title: miRNA healthy controls replicate3

description:
healthy controls replicate3
miRNA expression in healthy knee


title: WCJLS_MeRIP

status: Public on Jun 02 2021

type: SRA

city: shanghai

first: jiaxiang

last: zhang

state: shanghai

address: 650 Xinsongjiang Rd

department: Department of Critical Care Medicine

country: China

institute: Shanghai Jiaotong University

library_source: transcriptomic

data_processing:
Illumina Bcl2FastQ  software used for basecalling
Adaptor and low-quality bases were trimmed with Trimmomatictools(version:0.36), and the clean reads undergone rRNA deleting through RNAcentral to get effective reads.Genomic alignment (hg19 from UCSC genome browser) was using Tophat(version:2.0.13)to get uniquely mapping reads.
MACS2(version 2.1.0.20151222) was employed to perform m6A peak calling.Then using Hommer(version:4.8)  to annotate the m6A Peaks.The nucleotides in m6A Peaks region were used for detection of the consensus  m6A motif by DREME (version:4.11.1) and MEME(version:4.11.1). Motif central enrichment was performed by  CentriMo (version:4.11.1).Differential methylation was determined by Pyicoenrich(version:2.0.7)
Genome_build: hg19
Supplementary_files_format_and_content: peak.txt：a tabular file which contains information about called peaks
Supplementary_files_format_and_content: CentriMo (version:4.11.1).Differential methylation was determined by Pyicoenrich(version:2.0.7)

molecule: total RNA

organism: Homo sapiens

source_name: fibrotic lung

extract_protocol:
50 μg RNA was isolated from human lung tissues using Trizol reagent followed by purification using RiboMinusTM Eukaryote Kit v2 (A15020, Invitrogen). Purified RNA was chemically fragmented into approximately 100 nt using Ambion RNA fragmentation regents and subjected to immunoprecipitation using m6A antibody.
library strategy: MeRIP-seq

tag: tissue

value: lung

tag: source

value: IPF lung tissue

tag: merip antibody

value: Synaptic Systems, 202003


title: miRNA healthy controls replicate1

type: RNA

city: Guangzhou

first: Jun

last: Jing

state: Guangdong

address: 107 Riverside Road, Guangzhou, Guangdong Province 510120, China

department: Department of Rheumatology

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

description:
healthy controls replicate1
miRNA expression in healthy knee

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v14.9 software package (Agilent Technologies).

source_name: healthy Knee

label_protocol: total miRNA from each sample was labeled with Cyanine 3-pCp under the action of T4 RNA ligase.

extract_protocol: The cartilage of KOA patients and healthy volunteers were collected from tibia plateau. All samples were immediately frozen in liquid nitrogen before RNA isolation.

value: cartilage


title: VirE2 Induced + Agro 3 hours replicate 3

city: WEST LAFAYETTE

first: Shaojun

last: Xie

state: Indiana

address: 3135 Decatur Street

country: USA

institute: Purdue University

description:
3 hours in induction solution (B5 liquid media plus 1 µM β-estradiol) plus A. tumefaciens strain A136 at 10^8 cfu/mL
Treated3hRep3

data_processing:
RNA was submitted to the Purdue Genomics Core Facility for sequencing after treatment with DNase I to remove any contaminating genomic DNA (Pilot Study-Replicate 1). Ribosomal RNA was depleted and cDNA libraries (stranded) were prepared from each of the samples before sequencing. Between 15 to 23 million reads were obtained for each sample (100 nucleotides per read) which were quality trimmed and mapped to the A. thaliana genome using TopHat (Trapnell et al., 2010). Differentially expressed genes were determined from the mapped (bam) files using Cuffdiff from the Cufflinks suite of programs (Trapnell et al., 2010). Custom perl scripts were used to extract genes for which fold-changes of 3 or greater occurred between the induced and non-induced control samples at their respective time points. The resulting genes were annotated by hand and separated into categories based on their Gene Ontology (GO) functions.
Second study (replicates 2 and 3): Sequence quality was assessed using FastQC (v 0.11.7) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) for all samples and quality and adapter trimming was done using TrimGalore (0.4.4) (Krueger, 2017) to remove the sequencing adapter sequences and bases with Phred33 scores less than 30. The resulting reads of length >25 bases were retained (original read length = 50 and lib type = unstranded) respectively. The quality trimmed reads were mapped against the reference genome using STAR (Dobin et al., 2013) (v 2.5.4b). STAR derived mapping results and annotation (GTF/GFF) file for reference genome were used as input for HTSeq (Anders et al., 2015) package (v 0.7.0) to obtain the read counts for each gene feature for each replicate. Counts from all replicates were merged using custom Perl scripts to generate a read count matrix for all samples.
The merged counts matrix was used for downstream differential gene expression analysis. Genes that did not have counts in all samples were removed from the count matrix and genes that had counts in some samples but not in others were changed from 0 to 1 in order to avoid having infinite values calculated for the fold change. Differential gene expression (DEG) analysis between treatment and control was carried out using ‘R’ (v 3.5.1; http://www.r-project.org/) with two different methods (DESeq2 and edgeR). Basic exploration of the read count data file such as accessing data range, library sizes, etc. was performed to ensure data quality. An edgeR object was created by combining the count's matrix, library sizes, and experimental design using the edgeR (Robinson et al., 2010) (v 3.24.3) package. Normalization factors were calculated for the count's matrix, followed by estimation of common dispersion of counts. An exact test for differences between the negative binomial distribution of counts for the two experimental conditions resulted in finding differential expression, which was then adjusted for multiple hypothesis testing. DESeq2 (Love et al., 2014) (v 1.22.2) was also used to find differentially expressed genes. Both use an estimate variance-mean test based on a model using the negative binomial distribution. The significant genes were identified by examining the adjusted p-value.
Additionally, STAR mapping (bam) files were used for analysis by the Cuffdiff from Cufflinks (v 2.2.1) (Trapnell et al., 2010) suite of programs which perform DE analysis based on FPKM values. Cuffdiff uses bam files to calculate Fragments per Kilobase of exon per Million fragments mapped (FPKM) values, from which differential gene expression between the pairwise comparisons can be ascertained. Differentially expressed gene lists detected by at least two or more methods (DESeq2, edgeR, and Cufflinks) were generated using custom Perl scripts.
Gene annotations were retrieved from BioMart databases using biomartr package in ‘R’. The "transcript_biotype", "description" attributes were extracted using mart = "plants_mart" and dataset = "athaliana_eg_gene". GO enrichment analysis was also performed using DEGs from two or more methods while using two replicates. Singular Enrichment Analysis (SEA) from agriGO (Du et al, 2010) was used to perform GO enrichment analysis (count = 5 with Fisher exact t-test with multiple testing). A GO enrichment analysis was performed using the PANTHER Classification system and online tools (http://geneontology.org/docs/go-enrichment-analysis/).
Supplementary_files_format_and_content: Count_matrix.txt

organism: Arabidopsis thaliana

source_name: Root tissue

growth_protocol: Inducible VirE2 seedlings (T3 generation) were germinated on B5 medium containing 100 mg/mL Timentin and 20 mg/mL hygromycin. The seedlings were transferred after two weeks to plates containing B5 medium lacking antibiotics. These plates were placed vertically in racks to promote root growth on the surface of the medium.

extract_protocol:
RNA was isolated from non-induced and induced roots in the presence of Agrobacterium after 0, 3, and 12 h of treatment using TriZol reagent (http://www.thermofischer.com). A total of 2 µg of total RNA was treated with Ambion DNase I (Thermo Fisher Scientific) before submitting the RNA for sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After 10 days of growth (see above), the plates were placed horizontally and B5 liquid medium containing 1 mM β-estradiol dissolved in DMSO (b-estradiol solution) or B5 plus DMSO only (control solution) with A. tumefaciens strain A136 at a concentration of 10^8 cfu/mL was pipetted onto the surface until a thin layer covered the root tissue (4-5 mL). Roots from 30 plants were cut after 0, 3, or 12 hours treatment, rinsed with sterile water, dried on a paper towel, and frozen in liquid nitrogen before RNA extraction.

tag: parental ecotype

tag: transgenic line

value: Inducible VirE2 Line 10-9 T3 generation

tag: agent

value: induction solution (B5 liquid media plus 1 microM Beta-estradiol) plus A. tumefaciens strain A136 at 10^8 cfu/mL

tag: time point

value: 3 hours


title: VirE2 Non-induced + Agro 12 hours replicate 1

description:
12 hours in control solution (B5 liquid media plus DMSO) plus A. tumefaciens strain A136 at 10^8 cfu/mL
Mock12hRep1

value: 12 hours


title: VirE2 Non-induced  + Agro 3 hours replicate 2

description:
3 hours in control solution (B5 liquid media plus DMSO) plus A. tumefaciens strain A136 at 10^8 cfu/mL
Mock3hRep2


title: SLF_MeRIP


title: SLF_Input


title: VirE2 Induced + Agro 3 hours replicate 2

description:
3 hours in induction solution (B5 liquid media plus 1 µM β-estradiol) plus A. tumefaciens strain A136 at 10^8 cfu/mL
Treated3hRep2


title: VirE2 Induced + Agro 3 hours replicate 1

description:
3 hours in induction solution (B5 liquid media plus 1 µM β-estradiol) plus A. tumefaciens strain A136 at 10^8 cfu/mL
Treated3hRep1


title: HJP_Input


title: VirE2 Non-induced  + Agro 3 hours replicate 1

description:
3 hours in control solution (B5 liquid media plus DMSO) plus A. tumefaciens strain A136 at 10^8 cfu/mL
Mock3hRep1


title: HJP_MeRIP


title: C-4_Input

source_name: non fibrotic lung

value: noncancerous areas of the lungs from patients with lung cancer.


title: C-4_MeRIP


title: VirE2 untreated replicate 2

value: Untreated


title: KO2

city: Fukuoka

first: YUJI

last: ISHII

state: Fukuoka

address: Maidashi, 3-1-1, Higashiku

department: Faculty of Pharmaceutical Sciences

country: Japan

institute: Kyushu university

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K v2 ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

organism: Mus musculus

source_name: Kidney,knockout

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

treatment_protocol: The left kidneys were removed from male Selenbp1-KO and WT mice, and each dissected sample was rapidly put into a tube filled with RNAlater® and used for RNA extraction without freezing

tag: strain

tag: genotype

value: Kidney

tag: age

value: 8 weeks


title: W4

source_name: Kidney, wild-type

value: WT


title: C-3_MeRIP


title: KO1


title: W2


title: KO3


title: W3


title: C-1_MeRIP


title: C-3_Input


title: ECRT-SMARCA4, Patient_4

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

data_processing:
Reads Per Kilobase of exon per Megabase of library size (RPKM) 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.
Quality control: sequenced reads quality were assessed using fastqc v0.11.5
Mapping: sequenced reads were aligned with hg19 human genome reference using STAR v2.5.3a
Reads counting: reads aligned in each gene are counted using STAR v2.5.3a and the and the refFlat table gene annotation (downloaded in GTF format on October 2nd, 2018 from UCSC website)
Transcript Per Million (TPM) normalized count were calculated based on library size and gene length using an in-house script
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with TPM normalized gene count for every gene and every sample in tab-delimited text file
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample in tab-delimited text file

source_name: tumor sample

extract_protocol:
Total RNAs were obtained from tumor frozen samples using Qiagen RNAeasy kit, according to the manufacturer's procedures (Qiage, Venlo, Netherlands)
Barcoded Illumina compatible libraries were generated from 750 ng of total RNA for each sample using TruSeq Stranded mRNA Library Preparation Kit (Illumina, San Diego, California, U.S.)
Library werer sequenced using the Illumina HiSeq 2500 platform in the 100 bp paired-end mode

tag: tumor type

value: ECRT

value: soft parts

tag: Sex

value: M


title: ECRT-SMARCA4, Patient_3

value: bladder

value: F


title: ECRT-SMARCA4, Patient_2

value: kidney


title: CAh12-6_CTR

city: Boston

first: Cameron

last: McAlpine

address: 185 Cambridge Street

institute: Massachusetts General Hospital

data_processing:
Sequencing was performed on Illumina HiSeq 2500 instrument, resulting in approximately 30 million of 50 bp reads per sample. Sequencing reads were mapped in a splice-aware fashion to the Ensembl annotation of the mouse GRCm37/mm9 transcriptome using STAR (Dobin et al., 2013). Read counts over transcripts were calculated using HTSeq (Anders et al., 2015), followed by the differential expression analysis using EdgeR (Robinson et al., 2010). Genes were claddified as differentially expressed based on the cutoffs of log2-fold change 1.6 in expression value and false discovery rates (FDR) below 0.05.
Genome_build: mm9
Supplementary_files_format_and_content: gene expression counts per million

extract_protocol:
Brain was excised after PBS (Thermo Fisher Scientific) perfusion, minced and digested with 450 U ml-1 collagenase I, 125 U ml−1 collagenase XI, 60 U ml−1 DNase I and 60 U ml−1 hyaluronidase (Sigma) in PBS for 40 min at 37 °C. Samples were passed through a 70-μm cell strainer and mixed with 30% percol layered on-top of 70% percol. The percol gradient was centrifuged at 500g for 30 mins with brake off. The cell fraction was collected and washed with PBS. Microglia were identified as live (7AAD-), CD45+, CD11b+ and sorted using a FACS Aria II cell sorter (BD Biosciences). Microglia were pooled as described above and total RNA was isolated using E.Z.N.A micro elute total RNA kit according to the manufacturer’s instructions (Omega Biotek).
NEBNext PolyA Directional RNA Library Prep Kit for Illumina

value: brain

tag: cell type

value: Microglia


title: CAh12-5_CTR


title: CAh12-1_KO


title: CAh12-2_KO


title: CAh12-3_KO


title: CAh12-4_CTR


title: Neural progenitor cells, B145T30

first: Dina

last: Zielinski

description:
NPC_F5
polyA enrichment

data_processing:
Strain-specific SNPs were used to generate a FASTA file N-masked at high quality homozygous SNPs differing between the two parental strains with SNPsplit (0.3.2).
Reads were aligned to the N-masked genome using Tophat (2.1.0)/Bowtie2 (2-2.2.5).
Reads spanning N-masked sites were assigned to the maternal or paternal allele using SNPsplit.
Strand-specific read counts (reverse stranded) were assigned to each parental genome using FeatureCounts (1.5.1) .
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: allele-specific counts

source_name: Neural progenitor cells

growth_protocol: ESCs were plated in N2B27 medium for 7 days. At day 7, cells were dissociated and plated in a non-adherent cell culture dish in N2B27 medium supplemented with EGF and FGF2 (10ng/mL each) for 3 days. Cellular aggregates were then transferred in a gelatin-coated flask, in N2B27+EGF+FGF2, for attachment and NPC expansion. NPC clones were subsequently generated following manual colony picking after limited dilution of the NPC population.

extract_protocol:
Total RNAs were extracted using Qiagen RNeasy plus mini kit and treated with DNase1 using the RNase-free DNase set (Qiagen).
1 microgram of total RNA was used for polyA enrichment or ribosomal RNA depletion.

value: ES cell derived-neural progenitor clonal cell line

value: 129Sv x Cast/EiJ

value: female


title: Neural progenitor cells, B145T31

description:
NPC_mG2
polyA enrichment

value: male


title: ECRT-SMARCA4, Patient_5


title: VirE2 untreated replicate 1

value: Inducible VirE2 Line 10-9 T3 generation


title: Neural progenitor cells, Ch8_2

description:
Ch8_2
ribosomal RNA depletion


title: C-1_Input

value: lung

value: noncancerous areas of the lungs from patients with lung cancer.


title: Neural progenitor cells, Ch8_1

description:
Ch8_1
ribosomal RNA depletion


title: Neural progenitor cells, Ch7_2

description:
Ch7_2
ribosomal RNA depletion


title: 10_YES_RIP_hB7_8651

type: genomic

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

institute: INSERM

hyb_protocol: DNA was hybridized to each array according to the manufacturer's instructions using Genome-Wide SNP 6.0 Assaykit.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: The array image was acquired using Affymetrix Genotyping Console (version 4.2.0.26). SNP calls were extracted and converted from CEL files into signal intensities using Genotyping Console (version 4.2.0.26) software and BRLMM algorithm.

label: Biotin

molecule: genomic DNA

label_protocol: DNA was restriction digested, PCR amplified, fragmented and labeled according to the manufacturer's instructions using Genome-Wide SNP6.0 Assay kit.

growth_protocol: All mice were maintained under specific pathogen-free conditions and experimental studies were performed in accordance with the Institutional Animal Care and Use Guidelines and accredited by the ethic committee under the number CEEA34.CB.024.11.

extract_protocol: DNA extraction were realized from tails by 20 mg/ml proteinase K (Invitrogen) degradation, saturated NaCl/propanol DNA precipitation and DNA re-suspension 2 hours in TE10-4 buffer at 42°C.

treatment_protocol: No treatment of mice before DNA extraction

value: tail


title: 11_YES_RIP_hB7_num1


title: Neural progenitor cells, Ch5_2

description:
Ch5_2
ribosomal RNA depletion


title: Neural progenitor cells, Ch7_1

description:
Ch7_1
ribosomal RNA depletion


title: Neural progenitor cells, Ch5_1

description:
Ch5_1
ribosomal RNA depletion


title: Neural progenitor cells, Ch3_2

description:
Ch3_2
ribosomal RNA depletion


title: Astrocytes, B129T2

description:
Astro_G4
polyA enrichment

source_name: Astrocytes

value: Astrocytes derived from clonal NPC cell line


title: Astrocytes, A234T14

description:
Astro_mC3
polyA enrichment


title: Neural progenitor cells, Ch3_1

description:
Ch3_1
ribosomal RNA depletion


title: Astrocytes, B129T1

description:
Astro_C2
polyA enrichment


title: 12_YES_RIP_hB7_num2


title: 13_YES_RIP_hB7_num3


title: Astrocytes, A234T13

description:
Astro_mE6
polyA enrichment


title: Astrocytes, A234T12

description:
Astro_129
polyA enrichment


title: Neural progenitor cells, B145T32

description:
NPC_mG6
polyA enrichment


title: ΔpBK-SC-ITIH5 59

city: Aachen

first: Lin

last: Gan

address: Pauwelsstr. 30

department: IZKF

country: Germany

institute: University Hospital Aachen

hyb_protocol: Overnight hybridization of end-labelled cDNA was applied on the HTA 2.0 Human (Affymetrix) arrays for 16 hours, at 60 rpm, at 45ºC in a Hybridization Oven 645 (Affymetrix). Washing and staining of the arrays were done on an Affymetrix 450 Fluidics Station using the protocol FS450_0001.

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the manufacture manual

data_processing: CEL files were generated in Affymetrix® GeneChip® Command Console® Software (Affymetrix, USA) with default settings. Gene expression intensities were normalized and summarized with robust multiarray average algorithm (RMA) by using EnsMart72 database, which was performed by using program package of AltAnalyze (version 2.1.3) (Emig et al., 2010).

label: biotin

source_name: cells derived from squamous-like bladder cancer

label_protocol: Total RNA was process with Affymetrix GeneChip WT Plus Reagent Kit.

growth_protocol: Eagle's Minimum Essential Medium 10% FCS; L-Glutamine

extract_protocol: Total RNA from cultured cells was prepared by using TRIzol reagent (Invitrogen) according to the manufacture manual.

treatment_protocol: SCaBER cells  were transfected with either the ITIH5-pBK-CMV expression vector, containing the full-length human ITIH5 cDNA, or the empty vector alone.

tag: genetic modification

value: 2n=46 the stemline chromosome number is hypotriploid with the 2S component occuring at 9.2%

tag: cell line

value: SCaBER cell line

tag: individual


title: ΔpBK-SC-ITIH5 45


title: ΔpBK-SC-ITIH5 17


title: ΔpBK-SC-mock 9

value: stable mock clones (empty vector)


title: ΔpBK-SC-mock 8

value: bladder


title: ΔpBK-SC-mock 1


title: Capsicum_47-2

city: A Coruña

first: Javier

last: Veloso

state: A Coruña

address: Campus da Zapateira s/n

country: Spain

institute: Universidad de A Coruña

description: Stem 48h after inoculation with Fo47, biological rep2

hyb_protocol: 5 ug of fragmented and labeled aRNA were hybridized for 16 hr at 45ºC on GeneChip® Tomato Genome Array. GeneChips® were washed and stained in the Affymetrix GeneChip® Fluidics Station 450.

scan_protocol: GeneChip® scanning was carried out in the GeneChip® Scanner 3000 7G.

data_processing: GeneChip® data quality control, background correction, normalization and summarization methods were carried out with Affymetrix Expression Console® Software. Data of the 6 GeneChips® were analyzed together performing a Significance Analysis of Microarrays (SAM) in the TM4 Microarray Software Suite (MeV 4.8.1) to determine gene expression differences. Default settings were used for SAM. The delta value for SAM was 1.3095916509628296.

organism: Capsicum annuum

source_name: Capsicum annuum stems 48 hours after root inoculation with Fo47

label_protocol: In vitro transcription synthesizes aRNA and incorporates a biotin-congugated nucleotide (aRNA is also known as cRNA). GeneChip® 3’ IVT Express Kit User Manual P/N 702646 Rev. 8

growth_protocol: Seeds of Capsicum annuum were disinfected by incubation in 10% (v/v) commercial bleach for 30 min. Seeds were then washed and soaked overnight in distilled water before being sown in sterile vermiculite. Plants were grown in a growth chamber at 25 ºC and a photoperiod of 16 h light and 8 h darkness. Plants were used for inoculation 30 days after sowing.

extract_protocol: Samples of stems were collected 48 h after induction with Fo47 and homogenized in mortar cooled with liquid nitrogen. Total RNA was extracted from the homogenized samples as described in the protocol of the BioRad AurumTM Total RNA Mini kit.

treatment_protocol: The roots were dipped into a 10^6 conidia per ml conidial suspension for 3 h. Control plants were treated with sterile distilled water instead of Fo47 conidia.

value: Stem

tag: cultivar

value: Padron

value: 15 days after plant emergence.


title: Capsicum_47-1

description: Stem 48h after inoculation with Fo47, biological rep1

tag: tissue


title: Capsicum_Co-3

description: Stem 48h after inoculation with water, biological rep3

source_name: Capsicum annuum stems 48 hours after root inoculation with water


title: Capsicum_Co-2

description: Stem 48h after inoculation with water, biological rep2


title: Neutrophils treated after Staphylococcus aureus for 4 hours

city: Taipei

first: Li-Wen

last: Lo

address: 128 Academia Road, Section 2, Nankang, Taipei

country: Taiwan

institute: Academia sinica

hyb_protocol: Biotinylated cRNA was hybridized to Clarion D Mouse Array (Affymetrix) via Hybridization Oven 645 (Affymetrix)

scan_protocol: The array data were acquired with GeneChip® Scanner 3000.

data_processing: The data from MZ B cells and neutrophils were analyzed with GeneSpring GX.

source_name: Neutrophills treated after Staphylococcus aureus for 4 hours

label_protocol: Total RNA was subjected to reverse transcription and biotin-conjugated nucleotide incorporation by using GeneChip WT PLUS Reagent Kit (Affymetrix)

growth_protocol: Mice were bred under specific pathogen-free conditions

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer's instructions

treatment_protocol: Target cells were prepared from FACS-sorted MZ B cells (B220+CD21hi CD23lo) and negative selection beads (Stemcell Technology) isolated neutrophils before and 4 hours after S. aureus infection.

value: Neutrophils

tag: treatment

value: after Staphylococcus aureus infection for 4 hours


title: ileum organoid, 2D collagen I, IL22, replicate 3

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 2.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations.

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

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.34.2)

source_name: organoid isolated from mouse Ileum, grown on collagen (2D structure), treated with mIL22 (5 ng/ml) for 24 hrs

label_protocol: Total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: Crypt isolation: a female mouse C57/BL6, 6 months of age was sacrificed using carbon dioxide. The intestine was removed and the ileum isolated. Villi were removed from the ileum by scraping with a scalpel and the tissue was cut into small pieces, transferred to a tube with ice-cold PBS and washed three times with PBS (spun down at 335x g for 5 minutes between every wash step). A Polter-Elvehjem tube was then used to fragment the tissue and the cell suspension was transferred to a tube with ice-cold PBS, washed three times with PBS and subsequently filtered through a 100 μm filter. The now isolated crypts were spun down at 335x g for 5 minutes at room temperature and supernatant was removed. The crypts were resuspended in Matrigel (Corning; 356231), and drops of 25 μl suspension were added to each well (Corning Costar). The plates were then incubated for 15 minutes at 37 ˚C until the droplets had solidified. One ml of organoid culture medium supplemented with 10% FCS, 10 µM Y27632 (Selleckchem; S1049),  CHIR 4,3 µM, (Sigma; SML 1046) and 2-Propylpentanoic acid (Sigma; P6273; 1:8000). After 3 days of incubation at 37˚C and 5% CO2, medium was replaced by normal culture medium: DMEM/F12 medium containing GlutaMAX supplement, 1mM sodium pyruvate, MEM Non-Essential Amino Acids, 100U/ml Penicillin-Streptomycin, R-spondin 1 (homebrew), WNT (homebrew) and the BMP4 inhibitor DMH1 0.5ug/ml (Sigma; D8946) to stimulate organoid formation. These organoids were passaged once a week in a 1:4 ratio.

extract_protocol: Total RNA was prepared from the organoid samples using TRIzol reagent, whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Ileum organoids were grown in 3D in 25 ul Matrigel droplets in DMEM/F12 medium containing GlutaMAX supplement, 1mM sodium pyruvate, MEM Non-Essential Amino Acids, 100U/ml Penicillin-Streptomycin, R-spondin 1 (homebrew), WNT (homebrew) and the BMP4 inhibitor DMH1 0.5ug/ml (Sigma; D8946) to stimulate organoid formation. These organoids were passaged once a week in a 1:4 ratio or used for IL22 stimulation in 3D. 2D Ileum organoids: 3D cultures were collected (1 3D cultures was used per 2D culture) and spun down at 335x g for 5 minutes at room temperature. supernatant and excess of matrigel was carefully removed and pellet was resuspended in 10 ml culture medium. cells were spun down again and supernatant and excess of matrigel was removed. cells were resuspended in 100 ul culture medium and added to the collagen coated plates. preparation of collagen coated plates:. 24 wells plates were coated with a thin layer of 3 ug/ml rat tail Collagen I (IBIDI GmbH; 50201). After solidification of the Collagen I coating, a suspension of organoids in medium supplemented with 10% FCS, 10 µM Y27632 (Selleckchem; S1049),  CHIR 4,3 µM, (Sigma; SML 1046) and  2-Propylpentanoic acid (Sigma; P6273; 1:8000) was added to each well. The organoids were grown for 2 days at 37°C and 5% CO2.

tag: sexe

tag: culture

value: 2D (Collagen I)

value: IL22 (5 ng/ml)

tag: treatment duration (h)

tag: mouse strain


title: Arabidopsis ccd4 x clb5 first true leaves (sample-3)

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

data_processing:
All reads from RNA-seq libraries were trimmed to remove adapter sequences using  The quality of sequences was analyzed with Trimmomatic (Bolger et al., 2014).  We developed the website and database using the Arabidopsis TAIR10 genome, to  store and analyze all libraries; we used these visualization tools extensively  for this analysis.
Genome_build: Arabidopsis TAIR10
Supplementary_files_format_and_content: tag count

source_name: Arabidopsis first true leaves

extract_protocol:
Total RNA was isolated using Plant RNA Reagent (Invitrogen, Carlsbad, CA).
RNA-seq libraries were constructed using TruSeq Stranded RNA preparation kit (Illumina, San Diego, CA). All libraries were sequenced on an Illumina Hi-Seq 2500 instrument at the Delaware Biotechnology Institute, Newark, DE.

value: ccd4 x clb5

value: first true leaves


title: MZ B cells treated after Staphylococcus aureus for 4 hours

value: B cells


title: Arabidopsis ccd4 x clb5 first true leaves (sample-2)


title: ileum organoid, 2D collagen I, IL22, replicate 1

value: female


title: MZ B cells untreated

source_name: MZ B cells untreated

value: before infection


title: Capsicum_Co-1

description: Stem 48h after inoculation with water, biological rep1


title: Arabidopsis ccd4 x clb5 first true leaves (sample-1)


title: ileum organoid, 2D collagen I, IL22, replicate 2


title: ileum organoid, 2D collagen I, vehicle, replicate 3

source_name: organoid isolated from mouse Ileum, grown on collagen (2D structure), treated with vehicle for 24 hrs

value: vehicle (PBS)


title: Capsicum_47-3

description: Stem 48h after inoculation with Fo47, biological rep3


title: Neutrophils untreated

source_name: Neutrophils untreated


title: ileum organoid, 2D collagen I, vehicle, replicate 2


title: ileum organoid, 3D matrigel, IL22, replicate 2

source_name: organoid isolated from mouse Ileum, grown in matrigel (3D structure), treated with mIL22 (5ng/ml) for 24 hrs

value: 3D (matrigel)


title: ileum organoid, 2D collagen I, vehicle, replicate 1


title: Arabidopsis pds3 first true leaves (sample-3)


title: 387_SgCHMP2A_3-2

city: La Jolla

first: Davide

last: Bernareggi

state: CA

address: 9500 Gilman Drive

institute: UCSD

data_processing:
Data were trimmed with TrimGalore version 0.5.0
Salmon version 0.8.2 was used for mapping to the human genome with correction for position bias and sequence bias
DESeq2 was used for differential expression analysis
Genome_build: hg38, Gencode version 27
Supplementary_files_format_and_content: CHMP2A RNAseq Abundance and Differential Expression

source_name: Glioblastoma stem cells

extract_protocol: Trizol reagent (Sigma-Aldrich) was used to isolate total cellular RNA from cell pellets.

value: glioblastoma stem cell line 387


title: Arabidopsis pds3 first true leaves (sample-2)


title: ileum organoid, 3D matrigel, vehicle, replicate 2

source_name: organoid isolated from mouse Ileum, grown in matrigel (3D structure), treated with vehicle for 24 hrs


title: ileum organoid, 3D matrigel, IL22, replicate 3


title: ileum organoid, 3D matrigel, vehicle, replicate 3


title: 387_SgCHMP2A_3-1


title: Arabidopsis pds3 first true leaves (sample-1)


title: 387_SgNT-2


title: circRNA Knee Osteoarthritis patients replicate3

description:
Knee Osteoarthritis patients replicate3
circRNA
circRNA expression in Osteoarthritis Knee

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays V2 (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

data_processing: A series of data processing including quantile normalization were performed using the R software limma package. Differentially expressed circRNAs with statistical significance between two samples or two groups were identified using fold change cutoff or through Volcano Plot filtering respectively.

source_name: Osteoarthritis Knee

label_protocol: Total RNA from each sample was treated with Rnase R to enrich circular RNA. The enriched circular RNA was then amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol

extract_protocol: Total RNA was isolated from cartilage of KOA patients and healthy volunteers using TRIzol reagent. RNA integrity was assessed by standard denaturing agarose gel electrophoresis. The RNA samples were labeled, purified and amplified. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner

treatment_protocol: The cartilage of KOA patients and healthy volunteers were collected from tibia plateau. All samples were immediately frozen in liquid nitrogen before RNA isolation.

value: cartilage


title: Arabidopsis clb5 first true leaves (sample-3)


title: ileum organoid, 3D matrigel, vehicle, replicate 1


title: Arabidopsis clb5 first true leaves (sample-2)


title: circRNA Knee Osteoarthritis patients replicate2

description:
Knee Osteoarthritis patients replicate2
circRNA
circRNA expression in Osteoarthritis Knee


title: WFY10YM3

city: 南昌

first: Jianmin

last: Bian

state: 江西 (Jiāngxī)

address: 志敏大道1101

institute: 江西农业大学

description: WFY1YMVSWFY10YM_Gene_differential_expression

data_processing:
A cDNA library constructed by technology from leaves of rice was sequenced run with Illumina 4000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon paired-end reads of bp length. This yielded gigabases (Gb) of sequence.
we aligned reads to rice reference genome using HISAT package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
HISAT allows multiple alignments pe read (up to 20 by default) and a maximum of two mismatchs when mapping the reads to the reference.HISAT build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions.
The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using perl scripts. After the ﬁnal transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM. The differentially expressed mRNAs and genes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package.
Genome_build: https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Osativa
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Oryza sativa

source_name: leaf

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure.
Following purification, the mRNA is fragmented into smallpieces 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 mRNASeq sample preparation kit (Illumina, San Diego, USA).
Paired-end RNA-seq

tag: variety type

tag: Stage

value: on the tenth day after flowering

tag: enviroment

value: middle rice


title: WFY10YM1


title: ileum organoid, 3D matrigel, IL22, replicate 1


title: Arabidopsis clb5 first true leaves (sample-1)

tag: genotype


title: circRNA healthy controls replicate1

description:
healthy controls replicate1
circRNA
circRNA expression in healthy knee

source_name: healthy Knee


title: circRNA healthy controls replicate2

description:
healthy controls replicate2
circRNA
circRNA expression in healthy knee


title: circRNA Knee Osteoarthritis patients replicate1

description:
Knee Osteoarthritis patients replicate1
circRNA
circRNA expression in Osteoarthritis Knee


title: WFY1YM3

value: on the first day after flowering


title: CW468_SgCHMP2A_3-2

value: glioblastoma stem cell line CW468


title: CW468_SgCHMP2A_3-1


title: WFY1YM2


title: Arabidopsis ccd4 x clb5 expanded cotyledon (sample-3)

source_name: Arabidopsis expanded cotyledon

value: expanded cotyledon


title: CH10YM3

description: CH1YMVSCH10YM_Gene_differential_expression.tsv


title: CW468_SgNT-2


title: VirE2 Non-induced + Agro 3 hours replicate 3

description:
3 hours in control solution (B5 liquid media plus DMSO) plus A. tumefaciens strain A136 at 10^8 cfu/mL
Mock3hRep3

source_name: Root tissue

tag: parental ecotype

tag: transgenic line

value: Inducible VirE2 Line 10-9 T3 generation

tag: agent

tag: time point

value: 3 hours


title: CW468_SgNT-1

tag: cell line


title: WFY1YM1


title: CH10YM2


title: CH10YM1


title: Arabidopsis ccd4 x clb5 expanded cotyledon (sample-2)


title: Arabidopsis ccd4 x clb5 expanded cotyledon (sample-1)


title: CH1YM3


title: CH1YM2


title: CW468_Sh-CHMP2A_1-1


title: Arabidopsis pds3 expanded cotyledon (sample-3)


title: CH1YM1


title: circRNA healthy controls replicate3

description:
healthy controls replicate3
circRNA
circRNA expression in healthy knee


title: WFB10YM2

description: WFB1YMVSWFB10YM_Gene_differential_expression

value: WFB


title: 9_YES_RIP_hB7_8776

tag: strain

value: tail


title: WFB1YM3


title: CW468_Sh-CHMP2A_1-2


title: WFB10YM1


title: WFB10YM3


title: Arabidopsis pds3 expanded cotyledon (sample-1)


title: CW468_ShNT-1


title: WFB1YM2


title: Arabidopsis clb5 expanded cotyledon (sample-3)


title: 1517 nk

library_source: genomic

data_processing:
FASTQ files were trimmed to 20 bp CRISPR guide sequences using BBDuk from the BBMap (B. Bushnell) toolkit and quality control as performed using FastQC (Babraham Bioinformatics).
FASTQs were aligned to the library and processed into counts using the MAGECK ‘count’ function. Genes were then filtered such that the sum of normalized counts > 10. Hits were ranked by RIGER using the Kolmogorov-Smirnov algorithm.
Supplementary_files_format_and_content: CRISPR Screen Hits and scores.csv

extract_protocol:
gDNA extraction was performed using the gDNA extraction kit from Zymo following the protocol from the manufacturer
Library construction and sequencing were performed following the protocols from Adgene related to the Brunello CRISPR KO library: https://www.addgene.org/pooled-library/broadgpp-human-knockout-brunello/

value: glioblastoma stem cell line 1517

tag: challenge

value: nk


title: Arabidopsis pds3 expanded cotyledon (sample-2)

tag: tissue


title: Arabidopsis clb5 expanded cotyledon (sample-2)


title: WFY10YE3

description: WFY1YEVSWFY10YE_Gene_differential_expression

value: early rice


title: WFY10YE1


title: CW468_ShNT-2

tag: treatment


title: WFY10YE2


title: Arabidopsis clb5 expanded cotyledon (sample-1)


title: WFY1YE3


title: VirE2 untreated replicate 3

value: Untreated


title: 387 nk


title: WFY1YE2


city: Merced

first: Hans

middle: Tomas

last: Rube

address: 5200 North Lake Rd.

department: Bioengineering

institute: UC Merced

description:
synthetic DNA, 5mCG
EpiSELEX-seq for ATF4
run_10_05_17__R1_ATF4-CEBPg_50nM_highBand__5mCG.100000.tsv.gz

data_processing:
Library strategy: SELEX-seq
SELEX-seq/EpiSELEX-seq/K_D-seq: Low-quality reads were filtered out using fasts_quality_filter -Q 33 -q 20 -p 10 (FASTX toolkit 0.0.12; Hannon lab). Reads with the correct flanking identified, retained, trimmed, and the remaining variable sequence was, if needed, reverse reverse-complemented. Kinase sequencing: The deep sequencing data was processed as described previously (Shah, eLife, 2018). The paired-end reads were merged using FLASH and the adapter sequences were trimmed using the software Cutadapt. The remaining sequences were translated into amino acid codes, and sequences containing stop codons were removed.
Next count tables were generated. These enumerate the probes in each SELEX round (for SELEX-seq and EpiSELEX-seq), in the input/bound/free libraries (for K_D-seq), and in the input/modified libraries (for Kinase sequencing). Because ProBound only needs a limited number of reads, the data was randomly down-sampled to 100k reads for SELEX-seq and EpiSELEX-seq and 1M reads for K_D-seq, and binding models were learned by ProBound using the resulting tables.
Supplementary_files_format_and_content: Tab-separated files enumerating the occurrence of each probe sequence (first column) in each sequencing library (following columns). Because ProBound only needs limited data, each library was randomly downsampled to 100k reads for the SELEX-seq and EpiSELEX-seq and 1M reads for the K_D-seq.

source_name: in-vitro purification

extract_protocol: SELEX-seq: The Hth-Exd-Ubx SELEX experiment was carried out following previously published methods (Slattery, Cell, 2011). Briefly, after expressing and purifying the wild-type homeodomain proteins, a final concentration of ~50 nM was assembled, incubated with excess DNA (10-20 fold) for 30 minutes, and loaded onto an EMSA gel. A DNA library with 30 randomized bases was used. The TF-bound fraction was isolated from the gel, amplified, and either subjected to another round of enrichment or prepared for sequencing. An all, three rounds of enrichment were performed. After each selection round, the DNA was extracted from the gel and amplified by using Ilumina’s small RNA primer sets. Sequencing barcodes were added in a five cycle PCR step and the final library was gel-purified using a native TBE-gel before sequencing. Libraries were sequenced at the New York Genome Center using separate lanes on an Illumina HiSeq 2000 sequencing machine. EpiSELEX-seq:  ATF4 protein purification and EpiSELEX-seq experiments were performed as described previously (Kribelbauer, Cell reports, 2017). Purified CEBPg protein was kindly donated by the Lomvardas lab at the Zuckerman Institute at Columbia University. To generate randomized 5hmC or 6mA libraries, single-stranded oligos with a 16-bp randomized region were ordered from TriLink Biotechnologies, substituting i) deoxycytidine triphosphate (dCTP) with deoxy-(5hm)-cytidine triphosphate (d5hmCTP), or ii) deoxyadenosine triphosphate (dATP) with deoxy-(6m)-adenosine triphosphate (d6ATP) during the synthesis step. For double-stranding, a standard mix of deoxy-nucleotides was used, resulting in hemi-modified libraries. 5mCpG libraries were generated by enzymatic treatment with M.SssI (NEB). The library sequences consisted of constant  left (GGTAGTGGAGG-) and right (-CCAGGGAGGTGGAGTAGG) adapters flanking a library specific barcode and a 16bp randomized sequence: -TGGG-CCTGG-N16- (no modification), -GCAC-CCTGG-N16- (5mCpG), -CAGT-CCTGG-N16- (5hmC), and -AGTG-CCTGG-N16- (6mA). K_D-seq: 6xHis tagged Drosophila Distalless (Dll) protein lacking amino acids N terminal to its homeodomain was purified by standard procedures. The 10mer R0 library was generated by annealing the library oligo GTTCAGAGTTCTACAGTCCGACCTGG-10N-CCAGGACTCGGACCTGGACTAGG and the SELEX-R primer CCTAGTCCAGGTCCGAGT, followed by a Klenow mediated primer extension reaction. The SELEX procedure was largely the same as previously described (Slattery, Cell, 2011), except that a Cy5 labeled DNA probe, instead of a P32 labeled probe, was used as the marker to indicate where the bound and unbound fractions were. For each SELEX condition, 15ul of protein solution (at 2x final concentration) in dialysis buffer (20mM HEPES pH8.0, 200mM NaCl, 10% glycerol, 2mM MgCl2, 0.05% Tween-20) was made. The library mixture was made by adding desired amount of the R0 library to 6ul of 5x binding buffer (50mM Tris-HCl pH7.5, 250mM NaCl, 5mM MgCl2, 20% glycerol, 2.5mM DTT, 2.5mM EDTA, ~125ng/ul polydIdC, 100ng/ul BSA, 0.125% Tween-20), and filling to 15ul with H2O. The protein and DNA parts were mixed and incubated at room temperature for 30 to 40 minutes before loading the gel. After running the gel, gel slices corresponding to the bound and unbound fractions were cut from the gel and purified. Each purified SELEX DNA was properly diluted such that the PCR program gave good library yield for all samples. The libraries were pooled and sequenced using Illumina Nextseq 550, following standard procedures. Kinase sequencing: The degenerate peptide library contained 11-residue sequences with five randomized amino acids flanking either side of a fixed central tyrosine residue: GCTGGCCAGTCTGGCCAG-NNSNNSNNSNNSNNStatNNSNNSNNSNNSNNS-GGAGGGCAGTCTGGGCAGTCTG. These sequences were fused to the eCPX bacterial surface display scaffold (Rice, Protein Engineering, Design & Selection, 2008). This construct was inserted into the SfiI-digested pBAD33-eCPX plasmid, as described previously (Shah, eLife, 2018). Transformed DH5a cells were grown overnight in liquid culture and the plasmid DNA library was extracted and purified using a commercial midiprep kit. A phosphotyrosine monoclonal antibody, pY20, conjugated to the fluorophore, perCP-eFluor 710 (Invitrogen), was biotinylated before use in the specificity screen. The catalytic domain of the human tyrosine kinase c-Src was screened against the degenerate peptide library as described previously (Shah, eLife, 2018), with one main difference being the use of magnetic beads to isolate phosphorylated cells, rather than fluorescence-activated cell sorting. Time points were taken at 5, 20, and 60 minutes. The phosphorylated cells were isolated with Dynabeads FlowComp Flexi (Invitrogen) following the manufacturer’s protocol. In total, two populations were collected for each time point: cells that did not bind to the magnetic beads and eluted after each wash (unbound) and cells that bound to the magnetic beads and eluted after the addition of the release buffer (bound). After isolation of these two populations, the cell pellet was collected, lysed, and used as a template in a PCR reaction (Shah, eLife, 2018). The product of this PCR reaction was then used as a template for a second PCR reaction to append a unique 5’ and 3’ indices. Each sample was pooled to equal molarity and sequenced by paired-end Illumina sequencing on a MiSeq instrument.

tag: variable region length

tag: left flank

value: GGTAGTGGAGGGCACCCTGG

tag: right flank

value: CCAGGGAGGTGGAGTAGG

tag: round / concentrations


title: 387 ctrl

value: glioblastoma stem cell line 387

value: ctrl


title: WFY1YE1

tag: variety type


title: CH10YE3

description: CH1YEVSCH10YE_Gene_differential_expression.tsv

tag: Stage

value: on the tenth day after flowering


title: run_10_05_17__R1_ATF4-CEBPg_50nM_highBand__None

description:
synthetic DNA
EpiSELEX-seq for ATF4
run_10_05_17__R1_ATF4-CEBPg_50nM_highBand__.100000.tsv.gz

value: GGTAGTGGAGGTGGGCCTGG


title: CW468 nk


title: CH10YE1

tag: enviroment


title: CH1YE3

value: on the first day after flowering


description:
synthetic DNA, 5hmC
EpiSELEX-seq for CEBPg
run_06_05_17__R1_CEBPg_homo_75nM_lowBand__5hmC.100000.tsv.gz

value: GGTAGTGGAGGCAGTCCTGG


title: D456 ctrl

value: glioblastoma stem cell line D456


title: WFB10YE1

description: WFB1YEVSWFB10YE_Gene_differential_expression


description:
synthetic DNA, 5mCG
EpiSELEX-seq for CEBPg
run_06_05_17__R1_CEBPg_homo_75nM_lowBand__5mCG.100000.tsv.gz


title: WFB1YM1

value: middle rice


title: run_2_06_17__R0_Mlibmix_1256_hemi_264__6mA

description:
synthetic DNA, 6mA
EpiSELEX-seq input

value: GGTAGTGGAGGAGTGCCTGG


title: FRAL190074270

city: Wenzhou

first: Xiaofang

last: Zhu

state: Zhejiang Province

address: Nan Bai Xiang Street

department: Rheumatology

institute: First Affiliated Hospital of Wenzhou Medical University

data_processing:
Illumina bcl2fastq software used for basecalling.
Using Cutadapt adapters and TrimGalore, raw reads were trimmed and low-quality reads were filtered. Quality-control reports of sequence reads were obtained using FastQC software.
The sequencing data were aligned to the human reference genome "hg38" using STAR software.
The read count files were filtered with low expression and normalized using the DESeq2 package.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample

source_name: salivary glands

extract_protocol:
Total RNA was isolated from frozen salivary gland samples using TRIzol Reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. RNA purity was checked using a Nano Photometer spectrophotometer (IMPLEN, Westlake Village, CA, USA).
The quality of the RNA used to construct the cDNA library was verified (RNA integrity numbers >9) using an RNA 6000 Nano kit with the Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA). With input material of 3 mg RNA per sample, we constructed sequencing libraries using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) and subsequently performed the sequence on an Illumina HiSeq platform.

value: salivary glands

tag: disease state

value: non-ILD-pSS


title: HEK293-control_rep2

city: Shanghai

first: Bo

last: Wang

address: 1678 Dongfang Road

institute: Shanghai Children's Medical Center

data_processing:
Read pairs with low quality (e.g. proportion of bases with sQ<=5 greater than 50%; proportion of N greater >10%; 5’adaptor contamination) were removed.
The remaining clean data were aligned to human reference genome (version GRCh38) using STAR
The remaining clean data were aligned to human reference genome (version GRCh38) using STAR (Dobin et al., 2013) with ENCODE (Encyclopedia of DNA Elements, https://www.encodeproject.org/) standard options for long RNA-seq pipeline
Gene level read counts were featureCounts
Genome_build: GRCh38
Supplementary_files_format_and_content: raw read counts

extract_protocol:
Cells were harvested using Trizol reagent. 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard BGI protocols

value: empty vector control

tag: cell type

value: fetal kidney


title: HEK293-lnc-TSSK2-8-Overexpression_rep3

value: Overexpression


title: HEK293-lnc-TSSK2-8-Overexpression_rep2


title: FRAL190036196


title: run_2_06_17__R0_Mlibmix_1256_hemi_264__None

description:
synthetic DNA
EpiSELEX-seq input


title: HEK293-lnc-TSSK2-8-Overexpression_rep1


title: HEK293-control_rep1


title: CH1YE2

value: early rice


title: FRAL190074305


title: CW468 ctrl

value: glioblastoma stem cell line CW468


description:
synthetic DNA, 6mA
EpiSELEX-seq for CEBPg
run_06_05_17__R1_CEBPg_homo_75nM_lowBand__6mA.100000.tsv.gz

value: CCAGGGAGGTGGAGTAGG


title: run_2_06_17__R0_Mlibmix_1256_hemi_264__mCG

description:
synthetic DNA, 5mCG
EpiSELEX-seq input

value: GGTAGTGGAGGGCACCCTGG


title: FRAS190036186


title: D456 nk

value: nk


title: Single cell sgRNA library

city: duarte

first: LU

last: YANG

address: 1500 duarte rd

institute: city of hope

data_processing:
library strategy: sc-RNAseq and direct-capture Perturb-seq
Illumina RTA was used to create .bcl files, and bcl2fastq v2.20.0.422 software was used for base calling (for samples split between flowcells and later merged per run)
CellRanger 5.0.0 by 10x genomics were used to perfrom alignment, filtering, barcode counting and UMI counting from fastq files. It genarates feature-barcode matrices to be used in the downstream analysis.
Seurat v3.0 was used to determine the single cell clusters based on gene expression profiles and identify the correlated sgRNA sequences information.
Genome_build: Genome Reference Consortium GRCh38
Supplementary_files_format_and_content: Feature-barcode Matrix in MTX format; Features and barcode sequences in gzipped TSV files

source_name: Leukemia

growth_protocol: MLL-AF9-Cas9+ leukemic cells were cultured in vitro in Iscove's Modified Dulbecco's Medium (IMDM; Gibco) plus 15% FBS (Gibco) supplemented with 20 ng/ml mouse SCF (PeproTech), 10 ng/ml mouse IL-3 (PeproTech), 10 ng/ml mouse IL-6 (PeproTech), penicillin (100 units/ml; Gibco), streptomycin (100 μg/ml; Gibco), and plasmocin (5 μg/ml; InvivoGen).

extract_protocol:
Single cells were isolated using a 10X Chromium and 10X GEM v3.1 kit.
10X Genomics GEM v3.1 library prep protocol.

treatment_protocol: MLL-AF9-Cas9+ leukemic cells were transduced with a lentiviral library expressing sgRNAs with CS1 capture sequence.

value: MLL-AF9 leukemia

tag: capture method

value: CS1 in 10X GEM v3.1 kit

tag: molecule type

value: sgRNA library


title: i48_SF_P310_AF2

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road

department: NDORMS

country: United Kingdom

institute: University of Oxford

data_processing:
The raw FASTQ files were processed using CGAT-flow readqc and mapping workflows (https://github.com/cgat-developers/cgat-flow)
The quality of the reads was assessed using FASTQC and ReadQC.
Genome_build: Raw reads were aligned to the GRCh38 reference genome using HiSat2 (v2.0.5). The quantification of mapped reads against GCRh38 reference genome annotation was carried out using FeatureCounts (v1.5.0).

molecule: polyA RNA

source_name: Osteoarthritic knee synovium

growth_protocol: Collagenase-digested tissue was filtered through a 70m cell strainer, and cells were plated out in 10-cm dishes in D10 (DMEM-F12 (Gibco, supplied by Fisher Scientific, Loughborough, UK) with 10% Foetal Bovine Serum (FBS) (Labtech International, Heathfield, UK) and 1% Penicillin/Streptomycin (P/S) (Gibco)). Once 95% confluent, chondrocytes were cryopreserved, while synovial fibroblasts were passaged once (p=1) and then cryopreserved.

extract_protocol:
RNA was extracted using a Direct-zol MicroPrep kit with DNase treatment (Zymo Research, Irvine, CA, USA) following the manufacturer’s instructions.
RNA was extracted using a Direct-zol MicroPrep kit with DNase treatment (Zymo Research, Irvine, CA, USA) following the manufacturer’s instructions. RNA concentration was measured using a NanoDrop spectrophotometer. RNA quality of eight randomly chosen samples were assessed using High Sensitivity RNA ScreenTapes (Agilent) on an Agilent 2200 TapeStation. Library preparation was done using a NEBNext Ultra II Directional RNA Library Prep Kit for Illumina with poly-A selection (Illumina, San Diego, CA, USA) following the manufacturer’s instructions. Every library was quantified for DNA content with High Sensitivity DNA ScreenTapes (Agilent). Libraries from 24 samples with unique identifiers were pooled and run on an Illumina NextSeq 500 using the 75 cycles NextSeq High Output kit (Illumina).
bulk RNA-Seq

treatment_protocol: Chondrocytes (n=6 patients) were expanded to p=2 and synovial fibroblasts (n=6 patients) to p=3 in D10 after which they were plated out in 12-well plates. Cells were left to attach for 24 hours, before medium was changed to serum-free DMEM-F12 with P/S (D0) and left for 24 hours. On the day of the experiments, vehicle control, and 10ng/ml IL-17A, IL-17F, or IL-17AF (all from Biolegend UK Ltd, London, UK) was made up in D0. Old D0 was removed and D0 with vehicle control or IL-17 was added. After 24 hours, treatment medium was removed and cells were washed with PBS, before being harvested in Trizol (Invitrogen, supplied by ThermoFisher Scientific, Waltham, MA, USA), and stored at -80'C.

value: Synovium (knee)

tag: cells

value: Synovial fibroblasts

value: End-stage osteoarthritis

value: IL-17AF (10 ng/ml) for 24 hours

tag: patient id


title: 387_SgNT-1

tag: cell line

value: glioblastoma stem cell line 387


title: WFB10YE3

value: WFB

value: on the tenth day after flowering


title: CH10YE2


title: CH1YE1

value: on the first day after flowering


title: FRAS190036187

value: salivary glands

value: non-ILD-pSS


title: Single cell mRNA library

tag: strain

value: poly(T) in 10X GEM v3.1 kit

value: mRNA library


title: i47_SF_P310_F2

tag: tissue

value: IL-17F (10 ng/ml) for 24 hours


title: FRAS190036189


title: KO_Tumor_3

city: Bethesda

first: Stephen

middle: R

last: Brooks

state: MD

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

data_processing:
Demultiplex and convert to FastQ (bcl2fastq v2.20.0.422)
Map to mm10 (tophat/2.1.1 bowtie/2-2.3.4)
Calculate RPKM (Partek GS 7.0)
ANOVA comparison (Partek GS 7.0)
Genome_build: mm10
Supplementary_files_format_and_content: Excel files with RPKM and ANOVA results

source_name: skin

extract_protocol:
RNA was extracted from snap frozen tumor and skin sample stored in RNAlater solution . Total RNA was isolated using RNeasy Mini Kits (Qiagen).
Total RNA from mouse skin was used to create ribosomal RNA-depleted cDNA libraries (NEBNext® Ultra™ RNA Library Prep Kit).
Each sample was sequenced to 40 million raw reads in a single end 50bp sequencing run on the Illumina Hiseq3000 or Novaseq6000.

treatment_protocol: Three doses of DMBA (100ug/200ul) were topically administered on the dorsal side of DLX3cKO and WT mice. The time interval between treatments was one week. Animals were euthanized 31 weeks after the initiation of the protocol, and tumors and skin samples were collected.

tag: genotype

value: Dlx3 KO

value: Tumor


title: WFB10YE2

value: early rice


title: FRAS190036193


title: i46_SF_P310_A2

tag: treatment

value: IL-17A (10 ng/ml) for 24 hours


title: KO_Tumor_1


title: i45_SF_P310_C2

value: Synovium (knee)

value: Control (vehicle) for 24 hours


title: KO_Tumor_2


title: ST control at D8 (rep2)

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

institute: National Taiwan University Hospital

description:
ST control at D8
D8-ST-2

data_processing:
Adaptor trimming by cutadapt
Alignment by bowtie2
Expression quantification by RSEM
Genome_build: Am_3.4
Supplementary_files_format_and_content: Tab-delimited text file includes transcript expression level represented by TPM

organism: Ambystoma mexicanum

source_name: Soft tissue

growth_protocol: All the axolotls were kept in modified Holtfreter's solution.

extract_protocol:
Tissues from axolotls were subjected to total RNA extraction using TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s instructions. RNA samples were purified using a RNeasy Mini Kit (Qiagen, Hilden, Germany), then quantified on a Qubit 4 fluorometer (Invitrogen, CA, USA) and Qsep100 capillary gel electrophoresis (BiOptic, New Taipei City, Taiwan).
Libraries were constructed uing SureSelect Strand Specific RNA Library kit according to the manufacturers

treatment_protocol: Two microliters of 25 mM MS-275 (Selleckchem, Houston, TX, USA) was injected into the stumps immediately beneath the WE of juveniles every other day after amputation.

value: DMSO

value: Soft tissue

tag: days after amuptation


title: KO_Skin_1

value: Skin


title: FAPs-Prdm16-rep2

city: Rome

first: Chiara

last: Mozzetta

address: P.le Aldo Moro 5

department: IBPM

country: Italy

institute: CNR

description:
PolyA RNA
processed data file: Raw_counts.tsv
processed data file: Normalized_counts.tsv
processed data file: Prdm16-vs-WT_diffexp_log2fc0.5_pval0.1.tsv

data_processing:
Paired-end reads were aligned to the mouse reference genome mm10, or mm10 and dm6 for histone ChIP-Rx, using Bowtie v1.2.2 (Langmead et al., 2009) and parameters -k1 -I 10 -X 1000. PCR duplicates were removed using samblaster (Faust and Hall, 2014). Ambiguous reads mapping to both mm10 and dm6 were discarded. H3K9me2 and LamininB1 domains were calling using edd.
Reads were aligned to the mouse reference genome mm10 using STAR v2.7 without allowing multimapping reads (--outFilterMultimapNmax 1). PCR duplicates were removed using samblaster (Faust and Hall, 2014). Gene counts were calculated using featureCounts (Liao et al., 2014) with parameters -s 0 -t exon -g gene_name using Gencode M21 (GRCm38) annotation downloaded from (https://www.gencodegenes.org/mouse/). Differential expression analyses were performed using the R package DESeq2 v1.20 (Love et al., 2014) using default parameters. Log2FoldChanges and adjusted p-values were corrected using the apeglm (Zhu et al., 2019) and IHW (Ignatiadis et al., 2016) packages, respectively. Genes with an absolute log2 fold change of 1.5 and FDR < 0.05 were considered as differentially expressed.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Raw_counts.tsv: Raw counts
Supplementary_files_format_and_content: Normalized_counts.tsv: Normalized counts
Supplementary_files_format_and_content: Prdm16-vs-WT_diffexp_log2fc0.5_pval0.1.tsv: Differential expression
Supplementary_files_format_and_content: *_peaks.bed: BED files

source_name: FAPs

growth_protocol: FAPs were FACS-isolated as described in Methods and expanded in growth medium (Cytogrow; TGM-9001-B) for 4/5 days.

extract_protocol:
The mice were treated for 5 consecutive days with tamoxifen, by intraperitoneal injection. After 7 days, muscle regeneration was induced with cardiotoxin (CTX), via intra-muscular injection. Muscles and FAPs were then isolated 5 days post-injury (d.p.i). FAPs were expanded on ECM-coated dishes for 4/5 days and total RNA was extracted with Tri-reagent (Sigma) following manufacturer's instructions.
RNA-seq was performed following SMART-seq2 protocol (Picelli et al., 2014).

value: Skeletal muscle fibro-adipogenic progenitors

tag: genotype/variation

tag: developmental stage

value: Adult


title: i44_SF_P317_AF2

value: Synovial fibroblasts

value: End-stage osteoarthritis

value: IL-17AF (10 ng/ml) for 24 hours


title: KO_Tumor_4


title: WFB1YE2

tag: variety type

value: WFB

value: on the first day after flowering


title: ST control at D8 (rep1)

description:
ST control at D8
D8-ST-1


title: FRAS190036201

value: salivary glands

value: non-ILD-pSS


title: WFB1YE3

tag: Stage


title: run_2_06_17__R0_Mlibmix_1256_hemi_264__5hmC

description:
synthetic DNA, 5hmC
EpiSELEX-seq input

tag: variable region length

tag: left flank

value: GGTAGTGGAGGCAGTCCTGG

tag: right flank

value: CCAGGGAGGTGGAGTAGG

tag: round / concentrations


title: WFY10YM2

description: WFY1YMVSWFY10YM_Gene_differential_expression

value: on the tenth day after flowering

tag: enviroment

value: middle rice


title: FAPs-Prdm16-rep1

tag: cell type


title: i43_SF_P317_F2

value: Synovium (knee)

tag: cells

tag: disease state

value: IL-17F (10 ng/ml) for 24 hours

tag: patient id


title: WFB1YE1

value: early rice


title: run_06_05_17__R1_CEBPg_homo_75nM_lowBand__None

description:
synthetic DNA
EpiSELEX-seq for CEBPg
run_06_05_17__R1_CEBPg_homo_75nM_lowBand__.100000.tsv.gz

value: GGTAGTGGAGGTGGGCCTGG


title: FRAS190036202

tag: tissue


title: 1517 ctrl

tag: cell line

value: glioblastoma stem cell line 1517

tag: challenge

value: ctrl


title: FAPs-WT-rep3

value: Skeletal muscle fibro-adipogenic progenitors

value: Adult


title: i42_SF_P317_A2

value: Synovial fibroblasts

value: End-stage osteoarthritis

tag: treatment

value: IL-17A (10 ng/ml) for 24 hours


title: WE control at D8 (rep1)

description:
WE control at D8
D8-WE-1

source_name: Wound epidermis

value: DMSO

value: Wound epidermis

tag: days after amuptation


title: WE control at D8 (rep2)

description:
WE control at D8
D8-WE-2


title: FRAS190036203

value: salivary glands

value: non-ILD-pSS


title: FRAL190053199


title: FRAS190036199


title: HEK293-control_rep3

value: empty vector control

value: fetal kidney


title: FAPs-WT-rep2

tag: genotype/variation

tag: developmental stage


title: i41_SF_P317_C2

value: Synovium (knee)

value: Control (vehicle) for 24 hours


title: FAPs-WT-rep1


title: FRAS190036204


title: ST control at D3 (rep2)

description:
ST control at D3
D3-ST-5

value: Soft tissue


title: i40_SF_P377_AF2

value: IL-17AF (10 ng/ml) for 24 hours


title: ST control at D3 (rep1)

description:
ST control at D3
D3-ST-4


title: i39_SF_P377_F2

value: IL-17F (10 ng/ml) for 24 hours


title: FRAS190036205


title: FRAS190036209


title: i38_SF_P377_A2


title: WE control at D3 (rep2)

description:
WE control at D3
D3-WE-3


title: WT-LamininB1-rep1

extract_protocol:
The mice were treated for 5 consecutive days with tamoxifen, by intraperitoneal injection. After 7 days, muscle regeneration was induced with cardiotoxin (CTX), via intra-muscular injection. Muscles and FAPs were then isolated 5 days post-injury (d.p.i). FAPs were expanded on ECM-coated dishes for 4/5 days and were cross-linked with 1% formaldehyde. Chromatin sonicated to an average size of 200-150 bp. Chromatin was precipitated with specific antibody, which was further purified using magnetic protein A/G coupled beads, and recovered DNA was used for high-throughput sequencing.
DNA libraries were prepared with 2–10 ng of DNA using an in-house protocol (Blecher-Gonen et al., 2013) by the IEO genomic facility.

tag: chip antibody

value: LaminB1 (ab16048; Abcam)


title: WT-input-rep3

value: Skeletal muscle fibro-adipogenic progenitors


title: FRAS190036210


title: ST control at D0 (rep2)

description:
ST control at D0
O-ST-4


title: FRAS190036211


title: WT-input-rep2

value: Adult


title: i37_SF_P377_C2

value: Synovial fibroblasts


title: i36_SF_P368_AF2

value: End-stage osteoarthritis


title: WT-input-rep1


title: i35_SF_P368_F2


title: ST with MS-275 at D8 (rep2)

description:
ST with MS-275 at D8
D8-ST-M2


title: WE control at D0 (rep2)

description:
WE control at D0
O-WE-3


title: WT-H3K9me2-rep3

value: H3K9me2 (ab1220; Abcam)


title: FRAS190036215


title: ST with MS-275 at D8 (rep1)

description:
ST with MS-275 at D8
D8-ST-M1


title: WE control at D3 (rep1)

description:
WE control at D3
D3-WE-2

value: DMSO


title: i33_SF_P368_C2


title: FRAS190036216


title: WTlaminin-input-rep1


title: WE with MS-275 at D8 (rep2)

description:
WE with MS-275 at D8
D8-WE-M2

value: Wound epidermis


title: FRAS190036217

value: salivary glands


title: WT-H3K9me2-rep2


title: WT-H3K9me2-rep1


title: WE with MS-275 at D8 (rep1)

description:
WE with MS-275 at D8
D8-WE-M1


title: Prdm16laminin-input-rep1


title: i32_SF_P299_AF2


title: FRAS190036218

value: non-ILD-pSS


title: i31_SF_P299_F2


title: FRAS190036213


title: ST with MS-275 at D3 (rep2)

description:
ST with MS-275 at D3
D3-ST-M2


title: FRAS190036222


title: i30_SF_P299_A2

value: IL-17A (10 ng/ml) for 24 hours


title: Prdm16-LamininB1-rep1


title: i34_SF_P368_A2


title: ST with MS-275 at D3 (rep1)

description:
ST with MS-275 at D3
D3-ST-M1


title: Prdm16-input-rep3


title: WE with MS-275 at D3 (rep2)

description:
WE with MS-275 at D3
D3-WE-M2


title: i29_SF_P299_C2


title: FRAS190036233


title: i28_SF_P330_AF2


title: Prdm16-input-rep2


title: FRAS190036234


title: Prdm16-input-rep1


title: FRAS190036237


title: WE with MS-275 at D3 (rep1)

description:
WE with MS-275 at D3
D3-WE-M1


title: FRAS190036238


title: Prdm16-H3K9me2-rep3


title: i27_SF_P330_F2


title: i26_SF_P330_A2


title: Prdm16-H3K9me2-rep1


title: Prdm16-H3K9me2-rep2


title: ST control at D0 (rep1)

description:
ST control at D0
O-ST-2


title: i25_SF_P330_C2


title: FRAS190036242


title: KO_Skin_3

tag: genotype

value: Dlx3 KO

value: Skin


title: FRAS190036243


title: FRAS190036232


title: i23_HAC2_P4_F2_S24

source_name: Osteoarthritic knee cartilage

value: Cartilage (knee)

value: Chondrocytes


title: KO_Skin_2


title: FRAS190036244


title: i22_HAC2_P4_A2_S12


title: WT_Skin_3

value: WT


title: i21_HAC2_P4_C2_S22

value: Control (vehicle) for 24 hours


title: WT_Skin_2


title: WE control at D0 (rep1)

description:
WE control at D0
O-WE-2


title: FRAS190053149


title: KO_Tumor_5

value: Tumor


title: i20_HAC2_P226_AF2_S1

value: IL-17AF (10 ng/ml) for 24 hours


title: WT_Skin_1


title: i24_HAC2_P4_AF2_S19


title: FRAS190053155


title: FRAS190053160


title: i19_HAC2_P226_F2_S23

value: IL-17F (10 ng/ml) for 24 hours


title: i18_HAC2_P226_A2_S10


title: FRAS190053174


title: i17_HAC2_P226_C2_S15


title: FRAS190053175


title: i16_HAC2_P39_AF2_S7


title: FRAS190053151


title: FRAS190053176


title: Natolen128_salt_rep1

city: Nara

first: Kaori

last: Sako

state: Nara

address: 3327-204, Nakamachi

department: Department of Advanced Bioscience

institute: Kindai University

hyb_protocol: 600 ng of cRNAs was hybridized to the microarray (GPL19830) 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.

label_protocol: 200 ng of each RNA sample was used to prepare for Cy3-labeled cRNA, using Low Input Quick Amp Labeling Kit (Agilent).

growth_protocol: four-day-old wild-type plants (Arabidopsis thaliana ecotype Columbia) were grown on 1/2 MS, 0.1 % Agar medium.

extract_protocol: Total RNA was extracted from whole plants using RNeasy Plant Mini Kit  (QIAGEN).

treatment_protocol: The plants were treated 2 uM  Natolen128 or 2 uM Necolen124 for 24 hours and supplied 100 mM NaCl for two hours.

tag: ecotype

value: Columbia

value: whole plant

tag: stress condition

value: salinity stress condtion

value: with Natolen128


title: FRAS190053183


title: FRAS190053184


title: Natolen128_salt_rep2


title: Necolen124_salt_rep2

value: with Necolen124


title: i13_HAC2_P39_C2_S4

value: End-stage osteoarthritis


title: FRAS190053185

value: salivary glands

value: non-ILD-pSS


title: Natolen128_salt_rep3


title: Necolen124_salt_rep1


title: i12_HAC2_P3_AF2_S5


title: Natolen128_con_rep3

value: unstress condition


title: i10_HAC2_P3_A2_S9

value: IL-17A (10 ng/ml) for 24 hours


title: FRAS190053195


title: i09_HAC2_P3_C2_S17

value: Cartilage (knee)


title: DNA methylation from liver sample 137

city: New York

first: Gabriela

last: Hernandez-Meza

state: New York

address: 1 Gustave L. Levy Place

institute: Mount Sinai

description:
9247377175_R01C02
Dysplastic liver sample

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450k BeadChip using standard Illumina protocol.

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

data_processing:
BeadStudio software v3.2
Unmethylated_methylated_signal_intensities.txt: Unmethylated and methylated signal intensities, p-values.

label: not provided

source_name: Liver sample 137

label_protocol: Standard Illumina Protocol.

extract_protocol: For DNA extraction, we used the Qiagen RNeasy Mini and Invitrogen ChargeSwitch genomic DNA Mini Tissue according to standard instructions.

value: Liver

tag: diagnosis

value: Dysplastic


title: FRAS190053192


title: FRAS190053196


title: DNA methylation from liver sample 133

description:
9257625055_R06C01
Dysplastic liver sample

source_name: Liver sample 133


title: Necolen124_salt_rep3


title: Necolen124_con_rep3


title: Necolen124_con_rep2


title: DNA methylation from liver sample 131

description:
9247377204_R06C01
Dysplastic liver sample

source_name: Liver sample 131


title: i08_HAC2_P332_AF2_S11

value: Chondrocytes


title: i11_HAC2_P3_F2_S6


title: FRAS190053191


title: DNA methylation from liver sample 136

description:
9247377203_R06C01
Dysplastic liver sample

source_name: Liver sample 136


title: DNA methylation from liver sample 135

description:
9257625023_R06C01
Dysplastic liver sample

source_name: Liver sample 135


title: FRAS190053200


title: i14_HAC2_P39_A2_S13


title: i15_HAC2_P39_F2_S3


title: i07_HAC2_P332_F2_S16


title: DNA methylation from liver sample 132

description:
9257625022_R06C01
Dysplastic liver sample

source_name: Liver sample 132


title: DNA methylation from liver sample 138

description:
9257625025_R01C02
Dysplastic liver sample

source_name: Liver sample 138


title: 200205_Src-Kinase_60m

description:
peptide (bacterial display)
Kinase sequencing for Src
200205_Src-Kinase_60m.10000000.tsv.gz

tag: variable region length

tag: left flank

value: TAGTSVAGQSGQ

tag: right flank

value: GGQSGQSGDYNK

tag: round / concentrations

value: R0, input


title: FRAS190053201

tag: disease state


title: Necolen124_con_rep1

value: Columbia

tag: tissue


title: Natolen128_con_rep1

value: whole plant


title: Natolen128_con_rep2


title: DNA methylation from liver sample 134

description:
9257625047_R06C01
Dysplastic liver sample

source_name: Liver sample 134


title: DNA methylation from liver sample 128

description:
9247377203_R04C02
Cirrhosis liver sample

source_name: Liver sample 128

value: Cirrhosis


title: DNA methylation from liver sample 129

description:
9247377203_R05C02
Cirrhosis liver sample

source_name: Liver sample 129


title: i05_HAC2_P332_C2_S21

tag: cells

value: Control (vehicle) for 24 hours

tag: patient id


title: FRAS190053209

source_name: salivary glands


title: FRAS190053218


title: 200205_Src-Kinase_Unsel

description:
peptide (bacterial display)
Kinase sequencing for Src

source_name: in-vitro purification

value: R1, modified


title: DNA methylation from liver sample 126

description:
9247377203_R02C02
Cirrhosis liver sample

source_name: Liver sample 126


title: i06_HAC2_P332_A2_S20

value: End-stage osteoarthritis

tag: treatment


title: FRAS190053219

value: salivary glands


title: DNA methylation from liver sample 130

description:
9247377203_R06C02
Cirrhosis liver sample

source_name: Liver sample 130


title: i02_HAC2_P33_A2_S18


title: i03_HAC2_P33_F2_S2

value: IL-17F (10 ng/ml) for 24 hours


title: FRAS190053223

value: non-ILD-pSS


title: i01_HAC2_P33_C2_S8


title: 200205_Src-Kinase_5m

description:
peptide (bacterial display)
Kinase sequencing for Src
200205_Src-Kinase_5m.10000000.tsv.gz


title: DNA methylation from liver sample 123

description:
9247377203_R04C01
Cirrhosis liver sample

source_name: Liver sample 123


title: FRAS190053274


title: N4.holo

city: Frankfurt

first: Tobias

last: Schmid

address: Theodor-Stern-Kai 7

department: Institute of Biochemistry I

institute: Goethe University Frankfurt

data_processing:
joint report was created with MultiQC
umi2index
FastQC
Alignment: STAR Aligner with modified ENCODE settings
UMI collapse
Gene Read Counting: HTSeq-count with kit-specic options (FWD)
differential analysis: edgeR
Genome_build: Human (GRCh38)
Supplementary_files_format_and_content: text files containing the normalized read counts for contol or holo Lcn-2 stimulated CAKI1 cells

source_name: CAKI1 Cells

growth_protocol: Human renal CAKI1 tumor cells were cultured in Dulbecco’s modified Eagle medium (DMEM) with high glucose (Gibco, Dreieich, Germany), supplemented with 100 U/ml penicillin (Sigma-Aldrich, Taufkirchen, Germany), 100 µg/ml streptomycin (Sigma-Aldrich), and 10% fetal bovine serum (FBS; Capricorn Scientific, Ebsdorfergrund, Germany). Tumor cells were cultivated in a humidified atmosphere with 5% CO2 at 37°C and passaged 3 times per week. 24 h prior to stimulation, cells were serum starved. Cells were routinely tested for mycoplasma.

extract_protocol:
Total RNA was isolated using RNeasy Micro Kit (Qiagen) according to the manufacturer’s protocol
Libraries were prepared using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD from Illumina (Lexogen)

treatment_protocol: Cells were stimulated with 5 µg/ml hLcn-2 for 24 h.

value: holo Lcn-2

tag: concentration

tag: cell-line


title: FRAS190053273


title: DNA methylation from liver sample 124

description:
9247377203_R05C01
Cirrhosis liver sample

source_name: Liver sample 124


title: DNA methylation from liver sample 127

description:
9247377203_R03C02
Cirrhosis liver sample

source_name: Liver sample 127


title: N3.holo


title: DNA methylation from liver sample 122

description:
9247377203_R03C01
Cirrhosis liver sample

source_name: Liver sample 122


title: DNA methylation from liver sample 125

description:
9247377203_R01C02
Cirrhosis liver sample

source_name: Liver sample 125


title: FRAS190053277


title: i04_HAC2_P33_AF2_S14

source_name: Osteoarthritic knee cartilage

value: Cartilage (knee)

value: IL-17AF (10 ng/ml) for 24 hours


title: FRAS190053276


title: N3.control

value: control


title: HCC38 5µM Tubacin-3

city: HOUGHTON

first: TAHIYAT

last: ALOTHAIM

state: MI

address: DOW 514,1400 Townsend Dr

department: Department of Biological Sciences

institute: Michigan Technological University

hyb_protocol: Hybridized to GeneChip® arrays in Affymetrix GeneChip® hybridization oven 645, washed in Affymetrix GeneChip® Fluidics Station 450

scan_protocol: scanned with Affymetrix GeneChip® Scanner 7G according to standard Affymetrix GeneChip® Hybridization, Wash, and Stain protocols. (Affymetrix, Santa Clara,CA).

data_processing: The gene expression pattern of the RNA samples were interrogated with Affymetrix U133A genechips and normalized by the RMA (Robust Multi-Array) algorithm

source_name: Triple negetive  breast cancer cell line HCC46

label_protocol: Hybridization targets were prepared with MessageAmp™ Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX) from total RNA

growth_protocol: HCC38 cells seeded in DMEM media supplement with 10% FBS and Penicillin/Stertomycin for 48hours pre-treatment, and treated for 18hours

extract_protocol: Samples were collected on ice and RNA was isolated with QIAGEN’s RNeasy Kit according to the manufacturer's protocol

treatment_protocol: HCC38 cells were treated for 18hours with DMSO as control C sample, 5µM Erastin E, 5µm Tubacin T , or the combnation of Erastin and tubacin E+T, the RNA collected 18h post treatment

tag: cell line

value: 5µM Tubacin for 18 hours


title: FRAS190053285


title: HCC38 E+T-2

source_name: Triple negetive  breast cancer cell line HCC48

value: combination of 5µM Erastin and 5µM Tubacin for 18 hours


title: FRAS190053206


title: N2.holo


title: HCC38 5µM Tubacin-1

source_name: Triple negetive  breast cancer cell line HCC44


title: HCC38 5µM Tubacin-2

source_name: Triple negetive  breast cancer cell line HCC45


title: FRAS190053290


title: N2.control


title: DNA methylation from liver sample 119

description:
9257625023_R06C02
Cirrhosis liver sample

source_name: Liver sample 119

value: Liver


title: HCC38 5µM Erastin-3

source_name: Triple negetive  breast cancer cell line HCC43

value: 5µM Erastin for 18 hours


title: FRAS190053300

source_name: salivary glands


title: DNA methylation from liver sample 120

description:
9247377203_R01C01
Cirrhosis liver sample

source_name: Liver sample 120


title: N1.holo


title: DNA methylation from liver sample 117

description:
9257625023_R04C02
Cirrhosis liver sample

source_name: Liver sample 117


title: N1.control


title: HCC38 E+T-1

source_name: Triple negetive  breast cancer cell line HCC47


title: HCC38 5µM Erastin-2

source_name: Triple negetive  breast cancer cell line HCC42


title: DNA methylation from liver sample 121

description:
9247377203_R02C01
Cirrhosis liver sample

source_name: Liver sample 121


title: HCC38 Con-2

source_name: Triple negetive  breast cancer cell line HCC39

value: DMSO as a control sample for 18 hour


title: FRAS190053311


title: HCC38 5µM Erastin-1

source_name: Triple negetive  breast cancer cell line HCC41


title: SCCOHT, UGS669

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

institute: Institut Curie

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human EPIC Beadchip using Illumina protocol

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

data_processing:
RnBeads Bioconductor R package (version 1.6.1)
matrix processed value definition: beta-value

label: cy3, cy5

source_name: Fresh frozen sample

label_protocol: Illumina Protocol

extract_protocol: Illumina Protocol

tag: gender

value: Female

tag: sample type

value: SCCOHT

value: tumour


title: DNA methylation from liver sample 113

description:
9257625023_R05C01
Cirrhosis liver sample

source_name: Liver sample 113

value: Cirrhosis


title: SCCOHT, UGS668


title: FRAS190053314


title: 200205_Src-Kinase_20m

description:
peptide (bacterial display)
Kinase sequencing for Src
200205_Src-Kinase_20m.10000000.tsv.gz

source_name: in-vitro purification

value: TAGTSVAGQSGQ

value: GGQSGQSGDYNK

value: R1, modified


title: DNA methylation from liver sample 115

description:
9257625023_R02C02
Cirrhosis liver sample

source_name: Liver sample 115


title: HCC38 Con-1

source_name: Triple negetive  breast cancer cell line HCC38


title: SCCOHT, UGS667


title: DNA methylation from liver sample 111

description:
9257625023_R03C01
Cirrhosis liver sample

source_name: Liver sample 111


title: DNA methylation from liver sample 112

description:
9257625023_R04C01
Cirrhosis liver sample

source_name: Liver sample 112


title: FRAS190053320

value: salivary glands

value: non-ILD-pSS


title: FRAS190053318


title: DNA methylation from liver sample 114

description:
9257625023_R01C02
Cirrhosis liver sample

source_name: Liver sample 114


title: FRAS190053325


title: FRAS190053327


title: HCC38 Con-3

source_name: Triple negetive  breast cancer cell line HCC40


title: FRAS190053329

source_name: salivary glands


title: HCC38 E+T-3

source_name: Triple negetive  breast cancer cell line HCC49


title: FRAS190053333


title: FRAS190053339


title: FRAS190053342


title: FRAS190074232


title: DNA methylation from liver sample 108

description:
9257625047_R06C02
Cirrhosis liver sample

source_name: Liver sample 108


title: FRAS190074233


title: DNA methylation from liver sample 109

description:
9257625023_R01C01
Cirrhosis liver sample

source_name: Liver sample 109


title: FRAS190074249


title: DNA methylation from liver sample 105

description:
9257625047_R03C02
Cirrhosis liver sample

source_name: Liver sample 105


title: SCCOHT, UGS666


title: N4.control

source_name: CAKI1 Cells


title: DNA methylation from liver sample 116

description:
9257625023_R03C02
Cirrhosis liver sample

source_name: Liver sample 116


title: DNA methylation from liver sample 106

description:
9257625047_R04C02
Cirrhosis liver sample

source_name: Liver sample 106


title: FRAS190074260


title: FRAS190074252


title: FRAS190074246


title: FRAS190053303


title: DNA methylation from liver sample 107

description:
9257625047_R05C02
Cirrhosis liver sample

source_name: Liver sample 107


title: DNA methylation from liver sample 110

description:
9257625023_R02C01
Cirrhosis liver sample

source_name: Liver sample 110


title: FRAS190053297


title: FRAS190074264


title: FRAS190074266


title: DNA methylation from liver sample 102

description:
9257625047_R05C01
Cirrhosis liver sample

source_name: Liver sample 102


title: FRAS190074269


title: FRAS190053309


title: FRAS190074273


title: DNA methylation from liver sample 99

description:
9257625047_R02C01
Cirrhosis liver sample

source_name: Liver sample 99


title: FRAS190074277


title: SCCOHT, UGS663

source_name: Fresh frozen sample


title: FRAS190074284


title: DNA methylation from liver sample 103

description:
9257625047_R01C02
Cirrhosis liver sample

source_name: Liver sample 103


title: sh-FGD5-AS1 rep3

first: Xingyu

last: Zhang

address: No.1678, Dong Fang Road

institute: Shanghai Jiaotong University School of Medicine

data_processing:
Sequence quality was analyzed by FastQC v 0.11.9. Read pairs with low quality were removed using Trim_Galore! v 0.6.5.
The clean data were aligned to human reference genome  using BWA v0.7.17 and duplicated pairs were removed by Picard v2.23.1.
BedGraph files were generated from replicate concatenated processed ATAC-seq reads and .bed files  scaled to 1 million mapped reads were created with BEDTools v2.29.2  which were then converted to .bigWig files using the ENCODE program bedGraphToBigWig.
broad/narrow peaks were called using MACS v2.2.7.1 and  peaks relative to gene features were annoated by HOMER v4.11.
Gene count reads in consensus peaks  were summarized using  featureCounts v 2.0.0.
Genome_build: GRCh38
Supplementary_files_format_and_content: bigwig files
Supplementary_files_format_and_content: peak text files

source_name: human embryonic heart tissue

growth_protocol: The CCC-HEH-2 human cardiac myocytes were were cultured in Dulbecco's modified Eagle's medium  containing 10% fetal bovine serum at 37°C with 5% CO2.

extract_protocol:
Lysates were clarified from sonicated nuclei and were carried out immediately in the prepared transposition reaction mix which contained Nextera Tn5 Transposase from Nextera kit.
Libraries were generated by PCR amplification using NEBNext High-Fidelity 2X PCR Master Mix (NEB).

value: human embryonic heart tissue

value: male

tag: age

value: 11 weeks


title: ECRT-SMARCB1, INI289

value: Male

value: ECRT


title: DNA methylation from liver sample 100

description:
9257625047_R03C01
Cirrhosis liver sample

source_name: Liver sample 100

value: Liver


title: DNA methylation from liver sample 95

description:
9257625055_R04C02
Cirrhosis liver sample

source_name: Liver sample 95


title: sh-FGD5-AS1 rep2


title: FRAS190074291

source_name: salivary glands


title: DNA methylation from liver sample 104

description:
9257625047_R02C02
Cirrhosis liver sample

source_name: Liver sample 104


title: sh-FGD5-AS1 rep1


title: FRAS190074303


title: sh-NC rep3

value: sh-NC


title: DNA methylation from liver sample 94

description:
9257625055_R03C02
Cirrhosis liver sample

source_name: Liver sample 94


title: DNA methylation from liver sample 96

description:
9257625055_R05C02
Cirrhosis liver sample

source_name: Liver sample 96


title: sh-NC rep2


title: DNA methylation from liver sample 93

description:
9257625055_R02C02
Cirrhosis liver sample

source_name: Liver sample 93


title: FRAS190074289


title: DNA methylation from liver sample 97

description:
9257625055_R06C02
Cirrhosis liver sample

source_name: Liver sample 97


title: DNA methylation from liver sample 98

description:
9257625047_R01C01
Cirrhosis liver sample

source_name: Liver sample 98


title: FRAS190074321


title: sh-NC rep1


title: FRAS190074285


title: DNA methylation from liver sample 89

description:
9257625055_R03C01
Cirrhosis liver sample

source_name: Liver sample 89


title: DNA methylation from liver sample 101

description:
9257625047_R04C01
Cirrhosis liver sample

source_name: Liver sample 101


title: L428-shNTC-day5_rep3 (RNA-seq)

city: CANBERRA

first: Jiayu

last: Wen

state: ACT

address: 133 Garran Rd

department: Department of Genome Science

country: Australia

institute: John Curtin School of Medical Research, The Australian National University

description:
L428-shNTC-day5_rep3 (RNA-seq)
L428_RNAseq_counts.xlsx

data_processing:
The CUT&RUN samples were mapped to the Homo sapiens (hg38) genome assembly using Bowtie2 with the default parameters, after the adaptor trimming by Trimmomatic. The high quality and uniquely mapped reads with a mapping quality MAPQ > 20 were used for further analysis. We obtained the spike-in reads by mapping the reads to the Drosophila melanogaster (dm6) genome assembly. We generated coverage tracks for CUT&RUN samples, which were normalized to spike-ins.
The ATAC-seq samples in two biological replicates in two cell lines were mapped to the Homo sapiens (hg38) genome assembly using Bowtie2 with default parameters after adaptor trimming by Trimmomatic. The high quality and uniquely mapped reads (MAPQ > 20) and the reads filtered for PCR-duplicates by Picard were used for further analysis.
After trimming the adaptor sequences using Trimmomatic, the RNA-seq samples in three replicates from the wild type and H2A.B mutant in two cell lines, L1236 and L428, were mapped to the Homo sapiens (hg38) genome assembly using HISAT2. Gene annotation was obtained from the UCSC hg38 gene annotation in iGenomes. The sequencing reads were assigned to genes by featureCounts in Rsubread package in Bioconductor.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig for coverage and RNA-seq counts for all genes

source_name: L428 cell line

growth_protocol: The L1236 and L428 cell lines with doxycycline-inducible shNTC or shH2A.B expression were routinely cultured in RPMI-1640 growth medium supplemented with 10% heat-inactivated foetal bovine serum (HI-FBS), 1% L-glutamine (200 mM stock), and 1% Penicillin-Streptomycin (10,000 units penicillin and 10 mg streptomycin/mL stock), and 0.2 μg/mL puromycin. Cells were cultured in T75 flasks and maintained in a humidified cell culture incubator at 37 ˚C and 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent (Thermo Fisher Scientific) .The genomic DNA was removed using the  TURBO DNA-free kit (Thermo Fisher Scientific)  following the kit manual.
The sequencing libraries  for L1236 were prepared using the Illumina TruSeq Stranded mRNA library prep kit coupled with poly-A selection, using standard Illumina protocols. The sequencing libraries for L428  were prepared using the Illumina TruSeq RNA Sample Prep Kit coupled with poly-A selection, using standard Illumina protocols.

treatment_protocol: 0.5 x106 cells were seeded per well in 4 mL RPMI-1640 grwoth medium in 6-well plates. Eeach well was supplemented with 0.1 μg/mL doxycycline for induction of shRNA expression.  Three replicates of each L1236- shNTC and L1236-shH2A.B cells were collected for RNA extraction on day 2 and day 5 post doxycyline induction.

tag: cut&run antibody

value: shNTC (Non-targeting control)

value: Day 5


title: DNA methylation from liver sample 87

description:
9257625055_R01C01
Cirrhosis liver sample

source_name: Liver sample 87

tag: diagnosis


title: DNA methylation from liver sample 118

description:
9257625023_R05C02
Cirrhosis liver sample

source_name: Liver sample 118


title: FRAS190074313


title: FRAS190074329


title: FRAS190074333


title: L428-shH2A.B-day5_rep3 (RNA-seq)

description:
L428-shH2A.B-day5_rep3 (RNA-seq)
L428_RNAseq_counts.xlsx


title: DNA methylation from liver sample 88

description:
9257625055_R02C01
Cirrhosis liver sample

source_name: Liver sample 88


title: DNA methylation from liver sample 92

description:
9257625055_R01C02
Cirrhosis liver sample

source_name: Liver sample 92


title: L428-shH2A.B-day5_rep2 (RNA-seq)

description:
L428-shH2A.B-day5_rep2 (RNA-seq)
L428_RNAseq_counts.xlsx


title: DNA methylation from liver sample 86

description:
9257625022_R06C02
Cirrhosis liver sample

source_name: Liver sample 86


title: DNA methylation from liver sample 91

description:
9257625055_R05C01
Cirrhosis liver sample

source_name: Liver sample 91


title: FRAS190074325


title: FRAS190074336


title: L428-shH2A.B-day5_rep1 (RNA-seq)

description:
L428-shH2A.B-day5_rep1 (RNA-seq)
L428_RNAseq_counts.xlsx


title: FRAS190074337


title: L1236-shNTC-day5_rep3 (RNA-seq)

description:
L1236-shNTC-day5_rep3 (RNA-seq)
L1236_RNAseq_counts.xlsx

source_name: L1236 cell line


title: DNA methylation from liver sample 85

description:
9257625022_R05C02
Cirrhosis liver sample

source_name: Liver sample 85


title: DNA methylation from liver sample 83

description:
9257625022_R03C02
Cirrhosis liver sample

source_name: Liver sample 83


title: FRAS190074354

source_name: salivary glands


title: DNA methylation from liver sample 90

description:
9257625055_R04C01
Cirrhosis liver sample

source_name: Liver sample 90


title: DNA methylation from liver sample 84

description:
9257625022_R04C02
Cirrhosis liver sample

source_name: Liver sample 84


title: SCCOHT, UGS653

source_name: Fresh frozen sample

value: Female

value: SCCOHT


title: FRAS190074343


title: DNA methylation from liver sample 79

description:
9257625022_R04C01
Cirrhosis liver sample

source_name: Liver sample 79

value: Cirrhosis


title: FRAS190074355


title: DNA methylation from liver sample 78

description:
9257625022_R03C01
Cirrhosis liver sample

source_name: Liver sample 78


title: L1236-shNTC-day5_rep1 (RNA-seq)

description:
L1236-shNTC-day5_rep1 (RNA-seq)
L1236_RNAseq_counts.xlsx


title: L1236-shH2A.B-day5_rep3 (RNA-seq)

description:
L1236-shH2A.B-day5_rep3 (RNA-seq)
L1236_RNAseq_counts.xlsx


title: DNA methylation from liver sample 81

description:
9257625022_R01C02
Cirrhosis liver sample

source_name: Liver sample 81


title: SCCOHT, UGS652

value: tumour


title: FRAS190074368


title: L1236-shH2A.B-day5_rep2 (RNA-seq)

description:
L1236-shH2A.B-day5_rep2 (RNA-seq)
L1236_RNAseq_counts.xlsx


title: SCCOHT, UGS650


title: FRAS190074370


title: L1236-shH2A.B-day5_rep1 (RNA-seq)

description:
L1236-shH2A.B-day5_rep1 (RNA-seq)
L1236_RNAseq_counts.xlsx


title: DNA methylation from liver sample 76

description:
9257625022_R01C01
Cirrhosis liver sample

source_name: Liver sample 76


title: Lml_axenic_C

city: Thiverval-Grignon

first: Jessica

middle: Louise

last: SOYER

address: Avenue Lucien Brétignières

department: SPE

institute: INRAE

data_processing:
Mapping against the reference genome of Lmb (Dutreux et al., 2018) or Lml (Grandaubert et al., 2014) using STAR (Langmead and Salzberg, 2012) with default parameters
Genome_build: Lmb (Dutreux et al., 2018); Lml (Grandaubert et al., 2014)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample, rpkm values estimated with function rpkm_count of EdgeR (Robinson et al., 2010)

organism: Plenodomus lingam/Leptosphaeria maculans 'lepidii' group

source_name: mycelium

growth_protocol: mycelium of Lmb and Lml were grown on V8 agar medium at 25°C for seven days. Then 10 plugs of mycelium were inoculated into 100 ml of Fries liquid medium in Roux bottle. Mycelia were harvested after growing for 7 days at 25°C

extract_protocol:
Total RNA was extracted following protocol by Fudal et al. (2007)
The NEBNext Ultra Directional RNA Library Prep Kit for Illumina (cat. # E7420L New England BioLabs) was used to prepare all RNA-seq libraries, following the manufacturer’s instructions. Sequencing was performed by the GenomEast platform, a member of the ‘France Génomique’ consortium (ANR-10-INBS-0009). Samples were run in 9-plex on an Illumina HiSeq 4000 in paired mode, 2x50 bp.

treatment_protocol: mycelium was filtered and washed thoroughly with distilled water, placed in liquid nitrogen until RNA extraction

tag: strain

value: IBCN84 (Grandaubert et al., 2014)

value: mycelium

tag: growth condition

value: axenic