title: mAktKO 2

city: Bunkyo-ku

first: Hiroshi

last: Asahara

state: Tokyo

address: 1-5-45 Yushima

department: Department of Systems BioMedicine

institute: Institute of Science Tokyo

data_processing:
bcl2fastq was used for basecall
Sequenced reads were  mapped to mouse genome (mm10) using STAR v2.6.1b  with default parameters
Raw gene counts were caliculated with RSEM v1.3.1
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Extensor digitorum longus

extract_protocol:
Extensor digitorum longus was removed and frozen in liquid nitrogen, and RNA was harvested using RNeasy Mini Kit after incubation with Proteinase K with 1 ug of total RNA for the construction of sequencing libraries.
Libraries were prepared by NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760) according to manufacturer's instruction

tag: genotype/variation

tag: age

value: 50 weeks old


title: GFP-TRIM66-replicate1

status: Public on Jun 02 2022

type: SRA

city: Beijing

first: Zuo

last: Feifei

address: Zhongguancun Street, Haidian District

country: China

institute: Tsinghua University

library_source: transcriptomic

data_processing:
For ChIP-seq analysis, the data were trimmed using TrimGalore and then aligned to mm10 using Bowtie2.We chose MACS2 to call the peaks using the ‘‘broad peaks’’ setting for GFP-Trim66, GFP-Dax1, H3K9me3 and H3K18ac. GFP-Dax1 ChIP-seq peaks that were significantly increased in the presence of Trim66 were then identified using the DiffBind package in R. We subsequently generated bigwig files from the bam files using the Coverage function in deepTools.
RNA-seq data were mapped to the mouse reference genome (mm10) using HISAT2 (version 2.1.0) and removed duplicates using PicardTools. The levels of gene expression were calculated by Cufflinks (version 2.2.1) based on mm10 annotations. Differential testing and log2 fold change calculations were performed using TEanalysis (version 4.6), with the implementation of two biological replicates. Volcano plots were generated by ggplot2 showing the log transformed p values in the y-axis and the log2 fold-change in the x-axis.
Genome_build: mm10
Supplementary_files_format_and_content: We subsequently generated bigwig files from the bam files using the Coverage function in deepTools. For visualization purposes, we normalized the data to 1X genome coverage (mm10), ignoring PCR duplicates. Representative track diagrams were generated using the Integrated Genomics Viewer software

molecule: total RNA

organism: Mus musculus

source_name: mouse embryonic stem cell

growth_protocol: mESCs were cultured on gelatin coated plates with 15% serum ESC culture medium and then Cells were harvested for ChIP or RNA extraction.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with GFP-trapped beads or antibody. Total RNA was extracted by commerical RNA extraction Kit.
DNA and RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: ESCs

tag: strain

tag: genotype

value: TRIM66 overexpression

tag: treatment

value: untreated

tag: chip antibody


title: flox 3

country: Japan


title: GFP-EV-replicate2

value: GFP overexpression


title: flox 2


title: G555-24

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

country: USA

institute: Penn State University

data_processing:
Bcl converion and demultiplexing using Illumina bcl2fastq (released version 2.18.0.12) allowing no mismatches in the index read. Adapter masked fastq files were generated.
Quality filter by FASTQC 0.11.6
Read alignment using RNA STAR (Galaxy version 2.5.2b-0). BAM files were generated.
Reads were counted using HTSeq-Count set to union mode with a minimum alignment quality of 10 (Galaxy version 0.6.1galaxy3).
Genome_build: hg19
Supplementary_files_format_and_content: xlsx file of raw read counts

molecule: polyA RNA

organism: Homo sapiens

source_name: ileum tissue

extract_protocol:
Surgical specimens were transferred immediately from the operating room to the surgical pathology lab where a section of full-thickness ileum was obtained from a site of active inflammation and stored in RNAlater. RNA was extracted from tissue samples using trizol reagent followed by purification with the Qiagen RNeasy Mini Kit.
The cDNA libraries were prepared using the TruSeq® Stranded mRNA Library Prep Kit (Illumina) as per the manufacturer’s instructions. Briefly, polyA RNA was purified from 200 ng of total RNA using oligo (dT) beads. The extracted mRNA fraction was subjected to fragmentation, reverse transcription, end repair, 3’– end adenylation, and adaptor ligation, followed by PCR amplification and SPRI bead purification (Beckman Coulter). The unique dual index sequences (NEXTFLEX® Unique Dual Index Barcodes, BioO Scientific) were incorporated in the adaptors for multiplexed high-throughput sequencing. The final product was assessed for its size distribution and concentration using Bio Analyzer High Sensitivity DNA Kit (Agilent Technologies). The libraries were pooled and diluted to 3 nM using 10 mM Tris-HCl, pH 8.5 and then denatured using the Illumina protocol. The denatured libraries were loaded onto an S1 flow cell on an Illumina NovaSeq 6000 (Illumina) and run for 2X50 cycles according to the manufacturer's instructions.

tag: disease

value: CD

tag: tissue

value: ileum

tag: Sex

value: Female

tag: smoking history

value: Never Smoked

tag: age at diagnosis

tag: age at surgery

tag: bmi


title: G555-25


title: GFP-EV-replicate1


title: G555-22

value: Male

value: Ex-smoker


title: mAktKO 1


title: flox 1


title: H1_GABA_IgG_Rep1

city: New York

first: Matthew

middle: A

last: Lalli

state: NY

address: 1 Gustave L. Levy Pl

department: Psychiatry

institute: Icahn School of Medicine at Mount Sinai

description: DNA released from nuclei

library_source: genomic

data_processing:
Library strategy: CUT&RUN
Illumina adapters were trimmed from reads using trimmomatic:  trimmomatic PE -threads 8 -phred33 R1_001.fastq.gz R2_001.fastq.gz ILLUMINACLIP:$adapterpath/TruSeqAdapters.fa:2:15:4:4:true LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:25
Trimmed reads were mapped to the human genome (hg38) using bowtie2:  bowtie2 -p 8 --dovetail --phred33 --local --very-sensitive-local --no-unal --no-mixed --no-discordant -I 10 -X 700 -x $bt2idx/GRCh38_noalt_as
Aligned reads were sorted and indexed using samtools
Bigwig files were gneerated for visualizing sample using bamCoverage:  bamCoverage -b  aligned_sorted.bam -o aligned.bigwig -p 4 --normalizeUsing RPKM --extendReads 160
Broad peaks were called using MACS2:  macs2 callpeak -t sorted_sample.bam -c sorted_control.bam-f BAMPE -g hs --nomodel --keep-dup all --broad
Genome_build: hg38 (GRCh38_noalt_as)
Supplementary_files_format_and_content: Bigwig files (.bigwig) can be used to visualize each sample on a gennome browser
Supplementary_files_format_and_content: Peak files (.broadPeak) contain the called peaks from MACS2

molecule: genomic DNA

source_name: WA01 (H1 ES)

extract_protocol:
CUT&RUN was performed as previously described. Nuclei (50,000) were extracted from neurons using NE1 buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 0.5 805 mM Spermidine, 0.1% Triton X-100, 20% Glycerol and Roche Complete Protease Inhibitor EDTA-Free and used as the input source. Nuclei bound to Concanavalin-coated magnetic beads (Bangs Laboratories BP531) were incubated with the relevant antibody: H3K27ac (Abcam AB4729), FOS (Abcam AB208942), rabbit IgG (Abcam AB46540) or guinea pig IgG (Novus NBP1-2763). The next day, the beads were placed on a magnet to remove supernatant, washed, and incubated with Protein AG-MNase. To fragment the DNA, samples were first chilled to 0º C, the digestion was then activated by the addition of 2 mM of CaCl2. Reactions were stopped by 2×Stop buffer (340mM NaCl, 20mM EDTA, 4mM EGTA (Alfa Aesar J60767), 0.05% Digitonin, 100ug/mL RNAse A (Thermo Fisher Scientific EN0531), 50ug/mL Glycogen).
DNA fragments released from the nuclei were purified by extraction with phenol-chloroform and ethanol precipitated. DNA was quantified with a fluorescence-based method using Qubit 4 Fluorometer dsDNA HS assay. CUT&RUN DNA (10ng) was processed using NEBNext Ultra II DNA Library Prep Kit (New England Biolabs 816 E7645) for library preparation according to manufacturer’s instructions. Briefly, purified DNA was repaired, ligated with 1.5μM NEBNext Adaptors and amplified for 14 cycles by PCR. DNA was enriched for fragments of size 150-350bp for transcription factor and 150-800 bp for histone markers using Ampure XP beads. Final libraries were quantified with Qubit dsDNA HS assay and the size distribution was determined by Agilent 4200 TapeStation. Libraries were mixed at an equal ratio to achieve a final concentration as recommended by the manufacturer and sequenced on an Illumina HiSeq 4000 system.

treatment_protocol: Prior to depolarization, medium was replaced with serum free Neurobasal A/B27/Glutamax for 3 days. The neuronal culture was then silenced using 1μM of Tetrodotoxin citrate (TTX) (Labome 1069/1) and 100μM of DL-2-amino-5-phosphopentnoic acid (DL-AP5) (Abcam ab120271) for 12-16h. The neurons were then depolarized by adding depolarization buffer (170 mM KCl, 2 mM CaCl2, 1 mM MgCl and 10 mM HEPES directly into the media to a final concentration of 30% of the total culture media. Neurons were collected at different time points after depolarization for experiments.

value: induced GABAergic neurons

value: depolarization

tag: timepoint (minutes)


title: Trim66-KO-2-replicate2

value: Trim66 Knockout


title: Trim66-KO-2-replicate1


title: H1_GABA_H3K27ac_t90_Rep1

description: DNA released from nuclei


title: G555-19


title: H1_GABA_H3K27ac_t30_Rep2

description: DNA released from nuclei


title: H1_GABA_H3K27ac_t30_Rep1

description: DNA released from nuclei


title: Plg-KO-3

city: Bethesda

first: Niki

last: Moutsopoulos

address: 30 convent Dr

institute: NIDCR

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sequenced reads were mapped to GRCm38.p3 mouse genome using STAR v2.5.2a in  single-pass mode. With the following parameters:  --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField None --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterMatchNminOverLread 0.25 --outFilterScoreMinOverLread 0.25 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000  --outSAMtype BAM SortedByCoordinate --bamRemoveDuplicatesType UniqueIdentical --quantMode GeneCounts
Gene counts were generated with STAR v2.5.2a built-in counting option --quantMode GeneCounts against a customized Gencode GRCm38 vM11 genome annotation GTF which included ERCCs.
A expression matrix was assembled using R. Genes with less than 5 reads in at least one of the samples were filtered out before differential gene expression analysis.
Differential expression was performed using the DESeq2, EdgeR and Limma-Voom R packages.
Genome_build: Custom mm10/GRCm38.vM11+ERCCs
Supplementary_files_format_and_content: Tab delimited files include a raw counts and TMM-normalized expression matrices.

source_name: Gingiva

extract_protocol:
Gingiva was removed from 12-weeks old mice and processed into total RNA.
Sequencing libraries were prepared by the Illumina Nextera XT method following manufacturer’s recommendations (Illumina, San Diego, CA). The multiplexed libraries were sequenced in a NextSeq500 instrument in 37bp paired end mode.

value: 12 weeks

value: oral mucosa

value: Plg KO


title: H1_GABA_H3K27ac_t0_Rep2

description: DNA released from nuclei


title: G555-23


title: Plg-KO-2


title: mAktKO 3

value: 50 weeks old


title: Trim66-KO-1-replicate2

value: ESCs


title: G555-17


title: G555-18


title: Trim66-KO-1-replicate1


title: Plg-KO-1


title: G555-16


title: G555-15


title: Trim66-WT-replicate2

value: WT


title: H1_GABA_H3K27ac_t0_Rep1

description: DNA released from nuclei


title: Trim66-WT-replicate1

value: untreated


title: Plg-WT-3

value: Plg WT


title: Plg-WT-1


title: H3K18ac_WT-ChIP

value: H3K18ac (Abcam ab1191)


title: T114

type: RNA

city: Oxford

middle: J

last: Bottomley

state: Oxfordshire

address: Old Road Campus

department: Nuffield Department of Medicine

country: United Kingdom

institute: University of Oxford

hyb_protocol: 25ng total RNA was hybridised to fluorescent barcode labelled probes from the nCounter Myeloid Innate Immunity v2 panel, as per manufacturer's instructions

scan_protocol: Data was acquired on a Nanostring nCounter Sprint platform

data_processing: Normalization was performed using the ROSALIND platform and calculated using criteria provided by Nanostring, following the nCounter Advanced Analysis protocol of dividing counts within a lane by the geometric mean of the normalizer probes from the same lane. Housekeeping probes to be used for normalization were selected based on the geNorm algorithm as implemented in the NormqPCR R library

label: not provided

source_name: Enriched monocytes, peripheral blood

label_protocol: manufacturer's protocol

growth_protocol: Monocytes from transplant recipients with high and low mHLA-DRd, matched by prednisolone use and age, were enrichment from peripheral blood mononuclear cells using magnetic beads (EasySep Human Monocyte Enrichment Kit without CD16 depletion) according to manufacturer's instructions

extract_protocol: Total RNA was extracted by column-based isolation, using the Qiagen RNEasy Micro Kit, according to manufacturer's instructions

tag: prednisolone use at sampling

value: No

tag: enrichment purity

tag: monocytic hla-dr density (ab/cell)

tag: induction therapy at time of transplant

tag: immunosuppression duration (months)


title: T098

value: Female

value: Yes

tag: age


title: H3K18ac_Trim66-KO-ChIP

tag: cell type

tag: strain

tag: genotype


title: G555-14

tag: disease

value: CD

value: ileum

value: Never Smoked


title: T078


title: G555-11

tag: tissue

value: Ex-smoker


title: genomic DNA from skull base chordomas 18

type: genomic

first: Xulei

last: Huo

address: Beijing

institute: Beijing tiantan hospital

description: tumor sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

label: Cy5 and Cy3

source_name: skull base chordomas 18

label_protocol: Standard Illumina Protocol

growth_protocol: Not applicable

extract_protocol: genomic DNA was extracted and purified from chordoma samples according to standard instructions

treatment_protocol: Not applicable

tag: Sex

value: male

value: chordoma

tag: disease state

value: tumor


title: genomic DNA from skull base chordomas 19

description: tumor sample

source_name: skull base chordomas 19


title: T129

value: Male

value: Basiliximab


title: genomic DNA from skull base chordomas 17

description: tumor sample

source_name: skull base chordomas 17


title: T066


title: Plg-WT-2

value: 12 weeks

value: oral mucosa


title: G555-10

tag: smoking history

value: Current Smoker

tag: age at diagnosis


title: H3K9me3_WT-ChIP

value: ESCs

value: WT

tag: treatment

value: untreated

tag: chip antibody

value: H3K9me3 (Active motif 61063)


title: T040

tag: prednisolone use at sampling

value: No


title: T045

value: Yes

tag: enrichment purity


title: GFP-TRIM66-PB-del-ChIP

value: TRIM66-PB-del overexpression


title: G555-08

value: CD

value: ileum

tag: age at surgery

tag: bmi


title: G555-05

value: Female


title: genomic DNA from skull base chordomas 11

description: tumor sample

source_name: skull base chordomas 11

value: male

value: chordoma


title: H3K9me3_Trim66-KO-ChIP

value: Trim66 Knockout


title: genomic DNA from skull base chordomas 13

description: tumor sample

source_name: skull base chordomas 13

value: tumor


title: T029

value: Male

tag: monocytic hla-dr density (ab/cell)

tag: induction therapy at time of transplant

value: Basiliximab

tag: immunosuppression duration (months)


title: INPUT-ChIP

tag: cell type

tag: strain

value: TRIM66 overexpression


title: G555-07

tag: disease

value: Never Smoked


title: GFP-TRIM66-ChIP

value: ESCs

tag: genotype


title: T021

tag: Sex

tag: age


title: G555-04

tag: tissue

tag: smoking history

value: Current Smoker


title: genomic DNA from skull base chordomas 8

description: tumor sample

source_name: skull base chordomas 8

tag: disease state


title: genomic DNA from skull base chordomas 16

description: tumor sample

source_name: skull base chordomas 16


title: T019


title: G555-03

tag: age at diagnosis


title: GFP-DAX1-ChIP

value: Dax1 overexpression

tag: treatment

value: untreated

tag: chip antibody


title: G555-02

tag: age at surgery


title: G555-01

tag: bmi


title: T017

tag: prednisolone use at sampling

value: No

tag: enrichment purity

tag: monocytic hla-dr density (ab/cell)


title: T003

tag: induction therapy at time of transplant

tag: immunosuppression duration (months)


title: genomic DNA from skull base chordomas 3

description: tumor sample

source_name: skull base chordomas 3

tag: disease


title: genomic DNA from skull base chordomas 4

description: tumor sample

source_name: skull base chordomas 4


title: GFP-DAX1-ChIP_TRIM66 OE

tag: cell type

tag: strain

tag: genotype

value: Dax1-TRIM66 double overexpression


title: genomic DNA from skull base chordomas 7

description: tumor sample

source_name: skull base chordomas 7

tag: Sex


title: BMDM_AS1_plasma_48h_Replicate3

status: Public on Jun 01 2022

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

country: Germany

institute: University Heidelberg

description: Day 6 after isolation, after 48h treatment with 10% Plasma (see: characteristics) instead of FCS

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of human Mogene-2_0-type from Affymetrix. A Custom CDF Version 22 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

label: biotin

source_name: Bone marrow derived macrophages

label_protocol: Biotinylated cRNA samples were prepared according to the standard Affymetrix protocol.

growth_protocol: Cells were cultured in DMEM containing 10% FCS; 0,5% Penicillin; 0,5% Streptavidin and MCSF 30 ng/ml (Peprotech; cat. no. 315-02).

extract_protocol: The RNA isolation was performed with microRNA Isolation kit II according to the manufacturer’s instructions (Bioline; cat. no. Bio-52075).

treatment_protocol: After 4 days of culturing in DMEM containing 10% FCS; 0,5% Penicillin; 0,5% Streptavidin and MCSF 30 ng/ml (Peprotech; cat. no. 315-02), the initial medium was replaced with DMEM containing 10% plasma of Wildtype (WT), ApoE-KO (ApoE), ApoE-Stab1-KO (AS1) and ApoE-Stab2-KO (AS2) mice after 8 weeks of Western Diet treatment. The RNA was isolated 48 hours after cultivation with the corresponding plasma.

value: ApoE-Stab1-KO C57BL/6J

value: Bone marrow derived macrophages


title: BMDM_ApoE_plasma_48h_Replicate3

value: ApoE-KO C57BL/6J


title: BMDM_ApoE_plasma_48h_Replicate4


title: BMDM_WT_plasma_48h_Replicate4

value: Wildtype C57BL/6J


title: BMDM_WT_plasma_48h_Replicate1


title: BMDM_AS2_plasma_48h_Replicate4

value: ApoE-Stab2-KO C57BL/6J


title: BMDM_AS2_plasma_48h_Replicate3


title: BMDM_WT_plasma_48h_Replicate3


title: BMDM_ApoE_plasma_48h_Replicate5


title: BMDM_WT_plasma_48h_Replicate2


title: BMDM_AS2_plasma_48h_Replicate2


title: BMDM_AS2_plasma_48h_Replicate5


title: MAOEC_WT_plasma_48h_Replicate6

description: Grown to confluency, subsequently harvested after 48h treatment with 10% Plasma (see: characteristics) instead of FCS

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Primary mouse aorta endothelial cells (MAOEC) (Pelo Biotech; cat. no. C57-6052) were grown to confluence in 6-well plates supplied with Endothelial Cell Medium (Pelo Biotech) containing 10% FCS.

treatment_protocol: At confluency, the Endothelial Cell Medium was supplemented with 10% plasma of ApoE-KO, ApoE-Stab1-KO and ApoE-Stab2-KO mice after 8 weeks of Western Diet treatment instead of FCS. After 48 hours of incubation, the RNA of the MAOEC was isolated.

value: Wildtype


title: BMDM_AS1_plasma_48h_Replicate1


title: MAOEC_WT_plasma_48h_Replicate5

source_name: Primary mouse aorta endothelial cells (MAOEC)


title: BMDM_AS1_plasma_48h_Replicate2


title: BMDM_AS2_plasma_48h_Replicate1


title: MAOEC_WT_plasma_48h_Replicate4


title: MAOEC_WT_plasma_48h_Replicate3


title: MAOEC_WT_plasma_48h_Replicate2


title: genomic DNA from skull base chordomas 10

description: tumor sample

source_name: skull base chordomas 10

value: male

value: chordoma

value: tumor


title: MAOEC_AS2_plasma_48h_Replicate5


title: genomic DNA from skull base chordomas 6

description: tumor sample

source_name: skull base chordomas 6


title: MAOEC_WT_plasma_48h_Replicate1


title: MAOEC_AS2_plasma_48h_Replicate2


title: ZMYND11-MBTD1 fusion 3xFlag-2xstrep in ZMYND11 KO-clone #2

city: Quebec City

first: Samer

last: Hussein

state: Quebec

address: 9 rue Mcmahon

department: Departement of medecine

country: Canada

institute: CHU de Québec - Université Laval

data_processing:
For ChIP-seq, the single-end reads were mapped on the human genome build hg19 using bowtie version 2.1.6 (Langmead et al., 2009), using the pre-set sensitive parameter.
MACS version 2.0.10 (model-based analysis of ChIPseq) peak finding algorithm was used to identify regions of ChIP-seq enrichment over the background (Feng et al., 2012), using broad peaks parameters.
Unique mapped read values were normalized to library size. Peaks were annotated as per human genome EnsDb.Hspaiens.v75 - hg19
For long-read RNAseq, raw fast5 files were basecalled using Guppy v.4.2.2 using fast basecalling settings, and samples were demultiplexed according to barcodes with the guppy_barcoder.
The resulting FASTQ reads were aligned to the GRCh38 human reference with Minimap2 version 2.17-r941
Raw read counts were obtained with the featureCounts tool from the Subread package v 2.0.0, using the exon counting mode (Li, 2018; Liao et al., 2014) and normalized as Counts per Million (CPM).
Genome_build: hg19
Supplementary_files_format_and_content: MBTD1_Flag.IgG.broad_peaks.broadPeak is a bed file containing significant MACS-called broad peaks for the MBTD1 3xFlag-2xstrep ChIP sample using the IgG control sample as input sample.
Supplementary_files_format_and_content: WTZMYND11_Flag.IgG.broad_peaks.broadPeak is a bed file containing significant MACS-called broad peaks for the full length (WT) ZMYND11 3xFlag-2xstrep ChIP sample using the IgG control sample as input sample.
Supplementary_files_format_and_content: trZMYND_Flag.IgG.broad_peaks.broadPeak is a bed file containing significant MACS-called broad peaks for the truncated ZMYND11 [aa1-409] 3xFlag-2xstrep ChIP sample using the IgG control sample as input sample.
Supplementary_files_format_and_content: Fusion_Flag.IgG.broad_peaks.broadPeak is a bed file containing significant MACS-called broad peaks for the ZMYND11-MBTD1 fusion 3xFlag-2xstrep ChIP sample using the IgG control sample as input sample.
Supplementary_files_format_and_content: JC_MD_exp.genes.cpm.txt is a tab separated text file containing read counts for genes normalized to CPM for all long-read RNA-seq samples.
Supplementary_files_format_and_content: JC_MD_exp.transcripts.cpm.txt is a tab separated text file containing read counts for transcripts normalized to CPM for all long-read RNA-seq samples.

source_name: K562 from ATCC

growth_protocol: RPMI, 10% NBCS, 1ug/ml Puromycin

extract_protocol:
For long-read RNA-seq, total RNA was extracted with Rneasy mini columns (QIAGEN), TURBO Dnase treated (ThermoFisher Scientific) and poly(A) enriched with NEBNext poly(A) mRNA Magnetic Isolation Module (NEB).
Libraries were prepared according to Oxford Nanopore Technologies' instructions for the ONT SQK-DCS109 kit, with each sample barcoded with the ONT EXP-NBD104 kit. Briefly, poly(A) RNA was reverse-transcribed into cDNA with the Maxima H Minus RT (ThermoFisher Scientific) and second strand synthesis was accomplished using LongAmp Taq polymerase (NEB). The blunt DNA ends were prepared using the NEBNext Ultra II End Repair/dA-Tailing module (NEB), adding a 3' dA tail and phosphorylating the 5' end. Barcodes were ligated to the DNA fragments with a Blunt/TA ligase (NEB) and motor protein adapters were finally ligated with the NEBNext Quick Ligation Module (NEB). Purification of DNA between each step was performed with KAPA Hyperpure Beads (Roche). Libraries were sequenced on ONT's MinION Mk1B using four R9 flowcells.

tag: cell line

value: lymphoblast from chronic myelogenous leukemia (CML)

tag: growth conditions

value: normal growth conditions

value: ZMYND11 KO by CRISPR/Cas9 and insertion of Tag only at the AAVS1 locus by Zinc finger Nuclease.

tag: expressing

value: ZMYND11-MBTD1 fusion 3xFlag-2xstrep


title: MAOEC_AS2_plasma_48h_Replicate4


title: MBTD1 3xFlag-2xstrep in ZMYND11 KO-clone #1

tag: treatment

value: MBTD1 3xFlag-2xstrep


title: MBTD1 3xFlag-2xstrep-rep2


title: ZMYND11-MBTD1 fusion 3xFlag-2xstrep in ZMYND11 KO-clone #1


title: MAOEC_AS2_plasma_48h_Replicate3


title: MAOEC_ApoE_plasma_48h_Replicate4

value: ApoE-KO


title: MAOEC_ApoE_plasma_48h_Replicate1


title: MAOEC_AS1_plasma_48h_Replicate4


title: MAOEC_AS1_plasma_48h_Replicate3


title: MAOEC_AS2_plasma_48h_Replicate6


title: MAOEC_AS2_plasma_48h_Replicate1


title: MAOEC_AS1_plasma_48h_Replicate2


title: MAOEC_AS1_plasma_48h_Replicate6


title: MAOEC_ApoE_plasma_48h_Replicate5


title: MBTD1 3xFlag-2xstrep in ZMYND11 KO-clone #2


title: MAOEC_AS1_plasma_48h_Replicate1


title: MAOEC_ApoE_plasma_48h_Replicate2


title: truncated ZMYND11 [aa1-409] 3xFlag-2xstrep in ZMYND11 KO-clone #1


title: Vh_0

city: Guangzhou

first: Yiqin

last: Deng

state: Guangdong

address: 231 Xingang West Road, Haizhu District, Guangzhou, Guangdong, China

institute: South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences

data_processing:
A Perl program was written to remove low-quality sequences, reads with more than 5% of N bases (unknown bases) and reads containing adaptor sequences, obtaining clean reads.
The high quality reads in each sample were mapped to the referent V. harveyi (PRJNA418027) genome by Bowtie2 (Langmead and Salzberg, 2012).
Transcript per million (TPM) mapped reads was calculated by RSEM (Dewey and Li, 2011) to assessment the gene expression.
Genome_build: Vibrio harveyi 345 (PRJNA418027)
Supplementary_files_format_and_content: Matrix table with tpm gene counts for every gene of every sample
Supplementary_files_format_and_content: Matrix table with tpm gene counts for different expressed gene of every sample

organism: Vibrio harveyi

source_name: Vibrio harveyi 345

growth_protocol: Overnight culture was diluted into OD600=0.01 with fresh LBS medium, then was cultured at 28 degree, 200 rpm, until OD600=3.5

extract_protocol:
Then TRIzol® Reagent was used to extracted the total RNA according the manufacturer’s instructions (Invitrogen, USA) and DNase I was used to remove the genomic DNA (TaKara, Japan).
TruSeqTM RNA sample preparation Kit (Illumina, San Diego, CA)) was used to prepare RNA-seq transcriptome library using 2μg of total RNA. The Illumina HiSeq×TEN was performed to sequence the paired-end RNA-seq sequencing library (2 × 150bp read length).

treatment_protocol: The bacterial cells were collected by centrifugation and quickly frozen in liquid nitrogen.

tag: tissue

value: mid-log bacterial cells

tag: concentration

value: wild type


title: truncated ZMYND11 [aa1-409] 3xFlag-2xstrep in ZMYND11 KO-clone #2


title: AhR-1 KO/WT R3

city: PARIS

first: LINH CHI

last: BUI

address: 45 rue des Saints-Pères

department: INSERM

country: France

institute: Université de Paris

description: Biological replicate 1 of 4.

hyb_protocol: The probes (1 µg each of a biopsy sample and of the reference, direct design) were hybridized to a “pan-genomic C. elegans 4*44K” microarray (Agilent ID_015061) containing with over 21,000 predicted genes from WormBase, a public C. elegans genome database. Hybridization was performed for 17 hours at 60°C with rotation in a hybridization oven (Agilent) as described by the manufacturer. The microarrays were washed as described in the manufacturer’s protocol and dried immediately in a speed-vac centrifuge for 2 minutes.

scan_protocol: Array images were digitized using ScanArray (Agilent Technologies) in XDR mode at 5 µm resolution and then quantified with Feature Extraction software (version 9.5.3).

data_processing: Genes differentially expressed between AhR KO and Wild type condition in the microarray study were first normalized using R loess function then analyzed with Focus software (Cole SW, Galic Z, Zack JA (2003) Controlling false-negative errors in microarray differential expression analysis: a PRIM approach. Bioinformatics 19: 1808-1816.)

organism: Caenorhabditis elegans

source_name: embryonic cells obtained by  fluorescence activated cell sorting

label_protocol: Total RNA were amplified with the MessageAmp kit (Ambion). After amplification, RNA concentration has been determined using a nanodrop spectrophotometer then 200ng submitted to indirect Cy3/Cy5 labeling using the CyScribe Post Labeling Kit (GE Healthcare Amersham Biosciences).

growth_protocol: The nematodes were grown in standard laboratory conditions (S. Bernner et. al, 1974).

extract_protocol: Embryos were isolated from gravid adults following lysis in a hypochlorite solution. Eggshells were removed by incubation in 0.5 ml chitinase/chymotrypsine (1 U/ml and 3,000 U/ml, respectively, in egg buffer) for 20 min. Following resuspension in egg buffer, the embryos were dissociated by 0.25% trypsin treatment for 5 min and resuspended in L-15 supplemented with antibiotics and 20% FBS (L15-CM). Cells were plated on TESPA (4%, Sigma) coated glass plates at a density of 300,000 cells/cm2 and maintained in L15-CM media. Cells were incubated at 20°C overnight.   Enriched population of AhR-1 expressing neurons in both wild-type GFP and mutant AhR-1:GFP were generated using fluorescence activated cell sorting (FACS). Cell sorting experiments were performed on a Moflo flow cytometer (Dako). GFP-positive cells were directly collected in trizol LS (Invitrogen) after sorting and total RNAs extracted according to the manufacturer's protocol. Four independent batches of total RNA from wild-type (N2 and WT-GFP) and mutant (ahr-1(ia03) and KO-GFP) cells were isolated and the quality of the samples was analyzed using a bioanalyzer (Agilent).

value: pmec3:gfp ::ahr-1(ia03)


title: AhR-1 KO/WT R4

description: Biological replicate 1 of 4.


title: MAOEC_ApoE_plasma_48h_Replicate3


title: AhR-1 KO/WT R2

description: Biological replicate 1 of 4.


title: MBTD1 3xFlag-2xstrep-rep1


title: AhR-1 KO/WT R1

description: Biological replicate 1 of 4.


title: hfq_0

source_name: Vibrio harveyi 345∆hfq

value: hfq mutant


title: 5FU 1um sup

type: protein

city: North Grafton

first: Jillian

middle: M

last: Richmond

state: Massachusetts

address: 200 Westboro Road

department: Comparative Pathobiology

institute: Tufts Cummings School of Veterinary Medicine

description: raw data file: slide 2.xlsx

hyb_protocol: Binding was performed per RayBiotech manufacturer's protocol

scan_protocol: Slides were shipped to RayBiotech manufacturer for their in-house Quantibody testing service

data_processing: Backgound median fluorescence intensity was subtracted from sample median fluorescence intensity

label: fluorescent antibody quantitative detection

molecule: protein

source_name: cultured DO.11 T cells

growth_protocol: For cultures, DO.11 T cells were isolated from donor spleens, activated with ova-pulsed splenocytes, skewed with cytokines and antibodies towards Th0, Th1 or Th2, and expanded with IL-2 for a total of 10 days (see also Mande et al JCI 2018 PMID: 29889098). For ex vivo analysis, DO.11 T cells were enriched from digested lesional skin tissue using Miltenyi CD3 bead isolation kits. For serum analysis, mice were bled at first disease presentation (approximately week 4) or flare (approximately week 12).

extract_protocol: Cell culture supernatants or sera were isolated after centrifugation at 330 x g for 5 min and were stored at -70C until used in assays. Samples were prepared per the manufacturer's instructions (RayBiotech).

treatment_protocol: For drug treatments, Th0 unskewed DO.11 T cells were cultured in the presence of 100uM hydrochlorothiazide (HCTZ), 1uM 5' fluorouracil (FU), 10uM terbinafine (Ter), or vehicle control (Veh) and ova peptide pulsed APCs for a total of 10 days as for skewing growth protocol.

tag: pre vs post injection

value: Pre

tag: cle disease first vs flare

tag: th skewing

tag: mouse cle skin disease score


title: No ova sup

description: raw data file: slide 2.xlsx


title: Ter 10um sup

description: raw data file: slide 2.xlsx


title: GVH37/38-11+12 sup restim

description: raw data file: slide 2.xlsx

value: Post

value: Flare

value: Th2 (source)


title: GVH35-1 flare serum (1:10)

description: raw data file: slide 1.xlsx

source_name: serum


title: Veh sup

description: raw data file: slide 2.xlsx


title: GVH37/38-13 flare serum (1:5)

description: raw data file: slide 2.xlsx


title: GVH37/38-12 flare serum (1:5)

description: raw data file: slide 1.xlsx


title: GVH37/38-10 flare serum (1:5)

description: raw data file: slide 1.xlsx


title: GVH35-5 serum (1:5)

description: raw data file: slide 1.xlsx

value: First


title: HCTZ 100um sup

description: raw data file: slide 2.xlsx


title: Th1 sup

description: raw data file: slide 1.xlsx


title: Th2 sup GVH38

description: raw data file: slide 2.xlsx


title: GVH35-4 serum (1:5)

description: raw data file: slide 1.xlsx


title: Th2 sup GVH37

description: raw data file: slide 1.xlsx


title: T0 sup

description: raw data file: slide 1.xlsx


title: PRELP knockout 1

city: London

first: Alex

last: Leung

state: London

address: 11-43 Bath Street

institute: UCL Institute Of Ophthalmology

data_processing:
Data demultiplexed and converted to fastq ising Ilumina bcl2fastq conversion software v2.19
Fastq files were converted into BAM files and aligned to Mus musculus GRCm38 genome using RNA-STAR 2.5.2b and UMI de-duplicated using Je-Suite using HISAT2 at UseGalaxy.com
Reads per transcript counted using FeatureCounts at UseGalaxy.com
Samples pooled and differential expression of genes calculated using DESeq2 at UseGalaxy.com
Assembly: m38.96
Supplementary files format and content: tab-delimited text files from FeatureCounts contain raw counted reads, per gene, per row, for each sample
Supplementary files format and content: tab-delimited text file from DESeq2 contain log2 fold change of each read between pooled control and treated samples per gene with p and q-values

source_name: Meninges

extract_protocol:
Retinas were removed using Papain kit and RNA harvested using ARCTURUS PicoPure RNA isolation kit
Samples prepared using KAPA mRNA HyperPrep kit and sequenced using standard ilumina protocols

value: Meninges

value: PRELP-/-


title: Wild type 3

value: Wild type


title: PRELP knockout 3


title: BMDM_AS2_plasma_48h_Replicate6

value: ApoE-Stab2-KO C57BL/6J

value: Bone marrow derived macrophages


title: BCAS LCM Neurons_5

city: SHEFFIELD

first: Rachel

last: Waller

state: South Yorkshire

address: SITraN, 385A Glossop Road

department: Neuroscience

institute: The University of Sheffield

description: Gene expression data from BCAS neurons

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

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

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

label: Biotin

source_name: Laser capture miscrodissected neurons from mouse BCAS brain tissue

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

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

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

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

tag: gender

tag: condition

value: BCAS


title: Wild type 1


title: young_rep1

city: Osaka-Sayama

first: Toshiyuki

last: Takehara

state: Osaka

address: 377-2, Ohno-Higashi

department: Faculty of Medicine

institute: Kindai Universty Hospital

hyb_protocol: Following fragmentation, 5 ug of fragmented and labeled ss-cDNA were hybridized for 16 hr at 45℃ on GeneChip Clariom S array, mouse. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Gene chip Scanner 7G, affymetrix.

data_processing: The raw data of the array were collected as CEL files and analysed using the Transcriptome Analysis Console (TAC 4.1) software. The gene expression was analysed with the Gene Level SST-RMA summarization method.

source_name: young muscle progenitor cell

label_protocol: Biotinylated ss-cDNA were prepared according to the standard Affymetrix protocol from 1 ng total RNA(Gene Chip WT Pico kit, Affymetrix)

extract_protocol: Trizol extraction of total RNA and DNase treatment were performed according to the manufacturer's instructions

treatment_protocol: The cells obtained by collagenase treatment of muscle tissue from aged and young mice were labeled with antibodies and sorted the CD29/ITGA7 positive MPSCs by FACS Aria II after two washes.

value: Muscle

value: progenitor cells

tag: age

value: 5 weeks-old


title: Wild type 2


title: BCAS LCM Neurons_2

description: Gene expression data from BCAS neurons


title: Inflamed2

city: Boston

first: Ilya

last: Korsunsky

state: MA

address: 77 Avenue Louis Pasteur

institute: Brigham and Women's Hospital

data_processing:
UMI counts with kallisto bustools v0.24.4
Genome_build: GRCm38, Gencode M25
Supplementary_files_format_and_content: Raw UMI count matrices

source_name: Stromal joint cells

extract_protocol:
For collagen induced arthritis, bovine type II collagen (CII; generously provided by Prof. Richard Williams, Kennedy Institute Oxford) was dissolved in 0.1M acetic acid at 4mg/mL. Complete Freund’s adjuvant (CFA) was generated using incomplete Fruend’s adjuvant (IFA; BD Difco, #BD263910) containing Mycobacterium tuberculosis H37Ra (4mg/ml; BD Difco, #BD231141). Male DBA/1 mice were immunised with 200μg of CII emulsified 1:1 in CFA and were boosted 21 days later with 200μg CII in IFA. Onset of arthritis was determined by a paw score ≥2. 5-7 days following onset, mice were culled and inflamed rear limbs were harvested. Mouse rear limb were dissected and bones (including femur, tibia, fibular; and rear foot bones calcaneus, tarsals, metatarsals and phalanges) with intact joint tissue were transferred into RPMI-1640 media (+2% FCS) containing 0.1g/mL Collagenase D (Roche), 0.01g/ml of DNase I (Sigma-Aldrich). Samples were incubated at 37°C, 45min, followed by a second incubation with RPMI-1640 media (+2% FCS) containing 0.1g/mL Collagenase Dispase (Roche) and 0.01g/mL DNase I at 37°C for 30min. Cells were labelled with anti-mouse CD45 APC-cy7 (1/500, 30-F11; BioLegend, #103116) and 7-AAD (7-Aminoactinomycin D, 1/1000; ThermoFisher, #A1310) viability dye. From this, live, CD45 negative cells were sorted using a MoFlow Astrios EQ (100µM nozzle size).
Cells were counted and loaded into 10X chromium controller for a 5000 cell target recovery.

tag: disease

value: collagen induced arthritis

tag: cell type

value: CD45-negative joint cells


title: Inflamed3


title: aged_rep2

source_name: aged muscle progenitor cell

value: 2 years-old

tag: strain


title: young_rep2


title: Control2

value: Control


title: SHAM LCM Neurons_2

description: Gene expression data from SHAM neurons

source_name: Laser capture miscrodissected neurons from mouse SHAM brain tissue

value: SHAM


title: Inflamed1


title: BCAS LCM Neurons_1

description: Gene expression data from BCAS neurons


title: SHAM LCM Neurons_4

description: Gene expression data from SHAM neurons


title: PRELP knockout 2

tag: genotype


title: SHAM LCM Neurons_5

description: Gene expression data from SHAM neurons


title: BCAS LCM Neurons_3

description: Gene expression data from BCAS neurons


title: SHAM LCM Neurons_1

description: Gene expression data from SHAM neurons


title: BCAS LCM Neurons_4

description: Gene expression data from BCAS neurons


title: BMDM_ApoE_plasma_48h_Replicate1

value: ApoE-KO C57BL/6J


title: Control1


title: Control3


title: aged_rep1


title: C3TAG mammary gland Tumor 2 for scRNAseq

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

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

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

institute: University of North Carolina at Chapel Hill

data_processing:
For scRNA-Seq, the Cell Ranger Single Cell Software Suite, version 3.1 was used for de-multiplexing, barcode ad UMI processing, and single-cell 3′ gene counting. Reads were mapped to the mm10 genome along with an added vector gene for SV large T antigen.
Flash frozen, bulk mRNA-Seq libraries were aligned to the mouse mm10 reference genome using the STAR aligner algorithm. Resulting BAM files were sorted and indexed using Samtools and QC was performed using Picard. Tran-script read counts were determined was performed using Salmon
Genome_build: mm10
Supplementary_files_format_and_content: Cell Ranger output

source_name: Mammary Tumor

extract_protocol:
For scRNAseq, whole mammary glands and mammary tumors were placed in 10 ml of a digestion medium containing EpiCultTM-B Mouse Medium Kit (#05610, StemCell Technologies), Col-lagenase/Hyaluronidase (#07912, StemCell Technologies) and 1% penicillin streptomycin (Gibco). The glands and tumors were digested overnight in a thermocycler maintained at 37 C with continuous rotation. For bulk RNAseq; the flash frozen whole mammary gland and tumors were homogenized and RNA was isolated using the RNeasy Mini Kit (#74104, Qiagen) according to manufacturer protocol. Single cell suspensions were input to a 10x Genomics Chromium machine to establish single-cell gel beads in emulsion (GEMs) for directed retrieval of approximately 5000-10000 cells
scRNA-Seq libraries were prepared following the Single Cell 30 Reagent Kits v2 User Guide (Manual Part # CG00052 Rev A) using the following Single Cell 30 Reagent Kits v2: ChromiumTMSingle Cell 3' Library & Gel Bead Kit v2, PN-120237, Single Cell 3' Chip Kit v2 PN-120236, and i7 Multiplex Kit PN-120262 (10X Genomics). Bulk RNA-Seq were made using total RNA and the Illu-mina TruSeq mRNA sample preparation kit.
scRNA-Seq Libraries were run on an Illumina NextSeq 500 paired-end reads. For bulk mRNA-Seq Paired end (2 50bp) sequencing was performed on the Illumina HiSeq 2000/2500 sequencer

value: >18 weeks old

value: Palpable C3Tag mouse Tumor harvested and made into a single cell suspension for scRNAseq

tag: model

tag: Sex

value: female


title: ID8-12

city: Ottawa

first: David

last: Cook

state: ON

address: 501 Smyth Rd

department: Cancer Therapeutics Program

institute: Ottawa Hospital Research Institute

description:
10x Genomics 3' scRNA-seq library
combined_cell_metadata.csv
combined_umi_matrix.csv

data_processing:
Raw sequencing reads were processed using CellRanger v3.0.2 and the mm10 build of the mouse genome. Default settings were used for both libraries.
Genome_build: mm10
Supplementary_files_format_and_content: Cell metadata table: Various metadata (sample ID, cluster, etc) for each cell contained in the UMI count matrix. UMI count matrix: Matrix containing UMI counts for all cells passing quality control filters. Cellranger barcode list: Cellranger barcode list from filtered_feature_bc_matrix directory. Cellranger gene list: Cellranger gene list output from filtered_feature_bc_matrix directory. Cellranger UMI matrix: Cellranger UMI matrix output from filtered_feature_bc_matrix directory.

source_name: ID8 intrabursal tumor

growth_protocol: Animal experiments were carried out using protocols approved by the Animal Care Committee at the University of Ottawa and conforming to or exceeding the standards defined by the Canadian Council on Animal Care. FVB/N mice (for STOSE and  MOE cell lines) were acquired from Charles River and C57BL/6 mice (for ID8 and derivatives) were purchased from Jackson Laboratories. Intrabursal (IB) injections of cell lines (0.15 x 10^6 cells) were performed as previously described (35). Intraperitoneal (IP) injections of 5 x 10^6 cells were delivered to a subset of the mice. As the mice developing IB tumors neared humane endpoint, primary tumors, abdominal metastases, spleens, and ascites were collected for flow cytometry, immunohistochemistry (frozen and fixed), immunofluorescence, qPCR, and single cell-RNAseq analysis.

extract_protocol:
Tumors (maximum 1g) were cut into tiny pieces using a razor blade in 2.5 mL of digestion solution following the manufacturer’s protocol using the mouse Tumor Dissociation Kit (Miltenyi) and a gentleMACS™ Octo Dissociator with heaters (protocol tumor 37⁰C_m_TDK_1). Following the dissociation protocol, the suspension was filtered, and remaining tumor pieces were further disrupted using a syringe plunger on a 70μm filter in order to generate a single-cell suspension. All samples underwent blood cell lysis with ACK Lysing Buffer (VWR). Cells were counted to assess viability (Trypan-blue exclusion) prior to staining. Dead cells were removed from the single-cell suspension using the microbead-based Dead Cell Removal Kit (Miltenyi Biotec) according to the manufacturer’s protocol. Briefly, <10 7 cells were centrifuged at 300xg for 10 minutes and resuspended in 100μl of Dead Cell Removal MicroBeads. After 15 minutes of incubation at RT, the sample was passed through MACS MS columns (Miltenyi Biotec) and washed, collecting the flow-through of unlabelled live cells. After removal each sample had >80% viable cells.
Single-cell suspensions were processed using the 10x Genomics Single Cell 3’ RNA-seq kit (v3), loaded to target a yield of 10,000 cells per sample. Cell cDNA libraries were prepared according to the manufacturer’s protocol and libraries were assessed using the Fragment Analyzer (Agilent).
3' scRNA-seq

value: ID8 intrabursal tumor


title: BMDM_ApoE_plasma_48h_Replicate2

source_name: Bone marrow derived macrophages


title: C3TAG mammary gland Tumor 1 for scRNAseq


title: SHAM LCM Neurons_3

description: Gene expression data from SHAM neurons


title: FF-2

city: Cincinnati

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

description: selected for 5 days

data_processing:
Library strategy: CRISPR gRNA Enrichment Screen
Basecalls performed using CASAVA version 1.4
The quality of paired reads were checked using FASTQC (v0.11.7)
For the genome-scale CRISPR-Cas9 knockout screen, MAGeCK (v0.5.9) was used.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited Mageck output

source_name: bone marrow

growth_protocol: Bone marrow mononuclear cells were harvested according to standard protocols and the lineage-negative cells were purified using EasySep Hematopoietic Progenitor Enrichment kit. The cells were grown in IMDM containing 10% FCS and 50ng/ml mouse IL-3, mouse SCF, mouse FLT3L, human TPO, and human IL-6.

extract_protocol:
Total DNA was extracted from the remaining culture using Nucleobond CB-100 columns
The section of the vector comprising the gRNA sequence was PCR amplified using primers containing the illumina sequencing primer and flowcell attachment sequences according to the Broad protocol provided on addgene.

treatment_protocol: The cells were transduced with viral particles to achieve approximately 30% transduction efficiency. 4-OH-Tamoxifen was added after the transduction and the cells were grown in the same media for 5 days.

value: bone marrow

value: lineage-negative cells


title: C3TAG DCIS containing whole mammary gland 1 for scRNAseq

source_name: Whole mammary gland

value: 14 weeks old

value: Whole mouse gland harvested from 14 weeks old C3Tag mouse and made into a single cell suspension for scRNAseq


title: C3TAG prepuberty mammary gland 1 for scRNAseq

value: 5 weeks old

value: Whole mouse gland harvested from 5 weeks old C3Tag mouse and made into a single cell suspension for scRNAseq


title: C3TAG DCIS containing whole mammary gland 2 for scRNAseq


title: Control

description: sequencing on day after transduction

value: wild-type


title: WT-2

description: selected for 5 days


title: WT-3

description: selected for 5 days


title: FF-1

description: selected for 5 days


title: WT-1

description: selected for 5 days


title: ectopic_Prox1_Mutant Replicate 3

city: Chicago

first: Beatriz

last: Sosa-Pineda

state: IL

address: 303 E Superior SQI 8-520

department: Medicine

institute: Northwestern University

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned to mm10 using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited file with read counts per gene

source_name: whole pancreas

extract_protocol:
Individual pancreata were dissected and placed in RNA TM later (Invitrogen) overnight at 4 C and subsequently at -80 C until ready to process. Total RNA was extracted using TRIzol reagent (AMBION) and PureLinkTM RNA Mini Kit (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: NMRI

value: postnatal day 7

value: pancreas


title: ectopic_Prox1_Mutant Replicate 2


title: Cre-only_Control Replicate 3

value: Ptf1a cre/+


title: ectopic_Prox1_Mutant Replicate 1


title: Cre-only_Control Replicate 2


title: STOSE-4

source_name: STOSE intrabursal tumor

value: STOSE intrabursal tumor


title: C3TAG prepuberty mammary gland 2 for scRNAseq


title: Mutant Replicate 1

description: mutant -1

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned to mm10 using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited file with raw read counts per gene

source_name: embryonic pancreas

extract_protocol:
Individual pancreata were dissected and flash frozen on dry ice. RNA was harvested from pools containing 5-6 pancreata of the same genotype using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 2-3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: Mutant Replicate 2

description: mutant -2


title: Control Replicate 3

description: control -3

value: wildtype


title: Capture_Dt1t2_ter119_exp2_rep3

city: Headington

first: Jim

middle: R

last: Hughes

address: MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine

department: MRC WIMM

description:
DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown.
Exp2_supp_file.tab

data_processing:
Library strategy: NG Capture-C
Adaptor Removal: Trim Galore
Fragment reconstruction into a single read: Flash
In silico restriction enzyme digestion of FASTQ file (dpnIIPE.pl).
Alignment: Bowtie
Processing: Removal of PCR duplicates; Parsing of informative reads and mapping to restriction enzyme fragments (CCanalyser2.pl).
Processing: Combining data from multiple replicates (custom scripts).
Processing: Removal of ploidy regions and off target capture (custom scripts).
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *interaction_counts.tab: Interaction calls; custom format (chr start stop interactions viewpoint).
Supplementary_files_format_and_content: Exp*_supp_file.tab: Files show the DpnII fragments that were used as hybridisation viewpoints for NG Capture-C for the two separate experiments, in bed file format for the mm9 genome build.

source_name: Primary erythroid cells (Spleen)

growth_protocol: Primary Ter119+ erythroid cells were obtained from the spleens of adult mice that were treated with phenylhydrazine as described previously (Spivak et al., 1973). Spleens were mechanically dissociated into single cells suspensions in cold phosphate-buffered saline (PBS; Gibco: 10010023)/10% fetal bovine serum (FBS; Gibco: 10270106) and passed through a 70 μm filter to remove clumps. Cells were washed with cold PBS/10% FBS and resuspended in 10 μl of cold PBS/10% FBS per 10e6 cells and stained with a 1/100 dilution of anti-Ter119-PE antibody (Miltenyi Biotec: 130-102-336) at 4 °C for 20 minutes. Stained cells were washed with cold PBS/10% FBS and resuspended in 8 μl of cold PBS/0.5% BSA/2 mM EDTA and 2 μl of anti-PE MACS microbeads (Miltenyi Biotec: 130-048-801) per 10e6 cells and incubated at 4 °C for 15 minutes. Ter119+ cells were positively selected via MACS lineage selection columns (Miltenyi Biotec: 130-042-401) and processed for downstream applications. Purity of the isolated erythroid cells was routinely verified by Fluorescence-Activated Cell Sorting (FACS).

extract_protocol:
3C Libraries were generated according to the NG Capture-C protocol (Davies et al. 2016). Briefly, cells were crosslinked with 2% formaldehyde (10 minutes, room temperature); quenched with cold glycine; washed in phosphate buffered saline; resuspended in cold lysis buffer (tris 10mM, NaCl 10mM, NP40 0.2%, complete proteinase inhibitor (Roche)) and snap frozen to -80. Cells were thawed on ice, washed in milliq dH2O and Dounce homogenised on ice (x 40 strokes). Cells were then resuspended with 0.25% SDS and restriction enzyme buffer and incubated at 37C for 1h at 1400rpm on a Comfort Thermomixer (Eppendorf) followed by a further incubation of 1h following the addition of Triton X100 (final concentration 1.67%). An overnight digestion was performed using Dpn II (500U /ml (NEB) at 37C / 1400 rpm). The digested chromatin was ligated overnight (Fermentas HC Ligase final concentration 10U/ml) at 16 degrees at 1400 rpm on the Thermomixer. The samples were then decrosslinked overnight at 65C with Proteinase K (Roche) followed by a 30 min incubation at 37C with RNase (Roche). Phenol/Chloroform extraction was then performed followed by an Ethanol precipitation and a wash with 70% Ethanol. Digestion efficiencies were assessed by gel electrophoresis (1% agarose) and RT-PCR (Taqman), which showed digestion efficiencies in excess of 70%. DNA content of the Dpn II 3C libraries were quantitated using a Qubit fluorometer (Life Technologies).
5-10ug of each library was sheared using a Covaris S2 in milliq dH2O. Covaris settings used were: duty cycle 10%, Intensity 5, Cycles/burst 200, Time 6 cycles of 60seconds, Set Mode Frequency sweeping Temperature 4 to 7 degrees. Following shearing DNA was purified using AMPureXP beads (Agencourt) and DNA quality assessed on a Bioanalyser 2100 using a DNA High Sensitivity Chip (Agilent). DNA end repair and adapter ligation was performed using the NEB Next or NEB Ultra DNA sample preparation reagent kits, depending on the amount of DNA available, using the standard protocol. Biotinylated capture oligonucleotides were designed to the ends of the viewpoint fragments. Where possible 1-2ug of each adapter ligated library were hybridized with the biotinylated capture oligonucleotides, using the Nimblegen SeqCap reagents and an adapted protocol. The quality of the resultant captured library was assessed by Agilent tapestation or bioanalyser (D1000). The resulting libraries were sequenced using Illumina Nextseq 500 (150 bp paired-end reads).

tag: strain/background

tag: genotype/variation

value: Adult

value: Erythroid


title: Mutant Replicate 3

description: mutant -3

tag: tissue


title: FF-3

description: selected for 5 days


title: Control Replicate 1

description: control -1


title: Control Replicate 2

description: control -2


title: Cre-only_Control Replicate 1


title: Capture_Dtheta2_ter119_exp2_rep2


title: Capture_Dtheta2_ter119_exp2_rep3


title: Capture_Dt1t2_ter119_exp2_rep2


title: Capture_Dt1t2_ter119_exp2_rep1


title: Capture_Dtheta2_ter119_exp2_rep1


title: Capture_Dtheta1_ter119_exp2_rep3


title: MAOEC_AS1_plasma_48h_Replicate5

source_name: Primary mouse aorta endothelial cells (MAOEC)


title: Capture_WT_ter119_exp1_rep3

description:
DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown.
Exp1_supp_file.tab

value: WT


title: Capture_D4448_ter119_exp1_rep3


title: Capture_WT_ter119_exp1_rep2


title: Capture_Dtheta1_ter119_exp2_rep1


title: Capture_WT_ter119_exp2_rep1


title: Capture_D4448_ter119_exp1_rep1


title: Capture_WT_ter119_exp2_rep3


title: Capture_D4448_ter119_exp1_rep2


title: Capture_WT_ter119_exp1_rep1


title: ATAC_Dtheta2_ter119_rep1

description: Genome-wide library of tagmented fragments.

data_processing:
Mapping: bowtie -m 2 --maxIns 350, mm9
For un-mapping reads: trimming adaptors trim_galore -- length 10, combining overlapping R1-R2 reads : flash -m 9 -x 0.125
Combining trimmed+flashed and originally mapped reads, mapping again with bowtie -m 2 --maxIns 350
Removing read pairs overlapping Blacklisted regions.
Removing duplicates: samtools rmdup
Reconstructing sequenced fragments from R1+R2 read pairs (bedtools bedpe | cut -f 1,2,6) - for visualisation.
Pileup of fragments (bedtools genomecov -counts).
Generating bigwig tracks.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: bigWig: (DEEPtools) bamCoverage conversion of filtered fragments (reconstructed, duplicate-filtered fragments : see above) from bam to bigwig, (--binSize 50 --normalizeUsingRPKM --ignoreForNormalization chrM)

extract_protocol:
Assay for transposition of active chromatin sequencing (ATAC-Seq) was performed as previously published (Buenrostro, 2013) on single cell suspensions. 60000-80000 cells were used per biological replicate. Cells were lysed and nuclei were isolated prior to transposition with Tn5 transposase (Nextera, Illumina) for 30 minutes at 37°C. DNA was purified using a MinElute kit (Qiagen).
Libraries were amplified and barcoded using the NEBNext 2xMastermix (NEB) and the custom primers as published in Buenrostro et al., 2013. ATAC-Seq libraries profiles were visualized using D1000 tape on the Tapestation (Agilent). The libraries were quantified using the universal library quantification kit (KAPA Biosystems).


title: ATAC_Dt1t2_ter119_rep1


title: ATAC_Dtheta1_ter119_rep3


title: ATAC_Dtheta2_ter119_rep2


title: ATAC_Dtheta1_ter119_rep1


title: ATAC_Dt1t2_ter119_rep2


title: ATAC_Dt1t2_ter119_rep3


title: ATAC_Dtheta2_ter119_rep3


title: Capture_WT_ter119_exp2_rep2


title: ATAC_Dtheta1_ter119_rep2


title: ATAC_D4448_ter119_rep3


title: Capture_Dtheta1_ter119_exp2_rep2


title: ATAC_D4448_ter119_rep1


title: ATAC_D4448_ter119_rep2


title: ChIP_CTCF_Dt1t2_ter119_rep1

description: Genome-wide library of Immunoprecipitated fragments.

data_processing:
Mapping: bowtie -m 2 --maxIns 350, mm9
For un-mapping reads: trimming adaptors trim_galore -- length 10, combining overlapping R1-R2 reads : flash -m 9 -x 0.125
Combining trimmed+flashed and originally mapped reads, mapping again with bowtie -m 2 --maxIns 350.
Removing read pairs overlapping Blacklisted regions.
Removing duplicates: samtools rmdup
Reconstructing sequenced fragments from R1+R2 read pairs (bedtools bedpe | cut -f 1,2,6) - for visualisation.
Pileup of fragments (bedtools genomecov -counts).
Generating bigwig tracks.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: bigWig: (DEEPtools) bamCoverage conversion of filtered fragments (reconstructed, duplicate-filtered fragments : see above) from bam to bigwig, (--binSize 50 --normalizeUsingRPKM)

extract_protocol:
CTCF Chromatin immunoprecipitation (ChIP) was performed on 1 x 10e7 Ter119+ erythroid cells using a ChIP Assay Kit (Millipore: 17-295) according to the manufacturer’s instructions. Cells were crosslinked by a single 10 min 1% formaldehyde fixation. Chromatin fragmentation was performed with the Bioruptor Pico sonicator (Diagenode) for a total sonication time of 4 min (8 cycles) at 4°C to obtain an average fragment size between 200 and 400 bp. Immunoprecipitation was performed overnight at 4 °C with an anti-CTCF antibody (10 µl 07-729, lot: 2836926; Millipore).
DNA was purified by phenol-chloroform extraction with PhaseLock tubes (5Prime) and ethanol precipitation with NaOAc, and 2 µl GlycoBlue (Invitrogen). ChIP enrichment was determined by RT-qPCR.
NEBNext Ultra II DNA Library Prep kit for Illumina (New England Biolabs).

tag: chip antibody


title: ChIP_CTCF_Dtheta2_ter119_rep2


title: ChIP_CTCF_Dt1t2_ter119_rep2


title: ChIP_CTCF_Dtheta2_ter119_rep3


title: RNA_WT_ter119_rep1

data_processing:
Mapping: STAR --outFilterMultimapNmax 2
Duplicate removal: samtools rmdup
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: bigwig: forward reads (deeptools) - bamCoverage --binSize 1 --normalizeUsingRPKM --filterRNAstrand forward --ignoreForNormalization chrM chrX chrY
Supplementary_files_format_and_content: bigwig: reverse reads (deeptools) - bamCoverage --binSize 1 --normalizeUsingRPKM --filterRNAstrand reverse --ignoreForNormalization chrM chrX chrY

extract_protocol:
Total RNA was isolated from 5 x 10e6 Ter119+ erythroid cells lysed in TRI reagent (Sigma-Aldrich: T9424) using a Direct-zol RNA MiniPrep kit (Zymo Research: R2050). DNase I treatment was performed on the column as recommended in the manufacturer’s instructions but with an increased incubation of 30 min at room temperature (rather than 15 min).
For RNA-seq libraries, 1-2 μg of total RNA was depleted of rRNA and globin mRNA using the Globin-Zero Gold rRNA Removal Kit (Illumina: GZG1224) according to the manufacturer’s instructions. To enrich for mRNA, poly(A)+ RNA was isolated, strand-specific cDNA was synthesised, and the resulting libraries prepared for Illumina sequencing using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs: E7490) and the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs: E7760) following the manufacturer’s instructions.


title: ChIP_CTCF_D4448_ter119_rep3


title: ChIP_CTCF_Dtheta1_ter119_rep1


title: RNA_Dtheta2_ter119_rep1


title: ChIP_CTCF_Dtheta2_ter119_rep1


title: RNA_Dt1t2_ter119_rep3


title: ChIP_CTCF_D4448_ter119_rep1


title: RNA_Dt1t2_ter119_rep2


title: ChIP_CTCF_D4448_ter119_rep2


title: RNA_WT_ter119_rep3


title: RNA_WT_ter119_rep2


title: ChIP_CTCF_Dtheta1_ter119_rep3


title: ChIP_CTCF_Dtheta1_ter119_rep2


title: RNA_Dt1t2_ter119_rep1


title: RNA_Dtheta1_ter119_rep1


title: RNA_Dtheta1_ter119_rep3


title: RNA_Dtheta2_ter119_rep3


title: RNA_Dtheta1_ter119_rep2


title: RNA_Dtheta2_ter119_rep2


title: ap2-12 IV

city: Cologne

first: Alice

last: Vayssieres

address: Carl-von-Linne-Weg 10

institute: Max Planck Institute for Plant Breeding Research

description: ap2-12 rep IV

data_processing:
RNA-Seq reads were then mapped to A. thaliana TAIR10 using tophat2 under default settings (Kim et al., 2013), except only a single alignment was permitted per read and the coverage based junction search was disabled (settings: -g 1 –no-coverage-search).
Samtools was used to sort and index BAM alignment files and to calculate BAM file statistics (Li et al., 2009).
HTSeq was used to tabulate the number of reads mapping to each genomic feature, with counts tabulated only for genes that completely overlapped a given feature (Anders et al., 2015).
Genome_build: TAIR10
Supplementary_files_format_and_content: gene_expression_reads_count.xlsx: Excel table contains counts.

organism: Arabidopsis thaliana

source_name: Shoot apices

growth_protocol: Plants were grown in long day conditions (16h light/ 8h dark). Samples were collected when the main inflorescence stem had reached a height of 1 cm (1-cm-bolting stage).

extract_protocol:
Total RNA was extracted from 4 independent biological replicates of shoot 15 apices by using the RNeasy Plant Mini Kit (Qiagen) and treated with DNase (Ambion) to remove residual genomic DNA.
Library for sequencing was prepared using the Illumina TruSeq library preparation kit according to the manufacturer’s protocol at the Cologne Genome Centre and sequencing was carried out using a HiSeq3000 (Illumina) with 1 x 150 bp single reads.

value: ap2-12 mutant

value: Shoot apices

tag: replicate

value: rep 4


title: rAP2-V #A6 IV

description: rAP2-VENUS rep IV

value: rAP2-VENUS line #A6


title: rAP2-V #A6 III

description: rAP2-VENUS rep III

value: rep 3


title: ap2-12 III

description: ap2-12 rep III


title: WT IV

description: Col-0 rep IV

value: WT (Col-0)


title: rAP2-V #A6 II

description: rAP2-VENUS rep II

value: rep 2


title: MD741-7-S1

city: Hangzhou

first: Daoqiong

last: Zheng

state: Zhejiang

address: 866 Yuhangtang Road

department: Institute of Microbiology

institute: College of Life Sciences, Zhejiang University

description: Genotypes of MD741-7-S1

hyb_protocol: The hybridization reactions were prepared using an Agilent Oligo aCGH/ChIP-on-Chip Hybridization kit (5188-5220) following kit instructions. Arrays were incubated for 24 hours at 62°. Following hybridization, the arrays were washed for 5 minutes in Oligo aCGH/ChIP-on-Chip Wash Buffer 1 (Agilent 5188-5221) and 1 minute in Oligo aCGH/ChIP-on-Chip Wash Buffer 2 (Agilent 5188-5222) that was pre-warmed to 37°. The arrays were then scanned at wavelengths of 635 and 532 nm using the GenePix scanner and the GenePix Pro software using settings recommended by the manufacturer.Microarrays could be re-used approximately 4-6 times by removing the hybridized labeled DNA sequences from the oligonucleotides. Microarrays and gasket slides were stripped separately in 1x stripping buffer (10 mM potassium phosphate, pH6.6). The slides were slowly heated to the boiling point in the stripping buffer for 30-45 minutes. After stripping, they were transferred to deionized water, and then slowly removed and stored in a nitrogen cabinet. The gasket slides were centrifuged at 500 rpm to remove excess liquid. Labels on microarrays were removed prior to stripping.

scan_protocol: The data generated by GenePix Pro were exported as .gpr files and analyzed with a homemade software pipeline. Probes that were flagged by the software were deleted from the analysis.

data_processing: The data generated by GenePix Pro were exported to text files and analyzed with Microsoft Excel. The 635 nm/532 nm ratio was analyzed for each oligonucleotide. The average value of the median ratios of the control probes was calculated and used to normalize the ratios of the experimental probes to a value of 1 by dividing each probe ratio by the average control probe ratio. The Whole genome arrays were completed with Agilent platform with Design ID Agilent-027438 was used. Sectored colonies were mapped using Agilent platforsm with Design IDs Agilent-031671, which contains probes specific only to chromosome IV, and Agilent-047217, which contains many probes on chromsome IV, but few probes near the telomere and centromere of all chromosomes.

organism: Saccharomyces cerevisiae

source_name: cell culture of MD741-7-S1

label_protocol: DNA from these colonies was labeled with Cy5, and mixed with control DNA (DNA from the strain MD703) labeled with Cy3. The two samples were mixed and competitively hybridized to the SNP microarrays.

growth_protocol: Yeast cells were grown in YPD medium at 30 degree.

extract_protocol: Genomic DNA were prepared by standard procedures (St. Charles et al., 2012)

treatment_protocol: MD704 cells were culture with 2% Galactose medium for long-term or transient (2 hours or 4 hours) exposure of CRISPR/Cas9.

source_name: cell culture of MD703

tag: tag


title: ap2-12 II

description: ap2-12 rep II


title: MD704-2h-7

description: Genotypes of MD704-2h-7

source_name: cell culture of MD704-2h-7


title: MD741-5-S2

description: Genotypes of MD741-5-S2

source_name: cell culture of MD741-5-S2


title: MD704-4h-8

description: Genotypes of MD704-4h-8

source_name: cell culture of MD704-4h-8


title: MD741-3-S1

description: Genotypes of MD741-3-S1

source_name: cell culture of MD741-3-S1


title: MD741-7-S2

description: Genotypes of MD741-7-S2

source_name: cell culture of MD741-7-S2


title: MD741-3-S2

description: Genotypes of MD741-3-S2

source_name: cell culture of MD741-3-S2


title: MD741-6

description: Genotypes of MD741-6

source_name: cell culture of MD741-6


title: MD704-4h-12

description: Genotypes of MD704-4h-12

source_name: cell culture of MD704-4h-12


title: MD741-6-S2

description: Genotypes of MD741-6-S2

source_name: cell culture of MD741-6-S2


title: MD741-5

description: Genotypes of MD741-5

source_name: cell culture of MD741-5


title: rAP2-V #A6 I

description: rAP2-VENUS rep I

value: rep 1


title: WT II

description: Col-0 rep II


title: MD704-4h-6P

description: Genotypes of MD704-4h-6P

source_name: cell culture of MD704-4h-6P


title: MD704-4h-1

description: Genotypes of MD704-4h-1

source_name: cell culture of MD704-4h-1


title: WT III

description: Col-0 rep III


title: MD741-7

description: Genotypes of MD741-7

source_name: cell culture of MD741-7


title: MD741-3

description: Genotypes of MD741-3

source_name: cell culture of MD741-3


title: MD741-6-S1

description: Genotypes of MD741-6-S1

source_name: cell culture of MD741-6-S1


title: WT I

description: Col-0 rep I

source_name: Shoot apices


title: MD704-2h-26

description: Genotypes of MD704-2h-26

source_name: cell culture of MD704-2h-26

source_name: cell culture of MD703


title: ap2-12 I

description: ap2-12 rep I


title: MD741-5-S1

description: Genotypes of MD741-5-S1

source_name: cell culture of MD741-5-S1


title: sk-Hep1-HDGF cell

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

description: 52 years, male, Caucasian

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: hepatoma

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray, Kamakura, Japan)

growth_protocol: Cells were cultured in DMEM medium with 10% fetal bovine serum (Sigma-Aldrich Japan, Tokyo, Japan).

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Qiagen).

treatment_protocol: Cells were plated into 12 well-dishes (Corning International, Tokyo, Japan) at a density of 1×105 cells/well. Twenty-four hours after the inoculation, the cells were exogenously stimulated with the administration of recombinant HDGF (abcam, Tokyo, Japan; product code: ab132259) for 48 h (final concentration: 100 ng/mL).

tag: cell line

tag: cell line source

value: An immortal, human cell line derived from the ascitic fluid of a patient with adenocarcinoma of the liver.


title: sk-Hep1-control cell

description: 52 years, male, Caucasian


title: HepG2-control cell

description: 15 years, male, Caucasian

value: Isolated from a liver biopsy of a male Caucasian aged 15 years, with a well differentiated hepatocellular carcinoma


title: PC9 si#3 96h m6A biological rep2

city: Hamamatsu

first: Kazuo

last: Tsuchiya

department: Tumor pathology

institute: Hamamatsu University School of Medicine

description: PC9 siALKBH5#3 biological rep2 at 96h after transfection

hyb_protocol: The cRNA mixture was fragmented by adding 5 μL Blocking Agent and 1 μL of Fragmentation Buffer, heated at 60°C for 30 min, and combined with 25 μL hybridization buffer. 50 μL hybridization solution was dispensed into the gasket slide and assembled to the m6A-mRNA&lncRNA Epitranscriptomic Microarray slide. The slides were incubated at 65°C for 17 hours in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using an Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Raw intensities of IP (immunoprecipitated, Cy5-labelled) and Sup (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities. After Spike-in normalization, the probe signals having Present (P) or Marginal (M) QC flags in at least 3 out of 9 samples were retained as “All Targets Value” in the Excel sheet for further “m6A methylation level” and “m6A quantity” analyses. “m6A methylation level” was calculated for the percentage of modification based on the IP (Cy5-labelled) and Sup (Cy3-labelled) normalized intensities. “m6A quantity” was calculated for the m6A methylation amount based on the IP (Cy5-labelled) normalized intensities.

source_name: PC9 siALKBH5#3_IP

label_protocol: The “IP” RNA and “Sup” RNAs were added with equal amount of calibration spike-in control RNA, separately amplified and labeled with Cy3 (for “Sup”) and Cy5 (for “IP”) using Arraystar Super RNA Labling Kit.

growth_protocol: Cells were maintained in a 5% CO2 and 95% air incubator at 37℃.

extract_protocol: Total RNA was extracted using RNeasy Plus Mini Kit (#74136, Qiagen) according to the manufacturer’s instructions.

treatment_protocol: Cells were cultured for 24 hours prior to transfection and transfected with 15 nM of final concentrations of siRNAs. Total RNA were extracted from ALKBH5 knockdown PC9 cells at 96 h after transfection.

value: lung adenocarcinoma cell line

value: ALKBH5 knockdown

tag: sample type

value: immunoprecipitated

source_name: PC9 siALKBH5#3_Sup

value: Lung

value: supernatant


title: PC9 Ctrl 96h m6A biological rep2

description: PC9 siControl biological rep2 at 96h after transfection

source_name: PC9 siControl_IP

value: control

source_name: PC9 siControl_Sup


title: PC9 si#3 96h m6A biological rep3

description: PC9 siALKBH5#3 biological rep3 at 96h after transfection


title: PC9 si#3 96h m6A biological rep1

description: PC9 siALKBH5#3 biological rep1 at 96h after transfection


title: ColonCancerCellLineHCT8_control_plasma_rep2

city: Prague 10

first: Veronika

last: Boušková

address: Srobarova 48

country: Czech Republic

institute: National Institute of Public Health

description:
Array 2
HCT8_CTRL_P_2

hyb_protocol: protocol for miRNA Microarray System with miRNA Complete Labeling and Hyb Kit (Version 3.1, Agilent Technologies)

scan_protocol: scanning protocol: AgilentG3_miRNA high-sensitivity

data_processing: data extraction: Feature Extraction version software (v12.1, Agilent) with default parameters for miRNA (Grid: 070156_D_F_20141006)

source_name: Plasma samples from the mice with implemented colon cancer cell line HCT8

growth_protocol: Frozen HCT8 cancer cell lines were resuscitated for every set of experiments (lasted 3-9 weeks) and cultures in DMEM supplemented with 10% FBS and 0.5% penicillin/streptomycin. Cells were cultured in incubators with a humidified atmosphere containing 5% CO2 at 37°C. Further manipulation with cell cultures was described hier (DOI: 10.5507/bp.2017.040).

extract_protocol: Tri Reagent (Molecular Research Centre)

treatment_protocol: no treatment protocol

value: plasma


title: ColorectalCancerPrimocultures_Patient1_rep2

description:
Array 3
T47B_2

source_name: Patient-derived xenograft tumor

label_protocol: protocol for miRNA Microarray System with miRNA Complete Labeling and Hyb Kit (Version 3.1, Agilent Technologies)

value: tumor tissue


title: ColonCancerCellLineHCT8_control_plasma_rep3

description:
Array 2
HCT8_CTRL_P_3


title: ColonCancerCellLineHCT8_N-cadherinOverexpressed_plasma_rep3

description:
Array 2
HCT8_N-cad_P_3

source_name: Plasma samples from the mice with implemented colon cancer cell line HCT8_N-cad


title: ColorectalCancerPrimocultures_Patient1_rep1

description:
Array 3
T47B_1


title: ColorectalCancerPrimocultures_Patient2_rep1

description:
Array 3
T48B_1


title: ColonCancerCellLineHCT8_N-cadherinOverexpressed_plasma_rep4

description:
Array 2
HCT8_N-cad_P_4


title: ColorectalCancerPrimocultures_Patient2_rep2

description:
Array 3
T48B_2


title: ColonCancerCellLineHCT8_control_plasma_rep4

description:
Array 2
HCT8_CTRL_P_4


title: ColonCancerCellLineHCT8_N-cadherinOverexpressed_plasma_rep2

description:
Array 2
HCT8_N-cad_P_2


title: PC9 si#1 96h m6A biological rep3

description: PC9 siALKBH5#1 biological rep3 at 96h after transfection

source_name: PC9 siALKBH5#1_IP

source_name: PC9 siALKBH5#1_Sup


title: PC9 Ctrl 96h m6A biological rep3

description: PC9 siControl biological rep3 at 96h after transfection


title: ColonCancerCellLineHCT8_control_tissue_rep4

description:
Array 1
HCT8_CTRL_T_4

source_name: HCT8 colon cancer cell line-derived xenograft tumor


title: PC9 si#1 96h m6A biological rep1

description: PC9 siALKBH5#1 biological rep1 at 96h after transfection


title: PC9 si#1 96h m6A biological rep2

description: PC9 siALKBH5#1 biological rep2 at 96h after transfection


title: PC9 Ctrl 96h m6A biological rep1

description: PC9 siControl biological rep1 at 96h after transfection


title: ColonCancerCellLineHCT8_N-cadherinOverexpressed_tissue_rep1

description:
Array 1
HCT8_N-cad_T_1

source_name: HCT8_N-cad colon cancer cell line-derived xenograft tumor


title: ColonCancerCellLineHCT8_N-cadherinOverexpressed_tissue_rep2

description:
Array 1
HCT8_N-cad_T_2


title: ColonCancerCellLineHCT8_N-cadherinOverexpressed_tissue_rep3

description:
Array 1
HCT8_N-cad_T_3


title: HepG2-HDGF cell

description: 15 years, male, Caucasian


title: ColonCancerCellLineHCT8_control_plasma_rep1

description:
Array 2
HCT8_CTRL_P_1


title: ColonCancerCellLineHCT8_control_tissue_rep2

description:
Array 1
HCT8_CTRL_T_2


title: ColonCancerCellLineHCT8_N-cadherinOverexpressed_plasma_rep1

description:
Array 2
HCT8_N-cad_P_1


title: ColonCancerCellLineHCT8_control_tissue_rep3

description:
Array 1
HCT8_CTRL_T_3


title: ColonCancerCellLineHCT8_N-cadherinOverexpressed_tissue_rep4

description:
Array 1
HCT8_N-cad_T_4


title: ColonCancerCellLineHCT8_control_tissue_rep1

description:
Array 1
HCT8_CTRL_T_1


title: Bhas 42, Min-U-Sil 5, replicate 1

city: Vandœuvre-lès-Nancy

first: Hélène

last: Dubois-Pot-Schneider

address: Site CRAN/Faculté de Médecine - Bâtiment D, 1er étage 9 avenue de la Forêt de Haye, BP 184

department: CRAN

institute: Université de Lorraine - UMR7039 CRAN

description: Gene expression of Bhas 42 cells after 48h treatment with Min-U-Sil 5 (20 µg/cm²)

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer (HI-RPM) was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE v2 8x60K for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565) using one color scan setting for 8x60k array slides (profile Agilent G3-GX-1color).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using protocol GE_1100 Jul_11 and Grid: Design 074809_D_F_20150624. Gene expression data were further analyzed by using the GeneSpring software (Agilent Technologies). Filtration by flag and signal intensity was applied. Briefly, were retained only the entities in which at least 75% of the values in at least one condition  had a detected flag (i.e. a positive  and significant feature as defined by GeneSpring). For the filtration by signal intensity, were retained the entities in which 75% of the values in at least one condition were within the range of interest (i.e. 20-100th percentile).

source_name: Bhas 42, Min-U-Sil 5, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low RNA Input Quick Amp Labelling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the Implen Nanophotometer.  Amplification yield was 3.15 ± 0.96 µg cRNA and specific activity was 11.20 ± 4.06 pmol Cy3 per µg cRNA.

growth_protocol: Cells were seeded at a density of 1460 cells/cm²  and cultured in Dulbecco’s modified Eagle’s medium/Ham’s F12 (Invitrogen) supplemented with 1% antibiotic (Streptomycin and Penicillin, Invitrogen) and 5% fetal bovine serum (FBS, Dutscher, France). Then, cells were treated, on Day 4 (4 days after seeding) with different compounds. Finally, cells were collected after 48h-treatment on Day 6.

extract_protocol: RNA extractions were performed with RNeasy mini kit (Qiagen)  following the manufacturer's recommendations. RNA was quantified using a Implen Nanophotometer.

treatment_protocol: At day 4, Bhas 42 cells were treated for 48h with 3 doses of NM-203 (1 µg/cm²; 2 µg/cm² and 5 µg/cm²), Min-U-Sil 5 (20 µg/cm²) or DE (diatomaceous earth; 5 µg/cm²). Treatment with H2O 2%  was used as control.  Cells were also treated with TPA (12-O-tetradecanoylphorbol-13-acetate; 0.05 µg/ml) or its control DMSO (0.1%) .

value: Bhas 42 cells

tag: compound

value: Min-U-Sil 5

tag: dose

value: 20 µg/cm²


title: Bhas 42, TPA, replicate 3

description: Gene expression of Bhas 42 cells after 48h treatment with TPA (0.05 µg/ml)

source_name: Bhas 42, TPA, replicate 3


title: Bhas 42, TPA, replicate 4

source_name: Bhas 42, TPA, replicate 4


title: Bhas 42, H2O (Min-U-Sil 5), replicate 2

description: Gene expression of Bhas 42 cells after 48h treatment with H2O 2%

source_name: Bhas 42, H2O (Min-U-Sil 5), replicate 2

value: H2O (Min-U-Sil 5)


title: Bhas 42, DMSO, replicate 2

description: Gene expression of Bhas 42 cells after 48h treatment with DMSO 0.1%

source_name: Bhas 42, DMSO, replicate 2

value: DMSO


title: Bhas 42, TPA, replicate 2

source_name: Bhas 42, TPA, replicate 2


title: Bhas 42, Min-U-Sil 5, replicate 2

source_name: Bhas 42, Min-U-Sil 5, replicate 2


title: Bhas 42, Min-U-Sil 5, replicate 4

source_name: Bhas 42, Min-U-Sil 5, replicate 4


title: Bhas 42, Min-U-Sil 5, replicate 3

source_name: Bhas 42, Min-U-Sil 5, replicate 3


title: Bhas 42, H2O (Min-U-Sil 5), replicate 1

source_name: Bhas 42, H2O (Min-U-Sil 5), replicate 1


title: Bhas 42, DMSO, replicate 4

source_name: Bhas 42, DMSO, replicate 4


title: Bhas 42, TPA, replicate 1

source_name: Bhas 42, TPA, replicate 1


title: Bhas 42, H2O (Min-U-Sil 5), replicate 4

source_name: Bhas 42, H2O (Min-U-Sil 5), replicate 4


title: Bhas 42, H2O (Min-U-Sil 5), replicate 3

source_name: Bhas 42, H2O (Min-U-Sil 5), replicate 3


title: Bhas 42, DMSO, replicate 3

source_name: Bhas 42, DMSO, replicate 3


title: Bhas 42, DMSO, replicate 1

source_name: Bhas 42, DMSO, replicate 1


title: Bhas 42, DE, replicate 3

description: Gene expression of Bhas 42 cells after 48h treatment with DE (5 µg/cm²)

source_name: Bhas 42, DE, replicate 3

value: DE (diatomaceous earth)

value: 5 µg/cm²


title: Bhas 42, DE, replicate 4

source_name: Bhas 42, DE, replicate 4


title: Bhas 42, NM-203, 2µg/cm², replicate 3

description: Gene expression of Bhas 42 cells after 48h treatment with NM-203 (2 µg/cm²)

source_name: Bhas 42, NM-203, 2 µg/cm², replicate 3

value: 2 µg/cm²


title: Bhas 42, DE, replicate 2

source_name: Bhas 42, DE, replicate 2


title: Bhas 42, DE, replicate 1

source_name: Bhas 42, DE, replicate 1


title: Bhas 42, NM-203, 5µg/cm², replicate 3

description: Gene expression of Bhas 42 cells after 48h treatment with NM-203 (5 µg/cm²)

source_name: Bhas 42, NM-203, 5 µg/cm², replicate 3


title: Bhas 42, NM-203, 5µg/cm², replicate 1

source_name: Bhas 42, NM-203, 5 µg/cm², replicate 1


title: Bhas 42, NM-203, 1µg/cm², replicate 4

description: Gene expression of Bhas 42 cells after 48h treatment with NM-203 (1 µg/cm²)

source_name: Bhas 42, NM-203, 1 µg/cm², replicate 4

value: 1 µg/cm²


title: Bhas 42, NM-203, 5µg/cm², replicate 2

source_name: Bhas 42, NM-203, 5 µg/cm², replicate 2


title: Bhas 42, NM-203, 2µg/cm², replicate 4

source_name: Bhas 42, NM-203, 2 µg/cm², replicate 4


title: Bhas 42, NM-203, 5µg/cm², replicate 4

source_name: Bhas 42, NM-203, 5 µg/cm², replicate 4


title: K562.SSedit.2.3_S11

city: Columbus

first: Maciej

last: Pietrzak

state: OH

address: 1800 Cannon Drive, 340C Lincoln Tower

department: Department of Biomedical Informatics College of Medicine

institute: Ohio State University

data_processing:
Illumina BaseCalling pipeline
RNA-Seq reads were first mapped to the human genome GRCh38 using Hierarchical Indexing for Spliced Alignment of Transcripts (HISAT2).
Raw read counts for each gene were quantified by using featureCounts software. Then RNA-seq counts were obtained by using GENCODE v.27 Gene Transfer Format (GTF) file as a transcript reference (GENCODE annotation).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw read counts
Supplementary files format and content: raw counts

source_name: CRISPR/Cas 9 edited K562 cells

growth_protocol: Cells were maintained in DMEM/10% FBS. All experiments were performed utilizing cells growing in mid-log phase.

extract_protocol:
Qiagen Rneasy prep kit
Illumina - performed by Genomics core at OSU

treatment_protocol: Genome editing of the TOP2α E19/I19 5′ SS was performed as follows:  sgRNA #1 (0.5 µg) was incubated with 2 µg TrueCut Cas9 Protein v2 and 5 µM TOP2α E19/I19 repair template.

value: CRISPR/Cas 9 edited K562 cells

value: leukemia cell line

tag: treatment

value: CRISPR/Cas 9 edited


title: K562.SSedit.2.4_S12

tag: cell type


title: K.VP.5.2_S6

source_name: etoposide resistant K562 cells

value: etoposide resistant K562 cells


title: K562.SSedit.2.1_S9


title: K562.2_S2

source_name: K562 cells

value: K562 cells


title: K562.SSedit.2.2_S10


title: K.VP.5.3_S7


title: A4141_120

city: Ecublens

first: Chris

last: Rinsch

address: EPFL Innovation Park, Building C

country: Switzerland

institute: Amazentis SA

data_processing:
RNA-seq run was performed using the Illumina HiSeq 4000 sequencing platform with single reads (1 x 50 bp)
quantification of mRNA from the RNA-seq FASTQ files was performed using Salmon
Sample-wise quant.sf files containing raw transcript-level read estimates were read into R, v. 4.0.3 and were combined into a data matrix. Transcripts with very low total counts (< 10) across all samples were filtered out.
The data was transformed using the variance stabilizing transformation (VST) method of R package DESeq2, v. 1.30.0
Data transformation and PCA was also done separately for each treatment group. Based on the PCAs, probable outlier samples were excluded and new PCAs were plotted without these samples
The raw transcript-level read count estimates were read in R and summarized to gene-level counts based on the provided transcript and gene ID annotations using summarizeToGene function of R package tximport, v. 1.18.0. DESeqDataSetFromTximport function of DESeq2 was then used for constructing a DESeqDataSet object for DE analysis. Pre-filtering was applied before the DE analysis by excluding genes with < 10 total counts across samples
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Vastus lateralis muscle

extract_protocol:
muscle biopsy portion was added in RNA-later containing 2ml Eppendorf tubes. RNA was extracted using automated extraction protocols on the QiaSymphony platform using the QiaSymphony RNA extraction kit (cat. 931636). RNA is quantified by Agilent Fragment Analyzer.
Library preparation and was performed using the Strand-specific cDNA library. RNA samples were subjected to purification of poly-A containing mRNA molecules, fragmented mRNA fragmentation. Random primed cDNA synthesis (strand-specific) and adapter ligation and adapter specific PCR amplification was then performed.

treatment_protocol: Administration of Placebo, Urolithin A 500 mg  and Urolithin A 1000 mg softgels for 4 month

value: Vastus lateralis muscle

tag: timepoint

value: 4 months

value: Urolithin A 1000 mg


title: K.VP.5.1_S5


title: K562.4_S4


title: K562.3_S3


title: A4141_115

value: Urolithin A 500 mg


title: A4141_114


title: A4141_118


title: A4141_117

value: Placebo


title: K562.1_S1


title: Bhas 42, NM-203, 1µg/cm², replicate 2

source_name: Bhas 42, NM-203, 1 µg/cm², replicate 2

value: Bhas 42 cells


title: A4141_112


title: A4141_116


title: Bhas 42, NM-203, 2µg/cm², replicate 1

source_name: Bhas 42, NM-203, 2 µg/cm², replicate 1


title: Bhas 42, H2O, replicate 3

source_name: Bhas 42, H2O, replicate 3


title: Bhas 42, H2O, replicate 1

source_name: Bhas 42, H2O, replicate 1


title: Bhas 42, NM-203, 1µg/cm², replicate 1

source_name: Bhas 42, NM-203, 1 µg/cm², replicate 1


title: Bhas 42, H2O, replicate 4

source_name: Bhas 42, H2O, replicate 4


title: Bhas 42, NM-203, 1µg/cm², replicate 3

source_name: Bhas 42, NM-203, 1 µg/cm², replicate 3


title: Bhas 42, H2O, replicate 2

source_name: Bhas 42, H2O, replicate 2


title: A4141_119


title: A4141_109


title: A4141_111


title: A4141_110


title: A4141_105


title: A4141_107


title: A4141_106


title: A4141_104


title: A4141_102


title: A4141_113


title: A4141_103


title: A4141_100


title: A4141_096


title: A4141_099


title: A4141_101


title: K.VP.5.4_S8


title: A4141_094


title: A4141_098


title: A4141_097


title: A4141_095


title: A4141_093


title: A4141_092


title: A4141_089


title: A4141_090


title: A4141_088


title: A4141_087


title: A4141_086


title: A4141_079


title: A4141_078


title: A4141_084


title: A4141_085


title: A4141_083


title: A4141_080


title: A4141_082


title: A4141_077


title: A4141_070


title: A4141_076


title: A4141_065


title: A4141_064


title: A4141_066


title: A4141_108


title: A4141_075


title: A4141_060

value: Baseline


title: A4141_059


title: A4141_074


title: A4141_073


title: A4141_071


title: A4141_057


title: A4141_058


title: A4141_091


title: A4141_063


title: A4141_068


title: A4141_072


title: A4141_061


title: A4141_056


title: A4141_055


title: A4141_069


title: A4141_062


title: A4141_054


title: A4141_051


title: A4141_053


title: A4141_044


title: A4141_047


title: A4141_046


title: A4141_049


title: A4141_042


title: A4141_041


title: A4141_038


title: A4141_048


title: A4141_036


title: A4141_037


title: A4141_040


title: A4141_043


title: A4141_035


title: A4141_039


title: A4141_032


title: A4141_052


title: A4141_033


title: A4141_050


title: A4141_029


title: A4141_031


title: A4141_028


title: A4141_030


title: A4141_027


title: A4141_034


title: A4141_026


title: A4141_025


title: A4141_045


title: A4141_019


title: A4141_023


title: A4141_021


title: A4141_020


title: A4141_017


title: A4141_018


title: A4141_016


title: A4141_014


title: A4141_015


title: A4141_010


title: A4141_012


title: A4141_011


title: A4141_009


title: A4141_013


title: A4141_006


title: A4141_004


title: Bhas 42, NM-203, 2µg/cm², replicate 2

source_name: Bhas 42, NM-203, 2 µg/cm², replicate 2


title: A4141_001


title: A4141_002


title: A4141_005


title: 45

city: NEW YORK

first: RUI

last: FU

address: 101 6th Ave

department: Computational Biology

institute: New York Genome Center

data_processing:
Raw sequencing reads were demultiplexed, mapped to the human reference genome (build GRCh38) as appropriate and gene-expression matrices were generated using CellRanger (version 3.1.0). The resulting count matrices were further filtered in Seurat 4.0.1 (https://satijalab.org/seurat/) to remove cell barcodes with less than 500 or more than 7000 genes, more than 20% of UMIs derived from mitochondrial genes.
Genome_build: GRCh38
Supplementary_files_format_and_content: UMI count matrices and associated cell-level metadata

source_name: bronchoalveolar lavage sample, Chronic beryllium disease

extract_protocol:
Bronchoalveolar lavage samples were collected from two Be-exposed subjects at National Jewish Health (NJH) Granuloma Clinic
3' end 10x Genomics library prep (v2)

value: bronchoalveolar lavage


title: Pol II_shYY1

city: Shanghai

first: Zhixin

last: Qiu

address: Dongan Road

institute: Fudan University

data_processing:
Raw FASTQ files were trimmed using TrimGalore and aligned to the hg19 human genome using Bowtie2.
SamTools was used to sort and index the BAM files.
The bigwig files were generated using the DeepTools “bamCoverage”
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

source_name: patient-derived cells

extract_protocol:
ChIP was performed using Magna ChIP™ A/G Chromatin Immunoprecipitation Kit (MilliporeSigma, 17-10085) according to the manufacturer’s instructions
Library was constructed using NEB NEBNext® Ultra™ DNA Library Prep Kit for Illumina for sequencing

value: patient-derived glioblastoma stem cells

tag: antibody

value: Pol II antibody (Sigma-Aldrich, cat # 05-623)


title: Pol II_shCONT

value: shCONT


title: 29

source_name: bronchoalveolar lavage sample, beryllium-exposed


title: A4141_024