title: KO_LPS

first: Zhongfei

last: Ma

address: 5, DongDan SanTiao, Dongcheng district

department: Department of Immunology

institute: Chinese Academy of Medical Sciences

data_processing:
Illumina CASAVA 1.8 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mouse genome (GRCm38/mm10).
Paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM value and gene count for each sample

source_name: RAW 264.7 cells

extract_protocol:
RNA was harvested using Trizol reagent. A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.
Library was constructed by Novogene China Co. Ltd. Briefly, fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: "WT" and "KO" cells were untreated; "WT_LPS" and "KO_LPS" cells were treated with LPS (100 ng/ml)

value: murine macrophage cells

value: treated with 100 ng/ml LPS for 10 h


title: H95_35062128235_v1: Newly diagnosed MM_109

status: Public on Jun 01 2022

type: SRA

city: Rotterdam

first: Mark

last: van Duin

address: Wytemaweg 80

country: Netherlands

institute: Erasmus MC

library_source: transcriptomic

data_processing:
Paired end sequencing was performed on an Illumina NovaSeq 6000 using 101 cycles for each mate.
Fastq files were constructed using bcl2fastq (v2.20.0.422).
Illumina universal adapters   were removed using trim_galore (v0.4.4).
Pseudo counts were measured on the trimmed Fastq files using  salmon (v1.3.0) using the default settings.
Salmon performed according to reference DOI:10.1038/NMETH.4197
Genome_build: GRCh37
Supplementary_files_format_and_content: Salmon, read counts

molecule: polyA RNA

organism: Homo sapiens

source_name: bone marrow aspirate

growth_protocol: primary human tissue

extract_protocol:
RNeasy
RNA Seq libraries were generated with the mRNA HyperPrep Kit (KAPA, catalog number 08105952001/KK8544), according to manufacturer’s instructions.

treatment_protocol: Patients were treatment naive

tag: tissue

value: bone marrow aspirate

tag: gender

value: Male

tag: age

tag: disease state

value: multiple myleoma


title: ImPACCT-01-013-I-1-RNA

city: Utrecht

first: Onno

last: Kranenburg

address: Heidelberglaan 100

institute: UMC Utrecht

data_processing:
Illumina NextSeq500 High Output: 1x 75 bp
Quality control on the sequence reads from the raw FASTQ files was done with FastQC (v0.11.4)
Reads were aligned to the reference genome fasta (Homo_sapiens.GRCh37) using star (v2.4.2a) aligner
Readgroup were added using Picard (v1.141)
Readcounts were generated using the HTSeq-count (v0.6.1) with the Homo_sapiens.GRCh37.74.gtf gtf file as annotation
Normalization was done using R-packages DeSeq (v1.18.0) and edgeR (v3.8.6)
Genome_build: Homo_sapiens.GRCh37
Supplementary_files_format_and_content: tab-delimited text files include raw reads count for each sample
Supplementary_files_format_and_content: tab-delimited text file with size factor normalized (DESeq) read counts of all samples

molecule: total RNA

source_name: Colorectal cancer

extract_protocol:
In brief, biopsies were homogenized using the tissue homogenizing CKMix ceramic beads (Precellys, P000918-LYSK0-A) and subsequently processed for RNA isolation using the column-based RNA isolation (RNeasy Kit, Qiagen). RNA yield and quality were evaluated using spectrometry (Nanodrop 2000/200c, Thermo Fisher) and the BioAnalyzer (2100 Bioanalyzer, Agilent), respectively.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Colorectal cancer

tag: subject id

tag: rf cms4 probability

tag: imatinib

value: Post-imatinib


title: H95_14482288896_v1: Newly diagnosed MM_113


title: WT_LPS

city: Beijing

country: China

organism: Mus musculus

tag: cell type

tag: treatment

tag: genotype

value: wild type


title: H95_82543072604_v1: Newly diagnosed MM_108

value: Female


title: Mono-enriched-PBMC_AMCP_3hr_subj3

type: RNA

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Human Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.28.2).

label: biotin

source_name: Monocyte-enriched peripheral blood mononuclear cells, 3hr incubation with synthetic AMCP nanoparticles, subject 3

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: Leukocyte cones (n=7) were purchased from the National Blood Service (Cambridge, UK) and peripheral blood mononuclear cells (PBMC) isolated by Lymphoprep (Axis Shield Diagnostics Ltd, Scotland) density gradient centrifugation. PBMC were further enriched for monocytes by a second density gradient centrifugation over Percoll (Sigma-Aldrich Ltd, UK) density medium, and were re-suspended at 1.10^6 cells/ml in RPMI-1640 medium (Sigma-Aldrich), supplemented with 10 % Fetal Calf Serum (PAA Laboratories Ltd, UK), 2 mM L-glutamine (Sigma-Aldrich), 100 U/ml penicillin (Sigma-Aldrich) and 100 μg/ml streptomycin (Sigma-Aldrich).

extract_protocol: Total RNA was purified using an Abi Prism 6100 Nucleic Acid PrepStation (Applied Biosystems, UK) following manufacturer’s instructions and including a wash step with AbsoluteRNA wash solution (Applied Biosystems), again as per manufacturer’s instructions. On occasions and to increase nucleotide concentration, a second purification procedure was performed using RNeasy MinEluteTM Cleanup Kit (Qiagen Ltd, UK) according to manufacturer’s protocol. Samples were stored at -80 °C until further microarray processing.

treatment_protocol: Culture and stimulation of monocyte-enriched PBMC were performed in sterile 15 ml Falcon tubes (Starlab UK Ltd, UK) at 1.10^6 cells/ml and at 37 °C/ 5 % CO2. Freshly isolated monocyte-enriched PBMC were rested overnight, following which they were replenished with Dulbecco’s Modified Eagle’s Medium (Sigma-Aldrich), supplemented with 10 % Fetal Calf Serum, 2 mM L-glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin. 5.10^6 cells were then stimulated for 3 hr with vehicle, synthetic AMCP nanoparticles or with a final concentration of 4 µg/ml soluble peptidoglycan (from Escherichia coli; Source BioScience plc, UK), alone or trapped within synthetic AMCP (AMCP/sPg). After challenge, stimulants were removed and cells washed twice in Hank’s Balanced Salt Solution (Sigma-Aldrich) before being lysed with Nucleic Acid Purification Solution (Life Technologies Ltd, UK) and stored at -80 °C prior to RNA isolation.

value: blood

value: cultured monocyte-enriched peripheral blood mononuclear cells

value: synthetic AMCP nanoparticles


title: Mono-enriched-PBMC_AMCP_3hr_subj4

source_name: Monocyte-enriched peripheral blood mononuclear cells, 3hr incubation with synthetic AMCP nanoparticles, subject 4


title: H95_29140118011_v1: Newly diagnosed MM_107


title: KO

value: untreated


title: Mono-enriched-PBMC_AMCP_3hr_subj2

source_name: Monocyte-enriched peripheral blood mononuclear cells, 3hr incubation with synthetic AMCP nanoparticles, subject 2


title: WT


title: H95_17665771071_v1: Newly diagnosed MM_106


title: ImPACCT-01-005-II-2-RNA


title: ImPACCT-01-005-I-2-RNA


title: H95_42826179782_v1: Newly diagnosed MM_105


title: Mono-enriched-PBMC_AMCP_3hr_subj1

source_name: Monocyte-enriched peripheral blood mononuclear cells, 3hr incubation with synthetic AMCP nanoparticles, subject 1


title: Mono-enriched-PBMC_ctrl_3hr_subj7

source_name: Monocyte-enriched peripheral blood mononuclear cells, 3hr incubation with tissue culture medium D10 (control), subject 7


title: ImPACCT-01-006-III-2-RNA


title: ImPACCT-01-005-III-2-RNA


title: H95_46241617256_v1: Newly diagnosed MM_103


title: H95_43459586815_v1: Newly diagnosed MM_104


title: ImPACCT-01-006-II-2-RNA


title: H95_95268571667_v1: Newly diagnosed MM_102


title: ImPACCT-01-006-I-1-RNA


title: d12_RNA_KO_LZ_rep1

first: Chunsheng

last: Han

state: Beijing

address: 1-5 Beichen West Road, Chaoyang District

department: Institute of Zoology

institute: Chinese Academy of Sciences

data_processing:
Paired-end reads were aligned with Hisat2 using default parameters, and only uniquely mapping reads were retained for further analysis
Differentially expressed genes were identified by using the DESeq2 R package.
Genome_build: mm10
Supplementary_files_format_and_content: bw files

source_name: spermatocytes

extract_protocol:
Total RNA from spermatocytes were isolated by TRIzol,  and oligo (dT) beads (NEB) were used to isolate poly(A) mRNAs
poly(A) mRNA libraries were constructed at the same time using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7760) according to the manufacturer’s recommendations.

tag: strain

tag: developmental stage

value: Bend2 KO


title: Mono-enriched-PBMC_ctrl_3hr_subj6

source_name: Monocyte-enriched peripheral blood mononuclear cells, 3hr incubation with tissue culture medium D10 (control), subject 6

value: tissue culture medium D10 (control)


title: d12_RNA_KO_LZ_rep4


title: H95_25293719664_v1: Newly diagnosed MM_101


title: D5_12(KO of YY1 BS in the promoter) [HBL_12_S12]

city: Bethesda

first: Thomas

middle: Joshua

last: Meyer

state: Maryland

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

country: USA

institute: National Institutes of Health

data_processing:
Each sample has 123 to 140 million of passed filter reads with more than 89% of bases above the quality score of Q30. Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt before alignment with the reference genome (Human - hg38) and the annotated transcripts using STAR.
12 RNA-Seq samples were pooled and sequenced on NextSeq using Illumina TruSeq Stranded Total RNA Library Prep and paired-end sequencing.
Basecalling was performed by RTA (version 1.18.64).
Demultiplexing and FASTQ generation was performed using bcl2fastq (version 2.17) allowing 1 mismatch.
Reads were filtered with a base call quality >94% of bases with Q30 and and above.
Trimming of adapters and low-quality bases was performed using Trimmomatic (version 0.33).
First pass alignment of reads to the hg38 reference genome was performed using STAR (version 2.5.2b) with parameters: STAR --genomeDir /path/to/genomeDir --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField None --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1  --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000  --clip3pAdapterSeq - --readFilesIn /path/to/read1.fastq.gz /path/to/read2.fastq.gz --readFilesCommand zcat --runThreadN 32 --outFileNamePrefix <prefix> --outSAMtype BAM Unsorted
Second pass alignment of reads to the hg38 reference genome was performed using STAR (version 2.5.2b) with parameters: STAR --genomeDir /path/to/genomeDir --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField None --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1  --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000  --clip3pAdapterSeq - --readFilesIn /path/to/read1.fastq.gz /path/to/read2.fastq.gz --readFilesCommand zcat --runThreadN 32 --outFileNamePrefix <prefix> --outSAMunmapped Within --outWigType None --outWigStrand Stranded --sjdbFileChrStartEnd /path/to/sjdbFile.txt --sjdbGTFfile /path/to/annotations.gtf --limitSjdbInsertNsj 4000000 --quantMode TranscriptomeSAM GeneCounts --outSAMtype BAM SortedByCoordinate
Gene-level expression quantificiation and library size normalization in counts-per-million was performed using RSEM (version 1.3.0) and the hg38 v28 gene annotation.
Quantile-normalization and differential expression was performed using limma-voom (version 3.34.5).
Alignment was performed to the genome (hg38, GRCh38).
Genome_build: hg38
Supplementary_files_format_and_content: filtered raw counts produced by RSEM, limma-voom normalized differential expression output

source_name: CaSki

growth_protocol: Both WT and Knock-out CaSki  cells were maintained in DMEM media supplemented with 10% fetal bovine serum (FBS) and 1x penicillin, streptomycin, glutamine (Thermo Fisher Scientific).

extract_protocol:
Total RNA was isolated using Tripure reagent (Roche, cat. no. 11667165001).
Four RNA-Seq samples for each cell were pooled and sequenced on NextSeq using Illumina TruSeq Stranded Total RNA Library Prep and paired-end sequencing.

treatment_protocol: Both WT and Knock-out cells were cultured for 24 hours in 10cm dish, then total RNA was isolated.

tag: cancer type

value: Cervical cancer positive for human papillomavirus type 16

tag: cell line

value: CaSki

tag: genotype/variation

value: KO of YY1 BS in the promoter


title: d12_RNA_WT_LZ_rep4

value: Bend2 WT


title: d12_RNA_WT_LZ_rep3


title: d12_RNA_KO_LZ_rep3


title: D5_11(KO of YY1 BS in the promoter) [HBL_11_S11]


title: H95_51074988620_v1: Newly diagnosed MM_100

value: bone marrow aspirate


title: d12_RNA_KO_LZ_rep2


title: d12_RNA_WT_LZ_rep2


title: H95_70289119654_v1: Newly diagnosed MM_98

value: Male


title: d12_RNA_WT_LZ_rep1


title: H95_31765020247_v1: Newly diagnosed MM_99

value: multiple myleoma


title: H95_63502541661_v1: Newly diagnosed MM_97


title: H95_32313700572_v1: Newly diagnosed MM_96


title: Control3

city: Hefei

first: Kuokuo

last: Li

institute: Anhui Medical University

data_processing:
Illumina bcl2fastq 2.0 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using HISAT2
Transcript abundance values were obtained from gene-level count matrices were generated by StringTie
Gene counts were normalized using geometric mean (GEO) in DESeq2 package and log2 transformed. Removal of unwanted variation (RUV) was used to remove batch effects and genes with no counts in over 50% of the samples were removed.
Differential gene expression by DEseq2 was performed on normalized gene counts, using batch effects and the Sertoli cells .
Genome_build: Genome_build: hg38
Supplementary_files_format_and_content: raw count file
Supplementary_files_format_and_content: FPMK file

source_name: Testis

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease

value: Control


title: H95_73535534583_v1: Newly diagnosed MM_95


title: Control2


title: H95_41639388983_v1: Newly diagnosed MM_94


title: Control1


title: NOA3

value: Non-obstructive azoospermia


title: H95_25158603699_v1: Newly diagnosed MM_92


title: H95_16722157346_v1: Newly diagnosed MM_93


title: A9_7(KO of lncFANCI2Promoter) [HBL_7_S7]

value: KO of lncFANCI2Promoter


title: A9_5(KO of lncFANCI2Promoter) [HBL_5_S5]


title: WT_4 [HBL_4_S4]

value: wild type


title: D5_9(KO of YY1 BS in the promoter) [HBL_9_S9]


title: D5_10(KO of YY1 BS in the promoter) [HBL_10_S10]


title: A9_8(KO of lncFANCI2Promoter) [HBL_8_S8]


title: WT_3 [HBL_3_S3]


title: A9_6(KO of lncFANCI2Promoter) [HBL_6_S6]


title: KLF4-KO-RNApol2-HiChIP-Rep2

city: Tianjin

first: Niannian

state: Tianjin

address: No. 94 Weijin Road, Nankai District, Tianjin

department: college of Life Sciences

institute: Nankai University

library_source: genomic

data_processing:
Clean reads of RNA-seq were mapped to mm10 using HISAT2(2.1.0)
Expression levels of all genes were counted and expression profile matrix was constructed with HTSeq (0.9.1)
Differential expression analysis was calculated in R using DESeq2(1.18.1), with p value < 0.05 and fold change > 2 or < 1/2
Clean reads of HiChIP were mapped to mm10 with HIC-Pro (2.11.4)
HiChIP loops was called by hichipper(0.7.7)
Genome_build: mm10
Supplementary_files_format_and_content: Text files include genes counts values and bedpe files include HiChIP loops

molecule: genomic DNA

source_name: Embryonic stem cells

growth_protocol: Mouse ESCs E14 was cultured as the previous scheme with a few modifications. ESCs were grown in culture dishes coated with 0.1% gelatin (Sigma, Lot # SLBQ9498V) in Dulbecco's Modified Eagle's Medium (DMEM, Gibco, Lot # 8119213) supplemented with 15% fetal bovine serum (FBS, AusGeneX, Lot # FBS00717-1), 100 nM nonessential amino acids (100x, Gibco, Lot # 2027433), 200 mM L-Glutamate (100x, Gibco, Lot # 2085472), 1% Penicillin-streptomycin (Gibco, Lot # 2029632), 50 μM β-mercaptoethanol (Sigma, Cas # 60-24-2), 10 ng/mL LIF (ESGRO, Lot # ESG1107), 1 μM PD0325901 (a MEK inhibitor, MedChemExpress, Lot # HY-10254) and 3 μM CHIR99021 (a GSK inhibitor, MedChemExpress, Lot # HY-10182). The medium was replaced every 1 - 2 days. All cells are maintained at 37 °C in a 5% CO2 incubator.

extract_protocol:
For RNA -seq: cells were lysed with Trizol reagent (Life Technologies) and RNA was extracted according to the manufacturer's instructions; For HiChIP libraries, DNA was extracted according to the manufacturer's instructionsQIAseq FX DNA Library Kits were used to generate the sequencing library. HiChIP libraries were size-selected to 300–700 bp using AMPure XP beads (Beckman) and subjected to 2 × 150-bp paired-end sequencing on HiSeq XTen (Illumina). Two biological replicates were analyzed for each experimental condition.
RNA libraries and HiChIP libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
Mouse ESCs E14 were grown in cell culture dishes coated with 0.1% gelatin (Sigma, 9000-70-8) in DMEM medium (Gibco) supplemented with 15% FBS (AusGeneX) 1,000 U/mL of LIF (Millipore), non-essential amino acids (Gibco), 1 mM of glutamax (ThermoFisher,), 100 U/mL of penicillin and streptomycin (ThermoFirsher) and 0.1 mM of β-mercaptoethanol (Sigma). Medium was changed every 2 days and cells were passaged every two days using Trypsin-EDTA (0.25%) (Gibco).
The KLF4-KO E14 cells were control groups for the same conditions with WT

value: embryo, blastocyst embryo, blastocyst


title: KLF4-KO-RNA-seq-Rep1


title: WT-RNApol2-HiChIP-Rep1


title: KLF4-KO-RNA-seq-Rep2


title: KLF4-KO-RNApol2-HiChIP-Rep1


title: WT-RNApol2-HiChIP-Rep2


title: NOA2


title: WT-RNA-seq-Rep2 (KLF4 control)


title: WT_2 [HBL_2_S2]


title: WT_1 [HBL_1_S1]


title: Mono-enriched-PBMC_ctrl_3hr_subj5

source_name: Monocyte-enriched peripheral blood mononuclear cells, 3hr incubation with tissue culture medium D10 (control), subject 5

value: blood

value: cultured monocyte-enriched peripheral blood mononuclear cells


title: WT-RNA-seq-Rep1 (KLF4 control)


title: NOA1


title: RNA_KO_zyg_rep2

data_processing:
Paired-end reads were aligned with Hisat2 using default parameters, and only uniquely mapping reads were retained for further analysis
Differentially expressed genes were identified by using the DESeq2 R package.
Genome_build: mm10
Supplementary_files_format_and_content: GTF files

source_name: zygotene spermatocytes

extract_protocol:
Total RNA from spermatocytes were isolated by TRIzol.
All RNA libraries were constructed at the same time using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7760) according to the manufacturer’s recommendations.

tag: tissue/cell type

value: zygotene spermatocytes


title: H95_16923322959_v1: Newly diagnosed MM_90

tag: tissue


title: H95_94551085868_v1: Newly diagnosed MM_89

tag: gender


title: SF-CON_L4_382382

first: Shengde

last: Liu

address: 38 Xueyuan Rd , Haidian District

institute: Peking University Health Science Center

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
FPKM were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.

organism:
Homo sapiens
Human alphaherpesvirus 1

source_name: Hela

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

value: stably expresses the plasmid of SAFA

tag: host

value: HeLa cells


title: H95_35677547599_v1: Newly diagnosed MM_91

tag: age

tag: disease state


title: SF-CD_L4_383383

value: stably expresses the plasmid of SAFA-ADAR1 catalytic domain(SAFA-ADAR1cd)


title: SF-CD488_L4_384384

value: stably expresses the plasmid of SAFA-ADAR1 catalytic domain E488Q(SAFA-ADAR1cd E488Q)


title: RNA_KO_zyg_rep1

value: Bend2 KO


title: Mono-enriched-PBMC_ctrl_3hr_subj1

source_name: Monocyte-enriched peripheral blood mononuclear cells, 3hr incubation with tissue culture medium D10 (control), subject 1

tag: subject id

value: tissue culture medium D10 (control)


title: RNA_WT_zyg_rep2

value: Bend2 WT


title: Donor3_siNrf2_2

city: Lyon

first: Florence

last: Ruggiero

address: 32 avenue Tony Garnier

country: France

institute: ENS de Lyon - IGFL

data_processing:
Reads were mapped to the human genome reference GRCh38.p12 and quantified using STAR (Dobin et al., 2013) (with parameters  --outFilterType BySJout, --outSAMtype BAM Unsorted, and --quantMode GeneCounts).  This last parameter allows direct conversion of the mappings into gene counts.
Then, differential gene expression (DGE) analysis was performed using DESeq2 package (Anders and Huber, 2010) with a filtering step (genes that did not have more than 0.339 count per million counts in at least 2 samples were filtered out) and corrections (to remove library size and technical effects).
The differentially expressed (DE) genes were further analysed considering various thresholds.
Only DE genes with adjusted p-value <0.05 were considered as significantly expressed.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Breast skin

growth_protocol: Fibroblasts were cultured in T25 flasks.

extract_protocol:
mRNA were extracted from T25 flasks using the RNeasy kit (Qiagen). Concentration and quality of the RNA samples were assessed using Qubit 2.0 (Thermo Fischer Scientific) and TapeStation 2200 (Agilent Technologies) respectively.
Barcoded libraries were built using SENSE mRNA-seq Library Prep Kit V2 (Lexogen) following the manufacturer's instructions. Libraries were pooled in equimolar ratios and sequenced on Illumina NextSeq 500 sequencing platform in single end (75 bp).

treatment_protocol: Fibroblasts were cultured in 2% serum with or without siRNA during 72 hours.

value: Primary papillary skin fibroblasts

value: transfected with siNrf2_2


title: Mono-enriched-PBMC_ctrl_3hr_subj3

source_name: Monocyte-enriched peripheral blood mononuclear cells, 3hr incubation with tissue culture medium D10 (control), subject 3


title: Donor3_siNrf2_1

value: transfected with siNrf2_1


title: C3TAG mammary gland Tumor 1 for bulk DNA arrayCGH

type: genomic

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

description: C3Tag/ female

hyb_protocol: For arrayCGH; The Cy3 and Cy5 labeled genomic DNA WERE hybridized to Agilent 244k CGH arrays (model G4415A)

scan_protocol: Scanned on Agilent scanner (model G2505B)

data_processing: Data for both channels were Lowess-normalized and then the log(2) ratio was taken

source_name: FVB normal mammary gland reference

label_protocol: For arrayCGH; genomic DNA was labeled according to the direct incorporation method (Agilent)Labeling Kit PLUS (Catalog Number 5188–5309). Channel 1 was DNA reference from FVB normal mammary gland with Cy3 label; Channel 2 was the C3Tag DCIS or tumor genomic DNA with Cy5 label

extract_protocol: the genomic DNA was isolated using Dneasy kit (Qiagen)

tag: referece

value: normal reference

source_name: Mammary Tumor

value: >18 weeks old

tag: test

value: Palpable C3Tag mouse Tumor flash frozen for bulk DNA arrayCGH


title: H95_88467538747_v1: Newly diagnosed MM_87

source_name: bone marrow aspirate

value: bone marrow aspirate

value: Female

value: multiple myleoma


title: Mono-enriched-PBMC_ctrl_3hr_subj2

source_name: Monocyte-enriched peripheral blood mononuclear cells, 3hr incubation with tissue culture medium D10 (control), subject 2

value: blood

tag: cell type

value: cultured monocyte-enriched peripheral blood mononuclear cells

tag: treatment


title: C3TAG mammary gland Tumor 2 for bulk DNA arrayCGH

description: C3Tag/ female


title: C3TAG DCIS containing whole mammary gland 3 for bulk DNA arrayCGH

description: C3Tag/ female

source_name: Whole mammary gland

value: 18 weeks old

value: Whole mouse gland from 18 weeks old C3Tag mouse, flash frozen for bulk DNA arrayCGH


title: H95_27201492856_v1: Newly diagnosed MM_88


title: Mono-enriched-PBMC_ctrl_3hr_subj4

source_name: Monocyte-enriched peripheral blood mononuclear cells, 3hr incubation with tissue culture medium D10 (control), subject 4


title: RNA_WT_zyg_rep1

tag: strain

tag: genotype

value: zygotene spermatocytes


title: C3TAG mammary gland Tumor 3 for bulk DNA arrayCGH

description: C3Tag/ female


title: Donor3_siScramble

value: transfected with a scramble siRNA


title: Donor3_untreated

value: no treatment


title: H95_88927351997_v1: Newly diagnosed MM_86

value: Male


title: ImPACCT-02-004-I-2-RNA

source_name: Colorectal cancer

value: Colorectal cancer

tag: rf cms4 probability

tag: imatinib

value: Post-imatinib


title: H95_81588441726_v1: Newly diagnosed MM_85


title: 419-20

city: Frederiksberg

first: Xiaoyu

last: Pan

address: Dyrlægevej 68

department: Department of Veterinary and Animal Sciences

country: Denmark

institute: University of Copenhagen

data_processing:
Quality and adapter trimming of raw reads were performed using TrimGalore (Babraham Binoinformatics).
The remaining clean reads were aligned to the porcine genome (Sscrofa11.1) using HISAT2
The annotated gene information of porcine genome was downloaded from Ensembl (release 99).
The script htseq-count was used to generate gene count matrix.
The gene count was normalized using DESeq2.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: Raw counts of sequencing reads for each gene (Ensembl gene IDs) generated from htseq-count.

organism: Sus scrofa

source_name: cerebellum

extract_protocol:
Total RNA was isolated with RNeasy Lipid Tissue Mini Kit  (Qiagen).
RNA libraries were prepared by Novogene Europe (Cambridge, UK) and sequenced on the Illumina NovaSeq platform with paired-end 150-bp reads production.

tag: body weight

tag: Sex

value: F

value: BDL


title: RNA_KO_lep_rep2

source_name: leptotene spermatocytes

tag: developmental stage

value: Bend2 KO

tag: tissue/cell type

value: leptotene spermatocytes


title: Donor2_siNrf2_3

value: Primary papillary skin fibroblasts

value: transfected with siNrf2_3


title: 421-20

value: M


title: RNA_KO_lep_rep1


title: H95_51513539224_v1: Newly diagnosed MM_84

tag: tissue

value: bone marrow aspirate

tag: gender

value: Female

value: multiple myleoma


title: RNA_WT_lep_rep2

value: Bend2 WT


title: 420-20

value: SHAM


title: H95_36204590648_v1: Newly diagnosed MM_83

tag: age


title: Donor2_siScramble

value: transfected with a scramble siRNA


title: C3TAG DCIS containing whole mammary gland 2 for bulk DNA arrayCGH

description: C3Tag/ female

value: normal reference

value: 16 weeks old

value: Whole mouse gland from 18 weeks old C3Tag mouse, flash frozen for bulk DNA arrayCGH


title: C3TAG DCIS containing whole mammary gland 1 for bulk DNA arrayCGH

description: C3Tag/ female

value: 18 weeks old


title: H95_98855783526_v1: Newly diagnosed MM_82

tag: disease state


title: 418-20

value: F


title: RNA_WT_lep_rep1


title: 417-20

value: BDL


title: ATAC_KO_rep2

data_processing:
Paired-end reads were aligned with Bowtie2 using default parameters, and only uniquely mapping reads were retained for further analysis
Peak calling was executed using MACS2 (v2.2.7.1).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files

extract_protocol:
Cells were lysed and nucleus were incubated with Tn5 reaction mix.
Fragments were purified and library amplification was performed using the TruePrep DNA Library Prep Kit V2 for Illumina (TD501, Vazyme).

value: Bend2 KO

value: zygotene spermatocytes


title: 416-20


title: H95_30114194799_v1: Newly diagnosed MM_81

value: Male


title: ATAC_KO_rep1


title: H95_99118191515_v1: Newly diagnosed MM_80


title: 415-20


title: Donor2_siNrf2_2

value: Primary papillary skin fibroblasts

value: transfected with siNrf2_2


title: Donor2_untreated

value: no treatment


title: Donor1_siNrf2_3

value: transfected with siNrf2_3


title: Donor2_siNrf2_1

value: transfected with siNrf2_1


title: Donor1_siNrf2_1


title: Donor1_siNrf2_2


title: H95_43027278927_v1: Newly diagnosed MM_78

value: bone marrow aspirate

value: Female

value: multiple myleoma


title: H95_19105755822_v1: Newly diagnosed MM_79


title: ATAC_WT_rep2

value: Bend2 WT


title: Donor1_siScramble

value: transfected with a scramble siRNA


title: H95_72661535288_v1: Newly diagnosed MM_77


title: H3K27me3_WT_rep1

data_processing:
library strategy: CUT&RUN
ChIP-seq reads were mapped to the UCSC mm10 genome using Bowtie2 (v2.4.1) with default parameters.
Peak calling was performed using MACS2 (v2.2.7.1) with default parameters, except that the q value was less than 0.01.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files

extract_protocol:
Cells were binded to concanavalin A beads and histones were recognized by antibodies then combined with pA/G-MNase. DNA binds to histones were digested by pA/G-MNase and released into suspension after treated with calcium ion.
Extracted DNA was used to construct libraries with the NEBNext Ultra II DNA library Prep Kit for Illumina (E7645, NEB), and qualified libraries were sequenced with an Illumina Novaseq 6000 to obtain paired-end 150-nt reads.

tag: H3K27me3 (Cell Signaling Technology, 9733, C36B11)


title: 410-20

value: M

value: SHAM


title: CB-HSPC - SR1_rep3

city: Seoul

first: Dong-Yeop

last: Shin

address: 101 Daehak-ro, Jongno-gu

department: College of Medicine

country: South Korea

institute: Seoul National University

data_processing:
We arranged reads to the reference genome using STAR software, and quantified aligned reads using Cufflinks.
Based on the gene annotation of the reference genome hg19, Fragments per Kilobase of transcript per Million fragments mapped (FPKM) unit was calculated.
Differentially expressed genes (DEGs) were calculated and analyzed using Cuffdiff software in the Cufflinks package.
Clustered expression values were further analyzed using in-house R script, and Gene Ontology, KEGG pathway, and Reactome pathway terms were used through g: Profiler.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files of FPKM values

source_name: Hematopoietic stem/progenitor cells (HSPCs)

growth_protocol: CD34+cells were isolated from cord blood and cultured in Serum-Free Expansion Medium II (SFEM II, STEMCELL Technologies, 09650) supplemented with four growth factors; recombinant human Stem cell factor (rhSCF, Peprotech, 300-07), Fms-related tyrosine kinase 3 ligand (rhFLT3-L, Peprotech, 300-19), Thrombopoietin (rhTPO, Peprotech, 300-18), and Interleukin-3 (rhIL-3, Peprotech, 200-03).

extract_protocol:
Total RNA is manually extracted using Trizol from lysates of cultured HSPCs.
Using Illumina TruSeq Stranded mRNA Sample Preparation kit, mRNA sequencing library were prepared. Library size and quality were confirmed by Agilent 2100 bioanalyzer DNA kit (Agilent). Libraries were quantified (qPCR using CFX96 Real Time System, Biorad) and equenced on the NextSeq500 sequencers (Illumina).

treatment_protocol: Cells were cultured with either of two AhR antagonists Stem Regenin 1 (SR1, Selleckchem, S2858) and CH223191 (Selleckchem, S7711) in designated concentrations, and culture media changed every 2-3 days during 7 days of culture.

value: Umbilical cord blood-HSPCs

tag: culture period

value: Day 7

value: treated with StemRegenin1


title: ATAC_WT_rep1

value: zygotene spermatocytes


title: 412-20

value: F


title: H3K27me3_WT_rep2


title: 411-20

value: BDL


title: 409-20


title: H3K27me3_KO_rep2

value: Bend2 KO


title: 408-20


title: H3K4me3_KO_rep2


title: H95_54073444830_v1: Newly diagnosed MM_75


title: CB-HSPC - SR1_rep2


title: 414-20


title: Donor1_untreated

value: Primary papillary skin fibroblasts

value: no treatment


title: H95_18039603324_v1: Newly diagnosed MM_74

value: Male


title: H95_60725268705_v1: Newly diagnosed MM_73

value: bone marrow aspirate


title: 413-20


title: H3K4me3_KO_rep1


title: H95_63575013733_v1: Newly diagnosed MM_72


title: H95_55663140178_v1: Newly diagnosed MM_71

value: Female


title: CB-HSPC - CH223191_rep2

value: treated with CH223191


title: CB-HSPC - CH223191_rep1


title: H95_25778709384_v1: Newly diagnosed MM_70

value: multiple myleoma


title: 405-20


title: CB-HSPC - SR1_rep1


title: H95_89673138286_v1: Newly diagnosed MM_69


title: CB-HSPC - CH223191_rep3


title: 404-20


title: BEND2_input_rep5

data_processing:
ChIP-seq reads were mapped to the UCSC mm10 genome using Bowtie2 (v2.4.1) with default parameters.
Peak calling was performed using Pepr with default parameters and the corresponding inputs as background, and peaks that mapped to blacklist regions were removed.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files

source_name: testes

extract_protocol:
Testicular lysates were clarified from sonicated nuclei and protein-DNA complexes were precipited by antibody.
Extracted DNA was used to construct libraries with the NEBNext Ultra II DNA library Prep Kit for Illumina (E7645, NEB), and qualified libraries were sequenced with an Illumina Novaseq 6000 to obtain paired-end 150-nt reads.

value: testes

tag: chip antibody


title: H95_95730729146_v1: Newly diagnosed MM_76


title: 407-20

value: M


title: H3K27me3_KO_rep1


title: 406-20

value: SHAM


title: BEND2_input_rep6


title: 400-20


title: 403-20


title: CB-HSPC - DMSO_rep2

tag: cell type

value: Umbilical cord blood-HSPCs

value: DMSO


title: BEND2_input_rep4


title: H3K4me3_WT_rep2

value: Bend2 WT


title: H3K4me3_WT_rep1

value: zygotene spermatocytes


title: H95_45211526870_v1: Newly diagnosed MM_68


title: BEND2_input_rep1


title: CB-HSPC - ChIP_SR1_input

data_processing:
We aligned the reads using Bowtie (version 1.1.2 parameter set -n 2 -m 1 -X 500).
The mapped reads were sorted and indexed through SAMtools (version 1.9), and duplicate reads were removed through the MarkDuplicates module in Picard (version 1.118).
Through MACS2 version 2.1.1, peak calling was performed on the IP sample compared to the input control in the aligned sequences.
Genes nearby the peaks were distinguished by annotating the identified peaks using ChIPseeker of R.
Genome_build: GRCh38
Supplementary_files_format_and_content: peak files

extract_protocol:
Cultured cells were lysated by ultrasonication. Using Agarose ChIP assay kit (Pierce Biotechnology, 25156), Chromatin complexes were immunoprecipitated isolated with AhR specific antibody (Cell signaling technology, #83200).
Libraries were constructed (TruSeq ChIP Library Preparation Kit, Illumina). Paired end reads were sequenced with a length of 151 bp using an Illumina instrument and sequence quality was confirmed by FASTQC (version 0.11.7). Adaptor sequences were removed by Trimmomatic (Ver. 0.38) (Bolger et al, 2014), and low quality base (lower than three) were trimmed from the reads.

treatment_protocol: Cells were cultured with either of two AhR antagonists Stem Regenin 1 (SR1, Selleckchem, S2858) and CH223191 (Selleckchem, S7711) in designated concentrations, and culture media containing AhR antagonists changed every 2-3 days during 14 days of culture.

value: Day 14

tag: treatment

value: treated with StemRegenin1

tag: chip-antibody


title: CB-HSPC - ChIP_CH223191_IP

value: anti-hAhR (Cell signaling, #83200)


title: H95_27225006672_v1: Newly diagnosed MM_64

data_processing:
Paired end sequencing was performed on an Illumina NovaSeq 6000 using 101 cycles for each mate.
Fastq files were constructed using bcl2fastq (v2.20.0.422).
Illumina universal adapters   were removed using trim_galore (v0.4.4).
Pseudo counts were measured on the trimmed Fastq files using  salmon (v1.3.0) using the default settings.
Salmon performed according to reference DOI:10.1038/NMETH.4197
Genome_build: GRCh37
Supplementary_files_format_and_content: Salmon, read counts

extract_protocol:
RNeasy
RNA Seq libraries were generated with the mRNA HyperPrep Kit (KAPA, catalog number 08105952001/KK8544), according to manufacturer’s instructions.


title: BEND2_rep6

tag: strain

tag: genotype

value: ANTI-FLAG M2 (SIGMA F1804 SLBW3851)


title: CB-HSPC - DMSO_rep1

value: Day 7


title: CB-HSPC - ChIP_SR1_IP


title: H95_57558990134_v1: Newly diagnosed MM_66


title: H95_71035164901_v1: Newly diagnosed MM_67

value: Male


title: 401-20


title: CB-HSPC - ChIP_CH223191_input


title: BEND2_input_rep2


title: River water, rep9

city: Ste-Anne-de-Bellevue

first: Jessica

last: Head

state: Quebec

address: 21111 Lakeshore

department: Natural Resource Sciences

country: Canada

institute: McGill University

data_processing:
All the FASTQ read files were submitted to Seq2Fun (www.seq2fun.ca) with default parameters to conduct Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthologues (KOs) abundance quantification. Seq2Fun is a profiling tool for RNAseq data analysis for organisms without reference genomes, such as many endangered species (Liu et al. 2021). Quality checks were first performed on paired-end reads and sequencing adaptors, and low quality bases/reads and polyAtails were removed. Sequencing errors were corrected and merged into a single end clean read when overlapping. The clean reads were then translated into all possible amino acid (AA) sequences with six open reading frames, followed by a homology search in a protein database consisting of 2,446,258 proteins and 12,984 KOs (of which 783,801 proteins and 10,510 KOs were from multiple fish species), using Burrow Wheeler Transform (BWT) and Fowlkes Mallows Index (FMI). A KO abundance table was produced.
The produced KO abundance table was uploaded to NetworkAnalyst (www.networkanalyst.ca) for analysis of differential gene expression (Zhou et al. 2019). Differentially expressed genes (DEGs) were identified using EdgeR between lab and river water groups using the combination of fold-change expression (log2FC ³ 1) and adjusted p-value based on the false discovery rate (FDR < 0.05).
Supplementary_files_format_and_content: tab-delimited text files include KOs count values for each sample
Supplementary_files_format_and_content: Matrix table with raw KOs counts for every gene and every sample

organism: Moxostoma hubbsi

source_name: Copper redhorse larvae

extract_protocol:
Larvae were taken out of water and flash frozen on dry ice, and RNA was extracted using a Rneasy Mini QIAcube kit (Qiagen). Larval tissue was homogenized in buffer RLT using a TissueLyser II (Qiagen). Dnase I (Qiagen) was used to prevent genomic DNA contamination. QIAxpert (Qiagen) was used to spectrophotometrically measure RNA concentration (260/280 ratio between 2 and 2.3) and purity.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 14 days post fertilization

value: 5 x Whole larvae

value: River water


title: 402-20

value: F

value: BDL


title: River water, rep7


title: River water, rep8


title: BEND2_rep5

value: testes


title: H95_40001226014_v1: Newly diagnosed MM_62

value: bone marrow aspirate

value: multiple myleoma


title: River water, rep6


title: BEND2_input_rep3


title: CB-HSPC - ChIP_C_IP

value: Umbilical cord blood-HSPCs

value: DMSO


title: H95_49394683789_v1: Newly diagnosed MM_65


title: BEND2_rep3


title: H95_68858331506_v1: Newly diagnosed MM_61

value: Female


title: H95_68829024685_v1: Newly diagnosed MM_59


title: CB-HSPC - ChIP_C_input

value: Day 14


title: H95_72699532466_v1: Newly diagnosed MM_60


title: River water, rep5


title: BEND2_rep1


title: BEND2_rep2


title: R3_GFP_negC

city: Jerusalem

first: Dan

last: Vershkov

address: The Edmond J. Safra Campus

country: Israel

institute: Hebrew University of Jerusalem

description: control for 3rd+4th experiment - 3rd GFP(-) sample

data_processing:
Align the fastq files against the library’s sgRNAs sequences list using Bowtie2
Genome_build: The sgRNAs sequences as appear in Table S1 of Wang, T. et al. Identification and characterization of essential genes in the human genome. Science 350, 1096–1101 (2015).
Supplementary_files_format_and_content: comma separated values (csv) file contains sgRNA counts for each sample.

source_name: CRISPR/Cas9 mutant library in h-pES10

growth_protocol: Human haploid embryonic stem cells were cultured at 37 °C with 5% CO2 in feeder-free conditions using matrigel-coated plates (Corning) and mTeSR1 medium (STEMCELL Technologies) supplemented with 10μM ROCK inhibitor (Y27632, Stemgent) for one day after thawing or splitting.

extract_protocol:
Genomic DNA was extracted using the gSYNC DNA extraction kit (Geneaid).
The sgRNA integration-containing region was amplified, and the DNA library was established as previously described (Yilmaz et al., 2020. PMID: 32735778).

treatment_protocol: 10µM ROCK inhibitor (Y27632) was added 1 hour prior to trypsinization and transfection. Library cells were harvested using TrypLE™ Select Enzyme solution (Thermo Fisher Scientific, Cat# 12563029) in a single cell state. Following the first centrifugation, cells were re-suspended twice with DMEM/F12 and centrifuged again before incubation with the plasmid DNA. Transfection was performed using the Xtreme Gene9 reagent (Roche), using standard conditions. 48 hours following transfection, cells were washed with PBS, harvested using TrypLE™ Select, resuspended in PBS supplemented with 15% fetal bovine serum (FBS), and filtered through a 70-µm cell strainer (Corning) and sorted using BD FACDAria III.

value: haploid human embryonic stem cells

tag: population

value: GFP negative

tag: replicate

value: R3 + R4 - control


title: H95_43919813020_v1: Newly diagnosed MM_63


title: H95_76299194805_v1: Newly diagnosed MM_58


title: River water, rep3


title: River water, rep2


title: BEND2_rep4

value: ANTI-FLAG M2 (SIGMA F1804 SLBW3851)


title: H95_17121435841_v1: Newly diagnosed MM_57

value: Male


title: R3_GFP_negA

description: control for 3rd+4th experiment - 1st GFP(-) sample


title: R3_GFP_negB

description: control for 3rd+4th experiment - 2nd GFP(-) sample


title: R2_GFPminusC

description: 2nd experiment - 2nd GFP(-) sample

value: R2 - control


title: R2_GFPminusB

description: 2nd experiment - 1st GFP(-) sample


title: River water, rep1

value: 14 days post fertilization

value: 5 x Whole larvae


title: CD45+ cells - 27HC.3

city: Urbana

first: Erik

last: Nelson

state: Illinois

address: 407 S Goodwin Ave

department: Molecular and Integrative Physiology

institute: University of Illinois at Urbana Champaign

data_processing:
Base-calling and demultiplexing of raw data was done with the mkfastq command of the software Cell Ranger 4.0 (10x Genomics).
The sequenced libraries were reference mapped and quantified using CellRanger Count v5.0 (mouse GRCm39, GENCODE M26).
Genome_build: GRCm39
Supplementary_files_format_and_content: filtered count h5 matrix output from CellRanger Count

source_name: CD45+ cells from metastatic mouse lung

extract_protocol:
A total of 12 flow sorted single-cell suspensions with an average viability of 90-99% by AO/PI staining on the Nexcelom K2 (Nexcelom Bioscience, Lawrence, MA) were converted into individually barcoded cDNA libraries with the Chromium Next GEM Single-Cell 3’ dual-index kit version 3.1 from 10X Genomics (Pleasanton, CA).
Following ds-cDNA synthesis, individually barcoded dual-indexed libraries compatible with the Illumina chemistry were constructed. The final libraries were quantitated on Qubit and the average size determined on the AATI Fragment Analyzer. Libraries were pooled evenly, and the final pool was diluted to 5nM concentration and further quantitated by qPCR on a Bio-Rad CFX Connect Real-Time System. The final library pool was sequenced on three lanes of an Illumina NovaSeq 6000 S4 flowcell as paired-reads with 28 cycles for read 1, 10 cycles for each index read, and 150 cycles for read 2, to target 100k cDNA reads per cell.

value: CD45+ cells

value: lung


title: River water, rep4

value: River water


title: Lab water, rep9

value: Laboratory water (control)


title: CD45+ cells - GW273297X.3


title: CD45+ cells - GW3965.3


title: CD45+ cells - 27HC.2


title: H95_33374926438_v1: Newly diagnosed MM_55

value: bone marrow aspirate

value: multiple myleoma


title: R1_GFP_neg_3_ii

description: 1st experiment - 3rd GFP(-) sample  - technical replicate ii

value: R1 - control


title: H95_28487116855_v1: Newly diagnosed MM_54

value: Female


title: R1_GFP_neg_3_i

description: 1st experiment - 3rd GFP(-) sample  - technical replicate i


title: H95_27178908090_v1: Newly diagnosed MM_53


title: CD45+ cells - Vehicle.3

value: Vehicle


title: R1_GFP_neg_2_ii

description: 1st experiment -2nd GFP(-) sample  - technical replicate ii

value: haploid human embryonic stem cells


title: CD45+ cells - GW273297X.2


title: Lab water, rep7


title: H95_38004909435_v1: Newly diagnosed MM_52


title: Lab water, rep6


title: R1_GFP_neg_2_i

description: 1st experiment -2nd GFP(-) sample  - technical replicate i

value: GFP negative


title: H95_25459089354_v1: Newly diagnosed MM_50


title: H95_93707430173_v1: Newly diagnosed MM_51


title: Lab water, rep5


title: CD45+ cells - GW3965.2


title: R1_GFP_neg_1_i

description: 1st experiment - 1st GFP(-) sample  - technical replicate i


title: H95_44330907233_v1: Newly diagnosed MM_56


title: Lab water, rep8


title: H95_32948916566_v1: Newly diagnosed MM_49


title: H95_54622906537_v1: Newly diagnosed MM_48


title: CD45+ cells - Vehicle.2


title: Lab water, rep2


title: Lab water, rep3


title: H95_70997597735_v1: Newly diagnosed MM_47


title: CD45+ cells - 27HC.1


title: CD45+ cells - GW273297X.1


title: R3_GFP_pos3

description: 4th experiment - 1st GFP(+) sample

value: GFP positive


title: CD45+ cells - GW3965.1


title: R3_GFP_pos4

description: 4th experiment -2nd GFP(+) sample


title: Lab water, rep1


title: Lab water, rep4


title: R1_GFP_neg_1_ii

description: 1st experiment - 1st GFP(-) sample  - technical replicate ii


title: CD45+ cells - Vehicle.1


title: R3_GFP_pos1

description: 3rd experiment - 1st GFP(+) sample


title: H95_75486530924_v1: Newly diagnosed MM_46


title: BMDM - GSK2033 + 27HC.5

data_processing:
The abundance of transcript was quantified using Kallisto (v0.44.0) pseudoalignment, using index built from a transcriptome fasta of Mus Musculus build GRCm38. Transcript abundance was subsequently summarized to gene-level using R package Tximport.
After keeping all the genes that were expressed in at least 1 sample, 24671 genes were left for downstream analysis.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited txt file of gene counts of each sample

source_name: BMDM_GSK2033 + 27HC

extract_protocol:
Genomic DNA removal and total RNA extraction from BMDMs were performed using Qiagen RNeasy Plus Mini Kit (Cat. #74136).
RNAseq libraries were constructed from PolyA+ RNA using the TruSeq Stranded RNA Sample Preparation Kit (Illumina San Diego, CA). The final stranded RNASeq library pool consisting of 46 libraries was sequenced on 3 lanes of an Illumina NovaSeq 6000 SP flowcell as single-reads with 100nt length, to generate an average of 35M reads per sample. The run generated .bcl files which were converted into adaptor-trimmed demultiplexed fastq files using bcl2fastq v2.20 Conversion Software (Illumina, CA).

value: Bone marrow-derived macrophages (BMDM)


title: H95_59287418008_v1: Newly diagnosed MM_45

value: Male


title: BMDM - GSK2033 + 27HC.4


title: R2_GFPplusB

description: 2nd experiment - 2nd GFP(+) sample


title: Th2_ex_vivo_DO.11_expt2_mouse12_flare

city: North Grafton

first: Jillian

middle: M

last: Richmond

state: Massachusetts

address: 200 Westboro Road

department: Comparative Pathobiology

institute: Tufts Cummings School of Veterinary Medicine

description: GVH37 mouse 12 flare

hyb_protocol: Hybridizations were performed per NanoString manufacturer's protocol overnight for 18h in a BioRad C1000 touch thermocycler

scan_protocol: Cartridges were run on a NanoString Sprint machine.

data_processing: Data were analyzed with nSolver software version 4.0 and with ROSALIND software OnRamp Bio.

label: fluorescent probe

source_name: ex vivo enriched DO.11 T cells

label_protocol: Probe labeling was performed per NanoString manufacturer's protocol.

growth_protocol: For cultures, DO.11 T cells were isolated from donor spleens, activated with ova-pulsed splenocytes, skewed with cytokines and antibodies towards Th0, Th1 or Th2, and expanded with IL-2 for a total of 10 days (see also Mande et al JCI 2018 PMID: 29889098). For ex vivo analysis, DO.11 T cells were enriched from digested lesional skin tissue using Miltenyi CD3 bead isolation kits.

extract_protocol: RNA was extracted from T cells using Qiagen RNEasy mini kits per the manufacturer's instructions.

tag: pre vs post injection

value: Post

tag: cle disease first vs flare

value: Flare

tag: th skewing

value: Th2 (source)

tag: mouse cle skin disease score


title: H95_20532640307_v1: Newly diagnosed MM_44

tag: tissue

tag: gender


title: BMDM - GSK2033 + 27HC.3


title: H95_34136296948_v1: Newly diagnosed MM_43

tag: age

tag: disease state


title: R3_GFP_pos2

description: 3rd experiment - 2nd GFP(+) sample


title: BMDM - GSK2033 + 27HC.2


title: R1_GFP_pos_5_ii

description: 1st experiment - 5th GFP(+) sample  - technical replicate ii


title: R2_GFPplusA

description: 2nd experiment - 1st GFP(+) sample


title: Th2_cultured_DO.11_female_expt2

description: Th2 female GVH37

source_name: cultured DO.11 T cells

value: Pre


title: Th2_cultured_DO.11_male_expt2

description: Th2 male GVH37


title: H95_61064339613_v1: Newly diagnosed MM_42


title: R1_GFP_pos_4_ii

description: 1st experiment - 4th GFP(+) sample  - technical replicate ii


title: BMDM - GSK2033 + 27HC.1


title: H95_80428083070_v1: Newly diagnosed MM_41


title: Th1_cultured_DO.11_expt2

description: Th1 GVH37


title: BMDM - ICI + 27HC.5

source_name: BMDM_ICI + 27HC

value: ICI + 27HC


title: Th0_cultured_DO.11_expt2

description: T0 GVH37


title: H95_82069194919_v1: Newly diagnosed MM_40


title: Th2_ex_vivo_DO.11_expt1_mouse2_flare

description: GVH35 mouse 2 flare


title: H95_42265336143_v1: Newly diagnosed MM_39


title: R1_GFP_pos_4_i

description: 1st experiment - 4th GFP(+) sample  - technical replicate i


title: BMDM - ICI + 27HC.4


title: BMDM - ICI + 27HC.3


title: Th2_ex_vivo_DO.11_expt1_mouse6_first

description: GVH35 mouse 6

value: First


title: H95_47363361239_v1: Newly diagnosed MM_38


title: Th2_ex_vivo_DO.11_expt1_mouse1_flare

description: GVH35 mouse 1 flare


title: R1_GFP_pos_3_i

description: 1st experiment - 3rd GFP(+) sample  - technical replicate i


title: R1_GFP_pos_3_ii

description: 1st experiment - 3rd GFP(+) sample  - technical replicate ii


title: BMDM - ICI + 27HC.2


title: H95_63571029752_v1: Newly diagnosed MM_37


title: R1_GFP_pos_5_i

description: 1st experiment - 5th GFP(+) sample  - technical replicate i


title: Th2_ex_vivo_DO.11_expt1_mouse3_first

description: GVH35 mouse 3


title: R1_GFP_pos_2_ii

description: 1st experiment -2nd GFP(+) sample  - technical replicate ii


title: BMDM - ICI + 27HC.1


title: BMDM - GW3965 + 27HC.5

source_name: BMDM_GW3965 + ICI

value: GW3965 + ICI


title: H95_22514675883_v1: Newly diagnosed MM_36

source_name: bone marrow aspirate

value: bone marrow aspirate


title: R1_GFP_pos_2_i

description: 1st experiment -2nd GFP(+) sample  - technical replicate i


title: Th2_ex_vivo_DO.11_expt1_mouse1_first

description: GVH35 mouse 1


title: BMDM - GW3965 + 27HC.4


title: R1_GFP_pos_1_ii

description: 1st experiment - 1st GFP(+) sample  - technical replicate ii


title: BMDM - GW3965 + 27HC.3


title: Th2_cultured_DO.11_expt1

description: Th2 GVH35 setup


title: H95_62341947243_v1: Newly diagnosed MM_33

value: multiple myleoma


title: H95_67510998658_v1: Newly diagnosed MM_34


title: R1_GFP_pos_1_i

description: 1st experiment - 1st GFP(+) sample  - technical replicate i


title: Th1_cultured_DO.11_expt1

description: Th1 GVH35 setup


title: BMDM - GW3965 + 27HC.2


title: FXS-iPSCs DNMT1 rep3

data_processing:
Raw RNA sequencing samples were aligned to the human reference genome using STAR 2.4.0.1  software.
Sequences originating from the feeder layer of mouse embryonic fibroblasts were filter using the XenofilteR software.
Following the filtering of mouse sequences, normalization of the read counts and identification of statistically significant differentially expressed genes were performed using edgeR.
Genome_build: GRCh38/hg38

source_name: induced pluripotent stem cells

growth_protocol: FXS-iPSCs were cultured at 37°C and 5% CO2 on growth-arrested mouse embryonic fibroblasts (MEF) in KnockOut Dulbecco's modified Eagle's medium (Gibco-Invitrogen, CA) supplemented with 15% KnockOut Serum Replacement (Gibco-Invitrogen, CA), 1mM glutamine, 0.1mM ß-mercaptoethanol (Sigma-Aldrich, MO), 1% nonessential amino acids stock (Gibco-Invitrogen, CA), penicillin (50units/ml), streptomycin (50μg/ml), and 8ng/ml FGF2 (Gibco-Invitrogen, CA).

extract_protocol:
Total RNA was isolated using NucleoSpin RNA Plus kit (Macherey-Nagel) or the RNeasy Mini Kit (Qiagen) and reverse transcribed using the qScript® cDNA Synthesis Kit.
RNA sequencing libraries were created using TruSeq RNA Library Prep Kit (Illumina) and sequenced using Illumina NextSeq 500 with 75 bp single-end reads.

treatment_protocol: FXS-iPSCs were infected with an sgRNA that targets the open reading frame of DNMT1. The sgRNA sequence was cloned into the lentiCRISPR v2 plasmid and transformed into Stbl3 chemically competent bacteria. Following plasmid isolation, 293T cells in 10cm culture plates were transfected with sgRNA-containing lentiCRISPR V2, pCMV-VSV-G (a gift from Bob Weinberg, Addgene cat. no. 8454) and psPAX2 (a gift from Didier Trono, Addgene cat. no. 12260) plasmids at a ratio of 5.32:2.64:4, respectively, in the presence of polyethylenimine ‘Max’ (Polysciences) at 1:2 ratio of DNA to PEI-Max. Medium was exchanged after 16-24 hours to fresh hESC growth medium, and lentiviral particle-containing supernatant was collected ~65 hours after transfection, centrifuged at 3000 rpm for 10 minutes at 4°C and filtered using 0.45µM cellulose acetate filters (Millipore). For transduction, FXS-iPSCs were harvested using Trypsin-EDTA, centrifuged, and suspended in embryonic stem cell medium supplemented with 10µM ROCK inhibitor (Y27632) and 8 µg/ml polybrene (Sigma). The viruses were added to the cell suspension, and the cells were plated on MEFs overnight. After ~36 hours, the cells’ medium was replaced with puromycin-containing medium (0.3 mg/ml, Sigma). After 2-14 days selection with puromycin, cells were harvested for RNA extraction.

value: induced pluripotent stem cells

tag: infection

value: infected with lentiviral vector containing Cas9 and sgRNA targeting DNMT1


title: BMDM - GW3965 + 27HC.1


title: FXS-iPSCs DNMT1 rep2


title: H95_33103500276_v1: Newly diagnosed MM_31


title: H95_93029417313_v1: Newly diagnosed MM_32


title: CB-HSPC - DMSO_rep3

value: Umbilical cord blood-HSPCs

tag: culture period

value: Day 7

value: DMSO


title: H95_44393599343_v1: Newly diagnosed MM_35


title: PSND LCM EndCells_10

city: SHEFFIELD

first: Rachel

last: Waller

state: South Yorkshire

address: SITraN, 385A Glossop Road

department: Neuroscience

country: United Kingdom

institute: The University of Sheffield

description: Gene expression data from PSND endothelial cells

hyb_protocol: Approximately 5.5 μg amplified cDNA was fragmented, labelled and hybridised to Affymetrix Clariom S Array chips for 16 h at 45 °C in a rotating oven at 60 rpm

scan_protocol: Using the Fluidics Station 400, and Gene Chip Operating System, the hybridisation cocktail was removed, and a series of stringency washing steps followed to remove any unbound DNA, before each microarray was stained. Each microarray chip was scanned using the GeneChip 3000 scanner to determine the fluorescence intensity of hybridised transcripts.

data_processing: Transcription Analysis Console (TAC) was used for quality control and analysis of the data, the .CEL files were imported into TAC version 4.0.1 (Applied Biosystems, USA) and normalised to the median of all genes, prior to statistical analysis, to identify differentially expressed genes (DEGs). Transcripts were defined as being significantly differentially expressed if they showed a p-value of < 0.05 (unpaired t-test). DEGs were classified according to their biological function using the Database for Annotation Visualisation and Integrated Discovery (DAVID)  using Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis to identify specific pathways while Functional Annotation Clustering (FAC) was used to cluster together functionally similar genes. In the case of a significant result, the p value was adjusted for multiple testing using the Bonferroni correction method and considered significant if p < 0.05

label: Biotin

source_name: Laser capture miscrodissected endothelial cells from human PSND brain tissue

label_protocol: Target labelled mRNA was prepared following the GeneChip WT Pico amplification protocol (Affymetrix). RNA amplification was achieved using low-cycle PCR followed by amplification using T7 in vitro transcription. The cRNA was converted to biotinylated sense-strand DNA hybridisation targets.

growth_protocol: All samples were snap frozen and stored at -80°C

extract_protocol: Total RNA was extracted from each isolated group of cells using the PicoPure RNA isolation kit

treatment_protocol: Toluidine blue histologically stained pyramidal neurons, glial fibrillary acidic protein-positive (GFAP+)- astrocytes and collagen IV-positive (Coll-IV+)- endothelial cells were isolated from each human case (PSD, PSND and Control) using a PixCell II laser capture microdissection (LCM) system. Toluidine blue histologically stained pyramidal neurons were isolated from each mouse case (BCAS and SHAM) using a PixCell II laser capture microdissection (LCM) system.

value: M

tag: condition

value: PSND


title: BMDM - GSK2033.5

tag: treatment

tag: cell type

value: Bone marrow-derived macrophages (BMDM)


title: H95_97651650339_v1: Newly diagnosed MM_30

first: Mark

institute: Erasmus MC

value: Male


title: FXS-iPSCs Control rep4

value: infected with lentiviral vector containing Cas9 without a specfic sgRNA


title: BMDM - GSK2033.4


title: FXS-iPSCs Control rep3


title: H95_30933175219_v1: Newly diagnosed MM_29


title: H95_68092466641_v1: Newly diagnosed MM_28


title: FXS-iPSCs DNMT1 rep1


title: FXS-iPSCs Control rep2


title: FXS-iPSCs Control rep1


title: BMDM - GSK2033.3


title: BMDM - GSK2033.1


title: PSND LCM EndCells_9

value: F


title: Control LCM EndCells_10

description: Gene expression data from control endothelial cells

source_name: Laser capture miscrodissected endothelial cells from human control brain tissue

value: Control


title: BMDM - GSK2033.2


title: PSD LCM EndCells_9

description: Gene expression data from PSD endothelial cells

source_name: Laser capture miscrodissected endothelial cells from human PSD brain tissue

value: PSD


title: Control LCM EndCells_9


title: PSD LCM EndCells_10


title: H95_30406789186_v1: Newly diagnosed MM_26

value: Female


title: Control LCM EndCells_8


title: H95_60297585008_v1: Newly diagnosed MM_27


title: BMDM - GW3965.5


title: BMDM - GW3965.4


title: PSND LCM EndCells_8


title: H95_86492226861_v1: Newly diagnosed MM_24


title: BMDM - GW3965.3


title: U251T_vehicle_2

city: Huntsville

first: Sara

last: Cooper

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

data_processing:
Lexogen's QuantSeq Bluebee data analysis pipeline used for data processing
Genome_build: hg38
Supplementary_files_format_and_content: raw count table at the gene level for all 12 samples

growth_protocol: Gibco phenol red-free DMEM/F12 containing 2.5 mM L-glutamine and 17.5 mM glucose and supplemented with 10% FBS, B27 equivalent-Gem 21 (Gemini Biosciences), 20 ng/ml epidermal growth factor and fibroblast growth factor basic, 1% sodium pyruvate, and 1% penicillin/streptomycin. 5% CO2 and 21% O2

extract_protocol:
RNA was extracted with Total RNA Extration Kit with DNAse (Norgen)
QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen)

treatment_protocol: For these samples, cells were seeded and allowed to adhere. Then, they were serum starved overnight (16hr) followed by 24hr in the presence of the full media with DMSO or carmofur. Cell pellets were isolated at the end of that 24hr.

tag: cell line

tag: replicate #


title: U251T_vehicle_1


title: Control LCM EndCells_7


title: BMDM - GW3965.2


title: U251T_vehicle_3


title: H95_44945778546_v1: Newly diagnosed MM_22

city: Rotterdam

last: van Duin

address: Wytemaweg 80


title: U251T_Carm_2

value: Carmofur


title: U251T_Carm_1


title: H95_33350375676_v1: Newly diagnosed MM_20

value: bone marrow aspirate


title: BMDM - GW3965.1


title: H95_43011810355_v1: Newly diagnosed MM_21

value: multiple myleoma


title: BMDM - ICI.5

value: ICI


title: PSND LCM EndCells_7


title: H95_45295560206_v1: Newly diagnosed MM_25


title: BMDM - ICI.4


title: U251P_vehicle_3


title: Control LCM EndCells_6


title: PSD LCM EndCells_7


title: BMDM - ICI.3


title: PSD LCM EndCells_6


title: H95_26506671996_v1: Newly diagnosed MM_23


title: Control LCM EndCells_5


title: U251P_vehicle_1


title: H95_66242972109_v1: Newly diagnosed MM_17


title: H95_41822734775_v1: Newly diagnosed MM_18


title: U251P_Carm_3


title: PSD LCM EndCells_5


title: BMDM - ICI.2


title: H95_48538742214_v1: Newly diagnosed MM_19


title: U251T_Carm_3


title: BMDM - ICI.1


title: H95_73938687550_v1: Newly diagnosed MM_16


title: BMDM - E2.5


title: U251P_Carm_2


title: U251P_vehicle_2


title: H95_64091355837_v1: Newly diagnosed MM_15


title: PSND LCM EndCells_5


title: THP1 cells 1mM WFA 6 hours, rep3

city: London

first: Owen

last: Williams

address: 30 Guilford Street

department: Cancer section

institute: UCL GOS ICH

data_processing:
All tools in the analysis were invoked through the Galaxy Project for NGS analysis, as follows:
Fastq was demultiplexed and generated using Illumina bcl2fastq v2.19 before pre-processing (trimmomatic) to remove adapter read-through and poor quality sequences.
Pre-processed data were then aligned to the genome (UCSC hg38) with Bowtie 2 and deduplicated using Picard.
Reads-per-transcript were counted by FeatureCounts, before differential expresson analysis by SARTools, a DESeq2 wrapper.
Genome_build: hg38
Supplementary_files_format_and_content: complete_WFA_vs_DMSO.csv: average count values for each sample

growth_protocol: THP1 cells (AML cell line) (ATCC, Manassas, Virginia, United States) were maintained in culture in RPMI 1640 medium containing 10% fetal bovine serum, 100 units/ml penicillin and 100 ug/ml streptomycin at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted with RNeasy Plus Mini Kit according to manufacturers instructions
Indexed RNA libraries were prepared for sequencing using standard Illumina TruSeq RNA v2 protocols

treatment_protocol: THP1 cells were treated for 6 hours with DMSO or 1mM WFA.

tag: agent

value: WFA 1mM


title: H95_36160911021_v1: Newly diagnosed MM_14


title: U251P_Carm_1


title: BMDM - E2.4


title: BMDM - E2.3


title: H95_45671714120_v1: Newly diagnosed MM_13


title: PSND LCM EndCells_4


title: H95_70590289754_v1: Newly diagnosed MM_12


title: BMDM - E2.2


title: THP1 cells 1mM WFA 6 hours, rep2


title: BMDM - E2.1


title: THP1 cells DMSO 6 hours, rep3


title: BMDM - 27HC.5


title: H95_79093593121_v1: Newly diagnosed MM_10


title: BMDM - 27HC.4


title: THP1 cells DMSO 6 hours, rep1


title: H95_49394530211_v1: Newly diagnosed MM_9


title: BMDM - 27HC.3


title: PSND LCM EndCells_3


title: BMDM - 27HC.2


title: PSND LCM EndCells_6


title: PSD LCM EndCells_4


title: THP1 cells 1mM WFA 6 hours, rep1


title: H95_28035359704_v1: Newly diagnosed MM_8


title: CD4-T-cell HIV IFNb 8hr D2

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

description: G008_HIV01_scLatency_CD4-T-cell_HIV_IFNb_8hr_D2_Lib1

data_processing:
Read quality and alignment was performed with CellRanger count
Genome_build: hg19
Supplementary_files_format_and_content: these compressed files contain the barcode.tsv, feature.tsv and matrix.tsv files, the count data produced by CellRanger, that can easily be uploaded into Seurat or other analysis software

source_name: CD4-T-cell HIV IFNb 8hr

growth_protocol: PBMC were washed with complete RPMI and passed through mesh filters. CD4+ T cells were purified from PBMC by negative magnetic separation with a CD4+ T cell isolation kit (Miltenyi) using a QuadroMACS separator (Miltenyi) according to the manufacturer's instructions. Purified CD4+ T cells were cultured at 37°C and 5% CO2 in RPMI media supplemented with 10% FBS, 1% L-glutamine, 1% non-essential amino acids, 1% sodium pyrvuate, and 1% antibiotic/antimycotic cocktail (complete RPMI). Cells were cryopreserved in FBS containing 10% DMSO and stored at -80°C.

extract_protocol:
Cells were washed twice with cold PBS then viability assessed by Trypan Blue exclusion. Viable cell suspension was adjusted to 5 x 10^6 cells/ml in 200 μl cold PBS, then 800 μl cold methanol slowly added. Methanol-fixed cells were stored at -20°C until further sample processing. After two weeks, fixed cells were thawed, centrifuged and supernatant removed, then resuspended in rehydration buffer (SSC buffer supplemented with 1% BSA, 20 U/μl Superasein, and 1 M DTT). Single-cell suspensions were diluted to a cell concentration of 1,000 cells/µl for single-cell RNAseq.
Indexed libraries were prepared from 10 µl of cDNA using Chromium Next GEM Single Cell 3’ Reagent Kits v3 (10x Genomics). Library and cDNA quality were evaluated using the Agilent 2100 Bioanalyzer Instrument (Agilent) and quantified using the ViiA 7 Real-Time PCR system (ThermoFisher).
Constructed libraries were sequenced on an Illumina NextSeq 500/550 High Output v2 kit (Illumina). Each sample was sequenced to a depth of 40,000 reads per cell.

treatment_protocol: Thawed CD4+ T cells were cultured for 5 days in complete RPMI supplemented with homeostatic cytokines (IL-2, IL-7, IL15). CD4+ T cells were then seeded at a concentration of 2 x 10^6 cells/ml in 6-well plates and were spinoculated with complete RPMI media (mock control) or NanoLuc HIV (MOI 2.0) for 2h at 2400 rpm. Cells were washed three times with RPMI and cultured in T25 flasks for 24h in complete RPMI supplemented 20 U/ml IL-2, 10 ng/ml IL-7, and 50 ng/ml recombinant human IL-15. HIV replication was then suppressed for 7 days by treatment with ART consisting of 10 μM Raltegravir and 1 μM Efavirenz. Suppressed cells at 8 dpi were also seeded in 6-well plates at 2 x 10^6 cells per ml in complete RPMI + cytokines + ART, and were stimulated for 8h with 100 IU/ml IFN-β then fixed in methanol for single cell sequencing analysis

tag: subject id

value: Donor 2

tag: Sex

tag: smoking status

value: nonsmoker

tag: cmv status

value: CMV negative

value: Primary CD4 T cells

value: HIV infected + IFNb Treated


title: Control LCM EndCells_4


title: Control LCM EndCells_2


title: Control LCM EndCells_3

value: M


title: CD4-T-cell HIV 8hr D2

description: G007_HIV01_scLatency_CD4-T-cell_HIV_8hr_D2_Lib1

source_name: CD4-T-cell HIV 8hr

value: Male

value: HIV infected


title: BMDM - 27HC.1

value: Bone marrow-derived macrophages (BMDM)


title: PSND LCM EndCells_2

value: PSND


title: THP1 cells DMSO 6 hours, rep2

value: DMSO


title: CD4-T-cell M IFNb 8hr D2

description: G006_HIV01_scLatency_CD4-T-cell_M_IFNb_8hr_D2_Lib1

source_name: CD4-T-cell M IFNb 8hr

value: IFNb Treated


title: H95_44472878275_v1: Newly diagnosed MM_11

value: Female


title: H95_75107900786_v1: Newly diagnosed MM_6

value: bone marrow aspirate


title: H95_46490107996_v1: Newly diagnosed MM_7

value: multiple myleoma


title: BMDM - Vehicle.5

value: Vehicle


title: H95_93466300400_v1: Newly diagnosed MM_5


title: BMDM - Vehicle.4


title: CD4-T-cell HIV IFNb 8hr D1

description: G004_HIV01_scLatency_CD4-T-cell_HIV_IFNb_8hr_D1_Lib1

value: Donor 1


title: H95_21787494486_v1: Newly diagnosed MM_4


title: CD4-T-cell HIV 8hr D1

description: G003_HIV01_scLatency_CD4-T-cell_HIV_8hr_D1_Lib1


title: CD4-T-cell M IFNb 8h D1 IFNb treated

description: G002_HIV01_scLatency_CD4-T-cell_M_IFNb_8hr_D1_Lib1

source_name: CD4-T-cell M IFNb 8h IFNb treated


title: BMDM - Vehicle.3


title: H95_63759484796_v1: Newly diagnosed MM_2


title: CD4-T-cell M 8hr D2

description: G005_HIV01_scLatency_CD4-T-cell_M_8hr_D2_Lib1

source_name: CD4-T-cell M 8hr

value: Donor 2

value: mock


title: BMDM - Vehicle.2


title: H95_89034225809_v1: Newly diagnosed MM_3


title: CD4-T-cell M 8hr D1 mock

description: G001_HIV01_scLatency_CD4-T-cell_M_8hr_D1_Lib1

source_name: CD4-T-cell M 8hr mock

value: nonsmoker

value: CMV negative


title: H95_79099048168_v1: Newly diagnosed MM_1


title: BMDM - Vehicle.1


title: H143_99912777286_v1: Newly diagnosed MM_45

value: multiple myeloma


title: BMDM - Vehicle.6


title: PSD LCM EndCells_1

value: M

value: PSD


title: PSND LCM EndCells_1

value: F


title: PSND LCM Neurons_9

description: Gene expression data from PSND neurons

source_name: Laser capture miscrodissected neurons from human PSND brain tissue


title: PSND LCM Neurons_10

description: Gene expression data from PSND neurons


title: PSD LCM Neurons_10

description: Gene expression data from PSD neurons

source_name: Laser capture miscrodissected neurons from human PSD brain tissue


title: Control LCM Neurons_10

description: Gene expression data from control neurons

source_name: Laser capture miscrodissected neurons from human control brain tissue

value: Control


title: PSD LCM EndCells_3


title: Control LCM EndCells_1


title: PSD LCM EndCells_2


title: DSS_D14_F

city: Boston

first: Ilya

last: Korsunsky

state: MA

address: 77 Avenue Louis Pasteur

institute: Brigham and Women's Hospital

data_processing:
Reads mapped with Kallisto
Genome_build: GRCm 38, Gencode M25
Supplementary_files_format_and_content: Matrix of gene counts

source_name: Cd45-Epcam-Cd31-Pdpn+Pdgfra+ dissociated gut cells

extract_protocol:
Animal experiments were carried out under the relevant Home Office license at the University of Oxford (PPL: P508FFA1F). Female 7-week–old C57BL/6J mice were obtained from The Jackson Laboratory and housed in ventilated cages with 12-hour light cycles under specific pathogen-free conditions (SPF). They received food and water ad libitum. For induction of colitis, 2.5% w/v dextran sulfate sodium (DSS; MP Biomedicals) was supplemented in drinking water and given to mice for six consecutive days, with renewal on day three. After the treatment was ceased, mice returned to receiving standard water for the remaining time. Mice were monitored every day for alterations in body weight and clinical disease scores, until euthanised with carbon dioxide. Colons were resected, cleaned and washed in RPMI1640 supplemented with 5% fetal calf serum (FCS), 1% Penicillin-Streptomycin and 5mM EDTA for two total washes of 30 minutes and 20 minutes respectively at 37C to remove bulk epithelium. This was followed by tissue digestion using 100 g /ml Liberase TL and 40 g/ml DNAse for 3 x 1-hour cycles to dissociate all tissue into single-cell suspension. These were then stained with relevant reagents and antibodies (below) and FACS sorted (BD FACSAria III and BD FACSDiva 8.0.1) for live fibroblasts on CD45 -ve, EpCAM -ve, CD31 -ve, Podoplanin +ve, Pdgfra +ve cells at the time points described.
Cells were directly sorted into RNA lysis buffer and RNA was isolated using Zymo Quick RNA 96 kits as per the manufacturer’s instructions. Libraries were prepared using NEBNext ultra-low input RNA library prep with 1ng of RNA per sample and sequenced on a NovaSeq6000 (150 paired-end).
cDNA and library generation per manufacturer protocol.

tag: diease

value: DSS induced colitis

tag: day

tag: cage


title: H143_99804551870_v1: Newly diagnosed MM_44

tag: gender

value: Male

tag: age

tag: tissue


title: CC3-5

city: Chicago

first: Cambrian

middle: Yangshao

state: IL

address: 5841 S Maryland Ave

department: Department of Medicine

institute: The University of Chicago

description:
FT-SA08928_S33_L008
patient-derived iPSCs with NEUROG3-null mutation corrected by CRISPR/Cas9, line CC3, differentiated to pancreatic endocrine progenitor stage

data_processing:
Illumina Casava software was used for basecalling.
Abundance measurements (transcripts per million, tpm) were generated from pseudoalignment procedures in kallisto.
Genome_build: hg38
Supplementary_files_format_and_content: Comma-separated file includes tpm levels of individual transcripts for each sample.

source_name: patient iPSCs, then differentiated in vitro

growth_protocol: iPSCs were differenitated to the pancreatic endoderm and pancreatic progenitor stages using STEMCELL Technologies STEMdiff Pancreatic Progenitor Kit. Cells were further differentiated to pancreatic endocrine progenitor stage using the Kieffer 2014 protocol wherein MCDB131 media is supplemented with gamma secretase inhibitor, ALK5II, LDN193189, T3, Zinc sulfate, heparin, and ITS-X.

extract_protocol:
Samples were washed twice in PBS, and subjected to the RNAqueous kit by Invitrogen for RNA extraction.
Libraries were constructed using the Illumina Stranded mRNA library preparation kit and sequenced to obtain paired-end reads.

treatment_protocol: These cells were not treated with any factors not listed in the defined differentiation media.

value: corrected


title: DSS_D14_E

value: E


title: H143_97284639677_v1: Newly diagnosed MM_43

tag: disease state

value: bone marrow aspirate


title: DSS_D14_C

value: C


title: PSD LCM Neurons_9

description: Gene expression data from PSD neurons

tag: condition


title: DSS_D14_B

value: B


title: CC3-4

description:
FT-SA08927_S32_L008
patient-derived iPSCs with NEUROG3-null mutation corrected by CRISPR/Cas9, line CC3, differentiated to pancreatic progenitor stage


title: Control LCM Neurons_9


title: CC3-3

description:
FT-SA08912_S17_L008
patient-derived iPSCs with NEUROG3-null mutation corrected by CRISPR/Cas9, line CC3, differentiated to pancreatic endoder, stage


title: H143_95512868312_v1: Newly diagnosed MM_41


title: NN2-3

description:
FT-SA08929_S34_L008
patient-derived iPSCs, line NN2, differentiated to pancreatic endoderm stage

value: mutant


title: CC10-5

description:
FT-SA08926_S31_L008
patient-derived iPSCs with NEUROG3-null mutation corrected by CRISPR/Cas9, line CC10, differentiated to pancreatic endocrine progenitor stage


title: DSS_D14_A

value: A


title: H143_94102396117_v1: Newly diagnosed MM_40


title: Control LCM Neurons_8


title: PSND LCM Neurons_8

description: Gene expression data from PSND neurons

value: PSND


title: DSS_D11_F


title: DSS_D11_E


title: H143_93624264385_v1: Newly diagnosed MM_39

value: Female


title: CC10-4

description:
FT-SA08925_S30_L008
patient-derived iPSCs with NEUROG3-null mutation corrected by CRISPR/Cas9, line CC10, differentiated to pancreatic progenitor stage


title: NN2-5

description:
FT-SA08924_S29_L008
patient-derived iPSCs, line NN2, differentiated to pancreatic endocrine progenitor stage


title: H143_90232462705_v1: Newly diagnosed MM_38


title: H143_96755058147_v1: Newly diagnosed MM_42


title: PSD LCM EndCells_8

description: Gene expression data from PSD endothelial cells


title: NN2-4

description:
FT-SA08923_S28_L008
patient-derived iPSCs, line NN2, differentiated to pancreatic progenitor stage


title: DSS_D11_D

value: D


title: NN3-5

description:
FT-SA08922_S27_L008
patient-derived iPSCs, line NN3, differentiated to pancreatic endocrine progenitor stage


title: H143_87595859584_v1: Newly diagnosed MM_36

value: multiple myeloma


title: DSS_D11_C


title: H143_84330021249_v1: Newly diagnosed MM_35


title: H143_89726683769_v1: Newly diagnosed MM_37


title: DSS_D11_B


title: NN3-4

description:
FT-SA08921_S26_L008
patient-derived iPSCs, line NN3, differentiated to pancreatic progenitor stage


title: DSS_D11_A


title: NN3-3

description:
FT-SA08920_S25_L008
patient-derived iPSCs, line NN3, differentiated to pancreatic endoderm stage


title: PSD LCM Neurons_7

description: Gene expression data from PSD neurons

value: M


title: H1-5

description:
FT-SA08919_S24_L008
H1 ESCs differentiated to pancreatic endocrine progenitor stage

source_name: human H1 ESC line, then differentiated in vitro

value: control


title: H143_78086106590_v1: Newly diagnosed MM_34

source_name: bone marrow aspirate


title: Control LCM Neurons_7

value: F


title: PSD LCM Neurons_8

description: Gene expression data from PSD neurons

value: PSD


title: H143_75736348582_v1: Newly diagnosed MM_33


title: DSS_D9_E

value: DSS induced colitis


title: PSND LCM Neurons_7

description: Gene expression data from PSND neurons


title: Control LCM Neurons_6

value: Control


title: DSS_D9_D


title: H1-3

description:
FT-SA08917_S22_L008
H1 ESCs differentiated to pancreatic endoderm stage


title: PSD LCM Neurons_6

description: Gene expression data from PSD neurons


title: Control LCM Neurons_5


title: H143_69254957465_v1: Newly diagnosed MM_30

value: Male


title: H143_69507292376_v1: Newly diagnosed MM_31


title: DSS_D9_C


title: DSS_D9_B


title: H143_67136338923_v1: Newly diagnosed MM_28


title: PSD LCM Neurons_5

description: Gene expression data from PSD neurons


title: PSND LCM Neurons_6

description: Gene expression data from PSND neurons


title: PSND LCM Neurons_4

description: Gene expression data from PSND neurons


title: DSS_D9_A


title: PSND LCM Neurons_5

description: Gene expression data from PSND neurons


title: H143_62146312806_v1: Newly diagnosed MM_27


title: DSS_D7_E

value: E


title: DSS_D9_F


title: H1-4

description:
FT-SA08918_S23_L008
H1 ESCs differentiated to pancreatic progenitor stage


title: H143_73592528004_v1: Newly diagnosed MM_32

value: bone marrow aspirate


title: H143_61936532503_v1: Newly diagnosed MM_26


title: H143_60925049292_v1: Newly diagnosed MM_25


title: DSS_D7_C

value: C


title: DSS_D7_D


title: H143_68173853894_v1: Newly diagnosed MM_29


title: DSS_D7_B

value: B


title: PSD LCM Neurons_4

description: Gene expression data from PSD neurons


title: H143_59458239686_v1: Newly diagnosed MM_23


title: DSS_D7_F


title: DSS_D7_A


title: H143_50271695959_v1: Newly diagnosed MM_22


title: Control LCM Neurons_4


title: H143_49921048448_v1: Newly diagnosed MM_21


title: DSS_D4_F


title: PSND LCM Neurons_2

description: Gene expression data from PSND neurons


title: PSND LCM Neurons_3

description: Gene expression data from PSND neurons


title: H143_43886189351_v1: Newly diagnosed MM_20


title: H143_42664338057_v1: Newly diagnosed MM_19


title: DSS_D4_C


title: H143_59902067724_v1: Newly diagnosed MM_24


title: Control LCM Neurons_2


title: Control LCM Neurons_3


title: PSD LCM Neurons_1

description: Gene expression data from PSD neurons


title: H143_36676992427_v1: Newly diagnosed MM_17


title: DSS_D4_B


title: H143_37852117733_v1: Newly diagnosed MM_18


title: DSS_D4_E


title: Siha_ECD_Si_III

city: Omaha

first: Jordan

last: Rowley

state: NE

address: 3828 Jones St, Apt 202

institute: University of Nebraska Medical Center

data_processing:
Reads were aligned and mapped to reference genome using STAR
Peaks from bigwig files were visualized using IGV
TPM values were calculated using DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Cervical cancer cell line

growth_protocol: 293T cells were grown inDulbecco modified Eagle medium (Life Technologies, Grand Island,N.Y.) supplemented with 10% fetal calf serum(FCS) (Hyclone). Human cervical carcinoma cell lines HeLa(HPV18-positive), SiHa(HPV16-positive), CaSKi (HPV16-positive), were obtained from the American Type Culture Collection (Manassas, VA). Two independently-derived primary human foreskin keratinocyte lines (designated as 10HFK and 11HFK)were cultured in KGM medium (KGMTMKeratinocyte Growth Medium BulletKitTM, Lonza,). NTERT1 cell line (TERT immortalized keratinocytes) was kindly provided by Dr. James Rheinwald and has been described previously(Ref). The human immortalized keratinocyte cell line, HaCaT, were maintained in Dulbecco’s modified Eagle’s medium (DMEM) with 10% fetal bovine serum . HNCC cells SCC1, SCC10B, SCC11 and HCC38 were obtained (from Dr. Thomas Carey, University of Michigan, Ann Arbor, MI) and HPV+ve HNCC cell lines, UPCI:SCC090, UPCI:SCC152, and UPCI:SCC154, were obtained from S. Gollin, University of Pittsburgh Cancer Institute.These cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) with 10% fetal bovine serum. Cells were grown at 37°C in a humidified atmosphere with 5% CO2in alpha-MEM supplementedwith 10% FCS. Mycoplasmacontamination was examined by DAPI staining/fluorescence microscopy.

extract_protocol:
TRIzol reagent (Invitrogen) was used to isolate total RNA.
RNA libraries were prepared for sequecing using standard Illumina protocols

treatment_protocol: SiHacells were  transfected with Control siRNA and siRNA against ECD, PRPF8 orDDX39A,cells  were  collected  using  Trizol  reagent  and  RNA  was  isolated. RNA  was  analyzed  by UNMC genome facility for BIOANALYZERforpurity and then subjected to sequencing. Beginning with 800 ng of total RNA from each sample, RNAseq libraries were generated using the TruSeq Stranded RNA Library preparation kit (Illumina) per manufacturers recommended protocol. Libraries were multiplexed  together  and subjected  to  75 bp paired  end  sequencing  on  an  Illumina  NextSeq  500 instrument to generate approximately 25 M pairs of reads per sample. FASTq files were provided to the Bioinformatics and Systems Biology Core for further analysis.

tag: strain

value: SiHa


title: H143_36215534375_v1: Newly diagnosed MM_16


title: DSS_D4_A

value: A


title: DSS_D2_F


title: PSD LCM Neurons_2

description: Gene expression data from PSD neurons


title: PSND LCM Astrocytes_10

description: Gene expression data from PSND astrocytes

source_name: Laser capture miscrodissected astrocytes from human PSND brain tissue

value: PSND


title: PSND LCM Astrocytes_9


title: Control LCM Neurons_1

description: Gene expression data from control neurons


title: H143_35481538763_v1: Newly diagnosed MM_15


title: PSD LCM Astrocytes_10

description: Gene expression data from PSD astrocytes

source_name: Laser capture miscrodissected astrocytes from human PSD brain tissue


title: H143_34221056807_v1: Newly diagnosed MM_14

value: Female


title: Siha_ECD_Si_I


title: DSS_D2_D

value: D


title: DSS_D2_E


title: Siha_Ctl_III


title: H143_34194087698_v1: Newly diagnosed MM_13

value: multiple myeloma


title: Siha_Ctl_II


title: DSS_D2_C


title: H143_32025485018_v1: Newly diagnosed MM_12


title: H143_30826692821_v1: Newly diagnosed MM_11


title: Control LCM Astrocytes_9

description: Gene expression data from control astrocytes

source_name: Laser capture miscrodissected astrocytes from human control brain tissue


title: DSS_D2_A


title: Siha_ECD_Si_II


title: PSD LCM Astrocytes_9

value: M


title: H143_29580873118_v1: Newly diagnosed MM_10


title: PRP8_III


title: PSND LCM Astrocytes_8


title: H143_27424011493_v1: Newly diagnosed MM_9


title: Control LCM Astrocytes_7


title: SS_D14_G

value: Steady State

value: G


title: PRP8_II


title: PSD LCM Astrocytes_8

value: F

value: PSD


title: SS_D9_G


title: Control LCM Astrocytes_8

value: Control


title: Control LCM Astrocytes_6


title: H143_23906322534_v1: Newly diagnosed MM_8

value: Male


title: SS_D7_G


title: DSS_D2_B

value: DSS induced colitis


title: PRP8_I


title: PSD LCM Neurons_3

description: Gene expression data from PSD neurons


title: PSND LCM Astrocytes_7


title: H143_22685180872_v1: Newly diagnosed MM_7

value: bone marrow aspirate


title: MDMs_RNAseq_UT-rep4

city: Oxford

first: Ping

last: Zhang

address: Roosevelt Drive

department: Wellcome Centre for Human Genetics

institute: University of Oxford

description: MDMs_UT_rep123456_RPKM.bw; MDMs_UT_rep123456_RPKM_FR.bedgraph.gz.tbi;MDMs_UT_rep123456_RPKM_FR.bedgraph.gz

data_processing:
RNA Sequencing reads were trimmed using Trim Galore (version 0.6.2), and mapped to human genome assembly hg38 using the HISAT2 (version 2.1.0).  The aligned Binary-sequence Alignment Format (BAM) files were used to determine the transcript counts through featureCounts (version 1.6.2) and GENCODE annotations (release 31). For gene differential expression analysis, the raw read counts were used as input into the R package DESeq2 (version 1.28.1) for pair-wise comparisons. For differential exon usage analysis, a featureCounts readable GTF file for exonic regions was generated through (https://github.com/vivekbhr/Subread_to_DEXSeq). The number of reads overlapping with each exonic region was counted by featureCounts with parameters -p -f -O -s 2 -t exonic_part. The exonic regions with read counts ≥ 10 in at least 30% of samples were used as input into the R package DEXSeq (version 1.32.0). The strandedness of the RNA-seq reads was extracted using Samtools, and the normalized bidirectional bedgrapgh files were generated using Bedtools and Bedops. The RPKM (Reads Per Kilobase per Million mapped reads) normalized bigwig files were generated using the bamCoverage function of deepTools (version 3.3.1).
Differential analyses for chromatin accessibility (ATAC) and histone modifications (H3K27ac and H3K4me3) were processed via an in-house pipeline. Briefly, sequencing reads were aligned to human genome assembly hg38 using bowtie2. The resulting BAM files were filtered to remove non-uniquely mapped reads, non-properly paired reads, reads mapped to mitochondrial chromosome, duplicate reads and reads with a mapping quality score less than 30 using Picard (version 2.0.1) and Samtools (version 1.9). Peaks were called using MACS2 (version 2.1.0) with the appropriate input dataset (paired non-ChIP data were used as controls for histone modifications). ATAC peaks were called using parameters --nomodel --shift -100 --extsize 200, and H3K27ac and H3K4me3 peaks were called using --bw 200. Peaks that overlay the ENCODE Blacklist and with p value > 1e-08 were filtered out. Peaks called in at least 30% of samples were defined as recurrent, and merged as a list of coordinates to count the number of overlapping reads in each condition using htseq-count (version 0.6.1). Finally, the reads were normalized using DESeq2 and then pair-wise comparisons were performed to determine the differential (fold change >2, FDR < 0.05) ATACs and histone modifications per condition. Potential batch effect or technical variable was examined by principal component analysis and was included as a covariate in DESeq2 design formula. The normalized bigwig files showing the average sequencing depth across samples with same treatment were generated using wiggletools and wigToBigWig.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig; bedgraph

source_name: MDMs

growth_protocol: Peripheral blood samples were obtained from healthy volunteers and PBMC isolated by Ficoll-Paque centrifugation. Monocytes (CD14+), T-cells (CD4+ and CD8+) and B-cells (CD19+) were separated from peripheral blood mononuclear cells (PBMCs) by positive selection with magnetic MicroBeads (Miltenyi Biotec). The isolated CD14 monocytes were differentiated into macrophages (MDMs) by culturing cells for 6 days in RPMI-1640 (Sigma) supplemented with 20% FBS (Sigma), L-glutamine (Sigma), sodium pyruvate (Sigma), non-essential amino acids (Sigma) and 20 ng/mL M-CSF (Gibco). Induced pluripotent stem cell (iPSC) line (SFC840-03-03) was reprogramed from dermal fibroblasts from a healthy donor recruited by the Oxford Parkinson’s Disease Centre, and cultured with feeder-free TeSR-E8 media (STEMCELL) on tissue culture plates coated with Matrigel (Corning). iPSCs were then transferred into AggreWell plate (STEMCELL) with E8 media (Gbico) supplemented with 50ng/mL BMP4 (ThermoFisher), 50 ng/mL VEGF (ThermoFisher) and 20 ng/mL SCF (Miltenyi) for four days to generate Embryoid Bodies (EBs) which were then used for generation of macrophage precursor in XVIVO-15 media (Lonza) supplemented with 25 ng/mL IL-3 (Gibco), GlutaMax, 2-mercaptoethanol and 100 ng/mL M-CSF.

extract_protocol: RNA-seq library was prepared using a standardised rRNA depletion and dUTP protocol (NEB) followed by sequencing on either a HiSeq4000 or NextSeq500 platform.(Illumina) at the Oxford Genomics Centre (Wellcome Centre for Human Genetics, Oxford, UK). Omni-ATAC-seq and ChIP for histone modifications were amplified for optimized cycles and were subjected to sequencing using a HiSeq4000 platform (Illumina).

treatment_protocol: Cells were treated with 20 ng/ml LPS for 6 hours (HD) or 2 ng/ml LPS for 16 hours and subsequent 20 ng/ml LPS challenge for 6 hours (LDHD).

tag: cell type

value: monocyte-derived macrophage


title: SS_D4_G


title: MDMs_RNAseq_UT-rep3


title: SS_D2_G


title: MDMs_RNAseq_UT-rep2

description: MDMs_UT_rep123456_RPKM.bw; MDMs_UT_rep123456_RPKM_FR.bedgraph.gz.tbi;


title: PSD LCM Astrocytes_7


title: H143_17006911740_v1: Newly diagnosed MM_4


title: TNF_K 3

city: Beijing

last: Wu

address: No. 16, Nei Nanxiao Street, Dongzhimen, Dongcheng District

institute: Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences

description: gene_fpkm_all_samples.txt;transcript_fpkm_all_samples.txt

data_processing:
Briefly, The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads.
Following purification, the mRNA is fragmented into small pieces using divalent cations under 94℃ for 8 min. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers.
This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H.
These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters.
The products are then purified and enriched with PCR to create the final cDNA library.
Purified libraries were quantified by Qubit® 2.0 Fluorometer (Life Technologies, USA) and validated by Agilent 2100 bioanalyzer (Agilent Technologies, USA) to confirm the insert size and calculate the mole concentration. Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina NovaSeq 6000 (Illumina, USA).
Supplementary_files_format_and_content: Expression value of genes and transcripts

source_name: murine macrophage-like cell line

growth_protocol: The murine macrophage-like cell line (RAW264.7) was obtained from Cell Resource Center, IBMS, CAMS/PUMC (Beijing, China) and cultured in DMEM supplemented with 10% heat-inactivated fetal bovine serum and antibiotics (100 U/mL penicillin and 100 U/mL streptomycin) at 37 °C in a humidified atmosphere containing 95% O2 and 5% CO2 atmosphere.

extract_protocol:
Total RNA was isolated using an RNeasy mini kit (Qiagen, Germany) according to the manufacturer’s protocol. RNA integrity was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The quantity of total RNA in the samples was measured using a Qubit®3.0 Fluorometer (Thermo Fisher Scientific, USA) and NanoDrop One (Wilmington, DE, USA).
Paired-end libraries were synthesized by using the TruSeq™ RNA Sample Preparation Kit (Illumina, USA) following TruSeq™ RNA Sample Preparation Guide. Briefly, the poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under 94℃ for 8 min. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library. Purified libraries were quantified by Qubit® 2.0 Fluorometer (Life Technologies, USA) and validated by Agilent 2100 bioanalyzer (Agilent Technologies, USA) to confirm the insert size and calculate the mole concentration. Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina NovaSeq 6000 (Illumina, USA). The sequencing work was undertaken by Beijing Zhimei Yinuo Biotechnology Co., Ltd (Beijing, China).

value: macrophage

tag: treatment

value: treated with WBG and TNF-α for 24 hours

value: BALB/c


title: H143_17226505219_v1: Newly diagnosed MM_5

growth_protocol: primary human tissue


title: Control LCM Astrocytes


title: Control LCM Astrocytes_5


title: H143_12250278397_v1: Newly diagnosed MM_2


title: MDMs_RNAseq_LDHD-rep3

description: MDMs_LDHD_rep123456_RPKM.bw; MDMs_LDHD_rep123456_RPKM_FR.bedgraph.gz.tbi;  MDMs_LDHD_rep123456_RPKM_FR.bedgraph.gz


title: PSD LCM Astrocytes_6


title: TNF_K 2


title: SS_D0_G


title: PSND LCM Astrocytes_6

value: PSND


title: PSD LCM Astrocytes_5


title: PSND LCM Astrocytes_5


title: H143_15899371102_v1: Newly diagnosed MM_3

value: Female


title: MDMs_RNAseq_UT-rep1

description: MDMs_UT_rep123456_RPKM.bw; MDMs_UT_rep123456_RPKM_FR.bedgraph.gz.tbi;   MDMs_UT_rep123456_RPKM_FR.bedgraph.gz


title: PSND LCM Astrocytes_4


title: MDMs_RNAseq_LDHD-rep4


title: PSND LCM Astrocytes_3


title: H143_19913049186_v1: Newly diagnosed MM_6


title: MDMs_RNAseq_LDHD-rep2


title: ESO-51

city: Cambridge

first: David

last: Shorthouse

address: Hutchison/MRC Research Centre

institute: MRC Cancer Unit

data_processing:
Quality control of raw sequencing reads was performed using FastQC v0.11.7.
Reads were aligned to GRCh37 using STAR v2.6.1d.
Read counts were generated within R 3.6.1 summarizeOverlaps. Reads are pooled from 3 lanes
Genome_build: GRCh37
Supplementary_files_format_and_content: comma delimited file containing read counts for every gene in every sample
Supplementary_files_format_and_content: tab delimited file for each sample containing FPKM values for each gene

source_name: Gastric cardia adenocarcinoma

growth_protocol: Human oesophageal cancer cell lines; OACP4 C (RRID: CVCL_1843), OE19 (RRID: CVCL_1622), FLO-1 (RRID: CVCL_2045), SK-GT-4 (RRID: CVCL_2195), ESO-26 (RRID: CVCL_2035), OE33 (RRID: CVCL_0471), ESO-51 (RRID: CVCL_2036), OAC,5.1 C (RRID: CVCL_1842), JH-EsoAd1 (RRID: CVCL_8098) were  preserved in a cell culture incubator set at 5% CO2, 37°C and subcultured to 80% confluency according to supplier instructions.

extract_protocol:
Cell pellets were homogenised using QIAshredder columns (Qiagen, 79656) and total RNA was purified using the RNeasy Mini Kit (Qiagen, 74106) as per manufacturer instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Oesophageal Adenocarcinoma

tag: cell line

value: ESO-51 (RRID:CVCL_2036)


title: H143_11405259490_v1: Newly diagnosed MM_1

data_processing:
Paired end sequencing was performed on an Illumina NovaSeq 6000 using 101 cycles for each mate.
Fastq files were constructed using bcl2fastq (v2.20.0.422).
Illumina universal adapters   were removed using trim_galore (v0.4.4).
Pseudo counts were measured on the trimmed Fastq files using  salmon (v1.3.0) using the default settings.
Salmon performed according to reference DOI:10.1038/NMETH.4197
Genome_build: GRCh37
Supplementary_files_format_and_content: Salmon, read counts

extract_protocol:
RNeasy
RNA Seq libraries were generated with the mRNA HyperPrep Kit (KAPA, catalog number 08105952001/KK8544), according to manufacturer’s instructions.

value: multiple myeloma


title: MDMs_RNAseq_HD-rep3

description: MDMs_HD_rep123456_RPKM.bw; MDMs_HD_rep123456_RPKM_FR.bedgraph.gz.tbi;  MDMs_HD_rep123456_RPKM_FR.bedgraph.gz


title: TNF_K 1


title: PSD LCM Astrocytes_4

value: M