title: OVX.VEH4

value: Mice of this group were exposed to ovariectomy procedure (OVX) at the beginning of experiment and then at day 7 post operational procedure, each mouse of this group received intraperitoneal injection of normal saline only. Intramuscular injection of Diethylstilbestrol to replace natural estrogen was given  every 5 days started from day of ovariectomy till the end of the experiment.


title: C6_m15_cDC2

status: Public on Dec 08 2023

type: SRA

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

country: USA

institute: Benaroya Research Institute

library_source: transcriptomic

data_processing:
Base call quality-trimming step was applied to remove low-confidence base calls from the ends of read using trimmomatic v0.39 (LEADING:3 SLIDINGWINDOW:4:20 MINLEN:8)
Trimmed sequence read were mapped to GRCm38.91 using star (v2.7.11a)
Duplicates were removed from aligned reads using Picard (v3.1.0) and samtools (v1.16)
Gene counts were generated using htseq-count v2.0.2
Assembly: GRCm38.91
Supplementary files format and content: csv of raw gene counts

molecule: total RNA

organism: Mus musculus

source_name: Lin- CD11c+ MHC II+ 33D1+ DCs

extract_protocol:
300 cells per population were sorted (FACS Aria II, Becton Dickinson) into lysis buffer, and cDNA was prepared using the SMART-Seq Ultra Low Input RNA Kit for Sequencing (Takara Bio).
Reverse transcription was performed followed by PCR amplification to generate full-length amplified cDNA.  Sequencing libraries were constructed using a modified protocol of the Nextera XT DNA Sample Preparation Kit (Illumina) to generate Illumina-compatible barcoded libraries

tag: cell type

value: Lin- CD11c+ MHC II+ 33D1+ DCs

tag: mouseid

tag: treatment


title: HEK293T, Control-sh control-plasmid YH2AX Rep1

city: London

first: Pradeepa

middle: M

last: Madapura

state: UK

address: 4 Newark Street, Whitechapel

country: United Kingdom

institute: Queen Mary University of London

library_source: genomic

data_processing:
150bp paired-end reads for the CUT&Tag-seq were trimmed for adapters using the Trimmomatic tool and aligned to the hg38 genome through local Bowtie2 (version 2.4.5) with these parameters for pair-end mapping: --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700. The bam files were sorted and indexed using the samtools (version 1.9) sort and the samtools index. Merging of multiple replicates was performed using samtools merge.
The sorted bam files were used to generate bed, bedgraph and bigwig formats for individual modifications. Sorted bam files were subjected to bigwig generation via deepTools (version 3.5.1) bamCoverage tool with --binSize 20 --scaleFactor=1.0 --smoothLength 60 --extendReads 150 --centerReads options. The corresponding bigwig files were normalized by log2raio option for Antibody against IgG.
Peak-calling and analyses The reads were extracted from the bam to bed by the bedtools bamtobed option. Further reads were processed as mentioned in the SEACR (version 1.3) manual to get the bedgraph. These bedgraph files were subjected to peak calling through SEACR keeping IgG as a background with the norm and relaxed options for individual replicates. Peaks consistenet in both replicates were reatins and the coordinates were merged.
Assembly: hg38
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: HEK293T cells were grown on 100 mm culture dishes (Corning Falcon product number: 353003 ) in Delbecco's Modified Eagle's Medium (Gibco, 41966-029) supplemented with 100 U/ml penicillin-streptomycin (Gibco, 15140122) and 10% FBS (Sigma, F7524). The cells were passaged every 3-4 days. All the cell lines were tested for Mycoplasma contamination using EZ-PCR Kit (Geneflow, K1-0210).

extract_protocol:
CUT&Tag was performed according to the protocol of Kaya-Okur et al (1) with modifications to tissue processing as described below. ~100,000 cells were pelleted by centrifugation for 3 min at 600 x g at room temperature and resuspended in 500μl of ice-cold NE1 buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 0.5 mM spermidine, 1% Triton X-100, and 20 % glycerol and cOmplete EDTA free protease inhibitor tablet) and was let to sit for 10 min on ice. Nuclei were pelleted by centrifugation for 4 min at 1300 x g at 4°C, resuspended in 500μl of wash buffer and held on ice until beads were ready. Required amount of BioMag Plus Concanavalin-A-conjugated magnetic beads (ConA beads, Polysciences, Inc) were transferred into binding buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 1mM CaCl2 and 1mM MnCl2), washed once in the same buffer, each time placing them on a magnetic rack to allow the beads to separate from the buffer and resuspended in binding buffer. 10 μl of beads was then added to each tube containing cells and rotated on an end-to-end rotator for 10 minutes. After a quick spin to remove liquid from the cap, tubes were placed on a magnet stand to clear, the liquid was withdrawn and 800μl of antibody buffer containing 1μg of primary antibodies: normal rabbit IgG (Santa Cruz Cat no sc-2027), PSIP1 (Bethyl Laboratory, A300-848A), S9.6 (Millipore, MABE 1095), YH2AX (Abcam, ab81299) was added and incubated at 4ºC overnight in a nutator. Secondary antibodies (guinea pig α-rabbit antibody, Antibodies online, ABIN101961) were added 1:100 in Dig-wash buffer (5% digitonin in wash buffer) and 100 µL was squirted in per sample while gently vortexing to allow the solution to dislodge the beads from the sides and incubated for 60 min on a nutator. Unbound antibodies were washed in 1 ml of Dig-wash buffer three times. 100 μl of (1:250 diluted) protein-A-Tn5 loaded with adapters in Dig-300 buffer (20 mM HEPES pH 7.5, 300 mM NaCl, 0.5 mM spermidine with Roche cOmplete EDTA free protease inhibitor) was added to the samples, placed on nutator for 1 hour and washed three times in 1 ml of Dig-300 buffer to remove unbound pA-Tn5. 300 µL Tagmentation buffer (Dig-300 buffer + 5 mM MgCl2) was added while gentle vortexing and samples were incubated at 37ºC for 1 hr on an incubator. Tagmentation was stopped by adding 10 µL 0.5M EDTA, 3 µL 10% SDS and 2.5 µL 20 mg/mL Proteinase K to each sample. Samples were mixed by full speed vortexing for ~2 seconds and incubated for 1 hr at 55ºC to digest proteins. DNA was purified by phenol: chloroform extraction using phase-lock tubes (Quanta Bio) followed by ethanol precipitation.
Libraries were prepared using NEBNext HiFi 2x PCR Master mix (M0541S) with a 72ºC gap-filling step followed by 13 cycles of PCR with 10-second combined annealing and extension for the enrichment of short DNA fragments. Libraries were sequenced in Novaseq 6000 (Novogene) with 150bp paired-end reads.

treatment_protocol: Control or RNASEH overexpressing plasmid transfected HEK293T cells were transduced with either control shRNA or PSIP1 shRNA and grown in a medium containing 2ug/ml puromycin.

tag: cell line

value: Human Embryonic Kidney cells with large T antigen

tag: antibody

value: YH2AX(Abcam, AB81299)


title: C8_m16_cDC2


title: sample.hoxpkd1het_p15_1

city: Saint Louis

first: Tao

last: Cheng

state: MO

address: MSB Room 880M, Nephrology Division,425 South Euclid Ave, Box 8126, St Louis, MO  63110

institute: Washington University in St. Louis

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read. RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a. Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5. Isoform expression of known Ensembl transcripts were estimated with Salmon version 0.8.2. Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected. The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.6.2.
Assembly: mm9
Supplementary files format and content: excelsheet files
Supplementary files format and content: DEG

source_name: kidney

extract_protocol:
For analysis of gene expression changes in fibrocystic kidneys of postnatal mice, whole kidneys were isolated from wildtype and Hoxb7-Cep120 animals at P15. The kidneys were weighed and then grounded using pestle and mortar in liquid N2 bath and then lysed in Trizol, then total RNA was isolated using Direct-zolTM RNA MiniPrep Plus (Zymo Research).
ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol

tag: tissue

value: kidney

value: whole kidney

value: whole kidney cells

tag: genotype

value: WT

tag: developmental stage


title: RNA-Seq BM-12

city: Rochester

first: Surendra

last: Dasari

state: MN

address: 200 First Street SW

department: Quantitative Health Sciences Research

institute: Mayo Clinic

data_processing:
The raw RNA-seq reads were processed through the Mayo Clinic RNA-seq bioinformatics pipeline, MAP-RSeq version 3.0, as previously described. Briefly, MAP-RSeq used the STAR tool to align reads to the reference human genome build hg38. Gene and exon expression quantification were performed using the Subread package to obtain raw counts. We further removed genes with a median count below. We next computed transcripts per million (TPM) for the expression data. For our gene expression clustering, we used the nonnegative matrix factorization (NMF) unsupervised clustering approach that ensure robustness of clustering. Only protein coding genes, with the exclusion of mitochondrial genes and sex chromosome genes, were used for the NMF and principal component analysis (PCA).
Assembly: hg38
Supplementary files format and content: tab-delimited file of normalized read counts

source_name: Plasma cells

extract_protocol:
Total RNA was extracted using the Qiagen miRNeasy Micro Kit (217004). The library was prepared using the RNA access kit TruSeq Stranded Total RNA v2 from Illumina.
Total RNA was extracted using the Qiagen miRNeasy Micro Kit (217004). The library was prepared using the RNA access kit TruSeq Stranded Total RNA v2 from Illumina.

value: Plasma cells

value: Sorted Plasma Cells

value: WM


title: sample.hoxpkd1het_p15_2


title: C4_m14_cDC2


title: C3_m14_cDC1

source_name: Lin- CD11c+ MHC II+ 33D1- CD8+ DCs

value: Lin- CD11c+ MHC II+ 33D1- CD8+ DCs


title: OVX.VEH3

city: Columbia

first: Mitzi

last: Nagarkatti

state: SC

address: 6439 Garners Ferry Rd

department: PMI

institute: University of South Carolina School of Medicine

description:
predicted_metagenomes.L3_L3.txt
table_mc17612_sorted_L6.txt

data_processing:
Sequenced data by Illumina Miniseq system in FASTQ files along with mapfile in excel format were uploaded to the online 16s analysis platform, Nephele (https://nephele.niaid.nih.gov/) supported by Cyber Infrastructure and Computational Biology (OCICB), National Institute of Allergy and Infectious Diseases (NIAID), NIH.
The 16S metagenomics was analyzed through 16S Paired-end QIIME method, the groups of related DNA se-quences were assigned to operational taxonomic units (OTUs), and Nephele-generated output pipeline files were analyzed to determine targeted tissue-microbial compositions.
The default setting of Nephele was excluding any samples with the median OUT less than 0.2 OUT fractions of the highest sample in the same run in order to increase the quality of the reads, and then the generated FASTA files were blasted into Greengenes_99 database at 70% cutoff similarity.
Assembly: Greengenes_99
Supplementary files format and content: Text file includes raw total counts of OTUs for each sample
Supplementary files format and content: Text file includes raw counts of OTUs for each predicted metagenomic metabolism process
Library strategy: 16S ribosomal RNA sequencing

organism: mouse gut metagenome

source_name: Colonic contents

extract_protocol:
Colon flush was performed of the excised whole colon using sterile PBS. Bacterial genomic DNA was isolated from colon contents using QIAamp DNA Stool Mini Kit (Qiagen, Valencia, CA) and quantified using a Qubit 4 Fluorometer (ThermoFisher, Waltham, MA). Purified DNA was used in the library preparation for 16S ribosomal RNA sequencing using 16S Metagenomic Sequencing Library Preparation Kit (Illumina, San Diego, CA) according to the manufacturer’s instructions. Briefly, the purified DNA was amplified by PCR using bacterial/archaeal sense 319 F primer and anti-sense 806 R primer to amplify the V3-V4 hypervariable regions of 16S rRNA. After clean-up, the amplified PCR products were then amplified again by PCR using dual indices and sequencing adaptors for 16S rRNA sequencing.
Purified DNA was used in the library preparation for 16S ribosomal RNA sequencing using 16S Metagenomic Sequencing Library Preparation Kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

treatment_protocol: Mature Balb\c mice were used in current experimental design. All the experimental mice were housed and managed at same condiotions with no restriction in standard food or drink. Some Balb\c mice were kept as naive and some underwent ovariectomy (OVX) under isoflurane anasthesia and then 7 days later some of these OVX mice assigned as donor mice and the rest was assigned as recipient mice (OVX) in rate of one donor for every 2 recipients mice. The donor mice went through euthanasia by using overdose of isoflurane to collect the uterie horns to appeal the endometrial tissue for transplantation. Naive and OVX then divided into four groups. Naïve group, mice of this group were kept as control wihtout any treatment to normalized collected data. Naive+END group, mice of this group are having intact ovaries but received endometrial tissue transplant taken from ovariectomized donor mice. OVX mice received either intraperitoneal load of endometrial tissue (END) in normal saline and assigned as OVX+END or received intraperitoneal injection of normal saline namely, OVX+VEH. At the endpoint of the experiment, the uterine horns, blood samples, peritoneal wash and colonic fulshes were collected for downstream analysis.

value: Colonic contents

tag: strain

value: Balb\c


title: HEK293T, Control-sh RNASEH S96 Rep1

value: S9.6(Millipore, MABE 1095)


title: C2_m13_cDC2


title: OVX.VEH1


title: OVX.VEH2


title: sample.hoxpkd1het_p15_3


title: HEK293T, Control-sh control-plasmid IgG Rep2

value: IgG(Abcam, ab4729)


title: C1_m13_cDC1


title: Naive.END4

value: Five mg of endometrial tissue (END) was collected from ovariectomized-donor mice and then transplanted intraperitoneally into ovary-intacted recipient mice (Naive). Mice of this group did not receive any treatment rather than transplanted endometrial tissue.


title: outflow vein

city: New Haven

first: Yuichi

last: Ohashi

state: CT

address: 10 Amistad Street #414J

department: Surgery

institute: Yale University School of Medicine

description: 2 samples were combined into 1 RNA library

data_processing:
Data generated during sequencing runs were simultaneously transferred to the YCGA high-performance computing cluster. The FASTQ files of raw sequencing reads were imported into a cumputing cluster based on Red Hat Linux computing system and analyzed. For the purpose of quality control, poly A and poly T seequences, Illumina adaptor sequences and low-quality sequenes in the reads were deleted using PRINSEQv0.20.4 and Trimmomatic v0.39 software. The trimmed sequencing data were aligned to the GRCm39 reference genome with the gene annotation information (Ensembl release 106), and expression values for each gene were counted using STAR v2.7.11a and RSEM v1.3.3 software.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

molecule: polyA RNA

source_name: outflow vein

extract_protocol:
On postoperative day 7, the anastomotic neointimas (combined from 4 mice) and outflow veins (combined from 2 mice) were carefully harvested and immediately submerged in RNA protect Tissue Reagent (QIAGEN, Hilden, Germany) and incubated overnight at 4°C, then stored at -80°C without the reagent. Total RNA was extracted using RNeasy Mini Kit with DNase I (QIAGEN, Hilden, Germany) according to the manufacturer’s protocol. Total RNA quality and concentration were estimated with A260/A280 and A260/A230 ratios measured using a NanoDrop spectrophotometer (Thermo Scientific, Wilmington, DE, USA). Preparation and sequencing of poly-A mRNA sequencing libraries were performed by the Yale Center for Genome Analysis (YCGA). RNA integrity was estimated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Samples with RNA integrity number (RIN) values of ≥ 8.0 were used for analysis.
Poly-A mRNA was purified from approximately 200 ng of total RNA and the stranded mRNA sequencing libraries were constructed using KAPA mRNA HyperPrep Kit for Illumina sequencing (Roche, Basel, Switzerland). Indexed libraries were quantified by qRT-PCR using KAPA Library Quantification Kits (Roche, Basal, Switzerland) and insert size distribution was determined using an Agilent 2100 Bioanalyzer. Samples with a yield of ≥ 0.5 ng/µL and a size distribution of 150 - 300 bp were sequenced. Sample concentrations were normalized to 1.2 nM and loaded onto an Illumina NovaSeq flow cell (Illumina, San Diego, CA, USA) at a concentration that yielded 25 million passing filter clusters per sample. Samples were sequenced using 101 bp paired-end sequencing on an Illumina NovaSeq 6000 (Illumina, San Diego, CA, USA).

value: outflow vein

value: AVF creation


title: C5_m15_cDC1


title: N2a_TG

city: Hefei

first: Xiaolin

last: Wang

address: Huangshan Road

country: China

institute: USTC

data_processing:
The adaptors were trimmed with Cutadapt to obtain clean reads. The data quality was then checked with FastQC and the low-quality (Q value ≤ 20) reads were removed.
Reads were aligned to the human reference genome (hg19 or mm10) with Bowtie2. For linear RNAs including lncRNAs and mRNAs, the corresponding reads were counted with BEDtools and read per million (RPM) was used to calculate levels for lncRNAs and mRNAs.
Assembly: hg19 and mm10
Supplementary files format and content: tab-delimited text files include reads for each Sample

source_name: N2a cells

extract_protocol:
Total RNA was extracted by TRIzol reagent (Invitrogen, 15596026) according to the manufacturer’s instructions.
Libraries were constructed by the TruSeq Ribo Profile Library Prep Kit (Illumina, RPHMR12126) according to the manufacturer’s instructions.

value: N2a cells

value: Mouse neuroblastomaN2a cells

value: 300 nM TG  for 6 h


title: Naive.END3


title: B12_m12_cDC2

value: Lin- CD11c+ MHC II+ 33D1+ DCs


title: anastomotic neointima

description: 4 samples were combined into 1 RNA library

source_name: anastomotic neointima

value: anastomotic neointima


title: B11_m12_cDC1


title: HEK293T, Control-sh RNASEH PSIP1 Rep1

value: Human Embryonic Kidney cells with large T antigen

value: PSIP1(Bethyl Laboratory, A300-848A)


title: B10_m11_cDC2


title: N2a_GD

value: WT

value: Glucose deprivation for 24h


title: Naive.END1


title: Naive.END2


title: HEK293T, Control-sh RNASEH S96 Rep2


title: HEK293T, Control-sh RNASEH IgG Rep2


title: N2a_REG

value: Mock


title: HEK293T, Control-sh RNASEH IgG Rep1


title: B8_m10_cDC2


title: Naive4

value: Colonic contents

value: Mice of this group kept as control group without any treatment.


title: HEK293T, Control-sh RNASEH YH2AX Rep2

value: YH2AX(Abcam, AB81299)


title: Naive3

value: Balb\c


title: HEK293T, Control-sh RNASEH PSIP1 Rep2


title: B9_m11_cDC1

value: Lin- CD11c+ MHC II+ 33D1- CD8+ DCs


title: HEK293T, Control-sh RNASEH YH2AX Rep1


title: Naive2


title: B7_m10_cDC1


title: B6_m9_cDC2


title: PS19-Ch25hKO, 9 months

city: St. Louis

first: Jason

last: Ulrich

address: 660 S Euclid

department: Neurology

institute: Washington University

description: one sample run over two lanes

library_source: transcriptomic single cell

data_processing:
quality control, Cell Ranger Single Cell Software Suite (v3.0.2)
sample de-multiplexing, Cell Ranger Single Cell Software Suite (v3.0.2)
barcode processing, Cell Ranger Single Cell Software Suite (v3.0.2)
single-cell 3' gene counting, Cell Ranger Single Cell Software Suite (v3.0.2)
alignment, Cell Ranger Single Cell Software Suite (v3.0.2)
Assembly: mm10
Supplementary files format and content: Filtered matrix of gene by cell expression, file with barcodes and file with expressed genes. Files are ready to be imported to Seurat package.

molecule: nuclear RNA

source_name: hippocampus

growth_protocol: Mice housed in SPF facility

extract_protocol:
Mice were aged to 6 or 9 months of age. Upon tissue harvest, mice were euthanized and perfused with 1U/ml heparin in PBS. Left hemisphere of the brains were dissected out and flash frozen on dry ice. Flash frozen brain tissue was homogenized in a Dounce homogenizer in Lysis Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.025% NP-40), and incubated on ice 15 minutes. The suspension was filtered through a 30 um filter to remove debris and pelleted at 500 x g 5 min at 4o C. Nuclei were washed and filtered twice with Nuclei Wash (1% BSA in PBS with 0.2 U/uL RNasin (Promega)). Nuclei pellets were resuspended in 500 uL Nuclei Wash and 900 uL 1.8 M Sucrose. This 1400 uL mixture was carefully layered on top of 500 uL 1.8 M sucrose and centrifuged at 13,000 x g 45 min 4oC to separate the nuclei from myelin debris. The nuclei pellet was resuspended in Nuclei wash at 1200 nuclei/uL and filtered through a 40 um FlowMi Cell Strainer.
Isolated single nuclei were subjected to droplet-based 3’ end massively parallel single-cell RNA sequencing using Chromium Single Cell 5’ Reagent Kits as per manufacturer’s instructions (10x Genomics) The generated scRNAseq libraries were sequenced using an Illumina sequencer.
snRNAseq

value: hippocampus

tag: age

value: 9 months


title: HEK293T, PSIP1-sh control-plasmid S96 Rep1

value: S9.6(Millipore, MABE 1095)


title: PS19, 9 months


title: sr34a-1 germinated seeds submitted to ABA treatment biol rep 3

city: Oeiras

first: Tom

last: Laloum

address: Rua da Quinta Grande, 6

country: Portugal

institute: Instituto Gulbenkian de Ciencia

data_processing:
Gene expression (GE) quantification is performed using vast-tools. vast-tools maps the first 50 nucleotides of the forward read (if longer and paired end) to a library with one reference transcript per gene, the *.1 transcript according to the TAIR 10 nomenclature or else that with the lowest suffix (33,602 genes in total). GE levels are provided using the cRPKM metric (corrected [for mappability] Reads Per Kilobasepair and Million mapped reads), as detailed in Labbé et al., Stem Cells 2012. cRPKM can be converted to TPMs applying the following formula: TPM = 10^6 * cRPKM/sum_all(cRPKM).
Alternative splicing (AS) quantification is performed using vast-tools. vast-tools maps the RNA-seq data to the araTha10 library, based on Ensembl Plants v31 and composed of an extended annotation with all exon-exon and exon-intron junction sequences found in the Arabidopsis thaliana genome. vast-tools then quantifies intron retention, exon skipping, alternative 5' splice site and alterntive 3' splice site events and provides the percentage of inclusion (PSI) of the putative alternative sequence using only exon-exon (or exon-intron for IR) junction reads.
Assembly: TAIR10
Supplementary files format and content: Tab-delimited text file including cRPKM values for each gene
Supplementary files format and content: Tab-delimited text file including PSI values for each alternative splicing event

organism: Arabidopsis thaliana

source_name: 44h germinated seeds + 2h ABA treatment

growth_protocol: Stratified seeds were grown on MS medium in continuous white light  (100 µmol/m2) at 21 ºC for 44h

extract_protocol:
Total RNA was extracted from whole Arabidopsis seedlings using the innuPREP Plant RNA kit (Analytik Jena BioSolutions).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 44h germinated seeds were transferred to MS medium (Control) or MS medium supplemented with 0.5 µM ABA during 2h

value: 44h germinated seeds + 2h ABA treatment

value: ABA 0.5 µM


title: Naive1


title: B5_m9_cDC1


title: HEK293T, PSIP1-sh control-plasmid PSIP1 Rep2


title: B3_m8_cDC1

value: PBS/LPS


title: B4_m8_cDC2

value: Lin- CD11c+ MHC II+ 33D1+ DCs


title: sr34a-1 germinated seeds submitted to ABA treatment biol rep 1


title: PS19, 6 months

description: one sample run over two lanes

value: 6 months


title: sr34a-1 germinated seeds submitted to ABA treatment biol rep 2


title: HEK293T, PSIP1-sh control-plasmid IgG Rep2

value: Human Embryonic Kidney cells with large T antigen

value: IgG(Abcam, ab4729)


title: HEK293T, PSIP1-sh control-plasmid PSIP1 Rep1

value: PSIP1(Bethyl Laboratory, A300-848A)


title: TE4-LXR [al-30]

first: Eric

last: Tycksen

state: Missouri

address: 4444 Forest Park Avenue

department: McDonnell Genome Institute

institute: Washington University in St. Louis School of Medicine

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.7.9a
Gene counts quantitated with Subread:featureCount 2.0.3 with CPM and RPKM transformations added with custom Rscripting.
Assembly: Ensembl GRCm38.101
Supplementary files format and content: Gene counts with CPM and RPKM in tab-delimitted text format

extract_protocol:
Mice were aged to 9.5 months of age. Upon tissue harvest, mice were euthanized and perfused with 1U/ml heparin in PBS. Left hemisphere of the brains were dissected out and flash frozen on dry ice. Total RNA was extracted from frozen brain tissues using RNeasy mini kit (Qiagen, 71404) with Trizol.
Takara Clontech SMARTer

treatment_protocol: Mice were fed with a control diet or with diet supplemented with 10 mg/kg dosage of GW3965 from 6 to 9.5 months of age

tag: strain background


title: B2_m7_cDC2


title: WT, 9 months


title: TE4-LXR [al-29]


title: HEK293T, PSIP1-sh control-plasmid YH2AX Rep2


title: WT germinated seeds submitted to ABA treatment biol rep 2


title: HEK293T, PSIP1-sh control-plasmid IgG Rep1


title: HEK293T, PSIP1-sh control-plasmid S96 Rep2


title: PS19-Ch25hKO, 6 months


title: TE4-LXR [al-28]


title: A12_m6_cDC2


title: HEK293T, PSIP1-sh control-plasmid YH2AX Rep1


title: A8_m4_cDC2

value: PBS/Ctrl


title: WT germinated seeds submitted to ABA treatment biol rep 3


title: TE4-LXR [al-25]


title: HEK293T, PSIP1-sh RNASEH S96 Rep1


title: TE4-LXR [al-27]


title: A7_m4_cDC1


title: TE4-LXR [al-26]


title: sr34a-1 germinated seeds submitted to mock treatment biol rep 3

source_name: 44h germinated seeds + 2h mock treatment

value: Control


title: sr34a-1 germinated seeds submitted to mock treatment biol rep 2

value: 44h germinated seeds + 2h mock treatment


title: WT germinated seeds submitted to ABA treatment biol rep 1


title: TE4-LXR [al-24]


title: TE4-LXR [al-23]


title: A6_m3_cDC2


title: HEK293T, PSIP1-sh RNASEH PSIP1 Rep2


title: HEK293T, PSIP1-sh RNASEH S96 Rep2


title: WT germinated seeds submitted to mock treatment biol rep 3


title: B1_m7_cDC1


title: TE4-LXR [al-22]


title: HEK293T, PSIP1-sh RNASEH PSIP1 Rep1


title: WT germinated seeds submitted to mock treatment biol rep 2


title: HEK293T, PSIP1-sh RNASEH IgG Rep2


title: A4_m2_cDC2


title: A11_m6_cDC1


title: HEK293T, PSIP1-sh RNASEH IgG Rep1


title: A3_m2_cDC1


title: TE4-Ctrl [al-20]

value: Ctrl


title: TE4-Ctrl [al-19]


title: WT_10DAG_roots_mannitoll_rep2

city: Busan

first: Yong-Hwan

last: Moon

address: Busandaehak-ro 63Beon-gil 2, Geumjeong-gu

department: Molecular Biology

country: South Korea

institute: Pusan National University

description: Gene expression in 10-day-old seedlings of WT grown under SD conditions (8-h-light and 16-h-dark cycle) after 1, 2, and 4 h of 300 mM mannitol treatment. Roots were sampled and total RNA was analyzed.

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to TAIR10 whole genome using Tophat
FPKM calculation using Cufflink
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: roots

growth_protocol: Arabidopsis plants were of the Columbia (Col-0) ecotype background. Arabidopsis seeds were surface-sterilized and water-imbibed in the dark for 2 d at 4℃. The seeds were sown on 0.7% (w/v) agar plates containing on-half-strength Murashige and Skoog (MS) media supplemented with B5 vitamins and 1.5% (w/v) sucrose. They were grown at 22℃ under SD conditions (8-h-light/16-h-dark cycle).

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the NEBNext Ultra II Directional RNA-Seq Kit standard protocols.

treatment_protocol: 10-day-old WT seedlings grown under SD conditions (8-h-light/16-h-dark cycle) were placed on ﬁlter papers soaked in MS solution containing 150 mM NaCl or 300 mM mannitol. After 0, 1, 2, and 4 h, the seedlings were harvested and prepared as whole seedlings or cut as shoots and roots.

value: roots

value: WT (Col-0)

value: 300 mM mannitol for 1, 2, and 4 h


title: A2_m1_cDC2


title: sr34a-1 germinated seeds submitted to mock treatment biol rep 1


title: A1_m1_cDC1

value: Lin- CD11c+ MHC II+ 33D1- CD8+ DCs


title: WT_10DAG_roots_mannitoll_rep1


title: ALDH9A1B +/+ +tt-DDE5

city: Mannheim

first: Xin

last: Qian

state: Baden-Wuerttemberg

address: Ludolf-Krehl-Str. 13-17

department: Vascular Biology&Tumor Angiogenesis

country: Germany

institute: Medical Faculty Mannheim, Heidelberg University

data_processing:
QC with fastqc  nersion 0.11.9  Parameters:fastqc *.fastq
trimmed with trim_galore version 0.6.7. Parameters: trim_galore phred33 -q 30 --length 36 --stringency 3
alignment with hisat2  version 2.2.1 . Parameters: hisat2 -t -p 30 -x
Get raw counts with featureCounts Version 2.0.1. Parameters: featureCounts -T 5 -p -t exon -g gene_id -a
Assembly: GRCz11
Supplementary files format and content: Raw counts generated with featureCounts Version 2.0.1.

organism: Danio rerio

extract_protocol:
Total RNA was extracted using TRIzol method
RNA libraries were prepared for sequencing using standard BGISeq-500 protocols

value: larvae

value: yes, treated with tt-DDE

value: WT


title: TE4-LXR [al-21]

value: hippocampus


title: HEK293T, PSIP1-sh RNASEH YH2AX Rep1

value: YH2AX(Abcam, AB81299)


title: A5_m3_cDC1


title: MCviPI_FFA_1

city: Wilrijk

first: Claudia

last: Theys

state: Antwerpen (nl)

department: FBD

country: Belgium

institute: Universiteit Antwerpen

data_processing:
The quality of the raw sequencing reads was evaluated using FastQC (v0.11.5)
Alignment to genome reference consortium mouse build 38 (GRCm38) was performed with the STAR (v.2.7.3a) tool
Differential gene expression and pathway analysis were performed using DESeq2 R package software41 and the Omics Playground tool (v2.8.12) platform
Assembly: GRCh37
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: HepG2 cells

growth_protocol: The Human hepatoma cells (HepG2) cell lines overexpressing mitochondria targeted DNMTs MCviPI, MSssI or inactivated MCviPI (MCviPI mutant) were cultured in Dulbecco’s modified Eagle medium (DMEM, Gibco, Thermo Fisher Scientific, 41965039) supplemented with 10% foetal bovine serum (Gibco, Thermo Fisher Scientific, 10270106), 1% penicillin-streptomycin solution (Gibco, Thermo Fisher Scientific, 15140122) and 1mM pyruvate. Both cell lines were cultured in T75 or T25 flasks in a humidified atmosphere (37°C and 5% CO2).

extract_protocol:
Total RNA was extracted from fresh cell pellets with the RNeasy kit (Qiagen, 75162), according to the manufacturer’s protocol
The non-directoinaly librabry protocol of Novogene was performed on site. Briefly, Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads.After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP for non-directional library. The cDNA was ready for sequencing after end repair, A-tailing, adapter ligation, size selection, amplification, and purification

treatment_protocol: 24h treatment with 1mM FFA (Oleic acid and palmitic acid in a 2:1 ratio)

value: HepG2 cells

value: liver

value: MCviPI DNMT overxpressing

value: 1mM FFA


title: ALDH9A1B +/+ +tt-DDE4


title: TE4-Ctrl [al-17]


title: TE4-Ctrl [al-15]


title: TE4-Ctrl [al-18]


title: WT_10DAG_roots_NaCl_rep2

description: Gene expression in 10-day-old seedlings of WT grown under SD conditions (8-h-light and 16-h-dark cycle) after 1, 2, and 4 h of 150 mM NaCl treatment. Roots were sampled and total RNA was analyzed.

value: 150 mM NaCl for 1, 2, and 4 h


title: MCviPI_FFA_3


title: MCviPI_FFA_4


title: WT_10DAG_roots_control_rep2

description: Gene expression in 10-day-old seedlings of WT grown under SD conditions (8-h-light and 16-h-dark cycle). Roots were sampled and total RNA was analyzed.

value: no treatment


title: MCviPI_4


title: MCviPI_FFA_2


title: WT_10DAG_roots_NaCl_rep1


title: ALDH9A1B +/+ +tt-DDE3


title: WT_10DAG_roots_control_rep1


title: WT germinated seeds submitted to mock treatment biol rep 1

value: 44h germinated seeds + 2h mock treatment

value: Control


title: TE4-Ctrl [al-14]

value: Ctrl


title: ALDH9A1B +/+ +tt-DDE2


title: ALDH9A1B +/+ +tt-DDE1


title: MCviPI_3


title: TE4-Ctrl [al-13]


title: TE4-Ctrl [al-16]


title: WT_10DAG_whole_seedlings_mannitol_rep1

description: Gene expression in 10-day-old seedlings of WT grown under SD conditions (8-h-light and 16-h-dark cycle) after 1, 2, and 4 h of 300 mM mannitol treatment. Whole seedlings were sampled and total RNA was analyzed.

source_name: whole seedlings

value: whole seedlings

value: WT (Col-0)


title: WT_10DAG_whole_seedlings_mannitol_rep2

value: 300 mM mannitol for 1, 2, and 4 h


title: TE4-Ctrl [al-12]


title: ALDH9A1B -/- 4

value: larvae

value: no

value: KO


title: MCviPI_1


title: TE4-Ctrl [al-11]

value: hippocampus


title: WT_10DAG_whole_seedlings_NaCl_rep2

description: Gene expression in 10-day-old seedlings of WT grown under SD conditions (8-h-light and 16-h-dark cycle) after 1, 2, and 4 h of 150 mM NaCl treatment. Whole seedlings were sampled and total RNA was analyzed.


title: WT_10DAG_whole_seedlings_NaCl_rep1


title: ALDH9A1B -/- 3


title: MSSSI_FFA_4

value: MSssI  DNMT overxpressing


title: ALDH9A1B -/- 2


title: MSSSI_FFA_3

value: HepG2 cells


title: WT_10DAG_whole_seedlings_control_rep2

description: Gene expression in 10-day-old seedlings of WT grown under SD conditions (8-h-light and 16-h-dark cycle). Whole seedlings were sampled and total RNA was analyzed.


title: WT_10DAG_whole_seedlings_control_rep1


title: MSSSI_FFA_1

value: liver


title: MSSSI_FFA_2


title: E4-LXR [al-10]


title: E4-LXR [al-9]


title: ALDH9A1B -/- 1


title: ALDH9A1B +/+ 4

value: WT


title: E4-LXR [al-7]


title: MCviPI_2

value: MCviPI DNMT overxpressing


title: E4-LXR [al-6]


title: MSSSI_4


title: ALDH9A1B +/+ 3


title: ALDH9A1B +/+ 2


title: MSSSI_3


title: E4-Ctrl [al-5]


title: endothelial cells adipose tissue - Gluteofemoral - donor 5

type: RNA

city: Toulouse

first: Anaïs

last: Briot

address: 1 avenue Jean Poulhès

department: UMR1297, I2MC

country: France

institute: Inserm

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE v3 microarray (8X60K, Design 072363  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 072363_D_F_20150612). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 7 out of 8 microarrays or with a minimal weight of 2 per group from at least one experimental group. At this step, 31665 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 29093 rows each corresponding to a unique ProbeName (provided as data Matrix).

source_name: endothelial cells adipose tissue

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

growth_protocol: Cells were studied in native state

extract_protocol: Total RNA was isolated from endothelial cells using Rneasy Mini kit Plus (Qiagen) following the manufacturer's recommendations

treatment_protocol: Endothelial cells from human adipose tissue  were isolated by immunoselection (CD45NEG,CD34POS,CD31POS)

tag: territory

value: Gluteofemoral

tag: gender

value: female


title: E4-LXR [al-8]


title: MSSSI_2


title: MSSSI_1

value: MCviPI mutant DNMT overxpressing

value: 1mM FFA


title: E4-Ctrl [al-3]

value: Ctrl


title: E4-Ctrl [al-4]


title: Amor_P1_uPAR_positive

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

description: 10x Genomics

data_processing:
Sequencing data was demultiplexed, mapped, and processed into gene/cell expression matrices using 10X Genomics' Cell Ranger software v7.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). Gene expression reads were aligned to the mouse reference genome version gex-mm10-2020-A, available from the 10X Genomics website.
Assembly: mm10
Supplementary files format and content: Filtered single cell 3' cell/gene matrices in .h5 format generated by Cell Ranger for Liver + Adipose tissues
Supplementary files format and content: Filtered single cell 3' cell/gene matrices in .h5 format generated by Cell Ranger for Pancreas tissue

source_name: Pancreas

extract_protocol:
Live uPAR positive or negative cells were sorted by uPAR staining (R&D, FAB531P) on a SONY SH800 cell sorter, stained with AO/PI (acridine orange/propidium iodide, Nexcelon ViaStain) and checked for viability >80% using a Countess FL II Automated cell counter.
10X Genomics NextGEM v3.1 Single Cell 3' Gene Expression libraries were prepared from sorted cells according to the manufacturer's instructions and sequenced on Illumina NextSeq2000 flow cells.

value: Pancreas

value: Untreated

tag: Sex

value: Female


title: Mutant_FFA_4


title: E4-Ctrl [al-2]


title: Amor_P2_uPAR_positive

description: 10x Genomics

value: Male


title: Amor_AT1_uPAR_positive

description: 10x Genomics

source_name: Gonadal adipose tissue

value: Gonadal adipose tissue


title: Mutant_FFA_3


title: E4-Ctrl [al-1]


title: Amor_L3_uPAR_positive

description: 10x Genomics

source_name: Liver

value: Liver


title: ALDH9A1B +/+ 1

value: larvae

value: no


title: PS19-APOE4, GW3965_2

description: Technical replicate  2

data_processing:
quality control, Cell Ranger Single Cell Software Suite (v3.0.2)
sample de-multiplexing, Cell Ranger Single Cell Software Suite (v3.0.2)
barcode processing, Cell Ranger Single Cell Software Suite (v3.0.2)
single-cell 3' gene counting, Cell Ranger Single Cell Software Suite (v3.0.2)
alignment, Cell Ranger Single Cell Software Suite (v3.0.2)
Assembly: mm10+ human APOE
Supplementary files format and content: Filtered matrix of gene by cell expression, file with barcodes and file with expressed genes. Files are ready to be imported to Seurat package.

extract_protocol:
Mice were aged to 9 months of age. Upon tissue harvest, mice were euthanized and perfused with 1U/ml heparin in PBS. Left hemisphere of the brains were dissected out and flash frozen on dry ice. Flash frozen brain tissue was homogenized in a Dounce homogenizer in Lysis Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.025% NP-40), and incubated on ice 15 minutes. The suspension was filtered through a 30 um filter to remove debris and pelleted at 500 x g 5 min at 4o C. Nuclei were washed and filtered twice with Nuclei Wash (1% BSA in PBS with 0.2 U/uL RNasin (Promega)). Nuclei pellets were resuspended in 500 uL Nuclei Wash and 900 uL 1.8 M Sucrose. This 1400 uL mixture was carefully layered on top of 500 uL 1.8 M sucrose and centrifuged at 13,000 x g 45 min 4oC to separate the nuclei from myelin debris. The nuclei pellet was resuspended in Nuclei wash at 1200 nuclei/uL and filtered through a 40 um FlowMi Cell Strainer.
Isolated single nuclei were subjected to droplet-based 3’ end massively parallel single-cell RNA sequencing using Chromium Single Cell 5’ Reagent Kits as per manufacturer’s instructions (10x Genomics) The generated scRNAseq libraries were sequenced using an Illumina sequencer.

value: hippocampus

value: 9.5 months

value: GW3965 diet


title: PS19-APOE4, GW3965_1

description: Technical replicate 1


title: Mutant_FFA_1

value: HepG2 cells

value: liver


title: Pcrg1:grx4, glucose, 24hours, rep3

city: Vancouver

first: James

last: Kronstad

state: BC

address: 2185 E Mall

department: Mircobiology and Immunology

country: Canada

institute: University of British Columbia

data_processing:
Raw reads were checked for quality using FastQC
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36
The trimmed reads were mapped to the ustilago_maydis reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
Differential gene expression was preformed using the DEseq2 package in R
Assembly: Ustilago maydis 521 v2.0
Supplementary files format and content: Processed files represent the differential gene expression information for all genes between specific comparisons. Files are in .csv format

organism: Mycosarcoma maydis

growth_protocol: Samples were grown in PDB media overnight before treatment.

extract_protocol:
RNA was extracted using the Qiagen RNA mini kit
The library construction was completed according to protocols from Genewiz.

treatment_protocol:
grown in minimal media with 2% glucose for 24 hours
"moved to SAMPLES" section

value: glucose


title: endothelial cells adipose tissue - Gluteofemoral - donor 3

value: Gluteofemoral

value: female


title: Mutant_FFA_2

value: MCviPI mutant DNMT overxpressing

value: 1mM FFA


title: endothelial cells adipose tissue - Abdominal - donor 4

value: Abdominal


title: Pcrg1:grx4, glucose, 24hours, rep2


title: Mutant_ 4


title: endothelial cells adipose tissue - Abdominal - donor 3


title: endothelial cells adipose tissue - Gluteofemoral - donor 4


title: endothelial cells adipose tissue - Abdominal - donor 5


title: endothelial cells adipose tissue - Gluteofemoral - donor 2


title: endothelial cells adipose tissue - Abdominal - donor 2


title: Amor_P2_uPAR_negative

description: 10x Genomics

value: Pancreas

value: WT

value: Untreated


title: PS19-APOE4, Ctl_2

description: Technical replicate  2

value: Control diet


title: Mutant _2


title: Amor_L1_uPAR_positive

description: 10x Genomics

value: Liver

value: Female


title: Pcrg1:grx4, glucose, 24hours, rep1


title: Amor_AT3_uPAR_positive

description: 10x Genomics

value: Gonadal adipose tissue

value: Male


title: Amor_P1_uPAR_negative

description: 10x Genomics


title: Pcrg1:grx4, arabinose, 24hours, rep2

treatment_protocol:
grown in minimal media with 2% arabinose for 24 hours
"moved to SAMPLES" section

value: arabinose


title: Amor_AT1_uPAR_negative

description: 10x Genomics


title: APOE4, GW3965_2

description: Technical replicate  2

value: hippocampus

value: 9.5 months

value: GW3965 diet


title: PS19-APOE4, Ctl_1

description: Technical replicate 1


title: Pcrg1:grx4, arabinose, 24hours, rep3


title: APOE4, GW3965_1

description: Technical replicate 1


title: PFCH6-Y

city: Basel

first: Ilya

middle: M.

last: Flyamer

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

data_processing:
Raw reads were processed using the distiller-nf pipeline (https://github.com/open2c/distiller-nf) with a project file available here: https://gist.github.com/Phlya/b1cdceb8124d787731e654a7edaedb82
Briefly, reads were mapped using bwa mem to the hg38 reference genome. Resulting .bam files were parsed using pairtools parse into pairs, which were deduplicated with max_mismatch_bp=1. Deduplicated pairs with mapq>=30 were binned using cooler cload pairs to create 1000 bp resolution cooler files, which were then coarsegrained to multiple resolution using cooler zoomify. All resolutions were then balanced to create three different weights: genome-wide, cis-only, and trans-only.  Depending on the analysis, cis-only or trans-only weights were used. All datasets were subsampled to the same number of reads using cooltools random-sample.
Assembly: hg38
Supplementary files format and content: .mcool - genome-wide contact matrices at various resolutions, subsampled to the same number of reads

source_name: fibroblasts

growth_protocol: Human primary fibroblasts were obtained from the collection of Research Centre for Medical Genetics (Moscow, Russia) and Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University (Moscow, Russia). Fibroblasts were grown in Dulbecco’s Modified Eagle’s Medium (DMEM), supplemented with 10% fetal calf serum, at 37 o C and 5% of CO 2.Chorion cells were isolated from donors in Medical genetic center LLC Progen (Moscow, Russia). Chorionic villi were cut with sterile scissors, and unicellular suspension was obtained by incubating the sample with collagenase I (1 mg/ml) in DMEM, supplemented with 10% fetal calf serum, at 37 o C for 40 min.

extract_protocol:
Hi-C libraries were prepared as described previously, with minor modifications. A total of 5-10 million fibroblasts or chorion cells were fixed in 1× PBS containing 2% formaldehyde (Sigma-Aldrich) for 10 min, with occasional mixing. The reaction was quenched with by the addition of 2 M glycine (Sigma-Aldrich), to a final concentration of 125 mM. Cells were pelleted by centrifugation (1,000 x g, 10 min, 4 °C), resuspended in 50 ul 1× PBS, snap-frozen in liquid nitrogen, and stored at -80°C. Cells were lysed in 1.5 ml isotonic buffer [50 mM Tris-HCl pH 8.0 (Sigma-Aldrich), 150 mM NaCl (Sigma-Aldrich), 0.5% (v/v) NP-40 substitute (Fluka), 1% (v/v) Triton-X100 (Sigma-Aldrich), 1× Halt™ Protease Inhibitor Cocktail (Thermo Scientific)], on ice for 15 min. Cells were pelleted by centrifugation at 2,500g for 5 min, resuspended in 100 ul 1× DpnII buffer (New England Biolabs), and pelleted again. The pellet was resuspended in 200 ul 0.3% SDS (Sigma-Aldrich) in 1.1× DpnII buffer (New England Biolabs) and incubated at 37°C for 1 h. Then, 330 ul 1.1× DpnII buffer and 53 ul 20% Triton X-100 were added, and the suspension was incubated at 37°C for 1 h. Next, 600 U DpnII enzyme (New England Biolabs) were added, and the chromatin was digested overnight (14-16 h), at 37°C, with shaking (1,400 rpm). In the morning, 200 U DpnII enzyme was added, and the cells were incubated for 2 h. DpnII was then inactivated by incubation at 65°C for 20 min. The nuclei were harvested for 10 min at 5,000 g, washed with 100 ul 1× NEBuffer 2 (New England Biolabs), and resuspended in 125 ul 1.2× NEBuffer 2. Cohesive DNA ends were biotinylated by adding 25 ul biotin fill-in mixture [0.025 mM dATP (Thermo Scientific), 0.025 mM dGTP (Thermo Scientific), 0.025 mM dTTP (Thermo Scientific), 0.025 mM biotin-14-dCTP (Invitrogen), 0.8 U/μl Klenow enzyme (New England Biolabs)]. The samples were incubated at 37°C for 75 min, with shaking (1,400 rpm). Nuclei were pelleted by centrifugation at 3,000 x g for 5 minutes, resuspended in 300 ul 1× T4 DNA ligase buffer (Thermo Scientific), and pelleted again. The pellet was resuspended in 300 ul 1× T4 DNA ligase buffer, and 75 U T4 DNA ligase (Thermo Scientific) was added. Chromatin fragments were ligated at 20°C for 6 h. The cross-links were reversed by overnight incubation at 65°C in the presence of proteinase K (100 μg/ml) (Sigma-Aldrich). After cross-link reversal, the DNA was purified by single phenol-chloroform extraction, followed by ethanol precipitation [glycogen (Thermo Scientific) at a concentration of 20 μg/ml was used as co-precipitator]. After precipitation, the pellets were dissolved in 100 μl 10 mM Tris-HCl, pH 8.0. To remove residual RNA, samples were treated with 50 ug RNase A (Thermo Scientific) for 45 min at 37°C. To remove residual salts and DTT, the DNA was purified using Agencourt AMPure XP beads (Beckman Coulter). Biotinylated nucleotides from the non-ligated DNA ends were removed by incubating the Hi-C libraries (2 μg) in the presence of 6 U T4 DNA polymerase (New England Biolabs) in NEBuffer 2, supplemented with 0.025 mM dATP and 0.025 mM dGTP, at 20°C for 4 h. Next, the DNA was purified using Agencourt AMPure XP beads.
The DNA was then dissolved in 500 ul sonication buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 0.1% SDS) and was sheared to a size of approximately 100-1,000 bp, using a VirSonic 100 (VerTis). The samples were concentrated (and simultaneously purified), using AMICON Ultra Centrifugal Filter Units (Merck), to a total volume of approximately 50 ul. The DNA ends were repaired by adding 62.5 ul MQ water, 14 ul 10× T4 DNA ligase reaction buffer, 3.5 ul 10 mM dNTP mix (Thermo Scientific), 5 ul 3 U/ul T4 DNA polymerase (New England Biolabs), 5 ul 10 U/ul T4 polynucleotide kinase (New England Biolabs), and 1 ul 5 U/ul Klenow DNA polymerase (New England Biolabs) and incubating at 20°C for 30 min. The DNA was purified with Agencourt AMPure XP beads and eluted with 50 ul 10 mM Tris-HCl (pH 8.0). To perform an A-tailing reaction, the DNA samples were supplemented with 6 ul 10× NEBuffer 2, 1.2 ul 10 mM dATP, 1 ul MQ water and 3.6 ul 5 U/ul Klenow (exo-) (New England Biolabs). The reactions were performed for 30 min at 37°C in a PCR machine, and the enzyme was then heat-inactivated by incubation at 65°C for 20 min. The DNA was purified using Agencourt AMPure XP beads and eluted with 200 ul 10 mM Tris-HCl (pH 8.0). Biotin pulldown of the ligation junctions was performed as described previously, with minor modifications. Briefly, 10 ul MyOne Dynabeads Streptavidin C1 (Invitrogen) beads were used to capture the biotinylated DNA, and the volumes of all buffers were decreased by 4-fold. The washed beads attached to captured ligation junctions were resuspended in 50 ul adapter ligation mixture, composed of 41.5 ul MQ water, 5 ul 10× T4 DNA ligase reaction buffer (Thermo Scientific), 2.5 ul Illumina TruSeq adapters and 1 ul 5 U/ul T4 DNA ligase (Thermo Scientific). Adapter ligation was performed at 22°C, for 2.5 h, and the beads were washed twice with 100 ul TWB (5 mM Tris-HCl, pH 8.0, 0.5 mM EDTA, 1 M NaCl, 0.05% Tween-20 (Sigma-Aldrich)), once with 100 ul 1× binding buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 2 M NaCl), and once with 100 ul CWB (10 mM Tris-HCl, pH 8.0 and 50 mM NaCl), and then resuspended in 20 ul MQ water. Test PCR reactions containing 4 ul streptavidin-bound Hi-C library were performed to determine the optimal number of PCR cycles necessary to generate sufficient PCR products for sequencing. The PCR reactions were performed using KAPA High Fidelity DNA Polymerase (KAPA) and Illumina PE1.0 and PE2.0 PCR primers (10 pmol each). The temperature profile was 5 min at 98°C, followed by 6, 9, 12, 15, and 18 cycles of 20 s at 98°C, 15 s at 65°C, and 20 s at 72°C. The PCR reactions were separated on a 2% agarose gel supplemented with ethidium bromide, and the number of PCR cycles necessary to obtain a sufficient amount of DNA was determined based on the visual inspection of gels (typically 9-12 cycles). Four preparative PCR reactions were performed for each sample. The PCR mixtures were combined, and the products were purified using Agencourt AMPure XP beads.

value: fibroblasts

tag: karyotype

value: normal

tag: donor


title: Pcrg1:grx4, arabinose, 24hours, rep1


title: Amor_AT3_uPAR_negative

description: 10x Genomics


title: PFCH6-G

value: female


title: APOE4, Ctl_2

description: Technical replicate  2


title: Amor_L3_uPAR_negative

description: 10x Genomics


title: HF18-Y

description: sextra 18.hg38.mapq_30.1000.sampled.mcool

value: extra 18


title: APOE4, Ctl_1

description: Technical replicate 1


title: wildtype, glucose, 24hours, rep3

source_name: wildtype

value: wildtype

value: glucose


title: wildtype, glucose, 24hours, rep1


title: Mutant _1

value: HepG2 cells

value: liver

value: MCviPI mutant DNMT overxpressing


title: wildtype, arabinose, 24hours, rep3


title: wildtype, glucose, 24hours, rep2


title: Amor_L1_uPAR_negative

description: 10x Genomics

value: Liver

value: WT

value: Untreated


title: CD8+ T cells VDJ seq, Lgr5-GFP+ mice

first: Craig

middle: B

last: Wilen

address: 789 Howard Avenue, Clinic Building Rm 438

department: Immunobiology

institute: Yale University

description: age 7-16 wks

data_processing:
mm10
Hierarchical data format and comma-separated value

source_name: Large intestine

growth_protocol: Mice were sacrificed and the full large intestine were harvested. Fat and connective tissue were removed. Tissues were placed in ice cold 1X HBSS without calcium or magnesium (Gibco). Large intestines were cut longitudinally and impacted feces were cleared. One to two mice per tissue were combined for tissue processing and sample analysis. Tissues were washed three times in cold 1X HBSS and stored in cold RPMI 1640 (Gibco) lymphocyte media containing 25 mM HEPES (Gibco), 1% Penicillin/Streptomycin, 1% Glutamax (1000X stock, Gibco), 50 μM β-mercaptoethanol (Gibco), and supplemented with 10% FBS. Intestinal tissues were then cut into 1-2 cm pieces and transferred to a flask containing pre-warmed (37°C) RPMI 1640 lymphocyte media supplemented with 3% FBS, 5 mM EDTA, and 0.145 mg/mL DTT per intestine. Tissue was stirred continually at ~400 rpm on a 9 x 250 mL stirrer (Corning) at 37°C/5% CO2 for exactly 20 minutes. Contents of the flask were strained over a fine-meshed kitchen strainer into a beaker on ice. Intestinal pieces were recollected from the strainer into a 50 mL conical tube with room temperature serum-free RPMI 1640 lymphocyte media + 2 mM EDTA and were shaken vigorously for 30 seconds. Cells were filtered over the same kitchen strainer (1 per tissue per mouse) into a beaker on ice. The shaking procedure was repeated for a total of three times. Cellular filtrates were passed through a 70 μM cell strainer (Falcon) and centrifuged at 1500 rpm for 8 min at 4°C. Pellets were resuspended in RPMI 1640 lymphocyte media + 3% FBS and passed through a 40 μM cell strainer (Falcon). Samples were centrifuged again at 1500 rpm for 8 min at 4°C. Cell pellets were resuspended in 30 mL of 27% Percoll (Cytiva) prepared in 1X PBS. Samples were centrifuged at 1600 rpm for 20 min at room temperature. Cells were then resuspended in 1 mL cold RPMI 1640 lymphocyte media + 10% FBS for counting. After counting, cells were processed for flow cytometry, including mouse Fc block (1:50, BioLegend) and stained with α-CD8a (APC-Fire750 or APC, 1:200; BioLegend), α-CD45.2 (PacBlue, 1:200; BioLegend), and α-CD45.1 (PE, 1:200; BioLegend). Cells were washed twice with FACS buffer (1400 rpm for 15 min at 4°C) and were resuspended to a concentration of ~6 x 106 cells/mL. Live CD8+ T cells (JEDI and endogenous) were purified from both Gfi1b-GFP+/- and Lgr5-GFP+/- recipient mice via FACS-based sorting (Sony MA900). JEDI CD8+ T cells were gated as live singlet CD8+CD45.1+CD45.2-, and endogenous CD8+ T cells were gated as live singlet CD8+CD45.1-CD45.2 cells. Post-sort purity was confirmed to exceed 85%. Cells were centrifuged at 1400 rpm for 15 min at 4°C and supernatant was carefully removed prior to resuspension in RPMI + 10% FBS. Cells were counted and combined at approximately a 1:1 ratio of CD45.1:CD45.2 cells.

extract_protocol:
10x scRNA-seq
5P single-cell RNA-seq and TCR-seq data from sorted colonic intraepithelial CD8+ T cells was processed with Cell Ranger 7.1.0 using the mm10 mouse genome indices from 10X Genomics. 7477 and 5332 cells were detected from Gfi1b and Lgr5 samples respectively. R (v4.2.1) was used for analysis and the packages Seurat (v4.3.0), DoubletFinder (v2.0.3), and SingleR (v1.10.0) were used to preprocess the data. Briefly, only cells with greater than 200 features and less than 5% mitochondrial reads were included. Further, the data was subset on predicted singlets as assigned by DoubletFinder and predicted T cells or NK cells as assigned by SingleR using the mouse bulk RNA-seq reference data (MouseRNAseqData) from celldex (v1.6.0). Cell cycle scoring was performed using Seurat’s CellCycleScoring function. To specifically visualize the JEDI T cells, cells from both samples were merged and only cells belonging to that JEDI clonotype were analyzed. Traditional Seurat processing was performed: NormalizeData, FindVariableFeatures, ScaleData, RunPCA, RunUMAP, FindNeighbors, FindClusters. 2000 variable features were used and RunUMAP was performed with the top 30 dimensions. Clustering was performed with a resolution of 0.35. DEGs were calculated using the functions FindAllMarkers or FindMarkers for pairwise comparisons. For gene set enrichment analysis, escape (v1.6.0) was used whereby gene sets were customized to include canonical exhaustion, effector, tissue resident, or central memory genes. The AverageExpression function was performed to facilitate heat map creation. The package dittoSeq (v1.8.1) was also used to perform some visualizations. Monocle3 (v1.2.9) was used to infer pseudotime on non-proliferating cells using the package SeuratWrappers (v0.3.0) and setting those cells with highest Sell expression as the root node. Analysis of all bystander cells was performed in a similar fashion as above by excluding those cells with the JEDI T cell clonotype.

treatment_protocol: Library was prepared according to manufacturer's protocol (5' single cell v2, 10x Genomics)

value: Large intestine

value: CD8+ T cells

value: Lgr5-EGFP-IRES-CreERT2 B10.D2

value: 6 days post-adoptive transfer of 5e6 JEDI CD8+ T cells


title: CD8+ T cells scRNA, Lgr5-GFP+ mice

description: age 7-16 wks


title: BMSC ko 1

city: Shen Zhen

first: Guozhi

last: Xiao

state: Guang Dong

address: No. 1088, Xueyuan Road

department: Biology

institute: Southern University of Science and Technology

description: 10X Chromium Single Cell 3ʹ Reagent Kits v3

data_processing:
Raw sequencing data was processed with Cell Ranger (v3.0.1)
Genome_build: mm10
Supplementary_files_format_and_content: feature barcode matrices were generated using Cell Ranger (v3.0.1)

source_name: bone marrow non-hematopoietic cell

extract_protocol:
All bone marrow cells hematopoietic cells were extracted from bone marrow, and bone marrow non-hematopoietic cells were extracted and sorted by FACS. Then, cells were loaded to 10X Chromium Single Cell Controler.
Libraries were constructed according to 10X Chromium Single Cell 3ʹ Reagent Kits v2 or v3 protocols

value: bone marrow


title: BMSC ctrl 1


title: BMHC ko 2

description: 10X Chromium Single Cell 3ʹ Reagent Kits v2

source_name: bone marrow hematopoietic cell


title: 3525b_S10

source_name: chorion

value: chorion


title: CD8+ T cells VDJ seq, Gfi1b-GFP+ mice

description: age 7-16 wks

value: Gfi1b-GFP B10.D2


title: HF18-G

value: fibroblasts

value: female


title: wildtype, arabinose, 24hours, rep2

value: wildtype

value: arabinose


title: wildtype, arabinose, 24hours, rep1


title: BMHC ctrl 2


title: 3524I

value: normal


title: 3525a_S9


title: CD8+ T cells scRNA, Gfi1b-GFP+ mice

description: age 7-16 wks


title: BMHC ko 1


title: 3518I

value: male


title: Lung, ML364_Rep5

city: Boston

first: Fabin

last: Dang

address: 3 Blackfan Circle

institute: Beth Israel Deaconess Medical Center

data_processing:
Raw data was filtered through removing the reads with 3'-end adapters and those with an average quality score lower than Q20
Mapping the filtered reads to the gemome using HISAT2
Differential genes were determined using DESeq.
Assembly: GRCm39
Supplementary files format and content: csv files containing abundance measurements and DEGs

source_name: K18-hACE2 transgenic mice infected with SARS-CoV-2 (Wuhan strain)

growth_protocol: The K18-hACE2 transgenic mice were housed on a 12 light/12-dark cycle, temperature 70° ± 5 F, and humidity 40–60%.

extract_protocol:
For RNA-seq, total RNA was purified using trizol reagent
Libraries were prepared using Illumina TruSeq mRNA sample preparation kits from 500 ng of purified total RNA

treatment_protocol: The K18-hACE2 transgenic mice were intraperitoneally administered either a solvent or ML364 (50 mg/kg) for four days prior to the SARS-CoV-2 challenge. On day five, both groups were lightly anesthetized with isoflurane and intranasally infected with 250 PFU of SARS-CoV-2 (strain IVCAS 6.7512) in a total volume of 50 μl DMEM. The mice were then given either a solvent or ML364 once daily until five days post-challenge. On day 10, the mice were euthanized, and lung tissues were collected for further analysis.

tag: infection

value: SARS-CoV-2 (Wuhan strain)

value: lung


title: Xanthomonas L148_Col-0_3_4

city: Cologne

first: Frederickson

last: Entila

state: Nordrhein-Westfalen

address: Carl-von-Linne-Weg 10

department: Plant-Microbe Interactions

institute: MPIPZ

description:
F_20220706_3_4
5732_F_run775_ACTCCTAC_S2_L002_R1_001.fastq.gz.subread.BAM

data_processing:
R software
sequences were mapped using the align() function in Rsubread package resulting to BAM files
raw read counts were extracted from the BAM files using featureCounts() function in edgeR package
the matrix of raw counts were normalized using the voom() function in limma package
Assembly: Leaf148.gff (http://www.at-sphere.com/)
Supplementary files format and content: voom normalized count matrix

organism: Xanthomonas sp. Leaf148

source_name: plant shoot

growth_protocol: The in planta bacterial RNA-Seq was done in accordance to Tatsuya et al, 2018. Briefly, 2-week-old plants grown in gnotobiotic agar system were inoculated with the strains (OD600=0.005) and approximately 150 shoots were harvested and pooled per sample 2 dpi were bacterial populations are still similar between Col-0 and rbohD plants.

extract_protocol:
RNA was extacted using TRIzol, DNAse treated, and 10ng was used for library construction
library was generated using Prokaryotic kit of NuGEN with plant ribo-depletion

value: plant shoot

tag: time

value: flood inoculation

tag: biol rep

tag: date received

tag: date experiment

tag: tech rep


title: Lung, ML364_Rep6

tag: tissue

tag: treatment


title: BMHC ctrl 1


title: MEEC+OP9-Jag1_24h.3 RNA

city: Madrid

first: Jose Luis

last: de la Pompa

state: MADRID

address: Melchor Fernández Almagro 3

country: Spain

institute: Centro Nacional de Investigaciones Cardiovasculares (CNIC)

data_processing:
Sequencing reads were pre-processed using FastQC and Cutadapt to remove Illumina adapter contamination.
Resulting reads were mapped against reference transcriptome GRCm38.91 and quantified using RSEM.
Expected expression counts calculated with RSEM were then processed with the Bioconductor package Limma for normalization (using TMM method).
Assembly: GRCm38.91
Supplementary files format and content: Normalized counts (TMM method) in each sample, for genes with at least 1 CPM in at least 3 samples.

source_name: MEEC

growth_protocol: MEECs were cultured on 0.1% gelatin-coated dishes and maintained in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin. GFP-, Jag1- or Dll4-expressing OP9 cells were cultured on 0.1% gelatin-coated dishes and maintained in MEM Alpha (1X) supplemented with 20% FBS and 1% penicillin/streptomycin. Cultures were incubated at 37 °C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA from cells was extracted with the PicoPure RNA Isolation Kit (ThermoFisher)
Total RNA was used to generate barcoded RNA-seq libraries using the NEBNext Ultra RNA Library preparation kit (New England Biolabs)

treatment_protocol:
Co-culture with OP9 cells: To define the effect of Dll4- and Jag1-mediated cell-to-cell signaling, MEECs were co-cultured for 6h (50% confluency) and 24h (25% confluency) over GFP-, Jag1- or Dll4-expressing OP9 cells at 90% confluence. To define the effect of NICD nuclear translocation inhibition, MEECS were cultured with DMSO (vehicle) or 20 μM of the γ-secretase inhibitor RO4929097 for 24 h. Next, MEECs were co-cultured for 6h (50% confluency) over GFP-expressing OP9 cells at 90% confluence.
Culture with Recombinant Ligands: Recombinant NOTCH ligands DLL4-His (R&D Systems 1389-D4-050) and JAG1-Fc (R&D Systems 599-JG-100) were attached to 24 x well dishes as described in (Torregrosa-Carrión et al., 2019). Once MEEC were seeded, DMSO was added to control and recombinant-ligand stimulated cells, and 20 μM RO4929097 (Selleck Chemicals S1575) to inhibit Notch activity. After 24 h at 37 °C, cells were washed twice with PBS and incubated for an additional 14 h in serum-free DMEM together with RO4929097 or DMSO as appropriate.

tag: cell line

value: MEEC

tag: cell type

value: Mouse embryonic endocardial cells

tag: genotype

value: WT

value: coculture with OP9-Jag1 cells

value: 24 hours


title: Xanthomonas L148_Col-0_3_3

description:
F_20220706_3_3
5732_F_run775_ACTCCTAC_S2_L001_R1_001.fastq.gz.subread.BAM


title: MEEC+OP9-Jag1_24h.2 RNA


title: Lung, ML364_Rep4


title: Xanthomonas L148_Col-0_3_2

description:
F_20220706_3_2
5732_F_run774_ACTCCTAC_S18_L002_R1_001.fastq.gz.subread.BAM


title: Lung, ML364_Rep3


title: 3494-Y

value: chorion


title: 3492-Y


title: MEEC+OP9-Jag1_24h.1 RNA


title: Lung, ML364_Rep1


title: Xanthomonas L148_rbohD_3_2

description:
E_20220706_3_2
5732_E_run774_GACTACGA_S17_L002_R1_001.fastq.gz.subread.BAM

value: rbohD


title: 3494-G


title: Lung, ML364_Rep2


title: Xanthomonas L148_Col-0_3_1

description:
F_20220706_3_1
5732_F_run774_ACTCCTAC_S18_L001_R1_001.fastq.gz.subread.BAM


title: 3518II


title: Xanthomonas L148_rbohD_3_1

description:
E_20220706_3_1
5732_E_run774_GACTACGA_S17_L001_R1_001.fastq.gz.subread.BAM


title: 3475-Y

description: sextra 13.hg38.mapq_30.1000.sampled.mcool

value: extra 13


title: 3492-G

value: female


title: Lung, Vehicle_Rep6

value: vehicle


title: 3475-G


title: Xanthomonas L148_rbohD_2_2

description:
D_20220604_2_2
5732_D_run774_TCTTCGAC_S16_L002_R1_001.fastq.gz.subread.BAM


title: MEEC+OP9-Dll4_24h.1 RNA

value: coculture with OP9-Dll4 cells


title: MEEC+OP9-Dll4_24h.3 RNA


title: MEEC+OP9-Dll4_24h.2 RNA


title: Lung, Vehicle_Rep5


title: 3471-Y

description: sextra 16.hg38.mapq_30.1000.sampled.mcool

value: extra 16


title: Xanthomonas L148_rbohD_2_1

description:
D_20220604_2_1
5732_D_run774_TCTTCGAC_S16_L001_R1_001.fastq.gz.subread.BAM


title: 3471-G

value: male


title: MEEC+OP9-GFP_24h.3 RNA

value: coculture with OP9-GFP cells


title: Lung, Vehicle_Rep4

value: SARS-CoV-2 (Wuhan strain)

value: lung


title: Lung, Vehicle_Rep3


title: Xanthomonas L148_Col-0_2_2

description:
C_20220604_2_2
5732_C_run774_CTCCTAGT_S15_L002_R1_001.fastq.gz.subread.BAM

value: plant shoot

value: flood inoculation


title: Xanthomonas L148_Col-0_2_1

description:
C_20220604_2_1
5732_C_run774_CTCCTAGT_S15_L001_R1_001.fastq.gz.subread.BAM


title: Lung, Vehicle_Rep2


title: MEEC+OP9-GFP_24h.2 RNA

value: MEEC

value: Mouse embryonic endocardial cells


title: MEEC+OP9-GFP_24h.1 RNA

value: WT


title: PIEZO1_Control_NCI-N87

city: Hong Kong

first: Bonan

last: Chen

address: The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, The People's Republic of China

country: Hong Kong

institute: the Chinese University of Hong Kong

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Trimmed sequence reads were mapped to GrCh38/hg38 using lab server.
Read count extraction and normalization were performed using lab server.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes RPKM values for each Sample

extract_protocol:
RNA was harvested using RNA Extraction Kits (QIAGEN). 1 ug of total RNA was used for the construction of sequencing libraries.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 m in followed by 5 min at 95 °Cbefore PCR. Then PCR was performed with Phusion High -Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Lipofectamine™ 2000 Transfection

value: gastric cancer cell

value: control


title: Lung, Vehicle_Rep1


title: PIEZO1_Yoda1_NCI-N87

value: PIEZO1 stimulation by Yoda1 treatment


title: Xanthomonas L148_rbohD_1_4

description:
B_20220513_1_4
5732_B_run775_GCACACAA_S1_L002_R1_001.fastq.gz.subread.BAM

value: rbohD


title: PIEZO1_siScramble_NCI-N87

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Trimmed sequence reads were mapped to GrCh38/hg38 using lab server.
Read count extraction and normalization were performed using lab server.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes RPKM values for each Sample

value: siCtrl


title: PIEZO1_siPIEZO1_NCI-N87

value: PIEZO1 knockdown


title: MEEC+OP9-Jag1_6h.2 RNA

value: coculture with OP9-Jag1 cells

value: 6 hours


title: Sperm, Veh, rep2

city: Zurich

first: Vincent

middle: Valentin Tobias

last: Fischer

address: Wintherthurerstrasse 190

department: INS

institute: ETH Zurich

data_processing:
Adapters were trimmed with trimmomatic and reads were aligned to GRCm38 using bowtie2 (2.3.4.3) end-to-end alignment (with --no-unal -X 2000 --no-mixed --no-discordant --score-min L,-0.4,-0.4). Duplicated fragments were marked with Picard (2.18.27).
For Dex vs Veh, fragments with MAPQ >= 30 and length between 50 and 115, excluding chrM and ENCODE blacklisted regions, were retained as nucleosome-free. The retained fragments were shifted and merged across samples before running MACS 2.2.5 (BAMPE mode) to identify nucleosome-free regions. BigWig tracks were generated with bamCoverage and CPM normalization
bigWig track files were generated with the r package epiwraps 0.99 bam2bw.
For tdg+/- vs wt, all fragments were used to call general accessible regions with MACS --broad, while shifted fragments of length 40 to 120 with MAPQ>=20 were used to call nucleosome-free regions (narrowPeaks). BigWig tracks were generated with bamCoverage and CPM normalization.
Assembly: GRCm38
Supplementary files format and content: bw,narrowPeak,broadPeak
Supplementary files format and content: bed.zip; merged narrowPeaks for Dex_Veh "NFA"

source_name: Sperm

extract_protocol:
Cauda epididymis and vas deferens were minced and placed in 37°C warm M2 medium for at least 15 minutes. Sperm cells were separated from contaminating tissue by filtration through a 70 um Nylon mesh using several rinses with PBS. Cells were inspected for impurities under the microscope followed by cell counting and aliquoting.
100 000 fresh PBS washed sperm cells were incubated on ice for 3 minutes in resuspension buffer (0.1% v7v NP-40, 0.1% v/v Tween-2 and 0.01% v/v Digitonin, 10mM Tris-HCL pH7.5, 10mM NaCl, 3mM MgCl2), after a washing step (10mM Tris-HCL pH7.5, 10mM NaCl, 3mM MgCl2) nuclei were recovered by centrifugation (500g, 10 min, 4°C). Nuclei were transposed in TD Buffer supplemented with Tween-20 0.1% v/v, Digitonin 0.01% v/v and 2.5 ul Tn5 Transposase for 30 min at 37°C while shaking (1.000rpm). DNA was purified using the Qiagen MinElute Reaction Cleanup and amplified using the NEBNext high-Fidelity 2X master mix and 2.5uM nextera primers for 72°c for 5 minutes, 98°C for 30 sec and 6 cycles of 98°C for 10 sec and 63§C for 30 sec, followed by 1 minute at 72°C. A subfraction of the amplification product was then subjected to q-PCR to evaluate how many additional PCR cycles would be required. Remaining PCR product was then amplified for additional cycles before double sided bead purification with AmPure XP beads. Libraries were inspected quantitatively and qualitatively on an Agilent Bioanalyzer. Sequencing aimed at 50 Million reads/sample.

treatment_protocol: For Dex vs. Veh: Mature male C57BL/6J mice (12 weeks old) were injected with 2mg/kg Dexamethasone (D4902 Sigma Aldrich) dissolved in DMSO (10%) and 0.9% saline and eight control males were injected with vehicle consisting of 10% DMSO and 0.9% saline. Animals were sacrificed 14 days later for sperm collection.

value: Sperm

value: wt

tag: strain

value: DMSO


title: Sperm, Veh, rep1


title: MEEC+OP9-Jag1_6h.1 RNA


title: Xanthomonas L148_rbohD_1_2

description:
B_20220513_1_2
5732_B_run774_GCACACAA_S14_L002_R1_001.fastq.gz.subread.BAM


title: MEEC+OP9-Dll4_6h.3 RNA

value: coculture with OP9-Dll4 cells


title: MEEC+OP9-Jag1_6h.3 RNA


title: MCF-7, abemaciclib-96h, biol rep 2

city: Kyoto

first: Wei

last: Li

address: 54 Shogoin-kawaharacho

department: Breast surgery

country: Japan

institute: Kyoto university

data_processing:
RNA sequencing  was performed by Illumina NovaSeq 6000 and total RNA integrity using an TapeStation RNA Screen Tape with an RNA Integrity Number (RIN) value greater than or equal to 9.
Read quality were checked for quality by FastQC.
Human reference genome (GRch38/hg38) with HISAT2 for for alignment into BAM files.
assigned sequence reads to reference genomic features by FeatureCounts.
Gene counts were scaled and normalized into Transcripts Per Kilobase Million (TPM)
Assembly: GRch38/hg38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: cell

growth_protocol: Cells were maintained in DMEM containing 10% FBS and 0.01% penicillin/streptomycin . All cell lines were cultured at 37 °C in a 5% v/v CO2 atmosphere.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.0 ug of total RNA was used for the TruSeq stranded mRNA Library.
1 μg total RNA was enriched polyA + RNA, and sequencing libraries were sequenced with TruSeq stranded mRNA Library.

treatment_protocol: The cells were treated with doxorubicin at 100 nM and abemaciclib at 500 nM for the 96 hours.

value: cell

value: breast cancer cells

value: abemaciclib


title: Sperm, Dex-treated, rep3

value: Dexamethasone


title: Sperm, Dex-treated, rep2


title: MCF-7, abemaciclib-96h, biol rep 3


title: Xanthomonas L148_Col-0_1_2

description:
A_20220513_1_2
5732_A_run774_ATGACAGG_S13_L002_R1_001.fastq.gz.subread.BAM

value: plant shoot

value: flood inoculation


title: MEEC+OP9-Dll4_6h.2 RNA

value: MEEC

value: Mouse embryonic endocardial cells

value: WT


title: MCF-7, abemaciclib-96h, biol rep 1


title: Sperm, Dex-treated, rep1


title: MEEC+OP9-Dll4_6h.1 RNA


title: MCF-7, doxorubicin-96h, biol rep 3

value: doxorubicin


title: Xanthomonas L148_rbohD_1_3

description:
B_20220513_1_3
5732_B_run775_GCACACAA_S1_L001_R1_001.fastq.gz.subread.BAM

value: rbohD


title: Sperm, wt, rep2


title: J01-4-10HAT

city: Fort Collins

first: Todd

last: Gaines

state: CO

address: 1177 Campus Delivery

department: Agricultural Biology

institute: Colorado State University

data_processing:
Basecalling completed with DNBSEQ, a smiliar platform to illumina
Alignment with HISAT2, version 2.1.0
Differential expression analysis with DESeq2, version 1.28.1
Variant calling and annotatin with Platypus and SNPEff version
Genome_build: Bs_v2.OGS_CDS.fna
Supplementary_files_format_and_content: for processed data deseq_normalized_cts.csv, data is a matrix of gene names and sample ID's with normalized counts following DEseq2 processing, Bs_v2_OGS.genes.gff3 is the GFF3 file, and Bs_v2_OGS.CDS.fna is the fasta file used for alignment.

organism: Bassia scoparia

source_name: kochia meristem tissue

extract_protocol:
Young leave tissue was removed and flash frozen in liquid Nitrogen. QIAGEN RNeasy plant extraction kit was used with 10-15mg tissue
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: treatment/timepoint

value: 10 hours after treatment

value: kochia meristem tissue


title: MCF-7, doxorubicin-96h, biol rep 2


title: MCF-7, doxorubicin-96h, biol rep 1


title: J01-3-10HAT


title: MEEC+OP9-GFP_6h.2 RNA

value: coculture with OP9-GFP cells

value: 6 hours


title: Xanthomonas L148_rbohD_1_1

description:
B_20220513_1_1
5732_B_run774_GCACACAA_S14_L001_R1_001.fastq.gz.subread.BAM


title: MCF-7, Control, biol rep 3

value: Control

value: no exposure 96 h


title: Sperm, Tdg +/-, rep3

value: Sperm

value: Tdg +/-

value: 129P2/OlaHsd * C57BL/6


title: MEEC+OP9-GFP_6h.1 RNA


title: MCF-7, Control, biol rep 2

value: cell

value: breast cancer cells


title: Sperm, Tdg +/-, rep2


title: MEEC+OP9-GFP+RO_6h.4

data_processing:
Fastq files were pre-processed using FastQC and Cutadapt, to remove Illumina and Nextera adapter contamination.
Resulting reads were then mapped against reference genome GRCm38/MM10 with bowtie2 as aligner, Piccard to mark duplicate alignments, and samtools   to eliminate duplicate, chimeric and sub-optimally multi-mapped alignments, keeping only properly paired and mapped reads. Alignments against the mitochondrial genome and chromosome Y were also removed.
Once filtered alignments had been obtained, peaks (accessible DNA regions) were called with MACS2 using parameters "--nomodel --shift -100 –extsize  200", and "-q 0.05" as the false discovery rate cut-off.
Assembly: GRCm38/MM10
Supplementary files format and content: ATAC-Seq peaks called with MACS2, in narrowPeak (XLS) format.

extract_protocol:
50,000 cells were lysated with cold lysis buffer (10mM Tris-HCl pH 7.4, 10mM MgCl2, 0.1% IGEPAL CA-630) spinning for 15 at 500g (4C), and DNA tagmentated with Nextera DNA Library Prep Kit (Illumina)
ATAC-seq libraries were prepared using the NEB Next High-Fidelity 2x PCR Mastermix (New England BioLabs). Libraries were size selected using Agencourt AMPure XP beads from Beckman Coulter.

treatment_protocol: Co-culture with OP9 cells: To define the effect of Dll4- and Jag1-mediated cell-to-cell signaling, MEECs were co-cultured for 6h (50% confluency) and 24h (25% confluency) over GFP-, Jag1- or Dll4-expressing OP9 cells at 90% confluence. To define the effect of NICD nuclear translocation inhibition, MEECS were cultured with DMSO (vehicle) or 20 μM of the γ-secretase inhibitor RO4929097 for 24 h. Next, MEECs were co-cultured for 6h (50% confluency) over GFP-expressing OP9 cells at 90% confluence.

tag: chip antibody

value: ATAC-seq


title: MEEC+OP9-GFP+RO_6h.3

value: MEEC


title: Xanthomonas L148_Col-0_1_1

description:
A_20220513_1_1
5732_A_run774_ATGACAGG_S13_L001_R1_001.fastq.gz.subread.BAM

value: plant shoot

value: flood inoculation


title: Sperm, Tdg +/-, rep1


title: Sperm, wt, rep1

value: wt


title: J01-1-UNT

value: Untreated


title: J01-1-3HAT

value: 3 hours after treatment


title: MDA-MB-231, abemaciclib-96h, biol rep 3

value: abemaciclib


title: MEEC+OP9-GFP+RO_6h.2

value: Mouse embryonic endocardial cells


title: J01-4-3HAT

value: kochia meristem tissue


title: high fat diet #6

city: Ann Arbor

first: Dave

last: Bridges

state: MI

address: 1415 Washington Heights

department: Nutritional Sciences

institute: University of Michigan

data_processing:
Reads were mapped to mm10 using Salmon v1.9.0
Transcripts were mapped to the genes using EnsDb.Mmusculus.v79 and tximport
Removed genes with <10 reads across all samples
Differential expression performed using DESeq2 v1.36
Assembly: mm10
Supplementary files format and content: quant.sf file containing one row per transcript (ENSEMBLID), length, TPM and number of reads

source_name: GWAT

extract_protocol:
Qiagen RNEasy Mini Prep kit
Lexogen quantseq

value: GWAT

tag: Sex

value: male

tag: age

value: postnatal day 16

value: high fat diet


title: MEEC+OP9-GFP_6h.3 RNA

value: WT

value: coculture with OP9-GFP cells

value: 6 hours


title: B3-4-10HAT

value: 10 hours after treatment


title: MDA-MB-231, abemaciclib-96h, biol rep 2

value: cell

value: breast cancer cells


title: control #5

value: control


title: MEEC+OP9-GFP+DMSO_6h.4

value: MEEC

value: ATAC-seq


title: J01-2-10HAT


title: B3-3-10HAT


title: MDA-MB-231, abemaciclib-96h, biol rep 1


title: high fat diet #5


title: MDA-MB-231, doxorubicin-96h, biol rep 3

value: doxorubicin


title: MEEC+OP9-GFP+DMSO_6h.3


title: high fat diet #4


title: B3-2-10HAT


title: J01-4-UNT

value: Untreated


title: MCF-7, Control, biol rep 1

value: Control

value: no exposure 96 h


title: MEEC+OP9-GFP+DMSO_6h.2

value: Mouse embryonic endocardial cells


title: control #6

value: GWAT

value: male


title: MDA-MB-231, doxorubicin-96h, biol rep 1


title: high fat diet #3

value: postnatal day 16

value: high fat diet


title: MEEC+OP9-GFP+RO_6h.1


title: MEEC+OP9-GFP+DMSO_6h.1


title: MEEC+OP9-Jag1_24h.4


title: control #3


title: B3-3-3HAT

value: 3 hours after treatment

value: kochia meristem tissue


title: MDA-MB-231, Control, biol rep 3


title: high fat diet #2


title: MEEC+OP9-Jag1_24h.3


title: MDA-MB-231, Control, biol rep 2


title: B3-2-3HAT


title: MEEC+OP9-Jag1_24h.2


title: control #2


title: MDA-MB-231, Control, biol rep 1


title: B3-4-UNT


title: MEEC+OP9-Jag1_24h.1


title: high fat diet  #1


title: B3-3-UNT


title: B3-1-10HAT

value: 10 hours after treatment


title: MDA-MB-231, doxorubicin-96h, biol rep 2

value: cell


title: control #1


title: B3-4-3HAT


title: B3-2-UNT


title: RWPE, Control-sh TT-seq Rep2

city: London

first: Pradeepa

last: Madapura

address: 4 Newark Street, Whitechapel

institute: Queen Mary University of London

data_processing:
The reads were processed and mapped using Lexogen Bluebee pipeline. The mapped data obtained as bam files were further used for sorting and indexing. The sorted bam files were merged for replicates and converted to bigwigs via deepTools (version 3.5.1) bamCoverage tool with --binSize 20 –normalizeUsing RPKM --smoothLength 60 --extendReads 150 --centerReads options.
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: RWPE-1 cells were grown on 100 mm culture dishes (Corning Falcon product number: 353003 ) in keratinocytes serum-free medium (Gibco, 10724-011) supplemented with 100 U/ml penicillin-streptomycin (Gibco, 15140122) and 10% FBS (Sigma, F7524). The cells were passaged every 3-4 days. All the cell lines were tested for Mycoplasma contamination using EZ-PCR Kit (Geneflow, K1-0210).

extract_protocol:
TT-seq was performed according to the protocol described in Vlaming et al 2022 (PMID: 35681023).
CORALL total RNAseq library preparation kit (Lexogen Cat. no. 147.24) was used for sequencing library preparation. Libraries were sequenced as 150 bp paired-end reads using Novaseq 6000.
Transient Transcriptome Seq (TT-seq)

treatment_protocol: Cells were transduced with either control shRNA or PSIP1 shRNA and grown in a medium containing 2ug/ml puromycin

value: Human Prostate Epithelial cells

tag: antibody


title: RWPE, PSIP1-sh TT-seq Rep1


title: 9425-4-10HAT


title: MEEC+OP9-Dll4_24h.4


title: MEEC+OP9-Dll4_24h.3


title: VE.3296.EXP.22.BY8608.C2

city: Uppsala

first: Christopher

last: von Beek

address: Husargatan 3

department: IMBIM

country: Sweden

institute: Uppsala University

description: Experiment2, ON2

data_processing:
Illumina NovaSeq 6000. Demultiplexing and conversion to FASTQ performed using the bclfastq2 (2.20.0.422) software.
https://nf-co.re/rnaseq/output
Supplementary files format and content: Tab-delimited text file containing count matrix of merged gene counts from STAR mapping of all samples (salmon.merged.gene_counts.tsv).
Supplementary files format and content: Tab-delimited text file containing count matrix of merged gene counts adjusted for gene length from STAR mapping of all samples (salmon.merged.gene_counts_length_scaled.tsv).

growth_protocol: BMMC were maintained in DMEM GlutaMAX, 10% FBS, 1% PenStrep at 37°, 5 CO2. Salmonella Typhimurium SL1344 strains were inoculated from crytotubes into 15 ml falcon tube with 3 ml LB 0.3 M NaCl + 50 µg/ml streptomycin. After exactly 12 h incubation at 37 °C on a rotating wheel (20 rpm), cultures were diluted 1:20 into LB 0.3 M NaCl without antibtioics.

extract_protocol:
Total RNA was extracted with the RNeasy Micro Kit (Qiagen, #74004) and stored at -80 C until submission.
Sequencing libraries were prepared from 500ng total RNA using the TruSeq stranded mRNA library preparation kit (cat# 20020595, Illumina Inc.) including polyA selection. Unique dual indexes (cat# 20022371, Illumina Inc.) were used. The library preparation was performed according to the manufacturers’ protocol.
The quality of the libraries was evaluated using the Fragment Analyzer from Advanced Analytical Technologies Inc., using the DNF-910 dsDNA kit. The adapter-ligated fragments were quantified by qPCR using the Library quantification kit for Illumina (KAPA Biosystems) on a CFX384 Touch instrument (Bio-Rad) prior to cluster generation and sequencing.

treatment_protocol: BMMC were washed 2x in DPBS and resuspended in DMEM GlutaMAX, 10% FBS. 500 µl of BMMC (0.5 x 10^6 cells) were placed into a 24 well plate, 25 µl of S.Tm (MOI 50), resuspended in the same medium, were added to the cells and the plate was incubated for 30 min at 37 °C, 5% CO2. After 30 min, 25 µl of 20x gentamycin in medium were added to a final conc. of 90 µg/ml. Cells were harvested (5 min, 400 x g) 3.5 h later.

value: Bone marrow-derived mast cells

value: Mast cell

value: Uninfected


title: RWPE, Control-sh TT-seq Rep1


title: 9425-3-10HAT


title: VE.3296.EXP.22.BY8606.C2

description: Experiment1, ON2


title: MEEC+OP9-Dll4_24h.1

value: MEEC

value: ATAC-seq


title: MEEC+OP9-Dll4_24h.2


title: 9425-2-10HAT


title: MEEC+OP9-GFP_24h.4


title: VE.3296.EXP.22.BY8606.C1

description: Experiment1, ON1


title: RWPE, PSIP1-sh TT-seq Rep2


title: 9425-1-10HAT


title: RWPE, PSIP1-sh RNAseq Rep2

data_processing:
The reads were processed and mapped following Lexogen Bluebee pipeline. The bam files were sorted and indexed uisng samtools. The sorted bam files were merged for replicates, sorted and indexed and converted to bigwigs via deepTools (version 3.5.1) bamCoverage tool with --binSize 20 –normalizeUsing RPKM --smoothLength 60 --extendReads 150 --centerReads options.
Assembly: hg38

extract_protocol:
RNA was isolated using an RNeasy mini kit (Qiagen Cat no: 74106). Then mRNA was isolated using Poly (A) mRNA magnetic isolation kit (NEB cat no: E7490L)
RNA seq library was prepared using NEBNext Ultra II directional RNA library preparation kit (NEB cat no: E7760L) by following the manufacturer's protocol. Libraries were sequenced as 150 bp paired-end reads using Novaseq 6000.


title: VE.3296.EXP.22.BY8608.dinvG2

description: Experiment2, ON2

value: S.Tm {delta}invG infected


title: RWPE, PSIP1-sh RNAseq Rep1


title: MEEC+OP9-GFP_24h.3


title: 9425-4-3HAT


title: MEEC+OP9-GFP_24h.2


title: RWPE, Control-sh RNAseq Rep3


title: MEEC+OP9-GFP_24h.1


title: 9425-2-3HAT


title: RWPE, Control-sh RNAseq Rep2


title: VE.3296.EXP.22.BY8606.dinvG1

description: Experiment1, ON1


title: VE.3296.EXP.22.BY8608.C1

description: Experiment2, ON1


title: VE.3296.EXP.22.BY8606.dinvG2

description: Experiment1, ON2


title: 9425-3-3HAT


title: VE.3296.EXP.22.BY8608.WT2

description: Experiment2, ON2

value: S.Tm WT infected


title: MEEC+OP9-Jag1_6h.4

value: Mouse embryonic endocardial cells


title: RWPE, PSIP1-sh RNAseq Rep3


title: 9425-2-UNT

value: Untreated


title: RWPE, Control-sh RNAseq Rep1


title: MEEC+OP9-Jag1_6h.3


title: VE.3296.EXP.22.BY8608.WT1

description: Experiment2, ON1


title: RWPE1, PSIP1-sh YH2AX Rep2

data_processing:
150bp paired-end reads for the CUT&Tag-seq were trimmed for adapters using the Trimmomatic tool and aligned to the hg38 genome through local Bowtie2 (version 2.4.5) with these parameters for pair-end mapping: --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700. The bam files were sorted and indexed using the samtools (version 1.9) sort and the samtools index. Merging of multiple replicates was performed using samtools merge.
The sorted bam files were used to generate bed, bedgraph and bigwig formats for individual modifications. Sorted bam files were subjected to bigwig generation via deepTools (version 3.5.1) bamCoverage tool with --binSize 20 --scaleFactor=1.0 --smoothLength 60 --extendReads 150 --centerReads options. The corresponding bigwig files were normalized by factoring in the reads mapped to E. coli in Control-sh and PSIP1-sh.
Peak-calling and analyses  The reads were extracted from the bam to bed by the bedtools bamtobed option. Further reads were processed as mentioned in the SEACR (version 1.3) manual to get the bedgraph. These bedgraph files were subjected to peak calling through SEACR keeping IgG as a background with the norm and relaxed options for individual replicates. Peaks consistenet in both replicates were reatins and the coordinates were merged.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
CUT&Tag was performed according to the protocol of Kaya-Okur et al (1) with modifications to tissue processing as described below. ~100,000 cells were pelleted by centrifugation for 3 min at 600 x g at room temperature and resuspended in 500μl of ice-cold NE1 buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 0.5 mM spermidine, 1% Triton X-100, and 20 % glycerol and cOmplete EDTA free protease inhibitor tablet) and was let to sit for 10 min on ice. Nuclei were pelleted by centrifugation for 4 min at 1300 x g at 4°C, resuspended in 500μl of wash buffer and held on ice until beads were ready. Required amount of BioMag Plus Concanavalin-A-conjugated magnetic beads (ConA beads, Polysciences, Inc) were transferred into binding buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 1mM CaCl2 and 1mM MnCl2), washed once in the same buffer, each time placing them on a magnetic rack to allow the beads to separate from the buffer and resuspended in binding buffer. 10 μl of beads was then added to each tube containing cells and rotated on an end-to-end rotator for 10 minutes. After a quick spin to remove liquid from the cap, tubes were placed on a magnet stand to clear, the liquid was withdrawn and 800μl of antibody buffer containing 1μg of primary antibodies: normal rabbit IgG (Santa Cruz Cat no sc-2027), H3K27ac (Abcam, ab4729), H4K16ac (Abcam, ab109463), H3K122ac (Abcam, ab33309), H3K4me1(Abcam, ab8895), H3K36me3 (Abcam, ab9050)) H3K4me3 (Millipore, 07-473),  H3K27me3 (Abcam, ab192985) and H3K9me3 (Abcam, ab176916)) was added and incubated at 4ºC overnight in a nutator. Secondary antibodies (guinea pig α-rabbit antibody, Antibodies online, ABIN101961) were added 1:100 in Dig-wash buffer (5% digitonin in wash buffer) and 100 µL was squirted in per sample while gently vortexing to allow the solution to dislodge the beads from the sides and incubated for 60 min on a nutator. Unbound antibodies were washed in 1 ml of Dig-wash buffer three times. 100 μl of (1:250 diluted) protein-A-Tn5 loaded with adapters in Dig-300 buffer (20 mM HEPES pH 7.5, 300 mM NaCl, 0.5 mM spermidine with Roche cOmplete EDTA free protease inhibitor) was added to the samples, placed on nutator for 1 hour and washed three times in 1 ml of Dig-300 buffer to remove unbound pA-Tn5. 300 µL Tagmentation buffer (Dig-300 buffer + 5 mM MgCl2) was added while gentle vortexing and samples were incubated at 37ºC for 1 hr on an incubator. Tagmentation was stopped by adding 10 µL 0.5M EDTA, 3 µL 10% SDS and 2.5 µL 20 mg/mL Proteinase K to each sample. Samples were mixed by full speed vortexing for ~2 seconds and incubated for 1 hr at 55ºC to digest proteins. DNA was purified by phenol: chloroform extraction using phase-lock tubes (Quanta Bio) followed by ethanol precipitation.
Libraries were prepared using NEBNext HiFi 2x PCR Master mix (M0541S) with a 72ºC gap-filling step followed by 13 cycles of PCR with 10-second combined annealing and extension for the enrichment of short DNA fragments. Libraries were sequenced in Novaseq 6000 (Novogene) with 150bp paired-end reads.

value: YH2AX(Abcam, ab8895)


title: RWPE1, PSIP1-sh YH2AX Rep1


title: 9425-1-UNT


title: MEEC+OP9-Jag1_6h.2


title: VE.3296.EXP.22.BY8608.dinvG1

description: Experiment2, ON1


title: VE.3296.EXP.22.BY8606.WT2

description: Experiment1, ON2


title: MEEC+OP9-Jag1_6h.1


title: VE.3296.EXP.22.BY8606.WT1

description: Experiment1, ON1


title: MEEC+OP9-Dll4_6h.4


title: CaOV3 GFP + DOX, biological rep3

first: Alex

last: Miranda Rodriguez

state: Massachusetts

address: 55 Fruit St.

department: Massachusetts General Hospital

institute: Harvard Medical School

description: Gene expression data from a human ovarian cell line with TET-On inducible expression of the MYCN oncogene.

hyb_protocol: Performed by Genome Quebec

scan_protocol: Performed by Genome Quebec

data_processing:
Data was preprocessed using the R package OLIGO and limma to identify differentially expressed genes.
RMA based normalized intensity summarized at gene level

label: biotin

source_name: CaOV3 GFP TET-On cells, Doxycycline (1ug/ml) 72 hours

label_protocol: Performed by Genome Quebec

growth_protocol: 2x105 CaOV3 TET-On MYCN-GFP and GFP control cells were cultured in triplicate in wells of a 6-well plate during 72 hours.

extract_protocol: Total RNA was isolated using the RNeasy plus kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Cells were cultured in the presence or absence of 1 ug/ml of Doxycycline (DOX) for 3 days.

value: High grade ovarian serous carcinoma cell line


title: RWPE1, Contol-sh YH2AX Rep2


title: CaOV3 GFP + DOX, biological rep2


title: Wildtype E16.5 Sample 5 [WT_ATF4_E16_5_9_S98]

city: Newark

first: Melinda

last: Duncan

state: DE

address: 105 The Green

department: Biological Sciences

institute: University of Delaware

data_processing:
Aggregate individual lane files (4 per sample) into a single file for each sample
Trim reads using trimgalore
Remove reads aligning to the Rn45s prespliced transcript using HISAT2
Align "non-ribosomal" reads using HISAT2 (-fr --rna-strandness RF --dta)
Quantify genes using htseq-count
Normalize counts using TMM using edgeR
Test for differential expression using edgeR's Exact test
Assembly: GRCm39 / Ensembl v104
Supplementary files format and content: Gene level counts for each sample in text file
Supplementary files format and content: Gene level counts and Differential Expression analysis in excel spreadsheet

source_name: whole lens

extract_protocol:
mirVana mirRNA Isolation Kit, with phenol
Takara SMARTer Stranded Pico v2

value: whole lens

value: Mouse embryonic lens cells

value: WT


title: CaOV3 GFP + DOX, biological rep1


title: MEEC+OP9-Dll4_6h.3


title: RWPE1, PSIP1-sh S9.6 Rep2

state: UK


title: RWPE1, PSIP1-sh S9.6 Rep1


title: Wildtype E16.5 Sample 4 [WT_ATF4_E16_5_6_S95]


title: MEEC+OP9-Dll4_6h.2


title: Wildtype E16.5 Sample 3 [WT_ATF4_E16_5_5_S97]