title: CC002d5_3

data_processing:
Reads were quality checked with package FastQC, then trimmed using Trimgalore with default settings.
Trimmed reads were mapped to mouse genome annotation mm10 using STAR aligner with default settings.
Mapped reads were feature counted (per gene) using RsubRead. Raw counts from mouse genome and virus mapping were then combined, an offset of 1 was added and counts were then normalized using DESeq2. After normalization, single extreme outlier points were razorized.
Log2 transformed, normalized expression levels were then batch corrected using package sva.
Extreme outlier samples were identified in principle component analyses and removed. For each group, 3-4 replicates were retained. Log2 transformed, normalized and batch corrected expression levels were then used for further analyses.
Genome_build: mouse mm10
Supplementary_files_format_and_content: txt matrix with log2 normalized values per sample.

tag: Sex

tag: strains


title: Sample 129_WT.4R

status: Public on Jul 08 2020

type: SRA

city: Charlottesville

first: David

middle: Michael

last: Johanson

state: VA

address: 200 Jeanette Lancaster Way

department: Department of Neuroscience

country: USA

institute: UVa School of Medicine

library_source: genomic

data_processing:
Reads with an average quality score below 25 (from any 10-bp window) or a mismatched barcode were removed
Paired-end reads were then merged using the software FLASH
Merged reads were analyzed using the QIIME pipeline with default parameters to remove chimeric, pick 97%-identity OTUs and assign taxonomy
Genome_build: Greengenes 13_8
Supplementary_files_format_and_content: csv: Includes OTUs and abundances that were detected in the dataset as well as taxonomic lineages for OTUs

molecule: genomic DNA

organism: Mus musculus

source_name: WT_chronic stress_47_cecal tissue

growth_protocol: The mice were maintained on a 12 hours light/dark cycle with lights on at 7am. Animals were housed 2–3 per cage and cages were randomly assigned to control or experimental groups.

extract_protocol:
Whole genomic DNA was isolated via phenol-chloroform extraction. Briefly, a fecal pellet was placed in a 2 mL tube containing 200 μL silica-zirconia beads (0.1 mm). The tube was filled with 750 μL extraction buffer, 200 μL 20% SDS and 750 μL phenol-chloroform-isoamyl alcohol (25:24:1). After disruption, the aqueous phase was separated by centrifugation and cleaned up with two washes of chloroform-isoamyl alcohol (24:1). The DNA was precipitated and resuspended in 10 mM Tris solution.
For 16S rRNA sequencing, the V3-V4 region of the 16S rRNA gene was amplified for 25 cycles using specific primers with adapter overhangs as per the Illumina library preparation guide. Following purification of the PCR products, individual indexes were added to the amplicons by PCR. The amplicons were purified, pooled in equal quantities, and then sequenced on the Illumina MiSeq platform.

treatment_protocol: Chronic stress was started after at least 1 week of acclimation. All behavioral interventions were performed between 4 pm and 7 pm and take-downs were performed between 11am and 2 pm. Animals were excluded from the experiments if they developed illnesses (e.g. dermatitis) that might affect the outcome of the results. Mice were subjected daily to an acute stressor (1–2 hours: restraint, loud white noise, crowded housing, strobe light) and an overnight stressor (12–24 hours: 45° cage tilting, repeated cage changes, wet bedding, dark deprivation) presented in a randomized fashion. For restraint stress, mice were placed in clean 50 mL conical tubes with pierced holes for ventilation for 1 hour. For crowded housing stress, mice were placed on top of the cage wire for 2 hours, after which their cage was changed. For wet bedding stress, 200 mL of water was added to the bedding of a clean cage. All procedures used autoclaved, sterile materials (bedding, water) in order to prevent contamination.

tag: strain background

tag: age

value: 8 weeks

tag: genotype

value: WT

tag: treatment

value: chronic stress

tag: experiment day

tag: sample type

value: cecal tissue


title: maize_ligular_region_mRNA_SEQ_Sdw3_rep1

city: Beijing

first: Hongchao

last: Li

address: No.2 Yuanmingyuan West Road

department: Crop Genetics and Breeding

country: China

institute: China Agricultural University

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.8
Raw reads analyzed using Bcl2Fastq
Raw data can be filtered according to NEBNext Ultra RNA Library Prep Kit. The RNA 5' Adapter AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT; the RNA 3' Adapter GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG
Clean data were mapped to the maize genome with TopHat (V2.1.0)
The Cufflinks package was used to assemble transcripts, compare and merge assembles, and identify differentially expressed genes (DEGs).
Genome_build: Zea mays B73 RefGen_v3
Supplementary_files_format_and_content: log2(fold_change（Sdw3/N18)

molecule: total RNA

organism: Zea mays

source_name: ligular region

extract_protocol:
Total RNA was extracted from the samples using a Plant RNA Isolation Kit (Waryong, China) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: developing ligular region of leaf8 and leaf9

tag: developmental stage

tag: cultivar


title: maize_ligular_region_mRNA_SEQ_N18_rep3


title: CC002d5_2

city: Münster

first: Klaus

last: Schughart

address: Von-Esmarch-Str 56

department: Virology

country: Germany

institute: University Münster

source_name: lung

extract_protocol:
For tissue preparation, mice were sacrificed and entire lungs were extracted. Lungs were immediately transferred to RNAlater solution, kept at 4°C for one day and subsequently stored at -20°C. RNA was isolated using Qiagen Midi Kit as described previously. RNA quality was controlled on a 2100 Bioanalyzer Instrument (Agilent).
500ng of total RNA was used to prepare libraries for sequencing using the Lexogen SENSE mRNA-seq library kit for Ion Torrent. Libraries amplified for 11 cycles as the final step of library preparation. Before sequencing, 1ul aliquots of this material was pooled and sequenced on an Ion Torrent PGM 314 chip. Barcode quantification data from the PGM were used to balance the barcodes for final pooling before sequencing. Following this final pooling, the library pools were sized to a target size of 260bp on a Pippin Prep instrument using the 2% Pippin Agarose gel. The sized libraries were examined on an Agilent High Sensitivity DNA chip, quantified using real-time PCR, and used to prepare spheres using a One-Touch 2 device.
RNA-Seq; These spheres were then sequenced on an Ion Torrent Proton sequencer with a P1 chip. The mean number of reads per sample was 24 million.

treatment_protocol: Female, 8-12 weeks old mice were anesthetized by intra-peritoneal injection with Ketamine/Xylazine. Mice were then intra-nasally infected with 20µl virus solution (10 ffu) and body weight, survival and well-being of mice was monitored for the following 14 days.

tag: agent

value: mouse-adapted H3N2 virus

tag: day

tag: ffu

value: female


title: CU-OP-17 (2 Gy)

city: CARDIFF

first: Peter

last: Giles

address: Heath Park

country: United Kingdom

institute: Cardiff University

description: CU-OP-17 (2 Gy) - Tonsil squamous cell carcinoma (cell line) - HPV-negative - Irradiated: 2 Gy

data_processing:
Trimming to remove adapter sequencer and poor quality ends of reads was performed by Trim Galore ( a wrapper to cutadapt). Trimming was performed using default parameters in paired-end mode.
Trimmed paired-end reads were aligned to the GRCm38 reference using STAR (v2.5.1b), an ultrafast universal RNA-seq aligner, following the 2-pass method.  STAR mapping was carried out using the MultimapNMax=1 flag, whereby reads that map to more than one genomic location are treated as being unmapped so as to excluded them from downstream analysis*.
Transcript level counts were calculated using Subread featureCounts Version 1.5.1. Transcript and locations used in the analysis derive from the UCSC ref_gene annotation combined with that of HPV16 (from NC_001526.2 ref_seq)
Genome_build: Combined hg19 and HPV16 (NC_001526.2)
Supplementary_files_format_and_content: tab-delimited text files containing: ensemble transcript ID, chromosome, start and end locations, strand, transcripts length and counts in STAR mapped bam file.

organism: Homo sapiens

growth_protocol: The novel cell lines CU-OP-17 and CU-OP-20 were derived from tonsil tumour biopsies that were obtained from patients prior to treatment at Cardiff and Vale University Health Board, from March 2015 to August 2016.   The study was conducted with NHS Research Ethics Committee approval: Research Ethics Committee for Wales 13/WA/0002, with written consent of patients. The study was performed in accordance with the Declaration of Helsinki.   CU-OP cell lines (CU-OP-2, -3, -17 and -20) were growing in GMEM media with additional supplements and 60 Gy irradiated 3T3 fibroblasts, which were removed prior to RNA extraction (described in detail in"Sensitivity to inhibition of DNA repair by Olaparib in novel oropharyngeal cancer cell lines infected with Human Papillomavirus" by Pirotte et al).   The remaining cell lines of this study were grown in DMEM with 10% Fetal Bovine Serum: UM-SCC-47 (HPV-positive), UM-SCC-6 (HPV-negative), UM-SCC-4 (HPV-negative), UM-SCC-19 (HPV-negative), UM-SCC-74a (HPV-negative), cell lines were obtained from Professor Thomas Carey (University of Michigan, USA). UPCI-SCC-90 (HPV-positive) was purchased from DSMZ (Braunschweig, Germany). All cell cultures were incubated at 37°C in 5% CO2.

extract_protocol: Cells (non-irradiated and irradiated with 2 Gy) were collected 24 h after treatment. RNA was extracted with QiaAMP RNA Mini Kits (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. Wales Gene Park (Cardiff University, UK) performed the RNA transcriptome sequencing. Library preparation was performed by using the Illumina® TruSeq® Stranded Total RNA with Ribo-Zero Gold™ kit (Illumina Inc.) following manufacturer’s instructions. On the Illumina® HiSeq2500 in high-output mode, a 75-base paired-end dual index read format was used

treatment_protocol: 20 samples (10 non-irradiated and 10 irradiated with 2 Gy and collected after 24 h)

tag: hpv status

value: HPV-negative

tag: p53 status

value: p53 wild-type

value: irradiated with 2 Gy


title: Sample 128_WT.4L


title: CU-OP-3 (2Gy)

description: CU-OP-3 (2Gy) - Tonsil squamous cell carcinoma (cell line) - HPV-positive - Irradiated: 2 Gy

source_name: Tonsil sqamous cell carcinoma (cell line)

value: HPV-positive


title: CC002d3_4


title: maize_ligular_region_mRNA_SEQ_N18_rep2


title: CU-OP-2 (2 Gy)

description: CU-OP-2 (2 Gy) - Tonsil squamous cell carcinoma (cell line) - HPV-positive - Irradiated: 2 Gy


title: maize_ligular_region_mRNA_SEQ_N18_rep1


title: Sample 127_SCID.4R

source_name: SCID_Naive_49_fecal pellet

value: SCID

value: Naive

value: fecal pellet


title: CC002d3_3


title: maize_internode_mRNA_SEQ_Sdw3_rep3

source_name: internode

value: developing internode between leaf7 and leaf8


title: Sample 125_SCID.3R


title: UPCI-SCC-90 (2 Gy)

description: UPCI-SCC-90 (2 Gy) - Base of tongue squamous cell carcinoma (cell line) - HPV-positive - Irradiated: 2 Gy


title: UM-SCC-47 (2 Gy)

description: UM-SCC-47 (2 Gy) -   Lateral tongue squamous cell carcinoma (cell line) - HPV-positive - 2Gy Irradiated


title: Sample 130_WT.5L


title: maize_internode_mRNA_SEQ_Sdw3_rep2


title: Sample 124_SCID.3L


title: CC002d3_2


title: maize_internode_mRNA_SEQ_Sdw3_rep1


title: UM-SCC-19

description: UM-SCC-19 - Base of tongue squamous cell carcinoma (cell line) - HPV-negative

value: p53 mutant


title: CC002cd3_7

value: ctrl


title: CC002cd3_6


title: Sample 123_WT.7R

source_name: WT_Naive_49_fecal pellet

value: 8 weeks


title: maize_internode_mRNA_SEQ_N18_rep3


title: Sample 121_WT.6R

value: WT


title: CC002d5_1


title: UM-SCC-74a

description: UM-SCC-74a - Base of tongue squamous cell carcinoma (cell line) - HPV-negative


title: CC002cd3_4


title: Sample 126_SCID.4L


title: UM-SCC-6

description: UM-SCC-6 - Base of tongue squamous cell carcinoma (cell line) - HPV-negative


title: Sample 120_WT.6L


title: maize_internode_mRNA_SEQ_N18_rep2


title: UM-SCC-4

description: UM-SCC-4 - Tonsil squamous cell carcinoma (cell line) - HPV-negative


title: CC002cd3_3


title: maize_internode_mRNA_SEQ_N18_rep1


title: Sample 118_SCID.1L

source_name: SCID_chronic stress_47_fecal pellet

value: chronic stress


title: CC001d5_3


title: Sample 117_WT.5L

source_name: WT_chronic stress_47_fecal pellet


title: evolved Pseudomonas putida KT2440 in the glucose M9 (rep 2)

city: San Diego

first: Bernhard

middle: O.

last: Palsson

state: California

address: 9500 Gilman Dr

department: Bioengineering

institute: University of California, San Diego

description:
T9__glc__2
Total RNA with depleted ribosomal RNA

data_processing:
Raw RNA-Seq reads were mapped to the original reference genome using Bowtie2 and transcript abundance was analyzed using summarizeOverlaps (Lawrence et al., 2013). Calculation of transcripts per million (TPM) and prediction of differentially expressed genes were conducted using DESeq2 (Love et al., 2014).
Genome_build: NC_002947.4

organism: Pseudomonas putida KT2440

source_name: Pseudomonas putida KT2440 TA9_F60_I1

growth_protocol: All microbial cultures were conducted at 30 ˚C using either the modified minimal M9 medium (4 g/L glucose, 2 g/L (NH4)2SO4, 6.8 g/L Na2HPO4, 3 g/L KH2PO4, 0.5 g/L NaCl, 2 mM MgSO4, 0.1 mM CaCl2, 500 μL/L 2000X trace element solution). The composition of the trace element solution is 4.5 g/L ZnSO4⋅7H2O, 0.7 g/L MnCl2⋅4H2O, 0.3 g/L CoCl2⋅6H2O, 0.2 g/L CuSO4⋅2H2O, 0.4 g/L Na2MoO4⋅2H2O, 4.5 g/L CaCl2⋅2H2O, 3.0 g/L FeSO4⋅7H2O, 1.0 g/L H3BO3, 0.1 g/L KI, 15 g/L disodium ethylenediaminetetraacetate (Mohamed et al., 2017).

extract_protocol:
For transcriptomic analysis, cell cultures at the exponential phase (OD600 0.4-0.6) were mixed with two volumes of RNA protect Bacteria Reagent (Qiagen, Hilden, Germany) for stabilization and their total RNA was extracted by using Quick-RNA Fungal/Bacterial Miniprep Kit (Zymo Research). Residual genomic DNA was removed by incubating the samples with DNase I (RNase-free, NEB). Ribosomal RNA was removed by hybridizing with 30-bp oligonucleotides designed to bind the ribosomal RNA of KT2440 specifically and treating with Thermostable RNase H purchased from Lucigen (Middleton, WI, USA). The remaining oligonucleotides were removed by incubating the resulting samples with DNase I (NEB). The samples were purified by using an RNA Clean & Concentrator Kit (Zymo Research).
Paired-end RNA-Seq libraries were constructed using a KAPA RNA HyperPrep kit from Kapa Biosystems (Wilmington, MA, USA).

treatment_protocol: The IL stock solutions were additionally added for the preparation of the IL-containing minimal media. When [TEA][HS] was added, the media were neutralized (pH 7) by the addition of 10 M NaOH solution.

tag: growth

value: in the glucose M9

tag: strain

value: evolved


title: CU-OP-20

description: CU-OP-20 - Tonsil squamous cell carcinoma (cell line) - HPV-positive


title: CU-OP-17

description: CU-OP-17 - Tonsil squamous cell carcinoma (cell line) - HPV-negative


title: CC001d5_2

value: mouse-adapted H3N2 virus

tag: Sex

tag: strains


title: Sample 116_WT.4R

tag: strain background

tag: age


title: evolved Pseudomonas putida KT2440 in the glucose M9 (rep 1)

description:
T9__glc__1
Total RNA with depleted ribosomal RNA

tag: genotype


title: CC001d5_1

value: female


title: CU-OP-2

description: CU-OP-2 - Tonsil squamous cell carcinoma (cell line) - HPV-positive


title: Sample 113_WT.3L

source_name: WT_EAE_39_fecal pellet

tag: treatment

value: EAE

tag: experiment day


title: evolved Pseudomonas putida KT2440 in the glucose acetate M9 (rep 2)

description:
T8__glc_ace__2
Total RNA with depleted ribosomal RNA

source_name: Pseudomonas putida KT2440 TA8_F83_I1

value: in the glucose acetate M9


title: UPCI-SCC-90

description: UPCI-SCC-90 - Base of tongue squamous cell carcinoma (cell line) - HPV-positive

value: p53 wild-type


title: Pseudomonas putida KT2440 with a 9bp deletion in its PP_5350 in the glucose acetate M9 (rep 2)

description:
PP5350__glc_ace__2
Total RNA with depleted ribosomal RNA

source_name: Pseudomonas putida KT2440 PP_5350'

value: 9bp deletion in its PP_5350


title: CC001d3_3


title: evolved Pseudomonas putida KT2440 in the glucose acetate M9 (rep 1)

description:
T8__glc_ace__1
Total RNA with depleted ribosomal RNA


title: CC001d3_2


title: Sample 110_WT.1R

tag: sample type


title: UM-SCC-47

description: UM-SCC-47 -   Lateral tongue squamous cell carcinoma (cell line) - HPV-positive

value: HPV-positive


title: CC001d3_1


title: Pseudomonas putida KT2440 with a 9bp deletion in its PP_5350 in the glucose acetate M9 (rep 1)

description:
PP5350__glc_ace__1
Total RNA with depleted ribosomal RNA


title: Sample 108_SCID.4R

source_name: SCID_Naive_39_fecal pellet

value: SCID

value: Naive


title: Sample 109_WT.1L

value: fecal pellet


title: wildtype Pseudomonas putida KT2440 in the glucose acetate M9 (rep 2)

description:
WT__glc_ace__2
Total RNA with depleted ribosomal RNA

source_name: Pseudomonas putida KT2440

value: wild type


title: CU-OP-3

description: CU-OP-3 - Tonsil squamous cell carcinoma (cell line) - HPV-positive


title: RAW_sh1_GIV_LPS_5hr

first: Pradipta

last: Ghosh

state: CA

department: Cellular and Molecular Medicine

institute: University of California San Diego

data_processing:
fastq files were aligned and quantified to the mouse transcriptome using the GRCm38 M24 GENCODE release, using Salmon and Tximport software.
Expression data was normalized using the DESeq function from the DESeq2 package in Bioconductor.
Differentially expressed genes were identified by the DESeq2 model with a significant cutoff of padj £5%
Tab-delimited text file including the normalized counts from the DESeqDataSet object  used for DE analysis.
Genome_build: version 79 of mouse reference genome GRCm38
Supplementary_files_format_and_content: tab-delimited text files include log2 counts per million (CPM) values for each Sample ...

source_name: RAW 267.4 macrophages

growth_protocol: 5x10^5 RAW 264.7/well were plated in 6-well tissue culture-treated dishes and placed in a 5% CO2 37 °C incubator overnight

extract_protocol:
RNA was isolated using the Direct-zol RNA Miniprep Kit (Zymo Research) and processed as per manufacturer’s instructions.
Libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit, according to the manufacturer’s instructions.

treatment_protocol: RAW 264.7 cells were stimulated with LPS (100 ng/mL) for 5 hrs.

tag: background strain

value: BALB/c

value: male

value: GIV-depleted

value: LPS 5hr


title: CC001cd3_2

value: ctrl


title: RAW_shC_LPS_5hr

value: wild-type


title: CC001cd3_1


title: Sample 107_SCID.4L

value: 8 weeks


title: Sample 106_SCID.3R


title: wildtype Pseudomonas putida KT2440 in the glucose M9 supplemented with 2 g/L triethylamine hydrogen sulfate (rep 2)

description:
WT__IL2__2
Total RNA with depleted ribosomal RNA


title: FSNCH 846_CH_F_NuAcc

city: Potsdam

first: Rachel

last: Lippert

address: Arthur-Scheunert-Allee 114-116

institute: German Institte of Human Nutrition

description:
FSNCH
CH
high fat

data_processing:
Illumina TruSeq mRNA stranded protocol and the HiSeq 4000 sequencer with a PE75 read length run
Sequenced reads were aligned to the reference genome using hisat 2.1.0.
Transcript abundance was derived using stringtie 1.3.4d.
Differential gene expression analysis was carried out using cuffdiff 2.2.1
Genome_build: GRCm38.p6 (Genome Reference Consortium Mouse Reference 38), INSDC Assembly GCA_000001635.8, Jan 2012
Supplementary_files_format_and_content: Excel speadsheet containing mean expression levels per group, fold change and significance level for each annotated gene.

source_name: NuAcc

extract_protocol:
Samples were homogenize din Trizol LS, extracted with Chloroform, precipitated with isopropranol, washed with 80% Ethanol, resuspende din Nuclease free water and treated with DNAse I.  Concentraiton was analyzed using QuBit/Bioanalyzer and remaining samples were stored at -80 C until sequencing.
Total RNA was used for first strand cDNA synthesis, using both poly(T) and random primers, followed by second strand synthesis and isothermal strand-displacement amplification. For library preparation, the Illumina Nextera XT DNA sample preparation protocol was used, with 1 ng cDNA input. After validation (Agilent 2200 TapeStation) and quantification (Invitrogen Qubit System) all 24 transcriptome libraries were pooled. The pool was quantified using the Peqlab KAPA Library Quantification Kit and the Applied Biosystems 7900HT Sequence Detection and sequenced on a Illumna NovaSeq S2 flowcell with a PE100 protocol. The RNA sequencing pipeline utilizes the GRCm38 assembly of the mouse genome as gene sets from Ensembl release 96 (Yates et al., 2015).

treatment_protocol: All mice were rapidly decapitated and tissue was taken between 13-17h

tag: tissue

value: Ventral Striatum

value: 24-26 weeks

tag: gender

value: Female


title: wildtype Pseudomonas putida KT2440 in the glucose M9 supplemented with 2 g/L triethylamine hydrogen sulfate (rep 1)

description:
WT__IL2__1
Total RNA with depleted ribosomal RNA


title: w4_Tak1_HEP_Ripk1D138N_D138N_rep2

city: shanghai

first: jing

last: zhao

address: Qiuyue Road

institute: IRCBC

data_processing:
For RNA-Seq comparison, Sequencing reads were mapped to rat with STAR by default parameter. The read counts for each genes were calculated by featurecounts. The count files were used as input to DESeq2 for differential expression analysis. And for sc-seq comparison, Sequencing reads were mapped to dme with cellranger count by default parameter. The count files were used as input to Seurat for downstream analysis.
Genome_build: mm19
Supplementary_files_format_and_content: DESeq was used for calling differential expression.tab-delimited text files include normalized read counts,foldChange,pvalue. And Seurat was used for single cell downstream analysis

molecule: polyA RNA

extract_protocol:
Total RNA was extracted and purified using RNAiso Plus (TaKaRa) and single cell isolated by cell strainer (Falcon, 352340)
RNA libraries were prepared according to instructions of Vazyme VAHTS mRNA-seq V3 Library Prep Kit for Illumina(NR611-01) and sc-seq libraries were prepared according to instructions of 10X single cell  library  kit v3 (Chromiun, 1000078).

value: 4 weeks

value: Liver


title: Sample 104_WT.7R

source_name: WT_Naive_39_fecal pellet

value: WT


title: RAW_sh2_GIV_LPS_5hr


title: wildtype Pseudomonas putida KT2440 in the glucose M9 supplemented with 0.5 g/L triethanolamine acetate (rep 2)

description:
WT__IL1__2
Total RNA with depleted ribosomal RNA


title: w6_Tak1f_f_rep1

value: 6 weeks


title: FSNCH 825_CH_F_NuAcc

description:
FSNCH
CH
high fat


title: FSNCH 845_CH_F_NuAcc

description:
FSNCH
CH
high fat


title: Sample 103_WT.7L

value: Naive


title: wildtype Pseudomonas putida KT2440 in the glucose M9 supplemented with 0.5 g/L triethanolamine acetate (rep 1)

description:
WT__IL1__1
Total RNA with depleted ribosomal RNA


title: FSNCH 824_CH_F_NuAcc

description:
FSNCH
CH
high fat


title: Sample 102_WT.6R

value: fecal pellet


title: wildtype Pseudomonas putida KT2440 in the glucose acetate M9 (rep 1)

description:
WT__glc_ace__1
Total RNA with depleted ribosomal RNA

value: in the glucose acetate M9

value: wild type


title: FSNCH 823_CH_F_NuAcc

description:
FSNCH
CH
high fat


title: wildtype Pseudomonas putida KT2440 in the glucose M9 (rep 4)

description:
WT__glc__4
Total RNA with depleted ribosomal RNA

value: in the glucose M9


title: HD7

type: RNA

city: Créteil

first: cecile

last: lefebvre

address: 51 Avenue du Marechal De Lattre de Tassigny

country: France

institute: INSERM U955_VRI

hyb_protocol: Whole-Genome Gene Expression Direct Hybridization Assay

scan_protocol: iScan Illumina scanning protocol using iScan control software

data_processing: Differentially expressed genes were identified using quantile normalized data of genes as input to Gene-specific analysis (GSA) (Partek® Flow® software, Copyright ©; 2019 Partek Inc.)

source_name: hair follicle stem cells; Outer Root Sheath Cells (ORS)

label_protocol: In vitro transcription was generated from 100 ng of RNA using Ambion Illumina TotalPrep RNA Amplification Kits (Applied Biosystems/Ambion).

extract_protocol: RNA were purified using RNeasy Plus Micro Kit (Qiagen, France) and quantified using a ND-8000 spectrophotometer (NanoDrop Technologies) before being checked for integrity on the 2100 BioAnalyzer (Agilent Technologies).

tag: cell type

tag: disease state

value: healthy


title: Sample 101_WT.6L


title: wildtype Pseudomonas putida KT2440 in the glucose M9 (rep 3)

description:
WT__glc__3
Total RNA with depleted ribosomal RNA


title: FSNCH 811_CH_F_NuAcc

description:
FSNCH
CH
high fat


title: HD4

value: hair follicle stem cells; Outer Root Sheath Cells (ORS)


title: HD5


title: Sample 105_SCID.3L

value: SCID


title: wildtype Pseudomonas putida KT2440 in the glucose M9 (rep 2)

description:
WT__glc__2
Total RNA with depleted ribosomal RNA


title: FSNCC 818_CC_F_NuAcc

description:
FSNCC
CC
control


title: Sample 100_SCID.1R

source_name: SCID_chronic stress_39_fecal pellet

value: chronic stress


title: CC001cd3_3

source_name: lung

value: ctrl

tag: day

tag: ffu

value: female


title: wildtype Pseudomonas putida KT2440 in the glucose M9 (rep 1)

description:
WT__glc__1
Total RNA with depleted ribosomal RNA

tag: growth


title: FSNCC 766_CC_F_NuAcc

description:
FSNCC
CC
control

tag: strain

value: Ventral Striatum

value: 24-26 weeks


title: HD2


title: HS7

value: Hidradenitis suppurativa


title: Sample 99_SCID.1L

value: 8 weeks


title: Sample 114_WT.3R

value: WT

value: EAE


title: HD3


title: HS6


title: Sample 96_WT.4L

source_name: WT_chronic stress_39_fecal pellet


title: FSNCC 754_CC_F_NuAcc

description:
FSNCC
CC
control

value: Female


title: Sample 85_WT.7R

source_name: WT_Naive_32_fecal pellet

value: Naive

value: fecal pellet


title: MSNCH 807_CH_M_NuAcc

description:
MSNCH
CH
high fat

value: Male


title: ChIP_seq_INPUT_T

city: Cuernavaca

first: Mario

last: Zurita

state: Morelos

address: Av. Universidad 2001

country: Mexico

institute: UNAM

data_processing:
After filtering, clean reads are mapped to reference using BWA / Bowtie2  tool
Genes expression level is quantified by a software package called RSEM
The file all.gene. FPKM.txt is a expression table for all samples with brief gene description and annotation.
Then they used the alignment result to calling peak (MACS (Model-based Analysis for ChIP -seq, version: MACS-1.4.2)
We used HOMER for the differential analysis
Supplementary_files_format_and_content: bigwig, peak, FPKM

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cell tratment wiht DMSO or TPL for 4 h

value: Breast

tag: cell line

tag: antibody

tag: agent

value: DMSO


title: NO_RNA_BLANK_31-32_43-46_59-63

city: Aurora

first: Michael

middle: S

last: Kriss

state: CO

institute: University of Colorado School of Medicine

hyb_protocol: Samples were cooled to 4°C at completion of hybridization time cycle.  Further purification and binding of the hybridized probes to the optical cartridge was performed on the nCounter Prep Station using high sensitivity settings

scan_protocol: The cartridge was scanned on the nCounter Digital Analyzer

data_processing:
Raw counts from each gene were imported into the nSolver Analysis Software and normalized against background and housekeeping genes, and overall assay performance was assessed through evaluation of built-in positive controls.  A total of 594 immunology-related human genes and 15 internal reference genes were implemented in the digital transcript counting (nCounter® Human Immunology Panel v2 kit assay NanoString®, Seattle, WA)
Data were analyzed using the nSolver Analysis Software v2.6 gene expression analysis module (NanoString®).

molecule: other

organism: blank sample

label_protocol: Depending on RNA integrity, 300-350ng of the purified RNA was hybridized with the Human Immunology v2 Code Set (NanoString Technologies) using the XT protocol at 65C for 19hours.

extract_protocol: Two to four curls from continuous FFPE tissue sections per specimen were collected in 1.5mL centrifuge tubes used for RNA isolation.  The tubes containing the tissue curls were deparaffinized following the protocol for tube-sections in the Roche HighPure FFPET RNA Isolation spin-column kit (Catalog #06650775001) with the following modifications: maximum 10µM sections used were increased up to 4 curls rather than 1 per tube and d-limonene (histology grade) was used in place of xylene. The tissue sections were allowed to dry completely before proceeding to the RNA Isolation protocol.  RNA isolation was performed using the same Roche HighPure FFPET RNA Isolation spin-column kit according to manufacturer’s specifications.

treatment_protocol: Formalin-fixed, paraffin-embedded liver tissue

value: blank


title: NO_RNA_BLANK_33-34_47-50_64-66


title: NO_RNA_BLANK_28-30_39-42_55-58


title: ChIP_seq_INPUT_NT


title: Sample 83_WT.6R

tag: strain background

tag: age


title: HS4

value: hair follicle stem cells; Outer Root Sheath Cells (ORS)


title: FSNCC 762_CC_F_NuAcc

description:
FSNCC
CC
control


title: HS2


title: Sample 82_WT.6L

tag: genotype

tag: treatment


title: MSNCH 302_CH_M_NuAcc

description:
MSNCH
CH
high fat


title: ChIP_seq_TT-2

description:
TPL-125nM-4h
TSS_InPeaks_TTc_unique.bed.gz

value: RNAPII


title: Sample 81_SCID.1R

source_name: SCID_chronic stress_32_fecal pellet

value: SCID

value: chronic stress

tag: experiment day

tag: sample type


title: HS3


title: FSNCC 756_CC_F_NuAcc

description:
FSNCC
CC
control

tag: tissue

value: Ventral Striatum


title: NO_RNA_BLANK_1-24


title: Liver_RNA-65_CTRL

description: RNA extracted from formalin-fixed, paraffin-embedded liver tissue

label: NanoString oligonucleotide probes

value: liver

tag: Sex

value: M

tag: ethnicity

value: Hispanic

tag: bmi

value: N

tag: insulin

tag: hypertension

tag: hyperlipidemia

tag: statin/fibrate

tag: osa

tag: pcos

tag: hypothyroidism

tag: cardiovascular disease

tag: ast (units/l)

tag: alt (units/l)

tag: alkaline phosphatase (units/l)

tag: total bilirubin (mg/dl)

tag: albumin (g/dl)

tag: total protein (g/dl)

tag: nas

value: Lobular inflammation:0

value: Total score:0


title: Liver_RNA-66_CTRL

tag: tissue

tag: age

tag: Sex

value: F

tag: ethnicity

value: Y


title: MSNCH 1468_CH_M_NuAcc

description:
MSNCH
CH
high fat

tag: strain

value: 24-26 weeks

tag: gender

value: Male


title: HS5

tag: cell type

tag: disease state

value: Hidradenitis suppurativa


title: ChIP_seq_TT-1

value: Breast

tag: cell line

tag: antibody

tag: agent


title: Sample 80_SCID.1L

tag: strain background

value: 8 weeks

tag: genotype

tag: treatment

tag: experiment day

tag: sample type

value: fecal pellet


title: MSNCH 3033_CH_M_NuAcc

description:
MSNCH
CH
high fat


title: NO_RNA_BLANK_25-27_35-38_51-54

value: blank


title: Sample 97_WT.4R

value: WT

value: chronic stress


title: MSNCH 842_CH_M_NuAcc

description:
MSNCH
CH
high fat

value: Ventral Striatum


title: Liver_RNA-64_CTRL

value: liver

value: M

value: White

tag: bmi

tag: insulin

tag: hypertension

tag: hyperlipidemia

tag: statin/fibrate

tag: osa

tag: pcos

tag: hypothyroidism

tag: cardiovascular disease

tag: ast (units/l)

tag: alt (units/l)

tag: alkaline phosphatase (units/l)

tag: total bilirubin (mg/dl)

tag: albumin (g/dl)

tag: total protein (g/dl)

tag: nas


title: ChIP_seq_T-1

description:
DMSO-4h
TSS_InPeaks_Tc_unique.bed.gz

tag: cell type

tag: cell line

tag: antibody

value: RNAPII

tag: agent

value: DMSO


title: Sample 78_WT.4R

source_name: WT_chronic stress_32_fecal pellet

tag: strain background

tag: age

tag: genotype

tag: treatment

tag: experiment day

tag: sample type


title: Liver_RNA-63_CTRL

tag: tissue

tag: Sex

value: F

tag: ethnicity

tag: bmi

value: N

tag: insulin

tag: hypertension

tag: hyperlipidemia

tag: statin/fibrate

tag: osa

tag: pcos

tag: hypothyroidism

tag: cardiovascular disease

tag: ast (units/l)

value: Lobular inflammation:0

value: Total score:0


title: ChIP_seq_NTT-2

description:
TPL-125nM-4h
TSS_InPeaks_NTTc_unique.bed.gz

tag: cell type

tag: cell line

tag: antibody

tag: agent


title: Sample 77_WT.4L

tag: strain background

tag: age

tag: genotype

tag: treatment

tag: experiment day

tag: sample type


title: MSNCC 827_CC_M_NuAcc

description:
MSNCC
CC
control

tag: strain

tag: tissue

value: 24-26 weeks

tag: gender

value: Male


title: MSNCC 860_CC_M_NuAcc

description:
MSNCC
CC
control


title: Sample 75_WT.3L

source_name: WT_EAE_26_fecal pellet

value: 8 weeks

value: EAE


title: ChIP_seq_NTT-1

value: Breast


title: Liver_RNA-62_CTRL

tag: Sex

tag: ethnicity

tag: bmi

tag: insulin

tag: hypertension

tag: hyperlipidemia

tag: statin/fibrate

tag: osa

tag: pcos

tag: alt (units/l)

tag: alkaline phosphatase (units/l)

tag: total bilirubin (mg/dl)

tag: albumin (g/dl)

tag: total protein (g/dl)

tag: nas


title: Liver_RNA-61_CTRL

tag: tissue

tag: age

value: Y

tag: hypothyroidism

tag: cardiovascular disease

tag: ast (units/l)


title: ChIP_seq_NT-2

description:
DMSO-4h
TSS_InPeaks_NTc_unique.bed.gz

tag: cell type

tag: cell line

tag: antibody

tag: agent


title: ChIP_seq_T-2

description:
DMSO-4h
TSS_InPeaks_Tc_unique.bed.gz


title: Sample 79_WT.5L

tag: strain background

tag: genotype

value: WT

tag: treatment

value: chronic stress

tag: experiment day

tag: sample type

value: fecal pellet


title: MSNCC 859_CC_M_NuAcc

description:
MSNCC
CC
control

tag: strain

value: Ventral Striatum

tag: gender


title: MSNCC 828_CC_M_NuAcc

description:
MSNCC
CC
control


title: MSNCH 1469_CH_M_NuAcc

description:
MSNCH
CH
high fat


title: MSNCC 395_CC_M_NuAcc

description:
MSNCC
CC
control


title: Sample 73_WT.2L


title: Sample 71_WT.1L


title: Sample 70_SCID.4R

source_name: SCID_Naive_25_fecal pellet

value: SCID

value: Naive


title: Liver_RNA-60_CTRL

value: liver

tag: Sex

tag: ethnicity

value: White

tag: bmi

tag: insulin

tag: hypertension

tag: hyperlipidemia

tag: statin/fibrate

tag: osa

tag: pcos

tag: alt (units/l)

tag: alkaline phosphatase (units/l)

tag: total bilirubin (mg/dl)

tag: albumin (g/dl)

tag: total protein (g/dl)

tag: nas


title: FSNCH 846_CH_F_Cpu

description:
FSNCH
CH
high fat

source_name: CPU

tag: strain

tag: tissue

value: Dorsal Striatum

tag: age

value: Female


title: Sample 98_WT.5L

tag: strain background

tag: genotype

tag: treatment

tag: experiment day

tag: sample type


title: Sample 68_SCID.3R


title: FSNCH 825_CH_F_Cpu

description:
FSNCH
CH
high fat

tag: gender


title: simulated graivty group pool 3

city: Haidian District

first: Zhongquan

last: Dai

state: Beijing

address: No. 26 Beiqing Road

institute: Astronaut Research and training Center

description: miRNA level in rat blood after 28-day hindlimb suspenstion to simulated microgavity

hyb_protocol: 0.6 μg of Cy3-labelled purified miRNA was added with Hyb Spike-in, 10* GE Blocking agent and Hi-RPM Hydridizaiton buffer in the total reaction volume of 45μL, followed with 100°C incubation for 5 minutes and ice water bath for 5 minutes. Then the mixture reaction was hybridized to Agilent Rat miRNA (8*60K)for 20 hours at 55°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 2 (Agilent) and 5 minute with 37°C GE Wash buffer 3 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner G2505C (Agilent) using one color scan setting (Scan Area 61x21.6 mm, Scan resolution 5μm, Dye channel is set to Green and Green PMT is set XDR Hi 100% and XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 12.5 (Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

organism: Rattus norvegicus

source_name: serum simulated microgravitry

label_protocol: Cyanine-3(Cy3) labeled cRNA was prepared from 0.2ug RNA using for the One-Color low RNA Inpiut Linear Amplification PLUS Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen, Valencia Ca). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted by mirVana™ PARIS™ Kit (Applied Biosystem p/n AM1556) according to the manufacturer’s instructions and qualitified by NanoDrop ND2000 (Thermo Scientific) Agilent Bioanalyzer 2100 (Agilent).

value: Serum

value: male

value: SD


title: simulated graivty group pool 4


title: FSNCH 824_CH_F_Cpu

description:
FSNCH
CH
high fat

value: 24-26 weeks


title: ChIP_seq_NT-1

description:
DMSO-4h
TSS_InPeaks_NTc_unique.bed.gz

tag: cell type

tag: cell line

tag: antibody

value: RNAPII

tag: agent

value: DMSO


title: FSNCH 823_CH_F_Cpu

description:
FSNCH
CH
high fat


title: simulated graivty group pool 2


title: Liver_RNA-58_CTRL

tag: Sex

value: M

tag: ethnicity

tag: bmi

value: N

tag: insulin

tag: hypertension

tag: hyperlipidemia

tag: statin/fibrate

tag: osa

tag: pcos

tag: hypothyroidism

tag: cardiovascular disease

tag: ast (units/l)

tag: alt (units/l)

tag: alkaline phosphatase (units/l)

tag: total bilirubin (mg/dl)

value: Lobular inflammation:0

value: Total score:0


title: Liver_RNA-57_CTRL

tag: tissue

tag: age

value: F

value: Y

tag: albumin (g/dl)

tag: total protein (g/dl)

tag: nas


title: Liver_RNA-56_CTRL

tag: Sex

tag: ethnicity

tag: bmi

tag: insulin


title: Liver_RNA-59_CTRL

tag: hypertension

tag: hyperlipidemia

tag: statin/fibrate

tag: osa


title: Liver_RNA-54_CTRL

tag: pcos

tag: hypothyroidism

tag: cardiovascular disease

tag: ast (units/l)


title: Liver_RNA-55_CTRL

tag: tissue

tag: alt (units/l)

tag: alkaline phosphatase (units/l)

tag: total bilirubin (mg/dl)


title: control group pool 3

description: miRNA level in control rat blood

source_name: serum control

tag: gender

tag: strain


title: simulated graivty group pool 1


title: Sample 69_SCID.4L

tag: strain background

tag: age

value: 8 weeks

tag: genotype

value: SCID

tag: treatment

value: Naive

tag: experiment day

tag: sample type

value: fecal pellet


title: FSNCC 818_CC_F_Cpu

description:
FSNCC
CC
control

value: Dorsal Striatum

value: Female


title: FSNCH 845_CH_F_Cpu

description:
FSNCH
CH
high fat


title: Liver_RNA-53_CTRL

value: liver

tag: Sex

tag: ethnicity

value: White

tag: bmi

tag: insulin

tag: hypertension

tag: hyperlipidemia

tag: statin/fibrate

tag: osa

tag: albumin (g/dl)

tag: total protein (g/dl)

tag: nas


title: control group pool 2

description: miRNA level in control rat blood

tag: tissue

value: Serum

tag: gender

value: male

tag: strain

value: SD


title: Sample 47_WT.7R

source_name: WT_Naive_18_fecal pellet

tag: strain background

tag: age

tag: genotype

value: WT

tag: treatment


title: Sample 50_SCID.4L

source_name: SCID_Naive_18_fecal pellet

tag: experiment day

tag: sample type


title: control group pool 1

description: miRNA level in control rat blood


title: Sample 48_SCID.3L


title: Liver_RNA-51_CTRL

tag: Sex

tag: ethnicity

tag: bmi

value: N

tag: insulin

tag: pcos

tag: hypothyroidism

tag: cardiovascular disease

tag: ast (units/l)

tag: alt (units/l)

tag: alkaline phosphatase (units/l)

tag: total bilirubin (mg/dl)


title: Liver_RNA-52_CTRL

tag: tissue

tag: hypertension

tag: hyperlipidemia

tag: statin/fibrate

tag: osa

tag: albumin (g/dl)

tag: total protein (g/dl)

tag: nas

value: Lobular inflammation:0


title: Sample 46_WT.7L

tag: strain background

tag: age

tag: genotype

tag: treatment

tag: experiment day

tag: sample type


title: Liver_RNA-50_NAS3

tag: Sex

tag: ethnicity

tag: bmi

tag: insulin

tag: pcos

tag: hypothyroidism

tag: cardiovascular disease

tag: ast (units/l)

tag: alt (units/l)

value: Lobular inflammation:1

value: Total score:3


title: FSNCC 766_CC_F_Cpu

description:
FSNCC
CC
control

tag: strain

tag: tissue

value: 24-26 weeks

tag: gender


title: Sample 45_WT.6R

tag: strain background

tag: age

value: 8 weeks


title: FSNCC 762_CC_F_Cpu

description:
FSNCC
CC
control


title: Sample 44_WT.6L

tag: genotype

tag: treatment


title: L1353-Triptolide_time_course_48h_high_dose-Hi-C

city: Stanford

first: Georgi

middle: Kolev

last: Marinov

address: 279 Campus Drive West, Beckman Center, B-257A/259

department: Genetics

institute: STANFORD UNIVERSITY

data_processing:
read alignment: juicer_tools.1.8.9
.hic file generation juicer_tools.1.8.9
Genome_build: custom
Supplementary_files_format_and_content: bedGraph of read coverage, normalized to RPM (Read Per Million) except for dSMF samples, where the bedGraph shows the methylation percentage

organism: Breviolum minutum

source_name: SSBO1 cells

extract_protocol: Symbiodinium minutum SSBO1 cells were first crosslinked using 37% formaldehyde (Sigma) at a final concentration of 1% for 15 minutes at room temperature. Formaldehyde was then quenched using 2.5 M Glycine at a final concentration of 0.25 M. Cells were subsequently centrifuged at 2,000 g for 5 minutes, washed once in 1X PBS, and stored at -80C.

value: triptolide treatment, 40uM, 48h


title: L1352-Triptolide_time_course_48h_normal_dose-Hi-C

value: triptolide treatment, 10uM, 48h


title: L1351-Triptolide_time_course_48h_NT-HiC

value: triptolide treatment 0uM 48h


title: FSNCC 756_CC_F_Cpu

description:
FSNCC
CC
control

value: Dorsal Striatum


title: Sample 43_SCID.1R

source_name: SCID_chronic stress_18_fecal pellet

value: SCID

value: chronic stress

tag: experiment day

tag: sample type

value: fecal pellet


title: L1350-Triptolide_time_course_24h_high_dose-Hi-C

value: triptolide treatment, 40uM, 24h


title: FSNCC 754_CC_F_Cpu

description:
FSNCC
CC
control

value: Female


title: FSNCH 811_CH_F_Cpu

description:
FSNCH
CH
high fat


title: L1349-Triptolide_time_course_24h_normal_dose-Hi-C

value: triptolide treatment, 10uM, 24h


title: MSNCH 807_CH_M_Cpu

description:
MSNCH
CH
high fat

value: Male


title: L1348-Triptolide_time_course_24h_NT-HiC

value: triptolide treatment 0uM 24h


title: Sample 42_SCID.1L


title: Liver_RNA-49_NAS3

value: liver

tag: Sex

value: M

tag: ethnicity

value: Hispanic

value: Y

value: N

tag: hypertension

tag: hyperlipidemia

tag: statin/fibrate

tag: osa

tag: alkaline phosphatase (units/l)

tag: total bilirubin (mg/dl)

tag: albumin (g/dl)

tag: total protein (g/dl)

tag: nas


title: Liver_RNA-47_NAS3

tag: tissue

value: White

tag: bmi

tag: insulin

tag: pcos

tag: hypothyroidism

tag: cardiovascular disease

tag: ast (units/l)

tag: alt (units/l)

value: Lobular inflammation:1

value: Total score:3


title: L1347-Triptolide_time_course_8h_high_dose-Hi-C

tag: strain

tag: treatment

value: triptolide treatment, 40uM, 8h


title: MSNCH 842_CH_M_Cpu

description:
MSNCH
CH
high fat

value: Dorsal Striatum

tag: age

value: 24-26 weeks

tag: gender


title: Sample 41_WT.5L

source_name: WT_chronic stress_18_fecal pellet

tag: strain background

value: 8 weeks

tag: genotype

value: WT

value: chronic stress

tag: experiment day

tag: sample type

value: fecal pellet


title: L1346-Triptolide_time_course_8h_normal_dose-Hi-C

value: triptolide treatment, 10uM, 8h


title: Liver_RNA-46_NAS3

tag: Sex

value: F

tag: ethnicity

tag: hypertension

tag: hyperlipidemia

tag: statin/fibrate

tag: osa

tag: alkaline phosphatase (units/l)

tag: total bilirubin (mg/dl)

tag: albumin (g/dl)

tag: total protein (g/dl)

tag: nas


title: Sample 40_WT.4R

tag: age

tag: treatment


title: MSNCH 302_CH_M_Cpu

description:
MSNCH
CH
high fat

tag: strain

tag: tissue

tag: gender

value: Male


title: Liver_RNA-45_NAS3

value: liver

tag: bmi

tag: insulin

tag: pcos

tag: hypothyroidism

tag: cardiovascular disease

tag: ast (units/l)

tag: alt (units/l)


title: Liver_RNA-44_NAS3

tag: Sex

tag: ethnicity

tag: hypertension

tag: hyperlipidemia

tag: statin/fibrate

tag: osa

tag: alkaline phosphatase (units/l)

value: Lobular inflammation:2


title: Sample 51_SCID.4R

tag: strain background

tag: age

tag: genotype

value: SCID

tag: treatment

value: Naive

tag: experiment day

tag: sample type


title: Liver_RNA-48_NAS3

tag: tissue

value: M

value: White

tag: bmi

value: N

tag: insulin

value: Y

tag: pcos

tag: hypothyroidism

tag: total bilirubin (mg/dl)

tag: albumin (g/dl)

tag: total protein (g/dl)

tag: nas


title: Sample 39_WT.4L


title: Liver_RNA-43_NAS3

tag: Sex

tag: ethnicity

tag: hypertension

tag: hyperlipidemia

tag: statin/fibrate

tag: osa

tag: cardiovascular disease

tag: ast (units/l)

tag: alt (units/l)

value: Lobular inflammation:1

value: Total score:3


title: L1344-Triptolide_time_course_0h_NT-HiC

tag: strain

tag: treatment

value: triptolide treatment 0uM 0h


title: Sample 38_SCID.4R

source_name: SCID_Naive_11_fecal pellet

tag: strain background

tag: age

value: 8 weeks

tag: genotype

tag: experiment day

tag: sample type


title: L1337-SSB01-a_amanitin_high-48h-Hi-C-V2

value: a-amanitin treatment, 4ug/mL, 48h


title: MSNCH 3033_CH_M_Cpu

description:
MSNCH
CH
high fat

tag: tissue

value: Dorsal Striatum

value: 24-26 weeks

tag: gender


title: MSNCH 1469_CH_M_Cpu

description:
MSNCH
CH
high fat


title: Sample 37_SCID.4L

value: fecal pellet


title: Liver_RNA-42_NAS3

tag: Sex

value: F

tag: ethnicity

tag: bmi

tag: insulin

tag: pcos

tag: hypothyroidism

tag: alkaline phosphatase (units/l)

tag: total bilirubin (mg/dl)

tag: albumin (g/dl)

tag: total protein (g/dl)

tag: nas


title: Liver_RNA-41_NAS3

value: liver

tag: age

tag: hypertension

tag: hyperlipidemia

tag: statin/fibrate

tag: osa

tag: cardiovascular disease

tag: ast (units/l)

tag: alt (units/l)


title: L1336-SSB01-a_amanitin_high-24h-Hi-C-V2

tag: strain

tag: treatment

value: a-amanitin treatment, 4ug/mL, 24h


title: Sample 36_SCID.3R

tag: strain background

tag: genotype

value: SCID

tag: experiment day

tag: sample type


title: Sample 35_SCID.3L

value: Naive


title: MSNCC 860_CC_M_Cpu

description:
MSNCC
CC
control

tag: tissue

tag: gender

value: Male


title: L1334-SSB01-a_amanitin_high-48h-Hi-C


title: MSNCC 859_CC_M_Cpu

description:
MSNCC
CC
control


title: L1332-SSB01-a_amanitin-0h-Hi-C

value: a-amanitin treatment, 1ug/mL, 0h


title: L1333-SSB01-a_amanitin-48h-Hi-C-rep1

value: a-amanitin treatment, 1ug/mL, 48h


title: Liver_RNA-38_NAS3

tag: Sex

value: M

tag: ethnicity

value: White

tag: bmi

value: N

tag: insulin

value: Y

tag: pcos

tag: hypothyroidism

tag: alkaline phosphatase (units/l)

tag: total bilirubin (mg/dl)

tag: albumin (g/dl)

tag: total protein (g/dl)

tag: nas


title: Sample 34_WT.7R

source_name: WT_Naive_11_fecal pellet

tag: strain background

tag: age

value: 8 weeks

value: WT

tag: treatment


title: Sample 33_WT.7L

tag: genotype

tag: experiment day

tag: sample type


title: L1247-SSB01-a_amanitin_high-48h-Hi-C

tag: strain

value: a-amanitin treatment, 4ug/mL, 48h


title: Liver_RNA-39_NAS3

tag: tissue

tag: Sex

tag: ethnicity

tag: hypertension

tag: hyperlipidemia

tag: statin/fibrate

tag: osa

tag: cardiovascular disease

tag: ast (units/l)

tag: alt (units/l)

value: Lobular inflammation:0

value: Total score:3


title: MSNCC 395_CC_M_Cpu

description:
MSNCC
CC
control

value: Dorsal Striatum

value: 24-26 weeks

tag: gender


title: MSNCH 1468_CH_M_Cpu

description:
MSNCH
CH
high fat

tag: age


title: Sample 32_WT.6R

tag: strain background

tag: treatment

value: fecal pellet


title: Liver_RNA-37_NAS3

value: liver

value: F

tag: bmi

tag: insulin

tag: pcos

tag: hypothyroidism

tag: alkaline phosphatase (units/l)

tag: total bilirubin (mg/dl)

tag: albumin (g/dl)

tag: total protein (g/dl)

tag: nas

value: Lobular inflammation:1


title: MSNCC 828_CC_M_CPu

description:
MSNCC
CC
control

tag: strain

tag: tissue

value: Male


title: Sample 31_WT.6L

tag: genotype

value: Naive

tag: experiment day

tag: sample type


title: Liver_RNA-36_NAS3

tag: age

tag: Sex

value: M

tag: ethnicity

tag: hypertension

tag: hyperlipidemia

tag: statin/fibrate

tag: osa

tag: cardiovascular disease

tag: ast (units/l)

tag: alt (units/l)

value: Total score:2


title: L1246-SSB01-a_amanitin-48h-Hi-C-rep2

tag: treatment

value: a-amanitin treatment, 1ug/mL, 48h


title: FSNCH 846_CH_F_VTA

description:
FSNCH
CH
high fat

source_name: VTA

value: Mibrain

tag: gender

value: Female


title: MSNCC 827_CC_M_Cpu

description:
MSNCC
CC
control

tag: strain


title: Sample 30_SCID.2R

source_name: SCID_chronic stress_11_fecal pellet

tag: strain background

value: 8 weeks

value: SCID

value: chronic stress


title: FSNCH 845_CH_F_VTA

description:
FSNCH
CH
high fat

tag: tissue


title: L1244-SSB01-a_amanitin-24h-Hi-C-rep2

value: a-amanitin treatment, 1ug/mL, 24h


title: Liver_RNA-40_NAS3

value: White

tag: bmi

value: Y

tag: insulin

value: N

tag: pcos

tag: hypothyroidism

tag: alkaline phosphatase (units/l)

tag: total bilirubin (mg/dl)

tag: albumin (g/dl)

tag: total protein (g/dl)

tag: nas

value: Total score:3


title: FSNCH 825_CH_F_VTA

description:
FSNCH
CH
high fat

tag: age

value: 24-26 weeks


title: Sample 29_SCID.2L

tag: genotype

tag: experiment day

tag: sample type

value: fecal pellet


title: Sample 28_SCID.1R

tag: treatment


title: Liver_RNA-35_NAS3

value: liver

tag: Sex

value: F

tag: ethnicity

value: AA

tag: hypertension

tag: hyperlipidemia

tag: statin/fibrate

tag: osa

tag: cardiovascular disease

tag: ast (units/l)

tag: alt (units/l)

value: Lobular inflammation:1


title: L1243-SSB01-a_amanitin-24h-Hi-C-rep1

tag: strain


title: FSNCH 824_CH_F_VTA

description:
FSNCH
CH
high fat

tag: tissue

tag: gender


title: L1242-SSB01-a_amanitin-16h-Hi-C-rep2

value: a-amanitin treatment, 1ug/mL, 16h


title: Sample 27_SCID.1L

tag: strain background

tag: age


title: FSNCH 823_CH_F_VTA

description:
FSNCH
CH
high fat

value: Mibrain


title: Liver_RNA-33_NAS5

value: Hispanic

tag: bmi

tag: insulin

tag: pcos

tag: hypothyroidism

tag: alkaline phosphatase (units/l)

tag: total bilirubin (mg/dl)

tag: albumin (g/dl)

tag: total protein (g/dl)

tag: nas

value: Lobular inflammation:2

value: Total score:6


title: Sample 26_WT.5R

source_name: WT_chronic stress_11_fecal pellet

value: 8 weeks

tag: genotype

value: WT

tag: treatment

value: chronic stress

tag: experiment day

tag: sample type


title: Liver_RNA-32_NAS5

tag: tissue

tag: Sex

tag: ethnicity

tag: hypertension

value: Y

tag: hyperlipidemia

tag: statin/fibrate

tag: osa

tag: cardiovascular disease

tag: ast (units/l)

tag: alt (units/l)


title: FSNCH 811_CH_F_VTA

description:
FSNCH
CH
high fat

tag: strain

tag: age

tag: gender

value: Female


title: Liver_RNA-31_NAS5

value: White

tag: bmi

value: N

tag: insulin

tag: pcos

tag: hypothyroidism

tag: alkaline phosphatase (units/l)

tag: total bilirubin (mg/dl)

tag: albumin (g/dl)

tag: total protein (g/dl)

tag: nas


title: L1240-SSB01-a_amanitin-0h-Hi-C

tag: treatment

value: a-amanitin treatment, 1ug/mL, 0h


title: Liver_RNA-30_NAS5

tag: tissue

value: liver

tag: Sex

tag: ethnicity

tag: hypertension

tag: hyperlipidemia

tag: statin/fibrate

tag: osa

value: Lobular inflammation:3


title: L1245-SSB01-a_amanitin-48h-Hi-C-rep1

tag: strain

value: a-amanitin treatment, 1ug/mL, 48h


title: FSNCC 818_CC_F_VTA

description:
FSNCC
CC
control

tag: age

value: 24-26 weeks

tag: gender


title: L534-Symbiodinium_34C_Hi-C

value: heat stress, 34C


title: Sample 24_WT.4R

tag: strain background

tag: genotype

tag: experiment day

tag: sample type

value: fecal pellet


title: Liver_RNA-29_NAS5

value: F

tag: bmi

tag: insulin

tag: pcos

tag: hypothyroidism

tag: cardiovascular disease

tag: ast (units/l)

tag: alt (units/l)

tag: alkaline phosphatase (units/l)

tag: total bilirubin (mg/dl)

tag: albumin (g/dl)

tag: total protein (g/dl)

value: Lobular inflammation:1


title: Liver_RNA-34_NAS5

tag: tissue

tag: age

tag: Sex

tag: ethnicity

tag: hypertension

tag: hyperlipidemia

tag: statin/fibrate

tag: osa

tag: nas

value: Total score:5


title: L533-Symbiodinium_27C_Hi-C

tag: strain

tag: treatment

value: not treated, 27C


title: FSNCC 766_CC_F_VTA

description:
FSNCC
CC
control

value: Mibrain

tag: gender


title: FSNCC 762_CC_F_VTA

description:
FSNCC
CC
control


title: Sample 22_SCID.4R

source_name: SCID_Naive_1_fecal pellet

tag: strain background

value: 8 weeks

tag: genotype

value: SCID

value: Naive

tag: experiment day

tag: sample type


title: L142-Symbiodinium_minutum_SSb01-HIC

value: not treated


title: Sample 23_WT.4L

value: WT

value: chronic stress


title: L1241-SSB01-a_amanitin-16h-Hi-C-rep1

value: a-amanitin treatment, 1ug/mL, 16h


title: FSNCC 756_CC_F_VTA

description:
FSNCC
CC
control

value: Female


title: Sample 21_SCID.4L


title: REM_RR_8h_2g

city: Edinburgh

first: Carlos

last: Martinez-Perez

address: Western General Hospital, Crewe Road South

department: Institute of Genetics and Molecular Medicine

institute: The University of Edinburgh

description: REMData_Raw.txt, REMData_Processed.txt, ProcessedData_Combined_QN.txt

data_processing:
Total RNA samples underwent quality control using Agilent Bioanalyser and RNA 600 Nanochips and quantified using the Qubit 2.0 fluorometer and the RNA BR assay.
Libraries generated from 500ng of each total RNA sample using the Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit for Illumina (FWD).
After amplification and purification, libraries were quantified using the Qubit dsDNA HS assay kit and assessed for size/quality using Agilent DNA HS kit.
Sequencing performed using the NextSeq 500/550 High-Output v2 kit (#FC-404-2005) on the NextSeq 550 platform (Illumina, #SY-415-1002).
Demultiplexed FASTQ files were generated using Bcl2fastq2 v2.17.1.14 software provided by Illumina.
Individual FASTQ files processed using the BlueBee software provided by Lexogen: trimming of low quality tails and adapter contamination, alighment with ENCODE settings and generate read counts using HTSeq-count.
Working on MS Excel: transfer gene read counts from each sample on to a single file, filter genes with low read counts for the majority of samples, relabel genes to Ensemble IDs obtained from Biomart and do log2 transformation.
Further filtering performed to select only genes that mapped across species.
All preprocessed data was combined and quantile normalisation was performed using R the preprocessorCore package by Bioconductor.
Where data had to be integrated with data from publically-available datasets, integration batch effects were corrected using ComBat (Bioconductor).
Genome_build: GRCh38
Supplementary_files_format_and_content: .txt file containing read counts per gene for every samples after filtering, log2 transformation, filtering and quantile normalisation as decribed.
Supplementary_files_format_and_content: REMData_Raw.txt: Original REM unfiltered data containing raw counts – gene IDs are ENSCAFG from the Canis genome
Supplementary_files_format_and_content: REMData_Processed.txt: Processed REM data after log2 transformation and filtering – to include only genes expressed across all samples and only genes which mapped to ENSM (human IDs).
Supplementary_files_format_and_content: ProcessedData_Combined_QN.txt: Processed data from all samples (canine and human breast cancer cell lines) combined and quantile-normalised.

organism: Canis lupus familiaris

source_name: Dog breast cancer cell line model

growth_protocol: All cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% foetal calf serum (FCS), 50 U ml-1 penicillin and 50 mg ml-1 streptomycin and incubated at 37oC in a humidified atmosphere with 5% CO2.

extract_protocol:
Pellets of up to 1x10^7 cells were collected by trypsinization at 0, 2 and 8 h post-radiation, snap-frozen on dry ice and stored at – 70oC for subsequent RNA extraction. Total RNA was extracted from cells with the RNeasy Mini Kit using QIAshredder technology (UK Qiagen, Ltd). The manufacturer’s protocol for purification of total RNA from animal cells using spin technology was followed.
Prepared using the standard protocol for the Lexogen QuantSeq 3' mRNA-Seq Prep Kit for Illumina (FWD).

treatment_protocol: Cells were irradiated using a Faxitron cabinet X-ray system 43855D. Radioresistant cells (REM-RR) were developed from their parental cell line (REM) by weekly exposure to single fractions of radiation. Radiation doses were increased from 0.5 Gy to 10 Gy over a period of 12 weeks and then maintained by weekly doses.

tag: cell type

value: Canine breast cancer

tag: parental cell line

value: REM

tag: timepoint

value: 8h post-treatment

value: 2 Gray radiation dose


title: Liver_RNA-28_NAS5

tag: tissue

value: liver

tag: age

tag: Sex

value: F

value: White

tag: bmi

value: N

tag: insulin

value: Y

tag: pcos

tag: hypothyroidism

tag: cardiovascular disease

tag: ast (units/l)

tag: alt (units/l)

tag: alkaline phosphatase (units/l)

tag: total bilirubin (mg/dl)

tag: albumin (g/dl)

tag: total protein (g/dl)

value: Total score:6


title: Sample 25_WT.5L

tag: strain background

value: 8 weeks

tag: genotype

tag: treatment

tag: experiment day

tag: sample type

value: fecal pellet


title: REM_RR_8h_0g

tag: cell type

tag: parental cell line

tag: timepoint

value: Untreated


title: MSNCH 807_CH_M_VTA

description:
MSNCH
CH
high fat

tag: strain

tag: tissue

value: Mibrain

tag: age

value: 24-26 weeks

tag: gender

value: Male


title: Liver_RNA-26_NAS5

tag: Sex

value: M

tag: ethnicity

tag: bmi

tag: insulin

tag: hypertension

tag: hyperlipidemia

tag: statin/fibrate

tag: osa

tag: pcos

tag: hypothyroidism

tag: cardiovascular disease

tag: ast (units/l)

tag: alt (units/l)

tag: nas

value: Lobular inflammation:1

value: Total score:5


title: Liver_RNA-27_NAS5

tag: tissue

tag: alkaline phosphatase (units/l)

tag: total bilirubin (mg/dl)

tag: albumin (g/dl)

tag: total protein (g/dl)

value: Lobular inflammation:2


title: REM_RR_2h_2g

tag: cell type

value: Canine breast cancer

tag: parental cell line

value: REM

tag: timepoint

value: 2h post-treatment

tag: treatment

value: 2 Gray radiation dose


title: MSNCH 842_CH_M_VTA

description:
MSNCH
CH
high fat

tag: strain

tag: age

tag: gender


title: Sample 20_SCID.3R

tag: strain background

tag: genotype

value: SCID

value: Naive

tag: experiment day

tag: sample type


title: Sample 19_SCID.3L


title: Liver_RNA-25_NAS5

value: liver

tag: Sex

tag: ethnicity

value: White

tag: bmi

value: N

tag: insulin

tag: hypertension

tag: hyperlipidemia

tag: statin/fibrate

tag: osa

tag: pcos

tag: hypothyroidism

tag: cardiovascular disease

tag: ast (units/l)

tag: alt (units/l)

tag: nas


title: REM_RR_2h_0g

tag: cell type

tag: parental cell line

tag: timepoint

tag: treatment

value: Untreated


title: Liver_RNA-22_CTRL

tag: tissue

tag: age

tag: Sex

value: F

tag: ethnicity

tag: alkaline phosphatase (units/l)

tag: total bilirubin (mg/dl)

tag: albumin (g/dl)

tag: total protein (g/dl)

value: Lobular inflammation:0

value: Total score:0


title: MSNCH 302_CH_M_VTA

description:
MSNCH
CH
high fat

tag: strain

value: Mibrain

value: 24-26 weeks

tag: gender

value: Male


title: Sample 18_SCID.2R

source_name: SCID_chronic stress_1_fecal pellet

tag: strain background

value: 8 weeks

tag: genotype

value: chronic stress

tag: experiment day

tag: sample type

value: fecal pellet


title: Sample 17_SCID.2L


title: REM_RR_0h_0g

tag: cell type

value: Canine breast cancer

tag: parental cell line

value: REM

value: 0h post-treatment


title: Liver_RNA-20_CTRL

value: M

tag: bmi

tag: insulin

tag: hypertension

tag: hyperlipidemia

tag: statin/fibrate

tag: osa

tag: pcos

tag: hypothyroidism

tag: cardiovascular disease

tag: ast (units/l)

tag: alt (units/l)

tag: nas


title: Liver_RNA-21_CTRL

tag: tissue

value: liver

tag: age

tag: Sex

tag: ethnicity

value: Hispanic

tag: alkaline phosphatase (units/l)

tag: total bilirubin (mg/dl)

tag: albumin (g/dl)

tag: total protein (g/dl)


title: MSNCH 1468_CH_M_VTA

description:
MSNCH
CH
high fat

tag: strain

tag: gender


title: Sample 16_SCID.1R

tag: strain background

tag: genotype

value: SCID

tag: treatment

tag: experiment day

tag: sample type


title: REM_8h_2g

tag: cell type

tag: parental cell line

tag: timepoint

value: 8h post-treatment

value: 2 Gray radiation dose


title: FSNCC 754_CC_F_VTA

description:
FSNCC
CC
control

tag: tissue

tag: age

value: Female


title: REM_8h_0g

value: Untreated


title: Liver_RNA-19_CTRL

tag: Sex

value: F

tag: ethnicity

value: White

tag: bmi

value: N

tag: insulin

tag: hypertension

tag: hyperlipidemia

tag: statin/fibrate

tag: osa

tag: pcos

tag: hypothyroidism

tag: cardiovascular disease

tag: ast (units/l)

tag: alt (units/l)

tag: nas

value: Lobular inflammation:0

value: Total score:0


title: Liver_RNA-17_CTRL

tag: alkaline phosphatase (units/l)

tag: total bilirubin (mg/dl)

tag: albumin (g/dl)

tag: total protein (g/dl)


title: MSNCH 1469_CH_M_VTA

description:
MSNCH
CH
high fat

tag: strain

tag: tissue

value: Mibrain

tag: age

value: 24-26 weeks

tag: gender

value: Male


title: MSNCC 860_CC_M_VTA

description:
MSNCC
CC
control


title: REM_2h_2g

tag: cell type

value: Canine breast cancer

tag: parental cell line

value: REM

tag: timepoint

value: 2h post-treatment

tag: treatment


title: Sample 15_SCID.1L

tag: strain background

value: 8 weeks

tag: genotype

value: chronic stress

tag: experiment day

tag: sample type

value: fecal pellet


title: Sample 14_WT.7R

source_name: WT_Naive_1_fecal pellet

value: WT

value: Naive


title: REM_2h_0g

value: Untreated


title: MSNCC 827_CC_M_VTA

description:
MSNCC
CC
control


title: REM_0h_0g

value: 0h post-treatment


title: Liver_RNA-16_NAS3

value: liver

tag: Sex

value: M

tag: ethnicity

value: Hispanic

tag: bmi

value: Y

tag: insulin

tag: hypertension

tag: hyperlipidemia

tag: statin/fibrate

tag: osa

tag: pcos

tag: hypothyroidism

tag: cardiovascular disease

tag: ast (units/l)

tag: alt (units/l)

tag: nas

value: Lobular inflammation:1

value: Total score:3


title: Sample 12_WT.6R

tag: strain background

tag: age

tag: genotype

tag: treatment


title: DXlg03 [miRNA-seq]

city: Lanzhou

first: Qianyun

last: Ge

state: Gansu

address: NO.1 yingmen village, Anning district

institute: Gansu Agricultural University

data_processing:
Reads obtained from the sequencing machines included raw reads containing adapters or low quality bases which would affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered according to the following rules: 1) Remove the 3’ linker sequence, remove the sequence containing the fuzzy base N; 2) Remove low-quality reads so that at least 95% of the bases have a quality score of not less than 20; 3) Remove reads containing polyA/polyT, remove reads outside the miRNA length range (15-34nt).
Pipette 1µL library to Qubit Fluorometer (Invitogen) for detection. The library concentration, greater than 1.0ng/µL is qualified library.
Use Bio-Q100 to detect library length distribution and concentration.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

organism: Bos grunniens

source_name: lung tissue

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. A small RNA library of about 150 bp was recovered using PAGE (polyacrylamide) gel electrophoresis.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: altitude

tag: tissue

value: lung tissue

tag: breed

value: yak


title: Liver_RNA-15_NAS3

tag: Sex

tag: ethnicity

tag: bmi

value: N

tag: insulin

tag: hypertension

tag: alkaline phosphatase (units/l)

tag: total bilirubin (mg/dl)

tag: albumin (g/dl)

tag: total protein (g/dl)


title: MSNCC 859_CC_M_VTA

description:
MSNCC
CC
control

tag: strain

value: Mibrain

value: 24-26 weeks

tag: gender

value: Male


title: Liver_RNA-13_NAS3

tag: age

value: F

value: White

tag: hyperlipidemia

tag: statin/fibrate

tag: osa

tag: pcos

tag: hypothyroidism

tag: cardiovascular disease

tag: ast (units/l)

tag: alt (units/l)

tag: nas


title: Liver_RNA-14_NAS3

tag: tissue

tag: Sex

tag: ethnicity

tag: bmi

tag: insulin

tag: hypertension


title: Sample 11_WT.6L

tag: strain background

value: 8 weeks

tag: genotype

value: WT

tag: treatment

value: Naive

tag: experiment day

tag: sample type

value: fecal pellet


title: MSNCH 3033_CH_M_VTA

description:
MSNCH
CH
high fat

tag: strain

tag: age

tag: gender


title: BGlg02 [miRNA-seq]

tag: altitude

tag: breed


title: MSNCC 828_CC_M_VTA

description:
MSNCC
CC
control


title: Sample 10_WT.5R

source_name: WT_chronic stress_1_fecal pellet

value: chronic stress


title: Liver_RNA-12_NAS3

value: liver

tag: hyperlipidemia

tag: statin/fibrate

tag: osa

tag: pcos

tag: hypothyroidism

tag: cardiovascular disease

tag: ast (units/l)

tag: alt (units/l)

tag: alkaline phosphatase (units/l)

tag: total bilirubin (mg/dl)

tag: albumin (g/dl)

tag: total protein (g/dl)

tag: nas


title: LZlg01 [miRNA-seq]

tag: tissue


title: FSNCH 846_CH_F_SN

description:
FSNCH
CH
high fat

source_name: SN

tag: strain

tag: age

tag: gender

value: Female


title: ADlg03 [miRNA-seq]

tag: altitude

tag: breed


title: MSNCC 395_CC_M_VTA

description:
MSNCC
CC
control


title: Liver_RNA-11_NAS3

tag: Sex

value: M

tag: ethnicity

tag: bmi

tag: insulin

tag: hypertension

value: Y

tag: hyperlipidemia

tag: statin/fibrate

tag: osa

value: Lobular inflammation:1


title: Sample 13_WT.7L

tag: strain background

tag: genotype

tag: treatment

tag: experiment day

tag: sample type


title: Sample 4_WT.2R

source_name: WT_EAE_1_fecal pellet

tag: age

value: EAE


title: Liver_RNA-09_NAS3

tag: tissue

value: N

tag: pcos

tag: hypothyroidism

tag: cardiovascular disease

tag: ast (units/l)

tag: alt (units/l)

tag: alkaline phosphatase (units/l)

tag: total bilirubin (mg/dl)

tag: albumin (g/dl)

tag: total protein (g/dl)

tag: nas

value: Total score:3


title: FSNCH 825_CH_F_SN

description:
FSNCH
CH
high fat

tag: strain

value: Mibrain

value: 24-26 weeks

tag: gender


title: Sample 9_WT.5L

tag: strain background

tag: genotype

tag: treatment


title: Liver_RNA-07_NAS5

tag: age

tag: Sex

tag: ethnicity

tag: bmi

tag: insulin

tag: hypertension

tag: hyperlipidemia

tag: statin/fibrate

tag: osa

value: Lobular inflammation:2

value: Total score:5


title: Liver_RNA-08_NAS5

tag: tissue

value: Hispanic

tag: pcos

tag: hypothyroidism

tag: cardiovascular disease

tag: ast (units/l)

tag: alt (units/l)

tag: alkaline phosphatase (units/l)

tag: total bilirubin (mg/dl)

tag: albumin (g/dl)


title: FSNCH 845_CH_F_SN

description:
FSNCH
CH
high fat

tag: strain

tag: age

tag: gender


title: Sample 2_WT.1R

tag: strain background

value: 8 weeks

tag: genotype

value: WT

tag: treatment

tag: experiment day

tag: sample type


title: ADlg01 [miRNA-seq]

tag: altitude

tag: tissue

value: lung tissue

tag: breed

value: yak


title: MQlg03 [miRNA-seq]


title: FSNCH 824_CH_F_SN

description:
FSNCH
CH
high fat


title: FSNCH 823_CH_F_SN

description:
FSNCH
CH
high fat


title: Liver_RNA-04_NAS5

value: liver

tag: Sex

value: F

tag: ethnicity

value: White

tag: bmi

tag: insulin

tag: hypertension

tag: hyperlipidemia

tag: statin/fibrate

tag: osa

tag: pcos

tag: hypothyroidism

tag: cardiovascular disease

tag: total protein (g/dl)

tag: nas

value: Total score:6


title: MQlg02 [miRNA-seq]


title: FSNCH 811_CH_F_SN

description:
FSNCH
CH
high fat

tag: strain

tag: age

tag: gender

value: Female


title: MQlg01 [miRNA-seq]

tag: altitude

tag: tissue

tag: breed


title: H3K4me3_LPS_12h

city: Chiba

first: Ichiro

last: Manabe

address: 1-8-1 Inohana, Chuo

country: Japan

institute: Chiba University

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using STAR aligner.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files were generated using Homer.

source_name: Bone marrow-derived macrophage

growth_protocol: Bone marrow cells were flushed from femurs and tibias of male mice between 6 and 9 weeks of age, and were grown in DMEM/F12 (Thermo Fisher) supplemented with 10% FBS (HyClone), 1% penicillin–streptomycin (Thermo Fisher), 1% l-glutamine (Thermo Fisher), and 40 ng/ml of recombinant mouse M-CSF (576406; BioLegend) for 7-8 days. The medium was changed every 3 days. Differentiated BMDMs were detached from plates using StemPro Accutase Cell Dissociation Reagent (Thermo Fisher) and replated into 12-well tissue culture dishes at a density of 5 x 105 cells per well prior to cell stimulation.

extract_protocol: ChIP-seq libraries were prepared using a TruSeq ChIP Library Preparation kit (Illumina) according to the manufacturer’s protocol.

treatment_protocol: For LPS treatment, 100 ng/ml of LPS (Sigma-Aldrich) was added to the medium.

tag: chip antibody

value: H3K4me3 (Active Motif, 39159)

tag: treatment

value: LPS 12h


title: Sample 8_WT.4R

tag: strain background

tag: genotype

value: chronic stress

tag: experiment day

tag: sample type

value: fecal pellet


title: Sample 1_WT.1L

value: EAE


title: Liver_RNA-06_NAS5

tag: Sex

tag: ethnicity

tag: bmi

value: N

tag: insulin

tag: hypertension

value: Y

tag: hyperlipidemia

tag: statin/fibrate

tag: osa

tag: pcos

tag: ast (units/l)

tag: alt (units/l)

tag: alkaline phosphatase (units/l)

tag: total bilirubin (mg/dl)

tag: albumin (g/dl)

value: Lobular inflammation:2


title: FSNCC 818_CC_F_SN

description:
FSNCC
CC
control

tag: strain

tag: tissue

value: Mibrain

tag: age

value: 24-26 weeks

tag: gender


title: Liver_RNA-03_NAS5

tag: Sex

tag: ethnicity

tag: hypothyroidism

tag: cardiovascular disease

tag: total protein (g/dl)

tag: nas

value: Lobular inflammation:1

value: Total score:5


title: ADlg02 [miRNA-seq]

tag: altitude

value: lung tissue

tag: breed

value: yak


title: H3K4me3_LPS_4h

tag: chip antibody

tag: treatment

value: LPS 4h


title: FSNCC 766_CC_F_SN

description:
FSNCC
CC
control


title: DXlg03 [RNA-seq]

data_processing:
Reads obtained from the sequencing machines included raw reads containing adapters or low quality bases which would affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered according to the following rules: 1) Removing reads containing adapters; 2) Removing reads consisting of all A bases; 3) Removing reads containing more than 10% of unknown nucleotides (N); 4) Removing low quality reads containing more than 50% of low quality (Q-value≤20) bases
Short reads alignment tool Bowtie2 (2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads were then removed. The remaining reads were further used in assembly and analysis of transcriptome.
The rRNA removed reads of each sample were then mapped to reference genome by TopHat2 (version 2.1.1), respectively. The alignment parameters were as follows: 1) Maximum read mismatch is 2 2) Disables the coverage based search for junctions 3) The distance between mate-pair reads is 50bp 4) The standard deviation for the distribution on inner distance between mate-pair reads is 80bp
After aligned with reference genome, unmapped reads (or mapped very poorly) were then re-aligned with Bowtie2, the enriched unmapped reads were split into smaller segments which were then used to find potential splice sites. The section and the section position of these short segments were predicted as well. A set of splice sites was built with initial unmapped reads by TopHat2 without relying on the known genes annotation. Not only be used for identifying expressed genes and their quantitative expression, the sequence alignment will also be helpful to find alternative splicing and new transcripts.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

source_name: lung tissues

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: Liver_RNA-01_NAS5

value: liver

value: F

value: White

tag: bmi

tag: insulin

tag: hypertension

tag: hyperlipidemia

tag: statin/fibrate

tag: osa

tag: pcos

tag: ast (units/l)

tag: alt (units/l)

tag: alkaline phosphatase (units/l)


title: H3K4me3_LPS_0h

tag: strain

value: H3K4me3 (Active Motif, 39159)

value: LPS 0h


title: BGlg02 [RNA-seq]

tag: tissue


title: [BIG+] replicate 5

city: Eugene

middle: M

last: Garcia

state: OR

address: 1318 Franklin Blvd.,, Room 273 Onyx Bridge

department: Biology

institute: University of Oregon, Institute of Molecular Biology

description:
total RNA with rRNA depletion
YDJ1952_5

data_processing:
Pre-processing performed by Beijing Genomics Institute
Alignment was performed using Bowtie2 (Langmead and Salzberg, 2012)
HT-Seq (Anders et al., 2015) was used to prepare read counts.
DE-Seq2 (Love et al., 2014) was used in R to perform differential gene expression analysis
Genome_build: S. cerevisiae strain S288C reference genome R64-2-1
Supplementary_files_format_and_content: Genes (systematic name) are listed in rows, samples listed in columns, values are TPM (Transcirpts Per kilobase Million)

organism: Saccharomyces cerevisiae

source_name: budding yeast

growth_protocol: Five independent colonies of naïve and [BIG+] cells were grown in 5 mL YPD cultures on a culture roller drum wheel overnight at 30°C. Saturated cultures were added to 700 mL YPD cultures in 2 L narrow mouthed baffled flasks, pre-incubated to 30°C. These were grown until a cuvette reading of OD 1.0. (700 mL cultures were used to provide enough material for other sample-intensive experiments done in parallel).

extract_protocol:
Cultures were pelleted in large table-top centrifuge with swing-bucket rotor at 4300 x g at 4°C for 20 minutes, washing once with ice-cold 1X TBS. RNA was harvested as described in (Carlile et al., 2015). Total RNA was treated with RiboZero (Illumina, San Diego, CA) to remove most rRNAs but retain mRNAs and other ncRNAs. RNA was fragmented and submitted for Illumina sequencing
Library preparation and Illumina sequencing was performed at the Beijing Genomics Institute in late 2017.

tag: strain background

tag: genotype

value: WT

tag: prion

value: [BIG+]


title: LZlg01 [RNA-seq]

tag: altitude

tag: breed


title: FSNCC 762_CC_F_SN

description:
FSNCC
CC
control

tag: age

tag: gender

value: Female


title: KO_LPS12h

data_processing:
Reads were aligned to the mm9 mouse genome using STAR.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files were generated using Homer.

extract_protocol: Poly-A mRNA was extracted from total RNA by using an Oligo-dT beads of TruSeq RNA Sample Prep Kit v2 (Illumina), after which RNA-seq libraries were prepared using a ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre) according to the manufacturer’s protocol.

tag: genotype/variation

value: lncFAO knockout

tag: treatment

value: LPS 12h


title: ADlg03 [RNA-seq]


title: FSNCC 756_CC_F_SN

description:
FSNCC
CC
control

value: Mibrain


title: [BIG+] replicate 3

description:
total RNA with rRNA depletion
YDJ1952_3


title: [BIG+] replicate 4

description:
total RNA with rRNA depletion
YDJ1952_4


title: WT_LPS12h

value: contro wild-type for lncFAO knockout


title: Liver_RNA-02_NAS5

tag: Sex

value: M

tag: ethnicity

tag: bmi

value: N

tag: insulin

tag: hypertension

tag: hyperlipidemia

tag: statin/fibrate

tag: hypothyroidism

tag: cardiovascular disease

tag: total bilirubin (mg/dl)

tag: albumin (g/dl)

tag: total protein (g/dl)

tag: nas

value: Lobular inflammation:2


title: H3K4me3_LPS_24h

tag: strain

tag: chip antibody

value: LPS 24h


title: FSNCC 754_CC_F_SN

description:
FSNCC
CC
control

tag: tissue

tag: age

value: 24-26 weeks

tag: gender


title: ADlg02 [RNA-seq]

tag: altitude

value: lung tissue

tag: breed

value: yak


title: ADlg01 [RNA-seq]


title: silncFAO2

tag: genotype/variation

value: transfected with siRNA against lncRNA


title: MSNCH 842_CH_M_SN

description:
MSNCH
CH
high fat

value: Male


title: [BIG+] replicate 1

description:
total RNA with rRNA depletion
YDJ1952_1

tag: strain background

tag: genotype

tag: prion


title: naïve replicate 5

description:
total RNA with rRNA depletion
YDJ128_5


title: silncFAO1


title: siControl

value: transfected with control siRNA


title: MQlg03 [RNA-seq]


title: MSNCH 302_CH_M_SN

description:
MSNCH
CH
high fat


title: BMDM_LPS24h

value: wild-type

tag: treatment


title: MQlg02 [RNA-seq]


title: BMDM_LPS12h


title: naïve replicate 4

description:
total RNA with rRNA depletion
YDJ128_4

value: WT


title: MQlg01 [RNA-seq]


title: MSNCH 1468_CH_M_SN

description:
MSNCH
CH
high fat


title: naïve replicate 3

description:
total RNA with rRNA depletion
YDJ128_3


title: MSNCH 3033_CH_M_SN

description:
MSNCH
CH
high fat


title: BMDM_LPS4h

value: LPS 4h


title: 4 Gy + ONC201 48h rep3

city: Los Angeles

first: Frank

last: Pajonk

address: 10833 Le Conte Ave

institute: UC Los Angeles

data_processing:
Novogene Standard RNA-Seq pipeline
Genome_build: Homo_sapiens_hg38
Supplementary_files_format_and_content: counts

growth_protocol: well density in a 6-well plate with complete media.

extract_protocol:
Total RNA was isolated using Trizol reagent. The treated cells were lysed in 1 ml of Trizol reagent, rocked for 5 min to obtain a homogenous mixture and then transferred to RNAeasy mini kit (Qiagen) colimns for RNA isolation by following manufacturer's protocol.
uL before checking insert size on an Agilent Technologies 2100 Bioanalyzer (Agilent Technologies; Waldbronn, Germany) and quantifying to greater accuracy by quantitative Q-PCR (library molarity >2 nM). The library was sequenced on Illumina NovaSeq6000 with an average of 20M reads per RNA sample.

treatment_protocol: min. The X-ray beam was operated at 300 kV and hardened using a 4 mm Be, a 3 mm Al, and a 1.5 mm cu filter and calibrated using NIST-traceable dosimetry). Corresponding control cells were sham irradiated. The cells were then incubated and the RNA samples extracted at 48 hours post irradiation.

tag: condition

value: Glioblastoma

tag: sample type

value: patient-derived


title: BMDM_LPS0h

value: LPS 0h


title: naïve replicate 1

first: David

description:
total RNA with rRNA depletion
YDJ128_1


title: naïve replicate 2

description:
total RNA with rRNA depletion
YDJ128_2


title: 4 Gy + ONC201 48h rep2


title: MSNCH 807_CH_M_SN

description:
MSNCH
CH
high fat

value: Mibrain


title: 4 Gy + ONC201 48h rep1


title: RNAseq_12hr_Rep2

city: Ames

first: Wyatt

middle: Allen

last: Miller

state: IA

address: 2213 Pammel Dr

department: Plant Pathology & Microbiology

institute: Iowa State University

description: RNA-seq data

data_processing:
de-multiplexed sequenced data (fastq) files were obtained from the DNA facility at Iowa State University. The quality of raw sequencing reads was assessed using FastQC. Cutadapt 1.16 was used to remove adapters from raw sequencing reads using the following parameters: “ -a TGGAATTCTCGGGTGCCAAGG --discard-untrimmed --minimum-length 23.” Adapter trimmed reads were further processed to trim the four random bases, that were added to both ends of riboseq and RNAseq reads during library preparation, using cutadapt 1.16 with the following parameters: “-u 4 -u -4”. Subsequently, riboseq reads that were 27 nt to 32 nt in length and RNAseq reads from 25 nt to 40 nt were retained, and the rest were filtered out.
Subsequently, noncoding RNA (rRNA, snoRNA and tRNA) was depleted by mapping the reads to the maize ncRNA reference file (ftp://ftp.gramene.org/pub/gramene/CURRENT_RELEASE/fasta/zea_mays/ncrna/) using bowtie 1.2 with the following parameters: “-n 0 -l 23” and retaining only the unmapped reads. ncRNA depleted reads were subsequently mapped to maize cDNA and CDS reference transcriptomes (ftp://ftp.gramene.org/pub/gramene/CURRENT_RELEASE/fasta/zea_mays) using bowtie 1.2 with following parameters: “-l 23 -v 2 -m 20 --best -k 1” and only aligned reads were retained. cDNA and CDS aligned files were converted from sam to bam, sorted, indexed and read counts were extracted from CDS-aligned files using samtools view, sort, index and idxstats tools respectively. All transcriptome-level read counts were consolidated as gene-level read counts.
For gene-expression analysis, CDS-aligned read count table was used that is attached as the PROCESSED DATA FILES.
Genome_build: Zea_mays.AGPv4.ncrna.fa.gz
Genome_build: Zea_mays.AGPv4.cdna.all.fa.gz
Genome_build: Zea_mays.AGPv4.cds.all.fa.gz
Supplementary_files_format_and_content: excel sheet (.xlsx)  consisting of raw count data of CDS-aligned riboseq and RNAseq reads

source_name: maize seedling roots

growth_protocol: sterile maize B73 seeds were placed in sterile Sigma bottles (Cat No V8630-E100) with two layers of wet filter paper. The seeds were incubated at 30°C for two days then transferred to an illuminated incubator at 23°C for 7 days.

extract_protocol:
Total RNA was extracted from 300 uL aliquoted clarified lysate using a Trizol extraction method until the phase separation step and was followed by adding an equal volume of ice cold 100% ethanol to the aqueous phase and further purification using Zymo RNA clean & concentrator -5 columns (Zymo R1016) according to manufacturer’s protocol and quantified using a Nanodrop spectrophotometer. Integrity of total RNA was assessed by electrophoresis followed by DNase treatment and integrity assessment of DNase-treated total RNA for riboseq samples. rRNA depletion was carried out using half reactions of Ribo-Zero for plant seed/root kit (Illumina MRZSR116) per ~5 ug of DNAse-treated total RNA sample followed by RNA clean up using Zymo RNA clean & concentrator -5 columns (Zymo R1016) according to the Illumina TruSeq Ribo Profile kit protocol (Illumina 15066016). Total RNA was subjected to random fragmentation by alkaline hydrolysis as follows: 10 uL total RNA (~1 ug) mixed with 10 uL 2x fragmentation buffer (2 mM EDTA (pH 8), 12 mM Na2CO3, 88 mM NaHCO3), incubated at 95 ˚C in a thermocycler for 20 min.  The reaction was terminated by addition of 280 uL stop solution (0.3 M NaOAc, 53.6 ug/mL Glyco Blue) and 750 uL ice cold 100% ethanol followed by precipitation at -80˚C for 3 hr. RNA was precipitated by centrifugation at 21k g for 45 minutes at 4˚C and washed with ice cold 80% ethanol and resuspended in water. For size-selections, denatured rRNA-depleted fragmented RNA was subjected to electrophoresis on a 15% TBE-Urea gel (Invitrogen EC6885BOX) at 120V for 5 min and 170V for 85 min, stained in the gel with SYBR gold (Invitrogen S11494), and visualized on a blue light transilluminator.  The gel region between 28 nt and 34 nt RNA size markers was excised and transferred to a 0.5 ml tube with a hole at the bottom made by a 18 G syringe needle, and the tube was placed a 2 mL microfuge tube.  The tube was then centrifuged at 21k g for 2 min at 4˚ C to crush the gel slice and transfer its contents to the 2 mL microfuge tube. 500 uL RNA gel extraction buffer (0.3 M NaOAc (pH5.5), 1 mM EDTA (pH 8), 10 mM Tris-HCl (pH 7.5), 0.25% (w/v) SDS) was added and incubated overnight at 4 ˚C on a shaker. Eluted RNA were filtered through 0.22 µ SpinX cellulose acetate filter columns (Sigma-Aldrich CL8161). 2 uL Glyco Blue (Ambion AM9516) and equal volume of ice cold 100% isopropanol were added to the supernatant, and RNA were precipitated at -80 ˚C for 3 hours followed by centrifugation for 45 min at 21k g at 4 ˚C, washing with ice cold 80% ethanol and resuspending the pellet in 3.5 uL water.
250 mg of 10-day old maize B73 seedling roots (in biological duplicates) were ground with liquid N2 in 2.5 mL of polysome extraction buffer (PEB; 50 mM Tris-Acetate (pH 8), 200 mM KCl, 15 mM MgCl2, 1% (v/v) Triton X-100, 2% (v/v) polyoxyethelene 10-tridecylether, 200 mM sucrose, 100 g/mL cycloheximide, 100 g/mL chloramphenicol, 20 mM -mercaptoethanol). The crude lysate was filtered through a 40 µm cell strainer (Falcon 08-771-1) by centrifugation at 4000 g for 2 minutes. The flow through supernatant was further clarified by centrifugation at 21k g for 15 min. 300 l of clarified lysate were aliquoted for total RNA extraction.  Subsequent steps for ribosome profiling and RNAseq are described above in SAMPLES section
cDNA libraries were prepared using Nextflex small RNA-Seq kit v3 (Bioo Scientific 5132-05) according to manufacturer’s protocol and 12 cycles of PCR. Quality of the libraries was assessed using an Agilent bioanalyzer high sensitivity DNA Assay kit. Libraries were quantified using Qubit dsDNA HS Assay kit (Invitrogen Q32854) and diluted to same concentration. The riboseq and RNAseq libraries were pooled together for multiplexing and sequenced in two lanes using an Illumina HiSeq 3000 to yield single-end 50 bp reads. Because of low depth of riboseq sequences, riboseq samples were pooled and resequenced in additional two lanes using Illumina HiSeq 3000 to yield single-end 50 bp reads.
Ribo-seq and RNA-seq

treatment_protocol: 7-day old seedlings were treated with 5ug/ml tunicamycin in DMSO for 0, 6 and 12 hours

value: seedling roots

value: 12 hour tunicamycin treatment

tag: cultivar


title: MSNCC 827_CC_M_SN

description:
MSNCC
CC
control


title: ONC201 48h rep3


title: RNAseq_12hr_Rep1

description: RNA-seq data


title: RNAseq_6hr_Rep2

description: RNA-seq data

value: 6 hour tunicamycin treatment


title: ONC201 48h rep2


title: MSNCC 395_CC_M_SN

description:
MSNCC
CC
control


title: MSNCC 828_CC_M_SN

description:
MSNCC
CC
control


title: MSNCH 1469_CH_M_SN

description:
MSNCH
CH
high fat


title: 4 Gy 48h rep2


title: RNAseq_0hr_Rep2

description: RNA-seq data

value: 0 hour tunicamycin treatment


title: SARS-CoV-2-infected 24h 3

city: Bethesda

first: Eytan

last: Ruppin

address: 9000 Rockville Pike

institute: National Institutes of Health

data_processing:
Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt before alignment with the reference genome and the annotated transcripts using STAR (v2.7.3a).
The gene expression quantification analysis was performed for all samples using STAR/RSEM tools (v1.3.2).
Genome_build: Chlorocebus sabaeus genome (https://useast.ensembl.org/Chlorocebus_sabaeus/Info/Annotation); SARS-CoV-2 genome (https://www.ncbi.nlm.nih.gov/nuccore/NC_045512).
Supplementary_files_format_and_content: The RSEM result for each sample is given in a separate file, containing the expected read count, TPM and FPKM across genes and transcripts

organism:
Chlorocebus sabaeus
Severe acute respiratory syndrome coronavirus 2

source_name: SARS-CoV-2-infected Vero E6 cells

growth_protocol: Vero E6 cells were maintained in Dulbecco’s modified eagle medium (DMEM, Gibco) supplemented with 10 % heat-inactivated fetal bovine serum (FBS, Gibco), 50 U/mL penicillin, 50 μg/mL streptomycin, 1 mM sodium pyruvate (Gibco), 10 mM 4-(2-hydroxyethyl)-1- piperazineethanesulfonic acid (HEPES, Gibco), and 1X MEM non-essential amino acids solution (Gibco).

extract_protocol:
Cells were harvested, and total RNA was extracted using the Qiagen RNeasy Plus Mini Kit. The quality of the extracted RNA was assessed with the Agilent 2100 Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Vero E6 cells were either mock-infected or infected with SARS-CoV-2 USA-WA1/2020 (MOI = 0.3) for 24 hours.

tag: cell

value: Vero E6 cells

value: SARS-CoV-2 infection

tag: time


title: MSNCC 860_CC_M_SN

description:
MSNCC
CC
control

tag: strain

value: 24-26 weeks


title: SARS-CoV-2-infected 24h 2


title: RNAseq_0hr_Rep1

description: RNA-seq data


title: RNAseq_6hr_Rep1

description: RNA-seq data


title: MSNCC 859_CC_M_SN

description:
MSNCC
CC
control


title: 4 Gy 48h rep1


title: SARS-CoV-2-infected 24h 1


title: WT Tnaive

city: Ichikawa

first: Takashi

last: Sekiya

state: Chiba

address: 1-7-1 Kohnodai

institute: National Center for Global Health and Medicine

description: Gene expression of wild type naive CD4+ T cells.

hyb_protocol: Using Gene Expression Hybridiation kit (Agilent), 600 ng of Cy3-labelled cRNA (Cy3 incorporation > 6) was fragmented at 60°C for 30 minutes following the manufacturers instructions. On completion of the fragmentation reaction, samples were hybridized to SurePrint G3 Mouse GE microarray kit 8x60k ver 2.0  (G4858A, Agilent) for 17 hours at 65°C, rotating in hybridization oven (G2545A , Agilent) at 10 rpm.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan (G4900DA) using a setting AgilentG3_GX_1color (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction 11.5.1.1 (Agilent) using default parameters (protocol GE１_1010_Sep10, QC metric GE１_QCMT_Sep10, and Grid: 028005_D_F_20131202) to obtain background subtracted and spatially detrended Processed Signal intensities.  Output data were further analyzed with GeneSpring GX 12.6.1 with a default setting, with Prcentile=75, to generate values of normalized signal intensity.

source_name: Naive CD4+T cells from wild type mice

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the Low input Quick Amp labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy mni kit purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted with RNAiso PLUS (TAKARA). Samples were further cleaned using an NucleoSpin RNA Clean-up XS (MACHEREY-NAGEL). RNA was quantified using a Quantus fluorometer (Promega) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Naive CD4+T cells were obtained by sorting spleen and lymph nodes with the surface expression profiles of: CD4+, CD25low, CD44low, CD62L-high, and Foxp3-. To obtain iTreg 3 h cells, Primary naïve CD4+ T cells were cultured for 3 h in RPMI1640 medium supplemented with plate-coated anti-CD3 (clone 2C11, 2 μg/ml), anti-CD28 (clone 57.31, 0.5 μg/ml) antibodies, 2-Mercaptoethanol (Invitrogen, 55 μM), 10% fetal bovine serum, and further supplemented with anti-IFN-γ (clone R4-6A2, 1 μg/ml), anti-IL-4 (clone 11B11, 1 μg/ml) antibodies, IL-2 (10 ng/ml, PeproTech) and recombinant human TGF-β1 (0.2 or 0.5 ng/ml, BioLegend).

tag: cell subset

value: Naive CD4+ T cells

value: Wild type


title: Nr4a-TKO iTreg 3 h

description: Gene expression after 3 h in iTreg cell differentiation condition of Nr4a-TKO naive CD4+ T cells.

source_name: In vitro induced Treg (iTreg) of Nr4a-TKO cells, 3 h

value: iTreg cells

value: Nr4a triple knockout


title: WT iTreg 3 h

description: Gene expression after 3 in iTreg cell differentiation condition of wild type naive CD4+ T cells.

source_name: In vitro induced Treg (iTreg) of wild type cells, 3 h


title: Riboseq_12hr_Rep2

description: Ribosome profiling data

extract_protocol:
For RPF generation, the remaining lysate was adjusted to A254 = ~10  (Lysate - PEB) with PEB. 600 ul of the adjusted lysate were digested with 15 ul RNase1 (Ambion AM2295) for 30 min at 28 ˚C on a shaker with slow speed. To terminate RNase digestion, 15 ul superase-IN (Ambion AM2696) were added. For each sample, two-aliquots of 600 ul (technical reps) were used and pooled after ultracentrifugation. The RNAse-digested lysate was layered on a precooled 330 ul sucrose cushion (1M sucrose, 40 mM Tris-acetate (pH 8), 100 mM KCl, 15 mM MgCl2, 100 ug/mL cycloheximide, 100 ug/mL chloramphenicol, 10 mM B-mercaptoethanol) in ultracentrifuge tubes (ThermoScientific #45237) and subjected to ultracentrifugation at 131k g (57000 rpm) for 90 minutes at 4˚ C in a Sorvall mini ultracentrifuge (Discovery M150) with S150-AT fixed angle rotor (ThermoScientific 45582). The pellet was resuspended in 150 uL ribosome dissociation buffer (10 mM Tris-HCl (pH 7.5), 10 mM EDTA (pH 8), 5 mM EGTA (pH 8), 100 mM NaCl).   RNA was purified by Trizol extraction method until the phase separations step followed by addition of an equal volume of ice cold 100% ethanol to the aqueous phase and further purification using Zymo RNA Clean & ConcentratorTM-5 columns (Zymo R1016) according to manufacturer’s protocol and quantified using a Nanodrop spectrophotometer. Quality of RPFs was assessed by electrophoresis of denatured RNA in a 15% TBE-Urea gel (Invitrogen EC6885BOX) at 120V for 5 minutes and 200V for 55 minutes, staining the gel with SYBR gold (Invitrogen S11494) and determining the sharpness of the RPF band between the 28 nt and 34 nt RNA size markers. If the RPF bands appeared sharp for all samples, the RNAs from two technical duplicates were pooled for each sample. Subsequently, 10 ug RNA were treated with 1 uL Turbo DNase (Ambion AM2238) in a 50 uL reaction with 1x Turbo DNase buffer at 37 ˚C for 30 min followed by addition of 1 uL more Turbo DNase and incubation at 37 ˚C for additional 30 min, purification by Zymo RNA clean & concentrator -5 columns (Zymo R1016) and quantification with a Nanodrop spectrophotometer. Quality of the DNase-treated RNA was assessed as above. rRNA depletion was carried out using a half reaction of Ribo-Zero for plant seed/root kit (Illumina MRZSR116) per ~5-10 ug of DNAse treated RNA sample followed by RNA clean up using Zymo RNA clean & concentrator -5 columns (Zymo R1016) according to the Illumina TruSeq Ribo Profile kit protocol (Illumina 15066016). RNA was quantified using a Qubit RNA HS kit (Invitrogen Q32852) yielding ~20% recovery from the input.   For size-selecting the RPFs, denatured rRNA-depleted RNA was subjected to electrophoresis on a 15% TBE-Urea gel (Invitrogen EC6885BOX) at 120V for 5 min and 170V for 85 min, stained in the gel with SYBR gold (Invitrogen S11494), and visualized on a blue light transilluminator.  The gel region between 28 nt and 34 nt RNA size markers was excised and transferred to a 0.5 ml tube with a hole at the bottom made by a 18 G syringe needle, and the tube was placed a 2 mL microfuge tube.  The tube was then centrifuged at 21k g for 2 min at 4˚ C to crush the gel slice and transfer its contents to the 2 mL microfuge tube. 500 uL RNA gel extraction buffer (0.3 M NaOAc (pH5.5), 1 mM EDTA (pH 8), 10 mM Tris-HCl (pH 7.5), 0.25% (w/v) SDS) was added and incubated overnight at 4 ˚C on a shaker. Eluted RPFs were filtered through 0.22 µ SpinX cellulose acetate filter columns (Sigma-Aldrich CL8161). 2 uL Glyco Blue (Ambion AM9516) and equal volume of ice cold 100% isopropanol were added to the supernatant, and RPFs were precipitated at -80 ˚C for 3 hours followed by centrifugation for 45 min at 21k g at 4 ˚C, washing with ice cold 80% ethanol and resuspending the pellet in 3.5 uL water.  Prior to library preparation, RPF ends were repaired as follows using T4PNK kit (ThermoScientific EK0031): incubate 3.25 uL RNA at 70˚ C for 3 min, transfer to ice and centrifuge, add 0.5 uL 10 x T4 PNK buffer A (no ATP), 0.25 uL superase-IN, 0.5 uL T4PNK enzyme, incubate at 37 ˚C for 30 min, add 0.5 uL 10 mM ATP, incubate at 37 ˚C for 1 hr, add 5.5 uL water, deactivate the reaction by incubating at 75 ˚C for 10 min and transfer to ice.
250 mg of 10-day old maize B73 seedling roots (in biological duplicates) were ground with liquid N2 in 2.5 mL of polysome extraction buffer (PEB; 50 mM Tris-Acetate (pH 8), 200 mM KCl, 15 mM MgCl2, 1% (v/v) Triton X-100, 2% (v/v) polyoxyethelene 10-tridecylether, 200 mM sucrose, 100 g/mL cycloheximide, 100 g/mL chloramphenicol, 20 mM -mercaptoethanol). The crude lysate was filtered through a 40 µm cell strainer (Falcon 08-771-1) by centrifugation at 4000 g for 2 minutes. The flow through supernatant was further clarified by centrifugation at 21k g for 15 min. 300 l of clarified lysate were aliquoted for total RNA extraction.  Subsequent steps for ribosome profiling and RNAseq are described above in SAMPLES section
cDNA libraries were prepared using Nextflex small RNA-Seq kit v3 (Bioo Scientific 5132-05) according to manufacturer’s protocol and 12 cycles of PCR. Quality of the libraries was assessed using an Agilent bioanalyzer high sensitivity DNA Assay kit. Libraries were quantified using Qubit dsDNA HS Assay kit (Invitrogen Q32854) and diluted to same concentration. The riboseq and RNAseq libraries were pooled together for multiplexing and sequenced in two lanes using an Illumina HiSeq 3000 to yield single-end 50 bp reads. Because of low depth of riboseq sequences, riboseq samples were pooled and resequenced in additional two lanes using Illumina HiSeq 3000 to yield single-end 50 bp reads.
Ribo-seq and RNA-seq

tag: tissue


title: Control (mock-infected) 3

organism: Chlorocebus sabaeus

source_name: Vero E6 cells

value: Control (mock infection)


title: ONC201 48h rep1