title: cko_2

city: Peking

first: Yue

last: Deng

address: Yinghua street

institute: Peking University

data_processing:
Reference genome and gene model annotation files were downloaded from genome website directly
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene
Assembly: mm10

extract_protocol: Lung endothelial cells were isolated by MACS. RNA was harvested using TRIzol reagent.

treatment_protocol: WT mice were injected intratracheally with 10 mg/kg LPS or saline, while cko mice and  its control wt mice were injected intratracheally with 2 mg/kg LPS to maintain their survival.

value: lung

value: EC

value: intratracheal injection of LPS


title: 1313_GA_Lysate

status: Public on Mar 29 2023

type: SRA

city: La Jolla

first: Cecilia

middle: Sofie

last: Lindestam

state: CA

address: 9420 Athena Circle

department: Sette

country: USA

institute: La Jolla Institute for Immunology

library_source: transcriptomic

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr)
Filtered reads were against the GRCh38 reference genome and Gencode v27 annotations using STAR v2.6.1 (default options)
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using HTSeq-count v0.7.1 (-m union -s yes -t exon -i gene_id) and features with 0 counts across all samples were removed
Assembly: GRCh38.gencode.v27B
Supplementary files format and content: read count matrix with rows as genes and columns as cells

molecule: total RNA

organism: Homo sapiens

source_name: blood - PBMC

growth_protocol: PBMC were thawed and added at a density of 1 million cells per well to a round-bottom 96-well plate.

extract_protocol:
After 24 hrs, cells were resuspended in PBS with 10% (v/v) FBS and incubated at 4C for 10 min. Cells were then stained with fixable viability dye eFluor506 (eBioscience) and an antibody mixture containing anti-human CD3-AF700 (UCHT1; ThermoFisher), CD4-APCeFluor780 (RPA-T4; eBioscience), CD8-BV650 (RPA-T8; BioLegend), CCR7-PerCPCy5.5 (G043H7, Biolegend) CD14-V500 (M5E2; BD Bioscience), CD19-V500 (HIB19; BD Bioscience), CD25-FITC (M-A251; BD Bioscience), CD45RA-eFluor450 (HI100, eBiosciences), CD137-APC (4B4-1; BioLegend), OX40-PECy7 (Ber-ACT35; BioLegend), and PD-L1-PE (29E.2A3; BioLegend) for 20 min at room temperature. Cells were washed and resuspended in PBS before being transferred into a 5 ml polypropylene FACS tube (BD Bioscience). PBMCs were sorted, based on forward and side scatter excluding debris and doublets, on a FACSAria into TRIzol LS (Thermo Fisher). Acquisition files were analyzed using FlowJo. Total RNA was extracted from ~100,000 cells in TRIzol LS using the miRNeasy Micro Kit (Qiagen) on a QIAcube (Qiagen). Total RNA was amplified according to Smart Seq protocol (2). cDNA was purified using AMPure XP beads. cDNA was used to prepare a standard barcoded sequencing library (Illumina). Samples were sequenced using an Illumina HiSeq2500 to obtain 50-bp single end reads. Samples that failed to be sequenced due to limited sample availability or failed the quality control were eliminated from further sequencing and analysis. The full protocol can be found at protocols.io (http://dx.doi.org/10.17504/protocols.io.bxr6pm9e).
Sequencing was performed according to a paired-end strategy using the NovaSeq sequencer (Illumina). Samples that failed quality control standards were eliminated from further analysis21.

treatment_protocol: PBMCs were stimulated for 24hrs at 37 degree C with MTB300, Mtb whole cell lysate, as well as left unstimulated as a negative control. After 24hrs cells were stained for sorting

tag: with susceptibiliy allele

value: no

tag: stimulation

value: Lysate

tag: cell type

value: PBMC


title: cko_1

country: China

organism: Mus musculus

source_name: lung

tag: tissue

tag: time

tag: genotype

tag: treatment


title: 1310_GA_Lysate


title: cutaneous wound, P-F127, Day3 rep3

city: Taipei

first: SU-YI

last: SU

address: No. 280, Sec. 4, Renai Rd.,

department: Department of Medical Research

country: Taiwan

institute: Cathay General Hospital

data_processing:
BaseCall Conversion: Illumina's official basecalling program, the bcl2fastq conversion software v2.20, was used to convert BCL files from all Illumina sequencing platforms into FASTQ reads.
Adaptor Clipping: Adaptors are short nucleotide sequences which have to be ligated to every single DNA molecule during library preparation, and allow DNA fragments to bind to a flow cell for next generation sequencing. Removal of adapter sequences, a process called 'adaptor trimming', or clipping, is one of the first steps in analyzing NGS data.
Sequence Quality Trimming: Quality trimming was proformed to remove low quality reads/bases. Lower quality bases from the the 3' end were removed using a sliding-window approach as the per base quality gradually drops toward the 3' end of reads.
Both adaptor clipping and sequence quality trimming were performed using Trimmomatic v0.36 with a sliding-window approach.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: cutaneous wound

extract_protocol:
Total RNA was extracted using Trizol® Reagent (Invitrogen, USA) according to the instruction manual. Purified RNA was quantified at OD260nm using a ND-1000 spectrophotometer (Nanodrop Technology,USA) and qualitated by using a Bioanalyzer 2100 (Agilent Technology, USA) with RNA 6000 LabChip kit (Agilent Technology, USA).
RNA libraries for RNA-seq were prepared using SureSelect XT HS2 mRNA Library Preparation kit (Agilent, USA) following manufacturer's protocols.

treatment_protocol:
The experimental mice (10 µM capsaicin) were received 200 µL of capsaicin (10 µM, Sigma-Aldrich Corp., St. Louis, MO, USA) once daily, through Pluronic F127 gel (25% in saline; Merck, Darmstadt, Germany) topically.
Aliquots of 200 µL of Pluronic F127 were applied on the wounds once daily in the sham group (Pluronic-F127) for the same duration.

value: cutaneous wound

tag: strain

tag: Sex

value: male

value: Pluronic F127

value: Day 3


title: cutaneous wound, P-F127, Day3 rep2


title: wt_3

value: Fgfr1loxp/loxp mice


title: wt_2


title: wt_1


title: LPS_ 6

value: WT


title: IMR32tetHAND2_Ctrl_Input_6h

city: bethesda

first: Jack

last: Shern

state: MD

address: 10 Center drive

institute: NCI

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 genome using bwa and then use the MACS2 for peak calling
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using deeptools. The coverage is calculated as the number of reads per bin.

molecule: genomic DNA

source_name: IMR32_Input DNA

growth_protocol: The HAND2 stably transfected IMR32 cells (IMR32tetHAND2) are cultured in RPMI 1640 containing 10% FBS. HAND2 expression is induced by Dox treatment.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody following the Active Motif's instructions of the ChIP-IT High Sensitivity Kit.
Libraries were prepared according to Illumina's TruSeq ChIP Sample Preparation Guide.

treatment_protocol: ChIP experiments were performed after IMR32tetHAND2 cells being treated with or without Dox for 6 hr or 36 hr.

tag: cell line

value: Neuroblastoma

tag: chip antibody


title: IMR32tetHAND2_Ctrl_HAND2_6h

value: HAND2 (Abcam ab204000)


title: IMR32tetHAND2_Dox_MYCN_6h

value: MYCN (Active motif,  61185)


title: LPS_ 5


title: IMR32tetHAND2_Dox_Input_6h


title: IMR32tetHAND2_Ctrl_MYCN_6h


title: LPS_ 4


title: IMR32_3_siMYCN_r1

data_processing:
Basecalls performed using CASAVA version 1.4
Data was analyzed by Encode ATAC-seq pipeline
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using deeptools. The coverage is calculated as the number of reads per bin.

source_name: IMR32 Cells

growth_protocol: IMR32 cells are maintained in growth medium. Growth medium: RPMI-1640, 10% fetal calf serum, 100µg/mL streptomycin, 100U/mL penicillin, and L-glutamine.

extract_protocol:
Chromatin extraction and ATAC-seq was performed as previously described by William J Greenleaf and Howard Y Chang's group (Nature Methods. 960 | VOL.14 NO.10 | OCTOBER 2017, PMID 28846090).
Libraries were prepared according to the protocol from William J Greenleaf and Howard Y Chang's group using Illumina's Nextera DNA library prep kit.

treatment_protocol: siRNAs were transiently transfected into IMR32 cells using Nucleofector electroporation (Lonza) and cultured in growth medium for 24hr or 72 hr, then ATAC-seq experiment was performed.

tag: transfection

value: siMYCN


title: LPS_ 3


title: 1299_GA_Lysate


title: 1156_GA_Lysate


title: cko_3


title: IMR32tetHAND2_Dox_MYCN_36h


title: LPS_ 2


title: IMR32tetHAND2_Ctrl_HAND2_36h


title: LPS_ 1


title: IMR32tetHAND2_Dox_HAND2_6h


title: IMR32tetHAND2_Ctrl_Input_36h


title: IMR32tetHAND2_Dox_Input_36h


title: IMR32_19_siHAND2_Input_72h

treatment_protocol: siRNAs were transiently transfected into IMR32 cells using Nucleofector electroporation (Lonza) and cultured in growth medium for 24hr or 72 hr, then ChIP experiment was performed.

value: none (input)


title: saline_3

value: lung

value: intratracheal injection of saline


title: saline_4

value: EC


title: saline_2


title: A549 trame 3

city: Shang Hai

first: zhengke

last: lian

address: 500 Dongchuan Rd

institute: East China Normal University

data_processing:
Basecalls performed using Illumina NovaSeq 6000
clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1).
Genome_build: Hissat2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: lung adenocarcinoma cell

growth_protocol: H460 and A549 cells were cultured in RPMI 1640 with 10% FBS and 1% Penicillin/Streptomycin (typically 1-3 × 106 cells into a 6cm dish) supplemented with a humidified 95:5 (%; v/v) mixture of air and CO2 at 37℃.

extract_protocol:
Total RNA samples were extracted with RNA TRIzol Reagent (Magen) according to the manufacture’s manual.
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: One replicate of H460 was 5μM trametinib treated for 24 hours while the replicate of A549 was 100nM trametinib treated

tag: response to meki

value: sensitive to MEKi(trametinib)

value: 100nM trametinib for 24h

value: Non-Small Cell Lung Cancer


title: IMR32tetHAND2_Dox_HAND2_36h


title: IMR32_17_siCtrl_Input_72h


title: saline_1


title: A549 trame 2


title: IMR32_14_siHAND2_HAND2_72h


title: A549 trame 1


title: A549 3

value: 0.1% DMSO for 24h


title: HCD3

city: CHONGQING

first: Chaonan

last: Liu

address: Gaotanyan Street

institute: the Army Medical University

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp.
We used HISAT2 (https://ccb.jhu.edu/software/hisat2) to map reads to the reference genome of Mus musculus GRCm38.
The mapped reads of each sample were then assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters.
All the transcriptomes were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/).
After the final transcriptome was generated, StringTie was used to perform expression level for mRNAs by calculating FPKM.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Bone marrow

growth_protocol: All mice used were randomized, background-matched. All mice used were housed in individually ventilated specific pathogen-free (SPF) conditions and fed with autoclaved water and food.

extract_protocol:
LT-HSCs were sorted from the BM of mice with control diet (CD) or high cholesterol diet (HCD)  for 3 months.RNA was extracted from sorted cells using a RNeasy Micro Kit (QIAGEN) following the manufacturer's introductions. The RNA amount and purity were quantified using NanoDrop ND-1000 (NanoDrop).
Libraries for RNA-seq were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

value: Bone marrow

value: hematopoietic stem cells

value: high cholesterol diet (HCD)


title: IMR32_13_siCtrl_HAND2_72h


title: HCD2


title: IMR32_10_siHAND2_RNA_P_IIS2_72h

value: RNA_P_IIS2 (Active motif,61083)


title: A549 2


title: A549 1


title: IMR32_8_siHAND2_RNA_Pol_II_72h

value: RNA_PII (Active motif, 39097)


title: IMR32tetHAND2_Ctrl_MYCN_36h

value: Neuroblastoma


title: HCD1

value: WT


title: CD2

value: control  diet (CD)


title: IMR32_7_siCtrl_RNA_Pol_II_72h


title: IMR32_9_siCtrl_RNA_P_IIS2_72h


title: CD3


title: H460 trame 3

value: resistant to MEKi(trametinib)

value: 5uM trametinib for 24h


title: CD1


title: H460 trame 1


title: IMR32_5_siCtrl_H3K27me3_72h

value: H3K27me3 (Millipore, 07-449)


title: Soleus, MCK-RIP140KO, rep3

city: Philadelphia

first: Daniel

last: Kelly

state: PA

address: 3400 Civic Center Blvd

department: Penn Cardiovascular Institute

institute: University of Pennsylvania

data_processing:
Expression of transcripts of the GRCm38 (mm10) genome was quantified using Salmon 1.3.0
The transcripts expression was then summarized at the gene level, and differentially expressed genes were found using DESeq2 1.36.0 with ashr adaptive shrinkage estimator
Genes with FDR < 0.05, when comparing conditions of interest, were selected as differentially expressed. Furthermore, we only consider those genes which change at least 1.2-fold, in any direction.
Assembly: mm10
Supplementary files format and content: Tab-separated files contain gene name, log2 fold change, and FDR values for each differentially expressed gene in a comparison between two conditions

source_name: Striated muscle RIP140 KO - MCK-RIP140KO in Soleus

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen) and RNase-Free DNase Set (Qiagen) according to the manufacturer’s instructions. cDNAs were synthesized using the Affinity Script cDNA Synthesis Kit (Agilent) with 0.5 μg of total RNA.
RNA library preparations and sequencing reactions were conducted at GENEWIZ, LLC. (South Plainfield, NJ, USA). RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA).  RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were clustered on a single (two lanes in 30-209309547) lane of a flowcell. After clustering, the flowcell was loaded on the Illumina HiSeq instrument (4000 or equivalent) according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.

treatment_protocol: Transverse aortic constriction combined with small apical myocardial infarction (TAC/MI) surgeries were performed on 8 week-old male mice. Mice were anesthetized with ketamine [90mg/kg] / xylazine [10mg/kg] / Acepromazine [2mg/kg], intubated and ventilated (Harvard Apparatus). TAC was performed on anesthetized mice by first freeing the aortic arch by blunt dissection. A 7-0 silk suture was passed under the aorta. The suture was then tied around a blunt needle (25 to 28 gauge depending on size of animal) lying on the artery, and the blunt needle was removed to induce constriction. Second, to generate a small myocardial infarction (MI), the chest wall was retracted through the 4th intercostal space to clearly visualize the left ventricle and the left anterior descending artery. The left anterior descending branch (LAD) of the left coronary artery was ligated with a 8-0 nylon suture. Prior to analysis of all TAC/MI samples, the infarcted apical region was removed from the hearts (and the corresponding cardiac tissue region was removed from sham operated controls). Post-weaning aortic banding (PWAB) surgeries were performed on 21- to 28-day-old mice, weighing 7–13 g, received ascending aortic constrictions as described above (26 gauge).

value: Soleus

value: Nrip1 f/f Cre+


title: H460 3


title: Soleus, MCK-RIP140KO, rep2


title: H460 2


title: Soleus, MCK-RIP140KO, rep1


title: IMR32_4_siHAND2_H3K4me3_72h


title: H460 1


title: Soleus, Control, rep3

source_name: Striated muscle RIP140 KO - Control in Soleus

value: Nrip1 f/f Cre-


title: FLASH-RT_10Gy_Physioxia_4%O2_Rep3

city: Stanford

first: Richard

middle: L

last: Frock

state: California

address: 269 Campus Drive

department: Radiation Oncology

institute: Stanford University

data_processing:
Data processing is described in Hu et al., 2016 Nature Protocols (PMC4895203) and Liang et al., 2021 PNAS (PMC8166026)
Standard basecalling formats for Illumina reads
Illumina reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the hg38 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) to map translocations
Reads were aligned to the bait and the prey region using Bowtie2 and filtered to identify rejoining events and then combined to translocations using JoinT
Assembly: hg38
Supplementary files format and content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); and the entire stitched paired end read sequence (Seq)
Supplementary files format and content: The processed data files are the data files used for analysis.
Library strategy: JoinT-seq

growth_protocol: HEK293T cells were cultured at 37°C, 5% CO2 using DMEM supplemented with glutamine, 10% FCS and 0.5% penicillin/streptomycin

extract_protocol:
Genomic DNA was isolated using protocol described in Hu et al., 2016 Nature Protocols (PMC4895203)
Libraries were generated as described in Hu et al., 2016 Nature Protocols (PMC4895203), with the enzyme blocking step being omitted, using primers associated with the target locus and Illumina Miseq or Novaseq sequencing

treatment_protocol: HEK293T cells were cultured in Normoxia/Air (21% O2), Physioxia (4%O2), Physiological hypoxia (2% O2), or Pathological hypoxia (0.5% O2) and optionally exposed to electron beam ionizing radiation at CONV (0.06-0.21 Gy/sec) or FLASH (100-1,000Gy/sec) dose rates.

tag: nuclease delivery

tag: transfection protocol

value: FuGENE; 48 hour culture post transfection

tag: oxygen tension (o2)

value: 4% O2; Physioxia

tag: radiation treatment (rt) type

value: FLASH-RT

tag: dose

tag: radiation facility

value: LINAC; Lausanne

tag: treatment protocol

value: Trypsinize cells 24 hour post transfection at 4% O2, radiation exposure, replate cells for another 24 hours and then collect gDNA

tag: target locus

value: RAG1 (spCas9:RAG1B gRNA)

tag: extract_protocol (dna fragmentation)

value: Sonication

tag: illumina sequencing

value: Illumina MiSeq System; 250PE

tag: figure displaying results for this library

value: Fig 3

tag: number of raw reads used for normalization

tag: pipeline used for the analysis

value: JoinT-seq


title: IMR32_2_siHAND2_H3K27AC_72h

tag: cell line

tag: cell type

value: Neuroblastoma

value: H3K27ac  (Active motif, 39133)


title: Soleus, Control, rep1

tag: tissue

tag: genotype


title: IMR32_1_siCtrl_H3K27AC_72h

tag: chip antibody


title: Soleus, Control, rep2


title: FLASH-RT_10Gy_Physioxia_4%O2_Rep2

value: WT

tag: nuclease delivery

tag: transfection protocol


title: H460 trame 2

tag: response to meki

value: resistant to MEKi(trametinib)

tag: treatment

value: 5uM trametinib for 24h

value: Non-Small Cell Lung Cancer


title: Gastrocnemius, MCK-RIP140KO, rep3

source_name: Striated muscle RIP140 KO - MCK-RIP140KO in Gastrocnemius

value: Gastrocnemius

value: Nrip1 f/f Cre+


title: IMR32_34_siHAND2_GATA3ab_24h

tag: genotype/variation

value: GATA3 (Abcam, ab199428)


title: IMR32_32_siHAND2_HAND2_24h

value: HAND2 (Abcam ab204000)


title: CONV-RT_10Gy_Physioxia_4%O2_Rep2

value: FuGENE; 48 hour culture post transfection

tag: oxygen tension (o2)

value: 4% O2; Physioxia

tag: radiation treatment (rt) type

value: CONV-RT

tag: dose

tag: radiation facility

value: LINAC; Lausanne

tag: treatment protocol


title: CONV-RT_10Gy_Physioxia_4%O2_Rep3

value: Trypsinize cells 24 hour post transfection at 4% O2, radiation exposure, replate cells for another 24 hours and then collect gDNA

tag: target locus

value: RAG1 (spCas9:RAG1B gRNA)

tag: extract_protocol (dna fragmentation)

value: Sonication

tag: illumina sequencing

value: Illumina MiSeq System; 250PE

tag: figure displaying results for this library

tag: number of raw reads used for normalization


title: IMR32_6_siHAND2_H3K27me3_72h

tag: cell line

tag: cell type

value: Neuroblastoma

value: H3K27me3 (Millipore, 07-449)


title: IMR32_31_siHAND2_MYCN_24h

tag: chip antibody

value: MYCN (Active motif,  61185)


title: Gastrocnemius, MCK-RIP140KO, rep1

tag: tissue

tag: genotype


title: IMR32_33_siHAND2_PHOX2B_24h

value: PHOX2B (santa cruze, sc-376997 X)


title: CONV-RT_10Gy_Physioxia_4%O2_Rep1

value: WT

tag: nuclease delivery

tag: transfection protocol

value: Fig 3

tag: pipeline used for the analysis

value: JoinT-seq


title: Xray_10Gy_Physioxia_4%O2_Rep3

tag: oxygen tension (o2)

tag: radiation treatment (rt) type

value: X-Ray

value: X-Ray Tube; Lausanne


title: IMR32_30_siCtrl_GATA3ab_24h

tag: genotype/variation

value: siCtrl

value: GATA3 (Abcam, ab199428)


title: Gastrocnemius, Control, rep2

source_name: Striated muscle RIP140 KO - Control in Gastrocnemius

value: Gastrocnemius

value: Nrip1 f/f Cre-


title: Gastrocnemius, Control, rep3


title: Xray_10Gy_Physioxia_4%O2_Rep2

value: FuGENE; 48 hour culture post transfection

value: 4% O2; Physioxia

tag: dose

tag: radiation facility

tag: treatment protocol

value: Trypsinize cells 24 hour post transfection at 4% O2, radiation exposure, replate cells for another 24 hours and then collect gDNA


title: IMR32_29_siCtrl_PHOX2B_24h


title: Gastrocnemius, Control, rep1


title: IMR32_28_siCtrl_HAND2_24h

value: HAND2 (Abcam ab204000)


title: Xray_10Gy_Physioxia_4%O2_Rep1

tag: target locus

value: RAG1 (spCas9:RAG1B gRNA)

tag: extract_protocol (dna fragmentation)

value: Sonication

tag: illumina sequencing

value: Illumina MiSeq System; 250PE


title: FLASH-RT_10Gy_Physioxia_4%O2_Rep1

tag: cell line

value: FLASH-RT

value: LINAC; Lausanne

tag: figure displaying results for this library

tag: number of raw reads used for normalization


title: Heart, MCK-RIP140KO, rep3

source_name: Striated muscle RIP140 KO - MCK-RIP140KO in Heart

tag: tissue

value: Heart

value: Nrip1 f/f Cre+


title: IMR32_3_siCtrl_H3K4me3_72h

tag: cell type

value: Neuroblastoma

tag: chip antibody


title: Heart, MCK-RIP140KO, rep1

tag: genotype


title: IMR32_26_siHAND2_24h_Input_72h

value: none (input)


title: Control_NoRT_Physioxia_4%O2_Rep2

value: WT

tag: nuclease delivery

tag: transfection protocol

value: NoRT

value: Trypsinize cells 24 hour post transfection at 4% O2, NO radiation exposure, replate cells for another 24 hours and then collect gDNA

value: Fig 3

tag: pipeline used for the analysis

value: JoinT-seq


title: Heart, MCK-RIP140KO, rep2


title: IMR32_25_siCtrl_24h_Input_72h

tag: genotype/variation

value: siCtrl


title: IMR32_13_siGATA3_GATA3_ab_72h

value: GATA3 (Abcam, ab199428)


title: Heart, Control, rep3

source_name: Striated muscle RIP140 KO - Control in Heart

value: Nrip1 f/f Cre-


title: Control_NoRT_Physioxia_4%O2_Rep1

value: FuGENE; 48 hour culture post transfection

tag: oxygen tension (o2)

value: 4% O2; Physioxia

tag: radiation treatment (rt) type

tag: dose

value: RAG1 (spCas9:RAG1B gRNA)


title: IMR32_12_siPHOX2B_GATA3_ab_72h


title: IMR32_11_siCtrl_GATA3_ab_72h


title: Heart, Control, rep2


title: Cardiomyocytes, Nkx2.5-RIP140KO, IgG, rep3

description: Cardiac-specific RIP140 KO - KO - IgG

data_processing:
Reads were aligned to the GRCm38 reference genome with bowtie2 v2.4.2 using command line parameters: -N 1
Duplicate reads were removed with samtools rmdup
Further processing was performed with Homer v4.11.1 Tag directories were created with Homer's makeTagDirectory
H3K27ac-enriched regions were called for each biological replicate separately with Homer's findPeaks, against the IgG background, using parameters: -style histone
Reliable H3K27ac-high regions were identified as those where enrichment was detected in at least 2 out of 3 replicates, using Homer's mergePeaks
Assembly: mm10
Supplementary files format and content: BED file with H3K27ac-rich DNA regions
Library strategy: CUT&RUN

source_name: Heart

extract_protocol:
Adult cardiomyocytes were isolated from 10-12-week old mice by Langendorff perfusion. Cardiomyocyte fraction was enriched by low-speed centrifugation at 50g for 5 min.  H3K27ac Cut&Run was performed in cardiomyocytes as previously described . 200,000 cardiomyocytes are used for each Cut&Run experiment. H3K27ac (Cell Signaling Technology #8173) or Rabbit IgG (Cell Signaling Technology #3900) at 1:100 was incubated with cardiomyocytes which were attached to Concanavalin A coated magnetics beads (Bangs Laboratories #BP531) overnight at 4⸰C. 2.5 ul of pA-MNase from 1:10 dilution of the original stock provided by Henikoff lab was applied to cell-beads mixture and incubated at room temperature for 10min. Pull-down DNA was extracted in phase-lock tubes using phenol-chloroform method.
DNA library was prepared using Hyper-prep kit (KAPA Biosystems KK8502) and submitted to Next-Generation Sequencing Core in University of Pennsylvania for sequencing. 40bp X 40bp paired-end sequencing was adopted.

value: Cardiomyocytes

tag: cut&run antibody

value: IgG


title: IMR32_43_siGATA3_Input_3_72h


title: IMR32_42_siPHOX2B_Input_3_72h


title: Cardiomyocytes, Nkx2.5-RIP140KO, IgG, rep2

description: Cardiac-specific RIP140 KO - KO - IgG

value: Heart


title: Genomic DNA from Skeletal Muscle Biopsy_204963470136_R07C01_Participant 9_ED-LF_30mins

type: genomic

city: Oslo

first: Adam

middle: P

last: Sharples

address: 220 Sognsveien

country: Norway

institute: Norwegian School of Sport Sciences

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using Infinium Methylation NXT setting

data_processing:
Following MethylationEPIC BeadChip arrays, raw .IDAT files were processed using Partek Genomics Suite V.7 (Partek Inc. Missouri, USA) and annotated using the MethylationEPIC_v-1-0_B4 manifest file. The mean detection p-value for all samples was 0.0002, which was well below the recommended 0.01 (6). The difference between the average median methylated and average median unmethylated signal was 0.08, well below the recommended difference of less than 0.5 (6). Upon import of the data we filtered out probes located in known single nucleotide polymorphisms (SNPs) and any known cross-reactive probes using previously defined SNP and cross-reactive probe lists from EPIC BeadChip 850K validation studies (7). Although the average detection p-value for each sample across all probes was very low (on average 0.0002), we also excluded any individual probes with a detection p-value that was above 0.01 as recommended previously (6). Out of a total of 865,860 probes in the EPIC array, removal of known SNPs, cross-reactive probes, those with a detection p-value above 0.01 resulted in 809,832 probes being taken forward for downstream analysis. Following this, background normalisation was performed via functional normalisation (with noob background correction) as previously described (8). After functional normalisation, we also undertook quality control procedures via principal component analysis (PCA). One sample in the EB-HF trial was removed due to a larger variation than that expected within that condition (variation defined as values above 2.2 standard deviations for that condition). Following normalisation and quality control procedures, we undertook differentially methylated position (DMP) analysis by converting β-values to M-values (M-value = log2(β / (1 - β)), as M-values show distributions that are more statistically valid for the differential analysis of methylation levels (9). We then performed a two-way ANOVA for condition (high-fat, energy balance/EB-HF and low-fat energy deficit/ED-LF) and time (baseline, 30 minutes, 3.5 hrs) with planned contrast/pairwise comparisons of: EB-HF baseline vs. ED-LF baseline, EB-HF 30 min vs. ED-LF 30 min, EB-HF 3.5 hrs vs. ED-LF 3.5 hrs. For initial discovery of CpG sites that were deemed statistically significant, DMPs with an unadjusted P value of ≤ 0.01 were accepted for downstream analysis (Kyoto Encyclopedia of Genes and Genomes/KEGG pathway, Gene Ontology/GO and differentially methylated region/DMR analysis - see below). We then undertook CpG enrichment analysis on these DMPs within GO terms and KEGG pathways (10-12) using Partek Genomics Suite and Partek Pathway software at the significance level of FDR ≤ 0.05. Differentially methylated region (DMR) analysis was performed to identify where several CpGs were differentially methylated within a short chromosomal locations/regions, undertaken using the Bioconductor package DMRcate (DOI: 10.18129/B9.bioc.DMRcate). Finally, to plot and visualise temporal changes in methylation across the post-exercise period (baseline, 30 min and 3.5 hr) within each condition (EB-HF and ED-LF) we implemented Self Organising Map (SOM) profiling of the change in mean methylation within each condition using Partek Genomics Suite.
Data is normalised via functional normalisation (with noob background correction)

label: biotin

source_name: DNA from Vastus Lateralis Muscle_204963470136_R07C01_Participant 9_ED-LF_30mins

label_protocol: Labels (Beadchip Barcode_Beadchip position_Participant_Condition_Timepoint)

extract_protocol: Muscle samples were homogenized for 45 seconds at 6,000 rpm × 3 (5 min on ice in-between intervals) in lysis buffer (180 µl buffer ATL with 20 µl proteinase K) provided in the DNeasy spin column kit (Qiagen, UK) using a Roche Magnalyser instrument and homogenization tubes containing ceramic beads (Roche, UK). The DNA was then isolated using the DNeasy spin column kit (Qiagen, UK)  bisulfite converted using the EZ DNA Methylation Kit (Zymo Research, CA, United States) as per the manufacturer’s instructions.

treatment_protocol:
Dietary interventions : Diet was controlled and standardised for both interventions for the 24 hrs before visiting the laboratory. Specifically, the diets were pre-packaged and provided 40 kcal/kg FFM/day containing 1.2, 6.0 and 1.35 g/kg FFM/day of fat, CHO, and protein, respectively. Immediately after the exercise in the evening of Day 1, participants consumed one of two low-CHO diets: either a high-fat, energy balance diet (EB-HF), which provided 30 kcal/kg FFM, completely replacing the energy expended during exercise and was composed of 2.5 g/kg FFM (73% energy) fat, 1.2 g/kg FFM (16% energy) CHO and 0.84 g/kg FFM (11% Energy) protein, or a low-fat, energy deficit (ED-LF) diet which provided 9 kcal/kg FFM, partially replacing the energy expended during exercise and was composed of 0.1 g/kg FFM (10% energy) fat, 1.2 g/kg FFM (53% energy) CHO and 0.84 g/kg FFM (37% energy) protein. On day 2, both groups ingested a recovery drink 30 min after the morning exercise containing: 1.2 g/kg FFM CHO and 0.38 g/kg FFM of protein, as this nutrient composition is common practice for athletes to maximise training adaptation (3). Diets were designed to provide the same amount of CHO and protein while providing divergent amounts of energy (deficit and balance), with the energy difference depending solely on the difference in exogenous fat consumption.
Biopsies : Muscle biopsies were taken from the vastus lateralis using a 6 mm Bergström needle modified for manual suction, following local anaesthesia (1% lidocaine, AstraZeneca, Cambridge, UK). Muscle biopsies were taken on day 2 at rest immediately before the start of exercise (baseline), and at 30 mins and 3.5 h after the exercise bout. From the 9 subjects completing the study, we identified a random subpopulation of 4 participants biopsies from each condition and each time point to analyse genome-wide DNA methylation (detailed methods below). Based on the genes identified to possess alterations in DNA methylation, we then validated those changes with gene expression of the same genes across the entire cohort of 9 participants (see ´RNA isolation, primer design & gene expression analysis´ methods section below). This helped to determine whether the identified changes at the genome-wide DNA methylation level in the subpopulation were associated with changes in gene expression of the entire cohort. Baseline characteristics of subpopulation for DNA methylome analysis were: VO2max: 70 ± 5 ml/kg/min, height: 185 ± 6 cm, body mass: 77 ± 6 kg, body fat: 14 ± 4%.

tag: gender

value: Male

value: Skeletal Muscle - Vastus Lateralis

tag: subject

value: Participant 9

tag: treatment group

value: ED-LF

tag: timepoint


title: Genomic DNA from Skeletal Muscle Biopsy_204963470136_R05C01_Participant 9_EB-HF_3.5hrs

source_name: DNA from Vastus Lateralis Muscle_204963470136_R05C01_Participant 9_EB-HF_3.5hrs

value: EB-HF


title: Genomic DNA from Skeletal Muscle Biopsy_204963470136_R06C01_Participant 9_ED-LF_Baseline

source_name: DNA from Vastus Lateralis Muscle_204963470136_R06C01_Participant 9_ED-LF_Baseline

value: Baseline


title: Genomic DNA from Skeletal Muscle Biopsy_204963470136_R04C01_Participant 9_EB-HF_30mins

source_name: DNA from Vastus Lateralis Muscle_204963470136_R04C01_Participant 9_EB-HF_30mins


title: Genomic DNA from Skeletal Muscle Biopsy_204963470136_R03C01_Participant 9_EB-HF_Baseline

source_name: DNA from Vastus Lateralis Muscle_204963470136_R03C01_Participant 9_EB-HF_Baseline


title: Control_NoRT_Physioxia_4%O2_Rep3

tag: cell line

value: WT

value: NoRT

tag: radiation facility

tag: treatment protocol

value: Trypsinize cells 24 hour post transfection at 4% O2, NO radiation exposure, replate cells for another 24 hours and then collect gDNA

tag: target locus

tag: extract_protocol (dna fragmentation)

value: Sonication

tag: illumina sequencing

value: Illumina MiSeq System; 250PE

tag: figure displaying results for this library

value: Fig 3

tag: number of raw reads used for normalization


title: IMR32_27_siCtrl_MYCN_24h

tag: cell type

value: Neuroblastoma

tag: genotype/variation

value: siCtrl

tag: chip antibody

value: MYCN (Active motif,  61185)


title: IMR32_41_siCtrl_Input_3_72h

value: none (input)


title: Cardiomyocytes, Nkx2.5-RIP140KO, H3K27ac, rep3

description: Cardiac-specific RIP140 KO - KO - H3K27ac

tag: tissue

value: Heart

value: Cardiomyocytes

tag: genotype

value: Nrip1 f/f Cre+


title: IMR32_35_siGATA3_PHOX2B_3_72h

value: PHOX2B (santa cruze, sc-376997 X)


title: Genomic DNA from Skeletal Muscle Biopsy_204963470136_R08C01_Participant 9_ED-LF_3.5hrs

source_name: DNA from Vastus Lateralis Muscle_204963470136_R08C01_Participant 9_ED-LF_3.5hrs

tag: gender

value: Male

value: Skeletal Muscle - Vastus Lateralis

value: Participant 9

value: ED-LF


title: IMR32_34_siGATA3_HAND2_3_72h

value: HAND2 (Abcam ab204000)


title: Heart, Control, rep1

value: Nrip1 f/f Cre-


title: Genomic DNA from Skeletal Muscle Biopsy_204963470136_R02C01_Participant 7_ED-LF_3.5hrs

source_name: DNA from Vastus Lateralis Muscle_204963470136_R02C01_Participant 7_ED-LF_3.5hrs

tag: subject

value: Participant 7


title: Cardiomyocytes, Nkx2.5-RIP140KO, H3K27ac, rep2

tag: cut&run antibody


title: IMR32_33_siGATA3_MYCN_3_72h


title: Genomic DNA from Skeletal Muscle Biopsy_204963470136_R01C01_Participant 7_ED-LF_30mins

source_name: DNA from Vastus Lateralis Muscle_204963470136_R01C01_Participant 7_ED-LF_30mins

tag: treatment group

tag: timepoint


title: Genomic DNA from Skeletal Muscle Biopsy_204963470085_R06C01_Participant 6_ED-LF_3.5hrs

source_name: DNA from Vastus Lateralis Muscle_204963470085_R06C01_Participant 6_ED-LF_3.5hrs

value: Participant 6


title: Genomic DNA from Skeletal Muscle Biopsy_204963470085_R05C01_Participant 6_ED-LF_Baseline

source_name: DNA from Vastus Lateralis Muscle_204963470085_R05C01_Participant 6_ED-LF_Baseline

value: Baseline


title: Cardiomyocytes, Control, IgG, rep3

description: Cardiac-specific RIP140 KO - Control - IgG

value: IgG


title: IMR32_30_siPHOX2B_HAND2_3_72h

tag: cell line

value: Neuroblastoma


title: Cardiomyocytes, Nkx2.5-RIP140KO, IgG, rep1

description: Cardiac-specific RIP140 KO - KO - IgG


title: Genomic DNA from Skeletal Muscle Biopsy_204963470041_R08C01_Participant 7_ED-LF_Baseline

source_name: DNA from Vastus Lateralis Muscle_204963470041_R08C01_Participant 7_ED-LF_Baseline


title: IMR32_31_siPHOX2B_PHOX2B_3_72h


title: IMR32_29_siPHOX2B_MYCN_3_72h

value: MYCN (Active motif,  61185)


title: Cardiomyocytes, Control, IgG, rep2


title: IMR32_27_siCtrl_PHOX2B_3_72h

value: siCtrl


title: Cardiomyocytes, Control, H3K27ac, rep3

description: Cardiac-specific RIP140 KO - Control - H3K27ac

value: Heart


title: IMR32_26_siCtrl_HAND2_3_72h


title: Genomic DNA from Skeletal Muscle Biopsy_204963470041_R05C01_Participant 7_EB-HF_Baseline

source_name: DNA from Vastus Lateralis Muscle_204963470041_R05C01_Participant 7_EB-HF_Baseline

value: EB-HF


title: Cardiomyocytes, Control, H3K27ac, rep1

value: Cardiomyocytes


title: Gastrocnemius, MCK-RIP140KO, rep2

source_name: Striated muscle RIP140 KO - MCK-RIP140KO in Gastrocnemius

value: Gastrocnemius

value: Nrip1 f/f Cre+


title: Genomic DNA from Skeletal Muscle Biopsy_204963470041_R07C01_Participant 7_EB-HF_3.5hrs

source_name: DNA from Vastus Lateralis Muscle_204963470041_R07C01_Participant 7_EB-HF_3.5hrs

value: Male

value: Skeletal Muscle - Vastus Lateralis


title: Cardiomyocytes, Control, H3K27ac, rep2


title: Genomic DNA from Skeletal Muscle Biopsy_204963470041_R03C01_Participant 6_ED-LF_30mins

source_name: DNA from Vastus Lateralis Muscle_204963470041_R03C01_Participant 6_ED-LF_30mins

value: ED-LF


title: Genomic DNA from Skeletal Muscle Biopsy_204963470041_R01C01_Participant 6_EB-HF_3.5hrs

source_name: DNA from Vastus Lateralis Muscle_204963470041_R01C01_Participant 6_EB-HF_3.5hrs


title: Cardiomyocytes, Control, IgG, rep1

source_name: Heart


title: IMR32_25_siCtrl_MYCN_3_72h


title: VLDL_4

city: Amsterdam

first: Esther

last: Lutgens

address: Meibergdreef 15

department: Medical Biochemistry

country: Netherlands

institute: Amsterdam UMC, location AMC

data_processing:
Bases were called using Illumina CASAVA 1.8.2
Reads were aligned to the mouse genome mm10 by STAR 2.5.2b
BAM files were indexed and filitered on MAPQ > 15 with SAM Tools 1.3.1
Raw tag counts per gene were counted using HOMER2's analyzeRepeats.pl script
Genome_build: mm10
Supplementary_files_format_and_content: matrix of raw reads

source_name: Spleen

growth_protocol: Single cell suspensions were prepared by meshing spleens through a 70um cell strainer and after erythrocyte lysis, CD4+ T cells were isolated using CD4 microbeads (Miltenyi) and cultured in in RPMI 1640 Medium with HEPES (Thermo Fisher Scientific) supplemented with 10% FCS (Gibco), Pen/Strep (Gibco), 50 μM 2-Mercaptoethanol (Sigma) and 20 ng/ml IL-2 (R&D systems)

extract_protocol:
Cells were lysed in RLT buffer and total RNA was isolated using the RNeasy mini kit with on-column DNase treatment (Qiagen)
RNA seq libraries were generated using the KAPA mRNA Hyperprep kit protocol

treatment_protocol: Cells were activated by adding anti-CD3/CD28 beads (Thermo Fisher Scientific) in a 1:1 cell to bead ratio and exposed to either 5 μg/ml LDL (STEMCELL Technologies) or 5 μg/ml VLDL (Sigma) and left to divide for 72 hours before medium and beads were removed.

tag: strain

value: Ldlr-/-

value: CD4+ T cell

tag: stimulus

value: VLDL


title: IMR32_7_siMYCN_HAND2_72h

value: siMYCN

value: HAND2 (Abcam ab204000)


title: Genomic DNA from Skeletal Muscle Biopsy_204963470032_R08C01_Participant 6_EB-HF_30mins

source_name: DNA from Vastus Lateralis Muscle_204963470032_R08C01_Participant 6_EB-HF_30mins

value: Participant 6


title: Cardiomyocytes, Nkx2.5-RIP140KO, H3K27ac, rep1


title: Genomic DNA from Skeletal Muscle Biopsy_204963470032_R07C01_Participant 6_EB-HF_Baseline

source_name: DNA from Vastus Lateralis Muscle_204963470032_R07C01_Participant 6_EB-HF_Baseline

value: Baseline


title: VLDL_3


title: VLDL_1


title: Genomic DNA from Skeletal Muscle Biopsy_204963470032_R06C01_Participant 3_ED-LF_3.5hrs

source_name: DNA from Vastus Lateralis Muscle_204963470032_R06C01_Participant 3_ED-LF_3.5hrs

value: Participant 3


title: IMR32_4_siHAND2_PHOX2B_72h

value: Neuroblastoma

value: PHOX2B (santa cruze, sc-376997 X)


title: IMR32_2_siCtrl_GATA3_ab_72h

value: siCtrl

value: GATA3 (Abcam, ab199428)


title: IMR32_5_siHAND2_GATA3_ab_72h


title: Genomic DNA from Skeletal Muscle Biopsy_204963470032_R05C01_Participant 3_ED-LF_30mins

source_name: DNA from Vastus Lateralis Muscle_204963470032_R05C01_Participant 3_ED-LF_30mins


title: LDL_4

value: LDL


title: LDL_3


title: Genomic DNA from Skeletal Muscle Biopsy_204963470032_R04C01_Participant 3_ED-LF_Baseline

source_name: DNA from Vastus Lateralis Muscle_204963470032_R04C01_Participant 3_ED-LF_Baseline


title: LDL_2


title: IMR32_20_siMYCN+siHAND2_Input_72h

source_name: IMR32_Input DNA

value: none (input)


title: LDL_1


title: IMR32_18_siMYCN_Input_72h


title: Ctrl_4

value: untreated


title: Genomic DNA from Skeletal Muscle Biopsy_204963470032_R02C01_Participant 3_EB-HF_30mins

source_name: DNA from Vastus Lateralis Muscle_204963470032_R02C01_Participant 3_EB-HF_30mins

value: Male

value: Skeletal Muscle - Vastus Lateralis

value: EB-HF


title: Ctrl_3

value: Ldlr-/-

value: CD4+ T cell


title: Genomic DNA from Skeletal Muscle Biopsy_204963470032_R01C01_Participant 3_EB-HF_Baseline

source_name: DNA from Vastus Lateralis Muscle_204963470032_R01C01_Participant 3_EB-HF_Baseline


title: DS_6

extract_protocol:
Single cell suspensions were prepared by meshing spleens through a 70um cell strainer and after erythrocyte lysis, CD4+ T cells, defined as CD3+CD4+CD8-CD19-CD25-, were sorted from the cell suspension using a FACSAria II cell sorter (BD Biosciences). Sorted cells were lysed in RLT buffer and total RNA was isolated using the RNeasy mini kit with on-column DNase treatment (Qiagen)
RNA seq libraries were generated using the KAPA mRNA Hyperprep kit protocol

value: diet switch


title: IMR32_16_siMYCN+siHAND2_MYCN_72h

value: MYCN (Active motif,  61185)


title: DS_5


title: Genomic DNA from Skeletal Muscle Biopsy_204963470032_R03C01_Participant 3_EB-HF_3.5hrs

source_name: DNA from Vastus Lateralis Muscle_204963470032_R03C01_Participant 3_EB-HF_3.5hrs


title: DS_4


title: IMR32_15_siMYCN_MYCN_72h

value: siMYCN


title: IMR32_12_siHAND2_MYCN_72h


title: Ctrl_2


title: Ctrl_1


title: DS_3


title: IMR32_11_siCtrl_MYCN_72h


title: DS_2


title: Infected, 5°C, replicate 3

city: Paris

first: Hugo

last: Varet

address: 28 rue du Docteur Roux

country: France

institute: Institut Pasteur

data_processing:
The bioinformatic analysis was performed using the RNA-seq pipeline from Sequana.
Sequencing reads were cleaned of adapter and low-quality sequences using cutadapt version 2.6.
STAR version 2.7.3a was used for the alignment onto the reference genome (Myotis lucifugus 2.0 on Ensembl 99)
featureCounts version 2.0.0 was used to count the number of reads mapped on each gene.
Count data were analyzed using R version 3.6.1 and the Bioconductor package DESeq2 version 1.26.0.
Assembly: Myotis lucifugus 2.0 on Ensembl 99
Supplementary files format and content: Raw counts from featureCounts

organism: Myotis myotis

source_name: olfactory nerve-derived cell

extract_protocol:
After a total of 54h post-infection (hpi), the supernatants were collected and stored at −80◦C. The cells were lysed with 1 mL of TRIzol (ThermoFisher) and RNA was extracted using Direct-zol RNA Miniprep Kit (Zymo Research) according to the manufacturer’s instructions (including a DNAse I treatment), and eluted into 50 µL RNAse free water.
Strand-specific single-end cDNA libraries were prepared using TruSeq Stranded mRNA sample prep kit, Illumina according to the manufacturers’ instructions and sequenced using Illumina NextSeq 500 sequencer.

value: olfactory nerve-derived cell

tag: temperature

tag: infection


title: IMR32_1_siCtrl_PHOX2B_72h


title: DS_1


title: Infected, 37°C, replicate 3


title: Infected, 5°C, replicate 1


title: HCD_6

value: high cholesterol diet


title: Infected, 37°C, replicate 2


title: E8.5_DKO_hic_rep1

city: Beijing

first: Yaxi

address: 5 Yiheyuan Road

description: Hi-C library with U1U2-DKO E8.5 mouse heart

data_processing:
Library strategy: Hi-C
HiCExplorer (v.3.4.2) was used for the pre-processing of Hi-C  sequencing data with default parameters.
During the pre-processing, read pairs which were not uniquely mapped were filtered out (MAPQ < 10). Dangling end reads, same fragment reads, selfcircled reads, self-ligated reads and other invalid Hi-C reads were also discarded.
Valid reads were used to generate raw Hi-C matrix at 5kb,10 kb, 20 kb resolution using Python package cooler (v.0.8.5)
After filtering low-count bins, the matrices were corrected by the KR using hicCorrectMatrix (v.3.4.2) in HiCExplorer (14). Then the Hi-C libraries were normalized in the way that the total read count of each matrix is equal to the read count of the matrix with the smallest read count of all input matrices by using hicNormalize (v.3.4.2) in HiCExplorer suite with parameters “--normalize smallest”.
Loops were identified by hicDetectLoops tools with Hi-C matrices at 10 kb resolution.
Genome_build: mm10
Supplementary_files_format_and_content: The processes files were cool files.

source_name: E8.5 heart

growth_protocol: All animal were fed according to protocols (protocol #, Lsc-HeAB-1) approved by the Institutional Animal Care and Use Committees of Peking University.

extract_protocol:
The hearts of E8.5 mouse embryo were isolated and fixed with 1% formaldehyde for 10 min at RT, then used for Hi-C.
The Hi-C fragments were amplified with Extaq (Takara), followed by size selection with AMPure XP beads (0.48 X + 1 X).

treatment_protocol: The hearts were fixed with 1% formaldehyde for 10 min at RT after being taken out.

value: E8.5 heart

value: embryonic heart cells

tag: treatment

value: PFA fixed


title: E8.5_DKO_hic_rep2


title: HCD_4


title: E8.5_WT_hic_rep1

description: Hi-C library with WT E8.5 mouse heart

value: WT


title: Infected, 5°C, replicate 2


title: Not infected, 5°C, replicate 3

value: No


title: E8.5_WT_hic_rep2

description: Hi-C library with WT E8.5 mouse heart


title: HCD_3


title: Infected, 37°C, replicate 1


title: HCD_2


title: Not infected, 5°C, replicate 2


title: Not infected, 5°C, replicate 1


title: HCD_1


title: NCD_6

value: normal cholesterol diet


title: WT_arabinan_4h_2

city: Tianjin

first: Jingen

last: Li

address: Xiqi Dao 32, Tianjin Airport Economic Area

institute: Tianjin institute of industrial biotechnology,Chinses Academy of Sciences

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with NGSQCToolkit (v2.3).
Clear reads were mapped to Myceliophthora thermophila ATCC 42464 genome using Tophat (version 2.0.8b) with parameters -i 10 -g 1 --segment-length 24 --b2-very-sensitive --no-convert-bam --library-type fr-unstranded.
The counts of reads uniquely mapped to only one gene for each gene were calculated by HTseq-count(version 0.13.5).
Assembly: Myceliophthora thermophila ATCC 42464(https://genome.jgi.doe.gov/Spoth2/Spoth2.home.html)
Supplementary files format and content: tab-delimited text files including Reads count for each sample.

organism: Thermothelomyces thermophilus

source_name: Mycelium

growth_protocol: Precultured mycelium from M. thermophila WT strain (ATCC42464) were shifted into 1×Vogel’s salt with 2% D-glucose, 2% D-xylose, 2% L-arabinose, arabinan, or no carbon for the induciton of additional 4 h.

extract_protocol:
Mycelia were harvested by vacuum filtration with Whatman filter paper, frozen immediately in liquid nitrogen. Total RNA from frozen samples was isolated using TRIzol reagent and an additional clean-up was performed for DNA degradation using the RNeasy mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Mycelium

value: fungal cell


title: MtAra-1_arabinan_4h_1

growth_protocol: Precultured mycelium from M. thermophila strain ΔMtara-1 were shifted into 1×Vogel’s salt with  2% D-xylose, 2% L-arabinose, or 2% arabinan for the induciton of additional 4 h.


title: WT_arabinan_4h_1


title: MtAra-1_arabinan_4h_2


title: Lung fibroblasts (Fbs) Wildtype (WT)

type: RNA

city: Munich

first: Maximilian

last: Fischer

address: Marchioninistr. 15

country: Germany

institute: LMU University

description: m Lung

hyb_protocol: Panel was hybridized to both Mouse 430 and MG-U74v2 arrays; Mouse 430 array results are presented here.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were processed with the Exon Array Computational Tool (ExACT) (Affymetrix) for background correction and normalization. Data analysis and statistical evaluations were performed Affymetrix.

source_name: C57Bl/6N lung

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

extract_protocol: RNA was isolated from tissue and cells with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

tag: disease state

value: healthy

tag: Sex

value: male

tag: age

value: 6 months old

value: lung

value: Lung fibroblasts


title: MtAra-1_xylose_4h_2

tag: cell type


title: NCD_5

value: Ldlr-/-

value: CD4+ T cell


title: Not infected, 37°C, replicate 2

value: olfactory nerve-derived cell


title: HCD_5

value: high cholesterol diet


title: NCD_4


title: Not infected, 37°C, replicate 3


title: MtAra-1_xylose_4h_1

tag: tissue


title: mouse failing cardiac fibroblasts (mF CFb), beta1-adrenergic transgenic mice

description:
mF CF
beta1-adrenergic transgenic mice (see PMID: 11562432)

source_name: beta1-adrenergic transgenic mouse heart

value: beta1-adrenergic transgenic

value: heart failure

value: heart

value: failing cardiac fibroblasts


title: NCD_2


title: MtAra-1_arabinose_4h_2

tag: genotype


title: mouse non-failing cardiac fibroblasts (mNF CFb)

description: mNF CF

source_name: C57Bl/6N heart

value: non-failing cardiac fibroblasts


title: LA, ULO, rep3

city: San Michele all'Adige

first: Fabrizio

last: Costa

state: N/A = Not Applicable

address: Via Mach 1

department: Center Agriculture Food Environment

country: Italy

institute: University of Trento

data_processing:
RNASeq data were aligned on the Malus domestica genome using the new Tuxedo protocol. Alignment was carried out with HiSAT2, while read counting analysis was performed with StringTie. For the analysis fo the genes differentially expressed was used DEseq2.
Assembly: ASM211411v1
Supplementary files format and content: Excel file with FPKM values for each Sample/Replicate

organism: Malus domestica

source_name: apple skin

extract_protocol:
RNA extraction was performed, for each of the three biological replicates with the Spectrum Plant total RNA kit (Sigma-Aldrich Co., St. Luis, MO, USA). RNA was quantified using a NanoDrop ND-8000 spectrophotometer (Thermo Scientific, Waltham, MA, USA), while its purity and integrity was assessed with a 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA).
For each replicate/sample, 3 mg of RNA was used for the construction of a non-directional Illumina RNA-seq library, using TrySeq RNA sample preparation kits, v2 (Illumina, San Diego, CA, USA). Libraries were quantified using quantitative PCR and quality control was performed with the DNA 1000 series II chip bioanalyzer (Agilent, Santa Clara, CA, USA). Sequencing of libraries was performed with an Illumina HiSeq 1000 Sequencer using TruSeq SBS v3-HS kit (100 cycles) and TruSeq SR Cluster v3-cBot-HS kits (Illumina, San Diego, CA, USA) generating 100-bp reads.

treatment_protocol: 1-MCP is a treatment with 1-methylcyclopropene operated on harvest fruit overnight in a sealed container according to the manufacturer instruction (AgroFresh). Low oxygen storage has been carried out lowering down the concentration of oxygen at 1%

value: apple skin

value: apples stored at low oxygen

tag: cultivar

value: cv. Ladina


title: Yeast spt8 deletion

city: Fukui-city

first: Takahito

last: Ayano

state: Fukui

address: 3-9-1, Bunkyo

department: Graduate school engineering

country: Japan

institute: University of Fukui

hyb_protocol: Following fragmentation, 7.5 μg of aRNA were hybridized for 16 hr at 45ºC on GeneChip Yeast Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing:
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.
affymetrix-algorithm-name = ExpressionStat
affymetrix-algorithm-version = 5.0
program-name = Expression Console
program-id = 1.1.2800.19935

organism: Saccharomyces cerevisiae

source_name: spt8 deleted yeast strain

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 200ng total RNA (GeneChip®  3’ IVT Express Kit user Manual, 2010, Affymetrix).

growth_protocol: Yeast cells were grown in 5ml YPD until exponential phase (optimal density of 0.7).

extract_protocol: Total RNA was extracted by acid phenol-chloroform extraction.

treatment_protocol: Deletion strains were constructed by homologous recombination utilizing a KanMX gene.

value: spt8 deletion

tag: strain background


title: Yeast BY4742

source_name: Wild type yeast strain

value: Wild type


title: Yeast spt3 deletion

source_name: spt3 deleted yeast strain

value: spt3 deletion


title: heart WT (left ventricle)

description: mHeart

value: healthy

value: male

value: 6 months old

value: left ventricle


title: NCD_1

source_name: Spleen

value: Ldlr-/-

value: CD4+ T cell

value: normal cholesterol diet


title: LA, ULO, rep2


title: MtAra-1_arabinose_4h_1

value: Mycelium

value: fungal cell


title: mouse cardiomyocyte (CM) wildtype (WT)

description: mCM

value: heart

value: cardiomyocyte


title: MtLat-1_arabinan_4d_2

growth_protocol: When grown on 2% arabinan, the cultures of strains WT and ΔMtlat-1 were collected after the cultivation of 2 d and 4 d.


title: LA, 1-MCP, rep3

value: apple skin

value: apples treated with 1-MCP


title: MtLat-1_arabinan_4d_1


title: LDHB KO-TH17 5%O2_5

city: columbus

first: Ruoning

last: Wang

state: OH

address: 700 Children's Drive

institute: Nationwide children's hospital

data_processing:
Total stranded RNA sequencing data were processed by  the internal AutoMapper pipeline.First the raw reads were firs trimmed (Trim-Galore version 0.60),  mapped to human genome assembly (hg19) (STAR v2.7).
The gene level expression values were quantified (RSEM v1.31) based on GENCODE annotation (v19) .
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: T cell

growth_protocol: The naïve CD4 T cells were polarization under TH17 condition for 3 days

extract_protocol:
Total RNA was isolated according to the RNeasy Mini Kit (Qiagen) and treated with DNase I.
RNA libraries were prepared for sequencing using standard Illumina protocols at the Nationwide Children's hospital.

treatment_protocol: no treatment

value: T cell

value: 9 weeks

value: LDHB KO


title: LDHB KO-TH17 5%O2_6

value: 10 weeks


title: LA, ULO, rep1

value: apples stored at low oxygen

value: cv. Ladina


title: Not infected, 37°C, replicate 1

value: olfactory nerve-derived cell

value: No


title: Donor 10: Human_Vdelta2 T cells

city: Washington

first: Natalia

last: Soriano-Sarabia

state: DC

address: 2300 I St. NW

department: Microbiology Immunology and tropical Medicine

institute: George Washington University

hyb_protocol: The Cy3- labeled cDNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Human Genome Oligo Microarrays 4 x 44K using Agilent’s recommended hybridization chamber and oven. Finally, the microarrays were washed once with 6x SSPE buffer containing 0.005% N-lauroylsarcosine for 1 min at room temperature followed by a second wash with pre-heated 0.06x SSPE buffer (37 °C) containing 0.005% N-lauroylsarcosine for 1 min.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies). The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files.

data_processing:
For determination of differential gene expression FES derived output data files were further analyzed using the Rosetta Resolverâ gene expression data analysis system (Rosetta Biosoftware).
Ratios were calculated by dividing sample signal intensity through control signal intensity (automated data output of the Resolverâ system).

source_name: Human FACS-sorted

label_protocol: 250 ng of each of the cDNAs were used as template for Cy3 labeling which was performed according to Miltenyi Biotec’s undisclosed protocol.

growth_protocol: Ex vivo FACS-sorted Vdelta1 and Vdelta2 T cells from isolated peripheral blood mononuclear cells

extract_protocol: RNA was isolated using Trizol, and quality control on total isolated RNA was performed using the Agilent 2100 Bioanalyzer expert software that allows for visual control and generation of an RNA integrity Number (RIN) for integrity and overall quality of the samples

treatment_protocol: Cells were stained with a cocktail of monoclonal antibodies

value: Isolated cells from PBMCs

tag: self-reported sex

value: Healthy-female


title: LA, 1-MCP, rep2


title: MtLat-1_arabinan_2d_1


title: MtLat-1_arabinan_2d_2


title: LA, 1-MCP, rep1


title: LDHB KO-TH17 5%O2_4

value: 8 weeks


title: LA, RA, rep3

value: control Regular Atmosphere


title: Donor 16: Human_Vdelta2 T cells

value: Healthy-male


title: Donor 16: Human_Vdelta1 T cells


title: WT-TH17 5%O2_2

value: Wild Type


title: LA, RA, rep2


title: WT_arabinan_4d_1

value: WT

value: Mycelium

value: fungal cell


title: Lagrue high night temperature (HNT)  R6 stage Replicate 1

city: Fayettiville

first: Julie

last: ThomaS

state: AR

address: 115 Maple Street

department: CSES

institute: University of arkansas

data_processing:
https://usegalaxy.org/- Trim sequences
Sequence reads were trimmed for adaptor sequence/low-quality sequence-The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
Trimmed sequence reads were mapped to rice reference genome sequence (MSU 7.0) with Tophat 2 used for alignment
Read count extraction and normalization were performed using  DESeq
Assembly: Oryza_sativa.IRGSP-1.0.24.dna.toplevel.fa
Assembly: Oryza_sativa.IRGSP-1.0.24.gtf

organism: Oryza sativa

source_name: seed, endosperm

growth_protocol: At 10 days after germination, equal-sized seedlings of each RIL and both parents (Cypress and Lagrue)  were transplanted in 3-gallon-plastic pots filled with a mixture of potting mix and field soil.The RILs and parents were then grown in the greenhouse until booting stage (R2). For greenhouse conditions, the temperature was set to 30 ± 1°C (86 ± 1°F) during the day and 22.2 ± 1°C (72 ± 1°F) at night71. The light was set to a light/dark 13/11-h cycle with maximum photo-synthetically active radiant (800-1,000 μmolPAR m-2 s-1) light and 60–65% relative humidity (RH) for the growth of the rice plants.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1ug of total RNA was used for the construction of sequencing libraries.
RNA was isolated from R6 stage caryopsis ( milky stage) treated to HNT and sequenced using Illumina High-Seq 2000 platform (Michigan State University Genomics core facility)

treatment_protocol: At booting stage (R2), three major panicles per plant were tagged in each 185 RILs and both parents. The plants with tagged panicles were then moved to the greenhouse with the HNT stress treatment that was maintained at a day/night temperature of 30°C (86°F)/28°C (82.4°F) for 10 h (20:00–6:00) while the control treatment was set at a day/night temperature of 30°C (86°F)/22.2°C (72°F) until harvest maturity (approximately 18–20% grain moisture content)

value: seed, endosperm

value: R6 caryopsis

value: Lagrue high night temperature (HNT)

value: High night temperature


title: WT-TH17 5%O2_1

value: T cell


title: WT_arabinan_4d_2


title: LA, RA, rep1

value: apple skin

value: cv. Ladina


title: WT_arabinan_2d_2


title: Lagrue control  R6 stage Replicate 2

value: Lagrue control

value: control


title: GS, ULO, rep3

value: apples stored at low oxygen

value: cv. Granny Smith


title: Donor 3: Human_Vdelta2 T cells

value: Isolated cells from PBMCs

value: Healthy-female


title: Lagrue control R6 stage Replicate 1


title: WT-TH17 5%O2_3

value: 8 weeks

value: Wild Type


title: Donor 7: Human_Vdelta2 T cells

value: Healthy-male


title: Donor 10: Human_Vdelta1 T cells


title: siSFV1-200 #2

city: Wuhan

first: Yang

last: Qiu

state: Hubei

address: No. 44 Xiaohongshan Central District, Wuchang District,

institute: Wuhan institue of virology, CAS

description: siEGFP1-200_siSFV1-200_expression_matrix.txt

data_processing:
Fo small RNAs, libraries of small RNAs were constructed using TruSeq Small RNA Library Preparation Kits (Illumina) according to manufacturer’s protocols, and then sequenced by Illumina HiSeq 2000 at Bioacme (Wuhan, China). Quality control and adapter trimming were performed using Trim Galore (v0.6.4) with default parameters, and reads length between 17 and 70 were used for subsequent analyses. The sequenced reads were mapped to the human genome (release hg19), mouse genome (release GRCm38), and mosquito genome (AaeGL5.0) by using Bowite 2.2.5, and the cellular miRNA expression level was determined on the basis of the number of reads, which were 100% identical to the annotated miRNA sequences in miRBase version 22 (https://www.mirbase.org/ftp/CURRENT/genomes/dme.gff3). The vsRNA reads that cannot be mapped to the host genome were then mapped to the viral genome allowing 2 nt mismatch. The vsRNA reads were counted and normalized by the number of total vsRNA reads (counts per million of total vsRNA reads) to show the size distribution and abundance of vsRNAs in different size, and 21-23 nt size vsRNA reads mapping to the viral genome were counted to show the distribution across the viral genome. The vsRNA Reads mapped to (+)-strand and (-)-strand of the viral genome were intersected using BedTools (v2.29.2).
For total RNAs, libraries of total RNAs were constructed using MGIEasy RNA Library Preparation Kits (BGI) according to manufacturer’s protocols, and then sequenced by MGISEQ2000 (BGI) at Wuhan Institute of Virology, CAS. Quality control and adapter trimming were performed using Trim Galore (v0.6.4) with default parameter. Then all reads were mapped to the human genome (release hg19) using Hisat2. DEseq2 (v1.34.0) was used to detect differentially expressed genes.
Assembly: Human genome (release hg19), mouse genome (release GRCm38), and mosquito genome (AaeGL5.0)
Supplementary files format and content: bam files generated by Bowite 2.2.5

source_name: Human  HEK293T cells

extract_protocol: TruSeq Small RNA Library Preparation Kits (Illumina) (for small RNAs); MGIEasy RNA Library Preparation Kits (BGI) (for total RNAs)

value: transfection of siRNA from dsSFV1-200 for 24 hours


title: GS, ULO, rep2


title: Donor 7: Human_Vdelta1 T cells


title: WT_arabinose_4h_2

value: WT

value: Mycelium

value: fungal cell


title: siSFV1-200 #1


title: Cypress high night temperature (HNT) R6 stage Replicate 2

value: seed, endosperm

value: R6 caryopsis

value: Cypress high night temperature (HNT)

value: High night temperature


title: Lagrue high night temperature (HNT) R6 stage  Replicate 2

value: Lagrue high night temperature (HNT)


title: GS, 1-MCP, rep3

value: apple skin

value: apples treated with 1-MCP


title: siEGFP1-200 #3

value: transfection of siRNA from dsEGFP1-200 for 24 hours


title: WT_arabinose_4h_1


title: Cypress high night temperature (HNT) R6 stage Replicate 1


title: GS, ULO, rep1

value: apples stored at low oxygen

value: cv. Granny Smith


title: WT_xylose_4h_2


title: siSFV1-200 #3


title: Cypress control R6 stage_Replicate 2

value: Cypress control

value: control


title: siEGFP1-200 #2


title: siEGFP1-200 #1


title: Cypress control R6 stage_Replicate 1


title: WT_arabinan_2d_1


title: GS, 1-MCP, rep1


title: SFV in NoDice_RNase L-KO #2

value: Semliki Forest virus

value: SFV4 strain (GenBank:KP699763.1)

tag: molecule subtype

value: small RNA


title: Donor 3: Human_Vdelta1 T cells

value: Isolated cells from PBMCs

value: Healthy-female


title: GS, RA, rep3

value: control Regular Atmosphere


title: WT_glucose_4h_2

value: WT

value: Mycelium

value: fungal cell


title: WT_glucose_4h_1


title: No.3: pitavastatin 0hr

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: HeLa cells

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: HeLa  cells were cultured in Eagle-MEM with heat-inactivated 10% FCS in a 24-well plate.

extract_protocol: Total RNA was extracted using TRIZOL reagents according to the manufacture's protocol.

treatment_protocol: 2µM of pitavastatin or control DMSO (0.1%) was subjectd to HeLa cells. 24 hr after treatment, HeLa cells were infected with/without Sendai virus for 24 hr .

value: HeLa

value: pitavastatin 0hr


title: WT_NoCarbon_4h_2


title: hepatocyte, lipid and itaconate treated, replicate C [12_hep_C_both]

status: Public on Mar 28 2023

city: Frederick

first: Ian

last: Bettencourt

address: 1050 Boyles Street Rm 31-16A

department: CIL

institute: NCI

data_processing:
Basecalling with RA 3.9.25
Demultiplexing with Bcl2Fastq v2.20
Filtering (adaptor and quality) with Cutadapt 1.18
Alignment with STAR 2.7.0f
RNA Statistics and Duplication Statistics with Picard 2.18.26
Quantification with RSEM 1.3.1
Assembly: mm10
Supplementary files format and content: tab-delimited text file with raw count values for each sample.  Gene names are structured as Ensembl ID and gene symbol separated by an underscore

source_name: liver

growth_protocol: Cultured hepatocytes were treated overnight in complete media (DMEM supplemented with 5% FBS, 1x insulin-transferrin-selenium (Thermo Fisher Scientific)

extract_protocol:
Total RNA was isolated from treated hepatocytes using a PureLink RNA Mini kit with on-column DNAse digestion (Invitrogen). All samples met quality control of RIN > 8.0 using a Bioanalyzer.
500ng total RNA was used via the stranded mRNA ligation kit (Illumina) as input to an mRNA capture, cDNA synthesis, and standard Illumina library prep prior to sequencing.

treatment_protocol: Cells were untreated, treated with 10mM sodium itaconate, a 1:10 dilution of sterile, chemicalyl defined lipid mixture 1 (2ug/mL arachidonic acid; 10ug/ml each linoleic, myristic, oleic, palmitic, and stearic acids; 0.22mg/mL cholesterol) (Sigma-Aldrich), or both itaconate and lipid

value: liver

value: hepatocyte

value: Wildtype

value: Lipid + Itaconate


title: WT_xylose_4h_1


title: SFV in NoDice_RNase L-KO #1


title: GS, RA, rep2

value: apple skin

value: cv. Granny Smith


title: hepatocyte, lipid and itaconate treated, replicate A [4_hep_A_both]


title: hepatocyte, untreated, replicate D [13_hep_D_UT]

value: Untreated


title: hepatocyte, itaconate treated, replicate C [11_hep_C_ITA]

value: Itaconate


title: GS, 1-MCP, rep2

value: apples treated with 1-MCP


title: hepatocyte, lipid treated, replicate B [6_hep_B_lipid]

value: Lipid


title: hepatocyte, itaconate treated, replicate B [7_hep_B_ITA]


title: GS, RA, rep1


title: hepatocyte, lipid treated, replicate D [14_hep_D_lipid]


title: hepatocyte, itaconate treated, replicate D [15_hep_D_ITA]


title: hepatocyte, lipid and itaconate treated, replicate D [16_hep_D_both]


title: hepatocyte, untreated, replicate B [5_hep_B_UT]

value: untreated


title: WT_NoCarbon_4h_1


title: hepatocyte, lipid and itaconate treated, replicate B [8_hep_B_both]


title: hepatocyte, untreated, replicate A [1_hep_A_UT]


title: hepatocyte, lipid treated, replicate A [2_hep_A_lipid]


title: hepatocyte, itaconate treated, replicate A [3_hep_A_ITA]


title: N25 fragments

city: Shenzhen

first: Qing

address: No 7,Pengfei Road,Dapeng District

institute: Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences,

description: PCR product

data_processing:
The raw data (raw reads) of fastq format are firstly trimmed by cutadapt (v1.16) to remove adaptor and homologous arm   sequences
Low quality reads are filtered by fastx-toolkit.Only the sequences which the number of bases with a minimum Phred-score quality score of 20 accounted for more than 50% of the total would be saved.
The sequences are processed through Fastuniq (https://sourceforge.net/projects/fastuniq/) to remove the duplicated sequences
The 25bp reads are picked out and aligned to reference genome using Bowtie2 with parameters -D 20 -R 3 -N 0 -L 17 -i S,1,0.50 --end-to-end. The unique mapping sequences which have no deletion and insertion compared with the reference are kept
Genome_build: hg19
Supplementary_files_format_and_content: text files include peak scores and annotation information of loci identified by MEA-seq

source_name: random DNA library

growth_protocol: Cell cultures are inoculated into 100 mm DMEM (ThermoFisher; Cat. No.10566024) containing 10% FBS (Gibco; Cat. No.10437028) and 1% Penicillin Streptomycin P/S (Sigma; Cat. No. P0781) at 37 ℃ cell incubator.

extract_protocol:
Transfection of plasmid libraries (4µg DNA/1x106
cells) is performed with cells at 70-80% confluence using HD Transfection Reagent (FuGENE; Cat. No. E2311). Fluorescence cells are then collected 24 hours after transfection.
DNA is extracted from the collected fluorescent cells and amplified for 7 cycles using primers containing reporter vector sequence (forward: TGCAGGTGCCAGAACATTTC, reverse: GTGGCTTTACCAACAGTACC). The amplified products are electrophoresed in 2% agarose gel for 35 min (120v,130mA) and recovered through gel recycling. The recovered product is subjected to 4 cycles of amplification using KAPA kit (KAPA, Cat. No. KK2620) and sent for high-throughput sequencing.
MAE-seq

value: HEK293T cell

tag: passages


title: No.1: DMSO 0hr

tag: cell line

value: DMSO 0hr


title: hepatocyte, untreated, replicate C [9_hep_C_UT]


title: No.2: DMSO 24hr+SeV

value: DMSO 24hr+SeV


title: hepatocyte, lipid treated, replicate C [10_hep_C_lipid]


title: Ifnar1 WT ID8 cells, untreated, replicate 2

city: Melbourne

first: Jamie

last: Gearing

address: 27-31 Wright St

country: Australia

institute: Hudson Institute of Medical Research

data_processing:
Base calling was perfromed using Dragen BCLConvert (v3.7.4).
RNA-seq read alignment and UMI counting was performed in R (v3.6.2). The scPipe package (v1.8.0) was employed to process and de-multiplex the data. A combined multiplexed FASTQ file was created from the R1 and R2 FASTQ files, by trimming the sample index and UMI sequences and storing them in the read header, using the sc_trim_barcode function (with bs2 = 0, bl2 = 8, us = 8, ul = 10).
Additionally, the original multiplexed R1 and R2 FASTQ files were de-multiplexed using cutadapt v3.0 (with error rate 1 and action none).
Read alignment was performed using the RSubread package (v2.0.0). An index was built using the mouse (GRCm38) Ensembl primary assembly genome files and alignment was performed with default settings.
Aligned reads were mapped to exons using the sc_exon_mapping function with the Ensembl Mus musculus GRCm38 v102 GFF3 genome annotation file. The resulting BAM file was de-multiplexed and reads mapping to exons were associated with each individual sample using the sc_demultiplex function, taking the UMI into account, and an overall count for each gene for each was sample was generated using the sc_gene_counting function (with UMI_cor = 1).
UMI gene counts were processed in R (v.4.1.2) using the edgeR package (v3.36.0). Lowly expressed genes were removed using the filterByExpr function and normalisation factors were calculated using the TMM method.
Differential gene expression analyses were performed using the limma package (v3.50.0), with the voom, lmFit, contrasts.fit, eBayes and treat functions.
Assembly: mm10
Supplementary files format and content: Matrix table with UMI gene counts for every gene and every sample.

source_name: ID8 WT

growth_protocol: Trp53 Brca2 double knockout ID8 murine ovarian cancer cells (Roby KF et al., Carcinogenesis 2000; Walten J et al., Cancer Research 2016) were cultured in RPMI 1640 (GibcoBRL, Ontario, Canada) supplemented with 4% heat-inactivated foetal calf serum (FCS; GibcoBRL).

extract_protocol:
RNA was extracted using a QIAGEN RNeasy mini-kit (QIAGEN, Germany)  as per the manufacturer’s protocol. Cells were harvested in RLT buffer and RNA was on-column DNase treated using the QIAGEN RNase-free DNase Set according to manufacturer’s instructions. RNA yield and quality were then assessed using a NanoDrop ND-1000 spectrophotometer and stored at −80°C.
Libraries were generated using an in-house multiplex RNA-seq method (MHTP, Medical Genomics Facility) and were prepared using 20 ng of total RNA input. An 8 bp sample index and a 10 bp unique molecular identifier (UMI) were added during initial poly(A) priming and pooled samples were amplified using a template switching oligonucleotide. The Illumina P5 and P7 sequences were added by PCR and Nextera transposase, respectively. The library was designed so that the forward read (R1) utilised a custom primer (5' GCC TGT CCG CGG AAG CAG TGG TAT CAA CGC AGA GTA C 3') to sequence directly into the index and then the 10 bp UMI. The reverse read (R2) used the standard R2 primer to sequence the cDNA in the sense direction for transcript identification. Paired-end sequencing (R1 19 bp; R2 101 bp) was performed on the NextSeq 2000 (Illumina), using a P2 100 cycle kit.

treatment_protocol: Cell lines were plated (50,000 cells/well) in a 24-well plate 24 hours prior to stimulation with recombinant murine IFN beta at 10,000 IU/ml. Cells were then incubated at 37°C for 3 hours prior to mRNA extraction.

value: ID8 WT

value: Ifnar1 WT

value: UT

tag: replicate


title: Ifnar1 WT ID8 cells, untreated, replicate 1


title: No.4: pitavastatin 24hr+SeV

value: HeLa

value: pitavastatin 24hr+SeV


title: Ifnar1 WT ID8 cells, IFNB, replicate 3

value: IFN


title: Ifnar1 WT ID8 cells, IFNB, replicate 2


title: Ifnar1 WT ID8 cells, empty vector, untreated, replicate 3

source_name: ID8 EV

value: ID8 EV


title: Ifnar1 WT ID8 cells, empty vector, untreated, replicate 2


title: Ifnar1 WT ID8 cells, untreated, replicate 3


title: Ifnar1 WT ID8 cells, IFNB, replicate 1


title: Ifnar1 WT ID8 cells, empty vector, IFNB, replicate 3


title: Ifnar1 WT ID8 cells, empty vector, IFNB, replicate 2


title: Ifnar1 WT ID8 cells, empty vector, IFNB, replicate 1


title: Ifnar1 KO ID8 cells, clone 1CF10, untreated, replicate 3

source_name: ID8 1CF10

value: ID8 1CF10

value: Ifnar1 KO


title: Ifnar1 KO ID8 cells, clone 2CD7, untreated, replicate 2

source_name: ID8 2CD7

value: ID8 2CD7


title: Ifnar1 KO ID8 cells, clone 1CF10, untreated, replicate 2


title: Ifnar1 KO ID8 cells, clone 2CD7, IFNB, replicate 2


title: Ifnar1 KO ID8 cells, clone 2CD7, untreated, replicate 1


title: Ifnar1 KO ID8 cells, clone 1CF10, untreated, replicate 1


title: Ifnar1 KO ID8 cells, clone 1CF10, IFNB, replicate 3


title: Ifnar1 KO ID8 cells, clone 1CF10, IFNB, replicate 1


title: Ifnar1 KO ID8 cells, clone 1CF10, IFNB, replicate 2


title: shEZH2_rep3

city: Los Angeles

first: Nikhil

middle: Baban

last: Ghate

address: 1450 Biggy st, Norris Research Tower

department: Biochemistry and Molecular Medicine

institute: University of Southern California

data_processing:
Sequenced RNA-seq reads were mapped to hg38 GENCODE version 29 using STAR 2.6.1d. Aligned reads were quantified at gene levels, and gene counts were normalized using the upper quartile normalization method. After principal components analysis with normalized gene counts, differentially expressed genes were selected by using the Gene Specific Algorithm from Partek® Flow® software (Partek Inc., MO, USA). We used a false discovery rate cut-off of 0.05 and absolute fold change > 1.5 to select statistically significantly differently expressed genes.
Genome_build: hg38 GENCODE version 29
Supplementary_files_format_and_content: Normalized counts in text format

source_name: EZH2-knocked down colon cancer cell line (SW620)

extract_protocol: RNA was prepared from SW620 cells using the Qiagen RNeasy kit (Qiagen Inc., CA, USA) according to the manufacturer’s instructions  Strand specific libraries were prepared using a KAPA Stranded mRNA-Seq Kit with KAPA mRNA Capture Beads (KAPA Biosystem Inc., MA, USA), and validated on an Agilent Bioanalyzer with the DNA1000 kit. Pooled libraries were prepared, denatured, diluted to 15 pM, and then clonally clustered onto the sequencing flow cell using the Illumina cBOT Cluster Generation Station and Cluster Kit v3-cBot-HS. The clustered flow cell was sequenced with 1X50 SE reads on the Illumina HiSeq2000 according to manufacturer’s protocol. Base conversion was made using OLB version 1.9, de-multiplexed, and converted to Fastq using CASAVA version 1.8 (Illumina, CA, USA).

treatment_protocol: DNA oligonucleotides encoding shRNAs speciﬁc for EZH2 (TATGATGGTTAACGGTGATCA) coding region were annealed and ligated into the lentiviral expression vector pLKO.1 (Addgene). Lentiviral particles were generated in 293T cells by transfecting plasmids encoding VSV-G, NL-BH, and the shRNA. Two days after transfection, the soups containing viruses were collected and used to infect SW620 colon cancer cells in the presence of polybrene (8 μg/ml). Cells with stable integration of shRNA constructs were selected for two weeks in the presence of puromycin (2 μg/ml). Cells were then allowed to grow in absence of puromycin for one week and harvested for further processing.


title: shEZH2_rep2


title: shEZH2_rep1


title: Ifnar1 WT ID8 cells, empty vector, untreated, replicate 1


title: Ifnar1 KO ID8 cells, clone 2CD7, untreated, replicate 3


title: Ifnar1 KO ID8 cells, clone 2CD7, IFNB, replicate 1


title: Ifnar1 KO ID8 cells, clone 2CD7, IFNB, replicate 3


title: PANC-1 cells, GW3965 treatment, bio rep 3

city: Houston

first: Chin-Yo

last: Lin

state: Texas

address: 3517 Cullen Blvd, SERC, Third Floor, Room 3018, SERC, Third Floor, Room 3018

institute: University of Houston

data_processing:
Paired-end FASTQ files were adapter and quality trimmed with Trim Galore v.0.4.4 (default parameters)
Trimmed sequence reads were mapped to indexes built with Homo_sapiens.GRCh38.dna.primary_assembly with HISAT2 v.2.0.2 (default parameters)
SAM files were sorted and converted to BAM format using SAMtools v.1.3 (default parameters)
Transcripts were assembled and quantified with Homo_sapiens.GRCh38.99.gtf using StringTie v.1.3.1c (default parameters)
Assembly: hg38
Supplementary files format and content: comma-delimited text file includes a gene count matrix of all samples

growth_protocol: BxPC-3 cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and MIA PaCa-2 and PANC-1 cells were maintained in DMEM (high glucose and HEPES) supplemented with 10% FBS in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared with QIAseq Stranded Total RNA library Kit (Qiagen)

treatment_protocol: 48 hr treatments of ligands at 10µM

value: PDAC

value: LXR agonist GW3965

tag: time

value: 48 hr


title: PANC-1 cells, 1E5 treatment, bio rep 2

value: LXR inverse agonist 1E5


title: PANC-1 cells, DMSO treatment, bio rep 1

value: Vehicle


title: PANC-1 cells, 3A4 treatment, bio rep 2

value: LXR inverse agonist 3A4


title: PANC-1 cells, GW3965 treatment, bio rep 1


title: PANC-1 cells, DMSO treatment, bio rep 2


title: PANC-1 cells, 1E5 treatment, bio rep 1


title: PANC-1 cells, 3A4 treatment, bio rep 3


title: PANC-1 cells, GW3965 treatment, bio rep 2


title: PANC-1 cells, 3A4 treatment, bio rep 1


title: MIA PaCa-2 cells, GW3965 treatment, bio rep 3

source_name: MIA PaCa-2

value: MIA PaCa-2


title: PANC-1 cells, 1E5 treatment, bio rep 3


title: PANC-1 cells, DMSO treatment, bio rep 3


title: Unstimulated vs IL-13 stimulated cells from donor #2

city: Tampere

first: Ilkka

last: Junttila

state: Tampere

address: Arvo Ylpön katu 34

department: Institute of Medical and Life Science

country: Finland

institute: University of Tampere

description: Biological replicate 2 of 3. Flipped labeling.

hyb_protocol: Standard Agilent protocol

scan_protocol: Agilent Technologies Scanner G2505C - 5 microns per pixel

data_processing: Agilent Feature extraction version GE2_105_Dec08

molecule: polyA RNA

source_name: neutrophils isolated from blood

label_protocol: Nugen Ovation V2, Nugen FL-Ovation cDNA Fluorescent Module

growth_protocol: Freshly isolated human neutrophils

extract_protocol: Qiagen RNAeasy (#74104) kit protocol

treatment_protocol: unstimulated or stimulated with 10ng/ml IL-13

tag: donor number

value: Donor 2

tag: stimulation type

tag: stimulation

value: Unstimulated


title: Unstimulated vs IL-13 stimulated cells from donor #1

description: Biological replicate 1 of 3. Flipped labeling.

value: Donor 1


title: IL-13 stimulated cells vs Unstimulated from donor #3

description: Biological replicate 3 of 3.

value: Donor 3


title: MIA PaCa-2 cells, DMSO treatment, bio rep 3

tag: treatment


title: IL-13 stimulated cells vs Unstimulated from donor #2

description: Biological replicate 2 of 3.


title: Unstimulated vs IL-13 stimulated cells from donor #3

description: Biological replicate 3 of 3. Flipped labeling.


title: IFNg stimulated cells vs Unstimulated from donor #3

description: Biological replicate 3 of 3.

treatment_protocol: unstimulated or stimulated with 10ng/ml IFNg

value: IFNg


title: Unstimulated vs IFNg stimulated cells from donor #1


title: MIA PaCa-2 cells, 1E5 treatment, bio rep 3


title: MIA PaCa-2 cells, GW3965 treatment, bio rep 2


title: IFNg stimulated cells vs Unstimulated from donor #2

description: Biological replicate 2 of 3.


title: MIA PaCa-2 cells, DMSO treatment, bio rep 2


title: MIA PaCa-2 cells, 3A4 treatment, bio rep 2


title: Unstimulated vs IFNg stimulated cells from donor #2


title: MIA PaCa-2 cells, GW3965 treatment, bio rep 1


title: MIA PaCa-2 cells, 3A4 treatment, bio rep 1


title: BxPC-3 cells, DMSO treatment, bio rep 3


title: MIA PaCa-2 cells, 1E5 treatment, bio rep 1


title: BxPC-3 cells, GW3965 treatment, bio rep 3


title: BxPC-3 cells, 1E5 treatment, bio rep 3


title: Unstimulated vs IFNg stimulated cells from donor #3


title: IL-13 stimulated cells vs Unstimulated from donor #1

description: Biological replicate 1 of 3.


title: BxPC-3 cells, GW3965 treatment, bio rep 2


title: BxPC-3 cells, 3A4 treatment, bio rep 3


title: MIA PaCa-2 cells, DMSO treatment, bio rep 1


title: BxPC-3 cells, DMSO treatment, bio rep 2


title: BxPC-3 cells, 3A4 treatment, bio rep 2


title: BxPC-3 cells, 1E5 treatment, bio rep 2


title: BxPC-3 cells, 3A4 treatment, bio rep 1


title: BxPC-3 cells, DMSO treatment, bio rep 1


title: IFNg stimulated cells vs Unstimulated from donor #1

description: Biological replicate 1 of 3.


title: BxPC-3 cells, 1E5 treatment, bio rep 1


title: MIA PaCa-2 cells, 3A4 treatment, bio rep 3


title: MIA PaCa-2 cells, 1E5 treatment, bio rep 2


title: aspirin treated 1

city: Newark

first: Pranela

last: Rameshwar

state: NJ

address: 185 South Orange Avenue

department: Medicine

institute: Rutgers NJ Medical School

description: patient 1

data_processing:
STAR 2.6.1 aligned to HG38.
Quantified to Ensembl human genome 92.
Normalized via Log2 Counts per million with offset of 1.
Log normal shrinkage was used to remove batch effect between runs.
Counts with a maximum of less than 2 were filtered out for a normal distribution.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: Excel files include RPKM values for each sample.

source_name: placenta-derived MSCs

growth_protocol: Primary MSC were isolated from the chorionic membrane of placentas and cultured in DMEM supplemented with 10% FCS and glutamine.

extract_protocol:
Total RNA was extracted from the cells according to manufacturer’s protocols with the RNeasy Mini Kit (Qiagen).
Libraries were prepared using the NEB Ultra II Library Preparation Kit and NEBNext® Multiplex Oligos for Illumina (Dual Index Primers Set 1) (New England BioLabs) following the manufacturer’s protocol.

treatment_protocol: Aspirin treated MSC were cultured with aspirin in normal culture media for 24 hrs.

tag: tissue source

value: placenta, chorionic membrane

value: placenta-derived MSCs

tag: passage

value: aspirin


title: aspirin treated 2

description: patient 2

tag: cell type


title: untreated

description: untreated

value: untreated


title: aspirin treated 3

description: patient 3


title: Control_8 iWAT

city: St Louis

first: Irfan

middle: J

last: Lodhi

state: MO

address: 660 S Euclid Ave Campus box 8127

institute: Washington University School of Medicine in St. Louis

data_processing:
All sequencing data were generated by the Washington University Genome Technology Access Center (GTAC)
Reads were Aligned to m_musculus reference build Ensembl_R76 with STAR v2.0.4b
Gene counts were obtained using the Subread featureCount probram (v1.4.5)
differential expression analysis was performed from gene-level counts using edgeR
Assembly: m_musculus reference build Ensembl_R76
Supplementary files format and content: Gene level CPM normalized counts matrix (all.gene_counts.csv)

source_name: inguinal white adipose tissue (iWAT)

growth_protocol: Male control or PexRAP-AKO mice were fed chow diet for 8 weeks prior to tissue harvesting for RNAseq

extract_protocol:
RNA was harvested using RNeasy Lipid Tissue Mini Kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared following manufacturer (Illumina) protocols.

tag: tissue

value: inguinal white adipose tissue (iWAT)

tag: Sex

value: male

value: Control

value: 8 weeks old male mice fed chow diet


title: Control_7 iWAT

tag: genotype


title: PexRAP-AKO_5 iWAT

value: PexRAP-AKO


title: Control_2 iWAT


title: PexRAP-AKO_1 iWAT


title: PexRAP-AKO_6 iWAT


title: Liver-T4

city: Shanghai

first: Cenxi

last: Liu

address: Songhu Road 2005

institute: Fudan University

description: liver, low BCAA

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for  low-quality sequence, then mapped to mm10 whole genome using Hisat2
Stringtie was used to quantify
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Total RNA was extracted from tissues by using TRIzol reagent (Invitrogen). Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

value: low BCAA


title: Liver-T6

description: liver, low BCAA


title: Liver-T3

description: liver, low BCAA


title: Liver-T5

description: liver, low BCAA


title: BxPC-3 cells, GW3965 treatment, bio rep 1

value: PDAC

value: LXR agonist GW3965

value: 48 hr


title: Liver-T2

description: liver, low BCAA


title: Liver-C4

description: liver, control

value: control


title: Liver-C5

description: liver, control


title: Liver-C3

description: liver, control


title: Liver-C6

description: liver, control


title: Liver-C2

description: liver, control


title: Liver-C1

description: liver, control


title: Control_5 iWAT


title: Control_3 iWAT


title: PexRAP-AKO_3 iWAT


title: PexRAP-AKO_2 iWAT


title: M_o_34

city: nanjing

first: Xiangyu

last: Ma

state: JIANGSU

address: No. 2, Sipai Building, Dashiqiao Community, Xinjiekou Street, Xuanwu District, Nanjing

institute: Southeast University

description:
M_o_34
This sample represents a single cell.

data_processing:
Sample quality and yield were determined with a Bioanalyzer (Agilent). The DNA was sequenced from the 43 bp-end with both i5 and i7 indices (6 bp each) using an Illumina HiSeq 2500. And then, raw reads were filtered with Trimmomatic software and aligned to the GRCm38 mm10 assembly reference genome with hisat2 . Reads mapped to the mouse transcriptome were counted using the featureCounts program in the Subread package (v 1.4.6).
Genome_build: mm10

source_name: cochlea

extract_protocol:
Sample quality and yield were determined with a Bioanalyzer (Agilent). The DNA was sequenced from the 43 bp-end with both i5 and i7 indices (6 bp each) using an Illumina HiSeq 2500
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cochlea

tag: region

value: outer hair cells/middle

tag: age


title: M_o_32

description:
M_o_32
This sample represents a single cell.


title: M_o_40

description:
M_o_40
This sample represents a single cell.


title: M_o_39

description:
M_o_39
This sample represents a single cell.


title: M_o_35

description:
M_o_35
This sample represents a single cell.


title: M_o_37

description:
M_o_37
This sample represents a single cell.


title: M_o_28

description:
M_o_28
This sample represents a single cell.


title: M_o_36

description:
M_o_36
This sample represents a single cell.


title: M_o_38

description:
M_o_38
This sample represents a single cell.


title: M_o_30

description:
M_o_30
This sample represents a single cell.


title: Liver-T1

description: liver, low BCAA


title: M_o_23

description:
M_o_23
This sample represents a single cell.


title: M_o_107

description:
M_o_107
This sample represents a single cell.


title: M_o_29

description:
M_o_29
This sample represents a single cell.


title: M_o_108

description:
M_o_108
This sample represents a single cell.


title: M_o_27

description:
M_o_27
This sample represents a single cell.


title: M_o_24

description:
M_o_24
This sample represents a single cell.


title: M_o_105

description:
M_o_105
This sample represents a single cell.


title: aspirin treated 4

description: patient 4

value: placenta, chorionic membrane


title: M_o_31

description:
M_o_31
This sample represents a single cell.


title: M_o_106

description:
M_o_106
This sample represents a single cell.


title: M_o_25

description:
M_o_25
This sample represents a single cell.


title: M_o_104

description:
M_o_104
This sample represents a single cell.


title: M_o_102

description:
M_o_102
This sample represents a single cell.


title: M_o_101

description:
M_o_101
This sample represents a single cell.


title: M_i_55

description:
M_i_55
This sample represents a single cell.

value: inner hair cells/middle


title: M_i_56

description:
M_i_56
This sample represents a single cell.


title: M_i_52

description:
M_i_52
This sample represents a single cell.


title: M_i_54

description:
M_i_54
This sample represents a single cell.


title: M_i_45

description:
M_i_45
This sample represents a single cell.


title: M_i_53

description:
M_i_53
This sample represents a single cell.


title: M_i_44

description:
M_i_44
This sample represents a single cell.


title: M_i_50

description:
M_i_50
This sample represents a single cell.


title: M_i_43

description:
M_i_43
This sample represents a single cell.


title: M_i_51

description:
M_i_51
This sample represents a single cell.


title: M_i_42

description:
M_i_42
This sample represents a single cell.


title: M_i_41

description:
M_i_41
This sample represents a single cell.


title: M_i_40

description:
M_i_40
This sample represents a single cell.


title: Cap_9

city: Yantai

first: Xicheng

last: Song

address: No.20, Yuhuangding East Road, Zhifu District, Yantai City, Shandong Province

department: Department of Otorhinolaryngology, Head and Neck Surgery

institute: Qingdao University Affiliated Yantai Yuhuangding Hospital

data_processing:
The sequenced data are called raw reads. first, we filter out the rRNA, low quality, junctional contamination and high content of unknown base N reads, and the filtered data are called clean reads. then the clean reads are compared to the reference genome and transcriptome respectively. In this project, we used UW's self-developed filtering software SOAPnuke for filtering, HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts) software for genome comparison, and Bowtie2 to align the clean reads to the reference genes. Reference genome version: GCF_000001405.39_GRCh38.p13.
Supplementary files format and content: Processed data are formatted for Microsoft Excel (.xls extension). Files contain Transcript per Kilobase per Million mapped reads (TPM) reads of samples of interest.

source_name: Paraneoplastic tissue of laryngeal squamous cell carcinoma

extract_protocol: The extracted total RNA was first removed from the ribosomal rRNA using the MGIEasy rRNA removal kit. after purification, the RNA was fragmented at a certain temperature and ionic environment. The cDNA first strand is then synthesized using random primers and reverse transcriptase from the MGIEasy RNA Directional Library Preparation Kit, followed by the synthesis of double-stranded cDNA using DNA polymerase I and RNaseH. During cDNA second-strand synthesis, the RNA template is removed and dTTP is replaced by dUTP. dUTP involvement prevents the cDNA second strand from being amplified in subsequent processes amplified in subsequent processes because the polymerase is unable to cross the dUTP site on the template during extension. The double-stranded cDNA product is then ligated with an "A" base and a splice. The ligated product is amplified, the PCR product is heat denatured to a single strand, and a bridge primer is used to loop the single stranded DNA to obtain a single stranded circular DNA library for sequencing.

value: Normal human epithelial tissue