normal

value: pool of 6 normal oviducts

value: no

value: varies for pooled samples


title: 13604T

value: tumor

value: primary


title: Od2

value: yes


title: Od1


title: Ov3

source_name: ovary

value: pool of 4 normal ovaries


title: Ov2

value: mixed background


title: sample_08 [miRNA-Seq]

city: Biberach an der Riß

first: Kolja

last: Becker

address: Birkendorfer Str. 65

department: Global Computational Biology and Digital Sciences

country: Germany

institute: Boehringer Ingelheim Pharma GmbH & Co. KG

description: small RNA

data_processing:
Filtered reads were mapped against the Homo sapiens (human) genome hg38/GRCh38 (primary assembly, excluding alternate contigs) using the STAR aligner software (STAR version 2.5.2b) allowing for soft clipping of adapter sequences. Sequenced read quality was checked with FastQC (FastQC version 0.11.5). Subsequently miRNA-sequencing read adapters were detected using minion and trimmed using reaper from the kraken package (kraken version 13-274). The trimmed reads were aligned using the STAR Aligner (version 2.3.0e) on the miRBase 21 reference. In the following miRNA read counts were quantified using subread (version 1.4.5-PR1).
Threshold for filtering expressed/active miRNA was set at voom normalized log2 CPM > 100 for any of the available samples. miRNA expression values were corrected for age using the same confounder correction method as described above.
Genome_build: hg38/GRCh38
Supplementary_files_format_and_content: human_retina_DR_smallRNA_normalized_cpm.txt - normalized cpm values for each miRNA

source_name: Retina Macula

extract_protocol:
Post-mortem human eyes from 43 donors were obtained through the Iowa Lions Eye Bank (Coralville, IA) after written informed consent of the next-of-kin was obtained and preserved within 6 hours post-mortem. Donors were categorized into one of four disease groups: a) diabetic donors with no apparent visual impairment or visible pathology of the retina at last eye exam, b) donors diagnosed with non-proliferative diabetic retinopathy (NPDR) but without diabetic macular edema (DME), c) patients diagnosed with NPDR with additional indication of DME, or d) donors diagnosed with proliferative diabetic retinopathy (PDR) and DME. The diagnosis was based on the early treatment diabetic retinopathy study Diabetic Retinopathy Severity Score (ETDRS-DRSS). Additional retinal samples were taken from healthy donors to serve as the control group. The study was designed such that donors of all groups approximately matched in age and gender distribution. Note that none of the donors received treatment for their retinal indication. The study design was reviewed by the University of Iowa Institutional Review Board and found not to involve human subjects research. From each donor group (healthy control, diabetic, NPPR, and NPDR/PDR + DME), 10 tissue samples were collected from the macula region as well as the retinal periphery. All tissue samples were taken with a 6mm biopsy punch, snap frozen in liquid nitrogen, and preserved at -80C until use. Both miRNA and total RNA was extracted using miRNeasy kits (Qiagen) after homogenization of the retina with Qiashredders (Qiagen). RNA was eluted into 30 μl of dH2O. RNA was quantitatively and qualitatively assessed using the fluorescence-based Broad Range Quant-iT RNA Assay Kit (ThermoFisher) and the Standard Sensitivity RNA Analysis DNF-471 Kit on a 48-channel Fragment Analyzer (Agilent), respectively. Concentrations averaged at 100ng/µL while RIN ranged from 4 to 9.
RNA sequencing libraries were prepared using QIASeq miRNA Library Kit (Qiagen) according to the manufacturer’s instructions. In brief, 200ng of RNA was used for the 3' Adapter Ligation to the RNA followed by the 5`Adapter Ligation. The tagged RNA library was translated into cDNA using reverse-transcription primer that contain integrated UMIs (Unique Molecular Indices), a universal sequence was also added in reverse transcription (RT) that is recognized by sample indexing primers during library amplification. RT was followed by a cDNA cleanup. During PCR amplification specific index PCR reverse primer were used and RT product was enriched to the final cDNA library. This was followed by a size selection purification via Magnetic beads. The library concentrations were quantified with the Quant-iT PicoGreen dsDNA Assay Kit (Quant-iTTM) using CLARIOstar (BMG LABTECH) and the library quality was determined by checking cDNA fragment size using a High Sensitivity DNA Kit on the Agilent Bioanalyzer 2100 (Agilent). miRNA Libraries were normalized to 8nM and subjected to cluster generation on a cBot system, followed by sequencing on an Illumina HiSeq4000 instrument (Illumina).

tag: tissue

value: Retina Macula

tag: sampleID

tag: samplenumber

tag: donor

tag: gender

value: female

tag: age

value: Protonix, methotrexate, prednisone, folic acid, captopril, Fosamax, calcium

tag: comorbidities

value: failure to thrive, COPD, hypertension arthritis, osteoporosis, coronary artery disease, CHF, fractures

value: corneal dystrophy

value: Control

tag: dme

value: FALSE

tag: eye

value: OD

value: Macula

tag: buffer

value: Water

value: ul

value: ng/ul

tag: rin

value: min


title: sample_79 [miRNA-Seq]

description: small RNA

source_name: Retina Periphery

value: Retina Periphery

value: unkown, but >8 years

value: metformin, humalog, lantus

value: Aggrenox, amitriptyline, avapro, furosemide, lipitor, metoprolol,  omeprazole, systane

value: hypertension, GERD, hyperlipidimia

value: DME OD>OS

value: mild ARMD

value: NPDR

value: TRUE

value: NPDR/PDR + DME

value: NPDR + DME

value: Periphery


title: sample_78 [miRNA-Seq]

description: small RNA

value: female

value: >17 years

value: Lantus, Humalog

value: allopurinol, ammonium lactate, atorvastatin, diphenhydramine, fuosemide, metoprolol

value: endometrial cancer, septic shock, acute renal failure, hypertension, heart failure, a fib, diabetes type II, GERD,tinnitus, obesity,

value: pan retinal photocoagulation

value: PDR

value: PDR + DME

value: OS


title: sample_77 [miRNA-Seq]

description: small RNA

value: Retina Periphery

value: 7 years

value: glipizide

value: furosemide, verapamil, xopenex, crestor, nexium, venlafaxine, prednisone, hydralazine, azithromysin, spriva, levothyroxine

value: pulmonary hypertension, hypothyroidism, diabetes type II, reflux disease, COPD, mastectomy due to breast cancer, knee replacement, Gravesâ€™ disease, depression

value: glaucoma suspect

value: OD

value: Water

value: ul

value: ng/ul

value: min


title: sample_80 [miRNA-Seq]

description: small RNA

value: female

value: unkown, but >8 years

value: metformin, humalog, lantus

value: Aggrenox, amitriptyline, avapro, furosemide, lipitor, metoprolol,  omeprazole, systane

value: hypertension, GERD, hyperlipidimia

value: DME OD>OS

value: mild ARMD

value: NPDR

value: TRUE

value: NPDR/PDR + DME

value: NPDR + DME

value: Periphery


title: Ov4

tag: normal or tumor source

value: normal

tag: primary, organoid, or organoid cultured in monolayer

value: primary

tag: tumor type

tag: used in our analysis

value: yes

tag: pooling information

value: pool of 4 normal ovaries

tag: strain

value: mixed background

tag: tamoxifen treatment

value: no

tag: brca1 germline genotype

value: fl/fl

tag: trp53 germline genotype

value: wt/wt

value: varies for pooled samples


title: sample_74 [miRNA-Seq]

description: small RNA

tag: tissue

value: Retina Periphery

tag: sampleID

tag: samplenumber

tag: donor

value: female

value: >15 years

value: Insulin, glipizide,

value: celebrex, ASA, trazodone, norvascstatin, lipitor, hydorchlorothiazide

value: hypertension, heart attack, acid reflux, congestive heart failure, COPD, aortic valve stenosis

value: AION, pseudophakia

value: OS

value: Water

value: ul

value: ng/ul

value: min


title: sample_09 [miRNA-Seq]

description: small RNA

value: Retina Macula

tag: gender

value: male

tag: age

value: laspofunginin, posacandozole, neupogen, heparin, coumadin, zosyn, vancomycin

tag: comorbidities

value: ulcerative colitis, bone marrow failure, rhizopus lung infection, refractory anemia with myelodysplasia, pulmonary embolus, HTN, myelodysplasia, dyslipidemia

value: pterygium removed, glasses

value: Control

tag: dme

value: FALSE

value: Macula


title: Ov1

tag: normal or tumor source

value: normal

value: primary

value: yes

value: pool of 4 normal ovaries

value: mixed background

value: no

value: fl/fl

tag: rb1 germline genotype

tag: nf1 germline genotype

tag: apc germline genotype

value: wt/wt

tag: pten germline genotype

tag: age (months)

value: varies for pooled samples


title: sample_75 [miRNA-Seq]

description: small RNA

value: Retina Periphery

value: female

value: 23 years, DR 7 years

value: insulin

value: Diovan, Norvasc, plavix, lopressor, foltex, furosemide, pyridoxine, iron, calcium carbonate, diltiazem, allegra, protoniox, levaquin, coumadin, flagyl

value: DM type 1, stroke, Afib, hpertension, renal disease, peripheral neuropathy, ischemic bowl disease

value: focal macula laser, IOL

value: drusen

value: NPDR

value: TRUE

value: NPDR/PDR + DME

value: NPDR + DME

tag: eye

value: OD

value: Periphery

tag: buffer

value: Water

value: ul

value: ng/ul

tag: rin

value: min


title: sample_72 [miRNA-Seq]

description: small RNA

tag: tissue

value: Retina Periphery

value: male

value: >25 years

value: pamelor, lisonopril, furosemide, glyburide, atenolol, paxil, insulin

value: cellulitis with Staph Aureus sepsis, hypertension, coronary atery disease, anxiety, CHF

value: focal grid laser to macula, IOL, YAG, PVD

value: OS


title: sample_70 [miRNA-Seq]

description: small RNA

value: Retina Macula

tag: sampleID

value: female

value: unkown, but >8 years

value: metformin, humalog, lantus

value: Aggrenox, amitriptyline, avapro, furosemide, lipitor, metoprolol,  omeprazole, systane

value: hypertension, GERD, hyperlipidimia

value: DME OD>OS

value: mild ARMD

value: NPDR

value: Macula


title: sample_71 [miRNA-Seq]

description: small RNA

value: Retina Periphery

tag: samplenumber

value: >15 years

value: Insulin, glipizide,

value: celebrex, ASA, trazodone, norvascstatin, lipitor, hydorchlorothiazide

value: hypertension, heart attack, acid reflux, congestive heart failure, COPD, aortic valve stenosis

value: TRUE

value: NPDR/PDR + DME

value: NPDR + DME

value: OD

value: Periphery

value: Water

value: ul

value: ng/ul

value: min


title: sample_76 [miRNA-Seq]

description: small RNA

tag: donor

value: female

value: 23 years, DR 7 years

value: insulin

value: Diovan, Norvasc, plavix, lopressor, foltex, furosemide, pyridoxine, iron, calcium carbonate, diltiazem, allegra, protoniox, levaquin, coumadin, flagyl

value: DM type 1, stroke, Afib, hpertension, renal disease, peripheral neuropathy, ischemic bowl disease

value: grid focal laser, IOL

value: drusen

value: OS


title: sample_69 [miRNA-Seq]

description: small RNA

value: Retina Macula

tag: gender

value: unkown, but >8 years

value: metformin, humalog, lantus

value: Aggrenox, amitriptyline, avapro, furosemide, lipitor, metoprolol,  omeprazole, systane

value: hypertension, GERD, hyperlipidimia

value: DME OD>OS

value: mild ARMD

value: NPDR

value: TRUE

value: Macula


title: sample_68 [miRNA-Seq]

description: small RNA

value: female

tag: age

value: >17 years

value: Lantus, Humalog

value: allopurinol, ammonium lactate, atorvastatin, diphenhydramine, fuosemide, metoprolol

value: endometrial cancer, septic shock, acute renal failure, hypertension, heart failure, a fib, diabetes type II, GERD,tinnitus, obesity,

value: pan retinal photocoagulation

value: PDR

value: NPDR/PDR + DME

value: PDR + DME

value: Water

value: ul

value: ng/ul

value: min


title: 2611T

value: tumor

tag: primary, organoid, or organoid cultured in monolayer

value: primary

tag: tumor type

value: High Grade Serous Carcinoma (HGSC)

tag: used in our analysis

value: yes

tag: pooling information

value: no pooling

tag: strain

value: mixed background

tag: tamoxifen treatment

tag: brca1 germline genotype

value: fl/fl

tag: trp53 germline genotype

value: fl/wt

value: wt/wt


title: Od3

tag: normal or tumor source

value: normal

value: pool of 6 normal oviducts

value: no

tag: rb1 germline genotype

tag: nf1 germline genotype

tag: apc germline genotype

tag: pten germline genotype

tag: age (months)

value: varies for pooled samples


title: sample_66 [miRNA-Seq]

description: small RNA

tag: tissue

value: Retina Macula

tag: sampleID

tag: samplenumber

tag: donor

value: female

value: 23 years, DR 7 years

value: insulin

value: Diovan, Norvasc, plavix, lopressor, foltex, furosemide, pyridoxine, iron, calcium carbonate, diltiazem, allegra, protoniox, levaquin, coumadin, flagyl

tag: comorbidities

value: DM type 1, stroke, Afib, hpertension, renal disease, peripheral neuropathy, ischemic bowl disease

value: grid focal laser, IOL

value: drusen

value: NPDR

tag: dme

value: TRUE

value: NPDR/PDR + DME

value: NPDR + DME

tag: eye

value: OS

value: Macula

tag: buffer

value: Water

tag: rin


title: sample_67 [miRNA-Seq]

description: small RNA

tag: gender

value: male

tag: age

value: unkown

value: unknown

value: CAD, CHF, COPD, DM type II, HTN, hyperlipidemia, cor pulmonae, ischemic heart disease, morbid obesity, MI, obstructive sleep apnea, tobacco use

value: ul

value: ng/ul

value: min


title: sample_64 [miRNA-Seq]

description: small RNA

value: Retina Macula

value: female

value: 34 years

value: insulin

value: oxygen, ASA, synthroid, diatx, allopurinol, tums, iron, BiPAP, vit E, fish oil, benicar, allegra

value: heart failure, cor pumonale and oxygen support, lower extremity lymphedema

value: repeated pan retinal photocoagulation

value: PDR

value: PDR + DME


title: sample_63 [miRNA-Seq]

description: small RNA

value: TRUE

value: NPDR/PDR + DME

value: OD

value: Macula

value: Water


title: sample_62 [miRNA-Seq]

description: small RNA

value: >15 years

value: Insulin, glipizide,

value: celebrex, ASA, trazodone, norvascstatin, lipitor, hydorchlorothiazide

value: hypertension, heart attack, acid reflux, congestive heart failure, COPD, aortic valve stenosis

value: AION, pseudophakia

value: NPDR

value: NPDR + DME

value: OS

value: ul


title: sample_60 [miRNA-Seq]

description: small RNA

value: Retina Periphery

value: male

value: unknown

value: glimepiride

value: atenolol, atorvastatin, Azor, furosemide

value: type II diabetes mellitus, acute pulmonary edema, renal failure, gastrointestinal hemorrhage,

value: lattice degeneration, vitreous detachment, mild  ARMD, pseudophakia

value: FALSE

value: Periphery

value: ng/ul

value: min


title: sample_61 [miRNA-Seq]

description: small RNA

value: Retina Macula

value: >25 years

value: insulin

value: pamelor, lisonopril, furosemide, glyburide, atenolol, paxil, insulin

value: cellulitis with Staph Aureus sepsis, hypertension, coronary atery disease, anxiety, CHF

value: focal grid laser to macula, IOL, YAG, PVD

value: TRUE

value: NPDR/PDR + DME

value: OD

value: Macula

value: Water


title: sample_06 [miRNA-Seq]

description: small RNA

value: female

value: unknown

value: ovarian CA, mitral regurg, choesystectomy, tonsillectomy

value: corneal stromal scar, cataract

value: Control

value: OS

value: ul


title: sample_65 [miRNA-Seq]

description: small RNA

value: Retina Macula

value: 23 years, DR 7 years

value: Diovan, Norvasc, plavix, lopressor, foltex, furosemide, pyridoxine, iron, calcium carbonate, diltiazem, allegra, protoniox, levaquin, coumadin, flagyl

value: DM type 1, stroke, Afib, hpertension, renal disease, peripheral neuropathy, ischemic bowl disease

value: focal macula laser, IOL

value: drusen

value: NPDR

value: NPDR + DME

value: ng/ul

value: min


title: sample_58 [miRNA-Seq]

description: small RNA

value: Retina Periphery

value: male

value: 19 years

value: insulin

value: clonidine,  fluoxetine, gabapentin, hydrocodone, simvastatin,  omeprazole, lisinopril, cephalexin, tirosint, diltiazem, hydralazine

value: type I diabetes, hypothyroidism, high cholesterol, hypertension, neuropathy

value: glaucoma suspect due to large cups, but not frank glaucoma

value: FALSE

value: Periphery

value: Water


title: sample_54 [miRNA-Seq]

description: small RNA

value: 13 yrs

value: Insulin

value: Furosemide, spironolactone, methotrexate, aranesp

value: HTN, ascites of unclear etiology, psoriasis, ostheoarthritis.

value: macular pucker

value: OS

value: ul


title: sample_73 [miRNA-Seq]

description: small RNA

value: Retina Periphery

value: female

value: 34 years

value: oxygen, ASA, synthroid, diatx, allopurinol, tums, iron, BiPAP, vit E, fish oil, benicar, allegra

value: heart failure, cor pumonale and oxygen support, lower extremity lymphedema

value: repeated pan retinal photocoagulation

value: PDR

value: TRUE

value: NPDR/PDR + DME

value: PDR + DME

value: OD

value: ng/ul

value: min


title: sample_55 [miRNA-Seq]

description: small RNA

value: male

value: 17 yrs

value: glipizide

value: Ranexa, hydralazine, tranexamic acid, Ativan, Lasix, potassium chloride, metoprolol, nitroglycerin, imdur, multivitamin, Colace, Motrin, Haldol, roxanol, Zocor, trazodone, allopurinol, digoxin, torsemide

value: Ischemic cardiomyopathy, CHF, CAD s/p CABG, hyperlipidemia, renal insufficiency/failure, gout, cerebrovascular disease and carotid bruit, HTN, chronic back discomfort, spinal stenosis, atrial fibrillation, heart block with prior pacemaker implantation, anemia, peripheral vascular disease, ex-smoker

value: cataract extraction, PVD

value: allopurinol, amlopidine, asperin, atenolol, gabapentin, omeprazole, furosemide, lorazepam,

value: NPDR

value: FALSE

value: Periphery

value: Water


title: sample_56 [miRNA-Seq]

description: small RNA

value: Retina Periphery

value: 5 yrs

value: carvedilol, warfarin, cozaar, digoxin, diltiazem, flector, fluticasone inhalation, furosemide,  januvia, KCl, neurontin, oxycontin, valium, Vicodin, Vit C, Vit E

value: PVD, chronic left foot ischemia and gangrenous tissue, CHF, suicidal thoughts, chronic severe pain, A-fib, BPH, HTN, chronic back pain, vertigo, constipation

value: ul


title: sample_52 [miRNA-Seq]

description: small RNA

value: >12 years

value: glipizide, pioglitazone

value: Fosamax, aspirin, atorvastatin, calcium, cefaclor, citalopram, furosemide, gabapentin,  insulin, levothyroxine, mitazapine, omeprazole, polyethilene glycol, repaglinide, triamcinolone

value: Diabetes mellitus type II, hypothyroidism, hyperlipidemia

value: Glaucoma suspect, Cataract extraction

value: OD

value: ng/ul

value: min


title: sample_53 [miRNA-Seq]

description: small RNA

value: male

value: >25 yrs

value: Insulin

value: allopurinol, amlopidine, asperin, atenolol, gabapentin, omeprazole, furosemide, lorazepam

value: DM type 2, IDDM, chronic kidney disease, HTN, prostate adeno CA, melanoma, gout, hyperlipidemia, hypercalcemia.

value: cateract extraction

value: Toe amputation 1 yr prior to death

value: NPDR


title: sample_51 [miRNA-Seq]

description: small RNA

value: Retina Periphery

value: female

value: unkown

value: insulin (lantus, humalog)

value: allopurinol, ASA, lipitor, plavix, lanoxin, furosemide, indomethacin,  isosorbide, synthroid, toprol, nitroclycerin, altace

value: CAD, ischemic cardiomyopathy, chronic kidney dz, HTN, anemia, PVD, hypothyroidism, DM type 2, hyperlipidemia, asthma.

value: iris neovascularization

value: FALSE

value: Periphery

value: Water

value: ul


title: sample_07 [miRNA-Seq]

description: small RNA

value: Retina Macula

value: male

value: Heparin, lasix, lactulose, protonix, paroxetine, vitamin K

value: liver cirrhosis, alpha-1-AT deficiency diagnosed 2 yrs ago, UTI, HTN, nephrolithiasis, OSA on CPAP at night

value: Control

value: OD

value: Macula

value: ng/ul

value: min


title: sample_48 [miRNA-Seq]

description: small RNA

value: 19 years

value: insulin

value: clonidine,  fluoxetine, gabapentin, hydrocodone, simvastatin,  omeprazole, lisinopril, cephalexin, tirosint, diltiazem, hydralazine

value: type I diabetes, hypothyroidism, high cholesterol, hypertension, neuropathy

value: glaucoma suspect due to large cups, but not frank glaucoma

value: NPDR

value: OS


title: sample_46 [miRNA-Seq]

description: small RNA

value: 5 yrs

value: glipizide

value: carvedilol, warfarin, cozaar, digoxin, diltiazem, flector, fluticasone inhalation, furosemide,  januvia, KCl, neurontin, oxycontin, valium, Vicodin, Vit C, Vit E

value: PVD, chronic left foot ischemia and gangrenous tissue, CHF, suicidal thoughts, chronic severe pain, A-fib, BPH, HTN, chronic back pain, vertigo, constipation

value: cataract extraction, PVD

value: FALSE

value: Water

value: ul


title: sample_49 [miRNA-Seq]

description: small RNA

value: Retina Macula

value: female

value: >15 years

value: unknown

value: diabetes type 2, cardiomyopathy peripheral artery disease, hypertension, CAD, osteoarthritis, atrial fibrillation, depression, anxiety, history of gangrene

value: This donor had very limited health care

value: OD

value: Macula

value: ng/ul


title: sample_44 [miRNA-Seq]

description: small RNA

value: male

value: 13 yrs

value: Insulin

value: Furosemide, spironolactone, methotrexate, aranesp

value: HTN, ascites of unclear etiology, psoriasis, ostheoarthritis.

value: macular pucker

value: NPDR

value: min


title: sample_43 [miRNA-Seq]

description: small RNA

value: Retina Macula

value: >25 yrs

value: allopurinol, amlopidine, asperin, atenolol, gabapentin, omeprazole, furosemide, lorazepam

value: DM type 2, IDDM, chronic kidney disease, HTN, prostate adeno CA, melanoma, gout, hyperlipidemia, hypercalcemia.

value: cateract extraction

value: Toe amputation 1 yr prior to death

value: FALSE

value: Water

value: ul


title: sample_42 [miRNA-Seq]

description: small RNA

value: male

value: >12 years

value: glipizide, pioglitazone

value: Fosamax, aspirin, atorvastatin, calcium, cefaclor, citalopram, furosemide, gabapentin,  insulin, levothyroxine, mitazapine, omeprazole, polyethilene glycol, repaglinide, triamcinolone

value: Diabetes mellitus type II, hypothyroidism, hyperlipidemia

value: Glaucoma suspect, Cataract extraction

value: OD

value: Macula

value: ng/ul


title: sample_41 [miRNA-Seq]

description: small RNA

value: Retina Macula

value: female

value: unkown

value: insulin (lantus, humalog)

value: allopurinol, ASA, lipitor, plavix, lanoxin, furosemide, indomethacin,  isosorbide, synthroid, toprol, nitroclycerin, altace

value: CAD, ischemic cardiomyopathy, chronic kidney dz, HTN, anemia, PVD, hypothyroidism, DM type 2, hyperlipidemia, asthma.

value: iris neovascularization

value: NPDR

value: min


title: sample_04 [miRNA-Seq]

description: small RNA

value: male

value: atenolol, DECADRON (STEROIDS), paroxetine, ASA, Aricept, folic acid

value: metastatic lung CA, HTN, depression

value: cataract extraction

value: Control

value: FALSE

value: Water

value: ul


title: sample_39 [miRNA-Seq]

description: small RNA

value: Retina Periphery

value: >15 years

value: Plavix, metoprolol,dyrenium, gabapentin, multivitamin

value: DM, HTN, hypothyroidism, depression CHF, osteoarthritis

value: Phaco, trabeculectomy

value: Diabetic

value: OD

value: Periphery

value: ng/ul


title: sample_37 [miRNA-Seq]

description: small RNA

value: female

value: 7 yrs

value: humalog, glucophage, lantus

value: fentanyl, Haldol, heparin, Ativan, levothyroxin, lisinopril, protonix, pantoprazole

value: acute chronic kidney injury,acute hepatic encephalopathy, heart-to-heart cirrhosis of liver, hypertension, hypothyroidism, obesity, pneumonia, diabetes mellitus type II, IDDM

value: OS

value: min


title: sample_38 [miRNA-Seq]

description: small RNA

value: unknown

value: metformin (1000 mg)

value: mapap

value: paroxysmal a-fib on chronic anticoagulation, mild to moderate mitral regurgitation and stenosis, IDDM, HTN, CAD.

value: hypertensive retinopathy

value: FALSE

value: Water

value: ul


title: sample_59 [miRNA-Seq]

description: small RNA

value: Retina Periphery

value: male

value: >10 years

value: Humalog, Lantus

value: aspirin, fish oil, Lasix, Lipitor, lisinopril, warfarin, metolazone

value: kidney failure, hypertension, melanoma, heart bypass

value: pseudophakia, epiretinal membrane

value: NPDR

value: OD

value: Periphery


title: sample_36 [miRNA-Seq]

description: small RNA

value: female

value: >12 yrs

value: metformin

value: allopurinol, aspirin, ferrous sulfate, neurontin, omeprazole, KCl, PreserVision, Restasis, Demadex, Tyvaso inhaler, Zetia

value: heart failure, atrial flutter, chronic renal insufficiency, pulmonary hypertension, Sjogrenâ€™s syndrome, DM, osteoarthritis

value: Sjogrenâ€™s, Fuchsâ€™, early ARMD

value: A1C between 6 and 7 over the years

value: Diabetic

value: ng/ul

value: min


title: sample_34 [miRNA-Seq]

description: small RNA

value: Retina Periphery

value: male

value: unknown

value: Lantus insulin, Humalog insulin

value: fish oil, lasix, Avapro, isosorbide, metroprolol XL, omeprazole, KCl, Crestor, Vit D, nitroglycerin prn

value: IDDM type 2, adematous colon polyp, hypercholesterolemia, HTN, A-fib w/ ablation, CAD, back pain, stroke, kidney failure, acid reflux, arthritis, atrial flutter, GERD, cataracts, tobacco use.

value: IOL, drusen

value: FALSE

value: OS

value: Water

value: ul


title: sample_57 [miRNA-Seq]

description: small RNA

value: 40 yrs

value: insulin

value: hydralazine, Metalozone

value: colon cancer with pulmonary adn bladder mets, bladder bleeding, bladder clots and occlusion, heart disease, popliteal aneurysm, HTN, CAD in native artery, chronic systolic CHF, CKD, acute on chronic combined systolic and diastolic heart failure, PE, A-fib, gross hematuria, urinary tract obstruction, hypotension, slow transit constipation.

value: PVD

value: NPDR

value: OD

value: Periphery


title: sample_33 [miRNA-Seq]

description: small RNA

value: Retina Periphery

value: male

value: >25 years

value: Glimepiride, Novolin

value: isosorbide, metoprolol, allopurinol, lisinopril, lasix, ASA, Crestor,  Zetia, sulfasalazine, digoxin

value: ischemic cardiomyopathy, CAD, aortic stenosis, DM, renal insufficiency, hyperlipidemia, HTN, TIA, spinal stenosis, ulcerative colitis, left ulnar palsy,

value: Diabetic

value: ng/ul

value: min


title: sample_50 [miRNA-Seq]

description: small RNA

value: Retina Macula

value: unknown

value: glimepiride

value: atenolol, atorvastatin, Azor, furosemide

value: type II diabetes mellitus, acute pulmonary edema, renal failure, gastrointestinal hemorrhage,

value: lattice degeneration, vitreous detachment, mild  ARMD, pseudophakia

value: FALSE

value: Macula

value: Water

value: ul


title: sample_28 [miRNA-Seq]

description: small RNA

value: female

value: metformin (1000 mg)

value: mapap

value: paroxysmal a-fib on chronic anticoagulation, mild to moderate mitral regurgitation and stenosis, IDDM, HTN, CAD.

value: hypertensive retinopathy

value: OS


title: sample_03 [miRNA-Seq]

description: small RNA

value: levoxyl, atenolol, avapro, dilantin, DDAVP, omepraxole, MVI, ASA

value: breast CA with brain mets, DI, HTN, hypothyroidism, GRD

value: cataracts

value: Control

value: OD

value: ng/ul

value: min


title: sample_31 [miRNA-Seq]

description: small RNA

value: Retina Periphery

value: 10 yrs

value: atenolol/chlorthalidone, monopril, synthroid, ambien, tylenol .3, amitriptyline

value: DM, HTN, hypothyroidism, depression CHF, osteoarthritis

value: cataracts, Fuchs., glaucoma suspect, corneal dystrophy

value: Diabetic

value: FALSE

value: Periphery


title: sample_05 [miRNA-Seq]

description: small RNA

value: Retina Macula

value: female

value: Plavix, demadex, levothyroxine, folic acid, metoprolol, amlodipine, hydralzine, ASA, fosamax, isosorbide, Douvent nebulizer, PULMICORT INHALER,

value: CAD, s/p MI, angina, CHF, COPD, pulmonary HTN, hypothyroidism, breast CA, osteoprosis/OA, vocal cord paralysis, RA, PUD, vitiligo, HTN

value: pseudophakia, Fuchâ€™s endo dystrophy, choroidal nevi

value: Macula

value: Water

value: ul


title: sample_30 [miRNA-Seq]

description: small RNA

value: male

value: 16 years

value: metformin

value: aspirin, levothyroxine,cloidogrel

value: none noted

value: AMD, cataract extraction, PVD

value: OS

value: ng/ul

value: min


title: sample_32 [miRNA-Seq]

description: small RNA

value: Retina Periphery

value: >12 years

value: glyburide, insulin

value: atenolol, lisinopril

value: pancreatic cancer, dyspnea from pleural effusion, DM, Afib.

value: cataract

value: Diabetic

value: FALSE

value: OD

value: Periphery


title: sample_29 [miRNA-Seq]

description: small RNA

value: Retina Macula

value: female

value: 7 yrs

value: humalog, glucophage, lantus

value: fentanyl, Haldol, heparin, Ativan, levothyroxin, lisinopril, protonix, pantoprazole

value: acute chronic kidney injury,acute hepatic encephalopathy, heart-to-heart cirrhosis of liver, hypertension, hypothyroidism, obesity, pneumonia, diabetes mellitus type II, IDDM

value: Macula

value: Water

value: ul


title: sample_26 [miRNA-Seq]

description: small RNA

value: 8 years

value: metformin

value: allopurinol, aspirin, ferrous sulfate,  neurontin, omeprazole, KCl, PreserVision, Restasis, Demadex, Tyvaso inhaler, Zetia

value: breast CA, CHF, A-fib, HTN, pulmonary artery fibrillation/flutter-unsuccessful R atrial ablation; non ischsmic dilated cardiomyopathy, hysterectomy 1992; bowel obstruction

value: asteroid hyalosis, choroiodal nevus

value: OS

value: ng/ul

value: min


title: sample_47 [miRNA-Seq]

description: small RNA

value: Retina Macula

value: male

value: 40 yrs

value: insulin

value: hydralazine, Metalozone

value: colon cancer with pulmonary adn bladder mets, bladder bleeding, bladder clots and occlusion, heart disease, popliteal aneurysm, HTN, CAD in native artery, chronic systolic CHF, CKD, acute on chronic combined systolic and diastolic heart failure, PE, A-fib, gross hematuria, urinary tract obstruction, hypotension, slow transit constipation.

value: PVD

value: NPDR

value: FALSE

value: OD


title: sample_25 [miRNA-Seq]

description: small RNA

value: female

value: 7 yrs

value: Glimepiride, metformin

value: prednisone, lisinopril/HCTZ, bisoprolol

value: paratracheal mass, lupus, autoimmune hepatitis, NIDDM, HTN, high creatinine levels.

value: cataracts

value: Diabetic

value: Macula

value: Water

value: ul


title: sample_27 [miRNA-Seq]

description: small RNA

value: Retina Macula

value: >15 years

value: Plavix, metoprolol,dyrenium, gabapentin, multivitamin

value: DM, HTN, hypothyroidism, depression CHF, osteoarthritis

value: Phaco, trabeculectomy

value: ng/ul

value: min


title: sample_22 [miRNA-Seq]

description: small RNA

value: male

value: >12 years

value: glyburide, insulin

value: atenolol, lisinopril

value: pancreatic cancer, dyspnea from pleural effusion, DM, Afib.

value: cataract

value: FALSE

value: OD


title: sample_21 [miRNA-Seq]

description: small RNA

value: female

value: 10 yrs

value: atenolol/chlorthalidone, monopril, synthroid, ambien, tylenol .3, amitriptyline

value: cataracts, Fuchs., glaucoma suspect, corneal dystrophy

value: Diabetic

value: Macula

value: Water


title: sample_24 [miRNA-Seq]

description: small RNA

value: Retina Macula

value: 9 years

value: Insulin (Humalin)

value: digoxin, prednisone, coumarin

value: cholecystectomy, prostrate surgery

value: PVD, cataracts

value: ul

value: ng/ul


title: sample_23 [miRNA-Seq]

description: small RNA

value: male

value: >25 years

value: Glimepiride, Novolin

value: isosorbide, metoprolol, allopurinol, lisinopril, lasix, ASA, Crestor,  Zetia, sulfasalazine, digoxin

value: ischemic cardiomyopathy, CAD, aortic stenosis, DM, renal insufficiency, hyperlipidemia, HTN, TIA, spinal stenosis, ulcerative colitis, left ulnar palsy,

value: FALSE

value: min


title: sample_40 [miRNA-Seq]

description: small RNA

value: Retina Periphery

value: 16 years

value: metformin

value: aspirin, levothyroxine,cloidogrel

value: none noted

value: AMD, cataract extraction, PVD

value: Diabetic

value: OS

value: Periphery


title: sample_02 [miRNA-Seq]

description: small RNA

value: Retina Macula

value: isoptin, imdur, prozac, trazodone, ASA

value: CAD, s/p coronary angioplasties, HTN, COPD, hyperlipidemia, anxiety, depression, s/p appendectomy, s/p hemorrhoidectomy.

value: cataracts

value: Control

value: OD

value: Macula

value: Water

value: ul

value: ng/ul


title: sample_19 [miRNA-Seq]

description: small RNA

value: Retina Periphery

value: male

value: Levaquin, zosyn, Flomax, hydrochlorothiazide, Compazine, lorazepam, nystatin, warfarin, gabapentin, librax, tarceva,

value: metastatic adenocarcinoma of lung, lung cancer, pulmonary embolism, Waldenstrom macroglobulinemia, hypertension, familial tremor, gastroesophageal disease, asthma, recurring pneumonia

value: cataract extraction

value: FALSE

value: min


title: sample_18 [miRNA-Seq]

description: small RNA

value: female

value: Tylenol, haldol, ativan, morphine,mylicon

value: Cholangiocarcinoma, sepsis, diabetes type II, coronary artery disease, diverticulitis, liver disease,

value: OS

value: Periphery


title: sample_35 [miRNA-Seq]

description: small RNA

value: >15 years

value: Plavix, metoprolol,dyrenium, gabapentin, multivitamin

value: DM, HTN, hypothyroidism, depression CHF, osteoarthritis

value: Phaco, trabeculectomy

value: Diabetic

value: OD


title: sample_17 [miRNA-Seq]

description: small RNA

value: Retina Periphery

value: Protonix, methotrexate, prednisone, folic acid, captopril, Fosamax, calcium

value: failure to thrive, COPD, hypertension arthritis, osteoporosis, coronary artery disease, CHF, fractures

value: corneal dystrophy

value: Control

value: Water

value: ul

value: ng/ul


title: sample_16 [miRNA-Seq]

description: small RNA

value: male

value: Heparin, lasix, lactulose, protonix, paroxetine, vitamin K

value: liver cirrhosis, alpha-1-AT deficiency diagnosed 2 yrs ago, UTI, HTN, nephrolithiasis, OSA on CPAP at night

value: FALSE

value: min


title: sample_15 [miRNA-Seq]

description: small RNA

value: female

value: unknown

value: ovarian CA, mitral regurg, choesystectomy, tonsillectomy

value: corneal stromal scar, cataract

value: Periphery


title: sample_14 [miRNA-Seq]

description: small RNA

value: Retina Periphery

value: Plavix, demadex, levothyroxine, folic acid, metoprolol, amlodipine, hydralzine, ASA, fosamax, isosorbide, Douvent nebulizer, PULMICORT INHALER,

value: CAD, s/p MI, angina, CHF, COPD, pulmonary HTN, hypothyroidism, breast CA, osteoprosis/OA, vocal cord paralysis, RA, PUD, vitiligo, HTN

value: pseudophakia, Fuchâ€™s endo dystrophy, choroidal nevi

value: OD


title: sample_12 [miRNA-Seq]

description: small RNA

value: laspofunginin, posacandozole, neupogen, heparin, coumadin, zosyn, vancomycin

value: ulcerative colitis, bone marrow failure, rhizopus lung infection, refractory anemia with myelodysplasia, pulmonary embolus, HTN, myelodysplasia, dyslipidemia

value: pterygium removed, glasses

value: Control

value: OS

value: Water

value: ul


title: sample_13 [miRNA-Seq]

description: small RNA

value: male

value: atenolol, DECADRON (STEROIDS), paroxetine, ASA, Aricept, folic acid

value: metastatic lung CA, HTN, depression

value: cataract extraction

value: FALSE

value: ng/ul

value: min


title: sample_11 [miRNA-Seq]

description: small RNA

value: Retina Periphery

value: female

value: ASA, levoxyl, verpamil, aldactone, nasonex nasal srapy, vicodin, toprol, mirtazapine, pulmicort puff (glucocorticoid), albuterol inhaler 2 puff, home oxygen, Mg tablets,

value: hypertension (HTN), congestive heart failure (CHF), asthma, history of Vfib with MI x 2 s/p AICD placement in 1999.  Atrial fib, hypothyroidism

value: pseudophakia with YAG

value: Periphery


title: sample_08

data_processing:
Filtered reads were mapped against the Homo sapiens (human) genome hg38/GRCh38 (primary assembly, excluding alternate contigs) using the STAR aligner software (STAR version 2.5.2b) allowing for soft clipping of adapter sequences. For quantification of transcript levels the annotation files from Ensembl version 86 were used, which corresponds to GENCODE 25. Samples were quantified with the above annotations, using RSEM (RSEM version 1.3.0) and featureCount (featureCount version 1.5.1). Quality controls were implemented using FastQC (FastQC version 0.11.5), picardmetrics (picardmetrics version 0.2.4), and dupRadar (dupRadar version 1.0.0) at the respective steps.
Normalized log2 Counts Per Million (CPM) mRNA expression values were calculated using the voom function provided by the limma R package (limma version 3.42.0).
mRNA were filtered by minimum read counts using the filterByExpr function of the edgeR package (edgeR version 3.26.5) and. In addition, a Gaussian mixture model (mclust version 5.4.5) was applied, fitting two Gaussian distributions to mean CPM expression data. mRNA assigned to the cluster with higher mean were retained.
Surrogate variables describing a technical confounder effect were estimated using the sva R package (sva version 3.34.0). mRNA expression was corrected for donor age as well as the estimated surrogate variable. In more detail, we designed linear models with mRNA expression of each individual transcript as response, and donor age as well as the estimated surrogate variable as covariates. For each linear model, a t-test was performed on the covariate to assess its statistical significance. In case the p-value for a transcript was below 0.05, the expression values of that transcript were replaced by the residuals of the linear model plus the intercept of the model.
Genome_build: hg38/GRCh38
Supplementary_files_format_and_content: human_retina_DR_totalRNA_normalized_cpm.txt - normalized cpm values for each gene

extract_protocol:
Post-mortem human eyes from 43 donors were obtained through the Iowa Lions Eye Bank (Coralville, IA) after written informed consent of the next-of-kin was obtained and preserved within 6 hours post-mortem. Donors were categorized into one of four disease groups: a) diabetic donors with no apparent visual impairment or visible pathology of the retina at last eye exam, b) donors diagnosed with non-proliferative diabetic retinopathy (NPDR) but without diabetic macular edema (DME), c) patients diagnosed with NPDR with additional indication of DME, or d) donors diagnosed with proliferative diabetic retinopathy (PDR) and DME. The diagnosis was based on the early treatment diabetic retinopathy study Diabetic Retinopathy Severity Score (ETDRS-DRSS). Additional retinal samples were taken from healthy donors to serve as the control group. The study was designed such that donors of all groups approximately matched in age and gender distribution. Note that none of the donors received treatment for their retinal indication. The study design was reviewed by the University of Iowa Institutional Review Board and found not to involve human subjects research. From each donor group (healthy control, diabetic, NPPR, and NPDR/PDR + DME), 10 tissue samples were collected from the macula region as well as the retinal periphery. All tissue samples were taken with a 6mm biopsy punch, snap frozen in liquid nitrogen, and preserved at -80C until use. Both miRNA and total RNA was extracted using miRNeasy kits (Qiagen) after homogenization of the retina with Qiashredders (Qiagen). RNA was eluted into 30 μl of dH2O. RNA was quantitatively and qualitatively assessed using the fluorescence-based Broad Range Quant-iT RNA Assay Kit (ThermoFisher) and the Standard Sensitivity RNA Analysis DNF-471 Kit on a 48-channel Fragment Analyzer (Agilent), respectively. Concentrations averaged at 100ng/µL while RIN ranged from 4 to 9.
Retina-derived RNA samples were normalized on the MicroLab STAR automated liquid platform (Hamilton). Total RNA input of 240ng was used for library construction with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina #E7760, together with the NEBNext rRNA depletion Kit #E6310 upstream and the NEXNext Multiplex Oligos for Illumina #E7600 downstream (all New England Biolabs). The only deviation from the manufacturer’s protocol was the use of Ampure XP beads (Beckman Coulter) at the double-stranded cDNA purification step, instead of the recommended SPRIselect Beads. Final sequencing libraries were quantified by the fluorescence dye-based methodology High Sensitivity dsDNA Quanti-iT Assay Kit (ThermoFisher) on a Synergy HTX (BioTek). Total RNA libraries were also assessed for size distribution and adapter dimer presence by the High Sensitivity NGS Fragment DNF-474 Kit on a 48-channel Fragment Analyzer (Agilent). Sequencing libraries were normalized on the MicroLab STAR (Hamilton), pooled as two 40-plex pools and spiked in with PhiX Control v3 (Illumina). The two individual pools were then separately clustered on a cBot instrument with a HiSeq 3000/4000 PE Cluster Kit and subsequently sequenced on a HiSeq 4000 Sequencer (all Illumina) with dual index, paired-ends reads at 75 bp length (Read parameters: Rd1: 76, Rd2: 8, Rd3: 8, Rd4: 76) to reach a minimum depth of 50 million Pass-filter reads per sample.

value: Retina Macula

value: Protonix, methotrexate, prednisone, folic acid, captopril, Fosamax, calcium

value: failure to thrive, COPD, hypertension arthritis, osteoporosis, coronary artery disease, CHF, fractures

value: corneal dystrophy

value: Control

value: OD

value: Macula


title: sample_80

value: unkown, but >8 years

value: metformin, humalog, lantus

value: Aggrenox, amitriptyline, avapro, furosemide, lipitor, metoprolol,  omeprazole, systane

value: hypertension, GERD, hyperlipidimia

value: DME OD>OS

value: mild ARMD

value: NPDR

value: TRUE

value: NPDR/PDR + DME

value: NPDR + DME

value: OS

value: Water

value: ul


title: sample_79

value: Retina Periphery

value: female

value: Periphery

value: ng/ul

value: min


title: sample_78

value: >17 years

value: Lantus, Humalog

value: allopurinol, ammonium lactate, atorvastatin, diphenhydramine, fuosemide, metoprolol

value: endometrial cancer, septic shock, acute renal failure, hypertension, heart failure, a fib, diabetes type II, GERD,tinnitus, obesity,

value: pan retinal photocoagulation

value: PDR

value: PDR + DME


title: sample_20 [miRNA-Seq]

description: small RNA

value: Haldol, lorazepam, melatonin, nystatin, omeprazole, Zofran, oxycodone

value: metastatic duodenal cancer, chemotherapy, small bowel obstruction, hernia repair, hyponatremia, hypertension hyperlipidemia,

value: Control

value: FALSE

value: OD


title: sample_72

value: Retina Periphery

value: male

value: >25 years

value: insulin

value: pamelor, lisonopril, furosemide, glyburide, atenolol, paxil, insulin

value: cellulitis with Staph Aureus sepsis, hypertension, coronary atery disease, anxiety, CHF

value: focal grid laser to macula, IOL, YAG, PVD

value: NPDR

value: TRUE

value: NPDR/PDR + DME

value: NPDR + DME

value: OS

value: Water

value: ul


title: sample_09

value: Retina Macula

value: laspofunginin, posacandozole, neupogen, heparin, coumadin, zosyn, vancomycin

value: ulcerative colitis, bone marrow failure, rhizopus lung infection, refractory anemia with myelodysplasia, pulmonary embolus, HTN, myelodysplasia, dyslipidemia

value: pterygium removed, glasses

value: Control

value: Macula

value: ng/ul

value: min


title: sample_74

value: Retina Periphery

value: female

value: >15 years

value: Insulin, glipizide,

value: celebrex, ASA, trazodone, norvascstatin, lipitor, hydorchlorothiazide

value: hypertension, heart attack, acid reflux, congestive heart failure, COPD, aortic valve stenosis

value: AION, pseudophakia

value: Periphery


title: sample_73

value: 34 years

value: insulin

value: oxygen, ASA, synthroid, diatx, allopurinol, tums, iron, BiPAP, vit E, fish oil, benicar, allegra

value: heart failure, cor pumonale and oxygen support, lower extremity lymphedema

value: repeated pan retinal photocoagulation

value: PDR

value: TRUE

value: NPDR/PDR + DME

value: PDR + DME

value: OD

value: Water

value: ul


title: sample_71

value: Retina Periphery

value: female

value: >15 years

value: Insulin, glipizide,

value: NPDR

value: NPDR + DME

value: ng/ul

value: min


title: sample_68

value: Retina Macula

value: >17 years

value: Lantus, Humalog

value: allopurinol, ammonium lactate, atorvastatin, diphenhydramine, fuosemide, metoprolol

value: endometrial cancer, septic shock, acute renal failure, hypertension, heart failure, a fib, diabetes type II, GERD,tinnitus, obesity,

value: pan retinal photocoagulation

value: OS

value: Macula


title: sample_69

value: unkown, but >8 years

value: metformin, humalog, lantus

value: Aggrenox, amitriptyline, avapro, furosemide, lipitor, metoprolol,  omeprazole, systane

value: hypertension, GERD, hyperlipidimia

value: DME OD>OS

value: mild ARMD

value: TRUE

value: NPDR/PDR + DME

value: OD

value: Water

value: ul


title: sample_76

value: Retina Periphery

value: female

value: 23 years, DR 7 years

value: insulin

value: Diovan, Norvasc, plavix, lopressor, foltex, furosemide, pyridoxine, iron, calcium carbonate, diltiazem, allegra, protoniox, levaquin, coumadin, flagyl

value: DM type 1, stroke, Afib, hpertension, renal disease, peripheral neuropathy, ischemic bowl disease

value: grid focal laser, IOL

value: drusen

value: NPDR

value: NPDR + DME

value: Periphery

value: ng/ul

value: min


title: sample_70

value: Retina Macula

value: unkown, but >8 years

value: metformin, humalog, lantus

value: Aggrenox, amitriptyline, avapro, furosemide, lipitor, metoprolol,  omeprazole, systane

value: hypertension, GERD, hyperlipidimia

value: DME OD>OS

value: mild ARMD

value: TRUE

value: NPDR/PDR + DME

value: OS

value: Macula


title: sample_07

value: male

value: Heparin, lasix, lactulose, protonix, paroxetine, vitamin K

value: liver cirrhosis, alpha-1-AT deficiency diagnosed 2 yrs ago, UTI, HTN, nephrolithiasis, OSA on CPAP at night

value: Control

value: FALSE

value: OD

value: Water

value: ul


title: sample_66

value: Retina Macula

value: female

value: 23 years, DR 7 years

value: insulin

value: Diovan, Norvasc, plavix, lopressor, foltex, furosemide, pyridoxine, iron, calcium carbonate, diltiazem, allegra, protoniox, levaquin, coumadin, flagyl

value: DM type 1, stroke, Afib, hpertension, renal disease, peripheral neuropathy, ischemic bowl disease

value: grid focal laser, IOL

value: drusen

value: NPDR

value: NPDR + DME

value: ng/ul

value: min


title: sample_67

value: male

value: unkown

value: unknown

value: CAD, CHF, COPD, DM type II, HTN, hyperlipidemia, cor pulmonae, ischemic heart disease, morbid obesity, MI, obstructive sleep apnea, tobacco use

value: TRUE

value: NPDR/PDR + DME

value: OS

value: Macula


title: sample_75

value: Retina Periphery

value: female

value: 23 years, DR 7 years

value: insulin

value: focal macula laser, IOL

value: OD

value: Periphery

value: Water

value: ul


title: sample_65

value: Retina Macula

value: Diovan, Norvasc, plavix, lopressor, foltex, furosemide, pyridoxine, iron, calcium carbonate, diltiazem, allegra, protoniox, levaquin, coumadin, flagyl

value: DM type 1, stroke, Afib, hpertension, renal disease, peripheral neuropathy, ischemic bowl disease

value: drusen

value: NPDR

value: NPDR + DME

value: ng/ul

value: min


title: sample_62

value: >15 years

value: Insulin, glipizide,

value: celebrex, ASA, trazodone, norvascstatin, lipitor, hydorchlorothiazide

value: hypertension, heart attack, acid reflux, congestive heart failure, COPD, aortic valve stenosis

value: AION, pseudophakia

value: TRUE

value: NPDR/PDR + DME

value: OS

value: Macula


title: sample_61

value: Retina Macula

value: male

value: >25 years

value: insulin

value: pamelor, lisonopril, furosemide, glyburide, atenolol, paxil, insulin

value: cellulitis with Staph Aureus sepsis, hypertension, coronary atery disease, anxiety, CHF

value: focal grid laser to macula, IOL, YAG, PVD

value: OD

value: Water

value: ul


title: sample_63

value: female

value: 34 years

value: oxygen, ASA, synthroid, diatx, allopurinol, tums, iron, BiPAP, vit E, fish oil, benicar, allegra

value: heart failure, cor pumonale and oxygen support, lower extremity lymphedema

value: repeated pan retinal photocoagulation

value: PDR

value: PDR + DME

value: ng/ul

value: min


title: sample_64

value: Retina Macula

value: TRUE

value: NPDR/PDR + DME

value: OS

value: Macula


title: sample_10 [miRNA-Seq]

description: small RNA

value: Haldol, lorazepam, melatonin, nystatin, omeprazole, Zofran, oxycodone

value: metastatic duodenal cancer, chemotherapy, small bowel obstruction, hernia repair, hyponatremia, hypertension hyperlipidemia,

value: Control

value: FALSE

value: OD


title: sample_60

value: Retina Periphery

value: male

value: unknown

value: glimepiride

value: atenolol, atorvastatin, Azor, furosemide

value: type II diabetes mellitus, acute pulmonary edema, renal failure, gastrointestinal hemorrhage,

value: lattice degeneration, vitreous detachment, mild  ARMD, pseudophakia

value: NPDR

value: Periphery

value: Water

value: ul


title: sample_59

value: >10 years

value: Humalog, Lantus

value: aspirin, fish oil, Lasix, Lipitor, lisinopril, warfarin, metolazone

value: kidney failure, hypertension, melanoma, heart bypass

value: pseudophakia, epiretinal membrane

value: ng/ul

value: min


title: sample_06

value: Retina Macula

value: female

value: ovarian CA, mitral regurg, choesystectomy, tonsillectomy

value: corneal stromal scar, cataract

value: Control

value: FALSE

value: OS

value: Macula


title: sample_58

value: Retina Periphery

value: male

value: 19 years

value: insulin

value: clonidine,  fluoxetine, gabapentin, hydrocodone, simvastatin,  omeprazole, lisinopril, cephalexin, tirosint, diltiazem, hydralazine

value: type I diabetes, hypothyroidism, high cholesterol, hypertension, neuropathy

value: glaucoma suspect due to large cups, but not frank glaucoma

value: NPDR

value: Periphery

value: Water


title: sample_77

value: female

value: 7 years

value: glipizide

value: furosemide, verapamil, xopenex, crestor, nexium, venlafaxine, prednisone, hydralazine, azithromysin, spriva, levothyroxine

value: pulmonary hypertension, hypothyroidism, diabetes type II, reflux disease, COPD, mastectomy due to breast cancer, knee replacement, Gravesâ€™ disease, depression

value: glaucoma suspect

value: TRUE

value: NPDR/PDR + DME

value: NPDR + DME

value: OD

value: ul

value: ng/ul

value: min


title: sample_55

value: Retina Periphery

value: male

value: 17 yrs

value: Ranexa, hydralazine, tranexamic acid, Ativan, Lasix, potassium chloride, metoprolol, nitroglycerin, imdur, multivitamin, Colace, Motrin, Haldol, roxanol, Zocor, trazodone, allopurinol, digoxin, torsemide

value: Ischemic cardiomyopathy, CHF, CAD s/p CABG, hyperlipidemia, renal insufficiency/failure, gout, cerebrovascular disease and carotid bruit, HTN, chronic back discomfort, spinal stenosis, atrial fibrillation, heart block with prior pacemaker implantation, anemia, peripheral vascular disease, ex-smoker

value: cataract extraction, PVD

value: allopurinol, amlopidine, asperin, atenolol, gabapentin, omeprazole, furosemide, lorazepam,

value: FALSE


title: sample_56

value: 5 yrs

value: glipizide

value: carvedilol, warfarin, cozaar, digoxin, diltiazem, flector, fluticasone inhalation, furosemide,  januvia, KCl, neurontin, oxycontin, valium, Vicodin, Vit C, Vit E

value: PVD, chronic left foot ischemia and gangrenous tissue, CHF, suicidal thoughts, chronic severe pain, A-fib, BPH, HTN, chronic back pain, vertigo, constipation

value: NPDR

value: Periphery

value: Water


title: sample_53

value: >25 yrs

value: Insulin

value: allopurinol, amlopidine, asperin, atenolol, gabapentin, omeprazole, furosemide, lorazepam

value: DM type 2, IDDM, chronic kidney disease, HTN, prostate adeno CA, melanoma, gout, hyperlipidemia, hypercalcemia.

value: cateract extraction

value: Toe amputation 1 yr prior to death

value: OD

value: ul

value: ng/ul


title: sample_54

value: Retina Periphery

value: male

value: 13 yrs

value: Furosemide, spironolactone, methotrexate, aranesp

value: HTN, ascites of unclear etiology, psoriasis, ostheoarthritis.

value: macular pucker

value: FALSE

value: OS

value: min


title: sample_52

value: >12 years

value: glipizide, pioglitazone

value: Fosamax, aspirin, atorvastatin, calcium, cefaclor, citalopram, furosemide, gabapentin,  insulin, levothyroxine, mitazapine, omeprazole, polyethilene glycol, repaglinide, triamcinolone

value: Diabetes mellitus type II, hypothyroidism, hyperlipidemia

value: Glaucoma suspect, Cataract extraction

value: NPDR

value: Periphery

value: Water


title: sample_05

value: Retina Macula

value: female

value: Plavix, demadex, levothyroxine, folic acid, metoprolol, amlodipine, hydralzine, ASA, fosamax, isosorbide, Douvent nebulizer, PULMICORT INHALER,

value: CAD, s/p MI, angina, CHF, COPD, pulmonary HTN, hypothyroidism, breast CA, osteoprosis/OA, vocal cord paralysis, RA, PUD, vitiligo, HTN

value: pseudophakia, Fuchâ€™s endo dystrophy, choroidal nevi

value: Control

value: OD

value: Macula

value: ul

value: ng/ul


title: sample_50

value: male

value: unknown

value: glimepiride

value: atenolol, atorvastatin, Azor, furosemide

value: type II diabetes mellitus, acute pulmonary edema, renal failure, gastrointestinal hemorrhage,

value: lattice degeneration, vitreous detachment, mild  ARMD, pseudophakia

value: FALSE

value: min


title: sample_51

value: Retina Periphery

value: female

value: unkown

value: insulin (lantus, humalog)

value: allopurinol, ASA, lipitor, plavix, lanoxin, furosemide, indomethacin,  isosorbide, synthroid, toprol, nitroclycerin, altace

value: CAD, ischemic cardiomyopathy, chronic kidney dz, HTN, anemia, PVD, hypothyroidism, DM type 2, hyperlipidemia, asthma.

value: iris neovascularization

value: NPDR

value: Periphery

value: Water


title: sample_48

value: Retina Macula

value: male

value: 19 years

value: insulin

value: clonidine,  fluoxetine, gabapentin, hydrocodone, simvastatin,  omeprazole, lisinopril, cephalexin, tirosint, diltiazem, hydralazine

value: type I diabetes, hypothyroidism, high cholesterol, hypertension, neuropathy

value: glaucoma suspect due to large cups, but not frank glaucoma

value: OS

value: Macula

value: ul

value: ng/ul


title: sample_47

value: 40 yrs

value: hydralazine, Metalozone

value: colon cancer with pulmonary adn bladder mets, bladder bleeding, bladder clots and occlusion, heart disease, popliteal aneurysm, HTN, CAD in native artery, chronic systolic CHF, CKD, acute on chronic combined systolic and diastolic heart failure, PE, A-fib, gross hematuria, urinary tract obstruction, hypotension, slow transit constipation.

value: PVD

value: FALSE

value: OD

value: min


title: sample_44

value: Retina Macula

value: male

value: 13 yrs

value: Insulin

value: Furosemide, spironolactone, methotrexate, aranesp

value: HTN, ascites of unclear etiology, psoriasis, ostheoarthritis.

value: macular pucker

value: NPDR

value: Water


title: sample_43

value: >25 yrs

value: allopurinol, amlopidine, asperin, atenolol, gabapentin, omeprazole, furosemide, lorazepam

value: DM type 2, IDDM, chronic kidney disease, HTN, prostate adeno CA, melanoma, gout, hyperlipidemia, hypercalcemia.

value: cateract extraction

value: Toe amputation 1 yr prior to death

value: Macula

value: ul

value: ng/ul


title: sample_49

value: Retina Macula

value: female

value: >15 years

value: unknown

value: diabetes type 2, cardiomyopathy peripheral artery disease, hypertension, CAD, osteoarthritis, atrial fibrillation, depression, anxiety, history of gangrene

value: This donor had very limited health care

value: FALSE

value: OD

value: min


title: sample_46

value: male

value: 5 yrs

value: glipizide

value: carvedilol, warfarin, cozaar, digoxin, diltiazem, flector, fluticasone inhalation, furosemide,  januvia, KCl, neurontin, oxycontin, valium, Vicodin, Vit C, Vit E

value: PVD, chronic left foot ischemia and gangrenous tissue, CHF, suicidal thoughts, chronic severe pain, A-fib, BPH, HTN, chronic back pain, vertigo, constipation

value: cataract extraction, PVD

value: NPDR

value: Water


title: sample_41

value: Retina Macula

value: unkown

value: insulin (lantus, humalog)

value: allopurinol, ASA, lipitor, plavix, lanoxin, furosemide, indomethacin,  isosorbide, synthroid, toprol, nitroclycerin, altace

value: CAD, ischemic cardiomyopathy, chronic kidney dz, HTN, anemia, PVD, hypothyroidism, DM type 2, hyperlipidemia, asthma.

value: iris neovascularization

value: Macula

value: ul

value: ng/ul


title: sample_40

value: Retina Periphery

value: male

value: 16 years

value: metformin

value: aspirin, levothyroxine,cloidogrel

value: none noted

value: AMD, cataract extraction, PVD

value: Diabetic

value: FALSE

value: OS

value: Periphery

value: min


title: sample_36

value: female

value: >12 yrs

value: allopurinol, aspirin, ferrous sulfate, neurontin, omeprazole, KCl, PreserVision, Restasis, Demadex, Tyvaso inhaler, Zetia

value: heart failure, atrial flutter, chronic renal insufficiency, pulmonary hypertension, Sjogrenâ€™s syndrome, DM, osteoarthritis

value: Sjogrenâ€™s, Fuchsâ€™, early ARMD

value: A1C between 6 and 7 over the years

value: OD

value: Water


title: sample_04

value: Retina Macula

value: male

value: atenolol, DECADRON (STEROIDS), paroxetine, ASA, Aricept, folic acid

value: metastatic lung CA, HTN, depression

value: cataract extraction

value: Control

value: Macula

value: ul

value: ng/ul


title: sample_35

value: Retina Periphery

value: female

value: >15 years

value: Plavix, metoprolol,dyrenium, gabapentin, multivitamin

value: DM, HTN, hypothyroidism, depression CHF, osteoarthritis

value: Phaco, trabeculectomy

value: Diabetic

value: FALSE

value: Periphery

value: min


title: sample_42

value: Retina Macula

value: male

value: >12 years

value: glipizide, pioglitazone

value: Fosamax, aspirin, atorvastatin, calcium, cefaclor, citalopram, furosemide, gabapentin,  insulin, levothyroxine, mitazapine, omeprazole, polyethilene glycol, repaglinide, triamcinolone

value: Diabetes mellitus type II, hypothyroidism, hyperlipidemia

value: Glaucoma suspect, Cataract extraction

value: NPDR

value: OD

value: Water


title: sample_37

value: Retina Periphery

value: female

value: 7 yrs

value: humalog, glucophage, lantus

value: fentanyl, Haldol, heparin, Ativan, levothyroxin, lisinopril, protonix, pantoprazole

value: acute chronic kidney injury,acute hepatic encephalopathy, heart-to-heart cirrhosis of liver, hypertension, hypothyroidism, obesity, pneumonia, diabetes mellitus type II, IDDM

value: OS

value: ul

value: ng/ul


title: sample_38

value: unknown

value: metformin (1000 mg)

value: mapap

value: paroxysmal a-fib on chronic anticoagulation, mild to moderate mitral regurgitation and stenosis, IDDM, HTN, CAD.

value: hypertensive retinopathy

value: Diabetic

value: FALSE

value: Periphery

value: min


title: sample_01 [miRNA-Seq]

description: small RNA

value: Retina Macula

value: female

value: ASA, levoxyl, verpamil, aldactone, nasonex nasal srapy, vicodin, toprol, mirtazapine, pulmicort puff (glucocorticoid), albuterol inhaler 2 puff, home oxygen, Mg tablets,

value: hypertension (HTN), congestive heart failure (CHF), asthma, history of Vfib with MI x 2 s/p AICD placement in 1999.  Atrial fib, hypothyroidism

value: pseudophakia with YAG

value: Control

value: OD

value: Macula

value: Water


title: sample_33

value: Retina Periphery

value: male

value: >25 years

value: Glimepiride, Novolin

value: isosorbide, metoprolol, allopurinol, lisinopril, lasix, ASA, Crestor,  Zetia, sulfasalazine, digoxin

value: ischemic cardiomyopathy, CAD, aortic stenosis, DM, renal insufficiency, hyperlipidemia, HTN, TIA, spinal stenosis, ulcerative colitis, left ulnar palsy,

value: ul

value: ng/ul


title: Series#3: siFus#1

city: Fujisawa

first: MASAHIRO

last: NOGAMI

state: Kanagawa

address: 26-1, Muraoka-Higashi 2-Chome

department: Research

country: Japan

institute: Takeda Pharmaceutical Company Limited

data_processing:
Sequenced reads were trimmed for adaptor sequence with Trimmomatic_ver.0.36 PE -phred 33 -trimlog ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10
Sequenced reads were masked for low-complexity or low-quality sequence with PRINSEQ_ver. 2.20.4 -fastq -fastq2 -out_good -out_bad -out_format 3 -trim_left 5 -trim_tail_right 5 -trim_qual_right 30 -ns_max_p 20 -min_len 30
Mapping to GRCm38.p6 whole genome using STAR_ver.2.5.4b --runMode alignReads --runThreadN 9 --genomeDir --sjdbScore 1 --sjdbGTFfile --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --outSAMattributes All --outFilterIntronMotifs RemoveNoncanonical --readFilesCommand zcat --readFilesIn --outFileNamePrefix --outFilterMultimapNmax 8 --outFilterMismatchNmax 4 --outFilterType BySJout --outFilterMismatchNoverReadLmax 0.04 --outReadsUnmapped Fastx --alignIntronMin 20 --alignIntronMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignMatesGapMax 1000000
The number of reads count in the exons of were counted. featureCounts_ver. 1.61 -T 9 -F GTF -O -p -t exon -g gene_id -a gencode.vM17.chr_patch_hapl_scaff.annotation.gtf -o
Genome_build: GRCm38.p6, gencode.vM17.chr_patch_hapl_scaff.annotation.gtf

source_name: NSC-34 cell treated with siFus#1 and RNAiMAX.

growth_protocol: NSC-34 cells were maintained in DMEM (Sigma; # D5796-500ML) with 10% FBS (ATCC, #30-2020) and 100 U/ml Penicillin-Streptomycin (Invitrogen, #15140122) in 5% CO2 at 37 °C.

extract_protocol:
After 72 hours from siRNA transfection, total RNA were extracted from the cells by miRNeasy Kit with QIAzol (QIAGEN).
Illumina Strand-Specific RNA library preparation with polyA selection

treatment_protocol: 400,000 NSC-34 cells/well (6 well plate) were plated on collagen coated plate and 60 nM siNC#1, siNC#2, siFus#1, siFus#4 and siFus#5 were transfected with Lipofectamine RNAiMAX reagent.

value: NSC-34 cells

tag: cell type

value: mouse motor neuron-like cells


title: Series#3: siFus#5

source_name: NSC-34 cell treated with siFus#5 and RNAiMAX.


title: sample_32

value: >12 years

value: glyburide, insulin

value: atenolol, lisinopril

value: pancreatic cancer, dyspnea from pleural effusion, DM, Afib.

value: cataract

value: Diabetic

value: FALSE

value: Periphery

value: min


title: Series#3: siNC#2

source_name: NSC-34 cell treated with siNC#2 and RNAiMAX.


title: sample_31

value: Retina Periphery

value: female

value: 10 yrs

value: atenolol/chlorthalidone, monopril, synthroid, ambien, tylenol .3, amitriptyline

value: DM, HTN, hypothyroidism, depression CHF, osteoarthritis

value: cataracts, Fuchs., glaucoma suspect, corneal dystrophy

value: OD

value: Water


title: Series#3: siNC#1

source_name: NSC-34 cell treated with siNC#1 and RNAiMAX.

value: NSC-34 cells

value: mouse motor neuron-like cells


title: sample_57

value: male

value: 40 yrs

value: insulin

value: hydralazine, Metalozone

value: colon cancer with pulmonary adn bladder mets, bladder bleeding, bladder clots and occlusion, heart disease, popliteal aneurysm, HTN, CAD in native artery, chronic systolic CHF, CKD, acute on chronic combined systolic and diastolic heart failure, PE, A-fib, gross hematuria, urinary tract obstruction, hypotension, slow transit constipation.

value: PVD

value: NPDR

value: ul

value: ng/ul


title: sample_30

value: Retina Macula

value: 16 years

value: metformin

value: aspirin, levothyroxine,cloidogrel

value: none noted

value: AMD, cataract extraction, PVD

value: Diabetic

value: FALSE

value: OS

value: Macula

value: min


title: sample_03

value: female

value: levoxyl, atenolol, avapro, dilantin, DDAVP, omepraxole, MVI, ASA

value: breast CA with brain mets, DI, HTN, hypothyroidism, GRD

value: cataracts

value: Control

value: OD

value: Water


title: Series#2: pre-miR-125b

source_name: NSC-34 cell treated with pre-miR-125b and RNAiMAX.

extract_protocol:
After 48 hours from miRNA mimic transfection, total RNA were extracted from the cells by miRNeasy Kit with QIAzol (QIAGEN).
Illumina Strand-Specific RNA library preparation with polyA selection

treatment_protocol: 400,000 NSC-34 cells/well (6 well plate) were plated on collagen coated plate and 60 nM siNC#1, siNC#2, miR-125b-5p-mimics and pre-miR-125b were transfected with Lipofectamine RNAiMAX reagent.

value: NSC-34 cells

value: mouse motor neuron-like cells


title: Series#3: siRNA (-)

source_name: NSC-34 cell treated with RNAiMAX only.


title: sample_29

value: Retina Macula

value: 7 yrs

value: humalog, glucophage, lantus

value: fentanyl, Haldol, heparin, Ativan, levothyroxin, lisinopril, protonix, pantoprazole

value: acute chronic kidney injury,acute hepatic encephalopathy, heart-to-heart cirrhosis of liver, hypertension, hypothyroidism, obesity, pneumonia, diabetes mellitus type II, IDDM

value: ul

value: ng/ul


title: sample_27

value: >15 years

value: Plavix, metoprolol,dyrenium, gabapentin, multivitamin

value: DM, HTN, hypothyroidism, depression CHF, osteoarthritis

value: Phaco, trabeculectomy

value: Diabetic

value: FALSE

value: Macula

value: min


title: Series#2: miR-125b mimic

source_name: NSC-34 cell treated with miR-125b-5p mimic and RNAiMAX.

value: NSC-34 cells


title: sample_28

value: female

value: unknown

value: metformin (1000 mg)

value: mapap

value: paroxysmal a-fib on chronic anticoagulation, mild to moderate mitral regurgitation and stenosis, IDDM, HTN, CAD.

value: hypertensive retinopathy

value: OS

value: Water


title: Series#2: siNC#2

value: mouse motor neuron-like cells


title: Series#2: siNC#1


title: sample_34

value: Retina Periphery

value: male

value: Lantus insulin, Humalog insulin

value: fish oil, lasix, Avapro, isosorbide, metroprolol XL, omeprazole, KCl, Crestor, Vit D, nitroglycerin prn

value: IDDM type 2, adematous colon polyp, hypercholesterolemia, HTN, A-fib w/ ablation, CAD, back pain, stroke, kidney failure, acid reflux, arthritis, atrial flutter, GERD, cataracts, tobacco use.

value: IOL, drusen

value: Periphery

value: ul

value: ng/ul


title: sample_25

value: Retina Macula

value: female

value: 7 yrs

value: Glimepiride, metformin

value: prednisone, lisinopril/HCTZ, bisoprolol

value: paratracheal mass, lupus, autoimmune hepatitis, NIDDM, HTN, high creatinine levels.

value: cataracts

value: Diabetic

value: FALSE

value: Macula

value: min


title: Series#3: siFus#4

source_name: NSC-34 cell treated with siFus#4 and RNAiMAX.

value: NSC-34 cells

value: mouse motor neuron-like cells