title: Neuroepithelial stem cells - CTRL7 (P10052_111)

description:
Sample 4
P10052_111
This cell line served as reference


title: Naïve MGPP3

status: Public on Jan 09 2022

type: SRA

city: New York

first: Michael

middle: G

last: Argenziano

state: New York

address: 1130 St. Nicholas Ave

country: USA

institute: Columbia University Vagelos College of Physicians and Surgeons

description:
PT001
murine glioma (brain)

library_source: transcriptomic

data_processing:
Raw sequencing data were processed using the 10x Genomics Cell Ranger pipeline version 2.2.0 with default parameters.
Genome_build: GRCh38
Supplementary_files_format_and_content: *.countmatrix.txt: Tab-delimited text files include transcript count abundances.

molecule: total RNA

organism: Mus musculus

source_name: Naïve MGPP3

growth_protocol: Growth protocol described here: https://link.springer.com/article/10.1007/s11060-013-1082-x

extract_protocol:
RNA was extracted and poly(A) mRNA was converted into barcoded cDNA using the 10x Genomics Chromium platform.
scRNA-seq libraries were constructed using the 10x Genomics Gene Expression 3' v2 chemistry.

treatment_protocol: Basal conditions or 75uM ispinesib for 21 days.

tag: cell line

tag: cell type

value: Glioma cell line

tag: genotype

value: PDGFB, PTEN-/-, p53 -/-

tag: condition

value: Basal

tag: phenotype

value: Naive


title: Neuroepithelial stem cells - CTRL11 (P10052_126)

city: Stockholm

first: Jakob

last: Schuy

address: Akademiska stråket 1

country: Sweden

institute: Karolinska Institutet

description:
Sample 6
P10052_126
This cell line served as reference

data_processing:
Transcript abundance: Salmon V1.1.0
Gene expression changes: DeSeq2 package in R (Love et al., 2014)
Tx2Gene list: GRCh38.p13/hg38, release 36
Gene annotations: BioMart - Ensembl for gene annotation
Genome_build: GRCh38.p13/hg38
Supplementary_files_format_and_content: Excel files contain the DeSeq2 output for Samples 1-3 compared to the merged control lines (e.g. Sample1 compared to Sample4-6) including gene annotation and statistics

molecule: polyA RNA

organism: Homo sapiens

source_name: Neuroepithelial stem cells

growth_protocol: The iPSC colonies were neurally induced to capture neuroepithelial stem cells (NESCs) (Falk et al., 2012). Briefly, neural induction was achieved by culturing the iPSCs in 0.5 ng/mL hNoggin and 3.3 µM CHIR99021 until day 10. The medium was supplemented with 10 µM SB431542 until day 4. The cells were replated at 40,000 cells/cm2 onto 0.1 mg poly-l-ornithine 1 μg/ml laminin L2020–coated plates in medium containing Dulbecco modified eagle medium/F-12 GlutaMAX, 1% N2, 0.1% B27, 10 ng/mL FGF2, 10 ng/mL EGF, and 1% Pen/Strep.

extract_protocol:
Illumina TrueSeq Stranded mRNA kit
Nova-Seq 6000 platform

value: Neuroepithelial stem cells

tag: cell source

value: iPSC-derived

tag: disease state

value: Control cell line


title: Ispinesib Resistant MGPP3

description:
PT002
murine glioma (brain)

source_name: Ispinesib Resistant MGPP3

value: 75uM ispinesib x 21 days

value: Ispinesib Resistant


title: Neuroepithelial stem cells - DSB3 (P10052_123)

description:
Sample 3
P10052_123
DESeq2_output_DSB3_comparedToAllCTRL.xlsx

value: Trisomy 21


title: Neuroepithelial stem cells - DSB2 (P10052_135)

description:
Sample 2
P10052_135
DESeq2_output_DSB2_comparedToAllCTRL.xlsx


title: Neuroepithelial stem cells - DSB3 (P10052_110)

description:
Sample 3
P10052_110
DESeq2_output_DSB3_comparedToAllCTRL.xlsx


title: NAMPT+ statuses CIA rats peripheral leukocytes RNA, rep4

city: wuhu

first: qing

middle: meng

last: tao

address: Wenchang road

country: China

institute: Wannan Medical College

data_processing:
Total RNA was extracted using Trizol reagent, after that, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification.
Then, mRNA was fragmented into short fragments and were reverse-transcribed to create the cDNA.
Illumina Novaseq™ 6000 was used to sequence following the vendor's recommended protocol.
cutadapt(v 1.9) was introduced to removes adapter sequences. Hisat2(v 2.0.4) was introduced to map genome and StringTie(v 1.3.4) was performed to assemble the mappped reads.
FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated by StringTie and ballgown.
Genome_build: rno ensembl v96
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values and row counts for each Sample

organism: Rattus norvegicus

source_name: Peripheral leukocytes

growth_protocol: The rats in CIA control group received a boost IFA-CII injection on day 7, and collected peripheral blood through fossa orbitalis vein started the next day to cover pre-clinical stages of CIA.The blood was centrifugated to obtain  precipitation, then resuspended in red blood cell lysis buffer, and incubated at room temperature for 5 min. After erythrolysis, WBCs were obtained. Total RNA within these cells were exacted by TRNzol reagent.

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

treatment_protocol: RNA was extracted directly from leukocytes in peripheral blood of normal and CIA rats

tag: strain

value: Wistar

value: collagen-induced arthritis (CIA)

tag: status

value: NAMPT+

value: Peripheral leukocytes


title: NAMPT++ statuses CIA rats peripheral leukocytes RNA, rep4

value: NAMPT++


title: NAMPT+ statuses CIA rats peripheral leukocytes RNA, rep3


title: Neuroepithelial stem cells - RD_P26 (P10052_134)

description:
Sample 1
P10052_134
DESeq2_output_RD_P26_comparedToAllCTRL.xlsx

value: Ring chromosome 21


title: Neuroepithelial stem cells - DSB2 (P10052_122)

description:
Sample 2
P10052_122
DESeq2_output_DSB2_comparedToAllCTRL.xlsx


title: NAMPT++ statuses CIA rats peripheral leukocytes RNA, rep1


title: NAMPT+ statuses CIA rats peripheral leukocytes RNA, rep1


title: NAMPT++ statuses CIA rats peripheral leukocytes RNA, rep3


title: NAMPT++ statuses CIA rats peripheral leukocytes RNA, rep2


title: Neuroepithelial stem cells - RD_P26 (P10052_121)

description:
Sample 1
P10052_121
DESeq2_output_RD_P26_comparedToAllCTRL.xlsx


title: NAMPT+ statuses CIA rats peripheral leukocytes RNA, rep2


title: HCI-011_PDX_18708X9

city: Salt Lake CIty

first: Jason

last: Gertz

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: University of Utah

library_source: genomic

data_processing:
Sequencing data quality was assessed using FastQC v0.11.4 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) to ensure the read starts with the MspI recognition sequence, and includes adequate base balancing (20-40% A,C,G and T at each cycle after the MspI recognition sequence).
Adapters were trimmed from the sequencing reads using Trim Galore! v0.4.4 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), using the options --rrbs and --fastqc.
Alignment to the hg19 reference genome was performed using Bismark v0.19.0108, using the options -bowtie2, --non_bs_mm, -N 1, and --multicore 6.
Library quality was considered sufficient if greater than 60% of reads uniquely aligned to the genome. Conversion efficiency was considered sufficient when the percent of methylation observed in the CHH genome context was less than 3%. Library genome coverage was considered sufficient if more than 700,000 CG positions in the genome had a depth of at least 10 reads.
For each library that met these quality metrics, methylation percentages at individual CpG positions in the reference genome were quantified using the Bismark Methylation Extractor v0.19.0 program, using the options --zero_based and --bedGraph.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix of percent methylated values

molecule: genomic DNA

growth_protocol: The growth of mouse xenograft tumors and the growth of organoid cultures from these xenograft tumors is described in detail in Guillen, Katrin P. , et al. A breast cancer patient-derived xenograft and organoid platform for drug discovery and precision oncology. BioRxiv. 2021. doi: https://doi.org/10.1101/2021.02.28.433268.

extract_protocol:
Genomic DNA was extracted from each sample using the Qiagen AllPrep DNA/RNA Mini kit.
Reduced representation methylation sequencing was performed on 500ng of genomic DNA isolated from each sample. Briefly, DNA is digested with MspI to enrich for CG rich regions of the genome. DNA fragment overhangs are filled with Klenow Fragment (3’-5’ exo-) (NEB) to leave an A-overhang. Adapters containing methyl-C are ligated to create a library. The library is treated with sodium bisulfite (EZ DNA Methylation Gold Kit; Zymo Research), or enzymatic methylation conversion (Enzymatic Methyl-seq Conversion Module, NEB Product #E7125L) to convert unmethylated cytosine to uracil.  The converted library is PCR amplified using Taq polymerase and barcoded primers. During PCR uracil is copied as a thymine and methyl-cytosine is copied as cytosine. Equimolar quantities of barcoded libraries are pooled and sequenced on the illumina HiSeq 2500 or NovaSeq to obtain at least 50 million reads per sample. PhIX genome control library (Illumina) is included at 20-25% in each sequencing lane to improve cluster identification and base-balancing during sequencing.
Other: Reduced representation methylation sequencing using either sodium bisulfite conversion (RRBS) or enzymatic methylation conversion (RREMS).

tag: modeltype

value: PDX

tag: method

value: RREMS

value: Breast Cancer


title: Normal rats peripheral leukocytes RNA, rep3

description: Normal 3

value: healthy control

value: control


title: HCI-011_PDxO_18708X7

value: PDXO


title: Neuroepithelial stem cells - RD_P26 (P10052_108)

description:
Sample 1
P10052_108
DESeq2_output_RD_P26_comparedToAllCTRL.xlsx

value: Neuroepithelial stem cells

value: iPSC-derived


title: HCI-011_Patient_18708X8

value: Patient


title: Neuroepithelial stem cells - DSB2 (P10052_109)

description:
Sample 2
P10052_109
DESeq2_output_DSB2_comparedToAllCTRL.xlsx


title: Normal rats peripheral leukocytes RNA, rep1

description: Normal 1


title: HCI-005_PDX_18708X6


title: HCI-005_PDxO_18733X2


title: Urine, right after exercise

city: Seoul

first: Suhong

last: Park

address: 1, Gwanak-ro, Gwanak-gu,

department: Exercise Science

country: South Korea

institute: Seoul National University

data_processing:
Adapter trimming:  The raw reads of small RNAs were pre-processed to eliminate adapter sequences. Adapters in the raw reads were trimmed using cutadapt program. The first 3nt of all reads were trimmed to remove extra bases, which were inserted during the SMART template-switching activity process. If a sequence was matched to more than the first 5 bp of 3' adapter sequence, it was regarded as an adapter sequence, and then trimmed from the read. Trimmed reads, whose length is longer than 18 bp, were selected for mapping reliability. Then, the remaining reads are classified into non-adapter reads, whose adapter sequences were not sequenced. In this analysis, trimmed and non-adapter reads were combined and regarded as processed reads for downstream analysis.
Clustering:  To minimize the sequence redundancy for computational efficiency, processed reads were clustered by a sequence. A unique cluster consists of the reads whose sequences and length are same.
Ribosomal RNA filtering:  In order to eliminate rRNA, reads were excluded that aligned to the 45S pre-rRNA and mitochondrial rRNA of Homo sapiens.
Identification of known miRNA reads:  Sequence alignment and detection of known and novel microRNAs were performed using miRDeep2 software algorithm. rRNA-filtered reads were aligned to the matured and precursor miRNAs of Homo sapiens obtained from miRBase v22.1 using miRDeep2 quantifier module. The miRDeep2 algorithm is based on the miRNA biogenesis model; it aligns reads to potential hairpin structures to check whether their mapping context is consistent with Dicer processing, and assigns scores representing the probability that hairpins are true miRNA precursors.
Novel miRNAs prediction:  The reference genome of Homo sapiens, release GRCh38, was retrieved from RefSeq. The reference genome was indexed and rRNA-filtered reads were mapped to it using Bowtie (1.1.2). Novel microRNAs were predicted from the mature, star and loop sequence according to the RNAfold algorithm using miRDeep2. The RNAfold function uses the nearest-neighbor thermodynamic model to predict the minimum free-energy secondary structure of an RNA sequence.
mRNA expression profiling:  The reference gene annotation for Homo sapiens (GRCh38; release 109.20190607) was retrieved from NCBI. Since the produced read contains not only small RNA but also mRNA, mRNA expression profiling was performed using RSEM (v1.3.1) with options (--estimate-rspd --seed-length 15 --strandedness forward).
Proportion of miRNA and other RNA categories:  Uniquely clustered reads are then sequentially aligned to reference genome, miRBase v21 and non-coding RNA database RNAcentral release 14.0 to identify known miRNAs and other types of RNA for classification.
Statistical analysis of differential miRNA expression:  Raw data (the reads for each miRNA) was normalized by Trimmed mean of M value (TMM) method with edgeR. For pre-processing, miRNAs with zero-count in more than one sample were excluded leaving 350 mature miRNAs for downstream analysis. A dummy variable “1” was added to the normalized read count of the filtered miRNAs to facilitate log2 transformation for plotting. For each miRNA, logCPM (Counts Per Million) and log fold change were calculated between case and control. Statistical hypothesis test for comparison of two groups was conducted using the exact test in edgeR. Differentially expressed miRNAs between two groups were determined by the criteria: |fold change|≥2 & p-value < 0.05.
Genome_build: GRCh38
Supplementary_files_format_and_content: MatureBased_expression.txt (RPMs, Counts)

source_name: Urinary exosome

extract_protocol:
Exosomal fractions from filtered urine samples were isolated by using miRCURY Exosome Cell/Urine/CSF kit(Cat#76743). SMARTer smRNA-Seq Kit for Illumina (Takara Bio, Shiga, Japan) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Participants were encouraged to finish 20 m shuttle run with their maximal effort.

tag: age

value: Twenties

tag: gender

value: Male

tag: sample type

value: Exosomal fraction from urine

tag: time

value: Post


title: Morning first urine

value: Pre


title: Urine, 1 hour rest after exercise

value: Post 1h


title: HCI-005_Patient_18708X5


title: HCI-027_PDxO_15261X5

value: RRBS


title: HCI-003_PDxO_18708X1


title: HCI-027_PDX_15261X4


title: HCI-003_PDX_18708X3.18733X1


title: HCI-027_Patient_14561X5


title: HCI-003_Patient_18708X2


title: HCI-010_PDxO_14561X8


title: HCI-010_PDX_15261X3


title: HCI-017_PDxO_18708X10


title: Normal rats peripheral leukocytes RNA, rep2

description: Normal 2

value: Wistar

value: Peripheral leukocytes


title: HCI-017_PDX_18708X11

value: PDX

value: RREMS


title: HCI-001_PDxO_14561X6

value: Breast Cancer


title: HCI-032_PDxO_S18088X2


title: HCI-001_PDX_15261X1


title: HCI-001_Patient_14561X11


title: HCI-032_Patient_S18061X5


title: HCI-002_PDxO_14561X7


title: HCI-028_PDxO_S18061X4


title: Ispinesib Resistant MGPP3 [SP064]

description:
SP064
murine glioma (brain)

data_processing:
RTA (Illumina) for base calling.
bcl2fastq2 (version 2.19) for converting BCL to fastq format.
Pseudoalignment to a kallisto index created from transcriptomes (Human: GRCh38; Mouse: GRCm38) using kallisto (0.44.0).
Genome_build: GRCm38
Supplementary_files_format_and_content: *.tsv: Tab-delimited text files include transcript abundances.

extract_protocol:
We use poly-A pull-down to enrich mRNAs from total RNA samples.
Illumina TruSeq

value: Glioma cell line

value: PDGFB, PTEN-/-, p53 -/-

value: 75uM ispinesib x 21 days

value: Ispinesib Resistant


title: HCI-002_PDX_15261X2


title: HCI-028_PDX_S18061X3


title: HCI-002_Patient_13697X7

value: Patient


title: Ispinesib Resistant MGPP3 [SP063]

description:
SP063
murine glioma (brain)


title: HCI-028_Patient_S18061X1


title: KD-R3me2a

city: Shanghai

first: Charilie

middle: Degui

last: Chen

address: No. 320 YueYang Road

institute: SIBCB

data_processing:
ChIP-seq reads were aligned to the UCSC hg19 genome assembly using bowtie2 version 2.2.6 with the default --end-to-end configurations.
Aligned sam files were converted to bam files using samtools version 0.1.19-44428cd.
Bam files were converted to bw files using bamCoverage version 1.5.12.
Genome_build: UCSC hg19 genome assembly (GRCh37)
Supplementary_files_format_and_content: *.bed: Peaks were called using MACS version 1.4.2 with the following setting: --nomodel --shift 100.
Supplementary_files_format_and_content: *bw: bigWig files

source_name: MCF7 cells

growth_protocol: MCF7 cells are cultured under ATCC instruction.

extract_protocol:
Lysates were clarified from MNase digested nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared by BerryGenomic (Beijing, China).

treatment_protocol: Lentivirus are used to knockdown RDMe1.

tag: passage

tag: genotype/variation

tag: chip antibody

value: anti-H4R3me2a (in-house)


title: HCI-039_PDxO_S18036X4

value: PDXO


title: Naïve MGPP3 [SP059]

description:
SP059
murine glioma (brain)

tag: cell line

tag: cell type

value: Basal

value: Naive


title: RDme1 ChIPSeq

value: WT RDme1

value: anti-RDme1 (in-house)


title: Ctr-R3me2a

value: sh-Control


title: HCI-032_PDX_S18088X1.S18131X1


title: Human dermal fibroblasts_2D_irradiated_rep2 (mRNA)

type: RNA

city: Saint-Viance

first: Pauline

last: Rouaud-Tinguely

address: ZI de la Nau

department: R&D

country: France

institute: SILAB

description:
S6
Gene expression after 4 days of irradiation

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutesusing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K Microarrays (G4851B) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2600D) using one color scan setting for AgilentG3 GX array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11_5_1_1 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Human dermal fibroblasts, 4 days of irradiation

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low Input Quick Amp labeling  kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000c Spectrophotometer.

growth_protocol: Normal human fibroblasts (NHF) were isolated from human breast skin, collected from healthy female (aged 20-28 years) undergoing plastic surgery. The skin was collected after written informed consent from the donors, institutional approval, and handled according to the Declaration of Helsinki Principles. Fibroblasts were cultured in monolayer at 37°C under 5% CO2 in Minimal Essential Medium (MEM; Gibco; Inchinnan Business Park, UK) supplemented with 10% fetal bovine serum (FBS; Sigma), 1% penicillin/streptomycin (Gibco; Inchinnan Business Park, UK), 0.1% fungizone (Gibco; Inchinnan Business Park, UK). Cells were used at passage 5 and 6, grown to 80% confluency before treatment.

extract_protocol: Total RNA was extracted using the RNeasy Kit (Qiagen). Quantification and quality assessment of the isolated RNA samples were performed and verified using a NanoDrop 2000c spectrophotometer (ThermoFisher) and an Agilent Bioanalyzer2100 (Agilent Technologies) according to the manufacturer's instructions.

treatment_protocol: Prior to irradiation, the growth medium was removed and the cell monolayer was rinsed with PBS. Cells were then covered with PBS and irradiated at 25°C every day during 4 consecutive days with a dose of 26J/cm² during 15 minutes, with a solar simulator « CPS+» (Atlas; Linsengericht, Germany). Between each treatment, cells were cultivated with MEM supplemented with 2% FBS at 37°C. One day after the last irradiation, stress-induced senescence (SIS) fibroblasts were used for following experiments. Control cells were held on 25 °C under similar conditions without irradiation.

tag: stress

value: irradiation

value: dermal fibroblasts


title: Human dermal fibroblasts_2D_irradiated_rep4 (mRNA)

description:
S8
Gene expression after 4 days of irradiation


title: Human dermal fibroblasts_2D_normal medium_rep2 (mRNA)

description:
S2
Gene expression without irradiation

source_name: Human dermal fibroblasts, 4 days with normal medium

value: control


title: Human dermal fibroblasts_2D_normal medium_rep1 (mRNA)

description:
S1
Gene expression without irradiation


title: Human dermal fibroblasts_2D_normal medium_rep4 (mRNA)

description:
S4
Gene expression without irradiation


title: Human dermal fibroblasts_2D_irradiated_rep3 (mRNA)

description:
S7
Gene expression after 4 days of irradiation


title: Human dermal fibroblasts_2D_normal medium_rep3 (mRNA)

description:
S3
Gene expression without irradiation


title: Naïve MGPP3 [SP061]

description:
SP061
murine glioma (brain)

tag: genotype

tag: condition

tag: phenotype


title: Human dermal fibroblasts_2D_irradiated_rep1 (mRNA)

description:
S5
Gene expression after 4 days of irradiation


title: HCI-039_PDX_S18036X3

value: PDX

value: RREMS

tag: disease state


title: input DNA


title: Naïve MGPP3 [SP060]

description:
SP060
murine glioma (brain)

value: Glioma cell line


title: HCI-039_Patient_S18036X1

value: Breast Cancer


title: Ispinesib Resistant MGPP3 [SP062]

description:
SP062
murine glioma (brain)

value: PDGFB, PTEN-/-, p53 -/-

value: 75uM ispinesib x 21 days


title: Non-treated gshA:Tn cells replicate 2

status: Public on Jan 08 2022

city: Fresno

first: Mamta

last: Rawat

state: CA

address: 2555 E. San Ramon Ave. MS S/B 73

department: Biology

institute: California State University, Fresno

data_processing:
Reads were mapped to the reference genome for A. baumannii (RefSeq GCF_000963825.1) using Rsubread version 2.4.0
EdgeR was used to normalize gene expression using trimmed means of M-values (TMM) and to identify differentially expressed genes and statistical analysis
Only mapped reads equal to or greater than 10 counts per million reads, and a cut-off of p-value < 0.05 were considered for further analysis.
Genome_build: RefSeq GCF_000963825.1
Supplementary_files_format_and_content: abuw_rawcounts contains the raw counts for each set of aligned reads for each individual sample. abuw_processed contains an excel file containing the gene ID, gene description, log2FC of the gshA mutant compared to the wildtype strain, and p-value.

organism: Acinetobacter baumannii

source_name: whole cell

growth_protocol: A. baumannii was grown in TSB and collected at mid-logarithmic phase (OD600 0.4 - 0.6) grown while shaken at 37C

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen), according to manufacturer instructions with the following exception: samples were lysed by bead-beating using a BeadBlaster 24 (Benchmark Scientific). To remove ribosomal RNAs, high-quality total RNA was processed using Illumina’s Ribo-Zero Bacteria kit (Illumina, San Diego, CA).
cDNA libraries were generated with rRNA depleted mRNA using the KAPA RNA Hyper Plus Kit (Roche, Indianapolis, IN) following the manufacturer’s instructions

treatment_protocol: No treatments were applied, rather a comparison between the wildtype and transposon mutated strain were compared.

tag: mutant

value: gshA transposon mutant

tag: strain


title: Non-treated gshA:Tn cells replicate 3


title: Non-treated gshA:Tn cells replicate 1


title: Non-treated wildtype cells replicate 3

value: wildtype strain


title: Non-treated wildtype cells replicate 2


title: Non-treated wildtype cells replicate 1


title: IXA4-8

city: La Jolla

first: R. Luke

last: Wiseman

address: 10550 North Torrey Pines Road

department: Molecular Medicine

institute: The Scripps Research Institute

data_processing:
Basescaling was performed by BGI
Single end, 50 bp-long reads from RNA Seq experiments were aligned to the Mus musculus MGSCv37 NCBI build 37.2 mouse genome reference assembly using SeqMan NGen 11.2.1 or 12.2.0 (DNAStar Inc.) using default parameters.
The assembly data were imported into ArrayStar 12.2 with Qseq (DNAStar Inc.) to quantify the gene expression levels. The sequence counts were normalized to reads per kilobase per million (RPKM) after filtering out non-mRNA sequence features.
Counts Data were analyzed using DESeq
Genome_build: Mus musculus MGSCv37 NCBI build 37.2 mouse genome reference assembly
Supplementary_files_format_and_content: XLSX files contain counts data for each sample and DESeq differential expression analysis of IXA4 vs. Vehicle

source_name: liver

growth_protocol: Male C57BL/6N diet-induced obese (DIO) mice (14-week-old) were purchased from Taconic Biosciences. DIO mice were maintained on a 60% kcal high fat diet (Research Diets D12492) for 3 weeks prior to IXA4 treatment.

extract_protocol:
Four biological replicates were studied for each treatment condition. RNA was isolated from livers of DIO mice treated with IXA4 or vehicle using the Zymo Research Quick-RNA Miniprep Kit according to the manufacturer’s instructions.
Libraries were constructed using standard protocols at BGI

treatment_protocol: IXA4 was formulated in 10% DMSO, 30% Kolliphor EL:Ethanol (2:1 ratio), 60% saline and kept warm until use. Chow-fed or DIO mice were administered IXA4 (50 mg/kg) or vehicle once daily via intraperitoneal injection for up to 8 weeks

tag: growth conditions

value: DIO

tag: treatment


title: IXA4-6


title: pat35_normal [methylation]

type: genomic

city: Boston

first: JAE WON

last: CHO

state: MA

address: 60 Fenwood Road

department: Neurology

institute: Brigham and Women's Hospital

hyb_protocol: Bisulphite coverted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation850 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using iScan System.

data_processing:
Cpgsite filtering: Rnbeads package
Additional filtering: SNP region from KOVA and KRGDB
Normalization: Functional normalization

label: Cy3 and Cy5

source_name: lung biopsies

label_protocol: Standard Illumina labelling protocol (label: Cy3 and Cy5)

extract_protocol:
Extraction was performed by Quant-iT PicoGreen (Invitrogen) quantitation.
EZ DNA methylation kit (Zymo Research) protocols

tag: tumor

value: normal


title: IXA4-5


title: pat37_normal [methylation]


title: pat38_normal [methylation]


title: pat36_normal [methylation]


title: IXA4-1


title: Veh-4

value: Vehicle


title: pat34_normal [methylation]


title: pat36_tumor [methylation]

value: tumor


title: pat39_normal [methylation]


title: pat37_tumor [methylation]


title: pat39_tumor [methylation]


title: pat38_tumor [methylation]


title: pat35_tumor [methylation]


title: Veh-2


title: Veh-1


title: pat33_normal [methylation]


title: Veh-3


title: rep2-igG

city: beijing

first: pengyu

last: li

address: beijing

institute: Beijing Union Medical College

data_processing:
Library strategy: CUT&Tag
We used the CUT&Tag 2.0 High-Sensitivity Kit (Novoprotein Scientific Inc., Cat# N259-YH01) to perform the CUT&Tag assay
Trim_galore (v0.5.0) was used to remove low-quality and adapter sequences to facilitate analysis of the raw sequence data.
Bowtie2 (v2.2.5) was used to align all reads generated by CUT&Tag with the mm10 mouse genome, and MACS2 (v2.1.2) was used to enrich the binding genome regions (peaks).
Genome_build: mm10
Supplementary_files_format_and_content: peak text files

source_name: spermatogonial

extract_protocol:
The DNA fragments were extracted by phenol chloroform
We used the CUT&Tag 2.0 High-Sensitivity Kit (Novoprotein Scientific Inc., Cat# N259-YH01) to perform the CUT&Tag assay according to the manufacturer's description. Briefly, the mouse testes were digested into single cells with the above method, and 100,000 cells were enriched in Digwash Buffer with ConA-magnetic beads. The primary antibody was diluted 1:100 in Digwash Buffer and incubated with ConA beads overnight. After that, the secondary antibody was incubated with the ConA beads for 1 hour, and the beads were washed three times in DigHisalt Buffer. Cells were incubated with protein A/G-Tn5 transposome for 1 hour, followed by incubation in DigHisalt Buffer containing 10 mM MgCl2 at 37°C for 1 hour. The reaction was then terminated by adding 0.5 M EDTA, 10% SDS, and 20 mg/mL proteinase K at 55°C for 1 hour. The DNA fragments were extracted with phenol chloroform and sequenced on the Illumina NovaSeq platform.

value: spermatogonial

value: Rabbit Anti-Mouse IgG H&L (HRP) (Abcam ab6728)


title: pat30_normal [methylation]


title: pat33_tumor [methylation]


title: pat28_normal [methylation]


title: Card11dLinker 3 [31_S19]

city: Munich

first: Zsuzsanna

last: Kurgyis

address: Ismaningerstr. 22

country: Germany

institute: Technical University of Munich

data_processing:
The demultiplexed fastq files were aligned with hisat2 and samtools was used to sort the aligned files.
StringTie was used for assembling the alignments into transcripts.
Further, prepDE.py script provided by Stringtie was used to get data table to perform differential analysis in Deseq2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file including FPKM values for each Sample
Supplementary_files_format_and_content: tab-delimited text file including raw gene counts for every gene and every sample

growth_protocol: Cells were grown on collagen-treated wells in Keratinocyte Serum-free Medium (Gibco) with 0.05mM CaCl2

extract_protocol:
Keratinocytes were harvested in RLT Buffer, and RNA was isolated using Rneasy Plus Micro Kits. Library preparation from 100 ng of total RNA was performed using the NEBNext Ultra II RNA Library Prep Kit for Illumina and NEBNext Poly(A) mRNA Magnetic Isolation Module
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were left unstimulated

value: R26Card11DL, not congenic

tag: age

value: postnatal day 4-5

tag: tissue

value: Skin

value: primary murine keratinocytes

value: unstimulated


title: pat29_normal [methylation]


title: pat27_normal [methylation]


title: pat32_tumor [methylation]


title: pat34_tumor [methylation]


title: pat32_normal [methylation]


title: pat29_tumor [methylation]


title: rep1-igG


title: Card11dLinker 2 [26_S16]


title: rep2-chd4

value: CHD4  (Abcam, ab70469)


title: pat31_tumor [methylation]


title: Card11dLinker 1 [21_S13]


title: pat31_normal [methylation]


title: pat28_tumor [methylation]


title: pat26_normal [methylation]


title: WT 2 [6_S4]

source_name: primary murine keratinocytes_K14Cre

value: Tg (KRT14-cre) 1Amc/J


title: WT 4 [16_S10]


title: rep1-chd4

value: CHD4 (Abcam, ab70469)


title: Control C2

data_processing:
equencing was carried out on the Illumina NovaSeq platform with 150 bp paired-end reads.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie  with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
DEG analysis was carried out using the DESeq2 R software package.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: testes

growth_protocol: The SSCs were isolated, enriched, and cultured as described in the literature (20). In summary, the testes of P 5-P 7 mice (progenies of C57BL6 and DBA/2) were digested with type-IV collagenase (1 mg/ml) and trypsin (0.25%). Isolated cells were centrifuged in 30% percoll solution, then MACS was used to enrich for Thy1+spermatogonia. SSCs were cultured with mouse embryonic fibroblasts treated with mitomycin C

extract_protocol:
Total RNA was extracted from the cultured SSCs by Trizol reagent and quantified in a NanoDrop 2000 spectrophotometer (Thermo Scientific). RNA-seq libraries were constructed using polyadenylated RNA and standard Illumina RNA-seq protocols according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: We infected SSCs with the lentivirus to obtain Chd4-knockdown cells (shCHD4) or with scrambled RNA to obtain negative control (shCtrl) cells. Then, EGFP+cells were isolated by flow cytometry to confirm infection with the lentivirus and cultured for 5 days.

value: spermatogonial stem cells

value: testes

value: wild type


title: Bcl10+/− unstim 3 [37_S37_R1_001]

data_processing:
The demultiplexed fastq files were aligned with hisat2 and samtools was used to sort the aligned files.
StringTie was used for assembling the alignments into transcripts.
Further, prepDE.py script provided by Stringtie was used to get data table to perform differential analysis in Deseq2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file including FPKM values for each Sample

source_name: primary murine keratinocytes

treatment_protocol: Cells were left unstimulated or were stimulated with 200ng/mL recombinant mouse IL-17A for 5 hours


title: Control C3


title: WT 1 [1_S1]


title: pat27_tumor [methylation]


title: WT 3 [11_S7]


title: Bcl10+/− IL17A 3 [38_S38_R1_001]

value: IL-17A stimulated


title: pat26_tumor [methylation]


title: pat25_tumor [methylation]


title: Control C1


title: Bcl10+/− unstim 2 [33_S33_R1_001]


title: pat30_tumor [methylation]


title: Bcl10+/− IL17A 1 [14_S14_R1_001]


title: pat23_normal [methylation]

value: normal


title: pat25_normal [methylation]


title: Bcl10+/− unstim 1 [13_S13_R1_001]


title: CHD4 B3


title: CHD4 B2


title: Bcl10−/− IL17A 2 [10_S10_R1_001]


title: Bcl10−/− IL17A 1 [2_S2_R1_001]


title: Bcl10−/− unstim 2 [9_S9_R1_001]


title: Bcl10−/− unstim 1 [1_S1_R1_001]


title: Bcl10+/− IL17A 2 [34_S34_R1_001]


title: CHD4 B1


title: pat24_tumor [methylation]


title: pat24_normal [methylation]


title: High-density-Rep3

city: Rennes

first: Herve

last: Colinet

address: UMR CNRS 6553 EcoBio

institute: University of Rennes

description:
H3
pool of 10 larvae

data_processing:
Bases with a phred score below 20 and Illumina adapter read-through of at least 3 bp were trimmed from the 3’ end using TRIMGALORE 0.6.4
Trimmed reads were aligned to the D. melanogaster release 6 genome (GCF_000001215.4) using HISAT 2.1.0 and alignments were processed using SAMTOOLS 1.9
Read alignments were quantified against exon annotations and summarised at the gene level using FEATURECOUNTS 1.6.2 with -M --fraction -C -B options
Differential gene expression analysiswas carried out with DESeq2 1.26.0 in R 3.6.1, shrinking fold-changes of low-count genes using the apeglm method
Genome_build: dm6
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Drosophila melanogaster

source_name: whole larva

growth_protocol: Larvae were grown in sugar-yeast diet until the third instar was reached. Only wandering larvae were collected, randomly, for analysis.

extract_protocol:
Larvae were snap-frozen in liquid nitrogen and ground to fine powder. RNA was extracted with the Nucleospin® RNA extraction kit
Illumina TruSeq stranded mRNA library

treatment_protocol: Following published protocols (Henry et al., 2020 FEMS Microb), the number of larvae was manipulated by counting individual first-instar larvae and allocating randomly to treatment groups.

tag: developmental stage

value: third-instar larva

tag: larval density

value: high


title: Pulmonary valve Control-L279

city: Liege

first: Zheshen

last: Jiang

state: Liege

address: Avenue de l'hopital, 1

department: GIGA

country: Belgium

institute: University of Liege

data_processing:
Basecalling performed using Illumina bcl2fastq v2.20
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Reads were processed for mapping and quantification using nf-core rnaseq pipeline v1.4.2 (https://nf-co.re/rnaseq/1.4.2/usage) and using Gene set from Ensembl.org release 099.
Genome_build: OryCun2.0
Supplementary_files_format_and_content: tab-delimited text file include raw counts for annotations for all Sample

organism: Oryctolagus cuniculus

source_name: heart

growth_protocol: Animals were kept in a temperature and humidity-controlled environment in an air-conditioned room with standard rabbit chow and tap water ad libitum. After 2 weeks of acclimation, rabbits were randomly assigned in seven different groups and diet habituation was conducted for 2 weeks.

extract_protocol:
Aorta ring (Ao) and heart valves (AoV, MV, PV, TV) were dissected at the end of the 16-week protocols, snap frozen in liquid nitrogen and stored at -80°C until RNA extraction. Total RNA was extracted by use of miRNeasy Mini Kit (Qiagen) according to manufacturer’s instructions.
RNA librairies were prepared with 10ng of RNA using the SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara Bio USA, Inc.) according to manufacturer’s instructions.
Sequencing of the libraries was performed on a NovaSeq6000 System (Illumina) with a S4 reagent kit (300 cycles) and 1.2nM library loading.

treatment_protocol: Protocols started when rabbits were 12 weeks old and lasted 16 weeks. Control group (Ctrl, n=13) received standard chow diet. Vitamin D2 group (Vit.D2, n=7) received chow diet with 15 days of Vitamin D2 supplementation (ergocalciferol, Sigma-Aldrich) in drinking water at the beginning of the protocol (25,000U/day/2.5Kg). Cholesterol-enriched diet group (CHT, n=17) was treated with 0.3% cholesterol-enriched diet and received vitamin D2 (Vit.D2) supplementation as the Vit.D2 group. Lard-enriched diet group (Lard, n=13) received 5%-lard enriched diet(17) with Vit.D2 supplementation. Irradiation group (IR, n=7) received chow diet and underwent X-ray cardiac irradiation focused on the aortic valve and the thoracic aorta during the first week of the protocol (24Gy dose divided in 3 fractions of 8Gy delivered at 48-hour intervals, chosen to mimic clinically relevant doses used for anticancer radiotherapy) using image-guided radiation on an irradiator specifically made for small animals (X-Rad 225Cx, Precision X-Ray, Inc.). Irradiation combined with cholesterol-enriched diet group (IR/CHT, n=15) received 0.3% cholesterol-enriched diet plus Vit.D2 supplementation and underwent cardiac irradiation at mid protocol (e.g., after 8 week of cholesterol-rich diet). Cholesterol- and lard-enriched diets were produced by Safe (France).

tag: breed

value: New Zealand White

tag: Sex

value: male

value: heart (Pulmonary valve)

value: Control


title: High-density-Rep2

description:
H2
pool of 10 larvae


title: pat22_normal [methylation]


title: pat22_tumor [methylation]

value: tumor


title: pat23_tumor [methylation]


title: High-density-Rep1

description:
H1
pool of 10 larvae


title: Mitral valve Control-L278

value: heart (Mitral valve)


title: Medium-density-Rep3

description:
M3
pool of 10 larvae

value: medium


title: Medium-density-Rep2

description:
M2
pool of 10 larvae


title: Low-density-Rep2

description:
L2
pool of 10 larvae

value: low


title: Aortic valve Control-L277

value: heart (Aortic valve)


title: Low-density-Rep3

description:
L3
pool of 10 larvae


title: Tricuspid valve Cholesterol+IR-L276

value: heart (Tricuspid valve)

value: Cholesterol+IR


title: Low-density-Rep1

description:
L1
pool of 10 larvae


title: Pulmonary valve Cholesterol+IR-L275


title: pat21_normal [methylation]


title: Mitral valve Cholesterol+IR-L274


title: 3B rep4 [ncRNA-Seq]

city: Hangzhou

first: Xiaowen

last: Shi

state: Zhejiang

address: 866 Yuhangtang Road NongshenghuanA443

department: College of Agriculture and Biotechnology

institute: Zhejiang University

data_processing:
For mRNA-seq: 1. the 3' end of the reads was trimmed for Illumina adapters, for ambiguous nucleotides (N's), and for artificial poly-G using cutadapt version 1.16; 2. Low quality reads were removed; 3. ERCC reads were selected and mapped to ERCC references independently; 4. Reads with ERCC removed were mapped to W22 genome v2 using tophat2, then to B73 genome v4 using tophat2,  finally to TE sequences using bowtie2; 5. Read counts were normarlized with RPKM; 6. Differential gene expression analysis were performed via edgeR.
For sRNA-seq: 1. the 3' end of the reads was trimmed for Illumina adapters, for ambiguous nucleotides (N's), and for artificial poly-G using cutadapt version 1.16; 2. Low quality reads were removed; 3. Reads were mapped to W22 genome v2 and transposable element seqeunes respectively using shortstack; 4. Read counts were normarlized with RPM; 5. Differential gene expression analysis were performed via edgeR.
Genome_build: W22v2 & TE sequences from W22 genome annotation
Supplementary_files_format_and_content: Tab-delimited text files include raw counts table, normalized counts table, differential gene expression analysis (edgeR) for each sample in mRNA-seq experiments; raw count table of mapped sRNA and RPM counts by ShortStack.
Supplementary_files_format_and_content: Counts_ERCC.txt: raw count table.
Supplementary_files_format_and_content: Counts_miRNA.txt: raw count table by ShortStack.
Supplementary_files_format_and_content: Counts_gene.txt: raw count table.
Supplementary_files_format_and_content: Counts_TE.txt: raw count table.
Supplementary_files_format_and_content: Counts_TE_RPKM.txt: RPKM normalized count table.
Supplementary_files_format_and_content: DGE_analysis.txt: Cuffdiff normalized count table.
Supplementary_files_format_and_content: EdgeR_miRNA.txt: edgeR.
Supplementary_files_format_and_content: EdgeR_TE.txt: edgeR.
Supplementary_files_format_and_content: Counts_miRNA_rpm.txt: RPM normalized count table.

organism: Zea mays

source_name: Leaf tissue

growth_protocol: 45-day grown in the greenhouse

extract_protocol:
Extracted by mirVana™ miRNA Isolation Kit
RNA libraries were prepared for sequencing using standard Illumina protocols


title: 2B rep4 [ncRNA-Seq]


title: Medium-density-Rep1

description:
M1
pool of 10 larvae


title: Aortic valve Cholesterol+IR-L273


title: 4B rep4 [ncRNA-Seq]


title: 7B rep3 [ncRNA-Seq]


title: Pulmonary valve Lard-L271

value: Lard


title: 6B rep3 [ncRNA-Seq]


title: 1B rep4 [ncRNA-Seq]


title: Tricuspid valve Lard-L272


title: pat19_tumor [methylation]


title: pat19_normal [methylation]


title: PC3 Control

city: Shinjuku-ku

first: Hiroshi

last: Hongo

state: Tokyo

address: 35, Shinanomachi

department: Urology

country: Japan

institute: Keio University School of Medicine

description: strain: PC3  cell type: Prostate cancer  tissue: prostate

hyb_protocol: Following fragmentation, 5.5 ug of cDNA were hybridized on the GeneChip Human Gene 2.0 ST Array using  the GeneChip Hybridization Oven 645. GeneChips were washed and stained in the  GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Expression Console v1.4(Affymetrix) and Transcriptome Analysis Console v3.1 (Affymetrix). RMA was used as summarization algorithm.

label: biotin

source_name: Prostate cancer

label_protocol: cDNA synthesis, amplification and labeling were performed with WT PLUS Reagent Kit (Affymetrix).

growth_protocol: PC3 cells were routinely maintained in RPMI-1640 (Invitrogen, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (Dainippon Pharmaceutical, Tokyo, Japan) at 37°C in a humidified 5% CO2 atmosphere.

extract_protocol: Total RNA was isolated purified using RNeasy Mini kit (Qiagen).

treatment_protocol: PC3 cells after treatment of DMSO (control) or 10uM fluphenazine were used for microarray.

tag: cell line

value: Prostate cancer

tag: agent

value: DMSO


title: PC3 Fluphenazine

value: 10uM fluphenazine


title: pat20_normal [methylation]

value: normal


title: 6B rep2 [ncRNA-Seq]

tag: genotype


title: pat20_tumor [methylation]


title: Mitral valve Lard-L270


title: 2B rep3 [ncRNA-Seq]


title: pat17_normal [methylation]


title: 5B rep2 [ncRNA-Seq]


title: 1B rep2 [ncRNA-Seq]


title: 4B rep2 [ncRNA-Seq]


title: 1B rep3 [ncRNA-Seq]


title: Aortic valve Lard-L269


title: pat16_normal [methylation]


title: pat18_normal [methylation]


title: 1B rep1 [ncRNA-Seq]


title: pat17_tumor [methylation]


title: Aortic valve Control-L261


title: Pulmonary valve Lard-L250


title: 3B rep2 [ncRNA-Seq]


title: 3B rep3 [ncRNA-Seq]


title: 2B rep2 [ncRNA-Seq]


title: pat18_tumor [methylation]


title: pat16_tumor [methylation]


title: pat14_tumor [methylation]


title: 5B rep1 [ncRNA-Seq]


title: 3B rep1 [ncRNA-Seq]


title: pat12_tumor [methylation]


title: pat14_normal [methylation]


title: Pulmonary valve Cholesterol-L246

value: Cholesterol


title: 2B rep1 [ncRNA-Seq]


title: 4B rep1 [ncRNA-Seq]


title: Pulmonary valve Control-L242

value: New Zealand White


title: Aortic valve Lard-L248

value: male


title: pat11_normal [methylation]


title: pat12_normal [methylation]


title: Control rep3 [ncRNA-Seq]


title: Mitral valve Control-L241


title: pat15_tumor [methylation]


title: 7B rep2 [ncRNA-Seq]


title: 6B rep1 [ncRNA-Seq]


title: Control rep4 [ncRNA-Seq]


title: Tricuspid valve Cholesterol-L231


title: 3B rep4 [RNA-Seq]


title: pat15_normal [methylation]


title: Control rep1 [ncRNA-Seq]


title: 2B rep4 [RNA-Seq]


title: pat21_tumor [methylation]


title: 7B rep1 [ncRNA-Seq]


title: Aortic valve Control-L240


title: 6B rep3 [RNA-Seq]


title: pat10_normal [methylation]


title: Tricuspid valve Cholesterol+IR-L197


title: 7B rep3 [RNA-Seq]


title: pat11_tumor [methylation]


title: 4B rep4 [RNA-Seq]


title: Pulmonary valve Cholesterol-L230

value: heart (Pulmonary valve)


title: pat9_normal [methylation]


title: Mitral valve Cholesterol+IR-L195


title: 1B rep4 [RNA-Seq]


title: 5B rep2 [RNA-Seq]


title: 6B rep2 [RNA-Seq]


title: 1B rep3 [RNA-Seq]


title: pat10_tumor [methylation]


title: Mitral valve Lard-L191


title: 1B rep2 [RNA-Seq]


title: Aortic valve Cholesterol+IR-L194


title: 2B rep3 [RNA-Seq]


title: 4B rep3 [RNA-Seq]


title: 4B rep2 [RNA-Seq]


title: 3B rep3 [RNA-Seq]


title: Tricuspid valve Cholesterol-L268


title: 1B rep1 [RNA-Seq]


title: 3B rep2 [RNA-Seq]


title: 2B rep2 [RNA-Seq]


title: Pulmonary valve Cholesterol+IR-L549


title: 5B rep1 [RNA-Seq]


title: 3B rep1 [RNA-Seq]


title: pat9_tumor [methylation]


title: Aortic valve Lard-L190


title: pat8_tumor [methylation]


title: 2B rep1 [RNA-Seq]


title: Aortic valve Cholesterol+IR-L547


title: pat7_normal [methylation]


title: Mitral valve Cholesterol+IR-L548


title: Control rep2 [ncRNA-Seq]

value: Control


title: 4B rep3 [ncRNA-Seq]


title: 4B rep1 [RNA-Seq]


title: Tricuspid valve Cholesterol+IR-L550


title: 6B rep1 [RNA-Seq]


title: flrA null mutant 3

first: Chongtao

last: Guo

address: 866 Yuhangtang Road

department: College of life science

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
FPKM were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GCF_000280675.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM and count values for each Sample

organism: Beauveria bassiana

source_name: hyphal culture 3

growth_protocol: Aliquots (100 microliter) of a 107 conidia/mL were spread on SDAY plates and incubated for 3 days at an optimal regime (25 degree centigrade and light/dark cycle of 12:12 h).

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: liquid nitrogen preservation

value: ARSEF 2860

value: hyphae

value: flrA null mutant

value: 3-day-old culture


title: Aorta Cholesterol+IR-L582

value: heart (Aorta)


title: 7B rep2 [RNA-Seq]


title: flrA null mutant 2

source_name: hyphal culture 2


title: pat7_tumor [methylation]

value: tumor


title: Control rep4 [RNA-Seq]


title: Control rep3 [RNA-Seq]


title: flrA null mutant 1

source_name: hyphal culture 1


title: Aorta Cholesterol+IR-L579

value: Cholesterol+IR


title: Control rep2 [RNA-Seq]


title: 7B rep1 [RNA-Seq]


title: fluG null mutant 3

value: fluG null mutant


title: Control rep1 [RNA-Seq]


title: Aorta Cholesterol+IR-L567


title: Aorta Cholesterol+IR-L566


title: pat6_normal [methylation]


title: fluG null mutant 2


title: HRA_RNA_rep3

city: Montpellier

first: Guillaume

last: Bossis

address: 1919 Route de Mende

department: IGMM

institute: CNRS

data_processing:
Basecalls performed with Real-Time Analysis software (Illumina)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat2 2.1.1 based on Bowtie2 2.3.5.1
Duplicated were removed using Picard. The reproducibility of replicate was quantified using cufflinks 2.2.1
The read count on gene performed using HTseq-count tool 0.11.1 and the differential expression analysis was performed with DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: tab-sep table of the DeSeq2 analysis

source_name: acute myeloid leukemia

growth_protocol: Cells were cultured in RPMI (Eurobio) supplemented with 10% decomplemented (30 min at 56°C) fetal bovine serum (FBS) and penicillin and streptomycin at 37°C in the presence of 5% CO2. After thawing, cells were spitted at 0.3.106/mL every 2 to 3 days for no more than 10 passages.

extract_protocol:
Total RNAs were purified using the GenElute Mammalian Total RNA kit (Sigma-Aldrich), treated with DNase I (4U, New England Biolabs) and RNasin (2.5U, Promega) and re purified. RNA quality was assessed using a BioAnalyzer Nano 6000 chip (Agilent).
Libraries were prepared using TruSeq®Stranded mRNA Sample Preparation kit (Illumina)

treatment_protocol: HL-60 cells resistant to Ara-C (HRA) were cultured in the presence of 100nM Ara-C. HL-60 cells resistant to DNR (HRD) were cultured in the presence of 30nM DNR

tag: resistance

value: resistant to Ara-C


title: HL-60_RNA_rep3

value: parental


title: fluG null mutant 1


title: pat5_tumor [methylation]


title: Aorta Cholesterol+IR-L565


title: HRD_RNA_rep2

value: resistant to DNR


title: pat6_tumor [methylation]


title: pat5_normal [methylation]

value: normal


title: pat8_normal [methylation]


title: Aorta Cholesterol+IR-L581


title: HRA_RNA_rep2


title: wild-type strain 3

value: wild-type


title: HL-60_RNA_rep2


title: Aorta Cholesterol+IR-L580

value: New Zealand White


title: HRD_RNA_rep1


title: wild-type strain 2


title: Tricuspid valve Control-L168

value: male

value: heart (Tricuspid valve)


title: HRA_RNA_rep1


title: HL-60_RNA_rep1


title: pat4_normal [methylation]


title: pat39_normal [RNA-seq]

description: counts.txt

data_processing:
Read mapping: STAR-2.5.2a
Quantification: FeatureCounts
Genome_build: GRCH37.p13, release 19
Supplementary_files_format_and_content: tab-delimited text files include counts for each Sample ...

extract_protocol:
Next-Gen Sequecing Sample Specification and Submission Guideline: RNA extraction protocol
TruSeq RNA Access Library Prep Guide Part # 15049525 Rev. B with TruSeq RNA Access Library Prep Kit


title: Aortic valve Control-L166

value: heart (Aortic valve)

value: Control


title: pat38_normal [RNA-seq]

description: counts.txt


title: pat39_tumor [RNA-seq]

description: counts.txt


title: 1uM_MS023_+ActD_RepC

city: New York

first: Omar

last: Abdel-Wahab

address: 1275 York Ave

department: Molecular Pharmacology Program

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Adapter trimming accomplished with trim_galore v0.6.5 (trim_galore --paired -j 8 $file ${fn}_2.fastq.gz)
Alignment performed with STAR v2.4.2a (STAR --genomeDir $GENDIR --readFilesIn ${fn}_1.fq.gz ${fn}_2.fq.gz --readFilesCommand zcat --outFileNamePrefix ${fn}_ --runThreadN 12 --outSAMtype BAM Unsorted --outSAMstrandField intronMotif --outSAMattributes All --outFilterMultimapNmax 1 --outFilterScoreMinOverLread 0.51 --outFilterMatchNminOverLread 0.51 --outFilterMismatchNmax 4 --alignIntronMax 50000 --sjdbGTFfile $GENDIR/genes.gtf --quantMode TranscriptomeSAM GeneCounts --twopassMode Basic)
Duplicate control Picard tools 2.3.0 (java -jar `which picard.jar` MarkDuplicates INPUT=${fn}_Aligned.sortedByCoord.PEonly.bam OUTPUT=${fn}_Aligned.sortedByCoord.PEonly_marked.bam METRICS_FILE=${fn}_Aligned.sortedByCoord.PEonly_marked_metrics CREATE_INDEX=true)
Genome_build: hg19
Supplementary_files_format_and_content: Aligned reads are provided as bigwig files generated using deepTools v3.3.1 (bamCoverage -b $file -o ${fn}.bw  -p 35 -bs 1  -v --ignoreDuplicates)

extract_protocol:
RNA was extracted using RNeasy® Mini Kit (Qiagen, 74104) following the manufacturer’s protocol.
Stranded RNA seq libraries were constructed by Novogene Genetics US. The barcoded libraries were sequenced by Novogene on an Illumina platform using 150nt paired end libraries generating ~30-40 million reads per replicate.

tag: rna population

value: poly(A) RNA


title: Tricuspid valve Control-L280


title: pat4_tumor [methylation]


title: pat38_tumor [RNA-seq]

description: counts.txt


title: pat2_normal [methylation]


title: pat37_normal [RNA-seq]

description: counts.txt


title: 1uM_GSK591_+ActD_RepC


title: Tricuspid valve Lard-L546

value: Lard


title: pat36_normal [RNA-seq]

description: counts.txt


title: pat3_tumor [methylation]


title: Pulmonary valve Lard-L545

value: heart (Pulmonary valve)


title: pat37_tumor [RNA-seq]

description: counts.txt


title: pat36_tumor [RNA-seq]

description: counts.txt


title: 0.01%_DMSO_+ActD_RepC


title: pat3_normal [methylation]


title: pat34_normal [RNA-seq]

description: counts.txt


title: pat2_tumor [methylation]


title: pat35_normal [RNA-seq]

description: counts.txt


title: Mitral valve Lard-L544

value: heart (Mitral valve)


title: Aortic valve Lard-L543


title: 1uM_MS023_-ActD_RepC


title: Aorta Lard-L578

value: heart (Aorta)


title: 0.01%_DMSO_-ActD_RepC


title: pat33_tumor [RNA-seq]

description: counts.txt

value: tumor


title: 1uM_MS023_+ActD_RepB


title: pat32_normal [RNA-seq]

description: counts.txt


title: pat35_tumor [RNA-seq]

description: counts.txt


title: Aorta Lard-L577


title: pat32_tumor [RNA-seq]

description: counts.txt


title: 1uM_GSK591_+ActD_RepB


title: pat31_normal [RNA-seq]

description: counts.txt


title: Aorta Lard-L576


title: pat31_tumor [RNA-seq]

description: counts.txt


title: Aorta Cholesterol-L574

value: Cholesterol


title: 1uM_GSK591_-ActD_RepC


title: pat30_tumor [RNA-seq]

description: counts.txt


title: 1uM_MS023_-ActD_RepB


title: pat29_tumor [RNA-seq]

description: counts.txt


title: 1uM_GSK591_-ActD_RepB


title: pat29_normal [RNA-seq]

description: counts.txt


title: Aorta Cholesterol-L572


title: Aorta Cholesterol-L573


title: pat28_tumor [RNA-seq]

description: counts.txt


title: pat28_normal [RNA-seq]

description: counts.txt


title: pat34_tumor [RNA-seq]

description: counts.txt


title: pat33_normal [RNA-seq]

description: counts.txt


title: 0.01%_DMSO_-ActD_RepB


title: pat27_normal [RNA-seq]

description: counts.txt


title: Aorta Lard-L575


title: pat27_tumor [RNA-seq]

description: counts.txt


title: wild-type strain 1

value: ARSEF 2860

value: hyphae

value: 3-day-old culture


title: 1uM_MS023_+ActD_RepA


title: pat26_normal [RNA-seq]

description: counts.txt

value: normal


title: Aorta Lard-L564


title: pat26_tumor [RNA-seq]

description: counts.txt


title: Aorta Cholesterol-L561


title: pat25_normal [RNA-seq]

description: counts.txt


title: 0.01%_DMSO_+ActD_RepB


title: pat25_tumor [RNA-seq]

description: counts.txt


title: 1uM_GSK591_+ActD_RepA


title: pat30_normal [RNA-seq]

description: counts.txt


title: pat24_normal [RNA-seq]

description: counts.txt


title: pat24_tumor [RNA-seq]

description: counts.txt


title: pat23_normal [RNA-seq]

description: counts.txt


title: pat23_tumor [RNA-seq]

description: counts.txt


title: Pulmonary valve Lard-L541


title: 1uM_GSK591_-ActD_RepA


title: pat22_tumor [RNA-seq]

description: counts.txt


title: Mitral valve Lard-L540


title: Tricuspid valve Lard-L542


title: Aorta Lard-L563


title: pat21_tumor [RNA-seq]

description: counts.txt


title: 1uM_MS023_x_7_days_Rep3

data_processing:
Adapter trimming accomplished with trim_galore v0.6.5 (trim_galore --paired -j 8 $file ${fn}_2.fastq.gz)
Alignment performed with STAR v2.4.2a (STAR --genomeDir $GENDIR --readFilesIn ${fn}_1_val_1.fq.gz ${fn}_2_val_2.fq.gz --readFilesCommand zcat --outFileNamePrefix ${fn}_ --runThreadN 12 --outSAMtype BAM Unsorted --outSAMstrandField intronMotif --outSAMattributes All --outFilterMultimapNmax 1 --outFilterScoreMinOverLread 0.51 --outFilterMatchNminOverLread 0.51 --outFilterMismatchNmax 4 --alignIntronMax 50000 --sjdbGTFfile $GENDIR/genes.gtf --quantMode TranscriptomeSAM GeneCounts --twopassMode Basic)
Duplicate control Picard tools 2.3.0 (java -jar `which picard.jar` MarkDuplicates INPUT=${fn}_Aligned.sortedByCoord.PEonly.bam OUTPUT=${fn}_Aligned.sortedByCoord.PEonly_marked.bam METRICS_FILE=${fn}_Aligned.sortedByCoord.PEonly_marked_metrics CREATE_INDEX=true)
Splicing analysis rMATs v4.0.2 (rmats.py --b1 $fn --b2 $file --gtf gencode.v19.annotation.gtf --od ${file%.txt} --tmp ${file%.txt}_tmp -t single --readLength 150 --nthread 35)
Genome_build: hg19
Supplementary_files_format_and_content: SKaTER aligned reads are provided as bigwig files generated using deepTools v3.3.1 (bamCoverage -b $file -o ${fn}.bw  -p 35 -bs 1  -v --ignoreDuplicates). rMATS summary files are rMATs JCEC output concatenated into a single text file for each condition.

extract_protocol:
Poly(A) RNA seq: RNA was extracted using RNeasy® Mini Kit (Qiagen, 74104) following the manufacturer’s protocol. SKaTER-seq: RNA was isolated using TRIzol (Thermo, 15596026) at -80 °C. RNA isolation was followed by poly(A)-depletion using the NEBNext Poly(A) mRNA magnetic isolation mod-ule (NEB, E7490L).
Poly(A) RNA seq: Stranded RNA seq libraries were constructed by Novogene Genetics US. The barcoded libraries were sequenced by Novogene on an Illumina platform using 150nt paired end libraries generating ~30-40 million reads per replicate. SKaTER-seq: Stranded RNA-seq libraries were prepared using the KAPA RNA HyperPrep Kit with RiboErase (HMR) and KAPA Unique Dual-Indexed Adapters (Roche) according to instructions provided by the manufacturer.


title: 1uM_MS023_-ActD_RepA


title: pat20_normal [RNA-seq]

description: counts.txt


title: pat22_normal [RNA-seq]

description: counts.txt


title: 0.01%_DMSO_-ActD_RepA


title: pat19_normal [RNA-seq]

description: counts.txt


title: pat21_normal [RNA-seq]

description: counts.txt


title: 1uM_MS023_x_7_days_Rep2


title: pat20_tumor [RNA-seq]

description: counts.txt


title: Aorta Lard-L562


title: pat19_tumor [RNA-seq]

description: counts.txt


title: pat18_normal [RNA-seq]

description: counts.txt


title: Aorta Cholesterol-L559


title: pat18_tumor [RNA-seq]

description: counts.txt


title: pat17_normal [RNA-seq]

description: counts.txt


title: 1uM_GSK591_x_7_days_Rep3


title: Aorta Cholesterol-L560


title: pat17_tumor [RNA-seq]

description: counts.txt


title: Aorta Control-L570


title: pat16_normal [RNA-seq]

description: counts.txt


title: pat16_tumor [RNA-seq]

description: counts.txt


title: 1uM_GSK591_x_7_days_Rep1


title: Aorta Control-L571


title: pat15_normal [RNA-seq]

description: counts.txt


title: pat15_tumor [RNA-seq]

description: counts.txt


title: DMSO_control_(0.01%)_x_7_days_Rep3

description: no processed data provided


title: pat14_normal [RNA-seq]

description: counts.txt


title: Aorta Control-L568


title: Aorta Control-L553


title: pat14_tumor [RNA-seq]

description: counts.txt


title: pat12_tumor [RNA-seq]

description: counts.txt


title: pat12_normal [RNA-seq]

description: counts.txt


title: DMSO_control_(0.01%)_x_7_days_Rep2

description: no processed data provided


title: 1uM_MS023_x_7_days_Rep1


title: pat11_normal [RNA-seq]

description: counts.txt


title: pat11_tumor [RNA-seq]

description: counts.txt


title: Aorta Control-L552


title: pat10_normal [RNA-seq]

description: counts.txt


title: Aorta Control-L569


title: pat9_normal [RNA-seq]

description: counts.txt


title: 1uM_GSK591_x_7_days_Rep2


title: pat10_tumor [RNA-seq]

description: counts.txt


title: DMSO_control_(0.01%)_x_4_days_Rep2

description: no processed data provided


title: pat9_tumor [RNA-seq]

description: counts.txt


title: DMSO_control_(0.01%)_x_4_days_Rep1

description: no processed data provided


title: pat8_normal [RNA-seq]

description: counts.txt


title: Pulmonary valve Cholesterol-L267


title: pat8_tumor [RNA-seq]

description: counts.txt


title: 1uM_MS023_x_4_days_Rep3


title: Mitral valve Cholesterol-L266


title: HRD_RNA_rep3

value: resistant to DNR


title: pat7_tumor [RNA-seq]

description: counts.txt


title: pat6_normal [RNA-seq]

description: counts.txt


title: pat6_tumor [RNA-seq]

description: counts.txt


title: DMSO_control_(0.01%)_x_7_days_Rep1

description: no processed data provided


title: Aorta Control-L551

value: New Zealand White


title: Tricuspid valve Control-L264

value: male


title: 1uM_MS023_x_4_days_Rep2


title: 1uM_MS023_x_4_days_Rep1


title: pat5_normal [RNA-seq]

description: counts.txt


title: DMSO_control_(0.01%)_x_4_days_Rep3

description: no processed data provided


title: Pulmonary valve Control-L263


title: pat5_tumor [RNA-seq]

description: counts.txt


title: pat4_normal [RNA-seq]

description: counts.txt


title: 1uM_GSK591_and_1uM_MS023_x_4_days_Rep2


title: pat4_tumor [RNA-seq]

description: counts.txt


title: Mitral valve Lard-L158


title: pat3_tumor [RNA-seq]

description: counts.txt


title: 1uM_GSK591_and_1uM_MS023_x_4_days_Rep1


title: pat2_tumor [RNA-seq]

description: counts.txt


title: pat2_normal [RNA-seq]

description: counts.txt


title: Mitral valve Cholesterol-L157


title: 1uM_GSK591_x_4days_Rep3


title: pat7_normal [RNA-seq]

description: counts.txt


title: Tricuspid valve Cholesterol+IR-L260

value: heart (Tricuspid valve)

value: Cholesterol+IR


title: Aortic valve Cholesterol-L265

value: heart (Aortic valve)


title: Pulmonary valve Cholesterol+IR-L259


title: Mitral valve Cholesterol+IR-L258


title: 1uM_GSK591_x_4days_Rep1

value: poly(A) RNA


title: 1uM_MS023_x_2_days_Rep3


title: 1uM_GSK591_and_1uM_MS023_x_4_days_Rep3


title: Aortic valve Cholesterol+IR-L257


title: 1uM_MS023_x_2_days_Rep2


title: Mitral valve Control-L262

value: Control


title: 1uM_MS023_x_2_days_Rep1


title: Tricuspid valve Lard-L251

value: Lard


title: Mitral valve Lard-L249

value: heart (Mitral valve)


title: 0.01%_DMSO_+ActD_RepA


title: 1uM_GSK591_and_1uM_MS023_x_2_days_Rep2


title: 1uM_GSK591_x_4days_Rep2


title: 1uM_GSK591_and_1uM_MS023_x_2_days_Rep1


title: Mitral valve Cholesterol-L245


title: Mitral valve Control-L156


title: 1uM_GSK591_x_2days_Rep3


title: Aortic valve Cholesterol-L244


title: 1uM_GSK591_and_1uM_MS023_x_2_days_Rep3


title: Tricuspid valve Cholesterol-L247


title: Tricuspid valve Control-L243


title: 1uM_GSK591_x_2days_Rep2


title: 1uM_MS023_SKaTER_2_days_+DRB_(35_min)_Rep_2

data_processing:
Library strategy: SKaTER-seq
Adapter trimming accomplished with trim_galore v0.6.5 (trim_galore --paired -j 8 $file ${fn}_2.fastq.gz)
Alignment performed with STAR v2.4.2a (STAR --genomeDir $GENDIR --readFilesIn ${fn}_1_val_1.fq.gz ${fn}_2_val_2.fq.gz --readFilesCommand zcat --outFileNamePrefix ${fn}_ --runThreadN 12 --outSAMtype BAM Unsorted --outSAMstrandField intronMotif --outSAMattributes All --outFilterMultimapNmax 1 --outFilterScoreMinOverLread 0.51 --outFilterMatchNminOverLread 0.51 --outFilterMismatchNmax 4 --alignIntronMax 50000 --sjdbGTFfile $GENDIR/genes.gtf --quantMode TranscriptomeSAM GeneCounts --twopassMode Basic)
Duplicate control Picard tools 2.3.0 (java -jar `which picard.jar` MarkDuplicates INPUT=${fn}_Aligned.sortedByCoord.PEonly.bam OUTPUT=${fn}_Aligned.sortedByCoord.PEonly_marked.bam METRICS_FILE=${fn}_Aligned.sortedByCoord.PEonly_marked_metrics CREATE_INDEX=true)
Splicing analysis rMATs v4.0.2 (rmats.py --b1 $fn --b2 $file --gtf gencode.v19.annotation.gtf --od ${file%.txt} --tmp ${file%.txt}_tmp -t single --readLength 150 --nthread 35)
Genome_build: hg19
Supplementary_files_format_and_content: SKaTER aligned reads are provided as bigwig files generated using deepTools v3.3.1 (bamCoverage -b $file -o ${fn}.bw  -p 35 -bs 1  -v --ignoreDuplicates). rMATS summary files are rMATs JCEC output concatenated into a single text file for each condition.

value: nascent RNA


title: 15D

city: Marseille

last: Brochet

address: 13288 MARSEILLE cedex 09

description: Peripheral blood samples were collected in BD Vacutainer® CPT™ BD tubes containing sodium citrate, separator gel and Ficoll ™ Hypaque ™ solution. The samples were centrifuged for 30min at 2.300 rpm at room temperature. The pellet was washed with Hanks Buffer (HBSS- Gibco™ -Thermofisher), centrifugated at 1.800 rpm for 10min, lysed with ACK lysing buffer –Gibco™, washed again with the same buffer and centrifuged. The PBMC pellet was re-suspended in RNAlater reagent (Ambion- Thermofisher, USA and stored at freezer -80°C. The RNA extraction used the RNeasy Mini Kit (QiagenGermany) according to the manufacturer’s protocol. Total RNA purity was certificated in a NanoDrop ND-2100 spectrophotometer (Thermofisher-USA), evidencing values for the ratio optical density OD260/OD280 superior to 1.8. The RNA integrity was obtained using the RNA 6000 Nano kit on BioAnalyzer 2100 (Agilent- Technologies, USA). All samples presented RNA Integrity Number (RIN) ≥ 8.0, exhibiting the presence of distinct ribosomal bands 28SrRNA and 18SrRNA, with 2:1 intensity ratio, demonstrating that the RNA was intact. Gene expression profile determination used a 60,901 probe sets microarray (SurePrint G3 Human Gene Expression v3 8x60K Microarray, G4858A-072363- Agilent Technologies, Inc., Santa Clara, CA, USA). The procedures for hybridization, using the fluorescent dye Cy3 followed the manufacturer’s protocol (One Color Microarray-Based Gene Expression Analysis-Low Input Quick Amp Labeling Agilent Technologies, USA). The Agilent One-Color Microarray-based Gene Expression Analysis uses cyanine 3-labelled targets to measure gene expression in experimental and control samples and Oligo dT-Promoter Primer and T7 RNA Polymerase to generate cRNA. The total RNA (100ng) containing 2mL of spike-in control was amplified, fluorescently labeled, and hybridized to microarray chips according to the manufacturer’s instruction. The hybridization process was performed for 17 h at 65°C into the hybridization oven rotator rack at a speed of four rounds per minute. After hybridization, appropriate washing steps followed the manufacturer’s protocol. The microarray images were captured by the reader Agilent Bundle according to parameters recommended for bio-arrays and extracted by Agilent Feature Extraction software version 10.7.3 for gene expression.

hyb_protocol: The hybridization was performed for 17 hours at 10 rpm and 65°C in a Hybridization Oven (Robbins Scientific). Slide Wash was done according to the manufacturer's recommendation.

scan_protocol: Cy3 intensities were detected by one-color scanning using Agilent DNA microarray scanner at 3 micron resolution. Raw data from scanned image files were extracted using Feature Extraction software (10.7.3.1). Spike-in used in the experiment gave reliable data and all arrays passed the quality control.

data_processing: The microarrays were therefore analyzed using both GeneSpring software (11.5.1). Threshold raw signals to 1.0. Normalization algorithm: Percentile shift. Percentile target: 75. Baseline option: baseline to median of all samples. Group comaraison: Moderated T-Test.

source_name: PBMC

label_protocol: Microarrays were done using the Low Input Quick Amp Labeling One-Color Kit (Agilent Technologies) and the One-color RNA Spike-in Kit (Agilent Technologies) following the manufacturer's standard protocol (Agilent One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling). 100 ng of total RNA input was used. After cDNA synthesis, amplification, labeling and purification, the reaction efficacy was checked using the NanoDrop.

extract_protocol: Tissue (20-30mg of tissue) homogenization was carried out with the Precellys-24 device (Bertin Technologies, Ozyme), with ceramic beads (1.4mm in diameter, CK14), in 400 µl of lysis buffer RLT plus (Qiagen) supplemented with 4µl β-mercapto-ethanol. RNA was recovered with the RNeasy plus following the manufacturer's instructions (Qiagen). RNA integrity was assessed with a 2100 Bioanalyzer (Agilent). Total RNA (1µg), with a RIN > 7, was reverse-transcribed with the high Capacity cDNA Reverse Transcription Kit (Applied Biosystems).

tag: cell type

value: PBMC

tag: diagnosis

value: recent-onset T1D


title: 11D


title: 9D


title: Pulmonary valve Cholesterol+IR-L238

value: heart (Pulmonary valve)


title: 2D


title: 5D


title: 3D


title: 17D


title: 13D


title: 1D


title: 18D


title: 1uM_GSK591_x_2days_Rep1


title: Hip-CLO50-6

city: Toyama

first: Tetsushi

last: Hirano

state: Toyama

address: 2630 sugitani

institute: University of Toyama

hyb_protocol: The biotinylated cRNA was hybridized to arrays at 45°C for 16 hours.

scan_protocol: The arrays were washed and stained using wash and stain kit on the Affymetrix Fluidics Station 450 (Affymetrix).

data_processing: The data were normalized with the SST-RMA algorism using a Transcriptome analyses console (Affymetrix) software.

source_name: exposure group

label_protocol: The total RNA (250 ng) was used to synthesize cRNA with a GeneChip WT Amplification Kit. The cDNA was fragmentated and labeled with a GeneChip WT Terminal Labeling Kit (Affymetrix).

growth_protocol: On the end of 2 weeks expsure of CLO, brains were dissected.

extract_protocol: Total RNA was extracted from brain tissue using a NucleoSpin®  RNA plus isolation kit (MACHEREY-NAGEL, GmbH).  The quality of total RNA was analyzed using a Bioanalyzer 2100 (Agilent Technologies, Inc.). The RNA samples with RIN (RNA integrity number) values > 7.0 were considered acceptable.

tag: strain

value: 12 weeks

value: hippocampus


title: 14D


title: 19D


title: 16D


title: 6D


title: 20D


title: Tricuspid valve Cholesterol+IR-L239


title: Hip-Ctrl-6

source_name: control group


title: 19C

value: healthy control


title: 8D


title: 4D


title: 12D


title: 7D


title: 20C


title: 10D


title: 1uM_MS023_SKaTER_2_days_+DRB_(30_min)_Rep_2


title: Mitral valve Cholesterol+IR-L237


title: 1uM_MS023_SKaTER_2_days_+DRB_(25_min)_Rep_2


title: Aortic valve Cholesterol+IR-L236


title: Hip-CLO50-3


title: 1uM_MS023_SKaTER_2_days_+DRB_(15_min)_Rep_2


title: Pulmonary valve Lard-L155


title: 1uM_MS023_SKaTER_2_days_+DRB_(10_min)_Rep_2


title: Pulmonary valve Lard-L234


title: Mitral valve Lard-L233


title: Aortic valve Lard-L232


title: Col-0 floral bud PacBio (biorep #2)

city: Wageningen

first: Michael

middle: D

last: Nodine

state: Gelderland

address: Radix West

department: Plant Sciences

country: Netherlands

institute: Wageningen University & Research

description: PacBio reads from second biological replicate of Col-0 floral buds

data_processing:
Library strategy: Iso-seq
Raw Arabidopsis PacBio reads were converted to Circular Consensus Sequences using Iso-seq3 software with the command ccs --min-passes 2 --min-rq .9, and CCS reads were converted to full-length non-chimeric (FLNC) reads using lima and isoseq3 refine --require-polya --min-rq -1 --min-polya-length 10.
FLNC reads were aligned to the Arabidopsis genome with the command minimap2 -G 5000 -H -ax splice --MD -C 5 -u f -p 0.9 --junc-bed [TAIR10 transcript BED12].
Aligned unsorted SAM files were converted to ELR with the command bookend elr --stranded -s -e --start_seq ATGGG --genome [TAIR10.fa].
Genome_build: TAIR10
Supplementary_files_format_and_content: BED12+3 columns that store the source, weight, and ELCIGAR (record of end labels) for every read

organism: Arabidopsis thaliana

source_name: Inflorescences containing unopened floral buds

growth_protocol: Arabidopsis thaliana accession Columbia-0 (Col-0) were grown in controlled growth chambers at 20-22˚C under a 16-h light/8-h dark cycle with incandescent lights (130 to 150 µmol/m2/s).

extract_protocol:
TRIzol reagent (Thermo Fisher Scientific)
SMRTbell Template Preparation, PacBio Sequel SMRT Cell 1M

tag: ecotype

value: wild type


title: Col-0 floral bud PacBio (biorep #1)

description: PacBio reads from first biological replicate of Col-0 floral buds


title: 1uM_MS023_SKaTER_2_days_+DRB_(0_min)_Rep_2


title: 1uM_MS023_SKaTER_2_days_-DRB_Rep_2


title: 1uM_MS023_SKaTER_2_days_+DRB_(20_min)_Rep_2


title: Mitral valve Cholesterol-L229

value: New Zealand White

tag: treatment

value: Cholesterol


title: Tricuspid valve Lard-L235

value: male

value: heart (Tricuspid valve)


title: 1uM_GSK591_SKaTER_2_days_+DRB_(30_min)_Rep_2


title: Aortic valve Cholesterol-L228

value: heart (Aortic valve)


title: 1uM_GSK591_SKaTER_2_days_+DRB_(25_min)_Rep_2


title: Surgery_72h_rep5

city: Stockholm

first: Souren

last: Mkrtchian

address: Solnavägen 9

department: Physiology and Pharmacology

institute: Karolinska Institutet

data_processing:
Illumina NextSeq 500/550
The raw sequence reads in FastQ format were cleaned from adapter sequences and size-selected for 14-34 base-long inserts (plus 8 random adapter bases) using cutadaptv.2.4
For miRNA-focused analysis, the genome-aligned reads in SAM format were selected in the size range 20-24 bases using GNUAwkand Samtoolsv.1.10, converted into sorted BAM files with Samtools, and read counts were summarized either per miRNA locus or per mature miRNA using featureCountsusing miRNA annotation either from Gencode M25 or from miRBase v.22
Genome_build: mm10 and miRBase v. 22
Supplementary_files_format_and_content: Matrix table in tab delimited txt format with raw gene counts for every miRNA and every sample

source_name: serum EVs

extract_protocol:
EVs were isolated from the mice serum and total RNA was extracted using the Exosomal RNA isolation kit from Norgen Biotek Corp. 2.3 ng of RNA were used for the construction of small RNA libraries
Small RNA libraries were constructed using the NEXTFLEX® Small RNA-Seq Kit v3 (Bioo Scientic Corp.).

value: serum

value: 14-16 weeks

tag: time point

value: tibia surgery


title: Surgery_72h_rep6

tag: age


title: Surgery_72h_rep4

tag: tissue


title: Tricuspid valve Control-L201

value: Control


title: 17C


title: Hip-Ctrl-1


title: 13C


title: 1uM_GSK591_SKaTER_2_days_+DRB_(20_min)_Rep_2

value: nascent RNA


title: 16C

value: PBMC


title: 15C


title: Ctx-Ctrl-6

value: cerebral cortex


title: Surgery_72h_rep3


title: 11C


title: 14C


title: 18C


title: Ctx-CLO50-3


title: 1uM_GSK591_SKaTER_2_days_+DRB_(35_min)_Rep_2


title: Pulmonary valve Control-L200

value: heart (Pulmonary valve)


title: 12C


title: Ctx-CLO50-6

value: 12 weeks


title: 1uM_GSK591_SKaTER_2_days_+DRB_(15_min)_Rep_2


title: Pulmonary valve Cholesterol-L154


title: Surgery_72h_rep2


title: 9C


title: 10C


title: Ctx-Ctrl-1


title: 8C


title: Mitral valve Control-L199

value: heart (Mitral valve)


title: 1uM_GSK591_SKaTER_2_days_+DRB_(10_min)_Rep_2


title: Surgery_72h_rep1


title: Surgery_24h_rep6


title: 7C

value: healthy control


title: 1uM_GSK591_SKaTER_2_days_+DRB_(0_min)_Rep_2


title: Aortic valve Control-L198


title: 1uM_GSK591_SKaTER_2_days_-DRB_Rep_2


title: Surgery_24h_rep5

value: wild type


title: Pulmonary valve Cholesterol+IR-L196

value: New Zealand White

value: Cholesterol+IR


title: Surgery_24h_rep4


title: Tricuspid valve Lard-L193

value: male

value: Lard


title: 0.01%_DMSO_SKaTER_2_days_+DRB_(30_min)_Rep_2


title: 0.01%_DMSO_SKaTER_2_days_+DRB_(35_min)_Rep_2


title: Pulmonary valve Lard-L192


title: Surgery_24h_rep3


title: 6C


title: 0.01%_DMSO_SKaTER_2_days_+DRB_(25_min)_Rep_2


title: Pulmonary valve Control-L153


title: Surgery_24h_rep2


title: 0.01%_DMSO_SKaTER_2_days_+DRB_(20_min)_Rep_2


title: Tricuspid valve Cholesterol-L189

value: heart (Tricuspid valve)

value: Cholesterol


title: HMDP Treatment

city: Los Angeles

first: Takeru

last: Kondo

state: California

address: 10824 Lindbrook Dr. #304

institute: UCLA School of Dentistry

description: single cell RNA

data_processing: The Cell Ranger output of single cell RNA sequencing data were analyzed using R-program (Seurat, https://satijalab.org/seurat/).

source_name: Palatal gingiva

extract_protocol:
After the HMDP-DNV treatment of the BRONJ mice, the gingival tissue from the tooth extraction side of the palate was harvested (n=4). The gingival tissue of untreated BRONJ mice was also harvested (n=4). Gingival tissues were cut into 1-mm pieces and placed in digestion buffer containing 1 mg/ml collagenase II (Life Technologies, Grand Island, NY), 10 units/ml DNase I (Sigma-Aldrich) and 1% bovine serum albumin (BSA; Sigma-Aldrich) in Dulbecco’s modified Eagle’s medium (DMEM; Life Technologies) for 20 min at 37°C on a 150 rpm shaker. The tissues were passed through a 70µm cell strainer. The collected cells were pelleted at 1,500 rpm for 10 min at 4°C and resuspended in phosphate buffered saline (PBS; Life Technologies) that was supplemented with 0.04% BSA (Cell suspension A).  The remaining tissues were further incubated in 0.25% trypsin (Life Technologies) and 10 units/ml DNase I for 30 min at 37 ℃ on a 150 rpm shaker.
The combined trypsin-released cells and collagenase II-released cells were counted and the equal number of cells (2,000~3,000) from each animal were combined in the group for single cell RNA sequencing (10X Genomics, San Francisco, CA).

treatment_protocol: Female C57Bl6/J mice received a bolus intravenous injection of ZOL (500 µg/Kg in saline solution) from the retro-orbital venous plexus. One (1) week later, the maxillary left first molar was extracted under general anesthesia by isoflurane. Delayed healing and BRONJ-like jawbone exposure were confirmed 1 week after tooth extraction. HMDP-DNV in 3 µl MQW (1.5 pmol/100 µM) was topically applied to the BRONJ lesion and surrounding gingival tissue. This treatment was applied 2 times total in a week. The BRONJ control group did not receive the HMDP-DNV treatment.

value: Gingiva

value: 11-13 weeks old


title: BRONJ Control

description: single cell RNA


title: 0.01%_DMSO_SKaTER_2_days_+DRB_(15_min)_Rep_2


title: Surgery_6h_rep6

value: serum

value: 14-16 weeks

value: tibia surgery


title: 5C

first: Pauline

value: PBMC


title: Pulmonary valve Cholesterol-L188

value: heart (Pulmonary valve)


title: 0.01%_DMSO_SKaTER_2_days_+DRB_(10_min)_Rep_2

value: nascent RNA


title: 3C


title: PS-21

city: INDIANAPOLIS

first: Xiaoyu

last: Lu

state: IN

address: 410W 10TH ST

department: school of medicine

institute: INDIANA UNIVERSITY

data_processing:
Data is mapping to genome UCSC mm10 using STAR software
counts data are extract using featureCounts
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Gene counts for each sample in spreadsheet

source_name: Bone Marrow Tissue

growth_protocol: Tet2-defient mice (Tet2-/-, donor, CD45.2), competitor Boy/J (CD45.1) mice and recipient Leptin deficient Ob/Ob mice (lethally irradiated) and C57Bl/6J mice (lethally irradiated) were used for BM collection and transplantation studies. Ob/Ob mice were obtained from Jackson Laboratory (Stock No: 000632). C57Bl/6J and Boy/J mice were obtained from the In Vivo Therapeutics core facility at the Indiana University School of Medicine. Mice husbandry and care were performed under 21-24°C temperature- and 12-hour light,12-hour dark cycle; group-housed according to age, sex, and genotype; and fed ad libitum. Tet2-/- (donor, CD45.2) and Boy/J (donor, CD45.1) mice were 6-8 months of age when utilized. Ob/Ob and C57Bl/6J recipient mice were 10-12 weeks of age when used for experiments. Both male and female mice were used as donors, competitors, and recipients for experiments. All experiments were matched for age and sex for each experiment. We did not observe any difference in function or phenotypes between males and females.

extract_protocol:
Total RNA was isolated from the BM cells of 7 different drug treatment groups (Group 1: Vehicle, Group 2: Metformin, Group 3: Pioglitazone, Group 4: Nifedipine, Group 5: metformin+pioglitazone+MCC950+anakinra, Group 6: metformin+nifedipine+MCC950+anakinra and Group 7: Tet2-/-+Boy/J to WT (Un-treated) mice) using Qiagen RNeasy Plus Micro Kit. RNA with Agilent Bioanalyzer RIN of > 7 were selected for library preparation.
Library preparation was performed using New England Biolabs Single Cell/Low Input RNA Library Prep Kit for Illumina. Paired-end RNA-sequencing (RNA-seq) was performed on Illumina HiSeq 4000 by IU School of Medicine Medical Genomics core. Each group/condition consists of four matched biological replicates and ~30 million reads were obtained per sample.

treatment_protocol: The CD45.2 donor BM cells from Tet2-/- mice were mixed with Boy/J CD45.1 competitor BM donor cells (with an equal number of viable total cells, 500K:500K). Recipient mice (Ob/Ob and WT) were lethally irradiated (700 cGy + 400 cGy) one day prior to transplantation (intravenous tail injection) of donor cells. At 8 weeks post-transplantation, the Ob/Ob recipient mice were treated with Group I: Vehicle (PBS), Group II: Metformin 100 mg/kg (Glucose inhibitor; oral, 30 days) (Cat no: S1950, Selleckchem), Group III: pioglitazone 20 mg/kg (PPARγ agonist; oral, 30 days) (Cat no: HY-13956, Med Chem Express), Group IV: Nifedipine 100 mg/kg, (calcium channel (Ca2+) blocker; oral, 30 days) (Cat no: Ab120135, Abcam), Group V: Metformin 100 mg/kg (oral; 30 days) + Pioglitazone 20 mg/kg (oral; 30 days) + MCC950 30mg/kg (a small molecule inhibitor of the NLRP3 inflammasome; oral, 30 days) (Cat no: S7809, Selleckchem) + Anakinra 10 mg/kg (i.p; 10 days) (Cat no: HY-108841, Med Chem Express), Group VI: Metformin 100 mg/kg (oral; 30 days) + Nifedipine 100 mg/kg, (oral; 30 days) + MCC950 30mg/kg, (oral; 30 days) + Anakinra 10 mg/kg (i.p; 10 days), Group VII: Tet2-/- + Boy/J into WT recipients (Untreated).

tag: genotype/variation

value: Tet2-/- + Boy/J to Ob/Ob

value: Metformin + Pioglitazone + MCC950 + Anakinra

value: bone marrow


title: 1C

value: healthy control


title: 4C


title: PS-20


title: Surgery_6h_rep4

value: wild type


title: Surgery_6h_rep5


title: 2C


title: Aortic valve Cholesterol-L186

value: New Zealand White

value: male

value: heart (Aortic valve)


title: 0.01%_DMSO_SKaTER_2_days_+DRB_(0_min)_Rep_2


title: 0.01%_DMSO_SKaTER_2_days_-DRB_Rep_2


title: Tricuspid valve Control-L185

value: heart (Tricuspid valve)

value: Control


title: PS-18

value: Nifedipine


title: 1uM_MS023_SKaTER_2_days_+DRB_(35_min)_Rep_1


title: Surgery_6h_rep2

value: serum


title: PS-17


title: Surgery_24h_rep1

value: 14-16 weeks


title: PS-19


title: Pulmonary valve Control-L184


title: 1uM_MS023_SKaTER_2_days_+DRB_(30_min)_Rep_1


title: Surgery_6h_rep1

value: tibia surgery


title: Mitral valve Control-L183

value: heart (Mitral valve)


title: 1uM_MS023_SKaTER_2_days_+DRB_(25_min)_Rep_1


title: Control_ rep6

value: control


title: PS-16


title: Mitral valve Cholesterol-L187

value: Cholesterol


title: PS-15

value: Tet2-/- + Boy/J to Ob/Ob

value: Pioglitazone


title: Control_ rep5


title: 1uM_MS023_SKaTER_2_days_+DRB_(20_min)_Rep_1

value: nascent RNA


title: Tricuspid valve Cholesterol+IR-L181

value: Cholesterol+IR


title: 1uM_MS023_SKaTER_2_days_+DRB_(15_min)_Rep_1


title: Pulmonary valve Cholesterol+IR-L180

value: heart (Pulmonary valve)


title: PS-13

value: bone marrow


title: Control_ rep3

value: wild type


title: 1uM_MS023_SKaTER_2_days_+DRB_(10_min)_Rep_1


title: Aortic valve Lard-L152

value: New Zealand White

value: male

value: heart (Aortic valve)

value: Lard


title: Surgery_6h_rep3

value: serum


title: PS-12

value: Tet2-/- + Boy/J to WT

value: Un-treated


title: 1uM_MS023_SKaTER_2_days_+DRB_(0_min)_Rep_1


title: Mitral valve Cholesterol+IR-L179

value: heart (Mitral valve)


title: 1uM_MS023_SKaTER_2_days_-DRB_Rep_1


title: Control_ rep1

value: 14-16 weeks

value: control


title: PS-11


title: PS-14

value: Tet2-/- + Boy/J to Ob/Ob


title: Control_ rep4


title: PS-10


title: 1uM_GSK591_SKaTER_2_days_+DRB_(35_min)_Rep_1


title: Control_ rep2


title: Tricuspid valve Cholesterol+IR-L177

value: heart (Tricuspid valve)


title: PS-9

value: Vehicle


title: 1uM_GSK591_SKaTER_2_days_+DRB_(30_min)_Rep_1

value: nascent RNA


title: Aortic valve Control-L182

value: Control


title: Pulmonary valve Cholesterol+IR-L176

value: heart (Pulmonary valve)

value: Cholesterol+IR


title: J_7136_hom_p

city: Dresden

first: Francis

last: Stewart

address: Tatzberg 47-49

institute: BIOTEChnology Center TU Dresden

data_processing:
bcl2fastq2 2.19.1
Fastq files were alignment with gsnap (2018-07-04) to the mm10 reference which was obtained from Ensembl. Additionally Ensembl annotation version 92 from mm10 was used to support splicesite detection for gsnap (-d mm10 --gunzip -A sam -t 16 -n 1 -s EnsemblGene-92.ss.mm10.iit -N 0)
FeatureCounts (1.6.3) was used to count fragments per gene. Ensembl annotation version 92 as gtf file was used to detect genomic coordinates of genes (-s 0 -Q 1 -T 8)
Genome_build: mm10
Supplementary_files_format_and_content: tab separated file where the first columns provide details about the genes (ID, start, end, chromosome, strand) which is followed by the fragment counts per gene per sample

source_name: Mll1-/- (knockout) _Paneth cells

extract_protocol:
At 10 days after the induction of mutagenesis, intestinal crypts were dissociated into single cells with TrypLE Express (Thermo Fisher Scientific) for 30min at 37°C. Dissociated cells were passed through 70µm cell strainer and washed wit 5% FBS/PBS. Cells were stained with PE-conjugated anti-CD24, APC-conjugated anti‑326 (EpCAM) antibody and Alexa-Fluor 700 CD45 antibody for 45min on ice. Stained cells were collected by centrifugation and resuspended in SYTOX blue dead cell stain. FACS sorting was performed on a FACS AriaTM III cell sorter (BD).
Cells are FACsorted into a PCR tube containing 2 ul of nuclease free water with 0.2% Triton-X 100 and 4 U murine RNase Inhibitor (NEB), spun down and frozen at -80°C. After thawing the samples, RNA is denatured for 3 minutes at 72 °C in the presence of 2.4 mM dNTP (Invitrogen), 240 nM dT-primer* and 4 U RNase Inhibitor (NEB). The reverse transcription and addition of the template switch oligo is performed at 42°C for 90 min after filling up to 10 µl with RT buffer mix for a final concentration of 1x superscript II buffer (Invitrogen), 1 M betaine, 5 mM DTT, 6 mM MgCl2, 1 µM TSO-primer*, 9 U RNase Inhibitor and 90 U Superscript II. The reverse transcriptase is inactivated at 70 °C for 15 min. The single stranded cDNA is subsequently amplified using Kapa HiFi HotStart Readymix (Roche) at a 1x concentration together with 250 nM UP-primer* under following cycling conditions: initial denaturation at 98°C for 3 min, 16 cycles [98°C 20 sec, 67°C 15 sec, 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 1x volume of Sera-Mag SpeedBeads (GE Healthcare) resuspended in a buffer consisting of 10 mM Tris, 20 mM EDTA, 18.5 % (w/v) PEG 8000 and 2 M sodium chloride solution. The cDNA quality and concentration is determined with the Fragment Analyzer (Agilent). For library preparation 1.5 ng cDNA was tagmented using 0.5 µl TruePrep Tagment Enzyme V50 and 1x TruePrep Tagment Buffer L (TruePrep DNA Library Prep Kit V2 for Illumina, Vazyme), followed by an incubation step at 55 °C for 10 min. Next, Illumina indices are added during PCR (72 °C 3 min, 98 °C 30 sec, 12 cycles [98 °C 10 sec, 63 °C 20 sec, 72 °C 1 min], 72°C 5 min) with 1x concentrated KAPA Hifi HotStart Ready Mix and 300 nM dual indexing primers. After PCR, libraries are purified twice with 1x volume Sera-Mag SpeedBeads and quantified with the Fragment Analyzer, followed by Illumina sequencing on a Nextseq500 with a sample sequencing depth of 30 mio reads on average.

treatment_protocol: Mutagenesis was induced in mice by intraperitoneal injections of 1mg  tamoxifen on 3 consecutive days.

value: Mll1-/- (knockout)

value: small intestine

value: Paneth cells


title: J_7135_hom_p


title: PS-8

value: Metformin + Nifedipine + MCC950 + Anakinra

value: bone marrow


title: 1uM_GSK591_SKaTER_2_days_+DRB_(25_min)_Rep_1


title: PS-7


title: 1uM_GSK591_SKaTER_2_days_+DRB_(20_min)_Rep_1


title: Mitral valve Cholesterol+IR-L175

value: New Zealand White

value: male


title: Aortic valve Cholesterol+IR-L174

value: heart (Aortic valve)


title: J_7134_het_p

source_name: Mll1+/- (control)_Paneth cells

value: Mll1+/- (control)


title: PS-6

value: Metformin


title: 1uM_GSK591_SKaTER_2_days_+DRB_(15_min)_Rep_1


title: J_7100_het_p


title: PS-5

value: Tet2-/- + Boy/J to Ob/Ob


title: J_7096_hom_p


title: 1uM_GSK591_SKaTER_2_days_+DRB_(10_min)_Rep_1


title: PS-4


title: Tricuspid valve Cholesterol-L172

value: heart (Tricuspid valve)

value: Cholesterol


title: 1uM_GSK591_SKaTER_2_days_+DRB_(0_min)_Rep_1

value: nascent RNA


title: J_7079_het_p


title: Aortic valve Cholesterol+IR-L178


title: Pulmonary valve Cholesterol-L171


title: PS-3


title: J_7136_het_p


title: 1uM_GSK591_SKaTER_2_days_-DRB_Rep_1


title: J_7075_hom_p


title: Mitral valve Cholesterol-L170

value: heart (Mitral valve)


title: 0.01%_DMSO_SKaTER_2_days_+DRB_(35_min)_Rep_1


title: PS-2

value: Vehicle


title: Aortic valve Cholesterol-L151


title: PS-1


title: 0.01%_DMSO_SKaTER_2_days_+DRB_(30_min)_Rep_1


title: OE--U3-2

city: shanghai

first: Xin

last: Zhang

state: Shanghai

address: 450 tengyue road

department: Ophthalmology

institute: Yangpu Hospital, School of Medicine, Tongji University

data_processing:
Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA)
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v4-cBot-HS (Illumia)
The raw reads were further processed with a bioinformatic pipeline tool, BMKCloud (www.biocloud.net) online platform.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
Genome_build: mm9
Supplementary_files_format_and_content: All.DEG.final files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: human pterygium fibroblasts

growth_protocol: Tissue blocks were incubated with DMEM/F12, until a sufficient number of fibroblasts crawl out from each tissue blocks.

extract_protocol:
Total RNA is isolated with TRIzol reagent (Invitrogen).
According to the manufacturer's instructions, the clustering of the index-coded samples was performed on a cBot Cluster Generation System using a TruSeq PE Cluster Kit v4-cBot-HS (Illumina). After cluster generation, the library preparations were sequenced on an Illumina platform, and paired-end reads were generated.

treatment_protocol: untreated

value: conjunctiva

tag: disease state

value: pterygium

tag: culture method

value: primary culture

value: overexpressing U3 snoRNA


title: OE-U3-1


title: Aortic valve Cholesterol-L169

data_processing:
Basecalling performed using Illumina bcl2fastq v2.20
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Reads were processed for mapping and quantification using nf-core rnaseq pipeline v1.4.2 (https://nf-co.re/rnaseq/1.4.2/usage) and using Gene set from Ensembl.org release 099.
Genome_build: OryCun2.0
Supplementary_files_format_and_content: tab-delimited text file include raw counts for annotations for all Sample

source_name: heart

tag: breed

tag: Sex


title: 0.01%_DMSO_SKaTER_2_days_+DRB_(25_min)_Rep_1

tag: cell line


title: TSK-KO-3 RNAseq

city: Ann Arbor

first: Jiandie

last: Lin

state: MI

address: 210 Washtenaw Ave

department: Cell & Developmental Biology, Life Science Institute

institute: University of Michigan

description: Mouse quadriceps was harvested and immediately frozen into liquid nitrogen. RNA was extract by TRIzol.  Sequencing library was constructed from more than 400ng of total RNA by BGI sequencing service.

data_processing:
FastQC was used to assess the sequencing quality on fastq files.
STAR was used for alignment to generate bam files.
The reads aligned to each gene feature were counted by htseq.
R package DESeq2 was used for differential expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files contain DESeq2-normalized read counts from bulk RNA-seq

source_name: quadriceps

value: quadriceps

tag: phenotype

value: TSK-KO


title: Control-2

tag: genotype

value: control


title: Pulmonary valve Control-L167

value: New Zealand White

value: male

value: heart (Pulmonary valve)

value: Control


title: TSK-KO-2 RNAseq

extract_protocol: Mouse quadriceps was harvested and immediately frozen into liquid nitrogen. RNA was extract by TRIzol.  Sequencing library was constructed from more than 400ng of total RNA by BGI sequencing service.


title: Control-1


title: 0.01%_DMSO_SKaTER_2_days_+DRB_(20_min)_Rep_1

tag: rna population


title: TSK-KO-1 RNAseq


title: Aortic valve Lard-L173

extract_protocol:
Aorta ring (Ao) and heart valves (AoV, MV, PV, TV) were dissected at the end of the 16-week protocols, snap frozen in liquid nitrogen and stored at -80°C until RNA extraction. Total RNA was extracted by use of miRNeasy Mini Kit (Qiagen) according to manufacturer’s instructions.
RNA librairies were prepared with 10ng of RNA using the SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara Bio USA, Inc.) according to manufacturer’s instructions.
Sequencing of the libraries was performed on a NovaSeq6000 System (Illumina) with a S4 reagent kit (300 cycles) and 1.2nM library loading.

value: heart (Aortic valve)

value: Lard


title: Tricuspid valve Lard-L161

value: heart (Tricuspid valve)


title: 0.01%_DMSO_SKaTER_2_days_+DRB_(15_min)_Rep_1

value: nascent RNA


title: Silence_RNASeq_Rep2

city: Nanjing

first: Keith

last: Ma

address: No.44 Baiziting Road

institute: Nanjing Medical University

description: Gnen expression data from H1299 cells treated with si-circZFR

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Clean Reads mapped to human genome using Mapsplice v2.1.8 with parameters -s 22 -p 15 --ins 6 --del 6 --non-canonical --bam -o count counting
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

growth_protocol: H1299 cells plated in 6-well dishes the night before treatment in RPMI containing 10% fetal calf serum were treated

extract_protocol:
Total RNA was extracted from cell  by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.  The RNA with RIN >6.0 is right for experiment.
RNA library using standard Ion proton RNA-Seq Kit v2.0 protocol according to the manufacturer’s instructions.

treatment_protocol: H1299 cells were transfected with circZFR siRNA or control for 24h, respectively.

tag: cell type

value: lung adenocarcinoma

value: si-circZFR


title: Tricuspid valve Cholesterol-L160

value: Cholesterol


title: 0.01%_DMSO_SKaTER_2_days_+DRB_(10_min)_Rep_1


title: Aortic valve Control-L150


title: Silence_RNASeq_Rep1

source_name: H1299 cells were transfected with circZFR siRNA


title: Tricuspid valve Control-L159


title: WT-2 RNAseq

value: WT


title: Control_RNASeq_Rep2

description: Gnen expression data from H1299 cells treated with negative control

source_name: H1299 cells were transfected with negative control

value: negative control


title: 0.01%_DMSO_SKaTER_2_days_+DRB_(0_min)_Rep_1


title: 0.01%_DMSO_SKaTER_2_days_-DRB_Rep_1


title: Control_RNASeq_Rep1