title: DK_mta_1

city: fuzhou

first: Lianfeng

last: Gu

address: No.15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province, China

country: China

institute: Fujian Agriculture and Forestry University

description: RNA-seq of mta in the dark

data_processing:
The RNA-seq reads were aligned to the arabidopsis genome (TAIR10) using tophat-2.0.11 (Trapnell et al., 2009) with anchor length more than 8nt for spliced alignments. Only uniquely mapped reads were retained for subsequent analysis.
Assembly: TAIR10
Supplementary files format and content: bigWig

organism: Arabidopsis thaliana

growth_protocol: the seedling were grown in greenhouse

extract_protocol:
The total RNA was extracted using TRIZOL reagent.
Strand-specific RNA-Seq libraries generated from samples above were constructed using dUTP method (Parkhomchuk et al., 2009) and sequenced on Illumina Hiseq 2500.

treatment_protocol: Continuous blue light or darkness

value: seedling

tag: developmental stage

value: mta

value: dark


title: Input for K562 cells with depleted BORIS

status: Public on Jan 03 2024

type: SRA

city: Bethesda

first: Elena

last: Pugacheva

state: MD

department: NIAID

country: USA

institute: NIH

library_source: genomic

data_processing:
ChIP-seq, ATAC-seq, CAGE-seq data: single-end or paired-end reads were aligned either to the UCSC hg19 (human samples) or UCSC mm9 (mouse samples) genome using Bowtie version 2 under default parameters.
RNA-seq data: FASTQ files were either mapped to the UCSC mouse (build mm9) or human ((build hg19) reference genomes using STAR with default settings. Normalized gene counts and differentially expressed genes (DEG) were obtained with the R package DESeq2.
For ChIP-seq and ATAC-seq data, output BAM files were converted into bdg track files using MACS2
For CAGE-seq, ChIP-seq, ATAC-seq data, output BAM files were converted into bigwig files using bamCoverage option in deepTools 3.5.0 in order to display normilized coverage throughout the genome (in RPKM).
ChIP-seq and ATAC-seq peaks were called using Model-based Analysis for ChIP-seq (MACS2) using default parameters.
CAGE-seq clusters were called using MACS2  with parameters (--nomodel --shift -1)
bdg files were generated using  MACS2  with default settings.
Assembly: hg19 (for human) amd mm9 (for mouse)
Supplementary files format and content: bdg, xlsx (differentially expressed genes (DEG) were obtained with the R package DESeq2), bigwig (BAM files normilized using bamCoverage option in deepTools 3.5.0 (in RPKM))

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: DMEM (NIH3T3, 293T, MDA-MB-435, MCF7 cells), RPMI (K562, CH12cells), 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2. Stable NIH3T3, MDA-MB-435 and MCF7 clones were maintained under 150 mkg/ml of Hygromycin B.

extract_protocol:
ChIP-seq protocol: 2x106 asynchronously growing cells were crosslinked with 1% formaldehyde for 10 min at room temperature, followed by quenching with 125 mM glycine for 10 min, washed twice with 1×phosphate buffered saline (PBS), and resuspended in chromatin immunoprecipitation (ChIP) lysis buffer (150 mM NaCl, 1 % Triton X-100, 0.1 % SDS, 20 mM Tris–HCl pH8.0, 2 mM EDTA). Chromatin was sheared to 200–600 bp and immunoprecipitated with 5 μg of antibody. Immunoprecipitated DNA was purified with QIAquick columns (ZymaResearch).
ATAC-seq protocol:NIH3T3 cells (5 × 104) were pelleted by centrifugation and resuspended in 50 µL of cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630), gently pipetting up and down 10 times. Nuclei were pelleted by centrifugation at 2500g for 10 min at 4°C and resuspended in 25 µL of 2x TD Buffer (Illumina Cat #FC-121-1030), containing 8 µL of Tn5 Transposes (Illumina Cat #FC-121-1030) and 17 µL of nuclease free water. The rection was incubated for 30 min at 37°C. Tagmented DNA was purified by using a Zymo Research DNA Clean & Concentrator™-5 - Capped Columns.
RNA-seq protocol:The RNA sequencing library preparation and sequencing procedures were carried out according to Illumina protocols. Briefly, poly(A)-mRNA was purified from 5 μg of RNA with streptavidin-coated magnetic beads. After chemical fragmentation, mRNA fragments were reverse-transcribed and converted into double-stranded cDNA. Following end repair and A-tailing, paired-end adaptors were ligated to the ends of the DNA fragments. The ligated products were amplified with 18 cycles of PCR followed by purification using AMPure beads (Beckman Coulter). The enriched libraries were diluted to a final concentration of 5 nM.
ChIP-seq libraries were prepared using TruSeq ChIP Sample Preparation Kit (Illumina, Inc., USA) or NEBNext UltraII DNA Library Prep Kit for Illumina (BioLabs, catalog # E7645S).  Libraries were amplified using 15 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.
RNA-seq library were prepared using TruSeq RNA Library Prep Kit (Illumina, Inc., USA)
ATAC-seq libraries were amplified using NEBNext High-Fidelity 2× PCR Master Mix (New England Biolabs). The libraries were size-selected  by adding 1.8X volume Agencourt AMPure XP beads (Beckman, 63881).
CAGE-seq libraries were prepared by DNAFORM (Yokohama, Kanagawa, Japan).

tag: cell line

tag: cell type

value: Human immortalised myelogenous leukemia cell line

tag: chip antibody

tag: treatment

value: Zinc Finger Nuclease treatment to downregulate BORIS expression

tag: genotype

value: K562 mutant, BORIS downregulation


title: DK_fio1_3

description: RNA-seq of fio1 in the dark

library_source: transcriptomic

molecule: total RNA

tag: tissue


title: ChIP-seq with BORIS Abs in 293T+BORIS cells

value: Human embryonic kidney 293 cells

value: BORIS custom-made mouse monoclonal (characterized in  PMID:21659515)

value: Transient ectopic expression of of BORIS from CpG-free plasmid (InvivoGen)

value: 293T transiently expressing BORIS


title: RSV convalescence, comorbidity [A4398_287]

type: RNA

city: Leuven

first: Deniz

last: Oner

address: Gaston Geenslaan

country: Belgium

institute: KU Leuven

description: Gene expression data of infants from RESCEU case-control cohort

hyb_protocol: After fragmentation, denaturation and end-labeling the targets are hybridized on the single GO Screen plate, according to manufacturer’s instructions (Thermo Fisher; GeneChip Pico Reagent Kit).

scan_protocol: Single sample cartridge arrays were stained on a GeneChip Fluidics Station 450 and scanned on a GeneChip scanner 3000 7G while array plates were stained and imaged on the GeneTitan Multi-Channel Instrument.

data_processing:
Microarray data were preprocessed using R, Bioconductor package 40,41. Robust Multi-Array Average (RMA) function was used to normalize the raw data 42. Outliers were removed from the downstream data analysis based on visual guidance on principal component (PC) spectral map and sample clustering (Pearson correlation with complete linkage).
The clinical data necessary for batch correction (site of sample collection) is accessible by request only from the submitting party.

label: biotin

source_name: whole blood

label_protocol: First strand cDNA was synthesized with a combination of a Poly-dT and random primers containing a 5′-adaptor sequence. A 3’-adaptor was added to the single stranded cDNA followed by low-cycle PCR amplification. The cDNA was used as a template for in vitro transcription (IVT) that produces amplified amounts of antisense mRNA, (cRNA). The cRNA was then used as input for a second round of cDNA synthesis, producing double stranded cDNA.

extract_protocol: The whole blood samples were collected in Paxgene tubes (PAXgene® Blood RNA Tube, BD) and stored at –80 °C until the processing. The RNA was extracted using QIAsymphony PAXgene Blood RNA Kit (QIAGEN) according to the manufacturer’s instructions. After the quality control, the RNA was further processed for Clariom™ GOScreen microarray (Thermo Fisher).

value: whole blood

tag: gender / sex

value: Male

tag: age in days

tag: age group

tag: visit

value: RSV convalescence visit

tag: disease classification at rsv visit based on resvinet score

value: 3 - Moderate


title: RSV convalescence, comorbidity [A4398_293]


title: ChIP-seq with H2AZ Abs in K562 cells with depleted BORIS

value: H2A.Z (Abcam, catalog # ab4174)


title: RSV convalescence, comorbidity [A4398_257]

value: Female


title: AC-30d-rep2

city: Bundoora

first: Mathew

middle: G

last: Lewsey

state: VIC

address: AgriBio, 5 Ring Rd

department: Animal, Plant and Soil Sciences

country: Australia

institute: La Trobe University

description: raw count and normalized data were provided as processed data file

data_processing:
Sequence data quality were assessed using FastQC and Trim Galore were used to trim adaptor sequence and low-quality data.
The trimmed reads were align to SortMeRNA rRNA database using bowtie2 and unaligned reads were extracted and quantified using Salmon with the OT3098 Version 2 reference transcripts database.
Quantified reads counts were used for differential gene expression analysis using Deseq2.
Assembly: OT3098 Version2
Supplementary files format and content: tab-delimited text files include normalized values using variance stabilizing transformation (VST) for each Sample

organism: Avena sativa

source_name: whole grain

growth_protocol: Avena sativa cv. Morgan (AC) and Morrison (CDC) grains were germinated for 3, 6, 24 and 48 h in controlled growth chambers under long day conditions (23˚C 14h day/19˚C 10h night) on 3 layers of sterilised Whatman paper damp with sterile water.

extract_protocol:
The RNA was extracted using Spectrum™ Plant Total RNA Kit from Sigma-Aldrich (ref. STRN250-1KT) with some additional optimisation steps. Samples were pre-treated with 0.03% (v/v) α-amylase (Sigma-Aldrich, ref. A4551-100MG) in the lysis buffer. Ground frozen samples were vortexed for 1 min with the mixture and incubated at RT for 6 min. 0.01 % (v/v) β-mercaptoethanol was added to the samples and vortexed again for 30 sec. Samples were centrifuged at RT for 5 min at max r.p.m. Supernatant was transferred to the filtering columns and Spectrum™ Plant Total RNA protocol was used following manufacturer’s instructions including the on-column DNase treatment. Protocol A was used for the binding buffer solution. Samples were further cleaned up using RNA Clean & Concentrator-5 kit (Zymo Research, ref. R1016) to ensure purity and concentration.
Libraries were generated using TruSeq® Stranded mRNA Library Prep Kit (Illumina) according to manufacturer’s instructions and sequenced on a Nextseq 500 platform (Illumina) as single-end reads.

value: whole grain

value: developing grain

value: AC Morgan

tag: time

value: Day 30


title: DK_cry1cry2_2

description: RNA-seq of cry1cry2 in the dark

value: seedling

value: dark


title: DK_mta_3

description: RNA-seq of mta in the dark

value: mta


title: DK_Col_3

description: RNA-seq of WT in the dark

value: WT


title: AC-30d-rep1


title: DK_mta_2

description: RNA-seq of mta in the dark


title: AC-30d-rep3


title: DK_cry1cry2_3

description: RNA-seq of cry1cry2 in the dark


title: AC-25d-rep3

value: Day 25


title: DK_Col_2

description: RNA-seq of WT in the dark


title: AC-40d-rep3

value: Day 40


title: DK_fio1_1

description: RNA-seq of fio1 in the dark


title: AC-35d-rep1

value: Day 35


title: DK_cry1cry2_1

description: RNA-seq of cry1cry2 in the dark


title: BL_mta_3

description: RNA-seq of mta in blue light(30 μmol m−2 s−1)

value: blue light(30 micromol m−2 s−1)


title: DK_fio1_2

description: RNA-seq of fio1 in the dark


title: RSV convalescence, comorbidity [A4398_224]

value: whole blood


title: RSV convalescence, comorbidity [A4398_238]

value: Male

value: RSV convalescence visit


title: RSV convalescence, comorbidity [A4398_181]

value: 3 - Moderate


title: RSV convalescence, comorbidity [A4398_271]

value: Female


title: AC-25d-rep2

value: whole grain


title: RSV convalescence, comorbidity [A4398_179]


title: BL_mta_2


title: BL_fio1_2

description: RNA-seq of fio1 in blue light(30 μmol m−2 s−1)


title: BL_mta_1


title: BL_fio1_1


title: BL_cry1cry2_3

description: RNA-seq of cry1cry2 in blue light(30 μmol m−2 s−1)


title: AC-25d-rep1

value: developing grain


title: AC-20d-rep2

value: AC Morgan

value: Day 20


title: BL_fio1_3

value: seedling


title: RSV convalescence, comorbidity [A4398_178]


title: DK_Col_1

description: RNA-seq of WT in the dark

value: dark


title: AC-20d-rep3


title: BL_cry1cry2_2


title: BL_cry1cry2_1


title: AC-20d-rep1


title: AC-15d-rep3

value: Day 15


title: BL_Col_2

description: RNA-seq of WT in blue light(30 μmol m−2 s−1)

value: WT


title: RSV convalescence, comorbidity [A4398_164]


title: BL_Col_1


title: RSV convalescence, comorbidity [A4397_1087]


title: Biol Rep 403_3

city: London

first: Seda

last: Eminaga

address: Westminster Bridge Road, St Thomas's Hospital

department: Cardiovascular Division

country: United Kingdom

institute: King's College London

description: 403_3 (norm)

data_processing:
Data was processed according to a detailed protocol published in Eminaga et al CPMB 2013. Briefly, BioPerl module for SAGE comparison (http://search.cpan.org/∼scottzed/ Bio-SAGE-Comparison-1.00/) and custom analysis package was used.  After the  removal of 3' adapter and barcode sequences, the sequences with <17 nucleotides were eliminated and the remaining sequencing reads were matched to reference mature miRNA sequences downloaded from miRBase.  Next, the read counts were normalised to counts per million by dividing the total read counts of a single miRNA by the total read counts of the sample and multiplying by 10^6.
Assembly: https://www.mirbase.org/ftp/15/
Supplementary files format and content: .xlsx files contain normalised read counts per million

organism: Mus musculus

source_name: left ventricle-heart

extract_protocol:
Total RNA was isolated using miRVana miRNA isolation kit (Ambion, cat no AM1560) according to manufacturer's instructions.
The multiplexed miRNA libraries were prepared as described in detail in Eminaga et al, 2013 (Curr Protoc Mol Biol. 2013 Jul;Chapter 4:Unit 4.17) and Vigneault et al 2012 (Curr Protoc Hum Genet. 2012 Apr;Chapter 11:11.12.1-11.12.10).

treatment_protocol: Aged mice >50 weeks of age

value: left ventricle-heart

value: mutant (aMHC403/+)

value: Aged mice


title: Biol Rep 403_2

description: 403_2 (norm)


title: AC-15d-rep2


title: Biol Rep WT_3

description: WT_3 (norm)


title: Biol Rep 403_1

description: 403_1 (norm)


title: AC-15d-rep1


title: RSV convalescence, comorbidity [A4398_299]

value: 2 - Mild


title: Biol Rep WT_1

description: WT_1 (norm)


title: AC-10d-rep3

value: Day 10


title: BL_Col_3

value: blue light(30 micromol m−2 s−1)


title: Prime editing library of CTT insertions in synHEK3 reporters in wild-type K562 cells Pool1

city: Seattle

first: Xiaoyi

last: Li

state: WA

address: 3720 15th Ave NE

department: Department of Genome Sciences

institute: University of Washington

description: synHEK3 amplicon sequencing library

data_processing:
T7-assisted reporter mapping: Sequencing reads were first demultiplexed using the bcl2fastq software. Under the current library design and sequencing scheme, Read1 started from genomic sequence and extended into the integrated synHEK3 construct, while Read2 contained reporter barcode information. Therefore, 1) for each sequencing read pair, the 16-bp reporter barcode was extracted from Read 2 and attached to the read name of Read 1. 2) Read1 was trimmed using cutadapt (v4.1) with following parameters: --cores=4 --discard-untrimmed -e 0.2 -m 10 -O 8 -a CCCTAGAAAGATAGTCTGCGTAAAATTGACGCATG. The adapter corresponded to the 3’ITR of piggyBac transposon. Since parameter “--discard-untrimmed” was used, only reads spanning insertion junctions were kept and trimmed. 3) Trimmed sequences were aligned to the GRCh38 reference genome using bwa mem (v0.7.17). The “-Y” option was used to enable soft clipping for supplementary alignments. 4) Reads uniquely (without XA:Z tag) and contiguously mapped near putative piggyBac landing pads (TTAA motifs) were kept using samtools (v1.9) and a custom script. 5) Aligned reads were converted to BED format using the sam2bed function in bedops (v2.4.35). Reads aligned to standard chromosomes were kept. 6) Insertion points were calculated for all reads based on strand of alignment. And reads were sorted by the insertion coordinates. 7) The first 8-bp of reads were used as UMIs. A custom script was used to collapse reads at a per-location, per-barcode, per UMI basis. A barcode-location-UMI count table was generated. 8) synHEK3 barcodes <3 Levenshtein Distance at each location were collapsed and barcodes with > 3 UMIs were kept. 9) The count table was converted to a GenomicRanges object in R. Coordinates of the last 4 base pairs of aligned reads were designated as genomic locations of the inserted synHEK3 reporters. 10) “Landing pads” of the mapped synHEK3 reporters were retrieved using the getSeq() function in the BSgenome package. Reporters that didn’t have a TTAA sequence (which could be due to PCR error, mapping error, or the use of non-canonical landing pads) were removed. 11) SynHEK3 barcodes mapped to more than one location were removed.
SynHEK3 amplicon sequencing library: Sequencing reads from the Illumina NextSeq platforms were first demultiplexed using the bcl2fastq software. The 16-bp reporter barcodes were extracted from read and attached to its read name. Sequences around the CRISPR cut site were extracted for all reads. A barcode-editing outcome table was generated. For prime editing experiments, a custom script was used to align sequences to a reference sequence and count mutation frequency for every barcode. For Cas9 mutagenesis analysis, all sequences were aggregated and editing outcomes (alleles) with the highest number of counts were selected. These most frequent alleles were then aligned to reference sequences using needleall with the following parameters: -gapopen 20 -gapextend 0.5 -endopen 20. A custom script was used to annotate the mutational events.
Amplicon sequencing of endogenous genes: Sequencing reads were demultiplexed using the bcl2fastq software (Illumina). A custom script was used to determine frequencies of the introduced substitutions.
Assembly: GRCh38
Supplementary files format and content: CRISPRa_K562_new.csv contains editing efficiencies in the CRISPRa experiments in K562 cells
Supplementary files format and content: CRISPRa_WTC11_new.csv contains editing efficiencies in the CRISPRa experiments in WTC11 cells
Supplementary files format and content: PE2max_endogenous_121_K562.csv contains editing efficiencies of the 121 epegRNAs in K562 cells
Supplementary files format and content: PE_IL2RB_libraries.csv contains corrected editing efficiencies of epegRNA pools targeting IL2RB (with and without CRISPR activation of IL2RB)
Supplementary files format and content: T7-WT-Pool1.csv contains mapped locations, editing outcomes, and chromatin scores of synHEK3 reporters in wild-type K562 cells
Supplementary files format and content: T7-WT-Pool2.csv contains mapped locations, editing outcomes, and chromatin scores of synHEK3 reporters in wild-type K562 cells

growth_protocol: K562 cells (CCL-243) were purchased from ATCC and maintained in RPMI 1640 medium (Gibco) supplied with 10% FBS (Hyclone) and penicillin/streptomycin (Gibco, 100 U/ mL). The DHFR-dCas9-VPH (VP48-P65-HSF1) WTC11 (human iPSCs) line was generated by the Martin Kampmann lab (Tian et al. 2021). Cells were maintained on Geltrex (Gibco) coated plates in the mTeSR Plus medium (STEMCELL Technologies) supplied with 10 uM Y-27632 (Stemgent). 20 uM trimethoprim was added to culture for stabilization of dCas9-VPH. All cells were kept in a humidified incubator at 37 oC, 5% CO2.

extract_protocol:
K562 and WTC11 cells were lysed in a lysis buffer [100 mM Tris-HCl pH8.0, 0.05% SDS and 0.04 mg/mL proteinase K(Thermo Scientific)], and incubated at 50 oC 60 min and 80 oC 30 min.
T7-assisted reporter mapping: gDNA of K562 cells was purified using the DNeasy Blood & Tissue Kit (QIAGEN) and in vitro transcribed with the HiScribe T7 High Yield RNA Synthesis Kit (New England Biolabs). Briefly, each reaction (20 uL) contained 0.3~1 ug gDNA, NTPs (10 mM each) and 2 ul T7 RNA Polymerase Mix. The reaction mixture was incubated at 37 oC for 16 hours. Then, gDNA was digested with 2.5 uL DNase (Qiagen) in a 100 uL reaction at room temperature for 30 min. RNA was extracted with TRIzol LS Reagent (Invitrogen), and aqueous phase was precipitated with 1 volume of isopropanol and 5 ug Glycogen (Invitrogen) at -80 oC for 1 hour. RNA pellet was collected by centrifugation at 21,000 x g at 4 oC for 1 hour. The pellet was washed with 80% ice-cold ethanol and resuspended in 11.5 uL nuclease-free water. For reverse transcription, RNA was incubated with 0.5 uL 100 uM RT primer p6 (5’-TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGNNNNNNNN-3’) and 1 uL 10 mM dNTP at 65 oC for 5 min and cooled on ice. Then, 4 uL 5X RT buffer, 1 uL 100 mM DTT, 1 uL RNaseOUT (40 U/uL) and 1 uL SuperScript IV RT (200 U/uL, Invitrogen) were added and the reaction mixture was incubated at 23 oC for 10 min, 50  oC for 15 min and 80 oC for 10 min. cDNA library was amplified with KAPA2G Robust HotStart polymerase, using primers p7 (5’- GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGAAAGGAAGCCCTGCTTCCTCCAGAGGG-3’, 0.5 uM) and p8 (5’- TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG-3’, 0.5 uM). PCR reaction was performed as follows: 95 oC 3 min; 95 oC 15 s, 65 oC 15 s, 72 oC 30 s, 16~18 cycles; and 72 oC 1 min. The PCR product was subjected to double-sided size selection (0.5X, 0.9X) and cleaned up with AMPure XP beads. The resulting product ranged from 200 to 1000 bp. To prepare Illumina sequencing libraries, 5-10 ng PCR product was re-amplified with the Nextera P5 and TruSeq P7 library index primers for 5 cycles. The final PCR product underwent another round of double-sided size selection (0.5X, 0.9X) and cleaned up with AMPure XP beads. The library was sequenced on an Illumina MiSeq in paired-end mode (Read 1: 254 bp; Read2: 55bp). Amplicon sequencing of synHEK3 reporters: 100~250 ng gDNA or cell lysates were amplified using KAPA2G Robust HotStart ReadyMix with primers p9 (5’-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTCTACCCCGACCACATGAAGCAGC-3’, 0.5 uM) and p10 (5’-TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGNNNNNNNNNNGACCATGTCATCGCGCTTCTCGT-3’, 0.5 uM). PCR reaction was performed as follows: 95 oC 3 min; 95 oC 15 s, 68-N oC 15 s, 72 oC 30 s, for 9 cycles (N was cycle number); 95 oC 15 s, 65 oC 15 s, 72 oC 30 s, for 11 cycles; and 72 oC 1 min. To ensure enough coverage and accurate measurement of editing efficiencies, for the K562 synHEK3 pool, we pooled products from at least 16 PCR reactions. The PCR product was purified with AMPure XP beads. 5 ng PCR product was re-amplified with the Nextera P5 and TruSeq P7 library index primers for 5 cycles.  Other amplicon sequencing: Cell lysates or plasmids were directly used for PCR with the KAPA2G Robust HotStart ReadyMix with primers (0.5 uM each) designed for the endogenous targets. PCR reaction was performed as follows: 95 oC 3 min; 95 oC 15 s, 66-N oC 15 s, 72 oC 40 s, for 8 cycles (N was cycle number); 95 oC 15 s, 60 oC 15 s, 72 oC 40 s, for 11 cycles; and 72 oC 1 min. The PCR product was purified with AMPure XP beads. 5 ng PCR product was re-amplified with the Nextera P5 and TruSeq P7 library index primers for 5 cycles.
Amplicon sequencing

treatment_protocol: Transfections of K562 cells were performed using a Lonza Bioscience 4D-Nucleofector system and the SF Cell Line 4D-Nucleofector X kits (Lonza). For single nucleocuvettes (100 uL), 1-2 x 106 cells were transfected with up to 4 ug DNA. For 96-well Nucleocuvette plates (20 uL), 2 x 105 ~ 5 x 105 cells were transfected with up to 2 ug DNA. Program code was FF-120. CRISPRa experiments (K562): On Day 0, 4 x 105 K562 dCas9-VP64 cells were transfected with PB-CMV-MCP-XTEN80-p65-Rta-3xNLS-P2A-T2A-mPlum (600 ng) and paired pU6-Sp-gRNA-2XMS2 (200 ng each) plasmids targeting the same promoter. On Day 2, 4 x 105 cells from the previous transfection were transfected with pCMV-PEmax (Addgene: 174820) or PB-UCOE-EF1a-PE2max-P2A-mCherry-PGK-Blast (800 ng) and the pU6-Sp-pegRNA plasmids (400 ng). All transfections were performed using the SF Cell Line 96-well Nucleofector Kit (Lonza) with program FF-120. Cells transfected with PB-UCOE-EF1a-PE2max-P2A-mCherry-PGK-Blast were selected with 2 ug/mL Puromycin 24 hours after transfection for 2 days. Cells were lysed at Day 5 or 6 for gDNA collection. CRISPRa experiments (WTC11): On Day 0, 2 x 105 the DHFR-dCas9-VPH WTC11 cells were transfected with PB-CMV-MCP-XTEN80-p65-Rta-3xNLS-P2A-T2A-mPlum (2100 ng) and paired pU6-Sp-gRNA-2XMS2 (700 ng each) plasmids targeting the same promoter. 20 uM Trimethoprim was added to induce dCas9-VPH. On Day 3, 2 x 105 cells from the previous transfection were transfected with PB-UCOE-EF1a-PE2max-P2A-mCherry-PGK-Blast (2000 ng) and the pU6-Sp-pegRNA plasmids (1000 ng). All transfections were performed using the P3 Prime Cell 96-well Nucleofector Kit (Lonza) with program CB-150. Cells were continued to be treated with 20 uM Trimethoprim and were selected with 2 ug/mL Puromycin 24 hours after transfection for 1 day. Cells were lysed at Day 5 or 6 for gDNA collection.

value: lymphoblast

value: wild-type


title: Biol Rep WT_2

description: WT_2 (norm)


title: Prime editing library of CTT insertions in synHEK3 reporters in wild-type K562 cells Pool2

description: synHEK3 amplicon sequencing library


title: CD26KD / TGF-β1 4

city: Chiba

first: Takeshi

last: Kawasaki

address: 1-8-1, Inohana, Chuoku

department: Respirology

country: Japan

institute: Chiba University

data_processing:
Removal of poly A tail and adapter sequences were performed using BBDuk (BBMap version 38.96) with the following settings (k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20).
Trimmed reads were mapped to hg38 using STAR version 2.7.6a with the following settings (--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000).
Read counts for each gene were obtained using HTSeq-count version 1.99.2 with the following settings (-m intersection-nonempty -s yes).
Assembly: hg38
Supplementary files format and content: xlsx files include raw conts for each sample
Supplementary files format and content: xlsx files include RPM values for each sample

source_name: palmonary artery smooth muscle cell

extract_protocol:
RNA was harvested using ISOGEN reagent (Life Technologies, Carlsbad, CA, USA).
Purified total RNA (200 ng) was used for RNA library preparation, according to the instructions of the Quant Seq 3' mRNA-seq library preparation kit FWD of Illumina (Lexogen, Vienna, Austria). The RNA libraries were sequenced on an Illumina NextSeq 500 system with 75-nt-long reads.

value: palmonary artery smooth muscle cell

tag: age

tag: Sex

value: male

tag: race

value: Caucasian


title: RSV convalescence, comorbidity [A4398_329]

value: whole blood

value: Male

value: RSV convalescence visit


title: AC-10d-rep1

value: whole grain

value: developing grain

value: AC Morgan


title: CD26KD / TGF-β1 3


title: RSV convalescence, comorbidity [A4398_208]


title: RSV convalescence, comorbidity [A4398_159]

value: 3 - Moderate


title: CD26KD / TGF-β1 2


title: CD26KD / TGF-β1 1


title: AC-5d-rep3

value: Day 5


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_167rr]

value: Female


title: CD26KD / PBS 4

value: PBS


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_137]


title: AC-5d-rep2


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_024rr]


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4397_1081]


title: CD26KD / PBS 3


title: AC-10d-rep2

value: Day 10


title: Control / TGF-β1 4

value: Control


title: AC-5d-rep1


title: CD26KD / PBS 2


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_507]

value: 2 - Mild


title: CD26KD / PBS 1


title: Control / TGF-β1 3


title: Control / TGF-β1 2


title: Control / TGF-β1 1


title: HSVTK_GANC_1

city: Kunming

first: Li

middle: Qiao

last: hua

state: Yunnan

address: No. 727, Jingming South Road, Chenggong District

institute: Kunming University of Science and Technology

data_processing:
Raw data were filtered using fastp software (v 0.23.2), and reads were mapped to GRCm39 using HISAT2 (v 2.1.0), featureCounts (v 2.0.1) is used to count the reads mapped to each gene
Differential expression analysis between the two comparison sets was performed using DESeq2 software (1.40.2)
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: mouse embryonic stem cells

extract_protocol:
RNA extraction using the phenol/chloroform method,1 ug total RNA of each sample was used as the starting material to construct a transcriptome sequencing library
According to the operating instructions of VAHTS Universal V6 RNA-Seq Library Prepkit for Illumina (NR 604-01/02)

value: mouse embryonic stem cells

tag: group

value: HSVTK

value: GANC


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_487]


title: Control / PBS 3

value: palmonary artery smooth muscle cell

value: male

value: Caucasian


title: Control / PBS 1


title: Control / PBS 4


title: HSVTK_DMSO_1

value: DMSO


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_337]

value: whole blood

value: RSV convalescence visit


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_461]


title: Control_GANC_2

value: control


title: MIO-M1-secreted EV, P25

first: William

last: Lamb

state: England

address: UCL Institute of Ophthalmology, 11-43 Bath Street, 11-43 Bath Street

institute: UCL Institute Ophthalmology

data_processing:
Sequence reads were demultiplexed and text-based fastq.gz files storing sequence and quality scores for each sample were generated using the software bcl2fastq.gz (Illumina).
Adapters were trimmed using "Cutadapt" tool, raw reads were aligned to miRbase database (release 21) using the "Bowtie2" read alignment tool.
R-Bioconductor statistical package DESeq2
Assembly: miRBase (release 21)
Supplementary files format and content: Tab-deliminated text file includes raw counts for each sample.

growth_protocol: MIO_M1 cells were cultured under normal conditions (36 C, 5% CO2) in DMEM containing 10% FCS and 1% penicillin/ streptomycin.

extract_protocol:
Qiagen Rneasy kit was used to isolate total RNA samples from cell pellets (Qiagen). Total Exosome RNA Isolation Kit (Invitrogen™) was used to isolate total RNA from EV pellets.
The QIAseq miRNA Library Kit (Qiagen) was used to prepare miRNA libraries according to manufacturers instructions.

treatment_protocol: Cultures of 80% confluence were washed 5 x with sterile, particle-depleted PBS, and cultured in serum-free DMEM for 24 hours. Culture supernatants were then collected, and processed for isolation of secreted extracellular vesicles by sequential rounds of centrifugation.

value: Muller glia

value: WT

tag: fraction

value: secreted EV


title: MIO-M1-secreted EV, P27

tag: cell line


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_473]

value: Female


title: Control_GANC_1

tag: cell type


title: HSVTK_GANC_2


title: MIO-M1-secreted EV, P23


title: MIO-M1 whole cell RNA, P26

value: whole cell RNA


title: MIO-M1 whole cell RNA, P24


title: Control_DMSO_2


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_216]

value: 3 - Moderate


title: MIO-M1 whole cell RNA, P22


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_022rr]

value: 2 - Mild


title: Control_DMSO_1

value: mouse embryonic stem cells


title: P42

city: Torino

first: Giovanni

last: Birolo

state: TO

address: Via Santena 19

department: Medical Sciences

country: Italy

institute: University of Turin

data_processing:
Adapter removal (cutadapt).
Alignment (bwa).
Alignment filtering (custom script).
Sample merging into raw count table.
Assembly: miRBase 22
Supplementary files format and content: *_clean_raw_counts.tsv: Tab-delimited text file includes raw (unnormalized) sncRNA expression counts.

source_name: Plasma Evs

extract_protocol:
Standard phenol-chloroform method.
NEBNext Multiplex Small RNA Library Prep Set for Illumina (Protocol E7330, New England BioLabs Inc., USA).

value: Plasma Evs

value: female

tag: disease

value: Stomach cancer

tag: caco


title: HSVTK_DMSO_2

value: HSVTK

tag: treatment


title: Control / PBS 2

tag: tissue

value: palmonary artery smooth muscle cell

value: male

value: Caucasian

tag: genotype

value: Control

value: PBS


title: P43


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_215]

value: whole blood

tag: gender / sex

tag: age in days

value: RSV convalescence visit


title: P41

value: Pancreas cancer


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_143]

value: Female

tag: age group

tag: visit


title: P39

value: Colon cancer


title: P38


title: P40


title: Neonate Urothelium Replicate 3

city: Columbus

first: Xin

last: Wang

state: OH

address: 700 Children's Dr,

department: The Kidney and Urinary Tract Center

institute: Nationwide Children's hosptial

description: FACS enriched Krt5-tdT-positive bladder urothelial cells

data_processing:
Demultiplexed FASTQ files were utilized for a comprehensive analysis pipeline encompassing data normalization, differential gene expression detection, and functional enrichment. We obtained the mm10 mouse genome and its corresponding reference gene set from UCSC. Adapter sequences were removed, and high-quality filtered reads were generated using Trim Galore v0.6.6.
Tophat v2.1.2 was used to map these high-quality reads to the mm10 genome. Successfully mapping reads were sorted, and unique mapped reads was retained by SAMtools v1.15. Quantification of reads per gene was performed by Htseq-count v0.12.4 with a union gene region parameter. EdgeR_3.42.4 was used to identify differentially expressed genes (DEGs). We filtered out any gene that is sparsely quantified in samples with loose criteria, i.e., a total count less than five across all samples, and more than two sample with cpm greater than 0.5. Then, quantile normalization method was used to eliminate or minimize technical variability. Principal component analysis (PCA) was used as an unsupervised dimensionality for gene abundance levels across samples.
We defined DEGs as those with a fold change greater than 1.5 and an adjusted P value smaller than 0.05. Gene ontology (GO) analysis for the functional enrichments of up-regulated and down-regulated genes was performed by clusterProfiler_4.8.2. A Chi-square test was used to test for statistically enriched pathways and an FDR of < =0.05 was used as the significance threshold to detect enriched molecular functions, biological processes, and cellular components. Finally, transcription factors and their activities were predicted and estimated by decoupleR 2.5.3. For data visualization, we mainly used a series of R packages such as "ggplot2", "enrichplot", “pheamap” to create heatmaps, volcano plots, bar plots and venn diagrams.
Assembly: mm10
Supplementary files format and content: Ensembl gene ID, Count

source_name: bladder

growth_protocol: Animals were maintained in accordance to Public Health Service Animal Welfare Assurance no. A3544-01 and Institutional Animal Care and Use Committee no. AR16-00058.

extract_protocol:
Cells were sorted directly into the Takara SMART-Seq HT lysis buffer containing RNase Inhibitor + 3’ SMART-Seq CDS Primer II A (SMART-Seq® HT Kit, Takara Bio USA, Ann Arbor, MI). Samples were immediately frozen on dry ice, stored at -80ºC, then transported to The Ohio State University Comprehensive Cancer Center NextGen Sequencing Shared Resource facility.
lcRNAseq libraries were generated using the Takara SMART-Seq HT Kit, Nextera XT DNA Library Preparation and Nextera XT Index kits (Illumina, Inc., San Diego, CA). Samples were evaluated using a High Sensitivity DNA Bioanalyzer and Tapestation HS-DNA1000 Bioanalyzer (Agilent), and Qubit (ThermoFisher).
Sequencing was performed using a NovaSeq6000 SP 200 cycle (≤2x100bp) flow cell.

treatment_protocol: The Adult cohort received tamoxifen (75mg/kg body weight in corn oil, via ip) at postnatal day 35, and were euthanized at postnatal day 42. The Neonate cohort received tamoxifen (75mg/kg body weight in corn oil, via ip) at postnatal day 5, and were euthanized at postnatal day 7. Bladders were harvested in ice cold 1X PBS, everted with blunt forceps, and incubated with Dispase II (2.5 mg/mL, Sigma-Aldrich, St. Louis, MO) in 1X PBS/50mM HEPES for 1 hour at 37ºC. Urothelium was scraped, disaggregated in TrypLE Express (Sigma-Aldrich, St. Louis, MO), then passed through a 70 µm strainer. Red blood cells were lysed using Ammonium-Chloride-Potassium (ACK; Thermofisher, Waltham, MA) lysis solution, and cells were resuspended in 1X PBS containing 2% Fetal Bovine Serum (FBS, Thermofisher, Waltham, MA). The BD Influx System (BD Biosciences, San Jose, CA, USA) was used to sort 300 tdTK5

value: bladder

value: bladder urothelium Krt5 cell

tag: strain background

value: Neonate (Tamoxifen (ip) at postnatal day 5, euthanized at postnatal day 7)


title: Neonate Urothelium Replicate 4


title: P36

value: Plasma Evs

tag: age


title: Neonate Urothelium Replicate 2


title: P35

tag: Sex


title: Neonate Urothelium Replicate 1


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_539]

tag: disease classification at rsv visit based on resvinet score

value: 2 - Mild


title: P34

value: female


title: P32


title: P33


title: P31


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_538]


title: P30


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_535]


title: P29


title: P28


title: Adult Urothelium Replicate 2

value: Adult (Tamoxifen (ip) at postnatal day 35, euthanized at postnatal day 42)


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_528]


title: P24

value: Stomach cancer


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_482]


title: P37

value: male


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_542]


title: Adult Urothelium Replicate 1


title: P22


title: RNA-seq in NIH3T3_pBIG_BORIS cells_transfected with siH2AZRNA,  Dox treatment for 48h

value: Mouse immortalized embryonic fibroblast cell line

tag: chip antibody

value: The cells were cultured in the presence of doxycycline (Dox) concentration (1 μg/mL) for 48h

value: NIH3T3 stably transfected with dox-inducable pBIGi BORIS-expressing plasmid (pBIG_BORIS) and transiently transfected with siH2AZRNAs to downregulate H2az1 gene expression


title: P21


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_525]

value: whole blood


title: RNA-seq in NIH3T3_pBIG_BORIS cells_transfected with siCtrlRNA,  Dox treatment for 48h

value: NIH3T3 stably transfected with dox-inducable pBIGi BORIS-expressing plasmid (pBIG_BORIS) and transiently transfected with siCtrlRNAs


title: P19


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_465]

value: RSV convalescence visit


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_404]

value: Female


title: P20

value: Colon cancer


title: RNA-seq in NIH3T3_pBIG_BORIS cells_transfected with siCtrlRNA, no Dox treatment

value: The cells were cultured in the absence of doxycycline (noDox), under regular culturing conditions.


title: Adult Urothelium Replicate 3

value: bladder

value: bladder urothelium Krt5 cell


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_355]


title: P16

value: Plasma Evs

value: Control


title: RNA-seq in NIH3T3_pBIG_BORIS cells_with_WashOffDox_24h

value: The cells were cultured in the presence of doxycycline (Dox) concentration (1 μg/mL) for 5 days, with the refreshment of dox every two days. After Dox treatment, the media was replaced with regular media (without dox). The cells were allowed to grow for 24h (washing off Dox).

value: NIH3T3 stably transfected with dox-inducable pBIGi BORIS-expressing plasmid (pBIG_BORIS)


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_469]

value: 2 - Mild


title: P15

value: female


title: RNA-seq in NIH3T3_pBIG_BORIS cells_with_Dox_24h

value: Mouse immortalized embryonic fibroblast cell line

value: The cells were cultured in the presence of doxycycline (Dox) concentration (1 μg/mL) for 24h


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_315]


title: P13

value: male

value: Stomach cancer


title: P12


title: P11


title: RNA-seq in NIH3T3_pBIG_BORIS cells_with_Dox_12h

value: The cells were cultured in the presence of doxycycline (Dox) concentration (1 μg/mL) for 12h


title: P14


title: P23

value: Pancreas cancer


title: P18


title: RNA-seq in NIH3T3_pBIG_BORIS cells_with_Dox_8h

value: The cells were cultured in the presence of doxycycline (Dox) concentration (1 μg/mL) for 8h


title: P9


title: P10


title: P7


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_213]

value: whole blood

value: Female

value: RSV convalescence visit


title: P8


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_220]


title: P17

value: Colon cancer


title: P5

value: Plasma Evs


title: ChIP-seq with HCFC1 Abs in NIH3T3+EV cells

value: HCFC1 (Novus Biologicals, catalog # NB100-68209)

value: Stable ectopic expression of Empty Vector (EV) from CpG-free plasmid (InvivoGen)

value: NIH3T3 stably expressing EV


title: P6

value: Control


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_141]

value: 2 - Mild


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_254]


title: P4


title: ChIP-seq with TBP Abs in NIH3T3+EV cells

value: Mouse immortalized embryonic fibroblast cell line

value: TBP (Abcam, catalog # ab220788)


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_140]


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_136]


title: P3

value: female


title: P1

value: male


title: M43

source_name: Muscle

value: Muscle

value: Stomach cancer


title: ChIP-seq with TBP Abs in NIH3T3+EV cells (clone#1)

value: Stable ectopic expression of Empty Vector (EV) from CpG-free plasmid (InvivoGen) - Clone#1


title: M42


title: ChIPReChIP with BORIS first, followed with CTCF Abs in NIH3T3+EV cells

value: 1st - BORIS custom-made mouse monoclonal (characterized in  PMID:21659515); 2nd:CTCF custom-made mouse monoclonal (characterized in PMID:15731119)


title: M41

value: Pancreas cancer


title: RNA-seq in NIH3T3_pBIG_EV cells_with_Dox_12h

value: The cells were cultured in the presence of doxycycline (Dox) concentration (1 μg/mL) for 12h

value: NIH3T3 stably transfected with dox-inducable pBIGi_EV (Empty Vector (luciferase) expressing plasmid (pBIG_EV)


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_085]

value: whole blood

value: Female

value: RSV convalescence visit


title: M39

value: Colon cancer


title: ChIPReChIP with BORIS first, followed with CTCF Abs in NIH3T3+BORIS (Clone#2) cells

value: Stable ectopic expression of BORIS from CpG-free plasmid (InvivoGen) - Clone#2

value: NIH3T3 stably expressing BORIS


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_076]

value: 2 - Mild


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_074]


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_073]


title: M37


title: M38


title: M35

value: Control


title: ChIP-seq with H3K4me3 Abs in NIH3T3+BORIS cells (clone#4)

value: Mouse immortalized embryonic fibroblast cell line

value: H3K4me3 (Abcam, catalog # ab8580)

value: Stable ectopic expression of BORIS from CpG-free plasmid (InvivoGen) - Clone#4


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_053]


title: ChIP-seq with H3K4me3 Abs in NIH3T3+BORIS cells (clone#3)

value: Stable ectopic expression of BORIS from CpG-free plasmid (InvivoGen) - Clone#3


title: M34

value: Muscle

value: female


title: M32

value: male


title: ChIP-seq with TBP Abs in NIH3T3+BORIS cells (clone#2)

value: TBP (Abcam, catalog # ab220788)


title: ChIP-seq with TBP Abs in NIH3T3+BORIS cells (clone#4)


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_008rr]


title: M33


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_023]


title: M31

value: Pancreas cancer


title: M40


title: ChIP-seq with TBP Abs in NIH3T3+BORIS cells (clone#3)


title: M29


title: M28


title: ChIP-seq with HCFC1 Abs in NIH3T3+BORIS cells (clone#2)

value: HCFC1 (Novus Biologicals, catalog # NB100-68209)


title: M36


title: M23


title: M22


title: ChIP-seq with HCFC1 Abs in NIH3T3+BORIS cells (clone#4)


title: M21


title: Healthy [A4398_520rr]

value: whole blood

value: Female

value: Healthy

value: 1 - Healthy controls


title: Healthy [A4398_501]


title: ChIP-seq with HCFC1 Abs in NIH3T3+BORIS cells (clone#3)

value: NIH3T3 stably expressing BORIS


title: M20

value: Colon cancer


title: M19

value: Stomach cancer


title: M30

value: Control


title: ChIP-seq with H2AZ Abs in NIH3T3+EV cells (clone#1)

value: Mouse immortalized embryonic fibroblast cell line

value: H2A.Z (Abcam, catalog # ab4174)

value: Stable ectopic expression of Empty Vector (EV) from CpG-free plasmid (InvivoGen) - Clone#1

value: NIH3T3 stably expressing EV


title: M17

value: Muscle


title: ChIP-seq with H2AZ Abs in NIH3T3+BORIS cells (clone#4)

value: Stable ectopic expression of BORIS from CpG-free plasmid (InvivoGen) - Clone#4


title: M16

value: male


title: Healthy [A4398_429]


title: ChIP-seq with H2AZ Abs in NIH3T3+BORIS cells (clone#3)

value: Stable ectopic expression of BORIS from CpG-free plasmid (InvivoGen) - Clone#3


title: M15

value: female


title: M24


title: M14


title: Healthy [A4398_437]

value: whole blood


title: Healthy [A4398_438]

value: Female


title: M13


title: ChIP-seq with TBP Abs in NIH3T3+pBIGi_BORIS cells_Treated with WashOff DOX

value: TBP (Abcam, catalog # ab220788)

value: The cells were cultured in the presence of doxycycline (Dox) concentration (1 μg/mL) for 5 days, with the refreshment of dox every two days. After Dox treatment, the media was replaced with regular media (without dox). The cells were allowed to grow for 24h (washing off Dox).

value: NIH3T3 stably transfected with dox-inducable pBIGi BORIS-expressing plasmid (pBIG_BORIS)


title: Healthy [A4398_423]

value: Healthy

value: 1 - Healthy controls


title: M11

value: Control


title: Healthy [A4398_420]


title: M12


title: M18

value: Stomach cancer


title: Healthy [A4398_418]


title: Healthy [A4398_427]


title: M9


title: ChIP-seq with TBP Abs in NIH3T3+pBIGi_BORIS cells_Treated with DOX for 8h

value: Mouse immortalized embryonic fibroblast cell line

value: The cells were cultured in the presence of doxycycline (Dox) concentration (1 μg/mL) for 8hours


title: M8


title: ChIP-seq with TBP Abs in NIH3T3+pBIGi_BORIS cells_Treated with DOX for 24h

value: The cells were cultured in the presence of doxycycline (Dox) concentration (1 μg/mL) for 24hours


title: Healthy [A4398_190]


title: Healthy [A4398_133]


title: M6

value: Muscle


title: M5


title: ChIP-seq with TBP Abs in NIH3T3+pBIGi_EV cells_Treated with DOX for 24h

value: The cells were cultured in the presence of doxycycline (Dox) concentration (1 μg/mL) for 24h

value: NIH3T3 stably transfected with dox-inducable pBIGi_EV (Empty Vector (luciferase) expressing plasmid (pBIG_EV)


title: M2


title: M3

value: Pancreas cancer


title: ChIP-seq with H3K4me3 Abs in NIH3T3+pBIGi_BORIS cells_Treated with WashOff DOX

value: H3K4me3 (Abcam, catalog # ab245240)


title: M1

value: male


title: ChIP-seq with H2AZ Abs in K562 cells

value: Human immortalised myelogenous leukemia cell line

value: H2A.Z (Abcam, catalog # ab4174)

value: wild type


title: ChIP-seq with H3K4me3 Abs in NIH3T3+pBIGi_BORIS cells_Treated with DOX for 24h

value: NIH3T3 stably transfected with dox-inducable pBIGi BORIS-expressing plasmid (pBIG_BORIS)


title: M10

value: female


title: Healthy [A4398_132]

value: whole blood

value: Female

value: Healthy

value: 1 - Healthy controls


title: Healthy [A4398_131]


title: ChIP-seq with H3K4me3 Abs in NIH3T3+pBIGi_BORIS cells_Treated with DOX for 8h

value: Mouse immortalized embryonic fibroblast cell line

value: H3K4me3 (Abcam, catalog # ab8580)

value: The cells were cultured in the presence of doxycycline (Dox) concentration (1 μg/mL) for 8hours


title: M7

value: Muscle


title: ChIP-seq with H2AZ Abs in MCF7+BORIS cells

value: Human breast cancer cell line

value: Ectopic expression of BORIS from CpG-free plasmid (InvivoGen)

value: MCF7 stably expressing BORIS


title: ChIP-seq with H2AZ Abs in MDA-MB-435+EV cells

value: Human melanoma cancer cell line

value: Stable ectopic expression of a control plasmid (empty vector, EV), expressing beta-galactosidase (CpG-free plasmid (InvivoGen))

value: MDA-MB-435 stably expressing EV (Empty Vector)


title: ChIP-seq with H2AZ Abs in MCF7+EV cells

value: H2A.Z (Abcam, catalog # ab4174)

value: Ectopic expression of a control plasmid (empty vector, EV), expressing beta-galactosidase (CpG-free plasmid (InvivoGen))

value: MCF7 stably expressing EV (Empty Vector)


title: Healthy [A4398_130]

value: whole blood


title: ChIP-seq with TBP Abs in NIH3T3+pBIGi_BORIS cells_Treated with no DOX

value: TBP (Abcam, catalog # ab220788)

value: The cells were cultured in the absence of doxycycline (noDox), under regular culturing conditions.

value: NIH3T3 stably transfected with dox-inducable pBIGi BORIS-expressing plasmid (pBIG_BORIS)


title: 1817_Tumor

city: Guangzhou

first: Jinxin

last: Bei

state: Guangdong

address: No. 651, Dongfeng Road East

institute: Sun Yat-sen University Cancer Center

library_source: transcriptomic single cell

data_processing:
Droplet-based sequencing data were aligned and quantified using Cell Ranger (v3.0.2) against the human reference genome (hg38) and EBV reference sequence (Akata; https://github.com/flemingtonlab/public/tree/master/annotation).
Raw gene expression matrices generated from Cell Ranger count were converted to Seurat objects using the Seurat package (v3.2.3).
Assembly: hg38 and Akata
Supplementary files format and content: expression matrix (normalized data; for PBMC and Tumor, respectively)
Supplementary files format and content: cell metadata

molecule: polyA RNA

source_name: Tumor

extract_protocol:
Viable single cells were prepared from the PBMC and tumor biopies of 10 patients with extranodal natural killer/T-cell lymphoma. The concentration of single cell suspension was determined using a Cellometer Auto 2000 instrument (Cellometer) and adjusted to 1,000 cells/μl.
Approximately 14,000 cells were loaded into a CHROMIUM instrument (10x Genomics, USA) according to the standard protocol of the Chromium Single Cell 5' Library Construction Kit (10x Genomics) in order to capture 5,000 ~ 10,000 cells per channel. Briefly, mRNA transcripts were reversely transcribed into cDNA with barcoded indexes at 5'-end, followed by cDNA amplification on a thermal cycler (C1000; Bio-Rad, USA). Amplified cDNA was then used for 5' gene expression library construction and further high-throughput sequencing.

value: NKTCL

value: Tumor


title: ChIP-seq with H3K4me3 Abs in NIH3T3+pBIGi_BORIS cells_Treated with no DOX

value: Mouse immortalized embryonic fibroblast cell line

value: H3K4me3 (Abcam, catalog # ab8580)


title: Healthy [A4398_106]

value: Female

value: Healthy

value: 1 - Healthy controls


title: Healthy [A4398_129]


title: DP710

city: Hangzhou

first: Jiucheng

last: Chen

state: Zhejiang

address: No.866 Yuhangtang Road

institute: Zhejiang University

description: Endometrial tissue collected on day P+7 (7th day of progesterone management) of a hormone replacement therapy (HRT) cycle

data_processing:
Use the fastp tool for quality control of sequencing data. Remove sequences with the following low-quality criteria: Sequences with unknown bases numbering 5 or more. Sequences with a length less than 75bp. Sequences with an average base quality value less than 15. The resulting data after this step is termed Clean Data.
Use the sortmerna tool to align the Clean Data against a ribosomal database. Exclude sequences that align to the ribosomal database. The data obtained after this step is termed de-rRNA Clean Data.
Use the STAR tool to align the de-rRNA Clean Data to the reference genome.
Use the RSeQC tool to assess the quality of the alignment results from STAR.
Use the featureCounts tool to quantify gene expression from the alignment results.
Use the edgeR tool for differential gene expression analysis.
Assembly: hg19
Supplementary files format and content: tab-delimited rawcount files for each samples
Supplementary files format and content: tab-delimited FPKM files for each samples

source_name: endometrium tissue

growth_protocol: All endometrial biopsy samples were obtained with disposable uterine-cavity tissue-suction tubes (Runting), and all the collected samples were stored in All protect Tissue Reagent (QIAGEN). The samples were transported to our laboratory on ice packs and stored at -80°C before processing.

extract_protocol:
RNA was extracted from endometrial tissue using RNAprep Pure Tissue Kit (DP341; Tiangen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using a KAPA Stranded RNA-Seq Library Preparation Kit (KR0934, KAPA Biosystems), following the manufacturer’s instructions.

treatment_protocol: The estradiol administration of all patients was started from the second day of menstruation with 4 mg estradiol valerate (Progynova; Bayer, Leverkusen, Germany) per day. When endometrial thickness was at least 7 mm and endogenous progesterone level was less than 1.5 ng/ml, 90 mg progesterone sustained-release vaginal gel (Crinone; Merck-Serono, Darmstadt, Germany) was applied transvaginally per day. The initial day of progesterone administration was recognized as “P+0” and endometrial biopsies were respectively taken on days P+3, P+5, and P+7 for each patient by a dedicated physician.

value: endometrium tissue

tag: time

value: day P+7


title: 1815_Tumor


title: Healthy [A4398_104]


title: 1814_PBMC

source_name: PBMC

value: PBMC


title: ChIP-seq with H2AZ Abs in NIH3T3+pBIGi_BORIS cells_Treated with WashOff DOX

tag: cell line

value: H2A.Z (Abcam, catalog # ab4174)

value: The cells were cultured in the presence of doxycycline (Dox) concentration (1 μg/mL) for 5 days, with the refreshment of dox every two days. After Dox treatment, the media was replaced with regular media (without dox). The cells were allowed to grow for 24h (washing off Dox).


title: 1815_PBMC


title: 1814_Tumor


title: ChIP-seq with H3K4me3 Abs in NIH3T3+pBIGi_EV cells_Treated with DOX for 24h

tag: cell type

value: The cells were cultured in the presence of doxycycline (Dox) concentration (1 μg/mL) for 24h

value: NIH3T3 stably transfected with dox-inducable pBIGi_EV (Empty Vector (luciferase) expressing plasmid (pBIG_EV)


title: ChIP-seq with H2AZ Abs in MDA-MB-435 cells

value: Human melanoma cancer cell line

value: Stable ectopic expression of BORIS from CpG-free plasmid (InvivoGen)

value: MDA-MB-435 stably expressing BORIS


title: ChIP-seq with H2AZ Abs in NIH3T3+pBIGi_BORIS cells_Treated with DOX for 24h

value: The cells were cultured in the presence of doxycycline (Dox) concentration (1 μg/mL) for 24 hours

value: NIH3T3 stably transfected with dox-inducable pBIGi BORIS-expressing plasmid (pBIG_BORIS)


title: Healthy [A4398_087]

value: whole blood


title: 1813_Tumor

tag: disease

value: NKTCL

value: Tumor


title: DP708


title: DP709


title: 1813_PBMC


title: 1812_Tumor


title: 1811_Tumor


title: 1812_PBMC


title: ChIP-seq with H2AZ Abs in NIH3T3+pBIGi_BORIS cells_Treated with DOX for 8h

value: Mouse immortalized embryonic fibroblast cell line

value: The cells were cultured in the presence of doxycycline (Dox) concentration (1 μg/mL) for 8 hours


title: DP706

value: endometrium tissue


title: DP707

value: day P+7


title: 1817_PBMC

value: PBMC


title: ChIP-seq with H2AZ Abs in NIH3T3+pBIGi_BORIS cells_Treated with no DOX

value: H2A.Z (Abcam, catalog # ab4174)

value: The cells were cultured in the absence of doxycycline (noDox), under regular culturing conditions.


title: ChIP-seq with H2AZ Abs in NIH3T3+pBIGi_EV cells_Treated with DOX

value: The cells were cultured in the presence of doxycycline (Dox) concentration (1 μg/mL) for 24h


title: 1811_PBMC


title: 1808_PBMC


title: DP705


title: DP703


title: ChIP-seq with BORIS Abs in NIH3T3+pBIGi_BORIS cells_Treated with WashOff DOX_24h

value: BORIS custom-made mouse monoclonal (characterized in  PMID:21659515)

value: The cells were cultured in the presence of doxycycline (Dox) concentration (1 μg/mL) for 5 days, with the refreshment of dox every two days. After Dox treatment, the media was replaced with regular media (without dox). The cells were allowed to grow for 24h (washing off Dox).


title: 1807_PBMC


title: 1806_PBMC


title: ChIP-seq with BORIS Abs in NIH3T3+pBIGi_BORIS cells_Treated with DOX for 24h

value: The cells were cultured in the presence of doxycycline (Dox) concentration (1 μg/mL) for 24hours


title: 1802_Tumor


title: 1802_PBMC


title: ChIP-seq with BORIS Abs in NIH3T3+pBIGi_BORIS cells_Treated with DOX for 12h

value: The cells were cultured in the presence of doxycycline (Dox) concentration (1 μg/mL) for 12hours


title: DP510

description: Endometrial tissue collected on day P+5 (5th day of progesterone management) of a hormone replacement therapy (HRT) cycle

value: day P+5


title: DP701


title: ChIP-seq with BORIS Abs in NIH3T3+pBIGi_BORIS cells_Treated with DOX for 8h

value: The cells were cultured in the presence of doxycycline (Dox) concentration (1 μg/mL) for 8hours

value: NIH3T3 stably transfected with dox-inducable pBIGi BORIS-expressing plasmid (pBIG_BORIS)


title: Rpl8_2nd

city: wuhan

first: dong

last: chen

state: Hubei

address: GaoXin 2nd Road

institute: ablife

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2  Qvalue < =0.05
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample

source_name: hela cell

growth_protocol: The human HeLa cell line was purchased from the Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China. Cells were seeded into a petridish (100 mm) at a density of 1 × 105 cells/mL per well, and cultured at 37 ℃with 5% CO2 in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal bovine serum (FBS) (Hyclone), penicillin (100 U/ml) and streptomycin (100 g/ml). RPL8 overexpression plasmid transfection of HeLa cells was performed using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's instructions. Transfected cells were harvested after 48 h.

extract_protocol:
Total RNA was extracted by the TRIZOL (Ambion). The RNA was further purified with two phenol-chloroform treatments and then treated with RQ1 DNase (Promega) to remove DNA. The quality and quantity of the purified RNA were redetermined by measuring the absorbance at 260 nm/280 nm (A260/A280) using Smartspec Plus (BioRad). The integrity of RNA was further verified by 1.5% agarose gel electrophoresis.
For each sample, 1μg of total RNA was used for RNA-seq library preparation by VAHTS Stranded mRNA-seq Library Prep Kit (Vazyme). Polyadenylated mRNAs were purified and fragmented, and then converted into double strand cDNA. After the step of end repair and A tailing, the DNAs were ligated to VAHTS RNA Adapters (Vazyme). Purified ligation products corresponding to 200-500 bps were digested with heat-labile UDG, and the single strand cDNA was amplified, purified, quantified and stored at -80℃ before sequencing.
For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina HiSeq X Ten system for 150 nt paired-end sequencing.

value: RPL8 overexpression

value: HeLa


title: ChIP-seq with BORIS Abs in NIH3T3+pBIGi_EV cells_Treated with DOX for 24h

value: Mouse immortalized embryonic fibroblast cell line

value: NIH3T3 stably transfected with dox-inducable pBIGi_EV (Empty Vector (luciferase) expressing plasmid (pBIG_EV)


title: DP508

value: endometrium tissue


title: ChIP-seq with BORIS Abs in NIH3T3+pBIGi_BORIS cells_Treated with no DOX


title: DP509


title: Ctrl_1st

value: control plasmid


title: Rpl8_1st


title: 1808_Tumor

value: NKTCL

value: Tumor


title: Set1 Knockdown rep 3

city: Baltimore

first: Hangnoh

middle: Joseph

last: Lee

address: 670 W Baltimore St

institute: University of Maryland School of Medicine

data_processing:
The short reads were mapped using STAR aligner version 2.7.10a (PMID: 23104886) with the --alignIntronMax 250000 --alignMatesGapMax 1000000 parameters.
The mapped reads were then counted using RSEM version 1.3.3 with its default parameters (PMID: 21816040).
For the mapping and counting processes, the Drosophila gene annotation from Ensembl (Release 100, corresponding to Flybase 6.28) was used with the Berkeley Drosophila Genome Project (BDGP) reference genome release 6.
Berkeley Drosophila Genome Project (BDGP) reference genome release 6
Supplementary files format and content: Tab-delimited text files include Flybase gene IDs and corresponding expression levels in TPM (transcripts per kilobase million) for each sample.

organism: Drosophila melanogaster

source_name: Heart

growth_protocol: Flies were crossed, reared, and kept on standard food at 25°C.

extract_protocol:
For each of the heart samples,50 one-week old adult fly hearts were dissected and collected into ice-cold TRIzol LS reagent. Total RNA extraction followed the manufacturer's instructions (Direct-zol RNA Microprep, Zymo Research). The quality and concentration of RNA were assessed using agarose gel electrophoresis, NanoDrop 8000 Spectrophotometer, and Agilent 2100.
The preparation of RNA libraries was conducted by Novogene (Beijing, China) using standard Illumina protocols.

treatment_protocol: twi-Gal4 was applied to tissue specifically knockdown (RNAi) targeting Set1, trx, or trr. Hand-GFP was used to visualize the heart cells (labels the nuclei). Fly hearts were dissected from 50 one-week-old adult female flies.

value: Heart

value: trx-IR


title: Set1 Knockdown rep 2


title: Set1 Knockdown rep 1


title: DP507


title: Notch2 mutant osteoclasts Hes1 deletion, biological rep 3

city: Farmington

first: Ernesto

last: Canalis

state: CT

address: 263 Farmington Avenue

department: Orthopaedic Surgery

institute: UConn Health

data_processing:
Raw reads were trimmed with Sickle, with a quality threshold of 30 and length threshold of 45, following that the trimmed reads were mapped to Mus Musculus genome (GRCm38) with HISAT2 .
The resulting SAM files then converted into BAM format using samtools, and the PCR duplicates were removed using PICARD (http://broadinstitute.github.io/picard/).
The counts were generated against the features with htseq-count.
The differential expression of genes between conditions was evaluated using DESeq2.
Covariates were introduced in the DESeq2 analysis to increase the accuracy of results, and genes showing less than 10 counts across the compared samples were excluded from the analysis.
Genes with a false discovery rate (FDR) < 0.05 were considered significant and used in the downstream analysis.
Assembly: Mus Musculus genome (GRCm38 ensembl release 97)
Supplementary files format and content: COUNTS File (*.counts) and counts

source_name: Osteoclast

growth_protocol: Plated wt and Notch2 Hes1 BMMs with MCSF on uncoated petri dishes.

extract_protocol:
Cells were lifted and the RNA extracted using Qiagen Rneasy Mini Kit.
Total RNA samples were prepared for mRNA-Sequencing using the Illumina TruSeq Stranded mRNA Sample Preparation kit following the manufacturer’s protocol (Illumina, San Diego, CA).
Libraries were validated for length and adapter dimer removal using the Agilent TapeStation 4200 D1000 High Sensitivity assay (Agilent Technologies), and then they were quantified and normalized using the dsDNA High Sensitivity Assay for Qubit 3.0 (Thermo Fisher Scientific).
Sample libraries were prepared for Illumina sequencing by denaturing and diluting the libraries per manufacturer’s protocol (Illumina).
All samples were pooled into one sequencing pool, equally normalized, and run as one sample pool across the Illumina NextSeq 500 using version 2.5 chemistry.
Target read depth was achieved for each sample with paired end 75bp reads.

treatment_protocol: On day 3 the wt and Notch2 Hes1 BMMs with MCSF and RankL for 4 days until osteoclasts formed.

value: Osteoclast

value: Notch2 mutant

value: male

value: 7-8 weeks


title: 1807_Tumor


title: DP506

value: day P+5


title: 1806_Tumor


title: DP702

value: day P+7


title: Notch2 mutant osteoclasts Hes1 deletion, biological rep 2


title: DP505


title: Trx Knockdown rep 2

value: trr-IR


title: Notch2 mutant osteoclasts Hes1 deletion, biological rep 1


title: Trx Knockdown rep 1


title: Trr Knockdown rep 3


title: DP504


title: Ctrl_2nd


title: Trr Knockdown rep 2


title: Wild type osteoclasts Hes1 deletion, biological rep 3

value: Wild type


title: Trr Knockdown rep 1


title: DP503


title: Control

value: control

value: Hand-GFP;twi-Gal4+/- (Gal4 crossed with w1118)


title: DP502


title: Wild type BMMs with M-CSF and RANKL

description:
10x Genomics
Sample3_Control_M-CSF_RANKL

data_processing:
Demultiplexing, barcode processing, gene counting, and aggregation made using CellRanger software v.7.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10-2020-A
Supplementary files format and content: .h5 filtered features, matrix, barcoded files
Supplementary files format and content: Tab-separated values files and matrix files

source_name: bone marrow derived macrophage

growth_protocol: Plated wt and Notch2 BMMs with MCSF on uncoated petris.

extract_protocol:
Collagenase was used to lift cells and proceed with single cell protocol.
A 10x genomics kit for library construction.

treatment_protocol: On day 3 cells were plated on collagen with half of the groups being trated with MCSF and RankL and the other half with just MCSF for 3 days.

value: bone marrow derived macrophage

value: M-CSF+RANKL


title: Notch2 mutant BMMs with M-CSF

description:
10x Genomics
Sample2_Notch2_M-CSF

value: M-CSF


title: Trx Knockdown rep 3


title: Wild type osteoclasts Hes1 deletion, biological rep 2


title: Notch2 mutant BMMs with M-CSF and RANKL

description:
10x Genomics
Sample4_Notch2_M-CSF_RANKL


title: DP501

value: endometrium tissue


title: Notch2 mutant osteoclasts Hes1 loxP, biological rep 3


title: Wild type BMMs with M-CSF

description:
10x Genomics
Sample1_Control_M-CSF


title: Wild type osteoclasts Hes1 deletion, biological rep 1


title: DP309

description: Endometrial tissue collected on day P+3 (3th day of progesterone management) of a hormone replacement therapy (HRT) cycle

value: day P+3


title: Fbxo2GAP_D96

city: Houston

first: Chenghang

last: Zong

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

data_processing:
The fastq files of read 1 were mapped to the reference transcriptome by using STAR.
The reads were assigned to genes by using htseq-count.
The UMI sequences were extracted from read 2 (the first five bases).
The reads with the same UMI were collapsed. The number of UMIs of each gene were counted.
Assembly: mm10
Supplementary files format and content: Tab-separated UMI count matrix; Files: Exon_UMI_matrix.txt

source_name: cochlea

extract_protocol:
After tissue dissociation, single cells are sorted into 96-well plate by FACS.
Libraries were constructed by following SMART-MATQ protocol.

treatment_protocol: Animal were treated with tamoxifen at 3 weeks and cells were harvested at 5 weeks.

value: cochlea

value: tamoxifen at 3 weeks, dissociation with Papain at 5 weeks.


title: Fbxo2GAP_D94


title: Notch2 mutant osteoclasts Hes1 loxP, biological rep 2

value: Osteoclast


title: Fbxo2GAP_D93


title: DP308


title: Notch2 mutant osteoclasts Hes1 loxP, biological rep 1

value: Notch2 mutant


title: Fbxo2GAP_D91


title: Fbxo2GAP_D92


title: Fbxo2GAP_D90


title: Wild type osteoclasts Hes1 loxP, biological rep 3

value: male


title: Wild type osteoclasts Hes1 loxP, biological rep 2

value: 7-8 weeks


title: DP306


title: Fbxo2GAP_D89


title: Fbxo2GAP_D88


title: Wild type osteoclasts Hes1 loxP, biological rep 1


title: DP304


title: Fbxo2GAP_D87


title: WT_lowOD_2

city: Aurora

first: Matthew

last: Taliaferro

state: CO

department: Biochemistry and Molecular Genetics

institute: University of Colorado Anschutz Medical Campus

data_processing:
Adapters were removed using cutadapt.
Transcript abundances were calculated using salmon v 1.9
Changes in splice isoform abundances were calculated using junctionCounts
Assembly: SacCer3
Supplementary files format and content: transcript abundances calculated by salmon

organism: Saccharomyces cerevisiae

source_name: wildtype

growth_protocol: All strains were grown on YPD or in appropriate dropout media.

extract_protocol:
RNA was extracted using hot phenol and DNase treated.
Standard poly-A selected RNAseq libraries were prepared.

treatment_protocol: For degron-containing samples, cells were treataed with beta-estradiol and IAA for 6 hrs to deplete degron-tagged proteins

value: wildtype

value: low OD


title: WT_lowOD_3


title: WT_highOD_3

value: high OD


title: WT_lowOD_1


title: DP303


title: d12

first: Emilie

last: Pollenus

address: Herestraat 49 bus 1044

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.2
Assembly: mm10
Supplementary files format and content: Tab-separated values and matrix files (barcodes.tsv.gz, genes.tsv.gz, matrix.tsv.gz)

source_name: Lungs

extract_protocol:
Single cell suspensions were prepared from lungs of uninfected control C57BL/6 mice (CON), Untreated, PbNK65-infected C57BL/6 mice dissected at 8 days post infection (d8) and antimalarial drug-treated, PbNK65-infected C57BL/6 mice dissected at 12 days post infection (d12).
Samples of 4 mice per condition were labeled using Totalseq B Hashtag oligo's (Biolegend), pooled together and loaded onto a Chromium controller (10X Genomics). Library was generated according to the manufacturer's instructions (single cell 3' v2 protocol, 10X Genomics). Sequencing was performed on Illumina NovaSeq 6000 according to manufacturer's recommendations.

treatment_protocol: Mice were infected with Plasmodium berghei NK65. At 8 days post infection, untreated mice were dissected (d8 sample). For the d12 sample, PbNK65-infected C57BL/6 mice were treated daily with antimalarial drugs, artesunate and chloroquine starting at 8 days post infection and dissected at 12 days post infection

value: Lungs

value: All pulmonary cells


title: DP302


title: Fbxo2GAP_D85


title: Fbxo2GAP_D86


title: d8

description: 10X Genomics

value: PbNK65-infected C57BL/6 mice dissected at 8 days post infection (d8)


title: WT_highOD_2


title: DP301


title: CON

description: 10X Genomics

value: uninfected control mice (CON)


title: Luc7T_3

source_name: Luc7 triple mutant

value: Luc7 triple mutant


title: Sinus+Artery, Klf4WT, YFPplus_control_0

first: Mary

last: Weiser-Evans

address: 12700 East 19th Avenue, C281

department: Renal Diseases & Hypertension

description: 10x Genomics

data_processing:
Fastq files were aligned  to a custom build reference genome (Ensembl GRCm39 release 104) containing eYFP ORF sequence using Cell Ranger 6.1.2.
Based on single-cell best practices, Seurat 4.1.0 was used for the downstream analysis including quality control, normalization, and clustering; exact algorithm can be found at https://github.com/weiserevanslab/adubner
Cells with less than 500 or greater than 6,500 genes were filtered out. Cells with total molecules greater than 45,000 or less than 500 were filtered out. Cells with a percentage of mitochondrial counts exceeding 15 %  were also removed.
Assembly: GRCm39 (Ensembl, r104)
Supplementary files format and content: counts.csv.gz contains the count matrix file
Supplementary files format and content: metadata.csv.gz contains metadata describing the cells
Supplementary files format and content: umap_embedding.csv.gz contains umap embedding for the cells

source_name: Aortic root, aortic arch, BCA, carotids

extract_protocol:
Single cell suspension was prepared and fluorescence activated cell sorting (FACS) was performed to separate YFP+ and YFP- cells. Each sample (condition) consisted of pooled aortic root/aortic arch/BCA/carotid arteries from 3 animals.
YFP+ and YFP- samples for each condition were subjected to scRNA-seq using the Chromium Single Cell 3’ Library and Gel Bead Kit (v3.1 10x Genomics, Pleasanton, CA) and the Chromium X.

value: Aortic root, aortic arch, BCA, carotids

value: 8-10 weeks old

value: Klf4 WT

value: Control

value: 0 weeks post tamoxifen


title: NP710

value: endometrium tissue

value: day P+7


title: Fbxo2GAP_D83

value: cochlea

value: tamoxifen at 3 weeks, dissociation with Papain at 5 weeks.


title: Fbxo2GAP_D84


title: DP305

value: day P+3


title: Sinus+Artery, Klf4WT, YFPminus_control_0

description: 10x Genomics


title: Luc7T_2

value: low OD


title: Fbxo2GAP_D82


title: Sinus+Artery, Klf4KO, YFPplus_control_0

description: 10x Genomics

value: Klf4 KO


title: NP709


title: Fbxo2GAP_D81


title: Luc7D_uninduced_3

source_name: Luc7 degron

value: Luc7 degron

value: minus IAA


title: Sinus+Artery, Klf4KO, YFPminus_control_0

description: 10x Genomics


title: NP708


title: Sinus+Artery, Klf4KO, YFPplus_control_16

description: 10x Genomics

value: 24-26 weeks old

value: 16 weeks post tamoxifen


title: Fbxo2GAP_D80


title: WT_highOD_1

value: wildtype

value: high OD


title: Sinus+Artery, Klf4KO, YFPminus_control_16

description: 10x Genomics

value: Aortic root, aortic arch, BCA, carotids


title: Luc7D_uninduced_2


title: NP706


title: NP704


title: Luc7D_uninduced_1


title: Fbxo2GAP_D78


title: Sinus+Artery, Klf4KO, YFPplus_athero_16

description: 10x Genomics

value: Athero


title: Fbxo2GAP_D77


title: Luc7D_induced_3

value: plus IAA


title: NP703


title: Luc7D_induced_2


title: Sinus+Artery, Klf4KO, YFPminus_athero_16

description: 10x Genomics


title: Fbxo2GAP_D76


title: Sinus+Artery, Klf4WT, YFPplus_control_16

description: 10x Genomics

value: Klf4 WT

value: Control


title: Luc7D_induced_1


title: NP702

value: endometrium tissue

value: day P+7


title: Luc7T_1

value: Luc7 triple mutant


title: NP701


title: NP707


title: Fbxo2GAP_D75

value: cochlea

value: tamoxifen at 3 weeks, dissociation with Papain at 5 weeks.


title: DP307

value: day P+3


title: Sinus+Artery, Klf4WT, YFPminus_control_16

description: 10x Genomics


title: Fbxo2GAP_D74


title: Fbxo2GAP_D79


title: h_yU1C_lowOD_3

source_name: humanized yeast U1C

value: humanized yeast U1C

value: low OD


title: Sinus+Artery, Klf4WT, YFPplus_athero_16

description: 10x Genomics

value: 24-26 weeks old


title: NP510

value: day P+5


title: NP509


title: Fbxo2GAP_D73


title: h_yU1C_lowOD_1


title: NP508


title: Sinus+Artery, Klf4WT, YFPminus_athero_16

description: 10x Genomics

value: 16 weeks post tamoxifen


title: D5

city: Xi'an

first: Tong

last: Chang

state: Shaanxi Province

address: No.169, Changle West Road

department: School of Aerospace Medicine

institute: Air Force Medical university

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2.2.4 and other parameters set as a default
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach
RNAs differential expression analysis was performed by DESeq2 software between two different groups
Assembly: Ensembl_release109
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: D-V group

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol
RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads.Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).Ligated fragments were subjected to size selection by agarose gel electrophoresis and polymerase chain reaction (PCR) amplified.The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).

value: hippocampus

value: This group was referred to as the Coriolis illusion（bidirectional rotational motion with visual occlusion）


title: D4


title: h_yU1C_highOD_2

value: high OD


title: h_yU1C_highOD_3


title: h_yU1C_lowOD_2


title: NP505


title: Fbxo2GAP_D68


title: D2


title: Fbxo2GAP_D67


title: mock-9h_rep2

city: Pyeongchang

first: Jun Sung

last: Seo

state: Gangwon

address: Pyeongchangdaero 1447

department: Company-affiliated research institute

country: South Korea

institute: LaSemilla Co. Ltd.

description: Oryza sativa (japonica)

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 IRGSP-1.0 whole genome using HISAT2 through bowtie2 aligner
Gene/transcript was assemblied using reference gene model by StringTie program. Trancript abundance measurement was calculated by read count and FPKM value.
Genome_build: IRGSP-1.0
Supplementary_files_format_and_content: Gtf files by Stringtie include FPKM values for each Sample.

organism: Oryza sativa Japonica Group

source_name: rice seedlings

growth_protocol: Rice plants were grown in MS media for 10 days at 30 °C with a cycle of 16 h light/ 8 h dark having light intensity of 200 µmol m-2 s-1

extract_protocol:
10-day-old rice seedlings were ground with liquid nitrogen, and total RNA was extracted using Rneasy plant mini kit (Qiagen). Illumina TruSeq mRNA LT Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
TruSeq Stranded mRNA Sample Preparation Guide, Part # 15031047 Rev. E

treatment_protocol: dexamethasone(DEX) or mock treatment

tag: growth stage

tag: cultivar

value: Dongjin


title: D3

tag: tissue

tag: treatment


title: D1


title: NP503


title: C5

source_name: D+V group

value: This group underwent bidirectional rotational motion without visual occlusion.


title: mock-9h_rep1

description: Oryza sativa (japonica)

tag: genotype


title: NP504


title: mock-3h_rep2

description: Oryza sativa (japonica)


title: NP502


title: Fbxo2GAP_D65


title: C4


title: Fbxo2GAP_D71


title: Fbxo2GAP_D66


title: mock-3h_rep1

description: Oryza sativa (japonica)


title: NP501


title: Fbxo2GAP_D64


title: Fbxo2GAP_D70


title: Fbxo2GAP_D69


title: NP506


title: DEX-9h_rep2

description: Oryza sativa (japonica)


title: h_yU1C_highOD_1


title: NP507


title: NP310


title: Fbxo2GAP_D63


title: DEX-9h_rep1

description: Oryza sativa (japonica)


title: NP309


title: C2


title: DEX-3h_rep2

description: Oryza sativa (japonica)


title: C1


title: Fbxo2GAP_D62


title: B5

source_name: S-V group

value: This group underwent unidirectional rotation motion with visual occlusion.


title: NP308

source_name: endometrium tissue

value: endometrium tissue


title: Fbxo2GAP_D61


title: NP307


title: NP306


title: DEX-3h_rep1

description: Oryza sativa (japonica)


title: B3


title: ATAC-seq on NIH3T3+BORIS (Clone#2) cells

city: Bethesda

first: Elena

last: Pugacheva

institute: NIH

data_processing:
ChIP-seq, ATAC-seq, CAGE-seq data: single-end or paired-end reads were aligned either to the UCSC hg19 (human samples) or UCSC mm9 (mouse samples) genome using Bowtie version 2 under default parameters.
RNA-seq data: FASTQ files were either mapped to the UCSC mouse (build mm9) or human ((build hg19) reference genomes using STAR with default settings. Normalized gene counts and differentially expressed genes (DEG) were obtained with the R package DESeq2.
For ChIP-seq and ATAC-seq data, output BAM files were converted into bdg track files using MACS2
For CAGE-seq, ChIP-seq, ATAC-seq data, output BAM files were converted into bigwig files using bamCoverage option in deepTools 3.5.0 in order to display normilized coverage throughout the genome (in RPKM).
ChIP-seq and ATAC-seq peaks were called using Model-based Analysis for ChIP-seq (MACS2) using default parameters.
CAGE-seq clusters were called using MACS2  with parameters (--nomodel --shift -1)
bdg files were generated using  MACS2  with default settings.
Assembly: hg19 (for human) amd mm9 (for mouse)
Supplementary files format and content: bdg, xlsx (differentially expressed genes (DEG) were obtained with the R package DESeq2), bigwig (BAM files normilized using bamCoverage option in deepTools 3.5.0 (in RPKM))

extract_protocol:
ChIP-seq protocol: 2x106 asynchronously growing cells were crosslinked with 1% formaldehyde for 10 min at room temperature, followed by quenching with 125 mM glycine for 10 min, washed twice with 1×phosphate buffered saline (PBS), and resuspended in chromatin immunoprecipitation (ChIP) lysis buffer (150 mM NaCl, 1 % Triton X-100, 0.1 % SDS, 20 mM Tris–HCl pH8.0, 2 mM EDTA). Chromatin was sheared to 200–600 bp and immunoprecipitated with 5 μg of antibody. Immunoprecipitated DNA was purified with QIAquick columns (ZymaResearch).
ATAC-seq protocol:NIH3T3 cells (5 × 104) were pelleted by centrifugation and resuspended in 50 µL of cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630), gently pipetting up and down 10 times. Nuclei were pelleted by centrifugation at 2500g for 10 min at 4°C and resuspended in 25 µL of 2x TD Buffer (Illumina Cat #FC-121-1030), containing 8 µL of Tn5 Transposes (Illumina Cat #FC-121-1030) and 17 µL of nuclease free water. The rection was incubated for 30 min at 37°C. Tagmented DNA was purified by using a Zymo Research DNA Clean & Concentrator™-5 - Capped Columns.
RNA-seq protocol:The RNA sequencing library preparation and sequencing procedures were carried out according to Illumina protocols. Briefly, poly(A)-mRNA was purified from 5 μg of RNA with streptavidin-coated magnetic beads. After chemical fragmentation, mRNA fragments were reverse-transcribed and converted into double-stranded cDNA. Following end repair and A-tailing, paired-end adaptors were ligated to the ends of the DNA fragments. The ligated products were amplified with 18 cycles of PCR followed by purification using AMPure beads (Beckman Coulter). The enriched libraries were diluted to a final concentration of 5 nM.
ChIP-seq libraries were prepared using TruSeq ChIP Sample Preparation Kit (Illumina, Inc., USA) or NEBNext UltraII DNA Library Prep Kit for Illumina (BioLabs, catalog # E7645S).  Libraries were amplified using 15 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.
RNA-seq library were prepared using TruSeq RNA Library Prep Kit (Illumina, Inc., USA)
ATAC-seq libraries were amplified using NEBNext High-Fidelity 2× PCR Master Mix (New England Biolabs). The libraries were size-selected  by adding 1.8X volume Agencourt AMPure XP beads (Beckman, 63881).
CAGE-seq libraries were prepared by DNAFORM (Yokohama, Kanagawa, Japan).

value: Mouse immortalized embryonic fibroblast cell line

value: Stable ectopic expression of BORIS from CpG-free plasmid (InvivoGen) - Clone#2

value: NIH3T3 stably expressing BORIS


title: B4


title: Fbxo2GAP_D60

value: cochlea

value: tamoxifen at 3 weeks, dissociation with Papain at 5 weeks.


title: NP305

value: day P+3


title: Fbxo2GAP_D59


title: ChIP-seq with H3K27me3 Abs in NIH3T3+BORIS cells

value: H3K27me3 (Diagenode, catalog # C15410195)


title: NP304


title: ATAC-seq on NIH3T3+EV cells

value: Stable ectopic expression of a control plasmid (empty vector, EV), expressing beta-galactosidase (CpG-free plasmid (InvivoGen))

value: NIH3T3 stably expressing EV (Empty Vector)


title: B2


title: Fbxo2GAP_D58


title: B1


title: Fbxo2GAP_D57


title: NP303


title: ChIP-seq with H3K27me3 Abs in NIH3T3+EV cells


title: ChIP-seq with H3K36me3 Abs in NIH3T3+BORIS cells

value: H3K36me3 (Diagenode, catalog # C15410058)


title: Fbxo2GAP_D56


title: C3

value: hippocampus


title: NP302


title: A3

source_name: Control group

value: Blank control


title: Fbxo2GAP_D54


title: NP301


title: ChIP-seq with SRCAP Abs in NIH3T3+BORIS cells

value: SRCAP (Kerafast, catalog # ESL103)


title: A2


title: A1


title: AP706

value: day P+7


title: ChIP-seq with H3K36me3 Abs in NIH3T3+EV cells


title: Fbxo2GAP_D53


title: ChIP-seq with SRCAP Abs in NIH3T3+EV cells


title: ChIP-seq with HCFC1 Abs in NIH3T3+BORIS cells

value: HCFC1 (Novus Biologicals, catalog # NB100-68209)


title: Heme 2

city: Zurich

first: Florence

last: Vallelian

address: Rämistrasse 100

country: Switzerland

institute: University Hospital Zürich

data_processing:
Read alignment using STAR (version 2.7.0)
Read summarization using featureCounts (Rsubread version 1.22.2)
Assembly: Ensembl/GRCm38.p5/Annotation/Release_91-2018-02-26
Supplementary files format and content: .txt: Contains feature (gene) counts

source_name: BMDM

growth_protocol: BM cells were isolated by flushing the femurs and tibias of 8- to 10-week-old C57BL/6J mice and passed through a 70-μm filter. The BM cells were plated at a density of 3 x 105 cells/ml on tissue culture-treated 60 mm UpCell dish (Nunc™ UpCell™, ThermoFisher) in complete RPMI-1640 medium (10% fetal calf serum (FCS), 1% L-glutamine and 1% P/S) supplemented with 100 ng/ml recombinant mouse M-CSF (PeproTech). On day 3, half of the medium was replaced. Cultures were treated on day 3 as indicated in the results section with 300 μM heme-albumin or albumin (as vehicle/control). The BM cells were harvested for analysis on day 7 from the temperature responsive cell culture plates after cooling to room temperature. Cells were washed in PBS and centrifuged (300 g, 10 min) before processing.

extract_protocol:
RNA was extracted from cells using the RNeasy Micro kit (Qiagen) according to the manufacturer's protocol, including on-column DNase I treatment.
RNA quality was validated an Agilent Technologies 2100 Bioanalyzer using an RNA chip, and only samples with an RNA integrity number (RIN) of > 9 were used for sequencing. cDNA libraries were generated from the RNA samples using the Illumina TruSeq RNA stranded kit following the manufacturer’s instructions. Libraries were amplified by PCR (total of 15 cycles) and their quality and concentration determined using an Agilent Fragment Analyzer with DNA High-Sensitivity Chips. The libraries were pooled in equimolar amounts.

value: BMDM

value: heme


title: AP705

value: endometrium tissue


title: Heme 3


title: Fbxo2GAP_D51


title: Heme 1


title: Fbxo2GAP_D50


title: Control 3

value: control


title: ChIP-seq with HCFC1 Abs in NIH3T3+EV cells

value: Mouse immortalized embryonic fibroblast cell line


title: AP704


title: ChIP-seq with MXI1 Abs in NIH3T3+BORIS cells

value: MXI1 (R&D Systems, catalog # AF4185)

value: Stable ectopic expression of BORIS from CpG-free plasmid (InvivoGen) - Clone#2

value: NIH3T3 stably expressing BORIS


title: AP703


title: Fbxo2GAP_D55

value: cochlea

value: tamoxifen at 3 weeks, dissociation with Papain at 5 weeks.


title: AP506

value: day P+5


title: Fbxo2GAP_D48


title: AP505


title: Fbxo2GAP_D47


title: ChIP-seq with MAZ Abs in NIH3T3+BORIS cells

value: MAZ (Abcam, catalog # ab85725)


title: Control 1


title: Fbxo2GAP_D52


title: Fbxo2GAP_D46


title: AP504


title: ChIP-seq with MXI1 Abs in NIH3T3+EV cells

value: Stable ectopic expression of a control plasmid (empty vector, EV), expressing beta-galactosidase (CpG-free plasmid (InvivoGen))

value: NIH3T3 stably expressing EV (Empty Vector)


title: Control 2


title: Fbxo2GAP_D45


title: ChIP-seq with MAZ Abs in NIH3T3+EV cells


title: sample 2 (B23-0402-001)

data_processing:
Read alignment using SpaceRanger (cellranger-6.1.2)
Preprocessing: Filtering, normalization and log(x+1)-transformation, dimensionality reduction and UMAP
Scoring of gene sets
Assembly: GENCODE/GRCm39/Annotation/Release_M31-2023-01-30
Supplementary files format and content: *.jpg, *.h5, *.json, *.png: aoutput of spaceranger
Supplementary files format and content: *.h5ad: combined processed samples
Library strategy: Spatial Transcriptomics

source_name: tumor

growth_protocol: Once confluent, MC38-GFP tumor cells were harvested using 5mM EDTA (Gibco) (4 min at 37°C), washed twice in PBS. 2 x 106 MC38 cells in culture medium were mixed with 350 µl Geltrex (ThermoFisher) and injected subcutaneously into the mouse flanks. Agonistic anti-CD40 treatment (20 mg/kg, InVivoPlus) or an isotype control antibody was administered intravenously 7 days after tumor cell injection. Mice were euthanized, and tumors were collected 72 hours after antibody administration.

extract_protocol:
Mice were anesthetized by intraperitoneal injection of ketamine (80 mg/kg), xylazine (16 mg/kg), and acepromazine (3 mg/kg) and transcardially perfused with cold PBS. Organs were placed in 10% formalin and after 24 h transferred in 70% ethanol before embedding in paraffin blocks. Microtome sections (2-2.5 µm) were cut for hematoxylin and eosin staining.
Microtome sections on regular glass slides were deparaffinized and stained for H&E as described in Visium CytAssist Spatial Gene Expression for FFPE (10X Genomics, CG000520). Regions of interest on the tumor sections were then chosen by means of the H&E stain and were aligned in the tissue slide cassette 6.5mm. After destaining and decrosslinking, sections were immediately subjected to probe hybridization overnight followed by probe ligation, release and extension and spatial library construction as described in Visium CytAssist Spatial Gene Expression for FFPE (10X Genomics, CG000495).

value: tumor


title: AP503


title: ChIP-seq with PHF8 Abs in NIH3T3+BORIS cells

value: PHF8  (Bethyl Laboratories, catalog # A301-772A)


title: Fbxo2GAP_D44


title: KeapKO Control, CMO310

data_processing:
Demultiplexing and read alignment using CellRangerMulti (cellranger-7.0.0)
Filtering, normalization and log(x+1)-transformation, dimensionality reduction and UMAP
Assembly: Mus_musculus/GENCODE/GRCm39/Annotation/Release_M26-2021-04-20
Supplementary files format and content: *_sample_alignments.bam: demultiplexed raw data
Supplementary files format and content: .h5 output of CellRangerMulti
Supplementary files format and content: .h5ad containing processed data of the combined experiments

growth_protocol: BM cells were isolated by flushing the femurs and tibias of 8- to 10-week-old C57BL/6J mice and passed through a 70-μm filter. The BM cells were plated at a density of 3 x 105 cells/ml on tissue culture-treated 60 mm UpCell dish (Nunc™ UpCell™, ThermoFisher) in complete RPMI-1640 medium (10% fetal calf serum (FCS), 1% L-glutamine and 1% P/S) supplemented with 100 ng/ml recombinant mouse M-CSF (PeproTech). On day 3, half of the medium was replaced. Cultures were treated on day 3 as indicated in the results section with 300 μM heme-albumin or albumin (as vehicle/control). For inflammatory polarization, INFγ (10 ng/ml, PeproTech) or LPS (10 ng/ml, Sigma) was added on day 6 for 24 hours

extract_protocol:
The BM cells were harvested for analysis on day 7 from the temperature responsive cell culture plates after cooling to room temperature. Cells were washed in PBS and centrifuged (300 g, 10 min) before processing.
GEM generation and library preparation was performed according to 10X Genomics protocol (CG000388 Demonstrated Protocol Chromium Next GEM Single Cell 3ʹ v3.1 (Dual Index) with Feature Barcode technology for Cell Multiplexing Rev B) targeting a cell recovery rate of 10’000 cells.

value: KeapKO


title: ChIP-seq with PHF8 Abs in NIH3T3+EV cells


title: WT Heme, CMO309

value: BMDM

value: WT


title: ChIP-seq with TBP Abs in NIH3T3+BORIS cells

value: TBP (Abcam, catalog # ab220788)


title: AP306

value: endometrium tissue

value: day P+3


title: Fbxo2GAP_D43


title: Fbxo2GAP_D42


title: WT Control, CMO308


title: ChIP-seq with TBP Abs in NIH3T3+EV cells

value: Mouse immortalized embryonic fibroblast cell line


title: AP305


title: Tumor cells CMO305

data_processing:
Demultiplexing and read alignment using CellRangerMulti (cellranger-7.0.0)
Preprocessing: Filtering, normalization and log(x+1)-transformation, dimensionality reduction and UMAP
downstream analysis
Assembly: Mus_musculus/GENCODE/GRCm39/Annotation/Release_M26-2021-04-20
Supplementary files format and content: *_sample_alignments.bam: demultiplexed raw data
Supplementary files format and content: .h5 output of CellRangerMulti
Supplementary files format and content: .h5ad containing processed data of the combined experiments

growth_protocol: MC38-GFP cells were from L.Borsig and cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS, Gibco), 1% penicillin/streptomycin (P/S, Gibco), 1% non essential amino acids (NEAA, Gibco) and 1% sodium-pyruvate (Gibco). BM cells were isolated by flushing the femurs and tibias of 8- to 10-week-old C57BL/6J mice and passed through a 70-μm filter. The BM cells were plated at a density of 3 x 105 cells/ml on tissue culture-treated 60 mm UpCell dish in complete RPMI-1640 medium supplemented with 100 ng/ml recombinant mouse M-CSF (PeproTech). On day 3, half of the medium was replaced. Cultures were treated on day 3 with 300 μM heme-albumin or albumin (as vehicle/control). For inflammatory polarization, INFγ (10 ng/ml, PeproTech) was added on day 6 for 24 hours. The BM cells were harvested for analysis on day 7 from the temperature responsive cell culture plates after cooling to room temperature. Cells were washed in PBS and centrifuged (300 g, 10 min) before processing. 5 x 104  MC38-GFP cells +/- BMDMs in 1-1 ratio were seeded in 800 μl tumor cell medium with M-CSF (100 ng/ml) in 24-well microwell Sphericalplate® 5D (Kugelmeiers). 800 μl fresh culture cell medium was added on day 2-3.

extract_protocol:
Spheroids were dissociated in 2 ml digestion medium (RPMI medium (Gibco) + 25 µg/ml Liberase ™ (Roche) + 40 µg/ml DNase I (Roche; 2000 U/ml) and incubated for 30-45 min in a water bath at 37°C with gentle shaking every 5 min. 4 ml PBS + 0.04% BSA was added to stop the digestion.
Cell Multiplexing Oligos (CMO) labels B301 - B305 (3’ CellPlex Kit Set A) were used to label the 5 samples. After labeling, cell suspensions were counted again and the 5 samples were pooled according to the pooling calculations in appendix of the labeling protocol (CG00391) in equivalent ratios. The pool was then directly used for GEM generation following 10X Genomics protocol (CG000388 Demonstrated Protocol Chromium Next GEM Single Cell 3ʹ v3.1 (Dual Index) with Feature Barcode technology for Cell Multiplexing Rev B) targeting a cell recovery rate of 10’000 cells.


title: ChIP-seq with RNAPII Abs in NIH3T3+BORIS cells

value: RNAPII (anti-RNA Polymerase II Antibody, CTD Antibody, clone 8WG16 (Millipore, catalog #05-952-I-100UG))

value: Stable ectopic expression of BORIS from CpG-free plasmid (InvivoGen) - Clone#2


title: AP303


title: Fbxo2GAP_D39

value: cochlea


title: ChIP-seq with RNAPII Abs in NIH3T3+EV cells


title: Fbxo2GAP_D38

value: tamoxifen at 3 weeks, dissociation with Papain at 5 weeks.


title: Heme Interferon gamma CMO304

source_name: MC38-GFP & BMDM

value: MC38-GFP & BMDM

value: BMDM:Heme & Interferon gamma


title: AP502

value: day P+5


title: Fbxo2GAP_D37


title: sample 1 (B23-0396-001)


title: AP304


title: AP501


title: Heme CMO303