title: Control_48hpf_Replicate-1

description:
Control_48hpf_1
Total RNA isolated from untreated control zebrafish embryos at 48 hpf.


title: Control_48hpf_Replicate-2

status: Public on Apr 20 2022

type: SRA

city: Corvallis

first: Christopher

middle: Michael

last: Sullivan

state: OR

address: Sinnhuber Aquatic Research Laboratory, 28645 East HWY 34

department: Environmental & Molecular Toxicology

country: USA

institute: Oregon State University

description:
Control_48hpf_2
Total RNA isolated from untreated control zebrafish embryos at 48 hpf.

library_source: transcriptomic

data_processing:
SOAPnuke for read filter.
HISAT2 for genome mapping.
Bowtie2 for reference genome map.
DESeq2 for differential expression.
Genome_build: GCF_000002035.6_GRCz11
Supplementary_files_format_and_content: Excel files with compiled normalized count and clean read files for all samples.
Supplementary_files_format_and_content: AllSamples.GeneExpression.FPKM.xlsx: FPKM normalized read counts.
Supplementary_files_format_and_content: FilterSummary.xlsx: Read percentages.
Supplementary_files_format_and_content: GeneExpressionSummary.xlsx: Clean read and mapping %.

molecule: total RNA

organism: Danio rerio

source_name: Zebrafish embryonic total RNA

extract_protocol:
Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf.
Library prep and sequencing were done on a Beijing Genomics Institute DNBseq-G50 platform, with 100 bl PE.

treatment_protocol: Zebrafish embryos were untreated or treated with 3.5 GHz RFR from 6-48 hpf.

tag: tissue

value: whole embryos

tag: developmental stage

value: 48 hpf

tag: treatment

value: Control


title: 8h_WT_M4_pIC

city: Epalinges

first: Nicolas

last: Fasel

address: Chemin des Boveresses 155

department: Department of Biochemistry

country: Switzerland

institute: University of Lausanne

data_processing:
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.8, Martin 2011).
Reads matching to ribosomal RNA sequences were removed with fastq_screen (v. 0.11.1). Remaining reads were further filtered for low complexity with reaper (v. 15-065, Davis et al. 2013)
Reads were aligned against the Mus musculus.GRCm38.92 genome using STAR (v. 2.5.3a, Dobin et al. 2013). The number of read counts per gene locus was summarized with htseq-count (v. 0.9.1, Anders et al. 2014) using Mus musculus.GRCm38.92 gene annotation.
Quality of the RNA-seq data alignment was assessed using RSeQC (v. 2.3.7, Wang et al. 2012). Reads were also aligned to the Mus musculus.GRCm38.92 transcriptome using STAR (v. 2.5.3a, Dobin et al. 2013) and the estimation of the isoforms abundance was computed using RSEM (v. 1.2.31, Li and Dewey 2011).
Statistical analysis was performed for genes independently in R (R version 3.4.4). Genes with low counts were filtered out according to the rule of 1 count(s) per million (cpm) in at least 1 sample. Library sizes were scaled using TMM normalization. Subsequently, the normalized counts were transformed to cpm values, and a log2 transformation was applied, by means of the function cpm with the parameter setting prior.counts = 1 (EdgeR v 3.20.9; Robinson et al. 2010).

organism: Mus musculus

source_name: Bone marrow derived macrophages

growth_protocol: Macrophages were isolated from bone marrow of C57BL/6 mice (wild-type or knock-out). Hind leg bones were collected and the bone marrow was flushed out with complete DMEM medium, containing DMEM (Dulbecco’s modified Eagle’s medium, Gibco), supplemented with 10% heat-inactivated FBS (Gibco), 1% Penicillin-Streptomycin Solution (BioConcept) (i.e. 100 IU/ml and 100 µg/ml respectively), 1% HEPES (BioConcept) (i.e. 10mM). The cells were differentiated into macrophages for 6 days in complete DMEM medium containing 50 ng/ml recombinant mouse Macrophage Colony Stimulating Factor (rmM-CSF, ImmunoTools), at 37°C and 5% CO2, in Sterilin Petri Dish (Thermo Scientific). Then, the bone marrow-derived macrophages (BMDMs) were detached with 1X DPBS (Gibco) containing 5 mM EDTA, washed and resuspended with complete DMEM medium. The cells were plated in 12-well plates (TPP) with 1.95 million cells per well. They were finally put back in culture at 37°C and 5% CO2.

extract_protocol:
BMDMs were cleared out of supernatants and lysed with 350 µl RLT buffer (Qiagen) supplemented with 40 mM DTT (Dithiotreitol) for RNA extraction. Plates were then frozen at -80°C until the RNA purification. The RNA samples were purified with the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s instructions. Purified RNA was eluted with 30 µl RNase-free water (Qiagen).
Library preparation and sequencing were performed at the Lausanne Genomic Technologies Facility (GTF), University of Lausanne (UNIL), Switzerland

treatment_protocol: One day after their plating, murine BMDMs were infected with stationary-phase Leishmania promastigotes with a multiplicity of infection of 5. Cells were also alternatively treated with Poly(I:C) (HMW), a TLR3 agonist (mimicking dsRNA), or FSL1, a TLR2 agonist.  As controls, non treated or non infected (Medium) wells were filled with complete DMEM medium alone. The cells were incubated at 35°C and 5% CO2 until 8 and 24 hrs post -infection or -treatment (h post-treatment).

tag: strain

tag: genotype

value: WT

tag: time-point

value: Poly IC


title: Control_120hpf_Replicate-3

description:
Control_120hpf_3
Total RNA isolated from untreated control zebrafish embryos at 120 hpf.

value: 120 hpf


title: 8h_WT_M4_FSL1


title: 4h_PRX5neg_M1_H2O2_4h

tag: gender

value: female

value: H2O2 4h


title: 4h_NRF2_M4_H2O2_2h

value: H2O2 2h


title: Control_120hpf_Replicate-2

description:
Control_120hpf_2
Total RNA isolated from untreated control zebrafish embryos at 120 hpf.


title: Control_120hpf_Replicate-1

description:
Control_120hpf_1
Total RNA isolated from untreated control zebrafish embryos at 120 hpf.


title: 8h_WT_M4_Vneg


title: 4h_NRF2_M4_Medium

value: Non-treated


title: 5G_48hpf_Replicate-4

description:
5G_48hpf_4
Total RNA isolated from zebrafish embryos treated with 3.5 GHz RFR from 6-48 hpf and collected at 48 hpf.


title: 4h_PRX5pos_M1_H2O2_2h


title: 8h_WT_M4_Vpos


title: 4h_PRX5pos_M1_H2O2_4h


title: 4h_NRF2_M4_H2O2_4h


title: 8h_WT_M4_Vpos_FSL1

value: LgyLRV1+ and FSL1


title: 8h_WT_M4_Medium


title: 5G_48hpf_Replicate-1

description:
5G_48hpf_1
Total RNA isolated from zebrafish embryos treated with 3.5 GHz RFR from 6-48 hpf and collected at 48 hpf.


title: 5G_48hpf_Replicate-2

description:
5G_48hpf_2
Total RNA isolated from zebrafish embryos treated with 3.5 GHz RFR from 6-48 hpf and collected at 48 hpf.


title: 5G_120hpf_Replicate-3

description:
5G_120hpf_3
Total RNA isolated from zebrafish embryos treated with 3.5 GHz RFR from 6-48 hpf and collected at 120 hpf.


title: 4h_PRX5neg_M3_H2O2_4h


title: 8h_iNOS_M1_pIC

value: inos-/-


title: 5G_120hpf_Replicate-4

description:
5G_120hpf_4
Total RNA isolated from zebrafish embryos treated with 3.5 GHz RFR from 6-48 hpf and collected at 120 hpf.


title: 8h_iNOS_M1_Vneg


title: 5G_120hpf_Replicate-1

description:
5G_120hpf_1
Total RNA isolated from zebrafish embryos treated with 3.5 GHz RFR from 6-48 hpf and collected at 120 hpf.


title: 5G_120hpf_Replicate-2

description:
5G_120hpf_2
Total RNA isolated from zebrafish embryos treated with 3.5 GHz RFR from 6-48 hpf and collected at 120 hpf.


title: Control_120hpf_Replicate-4

description:
Control_120hpf_4
Total RNA isolated from untreated control zebrafish embryos at 120 hpf.


title: 8h_iNOS_M1_Vpos


title: 4h_PRX5neg_M3_Medium


title: 7_2

city: Shihezi

first: li

middle: guo

last: zhi

state: xinjiang

address: Xiangyang Street

department: College of Life Sciences

country: China

institute: Shihezi University

description: G. uralensis underground parts CK

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp (https://github.com/OpenGene/fastp) with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml) software. The mapped reads of
each sample were assembled by StringTie(https://ccb.jhu.edu/software/stringtie/index.shtml? t=example) in a reference-based approach.
To identify DEGs (differential expression genes) between two different samples, the expression level of each transcript was calculated according to the transcripts per million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances. Essentially, differential expression analysis was performed using the DESeq2/DEGseq/EdgeRwith Q value ≤ 0.05, DEGs with |log2FC|>1 and Q value <= 0.05(DESeq2 or EdgeR) /Q value <= 0.001(DEGseq) were considered to be significantly different expressed genes). In addition, functional-enrichment analysis including GO and KEGG were performed to identify which DEGs were significantly enriched in GO terms and metabolic pathways at Bonferroni-corrected P-value ≤0.05 compared with the whole-transcriptome background. GO functional enrichment and KEGG pathway analysis were carried out by Goatools (https://github.com/tanghaibao/Goatools) and KOBAS (http://kobas.cbi.pku.edu.cn/home.do).
Genome_build: The results of expression quantification are expressed in TPM, and the homogenisation process of TPM results in consistent total expression across samples.

organism: Glycyrrhiza uralensis

source_name: underground parts

extract_protocol:
Total RNA was extracted from the tissue using Plant RNA Purification Reagent for plant tissue according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample(OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥8.0, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The G. uralensis seedlings were grown hydroponically for 1 week and then subjected to a simulated drought treatment (MS nutrient solution containing 150 mM NaCl ) for 0, 2, 6 and 12. The 0 h sample served as the control group.

value: root

tag: age

value: seedlings of 60 days

value: distilled water


title: 8h_iNOS_M1_Medium


title: 4h_PRX5neg_M3_H2O2_2h


title: 5G_48hpf_Replicate-3

description:
5G_48hpf_3
Total RNA isolated from zebrafish embryos treated with 3.5 GHz RFR from 6-48 hpf and collected at 48 hpf.


title: 4h_NRF2_M2_H2O2_4h


title: 4h_PRX5pos_M1_Medium


title: 8h_IFNAR_M4_Vpos_FSL1

value: Ifnar-/-


title: 4h_NRF2_M2_H2O2_2h


title: R6

description: G. uralensis underground parts salt stress 6h

value: 150 mM NaCl for 6h


title: R7

description: G. uralensis underground parts salt stress 12h

value: 150 mM NaCl for 12h


title: R5


title: R8


title: 8h_IFNAR_M4_Vneg_FSL1

value: LgyLRV+- and FSL1


title: 4h_NRF2_M2_Medium


title: R3

description: G. uralensis underground parts salt stress 2h

value: 150 mM NaCl for 2h


title: R2


title: R4


title: 4h_WT-F_M4_H2O2_4h

value: WT


title: 9_2

description: G. uralensis underground parts CK


title: R1


title: 8h_IFNAR_M4_Vneg


title: 8_2

description: G. uralensis underground parts CK


title: 8h_IFNAR_M4_Vpos


title: R9


title: 4h_WT-F_M4_Medium


title: 8h_IFNAR_M4_Medium


title: Kotho-treated H3K27me2/3 ChIP

city: Los Angeles

first: James

middle: G

last: Tidball

state: CA

address: 610 Charles E Young Drive E

department: Integrative Biology and Physiology

institute: University of California, Los Angeles

library_source: genomic

data_processing:
Raw fastq files were aligned to the mm10 genome using Bowtie2 (PMID: 22388286) with default parameters, achieving an alignment rate between 95-98%.  Resulting SAM files were converted to BAM format and sorted using Samtools (PMID: 19505943).
Genome_build: mm10
Supplementary_files_format_and_content: bigWigs showing read density are provided

molecule: genomic DNA

source_name: C2C12 cells

growth_protocol: C2C12 myoblasts were seeded on 60 mm culture plates at 100,000 cells per dish or in 6-well plates at 40,000 cell per well. Myoblasts were maintained in growth medium (Dulbecco’s Modified Eagle Medium (DMEM) containing 10% FBS, penicillin and streptomycin) at 37°C and in 5% CO2. Culture medium was refreshed every other day unless otherwise stated.

extract_protocol:
C2C12 myoblasts were seeded at 2.0 x 105 on 100 mm culture dishes and maintained in growth medium and treated with Klotho as outlined above. Following 48 hours of stimulation cells were washed with DPBS, released with 0.05% trypsin EDTA (Gibco) and quenched with growth medium. Cells were fixed in 1% formaldehyde on an end-to-end rotator (Barnstead/Thermolyne) for 10 minutes at room temperature. 1% formaldehyde solution was quenched with 2 M glycine for a final concentration of 125 mM glycine and incubated on rotation for 10 minutes. Cells were washed 3 times with cold DPBS prior to lysing. Subsequent steps were done following the ChIP-IT High Sensitivity Kit (Active Motif #53040) manufacturer’s protocol. Cells were lysed in chromatin prep buffer (from the Active Motif kit) containing proteinase inhibitor cocktail and 100 mM phenylmethylsulfonyl fluoride (PMSF) and incubated on ice for 10 minutes. The lysate was transferred to an ice-cold Dounce homogenizer for mechanical dissociation. The homogenate was then centrifuged at 2350 rpm for 3 minutes at 4°C. The pellet fraction was resuspended in ChIP buffer containing proteinase inhibitor cocktail and PMSF, transferred to a 1.5 ml sonication tube (Active Motif) and incubated on ice for 10 minutes. Chromatin was sheered by sonication (Active Motif ) at 20 amp for cycles of 15 seconds on and 15 seconds off to reach a fragment side of approximately 200 bp. DNA fragments were electrophoresed on a 2.0% agarose gel and digitally visualized (SynGene PXi) with gel red staining. ~17 µg of chromatin were incubated with ChIP-verified anti-H3K27me2/3 (Active Motif #39535, RRID:AB_2793246) or IgG negative control antibodies on end-to-end rotation overnight at 4°C. The following day, Protein G agarose beads were washed and added to each sample for chromatin immunoprecipitation (ChIP). The chromatin-bead mixtures were incubated for 3.5 hours on an end-to-end rotator at 4°C. Each sample was loaded on to a ChIP filtration column, washed and dried by centrifugation at 1250 g for 3 minutes at room temperature. ChIP DNA was eluted twice with 50 µl of Elution Buffer AM4. ChIP-DNA was reverse cross-linked and purified with the ChIP-IT DNA Isolation Kit (Active Motif) per manufacturer’s protocol. Briefly, eluted ChIP DNA was mixed with Proteinase K and incubated in a thermomixer (Eppendorf) set to at 900 rpm and 55°C for 30 minutes, followed by 80°C for 2 hours. DNA was diluted with DNA Purification Binding Buffer with 10 µl of 3 M sodium acetate for pH adjustment yielding a bright yellow reaction mixture. Each sample was placed in a DNA purification column and washed with DNA Purification Wash Buffer. Purified DNA was eluted in 40 µl of DNA Purification Elution Buffer and stored at -20°C prior to DNA sequencing.
DNA quality control and sequencing were done at the UCLA Technology Center for Genomics and Bioinformatics at the University of California, Los Angeles. Single-end DNA sequencing was performed on an Illumina HiSeq 3000  instrument, with ~39-45 million reads per sample and a read length of 50 base-pairs (bp).

treatment_protocol: C2C12 myoblasts were seeded and cultured as outline above. Cultures were stimulated with heparin (10 µg/ml, Sigma) or heparin and Klotho (1 µg/ml, R&D Systems #1819-KL) in growth medium at 24- and 48-hours post-plating.

value: Klotho


title: 4h_PRX5pos_M2_H2O2_4h


title: 12_1

description: G. uralensis aboveground parts CK

source_name: aboveground parts

value: stems and leaves


title: 11_1

description: G. uralensis aboveground parts CK


title: Klotho-treated Input


title: 10_1

description: G. uralensis aboveground parts CK


title: 8h_IFNAR_M4_FSL1


title: 8h_Prx5_M4_pIC

value: Poly IC


title: Vehicle-treated H3K27me2/3 ChIP

value: vehicle


title: L9

description: G. uralensis aboveground parts salt stress 12h


title: 8h_Prx5_M4_Vneg


title: Vehicle-treated Input


title: 8h_Prx5_M4_Vpos


title: 4h_PRX5pos_M2_H2O2_2h

value: female

value: H2O2 2h


title: 8h_Prx5_M4_Medium

value: Non-treated


title: L8


title: 4h_PRX5pos_M2_Medium


title: 4h_PRX5neg_M2_H2O2_4h

value: H2O2 4h


title: 4h_PRX5neg_M2_H2O2_2h


title: 8h_IFNg_M3_Vneg

value: Ifng-/-


title: 4h_WT-F_M4_H2O2_2h


title: L7

value: seedlings of 60 days


title: L6

description: G. uralensis aboveground parts salt stress 6h


title: 8h_IFNg_M3_Vpos


title: Cochlea E17.5 PVcre;Ai14 [SS2_20_143]

city: New York

first: Louis

last: Faure

state: NY

address: 321 E 61st Street

institute: Memorial Sloan Kettering Cancer Center

description: corresponding raw files include SS2_20_143 in the filename

data_processing:
The samples were analyzed by first demultiplexing the fastq files using deindexer (http://github.com/ws6/deindexer) using the nextera index adapters and the 384 well layout.
Individual fastq files were then mapped to the relevant genome assembly using the STAR aligner (Dobin et al. Bioinformatics 2013) using 2-pass alignment to have improved performance of de novo splice junction reads, filtered for only uniquely mapping reads that are saved in the BAM  file.
The expression values were computed per gene as described in Ramsköld et al. (2009 PLoS Comp Biol), using uniquely aligned reads and correcting for the uniquely alignable positions using MULTo (Storvall et al. 2013 PLoS ONE).
BAM files from each plate were processed using python command-line velocity tool10, using run-smartseq2 command with GENCODE M21 genome and repeat masker annotation files
count matrix was pre-processed using scanpy and scFates, which includes normalization, clustering of cells, and projection on low embedding for visualization
Genome_build: mm10
Supplementary_files_format_and_content: counts.csv contains compiled count data from all plates, plate id is mentioned in cell name. Files starting with "adata" are anndata object that can be read and analyised by scanpy or scFates. adata_raw is the starting point, it contains the same data as counts.csv. adata_aligned.h5ad is the data cleaned up from glial contamination and hamrony timepoints aligned. adata_HC contains cochlear hair cells only. adata_SGN_tree contains SGN cells with final tree and fitted gene expression. files starting with "p2w" are pagoda2 web objects, that can be opened on http://adameykolab.srv.meduniwien.ac.at/pagoda2/ (BIN format). p2w files with imputed in thier names contain MAGIC imputed count matrix. p2w files with knn in their names contain knn smoothed expression matrix.

molecule: polyA RNA

source_name: Cochlea

extract_protocol:
The same dissociation protocol was used for SGs of all stages. First, the presence of tdTomato signal was verified under a fluorescence stereomicroscope. From tdTomato positive animals, the cochlea was carefully dissected from the temporal bone as described above. Upon removal of the cochlear capsule, the spiral ganglia (SG) were dissected and collected on ice in Leibovit’z L-15 medium (Life technologies). For E14.5 and E15.5 tissue sample, the cochlea was cut open, and the modiolus region was dissected out. Tissue samples were then digested in a papain-DNAse solution (1.5 ml of papain at 1 mg/ml, 0.5 ml of DNAse at 0.1%) for 20 min, shaking at 700 RPM. After centrifugation of the partially digested tissue at 400 RCF for 10 min, the dissociation mix-solution was removed, and the cell pellet gently resuspended in Dulbecco’s modified Eagle’s medium (DMEM) F-12 (Life technologies). Subsequently, to break up the tissue fragments, cells were mechanically triturated using fire polished Pasteur pipettes coated with 0.2% bovine serum albumin until a homogenized solution was achieved. To remove residual cell aggregates and to generate a single cell suspension, the cell homogenate was then passed through a 70μm nylon cell strainer (BD Biosciences). Single RFP+ cells were sorted by fluorescence-activated cell sorting (FACS) into individual wells containing lysis buffer in a 384-well plate. The plates were immediately placed on dry ice and stored at -80°C before processed for Smart-seq2 protocol. We used 3-4 animals (6-8 cochlea) per experiment, with several rounds of experiments and plates per time-point.
RNA libraries were prepared according to Smart-seq2 protocol.

value: Cochlea


title: L5


title: Cochlea E16.5 PVcre;Ai14 [SS2_20_139]

description: corresponding raw files include SS2_20_139 in the filename


title: Cochlea E14.5 TrkCcre [SS2_20_133]

description: corresponding raw files include SS2_20_133 in the filename

value: TrkCcre


title: L4

value: 150 mM NaCl for 6h


title: 4h_PRX5neg_M2_Medium


title: 4h_NRF2_M1_H2O2_2h


title: 8h_IFNg_M3_Medium


title: 4h_NRF2_M1_H2O2_4h


title: Cochlea E15.5 PVcre;Ai14 [SS2_20_151]

description: corresponding raw files include SS2_20_151 in the filename


title: 8h_NOX2_M3_Vneg


title: Cochlea E14.5 PVcre;Ai14 [SS2_20_135]

description: corresponding raw files include SS2_20_135 in the filename


title: Cochlea E15.5 PVcre;Ai14 [SS2_20_153]

description: corresponding raw files include SS2_20_153 in the filename


title: L3

description: G. uralensis aboveground parts salt stress 2h


title: L2


title: 4h_NRF2_M1_Medium


title: L1


title: 4h_WT-F_M5_H2O2_4h


title: 4h_WT-F_M5_H2O2_2h


title: UK5099-treated replicate 2

city: Lausanne

first: Tania

last: Wyss

address: Rue du Bugnon 25A

institute: SIB Swiss Institute of Bioinformatics

data_processing:
Fastq files were generated using bcl2fastq v.2.19.1
Low quality reads were filtered and trimmed using AdapterRemoval (v. 2.1.7).
Reads were aligned to the Mus musculus genome (v. GRCm38, release 94) using Bowtie 2 (v. 2.3.4.1) with default parameters. Next, we used samtools to convert and sort sam files to sorted bam files, as well as to mark duplicates using the markdup function of samtools (v. 1.8).
Finally, we retained reads aligning to the primary assembly only, removing the reads aligned to the mitochondrial chromosome or alternate locus groups.  The callpeak function of MACS2 (v. 2.1.1.20160309) was used for peak calling, combining the sorted and filtered bam files of all replicates per condition, and using the --broad option.
bigWig files were generated using the bamCoverage function of deepTools (v. 2.5.4).
Differential chromatin accessibility analysis between MPCi-treated and DMSO-treated samples was performed using R (v. 3.5.1). Number of reads overlapping each broad peak called by MACS2 were counted using the dba.count function of the DiffBind package (v. 2.10.0), with parameters minOverlap = 2 and score=DBA_SCORE_TMM_READS_FULL. The edgeR method implemented in the dba.analyze and dba.report functions of DiffBind was used to statistically compare the accessibility of genomic regions, considering the regions with an FDR<0.05 as statistically significant. Using the ChIPpeakAnno package (v. 3.16.1), differentially accessible regions were annotated to neighboring genes with the annotatePeakInBatch function with default parameters and the mouse TSS annotation data (TSS.mouse.GRCm38), and gene symbols were obtained with the addGeneIDs function.
Genome_build: Mus musculus v. GRCm38, release 94
Supplementary_files_format_and_content: For each sample, a bigWig file was generated using as input bam files that were sorted by position and filtered to remove mitochondrial and non-conventional chromosomes. The bed file "DA_regions_DMSO_vs_UK5099_ATACseq.bed" contains differentially accessible regions identified using DiffBind, and annotated to closest genes (indicated as gene symbols when available in the fourth column of the bed file).

source_name: Splenic CD8 T cells

growth_protocol: Splenocytes were cultured in RPMI medium (Gibco 61870-01) supplemented with 10% FBS, (Gibco 10270-106), 1% Penicillin/Streptomycin (Gibco 15070-063), 50µM ß-mercaptoethanol, 1% HEPES (Gibco 15630-080), 1x Non-essential amino acids (Gibco 11140-035), 1% L-glutamine (Gibco 25030-081) and 1mM Sodium Pyruvate (Gibco 11360-039). Cells were additionally supplemented with recombinant human (rh) IL-2 100IU/ml (in house) and ovalbumin peptide (SIINFEKL) 1µg/ml and either with 20 µM UK5099 (Sigma Aldrich) or with their solvent DMSO as a control. Splenocytes were collected at day 3, washed and split, and cells were cultured for 4 additional days with 100U/ml rhIL-2 and 10ng/ml rhIL-7 (Peprotech 200-07) without small molecule inhibitor.

extract_protocol:
50 000 T cells were washed 1x with PBS and prepared for transposase treatment
T cell pellet was resuspended in 50 microliter of ice-cold lysis buffer (10mM Tris-Cl (pH 7.4), 10mM NaCl, 3mM MgCl2 and 0.1% (v/v) of NP-40. Cells were centrifuged immediately and the resulting pellet (nuclei) was resuspended in 50 microliter of transposase reaction mix  (Illumina), followed by incubation at 37°C for 30min. Tagmented DNA was cleaned using QIAGEN MinElute PCR Purification kit as described in the kit’s protocol. Library preparation was performed using Indexes (R#20027213) and NEBNext High-Fidelity 2X PCR Master Mix(M0541), using the following program: 5 min 72°C, 30 s 98°C; 10 cycles: 10 s 98°C, 30 s 63°C, 1 min 72C°. The libraries were then cleaned using Agencourt AMPure XP magnetic beads (A63880, Beckman).

treatment_protocol: T cells were treated for the first 72 hours with either DMSO or 75 micromolar UK5099

tag: cell type

value: Splenic CD8 T cells


title: 4h_WT-F_M5_Medium


title: 8h_NOX2_M3_Medium


title: 8h_NLRX1_M4_pIC


title: UK5099-treated replicate 1


title: Trunk treatment-rod rep4

city: GAINESVILLE

first: FAHONG

last: YU

state: FL

address: 2033 Mowry Rd

department: ICBR

institute: UNIVERSITY OF FLORIDA

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads acquired from the Illumina NextSeq 500 platform were cleaned up with the cutadapt program to trim off sequencing adaptors and low-quality bases with a quality phred-like score <20. Reads <40 bases were excluded from RNA-seq analysis.
ICBR scripts along with SAMtools and the DESeq, EdgeR, and Bayseq (DEB) computational applications were applied to generate the gene expression data, including fold changes and p-values, to remove duplicates or artifacts from PCR, and choose uniquely mapped reads for gene expression analysis. Digital gene expression was assessed by counting the number of transcripts that mapped to a gene sequence
Genome_build: LMB_Assem_assem6.fsa
Supplementary_files_format_and_content: tab-delimited text files include the mapped read counts for each Sample

organism: Micropterus salmoides

source_name: Trunk kidney

extract_protocol:
Total RNA was isolated from males only using 30-50 mg of the frozen trunk and head kidney tissue using Stat-60 (Tel-test Friendswood, TX, USA) reagent. Each tissue was homogenized in 700 µl Stat-60, 150 µl chloroform was added and the samples were centrifuged at 20,800 x g for 15 min at 4ºC. This extraction was repeated with fresh STAT-60, and the RNA was precipitated overnight at -20 ºC in isopropanol with the addition of 1.5 µL of GlycoBlueTM (Ambion, Invitrogen, Austin, TX) as a coprecipitant. Following centrifugation at 20,800 x g for 45 minutes, the pellet was washed twice with 70% ethanol, air-dried, and resuspended in 20 mL of RNA secure and heated up at 60ºC for 10 minutes (Ambion, Austin, TX, USA). We performed DNase treatment to remove possible contamination with genomic DNA using Turbo DNA-freeTM kit (Ambion, Austin, TX, USA).
The RNA-seq library was performed by using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, catalog # E7490) and the NEBNext Ultra II  Directional RNA Library Prep Kit (New England Biolabs, catalog #E7760) according to the manufacturer's user guide. Briefly, 250 ng of total RNA was used for Poly(A) selection, then  fragmented in NEBNext First Strand Synthesis Buffer via incubation at 94 °C for 10min. The first-strand cDNA synthesis using reverse transcriptase and random hexamer primer.  Synthesis of ds-cDNA was performed using the 2nd strand master mix provided in the kit, followed by end-repair and adaptor ligation.  At this point, Illumina adaptors were ligated to the sample.  Finally, each library (uniquely barcoded) was enriched by 10 cycles of amplification, and purified with Agencourt AMPure beads (Beckman Coulter, catalog # A63881). The barcoded libraries were sized on the Bioanalyzer and quantified with the Qubit® 2.0 Fluorometer. Finally, individual libraries were pooled in equimolar concentration.

treatment_protocol: The largemouth bass in glass tanks of 38 L for 21 days. Each treatment consisted of 4 individuals per tank in quadruplicate. Largemouth bass were kept in a controlled environment where the temperature was 22.3 ± 0.6 ºC and the bass were fed every 3 days with Salmon broodstock feed (Skretting, UT, USA). The total ammonium, chlorine and nitrite levels were 0 mg L-1 and were measured using CHEMets (Midland, VA, USA) colorimetric kits. At the termination of the experiment, the individuals were anesthetized with 250 mg L-1 buffered Tricaine methane-sulfonate (MS-222) and sacrificed by cervical dislocation. . The trunk and head kidneys of each animal were dissected, a portion was flash-frozen in liquid nitrogen, and stored at -80ºC until RNA was isolated. Another portion was preserved in 10% formalin buffer for gonad sex and stage determination.

tag: location

value: USA:Florida:Terry Town:Richloam State Hatchery

value: Adult

tag: Sex

value: male

value: trunk kidney


title: Trunk treatment-rod rep3


title: DMSO-treated replicate 2

value: DMSO


title: DMSO-treated replicate 3


title: 8h_NOX2_M3_Vpos


title: 24h_NRF2_M3_tBHQ

value: tBHQ


title: 24h_NRF2_M3_Vneg


title: DMSO-treated replicate 1


title: 8h_NLRX1_M4_Vpos


title: Trunk treatment-rod rep1


title: 8h_NLRX1_M4_Vneg


title: 8h_NLRX1_M4_Medium


title: Trunk treatment-gly rep4


title: 8h_WT_M2_Vneg_FSL1

value: WT

value: LgyLRV+- and FSL1


title: 24h_NRF2_M3_Medium

value: female


title: 24h_NRF2_M3_Vpos


title: Trunk treatment-rod rep2


title: Cochlea E18.5 PVcre;Ai14 [SS2_19_166]

description: corresponding raw files include SS2_19_166 in the filename

data_processing:
The samples were analyzed by first demultiplexing the fastq files using deindexer (http://github.com/ws6/deindexer) using the nextera index adapters and the 384 well layout.
Individual fastq files were then mapped to the relevant genome assembly using the STAR aligner (Dobin et al. Bioinformatics 2013) using 2-pass alignment to have improved performance of de novo splice junction reads, filtered for only uniquely mapping reads that are saved in the BAM  file.
The expression values were computed per gene as described in Ramsköld et al. (2009 PLoS Comp Biol), using uniquely aligned reads and correcting for the uniquely alignable positions using MULTo (Storvall et al. 2013 PLoS ONE).
BAM files from each plate were processed using python command-line velocity tool10, using run-smartseq2 command with GENCODE M21 genome and repeat masker annotation files
ount matrix was pre-processed using scanpy and scFates, which includes normalization, clustering of cells, and projection on low embedding for visualization
Genome_build: mm10
Supplementary_files_format_and_content: counts.csv contains compiled count data from all plates, plate id is mentioned in cell name. Files starting with "adata" are anndata object that can be read and analyised by scanpy or scFates. adata_raw is the starting point, it contains the same data as counts.csv. adata_aligned.h5ad is the data cleaned up from glial contamination and hamrony timepoints aligned. adata_HC contains cochlear hair cells only. adata_SGN_tree contains SGN cells with final tree and fitted gene expression. files starting with "p2w" are pagoda2 web objects, that can be opened on http://adameykolab.srv.meduniwien.ac.at/pagoda2/ (BIN format). p2w files with imputed in thier names contain MAGIC imputed count matrix. p2w files with knn in their names contain knn smoothed expression matrix.

source_name: Cochlea E18.5 PVcre;Ai14

tag: strain/genotype


title: Cochlea E18.5 PVcre;Ai14 [SS2_19_168]

description: corresponding raw files include SS2_19_168 in the filename


title: Trunk treatment-gly rep3


title: 24h_NLRX1-M_M4_pIC

value: Poly I:C


title: 8h_WT_M2_Vpos_FSL1

value: LgyLRV1+ and FSL1


title: Cochlea E16.5 PVcre;Ai14 [SS2_18_349]

description: corresponding raw files include SS2_18_349 in the filename

source_name: Cochlea E16.5 PVcre;Ai14


title: Cochlea E16.5 PVcre;Ai14 [SS2_18_350]

description: corresponding raw files include SS2_18_350 in the filename


title: Trunk treatment-gly rep2


title: 8h_WT_M2_FSL1


title: 24h_NLRX1-M_M4_Vneg


title: Cochlea P3 PVcre;Ai14 [SS2_15_0144]

description: corresponding raw files include SS2_15_0144 in the filename

source_name: Cochlea P3 PVcre;Ai14


title: 24h_NLRX1-M_M4_Vpos


title: 8h_WT_M2_pIC

value: Poly IC


title: 24h_NLRX1-M_M4_Medium

value: Non-treated


title: Trunk treatment-gly rep1


title: Trunk control rep2


title: Cochlea P3 PVcre;Ai14 [SS2_15_0135]

description: corresponding raw files include SS2_15_0135 in the filename

value: Cochlea


title: 24h_NLRX1-F_M4_pIC


title: 24h_NLRX1-F_M4_Vpos


title: 3T3L1_Ser2_vehicle_rep2_ChIPSeq

city: Durham

first: Zhong

last: Chen

state: NC

address: 905 S. LaSalle Street

department: Pathology

institute: Duke University

data_processing:
ChIP-seq reads were aligned to the hg19 and mm10 genome assembly using bowtie-1.0.0 with the following parameters -v 3 -k 3 -m 2. And only those reads with unique or two mapped locations are remained for further analysis.
Each mapped reads has been extended into a 300 bp fragment (presumably coinciding with library size) in a direction from 5'-3' along with chromosome axis. And the bigwig files would be made on these processed alignments.
Genome_build: hg19 and mm10

source_name: adipocyte

growth_protocol: LNCaP-abl cells were cultured in RPMI 1640 (Invitrogen) supplemented with 10% charcoal-stripped FBS (Omega Scientific) and 1mM L-glutamine.

extract_protocol:
cells were grown to 70%-80% confluence, and crosslinked with 1% formaldehyde for 10 min at room temperature. After washing twice with cold PBS, cells were collected and resuspended in lysis buffer (1% SDS, 5 mM EDTA, 50 mM Tris (pH 8.0), 1x protease and phosphatase inhibitors). After sonication, the soluble chromatin was diluted in 1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris (pH 8.0), 1x protease and phosphatase inhibitors). Then samples were precleared and immunoprecipitated with the appropriate antibodies overnight at 4°C. The next day, protein A or G beads blocked with BSA were added for 2 h at 4°C, and then washed sequentially for 10 min with TSE I (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris (pH 8.0), 150 mM NaCl), TSE II (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris (pH 8.0), 500 mM NaCl), buffer III (0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris (pH 8.0), and TE buffer (10 mM Tris (pH 8.0), 1mM EDTA (pH 8.0)). DNA was eluted in Elution buffer (1% SDS, 0.1M NaHCO3) at room temperatue for 30 min. The crosslinking was reversed by incubation for 16 h at 65°C. During the purification, ChIP DNA was treated with DNase-free RNase for 30 min at 37°C.
Libraries were prepared according to NEBNext ChIP-Seq Library Prep Master Mix Set (E6240L). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 10 or 14 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an E-gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq2000 following the manufacturer's protocols.

treatment_protocol: Cells were treated with 300 nM FP for indicated time.

value: adipocytes

tag: chip antibody

value: phosphorylated RNA pol II (Abcam, phospho S2)


title: 8h_WT_M2_Vpos


title: 3T3L1_Ser2_vehicle_rep1_ChIPSeq


title: 8h_iNOS_M3_pIC

value: inos-/-


title: Trunk control rep1

value: USA:Florida:Terry Town:Richloam State Hatchery


title: Head treatment-rod rep4

source_name: Head kidney

value: Adult

value: head kidney


title: 8h_iNOS_M3_Vneg


title: 3T3L1_pMed1_vehicle_rep1_ChIPSeq

value: pMED1 (Yenzyme, Custom antibody)


title: Trunk control rep4

value: male

value: trunk kidney


title: 8h_iNOS_M3_Vpos


title: 24h_NLRX1-F_M4_Medium


title: Head treatment-rod rep2


title: 8h_WT_M2_Vneg

value: WT


title: ABL_H3K36Me3_rep2_ChIPSeq

organism: Homo sapiens

source_name: prostate

value: prostate cancer cells

tag: passages

value: LNCaP-abl

value: H3K36me3 (Abcam, ab9050)


title: 8h_iNOS_M3_Medium


title: Head treatment-rod rep3


title: Head treatment-rod rep1


title: Trunk control rep3


title: ABL_H3K36Me3_rep1_ChIPSeq


title: 24h_NLRX1-F_M4_Vneg

value: female


title: 8h_WT_M2_Medium


title: 24h_WT-M_M3_Vneg


title: 8h_IFNAR_M2_Vneg_FSL1

value: Ifnar-/-

value: LgyLRV+- and FSL1


title: ABL_H3K4Me3_rep2_ChIPSeq

value: H3K4me3 (Abcam, ab8580)


title: 24h_WT-M_M3_Vpos


title: ABL_H3K4Me3_rep1_ChIPSeq


title: 8h_IFNAR_M2_Vpos_FSL1

value: LgyLRV1+ and FSL1


title: 24h_WT-M_M3_Medium

value: Non-treated


title: 24h_WT-M_M3_pIC

value: Poly I:C


title: 8h_IFNAR_M2_FSL1


title: ABL_H3K4Me2_rep2_ChIPSeq

value: H3K4me2 (Abcam, ab7766)


title: 24h_WT-F_M6_tBHQ

value: tBHQ


title: Head control rep4

value: USA:Florida:Terry Town:Richloam State Hatchery

value: Adult

value: head kidney


title: Head treatment-gly rep1

value: male


title: Liver post HFD feeding, rep 3

type: RNA

city: Hong Kong

first: Chi Bun

last: Chan

address: 5N10, SBS, HKU

department: School of Biological Sciences

country: Hong Kong

institute: The University of Hong Kong

description:
Hepatic gene expression data for mice fed with HFD diet
Mouse_Liver_HFD_R3

hyb_protocol: 10 ug cDNA were hybridized for 16 h at 45C on GeneChip Mouse Gene 1.0 ST Arrays (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Gene level expression index was generated using the Affymetrix MAS 5.0 software.

label: Biotin

source_name: Liver, HFD, 12 weeks

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA.

growth_protocol: Female C57BL/6 mice (3-month-old) were fed with chow or high fat-diet (HFD, 60% kCal, Research Diet Inc.) for 20 weeks.

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

treatment_protocol: The livers were collected and snap frozen in liquid nitrogen. The tissues were then stored in -70 deg Celsius

value: liver

tag: diet

value: HFD


title: 24h_WT-F_M6_Vpos

value: WT


title: ABL_H3K4Me2_rep1_ChIPSeq

value: prostate cancer cells

value: LNCaP-abl


title: 8h_IFNAR_M2_Medium

value: Ifnar-/-


title: Head control rep3


title: Head treatment-gly rep2


title: Liver post chow feeding, rep 3

description:
Hepatic gene expression data for mice fed with chow diet
Mouse_Liver_Chow_R3

source_name: Liver, Chow, 12 weeks

value: female

value: chow


title: 24h_WT-F_M6_Vneg


title: Liver post HFD feeding, rep 1

description:
Hepatic gene expression data for mice fed with HFD diet
Mouse_Liver_HFD_R1


title: 8h_IFNAR_M2_Vpos


title: 8h_IFNAR_M2_Vneg


title: 24h_WT-F_M6_pIC


title: Head control rep1


title: 8h_Prx5_M3_Vneg


title: 24h_WT-F_M6_Medium


title: Head control rep2


title: Liver post chow feeding, rep 2

description:
Hepatic gene expression data for mice fed with chow diet
Mouse_Liver_Chow_R2


title: Head treatment-gly rep4


title: 24h_NRF2_M4_Vneg


title: RRBS D14 Control rep2

city: Taipei

first: Pao-Yang

address: 128 Sec. 2, Academia Rd, Nankang,

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

data_processing:
BS-seq reads were trimmed (removing sequencing adapter and low-quality reads) by using Trimmomatic.
BS-seq reads were aligned to the human  genome hg19 using BS-Seeker2, and in each read, at most 4 bp mismatches will be allowed. If multiple alignments mapped to the same location only one is kept.
Calling methylation levels and removing BS-seq reads with incomplete bisulfite conversion (#(mCH sites)/#(all CH sites)>0.8 and #(mCH sites)>5 for one read) by using BS-Seeker2.
The RNA-seq reads were aligned using HISAT2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cuffdiff
Genome_build: hg19
Supplementary_files_format_and_content: Processed data (CGmap) is in text format.  column 1=chromosome id; column 2=C/G (G stands for C on the opposite strand); column 3= chromosomal location; column 4=sequence context (CG/CHG/CHH); column 5=sequence context (CA/CT/CC/CG); column 6=methylation fraction #C/(#C+#T); column 7=number of C (#C); column 8 #C+#T.

source_name: Abdominal preadipocyte cells

growth_protocol: Preadipocytes were cultured in Dulbecco's modified Eagle's medium/F12 Ham's nutrient mixture (v/v, 1:1) containing 17.5 mM glucose and supplemented with 10% foetal calf serum, 0.25 ng/ml fibroblast growth factor, 2 mM glutamine, 100 units/ml penicillin and 100 µg/ml streptomycin.

extract_protocol:
RRBS: Genomic DNA was extracted using the GenEluteTM Mammalian Genomic DNA Miniprep Kit (Sigma)
RRBS libraries were constructed using Ovation® RRBS Methyl-Seq with TrueMethyl® oxBS preparation kit.
RNA-Seq: Use poly-T oligo-attached beads to purify and fragment mRNA for cDNA synthesis.
Then, a single ‘A’ nucleotide was added to 3’ end of ds cDNA, multiple indexing adaptors were ligated to 5’ and 3’ of the ends of ds cDNA, following with PCR amplification,

treatment_protocol: For adipogenesis, immortalized preadipocytes were cultured in growth medium first. Then, two days after full confluence (differentiation day 0), the cells were treated with adipogenic differentiation medium for 14 days. The differentiation medium is growth medium with Troglitazone (4 μM) and 3-isobutyl-1-methylxanthine (0.25 mM)

value: Control

tag: differentiation time


title: Liver post chow feeding, rep 1

description:
Hepatic gene expression data for mice fed with chow diet
Mouse_Liver_Chow_R1


title: Head treatment-gly rep3


title: 8h_Prx5_M3_Vpos


title: Liver post HFD feeding, rep 2

description:
Hepatic gene expression data for mice fed with HFD diet
Mouse_Liver_HFD_R2


title: 8h_Prx5_M3_pIC

value: Poly IC


title: Leaf_Fen_48h_2

city: Malaga

first: Carlos

middle: Molina

last: Santiago

state: Malaga

address: Bulevar Louis Pasteur 49

department: MIcrobiology

country: Spain

institute: UMA

data_processing:
The raw reads were pre-processed with SeqTrimNext using the specific NGS technology configuration parameters (Falgueras et al., 2010). This pre-processing removes low quality, ambiguous and low complexity stretches, linkers, adapters, vector fragments, and contaminated sequences while keeping the longest informative parts of the reads. SeqTrimNext also discarded sequences below 25 bp. Subsequently, clean reads were aligned and annotated using the Cucumis melo genome as the reference with Bowtie2 (Langmead and Salzberg, 2012) in BAM files, which were then sorted and indexed using SAMtools v1.484110 (Li et al., 2009).
Uniquely localized reads were used to calculate the read number value for each gene via Sam2counts (https://github.com/vsbuffalo/sam2counts). Differentially expressed genes (DEGs) between treatments were analyzed via DEgenes Hunter, which provides a combined p value calculated (based on Fisher’s method) using the nominal p values provided by from edgeR113 (Robinson et al., 2010) and DEseq2114 (Anders and Huber, 2010).
Genome_build: ASM31304v1
Supplementary_files_format_and_content: tab-delimited excel files include Log2FC of the comparison between treated and non-treated seeds and leaves, with p-value, gene names and descriptions

organism: Cucumis melo

source_name: cucumis melo leaves treated with fengycin

extract_protocol:
Total RNA was extracted from frozen tissues, harvested at different times after treatment, by phenol/chloroform extraction followed by precipitation with 1.5 m LiCl and sodium acetate.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: leaves

value: treatment with fengycin

value: adult plant + 48h


title: RRBS D14 HOTAIR-OE rep1

value: HOTAIR-OE


title: RRBS D14 Control rep1


title: Leaf_Fen_48h_1


title: 3T3L1_pMed1_vehicle_rep2_ChIPSeq

value: adipocytes

value: pMED1 (Yenzyme, Custom antibody)


title: 24h_NRF2_M4_Medium

source_name: Bone marrow derived macrophages

value: Non-treated


title: 8h_Prx5_M3_Medium


title: 24h_NRF2_M4_tBHQ

value: tBHQ


title: 24h_NRF2_M4_Vpos


title: RRBS D0 Control rep1


title: Leaf_Control_48h_1

source_name: cucumis melo leaves control

value: control


title: RRBS D14 HOTAIR-OE rep2


title: 8h_IFNg_M1_Vneg

value: Ifng-/-


title: 8h_IFNg_M1_Vpos


title: 8h_NOX2_M1_Vneg


title: 24h_NLRX1-M_M3_Vneg

value: male


title: 24h_NLRX1-M_M3_pIC

value: Poly I:C


title: RRBS D0 Control rep2


title: Leaf_Fen_0h_2

value: adult plant


title: 8h_NOX2_M1_Vpos


title: RRBS D0 HOTAIR-OE rep2


title: 24h_NLRX1-M_M3_Medium


title: Leaf_Fen_0h_1


title: 24h_NLRX1-F_M1_pIC

value: female


title: 8h_NOX2_M1_Medium


title: 24h_NLRX1-M_M3_Vpos


title: Leaf_Control_48h_2


title: 8h_IFNg_M1_Medium


title: RRBS D0 HOTAIR-OE rep1


title: 8h_NLRX1_M2_pIC


title: RNA-seq D14 Control rep2


title: 8h_NLRX1_M2_Vneg


title: Leaf_Control_0h_2


title: 24h_NLRX1-F_M1_Vpos


title: 24h_WT-M_M2_pIC

value: WT


title: 24h_NLRX1-F_M1_Vneg


title: Seed_3610_2

source_name: cucumis melo seeds treated with B. subtilis

value: seeds

value: treatment with B. subtilis

value: 5 days


title: Seed_3610_1


title: RNA-seq D14 Control rep1

value: Control


title: 24h_NLRX1-F_M1_Medium


title: Leaf_Control_0h_1

value: leaves


title: 8h_NLRX1_M2_Medium


title: 24h_WT-M_M2_Vpos


title: 24h_WT-M_M2_Vneg


title: RNA-seq D14 HOTAIR-OE rep3

value: HOTAIR-OE


title: RNA-seq D14 Control rep3


title: RNA-seq D14 HOTAIR-OE rep2


title: 8h_NLRX1_M2_Vpos


title: RNA-seq D4 Control rep3


title: 8h_WT_M1_FSL1


title: RNA-seq D14 HOTAIR-OE rep1


title: 8h_WT_M1_Vneg_FSL1

value: LgyLRV+- and FSL1


title: Sample_14983 [Control]

type: genomic

city: Royal Oak

first: Stewart

middle: F

last: Graham

state: Michigan

address: 3811 West 13 Mile Road, Suite 415

department: OBGYN

institute: Corewell Health - Research Institute

description: Normal Brain tissue

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Infinium MethylationEPIC-8+ v1.0 Kit (32 samples) 20020531 using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
R package based
Normalized (Noob normalization)

label: Cy3, Cy5

source_name: Brain

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from the lyophilized and milled brain tissue using the QIAamp DNA Mini Kit (Qiagen)

treatment_protocol: lyophilized and milled brain tissue

value: Normal Brain tissue

value: M

tag: pmi

tag: repository

value: Mount Sinai

tag: race

value: Hispanic

tag: group


title: 8h_WT_M1_Vpos_FSL1

tag: strain

tag: treatment

value: LgyLRV1+ and FSL1


title: Seed_Control_1

source_name: cucumis melo seeds control

tag: tissue

value: control


title: Sample_14982 [Control]

description: Normal Brain tissue

value: White


title: 24h_WT-M_M2_Medium

tag: genotype

tag: gender

value: male

tag: time-point

value: Non-treated


title: Seed_Control_2

tag: age


title: 24h_WT-F_M3_tBHQ

value: WT

value: female

value: tBHQ


title: RNA-seq D4 Control rep2


title: Sample_14981 [Control]

description: Normal Brain tissue

tag: Sex

value: Asian


title: RNA-seq D4 Control rep1

value: Control


title: 8h_WT_M1_pIC

value: Poly IC


title: Sample_14980 [Control]

description: Normal Brain tissue


title: 8h_WT_M1_Vneg


title: 24h_WT-F_M3_pIC

value: Poly I:C


title: 24h_WT-F_M3_Vneg


title: Sample_14979 [Control]

description: Normal Brain tissue

value: F

value: Black


title: 24h_WT-F_M3_Vpos


title: 24h_WT-F_M3_Medium


title: 24h_NRF2_M2_tBHQ


title: RNA-seq D4 HOTAIR-OE rep1

value: HOTAIR-OE


title: Sample_14974 [Control]

description: Normal Brain tissue

value: Normal Brain tissue

value: Harvard

value: Unknown


title: 8h_WT_M1_Vpos


title: RNA-seq D4 HOTAIR-OE rep3


title: Neonatal B cells_7h culture_anti-IgM stimulated_rep1

city: Silver Spring

first: Jiro

last: Sakai

state: Maryland

address: 10903 New Hampshire Avenue

institute: US Food and Drug Administration

data_processing:
FDA HIVE platform v2.4
Quality of sequence reads was inspected using HIVE's native multi-QC tool
Sequence reads were mapped to GRCm38.p6 transcriptome (G CF_000001635.26) using HIVE's native NGS aligner Hexagon (v2.4)
Gene-level feature counts were quantified using HIVE's native feature mapping tool, HIVE Alignment Comparator (v2.4) and normalized to FPKM

source_name: Spleen

growth_protocol: Isolated splenic B cells were maintained in ex vivo culture.

extract_protocol:
RNA was extracted with QIAGEN RNeasy Plus mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
Clontech SMART-Seq v4 Ultra Low Input RNA Kit for Illumina Sequencing
(first-strand cDNA synthesis; full-length double strand cDNA amplification by LD-PCR; amplified cDNA purification and validation). The cDNAs were then further prepared using Illumina (San Diego, CA) Nextera DNA Library Preparation Kit (tagmentation; PCR amplification; clean-up and validation).

treatment_protocol: Isolated splenic B cells were stimulated ex vivo with anti-IgM for 0 or 7 hours.

value: 1 week

value: wild type

value: Spleen

tag: cell type

value: B cells

value: anti-IgM

tag: time

value: 7h culture


title: Sample_14976 [PD]

description: Parkinson's disease Affected Brain tissue

value: Parkinson's disease (PD)


title: Sample_14975 [PD]

value: Parkinson's disease Affected Brain tissue

value: M

value: White


title: RNA-seq D0 Control rep3

value: Control


title: 24h_NRF2_M2_Vneg

value: female


title: 24h_NRF2_M2_Vpos


title: Sample_14977 [Control]

description: Normal Brain tissue

value: F


title: Sample_14972 [Control]

description: Normal Brain tissue


title: RNA-seq D4 HOTAIR-OE rep2

value: HOTAIR-OE


title: Neonatal B cells_7h culture_anti-IgM stimulated_rep2


title: 8h_WT_M1_Medium

value: WT

value: Non-treated


title: RNA-seq D0 HOTAIR-OE rep3


title: Neonatal B cells_7h culture_anti-IgM stimulated_rep3


title: RNA-seq D0 Control rep1


title: Neonatal B cells_0h culture_rep3

value: unstimulated


title: RNA-seq D0 Control rep2


title: 24h_NLRX1-M_M2_Vneg

value: male


title: Neonatal B cells_0h culture_rep2

value: 1 week

value: wild type


title: Neonatal B cells_7h culture_unstimulated_rep3

value: Spleen

value: B cells


title: 24h_NLRX1-M_M2_Vpos


title: RNA-seq D0 HOTAIR-OE rep2


title: R_6545_ST [PCHT116]

city: JOUY-en-JOSAS

first: gilles

last: charpigny

state: ILe de France

address: domaine de Vilvert

department: Physiologie Animale Systeme Elevage

country: France

institute: INRAE

description: re-analysis of GSM5543438

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: PCHT*.quant.sf is the quantification file output of Salmon (quasi-mapping and transcript quantification tool for RNA-seq data). This is a plain text, tab-separated file. The columns have the following interpretation:  Name: the name of the target transcript.  Length: the length of the target transcript in nucleotides.  EffectiveLength: the computed effective length of the target transcript.  TPM: salmon's estimate of the relative abundance of this transcript in units of Transcripts Per Million (TPM). TPM is the recommended relative abundance measure to use for downstream analysis.  NumReads: Salmon's estimate of the number of reads mapping to each transcript that was quantified. It is an estimate insofar as it is the expected number of reads that have originated from each transcript given the structure of the uniquely mapping and multi-mapping reads and the relative abundance estimates for each transcript.

organism: Bos taurus

source_name: endometrium

extract_protocol:
Total RNA was extracted using the Arcturus PicoPure RNA isolation kit (Applied Biosystems, Life Technologies), according to the manufacturer’s instructions
Full length cDNA were generated from 2.5 ng of total RNA using Clontech SMART-Seq v4 Ultra Low Input RNA kit for Sequencing (Takara Bio Europe, Saint Germain en Laye, France) according to manufacturer's instructions with 10 cycles of PCR for cDNA amplification by Seq-Amp polymerase. Six hundreds pg of pre-amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit (96 samples) (Illumina, San Diego, CA) followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads (Beckman-Coulter, Villepinte, France), the size and concentration of libraries were assessed by capillary electrophoreris.

treatment_protocol: The three endometrial cell types (luminal epithelium, glandular epithelium and stroma cells) were collected by laser microdissection from endometrial biopsies performed at 45 days postpartum

tag: breed

value: Holstein

value: stromal cell

tag: animal group


title: R_6545_GE [PCHT115]

description: re-analysis of GSM5543436

value: glandular cell


title: Sample_14973 [Control]

description: Normal Brain tissue

value: Normal Brain tissue

value: M

value: Harvard

value: Unknown


title: 24h_NLRX1-F_M2_pIC

value: female

value: Poly I:C


title: Sample_14969 [PD]

value: Parkinson's disease Affected Brain tissue

value: White

value: Parkinson's disease (PD)


title: 24h_NLRX1-M_M2_pIC

value: male


title: 24h_NRF2_M2_Medium

value: Non-treated


title: Neonatal B cells_7h culture_unstimulated_rep2

value: 1 week

value: wild type

value: unstimulated

value: 7h culture


title: Sample_14970 [PD]

value: F


title: R_6494_ST [PCHT113]

description: re-analysis of GSM5543435

value: Holstein

value: stromal cell


title: R_6494_GE [PCHT112]

description: re-analysis of GSM5543433

value: glandular cell


title: 24h_NLRX1-M_M2_Medium


title: RNA-seq D0 HOTAIR-OE rep1

value: HOTAIR-OE

tag: differentiation time


title: Sample_14968 [Control]

description: Normal Brain tissue

value: Normal Brain tissue

value: M

tag: pmi

value: Harvard

value: Unknown

value: Control


title: R_6545_LE [PCHT114]

description: re-analysis of GSM5543437

value: luminal cell


title: Neonatal B cells_7h culture_unstimulated_rep1

value: Spleen

value: B cells


title: Sample_14971 [Control]

description: Normal Brain tissue

tag: repository

value: White


title: Adult B cells_7h culture_unstimulated_rep1

value: 8 weeks

value: wild type


title: Sample_14962 [Control]

description: Normal Brain tissue

tag: race


title: 24h_NLRX1-F_M2_Vneg

value: female


title: Adult B cells_7h culture_anti-IgM stimulated_rep3

value: anti-IgM

value: 7h culture


title: Sample_14967 [PD]

value: Parkinson's disease Affected Brain tissue

tag: group

value: Parkinson's disease (PD)


title: Adult B cells_7h culture_anti-IgM stimulated_rep1

tag: strain


title: Adult B cells_0h culture_rep3

tag: treatment

value: unstimulated


title: Adult B cells_7h culture_anti-IgM stimulated_rep2

tag: tissue


title: 24h_NLRX1-F_M2_Vpos

tag: genotype


title: Adult B cells_7h culture_unstimulated_rep3


title: R_6492_GE [PCHT109]

description: re-analysis of GSM5543430

value: Holstein

value: glandular cell


title: Sample_14965 [PD]

value: F

value: Harvard


title: Adult B cells_0h culture_rep2


title: R_6492_LE [PCHT108]

description: re-analysis of GSM5543431


title: Sample_14966 [PD]


title: Adult B cells_0h culture_rep1


title: Sample_14959 [PD]

value: M

value: Unknown


title: Neonatal B cells_0h culture_rep1

value: 1 week

value: Spleen


title: 24h_NLRX1-F_M2_Medium

tag: gender

value: Non-treated


title: R_6494_LE [PCHT111]

description: re-analysis of GSM5543434

value: luminal cell


title: 24h_WT-M_M1_pIC

value: WT

value: male

tag: time-point

value: Poly I:C


title: 24h_WT-M_M1_Vneg


title: Sample_14964 [PD]

tag: age

value: White


title: R_6492_ST [PCHT110]

description: re-analysis of GSM5543432

value: stromal cell


title: Sample_14960 [PD]

value: Parkinson's disease Affected Brain tissue

tag: Sex

value: Parkinson's disease (PD)


title: Sample_14957 [PD]


title: 24h_WT-M_M1_Medium


title: Adult B cells_7h culture_unstimulated_rep2

value: 8 weeks

value: wild type

tag: cell type

value: B cells

value: unstimulated

value: 7h culture


title: 24h_WT-M_M1_Vpos


title: R_5771_ST [PCHT104]

description: re-analysis of GSM5543426

value: Holstein


title: R_5780_GE [PCHT106]

description: re-analysis of GSM5543427

value: glandular cell


title: R_5780_ST [PCHT107]

description: re-analysis of GSM5543429


title: Sample_14956 [PD]

value: F

value: Harvard

value: Unknown


title: Uninfected_A

first: David

middle: William

last: McKellar

address: 101 6th Ave

institute: New York Genome Center

description: Small RNA-sequencing was perforemed on OCT-embedded frozen mouse heart after saline injection (as a control)

data_processing:
Reads were trimmed and aligned using the miRge3.0 v0.0.9 pipeline
Assembly: mirbase
Supplementary files format and content: Raw counts for mature microRNAs are provided as .csv file

source_name: heart

extract_protocol:
For skeletal muscle samples, following the injury time course, tibialis anterior muscles were dissected and snap frozen with liquid nitrogen. The Norgen Total RNA Purification Kit (Cat. 17200) was used to extract RNA from 10 mg of tissue for each sample. For heart samples, following the infection time course, hearts were dissected, embedded in OCT, and frozen in liquid nitrogen. RNA was extracted with Trizol (Invitrogen, Cat. 15596026) and glycogen precipitation for a small fraction of each of the heart samples. RNA quality was assessed via High Sensitivity RNA ScreenTape Analysis (Agilent, Cat. 5067-5579) and all samples had RNA integrity numbers greater than or equal to 7.
Libraries were prepared using the TriLink CleanTag Small RNA Ligation kit (TriLink Biotechnologies, San Diego, CA)

value: heart

value: Mock/saline injection (7dpi)

tag: injury


title: Uninfected_B

value: male


title: Infected_B

description: Small RNA-sequencing was perforemed on OCT-embedded frozen mouse heart after oral infection of Type 1-Lang Reovirus

value: female

value: Oral infection with Reovirus Type 1-Lang, 7dpi


title: Infected_A


title: R_5780_LE [PCHT105]

description: re-analysis of GSM5543428

tag: breed

value: luminal cell


title: R_5771_GE [PCHT103]

description: re-analysis of GSM5543424

tag: animal group


title: 24h_WT-F_M4_tBHQ

value: WT

value: tBHQ


title: Sample_14954 [PD]

value: Parkinson's disease Affected Brain tissue

value: M

value: White

value: Parkinson's disease (PD)


title: Sample_14958 [Control]

description: Normal Brain tissue

value: Normal Brain tissue

value: Control


title: 24h_WT-F_M4_Medium

value: Non-treated


title: D7_B

description: Small RNA-sequencing was perforemed on snap frozen mouse tibialis anterior muscle (7 days post-injury, notexin injection)

source_name: muscle

value: muscle

value: Notexin (7dpi)


title: Sample_14961 [PD]

value: Harvard


title: 24h_WT-F_M4_Vneg


title: D7_A


title: 8h_NRF2_M3_tBHQ


title: 24h_WT-F_M4_Vpos


title: R_5771_LE [PCHT102]

description: re-analysis of GSM5543425

value: Holstein


title: Sample_14952 [PD]

value: F


title: R_5626_GE [PCHT100]

description: re-analysis of GSM5543422

value: glandular cell


title: 8h_NRF2_M3_Vpos

value: female


title: D5_B

description: Small RNA-sequencing was perforemed on snap frozen mouse tibialis anterior muscle (5 days post-injury, notexin injection)

value: Notexin (5dpi)


title: R_5626_ST [PCHT101]

description: re-analysis of GSM5543423

value: stromal cell


title: Sample_14951 [PD]

value: Unknown


title: D5_A


title: Sample_14953 [PD]

value: Parkinson's disease Affected Brain tissue


title: R_5614_ST [PCHT99]

description: re-analysis of GSM5543421


title: 8h_NRF2_M3_Medium


title: 8h_NLRX1-M_M4_pIC

value: male

value: Poly I:C


title: 24h_WT-F_M4_pIC

value: WT


title: G_6480_GE [PCHT96]

description: re-analysis of GSM5543418

value: Healthy (H)


title: Sample_14949 [PD]

value: M

value: White

value: Parkinson's disease (PD)


title: 8h_NLRX1-M_M4_Vneg


title: G_6480_LE [PCHT95]

description: re-analysis of GSM5543419

value: luminal cell


title: 8h_NRF2_M3_Vneg


title: D2_A

description: Small RNA-sequencing was perforemed on snap frozen mouse tibialis anterior muscle (2 days post-injury, notexin injection)

value: muscle

value: Notexin (2dpi)


title: G_6460_ST [PCHT94]

description: re-analysis of GSM5543417

value: Holstein


title: Sample_14947 [PD]

value: Harvard


title: G_6450_ST [PCHT92]

description: re-analysis of GSM5543416


title: D0_A

description: Small RNA-sequencing was perforemed on snap frozen mouse tibialis anterior muscle (uninjured)

value: female

value: Uninjured


title: 8h_NLRX1-M_M4_Medium

value: Non-treated


title: Sample_14948 [Control]

description: Normal Brain tissue

value: Normal Brain tissue

value: Unknown

value: Control


title: 8h_NLRX1-F_M4_pIC

value: Poly I:C


title: G_6480_ST [PCHT97]

description: re-analysis of GSM5543420

value: stromal cell


title: Sample_14950 [PD]

value: Parkinson's disease Affected Brain tissue


title: G_6450_GE [PCHT91]

description: re-analysis of GSM5543415

value: glandular cell

value: Healthy (H)


title: D2_B


title: 4T07 tumor infiltrates 1

city: Boston

first: Judith

last: Agudo

state: MA

address: 1 Jimmy fund way

institute: Dana Farber Cancer Institute

description:
scRNAseq from 4T07 infilrates after PADMEseq protocol to identify microregions labeled by hashtags before the 10x pipeline
UMAP_all_infiltrates.rds; UMAP_t_cells.rds; 703_barcodes.tsv; 703_features.tsv; 703_matrix.mtx.gz

data_processing:
The BWH Single Cell Genomics Core performed basic computational analysis using Cell Ranger pipeline.
Seurat v4.0.3 package for R was used to analyze the scRNA-seq data. Following Seurat-guided clustering tutorial.
Cells were filtered using <15% of mitochondrial genes reads to eliminate dead cells. We distinguish unique hashtags from each cell by excluding the cells that have > 250 read count in both hashtags.  We excluded cells outlier to the 200-25000 read count (nCount RNA) to eliminate doublets and debris.
Assembly: mm10
Supplementary files format and content: Cellranger outputs a .mtx.gz file with the gene-barcode matrix. This matrix contains the counts of molecules per cell (UMI/cell) as determined after filtering and counting by Cellranger. The matrix is in market exchange format while the row (gene names) and columns (cell barcodes) are provided as TSV files. File formats are documented in Cellranger software manual.
Supplementary files format and content: Seurat object in .rds format containing the anotated clusters identified by well known markers of the respective immune populations.

source_name: Tumor infiltrates

growth_protocol: 250000 p27k-tdtomato-transduced 4T07 cells were injected into the mammary fat pad of Balb/c x Kaede F1 mice.

extract_protocol:
FACS-sorted live cells were submitted to the Bigham and Women’s Hospital Single Cell Genomics Core for 10x genomics. Samples from different areas were tagged using hashed antibodies and then pooled to reduce technical variability in the preparation of the 10X library following an approved protocol from the core
The BWH Single Cell Genomics Core performed basic computational analysis using Cell Ranger pipeline.

treatment_protocol: Tumors were harvested and embedded in 2% low melting agarose and cut into 300μm slices by the Compresstome VF 310-0Z vibrating microtome (Precisionary Instruments). Photoconversion of Kaede was performed using a 405nm 30mW diode AOTF modulated line set to 0.2 % transmittance laser and a time series of 325 cycles at a 1.58msec/pixel pixel dwell times, using a 405 long-pass dichroic mirror. Photoconverted slices were digested in collagense IV + hyaluronidase + DNAse. Samples were digested for 15 min at 37°C and pass through a 100μm cell strainer followed by RBC lysis. Cells were washed and resuspended in 1mL flow buffer with DAPI (1:10,000) for sorting. Green/red double positive live cells were considered as the successful photoconverted ones and FACS-sorted into 1.5mL Eppendorf tubes with 500μL media at AriaIII.

value: Balb/c x Kaede F1

tag: tumor

tag: hashtags

value: Hashtag 7 = QCC areas Hashtag 8= proliferative areas


title: Sample_14946 [Control]

description: Normal Brain tissue

value: F

tag: pmi

tag: repository

value: White


title: 8h_NLRX1-F_M4_Vneg


title: Sample_14944 [Control]

description: Normal Brain tissue

value: M

tag: race

tag: group


title: D0_B

value: muscle

tag: treatment


title: G_5645_ST [PCHT90]

description: re-analysis of GSM5543414

value: Holstein


title: 4T07 p27k Neg 4

description: Proliferative cells sorted  paired with QCC from 4T07 tumor

data_processing:
Genewix performed basic computational analysis for quality controls and constructed the gene matrices.
Gene matrices were normalized using DESeq2 size factors and filtering for a minimum of 10 read per condition (60-80 rowSums).
Gene matrices were normalized using reads per million counts
Assembly: mm10
Supplementary files format and content: Gene count matrix with genes organized in rows and identified by official gene symbol and samples from the same experiment organized in columns
Supplementary files format and content: DESeq2 output files analyzed using p27high vs p27low considering paired samples form the same tumor

source_name: 4T07 tumor

growth_protocol: 250000 mCherry and mVenus-p27k-transduced 4T07, D2A1 and EMT6 cells were injected into the mammary fat pad of Balb/cJ mice. Tumors were harvested 14 days after injection.

extract_protocol:
RNA was extracted with miRNeasy Micro kit (QIAGEN) following the manufacturer’s instructions
RNA samples were submitted to GENEWIZ for bulk RNA-sequencing. Were they performed basic computational analysis to generate the genecount matrices

treatment_protocol: Tumors were digested in collagense IV + hyaluronidase + DNAse. Samples were digested for 20 min at 37°C and pass through a 100μm cell strainer followed by RBC lysis. Cells were stained with CD45 and resuspended in 1mL flow buffer with DAPI (1:10,000) for sorting at an AriaIII (BD).

tag: strain

value: Balb/cJ

tag: tumor cell line

value: 4T07 tumor

tag: tumor id

tag: rnaseq run


title: 4T07 tumor infiltrates 2

description:
scRNAseq from 4T07 infilrates after PADMEseq protocol to identify microregions labeled by hashtags before the 10x pipeline
UMAP_all_infiltrates.rds; UMAP_t_cells.rds; 705_barcodes.tsv; 705_features.tsv; 705_matrix.mtx.gz

value: Hashtag 9 = QCC areas Hashtag 10 = proliferative areas


title: 8h_NLRX1-F_M4_Vpos

data_processing:
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.8, Martin 2011).
Reads matching to ribosomal RNA sequences were removed with fastq_screen (v. 0.11.1). Remaining reads were further filtered for low complexity with reaper (v. 15-065, Davis et al. 2013)
Reads were aligned against the Mus musculus.GRCm38.92 genome using STAR (v. 2.5.3a, Dobin et al. 2013). The number of read counts per gene locus was summarized with htseq-count (v. 0.9.1, Anders et al. 2014) using Mus musculus.GRCm38.92 gene annotation.
Quality of the RNA-seq data alignment was assessed using RSeQC (v. 2.3.7, Wang et al. 2012). Reads were also aligned to the Mus musculus.GRCm38.92 transcriptome using STAR (v. 2.5.3a, Dobin et al. 2013) and the estimation of the isoforms abundance was computed using RSEM (v. 1.2.31, Li and Dewey 2011).
Statistical analysis was performed for genes independently in R (R version 3.4.4). Genes with low counts were filtered out according to the rule of 1 count(s) per million (cpm) in at least 1 sample. Library sizes were scaled using TMM normalization. Subsequently, the normalized counts were transformed to cpm values, and a log2 transformation was applied, by means of the function cpm with the parameter setting prior.counts = 1 (EdgeR v 3.20.9; Robinson et al. 2010).

tag: genotype

tag: gender

value: female

tag: time-point


title: Sample_14943 [PD]

tag: tissue

tag: age

tag: Sex

value: Harvard

value: Parkinson's disease (PD)


title: 4T07 p27k Neg 3


title: 8h_NLRX1-F_M4_Medium

value: Non-treated


title: G_5645_GE [PCHT89]

description: re-analysis of GSM5543412

tag: breed

tag: cell type

tag: animal group


title: G_5645_LE [PCHT88]

description: re-analysis of GSM5543413

value: luminal cell


title: Sample_14942 [PD]

value: Parkinson's disease Affected Brain tissue

tag: pmi

tag: repository

value: Unknown


title: 4T07 p27k Neg 2


title: 8h_WT-M_M3_pIC

value: WT

value: male

value: Poly I:C


title: 8h_WT-M_M3_Vneg


title: 4T07 p27k Neg 1


title: G_4463_GE [PCHT86]

description: re-analysis of GSM5543411

value: glandular cell

value: Healthy (H)


title: Sample_14945 [PD]

value: M

tag: race

tag: group


title: Sample_14940 [PD]

value: White


title: 4T07 p27k High 4

description: QCC cells sorted from 4T07 tumor

tag: strain

value: Balb/cJ


title: G_3030_ST [PCHT84]

description: re-analysis of GSM5543410

value: Holstein

value: stromal cell


title: E_6608_ST [PCHT83]


title: Sample_14939 [PD]


title: 8h_WT-M_M3_Vpos

tag: treatment


title: 4T07 p27k High 3

description: QCC cells sorted from 4T07 tumor

tag: tumor cell line

value: 4T07 tumor

tag: tumor id


title: Sample_14938 [Control]

description: Normal Brain tissue

value: Normal Brain tissue

value: F

value: Harvard

value: Control


title: 4T07 p27k High 2

description: QCC cells sorted from 4T07 tumor

tag: rnaseq run


title: Sample_14955 [PD]

value: Parkinson's disease Affected Brain tissue

value: Parkinson's disease (PD)


title: 4T07 p27k High 1

description: QCC cells sorted from 4T07 tumor


title: Sample_14937 [Control]

description: Normal Brain tissue


title: E_6608_GE [PCHT82]


title: E_6608_LE [PCHT81]

value: luminal cell


title: 8h_WT-F_M6_pIC

tag: genotype

value: WT

tag: gender

value: female


title: 8h_WT-M_M3_Medium

value: male

tag: time-point

value: Non-treated


title: E_6575_ST [PCHT80]


title: EMT6 p27k Neg 4

description: Proliferative cells sorted  paired with QCC from EMT6 tumor

source_name: EMT6 tumor

value: EMT6 tumor


title: Sample_14935 [PD]

tag: tissue

tag: age

value: Unknown


title: 8h_WT-F_M6_tBHQ

value: tBHQ


title: E_6575_GE [PCHT79]

tag: breed

value: Holstein

value: glandular cell


title: EMT6 p27k Neg 3

value: Balb/cJ


title: EMT6 p27k Neg 2


title: E_6523_ST [PCHT77]

tag: cell type

value: stromal cell


title: Sample_14936 [Control]

description: Normal Brain tissue

value: Normal Brain tissue

tag: Sex

value: F


title: Sample_14941 [PD]

tag: pmi

value: Harvard


title: 8h_WT-F_M6_Vneg


title: Sample_14934 [PD]

value: Parkinson's disease Affected Brain tissue

value: M

tag: repository

value: White


title: Sample_14933 [PD]

tag: race

value: Parkinson's disease (PD)


title: 8h_WT-F_M6_Vpos

value: WT

value: female


title: E_6523_GE [PCHT76]

tag: animal group


title: EMT6 p27k Neg 1

tag: strain


title: E_5777_ST [PCHT75]


title: Sample_14932 [Control]

description: Normal Brain tissue

tag: group

value: Control


title: 8h_WT-F_M6_Medium

tag: treatment

value: Non-treated


title: 8h_NRF2_M4_tBHQ


title: EMT6 p27k High 4

description: QCC cells sorted from EMT6 tumor

tag: tumor cell line

value: EMT6 tumor

tag: tumor id


title: 8h_NRF2_M4_Vneg

tag: genotype


title: E_5734_ST [PCHT72]


title: Sample_14931 [Control]

description: Normal Brain tissue

value: Unknown


title: EMT6 p27k High 2

description: QCC cells sorted from EMT6 tumor

tag: rnaseq run


title: Sample_14930 [Control]

description: Normal Brain tissue


title: EMT6 p27k High 3

description: QCC cells sorted from EMT6 tumor


title: E_5734_GE [PCHT71]

value: Holstein


title: 8h_NRF2_M4_Vpos

tag: gender

tag: time-point


title: 8h_NRF2_M4_Medium


title: Sample_14929 [Control]

description: Normal Brain tissue

tag: tissue

tag: age


title: EMT6 p27k High 1

description: QCC cells sorted from EMT6 tumor


title: Sample_14928 [PD]


title: E_5703_GE [PCHT68]

tag: breed

tag: cell type

value: glandular cell


title: Sample_14927 [PD]

tag: Sex

tag: pmi


title: 8h_NLRX1-M_M3_pIC

value: male

value: Poly I:C


title: D2A1 p27k Neg 3

description: Proliferative cells sorted  paired with QCC from D2A1 tumor

source_name: D2A1 tumor

value: Balb/cJ

value: D2A1 tumor


title: 8h_NLRX1-M_M3_Vneg


title: E_5703_LE [PCHT67]

value: luminal cell


title: Sample_14926 [PD]

value: Parkinson's disease Affected Brain tissue

value: F

tag: repository

value: Harvard

tag: race


title: D2A1 p27k Neg 4

tag: strain


title: 8h_NLRX1-M_M3_Vpos


title: D2A1 p27k Neg 2


title: E_5638_ST [PCHT66]

value: stromal cell

tag: animal group


title: D2A1 p27k Neg 1


title: Sample_14925 [PD]

value: White

tag: group

value: Parkinson's disease (PD)


title: 8h_NLRX1-M_M3_Medium

tag: treatment


title: E_5638_GE [PCHT65]


title: Sample_14923 [Control]

description: Normal Brain tissue

value: Normal Brain tissue

value: M

value: Control


title: D2A1 p27k High 4

description: QCC cells sorted from D2A1 tumor

tag: tumor cell line

tag: tumor id


title: D2A1 p27k High 3

description: QCC cells sorted from D2A1 tumor

tag: rnaseq run


title: 8h_NLRX1-F_M1_Vpos

tag: genotype

tag: gender

value: female


title: 8h_NLRX1-F_M1_Vneg

tag: time-point


title: Sample_14922 [PD]

tag: tissue

tag: age


title: E_5734_LE [PCHT70]

tag: breed

value: Holstein

tag: cell type


title: D2A1 p27k High 2

description: QCC cells sorted from D2A1 tumor


title: Sample_14921 [PD]

tag: Sex

tag: pmi


title: Sample_14920 [Control]

description: Normal Brain tissue

tag: repository

tag: race

value: Unknown


title: D2A1 p27k High 1

description: QCC cells sorted from D2A1 tumor

tag: strain


title: E_4454_LE [PCHT61]

tag: animal group


title: E_4423_ST [PCHT60]


title: mCherry_3

description: 4T07 mcherry control tumors without GFP cells or Jedi injection

data_processing:
Genewix performed basic computational analysis for quality controls and constructed the gene matrices.
Gene matrices were normalized using DESeq2 size factors and filtering for a minimum of 10 read per condition (60-80 rowSums).
Gene matrices were normalized using reads per million counts
Assembly: mm10
Supplementary files format and content: Gene count matrix with genes organized in rows and identified by official gene symbol and samples from the same experiment organized in columns
Supplementary files format and content: DESeq2 output files analyzed using GFP vs mCherry considering paired samples form the same tumor

source_name: mcherry 4T07 control tumors

growth_protocol: 250000 GFP and mCherry-transduced 4T07 cells were injected forming a 1:1 mix ratio into the mammary fat pad of Balb/cJ x Bl6 mice. 7M PD1KO Jedi T cells was injected tail vein at day 7 or 15 from tumor growth. Tumors were harvested 7 days after Jedi injection.

extract_protocol:
RNA was extracted with miRNeasy Micro kit (QIAGEN) following the manufacturer’s instructions or by GENEWIZ company using their low input RNA protocol
RNA samples were submitted to GENEWIZ for bulk RNA-sequencing. Were they performed basic computational analysis to generate the genecount matrices

value: C57BL/6J x Balb/cJ F16


title: Sample_14918 [PD]

tag: group


title: 8h_WT-M_M2_pIC

extract_protocol:
BMDMs were cleared out of supernatants and lysed with 350 µl RLT buffer (Qiagen) supplemented with 40 mM DTT (Dithiotreitol) for RNA extraction. Plates were then frozen at -80°C until the RNA purification. The RNA samples were purified with the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s instructions. Purified RNA was eluted with 30 µl RNase-free water (Qiagen).
Library preparation and sequencing were performed at the Lausanne Genomic Technologies Facility (GTF), University of Lausanne (UNIL), Switzerland

value: WT

value: male

tag: treatment

value: Poly I:C


title: E_4423_GE [PCHT59]

value: glandular cell


title: 8h_NLRX1-F_M1_pIC


title: E_5638_LE [PCHT64]

value: luminal cell


title: 8h_NLRX1-F_M1_Medium

value: Non-treated


title: mCherry_1

value: C57BL/6J x Balb/cJ F14

tag: tumor cell line

tag: tumor id


title: Sample_14916 [PD]

value: Parkinson's disease Affected Brain tissue

value: Harvard


title: E_4454_ST [PCHT63]

value: stromal cell


title: mCherry_2

value: C57BL/6J x Balb/cJ F15

tag: rnaseq run


title: 8h_WT-M_M2_Vpos

tag: genotype

tag: gender


title: E_2333_ST [PCHT58]


title: E_2333_GE [PCHT57]


title: 8h_NLRX1-M_M4_Vpos

tag: time-point


title: mCherry_0

value: C57BL/6J x Balb/cJ F13


title: E_4454_GE [PCHT62]


title: 8h_WT-F_M3_tBHQ

value: tBHQ


title: Sample_14914 [PD]

tag: tissue

tag: age

value: M

value: White

value: Parkinson's disease (PD)


title: E_2333_LE [PCHT56]

tag: breed

value: Holstein

tag: cell type


title: 8h_WT-F_M3_pIC

value: WT

value: female


title: Sample_14912 [Control]

description: Normal Brain tissue

value: Normal Brain tissue

tag: Sex

value: F

tag: pmi

value: Miami

value: Control


title: 8h_WT-M_M2_Vneg

value: male


title: E_2297_ST [PCHT55]


title: Da15_mCherry_3

description: 4T07 mCherry control cells that were tumor counterparts of the GFP cells while Jedi killing in vivo

source_name: mCherry 4T07 tumors cells after Jedi killing

value: C57BL/6J x Balb/cJ F12

tag: t cell injection day


title: E_2297_GE [PCHT54]

value: glandular cell


title: Da15_mCherry_2

tag: strain

value: C57BL/6J x Balb/cJ F11


title: 8h_WT-F_M3_Vneg


title: Sample_14910 [Control]

description: Normal Brain tissue

tag: repository

tag: race


title: Sample_14911 [Control]

description: Normal Brain tissue

tag: group


title: 8h_WT-F_M3_Vpos

tag: treatment


title: 8h_WT-M_M2_Medium

value: Non-treated


title: Da15_GFP_3

description: 4T07 GFP surviving cells after Jedi killing in vivo

source_name: GFP 4T07 tumors cells after Jedi killing

value: C57BL/6J x Balb/cJ F9

tag: tumor cell line

tag: tumor id


title: Sample_14908 [Control]

description: Normal Brain tissue


title: Sample_14915 [PD]

value: Parkinson's disease Affected Brain tissue

value: Harvard


title: Da15_GFP_1

value: C57BL/6J x Balb/cJ F7

tag: rnaseq run


title: 8h_WT-F_M3_Medium

tag: genotype

tag: gender


title: Sample_14907 [Control]

description: Normal Brain tissue

tag: tissue

value: White


title: 8h_NRF2_M2_Vneg

tag: time-point


title: Day7_mCherry_3

value: C57BL/6J x Balb/cJ F6


title: Day7_mCherry_2

value: C57BL/6J x Balb/cJ F5


title: Sample_14906 [Control]

description: Normal Brain tissue

tag: age


title: Da15_mCherry_1

value: C57BL/6J x Balb/cJ F10


title: Day7_mCherry_1

value: C57BL/6J x Balb/cJ F4


title: Sample_14905 [Control]

description: Normal Brain tissue

value: Normal Brain tissue

value: F


title: 8h_NLRX1-M_M2_pIC

value: Poly I:C


title: Sample_14909 [Control]

description: Normal Brain tissue

value: Miami

value: Control


title: Day7_GFP_3

value: C57BL/6J x Balb/cJ F3


title: 8h_NRF2_M2_Medium

value: female


title: 8h_NRF2_M2_tBHQ

value: tBHQ


title: Sample_14903 [Control]

description: Normal Brain tissue

value: M


title: Day7_GFP_2

value: C57BL/6J x Balb/cJ F2


title: Da15_GFP_2

value: C57BL/6J x Balb/cJ F8


title: 8h_NRF2_M2_Vpos


title: OLAP-HuR, biological rep 1

city: Philadelphia

first: Aditi

last: Jain

state: PA

address: 1015 Walnut Street

department: Surgery

institute: Thomas Jefferson University

description: Gene expressiond data from cytoplasmic extracts subjected to HuR IP

hyb_protocol: Affymetrix gene chips Human Clariom D array was hybridized with fragmented and biotin-labeled target (5 µg) in 220 ul of hybridization cocktail. Target denaturation was performed at 99°C for 5 min. and then 45°C for 5 min, followed by hybridization for 16-18 h.

scan_protocol: Chips Human Clariom D arrays were scanned on an Affymetrix Gene Chip Scanner 3000, using Command Console Software.

data_processing:
Chp files were generated by Gene Level-SST-RMA normalization from Affymetrix cel file by using Expression Console Software 1.4.
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = Clariom_D_Human
program-name = Expression Console
program-version = 1.4.1.46

label: biotin

source_name: Mia PaCa-2_RNA extracts from cytoplasmic HuR-IP of OLAP treated cells

label_protocol: Fragmented biotin labeled cDNA (from 10 ng of RNA) was synthesized using the Affymetrix GeneChip WT Pico kit

growth_protocol: Cells were grown in DMEM + 10% FBS at 37˚C and 5% C02

extract_protocol: Cytoplasmic HuR was immunopreciptated using HuR specific antibody and bound immunoprecipitated RNA was extracted using Trizol RNA extraction method.

treatment_protocol: Cells were treated with olaparib (10µM) or gemcitabine (1µM) for 16 hours in complete growth medium

tag: cell line

value: Mia PaCa-2

tag: tissue source

value: pancreas

tag: cell type

value: pancreatic ductal adenocarcinoma (PDAC) cell line

value: olaparib (10µM) for 16 h

tag: ip

value: HuR-IP

tag: molecule subtype

value: cytoplasmic RNA


title: GEM-HuR, biological rep 1

source_name: Mia PaCa-2_RNA extracts from cytoplasmic HuR-IP of GEM treated cells

value: gemcitabine (1µM) for 16 h


title: Sample_14902 [Control]

description: Normal Brain tissue

value: Normal Brain tissue

tag: Sex

tag: pmi

tag: repository

value: White


title: 8h_NLRX1-M_M2_Vpos

source_name: Bone marrow derived macrophages

tag: strain

value: male

tag: treatment


title: OLAP-HuR, biological rep 2


title: OLAP-IgG, biological rep 2

description: Gene expressiond data from cytoplasmic extracts subjected to IgG IP

source_name: Mia PaCa-2_RNA extracts from cytoplasmic IgG-IP of OLAP treated cells

value: IgG-IP


title: Day7_GFP_1

value: C57BL/6J x Balb/cJ F1

tag: tumor cell line

tag: t cell injection day

tag: tumor id


title: GEM-HuR, biological rep 2


title: 8h_NLRX1-M_M2_Vneg

tag: genotype

tag: gender


title: OLAP-IgG, biological rep 1


title: Sample_14901 [Control]

description: Normal Brain tissue

source_name: Brain

tag: tissue

value: F

value: Miami

tag: race

tag: group

value: Control


title: 8h_NLRX1-M_M2_Medium

tag: time-point

value: Non-treated


title: GEM-IgG, biological rep 2

source_name: Mia PaCa-2_RNA extracts from cytoplasmic IgG-IP of GEM treated cells

tag: cell line

tag: tissue source

tag: cell type


title: E13.5 FlashTag collected at P7 IL12_Pool1

city: Geneva

first: Denis

last: Jabaudon

address: Rue Michel-Servet 1

institute: University of Geneva

data_processing:
Reads were aligned with STAR aligner
The count matrix were generated with HTSeq
cells expressing less <2000 genes or >12% of mitochondrial RNAs were excluded
Genome_build: Genome_build: mm10
Supplementary_files_format_and_content: RPM normalized matrix

source_name: Neurons

extract_protocol:
SMART-Seq v4 3’ DE Kit
Single cells were collected into tubes and the library was constructed with Nextera XT library prep kit according to manufacturers

value: WT

tag: age


title: Sample_14904 [Control]

description: Normal Brain tissue

tag: Sex

value: M

tag: pmi


title: GEM-IgG, biological rep 1

value: Mia PaCa-2

value: pancreas

tag: ip

tag: molecule subtype


title: E13.5 FlashTag collected at P7 IL10_Pool5

tag: strain


title: 8h_NLRX1-F_M2_Vneg

first: Nicolas

address: Chemin des Boveresses 155

institute: University of Lausanne

value: female

tag: treatment


title: 8h_NLRX1-F_M2_pIC

value: Poly I:C


title: 8h_NLRX1-F_M2_Vpos


title: AERD_28_TK240s1

city: Vienna

first: Christine

last: Bangert

address: Waehringer Guertel 18-20

department: Department of Dermatology

country: Austria

institute: Medical University of Vienna

data_processing:
The raw sequencing reads were aligned to the reference genome GRCh38 and demultiplexed using Cell Ranger 3.0.2
The resulting count-matrices were then imported into R for further analysis using the Seurat package v3
Cells were filtered based on their number of unique reads, number of expressed features and the percentage of mitochondrial reads present to ensure cell quality .
Samples were normalized with Seurat’s NormalizeData function using log normalisation.
Genome_build: GRCh38
Supplementary_files_format_and_content: individual gene expression matrix per patient, in .csv format containing log-normalized cell-counts

source_name: nasal polyps

extract_protocol:
Biopsies were taken during endoscopy and kept in phosphate buffered saline (PBS) on ice until further processing.
The partial nasal biopsy was enzymatically digested for one hour at 37°C using RPMI-1640 medium (Thermo Fisher Scientific, Waltham, Massachusetts, USA) supplemented with 2.8 mg/ml Collagenase IV Thermo Fisher Scientific) and 0.03 mg/ml DNAse (Merck, Burlington, Massachusetts, USA). Single cell suspension was obtained by passing the tissue through a 70 µm cell strainer (BD, Franklin Lakes, New Jersey, USA) and washing it twice with RPMI-1640 medium supplemented with 20% foetal bovine serum (FBS, Thermo Fisher Scientific). Thereafter cells were blocked with 10% mouse serum (Thermo Fisher Scientific) in MACS buffer (Miltenyi Biotec, Bergisch Gladbach, Germany) on ice for 5 minutes. Preparing cell suspensions for FACS sorting, cells were stained with anti-human CD15 FITC (clone W6D3, Biolegend), anti-human CD94 PE (clone DX22, Biolegend), anti-human CD14 APC (clone HCD14, Biolegend), anti-human HLA-DR BV421 (clone L243, Biolegend), anti-human CD45 PE-CF594 (clone HI30, BD BioSciences), anti-human CD11c PE-Cy7 (clone 3.9, Biolegend), anti-human CD20 APC-Cy7 (clone 2H7, Biolegend) and anti-human CD3 BV605 (clone SK7, Biolegend) with an incubation period of 30 minutes on ice under light protection. Cells were then subjected to FACS sorting (FACSAria III, BD Biosciences, Franklin Lakes, NJ) for enrichment of CD45+ leukocyte subsets to obtain comparable numbers between all samples allowing for comparison of small cell populations. Up to 18,000 sort-purified cells from each sample were suspended in reverse transcription reagents, along with gel beads, and then segregated into aqueous nanoliter-scale gel bead-in-emulsions. After gel bead-in-emulsions reverse transcription, single-cell droplets were broken, and the single-strand cDNA was isolated and amplified. Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed, and index adaptor ligated followed by post-ligation amplification. The sequencing-ready libraries were sequenced by the Biomedical Sequencing Facility at the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, using the Illumina HiSeq 3000/4000 platform and the 75 bp paired-end configuration.

treatment_protocol: Prior to polyp biopsy, patients received local anasthetics and decongestants.

tag: 10x chromium chemistry version

tag: condition

value: AERD


title: E13.5 FlashTag collected at P7 IL10_Pool1

tag: genotype


title: E13.5 FlashTag collected at P7 IL11_Pool1


title: DMSO-IgG, biological rep 2

source_name: Mia PaCa-2_RNA extracts from cytoplasmic IgG-IP of DMSO treated cells

value: pancreatic ductal adenocarcinoma (PDAC) cell line

value: DMSO

value: cytoplasmic RNA


title: DMSO-HuR, biological rep 1

source_name: Mia PaCa-2_RNA extracts from cytoplasmic HuR-IP of DMSO treated cells

value: HuR-IP


title: 8h_NLRX1-F_M2_Medium

city: Epalinges

last: Fasel

tag: gender


title: 8h_WT-M_M1_Vneg

value: male


title: OC cells_OVCAR-8_resistant

city: Vejle

first: Silvia

middle: Regina

last: Rogatto

address: Beriderbakken 4

department: Clinical Genetics

country: Denmark

institute: Vejle Hospital

description: carboplatin-resistant

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using the Illumina HiScan system.

data_processing: Methylation data were analyzed using the minfi R package. Quality control, p-value for all probes, background noise detection, and adjustment were performed using the same package. Differences Type-I and Type-II probes adjustment and normalization of β values were performed using the BMIQ model. Batch effects were removed using SVA package. Probes with low quality (detection p-value >0.05), mapped in X/Y chromosomes, and cross-reactive were filtered out, and those mapped to SNPs were removed (package minfi). DMPs were identified using the R package limma. Probes with p-value <0.01 and |∆β| > 0.1 were considered significant and annotated using the Illumina manifest file.

label: Cy5 and Cy3

growth_protocol: The cell lines were cultured in RPMI medium (Sigma Aldrich, Saint Louis, USA) (cell lines IGROV1, OVCAR3, and OVCAR4) or Dulbecco’s modified Eagle medium (DMEM, Sigma Aldrich) (OVCAR5, OVCAR8, and Ovc316), as recommended. The media were supplemented with 10% FBS (Biological Industries) and 1% antibiotic-antimycotic (Thermo Fisher).

extract_protocol: Genomic DNA was extracted using DNeasy Blood & Tissue Kit (Qiagen, Valencia, CA, USA).

value: ovarian cancer cell line

value: Not applicable


title: DMSO-HuR, biological rep 2


title: E13.5 FlashTag collected at P7 IL09_Pool4


title: E13.5 FlashTag collected at P7 IL09_Pool5


title: OC cells_Ovc316_resistant

description: carboplatin-resistant


title: AERD_22_TK221s1

value: CRSwNP


title: 8h_WT-M_M1_Vpos


title: E13.5 FlashTag collected at P7 IL09_Pool2


title: AERD_24_TK221s2


title: AERD_27_TK233s1

value: F


title: DMSO-IgG, biological rep 1

value: IgG-IP


title: AERD_20_TK219s2


title: E13.5 FlashTag collected at P7 IL09_Pool3

value: WT


title: AERD_18_TK219s1


title: 8h_WT-M_M1_Medium

value: Non-treated


title: 8h_WT-M_M1_pIC


title: Sample_14917 [Control]

description: Normal Brain tissue

tag: tissue

value: Normal Brain tissue

value: M

tag: repository

value: Harvard

tag: race

value: Unknown

value: Control


title: OC cells_IGROV-1-R1_resistant

description: carboplatin-resistant

tag: cell line

value: To establish resistant cell lines, the baseline schedule consisted of four days treatment with 1 µM of carboplatin in the culture media followed by three recovery days in media without carboplatin. For cell lines tolerating this treatment well, the concentration was increased gradually (1-5-10-15 µM) when the cells reached a high confluency. For cell lines not tolerating the treatment well, the recovery was extended, and the low dose was maintained.


title: OC cells_OVCAR-3-R2_resistant

description: carboplatin-resistant


title: OC cells_OVCAR-3-R1_resistant

description: carboplatin-resistant


title: 8h_WT-F_M4_tBHQ

value: female

tag: time-point

value: tBHQ


title: E13.5 FlashTag collected at P7 IL08_Pool5


title: AERD_16_TK209s2


title: 8h_WT-F_M4_pIC

value: Poly I:C


title: AERD_14_TK206s3

value: AERD


title: E13.5 FlashTag collected at P7 IL08_Pool4


title: OC cells_OVCAR-5-R1_resistant

description: carboplatin-resistant

tag: cell type

value: ovarian cancer cell line


title: OC cells_OVCAR-5_sensitive

description: carboplatin-sensisitive

value: Not applicable


title: AERD_13_TK206s2


title: 8h_WT-F_M4_Vneg


title: OC cells_OVCAR-4_sensitive

description: carboplatin-sensisitive


title: 8h_WT-F_M4_Vpos


title: E13.5 FlashTag collected at P7 IL08_Pool2

tag: age


title: Wrinkly Speader1 Rep 4

city: Christchurch

first: Heather

last: Hendrickson

department: Biological Sciences

country: New Zealand

institute: University of Cantebury

data_processing:
reads were aligned to the Acanthamoeba reference genome (Acanthamoeba castellanii strain NEFF GCA_000313135.1) using HiSat2
unused reads were then aligned to the bacterial reference genome (Pseudomonas fluorescens SBW25 GCA_000009225.1) using Bowtie2
Sequence reads were assigned to genomic features using featureCounts
Differential expression using GLM and count normalisation was calculated with edgeR, Counts were normalised by library size (counts per million, CPM) with log2 transformation.
Assembly: GCA_000313135.1, GCA_000009225.1
Supplementary files format and content: tab-delimited text files include CPM values per sample

organism: Pseudomonas fluorescens

source_name: Bacteria

growth_protocol: Individual colonies of bacterial strains pre-cultured on LB agar were homogenised in LB broth and spread in single lines across PM agar plates using a 1ul transfer loop. Plates were allowed to dry before applying 2 ul of suspension containing ~103 Acanthamoeba cysts µl-1 at one end of the bacterial line. Plates were incubated at 28˚C for up to 1 week and the interaction zone was collected once the amoeba had formed a visible clearing. Pseudomonas fluorescens SBW25 strains were collected with Acanthamoeba from the bacteria-protozoa interaction zone and alone from the opposite end of the culture line with a transfer loop and immediately homogenised in RNA shield (n=4

extract_protocol:
Total RNA was extracted from bacterial and amoebae cells using the Quick-RNA MiniPrep Kit (Zymo Research, USA)
Preparations were dried in GenTegra RNA tubes according to manufacturer’s instructions (Gentegra, USA) and sent to the Microbial Genome Sequencing (MiGS, USA) Center for Illumina Stranded RNA library preparation with RiboZero Plus rRNA depletion and sequencing on the NextSeq 550 platform.

value: SBW25 WS1


title: AERD_10_TK214s1

tag: Sex

value: F


title: Wrinkly Speader1 Rep 3


title: OC cells_OVCAR-3_sensitive

description: carboplatin-sensisitive


title: E13.5 FlashTag collected at P7 IL08_Pool3


title: AERD_12_TK206s1


title: 8h_WT-F_M4_Medium


title: E13.5 FlashTag collected at P7 IL08_Pool1


title: SCF-3

city: Beijing

first: Xi

address: 95 Yongan Rd

institute: Beijing Friendship Hospital

description: NMDA exposed mice with SCF treatment

data_processing:
The corresponding cDNA libraries were produced and qualified using an Agilent 2100 Bioanalyzer and an ABI StepOnePlus Real-Time PCR System.
Primary raw reads produced by HiSeq 4000 (Illumina, United States) were qualified and filtered to obtain clean reads.
Illumina Casava1.7 software used for basecalling.
A heatmap analysis of gene expression levels were created based on the averaged fragments per kilobase of exon per million fragments mapped (FPKM) values of genes.
Annotation analysis of Gene Ontology (GO) was performed to determine the on-going biological process.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Retina

extract_protocol:
Retinas were removed, flash frozen on dry ice. The mRNA sample was enriched using oligo (dT) magnetic beads and fragmented into short fragments using fragmentation buffer.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Two days post NMDA challenge, intravitreal injection of recombinant SCF was performed.

value: retina

value: post natal week 5

value: wild type


title: E13.5 FlashTag collected at P7 IL07_Pool5

value: WT


title: Wrinkly Speader1 Rep 2


title: AERD_09_TK196s2

value: M


title: AERD_08_TK196s1


title: OC cells_IGROV-1_sensitive

description: carboplatin-sensisitive


title: Wrinkly Speader1 Rep 1


title: E13.5 FlashTag collected at P7 IL07_Pool4


title: SCF-2

description: NMDA exposed mice with SCF treatment


title: WT Rep 4


title: SCF-1

description: NMDA exposed mice with SCF treatment


title: AERD_07_TK191s2


title: E13.5 FlashTag collected at P7 IL07_Pool3


title: WT Rep 3


title: E13.5 FlashTag collected at P7 IL07_Pool2


title: NMDA-3

description: NMDA exposed mice


title: AERD_05_TK188s1

value: CRSwNP


title: WT Rep 2


title: NMDA-2

description: NMDA exposed mice


title: AERD_04_TK187s1


title: E13.5 FlashTag collected at P7 IL07_Pool1


title: WT Rep 1


title: E13.5 FlashTag collected at P7 IL06_Pool5


title: Wrinkly Fried Egg Rep 4

value: SBW25 WFE


title: Tram -/- high dose LPS neutrophil

city: Blacksburg

first: Liwu

last: Li

state: VA

address: 1015 Life Science Cir

institute: Virginia Tech

data_processing:
Cellranger
Genome_build: mm10
Supplementary_files_format_and_content: matrix table

source_name: neutrophil

growth_protocol: Murine bone marrow neutrophils were purified by the percoll gradient method, and cultured in complete RPMI medium (10% fetal bovine serum, 2 mM L-glutamine, and 1% penicillin/streptomycin) supplemented with 100 ng/ml G-CSF.

extract_protocol:
cDNA libraries were generated from treated cells by using the 10X Genomics Chromium Single Cell 3' Reagent Kits (version 3 Chemistry)
ingle-cell suspensions were loaded onto the Chromium Controller to generate 1,000 single-cell gel beads in emulsion per sample. The cDNA of each sample after amplification of 12 cycles was quantified by Qubit and quality-checked by Bioanalyzer to verify the size distribution of cDNA samples and determine indexed PCR amplification of 15 cycles to yield a sufficient and unbiased library for sequencing. After library quality control by Tapestation, indexed library samples were quantified by KAPA library quantification kit (Universal) and pooled with 15 ul of 5 nM for each sample.

treatment_protocol: Cultured bone marrow neutrophils from WT and TRAM knockout mice were treated with PBS or 1mM 4-PBA for 24 h.

value: BM derived

value: High dose LPS

value: Tram -/-


title: AERD_02_TK186s2


title: NMDA-1

description: NMDA exposed mice


title: Tram -/- PBS neutrophil

value: PBS


title: AERD_01_TK186s1


title: Wrinkly Fried Egg Rep 2


title: E13.5 FlashTag collected at P7 IL06_Pool3


title: E13.5 FlashTag collected at P7 IL06_Pool2


title: Wrinkly Fried Egg Rep 1


title: WT 4PBA neuutrophil


title: E13.5 FlashTag collected at P7 IL06_Pool1