title: Yki-head-2

city: Daejeon

first: Kyu-Sun

last: Lee

address: 125 Gwahak-ro

country: South Korea

institute: KRIBB

data_processing:
Alignment: Transcriptome with novel splices
Quality Trimming: >average Q20
Normalization Method: Global normalization(RC)
Genome_build: dm6 (UCSC)
Supplementary_files_format_and_content: tab-delimited text files include RC values for each Sample ...

organism: Drosophila melanogaster

source_name: head

extract_protocol:
To extract total RNAs for RNA sequencing (RNA-seq) experiments, 30 adult heads were dissected and isolated with easy-BLUE™ reagent (iNtRON biotechnology). RNA quality control and data analyses were performed by ebiogen (ebiogen.com).
RNA libraries were constructed by Lexogen SENSE mRNA Library Preparation Kit

value: head

tag: genotype

value: GMR>yki S168A


title: DNAse_seq-B6xCAST-B_cell-DS35986B

status: Public on Nov 25 2020

type: SRA

city: New York

first: Matthew

middle: T

last: Maurano

state: NY

address: 435 East 30th Street

department: Institute for Systems Genetics

country: USA

institute: NYU School of Medicine

library_source: genomic

data_processing:
Trimmed to remove low-quality sequence or adapter contamination using the trimmomatic tool (Parameters: TOPHRED33 ILLUMINACLIP: TruSeq3-PE2.fa:2:5:5:1:true MAXINFO:27:0.95 TRAILING:20 MINLEN:27')
Reads were mapped with Burrows-Wheeler Aligner to the mouse reference assembly and the strain-specific genome (Parameters: bwa aln -n 0.04 -l 32 -t 2 -Y)
Alignments were post-processed with a custom Python script using pysam to retain only properly-paired or single-end reads mapping  uniquely to the autosomes and chrX with a mapping quality of at least 20. Paired end reads were required to have an inferred template length of less than 500 bp.
Duplicate reads were flagged on a per-library basis using Samblaster
Mapped tags were converted to BED format using awk and bedops
DNase I hypersensitive sites were identified using hotspot2
RNA-seq eads were mapped to the mm10 reference and strain-specific genomes in parallel using STAR
Transcript counts were calculated using RSEM
Genome_build: mm10
Supplementary_files_format_and_content: bed.gz file containing DHS hotspots
Supplementary_files_format_and_content: bigWig files indicate DHS density
Supplementary_files_format_and_content: tsv file containing count data for Gencode M10 transcripts
Supplementary_files_format_and_content: bigWig indicating RNA-seq read denisty

molecule: genomic DNA

organism: Mus musculus

source_name: B cell

extract_protocol:
Whole liver (all lobes), both kidneys and all lobes of the lungs were rapidly dissected from sacrificed mice. Tissues were minced in 2 mm square pieces and resuspended in 5 mL of homogenization buffer per tissue. Nuclei were released using 5-10 strokes in a Dounce homogenizer with a loose-fitting type-A pestle and the resulting homogenate was filtered through a 120µm filter. Marrow was obtained from femurs of 8 week old female mice. B cells were isolated using an AutoMACS (Miltenyi Biotech) to deplete CD43 and Mac-1/CD11b markers. Nuclei were extracted by resuspending cells in buffer A supplemented with 0.015% detergent (IGEPAL-CA630) (Sigma) and incubating for 5-10 minutes on ice.
Fresh nuclei were digested with DNase I for 3 minutes. Fragments <250 bp were recovered by sucrose ultracentrifugation, end-repaired and ligated with adapters compatible with the Illumina sequencing platform. Libraries were amplified using minimal PCR cycles based on a trial qPCR amplification. Total RNA was isolated using the mirVana miRNA Isolation Kit with phenol (AM1560). Spike-in controls were mixed in (Ambion-ERCC Mix, Cat no. 4456740) and Illumina sequencing libraries were made using the RNA TruSeq Stranded total RNA (Illumina).

tag: strain

tag: tissue

value: B cell


title: Yki-head-1

library_source: transcriptomic

molecule: total RNA


title: DNAse_seq-B6xPWK-Kidney-DS36649B

source_name: Kidney

value: Kidney


title: DNAse_seq-B6xPWK-Lung-DS36657B

source_name: Lung

value: Lung


title: DNAse_seq-B6xPWK-Liver-DS36641B

source_name: Liver

value: Liver


title: control head-2


title: control head-1


title: DNAse_seq-B6xCAST-B_cell-DS35978A


title: DNAse_seq-B6xCAST-Kidney-DS35927B


title: DNAse_seq-B6xCAST-Lung-DS35910B


title: DNAse_seq-B6xCAST-Kidney-DS35927A


title: DNAse_seq-B6xCAST-Lung-DS35909A


title: larval CNS SKD-2

city: Cambridge

first: Rishav

last: Mitra

state: Massachusetts

address: 16 Divinity Avenue

institute: Harvard University

data_processing:
Reads were aligned to the genome using HISAT2 (Kim et al., 2015, 2019)
Mapped sequence reads were aligned to the genome to obtain read counts using Featurecounts (Liao et al., 2014)
Differential expression analysis was performed using two independent methods: DESeq2 (Love et al., 2014) and edgeR (Robinson et al., 2009)
Genome_build: dm3

source_name: CNS

growth_protocol: Drosophila strains were grown on standard cornmeal medium supplemented with yeast (ND) at 25°C under a light-dark cycle of 12h and 12h

extract_protocol:
RNA-seq from larval CNSs: RNA isolation was performed from 15 larval CNSs of 84h AEL larvae of both  genotypes using Trizol (Thermo Fisher Scientific)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: dSET2 RNAi/+; elavC155GAL4

value: larval CNS

tag: dev stage

value: 3rd instar (84h AEL)


title: larval CNS SKD-1


title: DNAse_seq-B6xCAST-Lung-DS35898B


title: larval CNS SKD-3


title: DNAse_seq-B6xCAST-Lung-DS35909B


title: larval CNS SC-2

value: dSET2 RNAi/+; Canton S


title: DNAse_seq-B6xCAST-Lung-DS35898A


title: DNAse_seq-B6xCAST-Lung-DS35897B


title: larval CNS SC-3


title: M130425

city: Geneva

first: Phil

middle: Fang

last: Cheng

address: Rue Gabrielle-Perret-Gentil 4

department: Oncology

country: Switzerland

institute: Hopitaux universitaires de Geneve

data_processing:
bcl2Fastq v2.19 software for demultiplexing + basecalling
reads trimmed with skewer v0.2.1
reads mapped with STAR v2.6.0a with default options
counts with STAR --quantmode GeneCounts
differential expression with limma/voom
Genome_build: GRCh38, gencode v22
Supplementary_files_format_and_content: tab-delimited files include stranded alignment for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and sample

organism: Homo sapiens

source_name: melanoma cells

growth_protocol: Melanoma cells were grown in RPMI 1640 with 10% FCS, 5 mM glutamine, and 1 mM sodium pyruvate.

extract_protocol:
RNA was extracted with QIAGEN RNeasy mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: melanoma cell culture

tag: treatment

value: Relapsed


title: MM130427


title: larval CNS SC-1


title: DNAse_seq-B6xCAST-Liver-DS35890B


title: DNAse_seq-B6xCAST-Lung-DS35897A


title: M130421


title: M130420


title: DNAse_seq-B6xCAST-Liver-DS35890A


title: DNAse_seq-B6xCAST-Liver-DS35889B


title: MM121224


title: MM130434


title: M130830


title: DNAse_seq-B6xCAST-Liver-DS35884B


title: DNAse_seq-B6xCAST-Liver-DS35884A


title: DNAse_seq-B6xCAST-Liver-DS35884C


title: DNAse_seq-B6xCAST-Liver-DS35889A


title: MM140902


title: MM131206


title: M150404

value: Before


title: DNAse_seq-B6xCAST-Liver-DS35877A


title: DNAse_seq-B6xC3H-B_cell-DS34569A


title: MM131205


title: DNAse_seq-B6xC3H-B_cell-DS34565A


title: DNAse_seq-B6xC3H-B_cell-DS34563A


title: DNAse_seq-B6xCAST-Liver-DS35877B


title: MM130106


title: MM130626


title: DNAse_seq-B6xC3H-Kidney-DS33568A


title: DNAse_seq-B6xC3H-Kidney-DS33567C


title: M130107


title: M980513


title: M121102


title: MM130926


title: DNAse_seq-B6xC3H-Kidney-DS33567A


title: DNAse_seq-B6xC3H-Kidney-DS33567B


title: B10APb_3

city: Brasília

first: Fabián

middle: Andrés

last: Hurtado Erazo

state: DF

address: Campus universitário Darcy Ribeiro. Asa Norte

department: University of Brasília Medical School

country: Brazil

institute: University of Brasília

description: B10APb experiment

data_processing:
Quality check was performed by FastQC v0.11.2 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), adaptor removal using Cutadapt v1.7.1 (Martin, 2011), and read trimming using PRINSEQ (Schmieder and Edwards, 2011)
Alignments to the Mouse reference genome GRCh38.75 were performed by Tophat v2.0.11 (Trapnell et al., 2009)
HTSeq-count v0.5.0 (Anders and Huber, 2014) was used to count and compare aligned reads to annotated mouse genes
The relative gene expression was calculated using EdgeR v3.30.3 (Robinson et al., 2009) in R v4.0.1
Genome_build: Mus musculus GRCm38.75
Supplementary_files_format_and_content: tab-delimited text files include Matrix table with raw gene counts for every gene and every sample

source_name: Bone Marrow derived dendritic cells

growth_protocol: BMDCs were derived from the bone marrow of the A/J and B10.A strains were obtained by the method described by Lutz et al. (1999) with the use of GM-CSF (Recombinant PEPROTECH cat no: 315-03). Lutz, Manfred B., et al. "An advanced culture method for generating large quantities of highly pure dendritic cells from mouse bone marrow." Journal of immunological methods 223.1 (1999): 77-92.

extract_protocol:
The total RNA of the cultured BMDCs was obtained employing the RNAeasy® Plus Mini Kit (QIAGEN cat. No. 74134), in accordance with the manufacturer's protocol. After the quality analysis (Bioanalyser 2100 - Agilent) and quantification (Qubit® 2.0 Fluorometer - Life Technologies),  the samples from the different experimental conditions were prepared for the Stable transport at room temperature with the RNAstable kit (Biomatrica cat no. 93221-001), according to the manufacturer's recommendations. The dried samples were sent to the Scripps Research Institute for sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: BMDCs infected or not with P. brasiliensis (Pb18) at a cell-to-yeast ratio of 5:1 (multiplicity of infection, MOI: 5:1) for 6 hours in a humidified atmosphere of 5% CO2  at 37ºC

value: dendritic cells

tag: mice strain

tag: phenotype

value: susceptible

tag: age

value: 6-12 weeks

value: Paracoccidioides brasiliensis for 6 hours


title: B10APb_2

description: B10APb experiment


title: MM140905


title: DNAse_seq-B6xC3H-Kidney-DS33566C


title: DNAse_seq-B6xC3H-Kidney-DS33566B


title: MM150604


title: M121008


title: B10A_1

description: Control

value: untreated


title: B10APb_1

description: B10APb experiment


title: B10A_2

description: Control


title: MM150325


title: B10A_3

description: Control


title: AJPb_3

description: AJPb experiment

value: A/J

value: resistant


title: BMECs, EEF1D-1357 shRNA, replicate 3

type: RNA

city: Beijing

first: Shan

last: Lin

address: No.2 Yuan Mingyuan West Road

country: China

institute: China Agricultural University

description: Gene expression after RNAi with EEF1D-1357

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Genome Oligo Microarrays (G4112A) 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), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Bos taurus

source_name: BMECs, EEF1D-1357 shRNA

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS 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 NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted and purified, reversely transcribed into cDNA, and synthesized into cRNAs labeled with Cy3 using a Quick Amp Labeling Kit (Agilent).

treatment_protocol: Using the blocks of fresh mammary gland epithelial tissue collected from a lactating Holstein cow as the abovementioned, the primary BMECs were isolated, cultured and purified by tissue block culture and enzyme digestion method. The BMECs at the fifth passage were used for subsequent experiments.

value: Bovine mammary epithelial cell (BMEC)

tag: passage

value: fifth passage

value: EEF1D-1357 shRNA

value: EEF1D knockdown


title: BMECs, EEF1D-1357 shRNA, replicate 2


title: BMECs, without shRNA, replicate 1

description: Gene expression without RNAi

source_name: BMECs, without shRNA

value: control


title: BMECs, EEF1D-1357 shRNA, replicate 1


title: BMECs, EEF1D-1893 shRNA, replicate 1

description: Gene expression after RNAi with EEF1D-1893

source_name: BMECs, EEF1D-1893 shRNA

value: EEF1D-1893 shRNA


title: BMECs, without shRNA, replicate 2

description: Gene expression without RNAi


title: DNAse_seq-B6xC3H-Kidney-DS33566A

value: Kidney


title: BMECs, EEF1D-1893 shRNA, replicate 2


title: BMECs, EEF1D-1893 shRNA, replicate 3


title: AJ_3

description: Control


title: AJPb_1

description: AJPb experiment


title: MM130820

value: melanoma cell culture


title: AJPb_2

description: AJPb experiment


title: DNAse_seq-B6xC3H-Liver-DS33563A

value: Liver


title: DNAse_seq-B6xC3H-Liver-DS33561C


title: SNU16_H3K27ac_HiChIP

city: Stanford

first: Howard

middle: Y

last: Chang

state: CA

address: CCSR 2130, 269 Campus Drive

department: Center for Personal Dynamic Regulomes

institute: Stanford University

description: H3K27ac HiChIP library

data_processing:
Library strategy: HiChIP
Sequencing reads were aligned and paired, filtered for long-range contacts, and removed of duplicates using the HiC-Pro pipeline (PMID: 26619908)
Filtered reads were converted to a .hic file for visualization with Juicebox (PMID: 25497547)
Genome_build: hg19
Supplementary_files_format_and_content: HiC output from the Juicebox Tools pipeline. Matrix file to visualize long-range interactions with Juicebox.

source_name: SNU16 cells

growth_protocol: Cells were maintained in DMEM/F12  (Gibco, #11320-082) supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin.

extract_protocol:
HiChIP libraries were generated as described previously (PMID: 27643841).
Nextera

tag: chip antibody

value: H3K27ac (Abcam ab4729)


title: KO_Dam_control

city: Edinburgh

first: Jose

middle: Ignacio

last: de las Heras

address: Max Born Crescent

department: Wellcome Trust Centre

country: United Kingdom

institute: University of Edinburgh

description: KO Dam control

data_processing:
Library strategy: DamID-seq
Basecalls and quality filtering performed by BGI according to their standard procedures
Clean reads were aligned to the mouse mm9 genome using the Burrows-Wheeler aligner bwa mem. Mitochondrial sequences (a common contaminant in these experiments) and unaligned reads were filtered out.
Reads were counted per DpnI fragment (genomic sequence flanked by GATC motifs), and log2(ratio LaminB1/dam) measurements were obtained for WT and KO samples. The log2 ratios were then normalised using quantile normalisation (Bioconductor Limma package) and converted to bigwig format for visualisation purposes.
To identify LADs, we used a circular binary segmentation algorithm (CBS) from the R/Bioconductor package 'DNAcopy' (Venkatraman E. Seshan and Adam Olshen (). DNAcopy: DNA copy number data analysis. R package version 1.44.0) using default parameters. Positive signal segments identified by the CBS algorithm were merged if closer than 5Kb, and then any regions smaller than 10Kb were removed.
Regions that change peripheral association between conditions (PI regions represent loss of peripheral association after activation, and IP regions represent a gain) were then identified by comparing the LAD regions between the two conditions. Regions smaller than 10Kb were discarded.
Genome_build: mm9
Supplementary_files_format_and_content: LADs_N_wt_10cut_sm20_t01.bed -  LAD peaks (BED format) for WT hepatocytes
Supplementary_files_format_and_content: LADs_N_wt_10cut_sm20_t01.bed -  LAD peaks (BED format) for Tm7sf2/NET47 KO hepatocytes
Supplementary_files_format_and_content: DR_12_WT.bed - contains coordinates for differential regions (DR) that appear more associated with the nuclear envelope in the WT hepatocytes (PI regions)
Supplementary_files_format_and_content: DR_12_KO.bed - contains coordinates for differential regions (DR) that appear more associated with the nuclear envelope in the KO hepatocytes (IP regions)
Supplementary_files_format_and_content: sq3_smooth_20_wt.bw - contains DamID profiles for WT hepatocytes as log2(LaminB1/Dam-control), for visualisation purposes
Supplementary_files_format_and_content: sq3_smooth_20_ko.bw - contains DamID profiles for KO hepatocytes as log2(LaminB1/Dam-control), for visualisation purposes

source_name: primary hepatocyte

growth_protocol: Mice were maintained and primary hepatocytes obtained as described in Gatticchi et al. (2019) Methods 157:88-99 (PMID 30445179)

extract_protocol:
DamID protocol: Lentivirus encoding the control Dam, or LaminB1-Dam fusion, were used to transduce hepatocytes from WT of Tm7sf2/NET47 KO mice, and genomic DNA extracted and processed for DamID as described in Gatticchi et al. (2019) Methods 157:88-99 (PMID 30445179)
Genomic DNA was extracted using Qiagen DNA-Easy kit, following manufacturer's instructions.
DamID enrichment protocol: Dam-methylated genomic DNA was enriched using the standard protocol as described by Vogel et al. (2007) Nature Protocols 2:1467-1478. It involves digesting gDNA with DpnI enzyme, which cuts at non-Adenine-methylated GATC motifs.
Libraries were prepared by Beijing Genomics Institute (BGI) to Illumina's specifications

treatment_protocol: Tm7sf2/NET47 mouse KO was generated as described in Bennati et al. (2008) FEBS J. 20:5034-5047 (PMID 18785926)

value: hepatocyte

value: Tm7sf2/NET47 KO

tag: damid

value: Dam


title: KO_LaminB1-Dam

description: KO LaminB1-Dam


title: COLO320DM_H3K27ac_HiChIP

description: H3K27ac HiChIP library

source_name: COLO320-DM cells

growth_protocol: Cells were maintained in RPMI (Life Technologies, #11875-119) supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin.


title: WT_LaminB1-Dam

description: WT LaminB1-Dam

value: WT


title: SNU16_input

description: Input DNA for ChIP-seq library

data_processing:
Paired-end reads were aligned to the hg19 genome using Bowtie2 with the --very-sensitive option following adapter trimming with Trimmomatic.
Reads with MAPQ values less than 10 were filtered using samtools and PCR duplicates removed using Picard’s MarkDuplicates.
MACS2 was used for peak calling with the following parameters: macs2 callpeak -t  chip_bed -c input_bed -n output_file -f BED  -g hs -q 0.01 --nomodel --shift 0.
ChIP-seq signal was converted to bigwig format for visualization using deepTools bamCoverage with the following parameters: --bs 5 --smoothLength 105 --normalizeUsing CPM --scaleFactor 10.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig (bw) files contain normalized, smoothened ChIP-seq signal merged across technical replicates for visualization.

growth_protocol: Cells were maintained in DMEM/F12 (Gibco, #11320-082) supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin.

extract_protocol:
Sonicated chromatin from cross-linked cells was immunoprecipitated using H3K27ac (Abcam ab4729) and BRD4 (Bethyl Laboratories A301-985A100) antibodies. Following crosslink reversal, RNAse and Proteinase K treatment, immunoprecipitated DNA was purified using the ChIP DNA Clean & Concentrator kit (Zymo Research D5205).
Libraries were constructed using the NEBNext Ultra II DNA Library Prep Kit for Illumina kit.


title: SNU16_BRD4_rep2

description: BRD4 ChIP-seq library

value: BRD4 (Bethyl Laboratories A301-985A100)


title: AJ_2

description: Control

value: dendritic cells

value: A/J

value: 6-12 weeks

value: untreated


title: WT_Dam_control

description: WT Dam control


title: CUT&RUN_Nppa-bdKO_HOM3

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

country: Netherlands

institute: Amsterdam UMC

description: CRISPR deletion Nppa-Nppb

data_processing:
Reads were mapped to mm10 build of the mouse genome using BWA (Li et al., 2009) using default settings.
Peaks were called on each sample using MACS2. We used fixed background lambda as local lambda for every peak region. Q-value cut-off was set at 0.1. Otherwise default settings were used.
Genome_build: mm10
Supplementary_files_format_and_content: .bed files contain called peaks per sample. For .bigWig files the replicates per group were merged.

source_name: HOM

growth_protocol: Animal care and experiments conform to the Directive 2010/63/EU of the European Parliament. All animal work was approved by the Animal Experimental Committee of the Academic Medical Center, Amsterdam, and was carried out in compliance with the Dutch government guidelines. Myh6-MerCreMer (Sohal et al., 2001) , nTnG (JAX stock #023035) and Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/J (JAX stock #021039) mice were bred on the FVB/N background.

extract_protocol:
Cardiomyocyte nuclear isolation (Gilsbach et al Nat Commun 2014) was performed on left ventricular tissue followed by the CUT&RUN protocol (Hainer and Fazzio Curr Protoc Mol Biol 2019)
The NEBNext Ultra 2 DNA library preparation kit (NEB E7645S, E7335S)
CUT&RUN DNA library

treatment_protocol: Cardiomyocyte nuclei isolation: PCM-1 antibody (rabbit, Atlas antibodies HPA023370); CUT&RUN: H3K27ac antibody (Active Motif 39133)

value: FVB

value: 8-12 weeks

value: PCM-1 sort left ventricle


title: DNAse_seq-B6xC3H-Liver-DS33561B


title: DNAse_seq-B6xC3H-Liver-DS33561A


title: SNU16_BRD4_rep1

description: BRD4 ChIP-seq library


title: AJ_1

description: Control

value: resistant


title: DNAse_seq-B6xC3H-Liver-DS33560D


title: CUT&RUN_Nppa-bdKO_WT2

source_name: WT


title: SNU16_H3K27ac_rep2

description: H3K27ac ChIP-seq library


title: CUT&RUN_Nppa-bdKO_WT3


title: CUT&RUN_Nppa-bdKO_HOM1

description: CRISPR deletion Nppa-Nppb


title: DNAse_seq-B6xC3H-Liver-DS33560C


title: CUT&RUN_Nppa-bdKO_WT1


title: CUT&RUN_Nppa-bdKO_HOM2

description: CRISPR deletion Nppa-Nppb


title: DNAse_seq-B6xC3H-Liver-DS33560A


title: DNAse_seq-B6xC3H-Liver-DS33560B


title: DNAse_seq-B6xC3H-Lung-DS33554C

value: Lung


title: COLO320HSR_JQ1_input

description: Input DNA for ChIP-seq library

source_name: COLO320-HSR cells

value: 500 nM JQ1, 6 hours


title: COLO320HSR_JQ1_BRD4_rep2

description: BRD4 ChIP-seq library


title: MSC.MM28

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

country: Spain

institute: Josep Carreras Research Institute (IJC)

description: Gene expression data from human clinical samples

hyb_protocol: Hybridized to the Affymetrix GeneChip Human Gene 1.0 ST oligonucleotide microarray, after quality checking on GeneChips Test Arrays.

scan_protocol: Labeling and hybridization were performed according to protocols from Affymetrix.

data_processing: R studio

label: biotin

source_name: Bone marrow

growth_protocol: Primary MSCs from bone marrow (BM) samples of healthy donors (n=8), MGUS (n=10), SMM (n=10) and MM patients (n=24) were generated as described by Garayoa et al. 2009 (PMID:19357701). Ficoll-Paque density gradient separation medium was used to isolate mononuclear cells from BM aspirates. MSCs were selected by adherence to plastic and subsequently expanded until passage 2 when they were used for experiments.

extract_protocol: RNA isolation, labelling and microarray hybridization was done following the manufacturer’s protocols for the GeneChip platform: Human Gene 1.0 ST oligonucleotide arrays (Affymetrix).

treatment_protocol: MSCs were recovered by trypsinization, washed once in PBS and stored at -20°C in RLT buffer (Qiagen) until RNA extraction.

tag: gender

value: male

tag: disease state

value: multiple myeloma


title: MSC.MM27

label_protocol: Labeling and hybridization were performed according to protocols from Affymetrix.


title: COLO320HSR_JQ1_BRD4_rep1

description: BRD4 ChIP-seq library


title: DNAse_seq-B6xC3H-Lung-DS33554B


title: MSC.MM29

value: female


title: SNU16_H3K27ac_rep1

description: H3K27ac ChIP-seq library

value: H3K27ac (Abcam ab4729)


title: COLO320HSR_DMSO_BRD4_rep2

description: BRD4 ChIP-seq library

value: DMSO


title: MSC.MM26


title: MSC.MM25


title: DNAse_seq-B6x129-B_cell-DS33340B

source_name: B cell

value: B cell


title: DNAse_seq-B6x129-B_cell-DS33342A


title: DNAse_seq-B6x129-B_cell-DS33340A


title: COLO320HSR_DMSO_BRD4_rep1

description: BRD4 ChIP-seq library

value: BRD4 (Bethyl Laboratories A301-985A100)


title: COLO320HSR_DMSO_H3K27ac_rep2

description: H3K27ac ChIP-seq library


title: MSC.MM24


title: COLO320HSR_DMSO_H3K27ac_rep1

description: H3K27ac ChIP-seq library


title: MSC.MM17


title: COLO320HSR_DMSO_input

description: Input DNA for ChIP-seq library


title: DNAse_seq-B6xC3H-Lung-DS33554A


title: DNAse_seq-B6x129-B_cell-DS33334B


title: MSC.MM12


title: MSC.MM16


title: MSC.MM18


title: MSC.MM15


title: MSC.MM23


title: MSC.MM13


title: MSC.MM10


title: DNAse_seq-B6x129-B_cell-DS33334A


title: MSC.MM9


title: MSC.MM8


title: COLO320DM_JQ1_input

description: Input DNA for ChIP-seq library


title: MSC.MM11


title: COLO320DM_JQ1_BRD4_rep2

description: BRD4 ChIP-seq library


title: MSC.MM7


title: DNAse_seq-B6x129-Kidney-DS32759A

source_name: Kidney

value: Kidney


title: DNAse_seq-B6x129-Kidney-DS32758A


title: DNAse_seq-B6x129-Liver-DS32753E

value: Liver


title: MSC.MM4


title: DNAse_seq-B6xCAST-Lung-DS35910A

source_name: Lung


title: MSC.MM6


title: MSC.MM5


title: MSC.MM3


title: MSC.MM2


title: MSC.MM1


title: DNAse_seq-B6x129-Liver-DS32753D

source_name: Liver


title: COLO320DM_DMSO_BRD4_rep2

description: BRD4 ChIP-seq library


title: DNAse_seq-B6x129-Liver-DS32753C


title: DNAse_seq-B6x129-Liver-DS32753B


title: COLO320DM_DMSO_BRD4_rep1

description: BRD4 ChIP-seq library


title: COLO320DM_JQ1_BRD4_rep1

description: BRD4 ChIP-seq library


title: COLO320DM_DMSO_H3K27ac_rep2

description: H3K27ac ChIP-seq library


title: DNAse_seq-B6x129-Liver-DS32753A


title: COLO320DM_DMSO_H3K27ac_rep1

description: H3K27ac ChIP-seq library


title: DNAse_seq-B6x129-Liver-DS32752D


title: DNAse_seq-B6x129-Liver-DS32752B


title: ∆s14a_∆s14b_R136A_rep3

city: Solna

first: Vicent

last: Pelechano

address: Nobels väg 16

department: MTC

country: Sweden

institute: ScilifeLab - Karolinska Institutet

description: HT-5Pseq ∆s14a ∆s14b R136A mutant replicate 3

data_processing:
Base calling and demultiplexing was performed using bcl2fastq and a sample sheet, with default settings
Illumina sequencing adapters were trimmed from the reads using cutadapt
The first 8 bases of each read were extracted as the UMI with umi-tools
Reads were mapped to the R64-1-1 version of S. cerevisiae genome using STAR aligner
Mapped files were deduplicated using umi-tools
Deduplicated files were processed with the fivepseq pipeline  as of May 2020 (Nersisyan et al., https://doi.org/10.1101/2020.01.22.915421)
Deduplicated .bam files were converted to bedgraph using bedtools genomecov
Genome_build: R64-1-1
Supplementary_files_format_and_content: Strand-specific bedgraph files with coverage of only the 5' positions of reads across the genome

organism: Saccharomyces cerevisiae

growth_protocol: The strains were grown in liquid YPD medium at 30 ºC

extract_protocol:
RNA was extracted from yeast cells using the hot phenol procedure. The amount of RNA was quantified in a Nanodrop 2000 Spectrophotometer (Thermo Scientific) and RNA integrity was checked by agarose gel electrophoresis.
HT-5Pseq libraries were prepared as in (Y. Zhang & V. Pelechano, 2020 bioRxiv) from 6 µg total RNA per sample. Briefly, the RNA was treated with TURBO DNase (Thermo Fisher) to digest DNA. After inactivation of the DNase, RNA was precipitated with ethanol and sodium acetate. The pellet was resuspended directly in ligation mix. A single-stranded RNA adapter was ligated to the RNA using T4 RNA ligase (NEB) o/n at 16 degrees C. The sample was purified with 2 volumes of RNAClean XP beads (Beckman Coulter). The purified RNA was reverse-transcribed using Superscript II (Thermo Fisher) with a combination of two custom primers, each containing a partial Illumina adapter sequence and either a random hexamer or an oligo-dT sequence. RNA was depleted with NaOH treatment at 65 degrees C. cDNA was purified using 2 volumes RNAClean XP beads (Beckman Coulter). Ribosomal cDNA was depleted using duplex-specific nuclease and specific probes. Remaining cDNA was purified using 2 volumes RNAClean XP beads (Beckman Coulter). Illumina sequencing libraries were prepared from the cDNA by PCR using Phusion high-fidelity PCR master mix (Thermo Fisher). After PCR, libraries were size-selected with 0.7 and 0.9 volumes AMPure XP beads.

treatment_protocol: None. Cells were harvested at an OD600 of about 0.8

value: As W303-1B but MATa rps14A::HIS3MX6 rps14B::natNT2 [YCplac22-rps14A-R136A]

tag: parental strain


title: ∆s14a_∆s14b_R136A_rep2

description: HT-5Pseq ∆s14a ∆s14b R136A mutant replicate 2


title: COLO320DM_DMSO_input

description: Input DNA for ChIP-seq library


title: MSC.SM6

value: smoldering myeloma


title: ∆s14a_∆s14b_R136A_rep1

description: HT-5Pseq ∆s14a ∆s14b R136A mutant replicate 1


title: DNAse_seq-B6x129-Liver-DS32752A


title: MSC.SM11


title: MSC.SM8


title: MSC.SM5


title: MSC.SM4


title: MSC.MG10

value: MGUS


title: DNAse_seq-B6x129-Lung-DS32747A


title: ∆ltv1_rep3

description: HT-5Pseq in ∆ltv1 mutant replicate 3

value: As W303-1B but MATa ltv1::hphNT1


title: MSC.SM1


title: DNAse_seq-B6x129-Lung-DS32746C


title: MSC.MG9


title: MSC.MG8


title: P6.WT.6

city: Bethesda

first: Anand

last: Swaroop

state: MD

address: 6 Center Dr, Bldg 6, Room 303

department: NEI

institute: NIH

data_processing:
Demultiplexed NGS reads were quality checked and trimmed with FastQC and Trimmomatic (v3.6). Filtered paired end reads were aligned to the Mus musculus transcriptome reference ENSEMBL v84 using Kallisto (v0.44) quant to generate read counts for individual transcripts, which were subsequently imported in R and processed with the package tximport (v1.10.1) to generate aligned read counts for genes.
Finally, the gene count matrix was processed with functions of the edgeR (v3.24.2) and limma (v3.38.3) packages, to normalize to export CPM values.
Voom transformation was applied to the data and further differential expression analyses was performed using the standard linear bayes fit method, by creating appropriate design and contrast matrix corresponding to age-matched pairwise tests between WT and Rabgef1 KO samples.
Genome_build: Ensembl v84 annotations based on GRCm38

molecule: polyA RNA

source_name: retinal transcriptome at P6 of Rabgef1 WT mice

extract_protocol:
Directional RNA-seq library construction was performed from 100 ng of high quality RNA (RIN > 8.0) using the Illumina Stranded mRNA Library Prep Kit (Illumina).
Library construction from two or three biological replicates for all time points was performed.

treatment_protocol: BALB/cJ mice were purchased from Charles River Laboratories (Germantown, MD, USA). Generation of Rabgef1-/- mice was described previously {Tam, 2004}. Rabgef1+/- males (procured from the Galli lab at Stanford University) were crossed to wildtype BALB/cJ females to refresh the colony. The mice used for our study were subsequently generated from intercrosses of these heterozygous mice. Rabgef1 mice were genotyped for three alleles including the common allele (6505) 5’- TTA GAG GAG GTT GTG AGC TGCCAT-3’, Wildtype Allele (6506) 5’- TGC AGC TTA CTC AGG CAT GGA AGA-3’, and Mutant Allele (6534) 5’-GAC GTG CTA CTT CCA TTT GTC ACG -3’. The mutant band is 1000 bp, while the wildtype is 840 bp. The PCR was performed with the following steps: Step 1. 94°C for 60 sec. Step 2. 94°C for 15 sec. Step 3. 66°C for 60 sec. Step 4. 72°C 90 sec. Repeat steps 2, 3, and 4 for 35-40 cycles, depending on concentration of starting DNA. Step 5. 72°C 10 min. Step 6. 4°C. It should be noted that the Rabgef1 PCR reaction required 5M Betaine (Sigma) and 3% DMSO, in order to stabilize the DNA. To obtain tissues for analysis, we examined animals from Rabgef1 heterozygous intercrosses, with wildtype and heterozygous Rabgef1 mice serving as controls. Original founders were genotyped and found negative for RD1 and RD10 mutations, given that these are known to cause photoreceptor degeneration and are extremely common in a variety of inbred murine strains {Chang, 2013}.  Male and female mice in this study were used equally in all experimental procedures. Mice were maintained on a normal 12 h light/dark cycle (6:00 A.M. to 6:00 P.M) (unless otherwise noted) with unlimited access to food and water. All mouse procedures were approved by the Animal Care and Use Committees at the National Institutes of Health. Mice were used in accordance with the Statement for the Use of Animals in Ophthalmic and Vision Research of the Association for Research in Vision and Ophthalmology.

tag: genotype/variation

value: Rabgef1 WT

value: retina


title: MSC.SM10


title: MSC.SM2


title: MSC.MG6


title: P6.WT.4


title: MSC.SM3


title: P6.WT.2


title: MSC.MG7


title: ∆ltv1_rep1

description: HT-5Pseq in ∆ltv1 mutant replicate 1


title: ∆ltv1_rep2

description: HT-5Pseq in ∆ltv1 mutant replicate 2


title: ubi_∆ub3_∆zuo1_rep2

description: HT-5Pseq in ubi ∆ub3 ∆zuo1 mutant replicate 2

source_name: ORY

value: As W303-1B but ubi3<delta>ub-HA::kanMX4 zuo1::HIS3MX6


title: ubi_∆ub3_∆zuo1_rep1

description: HT-5Pseq in ubi ∆ub3 ∆zuo1 mutant replicate 1


title: MSC.SM12


title: P6.KO.5

source_name: retinal transcriptome at P6 of Rabgef1 KO mice

value: Rabgef1 KO


title: ubi_∆ub3_rep3

description: HT-5Pseq in ubi ∆ub3 mutant replicate 3

value: As W303-1B but ubi3<delta>ub-HA::kanMX4


title: ubi_∆ub3_∆zuo1_rep3

description: HT-5Pseq in ubi ∆ub3 ∆zuo1 mutant replicate 3


title: MSC.MG2

value: male


title: ubi_∆ub3_rep2

description: HT-5Pseq in ubi ∆ub3 mutant replicate 2


title: MSC.MG3


title: MSC.MG5

value: female


title: MSC.D9

value: healthy


title: P6.KO.3


title: P6.KO.1


title: MSC.D8


title: MSC.MG4


title: MSC.D5


title: P14.WT.3

source_name: retinal transcriptome at P14 of Rabgef1 WT mice


title: P14.WT.4


title: ubi_∆ub3_rep1

description: HT-5Pseq in ubi ∆ub3 mutant replicate 1


title: MSC.D3


title: ∆zuo1_rep3

description: HT-5Pseq in ∆zuo1 mutant replicate 3

value: As W303-1B but zuo1::HIS3MX6


title: P14.WT.1


title: MSC.D11


title: P14.KO.2

source_name: retinal transcriptome at P14 of Rabgef1 KO mice


title: ∆zuo1_rep1

description: HT-5Pseq in ∆zuo1 mutant replicate 1


title: MSC.D1


title: ∆zuo1_rep2

description: HT-5Pseq in ∆zuo1 mutant replicate 2


title: P14.KO.1


title: W303_rep3

description: HT-5Pseq in wildtype W303 replicate 3

value: MAT alpha ade2-1 his3-11,15 leu2-3,112 trp1-1 ura3-1


title: W303_rep2

description: HT-5Pseq in wildtype W303 replicate 2


title: MSC.D2


title: MSC.MG1


title: MSC.D4


title: P10.WT.3

source_name: retinal transcriptome at P10 of Rabgef1 WT mice


title: P10.WT.2


title: P10.WT.1


title: P10.KO.3

source_name: retinal transcriptome at P10 of Rabgef1 KO mice


title: W303_rep1

description: HT-5Pseq in wildtype W303 replicate 1


title: coIP RbpH::3xFLAG (26695)

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

country: Germany

institute: ZB MED - Information Centre for Life Sciences

description:
coIP_RbpH-3xFLAG_26695
RbpH-bound RNA

data_processing:
Demultiplexing
Fastq quality trimming using FastX and a cut-off value of 20
Fastq to fasta conversion using FastX
Size filtering: discarding reads shorter than 12 nt (READemption 0.3.3)
Read mapping using segemehl version 0.1.7 (READemption 0.3.3)
Coverage calculation and normalization (READemption 0.3.3)
Genome_build: H. pylori 26695: NC_000915.1; H. pylori G27: NC_011333.1, NC_011334.1
Supplementary_files_format_and_content: wiggle

organism: Helicobacter pylori

source_name: Helicobacter pylori 26695 cells

growth_protocol: Cells were grown to mid-exponential phase (~0.6 OD600) in Brain Heart Infusion medium (+10% FCS). Cells corresponding to 100 OD600 were harvested to perform coIP.

extract_protocol:
Phenol/Chloroform/Isoamyl alcohol RNA extraction (Rieder et. al., RNA Biology 2012)
The libraries were generated by Vertis Biotechnologie AG (Munich, Germany).

treatment_protocol: Cells were lysed and an anti-FLAG antibody (monoclonal anti-FLAG M2, Sigma, #F 1804)/sepharose beads (#P6649, Sigma) were used to co-immunoprecipitate RbpH-3xFLAG and bound RNA.

tag: rip antibody

value: monoclonal anti-FLAG M2 (Sigma, catalog# F1804)


title: coIP 26695 WT (control)

description:
coIP_WT_26695
RbpH-bound RNA

value: WT (control)


title: P10.KO.2


title: coIP G27 WT (control) replicate 2

description:
coIP_WT_G27_R2
RbpH-bound RNA

source_name: Helicobacter pylori G27 cells


title: P10.KO.1


title: coIP RbpH::3xFLAG (G27) replicate 2

description:
coIP_RbpH-3xFLAG_G27_R2
RbpH-bound RNA


title: G27 rbpH OE (overexpression) RNA-seq

data_processing:
Demultiplexing
Fastq quality trimming using FastX and a cut-off value of 20
Fastq to fasta conversion using FastX
Size filtering: discarding reads shorter than 12 nt (READemption 0.3.3)
Read mapping using segemehl version 0.1.7 (READemption 0.3.3)
Coverage calculation and normalisation (READemption 0.3.3)
Genome_build: H. pylori G27: NC_011333.1, NC_011334.1
Supplementary_files_format_and_content: wiggle

growth_protocol: Cells were grown to mid-exponential phase (~0.6 OD600) in Brain Heart Infusion medium (+10% FCS). Cells corresponding to 4 OD600 were harvested to isolate RNA.

extract_protocol:
Hot Phenol RNA extraction (Sharma et. al., Nature 2010)
The libraries were generated by Vertis Biotechnologie AG (Munich, Germany).

treatment_protocol: Cells were lysed by lysozyme/hot phenol/SDS and total RNA was purified by DNase treatment and ethanol precipitation

value: rbpH OE (overexpression)


title: Kras*+Injury_scATAC

city: New York City

first: Cassandra

last: Burdziak

state: New York

address: 417 E 68th St

institute: Memorial Sloan Kettering Cancer Center

description:
PE-50
DACD404-mKate2+

data_processing:
scATAC-seq data was processed with the CellRanger ATAC pipeline, version v1.1.0, with custom modifications (see Methods for full details).
Genome_build: mm10
Supplementary_files_format_and_content: cell by gene count matrices

source_name: sorted primary pancreatic epithelial cells

growth_protocol: 5 weeks-old KC;RIK (p48-Cre;RIK;LSLKrasG12D) littermate male mice were treated with 8 hourly intraperitoneal injections of 80 μg/kg caerulein (Bachem) or PBS for 2 consecutive days.

extract_protocol:
FACS-sorted cells were lysed in cold-lysis buffer (0.1% NP-40, 0.1% Tween 20, 0.01% Digitonin, 10 mM NaCl, 3 mM MgCl2 and 10 mM Tris-HCl [pH 7.4]), washed and processed according to “Nuclei Isolation for Single-Cell ATAC Sequencing” protocol (CG000169 RevD). Resulting nuclei suspension was subjected to transposition reaction for 60 min at 37°C and then encapsulated in microfluidic droplets using 10X Chromium instrument following manufacturer’s instructions with a targeted nuclei recovery ~ 5,000.
Barcoded DNA material was cleaned and prepared for sequencing according to the Chromium Single Cell ATAC Reagent Kits User Guide (10x Genomics; CG000168 RevA). Purified libraries were assessed using a Bioanalyzer High-Sensitivity DNA Analysis kit (Agilent) and sequenced on a Illumina HiSeq 2500 (High Output) platform at approx. 150M reads (R1 50bp, R2 50 bp, i7 8bp, i5 16bp) per 1 sample (~ 5000 nuclei) at MSKCC’s Integrated Genomics Operation Core.

treatment_protocol: Pancretata were harvested from the indicated mouse models and processed for FACS sorting using Collagenase (1mg/mL) & Dispase (2U/mL) mix digestion solution and Gentle-MACS dissociator (mTDK_1 protocol), followed by a 0.05% Trypsin-EDTA step. Cell suspensions were incubated with Fc block and CD45-APC antibody to mark immune cells. Live pancreatic epithelial cells (marked as mKate2- or GFP-positive, CD45-negative and DAPI-negative) were sorted using Aria3 sorter, and collected in 2% 1x PBS buffer containing 2% fetal bovine serum (FBS).

tag: experimental condition

value: Kras*+Injury

tag: model

value: KC;RIK GEMM

tag: alleles (gemm)

tag: oncotype (sorted cells)

value: Caerulein

tag: sample collection time point

value: Day 2 post-caerulein

value: pancreas

tag: sorting strategy

tag: age / stage (upon sample collection)

value: 5 - 6 weeks old

tag: Sex

value: Male


title: Kras*_scATAC

description:
PE-50
DACD408-mKate2+

value: Kras*

tag: treatment

value: PBS

value: Day 2 post-PBS

tag: tissue


title: G27 rbpH complementation RNA-seq

tag: strain

value: rbpH complementation


title: IMR32 cells, combination

type: genomic

city: Kitaadachi-gun

first: Hisanori

last: Takenobu

state: Saitama

address: 818, Komuro, Ina-machi

department: Research Institute for Clinical Oncology

country: Japan

institute: Saitama Cancer Center

hyb_protocol: Standard Illumina Protocol

scan_protocol: Arrays were imaged using Illumina iScan according to manufacturer's specifications (Illumina Inc.).

data_processing: The data were analyzed using GenomeStudio Methylation Module Software (v1.9.0). Beta values were obtained after background correction and normalization to internal controls.

label: Cy5 and Cy3

source_name: combination

label_protocol: Standard Illumina Protocol

growth_protocol: Human NB cell line IMR32 were cultured in RPMI1640 (Wako) supplemented with 10% heat-inactivated fetal bovine serum (Invitrogen) and 50 ?g/ml penicillin/streptomycin (Sigma–Aldrich) in an incubator with humidified air at 37 °C with 5% CO2

extract_protocol: Cells were lysed by proK treatment. After lysis, DNA were extracted using phenol/chloroform.

treatment_protocol: IMR32 cells were treated with 0.1% DMSO, 1 uM EPZ-6438, and/or 1 uM 5-Aza-dc for 5 days.

tag: cell line

value: neuroblastoma cell line IMR32

value: combination


title: IMR32 cells, mock

source_name: mock

value: mock


title: IMR32 cells, 5-aza-dc


title: MSC.MM10

description:
200340580024_R08C01
DNA methylation data from human clinical samples

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol

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

data_processing: Rstudio

label: Cy3, Cy5

source_name: Bone marrow

growth_protocol: Primary MSCs from bone marrow (BM) samples of healthy donors (n=8), MGUS (n=10) and SMM (n=8), multiple myeloma (MM) patients (n=9) were generated as described by Garayoa et al. 2009 (PMID:19357701). Ficoll-Paque density gradient separation medium was used to isolate mononuclear cells from BM aspirates. MSCs were selected by adherence to plastic and subsequently expanded until passage 2 when they were used for experiments.

extract_protocol: Genomic DNA was extracted using proteinase K according to standard protocols

treatment_protocol: MSCs were recovered by trypsinization, washed once in PBS and stored at -20°C in DNA extraction buffer

value: F

tag: age

tag: donor

value: MM

tag: batch


title: IMR32 cells, EPZ-6438


title: MSC.MM5

description:
200240850123_R07C01
DNA methylation data from human clinical samples

value: M


title: MSC.MM9

description:
200298840144_R03C01
DNA methylation data from human clinical samples


title: Injury_ATAC5

first: Richard

last: Koche

address: 417 East 68th St

department: Center for Epigenetic research

description:
D8_3
PE-50

data_processing:
ATAC-seq reads were filtered for quality and 3' trimmed for adapter sequences using trimgalore
Reads were aligned to mouse assembly mm9 using bowtie2 (v2.2.2) with default parameters.
Read count tables were created using featureCounts v1.6.0.
To create density files, the signal was normalized using the scalefactors from DESeq2 converted to BigWig using BEDTools.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files containing read densities normalized using DESeq2
Supplementary_files_format_and_content: ATAC_PeakNorm.txt: All ATAC peaks from all samples were merged by combining peaks within 500bp of each.  featureCount was used to count the mapped reads for each sample. The resulting peak atlas was normalized using DESeq2.

growth_protocol: For caerulein or PBS (control) treatments, 5 weeks-old KC;RIK (p48-Cre;RIK;LSLKrasG12D) or C;RIK (p48-Cre;RIK) littermate male mice were treated with 8 hourly intraperitoneal injections of 80 μg/kg caerulein (Bachem) or PBS for 2 consecutive days.

extract_protocol:
Lysis Buffer 10mM Tris·Cl, pH 7.4; 10mM NaCl; 3mM MgCl2; 0.1% (v/v) Igepal CA-630 (Buenrostro et al., 2015 protocol)
Buenrostro et al., 2015 protocol

value: Injury

value: C;RIK GEMM

value: KrasWT


title: G27 DrbpH (deletion) RNA-seq

tag: genotype/variation

value: DrbpH (deletion)


title: Injury_ATAC4

description:
D8_2
PE-50

value: Caerulein

value: Day 2 post-caerulein

value: pancreas


title: MSC.MM8

description:
200298840144_R02C01
DNA methylation data from human clinical samples


title: MSC.SMM4

description:
200325500026_R05C01
DNA methylation data from human clinical samples

value: SMM


title: MSC.MM2

description:
200240850123_R04C01
DNA methylation data from human clinical samples


title: Kras*_ATAC3

description:
D8_1
PE-50

value: Kras*

value: KC;RIK GEMM

value: PBS

value: 5 - 6 weeks old

value: Male


title: MSC.SMM7

description:
200240850123_R03C01
DNA methylation data from human clinical samples


title: G27 WT RNA-seq

value: WT


title: MSC.MM4

description:
200240850123_R06C01
DNA methylation data from human clinical samples


title: Normal_ATAC3

description:
D7_3
PE-50

value: Normal

value: Day 2 post-PBS


title: MSC.MM11

description:
200298840144_R04C01
DNA methylation data from human clinical samples

value: M

value: MM


title: MSC.SMM6

description:
200298840156_R03C01
DNA methylation data from human clinical samples

value: F


title: MSC.SMM1

description:
200240850070_R01C01
DNA methylation data from human clinical samples


title: MSC.SMM2

description:
200240850070_R02C01
DNA methylation data from human clinical samples


title: MSC.SMM8

description:
200240850070_R05C01
DNA methylation data from human clinical samples


title: MSC.MM3

description:
200240850123_R05C01
DNA methylation data from human clinical samples


title: MSC.SMM10

description:
200325500016_R05C01
DNA methylation data from human clinical samples


title: MSC.SMM9

description:
200325500026_R04C01
DNA methylation data from human clinical samples


title: MSC.MGUS11

description:
200340580024_R07C01
DNA methylation data from human clinical samples

value: MGUS


title: Liver metastasis of case 1

city: Kagoshima

first: Shunsuke

last: Misono

address: 8-35-1, Sakuragaoka

department: Pulmonary Medicine

institute: Kagoshima University Hospital

hyb_protocol: Gene Expression Hybridization Kit Protocol of Agilent Technologies

scan_protocol: The image of the DNA microarray was read by Agilent Microarray Scanner, and the trend signal of each spot was quantified by Feature Extraction Software (v.11.5.1.1).

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log10 of processed Green signal. Agilent software was used.

source_name: liver metastasis

label_protocol: Low Input Quick Amp Labeling Kit Protocol of Agilent Technologies

extract_protocol: Total RNA was extracted using Trizol following the manufacturer's instructions.

value: small cell lung cancer

tag: gender

value: male

tag: patient number


title: MSC.MGUS10

description:
200240850077_R02C01
DNA methylation data from human clinical samples


title: MSC.MGUS6

description:
200325500016_R04C01
DNA methylation data from human clinical samples


title: MSC.MGUS9

description:
200240850077_R07C01
DNA methylation data from human clinical samples


title: Kras*+Injury_ATAC5

description:
D7_1
PE-50

tag: experimental condition

value: Kras*+Injury

tag: model

value: Caerulein

value: Day 2 post-caerulein


title: MSC.MGUS5

description:
200240850070_R03C01
DNA methylation data from human clinical samples


title: WT_ST_Input

city: Denver

first: Hua

last: Huang

state: CO

address: 1400 Jackson St

department: Biomedical Research

institute: National Jewish Health

data_processing:
The adaptor sequences in raw reads (average 24.0 million reads, two biological replicates for each group) were trimmed using Trimmomatic (version 0.33) (Bolger et al., 2014) and the quality of trimmed sequence data was analyzed by FastQC (version 0.11.9).
The trimmed reads were aligned to the mm10 reference genome using Bowtie2 (version 2.3.5.1) (Langmead and Salzberg, 2012).
Peak calling was performed using MACS2 (version 2.1.2) with default parameters (Zhang et al., 2008).
Genome_build: mm10
Supplementary_files_format_and_content: Tdf and bedgraph files for each sample

source_name: BMMCs

growth_protocol: Bone marrow-derived mast cells (BMMCs) were cultured from bone marrow cells of Balb/c mice in Iscove’s DMEM (10016CV, CorningTM cellgroTM, Manassas, VA) plus 10% FBS,100 units/mL penicillin, 100 ug/mL streptomycin, and 2 mM beta-mercaptoethanol in the presence of 20 ng/mL IL-3 for four weeks. Over 99% of BMMCs were mast cells as determined by FACS analysis (FcεRIa+ c-Kit+).

extract_protocol:
Briefly, 1x10e7 BMMCs that were not treated or treated with IgE receptor crosslinking were fixed in complete medium with 1% Formaldehyde (Thermo Scientific, 28908). The fixation was quenched by adding glycine and then washed with ice-cold PBS. The cells were resuspended in lysis buffer with protease inhibitor cocktail (Sigma, SRE0055-1BO) and sonicated using Covaris S220 Focused-ultrasonicator (Covaris, Woburn, MA). The lysate was pre-cleared by incubating with protein A agarose/salmon sperm DNA slurry (Millipore, Cat# 16-157) and the supernatant was incubated with the anti-GATA2 antibody (ab109241, Abcam, Cambridge, MA) at 4 °C overnight. Then, the samples were incubated with salmon sperm DNA/protein A beads at 4 °C for one hour. The beads were washed using low salt immune complex wash buffer, high salt immune complex wash buffer once, LiCl immune complex wash buffer once and TE buffer twice. The beads were eluted with elution buffer. The crosslinking of eluted immunocomplexes was reversed by incubating with NaCl and RNase A (Roche, Cat# 11119915001) at 65 °C overnight, followed by incubation with Tris pH 6.5, EDTA pH 8.0, and Proteinase K at 55 °C for one hour. Finally, the recovered DNA was cleaned up using a QIAGEN QIAquick PCR purification kit (Qiagen, Valencia, CA).
ChIP-seq library was prepared using TruSeq ChIP Library Preparation Kit (IP-202-1024, Illumina, San Diego, CA) according to the manufacturer’s instructions. Briefly, 10 ng of ChIPed DNA was converted into blunt-ended fragments. A single adenosine nucleotide was added to the 3’ ends of the blunt-ended fragments before indexing adaptors were ligated to the adenylated 3' ends. The ligated product was purified, size-selected and PCR amplified according to the manufacturer’s instructions. The quality and quantity of the DNA library were assessed on an Agilent Technologies 2100 Bioanalyzer. The paired-ended sequencing was performed on an Illumina NovaSEQ6000 platform.

treatment_protocol: (Stimulation) BMMCs were sensitized with 1 ug/mL IgE anti-2, 4, 6-Trinitrophenyl (TNP) antibody (100 ng/mL) (IGEL 2a, ATCC, Manassas, VA). Twenty-four hours later, the cells were challenged with 100 ng/mL TNP-BSA (T-5050-100, LGC Biosearch Technologies, Novato, CA) for 2 additional hours before the cells were collected for further analysis.

tag: cell type

value: Bone-marrow derived mast cells

tag: chip antibody

value: none (input)

tag: genotype

value: wild type

value: IgE anti_TNP and TNP-BSA


title: WT_UN_Input


title: Kras*_ATAC2

description:
D6_3
PE-50

value: Kras*

value: KC;RIK GEMM

tag: alleles (gemm)

tag: oncotype (sorted cells)

value: PBS

tag: sample collection time point

value: pancreas

tag: sorting strategy

tag: age / stage (upon sample collection)

value: 5 - 6 weeks old

value: Male


title: Para-aortic lymph node metastasis of case 1

source_name: lymph node metastasis

tag: tissue


title: WT_ST_GATA2 rep2

tag: strain

value: Anti-GATA2, (Abcam, ab109241)

tag: treatment


title: MSC.MGUS7

description:
200240850077_R01C01
DNA methylation data from human clinical samples

tag: Sex

value: M

tag: age

tag: donor

value: MGUS

tag: batch


title: Mediastinal lymph node metastasis of case 1

value: small cell lung cancer

tag: gender

value: male

tag: patient number


title: Kras*+Injury_shBrd4_ATAC

description:
D4_1
PE-50

tag: experimental condition

tag: model

value: KC-shRNA GEMM

value: KrasG12D  (Brd4-knockdown)

value: Caerulein


title: MSC.MM7

description:
200298840144_R01C01
DNA methylation data from human clinical samples

value: F

value: MM


title: Right intrapulmonary metastasis of case 3

source_name: intrapulmonary metastasis


title: WT_ST_GATA2 rep1

tag: cell type

value: Bone-marrow derived mast cells

tag: chip antibody

tag: genotype

value: wild type

value: IgE anti_TNP and TNP-BSA


title: PDAC_ATAC4

description:
D22_3
PE-50

source_name: sorted PDAC cells

value: PDAC

value: Orthotopically transplanted pancreatic organoids (LSL-KrasG12D + AdCre + CRISPR-mediated Trp53 inactivation + MLP-GFP-shRen) in C57Bl6

tag: alleles (gemm)

tag: oncotype (sorted cells)

tag: sample collection time point

value: PDAC lesion


title: Lesser curvature lymph node metastasis of case 1

tag: tissue


title: MSC.MGUS2

description:
200325500026_R08C01
DNA methylation data from human clinical samples


title: Injury_ATAC3

description:
D6_1
PE-50

value: Injury

value: C-shRNA GEMM

value: p48Cre;RIK;TRE-GFP-shRen (On dox)

value: KrasWT

value: Day 2 post-caerulein

value: pancreas

tag: sorting strategy

tag: age / stage (upon sample collection)

value: 5 - 6 weeks old

value: Male


title: WT_UN_GATA2 rep2

tag: strain

value: Anti-GATA2, (Abcam, ab109241)

tag: treatment


title: Primary tumor of case3

source_name: small cell lung cancer primary tumor

value: small cell lung cancer

value: male


title: PDAC_ATAC1

description:
D2_1
PE-50

value: KPflC;RIK GEMM

tag: Sex


title: coIP G27 WT (control) replicate 1

description:
coIP_WT_G27_R1
RbpH-bound RNA

tag: genotype/variation

value: WT (control)

tag: rip antibody

value: monoclonal anti-FLAG M2 (Sigma, catalog# F1804)


title: MSC.MGUS3

description:
200325500016_R02C01
DNA methylation data from human clinical samples

value: F

tag: age

tag: donor

value: MGUS

tag: batch


title: Primary tumor of case2

tag: gender

tag: patient number


title: Kras*+Injury_ATAC4

description:
D4_2
PE-50

tag: experimental condition

value: Kras*+Injury-shRen

tag: model

value: KC-shRNA GEMM

value: Caerulein


title: MSC.HD13

description:
200298840156_R02C01
DNA methylation data from human clinical samples

value: M

value: HD


title: Kras*+Injury_ATAC3

description:
D19_3
PE-50

value: Kras*+Injury

value: KC;RIK GEMM

tag: alleles (gemm)

tag: oncotype (sorted cells)

value: Day 2 post-caerulein


title: Right hilar lymph node metastasis of case 2

tag: tissue


title: coIP RbpH::3xFLAG (G27) replicate 1

description:
coIP_RbpH-3xFLAG_G27_R1
RbpH-bound RNA


title: WT_UN_GATA2 rep1

tag: cell type

value: Bone-marrow derived mast cells

tag: chip antibody

tag: genotype

value: wild type


title: MSC.MGUS4

description:
200240850073_R06C01
DNA methylation data from human clinical samples


title: Cerebellum, Mn_0ppm_rep3

city: Ann Arbor

first: Shigeki

last: Iwase

address: 1241 E. Catherine St.

institute: University of Michigan

data_processing:
Read QC by FastQC
Read alignment by STAR
Transcript quantification by RSEM
Count table generated by RSEM, which is fed to Deseq2 for differential expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: Count table generated by RSEM

source_name: Cerebellum

extract_protocol:
Total RNA was isolated from fresh cerebellum tissue using the RNeasy mini kit (Qiagen, Valencia, CA). RNA concentration was measured on Epoch Microplate Spectrophotometer (BioTek Winooski, Vermont). RNA integrity assessment was performed on an Agilent Bioanalyzer 2100 using a Nano 6000 assay kit (Agilent Technologies, Santa Clara, CA). A RNA integrity number (RIN) > 7.2 was considered the minimum requirement for library preparation .
NEBNext Ultra II Directional RNA Library Prep Kit
Oligo dT

treatment_protocol: Mn 0ppm or Mn 35 ppm diet for two weeks in male adult mice.

value: Cerebellum

tag: strain

tag: treatment

value: Mn 0ppm diet


title: Kras*+Injury_ATAC6

city: New York

description:
D19_1
PE-50

tag: sample collection time point

value: pancreas

tag: sorting strategy

tag: age / stage (upon sample collection)

value: 5 - 6 weeks old

tag: Sex

value: Male


title: Normal lung tissue (upper lobe of the right lung) of case 2

source_name: normal lung tissue

value: normal lung tissue

value: male


title: Cerebellum, Mn_0ppm_rep2


title: Kras*+Injury_ATAC2

description:
D18_3
PE-50


title: Cerebellum, Mn_0ppm_rep1


title: Injury_ATAC2

description:
D14_2
PE-50

value: Injury

value: C-shRNA GEMM

value: p48Cre;RIK;TRE-GFP-shRen (On dox)

value: KrasWT


title: 7_F33R: MCA_tMCAO_occluded_3hrs

city: Calgary

first: Simona

middle: Denise

last: Frederiksen

state: Alberta

address: 3330 Hospital Dr NW

country: Canada

institute: University of Calgary

description: gene expression data from experimental stroke MCAs

hyb_protocol: 16h at 45 degrees celsius in an Affymetrix Gene Chip Hybridization 645 oven.

scan_protocol: Affymetrix GeneChip scanner 3000 7G.

data_processing: Expression Console Software (v1.1.2)

label: biotin allonamide triphosphate

organism: Rattus norvegicus

source_name: MCA, occluded, after tMCAO, 3 hrs

label_protocol: Biotin Allonamide Triphosphate-labelled, labelling reaction at 37 degrees celsius

growth_protocol: Environmental enriched cages with a 12-hour light/dark cycle (lights on 7am-7pm), climate- and humidity-controlled environment and with free access to food and water. Animals were subjected to an acclimatization period. Female rats in the high estrogen phase, proestrus, were not included.

extract_protocol: Nucleospin miRNA isolation kit (Machery-Nagel, Düren, Germany), following the manufactures instructions for extraction of total RNA.

treatment_protocol: MCA occlusion using the intraluminal filament technique, anesthesia induced by 3.5% isoflurane in N2O:O2 (70:30) and maintained by continuous inhalation of 2.5% isoflurane in N2O:O2 (70:30), allowed to recover with free access to food and water for 3 hours, euthanized with carbon dioxide and decapitation.

value: Wistar

value: middle cerebral artery

value: female

tag: weight

value: approx. 250 gram

value: tMCAO

tag: group

value: occluded MCA


title: 10_F15R: MCA_tMCAO_occluded_3hrs


title: 4CBS_downstream_rep2

city: La Jolla

first: Bing

last: Ren

address: 9500 Gilman Dr., CMM-East, Admin Area/Rm 2071

institute: University of California, San Diego School of Medicine

data_processing:
The RNA-Seq alignment and quantification pipeline is available at https://github.com/ren-lab/rnaseq-pipeline. Briefly, reads were aligned to mm10 (GRCm38) and GENCODE GTF version M25 with rnaSTAR77.
PCR duplicates were removed using Picard. Raw reads for each gene were quantified using featureCounts. RPKM values were calculated for each gene
Particularly, we created two extra chromosomes for the two tagged Sox2 alleles. Reads uniquely mapped to egfp and mCherry sequences were counted using samtools. Expression level of Sox2 gene from CAST and 129 allele was calculated by RPKM values of the egfp and mCherry gene, respectively.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: embryonic stem cells

growth_protocol: Cells were cultured on feeder-free, serum free 2i condition (Serum free mouse ES medium supplemented with 1uM PD03259010, 3uM CHIR99021, 2mM glutamine, 0.15uM Monothioglycerol, 1000U/ml LIF). The growth medium was changed every day. Cells were dissociated by Accutase (AT104) and passaged to onto 0.2% gelatin-coated plates every 2-3 days.

extract_protocol:
Total RNA from cells was extracted using the TRIzol Plus RNA purification kit (Thermo Fisher Scientific, Catlog: 12183555).
RNA-Seq libraries were prepared from 4 µg total RNA using the Illumina TruSeq Stranded mRNA Library Prep Kit Set A (RS-122-2101; Illumina) or Set B (RS-122-2102; Illumina). RNA-seq libraries were sequenced on illumine Next-seq 550 and Hi-seq4000 platforms (75-bp paired ends).

tag: cell line

value: F123 ESC

value: F1 hybrid (castaneus X 129/SvJae)


title: Normal lung tissue (lower lobe of the right lung) of case 3

tag: gender

tag: patient number


title: Cerebellum, Mn_35ppm_rep3

value: Cerebellum

value: Mn 35 ppm diet


title: 14_F8R: MCA_tMCAO_occluded_3hrs

tag: model


title: Kras*_ATAC1

description:
D13_3
PE-50

tag: experimental condition

value: Kras*

value: KC;RIK GEMM

tag: alleles (gemm)

tag: oncotype (sorted cells)

value: PBS

value: Day 2 post-PBS

value: pancreas

value: 5 - 6 weeks old

value: Male


title: MSC.HD12

description:
200325500016_R01C01
DNA methylation data from human clinical samples

value: F

tag: age

tag: donor

value: HD

tag: batch


title: Cerebellum, Mn_35ppm_rep2

tag: tissue

tag: strain

value: male

tag: treatment


title: MSC.HD11

description:
200325500026_R02C01
DNA methylation data from human clinical samples


title: Normal_ATAC2

description:
D13_2
PE-50

value: Normal

value: C;RIK GEMM

value: KrasWT

tag: sample collection time point

tag: sorting strategy

tag: age / stage (upon sample collection)


title: Normal lung tissue (lower lobe of the left lung) of case 1

value: normal lung tissue


title: 8_F10R: MCA_tMCAO_occluded_3hrs

value: Wistar

value: middle cerebral artery

tag: Sex

value: female

tag: weight

value: approx. 250 gram

value: tMCAO

tag: group

value: occluded MCA


title: Cerebellum, Mn_35ppm_rep1

value: Cerebellum

value: Mn 35 ppm diet


title: 4CBS_rep3

tag: cell line

value: F123 ESC

value: F1 hybrid (castaneus X 129/SvJae)

tag: genotype


title: MSC.MGUS1

description:
200240850123_R02C01
DNA methylation data from human clinical samples

value: M

value: MGUS


title: 19_F12R: MCA_tMCAO_occluded_3hrs

tag: model


title: Normal_ATAC1

description:
D1_2
PE-50

tag: experimental condition

value: C-shRNA GEMM

tag: alleles (gemm)

value: p48Cre;RIK;TRE-GFP-shRen (On dox)

value: PBS

value: Day 2 post-PBS

value: pancreas

value: 5 - 6 weeks old

value: Female


title: 4CBS_rep2


title: BMMCs, Gata2_KO_ST RNA rep2

data_processing:
The raw reads were analyzed and quality checked by FastQC.
The reads were aligned to the mm10 reference genome (GRCm38) using the Spliced Transcripts Alignment to a Reference (STAR, version 2.4.0.1) software (Dobin et al., 2013).
The aligned reads were assembled into reference transcripts using Cufflinks (version 2.2.1). The differential gene expression between the resting and stimulated samples was analyzed using Cuffdiff (Trapnell et al., 2012).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample .

extract_protocol:
To prepare RNA samples for RNA-seq, total RNA from 1x106 BMMCs that were not treated or treated with IgE receptor crosslinking were isolated using RNeasy mini kit (Qiagen), which was treated with DNase I according to manufacturer’s instructions. The quality of RNA was analyzed by using Agilent Technologies 2100 Bioanalyzer.
RNA-seq library was prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina (E7770S, New England Biolabs, Ipswich, MA). Briefly, polyA mRNA was purified using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490). The isolated mRNA was fragmented, reverse transcribed into cDNA, end-repaired, and adaptor-ligated. The ligated samples were USER enzyme digested and PCR amplified and purified using AMPure-XP beads (Beckman Coulter Life Sciences, A63881, Indianapolis, IN). The quality and quantity of RNA libraries were assessed on an Agilent Technologies 2100 Bioanalyzer.

treatment_protocol:
(Stimulation)  BMMCs were sensitized with 1 ug/mL IgE anti-2, 4, 6-Trinitrophenyl (TNP) antibody (100 ng/mL) (IGEL 2a, ATCC, Manassas, VA). Twenty-four hours later, the cells were challenged with 100 ng/mL TNP-BSA (T-5050-100, LGC Biosearch Technologies, Novato, CA) for 2 additional hours before the cells were collected for further analysis.
(Gata2 deletion)  BMMCs cultured from bone marrow cells of Gata2f/fRosaYfp/YfpTgCreErt2hemi mice or Gata2+/+RosaYfp/YfpTgCreErt2hemi mice were treated with 25 nM 4-hydroxytamoxifen (4-OHT; Calbiochem, Billerica, MA) for five days as described previously (Li et al., 2018; Li et al., 2015). The expression of FceR1a (PE-CY7–conjugated anti-FcεRIa (MAR-1), Biolegend, 134317) and c-Kit (allophycocyanin-CY7–conjugated anti–c-Kit (2B8), Biolegend, 105825) on mast cells were analyzed by Flow cytometry. The YFP+ cells were FACS-sorted and the deletion of the Gata2 gene was determined to be near 100%. The sorted cells were then used for the next-generation sequencing analysis.

tag: cell type

value: Bone-marrow derived mast cells

value: IgE anti_TNP and TNP-BSA


title: MSC.HD8

description:
200240850077_R05C01
DNA methylation data from human clinical samples

value: F

tag: age

tag: donor

value: HD


title: 4CBS_rep1


title: MSC.HD3.MM

description:
DNA methylation data from human clinical samples
201364900079_R02C01

growth_protocol: Primary MSCs from bone marrow (BM) samples of healthy donors mono-cultured (n=3) or co-cultured with the MM.1S cell line (n=3) were generated as described by Garayoa et al. 2009 (PMID:19357701). Ficoll-Paque density gradient separation medium was used to isolate mononuclear cells from BM aspirates. MSCs were selected by adherence to plastic and subsequently expanded until passage 2 when they were used for experiments.

tag: batch


title: Normal lung tissue (upper lobe of the left lung) of case 1

tag: tissue

value: normal lung tissue

tag: gender

value: male

tag: patient number


title: PDAC_ATAC2

description:
D12_1
PE-50

value: PDAC

value: Orthotopically transplanted pancreatic organoids (LSL-KrasG12D + AdCre + CRISPR-mediated Trp53 inactivation + MLP-GFP-shRen) in C57Bl6

tag: oncotype (sorted cells)

tag: treatment

tag: sample collection time point

value: PDAC lesion

tag: sorting strategy

value: Male


title: 18_F19L: MCA_tMCAO_nonoccluded_3hrs

source_name: MCA, non-occluded, after tMCAO, 3 hrs

tag: strain

value: Wistar

value: middle cerebral artery

tag: Sex

value: female

tag: weight

value: approx. 250 gram

value: tMCAO

tag: group

value: non-occluded MCA


title: PDAC_ATAC3

description:
D12_2
PE-50

tag: experimental condition

tag: model

value: pancreas

tag: age / stage (upon sample collection)


title: 4CBS_downstream_rep1

tag: cell line

value: F123 ESC

value: F1 hybrid (castaneus X 129/SvJae)

tag: genotype


title: WT_Rad21_rep3

data_processing:
Inserted sequence was add to the mm10 genome. And a customized mm10 genome was indexed by bowtie2-build
ChIP-seq sequencing data was trimmed and aligned to mm10 by bowtie2. Unmapped, multimapped and PCR duplicates were removed.
Genome_build: mm10
Supplementary_files_format_and_content: Signal tracks were generated by bamCoverage with parameters "--normalizeUsingRPKM -bs 50 --smoothLength 150" (deepTools)

extract_protocol: Crosslinked cells were processed by Covaris truChIP Chromatin Shearing kit and chromatin were sonicated to 300-500bp by Covaris M220. ChIP DNA and Input DNA were constucted into illumina Tru-seq libraries as previously described (Jian Yan et al., 2013), followed by size selection for 300-500bp.

value: F1 hybrid (castaneus x S129/SvJae)

tag: chip antibody

value: Wild-type


title: MSC.HD1

description:
200240850077_R06C01
DNA methylation data from human clinical samples

value: F

tag: age

tag: donor

value: HD

tag: batch


title: WT_CTCF_rep3


title: Injury_ATAC1

description:
D11_1
PE-50

value: Injury

value: C;RIK GEMM

tag: alleles (gemm)

tag: oncotype (sorted cells)

value: KrasWT

value: Caerulein

value: Day 2 post-caerulein

tag: tissue

value: 5 - 6 weeks old


title: MSC.HD6

description:
200240850073_R08C01
DNA methylation data from human clinical samples

value: M


title: BMMCs, Gata2_KO_UN RNA rep1

tag: cell type

value: Bone-marrow derived mast cells

tag: treatment


title: Syn1-6_Rad21_rep3

tag: strain


title: MSC.HD7

description:
200325500016_R06C01
DNA methylation data from human clinical samples

tag: Sex


title: 6_F10L: MCA_tMCAO_nonoccluded_3hrs

value: Wistar

value: middle cerebral artery

value: female

tag: weight

value: approx. 250 gram

value: tMCAO

tag: group


title: 1_F15L: MCA_tMCAO_nonoccluded_3hrs

tag: model

value: non-occluded MCA


title: Syn1-6_CTCF_rep4

value: F123 ESC

value: F1 hybrid (castaneus x S129/SvJae)


title: MSC.HD4

description:
200240850123_R08C01
DNA methylation data from human clinical samples

value: F

value: HD


title: BMMCs, Gata2_WT_ST RNA rep1

value: wild type

value: IgE anti_TNP and TNP-BSA


title: MSC.HD2

description:
DNA methylation data from human clinical samples
201364900029_R01C01


title: MSC.HD2.MM

description:
DNA methylation data from human clinical samples
201364900029_R02C01


title: BMMCs, Gata2_WT_UN RNA rep1


title: MSC.HD1.MM

description:
DNA methylation data from human clinical samples
201364900026_R03C01


title: 3_F21C: MCA_nonoperated_control

description: gene expression data from control MCAs

source_name: MCAs, non-operated, control

value: control

value: control MCAs


title: Syn1-6_10bp-adj_Rad21_rep2


title: Syn1-6_10bp-adj_Rad21_rep1


title: MSC.HD3

description:
DNA methylation data from human clinical samples
201364900079_R05C01


title: 15_F22C: MCA_nonoperated_control

description: gene expression data from control MCAs


title: IMR32 cells, input

data_processing:
Short reads were trimmed by trimmomatic.
Reads were mapped by bowtie2-2.3.1
Duplicated reads were removed by MarkDuplicates of Picard.
Peak call were performed by macs2 for MYCN, H3K27ac, H3M4me3. Peakcall were performed by Danpos2 for H3K27me3 and EZH2 with option “-q 40 -kw 750 -kd 1500”.
Bigwig files were generated by bamCompare with “--binSize 200”.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

growth_protocol: Human NB cell line IMR32 were cultured in RPMI1640 (Wako) supplemented with 10% heat-inactivated fetal bovine serum (Invitrogen) and 50 μg/ml penicillin/streptomycin (Sigma–Aldrich) in an incubator with humidified air at 37 °C with 5% CO2

extract_protocol:
ChIP assays were performed as previous papers (Orlando V et al., 1997, Methods, Fujimura Y et al., 2006, Development). Cross-linked chromatin prepared from the indicated cells was precipitated by each antibodies.
NEBNext Ultra DNA Library Kit for Illumina (NEB) was used to generate libraries from samples. All procedures were performed according to the protocols suggested by the manufacturers. The concentration of libraries was measured by Qubit 2.0 Fluorometer with Qubit dsDNA HS Assay Kit (Invitrogen).
Average length of libraries was analyzed on TapeStation with High Sensitivity D1000 ScreenTape (Agilent Technologies) according to the manufacturer's protocol. Finally, the molar concentration of each library was quantified by Library Quantification Kit (Takara). Single-read sequencing of libraries with a read length of 75 was performed with NextSeq 500 Sequencing System (Illumina)

treatment_protocol: without treatment

value: neuroblastoma cell line IMR32

value: input (without antibody treated input)


title: MSC.HD1

description:
DNA methylation data from human clinical samples
201364900026_R06C01


title: Syn1-6_10bp-adj_CTCF_rep2


title: BMMCs, WT_ST_RNA rep2

value: Balb/cJ

value: Bone-marrow derived mast cells


title: IMR32 cells, H3K27me3

value: H3K27me3 (Millipore 07-449)


title: BMMCs, WT_ST_RNA rep1


title: Syn1-6_10bp-adj_CTCF_rep1


title: 13_F16C: MCA_nonoperated_control

description: gene expression data from control MCAs

value: Wistar

value: middle cerebral artery

value: female


title: 20_F26C: MCA_nonoperated_control

description: gene expression data from control MCAs

value: approx. 250 gram


title: IMR32 cells, H3K27ac

value: H3K27ac (MBL MABI0309)


title: IMR32 cells, MYCN

value: MYCN (abcam NCM II 100)


title: nBd_Syn1-6_swap_CTCF_rep1

value: F123 ESC

value: F1 hybrid (castaneus x S129/SvJae)


title: nBd_Syn1-6_swap_CTCF_rep2


title: KO liver, rep1

description: replicate 1

hyb_protocol: labelled samples were hybridised to Affy MOE430 v2 chips according to Affymetrix standard protocols.

scan_protocol: Chips were scanned using an Affymetrix GeneChip Scanner3000 7G with standard parameters, and images analysed using GENECHIP v1.4 software

data_processing:
Raw data was read using the 'ReadAffy' function in Bioconductor's 'Affy' package. Data were then quantile-normalized, probesets aggregated using Tukey's median polish method
additional file: 200804_processed_data_matrix.xls - Bioconductor package 'limma' was used to determine probeset statistics, adjusted for multiple testing using the Benjamini & Hochberg method returning the false discovery rate (FDR); log2-transformed signal ratios KO/WT and associated FDR.

source_name: C57/B6 mouse liver

label_protocol: biotin-labelled cRNA was synthesised from 3ug total RNA according to the manufacturer (Affymetrix) standard protocols.

growth_protocol: 6 week old mice were used for gene expression analysis, as described in Bennati AM, Schiavoni G, Franken S, et al. (2008) FEBS Journal 275:5034-5047

extract_protocol: RNA from livers was extracted using Qiagen RNeasy Mini kit following the manufacturer's instructions

treatment_protocol: Tm7sf2 KO mouse was generated and backcrossed to C57/B6 background as described in Bennati AM, Schiavoni G, Franken S, et al. (2008) FEBS Journal 275:5034-5047

value: liver


title: 2_F36C: MCA_nonoperated_control

description: gene expression data from control MCAs


title: 16_F8L: MCA_tMCAO_nonoccluded_3hrs

value: tMCAO

value: non-occluded MCA


title: WT liver, rep1

description: replicate 1

value: WT


title: BMMCs, WT_UN_RNA rep2

value: wild type


title: Syn1-6_CTCF_rep3


title: IMR32 cells, H3K4me3

value: neuroblastoma cell line IMR32

value: H3K4me3 (abcam ab8580)


title: BMMCs, Gata2_KO_ST RNA rep1

value: Bone-marrow derived mast cells

value: IgE anti_TNP and TNP-BSA


title: Syn1-6_swap_CTCF_rep2


title: BMMCs, WT_UN_RNA rep1

value: Balb/cJ


title: KO liver, rep2

description: replicate 2


title: BMMCs, WT_UN_RNA rep3


title: Chopp29: Thpok KO Immature CD4SP thymocytes replicate 1

first: Remy

last: Bosselut

address: 9000 Rockville Pike, Building 37

department: Laboratory of Immune Cell Biology

institute: National Cancer Institute, National Institute of Health

data_processing:
Basecalls performed with Illumina RTA 1.18.66.3
Demultiplexing with Bcl2fastq 2.17
Filtering with Trimmomatic 0.36
Alignment--STAR aligner 2.4.0 to mm10
Counts per million normalized BigWig files performed with DeepTools
Read counts with HTSeq
Genome_build: mm10
Supplementary_files_format_and_content: Htseq count table, counts per million normalized bigwig

source_name: Thymus

extract_protocol:
RNA was isolated using the RNeasy Plus Micro kit (Qiagen)
SMART-seq Ultra Low Input RNA kit (Takara) and Nextera XT DNA (Illumina), paired-end 2x150

value: Thpok fl/fl ThpokGFP CD4-Cre positive

tag: surface markers

value: CD44low MHC-I-low CD8alow CD69+ ThpokGFP+ CD4+

value: Thymus


title: Chopp28: Mature CD8SP thymocytes replicate 3

value: Chimeric mice:Thpok-GFP Runx3-RFP reporter donor, C57BL/6 recipient

value: CD44low CD4low CD69- Runx3RFP+ CD8a+


title: Chopp30: Thpok KO Immature CD4SP thymocytes replicate 2


title: Kras*+Injury_ATAC1

description:
D11_3
PE-50

source_name: sorted primary pancreatic epithelial cells

tag: experimental condition

value: Kras*+Injury

value: KC-shRNA GEMM

value: Caerulein

tag: sample collection time point

value: Day 2 post-caerulein

value: pancreas

tag: sorting strategy

tag: age / stage (upon sample collection)

value: 5 - 6 weeks old

value: Male


title: BMMCs, Gata2_WT_UN RNA rep2

tag: genotype

value: wild type


title: Syn1-6_swap_CTCF_rep1

tag: cell line

value: F123 ESC

value: F1 hybrid (castaneus x S129/SvJae)

tag: chip antibody


title: BMMCs, Gata2_KO_ST_Input

extract_protocol:
Briefly, 1x10e7 BMMCs that were not treated or treated with IgE receptor crosslinking were fixed in complete medium with 1% Formaldehyde (Thermo Scientific, 28908). The fixation was quenched by adding glycine and then washed with ice-cold PBS. The cells were resuspended in lysis buffer with protease inhibitor cocktail (Sigma, SRE0055-1BO) and sonicated using Covaris S220 Focused-ultrasonicator (Covaris, Woburn, MA). The lysate was pre-cleared by incubating with protein A agarose/salmon sperm DNA slurry (Millipore, Cat# 16-157) and the supernatant was incubated with the anti-H3K4me1 antibody (ab8895, Abcam, Cambridge, MA) or anti-H3K27ac antibody (ab4729, Abcam) at 4 °C overnight. Then, the samples were incubated with salmon sperm DNA/protein A beads at 4 °C for one hour. The beads were washed using low salt immune complex wash buffer, high salt immune complex wash buffer once, LiCl immune complex wash buffer once and TE buffer twice. The beads were eluted with elution buffer. The crosslinking of eluted immunocomplexes was reversed by incubating with NaCl and RNase A (Roche, Cat# 11119915001) at 65 °C overnight, followed by incubation with Tris pH 6.5, EDTA pH 8.0, and Proteinase K at 55 °C for one hour. Finally, the recovered DNA was cleaned up using a QIAGEN QIAquick PCR purification kit (Qiagen, Valencia, CA).
ChIP-seq library was prepared using TruSeq ChIP Library Preparation Kit (IP-202-1024, Illumina, San Diego, CA) according to the manufacturer’s instructions. Briefly, 10 ng of ChIPed DNA was converted into blunt-ended fragments. A single adenosine nucleotide was added to the 3’ ends of the blunt-ended fragments before indexing adaptors were ligated to the adenylated 3' ends. The ligated product was purified, size-selected and PCR amplified according to the manufacturer’s instructions. The quality and quantity of the DNA library were assessed on an Agilent Technologies 2100 Bioanalyzer. The paired-ended sequencing was performed on an Illumina NovaSEQ6000 platform.

value: Bone-marrow derived mast cells

value: Gata2 -/-

value: IgE anti_TNP and TNP-BSA


title: Chopp27: Mature CD8SP thymocytes replicate 2


title: BMMCs, Gata2_KO_UN_Input


title: Chopp74: Donor3

data_processing:
Basecalls performed with Illumina RTA 2.4.6
Demultiplexing with Bcl2fastq 2.17
10x data for scATAC samples are run through cellranger ATAC (v1.1) software to produce the fastqfiles
The fastq files are processed through cellranger, including alignment, identification of cut sites, and peak calling.
Genome_build: hg38
Supplementary_files_format_and_content: raw_peak_bc_matrix.h5: Raw peak barcode matrix
Supplementary_files_format_and_content: fragments.tsv: Fragment file
Supplementary_files_format_and_content: fragments.tsv.gz.tbi: Fragment file index
Supplementary_files_format_and_content: singlecell.csv: Metadata

extract_protocol:
Nuclei were isolated following the recommended protocol from 10X Genomics. Transposition and scATACseq capture was performed with the 10X Chromium NextGem Single Cell ATAC Solution (v1.1) , following the manufacturer's recommended protocol
Libraries were run on a NextSeq500, Parameters:50bp (Read1), 8bp (Index1), 16bp (Index2), 50bp (Read2), Indexing 2 samples (SCAF1016_II, SI-NA-G5; SCAF1017_B, SI-NA-G6)

tag: gender

tag: flow markers

value: CD69+ mixed with CD69-CD8+CD4+


title: Chopp73: Donor2

value: Female

tag: tissue

value: Thymus


title: BMMCs, Gata2_WT_ST_Input

tag: cell type

tag: treatment


title: nBd_Syn1-6_scramble_CTCF_rep1

tag: strain


title: BMMCs, Gata2_WT_UN_Input


title: IMR32 cells, EZH2

value: neuroblastoma cell line IMR32

value: EZH2 (Millipore 07-689)


title: Chopp24: Immature CD8SP thymocytes replicate 2

value: Chimeric mice:Thpok-GFP Runx3-RFP reporter donor, I-AB deficient recipient

value: CD44low CD4low CD69+ Runx3RFP+ CD8a+


title: Chopp25: Immature CD8SP thymocytes replicate 3


title: BMMCs, Gata2_WT_ST RNA rep2


title: Syn1-6_scramble_CTCF_rep2


title: Chopp23: Immature CD8SP thymocytes replicate 1


title: Syn1-6_scramble_CTCF_rep1


title: BMMCs, Gata2_KO_ST_H3K27ac rep1

value: H3K27ac, (Abcam, ab4729)


title: Chopp65: Donor5_mix

data_processing:
Basecalls performed with Illumina RTA 2.4.6
Demultiplexing with Bcl2fastq 2.17
10x data for scRNA samples are run through cellranger (v3.1) software to produce the fastqfiles
The fastq files are processed throgh the cellranger count to get differential expression counts.
Genome_build: hg38
Supplementary_files_format_and_content: h5

extract_protocol:
Single Cell NextGem 5' chemistry from 10X genomics
Libraries were pooled and sequenced with paired-end reads of 26x98bp or 26x57bp on a NextSeq500 sequencer (Illumina)

value: male


title: Chopp67: Donor5_CD8SP


title: Chopp66: Donor5_CD4SP


title: BMMCs, Gata2_KO_UN RNA rep2


title: Chopp26: Mature CD8SP thymocytes replicate 1

value: Chimeric mice:Thpok-GFP Runx3-RFP reporter donor, C57BL/6 recipient

value: CD44low CD4low CD69- Runx3RFP+ CD8a+


title: Chopp22: Mature CD4SP thymocytes replicate 3

value: CD44low MHC-I+ CD8alow CD69- ThpokGFP+ CD4+


title: 4_F4C: MCA_nonoperated_control

description: gene expression data from control MCAs

value: Wistar

value: middle cerebral artery

tag: Sex

value: female

tag: weight

value: approx. 250 gram

value: control

value: control MCAs


title: BMMCs, Gata2_KO_UN_H3K27ac rep2

value: Bone-marrow derived mast cells

value: Gata2 -/-


title: Chopp21: Mature CD4SP thymocytes replicate 2

value: Thymus


title: Chopp64: Donor4_CD8SP


title: Hypoxia2

city: Göttingen

first: Hannelore

last: Ehrenreich

address: Hermann Rein Straße 3

department: Clinical Neuroscience

institute: Max Planck Institute of Experimental Medicine

description: Hypoxia

data_processing:
CellRanger v2.2.0 software was used to align sequence reads to the customized mouse mm10 reference genome to which the ODD and tdTomato sequences were added.
Genome_build: customized mm10 (tdTomato + ODD sequences added)
Supplementary_files_format_and_content: Butt_et_al_hypoxia_counts.csv file contains the final set of UMI counts of cells and genes included in the analyses after quality control (Seurat v2.3.0) and doublet removal (manual+DoubletFinder (McGinnis et al, 2019)). Butt_et_al_hypoxia_metadata.csv contains all relevant cell metadata, including UMI and feature counts per cell, initial and final cellular identity, sample ID and experimental group. Butt_et_al_hypoxia_Seurat.RDS is the final processed Seurat (v3; Stuart et al, 2019) object after QC, integration, clustering, annotation and doublet removal (manual+DoubletFinder (McGinnis et al, 2019)).

source_name: Hippocampus

extract_protocol:
CAG-CreERT2-ODD::R26R-tdTomato mice, 4 weeks old, received tamoxifen (100mg/kg/d) daily for 5 consecutive days before being exposed to either inspiratory hypoxia (6%O2) or normoxia (21%O2) for 6h each. Mice were handled identically and sacrificed on day 5 immediately after the last hypoxia/normoxia session. Hippocampi were dissected in Earle’s Balanced Salt Solution (EBSS1) and later digested with a working solution of Papain/DNaseI prepared in EBSS1, according to manufacturer’s instructions (Worthington Biochemical Corp). All steps were carried out on ice except the Papain/DNaseI dissociation. The samples were then incubated at 37°C for 40min with constant shaking in water bath and switched to 5%CO2 every 10min. Papain/DNaseI was removed and samples were further diluted in 5ml EBSS2. Dissociated tissues were manually triturated (avoid air bubbles), followed by centrifugation at 900rpm for 10min at 4°C. Supernatant was discarded and the cell pellet gently resuspended in 200µl of EBSS2 until a smooth and creamy suspension was obtained. Dissociated cells were washed frequently with DMEM/F12 (Sigma) without phenol-red containing 3% fetal bovine serum (FBS; Life Technologies) and centrifuged at 900rpm for 10min at 4°C. Cell pellet was resuspended in 1ml of DMEM/F12 and filtered through a 70µm strainer cap (Corning) smoothly to harvest a clear cell suspension. Cell viability and yield was calculated by mixing an equal volume of acridine orange and propidium iodide and checked at the cell counter (Nexcelom Bioscience, MA, USA). Cell suspension (1ml) was diluted with 3ml PBS containing 0.04% BSA and centrifuged. Supernatant was removed and cell pellet resuspended in 400µl PBS containing 0.04% BSA. Cells were fixed by adding 1.6ml methanol dropwise and kept at -20°C for 30min and stored at -80°C for further use.
The Methanol fixed cell suspensions were stored at -80°C for less than 7 days before processing. For each sample, approximately 1.5 million cells were taken for rehydration and downstream scRNA-seq experiment. Cells were first placed on ice and equilibrated to 4°C. After equilibration, cells were washed 2 times by 1ml pre-chilled rehydration buffer (1.0% BSA, 0.5U/µl RNAse inhibitor in 1x Dulbecco's Phosphate-Buffered Saline, DPBS). Centrifugation was done at 3000rcf for 10min at 4°C. Finally, cells were resuspended in pre-chilled 1xDPBS with 0.04% BSA and 0.5U/µl RNase inhibitor to achieve a concentration of 1,000 cells/µl. Rehydrated cells were immediately used for the scRNA-seq using the 10X genomics chromium single-cell gene expression platform. Around 35,000 cells from each sample were loaded on 1 well of 10X Single Cell A chip, where each single-cell was lysed and its transcriptome combined with a single barcoded gel bead in an oil droplet. Barcode cDNA libraries were then prepared using Chromium Single Cell 3’ Library and Gel-beads kit v2 according to the manufacturer’s instructions. Library quality was checked using Agilent High Sensitivity DNA chip on Agilent 2100 Bioanalyzer. High quality libraries were sequenced on Illumina HiSeq 4000 sequencer with an average depth of 200,000 reads per cell.

treatment_protocol: P28 male mice, 5xHypoxia (6% O2, 6h/day) or 5xNormoxia (21% O2, 6h/day), sacrificed immediately afterwards

tag: age


title: Normoxia2

description: Normoxia


title: BMMCs, Gata2_KO_UN_H3K27ac rep1


title: BMMCs, Gata2_KO_ST_H3K27ac rep2

value: IgE anti_TNP and TNP-BSA


title: Chopp20: Mature CD4SP thymocytes replicate 1

tag: surface markers


title: Chopp63: Donor4_CD4SP


title: BMMCs, Gata2_WT_ST_H3K27ac rep2

value: wild type


title: Chopp19: Semi-Mature CD4SP thymocytes replicate 3

value: Chimeric mice:Thpok-GFP Runx3-RFP reporter donor, b2m deficient recipient

value: CD44low MHC-I+ CD8alow CD69+ ThpokGFP+ CD4+


title: Chopp61: Donor3__mix_replicate2

value: male

value: CD69+ mixed with CD69-CD8+CD4+


title: Chopp18: Semi-Mature CD4SP thymocytes replicate 2


title: Chopp60: Donor3_mix_replicate1


title: BMMCs, Gata2_WT_UN_H3K27ac rep2

value: H3K27ac, (Abcam, ab4729)


title: BMMCs, Gata2_WT_ST_H3K27ac rep1


title: Normoxia1

description: Normoxia


title: NoTg-Day7DMXAA

city: Chapel Hill

first: Jonathan

middle: S

last: Serody

state: NC

address: 125 Mason Farm Rd.

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

data_processing:
The Cell Ranger Single Cell Software Suite, version 1.3 was used for de-multiplexing, barcode ad UMI processing, and single-cell 3′ gene counting. Reads were mapped to the mm10 genome.
The processing  followed the published protocol from cell ranger, as found in https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
Genome_build: mm10

source_name: Mammary tumor

growth_protocol: NT2 tumors were orthotopically injected to the second mammary gland pad. 21 days later therapy started as tumor area reach around 50mm2.

extract_protocol:
Tumors were bluntly resected and cut into small pieces and digested using Tumor Dissociation Kit, mouse (Miltenyi) in gentleMACS™ Dissociator (Miltenyi) according to manufacturer’s instruction. After digestion, dead and dying cells were magnetically separated using a Dead Cell Removal Kit (Miltenyi), after which immune cells were magnetically enriched using CD45 (TIL) MicroBeads (Miltenyi).
Single cells were partitioned using a Chromium Controller (10x Genomics), and gene expression sequencing libraries were generated using Chromium Single Cell 3′Library & Gel Bead Kit v3 (10x Genomics).
The libraries were pooled and sequenced using an Illumina NovaSeq 6000 (Illumina)

treatment_protocol: 1.5 million CAR expressing Th17 cells and 1.5 million CAR expressing Tc17 cells, with or without 500ug of DMXAA.

value: Mammary tumor

tag: time

value: 7 days after therapy

value: Th/Tc17 CAR-T cells and DMXAA treatment

value: FVB-Neu mice


title: BMMCs, Gata2_WT_UN_H3K27ac rep1


title: Chopp59: Donor2_mixture


title: 4-Day7NoTx

value: Th/Tc17 CAR-T cells treatment


title: 17-Day7DMXAA


title: 20-Day7NoTx


title: BMMCs, Gata2_KO_ST_H3K4me1 rep2

value: H3K4me1, (Abcam, ab8895)


title: Chopp58: Donor1_mixture


title: Chopp62: Donor4_mix

value: female


title: 16-Day7DMXAA


title: Chopp15: Immature CD4SP thymocytes replicate 2

value: CD44low MHC-I-low CD8alow CD69+ ThpokGFP+ CD4+


title: BMMCs, Gata2_KO_ST_H3K4me1 rep1

value: Bone-marrow derived mast cells

value: Gata2 -/-


title: Chopp14: Immature CD4SP thymocytes replicate 1

value: Thymus


title: 15-Day10DMXAA

value: 10 days after therapy


title: hESC-RPE, s21_MFG3

city: Dresden

first: Seba

last: Almedawar

address: Fetscherstrasse 105

institute: CRTD- TU Dresden

data_processing:
[basecalling] Basecalls were performed using Illumina bcl2fastq version 2.17.1.14.
[mapping]  Reads were aligned to the human genome assembly (hg38) using GSNAP (2017-08-15; parameters: --gunzip -A sam  --use-sarray=1 --input-buffer-size=500000 --output-buffer-size=500000 -B 5 -N 0 -n 1 -s EnsemblGene-81.ss.hg38.iit) with known splice sites from Ensembl (v81) as support.
[gene counting]  Uniquely aligned fragments and gene annotations from Ensembl (v81) were used for featureCounts (v1.5.3; parameters: -a EnsemblGene-81.hg38.TR.gtf -s 2 -Q 1 -T 8) to obtain a table with read counts per gene.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited counts table from featureCounts (bfx582.featureCounts.hg38.e81.txt.gz) with the following columns: Ensembl Gene ID, Chromosome, Gene Start, Gene End, Gene Length, then all sample counts; comments start with '#'

source_name: Human embryonic stem cells-derived retinal pigment epithelium

growth_protocol: Cells were differentiated from human embryonic stem cells according to the paper: Zhu, Y. et al. (2013) ‘Three-Dimensional Neuroepithelial Culture from Human Embryonic Stem Cells and Its Use for Quantitative Conversion to Retinal Pigment Epithelium’, PLoS ONE, 8(1), p. e54552. doi: 10.1371/journal.pone.0054552.

extract_protocol:
RNA was extracted using Qiagen RNeasy Mini kit by lysing the cells inside the wells.
mRNA enrichment and  reverse-transcription into cDNA was done with the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB) following manufacturer's protocol.

treatment_protocol: Cells were treated for 1 hour without POS at 37 degrees with 5% CO2 with the treatment without POS. POS were added and treatment was kept for three more hours. Cells were lysed and RNA was prepared for RNA seq.

tag: photoreceptor outer segment

value: No

value: MFGE8+GAS6 (2.5µg/ml)

tag: experiment time

value: 4 hours incubation


title: hESC-RPE, s20_MFG2

value: Human embryonic stem cells-derived retinal pigment epithelium


title: BMMCs, Gata2_KO_UN_H3K4me1 rep2

source_name: BMMCs


title: BMMCs, Gata2_KO_UN_H3K4me1 rep1


title: hESC-RPE, s19_MFG1


title: 12-Day10DMXAA


title: Chopp13: MHC-I signaled CD4+CD8int thymocytes replicate 2

value: Chimeric mice:Thpok-GFP Runx3-RFP reporter donor, I-AB deficient recipient

value: CD44low CD69+ ThpokGFP- Runx3RFP- CD8aint CD4+


title: Chopp16: Immature CD4SP thymocytes replicate 3

value: Chimeric mice:Thpok-GFP Runx3-RFP reporter donor, b2m deficient recipient


title: hESC-RPE, s18_POS_MFG3

value: Yes

value: 1 hour incubation without POS+3 hours with POS


title: Chopp11: MHC-II signaled CD4+CD8int thymocytes replicate 3


title: BMMCs, Gata2_WT_ST_H3K4me1 rep2

value: wild type

value: IgE anti_TNP and TNP-BSA


title: BMMCs, Gata2_WT_ST_H3K4me1 rep1

value: H3K4me1, (Abcam, ab8895)


title: hESC-RPE, s17_POS_MFG2


title: Chopp10: MHC-II signaled CD4+CD8int thymocytes replicate 2


title: BMMCs, Gata2_WT_UN_H3K4me1 rep2


title: hESC-RPE, s16_POS_MFG1


title: 12_F12L: MCA_tMCAO_nonoccluded_3hrs

value: Wistar

value: middle cerebral artery

value: female

value: approx. 250 gram

tag: model

value: tMCAO

tag: group

value: non-occluded MCA


title: Chopp9: MHC-II signaled CD4+CD8int thymocytes replicate 1

value: Thymus


title: Chopp8: MHC-I signaled DP thymocytes replicate2

value: CD44low CD69+ ThpokGFP- Runx3RFP- CD8a+ CD4+


title: BMMCs, WT_ST_Input

value: Balb/cJ

value: Bone-marrow derived mast cells

tag: genotype


title: hESC-RPE, s14_DMSO2

value: No

value: 4 hours incubation

value: Human embryonic stem cells-derived retinal pigment epithelium


title: BMMCs, WT_UN_Input

tag: chip antibody


title: Chopp7: MHC-I signaled DP thymocytes replicate1

value: Chimeric mice:Thpok-GFP Runx3-RFP reporter donor, I-AB deficient recipient


title: Chopp49: Thpok KO immature CD4SP thymocytes replicate 3

data_processing:
Basecalls performed with Illumina RTA 2.4.6
Demultiplexing with Bcl2fastq 2.17
Alignment--bowtie2 (v2.3.4) --end-to-end --sensitive -X 2000
Filtering with samtools (v1.6) -f -q 30
Sorting with samtools
Mark and remove duplicates with Picard (v2.2.8)
Index and remove mitochondrial reads with samtools
Convert to bed with bedtools (v2.29.2)
Peak calling with Macs2 (v2.2.4) --nomodel --nolambda --pvalue 1e-7 --keep-dup all
Generate counts per million normalized bigwig with Deeptools (v3.3.0)
Genome_build: mm10
Supplementary_files_format_and_content: Peak excel file, counts per million normalized bigwig

extract_protocol:
Nuclei were isolated as recommended in Buenrostro et al, 2013
ATAC-seq libraries were prepared as recommended in Buenerostro et al, 2013

value: Thpok fl/fl; ThpokGFP; Cd4-Cre positive

value: CD44low MHC-I-low CD8alow CD69+ ThpokGFP+ CD4+

tag: experimentdesig


title: 11-Day7NoTx

value: Mammary tumor

value: 7 days after therapy

value: Th/Tc17 CAR-T cells treatment

value: FVB-Neu mice


title: Chopp48: Thpok KO immature CD4SP thymocytes replicate 2

tag: flow markers


title: Chopp6: MHC-II signaled DP thymocytes replicate 3

value: Chimeric mice:Thpok-GFP Runx3-RFP reporter donor, b2m deficient recipient

tag: tissue


title: Chopp5: MHC-II signaled DP thymocytes replicate 2


title: Chopp47: Thpok KO immature CD4SP thymocytes replicate 1


title: hESC-RPE, s12_POS_DMSO3

value: Yes

value: 1 hour incubation without POS+3 hours with POS

tag: cell type


title: WT liver, rep2

city: Edinburgh

first: Jose

last: de las Heras

address: Max Born Crescent

institute: University of Edinburgh

description: replicate 2

value: WT

value: liver


title: BMMCs, WT_ST_H3K27ac rep2

value: Balb/cJ

value: H3K27ac, (Abcam, ab4729)

value: wild type

tag: treatment

value: IgE anti_TNP and TNP-BSA


title: hESC-RPE, s11_POS_DMSO2

value: Human embryonic stem cells-derived retinal pigment epithelium


title: hESC-RPE, s15_DMSO3

value: No

value: 4 hours incubation


title: Chopp72: Donor1

tag: gender

value: Female

value: CD69+ mixed with CD69-CD8+CD4+

value: Thymus


title: Chopp4: MHC-II signaled DP thymocytes replicate 1

tag: strain

value: CD44low CD69+ ThpokGFP- Runx3RFP- CD8a+ CD4+


title: Chopp46: WT immature CD4SP thymocytes replicate 3

value: Thpok fl/fl; ThpokGFP; Cd4-Cre negative

value: CD44low MHC-I-low CD8alow CD69+ ThpokGFP+ CD4+


title: hESC-RPE, s10_POS_DMSO1

value: Yes


title: BMMCs, WT_UN_H3K27ac rep2

value: Bone-marrow derived mast cells


title: hESC-RPE, s13_DMSO1


title: Chopp45: WT immature CD4SP thymocytes replicate 2


title: Chopp3: Unsignaled DP thymocytes replicate 3

value: Chimeric mice:Thpok-GFP Runx3-RFP reporter donor, C57BL/6 recipient

value: CD44low CD69- ThpokGFP- Runx3RFP- CD8a+ CD4+


title: BMMCs, WT_UN_H3K27ac rep1

value: Balb/cJ


title: BMMCs, WT_ST_H3K4me1 rep2

value: H3K4me1, (Abcam, ab8895)


title: Chopp44: WT immature CD4SP thymocytes replicate 1


title: Chopp1: Unsignaled DP thymocytes replicate 1


title: hESC-RPE, s8_Drug2

value: MFGE8 0.625 µg/ml+Ramoplanin (10µM)


title: BMMCs, Gata2_WT_UN_H3K4me1 rep1

value: wild type


title: Chopp43: Unsignaled DP thymocytes replicate 1

value: CD44low CD8a-CD4-CD69-


title: BMMCs, WT_ST_H3K27ac rep1

value: H3K27ac, (Abcam, ab4729)

value: IgE anti_TNP and TNP-BSA


title: hESC-RPE, s7_Drug1

value: No

value: 4 hours incubation

value: Human embryonic stem cells-derived retinal pigment epithelium