title: Subject9_0h_LA_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 9, before treatment with a Low Meal Frequency diet (t=0h)

tag: fasting insulin


title: S_95.1: Col-0_SynCom_BioRep2_S95TechRep2

status: Public on Nov 01 2020

type: SRA

city: Loughborough

first: Gabriel

last: Castrillo

address: Nr Loughborough

department: School of Biosciences

country: United Kingdom

institute: University of Nottingham

library_source: transcriptomic

data_processing:
Initial quality assessment of the Illumina RNA-Seq reads was performed using FastQC v0.11.8. (Babraham Bioinformatics, Cambridge, UK).
Trimmomatic v0.36  was used to identify and discard reads containing the Illumina adaptor sequence.
The resulting high-quality reads were then mapped against the TAIR10 Arabidopsis reference genome using HISAT2 v2.1.0 with default parameters
The featureCounts function from the Subread package (Liao et al., 2013) was then used to count reads that mapped to each one of the 27,206 nuclear protein-coding genes.
Genome_build: TAIR 10

molecule: total RNA

organism: Arabidopsis thaliana

source_name: root

growth_protocol: Sterilised Col-0 seeds were germinated on agar plate containing 0.5x MS medium solidified with 1% bacto-agar for a week. Ten seedlings of the different genotypes were then transferred to 0.5x MS agar plates inoculated with the 41-member synthetic community. In parallel 10 seedlings were also transferred to no bacteria control (agar plates inoculated with only 10 mM MgCl2). Plates were manually randomised and placed in a growth chambers and grown under a 16-h light/8-h dark regime at 21°C day/19°C night for another 7 days.

extract_protocol:
RNA was extracted from A. thaliana roots according to Logemann et al. We used three independent biological replicas per treatment and we repeated this experiment twice. Briefly, approximately 10 roots from 14-day-old seedlings were harvested from each sample and flash frozen using liquid N2. Frozen roots were pulverized using a TissueLyzer II (Qiagen), 2 cycles of 30 seconds, frequency 30 s-1, and 400 μL of Z6-buffer; 8 M guanidine HCl, 20 mM MES, 20 mM EDTA at pH 7.0 was added to the samples. Following the addition of 400 μL phenol:chloroform:isoamylalcohol; 25:24:1, samples were vortexed and centrifuged (20,000 g, 10 min) for phase separation. The aqueous phase was then transferred to a new 1.5 mL tube and 0.05 volumes of 1 N acetic acid and 0.7 volumes 96% ethanol were added. The RNA was precipitated at −20 °C overnight. Following centrifugation, (20,000 g, 10 min, 4 °C) the pellet was washed with 200 μL sodium-acetate (pH 5.2) and 70% ethanol. The RNA was dried and dissolved in 30 μL of ultrapure water and stored at −80 °C until use.
Before sequencing, RNA samples were quantified using the Qubit RNA BR Assay Kit (Invitrogen; Q10210) and quality was assessed using RNA Screen Tape (Agilent; 5067-5576) on the Agilent 4200 TapeStation System (Agilent; G2991A). Although TapeStation results showed RNA with high RNA integrity numbers (RINs > 8), indicative of good quality RNA, we detected the presence of high molecular weight nucleic acids typical of genomic DNA, therefore DNase treatment was carried out on the samples. TURBO DNase (Ambion; AM2238) was used to remove DNA from RNA samples. Briefly, 22.5 µL of RNA was combined with 2.5 µL of 10x TURBO DNase Buffer and 1 µL (2 Units) of TURBO DNAse and incubated at 37°C for 30 min. The RNA was then dissolved with 75 µL of nuclease free water and purified using the Qiagen RNeasy MinElute Cleanup Kit (Qiagen; 74204). The final elution was carried out with 15 µL of nuclease free water. For library construction, 200 ng of high-quality RNA was used as input into Lexogen Quant Seq 3’ mRNA Seq (FWD) Library Prep Kit (Lexogen; 015) and the standard protocol was followed. At the PCR stage 13 cycles of PCR were used. Library yield was measured by Qubit dsDNA HS (Invitrogen; Q32851) and library size was assessed using the High Sensitivity D1000 ScreenTape (Agilent; 5067- 5584) on the Agilent 4200 TapeStation System (Agilent; G2991A). Libraries were normalised to each other based on size and Qubit dsDNA HS concentration and pooled together. The pool was quantified by qPCR using the KAPA Library Quantification Kit for Illumina Platforms (KAPA Biosystems; KK4873)
The library pool was denatured and diluted according to the Illumina NextSeq System protocol (Illumina Document #15048776v09) and then sequenced on the Illumina NextSeq 500 on a NextSeq 500/550 High Output Kit v2.5 (75 Cycles) (Illumina; 20024906), to generate ~5 million 75bp single-end reads per sample

treatment_protocol: We used 5 replicas of each treatment and this experiment was repeated twice.

tag: genotype

tag: bacteria

value: SynCom

tag: biorep


title: Subject9_24h_HO_pbmc

type: RNA

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Human Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.24.2).

label: Biotin

organism: Homo sapiens

source_name: Peripheral blood mononuclear cells isolated from subject 9, 24h after treatment with a High Meal Frequency diet (t=24h)

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: Subjects were recruited by advertisements at local educational institutions and newspapers. Subjects with IGT were included according to the World Health Organization when glucose levels were lower than 7.0 mmol/L at fasting and 2 hours postload >7.8 mmol/L and <11.1 mmol/L. Glucose tolerance was determined with an Oral Glucose Tolerance Test (OGTT). Insulin sensitivity (IS) was assessed using the oral glucose insulin sensitivity (OGIS)-index. Additional inclusion criteria; weight stable over the past 3 months, no excess alcohol intake (28 drinks weekly), no major organ dysfunction, and no use of medication that could influence the results. For homogeneity reasons as well as to avoid menstrual cycle effects on energy expenditure, only Caucasian males were included. All subjects were informed about the nature of the study and written informed consent was obtained before study participation. The local Medical Ethical Committee of Maastricht University Medical Centre approved the study protocol.

extract_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from whole blood using BD Vacutainer Cell Preparation Tubes according to the manufacturers’ instructions. Total RNA was extracted using TRIzol reagent (Invitrogen, Breda, the Netherlands) and puriﬁed on columns using the Qiagen RNeasy Micro Kit (Qiagen, Venlo, Netherlands). RNA quantity was measured with the ND-100 spectrophotometer (Isogen Life Science, Ijsselstein, the Netherlands), and RNA integrity was analysed on an Agilent 2100 BioAnalyzer (Agilent Technologies, Amsterdam, The Netherlands) using nanochips according to manufacturer's instructions

treatment_protocol: The study had randomized, 2-way cross-over design with a wash-out period of at least two weeks. Each intervention lasted for 36 hours in a respiration chamber. All subjects randomly received the same iso-energetic diet with a Low meal Frequency (3x-LFr) or a High meal Frequency (14x-HFr). The diet consisted of 15 energy% (En%) dairy protein, 30 En% fat, and 55 En% carbohydrates. Peripheral blood mononuclear cells (PBMCs) were isolated from whole blood on T0 (fasting state), T13 (21.30h) and T24 (next morning at 08.00h in fasting state). A muscle biopsy was taken from the vastus lateralis muscle was taken after each respiration chamber stay in the fasting state (T24).

tag: tissue

value: PBMC

tag: subject number

tag: diet

tag: Sex

value: Male

tag: age(years)

tag: body mass index (bmi)

tag: body fat percentage (fm)

tag: blood pressure (bp)

tag: fasting glucose

value: 6.3 mmol/L


title: P517

city: rome

first: simona

last: giglio

state: rome

address: via di grottarossa

department: clinical and molecolar medicine

country: Italy

institute: Sapienza university

description: small-RNA

data_processing:
Basecalls performed using bcl2fastq version 2.20
Raw sequence files (.fastq files) underwent quality control analysis using FastQC of Babraham Bioinformatics group (version v0.11.5)
Small RNA-Seq data were analyzed using iSmaRT tool with standard parameters, using miRBase v21 as reference track
Only miRNA showing a raw expression value > 50 raw-reads in at least one sample were considered for further analysis
Differentially expressed miRNAs were identified using DESeq2 package, available on Bioconductor. A cutoff of |FC| ≥ 2 and FDR ≤ 0.001 were used to select differentially expressed miRNAs between ADK vs Prostatitis samples
Differentially expressed Analysis was performed considering, also, Gleason Score classification and using DESeq2 package. Therefore only those samples with the present gleason score were considered (32 ADK samples).
To investigate the independence of samples from PSA-value, Age and BMI, the Chi-Square (Pearson's Chi-squared test) and Differentially expressed Analysis wer performed considering only the  ADK samples with the PSA-value, Age and BMI classification.
Genome_build: hg19
Supplementary_files_format_and_content: excel file include normalized count and Differentially expressed Analysis results

source_name: Prostatitis

extract_protocol:
Plasma was isolated whit miRNeasy Serum / Plasma kit according to the manufacturer's protocol (Qiagen).  Illumina TruSeq RNA Sample Prep Kit  was used with 1 ug of total RNA for the construction of sequencing libraries.
Libraries were prepared according to Illumina's instructions accompanying the SmallRNA sample preparation kit

value: plasma

tag: patient diagnosis

value: Prostatitis

tag: patient age

tag: gleason score

value: Not Available (NA)

tag: cancer size

tag: psa-value

tag: bmi


title: S_94.3: Col-0_SynCom_BioRep2_S94TechRep4

tag: genotype

tag: bacteria


title: Subject9_13h_HO_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 9 treated with a High Meal Frequency diet for 13h

tag: tissue

value: after treatment with a High Meal Frequency diet (t=13h)

tag: fasting insulin


title: S_94.2: Col-0_SynCom_BioRep2_S94TechRep3

tag: biorep


title: S_95: Col-0_SynCom_BioRep2_S95TechRep1


title: Subject9_13h_LA_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 9 treated with a Low Meal Frequency diet for 13h

tag: subject number

tag: diet

tag: Sex


title: P504

description: small-RNA


title: S_94.1: Col-0_SynCom_BioRep2_S94TechRep2


title: P507

description: small-RNA


title: P491

description: small-RNA


title: Subject8_24h_LA_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 8, 24h after treatment with a Low Meal Frequency diet (t=24h)

tag: age(years)

tag: body mass index (bmi)

tag: body fat percentage (fm)

value: 6.9 mmol/L


title: Subject9_0h_HO_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 9, before treatment with a High Meal Frequency diet (t=0h)

tag: blood pressure (bp)

tag: fasting glucose


title: Subject8_0h_LA_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 8, before treatment with a Low Meal Frequency diet (t=0h)


title: Subject8_13h_LA_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 8 treated with a Low Meal Frequency diet for 13h


title: P489

description: small-RNA

tag: patient diagnosis

tag: patient age

tag: gleason score


title: P465

description: small-RNA

tag: cancer size

tag: psa-value

tag: bmi


title: P452

description: small-RNA

tag: tissue


title: S_66.2: Col-0_NB_BioRep2_S66TechRep3

tag: genotype

tag: bacteria

value: NB


title: S_66.1: Col-0_NB_BioRep2_S66TechRep2

tag: biorep


title: P449

description: small-RNA


title: S_94: Col-0_SynCom_BioRep2_S94TechRep1


title: P444

description: small-RNA


title: Subject8_0h_HO_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 8, before treatment with a High Meal Frequency diet (t=0h)

tag: subject number

tag: diet

tag: fasting insulin


title: S_65.3: Col-0_NB_BioRep2_S65TechRep4


title: S_65.2: Col-0_NB_BioRep2_S65TechRep3


title: S_65.1: Col-0_NB_BioRep2_S65TechRep2


title: Subject8_24h_HO_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 8, 24h after treatment with a High Meal Frequency diet (t=24h)

tag: Sex

tag: age(years)

tag: body mass index (bmi)


title: S_66.3: Col-0_NB_BioRep2_S66TechRep4


title: Subject7_24h_LA_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 7, 24h after treatment with a Low Meal Frequency diet (t=24h)

tag: body fat percentage (fm)

tag: blood pressure (bp)

tag: fasting glucose

value: 5.8 mmol/L


title: Subject7_13h_LA_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 7 treated with a Low Meal Frequency diet for 13h


title: Subject8_13h_HO_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 8 treated with a High Meal Frequency diet for 13h


title: P385

description: small-RNA

tag: patient diagnosis

tag: patient age

tag: gleason score


title: S_65: Col-0_NB_BioRep2_S65TechRep1


title: P35

description: small-RNA

tag: cancer size

tag: psa-value

tag: bmi


title: S_64.3: Col-0_NB_BioRep2_S64TechRep4

tag: genotype

tag: bacteria


title: S_66: Col-0_NB_BioRep2_S66TechRep1

tag: biorep


title: P337

description: small-RNA

tag: tissue


title: S_64.2: Col-0_NB_BioRep2_S64TechRep3


title: P391

description: small-RNA


title: P303

description: small-RNA


title: P727

description: small-RNA


title: P276

description: small-RNA


title: P190

description: small-RNA


title: P167

description: small-RNA


title: Subject7_0h_LA_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 7, before treatment with a Low Meal Frequency diet (t=0h)

tag: subject number

tag: diet

tag: fasting insulin


title: Subject7_13h_HO_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 7 treated with a High Meal Frequency diet for 13h

tag: Sex

tag: age(years)

tag: body mass index (bmi)


title: Subject7_0h_HO_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 7, before treatment with a High Meal Frequency diet (t=0h)

tag: body fat percentage (fm)

tag: blood pressure (bp)

tag: fasting glucose


title: Subject6_0h_LA_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 6, before treatment with a Low Meal Frequency diet (t=0h)

value: 4.8 mmol/L


title: S_64.1: Col-0_NB_BioRep2_S64TechRep2

source_name: root


title: Subject7_24h_HO_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 7, 24h after treatment with a High Meal Frequency diet (t=24h)


title: S_64: Col-0_NB_BioRep2_S64TechRep1


title: P129

description: small-RNA

source_name: Prostatitis

tag: patient diagnosis

tag: patient age

tag: gleason score


title: Subject6_13h_LA_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 6 treated with a Low Meal Frequency diet for 13h


title: S_6.1: Col-0_NB_BioRep1_S6TechRep2


title: S_6.2: Col-0_NB_BioRep1_S6TechRep3


title: Subject6_24h_LA_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 6, 24h after treatment with a Low Meal Frequency diet (t=24h)


title: A790

description: small-RNA

source_name: Adenocarcinoma of prostate (ADK)

value: Adenocarcinoma of prostate (ADK)

tag: cancer size

tag: psa-value

tag: bmi


title: Subject6_0h_HO_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 6, before treatment with a High Meal Frequency diet (t=0h)


title: S_6: Col-0_NB_BioRep1_S6TechRep1

tag: genotype

tag: bacteria

tag: biorep


title: Subject5_24h_LA_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 5, 24h after treatment with a Low Meal Frequency diet (t=24h)

tag: tissue

tag: subject number

tag: diet

value: 6.2 mmol/L


title: S_5.3: Col-0_NB_BioRep1_S5TechRep4


title: A781

description: small-RNA


title: Subject5_13h_LA_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 5 treated with a Low Meal Frequency diet for 13h

tag: Sex

tag: age(years)

tag: fasting insulin


title: S_6.3: Col-0_NB_BioRep1_S6TechRep4


title: Subject6_13h_HO_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 6 treated with a High Meal Frequency diet for 13h

tag: body mass index (bmi)

tag: body fat percentage (fm)

tag: blood pressure (bp)


title: Subject5_0h_LA_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 5, before treatment with a Low Meal Frequency diet (t=0h)

tag: fasting glucose


title: A758

description: small-RNA

tag: patient diagnosis

tag: patient age

tag: gleason score


title: S_5.2: Col-0_NB_BioRep1_S5TechRep3


title: S_5.1: Col-0_NB_BioRep1_S5TechRep2


title: S_48.3: myb36-2_SynCom_BioRep1_S48TechRep4


title: A734

description: small-RNA

tag: cancer size

tag: psa-value

tag: bmi


title: Subject5_24h_HO_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 5, 24h after treatment with a High Meal Frequency diet (t=24h)


title: A747

description: small-RNA


title: Subject6_24h_HO_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 6, 24h after treatment with a High Meal Frequency diet (t=24h)


title: A721

description: small-RNA


title: S_48.2: myb36-2_SynCom_BioRep1_S48TechRep3

tag: genotype

tag: bacteria

tag: biorep


title: A717

description: small-RNA

tag: tissue


title: S_48: myb36-2_SynCom_BioRep1_S48TechRep1


title: A700

description: small-RNA


title: Subject5_0h_HO_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 5, before treatment with a High Meal Frequency diet (t=0h)

tag: subject number

tag: diet

tag: Sex


title: Subject4_13h_LA_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 4 treated with a Low Meal Frequency diet for 13h

tag: age(years)

tag: body mass index (bmi)

value: 6.1 mmol/L

tag: fasting insulin


title: Subject4_24h_LA_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 4, 24h after treatment with a Low Meal Frequency diet (t=24h)

tag: body fat percentage (fm)

tag: blood pressure (bp)

tag: fasting glucose


title: Subject4_0h_LA_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 4, before treatment with a Low Meal Frequency diet (t=0h)


title: Subject4_13h_HO_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 4 treated with a High Meal Frequency diet for 13h


title: Subject4_0h_HO_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 4, before treatment with a High Meal Frequency diet (t=0h)


title: S_47.3: myb36-2_SynCom_BioRep1_S47TechRep4

source_name: root


title: Subject5_13h_HO_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 5 treated with a High Meal Frequency diet for 13h


title: A695

description: small-RNA

tag: patient diagnosis

tag: patient age

tag: gleason score


title: S_47.1: myb36-2_SynCom_BioRep1_S47TechRep2


title: S_47.2: myb36-2_SynCom_BioRep1_S47TechRep3


title: A755

description: small-RNA

tag: cancer size

tag: psa-value

tag: bmi


title: A724

description: small-RNA


title: S_5: Col-0_NB_BioRep1_S5TechRep1

tag: genotype

tag: bacteria

tag: biorep


title: A686

description: small-RNA

tag: tissue


title: A655

description: small-RNA


title: S_47: myb36-2_SynCom_BioRep1_S47TechRep1


title: Subject3_24h_LA_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 3, 24h after treatment with a Low Meal Frequency diet (t=24h)

tag: subject number

tag: diet

tag: Sex

value: 5.4 mmol/L


title: IS6A: HCASMC 1 dyne/cm2

city: Pisa

first: Federico

last: Vozzi

state: Tuscany

address: Via Moruzzi 1

department: Institute of Clinical Physiology

institute: CNR

data_processing:
Raw data were processed for basecalling and demultiplexing conversion and de-multiplexing by Bcl2Fastq 2.0.2 version of the Illumina pipeline
Removing lower quality bases and adapters by ERNE and Cutadapt software.
Reads were deduplicated based on unique molecular identifier (UMI) composed of 8 random bases for unambiguous identification of unique library molecules by IGATech proprietary script
Reads were aligned on reference GRCh38 genome/transcriptome with STAR (default parameters)
Assembling and quantification of full-length transcripts representing multiple spliced variants for each gene locus were performed by Stringtie (default parameters)
Htseq-count was used to preprocess RNA-Seq data for differential expression analysis by counting the overlap of reads with genes
DESeq2 is used to perform comparisons between expression levels of genes and transcripts.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample, a tab-delimited text file containing gene expression data used for differential expression analysis, a tab-delimited test file containing results data from DESeq2 analysis

source_name: Primary Human Coronary Artery

growth_protocol: Primary human coronary artery endothelial cells (HCAECs) were purchased from Promocell GmbH (Heidelberg, Germany) and cultured in the manufacturer’s recommended medium, designated as Endothelial Cell Growth Basal Medium MV 2 supplemented with Growth Medium MV 2 Supplement Pack, constituted by a mix of Fetal Calf Serum (FCS), Epidermal Growth Factor, Basic Fibroblast Growth Factor, Insulin-like Growth Factor, Vascular Endothelial Growth Factor 165, Ascorbic Acid and Hydrocortisone. Every 2 days media culture was changed, until the confluence. Primary human coronary artery smooth muscle cells (HCASMCs) were purchased from Thermo Scientific (Waltham, MA, USA) and cultured in the manufacturer’s recommended medium, designated as Medium 231 supplemented with Smooth Muscle Growth Supplement, constituted by a mix of Fetal bovine serum, Human basic fibroblast growth factor, Human epidermal growth factor, Heparin, Recombinant human insulin-like growth factor-I, BSA.

extract_protocol:
For molecular biology analysis, cells were washed with PBS and trypsinised with 200 μl/system. Once cells were detached, 1 ml of medium was added to block trypsin action and centrifuged. The pellet was washed once again with 1 ml of PBS, centrifuged and the final pellet was cryopreserved at -80°C.   Total RNA was extracted from on HCAECs and HCASMCs by a dedicated kit (RNeasy Plus Micro Kit, Qiagen SpA, Milano, Italy) accurately modified to purify total RNA (including miRNA) from small amounts of cells (<5*10^5); after re-suspension and lysis of the cells in a highly denaturing guanidine-isothiocyanate–containing buffer, which immediately inactivates RNases to ensure isolation of intact RNA, samples were selective passed through a gDNA Eliminator spin column. This column, in combination with the optimized high-salt buffer, efficiently removes genomic DNA.  Ethanol was added to the flow-through to provide appropriate binding conditions for RNA, and the samples were then applied to a silica-based membrane (RNeasy MinElute spin column), speeded on a microspin centrifuge; specific buffers allowed RNA to bind to the RNeasy silica membrane and contaminants were efficiently washed away. High-quality RNA was then eluted in 14 μl of RNAse free water without the need for additional DNase digestion.   The total RNA concentration was determined in all samples by measuring the spectrophotometer absorbance at 260 and 280 nm (NanoDrop Thermofisher) and calculated using the Beer-Lambert law, with expected values between 1.8-2.1. The RNA samples were stored at -80 °C for use in gene expression studies.
Ovation SoLo RNA-seq Library Preparation kit (NuGEN, Redwood City, CA) has been used for library preparation following the manufacturer’s instructions (library type: fr-second strand). RNA samples were quantified and quality tested by Agilent 2100 Bioanalyzer RNA assay (Agilent technologies, Santa Clara, CA) or Caliper (PerkinElmer, Waltham, MA). Final libraries were checked with both Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) and Agilent Bioanalyzer DNA assay or Caliper (PerkinElmer, Waltham, MA). Libraries were then prepared for sequencing and sequenced on single-end 75 bp mode on NextSeq 500 (Illumina, San Diego, CA).

tag: cell type

value: Human Coronary Artery Smooth Muscle Cells

tag: passages

tag: bvs+drug presence

value: N


title: S_48.1: myb36-2_SynCom_BioRep1_S48TechRep2

value: SynCom


title: S_46.3: myb36-2_SynCom_BioRep1_S46TechRep4


title: A649

description: small-RNA

source_name: Adenocarcinoma of prostate (ADK)


title: Subject3_13h_LA_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 3 treated with a Low Meal Frequency diet for 13h

value: PBMC

value: Male

tag: age(years)

tag: body mass index (bmi)

tag: body fat percentage (fm)

tag: blood pressure (bp)

tag: fasting glucose

tag: fasting insulin


title: Subject3_13h_HO_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 3 treated with a High Meal Frequency diet for 13h


title: S_46.2: myb36-2_SynCom_BioRep1_S46TechRep3


title: A642

description: small-RNA

value: plasma

tag: patient diagnosis

tag: patient age

tag: gleason score

tag: cancer size

tag: psa-value

tag: bmi


title: Subject3_24h_HO_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 3, 24h after treatment with a High Meal Frequency diet (t=24h)

tag: tissue

tag: subject number

tag: diet


title: S_46.1: myb36-2_SynCom_BioRep1_S46TechRep2

tag: genotype

tag: bacteria

tag: biorep


title: S_46: myb36-2_SynCom_BioRep1_S46TechRep1


title: A618

description: small-RNA


title: Subject3_0h_HO_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 3, before treatment with a High Meal Frequency diet (t=0h)

tag: Sex

tag: age(years)

tag: body mass index (bmi)


title: A640

description: small-RNA


title: A766

description: small-RNA


title: A607

description: small-RNA


title: S_4.2: Col-0_NB_BioRep1_S4TechRep3


title: Subject2_24h_LA_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 2, 24h after treatment with a Low Meal Frequency diet (t=24h)

tag: body fat percentage (fm)

tag: blood pressure (bp)

tag: fasting glucose


title: Subject3_0h_LA_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 3, before treatment with a Low Meal Frequency diet (t=0h)

tag: fasting insulin


title: S_4.3: Col-0_NB_BioRep1_S4TechRep4


title: A557

description: small-RNA

tag: patient diagnosis

tag: patient age

tag: gleason score


title: S_4.1: Col-0_NB_BioRep1_S4TechRep2


title: S_4: Col-0_NB_BioRep1_S4TechRep1


title: A512

description: small-RNA

tag: cancer size

tag: psa-value

tag: bmi


title: S_36.3: Col-0_SynCom_BioRep1_S36TechRep4


title: A426

description: small-RNA

tag: tissue


title: Subject1_24h_LA_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 1, 24h after treatment with a Low Meal Frequency diet (t=24h)

tag: subject number

tag: diet

value: 6.4 mmol/L


title: S_36.2: Col-0_SynCom_BioRep1_S36TechRep3

tag: genotype

tag: bacteria

tag: biorep


title: A350

description: small-RNA

value: Not Available (NA)


title: Subject2_0h_HO_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 2, before treatment with a High Meal Frequency diet (t=0h)

tag: Sex

tag: age(years)

tag: body mass index (bmi)


title: A346

description: small-RNA


title: S_36.1: Col-0_SynCom_BioRep1_S36TechRep2


title: CRISPR-LICHT PCR amplicon

city: Vienna

first: Christopher

last: Esk

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA - Institute of Molecular Biotechnology GmbH

library_source: genomic

data_processing:
demultiplexing
gRNA error correction
LID error correction (algorithm of Smith et al.)
UMI error correction (algorithm of Smith et al.)
UMI thresholding (TRUmiCount)
lineage size determination
LID cross-contamination filtering
Genome_build: -
Supplementary_files_format_and_content: tab-delimited text file with per lineage cell counts

molecule: genomic DNA

source_name: human cerebral organoids

extract_protocol:
Phenol/Chloroform
UMI-NOPE

value: cerebral organoids


title: Organoid lineage tracing

data_processing:
demultiplexing
LID error correction & filtering
lineage size determination
Supplementary_files_format_and_content: tab separeted text file with reads per lineage

extract_protocol:
Phenol/Chloroform
PCR introducing adaptors

tag: target tissue


title: Subject2_0h_LA_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 2, before treatment with a Low Meal Frequency diet (t=0h)

tag: body fat percentage (fm)

tag: blood pressure (bp)

tag: fasting glucose

tag: fasting insulin


title: Subject1_0h_LA_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 1, before treatment with a Low Meal Frequency diet (t=0h)


title: HCC827/Gefitinib

city: Zhengzhou

first: Xiangzhen

last: Kong

address: No.1 Jianshe road

country: China

institute: The First Affiliated Hospital of Zhengzhou University

data_processing:
performed on Illumina HiSeq2500
Illumina FastQC soft used for QC
The raw reads were subjected to the Illumina pipeline filter (Solexa 0.3), and then the dataset was further processed with an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats
unique sequences with length in 18~26 nucleotide were mapped to specific species precursors in miRBase 20.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs. Length variation at both 3’and 5 ends and one mismatch inside of the sequence were allowed in the alignment.
Supplementary_files_format_and_content: Expressed miRNA

source_name: drug-resistant NSCLC cell line

growth_protocol: The cisplatin-resistant non-small cell lung cancer cell line A549/DDP and the gefitinib-resistant cell line HCC827/GR were established by gradient dose treatment for almost 6 months. They and their parental cell lines were cultured in RPMI-1640 (Hyclone, MA, USA) with 10% fetal bovine serum (Gibco, NY, USA), 100 unit/ml of penicillin and 100 mg/ml of streptomycin. The drug concentrations for keeping the drug-resistance of A549/DDP or HCC827/GR were 8.3 μM and 2.5 μM, respectively.

extract_protocol:
Total RNA from the cell culture was isolated by TRIzol reagent (Invitrogen, CA, USA) and chloroform, according to the manufacturer’s protocol. Total RNA concentration and purity were measured by a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, MA, USA). RNA integrity was measured by 2100 Bioanalyzer (Agilent, CA, USA) and agarose electrophoresis.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: cell type

value: non-small cell lung cancer (NSCLC) cell line

tag: drug resistance

value: gefitinib-resistant


title: A336

description: small-RNA

tag: tissue

tag: patient diagnosis

tag: patient age

tag: gleason score

tag: cancer size

tag: psa-value

tag: bmi


title: Subject1_0h_HO_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 1, before treatment with a High Meal Frequency diet (t=0h)

tag: subject number

tag: diet

tag: Sex

tag: age(years)


title: A534

description: small-RNA


title: Subject1_24h_HO_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 1, 24h after treatment with a High Meal Frequency diet (t=24h)

tag: body mass index (bmi)

tag: body fat percentage (fm)

tag: blood pressure (bp)


title: A319

description: small-RNA


title: A549/DDP

tag: cell line

value: cisplatin-resistant


title: HCC827

source_name: drug-sensitive NSCLC cell line

tag: cell type

value: gefitinib-sensitive (parent cell line)


title: A308

description: small-RNA

value: Adenocarcinoma of prostate (ADK)


title: A549

tag: drug resistance

value: cisplatin-sensitive (parent cell line)


title: A254

description: small-RNA

tag: tissue


title: S_35.1: Col-0_SynCom_BioRep1_S35TechRep2

source_name: root

tag: genotype

tag: bacteria

tag: biorep


title: S_34.3: Col-0_SynCom_BioRep1_S34TechRep4


title: RNAseq HSB2

city: Birmingham

first: Maarten

last: Hoogenkamp

state: West Midlands

address: Vincent Drive

department: Institute of Cancer and Genomic Sciences

institute: University of Birmingham

description: poly(A)+ RNA

data_processing:
All the reads were filltered for the phred score higher than 30
RNA-Seq reads were mapped using TopHat 2.0.9
Transcripts were assembled using Cufflinks 2.0.0 based on the reference genome with quartile normalisation and effective length correction. A combined gtf file was produced using Cuffmerge 2.1.1 and used for determination of the differential gene expression using Cuffdiff 2.0.1.
Genome_build: hg38
Supplementary_files_format_and_content: bedgraph and tabular

source_name: HSB2 T-ALL cell line

extract_protocol:
RNA extraction using collumns
According to Illumina Sample Preparation Kit

value: T-ALL

value: SIL-TAL

tag: chip antibody


title: S_35: Col-0_SynCom_BioRep1_S35TechRep1


title: RNAseq CCRF_CEM

description: poly(A)+ RNA

source_name: CCRF CEM T-ALL cell line


title: A233

description: small-RNA

source_name: Adenocarcinoma of prostate (ADK)

tag: patient diagnosis

tag: patient age

tag: gleason score

tag: cancer size

tag: psa-value


title: S_34.2: Col-0_SynCom_BioRep1_S34TechRep3


title: A189

description: small-RNA

tag: bmi


title: A223

description: small-RNA


title: S_34.1: Col-0_SynCom_BioRep1_S34TechRep2


title: RNAseq DU528

description: poly(A)+ RNA

source_name: DU.528 T-ALL cell line


title: A158

description: small-RNA


title: S_36: Col-0_SynCom_BioRep1_S36TechRep1


title: RNAseq ARR

description: poly(A)+ RNA

source_name: ARR T-ALL cell line

value: unknown


title: S_35.3: Col-0_SynCom_BioRep1_S35TechRep4


title: S_35.2: Col-0_SynCom_BioRep1_S35TechRep3


title: S_18.3: myb36-2_NB_BioRep1_S18TechRep4

value: NB


title: S_34: Col-0_SynCom_BioRep1_S34TechRep1

value: SynCom


title: S_18.2: myb36-2_NB_BioRep1_S18TechRep3


title: Purified_AT2

city: Stanford

first: Ameen

middle: A

last: Salahudeen

state: CA

address: 265 Campus Drive

department: Medicine/Hematology

country: USA

institute: Stanford University School of Medicine

data_processing:
For Lung_1 through Lung_3, the Cell Ranger Single Cell Software Suite 1.1 was used to perform sample demultiplexing, barcode processing, and single cell 3’ gene counting (http://software.10xgenomics.com/single-cell/overview/welcome). UMI=5 for Lung_1 through Lung_3. For Purified AT2, data processing was carried out with Cell Ranger Single Cell Software Suite 1.2 and all sequencing parameters were according to manufacturer's protocol.
Genome_build: hg19
Supplementary_files_format_and_content: mtx: count matrix in a sparse matrix format; barcodes.tsv: barcode ids for each sample; genes.tsv: gene ids for each sample

growth_protocol: Organoid Culture with EN Media

extract_protocol:
Lung organoid cultures from separate individuals were dissociated 4 weeks after primary plating and subjected to droplet based scRNA-seq with the 10x Genomics Gemcode Single Cell 3’ platform with a 5 nucleotide UMI according to manufacturer’s protocol. Cell capture, library preparation, and sequencing were performed according to manufacturer's protocol.
Dissociated organoid cellular suspensions were loaded on a GemCode Single Cell Instrument (10x Genomics, Pleasanton, CA) to generate single-cell GEMs. Approximately 3-5,000 cells were loaded per channel for Lung_1 through Lung_3. Four technical replicates were generated per cell suspension, albeit for Lung_3 where one replicate failed to capture. Single-cell RNA-Seq libraries were prepared using GemCode Single Cell 3’ Gel Bead and Library Kit (now sold as P/N 120230, 120231, 120232, 10x Genomics) as per Zheng et al. Sequencing libraries were loaded at 2.1pM on an Illumina NextSeq500 with 2 × 75 paired-end kits using the following read length: 98bp Read1, 14bp I7 Index, 8bp I5 Index and 5bp Read2. Note that Lung_1 through Lung_3 libraries were generated before the official launch of GemCode Single Cell 3’ Gel Bead and Library Kit. Thus 5bp UMI was used (the official GemCode Single Cell 3’ Gel Bead contains 10bp UMI.). For the purified AT2 library, 10,000 cells were targeted in a single technical replicate. Libraries were generated with the 10x Genomics Chromium Single Cell 3’ platform v2 according to the manufacturer’s protocol. The library was sequenced using paired-end sequencing (26bp Read 1 and 98bp Read 2) with a single sample index (8bp) on an Illumina NextSeq 500.

tag: cell culture

value: d89 culture of purified AT2 cells

value: lung


title: S_18.1: myb36-2_NB_BioRep1_S18TechRep2


title: Lung_3_3

description: Each sub sample is a technical capture.

value: 1 month distal lung culture


title: Lung_3_2

description: Each sub sample is a technical capture.


title: S_18: myb36-2_NB_BioRep1_S18TechRep1


title: 252929711077_2_1

city: San Francisco

first: Valentina

last: Zavala

address: 1560 3rd street Apt 201

department: Medicine

institute: University of California San Francisco

description: microRNA expression in tumor sample

hyb_protocol: Cy3-labelled RNA was fragmented at 100°C for 5 minutes and then 5 minutes in ice water in a reaction volume of 45 ul containing 10x GE Blocking Agent  and Hi-RPM Hybridization Buffer, following the manufacturers instructions. Hibridization was performed on Agilent Whole Human Genome Oligo Microarrays (G4471A) for 20 hours at 55°C in a rotating hybridization oven.  After hybridization, microarrays were washed 5 minutes at room temperature with Gene Expression Wash buffer Buffer 1 (Agilent) and 5 minutes with 37°C Gene Expression Wash Buffer 2 (Agilent).

scan_protocol: Slides were scanned using an Agilent scanner (G2565).

data_processing: scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters.

source_name: Fresh frozen breast tumor

label_protocol: 100ng of total RNA was labeled with Cyanine-3 (Cy3) using the  miRNA Microarray System with miRNA Complete Labeling and Hyb Kit (G4170-90011, Agilent) according to the manufacturer's instructions, followed by purification using Micro Bio-Spin 6 columns.

extract_protocol: Total RNA was extracted from frozen tumor tissue using mirVana miRNA Isolation kit (Thermo Fisher Scientific, Inc., USA) according to the provided protocol.

tag: status


title: Lung_3_1

description: Each sub sample is a technical capture.


title: Lung_2_4

description: Each sub sample is a technical capture.


title: Lung_2_3

description: Each sub sample is a technical capture.


title: S_17.3: myb36-2_NB_BioRep1_S17TechRep4


title: S_17.2: myb36-2_NB_BioRep1_S17TechRep3


title: 252929711077_2_2

description: microRNA expression in tumor sample


title: 252929711077_1_4

description: microRNA expression in tumor sample


title: 252929711077_2_3

description: microRNA expression in tumor sample


title: Lung_2_2

description: Each sub sample is a technical capture.


title: 252929711077_1_3

description: microRNA expression in tumor sample


title: S_17: myb36-2_NB_BioRep1_S17TechRep1


title: S_17.1: myb36-2_NB_BioRep1_S17TechRep2


title: S_16.3: myb36-2_NB_BioRep1_S16TechRep4


title: 252929711077_1_2

description: microRNA expression in tumor sample


title: Lung_2_1

description: Each sub sample is a technical capture.


title: Lung_1_4

description: Each sub sample is a technical capture.


title: Lung_1_3

description: Each sub sample is a technical capture.


title: 252929711077_1_1

description: microRNA expression in tumor sample


title: 252929711076_2_4

description: microRNA expression in tumor sample


title: S_16.1: myb36-2_NB_BioRep1_S16TechRep2


title: Lung_1_2

description: Each sub sample is a technical capture.


title: 252929711076_2_2

description: microRNA expression in tumor sample


title: S_16: myb36-2_NB_BioRep1_S16TechRep1


title: 252929711076_2_3

description: microRNA expression in tumor sample


title: 252929711076_1_4

description: microRNA expression in tumor sample


title: 252929711076_2_1

description: microRNA expression in tumor sample


title: S_120.3: myb36-2_SynCom_BioRep2_S120TechRep4


title: 252929711076_1_3

description: microRNA expression in tumor sample


title: S_120.2: myb36-2_SynCom_BioRep2_S120TechRep3


title: Subject2_24h_HO_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 2, 24h after treatment with a High Meal Frequency diet (t=24h)

value: PBMC

tag: subject number

tag: diet

tag: Sex

value: Male

tag: age(years)

tag: body mass index (bmi)

tag: body fat percentage (fm)

tag: blood pressure (bp)

tag: fasting glucose

value: 4.8 mmol/L

tag: fasting insulin


title: S_120: myb36-2_SynCom_BioRep2_S120TechRep1

tag: genotype

tag: bacteria

tag: biorep


title: S_16.2: myb36-2_NB_BioRep1_S16TechRep3


title: S_120.1: myb36-2_SynCom_BioRep2_S120TechRep2


title: S_119.3: myb36-2_SynCom_BioRep2_S119TechRep4


title: S_119.2: myb36-2_SynCom_BioRep2_S119TechRep3


title: 252929711076_1_2

description: microRNA expression in tumor sample


title: S_119.1: myb36-2_SynCom_BioRep2_S119TechRep2


title: 252929711076_1_1

description: microRNA expression in tumor sample


title: 252929711075_2_4

description: microRNA expression in tumor sample


title: 252929711075_1_4

description: microRNA expression in tumor sample


title: S_119: myb36-2_SynCom_BioRep2_S119TechRep1


title: E14_Tooth_Br1

city: Helsinki

first: Jukka

last: Jernvall

address: P.O. Box 56 (Viikinkaari 9)

country: Finland

institute: University of Helsinki

hyb_protocol: The hybridization was done according to the manufacturer's instructions with minor modifications (GeneChip® WT Terminal Labeling and Hybridization User Manual for use with the Ambion® WT Expression Kit, P/N 702808 Rev. 7, Affymetrix  GeneChip® Expression Wash, Stain and Scan User Manual For Cartridge Arrays, P/N 702731 Rev. 3, Affymetrix). A hybridization cocktail is prepared including the labeled, fragmented target and hybridization controls. The target is then hybridized to the GeneChip array in cartridge format during 17-hour incubation at 45 °C. Immediately following hybridization, the array is washed and stained with streptavidin phycoerythrin conjugate using an automated protocol on the GeneChip® Fluidics Station 450.

scan_protocol: Affymetrix GeneChip® Scanner 3000

data_processing: The microarray gene signals were normalized with R aroma.affymetrix  package using Brainarray custom CDF (Version 23, released on 12th August 2019).

label: biotin

organism: Mus musculus

source_name: Molar 1 tissue

label_protocol: The labeling was done according to the manufacturer's instructions with minor modifications (GeneChip® WT Terminal Labeling and Hybridization User Manual for use with the Ambion® WT Expression Kit, P/N 702808 Rev. 7, Affymetrix). DNA is labeled by terminal deoxynucleotidyl transferase (TdT) with the Affymetrix® proprietary DNA Labeling Reagent that is covalently linked to biotin.

growth_protocol: Tooth germs were dissected carefully under microscope from E13.5 or E14.5 NMRI mice.

extract_protocol: 12-18 tooth germs were pooled and the RNA was extracted using Trizol-chloroform extraction follower uup Rneasy micro kit (Qiagen). cDNA syntehsis was done according to the manufacturer's instructions (Ambion WT Expression Kit for use with: Affymetrix GeneChip Whole Transcript (WT) Expression Arrays, User Guide, Part Number 4425209 Rev. D August 2011, Life Technologies).

tag: tissue

value: molar 1 tooth germ


title: S_118.3: myb36-2_SynCom_BioRep2_S118TechRep4


title: E14_Tooth_Br4


title: E14_Tooth_Br2


title: S_118.2: myb36-2_SynCom_BioRep2_S118TechRep3


title: E14_Tooth_Br5


title: 252929711075_1_1

description: microRNA expression in tumor sample


title: 252929711058_1_1

description: microRNA expression in tumor sample


title: E14_Tooth_Br6


title: E13_Tooth_Br2


title: S_118.1: myb36-2_SynCom_BioRep2_S118TechRep2


title: cerebral organoid 2

data_processing:
10x genomics cell ranger pipeline, version 2.1.1 (reference: GRCh38_p12_primary_assembly_genome)
Seurat 2.3 using marker genes for cluster analyses
Genome_build: GRCh38

source_name: eCas9 ready cerebral organoid, 2

extract_protocol:
Accutase / Trypsin
10x, V2

value: cerebral organoid

tag: age


title: cerebral organoid 1

source_name: eCas9 ready cerebral organoid, 1


title: 252929711075_1_3

description: microRNA expression in tumor sample


title: 252929711075_1_2

description: microRNA expression in tumor sample


title: 252929711057_2_4

description: microRNA expression in tumor sample


title: ST-06-42_Lu

city: Morgantown

first: Christina

middle: M

last: Umbright

state: WV

address: 1095 Willowdale Road

department: HELD

institute: DHHS/PHS/CDC/NIOSH

description:
total RNA including small RNAs
ST06Lu_Counts.txt
ST_06_BL_042_ST

data_processing:
Basecalls were performed using bcl2fastq/2.19.
Sequence reads were trimmed for adaptor sequence low-quality using Trimmomatic/0.35 with the following parameters ILLUMINACLIP:adapters/TruSeq2-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:85
Sequences were mapped  to Rnor6.0 whole genome using Hisat2/2.1.0 with the following parameters: -q --downstream-transcriptome-assembly --dta-cufflinks --fr --no-mixed --time --met-file
Aligned sequences were identified, sorted, and counted using Samtools/1.8 and HTSeq/0.11.2
Genome_build: Rnor6.0
Supplementary_files_format_and_content: tab-delimted text file including raw counts in a matrix containing all samples

organism: Rattus norvegicus

source_name: lung

growth_protocol: This experiment was conducted in an animal facility (NIOSH, Morgantown, WV) accredited by AAALAC International following a protocol approved by the Institutional Animal Care and Use Committee (IACUC). Male Fischer (CDF®) rats (F344/DuCrl) 3 months of age were purchased from Charles River Laboratories (Wilmington, MA). Rats were housed 2 per cage in a temperature (22-25oC) and humidity (40-60%) controlled environment following a 12hr light-dark schedule with free access to Harlan Teklad Global 18% Protein Rodent Diet, 2918 irradiated rodent chow, (Harlan Laboratories, Frederick, MD, USA) and tap water. Rodents were acclimated to the facility for 10 days before treatment commenced.

extract_protocol:
Total RNA, including miRNA and other small RNA molecules, was isolated from a piece of the lung tissue using the miRNeasy Mini Kit (Qiagen, Inc.; Valencia, CA) following the procedure provided by the manufacturer, including optional DNase treatment with RNase-Free DNase (Qiagen, Inc.; Valencia, CA).
One microgram total RNA/sample was used to create sequencing libraries using the Illumina TruSeq® Stranded Total RNA Library Prep  (Illumina, Inc., San Diego, CA) following the  manufacturer's protocol.  Briefly, following depletion of  ribosomal RNA (rRNA), the RNA samples were purified, fragmented (68°C for 5 minutes), and primed for cDNA synthesis.  The denatured and cleaved RNA fragments were purified using a bead cleanup and reverse transcribed into first strand cDNA using reverse transcriptase and random primers.  While synthesizing the double stranded cDNA, dUPT was incorporated in place of dTTP followed by the addition of a single ‘A’ nucleotide to the 3 prime ends to facilitate proper adapter ligation to each sample. Indexing adapters provided in the library preparation kit were ligated to the ends of the ds cDNA.  After adapter ligation, the samples were PCR amplified (12 cycles) to enrich the DNA fragments containing the adapter molecules and to enhance the amount of DNA in the library using a Veriti™ 96 Well Thermal Cycler (Applied Biosystems; Foster City, CA).

treatment_protocol: Exposures were performed in a whole-body inhalation chamber. Group 1: Six rats were exposed to air for 29 consecutive weeks. Group 2: Six rats were exposed to air for weeks 1 and 2; 15mg/m3, 6hours/day, 5days Min-U-Sil5 silica for week 3; and air for weeks 4-29. Group 3: Six rats were exposed to 40mg/m3, 3hours/day cigarette smoke on Tuesday and Friday of week 1; 80mg/m3, 3hours/day cigarette smoke on Tuesday and Friday of week 2; air for week 3; and 80mg/m3, 3hours/day cigarette smoke on Tuesday and Friday of weeks 4-29. Group 4: Six rats were exposed to 45mg/m3, 3hours/day cigarette smoke on Tuesday and Friday of week 1; 80mg/m3, 3hours/day cigarette smoke on Tuesday and Friday of week 2; 15mg/m3, 6hours/day, 5days Min-U-Sil5 silica for week 3; and 80mg/m3, 3hours/day cigarette smoke on Tuesday and Friday of weeks 4-29.

tag: strain

value: Fischer 344

value: male

tag: treatment

value: crystalline silica & cigarette smoke


title: E13_Tooth_Br5


title: 252929711057_2_3

description: microRNA expression in tumor sample

tag: status


title: IER3IP1_day42-53

data_processing:
Reads were preprocessed using umi2index (Lexogen) to add the UMI sequence to the read identifier, and trimmed using BBDuk v38.06 (ref=polyA.fa.gz,truseq.fa.gz k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10  minlength=20).
Reads mapping to abundant sequences included in the iGenomes UCSC hg38 reference (human rDNA, human mitochondrial chromosome, phiX174 genome, adapter) were removed using bowtie2 v2.3.4.1 alignment.
Remaining reads were analyzed using genome and gene annotation for the GRCh38/hg38 assembly obtained from Homo sapiens Ensembl release 94. Reads were aligned to the genome using star v2.6.0c, alignments were processed using collapse_UMI_bam (Lexogen) and reads in genes were counted with featureCounts (subread v1.6.2) using strand-specific read counting (-s 1) .
Differential gene expression analysis on raw counts, and principal component analysis on variance stabilized, transformed count data were performed using DESeq2 v1.18.1.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files with per gene read counts

source_name: human cerebral organoids, IER3IP1-KO

extract_protocol:
Qiagen RNEasy
Lexogen Quantseq kit, UMI inclusion

tag: time

value: cerebral organoids


title: 252929711057_2_1

description: microRNA expression in tumor sample


title: IER3IP1_day42-52


title: ST-06-40_Lu

description:
total RNA including small RNAs
ST06Lu_Counts.txt
ST_06_BL_040_ST


title: ST-06-41_Lu

description:
total RNA including small RNAs
ST06Lu_Counts.txt
ST_06_BL_041_ST


title: IER3IP1_day28-51


title: 252929711057_1_4

description: microRNA expression in tumor sample


title: IER3IP1_day28-50


title: ST-06-38_Lu

description:
total RNA including small RNAs
ST06Lu_Counts.txt
ST_06_BL_038_ST


title: ST-06-39_Lu

description:
total RNA including small RNAs
ST06Lu_Counts.txt
ST_06_BL_039_ST


title: S_118: myb36-2_SynCom_BioRep2_S118TechRep1


title: 252929711057_1_3

description: microRNA expression in tumor sample


title: 252929711048_2_4

description: microRNA expression in tumor sample


title: IER3IP1_day28-49


title: IER3IP1_day42-54


title: ST-06-37_Lu

description:
total RNA including small RNAs
ST06Lu_Counts.txt
ST_06_BL_037_ST


title: IER3IP1_day17-47


title: ST-06-29_Lu

description:
total RNA including small RNAs
ST06Lu_Counts.txt
ST_06_BL_029_TT

value: cigarette smoke


title: IER3IP1_day17-46


title: 252929711057_2_2

description: microRNA expression in tumor sample


title: ST-06-28_Lu

description:
total RNA including small RNAs
ST06Lu_Counts.txt
ST_06_BL_028_TT


title: 252929711048_2_3

description: microRNA expression in tumor sample


title: E13_Tooth_Br6


title: ST-06-27_Lu

description:
total RNA including small RNAs
ST06Lu_Counts.txt
ST_06_BL_027_TT


title: IER3IP1_day42-45


title: E13_Tooth_Br1


title: E13_Tooth_Br4


title: IER3IP1_day42-44


title: ST-06-26_Lu

description:
total RNA including small RNAs
ST06Lu_Counts.txt
ST_06_BL_026_TT


title: Lung_1_1

description: Each sub sample is a technical capture.

tag: cell culture


title: IER3IP1_day42-43


title: ST-06-25_Lu

description:
total RNA including small RNAs
ST06Lu_Counts.txt
ST_06_BL_025_TT

tag: Sex


title: ESC H3.3 CUT&RUN

city: Fukuoka

first: Takashi

last: Ishiuchi

address: 3-1-1 Maidashi, Higashi-ku

department: Medical Institute of Bioregulation

country: Japan

institute: Kyushu University

description:
processed data file:
ES_H33_CR_RPKM_bin1k.bw

data_processing:
For ChIP-seq data, paired-end reads were aligned to the mouse genome (mm10) using Bowtie2 with a default setting after removing adaptor sequences and low-quality reads by Trim Galore!.
Reads from PCR duplicates were removed by using Samtools ‘markdup’ with an option ‘-r’.
Input-normalized log2 fold enrichment in each bin was computed using deepTools bamCompare with an option '--binSize 1000'.
For CUT&RUN data, paired-end reads were aligned to the mouse genome (mm10) using Bowtie2 with an option '-X 700' after removing adaptor sequences and low-quality reads by Trim Galore!.
Reads from PCR duplicates were removed by using Samtools ‘markdup’ with an option ‘-r’.
Normalized read counts were computed using deepTools bamCoverage with options '--normalizeUsing RPKM' and '--binSize 1000'.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: ESC H3.3 CUT&RUN

growth_protocol: Male mouse ESCs (JM8A3N1) were cultured with the medium that consists of GMEM containing 15% FBS, 0.1 mM 2-mercaptoethanol, nonessential amino acid, sodium pyruvate, penicillin/streptomycin, LIF, 0.5 uM PD0325901, and 3 uM CHIR99021 on gelatin-coated plates. For ChIP-seq after mRNA injection, in vitro fertilization was performed.

extract_protocol:
For ChIP-seq, MNase-digested chromatin was used. For CUT&RUN, chromatin digested by protein A- protein G-MNase was used.
ULI-NChIP-seq protocol was used to prepare ChIP-seq libraries. CUT&RUN libraries were prepared as described before (Skene et al., eLife 2017).

treatment_protocol: For ULI-NChIP-seq for mRNA-injected 2-cell embryos, mRNA for EGFP or EGFP-p150DN (a dominant negetive p150) was injected into the cytoplasm of 1-cell embryos at 11 h post-insemination. Those developed to the late 2-cell stage were collected for ULI-N-ChIP-seq at 34 h post-insemination. For H3.3 CUT&RUN, wild-type or siRNA-transfected mESCs  were used.

tag: tissue/cell type

value: Embryonic stem cell

tag: antibody


title: IER3IP1_day17-48


title: 252929711047_2_4

description: microRNA expression in tumor sample


title: 252929711047_2_2

description: microRNA expression in tumor sample


title: ST-06-18_Lu

description:
total RNA including small RNAs
ST06Lu_Counts.txt
ST_06_BL_018_SS

value: crystalline silica


title: IER3IP1_day28-42


title: 252929711048_2_2

description: microRNA expression in tumor sample


title: IER3IP1_day28-41


title: 252929711047_1_3

description: microRNA expression in tumor sample


title: p150KD ESC H3.3 CUTandRUN rep2

description:
processed data file:
p150KDES_H33_CR_rep-merged_RPKM_bin1k.bw

source_name: p150KD ESC H3.3 CUTandRUN


title: 252929711047_1_2

description: microRNA expression in tumor sample


title: 252929711048_2_1

description: microRNA expression in tumor sample


title: 252929711047_2_3

description: microRNA expression in tumor sample


title: ST-06-17_Lu

description:
total RNA including small RNAs
ST06Lu_Counts.txt
ST_06_BL_017_SS


title: p150KD ESC H3.3 CUTandRUN rep1


title: IER3IP1_day28-40


title: ST-06-16_Lu

description:
total RNA including small RNAs
ST06Lu_Counts.txt
ST_06_BL_016_SS


title: 252929711057_1_2

description: microRNA expression in tumor sample


title: controlKD ESC H3.3 CUTandRUN rep2

description:
processed data file:
contKDES_H33_CR_rep-merged_RPKM_bin1k.bw

source_name: controlKD ESC H3.3 CUTandRUN


title: ST-06-15_Lu

description:
total RNA including small RNAs
ST06Lu_Counts.txt
ST_06_BL_015_SS


title: 252929711046_2_4

description: microRNA expression in tumor sample


title: IER3IP1_day17-39


title: controlKD ESC H3.3 CUTandRUN rep1

source_name: controlKD ESC H3.3 CUTandRUN rep1


title: IER3IP1_day17-38


title: ST-06-14_Lu

description:
total RNA including small RNAs
ST06Lu_Counts.txt
ST_06_BL_014_SS


title: NAIL_ΔNFκB_DSS_colon_rep2

city: Singapore

first: Vinay

last: Tergaonkar

address: 61 Biopolis Drive,  Proteos

country: Singapore

institute: Institute of Molecular and Cell Biology

data_processing:
By using HISAT2 v2.1, spliced alignment was performed on the quality trimmed sequences against Mus musculus (mm10) genome index, which consists of transcriptome splicing information.
Stranded alignment (first-strand) was applied and the alignment was finally coordinate sorted using Samtools v1.8.
Gene-level expression counts were quantified (strand-specific read counting) using featureCounts (subread-v1.6.2 package) by reference to the gene annotation obtained from Ensembl (version 96) database.
Genome_build: mm10
Supplementary_files_format_and_content: read counts

source_name: colon

extract_protocol:
RNA was isolated from the distal colon of the mice treated with or without DSS using Trizol followed by column purification and DNAse treatment.
RNA-Seq library was prepared by Illumina Truseq Total RNA sequencing kit according to manufacturer instructions.
Paired-end sequencing was performed using Illumina HiseqX, 2x150bp.

treatment_protocol: WT and NAIL-ΔNFκB  mice were treated with or without DSS (3%) for 4 days followed by 4 days of normal water.

value: colon

value: 8-10 weeks

value: NAIL-{delta}NFkappaB

value: DSS


title: IER3IP1_day17-37


title: ST-06-13_Lu

description:
total RNA including small RNAs
ST06Lu_Counts.txt
ST_06_BL_013_SS


title: NAIL_ΔNFκB_DSS_colon_rep1


title: 252929711048_1_3

description: microRNA expression in tumor sample


title: 252929711046_2_3

description: microRNA expression in tumor sample


title: IER3IP1_day00-36


title: 252929711048_1_4

description: microRNA expression in tumor sample


title: ST-06-06_Lu

description:
total RNA including small RNAs
ST06Lu_Counts.txt
ST_06_BL_006_AA

value: air


title: IER3IP1_day00-35


title: 252929711046_2_2

description: microRNA expression in tumor sample


title: NAIL_ΔNFκB_untreated_colon_rep1

value: untreated


title: 252929711047_1_1

description: microRNA expression in tumor sample


title: NAIL_ΔNFκB_untreated_colon_rep2


title: 252929711048_1_2

description: microRNA expression in tumor sample


title: ST-06-05_Lu

description:
total RNA including small RNAs
ST06Lu_Counts.txt
ST_06_BL_005_AA


title: IER3IP1_day00-34


title: ST-06-04_Lu

description:
total RNA including small RNAs
ST06Lu_Counts.txt
ST_06_BL_004_AA


title: 252929711046_2_1

description: microRNA expression in tumor sample


title: WT_day42-33

source_name: human cerebral organoids, H9

value: wild type


title: NAIL_WT_DSS_colon_rep1

value: WT


title: WT_day42-32


title: NAIL_WT_DSS_colon_rep2


title: ST-06-03_Lu

description:
total RNA including small RNAs
ST06Lu_Counts.txt
ST_06_BL_003_AA


title: ST-06-02_Lu

description:
total RNA including small RNAs
ST06Lu_Counts.txt
ST_06_BL_002_AA


title: WT_day42-31


title: NAIL_WT_untreated_colon_rep2


title: 252929711046_1_4

description: microRNA expression in tumor sample


title: ST-06-01_Lu

description:
total RNA including small RNAs
ST06Lu_Counts.txt
ST_06_BL_001_AA


title: 252929711048_1_1

description: microRNA expression in tumor sample


title: V7_EtOH rep3

city: Illkirch

first: Jocelyn

last: CERALINE

address: 1, rue Laurent Fries

department: IGBMC

country: France

institute: University of Strasbourg

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Alignment : Reads were mapped onto hg38 assembly of human genome using Tophat v2.0.14 and bowtie2 v2.1.0.
Quantification : Gene expression was quantified using HTSeq v0.6.1 and Ensembl release 84 annotations.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-separated values file containing raw read counts in each sample.

source_name: LNCaP cell line

growth_protocol: LNCaP cells, clone FGC (ECACC) were cultured in RPMI-1640 media supplemented with 10% tetracyclin-free fetal bovine serum (FBS), 10 mM HEPES, 2 mM L-glutamine, 100 U/mL penicillin, 100 μg/mL streptomyci  and 1 mM pyruvate.

extract_protocol:
Total RNA was extracted using Nucleospin® RNA II assay (Macherey-Nagel, France)
RNA-Seq libraries were generated from 500 ng of total RNA using TruSeq Stranded mRNA Sample Preparation Kit (Illumina, Part Number RS-122-2101). Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman Coulter) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

treatment_protocol:
Transduced-LNCaP cells were cultured in the presence of 20 ng/mL of Doxycycline and Ethanol as vehicle in place of 10 nM DHT
After 48h of starvation in hormone-depleted medium, cells were treated for 24h with 20 ng/mL doxycycline and 10 nM DHT or ethanol as vehicle as indicated.

tag: cell type

value: Prostate cancer cell

tag: cell line

value: LNCaP

tag: transduction

value: Transduction with lentiviral particles for doxycyclinbe-induced expression of EGFP-ARV7

tag: agent


title: NAIL_WT_untreated_colon_rep1

tag: genotype


title: WT_day28-29


title: WT_day28-28


title: V7_EtOH rep1

value: 20 ng/mL of Doxycycline and Ethanol as vehicle in place of 10 nM DHT


title: Frd05

city: Not Hispanic or Latino

first: Sheng

last: Zhao

address: #87, Dingjiaqiao, Gulouqu

department: Biochemistry and Molecular biology

institute: Southeast University

data_processing:
Illumina Hiseq X10 platform to get the raw data
Clean reads were generated from raw reads by Trimmomatic (ver. 0.36) using default parameters
The clean reads were mapped to reference genome (Ensembl Mus_musculus GRCm38.90) with Hisat2 (ver. 2.1.0)
Mapped data were assembled by Stringtie (ver. 1.3.3) with default parameters
Group comparison from Ballgown (ver. 2.5.3) R package was performed to estimate the differential gene expression by the fragment per kilobase per million mapped reads (FPKM)
Gene set enrichment analysis (GSEA) was then performed to generate the enrichment scores (ES)
Effectsize were calculated in volcano plot
Genome_build: Ensembl Mus_musculus GRCm38.90
Supplementary_files_format_and_content: Excel file of differential expressed genes (p<0.01, FPKM, the differential expression data and GSEA scores and Effectsize in volcano plot, etc.)

source_name: islets

growth_protocol: Standard animal care

extract_protocol:
Islets were isolated and stored in Trizol reagent and then flash frozen on dry ice.RNA was harvested using Trizol reagent.
prepared following manufacturer recommendations of VAHTSTM Total RNA-seq (H/M/R) Library Prep Kit for Illumina (Vazyme Biotech Co.,Ltd, Nanjing, China)

treatment_protocol: Normal food or high fat food feeding

value: pancreas

tag: tissue compartment

value: islets

tag: diet

value: high fat food for 22 weeks


title: V7_EtOH rep2


title: WT_day17-27

tag: tissue

value: cerebral organoids


title: Frd04


title: V7_DHT rep2

treatment_protocol:
Transduced-LNCaP cells were cultured in the presence of 20 ng/mL of Doxycycline and 10 nM DHT
After 48h of starvation in hormone-depleted medium, cells were treated for 24h with 20 ng/mL doxycycline and 10 nM DHT or ethanol as vehicle as indicated.

value: 20 ng/mL of Doxycycline and 10 nM DHT


title: V7_DHT rep3


title: Frd03


title: V7_DHT rep1


title: Ctr13

value: normal food for 22 weeks


title: WT_day42-15


title: Q640X_EtOH rep3

value: Transduction with lentiviral particles for doxycyclinbe-induced expression of EGFP-ARQ640X


title: Ctr12


title: WT_day42-14


title: Q640X_EtOH rep2


title: WT_day42-13


title: Q640X_EtOH rep1


title: IFN-β_RNA

city: Toronto

first: Melanie

last: Girard

address: 1 King's College Circle

department: Immunology

country: Canada

institute: University of Toronto

data_processing:
Library strategy: CITE-seq
Cellranger mkfastq v3.0.1 to generate FASTQ.
Cellranger count v3.0.1 to generate cDNA-derived count matrices. Set to 5000 cells.
CITE-seq-Count v1.4.2 to generate HTO and ADT derived expression matrices.
Genome_build: GRCh38
Supplementary_files_format_and_content: Filtered feature-barcode matrices for ADT, HTO and RNA data in Market Exchange Format for sparse matrices.

source_name: Peripheral blood CD1c+ DC and monocytes

growth_protocol: Human PBMC were isolated from peripheral blood using FICOLL density gradient centrifugation.

extract_protocol:
Cells were partitioned using the 10X Chromium controller.
cDNA libraries were prepared using the 10X Chromium Single Cell 3' v2 Reagent kit, while HTO and ADT-derived libraries were prepared according to the CITE-seq protocol developed by the Technology Innovation Lab at the New York Genome Center (https://cite-seq.com).

treatment_protocol: PBMC were cultured for 18h with or without recombinant human IFN-β (250 U/ml) prior to enrichment of CD1c+ dendritic cells and monocytes using positive and negative selection kits, respectively, and labelling with TotalSeq-A antibodies. Each donor was labeled with a unique hashtag antibody.

value: Peripheral blood CD1c+ dendritic cells and monocytes

value: 18h culture with IFN-beta

value: TotalSeq-A


title: WT_day28-12


title: IFN-β_HTO


title: WT_day28-11


title: WT_day17-26


title: Q640X_DHT rep3


title: Q640X_DHT rep2


title: IFN-β_ADT


title: WT_day17-9


title: Ctr07


title: CTRL_RNA

value: 18h culture without IFN-beta


title: Q640X_DHT rep1


title: WT_EtOH rep3

value: Transduction with lentiviral particles for doxycyclinbe-induced expression of EGFP-ARWT


title: CTRL_HTO


title: CTRL_ADT


title: WT_day17-8

value: wild type


title: WT_EtOH rep2

value: Prostate cancer cell


title: WT_day17-7


title: WT_day28-10


title: WT_EtOH rep1

value: LNCaP


title: WT_day00-6


title: H27948_stomach_sciRNA

city: Seattle

first: Junyue

last: Cao

state: WA

address: Foege Building S-210, 3720 15th Ave NE

department: Department of Genome Sciences

institute: University of Washington

data_processing:
Read alignment and gene count matrix generation for the single cell RNA-seq was performed using the pipeline that we developed for sci-RNA-seq3 (Cao et al. 2019) with minor modifications: Duplicates were removed using the unique molecular identifier (UMI) sequence (ED < 2, including insertions and deletions), reverse transcription (RT) index, hairpin ligation adaptor index and read 2 end-coordinate.
Genome_build: human reference genome (hg19)
Supplementary_files_format_and_content:
S1_metadata_cells.txt: Metadata of high-quality cells. Includes sample metadata and various per-cell QC stats, Louvain cluster id and cell type annotation, for each of the 4,062,965 high-quality cells used in the downstream analyses.
S2_Metadata_genes.txt: Metadata of genes. Includes gene id, short name and gene type information for each gene.
S3_gene_count.loom: Gene count matrix of cells. Includes expression UMI values for each gene in each cell. The gene count is stored in loom-formatted hdf5 file (read with function "scanpy.read_loom" in python)
S4_gene_expression_tissue.txt: Matrix of gene expression values across tissues. Includes normalized gene expression values (transcripts per million) for each tissue.
S5_gene_fraction_tissue.txt: Matrix of positive cell ratio for each gene across tissues. Includes the ratio number of cells expressing each gene in each tissue.
S6_gene_expression_celltype.txt: Matrix of positive cell ratio for each gene across tissues. Includes the ratio number of cells expressing each gene in each tissue.
S7_gene_fraction_celltype.txt: Matrix of positive cell ratio for each gene across main cell types. Includes the ratio number of cells expressing each gene for each type in each tissue.
S8_DE_gene_cells.txt: Differential gene expression test results for main cell types within each organ. For each gene, the “max_cell_type” is the cell type with the highest expression within the organ by transcripts per million (TPM) (“max.expr”). The “second_cell_type” is the cell type with the second highest expression within the organ by transcripts per million (TPM) (“second.expr”). The “fold.change” is the fold change between the max expression and second max expression. The “qval” is the false detection rate (one-sided likelihood ratio test with adjustment for multiple comparisons) for the differential gene expression test across different cell types within the organ.

molecule: polyA RNA

source_name: RNA-seq of Homo sapiens: Fetus stomach

growth_protocol: Human fetal tissues were obtained by the UW Birth Defects Research Laboratory (BDRL) under a protocol approved by the University of Washington Institutional Review Board. Gestational age, reported as the number of weeks post-fertilization, was estimated from fetal foot length. Tissues of interest were isolated and rinsed in 1X HBSS (with Ca2+ and Mg2+) then blotted dry on a semi-damp gauze. Dried tissue was placed on a heavy-duty foil or in cryotube, snap frozen in liquid nitrogen, and then stored at -80°C.

extract_protocol:
On the day of nuclei isolation, aliquots of tissue powder (0.1-1g) were first incubated with 1 mL ice-cold cell lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630 from (Buenrostro et al. 2013), modified to also include 1% SUPERase In (Thermo Fisher Scientific, AM2696) and 1% BSA (NEB, B9000S)) and then transferred to the top of a 40 µm cell strainer (VWR, 10199-654). Tissues were homogenized through the strainer with the rubber tip of a syringe plunger (VWR, BD309646) in 4 ml cell lysis buffer. The filtered nuclei were then transferred to a new 15 ml tube (VWR, 21008-936) and pelleted by centrifuge at 500xg for 5 min and washed once with 1 ml cell lysis buffer. The nuclei were fixed in 5 ml ice-cold 4% paraformaldehyde (EMS, 15-4-100) for 15 min on ice. After fixation, the nuclei were washed twice in 1 ml nuclei wash buffer (cell lysis buffer without IGEPAL), and re-suspended in 500 µl nuclei wash buffer. The samples were split into two tubes with 250 µl in each tube and flash frozen in liquid nitrogen. For human cell extraction in renal and digestive organs (kidney, pancreas, intestine, and stomach) and paraformaldehyde fixation, we followed the procedure described in (Thomsen et al. 2016).
sci-RNA-seq3 library: The paraformaldehyde fixed nuclei were processed similarly to the published sci-RNA-seq3 protocol (Cao et al. 2019). For paraformaldehyde fixed cells, frozen fixed cells were thawed on 37°C water bath, spun down at 500xg for 5 min, and incubated with 500ul PBSI (1 x PBS, pH 7.4, 1% BSA, 1% SuperRnaseIn)  including 0.2% Triton X-100 for 3min on ice. Cells were pelleted and resuspended in 500ul nuclease free water including 1% SuperRnaseIn. 3ml 0.1N HCl were added into the cells for 5min incubation on ice (Rosenberg et al. 2018). 3.5ml Tris-HCl (pH = 8.0) and 35ul 10% Triton X-100 were added into cells to neutralize HCl. Cells were pelleted and washed with 1ml PBSR. Cells were pelleted and resuspended in 100ul PBSI. The following steps were similar with the sci-RNA-seq3 protocol (with paraformaldehyde fixed nuclei) with slight modifications: (1) We distributed 20,000 fixed cells (instead of 80,000 nuclei) per well for reverse transcription. (2) We replaced all nuclei wash buffer in following steps with PBSI. (3) All nuclei dilution buffer were replaced with PBS + 1% BSA.

tag: development stage

value: Fetus tissues

value: Fetus stomach


title: H27948_pancreas_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus pancreas

value: Fetus pancreas


title: SUDEP DBA/1 mice-3

city: Chengdu

first: Ling

last: Liu

state: Sichuan

address: Wai Nan Guo Xue Lane 37 #

department: Department of neurology

institute: West China Hospital, Sichuan University

description: Biological replicate 3 of 4

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide.

scan_protocol: Scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies).
Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR.

source_name: Brain tissue

label_protocol: mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen).

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

tag: gender

value: male

tag: age

value: 5 weeks


title: SUDEP DBA/1 mice-4

description: Biological replicate 4 of 4


title: WT DHT 24h rep3


title: SUDEP DBA/1 mice-2

description: Biological replicate 2 of 4


title: SUDEP DBA/1 mice-1

description: Biological replicate 1 of 4


title: WT_day00-5

value: cerebral organoids


title: Normol DBA/1 mice-2

description: Biological replicate 2 of 4


title: Normol DBA/1 mice-3

description: Biological replicate 3 of 4


title: H27948_kidney_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus kidney

value: Fetus kidney


title: Normol DBA/1 mice-4

description: Biological replicate 4 of 4


title: ST-06-30_Lu

description:
total RNA including small RNAs
ST06Lu_Counts.txt
ST_06_BL_030_TT

tag: strain

value: Fischer 344

tag: treatment

value: cigarette smoke


title: WT_day00-4

tag: time


title: H27948_intestine_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus intestine

value: Fetus intestine


title: NUC treated HBV LDB_57

city: Bethesda

first: Barbara

last: Rehermann

state: Maryland

address: 10 Center Drive

department: Liver Diseases Branch

institute: National Institutes of Health

description: nothing special

hyb_protocol: Hybridization was performed according to hybridization protocol for nCounter XT CodeSet Gene Expression Assays Including Panels. Briefly, hybridization buffer and reporter codeset were mixed first, and this mastermix was added to samples (total RNA), finally hybridization reaction was completed by adding capture probeset.

scan_protocol: The cartridge was read with maximum sensitivity (280 FOV).

data_processing: Data from all runs were imported into nSolver version 4.0 (NanoString Technologies), matched to corresponding Reporter Library File (RLF), and subjected to quality control using the software quality metrics with default cutoff criteria

source_name: peripheral blood mononucler cells

extract_protocol: Total RNA was extracted from PBMC using QIAshredder and RNeasy Mini Kit (Qiagen, Germantown, MD), and 100 ng of total RNA was used for hybridization.

treatment_protocol: Frozen PBMCs were thawed and total RNA was extracted.

tag: diseases

value: chronic HBV

tag: hbeag (+/-)

value: HBeAg-

tag: therapy that the patient received

value: long term NUC


title: H27915_kidney_sciRNA


title: C3 EtOH 24h rep3

tag: cell type

value: Transduction with lentiviral particles for doxycyclinbe-induced expression of EGFP as control

value: 20 ng/mL of Doxycycline and Ethanol as vehicle in place of 10 nM DHT


title: NUC treated HBV LDB_55

description: nothing special


title: NUC treated HBV LDB_53

description: nothing special


title: WT DHT 24h rep1

value: Prostate cancer cell

tag: cell line

value: Transduction with lentiviral particles for doxycyclinbe-induced expression of EGFP-ARWT

value: 20 ng/mL of Doxycycline and 10 nM DHT


title: WT DHT 24h rep2

value: LNCaP

tag: transduction


title: H27915_intestine_sciRNA

value: Fetus tissues


title: Normol DBA/1 mice-1

description: Biological replicate 1 of 4

value: male


title: ∆FvstuA 2/8 rep 1

city: Athens

first: Anthony

middle: E.

last: Glenn

state: GA

address: 950 College Station Rd

department: Toxicology & Mycotoxin Research Unit

institute: USDA, ARS, USNPRC, R.B. Russell Research Center

description:
Deletion mutant ∆FvstuA_2/8, Rep1
FvstuA_2_8_FPKM

data_processing:
RNA Sequence data analysis was done with the Tuxedo suite of tools on the Galaxy server at the University of Georgia
FastQC
Paired end-reads mapped to F. verticillioides reference genome (FungiDB, www.fungidb.org, release 31, genome release date 2016-10-12) originally downloaded from the Broad Institute Fusarium Comparative Database but now available at FungiDB, with TopHat.
Mapped reads were assembled into transcriptome by Cufflinks and gene expression was quantified as fragments per kilobase per million mapped reads (FPKM).
Cuffdiff was used to perform differentially expressed (DE) genes between M3125 and ∆FvstuA strains, probability (p) ≤0.05 and false discovery rate (FDR; q value) < 0.05 was applied.
The DEGs were assigned functional categories as per the Gene Ontology (GO) system using Blast2GO and FungiDB.
Genome_build: Fusarium verticillioides genome originally downloaded from the Broad Institute Fusarium Comparative Database but now available at FungiDB, www.fungidb.org, release 31, genome release date 2016-10-12.
Supplementary_files_format_and_content: FPKM values in tab delimited table format for all treatments and genes (.txt file)

organism: Fusarium verticillioides

source_name: GYAM liquid culture

growth_protocol: Fungal spore suspensions (WT M3125 strain and the deletion mutants ∆FvstuA1/2, ∆FvstuA1/7, ∆FvstuA2/8) were grown in GYAM medium in sterile 14 ml snap-cap tubes and grown at 27°C at 225 rpm in the dark for 30 h with the caps unsnapped.

extract_protocol:
Fungal pellets were obtained by centrifuging fungal liquid cultures in Z matrix extraction tubes at 10,000 x g for 5 min at 4°C. The  pellets (with addition of lysis buffer from PureLink RNA kit) were homogenized in a Fast Prep-24 5G instrument and then vortexed for 20 min. Total RNA extraction from the resulting lysate was conducted with PureLink RNA Mini Kit as per the manufacturer’s instructions with On-column PureLink DNase Treatment.
Twelve RNA libraries (WT M3125 strain and the deletion mutants ∆FvstuA1/2, ∆FvstuA1/7, ∆FvstuA2/8, three biological replicates each) were made with the Illumina TruSeq Stranded mRNA Library Prep Kit

treatment_protocol: No treatment

tag: genotype/variation

value: Deletion mutant <delta>FvstuA_2/8

tag: time of growth

value: 30 hours


title: ∆FvstuA 2/8 rep 3

description:
Deletion mutant ∆FvstuA_2/8, Rep3
stuA_2_8_D


title: H27913_kidney_sciRNA

value: Fetus kidney


title: ∆FvstuA 2/8 rep 2

description:
Deletion mutant ∆FvstuA_2/8, Rep2
stuA_2_8_C


title: NUC treated HBV LDB_51

description: nothing special


title: ∆FvstuA 1/7 rep 3

description:
Deletion mutant ∆FvstuA_1/7, Rep3
FvstuA_1_7_FPKM

value: Deletion mutant <delta>FvstuA_1/7


title: C3 EtOH 24h rep1

tag: agent


title: C3 EtOH 24h rep2


title: H27913_intestine_sciRNA


title: C3 DHT 24h rep2


title: NUC treated HBV LDB_49

description: nothing special


title: H27909_stomach_sciRNA

value: Fetus stomach


title: NUC treated HBV LDB_47

description: nothing special

value: HBeAg+


title: H27909_kidney_sciRNA


title: C3 DHT 24h rep3


title: NUC treated HBV LDB_45

description: nothing special

value: chronic HBV


title: Hu2F High_3

city: New Haven

first: Xiao

last: Hu

state: CT

address: 10 Amistad ST

department: Cell Biology

institute: Yale University

data_processing:
RNA-seq reads were mapped to mouse genome (mm10) or human genome (hg38) with TopHat2. Gene abundance was calculated using cuffnorm, which outputs read counts and the number of mapped fragments per kilobase of exon per million fragments (RPKM). Genes with RPKM ≥1 in two or more samples were selected for further analysis. Differentially expressed genes were identified by Cuffdiff followed by cutting off with FDR-adjusted P value < 0.05 and fold change > 2.
Genome_build: mm10, hg38

source_name: Reprogramming human fibroblasts

growth_protocol: Reprogramming MEFs were cultured in mES medium + Dox (2 ug/mL). Medium was changed every other day. Reprogramming human secondary fibroblasts were cultured in mTeSRTM1 complete kit (STEMCELL technologies, 85850). Medium was changed every other day.

extract_protocol:
Total RNA was extracted with Trizol (ThermoFisher Scientific, invitrogen).
RNA-seq libraries were prepared with TruSeq Stranded mRNA Library Prep Kit (Illumina, RS-122-2101).

treatment_protocol: GFP low (10%) and GFP high (10%) cells were FACS-sorted.

value: human fibroblasts

tag: reprogramming day

value: Day 7


title: ∆FvstuA 1/7 rep 2

description:
Deletion mutant ∆FvstuA_1/7, Rep2
FvstuA_1_7_FPKM


title: H27909_intestine_sciRNA

tag: tissue

value: Fetus intestine


title: Hu2F High_2


title: ∆FvstuA 1/2 rep 3

description:
Deletion mutant ∆FvstuA_1/2, Rep3
FvstuA_1_2_FPKM

value: Deletion mutant <delta>FvstuA_1/2


title: ∆FvstuA 1/2 rep 2

description:
Deletion mutant ∆FvstuA_1/2, Rep2
FvstuA_1_2_FPKM


title: ∆FvstuA 1/2 rep 1

description:
Deletion mutant ∆FvstuA_1/2, Rep1
FvstuA_1_2_FPKM


title: NUC treated HBV LDB_43

description: nothing special

value: HBeAg-

value: long term NUC


title: H27876_stomach_sciRNA

tag: development stage


title: NUC treated HBV LDB_39

description: nothing special


title: ∆FvstuA 1/7 rep 1

description:
Deletion mutant ∆FvstuA_1/7, Rep1
FvstuA_1_7_FPKM


title: Hu2F High_1


title: NUC treated HBV LDB_41

description: nothing special


title: H27876_pancreas_sciRNA

value: Fetus pancreas


title: Hu2F Low_3


title: H27876_kidney_sciRNA


title: WT M3125 rep 3

description:
Wild type, control, Rep3
M3125_FPKM

value: Wild-type


title: NUC treated HBV LDB_37

description: nothing special


title: WT M3125 rep 2

description:
Wild type, control, Rep2
M3125_FPKM


title: H27876_intestine_sciRNA

value: Fetus tissues


title: NUC treated HBV LDB_35

description: nothing special


title: WT M3125 rep 1

description:
Wild type, control, Rep1
M3125_FPKM


title: Hu2F Low_2


title: Hu2F Low_1


title: H27870_pancreas_sciRNA


title: H27870_stomach_sciRNA


title: Cas9_NT_gRNA_2

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

description: poly(A)+ RNA

data_processing:
Raw reads were adapter-trimmed using Cutadapt (version 1.14)
Sequenced reads were aligned to hg19 genome using STAR (version 2.5.2b) and sorted using samtools (version 1.5)
Gene counts were quantified from sorted BAM files using featureCounts (version 1.5.0) of the Subread (Liao et al., Nucleic Acids Research 2013) package using "gene" as a metafeature. Annotated gene length and gene counts were subsequently used to calculate transcript per-million (TPM) for each gene in each library.
For downsampling prior to downstream editing analysis, samtools view -bs INT.FRAC was used for proportional downsampling of read pairs to achieve sampling depth between 15-35 million aligned reads
Aligned BAM files were run through SAILOR (v1.0.4) using the following parameters-- min_variant_coverage: 5, alpha: 0, beta: 0, edit_fraction: 0.01
BED files that are output corresponding to positive and negative strands of the genome from SAILOR are combined into one BED file and filtered based upon confidence score (Washburn et al., Cell Reports 2014)
Recurrent sites between replicates were determined using pybedtools (version 0.8.0) intersect with the following options: wo=True, s=True
Genome_build: hg19
Supplementary_files_format_and_content: Matrix tables containing normalized transcripts per-million (TPM) data for every annotated gene; BED files containing editing events per library

source_name: HEK293T cells

growth_protocol: HEK293T cells were maintained in DMEM supplemented with 10% Fetal Bovine Serum and routinely passaged 2-3 times per week upon reaching confluency

extract_protocol:
Total RNA was collected with TRIzol reagent using manufacturers' protocol
Libraries were constructed using the TruSeq Stranded mRNA Library Prep kit (Cat# 20020594) according to manufacturers' instructions
poly(A)+ RNA-seq

treatment_protocol: In a 24 well-plate format, cells were transfected with 100 ng Cas-ADAR2DD plasmid and 400 ng gRNA plasmid using Lipofectamine 3000 reagent and allowed to incubate for 48 hours

value: Immortalized human epithelial kidney cell

tag: treatmant

value: Transfected with dCas9-ADAR2(E488Q) + NT gRNA for 48 hours


title: uninfected control LDB_31

description: nothing special

value: uninfected control


title: H27870_kidney_sciRNA

value: Fetus kidney


title: uninfected control LDB_30

description: nothing special


title: uninfected control LDB_29

description: nothing special


title: NUC treated HBV LDB_33

description: nothing special


title: Cas9_CYFIP2_gRNA_2

description: poly(A)+ RNA

value: Transfected with dCas9-ADAR2(E488Q) + CYFIP2 gRNA for 48 hours


title: H27799_intestine_sciRNA


title: H27798_kidney_sciRNA


title: uninfected control LDB_28

description: nothing special


title: H27798_intestine_sciRNA


title: Liver - HFD_O3 - Rep4 [s3207]

city: clermont ferrand

first: frederic

last: capel

address: 28 place henri dunant

department: alimentation humaine

institute: INRA

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE v2 microarray (8X60K, Design 074809  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 074809_D_F_20150624). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 20 out of 24 microarrays or with a minimal weight of 4 per group from at least one experimental group. At this step, 34807 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 32176 rows each corresponding to a unique ProbeName (provided as data Matrix).

source_name: Liver - HFD_O3

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

extract_protocol: RNA were isolated using the Trizol reagent and washing steps with Isopropanol/Ethanol procedure before solubilization in sterile water

tag: Sex

value: male

tag: group id

tag: lineage

tag: diet

value: HFD

value: liver


title: uninfected control LDB_27

description: nothing special

tag: diseases


title: Ovarian Clear Cell Carcinoma cell line SMOV-2

type: genomic

city: London

first: Gabriel

middle: E

last: DiMattia

state: ONTARIO

address: 750 Base Line Rd E

department: Biochemistry

institute: Western University

description: Affymetrix CytoScan HD Reagent kit

hyb_protocol: 50°C, 60 rpm for 16 hr-18hr

scan_protocol: Affymetrix GeneChip Scanner 3000 (#3)

data_processing:
ChAS
Genotype Call (SNP call)

label_protocol: Affymetrix CytoScan HD Reagent kit

growth_protocol: Cell lines were cultured in Dulbecco’s modified Eagle medium/Ham’s F12 (Wisent) and supplemented with 10% FBS (Wisent). Cells were maintained in at 37 °C and a CO2 concentration of 5%. Cells were allowed to reach ~90% confluency at which point the media was aspirated and cells were washed with phosphate buffered saline (PBS) and exposed to 2 mL of trypsin/EDTA until cells detached from plate. Cells were resuspended in 10 mL of media and then split onto new plates at a minimum of a 1:3 dilution.

extract_protocol: Wizard Genomic DNA Purification Kit (Promega) was used to isolate DNA from cells as per manufacturers protocol.

value: Ovarian Clear Cell Carcinoma cell line


title: uninfected control LDB_26

description: nothing special

tag: hbeag (+/-)


title: Cas13b_NT_gRNA_1

description: poly(A)+ RNA

value: Transfected with dCas13b-ADAR2(E488Q) + NT gRNA for 48 hours


title: Cas9_CYFIP2_gRNA_1

description: poly(A)+ RNA


title: Ovarian Clear Cell Carcinoma cell line 105C

description: Affymetrix CytoScan HD Reagent kit


title: Liver - HFD_Cont - Rep6 [s3184]

source_name: Liver - HFD_Cont

tag: strain

value: Control fatty acid


title: Cas13b_NT_gRNA_2

description: poly(A)+ RNA

tag: cell type


title: Cas13b_CYFIP2_gRNA_2

description: poly(A)+ RNA

value: Transfected with dCas13b-ADAR2(E488Q) + CYFIP2 gRNA for 48 hours


title: Cas13b_CYFIP2_gRNA_1

description: poly(A)+ RNA


title: H27772_intestine_sciRNA

value: Fetus intestine


title: uninfected control LDB_23

description: nothing special

tag: therapy that the patient received


title: uninfected control LDB_25

description: nothing special


title: Liver - STD_Cont - Rep8 [s3186]

source_name: Liver - STD_Cont

value: STD


title: H27771_lung_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus lung

value: Fetus lung


title: Liver - HFD_Cont - Rep7 [s3185]


title: Liver - HFD_Cont - Rep4 [s3165]


title: Ovarian Clear Cell Carcinoma cell line OVSAYO

description: Affymetrix CytoScan HD Reagent kit


title: Liver - STD_Cont - Rep3 [s3149]


title: Cas9_NT_gRNA_1

description: poly(A)+ RNA


title: C3 DHT 24h rep1

value: Prostate cancer cell

tag: cell line

value: LNCaP

tag: transduction

value: Transduction with lentiviral particles for doxycyclinbe-induced expression of EGFP as control

value: 20 ng/mL of Doxycycline and 10 nM DHT


title: uninfected control LDB_22

description: nothing special

value: uninfected control


title: H27771_kidney_sciRNA

value: Fetus tissues

value: Fetus kidney


title: H27771_intestine_sciRNA


title: VC (control condition)

city: Gurugram

first: Mandira

last: Kochar

state: Haryana

address: Nanobiotechnology Centre, Sustainable Agriculture Division, TERI Gram, Gual Pahari, Gurugram-Faridabad Highway

department: Sustainable Agriculture Division

country: India

institute: The Energy and Resources Institute, New Delhi

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence using CutAdapt and Trimmomatic  v0.36
Filtered reads mapped to A. brasilense Sp245 whole genome (GenBank Assembly accession: GCA_000237365.1) using Bowtie v2.1.0
The aligned reads were used to generate counts data using Rsubread package (Version 1.16.1) in R using the GCF file of the reference genome
The gene counts were converted into RPKM values using the edgeR package in R.
Genome_build: A. brasilense Sp245 (GenBank Assembly accession: GCA_000237365.1)
Supplementary_files_format_and_content: tab-delimited text files include count values of the sequenced RNA reads in each Sample

organism: Azospirillum baldaniorum

source_name: isolated from surface sterilized wheat root

growth_protocol: The wild-type strain Sp245 was grown in buffered standard succinate medium (SSM) under two nutritional conditions: control (SSM with full strength of nitrogen) and stress-inducing (SSM with half strength of nitrogen). The temperature used for incubation was 30 degrees C and cells were grown for 12h prior to RNA  extraction.

extract_protocol:
Total RNA was extracted using the Ambion PureLink RNA Mini kit (Invitrogen).
Small RNA libraries were constructed for sequencing according to the Illumina TruSeq Small RNA library protocol

value: pure bacterial culture

tag: growth condition

value: strain Sp245


title: H27634_thymus_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus thymus

value: Fetus thymus


title: H27634_spleen_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus spleen

value: Fetus spleen


title: uninfected control LDB_20

description: nothing special


title: uninfected control LDB_21

description: nothing special


title: H27634_muscle_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus muscle

value: Fetus muscle


title: Ovarian Clear Cell Carcinoma cell line 105CT

description: Affymetrix CytoScan HD Reagent kit

source_name: Ovarian Clear Cell Carcinoma cell line OVSAYO

value: Ovarian Clear Cell Carcinoma cell line


title: MSR-3 (Clostridium thermocellum 1313 ∆hpt∆SO3R: sulfate)

city: Oak Ridge

first: Dawn

middle: Marie

last: Klingeman

state: TN

address: 1 Bethel Valley Rd building 15056 Rm 366  MS 6038

department: Biosciences Division

institute: Oak Ridge National Lab

data_processing:
Demultiplexing and file conversion performed by DRAGEN,  version 01.003.043.02.01.02.25767
RNAseq reads were aligned to the C. thermocellum DSM1313 (NC_017304.1) genome assembly using Fastq files imported into the CLCBio RNA-sequencing pipeline. Default settings were used for mismatch, insertion, and deletion costs.
Unique gene counts from the CLCBio mapping (DESeq_input.txt) were used for DESeq2 analysis to normalize and determine significant gene expression differences (DeSeq_output_all_pairwise_comparisons.xlsx)
Genome_build: NC_017304.1
Supplementary_files_format_and_content: Tab deliminated file includes unique read counts for each gene across the 4 conditions (with 3 biological replicates each) used in this study

organism: Acetivibrio thermocellus DSM 1313

source_name: Clostridium thermocellum_1313_ culture

growth_protocol: Strains were grown to mid-exponential phase (OD ~ 0.6) in sealed, N2 sparged 162 ml serum bottles containing 50 ml MTC (initial pH of 7.1) supplemented with 5 g/l cellobiose

extract_protocol:
Pelleted cells were  resuspended in TRIzol (Invitrogen, CA), throughly mixed and then refrozen.  The frozen TRIzol cell suspension was used for cell lysis by bead beating with 0.8 g of 0.1mm glass beads (Biospec Products) with 3 X 20 s bead beating treatments at 6,500 rpm in a Precellys 24 high-throughput tissue homogenizer (Bertin Technologies, Montigny-le-Bretonneux, France). The RNA from each cell lysate was purified and DNaseI treated (on column) using the Qiagen RNeasy kit. The RNA quantity and quality assessed by Nanodrop and Bioanalyzer respectively. Purified RNA was depleted of rRNA using the Ribo-Zero rRNA Removal kit for Bacteria (Epicentre/Illumina). The sample was then concentrated with RNA Clean & Concentrator-5 (Zymo Research, CA) following the manufacturer’s protocol.
Depleted RNA was used as the starting material for the Epicentre ScriptSeq™ v2 RNA-Seq Library preparation kit (Illumina compatible) utilising Epicentres Fail Safe PCR Enzyme mix (Epicentre, WI) and following the manufacturer’s protocol. cDNA, tagged with ScriptSeq adaptors (1-12), was purified with Agencourt AMPure XP magnetic beads (Beckman Coulter, IN ) and  eluted in water according to the ScriptSeq™ v2 RNA -Seq Library preparation kit protocol.  Twelve PCR cycles were used during library amplification and samples were purified with Agencourt AmPureXP magnetic beads and eluted with 20 µl of water. The final mRNA Seq library was quantified with a Qubit Fluorometer (Invitrogen, CA) and library quality was assessed with an Agilent Bioanalyzer DNA Chip (Agilent, CA). Samples were pooled and the concentration determined.  Pools of barcoded samples were sent to Hudson Alpha for SR50 sequencing run on an Illumina Hiseq 2500 platform.

treatment_protocol: Samples for RNA-seq were taken from mid-exponential phase (OD ~ 0.6) batch cultures grown in MTC on 5 g/l cellobiose. Control strain (∆hpt) and sulfite-reductase-mutant strain (∆hpt∆SO3R) were grown in the presence of either 5.7mM cysteine or 28.2mM sodium sulfate as the only sulfur source

tag: genotype/variation

tag: sulfur source

value: sulfate

value: sulfite reductase knockout strain


title: Ovarian Clear Cell Carcinoma cell line KOC-7c

description: Affymetrix CytoScan HD Reagent kit


title: untreated HBV LDB_19

description: nothing special

value: chronic HBV

value: HBeAg-

value: untreated


title: untreated HBV LDB_18

description: nothing special

value: HBeAg+


title: H27634_eye_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus eye

tag: tissue

value: Fetus eye