title: RNAseq_11321

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: eosinophil percent

tag: monocyte percent

tag: basophil percent


title: RNAseq_95479

status: Public on Dec 31 2020

type: SRA

city: Boston

first: Peter

last: Castaldi

state: Massachusetts

address: 181 Longwood Ave

country: USA

institute: Brigham and Women's Hospital

description:
gene_TMM_counts.csv
exon_TMM_counts.csv
isoform_TMM_counts.csv

library_source: transcriptomic

data_processing:
alignment: STAR, 2-pass
gene quantification: Salmon v0.12.0 and tximport
exon quantification: Rsubread v1.32.2
isoform quantification: Salmon v0.12.0
Genome_build: HG38 (GTF: Ensembl Homo_sapiens.GRCh38.94.gtf.gz)
Supplementary_files_format_and_content: count matrices

molecule: total RNA

organism: Homo sapiens

source_name: blood

extract_protocol:
Total RNA was extracted from PAXgene TM Blood RNA tubes using the Qiagen PreAnalytiX PAXgene Blood miRNA Kit (Qiagen, Valencia, CA).
Globin reduction and cDNA library preparation for total RNA was performed with the Illumina TruSeq Stranded Total RNA with Ribo-Zero Globin kit (Illumina, Inc., San Diego, CA).

tag: batch

tag: current smoker

tag: pack years

tag: age

tag: gender (1=male, 2=female)

tag: neutrophil percent

tag: lymphocyte percent


title: paraquat+highlight [PQ-HL_23]

city: Memphis

first: Soham

last: Sengupta

state: TN

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

data_processing:
Illumina's two-channel SBS sequencing
Quality control of reads were performed using FastQC v0.11.7
RNA-seq reads were aligned to Arabidopsis thaliana genome obtained from TAIR using STAR aligner v2.4.0.1
Differential gene expression analysis was performed using DeSeq2 v1.20.0
Genome_build: TAIR 10
Supplementary_files_format_and_content: tab-deliminated files included mean normalized counts for each sample

organism: Arabidopsis thaliana

growth_protocol: Seeds of Arabidopsis thaliana wild type Col-0 were sterilized and placed on 1% agar plates (0.5x Murashige and Skoog (MS) medium, pH 5.8) as controls. Similarly, sterilized seeds were placed on 1% agar MS medium supplemented by: Salt (50 mM NaCl); PQ (0.05 µM paraquat); Salt + PQ (50 mM NaCl + 0.05 µM paraquat). After being stratified at 4ºC for 12 hours in dark, seeds were germinated horizontally under controlled conditions (21°C, 50 µmol m-2 s-1). 10 days after germination, seedlings growing in the different plates were subjected to high light (700 µmol m-2 s-1), heat stress (33ºC) and the combination of high light and heat stress (700 µmol m-2 s-1; 33ºC) for 1.5 h. Immidiately after that, seedlings were frozen in liquid nitrogen.

extract_protocol:
Total RNA was isolated using Plant RNeasy kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Col-0 seedlings were subjected to salt, paraquat, high light, heat stress, and a combination of 2, 3 or 4 of those stresses as described in the groth protocol

tag: ecotype

tag: genotype

value: wild type

tag: treatment

value: paraquat+highlight

tag: tissue

value: Seedlings

tag: repeat


title: RNAseq_04552

tag: race (1=white, 2=black)


title: importin123 RNA-seq [imp2]

city: Austin

first: Sibum

last: Sung

state: TX

institute: University of Texas at Austin

data_processing:
Reads generated by Illumina NextSeq 500 platform were checked for quality using FastQC
After quality assessment, reads were aligned on TAIR10 genome using HISAT2
SAM files generated from mapping were then converted into BAM files and sorted using Samtools
For the gene counting bedtools program was used which generates raw count using BAM files
Raw count was then fed into R for differential gene expression analysis using edgeR and data visualization
Genome_build: TAIR10
Supplementary_files_format_and_content: Excel file containing raw read count of each sample and RPKM normalized read count of each sample

source_name: impα triple_seedling

growth_protocol: Whole seedlings were grown on ½ MS medium containing 0.8% sucrose under long-day (16 h light, 8 h dark) condition. Seedlings were collected at ZT12

extract_protocol:
Total RNAs were extracted by using TRIzol (Invitrogen) and treated with DNase I enzyme (Promega) to eliminate traces of genomic DNA
Sequencing libraries were prepared with 500 ng total RNA following NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7420). Quality of libraries was assessed on a Bioanalyzer (Agilent High Sensitivity DNA Assay)

tag: ecotype background

tag: genotype/variation

value: importin123 mutant

value: Seedling collected at ZT12


title: importin123 RNA-seq [imp1]


title: 12-9-W Wild type, 180 min after formaldehyde treatment

first: Jeffrey

middle: E.

last: Barrick

address: 2500 Speedway, Stop A4800

department: Molecular Biosciences

institute: The University of Texas at Austin

description: counts.csv

data_processing:
Read trimming was performed using Trimmomatic v0.38 in paired-end mode, if applicable, and removing reads trimmed to fewer than 30 bases.
Read alignment was performed using Bowtie2 v4.8.2 with the -k option, in paired-end mode for reads paired after trimming and in single read mode for others
Raw counts were generated using HTSeq v0.11.4 with options to count read pairs or singleton reads that unambiguously overlapped each gene
Normalized read counts were generated using DeSeq2 in R version 3.6.
Genome_build: NC_010172.1
Supplementary_files_format_and_content: CSV

organism: Methylorubrum extorquens

source_name: Bacterial cells

growth_protocol: From individual colonies, wild-type (CM2730) and the ΔefgA mutant (CM3745) were inoculated into 2 mL MP medium (3.5 mM succinate) and grown at 30 °C with shaking for 32 hr. Cells were subcultured (1/64) into fresh MP media twice: first into 35 mL (3.5 mM succinate, 24 hr incubation) and then into 2 L (15 mM succinate). When OD600 of 2 L cultures = 0.2 (~8 hr), 100 mL of each culture was used to harvest “pretreatment” cells for transcriptomic analysis and remaining cultures were divided into 100 mL aliquots in 250 mL flasks for treatment.

extract_protocol:
RNA was purified from cells for each sample using the RNAsnap method [1]. First, cell pellets were resuspended in 500 µl of RNA extraction buffer (18 mM EDTA, 0.025% w/v SDS, 1% v/v 2-mercaptoethanol, 95% v/v formamide) by vortexing. Following incubation at 95°C for 7 min, cell debris was pelleted by centrifugation at 16000 × g for 5 min at room temperature. The resulting supernatant was purified using the Clean & Concentrator kit incorporating the on-column DNase digestion step (Zymo Research). Yields were determined using a Qubit 2.0 fluorometer with the RNA BR assay kit (ThermoFisher). Then, 1.5 µg of purified RNA for each sample was processed using the Ribozero rRNA Removal Kit (Gram-negative bacteria) (Illumina) according to the manufacturer’s instructions except that reaction volumes were reduced by 50%. Depleted RNA samples were ethanol precipitated.
RNA-Seq library preparation from rRNA-depleted samples began by fragmenting them with the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs) for 110 s followed by ethanol precipitation. Fragmented RNA was treated with 10 U of T4 polynucleotide kinase (NEB) in 20 µl reactions containing 1 mM ATP. After another ethanol precipitation, the NEBNext small RNA Library Prep Set for Illumina (Multiplex Compatible) (New England Biolabs) was used to prepare samples according to recommended protocol, except all reaction volumes were reduced 50% and the SR RT primer concentration was reduced by an additional 50% in the RT primer hybridization step. After performing 15 cycles of PCR, samples were ethanol precipitated, and the DNA concentration was determined via the Qubit HS dsDNA assay kit (Thermofisher). For each sample, 200 ng of DNA was run on a 4% EX E-gel (ThermoFisher). DNA with a size of at least ~200 bases was excised and purified using a gel DNA recovery kit (Zymo Research) with elution in 50 µl of nuclease-free water.

treatment_protocol: When OD600 of 2 L cultures = 0.2 (~8 hr), 100 mL of each culture was used to harvest “pretreatment” cells for transcriptomic analysis and remaining cultures were divided into 100 mL aliquots in 250 mL flasks (18 hr for wild-type, 16 hr the ΔefgA mutant) and returned to the incubator for 30 min. All flasks were quickly removed from incubator and treated with i) 500 μL of 1 M formaldehyde (5 WT flasks, 4 ΔefgA mutant flasks), ii) 100uL of 50mg/mL kanamycin (4 flasks of each strain), or iii) left untreated (4 flasks of each strain). Flasks were well-sealed with foil and parafilm and returned to the shaker. Time of treatment is designated as t = 0, pretreatment therefore corresponds to -45 min. This growth regimen was executed on 6 consecutive days to obtain all treated samples in biological triplicate.

tag: strain

value: WT

value: form

tag: time

tag: biological replicate


title: H1_Hdac1/2-/-

city: Sherbrooke

first: Alexis

last: Gonneaud

state: QC

address: 3201 rue Jean-Mignault

department: Anatomie et biologie cellulaire

country: Canada

institute: Université de Sherbrooke

data_processing:
The mapping is performed with “Star 2.4.0f1”.
The basecalling is performed directly with the HiSeq instrument and run with the tool “Illumina RTA”
The “Illumina bcl2fastq 1.8.4” tool is used to generate the FASTQ prior to the alignment
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file with raw counts, normalized counts and analysis statistics

organism: Mus musculus

growth_protocol: Jejunal IEC from three-month-old wild-type (3 mice) and  villin-Cre Hdac1-/-; Hdac2-/- (3 mice) mice were enriched by EDTA treatment

extract_protocol:
Jejunal IEC RNAs were isolated with the ToTALLY RNA™ (Thermo Fisher Scientific) and Rneasy kits (Qiagen) (n=3). Samples with RNA integrity number over 6.5 were selected with a 2100 Bioanalyser (Agilent Technologies)
Libraries were generated from 250 ng of total RNA as following: mRNA enrichment was performed using the NEBNext Poly(A) Magnetic Isolation Module (New England BioLabs). cDNA synthesis was achieved with the NEBNext RNA First Strand Synthesis and NEBNext Ultra Directional RNA Second Strand Synthesis Modules (New England BioLabs). The remaining steps of library preparation were done using and the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs). Adapters and PCR primers were purchased from New England BioLabs. Libraries were quantified using the Quant-iT™ PicoGreen® dsDNA Assay Kit (Life Technologies) and the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (Kapa Biosystems). Average size fragment was determined using a LabChip GX (PerkinElmer) instrument.

value: Jejunum

tag: cell type

value: intestinal epithelial cells

value: villin-Cre Hdac1-/-; Hdac2-/-

value: 3 months


title: H5_Hdac1/2-/-


title: RNAseq_05261

tag: batch

tag: current smoker

tag: pack years

tag: fev1 % predicted

tag: eosinophil percent

tag: monocyte percent

tag: basophil percent


title: 11-3-W Wild type, 40 min after formaldehyde treatment

description: counts.csv

tag: genotype

tag: treatment


title: lhp1-3 RNA-seq [lhp2]

value: lhp1-3 mutant

tag: tissue


title: 4-3-W Wild type, 40 min after formaldehyde treatment

description: counts.csv


title: H9_Hdac1/2-/-

tag: age


title: RNAseq_94532

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: neutrophil percent

tag: lymphocyte percent


title: 10-9-W Wild type, 20 min after formaldehyde treatment

description: counts.csv

tag: strain

tag: time

tag: biological replicate


title: lhp1-3 RNA-seq [lhp1]

tag: ecotype background

tag: genotype/variation


title: Col-0 RNA-seq [Col2]

source_name: wild type_seedling


title: RNAseq_70158

tag: batch

tag: current smoker

tag: pack years

tag: fev1 % predicted


title: Control [CT_2]

tag: ecotype

tag: genotype

value: Control

tag: repeat


title: 3-9-W Wild type, 20 min after formaldehyde treatment

description: counts.csv

tag: treatment


title: C3_Ctr

source_name: Ctr

tag: tissue

tag: cell type

value: wildtype

tag: age


title: 3-3-W Wild type, 20 min after formaldehyde treatment

description: counts.csv


title: 7-3-W Wild type, 180 min after formaldehyde treatment

description: counts.csv


title: RNAseq_69180

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: neutrophil percent

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent

tag: basophil percent


title: Col-0 RNA-seq [Col1]

tag: ecotype background

tag: genotype/variation


title: RNAseq_16294

tag: batch

tag: current smoker

tag: pack years

tag: fev1 % predicted


title: C3-3_Ctr

tag: genotype


title: RNAseq_94879


title: 2-3-W Wild type, 5 min after formaldehyde treatment

description: counts.csv

tag: strain

tag: treatment

tag: time

tag: biological replicate


title: 2-9-W Wild type, 5 min after formaldehyde treatment

description: counts.csv


title: RNAseq_26824

tag: age

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)


title: 8-2-W Wild type, 360 min after kanamycin treatment

description: counts.csv

value: kan


title: mDex-exo rep3

city: Shenzhen

first: Guohua

last: Lai

state: Guangdong

address: NO.1333,Xinhu Road,Baoan District

country: China

institute: Shenzhen Hospital,Southern Medical University

description:
exosomes were isolated by differential ultracentrifugation
lncRNA

data_processing:
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.5)software
The transcript abundances for each sample was estimated with StringTie（1.3.1c）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0)
The mRNA reads were aligned to reference genome using STAR(2.5.2b)detecting backesplicec junction reads with CIRCexplore2 (2.2.6)
Genome_build: hg19
Supplementary_files_format_and_content: The Fastq format file contains the sequence of reads and the sequencing quality of base.

source_name: mmature bone marrow dendritic cells

growth_protocol: the mice were sacrificed by cervical dislocation and bone marrow progenitors were washed out from long bones (femur and tibia) and cultured in EV-depleted medium (10% EV-depleted FCS final) containing 20 ng/ml granulocyte-macrophage colony-stimulating factor and 10 ng/ml IL-4 (PeproTech). Non-adherent cells were gently washed out at 48 hrs. The remaining clusters, which were loosely adherent to Petri dish, were cultured and the medium was changed every other day. On day 7, the cells were collected for treatment and they were treated with different protocols depending on different studies subsequently conducted.For exosome isolation, DCs were treated with lipopolysaccharide (LPS, 5㎍/ml) or PBS for 24h and afterwards DCs were washed twice with PBS and replaced with fresh medium. After another 48h of continuous culturing, the culture medium was collected for exosome isolation.

extract_protocol:
Exosomes were isolated by differential ultracentrifugation and kept on dry ice. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: celltype

value: bone marrow derived dendritic cells

value: untreated


title: imDex-exo rep2

source_name: immature bone marrow dendritic cells


title: imDex-exo rep3


title: mDex-exo rep2


title: 7-2-W Wild type, 180 min after kanamycin treatment

description: counts.csv


title: mDex-exo rep1


title: RNAseq_72775

tag: neutrophil percent

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent


title: C1_Ctr

tag: tissue

tag: cell type


title: RNAseq_63244

tag: batch

tag: current smoker

tag: pack years

tag: basophil percent


title: imDex-exo rep1

tag: strain

tag: treatment


title: RNAseq_55893

tag: fev1 % predicted


title: 4-2-W Wild type, 40 min after kanamycin treatment

description: counts.csv

tag: genotype

tag: time

tag: biological replicate


title: 10-3-W Wild type, 5 min after formaldehyde treatment

description: counts.csv


title: RNAseq_48407

tag: age

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)


title: 13-1-W Wild type, 360 min after mock treatment

description: counts.csv


title: RNAseq_76071

tag: neutrophil percent

tag: lymphocyte percent

tag: eosinophil percent


title: RNAseq_89857

tag: monocyte percent


title: RNAseq_07730

tag: batch


title: TK1_WGS

city: Guangzhou

first: zhiwu

last: jiang

address: 190 Kai Yuan Avenue, Science Park

institute: GIBH

library_source: genomic

data_processing:
Library strategy: WGS
Sequencing-derived raw image files were processed by BGISEQ-500  basecalling Software for base-calling with default parameters and the sequence data of each  individual is generated as paired-end reads, which is defined as "raw data" and stored in FASTQ  format.
Burrows-Wheeler Aligner  (BWA)\[1\]\[2\] software was used to do the alignment.
Best Practices for variant analysis with the Genome Analysis Toolkit(GATK,  https://www.broadinstitute.org/gatk/guide/best-practices).
The genomic variations, including SNPs and InDels were detected by the state-of-the-art  software, such as HaplotypeCaller of GATK(v3.3.0). After that, the variant quality score recalibration  (VQSR) method, which uses machine learning to identify annotation profiles of variants that are likely  to be real, was applied to get high-confident variant calls. The Copy Number Variants ( CNVs ) were  called using the CNVnator\[6\] v0.2.7 read-depth algorithm. The structural variations ( SV ) were  detected using Breakdancer\[7\]\[8\] or CREST\[9\]. Then the SnpEff tool  (http://snpeff.sourceforge.net/SnpEff_manual.html) was applied to perform a series of annotations for  variants.
Genome_build: HG19

molecule: genomic DNA

source_name: T cells

growth_protocol: cells cultured in T551 H3 (Takara, Japan) medium supplemented with 5% heat-inactivated fetal bovine serum (FBS), 1000 IU/ml recombinant human IL-2, 10 mM HEPES, 2 mM glutamine and 1% penicillin/streptomycin.

extract_protocol:
To extract genomic DNA, sorted cells were incubated in 400 μl of lysis buffer (50mM Tris with pH 8.0, 100mM NaCl, 25 mM EDTA with pH 8.0, 0.5% SDS, and 0.5 mg/ml Proteinase K) at 65 oC for 2 hrs. Genomic DNA was precipitated by adding 500 μl of isopropanol into cell lysis buffer. After centrifugation, DNA was washed once with 500 μl 70% ethanol and air dried before being re-suspended as template for PCR.
The qualified genomic DNA sample was randomly fragmented by Covaris technology and the
fragment of 350bp was obtained after fragment selection

tag: tissue

value: Cord blood

tag: cell type

value: ITNK cells


title: RNAseq_04036

tag: current smoker

tag: pack years

tag: basophil percent


title: RNAseq_73518

tag: fev1 % predicted


title: 7-1-W Wild type, 180 min after mock treatment

description: counts.csv

tag: strain

tag: genotype

tag: treatment


title: RNAseq_29486

tag: age


title: 8-1-W Wild type, 360 min after mock treatment

description: counts.csv

tag: time

tag: biological replicate


title: 12-7-W Wild type, 180 min after mock treatment

description: counts.csv


title: GAR1961: Raw264.7_DexLPS_input

city: Freising

first: Franziska

last: Greulich

address: Gregor-Mendel-Str. 2

department: Metabolic Programming

country: Germany

institute: TU München

data_processing:
Reads were aligned to the mouse mm10 (GRCm38.6) or Drosophila melanogaster dm6 (BDGP6 release 78) reference genome using BWA-MEM version 0.7.13 with default parameter settings.
PCR duplicates were removed using Picard Tools version 2.0.1.
Peaks  were  called  using  MACS2 version  2.1.1.20160309 in paired-end mode with a FDR threshold of 0.05.
Blacklisted regions (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm10-mouse/mm10.blacklist.bed.gz) were removed from the called peaks.
Peaks were annotated to the closest TSS using the ChiPpeakAnno R package v3.18.2. (doi: 10.1186/1471-2105-11-237)
Genome_build: mm10, dm6
Supplementary_files_format_and_content: The .txt files containing the annotated peak positions called with MACS2. The .bw files contain coverage data for visualization in the genome browser.

growth_protocol: Raw264.7 cells were kept at subconfluent conditions in DMEM (Gibco) supplemented with 10% FBS (heat inactivated, Sigma) and 1% penicillin/streptomycin (Gibco). Cells were cultured at 5% CO2 at 37°C in humified incubators. Medium was changed every other day.

extract_protocol: For ChIP-Seq, 40 mio cells per sample or 20 mio cells in case of H3K4me1/me2/me3 were fixed as mentioned in the sample section either for 30 min in 2 mM DSG (#C1104 ProteoChem) and 10 min 1% MeOH-free formaldehye (#2890, ThermoFisher) or 10 min 1% formaldehyde at room temperature. Remaining formaldehyde was quenched with 150 uM glycin, cells collected and washed 2x in ice-cold D-PBS. Pellets were stored at -80°C until ChIP was performed. For ChIP-Seq nuclei were extracted in Fast-IP buffer (150 mM NaCl, 5 mM EDTA (pH=7.5), 5 mM Tris (pH=7.5), 1% Triton X-100, 0.5% NP40), chromatin sonicated in shearing buffer (1% SDS, 10 uM EDTA (pH=8),50 mM Tris (pH=8)) using the Bioruptor Pico (Diagenode) for 10-15 cycles (30s on/off) at high settings. Sonicated chromatin was diluted 1:10 in dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 uM EDTA (pH= 8), 16.7 uM Tris (pH=8), 167 mM NaCl) and the immunoprecipitation against the protein of interest was performed over night at 4°C. Antigen-antibody complexes were captured with protein A/G Dynabeads (Life Techn. #11202D or #11204D), 5x washed in Fast-IP buffer. Reverse crosslink was performed overnight at 65°C and proteins degraded with 100 uM proteinase K. The DNA was puriefied using Quiagen PCR purification kit according to manufacture?s manual (#28006).

treatment_protocol: Raw264.7 cells were either treated with 1 uM dexamethason (Dex, Sigma #D4902) or 0.1% EtOH (=vehicle) for 16 h followed by 3h treatment with 100 ng/ul LPS (Sigma #L2630).

value: Balb/c

tag: Sex

value: male

tag: spike-in

value: Drosophila melanogaster

value: 16h 1uM Dex, 3h 100ng/ul LPS

tag: fixation

value: 10min 1% FA

tag: antibody


title: RNAseq_91929

tag: batch

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: neutrophil percent

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent


title: 4-1-W Wild type, 40 min after mock treatment

description: counts.csv

tag: strain

value: WT


title: 10-7-W Wild type, 20 min after mock treatment

description: counts.csv

tag: genotype


title: 10-1-W Wild type, 5 min after mock treatment

description: counts.csv

tag: treatment


title: RNAseq_10618

tag: current smoker

tag: pack years

tag: age

tag: fev1 % predicted

tag: basophil percent


title: RNAseq_28895


title: 3-7-W Wild type, 20 min after mock treatment

description: counts.csv

tag: time

tag: biological replicate


title: RNAseq_27823

tag: batch


title: 2-1-W Wild type, 5 min after mock treatment

description: counts.csv


title: RNAseq_00601

tag: gender (1=male, 2=female)


title: 3-1-W Wild type, 20 min after mock treatment

description: counts.csv


title: RNAseq_88285

tag: race (1=white, 2=black)


title: RNAseq_28726

tag: neutrophil percent


title: 1-5-W Wild type, pretreatment

description: counts.csv

value: pre


title: RNAseq_73039

tag: lymphocyte percent


title: 2-7-W Wild type, 5 min after mock treatment

description: counts.csv


title: RNAseq_59124

tag: eosinophil percent


title: 11-1-W Wild type, 40 min after mock treatment

description: counts.csv


title: RNAseq_96454

tag: monocyte percent


title: RNAseq_98241


title: 1-1-W Wild type, pretreatment

description: counts.csv

tag: strain


title: 11-2-W Wild type, 40 min after kanamycin treatment

description: counts.csv

tag: genotype


title: RNAseq_77984


title: RNAseq_31006


title: RNAseq_03186


title: RNAseq_04565


title: CNC_20_54_Lu

city: Morgantown

first: Christina

middle: M

last: Umbright

state: WV

address: 1095 Willowdale Road

department: HELD

institute: DHHS/PHS/CDC/NIOSH

description: total RNA including microRNAs

data_processing:
Basecalls were performed using bcl2fastq/2.19.
Sequence reads were trimmed for adaptor sequence low-quality using Trimmomatic/0.35 with the following parameters ILLUMINACLIP:adapters/TruSeq2-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:60
Sequences were mapped  to Rnor6.0 whole genome using Hisat2/2.1.0 with the following parameters: -q --downstream-transcriptome-assembly --dta-cufflinks --fr --no-mixed --time --met-file
Aligned sequences were identified, sorted, and counted using Samtools/1.8 and HTSeq/0.11.2
Genome_build: Rnor6.0
Supplementary_files_format_and_content: tab-delimted text file including raw counts in a matrix containing all samples

organism: Rattus norvegicus

source_name: lung

growth_protocol: This experiment was conducted in an animal facility (NIOSH, Morgantown, WV) accredited by AAALAC International following a protocol approved by the Institutional Animal Care and Use Committee (IACUC). Male Fischer (CDF®) rats (F344/DuCrl) 3 months of age were purchased from Charles River Laboratories (Wilmington, MA). Rats were housed 3 per cage and maintained on a 12-hour light-dark cycle in a temperature (68-72oF) and humidity (30-70%) controlled room with free access to filtered tap water and Teklad rodent diet (Envigo, Indianapolis, IN).

extract_protocol:
Total RNA, including miRNA and other small RNA molecules, was isolated from a piece of the lung tissue using the miRNeasy Mini Kit (Qiagen, Inc.; Valencia, CA) following the procedure provided by the manufacturer, including optional DNase treatment with RNase-Free DNase (Qiagen, Inc.; Valencia, CA).
One microgram total RNA/sample was used to create sequencing libraries using the Illumina TruSeq Stranded mRNA Library Prep Kit   (Illumina, Inc., San Diego, CA) following the  manufacturer's protocol. The samples were PCR amplified (12 cycles) to enrich the DNA fragments containing the adapter molecules and to enhance the amount of DNA in the library using a Veriti™ 96 Well Thermal Cycler (Applied Biosystems; Foster City, CA).

treatment_protocol: Exposures were performed in a whole-body inhalation chamber. Groups (n=6) were exposed to air (controls) or crystallinenanocellulose (20 mg/m3, 6 hours/day for 5 days/week for a total of 14 days of exposure).

value: Fischer 344

tag: tissue

value: lung

tag: treatment group

value: crystalline nanocellulose

tag: crystalline nanocellulose concentration (20 mg/m3)

tag: post-exposure timepoint (days)


title: RNAseq_55418

tag: current smoker

tag: pack years

tag: age

tag: fev1 % predicted


title: RNAseq_36586

tag: batch

tag: basophil percent


title: RNAseq_11459

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)


title: RNAseq_48516

tag: neutrophil percent

tag: lymphocyte percent


title: RNAseq_85867

tag: eosinophil percent

tag: monocyte percent


title: macro_Setd1bKO_DexLPS_rep3

description:
macro_wtAndSetd1bKO_DexLPSoverLPS_TPMs.txt
GAR1179

data_processing:
Gene level quantification was performed with Salmon version 0.10.2 (https://combine-lab.github.io/salmon/). Settings:  -libType A, -gcBias, -biasSpeedSamp 5
Gene count normalization and differential expression analysis was performed with DESeq2 (doi: 10.1186/s13059-014-0550-8) version 1.22.0 (R version 3.6.0) after import of gene-level estimates with tximport (doi: 10.12688/f1000research.7563.1) in R.
For gene annotation Ensembl Transcript Ids were mapped to mgi_symbol using the Bioconductor package biomaRt (  doi:10.1093/bioinformatics/bti525) version 2.38 and information from Ensembl (GRCm38.p6)
Genome_build: mm10 (GRCm38.p6)
Supplementary_files_format_and_content: .txt file containing length normalized TPMs (transcripts per million) and log2FoldChanges, adjP and p-values for Dex+LPS over LPS treatment or for IFNb+LPS over LPS treatment as indicated in the file name.

molecule: polyA RNA

source_name: bone marrow-derived macrophage

growth_protocol: Macrophages were differentiated from the bone marrow of wild-type male mice. Shortly femur and tibia were dissected from mice and the bone marrow flushed into Falcon tubes with RPMI (ThermoFisher Scientific). AKC lysis was performed to remove erythrocytes and cells seperated from tissue residues by Ficoll gradient (Ficoll-Paque Premium; GE Healthcare #17-5442-02 ). The isolated bone marrow-derived cells were differentiated in DMEM (4.5 g/l glucose, Sigma) containing 30% of supernatant from L929 cells (producing M-CSF and GM-CSF), 20% heat-inactivated FBS and 1% Pen/Strep for 7 days on non-tissue culture treated plates. The medium was changed after 3 days. After 7 days the differentiated macrophages were dissociated using Versene (ThermoFischer Scientific #15040066) at RT and seeded at 2 mio cells/6-well in serum-free conditions (macrophage-SFM medium (ThermoFisher Scientific #12065074)) for treatment and RNA isolation. Raw264.7 cells were kept at subconfluent level in DMEM (Gibco) with 10% FBS at 37°C and 5% CO2.

extract_protocol:
RNA was extracted using the Quiagen Rneasy Mini Kit (Quiagen #74106) according to manufacture's manual.The quality of the RNA was verified by Agilent 2100 Bioanalyzer with RNA 6000Nano Reagents (Agilent Technologies).
Library preparation and rRNA depletion was performed using the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to manufacture's manual. 500 ng RNA were used as input for each sample.

treatment_protocol: Differentiated macrophages were treated for 16h with 0.1% EtOH and 0.1% D-PBS (veh), 16h with 0.1% EtOH and 6h 100 ng/ul LPS (LPS) or 16h with 1 uM Dex and 6h 100 ng/ul LPS (Dex+LPS) . Raw264.7 cells were either treated for 16 h as mentioned for macrophages or treated for 6h with 0.1% EtOH and 0.1% D-PBS (veh), 6h with 0.1% EtOH and 6h 100 ng/ul LPS (LPS), 6h with 1 uM Dex and 6h 100 ng/ul LPS (Dex+LPS), 6h with 1 uM Dex (Dex) or 6h with 100 ng/ml LPS and 10 ng/ml IFNB1 (IFNb1LPS). Treatment and timing as given in the sample discription.

tag: strain

tag: treatment

value: 16h 1 uM Dex, 6h 100 ng/ml LPS

tag: genotype

tag: Sex

value: female


title: CNC_20_48_Lu

description: total RNA including microRNAs

tag: tissue

tag: treatment group

tag: crystalline nanocellulose concentration (20 mg/m3)

tag: post-exposure timepoint (days)


title: RNAseq_30901

tag: current smoker

tag: pack years

tag: age

tag: fev1 % predicted


title: CNC_20_53_Lu

description: total RNA including microRNAs


title: CNC_20_45_Lu

description: total RNA including microRNAs


title: RNAseq_80597

tag: batch

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: basophil percent


title: macro_Setd1bKO_DexLPS_rep2

description:
macro_wtAndSetd1bKO_DexLPSoverLPS_TPMs.txt
GAR1178


title: macro_Setd1bKO_DexLPS_rep1

description:
macro_wtAndSetd1bKO_DexLPSoverLPS_TPMs.txt
GAR1177


title: macro_Setd1bKO_LPS_rep3

description:
macro_wtAndSetd1bKO_DexLPSoverLPS_TPMs.txt
GAR1176

value: 16h 0.1% EtOH, 6h 100 ng/ml LPS


title: RNAseq_44519

tag: neutrophil percent

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent


title: macro_Setd1bKO_LPS_rep2

description:
macro_wtAndSetd1bKO_DexLPSoverLPS_TPMs.txt
GAR1175

tag: strain

tag: treatment

tag: genotype

tag: Sex


title: RNAseq_96112


title: CNC_20_37_Lu

description: total RNA including microRNAs

tag: tissue

tag: treatment group

value: air

tag: crystalline nanocellulose concentration (20 mg/m3)

tag: post-exposure timepoint (days)


title: RNAseq_22301

tag: current smoker

tag: pack years

tag: age

tag: fev1 % predicted


title: CNC_20_43_Lu

description: total RNA including microRNAs


title: macro_Setd1bKO_LPS_rep1

description:
macro_wtAndSetd1bKO_DexLPSoverLPS_TPMs.txt
GAR1174


title: CNC_20_36_Lu

description: total RNA including microRNAs


title: RNAseq_84061

tag: batch

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: basophil percent


title: macro_Setd1bKO_veh_rep3

description:
macro_wtAndSetd1bKO_DexLPSoverLPS_TPMs.txt
GAR1173


title: macro_Setd1bKO_veh_rep2

description:
macro_wtAndSetd1bKO_DexLPSoverLPS_TPMs.txt
GAR1172


title: macro_Setd1bKO_veh_rep1

description:
macro_wtAndSetd1bKO_DexLPSoverLPS_TPMs.txt
GAR1171


title: CNC_20_35_Lu

description: total RNA including microRNAs


title: CNC_20_33_Lu

description: total RNA including microRNAs


title: CNC_20_32_Lu

description: total RNA including microRNAs


title: RNAseq_03978

tag: neutrophil percent

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent


title: RNAseq_77979


title: CNC_20_31_Lu

description: total RNA including microRNAs

tag: strain


title: CNC_20_44_Lu

description: total RNA including microRNAs

tag: tissue


title: macro_wt_DexLPS_rep3

description:
macro_wtAndSetd1bKO_DexLPSoverLPS_TPMs.txt
GAR1170

tag: treatment

tag: genotype

tag: Sex


title: macro_wt_LPS_rep3

description:
macro_wtAndSetd1bKO_DexLPSoverLPS_TPMs.txt
GAR1167


title: RNAseq_10967

tag: current smoker


title: RNAseq_38576

tag: pack years


title: macro_wt_DexLPS_rep1

description:
macro_wtAndSetd1bKO_DexLPSoverLPS_TPMs.txt
GAR1168


title: RNAseq_23613

tag: age


title: macro_wt_DexLPS_rep2

description:
macro_wtAndSetd1bKO_DexLPSoverLPS_TPMs.txt
GAR1169


title: RNAseq_42443

tag: fev1 % predicted


title: RNAseq_46316

tag: batch


title: RNAseq_67945

tag: gender (1=male, 2=female)


title: RNAseq_49508

tag: race (1=white, 2=black)


title: RNAseq_54294

tag: basophil percent


title: macro_wt_veh_rep3

description:
macro_wtAndSetd1bKO_DexLPSoverLPS_TPMs.txt
GAR1164


title: macro_wt_LPS_rep2

description:
macro_wtAndSetd1bKO_DexLPSoverLPS_TPMs.txt
GAR1166


title: RNAseq_14195

description:
gene_TMM_counts.csv
exon_TMM_counts.csv
isoform_TMM_counts.csv

tag: neutrophil percent


title: RNAseq_50492

tag: lymphocyte percent


title: macro_wt_veh_rep2

description:
macro_wtAndSetd1bKO_DexLPSoverLPS_TPMs.txt
GAR1163


title: RNAseq_52041

tag: eosinophil percent


title: RNAseq_97440

tag: monocyte percent


title: RNAseq_87558


title: macro_wt_veh_rep1

description:
macro_wtAndSetd1bKO_DexLPSoverLPS_TPMs.txt
GAR1162

tag: strain


title: Raw_Setd1aDel_6hDex_rep3

description:
Raw264_Setd1aDelSetvsWt_mRNA_DexLPSoverLPS_6h16hmerged_TPMs.txt
MUC9710

source_name: Raw264.7 cells

value: BALB/c

value: 6h 1 uM Dex


title: Raw_Setd1aDel_6hDex_rep2

description:
Raw264_Setd1aDelSetvsWt_mRNA_DexLPSoverLPS_6h16hmerged_TPMs.txt
MUC9709


title: RNAseq_40694


title: Bulk PM

city: Toronto

first: Alyssa

last: Molinaro

state: Ontario

address: 686 Bay Street

department: Molecular Genetics

institute: University of Toronto

data_processing:
Base calls and demultiplexing was performed with Illumina bcl2fastq version 1.8.3
Trimmed reads (3' 15 bp) were aligned to the transcriptome associated with NCBI BioProject PRJNA215411 using the program Bowtie2. Raw counts were extracted from resulting SAM files.
For bulk samples, raw counts were normalized to the number of mapped reads to calculate Reads Per Million (RPM) prior to analysis. For single cell samples, raw counts were log2 normalized with a small pseudocount of +1 prior to analysis.
Genome_build: NCBI BioProject 215411, SmedASXL_transcripts_20130210.nt
Supplementary_files_format_and_content: Excel tab delimited. Raw counts.

organism: Schmidtea mediterranea

source_name: planarian whole body

growth_protocol: The clonal strain of Schmidtea mediterranea, CIW4, was grown in a milli-Q-based salt solution on beef liver.

extract_protocol:
Bulk samples were RNA extracted in Trizol reagent.
Bulk samples were library prepped using Illumina's Truseq Library kits. Single cell samples were prepped using the Smart-seq2 protocol.

treatment_protocol: Animals were dissociated by douncing in cold CMF + 1% BSA and cells were stained with Hoechst and pyrnonin Y prior to FACS.

tag: facs gate

value: PM

tag: sample type

value: bulk

value: Hoechst/pyronin Y stain & FACS

tag: tissue

value: sorted cells

value: Asexual CIW4


title: Raw_Setd1aDel_6hDexLPS_rep3

description:
Raw264_Setd1aDelSetvsWt_mRNA_DexLPSoverLPS_6h16hmerged_TPMs.txt
MUC9707

tag: treatment

value: 6h 1 uM Dex, 6h 100 ng/ml LPS

tag: genotype

tag: Sex

value: male


title: RNAseq_17089

tag: current smoker

tag: pack years

tag: age


title: RNAseq_78086

tag: batch

tag: gender (1=male, 2=female)

tag: fev1 % predicted


title: Bulk S/G2/M


title: Raw_Setd1aDel_6hDex_rep1

description:
Raw264_Setd1aDelSetvsWt_mRNA_DexLPSoverLPS_6h16hmerged_TPMs.txt
MUC9708


title: Bulk G1


title: RNAseq_23389

tag: race (1=white, 2=black)

tag: neutrophil percent

tag: basophil percent


title: Raw_Setd1aDel_6hDexLPS_rep2

description:
Raw264_Setd1aDelSetvsWt_mRNA_DexLPSoverLPS_6h16hmerged_TPMs.txt
MUC9706


title: Bulk RNA-low

value: RNA-low


title: Plantaris LRT CTRL rep4

city: Gold Coast

first: Kevin

middle: John

last: Ashton

state: QLD

address: University Drive

department: Health Sciences & Medicine

country: Australia

institute: Bond University

data_processing:
Base calls performed using Illumina Real Time Analysis v2.4.11
Low-quality reads and 3' adapters were trimmed with BBDuk and then quasi-mapped to Ensembl Rnor_6.0 release 91 (cDNA and ncRNA) using Salmon v0.9.1
Transcript reads were imported into R/Bioconductor and summarised at the gene level using the tximport package
Genome_build: rn6

source_name: Plantaris muscle

extract_protocol:
Plantaris muscle (50-80mg) were homogenized in QIAzol with steel beads in a Bullet Blender. Total RNA was harvested using the miRNeasy minikit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Unilateral ablation of the gastrocnemius and soleus muscles was performed to induce functional overload of the plantaris muscle. After 14 days the plantaris muscle was excised, weighed and snap frozen in liquid nitrogen.

tag: line

value: LRT

value: plantaris

value: 14 months

value: control (CTRL)

tag: line generation

tag: rin


title: macro_wt_LPS_rep1

description:
macro_wtAndSetd1bKO_DexLPSoverLPS_TPMs.txt
GAR1165

tag: strain

value: female


title: RNAseq_38530

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent


title: Plantaris LRT CTRL rep6

tag: Sex

tag: tissue

tag: treatment


title: Raw_Setd1aDel_6hDexLPS_rep1

description:
Raw264_Setd1aDelSetvsWt_mRNA_DexLPSoverLPS_6h16hmerged_TPMs.txt
MUC9705

tag: genotype


title: Raw_Setd1aDel_6hLPS_rep3

description:
Raw264_Setd1aDelSetvsWt_mRNA_DexLPSoverLPS_6h16hmerged_TPMs.txt
MUC9704

value: 6h 0.1% EtOH, 6h 100 ng/ml LPS


title: RNAseq_59357

tag: batch

tag: current smoker

tag: pack years

tag: age


title: RNAseq_89984

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: neutrophil percent


title: Plantaris LRT FO rep5

tag: line

value: functional overload (FO)

tag: line generation

tag: rin


title: Raw_Setd1aDel_6hveh_rep2

description:
Raw264_Setd1aDelSetvsWt_mRNA_DexLPSoverLPS_6h16hmerged_TPMs.txt
MUC9700

tag: strain

value: BALB/c


title: Plantaris LRT CTRL rep5


title: Plantaris LRT FO rep4


title: RNAseq_50749

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent

tag: basophil percent


title: Raw_Setd1aDel_6hLPS_rep2

description:
Raw264_Setd1aDelSetvsWt_mRNA_DexLPSoverLPS_6h16hmerged_TPMs.txt
MUC9703

tag: treatment

tag: genotype

tag: Sex


title: Plantaris LRT CTRL rep3

tag: tissue


title: Raw_Setd1aDel_6hveh_rep3

description:
Raw264_Setd1aDelSetvsWt_mRNA_DexLPSoverLPS_6h16hmerged_TPMs.txt
MUC9701


title: Raw_Setd1aDel_6hLPS_rep1

description:
Raw264_Setd1aDelSetvsWt_mRNA_DexLPSoverLPS_6h16hmerged_TPMs.txt
MUC9702


title: Plantaris LRT FO rep3

tag: age


title: RNAseq_96656

tag: batch

tag: current smoker

tag: pack years

tag: gender (1=male, 2=female)


title: RNAseq_25973

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: neutrophil percent


title: Plantaris LRT CTRL rep2

tag: line

tag: line generation

tag: rin


title: Raw_wt_6hDex_rep1

description:
Raw264_Setd1aDelSetvsWt_mRNA_DexLPSoverLPS_6h16hmerged_TPMs.txt
MUC9696

tag: strain

value: 6h 1 uM Dex

value: Wild-type


title: RNAseq_08866

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent

tag: basophil percent


title: Plantaris LRT FO rep1

tag: Sex

tag: tissue

tag: treatment


title: Plantaris LRT CTRL rep1

tag: age


title: RNAseq_67936

tag: batch

tag: current smoker

tag: pack years


title: Raw_Setd1aDel_6hveh_rep1

description:
Raw264_Setd1aDelSetvsWt_mRNA_DexLPSoverLPS_6h16hmerged_TPMs.txt
MUC9699

tag: genotype


title: Raw_wt_6hDexLPS_rep1

description:
Raw264_Setd1aDelSetvsWt_mRNA_DexLPSoverLPS_6h16hmerged_TPMs.txt
MUC9693


title: Raw_wt_6hDexLPS_rep2

description:
Raw264_Setd1aDelSetvsWt_mRNA_DexLPSoverLPS_6h16hmerged_TPMs.txt
MUC9694


title: Raw_wt_6hDex_rep2

description:
Raw264_Setd1aDelSetvsWt_mRNA_DexLPSoverLPS_6h16hmerged_TPMs.txt
MUC9697


title: Raw_wt_6hDex_rep3

description:
Raw264_Setd1aDelSetvsWt_mRNA_DexLPSoverLPS_6h16hmerged_TPMs.txt
MUC9698


title: Raw_wt_6hDexLPS_rep3

description:
Raw264_Setd1aDelSetvsWt_mRNA_DexLPSoverLPS_6h16hmerged_TPMs.txt
MUC9695


title: Plantaris LRT FO rep2


title: Plantaris HRT CTRL rep6

value: HRT


title: Plantaris LRT FO rep6


title: Raw_wt_6hLPS_rep3

description:
Raw264_Setd1aDelSetvsWt_mRNA_DexLPSoverLPS_6h16hmerged_TPMs.txt
MUC9692


title: RNAseq_51729

description:
gene_TMM_counts.csv
exon_TMM_counts.csv
isoform_TMM_counts.csv

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: neutrophil percent


title: RNAseq_27013


title: Plantaris HRT CTRL rep5

tag: line

tag: line generation

tag: rin


title: RNAseq_04452

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent


title: Plantaris HRT CTRL rep4

tag: Sex

tag: tissue


title: Raw_wt_6hLPS_rep2

description:
Raw264_Setd1aDelSetvsWt_mRNA_DexLPSoverLPS_6h16hmerged_TPMs.txt
MUC9691

tag: strain

tag: treatment


title: RNAseq_86565

tag: batch

tag: current smoker

tag: age

tag: basophil percent


title: Raw_wt_6hLPS_rep1

description:
Raw264_Setd1aDelSetvsWt_mRNA_DexLPSoverLPS_6h16hmerged_TPMs.txt
MUC9690

tag: genotype


title: Plantaris HRT CTRL rep3


title: Raw_wt_6hveh_rep3

description:
Raw264_Setd1aDelSetvsWt_mRNA_DexLPSoverLPS_6h16hmerged_TPMs.txt
MUC9689


title: Plantaris HRT CTRL rep2


title: RNAseq_67430

tag: pack years

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: fev1 % predicted


title: RNAseq_33984

tag: neutrophil percent


title: Raw_wt_6hveh_rep2

description:
Raw264_Setd1aDelSetvsWt_mRNA_DexLPSoverLPS_6h16hmerged_TPMs.txt
MUC9688


title: RNAseq_50692

tag: lymphocyte percent


title: RNAseq_70670

tag: eosinophil percent


title: Raw_wt_6hveh_rep1

description:
Raw264_Setd1aDelSetvsWt_mRNA_DexLPSoverLPS_6h16hmerged_TPMs.txt
MUC9687


title: RNAseq_00513

tag: monocyte percent


title: Raw_Setd1aDel_16hDexLPS_rep2

description:
Raw264_Setd1aDelSetvsWt_mRNA_DexLPSoverLPS_6h16hmerged_TPMs.txt
MUC6825

value: 16h 1 uM Dex, 6h 100 ng/ml LPS

tag: Sex


title: Plantaris HRT FO rep4

tag: line

tag: tissue

tag: line generation

tag: rin


title: Plantaris HRT FO rep6

tag: treatment


title: Raw_Setd1aDel_16hDexLPS_rep3

description:
Raw264_Setd1aDelSetvsWt_mRNA_DexLPSoverLPS_6h16hmerged_TPMs.txt
MUC6826

tag: strain


title: Plantaris HRT FO rep5

tag: age


title: RNAseq_27677

tag: batch

tag: current smoker

tag: basophil percent


title: Plantaris HRT FO rep3


title: RNAseq_04920

tag: pack years

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)


title: RNAseq_87424

tag: fev1 % predicted

tag: neutrophil percent

tag: lymphocyte percent


title: Raw_Setd1aDel_16hDexLPS_rep1

description:
Raw264_Setd1aDelSetvsWt_mRNA_DexLPSoverLPS_6h16hmerged_TPMs.txt
MUC6824

tag: genotype

tag: Sex


title: RNAseq_82405

tag: eosinophil percent

tag: monocyte percent


title: Plantaris HRT FO rep2

tag: line

tag: tissue

tag: line generation

tag: rin


title: RNAseq_16059

tag: batch

tag: age


title: RNAseq_26668

tag: current smoker

tag: basophil percent


title: Plantaris HRT FO rep1

tag: treatment


title: Raw_Setd1aDel_16hveh_rep3

description:
Raw264_Setd1aDelSetvsWt_mRNA_DexLPSoverLPS_6h16hmerged_TPMs.txt
MUC6820

tag: strain


title: RNAseq_05564

tag: pack years

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: fev1 % predicted


title: RNAseq_12347

tag: neutrophil percent

tag: lymphocyte percent


title: Plantaris HRT CTRL rep1

tag: Sex


title: Raw_Setd1aDel_16hveh_rep1

description:
Raw264_Setd1aDelSetvsWt_mRNA_DexLPSoverLPS_6h16hmerged_TPMs.txt
MUC6818

tag: genotype


title: RNAseq_40764

tag: eosinophil percent

tag: monocyte percent


title: RNAseq_21342


title: Raw_Setd1aDel_16hveh_rep2

description:
Raw264_Setd1aDelSetvsWt_mRNA_DexLPSoverLPS_6h16hmerged_TPMs.txt
MUC6819


title: RNAseq_89528


title: RNAseq_79422


title: Raw_wt_16hDexLPS_rep3

description:
Raw264_Setd1aDelSetvsWt_mRNA_DexLPSoverLPS_6h16hmerged_TPMs.txt
MUC6817


title: RNAseq_85450


title: Raw_wt_16hLPS_rep3

description:
Raw264_Setd1aDelSetvsWt_mRNA_DexLPSoverLPS_6h16hmerged_TPMs.txt
MUC6814

value: 16h 0.1% EtOH, 6h 100 ng/ml LPS


title: Raw_wt_16hDexLPS_rep2

description:
Raw264_Setd1aDelSetvsWt_mRNA_DexLPSoverLPS_6h16hmerged_TPMs.txt
MUC6816


title: Raw_Setd1aDel_16hLPS_rep3

description:
Raw264_Setd1aDelSetvsWt_mRNA_DexLPSoverLPS_6h16hmerged_TPMs.txt
MUC6823


title: Raw_wt_16hDexLPS_rep1

description:
Raw264_Setd1aDelSetvsWt_mRNA_DexLPSoverLPS_6h16hmerged_TPMs.txt
MUC6815


title: RNAseq_97622

description:
gene_TMM_counts.csv
exon_TMM_counts.csv
isoform_TMM_counts.csv


title: RNAseq_53925


title: Raw_wt_16hLPS_rep2

description:
Raw264_Setd1aDelSetvsWt_mRNA_DexLPSoverLPS_6h16hmerged_TPMs.txt
MUC6813


title: Raw_Setd1aDel_16hLPS_rep2

description:
Raw264_Setd1aDelSetvsWt_mRNA_DexLPSoverLPS_6h16hmerged_TPMs.txt
MUC6822


title: Raw_wt_16hveh_rep3

description:
Raw264_Setd1aDelSetvsWt_mRNA_DexLPSoverLPS_6h16hmerged_TPMs.txt
MUC6811


title: 281_ind7-Sham

city: Gainesville

first: Svetlana

last: Yegorova

state: FL

address: 1864 Stadium Rd

institute: University of Florida

data_processing:
NextSeq500 Instrument Sequencing Output Files created with integrated instrument computers: BASE CALL FILES, BASE CALL INDEX FILEs, CLUSTER LOCATION FILES, INTEROP FILES, RTA CONFIGURATION FILE, RUN INFORMATION FILE, HUMBNAIL FILES.
*.bcl, *.bcl.gz, and *.bcl.bgzf files were converted into FASTQ files by using bcl2fastq2 Conversion Software v2.17
RNA-seq reads were aligned to Rattus norvegicus (UCSC rn5) genome assembly by using STAR_2.5.0a aligner( App RNA Express; BaseSpace Sequence Huband TopHat 2 aligner (AppTopHat Alignment; BaseSpace Sequence Hub) .
Alignment statistics, alignment distribution, transcript coverage distribution and Reference FPKM Values (FPKM-normalized abundance info at gene level) were obtained by using AppTopHat Alignment (BaseSpace Sequence Hub).
TopHat alignment output results were used for differential expression analysis (Cufflinks Assembly & DE App; BaseSpace Sequence Hub)
Genome_build: Rattus norvegicus (UCSC rn5)
Supplementary_files_format_and_content: table csv file includes merged gene counts, number of reads mapped to each gene for each sample (App RNA Express; BaseSpace Sequence Hub)

source_name: Diaphragm

extract_protocol:
Diaphragms were isolated, snap-frozen in liquid nitrogen, stored in vapor phase liquid nitrogen, and later processed for RNA isolation. Total RNA was isolated using TRI Reagent (Sigma, USA). RNA-Seq libraries were generated using the SMARTer® Ultra Low input RNA Kit (Clontech, USA) and KAPA Hyper Library Preparation Kit Illumina platforms (Kapa Biosystems, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: We caused myocardial infarction (MI) in rat via ligation of the left anterior descending coronary artery. We shaved the left side of the thorax and cleaned the surgical area with 4% chlorhexidine and sterile saline. Thereafter, we performed orotracheal intubation and connected the animal to a mechanical ventilator. While the animal was in the surgical plane of anesthesia (2% isoflurane), we exposed the heart via a left-sided thoracotomy in the fourth or fifth intercostal space, removed the pericardium, and ligated the left anterior descending coronary artery near the left atrium using a 6-0 PGA suture. After the ligation, we hyperinflated the lungs, approximated the ribs using a 6-0 PGA suture, and closed the skin incision with 3-0 suture. Once extubated, the animals were transferred to a heated pad for recovery. Sham surgeries were similar to the MI procedure, except that we skipped the ligation of the coronary artery.

tag: tissue

value: Diaphragm

value: Sprague-Dawley

value: Sham

value: 16-weeks post-surgery


title: RNAseq_08470

tag: batch


title: 280_ind6-Sham

tag: age


title: 255_ind5-Sham


title: 288_ind8-Sham


title: Raw_wt_16hveh_rep2

description:
Raw264_Setd1aDelSetvsWt_mRNA_DexLPSoverLPS_6h16hmerged_TPMs.txt
MUC6810

value: male


title: RNAseq_34556

tag: current smoker


title: RNAseq_53787

tag: basophil percent


title: Raw_wt_16hveh_rep1

description:
Raw264_Setd1aDelSetvsWt_mRNA_DexLPSoverLPS_6h16hmerged_TPMs.txt
MUC6809

tag: treatment


title: 276_ind4-MI

tag: strain

value: Myocardial infarction (MI)


title: BMDMs_DexLPS_rep3

data_processing:
Gene level quantification was performed with Salmon version 0.10.2 (https://combine-lab.github.io/salmon/). Settings:  -libType A, -gcBias, -biasSpeedSamp 5
Gene count normalization and differential expression analysis was performed with DESeq2 (doi: 10.1186/s13059-014-0550-8) version 1.22.0 (R version 3.6.0) after import of gene-level estimates with tximport (doi: 10.12688/f1000research.7563.1) in R.
For gene annotation Ensembl Transcript Ids were mapped to mgi_symbol using the Bioconductor package biomaRt (  doi:10.1093/bioinformatics/bti525) version 2.38 and information from Ensembl (GRCm38.p6)
Genome_build: mm10 (GRCm38.p6)
Supplementary_files_format_and_content: .txt file containing lenght normalized TPMs (transcripts per million) and log2FoldChanges, adjP and p-values for DexLPS over LPS tretament

source_name: bone marrow-derived macrophages

growth_protocol: Macrophages were differentiated from the bone marrow of wild-type male mice. Shortly femur and tibia were dissected from mice and the bone marrow flushed into Falcon tubes with RPMI (ThermoFisher Scientific). AKC lysis was performed to remove erythrocytes and cells seperated from tissue residues by Ficoll gradient (Ficoll-Paque Premium; GE Healthcare #17-5442-02 ). The isolated bone marrow-derived cells were differentiated in DMEM (4.5 g/l glucose, Sigma) containing 30% of supernatant from L929 cells (producing M-CSF and GM-CSF), 20% heat-inactivated FBS and 1% Pen/Strep for 7 days on non-tissue culture treated plates. The medium was changed after 3 days. After 7 days the differentiated macrophages were dissociated using Versene (ThermoFischer Scientific #15040066) at RT and seeded at 2 mio cells/6-well in serum-free conditions (macrophage-SFM medium (ThermoFisher Scientific #12065074)) for treatment and RNA isolation.

treatment_protocol: Differentiated macrophages were treated for 16h with 0.1% EtOH and 0.1% D-PBS (veh), 16h with 0.1% EtOH and 6h 100 ng/ul LPS (LPS) or 16h with 1 uM Dex and 6h 100 ng/ul LPS (DexLPS) .

value: 16h 1 uM Dex; 6h 100 ng/ml LPS


title: RNAseq_60479

tag: pack years


title: 275_ind3-MI


title: RNAseq_74980

tag: gender (1=male, 2=female)


title: BMDMs_DexLPS_rep2


title: 256_ind2-MI


title: RNAseq_25382

tag: race (1=white, 2=black)


title: BMDMs_DexLPS_rep1


title: Raw_wt_16hLPS_rep1

description:
Raw264_Setd1aDelSetvsWt_mRNA_DexLPSoverLPS_6h16hmerged_TPMs.txt
MUC6812


title: RNAseq_89744

tag: fev1 % predicted


title: Raw_Setd1aDel_16hLPS_rep1

description:
Raw264_Setd1aDelSetvsWt_mRNA_DexLPSoverLPS_6h16hmerged_TPMs.txt
MUC6821


title: BMDMs_LPS_rep3

value: 16h 0.1percent EtOH; 6h 100 ng/ml LPS


title: BMDMs_LPS_rep2


title: RNAseq_13754

tag: neutrophil percent


title: RNAseq_75538

tag: lymphocyte percent


title: BMDMs_LPS_rep1

tag: Sex


title: BTXA5.

city: Beijing

first: Mao

last: Qianying

address: No. 22 Zhong Guan Cun South Street, Haidian District,

department: Oral and Maxillofacial Surgery

institute: Peking University School and Hospital of Stomatology

data_processing:
After sequencing, the Solexa CHASTITY quanlity filtered reads were harvested as Clean Reads. The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15nt) were left.
miRDeep2 software was used to predict the novel miRNAs with these trimmed reads. Then, the trimmed reads were aligned to merged pre-miRNA databases (known pre-miRNA from miRBase v21 plus the newly predicted pre-miRNAs) using Novoalign software (v2.07.11) with at most one mismatch. Reads (counts < 2) were discarded when calculating the miRNA expression.
In order to characterize the isomiR variability, sequences that matched the miRNA precursors in the mature miRNAs region ±4 nt (no more than 1 mismatch) were accepted as mature miRNA isomiRs, which were grouped according to the 5-prime (5p) or 3-prime (3p) arm of the precursor hairpin. The numbers of mapped tags that were defined as the raw expression levels of that miRNA. To correct for the difference in tag counts between samples, the tag counts were scaled to TPM (the copy number of transcripts per million) based on the total number of tag aligned.Choosing a different isomiR sequence for measuring miRNA expression can affect the ability to detect differential miRNA expression. We use the most abundant isomiR, the mature miRNA annotated in miRBase and all isoforms of miRNA(5p or 3p) to calculate the miRNAs expression.
When comparing the differentially expressed miRNA profiles between two groups, fold change and p-value were calculated and used to identify significant differentially expressed miRNAs (Based on ALL_Isoform value). Differentially expressed miRNAs between two samples were filtered through Fold change (Based on ALL_Isoform value).
Genome_build: MmiRBase v21

source_name: WT+BTXA injection

growth_protocol: The submandibular glands of rats are preserved at -80 degrees Celsius.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s instructions.
Total RNA of each sample was used to prepare the miRNA sequencing library, which included the following steps:1) 3'-adaptor ligation;2) 5'-adaptor ligation;3) cDNA synthesis;4) PCR amplification;5) size selection of ~135-155 bp PCR amplified fragments (corresponding to ~15-35 nt small RNAs).The libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 50 cycles on Illumina NextSeq per the manufacturer's instructions.

value: BTXA injection

value: SD

value: submandibular gland

tag: gender


title: BTXA3.


title: RNAseq_80784

tag: eosinophil percent


title: BTXA2.


title: BMDMs_veh_rep3

value: 16h 0.1percent EtOH/D-PBS


title: BTXA1.


title: Ctrl4.

source_name: WT

value: control


title: BMDMs_veh_rep1


title: RNAseq_04838

source_name: blood

tag: monocyte percent


title: RNAseq_38101


title: BMDM_DexLPS_30_input

data_processing:
Reads were aligned to the mouse mm10 reference genome using BWA-MEM version 0.7.13 with default parameter settings.
PCR duplicates were removed using Picard Tools version 1.119.
Peaks  were  called  using  MACS2 version  2.1.0 in paired-end mode with a FDR threshold of 0.05.
Blacklisted regions (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm10-mouse/mm10.blacklist.bed.gz) were removed from the called peaks.
Peaks were annotated to the closest TSS using the ChiPpeakAnno R package v3.16.0. (doi: 10.1186/1471-2105-11-237)
Genome_build: mm10
Supplementary_files_format_and_content: The .txt files containing the annotated peak positions called with MACS2 version 2.1.0. The .bw files contain coverage data for visualization in the genome browser.

growth_protocol: Macrophages were differentiated from the bone marrow of wildtype male mice. Shortly femur and tibia were dissected from mice and the bone marrow flushed into Falcon tubes with RPMI (ThermoFisher Scientific). AKC lysis was performed to remove erythrocytes and cells seperated from tissue residues by Ficoll gradient (Ficoll-Paque Premium; GE Healthcare #17-5442-02 ). The isolated bone marrow-derived cells were differentiated in DMEM (4.5 g/l glucose, Sigma) containing 30% of supernatant from L929 cells (producing M-CSF and GM-CSF), 20% heat-inactivated FBS and 1% Pen/Strep for 7 days on non-tissue culture treated plates. The medium was changed after 3 days. After 7 days the differentiated macrophages were dissociated using Versene (ThermoFischer Scientific #15040066) at RT and seeded at 20 mio cells/15-cm plate in serum-free conditions (macrophage-SFM medium (ThermoFisher Scientific #12065074)) for treatment and fixation.

extract_protocol:
For ChIP-Seq, 40 mio cells per sample were fixed as mentioned in the sample section either for 30 min in 2 mM DSG (#C1104 ProteoChem) and 10 min 1% MeOH-free formaldehye (#2890, ThermoFisher) or 10 min/15 min 1% formaldehyde at room temperature. Remaining formaldehyde was quenched with 150 uM glycins, cells collected and washed 2x in ice-cold D-PBS. Pellets were stored at -80°C until ChIP was perormed. For ChIP-Seq nuclei were extracted in Fast-IP buffer (150 mM NaCl, 5 mM EDTA (pH=7.5), 5 mM Tris (pH=7.5), 1% Triton X-100, 0.5% NP40), chromatin sonicated in shearing buffer (1% SDS, 10 uM EDTA (pH=8),50 mM Tris (pH=8)) using the Bioruptor Pico (Diagenode) for 10-15 cycles (30s on/off) at high settings. Sonicated chromatin was diluted 1:10 in dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 uM EDTA (pH= 8), 16.7 uM Tris (pH=8), 167 mM NaCl) and the immunoprecipitation against the protein of interest was performed over night at 4°C. Antigen-antibody complexes were captured with protein A/G Dynabeads (Life Techn. #11202D or #11204D), 5x washed in Fast-IP buffer. Reverse crosslink was performed overnight at 65°C and proteins degraded with 100 uM proteinase K. The DNA was puriefied using Quiagen PCR purification kit according to manufacture‘s manual (#28006).
Library preperation was performed from 2 ng of ChIP DNA using the Kapa Hyper Prep Kit with PCR library amplification (#KK8504, KapaBiosystems) according to the manufactur's protocol. Shortly, ChIP DNA was end-repaired and A-tailed before adapter ligation. After adapter ligation, the ChIP DNA was purified with Agencourt AMPure XP beads (#A63880, Beckman Coulter) and size-selected for 360-600 bp using the Pippin Prep System from Saga Science. The size-selected library is amplified by PCR using the Kapa Hyper Prep Kit (#KK8504,KapaBiosystems) and purified terminally with Agencourt AMPure XP beads (#A63880, Beckman Coulter).

treatment_protocol: Macrophages were either treated with 1 uM dexamethason (Dex, Sigma #D4902) or 0.1% EtOH (=vehicle) for 16 h followed by 3h treatment with 100 ng/ul LPS (Sigma #L2630).

tag: spike-in

value: no

value: 16h 1uM Dex, 3h 100ng/ul LPS

tag: fixation

value: 30min 2mM DSG/10min 1% FA

tag: antibody


title: Ctrl1.

tag: age

tag: tissue


title: BMDM_LPS_input

value: Drosophila melanogaster

tag: treatment

value: 16h 0.1% EtOH, 3h 100ng/ul LPS

value: 10min 1% FA


title: RNAseq_59875

tag: batch

tag: current smoker

tag: basophil percent


title: RNAseq_37067

tag: pack years

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)


title: 253_ind1-MI

value: Diaphragm

tag: strain

value: Sprague-Dawley


title: BMDM_DexLPS_10m_input

tag: Sex

value: male


title: RNAseq_35090

tag: fev1 % predicted

tag: neutrophil percent

tag: lymphocyte percent


title: RNAseq_89107

tag: eosinophil percent

tag: monocyte percent


title: HD_MALE_10

city: Milano

first: Gualtiero

middle: Ivanoe

last: Colombo

address: Via Carlo Parea, 4

country: Italy

institute: Centro Cardiologico Monzino IRCCS

description:
Counts_Matrix.txt
FPKM_matrix.txt
Filtered_and_Normalized_Counts_Matrix.txt

data_processing:
We used XSQTools (Applied Biosystems) with default parameters to remove reads with low quality base values and to generate .csfasta and .QV.qual files for each samples.
Using TopHat v2.0.11 with Bowtie 1 to handle colour space reads, we mapped all reads to the human genome version HG38/GRCh38.83 downloaded from the Ensembl database. We excluded 'haplotypes' and 'patches' sequences from the reference, in order to focus on primary assembly and to avoid under-estimation of gene expression. Finally, we filtered out reads that aligned on genes coding for globin proteins, by the 'intersectBed' function implemented in Bedtools v2.23.0.
We implemented the reference annotation based transcript (RABT) procedure, using Cufflinks suite v2.1.1 to create a new assembly for downstream analysis, integrating the information about known genes and transcripts position in the genome (Ensemble GTF release 83) with those reads mapped in intergenic or intronic regions.
We estimated genes and transcripts expression levels by Cuffquant (using default parameters, apart from -multi-read-correct -frag-bias-correct 'reference.fasta' and -mux-bundle-frags 100000000) and then Cuffnorm (with default parameters, apart from -total-hits-norm).
For each feature we computed both reads counts and fragments per kilobase of transcript per million fragments mapped (FPKM) values. We selected genes with a FPKM value ≥ 0.03 in at least 50% of samples and with a length >= 100 nt. This threshold was obtained correlating RNA-Seq data with those from a qPCR gene expression array.
Genome_build: HG38/GRCh38.83
Supplementary_files_format_and_content: Tab-delimited text files include raw counts or FPKM values for each Sample. The header of the files reports gene name, Ensemble gene ID, chromosome location, gene length, biotype, biotype class and sample identifiers.

source_name: Peripheral blood

growth_protocol: Blood samples were collected and mantained into Tempus Blood RNA tubes until processing following manufacturer's instructions.

extract_protocol:
Total RNA was isolated using the Tempus Spin RNA Isolation Kit (Applied Biosystems) and was treated with RNase-free DNase-I to eliminate genomic contamination, following the manufacturer’s instructions.
Five µg of total RNA were precipitated, α- and β-globin mRNAs were depleted with GLOBINclear Whole Blood Globin Reduction kit (Applied Biosystems), and poly(A)+ RNA was enriched following MicroPoly(A) Purist kit protocol (Applied Biosystems). Libraries were prepared and pooled together using the multiplex SOLiD System Sequencing and Barcoding kits. Complementary DNA (cDNA) amplification reaction was conducted with 20 µL template in 100 µl end-volume reaction and with 16 PCR cycles. Clonally amplification of library templates was performed on SOLiD p1 DNA beads by emulsion PCR (ePCR) using 0.5 pM library template and E120 EZbeads scale.

value: Whole blood

value: Male

tag: age (years)

tag: country of origin

value: Italy


title: HD_MALE_8

tag: tissue


title: RNAseq_23751

data_processing:
alignment: STAR, 2-pass
gene quantification: Salmon v0.12.0 and tximport
exon quantification: Rsubread v1.32.2
isoform quantification: Salmon v0.12.0
Genome_build: HG38 (GTF: Ensembl Homo_sapiens.GRCh38.94.gtf.gz)
Supplementary_files_format_and_content: count matrices

tag: age


title: HD_MALE_9


title: RNAseq_49371

tag: batch


title: HD_MALE_5


title: HD_MALE_6


title: HD_MALE_7


title: RNAseq_98692

tag: current smoker


title: Ctrl3.

tag: treatment

tag: gender


title: RNAseq_60980

tag: pack years

tag: gender (1=male, 2=female)

tag: basophil percent


title: BMDMs_veh_rep2

tag: strain

tag: Sex


title: Ctrl2.


title: HD_MALE_2


title: RNAseq_64339

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: neutrophil percent


title: HD_MALE_3


title: RNAseq_28482

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent


title: RNAseq_19684


title: HD_FEMALE_9

tag: tissue

value: Female

tag: age (years)

tag: country of origin


title: HD_MALE_1


title: RNAseq_66588

tag: batch

tag: current smoker

tag: age


title: HD_FEMALE_8


title: RNAseq_24165

tag: pack years


title: HD_FEMALE_10


title: RNAseq_20828

tag: gender (1=male, 2=female)


title: HD_MALE_4


title: HD_FEMALE_7


title: HD_FEMALE_4


title: RNAseq_11805

tag: basophil percent


title: HD_FEMALE_6


title: RNAseq_10503


title: RNAseq_09631


title: HD_FEMALE_2


title: HD_FEMALE_5


title: RNAseq_56733


title: RNAseq_02069


title: RNAseq_14724


title: RNAseq_98081


title: RNAseq_29254


title: HD_FEMALE_1


title: HD_FEMALE_3


title: N2A_GFP-2

city: Athens

first: Panagiotis

last: Politis

address: Soranou Efessiou 4

country: Greece

institute: Biomedical Research Foundation, Academy of Athens (BRFAA)

data_processing:
Mapping of sequencing reads to mm10 reference genome was performed as recommended by the manufacturer and gene differential expression analysis was performed using Bioconductor package DESeq through metaseqR pipeline. Quality control of the data was done by Multidimensional scaling analysis to confirm high correlation and reproducibility among samples replicates of each group. Using Normalised counts tables generated by DEseq, we determined differentially esxpressed genes (DEGs) by filtering the genes with p-val < 0.05 and |Log2 FC| > 0.58. Downstream bioinformatics analysis was applied for generating 1) volcano plots in R using an in-house developed script and ggplot package, 2) Functional Annotation tables with Genecodis and 3) Gene Set Enrichment Analysis (GSEA) enrichment scores.
Genome_build: mm10
Supplementary_files_format_and_content: normalized read abundance measurements calculated by Deseq are given per gene: c1:gene_id c2:gene_name c3:rpgm_normalized_counts_sample (filtered genes)
Supplementary_files_format_and_content: normalized data for all genes are available in the file DEseq_output_ALL_genes.xlsx

source_name: GFP-Tet-On Neuro2A cells

growth_protocol: Mouse neuroblastoma Neuro2A cells inducible for overexpression of Prox1-Tet-On and GFP-Tet-On were previously described [Foskolou IP, Stellas D, Rozani I, Lavigne MD, Politis PK (2013) Prox1 suppresses the proliferation of neuroblastoma cells via a dual action in p27-Kip1 and Cdc25A. Oncogene 32 (8):947-960. doi:10.1038/onc.2012.129] and were cultured in DMEM with 1gr/L glycose supplemented with 10% FBS, 2mM L-Glutamine and 1% penicillin/streptomycin. For maintenance of stable cell line selection, G418 (300 μg/mL) and Hygromycine B (200 μg/ml) were used and purchased from Calbiochem and AppliChem, respectively.

extract_protocol:
Total RNA was isolated from mouse Neuro2A Prox1 and GFP overexpression cells (GFP-Tet-On and Prox1-Tet-On Neuro2A cells) using Trizol (ThermoFisher Scientific). The quantity and quality of RNA samples were analyzed using Agilent RNA 6000 Nano kit with the bioanalyzer from Agilent.
RNA samples with RNA Integrity Number (RIN) > 7 were used for library construction using the 3′mRNA-Seq Library Prep Kit Protocol for Ion Torrent (QuantSeq-LEXOGEN™) according to manufacturer’s instructions. DNA High Sensitivity Kit was used with the bioanalyzer to assess the quantity and quality of libraries. Libraries were then pooled and templated using the Ion PI™ HiQ OT2 200 Kit (ThermoFisher Scientific) on Ion One Touch System. Sequencing was performed in BSRC ‘Alexander Fleming’ Genomics Facility using the Ion PI™ HiQ Sequencing 200 Kit and Ion Proton PI™ V2 chips (ThermoFisher Scientific) on an Ion ProtonTM System, according to the manufacturer’s instructions.

treatment_protocol: Transgene expression was turned on with Dox (1μg/mL; AppliChem).

tag: cell line

tag: cell type

value: neuroblastoma

tag: genotype

value: GFP-Tet-On


title: RNAseq_17319

extract_protocol:
Total RNA was extracted from PAXgene TM Blood RNA tubes using the Qiagen PreAnalytiX PAXgene Blood miRNA Kit (Qiagen, Valencia, CA).
Globin reduction and cDNA library preparation for total RNA was performed with the Illumina TruSeq Stranded Total RNA with Ribo-Zero Globin kit (Illumina, Inc., San Diego, CA).

tag: race (1=white, 2=black)

tag: fev1 % predicted


title: RNAseq_98360

tag: neutrophil percent

tag: lymphocyte percent


title: RNAseq_52434

tag: eosinophil percent

tag: monocyte percent


title: N2A_Prox1-1

source_name: Prox1-Tet-On Neuro2A cells


title: N2A_GFP-1


title: RNAseq_28898


title: N2A_Prox1-2


title: RNAseq_11247


title: RNAseq_44439


title: RNAseq_17492


title: RNAseq_54375


title: RNAseq_96211


title: RNAseq_72179


title: RNAseq_07209


title: RNAseq_91824


title: s15: pdgfb_ret_ret_cortex_rep4

city: Zurich

first: Annika

last: Keller

address: Frauenklinikstrasse 10

department: Department of Neurosurgery

country: Switzerland

institute: University Hospital Zürich

data_processing:
RNAseq quantification was performed with kallisto 0.44.0 with sequence-based bias correction using transcript sequences obtained from ENSEMBL (GRCm38.p6). All other parameters were set to default when running kallisto.
Kallisto's transcript-level estimates were further summarized at the gene-level using tximport 1.8.0 from Bioconductor.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: CSV table of raw estimated counts as obtained from tximport. Rows represent genes and columns represent samples.

source_name: Brain

extract_protocol:
Brain calcifications are autofluorescent (Keller et al., 2013) and we exploited this characteristic to identify calcifications under a fluorescent stereomicroscope. Calcifications were surgically isolated from the brains of Pdgfb ret/ret animals. Brain tissue from the same anatomical regions was isolated from control animals. In addition, we also isolated tissue from non-calcification prone brain region (cortex) from both Pdgfb ret/ret and control animals. RNA was isolated using RNeasy micro kit (Qiagen) according to the manufacturer’s instructions.
RNA samples were polyA-enriched and libraries were prepared using the Illumina TruSeq® Stranded RNA kit.

value: Pdgfb ret/ret

tag: brain region

value: Cortex

tag: strain

tag: animal id

value: h

tag: tissue

value: Brain


title: RNAseq_07441

tag: batch

tag: current smoker

tag: age


title: GFP-Dam_GFP-Y59C_cec4_rep3

city: Seville

last: Askjaer

address: UPO Carretera de Utrera km 1

country: Spain

institute: Centro Andaluz de Biología del Desarrollo

description:
DamID (identification of methylated GATC fragments)
processed data file:
mapped_reads_10kb_ce11.txt
mapped_reads_100kb_ce11.txt
log2_10kb_ce11.txt
log2_100kb_ce11.txt

data_processing:
Libraries corresponding to replicas 1 and 2 were sequenced multiple times; raw fastq data from the separate runs were concatenated into single files that are submitted here. Most analyses were performed in R Studio (Version 1.0.153; RStudio Team 2016) using the damid.seq.R pipeline (Sharma et al, doi:10.1002/dvg.22925; available at github.com/damidseq/RDamIDSeq). This pipeline identifies and maps specifically those NGS reads that contain the DamID adapters (adapt.seq="CGCGGCCGAG”) and corresponds to genomic fragments flanked by GATC sites (restr.seq = "GATC"). Mapping was to the C. elegans genome release WBCel235 (species = "BSgenome.Celegans.UCSC.ce11"). The pipeline provides absolute and relative read counts both per GATC fragment and per user-defined bin size. 3.3-32.3 million uniquely mapped reads were obtained from each strain. Moreover, the pipeline computes the log2 ratio between relative Dam::EMR-1 and GFP::Dam reads across all replicas.
Genome_build: ce11
Supplementary_files_format_and_content: Output from the damid.seq.R pipeline organised in txt files. Pipeline used at 2 different bin sizes: 10 kb and 100 kb. Files named "mapped reads…" contain the number of reads of the individual samples. At 10 kb bin resolution, an artificially high number of reads at chrIII (6720001-6730000) and chrV (8650001-8660000) were replaced by "1". Files named "log2…" contain the log2 ratios between relative Dam::EMR-1 and GFP::Dam reads across all replicas. At 10 kb bin resolution, 1 pseudoread was added to all bins before calculation of log2 values to avoid -Inf, Inf and NA values.

organism: Caenorhabditis elegans

growth_protocol: We used the promoter of the heat shock-inducible gene hsp-16.41, and performed the DamID experiments without induction, in order to have only trace expression levels of Dam::EMR-1. Strains expressing a nuclear GFP::Dam fusion were used as a standard control for the experiments. Plates full of mix-staged worms growing on Dam- plates were washed with M9 and collected in 15 ml tubes. Worms were pelleted by centrifugation at 500g for 2 min and washed twice before adding 2 ml of bleach solution (5 ml H2O, 2ml NaOH 5M, 3 ml bleach). Tubes were agitated until half of the worms are broken up (max. 4 min). M9 was added and released embryos were washed ten times. Finally, embryos were resuspended in M9 and let hatch overnight. ~4000 L1s per plate were seeded onto four 10cm NGM plates previously seeded with E. coli GM119 Dam- bacteria as food source. Animals were incubated for 26h at 22.5°C until L3/L4 stage. Larvae were harvested by centrifugation, washed with M9 10 times and distributed in aliquots of 30 ul. Excess liquid was removed and aliquots were snap-frozen in liquid nitrogen and stored at -80°C.

extract_protocol:
Genomic DNA (gDNA) extraction from ~30 μl L3/L4s was performed by 5 rounds of rapid freeze/thaw cycles in liquid nitrogen and 37°C water bath to break the worm cuticle followed by purification using a DNeasy Blood and Tissue Kit (QIAGEN #69504). gDNA was eluted in two rounds in a total volume of 300 μl and precipitated using 0.1x volume NaAc 3M and 2.5x volume 96% ethanol. The final concentration after resuspension in 10 μl of 10mM Tris-Cl was measured by QUBIT.
200 ng gDNA were digested using 10 units DpnI (NEB #R0176S; cuts methylated GATC) in 10 μl for 6 hours at 37°C in a thermocycler. Next, DpnI was inactivated by heating to 80°C for 20 min. Double-stranded adaptors were prepared by heating a mixture of 50 μl primer AdRt (5’-CTAATACGACTCACTATAGGGCAGCGTGGTCGCGGCCGAGGA, 100 μM) and 50 μl AdRb (5’-TCCTCGGCCGCG; 100 μM) to 95°C and cooling slowly to room temperature. Next, 0.8 μl of the double-stranded adapters were ligated to the DpnI-digested gDNA in a volume of 20 μl at 16°C in a thermocycler overnight using T4 DNA ligase (Roche #10799009001), which later was inactivated by incubation for 10 min at 65°C. The ligated gDNA was purified with 1.8x volume Agencourt AMPure XP® beads (Beckman Coulter; #A63880) using a magnetic particle concentrator, washed with 180 μl of freshly prepared 70% ethanol and eluted in 20 μl elution buffer (EB; 10 mM Tris-Cl, pH 8.5). Unmethylated GATC sites were digested with 10 units of DpnII (NEB #R0543S) in a volume of 50 μl for 1 h at 37°C. Next, DpnII was inactivated by heating to 80°C for 20 min. The digested gDNA was re-purified with AMPure XP® beads as above and eluted in 25 μl. Methylated gDNA fragments were amplified using Taq DNA polymerase with ThermoPol buffer (NEB #M0267) in 50 μl reactions containing 5 μl 10x PCR reaction buffer, 25 μl DpnII digested DNA, 1.25 μl primer AdR (5’-NNNNGTGGTCGCGGCCGAGGATC; 50 μM), 4 μl dNTP mix (each 2.5 mM), 1 μl polymerase. PCR parameters were 1) 68°C 10 min; 2) 94°C 1 min; 3) 65°C 5 min; 4) 68°C 15 min; 5) 94°C 1 min; 6) 65°C 1 min; 7) 68°C 10 min; 8) Go to step 5 and repeat three times; 9) 94°C 1 min; 10) 65°C 1 min; 11) 68°C 2 min; 12) Go to step 9 and repeat 19 times. Five μl of each PCR reaction were analyzed by agarose gel electrophoresis: successful amplification of methylated DNA was confirmed by the presence of a 400–1000 bp smear which was not observed in controls without DpnI or T4 DNA ligase. Finally, the PCR products were purified using QIAquick PCR Purification Kit (QIAGEN #28104), eluted in 30 μl EB and their concentration was measured using QUBIT. 400 ng of PCR fragments were used as input in the NEBNext Ultra DNA Library Prep Kit for Illumina (E7370). The manufacturer’s instructions were used with the following conditions. Size selection was performed by first adding 30 μl of resuspended SpeedBead Magnetic Carboxylate Modified Particles, Azide 0.05% (GE65152105050250) to the 100 μl ligation reaction. The beads were discarded and the supernatant was mixed with 60 μl resuspended SpeedBeads. Then, the supernatant was discarded and the beads were washed with ethanol and DNA was eluted in 17 μl of 10mM Tris. Eight PCR cycles were performed to amplify the samples. The quality of the samples was verified by agarose gel electrophoresis and QUBIT analysis as above.

tag: Stage

value: L3/L4 larvae

tag: genotype/variation

value: body wall muscle


title: RNAseq_53355

last: Castaldi

institute: Brigham and Women's Hospital

tag: pack years

tag: gender (1=male, 2=female)

tag: basophil percent


title: RNAseq_53509

tag: race (1=white, 2=black)

tag: fev1 % predicted


title: RNAseq_76422

tag: neutrophil percent

tag: lymphocyte percent


title: s16: pdgfb_ret_ret_thalamus_rep4

tag: genotype

value: Thalamus


title: RNAseq_14391

tag: eosinophil percent

tag: monocyte percent


title: GFP-Dam_GFP-Y59C_rep3

tag: strain


title: s12: pdgfb_ret_ret_thalamus_rep2

tag: brain region

tag: animal id

value: f

tag: tissue


title: RNAseq_12911

tag: batch

tag: current smoker

tag: age


title: s14: pdgfb_ret_ret_thalamus_rep3

value: g


title: Dam-EMR_GFP-LMN_cec4_rep3

tag: Stage

tag: genotype/variation


title: RNAseq_97590

tag: pack years

tag: gender (1=male, 2=female)

tag: basophil percent


title: s9: pdgfb_ret_ret_cortex_rep1

value: e


title: RNAseq_08392

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: neutrophil percent


title: GFP-Dam_GFP-LMN_rep3


title: s8: pdgfb_ret_wt_thalamus_rep4

tag: genotype

value: Pdgfb ret/wt

value: d


title: s13: pdgfb_ret_ret_cortex_rep3


title: RNAseq_82888

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent


title: s7: pdgfb_ret_wt_cortex_rep4

tag: brain region

tag: strain

tag: animal id


title: GFP-Dam_GFP-Y59C_cec4_rep2

tag: tissue


title: s6: pdgfb_ret_wt_thalamus_rep3

tag: age

value: c


title: Dam-EMR_GFP-Y59C_rep2

tag: Stage


title: Dam-EMR_GFP-Y59C_cec4_rep3

tag: genotype/variation


title: RNAseq_41921

tag: batch

tag: current smoker

tag: pack years


title: GFP-Dam_GFP-LMN_cec4_rep3


title: Dam-EMR_GFP-Y59C_rep3


title: s4: pdgfb_ret_wt_thalamus_rep2

value: b


title: s5: pdgfb_ret_wt_cortex_rep3


title: RNAseq_65449

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: basophil percent


title: RNAseq_29290

tag: fev1 % predicted

tag: neutrophil percent


title: RNAseq_71609

tag: lymphocyte percent

tag: eosinophil percent


title: RNAseq_75217

tag: monocyte percent


title: s10: pdgfb_ret_ret_thalamus_rep1

tag: genotype

tag: brain region

tag: strain


title: Dam-EMR_GFP-Y59C_cec4_rep2

tag: tissue


title: s3: pdgfb_ret_wt_cortex_rep2

tag: age

tag: animal id


title: s2: pdgfb_ret_wt_thalamus_rep1

value: a


title: GFP-Dam_GFP-LMN_cec4_rep2

tag: Stage

tag: genotype/variation


title: GFP-Dam_GFP-LMN_rep2


title: Dam-EMR_GFP-LMN_rep2


title: RNAseq_47050

tag: batch

tag: current smoker

tag: pack years


title: GFP-Dam_GFP-Y59C_cec4_rep1


title: RNAseq_11039

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: basophil percent


title: s1: pdgfb_ret_wt_cortex_rep1


title: RNAseq_28450

tag: fev1 % predicted

tag: neutrophil percent

tag: lymphocyte percent


title: RNAseq_14973

tag: eosinophil percent

tag: monocyte percent


title: RNAseq_21142


title: RNAseq_31247


title: RNAseq_40013


title: RNAseq_47481


title: RNAseq_78456


title: Dam-EMR_GFP-Y59C_cec4_rep1

tag: strain


title: RNAseq_86070


title: RNAseq_07923


city: MARSEILLE

first: erinn

last: soucie

address: 27 Boulevard Lei Roure

country: France

institute: CRCM

description: Tet2pp-n31-GFPpos-W31p-Input-S001256_S6_L004_R1_001

data_processing:
Sequencing quality control was done with FastQC v0.11.6.
Cleaning up raw sequencing reads were performed with sickle v.0.6.3 (-q 20 , -l 25 parameters).
Cleaned Reads were mapped with the Bowtie2 V2.3.4.1 software to the mm10 (GRCm38), with on average 37 million, 35 million,38 million aligned reads/sample for PU.1, H3K27ac, H3K4me1 respectively.
SAM files where converted to BAM files and indexed using samtools V1.7.
The peak calling was carried out using MACS version 2.1.1.20160309 software (-q 0.01 for PU.1 ChiP, --broad for H3K27ac and H3K4me1 ChIP).
BedGraph control subtracted files were obtained using bdgcmp from same version of MACS.
Finaly BedGraph files were sorted and converted to bigwig files using bedGraphToBigWig V.4 for IGV visualization purpose.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using bedGraphToBigWig V.4 for IGV visualization purpose.

source_name: Tet2+/+ KitD816V_input DNA

growth_protocol: Primary mast cells were derived from bone marrow of either Tet2+/+ or Tet2-/- C57BL/6J Tet2LacZ  mice, isolated and cultured in OptiMEM/10% FCS (Life Technologies) media supplemented with 10 ng/ml IL3 (Peprotech), 50ug/ml Penicillin/streptomycin, and 1% beta-mercaptoethanol (both Life Technologies) on tissue culture treated plastic, at 37°C, 5% CO2. Non-adherent cells were selected for 15 days under these conditions, at which point cultures were infected with lenti-virus carrying the KitD816V allele and GFP (ires). For infection, we used a single 2h spinoculation in the presence of 6μg/ml polybrene. Infected cells were further expanded for 15 days, for a total of 30 days of in vitro culture, and then GFP-negative and GFP-positive fractions (cultures were 40-80% GFP-positive) were FACS sorted on FACSAria using DIVATM (Becton- Dickinson) software. Sorted cultures were expanded for 1-2 months in growth media. Fresh media was added to all cultures 1 day before fixation for ChIp. Fixed cell pellets were snap frozen in liquid nitrogen and stored at -80 degrees celcius.

extract_protocol:
The nuclei/chromatin suspension was sonicated using a Bioruptor Pico Sonnicator (Diagenode) for 20 cycles at 4°C. Sheared chromatin size was confirmed to be between 100-800 base-pairs on average by agarose gel. Two million cell equivalents were used for each ChIP. The following antibodies were used: H3K4me1 (Abcam, ab8895), H3K27ac (Abcam, ab4729), PU.1 (Santa Cruz Biotechnology, sc-352), Erg-1/2/3 (Santa Cruz Biotechnology, sc-354) and antibodies against total Stat5 (Santa Cruz, sc-835). ChIP samples were quantified using the Qubit Fluorometric quantification System (ThermoFisher) and using a DNA high sensitivity DNA kit on a Bioanalyzer (Agilent).
ChIP-seq libraries were made using the Multiplex Library Preparation Kit (Diagenode). Nine cycles of PCR were used for all libraries. After library DNA was purified, library concentration was measured by Qubit, and size distribution was determined by Bioanalyzer. Each ChIP-seq library was sequenced for single-end reads of Illumina HiSeq 4000 (between 100-800 bp read length). Biological replicates for ChIP-seq were performed on independently derived primary mast cell cultures from 2 different mice for each sample and both sequenced.

treatment_protocol: Primary mast cells cultures were fixed by the addition of 1/10 volume of freshly made cross- linking solution (11% formaldehyde, 100mM NaCl, 1mM EDTA, 0.5 mM EGTA, 50mM Hepes pH 7.8) directly to cell medium and incubation at room temperature (RT) for 10 minutes. Formaldehyde was then quenched for 5 minutes at RT by the addition of 2.5M Glycine solution to a final concentration of 125mM. Fixed cells were washed twice with cold PBS, counted, and transferred in 50ml Falcon tubes. Cells were then pelleted by centrifugation at 700g for 5 minutes at 4°C, snap-frozen in liquid nitrogen and stored at −80°C for storage or shipment on dry-ice. Each batch of 10 million cells was lysed and processed using reagents and according to the protocol provided by the ChIP-IT High Sensitivity® (HS) Kit (Active Motif).

value: C57BL/6J Tet2LacZ

value: Tet2+/+ KitD816V

tag: cell type

value: Primary murine mast cells derived from bone marrow

tag: chip antibody

value: none (input)


description: S001254_Tet2pp_n30_GFPpos_W30p_Input-11031_R1_001


title: RNAseq_78756

city: Boston

first: Peter

address: 181 Longwood Ave

tag: age


description: Tet2pp-n31-GFPpos-W31p-Input-S001256_S6_L003_R1_001


description: Tet2pp-n31-GFPpos-W31p-Input-S001256_S6_L002_R1_001


title: RNAseq_76700


description: Tet2pp-n30-GFPneg-W30m-Input-S001253_S5_L004_R1_001

source_name: Tet2+/+_input DNA


title: Dam-EMR_GFP-LMN_rep3

tag: Stage

tag: tissue


title: RNAseq_90658

tag: batch


title: RNAseq_65869

tag: current smoker


title: RNAseq_12549

tag: pack years


description: Tet2pp-n30-GFPneg-W30m-Input-S001253_S5_L003_R1_001

tag: genotype/variation


description: Tet2pp-n30-GFPneg-W30m-Input-S001253_S5_L002_R1_001


title: RNAseq_44331

description:
gene_TMM_counts.csv
exon_TMM_counts.csv
isoform_TMM_counts.csv

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)


title: RNAseq_68095

tag: fev1 % predicted

tag: basophil percent


title: GFP-Dam_GFP-Y59C_rep1


title: RNAseq_33475

tag: neutrophil percent

tag: lymphocyte percent


description: Tet2mm-n32-GFPpos-K32p-Input-S001258_S8_L001_R1_001

source_name: Tet2-/- KitD816V_input DNA

value: Tet2-/- KitD816V


title: RNAseq_77197

tag: eosinophil percent

tag: monocyte percent


description: S001251_Tet2mm_n29_GFPneg_K29m_Input-11029_R1_001

source_name: Tet2-/-_input DNA

tag: strain

tag: cell type


title: RNAseq_64516

tag: age


title: Dam-EMR_GFP-LMN_cec4_rep1

tag: Stage


title: RNAseq_61846


title: GFP-Dam_GFP-LMN_cec4_rep1

tag: tissue


title: Dam-EMR_GFP-LMN_rep1


description: Tet2mm-n32-GFPneg-K32m-Input-S001257_S7_L002_R1_001

tag: chip antibody


title: GFP-Dam_GFP-LMN_rep1


title: RNAseq_09040

tag: batch

tag: current smoker


title: RNAseq_86640

tag: pack years


title: Dam-EMR_GFP-Y59C_rep1

tag: genotype/variation


title: RNAseq_07802

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)


title: RNAseq_65462

tag: fev1 % predicted

tag: basophil percent


title: RNAseq_39749

tag: neutrophil percent

tag: lymphocyte percent


description: S001255_Tet2pp_n31_GFPneg_W31m_Input-11032_R1_001


description: Tet2pp-n31-GFPpos-W31p-Input-S001256_S6_L001_R1_001


title: RNAseq_86917

tag: eosinophil percent

tag: monocyte percent


title: H3K27ac ChIPSeq Tet2+/+ KitD816V,Lane4,Rep1

description:
processed data file: W31p_Chip_sorted_FE.bw
Tet2pp-n31-GFPpos-W31p-Chip-S001248_S2_L004_R1_001

source_name: H3K27ac ChIPSeq Tet2+/+ KitD816V

tag: strain

tag: cell type

value: H3K27ac(Abcam, ab4729)


title: RNAseq_29307

tag: age


title: RNAseq_72511


title: H3K27ac ChIPSeq Tet2+/+ KitD816V,Lane3,Rep1

description:
processed data file: W31p_Chip_sorted_FE.bw
Tet2pp-n31-GFPpos-W31p-Chip-S001248_S2_L003_R1_001


title: H3K27ac ChIPSeq Tet2+/+ KitD816V,Lane2,Rep1

description:
processed data file: W31p_Chip_sorted_FE.bw
Tet2pp-n31-GFPpos-W31p-Chip-S001248_S2_L002_R1_001


description: Tet2pp-n30-GFPneg-W30m-Input-S001253_S5_L001_R1_001


title: RNAseq_74143


title: Dam-EMR_GFP-LMN_cec4_rep2

description:
DamID (identification of methylated GATC fragments)
processed data file:
mapped_reads_10kb_ce11.txt
mapped_reads_100kb_ce11.txt
log2_10kb_ce11.txt
log2_100kb_ce11.txt

tag: Stage

value: L3/L4 larvae

tag: tissue


title: s11: pdgfb_ret_ret_cortex_rep2

tag: genotype

value: Pdgfb ret/ret

tag: brain region

value: Cortex

tag: animal id

value: Brain


title: RNAseq_28010

tag: batch

tag: current smoker

tag: pack years


title: H3K27ac ChIPSeq Tet2+/+,Lane3,Rep1

description:
processed data file: W30m_Chip_sorted_FE.bw
Tet2pp-n30-GFPneg-W30m-Chip-S001245_S1_L003_R1_001

source_name: H3K27ac ChIPSeq Tet2+/+

tag: genotype/variation

tag: chip antibody


description: S001252_Tet2mm_n29_GFPpos_K29p_Input-11030_R1_001


description: Tet2mm-n32-GFPpos-K32p-Input-S001258_S8_L004_R1_001


description: Tet2mm-n32-GFPpos-K32p-Input-S001258_S8_L003_R1_001


title: RNAseq_62585

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: neutrophil percent

tag: basophil percent


title: RNAseq_09728

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent


title: H3K27ac ChIPSeq Tet2+/+,Lane2,Rep1

description:
processed data file: W30m_Chip_sorted_FE.bw
Tet2pp-n30-GFPneg-W30m-Chip-S001245_S1_L002_R1_001

tag: strain

tag: cell type


title: RNAseq_33011

tag: age


description: Tet2mm-n32-GFPpos-K32p-Input-S001258_S8_L002_R1_001


description: Tet2mm-n32-GFPneg-K32m-Input-S001257_S7_L004_R1_001


title: RNAseq_70712

description:
gene_TMM_counts.csv
exon_TMM_counts.csv
isoform_TMM_counts.csv


description: Tet2mm-n32-GFPneg-K32m-Input-S001257_S7_L003_R1_001


title: H3K27ac ChIPSeq Tet2-/- KitD816V,Lane2,Rep1

description:
processed data file: K32p_Chip_sorted_FE.bw
Tet2mm-n32-GFPpos-K32p-Chip-S001250_S4_L002_R1_001

source_name: H3K27ac ChIPSeq Tet2-/- KitD816V


title: RNAseq_34981


title: RNAseq_18646


title: GFP-Dam_GFP-Y59C_rep2

tag: Stage

tag: tissue

value: body wall muscle


title: Chip IgG Tet2+/+KitD816V

source_name: Chip IgG Tet2+/+KitD816V


description: Tet2mm-n32-GFPneg-K32m-Input-S001257_S7_L001_R1_001


title: Chip IgG Tet2-/-

source_name: Chip IgG Tet2-/-


title: RNAseq_18429

tag: batch

tag: current smoker


title: H3K27ac ChIPSeq Tet2+/+,Lane4,Rep1

description:
processed data file: W30m_Chip_sorted_FE.bw
Tet2pp-n30-GFPneg-W30m-Chip-S001245_S1_L004_R1_001

tag: genotype/variation


title: RNAseq_30634

tag: pack years


title: RNAseq_33613

tag: gender (1=male, 2=female)


title: RNAseq_37008

tag: race (1=white, 2=black)


title: RNAseq_21201

tag: fev1 % predicted


title: H3K27ac ChIPSeq Tet2-/-,Lane2,Rep1

description:
processed data file: K32m_Chip_sorted_FE.bw
Tet2mm-n32-GFPneg-K32m-Chip-S001249_S3_L002_R1_001

source_name: H3K27ac ChIPSeq Tet2-/-

tag: chip antibody


title: H3K27ac ChIPSeq Tet2+/+ KitD816V,Lane1,Rep1

description:
processed data file: W31p_Chip_sorted_FE.bw
Tet2pp-n31-GFPpos-W31p-Chip-S001248_S2_L001_R1_001


title: H3K27ac ChIPSeq Tet2+/+,Lane1,Rep1

description:
processed data file: W30m_Chip_sorted_FE.bw
Tet2pp-n30-GFPneg-W30m-Chip-S001245_S1_L001_R1_001


title: RNAseq_62724

tag: neutrophil percent

tag: basophil percent


title: H3K27ac ChIPSeq Tet2-/-,Lane1,Rep1

description:
processed data file: K32m_Chip_sorted_FE.bw
Tet2mm-n32-GFPneg-K32m-Chip-S001249_S3_L001_R1_001


title: RNAseq_12343

tag: lymphocyte percent

tag: eosinophil percent


title: RNAseq_66431

tag: monocyte percent


title: H3K27ac ChIPSeq Tet2-/- KitD816V,Lane4,Rep1

description:
processed data file: K32p_Chip_sorted_FE.bw
Tet2mm-n32-GFPpos-K32p-Chip-S001250_S4_L004_R1_001

tag: strain

tag: cell type


title: RNAseq_42588

tag: age


title: RNAseq_84172


title: H3K27ac ChIPSeq Tet2-/- KitD816V,Lane3,Rep1

description:
processed data file: K32p_Chip_sorted_FE.bw
Tet2mm-n32-GFPpos-K32p-Chip-S001250_S4_L003_R1_001


title: RNAseq_33830


title: H3K27ac ChIPSeq Tet2-/-,Lane4,Rep1

description:
processed data file: K32m_Chip_sorted_FE.bw
Tet2mm-n32-GFPneg-K32m-Chip-S001249_S3_L004_R1_001


title: H3K27ac ChIPSeq Tet2-/- KitD816V,Lane1,Rep1

description:
processed data file: K32p_Chip_sorted_FE.bw
Tet2mm-n32-GFPpos-K32p-Chip-S001250_S4_L001_R1_001


title: RNAseq_27981


title: RNAseq_68434


title: H3K27ac ChIPSeq Tet2-/-,Lane3,Rep1

description:
processed data file: K32m_Chip_sorted_FE.bw
Tet2mm-n32-GFPneg-K32m-Chip-S001249_S3_L003_R1_001


title: RNAseq_44634


title: RNAseq_65943


title: RNAseq_87960


title: RNAseq_33631


title: RNAseq_10710


title: RNAseq_27491


title: RNAseq_51437


title: RNAseq_39529


title: RNAseq_51632


title: RNAseq_29933


title: RNAseq_05988


title: RNAseq_01802


title: RNAseq_84863


title: RNAseq_46661


title: RNAseq_82493


title: RNAseq_94153


title: RNAseq_29161


title: RNAseq_34710


title: RNAseq_73340


title: RNAseq_53335


title: RNAseq_33225


title: RNAseq_04441


title: RNAseq_76495


title: RNAseq_71865


title: RNAseq_99974


title: RNAseq_00813


title: RNAseq_46385


title: RNAseq_03485


title: Cut and Run  profiling using control IgG of OSCs with control knockdown and transfection of control plasmid

city: Vienna

first: Jakob

last: Schnabl

state: Vienna

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA - Institute of Molecular Biotechnology

data_processing:
Library strategy: CUT&RUN
reads were trimmed by removal of the adaptor sequences and to a length of 6-50 bases
reads were mapped to Drosophila melanogaster genome
Genome_build: dm6
Supplementary_files_format_and_content: all mapping and unique mapping bigwig files for sense and antisense

organism: Drosophila melanogaster

source_name: OSCs

growth_protocol: OSCs were grown at 27º C, 2.5% CO2

extract_protocol:
Cut and Run protocol V3
NEBNext Ultra II DNA Library Prep Kit
HiSeqV4

treatment_protocol: siRNA transfection + indicated plasmid transfection

value: Ovarian Somatic Cells (OSCs)

tag: knock-out or depletion

value: control depletion

tag: treatment

tag: antibody

value: Mouse IgG control antigbody (CST Cat #2729S)


title: RNAseq_60880

tag: batch

tag: current smoker


title: RNAseq_00955

tag: pack years

tag: gender (1=male, 2=female)


title: RNAseq_46642

tag: race (1=white, 2=black)

tag: fev1 % predicted


title: RNAseq_01520

tag: neutrophil percent


title: Cut and Run H3K9me3 profiling of OSCs with panx knockdown and transfection of Panx[dLC8-mut] plasmid replicate 1

value: panx depletion

value: anti-H3K9me3 antibody produced in rabbit (Active Motif Cat# 39161)


title: RNAseq_31179

tag: basophil percent


title: Cut and Run H3K9me3 profiling of OSCs with panx knockdown and transfection of Panx[dLC8-mut] plasmid replicate 2


title: Cut and Run H3K9me3 profiling of OSCs with panx knockdown and transfection of Panx[wildtype] plasmid replicate 2


title: RNAseq_70050

tag: lymphocyte percent


title: Sample M4D1 from D. melanogaster strain MUN-008 (aka MUN24) (Resistant to Copper stress) under Treated conditions

city: Barcelona

first: Gabriel

middle: Eduardo

last: Rech

address: Passeig Marítim de la Barceloneta 37-49

institute: Consejo Superior de Investigaciones Cientificas - Institute of Evolutionary Biology (CSIC-UPF)

description:
M4D1
Drosophila melanogaster strain MUN-008 (also knows as MUN24)

data_processing:
RNA-seq analysis was performed using the rnaseq pipeline (v1.2) from the nf-core community, a nextflow collection of curated bioinformatic pipelines (Di Tommaso et al. 2017; Ewels et al. 2020).
Briefly, sequencing quality was assessed using FastQC (v.0.11.8) (www.bioinformatics.babraham.ac.uk/projects/fastqc). TrimGalore (v.0.5.0) (www.bioinformatics.babraham.ac.uk/projects/trim_galore) was used for adapter removal and Cutadapt (v. 1.18) with default parameters was used for low-quality trimming (Martin 2011). Trimmed reads were mapped to the D. melanogaster genome r6.15 using STAR (v.2.6) (Dobin et al. 2012).
Technical duplications were explored using dupRadar (Sayols et al. 2016). Overall, we found no bias towards high number of duplicates at low read counts, so we did not remove duplicates from the alignments.
We used featureCounts (v.1.6.2) (Liao et al. 2014) for counting the number of reads mapping to genes (reverse-stranded parameter). Gene annotation r6.15.
Genome_build: dm6 (Release 6 plus ISO1 MT)
Supplementary_files_format_and_content: extra_and_finalnfcoreResultsSTAR_merged_gene_countsFinal_RMmales.txt: Tab-delimited text file includes RAW COUNTS reads for each sample.

source_name: whole body

growth_protocol: Flies were collected in 2015 from different European locations by members of the DrosEU consortium. Flies were inbred for 20 generations. Fly stocks were kept at 25 °C and 65% relative humidity with 12h day and night cycles.

extract_protocol:
RNA was extracted using GenElute™ Mammalian Total RNA Miniprep Kit from 20 whole female flies. RNA samples were treated with DNase I (Thermo Fisher Scientific) following manufacturer’s instructions. RNA concentration was checked with NanoDrop spectrophotometer (NanoDrop Technologies) and quality was assessed with Bioanalyzer.
1.5 µg of total RNA from each sample was used for library preparation and sequencing. Library preparation was performed using the TruSeq Stranded mRNA Sample Prep kit from Illumina following the manufacturer's instructions. Libraries were sequenced using Illumina 125 bp paired-end reads, obtaining between 27 and 41 million reads/sample.

treatment_protocol: Powdered Copper Sulphate (CuSO4) was reconstituted in a 5% sucrose solution. Food dye was added to aid visibility and even dispersal. An identical control solution without CuSO4 was prepared in the same manner. 250μl of the CuSO4 sucrose solution was pipetted onto 70x17mm slips of filter paper, which were then placed into 15ml Falcon tubes (manufacturer, CAT#), containing one ml on 1% agar at the bottom. Papers were allowed to dry for 15 minutes, after which the flies were added. Holes were made in the lids of the falcon tubes before they were re-affixed, to assist respiration. As Drosophila are known to show avoid food with a high concentration of heavy metals (Burke, the parkinsons group. Our prelim data) this assay also allows exposure to copper via contact.

tag: Sex

value: Female

tag: tissue

value: Whole body

tag: copper stress phenotype

value: Resistant

value: Copper treated


title: RNAseq_07134

source_name: blood

tag: eosinophil percent

tag: monocyte percent


title: Cut and Run H3K9me3 profiling of OSCs with panx knockdown and transfection of Panx[wildtype] plasmid replicate 1

tag: cell type

tag: knock-out or depletion


title: RNAseq_66901

tag: age


title: RNAseq_29071

tag: batch


title: Sample M4D4 from D. melanogaster strain MUN-008 (aka MUN24) (Resistant to Copper stress) under Treated conditions

description:
M4D4
Drosophila melanogaster strain MUN-008 (also knows as MUN24)

tag: strain

tag: treatment


title: Cut and Run H3K9me3 profiling of OSCs with control knockdown and transfection of control plasmid replicate 2

tag: antibody


title: Cut and Run H3K9me3 profiling of OSCs with control knockdown and transfection of control plasmid replicate 1


title: RNAseq_36890

tag: current smoker

tag: pack years

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)


title: Cut and Run H3K9me3 profiling of OSCs with panx knockdown and transfection of control plasmid replicate 2


title: RNAseq_27252

tag: fev1 % predicted

tag: neutrophil percent

tag: lymphocyte percent

tag: basophil percent


title: RNAseq_99006

tag: eosinophil percent


title: RNAseq_76747

tag: monocyte percent