title: PHYB-GFP/AbCDE, 5 minutes, rep 2

city: Szeged

first: Gabor

last: Grezal

state: Csongrád

address: Temesvári krt. 62.

department: Institute of Biochemistry

country: Hungary

institute: Biological Research Centre

data_processing:
Sequence reads were trimmed using TrimmomaticPE.0.39 with this parameters:ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10, LEADING:5 TRAILING:5, SLIDINGWINDOW:5:20, MINLEN:50.
Quality controlled reads (FastQC), were mapped to reference genom using bowtie v2.4.2
PCR duplicates were identified with PicardTools MarkDuplicates v.2.24.
Peaks were called using MACS2 v.2.2.7.1  with the significance cutoff <=0.05 with 147 base pair exact size.
Assembly: TAIR10
Supplementary files format and content: bw, narrowPeak

organism: Arabidopsis thaliana

source_name: 6-day-old etiolated seedlings (at 17 °C). Following a red light pulse at 50 µmol m-2 s-1 fluence rate for 5 min.

growth_protocol: Surface sterilised seeds were sowed on half-strength MS media and stratified for 3 days at 4 °C. Germination was induced by white light treatment for 6 h, then the plates were incubated in the darkness for 6 days at 17 °C.

extract_protocol:
The ChIP protocol by Werner Aufsatz (https://www.epigenome-noe.net/researchtools/protocol.php_protid=13.html) was applied with the following modifications. Chromatin samples were sonicated on ice six times for 10 s using a Vibra Cell sonicator (SONICS & MATERIALS Inc., Danbury, CT, USA) at 10% power. Sonicated and diluted chromatin samples were pre-cleared by 20 µl (bed volume) of binding control agarose beads (Chromotek GmbH, Germany) for 1 h at 4 °C. Chromatin was precipitated using 12.5 µl (bed volume) of GFP-Trap agarose beads (Chromotek GmbH, Germany) for 16 h at 4 °C. Precipitated chromatin was eluted from the beads, de-crosslinked and DNA was extracted using the NucleoSpin® Gel and PCR Clean-up kit (Macherey-Nagel, Düren, Germany) with Buffer NTB (Macherey-Nagel, Düren, Germany).
Library preparation was performed using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs) along with NEBNext Multiplex Oligos for Illumina (Index Primers Set 1 and 2, New England BioLabs) according to the manufacturer’s protocol. Final libraries were quality checked using D1000 ScreenTape and Reagents on TapeStation 2200 (all from Agilent); quantification was performed using Qubit dsDNA BR Assay kit (Thermo Fischer Scientific). Sequencing was performed on Illumina NextSeq 1000 instrument.

treatment_protocol: Following a red light pulse at 50 µmol m-2 s-1 fluence rate for 5 min, seedlings were fixed in 1 % (v/v) formaldehyde solution.

value: PHYB-GFP/AbCDE


title: R21792

status: Public on Jan 19 2024

type: SRA

city: Research Triangle Park

first: Dana

last: Hancock

state: NC

address: 3040 E Cornwallis Rd

country: USA

institute: RTI  International

library_source: transcriptomic

data_processing:
Transcripts were quantified using GENCODE v40 (GRCh38) transcriptome with Salmon (v 1.1.0).
Gene-level quantification was done with the tximport R package (v1.14.2).
Assembly: GRCh38/ GENCODE v40
Supplementary files format and content: compressed tab-deliminated text file including raw counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: DLPFC

extract_protocol:
Total RNA was extracted from ~100 mg of tissue using the RNeasy kit (Qiagen) according to the manufacturer's protocol.
Illumina TruSeq Total RNA Stranded RiboZero Gold (Illumina Inc, San Diego, CA) was used for library prep.

tag: tissue

value: DLPFC

tag: dsm-5 aud status

tag: Sex

value: M

tag: agedeath

tag: dsm-5 major depression diagnosis

tag: current smoker at death

value: Case

tag: pmi

tag: rin

tag: sample plate

tag: sample well

tag: brain number


title: R21791

value: F


title: R21797

value: Control


title: shTRA2A IP

city: Shenyang

first: li

last: bingwu

address: shenhe

country: China

institute: Shenyang Pharmaceutical University

data_processing:
Raw reads were trimmed by Trim Ggalore (version 0.6.7) with the parameter ‘--paired’ and were aligned to the human genome (GRCh38) using HISAT2 (version 2.2.1) with default parameters. Unmapped and multi-mapped reads were filtered out using samtools. Counts for annotated genes were generated using featureCounts (version 2.0.1) with the GENCODE V35 annotation file.  The raw counts were converted to TPM by using in house script and differential analysis was performed. exomePeak2 was used for m6A peak calling
Assembly: GRCh38
Supplementary files format and content: narrowPeak

source_name: U-251 MG cells

growth_protocol: U-251 MG cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM), 10% fetal bovine serum, 1× penicillin/streptomycin, 1×Myco-Blue Mycoplasma Detector. Cells were maintained at 37°C in a 5% CO2 atmosphere

extract_protocol:
Total RNAs were extracted utilizing RNA-easy Isolation Reagent (Vazyme, China) and treated with DNase I (Roche, Switzerland), which were then fragmented into 100-150 nt fragments with RNA Fragmentation Reagent (Invitrogen, USA).
The meRIP-seq libraries were used the SMARTer Stranded Total RNA-Seq Kit v2-Pico Input Mammalian (Takara, Japan). 10 ng of fragmented RNA from each sample was used as starting material for Input and IP samples. Amplification of libraries were performed with 14 cycles on the thermocycler. The samples were sequenced with paired-end on Illumina NovaSeq 6000.

tag: cell line

value: U-251 MG cells


title: PHYD-YFP/abCde, PHYB-GFP/AbCDE, PHYD-YFP/abcde mixture, 5 minutes, rep 1

library_source: genomic

molecule: genomic DNA

source_name: Mixture of samples

value: Mixture of samples

tag: genotype

tag: treatment

value: red light pulse at 50 µmol m-2 s-1 fluence rate for 5 min.


title: shMETTL3 Input


title: PHYD-YFP/abcde, 5 minutes, rep 3

value: 6-day-old etiolated seedlings (at 17 °C). Following a red light pulse at 50 µmol m-2 s-1 fluence rate for 5 min.

value: PHYD-YFP/abcde


title: PHYD-YFP/ab-C-de, 5 minutes, rep 3

value: PHYD-YFP/abCde


title: PHYD-YFP/ab-C-de, 5 minutes, rep 2


title: PHYD-YFP/abcde, 5 minutes, rep 2


title: PHYB-GFP/AbCDE, 5 minutes, rep 1


title: PHYD-YFP/ab-C-de, 5 minutes, rep 1


title: shMETTL3 IP


title: PHYD-YFP/abcde, 5 minutes, rep 1


title: CEG+Ri rep3

city: Duarte

first: Sarah

last: Shuck

state: CA

address: 1500 Duarte Rd, Fox North Room 216

institute: Beckman Research institute at City of Hope

data_processing:
The RNA-seq fastq reads were processed using Partek Flow Genomics pipeline version 10.0
Raw fastq reads were preprocessed to filter low quality reads and contaminants using Bowtie 2 and remove adapters using cutadapt.
The cleaned reads were aligned to the reference genome (Hg38) using STAR version 2.7.8a.
Gene counts were quantified using a modified form of the Expectation/Maximization algorithm (Partek E/M).
Counts normalization and differential gene expression analysis were performed using limma-voom.
Assembly: hg38
Supplementary files format and content: tab-delimited text file with columns containing raw gene counts from each sample.

source_name: HUVEC

extract_protocol:
Total RNA was isolated using Direct-zol RNA Miniprep Plus (Zymo).
RNA sequencing libraries were generated with Kapa RNA HyperPrep kit with RiboErase (Kapa Biosystems, KR1351) according to the manufacturer’s protocol. Total RNA (250 ng) from each sample was used for sequencing library preparation. The final libraries were validated with the Agilent Bioanalyzer DNA High Sensitivity Kit.

treatment_protocol: HUVECs were exposed to MG-adducts at a final concentration of 50 ng/mL of each diastereomer (R and S). Where indicated, HUVECs were pretreated with Ri at a final concentration of 100 µM for 1 hr before treatment with MG-adducts.

value: HUVEC

tag: cell type

value: Endothelial

value: CEG+Ri


title: PHYB-CFP, PHYD-YFP/abcde, 27 °C,  24 hours, rep 3

description: BBDox_24 hours_27deg_3

data_processing:
Sequence reads were trimmed using TrimmomaticPE.0.39 with this parameters:ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10, LEADING:5 TRAILING:5, SLIDINGWINDOW:5:20, MINLEN:50.
Quality controlled reads (FastQC), were mapped to reference genom using STAR.2.7.8a.
Raw count data were calculated with htseq-count.0.13.5.
In the next step, tRNA, rRNa, mithocondrial and chloroplast genes were removed from counts. Genes that have less than 5 counts per more than 75 percentage of the samples were also excluded.
Significant gene expression changes of light treatments were calculated from the log transformed quantile normalized intensities of the samples. For each temperature treatments, light exposure and genotypes, plants that kept in dark were used as dark control. The log2 fold changes and the FDR-adjusted p-values (q-values) were calculated with edgeR.3.38.4.
Assembly: TAIR10
Supplementary files format and content: Tab-delimited text files (.tsv) include raw gene counts for each Sample.

source_name: 4-day-old etiolated seedlings

growth_protocol: 4-day-old seedlings were grown on half-strength MS plates at 17 or 27 °C in the dark

extract_protocol:
Total RNA was extracted using RNeasy Miniprep Kits (Qiagen).
Poly(A)-enriched mRNA sequencing.

treatment_protocol: 0.1 g plant material was snap frozen in liquid nitrogen from etiolated or 1 h or 24 h R (50 µmol m-2 s-1) illuminated seedlings.

value: 4-day-old etiolated seedlings

value: PHYB-CFP, PHYD-YFP/abcde

tag: time point

value: 24 hours

value: 27 degreeC


title: PHYB-CFP, PHYD-YFP/abcde, 27 °C,  24 hours, rep 1

description: BBDox_24 hours_27deg_1


title: CEG+Ri rep2


title: R21787

value: DLPFC


title: PHYB-CFP/abcde, 27 °C,  24 hours, rep 2

description: BB_24 hours_27deg_2

value: PHYB-CFP/abcde


title: PHYB-CFP/abcde, 27 °C,  24 hours, rep 3

description: BB_24 hours_27deg_3


title: CEG+Ri rep1


title: aBcde, 27 °C,  24 hours, rep 2

description: B_24 hours_27deg_2

value: aBcde


title: aBcde, 27 °C,  24 hours, rep 3

description: B_24 hours_27deg_3


title: Single nucleus Hi-C cell P62E6

city: Cambridge

first: David

last: Lando

address: Department Biochemistry , Sanger Bulding, Tennis Court Road

department: Biochemistry

country: United Kingdom

institute: University of Cambridge

data_processing:
Single-cell Hi-C paired-end reads were processed using the NucProcessing software package (https://github.com/TheLaueLab/nuc_processing). Processed reads were aligned to the GRCm38/mm10 mouse genome reference using Bowtie 2 and filtered to retain reads that formed a valid Hi-C contact junction between two RE1 resriction sites. Output files were further processed to perform extra, single-cell specific processing and cleanup. These remove any pairs that represent only a single observation of a specific RE1-RE1 ligation junction after PCR amplification, while at least two separate, albeit sometimes identical, molecules must be paired-end sequenced to confirm a ligation junction. Next the sequence pairs were filtered to remove those with promiscuous ends: where the RE1 fragment at either end was involved in more than one ligation event. Finally, the redundancy in amplified RE1-RE1 ligation events was removed to create a single list of paired RE1 fragment ends.
Population Hi-C paired-end reads were processed using the NucProcessing software package (https://github.com/TheLaueLab/nuc_processing). Processed reads were aligned to the GRCm38/mm10 mouse genome reference using Bowtie 2 and filtered to retain reads that formed a valid Hi-C contact junction between two RE1 resriction sites. Output files were further processed to remove PCR redundancy in amplified RE1-RE1 ligation events to create a single list of paired RE1 fragment ends.
ChiP-seq paired-end reads were first mapped to the mouse genome reference sequence GRCm38/mm10 using Bowtie 2 v2.1.038 and filtered to retain reads with a mapping quality >30 using Samtools39. Peaks were called using MACS2 v2.1. Model-based analysis of ChIP-Seq data was carried out using MACS2 with a minimum FDR cut-off of 0.01 (-q 0.01) to find narrowPeaks (except for H3K9me3 and H3K27me3 which have broad peak features). For samples with the Drosophila spike-in, reads were mapped to the Drosophila genome (release 6/dm6) using Bowtie 2, but with a mapping quality cut-off equal to 10. The Drosophila spike-in read count was quantified using the Samtools Flagstat module. Bigwig files were normalised using the corresponding Drosophila spike-in read abundance with the –extendReads option in deepTools40.
Single-cell RNA-seq reads were aligned to the mouse reference genome GRCm38/mm10 with the GSNAP aligner (gmap-2014- 12-17) using the parameters -n 1 -N 1 for uniquely mapped reads and allowing for novel splicing sites. Gene read counts were assigned using HTSeq (v0.6.1) based on gene annotation from ensemble release 81. A quality control filtering was then applied to the cells using the R package Scater (1.2.0) : more that 5*10^5 reads per cell, more than 7000 individual features detected and less than 20% of the reads mapping to mitochondrial genes. The reads were then normalised for library size using the R package Scran (1.2.2).
Assembly: GRCm38/mm10
Supplementary files format and content: The Hi-C ncc file (.ncc) is a tab-separated text format file containing the Hi-C contacts for either single cell or population Hi-C samples. After the header line, each individual contact is represented on a line consisting of chromosome_1 seq_pos_1 chromosome_2 seq_pos_2
Supplementary files format and content: The n3d.txt (.n3d.txt) file format for single cell genomic 3D structure coordinate positions is a  simple whitespace-separated text format consisting of blocks of lines for separate  chromosomes. Each block consists of a header  line, giving the chrosome name, number of coordinates (i.e. number of particle  positions) and the number of alternative coordinate models. The subsequent  particle data lines for the chromosome contain the basebair sequence position  followed by cartesian (X, Y, Z) coordinates for each alternative model.
Supplementary files format and content: The bigWig (.bw) files are in an indexed binary format suitable for displaying data in a Genome Browser. No bigWig files for Input samples.
Supplementary files format and content: The peak files (.narrowPeak and .broadPeak) are files that contain called peaks of signal enrichement based on pooled, normalized data.The .narrowPeak files are in a BED6+4 format while the .broadPeak files are in a BED 6+3 format. No peak files for Input samples
Supplementary files format and content: The single-cell RNA-seq sample and barcode file (.samplebarcode.csv) is a file that lists all 96 cell sample names and there corresponding barcode name and sequence.
Supplementary files format and content: The single-cell RNA-seq expression read file (.tsv) is a file that lists the gene exprerssion read count for each different cell. The first column is the ensembl gene id. The remaining columns are the expression read counts for each individual cell.
Library strategy: Single-nucleus Hi-C

organism: Mus musculus

source_name: Yes

growth_protocol: For routine cell culture, cell lines were maintained in N2B27 media supplemented with 2i and mouse leukemia inhibitory factor (mLIF). 50 % DMEM/F-12 medium (Gibco, 21041025) and 50 % Neurobasal™ Medium (Gibco, 12348017) was supplemented with 1 x N2 to a final concentration of 2.5 µg/ml insulin (provided in-house by the Cambridge Stem Cell Institute), 0.5x B-27™ Supplement (Gibco, 17504044), 1x minimum essential medium non-essential amino acids supplement (Sigma-Aldrich, M7145), 2 mM L-glutamine (Life tech, 25030024), and 0.1 mM 2-mercaptoethanol (Life tech, 21985023), 2i inhibitors (1 µM PD0325901, 3 µM CHIR99021) and 10 ng/ml mLIF (provided by the Biochemistry Department, University of Cambridge). Cells were routinely screened for mycoplasma contamination.

extract_protocol:
Four to five million cells were fixed for 5 min with 2 % formaldehyde in PBS and then the reaction was quenched for another 5 min in 0.125 M glycine. Nuclei were then extracted by incubating cells on ice for 30 min (inverting every 10 min) in 10 mM Tris pH 8.0, 10 mM NaCl, 0.2 % NP-40 (IGEPAL CA-630) and protease inhibitor cocktail (Roche).
Single cell Hi-C libraries were prepared using an adaptor ligation method. Briefly, biotinylated junctions were captured on streptavidin M-280 dynabeads and digested with AluI enzyme to generate blunt ends. The blunt ends were A-tailed with Klenow (3'→5' exo-) before ligation with adaptor sequences containing unique barcode.  After adaptor ligation DNA was PCR amplified with Illumina primers for 25 cycles and library fragments of ~300-1000 bp (insert plus adaptor and PCR primer sequences) were isolated using AMPure beads (Beckman). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Hiseq 4000 following the manufacturer's protocols.

treatment_protocol: Naïve ES state cells were plated at a density of 10,000 cells/cm2 and grown in N2B27 with 2i and LIF for 48 hrs. 24 hr state cells were plated at the same density in N2B27 with 2i and no LIF. After 24 hrs the two inhibitors were removed and cells were grown in N2B27 only media for a further 24 hrs. To obtain 24 hr Rex1 High and 24hr Rex1 Low/formative state cells cells at the 24 hr stage were FACS sorted with gates set to collect cells with the highest and lowest 25% GFP expression, repectively. 48 hr primed state cells were plated and grown in the same way except that after removal of the two inhibitors cells were grown in N2B27 only media for 48 hrs.

value: Yes

value: haploid mESCs derived from strain 129/Ola

value: 24 hr Rex1 High


title: CEG rep3

value: CEG


title: CEG rep2


title: R17167

value: F

value: Control


title: PHYD-YFP/ab_C_de, 27 °C,  24 hours, rep 2

description: DoxC_24 hours_27deg_2

value: PHYD-YFP/abCde


title: PHYD-YFP/ab_C_de, 27 °C,  24 hours, rep 3

description: DoxC_24 hours_27deg_3


title: R17156

value: M

value: Case


title: CEG rep1

value: HUVEC

value: Endothelial


title: PHYD-YFP/ab_C_de, 27 °C,  24 hours, rep 1

description: DoxC_24 hours_27deg_1

value: 4-day-old etiolated seedlings


title: R21790


title: R17112


title: R17068


title: PHYB-CFP, PHYD-YFP/abcde, 27 °C,  24 hours, rep 2

description: BBDox_24 hours_27deg_2

value: PHYB-CFP, PHYD-YFP/abcde

value: 24 hours


title: R21789

value: DLPFC


title: PHYD-YFP/abcde, 27 °C,  24 hours, rep 3

description: Dox_24 hours_27deg_3

value: PHYD-YFP/abcde

value: 27 degreeC


title: CEdG+Ri rep3

value: CEdG+Ri


title: PHYB-CFP/abcde, 27 °C,  24 hours, rep 1

description: BB_24 hours_27deg_1

value: PHYB-CFP/abcde


title: aBcde, 27 °C,  24 hours, rep 1

description: B_24 hours_27deg_1

value: aBcde


title: PHYD-YFP/abcde, 27 °C,  24 hours, rep 2

description: Dox_24 hours_27deg_2


title: CEdG+Ri rep2


title: R17013


title: PHYD-YFP/abcde, 27 °C,  24 hours, rep 1

description: Dox_24 hours_27deg_1


title: PHYB-CFP, PHYD-YFP/abcde, 17 °C,  24 hours, rep 2

description: BBDox_24 hours_17deg_2

value: 17 degreeC


title: R16881

value: F


title: CEdG+Ri rep1


title: CEdG rep2

value: CEdG


title: genomic DNA from OPA1 treated-THP1 cells

type: genomic

city: Hangzhou

first: Jun

last: Lu

state: Zhejiang

address: 866 Yuhangtang Road

institute: Zhejiang University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised toheIllumina Infinium 850k Human MethylationEPIC BeadChip using standard Illumina protocol

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

data_processing: Bioconductor (version 3.3.3); BMIQ method used for normalization by CHAMP version  2.20.1. For normalization, functional normalization (Fortin et al., 2014) has been added as an option alongside beta-mixture quantile normalization. Singular value decomposition is used to correlate principal components to biological and technical factors.

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

growth_protocol: THP-1 cells were cultured in RPMI-1640 medium (Gibco, Grand Island, NY, USA), supplemented with 10% FBS (Gibco) and penicillin-streptomycin

extract_protocol: Genomic DNA was obtained from 5x106 cells with the Cell/Tissue DNA Isolation Mini Kit (Vazyme)

treatment_protocol: THP-1 cells were treated with DMSO or OPA1 for 48 hours

value: Human AML cells

value: OPA1 for 48 hours


title: R16834

value: M

value: Case


title: PHYB-CFP, PHYD-YFP/abcde, 17 °C,  24 hours, rep 3

description: BBDox_24 hours_17deg_3


title: aBcde, 17 °C,  24 hours, rep 2

description: B_24 hours_17deg_2


title: PHYB-CFP, PHYD-YFP/abcde, 17 °C,  24 hours, rep 1

description: BBDox_24 hours_17deg_1


title: CEdG rep3

value: HUVEC

value: Endothelial


title: PHYB-CFP/abcde, 17 °C,  24 hours, rep 2

description: BB_24 hours_17deg_2

value: 4-day-old etiolated seedlings


title: PHYB-CFP/abcde, 17 °C,  24 hours, rep 3

description: BB_24 hours_17deg_3

value: 24 hours


title: aBcde, 17 °C,  24 hours, rep 3

description: B_24 hours_17deg_3


title: genomic DNA from Ctrl treated-THP1 cells

source_name: Ctrl

value: DMSO for 48 hours


title: PHYD-YFP/ab_C_de, 17 °C,  24 hours, rep 3

description: DoxC_24 hours_17deg_3

value: PHYD-YFP/abCde


title: PHYD-YFP/ab_C_de, 17 °C,  24 hours, rep 2

description: DoxC_24 hours_17deg_2


title: R16740

value: DLPFC

value: Control


title: Control+Ri rep3

value: Ri


title: CEdG rep1


title: R16911


title: PHYD-YFP/ab_C_de, 17 °C,  24 hours, rep 1

description: DoxC_24 hours_17deg_1


title: Control+Ri rep2


title: R16653


title: PHYD-YFP/abcde, 17 °C,  24 hours, rep 3

description: Dox_24 hours_17deg_3

value: PHYD-YFP/abcde


title: PHYD-YFP/abcde, 17 °C,  24 hours, rep 2

description: Dox_24 hours_17deg_2

value: 17 degreeC


title: R16868

value: F


title: PHYD-YFP/abcde, 17 °C,  24 hours, rep 1

description: Dox_24 hours_17deg_1


title: R16643


title: PHYB-CFP, PHYD-YFP/abcde, 27 °C,  1 hour, rep 2

description: BBDox_1 hour_27deg_2

value: PHYB-CFP, PHYD-YFP/abcde

value: 1 hour

value: 27 degreeC


title: aBcde, 17 °C,  24 hours, rep 1

description: B_24 hours_17deg_1

value: aBcde


title: PHYB-CFP/abcde, 17 °C,  24 hours, rep 1

description: BB_24 hours_17deg_1

value: PHYB-CFP/abcde


title: PHYB-CFP, PHYD-YFP/abcde, 27 °C,  1 hour, rep 1

description: BBDox_1 hour_27deg_1


title: Control rep2

value: HUVEC


title: PHYB-CFP, PHYD-YFP/abcde, 27 °C,  1 hour, rep 3

description: BBDox_1 hour_27deg_3


title: R16376

value: M

value: Case


title: Control rep3

value: Endothelial


title: PHYB-CFP/abcde, 27 °C,  1 hour, rep 2

description: BB_1 hour_27deg_2

value: 4-day-old etiolated seedlings


title: Control rep1


title: PHYB-CFP/abcde, 27 °C,  1 hour, rep 3

description: BB_1 hour_27deg_3


title: R16257


title: PHYB-CFP/abcde, 27 °C,  1 hour, rep 1

description: BB_1 hour_27deg_1


title: aBcde, 27 °C,  1 hour, rep 3

description: B_1 hour_27deg_3


title: EZH2_H526_BRM014_Rep2

city: Chicago

first: Lu

last: Wang

state: Illinois

address: 303 E. Superior Street Simpson Querrey 7-414

department: Biochemistry and Molecular Genetics

institute: Northwestern University

data_processing:
Basecalls were performed using bcl2fastq v2.17 for NextSeq output.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC hg19 using Bowtie version 0.12.9. Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC hg19 using Tophat version 2.0.9. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Assembly: hg19
Supplementary files format and content: bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

growth_protocol: The SCLC cell lines NCI-H526, NCI-H211 and CORL311 were obtained from ATCC, and were maintained with ATCC-formulated RPMI-1640 medium containing 10% FBS (Sigma).

extract_protocol:
RNA was extracted using QIAGEN RNeasy kit. DNA after ChIP protocol was isolated using QIAGEN PCR purification kit. For ATAC-seq, frozen cells were thawed and washed once with PBS and then resuspended in 500 uL of cold ATAC lysis buffer. The cell number was assessed by Cellometer Auto 2000 (Nexcelom Bioscience). 50K to 100K nuclei were then centrifuge (pre-chilled) at 500 g for 10 min. Supernatant was then removed and the nuclei were resuspended in 50 uL of tagmentated DNA by pipetting up and down six times. The reactions were incubated at 37 °C for 30 min in a thermomixer shaking at 1,000 rpm, and then cleaned up by the MiniElute reaction clean up kit (Qiagen).
ChIP-seq: ChIP-sequencing libraries were prepared using KAPA HyperPrep Kit (Kapa Biosystems) following manufacturer’s recommendation. In brief, 500ng of input DNA sheared by Covaris LE220 ultrasonicator or 10 ng of immunoprecipitated DNA was end-repaired and 3'-dA tailed. Adapter was then ligated to the DNA, and ligated product was PCR amplified and cleaned up using SPRIselect Reagent (Beckman Coulter). for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-sequencing libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg of total RNA was used as starting material. Libraries were validated using the Agilent DNA 1000 Kit
RNA-seq: Paramagnetic beads coupled with oligo d(T) are combined with total RNA to isolate poly(A)+ transcripts based on NEBNext® Poly(A) mRNA Magnetic Isolation Module manual. Prior to first strand synthesis, samples are randomly primed (5´ d(N6) 3´ [N=A,C,G,T]) and fragmented based on manufacturer’s recommendation (NEBNext® Ultra™ II RNA Nondirectional Library Prep Kit for Illumina®). The first strand is synthesized with the Protoscript II Reverse Transcriptase with an longer extension period (40 minutes for 42◦C). All remaining steps for library construction were used according to the NEBNext® Ultra™ II RNA Nondirectional Library Prep Kit for Illumina®. Illumina 8-nt dual-indices were used. Samples were pooled and sequencing on a HiSeq with a read length configuration of 150 PE.
ATAC-seq: Tagmentated DNA was amplified with barcode primers. Library quality and quantity were assessed with Qubit 2.0 DNA HS Assay (ThermoFisher, Massachusetts, USA), Tapestation High Sensitivity D1000 Assay (Agilent Technologies, California, USA), and QuantStudio® 5 System (Applied Biosystems, California, USA). Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina® HiSeq (Illumina, California, USA) with a read length configuration of 150 PE for 50M PE reads (25M in each direction) per sample.

treatment_protocol: For GSK126, cells were treated with compound at 2 uM for 6 days; for BRM014, cells were treated with compoud at 1 uM for 24 hours. For sgRNA depletion, cells were infected with lentivirus containing sgRNAs and selected with puromycin for at least 2 days.

tag: antibody

value: small cell lung cancer

value: wild type


title: EZH2_H526_DMSO_Rep2

value: DMSO


title: aBcde, 27 °C,  1 hour, rep 2

description: B_1 hour_27deg_2

tag: tissue


title: R16148

value: DLPFC

tag: dsm-5 aud status


title: Control+Ri rep1

value: Ri


title: aBcde, 27 °C,  1 hour, rep 1

description: B_1 hour_27deg_1


title: PHYD-YFP/ab_C_de, 27 °C,  1 hour, rep 3

description: DoxC_1 hour_27deg_3

value: PHYD-YFP/abCde


title: PHYD-YFP/ab_C_de, 27 °C,  1 hour, rep 2

description: DoxC_1 hour_27deg_2


title: R16102

tag: Sex


title: PHYD-YFP/abcde, 27 °C,  1 hour, rep 3

description: Dox_1 hour_27deg_3

value: PHYD-YFP/abcde


title: R16099

value: F

tag: agedeath


title: R16259

tag: dsm-5 major depression diagnosis

value: Control


title: PHYD-YFP/abcde, 27 °C,  1 hour, rep 2

description: Dox_1 hour_27deg_2

value: 1 hour

value: 27 degreeC


title: H3K27me3_H526_DMSO_Rep2


title: PHYB-CFP, PHYD-YFP/abcde, 17 °C,  1 hour, rep 2

description: BBDox_1 hour_17deg_2

value: PHYB-CFP, PHYD-YFP/abcde

value: 17 degreeC


title: PHYB-CFP, PHYD-YFP/abcde, 17 °C,  1 hour, rep 1

description: BBDox_1 hour_17deg_1


title: R16002

value: M

tag: current smoker at death


title: R15981

tag: pmi


title: R16262

tag: rin


title: PHYD-YFP/ab_C_de, 27 °C,  1 hour, rep 1

description: DoxC_1 hour_27deg_1


title: PHYB-CFP/abcde, 17 °C,  1 hour, rep 3

description: BB_1 hour_17deg_3

value: PHYB-CFP/abcde


title: PHYD-YFP/abcde, 27 °C,  1 hour, rep 1

description: Dox_1 hour_27deg_1


title: BRG1_H526_sgPOU2AF2_2_Rep2

value: sgPOU2AF2 #2


title: R16078

tag: sample plate


title: R15977

value: Case

tag: sample well


title: BRG1_H526_sgNONT_Rep2

value: small cell lung cancer

value: sgRNA nontargeting


title: BRG1_H526_sgPOU2AF2_1_Rep2

value: wild type

value: sgPOU2AF2 #1


title: PHYB-CFP/abcde, 17 °C,  1 hour, rep 1

description: BB_1 hour_17deg_1

value: 4-day-old etiolated seedlings


title: EZH2_H526_sgPOU2AF2_2_Rep2


title: R15973

value: DLPFC

tag: brain number


title: aBcde, 17 °C,  1 hour, rep 3

description: B_1 hour_17deg_3

value: aBcde


title: PHYD-YFP/ab_C_de, 17 °C,  1 hour, rep 3

description: DoxC_1 hour_17deg_3

value: PHYD-YFP/abCde


title: aBcde, 17 °C,  1 hour, rep 2

description: B_1 hour_17deg_2


title: R15915

value: Control


title: H3K27me3_H526_BRM014_Rep2

tag: cell line


title: aBcde, 17 °C,  1 hour, rep 1

description: B_1 hour_17deg_1

tag: genotype

value: 1 hour


title: PHYB-CFP, PHYD-YFP/abcde, 17 °C,  1 hour, rep 3

description: BBDox_1 hour_17deg_3

tag: treatment


title: EZH2_H526_sgPOU2AF2_1_Rep2

tag: cell type


title: PHYD-YFP/ab_C_de, 17 °C,  1 hour, rep 1

description: DoxC_1 hour_17deg_1

tag: time point


title: EZH2_H526_sgNONT_Rep2

tag: antibody


title: H3K27me3_H526_sgPOU2AF2_2_Rep2


title: PHYD-YFP/ab_C_de, 17 °C,  1 hour, rep 2

description: DoxC_1 hour_17deg_2

tag: tissue


title: PHYD-YFP/abcde, 17 °C,  1 hour, rep 3

description: Dox_1 hour_17deg_3

value: PHYD-YFP/abcde


title: R15899

tag: dsm-5 aud status


title: R15908

tag: Sex


title: H3K27me3_H526_sgPOU2AF2_1_Rep2


title: PHYD-YFP/abcde, 17 °C,  1 hour, rep 1

description: Dox_1 hour_17deg_1


title: PHYB-CFP, PHYD-YFP/abcde, 27 °C,  Dark control, rep 3

value: PHYB-CFP, PHYD-YFP/abcde

value: dark, 27 degreeC


title: R21962

source_name: Nucleus Accumbens

value: Nucleus Accumbens

value: F

tag: agedeath


title: PHYB-CFP/abcde, 17 °C,  1 hour, rep 2

description: BB_1 hour_17deg_2

value: PHYB-CFP/abcde

value: 17 degreeC


title: PHYB-CFP, PHYD-YFP/abcde, 27 °C,  Dark control, rep 2


title: PHYB-CFP, PHYD-YFP/abcde, 27 °C,  Dark control, rep 1


title: R21961

tag: dsm-5 major depression diagnosis


title: H3K27me3_H526_sgNONT_Rep2

value: small cell lung cancer


title: PHYB-CFP/abcde, 27 °C,  Dark control, rep 3


title: Ventricular Fibroblasts, Donor 2, Rep 2

first: Salman

middle: R

last: Khetani

email: gbrown25@uic.edu, skhetani@uic.edu

state: IL

address: 851 S Morgan St, SEO 218

department: Biomedial Engineering

institute: University of Illinois at Chicago

data_processing:
Data was alined using the BioJupies online interface using the standard parameters and the raw counts were derived
The edgeR package in R was then utilized to normalize the data
Principal component analysis (PCA) was performed after normalization and differentially expressed genes (DEGs) were identified with false discovery rate (FDR) < 0.05 and an absolute log2 fold change of greater than 1.
The adjusted p-value was further assessed with the p-adjust function in edgeR.
Gene Ontology (GO) pathway analysis was performed in Cytoscape with the ClueGo package for analysis and visualization.
Assembly: Homo sapiens reference genome GRCh38 (hg38)
Supplementary files format and content: Processed data files are provided as .xlsx

source_name: Heart

growth_protocol: Cardiac fibroblasts were grown in Ham’s F-12 medium containing L-glutamine, 1% vol/vol penicillin/streptomycin, 4 ng/mL basic fibroblast growth factor, and 20 µg/mL human insulin. All cells were sequenced at passage 4 or 5.

extract_protocol:
RNA was isolated using the RNeasy kit from Qiagen
Strand-specific RNA-Seq libraries were prepared using a TruSEQ mRNA-SEQ library protocol (illinuma provided). Library quality and quantity was assessed using Agilent bio-analyzer and libraries were sequenced using an Illumina NovaSEQ6000.

value: Heart

tag: individual

value: Donor 2

value: Ventricular Fibroblast


title: R21960

value: M

tag: current smoker at death

tag: pmi


title: Ventricular Fibroblasts, Donor 2, Rep 1


title: PHYB-CFP/abcde, 27 °C,  Dark control, rep 2

value: 4-day-old etiolated seedlings


title: aBcde, 27 °C,  Dark control, rep 3

value: aBcde


title: PHYB-CFP/abcde, 27 °C,  Dark control, rep 1


title: Ventricular Fibroblasts, Donor 1, Rep 2

value: Donor 1


title: R21958

value: Control

tag: rin

tag: sample plate


title: PHYD-YFP/abcde, 27 °C,  Dark control, rep 3


title: R21959

tag: sample well

tag: brain number


title: PHYD-YFP/ab_C_de, 27 °C,  Dark control, rep 3

tag: genotype

value: PHYD-YFP/abCde


title: R21956

value: Case


title: PHYD-YFP/abcde, 17 °C,  1 hour, rep 2

description: Dox_1 hour_17deg_2

value: PHYD-YFP/abcde

value: 1 hour

tag: treatment


title: Atrial Fibroblasts, Donor 2, Rep 1

tag: cell type

value: Atrial Fibroblast


title: aBcde, 27 °C,  Dark control, rep 1

value: dark, 27 degreeC


title: PHYD-YFP/abcde, 27 °C,  Dark control, rep 1


title: aBcde, 27 °C,  Dark control, rep 2


title: Atrial Fibroblasts, Donor 1, Rep 2


title: Ventricular Fibroblasts, Donor 1, Rep 1


title: PHYD-YFP/abcde, 27 °C,  Dark control, rep 2


title: PHYD-YFP/ab_C_de, 27 °C,  Dark control, rep 2


title: PHYB-CFP, PHYD-YFP/abcde, 17 °C,  Dark control, rep 2

value: PHYB-CFP, PHYD-YFP/abcde

value: dark, 17 degreeC


title: Atrial Fibroblasts, Donor 2, Rep 2


title: R21954

value: Nucleus Accumbens


title: Atrial Fibroblasts, Donor 1, Rep 1

value: Heart


title: R21950


title: iPSCaCM, RandomMonoculture, rep 3

growth_protocol: iPSCs were maintained on human recombinant vitronectin coated plates in mTeSR medium. iPSCs were then differentiated using the cardiomyocyte differentiation kit (Gibco), and guided into atrial subtypes using 1µmol/l all-trans retinoic acid (protocol adapted from Devalla et al., 2015). At day 10, glucose starvation metabolic selection was used to enrich the iPSC-aCM culture. Thyroid hormone, insulin-like growth factor, dexamethasone, palmitic acid, and oleic acid were added to the foundational maintenance media after glucose starvation. At ~day 16, cells were replated onto either fibronectin coated plates (RM) or on micropatterned fibronectin plates with senquentially seeded atrial fibroblasts (PC). Media was changed every other day until day 45 where iPSC-aCMs were sorted via MACS and lysed for sequencing.

tag: cell line

value: iPSC-aCM

value: Random Monoculture


title: PHYB-CFP, PHYD-YFP/abcde, 17 °C,  Dark control, rep 3


title: R21952

value: M


title: R21955

value: F


title: PHYD-YFP/ab_C_de, 27 °C,  Dark control, rep 1

value: 4-day-old etiolated seedlings


title: R21951


title: R21945


title: R21948


title: PHYB-CFP/abcde, 17 °C,  Dark control, rep 3

value: PHYB-CFP/abcde


title: PHYB-CFP/abcde, 17 °C,  Dark control, rep 1


title: PHYD-YFP/ab_C_de, 17 °C,  Dark control, rep 3


title: PHYB-CFP/abcde, 17 °C,  Dark control, rep 2


title: R21944


title: PHYD-YFP/ab_C_de, 17 °C,  Dark control, rep 2


title: R21943


title: PHYD-YFP/ab_C_de, 17 °C,  Dark control, rep 1


title: iPSCaCM, PatternedCoculture, rep 2

value: Patterned Coculture


title: iPSCaCM, RandomMonoculture, rep 2


title: aBcde, 17 °C,  Dark control, rep 3

value: aBcde


title: PHYD-YFP/abcde, 17 °C,  Dark control, rep 1


title: aBcde, 17 °C,  Dark control, rep 2


title: iPSCaCM, RandomMonoculture, rep 1


title: aBcde, 17 °C,  Dark control, rep 1


title: R21942

value: Case


title: PHYB-CFP, PHYD-YFP/abcde, 17 °C,  Dark control, rep 1


title: iPSCaCM, PatternedCoculture, rep 3


title: PHYD-YFP/abcde, 17 °C,  Dark control, rep 3

value: PHYD-YFP/abcde


title: PHYD-YFP/abcde, 17 °C,  Dark control, rep 2


title: ATAC_H526_BRM014

data_processing:
Basecalls were performed using bcl2fastq v2.17 for NextSeq output.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC hg19 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC hg19 using Tophat version 2.0.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Assembly: hg19
Supplementary files format and content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

value: small cell lung cancer

value: wild type


title: R21941


title: iPSCaCM, PatternedCoculture, rep 1


title: R21940


title: WT2_M2G [Tn-seq]

city: Namur

first: Regis

last: Hallez

address: 61 Rue de Bruxelles

country: Belgium

institute: UNamur

data_processing:
*library strategy: Tn-seq
Around 3 x 10^7 paired-end sequence reads (2 x 75) were first filtered with the 5'-GGTTGAGATGTGTATAAGAGACAG sequence (corresponding to the mini-Tn5) and mapped on the genome of C. crescentus NA1000 (NC_011916.1) and converted to SAM using BWA and SAM tools from the sourceforge server (https://sourceforge.net/)
the number of reads overlapping each genomic position was computed using custom Python scripts.
The total number of reads for internal 80% of each ORF in each condition were then computed using custom Python scripts.
For comparing strains, the total number of reads was normalized by the ratio of the number of reads between the two strains.
Ward’s clustering analysis was performed to define the fitness categories as previously reported.
Assembly: NC_011916.1
Supplementary files format and content: The xls file reports Tn-Seq data. The different columns are organized as follows: column 1: Gene_ID (CCNA gene identification number); column 2: Start (coordinates for the start of the gene); column 3: End (coordinates for the end of the gene); column 4: Strand (Strand on which the gene is encoded); column 5: Name (Predicted function of the corresponding gene);[columns 6-13: WT_M2G; columns 14-21: WT_M2G-K]; columns 6&14: #Reads (number of normalized counts between the coordinates of the gene); columns 7&15: #Reads/bp (number of normalized counts divided by the length of the gene); columns 8&16: #Insertions (number of independent Tn insertions into the corresponding gene); columns 9&17: #Insertions/bp (number of independent Tn insertions divided by the length of the corresponding gene); columns 10&18: ES,#Reads (number of normalized counts between 80% of the coordinates of the gene); columns 11&19: ES,#Reads /bp (number of normalized counts divided by the 80% of length of the gene); columns 12&20: ES,#Insertions (number of independent Tn insertions into 80% of the corresponding gene); columns 13&21: ES,#Insertions/bp (number of independent Tn insertions divided by the 80% length of the corresponding gene)

organism: Caulobacter vibrioides

source_name: Colonies

growth_protocol: A mini-Tn5 was introduced into C. crescentus WT by bi-parental mating on PYE agar for 4h at 30 ° C. Cells were collected, resuspended in 10 ml M2G or M2G-K and washed twice with the same volume. Dilutions (10-6) were plated on M2G or M2G-K plates supplemented with aztreonam (5mg l-1) and kanamycin (5mg l-1) and incubated at 30 ° C for 5 days. Then, at least 3 x10^5 colonies were collected in M2G or M2G-K supplemented with 10% glycerol and stored at -80 °C.

extract_protocol:
Genomic DNA was then extracted following the Nucleospin Tissue Kit protocol (Macherey-Nagel) and resuspended in 50 µl elution buffer (5 mM Tris-HCl [pH 8.5]).
Tn-Seq libraries were prepared at the Fasteris company (Switzerland).

value: Colonies

value: WT

value: Colonies grown on M2G


title: R21938

value: Nucleus Accumbens


title: WT2_M2G-K [Tn-seq]

value: Colonies grown on M2G-K


title: EZH2_H526_DMSO

tag: antibody

value: DMSO


title: R21937

tag: tissue

value: Control


title: bzr1-1D brm_PPZ-bio3

city: Guangzhou

first: Tao

last: Zhu

address: 135 Xingang West Road, Guangzhou City

institute: Arabidopsis

description: Gene_differential_expression_testing_Col vs bzr1-1D brm-1.xlsx

data_processing:
Sequencing separately at Novogene, using Illumina = (Sequencing method: Novaseq-PE150).
Reads were mapped to the TAIR10 Arabidopsis genome using TopHat (Galaxy V2.1.1 in usegalaxy.org) with default settings, except that a minimum intron length of 20 bp and a maximum intron length of 4,000 bp were required (Paired-end). Then, mapped reads were assembled according to TAIR10 version of genome annotation using cufflinks (version 2.1.1) with default settings.
To analyze differential expression, the assembled transcripts from three independent biological replicates in Col and other mutants were included and compared using Cuffdiff (version 2.1.1) with default settings.
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include RPKM values for wt, bri1-701

source_name: Yong seedlings

growth_protocol: Plants were grown in 1/2MS media with 2 μM PPZ in the dark for five days

extract_protocol:
RNA was harvested using the HiPure Universal RNA Mini Kit (MAGEN, Cat. No. R4130). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Yong seedlings

value: bzr1-1D brm

tag: condition

value: dark and 2uM PPZ

tag: time

value: Day 5


title: brm_PPZ-bio1

description: Gene_differential_expression_testing_Col vs brm-1.xlsx

value: brm


title: ATAC_H526_DMSO


title: WT1_M2G-K [Tn-seq]


title: bzr1-1D_PPZ-bio3

description: Gene_differential_expression_testing_Col vs bzr1-1D.xlsx


title: WT1_M2G [Tn-seq]


title: R21939

tag: dsm-5 aud status

tag: Sex

value: M

tag: agedeath


title: brm_PPZ-bio3


title: endosperm, wild type, 16 days after pollination, rep3 [NT3]

city: Hefei

first: Di

last: Peng

address: Huangshan Road 443

institute: University of Science and Technology of China

data_processing:
The resulting clean reads were aligned to the B73 reference genome (Zm-B73-REFERENCE-NAM-5.0) using the HISAT2 program
Assembly: Zm-B73-REFERENCE-NAM-5.0
Supplementary files format and content: tab-delimited txt file include FPKM value for each sample

molecule: polyA RNA

organism: Zea mays

source_name: endosperm

extract_protocol:
Total RNA was extracted from maize endosperm using TRIzol reagent (Invitrogen). Kit for Illumina
Sequencing libraries were generated using VAHTSTM mRNA-seq V2 Library Prep Kit for Illumina.

value: endosperm

tag: age


title: bzr1-1D brm_PPZ-bio2


title: R21935

tag: dsm-5 major depression diagnosis

tag: current smoker at death

tag: pmi


title: endosperm, zmnac128 zmnac130, 16 days after pollination, rep3 [nac3]

value: zmnac128 zmnac130


title: bzr1-1D_PPZ-bio2


title: Mtphr2-AM-3

city: Changsha

first: Peng

address: Lushan Road

institute: Hunan Normal university

data_processing:
HISAT2
StringTie
DESeq2
Assembly: Medicago truncatula genome v4.0
Supplementary files format and content: expression browser

organism: Medicago truncatula

source_name: Root

extract_protocol:
Total RNA of wild-type R108 and Mtphr2 was extracted from the mycorrhizal roots using TRIzol® Reagent. Three technical replicates were used for each sample.
RNA samples were sequenced at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) using Illumina Novaseq 6000 platform. RNA-seq data were aligned and assembled to Medicago truncatula genome v4.0 using HISAT2 and StringTie software (Kim et al., 2015; Pertea et al., 2015).

value: Root

value: Root cell

value: Mtphr2 mutant


title: R21934

value: Case

tag: rin

tag: sample plate

tag: sample well


title: H3K27me3_H526_BRM014

value: small cell lung cancer

tag: genotype

value: wild type

tag: treatment


title: BRG1_H526_sgPOU2AF2_1

tag: cell line

tag: cell type

value: sgPOU2AF2 #1


title: brm_PPZ-bio2

tag: tissue


title: Mtphr2-AM-1


title: BRG1_H526_sgPOU2AF2_2

tag: antibody

value: sgPOU2AF2 #2


title: bzr1-1D brm_PPZ-bio1

tag: condition

tag: time


title: EZH2_H526_BRM014


title: bzr1-1D_PPZ-bio1


title: R21933

value: Nucleus Accumbens

tag: dsm-5 aud status

tag: Sex

tag: brain number


title: R21936

value: F

tag: agedeath

tag: dsm-5 major depression diagnosis

value: Control


title: H3K27me3_H526_DMSO

value: DMSO


title: Mtphr2-AM-2


title: WT_PPZ-bio2

value: Yong seedlings

value: dark and 2uM PPZ

value: Day 5


title: R108-AM-3

value: WT


title: SUZ12_H526_sgPOU2AF2_1


title: BRG1_H526_sgNONT

value: sgRNA nontargeting


title: WT_PPZ-bio3


title: R21929

value: M

tag: current smoker at death

tag: pmi


title: SUZ12_H526_sgPOU2AF2_2


title: R21932

tag: rin

tag: sample plate


title: R108-AM-2

value: Root

value: Root cell

tag: genotype


title: Empty Vector Control (LeGO-Ctl) tumor RNA-seq sample #3

city: Ithaca

first: Praveen

last: Sethupathy

email: as3999@cornell.edu, pr46@cornell.edu

state: NY

address: T7 006D Veterinary Research Tower, Box 17

department: Department of Biomedical Sciences

institute: Cornell University

description:
RNA-seq. Tumors derived from FLC monoclone implantation that harbor LINC00473 overexpression (LeGO-473ox) and empty vector control (LeGO-Ctl).
RKM7

data_processing:
Sequencing was aligned and quantified using STAR/Salmon (RNA-seq).
RNA-seq data was normalized using DESeq2.
Assembly: Single end RNA sequencing results were aligned to the human genome (hg38) using STAR (v2.4.2a) and quantified using Salmon (v0.8).
Supplementary files format and content: Normalized counts

source_name: Tumor

extract_protocol:
RNA was isolated from the new cohort using the Total RNA Purification Kit (Norgen Biotek).
Libraries were prepared with TruSeq Stranded mRNA Library Prep Kit (Illumina).

value: Tumor

value: Tumors derived from subcutaneous implantation of engineered FLC cells that were previously established from a patient-derived xenograft (PDX) mouse model

value: tumor stage


title: BRM-GFP_brm-1-PPZ-IP-bio2

data_processing:
The raw reads were mapped to the reference genome (Arabidopsis thaliana genome, TAIR10) with Bowtie for Illumina (Galaxy Version 1.1.2) for DNA sequencing on web https://usegalaxy.org/ with default setting, except that the paired-end was required.
MACS2 (Galaxy Version 2.1.1) was used for peak calling using the following parameters “gsize=119,667,750, bw=300, q=0.01, nomodel, extsize=200”.
The alignments were first converted to Wiggle (WIG) files and the bigwig files were generated using bamCoverage with “-bs 10”, “--normalizeUsing RPKM (reads per kilobase per million)” in DeepTools and then the data were imported into the Integrative Genomics Viewer (IGV) for visualization.
Assembly: TAIR10
Supplementary files format and content: bigWig, narrowPeak

source_name: Young seedlings

growth_protocol: Plants were grown in 1/2MS media with 22 degree in the dark for five days

extract_protocol:
Lysates were clarified from sonicated protein-DNA complexes were isolated with GFP antibody.
Two ng of ChIP DNA immuoprecipitated by anti-GFP antibody was used for ChIP-seq library construction. Blunting end, adapter ligation and amplification were carried out using Illumina Genomic DNA Sample Prep Kits according to the manufacturer's protocol. Illumina Novaseq was used for high-throughput sequencing of the ChIP-seq library.

treatment_protocol: 5-d-seedlings were treated with DMSO or 2 μM PPZ for 4 h

value: Young seedlings

tag: chip antibody

value: GFP (ab290, abcam)


title: Empty Vector Control (LeGO-Ctl) tumor RNA-seq sample #4

description:
RNA-seq. Tumors derived from FLC monoclone implantation that harbor LINC00473 overexpression (LeGO-473ox) and empty vector control (LeGO-Ctl).
RKM8

tag: cell line


title: R21931

value: Nucleus Accumbens

value: Case

tag: sample well


title: R108-AM-1

tag: tissue

tag: cell type


title: WT_PPZ-bio1

tag: condition


title: SUZ12_H526_sgNONT

tag: antibody

value: small cell lung cancer

value: wild type

tag: treatment


title: EZH2_H526_sgPOU2AF2_1

value: sgPOU2AF2 #1


title: R21927

tag: dsm-5 aud status

tag: Sex


title: EZH2_H526_sgPOU2AF2_2

value: sgPOU2AF2 #2


title: R21924

tag: agedeath

tag: brain number


title: R21928

tag: dsm-5 major depression diagnosis

tag: current smoker at death

value: Control


title: Empty Vector Control (LeGO-Ctl) tumor RNA-seq sample #1

description:
RNA-seq. Tumors derived from FLC monoclone implantation that harbor LINC00473 overexpression (LeGO-473ox) and empty vector control (LeGO-Ctl).
RKM5


title: BRM-GFP_brm-1-PPZ-IP-bio1


title: Empty Vector Control (LeGO-Ctl) tumor RNA-seq sample #2

description:
RNA-seq. Tumors derived from FLC monoclone implantation that harbor LINC00473 overexpression (LeGO-473ox) and empty vector control (LeGO-Ctl).
RKM6


title: EZH2_H526_sgNONT


title: R21926

value: F

tag: pmi

tag: rin


title: BRM-GFP_brm-1-DMSO-IP-bio2

tag: genotype


title: H3K27me3_H526_sgPOU2AF2_1


title: H3K27me3_H526_sgPOU2AF2_2


title: LINC00473-overexpression (LeGO-473ox) tumor RNA-seq sample #3

description:
RNA-seq. Tumors derived from FLC monoclone implantation that harbor LINC00473 overexpression (LeGO-473ox) and empty vector control (LeGO-Ctl).
RKM3


title: bri1-701-bio2

value: dark

tag: time

value: Day 5


title: R21920

value: M

tag: sample plate


title: BRM-GFP_brm-1-DMSO-IP-bio1

tag: chip antibody


title: R21921

tag: tissue

tag: sample well


title: RNA_H211_BRM014_Rep2

tag: cell line

tag: cell type


title: LINC00473-overexpression (LeGO-473ox) tumor RNA-seq sample #4

description:
RNA-seq. Tumors derived from FLC monoclone implantation that harbor LINC00473 overexpression (LeGO-473ox) and empty vector control (LeGO-Ctl).
RKM4


title: RNA_H211_BRM014_Rep1

tag: treatment


title: H3K27me3_H526_sgNONT

tag: antibody

value: sgRNA nontargeting


title: bri1-701-bio3

tag: condition


title: R21918

tag: dsm-5 aud status

tag: Sex

tag: agedeath


title: bri1-701-bio1


title: LINC00473-overexpression (LeGO-473ox) tumor RNA-seq sample #2

description:
RNA-seq. Tumors derived from FLC monoclone implantation that harbor LINC00473 overexpression (LeGO-473ox) and empty vector control (LeGO-Ctl).
RKM2

value: Tumor


title: R21919

tag: dsm-5 major depression diagnosis

tag: current smoker at death

tag: brain number


title: LINC00473-overexpression (LeGO-473ox) tumor RNA-seq sample #1

description:
RNA-seq. Tumors derived from FLC monoclone implantation that harbor LINC00473 overexpression (LeGO-473ox) and empty vector control (LeGO-Ctl).
RKM1

value: Tumors derived from subcutaneous implantation of engineered FLC cells that were previously established from a patient-derived xenograft (PDX) mouse model


title: WT-bio1

tag: genotype


title: WT-bio2

tag: time


title: RNA_H211_DMSO_Rep2

value: DMSO


title: H4K5ac-IP-bio1

data_processing:
The raw reads were mapped to the reference genome (Arabidopsis thaliana genome, TAIR10) with Bowtie for Illumina (Galaxy Version 1.1.2) for DNA sequencing on web https://usegalaxy.org/ with default setting, except that the paired-end was required.
MACS2 (Galaxy Version 2.1.1) was used for peak calling using the following parameters “gsize=119,667,750, bw=300, q=0.01, nomodel, extsize=200”.
The alignments were first converted to Wiggle (WIG) files and the bigwig files were generated using bamCoverage with “-bs 10”, “--normalizeUsing RPKM (reads per kilobase per million)” in DeepTools and then the data were imported into the Integrative Genomics Viewer (IGV) for visualization.
Assembly: TAIR10
Supplementary files format and content: bigWig

organism: Arabidopsis

source_name: five-day-old seedlings

extract_protocol:
Lysates were clarified from sonicated protein-DNA complexes were isolated with indicated antibody.
Two ng of ChIP DNA immuoprecipitated by indicated antibody was used for ChIP-seq library construction. Blunting end, adapter ligation and amplification were carried out using Illumina Genomic DNA Sample Prep Kits according to the manufacturer's protocol. Illumina Novaseq was used for high-throughput sequencing of the ChIP-seq library.

treatment_protocol: 5-d-seedlings were treated with indicated growth conditions

value: five-day-old seedlings

value: Anti-H4K5ac (07-327, Merck millipore)


title: H3K27me3-IP-bio2

value: Anti-H3K27me3 (ab6002,  abcam)


title: RNA_H211_DMSO_Rep1


title: R21915

value: Nucleus Accumbens

value: Case

tag: pmi

tag: rin

tag: sample plate


title: R21917

tag: tissue

tag: sample well


title: RNA_CORL311_BRM014_Rep2

tag: cell line

tag: cell type

value: small cell lung cancer

value: wild type


title: R21914


title: H3K27me3-IP-bio1

tag: chip antibody


title: RNA_CORL311_BRM014_Rep1

tag: treatment


title: R21913

tag: dsm-5 aud status


title: WT-bio3

value: Young seedlings

tag: condition


title: H4K5ac-IP-bio2


title: R21912

tag: Sex

tag: agedeath

value: Control


title: RNA_CORL311_DMSO_Rep1


title: H3K4me3-IP-bio2

value: Anti-H3K4me3 (07-473, Merck millipore)


title: RNA_CORL311_DMSO_Rep2


title: R21911

value: F

tag: dsm-5 major depression diagnosis

tag: current smoker at death


title: H3K4me3-IP-bio1

value: dark

tag: genotype


title: R21910

value: M

tag: brain number


title: RNA_H526_BRM014_Rep2


title: NHDF HCMV1

type: RNA

city: Hamamatsu-shi

first: Hideya

last: Kawasaki

state: Shizuoka-ken

country: Japan

institute: Hamamatsu University School of Medicine

description: Gene expression after 30min in MOI 10 HCMV infected NHDF cells

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 3°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction <version 10.10.1.1> (Agilent Technologies).

source_name: cultured NHDF cells, 30min, HCMV MOI 10, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Human iPSC generation from NHDFCs (derived from fetal skin fibroblasts and purchased from Lonza, Basel, Switzerland) was approved by the Ethics Committee of Hamamatsu University School of Medicine (approval number: 12-186). NHDFCs were cultured in Dulbecco’s modified Eagle Medium (DMEM), supplemented with 10% (v/v) fetal bovine serum (FBS). NHDFCs were transduced overnight with Sendai viruses containing human Oct3/4, Sox2, Klf4, and c-Myc (CytoTune®-iPS Sendai Reprogramming Kit; Thermo Fisher Scientific, Waltham, MA, USA) at a MOI of 15. The medium was changed daily for the next 2 days, and the cells were resuspended in expansion medium (Dulbecco’s modified Eagle Medium (DMEM) supplemented with 10% (v/v) fetal bovine serum (FBS)). On day 3, the cells were recovered via centrifugation (x 650 g for 5 min) and plated on mitomycin-C-treated mouse embryonic fibroblasts (feeder cells) in an expansion medium for 2 additional days. On day 6, half of the medium was changed to human pluripotent stem cell medium (DMEM/F12 supplemented with 20% Knock Out Serum Replacer, 1 mM L-glutamine, 1% (v/v) penicillin/streptomycin, and 100 μM 2-mercaptoethanol (all from Life Technologies, Waltham, MA, USA) or 20 ng/mL basic FGF (ReproCELL Inc. Kanagawa, Japan). For feeder-free culture, iMatrix-511 (0.5 ng/mL) was coated on the plate at 37°C for 1 h. ReproFF2 (ReproCELL Inc. Kanagawa, Japan) culture with 20 ng/mL bFGF was used for maintaining hiPSC proliferation.

extract_protocol: Total RNA was extracted from two independently prepared batches of 50000 control cells (NHDFCs and hiPSCs) and HCMV-infected cells (NHDFCs and hiPSCs) 30 min post infection at an MOI of 10. Total RNA was extracted from each sample using the RNeasy Mini Kit (QIAGEN, Tokyo, Japan) and diluted with RNase-free water.

treatment_protocol: Control cells (NHDFCs and hiPSCs) and HCMV-infected cells (NHDFCs and hiPSCs) 30 min post infection at an MOI of 10.

value: skin

tag: gender

value: male


title: BZR1-YFP-IP-bio1

value: GFP (ab290, abcam)


title: iPS HCMV2

description: Gene expression after 30min in MOI 10 HCMV infected iPS cells

source_name: cultured iPS cells, 30min, HCMV MOI 10, replicate 1


title: R21908

data_processing:
Transcripts were quantified using GENCODE v40 (GRCh38) transcriptome with Salmon (v 1.1.0).
Gene-level quantification was done with the tximport R package (v1.14.2).
Assembly: GRCh38/ GENCODE v40
Supplementary files format and content: compressed tab-deliminated text file including raw counts for each sample

tag: pmi

tag: rin


title: RNA_H526_BRM014_Rep1


title: BRM-GFP brm-1 bzr1-1D_PPZ_bio2

tag: tissue

value: dark and 2 μM PPZ

value: BRM-GFP brm-1 bzr1-1D


title: R21909

tag: sample plate

tag: sample well


title: RNA_H526_BRM014_0_Rep2

tag: cell line

tag: cell type

value: DMSO


title: R21904


title: NHDF cont1

description: Gene expression after 30min in MOI 0 HCMV infected NHDF cells

source_name: cultured NHDF cells, 30min, HCMV MOI 0, replicate 1


title: BRM-GFP brm-1 bzr1-1D_PPZ_bio1

value: five-day-old seedlings

tag: chip antibody


title: BRM-GFP brm-1_PPZ_bio1


title: RNA_H526_GSK126_Rep1

tag: treatment


title: RNA_H526_BRM014_0_Rep1


title: RNA_H526_GSK126_0_Rep2


title: R21906

value: Nucleus Accumbens

tag: dsm-5 aud status


title: BRM-GFP brm-1_PPZ_bio2

tag: condition


title: RNA_H526_GSK126_Rep2


title: BZR1-YFP-IP-bio2


title: R21902

tag: Sex

tag: agedeath


title: iPS HCMV1


title: R21905

tag: dsm-5 major depression diagnosis

tag: current smoker at death

value: Case


title: iPS cont2

description: Gene expression after 30min in MOI 0 HCMV infected iPS cells

source_name: cultured iPS cells, 30min, HCMV MOI 0, replicate 1


title: 48-N0027

city: Tokyo

first: Hiroaki

last: Hori

address: 4-1-1, Ogawahigashi, Kodaira

department: Department of Behavioral Medicine

institute: National Institute of Mental Health, National Center of Neurology and Psychiatry

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a Agilent fragmentation buffer and was hybridized at 65°C for 17 hr using Gene Expression Hybridization Kit.

scan_protocol: Microarray slides were scanned at 3 μm resolution using an Agilent SureScan (G4900DA).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1(Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Peripheral Blood

label_protocol: Agilent one-color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling protocol

extract_protocol: Venous blood was collected in PAXgene Blood RNA Tubes (PreAnalytiX, Hombrechtikon, Switzerland) from each participant, and RNA was extracted from whole blood according to the manufacturer’s guidelines using the PAXgene Blood RNA System Kit (PreAnalytiX, Hombrechtikon, Switzerland).

value: female

tag: age(years)

tag: diagnostic group

value: PTSD patient


title: iPS cont1

tag: gender


title: ATAC_brm-1_PPZ-bio2

extract_protocol:
Approximately 40,000 protoplasts were used for the isolation of nuclei. The purified nuclei were then incubated with Tn5 transposome and tagmentation buffer at 37 °C for 30 min
Genomic DNA breaked by Tn-5 transposable enzyme was used for ATAC-seq library construction. Blunting end, adapter ligation and amplification were carried out using TruePrep DNA Library Prep Kit V2  according to the manufacturer's protocol. Illumina Novaseq was used for high-throughput sequencing of the ATAC-seq library.

tag: genotype

tag: test kit

value: TD501, vazyme


title: ATAC_bzr1-1D brm-1_PPZ-bio2

tag: tissue

value: bzr1-1D brm-1


title: RNA_H526_GSK126_0_Rep1

value: small cell lung cancer

value: wild type


title: ATAC_bzr1-1D brm-1_PPZ-bio1


title: 47-N0026


title: non-malignant esophageal mucosa [E09SCN]

city: Fukuoka

first: Chikanori

last: Tsutsumi

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Surgery and Oncology, Graduate School of Medical Sciences

institute: Kyushu University

description: ESCC.integrated.rds

library_source: transcriptomic single cell

data_processing:
Raw sequencing reads were aligned to the human reference genome GRCh38 and processed to a matrix representing the UMI’s per cell barcode per gene using Cell Ranger v5.0.0 (10x Genomics)
Output files were analyzed with the R v3.6.3 package "Seurat v3.1.5".
Supplementary files format and content: To merge the data of all samples, we used the "SCTransform" package for the normalization and variance stabilization of molecular count data.

extract_protocol:
Single-cell library preparation was performed according to the manual of the Chromium Next GEM Single-cell 3' Reagent Kits v3.1. The cell suspensions were loaded on the Single-cell G Chip for gel bead-in-emulsion (GEM) generation and barcoding. cDNA library thus was generated with a droplet-based sequencing platform (10X Genomics). Next, reverse transcription, RT cleanup cDNA amplification, and quantification was performed to construct a 3’ gene library.
The libraries were sequenced on NovaSeq6000 (Illumina) or DNBSEQ-G400 (MGI Tech).

value: Esophagus

tag: disease state

value: non-malignant esophageal mucosa

tag: age

value: Female


title: 46-N0024


title: ATAC_bzr1-1D_PPZ-bio2


title: 43-N0019


title: R21900

extract_protocol:
Total RNA was extracted from ~100 mg of tissue using the RNeasy kit (Qiagen) according to the manufacturer's protocol.
Illumina TruSeq Total RNA Stranded RiboZero Gold (Illumina Inc, San Diego, CA) was used for library prep.

value: M

value: Control

tag: pmi

tag: rin

tag: sample plate

tag: sample well

tag: brain number


title: 45-WT0021


title: non-malignant esophageal mucosa [E15SCN]

description: ESCC.integrated.rds

tag: Sex

value: Male


title: ATAC_brm-1_PPZ-bio1

tag: condition

value: dark and 2 μM PPZ


title: R21897

tag: dsm-5 aud status

tag: agedeath

tag: dsm-5 major depression diagnosis


title: non-malignant esophageal mucosa [E14SCN]

description: ESCC.integrated.rds


title: 44-N0020

tag: age(years)

tag: diagnostic group


title: R21901

tag: current smoker at death


title: R21898


title: Esophageal squamous cell carcinoma [E07SCC]

description: ESCC.integrated.rds

value: Esophageal squamous cell carcinoma


title: ATAC_bzr1-1D_PPZ-bio1

value: five-day-old seedlings

tag: genotype

tag: test kit


title: R21899

tag: tissue

value: Nucleus Accumbens


title: R21896


title: R21894

value: Case


title: non-malignant esophageal mucosa [E08SCN]

description: ESCC.integrated.rds

tag: disease state

tag: age


title: ATAC_Col_PPZ-bio1


title: 39-N0015

tag: gender

value: female


title: 42-N0018

value: PTSD patient


title: 41-N0017


title: 40-N0016


title: ATAC_bri1-701-bio2

value: dark

value: TD501, vazyme


title: 37-N0012


title: A549 cells, pCMV6-Entry, rep4

city: Solna

first: Angela

last: Hoyer

address: Visionsgatan 4

country: Sweden

institute: Karolinska Institutet

data_processing:
During RNA sequencing (RNAseq) data preprocessing, the quality of the raw RNAseq reads was evaluated using FastQC (v0.11.1, Babraham Bioinformatics, UK) and then trimmed accordingly by Trim Galore (v0.6.1, Babraham Bioinformatics, UK) to achieve good quality reads with a Phred score of Q30. Cleaned reads were mapped to the human reference transcriptome (GRCh38.p13) downloaded from Ensembl (release 105, downloaded March 2022) to estimate the gene expression by Kallisto(24). Using R and Bioconductor packages, TPM (transcripts per million) values for each protein-coding transcript were extracted, collapsed at the gene level (with gene symbol), and analyzed for differential expression using edgeR (version 3.32.1). A generalized linear model design = ~ Cell-type (Treated (overexpressed) or non-treated (control)) was used to calculate differential gene expression between treated and non-treated cells. Log2 transformed fold change, p-value, FDR were calculated for each gene. We considered |log2FC| ≥ 2 and FDR < 0.05 as the cutoff values to identify differentially expressed genes (DEG).
Assembly: human reference transcriptome (GRCh38.p13)
Supplementary files format and content: TSV-fil (.tsv) include TPM values

extract_protocol:
Expression plasmids containing the human CST1 and CCL26 as well as the empty vector pCMV6-entry as control were obtained from OriGene Technologies Inc. (USA, Table 1). A549 cells were transfected with 1 µg plasmid DNA containing CST1 (CST1 overexpression) or CCL26 (CCL26 overexpression) separately in 24-well plates using Lipofectamine® 3000 (Thermofisher Scientific, USA), according to the manufacturer`s instruction. The cells were harvested for subsequent experiments 48 hours following transfection. All experiments were performed in biological quadruplicates. Total RNA was extracted with the Qiagen RNeasy Micro kit (Hilden, Germany) 48 hours after transfection and the concentrations were measured using QubitTM Flex Fluorometer (Thermofisher Scientific, USA). RIN values were obtained from Qsep100 Bio-Fragment Analyzers (Bioptic, Inc., Taiwan) and ranged between 8.9-10. Overexpression was confirmed using rt-qPCR (supplementary Figure 1). cDNA was synthesized using SuperScript III First-Strand Synthesis SuperMix (Thermofisher Scientific, USA), according to the manufacturer`s protocol. For rt-qPCR, 1 µl of cDNA was used in a 20 µl reaction volume, TaqMan gene expression Master Mix and pre-developed TaqMan gene expression assays (Thermofisher Scientific, USA). All samples were run in triplicates according to the manufacturer`s instructions. Each reaction was normalized to the GAPDH and PPIA content separately and the ΔΔCT method was used to determine the fold induction over cells transfected with the empty vector (control samples).
In total, 12 samples were included (4 samples CST1, 4 samples CCL26, 4 samples pCMV6-Entry). The libraries were prepared with the Illumina® TruSeq Stranded mRNA library preparation (Bravo) kit with 330 ng of each sample. The average library length for CST1 was equal to 362 bp, for CCL26 equal to 400 bp and for pCMV6-entry equal to 395 bp. Sequencing was performed on an IlluminaⓇ NovaSeq 6000 platform using the NovaSeq 6000 S4 Reagent Kit (35 cycles) (Illumina, San Diego, CA, USA). Sequencing was performed at the National Genomics Infrastructure in Stockholm, Sweden.

treatment_protocol: transfected with pCMV6-Entry plasmid with the Lipofectamine reagent, the RNA was extracted 48 hours after transfection

tag: cell line

tag: cell type

value: adenocarcinomic human alveolar basal epithelial cells

value: WT

tag: treatment


title: R21893

tag: Sex

tag: pmi

tag: rin

tag: sample plate

tag: sample well

tag: brain number


title: ATAC_bri1-701-bio1

tag: condition


title: ATAC_Col_PPZ-bio2


title: R21892

tag: dsm-5 aud status

tag: agedeath

tag: dsm-5 major depression diagnosis

tag: current smoker at death


title: ATAC_Col-bio1

tag: tissue

tag: genotype

tag: test kit


title: R21890


title: A549 cells, pCMV6-Entry, rep1

tag: cell line


title: 242_PHH_p100pop

city: Bochum

first: Nicola

last: Frericks

address: Universitätsstraße 150

country: Germany

institute: Ruhr-Universität Bochum

data_processing:
Transcriptomic analyses were performed using CLC Genomics Workbench Version 21.0.4 (Qiagen)
FASTQ files were aligned against the human reference genome GRCh38 (updated on the 24.11.2021)
Differentially expressed genes were identified by filtering on average expression for FDR correction and testing for differential expression due to infection while controlling for passage number/donor
Gene Ontology enrichment analysis were perforemed using following settings: mean RPKM >0.5, fold change >1.5 and FDR p-value <0.05
Results of the Gene Ontology enrichment analysis and KEGG pathway analysis were further processed in R using the gseKEGG function of the R package 'clusterProfiler' v4.7.1.001
Assembly: GRCh38
Supplementary files format and content: xlsx documents include expression browser (total counts, RPKM, fold change, log fold change, FDR p-value)
Supplementary files format and content: xlsx documents include Gene Ontology enrichment analyses (GO term, number and name of detected genes, FDR p-value, bonferroni) for both experimental settings (Huh-7, PHH) including all infection conditions

source_name: primary human hepatocytes

extract_protocol:
Total RNA was extracted using NucleoSpin RNA kit (Macherey-Nagel) according to manufracturer's instructions
For library preparation the NextSeq 500/550 High Output Kit v.2.5 (Ilumina) was used according to manufracturer's instructions

tag: donor id

value: donor 3

tag: cell type

value: primary human hepatocytes

tag: time point

value: 28 hours post inoculation

tag: read length


title: 242_PHH_Jc1-SP

tag: treatment


title: R21889

first: Dana

institute: RTI  International

tag: Sex

value: M

tag: pmi

tag: rin

tag: sample plate


title: A549 cells, CCL26, rep4

treatment_protocol: transfected with CCL26 plasmid with the Lipofectamine reagent, the RNA was extracted 48 hours after transfection


title: A549 cells, CCL26, rep3


title: 36-N0011

tag: gender

tag: age(years)

tag: diagnostic group


title: 38-N0013


title: A549 cells, pCMV6-Entry, rep3


title: 34-N0008


title: R21887

tag: dsm-5 aud status

value: F

tag: agedeath

tag: dsm-5 major depression diagnosis

tag: current smoker at death

tag: sample well

tag: brain number


title: A549 cells, CCL26, rep2

tag: cell line

tag: cell type

tag: genotype


title: R21886

tag: tissue

value: Control


title: ATAC_Col-bio2

tag: condition

tag: test kit


title: 33-N0007


title: 32-N0006


title: 168_PHH_p100pop

tag: donor id

value: donor 2

tag: treatment

tag: time point

tag: read length


title: 35-N0010

tag: gender

tag: age(years)

tag: diagnostic group


title: R21885

tag: dsm-5 aud status

tag: Sex

tag: agedeath

tag: dsm-5 major depression diagnosis

tag: pmi

tag: rin

tag: sample plate


title: 168_PHH_Jc1-SP

tag: cell type


title: R21891

tag: tissue

tag: current smoker at death

tag: sample well

tag: brain number


title: A549 cells, pCMV6-Entry, rep2

tag: cell line

tag: genotype

tag: treatment


title: A549 cells, CST1, rep4

treatment_protocol: transfected with CST1 plasmid with the Lipofectamine reagent, the RNA was extracted 48 hours after transfection


title: A549 cells, CCL26, rep1


title: 30-WT0024

tag: gender

tag: age(years)


title: 31-N0004

tag: diagnostic group


title: R21883

tag: dsm-5 aud status

tag: Sex


title: 168_PHH_condmed

tag: donor id

value: uninfected

tag: time point

tag: read length


title: A549 cells, CST1, rep3


title: 251_PHH_condmed

value: donor 4


title: A549 cells, CST1, rep2


title: R21881

value: Nucleus Accumbens

tag: agedeath

tag: dsm-5 major depression diagnosis

tag: pmi

tag: rin

tag: sample plate


title: 147_PHH_Jc1-SP

value: donor 1

tag: cell type


title: A549 cells, CST1, rep1

tag: cell line


title: R21880

tag: tissue

tag: current smoker at death

value: Case

tag: sample well

tag: brain number


title: 29-WT0023

tag: gender

value: female

tag: age(years)

tag: diagnostic group

value: PTSD patient


title: R21879

tag: dsm-5 aud status

tag: Sex


title: scRNA_HT-SncKD1

first: Zhen

last: Chen

address: 1500 E Duarte Rd

department: DMRI

institute: City of Hope

description: Single-cell RNA sequencing assay

data_processing:
10X Genomics cellranger (v3.1) was used to process sequencing data produced from Chromium Single Cell Gene Expression
Seurat 4.0 was used to analyze the scRNA-seq data
Assembly: hg38
Supplementary files format and content: Three processed data files per each sample: a matrix file (.mtx format) with UMI counts per each gene (rows) and single cell (columns); genes list (.tsv format) with the list of genes (features) detected; cell barcodes list (.tsv format) with the list of barcodes of the single cells in the sample.

source_name: Human Umbilical Vein Endothelial Cells transfected with LNA targeting SncmtRNA, treated with 25mM glucose + 5ng/ml TNFa and harvested after 72 hours

growth_protocol: HUVECs were cultured following the manufacturer's protocol

extract_protocol:
Single-cell suspension was prepared by using the 10XGenomics Chromium Controller
10X Genomics Single Cell 3' v3.1. gene expression

treatment_protocol: HUVECs were cultured in complete medium; transfected with either 20 nM scramble LNA (Scr) or 10nM LNA targeting SncmtRNA (Snc-KD) under HT conditions and then harvested after 72 hours post transfection.

value: HUVEC

value: Human Umbilical Vein Endothelial Cells

tag: treatment

tag: assay

value: scRNA-seq


title: scRNA_HT_SncKD2

description: Single-cell RNA sequencing assay

value: transfected with LNA targeting SncmtRNA, treated with 25mM glucose + 5ng/ml TNFa and harvested after 72 hours


title: 167_Huh7_p100pop

value: hepatocellular carcinoma

tag: time point

tag: read length


title: 28-WT0022


title: 27-WT0018


title: 26-WT0017


title: R21882

last: Hancock

address: 3040 E Cornwallis Rd

tag: agedeath

tag: dsm-5 major depression diagnosis

tag: pmi

tag: rin


title: scRNA_HT_Scr2

description: Single-cell RNA sequencing assay

source_name: Human Umbilical Vein Endothelial Cells transfected with scramble LNA, treated with  25mM glucose + 5ng/ml TNFa and harvested after 72 hours

tag: cell line

tag: cell type


title: 167_Huh7_Jc1SP

value: 28 hours post inoculation


title: R21878

source_name: Nucleus Accumbens

tag: tissue

value: M

tag: current smoker at death

tag: sample plate

tag: sample well


title: 147_PHH_p100pop

tag: donor id

value: primary human hepatocytes


title: scRNA_HT_Scr1

description: Single-cell RNA sequencing assay

value: transfected with scramble LNA, treated with  25mM glucose + 5ng/ml TNFa and harvested after 72 hours


title: R21876

tag: dsm-5 aud status

tag: brain number


title: 166_Huh7_p100pop

tag: treatment


title: 147_PHH_condmed


title: R19862

tag: Sex

value: F

value: Control


title: 166_Huh7_Jc1SP

tag: time point


title: 24-WT0014

tag: gender

tag: age(years)

tag: diagnostic group


title: snRNA_HT-SncKD1

description: Single-nuclear RNA sequencing assay

tag: assay

value: snRNA-seq


title: 25-WT0016


title: 23-WT0013


title: 22-WT0011


title: R21877

value: Nucleus Accumbens

tag: agedeath

tag: dsm-5 major depression diagnosis

tag: pmi

tag: rin


title: R19802

tag: tissue

tag: current smoker at death


title: 166_Huh7_condmed

tag: cell line

tag: cell type

value: uninfected

tag: read length


title: 20-WT0006


title: snRNA_HT_Scr2

description: Single-nuclear RNA sequencing assay


title: snRNA_HT_SncKD2

description: Single-nuclear RNA sequencing assay


title: 167_Huh7_condmed


title: 162_Huh7_Jc1SP


title: R19728

tag: dsm-5 aud status

tag: sample plate

tag: sample well

tag: brain number


title: HUVEC_AAV-SncOE3

description: polyA RNA enriched

data_processing:
Adaptors were timmed by Trimmomatic-0.39
Trimmed data was aligned to hg38 with STAR(2.7.10a)
reads map to genomic features were counted by FeatureCounts
Assembly: hg38
Supplementary files format and content: The processed counts.txt files are tab-delimited tables which includes annotation columns (‘Geneid’) and data columns (i.e. read counts for genes) for each library.

source_name: Human Umbilical Vein Endothelial Cells infected with adeno-associated virus expressing SncmtRNA for overexpression and harvested after 72 hours

extract_protocol:
Approximately 1 million cells were used for total RNA extraction and construction of strand-specific mRNA-seq library
The libraries were constructed using the KAPA mRNA stranded Hyper kit following the user manual

treatment_protocol: HUVECs were cultured in complete medium; transfected with either 20 nM scramble LNA (Scr) or 10nM LNA targeting SncmtRNA (Snc-KD) under NM or HT conditions and then harvested after 72 hours post transfection for SncmtRNA knockdown experiments. Alternatively, HUVECs were infected with AAV expressing Tdtomato (Ctrl) or SncmtRNA (SncOE) and collected after 72 hours for SncmtRNA overexpression experiments.

tag: treatment

value: RNA-seq


title: R19652

tag: Sex


title: 19-WT0005

tag: gender

value: female

tag: age(years)

tag: diagnostic group


title: HUVEC_AAV-Ctrl3

description: polyA RNA enriched

source_name: Human Umbilical Vein Endothelial Cells infected with adeno-associated virus expressing Tdtomato as control and harvested after 72 hours

tag: assay


title: 162_Huh7_condmed

tag: time point


title: HUVEC_AAV-SncOE2

description: polyA RNA enriched

value: infected with adeno-associated virus expressing SncmtRNA for overexpression and harvested after 72 hours


title: R19598

tag: agedeath

tag: dsm-5 major depression diagnosis

tag: pmi

tag: rin


title: 18-WT0004

value: PTSD patient


title: R19752

tag: tissue

tag: current smoker at death


title: 21-WT0009


title: R19592

tag: dsm-5 aud status


title: 162_Huh7_p100pop

tag: cell line

tag: cell type

tag: read length


title: 16-T0017

value: healthy control


title: snRNA_HT_Scr1

description: Single-nuclear RNA sequencing assay

value: HUVEC

value: Human Umbilical Vein Endothelial Cells

tag: treatment


title: HUVEC_AAV-Ctrl2

description: polyA RNA enriched

value: infected with adeno-associated virus expressing Tdtomato as control and harvested after 72 hours


title: Pooled control and treatment samples 3

city: Helsinki

first: Kuunsade

last: Maenpaa

address: Haartmaninkatu 3

country: Finland

institute: University of Helsinki

description: Sequencing was done using a strategy where 3'-UTRs were sequenced from mRNA fragments. In the process, all samples are pooled into a single library, where each sample is labeled with unique sample barcodes. After alignment each sample is demultiplexed using drop-seq tools and these 12bp long barcodes.

data_processing:
Raw sequence data was inspected using FastQC and multiQC. Reads were filtered to remove low quality reads and reads shorter than 20 bp using Trimmomatic. Reads passing the filter were then processed further using Drop-seq tools and the pipeline originally suggested in Drop-seq paper and adapted to 3' RNA-seq
The raw, filtered read libraries were converted to sorted BAM files using Picard tools. This was followed by tagging reads with sample specific barcodes and unique molecular identifiers (UMIs). Tagged reads were then trimmed for 5’ adapters and 3’ poly A tails. Alignment ready reads were converted from BAM formatted files to fastq files that were used as an input for STAR aligner.
Alignments and gene annotations were based on Gencode mouse Release M28 (GRCm39) reference genome and gene annotation files with default STAR settings. The uniquely aligned reads were sorted and merged with a previously unaligned tagged BAM file to regain barcodes and UMIs lost during the alignment step.
Annotation tags were added to aligned and barcode tagged BAM files to complete the alignment process. Drop-seq tools were used to detect and correct systematic synthesis errors present in sample barcode sequences. Digital expression matrices were then created by counting the total number of unique UMI sequences (UMI sequences that differ only by a single base were merged together) for each gene.
Gene count outputs from all sample pools were then compiled to form a single gene expression table for the whole dataset.
Assembly: Gencode mouse Release M28 (GRCm39) reference genome
Supplementary files format and content: Digital Gene Expression (DGE): xlsx file containing UMI read counts for each sample

source_name: upper back skin

extract_protocol:
Skin biopsies were transferred to 1 mL RL buffer (Norgen Biotek, Thorold, Canada) with a ¼ inch ceramic bead (MP Biomedicals, Santa Ana, CA, USA) and homogenised once or twice in the FastPrep machine (MP Biomedicals) at 6.0 m/s for 40 s. RNA was extracted using Total RNA Purification Plus Kit (Norgen Biotek) according to manufacturer’s instructions, except the samples were incubated for 2 min at RT before eluting to 50 μL of water. To remove traces of organic solvents, RNA was repurified using RNEasy Mini Cleanup kit (Qiagen, Venlo, Netherlands) according to the manufacturer’s instructions.
RNA sequencing method was designed based on the Drop-seq protocol described in (Macosko EZ et al. Cell 2015). 10 ng of RNA was mixed with Indexing Oligonucleotides and combined with Initial Mix (+10 mM dNTPs + RNAse Inhibitor +H2O). After 5 min incubation the RNA was combined with RT mix (1 x Maxima RT buffer, 10 U/µl Maxima H- RTase, 1 U/µl RNase inhibitor and 2.5 µM Template Switch Oligo (5M Betaine)). The reaction was performed according to manufacturer’s instruction, with the exception of the P5 SMART primer that was used instead of S5xx Nextera primer. Each set of samples that was pooled after the PCR reaction was tagmented with a different Nextera N7xx index.
Samples were incubated for 30 min at 22°C and 90 min at 52°C. The constructed cDNA was amplified by PCR. The PCR products were pooled together in sets containing different Indexing Oligos and purified with Agencourt AMPure XP Beads according to the manufacturer’s instructions. The 3’-end cDNA fragments for sequencing were prepared using the Nextera XT (Illumina) tagmentation reaction. Samples were PCR amplified and purified twice using Agencourt AMPure Beads. The libraries were sequenced on an Illumina NextSeq 500, with a custom primer producing read 1 of 21 bp and read 2 (paired end) of 62 bp.

value: upper back skin

tag: strain

value: Pooled samples with and without treatment


title: HUVEC_AAV-SncOE1

description: polyA RNA enriched


title: R19487

city: Research Triangle Park

tag: Sex

value: M

tag: sample plate

tag: sample well

tag: brain number


title: Pooled control and treatment samples 5


title: Pooled control and treatment samples 4


title: 17-WT0002

tag: gender

tag: age(years)

tag: diagnostic group


title: R19469

tag: agedeath

tag: dsm-5 major depression diagnosis

tag: pmi


title: Pooled control and treatment samples 2

tag: tissue


title: HUVEC_AAV-Ctrl1

description: polyA RNA enriched

tag: assay


title: 15-T0060


title: HUVEC_HT_SncKD2

description: polyA RNA enriched

tag: cell line

value: transfected with LNA targeting SncmtRNA, treated with 25mM glucose + 5ng/ml TNFa and harvested after 72 hours


title: 14-T0059


title: R19457

tag: dsm-5 aud status

tag: current smoker at death

value: Case

tag: rin


title: R19425

value: F


title: Pooled control and treatment samples 1

tag: strain

tag: treatment


title: HUVEC_HT_SncKD1

description: polyA RNA enriched

tag: cell type


title: 12-T0052


title: Sample pool containing treated and untreated control and MIRAS samples

first: Yilin

last: Kang

state: UUSIMAA

address: Biomedicum Helsinki 1 Haartmaninkatu 8 (C526)

description: Sequencing was done using a strategy where 3'-UTRs were sequenced from mRNA fragments. In the process, all samples are pooled into a single library, where each sample is labeled with unique sample barcodes. After  alignment each sample is demultiplexed using drop-seq tools and these 12bp long barcodes.

data_processing:
Sequencing with 75 cycles produced 21 bp Read 1 (bases 1-12 sample barcode, bases 13-20 UMI) and 62 bp Read 2 (sequence derived from the mRNA).
Raw sequence data was inspected using FastQC and multiQC to ensure the quality of sequencing results (Andrews S. FastQC: a quality control tool for high throughput sequence data. 2010. http://www.bioinformatics.babraham.ac.uk/projects/fastqc; Ewels P. MultiQC: Summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016).  Subsequently, reads were filtered to remove low quality reads and reads shorter than 20 bp using Trimmomatic (Bolgeret al. Trimmomatic: A flexible trimmer for Illumina Sequence Data. Bioinformatics. 2014).
Reads passing the filter were then processed further using Drop-seq tools and the pipeline originally suggested in Drop-seq paper (v. 2.3.0,Macoskoet al. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell. 2015). In brief, the raw, filtered read libraries were converted to sorted BAM files using Picard tools (http://broadinstitute.github.io/picard). This was followed by tagging reads with sample specific barcodes and unique molecular identifiers (UMIs). Tagged reads were then trimmed for 5’ adapters and 3’ poly A tails. Alignment ready reads were converted from BAM formatted files to fastq files that were used as an input for STAR aligner (Dobin A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013).
Alignments were done using data from GENCODE Release M28 mouse genome (GRCm39) and comprehensive gene annotation files (Frankish A. et al. GENCODE reference annotation for the human and mouse genomes. Nucleic Acids Res. 2019) with default STAR settings. Following the alignment, the uniquely aligned reads were sorted and merged with previous unaligned tagged BAM file to regain barcodes and UMI’s lost during the alignment step. Next, annotation tags are added to aligned and barcode tagged BAM files to complete the alignment process. Finally, Drop-seq tools are used to detect and correct systematic synthesis errors present in sample barcode sequences. Digital expression matrices are then created by counting the total number of unique UMI sequences (UMI sequences that differ only by a single base are merged together) for each transcript.
DESeq2 was then used to identify differentially expressed genes (Love MI. et al. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology. 2014).
Assembly: GENCODE Release M28 Mouse genome (GRCm39) and comprehensive gene annotation files.
Supplementary files format and content: Raw gene expression matrix (MS excel format) from drop-seq Digital Gene Expression (DGE) outputs.
Supplementary files format and content: List of samples and sample specific barcodes used for pooling (MS xlsx format).

source_name: Brain (cerebral cortex)

extract_protocol:
RNA was harvested using Trizol/chloroform method followed by purification using the RNeasy kit (Qiagen)
Custom library construction protocol.

treatment_protocol: Mice were either left untreated or infected with TBEV (inoculated intraperitoneally with 1000 PFU of TBEV) for 4 days prior to tissue collection

value: Brain (cerebral cortex)

tag: Sex

value: Female

tag: genotype

value: MIRAS & WT

value: Baseline, uninfected & Day 4 post TBEV infection


title: Neutrophils, KO, Sp, 3

city: Baltimore

first: Naina

last: Gour

state: MD

address: 745 N Wolfe st.

department: Neuroscience

institute: Johns Hokins University

data_processing:
Preprocesing and quality control of FASTQ files were done using fastp
Statistical comparison of RNAseq libraries replicates was done using Simple Error Ratio Estimate (SERE)
Transcript abundance was done using Salmon
Differential analysis of counts was done using DEseq2
Assembly: mm10
Supplementary files format and content: transcripts per million (TPM) for each sample was obtained from Salmon

source_name: Neutrophil

extract_protocol:
RNA was extracted with Qiagen Rneasy columns with on-column DNase digestion. 1 ng input was used to generate cDNA using SMART-Seq™ v4 Ultra™ Low Input RNA Kit for Sequencing
Libraries were made using Illumina Nextera XT DNA Library Preparation Kit

tag: infection

value: Streptococcus pneumoniae 6303

value: Neutrophil


title: R19362

value: Nucleus Accumbens

value: Control

tag: sample plate

tag: sample well

tag: brain number


title: HUVEC_HT_Scr2

city: Duarte

description: polyA RNA enriched

value: HUVEC

value: transfected with scramble LNA, treated with  25mM glucose + 5ng/ml TNFa and harvested after 72 hours

value: RNA-seq


title: Neutrophils, KO, Sp, 2


title: HUVEC_HT_Scr1

description: polyA RNA enriched

value: Human Umbilical Vein Endothelial Cells


title: R19315

tag: agedeath

tag: dsm-5 major depression diagnosis


title: 11-T0047

tag: gender

value: female

tag: age(years)

tag: diagnostic group

value: healthy control


title: R15480

tag: tissue

tag: dsm-5 aud status

tag: pmi


title: HUVEC_NM_SncKD2

description: polyA RNA enriched

source_name: Human Umbilical Vein Endothelial Cells transfected with LNA targeting SncmtRNA, treated with normal glucose + 25mM mannitol and harvested after 72 hours

tag: cell line

tag: assay


title: R15481

value: M

tag: current smoker at death

tag: rin


title: 9-T0041


title: 13-T0058


title: R15477

tag: Sex

value: Case


title: Neutrophils, wildtype, Sp, 3

tag: infection

tag: genotype

tag: cell type


title: HUVEC_NM_SncKD1

description: polyA RNA enriched

tag: treatment

value: transfected with LNA targeting SncmtRNA, treated with normal glucose + 25mM mannitol and harvested after 72 hours


title: Neutrophils, wildtype, Sp, 2


title: HUVEC_NM_Scr2

description: polyA RNA enriched

source_name: Human Umbilical Vein Endothelial Cells transfected with scramble LNA, treated with normal glucose + 25mM mannitol and harvested after 72 hours


title: Neutrophils, wildtype, Sp, 1


title: 8-T0001


title: 10-T0045


title: R15428

tag: agedeath

tag: sample plate

tag: sample well

tag: brain number


title: HUVEC_NM_Scr1

description: polyA RNA enriched

value: transfected with scramble LNA, treated with normal glucose + 25mM mannitol and harvested after 72 hours


title: 6-T0037

tag: gender

tag: age(years)

tag: diagnostic group


title: Neutrophils, KO, Sp, 1


title: 7-T0039


title: Neutrophils, KO, PBS, 1

value: PBS


title: R15402

tag: tissue

tag: dsm-5 aud status

tag: dsm-5 major depression diagnosis

tag: pmi


title: Neutrophils, KO, PBS, 2


title: R15399

tag: current smoker at death

tag: rin


title: 4-T0031


title: 5-T0035


title: Neutrophils, wildtype, PBS, 2

tag: infection


title: R15396

tag: Sex


title: R15395

value: F


title: Neutrophils, wildtype, PBS, 1

tag: genotype

tag: cell type


title: R15394

tag: agedeath


title: Knee joint articular cartilage, Tamoxifen injected Cbfβf/f;Aggrecan-CreERT

city: New Orleans

first: Yi-Ping

last: Li

state: LA

address: 1441 Canal St, Room 318

department: Pathology and Laboratory Medicine

institute: Tulane University School of Medicine

data_processing:
RNA-seq was performed using Illumina MiSeq (performed by Admera Health, LLC (South Plainfield, NJ)). The FASTQ files were checked for quality using FastQC (v0.11.3). STAR (v 2.0) with reference genome (Mouse, mmo) and annotation file (UCSC) were used for sequence alignment.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Knee joint articular cartilage

extract_protocol:
Total mRNA was isolated using TRIzol reagent (Invitrogen Corp., Carlsbad, CA) from the osteoblasts following the manufacturer's protocol
Admera Health (South Plainsfield, NJ) prepared the library using the NEBnext Ultra RNA—Poly-A kit.

value: Knee joint articular cartilage

value: Cbf{beta}f/f;Aggrecan-CreERT

tag: treatment

value: Tamoxifen injected


title: 3-T0028


title: Knee joint articular cartilage, Oil injected Cbfβf/f;Aggrecan-CreERT

value: Oil injected


title: Ctrl-input

city: Hangzhou

first: Jun

last: Lu

address: 866 Yuhangtang Road

institute: Zhejiang University

data_processing:
Sequencing was implemented on the platform of Illumina Hiseq2500.
The Bowtie2 (version 2.2.6) software was used to map the sequencing reads to UCSC GRCh38 human reference genome.
The MAC tool (version 1.4.2) software was used to handle peak calls for aligned reads.
Peaks were annotated with UCSC human genome GRCh38 by using annotatePeaks.pl, HOMER (Hypergeometric Optimization of Motif EnRichment) (version 3.12).
Genome_build: hg38
Supplementary_files_format_and_content: wig files were generated using MACS1.4 (Model-based Analysis o f ChIP -Seq); Scores represent the peak calling and the higher score, the more reliable of the peak.

source_name: THP1 cells

extract_protocol:
Lysates were collected from sonicated cells lysed with ChIP lysate buffer.
The DNA was mixed with end repair mix and incubated at 20℃ for 30 minutes. The end-repaired DNA was purified using the QIAquick PCR Purification Kit (Qiagen). Then A-tailing mix was added and the mixture was incubated at 37℃ for 30 minutes. The purified DNA, adapter and ligation mix was incubated at 20℃ for 15 minutes, and the adapter-ligated DNA was purified with the QIAquick PCR Purification Kit. After PCR amplification, the PCR products (about 100-300 bp) were separated through agarose gel running, and purified with QIAquick Gel Extraction kit (QIAGEN). The library was qualified with Qubit ssDNA kit. The sequencing was performed with the BGISEQ-500 sequencing system by BGI-Shenzhen, China.

tag: cell line

value: Human AML cells

value: DMSO

tag: chip antibody


title: R15207

value: Nucleus Accumbens

tag: sample plate

tag: sample well

tag: brain number


title: OPA1-TET2

value: TET2(Cell Signaling; 18950)


title: OPA1-input


title: Ctrl-TET2


title: 1-T0025

tag: gender

tag: age(years)

tag: diagnostic group


title: R15183

tag: tissue

tag: dsm-5 aud status

tag: dsm-5 major depression diagnosis

tag: pmi


title: Hip joint articular cartilage, Tamoxifen injected Cbfβf/f;Col2α1-CreERT

source_name: Hip joint articular cartilage

value: Hip joint articular cartilage


title: 2-T0026

value: female


title: OPA1-EGR1

value: EGR1(Cell Signaling; 4154s)


title: Hip joint articular cartilage, Cbfβf/f,

value: Cbf{beta}f/f


title: Ctrl-EGR1


title: R15181

tag: Sex

value: M

tag: current smoker at death

value: Case

tag: rin


title: non-malignant gastric mucosa [G40N]

data_processing:
Raw sequencing reads were aligned to the human reference genome GRCh38 and processed to a matrix representing the UMI’s per cell barcode per gene using Cell Ranger v5.0.0 (10x Genomics)
Output files were analyzed with the R v3.6.3 package "Seurat v3.1.5".
Assembly: GRCh38
Supplementary files format and content: To merge the data of all samples, we used the "SCTransform" package for the normalization and variance stabilization of molecular count data.

extract_protocol:
Single-cell library preparation was performed according to the manual of the Chromium Next GEM Single-cell 3' Reagent Kits v3.1. The cell suspensions were loaded on the Single-cell G Chip for gel bead-in-emulsion (GEM) generation and barcoding, aiming to recover 10,000 cells per sample. cDNA library thus was generated with a droplet-based sequencing platform (10X Genomics). Next, reverse transcription, RT cleanup cDNA amplification, and quantification was performed to construct a 3’ gene library.
The libraries were sequenced on NovaSeq6000 (Illumina) or DNBSEQ-G400 (MGI Tech).

tag: organ

value: stomach

tag: age

value: Male

value: non-malignant gastric mucosa