title: multimer_MSK1263_R7-R8_TCR

city: Stanford

first: Ansuman

middle: T

last: Satpathy

address: 240 Pasteur Drive

institute: Stanford University

data_processing:
Reads were processed with Cell Ranger v7.0.0
R1 contains barcode at 1-16bp and UMI at bp 17-26
R2 contains the biological sequence
I1 contains the i5 sample index
I2 contains the i7 sample index
Assembly: hg19
Supplementary files format and content: "clonotypes.csv" contains TCR clonotype information, "filtered_contig_annotations.csv" contains productive TCR contigs per cell, "consensus_annotations.csv" contains clonotype consensus annotations.
Library strategy: TCR-seq

molecule: polyA RNA

source_name: tumor

extract_protocol: 10x Chromium Next Gem Single Cell V(D)J Reagent Kit (v2)

tag: patient

tag: region

value: CD3+CD8+multimer+ lymphocytes


title: 16_ATAC_AK358_8hr_invading, biol rep 3

status: Public on Feb 13 2023

type: SRA

city: Philadelphia

first: Arjun

last: Raj

state: PA

address: 415/420 Clinical Research Building, 415 Curie Boulevard

department: Department of Bioengineering

country: USA

institute: University of Pennsylvania

description: Alignment reference genome hg38

library_source: genomic

data_processing:
ATAC reads were aligned to the human genome (hg38) assembly using bowtie2 v2.3.4.1, filtered out low-quality alignments with samtools v1.1, removed duplicate read pairs with picard 1.96, and generated artificial single-ended text-based alignment files containing inferred Tn5 insertion points with custom python scripts and bedtools v2.25.0.
Peaks from ATAC sequencing were called using MACS2 2.1.1.20160309 with the command, “macs2 callpeak --nomodel --nolambda --keep-dup all --call-summits -B --SPMR --format BED -q 0.05 --shift 75 --extsize 150”.
Assembly: hg38
Supplementary files format and content: Data provided as wiggle files and tab-delimited files of ATAC-seq peaks.

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: FS4 and 1205Lu cells were mantained in DMEM with glutamax and 10% serum at 37°C and 5% CO2.

extract_protocol:
Nuclei from early-, late-, and non-invaders were extracted from 50,000 lysed cells and collected in lo-bind tubes. DNA tagmentation was performed using the Illumina Tagment DNA Enzyme TDE1 (20034197).
Libraries were prepared using custom primer indices follwed by double-sided bead purification using Agencourt AM Pure XP magnetic beads (A63880).
Libraries were tested for average fragment length using Agilent High Sensitvity DNA Kit (5067-4626) and the concentration was tested using Qubit™ dsDNA HS kit (#Q32851, Invitrogen).
ATAC-seq; Samples were run as paired-end using 150-cycle NextSeq 500/550 High Output Kit v2.5.

treatment_protocol: Early-, late-, and non-invading cells were collected for analysis.

tag: cell line

tag: cell type

value: Melanoma cells

tag: treatment

value: invading, 8 hours


title: 11_ATAC_AK357_sema3c_high1, tech rep 1, biol rep 2

description: Alignment reference genome hg38


title: multimer_MSK1263_R7-R8_FB

state: CA

library_source: transcriptomic

data_processing:
Reads were processed with Cell Ranger v7.0.0.
R1 contains barcode at 1-16bp and UMI at bp 17-26.
R2 contains the biological sequence.
I1 contains the i5 sample index.
I2 contains the i7 sample index.
Assembly: hg19
Supplementary files format and content: "barcodes.tsv.gz" contains filtered cellular barcodes, "features.tsv.gz" contains genes and features, "matrix.mtx.gz" contains the barcoded gene expression and feature matrices.
Library strategy: Antigen associated capture

extract_protocol: 10x Chromium Next Gem Single Cell V(D)J Reagent Kit (v2).


title: multimer_MSK1263_R1-R6_TCR


title: multimer_MSK1263_A1-A4_TCR

source_name: adrenal tumor


title: multimer_MSK1263_LN7-9-10-12_FB

source_name: lymph node


title: multimer_MSK1263_R1-R6_RNA

data_processing:
Reads were processed with Cell Ranger v7.0.0.
R1 contains barcode at 1-16bp and UMI at bp 17-26.
R2 contains the biological sequence.
I1 contains the i5 sample index.
I2 contains the i7 sample index.
Assembly: hg19
Supplementary files format and content: "barcodes.tsv.gz" contains filtered cellular barcodes, "features.tsv.gz" contains genes and features, "matrix.mtx.gz" contains the barcoded gene expression and feature matrices.


title: multimer_MSK1263_R7-R8_RNA


title: multimer_MSK1263_A1-A4_FB


title: 10_ATAC_AK357_non_invading, biol rep 2

description: Alignment reference genome hg38

value: non invading


title: 8_ATAC_AK357_8hr_invading, biol rep 2

description: Alignment reference genome hg38


title: multimer_MSK1263_R1-R6_FB


title: XHT1

city: Changsha

first: Shiying

last: Zhang

address: Xueshi Road No. 300

country: China

institute: Hunan University of Chinese Medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.  We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
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. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as  differentially expressed.

molecule: total RNA

organism: Rattus norvegicus

source_name: Myocardial tissue

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

tag: tissue

value: Myocardial tissue

tag: genotype

value: Sprague-Dawley rats

value: XHT + Rat acute myocardial infarction model


title: multimer_MSK1263_LN7-9-10-12_RNA


title: 7_ATAC_AK357_parental_control, biol rep 2

description: Alignment reference genome hg38

value: parental


title: XHT2


title: 9_ATAC_AK357_16hr_invading, biol rep 2

description: Alignment reference genome hg38

value: invading, 16 hours


title: 6_ATAC_AK356_sema3c_low, biol rep 1

description: Alignment reference genome hg38


title: multimer_MSK1263_A1-A4_RNA


title: MSAMcyc4.2

city: Raleigh

first: Heike

last: Sederoff

state: NC

address: 851 Main Campus Dr

department: Plant & Microbial Biology

institute: North Carolina State University

data_processing:
QC metrics were obtained using FastQC and high-quality (Q>30) read pairs were mapped to RefSeq GCF_000188115.4 using HISAT2 with default parameter settings
Aligned reads were assigned genomic features according to Araport11 (arabidopsis) or Gifu v1.2 (lotus) annotations using featureCounts and read abundances quantified at the isoform level with default parameter settings
Raw counts were filtered for zero and low counts (<2) and library normalization was performed using DESeq2 size factor estimates
Assembly: Arabidopsis: TAIR10 INSDC Assembly GCA_000001735.1; Lotus: LotusBase Lotusjaponicus_Gifu_v1.2
Supplementary files format and content: Text files with counts for each sample by gene isoform

organism: Lotus japonicus

source_name: root

growth_protocol: Plants were grown in sterile conditions in a growth chamber on one of two media types, dependent upon treatment.

extract_protocol:
A PureLink RNA mini on-column kit with TRIzol with on-column DNAse treatment
The mRNA library was prepped by BGI Genomics Co., Ltd with polyA selection by an oligo dT library
Arabidopsis and lotus samples were multiplexed, pooled and loaded onto a DNBSEQ Technology Platform sequencer, separately by species

treatment_protocol: Plants were grown on either 1/2 MS medium or LN (low-nutrient) medium. +AM designated treatments were exposed to Rhizophagus AM fungi prior to root tissue sampling.

value: root

value: cyc4 mutant line

tag: background ecotype

value: gifu

tag: media

value: 1/2 MS medium

tag: am presence

value: +AM


title: MSAMcyc4.3


title: MOD3

value: Rat acute myocardial infarction model


title: MOD2


title: MSAMgifu4

value: wildtype

value: 1/2| +AM|gifu


title: MSAMcyc4.1


title: 5_ATAC_AK356_sema3c_high, biol rep 1

description: Alignment reference genome hg38


title: 4_ATAC_AK356_non_invading, biol rep 1

description: Alignment reference genome hg38


title: Donor 2, s-93

city: Oslo

first: Yohan

last: Lefol

state: Oslo

address: Sognsvannsveien 20 Rikshospitalet

department: Institute of Clinical Medicine

country: Norway

institute: University of Oslo

data_processing:
Sequencing was done on the Illumina NovaSeq platform using an S2 flow cell with 2*50 bp reads. 8’379’591’470 passed filter reads were produced with a mean Q of 36, equaling 63 Mio read pairs per sample on average. The produced double-end reads which passed Illumina’s chastity filter were subject to de-multiplexing and trimming of Illumina adaptor residuals using Illumina’s bcl2fastq software version 2.20.0.422 (no further refinement or selection). Quality of the reads in fastq format was checked with the software FastQC (17) (version 0.11.8). Raw reads having average Q-values below 20 or incorporating uncalled ‘N’ bases were filtered using the BBTools software suite (18) (version 38.86). The splice aware RNA mapping software STAR(19) (version 2.7.7a) was used to map the surviving reads to the reference genome UCSC hg38 provided by IGenomes. To count the uniquely mapped reads to annotated genes, the software htseq-count (20) (HTSeq version 0.13.5) was used. DNA extraction, library construction, sequencing and data analysis described in this section were performed by Microsynth AG (Balgach, Switzerland).
Assembly: reference genome UCSC hg38 provided by Igenomes
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: PBMC

extract_protocol:
Cells were pelleted by centrifugation and flash frozen with liquid nitrogen. Cell pellets were then shipped on dry ice. A human cell pellet from a blood sample was used as a positive control. Samples in 96-well plate were placed on dry ice and 3 times 150 ul of RNA shield (DNA/RNA Shield by Zymo, Cat. No. R1100-250) was added. The pellets were resuspended in RNA shield and the plate was transferred to room temperature and incubated at room temperature (RT) for 30 min. The plate was centrifuged for 4 min at 5,400 g. Supernatant was transferred to a new plate and remaining pellets were frozen. Qiagen’s RNeasy Plus 96 Kit (cat. no. 74192) was used for RNA isolation. RLT buffer was supplemented with β-mercaptoethanol (β-ME) before use. 1 volume of RLT plus buffer was added to samples, and samples were mixed by vigorous shaking. The following steps were according to the RNeasy® Plus 96 Handbook, as available from https://www. qiagen.com/de/resources/download.aspx? id=4842d50e-a987-477a-a819-98a017445ccd& lang=en. RNA was eluted with 45 ul of RNAse free water. Next, samples were quantified with RiboGreen RNA Reagent, RediPlate™96 RiboGreen™RNA Quantitation Kit, cat. No. R11490.
Libraries were prepared using an RNA Kit from Takara (Takara Bio USA, Inc. SMARTer® Stranded Total RNA- Seq Kit v2 - Pico Input Mammalian) according to the manufacturer’s instructions. Libraries were then pooled and analyzed by Agilent 5200 Fragment Analyzer system (Agilent Technologies) for quantity and size distribution.

value: PBMC

tag: individual

value: Donor 2

value: IgM

tag: time

value: Day 3


title: Donor 2, s-94

value: Day 9


title: multimer_MSK1263_LN7-9-10-12_TCR

value: CD3+CD8+multimer+ lymphocytes


title: MOD1

value: Myocardial tissue

value: Sprague-Dawley rats


title: MSAMgifu3


title: 3_ATAC_AK356_16hr_invading, biol rep 1

description: Alignment reference genome hg38

value: Melanoma cells

value: invading, 16 hours


title: XHT3

value: XHT + Rat acute myocardial infarction model


title: sams5_3

city: Worcester

first: Amy

middle: K

last: Walker

state: Massachusetts

address: Suite 137, Biotech 2, 373 Plantation St

department: Program in Molecular Medicine

institute: UMass Chan Medical School

data_processing:
RNA for deep sequencing was purified by Qiagen RNAeasy. Duplicate samples were sent for library construction and sequencing at BGI (China)
Raw sequencing reads were processed using an in-house RNA-Seq data processing software Dolphin at University of Massachusetts Medical School
The raw read pairs were first aligned to C. elegans reference genome with ws245 annotation. The RSEM method was used to quantify the expression levels of genes
Deseq was used to produce differentially expressed gene sets with more than a 2-fold difference in gene expression, with replicates being within 0.05 in a Students T test and a False Discovery Rate (FDR) under 0.01.
Statistics were calculated with DeBrowser
Assembly: ce11 with ws254 notations
Supplementary files format and content: abundance measurements

organism: Caenorhabditis elegans

source_name: C. elegans N2 ; sams5 RNAi

growth_protocol: C. elegans (N2) were cultured using standard laboratory conditions on E. coli OP50.  Adults were bleached onto RNAi plates and allowed to develop to the L4 to young adult at 20C

extract_protocol:
Young adult C. elegans were lysed in 0.5% SDS, 5% b-ME, 10 mM EDTA, 10 mM Tris-HCl pH 7.4, 0.5 mg/ml Proteinase K, then RNA was purified with Tri-Reagent (Sigma)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: whole body

tag: temperature

tag: strain

value: sams5 RNAi


title: sams5_2


title: 2_ATAC_AK356_8hr_invading, biol rep 1

description: Alignment reference genome hg38

value: invading, 8 hours


title: MSAMgifu2

value: root

value: gifu

value: 1/2 MS medium

value: +AM


title: MSAMgifu1

value: wildtype

value: 1/2| +AM|gifu


title: sams5_1


title: MSnoAMcyc4.3

value: cyc4 mutant line

value: -AM


title: Donor 2, s-88

value: PBMC

value: Donor 2

value: TGF

value: Day 3


title: Donor 2, s-84

value: LPS

value: Day 9


title: MSnoAMcyc4.2


title: Donor 2, s-87

value: Day 1


title: 21_AK472_cas9, biol rep 3

description: Alignment reference genome hg38

value: Melanoma cells

value: cas9 only


title: sams4_2

source_name: C. elegans N2 ; sams4 RNAi

value: whole body

value: sams4 RNAi


title: 23_AK472_sc2, tech rep 2, biol rep 3

description: Alignment reference genome hg38

value: AAVS control


title: Donor 2, s-83


title: sams4_1


title: 22_AK472_sc1, tech rep 1, biol rep 3

description: Alignment reference genome hg38


title: MSnoAMgifu4

value: root

value: gifu

value: 1/2 MS medium

value: 1/2| -AM|gifu


title: MSnoAMcyc4.1

value: cyc4 mutant line

value: -AM


title: sams4_3


title: 20_AK472_16, tech rep 3, biol rep 3

description: Alignment reference genome hg38

value: NKX2.2 knockdown


title: Donor 2, s-92

value: PBMC

value: Donor 2

value: IgM


title: Donor 2, s-89

value: TGF

value: Day 9


title: 19_AK472_14, tech rep 2, biol rep 3

description: Alignment reference genome hg38

value: Melanoma cells


title: Donor 2, s-79

value: Control


title: Donor 2, s-82

value: LPS

value: Day 1


title: sams3_2

source_name: C. elegans N2 ; sams3 RNAi

value: whole body

value: sams3 RNAi


title: MSnoAMgifu3

value: root

value: wildtype

value: gifu


title: MSnoAMgifu2

value: 1/2 MS medium

value: 1/2| -AM|gifu


title: 1_ATAC_AK356_parental_control, biol rep 1

description: Alignment reference genome hg38

value: parental


title: MSnoAMgifu1

value: -AM


title: Donor 2, s-78

value: PBMC

value: Donor 2

value: Day 3


title: 18_AK472_13, tech rep 1, biol rep 3

description: Alignment reference genome hg38

value: NKX2.2 knockdown


title: sams3_1


title: EV3

source_name: C. elegans N2 ; control RNAi

value: control RNAi


title: 16_AK470_sc3, tech rep 3, biol rep 2

description: Alignment reference genome hg38

value: Melanoma cells

value: AAVS control


title: 17_AK472_parental, biol rep 3

description: Alignment reference genome hg38


title: EV2


title: MIS55 SG NK cells, d120 ost MCMV infection

city: Clayton

first: David

middle: Richard

last: Powell

state: VIC

address: Wellington Road

department: Bioinformatics Platform

country: Australia

institute: Monash University

library_source: transcriptomic single cell

data_processing:
cellranger count
Assembly: mm10
Supplementary files format and content: HDF5 file containing matrix read counts for cells and genes

organism: Mus musculus

source_name: salivary glands

growth_protocol: cells were sequenced directly ex vivo from mouse salivary glands

extract_protocol:
10x
Single Cell 3' v3

treatment_protocol: Salivary glands were harvested from mice at day 120 post MCMV infection. A single cell suspension was prepared and stained with fluorescently conjugated antibodies to flow cytometrically sort NK cells (live CD45+TCRb- CD3-CD19-NKp46+CD49b+CD200r- cells) sequencing.

value: BALB/c

value: salivary glands

value: NK cells

tag: agent

value: Murine cytomegalovirus infection


title: sams3_3

value: whole body

value: sams3 RNAi


title: 14_AK470_sc1, tech rep 1, biol rep 2

description: Alignment reference genome hg38


title: Multiome_control_nr5a2_GFP_2.5dpf_head (snRNA-seq)

city: Los Angeles

first: Gage

last: Crump

state: California

address: 1425 San Pablo Street, BCC 403 Crump Lab

institute: Stem Cell Department at USC

description: genomic DNA and polyA RNA were collected from the same cell by 10x Genomics pipeline

data_processing:
Multi-omic libraries of snATACseq and snRNAseq from the same barcoded single nuclei were constructed per manufacturer’s instructions (10X Genomics, Chromium Next GEM Single Cell Multiome ATAC + Gene Expression, protocol CG000338). QC of libraries were checked with 4200 TapeStation system and Qubit dsDNA HS assay kit. Libraries were sequenced on Illumina HiSeq (control) or NextSeq (mutant) platforms. For sequencing snATACseq libraries, both Read1 and Read2 were extended to 60 cycles, whereas for sequencing snRNAseq libraries, Read2 was extended to 102 cycles for longer coverage. Sequencing reads were aligned to customized genome (built with GRCz11.fa, GRCz11.104.gtf and JASPAR2020.pfm and added GFP-CAAX and mCherry gene information). Alignment, peak calling for snATACseq data and cell calling were performed by Cell Ranger ARC v2.0.0 per manufacturer’s instructions (10X Genomics) to generate peak-by-cell and gene-by-cell count matrices.
Assembly: GRCz11
Supplementary files format and content: Each sample has one processed data output by Cell Ranger ARC v2.0.0: peak-by-cell and gene-by-cell count matrices in HDF5 format.

organism: Danio rerio

source_name: Jaw mesenchyme

growth_protocol: All experiments on zebrafish (Danio rerio) were approved by the Institutional Animal Care and Use Committee of the University of Southern California (IACUC protocol #20771 and #21151). Zebrafish are raised in vivarium under standard conditions maintained at 28.5°C with health and water conditions monitored daily.

extract_protocol:
Zebrafish embryos are screened for nr5a2:mGFP-DBD-del+ / scxa:mCherry+ and fin tips are collected for PCR-genotyping of oz3 allele (mutant) and wild-type allele (control) before 2 dpf. Control and mutant heads were decapitated between the eye and ear after anesthesia at 2.5 dpf. Dissected heads (twenty heads pre tube) were washed twice with fresh and iced Ringer’s solution (116mM NaCl, 2.6mM KCl, 5mM HEPES, pH 7.0), followed by dissociation at 28.5 °C for 40 min by mechanical - nutating and pipetting every 5 min and enzymatic - in pre-warmed protease solution (0.25% trypsin, 1 mM EDTA, pH 8.0, and 20 mg/mL Collagenase D (from stock of 400 mg/mL Collagenase D in HBSS) in PBS) until fully dissociated. Dissociation reaction is stopped by 6X stop solution (6 mM CaCl2 and 30% fetal bovine serum (FBS) in PBS). Dissociated cells were collected by centrifugation for 5 min, 2000 rpm at 4°C and washed by suspension solution (1% FBS, 0.8mM CaCl2, 50U/ml Penicillin, 0.05mg/ml Streptomycin in Leibovitz Medium) twice and filtered by cell strainer before sorting. Live cells were fluorescence-activated cell sorted (FACS) to isolate GFP+ and exclude the cytoplasmic stain Zombie Violet (control) or nuclear stain DAPI (mutant) into 0.04% BSA/ PBS at 4°C. Nuclei isolation was performed per manufacturer’s instructions (10X Genomics, protocol CG000169, low cell input protocol) with optimalization for zebrafish mesenchyme. FACS cells were pelleted for 15 min, 300 rcf at 4oC, and incubated with lysis buffer for 100 s on ice. Isolated nuclei were washed by Wash buffer and Nuclei buffer and checked for nucleus integrity under a fluorescence confocal microscope with DAPI staining before subjected to library construction.
To capture accessible chromatin and transcripts from the same cells per manufacturer’s instructions, accessible chromatin regions from isolated nuclei were first targeted and tagged by transposase. Tagged-chromatin and ployA mRNA from the same nuclei were pulled down and barcoded with the same sequences within isolated GEMs to achieve single-nuclei separation. Chromatin fragments were further indexed with sample-specific i7 indexes and linked with Illumina P5 and P7 sequences. Reverse transcription was performed in GEMs to synthesize cDNA from polyA mRNA. cDNAs were further fragmented and indexed with sample-specific i7 and i5 indexes and linked with Illumina P5 and P7 sequences. QC of libraries were checked with 4200 TapeStation system and Qubit dsDNA HS assay kit.

value: Jaw mesenchyme

tag: developmental stage

value: 2.5 dpf

tag: facs markers

value: Zombie- / GFP+


title: Donor 1, s-54

value: Donor 1

value: IgM

value: Day 9


title: Donor 1, s-53

value: PBMC

value: Day 3


title: EV1

value: control RNAi


title: Donor 1, s-52

value: Day 1


title: Multiome_control_nr5a2_GFP_2.5dpf_head (snATAC-seq)


title: Donor 1, s-49

value: TGF


title: Moricandia moricandioides, Re-Watering, water stress, biol rep M28s

city: Sesto Fiorentino

first: Giovanni

last: Emiliani

state: Firenze

address: vai Madonna del Piano, 10

country: Italy

institute: IPSP-CNR

data_processing:
Sequence assembly and expression statistics were performed by Nebion, and all the Moricandia RNAseq reads were aligned to a minimal set of coding sequences of the TAIR 10 release of the Arabidopsis genome (http://www.arabidopsis.org/) using BLAT (Kent, 2002) in protein space.
The expression values were computed by cross-mapping on a minimal Arabidopsis transcript reference. The mapping used BLAT with options "-t=dnax -q=dnax". TPM values and counts were computed from the best scoring mappings only: if reads mapped to multiple features, only the best mappings were kept.
Assembly: TAIR10
Supplementary files format and content: *.txt: Tab-delimited text files include TPM values for each Sample.

organism: Moricandia moricandioides

source_name: mature leaf

growth_protocol: Moricandia moricandioides (C3), Moricandia arvensis (C2) and Moricandia suffruticosa (C2) seeds were placed in trays containing Amsterdam medium (a 9:1 mix of washed sand and compost) and allowed to germinate. The trays were supplied with a commercially available nutrient solution (COMPO Concime Universale, NPK 7-5-7, B, Cu, Fe, Mn, Mo, Zn: COMPO Italia, Cesano Maderno, Italy) and kept within a plant growth room with a day/night temperature of 28/24˚C. Metal-halide lights were used to maintain a photosynthetically active radiation (PAR) of 800 μmol m-2 s-1 for 12 hours each day. After two weeks the plants were potted into 1.5 L square pots filled with Amsterdam medium and kept within the same growth room. The plants were watered to pot capacity every two days and each week provided with a commercial liquid plant fertiliser (COMPO Concime Universale) to facilitate nutrient availability at free access rates. The plants were grown for four weeks prior to the imposition of water deficit stress.

extract_protocol:
Total RNA was isolated using the RNeasy Plant Mini Kit (Qiagen, Germany) according to the manufacturer’s protocol and digested with DNase I using on-column Qiagen DNase, as per manufacturer’s instructions. The intactness of the RNA extracted was verified by 1% agarose-TBE gel electrophoresis total RNA concentration and purity was verified through NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific, USA) measurements.
After quality control on a Bioanalyzer 2100 (Agilent, Santa Clara, USA), RNASeq was performed on an Illumina HiSeq2500 platform at the Heinrich Heine University (Biologisch-Medizinisches Forschungszentrum.

treatment_protocol: The fraction of transpirable soil water (FTSW) method (Sinclair and Ludlow, 1986) was used to gauge the kinetics to soil drying of the Moricandia species with different photosynthetic physiologies. Thirty-five plants of equivalent size were selected for each species. On the evening prior to the imposition of water deficit, all of the plants were watered to pot capacity. The pots were then allowed to drain overnight and weighed the next morning and sealed within plastic bags to eliminate evaporation from the soil. The Gs of the plants was then recorded and assumed to represent 100% of potential Gs. The pots were weighed and Gs recorded every day. The water deficit treatment was imposed by withholding water from 15 of the pots and in the remaining pots water was replaced each day equivalent to the starting weight to serve as the control treatment. Opening of the bags for approximately 20 minutes each day enabled the exchange of gases between the soil and the atmosphere and prevented the soil becoming anoxic. When Gs declined to 10% of the starting Gs value in the water deficit treatment, or pot weight remained constant for three days, it was considered that all water within the soil available for transpiration had been exhausted (ie. 0% FTSW) and FTSW was calculated according to Sinclair and Ludlow (1986). After 10% Gs had been reached in the water deficit treatment, the plants were re-watered to their starting weight.

value: mature leaf

value: Water stress

value: Re-Watering

tag: stomatal conductance


title: 13_AK470_cas9, biol rep 2

description: Alignment reference genome hg38

value: Melanoma cells

value: cas9 only


title: 12_AK470_16, tech rep 3, biol rep 2

description: Alignment reference genome hg38

value: NKX2.2 knockdown


title: 15_AK470_sc2, tech rep 2, biol rep 2

description: Alignment reference genome hg38

value: AAVS control


title: Donor 2, s-77

value: Donor 2

value: Control


title: Moricandia moricandioides, Re-Watering, water stress, biol rep M26s


title: Moricandia moricandioides, Re-Watering, water stress, biol rep M27s


title: Donor 1, s-47

value: Donor 1


title: 11_AK470_14, tech rep 2, biol rep 2

description: Alignment reference genome hg38


title: Donor 1, s-48


title: 10_AK470_13, tech rep 1, biol rep 2

description: Alignment reference genome hg38


title: whole blood, 119_2

type: RNA

hyb_protocol: For hybridization on the microarrays 19 μl labelled cRNA were mixed with 10× Gene Expression Blocking Agent and 25× Fragmentation Buffer, incubated at 60°C for exactly 30 min before addition of 2× Hi-RPM Hybridization Buffer and 40 μl of the final hybridization mix were applied to SurePrint G3 Human Gene Expression v3 8x60K Microarrays (Agilent). The microarrays were hybridized at 65°C and 10 rpm for 17 hours in an Agilent Hybridization oven. After hybridization, the microarrays were disassembled in Gene Expression Wash Buffer 1 (Agilent) and washed in Gene Expression Wash Buffer 1 for 1 min followed by Gene Expression Wash Buffer 2 (Agilent) for 1 min. Triton X-102 was added to all wash buffers before use.

scan_protocol: The microarrays were scanned using the Agilent C microarray scanner and Agilent Scan Control software (v 8.4.1) and data extracted with Agilent Feature Extraction Software (v 10.7.3.1).

data_processing: Microarray data was processed/normalized using limma  version 3.48.1. Controls, outliers, and below background genes were removed, duplicate probes were then merged using the avereps function while using SustematicNames as the keys.

source_name: whole blood

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 25 ng total RNA using the the Low Input Quick Amp Labeling Kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions. The labelled cRNA were purified using RNeasy Mini Kit (Qiagen) and eluted in 30 μl nuclease-free water. cRNA yield and specific activity were assesed using NanoDrop ND-1000 UV-VIS Spectrophotometer.

extract_protocol: RNA was extracted from PAXgene RNA tubes using the PAXgene Blood miRNA Kit (Qiagen, Hilden, Germany) following the manufacturer's recommendations. RNA concentration and quality were assessed using NanoDrop ND-1000 UV-VIS Spectrophotometer (ThermoFisher, Waltham, MA) and the RNA was stored at -80°C.

value: patient 119

tag: disease state

tag: severity

value: Critical

value: whole blood


title: Donor 1, s-43

tag: cell type

value: PBMC

value: LPS

value: Day 3


title: whole blood, F008

value: patient F008

value: Healthy


title: Moricandia moricandioides, Re-Watering, control, biol rep M24c

value: mature leaf

tag: treatment


title: 8_AK468_sc3, tech rep 3, biol rep 1

description: Alignment reference genome hg38

tag: cell line


title: Moricandia moricandioides, Re-Watering, control, biol rep M23c

tag: tissue

tag: genotype

value: Re-Watering


title: Moricandia moricandioides, Re-Watering, control, biol rep M22c


title: whole blood, 138_1

value: patient 138

value: Non-critical


title: whole blood, 113_2

value: patient 113


title: Donor 1, s-39

value: Day 9


title: whole blood, 086_2

value: patient 086


title: whole blood, 059_2

value: patient 059


title: Donor 1, s-38

value: Donor 1

value: Control


title: Moricandia moricandioides, Re-Watering, control, biol rep M21c


title: 6_AK468_sc1, tech rep 1, biol rep 1

description: Alignment reference genome hg38

value: Melanoma cells

value: AAVS control


title: Moricandia moricandioides, Re-Watering, water stress, biol rep M25s

value: Water stress


title: Moricandia moricandioides, T2, water stress, biol rep M20s


title: 4_AK468_16, tech rep 3, biol rep 1

description: Alignment reference genome hg38

value: NKX2.2 knockdown


title: 5_AK468_cas9, biol rep 1

description: Alignment reference genome hg38

value: cas9 only


title: Donor 1, s-44

value: PBMC

value: LPS


title: Donor 1, s-37

value: Day 1


title: Moricandia moricandioides, T2, water stress, biol rep M19s

value: mature leaf


title: 9_AK470_parental, biol rep 2

description: Alignment reference genome hg38

value: parental


title: Donor 1, s-42


title: NPAD_52_OH_3_Day3

city: Iowa City

first: Aloysius

middle: John

last: Klingelhutz

state: IA

address: 3-604 BSB, 51 Newton Road

department: Microbiology and Immunology

institute: University of Iowa

data_processing:
Reads were converted from the native Illumina BCL format to fastq format, which were processed with a standard RNA-Seq pipeline, available through the open-source ‘bcbio-nextgen’ project (https://github.com/chapmanb/bcbio-nextgen).
The bcbio-nextgen pipeline runs qualimap, a computational tool that examines SAM/BAM alignment files and provides an overview of the data to detect common QC problems. Reads were aligned against the hg38 reference genomes using the ultra-rapid STAR aligner and concurrently pseudo-align reads to the transcriptome using the Salmon aligner.
Following alignment, expression values were summarized at the gene and transcript level. FeatureCounts was used for STAR-aligned data while Salmon performed its own internal quantitation, yielding estimated counts and values in length-normalized TPM (transcripts per million).
Raw counts at the gene and transcript level were used for differential gene expression (DEG) analysis using DESeq2. The sets of differentially expressed genes (DEGs) between PCB52- or 4-OH-PCB52-treated and DMSO-treated cells at the different time points were filtered to only include genes that showed an adjusted p-value  0.05. Lists were converted to Microsoft Excel format.

source_name: subcutaneous adipose tissue

growth_protocol: Immortal human subcutaneous preadipocytes were cultured in PGM2 media

extract_protocol:
RNA was extracted using Trizol followed by DNase treatment and column purification using Qiagen RNeasy columns
500 ng of Dnase treated total RNA was used to enrich for polyA containing transcripts using beads coated with oligo(dT) primers. The enriched RNA pool was fragmented, converted to cDNA and ligated to sequencing adaptors containing indexes using the Illumina TruSeq stranded mRNA sample prep kit. The molar concentrations of the indexed libraries were measured using the 2100 Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA) and combined equally into pools for sequencing.  The concentration of the pools were measured using the Illumina Library Quantification Kit (KAPA Biosystems, Wilmington, MA) and sequenced on the Illumina NovaSeq 6000 genome sequencer using 50 bp paired-end SBS chemistry with a minimum of 25 million reads per sample.

treatment_protocol: Cells were treated over a timecourse with 10 micromolar PCB52 or 4-OH-PCB52 or vehicle (DMSO)

value: preadipocytes

value: NPAD

tag: time of treatment

value: 3 days


title: NPAD_52_OH_2_Day3


title: 3_AK468_14, tech rep 2, biol rep 1

description: Alignment reference genome hg38


title: 7_AK468_sc2, tech rep 2, biol rep 1

description: Alignment reference genome hg38


title: NPAD_52_OH_1_Day3


title: whole blood, 129_1

value: patient 129

value: Critical

value: whole blood


title: 2_AK468_13, tech rep 1, biol rep 1

description: Alignment reference genome hg38


title: Moricandia moricandioides, T2, control, biol rep M16c

value: Control


title: whole blood, 046_2

value: patient 046

value: Non-critical


title: whole blood, 137_3

value: patient 137


title: whole blood, F006

value: patient F006

value: Healthy


title: Moricandia moricandioides, T2, control, biol rep M14c


title: 1_AK468_parental, biol rep 1

description: Alignment reference genome hg38

value: Melanoma cells


title: Moricandia moricandioides, T2, water stress, biol rep M17s

value: Water stress


title: NPAD_52_4_Day3


title: 21_AK485_parental, biol rep 3

description: Alignment reference genome hg38


title: 19_AK485_lateinvading, biol rep 3

description: Alignment reference genome hg38

value: late invading


title: 20_AK485_noninvading, biol rep 3

description: Alignment reference genome hg38

value: non invading


title: Moricandia moricandioides, T1, control, biol rep M10c

value: mature leaf


title: Moricandia moricandioides, T1, water stress, biol rep M8s


title: Moricandia moricandioides, T1, water stress, biol rep M12s


title: Moricandia moricandioides, T1, water stress, biol rep M7s


title: 18_AK485_fastinvading, biol rep 3

description: Alignment reference genome hg38

value: fast invading


title: NPAD_52_1_Day3

value: preadipocytes

value: NPAD


title: NPAD_52_2_Day3

value: 3 days


title: NPAD_52_3_Day3


title: NPAD_Veh_4_Day3

value: Vehicle


title: 17_AK485_parentalsort, biol rep 3

description: Alignment reference genome hg38


title: Moricandia moricandioides, T1, control, biol rep M9c


title: NPAD_Veh_2_Day3


title: Moricandia moricandioides, T1, control, biol rep M6c


title: NPAD_Veh_3_Day3


title: 16_AK485_sema3clow, biol rep 3

description: Alignment reference genome hg38


title: 15_AK485_sema3chigh, biol rep 3

description: Alignment reference genome hg38


title: NPAD_52_OH_4_Day1

value: 1 day


title: NPAD_Veh_1_Day3


title: 14_AK483_parental, biol rep 2

description: Alignment reference genome hg38

value: parental


title: 13_AK483_noninvading, biol rep 2

description: Alignment reference genome hg38


title: 12_AK483_lateinvading, biol rep 2

description: Alignment reference genome hg38


title: Moricandia moricandioides, T1, control, biol rep M5c

value: Control


title: Moricandia moricandioides, T0, control, biol rep M3s


title: Moricandia moricandioides, T0, control, biol rep M12c


title: Moricandia moricandioides, T0, control, biol rep M4s


title: whole blood, 119_1

value: patient 119

value: Critical

value: whole blood


title: NPAD_52_OH_3_Day1


title: NPAD_52_OH_2_Day1


title: Moricandia arvensis, Re-Watering, water stress, biol rep A42s

organism: Moricandia arvensis

value: IPK Gatersleben:MOR1

value: Re-Watering


title: Moricandia moricandioides, T0, control, biol rep M1c


title: whole blood, 127_3

value: patient 127


title: NPAD_52_4_Day1


title: whole blood, 086_1

value: patient 086


title: NPAD_52_OH_1_Day1


title: Moricandia arvensis, Re-Watering, water stress, biol rep A38s

value: Water stress


title: NPAD_52_3_Day1


title: whole blood, 059_1

value: patient 059

value: Non-critical


title: NPAD_52_2_Day1

value: preadipocytes


title: Moricandia arvensis, Re-Watering, water stress, biol rep A30s

value: mature leaf


title: NPAD_52_1_Day1

value: NPAD


title: 7_AK481_parental, biol rep 1

description: Alignment reference genome hg38

value: Melanoma cells


title: 9_AK483_sema3clow, biol rep 2

description: Alignment reference genome hg38


title: 8_AK483_sema3chigh, biol rep 2

description: Alignment reference genome hg38


title: 10_AK483_parentalsort, biol rep 2

description: Alignment reference genome hg38


title: 11_AK483_fastinvading, biol rep 2

description: Alignment reference genome hg38

value: fast invading


title: Moricandia arvensis, Re-Watering, water stress, biol rep A40s


title: whole blood, 137_2

value: patient 137


title: whole blood, 071_1

value: patient 071


title: 6_AK481_noninvading, biol rep 1

description: Alignment reference genome hg38

value: non invading


title: NPAD_Veh_4_Day1

value: Vehicle

value: 1 day


title: Moricandia arvensis, Re-Watering, control, biol rep A17c

value: IPK Gatersleben:MOR1

value: Control


title: whole blood, 043_2

value: patient 043

value: Critical

value: whole blood


title: Moricandia arvensis, Re-Watering, control, biol rep A13c

value: Re-Watering


title: 5_AK481_lateinvading, biol rep 1

description: Alignment reference genome hg38

value: late invading


title: whole blood, 071_2


title: whole blood, F005

value: patient F005

value: Healthy


title: whole blood, 046_1

value: patient 046

value: Non-critical


title: Moricandia arvensis, Re-Watering, control, biol rep A8c

value: mature leaf


title: Moricandia arvensis, Re-Watering, control, biol rep A10c


title: 3_AK481_parentalsort, biol rep 1

description: Alignment reference genome hg38

value: Melanoma cells


title: NPAD_Veh_3_Day1

value: preadipocytes

value: NPAD


title: NPAD_Veh_2_Day1

value: Vehicle


title: Moricandia arvensis, Re-Watering, control, biol rep A6c


title: whole blood, 058_2

value: patient 058


title: 2_AK481_sema3clow, biol rep 1

description: Alignment reference genome hg38


title: 1_AK481_sema3chigh, biol rep 1

description: Alignment reference genome hg38


title: whole blood, 127_1

value: patient 127


title: whole blood, 109_2

value: patient 109


title: Moricandia arvensis, T2, water stress, biol rep A44s

value: IPK Gatersleben:MOR1

value: Water stress


title: NPAD_52_OH_4_9h

value: 9 hours


title: NPAD_52_OH_3_9h


title: 4_AK481_fastinvading, biol rep 1

description: Alignment reference genome hg38

value: fast invading


title: whole blood, 113_1

value: patient 113

value: whole blood


title: NPAD_Veh_1_Day1

value: 1 day


title: Moricandia arvensis, T2, water stress, biol rep A37s


title: whole blood, 073_2

value: patient 073

value: Critical


title: whole blood, 127_2


title: whole blood, 109_1

value: Non-critical


title: whole blood, 137_1

value: patient 137


title: whole blood, 058_1


title: Moricandia arvensis, T2, water stress, biol rep A39s

value: mature leaf


title: whole blood, F004

value: patient F004

value: Healthy


title: RAMOS B cells, 1% oxygen + 1 µg/ml cyclosporine A, rep3

city: Rochester

first: Juilee

last: Thakar

state: New York

address: 601 Elmwood Ave

institute: University of Rochester

data_processing:
Data was formatted using bcltofastq-2.19.0
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic-0.36 with the following parameters: TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 SLIDINGWINDOW:4:20 MINLEN:35
Trimmed sequence reads were mapped to Reference Genome hg38/GencodeV28 using STAR_2.6.0c with the following parameters: --twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
Read quantification was performed using featureCounts from the R package subread version 1.34.7 using the GTF annotation file for genome assembly GRCh38.p12, setting parameters isGTFAnnotationFile=TRUE, GTF.attrType = 'gene_name" and isPairedEnd=FALSE and default values for other parameters.
Assembly: hg38/GencodeV28
Supplementary files format and content: counts_20221003.csv : comma-delimited text file with count values for each Sample in different columns
Supplementary files format and content: metadata.csv : comma-delimited text file with metadata for each Sample in different rows

source_name: RAMOS

growth_protocol: RAMOS cells were maintained in a 37 degree celsius, 5% CO2, humidified incubator in cR10 media (RPMI 1640 media supplemented with 10% heat inactivated fetal bovine serum (FBS), 50 U/mL Penicillin, 50 µg/mL Streptomycin and 50 µM 2-Mercaptoethanol).

extract_protocol: After incubation with CyA at the indicated oxygen conditions, cells were harvested by centrifugation and washed 3X with phosphate buffered saline (PBS). RNA was extracted from the resultant cell pellets using TRIzol™ Plus RNA Purification Kits according to the manufacturer's recommendations (Invitrogen).

treatment_protocol: RAMOS cells, in triplicate, were treated with either 0 or 1 µg/mL cyclosporine A (CyA) and incubated at either 19% oxygen (traditional tissue culture) or 1% oxygen for 24 hours.

value: RAMOS

value: B cells

value: 1% oxygen + 1 µg/ml cyclosporine A


title: NPAD_52_OH_2_9h

value: preadipocytes

value: NPAD


title: whole blood, 043_1

value: patient 043


title: RAMOS B cells, 1% oxygen + 1 µg/ml cyclosporine A, rep2


title: NPAD_52_OH_1_9h

value: 9 hours


title: whole blood, 062_3

value: patient 062


title: whole blood, 135_3

value: patient 135

value: whole blood


title: Moricandia arvensis, T2, water stress, biol rep A35s

value: IPK Gatersleben:MOR1

value: Water stress


title: whole blood, 096_2

value: patient 096

value: Non-critical


title: NPAD_52_4_9h


title: NPAD_52_3_9h


title: Moricandia arvensis, T2, water stress, biol rep A28s

value: mature leaf


title: RAMOS B cells, 1% oxygen, rep3

value: 1% oxygen


title: RAMOS B cells, 1% oxygen, rep2


title: whole blood, 091_2

value: patient 091


title: Moricandia arvensis, T2, control, biol rep A22c

value: Control


title: RAMOS B cells, 1% oxygen, rep1

value: RAMOS

value: B cells


title: RAMOS B cells, 1% oxygen + 1 µg/ml cyclosporine A, rep1

value: 1% oxygen + 1 µg/ml cyclosporine A


title: NPAD_52_2_9h

value: preadipocytes

value: NPAD


title: Moricandia arvensis, T2, control, biol rep A16c


title: NPAD_52_1_9h

value: 9 hours


title: RAMOS B cells, 19% oxygen + 1 µg/ml cyclosporine A, rep3

value: 19% oxygen + 1 µg/ml cyclosporine A


title: Moricandia arvensis, T2, control, biol rep A15c


title: whole blood, 073_1

value: patient 073

value: Critical


title: RAMOS B cells, 19% oxygen + 1 µg/ml cyclosporine A, rep2


title: whole blood, 022_2

value: patient 022

value: whole blood


title: RAMOS B cells, 19% oxygen + 1 µg/ml cyclosporine A, rep1


title: NPAD_Veh_2_9h

value: Vehicle


title: whole blood, 062_2

value: patient 062


title: Moricandia arvensis, T2, control, biol rep A9c

value: mature leaf

value: IPK Gatersleben:MOR1


title: whole blood, 057_2

value: patient 057

value: Non-critical


title: Moricandia arvensis, T2, control, biol rep A24c

value: Control


title: Moricandia arvensis, T1, water stress, biol rep A34s

value: Water stress


title: RAMOS B cells, 19% oxygen, rep3

value: RAMOS

value: B cells

value: 19% oxygen


title: NPAD_Veh_4_9h

value: preadipocytes

value: NPAD

value: 9 hours


title: NPAD_Veh_1_9h


title: RAMOS B cells, 19% oxygen, rep2


title: emphysema lung cells [TXP26]

city: San Francisco

first: Tien

last: Peng

address: 513 Parnassus Ave, Health Sciences East 1350

department: Department of Pulmonary Medicine

institute: University of California San Francisco

data_processing:
Data were processed according to the 10x Cellranger pipeline.
BAM files were generated with v2.1.1 10X Genomics Cellranger software using default parameters.
Gene-barcode matrices were generated from Cellranger v2.1.1 using default parameteres.
Genome_build: GRCh38
Supplementary_files_format_and_content: Cellranger outputs a .mtx file with the gene-barcode matrix. This matrix contains the counts of molecules per cell (UMI/cell) as determined after filtering and counting by Cellranger. The matrix is in market exchange format while the row (gene names) and columns (cell barcodes) are provided as TSV files. File formats are documented in Cellranger software manual.

source_name: Fresh sorted live human lung cells

extract_protocol:
Human lung distal fragments were digested with a cocktail of Collagenase Type I (225 U/ml, Thermo Fisher), Dispase (15 U/ml, Thermo Fisher) and Dnase (50 U/ml, Sigma). The cell suspension was then washed with FACS buffer (2% FBS in DMEM-F12). The mixture was passed through a 70 µm cell strainer and resuspended in RBC lysis buffer, before passing through a 40 µm cell strainer. DAPI was used to exclude dead cells. Doublets and dead cells were excluded based on forward scatter, side scatter, and DAPI fluorescence. Cells were sorted into FACS buffer. FACS analysis was performed by FACSDiva.
droplet-based single cell RNA-Seq: cDNA libraries were prepared for sequencing using standard protocol for the 10x Single Cell instrument, using Single cell 3' v2 chemistry kit.

tag: age

value: adult

value: lung (distal)

value: emphysema lung cells


title: whole blood, F002

tag: individual

value: patient F002

value: Healthy

value: whole blood


title: Moricandia arvensis, T1, control, biol rep A14c

value: mature leaf

value: IPK Gatersleben:MOR1

tag: time


title: RAMOS B cells, 19% oxygen, rep1


title: NPAD_Veh_3_9h

value: Vehicle


title: Moricandia arvensis, T1, control, biol rep A12c

value: Control


title: emphysema lung cells [TXP25]


title: emphysema lung cells [TXP24]


title: 220228_L2 ΔCTL0480 infected rep3

city: Omaha

first: Rey

last: Carabeo

state: Nebraska

address: 985900 Nebraska Medical Center

department: Pathology and Microbiology

institute: University of Nebraska Medical Center

data_processing:
CLC Genomics Workbench version 10.1.1 used for all data processing steps.
Adaptor sequences and low-quality reads were trimmed using default parameters, then aligned to the hg19 reference genome.
Transcripts per million (TPM) were calculated using default parameters.
An initial ANOVA-like pass of differential expression testing was performed. Genes that did not significantly vary between any of the three treatments were culled from downstream analysis.
Differential expression testing was performed using default paramters to identify differentially expressed genes in either L2-wt or L2ΔCTL0480-infected samples relative to the mock-infected control, accounting for variation between replicates.
Assembly: hg19
Supplementary files format and content: CLC file containing raw counts, TPM, and FDRP values for every gene and sample.

source_name: Primary endocervical epithelial cells

growth_protocol: Human primary endocervical epithelial cells (PCS-480-011, Lot 80306190) were cultured at 37C with 5% atmospheric CO2 in Cervical Epithelial Cell Basal Medium (CECBM, ATCC PCS-480-032) supplemented with all contents of the Cervical Epithelial Growth Kit (ATCC PCS-080-042), per manufacturer's instructions. Chlamydia trachomatis serovar L2/434/Bu was originally obtained from Dr. Ted Hackstadt (Rocky Mountain National Laboratory, NIAID), and the L2ΔCTL0480 mutant strain was provided by Dr. Derek Fisher and Dr. Erika Lutter.

extract_protocol:
Primary cells were harvested for Total RNA at 24 hpi using TRIzol (Thermo Fisher Scientific 15596026) and the DNA-free DNA removal kit (Thermo Fisher Scientific AM1906), according to manufacturers’ protocols, and were subsequently assayed for fragmentation using an Agilent Bioanalyzer 2100.
cDNA library preparation of intact samples was performed using the NuGEN Universal mRNA-Seq Library Preparation kit, according to the manufacturer's protocol.

treatment_protocol: Primary cells cultured to confluence (6-7 days) seeded on fibronectin-coated 6-well plates (Corning 354402) were washed with pre-warmed Hanks Buffered Saline Solution (HBSS) prior to inoculation with Chlamydia-containing CECBM at a multiplicity of infection (MOI) of 2. Tissue culture plates were centrifuged at 4C and 500 rcf (Eppendorf 5810 R tabletop centrifuge, A-4-81 rotor) for 15 minutes to synchronize infection. Inoculum was then aspirated, and cells were washed with chilled HBSS prior to the addition of pre-warmed KSFM. Infected cultures were then returned to the tissue culture incubator until 24 hours post-infection.

value: Primary endocervical epithelial cells

value: L2 deltaCTL0480 infected

tag: infection time

value: 24 hpi


title: whole blood, 091_1

value: patient 091

value: Non-critical


title: whole blood, 135_2

value: patient 135

value: Critical


title: Moricandia arvensis, T1, control, biol rep A3c


title: whole blood, 022_1

value: patient 022


title: normal human lung cells [NL_3]

value: adult

value: lung (distal)

value: normal human lung cells


title: 220228_L2 ΔCTL0480 infected rep1


title: whole blood, 057_1

value: patient 057


title: Moricandia arvensis, T1, control, biol rep A11c


title: 220228_L2 ΔCTL0480 infected rep2


title: Moricandia arvensis, T0, control, biol rep A48


title: whole blood, 066_2

value: patient 066

value: whole blood


title: whole blood, F009

value: patient F009

value: Healthy


title: Moricandia arvensis, T0, control, biol rep A46

value: mature leaf

value: IPK Gatersleben:MOR1

value: Control


title: whole blood, 096_1

value: patient 096


title: normal human lung cells [NL_2]


title: Moricandia arvensis, T0, control, biol rep A4


title: Moricandia arvensis, T0, control, biol rep A45


title: normal human lung cells [NL_1]


title: Moricandia suffruticosa, Re-Watering, water stress, biol rep S4s

organism: Moricandia suffruticosa

value: Royal Kew Garden:0105433

value: Water stress

value: Re-Watering


title: whole blood, 129_2

value: patient 129

value: Critical


title: MSK1344_R6_TCR

data_processing:
Library strategy: TCR-seq
Reads were processed with Cell Ranger v3.1.0
R1 contains barcode at 1-16bp and UMI at bp 17-26
R2 contains the biological sequence
I1 contains the i7 sample index
Genome_build: hg19
Supplementary_files_format_and_content: "clonotypes.csv" contains TCR clonotype information, "filtered_contig_annotations.csv" contains productive TCR contigs per cell, "consensus_annotations.csv" contains clonotype consensus annotations

source_name: tumor

extract_protocol: 10x Chromium Next Gem Single Cell V(D)J Reagent Kit (v1)

tag: patient

tag: region

value: CD3+ lymphocytes


title: whole blood, 086_3

value: patient 086


title: MSK1344_R7_TCR


title: MSK1344_R8_TCR


title: whole blood, 061_1

value: patient 061


title: whole blood, 113_3

value: patient 113

value: Non-critical


title: MSK1344_R5_TCR


title: Moricandia suffruticosa, Re-Watering, water stress, biol rep S3s


title: MSK1344_R3_TCR


title: Moricandia arvensis, T0, control, biol rep A1


title: Moricandia suffruticosa, Re-Watering, water stress, biol rep S2s


title: Moricandia suffruticosa, Re-Watering, water stress, biol rep S1s


title: L2 ΔCTL0480 infected rep2

data_processing:
CLC Genomics Workbench version 10.1.1 used for all data processing steps.
Adaptor sequences and low-quality reads were trimmed using default parameters, then aligned to the hg19 reference genome.
Transcripts per million (TPM) were calculated using default parameters.
Differential expression testing was performed using default paramters to identify differentially expressed genes in either L2 or B-infected samples relative to the mock-infected control, accounting for variation between replicates.
Genome_build: hg19
Supplementary_files_format_and_content: CLC file containing raw counts, TPM, and FDRP values for every gene and sample.
Supplementary_files_format_and_content: Expression_Browser files (differential expression analysis)

growth_protocol: Human endocervical epithelial HPV-16 E6/E7 transformed End1s (End1 E6/E7, ATCC CRL-2615) were cultured at 37C with 5% atmospheric CO2 in Keratinocyte Serum-Free Medium (KSFM, Thermo Fisher Scientific) supplemented with human recombinant epidermal growth factor, bovine pituitary extract, 5 ug/mL gentamicin, and 0.4 mM CaCl2. For all experiments, End1s were cultured between passages 3 and 15. Chlamydia trachomatis serovar L2/434/Bu and B/Jali was originally obtained from Dr. Ted Hackstadt (Rocky Mountain National Laboratory, NIAID).

extract_protocol:
End1s were harvested for Total RNA at 24 hpi using TRIzol (Thermo Fisher Scientific 15596026) and the DNA-free DNA removal kit (Thermo Fisher Scientific AM1906), according to manufacturers’ protocols, and were subsequently assayed for fragmentation using an Agilent Bioanalyzer 2100.
cDNA library preparation of intact samples was performed using the NuGEN Universal mRNA-Seq Library Preparation kit, according to the manufacturer's protocol.

treatment_protocol: End1s cultured to 125% of confluence seeded on fibronectin-coated 6-well plates (Corning 354402) were washed with pre-warmed Hanks Buffered Saline Solution (HBSS) prior to inoculation with Chlamydia-containing KSFM at a multiplicity of infection (MOI) of 2. Tissue culture plates were centrifuged at 4C and 500 rcf (Eppendorf 5810 R tabletop centrifuge, A-4-81 rotor) for 15 minutes to synchronize infection. Inoculum was then aspirated, and cells were washed with chilled HBSS prior to the addition of pre-warmed KSFM. Infected cultures were then returned to the tissue culture incubator until 24 hours post-infection.

value: Endocervical epithelial cells

tag: infection

value: L2 deltaCTL0480 infected

value: 24 hpi


title: L2 ΔCTL0480 infected rep3


title: MSK1344_R1_TCR


title: L2 ΔCTL0480 infected rep1


title: MSK1344_R2_TCR


title: MSK1344_R4_TCR


title: whole blood, 050_1

value: patient 050

value: whole blood


title: Moricandia suffruticosa, Re-Watering, control, biol rep S7c

value: mature leaf

value: Control


title: L2 wild-type infected rep3

value: L2 wild-type infected


title: L2 wild-type infected rep2


title: MSK1344_Normal_TCR

source_name: adjacent normal tissue

value: Normal


title: Moricandia suffruticosa, Re-Watering, control, biol rep S5c

value: Royal Kew Garden:0105433

value: Re-Watering


title: Moricandia suffruticosa, Re-Watering, control, biol rep S6c


title: MSK1302_R8_TCR


title: L2 wild-type infected rep1


title: whole blood, 141_1

value: patient 141


title: whole blood, 002_1

value: patient 002

value: Critical


title: whole blood, F013

value: patient F013

value: Healthy


title: Moricandia suffruticosa, T2, water stress, biol rep S8s

value: Water stress


title: MSK1302_R7_TCR

value: CD3+ lymphocytes


title: Moricandia suffruticosa, T2, water stress, biol rep S5s


title: whole blood, 130_1

value: patient 130

value: Non-critical


title: whole blood, 115_2

value: patient 115


title: Moricandia suffruticosa, T2, water stress, biol rep S4s


title: MSK1302_R5_TCR


title: MSK1302_R6_TCR


title: Blood sample 5 at 20 days-post-priming with MPXVac-097

city: West Haven

first: Sidi

last: Chen

state: CT

address: 850 West Campus Drive

institute: Yale University

description: VDJ sequencing

data_processing:
The bulk VDJ sequencing data was pre-processed on MiSeq local run manager to trim adaptors and separate reads based on sample index. The reads with an average quality score less 30 were removed from downstream analysis. Clonotypes were called using MiXCR v2.1.5 with the recommended settings for 5’ RACE (RNA alignment to V gene transcripts with P region). The output was further processed with Immunarch v0.6.6 R package for statistical analyses using standard analysis pipelines.
Assembly: Customized germline V and J gene references
Supplementary files format and content: tab-delimited text files with MIXCR clonotype output format.
Library strategy: VDJ-seq

source_name: Peripheral Blood

extract_protocol:
The collected blood was 1:1 diluted with 2% FBS and was added to 7ml of LymphoprepTM density gradient medium in SepMate-15 tubes (StemCell Technologies). The red blood cells, PBMCs and plasma were isolated from blood by centrifugation at 1200 x g for 20 min. After centrifugation, approximately 200 to 300ul plasma was collected from the surface layer and the PBMCs in the remaining solution at the top were poured to a new tube. The separated PBMCs were washed with 2% FBS and sample’s mRNA was extracted using RNeasy Plus Mini Kit (Qiagen).
Bulk TCR library was prepared using 200 ng mRNA extracted from PBMCs collected on day 0 (pre-vaccination) and day 20 (post boost) mice as described above. The SMARTer Mouse TCR a/b Profiling Kit (Takara, Cat. No. 634403) was used to amplify both TCRα and TCRβ sequences. The purified amplicon concentration and purity was determined using D5000 high sensitivity tapes on TapeStation (Agilent). Equal amount of TCR amplicons from each sample was pooled and diluted with water to get a 2nM library. The pooled library was denatured, mixed with 5% PhiX and sequenced on MiSeq (Illumina) using MiSeq V3 2 x 300 cycle kit (Illumina).

value: Peripheral Blood

value: Peripheral blood mononuclear cell

tag: vaccination

value: 20 days-post-priming with MPXVac-097


title: Blood sample 4 at 20 days-post-priming with MPXVac-097

description: VDJ sequencing


title: Moricandia suffruticosa, T2, water stress, biol rep S2s

value: mature leaf

tag: stomatal conductance


title: Blood sample 3 at 20 days-post-priming with MPXVac-097

description: VDJ sequencing


title: whole blood, 063_1

value: patient 063

tag: disease state

value: whole blood


title: MSK1302_R4_TCR


title: Blood sample 2 at 20 days-post-priming with MPXVac-097

description: VDJ sequencing


title: Moricandia suffruticosa, T2, control, biol rep S33c

value: Royal Kew Garden:0105433

value: Control


title: Blood sample 1 at 20 days-post-priming with MPXVac-097

description: VDJ sequencing


title: MSK1302_R3_TCR


title: whole blood, 002_3

value: patient 002

tag: severity


title: MSK1302_R1_TCR

tag: cell type


title: whole blood, 138_2

value: patient 138


title: whole blood, F003

value: patient F003


title: whole blood, 138_3


title: whole blood, 087_2

value: patient 087


title: Moricandia suffruticosa, T1, water stress, biol rep S15s

tag: treatment

value: Water stress


title: Blood sample 4 at 0 days-post-priming with MPXVac-097

description: VDJ sequencing

value: 0 days-post-priming with MPXVac-097


title: Blood sample 5 at 0 days-post-priming with MPXVac-097

description: VDJ sequencing


title: Moricandia suffruticosa, T2, control, biol rep S36c


title: Blood sample 3 at 0 days-post-priming with MPXVac-097

description: VDJ sequencing


title: MSK1302_Normal_TCR

value: Normal

value: CD3+ lymphocytes


title: whole blood, F011

value: patient F011

value: Healthy


title: whole blood, 115_1

value: patient 115

value: Critical


title: Blood sample 2 at 0 days-post-priming with MPXVac-097

description: VDJ sequencing

value: Peripheral Blood

value: Peripheral blood mononuclear cell


title: Moricandia suffruticosa, T1, water stress, biol rep S10s

value: mature leaf


title: whole blood, 050_2

value: patient 050

value: Non-critical

value: whole blood


title: whole blood, 061_2

value: patient 061


title: whole blood, 087_1


title: whole blood, 129_3

value: patient 129


title: MSK1263_R8_TCR


title: MSK1302_R2_TCR


title: Moricandia suffruticosa, T2, control, biol rep S28c

value: Royal Kew Garden:0105433

value: Control


title: Moricandia suffruticosa, T1, control, biol rep S35c


title: Blood sample 1 at 0 days-post-priming with MPXVac-097

description: VDJ sequencing

value: 0 days-post-priming with MPXVac-097


title: whole blood, 002_2

value: patient 002


title: oralmln3

city: Stony Brook

first: Brian

middle: S

last: Sheridan

state: NY

address: 100 Nicolls Road

institute: Stony Brook University

data_processing:
RNA seq and data analysis were performed by Macrogen
Analyze the quality control of the sequenced raw reads. Overall reads' quality, total bases, total reads, GC (%) and basic statistics are calculated.
In order to reduce biases in analysis, artifacts such as low quality reads, adaptor sequence, contaminant DNA, or PCR duplicates are removed.
Trimmed reads are mapped to reference genome with TopHat, splice-aware aligner.
Transcript is assembled by Cufflinks with aligned reads that contain paired-end information. This process provides information of known transcripts, novel transcripts, and alternative splicing transcripts.
Expression profiles of assembled transcripts for each sample are calculated by Cufflinks. Expression profiles are represented as normalization value which is based on transcript length and depth of coverage. The FPKM (Fragments Per Kilobase of transcript per Million Mapped reads) value is used as expression profile.
In groups with different conditions, genes or transcripts that express differentially are filtered out through statistical hypothesis testing.
Assembly: UCSC mm10
Supplementary files format and content: tab-delimited text file include RPKM values of known transcripts for all 9 samples, file name: AnnoOnly_FPKM_from_all_samples_in_mm10.transcript.addDesc
Supplementary files format and content: tab-delimited text file include RPKM values of known genes for all 9 samples, file name: AnnoOnly_FPKM_from_all_samples_in_mm10.gene.addDesc

source_name: MLN

extract_protocol:
RNA was extracted using QIAGEN RNeasy Plus Micro Kit (cat. no. 74034).
Libraries were prepared using Illumina TruSeq Stranded mRNA library kit at the Center for Genome Innovation at UCONN Storrs, Connecticut, USA

value: MLN

value: CD8+ T cells (OT-I cells)

value: MLN-primed


title: MSK1263_R7_TCR

value: CD3+ lymphocytes


title: Moricandia suffruticosa, T1, water stress, biol rep S13s

value: Water stress


title: Moricandia suffruticosa, T1, control, biol rep S24c


title: MSK1263_R6_TCR


title: MSK1302_LN_TCR

source_name: lymph node

value: LN


title: Moricandia suffruticosa, T1, control, biol rep S26c


title: Moricandia suffruticosa, T1, control, biol rep S18c


title: MSK1263_R4_TCR


title: oralmln1


title: MSK1263_R5_TCR


title: whole blood, 062_1

value: patient 062

value: Critical


title: oralmln2


title: whole blood, 051_2

value: patient 051


title: MSK1263_R3_TCR


title: Moricandia suffruticosa, T0, control, biol rep S43

value: mature leaf


title: ivspleen3

source_name: spleen

value: spleen

value: spleen-primed


title: MSK1263_R2_TCR


title: Moricandia suffruticosa, T0, control, biol rep S42


title: whole blood, 117_2

value: patient 117

value: Non-critical

value: whole blood


title: whole blood, 089_3

value: patient 089


title: Moricandia suffruticosa, T0, control, biol rep S39

value: Royal Kew Garden:0105433

value: Control


title: ivspleen1

value: CD8+ T cells (OT-I cells)


title: whole blood, 135_1

value: patient 135


title: MSK1263_R1_TCR

value: CD3+ lymphocytes


title: whole blood, 053_3

value: patient 053


title: Moricandia suffruticosa, T0, control, biol rep S38


title: MSK1263_Normal_TCR

value: Normal


title: ICIM3

first: Juan

last: Qin

address: 555 Mission Bay Boulevard South

institute: UCSF

data_processing:
Trimmed sequence reads were mapped to GrCM38 using the RNA STAR software (Version 2.7.3)
Reads (reads per kilobase million) were extracted from the mapped files using the Rsubread Bioconductor package (Version 3.1)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: whole mouse heart

extract_protocol:
Flash-frozen mouse tissue (cardiac ventricle) was homogenized using a TissueLyser II (Qiagen) for 2 min at 30 Hz. RNA was collected from dissociated tissue using Qiagen RNA Kit (Catalog#, 74136).
Libraries were prepared using Illumina TruSeq Stranded Total RNA Kit (Illumina, San Diego, CA, USA).
Sequencing was performed as paired-end sequencing, with a read length of 150 bps on the Illumina NovaSeq 6000 platform.

value: whole mouse heart

value: NO

value: 3-6 weeks old


title: whole blood, 066_1

value: patient 066


title: Naive2

value: spleen

value: naive


title: ivspleen2

value: spleen-primed


title: ICIM2


title: MSK1263_LN_TCR

value: LN


title: MSK1263_A4_TCR

source_name: adrenal tumor


title: FLC tumor cell smRNA-seq sample Treatment #4 [RetinoicAcid_3_T2_S15_R1_001]

city: Ithaca

first: Praveen

last: Sethupathy

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

address: T7 006D Veterinary Research Tower, Box 17

department: Department of Biomedical Sciences

institute: Cornell University

description:
smRNA-seq.  FLC tumor cells were treated with 4uM RA.
DESeq_normalized_miR_counts.csv

data_processing:
Sequencing was aligned and quantiitated using miRquant2.0 (small RNAseq), aligned and quantified using STAR/Salmon (RNA-seq).
RNA-seq and smRNA-seq  data was normalized using DESeq2.
Assembly: Paired end RNA sequencing reads were aligned to the human genome (hg38) using STAR. Small RNA sequencing was processed using miRquant 2.0 and aligned to the genome (hg19).
Supplementary files format and content: Normalized counts

source_name: FLC tumor cells in culture, established from a patient-derived xenograft (PDX) mouse model

extract_protocol:
Total RNA was isolated from ethanol and retinoic acid-treated FLC cells with the Total RNA Purification Kit (Norgen Biotek) as per the manufacturer’s instructions.  RNA purity was quantified with the Nanodrop 2000 instrument (Thermo Fisher Scientific, Waltham, MA) and RNA integrity was quantified with the Agilent 4200 Tapestation (Aglient Technologies, Santa Clara, CA).
Libraries were generated using the CleanTag Small RNA Library Prep Kit (TriLink Biotechnologies, San Diego, CA).

tag: trial #

value: One

value: FLC tumor cells

tag: Stage

value: tumor stage

value: 4uM RA

tag: molecule subtype

value: small RNA


title: MSK1263_A3_TCR

first: Ansuman

last: Satpathy

address: 240 Pasteur Drive

institute: Stanford University


title: FLC tumor cell smRNA-seq sample Treatment #3 [RetinoicAcid_2_T2_S19_R1_001]


title: CON4

tag: tissue

tag: genotype


title: MSK1263_A1_TCR


title: whole blood, 130_3

tag: individual

value: patient 130

value: Non-critical

value: whole blood


title: CON3

tag: time


title: FLC tumor cell smRNA-seq sample Treatment #2 [RetinoicAcid_1_T2_S18_R1_001]


title: MSK1344_R8_RNA

data_processing:
Reads were processed with Cell Ranger v3.1.0
R1 contains barcode at 1-16bp and UMI at bp 17-26
R2 contains the biological sequence
I1 contains the i7 sample index
Genome_build: hg19
Supplementary_files_format_and_content: "barcodes.tsv.gz" contains filtered cellular barcodes, "features.tsv.gz" contains genes, "matrix.mtx.gz" contains the barcoded gene expression matrix

value: CD3+ lymphocytes


title: Naive1

value: CD8+ T cells (OT-I cells)


title: CON2

value: whole mouse heart

value: NO


title: MSK1344_R7_RNA


title: ICIM1

value: 3-6 weeks old


title: FLC tumor cell smRNA-seq sample WT #4 [Ethanol_3_T1_S13_R1_001]

description:
smRNA-seq. FLC tumor cells were treated with EtOH as WT control.
DESeq_normalized_miR_counts.csv

value: EtOH as WT control


title: FLC tumor cell smRNA-seq sample WT #3 [Ethanol_2_T2_S17_R1_001]


title: CON1


title: MSK1344_R6_RNA


title: MSK1344_R5_RNA


title: Naive3

value: spleen

value: naive


title: SN4741_pcHiC_39_rep4

city: Baltimore

first: Andrew

middle: S.

last: McCallion

state: Maryland

address: 733 North Broadway

department: Genetic Medicine

institute: Johns Hopkins University School of Medicine

data_processing:
FASTQ files were mapped to mm10 using Bowtie2 (v.2.4.1) and filtered using HiCUP (v. 0.8) configured with the following parameters: FASTQ format (Format: Sanger), maximum di-tag length (Longest: 700), minimum di-tag length (shortest: 50)
BAM files were generated for each replicate using samtools (v.1.10). DeepTools (v.3.5.1) before read coverage similarities and replicate correlation was assessed using the function “multiBamSummary” (in bins mode) to analyze the entire genome.
The CHiCAGO (v. 1.18.0) pipeline was used to convert the merged BAM file into CHiCAGO format.
Assembly: mm10

growth_protocol: SN4741 cells were maintained in high glucose Dulbecco's Modified Eagle Medium, supplemented with 1% penicillin–streptomycin and 10% fetal bovine serum in a humidified 5% CO2 incubator at 37°C. Cells at 80% confluence were passaged by trypsinization approximately every 2-3 days.

extract_protocol:
SN4741 cells were cultured at the non-permissive temperature and plated at five million cells per 10cm dish. The cells were crosslinked using 1% formaldehyde, snap frozen using liquid nitrogen, and stored at -80°C. The cells were dounce homogenized and restriction enzyme digestion, using 400 units HindIII-HF overnight at 37°C. The total volume was maintained at 500µL, through addition of 1X NEBuffer 2.1. Heat inactivation was performed at 80°C for 20 minutes, and biotinylated-dCTP was used for biotin fill-in reaction. Blunt-end ligation was performed using Thermo T4 DNA ligase, with cohesive end units maintained at 15,000 and buffer and water volumes adjusted to ensure a total volume of 665µL was added to each Hi-C tube. Cross-linking was performed overnight, with additional (50μL) proteinase K added for two hours the following day. DNA purification was split across two reactions using 2mL PhaseLock tubes, and volumes were adjusted accordingly. Each PhaseLock reaction was split again into two vials for ethanol purification, and centrifugation at step 6.3.8 was performed at room temperature. The pellets were dissolved in 450µL 1X TLE and transferred to a 0.5mL 30kD Amicon Column. After washing, the column was inverted into a new container, and no additional liquid was added to raise the volume to 100µL. All four reactions were combined, the total volume determined, and RNAseA (1mg/mL) equal to 1% of the total volume was added for 30 minutes at 37°C.
The libraries were assessed for successful blunt-end ligation by a ClaI restriction enzyme digest of PCR products, as previously described  (Belaghzal, H., Dekker, J. and Gibcus, J.H., 2017. Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation. Methods, 123, pp.56-65.) . Biotin was removed from un-ligated ends and DNA was sheared to a size of 200-300bp using the Covaris M220 (High setting, 35 cycles of 30s “on” and 90s “off”; vortexing/spinning down samples and changing sonicator water every 5 cycles). Size selection was performed using AMpure XP magnetic beads, as described, except that all resuspension steps were increased by 5µL, so that 5μL could be used for QC with the High Sensitivity DNA Assay (Agilent) on the Agilent 2100 Bioanalyzer (at three stages: post-sonication, post-0.8x size-selection, and post-1.1x size-selection). The remaining protocol was performed as described. The remaining protocol was performed as described. Capture probes (Arbor Biosciences; https://github.com/nbbarrientos/SN4741_pcHiC) were designed against mouse (mm10) RefSeq transcription start sites, filtering out “XM” and “XR” annotated genes. The remaining promoters were intersected with the in silico digested HindIII mouse genome, to retain all HindIII fragments containing a promoter. Potential probes sites were assessed ±330bp of the HindIII cut site on either end of the fragment and finalized probe sets were filtered using no repeats and “strict” criteria, as defined by Arbor Biosciences. After generating a uniquely indexed HiC library with complete Illumina adapters, probes targeting promoter containing fragments were hybridized following Arbor Biosciences capture protocol (v4) at 65°C, 1µg DNA, and one round of capture.

treatment_protocol: To induce differentiation, 24 hours after the cells were passaged, media was replaced by DMEM supplemented with 1% penicillin–streptomycin and 0.5% FBS at 39°C. Cells were allowed to grow and differentiate in these conditions for 48 hours before harvesting for experimentation.

tag: cell line

value: Neural precursor cells

value: WT

value: 39°C Incubation


title: SN4741_pcHiC_39_rep3


title: FLC tumor cell smRNA-seq sample WT #2 [Ethanol_1_T2_S16_R1_001]

value: One

value: FLC tumor cells

value: tumor stage


title: MSK1344_R4_RNA

city: Stanford

tag: patient


title: SN4741_pcHiC_39_rep2


title: FLC tumor cell smRNA-seq sample Treatment #1 [RetinoicAcid_1_T1_S14_R1_001]

value: 4uM RA

value: small RNA


title: FLC tumor cell smRNA-seq sample WT #1 [Ethanol_1_T1_S11_R1_001]


title: whole blood, 117_1

value: patient 117

value: Non-critical

value: whole blood


title: whole blood, 018_3

value: patient 018

value: Critical


title: whole blood, 051_1

value: patient 051


title: whole blood, 063_3

value: patient 063


title: MSK1344_R3_RNA

tag: region

value: CD3+ lymphocytes


title: FLC tumor cell RNA-seq sample Treatment #5 [AF10]

description:
RNA-seq. Batch 2. FLC tumor cells were treated with 4uM RA.
DESeq_normalized_counts.csv

extract_protocol:
Total RNA was isolated from ethanol and retinoic acid-treated FLC cells with the Total RNA Purification Kit (Norgen Biotek) per manufacturer’s instructions.  RNA purity was quantified with the Nanodrop 2000 (Thermo Fisher Scientific, Waltham, MA) or Nanodrop One and RNA integrity was quantified with the Agilent 4200 Tapestation (Agilent Technologies, Santa Clara, CA).
Libraries were prepared by the Cornell Transcriptional Regulation and Expression (TREx) Facility using the NEBNext Ultra II Directional RNA kit.

value: Two


title: SN4741_pcHiC_39_rep1

value: Neural precursor cells


title: MSK1344_R2_RNA


title: FLC tumor cell RNA-seq sample Treatment #4 [AF9]


title: whole blood, F016

value: patient F016

value: Healthy


title: SN4741_scRNAseq_39_rep4

description: 10x Genomics

data_processing:
Paired-end reads were aligned to the mouse reference genome using the CellRanger v3.0.1 pipeline. Unique molecular identifier counts were quantified per gene per cell (“cellranger count”) and aggregated (“cellranger aggr”) across samples with no normalization.
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

extract_protocol:
Cell capture and cDNA generation was performed with the standard protocol for the Chromium Single Cell 3’ V3 reagent kit.
Library preparation was performed with the standard protocol for the Chromium Single Cell 3’ V3 reagent kit. Libraries were quantified with the Qubit dsDNA High Sensitivity Assay (Invitrogen) in combination with the High Sensitivity DNA Assay on the Agilent 2100 Bioanalyzer.

value: WT

value: 39°C Incubation


title: MSK1344_R1_RNA


title: SN4741_scRNAseq_39_rep3

description: 10x Genomics


title: FLC tumor cell RNA-seq sample WT #5 [AF8]

description:
RNA-seq. Batch 2. FLC tumor cells were treated with EtOH as WT control.
DESeq_normalized_counts.csv

value: FLC tumor cells

value: tumor stage

value: EtOH as WT control


title: MSK1344_Normal_RNA

value: Normal


title: FLC tumor cell RNA-seq sample WT #4 [AF7]


title: MSK1302_R8_RNA


title: SN4741_scRNAseq_39_rep1

description: 10x Genomics


title: FLC tumor cell RNA-seq sample Treatment #3 [AF6]

description:
RNA-seq. Batch 1. FLC tumor cells were treated with 4uM RA.
DESeq_normalized_counts.csv

value: One

value: 4uM RA


title: SN4741_scRNAseq_37_rep4

description: 10x Genomics

value: 37°C Incubation


title: FLC tumor cell RNA-seq sample Treatment #2 [AF5]


title: Multiome_mutant_nr5a2_GFP_2.5dpf_head (snRNA-seq)

value: Jaw mesenchyme

tag: developmental stage

value: 2.5 dpf

tag: facs markers

value: DAPI- / GFP+


title: SN4741_scRNAseq_37_rep3

description: 10x Genomics


title: FLC tumor cell RNA-seq sample Treatment #1 [AF4]


title: MSK1302_R5_RNA

value: CD3+ lymphocytes


title: Multiome_mutant_nr5a2_GFP_2.5dpf_head (snATAC-seq)


title: SN4741_scRNAseq_37_rep2

description: 10x Genomics


title: SN4741_scRNAseq_39_rep2

description: 10x Genomics


title: MSK1302_R4_RNA


title: SN4741_scRNAseq_37_rep1

description: 10x Genomics


title: MSK1302_R7_RNA


title: FLC tumor cell RNA-seq sample WT #2 [AF2]

description:
RNA-seq. Batch 1. FLC tumor cells were treated with EtOH as WT control.
DESeq_normalized_counts.csv


title: MSK1302_R6_RNA


title: FLC tumor cell RNA-seq sample WT #1 [AF1]


title: MSK1302_R2_RNA


title: MSK1302_R1_RNA


title: FLC tumor cell RNA-seq sample WT #3 [AF3]


title: MSK1302_Normal_RNA


title: MSK1302_R3_RNA


title: MSK1302_LN_RNA

value: LN


title: MSK1263_R8_RNA


title: sample4: HEK293T ORF57 (1)

city: Frederick

first: Zhi-Ming

last: Zheng

department: Center for Cancer Research

institute: National Cancer Institute

data_processing:
Illumina HiSeq 4000 (Illumina, Inc) reads were trimmed and clipped for quality control in Trimmomatic v0.27.
Read quality was checked for each sample using FastQC v0.10.1
High-quality reads were then aligned with STAR version 2.5.2b to create bam files.
Normalization of counts was performed using Limma package
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file containing gene names, read counts and statistics

growth_protocol: HEK293T (ATCC) cells were maintained in DMEM media supplemented with 10% fetal bovine serum (FBS) and 1x penicillin, streptomycin, glutamine (Thermo Fisher Scientific).

extract_protocol:
The cell pellet was lysed in 0.7ml of Tripure reagent (Roche, cat. no. 11667165001) for total RNA isolation using miRNeasy Mini kit (Qiagen, cat. No. , 217004) with DNase treatment.
RNA libraries were prepared by ACGT, inc (Germantown, MD). Indexed cDNA sequencing libraries were prepared from the RNA samples using the TruSeq Stranded mRNA Sample Preparation Kit, and bar-coded with individual tags, following the manufactures recommendations. Library preparation was performed using a 96-well plate method. The libraries were quantified using Qubit fluoroscopy and also with the NGS kit for Fragment Analyzer. Any failed results from the fragment analyzer were repeated using 2100 Bioanalyzer. Indexed libraries were combined as equimolar pools and run on HiSeq4000 (2x150 paired end runs) in order to generate 40 million paired-end reads per sample library.

treatment_protocol: Five millions cells were seeded in a 10 cm dish and 16h later transfected with 5 ug of ORF57-expressing  (pVM7) or empty vectors (pCMV5.1-FLAG) using LipoD293 reagent (SignaGen laboratories). Total RNA was extracted 24 hours after transfection using TriPure reagent (Roche) and subjected to RNA-seq.

value: ORF57 overexpression

tag: cancer type

value: Human Embryonic Kidney transformed with large T antigen


title: sample2: HEK293T control vector (2)

value: FLAG overexpression


title: sample1: HEK293T control vector (1)


title: sample5: HEK293T ORF57 (2)


title: sample6: HEK293T ORF57 (3)


title: sample3: HEK293T control vector (3)


title: SN4741_RNAseq_39_rep4

data_processing:
FASTQ files were aligned to the mouse reference genome (mm10) with HISAT2 (v2.0.5) and sample reads from different lanes were merged using samtools (v.1.10) function “merge.”.
Aligned reads from individual samples were quantified against the mm10 reference transcriptome with the subread (v1.6.1) function “featureCounts”, using -t exon and -g gene_id.
Assembly: mm10

extract_protocol:
Cells were run through QIAshredder (Qiagen) and total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s recommendations, except that RNA was eluted twice in 50μL of water. Total RNA integrity was determined with the RNA Pico Kit (Agilent) on the Agilent 2100 Bioanalyzer.
Library preparation was done using NEBNext Ultra II directional library prep kit with poly-A selection.

value: Neural precursor cells

value: WT


title: SN4741_RNAseq_39_rep1

value: 39°C Incubation


title: SN4741_RNAseq_39_rep3


title: SN4741_RNAseq_37_rep4


title: SN4741_RNAseq_37_rep3


title: SN4741_RNAseq_39_rep2


title: NULL, Donor 3

city: Tampa

first: Amer

last: Beg

state: FL

address: 12902 Magnolia Drive

institute: Moffitt Cancer Center

data_processing:
Paired-end RNA-seq reads were aligned to the GRCh37 human reference genome using STAR v2.5.3a following adaptor trimming by cutadapt v1.8.1.
Gene level expression was quantified using RSEM.
Read counts were normalized to TPM (transcript per million)
Assembly: hg19
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Human peripheral blood

growth_protocol: A549 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C. CD14+ PBMC were purified from healthy donor maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C and stimulated by IL-4 and GM-CSF.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA was isolated using a Qiagen RNeasy Kit, reverse transcribed and subjected to quantitative PCR analysis.

treatment_protocol: A549 were infected with NULL, ISF35 or/ and hIFNB viruses followed by cocultured with human Mo-DCs (CD14+ PBMC were purified and stimulated by IL-4 and GM-CSF for 6 days). 2 days later, all cells were collected for cell sorting.  RNA-seq was used to determine changes in gene expression after sorting HLA-DR+CD11c+ DCs derived from monocytes of 3 healthy donors.

value: Human peripheral blood

value: monocyte-derived DC

value: A549 were infected with NULL viruses, followed by cocultured with human Mo-DCs from Donor 3


title: COMBO treated, Donor 2

value: A549 were infected with ISF35 and hIFNB viruses, followed by cocultured with human Mo-DCs from Donor 2


title: ISF35 treated, Donor 3

value: A549 were infected with ISF35 viruses, followed by cocultured with human Mo-DCs from Donor 3


title: whole blood, 089_2

first: Yohan

last: Lefol

institute: University of Oslo

data_processing: Microarray data was processed/normalized using limma  version 3.48.1. Controls, outliers, and below background genes were removed, duplicate probes were then merged using the avereps function while using SustematicNames as the keys.

extract_protocol: RNA was extracted from PAXgene RNA tubes using the PAXgene Blood miRNA Kit (Qiagen, Hilden, Germany) following the manufacturer's recommendations. RNA concentration and quality were assessed using NanoDrop ND-1000 UV-VIS Spectrophotometer (ThermoFisher, Waltham, MA) and the RNA was stored at -80°C.

value: patient 089

tag: disease state

value: Critical

value: whole blood


title: IFNB treated, Donor 3

value: A549 were infected with hIFNB viruses, followed by cocultured with human Mo-DCs from Donor 3


title: COMBO treated, Donor 3

value: A549 were infected with ISF35 and hIFNB viruses, followed by cocultured with human Mo-DCs from Donor 3


title: SN4741_RNAseq_37_rep2

value: 37°C Incubation


title: IFNB treated, Donor 2

value: A549 were infected with hIFNB viruses, followed by cocultured with human Mo-DCs from Donor 2


title: SN4741_RNAseq_37_rep1


title: MSK1263_R4_RNA

value: CD3+ lymphocytes


title: MSK1263_R5_RNA


title: ISF35 treated, Donor 2

value: A549 were infected with ISF35 viruses, followed by cocultured with human Mo-DCs from Donor 2


title: NULL, Donor 2

value: A549 were infected with NULL viruses, followed by cocultured with human Mo-DCs from Donor 2


title: COMBO treated, Donor 1

value: A549 were infected with ISF35 and hIFNB viruses, followed by cocultured with human Mo-DCs from Donor 1


title: MSK1263_R3_RNA


title: MSK1263_R6_RNA


title: IFNB treated, Donor 1

value: A549 were infected with hIFNB viruses, followed by cocultured with human Mo-DCs from Donor 1


title: whole blood, 053_2

value: patient 053

tag: severity


title: MSK1263_R2_RNA

tag: cell type


title: NHEK_GFP-16E7-2

city: Hangzhou

first: Chunting

last: Hua

state: Zhejiang

address: 3 East Qingchun Road

institute: Sir Run Run Shaw Hospital

description:
1_genes_fpkm_expression.txt
2_transcripts_fpkm_expression.txt

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 hg38 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. 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.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: NHEK cells transfected with pEGFP-16E7 replicate 2

growth_protocol: NHEKs (ScienCell, Carlsbad, CA, USA) were cultured in 6-well plates using EPILIFE culture medium (MEPI500CA, Thermo, USA) containing 10% fetal bovine serum (FBS, Gibco, USA).

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, LifeTechnologies, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Agilent 2100 with RIN number >7.0.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: We transfected NHEK cell with pEGFP-16E7 as experimental group and pEGFP-C1 as control group by Lipofectamine 3000 reagent (Invitrogen, Carlsbad, CA, USA) until 80% confluence. Original culture medium was replaced with fresh culture medium after 6 hours.

value: skin

value: normal human epidermal keratinocytes

tag: hpv status

value: HPV 16E7 Positive


title: NHEK_GFP-16E7-3

source_name: NHEK cells transfected with pEGFP-16E7 replicate 3


title: NHEK_GFP-C1-1

source_name: NHEK cells transfected with pEGFP-C1 replicate 1

value: HPV-Negative


title: NHEK_GFP-16E7-1

source_name: NHEK cells transfected with pEGFP-16E7 replicate 1


title: NHEK_GFP-C1-3

source_name: NHEK cells transfected with pEGFP-C1 replicate 3


title: NHEK_GFP-C1-2

source_name: NHEK cells transfected with pEGFP-C1 replicate 2


title: SN4741_ATACseq_39_rep4

data_processing:
Reads were aligned to the mouse reference genome (mm10) in local mode with Bowtie2 (v2.4.1), using –X 1000 to specify an increased pair distance to 1000bp.
Samtools (v1.15.1) and Picard (v2.26.11; http://broadinstitute.github.io/picard/) were used to sort, deduplicate and index reads.
Peaks were called with MACS3 (v3.0.0a7; https://github.com/macs3-project/MACS) and specifying --nomodel and --nolambda for the `callpeaks()` command.
Peaks overlapping mm10 blacklisted/block listed regions called by ENCODE and in the original ATAC-seq paper were also removed with BEDTools (v2.30.0).
Assembly: mm10
Supplementary files format and content: xls peak files

extract_protocol:
Following the Omni-ATAC protocol, aliquots of 50,000 cells were centrifuged at 2000 x g for 20 mins at 4°C, and the resulting pellets were resuspended in 50μL of resuspension buffer. Cells were left to lyse for 3 minutes on ice before being centrifuged again at 2000 x g for 20 minutes at 4°C. The resulting nuclei pellets were then tagmented, as written, using 50μL of transposition mixture and then incubated at 37°C for 30 mins in a 1000 RPM thermomixer. After transposition, DNA was purified with the Zymo DNA Clean and Concentrator -5 Kit and eluted in 21μL of elution buffer.
Pre-amplification of transposed fragments was performed according to the conditions outlined in the Omni-ATAC protocol. 12 pre-amplification cycles were run in lieu of qPCR amplification to determine additional cycles. The amplified libraries were prepared according to the Nextera DNA Library Prep Protocol Guide, except that libraries were purified with 40.5μL AMPure XP beads, and 27.5μL of resuspension buffer was added to each sample. All libraries were quantified with the Qubit dsDNA High Sensitivity Assay (Invitrogen) in combination with the High Sensitivity DNA Assay (Agilent) on the Agilent 2100 Bioanalyzer.

value: Neural precursor cells

value: WT

tag: treatment

value: 39°C Incubation


title: SN4741_ATACseq_39_rep3


title: SN4741_ATACseq_37_rep4


title: MSK1263_Normal_RNA

value: Normal


title: SN4741_ATACseq_39_rep2


title: SN4741_ATACseq_39_rep1


title: ISF35 treated, Donor 1

value: Human peripheral blood

value: monocyte-derived DC

value: A549 were infected with ISF35 viruses, followed by cocultured with human Mo-DCs from Donor 1


title: NULL, Donor 1

value: A549 were infected with NULL viruses, followed by cocultured with human Mo-DCs from Donor 1


title: MSK1263_R1_RNA

value: CD3+ lymphocytes


title: End1/E6E7 cells, B-infected rep3

description: B R3

data_processing:
CLC Genomics Workbench version 10.1.1 used for all data processing steps.
Adaptor sequences and low-quality reads were trimmed using default parameters, then aligned to the hg19 reference genome.
Transcripts per million (TPM) were calculated using default parameters.
An initial ANOVA-like pass of differential expression testing was performed. Genes that did not significantly vary between any of the three treatments were culled from downstream analysis.
Differential expression testing was performed using default paramters to identify differentially expressed genes in either L2 or B-infected samples relative to the mock-infected control, accounting for variation between replicates.
Genome_build: hg19
Supplementary_files_format_and_content: CLC file containing raw counts, TPM, and FDRP values for every gene and sample.
Supplementary_files_format_and_content: Expression_Browser files (differential expression analysis)

extract_protocol:
End1s were harvested for Total RNA at 24 hpi using TRIzol (Thermo Fisher Scientific 15596026) and the DNA-free DNA removal kit (Thermo Fisher Scientific AM1906), according to manufacturers’ protocols. Extracted RNA was subsequently enriched for polyadenylated mRNA transcripts using the NucleoTrap mRNA enrichment kit (Macherey-Nagel), again according to the manufacturer’s protocol. For the comparison of Mock- and Ct serovar L2-infected transcriptomes, RNA samples were subsequently assayed for fragmentation using an Agilent 5200 Fragment Analyzer; intact samples were enriched for polyadenylated transcripts via the NucleoTrap kit a second time due to the high incidence of ribosomal RNA in the fragment analysis results.
cDNA library preparation was performed using the Ion Xpress Plus Fragment Library kit (Thermo Fisher Scientific 4471269), according to the manufacturer's protocol.

value: Endocervical epithelial cells

tag: infection

value: Serovar B/Jali-infected

tag: infection time

value: 24 hpi


title: MSK1263_A4_RNA


title: MSK1263_LN_RNA

value: LN


title: SN4741_ATACseq_37_rep1

value: 37°C Incubation


title: End1/E6E7 cells, B-infected rep2

description: B R2


title: End1/E6E7 cells, B-infected rep1

description: B R1


title: SN4741_ATACseq_37_rep2


title: KO_D1_Rep2

city: Diepenbeek

first: Ibrahim

last: HAMAD

state: Yes

address: Agoralaan Building C

department: Hasselt University

country: Belgium

data_processing:
Quality of raw sequence reads was checked using FastQC version 0.11.8, and nucleotide calls with a quality score of 28 or higher were considered high quality. Adapters were removed using cutadapt v.2.4. Reads were aligned to the hg19 genome reference, using STAR (2.5.0e) and amaximum of five mismatches were allowed.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include counts values for each Sample

source_name: Splenocytes

extract_protocol:
RNA was extracted with QIAzol reagent, followed by RNA extraction with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Splenocytes

value: Scd1-deficient C57BL/6


title: KO_D1_Rep3


title: KO_D1_Rep4


title: MSK1263_R7_RNA

source_name: tumor

extract_protocol: 10x Chromium Next Gem Single Cell V(D)J Reagent Kit (v1)


title: WT_D1_Rep3

value: wild type C57BL/6


title: whole blood, 053_1

city: Oslo

address: Sognsvannsveien 20 Rikshospitalet

source_name: whole blood

value: patient 053

value: Critical

tag: tissue

value: whole blood


title: whole blood, 089_1

value: patient 089


title: whole blood, 018_2

value: patient 018


title: whole blood, 018_1


title: Cx3cr1_Tam_3

city: Lisboa

first: Pedro

last: Sousa-Victor

address: Avenida Professor Egas Moniz

country: Portugal

institute: Instituto de Medicina Molecular (iMM)

description: macrophages, manfko, 3dpi

data_processing:
FPKM
Assembly: ensembl_mus_musculus_grcm38_p6_gca_000001635_8
Supplementary files format and content: excel file includes FPKM values for each Sample

source_name: Macrophages

extract_protocol: RNA was extracted with RNeasy Micro Kit

value: Macrophages

tag: genotype

value: Cx3cr1-CreER, Manffl/fl

value: Tamoxifen


title: whole blood, 130_2

tag: individual

value: patient 130

value: Non-critical


title: whole blood, 063_2

value: patient 063

tag: time


title: End1/E6E7 cells, L2-infected rep3

description: L2 R3

value: Endocervical epithelial cells

tag: cell line

value: Serovar L2/434/bu-infected

value: 24 hpi


title: whole blood, 141_2

value: patient 141


title: whole blood, F014

value: patient F014

value: Healthy


title: whole blood, 115_3

value: patient 115


title: WT_D1_Rep2

value: Splenocytes

value: wild type C57BL/6


title: SN4741_ATACseq_37_rep3

value: Neural precursor cells

value: WT

value: 37°C Incubation


title: MSK1263_A1_RNA

tag: patient

value: CD3+ lymphocytes


title: WT_D1_Rep4


title: Cx3cr1_Tam_2

description: macrophages, manfko, 3dpi

value: Macrophages

value: Cx3cr1-CreER, Manffl/fl

value: Tamoxifen


title: KO_D1_Rep1

value: Scd1-deficient C57BL/6


title: WT_D1_Rep1


title: Cx3cr1_Tam_1

description: macrophages, manfko, 3dpi


title: End1/E6E7 cells, L2-infected rep2

description: L2 R2

value: Endocervical epithelial cells


title: MSK1263_A3_RNA

tag: region