title: Cas12a Base editor 20220912_T1_wheat

city: Ghent

first: Thomas

last: Jacobs

address: Technologiepark-Zwijnaarde, 71

country: Belgium

institute: VIB Center for Plant Systems Biology

data_processing:
Reads were demultiplexed using Je-demultiplex (Girardot et al., 2016) and individual .fastq files were obtained as previously described (Bollier et al., 2020) using a Galaxy workflow (https://usegalaxy.be).
Base editing was calculated using CRISPResso2Pooled or CRISPRessoBatch (Clement et al., 2019) with the following settings to define the editing window and read quality: --cleavage_offset -1 --quantification_window_size 10 --quantification_window_center -12 --min_average_read_quality 30. Indels were calculated using CRISPResso2Pooled or CRISPRessoBatch with the following settings to define Cas12a cutting site and read quality: --cleavage_offset -4 --min_average_read_quality 30.
Spreadsheet generated from CRISPResso2 outputs and results from same experiments combined for analysis

organism: Triticum aestivum

source_name: Wheat leaf mesophyll

growth_protocol: Wheat seeds (Fielder) were processed by successive washes with sterilized water for 3 min, isopropanol for 45 sec, sterile water for 3 min and 6% sodium hypochlorite (Chem-lab nv) for 10 min. Sterilized seeds were washed six times with sterile water in a laminar flow cabinet and sown on sterile growth media containing 1/2 MS pH 5.7 (Duchefa Biochemie, , M0221.0050), 2.5 mM MES (Duchefa Biochemie, M1503.0100) and 0.5% plant tissue agar (NEOGEN , NCM0250A). Two seeds were sown per sterile, 175 ml cylindrical container (Greiner Bio-one, # 960162) and stratified for 3 days at 4°C in the dark. Plants were grown under SpectraluxPlus NL 36 W/ 840 Plus (Radium Lampenwerk) fluorescent bulbs under long days (16h light/8h dark) at 25°C.   B104 maize seeds were sown directly on Jiffy substrate (Jiffy Products International, No. 32170138). Seed germination was performed in long day (16h light/8h dark) conditions at 25°C, 55% relative humidity for 5 days under light provided by of high-pressure sodium vapor (RNP-T/LR/400W/S/230/E40; Radium) and metal halide lamps with quartz burners (HRI-BT/400W/D230/E40; Radium). Seedlings were transferred to the dark for 8 days prior to protoplast isolation.

extract_protocol:
For genotyping individual wheat transformed plants, DNA was isolated according to Edwards method (Edwards et al., 1991). A piece of leaf (0.5-1 cm), harvested in 1 ml tubes on 96-well plate (VWR, 732-3716) and flash frozen in liquid nitrogen. Two metal beads (3 mm) were added and tissue was ground to powder by shaking the plate at 20 Hz for 1 minute (Retsch, Mixer Mill MM 400). 400 µl of extraction buffer (100 mM Tris-HCl pH 8.0, 500 mM NaCl, 50 mM EDTA, 0.7% SDS) was added to individual samples and incubated 30 min at 60°C. Samples were centrifuged and 300 µl of the supernatant was mixed to 300 µl of isopropanol for DNA precipitation. Samples were then centrifuged and supernatant removed. The pellet was washed with 70% Ethanol,dried at room temperature, anddissolved in 100 µl of 10 mM Tris-HCl pH=8.0.  For sorted material, 2 μl of the solution containing sorted cells was used as template in a 20 µl total reaction volume for amplicon PCR using the Phire Plant Direct PCR Kit (Thermo Fisher Scientific, F160L) according to manufacturer’s recommendations.  For nCas9-BE, base editing efficiencies were measured by Sanger sequencing. 500-700 bp amplicons were designed to amplify target sites (Supplementary tables 2-3). 5 µl of the Phire PCR reaction was verified on a 1% agarose gel (Ultra-Pure agarose, Invitrogen, # 16500-500), with a 1kb bench top ladder (Promega, G754A). 15 µl was purified using 1.8× HighPrep™ PCR beads (MAGBIO Genomics, AC-60500), eluted in 35 μl 10mM Tris-HCl pH 8.0 and sent for Sanger sequencing (Eurofins, Mix2Seq). Chromatograms were processed using EditR to obtain base editing efficiencies (Kluesner et al., 2018). Statistical tests were conducted with GraphPad Prism 9.0.0 or VassarStats online tool (http://vassarstats.net/).    For dCas12-BE and nuclease-active LbCas12a, base editing and indel efficiencies were measured using NGS. 210-260 bp amplicons were designed to amplify target sites. 6-nt indices (Faircloth and Glenn, 2012) were added to forward and reverse primers for pooling and demultiplexing amplicon reads after sequencing (Supplemental table 2). 5 µl of the Phire PCR reaction was verified on a 2% agarose gel with a low molecular weight ladder (NEB, no. N3233S). 15 µl of PCR products were pooled and purified using PCR Purification Kit (Zymo Research Co., D4013). Depending on the amplicon, an extra gel purification was conducted (Zymo Research, D4002) to specifically isolate PCR band of the target site. The DNA concentration was measured with Qubit (Invitrogen) according to manufacturer’s protocol and adjusted to 2 ng µl-1. Paired end sequencing was performed with Eurofins NGSelect amplicons (5M reads 2x150bp). Reads were demultiplexed using Je-demultiplex (Girardot et al., 2016) and individual .fastq files were obtained as previously described (Bollier et al., 2020) using a Galaxy workflow (https://usegalaxy.be). Demultiplexing statistics can be found in Supplemental data 2.
Library was generated at Eurofins Genomics using NGSelect Amplicon Adaptor Ligation for 5M reads 2x150bp.
Amplicon-seq

treatment_protocol: Wheat protoplast isolation was adapted from (Shan et al., 2014). Wheat leaves were harvested 7 or 8 days after germination (DAG). Approximately 40-50 second leaves were cut into latitudinal 0.5-1 mm strips with a sharp razor blade and leaf strips were  incubated in 0.6 M D-mannitol (Sigma-Aldrich, M1902) for 10 min in the dark. The mannitol was removed and 25 ml cell wall enzyme solution (20 mM MES, 1.5% cellulase R10 (C8001.0010), 0.75% macerozyme R10 (M8002.0010), 0.6 M D-mannitol and 10 mM KCl, 0.1% BSA and 10 mM CaCl2) was added to protoplasts for 8 hours incubation in the dark at 25°C with 40 rpm shaking After enzymatic digestion, 25 ml of W5 solution (2 mM MES pH 5.7, 154 mM NaCl, 125 mM CaCl2 0,5 mM KCl) was added to release the protoplasts. Protoplasts were collected by filtering the mixture through a sterile 40 µm cell strainer (Corning, #431750) and centrifugation at 80g (slow acceleration and brake) for 3 min at room temperature. The supernatant was discarded and protoplasts were resuspended in 6 ml W5 solution and incubated on ice for 30 min. Protoplast yield was determined using a Neubauer chamber before adding MMGTa solution (4 mM MES pH 5.7, 0.4 M mannitol, 15 mM MgCl2) onto the cell pellet to reach a concentration of 1 × 106 cells ml-1.   Protoplasts were then incubated on ice for ~30 min before transfection. 12 µg of total plasmid DNA was added to MMGTa to a total volume of 20 µl in 1 ml strip tubes (National Scientific Supply Co, TN0946-08B). 100 μl of protoplasts (105 cells) and 110 μl of PEG solution (0.2 M mannitol, 100 mM CaCl2, 40% PEG (Sigma 81240) were added using a multichannel pipette to DNA and immediately mixed by slowly inverting the strip. For individual strips, 8 transfections were processed in parallel. Protoplasts were incubated for 15–20 min and W5 solution was added to stop the transfection. After centrifugation at 80g (slow acceleration and brake) for 3 min, the supernatant was discarded and the protoplast pellet resuspended in 1 ml of W5 solution. Cells were then transferred in 24-well plates (VWR 734-2325 EU catalog) and incubated in the dark at 25°C for 42 to 46 hours.   Maize protoplast isolation was adapted from (Cao et al., 2014; Yoo et al., 2007). Etiolated maize leaves were harvested at 12 or 13 DAG. The middle part of the second or third leaf was cut into 0.5mm strips. Strips were then infiltrated with 25 ml cell wall enzyme solution (0.6 M D-mannitol, 10 mM MES, 1.5% cellulose, 0.3% Macerozyme R10, 0.1% BSA and 1 mM CaCl2) using vacuum (50 mmMg) for 30 minutes in the dark and then incubated for 2 hours at 25°C with shaking (40rpm). The solution containing the protoplasts was filtered using a sterile 40 µm cell strainer (Corning) and collected by centrifugation at 100g (slow acceleration and brake) for 3 min. The supernatant was removed and protoplasts were washed with ice-cold 0.6 M D-mannitol by centrifugation at 100g (slow acceleration and brake) for 2 min. Cells were then resuspended in 5 ml of 0.6 M D-mannitol and incubated in the dark for 30 min. Protoplasts were resuspended in MMGZm solution (0.6 M mannitol, 15 mM MgCl2, 4 mM MES) and counted using a Neubauher chamber and adjusted to a concentration of 1 × 106 cells ml-1.   20 µg of total plasmid DNA was added to MMGZm to a total volume of 20 µl in 1 ml strip tubes. 100 μl of protoplasts (105 cells) and 110 μl of PEG (0.2 M mannitol, 100 mM CaCl2, 40% PEG (Sigma 81240) solution were added using a multichannel pipette to DNA and immediately mixed by inverting the strip. For individual strips, 8 transfections were processed in parallel. Cells were then incubated for 10–15 min in the dark and W5 solution was added to stop the transfection. After centrifugation at 100g (slow acceleration and brake) for 2 min, supernatant was discarded and the protoplast pellet resuspended in 1 ml of W5 solution. Cells were then transferred in 24-well plates (VWR) and incubated in the dark at 25°C with shaking (20 rpm) for 2 days. Two days after transfection, 500 μl of protoplast solution was used for sorting. Gating strategies for GFP were first established on cells expressing pZmUBI-GFP-NLS (p02243) and similar settings were used for all experiments in wheat and maize. The post-FACS fraction was imaged using the imaging system integrated in the FACS instrument. For both wheat and maize, a 130 μm nozzle was used and 1,000 to 5,000 cells were sorted into 1.5 ml Eppendorf tubes containing 10 μl of dilution buffer from the Phire Tissue Direct PCR Master Mix kit (Thermo Fisher Scientific, F160L).

value: Protoplasts

tag: cultivar

value: Fielder


title: ANFX2070

status: Public on Nov 21 2022

type: SRA

city: Ljubljana

first: Ales

last: Maver

address: Slajmerjeva 3

country: Slovenia

institute: Clinical institute of medical genetics Ljubljana Slovenia

library_source: transcriptomic

data_processing:
Demultiplexing and adaptor trimming was performed using the Illumina BCL2Fastq software
Alignments to the human reference genome (hg19) were performed  using bowtie and tophat algorithms
Transcript abundances were then estimated using read counts function in Subread package for R, followed by intersample normalization by variance modelling at the observational level (voom) approach implemented in limma Bioconductor package.
Differences in gene expression were estimated using linear modelling and significance estimation procedures in limma.
Assembly: hg19, mm10

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral blood

extract_protocol:
Whole blood samples were collected into Tempus™ Blood RNA tubes (Thermo Fisher Scientific, Waltham, MA, USA) or PAXgene blood tubes (Qiagen, Hilden, Germany) containing RNA stabilizing reagent. Total RNA was isolated using QuickGene blood cell kit (RB-S) and Fujifilm QuickGene-810 automated system (Fujifilm Life Sciences, Tokyo, Japan) or PAXgene Blood miRNA Kit and fully automated QIAcube system (Qiagen), according to manufacturer’s isolation protocol. The purity of isolated RNA was assessed using the NanoDrop 2000c spectrophotometer (Thermo Fisher Scientific) and integrity was determined on Agilent 2100 Bioan+alyzer using RNA 6000 Nano LabChip kit (Agilent Technologies, Santa Clara, CA, USA). All samples used for library preparation had RNA integrity values greater than 7.0. Extracted RNA samples were stored at -80ºC before further processing.
We performed library preparation using the TrueSeq stranded total RNA sample preparation kit (Illumina, San Diego, CA, USA), according to the manufacturer’s protocol. After Ribo-Zero rRNA depletion, the remaining RNA was purified, fragmented, and primed for first strand cDNA synthesis with reverse transcriptase (SuperScript II) and random primers, followed by second strand cDNA synthesis performed in the presence of dUTP. Blunt ended double strand DNA was 3’ adenylated and multiple indexing adapters (T-tailed) were ligated to the ends of the ds cDNA. Fragments with adapter molecules on both ends were selectively enriched with 15 cycles of PCR reaction. 44 libraries were normalized to the final concentration of 10 nM and then pooled in equimolar concentrations. Sequencing was performed on the Illumina Hiseq 2000 sequencing system in 2×100 sequencing cycles using pair-end sequencing mode.

tag: tissue

value: Peripheral blood

tag: anaphylaxis stage/severity

tag: individual


title: Cas12a Base editor  20220121_4_CG434_2

description: Cas12a Base editor

library_source: genomic

molecule: genomic DNA

tag: cell type


title: p35S-GFP-ZHD4; protoplast prep #2

city: Wuhan

first: Junpeng

last: Zhan

state: Hubei

address: 1 Shizishan Street, Hongshan District

country: China

institute: Huazhong Agricultural University

data_processing:
RNA-seq reads were mapped to the maize reference genomeusing Hisat v2.1.0. Reads mapped to each gene/locus were counted using the featureCounts program of the Subread package (v1.6.3). Read counts were normalized using edgeR v3.20.9.
Assembly: B73 RefGen_v3
Supplementary files format and content: tab-delimited text file including RPKM values

molecule: polyA RNA

organism: Zea mays

source_name: leaf protoplasts

growth_protocol: Seeds of the B73 maize were germinated and grown in constant darkness at 25oC and 50–70% humidity. Leaves were collected from more than 10 etiolated seedlings 10 to 12 days after germination for each protoplast isolation.

extract_protocol:
RNA was extracted using the TRI reagent (Sigma-Aldrich).
RNA-seq libraries were made using the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs) following the manufacturer’s protocol for use with the NEBNext Poly(A) mRNA magnetic isolation module.

value: leaf protoplasts

tag: genotype

tag: tf


title: iPSC-EC2_72_Carfilzomib

city: Palo Alto

first: Yu

last: Liu

state: CA

address: 1215 Welch Road

department: CVI

country: USA

institute: Stanford University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by TrimGalore
Trimmed data was mapped to hg38 whole genome using STAR
Assembly: hg38
Supplementary files format and content: Raw read counts from featureCounts

source_name: Endothelial cells

extract_protocol:
miRNeasy Micro Kit  (Qiagen)
Library construted by Novogene
bulk RNA-seq

value: iPSC-derived endothelial cells

tag: cell line

tag: treatment

value: Carfilzomib (0.025 uM)

tag: time

value: 72 hours


title: iPSC-EC2_72_Chloroquine

value: Chloroquine (1 uM)


title: ANFX2450


title: iPSC-EC2_72_Lapatinib

value: Lapatinib (1 uM)


title: iPSC-EC2_72_Bortezomib

value: Bortezomib (0.002 uM)


title: ANFX2100


title: ANFX2180


title: Cas12a Base editor  20220121_3_CG392_2

description: Cas12a Base editor


title: CUTRUN_State2_Klf4_BR3

city: Cambridge

first: Sofia

last: Hu

email: sofiahu@mit.edu, xsu@cpdr.org

state: MA

address: 500 Main Street

institute: MIT

description: CUT&RUN for Klf4 in State 2

data_processing:
CUT&RUN reads were trimmed using cutadapt (v1.16) (-m 10 -q 10). Paired-end reads were aligned to the mm10 reference genome and the E.coli MG1655 using bowtie2 with default parameters. The normalization factor for each replicate was calculated as 1/((unique E.coli reads⁄unique mouse reads)× 100%). Normalized bigWig files were generated for each replicate using the bamCoverage function in the deeptools package by inputting the normalization factor as the --scaleFactor parameter. Replicates were further normalized to IgG negative control using the bigwigCompare function with the parameter --operation log.
Assembly: mm10
Supplementary files format and content: CUT&RUN: bigWig format
Library strategy: CUT&RUN

organism: Mus musculus

source_name: State2, Klf4

growth_protocol: V6.5 mouse embryonic stem cells (mESC) were cultured on tissue culture-treated 10cm plates pre-coated with 0.2% gelatin in phosphate-buffered saline (PBS). ESC were cultured in Dulbecco’s Modified Eagle Medium (Fisher), plus 10% fetal bovine serum, 1x penicillin/streptomycin, 1x non-essential amino acids, 1x β-mercaptoethanol, and 1000 U ml-1 leukemia inhibitor factor. All cells were grown at 37C and 5% CO2 and passaged every two days to maintain 10-70% confluency.

extract_protocol: CUT&RUN was performed using CUTANA ChIC/CUT&Run Kit (Epicypher 14-1048) following manufacturer’s instruction in User Manual Version 2.1 or User Manual Version 3. Three technical replicates per antibody were performed. For sorted state populations, cells were harvested using versene, and 8x105 cells per replicate were isolated by flow cytometry. Harvested cells were permeabilized using 0.005% digitonin. Additionally, 1 ug of antibody per sample was added (Klf4 Abcam ab12947, Zfp281 Abcam ab10131), with Rabbit IgG antibody (CUTANA 13-0042) used as the negative control. E.coli spike-in DNA was also added to each sample.

value: embryonic stem cell line

tag: cut&run antibody

value: Klf4 (Abcam ab12947)

value: WT


title: iPSC-EC2_72_DMSO

value: DMSO


title: ANFX6300


title: iPSC-EC2_72_Aspirin

value: Aspirin (1 uM)

value: 24 hours


title: p35S-GFP-GBP15; protoplast prep #4


title: p35S-GFP-GBP15; protoplast prep #2


title: ANFX2020


title: iPSC-EC2_24_Sunitinib

value: Sunitinib (0.1 uM)


title: Cas12a Base editor  20220121_2_CG434_1

description: Cas12a Base editor

value: Protoplasts


title: p35S-GFP-EREB50; protoplast prep #4


title: ANFX2290


title: p35S-GFP-EREB50; protoplast prep #2


title: iPSC-EC2_24_Lapatinib


title: Cas12a Base editor  20220121_1_CG392_1

description: Cas12a Base editor

value: Fielder


title: iPSC-EC2_24_Doxorubicin

value: Doxorubicin (0.05 uM)


title: Cas12a Base editor  20211213_Library2

description: Cas12a Base editor


title: Cas12a Base editor  20211213_Library3

description: Cas12a Base editor


title: p35S-GFP-OFP9; protoplast prep #4

value: leaf protoplasts


title: ANFX1990

value: Peripheral blood


title: ANFX2030


title: p35S-GFP-OFP9; protoplast prep #2


title: iPSC-EC2_24_DMSO

value: iPSC-derived endothelial cells


title: Cas12a Base editor  20211213_Library1

description: Cas12a Base editor


title: iPSC-EC2_24_Cyclophosphamide

value: Cyclophosphamide (100 uM)


title: ANFX2060


title: iPSC-EC2_24_Chloroquine

value: Chloroquine (1 uM)


title: p35S-GFP-ABI5; protoplast prep #4


title: ANFX1960


title: p35S-GFP-ABI5; protoplast prep #2


title: iPSC-EC2_24_Carfilzomib

value: Carfilzomib (0.025 uM)


title: ANFX2270


title: Cas12a Base editor  20211025_multi_L3

description: Cas12a Base editor


title: p35S-GFP-bHLH97; protoplast prep #4


title: Cas12a Base editor  20211025_multi_L1

description: Cas12a Base editor


title: ANFX2010


title: Cas12a Base editor  20211025_multi_L2

description: Cas12a Base editor


title: iPSC-EC2_24_Bortezomib

value: Bortezomib (0.002 uM)


title: p35S-GFP-bHLH97; protoplast prep #2


title: iPSC-EC2_24_Aspirin


title: Negative control; p35S-GFP; protoplast prep #4

value: GFP


title: Cas12a Base editor  20211019_Cas12a_L3

description: Cas12a Base editor


title: ANFX2220


title: ANFX1950


title: iPSC-EC1_72_Sunitinib

value: 72 hours


title: Negative control; p35S-GFP; protoplast prep #2


title: iPSC-EC1_72_Lapatinib

value: Lapatinib (1 uM)


title: Cas12a Base editor  20211019_Cas12a_L1

description: Cas12a Base editor


title: Cas12a Base editor  20211018_Library3

description: Cas12a Base editor


title: ANFX1930


title: p35S-GFP-bHLH103; protoplast prep #3


title: ANFX2050


title: Cas12a Base editor  20211018_Library2

description: Cas12a Base editor


title: iPSC-EC1_72_dmso

value: DMSO


title: iPSC-EC1_72_Doxorubicin


title: ANFX2570


title: p35S-GFP-bHLH103; protoplast prep #1


title: Cas12a Base editor  20211018_Library1

description: Cas12a Base editor


title: p35S-GFP-DOF25; protoplast prep #3


title: iPSC-EC1_72_Cyclophosphamide


title: ANFX2532


title: iPSC-EC1_72_Chloroquine


title: Cas12a Base editor  NGS_20210824

description: Cas12a Base editor


title: p35S-GFP-HSF2; protoplast prep #3


title: Cas12a Base editor  20211019_Cas12a_L2

description: Cas12a Base editor


title: ANFX2580


title: iPSC-EC1_72_Carfilzomib


title: p35S-GFP-HSF2; protoplast prep #1


title: ANFX2470


title: iPSC-EC1_72_Bortezomib


title: Cas12a Base editor  NGS_4_31_05_21

description: Cas12a Base editor


title: Cas12a Base editor  NGS_3_31_05_21

description: Cas12a Base editor


title: iPSC-EC1_72_Aspirin

value: Aspirin (1 uM)


title: ANFX2390


title: p35S-GFP-NAC119; protoplast prep #1


title: p35S-GFP-NAC119; protoplast prep #3


title: Cas12a Base editor  NGS_2_31_05_21

description: Cas12a Base editor


title: ANFX2560


title: iPSC-EC1_24_Lapatinib

value: 24 hours


title: Cas12a Base editor  20211111_NGS_A3A

description: Cas12a Base editor

source_name: Maize leaf mesophyll


title: ANFX2460


title: Cas12a Base editor  20211028_Zm_Cas12a

description: Cas12a Base editor


title: p35S-GFP-ZIM13; protoplast prep #3


title: p35S-GFP-DOF25; protoplast prep #1


title: ANFX2520


title: ANFX2380


title: iPSC-EC1_24_Sunitinib

value: Sunitinib (0.1 uM)


title: iPSC-EC1_24_Doxorubicin


title: Cas12a Base editor  20211028_Zm_ABE

description: Cas12a Base editor

value: Protoplasts


title: p35S-GFP-CSD4; protoplast prep #3


title: ANFX2530


title: Cas12a Base editor  NGS_Maize_4

description: Cas12a Base editor


title: iPSC-EC1_24_DMSO


title: iPSC-EC1_24_Cyclophosphamide


title: ANFX2360


title: Cas12a Base editor  NGS_Maize_3

description: Cas12a Base editor


title: Cas12a Base editor  NGS_1_31_05_21

description: Cas12a Base editor

value: Fielder


title: p35S-GFP-EREB69; protoplast prep #4


title: iPSC-EC1_24_Chloroquine


title: ANFX2250


title: Cas12a Base editor  NGS_Maize_2

description: Cas12a Base editor


title: p35S-GFP-NAC29; protoplast prep #3


title: iPSC-EC1_24_Carfilzomib


title: Cas12a Base editor  NGS_Maize_1

description: Cas12a Base editor


title: p35S-ZFL2-GFP; protoplast prep #3


title: iPSC-EC1_24_Bortezomib


title: ANFX2272


title: ANFX2210


title: iPSC-EC1_24_Aspirin


title: p35S-ZFL2-GFP; protoplast prep #1


title: ONT_CpG_methyl_TTF_4

city: Quebec City

first: Samer

last: Hussein

state: Quebec

address: 9 rue Mcmahon

department: Departement of medecine

country: Canada

institute: CHU de Québec - Université Laval

data_processing:
Library strategy: Long-read DNA sequencing
For ChIP-seq, sequencing data were processed using the Illumina analysis pipeline
The quality of the sequence data was assessed using FastQC (Version 0.11.5).
Adaptors were trimmed using Trim Galore (Version 0.0.4).
FastQ format reads were aligned to the mm10 mouse reference using the Bowtie alignment algorithm. Bowtie version 2.1.0 was used with the pre-set sensitive parameter to align ChIP sequencing reads.
The MACS version 2.0.10 (model based analysis of ChIPseq) peak finding algorithm was used to identify regions of ChIP-Seq enrichment over background. Default parameters were used for H3K4me3, and broad peak parameters were used for H3K27me3 and H3K36me3 data.
Multicov command from Bedtools v2.17.0 was used to obtain raw read counts within each histone mark peak identified by MACS and input reads within these peaks. The number of reads per kilobase of peak per million reads (RPKM) was calculated for each peak and the corresponding input levels of that peak. The RPKM values for the histone mark peak were then subtracted by those of the input RPKM values to obtain a final and background-adjusted RPKM value, as modified from Hawkins et al. (https://doi.org/10.1016/j.stem.2010.03.018). Peak calls with background-adjusted RPKM values less than or equal to 0 were excluded from further analysis. The background adjusted RPKM values were averaged across -2 kb to +3 kb of a gene transcription start site (TSS), for downstream data analysis and visualization. Read densities and enrichment scores per locus, where defined, were normalized to the total number of million uniquely mapped reads producing values in units of reads per million mapped reads (RPM).
For long-read DNAseq, raw fast5 files were basecalled using the Guppy v.4.2.2 software, with the guppy_basecaller command and the dna_r9.4.1_450bps_modbases_dam-dcm-cpg_hac.cfg configuration file. GPU basecalling mode was employed with the following arguments: --num_callers 6 --gpu_runners_per_device 6 --chunks_per_runner 1000 --chunk_size 1000. Output fast5 files were generated with the --fast5_out argument.
The resulting FASTQ reads were concatenated and then indexed with Nanopolish version 0.13.2, using the nanopolish index command.
Reads were aligned to the mm10 mouse reference with Minimap2 version 2.17-r941 using the following parameters: -a -x map-ont.
BAM files were generated with SAMtools version 1.3.1.
CpG methylation was called using the call-methylation function of Nanopolish.
Methylation frequency for CpGs was analyzed using the calculate_methylation_frequency.py script from Nanopolish and fraction of methylated CpGs at gene TSS was calculated with a sliding window approach of 300 bp, sliding every 30 bp. Analysis was confined to -1 kb to +1 kb region of TSS as we found this to be the region frequently spanning hypomethylation for key genes in pluripotent stem cells.
To correct for sample-to-sample differences in CpG methylation percentages, values for fraction methylated CpGs were first subtracted to distribution means in each separate samples, and then averaged for two independent animal replicates.
Genome_build: mm10
Supplementary_files_format_and_content: DNAmethyl.CpG.TSS.table.txt
Supplementary_files_format_and_content: HistoneMarks_peak_gene.ids.rpkm.mean.txt

source_name: Induced pluripotent stem cells (iPSCs) derived from TTFs

extract_protocol:
For long-read DNA-seq, gDNA was extracted with Qiagen Genomic tip according to manufacturer's specifications.
gDNA was fragmented by sonication with a Bioruptor sonicator for 30 cycles of 5 seconds ON – 90 seconds OFF, using low intensity settings. gDNA was then purified with the Zymo DNA Clean & Concentrator™-5 columns (Zymo Research, D4013) and size selected with 0.4X volume of KAPA HyperPure Beads (ROCHE, 08963835001) to exclude small DNA fragments. 1 μg of sheared gDNA was used for library preparation using Ligation Sequencing Kits (Oxford Nanopore Technologies, LSK109 and LSK110) according to the manufacturer’s specifications. Samples were sequenced on a MinION sequencer on R9 Flow Cells (Oxford Nanopore Technologies FLO-MIN106D), using the MinKNOW software v19. Flowcells were washed and reloaded with the Flow Cell Wash Kit (Oxford Nanopore Technologies EXP-WSH003) to increase sequencing depth obtained per flowcell. Average read N50 for sequencing runs was 3 kilobases.

value: iPSCs


title: p35S-GFP-ZIM13; protoplast prep #1

value: leaf protoplasts


title: ANFX2510

value: Peripheral blood


title: UCHL1 overexpression-fibroblasts 4

city: Guangzhou

first: chipeng

last: guo

address: Yanjiang Road

institute: Sun Yat-sen Memorial Hospital

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
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
RSEM was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups was performed using the DESeq2 R package.

source_name: human skin

growth_protocol: Fibroblasts were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using TRIzol Reagent. 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 (CatalogE7530L, NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Lentivirus mixed with polybrene was added to the cell mediums according to the manufacturer’s instructions

value: human skin

value: primary fibroblasts

value: mesenchymal cell

value: UCHL1 overexpression-fibroblasts


title: p35S-GFP-CSD4; protoplast prep #1


title: p35S-GFP-TCP23; protoplast prep #1


title: ANFX2280


title: p35S-GFP-ZHD5; protoplast prep #3


title: UCHL1 overexpression-fibroblasts 2


title: ANFX2200


title: UCHL1 overexpression-fibroblasts 3


title: ANFX2440


title: p35S-GFP-NAC29; protoplast prep #1


title: ONT_CpG_methyl_PTC_11

source_name: Induced pluripotent stem cells (iPSCs) derived from PTCs


title: p35S-GFP-ZHD5; protoplast prep #1


title: UCHL1 overexpression-fibroblasts 1


title: ONT_CpG_methyl_TTF_1


title: ANFX1850


title: p35S-GFP-TCP23; protoplast prep #3


title: WGA_input

city: Taoyuang

first: Kou-Juey

last: Wu

state: Taiwan

address: No.15, Wenhua 1st Road, Gueishan Dist

department: Cancer Genome Research Center

country: Taiwan

institute: Chang Gung Memorial Hospital at Linkou

description:
N6mA_differential_compare1.txt.gz
N6mA_differential_compare2.txt.gz

data_processing:
Basecalls performed by Nextseq Control software.
Adpater sequence was trimmed by Trim galore.
Data was aligned to hg19 by bowtie2.
Aligned file was filtered by MAPQ > 20.
MACS2 was used by regular ChIP-seq peak calling.
For ChIP-exo-seq, after making genome windows, measure the abundance of 6mA signals. Comparing the different condition of 6mA signals by edgeR to identify the gain-of-6mA or loss-of-6mA region.
Assembly: hg19
Supplementary files format and content: bigwig file was produced by deeptools for signal visualization. After romiving PCR duplicates, transformed bam file into bed file for the measurement of 6mA signal abundance in each genome window. NarrowPeak region of HIF1 was called by MACS2.

source_name: FADU

growth_protocol: FADU cell were cultered in DMEM with 10% FBS, 1% antibiotic.

extract_protocol:
Genomic DNA was extracted by DNeasy.
6mA-ChIP-exo-seq library was constructed by following ChIP-exo-seq 5.0 (Ziyang Hao et al., 2020, Molecular Cell). Regular ChIP-seq was constructed by kapa hyper prep kit.

treatment_protocol: Cells were cultured under 1% O2 (hypoxia) or 18% O2 (normoxia) for 18 hr.

tag: condition

value: WGA control

value: FADU


title: p35S-GFP-OCL4; protoplast prep #3


title: ANFX1840


title: Negative control; p35S-GFP; protoplast prep #3

value: GFP


title: p35S-GFP-OCL4; protoplast prep #1


title: FADU_hypoxia_M4KD_input

value: hypoxia

tag: genometype


title: empty vector transfected-fibroblasts 2

value: empty vector transfected-fibroblasts


title: empty vector transfected-fibroblasts 3


title: ONT_CpG_methyl_PTC_12


title: FADU_hypoxia_input 2

value: Scramble-si


title: Negative control; p35S-GFP; protoplast prep #1


title: NKL IL18 treated Rep2

city: Boston

first: Sizun

last: Jiang

address: 3 Blackfan Circle

institute: BIDMC/Harvard

data_processing:
Sequencing QC with fastqc
Mapping to hg19 with Bowtie2 with parameters – very-sensitive
Duplicate reads were removed with Picard
Peak calling was performed by MACS2 in narrow peak mode with parameters −q 0.01, −nomodel, −shift 0
Overlapping peaks from all samples were merged into a consensus peak list, and the number of uniquely mapped and properly paired reads mapped to each peak for each individual sample was quantified to calculate the Pearson correlation.
For ATAC-seq signal intensity around TSSs, a 2-kbp window centered on a TSS was divided into 40 equally sized bins of 50 bp. The number of uniquely mapped and properly paired ATAC-seq tags overlapping each bin was counted. The replicates samples were merged and differential peak analysis of different conditions were performed with DESeq264
The motif enrichment analysis was performed with Homer using the whole genome as background
Mapped reads are normalized to their controls and converted into bigwig files for visualization on a genome browser. Replicates were pooled.
Differentially accessible regions were identified with DESeq and clustered with k means.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files and Bed files of final accessible peaks

source_name: NKL IL18 treated

growth_protocol: GM12878 cells were grown in RPMI 1640 (Life Technologies), 15% fetal bovine serum (FBS; Omega Scientific), and 2 mM L-glutamine (Life Technologies). Jurkat and K562 cells were grown in RPMI 1640, 10% FBS, and 2 mM L-glutamine. NKL cells were grown in RPMI 1640, 10% FBS, 2 mM L-glutamine, and 200 U/mL rhIL-2 (National Cancer Institute). HeLa cells were grown in DMEM (Life Technologies), 10% FBS and passaged with TrypLE Express (Gibco). Cells were maintained in 100 U/mL penicillin (Life Technologies) and 100 mg/mL streptomycin (Life Technologies) at 37 °C in 5% CO2 conditions.

extract_protocol:
ATAC-seq in GM12878 and NKL cells was performed using Illumina Tn5 transposase (Nextera kit; cat# FC-121-1030, Illumina), and GM12878 with Fluoro-Tn5 was performed as described previously. Briefly, 50,000 cells were centrifuged at 500 g for 5 min at 4 °C and washed once in cold PBS. The cell pellet was gently resuspended in 50 μl pre-chilled lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Igepal CA-630) and centrifuged immediately at 500 g for 10 min at 4 °C. The cell pellet was resuspended in 50 μl transposase mixture (25 μl 2× TD buffer (Nextera kit), 2.5 μl Illumina Tn5 transposase or final concentration of 100 nM Fluoro-Tn5, and nuclease-free water to a final volume of 40 μl) and incubated at 37 °C for 30 min. After purification with Qiagen Min-Elute PCR purification kit (cat# 28004, Qiagen), DNA was eluted in 10 μl Qiagen buffer EB.
Sequencing libraries were prepared following the original ATAC-seq protocol with slight modification1. A PCR library amplification step was performed with a final forward and reverse primer concentration of 0.625 µM. An AMPure XP (Beckman Coulter) purification step (1.8X volume) was performed in place of a PCR purification step after the PCR library amplification. Sequencing libraries were assessed via the 2100 Bioanalyzer (Agilent) for nucleosome profiles, and the library concentration estimated by analysis of library fragments between 50 bp and 450 bp. The sequencing was performed on Illumina NextSeq or HiSeq at the Stanford Functional Genomics Facility.

treatment_protocol: For cytokine treatment of NKL cells, cells were incubated with 200 U/mL rhIL-2 plus 20 ng/ml human IL-18 (R&D Systems) or 10 ng/ml human IL-12 (R&D Systems) for 24 h.

value: NKL

value: Natural killer cell lymphoblastic leukemia/lymphoma

tag: molecule subtype

value: Tagmented DNA fragments


title: FADU_normoxia_input

value: normoxia


title: NKL IL18 treated Rep1


title: empty vector transfected-fibroblasts 1


title: ANFX2000


title: FADU_hypoxia_rep5_N6mA_ChIPexo

data_processing:
Basecalls performed by Nextseq Control software.
Adpater sequence was trimmed by Trim galore.
Data was aligned to hg19 by bowtie2.
Aligned file was filtered by MAPQ > 20.
MACS2 was used by regular ChIP-seq peak calling.
For ChIP-exo-seq, after making genome windows, measure the abundance of 6mA signals. Comparing the different condition of 6mA signals by edgeR to identify the gain-of-6mA or loss-of-6mA region.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig file was produced by deeptools for signal visualization. After romiving PCR duplicates, transformed bam file into bed file for the measurement of 6mA signal abundance in each genome window. NarrowPeak region of HIF1 was called by MACS2.


title: NKL IL12 treated Rep2

source_name: NKL IL12 treated


title: FADU_hypoxia_rep4_N6mA_ChIPexo


title: RNAseq_WT_ESC_c3_BR2

description:
RNAseq
rRNA-depleted, steady state RNA

data_processing:
scRNAseq: Cellranger (v.3.1.0) mkfastq and count pipelines were used for: demultiplexing, converting to fastq format, combining sequencing results, alignment to GRCm38 (mm10) genome assembly and gene annotation, barcode processing, and UMI counting.
scATACseq: Cellranger ATAC (v.1.1.0) mkfastq and count pipelines were used for demultiplexing sequencing results and converting to fastq format, as well as alignment to GENCODE vM17 basic genome annotation, barcode processing, and UMI counting.
mPROseq: Raw reads were processed using fastxtoolkit (v.0.0.13). Fastq files were converted to fasta format using the fastq_to_fasta command with parameter -n. Adapter sequence was removed using fastx_clipper with parameters -n -a ATCTCGTATGCCGTCTTCTGCTTG -l 14. PCR duplicates were removed using fastx_collapser with default parameters. The 6bp unique molecular identifier (UMI) was removed using fastx_trimmer (-f 7). Then, libraries were demultiplexed using fastx_barcode_splitter with parameters --mismatches 2 --partial 1. Library barcodes were trimmed using fastx_trimmer (-f 10). The reverse complement of trimmed sequences were obtained using fastx_reverse_complement and aligned to the mm10 reference genome using Bowtie2 (v.2.3.5.1) with parameter --sensitive-local -f. Reads per genomic content (RPGC)-normalized bigWig files were generated from bam files using the BamCoverage function in the deeptools package (v.3.0.1) with parameters --normalizeUsing RPGC --effectiveGenomeSize 2652783500 --centerReads -e 150.
ATACseq: Reads were trimmed for adapter sequences using TrimGalore (v.0.6.5) (--paired --nextera). Paired-end reads were aligned to the mm10 reference genome using Bowtie2 (v.2.3.5.1) (--very-sensitive -k 10) and filtered for autosomal, properly-paired, mapped read pairs with mapping quality >= 30 using samtools (v.1.10) view (-b -h -f 3 -F 4 -F 8 -F 256 -F 1024 -F 2048 -q 30). Peak calling was performed separately for each sample using Genrich (-a 10 -j -r -e chrM,chrY), excluding ENCODE blacklisted regions (ENCFF547MET.bed, downloaded from https://www.encodeproject.org/files/ENCFF547MET/). Peaks called in each sample were collated, and overlapping peaks were merged to generate a consensus list of peaks using bedtools merge. Reads per genomic content (RPGC)-normalized bigWig files were generated from bam files using the BamCoverage function in the deeptools package (v.3.0.1) with parameters --normalizeUsing RPGC --effectiveGenomeSize 2652783500 --centerReads.
RNAseq: Reads were trimmed for adapter sequences using TrimGalore (--paired --illumina --length 20). Sequences were trimmed for read quality using fastq_quality_filter in fastxtoolkit (-Q33 -q 30 -p 90). Paired-end reads were aligned to the mm10 reference genome using hisat2 (v.2.2.0) (--rna-strandness FR). Aligned reads were counted to GENCODE vM15 genomic transcripts using featureCounts in the subread package (v.1.6.2) using default parameters. Reads per genomic content (RPGC)-normalized bigWig files were generated from bam files using the BamCoverage function in the deeptools package (v.3.0.1) with parameters --normalizeUsing RPGC --effectiveGenomeSize 2652783500 --centerReads.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: .tar archives include barcodes.tsv, features.tsv, and matrix.mtx files.
Supplementary_files_format_and_content: bigWig coverage files

source_name: mouse embryonic stem cell V6.5

growth_protocol: V6.5 mouse embryonic stem cells (ESC) were cultured on tissue culture-treated 10cm plates pre-coated with 0.2% gelatin in phosphate-buffered saline (PBS). ESC were cultured in Dulbecco’s Modified Eagle Medium (Fisher), plus 10% fetal bovine serum, 1x penicillin/streptomycin, 1x non-essential amino acids, 1x β-mercaptoethanol, and 1000 U ml-1 leukemia inhibitor factor. All cells were grown at 37C and 5% CO2 and passaged every two days to maintain 10-70% confluency.

extract_protocol: scRNAseq: Single-cell suspension of V6.5 mESC was made by treatment with 0.25% trypsin followed by inactivation in complete medium. Single-cell isolation and library preparation was done using a 10x Genomics Chromium machine in 3’ RNA digital gene expression mode. scATACseq: Single-nuclei suspension of V6.5 mESC was isolated following the 10x Genomics nuclei isolation protocol (CG000169 Rev D). mPROseq: The PROseq protocol established in Mahat et al. 2016 was modified to enable small cell input and performed. ATACseq: Library preparation was performed according to protocol established in Buenrostro et al. 2013 (PMID 24097267), Buenrostro et al. 2015 (PMID 25559105). RNAseq: RNA was extracted by standard Trizol protocol. rRNA-depleted RNA sequencing libraries were prepared using KAPA RNA HyperPrep Kit with RiboErase (Roche 08098140702) to manufacturer’s instructions.

value: embryonic stem cell line

tag: subpopulation

value: unsorted

value: WT

tag: biological replicate


title: RNAseq_WT_ESC_c3_BR3

description:
RNAseq
rRNA-depleted, steady state RNA


title: mCherry_3

city: Daegu

first: Ji Hwan

last: Park

state: Gyeongbuk

address: 333, Techno jungang-daero, Hyeonpung-eup, Dalseong-gun

department: Newbiology

country: South Korea

institute: DGIST

description: Gene expression in human dermal fibroblasts, pLenti transfected, mCherry overexpression [sample 3]

data_processing:
The adaptor sequences were trimmed by the trimmomatic (v0.38) and then aligned to the reference human genome (hg19) using the HISAT2 aligner(ver 2.1.0).
The align data were quantified to the gene features (RefSeq_2017_06_12) in gene count using StringTie (ver 1.3.4d).
Assembly: hg19

growth_protocol: Human dermal fibroblasts (HDFs) from neonatal foreskin were cultivated from supplemented with 10% fetal bovine serum, 100 units/mL penicillin, 10 μg/mL streptomycin, and 25 ng/mL amphotericin B. Cells were maintained at 37 °C in 5% CO2 and routinely split at ratios of 1:4 during early passages (up to passage 45), 1:3 (passages 46 and 47), or 1:2 during late passages (passages 48-50).

extract_protocol:
Total RNA was extracted from HDFs using the QIAzol Lysis Reagent on ice, following the manufacturer’s protocol. RNA purity and concentration were determined using NanoDrop One spectrophotometer. Integrity of RNA was confirmed in the lab.
Isolated RNA was fragmented using TruSeq Stranded mRNA LT Sample Prep Kit according to the manufacturer’s protocol, and libraries for sequencing were then generated based on NovaSeq 6000 S4 Reagent Kit and the protocols in Microgen Inc. (Seoul, South Korea). The libraries were sequenced using NovaSeq 6000 system.

treatment_protocol: Lnetiviral construct of ANT2 (tagged with expressing FLAG, Myc, and V5) and mCherry were generated by using Stbl3 competent E. coli. The viruses were produced in HEK293T cells and introduced to the HDFs.

value: Human dermal fibroblasts

tag: genotype/variation

value: mCherry overexpression

value: pLenti transfected


title: WGA_N6mA_ChIPexo


title: mCherry_2

description: Gene expression in human dermal fibroblasts, pLenti transfected, mCherry overexpression [sample 2]


title: RNAseq_WT_ESC_c3_BR1

description:
RNAseq
rRNA-depleted, steady state RNA


title: NKL IL12 treated Rep1


title: mCherry_1

description: Gene expression in human dermal fibroblasts, pLenti transfected, mCherry overexpression [sample 1]


title: FADU_hypoxia_HIF1_ChIP

value: empty


title: empty vector transfected-fibroblasts 4

value: human skin

value: primary fibroblasts

value: mesenchymal cell


title: FADU_hypoxia_M4KD_IgG_ChIPexo

value: FADU

value: hypoxia


title: ANT2_3

description: Gene expression in human dermal fibroblasts, pLenti transfected, ANT2 overexpression [sample 3]

value: ANT2 overexpression


title: RNAseq_WT_ESC_c2_BR2

description:
RNAseq
rRNA-depleted, steady state RNA


title: NKL IL2 treated control Rep1

source_name: NKL IL2 treated control

value: NKL


title: FADU_hypoxia_IgG_ChIPexo

value: Scramble-si


title: RNAseq_WT_ESC_c2_BR1

description:
RNAseq
rRNA-depleted, steady state RNA


title: ANT2_2

description: Gene expression in human dermal fibroblasts, pLenti transfected, ANT2 overexpression [sample 2]


title: FADU_normoxia_IgG_ChIPexo


title: ANT2_1

description: Gene expression in human dermal fibroblasts, pLenti transfected, ANT2 overexpression [sample 1]


title: ATAC-mass Tn5 Rep1

source_name: ATAC-mass Tn5

value: EBV transformed Lymphoblastoid Cells

value: Tn5 loaded with MIBI compatible adapters

value: Tagmented DNA fragments


title: RNAseq_WT_ESC_c1_BR3

description:
RNAseq
rRNA-depleted, steady state RNA

value: embryonic stem cell line

value: unsorted


title: FADU_hypoxia_input


title: Unperfused glomeruli replicant 3

city: Hamburg

first: Tianran

last: Zhang

address: Falkenried 94

country: Germany

institute: University Medical Center Hamburg-Eppendorf

data_processing:
The quality of the bulk RNA-seq reads was assessed using FastQC (v0.11.5).
The reads were aligned to the mouse reference genome (mm10) with Bowtie2 (v2.3.3.1) using RSEM (v1.3.0) with the default parameters.  The function rsem-calculate-expression was used to align the reads and quantify the gene and isoform abundance.
Assembly: mm10
Supplementary files format and content: plain file including read count and transcripts per million (TPM) value

source_name: Unperfused glomeruli r

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). Total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared by BGI

value: Unperfused glomeruli r

value: WT

value: Unperfused control


title: Unperfused glomeruli replicant 2


title: NKL IL2 treated control Rep2

value: Natural killer cell lymphoblastic leukemia/lymphoma


title: RNAseq_WT_ESC_c2_BR3

description:
RNAseq
rRNA-depleted, steady state RNA


title: RNAseq_WT_ESC_c1_BR2

description:
RNAseq
rRNA-depleted, steady state RNA


title: Unperfused glomeruli replicant 1


title: RNAseq_WT_ESC_c1_BR1

description:
RNAseq
rRNA-depleted, steady state RNA


title: C2013

city: Atlanta

first: Michael

last: Davis

state: GA

address: 2015 Uppergate Dr

institute: Emory University

description: lncRNA

data_processing:
Base calling was conducted with RTA v3.4.4 and demultiplexing was performed with bcl2fastq v2.20.0.422
Fastq files were aligned to the human genome (GRCh38) using the Qiagen GeneGlobe primary analysis tool
Supplementary_files_format_and_content: counts per gene

source_name: c-kit+ progenitor cell isolated from artial appendage

growth_protocol: CPCs were isolated by c-kit magnetic bead sorting from cardiac biopsies of congenital heart disease patients . CPCs were cultured using Hams F-12 medium with 10% fetal bovine serum, 1% Penicillin-Streptonmycin, 1% L-glutamine, and 0.04% fibroblast growth factor 2.

extract_protocol:
Qiagen miRNeasy kit was used to extract RNA from both CPCs and CPC sEVs.
1 ng of RNA was used as input for library preparation with the Qiagen QIAseq miRNA Library Prep Kit

treatment_protocol: CPCs were serum-depleted 24 h prior to isolate small extracellular vesicles (sEVs). 24 h after serum-depletion, conditioned media were collected and sEVs were isolated by serial ultracentrifugation (7,000 rpm for 30 mins, 32,000 rpm for 210 mins for twice).

tag: patient id

tag: sequence facility

value: Novogene

tag: heart chamber

value: Atrium

tag: age

value: 3 months

tag: Sex

value: Male

tag: diagnosis

value: Ventricular septal defect


title: C2016

description: lncRNA

value: 1-2 week

value: Female

value: Coarctation, atrial septal defe ct, ventricular septal defect


title: C1100

description: lncRNA

value: < 1 week

value: Hypoplastic left heart syndrome


title: FADU_hypoxia_M4KD_rep2_N6mA_ChIPexo

value: FADU

value: hypoxia

tag: genotype


title: FADU_hypoxia_M4KD_rep1_N6mA_ChIPexo

tag: cell line


title: Perfused glomeruli replicant 3

source_name: Perfused glomeruli

tag: cell type

value: Perfused glomeruli

tag: treatment

value: ex vivo kidney perfusion


title: RNAseq_Zfp281KO_ESC_c3_BR3

description:
RNAseq
rRNA-depleted, steady state RNA

value: embryonic stem cell line

value: unsorted

value: Zfp281 KO


title: ATAC-mass Tn5 Rep2

value: EBV transformed Lymphoblastoid Cells

value: Tn5 loaded with MIBI compatible adapters

value: Tagmented DNA fragments


title: C1099

description: lncRNA

value: Novogene

value: Atrium

value: 5 months

value: Complete atrioventricular canal defect, Downs syndrome


title: Perfused glomeruli replicant 2

value: WT


title: RNAseq_Zfp281KO_ESC_c2_BR3

description:
RNAseq
rRNA-depleted, steady state RNA


title: FADU_hypoxia_rep2_N6mA_ChIPexo

value: Scramble-si


title: C1092

description: lncRNA

value: 4 years

value: Female

value: Atrial septal defect


title: FADU_hypoxia_rep3_N6mA_ChIPexo

value: FADU

value: hypoxia


title: FADU_hypoxia_rep1_N6mA_ChIPexo


title: C1095

description: lncRNA

value: 3 months

value: Male

value: Double outlet right ventricle


title: Perfused glomeruli replicant 1

value: Perfused glomeruli

value: ex vivo kidney perfusion


title: RNAseq_Zfp281KO_ESC_c3_BR2

description:
RNAseq
rRNA-depleted, steady state RNA

value: embryonic stem cell line

value: unsorted

value: Zfp281 KO


title: FADU_hypoxia_M4KD_rep3_N6mA_ChIPexo


title: FADU_normoxia_rep3_N6mA_ChIPexo

value: normoxia


title: RNAseq_Zfp281KO_ESC_c2_BR2

description:
RNAseq
rRNA-depleted, steady state RNA


title: RNAseq_Zfp281KO_ESC_c3_BR1

description:
RNAseq
rRNA-depleted, steady state RNA


title: C1083

description: lncRNA

value: Novogene

value: Atrium

value: < 1 week

value: Interrupted aortic arch, ventricular septal defect


title: FADU_normoxia_rep1_N6mA_ChIPexo

value: Scramble-si


title: C1066

description: lncRNA

value: 6 months

value: Female

value: Tricuspid atresia, ventricular septal defect, atrial septal defect


title: RNAseq_Zfp281KO_ESC_c2_BR1

description:
RNAseq
rRNA-depleted, steady state RNA


title: C1063

description: lncRNA

value: 3 years

value: Ventricular septal defect


title: RNAseq_Zfp281KO_ESC_c1_BR3

description:
RNAseq
rRNA-depleted, steady state RNA


title: FADU_RP11-390F4.3_OE_rep2_RNA

description: processed data file: FADU_OE_cont_METTL4_RP11-390F4.3_normalizedTMM.txt.gz

data_processing:
Basecalls performed by Nextseq Control software.
Adpater sequence was trimmed by Trim galore.
Data was aligned to hg19 by hisat2.
Aligned file was filtered by MAPQ > 10.
The abundance of RNA fragments was counted by ht-seq.
Genome_build: hg19
Supplementary_files_format_and_content: TMM normalized gene abindance and differential gene analysis were performed by edgeR.

growth_protocol: FADU cell was cultered in DMEM with 10% FBS, 1% antibiotic

extract_protocol:
RNA was extracted by RNeasy kit.
Libarary was contructed by kapa Ribo minus with hyper prep stranded kit.

value: FADU


title: RNAseq_Zfp281KO_ESC_c1_BR2

description:
RNAseq
rRNA-depleted, steady state RNA


title: FADU_normoxia_rep2_N6mA_ChIPexo


title: C1097

description: lncRNA

value: 3 months

value: Male

value: Tetralogy of Fallot


title: C1050

description: lncRNA

value: 1 week

value: Hypoplastic left heart syndrome


title: FADU_RP11-390F4.3_OE_rep1_RNA

value: normoxia


title: RNAseq_Zfp281KO_ESC_c1_BR1

description:
RNAseq
rRNA-depleted, steady state RNA

value: embryonic stem cell line

value: unsorted

value: Zfp281 KO


title: C1048

description: lncRNA

value: Novogene

value: Atrium

value: 6 years

value: Atrial septal defect


title: RNAseq_Klf4KO_ESC_c3_BR3

description:
RNAseq
rRNA-depleted, steady state RNA

value: Klf4 KO


title: FADU_METTL4_OE_rep1_RNA


title: C1045

description: lncRNA

value: < 1 week

value: Female

value: Coarctation of the aorta, ventricular septal defect


title: RNAseq_Klf4KO_ESC_c3_BR2

description:
RNAseq
rRNA-depleted, steady state RNA


title: FADU_cont_OE_rep1_RNA

value: FADU

value: Control


title: RNAseq_Klf4KO_ESC_c3_BR1

description:
RNAseq
rRNA-depleted, steady state RNA


title: C1007

description: lncRNA

value: 6 months

value: Male

value: Ventricular septal defect, congenial/subaortic stenosis repair defect


title: C1006

description: lncRNA

value: Complete atrioventricular canal defect


title: CYT_IDL_IDC_1

type: RNA

city: Dallas

first: William

middle: R

last: Swindell

state: TX

address: 6201 Harry Hines Blvd

department: Internal Medicine

institute: UT Southwestern Medical Center

description: Gene expression data from CYT+IDL+IDC-treated RHE

hyb_protocol: Microarray hybridizations were performed using standard protocols by ThermoFisher (Waltham, MA).

scan_protocol: The standard Affymetrix protocol was following using the GeneChip™ Scanner.

data_processing: Raw CEL files were normalized using the robust multichip average (RMA) algorithm to generate log2-scaled signal intensities (Irizarry et al., 2003).

label: biotin

source_name: RHE

label_protocol: Biotinylated cDNA was prepared following the standard Affymetrix protocol using the GeneChip WT labeling kit.

growth_protocol: Pre-mature RHE tissues (4 days post airlift) were obtained from a commercial provider (Zen-Bio, Durham, NC) and maturation was continued in Zen-Bio Airlift Media (lot no. 011722) until day 11.

extract_protocol: RNA was extracted using the Qiagen (Hilden, Germany) RNAeasy Mini Plus kit.

treatment_protocol: Control (CTL) tissues were treated only with vehicle solution. On day 7 of air exposure, IL-4, IL-13, IL-31 and TNF-α were added to the culture medium at concentrations of 30 ng/ml, 30 ng/ml, 15 ng/ml and 3.5 ng/ml, respectively. On day 11, Zen-Bio Airlift Media was replaced with Zen-Bio assay media (lot. no. 042922) and test compounds (IDL and/or IDC) were applied topically at 10 mg/cm2. Cultures were continued until day 15.

value: CYT+IDL+IDC

tag: replicate

tag: tissue

value: RHE


title: CYT_IDL_2

description: Gene expression data from CYT+IDL-treated RHE

value: CYT+IDL


title: CYT_IDL_IDC_3


title: CYT_IDL_3


title: FADU_M4mut_clone2_hypoxia_RNA

description: processed data file: FADU_CRISPR_cont_M4mut_hypoixia_normalizedTMM.txt.gz

tag: condition

value: hypoxia


title: CYT_IDL_1


title: RNAseq_Klf4KO_ESC_c2_BR2

description:
RNAseq
rRNA-depleted, steady state RNA

value: embryonic stem cell line

value: unsorted


title: CYT_IDL_IDC_2


title: RNAseq_Klf4KO_ESC_c2_BR3

description:
RNAseq
rRNA-depleted, steady state RNA


title: CYT_IDC_3

description: Gene expression data from CYT+IDC-treated RHE

value: CYT+IDC


title: C1004

description: lncRNA

value: Novogene

value: Atrium

value: 12 months

value: Anomalous right superior vena cava to left atrium, no left superior vena cava


title: CYT_IDC_2


title: FADU_M4mut_clone1_hypoxia_RNA

value: FADU


title: RNAseq_Klf4KO_ESC_c2_BR1

description:
RNAseq
rRNA-depleted, steady state RNA

value: Klf4 KO


title: FADU_METTL4_OE_rep2_RNA

value: normoxia


title: FADU_CRISPRcont_hypoxia_RNA

value: WT


title: C985

description: lncRNA

value: 2 weeks

value: Male

value: Interrupted aortic arch


title: RNAseq_Klf4KO_ESC_c1_BR3

description:
RNAseq
rRNA-depleted, steady state RNA


title: CYT_2

description: Gene expression data from CYT-treated RHE

value: CYT

value: RHE


title: CYT_3


title: CYT_IDC_1


title: C1010

description: lncRNA

value: 9 weeks

value: Tetralogy of Fallot


title: FADU_cont_OE_rep2_RNA

value: Control


title: BFTC_hypoxia_M4KD_rep2_RNA

description: processed data file: BFTC_Normoxia_hypoxia_M4KD_normalizedTMM.txt.gz

value: hypoxia


title: C975

description: lncRNA

value: Novogene

value: 6 months


title: RNAseq_Klf4KO_ESC_c1_BR2

description:
RNAseq
rRNA-depleted, steady state RNA

value: embryonic stem cell line

value: unsorted


title: CYT_1


title: CTL_3

description: Gene expression data from CTL-treated RHE

value: CTL


title: BFTC_hypoxia_M4KD_rep1_RNA


title: BFTC_hypoxia_rep2_RNA

value: Scramble-si


title: C957

description: lncRNA

value: Atrium

value: 7 months

value: Partial anomalous pulmonary venous return


title: RNAseq_Klf4KO_ESC_c1_BR1

description:
RNAseq
rRNA-depleted, steady state RNA

value: Klf4 KO


title: ATACseq_WT_ESC_c3_BR1

description: ATACseq

value: WT


title: BFTC_normoxia_rep2_RNA

value: normoxia


title: S.aureus - pD4-19adapted (biol rep 3)

city: Tübingen

first: Kay

last: Nieselt

state: DE

address: Sand 14

department: Department for Computer Science

institute: Institute for Bioinformatics and Medical Informatics

data_processing:
All read mappings were performed against the previously sequenced and assembled genome S. aureus RN4220+pD4-19, from PRJNA855446.
The mappings of all samples were conducted with HISAT2 v2.1.0. Spliced alignment of reads was disabled (HISAT2 parameter --no-spliced-alignment). Library type was set to reverse (--rna-strandness)
resulting mapping files in SAM format were converted to BAM format using SAMtools v1.9
Gene counts for all samples were computed with featureCounts v1.6.4 based on the prokka (v1.14.6) annotation of the respective reference genome, where the selected feature type was set to transcript records (featureCounts parameter -t transcript)
Assembly: assembled genome  S. aureus RN4220+pD4-19 from PRJNA855446 using Unicycler v0.5.0 with gene annotation created using prokka (v1.14.6)
Supplementary files format and content: counts_for_publication.txt: A tab separated matrix with samples as columns and genes as rows

organism: Staphylococcus aureus subsp. aureus RN4220

source_name: bacterial cells

growth_protocol: Strains were grown over night, inoculated in fresh medium to OD600=0.1 and grown for 5 h at 37°C under continuous shaking.

extract_protocol:
1/10 volume EtOH/Phenol was added to 500 µl of sample and mixed for 1 min. After incubation on ice for 5 min, the samples were centrifuged for 1 min at 20 000 xg at 4°C. The supernatant was discarded, and the pellet was resuspended in 1 ml TRIzol. Each sample was transferred to one screw-cap tube with glass beads and cells were lysed via bead-beating for 2x 6.5 ms/s for 30 s. In between the two runs the cells were kept on ice for 2 min.  200 µl chloroform was added to the samples, mixed and incubated 2-3 min before centrifugation of the samples for 15 min, 12 000 xg, 4°C. The aqueous supernatant was taken, mixed with 500 µl isopropanol and samples were centrifuged for 10 min, 21 000 xg, 4°C. The supernatant was discarded, and the pellet was resuspended in 500 µl 75% EtOH. After centrifugation for 5 min, 20 000 xg, 4°C, the supernatant was discarded, and the pellet was dried at RT. The pellet was resuspended in 100 µl RNA-grade water and RNA was concentrated via the MN RNA clean up kit (Machery-Nagel).
RNA samples were DNase I digested (DNase I recombinant, Rnase-free, Millipore Sigma), cleaned up (RNA Clean & Concentrator-5, Zymo Research), quantified (Qubit RNA BR Assay Kit, ThermoFisher) and normalized to 100 ng in 11 µl nuclease-free water. Library preparation was performed according to the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus Reference Guide. Library concentration was measured with Qubit DNA HS Assay Kit, (ThermoFisher) on a Qubit Fluorometer (invitrogen) and fragment length was assessed with an Agilent 2100 Bioanalyzer (Agilent High sensitivity DNA Kit, Agilent). Samples were equimolarly pooled and sequenced on NextSeq™ 500 High Output Kit v2.5 (75 cycles) flow cell (Illumina) with 1 x 75 bp read length.

value: bacterial cells

value: adaptive evolution experiment


title: S.aureus - pD4-19adapted (biol rep 2)


title: C930

description: lncRNA

value: < 1 week

value: Male

value: Total anomalous pulmonary venous return, unbalanced atriovantricular canal defect


title: ATACseq_WT_ESC_c2_BR1

description: ATACseq


title: C938

description: lncRNA

value: Novogene

value: 5 years

value: Subaortic membrane resection, mitral valve ring


title: ATACseq_WT_ESC_c1_BR1

description: ATACseq

value: embryonic stem cell line

value: unsorted


title: S.aureus - pD4-19adapted (biol rep 1)


title: BFTC_normoxia_rep1_RNA

value: Scramble-si


title: C926

description: lncRNA

value: Atrium

value: 14 months

value: Ventricular septal defect


title: ATACseq_Zfp281KO_ESC_c3_BR1

description: ATACseq

value: Zfp281 KO


title: CTL_2

value: CTL

value: RHE


title: C925

description: lncRNA

value: Female

value: Total anomalous pulmonary venous return


title: FADU_hypoxia_M4KD_rep2_RNA

description: processed data file: FADU_Normoxia_hypoxia_M4KD_normalizedTMM.txt.gz

value: FADU

value: hypoxia


title: S.aureus - pD4-19 (biol rep 3)

value: bacterial cells

value: plasmid transfer


title: FADU_hypoxia_M4KD_rep1_RNA


title: S.aureus - pD4-19 (biol rep 2)


title: ATACseq_Zfp281KO_ESC_c2_BR1

description: ATACseq


title: C924

description: lncRNA

value: Novogene

value: 2 months

value: Male


title: C956

description: lncRNA

value: 5 months

value: Complete atrioventricular canal defect


title: CTL_1


title: BFTC_hypoxia_rep1_RNA

value: Scramble-si


title: ATACseq_Zfp281KO_ESC_c1_BR1

description: ATACseq

value: embryonic stem cell line

value: unsorted


title: S.aureus - pD4-19 (biol rep 1)


title: C903

description: lncRNA

value: Atrium

value: < 1 week

value: Hypoplastic left heart syndrome


title: ATACseq_Klf4KO_ESC_c3_BR1

description: ATACseq

value: Klf4 KO


title: S.aureus - WT (biol rep 3)

value: WT


title: FADU_hypoxia_rep1_RNA

value: FADU


title: C902

description: lncRNA

value: 4 years

value: Atrial septal defect


title: FADU_hypoxia_rep2_RNA

value: hypoxia


title: ATACseq_Klf4KO_ESC_c2_BR1

description: ATACseq


title: S.aureus - WT (biol rep 2)

value: bacterial cells


title: C896

description: lncRNA

value: Novogene

value: 12 months

value: Female

value: Ventricular septal defect


title: S.aureus - WT (biol rep 1)


title: FADU_normoxia_rep2_RNA

value: Scramble-si

value: normoxia


title: FADU_normoxia_rep1_RNA


title: Polysome-mRNA-seq-SNU449_shMETTL1_Heat treated

status: Public on Nov 20 2022

first: Shenghua

last: Zhu

address: 58 Zhong Shan Road 2

institute: The First Affiliated Hospital, Sun Yat-sen University

description: FPKM_polyribosome associated mRNA-seq-SNU449.txt

data_processing:
For RNA-Seq data analysis, after adapter trimming and low quality sequence filtering (Q30), the clean reads were mapped to human reference genome (GRCh38) using Bowtie2. The raw counts of reads mapping to the gencode genes (v19) were computed by HTSeq with ‘union’ overlap mode. The raw counts were then normalized as fractions per kilo base per million mapped reads (FPKM) using edegR.
For TRAC-Seq, after adaptor trimming and quality filtering, the clean sequencing data were first mapped to the tRNA sequences using Bowtie2. Then read count for each tRNA was calculated using the method in (Cozen et al., 2015). The read counts of tRNA are normalized as reads per million (RPM) by the total number of small RNA reads that are matched to tRNAs in each sample.

source_name: hepatocellular carcinoma cell line

growth_protocol: HCC cell lines were  cultrued in RMPI 1640 medium or DMEM medium. Cells were grown in a 5% CO2 cell culture incubator at 37℃.

extract_protocol:
Total RNA samples were isolated with Trizol following the manufacturer’s instructions. small RNAs (<200nt) were first purified using the mirVana miRNA Isolation Kit (Thermo Fisher Scientific).
Libraries were prepared according to Illumina's instructions accompanying the TrueSeq Stranded mRNA library preparation kit and the NEBNext® Small RNA Library Prep Set.

treatment_protocol: Mettl1 gene knockdown was mediated by short hairpin RNA.HCC cells was treated onto 46℃ constant temperature bathwater for 15 minutes.

value: Mettl1 knockdown

tag: sample type

value: polyribosome associated mRNA-seq


title: Polysome-mRNA-seq-SNU449_NC_Heat treated

value: wild type


title: Polysome-mRNA-seq-SNU449_NC_Heat treated_Input

value: RNA-Seq


title: Polysome-mRNA-seq-SNU449_NC_Input


title: Polysome-mRNA-seq-SNU449_shMETTL1_Heat treated_Input


title: Polysome-mRNA-seq-Huh7_Heat treated_repeat 1

description: FPKM_polyribosome associated mRNA-seq-Huh7.txt


title: peripheral blood mononuclear cells, STEMI26

city: Jinan

first: Jingbo

last: Xing

state: Shandong

address: No. 107, Wenhua West Road

institute: Shandong University

data_processing:
Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, USA).
Library sequencing was performed on an illumina Novaseq 6000 instrument with 150bp paired end reads.
Paired-end reads were harvested from Illumina Novaseq 6000 sequencer and controlled quality by Q30. After 3' adaptor-trimming and low-quality read removal by cutadapt [11] software (v1.9.3), the high-quality trimmed reads were used to analyze RNAs.
circRNA: The high quality reads were aligned to the reference genome/transcriptome with STAR software (v2.5.1b) and circRNAs were detected and identified with DCC software (v0.4.4). edgeR software (v3.16.5) was used to normalized the data and perform differentially expressed circRNA analysis. GO and KEGG analysis were performed for the differentially expressed circRNA-associated genes.
Assembly: mm10
Supplementary files format and content: An excel document contains CircRNAID, junction reads, the junction read number of each sample,logCPM by edgeR,the coordinates of circRNA, circBaseID, the source of the circRNA, the best transcript of the circRNA,the name of the circRNA-associated gene, the catalog of the circRNA, including exonic, intronic,predicted_sequence_length,circRNA-associated diseases.

source_name: peripheral blood

extract_protocol:
The total RNA was isolated from the PBMCs using TRIzol reagent (Life Technologies, Carlsbad, CA). NanoDrop ND-1000 instrument (Thermo Fisher Scientific, Waltham, MA, USA) was used to measure the RNA concentration of each sample. The OD260/OD280 value between 1.8 and 2.1 was considered an acceptable optical density (OD).
The selected total RNA was used for removing the rRNAs with NEBNext® rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA), following the manufacturer's instructions. RNA libraries were constructed using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, USA).

value: peripheral blood

value: mononuclear cells

tag: disease

value: STEMI

value: No


title: peripheral blood mononuclear cells, STEMI27


title: Polysome-mRNA-seq-Huh7_Ctrl_repeat 2


title: peripheral blood mononuclear cells, STEMI28


title: Polysome-mRNA-seq-Huh7_Ctrl_repeat 1


title: peripheral blood mononuclear cells, STEMI24


title: peripheral blood mononuclear cells, STEMI23


title: peripheral blood mononuclear cells, STEMI25


title: ATACseq_Klf4KO_ESC_c1_BR1

description: ATACseq

value: embryonic stem cell line

tag: subpopulation

value: unsorted

value: Klf4 KO

tag: biological replicate


title: Polysome-mRNA-seq-Huh7_Ctrl_Input_repeat 1


title: C894

description: lncRNA

source_name: c-kit+ progenitor cell isolated from appendage

tag: patient id

value: Novogene

value: Ventricle

value: 6 months

value: not collected


title: Polysome-mRNA-seq-Huh7_Ctrl_Input_repeat 2


title: peripheral blood mononuclear cells, STEMI20


title: peripheral blood mononuclear cells, STEMI19


title: Polysome-mRNA-seq-Huh7_Heat treated_Input_repeat 1


title: peripheral blood mononuclear cells, STEMI22


title: celecoxib + lactoferrin treatment group-3

city: beijing

first: yaonan

last: zhang

address: NO 1 Dahua Road, Dongdan, Beijing

institute: Beijing Hospital

data_processing:
seqenced reads were inmmed for adptor sequnce and masked for low-complexily sequence
mapped to human reference genome
Obtain mapped data(reads, etc., for subsequent transcription assembly and expression count
The distribution of reads compared to the genome in different regions of the reference genome was statistically analyzed, and the target regions were divided into CDS(coding region) Intron(Intron) Intergenic region and UTR(5' and 3 untranslated region).
The FPKM value of each gene/transcript in the sample was calculated, and the value was taken as the expression amount of gene/transcript in the sample
Assembly: GRCh38.p13
Supplementary files format and content: Gene/transcript COUNT expression matrix

organism: Rattus norvegicus

source_name: rat

extract_protocol:
HiSeq LncRNA-Seq
RNA libraries were prepared for sequencing using standard illumina protacal

value: tendon

value: teatment


title: Polysome-mRNA-seq-SNU449_NC


title: peripheral blood mononuclear cells, STEMI18


title: celecoxib + lactoferrin treatment group-1


title: peripheral blood mononuclear cells, STEMI17


title: celecoxib + lactoferrin treatment group-2


title: Polysome-mRNA-seq-Huh7_Heat treated_repeat 2


title: injury model group-3

value: not teatment


title: Polysome-mRNA-seq-Huh7_Heat treated_Input_repeat 2


title: in situ Hi-C in neuron 09_L5

first: Jingjing

last: Li

address: 3165 Porter Drive

description: library strategy: Hi-C

data_processing:
Hi-C protocol was based on the original publication by Rao, SS et al. 2014
Hi-C: Alignment by BWA
Hi-C: TADs were called from HI-C contact maps for each chromosome
Supplementary_files_format_and_content: Hi-C: TAD coordinates
Genome_build: hg19

source_name: iPSC derived human cortical neuron

growth_protocol: iPSC neurons were obtained from Cellular dynamics, and were harvested in post-plate day 14.

value: iPSC derived cortical neuron

tag: disease state

value: non-diseased


title: in situ Hi-C in neuron 08_L9

description: library strategy: Hi-C

extract_protocol: Hi-C protocol was based on the original publication by Rao, SS et al. 2014


title: injury model group-2


title: in situ Hi-C in neuron 09_L6

description: library strategy: Hi-C


title: in situ Hi-C in neuron 09_L7

description: library strategy: Hi-C


title: peripheral blood mononuclear cells, STEMI15


title: peripheral blood mononuclear cells, STEMI16


title: peripheral blood mononuclear cells, STEMI21


title: in situ Hi-C in neuron 09_L8

description: library strategy: Hi-C


title: in situ Hi-C in neuron 08_L8

description: library strategy: Hi-C


title: peripheral blood mononuclear cells, STEMI14


title: injury model group-1


title: in situ Hi-C in neuron 08_L7

description: library strategy: Hi-C


title: in situ Hi-C in neuron 08_L6

description: library strategy: Hi-C


title: in situ Hi-C in neuron 08_L5

description: library strategy: Hi-C


title: high glycolysis inhibition-rep2

city: Beijing

first: tongbiao

last: zhao

address: 1 Beichen West Road, Chaoyang District

institute: INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES

data_processing:
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data). The steps are:1) Trim Smart-seq2 public primer sequence from the Reads (If the length of trimmed Reads is lower than 30bp, reads should be discarded. If it is PE sequence, both of the reads must be removed );2) Remove the contaminated reads for adapters (The contaminated reads for adapters was defined that the Read Bases contained more than 5bp of adapter sequences. If either one of the PE Reads was polluted, we will remove both ends of the reads);3) Remove the low quality reads (The low quality reads was defined that the number of Reads Bases whose phred Quality value was less than or equal to 19 accounted for more than 15% . If either one of the PE Reads defined as low quality, we will remove both ends of the reads);4) Remove the reads whose N base more than 5% for total bases (If either one of the PE Reads had high Ns bases, we will remove both ends of the reads).
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0. with parameters (--dta dta –t –p 4 p)
StringTie1.3.2d was used for sequence assembly with parameter (-G ref .gtf)
Reads Count for each gene in each sample was counted by HTSeq v0.6.0 with parameters (-i gene_id -f bam -s no -a 10 -q)
Genome_build: Mus_musculus.GRCm38.90.chr
Supplementary_files_format_and_content: microsoft excel files include reads count and gene annotation for each sample

source_name: ESCs_10mM 2-DG

growth_protocol: ESCs were maintained in knockout DMEM with 15% fetal bovine serum, 2 mM glutamine, 1 mM sodium pyruvate, 0.1 mM nonessential amino acids, 1% penicillin/streptomycin, 0.055 mM β-mercaptoethanol, and 1,000 U/ml leukemia inhibitory factor .

extract_protocol:
Total RNA was extracted from samples with an RNeasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Low- and high-OXPHOS inhibition ESCs are cultured in the ESC medium containing 1 nM or 10 nM oligomycin  respectively. low- and high-glycolysis inhibition ESCs are cultured in the ESC medium containing 5 mM or 10 mM 2-DG respectively.

tag: strain

value: embryonic stem cells (ESCs)

value: 10mM 2-DG


title: high glycolysis inhibition-rep3


title: in situ Hi-C in neuron 07_L9

description: library strategy: Hi-C


title: CHIP-SEQ INPUT in neuron (for H3K27AC ctl)

data_processing:
CHIP-SEQ was based on Standard protocols used in ENCODE
CHIP-SEQ: Alignment by BWA
CHIP-SEQ: Peak call by GEM
Supplementary_files_format_and_content: CHIP-SEQ: Regulatory peaks are listed
Genome_build: hg19

tag: chip antibody


title: peripheral blood mononuclear cells, STEMI12

value: peripheral blood

value: mononuclear cells


title: peripheral blood mononuclear cells, STEMI13

value: STEMI

value: No


title: CHIP-SEQ H3K27AC in neuron

extract_protocol: CHIP-SEQ was based on Standard protocols used in ENCODE

value: H3K27Ac (ActiveMotif, catalog# 39133).


title: high glycolysis inhibition-rep1


title: peripheral blood mononuclear cells, STEMI11


title: low glycolysis inhibition-rep3

source_name: ESCs_5mM 2-DG

value: 5mM 2-DG


title: in situ Hi-C in neuron 07_L7

description: library strategy: Hi-C


title: CHIP-SEQ INPUT in neuron (for CHD8 ctl)


title: peripheral blood mononuclear cells, STEMI10


title: CHIP-SEQ CHD8 in neuron

value: CHD8 (Abcam, catalog# ab84527, lot# GR22849)


title: low glycolysis inhibition-rep1


title: peripheral blood mononuclear cells, STEMI9


title: in situ Hi-C in neuron 07_L5

description: library strategy: Hi-C


title: in situ Hi-C in neuron 07_L6

description: library strategy: Hi-C


title: ATAC-SEQ in neuron Rep2

description: library strategy: ATAC-SEQ

data_processing:
ATAC-SEQ protocol was based on the original publication Buenrostro, et al. 2013
ATAC-SEQ: Alignment by BWA
ATAC-SEQ: Peak call by MACS2
Supplementary_files_format_and_content: ATAC-SEQ: Regulatory peaks are listed
Genome_build: hg19


title: in situ Hi-C in neuron 07_L8

description: library strategy: Hi-C


title: ATAC-SEQ in neuron Rep1

description: library strategy: ATAC-SEQ

extract_protocol: ATAC-SEQ protocol was based on the original publication Buenrostro, et al. 2013


title: high OXPHO inhibition-rep3

source_name: ESCs_10nM oligomycine

value: 10nM oligomycine


title: peripheral blood mononuclear cells, STEMI7


title: peripheral blood mononuclear cells, STEMI8


title: MgB2_3

city: shanghai

first: yang

last: chen

address: siping road

institute: tongji university

data_processing:
The quality information of raw data in FASTQ  format was calculated and then the raw data was filtered using Cutadapt(v1.15) software.
Reference genome index was built by Bowtie2(v2.2.6) and the filtered reads were mapping to the reference genome using Bowtie2.
The gene read count value was counted using HTSeq(v0.9.1) as the original expression level of the gene.
FPKM(fragments per kilobaseof exon per million fragments mapped) is used to normalize the expression.
Assembly: https://www.ncbi.nlm.nih.gov/data-hub/genome/GCF_000404265.1/
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.

organism: Pseudomonas aeruginosa

growth_protocol: P. aeruginosa were grown in Luria-Broth medium (LB)

extract_protocol:
Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies), after which the concentration, quality and integrity were determined using a NanoDrop spectrophotometer. Three micrograms of RNA were used as input material for the RNA sample preparations.
Firstly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in an Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and Super Script II. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3′ ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for hybridization. To select cDNA fragments of the preferred 400-500 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter,Beverly, CA, USA).

value: bacterial cells

value: WT

value: treated with Nano-MgB2 3


title: in situ Hi-C in neuron 06_L9

description: library strategy: Hi-C


title: peripheral blood mononuclear cells, STEMI6


title: high OXPHO inhibition-rep1


title: in situ Hi-C in neuron 06_L8

description: library strategy: Hi-C


title: in situ Hi-C in neuron 06_L7

description: library strategy: Hi-C


title: high OXPHO inhibition-rep2


title: MgB2_2

value: treated with Nano-MgB2 2


title: peripheral blood mononuclear cells, STEMI5


title: peripheral blood mononuclear cells, STEMI4


title: MgB2_1

value: treated with Nano-MgB2 1


title: in situ Hi-C in neuron 06_L6

description: library strategy: Hi-C

value: iPSC derived cortical neuron


title: low OXPHO inhibition-rep3

source_name: ESCs_1nM oligomycine

value: 1nM oligomycine


title: low OXPHO inhibition-rep2

value: embryonic stem cells (ESCs)


title: peripheral blood mononuclear cells, STEMI3


title: B_3

value: no treatment 3


title: low glycolysis inhibition-rep2


title: in situ Hi-C in neuron 06_L5

description: library strategy: Hi-C

value: non-diseased


title: low OXPHO inhibition-rep1


title: B_2

value: no treatment 2


title: in situ Hi-C in neuron 05_L9

description: library strategy: Hi-C


title: peripheral blood mononuclear cells, STEMI2

value: peripheral blood

value: mononuclear cells

value: STEMI


title: peripheral blood mononuclear cells, STEMI1

value: No


title: in situ Hi-C in neuron 05_L8

description: library strategy: Hi-C


title: B_1

value: no treatment 1


title: conrol-rep3

value: mock


title: peripheral blood mononuclear cells, CCS28

value: CCS


title: in situ Hi-C in neuron 05_L6

description: library strategy: Hi-C


title: in situ Hi-C in neuron 05_L7

description: library strategy: Hi-C


title: conrol-rep1


title: Foxc1b_120hpf

city: Lexington

first: Oliver

last: Vöcking

state: KY

address: 675 Rose Street

department: Biology

institute: University of Kentucky

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCz11 assembly (NCBI Genome accession number: GCA_000002035.4)
Supplementary files format and content: Tab-separated values files and matrix files

organism: Danio rerio

source_name: Anterior Segment Mesenchyme

extract_protocol:
Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3-amino benzoic acid ethyl ester (Tricaine). Then, their eyes were dissected and subsequently collected on ice, before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. After filtering, the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

value: Anterior Segment Mesenchyme

value: AB

tag: developmental stage


title: in situ Hi-C in neuron 04_L9

institute: Stanford University

description: library strategy: Hi-C


title: Foxc1b_72hpf

description: 10x Genomics


title: Foxc1b_144hpf

description: 10x Genomics


title: Foxc1b_48hpf

description: 10x Genomics


title: in situ Hi-C in neuron 04_L8

description: library strategy: Hi-C


title: peripheral blood mononuclear cells, CCS25


title: Foxc1b_96hpf

description: 10x Genomics


title: RNA-SEQ in neuron

data_processing:
RNA-Seq: FASTQ alignment using TopHat v2.0.8 aginst the human RefSeq transcriptome downloaded from UCSC Table Browser.
RNA-Seq: Cufflinks were used for expression quantification
Supplementary_files_format_and_content: RNA-Seq: FPKM for each gene is listed
Genome_build: hg19

extract_protocol:
RNA-SEQ: Total RNA was treated with RNase-Free DNase (Qiagen) followed by purification with RNeasy MinElute Cleanup Kit (Qiagen) following the manufacturer’s instructions.
2 µg of total RNA each sample was subject to RNA-seq library preparation with ScriptSeq™ Complete Gold Kit from Epicentre (Cat. # SCL24EP, Madison, WI) following the manufacturer’s instructions. In brief, ribosomal RNA was depleted from total RNA using Ribo-Zero magnetic beads, then the ribosomal RNA depleted RNA was purified and fragmented. Random primer tailed with Illumina adaptor was used to perform reverse transcription to get cDNA library. Adaptor sequence was added to the other end of cDNA library with a Terminal-Tagging step. cDNA library was amplified with Illumina primers provided with this kit. The product was size selected (350~500 bp) from 2% agarose E-gels (Invitrogen) and sequenced in 1 lane per sample on Illumina’s HiSeq 2000 platform.


title: peripheral blood mononuclear cells, CCS26


title: Leaf, RNAi_1

city: Shanghai

first: Renyi

last: Liu

state: Shanghai

address: 3888 Chenhua Road

department: Bioinformatics

institute: Shanghai Center for Plant Stress Biology

description: The first true leaf of 20-day old CsTCP18a-RNAi line seedling was collected for RNA-seq analysis.

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads were first subject to 3’ adapter removal and quality filtering (Q > 17 and length >= 25 bp). Clean reads were mapped to the cucumber genome sequence (v2i; genome sequence and annotation data downloaded from http://cucumber.genomics.org.cn/page/cucumber/download.jsp (click link FTP2)) using TopHat. Read counts of each gene were summarized by the HTSeq-count. Lowly expressed genes were removed and only genes with an expression level of at least 1 CPM (counts per million) in at least one samples were kept for further analysis.
Genome_build: v2i
Supplementary_files_format_and_content: Tab-delimited text file include CPM(counts per Million) values for 4 Samples .

organism: Cucumis sativus

source_name: the first true leaf

growth_protocol: The cucumber seeds were germinated at 28°C in dark and then grown in a growth chamber at 16h day (25°C) and 8h night (18°C) until 20 days later.

extract_protocol:
The first true leaf of 20-day old wild type and CsTCP18a-RNAi line seedling were collected for RNA-seq analysis,and their total RNA was isolated with Transzol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A 402-bp specific fragment of the CsTCP18a coding sequence was used for generating the CsTCP18a-RNAi construct and the empty PFGC-1008 vector was used as transformation control (wild type). The recombinant construct was introduced into Agrobacterium strain GV3101 and transformed into cucumber inbred line R1461.

tag: age

value: 20-day old plant

value: leaf


title: Leaf, RNAi_2

tag: genotype


title: peripheral blood mononuclear cells, CCS24

tag: cell line


title: peripheral blood mononuclear cells, CCS23

tag: cell type


title: Leaf, WT_2

description: The first true leaf of 20-day old wild type seedling was collected for RNA-seq analysis.

value: wild type


title: in situ Hi-C in neuron 04_L6

city: Palo Alto

description: library strategy: Hi-C

value: iPSC derived cortical neuron


title: in situ Hi-C in neuron 04_L7

description: library strategy: Hi-C


title: conrol-rep2

value: embryonic stem cells (ESCs)

tag: treatment


title: peripheral blood mononuclear cells, CCS22


title: CHIP-SEQ CHD8 in BA44

source_name: human brain (Brodmann 44)

value: brain (Brodmann 44)

value: CHD8 (Abcam, catalog# ab84527, lot# GR22849)


title: in situ Hi-C in neuron 04_L5

description: library strategy: Hi-C

value: non-diseased


title: Leaf, WT_1


title: peripheral blood mononuclear cells, CCS27

value: peripheral blood


title: peripheral blood mononuclear cells, CCS21

value: mononuclear cells


title: in situ Hi-C in neuron 05_L5

description: library strategy: Hi-C


title: KO2

city: Nanjing

first: Xiaoming

last: Wang

state: jiangsu

address: 101 longmian avenue jiangning district

institute: Nanjing Medical University

data_processing:
Map the sequence reads to mm10 reference genome using Bowtie2 software.
Fragments Per Kilobase per Million were calculated with Cufflinks.
A threshold of fold change > 1.2 and p < 0.05 was used to determine the differential expression of genes.
Assembly: mm10
Supplementary files format and content: *.tsv: Tab-delimited text files include count values for each Sample.

source_name: spleen

extract_protocol:
B220+ B cells were sorted from the spleen of NSD1B WT and NSD1B KO mice with a BD Aria II. Sorting efficiency was tested, and only cells with high purity (>98%) were used for RNA extraction and library construction.
Sequencing were done by BGI Co.

value: spleen

value: B220+ Bcells

value: NSD1B KO


title: SZ-A-epididymal adipose tissue [SZ7]

first: Qian

middle: wen

last: Sun

state: Beijing

address: 1 Xian Nong Tan Street

institute: Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College

data_processing:
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene

source_name: epididymal adipose tissue

extract_protocol:
total RNA from eWAT was isolated using TRIzol reagent according to the manufacturer’s instructions, and RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer2100 system
libraries were constructed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® according to the manufacturer’s instructions.

value: epididymal adipose tissue

value: high-fat diet (HFD)/SZ-A


title: in situ Hi-C in neuron 03_L9

description: library strategy: Hi-C


title: peripheral blood mononuclear cells, CCS19

value: CCS

value: No


title: SZ-A-epididymal adipose tissue [SZ6]


title: KO1


title: SZ-A-epididymal adipose tissue [SZ5]


title: peripheral blood mononuclear cells, CCS20


title: peripheral blood mononuclear cells, CCS18


title: CHIP-SEQ INPUT in BA44


title: WT1

value: NSD1B WT


title: SZ-A-epididymal adipose tissue [SZ4]


title: in situ Hi-C in neuron 03_L6

description: library strategy: Hi-C


title: in situ Hi-C in neuron 03_L7

description: library strategy: Hi-C


title: peripheral blood mononuclear cells, CCS17


title: SZ-A-epididymal adipose tissue [SZ3]


title: GSK-treated Langerhans cells - 19D18

city: Debrecen

first: Attila

middle: Gábor

last: Szöllősi

address: Egyetem tér 1.

department: Department of Immunology

country: Hungary

institute: University of Debrecen

data_processing:
HISAT2 algorithm was used for alignment of raw sequencing reads to human reference genome version GRCh38.
StrandNGS software (www.strand-ngs.com) was used for further statistical analysis.
Aligned data were normalized by using DESeq algorithm, then differentially expressed genes were determined by moderated T-test. P value < 0.05 was considered to significant change.
Every alignment and genetic statement has also been manually checked using bowtie2 and samtools software packages against the GRCH38 P.13 human reference genome.
The genomic variants were listed and tested using Broad Institute's GATK4 and via scripts leveraging Python 3.8.X and Bioconda packages
Assembly: GRCH38 P.13 human reference genome
Supplementary files format and content: Tab-delimited text files for each sample containing gene IDs and read counts.

source_name: periphereal blood monocytes

growth_protocol: CD14+ monocytes were  cultured in RPMI 1640 medium containing 10% heat-inactivated FBS, 10% HEPES, 50 mM 2-mercaptoethanol, 1% penicillin. The cells were seeded in 12-well tissue-culture plates (1 000 000 per well) containing  media supplemented with GM-CSF (200 ng/mL), TGF-β1 (10 ng/mL), TNF-α (20 ng/mL), and IL-4 (20 ng/mL for the first 48 hrs) for 5 days at 37 °C to differentiate moLCs. GSK treated moLCs were treated from day 0 with 10 nM of GSK1016790A. iDC cultures were generated using GM-CSF (80 ng/ml) and IL-4 (20 ng/ml) for five days.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: monocyte-derived Langerhans cell

value: GSK treated LC


title: SZ-A-epididymal adipose tissue [SZ2]


title: peripheral blood mononuclear cells, CCS16


title: in situ Hi-C in neuron 03_L5

description: library strategy: Hi-C

value: iPSC derived cortical neuron


title: peripheral blood mononuclear cells, CCS15


title: in situ Hi-C in neuron 02_L9

description: library strategy: Hi-C


title: GSK-treated Langerhans cells - 19D10


title: in situ Hi-C in neuron 02_L8

description: library strategy: Hi-C


title: SZ-A-epididymal adipose tissue [SZ1]


title: in situ Hi-C in neuron 03_L8

description: library strategy: Hi-C


title: TRAC-Seq_MHCC97H_NC_Heat treated_Alkb_Treated_Input

city: Guangzhou

data_processing:
Library strategy: TRAC-Seq
For RNA-Seq data analysis, after adapter trimming and low quality sequence filtering (Q30), the clean reads were mapped to human reference genome (GRCh38) using Bowtie2. The raw counts of reads mapping to the gencode genes (v19) were computed by HTSeq with ‘union’ overlap mode. The raw counts were then normalized as fractions per kilo base per million mapped reads (FPKM) using edegR.
For TRAC-Seq, after adaptor trimming and quality filtering, the clean sequencing data were first mapped to the tRNA sequences using Bowtie2. Then read count for each tRNA was calculated using the method in (Cozen et al., 2015). The read counts of tRNA are normalized as reads per million (RPM) by the total number of small RNA reads that are matched to tRNAs in each sample.

value: wild type

value: small RNA-TRAC-Seq


title: TRAC-Seq_MHCC97H_NC_Heat treated_Alkb_and_NaBH4_treated


title: peripheral blood mononuclear cells, CCS14


title: HFD-epididymal adipose tissue [HFD6]

value: high-fat diet (HFD)/saline


title: GSK-treated Langerhans cells - 19D16


title: HFD-epididymal adipose tissue [HFD5]


title: peripheral blood mononuclear cells, CCS13


title: peripheral blood mononuclear cells, CCS12


title: TRAC-Seq_MHCC97H_NC_Alkb_and_NaBH4_Treated


title: peripheral blood mononuclear cells, CCS11


title: TRAC-Seq_MHCC97H_NC_Alkb_Treated_Input


title: peripheral blood mononuclear cells, CCS10


title: HFD-epididymal adipose tissue [HFD4]


title: in situ Hi-C in neuron 01_L9

description: library strategy: Hi-C

value: non-diseased


title: HFD-epididymal adipose tissue [HFD3]


title: peripheral blood mononuclear cells, CCS9

value: peripheral blood


title: genomic DNA from H446 cell/DDP line

type: genomic

city: Shiyan

first: Fuyun

last: Ji

address: South Renmin Road

department: Department of Medical Biology, School of Basic Medical Science

institute: Hubei University of Medicine

hyb_protocol: sodium bisulfite conversion with the EZ DNA methylation Gold Kit (Zymo Research, USA)

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

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: chemo-resistant H446/DDP(H446/R)

label_protocol: Standard Illumina Protocol

growth_protocol: Stadardized cell culture protocol

extract_protocol: DNA was isolated from H446 and H446/DDP cells with DNeasy Cell and Tissue Kit (Qiagen) in accordance with the standard protocols

treatment_protocol: H446/DDP cell line was screened with low dosage of DDP for over 6 months

value: lung

value: Small cell lung cancer


title: in situ Hi-C in neuron 01_L8

description: library strategy: Hi-C


title: HFD-epididymal adipose tissue [HFD2]


title: peripheral blood mononuclear cells, CCS8

value: mononuclear cells


title: Langerhans cells - 19D17

data_processing:
HISAT2 algorithm was used for alignment of raw sequencing reads to human reference genome version GRCh38.
StrandNGS software (www.strand-ngs.com) was used for further statistical analysis.
Aligned data were normalized by using DESeq algorithm, then differentially expressed genes were determined by moderated T-test. P value < 0.05 was considered to significant change.
Every alignment and genetic statement has also been manually checked using bowtie2 and samtools software packages against the GRCH38 P.13 human reference genome.
The genomic variants were listed and tested using Broad Institute's GATK4 and via scripts leveraging Python 3.8.X and Bioconda packages
Genome_build: GRCH38 P.13 human reference genome
Supplementary_files_format_and_content: Tab-delimited text files for each sample containing gene IDs and read counts.

growth_protocol: CD14+ monocytes were  cultured in RPMI 1640 medium containing 10% heat-inactivated FBS, 10% HEPES, 50 mM 2-mercaptoethanol, 1% penicillin. The cells were seeded in 12-well tissue-culture plates (1 000 000 per well) containing  media supplemented with GM-CSF (200 ng/mL), TGF-β1 (10 ng/mL), TNF-α (20 ng/mL), and IL-4 (20 ng/mL for the first 48 hrs) for 5 days at 37 °C to differentiate moLCs. iDC cultures were generated using GM-CSF (80 ng/ml) and IL-4 (20 ng/ml) for five days.


title: Langerhans cells - 19D19


title: in situ Hi-C in neuron 02_L7

description: library strategy: Hi-C


title: HFD-epididymal adipose tissue [HFD7]


title: in situ Hi-C in neuron 02_L6

description: library strategy: Hi-C


title: in situ Hi-C in neuron 01_L7

description: library strategy: Hi-C


title: Langerhans cells - 19D16


title: HFD-epididymal adipose tissue [HFD1]


title: genomic DNA from H446 cell line

source_name: parental H446


title: NC-epididymal adipose tissue [CHOW6]

value: normal chow


title: Langerhans cells - 19D12


title: in situ Hi-C in neuron 01_L5

description: library strategy: Hi-C


title: peripheral blood mononuclear cells, CCS6


title: Langerhans cells - 19D10


title: in situ Hi-C in neuron 00_L9

description: library strategy: Hi-C


title: NC-epididymal adipose tissue [CHOW5]

value: epididymal adipose tissue


title: peripheral blood mononuclear cells, CCS5


title: in situ Hi-C in neuron 02_L5

description: library strategy: Hi-C


title: immature dendritic cells - 19D19

value: immature dendritic cell


title: peripheral blood mononuclear cells, CCS4

value: CCS


title: in situ Hi-C in neuron 00_L8

description: library strategy: Hi-C


title: in situ Hi-C in neuron 00_L7

description: library strategy: Hi-C


title: immature dendritic cells - 19D17


title: NC-epididymal adipose tissue [CHOW2]


title: immature dendritic cells - 19D16


title: immature dendritic cells - 19D12


title: in situ Hi-C in neuron 01_L6

description: library strategy: Hi-C


title: peripheral blood mononuclear cells, CCS2

value: No


title: NC-epididymal adipose tissue [CHOW1]


title: peripheral blood mononuclear cells, CCS1


title: in situ Hi-C in neuron 00_L5

description: library strategy: Hi-C


title: peripheral blood mononuclear cells, CCS7


title: immature dendritic cells - 19D10


title: NC-epididymal adipose tissue [CHOW4]


title: peripheral blood mononuclear cells, CCS3


title: Con_7d_2

status: Public on Nov 19 2022

first: Qiankun

address: Fuxing Road

department: Department of Tissue Repair and Regeneration

institute: The First Medical Center Chinese PLA General Hospital

data_processing:
Raw reads were processed using Trimmomatic. The reads containing poly-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat 2.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
Assembly: mm10
Supplementary files format and content: FPKM.txt

source_name: skin wound tissue

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's protocol.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions.

value: skin wound tissue

value: untreated

tag: time point

value: 7 days


title: Con_3d_3

tag: tissue

value: 3 days


title: NC-epididymal adipose tissue [CHOW3]


title: SF_Exo_3d_2

value: SGM-miR146a-Exo@SFP treated


title: Con_7d_1


title: SF_Exo_7d_1


title: in situ Hi-C in neuron 00_L6

description: library strategy: Hi-C

value: iPSC derived cortical neuron


title: SF_Exo_3d_3


title: Con_3d_1


title: SF_Exo_3d_1


title: SF_Exo_7d_3


title: Con_7d_3


title: Con_3d_2


title: SF_Exo_7d_2


title: PHX-D7-2

first: Meng

middle: meng

last: Jiang

address: number 3728, Jinke Road

institute: Shanghai Institute of Materia Medica

data_processing:
RNA-seq data were uniquely mapped to mm10 reference genome by TopHat v1.4.1
Expression values were assigned to gene level by Cufflinks v1.3.0
Assembly: mm10
Supplementary files format and content: tab-delimited text files include gene id and RPKM value

source_name: liver

extract_protocol:
IL6 induced hepatocytes or mouse liver were removed, flash frozen on dry ice, total RNA was extracted using Trizol (Invitrogen) according to the manufacturer’s instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.
RNA library for RNA-seq was prepared as flows: mRNA was purified from total RNA using polyT and then fragmented into 300~350 bp fragments, the first strand cDNA was reverse-transcribed using fragmented RNA and dNTPs (dATP, dTTP, dCTP and dGTP) and second strand cDNA synthesis was subsequently performed. Remaining overhangs of double-strand cDNA were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, sequencing adaptors were ligated to the cDNA and the library fragments were purified. The template was enriched by PCR, and the PCR product was purified to obtain the final library

value: liver

value: WT

value: 2/3 partial hepatectomy