title: HLU 8

city: Boston

first: Frank

last: Ko

address: 330 Brooline Ave RN120

institute: Beth Israel Deaconess Medical Center

data_processing:
Samples were multiplexed (n = 8 per lane) for sequencing on a HiSeq (Illumina) platform and reads were aligned to reference genome (Tophat2). Differential gene expression was analyzed by DESeq2 and relevant biological processes associated with differentially expressed genes were analyzed by Gene Set Enrichment Analysis according to studies by Subramanian et al.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: cortical bone

extract_protocol:
After cutting the ends of bones and flushing marrow with PBS, the cortical bone was placed in an Eppendorf tube and immediately snap-frozen in liquid nitrogen.  Subsequently, Trizol was added while the bone is maintained frozen in an eppendorf tube placed in a liquid nitrogen bath, homogenized in the same eppendorf tube with the Fastprep24 machine (MP Biomdicals), and subsequently total RNA was isolated and purified using manufacture recommendations for the PureLink RNA kit (Life Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: female

value: cortical bone


title: HLU 7

status: Public on Mar 23 2021

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: Sex

tag: tissue


title: HLU 6


title: control_2011_Rep1

city: Fargo

first: David

last: Horvath

state: ND

address: 1605 Albrecht Blvd

department: Agr. Research Service

institute: US Dept. Agriculture

data_processing:
Raw sequence reads were checked for quality using the FastQC0.10.0 program and quality trimmed using the Sickle-quality-base-triming program in the iPlant discovery environment with the parameters minimum quality = 20 and minimum number of bases = 70.
The Tuxedo Suite (Tophat 1.0, Cufflinks 1.0 and Cuffdiff 1.0 for Single End reads) were used to map the quality trimmed sequences to the Glycine Max genome (Phytozome 9.0) in the iPlant archive (for only the first paired end reads since the quality of the second end was significantly less good).
The resulting FPKM values from the Cufflinks output files (genes.fpkm_tracking) were placed in a single file and those that matched known soybean gene models were kept.
FPKM values were log transformed (for use in follow-on programs to assess biological relevance).
Genome_build: Glycine Max genome (Phytozome 9.0)
Supplementary_files_format_and_content: Data table containing gene model, Protien name as indicated by most similar arabidopsis annotation, Most similar arabidopsis gene model name based on Phytozome 9.0 gene model annotation, Log2 transformed FPKM (fragments per kilobase per million reads) vales for indicated library, Average log ratio of the expression (weedy minus control) for the indicated year, P value as generated by CuffDiff program for weedy verses control from the two samples collected from indicated year Q value as generated by CuffDiff program for weedy verses control from the two samples collected from indicated year, and Functional annotation assigned to the gene model based on the Phytozome 9.0 database.

organism: Glycine max

source_name: Newly emerged unfolded trifoliate less than 2 cm in length from at least 8 plants per plot

growth_protocol: Soybean were grown to the V3 stage in field conditions near Brookings SDl. Soil consistes of loess over glacial outwash, and the soil series is Brandt silty clay loam.

extract_protocol:
RNA extraction was performed by grinding approximately 0.1 grams of frozen tissue in liquid nitrogen to a fine powder, and adding 1 ml Trizol reagent (Ambion/Life Technologies). Chloroform:Isoamyl (24:1) was added to the Trizol/tissue mixture, centrifuged, and RNA was extracted from the resulting supernatant using an RNeasy Plant Mini kit (Qiagen). Quality control was assessed using a nanodrop bioanalyzer on the RNA setting.
cDNA libraries were created following the Illumina TruSeq RNA Sample Preparation kit (Illumina). In short, 4000 ng of RNA was purified and fragmented into mRNA, followed by first and second strand cDNA synthesis. End repair and adenylation of 3’ ends preceded adapter ligation and PCR amplification. Library quality was assessed using an Agilent Bioanalyzer, and quantified for pooling by qRT-PCR using the PhiX Control Kit v2 according to manufacturer specifications. Libraries were paired-end sequenced on an Illumina HiSeq2000.

treatment_protocol: plants were either grown with various weeds (see "Weedy" treatment conditions in metaflie) or under weed free conditions (see "Control" conditions in metafile)

tag: cultivar

tag: treatment

value: "Control" with weeds controlled by application of Roundup Weather Max (glyphosate), Dual II Magnum (s-metolachlor), Poast (sethoxydim), and Pursuit (imazethapyr) were used at suggested rates and times.

tag: cummulative precipitation at sampling

tag: temperature at sampling

tag: r1.fastq spacing

value: R1.fastq (76 cm)

tag: sampling date


title: B19_084

city: Irvine

first: Zeba

middle: A

last: Wunderlich

state: CA

address: 4432 Natural Science II

department: Developmental and Cell Bio

institute: University of California Irvine

data_processing:
trimming and filtering: trimmomatic 0.35 with the following settings ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:6 SLIDINGWINDOW:4:15 MINLEN:30
Pseudoaligning and quantifying: Reads were Pseudo aligned tp the Iso1 DM6 transcriptome  using Salmon Aligner 0.12.0 using the quant functionality to generate Count data with the settings:  -l A --validateMappings
Assigning alleles
Aligning and quantifying allelic reads :Alleleic Reads were Pseudo aligned to either the A4 or the B6 transcriptome using Salmon Aligner 0.12.0 using the quant functionality to generate count data , with the settings:  -l A --validateMappings
Gene Summaries: Transcript level count  data was summarized to gene-level In R, using Tximport 1.12.3. These count data for all samples alligned to ISO-1, and parsed allelic reads aligned  to either A4 or B6, and  unparsed Reads aligned to either A4 or B6 where combined into a single DataMatrix in R.
Genome_build: dm6, Dmel_A4_1.0, ASM339711v2
Supplementary_files_format_and_content: Count matrix with rows of gene names and columns of samples either aligned to Iso 1, or allele-called reads alligned to the appropriate Genome with "g1" designating A4 alignment and "g2" representing B6, sample names with neither the "iso1", "g1" or "g2" indicators are unparsed homozygous samples aligned to thier corresponding genome (see meta data)

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: Fat body

growth_protocol: 25˚C on standard yeast-cornmeal fly food

extract_protocol:
Samples where brought to room temperature for 5 minutes and then homogenized, centrifuged for 10 minutes at 4˚C and supernatant mixed with equal parts 100% ethanol. mRNA was then purified from Trizol reagent using Zymo dirct-zol RNA extraction protocol.
Libraries where prepared using the modified SmartSeq2 protocol outlined in "Adapting trhe SmartSeq2 Protocol for Robust Single Worm RNA-seq". Libraries were then barcoded using Illumina/Nextera i5 common adapterand i7 index adapters

treatment_protocol: Microinjection of ~10000 CFUs of bacteria. dissection of fat body 3 hours post infection, (with three fat bodies collected per sample) and store in trizol and stored at -80˚C for extraction

value: Serratia marcescens infection

tag: paternal genotype

tag: maternal genotype

tag: extraction batch

tag: generation


title: B18_236


title: CL_39

city: Philadelphia

first: Camila

last: Farias Amorim

state: United States

address: 380 S University Ave

department: Pathobiology

institute: University of Pennsylvania

description: cutaneous

data_processing:
Raw reads from fastq files were mapped to the human reference transcriptome (Ensembl; Homo sapiens version 86) using Kallisto, version 0.44.0
All subsequent analyses were carried out using the statistical computing environment, R version 3.5.1 in RStudio version 1.1.456 and Bioconductor, version 3.8
Transcript-level counts and abundance data were imported into R and summarized to gene level using the TxImport package
Data was normalized using the TMM method in EdgeR
Normalized data was variance stabilized using the VOOM function in limma
Differentially expressed genes (FC>2 and FDR<.01) were identified on filtered-normalized, not batch-corrected gene expression matrix by linear modeling and Bayesian statistics using the Limma package, using the batch as factor for interception.
Genome_build: Ensembl; Homo sapiens version 86, GRCh38 Release 97
Supplementary_files_format_and_content: raw data file format and content: Tab-delimited text raw data includes raw gene counts summarized by tximport package
Supplementary_files_format_and_content: normalized data file format and content: Tab-delimited text filtered normalized data includes gene expression for each sample after normalization with EdgeR package (TMM method) and batch correction with Combat() function from the sva R package
Supplementary_files_format_and_content: study design: Comma-separated values file with study design including healthy subjects and cutaneous leishmaniasis patients clinical metadata

organism: Homo sapiens

source_name: cutaneous

growth_protocol: Before treatment, 3 ml of peripheral blood was collected from CL patients and 14 endemic non-L. braziliensis infected controls (healthy subjects, HS) in Corte de Pedra, Bahia, Brazil, and were stored in Tempus Tubes (Applied Biosystems) at -20oC

extract_protocol:
Frozen blood samples were shipped to the University of Pennsylvania, where RNA extraction, cDNA library preparation, and RNA sequencing were performed.  RNA was extracted using the Tempus Spin RNA Isolation Reagent Kit (Applied Biosystems)
Whole-transcriptome sequencing libraries were prepared with the TruSeq Stranded Total RNA with Ribo-Zero Globin (Illumina) and sequenced on an Illumina NextSeq 500 to produce 75 bp paired-end reads
RNA quality and quantification were assessed using a Tapestation 4200 (Agilent) and Qubit 3 (Invitrogen)

tag: age

value: M

value: Cure

value: neg

value: no

tag: dth


title: control day2 shoot replicate 3

type: RNA

city: Tsukuba

first: Yoshiki

last: Habu

state: Ibaraki

address: Kannondai 2-1-2

department: Institute of Agrobiological Sciences

country: Japan

institute: National Agriculture and Food Research Organization

description: Biological replicate 3 of 3. Control seedling shoot, harvested after 2 days.

hyb_protocol: Agilent protocol G4140-90050. 825 ng of each Cy-3- and Cy-5-labeled cRNAs were used for hybridization.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.11.5.1.1).

data_processing: Agilent Feature Extraction Software (v 11.5.1.1) was used for background subtraction.

organism: Oryza sativa

source_name: rice mock-treated seedling shoot day 2

label_protocol: 400 ng RNAs were labeled by Low RNA input Linear Amplification/Labeling Kit (Agilent).

growth_protocol: Rice seedlings were grown on soil in prastic pot (6 cm x 6 cm x 6 cm) at 30C under 14 hours light/10 hours dark light cycle for 2 weeks.

extract_protocol: Total RNA samples were prepared with RNeasy Plant Mini Kit (QIAGEN).

treatment_protocol: Pots containing two-weeks old seedlins were drained and soaked in 30 mM acetic acid, potassium acetate, or control water. Plants were grown for further 2 or 4 days.

value: shoot

value: mock-treated day 2

value: Nipponbare

value: 2 weeks

source_name: rice reference non-treated seedling shoot

value: untreated


title: CL_38

description: cutaneous

value: F

value: Failure


title: control day2 shoot replicate 2

description: Biological replicate 2 of 3. Control seedling shoot, harvested after 2 days.


title: HLU 5


title: control_2010_Rep1

value: "Control" with weeds controlled by application of Glyphosate was used at 1.2 L ha-3


title: CL_37

description: cutaneous


title: B18_235


title: HLU 4

value: female


title: CL_47

description: cutaneous


title: control_2009_Rep1

value: "Control" with weeds controlled by application of Poast (sethoxydim) (1.8 L ha-1) on June 26


title: HLU 3

value: cortical bone


title: CL_35

description: cutaneous


title: control_2010_Rep2

value: "Control" with weeds controlled by application of Glyphosate was used at 1.2 L ha-1

value: R1.fastq (18 cm)


title: CL_40

description: cutaneous

value: M


title: B18_205

value: Serratia marcescens infection


title: B18_234


title: HLU 2


title: B19_073


title: CL_34

description: cutaneous

value: neg


title: HLU 1


title: CL_33

description: cutaneous

value: Cure

value: no


title: CL_36

description: cutaneous


title: B18_220


title: control day2 shoot replicate 1

description: Biological replicate 1 of 3. Control seedling shoot, harvested after 2 days.

value: shoot

value: mock-treated day 2


title: Control 8


title: Control 7


title: Control 6


title: B18_203


title: CL_30

description: cutaneous


title: Vero E6 + SARS-CoV-2-S pseudovirions

city: Guangzhou

first: Fei

last: Li

address: Xingang West Road

department: School of Life Science

country: China

institute: Sun Yat-sen university

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Tophat2 tools soft were used to map with reference genome.
Gene function was annotated based on the following databases:Nr (NCBI non-redundant protein sequences)；Nt (NCBI non-redundant nucleotide sequences)；Pfam (Protein family)；KOG/COG (Clusters of Orthologous Groups of proteins)；Swiss-Prot (A manually annotated and reviewed protein sequence database)；KO (KEGG Ortholog database)；GO (Gene Ontology).
Picard - tools v1.41 and samtools v0.1.18 were used to sort, remove duplicated reads and merge the bam alignment results of each sample. GATK2 or Samtools software was used to perform SNP calling. Raw vcffiles were filtered with GATK standard filter method and other parameters ( clusterWindowSize: 10; MQ0 >= 4 and (MQ0/(1.0*DP)) > 0.1; QUAL < 10; QUAL < 30.0 or QD < 5.0 or HRun > 5), and only SNPs with distance > 5 were retained.
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.Quantification of gene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.
Genome_build: human NCBI genome build 36
Supplementary_files_format_and_content: LIST file includes FPKM values for each Sample

organism: Chlorocebus sabaeus

source_name: African green monkey kidney cells

growth_protocol: HEK293T-hACE2 and Vero E6 cells were treated Mock or SARS-CoV-2-S pseudovirions and cultured in 10%FBS BMEM medium

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen, Part#15596206) according to the manufacturer’s instructions.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase（RNase H-）. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H . Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 240 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: HEK293T-hACE2 and Vero E6 cells were treated Mock or SARS-CoV-2-S pseudovirions for 48h.

value: renal epithelial cells

value: SARS-CoV-2-S pseudovirions


title: B19_089

value: Entrerococcus faeicalis infection


title: CL_29

description: cutaneous


title: Vero E6 + Mock

value: mock


title: CL_28

description: cutaneous

value: F


title: Control 5

value: female


title: Control 3


title: control_2008_Rep1

value: "Control" with weeds controlled by application of Dual II Magnum (S-metolachlor) (1.9 L ha-1) on May 22

value: R1.fastq (76 cm)


title: B19_079


title: B18_226


title: HCT116, DUSP4 siRNA #2

city: Yufu

first: Naoki

last: Hijiya

state: Oita

address: 1-1, Idaigaoka Hasama-machi

department: Medicine

institute: Oita University

description: Cultured in accordance with the supplier's instructions. Total RNA for expression analysis was extracted using an RNeasy Mini kit (Qiagen).

hyb_protocol: Gene Expression Hybridization kit was used for hybridization in accordance with the manufacture's instructions (Agilent Technologies).

scan_protocol: Microarray images were obtained by using a laser confocal scanner G2565BA (Agilent Technologies).

data_processing:
Feature Extraction software (Version 9.1, Agilent Technologies) with the manufacturer’s recommended settings was applied for the microarray image analysis. Analysis of the microarray images was performed with Genespring 7.3.1 Software (Agilent Technologies).
The signal intensities of probe set data were median-normalized per chip, followed by filtering based on signal intensity and flagged values.The genes regulated by DUSP4 were identified using following filters: for 419 upregulated genes, (DUSP4 siRNA#1 ≥ 500, DUSP4 siRNA#1/control siRNA ≥ 1.6) and (DUSP4 siRNA#2 ≥ 500, DUSP4 siRNA#2/control siRNA ≥ 1.6), for 291 downregulated genes, (control siRNA ≥ 500, DUSP4 siRNA#1/control siRNA  ≤ 0.625) and  (control siRNA ≥ 500, DUSP4 siRNA#2/control siRNA  ≤ 0.625).

source_name: Colorectal cancer cell line

label_protocol: Cy3-labeled cRNA targets were generated using Quick Amp Labeling Kit, one-color (Agilent Technologies).

growth_protocol: All cell lines were cultured in accordance with the supplier's instructions.

tag: cell line

value: Colorectal cancer cell line HCT116

value: DUSP4 siRNA#2

tag: genotype

value: DUSP4 knockdown


title: Control 4

tag: strain

value: cortical bone


title: CL_27

description: cutaneous

tag: Sex

value: M

value: Failure

value: neg


title: B19_077


title: HCT116, no siRNA

extract_protocol: Total RNA for expression analysis was extracted using an RNeasy Mini kit (Qiagen).

value: no siRNA

value: control


title: Control 2

tag: tissue


title: B19_096


title: CL_26

description: cutaneous

value: Cure

value: no


title: HCT116, DUSP4 siRNA #1

value: DUSP4 siRNA#1


title: HCT116, control siRNA

value: control siRNA


title: B19_088

value: Entrerococcus faeicalis infection


title: CL_31

description: cutaneous


title: CL_32

description: cutaneous


title: B19_094


title: T9232

city: Houston

first: Yue

last: Lu

state: TX

address: 1881 East Road

department: Epigenetics & Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Illumina Casava software (version 1.8.2) was used for basecalling.
The reads were mapped to the mouse genome (mm9) using TopHat (V2.0.3).
The number of fragments in each known gene from RefSeq database (downloaded from UCSC Genome Browser on March 9, 2012) was enumerated using htseq-count from the HTSeq package (V0.5.3p9).
Genes with less than 10 fragments in all the samples were removed, and then the cpm (count per million fragments) value for each gene was calculated by R/Bioconductor package edgeR (V3.6.1).
Genome_build: mm9
Supplementary_files_format_and_content: The first column is gene symbol. The other columns are cpm values (estimated by edgeR) for all the samples.

source_name: mammay gland

growth_protocol: Transgenic female BK5.ATF3 mice were bred and raised in an A AALAC-accredited facility on standard lab chow.

extract_protocol:
Total RNA was extracted using Trizol following manufacturer's instructions.
Ovation RNA-Seq System V2 from NuGEN Technologies, Inc. was used to prepare RNA-Seq libraries following manufacturer's instructions.

treatment_protocol: Females were allowed to breed and raise one litter of pups. Mammary tumors arose in most transgenic mice between 6 months and 12 months of age. When tumors reached 1.5 cm in length, animals were sacrificed under CO2 and the tumor was quickly dissected. Adjacent normal mammary glands were obtained from each tumor-bearing mouse.

value: mammary gland

value: ATF3 transgenic

tag: tissue type

value: mammary tumor


title: CL_24

description: cutaneous


title: B19_076

tag: treatment


title: T11035


title: CL_23

description: cutaneous


title: M9232

source_name: mammary gland

value: normal mammary gland


title: CL_21

description: early

value: pos

value: yes

value: cutaneous


title: M11640


title: CL_20

description: cutaneous

value: M


title: M11035


title: Control 1

value: female

value: cortical bone


title: B19_081


title: B19_090


title: CL_18

description: cutaneous

value: neg


title: CL_17

description: cutaneous


title: CL_19

description: cutaneous


title: B19_095


title: B19_080


title: Otx1_mm10_E9.5_4C-seq

city: Berlin

first: Rafael

middle: Domínguez

last: Acemel

state: Berlin

address: Hannoversche Str. 28

department: Berlin Institute of Medical Systems Biology (BIMSB)

country: Germany

institute: Max Delbrück Center for Molecular Medicine (MDC)

description: 4C-seq experiments performed using as bait the specified promoter

library_source: genomic

data_processing:
Library strategy: 4C-seq
Demultiplexing: Different samples were demultiplexed using the primer sequences
Mapping: Reads were mapped to the Branchiostoma lanceolatum (Bl71nemr assembly), Mus musculus (mm10 assembly) or Danio rerio (danRer7 assembly) genomes using Bowtie software (http://bowtie-bio.sourceforge.net). Only uniquely mapped reads were kept.
Filtering: Only those reads that mapped withing fragments with a DpnII at one end and a Csp6I at the other end were kept.
Data visualization: Data were uploaded to UCSC Browser for visualization.
Genome_build: danRer7/mm10/Bl71nemr(http://amphiencode.github.io/Data/)
Supplementary_files_format_and_content: BEDGRAPH

molecule: genomic DNA

source_name: E9.5 mouse embryos

growth_protocol: CBA/Ca×C57Bl/10 crosses. Embryos taken at 9.5dpc, taking the day in which the plug was found as 0.5dpc.

extract_protocol:
Chromatin was extracted from single cells preparations from different samples. DNA was digested with DpnII and ligated. Then sample was de-crosslinked, digested with Csp6I and ligated again.
Primers with Illumina adaptors were used to amplify the library. Different samples were multiplexed for sequencing.

tag: 4c-seq bait

value: Otx1 promoter

value: whole embryos

tag: Stage


title: Isl2_mm10_E9.5_4C-seq

value: Isl2 promoter


title: B19_091


title: B19_097


title: CL_22

description: cutaneous

value: no


title: T11640


title: CL_15

description: cutaneous

value: Failure


title: KD_aff1_2

city: Nanjing

first: Xiaoxu

last: Liu

state: Jiangsu

address: 2 Sipailou

department: Institute of Life Sciences

institute: Southeast University

data_processing:
The clean reads were subjected to TopHat and Cufflinks pipeline based on Human genome (UCSC genome, GRCh37/hg19).
The Cuffdiff program within Cufflinks was used to test statistically significant differences of genes expressions between control and AFF1 knockdown.
The RNA-seq results are displayed as reads per kilobase million (RPKM).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig files

source_name: lung adenocarcinoma cells

growth_protocol: A549 cells were cultured in DMEM (Sigma) containing 10% FBS (Ex-Cell Bio) and 1% Penicillin-Streptomycin (HyClone) at 37℃ with 5% CO2 in a cell incubator.

extract_protocol:
For RNA-seq library preparation, polyadenylated RNA was purified from total RNA and fragmented. Double-stranded cDNA from the RNA fragments were ligated to adapters before subjected to deep sequencing (Illumina).
NEBNext® DNA Library Prep Master Mix Set for Illumina.

tag: cell type

value: lung adenocarcinoma cells

tag: genotype/variation

value: AFF1 knockdown


title: Isl1_mm10_E9.5_4C-seq

value: Isl1 promoter


title: CL_16

description: early


title: KD_aff1_1


title: B18_232

value: Control

tag: paternal genotype


title: B19_075

value: Entrerococcus faeicalis infection

tag: maternal genotype


title: B19_092

tag: extraction batch


title: CL_12

description: cutaneous

value: Cure


title: B18_230

tag: generation


title: SHC_2


title: CL_25

description: cutaneous

tag: age

value: F


title: SHC_1


title: B19_078


title: AFF1

data_processing:
ChipSeq samples were aligned using Bowtie2 (v2.2.5)  allowing uniquely mapping reads only
Peak calling was performed with MACS2 (v2.1.1) and filtered at FDR < 5 (0.05)
Genome_build: hg19

growth_protocol: A549  cells were cultured in DMEM (Sigma) containing 10% FBS (Ex-Cell Bio) and 1% Penicillin-Streptomycin (HyClone) at 37℃ with 5% CO2 in a cell incubator.

extract_protocol:
For ChIP-Seq, 5×107 cells were used per immunoprecipitation according to previously described protocols (Lee et al., 2006). ChIP-Seq libraries were prepared with Illumina's ChIP-Seq sample prep kit (0801-0303).
NEBNext® DNA Library Prep Master Mix Set for Illumina

tag: chip antibody


title: Otx2_mm10_E9.5_4C-seq

value: Otx2 promoter


title: B18_200


title: CL_11

description: cutaneous

value: yes

value: cutaneous

tag: dth


title: B19_085


title: B18_224


title: SirNeoblasts Cells 10x

city: Hangzhou

first: Kevin

last: Niu

state: Zhejiang

address: No.18 Shilongshanjie

institute: Westlake University

data_processing:
Using cellranger v 2.1.0 to generate fastq files
Using cellranger v 2.1.0 to perform alignments and get a count matrix
Genome_build: Using Schmidtea mediterranea transcriptome (GSE72389) as the ref genome
Supplementary_files_format_and_content: sirNeoblast-cells-10x.csv (cleaned counts)

organism: Schmidtea mediterranea

source_name: Sorted SirNeoblasts Cells

growth_protocol: Asexual Schmidtea mediterranea (strain CIW4) specimens were maintained and propagated at 20ºC in 1X Montjuïc salts.

extract_protocol: 10 X Genomics

value: asexual

value: Sorted SirNeoblasts Cells


title: B18_217


title: CL_10

description: cutaneous

value: pos


title: CL_14

description: cutaneous

value: M

value: neg


title: CL_07

description: cutaneous


title: CL_13

description: cutaneous


title: B18_198


title: B19_093


title: B19_086


title: CL_05

description: cutaneous


title: B18_233


title: CL_08

description: cutaneous


title: B18_231


title: CL_06

description: cutaneous


title: CL_04

description: cutaneous

value: no


title: B19_087


title: CL_09

description: cutaneous


title: B18_222


title: B18_216


title: B18_209


title: hey2_danRer_24hpf_4C-seq

data_processing:
Library strategy: 4C-Seq
Demultiplexing: Different samples were demultiplexed using the primer sequences
Mapping: Reads were mapped to the Branchiostoma lanceolatum (Bl71nemr assembly) or Danio rerio (danRer7 assembly) genomes using Bowtie software (http://bowtie-bio.sourceforge.net). Only uniquely mapped reads were kept.
Filtering: Only those reads that mapped withing fragments with a DpnII at one end and a Csp6I at the other end were kept.
Data visualization: Data were uploaded to UCSC Browser for visualization.
Genome_build: danRer7/Bl71nemr(http://amphiencode.github.io/Data/)
Supplementary_files_format_and_content: BEDGRAPH

organism: Danio rerio

source_name: 24 hpf zebrafish embryos

growth_protocol: Embryos were raised at 28ºC untill they reached the desired developmental stage. They were dechorionated with pronase before fixation.

value: hey2 promoter

value: whole embryos

value: 24 hpf


title: otx2_danRer_24hpf_4C-seq

value: otx2 promoter


title: isl2a_danRer_24hpf_4C-seq

value: isl2a promoter


title: isl1_danRer_24hpf_4C-seq

value: isl1 promoter


title: otx1b_danRer_24hpf_4C-seq

value: otx1b promoter


title: otx1a_danRer_24hpf_4C-seq

value: otx1a promoter


title: HS_04

description: control

source_name: control

value: control


title: HS_10

description: control


title: HS_13

description: control


title: HS_05

description: control

value: yes


title: HS_12

description: control


title: CL_03

description: cutaneous

value: Failure


title: CL_02

description: cutaneous


title: HS_14

description: control


title: HS_08

description: control


title: HS_07

description: control


title: HS_09

description: control


title: CL_01

description: cutaneous

value: Cure


title: HS_11

description: control


title: HS_06

description: control


title: HS_03

description: control


title: F0Saline-F1Saline (hMeDIP-seq)

city: Pittsburgh

first: wan-yee

last: tang

state: PA

address: 130 De Soto Street, PUBHL 4129

department: Dept of Environmental and Occupational Health

institute: University of Pittsburgh

description:
saline
NPB_hme

data_processing:
Library strategy: hMeDIP-seq
BaseCalling, Illumina Casava Pipeline 1.8.0
Sequencing Quality Control, FASTQC quality control tool version 0.10.0
Mapping, Bowtie v0.12.9
Peak generation and annonation, CLC Genomic Workbench 6.0.3, ChIP-seq platform (default)
Peak  calling, CLC Genomic Workbench 6.0.3, ChIP-seq platform (default)
Genome_build: Mouse Reference Genome Build NCBI38/mm10
Supplementary_files_format_and_content: Excel file; differential methylated peaks compared with other treatment groups; table includes peak location, center of peak, peak score and p value.

source_name: lung

growth_protocol: All mice were maintained at 22° C, and 12h light and 12h dark cycle. The mice were housed in polysulfone-ventilated cages (Technoplast, Exton, PA), and provided with Harlan Teklad Global 18% Protein Extruded Rodent Diet 2018SX and drinking water ad libitum.

extract_protocol:
DNA was isolated from lung tissues using AllPrep DNA/RNA/miRNA Universal Kit (QIAGEN, Germantown, MD), according to manufacturer’s instructions. Sample DNA concentrations were quantified with the Quanti-iTM Picogreen dsDNA assay kit (Invitrogen, CA).
DNA from each treatment group (pooled from mice of 3 individual dams) was fragmented on Covaris S2 and had an average length of 200 bp. Hydroxymethylated and methylated DNA was captured using the hMethylCap and MethylCap kit (Diagenode, NJ) respectively.  DNA was eluted from the protein complex. Two hundred fifty ng fragmented DNAs were amplified, ligated with linkers, and subjected to flow cells using the HiSeq2000 platform according to the manufacturer’s NGS ChIP protocol (Illumina, CA). We used the DNA Sample Prep Master Mix Set 1 (NEB E6040) in combination with the Multiplexing Sample Preparation Oligo Kit (96 samples, Illumina PE-400-1001). We used 250ng of fragmented DNA and performed Library preparation on Apollo 324 with PrepXDNA Library Kit 24 samples per kit (400007) or PrepX-32-DNA Library Kit 96 samples per kit (400021) according to the kit’s protocol.

treatment_protocol: Female nulliparous mice (F0) were sensitized to HDM (100µg of protein) or an equivalent volume of PBS via intraperitoneal injection (i.p.) two weeks prior to timed mating, and exposed to HDM (100 µg of protein) or an equivalent volume of PBS via intratracheal instillation (i.t.) three times a week during pregnancy and lactation, starting at embryonic day E0.5 and continuing for three weeks post parturition. Instillation was assisted by the use of an isoflurane vaporizer and an induction chamber.  Offspring were sex separated at four weeks of age and allowed to mature under the same housing conditions as mentioned in the Animal Husbandry section. Once the F1 male offspring reached six weeks of age, half of them were sensitized to HDM or saline (i.p) at day (d)0 and challenged with HDM or saline (i.t.) on d14, 18 and 21 before AHR measurement at d23.

value: male

tag: in utero treatment

value: saline

tag: adult treatment

value: lung


title: HS_01

description: control

tag: Sex


title: F0Saline-F1Saline (MeDIP-Seq)

description:
saline
NPB_me

data_processing:
BaseCalling, Illumina Casava Pipeline 1.8.0
Sequencing Quality Control, FASTQC quality control tool version 0.10.0
Mapping, Bowtie v0.12.9
Peak generation and annonation, CLC Genomic Workbench 6.0.3, ChIP-seq platform (default)
Peak  calling, CLC Genomic Workbench 6.0.3, ChIP-seq platform (default)
Genome_build: Mouse Reference Genome Build NCBI38/mm10
Supplementary_files_format_and_content: Excel file; differential methylated peaks compared with other treatment groups; table includes peak location, center of peak, peak score and p value.

tag: tissue


title: F0HDM-F1Saline (hMeDIP-seq)

description:
effect of in utero HDM exposure on lung reprogramming
YPB_hme
HM_YPB vs HM_NPB

value: house dust mite


title: F0Saline-F1HDM (hMeDIP-seq)

description:
effect of adult HDM exposure on allergen-induced AHR risk
NHB_hme
HM_NHB vs HM_NPB


title: HS_02

description: control


title: INF_VASC_2

city: Winnipeg

first: Philip

last: Walker

state: Manitoba

address: 104 Dunrobin Avenue

country: Canada

institute: Agriculture and AgriFood Canada

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads trimmed using trimmomatic v 0.36 for adaptor sequence and low-quality reads
Trimmed reads mapped to B. napus genome v4.1 using hisat2
The cufflinks suite (Trapnell et al. 2012) was used to generate normalized read counts in FPKM (fragments per kilobase of transcript per million mapped reads)
Genome_build: B. napus genome v4.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values

organism: Brassica napus

source_name: Infected vascular tissue from mature canola leaves

growth_protocol: B. napus planted in sunshine mix #1 soil and grown at 22°C (50-70% humidity) under long day conditions (16h light, 8h dark)

extract_protocol:
RNA was isolated using the Ambion® RNaqueous® micro kit according to manufacturers instructions and quality was analyzed using the Agilent 6000 Pico LabChip® and Agilent 2100 Bioanalyzer software
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Ascospore inoculum was prepared by suspending 8x104 spores/ml in a 15 ml distilled water and 0.01% tween solution. B. napus petals were inoculated with 30 µl of ascospore inoculum and stored at room temperature for 72 hours in a parafilm sealed petri plate. Control petals were inoculated with a 0.01% tween solution and stored under the same conditions. S. sclerotiorum infected and control petals were transferred to the adaxial side of canola leaves at the 30 – 50% bloom stage. Inoculated leaves were covered using plastic bags to increase humidity levels for optimal S. sclerotiorum pathogenicity. Infection sites were subsequently collected at 24 hours post inoculation

value: vascular

tag: disease state

value: infected (S. sclerotiorum 24hpi)


title: F0HDM-F1HDM (hMeDIP-seq)

description:
effect of in utero HDM exposure on allergen-induced AHR risk in adulthood
YHB_hme
HM_YHB vs HM_NHB


title: INF_VASC_3


title: INF_VASC_4


title: CTL_VASC_4

source_name: Uninfected vascular tissue from mature canola leaves

value: uninfected


title: 1302-ACP-0046: 1wk WD-Mphs_rep4

city: Nashville

first: Shristi

last: Shrestha

address: 2213 Garland Ave

institute: Vanderbilt University

data_processing:
Raw reads were mapped to reference mouse genome mm9 using TopHat v2.0 (Trapnell et al., 2009). Aligned reads were imported onto the Avadis NGS data analysis platform (Strand NGS, San Fransisco, CA, USA). Briefly imported mapped reads were first filtered on their quality metrics, and then duplicate reads were removed. Normalized gene expression was quantified using the TMM (Trimmed Mean of M-values) method (Dillies et al., 2012; Robinson and Oshlack, 2010). The transcriptional profile from each sample group (Sorted islet-derived beta cells, macrophages, and endothelial cells at No Dox, 1 week Dox, and 1 week withdrawl from Dox) was compared by principle component analysis (PCA) and hierarchal clustering analysis to determine the layout and spread of the samples. Differential expression between conditions was calculated on the basis of fold change (cutoff ≥2.0) and the p-value was estimated by z-score calculations (cutoff 0.05) as determined by the Benjamini Hochberg false discovery rate (FDR) method (Benjamini and Hochberg, 1995). Differentially expressed genes underwent gene set enrichment analysis (GSEA), gene ontology (GO) analysis, and pathway analysis using DAVID, and Ingenuity Pathway Analysis.
Genome_build: mm9
Supplementary_files_format_and_content: txt file contains normalized expressions for each sample in this submission plus GSM1864929, GSM1864931, GSM1864933, GSM1864930, GSM1864932, and GSM1864934 from GSE72546

source_name: CD11b+ islet-derived macrophages

extract_protocol:
Sorted islet-derived cells (8,000-400,000) were added to 200-400 ul lysis/binding solution in the RNAqueous small scale or micro scale phenol-free total RNA isolation kits (Ambion, Austin, TX). Trace contaminating DNA was removed with TURBO DNA-free kit (Ambion, Austin, TX). RNA quantification and quality analysis was performed using a Qubit Fluorometer and an Agilent 2100 Bioanalyzer.
RNA samples had RNA integrity number (RIN) ≥7.0. RNA was amplified using the NuGEN Technologies Ovation RNA amplification kit (Part # 7102-08) using manufacturer's instructions. Approximately, 2.5 µg amplified DNA from each sample was sheared on a Covaris S200 focused-ultrasonicator (Woburn, MA, USA) with a target yield of an average 200bp fragment size. The fragmented DNA was taken into standard library preparation protocol using NEBNext DNA Library Prep Master Mix Set for Illumina (New England BioLabs Inc., Ipswich, MA, USA) with slight modifications. Briefly, end-repair was done followed by polyA addition and custom adapter ligation. Post-ligated materials were individually barcoded with unique in-house genomics service lab (GSL) primers and amplified through 8 cycles of PCR using KAPA HiFi HotStart Ready Mix (Kapa  Biosystems, Inc., Woburn, MA, USA).  The quality of the libraries were assessed by Qubit 2.0 Fluorometer, and the concentration of the libraries was estimated by utilizing a DNA 1000 chip on an Agilent 2100 Bioanalyzer, respectively. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols.

tag: strain

value: MIP-GFP; RIP-rtTA; TetO-VEGF-A

tag: treatment

value: 1 week withdrawal from Dox

value: CD11b+ islet-derived macrophages


title: 1302-ACP-0045: 1wk WD-Mphs_rep3


title: Tongue_tissue_09

first: Zehang

last: Zhuang

address: No. 56 Lingyuan West Road

department: Department of Oral and Maxillofacial Surgery

institute: Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University

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

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, 20bit.

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

source_name: Tongue, patient 09

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

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

tag: individual

value: patient 09

tag: gender

value: tongue tissue

tag: tumor stage

value: adjacent non-cancerous tissue


title: Tongue_tissue_07

source_name: Tongue, patient 07

value: patient 07


title: Tongue_cancer_09

value: tongue squamous cell carcinoma


title: Tongue_tissue_10

source_name: Tongue, patient 10

value: patient 10

value: female


title: Tongue_tissue_06

source_name: Tongue, patient 06

value: patient 06


title: Tongue_cancer_07

value: male


title: B19_082

source_name: Fat body

value: Entrerococcus faeicalis infection

tag: paternal genotype


title: CTL_VASC_3


title: F0Saline-F1HDM (MeDIP-Seq)

description:
effect of adult HDM exposure on allergen-induced AHR risk
NHB_me
M_NHB vs M_NPB

value: saline

value: house dust mite

value: lung


title: INF_VASC_1

value: vascular

value: infected (S. sclerotiorum 24hpi)


title: Tongue_tissue_08

source_name: Tongue, patient 08

value: patient 08


title: Tongue_cancer_05

source_name: Tongue, patient 05

value: patient 05


title: F0HDM-F1Saline (MeDIP-Seq)

description:
effect of in utero HDM exposure on lung reprogramming
YPB_me
M_YPB vs M_NPB


title: 1302-ACP-0044: 1wk WD-Mphs_rep2

value: MIP-GFP; RIP-rtTA; TetO-VEGF-A

value: 1 week withdrawal from Dox

tag: cell type

value: CD11b+ islet-derived macrophages


title: CTL_VASC_2

value: uninfected


title: F0HDM-F1HDM (MeDIP-Seq)

description:
effect of in utero HDM exposure on allergen-induced AHR risk in adulthood
YHB_me
M_YHB vs M_NHB


title: 1302-ACP-0043: 1wk WD-Mphs_rep1


title: 1302-ACP-0055: 1wk WD-ECs_rep5

source_name: CD31+ islet-derived endothelial cells

value: CD31+ islet-derived endothelial cells


title: Tongue_cancer_04

source_name: Tongue, patient 04

value: patient 04

value: tongue squamous cell carcinoma


title: Tongue_tissue_05

value: tongue tissue

value: adjacent non-cancerous tissue


title: Tongue_cancer_10

value: patient 10

value: female


title: INF_MES_2

source_name: Infected mesophyll tissue from mature canola leaves

value: mesophyll


title: Tongue_cancer_08

value: male


title: Tongue_tissue_04


title: INF_MES_1


title: Tongue_cancer_06

value: patient 06


title: 1302-ACP-0053: 1wk WD-ECs_rep3


title: 1302-ACP-0052: 1wk WD-ECs_rep2


title: CTL_MES_2

source_name: Uninfected mesophyll tissue from mature canola leaves


title: heart, Non-transgenic control

city: Maywood

first: Michael

middle: J

last: Zilliox

state: IL

address: 2160 S. First Ave

department: Ophthalmology

institute: Loyola University Chicago

description: total heart RNA

data_processing:
STAR aligner was used to align sample reads to Mus musculus genome build mm10.
HTSeq was used to generate counts.
Genome_build: mm10
Supplementary_files_format_and_content: counts

source_name: SS1 - total heart mRNA

growth_protocol: Not applicable

extract_protocol:
Isolated hearts from NTG and TG mice were homogenized in 1 mL of TriZol (Bio-Rad,  Hercules, CA) using a bead homogenizer, and total RNA was extracted using the Aurum Total  RNA Fatty and Fibrous Tissue Kit (Cat. No. 732-6820, Bio-Rad Laboratories, Hercules, CA),  according to the manufacturer’s instructions.
mRNA in the total RNA  was translated into a library of template molecules of known strand origin using the TruSeq®  Stranded mRNA Library Prep kit (Cat. No. RS-122-2201, Illumina, Inc., San Diego, CA). Poly-T  oligos attached to magnetic beads were used to isolate the mRNA, which was then fragmented  and reverse transcribed. The resultant cDNA products were amplified, and cDNA libraries ready  for sequencing were created using sequencing adapters and barcodes ligated onto the cDNA  fragments for each respective sample.

treatment_protocol: Not applicable

value: 12 weeks old

value: FvB/N

tag: genotype

value: control

value: 3 hearts combined


title: heart, cMyBP-C delta C0-C1f transgenic

description: total heart RNA

source_name: SS3 - total heart mRNA

value: cMyBP-C delta C0-C1f transgenic


title: CTL_VASC_1

value: vascular


title: CTL_MES_1

value: uninfected


title: 1302-ACP-0056: 1wk WD-Beta_rep3

source_name: GFP+ islet beta cells

value: MIP-GFP; RIP-rtTA; TetO-VEGF-A

value: 1 week withdrawal from Dox

value: GFP+ islet beta cells


title: ebp1_knockdown_rnaseq_siEbp1_3

first: Matthew

middle: Lee

last: Kraushar

address: Ihnestrasse 63-73

department: Department of Computational Molecular Biology

institute: Max Planck Institute for Molecular Genetics

description: polyA enriched from lysate

data_processing:
Riboseq reads were stripped of adaptor sequences using cutdapt, and contaminants such as transfer RNAs (tRNAs) and rRNA were removed by alignment to a contaminants index via STAR 2.7.0, consisting of nucleotide sequences from known mouse rRNA and tRNA sequences drawn from the gencode annotation.
Unaligned reads from this analysis were then aligned to mouse genome version GRCm38 with the STAR v 2.7.0 splice-aware alignment tool allowing for up to 1 mismatch. The star genome index was built using GENCODE M12. Only uniquely aligning reads were used.
The RiboseQC pipeline v1.1 (https://github.com/ohlerlab/RiboseQC) was used to confirm 3-nucleotide periodicity of the data and deduce P-site positions from the Riboseq reads.
Ribosome P-site count metaplots and fold change were calculated by first normalizing the P-site coverage track for each gene to the gene's total density, excluding genes with < 32 reads or less (low count filtering), and then all genes’ tracks were added together to generate a mean P-site density at each point for each sample. Confidence intervals were calculated by resampling from the 3 replicates for each condition.
Genome_build: mouse GRCm38
Supplementary_files_format_and_content: counts_colrnm.tsv

source_name: Neuro2a cell line in culture

growth_protocol: Neuro2a cultures were prepared in biological triplicate, with 3x 10 cm plates per control and knockdown (mouse siEbp1) conditions. Growth in standard DMEM (Gibco, 31966047) with 10 % FBS (Gibco, 10270106) and 1 % penicillin-streptomycin (Gibco, 15140122) to a confluence of 90 % in humidified 37 °C, 5 % CO2.

extract_protocol:
400 µl mammalian polysome buffer (20 mMTris-HCl pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 µg/ml cycloheximide, 1 % Triton X-100 and 25 U/mL TurboDNase (Thermo Fisher, AM2238]) was added to each plate, which were then placed on ice. Cells were scraped into a slurry, and then passed 10 times through a 26 G needle. Lysates were cleared by centrifugation (20000 xg, 10 min, 4 °C). Ribosome-protected mRNA fragments were generated by adding 300 U RNase-I (Thermo Fisher, EN0601) for 45 min at room temperature with gentle agitation.
For total RNAseq, sequencing libraries were constructed with the NEBNext Ultra Directional RNA Library Prep Kit (Illumina, E7420L) according to manufacturer’s instructions. For Riboseq sequencing library preparation, the RNA was first ligated to a 3’ adapter 4N-RA3 (see below), and gel-purified using a 15 % denaturing urea-PAGE gel (Carl Roth). Next the 5’ adapter OR5-4N (see below) was ligated and gel purified. The RNA was reverse transcribed and PCR-amplified by Phusion High-Fidelity DNA polymerase (Thermo Fischer, F-530XL). The cDNA was visualized on a 2.5 % agarose gel, a ~150 bp sized fragment was excised and purified by Zymoclean Gel DNA Recovery kit (Zymo Research, D4007/D4008).

treatment_protocol: The mouse and human siEbp1 oligos were obtained from the Dharmacon SMARTpool ON-TARGETplus collection (mouse siPa2g4 #18813, L-042883-01-0005; human siPa2g4 #5036; L008860-00-0005) and compared to non-targeting siRNA control (D-001810-10-05). Transfection was performed with Lipofectamine RNAiMAX Transfection Reagent (Thermo Fisher, 13778075) according to the manufacturer’s protocol.

tag: cell line

value: Ebp1 siRNA knockdown oligo transfection


title: INF_EPI_3

source_name: Infected epidermis tissue from mature canola leaves

value: epidermis

value: infected (S. sclerotiorum 24hpi)


title: 1302-ACP-0037: 1wk WD-Beta_rep2


title: ebp1_knockdown_rnaseq_siEbp1_1

description: polyA enriched from lysate


title: 1302-ACP-0036: 1wk WD-Beta_rep1


title: mouse embryo 2

city: London

first: Clara

last: Collart

state: london

address: 1 Midland road

department: developmental biology

country: United Kingdom

institute: Crick

data_processing:
We used cell-ranger version 2.1.1 to deconvolve, align and quantify the per-cell transcriptomes. Reads were aligned to human transcriptome GRCh38-3.0.0 (software and data available from 10x genomics).
Genome_build: Mouse mm10 (m10-1.2.0 from cellranger)
Supplementary_files_format_and_content: tar file containing 10x counts matrix, features and barcode data

source_name: bottom

extract_protocol:
We followed the protocol described in (43) with minor modifications. Embryos were dissected in FHM medium (as described above). They were transferred onto a dish covered with a layer of 1% agarose in HBSS medium (Thermofisher Cat# 88284) and filled with HBSS with 5% Foetal Bovine Serum (FBS). The top and bottom (B part of 25 embryos (E7.25-E7.5) were sliced off, using a 13-Y1 micron wire tip cautery electrode with 1 mm loop from pProtech, mounted on a Model MC-2010 micro cautery instrument. Top and bottom parts were separated immediately after cutting and stored in Low-bind Eppendorf tubes (Cat# 022431021) filled with 500 ml recovery medium (HBSS with 5% FBS, rock inhibitor (10 mm, Sigma Aldrich Y-27632) and 1x non-essential amino acids (Thermofisher Cat# 11140050)) at 37C, until all pieces sank to the bottom of the tube. The recovery medium was removed by pipetting and 500 ml of dissociation medium (FACSmax cell dissociation solution (Amsbio T200100) with 10x papain (Sigma Aldrich Cat# 10108014001)) was added at 37C for a total time of 10. Every cells were pipetted up and down carefully with 200 ml MultiGuard Barrier Tips, Sorenson Cat#30550T. Cells were then pipetted through a cell restrainer (pluriSelect, pluristrainer 15 mm Cat# 43-50015-01), using a 1000 ml non-stick filter tip. Cells were spun down for 2 at 1300 rpm, the dissociation medium was removed and cells were re-dissociated in 500 ml recovery medium (see above). Cells were spun down for 2 at 1300 rpm for a second time and re-dissociated in recovery medium.
Cell size, number of cell aggregates, and percentage of live cells were used as measures of quality control, and only samples with a viability over 65% were used. A suspension of 10,000 single cells was loaded onto the 10x Genomics Single Cell 3 Chip, and cDNA synthesis and library construction were performed as per the manufacturer's protocol for the Chromium Single Cell 3 v2 protocol (10x Genomics; PN-120233). cDNA amplification involved 12 PCR cycles)

treatment_protocol: Top and bottom parts of 25 embryos (5 different litters, 5 embryos per litter) of mouse embryos between E7.25 and E7.5 were dissected, and the two parts were pooled separately and dissociated into single cells.

tag: mixed sample

value: embryo


title: mouse embryo 1

source_name: top


title: INF_EPI_1


title: 1302-ACP-0051: 1wk WD-ECs_rep1

value: CD31+ islet-derived endothelial cells


title: INF_EPI_2


title: ebp1_knockdown_rnaseq_scrambled-cntrl_3

description: polyA enriched from lysate

value: scrambled siRNA control oligo transfection


title: 1302-ACP-0058: 1wk Dox-Mphs_rep5

description: Other 1wk Dox-Mphs biological replicates are available in GSE72546 (GSM1864929, GSM1864931, GSM1864933)

source_name: CD11b+ islet-derived macrophages

value: 1 week Dox

value: CD11b+ islet-derived macrophages


title: ebp1_knockdown_rnaseq_scrambled-cntrl_2

description: polyA enriched from lysate


title: CTL_EPI_3

source_name: Uninfected epidermis tissue from mature canola leaves


title: ebp1_knockdown_rnaseq_siEbp1_2

description: polyA enriched from lysate


title: CTL_EPI_2


title: 1302-ACP-0057: 1wk Dox-Mphs_rep4


title: Tongue_tissue_02

source_name: Tongue, patient 02

value: patient 02

value: male

tag: age

value: tongue tissue

value: adjacent non-cancerous tissue


title: Tongue_tissue_03

source_name: Tongue, patient 03

value: patient 03


title: CB9

city: Valencia

first: Susana

last: Rovira-Llopis

address: Av Gaspar Aguilar 90

department: University Hospital Doctor Peset

country: Spain

institute: FISABIO

hyb_protocol: According to manufacturer's instructions

data_processing: Intensity backgrounds were corrected by RMA and normalized by quantiles. Normalization consists on isolating the statistical error in repeated easured data. This correction is required so that multiple chips can be compared to each other and analyzed together.

label: biotin

label_protocol: Extraction product was analyzed using Affymetrix miRNA 4.0  to study the differential expression of human miRNAs

extract_protocol: Serum circulating miRNAs were isolated using the miRNeasy Serum/Plasma Kit (Qiagen, Hilden, Germany), following the manufacturer's instructions.

tag: group

value: healthy


title: Tongue_cancer_02

value: tongue squamous cell carcinoma


title: 1302-ACP-0059: 1wk Dox-ECs_rep4

description: Other 1wk Dox-ECs biological replicates are available in GSE72546 (GSM1864930, GSM1864932, GSM1864934)

value: MIP-GFP; RIP-rtTA; TetO-VEGF-A


title: CTL_EPI_1

value: uninfected


title: Tongue_cancer_03


title: CB8

scan_protocol: According to manufacturer's instructions


title: ebp1_knockdown_rnaseq_scrambled-cntrl_1

description: polyA enriched from lysate


title: CB5


title: ebp1_knockdown_riboseq_siEbp1_1

description: Ribosome-protected mRNA fragments were generated by RNAse-I digestion

data_processing:
Library strategy: Ribo-seq
Riboseq reads were stripped of adaptor sequences using cutdapt, and contaminants such as transfer RNAs (tRNAs) and rRNA were removed by alignment to a contaminants index via STAR 2.7.0, consisting of nucleotide sequences from known mouse rRNA and tRNA sequences drawn from the gencode annotation.
Unaligned reads from this analysis were then aligned to mouse genome version GRCm38 with the STAR v 2.7.0 splice-aware alignment tool allowing for up to 1 mismatch. The star genome index was built using GENCODE M12. Only uniquely aligning reads were used.
The RiboseQC pipeline v1.1 (https://github.com/ohlerlab/RiboseQC) was used to confirm 3-nucleotide periodicity of the data and deduce P-site positions from the Riboseq reads.
Ribosome P-site count metaplots and fold change were calculated by first normalizing the P-site coverage track for each gene to the gene's total density, excluding genes with < 32 reads or less (low count filtering), and then all genes’ tracks were added together to generate a mean P-site density at each point for each sample. Confidence intervals were calculated by resampling from the 3 replicates for each condition.
Genome_build: mouse GRCm38
Supplementary_files_format_and_content: counts_colrnm.tsv

value: Ebp1 siRNA knockdown oligo transfection


title: ebp1_knockdown_riboseq_siEbp1_2


title: 1302-ACP-0034: 1wk Dox-Beta_rep4

value: GFP+ islet beta cells


title: 1302-ACP-0035: 1wk Dox-Beta_rep5


title: 1302-ACP-0033: 1wk Dox-Beta_rep3


title: CB6


title: ebp1_knockdown_riboseq_siEbp1_3


title: CB4


title: ebp1_knockdown_riboseq_scrambled-cntrl_3


title: 1302-ACP-0032: 1wk Dox-Bets_rep2


title: 1302-ACP-0054: 1wk WD-ECs_rep4

value: 1 week withdrawal from Dox


title: CB23


title: CB3


title: CB22

value: unhealthy


title: ebp1_knockdown_riboseq_scrambled-cntrl_2


title: Tongue_cancer_01

source_name: Tongue, patient 01

value: patient 01


title: CB20


title: CB21


title: CB1


title: Col-0 shoots, lowS, biological replicate 3

city: Warsaw

first: Agnieszka

last: Sirko

address: Pawinskiego 5A

country: Poland

institute: Institute of Biochemistry and Biophysics

description: Gene expression data from Arabidopsis thaliana shoots, 4 weeks old

hyb_protocol: Labelled samples were hybridized to the Arabidopsis Gene 1.1. ST array Strips (Aﬀymetrix, Santa Clara, CA).

scan_protocol: Microarrays were scanned with Aﬀymetrix GeneAtlas System and saved to CEL ﬁles.

data_processing: The CEL ﬁles were analyzed by Transcriptome Analysis Console (TAC) Software (version 4.0.1, Applied Biosystems) following manufacturer's specifications. Microarrays were normalized and summarized using RMA method (Robust Multiarray Averaging), followed by Anova (ebayes) method to investigate differential expression among different treatment. The obserbved p-values were corrected by Benjamin-Hochberg procedure. Genome version: tair10; annotation version: AraGene-1_1-st-v1.na36.tair10.transcript.csv.

organism: Arabidopsis thaliana

source_name: Arabidopsis ecotype Col-0, shoots

label_protocol: Samples containing 100 ng total RNA were reverse transcribed using the Ambion® WT Expression Kit and labelled with the Affymetrix GeneChip® WT Terminal Labelling Kit (ThermoScientific), according to the manufacturers’ protocols.

growth_protocol: Seeds were dry sterilised and placed on the solid medium with 0.8% Agargel (Sigma-Aldrich). Plants were grown in Araponic boxes (16 plants/box) kept in short day conditions (22 °C 8h day/18 °C 16h night) for about 4 weeks, with weekly changes of 0.5 x Hoagland medium. Individual plants were divided into shoot and root tissue and frozen in liquid nitrogen.

extract_protocol: Portions of plant material, drawn from at least 3 plants, were homogenised in TRI Reagent (Molecular Research Centre), and genomic DNA was removed with a RapidOut DNA removal kit (ThermoScientific). The quality, integrity and the concentration of RNA were evaluated using a Bioanalyzer 2100 (Agilent Technologies) and a Nano Drop ND-100 spectrophotometer.

tag: ecotype

value: wildtype

value: shoots


title: Col-0 shoots, lowS, biological replicate 1


title: ebp1_knockdown_riboseq_scrambled-cntrl_1

value: scrambled siRNA control oligo transfection


title: Col-0 shoots, lowS, biological replicate 2


title: CB18


title: 1302-ACP-0042: No Dox-Mphs_rep4

value: No Dox

value: CD11b+ islet-derived macrophages


title: 1302-ACP-0031: 1wk Dox-Beta_rep1

value: 1 week Dox


title: Tongue_tissue_01

value: male

value: tongue tissue

value: adjacent non-cancerous tissue


title: P0_2.fastq.gz

description: TPMs.tsv.gz

data_processing:
Reads were aligned to the mouse M12 genome using the splice aware aligner STAR (Dobin et al., 2013), and GENCODE (Frankish et al., 2019) gene annotation GRCm38.p5. We used the STAR parameters  ‘--alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999  --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20’ and default otherwise.
Gene-level counts were produced using the subread package, with duplicates and multi-mappers discarded.
TPMs were calculated using the total exon length for each gene.
Genome_build: Mus musculus GENCODE annotation GRCm38.p5
Supplementary_files_format_and_content: TPMs for each sample

source_name: neocortex

extract_protocol:
Frozen neocortex tissue was lysed in buffer containing detergent by crogenic pulverization, followed by lysate clarification with centrifugation, then RNA extraction with TriZOL LS according to the manufacturer's protocol
Libraries were constructed with the TruSeq Stranded mRNA kit (Illumina #20020594) according to manufacturer´s instructions

value: CD1 wild type

value: neocortex (brain)

tag: developmental stage


title: KO3 shoots, lowS, biological replicate 2

source_name: Arabidopsis KO3 line, NBR1 deletion, shoots

value: KO3 line, NBR1 deletion


title: 1302-ACP-0041: No Dox-Mphs_rep3

value: MIP-GFP; RIP-rtTA; TetO-VEGF-A


title: KO3 shoots, lowS, biological replicate 3


title: P0_1.fastq.gz

description: TPMs.tsv.gz


title: CB17


title: 1302-ACP-0040: No Dox-Mphs_rep2


title: E17_2.fastq.gz

description: TPMs.tsv.gz


title: KO3 shoots, lowS, biological replicate 1


title: 1302-ACP-0039: No Dox-Mphs_rep1


title: CB15


title: E155_2.fastq.gz

description: TPMs.tsv.gz


title: E155_1.fastq.gz

description: TPMs.tsv.gz


title: 1302-ACP-0050: No Dox-ECs_rep4

source_name: CD31+ islet-derived endothelial cells

value: CD31+ islet-derived endothelial cells


title: 1302-ACP-0049: No Dox-ECs_rep3


title: CB14


title: CB13


title: 1302-ACP-0048: No Dox-ECs_rep2


title: KO1 shoots, lowS, biological replicate 3

source_name: Arabidopsis KO1 line, NBR1 deletion, shoots

value: KO1 line, NBR1 deletion


title: E14_2.fastq.gz

description: TPMs.tsv.gz


title: KO1 shoots, lowS, biological replicate 2


title: KO1 shoots, lowS, biological replicate 1


title: Col-0 roots, lowS, biological replicate 2

description: Gene expression data from Arabidopsis thaliana roots, 4 weeks old

source_name: Arabidopsis ecotype Col-0, roots

value: roots


title: Col-0 roots, lowS, biological replicate 3


title: 1302-ACP-0047: No Dox-ECs_rep1


title: CB12

value: unhealthy


title: E14_1.fastq.gz

description: TPMs.tsv.gz


title: 1302-ACP-0030: No Dox-Beta_rep4

value: GFP+ islet beta cells


title: E17_1.fastq.gz

description: TPMs.tsv.gz


title: E125_2.fastq.gz

description: TPMs.tsv.gz


title: CB16


title: CB11


title: KO3 roots, lowS, biological replicate 3

source_name: Arabidopsis KO3 line, NBR1 deletion, roots


title: CB10

value: healthy


title: 1302-ACP-0029: No Dox-Beta_rep3

source_name: GFP+ islet beta cells


title: E125_1.fastq.gz

description: TPMs.tsv.gz


title: 1302-ACP-0027: No Dox-Beta_rep1


title: 1302-ACP-0028: No Dox-Beta_rep2


title: Main2.ADT.010819.l2

first: Kiya

middle: W

last: Govek

address: 3700 Hamilton Walk

department: Genetics

institute: University of Pennsylvania

data_processing:
Library strategy: CITE-seq
Basecalling with Illumina bcl2fastq
Read alignment, cell barcode demultiplexing, and UMI demultiplexing using cellranger 3.0.2
Cell barcodes were filtered out if they contained less than 1200 UMIs or >10% mitochondrial mRNA content.
Count matrices between mice were concatenated, discarding genes expressed in fewer than 15 cells
Genome_build: mm10
Supplementary_files_format_and_content: gene_matrix_all_new.csv is a csv file of a genes x cells count matrix for all samples; protein_expr_all.csv is a csv file of a cells x proteins count matrix for all samples

extract_protocol:
Spleens were removed from mice and mechanically dissociated with a syringe plunger over a 40 um strainer while being washed with 5 ml of PBS + 10% fetal calf serum. Suspensions were centrifuged briefly to pellet cells. Red blood cells were lysed with an RBC lysis buffer (155 mM NH4Cl, 12 mM NaHCO3, 0.1 mM EDTA) for 5 minutes and centrifuged again. 2 million cells from the resulting pellet were re-suspended in staining buffer (2% BSA, 0.01% Tween in PBS), and subsequently incubated with the antibody panel
cDNA libraries were prepared following the standard CITE-seq and 10x protocols

value: BALB/cJ

tag: Sex

value: Female

value: 9 months

value: spleen


title: CTL_MES_3

source_name: Uninfected mesophyll tissue from mature canola leaves

tag: tissue

value: mesophyll

value: uninfected


title: LNCaP-WT

city: Chicago

first: Feng

last: Yue

address: 303 E Chicago Ave. Simpson Querrey 7-518

department: Biochemistry and Molecular Genetics

institute: Northwestern University

data_processing:
The Hi-C data were processed using runHiC (0.8.3-r1, https://pypi.org/project/runHiC). Read alignment: The paired end reads were aligned using bwa version 0.7.17 (bwa mem -SP).
Filtering: PCR duplicates and read pairs that were mapped to the same restriction fragment were removed using pairtools (version 0.3.0). The output from this step is a pairs file containing a list of valid contacts.
Contact matrices at multiple resolutions (5kb, 10kb, 25kb, 50kb, 100kb, 250kb, 500kb, 1Mb, 2.5Mb, 5Mb) were constructed using cooler (version 0.8.6).
The original contact matrices were normalized using a modified matrix balancing method  to remove CNV (copy number variations) effects along with other systematic biases including mappability, GC content and restriction fragment sizes.
Genome_build: hg38
Supplementary_files_format_and_content: mcool format, multi-resolution Hi-C matrices

source_name: prostate cancer metastatic site

growth_protocol: LNCaP wild type and LNCaP M1-del cells were grown in RPMI-1640 medium with 10% FBS

extract_protocol:
ARIMA’s Hi-C kit (ARIMA Genomics) were applied for capturing proximally-ligated DNA. The biotinylated DNA was sheared to a size of 300–500 bp.
Libraries were constructed following Kapa Hyper Prep Kit (KAPA) protocols.

treatment_protocol: LNCaP M1-del cells were CRISPR/Cas9-mediated enhancer deletion cells. The LNCaP cell line (obtained from ATCC, https://www.atcc.org/) was transfected with two pairs of gRNA vector (backbone: pX458) aiming to upstream and downstream of the target region (named M1) and flow-sorted for GFP positive cells after 2 days. Single-cell clones were verified and crosslinked with final concentration of 2% formaldehyde (Sigma) in PBS.

value: LNCaP cells

tag: assay

value: Hi-C


title: HTBE-Mock-2

city: La Jolla

first: Max

last: Chang

address: 9500 Gilman Drive

institute: University of California, San Diego

data_processing:
Raw sequencing reads were aligned to the human hg38 genome with STAR
Read counts per gene were calculated using FeatureCounts
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited raw read counts per gene

source_name: tracheobronchial epithelial cells

extract_protocol:
8 hours after stimulation, cell extracts were collected with Trizol and total RNA was extracted using RNeasy Mini Kit (Qiagen).
Strand-specific rRNA-depleted sequencing libraries were produced according to standard Illumina protocols.

treatment_protocol: Samples were stimulated with 100 IU/ml universal type I interferon or a mock treatment. After 1 hour, cells were washed and then incubated with medium at 37 °C.

value: tracheobronchial epithelial cells

value: Mock

tag: replicate


title: KO Infl. rep4

city: Turku

first: Sina

last: Tadayon

address: Tykistökatu 6A, 4 floor

country: Finland

institute: Turku University

data_processing:
Single-end 50 bp reads were aligned to the mm10 mouse genome with STAR version 2.5.2b. Read counting was performed with subreads package.
Read counts were normalized and TPM were calculated.
The Bioconductor package Limma was used for differential expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited csv files include TPM values for each Sample ...

source_name: lymph node's lymphatic endothelial cells

extract_protocol:
Popliteal & brachial Lymph Node from WT and KO mice were removed, digested with collagenase and Live lymphatic endothelial cells (CD45- CD31+ Podoplanin+)  were sorted and RNA was extracted. cDNA was synthesized with SMART-Seq v4 ultra low input RNA kit.
Sequencing libraries were generated from the amplified cDNA using Nextera XT (Illumina)

tag: strain

value: Popliteal & brachial Lymph Node

value: Lymphatic endothelial cells

tag: treatment

value: 1 day after footpad injection of ovalbumin emulsified in complete Freund's adjuvant


title: KO1 roots, lowS, biological replicate 2

source_name: Arabidopsis KO1 line, NBR1 deletion, roots

value: KO1 line, NBR1 deletion

value: roots


title: Col-0 roots, lowS, biological replicate 1

value: wildtype


title: KO3 roots, lowS, biological replicate 1

value: KO3 line, NBR1 deletion


title: Main2.ADT.010819.l1

city: Philadelphia

value: BALB/cJ


title: KO3 roots, lowS, biological replicate 2


title: KO1 roots, lowS, biological replicate 1


title: KO1 roots, lowS, biological replicate 3


title: Ts_GC_3x salt_rep_4_Light

city: Wuerzburg

first: Sohail

middle: Mehmood

last: Karimi

state: Bavaria

address: Julius-von-Sachs-Platz 2,

department: Botany 1

institute: University of Wuerzburg

description: Gene expression after 75+150+200 mM salt treatment

hyb_protocol: For hybridization, the Agilent Gene Expression Hybridization Kit (Agilent Technologies) was used. 600 ng of each cRNA was hybridized on 8x60K microarray at 65°C for 17

scan_protocol: Fluorescence signals on microarrays were detected by the SureScan Microarray Scanner (Agilent Technologies) at a resolution of 3 micron for SurePrint G3 Gene Expression Microarrays and 5 micron for HD Microarray formats, generating a 20 bit TIFF file.

data_processing: Agilent's Feature Extraction software version 11 was used to read and process the TIFF files. Data pre-processing was performed using the Bioconductor software (Huber et al. 2015) with the statistical programming environment R (R Development Core Team, 2011). Normalization has been performed using negative control probes and quantile normalization using negative and positive control probes as implemented in the neqc function (Shi et al. 2010) of the Limma package (Ritchie et al. 2015).

organism: Eutrema salsugineum

source_name: Guard cells

label_protocol: For labeling, the Low Input QuickAmp Labeling Kit (Agilent Technologies) was used to generate fuorescent cRNA (complementary RNA). For 1st strand synthesis, either oligo-dT primer or random primer / oligo-dT primer mixture (WT primer) was used. After 2nd strand synthesis, an in vitro transcription for synthesis of cRNA labelled with cyanine 3-CTP was performed

growth_protocol: Thellngiella salsuginea (accession Sahandong) plants were grown in pots (7 cm diameter, 200 ml volume) filled with 91 ± 7 g soil (Einheitserde Typ P, Germany). Plants were illuminated for 12 hours (10 A.M. to 10 P.M.) with a light intensity of 80-110 μmol s-1 m-2 using fluorescent lamps (Osram, L58W/77 FLUORA; Munich, Germany) at 22°C in light and 16°C in dark and 60% relative air humidity.

extract_protocol: Total RNA was isolated using the NucleoSpin RNA kit (Macherey-Nagel, Gmbh& co. Germany) according to manufacturer’s protocol from salt (1x and 3x salt) and non-salt treated plants kept in light for four hours after beginning of the light period (from 10 am to 2 pm). Four guard cell samples of each treatment were prepared and hence, a total 12 samples for Thellungiella were used for microarray analysis.

treatment_protocol: Two different salt treatment protocols, a short- and long-term, were applied to 7 weeks old Thellungiella plants by soaking the soil pots in salt solutions each time for two hours. In the long-term salt stress experiment plants were treated three times : (i) On day 1 and 2 (75 mM NaCl), (ii) on day 7 and 8 (150 mM NaCl), and (iii) on day 13 and 14 (200 mM NaCl) named as 3x salt. In the short-term salt stress experiment plants were treated with 200mM NaCl on day 13 and 14 (named as 1x salt) while the control group faced tap water (named as (-) salt). All samples were collected at the end of the salt experiments on day 15 to ensure that plants have the same plant age and developmental stage.

value: 9 weeks


title: LNCaP-M1E10


title: KO Infl. rep3


title: Main2.ADT.113018.l2

value: Female

value: 9 months


title: HTBE-IFN-2

value: Interferon


title: Ts_GC_3x salt_rep_2_Light


title: Ts_GC_3x salt_rep_3_Light


title: Main2.ADT.113018.l1

value: spleen


title: KO Infl. rep2


title: HTBE-IFN-1


title: Ts_GC_1x salt_rep_4_Light

description: Gene expression after 200 mM salt treatment


title: Ts_GC_3x salt_rep_1_Light


title: Main1.ADT.010819.l2


title: KO Infl. rep1


title: Ts_GC_1x salt_rep_3_Light


title: Ts_GC_1x salt_rep_2_Light


title: A549-Mock-2

source_name: A549 cell line

value: A549 cell line


title: Main1.ADT.010819.l1


title: WT Infl. rep4

value: Wild type


title: A549-Mock-1


title: Main1.ADT.113018.l2


title: Ts_GC_non salt_rep_4_Light

description: Gene expression after non salt treatment


title: A549-IFN-2


title: WT Infl. rep3


title: Main1.ADT.113018.l1


title: WT Infl. rep2


title: Ts_GC_1x salt_rep_1_Light


title: Ts_GC_non salt_rep_3_Light


title: WT Infl. rep1


title: Main2.010819.l1


title: Main2.010819.l2


title: KO rep4

value: Steady State


title: Main2.113018.l2


title: KO rep3


title: Ts_GC_non salt_rep_1_Light


title: Main2.113018.l1


title: KO rep2


title: Control2

city: shanghai

first: Qi

last: yingxin

address: NO.800 Dongchuan Road, Shanghai

institute: shanghai jiao tong university

description:
C2
Gene expression data from control.

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
Genome_build: Rnor6
Supplementary_files_format_and_content: TXT file contains counts for each sample

organism: Rattus norvegicus

growth_protocol: Male Sprague-Dawley (SD) rats with an average weight of 400 g were anesthetized with isoflurane inhalation (MATRX VIP 3000, USA). The left carotid arteries were exposed, and a percutaneous transluminal angioplasty balloon dilatation catheter (2 F, 0.67 mm, Edwards Lifesciences, USA) was used to establish vascular intimal injury (Raugi et al., 1990). The arteries were then harvested after 2 wks, and the undamaged right carotid artery served as the self-control.

extract_protocol:
prefrontal cortex were rharvested , flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The intimal injury arteries harvested after 2 wks, and the undamaged right carotid artery served as the self-control, then performed transcriptome sequencing.

value: male

value: Sprague-Dawley (SD)

value: the undamaged carotid artery


title: Control1

description:
C1
Gene expression data from control.


title: WT rep4

value: Popliteal & brachial Lymph Node

value: Lymphatic endothelial cells


title: Main1.113018.l2


title: Main1.010819.l1


title: WT rep3


title: Neo3

description:
N3
Gene expression data from Intimal injury.

source_name: Intimal injury 3

value: the carotid artery at 2 wks after intimal injury


title: Main1.113018.l1


title: Neo2

description:
N2
Gene expression data from Intimal injury.

source_name: Intimal injury 2


title: Control4

description:
C4
Gene expression data from control.


title: Control3

description:
C3
Gene expression data from control.


title: WT rep1


title: SCC_4AKO_2

city: Shanghai

first: WUCHANG

last: ZHANG

state: Shanghai

address: 115 Jinzun Road

department: School of stomatology

institute: Shanghai Jiao Tong University

data_processing:
The reads were aligned to the mm9 build of the mouse genome using Tophat.
Expression of the transcript was determined using Cufflinks with Refseq mRNAs to guide assembly.
Genome_build: mm9

source_name: Primary SCC

growth_protocol: were not cultured

extract_protocol:
We extracted total RNA using Trizol reagent and then purified them using Dynabeads™ mRNA Purification Kit (Invitrogen, Cat No: 61006).
Libaray was constructed with Stranded RNA-Seq Library Preparation Kit (Kapa Biosystems, Cat No:KK8400)

treatment_protocol: KDM4A was knocked out in an inducible manner

value: squamous cell carcinoma

value: primary mouse SCCs

tag: genotype/variation

value: KDM4A knockout


title: v7_m2

city: Uppsala

first: Frauke

last: Augstein

address: Almas Allé 5

department: IOB

country: Sweden

institute: Uppsala University

data_processing:
Mapping to Arabidopsis thaliana reference genome with Hisat2
Generating of Count files with HTSeq
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: root

growth_protocol: Seeds were surface sterilized with ethanol, plated on 1/2MS+MES+bactoagar plates on mesh and stratified for 2 days. Seedlings were grown for 5 days in long day conditions, 16h light (22 C) and 8h darkness (20 C) at light intensity of 110µE/m2/s. Per sample 50-100 seedlings were pooled.

extract_protocol:
RNA was extracted using RNAeasy Plant Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using NEBNext®UltraTM RNA Library Prep Kit for Illumina® for paired-end sequencing with read length 150

treatment_protocol: Seedlings were transferred to plates containing 1µM ABA or mock and treated for 8h.

value: root

value: 5 days

value: mock


title: v7_m1


title: SCC_4AKO_1


title: S. aureus inoculum, Replicate 3

city: Hoersholm

first: Christian

last: Garde

address: Dr Neergaards Vej 5F

country: Denmark

institute: Evaxion Biotech

description:
4986
29213.tsv.gz

data_processing:
Fastq files were preprocessed using cutadapt and base qualities checked using fastqc.
The reads were mapped against the human reference genome hg38 using STAR. Unmapped reads were mapped to the NC_007795.1 reference genome using bwa mem.
Gene read coverages were computed using featureCounts.
Differential gene expression analysis was conducted using the DESeq2 workflow with the BH corrected Wald test and log2FC skrinkage
Genome_build: hg38, NC_007795.1
Supplementary_files_format_and_content: Tab separated text files with gene read coverages.

organism: Staphylococcus aureus

growth_protocol: The Staphylococcus aureus ATCC29213 reference strain and primary human umbilical cord endothelial cells (HUVEC from pooled donors, passage 2-3, PromoCell) were used for all experiments. Prior to experiments, the bacteria were grown until exponential growth phase in tryptic soy broth (2½h at 37°C), and bacterial stock solution could then be prepared by centrifugation and resuspension of pellet in phosphate buffered saline (PBS) followed by adjustment to OD600=0.1. HUVECs were grown until confluence in basal medium (Endothelial Cell Growth Medium 2, PromoCell) with fetal bovine serum (FBS) and penicillin-streptomycin (PS) and then split into microtiter plates. Prior to experiments, the confluent HUVEC microtiter plates were washed 3 times in PBS and filled with 0.5 ml basal medium+FBS without PS.

extract_protocol:
Pellets were resuspended in 700 μl acetate buffer (20 mM NaOAc, 1 mM EDTA, 0.5% SDS, pH 4.5) and transferred to FastPrep tubes containing lysing matrix B. Cells were lysed in a Thermo Savant FastPrep FP120 Cell Homogenizer at 6.0 m/sec for 3 x 40 sec with 1 min pause on ice in between runs, and then centrifuged for 5 min at 20,000 g. Lysate was transferred to tubes containing 500 μl phenol solution (2:1 phenol in water adjusted to pH 4.5 with NaOAc) and 100 μl chloroform followed by incubation at 65 °C at 1100 rpm in a thermomixer for 15 min with vortexing every 2 min. After centrifugation, the aqueous phase was transferred into tubes containing 500 μl chloroform followed by vortexing, centrifugation, and transferring to new tubes. The RNA was precipitated using 96% EtOH and 10vol% 3M NaOAc on ice for ≥1 hour. Tubes were centrifuged for 60 min at 4°C, and pellets were washed in ice cold 70% EtOH followed by centrifugation for 10 min. Supernatant was removed and pellets were then air-dried and dissolved in sterile ddH2O. RNA quantity was measured using Nanodrop spectrophotometer, and RNA quality was then verified by fragment analysis using a Fragment Analyzer (Agilent), followed by RiboZero Gold (MRZE724, Epidemiology/Illumina) treatment on the 3 samples from each group to remove both human and bacterial rRNA.
After DNase treatment, library preparation was performed using the NebNext® UltraTM Library prep kit (NEB) followed by quality assessment by the fragment analyzer

treatment_protocol: Microtiter plates were inoculated with 20 μl of bacterial stock suspension corresponding to a multiplicity of infection (MOI) of 16, followed by centrifugation at 300g for 5 min to sediment the bacteria. After 1½ hours post-infection (hpi), wells were supplemented with lysostaphin (10 μg/ml) + gentamicin (100 μg/ml). HUVEC samples were collected by washing 3 times in PBS followed by trypsination for 10 min, centrifugation, and washing the pellet followed by centrifugation and resuspension of the pellet in 100 μl PBS. Samples were then snap-frozen in liquid nitrogen and kept at -80°C until RNA isolation.

value: Inoculum

tag: s. aureus strain


title: v7_m3


title: SCC_Control_2

value: control


title: S. aureus inoculum, Replicate 2

description:
4985
29213.tsv.gz


title: v7_A3

value: 1µM ABA


title: S. aureus inoculum, Replicate 1

description:
4984
29213.tsv.gz


title: v7_A2


title: WT rep2

value: Wild type


title: v7_A1


title: keratinocytes in DKSFM rep2

city: Cincinanti

first: Ying

last: Xia

state: Ohio

address: 160 Panzeca Way

department: Department of Environmental and Public Health Sciences

institute: Univerisity of Cincinanti

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq via Illumina BaseSpace
fastq seqences were aligned using STAR via Illumina BaseSpace RNA-Seq Alignment v2.0.2 app
differential expression analysis was performed using DESeq2 via Illumina BaseSpace RNA-Seq Differential Expression app version 1.0.1 app
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited raw counts with genes in rows and samples in columns

source_name: Neonatal skin

growth_protocol: KSFM-Ca2+ cells were derived and cultured in KSFM-Ca2+ medium (Gibco, 37010-022). The DKSFM cells were derived from KSFM-Ca2+ cells, adapted and cultured in DKSFM (Gibco,10744019)

extract_protocol:
Total RNA was isolated from KSFM-Ca2+ and DKSFM cells using PureLink RNA Mini Kit (12183025, Invitrogen).
RNA libraries were prepared using standard Illumina protocols  for sequencing

treatment_protocol: No treatment

value: murine keratinocyte line adapted in DKSFM


title: v123_m3


title: Kasumi-1 treated with OGP46 2

city: Weifang

first: Liuya

last: Wei

address: 7166 number, Baotong West Street

institute: Weifang Medical University

description: *** Raw files were not submitted to GEO because they were lost and thus not available ***

data_processing:
Raw reads were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat 2.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with FPKM values for every gene and every sample

source_name: Kasumi-1 cell line treated with OGP46 2#

extract_protocol:
Total RNA was extracted using using Trizol reagent following the manufacturer's protocol.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions.

value: incubating with OGP46 for 48 h

value: 1 uM OGP46


title: Neo1

description:
N1
Gene expression data from Intimal injury.

source_name: Intimal injury 1

value: male

value: Sprague-Dawley (SD)


title: keratinocytes in DKSFM rep3


title: Kasumi-1 treated with OGP46 3

source_name: Kasumi-1 cell line treated with OGP46 3#


title: Kasumi-1 treated with OGP46 1

source_name: Kasumi-1 cell line treated with OGP46 1#


title: keratinocytes in DKSFM rep1


title: v123_m2


title: Dnmt3a_MAV_2

city: Houston

first: Katherine

middle: Y.

last: King

state: Texas

address: 1102 Bates Ave., Ste.1150

department: Pediatrics and Infectious diseases

institute: Baylor College of Medicine

description: Dnmt3a MAV vs Dnmt3a naïve

data_processing:
RNA-seq libraries were prepared by using SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara Bio Usa
Pico Input Mammalian (Takara Bio Usa). Illumina NovaSeq SP was used for sequencing with a paired-end sequencing length of 10bp.
FASTQ files were preprocessed using HTS stream (https://github.com/ibest/HTStream)
Clean FASTQ file were aligned using STAR
Differential expression (DE) analysis of gene expression was performed using Limma-Voom.
Genome_build: M22 (GRCm38.p6)
Supplementary_files_format_and_content: Counts.txt  (Normalized gene expression)
Supplementary_files_format_and_content: WT MAV vs WT naïve.xls  (Gene expression comparisons between WT infection (MAV) samples and WT naïve)
Supplementary_files_format_and_content: Dnmt3a MAV vs Dnmt3a naïve.xls  (Gene expression comparisons between Dnmt3a infection (MAV) samples and Dnmt3a naïve)

source_name: LT-HSCs

extract_protocol:
RNA was isolated with the NucleoSpin ® RNA Plus XS kit (Macherey Nagel)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 1 month of infection with M. avium

tag: infection

value: M. avium

value: HSCs


title: Kasumi-1 control 3

source_name: Kasumi-1 cell line treated with control 3#

value: incubating with control for 48 h

value: DMSO as control


title: Dnmt3a_MAV_1

description: Dnmt3a MAV vs Dnmt3a naïve

tag: cell type


title: v123_A3

tag: genotype


title: keratinocytes in KSFM-Ca2+ rep2

value: murine keratinocyte line grown in low calcium media


title: keratinocytes in KSFM-Ca2+ rep1


title: SCC_Control_1

value: squamous cell carcinoma

value: primary mouse SCCs


title: Dnmt3a_naive

description: Dnmt3a MAV vs Dnmt3a naïve

value: PBS


title: v123_A2

value: root

value: 5 days


title: Kasumi-1 control 1

source_name: Kasumi-1 cell line treated with control 1#

tag: cell line


title: Ts_GC_non salt_rep_2_Light

value: 9 weeks


title: WT_MAV_2

description: WT MAV vs WT naïve

value: WT


title: Ebp1_Total_Rep2

city: Berlin

description: ribosome-protected mRNA fragment

data_processing:
Raw reads were processed as described previously (Galmozzi et al., 2019) using standard analysis tools (Cutadapt, Bowtie2, TopHat2) and python scripts adapted to Mus musculus. In short, trimmed reads between 23 and 37 nucleotides in length were aligned to the mouse transcriptome (NCBI RefSeq mm10) by TopHat2 (Kim et al., 2013), allowing up to two mismatches.
Ribosomal A sites were statistically estimated by (virtually) cutting 11 nucleotides from both 5' and 3' read ends ('center weighting').
RPKM values were calculated using the Plastid CS program (Dunn and Weissman, 2016). Further analyses were performed using customized python scripts. SeRP analyses are based on two independent biological replicates that were highly reproducible. Genes were only considered for analysis if they fulfill the following requirements: i) at least 64 reads in all total and Ebp1-bound translatome datasets; ii) at least 2 RPKM in all total and Ebp1-bound translatome datasets.
For metagene enrichment analysis of Ebp1 binding, we aligned open reading frames (ORFs) as indicated and divided the mean RPM value of the IP translatome by the mean RPM value of the total translatome at each codon along the aligned ORFs. Values at each codon were smoothed using a 20 residue rolling average. Analyses were performed using either all genes that were detected in the dataset or by splitting genes into pre-defined subsets based on their cellular localization or protein features. Information about cellular localization and protein features were received from UniProt (www.uniprot.org).
Genome_build: mouse transcriptome (NCBI RefSeq mm10)
Supplementary_files_format_and_content: counts_table.csv

source_name: Neuro2a cell line in culture

growth_protocol: For each biological replicate (n=2), three 15 cm plates of Neuro2a cells were grown in standard DMEM (Gibco, 31966047) with 10 % FBS (Gibco, 10270106) and 1 % penicillin-streptomycin (Gibco, 15140122) to a confluence of 80 % in humidified 37 °C, 5 % CO2.

extract_protocol:
Cells were washed and detached in 10 mL ice-cold PBS supplemented with 12 mM MgCl2 and 100 µg/mL cycloheximide (Sigma-Aldrich, C7698) and centrifuged for 4 min at 300 xg, 4 °C. The cell pellet was lysed in 0.5 mL lysis buffer (20 mM Tris-HCl, pH 8.0, 140 mM KCl, 12 mM MgCl2, 5mM CaCl2, 0.5 % NP-40, 100 µg/mL cycloheximide, 25 U/mL DNase-I (Roche, 4716728001), 1x Protease Inhibitor cOmplete EDTA-free (Roche, 05056489001), 1 mM PMSF (Roth, 6367)). The lysate was passed five times through a 23 G needle and cleared by centrifugation (2 min at 13000 xg, 4 °C). After clearing the lysate by centrifugation (2 min at 13000 xg, 4 °C), the supernatant was divided for total (200 µL) and IP (400 µL) translatome samples. Total samples were digested with MNase (300 U / 1 A260 nm) for 30 min at 4 °C, under rotation. The reaction was terminated by addition of 10 mM EGTA and ribosomes were purified by sucrose cushion centrifugation (25 % sucrose, 20 mM Tris-HCl pH 8.0, 140 mM KCl, 12 mM MgCl2, 100 µg/mL cycloheximide, 1 mM PMSF) for 90 min, 75000 rpm, at 4 °C (Beckmann AT2 S120 rotor). Pelleted ribosomes were resuspended in lysis buffer lacking CaCl2 and subjected to phenol-chloroform extraction of RNA. IP samples were mixed with 100 µL Dynabeads (Life Technologies, 10008D) conjugated with 10 µg anti-Ebp1CT (Abcam, ab35424) and digested using MNase (300U / 1 A260nm) for 30 min at 4 °C, under rotation. The reaction was terminated by addition of 10mM EGTA and the beads were washed three times in 400 µL wash buffer (50 mM Tris-HCl pH 7.5, 150 mM NaCl, 12mM MgCl2, 1 mM PMSF, 100 µg/mL cycloheximide, 0.1 % NP-40) followed by phenol-chloroform extraction of RNA.
Gel purification and 3'-dephosphorylation of ribosome-protected footprints from total and IP samples was performed as previously described (Galmozzi et al., 2019). Footprints were then 5'-phosphorylated using T4 PNK (NEB, M0201S) and ATP for 1 hr at 37 °C. Deep sequencing libraries were prepared from these RNA fragments using the NEXTflex Small RNA-seq Kit v3 (Bio Scientific, NOVA-5132-06).

value: MNase digestion

tag: rip antibody


title: Ebp1_Total_Rep1

description: ribosome-protected mRNA fragment


title: v123_A1

tag: age

value: 1µM ABA


title: WT_MAV_1

description: WT MAV vs WT naïve


title: NB4 treated with OGP46 3

source_name: NB4 cell line treated with OGP46 3#

value: incubating with OGP46 for 48 h

value: 1 uM OGP46


title: Ebp1_IP_Rep2

description: ribosome-protected mRNA fragment


title: keratinocytes in KSFM-Ca2+ rep3


title: v123_m1

value: mock


title: NB4 treated with OGP46 1

source_name: NB4 cell line treated with OGP46 1#


title: WT_naive

description: WT MAV vs WT naïve


title: Sample Q001S0002B0011R3N

city: Ames

first: Roger

last: Wise

state: IA

address: Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, 1344 Advanced Teaching & Research Bldg., 2213 Pammel Dr.

department: CICGRU

institute: USDA/ARS

data_processing:
Library strategy: Amplicon-seq
Adapter Trimming - Each sample was processed using Trimmomatic to trim off adapters. Fastqc analysis revealed that most of the reads are of high quality. Hence, no quality trimming was performed.
Alignment - Reads from each sample were aligned to the genome of barley, Blumeria and vector sequences using STAR (dobin et. Al 2013).
Fusion read recognition - Custom python scripts were used to recognize fusion reads based on the partial alignment to the genomes and vector sequences. Vector portions were trimmed off from fusion reads.
Differential expression analysis - Salmon (Patro 2017) was used to obtain gene counts. Samples were size normalized and differential expression analysis was carried out using DESeq2 (Love 2014).
In-frame fusion reads  - Fusion reads expressed in-frame with the protein were recognized by translating the entire sequence and comparing with the protein.
Genome_build: Barley (Mascher 2017) and Blumeria (Ensembl Fungi Assembly EF 2) (Spanu 2018).
Supplementary_files_format_and_content: Read count data for barley and powdery mildew.

organism:
Hordeum vulgare
Blumeria hordei

source_name: Barley infected first leaf (PO:0007094)

growth_protocol: Yeast were grown at 28C shaking at 225rpm. Cells were subcultured once they reached saturation (OD600 >2.5).

extract_protocol:
Yeast cells were treated with lyticase to digest cell walls and Y2H plasmids were extracted using alkaline lysis and precipitation.
Libraries were constructed using the Nugen Ultralow System V2 with Custom AnyDeplete to reduce the abundance of an amplicon common to all libraries using the manufacturer's instructions.

treatment_protocol: Yeast were incubated in SC-Leu-Trp (no selection) or SC-Leu-Trp-His (reporter selection) liquid media. Two rounds of growth selection were performed.

tag: plant genotype

value: CI 16151 (Resistant progenitor), m19089 (resistant bln1 mutant), m18982 (susceptible mla6 mutant), m19028 (susceptible mla6 + bln1 double mutant), m11526 (susceptible rar3 mutant)

tag: fungal isolate

value: Bgh isolate 5874 (AVRa6)

value: Non-selected

tag: replication


title: Col0_A3


title: NB4 control 2

source_name: NB4 cell line treated with control 2#

value: incubating with control for 48 h

value: DMSO as control


title: Sample Q001S0002B0011R2N


title: Kasumi-1 control 2

source_name: Kasumi-1 cell line treated with control 2#


title: Col0_m1


title: Ebp1_IP_Rep1

first: Matthew

last: Kraushar

address: Ihnestrasse 63-73

institute: Max Planck Institute for Molecular Genetics

description: ribosome-protected mRNA fragment


title: Col0_A2


title: Col0_m3


title: Sample Q001S0002B0011R1N


title: NB4 control 1

source_name: NB4 cell line treated with control 1#


title: NB4 treated with OGP46 2

source_name: NB4 cell line treated with OGP46 2#


title: Col0_A1

source_name: root


title: Col0_m2


title: MF24_11 [RNA-Seq]

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

description:
Sample_135316
MF24hr.Control

data_processing:
Alignment with STAR
Raw counts with featureCounts
Genome_build: hg19
Supplementary_files_format_and_content: raw counts

source_name: normal adult human lung fibroblasts

growth_protocol: Cell culture was performed in low glucose Dulbecco’s modified Eagle’s medium (DMEM; Gibco Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum (FBS, Hyclone, Logan, UT), 100 Units/mL penicillin, and 100 µg/mL streptomycin (Invitrogen, Carlsbad, CA).  Cells were then serum-starved in FBS-free DMEM overnight and differentiation to myofibroblasts was induced by treatment with TGFβ for 48 h.

extract_protocol:
RNA extraction was performed using the Qiagen miRNeasy Mini kit per the manufacturer’s instructions to extract all RNA moieties >18nt. Genomic DNA was digested on-column per the manufacturer’s instructions using the RNase-Free DNase Set (New England Biolabs). Samples were split between total RNA and small RNA library preps.
NEBNext rRNA ultra II

treatment_protocol: CCL210 human adult lung fibroblasts were treated with PGE2, FGF2, or left untreated

value: CCL210 (ATCC)

value: Control

tag: time point


title: MC_NS102_48h_rep3, mast cells

city: Pittsburgh

first: Daniel

middle: H

last: Kaplan

address: 200 Lothrop Street

institute: University of Pittsburgh

data_processing:
RNA-sB68eq:  Paired-end reads were aligned using STAR aligner to mm9 genome assmebly. Cufflinks was used to measure transcripts abundance and report it as FPKM values.
Software used:  STAR aligner,  Cufflinks
Genome_build: mm9
Supplementary_files_format_and_content: RNA-seq data as cufflink reported FPKM values

growth_protocol: peritoneal-derived mast cells (PCMC) were cultured for 48 hours with vehicle or NS102; or PCMC cultured for 6 hours in glutamate-free Tyrode’s buffer supplemented with vehicle or 4 mM glutamate.

extract_protocol:
The whole skin tissues or sorted mast cells were homogenized using a homogenizer, and mRNA was processed using the Qiagen RNeasy Kit following the manufacturer’s instructions.
Illumina single and paired end libraries, RNA-seq and DNA-seq
Adapter ligation to fragements followed by pcr amplification using indexed primers for Illumnia HiSeq-2500

treatment_protocol: MrgprdDTR mice and control MrgprdCre mice were treated with DT for 3-4 weeks. Ear of WT mice were treated with 50 mM β-ala or vehicle once daily for two days.

value: Mast Cells

tag: sample derived from

value: Peritoneal


title: NB4 control 3

source_name: NB4 cell line treated with control 3#


title: FGMF24_12 [RNA-Seq]

description:
Sample_135317
FGF2.24hr


title: Sample Q001S0002B0011R3S

value: Selected


title: Sample Q001S0002B0011R2S


title: Q0990_m3

tag: tissue

value: root

value: 5 days


title: E2MF6_10 [RNA-Seq]

description:
Sample_135315
PGE2.6hr


title: Q0990_m1


title: MC_NS102_48h_rep2, mast cells


title: MF6_9 [RNA-Seq]

description:
Sample_135314
MF6hr.Control


title: Sample Q001S0002B0010R3N


title: MC_NS102_48h_rep1, mast cells


title: Q0990_A3


title: FGMF24_8 [RNA-Seq]

description:
Sample_135313
FGF2.24hr


title: Q0990_A2


title: Sample Q001S0002B0010R2N


title: MF24_7 [RNA-Seq]

description:
Sample_135312
MF24hr.Control


title: MC_vehicle_48h_rep4, mast cells


title: MC_NS102_48h_rep4, mast cells


title: MC_vehicle_48h_rep2, mast cells


title: MC_vehicle_48h_rep3, mast cells


title: Sample Q001S0002B0010R3S


title: J1721_m3


title: Q0990_A1


title: Q0990_m2


title: Neo4

description:
N4
Gene expression data from Intimal injury.

source_name: Intimal injury 4

tag: Sex

value: male

value: Sprague-Dawley (SD)

value: the carotid artery at 2 wks after intimal injury


title: MF6_5 [RNA-Seq]

description:
Sample_135310
MF6hr.Control


title: Sample Q001S0002B0010R2S


title: MC_vehicle_48h_rep1, mast cells

tag: strain


title: E2MF6_6 [RNA-Seq]

description:
Sample_135311
PGE2.6hr

tag: treatment


title: Sample Q001S0002B0011R1S


title: J1721_m2


title: HTBE-Mock-1

state: CA

source_name: tracheobronchial epithelial cells

value: tracheobronchial epithelial cells

value: Mock

tag: replicate