title: CSF3R.T618I+CEBPA.v314vw-INPUT

city: Portland

first: Theodore

middle: Paul

last: Braun

state: OR

address: 3181 SW Sam Jackson Park Road

department: Knight Cancer Institute

institute: OHSU

description: Cells immortalized through retroviral transduction with CSF3R.T618I and CEBPA.v314vw

data_processing:
Read qualities were evaluated using FastQC.
Reads were aligned to the mm10 reference using bwa-mem, with default single-end settings.
Using Samtools, alignments were converted to bam format and filtered to remove reads with mapping quality <30.
Alignments were combined between biological replicates.
We used MACS2 to predict ChIP-seq peaks and generate fold enrichment tracks againts appropriate INPUT sample.
Genome_build: mm10
Supplementary_files_format_and_content: BedGraph tracks contain fold enrichment values (calculated by MACS2, relative to INPUT) for each combination of ChIP for each of the cell groups.

source_name: Bone marrow

growth_protocol: HoxB8 cells were grown in RPMI +10% FCS and SCF-CHO conditioned media +estrogen as preaviously described (Wang et al, Nat Methods, 2006)

extract_protocol:
Cells were fixed and lysed to extract chromatin. Fixed chromatin was sheared and appropriate antibodies were used to perform the pull down. Aliquotes of the sheared chromatin were used as input.
ChIP and INPUT libraries were prepared using the NEB Ultra II kit (E7645S) according to manufacturer's instructions. Briefly, samples were end-prepped, adaptor ligated and cleaned with Agencourt Ampure XP magnetic beads. Adaptor ligated samples were then barcoded during PCR (10 cycles) and cleaned up.

treatment_protocol: Cells were retrovirally transduced with retrovirus harboring oncogenes, sorted for expression of both fluorescent proteins and allowed to recover for 1 week. Cells were washed 4x and cultured for 24 hours in estrogen free media

value: Bone marrow

tag: vector

value: CSF3R.T618I and CEBPA.v314vw

tag: chip marker

value: none (input)


title: WT_cells_d5_rep1 (RNA-seq)

status: Public on Dec 02 2019

type: SRA

city: Freiburg

first: Sebastian

middle: J.

last: Arnold

address: Albertstrasse 25

department: Pharmacology

country: Germany

institute: University of Freiburg

description:
processed data files:
bamCoverage_RNAseq_WT.bigwig
nrm-counts-avg-WT-BraKO-EoKO-dKO.xlsx
DE-sig-dKO-vs-WT_p0.05_l2FC2.5.xlsx
nrm-counts-avg-dKO-vs-WT.xlsx

library_source: transcriptomic

data_processing:
For differential gene expression analysis sequenced reads were mapped to the mouse reference genome GRCm38/mm10 (iGenomes, Illumina) containing the chromosomes 1-19, X, Y and M using Rsubread v1.28.1 package in R v3.4.3. The genomic annotations used for the mapping, counting and downstream analyses were contained in gtf files provided by the iGenomes reference genome bundles (archive-2015-07-17-32-40 and archive-2015-07-17-33-26 for GRCM38 and mm10, respectively). Genomic features were counted using the Rsubread::featureCounts function. Differential expression analysis was carried out using DESeq2 v1.18.1 in R, which applies Negative Binomial GLM fitting and Wald statistics on the count data. The results were filtered for adjusted p-value<0.05 and log2FC. Prior to fitting and statistical analysis, counts were normalized by library size (DESeq2::estimateSizeFactors) and gene-wise dispersion (DESeq2::estimateDispersions) to normalize the gene counts by gene-wise geometric mean over samples. Mapping for the creation of bigwig Coverage files was performed on Galaxy platform using Bowtie2 (v2.3.4) on mm10 reference genome with default settings. Obtained bam files from biological triplicates were merged using Merge BAM files tool in Galaxy (picard v1.56.0) and the duplicates were removed by RmDup tool (samtools v1.3.1). Coverage files were created using bamCoverage tool (deepTools v3.0.2) with bin size 10 bases and reads per kilobase per million (RPKM) normalization.
Mapping: For the RNA-seq results reads trimmed of the addapters were mapped to the mouse reference genome GRCm38/mm10 (iGenomes, Illumina), using Rsubread v1.28.1 package in R v3.4.3. For ATAC-seq and ChIP seq reads were mapped to mm10 genome using Bowtie2 v2.3.4 on the Galaxy platform.
Counting: Genomic features were counted for the RNA-seq analysis with the Rsubread::featureCounts function in Rsubread v1.28.1 package using genomic annotations as gtf files provided by the iGenomes reference genome bundles (archive-2015-07-17-32-40 and archive-2015-07-17-33-26 for GRCM38 and mm10, respectively).
Differential expression: Differential expression analysis was carried out using DESeq2 v1.18.1 in R, which applies Negative Binomial GLM fitting and Wald statistics on the count data. The results were filtered for adjusted p-value<0.05 and log2FC as indicated in the figure legends. Prior to fitting and statistical analysis, counts were normalized by library size (DESeq2::estimateSizeFactors) and gene-wise dispersion (DESeq2::estimateDispersions) to normalize the gene counts by gene-wise geometric mean over samples. Gene-wise scaling was performed on the normalized counts to cluster the counts for the expression tendency between the samples (stats::kmeans function). In addition, the counts were centered by setting the gene-wise mean to zero.
Coverage: For the generation of coverage files for RNA-seq, ATAC-seq and ChIP-seq analysis corresponding bam files from biological replicates were merged using Merge BAM files tool in Galaxy (picard v1.56.0) and the duplicates were removed by RmDup tool (samtools v1.3.1). Coverage files were created using bamCoverage tool (deepTools v3.0.2) with bin size 10 bases and reads per kilobase per million (RPKM) normalization.
Peak calling: Peaks were detected using MACS2 on the Galaxy platform (v2.1.1.20160309.4) with BAMPE format of the input file, default settings for building the shifting model and minimum q-value cut-off for detection of 0.05. For ChiP-seq of EoGFP and BraGFP peaks detected in the input control and dKO -dox control were subtracted from the genomic intervals detected in ChIP-seq treatment file using SubtractBed tool (bedtools v2.27.0) in Galaxy, where entire features were filtered out if the overlap of minimum 1 bp was found. For ChiP-seq of EoGFP and BraGFP peaks the resulting narrow peaks bed file was sorted and filtered for the pileup value (height of the peak at the summit, provided in the Peaks tabular file from MACS2) higher than 120 and 40, respectively.
Genome_build: mm10
Supplementary_files_format_and_content: Processed RNA-seq results showing differential gene expression between WT and dKO contain normalized and scaled counts (RPKM) in Tab delimited txt format. Coverage files in BigWig format  for RNA-seq and ChIP-seq reads are normalized to RPKM. Bed files for EoGFP and BraGFP ChIP-seq contain coordinates of the peaks recognized after MACS2 peak calling and subsequent filtering for the pileup value.

molecule: total RNA

organism: Mus musculus

source_name: 5 days A2lox.Cre embryoid bodies (ActA)

growth_protocol:
Prior to differentiation, ESCs were depleted of feeders by splitting for 2-3 passages onto 0.1% gelatin-coated 60 mm dishes. For embryoid body (EB) formation, 200 cells in 40 μl ESGRO Complete Basal medium were grown in ultra-low attachment 96-well plates (Greiner BioOne) for 2 days until single EB had formed in every well. EBs were subsequently transferred into 60 mm non-adhesive dishes and allowed to further differentiate in ESGRO Complete Basal medium with 30 ng/ml human recombinant ActivinA (ActA, R&D systems).
A2lox.Cre Mouse ESCs were grown in the standard serum containing conditions with 1000 U/ml LIF, 3 mM CHIR99021 and 1 mM OD0325901 on the monolayer of mitotically inactivated STO feeder cells (SNL76/7). Prior to differentiation cells were depleted of feeders and 200 cells per 40 ml of serum-free Basal medium were grown as embryoid bodies (EBs) in ultra-low attachment plates for 2 days, or alternatively, 2.5x10^5 cells were grown as EBs in 10 mm non-adherent dishes in Basal medium. Cells were further treated and grown for 2-3 more days.

extract_protocol:
RNA from differentiated embryoid bodies was extracted with RNeasy Mini Kit (Qiagen) with on-column DNAse digestion as recommended by the manufacturer.
Library preparation was carried out using 0.5 μg of RNA with NEBNext Ultra RNA library Prep Kit for Illumina (New England BioLabs).

treatment_protocol: Cells were either treated with 30 ng/ml human recombinant ActivinA (ActA) from day 2 to day 5 of differentiation, or for the NECtrl samples with 100 ng/ml Noggin and 10 mM SB431542 for 1 day followed by 1 day treatment with 100 ng/ml Noggin and 10 ng/ml ActA. Dox-inducible cells were stimulated with 5 mg/ml dox from day 2 to day 5 of differentiation in the appropriate medium.

tag: genotype/variation

value: WT

tag: day

tag: treatment

value: ActA


title: wlung_d14_1 [muc4637]

city: Houston

first: Lukas

last: Simon

address: 1 Baylor Plaza

department: THINC

country: USA

institute: Baylor College of Medicine

description:
Drop-seq
MUC4637_S7_L002

data_processing:
For the single-cell RNA-seq data the Drop-Seq core computational pipeline was used for processing next generation sequencing reads of the scRNA-seq data, as previously described (Pubmed ID: 26000488). For the whole lung tissue and flow-sorted bulk RNA-seq data, STAR (Pubmed ID:  23104886) was used to align the reads to reference genome mm10 followed by featureCounts (Pubmed ID: 24227677) for gene summarization.
Genome_build: mm10
Supplementary_files_format_and_content: For the "High resolution" experiment: Raw count matrix (HighResolution_rawcounts.mtx) from Drop-seq experiments with 24051 genes and 34068 cells in market matrix format and corresponding column (HighResolution_barcodes.txt) and row (HighResolution_genes.txt) labels and cell-level metadata (WholeLung_cellinfo.csv). For the "Whole lung" experiment: Raw count matrix (WholeLung_rawcounts.mtx) from Drop-seq experiments with 23400 genes and 29297 cells in market matrix format and corresponding column (WholeLung_barcodes.txt) and row (WholeLung_genes.txt) labels and cell-level metadata (WholeLung_cellinfo.csv).

source_name: whole_lung_Whole lung_day14

extract_protocol:
Lung single cell suspensions were generated in the following manner. Briefly, after euthanasia, lung tissue was perfused with sterile saline through the heart and the right lung was tied off at the main bronchus. The left lung lobe was subsequently filled with 4% paraformaldehyde for later histologic analysis. Right lung lobes were removed, minced (tissue pieces at approx. 1 mm2), and transferred for mild enzymatic digestion for 20-30 min at 37°C in an enzymatic mix containing dispase (50 caseinolytic U/ml), collagenase (2 mg/ml), elastase (1 mg/ml), and DNase (30 µg/ml). Single cells were harvested by straining the digested tissue suspension through a 40 micron mesh. After centrifugation at 300 x g for 5 minutes, single cells were taken up in 1 ml of PBS (supplemented with 10% fetal calf serum), counted and critically assessed for single cell separation and overall cell viability. For Dropseq, cells were aliquoted in PBS supplemented with 0.04% of bovine serum albumin at a final concentration of 100 cells/µl.
Single cell suspensions were processed through Drop-Seq to generate single-cell cDNA libraries attached to microbeads. Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA prepared for sequencing. For each sample, 1 ng of pre-amplified cDNA from an estimated 1000 cells was tagmented by Nextera XT (Illumina) with a custom P5 primer (Integrated DNA Technologies). Single cell libraries were sequenced in a 100 bp paired-end run on the Illumina HiSeq 4000 using 0.2 nM denatured sample and 5% PhiX spike-in. For priming of read 1, 0.5 µM Read1CustSeqB (primer sequence: GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC) was used.

tag: tissue

value: Whole lung

tag: injury timecourse

tag: experiment

tag: number of cells


title: CSF3R.T618I+CEBPA.v314vw-H3K4me3-ChIP-replicate.1

library_source: genomic

molecule: genomic DNA

tag: strain

tag: cell type


title: wlung_d10_1 [muc4635]

description:
Drop-seq
MUC4635_S5_L001

source_name: whole_lung_Whole lung_day10


title: D. Melanogaster_DGE_zt23_29C

city: Waltham

last: Kadener

state: MA

address: 415 South Street

institute: Brandeis University

data_processing:
Ribosomal RNA was taken out using Bowtie2 aligner against the ribosomal RNA
Reads were aligned to dm3 genome using TopHat
The aligned reads were analyzed with cufflinks
Genome_build: dm3
Supplementary_files_format_and_content: table of transcripts reads

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: fly heads

growth_protocol: Flies were grown at different temperatures

extract_protocol:
The precipitated RNAwas taken for library preparation.
3’-seq libraries were prepared as previously described (Shishki et al., Afik et al., 2017)

treatment_protocol: RNA extraction was done using TRI Reagent [SIGMA] following manufacturer´s protocol.

value: Canton-S

tag: circadian timepoints

tag: temperature

value: fly heads


title: D. Melanogaster_DGE_zt7_29C


title: CSF3R.T618I+CEBPA.v314vw-H3K4me1-ChIP-replicate.2


title: wlung_d10_3 [muc4646]

description:
Drop-seq
MUC4646_S16_L004


title: D. Melanogaster_DGE_zt23_25C


title: D. Melanogaster_DGE_zt11_29C


title: D. Melanogaster_DGE_zt15_29C


title: wlung_d10_2 [muc4636]

description:
Drop-seq
MUC4636_S6_L002


title: D. Melanogaster_DGE_zt18_29C


title: 744-16

type: RNA

city: Mexico City

first: Brenda

last: Cabrera

address: Periférico Sur

country: Mexico

institute: National Institute of Genomic Medicine

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalization with Limma in R; batch effects were removed with ARSyN package

label: biotin

organism: Homo sapiens

source_name: Dorsolateral prefrontal cortex

label_protocol: Biotinylated cRNA were prepared with the TargetAmpTM-Nano Labeling Kit (Epicentre)

growth_protocol: Fresh brain samples were stored in RNAlater

extract_protocol: RNA isolation was performed using the RNeasy kit from Qiagen™ following the manufacturer's instructions

tag: age

tag: gender

value: Female

tag: suicide

value: Suicide

tag: sud

value: Without SUD


title: 735-16

value: Male

value: SUD


title: CSF3R.T618I+CEBPA.v314vw-H3K4me1-ChIP-replicate.1

tag: vector


title: D. Melanogaster_DGE_zt3_29C


title: wlung_d7_4 [muc4634]

description:
Drop-seq
MUC4634_S4_L001

source_name: whole_lung_Whole lung_day7


title: wlung_d7_3 [muc4633]

description:
Drop-seq
MUC4633_S3_L001


title: WT_cells_d5_rep2 (RNA-seq)


title: MLL1-ChIP-Seq

city: Ann Arbor

first: Fengbiao

last: Mao

state: Michigan

address: 1301 Catherine St

department: Department of Pathology

institute: University of Michigan

data_processing:
All ChIP-seq data were mapped to the mm10 genome for mouse by using Bowtie2 (v2-2.2.4), which is ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. Then, we removed any duplicated reads for both pair-end and single-end data using SAMtools (v1.5)
For ChIP-seq data, the fold enrichment for visualization in IGV were normalized by MACS2 subcommands bdgopt and bdgcmp based on the ratio of tags after filtering between the treatment and input control.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig and peaks table

source_name: embryo

growth_protocol: mESCs were maintained in the presence of leukemia inhibitory factor (LIF, Millipore) in KO DMEM containing 5% ES qualified fetal calf serum and 15% KSR on Matrigel (feeder-free).

extract_protocol:
ChIP experiments were performed using ~4µg a-Mll1 antibody for 1E8 cells ; ~2ug a-H3K4me1/2/3 for 2E7 cells according to standard protocols. Crosslinking of the cells was performed with 1% PFA for 10 minutes, while ChIPed DNA was purified by Qiaquick PCR purification Kit (Qiagen).
Libraries were prepared with the Illumina TruSeq protocol according to the manufacturer’s protocol.

treatment_protocol: Treatment of MM401(100uM) or 4-Hydroxytamoxifen (4-OHT, 5µM ) on mESCs for three passage (9 day) in LIF/5%Serum/15%KSR/KO DMEM medium.

value: embryonic stem cell , blastocyst derived

tag: genotype

value: Mll1fl/fl; Cre-ER TM

tag: agent

value: untreated


title: D. Melanogaster_DGE_zt11_25C


title: 725-16


title: 4049-16


title: 724-16


title: 3393-16


title: 713-16


title: D. Melanogaster_DGE_zt18_25C


title: wlung_d7_2 [muc4632]

description:
Drop-seq
MUC4632_S2_L001


title: CSF3R.T618I+CEBPA.v314vw-H3K27ac-ChIP-replicate.2

tag: chip marker


title: D. Melanogaster_DGE_zt15_25C


title: CSF3R.T618I+CEBPA.v314vw-H3K4me3-ChIP-replicate.2


title: wlung_d7_1 [muc4171]

description:
Drop-seq
MUC4171_S12_L004


title: wlung_d3_1 [muc4631]

description:
Drop-seq
MUC4631_S1_L001

source_name: whole_lung_Whole lung_day3


title: CSF3R.T618I+CEBPA.v314vw-H3K27ac-ChIP-replicate.1

description: Cells immortalized through retroviral transduction with CEBPA.v314vw


title: wlung_PBS_4 [muc4173]

description:
Drop-seq
MUC4173_S14_L004

source_name: whole_lung_Whole lung_day0


title: 3887-16


title: CEBPA.v314vw-INPUT

value: CEBPA.v314vw only


title: 2836-16


title: D. Melanogaster_DGE_zt18_18C


title: D. Melanogaster_DGE_zt7_25C


title: wlung_PBS_3 [muc4172]

description:
Drop-seq
MUC4172_S13_L004


title: CEBPA.v314vw-H3K4me3-ChIP-replicate.2

value: Bone marrow


title: D. Melanogaster_DGE_zt3_25C


title: D. Melanogaster_DGE_zt15_18C


title: wlung_PBS_1 [muc4169]

description:
Drop-seq
MUC4169_S10_L003


title: 2536-16


title: 3278-16


title: D. Melanogaster_DGE_zt23_18C


title: 2446-16


title: hires_d13_2 [muc9296]

description:
Drop-seq
MUC9296_S6_L002

source_name: high_resolution_Lung epithelium_day13

value: Lung epithelium


title: CEBPA.v314vw-H3K4me1-ChIP-replicate.2


title: hires_d28_1 [muc9297]

description:
Drop-seq
MUC9297_S7_L002

source_name: high_resolution_Lung epithelium_day28


title: 3059-16


title: CEBPA.v314vw-H3K4me3-ChIP-replicate.1


title: CEBPA.v314vw--H3K4me1-ChIP-replicate.1


title: D. Melanogaster_DGE_zt11_18C


title: 2333-16


title: 2280-16


title: D. Melanogaster_DGE_zt7_18C


title: 2160-16


title: CSF3R.T618I-H3K4me3-ChIP-replicate.1

description: Cells immortalized through retroviral transduction with CSF3R.T618I

value: CSF3R.T618I only


title: CEBPA.v314vw-H3K27ac-ChIP-replicate.2


title: CEBPA.v314vw-H3K27ac-ChIP-replicate.1


title: CSF3R.T618I-H3K4me1-ChIP-replicate.2


title: wlung_PBS_2 [muc4170]

description:
Drop-seq
MUC4170_S11_L003


title: hires_d9_2 [muc9295]

description:
Drop-seq
MUC9295_S5_L002

source_name: high_resolution_Lung epithelium_day9


title: 2075-16


title: 2144-16


title: CSF3R.T618I-H3K4me1-ChIP-replicate.1


title: CSF3R.T618I-INPUT

value: none (input)


title: D. Melanogaster_DGE_zt3_18C


title: CSF3R.T618I-H3K4me3-ChIP-replicate.2


title: hires_d12_2 [muc9294]

description:
Drop-seq
MUC9294_S4_L001

source_name: high_resolution_Lung epithelium_day12


title: Drosophila Melanogaster_zt23_29C

data_processing:
Ribosomal RNA was taken out using Bowtie2 aligner against the ribosomal RNA
Reads were aligned to dm3 genome using TopHat
The aligned reads were analyzed with cufflinks
Genome_build: dm3
Supplementary_files_format_and_content: txt file with isoforms quantification

extract_protocol:
The precipitated RNAwas taken for library preparation.
Libraries were constructed using the protocol for ligation base libraries (Engreitz et al., 2013)


title: Drosophila Melanogaster_zt15_25C


title: hires_d3_2 [muc9292]

description:
Drop-seq
MUC9292_S2_L001

source_name: high_resolution_Lung epithelium_day3


title: hires_d8_2 [muc9291]

description:
Drop-seq
MUC9291_S1_L001

source_name: high_resolution_Lung epithelium_day8


title: hires_d10_2 [muc9293]

description:
Drop-seq
MUC9293_S3_L001

source_name: high_resolution_Lung epithelium_day10


title: Drosophila Melanogaster_zt3_29C


title: hires_d5_2 [muc9290]

description:
Drop-seq
MUC9290_S18_L005

source_name: high_resolution_Lung epithelium_day5


title: hires_d4_2 [muc9289]

description:
Drop-seq
MUC9289_S17_L005

source_name: high_resolution_Lung epithelium_day4


title: CSF3R.T618I-H3K27ac-ChIP-replicate.2

source_name: Bone marrow


title: Drosophila Melanogaster_zt15_29C


title: Drosophila Melanogaster_zt23_18C


title: Drosophila Melanogaster_zt3_25C


title: Drosophila Melanogaster_zt15_18C


title: hires_d13_1 [muc9288]

description:
Drop-seq
MUC9288_S16_L005


title: Empty-INPUT

description: Cells retrovirally tranduced with empty vector

value: Empty vector


title: hires_d0_2 [muc9287]

description:
Drop-seq
MUC9287_S15_L005

source_name: high_resolution_Lung epithelium_day0


title: Empty-H3K4me3-ChIP-replicate.2


title: Drosophila Melanogaster_zt3_18C

source_name: fly heads


title: 2074-16

source_name: Dorsolateral prefrontal cortex


title: Empty-H3K4me3-ChIP-replicate.1


title: hires_d21_1 [muc9286]

description:
Drop-seq
MUC9286_S14_L004

source_name: high_resolution_Lung epithelium_day21


title: 1921-16


title: 2066-16


title: 1896-16


title: hires_d10_1 [muc9285]

description:
Drop-seq
MUC9285_S13_L004


title: Empty-H3K4me1-ChIP-replicate.2


title: hires_d2_2 [muc9284]

description:
Drop-seq
MUC9284_S12_L004

source_name: high_resolution_Lung epithelium_day2


title: 1821-16


title: Empty-H3K4me1-ChIP-replicate.1


title: 1831-16


title: Ago29_21

data_processing:
Processing was done using miRExpress pipeline (Wang, W.C., et al., miRExpress: Analyzing high-throughput sequencing data for profiling microRNA expression. BMC Bioinformatics, 2009. 10(1): p. 328.) using miRBase 21 version
Genome_build: miRBase 21
Supplementary_files_format_and_content: txt file with miRNA quantification

source_name: AGO1-IP heads

extract_protocol:
RNA extraction was done using TRI Reagent [SIGMA] following manufacturer´s protocol. The precipitated RNAwas taken for library preparation.
Libraries were constructed using NEBNext® Small RNA Library Prep Set for Illumina.

treatment_protocol: Ago-IP was done as described at Kadener. S et al, Genes Dev 2009, with the following modifications: 200µl of fly heads were homogenized in 700 μL of lysis buffer (30 mM HEPES KOH at pH 7.4, 100 mM KAcetate, 2 mM MgAcetate, 5% glycerol, 0.5% IGEPAL CA-630, 1 mM EGTA, 1 mM DTT, 0.4 U/μL RNase OUT [Invitrogen], 1× EDTA free protease inhibitor [Roche]) using a motorized pellet pestle. The lysates were incubated for 10 min on ice and centrifuged at 21,000 rcf (Max speed) for 15 min at 4°C. 10% supernatant were used as input. For Ago IP, 2µg of anti-AGO-1 antibody (kindly provided by Prof. Mikiko C. Siomi , The University of Tokyo) was incubated for 2 hours at 4°C with rotation. Following incubation with protein G-plus magnetic bead slurry (Dynabeads.ThermoFisher Scientific) for an additional one hour (at 4°C with rotation), the beads were washed five times with 500μL of lysis buffer, with the magnet placed on ice.

tag: molecule subtype

value: small RNA


title: Ago29_15

value: Canton-S

tag: tissue


title: 1777-16


title: Ago29_9

value: fly heads


title: CSF3R.T618I-H3K27ac-ChIP-replicate.1


title: hires_d12_1 [muc9283]

description:
Drop-seq
MUC9283_S11_L003

tag: injury timecourse


title: Ago29_3


title: Empty-vector-replicate.2


title: hires_d6_1 [muc9282]

description:
Drop-seq
MUC9282_S10_L003

source_name: high_resolution_Lung epithelium_day6

tag: experiment


title: 1473-16


title: Empty-vector-replicate.1


title: hires_d36_2 [muc9281]

description:
Drop-seq
MUC9281_S9_L003

source_name: high_resolution_Lung epithelium_day36

tag: number of cells


title: Ago25_21

tag: strain


title: 1553-16


title: Root nodule - Na Sample 3

city: Durham

first: Louis

middle: S

last: Tisa

state: NH

address: 46 College Rd

department: MCBS

institute: University of New Hampshire

data_processing:
Illumina Casava1.8.3 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and mapped to SCBI whole genome using CLC workstation
Genome_build: Frankia sp. strain CcI3
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Frankia casuarinae

source_name: plant root nodule

growth_protocol: BD medium 28C for 21 days

extract_protocol:
LiCl method and Rneasy Kit
Stable Plant RNA was removed by the RiboZero Kit followed by stable bacterial RNA removal via the bacterial Ribo-Zero kit.   RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: stress status

value: Control

value: root nodule

tag: host

value: Casuarina glauca

tag: culture condition

value: 21 days


title: Ago25_15

tag: circadian timepoints

tag: temperature


title: 1445-16

tag: age

tag: gender

value: Male

tag: suicide

value: Suicide

value: Without SUD


title: 1442-16

value: Female

tag: sud


title: hires_d15_2 [muc9280]

description:
Drop-seq
MUC9280_S8_L003

source_name: high_resolution_Lung epithelium_day15


title: Ago25_9


title: Root nodule - Na Sample 2


title: hires_d54_1 [muc9279]

description:
Drop-seq
MUC9279_S7_L002

source_name: high_resolution_Lung epithelium_day54


title: hires_d5_1 [muc9278]

description:
Drop-seq
MUC9278_S6_L002


title: Ago25_3


title: Root nodule - Na Sample 1


title: hires_d11_2 [muc9277]

description:
Drop-seq
MUC9277_S5_L002

source_name: high_resolution_Lung epithelium_day11


title: Ago18_21


title: Root nodule + Na Sample 3

value: Na stressed


title: 1402-16


title: Ago18_15


title: 1343-16

value: SUD


title: Root nodule + Na Sample 2


title: hires_d15_1 [muc9276]

description:
Drop-seq
MUC9276_S4_L001

value: Lung epithelium


title: Root nodule + Na Sample 1


title: Ago18_9


title: 1236-16


title: 1338-16


title: hires_d4_1 [muc9275]

description:
Drop-seq
MUC9275_S3_L001


title: Ago18_3


title: 1233-16


title: 0987-16


title: hires_d3_1 [muc9273]

description:
Drop-seq
MUC9273_S1_L001

source_name: high_resolution_Lung epithelium_day3


title: hires_d2_1 [muc9274]

description:
Drop-seq
MUC9274_S2_L001


title: cell types 1, 2, and 3 in plate 105107

city: beijing

first: Xu

last: hanshi

address: 167 Beilishi Road

country: China

institute: State Key Laboratory of Cardiovascular Disease

data_processing:
Raw reads were filtered by cutadpt v1.8.1,-m 20 --trim-n --max-n 0.7 -q 20
Contaminants were filtered by fastq_screen (v0.5.1.4)
Clean reads were mapped to UCSC mm10 genome via STAR v2.5.2b
Reads were assigned to Ensembl genes by featureCounts (subread-1.4.6-p1 command line)
Genome_build: mm10
Supplementary_files_format_and_content: csv,gene expression matrix for single cell RNASeq

source_name: embryonic stem cell , blastocyst derived

extract_protocol:
Selected cells were removed from low temperature and reversed to get cDNA by a reaction including 5M Betaine Solution (Sigma B0300-1VL) 56 uL, 25 mM dNTP mix (Clontech 639132) 24 uL, 1M MgCl2 (Thermo Fisher Scientific AM9530G) 3.2 uL, 100 mM DTT (Sigma 43816-10ML) 8.8 uL, SMARTScribeTM 5X First-Strand Buffer (Clontech 639537) 61.9 uL, SeqAmpTM 2X PCR Buffer (Clontech 638504) 33.3 uL, 100 uM RT E5 Oligo (WaferGen 430-000240-0001) 4.0 uL, Amp Primer (WaferGen 430-000241-0001) and 100% Triton X-100 (Sigma T8787) 1.6 uL. ,
The library were prepared by using Nextera XT Library Prep Kit (illumina, 15032350) with some modification.

tag: genotype

value: Mll1fl/fl; Cre-ER TM; C57BL/6J

tag: sample group

value: cell type 1 - Mll1fl/fl control, cell type 2 - Mll1-/-, cell type 3 - Mll1 inhibition


title: cell types 1, 2, and 3 in plate 105106


title: hires_d7_2 [muc9272]

description:
Drop-seq
MUC9272_S29_L008

source_name: high_resolution_Lung epithelium_day7


title: cell types 1, 2, and 3 in plate 105102


title: hires_d0_1 [muc9271]

description:
Drop-seq
MUC9271_S28_L008


title: 0946-16


title: 0953-16


title: hires_d8_1 [muc9270]

description:
Drop-seq
MUC9270_S27_L008

source_name: high_resolution_Lung epithelium_day8


title: hires_d9_1 [muc9269]

description:
Drop-seq
MUC9269_S26_L008

source_name: high_resolution_Lung epithelium_day9


title: hires_d11_1 [muc9268]

description:
Drop-seq
MUC9268_S25_L007


title: Kidney_HOM_water_6 days_rep5

city: London

first: Mateja

last: Sborchia

state: Greater London

address: 150 Stamford Street

department: Analytical, Environmental and Forensic Sciences

country: United Kingdom

institute: King's College London

description: RMA expression value derived from Transcriptome Analysis Console; analysis with QLUCORE and MetaCore.

hyb_protocol: Hybridisation cocktails using the fragmented and biotin-labelled cDNA were prepared according to NuGen’s recommendations for mouse Clariom™ S Assay (Thermo Fisher Scientific) arrays. Hybridisation took place at 45°C for 16-20 hours at 60 rpm in a GeneChip™ Hybridization Oven 645 (Thermo Fisher Scientific). The arrays were washed and stained on a GeneChip™ Fluidics Station 450 (Thermo Fisher Scientific) by using a recommended fluidics protocol (FS450_0007, Affymetrix).

scan_protocol: The arrays were scanned with the GeneChip™ Scanner 3000 7G (Thermo Fisher Scientific).

data_processing: The data files were QC checked by using the Transcriptome Analysis Console (TAC) software (Thermo Fisher Scientific). This was performed by using standard metrics and guidelines for the microarray system. The data was normalised using the Robust Multi-array Average (RMA) sketch algorithm. The RMA normalised data were analysed visually with the Qlucore Omics Explorer software. Gene lists were created in Qlucore Omics Explorer according to the biological question taken into consideration and by taking the following parameters into account: p-value (p) < 0.05 and fold change cut-off ± 2. Statistical analyses in Qlucore Omics Explorer were based on an analysis of variance (ANOVA) test. The false discovery rate (FDR) was kept to approximately 15% and batch effects were also eliminated. Pathway analysis was carried out with the MetaCore™ software (Clarivate Analytics), particularly using the “Enrichment analysis in Pathway Maps” and “Compare Experiments Workflow” tools. Pathway significance was set to p<0.05.

label: Biotin

source_name: p53 homozygous mouse kidney exposed to water for 6 days

label_protocol: Total RNA (50 ng) was converted and amplified into cDNA with the Ovation® Pico WTA System V2 Kit (NuGEN) before hybridisation onto an array. A GeneChip™ Poly-A RNA Control (Thermo Fisher Scientific) was used as an amplification control. The SPIA® cDNA was fragmented and biotin-labelled with the Encore® Biotin Module (NuGen) according to the manufacturer’s instructions.

growth_protocol: Trp53(+/+), Trp53(+/-) and Trp53(-/-) male mice (9-11 weeks of age; n = 5/group) were treated with 3.5 mg/kg bw AAI by intraperitoneal injection daily for 6 days. Control mice (n = 5/group) were injected with water only.

extract_protocol: Total RNA was isolated by a modified method based on both TRIzol® (Thermo Fisher Scientific) and RNeasy Mini Kit (QIAGEN) protocols. A portion of tissue (15-35 mg) was placed in a tube containing a steel bead and 1 ml of TRIzol®. The tissue was homogenised twice with a TissueLyser II at 25 Hz for 2 minutes and it was placed at room temperature for 5 minutes. Following the addition of 200 µl of chloroform, it was centrifuged at 4°C at 13,000 rpm (5424R, Eppendorf™) for 20 minutes. The top layer was transferred to a tube and mixed with 350 µl of 70% ethanol. The sample was transferred to a RNeasy Mini Spin column and subsequent RNA isolation steps were performed according to the manufacturer’s instructions.

treatment_protocol: Mice were sacrificed 24 hours after the last treatment; and kidneys were collected, snap frozen in liquid nitrogen and stored at ‒80°C for further analysis.

value: Kidney

tag: p53 genotype

value: Homozygous

tag: Sex

tag: treatment

value: Water

tag: treatment duration

value: 6 days


title: 0895-16


title: Kidney_HOM_water_6 days_rep4

tag: tissue


title: hires_d7_1 [muc9267]

description:
Drop-seq
MUC9267_S24_L007

tag: injury timecourse

tag: experiment

tag: number of cells


title: EndoC-βH1 siSCD 3

city: Paris

first: Masaya

last: OSHIMA

address: 123 boulevard de Port Royal

country: France

institute: INSERM U1016

description: Gene expression data from siSCD EndoC-βH1

hyb_protocol: After control of fragmentation using Bioanalyzer 2100, cDNA is then hybridized to GeneChip® Human Gene 2.0 ST (Affymetrix) at 45°C for 17 hours.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing: The data were analyzed with R Bioconductor packages using RMA as normalization method

label_protocol: Total RNA is reverse transcribed following the GeneChip™ WT PLUS Reagent Kit (applied biosystems). Briefly, the resulting double strand cDNA is used for amplification based on SPIA technology. After purification according to Nugen protocol, 3,6 ug of Sens Target DNA are fragmented and biotin labelled using Encore Biotin Module kit (Nugen).   After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G. The scanned images are then analyzed with Expression Console software (Affymetrix) to obtain raw data (cel files) and metrics for Quality Controls. The observations of some of these metrics and the study of the distribution of raw data show no outlier experiment.

extract_protocol: RNeasy Micro kit (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

tag: cell type

value: Human beta cells


title: Kidney_HOM_water_6 days_rep1


title: H838 608.3_24h

city: Heidelberg

first: Nikolas

last: Gunkel

institute: DKFZ

description: replicate 3

hyb_protocol: Standard Illumina Hybridisation Protocol  Part # 11322355. Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays 750 ng of cRNA were hybridized for 17 hr at 58°C on Illumina Human HT-12-Microarray

scan_protocol: Gene Expression Microarrays were scanned using the Illumina iScan-Scanner according to Standard Illumina Scanning Protocol  Part # 11322355   (Whole-Genome Gene Expression  Direct Hybridization Assay Guide)

data_processing: The raw data were quantile-normalized using the Bioconductor package preprocessCore in R.

source_name: tissue culture

label_protocol: The Illumina total Prep RNA Amplification Kit (life technologies) is used to generate single-stranded cRNA from input amounts of 200ng total RNA. Label: Biotin, Cy3-Streptavidin

growth_protocol: 6x106 cells were seaded in T75 bottles in 25ml medium and incubated for 24h before addition of drug or carrier.

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. RNA quantification was performed on a Qubit 2.0 Flourometer and quality was assessed on an Agilent 2100 Bioanalyzer.

treatment_protocol: H209 and H838 lung cancer cells treated with 100nM DKFZ-608 formulated in 6.9µM cyclodextrin for 4, 8, or 24 hours or with cyclodextrin to the same time points

tag: cell line

value: 100nM DKFZ-608 formulated in cycodextrin

tag: time point


title: H838 608.3_8h

description: replicate 3


title: EndoC-βH1 siSCD 1


title: Kidney_HOM_AAI_6 days_rep5

source_name: p53 homozygous mouse kidney exposed to AAI for 6 days

value: Aristolochic acid I


title: wt_hepatocytes_2dpi

city: Vienna

first: Andreas

last: Bergthaler

address: Lazarettgasse 14 AKH BT25.3

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

data_processing:
Cell Ranger (v3.0.2) for demultiplexing, mapping and counting reads
UMI reads were processed with the R Bioconductor package Seurat v3.1.1
cells with more than 30% mitochondrial content or less than 0.5% Alb reads were discarded
Data was normalized with the SCTransform function in Seurat
UMAP low-dimensional projection was performed on the 3000 most variable genes and the 10 first principal components.
FindMarkers, Seurat function, with Wilcox test was employed for differential analysis between the 2 conditions.
Genome_build: mm10-3.0.0(based on GRCm38 and gene annotations V93 of 10X)
Supplementary_files_format_and_content: tab-delimited text files include UMI counts for each condition

source_name: liver

growth_protocol: cells were freshly isolated

extract_protocol:
standard 2 step liver perfusion protocol
10x Genomics Chromium Single Cell 3'V3

treatment_protocol: mice were infected with LCMV Cl13 for 2 days or kept naïve

tag: strain

value: liver

value: hepatocytes


title: EndoC-βH1 siCTRL 3

description: Gene expression data from siCTRL EndoC-βH1


title: Kidney_HOM_AAI_6 days_rep4

value: Male


title: Kidney_HOM_water_6 days_rep3


title: H838 608.3_4h

description: replicate 3


title: D28100

city: Beijing

first: Shaojun

last: Liang

address: 18 Shuangqing Road

institute: Chinese academy of sciences

data_processing:
Sequencing was performed with a BGISEQ-500 platform and generated 21,761,200 raw sequencing reads. Clean reads (21,628,715) were mapped to the reference genome (GCF_000001635.25_GRCm38.p5) using HISAT/Bowtie2 with a mean mapping rate of 86.03%.
The fragments per kilobase of exon per million fragments mapped (FPKM) method was used to calculated gene expression levels.
Differentially expressed genes (DEGs) were defined as log2-Ratio ≥ 1 and q-value (corrected p-value) £ 0.001.
Genome_build: GCF_000001635.25_GRCm38.p5
Supplementary_files_format_and_content: Text file and FPKM values for all samples

source_name: Embryoid body

extract_protocol:
RNA was harvested using Trizol reagent and purified with RNeasy Plus mini Kit
The procedures were performed at Beijing Genomics Institute (BGI), Wuhan, China. RNA samples were analyzed with a 2100 Bioanalyzer (Agilent Technologies, USA), and subjected to library preparation according to BGI standard protocols.

value: mESC

value: 100 nM TBBPA


title: Kidney_HOM_AAI_6 days_rep3


title: EndoC-βH1 siSCD 2


title: wt_hepatocytes_0dpi


title: Kidney_HOM_water_6 days_rep2


title: hires_d36_1 [muc9265]

description:
Drop-seq
MUC9265_S22_L007


title: Kidney_HOM_AAI_6 days_rep2


title: EndoC-βH1 siCTRL 1


title: Kidney_HET_water_6 days_rep5

source_name: p53 heterozygous mouse kidney exposed to water for 6 days

value: Heterozygous


title: H838 C3_24h

description: replicate 3

value: cyclodextrin alone


title: EndoC-βH1 siCTRL 2


title: H838 C3_8h

description: replicate 3


title: D2810

value: 10 nM TBBPA


title: Kidney_HOM_AAI_6 days_rep1


title: H838 C3_0h

description: replicate 3


title: Total peritoneal cells from Becn1f/f-LysMcre mice: Beclin_lysM

city: St. Louis

first: Maxim

last: Artyomov

state: Missouri

address: 425 S Euclid Ave

department: Pathology & Immunology

institute: WASHINGTON UNIVERSITY IN ST LOUIS

data_processing:
quality control, Cell Ranger Single Cell Software Suite (v2.0.1)
sample de-multiplexing,  Cell Ranger Single Cell Software Suite (v2.0.1)
barcode processing, Cell Ranger Single Cell Software Suite (v2.0.1)
single-cell 3′ gene counting , Cell Ranger Single Cell Software Suite (v2.0.1)
alignment, Cell Ranger Single Cell Software Suite (v2.0.1)
Genome_build: mm10
Supplementary_files_format_and_content: Filtered matrix of gene by cell expression, file with barcodes and file with expressed genes. Files are ready to be imported to Seurat package.

extract_protocol:
Peritoneal cells were harvested after a 5-ml injection of DMEM containing 2 mM EDTA and 2% FBS into the peritoneal space.
The cells are resuspended in final concentration of 1000cells/µL in 1X PBS containing 0.04% BSA to minimize cell loss and aggregation. ~17,400 cells are partitioned into nanoliter-scale Gel Bead-In-EMulsions (GEMs) to achieve single cell resolution for a maximum recovery of 10,000 individual cells per sample. Utilizing the v2 Chromium™ Single Cell 3’ Library Kit and Chromium instrument (10x Genomics), poly-adenylated mRNA from an individual cell is tagged with a unique 16bp 10x barcode and 10bp Unique Molecular Identifier. Full length cDNA is then amplified to generate sufficient mass for library construction. Enzymatic fragmentation and size selection are used to optimize the cDNA amplicon size (~400bp) for library construction. The final library is sequence ready and contains four unique sample indexes. The concentration of the 10x single cell library will be accurately determined through qPCR (Kapa Biosystems) to produce cluster counts appropriate for the HiSeq4000 platform (Illumina). 26x98nt read lengths are generated targeting 90,000 reads per cell.

tag: age

value: 8 weeks

tag: mouse genotype

tag: cell markers

value: Cd45+ cells

value: peritoneum


title: Kidney_HET_water_6 days_rep4

value: Kidney


title: H838 608.2_8h

description: replicate 2


title: H838 C3_4h

description: replicate 3


title: Total peritoneal cells from Becn1f/f mice: Beclin_flox


title: D28C2

value: 0.1% DMSO


title: D18100


title: netrin-1 rep2  [RRBS]

city: Lyon

first: Fabrice

last: Lavial

address: 28 rue Laennec

institute: CRCL

data_processing:
read quality: Quality of reads was assessed for each sample using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
sequence alignment: We used BS-Seeker21 to map RRBS data to the mouse genome mm10/GRCm38 and retrieve the number of methylated and unmethylated cytosines at each covered CpG site.
methylation rates analysis: Methylation rates were then integrated across CpG island (CGI)-based and gene-based features. CGI-based features were defined as follows: CpG islands (from UCSC database GRCm38/mm10), shores (2 kb on each side of the island) and shelves (2 kb on each side of the shores). DNA methylation outside CpG islands was analyzed by grouping CpG sites not located in CGI-based features every 100kb window. Gene-based features were defined based on Ensembl Mus musculus GRCm38.78 assembly. We calculated for each gene the methylation rate across the promoter region (TSS +/- 500bp) and the gene body.
Supplementary_files_format_and_content: xls files. Integrated DNA methylation values across genomic features are provided as Excel tables. The DNA_methylation_by_gene_features.xlsx table contains DNA methylation values in gene features (TSS, body), the DNA_methylation_by_CGI_features.xlsx table contains DNA methylation values in CGI features (islands, shores, shelves) and the DNA_methylation_by_100kb_windows.xlsx table contains DNA methylation values in 100kb-windows. For each feature, the number of values considered, the number of individual CpG sites and the average methylation value are indicated for each sample.

source_name: mouse embryonic stem cells

growth_protocol: mESC are grown in serum/LIF conditions

extract_protocol:
genomic DNA is extracted on colums
RRBS libraries prepared by inegragen: Msp1 enzymatic digestion, gel selection of DNA fragments, adaptor ligation, bisulfite conversion, libraries preparation, paired end sequencing 2x75bp on illumina hiseq4000

treatment_protocol: mESC are stably transfected with ppy-cagg-ires-puro vector epty or encoding a netrin-1 transgene.

value: CGR8 mESC

tag: transfection

value: empty ppy-cagg-netrin-ires-puro vector expressing the netrin-1 transgene


title: netrin-1 rep1  [RRBS]


title: H838 608.2_4h

description: replicate 2

value: 100nM DKFZ-608 formulated in cycodextrin


title: D1810


title: control rep2  [RRBS]

value: empty ppy-cagg-ires-puro vector


title: D18C2


title: control rep1  [RRBS]


title: D18C1


title: D28C1


title: D12100


title: wild-type retina_AAV viral vector bearing pre-miR-204 (AAV2/8.CMV.miR204), biol rep3 (animal n. 4, Left Eye OS)

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

description:
c57-Bl6_4_OS_204OE
wild-type c57BL/6 retina following subretinal injection of the AAV viral vector bearing the pre-miR-204 (AAV2/8.CMV.miR204), biological rep3 (animal n. 4, Left Eye OS)

data_processing:
Reads were aligned and assigned to Mouse ENSEMBLE transcripts and genes by using RSEM version 1.2.19 with standard parameters (Li & Dewey, 2011).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

source_name: Retina from c57BL/6 wild-type mouse

growth_protocol: Mice were maintained under SPF conditions and fed ad libitum. For the subretinal injections in the RHO-P347S background, pups were obtained by crossing the RHO-P347S (RHO-RHO-P347S+/+) transgenic mice (Li et al. 1996) with the C57BL/6 to obtain the RHO-RHO-P347S+/- genotype.

extract_protocol:
Extraction of total RNA was performed according to the manufacturer's instructions (miRNeasy kit (Qiagen, Inc., Hilden, Germany).
Libraries were prepared according manufacturer’s instructions (TruSeq RNA Sample Preparation kit, Illumina) starting from 4 μg of total RNA. Quality control of library templates was performed using a High Sensitivity DNA Assay kit (Agilent Technologies) on a Bioanalyzer (Agilent Technologies). The Qubit quantification platform (Qubit 2.0 Fluorometer, Life Technologies) was used to normalize samples for the library preparation.
The amplified fragmented cDNA of ~200 bp in size were sequenced in paired-end mode using the HiSeq 1000 (Illumina) with a read length of 2×100 bp

treatment_protocol: AAV vectors were delivered at the retina by subretinal injection at postnatal day (P)4. An equal load of viral genome copies (1x10^9 genome copies in 1 μl of injecting solution) of either the AAV2/8.CMV.miR204 or the control AAV2/8.CMV.miR204MUT vector were administered in each pair of eyes. Eyes were enucleated at P12 and total RNA was extracted. All surgery was performed under anesthesia, and all efforts were made to minimize suffering.

tag: individual

value: animal n. 4

value: retina

tag: eye

value: Left eye

tag: genotype

value: wild-type


title: H838 C2_24h

description: replicate 2

tag: treatment


title: Kidney_HET_water_6 days_rep2

tag: p53 genotype

tag: Sex

value: Male

value: Water

tag: treatment duration

value: 6 days


title: D1210

value: mESC

value: 10 nM TBBPA


title: wild-type retina_control AAV viral vector (AAV2/8.CMV.miR204MUT), biol rep3 (animal n. 4, Right Eye OD)

description:
c57-Bl6_4_OD_MUTATED
wild-type c57BL/6 retina following subretinal injection of control AAV viral vector (AAV2/8.CMV.miR204MUT), biological rep3 (animal n. 4, Right Eye OD)

tag: tissue

value: Right eye

value: injection of control AAV viral vector


title: wild-type retina_AAV viral vector bearing pre-miR-204 (AAV2/8.CMV.miR204), biol rep2 (animal n. 2, Left Eye OS)

description:
c57-Bl6_2_OS_204OE
wild-type c57BL/6 retina following subretinal injection of the AAV viral vector bearing the pre-miR-204 (AAV2/8.CMV.miR204), biological rep2 (animal n. 2, Left Eye OS)

value: animal n. 2


title: Kidney_HET_water_6 days_rep1

value: Kidney

value: Heterozygous


title: Kidney_HET_water_6 days_rep3


title: D12C2

value: 0.1% DMSO


title: wild-type retina_control AAV viral vector (AAV2/8.CMV.miR204MUT), biol rep2 (animal n. 2, Right Eye OD)

description:
c57-Bl6_2_OD_MUTATED
wild-type c57BL/6 retina following subretinal injection of control AAV viral vector (AAV2/8.CMV.miR204MUT), biological rep2 (animal n. 2, Right Eye OD)


title: H838 C2_8h

description: replicate 2

value: cyclodextrin alone


title: H838 H838.1_24h

description: replicate 1

value: 100nM DKFZ-608 formulated in cycodextrin


title: D12C1


title: H838 C2_0h

description: replicate 2


title: wild-type retina_AAV viral vector bearing pre-miR-204 (AAV2/8.CMV.miR204), biol rep1 (animal n. 1, Left Eye OS)

description:
c57-Bl6_1_OS_204OE
wild-type c57BL/6 retina following subretinal injection of the AAV viral vector bearing the pre-miR-204 (AAV2/8.CMV.miR204), biological rep1 (animal n. 1, Left Eye OS)

value: animal n. 1


title: Kidney_HET_AAI_6 days_rep5

source_name: p53 heterozygous mouse kidney exposed to AAI for 6 days

value: Aristolochic acid I


title: H838 C2_4h

description: replicate 2


title: D9100

value: 100 nM TBBPA


title: Kidney_HET_AAI_6 days_rep3


title: wild-type retina_control AAV viral vector (AAV2/8.CMV.miR204MUT), biol rep1 (animal n. 1, Right Eye OD)

description:
c57-Bl6_1_OD_MUTATED
wild-type c57BL/6 retina following subretinal injection of control AAV viral vector (AAV2/8.CMV.miR204MUT), biological rep1 (animal n. 1, Right Eye OD)

value: retina

value: wild-type


title: Kidney_HET_AAI_6 days_rep2

value: Male


title: D910


title: Kidney_HET_AAI_6 days_rep1

value: 6 days


title: Kidney_HET_AAI_6 days_rep4


title: H838 H838.1_8h

description: replicate 1


title: RHO-P347S retina_AAV viral vector bearing pre-miR-204 (AAV2/8.CMV.miR204), biol rep3 (animal n. 5, Left Eye OS)

description:
P347S_5_OS_204OE
RHO-P347S retina following subretinal injection of the AAV viral vector bearing the pre-miR-204 (AAV2/8.CMV.miR204), biological rep3 (animal n. 5, Left Eye OS)

source_name: Retina from RHO-P347S mouse

value: animal n. 5

value: Left eye


title: D9C2

value: mESC


title: Kidney_WT_water_6 days_rep4

source_name: p53 wild-type mouse kidney exposed to water for 6 days

value: Wild-type

value: Water


title: Kidney_WT_water_6 days_rep5

value: Kidney


title: RHO-P347S retina_control AAV viral vector (AAV2/8.CMV.miR204MUT), biol rep3 (animal n. 5, Right Eye OD)

description:
P347S_5_OD_MUTATED
RHO-P347S retina following subretinal injection of control AAV viral vector (AAV2/8.CMV.miR204MUT), biological rep3 (animal n. 5, Right Eye OD)

value: Right eye

value: injection of control AAV viral vector


title: H838 C1_24h

description: replicate 1

value: cyclodextrin alone


title: Kidney_WT_water_6 days_rep3


title: RHO-P347S retina_AAV viral vector bearing pre-miR-204 (AAV2/8.CMV.miR204), biol rep2 (animal n. 4, Left Eye OS)

description:
P347S_4_OS_204OE
RHO-P347S retina following subretinal injection of the AAV viral vector bearing the pre-miR-204 (AAV2/8.CMV.miR204), biological rep2 (animal n. 4, Left Eye OS)

value: animal n. 4


title: Kidney_WT_water_6 days_rep2


title: D9C1

value: 0.1% DMSO


title: H838 H838.1_4h

description: replicate 1

value: 100nM DKFZ-608 formulated in cycodextrin


title: H838 C1_0h

description: replicate 1


title: H838 C1_8h

description: replicate 1


title: H209 608.3_4h

description: replicate 3


title: H838 C1_4h

description: replicate 1


title: D4100

value: 100 nM TBBPA


title: H209 608.3_24h

description: replicate 3


title: RHO-P347S retina_control AAV viral vector (AAV2/8.CMV.miR204MUT), biol rep2 (animal n. 4, Right Eye OD)

description:
P347S_4_OD_MUTATED
RHO-P347S retina following subretinal injection of control AAV viral vector (AAV2/8.CMV.miR204MUT), biological rep2 (animal n. 4, Right Eye OD)

value: retina


title: D4C2


title: RHO-P347S retina_control AAV viral vector (AAV2/8.CMV.miR204MUT), biol rep1 (animal n. 2, Right Eye OD)

description:
P347S_2_OD_MUTATED
RHO-P347S retina following subretinal injection of control AAV viral vector (AAV2/8.CMV.miR204MUT), biological rep1 (animal n. 2, Right Eye OD)

value: animal n. 2


title: RHO-P347S retina_AAV viral vector bearing pre-miR-204 (AAV2/8.CMV.miR204), biol rep1 (animal n. 2, Left Eye OS)

description:
P347S_2_OS_204OE
RHO-P347S retina following subretinal injection of the AAV viral vector bearing the pre-miR-204 (AAV2/8.CMV.miR204), biological rep1 (animal n. 2, Left Eye OS)


title: Kidney_WT_AAI_6 days_rep5

source_name: p53 wild-type mouse kidney exposed to AAI for 6 days

value: Male

value: Aristolochic acid I


title: D410

value: 10 nM TBBPA


title: ES2

value: No treatment


title: Kidney_WT_AAI_6 days_rep4

value: 6 days


title: H209 C3_0h

description: replicate 3


title: Kidney_WT_AAI_6 days_rep2

value: Wild-type


title: Kidney_WT_AAI_6 days_rep1


title: Drosophila heads at 29C rep2 RNA immunoprecipitation AGO1-IP

description:
IP_29.2.
Drosophila_T2-2_IP

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: CEL files were imported to Affymetrix Expression Console program, and data were normalized using Robust Multichips Analysis. Differential expression was tested for probes that had expression levels above 4.0 (log2 scale)  in at least one group (mutants or WT). All other probes were excluded from the analysis.

source_name: Drosophila heads RNA at 29C IP of AGO1-Ip

label_protocol: RNA was then used to prepare a probe that was hybridized to Drosophila 2.0 gene expression arrays (Affymetrix) according to the manufacturer's protocol.

growth_protocol: FLies were grown at 18C, 25C, 29C

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Flies were grown at either 18, 25 or 19 degrees. Heads were collected and AGO1-IP was eprformed as in Kadener et al. 2009

value: Canton-S

value: adult flies

tag: temperature

value: heads


title: H209 C3_4h

description: replicate 3


title: H209 608.2_24h

description: replicate 2


title: H209 608.2_8h

description: replicate 2


title: ES1

tag: cell type

value: mESC


title: Drosophila simulans_zt15_29C

data_processing:
quantification of tim isoforms looking manually the exon-exon juntion reads
Genome_build: dm3, droAnanas2, droSim1, droViri3, droYak2
Supplementary_files_format_and_content: table of tim isoform analysis; transcript quantification

organism: Drosophila simulans

source_name: RNA from fly heads

growth_protocol: Flies were grown at different temperatures and heads were collected at different temperatures.

extract_protocol:
RNA extraction was done using TRI Reagent [SIGMA] following manufacturer´s protocol. The precipitated RNAwas taken for library preparation.
Libraries were constructed Stranded ligation-based, total-RNA libraries preparation was modified from (Engreitz et al., 2013) as described in Reddy et al 2018, Biorxiv.

tag: circadian timepoints

value: fly heads


title: D4C1

tag: cell line


title: Kidney_WT_AAI_6 days_rep3

value: Kidney


title: Drosophila simulans_zt3_29C


title: HoxB-CSF3R_T618I+CEBPA_V314VW-C

hyb_protocol: Following fragmentation, 2ug of cDNA were hybridized for 16hr at 45C to GeneChip Clariom S Mouse array. GeneChips were washed and stained using an Affymetrix Fluidics Station 450 with scrip FS450_0007.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the 7G upgrade.  Image processing was performed using Affymetrix Command Console (AGCC) v.3.1.1 software

data_processing: The data files were processed using Expression Console Software build 1.4.1.46 and RMA without normalization

source_name: HoxB8 cells transduced with CEBPA_V314VW MSCV-IRES-GFP/CSF3R_T618I MSCV-IRES-mCherry harvested 24 hours after estrogen withdrawal

label_protocol: Biotinylated-labeled cDNA were prepared using the Applied Biosystems WT Plus protocol with 100ng of total RNA input

extract_protocol: Total RNA was extracted using a Qiagen Rneasy Micro kit


title: HoxB-CSF3R_T618I+CEBPA_V314VW-B


title: Drosophila simulans_zt15_25C


title: Drosophila heads at 25C rep2 RNA immunoprecipitation AGO1-IP

description:
IP_25.2.
Drosophila_T1-2_IP

source_name: Drosophila heads RNA at 25C IP of AGO1-Ip

tag: strain


title: H209 C2_24h

description: replicate 2

value: cyclodextrin alone


title: Drosophila heads at 18C rep2 RNA immunoprecipitation AGO1-IP

description:
IP_18.2.
Drosophila_T0-2_IP

source_name: Drosophila heads RNA at 18C IP of AGO1-Ip

tag: age


title: Drosophila heads at 29C rep1 RNA immunoprecipitation AGO1-IP

description:
IP_29.1.
Drosophila_T2-1_IP


title: Drosophila heads at 25C rep1 RNA immunoprecipitation AGO1-IP

description:
IP_25.1.
Drosophila_T1-1_IP


title: Drosophila simulans_zt3_25C


title: HoxB-CSF3R_T618I+CEBPA_V314VW-A


title: HoxB-CEBPA_V314VW-C

source_name: HoxB8 cells transduced with CEBPA_V314VW MSCV-IRES-GFP/Empty MSCV-IRES-mCherry harvested 24 hours after estrogen withdrawal


title: H209 C2_8h

description: replicate 2

source_name: tissue culture

tag: time point


title: H209 C2_0h

description: replicate 2


title: Drosophila simulans_zt15_18C


title: H209 608.2_4h

description: replicate 2

value: 100nM DKFZ-608 formulated in cycodextrin


title: Drosophila heads at 18C rep1 RNA immunoprecipitation AGO1-IP

description:
IP_18.1.
Drosophila_T0-1_IP


title: Drosophila simulans_zt3_18C


title: HoxB-CEBPA_V314VW-B


title: HoxB-CEBPA_V314VW-A


title: H209 C2_4h

description: replicate 2


title: Drosophila heads at 29C rep1 RNA input from AGO1-IP

description:
INP_29.1.
Drosophila_T2-1_INPUT

source_name: Drosophila heads RNA at 29C input of AGO1-Ip


title: H209 608.1_24h

description: replicate 1


title: Drosophila heads at 29C rep2 RNA input from AGO1-IP

description:
INP_29.2.
Drosophila_T2-2_INPUT


title: HoxB-CSF3R_T618I-C

source_name: HoxB8 cells transduced with empty MSCV-IRES-GFP/CSF3R_T618I MSCV-IRES-mCherry harvested 24 hours after estrogen withdrawal


title: H3K9ac_Old

city: Kiel

first: Seyed Mohammd Mahdi

last: Rasa

state: Schleswig-Holstein

address: Michaelisstrasse 5

department: Institut for Immunology

institute: Universitätsklinikum Schleswig-Holstein

description: H3K9ac chromatin immunoprecipitation sequencing (ChIP-seq).

data_processing:
Fastq files quality check was performed using FastQC v0.11.5.
Fastq files mapping to Nothobranchius furzeri genome (http://nfingb.leibniz-fli.de) was performed using Bowtie (v1.1.2) with --best --strata -m 1 parameters.
Duplicate reads were removed using a custom script.
To make wig files, macs14 (v1.4.2) was used with --nolambda parameter and 1e-3 as p-value cutoffs.
igvtools (v2.3.97) were used to convert wig files to tdf.
Nfu_20150522(http://nfingb.leibniz-fli.de)
tdf files

organism: Nothobranchius furzeri

source_name: skeletal muscle

growth_protocol: Whole skeletal muscle was collected from male Nfu (strain MZM-04/10). Nfu samples were derived from fish at different ages: young (5 weeks) and old (27-40 weeks).

extract_protocol:
Around 20 mg of skeletal muscle tissue were chopped with a scalpel, harvested in 5 ml of PBS and crosslinked by adding formaldehyde to a final concentration of 1.5 %, incubated for 30 min at room temperature on a rotator, and quenched with 0.125 M glycine for 5 min at room temperature. After crosslinking, the tissue was washed two times in cold PBS and centrifuged at 1.000xg for 5 min at 4°C. The tissue pellet was resuspended in 0.25 ml of SDS lysis buffer (50 mM Tris pH 8.0, 1% SDS, 10 mM EDTA, anti-proteases), incubated on a rotator for 30 min at 4oC, sonicated for 18 cycles on high power setting (30s ON, 30s OFF) using the Bioruptor Next Gen (Diagenode) and centrifuged at 20.000xg for 10 min at 4°C.
The isolated chromatin was diluted 10-fold with ChIP dilution buffer (16.7 mM Tris-HCl pH 8.0, 0.01% SDS, 1.1 % Triton X-100, 1.2 mM EDTA, 167 mM NaCl) (1/10 was kept as input) and incubated with 4 µg of antibody overnight at 4°C on a rotator. Protein G-conjugated magnetic beads (Dynal, Thermo Fisher Scientific) were saturated with PBS/1% BSA overnight at 4°C. Next day, samples were incubated with saturated beads for two hours at 4°C on a rotator, and subsequently washed with 1 ml of cold Low salt buffer (20 mM Tris-HCl pH 8.0, 0.1 % SDS, 1% Triton X-100, 2 mM EDTA, 150 mM NaCl), 1 ml of cold High salt buffer (20 mM Tris-HCl pH 8.0, 0.1 % SDS, 1% Triton X-100, 2 mM EDTA, 500 mM NaCl), 1 ml of cold LiCl buffer (10 mM Tris-HCl pH 8.0, 1% DOC, 250 mM LiCl, 1 mM EDTA, 1% NP-40), and twice with 1 ml of cold TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA). The immunoprecipitated chromatin was eluted with 200 µl of Elution buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 1% SDS, 150 mM NaCl, 5mM DTT) for 30 min at RT on a rotator, and decrosslinked at 65°C overnight. The decrosslinked DNA was purified using QiaQuick PCR Purification Kit (Qiagen) according to the manufacture’s instruction. The following antibodies were used: rabbit anti-H3K9ac (ab4441, Abcam), rabbit anti-H3K27me3 (abe44, Millipore), rabbit anti-IgG (Millipore).
The purified ChIP DNA was end-repaired, dA-tailed, and adaptor-ligated using the NEBNext® DNA Library Prep Master Mix Set for Illumina (NEB) following the manufacturer’s instructions. The size of the library was checked using Fragment Analyzer (Agilent) and the library was sequenced on the NextSeq500 platform (illumina).

value: Skeletal muscle

value: Old (27-40 weeks)

tag: chip antibody


title: H3K27me3_Young

description: H3K27me3 chromatin immunoprecipitation sequencing (ChIP-seq).

data_processing:
Fastq files quality check was performed using FastQC v0.11.5.
Fastq files mapping to Nothobranchius furzeri genome (http://nfingb.leibniz-fli.de) was performed using Bowtie (v1.1.2) with --best --strata -m 1 parameters.
Duplicate reads were removed using a custom script.
To make wig files, macs14 (v1.4.2) was used with --nolambda parameter and 1e-3 as p-value cutoffs.
igvtools (v2.3.97) were used to convert wig files to tdf.
Nfu_20150522 (http://nfingb.leibniz-fli.de)
tdf files

value: Young (5 weeks)


title: H3K9ac_Young

value: Male


title: HoxB-CSF3R_T618I-B

city: Portland

last: Braun

institute: OHSU


title: H3K27me3_Old


title: H209 608.1_4h

description: replicate 1


title: Drosophila heads at 25C rep2 RNA input from AGO1-IP

description:
INP_25.2.
Drosophila_T1-2_INPUT

source_name: Drosophila heads RNA at 25C input of AGO1-Ip


title: Drosophila heads at 25C rep1 RNA input from AGO1-IP

description:
INP_25.1.
Drosophila_T1-1_INPUT


title: H209 608.1_8h

description: replicate 1


title: HoxB-CSF3R_T618I-A


title: H209 C1_24h

description: replicate 1


title: Drosophila heads at 18C rep2 RNA input from AGO1-IP

description:
INP_18.2.
Drosophila_T0-2_INPUT

source_name: Drosophila heads RNA at 18C input of AGO1-Ip


title: HoxB-Empty-Vector-B

source_name: HoxB8 cells transduced with empty MSCV-IRES-GFP/empty MSCV-IRES-mCherry harvested 24 hours after estrogen withdrawal


title: Drosophila heads at 18C rep1 RNA input from AGO1-IP

description:
INP_18.1.
Drosophila_T0-1_INPUT


title: HoxB-Empty-Vector-C


title: GFP overexpressing HUES6 cells

status: Public on Dec 01 2019

city: Nankang

first: Jean

last: Lu

state: Taipei

address: 128 Academia Road, Section 2, IBMS, N401F

department: Genomics Research Center

country: Taiwan

institute: Academia Sinica

description: Gene expression data from GFP overexpressing HUES6 cells

hyb_protocol: After aRNA fragmentation, 12.5 ug of fragmented aRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133 Plus 2.0 Array. Affymetrix Fluidics Station 450 was used for gene chips washing and staining.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and use Gene Spring Software 12 to normalize data (RMA mode).

source_name: GFP overexpressing HUES6 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250ng total RNA (GeneChip® 3’ IVT Express Kit, Affymetrix).

growth_protocol: HUES6 hESC cells were treated with accutase for 3 minutes in room temperature and washed cells with 1XPBS to remove MEF two times. After that, suspended cells in chemically defined medium (Essential 8 medium) and seeded cells density of 150,000 per one 6-well.

treatment_protocol: HUES6 hESCs were seeded on matrigel-coated plates and 2 hours later incubated in the supernatants containing lentivirus with 8 ug/ml protamine sulfate. After 24 hours, medium was replaced with fresh medium containing Blasticidin (5 ug/ml) antibiotic selection for 3 days.

value: embryonic stem cells

value: overexpressing GFP


title: PODXL overexpressing HUES6 cells

description: Gene expression data from PODXL overexpressing HUES6 cells

scan_protocol: GeneChip® Human Genome U133 Plus 2.0 Array

source_name: PODXL overexpressing HUES6 cells

value: overexpressing PODXL


title: H209 C1_4h

description: replicate 1


title: H209 C1_8h

description: replicate 1


title: H209 C1_0h

description: replicate 1


title: blood expression from subject Z037

city: Collegeville

first: David

last: Mayhew

state: PA

address: 1250 South Collegeville Road

department: Target Sciences, Computation Biology, R&D

institute: GlaxoSmithKline

hyb_protocol: The biotin labeled samples were then hybridized to a Human Genome U133 Plus 2.0 Array using a Genechip Hybridization Kit according to the manufacturer's instruction.

scan_protocol: The microarray chips were washed and stained using a Genechip Hybridization Wash and Stain Kit then scanned using a Genechip Scanner. All reagents and readers were used according to the manufacturer’s instruction.

data_processing:
The microarray gene expression data were analyzed using ArrayStudio 7.0.  Data were normalized using robust multiarray averaging and scaled to a mean target intensity of 150.  Differentially expressed transcripts were identified with a Student's t-test (p-value < 0.01 and at least 1.3 fold-change)
affymetrix-algorithm-name = Rma
affymetrix-algorithm-param-quantification-scale = log2
program-company = Omicsoft
program-name = oplatformlib
program-version = 1.0.0.0

source_name: whole blood_Obese Non-asthma subject

label_protocol: The RNA samples were converted to cDNA with Superscript Vilo cDNA synthesis Master Mix and cDNA samples were labeled with biotion with the FL-Ovation cDNA Biotin Module V2.

extract_protocol: Total mRNA was extracted from peripheral blood using Qiagen RNeasy kit (Qiagen, Valencia, CA) and quantified by NanoDrop (Thermo Fisher Scientific, Waltham, MA). RNA integrity was confirmed using the Agilent 2100 BioAnalyzer (Agilent, Palo Alto, CA).

treatment_protocol: Peripheral blood was collected in Paxgene tubes and immediately frozen at -80 °C until later analysis.

tag: subject id

tag: obesity status

value: Obese

tag: asthma status

value: Non-asthma

tag: bmi

value: Female

tag: location

value: Zurich, Switzerland

value: whole blood


title: blood expression from subject Z040


title: blood expression from subject Z039

source_name: whole blood_Obese Asthma subject

value: Asthma


title: blood expression from subject Z042


title: HoxB-Empty-Vector-A

first: Theodore

address: 3181 SW Sam Jackson Park Road


title: blood expression from subject Z038


title: blood expression from subject Z034


title: blood expression from subject Z041


title: blood expression from subject Z033


title: blood expression from subject Z025


title: blood expression from subject Z032

source_name: whole blood_Non-Obese Non-asthma subject

value: Non-Obese


title: blood expression from subject Z020

source_name: whole blood_Non-Obese Asthma subject


title: blood expression from subject Z023


title: blood expression from subject Z030


title: blood expression from subject Z026


title: blood expression from subject Z036


title: blood expression from subject Z018


title: blood expression from subject Z029


title: blood expression from subject Z031


title: blood expression from subject Z027


title: blood expression from subject Z035


title: blood expression from subject Z019


title: blood expression from subject Z017


title: blood expression from subject Z016


title: blood expression from subject Z015


title: blood expression from subject Z014


title: blood expression from subject Z022


title: blood expression from subject Z013


title: Kidney_WT_water_6 days_rep1

description: RMA expression value derived from Transcriptome Analysis Console; analysis with QLUCORE and MetaCore.

source_name: p53 wild-type mouse kidney exposed to water for 6 days

value: Kidney

tag: p53 genotype

value: Wild-type

tag: treatment

value: Water

value: 6 days


title: H209 C3_24h

description: replicate 3

value: cyclodextrin alone


title: blood expression from subject Z005

tag: Sex


title: blood expression from subject Z002

tag: tissue


title: blood expression from subject Z006


title: blood expression from subject Z003


title: blood expression from subject Z009


title: blood expression from subject Z004


title: blood expression from subject Z010


title: blood expression from subject Z007


title: blood expression from subject Z012


title: blood expression from subject Z011


title: blood expression from subject W120

value: Wroclaw, Poland


title: blood expression from subject W105


title: blood expression from subject W109


title: blood expression from subject W118

value: Male


title: blood expression from subject W114


title: blood expression from subject W115


title: blood expression from subject W112


title: blood expression from subject W104


title: blood expression from subject W119


title: blood expression from subject W110


title: blood expression from subject W113


title: blood expression from subject W116


title: blood expression from subject W106


title: blood expression from subject W111


title: blood expression from subject W108


title: blood expression from subject W103


title: blood expression from subject Z008


title: blood expression from subject W098


title: blood expression from subject W097


title: blood expression from subject W093


title: blood expression from subject W095


title: blood expression from subject W092


title: blood expression from subject W100


title: blood expression from subject W101


title: blood expression from subject W096


title: blood expression from subject W102


title: blood expression from subject W090


title: blood expression from subject W099


title: blood expression from subject Z001


title: blood expression from subject W091


title: blood expression from subject W087


title: blood expression from subject W086


title: blood expression from subject W094


title: blood expression from subject W088


title: blood expression from subject W083


title: blood expression from subject W082


title: blood expression from subject W085


title: blood expression from subject W079


title: blood expression from subject W076


title: blood expression from subject W077


title: blood expression from subject W071


title: blood expression from subject W070


title: blood expression from subject W068


title: blood expression from subject W072


title: blood expression from subject W078


title: blood expression from subject W067


title: blood expression from subject W084


title: blood expression from subject W075


title: blood expression from subject W081


title: blood expression from subject W065


title: blood expression from subject W064


title: blood expression from subject W066


title: blood expression from subject W063


title: blood expression from subject W073


title: blood expression from subject W089


title: blood expression from subject W069


title: blood expression from subject W080


title: blood expression from subject W060


title: blood expression from subject W074


title: blood expression from subject W061


title: blood expression from subject W056


title: blood expression from subject W057


title: blood expression from subject W054


title: blood expression from subject W062


title: blood expression from subject W055


title: blood expression from subject W059


title: blood expression from subject W058


title: blood expression from subject W051


title: blood expression from subject W048


title: blood expression from subject W045


title: blood expression from subject W039


title: blood expression from subject W047


title: blood expression from subject W042


title: blood expression from subject W049


title: blood expression from subject W053


title: blood expression from subject W041


title: blood expression from subject W033


title: blood expression from subject W052


title: blood expression from subject W030


title: blood expression from subject W027


title: blood expression from subject W024


title: blood expression from subject W043


title: blood expression from subject W050


title: blood expression from subject W025


title: blood expression from subject W038


title: blood expression from subject W044


title: blood expression from subject W036


title: blood expression from subject W117


title: blood expression from subject W037


title: blood expression from subject W032


title: blood expression from subject W046


title: blood expression from subject W026


title: blood expression from subject W031


title: blood expression from subject W023


title: blood expression from subject W040


title: blood expression from subject W029


title: blood expression from subject W028


title: blood expression from subject W022


title: blood expression from subject W020


title: blood expression from subject W019


title: blood expression from subject W018


title: blood expression from subject W010


title: blood expression from subject W016


title: blood expression from subject W017


title: blood expression from subject W021


title: blood expression from subject W008


title: blood expression from subject W014


title: blood expression from subject W011


title: blood expression from subject W004


title: blood expression from subject W013


title: blood expression from subject W006


title: blood expression from subject W015


title: blood expression from subject W012


title: blood expression from subject W007


title: MeT-5A-NF2-CDKN2A-KO#1

city: Nagakute

first: Karnan

last: Sivasundaram

state: Aichi

address: Yazakokarimata

department: Biochemisy

country: Japan

institute: Aichi Medical University

description: Gene expression in MeT-5A-NF2-CDKN2A-KO#1cell clone

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes according to the manufacturers instructions. After the fragmentation reaction, equal amount of Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G2519F-026652) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed for 1 minute at room temperature with GE Wash Buffer 1 (Agilent), for 1 minute with 37Â°C GE Wash buffer 2 (Agilent), and then dried for 1 minute at room temperature with acetonitrile.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 026652_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit  (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: MeT-5A were provided by the ATCC through the American Type Culture Collection , and were grown in RPMI containing 10% fetal bovine serum (FBS) at 37 °C in a 5% CO2 incubator.

extract_protocol: RNA was prepared using RNeasy Mini Kit (Qiagen) following the manufacturer's recommendations. RNA concentration was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Met-5A  and the established cell clones  were plated at 80% confluence and cultured for 24 hours

value: Human mesothelium

tag: gender

value: male

value: unknown


title: blood expression from subject W009

value: Obese


title: blood expression from subject W001

value: Non-asthma


title: blood expression from subject W002


title: blood expression from subject W005

value: Female


title: blood expression from subject W003


title: MeT-5A-NF2-CDKN2A-KO#2

description: Gene expression in MeT-5A-NF2-CDKN2A-KO#2cell clone

tag: cell type


title: scrambled antagomiR injected somites

city: Norwich

first: Tamas

last: Dalmay

address: Earlham Road

department: School of Biological Sciences

institute: University of East Anglia

data_processing:
only fragments with both 5' and 3' reads were considered for further analysis
the reads were mapped to the G. gallus genome full length, allowing up to 2 mis-matches
the calculation of gene expression was conducted as indicated in [Trapnell et al, 2010]
the normalization was RPKM [Mortazavi et al, 2008]
Genome_build: G. gallus 4.73
Supplementary_files_format_and_content: csv file containing the raw gene expression levels

organism: Gallus gallus

source_name: scrambled antagomiR injected somites

extract_protocol:
Trizol reagent was used for total RNA extraction
Performed by BaseClear (NL) in 2010-2011: 3 RNA samples were sequenced with PE50 sequencing protocol, each sample sequenced on one lane of the Genome Analyzer. We made libraries without barcoding and we used the standard mRNA-seq library preparation kit of Illumina that was available at that time. This approach resulted in a library with the following structure and sequence (indicated here is only the top strand): 5prime-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT (insert) AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG-3prime

tag: developmental stage

value: Hamburger-Hamilton stage 14 to 16

tag: tissue type

value: embryonic tissue, progenitors of musculoskeletal tissues


title: Control siRNA_48h

city: Seoul

first: Hyemin

last: Lee

address: Kyunghee-dae-ro 26

country: South Korea

institute: Kyunghee Univ

description: Gene expression after 48hr in control siRNA treated HCT116 cells

hyb_protocol: After checking labeling efficiency, fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60oC for 30 min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent’s Canine Oligo Microarray (44K). The arrays hybridized at 65oC for 17 hours using Agilent Hybridization oven (Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: All data normalization and further analysis were performed using GeneSpringGX 7.3 (Agilent Technology, USA).

label_protocol: Amplified and labeled cRNA was purified on cRNA Cleanup Module (Agilent Technology) according to the manufacturer’s protocol. Labeled cRNA target was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE).

growth_protocol: RPMI medium with 10% FBS, 2 μM L-glutamine and penicillin/streptomycin

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: HCT116 cells were transfected with ZNF746 siRNA plasmid for knockdown of their endogenous levels using INTERFERin® (Polyplus-transfection SA) transfection reagent

tag: cell line

tag: transfection

value: 48hr in control siRNA


title: non-injected_somites

source_name: non-injected somites from opposite side


title: MeT-5A-NF2-KO#2

description: Gene expression in MeT-5A-NF2-KO#2cell clone

tag: age


title: MeT-5A-CDKN2A-KO#1

description: Gene expression in MeT-5A-CDKN2A-KO#1cell clone


title: antagomiR-206 injected somites

source_name: antagomiR-206 injected somites


title: ZNF746siRNA_48h

description: Gene expression after 48hr in ZNF746 siRNA treated HCT116 cells

source_name: HCT116, ZNF_48hr

value: 48hr in ZNF746 siRNA


title: ZEV_nextseq_induced_R

city: Stanford

first: Christina

last: Smolke

state: CA

address: 443 Via Ortega

department: Bioengineering

institute: Stanford University

description:
Plasmid DNA and barcodes to assign an artificial promoter to an expression bin
means_nextseq_ZEV.csv

data_processing:
Library strategy: FACS-seq
Base-calling: default FASTQ output from Illumina bcl2fastq
Paired-end alignment (Miseq data only): PEAR 0.9.6 with flags -j 8 -v 1 -g 2 -n 20
Consensus sequence extraction (Miseq only): scripts to be deposited at github.com/smolkelab/promoter_design (mean_extraction/build_table_align.py)
Read table construction (Nextseqs and validation Miseq): scripts to be deposited at github.com/smolkelab/promoter_design (mean_extraction/build_table_exact.py)
Mean extraction: scripts to be deposited at github.com/smolkelab/promoter_design (mean_extraction/mean_fitting_likelihood_cuda.py)
Genome_build: not applicable – artificial sequence
Supplementary_files_format_and_content: means_nextseq_*.csv: comma-delimited table. No header – first column sequence, second column promoter activity in replicate A (GPD) or uninduced condition (others), third column activity in replicate B (GPD) or induced condition (others).
Supplementary_files_format_and_content: filtered_read_table_miseq_*.txt: comma-delimited table. No header – first column sequence, second column group identifier (from intermediate processing steps), following columns read counts in each bin, as assigned by ‘barcode_miseq_*.csv’ key tables in deposited code
Supplementary_files_format_and_content: final_means_ids_added.csv: comma-delimited table. “Seqs”: sequence.  “Means_A”: promoter activity, uninduced. “Means_B”: promoter activity, induced. “Experiment”: numerical ID of artificial promoter set this sequence is part of (cf. text Supplementary Tables 1 and 2), “None” if a mutant/mis-assembled sequence. “Design”: numerical ID of sequence within its “Experiment”, -1 if “Experiment” is None.

organism: synthetic construct

source_name: Synthetic promoter reporter gene assay

growth_protocol: Cells were grown in yeast nitrogen base media with 2 percent dextrose, lacking uracil, for three passages after library transformation. Passages were always at least 10 OD600*mL units.

extract_protocol:
PCR amplicons from random oligonucleotide pools, joined by Golden Gate assembly at constant regions encoding transcription factor binding sites based on the PZEV artificial promoter system.
After FACS-sorting and overnight regrowth in the same media used for growth, sorted fractions were miniprepped. PCR was used to verify that at least 10 plasmids were extracted per sorted cell; minipreps were PCR-amplified, further amplified with the addition of bin-specific barcodes, pooled, and amplified briefly again.

treatment_protocol: 1 micromolar beta-estradiol was added to culture media in the “induced” condition 18 hours presort.

tag: plasmid type

value: Synthetic promoter driving reporter gene


title: ZEV_nextseq_Q


title: ZEV_nextseq_induced_12


title: ZEV_nextseq_induced_X


title: ZEV_nextseq_Undetermined


title: ZEV_nextseq_induced_11


title: MeT-5A-NF2-KO#1

description: Gene expression in MeT-5A-NF2-KO#1cell clone


title: MeT-5A -parental

description: Gene expression in MeT-5A cells


title: ZEV_nextseq_induced_6


title: ZEV_nextseq_induced_5


title: ZEV_nextseq_induced_10


title: ZEV_nextseq_induced_8-1


title: ZEV_nextseq_induced_7


title: ZEV_nextseq_induced_9


title: ZEV_nextseq_induced_4


title: ZEV_nextseq_induced_3


title: ZEV_nextseq_induced_2


title: ZEV_nextseq_uninduced_R


title: ZEV_nextseq_induced_1


title: ZEV_nextseq_uninduced_12


title: ZEV_nextseq_uninduced_10


title: ZEV_nextseq_uninduced_11


title: ZEV_nextseq_uninduced_8-2


title: ZEV_nextseq_uninduced_8-1


title: ZEV_nextseq_uninduced_6


title: ZEV_nextseq_uninduced_7


title: ZEV_nextseq_uninduced_4


title: ZEV_nextseq_uninduced_5


title: ZEV_nextseq_uninduced_3


title: ZEV_nextseq_uninduced_2


title: ZEV_nextseq_uninduced_9


title: GPD_nextseq_BK727

description:
Plasmid DNA and barcodes to assign an artificial promoter to an expression bin
means_nextseq_GPD.csv

extract_protocol:
PCR amplicons from random oligonucleotide pools, joined by Golden Gate assembly at constant regions encoding transcription factor binding sites based on the PGPD promoter.
After FACS-sorting and overnight regrowth in the same media used for growth, sorted fractions were miniprepped. PCR was used to verify that at least 10 plasmids were extracted per sorted cell; minipreps were PCR-amplified, further amplified with the addition of bin-specific barcodes, pooled, and amplified briefly again.


title: GPD_nextseq_Undetermined


title: GPD_nextseq_BK729


title: GPD_nextseq_BK726


title: GPD_nextseq_BK728


title: 505449_rewilded

city: New York

first: Joseph

middle: C

last: Devlin

state: NY

address: 430 East 29th Street

department: Microbiology

institute: New York University Langone Health

data_processing:
Reads were mapped by Bowtie (v2.3.1) to the mm10 reference genome
Uniquely mapped indices (UMI) determined by HTSeq-counts
Normalized count tables were generated in R (v3.5.1) using DESeq2 (v1.18.1)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized count values for each Sample

growth_protocol: Primary mesenteric lymph node tissue was homogenized, resuspended with FACS buffer (1% BSA in HBSS containing 1mM EDTA) and made into a single-cell suspension.

extract_protocol:
RNA for each sample was then isolated with the RNeasy Plus Mini Kit (Qiagen) following the protocol with on column DNAse Digestion (Qiagen).
RNA libraries were prepared using standard CelSeq2 protocols.

tag: environment

value: rewilded

tag: genotype/variation

value: Primary mesenteric lymph node (MLN)


title: 515757_rewilded


title: 505248_rewilded


title: GPD_nextseq_BK724


title: ZEV_nextseq_uninduced_1


title: 515350_rewilded


title: 515155_rewilded


title: 515652_rewilded


title: 515056_rewilded


title: 515149_rewilded


title: 514957_rewilded


title: ZEV_nextseq_induced_8-2


title: GPD_nextseq_BK725


title: 505756_rewilded


title: 505751_rewilded


title: 515550_rewilded


title: 515749_rewilded


title: 515357_rewilded


title: 515057_rewilded


title: 505149_rewilded


title: 505748_rewilded


title: 515753_rewilded


title: 505054_rewilded


title: 505556_rewilded


title: 505349_rewilded


title: 505350_rewilded


title: 515251_rewilded


title: 515250_rewilded


title: 515450_rewilded


title: DamID AML12_shCtrl_rep1

type: genomic

city: Shanghai

first: Luzhang

last: Ji

address: 1239 Siping Rd.

institute: Tongji University

description: Replicate 1 of 2 shCtrl AML12 cells

hyb_protocol: Hybridized to Agilent-027414 arrays.

scan_protocol: Scanned on an Agilent Technologies Scanner G2505C.

data_processing: Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization. we also smoothed the probe signals using a moving average approach with a window size of 40k bps. The smoothing procedure takes into consideration of the spatial correlation of signals.

label_protocol: Genomic DNA samples were differentially labeled with Invitrogen’s BioPrime Total for Agilent aCGH labeling kit.

growth_protocol: AML12 cells were cultured in  DMEM/F12 supplemented with 10% fetal bovine serum,  ITS Liquid Media Supplement, and 0.1μM dexamethasone at 37 °C and 5% CO2.

extract_protocol: 2×106 AML12 cells were planted in 6-well plates, and infected with lenti-virus expressing Dam or Dam-Lamin B1 after 48 hours. gDNA was isolated with the Dneasy Tissue kit (Qiagen) per the manufacturers protocol after 72 hours. 2.5 μg of gDNA was digested with DpnI (New England Biolabs), adapters were ligated with T4 ligase (New England Biolabs), and the ligation reaction was subsequently digested with DpnII (New England Biolabs). 500 ng of the DpnII digested material was used as input for a PCR amplification of methylated fragments (MePCR),see Vogel et al., 2008, Nature Protocols for details.

treatment_protocol: The shRNA lentiviruses were prepared as previously described (Fu et al., 2015). Then AML12 cells were infected with 200 μl of virus concentrate in a well of six-well-plates. Medium was changed 24 hours after transfection, and then collect cells 5 days after transfection.

value: AML12 cells

tag: lenti-virus expression

value: Dam-only


title: 515249_rewilded


title: 515152_rewilded


title: 514851_rewilded


title: 505050_rewilded


title: 515050_rewilded


title: 515654_rewilded

value: WT


title: 505057_rewilded


title: DamID AML12_shSafb_rep1

description: Replicate 1 of 2 shSafb AML12 cells


title: 505750_rewilded


title: 514855_rewilded


title: 505150_rewilded


title: 514857_rewilded


title: 515055_rewilded


title: 505551_rewilded


title: 505749_rewilded


title: 505048_rewilded


title: 515255_rewilded


title: ADamID ML12_shSafb_rep2

description: Replicate 2 of 2 shSafb AML12 cells


title: DamID AML12_shCtrl_rep2

description: Replicate 2 of 2 shCtrl AML12 cells


title: 59-4_lab

value: lab


title: 59-5_lab


title: 59-2_lab


title: 66-4_lab


title: 515157_rewilded


title: 505049_rewilded


title: 515353_rewilded


title: 505452_rewilded


title: 66-3_lab


title: 66-2_lab


title: 61-4_lab


title: 66-1_lab


title: 59-1_lab


title: 61-2_lab


title: 61-1_lab


title: 61-3_lab


title: 32-8_lab


title: 32-2_lab


title: 32-1_lab


title: 86-8_lab


title: 86-3_lab


title: 76-4_lab


title: 76-5_lab


title: 86-7_lab


title: 86-9_lab


title: 30-10_lab


title: 59-3_lab


title: 30-21_lab


title: 30-9_lab


title: 30-33_lab


title: 78-85_lab


title: 76-3_lab


title: 66-5_lab


title: 30-36_lab


title: 76-2_lab


title: 78-84_lab


title: 32-5_lab


title: 71-9_lab


title: 86-6_lab


title: 71-8_lab


title: 71-7_lab


title: 71-3_lab


title: TCC-367_miRNA: CC026_D3_Mock_Liver_3_miRNA

first: Adam

last: Price

address: 722 West 168th St.

department: Center for Infection and Immunity

institute: Columbia University

description:
TCC-367_miRNA
TCC_miRNA_master_counts_1-370.txt
TCC_miRNA_master_targets.txt

data_processing:
Illumina adapters were trimmed from reads using Trimmomatic 0.38.
Reads were aligned to the reference genome using STAR 2.5.3
Transcript counts were quantified using rSubread-1.5.1 featureCounts utility.
Differential expression and analysis were performed using DESeq2 3.8 and DEvis 1.0.1.
miRNA and mRNA data were integrated based on the miRWalk 2.0 database.
Genome_build: Mus_musculus.GRCm38.91
Supplementary_files_format_and_content: Files representing transcript counts and associated sample metadata are provided in tab-delimited format.  These files represent quantified expression for each associated sample anad relevant points of metadata for each sample. Files are provided for both mRNA and miRNA.

source_name: Liver

growth_protocol: We used 6-8-week-old male Collaborative Cross (CC) mice obtained from the University of North Carolina Systems Genetics Core. Mice were acclimated to ABSL-4 containment for 5 days prior to beginning the experiment. Virus stocks were grown in Vero E6 cells and stored at -80 C. All mouse studies were performed under the oversight of the Rocky Mountain Laboratories (RML) Institutional Animal Care and Use Committee (IACUC) as well as the US Army Animal Care and Use Review Office (ACURO). All virus experiments were conducted in BSL-4/ABSL-4 containment at the RML Laboratory of Virology in compliance with federal law regarding handling and use of Select Agents.

extract_protocol:
Total RNA was isolated from liver and spleen frozen at -80 C in Trizol reagent. RNA was extracted using the Zymo Direct-zol MiniPrep RNA extraction kit. RNA quality was assessed using either the Agilent Bioanalyzer 2100 or Agilent TapeStation.
mRNA libraries were prepared from the poly-A fraction of total RNA using Illumina TruSeq v2 reagents. miRNA libraries were prepared from size-selected total RNA using Illumina TruSeq Small RNA reagents. All library preparations were performed according to the manufacturer's instructions. Completed libraries were run on the Illumina HiSeq 4000. We collected at least 30 million single-end 100 bp reads of mRNA sequence data and at least 5 million single-end 50 bp reads of miRNA sequence data.

treatment_protocol: Groups of at least 3 male CC mice per line per time point per condition were used to assess longitudinal disease progression at three time points post-infection (p.i.). Infected mice were injected intraperitoneally (i.p.) with 100 focus-forming units (FFU) of MA-EBOV in 0.2 mL total volume delivered bilaterally in 0.1 mL units using a 25-gauge needle. Time-matched mock-infected animals were i.p. injected in the same manner with 0.2 mL of virus stock buffer (complete DMEM medium) delivered as bilaterally in 0.1 mL units. Mice were humanely euthanized at days 1, 3, or 5 p.i. by exsanguination via cardiac puncture while under deep anesthesia with inhalational isoflurane, followed by isoflurane overdose. Gross pathological observations were recorded at necropsy. Spleen and liver samples were collected and frozen for subsequent viral titration, or preserved in RNAlater and subsequently frozen at -80 C in Trizol  reagent for downstream RNA extraction.

value: mock

value: Liver

tag: cc line

tag: infection condtion

value: Mock

tag: animal id

tag: day post-infection


title: TCC-365_miRNA: CC026_D3_Mock_Liver_1_miRNA

description:
TCC-365_miRNA
TCC_miRNA_master_counts_1-370.txt
TCC_miRNA_master_targets.txt

tag: treatment


title: TCC-369_miRNA: CC026_D5_Mock_Liver_2_miRNA

description:
TCC-369_miRNA
TCC_miRNA_master_counts_1-370.txt
TCC_miRNA_master_targets.txt

tag: tissue


title: TCC-368_miRNA: CC026_D5_Mock_Liver_1_miRNA

description:
TCC-368_miRNA
TCC_miRNA_master_counts_1-370.txt
TCC_miRNA_master_targets.txt


title: TCC-364_miRNA: CC026_D1_Mock_Liver_4_miRNA

description:
TCC-364_miRNA
TCC_miRNA_master_counts_1-370.txt
TCC_miRNA_master_targets.txt


title: TCC-362_miRNA: CC026_D1_Mock_Liver_2_miRNA

description:
TCC-362_miRNA
TCC_miRNA_master_counts_1-370.txt
TCC_miRNA_master_targets.txt


title: TCC-370_miRNA: CC026_D5_Mock_Liver_3_miRNA

description:
TCC-370_miRNA
TCC_miRNA_master_counts_1-370.txt
TCC_miRNA_master_targets.txt


title: TCC-366_miRNA: CC026_D3_Mock_Liver_2_miRNA

description:
TCC-366_miRNA
TCC_miRNA_master_counts_1-370.txt
TCC_miRNA_master_targets.txt


title: TCC-360_miRNA: CC026_D5_EBOV_Liver_4_miRNA

description:
TCC-360_miRNA
TCC_miRNA_master_counts_1-370.txt
TCC_miRNA_master_targets.txt

value: mouse-adapted Ebola virus

value: MA-EBOV infected


title: TCC-359_miRNA: CC026_D5_EBOV_Liver_3_miRNA

description:
TCC-359_miRNA
TCC_miRNA_master_counts_1-370.txt
TCC_miRNA_master_targets.txt


title: TCC-361_miRNA: CC026_D1_Mock_Liver_1_miRNA

description:
TCC-361_miRNA
TCC_miRNA_master_counts_1-370.txt
TCC_miRNA_master_targets.txt


title: TCC-351_miRNA: CC026_D1_EBOV_Liver_1_miRNA

description:
TCC-351_miRNA
TCC_miRNA_master_counts_1-370.txt
TCC_miRNA_master_targets.txt


title: TCC-350_miRNA: CC026_D5_Mock_Spleen_3_miRNA

description:
TCC-350_miRNA
TCC_miRNA_master_counts_1-370.txt
TCC_miRNA_master_targets.txt

source_name: Spleen

value: Spleen


title: TCC-353_miRNA: CC026_D1_EBOV_Liver_3_miRNA

description:
TCC-353_miRNA
TCC_miRNA_master_counts_1-370.txt
TCC_miRNA_master_targets.txt


title: TCC-355_miRNA: CC026_D3_EBOV_Liver_2_miRNA

description:
TCC-355_miRNA
TCC_miRNA_master_counts_1-370.txt
TCC_miRNA_master_targets.txt


title: TCC-354_miRNA: CC026_D3_EBOV_Liver_1_miRNA

description:
TCC-354_miRNA
TCC_miRNA_master_counts_1-370.txt
TCC_miRNA_master_targets.txt


title: TCC-363_miRNA: CC026_D1_Mock_Liver_3_miRNA

description:
TCC-363_miRNA
TCC_miRNA_master_counts_1-370.txt
TCC_miRNA_master_targets.txt


title: TCC-352_miRNA: CC026_D1_EBOV_Liver_2_miRNA

description:
TCC-352_miRNA
TCC_miRNA_master_counts_1-370.txt
TCC_miRNA_master_targets.txt


title: TCC-349_miRNA: CC026_D5_Mock_Spleen_2_miRNA

description:
TCC-349_miRNA
TCC_miRNA_master_counts_1-370.txt
TCC_miRNA_master_targets.txt


title: TCC-358_miRNA: CC026_D5_EBOV_Liver_2_miRNA

description:
TCC-358_miRNA
TCC_miRNA_master_counts_1-370.txt
TCC_miRNA_master_targets.txt


title: 71-6_lab


title: TCC-356_miRNA: CC026_D3_EBOV_Liver_3_miRNA

description:
TCC-356_miRNA
TCC_miRNA_master_counts_1-370.txt
TCC_miRNA_master_targets.txt


title: TCC-348_miRNA: CC026_D5_Mock_Spleen_1_miRNA

description:
TCC-348_miRNA
TCC_miRNA_master_counts_1-370.txt
TCC_miRNA_master_targets.txt


title: 76-1_lab


title: TCC-347_miRNA: CC026_D3_Mock_Spleen_3_miRNA

description:
TCC-347_miRNA
TCC_miRNA_master_counts_1-370.txt
TCC_miRNA_master_targets.txt


title: TCC-344_miRNA: CC026_D1_Mock_Spleen_4_miRNA

description:
TCC-344_miRNA
TCC_miRNA_master_counts_1-370.txt
TCC_miRNA_master_targets.txt


title: TCC-345_miRNA: CC026_D3_Mock_Spleen_1_miRNA

description:
TCC-345_miRNA
TCC_miRNA_master_counts_1-370.txt
TCC_miRNA_master_targets.txt


title: TCC-346_miRNA: CC026_D3_Mock_Spleen_2_miRNA

description:
TCC-346_miRNA
TCC_miRNA_master_counts_1-370.txt
TCC_miRNA_master_targets.txt


title: TCC-340_miRNA: CC026_D5_EBOV_Spleen_4_miRNA

description:
TCC-340_miRNA
TCC_miRNA_master_counts_1-370.txt
TCC_miRNA_master_targets.txt


title: TCC-341_miRNA: CC026_D1_Mock_Spleen_1_miRNA

description:
TCC-341_miRNA
TCC_miRNA_master_counts_1-370.txt
TCC_miRNA_master_targets.txt


title: TCC-339_miRNA: CC026_D5_EBOV_Spleen_3_miRNA

description:
TCC-339_miRNA
TCC_miRNA_master_counts_1-370.txt
TCC_miRNA_master_targets.txt


title: TCC-338_miRNA: CC026_D5_EBOV_Spleen_2_miRNA

description:
TCC-338_miRNA
TCC_miRNA_master_counts_1-370.txt
TCC_miRNA_master_targets.txt


title: TCC-331_miRNA: CC026_D1_EBOV_Spleen_1_miRNA

description:
TCC-331_miRNA
TCC_miRNA_master_counts_1-370.txt
TCC_miRNA_master_targets.txt


title: TCC-342_miRNA: CC026_D1_Mock_Spleen_2_miRNA

description:
TCC-342_miRNA
TCC_miRNA_master_counts_1-370.txt
TCC_miRNA_master_targets.txt


title: TCC-330_miRNA: CC057_D5_Mock_Liver_3_miRNA

description:
TCC-330_miRNA
TCC_miRNA_master_counts_1-370.txt
TCC_miRNA_master_targets.txt


title: TCC-329_miRNA: CC057_D5_Mock_Liver_2_miRNA

description:
TCC-329_miRNA
TCC_miRNA_master_counts_1-370.txt
TCC_miRNA_master_targets.txt


title: TCC-333_miRNA: CC026_D1_EBOV_Spleen_3_miRNA

description:
TCC-333_miRNA
TCC_miRNA_master_counts_1-370.txt
TCC_miRNA_master_targets.txt


title: TCC-324_miRNA: CC057_D1_Mock_Liver_3_miRNA

description:
TCC-324_miRNA
TCC_miRNA_master_counts_1-370.txt
TCC_miRNA_master_targets.txt


title: TCC-337_miRNA: CC026_D5_EBOV_Spleen_1_miRNA

description:
TCC-337_miRNA
TCC_miRNA_master_counts_1-370.txt
TCC_miRNA_master_targets.txt


title: TCC-335_miRNA: CC026_D3_EBOV_Spleen_2_miRNA

description:
TCC-335_miRNA
TCC_miRNA_master_counts_1-370.txt
TCC_miRNA_master_targets.txt


title: TCC-326_miRNA: CC057_D3_Mock_Liver_2_miRNA

description:
TCC-326_miRNA
TCC_miRNA_master_counts_1-370.txt
TCC_miRNA_master_targets.txt


title: TCC-332_miRNA: CC026_D1_EBOV_Spleen_2_miRNA

description:
TCC-332_miRNA
TCC_miRNA_master_counts_1-370.txt
TCC_miRNA_master_targets.txt


title: TCC-325_miRNA: CC057_D3_Mock_Liver_1_miRNA

description:
TCC-325_miRNA
TCC_miRNA_master_counts_1-370.txt
TCC_miRNA_master_targets.txt


title: TCC-327_miRNA: CC057_D3_Mock_Liver_3_miRNA

description:
TCC-327_miRNA
TCC_miRNA_master_counts_1-370.txt
TCC_miRNA_master_targets.txt