title: F1water_1

city: Los Angeles

first: Yen-Wei

address: 650 Charles E. Young Dr. South  16-035 Center for Health Sciences

department: IDP Molecular Toxicology

institute: University of California, Los Angeles

data_processing:
Data quality checks were performed using the Cellranger tool
Reads passing quality control were further aligned to pre-mRNA reference transcriptome generated by replacing “transcript” to “exon” in annotation GTF file.
Genome_build: ce10
Supplementary_files_format_and_content: filtered_feature_bc_matrix produced by Cellranger

organism: Caenorhabditis elegans

source_name: C. elegans whole worm body

growth_protocol: Worms were maintained on standard nematode growth medium (NGM) plates streaked with single colony Harvard OP50 E. coli. All experiments were grown at 20°C up until the generation right before sequencing during which they were moved at the L1 stage to 25°C and grown until day 2 of adulthood (i.e. 48 hours at 25°C). The JK560 (fog-1(q253) I.) strain used in this study was obtained from the C. elegans Genetics Center (CGC). This strain was chosen due to its defect in the last step of spermatogenesis. These mutants were observed to have a fully developed germline but not fertilized embryos.

extract_protocol:
All reagents except for Triton-X100, PBS-BSA 1%, and inhibitors were prepared the night before and all low retention 1.5mL microcentrifuge tubes were clearly labeled. The bench space and equipment used in this protocol were thoroughly sanitized with 70% ethanol and cleaned with RNaseZAP (AM9780 Fisher) before starting the dissociation. Reagents were prepared using RNase free water (BP2484100 Fisher). The FA lysis buffer was made using the following reagents: 50mM HEPES/NaOH pH 7.5, 1mM EDTA, 0.1% Triton X-100, 150mM NaCl, Protease inhibitor 0.5X (Roche 11697498001), RNase inhibitor 0.2U/μL (Thermo Fisher 10777019), and RNase free water and stored at 4°C or on ice. BSA was prepared to a final concentration of 1% in pH 7.4 1X PBS (AM9624 Thermo Fisher) using RNAse free water and RNAse free PBS. This solution was filtered using a 0.22μm pressure filter (Thermo Scientific 03-377-26, Fisher SLGP033RS). All equipment and reagents were moved to a 4°C cold room and subsequent steps were performed at 4°C.Homogenizers were stored pre-chilled in -20°C when not in use and moved to the 4°C room before starting the extraction. Each wheaton 1.5mL Dounce homogenizers (Z378623-1EA Sigma) was cleaned using 70% ethanol, RNaseZAP, and RNase free water. Homogenizers were rinsed twice with ethanol, twice with RNaseZAP, and 5 times with 1-2mL of RNase free water. The compact 30μL pellet of adult C. elegans was transferred to the dounce homogenizer and 400μL of ice cold FA buffer was used to rinse any remaining worms from the 1.5mL low bind microcentrifuge tube and 1000μL low bind pipette tip and added to the homogenizer. Worms were homogenized with 10 strokes of the dounce homogenizer using a corkscrew motion with a B (tight) pestle. Homogenized worms were transferred to a new low bind 1.5ml microcentrifuge tube and centrifuged at 100g for 1 minute to pellet debris. The supernatant containing the dissociated nuclei was removed using a 1000μL low bind tip and transferred to a fresh low bind 1.5mL microcentrifuge tube labeled pooled nuclei. 300μL of FA buffer was added to the debris remaining in the first microcentrifuge tube and homogenized using 10 strokes in a corkscrew fashion with an Eppendorf Dounce homogenizer. The newly homogenized sample was then centrifuged at 100g for 1 minute to pellet debris. The supernatant containing the newly dissociated nuclei was pooled with the previously dissociated nuclei and the previous steps with the Eppendorf Dounce homogenizer were repeated once more to further homogenize the sample. In total, worms were homogenized with 30 strokes: 10 strokes with the 1.5mL Wheaton Dounce homogenizer and 20 strokes with the Eppendorf dounce homogenizer. Between each homogenization step, debris was pelleted using 100g for 1 minute and the supernatant containing the dissociated nuclei was removed and added to a single 1.5mL microcentrifuge tube labeled pooled nuclei. Dissociated nuclei were removed after each set of 10 homogenization strokes to prevent overdigestion of nuclei. After homogenization, the pooled supernatant containing the dissociated nuclei was centrifuged at 100g for 1 minute to pellet any remaining or accidentally transferred debris. The top 900μL of supernatant containing nuclei was transferred to a clean low bind 1.5mL microcentrifuge tube, being careful not to disturb the debris pellet. These pooled nuclei were pelleted at 500g for 4 minutes. After pelleting, approximately 800μL of FA buffer was removed, being careful not to disrupt the nuclei pellet, and the pelleted nuclei was resuspended with 1000μL of PBS-BSA 1%. The nuclei was again centrifuged at 500g for 4 minutes and 1000μL of the PBS-BSA 1% supernatant was removed. Lastly, the nuclei pellet was resuspended in 750-850μL of PBS-BSA 1% (final volume was determined by examining the size of the nuclei pellet). After resuspension, the nuclei was filtered using a 40μm Flowmi tip filter (BAH136800040-50EA Sigma Aldrich). Filtered nuclei were transferred to a 1.5mL low retention microcentrifuge tube for FACS sorting or 10X sequencing.
Library preparation was performed by UCLA Technology Center for Genomics & Bioinformatics. Nuclei were isolated into single droplets and barcoded using the 10X platform. We sequenced using 50bp long paired end reads with the NovaSeq 6000 .

treatment_protocol: Worms were synchronized using a 10μm nylon mesh filter (NY1102500 EDM Millipore and SX00025000 EDM Millipore) which only allowed L1 staged worms to pass. The L1 worms were washed twice with M9 and centrifuged at 100g for 1 minute. These pellets were plated on fresh NGM plates and transferred to 25°C. Worms were grown for 62 hours at 25°C and were washed 5 times with M9. Between each wash, adult worms were centrifuged at 1300g for 1 minute to remove bacteria. After washing, worms were placed in 1mL of M9 in a 1.5mL low retention microcentrifuge tube and incubated in a rotator at 20°C for 30 minutes to remove residual OP50 from the worms gut. These microcentrifuge tubes were then set upright and the worms were allowed to settle by gravity for 5 minutes. The M9 supernatant was discarded and the final compact worm pellet volume was adjusted to 30μL.

tag: experiment design

value: water

tag: treatment group

value: whole worm body

tag: generation


title: F1ethanol_1

status: Public on Mar 31 2023

type: SRA

last: Chen

country: USA

library_source: transcriptomic

molecule: total RNA

value: 0.05% ethanol

value: ethanol

tag: tissue


title: F1water_2


title: F1ethanol_2


title: unexposed_5

value: unexposed


title: liver 661

type: genomic

city: Minneapolis

first: Maria

last: Razzoli

state: Minnesota

department: Integrative Biology and Physiology

institute: University of Minnesota

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Mouse Methylation Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software

label: biotin

molecule: genomic DNA

organism: Mus musculus

source_name: liver

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from liver samples using Qiagen DNeasy Kit according to standard instructions

tag: gender

value: Male

tag: sample type

value: frozen liver

tag: disease state

value: normal

tag: strain


title: unexposed_3


title: liver 662


title: liver 653


title: unexposed_4


title: H1N1_lnc-3

city: hangzhou

first: Hu

last: boli

state: zhejiang

address: Yuhangtang Road No.866

country: China

institute: Zijingang Campus of Zhejiang University

description: infected at MOI=10 and harvested at 18 hour post infection

data_processing:
The adaptors, low-quality reads and poly-N were removed by the Trim Galore_v0.4.2 (http://www.bioinformatics.babraham.ac.uk/projects/). Quality control analysis was performed by Fast QC_v0.11.5 software
Clean reads were mapped to the human reference genome (version: Homo_sapiens. GRCh38) by STAR_v2.5.2b software suite.
LncRNAs were identified using four predicted tools including predictor of lncRNAs based on Coding Potential Calculator (CPC2-beta) ，Coding Potential Assessment Tool (CPAT version 1.2.2)
The transcripts were assembled with the mapped reads using Stringtie_v1.3.1
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: tab-delimited excel files include  normalized  values for each Sample

organism: Homo sapiens

extract_protocol:
Total RNA was isolated from infected cells using SuPerfecTRITM Total RNA Isolation Reagent (Pufei) according to the manufacturer.
Ribo-zero-magnetic-kit (Epicentre, USA) was used to remove ribosomal RNA. RNA libraries were prepared using TruSeq® RNA LT Sample Prep Kit v2(illumine, USA). Library sequencing was performed on a Illumina Hiseq 3000 platform (Illumina Inc., San Diego, CA) in ShangHai Genergy Biotech (Shanghai, China).

treatment_protocol: A549 cells were infected with H1N1 at a multiplicity of infection (MOI) of 10 and harvested at 18 hour post infection or without, respectively.

tag: cell line

value: human lung epithelial cells

value: A/Puerto Rico/8/34(H1N1)

tag: genotype

tag: treatment

value: infected with H1N1


title: unexposed_2


title: liver 647


title: H1N1_lnc-2


title: H1N1_lnc-1


title: unexposed_1


title: liver 641


title: A549_lnc-3

description: control

value: uninfected


title: A549_lnc-1

description: control


title: A549_lnc-2

description: control


title: liver 640


title: LoNA KO 24h embryo with p300 inhibitor AcNPM1 rep3

city: Hefei

first: Ding

middle: feng

last: Li

address: Huang shan road 443

institute: USTC

description:
embryos AcNPM1 LoNA KO with p300
acNPM1 LoNA KO 24h embryos with p300 inhibitor normalized control 24h embryos .txt

library_source: genomic

data_processing:
bcl2fastq2 V2.2 software used for basecalling and parameter is default
inhouse scripts used for filtering
bowtie2 V2.1.0 used for alignment
MACS2 V2.1.1 used for peak-calling
normalization also used inhouse scripts and cauculated
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited txt files include normalized peak value for each group

source_name: embryos

growth_protocol: Normal culture condition for embryos

extract_protocol: HyperactiveTM In-Situ ChIP Library Prep Kit for Illumina (Vazyme, TD902)

treatment_protocol: p300 inhibitor

value: embryos

tag: antibody

value: AcNPM1 (Millipore,MABE938)


title: LoNA KO 24h embryo with p300 inhibitor AcNPM1 rep1


title: HC_2_IP

first: ming

state: Anhui

address: No.117 Meishan Road, Shushan District

department: Department of Rheumatology

institute: The First Affiliated Hospital of Anhui University of Chinese Medicine

data_processing:
Illumina bcl2fastq 2.0 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using HISAT2
Differential m6 A modified peaks between IP and input samples were identified using exomePeak
Gene counts were normalized using geometric mean (GEO) in DESeq2 package and log2 transformed.
Assembly: hg38

source_name: synovial

extract_protocol:
Total RNA was isolated using TRIzol reagent
m6A-IP and library preparation were performed per the reported protocol with some modifications.The purified mRNA fragments were then used to construct libraries with TruSeq Stranded mRNA Library Prep Kit

value: synovial

tag: disease

value: Healthy Control


title: liver 646


title: HC_1_Input


title: LoNA KO 24h embryo AcNPM1 rep3

description:
embryos AcNPM1 LoNA KO
acNPM1 LoNA KO 24h embryos normalized control 24h embryos .txt


title: HC_1_IP


title: HC_2_Input


title: liver 637


title: liver 630


title: LoNA KO 24h embryo AcNPM1 rep2


title: liver 643


title: liver 666


title: liver 629


title: RA_2_Input

value: Rheumatoid arthritis


title: liver 636


title: Control 24h embryo AcNPM1 rep3

description:
embryos AcNPM1 control
acNPM1 LoNA KO 24h embryos normalized control 24h embryos .txt


title: liver 627


title: Control 24h embryo AcNPM1 rep2


title: RA_2_IP


title: Control 24h embryo AcNPM1 rep1


title: liver 633


title: LoNA KO 24h embryo H3K4me3

description:
embryos H3K4me3 LoNA KO
H3K4me3 LoNA KO 24h embryos normalized control 24h embryos .txt

value: H3K4me3 (Abcam,ab8580 )


title: Control 24h embryo H3K4me3

description:
embryos H3K4me3 control
H3K4me3 LoNA KO 24h embryos normalized control 24h embryos .txt


title: RA_1_Input


title: LoNA KO 24h embryo AcNPM1 rep1


title: liver 670


title: lettingae_TMO_EXP_20MPa_rep3A

status: Public on Mar 30 2023

city: Marseille

first: Romain

last: Fenouil

address: Parc Scientifique et Technologique de Luminy - Case 906

department: CIML

country: France

institute: CNRS

data_processing:
In the preprocessing step, base-quality of raw and trimmed fastq files were analyzed with 'fastqc 0.11.5'.
Sequences were trimmed with 'TrimGalore 0.4.5' to remove low-quality bases (phred score <20) and eventual sequencing adapters before alignment to corresponding reference genome (p.elfii: GCF_000504085.1_ASM50408v1, p.lettingae: GCF_000017865.1_ASM1786v1) with 'STAR 2.5.3a' ('alignMatesGapMax'=10000, and disabling splicing alignment by setting 'alignSJoverhangMin'=999 and 'alignIntronMax'=1).
Post-alignment statistics were computed with 'RSeQC 2.6.4' 'preseq 2.0' and 'R 3.4.4' package 'dupradar'.
A summary of read counts for annotations categories was computed with the 'featurecount' from 'subread 1.6.0'.
Assembly: Pseudothermotoga lettingae:ASM1786v1(GCF_000017865.1), Pseudothermotoga elfii:ASM50408v1(GCF_000504085.1)
Supplementary files format and content: Text files (txt) contain gene counts computed by ‘featurecount’

molecule: polyA RNA

organism: Pseudothermotoga lettingae TMO

source_name: Cultured bacteria

extract_protocol:
RNAs were prepared using the Maxwell 16 LEV samples kit (Promega) and ribosomal RNAs were depleted using the Illumina Ribo-zero Plus rRNA depletion kit (Illumina, San Diego, CA, USA)
The sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina by following manufacturer’s recommendations (NEB, Ipswich, MA, USA). Sequencing libraries were validated using a DNA Chip on the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA, USA) as well as by quantitative PCR (Applied Biosystems, Carlsbad, CA, USA).
The sequencing libraries were multiplexed and clustered on six lanes of a flowcell. After clustering, the flowcell was loaded on the Illumina HiSeq 2500 instrument according to manufacturer’s instructions. The multiplexed libraries were sequenced using paired-end 150 cycle chemistry for the HiSeq 2500 (Illumina). Image analysis and base calling were conducted by the HiSeq Control Software (HCS) on the HiSeq 2500 instrument.

value: TMO

tag: cell type

value: Cultured bacteria

tag: growth phase

value: exponential

tag: growth pressure


title: lettingae_TMO_EXP_20MPa_rep2A


title: lettingae_TMO_EXP_0.1MPa_rep5AB


title: lettingae_TMO_EXP_0.1MPa_rep4AB


title: lettingae_TMO_EXP_20MPa_rep4A


title: lettingae_TMO_EXP_20MPa_rep1A


title: RA_1_IP


title: lettingae_TMO_EXP_0.1MPa_rep3AB


title: Control 24h embryo H3K27me3

description:
embryos H3K27me3 control
H3K27me3 LoNA KO 24h embryos normalized control 24h embryos .txt

value: H3K27me3 (arigo Biolaboratories,ARG54767 )


title: lettingae_TMO_EXP_0.1MPa_rep2AB


title: LoNA KO 24h embryo H3K27me3

description:
embryos H3K27me3 LoNA KO
H3K27me3 LoNA KO 24h embryos normalized control 24h embryos .txt


title: SGD_Chd1_ORC_mid_rep2

city: Planegg-Martinsried

first: Erika

last: Chacin

address: Grosshaderner Strasse 9

country: Germany

institute: BMC - Ludwig-Maximilians-Universität München

description: 50 bp

data_processing:
The data processing of the MNase-seq data was done as described before with modifications (Oberbeckmann, E. et al., 2021). Sequencing reads were mapped to the S. cerevisiae SacCer3 (R64-1-1 build) using Bowtie2 (version 2.3.5.1) (Langmead, B. and Salzberg, S.L., 2012) and reads aligning to multiple sites were removed. This was then imported into R Studio by using GenomicAlignments (Lawrence, M. et al., 2013). For the single-end data, reads were shifted by 73 bp and extended to 50 bp, while for the paired-end data, reads with a fragment length between 139 and 191 bp were selected and extended to 60 bp. The coverage was calculated and aligned to a list of ACS sites (Soriano, I. et al., 2014). The signal was normalized per ARS in a 2000 bp window centered at the ACS motif.
SacCer3
bw (bigwig) files were generated from genome coverage files using rtracklayer (Lawrence et al. 2009).

organism: Saccharomyces cerevisiae

source_name: yeast

extract_protocol: The reactions with reconstituted chromatin were incubated with 100 U MNase (Sigma-Aldrich) and 1.5 mM CaCl2 for 5 min at 30 °C. The digest was stopped by the addition of 10 mM EDTA and 0.5 % SDS. This was followed by a proteinase K treatment for 1 h at 37 °C and ethanol precipitation. The sequencing libraries of the vitro reconstituted chromatin samples were prepared as previously described (Oberbeckmann, E., Niebauer, V. et al., 2021; Oberbeckmann, E., Krietenstein, N. et al., 2021) by using 10-50 ng mononucleosomal DNA. The amplified DNA was run in a 1.5 % agarose gel, cut out, purified and the concentration was measured with the Qubit dsDNA HS Assay Kit (Fisher Scientific). The libraries were diluted to 10 nM, pooled according to the sequencing reads (~ 5 million reads/sample), and quantified via BioAnalyzer (Agilent). The pool was sequenced either on an Illumina HiSeq 1500 in 50 bp single-end mode or on an Illumina NextSeq 1000 in 60 bp paired-end mode (Laboratory for Functional Genome Analysis, LAFUGA, LMU Munich).

treatment_protocol: The in vitro remodeling assay was done as previously described with modifications (Oberbeckmann, E., Niebauer, V. et al., 2021; Oberbeckmann, E., Krietenstein, N. et al., 2021). The following concentrations of chromatin factors were used: 30 nM ORC, Orc1 mutants (BAH, IDR, Walker B, BAH-IDR); 20 nM INO80, Chd1; 10 nM ISW1a, ISW2, Fun30, RSC, SWI/SNF, SWR1, Asf1, CAF1, FACT, HIR, Nap1, Nhp6, Spt6, Rtt106, Vps75. The reactions were done in a buffer containing 20 mM HEPES pH 7.5, 50 mM NaCl, 3 mM MgCl2, 2.5 mM DTT, 2.5 mM ATP, 0.5 mM EGTA, 12 % glycerol and started by the addition of the SGD chromatin, incubated for 2 h at 30 ˚C and stopped by addition of 0.2 U apyrase (NEB), incubated at 30 ˚C for 20 min.

value: yeast

tag: chromatin

value: in vitro reconstituted chromatin

tag: histone type

value: Saccharomyces cerevisiae

tag: orc

value: ORC

tag: remodeler

tag: histone chaperone


title: lettingae_TMO_EXP_0.1MPa_rep1AB


title: SGD_Chd1_ORC_mid_rep1

description: 50 bp


title: lettingae_TMO_EXP_20MPa_rep5A


title: SGD_ISW2_ORC_mid_rep2

description: 50 bp


title: SGD_Chd1_ORC_rep4

description: 60 bp


title: SGD_INO80_ORC_mid_rep2

description: 60 bp


title: SGD_ISW1a_ORC_mid_rep1

description: 50 bp


title: SGD_INO80_ORC_mid_rep1

description: 60 bp


title: Orc1-IDR-rep2

description: 60 bp

data_processing:
The data processing of the MNase-seq data was done as described before with modifications (Oberbeckmann, E. et al., 2021). Sequencing reads were mapped to the S. cerevisiae SacCer3 (R64-1-1 build) using Bowtie2 (version 2.3.5.1) (Langmead, B. and Salzberg, S.L., 2012) and reads aligning to multiple sites were removed. This was then imported into R Studio by using GenomicAlignments (Lawrence, M. et al., 2013). For the single-end data, reads were shifted by 73 bp and extended to 50 bp, while for the paired-end data, reads with a fragment length between 139 and 191 bp were selected and extended to 60 bp. The coverage was calculated and aligned to a list of ACS sites (Soriano, I. et al., 2014). The signal was normalized per ARS in a 2000 bp window centered at the ACS motif.
genome build/assembly (used for read alignment): SacCer3
processed data files format and content: bw (bigwig) files were generated from genome coverage files using rtracklayer (Lawrence et al. 2009).

growth_protocol: A 500 mL YPDA culture was incubated at 30 °C for 16-20 h until reaching OD600 = 0.6-1.0 (measured with a GENESYS 20 Visible Spectrophotometer (Thermo Fisher)). The cells were collected by centrifugation and the nuclei isolation was performed as previously described with modifications (Oberbeckmann, E., Niebauer, V. et al., 2021; Almer, A. & Hörz, W., 1986). Spheroblasts were generated by incubation with zymolyase (MP Biomedicals zymolyase 100T) in 1 M sorbitol, washed and resuspended in a Ficoll solution (18 % Ficoll Type 400 (Sigma-Aldrich), 20 mM KH2PO4, 1 mM MgCl2, 0.25 mM EGTA pH 8.0, 0.25 mM EDTA pH 8.0). This was then aliquoted and centrifuged for 30 min at 22,550 g 4 °C. The nuclei pellets were frozen in a dry ice/ethanol bath and stored at - 80 °C.

extract_protocol:
The nuclei samples were digested with 16-32 U MNase in MNase buffer (150 mM Tris-HCl pH 7.5, 500 mM NaCl, 14 mM CaCl2, 2 mM EDTA, 2 mM EGTA and 50 mM β-mercaptoethanol) to get an 80 % mono- / 20 % di- nucleosome distribution. The reaction was stopped by addition of 10 mM EDTA and 0.5 % SDS. This was followed by a proteinase K digestion, phenol-chloroform extraction, ethanol precipitation, RNAse A digestion and isopropanol precipitation. The purified DNA was run in 1.5 % agarose gels for 1.5 h at 110 V constant in 1X TAE, the mononucleosomal DNA was cut out and purified using the PureLink Quick Gel Extraction kit (Invitrogen).
The libraries from in vivo samples were prepared with the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB). The amplified DNA was run in a 1.5 % agarose gel, cut out, purified and the concentration was measured with the Qubit dsDNA HS Assay Kit (Fisher Scientific). The libraries were diluted to 10 nM, pooled according to the sequencing reads (~ 5 million reads/sample), and quantified via BioAnalyzer (Agilent). The pool was sequenced either on an Illumina HiSeq 1500 in 50 bp single-end mode or on an Illumina NextSeq 1000 in 60 bp paired-end mode (Laboratory for Functional Genome Analysis, LAFUGA, LMU Munich).

value: in vivo chromatin


title: SGD_rep6

description: 50 bp


title: SGD_ISW2_ORC_mid_rep1

description: 50 bp


title: Orc1-IDR-rep1

description: 60 bp


title: SGD_rep5

description: 50 bp


title: Orc1-BAH_rep3

description: 60 bp


title: Orc1_rescue_rep4

description: 60 bp


title: Orc1_rescue_rep2

description: 60 bp


title: SGD_Vps75_ORC_rep1

description:
genomic DNA plasmid pool
50 bp

data_processing:
The data processing of the MNase-seq data was done as described before with modifications (Oberbeckmann, E. et al., 2021). Sequencing reads were mapped to the S. cerevisiae SacCer3 (R64-1-1 build) using Bowtie2 (version 2.3.5.1) (Langmead, B. and Salzberg, S.L., 2012) and reads aligning to multiple sites were removed. This was then imported into R Studio by using GenomicAlignments (Lawrence, M. et al., 2013). For the single-end data, reads were shifted by 73 bp and extended to 50 bp, while for the paired-end data, reads with a fragment length between 139 and 191 bp were selected and extended to 60 bp. The coverage was calculated and aligned to a list of ACS sites (Soriano, I. et al., 2014). The signal was normalized per ARS in a 2000 bp window centered at the ACS motif.
Assembly: SacCer3
Supplementary files format and content: bw (bigwig) files were generated from genome coverage files using rtracklayer (Lawrence et al. 2009).

value: Drosophila melanogaster embryos


title: SGD_Spt6_rep1

description:
genomic DNA plasmid pool
50 bp


title: SGD_Spt6_ORC_rep1

description:
genomic DNA plasmid pool
50 bp


title: Orc1-BAH_rep1

description: 60 bp


title: SGD_Vps75_rep1

description:
genomic DNA plasmid pool
50 bp


title: Orc1_rescue_rep3

description: 60 bp


title: SGD_SWR1_ORC_rep1

description:
genomic DNA plasmid pool
50 bp


title: QKO

description: 60 bp

data_processing:
The data processing of the MNase-seq data was done as described before with modifications (Oberbeckmann, E. et al., 2021). Sequencing reads were mapped to the S. cerevisiae SacCer3 (R64-1-1 build) using Bowtie2 (version 2.3.5.1) (Langmead, B. and Salzberg, S.L., 2012) and reads aligning to multiple sites were removed. This was then imported into R Studio by using GenomicAlignments (Lawrence, M. et al., 2013). Reads with a fragment length between 119 and 191 bp were selected and extended to 60 bp. The coverage was calculated and aligned to a list of ACS sites (Soriano, I. et al., 2014). The signal was normalized per ARS in a 2000 bp window centered at the ACS motif.
Assembly: SacCer3
Supplementary files format and content: bw (bigwig) files were generated from genome coverage files using rtracklayer (Lawrence et al. 2009).


title: SGD_SWI/SNF_rep1

description:
genomic DNA plasmid pool
50 bp

value: SWI/SNF


title: Orc1_rescue_rep1

description: 60 bp


title: SGD_ISW1a_ORC_mid_rep2

description: 50 bp


title: chd1Δ

description: 60 bp


title: SGD_SWI/SNF_ORC_rep1

description:
genomic DNA plasmid pool
50 bp


title: SGD_Sc_rep1

description:
genomic DNA plasmid pool
50 bp


title: isw2Δ

description: 60 bp

value: in vivo


title: isw1Δ

description: 60 bp


title: arp8Δ

description: 60 bp


title: SGD_rep1

description:
genomic DNA plasmid pool
50 bp


title: SGD_Rtt106_ORC_rep1

description:
genomic DNA plasmid pool
50 bp


title: BY4741_rep1

description: 60 bp


title: SGD_Rtt106_rep1

description:
genomic DNA plasmid pool
50 bp


title: Orc1-BAH_rep2

description: 60 bp


title: W303_rep2

description: 60 bp


title: SGD_RSC_rep1

description:
genomic DNA plasmid pool
50 bp

value: RSC


title: SGD_RSC_rep2

description:
genomic DNA plasmid pool
50 bp


title: SGD_SWR1_rep1

description:
genomic DNA plasmid pool
50 bp


title: SGD_RSC_ORC_rep1

description:
genomic DNA plasmid pool
50 bp


title: SGD_Vps75_rep2

description:
genomic DNA plasmid pool
60 bp


title: SGD_RSC_ORC_rep2

description:
genomic DNA plasmid pool
50 bp


title: SGD_Vps75_ORC_rep2

description:
genomic DNA plasmid pool
60 bp


title: SGD_ORC_rep1

description:
genomic DNA plasmid pool
50 bp


title: SGD_SWR1_rep2

description:
genomic DNA plasmid pool
60 bp


title: SGD_Nhp6_ORC_rep1

description:
genomic DNA plasmid pool
50 bp


title: SGD_Nhp6_rep1

description:
genomic DNA plasmid pool
50 bp


title: SGD_SWR1_ORC_rep2

description:
genomic DNA plasmid pool
60 bp


title: SGD_SWI/SNF_rep2

description:
genomic DNA plasmid pool
60 bp


title: SGD_Nap1_ORC_rep1

description:
genomic DNA plasmid pool
50 bp


title: SGD_Nap1_rep1

description:
genomic DNA plasmid pool
50 bp


title: SGD_SWI/SNF_ORC_rep2

description:
genomic DNA plasmid pool
60 bp


title: W303_rep1

description: 60 bp


title: SGD_rep4

description:
genomic DNA plasmid pool
60 bp


title: SGD_Sc_ISW2_ORC_rep1

description:
genomic DNA plasmid pool
50 bp


title: SGD_Sc_ISW1a_ORC_rep1

description:
genomic DNA plasmid pool
50 bp


title: SGD_ISW2_ORC_rep1

description:
genomic DNA plasmid pool
50 bp


title: SGD_rep2

description:
genomic DNA plasmid pool
60 bp


title: SGD_Rtt106_ORC_rep2

description:
genomic DNA plasmid pool
60 bp


title: SGD_Rtt106_rep2

description:
genomic DNA plasmid pool
60 bp


title: SGD_ISW1a_ORC_rep1

description:
genomic DNA plasmid pool
50 bp


title: SGD_Spt6_rep2

description:
genomic DNA plasmid pool
60 bp


title: SGD_rep3

description:
genomic DNA plasmid pool
60 bp


title: SGD_RSC_rep3

description:
genomic DNA plasmid pool
60 bp


title: SGD_Sc_INO80_ORC_rep1

description:
genomic DNA plasmid pool
50 bp


title: SGD_Spt6_ORC_rep2

description:
genomic DNA plasmid pool
60 bp


title: SGD_INO80_ORC_rep1

description:
genomic DNA plasmid pool
50 bp


title: SGD_RSC_ORC_rep3

description:
genomic DNA plasmid pool
60 bp


title: SGD_HIR_ORC_rep1

description:
genomic DNA plasmid pool
50 bp

value: HIR


title: SGD_ORC_rep2

description:
genomic DNA plasmid pool
60 bp


title: SGD_ORC_rep3

description:
genomic DNA plasmid pool
60 bp


title: SGD_HIR_rep1

description:
genomic DNA plasmid pool
50 bp


title: SGD_Nhp6_ORC_rep2

description:
genomic DNA plasmid pool
60 bp


title: SGD_FACT_ORC_rep1

description:
genomic DNA plasmid pool
50 bp

value: FACT


title: SGD_Fun30_rep1

description:
genomic DNA plasmid pool
50 bp


title: SGD_Fun30_ORC_rep1

description:
genomic DNA plasmid pool
50 bp


title: SGD_Chd1_rep2

description:
genomic DNA plasmid pool
50 bp


title: SGD_Sc_Chd1_ORC_rep1

description:
genomic DNA plasmid pool
50 bp


title: SGD_Nhp6_rep2

description:
genomic DNA plasmid pool
60 bp


title: SGD_Nap1_rep2

description:
genomic DNA plasmid pool
60 bp


title: SGD_Chd1_rep1

description:
genomic DNA plasmid pool
50 bp


title: SGD_ISW2_rep3

description:
genomic DNA plasmid pool
60 bp


title: SGD_Chd1_ORC_rep1

description:
genomic DNA plasmid pool
50 bp


title: SGD_ISW2_rep2

description:
genomic DNA plasmid pool
60 bp


title: SGD_Nap1_ORC_rep2

description:
genomic DNA plasmid pool
60 bp


title: SGD_ISW2_rep1

description:
genomic DNA plasmid pool
60 bp


title: LoNA KO 24h embryo with p300 inhibitor AcNPM1 rep2

tag: tissue

value: embryos

value: AcNPM1 (Millipore,MABE938)


title: SGD_FACT_rep1

description:
genomic DNA plasmid pool
50 bp


title: SGD_CAF1_ORC_rep1

description:
genomic DNA plasmid pool
50 bp


title: biol rep 3, S.aureus only, control, 1h

city: Tromsø

first: Anne

middle: Merethe

last: Hanssen

address: Hansine Hansens veg 18

department: Medical Biology

country: Norway

institute: University of Tromsø

data_processing:
RNA seq reads were generated from 14 samples in two runs of RNA-seq. Out fo these only 11 samples were processed for DEseq2 analysis.
Sequence reads were quality checked and trimmed for adaptor sequence/low-quality sequence using FASTQC (0.11.9-Java-11 ) and Trimmomatic (0.39-Java-11) respectively.Only those sequences with the quality score Q > equal to 20 and a minimum of 55 nucleotide sequence length were retained in the dataset.
Trimmed sequence reads were mapped to S. aureus TR145 throat isolate using Bowtie2 (2.4.4-GCC-10.3.0)
Reads mapped to each gene were identified using the HTSeq (v0.11.1) counting tool. After aligning reads to a reference and generating count files, it was further analyzed by DESeq2  (Bioconductor package) on the R platform to explore any DEGs present in the sample.
Deseq Normalization was performed followed by visualization of sample variance using principal component analysis (PCA). S. aureus only at 0h was not used for DESeq2 analysis. It was visualized only from PCA plot.
The DE was further curated to give only those genes which show p-value adjusted (padj) along the indication of the gene name. The threshold for padj was adjusted to less than 0.05 (padj < 0,05) and for log2foldchange greater than 2 (LFC> 2).
Assembly: GCA_949730015
Supplementary files format and content: raw RNA seq reads generated after RNA sequencing for each Samples
Supplementary files format and content: tab-delimited text files include count matrix complied after HTseq counting tool for each Sample

organism: Staphylococcus aureus

source_name: HTEpiC- Human tonsils epithelial cells

growth_protocol: HTEpiC- Human tonsil epithelial cells were cultured using Tonsil Epithelial Cell Medium (TEpiCM, Sciencell) supplemented with 1% Tonsil Epithelial Cell Growth Supplement (TEpiCGS) and penicillin/streptomycin solution (P/S) at 37°C in a 5% CO2 incubator. Prior to the culturing of HTEpiC, the T-75 tissue culture flask was coated with 2 µg/cm2 poly-L-lysin (PLL) and incubated at 37°C for 2h or overnight.

extract_protocol:
After 1 and 3h post-infection, the media was aspirated, and the host cells were washed twice with fresh media to remove unbound bacteria. The host cells were then trypsinized and lysed with Triton-X. The released bacteria were then collected from three technical replicates and pooled together for RNA extraction. Plate enumeration, adhesion assay and cytotoxicity assay were also performed.
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.2 ug of total RNA was used for the construction of sequencing libraries.
Prior to RNA libraries for RNA-seq, depletion of bacterial rRNA was performed with the RiboCop rRNA depletion kit for Gram-Positive Bacteria (G+), according to the manufacturer’s protocol. In total 15 samples were processed for libraries construction using Lexogen’s CORALLTM Total RNA-Seq Kit with RiboCop following  he manufacturer's protocols.

treatment_protocol: HTEpiC was seeded at a density of ~ 4 × e-5 viable cells per well in six-well plates coated with PLL. S. aureus TR145 at OD600nm of 0.4 was added to HTEpiC monolayer or to empty wells (coated with PLL) in a number corresponding to Multiplicity of Infection (MOI)=5 and incubated for 1h and 3h of exposure.

value: HTEpiC- Human tonsils epithelial cells

value: primary epithelial cell line

tag: time

value: without Host

tag: group


title: biol rep 3, S.aureus only, control, 3h


title: biol rep 3, S.aureus+ tonsillar cells , test, 3h

value: with HOST


title: biol rep 3, S.aureus+ tonsillar cells , test, 1h


title: biol rep 3, S.aureus only, control, 0h

value: inoculum used to infect HOST


title: biol rep 2, S.aureus+ tonsillar cells , test, 1h


title: SGD_Asf1_ORC_rep1

description:
genomic DNA plasmid pool
50 bp

value: in vitro reconstituted chromatin

value: yeast


title: SGD_ISW2_D569Y-ORC1_rep3

description:
genomic DNA plasmid pool
60 bp


title: SGD_CAF1_rep1

description:
genomic DNA plasmid pool
50 bp


title: SGD_ISW2_D569Y-ORC1_rep2

description:
genomic DNA plasmid pool
60 bp


title: SGD_Asf1_rep1

description:
genomic DNA plasmid pool
50 bp


title: biol rep 2, S.aureus only, control, 3h


title: biol rep 2, S.aureus+ tonsillar cells , test, 3h


title: biol rep 1, S.aureus+ tonsillar cells , test, 3h


title: P16: Plasma, Pellet

city: Saint-Petersburg

first: Aleksandr

last: Khudiakov

address: 2, Akkuratova

department: Institute of molecular biology and genetics

country: Russia

institute: Almazov National Medical Research Centre

description: Plasma pellet

data_processing:
Adapter sequences were removed by Illumina Miseq Control software.
Reads were filtered by length using BBDuk tool
Small RNAs annotation and expression analyses were performed using miRge3.0 tool
Counts were normalized and DESeq2 package version 1.34.0
Assembly: miRge3.0 libraries
Supplementary files format and content: Comma separated values table with normalized miRNA counts for every miRNA and every sample

source_name: blood

extract_protocol:
Peripheral blood samples from two healthy were collected into sterilize vacutainer blood collection tubes with K3-EDTA, pooled and processed within 6h after blood collection. Erythrocytes, leukocyte-platelet suspension and plasma fractions were collected after the first centrifugation of the whole blood sample at 1500 g for 10 minutes.  Platelets and leukocytes (CD45+cells) were obtained by highly sensitive fluorescence activated cell sorting. Subpopulations of plasma EVs were obtained using high-sensitivity fluorescence activated vesicle sorting. Additionally, 500 µl plasma sample collected after the whole blood centrifugation step described above was centrifuged at 16000 g for one hour at +4C, then 450 µl of the upper fraction supernatant (S16) was collected. Whereas, the pellet (P16) was resuspended in 100 µl PBS рН 7.4.
Small RNA libraries were generated using Small RNA-SeqKit (Lexogen, Vienna, Austria) according to manufacturer’s recommendations. The number of amplification cycles was 22 for sorted CD45+ cells and extracellular vesicle samples and 16 for other samples.

value: blood

value: Cell-free plasma


title: biol rep 1, S.aureus+ tonsillar cells , test, 1h


title: biol rep 2, S.aureus only, control, 0h


title: SGD_ISW2_ORC_rep4

description:
genomic DNA plasmid pool
60 bp

value: Drosophila melanogaster embryos

value: ORC


title: SGD_ISW2_D569Y-ORC1_rep1

description:
genomic DNA plasmid pool
60 bp


title: biol rep 1, S.aureus only, control, 3h


title: biol rep 1, S.aureus only, control, 0h


title: SGD_ISW2_ORC_rep3

description:
genomic DNA plasmid pool
60 bp


title: CD146: Extracellular vesicles, CD146-positive

description: Blood CD146-positive extracellular vesicles

value: Extracellular vesicles


title: SGD_ISW2_ORC_rep2

description:
genomic DNA plasmid pool
60 bp


title: CD45 : Extracellular vesicles, CD45-positive

description: Blood CD45-positive extracellular vesicles


title: CAU30 Dipeptides III

city: Paris

first: Philipp

last: Brandt

address: 25-28 Rue du Dr Roux

department: Mycology

institute: Institut Pasteur

data_processing:
Fastq files were assessed for sequence quality using FastQC (version 0.11.9) and a genome index from file C_auris_B8441_version_s01-m01-r21_chromosomes.fasta fom http://www.candidagenome.org/ was created with bowtie2 (version 2.3.5.1). Mapping of reads to the index was performed with bowtie2. Reads were counted and assigned to the corresponding genome using function featureCounts of R package Rsubread (version 2.2.6). Contrasts were calculated using R package DESeq2 (version 1.28.1). R version 4.0.4 was used.
Assembly: C_auris_B8441_version_s01-m01-r21_chromosomes.fasta
Supplementary files format and content: Raw.counts.B8441.S49.69.csv, Comma seperated text file containing counts of all samples

organism: Candidozyma auris

source_name: Planktonic cells

growth_protocol: C. auris was pre-grown overnight at 37°C in YPD (1% yeast extract, 2% peptone, 2% glucose) and used to set log-cultures in SD (0.17 yeast nitrogen base w/o ammonium sulfate and w/o amino cids, 0.5% ammonium sulfate, 2% glucose) at OD600 0.2. Log-cultures were incubated at 37°C until OD600 of ~1 was reached. Cells were collected, washed twice with PBS and resuspended in PBS and used to set OD600 to 0.2 in the respective test medium and incubated for 4 h at 37°C and shaking at 180 rpm.

extract_protocol:
For total RNA isolation cells were resuspended in 440 µl AE buffer with 10% SDS and 440 µl of Acid-phenol:Chloroform with isoamyl alcohol (Ambion, Germany) was added. The suspension was thoroughly mixed and incubated for 5 min at 65°C, frozen at -80°C for 30 min and subsequently thawed at 65°C for 5 min. The phases were separated via 4 min centrifugation at 13,000 g, the upper aqueous phase transferred and 1/10 of the volume sodium acetate (pH 5.3) and 1 volume of 2 propanol was added to precipitate the RNA overnight at -20°C. The supernatant was discarded after 10 min centrifugation at 12,000 g, the RNA pellet washed twice with 70 % ethanol and finally solved in 300 µl nuclease free H2O. Quality and quantity of the RNA was assessed using 2100 Bioanalyzer (Agilent Technologies, California, USA) and Nanodrop (Thermo Fischer Scientific, Massachusetts, USA) measurements.
A total amount of 0.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA. Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA by mRNAusing poly-T oligo-attached magnetic beads. Fragmentation was carried out by Covaris sonication. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using dTTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality and quantity are assessed by Qubit and real-time PCR. Sequencing platform was Illumina Novaseq 6000 PE150.
Paired end RNA sequencing of cDNA fragments of preferentially 150~200 bp in length.

treatment_protocol: Cells were separated from test medium by centrifugation 4 min at 4000g and 4ºC. Cells were shock frozen in liquid nitrogen and stored at -80°C until further processing.

value: yeast cells

tag: genotype/variation

value: B8441 clade I isolate

tag: medium type

value: 0.17% YNB w/o ammonium sulfate and w/o amino acids; 3.4 mM Ala-Gln, 3.3 mM Ala-Ser, 3.3 mM Arg-Asp; 1% Glucose; pH 5

tag: time point

value: 4 h


title: CAU30 Dipeptides I


title: CAU30 Dipeptides II


title: CD235: Extracellular vesicles, CD235a-positive

description: Blood CD235a-positive extracellular vesicles


title: AD, d21, Replicate 3

city: Munich

first: Dongsheng

last: Jiang

address: Max-Lebsche-Platz 31

department: Institute of Regenerative Biology and Medicine

institute: Helmholtz Zentrum München

data_processing:
RNA-Seq raw reads were mapped to the mouse genome build mm10 using the STAR in nf-core/rnasea. The mapped reads were then counted using salmon.
Raw counts were applyed differential gene expression analysis (DEG) using DEseq2 (version 1.34.0 with R version 4.1.2).
Normalized counts were scaled for Pearson’s correlation matrices and plotting feature genes expression in heat map.
Gene ontology (GO) enrichment of DEGs was done using clusterProfiler (version 4.2.2) and viewed by ggplot2 (Version 3.3.6)
Assembly: mm10
Supplementary files format and content: tsv files include raw coults for each Sample

source_name: Skin

extract_protocol:
Sorted GFP+ cells were lysed and cDNA synthesis and expansion were performed using the Smart-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Takara #634889), according to manufacturer’s instructions. The amplified cDNA was purified with NucleoMag NGS Clean-up and Size Select beads (Takara 7449705).
The library preparation were performed by Biomarker Technologies (BMKGene) GmbH (Münster, Germany). Double-stranded cDNA were ligated with adaptors, enriched by Agencourt AMPure XP beads (Beckman Coulter, Inc) and amplified by PCR.

treatment_protocol: 5-mm full-thickness excisional wounds were made on the back of AdipoqCre;R26mTmG and En1Cre;R26mTmG mice. Wounds were harvested at 10 days and 21 days after wounding. Adipocytes were FACS sorted as GFP+ cells from AdipoqCre;R26mTmG wounds, and fibroblasts were FACS sorted from En1Cre;R26mTmG wounds.

value: Skin

value: Adipocytes

tag: genotype

value: AdipoqCre+

tag: treatment

value: Excisional wound at day 21


title: CAU30 Proline III

value: 0.17% YNB w/o ammonium sulfate and w/o amino acids; 0.5% ammonium sulfate; 1% Proline; pH 5


title: CAU30 Proline II


title: CD41: Extracellular vesicles, CD41-positive

description: Blood CD41-positive extracellular vesicles


title: CAU30 Proline I


title: CD45Cells: Leucocytes

description: Leucocytes (CD45-positive)

value: Leucocytes


title: CAU30 α-ketoglutarate II

value: 0.17% YNB w/o ammonium sulfate and w/o amino acids; 0.5% ammonium sulfate; 1% α-ketoglutarate; pH 5


title: CAU30 α-ketoglutarate I


title: SGD_ISW2_ΔIDR-ORC1_rep3

description:
genomic DNA plasmid pool
60 bp

value: in vitro reconstituted chromatin

value: yeast


title: SGD_ISW2_ΔIDR-ORC1_rep2

description:
genomic DNA plasmid pool
60 bp


title: SGD_ISW2_ΔBAH-ORC1_rep3

description:
genomic DNA plasmid pool
60 bp


title: CAU30 α-ketoglutarate III


title: CAU30 Malic acid II

value: 0.17% YNB w/o ammonium sulfate and w/o amino acids; 0.5% ammonium sulfate; 1% malic acid; pH 5


title: CAU30 Malic acid III


title: SGD_ISW2_ΔIDR-ORC1_rep1

description:
genomic DNA plasmid pool
60 bp

value: Drosophila melanogaster embryos


title: SGD_ISW2_ΔBAH-ORC1_rep2

description:
genomic DNA plasmid pool
60 bp


title: Plt: Platelets

description: Platelets

value: blood

value: Platelets


title: S16: Plasma, Upper fraction

description: Plasma upper fraction supernatant

value: Cell-free plasma


title: biol rep 1, S.aureus only, control, 1h

tag: cell line

value: HTEpiC- Human tonsils epithelial cells

value: primary epithelial cell line

value: without Host


title: CAU30 Malic acid I

tag: cell type

value: yeast cells

value: B8441 clade I isolate

value: 4 h


title: CAU30 Glucose III

value: 0.17% YNB w/o ammonium sulfate and w/o amino acids; 0.5% ammonium sulfate; 1% glucose; pH 5


title: Rbc: Erythrocytes

description: Erythrocytes

value: Erythrocytes


title: CAU30 Glucose II


title: S4-8-2

city: Shanghai

first: Yuhang

address: 320 Yueyang Road

institute: Shanghai Institutes for Biological Sciences

data_processing:
Raw reads of fastq format were firstly processed using fastp1 and the low quality reads were removed to obtain the clean reads.
Then clean reads for each sample were retained for subsequent analyses.
The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples.
Assembly: hg19
Supplementary files format and content: Text files include FPKM values for each Sample

source_name: SUDHL-4 cells, FDX1-OE, ES 48h

growth_protocol: SUDHL-4 cells were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

treatment_protocol: ES (5 nM) or DMSO was added to the culture medium

value: cell line

value: DLBCL cells

value: FDX1 overexpression

value: Elesclomol


title: SGD_ISW2_ΔBAH-ΔIDR-ORC1_rep3

description:
genomic DNA plasmid pool
60 bp

value: in vitro reconstituted chromatin

value: yeast


title: S4-7-2

source_name: SUDHL-4 cells, control, ES 48h

value: WT


title: Treg10_hs_72h

city: Diepenbeek

first: Ibrahim

last: HAMAD

state: Yes

address: Agoralaan Building C

department: Hasselt University

country: Belgium

data_processing:
Quality of raw sequence reads was checked using FastQC version 0.11.8, and nucleotide calls with a quality score of 28 or higher were considered high quality. Adapters were removed using cutadapt v.2.4. Reads were aligned to the hg19 genome reference, using STAR (2.5.0e) and amaximum of five mismatches were allowed.
the raw counts were imported to R/Bioconductor package DESeq2 v.3.9 to identify differentially expressed genes among samples. The default DESeq2 options were used, including log fold change shrinkage.
Assembly: hg19 genome reference

source_name: T cells

growth_protocol: standard cell culture

extract_protocol:
QIAGEN total RNA extraction (Rneasy mico kit)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: changes in microenvironment

value: blood

value: +40mM NaCl


title: S4-8-1


title: Treg10_ctrl_72h

value: CTRL


title: Treg9_hs_72h


title: SGD_ISW2_ΔBAH-ΔIDR-ORC1_rep2

description:
genomic DNA plasmid pool
60 bp

value: Drosophila melanogaster embryos


title: S4-7-1

source_name: SUDHL-4 cells, control,ES 48h


title: Treg9_ctrl_72h


title: Treg2_hs_72h


title: SGD_ISW2_ΔBAH-ΔIDR-ORC1_rep1

description:
genomic DNA plasmid pool
60 bp


title: Treg7_hs_72h


title: Treg7_ctrl_72h


title: Treg1_ctrl_72h


title: SGD_ISW1a_rep1

description:
genomic DNA plasmid pool
60 bp


title: Treg2_ctrl_72h


title: SGD_ISW1a_rep3

description:
genomic DNA plasmid pool
60 bp


title: Treg5_AA_6h

value: AA


title: S4-2-1

source_name: SUDHL-4 cells, FDX1-OE, DMSO 48h

value: DMSO


title: S4-1-2

source_name: SUDHL-4 cells, control, DMSO 48h


title: SGD_ISW2_ΔBAH-ORC1_rep1

description:
genomic DNA plasmid pool
60 bp


title: Treg5_hs_6h


title: Treg5_ctrl_6h


title: SGD_ISW1a_D569Y-ORC1_rep1

description:
genomic DNA plasmid pool
60 bp


title: S4-1-1


title: Treg4_AA_6h


title: CAU30 Glucose I

value: yeast cells

value: B8441 clade I isolate


title: SGD_ISW1a_D569Y-ORC1_rep3

description:
genomic DNA plasmid pool
60 bp


title: Treg1_hs_72h


title: SGD_ISW1a_D569Y-ORC1_rep2

description:
genomic DNA plasmid pool
60 bp


title: Treg4_hs_6h


title: Treg2_hs_6h


title: S4-2-2


title: WSU-8-2

source_name: WSU-DLCL2 cells, FDX1-OE, ES 48h

growth_protocol: WSU-DLCL2 cells were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

treatment_protocol: ES (15 nM) or DMSO was added to the culture medium


title: Treg2_ctrl_6h


title: Treg3_AA_6h


title: SGD_ISW1a_rep2

description:
genomic DNA plasmid pool
60 bp


title: Treg3_hs_6h


title: Treg1_hs_6h


title: WSU-7-2

source_name: WSU-DLCL2 cells, control, ES 48h


title: Treg1_ctrl_6h


title: WSU-8-1


title: Treg3_ctrl_6h


title: SGD_ISW1a_ORC_rep2

description:
genomic DNA plasmid pool
60 bp

value: ORC


title: SGD_ISW1a_ORC_rep3

description:
genomic DNA plasmid pool
60 bp


title: SGD_ISW1a_ORC_rep4

description:
genomic DNA plasmid pool
60 bp


title: Treg2_ctrl_0h


title: Treg1_ctrl_0h


title: WSU-7-1

source_name: WSU-DLCL2 cells, control,ES 48h


title: SGD_ISW1a_ΔIDR-ORC1_rep3

description:
genomic DNA plasmid pool
60 bp


title: ALDH2*1/*2_1

city: Palo Alto

first: Yu

last: Liu

state: CA

address: 1215 Welch Road

department: CVI

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
Read counts of each gene was counted by featureCounts
Genome_build: hg38
Supplementary_files_format_and_content: Raw read counts in TXT format

source_name: Line 1 GA

extract_protocol:
hiPSC-ECs RNA was harvested using Trizol reagent
RNA libraries were pre

value: human induced pluripotent stem cell-derived endothelial cells (hiPSC-ECs)

tag: differentiation day

value: GA


title: ALDH2*1/*2_2

source_name: Line 2 GA


title: WSU-2-1

source_name: WSU-DLCL2 cells, FDX1-OE, DMSO 48h

value: cell line

value: DLBCL cells


title: Iso_GG_2

source_name: Line 2 GG

value: GG


title: SGD_ISW1a_ΔIDR-ORC1_rep2

description:
genomic DNA plasmid pool
60 bp

source_name: yeast

value: in vitro reconstituted chromatin


title: WSU-1-2

source_name: WSU-DLCL2 cells, control, DMSO 48h


title: Iso_GG_1

source_name: Line 1 GG


title: SGD_ISW1a_ΔIDR-ORC1_rep1

description:
genomic DNA plasmid pool
60 bp

value: yeast


title: SGD_ISW1a_ΔBAH-ORC1_rep3

description:
genomic DNA plasmid pool
60 bp


title: S25_17406

city: Coventry

first: Jan

middle: J

last: Brosens

address: University Hospital Coventry and Warwickshire

department: Warwick Medical School

country: United Kingdom

institute: University of Warwick

data_processing:
Raw base calls from sequencing were processed into FASTQ format using cellranger-atac mkfastq from 10x Genomics Cell Ranger ATAC v1.2.0.
The cellranger-atac count pipeline from 10x Genomics Cell Ranger ATAC v1.2 was used for alignment and generation of single-cell chromatin accessibility counts from each cell in the form of a peak-barcode matrix. Filtered peak-barcode matrices, without background and non-cellular barcodes, were used for further analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: 10X Genomics Cell Ranger ATAC filtered cell barcodes and fragment files in TSV format, filtered peak-barcode count matrices in MTX format, and peak locations in BED format.

source_name: Endometrial cells

extract_protocol:
Nuclei were extracted according to the 10X Genomics demonstrated protocol for frozen tissue (CG000212 Rev B), modified to include an additional wash with Wash buffer. Tissue homogenization was performed using a dounce homogenizer. Filtered nuclei suspension was  pelleted as instructed and then resuspended in 50 ul Storage Buffer from the EZ nuclei kit (Sigma Aldrich, NUC101). For downstream processing, nuclei were thawed briefly on ice, resuspended with 500 ul Wash Buffer and gently pipetted.  Nuclei were pelleted at 500 × g (5 min, 4 ˚C) then resuspended again in 500 ul Wash Buffer before counting and continuing to Chromium capture.
scATAC-seq libraries were generated according to the Chromium Single Cell ATAC protocol (10 × GENOMICS, CG000168) as described previously (Satpathy et al. 2019) and sequenced on the Illumina NextSeq 500 platform.

value: Endometrial cells

tag: age

tag: day of cycle

tag: live births

tag: miscarriages


title: S24_17667


title: SGD_ISW1a_ΔBAH-ORC1_rep2

description:
genomic DNA plasmid pool
60 bp

tag: chromatin

tag: histone type

tag: orc

tag: remodeler


title: WSU-1-1

tag: tissue

value: WT


title: S22_18061


title: SGD_ISW1a_ΔBAH-ORC1_rep1

description:
genomic DNA plasmid pool
60 bp

tag: histone chaperone


title: WSU-2-2

value: FDX1 overexpression


title: SGD_ISW1a_ΔBAH-ΔIDR-ORC1_rep3

description:
genomic DNA plasmid pool
60 bp


title: S21a_18325


title: S19_17204


title: SGD_ISW1a_ΔBAH-ΔIDR-ORC1_rep2

description:
genomic DNA plasmid pool
60 bp


title: PGP1_DE_CTD-2501M5.1-KO-RIP-IP-rep2

city: WuHan

first: Jie

last: Yang

state: Hubei Province

address: Donghu Road, No. 115

department: Medical Research Insitiute

institute: WuHan university

description:
RIPseq
CTD-2501M5.1-KO_RIP_summits.bed

data_processing:
Illumina bcl2fastq v2.20software used for basecalling.
Sequenced reads were trimmed for adaptor sequence by trim_glore version 0.6.6, the clean data were mapped to GRCh38 whole genome using HISAT2 version 2.1.0.
Raw RNAseq reads were performed with FeatureCounts (V2.0.1) using gencode v29 human gene annotation.
Raw counts were normalized to Transcripts Per Million (TPM).
Gene expression difference was analyzed by Bioconductor R package DESeq2. RIPseq peaks were analyzed by Macs2 callpeak (V2.1.1).
Assembly: GRCh38
Supplementary files format and content: TPM for RNAseq
Supplementary files format and content: peak bed for RIPseq

source_name: differentiated CTD-2501M5.1-KO endoderm cells

growth_protocol: hPSCs were treated with IMEM-F12 as basal medium, supplemented with 0.2% BSA, 1% Penicillin-Streptomycin and 100ng/mL Activin A  for the three days.

extract_protocol:
RNA was extracted with HiPure Total RNA Mini Kit (Magen, Cat#R4111-03).
RNA libraries were prepared for sequencing using standard Illumina protocols.


title: S21_18272


title: S20_18212


title: S19a_18189 Run2


title: S19a_18189 Run1


title: S18_18205


title: P10_182006


title: P7_182007


title: SGD_INO80_rep3

description:
genomic DNA plasmid pool
60 bp


title: roots_dm_lysoPAF_ONO_2

city: Wuhan

first: Qiang

state: Saskatchewan

address: #1 Shizishan Street

institute: Huazhong Agricultural University

data_processing:
Trimming using Trimmomatics-0.32
Read mapping using STAR-2.4.0j
Alignment using StringTie-1.0.3
Raw counts using htseq-count-0.6.0
Differentially expression analysis using DESeq2 1.12.4
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited .csv file includes annotation and normalized counts  for each sample

organism: Arabidopsis thaliana

growth_protocol: Arabidopsis thaliana Col-0 wild type and lpcat1/2 plants were grown at 22 ℃ with a 16-h photoperiod of ~125 μE m-2s-1.

extract_protocol:
RNA samples were extracted using the Plant RNA Isolation Mini Kit (Agilent Technologies) according to the manufacturer’s protocol.
Eighteen cDNA libraries were constructed using the TruSeq RNA Sample Preparation Kit v2 (Illumina).

treatment_protocol: Arabidopsis Col-0 wild type and lpcat1/2 plants were grown on 1/2 MS media (control), or 1/2 MS media containing 20ug/ml lyso-PAF or 20ug/ml lyso-PAF plus 50 µM ONO. Root tissues were collected at 5 days after germination, flash frozen in liquid nitrogen, and stored at -80 ℃ until required.

tag: time

value: 5 days after germination

value: lpcat1/2 double mutant

value: roots


title: roots_dm_lysoPAF_ONO_3


title: PGP1_DE_WT-RIP-IP-rep3

description:
RIPseq
WT_RIP_summits.bed

source_name: differentiated endoderm cells


title: S23_18016


title: PGP1_DE_CTD-2501M5.1-KO-RIP-IP-rep3

description:
RIPseq
CTD-2501M5.1-KO_RIP_summits.bed


title: SGD_INO80_rep2

description:
genomic DNA plasmid pool
60 bp

value: Drosophila melanogaster embryos


title: roots_dm_lysoPAF_ONO_1


title: PGP1_DE_WT-RIP-IP-rep2

description:
RIPseq
WT_RIP_summits.bed


title: roots_WT_lysoPAF_ONO_3

tag: ecotype

value: wild type


title: SGD_INO80_rep1

description:
genomic DNA plasmid pool
60 bp


title: PGP1_DE_CTD-2501M5.1-KO-RIP-IP-rep1

description:
RIPseq
CTD-2501M5.1-KO_RIP_summits.bed

tag: genotype


title: SGD_INO80_D569Y-ORC1_rep1

description:
genomic DNA plasmid pool
60 bp


title: SGD_ISW1a_ΔBAH-ΔIDR-ORC1_rep1

description:
genomic DNA plasmid pool
60 bp


title: roots_dm_lysoPAF_3

tag: treatment

value: lysoPAF


title: SGD_INO80_D569Y-ORC1_rep3

description:
genomic DNA plasmid pool
60 bp


title: PGP1_DE_WT-RIP-IP-rep1

description:
RIPseq
WT_RIP_summits.bed


title: SGD_INO80_ORC_rep4

description:
genomic DNA plasmid pool
60 bp

value: ORC


title: roots_WT_lysoPAF_ONO_2


title: IgG treated B16 tumor, rep4

city: New York

first: Levi Mark

middle: Bala

last: Mangarin

state: NY

address: 413 E 69th St

department: Meyer Cancer Center

institute: Weill Cornell Medical Center

description: Sample name: 1-4

data_processing:
Bulk RNAseq for each sample (FASTQ) were aligned to corresponding genome with STAR (v2.6.0)
Count based expression profiles were quantified using Subread featureCounts (v1.5.1)
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes count values for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen, QIACube). 800ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina 3000/4000 SBS Kit following manufacturer's protocols.

tag: cell line

value: Neutrophils

value: IgG


title: SGD_INO80_D569Y-ORC1_rep2

description:
genomic DNA plasmid pool
60 bp

tag: cell type


title: IgG treated B16 tumor, rep2

description: Sample name: 1-2


title: aOX40 treated B16 tumor, rep2

description: Sample name: O-2


title: IgG treated B16 tumor, rep3

description: Sample name: 1-3


title: IgG treated B16 tumor, rep5

description: Sample name: 1-5


title: aOX40 treated B16 tumor, rep3

description: Sample name: O-3


title: Islet128

city: Farmington

first: Efthymios

last: Motakis

state: CT

address: 10 Farmington Drive

department: Computational Sciences

institute: The Jackson Laboratory

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Reads alignment with STARsolo
Estimation and removal of ambient RNA by SoupX
Genetic demultiplexing for the 12 mutiplexed libraries by Demuxlet and removal of doublets
Cluster-based cell QC: the cell clusters are generated by Seurat's processing pipeline and the cells with > 500 features & < 50% MT & >1000 UMIs are kept for further analysis
Doublet identification by Scrublet, DoubletFinder and doublet visualization in the cell clusters
Second step cluster-based cell QC: the cell clusters are re-generated with the cleaner data by Seurat's processing pipeline and the cells with > 1400 features & < 40% MT are kept for further analysis. Keep cells of particular cell types (marker-based pre-annotation) even if the do not satisfy the features criterion.
Data integration by Harmony and integrated data clustering
Visualize the estimated doublets on the integrated data clusters, remove all scrublet doublets plus while custers if they are enriched in such doublets
Keep the clean data for downstream analysis: final cell annotation, differential expression, subclustering
Assembly: HG38
Supplementary files format and content: CellRanger output files

source_name: Pancreatic islets

growth_protocol: Cultured overnight in PIM(S) [ProdoLabs] prior to dissociation and 10X Genomics single cell capture

extract_protocol:
10X Genomics standard procedures for sample dilution and single cell capture
10X Genomcis standard procedures for library construction

treatment_protocol: Islets treated with Accutase for 10 minutes at 37 degrees Celsius and gentle pipetting

value: Pancreatic islets

tag: chemistry

tag: disease state

tag: Sex

value: Male

tag: bmi

tag: race

value: Hispanic

tag: unos

tag: center

value: southern California IsletCell Resource Center

tag: Cause of death

value: Cerebrovascular/stroke

tag: library id


title: IgG treated B16 tumor, rep6

description: Sample name: 1-6


title: roots_dm_lysoPAF_2

tag: tissue


title: SGD_INO80_ORC_rep3

description:
genomic DNA plasmid pool
60 bp

tag: chromatin

value: in vitro reconstituted chromatin

value: yeast

tag: histone type

tag: orc

tag: remodeler

tag: histone chaperone


title: SGD_INO80_ORC_rep2

description:
genomic DNA plasmid pool
60 bp


title: roots_WT_lysoPAF_3

tag: time

tag: ecotype

tag: genotype

tag: treatment


title: aOX40 treated B16 tumor, rep1

description: Sample name: O-1

tag: cell line

tag: cell type


title: Islet126

description: 10x Genomics

tag: chemistry

tag: disease state

tag: Sex

value: Female

tag: bmi

tag: race

value: AfricanAmerican

tag: age

value: UPenn

value: Anoxia


title: roots_WT_lysoPAF_ONO_1

value: 5 days after germination

tag: tissue

value: roots


title: Islet127

description: 10x Genomics

value: PreDiabetic

value: White

tag: unos

tag: center

tag: Cause of death

tag: library id


title: roots_WT_lysoPAF_2

tag: time

value: wild type

value: lysoPAF


title: aOX40 treated B16;B7H1 cells, HTO and ADT

description:
Hashtag-derived oligonucleotide (HTO), Antibody-derived oligonucleotide (ADT)
annotation.txt (HTO), count_matrix_adt.txt
processed_seurat_object.RData
The HTO and ADT matrices come from the same fastq batch.

library_source: other

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression, ADT and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline.
Further processing was done with Seurat v3.2.3 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Assembly: mm10
Supplementary files format and content: processed_seurat_object.RData
Supplementary files format and content: count_matrix_rna.txt
Supplementary files format and content: count_matrix_adt.txt
Supplementary files format and content: annotation.txt
Library strategy: CITE-seq

molecule: protein

source_name: Tumor

extract_protocol:
N/A (10X Genomics)
Chromium Single Cell 5' Reagent Kit
Chromium Single Cell 5' Feature Barcode Library Kit

treatment_protocol: Mice were implanted with mixed B16 and B78H1 cells at the same site. After 3 weeks, mice were injected with CTX. The next day mice were injected with Trp1 cells and anti-OX40 or IgG (controls). A separate cohort of mice was implanted with a mixture of B16 and B78H1 cells a week later as untreated controls. After 10 days, single-cell suspensions were prepared from tumors.

value: Tumor

value: Immune cells

value: aOX40 treated

tag: library type

value: HTO and ADT


title: Islet123

description: 10x Genomics

value: Pancreatic islets

value: NonDiabetic

value: Hispanic

value: Scharp-Lacy

value: Head trauma


title: IgG treated B16;B7H1 cells, HTO and ADT

value: IgG treated


title: roots_WT_lysoPAF_1

tag: ecotype

tag: genotype


title: SGD_INO80_ΔIDR-ORC1_rep2

description:
genomic DNA plasmid pool
60 bp

tag: chromatin

value: in vitro reconstituted chromatin

value: yeast

tag: histone type

value: Drosophila melanogaster embryos

tag: orc

tag: remodeler

tag: histone chaperone


title: Untreated B16;B7H1 cells, HTO and ADT

tag: cell type

tag: treatment

value: Untreated


title: roots_dm_3

value: 5 days after germination

value: lpcat1/2 double mutant

value: control

value: roots


title: Islet118/119_MS20087

description: 10x Genomics

tag: chemistry

tag: disease state

tag: Sex

value: Male/Female

tag: bmi

tag: race

value: White/AfricanAmerican

tag: age

value: Scharp-Lacy/Southern California IsletCell Resource Center

value: Head trauma/NA


title: SGD_INO80_ΔIDR-ORC1_rep1

description:
genomic DNA plasmid pool
60 bp


title: Islet118/119_MS20086

description: 10x Genomics

tag: tissue

value: Pancreatic islets

tag: unos

tag: center

tag: Cause of death

tag: library id


title: aOX40 treated B16;B7H1 cells, mRNA

description:
poly A RNA
count_matrix_rna.txt
processed_seurat_object.RData
none

value: Tumor

value: Immune cells

value: aOX40 treated

tag: library type

value: mRNA


title: SGD_INO80_ΔIDR-ORC1_rep3

description:
genomic DNA plasmid pool
60 bp

tag: chromatin

value: in vitro reconstituted chromatin

tag: histone type

tag: orc


title: IgG treated B16;B7H1 cells, mRNA

tag: cell type

value: IgG treated


title: Islet107

description: 10x Genomics

tag: treatment

value: NonDiabetic

value: Male

value: Hispanic

value: Scharp-Lacy

value: Head trauma


title: Untreated B16;B7H1 cells, mRNA

value: Untreated


title: roots_dm_2

tag: time

value: 5 days after germination

tag: genotype

value: lpcat1/2 double mutant

value: control

value: roots


title: roots_dm_lysoPAF_1

value: lysoPAF


title: SGD_INO80_ΔBAH-ΔIDR-ORC1_rep3

description:
genomic DNA plasmid pool
60 bp

value: yeast

value: Drosophila melanogaster embryos

tag: remodeler

tag: histone chaperone


title: Islet104

description: 10x Genomics

value: Pancreatic islets

tag: chemistry

tag: disease state

tag: Sex

tag: bmi

tag: race

value: AfricanAmerican

value: Cerebrovascular/stroke


title: roots_dm_1

tag: tissue


title: roots_WT_3

tag: ecotype

value: wild type


title: Islet101

description: 10x Genomics

value: PreDiabetic

value: White

tag: age

tag: unos

tag: center

tag: Cause of death

value: Anoxia

tag: library id


title: SGD_INO80_ΔBAH-ΔIDR-ORC1_rep2

description:
genomic DNA plasmid pool
60 bp

tag: chromatin

value: in vitro reconstituted chromatin

tag: cell type

tag: histone type

tag: orc


title: Islet91

description: 10x Genomics

tag: treatment

value: Male

value: Scharp-Lacy


title: roots_WT_2

tag: time

value: 5 days after germination

tag: genotype


title: roots_WT_1


title: SGD_INO80_ΔBAH-ΔIDR-ORC1_rep1

description:
genomic DNA plasmid pool
60 bp

tag: remodeler

tag: histone chaperone


title: Islet89

description: 10x Genomics

tag: chemistry

tag: disease state

tag: Sex

value: Female

tag: bmi

tag: race

value: Hispanic

value: Miami


title: C. elegans Serotonin Neurons Rep 1

first: Niels

last: Ringstad

address: 435 E. 30th Street

department: Cell Biology and Neuroscience Institute

institute: NYU School of Medicine

data_processing:
STAR aligner to align RNA sequences to genome
HTSeq to compute read counts
DESeq2 to identify differentially expressed transcripts
Assembly: WS243
Supplementary files format and content: bigwig files (RPKM) for each sample
Supplementary files format and content: counts.fpkm.xlsx
Supplementary files format and content: counts.normalized.xlsx

source_name: embryos and larvae

extract_protocol:
RNA was harvested using the Arcturus PicoPure RNA isolation kit (Life Technologies). 1-2 ngof total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Ovation RNA-seq system 2 (Nugen) following manufacturer's protocols.

tag: strain

value: serotonin neurons

value: WT

tag: tissue

value: embryos and larvae


title: SGD_INO80_ΔBAH-ORC1_rep3

description:
genomic DNA plasmid pool
60 bp

value: yeast

value: Drosophila melanogaster embryos


title: C. elegans Serotonin Neurons Rep 3


title: SGD_INO80_ΔBAH-ORC1_rep1

description:
genomic DNA plasmid pool
60 bp


title: SGD_INO80_ΔBAH-ORC1_rep2

description:
genomic DNA plasmid pool
60 bp


title: Islet84/85_MS19043

description: 10x Genomics

value: Pancreatic islets

value: Male/Male

value: Hispanic/Hispanic

tag: age

tag: unos

tag: center

value: Scharp-Lacy/Miami

tag: Cause of death

tag: library id


title: SGD_HIR_rep2

description:
genomic DNA plasmid pool
60 bp

tag: chromatin

tag: cell type

tag: histone type

tag: orc

value: HIR


title: hESC-derived Melanocyte P4 n1 (Batch2) [B_P4_n2]

city: Corbeil-Essonnes

first: Hélène

last: Polvèche

address: 28, Rue Henri Desbruères

institute: I-Stem

data_processing:
library strategy: Ampli-seq
Torrent Suite Software was used for basecalling, trimming of adaptator sequence, quality check and to generated FASTQ file FastQ files were exported to PartekFlow software (v6 Partek Inc) for alignement and quantification step.
Briefly sequence were mapped to hg19 reference genome using TOPHAT2 (v2.0.8). and bowtie 2 (v2.1.0) following the WT Pipeline for Ion Torrent. Mapped reads were annotated on Refseq release 84 and quantified with Partek E/M algorithm , normalised on total count and differential gene were identified using Partek Gene Specific Algorithm (GSA)
Assembly: hg19
Supplementary files format and content: csv file containing raw counting reads

molecule: other

source_name: hESC-derived Melanocyte P4

growth_protocol: This protocol is based on sequential application of molecules to specifically induce the differentiation of pluripotent stem cells into melanocytes. Functional melanocytes were obtained without being sorted in 40 days by the commitment of pluripotent stem cells into melanocytes precursors via neural crest state

extract_protocol:
Medium was removed and 350µl RLTplus were add. Sample were extracted on QIACUBE following the Rneasy Plus Mini kit protocole (Qiagen)
The Ion Ampliseq Transcriptome Human Gene expression kit was used with 50ng of mRNA for the construction of sequencing libraries following the manufacturer protcol. Ampliseq Transcriptome Human gene expression kit (Termofisher Scientific)

tag: cell line

tag: genotype

tag: extract

value: Total cells

tag: replicate

value: Replicate 1


title: SGD_HIR_ORC_rep2

description:
genomic DNA plasmid pool
60 bp

data_processing:
The data processing of the MNase-seq data was done as described before with modifications (Oberbeckmann, E. et al., 2021). Sequencing reads were mapped to the S. cerevisiae SacCer3 (R64-1-1 build) using Bowtie2 (version 2.3.5.1) (Langmead, B. and Salzberg, S.L., 2012) and reads aligning to multiple sites were removed. This was then imported into R Studio by using GenomicAlignments (Lawrence, M. et al., 2013). For the single-end data, reads were shifted by 73 bp and extended to 50 bp, while for the paired-end data, reads with a fragment length between 139 and 191 bp were selected and extended to 60 bp. The coverage was calculated and aligned to a list of ACS sites (Soriano, I. et al., 2014). The signal was normalized per ARS in a 2000 bp window centered at the ACS motif.
Assembly: SacCer3
Supplementary files format and content: bw (bigwig) files were generated from genome coverage files using rtracklayer (Lawrence et al. 2009).

extract_protocol: The reactions with reconstituted chromatin were incubated with 100 U MNase (Sigma-Aldrich) and 1.5 mM CaCl2 for 5 min at 30 °C. The digest was stopped by the addition of 10 mM EDTA and 0.5 % SDS. This was followed by a proteinase K treatment for 1 h at 37 °C and ethanol precipitation. The sequencing libraries of the vitro reconstituted chromatin samples were prepared as previously described (Oberbeckmann, E., Niebauer, V. et al., 2021; Oberbeckmann, E., Krietenstein, N. et al., 2021) by using 10-50 ng mononucleosomal DNA. The amplified DNA was run in a 1.5 % agarose gel, cut out, purified and the concentration was measured with the Qubit dsDNA HS Assay Kit (Fisher Scientific). The libraries were diluted to 10 nM, pooled according to the sequencing reads (~ 5 million reads/sample), and quantified via BioAnalyzer (Agilent). The pool was sequenced either on an Illumina HiSeq 1500 in 50 bp single-end mode or on an Illumina NextSeq 1000 in 60 bp paired-end mode (Laboratory for Functional Genome Analysis, LAFUGA, LMU Munich).

value: in vitro reconstituted chromatin

value: ORC

tag: remodeler

tag: histone chaperone


title: Islet84/85_MS19042

description: 10x Genomics

tag: treatment

tag: chemistry

tag: disease state

tag: Sex

tag: bmi

tag: race


title: Islet80

description: 10x Genomics

tag: tissue

value: NonDiabetic

value: Male

value: AfricanAmerican

tag: age

tag: unos

tag: center

tag: Cause of death

value: Head trauma

tag: library id


title: SGD_Fun30_rep3

description:
genomic DNA plasmid pool
60 bp

tag: chromatin

tag: cell type

tag: histone type

tag: orc


title: C. elegans Dopamine Neurons Rep 1

tag: strain

value: dopamine neurons

tag: genotype

value: WT


title: Islet73

description: 10x Genomics

tag: treatment

tag: chemistry

value: White

value: Scharp-Lacy

value: Cerebrovascular/stroke


title: SGD_Fun30_rep2

description:
genomic DNA plasmid pool
60 bp

value: yeast

value: Drosophila melanogaster embryos

tag: remodeler

tag: histone chaperone


title: hESC-derived Melanocyte days40 (P0) n3 (Batch2) [B_P0_n3]

source_name: hESC-derived Melanocyte days40 (P0)

tag: cell line

tag: extract

tag: replicate

value: Replicate 3


title: Melanocyte n2 (Batch2) [B_HEM_Ref_Mel_P5_704]

source_name: Melanocyte

value: mel 704 P5 Lonza

value: Replicate 2


title: Melanocyte n1 (Batch2) [B_HEM_Ref_Mel_P5_311]

value: mel 311 P5 Lonza

value: Total cells

value: Replicate 1


title: Islet70/71_MS19035

description: 10x Genomics

tag: tissue

value: Pancreatic islets

tag: disease state

tag: Sex

value: Female/Male

tag: bmi

tag: race

value: White/White

tag: age

tag: unos

value: Southern California IsletCell Resource Center/Scharp-Lacy


title: C. elegans Serotonin Neurons Rep 2

tag: cell type

value: serotonin neurons

value: embryos and larvae


title: CVA6-RD-C3

city: Beijing

first: Cong

middle: cong

last: Wang

address: 155 Changbai Road

institute: Chinese Center For Disease Control and Prevention

data_processing:
Nextseq 500
Sequence reads were trimmed for adaptor sequence/low-quality sequence using FastQC genomic benchwork (parameter- Quality limit: 0.05)
The Spliced Transcript Alignment to a Reference (STAR) aligner version 2.5.2b was used to align raw reads to build human gencode. Transcript abundance estimates were calculated internal to the STAR aligner using the algorithm of htseq-count
Read count extraction and normalization were performed using Qubit 2.0
Assembly: human gencod
Supplementary files format and content: The file name data format is fastq (fq for short), and the suffix is usually ".fq.gz.gz ".

source_name: RD

growth_protocol: RD cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using Trizol. 2 ug of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were prepared 359 using NEBNext® Ultra™ II Directional RNA Library Prep kit (New England Biolab) following 360 manufacturer’s instructions.

value: RD

value: tumor cells

value: Control

value: adipogenic differentiation


title: CVA6-RD-C2


title: SGD_Fun30_ORC_rep3

description:
genomic DNA plasmid pool
60 bp

tag: chromatin

value: in vitro reconstituted chromatin

value: yeast

tag: histone type

value: Drosophila melanogaster embryos

tag: orc

value: ORC


title: hESC-derived Melanocyte days40 (P0) n2 (Batch2) [B_P0_n4]

tag: genotype

value: WT

value: Replicate 2


title: CVA6-RD-C1

tag: treatment


title: Islet70/71_MS19034

description: 10x Genomics

tag: chemistry

tag: center

tag: Cause of death

value: Cerebrovascular/stroke

tag: library id


title: C. elegans Dopamine Neurons Rep 3

tag: strain

value: dopamine neurons

tag: tissue


title: Melanocyte n3 (Batch2) [B_HEM_Ref_Mel_P5_663]

tag: cell line

value: mel 663 P5 Lonza

tag: extract

value: Total cells

tag: replicate

value: Replicate 3


title: C. elegans Dopamine Neurons Rep 2


title: CVA6-RD-3


title: hESC-derived Melanocyte days40 (P0) n1 (Batch2) [B_P0_n2]

value: Replicate 1


title: SGD_Fun30_ORC_rep2

description:
genomic DNA plasmid pool
60 bp

tag: remodeler

tag: histone chaperone


title: Islet68

description: 10x Genomics

value: Pancreatic islets

tag: disease state

value: NonDiabetic

tag: Sex

value: Male

tag: bmi

tag: race

value: White

tag: age

tag: unos

value: Wisconsin

value: Head trauma


title: SGD_FACT_rep2

description:
genomic DNA plasmid pool
60 bp

tag: chromatin

value: in vitro reconstituted chromatin

tag: cell type

value: yeast

tag: histone type

tag: orc

value: FACT


title: hESC-derived Melanocyte P4 n1 (Batch3) [C_P4_n1]

tag: genotype

value: WT


title: CVA6-RD-2

value: RD

value: tumor cells

tag: treatment

value: adipogenic differentiation


title: Islet63

description: 10x Genomics

tag: tissue

tag: chemistry

value: PreDiabetic

value: AfricanAmerican

tag: center

value: Scharp-Lacy

tag: Cause of death

value: Anoxia

tag: library id


title: hESC-derived Melanocyte P4 n1 (Batch4) [D_P4_n2]

tag: cell line

tag: extract

value: Total cells

tag: replicate

value: Replicate 1


title: Islet62

description: 10x Genomics

value: Pancreatic islets

tag: disease state

tag: Sex

value: Male

tag: bmi

tag: race


title: CVA6-RD-1

tag: cell type


title: SGD_FACT_ORC_rep2

description:
genomic DNA plasmid pool
60 bp

tag: chromatin

tag: histone type

value: Drosophila melanogaster embryos

value: ORC

tag: remodeler

tag: histone chaperone


title: SGD_Chd1_rep3

description:
genomic DNA plasmid pool
60 bp

value: in vitro reconstituted chromatin

tag: orc


title: SGD_Chd1_D569Y-ORC1_rep1

description:
genomic DNA plasmid pool
60 bp

value: yeast


title: Islet61

description: 10x Genomics

tag: tissue

tag: treatment

tag: chemistry

value: NonDiabetic

value: Female

value: White

tag: age

tag: unos

value: Wisconsin

value: Cerebrovascular/stroke


title: hESC-derived Melanocyte days30 n3 (Batch1) [A_D30_n3]

source_name: hESC-derived Melanocyte days30

tag: cell line

tag: genotype

value: WT

tag: extract

value: Replicate 3


title: hESC-derived Melanocyte days30 n2 (Batch1) [A_D30_n2]

tag: replicate

value: Replicate 2


title: Wild type + DP - sample 3 (Bt - Wild type + DP - Bt_WT_DP_6_15_S46)

city: Richmond

first: Janina

middle: P

last: Lewis

state: VA

address: 521 North 11th Street

department: Philips Institute of OCMB

institute: Virginia Commonwealth University

description: Bt - Wild type + DP vs. Bt - Ox mut + DP and Bt - DP vs. Bt + DP

data_processing:
Base calls were done using CLC Genomic Workbench
Reads were aligned to the genome of Bacteroides thetaiotaomicron VPI - BT5482 NC_004663 using Genomic Workbench
Reads per gene were determined using Genomic Workbench
Statistical analysis was done using Genomic Workbench
Genome_build: Bacteroides thetaiotaomicron VPI-5482 NC_004663

organism: Bacteroides thetaiotaomicron

source_name: OxyR analysis - WT iron deplete

growth_protocol: Samples of wildtype and OxyR mutant B. thetaiotaomicron were grown in an overnight culture of BHI media. The overnight cultures served to inoculate cultures of BHI media starting at an OD660 of approximately 0.05. Cultures were grown with and without dipyridyl to mid-log phase, centrifuged, and stored at -20 °C.

extract_protocol:
RNA isolation was carried out using the RNeasy mini-kit (Qiagen) following manufacturers protocol. Residual DNA was removed using the DNA-free DNase kit (Ambion) following manufacturers protocol.
For RNA-seq library generation, the Ovation complete Prokaryotic RNA-Seq DR multiplex kit (Nugen) was used. The library was generated following the manufacturers protocol and fragment sizes from sonication during library generation was confirmed using a bioanalyzer (Agilent Technologies). Libraries were sequenced by VCU nucleic acid sequencing core using Miseq Illumina sequencing.

treatment_protocol: Dipyridyl (Fe Chelator) - 150uM

tag: phase of growth

value: logarithmic phase of growth

value: Wild type

tag: dp treatment

value: iron deplete

tag: strain


title: SGD_Chd1_D569Y-ORC1_rep2

first: Erika

address: Grosshaderner Strasse 9

description:
genomic DNA plasmid pool
60 bp

tag: chromatin

tag: cell type


title: Islet59/60_MS19020

description: 10x Genomics

value: Pancreatic islets

tag: disease state

tag: Sex

value: Male/Male

tag: bmi

tag: race

value: White/White

tag: center

value: Wisconsin/Scharp-Lacy

tag: Cause of death

tag: library id


title: Wild type - sample 4 (Bt - Wild Type  - Bt_WT_6_15_S45)

description: Bt - Ox mut vs. Bt - Wild Type and Bt Mut vs Bt - Wt - statistics

source_name: OxyR analysis - WT iron replete

value: iron replete


title: hESC-derived Melanocyte days30 n1 (Batch1) [A_D30_n1]

value: Total cells

value: Replicate 1


title: Wild type - sample 3 (Bt - Wild Type  - Bt_WT_6_12_S41)

description: Bt - Ox mut vs. Bt - Wild Type and Bt Mut vs Bt - Wt - statistics and Bt - DP vs. Bt + DP


title: hESC-derived Melanocyte days21 n3 (Batch1) [A_D21_n3]

source_name: hESC-derived Melanocyte days21


title: SGD_Chd1_ORC_rep2

description:
genomic DNA plasmid pool
60 bp

source_name: yeast

value: in vitro reconstituted chromatin

value: yeast

tag: histone type

value: Drosophila melanogaster embryos

tag: orc

value: ORC

tag: remodeler

tag: histone chaperone


title: SGD_Chd1_ORC_rep3

description:
genomic DNA plasmid pool
60 bp


title: Wild type + DP - sample 2 (Bt - Wild type + DP - Bt_WT_DP_6_12_S42)

description: Bt - Wild type + DP vs. Bt - Ox mut + DP and  Bt - DP vs. Bt + DP

tag: genotype


title: Islet60

description: 10x Genomics

tag: tissue

tag: treatment

tag: chemistry

value: Male

value: White

tag: age

tag: unos

value: Scharp-Lacy

value: Cerebrovascular/stroke


title: hESC-derived Melanocyte days21 n2 (Batch1) [A_D21_n2]

tag: cell line

value: WT

tag: extract

tag: replicate

value: Replicate 2


title: hESC-derived Melanocyte days21 n1 (Batch1) [A_D21_n1]


title: Islet57/58_MS19017

description: 10x Genomics

value: Pancreatic islets

tag: disease state

value: NonDiabetic/PreDiabetic

tag: Sex

value: Female/Male

tag: bmi

tag: race

value: White/Hispanic

value: Scharp-Lacy/Southern California IsletCell Resource Center

value: Cerebrovascular/stroke / Anoxia


title: SGD_Chd1_ΔIDR-ORC1_rep2

description:
genomic DNA plasmid pool
60 bp

tag: chromatin

tag: cell type

tag: histone type


title: Islet57/58_MS19016

description: 10x Genomics

tag: center

tag: Cause of death

tag: library id


title: SGD_Chd1_ΔBAH-ORC1_rep2

description:
genomic DNA plasmid pool
60 bp

tag: orc

tag: remodeler

tag: histone chaperone


title: Wild type + DP - sample 4 (Bt - Wild type + DP - Bt_WT_2_DP_6_6_S38)

tag: phase of growth

value: logarithmic phase of growth

tag: genotype

value: Wild type

tag: dp treatment

value: iron deplete

tag: strain


title: hESC-derived Melanocyte days14 n2 (Batch1) [A_D14_n2]

source_name: hESC-derived Melanocyte days14

tag: cell line

tag: extract

value: Total cells

tag: replicate


title: Wild type + DP - sample 1 (Bt - Wild type + DP - Bt_WT_2_DP_6_4_S34)


title: Islet58

description: 10x Genomics

tag: tissue

tag: treatment

tag: chemistry

tag: disease state

value: PreDiabetic

tag: Sex

tag: bmi

tag: race

value: Hispanic

tag: age

tag: unos

value: Southern California IsletCell Resource Center

value: Anoxia


title: Islet59

description: 10x Genomics

value: NonDiabetic

value: Male

value: White

tag: center

value: Wisconsin

tag: Cause of death

value: Cerebrovascular/stroke

tag: library id


title: Wild type - sample 2 (Bt - Wild Type  - Bt_WT_2_6_6_S37)

tag: phase of growth

tag: genotype

tag: dp treatment

value: iron replete


title: Wild type - sample 1 (Bt - Wild Type  - Bt_WT_2_6_4_S33)

tag: strain


title: Islet59/60_MS19021

description: 10x Genomics

value: Pancreatic islets

value: Male/Male

value: White/White

value: Wisconsin/Scharp-Lacy


title: hESC-derived Melanocyte days14 n1 (Batch1) [A_D14_n1]

tag: cell line

value: WT

tag: extract

tag: replicate

value: Replicate 1


title: Islet57

description: 10x Genomics

tag: tissue

tag: treatment

tag: chemistry

value: Female

value: Scharp-Lacy


title: SGD_Chd1_ΔBAH-ORC1_rep1

description:
genomic DNA plasmid pool
60 bp

tag: chromatin

value: in vitro reconstituted chromatin

tag: cell type

value: yeast

tag: histone type

value: Drosophila melanogaster embryos

tag: orc

tag: remodeler

tag: histone chaperone


title: OxyR mutant + DP - sample 4 (Bt - Ox mut + DP - Bt_Mut_DP_6_15_S48)

description: Bt - Wild type + DP vs. Bt - Ox mut + DP

source_name: OxyR analysis - mutant iron deplete

value: logarithmic phase of growth

value: OxyR mutant

value: iron deplete


title: hESC-derived Melanocyte days7 n3 (Batch1) [A_D7_n3]

source_name: hESC-derived Melanocyte days7

value: Total cells

value: Replicate 3


title: SGD_Chd1_ΔBAH-ΔIDR-ORC1_rep2

description:
genomic DNA plasmid pool
60 bp


title: OxyR mutant + DP - sample 3 (Bt - Ox mut + DP - Bt_Mut_DP_6_12_S44)


title: Islet56

description: 10x Genomics

tag: disease state

value: PreDiabetic

tag: Sex

tag: bmi

tag: race

value: White

tag: age

tag: unos

tag: center

value: Wisconsin

tag: Cause of death

value: Anoxia

tag: library id


title: hESC-derived Melanocyte days7 n2 (Batch1) [A_D7_n2]

tag: cell line

tag: genotype

tag: extract

tag: replicate

value: Replicate 2


title: SGD_Chd1_ΔBAH-ΔIDR-ORC1_rep1

description:
genomic DNA plasmid pool
60 bp

tag: chromatin

tag: cell type

tag: histone type


title: OxyR mutant - sample 4 (Bt - Ox Mutant  - Bt_Mut_6_15_S47)

description: Wild Type vs OxyR Mutant - all data and Bt Mut vs Bt - Wt - statistics

source_name: OxyR analysis - mutant iron replete

tag: phase of growth

tag: dp treatment

value: iron replete

tag: strain


title: Islet55

description: 10x Genomics

tag: tissue

value: Pancreatic islets

tag: treatment

tag: chemistry

tag: disease state

tag: Sex

value: Male

tag: bmi

value: Hispanic


title: hESC-derived Melanocyte days14 n3 (Batch1) [A_D14_n3]

value: WT


title: SGD_Chd1_ΔIDR-ORC1_rep1

description:
genomic DNA plasmid pool
60 bp

value: in vitro reconstituted chromatin

value: yeast

tag: orc

tag: remodeler

tag: histone chaperone


title: hESC-derived Melanocyte days7 n1 (Batch1) [A_D7_n1]

tag: cell line

tag: genotype

tag: extract

value: Replicate 1


title: SGD_CAF1_rep2

description:
genomic DNA plasmid pool
60 bp

tag: chromatin

tag: cell type

value: Drosophila melanogaster embryos


title: Islet54

description: 10x Genomics

value: NonDiabetic

tag: race

tag: age

tag: unos

tag: center

value: Southern California IsletCell Resource Center

tag: Cause of death

value: Head trauma

tag: library id


title: OxyR mutant - sample 3 (Bt - Ox Mutant  - Bt_Mut_6_12_S43)

tag: phase of growth

value: logarithmic phase of growth

value: OxyR mutant

tag: dp treatment

tag: strain


title: SGD_CAF1_ORC_rep2

description:
genomic DNA plasmid pool
60 bp

tag: histone type

tag: orc

value: ORC


title: SGD_Asf1_rep2

description:
genomic DNA plasmid pool
60 bp

tag: remodeler

tag: histone chaperone


title: OxyR mutant + DP - sample 2 (Bt - Ox mut + DP - Bt_Mut_2_DP_6_6_S40)

tag: genotype

value: iron deplete


title: hESC n2 (Batch1) [A_D0_hESC_n2]

source_name: hESC

tag: cell line

tag: extract

value: Total cells

tag: replicate

value: Replicate 2


title: Islet52

description: 10x Genomics

source_name: Pancreatic islets

tag: tissue

value: Pancreatic islets

tag: treatment

tag: chemistry

tag: disease state

tag: Sex

value: Female

tag: bmi

tag: race

value: White

value: Wisconsin

value: Cerebrovascular/stroke


title: SGD_Asf1_ORC_rep2

description:
genomic DNA plasmid pool
60 bp

tag: chromatin

value: in vitro reconstituted chromatin

tag: cell type

value: yeast


title: OxyR mutant + DP - sample 1 (Bt - Ox mut + DP - Bt_Mut_2_DP_6_4_S36)

tag: phase of growth

tag: dp treatment

tag: strain


title: Islet53

description: 10x Genomics

value: PreDiabetic

value: Male

value: Hispanic

tag: age

tag: unos

tag: center

value: Scharp-Lacy

tag: Cause of death

tag: library id


title: hESC n1 (Batch1) [A_D0_hESC_n1]

tag: cell line

tag: genotype

value: WT

tag: extract

tag: replicate

value: Replicate 1


title: OxyR mutant - sample 2 (Bt - Ox Mutant  - Bt_Mut_2_6_6_S39)

value: logarithmic phase of growth

value: OxyR mutant

value: iron replete


title: Islet50

description: 10x Genomics

tag: tissue

tag: treatment

tag: chemistry

tag: disease state

tag: Sex


title: OxyR mutant - sample 1 (Bt - Ox Mutant  - Bt_Mut_2_6_4_S35)

tag: phase of growth


title: Islet47/48_MS19007

description: 10x Genomics

value: Female/Female

tag: bmi

tag: race

value: White/Hispanic

value: Cerebrovascular/stroke / Head trauma


title: 16a: Asthma and lung cancer, amplified

city: Sharjah

first: Rifat

last: Hamoudi

address: University city

country: United Arab Emirates

institute: University of Sharjah

description: column H

data_processing:
Ion Torrent Suite software version 5.12.1
Fragments per kilobase million (FPKM) normalization
Burrows-Wheeler Aligner (BWA)-short, BWA-long, Sequence Search and Alignment by Hashing Algorithm (SSAHA) and Super-maximal Exact Matching (SMEM), within the TMAP suite were implemented
Assembly: hg19_AmpliSeq_Transcriptome_21K_v1
Supplementary files format and content: tab-delimited read counts in one file

source_name: Asthma and lung cancer, amplified

extract_protocol:
RNA was extracted using recover all (Invitrogen) kit
10 ng of RNA was used to prepare library using Ion Ampliseq Human gene expression kit

value: Atypical carcinoid lung tumour


title: 15a: Asthma and lung cancer, amplified

description: column G

value: Adenocracinoma, stage 3


title: Islet47/48_MS19006

description: 10x Genomics

value: Pancreatic islets

tag: age


title: 13a: Asthma and lung cancer, amplified

description: column E


title: hESC n3 (Batch1) [A_D0_hESC_n3]

value: Total cells

value: Replicate 3


title: Islet48

description: 10x Genomics

value: Female

tag: unos

value: Head trauma


title: 22: Severe asthma, unamplified

description: column L

source_name: Severe asthma, unamplified

value: bronchial biopsy


title: Islet47

description: 10x Genomics

value: NonDiabetic

value: White

tag: center

value: Scharp-Lacy

value: Cerebrovascular/stroke


title: paVICs, dantrolene+LPC, rep3

city: Houston

first: K.

middle: Jane

last: Grande-Allen

state: TX

address: 6500 Main St

department: Bioengineering

institute: Rice University

data_processing:
Novogene in-house perl script for adapter trimming and filtering of low quality reads
Trimmed, high quality reads were mapped to Sscrofa11.1 using Hisat2 v2.0.5
In R (v4.1.1), gene count matrices were built with Rsamtools (v2.8.0) and GenomicFeatures (v1.44.2).
Batch correction was performed using Combat_seq function of sva (3.40.0)
Count normalization and differential gene expression was performed using DESeq2 (1.32.0)
Normalized counts and differential genes were annotated using biomaRt (2.48.3)
Assembly: Sscrofa11.1
Supplementary files format and content: comma-separated text files include normalized counts for each sample
Supplementary files format and content: comma-separated text files include differential gene expression

organism: Sus scrofa

source_name: primary isolation 3

growth_protocol: Primarily isolated paVICs were thawed from freezing, passaged once and then seed on 10 cm petri dishes with 10% bovine growth serum (BGS) in 1:1 DMEM:F12 with 10 mM HEPES and antibiotics in a humidified incubator at 37C at 5% CO2.

extract_protocol:
RNA was harvested into TRIzol and purfied using a Direct-zol RNA microprep spin kit with DNAse treatment. RNA was eluted into RNAse free water.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strandsynthesis was performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. 3’ ends of fragments were adenylated and Adaptor with hairpin loop structure were ligated. Library fragments (~370-420 bp) were purified with AMPure XP system (Beckman Coulter, Beverly, USA). PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCRprimers and Index (X) Primer. PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Cells were treated with 1:1 DMEM:F12 with 1%BGS, 10 mM HEPES and antibiotics with the listed treatments for 24 hours in a humidified incubator at 37C at 5% CO2.

tag: cell type

value: aortic valve interstitial cells

value: WT

value: 60 uM dantrolene in DMSO + 10 uM LPC in EtOH


title: paVICs, dantrolene+LPC, rep2

source_name: primary isolation 2


title: paVICs, dantrolene+LPC, rep1

source_name: primary isolation 1


title: 21: Severe asthma, unamplified

description: column K


title: Islet45

description: 10x Genomics

value: Miami

tag: Cause of death

tag: library id


title: paVICs, dantrolene+ethanol, rep3

tag: genotype

value: 60 uM dantrolene in DMSO + 0.1% EtOH


title: 17: Severe asthma, unamplified

description: column I


title: Sample 4, 10µM vehicle Day 1

city: Erlangen

first: Christian

last: Büttner

address: Schwabachanlage 10

department: Institut of Human Genetics

institute: University Hospital Erlangen

data_processing:
After pooled sequencing 100 bp single-end reads on a HiSeq 2500 platform (Illumina) reads were converted to a FASTQ format with bcl2fastq (version 2.17.1.4).
Sequences were quality- and adapter-trimmed using cutadapt (version 1.18).
The pre-processed reads were mapped to the Mus musculus reference genome GRCm38.6 and Ensemble gene model 102, using spliced transcripts alignment to a reference (STAR) software (Version 2.7.8.a).
Strand specific gene level quantification with default parameters regarding overlap was performed using featureCounts (Version 2.0.1) relative to Ensembl gene model for mouse version 102.
Assembly: GRCm38.6
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

source_name: Oli-Neu

growth_protocol: The mouse oligodendrocyte precurser cell line Oli-Neu was grown in T75 cell culture flasks (Thermo Fisher Scientific, Waltham, USA) using SATO medium containing Dulbecco’s modified Eagle’s medium (DMEM; Thermo Fisher Scientific) supplemented with 2 %. heat-inactivated horse serum (Themo Fisher Scientific), 5 µg/ml insuline (Merck, Darmstadt, Germany), 1% penicilline/streptomycine (10.000 U/ml) (Thermo Fisher Scientific), 1% N2 supplement (Thermo Fisher Scientific), 5 ng/ml sodium selenite (Merck), 25 µg/ml gentamicine (Merck, Darmstadt, Germany), 400 nM 3,3′,5-triiod-L-thyronine (T3) (Merck) and 520 nM L-thyroxine (T4) (Merck). Cells were maintained at 37 °C and 5% CO2 and passaged when confluency of 70–80% was reached. All cell culture materials were coated overnight at 37 °C with 0.0001 poly-ornithine (PORN) (Merck) solution. Oli-Neu cells were differentiated using PD 174265, and isolated primary OPCs using PDGF-AA (Miltenyi Biotech, Bergisch Gladbach, Germany) and FGF2 (Miltenyi Biotech). For RNA isolation, the PureLinkTM Mini Kit with PureLinkTM-DNase set (Thermo Fisher Scientific) were used according to the manufacturer’s suggestions.

extract_protocol:
Total RNA was extracted using the PureLink RNA Mini Kit (Thermo Fisher Scientific), followed by DNase treatment.
Sequencing libraries were generated from 1 mg of high-quality RNA using the TruSeq Stranded mRNA Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: Cells were treated with 10 µM Nimodipine or DMSO (Thermo Fisher Scientific) as a vehicle control.

tag: cell line

value: Oli-Neu

value: oligodendrocyte precursor cells

value: 10µM vehicle

tag: time

value: Day 1


title: paVICs, dantrolene+ethanol, rep1


title: paVICs, dantrolene+ethanol, rep2


title: 16: Asthma and lung cancer, unamplified

description: column H

source_name: Asthma and lung cancer, unamplified

tag: tissue

value: Atypical carcinoid lung tumour


title: Islet42

description: 10x Genomics

value: Pancreatic islets

tag: treatment

value: Male


title: paVICs, DMSO+LPC, rep3

value: 0.6% DMSO + 10 uM LPC in EtOH


title: WT1

city: Birmingham

first: Laurie

middle: E

last: Harrington

state: AL

address: 845 19th Street S, BBRB 471

department: CDIB

institute: UAB

data_processing:
Total RNA was prepared for a standard RNA-seq library and sequenced on Illumina HiSeq 2500 (1x50 base paire, single-read). For the base-calling, Illumina Bal2fastq program, version 1.8.4 was used
Sequence reads were aligned to the mouse mm10 reference genome using TopHat 2.1.0.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated with Cufflinks version 2.2.1.0 and normalized expression levels were determined by Cuffnorm version 2.2.1.1
Significant changes in transcript expression were determined with Cuffdiff version 2.2.1.3
Assembly: mus musculus mm10
Supplementary files format and content: Tab-delimited TXT file containing FPKM gene expression values for each gene in each sample

source_name: Spleen

growth_protocol: 1x10^8 splenocytes from previously immunized mice (day 10 post EAE) were cultured with complete RPMI 1640 with 10ug/mL MOG35-55 peptide, 2.5ng/ml TGFb (Peprotech), 20ng/ml IL-6 (Peprotech), 10ng/mL IL-23 (Biolegend) and 10ug/mL anti-IFNγ (clone XMG1.2, Bio X Cell) and 10ug/ml anti-IL-4 (clone 11B11, Bio X Cell) for 72 hours at 37C.

extract_protocol:
Following culture, live CD4 T cells were isolated by centrifugation over Histopaque 1083 (Sigma) followed by Dynabeads FlowComp Mouse CD4 kit (Invitrogen).
RNA was isolated from WT and STAT4-/- CD4 cells using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s protocols. After RNA purification, cDNA synthesis and a standard RNA-seq library preparation was performed by GENEWIZ.

value: Spleen

value: CD4 T cells

value: MOG35-55 peptide, IL-23, αIFNγ


title: ST4KO3


title: WT3


title: WT2


title: ST4KO1


title: Islet41

description: 10x Genomics

tag: chemistry

value: AfricanAmerican

value: Scharp-Lacy

value: NR


title: ST4KO2