title: CRA_HIMT_4_rep3

description: Gene expression in Psa CRAFRU8.43 cells grown 4h in hrp-inducing medium supplemented with tomato extract, replicate 3

organism: Pseudomonas syringae pv. actinidiae str. CRAFRU8.43

source_name: Psa CRAFRU8.43 cells incubated in hrp-inducing medium supplemented with tomato extract for 4h, replicate 3


title: Sample 2_EB5 100% corrections

status: Public on Aug 25 2022

type: SRA

city: Wroclaw

first: Lukasz

last: Laczmanski

address: Weigla 12

country: Poland

institute: Hirszfeld Institute of Immunology and Experimental Therapy

library_source: transcriptomic

data_processing:
The HISAT2 software (Kim, Paggi, et al. 2019) as used to align reads to the human reference genome (Hg38).
SAMtools software were used to convert .sam to .bam files.
The featureCounts algorithm performed transcript assembly, quantification of expression as fragments per kilobase of transcript per million mapped reads (FPKM) values, and normalization
Normalized FPKM values were used for the differential expression analysis, which was performed using an ‘edger’ R script
Assembly: HG38
Supplementary files format and content: tab-delimited text files include R edger's analysis.

molecule: total RNA

organism: Homo sapiens

source_name: fibroblasts

extract_protocol:
RNA was isolated using the RNeasy Kit (Qiagen) according to manufacturer’s protocols
RNA-Sequencing libraries were prepared by KAPA RNA Hyper+RiboErase HMR Kit (Roche Corp.) according to the manufacturer’s standard protocol

tag: tissue

value: fibroblasts

tag: cell type

value: Fibroblasts after correction

tag: treatment


title: 697_0hr_Rep3_2-12hr_ATACseq

city: Memphis

first: Daniel

last: Savic

state: TN

address: 262 Danny Thomas Place

department: Pharmaceutical Sciences

country: USA

institute: St. Jude Children's Research Hospital

library_source: genomic

data_processing:
Reads were mapped to the human genome using bowtie2
Peak calling was performed using MACS2 using the default q value of 0.05
Differential analysis was performed using DESeq2
BigWig files were created using bedGraphToBigWig command in UCSC tools on bedgraphs output by MACS2
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak files for each experimental sample

molecule: genomic DNA

source_name: 697 (ALL cell line)

growth_protocol: Nalm6 and 697 cells were maintained with RPMI-1640 with 10% charcoal-stripped FBS, 2mM Glutamine, and Pen/Strep

extract_protocol:
Cells were transposed following to the FAST-ATAC protocol from the Greenleaf Lab
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with prednisolone at a concentration of 5uM (Nalm6 cells) or 10uM (697 cells) for 2, 6, 12, or 24 hours

tag: cell line

value: ALL

tag: replicate


title: 697_0hr_Rep2_2-12hr_ATACseq


title: Sample 1_EB5 control unedited

value: Primary patient fibroblasts


title: CRA_HIMT_4_rep2

type: RNA

city: Verona

first: Elodie

last: Vandelle

state: Verona

address: Strada Le Grazie, 15

department: Department of Biotechnology

country: Italy

institute: University of Verona

description: Gene expression in Psa CRAFRU8.43 cells grown 4h in hrp-inducing medium supplemented with tomato extract, replicate 2

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >15 pmol Cy3/ug cRNA) were fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing  25x Agilent fragmentation buffer and 10x Agilent blocking agent following manufacturer's instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer were added to the fragmentation mixture and hybridized to Agilent-078853 8x60K custom microarray chip for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarray chips were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute at 37°C with GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing using the Agilent DNA Microarray Scanner with one color scan settings for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to XDR Hi100%, XDR Lo 10%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.5.1 (Agilent) using default parameters (protocol GE1-105_Dec08 and Grid:078853_D_F_20151012) to substract the background and obtain spatially-detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Data were background corrected and quantile normalized.

source_name: Psa CRAFRU8.43 cells incubated in hrp-inducing medium supplemented with tomato extract for 4h, replicate 2

label_protocol: Cyanine-3 (Cy3)-labeled cRNA was prepared from 50 ng of RNA using the Low Input Quick Amp WT Labeling kit (Agilent Techonologies, Santa Clara, CA, USA) according to manufacturer's instructions for prokaryotic samples, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked using the NanoDrop 2000 instrument (Thermo Scientific, Wilmington, DE, USA).

growth_protocol: Bacterial cells were cultured in hrp-inducing medium supplemented or not with kiwifruit or tomato extract (1%, v/v) for 1h or 4 h at 28°C with shaking (200 rpm)

extract_protocol: Two ml of each bacterial suspension were centrifuged and total RNA was extracted from cell pellets using the Spectrum™ Plant Total RNA kit (Sigma-Aldrich, St. Louis, MO, USA). Total RNA quantity, integrity and purity were controlled using a Nanodrop 2000 instrument (Thermo Scientific, Wilmington, DE, USA) and a Bioanalyzer Chip RNA 7500 serie II (Agilent).

value: bacterial cells


title: Nalm6_12hr_Rep3_ATACseq

source_name: Nalm6 (ALL cell line)

value: PRED (5uM, 12hrs)


title: CRA_HIMT_1_rep3

description: Gene expression in Psa CRAFRU8.43 cells grown 1h in hrp-inducing medium supplemented with tomato extract, replicate 3

source_name: Psa CRAFRU8.43 cells incubated in hrp-inducing medium supplemented with tomato extract for 1h, replicate 3


title: HEK293T UL1KOKO CN 3 [CN_3_HEKUL1KO]

city: Poznan

first: Kishor

last: Gawade

address: Uniwersytetu Poznańskiego 10

department: Faculty of Biology

institute: Adam Mickiewicz University

data_processing:
The quality of the raw FASTQ files was assessed using fastqc/0.11.4.
Cutadapt 3.7 was used to remove adapter sequences and low-quality reads.
The processed FASTQ files were aligned to the GRCh38 human genome assembly using the STAR/2.7.8
A raw count matrix was obtained from the aligned BAM files using FeatureCounts.
Differentially expressed genes (DEGs) were obtained with DESeq2.
Assembly: Homo_sapiens.GRCh38 (NCBI)
Supplementary files format and content: Text file with Raw read counts matrix

source_name: HEK 293T

growth_protocol: HEK293T cells were grown in Dulbecco’s modified Eagle’s medium containing L-glutamine and 4.5 g/L glucose (DMEM; Lonza) and supplemented with 10% fetal calf serum (Gibco) and antibiotics (100 U/ml penicillin, 100 µg/ml streptomycin, 0.25 µg/ml amphotericin B (Sigma-Aldrich)) at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Nucleolar and cytoplasmic-nuclear fractionation was carried out according to the protocol. After fractionation, the following fractions are obtained: NO – nucleolar, CN – cytoplasmic-nuclear. RNA was isolated using the Quick-RNA MiniPrep Kit (Zymo Research, R1055) according to the manufacturer's protocol.
CORALL Total RNA-Seq library preparation Kit (Lexogen, Vienna, Austria) was used to prepare libraries, without ribosomal RNA depletion, following the manufacturer’s instructions.

value: HEK 293T

value: immortalised human embryonic kidney cells

tag: genotype

value: HNRNPUL1 knock-out

tag: rna fraction

value: Cytoplasmic-Nuclear RNA


title: 697_0hr_Rep1_2-12hr_ATACseq


title: CRA_HIMT_1_rep2

description: Gene expression in Psa CRAFRU8.43 cells grown 1h in hrp-inducing medium supplemented with tomato extract, replicate 2

source_name: Psa CRAFRU8.43 cells incubated in hrp-inducing medium supplemented with tomato extract for 1h, replicate 2


title: Wild Type Mouse Embryonic Fibroblast, rep3 (Hi-C)

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: Abu Dhabi

address: Saadiyat Campus, Abu Dhabi

department: Biology Department, Science Division

country: United Arab Emirates

institute: New York University Abu Dhabi

data_processing:
Raw fastq files were aligned and filtered using the HiCUP pipleline (Wingett, Steven et al. F1000Research vol. 4 1310. 20 Nov. 2015) with parameters specific to the arima protocol
Processed and filtered bam files were converted to HOMER tag directories followed by PCA analysis using HOMER command runHiCpca.pl (Heinz S, Benner C, Spann N, Bertolino E et al. Mol Cell 2010 May 28;38(4):576-589)
Assembly: mm10
Supplementary files format and content: bedGraph files with PC-1 values for 500kb bins

organism: Mus musculus

source_name: Mouse Embryonic Fibroblast

extract_protocol:
Cells were fixed with formaldehyde, pellets were washed twice by 1X PBS and stored at -80 deg. The frozen pellets were shipped on dry ice to Genome Technology Center at NYU Langone Health, NY. All subsequent processing was performed by Genome Technology Center at NYU Langone Health using standard DNA extraction and library preparation protocols.
Hi-C was performed at Genome Technology Center at NYU Langone Health, NY from cells cross-linked with formaldehyde. Experiments were performed in triplicates following the instructions from Arima Hi-C kit (Arima Genomics, San Diego, CA). Subsequently, Illumina-compatible sequencing libraries were prepared by using a modified version of KAPA HyperPrep library kit (KAPA BioSystems, Willmington, MA). Quality check steps were performed to assess the fraction of proximally ligated DNA labeled with biotin, and the optimal number of PCR reactions needed to make libraries. The libraries were loaded into an Illumina flowcell (Illumina, San Diego, CA) on a NovaSeq instrument for paired-end 50 reads.

value: Mouse Embryonic Fibroblast

tag: strain

value: BALB/c

value: Wild Type


title: HEK293T UL1KOKO CN 2 [CN_2_HEKUL1KO]


title: Wild Type Mouse Embryonic Fibroblast, rep2 (Hi-C)


title: CRA_HIMT_1_rep1

description: Gene expression in Psa CRAFRU8.43 cells grown 1h in hrp-inducing medium supplemented with tomato extract, replicate 1

source_name: Psa CRAFRU8.43 cells incubated in hrp-inducing medium supplemented with tomato extract for 1h, replicate 1


title: NM1 knockout Mouse Embryonic Fibroblast, rep2 (Hi-C)

value: NM1 knockout


title: Nalm6_12hr_Rep1_ATACseq


title: NM1 knockout Mouse Embryonic Fibroblast, rep1 (Hi-C)


title: HEK293T UL1KOKO CN 1 [CN_1_HEKUL1KO]


title: CRA_HIMT_4_rep1

description: Gene expression in Psa CRAFRU8.43 cells grown 4h in hrp-inducing medium supplemented with tomato extract, replicate 1

source_name: Psa CRAFRU8.43 cells incubated in hrp-inducing medium supplemented with tomato extract for 4h, replicate 1


title: NSCs ADV-GFP control 1

city: Hangzhou

first: sunli

last: cai

address: 866 Yuhangtang Rd

country: China

institute: Zhejiang University

description: control.txt

data_processing:
Illumina NovaSeq 6000
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Assembly: mm39
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: brain

growth_protocol: primary neural stem cells were isolated from the SVZ of adult C57BL/6 mice brain and maintained in Neuralbasal medium supplemented with 2% B27 in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
primary SVZ tissue were micro-dissected from adult C57BL/6 mice brain and dissociated by Neural Tissue Dissociation Kit - Papain (Miltenyi, 130-092-628)
RNA libraries were pereared for sequencing using standrard lllumina protocols

treatment_protocol: SETD4 overexpression was induced by treatment of 24 hour neural stem cells infected with ADV-SETD4-GFP, using ADV-GFP as a control.

value: brain

value: primary cell

value: neural stem cell

value: WT

value: ADV-GFP


title: Wild Type Mouse Embryonic Fibroblast, rep1 (Hi-C)


title: Nalm6_2hr_Rep3_ATACseq

value: ALL

value: PRED (5uM, 2hrs)


title: HEK293T WT CN 3 [X3_CN_3_HEKWT]

value: wild-type


title: CRA_HIMK_4_rep3

description: Gene expression in Psa CRAFRU8.43 cells grown 4h in hrp-inducing medium supplemented with kiwifruit extract, replicate 3

source_name: Psa CRAFRU8.43 cells incubated in hrp-inducing medium supplemented with kiwifruit extract for 4h, replicate 3

value: bacterial cells


title: HEK293T WT CN 2 [X2_CN_2_HEKWT]

value: HEK 293T


title: Nalm6_2hr_Rep2_ATACseq


title: HEK293T WT CN 1 [X1_CN_1_HEKWT]

value: immortalised human embryonic kidney cells


title: NM1 knockout Mouse Embryonic Fibroblast, rep3 (Hi-C)


title: CRA_HIMK_4_rep2

description: Gene expression in Psa CRAFRU8.43 cells grown 4h in hrp-inducing medium supplemented with kiwifruit extract, replicate 2

source_name: Psa CRAFRU8.43 cells incubated in hrp-inducing medium supplemented with kiwifruit extract for 4h, replicate 2


title: Nalm6_2hr_Rep1_ATACseq


title: CRA_HIMK_4_rep1

description: Gene expression in Psa CRAFRU8.43 cells grown 4h in hrp-inducing medium supplemented with kiwifruit extract, replicate 1

source_name: Psa CRAFRU8.43 cells incubated in hrp-inducing medium supplemented with kiwifruit extract for 4h, replicate 1


title: Nalm6_12hr_Rep2_ATACseq

value: PRED (5uM, 12hrs)


title: Wild Type Mouse Embryonic Fibroblast, rep2 (ATAC-Seq)

description: WT.bw

data_processing:
Raw reads quality trimmed using trim-galore with default settings and assessed with fastqc
Surviving paired reads were then aligned against the mouse reference genome mm10 using bwa-mem
Resulting BAM alignments were then processed through PICARD tools (http://broadinstitute.github.io/picard), to clean, sort and deduplicate (PCR and Optical duplicates).
RPKM normalized bamCoverage files were produced using deeptools2 for replicate-merged bams of each conditions
Assembly: GRCm38 (mm10)
Supplementary files format and content: bigwig files containing RPKM normalized ATAC signal for merged replicates of each condition

extract_protocol:
Samples were shipped in frozen medium on dry ice to Novogene (Beijing, China). All subsequent processing was performed by Novagene using standard DNA extraction and library preperation protocols.All processing was performed by Novagene (Beijing, China). Cell nuclei were isolated, mixed with Tn5 Transposase with two adapters and tagmentation was performed for 30 minutes at 37⁰C. The fragmented DNA was purified and amplified with limited PCR cycle using index primers. Llibraries were prepared according to recommended Illumina NovaSeq6000 protocols.
Library preperation and sequencing was performed by Novogene. Co Ltd using standard illumina protocols


title: HEK293T UL1KOKO NO 3 [NO_3_HEKUL1KO]

value: HNRNPUL1 knock-out

value: Nucleolar RNA


title: Nalm6_0hr_Rep3_2-12hr_ATACseq


title: Wild Type Mouse Embryonic Fibroblast, rep1 (ATAC-Seq)

description: WT.bw

value: Mouse Embryonic Fibroblast

value: BALB/c


title: HEK293T UL1KOKO NO 1 [NO_1_HEKUL1KO]


title: NM1 knockout Mouse Embryonic Fibroblast, rep2 (ATAC-Seq)

value: NM1 knockout


title: NM1 knockout Mouse Embryonic Fibroblast, rep3 (ATAC-Seq)


title: HEK293T UL1KOKO NO 2 [NO_2_HEKUL1KO]


title: Nalm6_0hr_Rep1_2-12hr_ATACseq


title: CRA_HIMK_1_rep1

description: Gene expression in Psa CRAFRU8.43 cells grown 1h in hrp-inducing medium supplemented with kiwifruit extract, replicate 1

source_name: Psa CRAFRU8.43 cells incubated in hrp-inducing medium supplemented with kiwifruit extract for 1h, replicate 1


title: mouse_D5all_10X

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

description: Single-cell RNA seq, 10X Chromium

data_processing:
Cell Ranger pipeline v.3.1.0 was used to align raw sequencing reads to a custom genome (based on the GRCm38 mouse genome, including the open reading frame encoding EYPF (Srinivas et al., 2001). Quality control (QC), normalization and gene expression analysis was performed using the CRAN R package Seurat v.3.1.2 (Butler et al., 2018; Stuart et al., 2019) in R v.3.6.2. Cells with <1,900 genes detected and >5% mitochondrial reads were excluded. Normalization was performed using SCTransform (Hafemeister and Satija, 2019) v.0.2.1 implemented in Seurat.
Genome_build: Custom genome based on the GRCm38 mouse genome, including the open reading frame encoding EYFP (Srinivas et al., 2001)
Genome_build: 10X barcode file: Tsv files contain barcodes of detected cells.
Genome_build: 10X feature file: Tsv files contain IDs of detected genes.
Genome_build: 10X matrix file: Mtx files contain matrix of raw count values.
Genome_build: 10X normalized count file: Txt files contain normalized and filtered count values with genes in rows and cells in columns.

source_name: Carotid artery

extract_protocol:
Cells were isolated from ligated right carotid arteries of VSMC lineage-labeled animals (Myh11-EYFP-Ki67/RFP) 5 days after surgery. EYFP+ VSMCs were mixed with EYFP- cells, and 10,000 cells were loaded onto the Chromium system (10x Genomics). Single cell preparation: Carotid arteries were dissected free of perivascular adipose tissue, cut open longitudinally and the endothelium was removed by gentle scraping with a cotton bud. Carotid arteries were then pre-digested in DMEM (Gibco) supplemented with 1 mg/mL Collagenase IV (Invitrogen) and 1 U/mL Elastase (Worthington) for 10 minutes at 37˚C to allow removal of the adventitial layer. The medial layer was transferred to fresh DMEM supplemented with 2.5 mg/mL Collagenase IV (Invitrogen) and 2.5 U/mL Elastase (Worthington) and digested to a single cell suspension at 37 ˚C.
A total of 10,000 cells were loaded onto a Chromium system (10x Genomics) and amplified cDNA libraries generated using the 3’ Gene Expression v3.0 kit (10x Genomics) were sequenced using 150 cycle paired end protocol (NovaSeq, Illumina).

tag: background


title: NM1 knockout Mouse Embryonic Fibroblast, rep1 (ATAC-Seq)


title: CRA_HIMK_1_rep2

description: Gene expression in Psa CRAFRU8.43 cells grown 1h in hrp-inducing medium supplemented with kiwifruit extract, replicate 2

source_name: Psa CRAFRU8.43 cells incubated in hrp-inducing medium supplemented with kiwifruit extract for 1h, replicate 2


title: Wild Type Mouse Embryonic Fibroblast, rep3 (ATAC-Seq)

description: WT.bw

value: Wild Type


title: mouse_D5_10X

description: Single-cell RNA seq, 10X Chromium

data_processing:
Cell Ranger pipeline v.3.1.0 was used to align raw sequencing reads to a custom genome (based on the GRCm38 mouse genome, including the open reading frame encoding EYPF (Srinivas et al., 2001). Quality control (QC), normalization and gene expression analysis was performed using the CRAN R package Seurat v.3.1.2 (Butler et al., 2018; Stuart et al., 2019) in R v.3.6.2. Cells with <5,000 UMI counts, <2,000 genes detected and >5% mitochondrial reads were excluded. Normalization was performed using SCTransform (Hafemeister and Satija, 2019) v.0.2.1 implemented in Seurat.
Genome_build: Custom genome based on the GRCm38 mouse genome, including the open reading frame encoding EYFP (Srinivas et al., 2001)
Supplementary_files_format_and_content: 10X Barcode file: Tsv files contain barcodes of detected cells.
10X feature file: Tsv files contain IDs of detected genes.
10X matrix file: Mtx files contain matrix of raw count values.
10X normalized count file: Txt files contain normalized and filtered count values with genes in rows and cells in columns.

extract_protocol:
For the D5 dataset, cells isolated from ligated left common carotid arteries of six VSMC lineage-labeled animals (Myh11-EYFP-Ki67/RFP) 5 days after surgery were pooled prior to FACS isolation of EYFP+ cells. 10,000 EYFP+ cells were loaded onto the Chromium system (10x Genomics). Single cell preparation: Carotid arteries were dissected free of perivascular adipose tissue, cut open longitudinally and the endothelium was removed by gentle scraping with a cotton bud. Carotid arteries were then pre-digested in DMEM (Gibco) supplemented with 1 mg/mL Collagenase IV (Invitrogen) and 1 U/mL Elastase (Worthington) for 10 minutes at 37˚C to allow removal of the adventitial layer. The medial layer was transferred to fresh DMEM supplemented with 2.5 mg/mL Collagenase IV (Invitrogen) and 2.5 U/mL Elastase (Worthington) and digested to a single cell suspension at 37 ˚C.
A total of 10,000 EYFP+ cells were loaded onto a Chromium system (10x Genomics) and amplified cDNA libraries generated using the 3’ Gene Expression v3.0 kit (10x Genomics) were sequenced using 150 cycle paired end protocol (NovaSeq, Illumina).


title: human_10X

description: Single-cell RNA seq, 10X Chromium

data_processing:
Raw sequences were aligned to GRCh38 using the Cell Ranger pipeline v.3.1.0. Quality control (QC), normalization and gene expression analysis was performed using the CRAN R package Seurat v.3.1.2 (Butler et al., 2018; Stuart et al., 2019) in R v.3.6.2. Cells with <35,000 UMI counts, <1,000 genes detected and >10% mitochondrial reads were excluded. Normalization was performed using scran (Lun et al., 2016a).
Genome_build: GRCh38
Supplementary_files_format_and_content: 10X Barcode file: Tsv files contain barcodes of detected cells.
10X feature file: Tsv files contain IDs of detected genes.
10X matrix file: Mtx files contain matrix of raw count values.
10X normalized count file: Txt files contain normalized and filtered count values with genes in rows and cells in columns.

source_name: Medial layer of human aorta

extract_protocol:
Healthy human aorta sample from a 65-year-old male was dissected to remove the adventitial and intimal layers. The medial layer was cut into 1 mm2 pieces, a single cell suspension was obtained by digestion in 3 mg/mL collagenase IV and 1 U/ml elastase.  Following staining with 7-Aminoactinomycin D (7-AAD), cells were fixed in Lomant’s Reagent (dithio-bis(succinimidyl propionate, DSP) at 4 °C overnight. Viable cells were isolated by FACS based on 7-AAD exclusion. Cells were de-crosslinked in dithiothreitol (DTT) at 37°C for 30 minutes. A total of 20,000 cells were loaded onto a 10X Chromium system.
A total of 20,000 cells were loaded onto a 10X Chromium system and amplified cDNA libraries generated using the 3’ Gene Expression v3.0 kit (10x Genomics) were sequenced using 150 cycle paired end protocol (NovaSeq, Illumina).

value: Anonymous


title: CRA_HIM_4_rep3

description: Gene expression in Psa CRAFRU8.43 cells grown 4h in hrp-inducing medium, replicate 3

source_name: Psa CRAFRU8.43 cells incubated in hrp-inducing medium for 4h, replicate 3


title: HEK293T WT NO 3 [X3_NO_3_HEKWT]


title: HEK293T WT NO 2 [X2_NO_2_HEKWT]


title: CRA_HIM_4_rep2

description: Gene expression in Psa CRAFRU8.43 cells grown 4h in hrp-inducing medium, replicate 2

source_name: Psa CRAFRU8.43 cells incubated in hrp-inducing medium for 4h, replicate 2


title: HEK293T WT NO 1 [X1_NO_1_HEKWT]


title: Nalm6_0hr_Rep2_2-12hr_ATACseq

source_name: Nalm6 (ALL cell line)


title: Tumor UNC1999 4

type: protein

city: Chiba

first: Junjie

last: Ao

state: Chiba

address: 1-8-1 Inohana, Chuo-ku

department: Department of Gastroenterology

country: Japan

institute: Graduate School of Medicine, Chiba University

description: Subcutaneous tumor tissues were homogenized to subjecte to a mouse chemokine array kit. Among 25 different antibodies to mouse chemokines, the screening identified 14 chemokines in control and UNC1999-treated tumors, respectively.

hyb_protocol: Pipette 2 mL of Array Buffer 6 into each well of the 4-Well Multi-dish to block the membranes, prepare samples by adding up to 1 mL of each sample to 0.5 mL of Array Buffer 4 in separate tubes. Adjust to a final volume of 1.5 mL with Array Buffer 6 as necessary. Carefully remove each membrane and place into individual plastic containers with 20 mL of 1X Wash Buffer. Return the membrane to the 4-Well Multi-dish containing the diluted Streptavidin-HRP. Chemi Reagent Mix was used to stain.

scan_protocol: Expose membranes to X-ray film for 1-10 minutes. Multiple exposure times are recommended. Images were captured with Bio-Rad Molecular Imager ChemiDoc XRS + Imaging System (Bio-Rad Laboratories, Inc., Hercules, CA).

data_processing: Dot densities were quantified using Image Lab 4.1 software (Bio-Rad Laboratories, Inc.)

label: Biotin

molecule: protein

source_name: Subcutaneous tumor

label_protocol: Add 15 μL of reconstituted Detection Antibody Cocktail to each prepared sample. Mix and incubate at room temperature for one hour.

growth_protocol: H22 cells were cultured in RPMI 1640 medium supplemented with 10% fetal calf serum and 1% penicillin/streptomycin.

extract_protocol: Nineteen days after UNC1999 treatment, mice were sacrificed to obtain tumor tissues, then tumor tissues were homogenized in PBS with protease inhibitors. After homogenization, add TritonTM X-100 to a final concentration of 1%. Freeze samples at ≤ -70 °C, thaw, and centrifuge at 10,000 x g for 5 minutes to remove cellular debris. Quantitation of sample protein concentrations using a total protein assay is recommended. Assay immediately or aliquot and store samples at ≤ -70 °C. Avoid repeated freeze-thaw cycles.

treatment_protocol: BALB/c mice were bred and maintained in accordance with our institutional guidelines for the use of laboratory animals. A total of 5 × 10^6 H22 cells were implanted into the subcutaneous spaces of BALB/c mice (6-week-old), UNC1999 were intraperitoneally administrated for 19 days after the tumor volume reached approximately 150 mm3.

value: Subcutaneous tumor

tag: age

value: 6-8 weeks

tag: Sex

value: Male

tag: tumor cell

value: 5 × 106 H22 cells


title: Tumor UNC1999 3


title: CRA_HIM_1_rep3

description: Gene expression in Psa CRAFRU8.43 cells grown 1h in hrp-inducing medium, replicate 3

source_name: Psa CRAFRU8.43 cells incubated in hrp-inducing medium for 1h, replicate 3


title: CRA_HIM_4_rep1

description: Gene expression in Psa CRAFRU8.43 cells grown 4h in hrp-inducing medium, replicate 1

source_name: Psa CRAFRU8.43 cells incubated in hrp-inducing medium for 4h, replicate 1


title: CRA_HIMK_1_rep3

description: Gene expression in Psa CRAFRU8.43 cells grown 1h in hrp-inducing medium supplemented with kiwifruit extract, replicate 3

source_name: Psa CRAFRU8.43 cells incubated in hrp-inducing medium supplemented with kiwifruit extract for 1h, replicate 3


title: CRA_HIM_1_rep2

description: Gene expression in Psa CRAFRU8.43 cells grown 1h in hrp-inducing medium, replicate 2

source_name: Psa CRAFRU8.43 cells incubated in hrp-inducing medium for 1h, replicate 2


title: CRA_HIM_1_rep1

description: Gene expression in Psa CRAFRU8.43 cells grown 1h in hrp-inducing medium, replicate 1

source_name: Psa CRAFRU8.43 cells incubated in hrp-inducing medium for 1h, replicate 1


title: 28d_ACLR_1_M+F

city: Ann Arbor

first: Tristan

last: Maerz

state: MI

address: 109 Zina Pitcher Place, Office 2017

institute: University of Michigan

description: 10x Genomics/BGI

library_source: transcriptomic single cell

data_processing:
Following sequencing, raw data were aligned to the GRCm38 (mm10) mouse genome using STAR, then pre-processing (demultiplexing, barcode processing, gene counting and aggregation) was performed using Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Pre-processed aligned data were read from Cell Ranger into Seurat (R, v4.1.0). Cells with less than 100 detected genes and genes expressed in less than 10 cells were excluded from Seurat object generation. Next, low-quality cells were filtered out based on number of expressed features (i.e. genes), with remaining cells having 200 < nFeature < 6000. Cells in which > 5% of all genes were mitochondrial-derived (percent.mt > 0.05) were also excluded. Canonical correlation analysis, which performs anchor-based integration, was used to integrate data across conditions (Sham, 7d ACLR, 28d ACLR) using the top 3000 variable features
ScaleData() was used to perform linear transformation and to regress out unwanted variation due to cell cycle and mitochondrial gene expression. Linear dimensionality reduction was performed using principal component analysis, and elbow plots and principal component heatmaps were used to determine the number of dimensions used in subsequent nonlinear dimensionality reduction via Uniform Manifold Approximation and Projection (UMAP). For the integrated object (all cells, all conditions), dimensions 1-25 were used. Unsupervised clustering was performed using FindNeighbors (dims = 1:25) and FindClusters (resolution = 0.3) to derive distinct cell clusters.
Assembly: GRCm38 (mm10)
Supplementary files format and content: gene list (_features.tsv.gz) and cell barcodes (_barcodes.tsv.gz) as well as gene/barcode matrices (_matrix.mtx.gz) are provided for each sample

source_name: Knee synovium

extract_protocol:
Synovium were dissected then digested for 35 minutes at 37C in a volume of 1.5ml containing DMEM with 400 μg/mL collagenase IV, 400 μg/mL liberase, 400 μg/mL DNaseI. Samples were vortexed for 10 seconds at 0, 15 and 30 minutes of digestion. Cells were then pelleted by centrifugation at 500 x g for 5 min (4C) then resuspended in DMEM for counting and submission.
Libraries were constructed according to the standard 10x Genomics Single Cell 3' protocol.

value: Knee synovium

value: ACLR, harvested 28d later


title: Tumor control 3


title: 28d_ACLR_2_M+F

description: 10x Genomics/BGI


title: Tumor UNC1999 1


title: Tumor control 1


title: 7d_ACLR_2_M+F

description: 10x Genomics/BGI

value: ACLR, harvested 7d later


title: ChIP replicate 1

city: Paris

first: Benoit

last: Miotto

address: 24 Rue du Faubourg Saint Jacques

department: Development, Reproduction and Cancer

country: France

institute: INSERM U1016, Institut Cochin

data_processing:
Sequencing quality was assessed with fastqc tool
Mapping was performed using bowtie 1.1.2 (Langmead et al, 2009) on the human reference genome (hg19), allowing two mismatches per read and not keeping reads with multiple alignments. Duplicated reads were removed with SAMtools tool.
Two ChIP replicates and the corresponding inputs were used to performed peak-calling with CisGenome tool (Ji et al, 2008) with a stringent cutoff at 5 and a maximal P-value set-up at 10-40
Genome_build: hg19
Supplementary_files_format_and_content: ZBTB38 enriched peaks (BED format)

source_name: HeLa cells

growth_protocol: HeLa-S3 cells overexpressing HA-Flag-ZBTB38 were maintained in DMEM supplemented with 10% fetal bovine serum.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
The libraries were prepared by the sequencing platform of the ‘Centre National de Génotypage’ (CEA, Evry, France) according to manufacturer recommendation using the NextFlexTM ChIP-sequencing kit (5143-01, BiooScientific, US) and adaptors NextFlexTM ChIP-seq barcodes (514120, BiooScientific, US). Twenty nanograms of ChIP and Input DNA were used as starting material, DNA extremities repaired and the resulting DNA PCR amplified (11-12 cycles). DNA materials were then size-selected and purified using agencourts AMPure XP magnetic beads (A63881, Beckman Coulter, US) prior to analysis on a Illumina Hi-seq 2000.

value: HeLa

tag: genotype/variation

tag: chip antibody

value: HA-tag (abcam; Ab9110)


title: 7d_ACLR_1_M+F

description: 10x Genomics/BGI


title: Tumor control 2


title: ChIP replicate 2


title: Input replicate 2


title: CRISPRi-seq, Ci, rep1-4

city: Lausanne

first: Johann

last: Mignolet

address: Biophore Quartier UNIL-SORGE

department: DMF

country: Switzerland

institute: UNIL

data_processing:
The MAGeCK algorithm (https://sourceforge.net/p/mageck/wiki/Home/) was used to map the reads on the HSISS4 genome. Approximatively 30% of total reads were mapped, producing about 10 M reads per replicate. Following the MAGeCK guidelines, we next pooled the reads from the 4 replicates, ultimately generating a total of around 40 M reads per condition. Total and normalized reads counts per condition (mock, Ci, Ci+C) are reported in Table S1B-D.
Assembly: NZ_CP013216.1
Supplementary files format and content: Table S1.xlsx contains 4 sheets. Sheet S1A lists all the sequences of gRNA and their genomics position. Sheets S1B, S1C and S1C reports total and normalized read counts for each gRNA in mock, Ci, and Ci+C condition, respectively.
Library strategy: CRISPRi-seq

organism: Streptococcus salivarius

extract_protocol:
After genomic extraction (GenElute, Sigma Aldrich) from at least 1.5 × 109 CFU per replicate, the locus containing the gRNAs was PCR-amplified prior to their deep sequencing. An optimized PCR protocol was used with high primer concentration (5 µM), low template genomic DNA (2 ng/µl), and low number of cycles (15 cycles) to avoid any chimeric products due to the highly randomized gRNA sequences. The 219-pb amplicons were next gel-purified (Monarch DNA Gel Extraction kit, NEB) and sent with a minimum amount of 4 pmol for Illumina sequencing. High-Seq Illumina sequencing was performed with 30% Phix and generated an average of 30 M reads per replicate.
The gRNA library was designed by selecting all the 20 nt followed by a PAM sequence within the genome of HSISS4. The library was filtered to keep only gRNAs targeting the coding strand in CDSs and targeting both strands in intergenic regions. We ended up with a high-density library of 83,104 gRNAs (Table S1A, random_gRNA_HSISS4). We ordered the gRNAs as single strand DNA (Twist BioSciences) and amplified the oligo-pool thanks to common upstream and downstream region using primers AK475 (CGGACTAGCCTTATTTAAAC) and AK476 (GTCCCCCTGGTATAATAACTATA). To reduce any amplification sequence-bias, we used 10 cycles of amplification. The PCR products were then purified (Monarch kit, NEB) and Gibson-joined to the pre-amplified upstream homologous region of the neutral locus gor (downstream of HSISS4_00325) containing an erythromycin resistance gene and to the downstream homologous region of the same locus fused to a P3 constitutive promoter. We performed 20 independent Gibson assemblies, which were latter transformed by natural transformation into 20 independent cultures of HSISS4 containing at least a lactose-inducible dCas9 module (PF6-lacI; Plac-dcas9). For every library produced, we calculated the number of transformants to obtain at least 15-fold transformants over the diversity rate, ensuring theoretically that 99,9% of the diversity would be present in the library. We finally pooled all the transformants in PBS and measured OD600 prior to storage at -80°C.

treatment_protocol: The gRNA library was spread onto three different solid media (M17-Glucose 1% [M17G], mock condition; M17G IPTG 100 µM, Ci condition; M17G IPTG 100 µM xylose 1%, Ci + C condition) resulting in an average of 9.6 × 106 CFU per large plate. Technical replicates (n = 4) were incubated 16 h at 37°C to yield an estimated mean of around 12 generations. Cells were then collected, pooled in PBS buffer and homogenized for each replicate

value: tRNAthr::PF6-lacI-lox72, tRNAser::Plac-dcas9-lox72, tnpII::PcomX-luxAB-lox72, suc::Pxyl2-comR-lox72, gor::P3-gRNA-erm

value: IPTG


title: CRISPRi-seq, Ci+C, rep1-4

value: IPTG + xylose


title: Tumor UNC1999 2


title: Tumor control 4


title: HFDPCs, TRI SQ

city: Tsukuba,

first: Meriem

last: Bejaoui

state: Ibaraki

address: 1 Chome-1-1 Tennodai

institute: University of Tsukuba

hyb_protocol: Following fragmentation, 250 ng of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array (HG-219). GeneChips were washed and stained in the Gene Atlas Fluidics Station 400

scan_protocol: GeneChips were scanned using the GeneAtlas Imaging Station

data_processing: The raw data were normalized using Expression Console Software provided by the Affymetrix following robust multichip average (RMA) algorithm (http://www.affymetrix.com). Subsequent analysis of the gene expression data was carried out in the freely available Transcriptome Analysis Console (TAC) version 4 (Thermofisher inc.). Further analysis was conducted using an online data mining tool DAVID (Database for Annotation, Visualization and Integrated Discovery, ver. 6.8). We used 'Functional Annotation' tool of DAVID to identify the most relevant biological terms, including gene ontology (GO) terms, biological pathways, tissue expression, and disease associations (Huang da et al., 2009). We also performed gene set enrichment analysis (GSEA) for the top DEGs.

label: biotin

source_name: cell treated with TRI SQ

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 9.4 ug total RNA

growth_protocol: HFDPCs were purchaced from Cell application and were maintained in Papilla cell culture meduim

extract_protocol: For RNA extraction, Isogen (Nippon Gene Co. Ltd., Toyama, Japan) was added and the cell suspensions were centrifuged for 5 minutes at 500 g and the pellet was stored at -80oC until use.

treatment_protocol: After the initial 24 hour seeding in 6-well-collagen-coated plates. The medium was changed with 0 (Control) and 2.5 % µM with SQ, Tetra SQ and Tri SQ for 48 h.

value: hair follicle dermal papilla cells

value: TRI SQ


title: Sham_28d_M+F

description: 10x Genomics/BGI

value: Sham (no injury), harvested 28d later


title: HFDPCs, TETRA SQ 2

source_name: cell treated with TETRA SQ

value: TETRA SQ


title: HFDPCs, TRI SQ 2


title: HFDPCs, SQ 2

source_name: cell treated with SQ

value: SQ


title: PAT WT LAD

city: Brussels

first: Didier

last: Communi

address: Route de Lennik 808

department: IRIBHM

country: Belgium

institute: Université Libre de Bruxelles

data_processing:
Sequenced reads were trimmed for adaptor sequence (Trimmomatic)
Paired-end reads were mapped against the mouse reference genome (GRCm38.p4/mm10) using the STAR software to generate read alignments.
The annotation file Mus_musculus.GRCm38.90.gtf was obtained from the ftp.Ensembl.org server.
Following transcript assembly, gene level counts were obtained using HTSeq.
Assembly: GRCm38.p4/mm10
Supplementary files format and content: Excel xlsx file includes counts per 20 millions of aligned reads values for each sample.

source_name: pericardial adipose tissue (PAT)

extract_protocol:
RNA was extracted from freshly harvested pericardial adipose tissue (PAT) using the RNeasy Mini Kit (Qiagen) after cells lysis in TRIzol Reagent Solution (Invitrogen) using the MagNA Lyser instrument (Roche).
TruSeq Stranded mRNA (Illumina)

value: pericardial adipose tissue (PAT)

value: wild type

tag: disease model

value: left anterior descending artery (LAD) ligation

tag: time

value: 24 hours after LAD ligation


title: PAT P2Y4 KO LAD

value: P2Y4 KO


title: HFDPCs, SQ


title: HFDPCs, Control 2

source_name: cell treated with medium

value: medium


title: HFDPCs, TETRA SQ


title: HFDPCs, Control


title: Input replicate 1


title: LY6934-veh-1

status: Public on Aug 24 2022

city: Waltham

first: Derek

middle: B

last: Oien

state: MA

address: 35 Gatehouse Dr

institute: AstraZeneca

data_processing:
Fastq files were aligned to GRCh38 and mm10 using HISAT2 (v2.1.0) and disambiguated using bcbio-nextgen v1.1.6
Counts were quanitied using Salmon (v0.8.2) using Ensembl v79 annotations.
tximport was used to generate gene level count data using option countsFromAbundance = "lengthScaledTPM" and a log2 transcripts per kilobase million, log2(TPM +0.01), abundance matrix.
Assembly: GRCh38
Supplementary files format and content: Count matrix.

growth_protocol: TMD8 human diffuse large B-cell lymphoma cells were obtained from Professor Daniel Krappmann and were grown in RPMI 1640, supplemented with 10% FBS, 2 mM L-glutamine, and 1% Penicillin-Streptomycin. All cells were maintained and propagated as suspension cultures at 37°C in a humidified 5% CO2 incubator. Cells were washed with buffer and injected into the right flank of female NSG mice aged 5 to 6 weeks. Cells were grown into a tumor (~1 week) prior to drug dosing. LY6934 tumors were from Crown Bioscience. These patient-derived xenografts were passaged between mice to grow tissue. Tissue size of ~ 8 mm3 was implanted subcutaneously with a trocar in the right flank of mice.

extract_protocol:
Xenograft tumors from TMD8 and LY6934 mouse models after dosing with AZD5153 and acalabrutinib were excised and snap frozen in liquid nitrogen. Tumor tissue was lysed and RNA was extracted using RNeasy kit (Qiagen, Hildren, Germany) according to manufacturer’s instructions. RNA concentration was quantified using the Qubit fluorometer (ThermoFisher, Waltham, MA). 15 RNA samples were sent to Novogene for library preparation and human RNA sequencing.
Illumina mRNA TruSeq library was used for library preparation at Novogene.
RNA-seq was sequenced on 9 lanes of Illumina HiSeq4000 with paired end 150bp reads by Novogene.

treatment_protocol: Treatments were A) TMD8 (4 hours): vehicle (0.5% hydroxymethylcellulose, 0.1% Tween80), 0.72 mg/kg AZD5153 QD, 20 mg/kg acalabrutinib BID, or 0.72 mg/kg AZD5153 QD + 20 mg/kg acalabrutinib BID, and B) LY6934 (25 days): vehicle (0.5% hydroxymethylcellulose, 0.1% Tween80) or 0.5 mg/kg AZD5153 QD + 20 mg/kg acalabrutinib

value: Vehicle

value: xenograft tumor


title: LY6934-veh-3


title: LY6934-Acala-AZD5153-0.5mgkg-2


title: LY6934-Acala-AZD5153-0.5mgkg-1


title: LY6934-veh-2


title: Sham_7d_M+F

description: 10x Genomics/BGI

value: Knee synovium

value: Sham (no injury), harvested 7d later


title: TMD8-AZD5153-0.72mgkg-3


title: TMD8-Acala-AZD5153-0.72mgkg-2


title: TMD8-Acala-AZD5153-0.72mgkg-1


title: TMD8-Acala-2

value: Acala


title: TMD8-AZD5153-0.72mgkg-1


title: TMD8-Acala-3


title: CRISPRi-seq, mock, rep1-4

value: tRNAthr::PF6-lacI-lox72, tRNAser::Plac-dcas9-lox72, tnpII::PcomX-luxAB-lox72, suc::Pxyl2-comR-lox72, gor::P3-gRNA-erm


title: TMD8-veh-3


title: TMD8-Acala-1


title: TMD8-veh-1


title: TMD8-veh-2


title: HeLa DHX34-1

city: Edinburgh

first: Javier

last: Caceres

address: Crewe Road

department: MRC HGU

institute: University of Edinburgh

data_processing:
pseudoalignment using Salmon
differential expression calling using Sleuth
splicing event calling using SUPPA2
Assembly: GRCh38.93
Supplementary files format and content: HeLa_sleuth.csv
Supplementary files format and content: HeLa_suppa2.csv

source_name: HeLa

growth_protocol: standard culture conditions , DMEM, 10% FCS, 1% Pen/Strep

extract_protocol:
Sequencing was done by  BGI TECH SOLUTIONS (HONGKONG) CO., LIMITED. They did not disclose how they made library so  state Illumina RNA seq library
Sequencing Platform & Strategy: RNA-Seq (transcriptome, 100PE, HiSeq4000)

treatment_protocol: siRNA transfection, harvest 4 days post transfection

value: HeLa

value: cervical cancer cell line


title: HeLa SCR-1


title: HeLa SCR-2


title: pooled sample, patients P0116; P0118; P0119; P0120_HTO

city: Berlin

first: Nikolaus

last: Rajewsky

address: Hannoversche Str. 28

department: BIMSB

country: Germany

institute: Max Delbrück Center for Molecular Medicine

data_processing:
fastqc to check quality of sequencing reads
bulit SARS-CoV1/2 genomic information reference if samples from COVID-19 patients
cellranger (v3.1) mkfastq to demultiplex fastq files
cellranger (v3.1) count to align sequencing files to a reference transcriptome
provide library.csv and feature_ref.csv for cellranger (v3.1) count of HTO samples
Assembly: GRCh38
Supplementary files format and content: Tab-separated UMI counts in matrix.mtx. List of genes in features.tsv List of cell barcodes in barcodes.tsv

molecule: polyA RNA

source_name: Urine

extract_protocol:
Samples were collected either as first morning void urine or via urinary catheter (using the pooled urine output of 4 hours) and stored on ice. Incubation with Actinomycin D for 30 min on ice was applied to prevent subsequent alteration of transcriptomes followed by blocking Fc receptors using human FcR blocking reagent (Miltenyi, Bergisch Gladbach, Germany). Cells were then incubated with fluorescent dyes and fluorochrome-conjugated monoclonal antibodies for fluorescence-activated cell sorting (FACS). The following antibodies and dyes were used for cell labeling: Calcein AM (BD Biosciences, San Jose, CA, USA, 564061), Hoechst 33342 (BD Biosciences, San Jose, CA, USA, 561908), AnnexinV-PE (Biolegend, San Diego, CA, USA, 640908), CD45-APC/Vio770 and CD66b-PE/Vio770 (both Miltenyi, 130-110-635 and 130-119-768). Cells were washed, filtered through a 70 Âµm cell strainer and labeled with To-Pro3 iodide (T3605, Life technologies, Eugene, Oregon) for dead cell discrimination immediately prior to sorting.  Samples were sorted using a Sony MA900 (Sony, Tokyo, Japan) with a 100Âµm nozzle into phosphate buffered saline (PBS) / 1 % BSA gating To-Pro3-AnnexinV- Hoechst33342+CalceinAM+ singlets for obtaining single viable urinary cells. Urinary granulocytes, which make up a large fraction of the urinary cellular signal (median 58% in FACS gating) but for which a renal tissue origin is not verifiable, and which may interfere with downstream analysis, were excluded. Relative single cell counts in sorted suspensions were counted using a MACSQuant Analyzer (Miltenyi). Cells were centrifuged, resuspended, and re-counted on a hemocytometer. Cell suspensions were subjected to single-cell sequencing following the 10x Genomics protocol for Chromium Next GEM Single Cell 3â€™ v3.1 chemistry targeting between 1000 - 10000 cells depending on sample cell count.
According to manufacturer recommendation of  Chromium Next GEM Single Cell 3Ê¹ GEM, Library & Gel Bead Kit v3.1

value: Urine

tag: kidney injury etiology

value: pneumonia / intesive care

tag: disease type

value: COVID


title: HeLa DHX34-2

tag: cell type


title: pooled sample, patients P0051; P0053; P0058; P0061_HTO

tag: tissue


title: pooled sample, patients P0048; P0054; P0060_HTO


title: pooled sample, patients P008; P009; P010; P012, CD45- urine cells_HTO

value: prerenal

value: Non-COVID


title: pooled sample, patients P008; P009; P010; P012, CD45+ urine cells_HTO


title: P023.4

value: Cardiac surgery associated


title: P022


title: pooled sample, patients P0048; P0054; P0060


title: pooled sample, patients P0116; P0118; P0119; P0120


title: P023.2


title: P023.3


title: P023.1


title: P024.2


title: pooled sample, patients P0051; P0053; P0058; P0061


title: P024.1


title: P021


title: HeLa DHX34-3

tag: cell line


title: P019.1


title: pooled sample, patients P0049; P0050; P0052; P0059_HTO


title: P018.1


title: pooled sample, patients P013; P014; P015; P016, CD45+ urine cells_HTO


title: pooled sample, patients P0049; P0050; P0052; P0059


title: TMD8-AZD5153-0.72mgkg-2

tag: treatment


title: P018.2


title: HeLa SCR-3


title: P017.1


title: P002.1


title: pooled sample, patients P013; P014; P015; P016, CD45- urine cells_HTO


title: P002.2


title: P019.2


title: pooled sample, patients P013; P014; P015; P016, CD45+ urine cells


title: pooled sample, patients P008; P009; P010; P012, CD45- urine cells


title: P006


title: Parental AT2 4-OHT 24h (2)

city: London

first: Miriam

last: Molina-Arcas

address: 1 Midland Road

institute: The Francis Crick Institute

data_processing:
Read trimming and adaptor removal with Trimmomatic (v 0.36)
Read alignment with STAR ( v 2.5.2a) and gene quantification with RSEM( v 1.2.31)
Differential expression analysis DESeq2
Genome_build: GRCm38 Ensembl release 89
Supplementary_files_format_and_content: tab separated counts per gene per sample

source_name: Parental AT2 cells

extract_protocol:
RNA was extracted via a column-based method
mRNA KAPA Hyper Prep

treatment_protocol: Cells were treated with vehicle, ARS-1620 or 4-OHT for different time points

value: AT2 parental

tag: replicate

value: replicate 2

tag: time point


title: P005


title: Parental AT2 4-OHT 24h (3)

value: replicate 3


title: pooled sample, patients P013; P014; P015; P016, CD45- urine cells


title: Parental AT2 4-OHT 24h (1)

value: replicate 1


title: Parental AT2 4-OHT 6h (3)


title: Parental AT2 4-OHT 30' (3)


title: Parental AT2 4-OHT 6h (1)


title: Parental AT2 4-OHT 30' (2)


title: P017.2


title: Parental AT2 4-OHT 6h (2)


title: P001


title: pooled sample, patients P008; P009; P010; P012, CD45+ urine cells


title: AT2 4-OHT 24h (3)

source_name: AT2 cells

value: AT2 KRAS-G12V-ER clone #6


title: AT2 4-OHT 24h (2)


title: Parental AT2 4-OHT 0h (3)

value: Ethanol control


title: Parental AT2 4-OHT 30' (1)


title: AT2 4-OHT 6h (3)


title: Parental AT2 4-OHT 0h (1)


title: AT2 4-OHT 6h (2)


title: AT2 4-OHT 24h (1)


title: Parental AT2 4-OHT 0h (2)


title: AT2 4-OHT 6h (1)


title: P007


title: AT2 4-OHT 30' (3)


title: A549 ARS-1620 24h (3)

source_name: A549 cells


title: AT2 4-OHT 0h (3)


title: AT2 4-OHT 30' (2)


title: AT2 4-OHT 30' (1)


title: AT2 4-OHT 0h (1)


title: A549 ARS-1620 8h (2)


title: A549 ARS-1620 8h (1)


title: A549 ARS-1620 8h (3)


title: A549 ARS-1620 2h (3)


title: A549 ARS-1620 2h (2)


title: A549 ARS-1620 0h (3)

value: DMSO control


title: A549 ARS-1620 24h (2)


title: A549 ARS-1620 24h (1)


title: A549 ARS-1620 0h (2)


title: H358 ARS-1620 8h (2)

source_name: H358 cells


title: H358 ARS-1620 24h (2)


title: H358 ARS-1620 2h (3)


title: A549 ARS-1620 0h (1)


title: H358 ARS-1620 24h (1)


title: H358 ARS-1620 24h (3)


title: H358 ARS-1620 8h (3)


title: H358 ARS-1620 8h (1)


title: H358 ARS-1620 2h (1)


title: H358 ARS-1620 2h (2)


title: H358 ARS-1620 0h (2)


title: AT2 4-OHT 0h (2)


title: H358 ARS-1620 0h (3)


title: A549 ARS-1620 2h (1)


title: H23 ARS-1620 24h (2)

source_name: H23 cells


title: H23 ARS-1620 8h (3)


title: H23 ARS-1620 24h (1)


title: H358 ARS-1620 0h (1)


title: H23 ARS-1620 8h (2)


title: H23 ARS-1620 8h (1)


title: H23 ARS-1620 2h (3)


title: Total RNA HL 800µE rep 2

city: ACTON

first: Marten

last: Moore

state: ACT

address: 134 Linnaeus Way

department: Research School of Biology

country: Australia

institute: The Australian National University

description: Total RNA

data_processing:
Quality control of sequencing data was performed with FastQC (v.0.11.5). Total RNA data had adapters removed using scythe (v.0.991) with a prior of 0.01, and quality trimmed with sickle (v.1.33) with a quality threshold of 20 and a minimum trimmed length of 20. Mapping to TAIR10 was performed with subjunc (v.1.4.5), reporting only reads with a single unambiguous mapping location [86]. RPF data was trimmed for adapter contamination and read quality using Cutadapt (v.1.9.1) with a minimum trimmed length of 20 bp and error rate of 0.1 (Martin M. 2011). Trimmed reads were mapped to TAIR10 using Bowtie2 (v2.2.9) requiring end-to-end alignment and a substring length of 10 (Lanfmead and Salzberg 2012).
Assembly: Tair10
Supplementary files format and content: h5: HDF5 file containing run info, abundance esimates (TPM), bootstrap estimates, and transcript length, .counts: gene-level raw counts.

organism: Arabidopsis thaliana

source_name: whole rosettes

growth_protocol: Arabidopsis seeds were sown onto moist soil (Seed Raising and Cutting Mix, Martins, NSW, Australia) supplemented with 1 g/L dry volume of soil Osmocote Exact Mini slow release fertilizer (Scotts, NSW, Australia) and 1 L of 0.3 % (v/v) AzaMax (OCP, NSW, Australia). Seeds were covered with a plastic hood and stratified at 4 °C in the dark for at least 72 hours to break dormancy and coordinate germination. Stratified seeds were transferred to a temperature controlled Conviron S10H growth chamber (Conviron, Winnipeg, MB, Canada), fitted with a mixture of 250 W metal halide lamps (Venture Lighting, MH 250W/U) and high pressure sodium lamps (Phillips, SON‐T 250 W E E40 SL/12), for cultivation under a 10-hour photoperiod (08:00-18:00) of 80-100 μ mol photons m-2 s -1, 22.5/20.5 °C day/night temperatures, and 57/55 % day/night relative humidity.

extract_protocol:
3 g of pulverized plant material was used with 6 mL polysomal extraction buffer (PEB; 0.2 M Tris, pH 9.0, 0.2 M KCl, 25 mM EGTA, 35 mM MgCl, 1 % Brij, 1 % Triton X-100, 1 % Tween 20, 1 % Igepal CA630, 1% sodium deoxycholate (DOC), 1 % polyethylene-10-tridecylether (PTE), 5 mM DTT, 1 mM PMSF, 100 µg/mL cycloheximide, 100 µg/mL chloramphenicol, 100 µg/mL lincomycin). The suspension was passed twice through MiraclothTM and subsequently cleared by centrifugation. Extracts were loaded on a sucrose cushion (0.2 M Tris, pH 9.0, 0.2 M KCl, 0.025 M EGTA, 0.035 M MgCl, 1.75 M sucrose, 5 mM DTT, 50 µg/mL cycloheximide, 50 µg/mL chloramphenicol, 50 µg/mL lincomycin) and centrifuged for 18 h at 100,000 xg in a Beckmann SW71Ti rotor. The sediment was suspended in 100 µL RNase digestion buffer (20 mM Tris-HCl, pH 8.0, 140 mM KCl, 35 mM MgCl2, 50 µg/µL cycloheximide, 50 µg/µL chloramphenicol, 50 µg/µL lincomycin) and used immediately for RNase If digestion. 500 µL of extract was combined with 1 mL of TriReagent, followed twice by extraction of the organic phase with 200 µL chloroform. RNA was precipitated with equal volume 100% isopropanol and incubated overnight at -20°C. The RNA was recovered by centrifugation and washed with 75% ethanol before resuspension in water. RNA quality was assessed using a LabChip GXII (Perkin-Elmer). Total RNA was DNase-treated using TURBO DNase (Invitrogen) following the manufacturer’s protocol.
Total RNA was DNase-treated using TURBO DNase (Invitrogen) following the manufacturer’s protocol. Preparation of total RNAseq libraries was carried out using Illumina TruSeq Stranded Total RNA with Ribo-Zero plant, scaled at half reaction volumes.  Libraries of ribosome-protected fragments (RPFs) were prepared from three biological replicates per time-point and sample following RNase If digestion (above) according to Juntawong et al. (2014) with minor modifications.

treatment_protocol: Three weeks old plants were transfered to 8 µmol photons m-2 s-1 (LL) for 10 days. Plants were transferred to 800 µmol photons m-2 s-1 (HL) for 10 min, while control plants remained in LL. Whole rosettes were harvested under control and HL conditions in the midday point of the light period to exclude circadian effects and immediately frozen in liquid nitrogen and stored at -80°C.

value: whole rosettes

tag: condition

value: stress

tag: genotype

value: high light (800µE) HL


title: Total RNA HL 800µE rep 3

description: Total RNA


title: RPF HL 800µE rep 3

description: RPF


title: RPF HL 800µE rep 2

description: RPF


title: Total RNA LL 8µE rep 3

description: Total RNA

value: controll

value: low light (8µE) LL


title: RPF LL 8µE rep 2

description: RPF


title: Total RNA LL 8µE rep 2

description: Total RNA


title: H23 ARS-1620 2h (2)


title: RPF LL 8µE rep 3

description: RPF


title: Total RNA HL 800µE rep 1

description: Total RNA


title: RPF HL 800µE rep 1

description: RPF


title: H23 ARS-1620 0h (2)


title: H23 ARS-1620 2h (1)


title: Total RNA LL 8µE rep 1

description: Total RNA


title: H23 ARS-1620 24h (3)


title: RPF LL 8µE rep 1

description: RPF


title: TMD8-Acala-AZD5153-0.72mgkg-3

value: xenograft tumor


title: H23 ARS-1620 0h (1)


title: 22Rv1_final_rep3

city: Istanbul

first: Ayse Derya

last: Cavga

address: Rumelifeneri Yolu, Sariyer

country: Turkey

institute: Koc University

description: Last collection. EPIKOL-transduced 22Rv1 cells were collected after 15 doublings.

data_processing:
Library strategy: CRISPR Amplicon Sequencing
Base calling was performed with Illumina HiSeq platforms (Genewiz, USA)
sgRNA counting, gene summarization and comparative analyses between samples were performed using MAGeCK version 0.5.8 (Li, W., et al., 2014) using median normalization and the RRA method. R1 fastq files were used in counting.
Genome_build: sgRNA counted by matching to custom CRISPR Screen library; Epigenetic Knock-out Library (EPIKOL)
Supplementary_files_format_and_content: txt files containing MAGeCK outputs; normalized counts, gene summary and sgRNA summary

source_name: prostate carcinoma cells

growth_protocol: MDA-MB-231 cells were cultured in DMEM supplemented with 10% fetal bovine serum and %1 Penicillin/Streptomycin. SUM159 and SUM149 cell lines were cultured with Ham’s F12 nutrient mix supplemented with 5% FBS, 5 µg/ml insulin, 1 µg/ml hydrocortisone and 10 mM HEPES. Immortalized human breast epithelial cells (HMLE) were cultured in MEGM medium. Briefly, MEGM Bullet Kit (Lonza,Swiss) (by excluding gentamicin/amphotericin-B) was used and supplemented with the same volume of DMEM:F12 (1:1), 10 µg/ml insulin, 0.5 µg/ml hydrocortisone, 20 ng/ml EGF, and %1 Penicillin/Streptomycin. All prostate cell lines except RWPE-1 were cultured in RPMI 1640 supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin. RWPE-1 cells were cultured in Keratinocyte SFM media supplemented with 0.05 mg/mL bovine pituitary extract and 5 ng/mL human recombinant epidermal growth factor.

extract_protocol:
Genomic DNA (gDNA) was isolated by NucleoSpin Tissue kit (Macherey-Nagel, Germany) for TNBC cell lines and by PureLink Genomic DNA mini kit (ThermoFischer K-1820) for PCa cell lines according to manufacturer’s instructions
Library was constructed with Illumina-compatible adapters. sgRNA cassettes were amplified from genomic DNA using pLentiGuide specific forward and reverse primers in the first PCR. For second PCR, %1-2.5 of the first PCR product was amplified with forward stagger and reverse index primers (specific to sample). Final library fragments of ~350 bp were agarose gel purified. Fragments were quality checked with fragment analyzer and sequenced with Illumina Hiseq (Genewiz, USA)

treatment_protocol: Cells were transduced with EPIKOL at low MOI (0.3-0.4) with 1000x coverage for TNBC and 500x coverage for PCa in the presence of 8 μg/ml protamine sulphate. Following three days of puromycin selection, initial reference point pellets were collected as 8 million cells for TNBC and 4 million cells for PCa. Later, cells were maintained with the indicated coverage for each line. After 15-16 population doublings, screens were ended and cell pellets were collected.

value: prostate carcinoma cells


title: sob3-6 RNA-seq ZT24 replicate 1

city: Yokohama

first: David

middle: Seth

last: Favero

state: International

address: 1-7-22 Suehirocho, Tsurumi-ku

department: CSRS

institute: RIKEN

description: RNA-seq for sob3-6 (dominant-negative ahl mutant) at ZT24 replicate 1

data_processing:
Generation of fastq files: Raw data files (bcl format) were converted to fastq files by bcl2fastq (Illumina).
Alignment: Reads were mapped to the Arabidopsis reference using Bowtie with the following parameters: '-all -best -strata'.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited data with transcript CPM (counts per million mapped reads) values for each sample

source_name: Whole plants

growth_protocol: 22°C constant temperature with short-day photoperiod (8h light/16h darkness) under white fluorescent light (~35-55 μmol/m2/sec) on 1X MS medium containing 0.6% Gelzan CM and 1% sucrose.

extract_protocol:
Total RNA was extracted using the RNeasy Plant Mini Kit (QIAGEN) according to manufacturer's instructions, including on-column DNase digestion to eliminate genomic DNA.
Isolated RNA was subjected to library preparation using the KAPA Stranded mRNA-Seq Kit (Kapa Biosystems) with NEBNext Multiplex Oligos for Illumina (New England Biolabs) used as adapters and Agencourt AMPure XP (Beckman Coulter) beads used instead of KAPA Pure Beads.

tag: ecotype

value: Columbia (Col-0)

tag: age

value: 6 days old

tag: time of harvest


title: sob3-6 RNA-seq ZT24 replicate 3

description: RNA-seq for sob3-6 (dominant-negative ahl mutant) at ZT24 replicate 3


title: sob3-6 RNA-seq ZT24 replicate 2

description: RNA-seq for sob3-6 (dominant-negative ahl mutant) at ZT24 replicate 2


title: P003

value: Urine

value: pneumonia / intesive care

value: COVID


title: sob3-6 RNA-seq ZT9 replicate 3

description: RNA-seq for sob3-6 (dominant-negative ahl mutant) at ZT9 replicate 3

value: 5 days old


title: H23 ARS-1620 0h (3)

value: replicate 3


title: sob3-6 RNA-seq ZT9 replicate 2

description: RNA-seq for sob3-6 (dominant-negative ahl mutant) at ZT9 replicate 2


title: sob3-6 RNA-seq ZT4 replicate 2

description: RNA-seq for sob3-6 (dominant-negative ahl mutant) at ZT4 replicate 2


title: sob3-6 RNA-seq ZT9 replicate 1

description: RNA-seq for sob3-6 (dominant-negative ahl mutant) at ZT9 replicate 1


title: 22Rv1_final_rep1


title: 22Rv1_initial_rep2

description: Initial collection (reference point). EPIKOL-transduced 22Rv1 cells were collected right after puromycin selection.


title: 22Rv1_initial_rep3


title: 22Rv1_initial_rep1


title: SOB3-D RNA-seq ZT24 replicate 3

description: RNA-seq for SOB3-D (AHL overexpressor) at ZT24 replicate 3


title: sob3-6 RNA-seq ZT4 replicate 3

description: RNA-seq for sob3-6 (dominant-negative ahl mutant) at ZT4 replicate 3


title: sob3-6 RNA-seq ZT4 replicate 1

description: RNA-seq for sob3-6 (dominant-negative ahl mutant) at ZT4 replicate 1


title: 22Rv1_final_rep2


title: SOB3-D RNA-seq ZT24 replicate 2

description: RNA-seq for SOB3-D (AHL overexpressor) at ZT24 replicate 2


title: SOB3-D RNA-seq ZT24 replicate 1

description: RNA-seq for SOB3-D (AHL overexpressor) at ZT24 replicate 1


title: DU145_final_rep3

description: Last collection. EPIKOL-transduced DU145 cells were collected after 15 doublings.


title: SOB3-D RNA-seq ZT9 replicate 2

description: RNA-seq for SOB3-D (AHL overexpressor) at ZT9 replicate 2


title: SOB3-D RNA-seq ZT9 replicate 3

description: RNA-seq for SOB3-D (AHL overexpressor) at ZT9 replicate 3


title: DU145_final_rep1


title: SOB3-D RNA-seq ZT9 replicate 1

description: RNA-seq for SOB3-D (AHL overexpressor) at ZT9 replicate 1


title: SOB3-D RNA-seq ZT4 replicate 2

description: RNA-seq for SOB3-D (AHL overexpressor) at ZT4 replicate 2


title: DU145_final_rep2


title: SOB3-D RNA-seq ZT4 replicate 3

description: RNA-seq for SOB3-D (AHL overexpressor) at ZT4 replicate 3


title: patient04-T

city: Nanjing

first: Feng

last: Jiang

state: Jiangsu

address: Baiziting 42

institute: Jiangsu Institute of Cancer Research

hyb_protocol: The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, SE-LncRNAs that at least 5 out of 10 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed SE-LncRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs between the two samples were identified through Fold Change filtering.

source_name: primary lung cancer

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen).

extract_protocol: We obtained tumor tissues with matched adjacent tissues from 5 patients who underwent radical surgery without neoadjuvant chemotherapy and who were diagnosed with LUAD at the Jiangsu Cancer Hospital (Nanjing, China). Each patient contains complete clinical and pathological information. 1. Cryopulverization of tissue using the Biopulverizer. a. Place the BioPulverizer™ in a shallow container and cool thoroughly with either liquid nitrogen. b. Place prefrozen tissue in the well of the mortar. c. Remove the mortar from the shallow container, place it on the lab bench and pulverize the tissue with one or two blows to the pestle with a hammer (models 59012MS). d. Empty the powdered contents for subsequent homogenization or extraction procedures. 2. Homogenization using the Mini-Bead-Beater-16. a. Fill the 2 ml screw-cap microtube one-half full with 1.0mm beads. Then add TRIzol and tissue, being sure to fill the microtube almost to the top. Exclude as much air from the microtube as possible. Use screw-cap microtubes with integral o-ring seals in order to eliminate aerosol formation during the homogenization. Be sure there are no beads on the threads of the microtubes when screwing down the cap. b. Insert 1 to 16 microtubes into the holder. Distribute them symmetrically as you would do with a centrifuge. Screw in the black plastic chamber cap until it is in contact with the tops of the microtube caps. Tighten the lid by hand so the vials are firmly held in place. Do not overtighten. c. Set the timer depending on the type of sample. Start the machine. Incubate the homogenized samples for 5 minutes at 15 to 30°C to permit the complete dissociation of nucleoprotein complexes. Add 0.2 ml of chloroform per 1 ml of TRIzol Reagent. Cap sample tubes securely. Shake tubes vigorously by hand for 15 seconds and incubate them at 15 to 30°C for 2 to 3 minutes. Centrifuge the samples at 12,000 × g for 15 minutes at 4°C. Following centrifugation, the mixture separates into a lower red, phenol-chloroform phase, an interphase, and a colorless upper aqueous phase. RNA remains exclusively in the aqueous phase. The volume of the aqueous phase is about 60% of the volume of TRIzol Reagent used for homogenization. Transfer the aqueous phase to a fresh tube. Precipitate the RNA from the aqueous phase by mixing with isopropyl alcohol. Use 0.5 ml of isopropyl alcohol per 1 ml of TRIzol Reagent used for the initial homogenization. Incubate samples at 15 to 30°C for 10 minutes and centrifuge at 12,000 × g for 10 minutes at 4°C. Remove the supernatant. Wash the RNA pellet once with 75% ethanol, adding at least 1 ml of 75% ethanol per 1 ml of TRIzol Reagent used for the initial homogenization. Mix the sample by vortexing and centrifuge at 7,500 × g for 5 minutes at 4°C. At the end of the procedure, air-dry the RNA pellet for 5-10 minutes. Dissolve RNA in 85ul or less RNase-free water by passing the solution a few times through a pipette tip, and incubating for 10 minutes at 55 to 60°C.

value: primary lung cancer

tag: gender

value: Female

tag: histology

value: AD


title: patient05-N

source_name: adjacent lung tissues

value: adjacent lung tissues

value: NC


title: patient05-T


title: patient03-T


title: SOB3-D RNA-seq ZT4 replicate 1

description: RNA-seq for SOB3-D (AHL overexpressor) at ZT4 replicate 1


title: DU145_initial_rep3

description: Initial collection (reference point). EPIKOL-transduced DU145 cells were collected right after puromycin selection.


title: SOB3-GFP Input ZT24

description: Input control for SOB3-GFP ChIP ZT24

data_processing:
Generation of fastq files: Raw data files (bcl format) were converted to fastq files by bcl2fastq (Illumina).
Alignment: Reads were mapped to the Arabidopsis reference using Bowtie with the setting "-m 1".
Generation of bigwig files: Fold-enrichment bdg format files were generated by using the treatment pileup and control lambda output files generated from MACS2 "callpeak" as inputs for the MACS2 "bdgcmp" command with the setting "-m FE". The bdg files were converted to bigwig format using the "bedGraphToBigWig" program (UCSC).
Genome_build: TAIR10
Supplementary_files_format_and_content: Fold enrichment bigwig files (ChIP vs Input) with replicates from the same time point analyzed together; peak calls in BED format from MACS2 for each individual ChIP sample

extract_protocol:
Frozen samples were ground to a fine powder using an MB1200 Multi-beads Shocker (Yasui Kikai). Ground tissue was mixed with nuclei isolation buffer and formaldehyde added to 1% final concentration. Fixation was stopped after 10 minutes by addition of glycine. Solution was filtered through miracloth and then centrifuged to pellet nuclei.  Pellet with nuclei was resuspended in nuclei isolation buffer, added on top of nuclei separation buffer containing 1 M sucrose, and then centrifuged to separate nuclei from debris. Nuclei were resuspended in SDS lysis buffer and incubated with rotation in order to lyse nuclei.  Subsequently, chromatin was sonicated in a Covaris S2 Focused-ultrasonicator (Covaris) to an average size of approximately 100-300 bp.
Libraries were constructed from input or ChIPed DNA using the KAPA Hyper Prep Kit for Illumina (KAPA Biosystems) and Illumina compatible adaptors (New England Biolabs). Qubit dsDNA HS Assay Kit was used with the Qubit 2.0 Fluorometer (Invitrogen) for quantitation of DNA.

value: ProSOB3::SOB3-GFP sob3-4

tag: chip antibody


title: SOB3-GFP ChIP ZT24 replicate 1

description: ChIP-seq for SOB3-GFP ZT24 replicate 1

value: Anti-GFP antibody - ChIP Grade (ab290, Abcam)


title: SOB3-GFP ChIP ZT9 replicate 3

description: ChIP-seq for SOB3-GFP ZT9 replicate 3


title: SOB3-GFP ChIP ZT24 replicate 2

description: ChIP-seq for SOB3-GFP ZT24 replicate 2


title: DU145_initial_rep2


title: SOB3-GFP ChIP ZT24 replicate 3

description: ChIP-seq for SOB3-GFP ZT24 replicate 3


title: LNCaP_final_rep3

description: Last collection. EPIKOL-transduced LNCaP cells were collected after 15 doublings.

value: LNCaP


title: patient02-T


title: SOB3-GFP Input ZT9

description: Input control for SOB3-GFP ChIP ZT9


title: patient04-N


title: patient03-N


title: DU145_initial_rep1


title: patient02-N


title: SOB3-GFP ChIP ZT9 replicate 1

description: ChIP-seq for SOB3-GFP ZT9 replicate 1


title: SOB3-GFP ChIP ZT9 replicate 2

description: ChIP-seq for SOB3-GFP ZT9 replicate 2


title: SOB3-GFP Input ZT4

description: Input control for SOB3-GFP ChIP ZT4


title: LNCaP_final_rep2


title: SOB3-GFP ChIP ZT4 replicate 2

description: ChIP-seq for SOB3-GFP ZT4 replicate 2


title: LNCaP_final_rep1


title: SOB3-GFP ChIP ZT4 replicate 3

description: ChIP-seq for SOB3-GFP ZT4 replicate 3


title: SOB3-GFP ChIP ZT4 replicate 1

description: ChIP-seq for SOB3-GFP ZT4 replicate 1


title: Wildtype, Nano-TiO2 Exposure, Fetal – 1

city: Morgantown

first: Quincy

middle: Alexander

last: Hathaway

state: WV

address: 1 Medical Center Drive

institute: West Virginia University

description: The protocol used in our study was adapted from m6A-RIP protocols described in “Refined RIP-seq protocol for epitranscriptome analysis with low input materials” and “Landscape and Regulation of m6A and m6Am Methylome across Human and Mouse Tissues”, with modifications. In a 1.5 mL microcentrifuge tube (per sample), 30 µL of protein-A magnetic beads (item no. 10002D; Thermo Fisher Scientific) and 30 µL of protein-G magnetic beads (item no. 10004D; Thermo Fisher Scientific) were mixed, magnetic field applied, and supernatant removed. The mixture of beads was washed twice with 400 µL of IPP buffer (10 mM Tris-HCl, 150 mM NaCl, pH 7.5; 0.1% IGEPAL CA-630) and resuspended in 500 µL of IPP buffer. 5 µg of affinity purified anti-m6A polyclonal antibody (item no. ABE572-I; MilliporeSigma, Burlington, MA) was added to the beads and incubated overnight at 4°C. An additional tube with the mixture of beads received 5 µg of the normal rabbit IgG control antibody (item no. 2729; Cell Signaling Technology (CST), Danvers, MA) and was also incubated overnight at 4°C. The magnetic field was applied, and supernatant removed, followed by washing the antibody-bead mixture twice with IPP buffer. In a 1.5 mL microcentrifuge tube, a 500 µL mixture was prepared containing 100 µL of 5X IPP buffer, fragmented total RNA (diluted with nuclease-free water to a volume of 395 µL), and 5 µL of RNasin Plus RNase Inhibitor (item no. N2611; Promega, Madison, WI). The antibody-bead mixture was resuspended in the 500 µL mixture containing the fragmented RNA and incubated with orbital rotation at 4°C for 2 hours, followed by application of the magnetic field, removal of the supernatant, and two washes with 1,000 µL of IPP buffer. The bead-antibody-RNA mixture was then washed twice with 1,000 µL of low-salt IPP buffer (10 mM Tris-HCl, 50 mM NaCl, pH 7.5; 0.1% IGEPAL CA-630) and twice with 1,000 µL of high-salt IPP buffer (10 mM Tris-HCl, 500 mM NaCl, pH 7.5; 0.1% IGEPAL CA-630). A competitive elution buffer was then prepared containing 6.7 mM N6-methyladenosine 5’- monophosphate sodium salt (item no. M2780, Sigma-Aldrich) in IPP buffer. Each immunoprecipitation (IP) sample was resuspended in 100 µL of the m6A competitive elution buffer with continuous shaking at 4°C for 1 hour. The magnetic field was applied, which allowed us to collect the supernatant (eluted m6A RNA) into a new tube. The eluted RNA was further purified using the RNeasy MinElute Cleanup Kit (item no. 74204; Qiagen) following manufacturer’s protocol. The m6A enriched RNA was eluted by adding 14 µL of ultrapure H2O directly to the center of the membrane and centrifuging for 1.5 mins at full speed. Samples were stored at –80°C until initiation of the library preparation procedure.

data_processing:
Adapters were trimmed from Fastq files through Flexbar v3.5.
The trimmed Fastq files were processed using paired-end alignment with HISAT2 v2.2.1 and the resulting BAM files were aligned to the mouse reference genome (Mus musculus, GRCm39, Ensemble version 104) for input and IP samples.
Peaks showing significant enrichment in the IP samples vs. corresponding input samples for all submitted replicates were detected using RADAR v0.2.1, with a fragment length of 297 base pairs and bin size of 25 base pairs.
Peak reads coverage for transcripts were visualized with RADAR and the Integrative Genomics Viewer (IGV) browser.
Input mRNA samples were further processed for full decoy-aware transcriptomic analyses using Salmon v1.5.2 on the mouse reference genome (Mus musculus, GRCm39, Ensemble version 104) and processed in R using tximport v1.22.0. Differential gene expression was performed through DESeq2 v1.34.0
Assembly: GRCm39
Supplementary files format and content: Fastq to quantification file through Salmon (v1.5.2)
Supplementary files format and content: CSV format of normalized reads for Input samples

source_name: Heart

growth_protocol: Friend Virus B NIH Jackson (FVB/NJ) wild type mice (14 females, 7 males at 10 weeks) were purchased from Jackson Laboratory (Bar Harbor, ME). Animals were housed in the West Virginia University Health Sciences Center Animal Facility with access to a standard chow diet and water ad libitum. All animals were allowed a 48-hour acclimation period before being handled. Females were housed in groups of 4 per cage and introduced to male bedding three days prior to being introduced to the males for breeding.

extract_protocol:
Total RNA was extracted from pooled fetal heart samples (sham, n =3; nano-TiO2, n=3) using QIAzol lysis reagent (item no. 79306, Qiagen). Samples were homogenized in QIAzol using a rotor-stator homogenizer and further processed using the miRNeasy Mini Kit (item no. 217004, Qiagen) per manufacturer’s protocol. Concentrations were determined for each sample using the NanoDrop ND-100 (Thermo Fisher Scientific, Waltham, MA). Spike-in controls obtained from the EpiMark N6-Methyladenosine Enrichment Kit (item no. E1610S; NEB) were prepared following the manufacturer’s protocol. The fetal cardiac total RNA samples (3 µg) were fragmented into ~250-350-nucleotide fragments using the NEBNext Magnesium RNA Fragmentation kit (item no. E6150S; New England Biolabs (NEB), Ipswich, MA) at 65°C for 5 minutes. The Monarch RNA Cleanup Kit (item no T2030L; NEB) was performed per manufacturer’s protocol. Samples were eluted with 20 µL of nuclease-dree water and concentrations were determined using the NanoDrop ND-100 (Thermo Fisher Scientific). 2 µL of fragmented total RNA was saved from each sample to be used as input and the rest was used for m6A RNA immunoprecipitation followed by sequencing (m6A-RIP-seq).
Library preparation was performed on immunoprecipitated (IP) and total (input) RNA samples from sham (n = 3) and nano-TiO2 (n = 3) gestationally-exposed fetal offspring hearts using the NEB® Single Cell/Low Input RNA Library Prep kit for Illumina® (item no. E6420S, NEB) and Illumina® compatible NEB® UDIs (item no. E6440S, NEB), which mitigate sample misassignment due to index-hopped reads. The Agilent 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA) was employed to determine the size distribution of RNA. Libraries were PCR amplified for 10 cycles and NEB UDIs were used for indexing by amplifying for 8 cycles. The RNA sample concentrations were quantified using a Qubit Fluorometer (Thermo Fisher Scientific). The samples were sequenced using the Illumina NextSeq 2000 (Illumina Inc., San Diego, CA) at Marshall University as paired end (PE) 2x50 bp reads.

treatment_protocol: A high-pressure acoustical generator (HPAG; IEStechno, Morgantown, WV) was utilized for nano-TiO2 aerosolization as has been previously done for rodent inhalation exposure studies. Using a whole-body exposure chamber, a target aerosol mass concentration of 12 mg/m3 of engineered nano-TiO2 was implemented for a period of 360 minutes per day for 6 non-consecutive days, over an 8-day period.

value: Heart

tag: strain

value: FVB/NJ

value: WT

value: Nano-TiO2 Exposure

tag: antibody

tag: Sex

value: pooled male and female


title: Wildtype, Nano-TiO2 Exposure, Fetal – 3


title: patient01-N


title: Wildtype, Nano-TiO2 Exposure, Fetal – 2


title: Wildtype, Sham Exposure, Fetal – 3

value: Sham Exposure


title: LNCaP_initial_rep3

description: Initial collection (reference point). EPIKOL-transduced LNCaP cells were collected right after puromycin selection.

value: prostate carcinoma cells


title: P_Pa4

city: Qingdao

first: Bin

last: Zhang

state: Shandong

address: Yanerdao Road 5

institute: Shangdong Eye Institue

data_processing:
The raw paired-end reads were trimmed and quality controlled by Trimmomatic with the default parameters.
Clean reads were separately aligned to the reference genome in orientation mode using Rockhopper software.
To identify DEGs between the two samples, the expression level for each transcript was calculated using the fragments per kilobase of read per million mapped reads (RPKM) method.
DEG analysis of the P. aeruginosa isolates was performed using edgeR.
Supplementary files format and content: genes.rpkm.anno.xls contains the FPKM and annotation of each genes in all samples.
Supplementary files format and content: PP1b-2.fna was the  genome assembly sequence.

organism: Pseudomonas aeruginosa

source_name: infected corneas with P. aeruginosa keratitis

extract_protocol:
The bacterial collection was added with phenol  and shaken to be mixed. The centrifuge tube was incubated at 65℃ with an oscillating metal bath at maximum speed for 30–60 minutes, cooled on ice for 5 minutes, then centrifuged at 4℃ for 10 minutes. The upper water phage was absorbed and added with 1/2 volume of TRK-1002 lysate. The concentration and purity of RNA were measured using an Agilent 2100 bioanalyzer.An RNA integrity number (RIN) >7.0 can be used to construct a cDNA library
Ribosomal RNA were removed from the total RNA by using a Ribo-Zero Magnetic Kit , and then the library was generated using an Illumina Truseq RNA Sample Preparation Kit according to the manufacturer’s recommendation. After digested into 200 nt fragments, double-stranded cDNAs were synthesized using uracil-N-glycosylase (UNG) to a cDNA cluster. The cDNAs were used to create the RNA-seq library by following the standard Illumina protocol.

tag: source


title: P_Pa5

value: infected corneas with P. aeruginosa keratitis


title: Wildtype, Sham Exposure, Fetal – 2

tag: tissue


title: patient01-T


title: P_Pa3


title: P_Pa2


title: LNCaP_initial_rep2

tag: cell line


title: NP_Pa3

source_name: conjunctival sacs of healthy eyes

value: conjunctival sacs of healthy eyes


title: RWPE_final_rep3

description: Last collection. EPIKOL-transduced RWPE-1 cells were collected after 15 doublings.

source_name: prostate epithelial cells

value: RWPE

value: prostate epithelial cells


title: NP_Pa2


title: NP_Pa1


title: Anti-m6A Wildtype, Nano-TiO2 Exposure, Fetal – 3

data_processing:
Adapters were trimmed from Fastq files through Flexbar v3.5.
The trimmed Fastq files were processed using paired-end alignment with HISAT2 v2.2.1 and the resulting BAM files were aligned to the mouse reference genome (Mus musculus, GRCm39, Ensemble version 104) for input and IP samples.
Peaks showing significant enrichment in the IP samples vs. corresponding input samples for all submitted replicates were detected using RADAR v0.2.1, with a fragment length of 297 base pairs and bin size of 25 base pairs.
Peak reads coverage for transcripts were visualized with RADAR and the Integrative Genomics Viewer (IGV) browser.
Input mRNA samples were further processed for full decoy-aware transcriptomic analyses using Salmon v1.5.2 on the mouse reference genome (Mus musculus, GRCm39, Ensemble version 104) and processed in R using tximport v1.22.0. Differential gene expression was performed through DESeq2 v1.34.0
Assembly: GRCm39
Supplementary files format and content: CSV format of normalized, filtered, and adjusted reads for IP samples

tag: treatment

value: anti-m6A polyclonal antibody (item no. ABE572-I; MilliporeSigma, Burlington, MA)


title: Anti-m6A Wildtype, Nano-TiO2 Exposure, Fetal – 2


title: RWPE_final_rep2


title: Anti-m6A Wildtype, Nano-TiO2 Exposure, Fetal – 1


title: GHCN12_3

city: Pamplona

first: Marta

middle: Maria

last: Alonso Roldán

state: Navarra

address: CIMA building , Pio XII 55

department: Dpt of Pediatrics

country: Spain

institute: University Hospital of Navarra

data_processing:
The quality of the samples was verified using FastQC v0.11.8 software.
FASTQ files were mapped to GRCm38 mouse assembly using STAR v2.6.1c with default parameters.
featureCounts v1.6.0 software and Gencode M25 release were used to obtain read counts at gene level considering only those genes aligned to exonic regions
Obtained gene counts were normalized using edgeR and voom function of limma
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include gene counts obtained with featureCounts for each sample.

source_name: K7M2 tumor

growth_protocol: Orthotopic K7M2 osteosarcoma mouse model was used

extract_protocol:
14 days posttreatment TRIzol Reagent was used for the RNA extraction.
Illumina protocol using Illumina Stranded mRNA Prep

treatment_protocol: Seven days after orthotopic K7M2 cell implantation (0D),  we treated mice by intratumorally injection with SFV-Gal3-N-C12, SFV-Luc or PBS (mock group).

value: Osteosarcoma primary tumor


title: GHCN12_2


title: RWPE_initial_rep3

description: Initial collection (reference point). EPIKOL-transduced RWPE-1 cells were collected right after puromycin selection.


title: GHCN12_1


title: GHCLUC_5

value: SFV-Luc


title: GHCLUC_2


title: Anti-m6A Wildtype, Sham Exposure, Fetal – 3


title: Anti-m6A Wildtype, Sham Exposure, Fetal – 2


title: GHCPBS_5

value: PBS


title: GHCLUC_4


title: RWPE_initial_rep2


title: GHCPBS_4


title: Wildtype, Sham Exposure, Fetal – 1


title: RWPE_initial_rep1


title: LNCaP_initial_rep1


title: GHCPBS_3


title: Anti-m6A Wildtype, Sham Exposure, Fetal – 1


title: GHCPBS_2


title: GHCPBS_1


title: GHCN12_5


title: SUM149_final_rep3

description: Last collection. EPIKOL-transduced SUM149 cells were collected after 16 doublings.

source_name: Breast ductal carcinoma cells

value: Breast ductal carcinoma cells


title: Microglia-CPEB1-KO-LPS-rep3

city: Worcester

first: Mariya

last: Ivshina

address: 373 Plantation st

institute: Umass Medical School

data_processing:
Sequenced reads were trimmed for adaptor and low quality sequences using cutadapt
Clean reads were then mapped to mm10 genome using RSEM
Quantification was done to calculate TPM and Counts using RSEM
Genome_build: mm10
Supplementary_files_format_and_content: read count, TPM values

source_name: microglia

extract_protocol:
Microglia were isolated  by Percoll gradients from WT or CEB1 KO mice, some of which were injected with LPS (4 variables, 3 replicates, 1 animal per replicate). Total RNA was extracted and polyA based libraries were constructed and sequenced by Novagen.
Standard polyA - based libraries were constructed by Novagen

value: microglia

tag: genotype/treatment

value: 3-4 months


title: RWPE_final_rep1


title: SUM149_final_rep2


title: Microbiota of stool from patient PST1 [FS80]

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

institute: University of Florence

description: 16s rRNA v3-v4 sequencing of human stool

data_processing:
demultiplexing: from raw to demultiplexed fastq files please contact IGA Technology Services (Udine, Italy)
primer check and trimming: qiime cutadapt trim-paired  --i-demultiplexed-sequences demux-paired-end.qza --p-adapter-f  CCTACGGGNGGCWGCAG   --p-adapter-r  GACTACNVGGGTWTCTAATCC  –o-trimmed-sequences trimmed-seqs.qza --p-discard-untrimmed --verbose
quality check: qiime demux summarize  --i-data trimmed-seqs.qza --o-visualization demux.qzv --p-n 500000
quality trimming, pair merging and ASV table creation: qiime dada2 denoise-paired --i-demultiplexed-seqs trimmed-seqs.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 244 --p-trunc-len-r 198 --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising-stats.qza --p-n-threads 8
taxonomic assignment (RDP): qiime feature-classifier classify-consensus-vsearch --i-query rep-seqs.qza --i-reference-reads silva-138-99-seqs.qza --i-reference-taxonomy silva-138-99-tax.qza --p-perc-identity 0.99 --p-threads 8 --o-classification taxonomy_vsearch.qza –verbose
further analyses: R phyloseq package (see https://github.com/matteoramazzotti/papers)
Supplementary files format and content: feature_table.csv: CSV text file containing the abundance table
Supplementary files format and content: taxonomy.tsv: TSV text file containing the complete taxonomic classification of the reference sequence
Supplementary files format and content: dna-sequences.fasta: fasta file containing the reference sequences used for taxonomy classification
Library strategy: paired-end (2x300) amplicon sequencing

organism: human feces metagenome

source_name: Stool

extract_protocol:
Genomic DNA was extracted using the DNeasy PowerSoil Pro Kit (Qiagen, Hilden, Germany)
Illumina 16S Metagenomic Sequencing Library Preparation protocol ( see https://emea.support.illumina.com)

value: Stool

tag: patient id

tag: timepoint

value: Pre-EVO

tag: diet

value: EVO


title: Microglia-CPEB1-KO-LPS-rep2


title: Microbiota of stool from patient PST8 [FS8]

value: Pre-ANG

value: ANG


title: Microglia-CPEB1-KO-LPS-rep1


title: Microglia-CPEB1-KO-rep3


title: SUM149_final_rep1


title: Microbiota of stool from patient PST20 [FS73]

value: Post-ANG


title: Microbiota of stool from patient PST19 [FS72]


title: Microglia-CPEB1-KO-rep1


title: SUM149_initial_rep3

description: Initial collection (reference point). EPIKOL-transduced SUM149 cells were collected right after puromycin selection.


title: Microbiota of stool from patient PST18 [FS71]

value: Post-EVO


title: Microbiota of stool from patient PST9 [FS9]


title: Microglia-WT-LPS-rep3

value: WT-LPS


title: Microbiota of stool from patient PST17 [FS70]


title: Microglia-WT-rep2

value: WT


title: Microglia-WT-rep3


title: SUM149_initial_rep1


title: SUM159_final_rep3

description: Last collection. EPIKOL-transduced SUM159 cells were collected after 16 doublings.

source_name: breast carcinoma cells

value: breast carcinoma cells


title: Microbiota of stool from patient PST7 [FS7]


title: Microglia-WT-rep1


title: SUM159_final_rep2


title: Rag1-1

city: St Louis

last: Gutmann

state: MO

address: 660 S Euclid Ave

department: Neurology

institute: Washington University in St Louis

description: Rag1_ 1 run_2947_s_5_withindex_sequence.txt_ACGCGGG

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 aligned to the Ensembl release 99 primary assembly with STAR version 2.5.3a
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file containing CPM normalized gene counts for each sample

extract_protocol:
Total RNA was extracted from snap-frozen brainstem tissue of three independent mice for each of the genotypes using QIAGEN RNeasy Mini Kit according to manufacturer’s instructions.
Samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina HiSeq by the Washington University GTAC core

tag: genotype/variation

tag: tissue/cell type

value: brainstem cells


title: Rag1-2

description: Rag1_2_run_2947_s_5_withindex_sequence.txt_CGCTACA


title: WT3

description: C57_3_run_2947_s_5_withindex_sequence.txt_GGAGTCC

value: wild type


title: WT2

description: C57_2_run_2947_s_5_withindex_sequence.txt_CCATCAT


title: SUM159_final_rep1


title: Microbiota of stool from patient PST13 [FS68]


title: WT1

description: C57_1_run_2947_s_5_withindex_sequence.txt_TGACTCT


title: Microglia-CPEB1-KO-rep2

tag: age


title: SUM149_initial_rep2


title: Microglia-WT-LPS-rep2


title: Microbiota of stool from patient PST12 [FS67]


title: Microglia-WT-LPS-rep1


title: SUM159_initial_rep2

description: Initial collection (reference point). EPIKOL-transduced SUM159 cells were collected right after puromycin selection.


title: SUM159_initial_rep3


title: Rag1-3

description: Rag1_3_run_2947_s_5_withindex_sequence.txt_ATGTTCT


title: Microbiota of stool from patient PST10 [FS65]


title: Microbiota of stool from patient PST11 [FS66]


title: SUM159_initial_rep1


title: MDA-MB-231_final_rep3

description: Last collection. EPIKOL-transduced MDA-MB-231 cells were collected after 16 doublings.

source_name: breast adenocarcinoma cells

value: breast adenocarcinoma cells


title: Microbiota of stool from patient PST9 [FS64]


title: Microbiota of stool from patient PST16 [FS69]


title: Microbiota of stool from patient PST8 [FS63]


title: CTN_20μM_rep3

city: Taipei

first: Jui-Feng

last: Tsai

address: No. 1, Sec. 1, Ren'Ai Rd,

department: Graduate Institute of Toxicology

country: Taiwan

institute: National Taiwan University

data_processing:
Fastqc for reads quality check
Cutadapt for adaptor trimming
STAR for alignment to human reference genome
RSeQC for post-alignment quality control
edgeR for normalization to CPM
Assembly: Homo sapiens GRCh38.105
Supplementary files format and content: Tab-delimited TXT file containing raw read counts of each gene for each sample

extract_protocol:
RNA extraction was performed with TRIzol reagent according to manufacturer’s instruction (Invitrogen, Waltham, MA). RNA quality assessment  was performed by Azenta Life Sciences, Inc. (Chelmsford, MA) according to manufacturers’ protocol.
cDNA library construction was performed by Azenta Life Sciences, Inc. (Chelmsford, MA) according to manufacturers’ protocol.

treatment_protocol: Human neuroblastoma cells SH-SY5Y were treated with 0, 10, or 20 μM CTN for 72 h in MEM/F12 medium containing 15% FBS.

tag: cell type

value: Neuroblastoma

value: CTN 20 μM

tag: time


title: Microbiota of stool from patient PST7 [FS62]


title: CTN_20μM_rep1


title: CTN_10μM_rep3

value: CTN 10 μM


title: Microbiota of stool from patient PST6 [FS61]


title: MDA-MB-231_final_rep1


title: MDA-MB-231_initial_rep3

description: Initial collection (reference point). EPIKOL-transduced MDA-MB-231 cells were collected right after puromycin selection.


title: CTN_10μM_rep2


title: melanoma tumor (mouse under HFD diet)_HFD diet2

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

institute: INSERM

hyb_protocol: After purification according to Thermofisher protocol, 5.5 ug of Sens Target DNA are fragmented and biotin labelled. After control of fragmentation using Bioanalyzer 2100, cDNA is then hybridized to GeneChip® MouseGene 2.0ST (Affymetrix) at 45°C for 17 hours.

scan_protocol: After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G

data_processing: The scanned images are then analyzed with Expression Console software (Thermofischer) to obtain raw data (cel files) and metrics for Quality Controls. The observations of some of these metrics and the study of the distribution of raw data show no outlier experiment.  RMA normalization is performed using R with CDF v21 of EntrezGene (Brain Array).

label_protocol: 100 ng of total RNA is reverse transcribed following the GeneChip® WT Plus Reagent Kit (Thermofisher). Briefly, the resulting double strand cDNA is used for in vitro transcription with T7 RNA polymerase (all these steps are included in the WT cDNA synthesis and amplification kit of Thermofisher).

growth_protocol: The melanoma B16F10 cells  (ATCC CRL6475) were cultured in RPMI supplemented with 10% fetal bovine serum (FBS), 2 mM glutamine, 50 U/ml penicillin and 100μg/ml streptomycin.

extract_protocol: Tumors were harvested, minced, lysed with 350ul RLT buffer containing 1% β-mercaptoethanol  and homogenize by using a seringue and a needle ( 10 times). Then RNA were extracted with RNAeasy microkit (Qiagen) according to manufactor's instructions. Total RNA were measured on Nanodrop and store at -80 until analysis.

treatment_protocol: Tumor cells ( 0.25x10^6 ) were  injected subcutaneously (s.c) in the abdominal flank of  mice fed with CD or HFHCD  and harvested at day 9 post tumor graft.

value: melanoma tumor


title: melanoma tumor (mouse under CD diet)_ctl2


title: melanoma tumor (mouse under HFD diet)_HFD diet4


title: melanoma tumor (mouse under CD diet)_ctl3


title: melanoma tumor (mouse under HFD diet)_HFD diet3


title: CTN_10μM_rep1


title: MDA-MB-231_initial_rep2


title: Microbiota of stool from patient PST5 [FS60]

value: Stool


title: melanoma tumor (mouse under CD diet)_ctl4


title: melanoma tumor (mouse under HFD diet)_HFD diet1


title: CTN_0μM_rep3

value: CTN 0 μM


title: MDA-MB-231_initial_rep1


title: MDA-MB-231_final_rep2


title: Microbiota of stool from patient PST6 [FS6]


title: CTN_0μM_rep1


title: HMLE_final_rep3

description: Last collection. EPIKOL-transduced HMLE cells were collected after 16 doublings.

source_name: mammary epithelium cells

value: HMLE

value: mammary epithelium cells


title: Microbiota of stool from patient PST4 [FS59]

value: EVO


title: melanoma tumor (mouse under CD diet)_ctl1


title: CTN_20μM_rep2


title: Microbiota of stool from patient PST3 [FS58]


title: Microbiota of stool from patient PST1 [FS56]


title: normal-1

city: Chengdu

first: Hao

last: Xu

state: China

address: No.17 section3 renmin south road, chengdu

institute: Sichuan university

description: 10x Genomics

data_processing:
The FASTQ files were analyzed with the Cell Ranger Software Suite (version 3.1; 10× Genomics).
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell.

source_name: buccal mucosa

extract_protocol:
Six tissue samples (normal = 1, NEOLP = 3, EOLP = 2) were washed by D-PBS twice and cut into fragments with a diameter of about 1-2mm, Infiltrating in the mixture of Whole Skin Dissociation Kit human (Miltenyi). The mixture was digested in water bath at 37 ℃ for 2.5 hours and dissociated by gentleMACSTM Octo Dissociator for 15 seconds every 0.5-1hours. Next, the mixture was filtered by 70 μm MACS Smartstrainers (Miltenyi), added 1ml DMEM to terminate digestion, and 4 ℃ centrifuged at 400rcf for 15 minutes. The cell precipitates were again subjected to lysis of red blood cells by Red Blood Cell Lysis Buffer (Abcam) and removal of dead cells by Easysep Dead Cell Removal (Annexin V) Kit (STEMCELL). Finally, single cell suspension was resuspended by D-PBS and counted through trypan blue.
The method of library establishment was as previous described (Xu et al., 2020). In brief, the single cell suspension was combined with barcoded beads to produce single-cell Gel Beads-in-Emulsion (GEMs) on the 10×Genomics platform. GEMs were dissolved, cells were lysed to release mRNA, and cDNAs were amplified. Library was constructed by the 10× Genomics Chromium Single Cell Kit (v3 chemistry) and sequenced on an Illumina NovaSeq 6000 System.

value: buccal mucosa


title: Microbiota of stool from patient PST2 [FS57]

value: Post-ANG

value: ANG


title: EOLP-1

description: 10x Genomics


title: NEOLP-2

description: 10x Genomics


title: NEOLP-1

description: 10x Genomics


title: NEOLP-3

description: 10x Genomics


title: EOLP-2

description: 10x Genomics


title: HMLE_final_rep1


title: HMLE_initial_rep3

description: Initial collection (reference point). EPIKOL-transduced HMLE cells were collected right after puromycin selection.


title: HMLE_initial_rep2


title: Microbiota of stool from patient PST20 [FS55]

value: Pre-ANG


title: CTN_0μM_rep2


title: K562 DHX34-2

data_processing:
pseudoalignment using Salmon
differential expression calling using Sleuth
splicing event calling using SUPPA2
Assembly: GRCh38.93
Supplementary files format and content: DHX34_sleuth.csv
Supplementary files format and content: DHX34_suppa2.csv
Supplementary files format and content: UPF1_sleuth.csv
Supplementary files format and content: UPF1_suppa2.csv

growth_protocol: standard culture conditions , RPMI, 10% FCS, 1% Pen/Strep

extract_protocol: mRNA library preparation (poly A enrichment) Library construction and sequencing was done by  Novogene

value: immortalised myelogenous leukemia cell line


title: HMLE_initial_rep1