title: LS8.5_3

city: Nanchang

first: Xiaosong

last: Peng

state: Jiangxi

address: No. 1101, Zhimin Avenue, Nanchang Economic Development Zone

department: College of Agronomy

institute: Jiangxi Agricultural University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value
Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package (3.18.1). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 and absolute foldchange of 2 were set as the threshold for significantly differential expression.
Genome_build: oryza indica ensemble 41
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Oryza longistaminata

source_name: Anther tissue

extract_protocol:
Anther were removed, flash frozen on dry ice, and RNA was harvested using the TRIzol reagent (Invitrogen). Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
The constructed sequencing libraries were sequenced on the Illumina Hiseq 2000 platform.

tag: tissue

value: Anther tissue

value: 8.5mm spikelet


title: LS8.5_2

status: Public on Jul 31 2021

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

tag: age


title: MEP_TFEB_3

city: Toronto

first: Laura

last: Garcia Prat

address: 101 College street

department: Princess Margaret Cancer Centre

country: Canada

institute: University Health Network

data_processing:
Equimolar quantities of libraries were pooled and sequenced with 4 cDNA libraries per lane on a High Throughput Run Mode Flowcell with v4 sequencing chemistry on the Illumina 30 HiSeq 2500 following manufacturer’s protocol generating paired-end reads of 125-bp in length to reach depth of 55-75 million reads per sample
Reads were then aligned with STAR v2.5.2b(49) against hg38 and annotated with ensembl v90. Default parameters were used except for the following: chimSegmentMin 12; chimJunctionOverhangMin 12; alignSJDBoverhangMin 10; alignMatesGapMax 100000; alignIntronMax 100000; chimSegmentReadGapMax parameter 3; alignSJstitchMismatchNmax 5 -1 5 5.
Read counts were generated using HTSeq v0.7.2(50) and general statistics were obtained from picard v2.6.0.

organism: Homo sapiens

source_name: Cord blood

growth_protocol: In vitro culture in X-Vivo 10, 1% BSA, L-Glutamine, Pen/Strep and cytokines SCF (100 ng/ml), Flt3L (100 ng/ml), TPO (50 ng/ml) and IL7 (IL-7; 10 ng/ml)

extract_protocol:
PicoPure RNA Isolation Kit (Thermo Fisher)
cDNA conversion was performed using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara) and libraries were prepared using Nextera XT DNA Library Preparation Kit (Illumina)
4 libraries were sequenced/lane on a HiSeq 2500 following manufacturer’s protocol generating paired-end reads of 125-bp in length

treatment_protocol: Lentiviral transduction, cells collected 6 days after transduction (7 days after sorting)

tag: group

value: TFEBWT

tag: cell type

value: Megakaryocyte-erythrocyte progenitor  (MEP)

tag: treatment

value: 3 days post-transduction

tag: genotype/variation

value: TFEB overexpression


title: LS8.5_1


title: MPP_GP91_1

treatment_protocol: Lentiviral transduction, cells collected 3 days after transduction (4 days after sorting)

value: CTRL

value: Short-term hematopoietic stem cells (ST-HSC)

value: 3 days post- transduction

value: GP91 overexpression (control)


title: LS6_3

value: 6mm spikelet


title: LS6_1


title: LS4_3

value: 4mm spikelet


title: PBMC unst NA high 13

city: Woolloongabba

first: Gayathri

last: Thillaiyampalam

state: QLD

address: 37 Kent Street

department: UQDI

country: Australia

institute: University of Queensland

data_processing:
Sequence reads (fastq files) were trimmed for adapter sequences usingCutadapt (version 1.11) and aligned using STAR (version 2.5.2a) to theGRCh37 assembly with the gene, transcript, and exon features of Ensembl (release 89) gene model. Qualitycontrol metrics were computed using RNA-SeQC (version 1.1.8) and expression was estimated using RSEM (version 1.2.30)
In normalising we corrected for library size by dividing each samples gene count by million reads mapped.This procedure is a common approach known as counts per million (CPM). We further corrected for differencesin RNA composition using a method proposed by Robinson and Oshlack (2010a) called trimmed mean of M-values (TMM). We used the function calcNormFactors()from the edgeR package to obtain TMM factors and used these to correct for differences in RNA composition.
Genes with less than 2 CPM were filtered out.
Function glmQLFit() from edgeR package fits a quasi-likelihood negative binomial generalised log-linear model to count data to identify differentially expressed genes. Significant genes were filtered with multiple testing corrected false discovery rate (FDR) < 0.05 and log fold-change > 1.
Genome_build: hg19
Supplementary_files_format_and_content: Raw counts, normalised counts matrix

source_name: PBMC

growth_protocol: Primary PBMC were isolated from whole blood and cultured for 24h

extract_protocol: Truseq mRNA kit

treatment_protocol: Rhinovirus stimulated cells were cultured with RV16 for 24h and unstimulated with media

value: Peripheral blood morphonuclear cell

tag: culture

value: Unstimulated

tag: asthma status

value: No

tag: ifn-α producer

value: high


title: MEP_TFEB_1


title: PBMC RV NA high 12

value: rhinovirus stimulated


title: MEP_GP91_2


title: LS4_1

value: Anther tissue


title: PBMC unst NA high 12


title: PBMC RV NA high 11


title: MEP_GP91_1


title: PBMC RV NA high 13


title: LS6_2


title: DCM serum [Sample 72]

type: RNA

city: Aurora

first: Danielle

middle: A.

last: Jeffrey

state: CO

department: Pharmacology

country: USA

institute: University of Colorado

data_processing:
Normalized to miR-320 (least variable miRNA in over 400 pediatric samples
1. AMP status: if no AMP then NA or 0 depending on the test.
2.If AMP: if Amp score <0.9 OR Ct >35 then NA or 0.
3.If Inconclusive: if AMP> 1 AND Ct<30 – Include. Has to meet both rules. If AMP<1 OR Ct>30, NA or 0.
4.Exclude subjects that do not amplify U6 in at least 3 of 4 wells. U6 is the only RNA that is amplified in 4 wells for each sample.
5.For each analysis done, exclude any miRs that are not expressed in at least 75% of any one group.

label: TaqMan probe

source_name: patient serum

extract_protocol: MegaPlex Pool and Taqman Low Density Arrays

treatment_protocol: three freeze-thaw cycles for serum aliquots

value: DCM serum

value: <18 years old (match to patient demographics table)


title: DCM serum [Sample 70]


title: PBMC unst NA high 11


title: DCM serum [Sample 71]


title: LT_HSC_TFEB_2

value: TFEBWT

value: Long-term hematopoietic stem cells (LT-HSC)


title: LT_HSC_TFEB_3

value: 3 days post-transduction

value: TFEB overexpression


title: LT_HSC_TFEB_1


title: PBMC RV A low 14

value: Asthma

value: low


title: DCM serum [Sample 68]


title: LT_HSC_GP91_3

value: CTRL

value: GP91 overexpression (control)


title: DCM serum [Sample 69]


title: LT_HSC_GP91_2


title: PBMC RV NA low 10


title: PBMC unst NA high 2


title: PBMC unst NA low 10


title: DCM serum [Sample 67]


title: MEP_TFEB_2

value: Megakaryocyte-erythrocyte progenitor  (MEP)


title: LS4_2

value: 4mm spikelet


title: PBMC RV A low 9

value: Peripheral blood morphonuclear cell


title: LT_HSC_GP91_1


title: DCM serum [Sample 66]


title: DCM serum [Sample 65]


title: PBMC unst A low 9

value: Unstimulated


title: HSC_T_2

value: shTFEB

value: 6 days post-transduction


title: PBMC RV A high 8

value: rhinovirus stimulated

value: high


title: DCM serum [Sample 64]

value: DCM serum

value: <18 years old (match to patient demographics table)


title: HSC_T_1

value: Long-term hematopoietic stem cells (LT-HSC)


title: DCM serum [Sample 63]


title: HSC_R_3

value: shCTRL

value: shRenilla


title: PBMC RV NA high 2

value: No


title: PBMC unst A high 8

value: Asthma


title: PBMC RV A low 75

value: low


title: DCM serum [Sample 62]


title: DCM serum [Sample 33]


title: PBMC unst A low 75


title: HSC_R_1


title: PBMC RV A high 1


title: DCM serum [Sample 58]


title: DCM serum [Sample 61]


title: LT_HSC_E_3

value: CTRL

value: empty vector


title: PBMC unst NA low 74


title: LT_HSC_MYC_3

value: MYCWT

value: MYC


title: PBMC unst A high 1

value: Peripheral blood morphonuclear cell

value: Unstimulated


title: HSC_R_2

value: 6 days post-transduction


title: DCM serum [Sample 55]


title: PBMC unst NA low 72


title: DCM serum [Sample 60]


title: LT_HSC_TFEB_1 [ATAC-Seq]

library_source: genomic

data_processing:
Reads were mapped to hg38 using BWA (0.7.15) using default parameters
Duplicate reads, reads mapped to mitochondria, an ENCODE blacklisted region or an unspecified contig were removed (Encode Project Consortium, 2012)
MACS (2.2.5) was used to call peaks in mapped reads. A catalogue of all peaks was obtained by concatenating all peaks and merging any overlapping peaks. Peaks were considered unique to one condition or another if they were present in at least 2 out of three replicates but not in the contrasting condition
Genome_build: hg38
Supplementary_files_format_and_content: ENCODE narrowPeak Format containing all called peaks per sample

molecule: genomic DNA

extract_protocol:
DNA purification following Buenrostro et al. 2013 protocol
Nextera DNA Sample Preparation kit (Illumina) following Buenrostro et al. 2013 protocol
4 libraries were sequenced/lane on a HiSeq 2500 following manufacturer’s protocol generating paired-end reads of 125-bp in length

value: TFEBWT

tag: genotype

value: TFEB overexpression


title: PBMC unst NA high 71

value: high


title: DCM serum [Sample 54]

value: DCM serum

value: <18 years old (match to patient demographics table)


title: PBMC RV A high 70

value: rhinovirus stimulated


title: DCM serum [Sample 47]


title: LT_HSC_MYC_2

value: Long-term hematopoietic stem cells (LT-HSC)


title: HSC_T_3

value: shTFEB


title: PBMC RV NA high 69

value: No


title: uninj_DMSO_MG_2

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

data_processing:
Adapter trimming with Trim Galore v0.4.5 and cutadapt v1.15
Alignment with bowtie2 v2.3.4.1 with -X 2000 --no-mixed --no-discordant
Deduplicate with picard v2.20.2
Filter alignments for MAPQ > 10
Peak calling with macs2 v2.1.2 with -f BAM --nomodel --shift -100 --extsize 200
Genome_build: danRer11
Supplementary_files_format_and_content: narrowPeak peak calls

organism: Danio rerio

source_name: Mueller Glia cells

growth_protocol: gfap:GFP transgenic zebrafish were maintained in aquaria at 28 degrees centrigrade

extract_protocol:
One day after treatment, retinas were isolated, dissociated, and GFP+ Muller glia purified by FACS.  Nuclei were isolated for ATACseq analysis.
ATACseq libraries prepared according to Buenrostro et al., Curr. Protoc. Mol. Biol. 109:21.29-1-21.29.9, 2015.

treatment_protocol: Fish were immersed in fish water containing either DMSO or DAPT

value: DMSO


title: DCM serum [Sample 59]


title: LT_HSC_MYC_1


title: DCM serum [Sample 53]


title: PBMC RV A low 73

value: Asthma

value: low


title: DCM serum [Sample 57]


title: LT_HSC_E_2

value: CTRL

value: empty vector


title: NF serum treated NRVMs [10+11]

description:
pooled samples
Sample10and11_pooled

data_processing:
Illumina hiSEQ4000
FastQC (filtering)
gsnap (alignment)
Genome_build: Rnor_5.0
Supplementary_files_format_and_content: cufflink

organism: Rattus norvegicus

source_name: neonatal rat ventricular myocyte cells

growth_protocol: 72 hour serum treatment

extract_protocol:
qiazol
150 bp ss

treatment_protocol: 1% serum

tag: strain

value: sprague dawley rats

value: post-natal 2 days

tag: serum patient id


title: DCM serum [Sample 48]


title: PBMC unst A high 73

value: Peripheral blood morphonuclear cell

value: Unstimulated


title: DCM serum [Sample 51]


title: LT_HSC_E_1

value: 6 days post-transduction


title: PBMC RV NA low 72


title: DCM serum [Sample 56]


title: LT_HSC_TFEB_3 [ATAC-Seq]

value: TFEBWT

value: TFEB overexpression


title: DCM serum [Sample 50]

value: DCM serum

value: <18 years old (match to patient demographics table)


title: DCM serum [Sample 28]


title: PBMC RV NA high 71

value: rhinovirus stimulated

value: high


title: LT_HSC_TFEB_2 [ATAC-Seq]

value: Long-term hematopoietic stem cells (LT-HSC)


title: PBMC RV NA low 74

value: No


title: LT_HSC_GP91_3 [ATAC-Seq]

value: GP91 overexpression (control)


title: PBMC unst A high 70

value: Asthma


title: LT_HSC_GP91_2 [ATAC-Seq]

value: CTRL


title: DCM serum [Sample 38]


title: PBMC RV A low 65

value: low


title: LT_HSC_GP91_1 [ATAC-Seq]


title: 8 weeks after pulmonary banding 3

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

country: Netherlands

institute: Amsterdam UMC

description: right ventricle pressure overload

data_processing:
RNA-seq: reads were mapped to rn6 build of the rat transcriptome using STAR (Dobin et al., 2013).
Differential expression analysis was performed using the DESeq2 package based on a model using the negative binomial distribution (Love, Huber, and Anders 2014).
Genome_build: rn6
Supplementary_files_format_and_content: RNA-seq: RAT-PB-counts.xlsx (Excel file with raw and normalized (DESeq2) count data per gene & differential expression analysis).

source_name: cardiac tissue right ventrcile

growth_protocol: The right ventrcile of cardiac tissue was isolated 4 weeks and 8 weeks after pulmonary banding or sham operation

extract_protocol:
RNA was isolated using Trizol, quantity was measured using the Qubit and quality was assessed using the Bioanalyzer RNA Chip
TruSeq Ribo-Zero Gold, RNA input: 800 ng

treatment_protocol: tissue was snap frozen and stored at -80 degree celcius

value: wistar

value: 11 weeks

value: right ventricle pressure overload


title: NF serum [Sample 22]

value: NF serum


title: 8 weeks after pulmonary banding 2

description: right ventricle pressure overload


title: DCM serum treated NRVMs [32+33]

description:
pooled samples
Sample32and33_pooled

value: sprague dawley rats

value: post-natal 2 days


title: PBMC unst NA high 69

value: Peripheral blood morphonuclear cell

value: Unstimulated


title: NF serum [Sample 23]

value: <18 years old (match to patient demographics table)


title: NF serum [Sample 21]


title: DCM serum [Sample 24]

value: DCM serum


title: NF serum [Sample 20]


title: NF serum treated NRVMs [10+11, pooled2]

description:
pooled samples
Sample10and11_pooled2


title: PBMC RV A low 68

value: rhinovirus stimulated


title: DCM serum [Sample 52]


title: PBMC unst A low 63


title: 4 weeks after pulmonary banding 3

description: right ventricle pressure overload

value: 7 weeks


title: DCM serum treated NRVMs [30+31]

description:
pooled samples
Sample30and31_pooled


title: PBMC RV NA high 62

value: No

value: high


title: PBMC unst A low 68

value: Asthma


title: PBMC unst NA high 62


title: DCM serum [Sample 31]


title: PBMC RV A low 63


title: 4 weeks after pulmonary banding 1

description: right ventricle pressure overload


title: NF serum [Sample 5]


title: PBMC RV NA low 61


title: PBMC RV A low 67


title: 8 weeks after sham operation 5

description: right ventrcle healthy

value: right ventrcle healthy


title: NF serum [Sample 4]


title: DCM serum [Sample 46]


title: DCM serum treated NRVMs [28+29]

description:
pooled samples
Sample28and29_pooled


title: PBMC RV A low 60

value: low


title: PBMC unst A low 67


title: NF serum treated NRVMs [8+9]

description:
pooled samples
Sample8and9_pooled


title: PBMC RV A low 66


title: 4 weeks after sham operation 5

description: right ventrcle healthy

value: wistar


title: 8 weeks after pulmonary banding 5

description: right ventricle pressure overload

value: 11 weeks


title: PBMC RV A high 7


title: PBMC unst A low 66


title: PBMC unst A high 7


title: DCM serum [Sample 49]


title: 4 weeks after sham operation 3

description: right ventrcle healthy


title: 8 weeks after pulmonary banding 4

description: right ventricle pressure overload

value: right ventricle pressure overload


title: 4 weeks after sham operation 2

description: right ventrcle healthy


title: PBMC unst A low 58


title: 203_K_HFS_HFS: GDM-High Fat and Sucrose 3

city: Winnipeg

first: Dr. Vernon

last: Dolinsky

state: Manitoba

address: 601 John Buhler Research Centre, 715 McDermot Avenue

department: Department of Pharmacology and Therapeutics

institute: University of Manitoba

data_processing:
The base calls were made by the RTA software on the computer running the instrument. The RTA for  Hiseq 4000 is v2.7.7 using default parameters.
Trim Galore was used to remove the Illumina TruSeq smRNA sequences form the reads and fastqc. After quality check the reads were aligned to Rnor_6 genome assembly using STAR v2.5.1b default parameters.
We have removed all the reads that were not mapped or did not have proper mate pairs using the tool jvarkit (GRADLE_VERSION=5.1.1)
All of the "chrUn" were not considered in the downstream analysis
To perform differential analysis HOMER (v4.9) software was used. First used homer script makeTagDirectory, the tag directories were made, which contains basic configuration information, such as the total number of reads, the total number of unique positions with aligned reads. Then homer script analyzeRepeats.pl was used to generate raw read counts based on exons, the counts were not adjusted and were condensed to genes. Further, the raw reads were subjected to homer script getDiffExpression.pl where we used edgeR to obtain the differentially regulated genes. We used a cutoff of ≥1.5 fold and FDR of ≤0.05 to find the significant genes.
Genome_build: Rattus norvegicus (Rnor_6) genome assembly

source_name: heart tissue

growth_protocol: To induce gestational diabetes mellitus (GDM) female Sprague-Dawley rats were fed a high fat and sucrose (HFS) diet prior to mating, throughout pregnancy and lactation. Lean control females received a low fat (LF) diet. Offspring from Lean and GDM dams were randomly assigned to HFS or LF diets after weaning at 3-weeks of age and maintained on their respective diets until 3-months (15-weeks of age).

extract_protocol:
Total RNA was isolated from cardiac tissue using RNeasy Fibrous Tissue Mini Kit (Qiagen).
Libraries were prepared using NEBNext rRNA Depletion Kit and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England BioLabs). The libraries were sequenced and pre-processed by Genome Quebec using an Illumina HiSeq4000 system, with paired-end reads of 100 base pairs and a total of 50 million reads per sample. FASTQ files were aligned and trimmed by Genome Quebec. Sequence alignment was performed using STAR (version 2.5.1b) and the genome assembly Rnor_6.0.

treatment_protocol: Whole hearts were collected from the four groups of young-adult rat offspring at 3-months of age for biochemical and gene expression (RNA-seq) analysis. Young-adult rat offspring were euthanized by a sodium pentobarbital overdose, and blood was drawn via a cardiac puncuture. The heart was then extracted, rinsed in sterile PBS and flash frozen in liquid N2.

value: Sprague Dawley

value: cardiac

value: 15-weeks of age


title: PBMC unst A low 65

value: Peripheral blood morphonuclear cell


title: 204_K_HFS_HFS: GDM-High Fat and Sucrose 2


title: PBMC unst A high 57

value: Unstimulated


title: PBMC RV A high 64


title: 8 weeks after pulmonary banding 1

description: right ventricle pressure overload


title: PBMC unst A high 64


title: 4 weeks after pulmonary banding 5

description: right ventricle pressure overload


title: PBMC RV NA low 56


title: NF serum [Sample 1]

value: NF serum

value: <18 years old (match to patient demographics table)


title: 4 weeks after pulmonary banding 4

description: right ventricle pressure overload


title: NF serum [Sample 7]


title: 217_K_HFS_LF: GDM-Low Fat 3


title: 4 weeks after pulmonary banding 2

description: right ventricle pressure overload


title: NF serum [Sample 19]


title: NF serum [Sample 6]


title: PBMC unst NA low 61


title: NF serum [Sample 18]


title: PBMC RV NA low 54

value: rhinovirus stimulated


title: 8 weeks after sham operation 4

description: right ventrcle healthy


title: PBMC unst A low 60


title: 200_K_LF_HFS: Lean-High Fat and Sucrose 2


title: PBMC unst NA low 54


title: NF serum [Sample 17]


title: 8 weeks after sham operation 2

description: right ventrcle healthy


title: PBMC RV A low 59


title: 8 weeks after sham operation 3

description: right ventrcle healthy


title: 8 weeks after sham operation 1

description: right ventrcle healthy


title: 202_K_LF_LF: Lean-Low Fat 2


title: PBMC unst NA high 6


title: PBMC unst A low 59


title: 4 weeks after sham operation 4

description: right ventrcle healthy

value: 7 weeks


title: PBMC unst NA low 51

value: No


title: CLas Month 8-F1 [MI8F1]

city: Davis

first: Christopher

last: McNeil

state: CA

address: One Shields Ave

institute: University of California Davis

data_processing:
Trimmomatic v 0.36  was used to remove adaptors and low quality reads using the following parameters: ILLUMINACLIP:TruSeq3-PE.fa:2:40:15 \LEADING:2 TRAILING:2 \SLIDINGWINDOW:4:20\MINLEN:36
Alignment to the Citrus sinensis genome version 2.0 (http://citrus.hzau.edu.cn/orange/download/index.php) was performed using STAR v 2.7.2a using default parameters for 150bp paired-end reads
The featureCount function of the Subread package v 1.6.3 was used to generate gene counts per sample and all counts were exported as a matrix table.
Genome_build: Csi_valencia_1.0
Supplementary_files_format_and_content: txt file containing a gene count table for all genes for all samples

molecule: polyA RNA

organism: Citrus sinensis

source_name: Clas_8m Leaf

growth_protocol: Plants grown under greenhouse conditions in a BSL Level III plant facility. Leaf samples were collected 2, 4, and 8 months after the completion of the grafts. The sampled leaves were immediately frozen in liquid nitrogen upon collection.

extract_protocol:
Total RNA was extracted from <100 mg of ground frozen leaf tissue using the Qiagen RNeasy Plant Mini Kit and treated with RNase-free DNase (Qiagen, Hilden, Germany) according to the manufacturer’s instructions, and then cleaned using a Zymo Research Clean and Concentrator kit (Zymo Research, Irvine, CA, USA) according to the manufacturer’s instructions.
RNA-seq libraries were generated from 400 ng of total RNA each, after poly-A enrichment, using the Kapa mRNA-seq Hyper kit (Kapa Biosystems-Roche, Basel, Switzerland) following manufacturer instructions.

treatment_protocol: Trees received a series of 3 grafts on the main stem of the tree from source material infected with the pathogens of interest. The control trees received grafts from plants known to be disease free.

value: Clas

tag: month

tag: developmental stage

value: Young tree

value: Leaf


title: PBMC RV A low 58

value: Asthma

value: low


title: 4 weeks after sham operation 1

description: right ventrcle healthy

value: wistar

value: right ventrcle healthy


title: PBMC RV A high 57

value: high


title: 211_K_HFS_HFS: GDM-High Fat and Sucrose 1

value: Sprague Dawley

value: cardiac


title: Stem-pitting CTV month 8-E5 [MI8E5]

source_name: Stem-pitting CTV (CCTEA-107)_8m Leaf

value: Stem-pitting CTV (CCTEA-107)


title: PBMC RV NA low 51

value: Peripheral blood morphonuclear cell


title: Stem-pitting CTV month 8-E4 [MI8E4]


title: CLas Month 8-F10 [MI8F10]


title: 209_K_HFS_LF: GDM-Low Fat 2

value: 15-weeks of age


title: PBMC unst A low 55

value: Unstimulated


title: 210_K_HFS_LF: GDM-Low Fat 1


title: 219_K_LF_HFS: Lean-High Fat and Sucrose 3


title: Mild CTV month 8-D1 [MI8D1]

source_name: Mild CTV (T30 isolate)_8m Leaf

value: Mild CTV (T30 isolate)


title: PBMC RV A low 53

value: rhinovirus stimulated


title: PBMC unst NA low 56

value: No


title: 199_K_LF_HFS: Lean-High Fat and Sucrose 1


title: PBMC RV A low 55


title: 221_K_LF_LF: Lean-Low Fat 3


title: PBMC RV NA high 6


title: 201_K_LF_LF: Lean-Low Fat 1


title: PBMC RV NA low 46


title: PBMC RV A high 52


title: S. citri Month 8-C5 [MI8C5]

source_name: S. citri_8m Leaf

value: S. citri


title: CLas Month 8-F7 [MI8F7]

value: Clas

value: Young tree


title: PBMC unst A high 52

value: Asthma


title: negative control SH-SY5Y cells, biological rep2

city: Xi'an

first: Fayi

last: Nie

state: China

address: YanTa Road 76

institute: Xi’an Jiaotong University Health Science Center

description: Gene expression data of total RNA from nagetive control SH-SY5Y cells samples

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The arrays were scanned by the GeneChip Scanner 3000 (Affymetrix).

data_processing: Affymetrix GeneChip Command Console (version 4.0, Affymetrix) was employed to analyze array images to get raw data, and normalized with the Robust Multi-array Average (RMA) algorithm.

label: biotin

source_name: negative control SH-SY5Y cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.

growth_protocol: SH-SY5Y cell line was cultured in growth medium (DMEM/Ham's F12 Medium, supplemented with 1.5 mM L-glutamine, 10% FBS, 100 U/mL penicillin, and 100 μg/mL streptomycin).

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

treatment_protocol: Lentiviral particles for EGR3 overexpression (OE) and negative control (NC) were used to infect SH-SY5Y cells. Three days post-infection, the medium was changed to growth medium supplemented with 1 μg/mL puromycin (Sigma, St. Louis, MO, USA), and the medium was changed every two days thereafter. The stable cells were acquired two weeks after selection.

value: negative control


title: S. citri Month 8-C4 [MI8C4]

value: Leaf


title: Stem-pitting CTV month 8-E9 [MI8E9]


title: PBMC unst A low 53

value: low


title: PBMC RV NA low 45


title: PBMC RV NA low 50


title: Stem-pitting CTV month 8-E8 [MI8E8]


title: PBMC unst NA low 50


title: negative control SH-SY5Y cells, biological rep1


title: PBMC RV NA low 49


title: PBMC unst NA low 49


title: PBMC RV NA high 48

value: high


title: PBMC unst NA low 44


title: PBMC unst NA high 48


title: Mild CTV month 8-D9 [MI8D9]


title: Combi_M7

city: Oxford

first: James

last: McAuliffe

state: Oxfordshire

address: Old Road Campus Research Building, Roosevelt Drive

department: Ludwig Institute for Cancer Research,

country: United Kingdom

institute: University of Oxford

data_processing:
The prepared sequencing libraries were size selected, multiplexed and QC’ed before 150bp paired end sequencing over one unit of a flow cell of an Illumina NovaSeq 6000. Samples were sequenced at a depth of approx 30,000,000 reads/sample.
Illumina Casava software was used for basecalling.
Sequenced reads were first masked for low-complexity or low-quality sequence, trimmed for adaptor sequences using Skewer and then mapped to GRCm38.ERCC (mm10) whole genome using the HISAT2 aligner with default parameters.
A counts matrix reporting the numbers of reads mapping to each gene was then generated for each sample using the featureCounts program (Liao Y. et al (2014), Bioinformatics) in the Subread UNIX package with parameters -t exon -T 4 -p -M --fraction -Q 4 -F GTF.  Genes expressed at a level <1 CPM in at least one condition were excluded from further analysis.
Gene expression was then calculated as counts per million (CPM). R package "edgeR" (Robinson MD. (2010), Bioinformatics) Bioconductor v3.11 R v4.0.1 was used for further data normalization and differential expression analysis. Counts data was normalized using the trimmed mean of M values (TMM) method and differential gene expression analysis between indicated samples determined using the glmQLFTest method. T-cell inflamed and IFN-g-related mRNA gene expression signatures were defined and associated gene expression signatures calculated using normalized counts data. Gene set variation analysis (GSVA) was performed using R package GSVA.
Genome_build: GRCm38.ERCC
Supplementary_files_format_and_content: A tab-delimited text file including a matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Tab-delimited text files including matrix tables with raw gene counts for every gene for each individual sample

organism: Mus musculus

source_name: 15V4T3 tumour

growth_protocol: 15V4T3 cells were expanded in culture and then implanted subcutaneously in the right-flanks of DBA/2 mice. Tumour growth was monitored upon the formation of palpable tumours. Mice were sacrificed and tumours excised 20 days following implantation

extract_protocol:
Tumours were surgically excised 20-days after implantation, and then snap-frozen using liquid nitrogen. Total RNA was then extracted by mechanical disruption of the tissue and using Qiagen RNeasy Mini kit reagents (Cat#74004) including on-column DNase digestion. The mRNA fraction was selected from the isolated total RNA by poly-A enrichment before being converted to cDNA for the construction of sequencing libraries. The cDNA was end-repaired, A-tailed and adapter-ligated.
RNA-seq libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Tumour-bearing mice were treated with a PBS control, anti-PD-1 inhibitor (3-doses of 100ug 3-days apart), ChAdOx/MVA P1A vaccine (10^7 IU / 10^6 PFU doses 1-week apart), or with vaccine + anti-PD-1 combination

value: tumour

value: WT

value: Vaccine + anti-PD-1


title: S. citri Month 8-C2 [MI8C2]


title: Combi_M35


title: PBMC RV A high 5

value: Peripheral blood morphonuclear cell


title: Mild CTV month 8-D4 [MI8D4]


title: Mild CTV month 8-D3 [MI8D3]


title: PBMC unst A high 5


title: Combi_M3


title: Mild CTV month 8-D2 [MI8D2]


title: PBMC RV A low 47


title: Stem-pitting CTV month 8-E10 [MI8E10]

value: Stem-pitting CTV (CCTEA-107)


title: Control Month 8-B5 [MI8B5]

source_name: Control_8m Leaf

value: Control


title: Vac_M24

value: Vaccine


title: PBMC unst A low 47

value: Unstimulated


title: S. citri Month 8-C6 [MI8C6]


title: negative control SH-SY5Y cells, biological rep3


title: PBMC unst NA low 46

value: No


title: S. citri Month 8-C3 [MI8C3]

value: S. citri


title: PBMC unst NA low 45


title: PBS_M5

value: PBS control


title: PBMC RV NA low 44

value: rhinovirus stimulated


title: Control Month 8-B8 [MI8B8]

value: Young tree


title: Control Month 8-B6 [MI8B6]


title: EGR3 overexpression SH-SY5Y cells, biological rep3

description: Gene expression data of total RNA from EGR3 overexpression SH-SY5Y cells samples

source_name: EGR3 overexpression SH-SY5Y cells

value: EGR3 overexpression


title: EGR3 overexpression SH-SY5Y cells, biological rep2


title: EGR3 overexpression SH-SY5Y cells, biological rep1


title: PBMC RV A low 43

value: Asthma


title: PBMC unst A low 43

value: low


title: Control Month 8-B3 [MI8B3]

value: Leaf


title: PBMC RV A low 42


title: Control Month 8-B10 [MI8B10]


title: PBMC unst A low 42


title: Vac_M6

value: tumour


title: CLas + Mild CTV Month 4-H5 [MI4H5]

source_name: Clas+T30_4m Leaf


title: CLas + Stem-pitting CTV Month 4-I7 [MI4I7]

source_name: Clas+CCTEA107_4m Leaf


title: aPD1_M22

value: WT


title: CLas + Mild CTV Month 4-H2 [MI4H2]


title: PBMC RV A high 41

value: high


title: CLas + Stem-pitting CTV Month 4-I6 [MI4I6]


title: Vac_M40


title: PBMC unst A high 41

value: Peripheral blood morphonuclear cell


title: PBMC RV A low 40


title: CLas + Stem-pitting CTV Month 4-I4 [MI4I4]


title: aPD1_M12


title: CLas + Mild CTV Month 4-H10 [MI4H10]


title: Curdlan-WT-neutrophils 2

first: Akihiro

last: Nakamura

state: Ontario

address: 399 Bathurst Street

data_processing:
The data analyses were performed in service of Princess Margaret Genomics Centre (Toronto) following a published protocol (Pertea. M, et al. 2016). Specifically, the raw sequence data was aligned to the mouse genome (GRCm38, Mus_musculus.GRCm38.84.gtf GTF definition file, index was downloaded from http://daehwankimlab.github.io/hisat2/) using the HISAT2 (v2.1.0). Accessory programs for the alignment stage include samtools (v1.9). Transcripts were assembled and gene expression levels were estimated with Stringtie (v.2.1.4). Stringtie output result was load into R (v3.6.1)/ballgown (v2.18.0) for differential gene expression analyses and graphing. The q-values were generated from the stattest function (https://rdrr.io/bioc/ballgown/man/stattest.html).
Genome_build: GRCm38
Supplementary_files_format_and_content: WT_vs_KO_neutro_transcript_results_all.tsv

source_name: Curdlan-WT neutrophils

extract_protocol:
Extracted total RNA from FACS-sorted mouse neutrophils (isolated from bone marrow and spleen) were purified with RNeasy Plus Mini Kit (Qiagen, cat# 74134) and subjected to the total RNA-seq. Four total RNA samples (2 from neutrophils in curdlan-treated WT SKG mice and 2 from neutrophils in curdlan-treated Mif KO SKG mice) were quantified by qubit RNA kit (Life Technologies) and quality assessed by Agilent Bioananlyzer (Agilent Technologies). The average of RNA integrity number (RIN) was 9.99 with minimum 9.9. Fifty nanograms of total RNA per sample were prepared using Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit as per manufaturer’s protocol (Illumina). Final cDNA libraries were size validated using Agilent Bioanalyzer or Tapestation and concentration validated by qPCR (Kapa Biosystems/Roche). All libraries were normalized to 1.5 nM and pooled together, denatured with 0.2N NaOH (Sigma), neutralized with 400mM Tris-HCL (Sigma). Library pools were loaded onto Illumina Novaseq 6000 for sequencing using paired end 100bp protocol to achieve ~40 Million reads per sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: BALB/c SKG

value: neutrophils

tag: time point

value: 8 weeks post curdlan

value: wild type


title: PBMC unst A high 37

source_name: PBMC

value: Unstimulated


title: aPD1_M11


title: CLas + Stem-pitting CTV Month 4-I3 [MI4I3]


title: dCas9-SET2-sgRNA-SRSF11_3_4

city: Philadelphia

first: Song-Jun

last: Xu

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description: processed data file: dCas9_SET2_RNA_seq_junction_counts.txt

data_processing:
RNA-seq reads were aligned against mouse reference genome (mm9 or mm10 ensemble annotation) using STAR (Version 2.4.1d)
ChIP-seq reads were aligned mouse reference genome (mm9, ensemble annotation) using Bowtie2
Cut&Run-seq reads were aligned mouse reference genome (mm9, ensemble annotation) using Bowtie2 with specifics --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700
Alternative splicing was analyzed by rMATS V3.2.4
Genome_build: mm9/mm10
Supplementary_files_format_and_content: bigwig; text file with exon skipping coordiates and their junction counts
Supplementary_files_format_and_content: IgG_1.bw: Merged bigwig files for dCas9-SET2-sgRNA-T1-C-1,dCas9-SET2-sgRNA-T1-C-2, and dCas9-SET2-sgRNA-T1-C-3
Supplementary_files_format_and_content: IgG_2.bw: Merged bigwig files for dCas9-SET2-sgRNA-NT-C-1,dCas9-SET2-sgRNA-NT-C-2, and dCas9-SET2-sgRNA-NT-C-3

source_name: Nucleus Accumbens

extract_protocol:
For tissue collection, mice were euthanized by cervical dislocation and the brain was placed in ice-cold phosphate buffered saline with protease inhibitor cocktail (Roche cOmplete Protease inhibitor). 1 mm thick sections of prefrontal cortex, nucleus accumbens and ventral tegmental area, brain regions were prepared using a cold tissue matrix and regions were micro-dissected with a 2- or 1.2-mm diameter micro-punch (Harris)
ChIP and RNA libraries were prepared for sequencing using standard Illumina protocols

value: Brain

value: 8 weeks


title: dCas9-SET2-sgRNA-SRSF11_3_3


title: CLas Month 4-F4 [MI4F4]

source_name: Clas_4m Leaf

value: Clas


title: CLas Month 4-F1 [MI4F1]

value: Young tree


title: dCas9-SET2-sgRNA-SRSF11_3_2


title: PBMC unst A high 35


title: CLas + Stem-pitting CTV Month 4-I1 [MI4I1]


title: PBMC RV A high 39

value: rhinovirus stimulated


title: dCas9-SET2-sgRNA-SRSF11_17_3


title: Stem-pitting CTV Month 4-E5 [MI4E5]

source_name: Stem-pitting CTV (CCTEA-107)_4m Leaf

value: Stem-pitting CTV (CCTEA-107)


title: dCas9-SET2-sgRNA-SRSF11_17_2


title: PBMC unst A low 40

value: Asthma

value: low


title: PBS_M2

value: tumour

value: PBS control


title: PBMC unst A high 39

value: high


title: PBS_M1

value: WT


title: PBMC RV NA high 32

value: Peripheral blood morphonuclear cell

value: No


title: dCas9-SET2-sgRNA-SRSF11_16_4


title: PBMC unst NA high 32


title: CLas + Mild CTV Month 4-H3 [MI4H3]

value: Leaf


title: Curdlan-Mif KO neutrophils 2

source_name: Curdlan-Mif KO neutrophils

value: BALB/c SKG

value: neutrophils

value: 8 weeks post curdlan

value: Mif -/- (Mif KO)


title: PBMC RV NA high 38


title: dCas9-SET2-sgRNA-SRSF11_16_3

value: Brain

value: 8 weeks

value: wild type


title: Curdlan-Mif KO neutrophils 1


title: PBMC RV A high 37

value: rhinovirus stimulated


title: CLas Month 4-F7 [MI4F7]

value: Clas

value: Young tree


title: PBMC RV NA high 31


title: dCas9-SET2-sgRNA-SRSF11_16_2


title: PBMC unst NA high 38

value: Unstimulated


title: Mild CTV Month 4-D4 [MI4D4]

source_name: Mild CTV (T30 isolate)_4m Leaf

value: Mild CTV (T30 isolate)


title: CLas Month 4-F5 [MI4F5]


title: PBMC RV A high 35

value: Asthma

value: high


title: CLas Month 4-F10 [MI4F10]


title: dCas9-SET2-sgRNA-SRSF11_3_1


title: PBMC unst A high 36

value: Peripheral blood morphonuclear cell


title: Stem-pitting CTV Month 4-E9 [MI4E9]

value: Stem-pitting CTV (CCTEA-107)


title: PBMC RV A high 36


title: PBMC RV A high 34


title: dCas9-SET2-sgRNA-SRSF11_17_4


title: PBMC unst NA high 4

value: No


title: Stem-pitting CTV Month 4-E4 [MI4E4]

value: Leaf


title: PBMC unst A high 34


title: PBMC RV A high 33


title: Stem-pitting CTV Month 4-E8 [MI4E8]


title: PBMC unst A high 33


title: dCas9-SET2-sgRNA-SRSF11_1_3


title: PBMC RV A high 30


title: S. citri Month 4-C5 [MI4C5]

source_name: S. citri_4m Leaf

value: S. citri


title: PBMC unst A high 30


title: Mild CTV Month 4-D9 [MI4D9]


title: S. citri Month 4-C4 [MI4C4]


title: Stem-pitting CTV Month 4-E10 [MI4E10]


title: CGA2023_NFM_LL_Suc rep2

city: Saint Paul

first: Kathryn

middle: R

last: Fixen

state: Minnesota

address: 1479 Gortner Ave. RM140

department: Plant and Microbial Biology

institute: University of Minnesota

description: ΔregSΔregR

data_processing:
Base-calling was performed by GENEWIZ, LLC (South Plainfield, NJ, USA) on an Illumina HiSeq instrument (Illumina, San Diego, CA, USA). Sequencing data were analyzed using the FastQC application v0.11.8 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) to verify high-quality base-calling.
TrimGalore v0.6.2 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was used to trim adapter sequences, process, and validate reads according to default parameters.
All subsequent steps were performed on the Avadis software package v3.1.1 (Strand Life Sciences, Bengaluru, India).
Trimmed reads were aligned to the published genome sequence of CGA009 (NC_005296). Residual rRNA and tRNA were removed, raw read counts were determined, and normalized RPKM values were calculated.
The DESeq2 package in R v3.6 (Love MI, Huber W, Anders S. 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology, 15, 550.) was used with default parameters to determine differentially expressed genes.
Genome_build: NC_005296 (Rhodopseudomonas palustris CGA009)
Supplementary_files_format_and_content: Expected/estimated read counts in tab-delimited format where rows represent genes and columns represent each sample

organism: Rhodopseudomonas palustris

source_name: Whole cells

growth_protocol: Rhodopseudomonas palustris was grown anaerobically in sealed hungate tubes containing 10 mL of liquid media with a headspace of primarily nitrogen gas. Carbon sources were added to the media after autoclaving from sterile, anaerobic stock solutions to a final concentration of 40 mM carbon. All strains were first grown in a defined mineral minimal medium (PM) supplemented with 20 mM acetate and 0.1% yeast extract, then diluted into either PM or nitrogen-fixing medium (NFM), which is PM medium without ammonium sulfate added. These cultures were then used to inoculate cultures in replicate for total RNA extraction. All cultures were incubated at 30℃ in either high-light (30 µmol photons/m^2/s) or low-light conditions (4 µmol photons/m^2/s) provided by a 60-W or a 15-W incandescent light bulb, respectively. Sodium bicarbonate was added to a final concentration of 10 mM for all cultures grown on benzoate. (For detailed media recipes, see the following: Kim, Min-Kyung; Hardwood CS. 1991. Regulation of benzoate-CoA ligase in Rhodopseudomonas palustris. FEMS Microbiol Lett 83:199–203.)

extract_protocol:
Cultures were grown to an optical density of 0.45-0.47 at 660nm. Each 10 mL culture was then pelleted to remove supernatant, cells were flash frozen with liquid nitrogen, and stored at -80℃ until extraction. To lyse cells, each pellet was resuspended in 1 mL of QIAzol Lysis Reagent (QIAGEN, Hilden, Germany) and samples were homogenized in a Mini BeadBeater-24 (BioSpec Products INC., Bartlesville, OK, USA). Cellular debris was removed via chloroform extraction and total RNA was isolated using the miRNAeasy Mini Kit (QIAGEN, Hilden, Germany). DNA was removed using TURBO DNase (Invitrogen, Carlsbad, CA, USA) and the RNeasy MinElute Cleanup Kit (QIAGEN, Hilden, Germany) was used to purify and concentrate total RNA.
Ribosomal RNA depletion, cDNA library construction, and sequencing reactions were performed at GENEWIZ, LLC (South Plainfield, NJ, USA). Briefly, rRNA depletion was performed using the Ribo-Zero rRNA Removal Kit (Illumina, San Diego, CA, USA) and cDNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit (NEB, Ipswich, MA, USA). Sequencing and base calling were performed on an Illumina HiSeq instrument (Illumina, San Diego, CA, USA).

tag: carbon source

value: Succinate

tag: nitrogen-fixing conditions?

value: Yes

tag: light intensity

value: Low:4 µmol photons/m^2/s (15-W)

value: {delta}regS{delta}regR


title: PBMC RV NA low 29

value: low


title: PBMC unst A low 29


title: dCas9-SET2-sgRNA-NT_3_4

value: Brain

tag: age

value: 8 weeks

value: wild type


title: S. citri Month 4-C3 [MI4C3]

value: Young tree

tag: tissue


title: PBMC unst NA high 31

tag: cell type

value: Unstimulated


title: dCas9-SET2-sgRNA-NT_3_3

tag: treatment


title: CGA2023_PM_HL_Ben rep2

description: ΔregSΔregR

value: Benzoate

value: High:30 µmol photons/m^2/s (60-W)


title: dCas9-SET2-sgRNA-SRSF11_16_1


title: S. citri Month 4-C2 [MI4C2]


title: PBMC RV NA high 3

value: Peripheral blood morphonuclear cell

tag: culture

value: rhinovirus stimulated

value: high


title: Mild CTV Month 4-D2 [MI4D2]

value: Mild CTV (T30 isolate)

value: Leaf


title: Control Month 4-B8 [MI4B8]

source_name: Control_4m Leaf

value: Control


title: PBMC unst NA high 3

tag: asthma status

value: No


title: PBMC RV NA high 4

tag: ifn-α producer


title: dCas9-SET2-sgRNA-SRSF11_1_4

tag: genotype


title: CGA2023_PM_HL_Ben rep1

description: ΔregSΔregR


title: dCas9-SET2-sgRNA-NT_3_1

tag: strain


title: CGA010_PM_HL_Ben rep2

description: wild type


title: S. citri Month 4-C6 [MI4C6]

value: S. citri


title: dCas9-SET2-sgRNA-SRSF11_17_1


title: CGA010_PM_HL_Ben rep1

description: wild type


title: dCas9-SET2-sgRNA-NT_17_3


title: dCas9-SET2-sgRNA-SRSF11_1_1


title: Mild CTV Month 4-D1 [MI4D1]


title: Control Month 4-B3 [MI4B3]


title: dCas9-SET2-sgRNA-SRSF11_1_2


title: CGA010_NFM_LL_Suc rep1

description: wild type

value: Succinate

value: Yes

value: Low:4 µmol photons/m^2/s (15-W)


title: Control Month 4-B10 [MI4B10]


title: CLas + Stem-pitting CTV Month 2-I7 [MI2I7]

source_name: Clas+CCTEA107_2m Leaf


title: PBMC unst A high 27

value: Asthma


title: CGA2023_NFM_LL_Suc rep1

description: ΔregSΔregR

value: {delta}regS{delta}regR


title: PBMC RV A high 27


title: CGA2023_NFM_HL_Mal rep2

description: ΔregSΔregR

value: Malate


title: CGA010_NFM_LL_Suc rep2

description: wild type

value: wild type


title: dCas9-SET2-sgRNA-NT_3_2

value: Brain

value: 8 weeks


title: Control Month 4-B5 [MI4B5]

value: Young tree


title: PBMC RV NA low 28

value: Peripheral blood morphonuclear cell

value: rhinovirus stimulated

value: low


title: CGA2023_NFM_LL_Ace rep1

description: ΔregSΔregR

value: Acetate


title: CGA2023_NFM_LL_Ace rep2

description: ΔregSΔregR


title: CGA010_NFM_HL_Mal rep2

description: wild type

value: High:30 µmol photons/m^2/s (60-W)


title: dCas9-SET2-sgRNA-NT_17_4


title: PBMC unst A high 26

value: Unstimulated

value: high


title: PBMC RV NA low 25

value: No


title: dCas9-SET2-sgRNA-NT_16_2


title: CLas + Stem-pitting CTV Month 2-I1 [MI2I1]

value: Leaf


title: CGA010_NFM_LL_Ace rep2

description: wild type

value: Yes

value: Low:4 µmol photons/m^2/s (15-W)


title: CGA010_NFM_LL_Ace rep1

description: wild type


title: dCas9-SET2-sgRNA-NT_16_1


title: dCas9-SET2-sgRNA-NT_17_2


title: PBMC unst NA low 28


title: dCas9-SET2-sgRNA-NT_17_1


title: CGA2023_NFM_HL_Suc rep2

description: ΔregSΔregR

value: Succinate

value: {delta}regS{delta}regR


title: CLas + Stem-pitting CTV Month 2-I6 [MI2I6]


title: PBMC RV A high 26

value: Asthma


title: CLas + Mild CTV Month 2-H3 [MI2H3]

source_name: Clas+T30_2m Leaf


title: CGA2023_NFM_HL_Mal rep1

description: ΔregSΔregR

value: Malate


title: CGA010_NFM_HL_Suc rep2

description: wild type

value: wild type


title: CLas + Stem-pitting CTV Month 2-I4 [MI2I4]

value: Young tree


title: dCas9-SET2-sgRNA-NT_16_3

value: Brain

value: 8 weeks


title: PBMC unst NA low 25

value: Peripheral blood morphonuclear cell

value: low


title: CLas + Stem-pitting CTV Month 2-I3 [MI2I3]


title: CGA010_NFM_HL_Mal rep1

description: wild type

value: High:30 µmol photons/m^2/s (60-W)


title: O_OE_AIMP1

city: Nanjing

first: Rong

middle: Fang

last: Wei

state: Jiangsu

address: 138 Xianlin Road

institute: Nanjing Unveristy of Chinese Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: multiple myeloma cells

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: multiple myeloma cells

tag: genotype/variation

value: overexpression

tag: cell line

value: OCI


title: CGA2023_PM_HL_Mal rep2

description: ΔregSΔregR

value: No


title: dCas9-SET2-sgRNA-NT_1_1


title: O_KD1_AIMP1

value: knockdown


title: O_KD2_AIMP1


title: CLas Month 2-F7 [MI2F7]

source_name: Clas_2m Leaf

value: Clas

tag: month

tag: developmental stage

value: Leaf


title: CLas Month 2-F5 [MI2F5]


title: Mice 2

city: Lübeck

first: Anke

last: Fähnrich

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: LIED

country: Germany

institute: University of Lübeck

data_processing:
Quality filtering - fastp - qualified_quality_phred=15 ,unqualified_percent_limit=30, detect_adapter_for_pe, trim_poly_g, trim_tail1=1, trim_tail2=1
Alignment - kallisto and bustools - whitelist constructed from available BD barcode sequences
Preprocessing - R, BUSpaRse - removed false positive empty barcodes by calculating the inflectionpoint of the ranked cell barcodes
Read in Seurat Object - R, Seurat - only kept genes expressed in at least 3 cells
Saved with R, saveRDS
Genome_build: GRCm38
Supplementary_files_format_and_content: List with both samples in SeuratObjects in RDS format

source_name: Hypothalamus

growth_protocol: 10 week old C57Bl/6N mice

extract_protocol:
Freshly harvested tissue blocks of the hypothalamus were transferred to a single-cell suspension by Papain Dissociation System (Worthington; LK003150). Isolation and labeling of the transcriptome was performed using the BD Rhapsody™ Single-Cell Analysis system. mRNA was barcoded using random primers and the transscriptome was sequenced using the Illumina system. Libraries were sequenced using High Output Sequencing Kits (75× 2bp) (Illumina) from a commercial supplier (Novogene).
RNA libraries were prepared for sequencing using BD Rhapsody WTA single cell RNA-seq protocol

treatment_protocol: non treatment

value: hypothalamus single cells

value: 10 weeks post natal

tag: strain background


title: dCas9-SET2-sgRNA-NT_16_4


title: O_WT_AIMP1

value: treated with protein


title: dCas9-SET2-sgRNA-NT_1_4

value: wild type


title: O_WT

value: wildtype


title: dCas9-SET2-sgRNA-NT_1_3

value: Brain


title: Mice 1


title: CGA010_NFM_HL_Suc rep1

description: wild type

tag: carbon source

value: Succinate


title: CLas + Mild CTV Month 2-H2 [MI2H2]

value: Young tree


title: CLas Month 2-F4 [MI2F4]


title: dCas9-SET2-sgRNA-NT_1_2

value: 8 weeks


title: CLas + Mild CTV Month 2-H5 [MI2H5]


title: CLas + Mild CTV Month 2-H10 [MI2H10]


title: H_OE_AIMP1


title: CGA2023_NFM_HL_Suc rep1

description: ΔregSΔregR

tag: nitrogen-fixing conditions?

value: High:30 µmol photons/m^2/s (60-W)

value: {delta}regS{delta}regR


title: H_WT

value: multiple myeloma cells


title: CGA010_PM_HL_Mal rep2

description: wild type

value: Malate

tag: light intensity


title: CGA2023_PM_HL_Mal rep1

description: ΔregSΔregR

value: No


title: CGA2023_PM_HL_Ace rep2

description: ΔregSΔregR

value: Acetate


title: H_WT_AIMP1


title: CGA010_PM_HL_Ace rep2

description: wild type


title: Stem-pitting CTV Month 2-E8 [MI2E8]

source_name: Stem-pitting CTV (CCTEA-107)_2m Leaf

value: Stem-pitting CTV (CCTEA-107)


title: WT_60light_R3

first: Javier

last: Avalos

address: Av. Reina Mercedes sn

department: Genetics

country: Spain

institute: University of Seville

data_processing:
Raw reads for all samples were trimmed, filtered and quality controlled with AfterQC (Chen et al., 2017; doi:10.1186/s12859-017-1469-3)
Read mapping to the reference genome was performed using Star (Dobin et al. 2013)
The annotation used was the corresponding one from the EnsemblFungi database (https://fungi.ensembl.org) for F. fujikuroi IMI58289.
Mapped sequences were analyzed using SeqMonk (version 1.45.4, https://github.com/s-andrews/SeqMonk)
Quantification was performed using the Seqmonk RNAseq quantitation pipeline, merging transcripts and counting reads over exons.
Deseq2 tool (Love et al., 2014; doi:10.1186/s13059-014-0550-8), implemented in SeqMonk, which uses raw counts for quantitation, was used to compare among conditions.
Genome_build: FMJU01
Supplementary_files_format_and_content: Processed data are described in a single tab-delimited text file that includes raw counts for all samples, indicating probe, chromosome, start and end positions, and feature. Transcripts with no equivalent in FFUJ annotation are indicated as "null"

organism: Fusarium fujikuroi

source_name: Wild type 60 min illumination

growth_protocol: the strains were grown in 100 ml of DG medium in 500 ml Erlenmeyer flasks, inoculated with 1000000 conidia. The flasks were kept in total darkness for three days at 30°C in an orbital shaker (150 rpm). Then, the cultures were transferred to four 25-ml Petri dishes under safe red light and kept in static conditions in the dark for 240 min. Subsequently, the Petri dishes were either kept in the dark or illuminated for 60 min.

extract_protocol:
RNA samples were extracted with Trizol (Invitrogen, Paisley, UK) using the protocol described by the manufacturer and further purified with the NucleoSpin RNA kit (Macherey-Nagel, GmbH & Co. KG Germany) following the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols
75 bp sequenced in single read mode

treatment_protocol: Illumination was provided by a set of four fluorescent tubes (Philips TL-D 18 W/840) at a distance of 60 cm, yielding a light intensity of 7 W/m2.

value: wild strain IMI58289

value: mycelium

value: illuminated for 60 min


title: Curdlan-WT_neutrophils 1

source_name: Curdlan-WT neutrophils

value: BALB/c SKG

value: neutrophils

tag: time point

value: 8 weeks post curdlan


title: Mild CTV Month 4-D3 [MI4D3]

value: Mild CTV (T30 isolate)

tag: tissue

value: Leaf


title: CGA010_PM_HL_Mal rep1

description: wild type

value: wild type


title: Stem-pitting CTV Month 2-E4 [MI2E4]

value: Young tree


title: RSLB1

city: Trivandrum

first: Rakesh

middle: S

last: Laishram

state: Kerala

address: Thycaud P O, Poojappura

department: Cardiovascular and Diabetes Biology Group

country: India

institute: Rajiv Gandhi Centre for Biotechnology(RGCB)

data_processing:
The raw data generated was checked for the quality with FastQC1 and pre-processed for removing adapter sequences and low quality bases using Genotypic's proprietary script. It was then aligned using Tophat-2.0.133  to Escherichia coli (K-12) Ensembl  (http://bacteria.ensembl.org/Escherichia_coli_str_k_12_substr_mg1655/Info/Index)
Transcript assembly was done using Cufflinks-2.2.14 which assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.
Using cuffmerge, cufflinks assemblies were combined followed by differntial gene expression analysis using "Cuffdiff"  to obtain the significant changes in transcript expression.
Uniprot knowledge base was used to annotate the genes for Gene Ontology (GO). Differential gene expression studies were carried out between PABPN1 expressed group versus wild type MG1655 samples.
Genome_build: Differentially expressed genes were further annotated for the protein name and Gene Ontology and heat map generated as a representation of the expression values (as colours).
Supplementary_files_format_and_content: Matrix table with log fold change

organism: Escherichia coli

source_name: Escherichia coli

growth_protocol: All bacterial strains were grown at 37°C in nutrient rich, Luria Bertani broth until OD600 = 0.6

extract_protocol:
Bacterial cells were grown in 37°C, harvested at OD600 of ~0.6 and total RNA was isolated by trizol method. 4 μg of QC passed total RNA was used for ribo-depletion using RiboMinus Bacterial Kit (Invitrogen). Further, 100 ng of Qubit quantified ribo-depleted RNA was taken for Transcriptome library preparation according to Sure Select Strand-Specific RNA Library Prep Kit protocol outlined in “SureSelect Strand-Specific RNA Library Prep for Illumina Multiplexed Sequencing” (Illumina).
Briefly, the RNA was fragmented for 4 minutes at 94oC in the presence of divalent cations and first strand cDNA was synthesised. The single stranded cDNA was cleaned up using High Prep (Magbio, Cat # AC-60050). Strand specificity was maintained by the addition of actinomycin D. Second strand cDNA was synthesised and end repaired using Second Strand Synthesis using End Repair mix. The cDNA was cleaned up using High Prep (Magbio, Cat # AC-60050). Adapters were ligated to the cDNA molecules after addition of “A” base. High Prep cleanup was performed post ligation. The library was indexed and enriched for adapter ligated fragments using 10 cycles of PCR. The prepared library was quantified using Qubit and validated for quality by running an aliquot on High Sensitivity Bioanalyzer Chip (Agilent). 150 (75X 2) bp Paired End Sequencing was carried out on Illumina platform to generate 20-25 million PE Reads per sample.

tag: transformed with

value: Chromosomal PABP


title: CGA2023_PM_HL_Ace rep1

description: ΔregSΔregR

value: High:30 µmol photons/m^2/s (60-W)

value: {delta}regS{delta}regR


title: GCSC-Tip-02

city: Shenzhen

first: Jixian

last: Xiong

state: Guangdong

address: Xueyuan Ave 1066

institute: Shenzhen University

data_processing:
Base-calling: bcl2fastq2 v2.20.0.422 with default parameters
Alignment: Reads in gzipped fastq format were aligned using  STAR (v2.4.2a) with default parameters to the Human genome hg19, Ensembl genome GRCh37.
Read counts (abundance measurement): Reads mapping uniquely to genes annotated in Ensembl genome GRCh37 were counted using RSEM (v1.2.29)
Normalized Counts: edgeR (v3.8.5) package in R was used to perform TMM (trimmed mean of M values) and CPM (count per million) normalization for the the gene expression
Genome_build: hg19
Supplementary_files_format_and_content: raw counts, TMM and CPM, differentially expressed genes

source_name: gastric cancer

extract_protocol:
RNA was extracted using TRIzol, and total RNA was polyA enriched. For each sample, RNA from biological replicates (n=3) were collected and  sequenced on Illumina NovaSeq platform as paired-end reads.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Fresh isolated, primary tumor-derived GCSC cells were treated with or without Tipranavir (20uM) for 24 h

value: gastric adenocarcinoma

tag: cell type

value: patient-derived gastric cancer stem cell

tag: group

value: Tipranavir

tag: treatment

value: treated with Tipranavir for 24 hours


title: GCSC-Tip-03


title: RSLA1


title: H_KD2_AIMP1

value: multiple myeloma cells

value: knockdown


title: Stem-pitting CTV Month 2-E10 [MI2E10]

value: Stem-pitting CTV (CCTEA-107)


title: Input Smad4 replicate2

city: Basel

first: Shalu

last: Jhanwar

address: Mattenstrasse 28

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

description: Input for Smad4 ChIP-seq at 25-30 somites

data_processing:
Hiigh quality reads for Smad4 were aligned on mm10 reference using Bowtie v2.2.9 while bwa was used to align single end reads of Gli3.
Mapped reads were filtered for duplicates using Picard. Filtered bam files were subsequently sorted and indexed using Samtools.
Peaks were called using Masc2 (Zhang et al. 2008).
Normalized profiles were generated in wig/bigWig format to visualize on UCSC genome browser.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: embryo

growth_protocol: Mice homozygous for the Smad43xFlag/3xFlag and the Gli33xFlag/3xFlag  were maintained in Swiss Albino and C57BL/6J backgrounds respectively in the animal facility under normal conditions. Date of vaginal plug was scored as embryonic day (E) 0.5 and pregnancy was confirmed by palpation.

extract_protocol:
For Gli3 ChIP, briefly limb buds at E10.5 and E11.5 were collected and pooled into ice-cold PBS prior to crosslinking them in 1% formaldehyde/PBS for 20min at room temperature and processed for ChIP as previously described in Peterson et al. 2012. For Smad4, embryos were cross-linked with 1%formaldehyde and chromatin immunoprecipitation was performed according to Sheth et al 2016.
For Gli3 ChIP, sequencing libraries were prepared according to manufacturer instructions (Takara Bio, Japan) and sequenced using a NextSeq instrument (Illumina) to generate single end reads. While for Smad4 ChIP, libraries were prepared with MicroPlex Library preparation kit V2 (Diagenode) according to the manufacture's instructions/protocol, and  sequenced using a NextSeq instrument (Illumina) to generate paired end reads.

value: Swiss albino

value: embryo

tag: chip antibody


title: ChIP Smad4 replicate2

description: ChIP-seq from whole embryos from SMAD4 flagged mice at 25-30 somites

tag: genotype

value: mouse monoclonal anti-FLAG (Sigma)


title: Stem-pitting CTV Month 2-E5 [MI2E5]


title: H_KD1_AIMP1


title: GCSC-Control-02

value: Control

value: untreated


title: CGA010_PM_HL_Ace rep1

description: wild type

value: Acetate

value: No

value: wild type


title: RSLD1

tag: strain

value: Plasmid PABP


title: WT_60light_R2

value: wild strain IMI58289

value: mycelium

value: illuminated for 60 min


title: Mild CTV Month 2-D3 [MI2D3]

source_name: Mild CTV (T30 isolate)_2m Leaf

value: Mild CTV (T30 isolate)

value: Young tree

value: Leaf


title: CLas Month 2-F1 [MI2F1]

value: Clas


title: WT_dark_R1

source_name: Wild type dark

value: dark for 60min


title: WT_dark_R2


title: Mild CTV Month 2-D2 [MI2D2]


title: CLas Month 2-F10 [MI2F10]


title: GCSC-Tip-01

value: gastric adenocarcinoma

value: patient-derived gastric cancer stem cell

value: Tipranavir

value: treated with Tipranavir for 24 hours


title: WT_60light_R1


title: WT_dark_R3


title: cytosolic RNA infected by bat morbillivirus

city: new york

first: satoshi

last: ikegame

state: new york

address: 1468 madison avenue, Annenbergbuilding 17-24

department: microbiology

institute: Icahn school of medicine at Mount Sinai

data_processing:
HiSeq Control software was used for basecalling
bowtie2 (version 2.3.4.3) for alignment
IGVtools (version 2.5.3) for exporting wig file.
Genome_build: bat morbillirus genome sequence (MW557651) were used for alignment.
Supplementary_files_format_and_content: processed data show the coverage of sequenced reads

organism: Myotis riparius

source_name: rectal swab from myotis riparius

extract_protocol:
Roche MagNA Pure 96
Total nucleic acid was DNase treated (DNase I; Ambion, Life Technologies, Inc.) and reverse transcribed using SuperScript III (Invitrogen, Life Technologies, Inc.) with random hexamer primers. The cDNA was treated with RNase H before second-strand synthesis by Klenow fragment (3′ to 5′ exonuclease) (New England Biolabs), then the double-stranded cDNA was sheared into average of 200 bps fragments using a Covaris focused ultrasonicator E210

treatment_protocol: no treatment

tag: sample type

value: rectal swab


title: Mild CTV Month 2-D1 [MI2D1]


title: RNA-seq FL bud E11.5 replicate 1

description:
HFK5FBGX5_E115A
HV2VFBGX3_E115A
RNA_FL_E11.5_repA
Total RNA extracted from forelimb buds of mouse at E11.5 stage

data_processing:
Raw single-end sequencing reads of 85 bp for mouse FLB (E9.75, E10.5 and E11.5) and chicken wing bud (HH20, HH22, HH24) were subjected to quality check using FASTQC (FastQC: a quality control tool for high throughput sequence data) and Trim Galore v 0.4.1.
High-quality sequencing reads were aligned on reference genome and transcriptome (ensembl release-91) of mouse (mm10) and chicken (galGal5) using a fast accurate aligner STAR v2.5.2 (Dobin A et al., 2012) following ENCODE settings.
bigWig profiles of normalized counts (reads per kilobase per million mapped reads) were generated using deeptools v3.0.0 (Ramírez, Fidel, et al., 2016).
Genome_build: mm10, galGal5
Supplementary_files_format_and_content: bigWig

source_name: forelimb buds

extract_protocol:
Per biological triplicates (n=3), a pair of mouse forelimb buds at E9.75 (28-30 somites), E10.5 (34-36 somites) and E11.5 (43-45 somites) stages and chicken wing buds at HH20, HH22 and HH24 stages and were microdissected in cold PBS. These samples were transferred to RNA later (SigmaR0901) after an overnight incubation at 4°C and samples were stored at -20°C. Total RNA was extracted using the RNeasy micro kit (Qiagen Ref.74004). Homogenization of tissue in RLT buffer was done by sheering the sample using a 25G needle for 20 times. An on column DNA digestion (Qiagen Ref.79254) was done during the extraction to minimize the gDNA contamination. RNA integrity was checked on a Agilent Fragment Analyser (RNA analysis kit DNF-472-0500). The RNA concentration was measured by QubitTM RNA HS Assay kit (Ref Q32855).
500ng total RNA was used to prepare RNA-seq libraries using NEB non directional NEBNext® Ultra™ II RNA Library Prep (E7775), using the polyA mRNA workflow and 9 cycles of PCR amplification. Barcoded poly-A RNA-seq libraries were pooled equal molar and sequenced on the Illumina Nextseq500.

value: Swiss albino

value: forelimb buds


title: GCSC-Control-03

value: Control

value: untreated


title: RNA-seq FL bud E11.5 replicate 3

description:
HFK5FBGX5_E115C
HV2VFBGX3_E115C
RNA_FL_E11.5_repC
Total RNA extracted from forelimb buds of mouse at E11.5 stage


title: Mild CTV Month 2-D4 [MI2D4]


title: RNA-seq FL bud E11.5 replicate 2

description:
HFK5FBGX5_E115B
HV2VFBGX3_E115B
RNA_FL_E11.5_repB
Total RNA extracted from forelimb buds of mouse at E11.5 stage


title: S. citri Month 2-C5 [MI2C5]

source_name: S. citri_2m Leaf

value: S. citri


title: RNA-seq FL bud E9.75 replicate 3

description:
HFK5FBGX5_E975C
HV2VFBGX3_E975C
RNA_FL_E9.75_repC
Total RNA extracted from forelimb buds of mouse at E9.75 stage


title: RNA-seq FL bud E9.75 replicate 2

description:
HFK5FBGX5_E975B
HV2VFBGX3_E975B
RNA_FL_E9.75_repB
Total RNA extracted from forelimb buds of mouse at E9.75 stage


title: GCSC-Control-01


title: S. citri Month 2-C3 [MI2C3]


title: carP_dark_R2

source_name: carP mutant SG268 dark

value: Mutant SG268

value: carP deletion mutant

value: mycelium


title: carP_60light_R2

source_name: carP mutant SG268 60 min illumination

value: illuminated for 60 min


title: carP_60light_R3


title: carP_dark_R1


title: RNA-seq FL bud E10.5 replicate 3

description:
HFK5FBGX5_E105C
HV2VFBGX3_E105C
RNA_FL_E10.5_repC
Total RNA extracted from forelimb buds of mouse at E10.5 stage


title: Mild CTV Month 2-D9 [MI2D9]

value: Mild CTV (T30 isolate)

value: Young tree

value: Leaf


title: 21MP3

first: Bin

last: Li

address: 50# Zhongling Street

department: Institute of Veterinary Medicine

hyb_protocol: Array hybridization using the NimbleGen Hybridization System and followed by washing with the NimbleGen wash buffer kit

scan_protocol: Array scanning using the Agilent Scanner G2505C.Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis.

data_processing: Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization. The 24 gene level files were imported into Agilent GeneSpring GX software (version 11.5.1) for further analysis. Genes that have values greater than or equal to lower cut-off: 50.0 in 1 out of 24 samples (“All Targets Value”) were chosen for data analysis. Significant differentially expressed genes were identified through Volcano Plot filtering. Pathway Analysis and GO analysis were applied to determine the roles of these differentially expressed genes played in these biological pathways or GO terms. Finally, Hierarchical Clustering was performed to show distinguishable gene expression profiling among samples.

organism: Sus scrofa

source_name: PAM collected from the piglets with Mhp+PRRSV infection

label_protocol: 5 mg cRNA was reverse transcribed to cDNA, fragmented, and then labeled with Cy3-dCTP (GE Healthcare) using Klenow.

growth_protocol: All animal experiments were approved by the Science and Technology Agency of Jiangsu Province. Approval was also granted by the Jiangsu Academy of Agricultural Sciences Experimental Animal ethics committee. All efforts were made to minimize the suffering of the animals. Five-week-old piglets were purchased from a healthy herd and were identified as negative for PCV, PRRSV and Mph. All piglets were randomly divided into four groups (six piglets for each group), which included the control group, PRRSV-infected group, Mph-infected group and the Mph-PRRSV coinfected group. Animals were given commercial feed and water at libitum throughout the experiment. The piglets in the PRRSV-infected group and coinfected group were infected with the HP-PRRSV NJGC strain (106.0TCID50/mL) through intranasal (2 mL) inoculation. Mph challenge, piglets in the Mph-infected group and the coinfected group were inoculated intranasally (5 mL) with Mph XLW-1 at a concentration of 1 ×105 CCU (color change unit)/mL.The piglets in the control group received PBS (2 ml).

treatment_protocol: Briefly, piglets were sedated using a Ketamine/Azaperone pre-medication mix and anaesthetized with Ketamine/Midazolam. Anesthesia throughout the procedure was maintained using Sevoflurane. PAMs were collected by broncho alveolar lavage (BAL) through an intubation with an air flow access. The lung segments were flushed in each animal using 2× 20 ml PBS. Fluid recovery was between 60–80%. Cells were collected by centrifugation for 10min at 800g from the BAL fluid and frozen at -80℃。  T

tag: agent

value: Mhp+PRRSV


title: carP_dark_R3

value: dark for 60min


title: S. citri Month 2-C2 [MI2C2]

tag: month


title: carP_60light_R1


title: RNA-seq FL bud E10.5 replicate 1

description:
HFK5FBGX5_E105A
HV2VFBGX3_E105A
RNA_FL_E10.5_repA
Total RNA extracted from forelimb buds of mouse at E10.5 stage

tag: developmental stage


title: RNA-seq FL bud E10.5 replicate 2

description:
HFK5FBGX5_E105B
HV2VFBGX3_E105B
RNA_FL_E10.5_repB
Total RNA extracted from forelimb buds of mouse at E10.5 stage


title: RNA-seq WB HH24 replicate 2

description:
HFK5FBGX5_HH24B
HV2VFBGX3_HH24B
RNA_WB_HH24_repB
Total RNA extracted from forelimb buds of mouse at HH24 stage

organism: Gallus gallus

source_name: wing buds

value: White Leghorn

value: wing buds


title: S. citri Month 2-C6 [MI2C6]


title: 21P3

institute: Jiangsu Academy of Agricultural Sciences

source_name: PAM collected from the piglets with PRRSV infection

value: PRRSV


title: Control Month 2-B8 [MI2B8]

source_name: Control_2m Leaf


title: S. citri Month 2-C4 [MI2C4]


title: 21P2


title: 21MP2


title: ATAC-seq forelimb bud E11.5 replicate 2 [re-analysis]

description:
e115_ATAC_rep2
ATAC_FL_E11.5_rep2
Raw sequencing data (fastq) generated in our lab was previously submitted; GSE126292 (sample GSM3595753)

data_processing:
Raw reads of 41 bp paired-end reads for developing mouse forelimb bud (E9.75, E10.5 and E11.5) and chicken wing bud (HH20, HH22 and HH24) stages were evaluated for quality using Trim galore v0.6.2 wrapper for Cutadapt (Martin, 2011) with --nextera --gzip --paired settings.
High-quality reads from mouse and chicken samples were aligned to the latest release of their respective reference genomes (mouse - GRCm38/mm10; chicken - Gallus_gallus-5.0/galGal5) using Bowtie2 v2.2.9 (Langmead B et al., 2012) following ENCODE settings.
CollectInsertSizeMetrics.jar and MarkDuplicates.jar utility from Picard v2.8.0 (BroadInstitute 2015) were used to generate fragment size statistics and eliminate PCR duplicates respectively. SAMtools commands utility (Li et al., 2009) was used for format conversion (view), indexing (index) and sorting (sort) of the alignment files.
bigWig profiles of normalized counts (reads per kilobase per million mapped reads) were generated using deeptools v3.0.0 (Ramírez, Fidel, et al., 2016).
Genome_build: mm10, galGal5
Supplementary_files_format_and_content: bigWig

extract_protocol:
Per biological replicate, a pair of forelimb bud of mouse at E9.75 and wing bud of chicken at HH20, HH22 and HH24 stages were microdissected in cold PBS. Cells were isolated from the tissue using a Dounce Tissue Grinder (VWR KT885300-002) pestl A for 20 strokes followed by B 20 strokes in 1ml cold PBS. Cells were counted using a Neubauer Counting chamber (VWR 631-0696)
75'000 cells were processed per sample for ATAC-Seq as described in Buenrostro et al., 2015.

value: Swiss albino


title: RNA-seq WB HH24 replicate 1

description:
HFK5FBGX5_HH24A
HV2VFBGX3_HH24A
RNA_WB_HH24_repA
Total RNA extracted from forelimb buds of mouse at HH24 stage


title: RNA-seq WB HH24 replicate 3

description:
HFK5FBGX5_HH24C
HV2VFBGX3_HH24C
RNA_WB_HH24_repC
Total RNA extracted from forelimb buds of mouse at HH24 stage


title: ATAC-seq forelimb bud E11.5 replicate 1 [re-analysis]

description:
e115_ATAC_rep1
ATAC_FL_E11.5_rep1
Raw sequencing data (fastq) generated in our lab was previously submitted; GSE126292 (sample GSM3595752)

value: forelimb buds


title: 21P1


title: Control Month 2-B3 [MI2B3]

value: Control


title: RNA-seq WB HH22 replicate 3

description:
HFK5FBGX5_HH22C
HV2VFBGX3_HH22C
RNA_WB_HH22_repC
Total RNA extracted from forelimb buds of mouse at HH22 stage


title: RNA-seq FL bud E9.75 replicate 1

description:
HFK5FBGX5_E975A
HV2VFBGX3_E975A
RNA_FL_E9.75_repA
Total RNA extracted from forelimb buds of mouse at E9.75 stage


title: ATAC-seq forelimb bud E10.5 replicate 2 [re-analysis]

description:
e105_ATAC_rep2
ATAC_FL_E10.5_rep2
Raw sequencing data (fastq) generated in our lab was previously submitted; GSE126292 (sample GSM3595751)


title: ATAC-seq forelimb bud E10.5 replicate 1 [re-analysis]

description:
e105_ATAC_rep1
ATAC_FL_E10.5_rep1
Raw sequencing data (fastq) generated in our lab was previously submitted; GSE126292 (sample GSM3595750)


title: RNA-seq WB HH22 replicate 2

description:
HFK5FBGX5_HH22B
HV2VFBGX3_HH22B
RNA_WB_HH22_repB
Total RNA extracted from forelimb buds of mouse at HH22 stage


title: Control Month 2- B6 [MI2B6]


title: ATAC-seq forelimb bud E9.75 replicate 2

description:
e975_ATAC_rep2
ATAC_FL_E9.75_rep2
ATAC-seq of mouse limb buds at E9.75 stage


title: Control Month 4- B6 [MI4B6]

source_name: Control_4m Leaf


title: RNA-seq WB HH20 replicate 3

description:
HFK5FBGX5_HH20C
HV2VFBGX3_HH20C
RNA_WB_HH20_repC
Total RNA extracted from forelimb buds of mouse at HH20 stage


title: RNA-seq WB HH20 replicate 2

description:
HFK5FBGX5_HH20B
HV2VFBGX3_HH20B
RNA_WB_HH20_repB
Total RNA extracted from forelimb buds of mouse at HH20 stage


title: Control Month 2-B10 [MI2B10]


title: RNA-seq WB HH22 replicate 1

description:
HFK5FBGX5_HH22A
HV2VFBGX3_HH22A
RNA_WB_HH22_repA
Total RNA extracted from forelimb buds of mouse at HH22 stage


title: 21M3

source_name: PAM collected from the piglets with Mhp infection

value: Mhp


title: Control Month 2-B5 [MI2B5]


title: Mild CTV Month 2-E9 [MI2E9]

source_name: Stem-pitting CTV (CCTEA-107)_2m Leaf

value: Stem-pitting CTV (CCTEA-107)


title: Mock Gli3 E10.5

description: Mock for GLI3 ChIPseq at E10.5

data_processing:
Hiigh quality reads for Smad4 were aligned on mm10 reference using Bowtie v2.2.9 while bwa was used to align single end reads of Gli3.
Mapped reads were filtered for duplicates using Picard. Filtered bam files were subsequently sorted and indexed using Samtools.
Peaks were called using Masc2 (Zhang et al. 2008).
Normalized profiles were generated in wig/bigWig format to visualize on UCSC genome browser.
Genome_build: mm10
Supplementary_files_format_and_content: wig, bigWig

source_name: limb buds

value: limb buds


title: Input Gli3 E10.5

description: Input for GLI3 ChIPseq at E10.5


title: 21M2


title: 21M1


data_processing:
Guppy (version 3.2.6)
minimap2 (version2.17-r941) for alignment
IGVtools (version 2.5.3) for exporting wig file.
Genome_build: bat morbillirus-eGFP genome sequence ( 1- 16,566 bp of MW553715) were used for alignment.
Supplementary_files_format_and_content: processed data show the coverage of sequenced reads

organism: Measles morbillivirus

source_name: african green monkey renal cells expressing batCD150

growth_protocol: Bat morbillivirus was infected to Vero-batCD150 cells at MOI=0.01. Cytosolic RNA was collected at day2.

extract_protocol:
Trizol
Direct RNA Sequencing Kit (SQK-RNA002) from Oxford nanopore technology was used by following manufacture's protocol.

value: Vero CCL81 cells expressing batCD150

tag: passages

value: passage 1


title: RNA-seq WB HH20 replicate 1

description:
HFK5FBGX5_HH20A
HV2VFBGX3_HH20A
RNA_WB_HH20_repA
Total RNAextracted from forelimb buds of mouse at HH20 stage


title: ATAC-seq forelimb bud E9.75 replicate 1

description:
e975_ATAC_rep1
ATAC_FL_E9.75_rep1
ATAC-seq of mouse limb buds at E9.75 stage


title: ChIP Gli3 E10.5 replicate2

description: GLI3 ChIPseq is done with GLI33xF E10.5 limb buds and normalised against input

value: mouse monoclonal anti-FLAG (Sigma, F1804, AB_262044)


title: 21C2

source_name: PAM  collected from the piglets without infection

value: uninfection


title: 21C1


title: 10MP3


title: ATAC-seq wing bud HH24 replicate 2

description:
h24_ATAC_rep2
ATAC_WB_HH24_rep2
ATAC-seq of chicken wing buds at HH24 stage


title: Mock Gli3 E11.5

description: Mock for GLI3 ChIPseq at E11.5


title: 21C3


title: ChIP Gli3 E10.5 replicate1


title: ATAC-seq wing bud HH24 replicate 1

description:
h24_ATAC_rep1
ATAC_WB_HH24_rep1
ATAC-seq of chicken wing buds at HH24 stage


title: ATAC-seq wing bud HH22 replicate 2

description:
h22_ATAC_rep2
ATAC_WB_HH22_rep2
ATAC-seq of chicken wing buds at HH22 stage


title: DCM patient plasma  [Sample 43]

type: protein

first: Danielle

last: Jeffrey

institute: University of Colorado

hyb_protocol: Following the manufacturer’s protocol and utilizing SOMAmer reagents immobilized on streptavidin beads, proteins from plasma samples were tagged with NHS-biotin reagent, captured as a SOMAmer reagent/protein complex, cleaved, denatured, eluted and hybridized to a custom Agilent DNA microarray. Additional details can be found at http://www.tandfonline.com/doi/abs/10.1586/erm.10.89 and Gold L et al. N Biotechnol. 2012 Jun 15;29(5):543-9.

scan_protocol: Microarrays were scanned with an Agilent SureScan scanner at 5 um resolution, and the Cy3 fluorescence readout was quantified. Additional information can be found in Gold L et al. N Biotechnol. 2012 Jun 15;29(5):543-9.

data_processing: Calibration normalizations, welch's t-test with adjusted FDR q<0.1

molecule: protein

source_name: patient plasma

extract_protocol: Performed by University of Colorado Genomics Core (Ref 53 in manuscript)

treatment_protocol: whole blood vacutainers with anticoagulant citrate dextrose - samples centrifuged @ 2200 g for 15 min at room temp, plasma layer aliquoted and stored at -80C

tag: disease

value: DCM patient

tag: age

value: <18 years old (match to patient demographics table)

value: plasma


title: NF patient plasma  [Sample 15]

label_protocol: Following the manufacturer’s protocol and utilizing SOMAmer reagents immobilized on streptavidin beads, proteins from plasma samples were tagged with NHS-biotin reagent, captured as a SOMAmer reagent/protein complex, cleaved, denatured, eluted and hybridized to a custom Agilent DNA microarray. Additional details can be found at http://www.tandfonline.com/doi/abs/10.1586/erm.10.89 and Gold L et al. N Biotechnol. 2012 Jun 15;29(5):543-9.

value: NF patient


title: ATAC-seq wing bud HH22 replicate 1

description:
h22_ATAC_rep1
ATAC_WB_HH22_rep1
ATAC-seq of chicken wing buds at HH22 stage

value: White Leghorn


title: ChIP Gli3 E11.5 replicate2

description: GLI3 ChIPseq is done with GLI33xF E11.5 limb buds and normalised against input


title: ATAC-seq wing bud HH20 replicate 2

description:
h20_ATAC_rep2
ATAC_WB_HH20_rep2
ATAC-seq of chicken wing buds at HH20 stage

value: wing buds


title: NF patient plasma  [Sample 13]


title: ChIP Gli3 E11.5 replicate1


title: 10MP2

value: Mhp+PRRSV


title: 10MP1


title: ATAC-seq wing bud HH20 replicate 1

description:
h20_ATAC_rep1
ATAC_WB_HH20_rep1
ATAC-seq of chicken wing buds at HH20 stage


title: Input Gli3 E11.5

description: Input for GLI3 ChIPseq at E11.5


title: 10P1

value: PRRSV


title: cytosolic RNA infected by bat morbillivirus 3

description: coverage.xlsx

data_processing:
MiSeq Control software (version 2.5.0.5) was used for basecalling
BBTools (version 37.77) for merging paired-end reads
bowtie2 (version 2.3.4.3) for alignment
IGVtools (version 2.5.3) for exporting wig file.
Genome_build: Part of bat morbillirus genome sequence ( 3150-3599 bp of MW553715) were used for alignment.
Supplementary_files_format_and_content: processed data show the coverage of sequenced reads

source_name: african green monkey renal cells expressing batCD152

extract_protocol:
Trizol
Total cytosolic RNA were reverse transcribed by poly-T primer. Then, cDNA were amplified by primer set of 'gggacctgttgcccgtttta' and 'tgtcggacctcttactactagact'


title: NF patient plasma  [Sample 14]


title: cytosolic RNA infected by bat morbillivirus 2

description: coverage.xlsx

source_name: african green monkey renal cells expressing batCD151


title: wt EC2_and_EC1_EC2

description: 4C-seq of Grem1 wildtype sample corresponding to del_EC2 genotype and del_EC1_EC2 genotype.

data_processing:
Library strategy: 4C-seq
Reads were aligned to the mouse reference genome (mouse mm10) using Bowtie v 2.2.9.
bedGraph formatted files of the read counts for each fragment or a specified window of fragments were generated
4C‐seq contacts were analyzed for the mouse region on chr2:113326224-113894862 that encompasses the Grem1-Fmn1 landscape
The viewpoint, adjacent undigested fragments and fragments 10 kb up- and downstream were excluded
Finally, a range of 5 informative fragments was used to normalize the data per million reads (RPM) over a sliding window using custom scripts and these continuous‐valued profiles were used to interpret 4C-seq outcome.
Genome_build: mm10
Supplementary_files_format_and_content: Smoothed/normalized data (bedGraph)

growth_protocol: Wild-type Swiss Albino mice were maintained in the animal facility under normal conditions. Date of vaginal plug was scored as embryonic day (E) 0.5 and pregnancy was confirmed by palpation.

extract_protocol:
4C-seq libraries were generated from 10-20 limb bud pairs (E11.0, 40-42 somites) as described by Noordermeer et al., 2011. For each sample, 2-4x106 cells were used. DpnII and NlaIII were used as primary and secondary restriction enzymes respectively. All samples except EC2-/- and EC1-/-EC2-/- genotypes was amplified in 10 PCR reactions (30 cycles with adapter + Viewpoint (VP) primer). For EC2-/- and EC1-/-EC2-/- samples, nested PCR was used as follows a) 1st PCR - 10 reactions with 150 ng with VP primer (no adapter), Column purification b) 2nd PCR - 1 reaction, 50 ng, 8 cycles with adapter +VP primer, AMPure size selection. Below are the primers used for the preparation of 4C libraries: Grem1_C1_TUA: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTCTTCCGTAGATGCTGGCCGAT, Grem1_C6_index12: CAAGCAGAAGACGGCATACGAGATTACAAGGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTAAGCACCAGGACCGAGTTTG, Grem1_C6_index2: CAAGCAGAAGACGGCATACGAGATACATCGGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTAAGCACCAGGACCGAGTTTG, Grem1_C6_index4: CAAGCAGAAGACGGCATACGAGATTGGTCAGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTAAGCACCAGGACCGAGTTTG, Grem1_C6_index5: CAAGCAGAAGACGGCATACGAGATCACTGTGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTAAGCACCAGGACCGAGTTTG, Grem1_C6_index6: CAAGCAGAAGACGGCATACGAGATATTGGCGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTAAGCACCAGGACCGAGTTTG, Grem1_C6_index7: CAAGCAGAAGACGGCATACGAGATGATCTGGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTAAGCACCAGGACCGAGTTTG, Grem1_C6_index9: CAAGCAGAAGACGGCATACGAGATCTGATCGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTAAGCACCAGGACCGAGTTTG
The libraries were generated for EC2-/- and EC1-/- EC2-/-  with a modified version of Krijger et al., 2020. All other samples were done according to modified version of  Noordermeer et al., 2011. These libraries were multiplexed and sequenced with Illumina Nextseq 500 to generate single or paired-end reads.

value: Swiss albino (mixed background)

value: wt


title: ChIP Smad4

description: ChIP-seq from whole embryos from SMAD4 flagged mice at 25-30 somites

source_name: embryo

value: Swiss albino

value: embryo


title: 10P3

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


title: 10P2


title: DCM patient plasma  [Sample 45]


title: DCM patient plasma  [Sample 44]


title: cytosolic RNA infected by bat morbillivirus 1

description: coverage.xlsx


title: 10M3

value: Mhp


title: 21MP1


title: wt Cis

description: 4C-seq of Grem1 wildtype sample corresponding to del_Cis genotype.

value: limb buds


title: NF patient plasma  [Sample 16]


title: X8: LPS+IFN-γ and Tub B rep2

first: Jie

last: Yao

address: Luohu district

institute: Shenzhen People’s Hospital

data_processing:
Illumina RTA software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR 2.7.0 with default parameters
The gene expression level was calculated by featureCounts with default parameters.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: macrophage

extract_protocol:
Total RNA was extracted by using EASYspin RNA Mini Kit (Aidlab RN07).
RNA-seq libraries were constructed by NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490) and NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module (NEB E6111).

value: LPS+IFN-γ and Tubuloside B


title: DCM patient plasma  [Sample 48]


title: 10M2


title: X7: LPS+IFN-γ and Tub B rep1


title: 10C3


title: 10M1


title: Input Smad4

description: Input for Smad4 ChIP-seq at 25-30 somites


title: wt CRM2

description: 4C-seq of Grem1 wildtype sample corresponding to del_CRM2 genotype.


title: DCM patient plasma  [Sample 47]


title: wt EC1

description: 4C-seq of Grem1 wildtype sample corresponding to del_EC1 genotype.


title: DCM patient plasma  [Sample 46]


title: DCM patient plasma  [Sample 31]


title: X6: LPS+IFN-γ rep2

value: LPS+IFN-γ


title: 10C2

value: uninfection


title: 10C1


title: del Cis

description: 4C-seq of del_Cis genotype. Sequencing libraries were prepared as described by Noordermeer et al., 2011 (refer extraction protocol).

value: Cis -/-


title: X5: LPS+IFN-γ rep1


title: DCM patient plasma  [Sample 42]

value: DCM patient

value: <18 years old (match to patient demographics table)


title: sigF-deletion CapSeq 6h

city: Stockton

first: Douglas

middle: D

last: Risser

state: California

address: 3601 Pacific Ave

department: Biology

institute: University of the Pacific

data_processing:
library strategy: Cappable-seq
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence at Vertis Biotechnologie AG prior to dissemination of data to the end user
The reads were mapped to the N. punctiforme genome using Bowtie2 local
TSSs were defined in the wild type strain using the following programs: bam2firstbasegtf.pl cutoff 1; cluster_tss.pl cutoff 5 (https://github.com/Ettwiller/TSS/)
Quantitation of TSSs in the sigma factor deletion strains was performed by running bam2firstbasegtf.pl cutoff 1 for each of the mutant strain libraries, and then retrieving the relative read score (RRS) at the position corresponding to each TSS defined in the wild-type strain
Genome_build: N. punctiforme genome
Supplementary_files_format_and_content: NOT PROVIDED

organism: Nostoc punctiforme PCC 73102

source_name: N. punctiforme

growth_protocol: Nostoc punctiforme strains were cultured in Allan and Arnon medium diluted four fould (AA/4), in the absence of a source of fixed nitrogen, as previously described (Campbell et al. 2007. Global gene expression patterns of Nostoc punctiforme in steady-state dinitrogen-grown heterocyst containing cultures and at single time points during the differentiation of akinetes and hormogonia. J. Bacteriol 189:5247-5256) with the exception that cultures were supplemented with 4 mM sucralose to suppress hormognium development prior to induction as previously described (Splitt and Risser, 2016. The non-metabolizable sucrose analog sucralose is a potent inhibitor of hormogonium differentiation in the filamentous cyanobacterium Nostoc punctiforme. Arch Microbiol. 2016 Mar;198(2):137-47)

extract_protocol:
RNA extractions were performed as previously described with a bead beater and phenol (Campbell et al. 2007. Global gene expression patterns of Nostoc punctiforme in steady-state dinitrogen-grown heterocyst containing cultures and at single time points during the differentiation of akinetes and hormogonia. J. Bacteriol 189:5247-5256)
Total RNA was used to generate libraries for Cappable-seq as previously described (Ettwiller et. al., BMC Genomics volume 17, Article number: 199 (2016)) by Vertis Biotechnologie AG

treatment_protocol: For hormogonium induction, culutres were harvested at 1000xg for 5 min, washed 3x with AA/4 to remove sucralose, and resuspended in AA/4 without sucralose

tag: strain/genotype

value: ATCC 29133; sigF-deletion

tag: filament type

value: developing hormogonia

tag: time following hormogonium induction

value: 6 h

tag: molecule subtype

value: 5'-Triphosphorylated RNA


title: del EC1_EC2

description: 4C-seq of del_EC1_EC2 genotype. Libraries were prepared using nested PCR (refer extraction protocol).

tag: tissue


title: X4: Tub B rep2

tag: cell type

value: Tubuloside B


title: X3: Tub B rep1

tag: treatment


title: X2: mock rep2

value: DMSO


title: X1: mock rep1


title: del CRM2

description: 4C-seq of del_CRM2 genotype. Sequencing libraries were prepared as described by Noordermeer et al., 2011 (refer extraction protocol).

value: Swiss albino (mixed background)

value: CRM2 /-


title: sigJ-deletion CapSeq 6h

value: ATCC 29133; sigJ-deletion


title: del EC1

description: 4C-seq of del_EC1 genotype. Sequencing libraries were prepared as described by Noordermeer et al., 2011 (refer extraction protocol).


title: WT CapSeq 6h


title: WT_ethanol_rep3

city: Yokohama

last: Matsui

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Sustainable Resource Science

country: Japan

institute: RIKEN

description: WT ethanol

hyb_protocol: 600 ng of cRNAs from Poly (A+) RNA samples were hybridized to the microarray (GPL22706) at 65 degree for 17 hours, using Gene Expression Hybridization kit. After hybridization, the microarray was washed with Gene Expression Wash Buffer 1 (Agilent) and Gene Expression Wash Buffer  (Agilent), and then dried immediately by brief centrifugation.

scan_protocol: The microarray was scanned by Agilent DNA Microarray Scanner G2539A ver. C and  raw data was extracted using Feature Extraction program ver 9.1.

data_processing: RMA normalization was performed for signals of microarray probes using limma package on R program.

organism: Arabidopsis thaliana

label_protocol: 200 ng of Total RNAs were used to prepare for Cy3-labeled cRNA, using Low Input Quick Amp Labeling Kit (Agilent).

growth_protocol: Arabidopsis thaliana wild-type plants (Col-0) were grown on MS medium at 22 ﾟC under 16 hr light and 8 hr dark condition.

extract_protocol: Total RNA was extracted from whole plants using Plant RNA Isolation Reagent (Life technologies).

treatment_protocol: WT seeds were sown on MS medium with and without 2 mM ethanol and grown for 2 weeks. Then whole plants were collected at ZT 5.

tag: ecotype

value: whole plant

value: ethanol


title: WT_con_rep3

description: WT control

value: control


title: sigC-deletion CapSeq 6h

value: ATCC 29133; sigC-deletion


title: WT_ethanol_rep1

description: WT ethanol


title: WT_ethanol_rep2

description: WT ethanol


title: 24_T23_FIBROB6_ENZA_ISO_S8

status: Public on Jul 30 2021

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

description: T23 tumor cells, co-cultured with human fibroblasts and treated with the combination of enzalutamide (ENZA) and  isoliquiritigenin (ISO), replicate 3

data_processing:
Bcl files were demultiplexed using the bcl2fastq tool v 2.20.0.422. Raw sequence reads (fastq) underwent quality control by means of FastQC 0.11.9. Trimming was performed with Cutadapt 2.9. Alignment was performed using STAR 2.6.1d against the mouse GRCm38 reference genome and reads were counted by means of FeatureCounts 2.0, asking for a gene-level report. Finally, the DeSeq2 package, available within Bioconductor, was used to normalize count data, estimate biological variance and determine differential expression.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw reads counts

source_name: T23 tumor cells + fibro + ENZA + ISO, rep 3

extract_protocol:
Total RNA was isolated from cell lines by means of miRNeasy Tissue/Cells Advanced Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. RNA quality and quantity were checked using Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, California, U.S.) and Nanodrop spectrophotometer (Thermo Fisher, Waltham, Massachusetts, U.S.).
500 ng of totRNA were used to prepare RNA libraries by means of the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, California, U.S.) following the manufacturer's protocol. Briefly, the mRNA fraction was purified from total RNA by polyA capture, fragmented and subjected to first-strand cDNA synthesis with random primers in the presence of Actinomycin D. The second-strand synthesis was performed incorporating dUTP instead of dTTP. Then a single ‘A’ nucleotide was added to the 3’ ends of the blunt fragments to prevent them to ligating to each other. Index adapters were ligated and cDNA was subjected to PCR amplification. Libraries were validated using Agilent bioanalyzer (DNA 1000 kit) and the concentration was evaluated by means of Qubit™ dsDNA HS Assay Kit (Thermo Fisher). Libraries were normalized, multiplexed and sequenced on the Illumina NextSeq 550 system.


title: 23_T23_FIBROB6_ENZA_ISO_S7

description: T23 tumor cells, co-cultured with human fibroblasts and treated with the combination of enzalutamide (ENZA) and  isoliquiritigenin (ISO), replicate 2

source_name: T23 tumor cells + fibro + ENZA + ISO, rep 2


title: del EC2

description: 4C-seq of del_EC2 genotype. Libraries were prepared using nested PCR (refer extraction protocol).

value: limb buds

tag: genotype


title: WT_con_rep1

description: WT control