title: Hep_Proliferating_2

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Trimmomatic (v0.36) was used to remove adaptor sequences. RNAseq reads were aligned to (GRCm38 - mm10) with STAR (v2.5.3a)
Genome wide transcript counting was performed by featureCounts (v1.6.3) to generate raw count table
Differential expression analysis was performed with DESeq2 (v1.20.0) package in R
Genome_build: GRCm38 - mm10
Supplementary_files_format_and_content: csv text file includes raw count value for each sample

growth_protocol: KP (KRASG12D,Tp53-/-) cells were grown in DMEM supplemented with 10% FBS and 100UI/ml penicillin/streptomycin.

extract_protocol:
Trizol RNA extraction protocol
Poly-A RNA-Seq / Paired-end 50

treatment_protocol: KP (KRASG12D,Tp53-/-) cells were treated for 8 days with either DMSO or the combination of MEK inhibitor (Trametinib) (25nM) and Cdk4/6 inhibitor (Palbociclib)  (500nM).After 8 days, the cells were harvested and subjected to RNAseq analysis. For the hydrodinamic tail vein injection experiments each mouse received 25ug of pT3-Caggs-NRASG12V-IRES-GFP plasmid and 5ug CMV-SB13 through hydrodynamic tail vein injection. Six days after, GFP-positive (NRASG12V overexpressing hepatocytes) and GFP-negative (untransduced hepatocytes) were isolated via low pressure fluorescence-activated cell sorting following liver perfusion and then were subjected to RNAseq analysis.

tag: model

value: Hydrodynamic tail vein injection of NRASG12V

value: Liver

value: Sorted primary hepatocytes

tag: oncotype (sorted cells)

value: Untransduced hepatocytes (GFP-)

tag: experimental condition

value: Proliferating

tag: age/stage (upon sample collection)

value: 12 weeks old

tag: sample collection time point

value: 6 days after hydrodynamic tail vein injection


title: Hep_Senescence_2

status: Public on Apr 18 2020

type: SRA

city: New York

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue source

tag: cell type

value: NRASG12V overexpression (GFP+)

value: Senescent


title: Hep_Senescence_1


title: P1228 (Smart-seq2)

city: Beijing

first: ZIyi

last: Li

address: No.5 Yiheyuan Road Haidian District

country: China

institute: Peking University

description:
CRC.Leukocyte.Smart-seq2.TPM.txt.gz
CRC.Leukocyte.Smart-seq2.Metadata.txt.gz

data_processing:
The Smart-seq2 data were first processed to filter out low-quality reads when: (1) “N” bases accounting for 10% read length; or (2) bases with quality < 5 account for 50% read length; or (3) containing adapter sequences. The remaining paired-end reads were aligned to the UCSC hg38 human genome reference using kallisto (version 0.43.1) with parameters “--bootstrap-samples=100 --threads=2”. The R package tximport (version 1.9.12) was used to summarize the transcript-level estimated counts into the matrix of gene-level counts.
Low-quality cells were discarded if the cell library size or the number of expressed genes (counts larger than 0) was smaller than pre-defined thresholds, which were the medians of all cells minus 3×median absolute deviation. Cells were also removed if their proportions of mitochondrial gene expression were larger than 10% (70% for CD45- cells).
In the droplet-based 10x data, the Cell Ranger toolkit (version 2.1.0) provided by 10x Genomics was applied to align reads and generate the gene-cell unique molecular identifier (UMI) matrix, using the reference genome GRCh38 and GRCm38. For each cell, we quantified the number of genes and UMIs, and kept high quality cells with the detection threshold of 600-4,000 genes and 1,600-25,000 UMIs. Cells with unusually high detection rate of mitochondrial gene expression were also excluded as described above.
Genome_build: hg38 downloaded from UCSC
Supplementary_files_format_and_content: tab-delimited text files include TPM values and metadata information for each Sample

organism: Homo sapiens

source_name: CD45+ and CD45- cells

extract_protocol: Single cells were sorted into 96-well plates (Axygen) chilled to 4°C, prepared with lysis buffer with 1 μl 10 mM dNTP mix (Invitrogen), 1 μl 10 μM Oligo dT primer, 1.9 μl 1% Triton X-100 (Sigma), and 0.1 μl 40 U/μl RNase Inhibitor (Takara). The single cell lysates were sealed and stored frozen at -80°C immediately.

tag: patient

value: CD45+ and CD45- cells


title: DLD-1 ZEB2 WT37 -DOX

city: Zwijnaarde

first: Jordy

last: De Coninck

address: Technologiepark 71

department: Department of Biomedical Molecular Biology

country: Belgium

institute: University Gent

description:
SG-23_S31
SG_23_DLD.1_TR21_ZEB2_WT37_mDOX

data_processing:
Samples were aligned to GRCh38 using STAR2.4.2a with default parameters.
Reads were count using STAR2.4.2a with default parameters and Ensembl v84 as reference.
Counts were normalized using the DESeq2 algorithm.
Genome_build: GRCh38
Supplementary_files_format_and_content: The processed file is counts table with in the rows the gene names (Ensembl ID) and in columns the different samples.

source_name: DLD-1 ZEB2 WT -DOX

extract_protocol:
RNA was extracted with the Nucleospin RNA Plus-kit (Machery-Nagel) according to the manufacturer’s instructions.
The mRNA libraries were prepared with the QuantSeq 3’ mRNA-Seq Library Prep FWD kit (Lexogen).

tag: cell line

tag: cell type background

value: epithelial colorectal cancer (CRC) cell line

value: colon

value: epithelial

tag: genotype/treatment

value: ZEB2 WT -DOX


title: WT_DRB.TTchemSeq_20min_release_rep2

city: London

first: Richard

middle: James

last: Mitter

state: LONDON

address: 1 Midland Road

department: Bioinformatics & Biostatistics

country: United Kingdom

institute: The Francis Crick Institute

description:
SC58
CUG506A58

data_processing:
library strategy: DRB/TTchem_Seq
DRB/TTchem-seq data were processed using previously a published protocol (Gregersen et al., 2020).
Reads were aligned to human GRCh38 Ensembl 86 using STAR 2.5.2a.
Sample scale factors were derived from a yeast spike-in, by aligning and counting against Saccharomyces cerevisiae R64-1-1 Ensembl 86.
Strand-specific, scaled bedgraph files were created from the aligments using BEDTools 2.27.1.  These were converted to bigWig format using the kentUtils bedGraphToBigWig function.
Genome_build: GRCh38
Supplementary_files_format_and_content: BigWig files contain sample-level, scaled read-depth coverage, split by strand.

growth_protocol: Cells were cultured in a 1:1 mixture of DMEM (Gibco) and Ham’s F10 (Invitrogen) supplemented with 10% FCS (Biowest) and 1% penicillin-streptomycin.

extract_protocol:
RNA was extracted by TRIzol (Thermo Fisher Scientific, 15596026) accordingly to the manufacturer’s instructions. As a control for equal sample preparation, we spiked-in S. cerevisiae (strain BY4741, MATa, his3D1, leu2D0, met15D0, ura3D0) 4-thiouracil (4TU)-labelled RNA. S. cerevisiae were grown in YPD medium overnight, diluted to an OD600 of 0.1, and grown to mid-log phase (OD600 of 0.8) and labelled with 5 mM 4TU (Sigma-Aldrich, 440736) for 6 min. Total RNA was extracted using the PureLink RNA Mini kit (Thermo Fisher Scientific, 12183020) following the enzymatic protocol. For purification of 4SU labelled RNA, 100 μg mammalian 4SU labelled RNA was spiked-in 1/100 of 4TU-labelled S. cerevisiae RNA. The 101 μg RNA was fragmented by addition of 20 μL 1 M NaOH to fragment RNA and left on ice for 20 min. Fragmentation was stopped by addition of 80 μL 1 M Tris pH 6.8 and cleaned up twice with Micro Bio-Spin™ P-30 Gel Columns (BioRad, 7326223) according to the manufacturer’s instructions. Biotinylation of 4SU-residues were carried out in a total volume of 250 μl, containing 10 mM Tris-HCl [pH 7.4], 1 mM EDTA and 5mg MTSEA biotin-XX linker (Biotium, BT90066) for 30 min at room temperature in the dark. RNA was then purified by phenol:chloroform extraction, denatured by 10 min incubation at 65°C and added to 200 μL μMACS Streptavidin MicroBeads (Miltenyi, 130-074-101). RNA was incubated with beads for 15 min at room temperature and beads applied to a μColumn in the magnetic field of a μMACS magnetic separator. Beads were washed twice with pull-out wash buffer (100 mM Tris-HCl, pH 7.4, 10 mM EDTA, 1 M NaCl and 0.1% Tween20). 4SU-RNA was eluted twice by addition of 100 mM DTT and RNA cleaned up using the RNeasy MinElute kit (Qiagen, 74204).
KAPA RNA HyperPrep Kit (Roche)

treatment_protocol: 3.5 hrs pre-treatment with 100uM DRB (5,6-dichloro-1-β-D-ribofuranosylbenzimidazole), followed by release from DRB inhibition for 10, 20, 30 or 40 min (including 10 min 1mM 4-thiouridine pulse)

tag: cell line background

value: colon cancer cell line

tag: genotype/variation

value: wild type

tag: treatment

value: 100uM DRB for 3.5 hrs, release from DRB inhibition for 20 min (including 10 min 1mM 4-thiouridine pulse)

tag: molecule subtype

value: Nascent RNA


title: KP_Proliferating_1

value: lung

value: KP

value: Murine Lung adenocarcinoma cell line (KrasG12D,Tp53-/-)

value: DMSO

value: After 8 days of treatment


title: shTROJAN-2 MCF7 cells

type: RNA

city: Shanghai

first: Xi

last: Jin

state: Shanghai

address: 270 Dong An Road, Build 7, RM301

institute: Fudan Universtiy Shanghai Cancer Canter

hyb_protocol: Hybridization of ST cDNA was performed on Affymetrix GeneChip HTA 2.0 Array as per the manufacturers protocol.

scan_protocol: Arrays were then washed and stained using the FS450_0001 fluidics protocol and scanned using an Affymetrix 3000 7G scanner.

data_processing: Initial Data processign was done with Affymetrix Expression Command Console software. Background correction was done by composition based and normalisation was done by IterativeProbe Logarithmic Intensity Error Estimation (iterPLIER) summarization algorithm with Global Median method.

label: biotin

source_name: breast cancer cells

label_protocol: Fragmentation and Biotin labelling and target preparation of the ST cDNA were performed using the NuGEN Encore Biotin Module.

growth_protocol: MCF7 cells were cultured in Dulbecco's Modified Eagle Medium

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: shCtrl or shTROJAN stable knockdown MCF7 cells

tag: genotype

value: shTROJAN


title: INT030-2: MDA-MB-453 scRNA

first: Sibo

last: Zhu

state: China

address: songhulu 2005

institute: Fudan University

description: single-cell transcriptome

data_processing:
Fastqc
Trimmomatic
hisat2
featureCounts
Genome_build: hg19
Supplementary_files_format_and_content: Expression Matrix

source_name: MDA-MB-453, spiked into blood and recovered

extract_protocol:
Manual picking
Smart-seq2

treatment_protocol: Blood spike-in; recovered by gradient-immunobeads based protocol (PLA), Aspirin (ASP), Ticagrelor (TIG), Clopidogrel (CHL), Cilostazol (CIL), Integrilin (INT), Tirofiban (TIR), and red blood lysis protocol (RBL).

value: Integrilin treated


title: INT030-1: MDA-MB-453 scRNA

description: single-cell transcriptome


title: shCtrl MCF7 cells

value: shCtrl


title: CIL030-5: MDA-MB-453 scRNA

description: single-cell transcriptome

value: Cilostazol treated


title: CIL030-2: MDA-MB-453 scRNA

description: single-cell transcriptome


title: CIL030-3: MDA-MB-453 scRNA

description: single-cell transcriptome


title: CM_stiff_1-m (S1841104)

city: Boulder

first: Corey

last: Neu

state: Colorado

address: 427 UCB - Mechanical Engineering, 1111 Engineering Drive

department: Mechanical Engineering

institute: University of Colorado, Boulder

data_processing:
Sequence quality was assessed using FastQC (v 0.11.2) for all samples and quality trimming was done using FASTX toolkit (v 0.0.13.2) to remove bases with less than Phred33 score of 30 and resulting reads of at least 50 bases were retained (typically more than 99% of total reads).
The quality trimmed reads were mapped against the bowtie2-indexed reference genome downloaded from Ensembl using Tophat (v 2.0.14) with default parameters.
HTSeq (v 0.6.1) was used to generate raw read counts from each sample for each gene feature using Tophat output and the gtf downloaded from Ensembl for protein coding genes (mRNA_counts.txt) and using Tophat output and gtf downloaded from NONCODE (NONCODEv4_mouse_lncRNA.gtf, http://www.noncode.org//datadownload/ncrna_NONCODEv4.fasta.tar.gz) (Version 4) for non coding genes (noncoding_counts.txt)
DE pairwise analysis between samples S184 and S527 using read counts matrix generated by HTSeq was performed using ‘R’ (Version 3.2.0) and two different methods (DESeq2,edgeR) and also using Cufflinks.
Any genes with 0 counts in all samples were removed from the count matrix and genes that had counts in some samples but not in others were changed from 0 to 1 in order to avoid having infinite values calculated for the fold change. Further filtering of genes with only read counts where 50% of samples in a group have greater than or equal to 5 counts were retained.
Genome_build: Mus_musculus.GRCm38.79.fa (Downloaded from Ensembl version 79)
Supplementary_files_format_and_content: Tab delimited files containing read counts for protein coding genes and noncoding genes from each sample

growth_protocol: Grown for 4 days (start beating before 24h) until confluent and at peak contraction in full growth medium (Advenaced DMEM, 10%FBS)

extract_protocol:
embryos are extracted from the mother at day 18 of gestation, embryonic hearts are then microdissceted out and digested to receive a single cell solution
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: plated on PDMS (polydimethylsiloxane) substrates with different elastic modulus

tag: organism age

tag: strain

value: embryonic cardiomyocytes

tag: substrate

value: stiff


title: CM_stiff_1-m (S1841103)


title: oe2.ribo: mimic miR-1271-5p 2

city: Callaghan

first: Dylan

last: Kiltschewskij

state: NSW

address: Room MS616, Level 6, Medical Sciences Building, University Drive

department: School of Biomedical Sciences and Pharmacy

country: Australia

institute: The University of Newcastle

data_processing:
Library strategy: Ribo-seq
Bcl files were demultiplexed and converted to fastq format using 'Bcl2fastq' version 2.2.
Lane data for each sample were merged.
Using 'Cutadapt' version 1.14, sequencing adapters were trimmed, low quality 3 prime nucleotides (Phred33 < 20) were removed and single 5 prime nucleotides were trimmed.
Reads were aligned to abundant short non-coding RNAs (rRNA, snRNA, snoRNA, miRNA) using 'Bowtie2' version 2.2.6. Unaligned reads were retained for further analysis.
Reads were mapped to the hg38 reference genome using 'Tophat2' version 2.1.1, and reads aligning to features were counted with 'HTSeq' version 0.7.2.
non.oe.ribo.cpm.txt: tab delimited text file containing Ribo-Seq gene-level counts per million for nonsense (scrambled siRNA) and overexpression (mimic) samples
kdctrl.kd.ribo.cpm.txt: tab delimited text file containing Ribo-Seq gene-level counts per million for knockdown control (inhibitor control) and knockdown (inhibitor) samples
Genome_build: hg38
Supplementary_files_format_and_content: Tab delimited text files containing read counts for each gene.

source_name: Neuronally differentiated SH-SY5Y

growth_protocol: SH-SY5Y cultures were neuronally differentiated using all-trans retinoic acid (ATRA, Sigma-Aldrich). One day prior to differentiation (day -1), cells were seeded into new 6 well plates at a density of 25,000 cells/cm2 in complete culture medium. The next day (day 0), standard culture medium was replaced with ATRA-supplemented medium (10µM final) and cells were wrapped in foil to protect from light exposure. ATRA-medium was subsequently replaced on day 2. On day 5, cells were washed with sterile PBS and returned to normal culture medium. Successful differentiation was confirmed by visual assessment of neurite outgrowth and quantification of neuronal marker genes (Fig 1A–C).

extract_protocol:
Cells were exposed to cycloheximide (0.1mg/mL) prior to detergent lysis and scraping as per the Illumina TruSeq Ribo Profile kit manual.
Ribosome profiling was conducted using the Illumina TruSeq Ribo Profile Kit (H/M/R) according to the manufacturer’s instructions, with minor amendments. To inhibit translational activity, transfected cells were treated with culture medium supplemented with 0.1mg/mL cycloheximide (CHX) for 1 min. Cells were subsequently washed with ice-cold CHX-supplemented PBS, then harvested on ice via the addition of 1mL mammalian lysis buffer (containing 200µL 5x mammalian polysome buffer, 2µL CHX and 10 units (U) DNase I) and extensive scraping. Ribosome foot-printing was performed by adding 90U RNase I to 300µL clarified lysate and incubating samples at room temperature for 45 min, after which reactions were stopped with 15µL SUPERase inhibitor (Invitrogen). Ribosome-protected RNA fragments (RPFs) were then enriched using MicroSpin S-400 columns (GE Life Sciences), prior to ribosomal RNA depletion, RPF size selection, end repair, adapter ligation, reverse transcription and PAGE purification, conducted according to the manufacturer’s instructions. RPF cDNA libraries were subsequently produced with 12 PCR cycles, following which adapter dimers were removed via 8% native polyacrylamide gel prior to library normalization and pooling. RPF libraries were then sequenced using the Illumina NextSeq 500 system, with a total of 76 single-end cycles performed.

treatment_protocol: Transfections were conducted 24 hours after removal of ATRA-medium. Each culture was transfected with 5µL Lipofectamine 2000 (L2K, ThermoFisher) and 100pmol of either miR-1271-5p mimic, mimic control (scrambled siRNA), inhibitor or inhibitor control (mirVana, ThermoFisher). Briefly, L2K and RNA were mixed separately in 500µL OptiMEM (ThermoFisher) at room temperature for 5 min, after which both were combined to a final volume of 1mL and incubated for an additional 25 min. Standard culture medium was then replaced with L2K/RNA/OptiMEM and cells were incubated at 37°C for 6 hours, following which cells were returned to normal culture medium. At 72 hours post-transfection, cells were harvested as per the ribosome profiling methodology (see below), with both total RNA and ribosome protected RNA collected. In parallel to this experiment, transfection efficiency was quantified by co-transfecting additional cells with 100pmol RNA and 2µg pEZ-Lv205CT empty vector control lentiviral expression plasmid, which contains the eGFP gene under the CMV promoter. The proportion of GFP+ cells was analysed via Countess II FL automated fluorescent cell counter 72 hours post-transfection, which revealed transfection efficiencies of: 52.5% (mimic), 75% (nonsense siRNA/mimic control), 72% (inhibitor) and 79% (inhibitor scramble control).

value: Neuronally differentiated SH-SY5Y

tag: passages

value: Ribosome protected mRNA


title: KP_Senescence_1

value: MEK inhibitor (Trametinib) (25nM) and Cdk4/6 inhibitor (Palbociclib) (500nM)

tag: experimental condition

value: Senescent


title: CM_soft_1-m (S527114)

value: soft


title: CIL030-4: MDA-MB-453 scRNA

description: single-cell transcriptome


title: CM_stiff_1-m (S1841102)


title: CIL030-1: MDA-MB-453 scRNA

description: single-cell transcriptome


title: shTROJAN-1 MCF7 cells


title: TIR030-5: MDA-MB-453 scRNA

description: single-cell transcriptome

value: Tirofiban treated


title: CM_soft_1-m (S527112)


title: CM_stiff_1-m (S1841101)


title: INT030-3: MDA-MB-453 scRNA

description: single-cell transcriptome


title: TIR030-6: MDA-MB-453 scRNA

description: single-cell transcriptome


title: KP_Proliferating_2

value: lung

value: Proliferating

tag: sample collection time point


title: CM_soft_1-m (S527111)


title: CM_soft_1-m (S527113)


title: TIR030-4: MDA-MB-453 scRNA

description: single-cell transcriptome


title: KP_Senescence_2

tag: tissue source

value: KP

value: Murine Lung adenocarcinoma cell line (KrasG12D,Tp53-/-)


title: CIL030-6: MDA-MB-453 scRNA

description: single-cell transcriptome


title: TIR030-3: MDA-MB-453 scRNA

description: single-cell transcriptome


title: TIR030-2: MDA-MB-453 scRNA

description: single-cell transcriptome


title: Hep_Proliferating_1

tag: model

value: Hydrodynamic tail vein injection of NRASG12V

value: Liver

tag: cell type

value: Sorted primary hepatocytes

tag: oncotype (sorted cells)

value: Untransduced hepatocytes (GFP-)

tag: age/stage (upon sample collection)

value: 12 weeks old

value: 6 days after hydrodynamic tail vein injection


title: SER030-6: MDA-MB-453 scRNA

description: single-cell transcriptome

source_name: MDA-MB-453, serum incubation

tag: cell line


title: TIR030-1: MDA-MB-453 scRNA

description: single-cell transcriptome


title: SER030-5: MDA-MB-453 scRNA

description: single-cell transcriptome


title: Erythroid differentiation Extra Loci S2 replicate 1

city: Oxford

first: A Marieke

last: Oudelaar

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Molecular Medicine

institute: University of Oxford

description:
Enriched 3C library
S2_Btg2_5000_iced.matrix
S2_CD47_5000_iced.matrix
S2_Slc25a37_2000_iced.matrix
S2_Tal1_5000_iced.matrix
Slc25a37_2000_coordinates.bed
Tal1_5000_coordinates.bed
Btg2_5000_coordinates.bed
CD47_5000_coordinates.bed

library_source: genomic

data_processing:
CCseqBasic pipeline (https://github.com/Hughes-Genome-Group/CCseqBasicF/releases)
Custom scripts (https://github.com/oudelaar/TiledC)
ICE normalization (Imakaev et al. Nature Methods 2012)
Genome_build: mm9
Supplementary_files_format_and_content: Sparse matrix format (bin1 \t bin2 \t ICE normalized interaction count \n) and bed file for bin number annotation. Processed data files have been down-sampled to be comparable between conditions as decribed in the Methods section of the paper.

molecule: genomic DNA

source_name: Primary haematopoietic/erythroid progenitor cells

growth_protocol: Cells were grown, treated and processed as described in the Methods section of the paper.

extract_protocol: Tiled-C combines 3C library preparation with oligonucleotide capture enrichment for deep, targeted sequencing of chromatin interactions within regions of interest. Details are described in the Methods section of the paper.

tag: tissue

value: Primary erythroid progenitor cells isolated from fetal liver

tag: immunophenotype

value: Lin- CD71:high Ter119:med

tag: regions analysed

value: slc25a37, tal1, cd47, btg2


title: Erythroid differentiation Extra Loci S3 replicate 1

description:
Enriched 3C library
S3_Btg2_5000_iced.matrix
S3_CD47_5000_iced.matrix
S3_Slc25a37_2000_iced.matrix
S3_Tal1_5000_iced.matrix
Slc25a37_2000_coordinates.bed
Tal1_5000_coordinates.bed
Btg2_5000_coordinates.bed
CD47_5000_coordinates.bed

treatment_protocol: Cells were grown, treated and processed as described in the Methods section of the paper.

value: Lin- CD71:high Ter119:high


title: SER030-2: MDA-MB-453 scRNA

description: single-cell transcriptome

tag: treatment


title: Erythroid differentiation Extra Loci S2 replicate 2


title: SER030-3: MDA-MB-453 scRNA

description: single-cell transcriptome


title: SER030-4: MDA-MB-453 scRNA

description: single-cell transcriptome


title: SER030-1: MDA-MB-453 scRNA

description: single-cell transcriptome


title: CHL030-5: MDA-MB-453 scRNA

description: single-cell transcriptome

value: Clopidogrel treated


title: Erythroid differentiation Extra Loci S0-medium replicate 2

description:
Enriched 3C library
S0M_Btg2_5000_iced.matrix
S0M_CD47_5000_iced.matrix
S0M_Slc25a37_2000_iced.matrix
S0M_Tal1_5000_iced.matrix
Slc25a37_2000_coordinates.bed
Tal1_5000_coordinates.bed
Btg2_5000_coordinates.bed
CD47_5000_coordinates.bed

value: Lin- CD71:med Ter119-


title: CHL030-4: MDA-MB-453 scRNA

description: single-cell transcriptome


title: Erythroid differentiation Extra Loci S0-medium replicate 1


title: CHL030-3: MDA-MB-453 scRNA

description: single-cell transcriptome


title: Erythroid differentiation Extra Loci S1 replicate 2

description:
Enriched 3C library
S1_Btg2_5000_iced.matrix
S1_CD47_5000_iced.matrix
S1_Slc25a37_2000_iced.matrix
S1_Tal1_5000_iced.matrix
Slc25a37_2000_coordinates.bed
Tal1_5000_coordinates.bed
Btg2_5000_coordinates.bed
CD47_5000_coordinates.bed

value: Lin- CD71:high Ter119-


title: Erythroid differentiation Extra Loci S1 replicate 1


title: Erythroid differentiation Extra Loci S0-low replicate 2

description:
Enriched 3C library
S0L_Btg2_5000_iced.matrix
S0L_CD47_5000_iced.matrix
S0L_Slc25a37_2000_iced.matrix
S0L_Tal1_5000_iced.matrix
Slc25a37_2000_coordinates.bed
Tal1_5000_coordinates.bed
Btg2_5000_coordinates.bed
CD47_5000_coordinates.bed

value: Lin- CD71- Ter119-


title: Erythroid differentiation Extra Loci S0-low replicate 1


title: MIR 7

city: Baltimore

first: Sheng

last: Wang

state: MD

address: 660 W Redwood Street, Howard Hall 564

department: Anesthesiology

institute: University of Maryland Baltimore

description:
cell-free RNA
SV18365-0014_S27_R1_001

data_processing:
Sequenced reads were first trimmed using Trim Galore software for adaptor sequence, and mapped to mouse genome (build mm9), genome-mappable reads were then mapped to mouse miRNA sequences (miRBase release 22.1) using the exceRpt Small RNA-Seq Pipeline.
Genome_build: mm9 and miRBase release 22.1
Supplementary_files_format_and_content: exceRpt_miRNA_ReadCounts.txt

source_name: Plasma

extract_protocol:
Plasma was prepared from EDTA anti-coagulated whole blood, and plasma RNA was harvested using Trizol LS reagent. NGS cDNA libraries were prepared using Norgen Biotek Small RNA Library Prep Kit. Library quality was validated prior to sequencing on an Illumina NextSeq 500 platform..
cDNA libraries were prepared for sequencing using standard Norgen protocols

value: Plasma

tag: age

value: 8 to 10 weeks

tag: genotype

value: wild type


title: CHL030-2: MDA-MB-453 scRNA

description: single-cell transcriptome


title: Erythroid differentiation Extra Loci S3 replicate 2

tag: strain


title: MIR 6

description:
cell-free RNA
SV18365-0013_S26_R1_001


title: MIR 8

description:
cell-free RNA
SV18365-0015_S28_R1_001


title: MIR 5

description:
cell-free RNA
SV18365-0012_S25_R1_001


title: CHL030-1: MDA-MB-453 scRNA

description: single-cell transcriptome


title: MIR 4

description:
cell-free RNA
SV18365-0011_S24_R1_001


title: RBL030-6: MDA-MB-453 scRNA

description: single-cell transcriptome

value: Red blood cell lysis buffer treated


title: MIR 3

description:
cell-free RNA
SV18365-0009_S22_R1_001


title: MIR 2

description:
cell-free RNA
SV18365-0008_S21_R1_001


title: RBL030-5: MDA-MB-453 scRNA

description: single-cell transcriptome


title: RBL030-4: MDA-MB-453 scRNA

description: single-cell transcriptome


title: MIR 1

description:
cell-free RNA
SV18365-0007_S20_R1_001


title: RBL030-3: MDA-MB-453 scRNA

description: single-cell transcriptome


title: CHL030-6: MDA-MB-453 scRNA

description: single-cell transcriptome


title: Sham 6

description:
cell-free RNA
SV18365-0006_S19_R1_001


title: RBL030-2: MDA-MB-453 scRNA

description: single-cell transcriptome


title: RBL030-1: MDA-MB-453 scRNA

description: single-cell transcriptome


title: PLA030-6: MDA-MB-453 scRNA

description: single-cell transcriptome


title: Sham 2

description:
cell-free RNA
SV18365-0002_S15_R1_001


title: PLA030-2: MDA-MB-453 scRNA

description: single-cell transcriptome


title: Sham 3

description:
cell-free RNA
SV18365-0003_S16_R1_001


title: Sham 4

description:
cell-free RNA
SV18365-0004_S17_R1_001


title: dm_t_tgfb_2

city: Basel

first: Ravi Kiran Reddy

last: KALATHUR

state: Basel

address: Mattenstrasse 28

department: Departement Biomedizin

country: Switzerland

institute: University of Basel

data_processing:
Base calling was done using Illumina software
Sequenced reads were mapped to MM10 version of mouse genome using RNA-STAR using parameters (outFilterMultimapNmax=10 and outFilterType="BySJout")
Counts are obtained using qcount in quasR and CPM (counts per million) was computed for each sample
Genome_build: mm10
Supplementary_files_format_and_content: txt file and contains counts as CPM values for each sample

molecule: polyA RNA

source_name: β-catenindm/- +TGFβ_2

growth_protocol: WT and mutant cell lines were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Sigma-Aldrich, D5671) supplemented with 10% Fetal Bovine Serum (FBS, 10%; Sigma-Aldrich), 2 mM glutamine (Sigma-Aldrich, G7513), 100 U penicillin (Sigma-Aldrich) and 0.1 mg/ml streptomycin (Sigma-Aldrich). All cell lines were grown at 37°C, 5% CO2, 95% humidity.

extract_protocol:
Total RNA was isolated from the samples above using the miRNeasy Mini Kit (Qiagen, 217004) with on-column DNAse digestion according to the manufacturer’s instructions.
RNA-sequencing libraries were prepared from total RNA using poly(A) enrichment with the TruSeq stranded mRNA Sample prep from Illumina using 200 ng input RNA. QC was performed with a fragment analyzer using DNF-473-33-SS NGS Fragment 1-6000bp kit. The RNA-sequence libraries were sequenced on a NextSeq 500 using 75 cycles kit High Output (Illumina).

treatment_protocol: For Wnt3a treatment, Pygo2 WT (+/+) and mutant (AE/AE) cell lines were treated with 100 ng/ml Wnt3a for 3 days. Medium was changed and fresh Wnt3a was added daily. Untreated cells served as control. For TGFb treatment, Pygo2 WT (+/+) and mutant (AE/AE) cell lines were treated with 2 ng/ml TGFb for 4 days. Medium was changed every second day with fresh addition of TGFb. Untreated cells served as control.

value: Breast cancer cells

value: MMTV-PyMT (FVB/N)

value: Tumor developed in mammary gland 2/3

tag: transgene

value: PyMT

tag: mutation

value: beta-catenindm/-

value: TGFb treated (4 days)


title: PLA030-5: MDA-MB-453 scRNA

description: single-cell transcriptome


title: dm_fl_ut_tgfb_2

source_name: β-catenindm/fl -TGFβ_2

value: beta-catenindm/fl

value: UT (4 days)


title: dm_ut_tgfb_2

source_name: β-catenindm/- -TGFβ_2


title: PLA030-1: MDA-MB-453 scRNA

description: single-cell transcriptome


title: Sham 1

description:
cell-free RNA
SV18365-0001_S14_R1_001


title: TIG030-4: MDA-MB-453 scRNA

description: single-cell transcriptome

value: Ticagrelor treated


title: PLA030-3: MDA-MB-453 scRNA

description: single-cell transcriptome


title: dc_t_tgfb_2

source_name: β-cateninΔC/- +TGFβ_2

value: beta-catenin{delta}C/-


title: dm_fl_t_tgfb_2

source_name: β-catenindm/fl +TGFβ_2


title: PLA030-4: MDA-MB-453 scRNA

description: single-cell transcriptome


title: TIG030-3: MDA-MB-453 scRNA

description: single-cell transcriptome


title: dc_ut_tgfb_2

source_name: β-cateninΔC/- -TGFβ_2


title: TIG030-5: MDA-MB-453 scRNA

description: single-cell transcriptome


title: TIG030-2: MDA-MB-453 scRNA

description: single-cell transcriptome


title: Sham 5

description:
cell-free RNA
SV18365-0005_S18_R1_001


title: da_t_tgfb_2

source_name: β-cateninD164A/- +TGFβ_2


title: dc_fl_ut_tgfb_2

source_name: β-cateninΔC/fl -TGFβ_2

value: beta-catenin{delta}C/fl


title: TIG030-1: MDA-MB-453 scRNA

description: single-cell transcriptome


title: BLK030-12: MDA-MB-453 scRNA

description: single-cell transcriptome

source_name: MDA-MB-453, culture medium


title: da_ut_tgfb_2

source_name: β-cateninD164A/- -TGFβ_2


title: BLK030-11: MDA-MB-453 scRNA

description: single-cell transcriptome


title: da_fl_t_tgfb_2

source_name: β-cateninD164A/fl +TGFβ_2


title: TIG030-6: MDA-MB-453 scRNA

description: single-cell transcriptome


title: BLK030-10: MDA-MB-453 scRNA

description: single-cell transcriptome


title: BLK030-8: MDA-MB-453 scRNA

description: single-cell transcriptome


title: bcatfl_fl_ut_tgfb_2

source_name: β-cateninfl/fl -TGFβ_2

value: beta-cateninfl/fl


title: da_fl_ut_tgfb_2

source_name: β-cateninD164A/fl -TGFβ_2


title: bcatfl_fl_t_tgfb_2

source_name: β-cateninfl/fl +TGFβ_2


title: BLK030-4: MDA-MB-453 scRNA

description: single-cell transcriptome


title: BLK030-6: MDA-MB-453 scRNA

description: single-cell transcriptome


title: BLK030-7: MDA-MB-453 scRNA

description: single-cell transcriptome


title: dm_t_tgfb_1

source_name: β-catenindm/- +TGFβ_1


title: BLK030-5: MDA-MB-453 scRNA

description: single-cell transcriptome


title: dm_fl_t_tgfb_1

source_name: β-catenindm/fl +TGFβ_1


title: dc_fl_t_tgfb_2

source_name: β-cateninΔC/fl +TGFβ_2


title: dm_fl_ut_tgfb_1

source_name: β-catenindm/fl -TGFβ_1


title: dm_ut_tgfb_1

source_name: β-catenindm/- -TGFβ_1


title: dc_t_tgfb_1

source_name: β-cateninΔC/- +TGFβ_1


title: BLK030-3: MDA-MB-453 scRNA

description: single-cell transcriptome


title: BLK030-1: MDA-MB-453 scRNA

description: single-cell transcriptome


title: dc_ut_tgfb_1

source_name: β-cateninΔC/- -TGFβ_1


title: ASP030-6: MDA-MB-453 scRNA

description: single-cell transcriptome

source_name: MDA-MB-453, spiked into blood and recovered

value: Aspirin treated


title: dc_fl_ut_tgfb_1

source_name: β-cateninΔC/fl -TGFβ_1


title: ASP030-5: MDA-MB-453 scRNA

description: single-cell transcriptome


title: da_t_tgfb_1

source_name: β-cateninD164A/- +TGFβ_1


title: da_ut_tgfb_1

source_name: β-cateninD164A/- -TGFβ_1


title: ASP030-4: MDA-MB-453 scRNA

description: single-cell transcriptome


title: BLK030-9: MDA-MB-453 scRNA

description: single-cell transcriptome

source_name: MDA-MB-453, culture medium


title: ASP030-3: MDA-MB-453 scRNA

description: single-cell transcriptome


title: ASP030-2: MDA-MB-453 scRNA

description: single-cell transcriptome


title: da_fl_ut_tgfb_1

source_name: β-cateninD164A/fl -TGFβ_1


title: ASP030-1: MDA-MB-453 scRNA

description: single-cell transcriptome


title: BLK030-2: MDA-MB-453 scRNA

description: single-cell transcriptome


title: bcatfl_fl_t_tgfb_1

source_name: β-cateninfl/fl +TGFβ_1


title: bcatfl_fl_ut_tgfb_1

source_name: β-cateninfl/fl -TGFβ_1


title: SAMPLEB1: HBRR bulkRNA

description: bulk transcriptome

source_name: HBRR, RNA

value: HBRR


title: dm_t_wnt3a_2

source_name: β-catenindm/- +Wnt3a_2

value: Wnt3a treated (3 days)


title: SAMPLEB2: HBRR bulkRNA

description: bulk transcriptome


title: SAMPLEA2: UHRR bulkRNA

description: bulk transcriptome

source_name: UHRR, RNA

value: UHRR


title: dc_fl_t_tgfb_1

source_name: β-cateninΔC/fl +TGFβ_1


title: dm_fl_ut_wnt3a_2

source_name: β-catenindm/fl -Wnt3a_2

value: UT (3 days)


title: dm_ut_wnt3a_2

source_name: β-catenindm/- -Wnt3a_2

value: Breast cancer cells


title: SAMPLEA1: UHRR bulkRNA

description: bulk transcriptome


title: dm_fl_t_wnt3a_2

source_name: β-catenindm/fl +Wnt3a_2

value: MMTV-PyMT (FVB/N)


title: TG6: MDA-MB-453 scRNA

description: single-cell transcriptome


title: dc_t_wnt3a_2

source_name: β-cateninΔC/- +Wnt3a_2

value: Tumor developed in mammary gland 2/3


title: dc_ut_wnt3a_2

source_name: β-cateninΔC/- -Wnt3a_2

value: PyMT


title: dc_fl_t_wnt3a_2

source_name: β-cateninΔC/fl +Wnt3a_2


title: TG4: MDA-MB-453 scRNA

description: single-cell transcriptome

source_name: MDA-MB-453, spiked into blood and recovered


title: TG3: MDA-MB-453 scRNA

description: single-cell transcriptome


title: da_fl_t_tgfb_1

source_name: β-cateninD164A/fl +TGFβ_1


title: da_t_wnt3a_2

source_name: β-cateninD164A/- +Wnt3a_2


title: TG2: MDA-MB-453 scRNA

description: single-cell transcriptome


title: da_ut_wnt3a_2

source_name: β-cateninD164A/- -Wnt3a_2


title: TG1: MDA-MB-453 scRNA

description: single-cell transcriptome


title: SAMPLEB3: HBRR bulkRNA

description: bulk transcriptome


title: TC5: MDA-MB-453 scRNA

description: single-cell transcriptome

source_name: MDA-MB-453, culture medium


title: TC4: MDA-MB-453 scRNA

description: single-cell transcriptome


title: SAMPLEA3: UHRR bulkRNA

description: bulk transcriptome


title: bcatfl_fl_ut_wnt3a_2

source_name: β-cateninfl/fl -Wnt3a_2


title: TC3: MDA-MB-453 scRNA

description: single-cell transcriptome


title: dm_t_wnt3a_1

source_name: β-catenindm/- +Wnt3a_1

value: beta-catenindm/-


title: bcatfl_fl_t_wnt3a_2

source_name: β-cateninfl/fl +Wnt3a_2


title: TC2: MDA-MB-453 scRNA

description: single-cell transcriptome


title: da_fl_t_wnt3a_2

source_name: β-cateninD164A/fl +Wnt3a_2


title: dm_ut_wnt3a_1

source_name: β-catenindm/- -Wnt3a_1


title: TG5: MDA-MB-453 scRNA

description: single-cell transcriptome


title: G155-27

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

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

source_name: sigmoid colon tissue

extract_protocol:
Surgical specimens were transferred immediately from the operating room to the surgical pathology lab where a section of full-thickness sigmoid colon was obtained from a site of active inflammation and stored in RNAlater. RNA was extracted from tissue samples using trizol reagent followed by purification with the Qiagen RNeasy Mini Kit.
The cDNA libraries were prepared using the NEXTflex™ Illumina Rapid Directional RNA-Seq Library Prep Kit (BioO Scientific) as per the manufacturer’s instructions. Briefly, polyA RNA was purified from 200 ng of total RNA using oligo (dT) beads. The extracted mRNA fraction was subjected to fragmentation, reverse transcription, end repair, 3’– end adenylation, and adaptor ligation, followed by PCR amplification and SPRI bead purification (Beckman Coulter). The unique index sequences were incorporated in the adaptors for multiplexed high-throughput sequencing. The final product was assessed for its size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent Technologies). Pooled libraries were diluted to 2 nM in EB buffer (Qiagen) and then denatured using the Illumina protocol. The denatured libraries were diluted to 10 pM by pre-chilled hybridization buffer and loaded onto a TruSeq v2 Rapid flow cell on an Illumina HiSeq 2500 and run for 50 cycles using a single-read recipe according to the manufacturer's instructions.

tag: disease

value: UC

value: sigmoid colon

tag: Sex

value: Male

tag: smoking history

value: ex smoker

tag: age at diagnosis

tag: age at surgery

tag: bmi


title: G155-25


title: TC1: MDA-MB-453 scRNA

description: single-cell transcriptome


title: dc_t_wnt3a_1

source_name: β-cateninΔC/- +Wnt3a_1

tag: cell type

value: beta-catenin{delta}C/-


title: dc_ut_wnt3a_1

source_name: β-cateninΔC/- -Wnt3a_1


title: dm_fl_t_wnt3a_1

source_name: β-catenindm/fl +Wnt3a_1

value: beta-catenindm/fl


title: G155-26

value: Never Smoked


title: dc_fl_ut_wnt3a_2

source_name: β-cateninΔC/fl -Wnt3a_2

value: beta-catenin{delta}C/fl


title: dm_fl_ut_wnt3a_1

source_name: β-catenindm/fl -Wnt3a_1


title: TC6: MDA-MB-453 scRNA

description: single-cell transcriptome

tag: cell line


title: G155-22

tag: tissue


title: G155-23

value: Female


title: G155-24


title: dc_fl_t_wnt3a_1

source_name: β-cateninΔC/fl +Wnt3a_1

value: Wnt3a treated (3 days)


title: dc_fl_ut_wnt3a_1

source_name: β-cateninΔC/fl -Wnt3a_1


title: da_t_wnt3a_1

source_name: β-cateninD164A/- +Wnt3a_1


title: da_fl_ut_wnt3a_2

source_name: β-cateninD164A/fl -Wnt3a_2


title: G155-20


title: da_ut_wnt3a_1

source_name: β-cateninD164A/- -Wnt3a_1


title: G155-19


title: da_fl_ut_wnt3a_1

source_name: β-cateninD164A/fl -Wnt3a_1


title: G155-18


title: G155-17


title: G155-16


title: bcatfl_fl_t_wnt3a_1

source_name: β-cateninfl/fl +Wnt3a_1

value: beta-cateninfl/fl


title: bcatfl_fl_ut_wnt3a_1

source_name: β-cateninfl/fl -Wnt3a _1

value: UT (3 days)


title: G155-15


title: G155-12


title: G155-11


title: G155-10


title: G155-13


title: G155-14


title: G155-09


title: G155-06


title: G155-07


title: G155-05


title: G155-08


title: da_fl_t_wnt3a_1

source_name: β-cateninD164A/fl +Wnt3a_1

value: Breast cancer cells


title: G155-04


title: G155-03


title: G155-02


title: G155-01


title: Liver_batch2_HBxs,src,p53-+DIO_OF+10Gy_replicate 4

city: Zhunan Town

first: Chiou-Hwa

last: Yuh

state: Miaoli County

address: #35 Keyan Road

country: Taiwan

institute: National Health Research Institutes

description: Gene expression data from adult HBx,src,p53- zebrafish diet-induced obesity with 10Gy γ-irradiation pretreated oligo-fucoidan, sample 4

hyb_protocol: An automated Hyb-Wash-Scan workflow with ZebGene1.1ST Array Plate was performed with the GeneTitan™ Multi-Channel (MC) Instrument (Thermo Fisher Scientific, US) according to the manufacturer manual (P/N 702933 Rev. 2).

scan_protocol: Hybridized arrays were washed and the signal intensity of the chip was scanned using a "High Throughput Array Scanner" .

data_processing: Data analysis was performed by Transcriptome Analysis Console (TAC) Software 4.0 (Thermo Fisher Scientific, US) according to the manufacturer manual (P/N 703150 Rev. 6).

organism: Danio rerio

label_protocol: Target cRNA and ss-cDNA samples were prepared stepwise from 100 ng of total RNA diluted into 3 ul of volume using GeneChip® WT PLUS Reagent Kit (Thermo Fisher Scientific, US) according to the manufacturer manual (P/N 703147 Rev. 3). The resulting purified ss-cDNA samples were fragmented and labelled with terminal deoxynucleotidyl transferase (TdT) using the Affymetrix proprietary DNA Labeling Reagent that was covalently linked to biotin (Thermo Fisher Scientific, US).

growth_protocol: The WT, HBx,Src and HBx,Src,p53–/+ transgenic zebrafish (Danio rerio) were used and growth for 6 months.

extract_protocol: Total RNA was isolated by NucleoSpin® RNA kit (MACHEREY-NAGEL, US) following the manufacturer manual, and RNA samples was eluted in 40 μl RNase-free water. RNA quantity and purity were assessed using NanoDrop ND-1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7.

treatment_protocol: The wild-type fish were normal diet with, the amount of Artemia fed was approximately 6.9 mg cysts/fish/day . Three-month-old female HBx,Src and HBx,Src,p53–/+ transgenic zebrafish were diet-induced obesity (DIO) fed with 12X of Artemia approximately 83 mg cysts/fish/day for two months. OF (300 mg/kg) was administrated by oral gavage for one month starting at 4 months of age for one month. Then, fish were exposed to 40 Gy γ-irradiation at 500 Gy/min followed by oral gavage with oligo-fucoidan thrice, with a one-week interval. The fish were sacrificed and the hepatic tissue was immediately frozen in liquid nitrogen and stored at −80 °C for later RNA extraction and hybridization on Affymetrix microarrays.

value: Liver

tag: group

value: diet-induced obesity (DIO)

tag: agent

value: oral gavage with OF (300 mg/kg) thrice a week for one month

tag: irradiation

value: 10 Gy γ-irradiation

value: 6 months


title: Liver_batch2_HBxs,src,p53-+DIO_OF+10Gy_replicate 3

description: Gene expression data from adult HBx,src,p53- zebrafish diet-induced obesity with 10Gy γ-irradiation pretreated oligo-fucoidan, sample 3

tag: age


title: Liver_batch2_HBxs,src,p53-+DIO_OF+10Gy_replicate 5

description: Gene expression data from adult HBx,src,p53- zebrafish diet-induced obesity with 10Gy γ-irradiation pretreated oligo-fucoidan, sample 5

tag: genotype


title: Liver_batch2_OF+10Gy_replicate 2

description: Gene expression data from adult WT zebrafish 10Gy γ-irradiation pretreated oligo-fucoidan, sample 2

value: WT

value: normal diet (NOR)


title: Liver_batch2_HBxs,src,p53-+DIO_OF+10Gy_replicate 2

description: Gene expression data from adult HBx,src,p53- zebrafish diet-induced obesity with 10Gy γ-irradiation pretreated oligo-fucoidan, sample 2


title: Liver_batch2_10Gy_replicate 2

description: Gene expression data from adult WT zebrafish 10Gy γ-irradiation, sample 2

value: no treatment (mock)


title: Liver_batch2_HBxs,src,p53-+DIO_10Gy_replicate 2

description: Gene expression data from adult HBx,src,p53- zebrafish diet-induced obesity with 10Gy γ-irradiation, sample 2


title: WT_ATAC-seq_rep3

city: Lyon

first: Thomas

last: Simonet

address: Faculté de Médecine Lyon Est, 8 Avenue Rockefeller

country: France

institute: Université de Lyon

data_processing:
Sequencing and Base-calling by BGI
Trimming of Nextera adapters from reads using Trimmomatic, with parameters : ILLUMINACLIP:Nextera.fa:2:30:10:2:true MINLEN:20
Mapping to the mm9 genome assembly using Bowtie2, with the local alignment mode (--local) and a maximum fragment length set to 2000bp (--maxins)
Filtering out of not properly paired, supplementary alignments using samtools view with parameters : -F 2572 -f 3
Filtering out of putative PCR duplicates using Picard Tools MarkDuplicates (REMOVE_DUPLICATES=true)
Bams to fragment ends files : bedtools bamtobed -i input.bam | grep -v '^chrM' | awk ‘BEGIN {OFS="\t"} { if ($6=="+") {print $1,$2,($2+1),".",$5,$6} else {print $1,($3-1),$3,".",$5,$6} }’
Fragment ends to peaks, modelled with a tn5-occupancy, using MACS2 : -q 0,01 --nomodel --shift -4 --extsize 9 --keep-dup all --call-summits --bdg –SPMR
Fold enrichment profiles to bigwig files, peak filtering and filtered peaks to bigbed files, as described in https://github.com/ENCODE-DCC/atac-seq-pipeline
High confidence peaks : for each condition, selection of intervals overlapped by at least 25% of their length by the two other replicates, taking the union of the three (using bedtools intersect)
Unions of high confidence peaks from both conditions, taking the union of regions overlapping by more than 50% of their length, or keeping not overlapped regions (or overlapped by less than 50%) with their boundaries unchanged (using bedtools intersect)
Bams to tn5 extended fragment ends files : bedtools bamtobed -i input.bam | grep -v '^chrM' | awk ‘BEGIN {OFS="\t"} { if ($6=="+") {start=$2-4; end=$2+5} else {start=$3-4; end=$3+5}; print $1,start,end,".",$5,$6 }’
Count of tn5 extended fragment ends falling within common peaks : bedtools intersect -c -sorted -g db/mm9/mm9_allChr.sizes -a union_peaks.bed -b tn5-ext_ends.bed
Differential peak enrichment between both conditions, using DESeq2
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file include peak coordinates, read count for each sample, and data computed with DESeq2

source_name: Tibialis Anterior muscle nuclei

extract_protocol:
Tibialis anterior (TA) muscle were dissected from mice and flash frozen in liquid nitrogen. After thawing of the sample, muscle were minced with scissors in a buffer containing 2,15M sucrose following by an ultraturrax treatment to release nuclei. After ultracentrifugation nuclei are washed to removed the sucrose and a small fraction is counted with DAPI under a microscope.
50 000 nuclei are used to perform the ATAC-Seq library according to Buenrostro et al 2013 (Nat Methods. 2013 Dec;10(12):1213-8)

tag: strain

value: 7 weeks

value: H2A.Z-1 flox/flox x H2A.Z-2 flox/flox x HSA CRE -


title: Liver_batch2_HBxs,src,p53-+DIO_OF+10Gy_replicate 1

description: Gene expression data from adult HBx,src,p53- zebrafish diet-induced obesity with 10Gy γ-irradiation pretreated oligo-fucoidan, sample 1


title: WT_ATAC-seq_rep2


title: dKO_ATAC-seq_rep3

value: H2A.Z-1 flox/flox x H2A.Z-2 flox/flox x HSA CRE +


title: Liver_batch1_HBxs,src+DIO_OF+40Gy_replicate 4

description: Gene expression data from adult HBx,src zebrafish diet-induced obesity with 40Gy γ-irradiation pretreated oligo-fucoidan, sample 4

value: HBx,src

value: 40 Gy γ-irradiation


title: Liver_batch2_HBxs,src,p53-+DIO_10Gy_replicate 3

description: Gene expression data from adult HBx,src,p53- zebrafish diet-induced obesity with 10Gy γ-irradiation, sample 3


title: Liver_batch1_HBxs,src+DIO_OF+40Gy_replicate 2

description: Gene expression data from adult HBx,src zebrafish diet-induced obesity with 40Gy γ-irradiation pretreated oligo-fucoidan, sample 2


title: WT_ATAC-seq_rep1


title: Liver_batch1_HBxs,src+DIO_OF+40Gy_replicate 3

description: Gene expression data from adult HBx,src zebrafish diet-induced obesity with 40Gy γ-irradiation pretreated oligo-fucoidan, sample 3


title: dKO_ATAC-seq_rep1


title: dKO_ATAC-seq_rep2


title: Liver_batch2_HBxs,src,p53-+DIO_10Gy_replicate 1

description: Gene expression data from adult HBx,src,p53- zebrafish diet-induced obesity with 10Gy γ-irradiation, sample 1


title: Liver_batch1_OF+40Gy_replicate 2

description: Gene expression data from adult WT zebrafish 40Gy γ-irradiation pretreated oligo-fucoidan, sample 2


title: Liver_batch1_HBxs,src+DIO_40Gy_replicate 2

description: Gene expression data from adult HBx,src zebrafish diet-induced obesity with 40Gy γ-irradiation, sample 2


title: Liver_batch1_HBxs,src+DIO_40Gy_replicate 1

description: Gene expression data from adult HBx,src zebrafish diet-induced obesity with 40Gy γ-irradiation, sample 1


title: Liver_batch1_HBxs,src+DIO_OF+40Gy_replicate 1

description: Gene expression data from adult HBx,src zebrafish diet-induced obesity with 40Gy γ-irradiation pretreated oligo-fucoidan, sample 1


title: Liver_batch1_OF+40Gy_replicate 1

description: Gene expression data from adult WT zebrafish 40Gy γ-irradiation pretreated oligo-fucoidan, sample 1


title: Liver_batch1_HBxs,src+DIO_40Gy_replicate 3

description: Gene expression data from adult HBx,src zebrafish diet-induced obesity with 40Gy γ-irradiation, sample 3


title: Liver_batch1_40Gy_replicate 2

description: Gene expression data from adult WT zebrafish 40Gy γ-irradiation, sample 2


title: Liver_batch2_10Gy_replicate 1

description: Gene expression data from adult WT zebrafish 10Gy γ-irradiation, sample 1


title: JLR541 WT_S3

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

hyb_protocol: Six micrograms of biotinylated cDNA was fragmented and then hybridized for 16 hr at 45C on an Affymetrix Clariom S mouse GeneChip. Following hybridization, GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the AffymetrixGeneChip Scanner 3000 7G.

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console software v1.1

source_name: iNKT cell developmental subsets

label_protocol: Total RNA (1 - 20 ng) were converted into biotinylated cDNA using the NuGEN WTA Pico v2 protocol and the NuGEN Encore Biotin module

growth_protocol: Total thymocytes were enriched for iNKT cells using the CD8+ microbeads positive-selecting kit (Miltenyi) and iNKT developmental stages were sorted using the Sony SY3200 sorter as follows: (S1, TCRb+CD1d-PBS57-tet+CD24–CD44–NK1.1–; S2, TCRb+CD1d-PBS57-tet+CD24–CD44+NK1.1–; or S3, TCRb+CD1d-PBS57-tet+CD24–CD44+NK1.1+)

extract_protocol: Total RNA samples were prepared according to the prototol of Rneasy Micro kit from Qiagen,

treatment_protocol: Sorted cells were lysed with lysis buffer from Rneasy Micro kit from Qiagen.

tag: sample type

value: iNKT cell developmental subsets

tag: genotype/stage


title: JLR543 dKOMst_S3


title: JLR540 WT_S3


title: JLR539 WT_S3


title: 1851013039-26_S61

city: Okhla Industrial Estate, Phase III

first: Arvind

last: Iyer

email: arvind16122@iiitd.ac.in, krishang@iiitd.ac.in, naveen.ramalingam@fluidigm.com, debarka@iiitd.ac.in

state: New Delhi

address: IIIT Delhi

department: Computational biology department

country: India

institute: IIIT Delhi

description: single circulating tumor cell

data_processing:
RSEM index generated on hg19
Read data aligned to index using RSEM/bowtie
Quantified gene expression levels in counts using RSEM v1.2.44
Genomic mappings(GM) performed with TopHat 2 v2.0.135 and GM percentages calculated using resulting alignments
Raw sequencing read data aligned to the human rRNA sequences using bowtie 2 v2.2.46, and calculated percentage of reads aligned to rRNA as reads aligned to sequences divided by the total reads
Genome_build: hg19
Supplementary_files_format_and_content: RSEM read count

source_name: Peripheral Blood of Cancer Patient

extract_protocol:
Circulating tumor cells enriched by ClearCell FX were captured by Polaris System(Fluidigm).  polyA RNA from each single cell was reverse transcribed and cDNA amplified using SMARTer kit (SMARTer Ultra Low RNA Kit for the Fluidigm C1 System,Clontech#634936)
Amplified cDNA was used as input to prepare sequencing libraries with the NexteraXT DNA Kit (Illumina #fc-131-1096) and with dual indices (PN FC-131-1002; Illumina); RNA-Seq, paired-end MiSeq 75bp sequencing

tag: subject id

tag: patient diagnosis

value: HER- Breast Cancer

value: Peripheral Blood

value: Circulating tumor cell


title: 1851013039-6_S89

description: single circulating tumor cell


title: Liver_batch1_40Gy_replicate 1

description: Gene expression data from adult WT zebrafish 40Gy γ-irradiation, sample 1

value: Liver


title: JLR536 dKOMst_S1_S2


title: 1851009049-9_S18

description: single circulating tumor cell


title: JLR537 dKOMst_S1_S2


title: 1851009049-8_S10

description: single circulating tumor cell


title: JLR534 WT_S1_S2


title: JLR535 WT_S1_S2


title: JLR528 Mst1KO_S3


title: JLR527 Mst1KO_S3


title: JLR533 WT_S1_S2


title: 1851009049-7_S2

description: single circulating tumor cell


title: 1851009049-5_S33

description: single circulating tumor cell


title: 1851009049-4_S25

description: single circulating tumor cell


title: 1851009049-17_S35

description: single circulating tumor cell


title: 1851009049-16_S27

description: single circulating tumor cell


title: JLR525 Mst1KO_S3


title: 1851009049-15_S19

description: single circulating tumor cell


title: JLR520 WT_S3


title: JLR526 Mst1KO_S3


title: JLR519 WT_S3


title: HCCLM3_PRRX1_shRNA_rep3

city: Nanjing

first: Weibo

last: Chen

state: Jiangsu

address: No. 321 Zhongshan Road

department: Department of Hepatobiliary Surgery

institute: Affiliated Drum Tower Hospital of Nanjing University Medical School

description: Gene expression data from HCCLM3 cells transfected with PRRX1 shRNA

hyb_protocol: Following fragmentation, 130 ul of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip primeview human Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000

data_processing: The data were analyzed with rma using Affymetrix default analysis settings and global scaling as normalization method.

label_protocol: Biotinylated cRNA were prepared according to the protocol of Affymetrix One-Cycle Target Labeling kit and Control Reagents kit(Affymetrix, Santa Clara, CA) from 10 ug total RNA.

growth_protocol: HCCLM3 cells were maintained in Dulbecco modified eagle medium (DMEM) (Gibco, Maryland, USA) supplemented with 10% fetal bovine serum (FBS) (Gibco) and cultured at 37 °C in a humidified atmosphere with 5% CO2.

treatment_protocol: HCCLM3 cells with PRRX1 knockdown were generated by transfection with lentivirus carrying short hairpin RNA (shRNA) targeting PRRX1. HCCLM3 cells transfected with lentivirus carrying shRNA for a non-targeting human gene were used as a control.

value: Human hepatocellular cell line

tag: genotype/variation

value: transfected with PRRX1 shRNA


title: JLR524 Mst1KO_S3


title: 1851009049-14_S11

description: single circulating tumor cell


title: HCCLM3_PRRX1_shRNA_rep1

source_name: HCCLM3 cells transfected with PRRX1 shRNA


title: 1851009049-11_S34

description: single circulating tumor cell


title: JLR517 WT_S3


title: 1851009049-10_S26

description: single circulating tumor cell


title: Liver_batch2_OF+10Gy_replicate 1

description: Gene expression data from adult WT zebrafish 10Gy γ-irradiation pretreated oligo-fucoidan, sample 1

value: oral gavage with OF (300 mg/kg) thrice a week for one month

value: 10 Gy γ-irradiation


title: HCCLM3_Control_shRNA_rep2

description: Gene expression data from HCCLM3 cells transfected with control shRNA

value: transfected with control shRNA


title: HCCLM3_Control_shRNA_rep3

source_name: HCCLM3 cells transfected with control shRNA


title: JLR511 Mst1KO_S1_S2


title: HCCLM3_PRRX1_shRNA_rep2


title: JLR518 WT_S3


title: 1850-061-049-CS29_S22

description: single circulating tumor cell


title: KO3

city: Rochester

first: Joseph

middle: M

last: Miano

state: NY

address: 601 Elmwood Avenue

institute: University of Rochester

data_processing:
DATA FORMATTING (Illumina -> FastQ) & DEMULTIPLEXING - bcltofastq-2.19.0
CLEANING - fastp 0.20.0, "--in1 ../${SAMPLE}_R1.fastq.gz --out1 clt_${SAMPLE}_R1.fastq.gz --length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -w 8 -y -r -j ${SAMPLE}_fastp.json"
MAPPING - STAR_2.7.0f, "--twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM Unsorted --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical"
READ COUNTING - subread-1.6.4, featurecounts, "-s 2 -t exon -g gene_name"
Genome_build: GRCm38 + Gencode-M22
Supplementary_files_format_and_content: tab-delimited text file includes raw count values for each sample

source_name: Aortae from homozygous floxed Srf with Itga8-CreERT2 driver

growth_protocol: Mice were maintained on a normal chow diet and allowed water ad libitum over the 10 days period following 5 sequential days of i.p. injection of Tamoxifen.  Please note that we have used the best possible control with heterozygous floxed Srf mice carrying the Itga8-CreERT2 allele and receiving the same schedule of tamoxifen injections as the experimental homozygous floxed Srf/Itga8CreERT2 mice.

extract_protocol:
Mice were euthanized and the aorta (from descending arch to the renal bifurcations) was rapidly excised and placed in ice cold PBS.  The adventitia and endothelium were gently removed to create as pure a population of medial smooth muscle cells as possible.  Aortae were individually snap frozen in liquid nitrogen and then homogenized with a Bertin Minilys Personal Homogenizer (Bertin Instruments) in a 1.5ml microfuge tube containing 1ml of Trizol.  Total RNA was isolated according to instructions by the manufacturer and then samples were treated with DNAse I for 15 minutes at 37C.  DNAse I was removed by phenol/chloroform extraction following by standard sodium acetate/ethanol preciptation.  Samples were resuspended in RNAse-free water and submitted to the University of Rochester Genomics Research Core for quality assessment and library construction.
Illumina TruSeq Stranded mRNA

value: aortae


title: HCCLM3_Control_shRNA_rep1


title: JLR509 Mst1KO_S1_S2


title: JLR510 Mst1KO_S1_S2


title: KO2

value: homozygous floxed Srf with Itga8-CreERT2 driver


title: 1850-061-049-CS26_S19

description: single circulating tumor cell


title: PW034-705

city: New York

first: Peter

middle: A

last: Sims

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

data_processing:
Read 1 and read 2 fastq files were generated on basespace.
Raw data obtained from the Illumina NovaSeq 6000 was first corrected for index swapping to avoid cross-talk between sample index sequences using the algorithm described by Griffiths et al, Nature Communications, 2018 before assigning read addresses for each sample.
12-nt cell barcodes (CBs) and 8-nt unique molecular identifiers (UMIs) were extracted from read 1. Degenerate CBs containing either 'N's or more than four consecutive 'G's were discarded. Synthesis errors, which can result in truncated 11-nt cell barcodes, were corrected.
Read 2 were trimmed to remove poly(A) tails (> dA(7)) from the 3'-ends of each read. Any resulting fragment shorter than 24 nucleotides were discarded.
Trimmed reads were then aligned to GRCh38 (GENCODE v.24) using STAR v.2.5.0 with parameters "-- sjdbOverhang 65 --twopassMode Basic --outSAMtype BAM Unsorted". Only reads with unique, strand-specific alignments to exons were kept for further analysis.
All reads with the same CB, UMI, and gene mapping were collapsed to represent a single molecule. To correct for sequencing errors in UMIs, we further collapsed UMIs that were within Hamming distance 1 of another UMI with the same barcode and gene. To correct for sequencing errors in cell barcodes, we then collapsed CBs that were within Hamming distance one of another cell barcode, had at least 20 unique IMI-gene pairs, and had at least 75% overlap of their UMI-gene pairs. A digital gene expression matrix was then generated from these corrected barcode-UMI-gene triplets.
We estimated the number of cell barcodes corresponding to beads associated with cells in our microwell system using the emptyDrops algorithm from Lun et al, Genome Biology, 2019.
We removed CBs that satisfied any of the following criteria 1) fractional alignment to the mitochondrial genome greater than 1.96 standard deviations above the mean, 2) ratio of molecules aligning to whole gene bodies (including introns) to molecules aligning exclusively to exons greater than 1.96 standard deviations above the mean, 3) average number of reads per molecule or average number of molecules per gene >2.5 standard deviations above the mean for a given sample, 4) more than 40% of UMI bases are T or where the average number of T-bases per UMI is at least 4..
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files that contain the gene expression level of each individual cell.

source_name: acute slice culture of glioma resection

growth_protocol: Tumor specimens were collected immediately after surgical removal  and kept in ice-cold artificial cerebrospinal fluid (ACSF) solution containing 210 mM sucrose, 10 mM glucose, 2.5 mM KCl, 1.25 mM NaH2PO4, 0.5 mM CaCl2, 7 mM MgCl2 and 26 mM NaHCO3 for transportation. Preparation of ex vivo tissue slices was modified from methods described previously4. Briefly, the collected tumor specimens were placed in a drop of ice-cold ACSF and sliced using a tissue chopper (McIlwain) at a thickness of 500 µm under sterile conditions. The slices were immediately transferred to the ice-cold ACSF solution in 6-well plates using a sterile plastic Pasteur pipette half filled with ice-cold ACSF solution followed by a 15 minutes recovery in ACSF to reach room temperature. Intact and well-shaped slices (approximately 5-10 mm diameter) were then placed on top of a porous membrane insert (0.4 µm, Millipore). Then the membrane inserts were placed into 6-well plates containing 1.5 mL maintenance medium consisting of F12/DMEM (Gibco) supplemented with N-2 Supplement (Gibco) and 1% penicillin/streptomycin (Sigma). To ensure proper diffusion into the slice, culture medium was placed under the membrane insert without bubbles. A drop of 10 µl of culture medium was added directly on top of each slice to prevent the slice surface from drying. The slices were first rested for 6 hrs with the maintenance medium in a humidified incubator at 37℃ and 5% CO2. Then, the medium was replaced with pre-warmed medium containing drugs with desired concentration (Table S1) or corresponding volume of vehicle (DMSO). Slices were then cultured with the treatment medium in a humidified incubator at 37℃ and 5% CO2 for 18 hrs before being collected for dissociation.

extract_protocol:
Collected tissue samples or tissue slices were dissociated using the Adult Brain Dissociation kit (Miltenyi Biotec) on gentleMACS Octo Dissociator with Heaters (Miltenyi Biotec) according to the manufacturer’s instructions.
mRNA molecues were captured using bead-bound oligo dT(30).
Captured mRNA molecues were reverse transcriped to obtain cDNA which is then amplified by PCR reactions. The cDNA PCR reaction product was then purified with AMPure XP beads. The purified cDNA PCR product was used as the input for Nextera XT reactions to generate sequencing library.

value: acute slice culture of glioma resection

tag: gender

value: F

tag: location

value: left parieto-occipital

tag: diagnosis

value: Glioblastoma, WHO Grade IV

tag: treatment

value: 0.2 uM panobinostat


title: 201883520002_R03C01

type: genomic

city: Toronto

first: George

middle: S.

last: Charames

state: ON

address: 600 University Ave, Ste 6-500

department: Pathology and Lab Medicine

country: Canada

institute: Mount Sinai Hospital

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChip array chips. In the overnight incubation at 48C, hybridization of DNA sample onto millions of loci, enzymatic single-base extension and allele-specific staining (XStain) with fluorescent dyes were performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining, BeadChips were coated with XC4/ethanol, dried for 1 hour and scanned on a BeadArray Reader (Illumina iScan or NextSeq 550) using a single bead type and a dual-color channel approach to interrogate up to millions of loci per DNA sample and to image all beads on the array. The scanner detects red and green fluorescence intensities for each locus to produce genotyping data.

data_processing: Genomic DNA extracted from saliva was genotyped using Infinium DrugDev Consortium Array (Illumina). Analysis using GenomeStudio 2.0 (Illumina).

label: Alexa555 and Alexa647

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37C using Infinium HD Assay Kit (WGS-PreLV1). Then amplified DNA was enzymatically fragmented with fragmentation solution (FMS), and the end-point fragmentation is used to prevent over-fragmentation and enables access to a vast majority of the genome. After fragmentation, DNA was precipitated with isopropanol and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA with ethanol precipitation protocol and prepIT•L2P reagent, from saliva samples collected with Oragene saliva collection kit (Oragene•DISCOVER | OGR-500) to maximize the recovery of DNA.

tag: sex

value: Male

tag: plasma thc - 5mg fast 2h

value: Int

tag: plasma thc - 10mg fast 2h

tag: plasma thc - 5mg fed 5h

tag: plasma thc - 10mg fed 5h

value: High

value: saliva


title: KO1

tag: tissue


title: JLR508 Mst1KO_S1_S2

value: iNKT cell developmental subsets


title: PW034-703

tag: age

value: 2.5 uM etoposide


title: JLR504 WT_S1_S2

tag: strain


title: 201883520003_R10C02

description: Genomic DNA extracted from saliva was genotyped using Infinium DrugDev Consortium Array (Illumina).

value: Low


title: PW034-702

value: vehicle (DMSO)


title: 201883520002_R09C01

value: Female


title: 201883520003_R11C02


title: JLR502 WT_S1_S2

tag: sample type


title: 201883520003_R12C02


title: 201883520003_R07C02


title: 201883520003_R02C02


title: Ctrl1

source_name: Aortae from heterozygous floxed Srf with Itga8-CreERT2 driver

tag: genotype


title: PW034-701


title: JLR501 WT_S1_S2

tag: genotype/stage


title: 201883520002_R05C01


title: Ctrl3

value: heterozygous floxed Srf with Itga8-CreERT2 driver


title: Ctrl2

value: aortae


title: Glomerulus_Obob_enarodustat_1

status: Public on Apr 17 2020

city: Bunkyo-ku

first: Mai

last: Sugahara

state: Tokyo

address: 7-3-1 Hongo

department: Nephrology and Endocrinology

country: Japan

institute: The University of Tokyo Graduate School of Medicine

description: Gene expression at the age of 22 weeks

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a Agilent fragmentation buffer and was hybridized at 65°C for 17 hr using Gene Expression Hybridization Kit.

scan_protocol: Microarray slides were scanned at 3 ìm resolution using an Agilent G4900DA SureScan Microarray Scanner System.

data_processing: The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction Software 11.5.1.1(Agilent).  Raw data were processed with the R package limma in Bioconductor to perform background correction and data normalization using the quantile normalization method.

source_name: Glomerulus, Obob, enarodusat, 1

label_protocol: Agilent one-color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling protocol.

extract_protocol: Total RNA was extracted using miRNeasy Mini Kit (Qiagen, Hilden, Germany).

treatment_protocol: The mice were fed with either vehicle- or enarodustat-containing food. After 18-week treatment, glomeruli were isolated using Dynabeads method.

value: BTBR ob/ob

value: male

value: 22 weeks

value: glomerulus


title: 201883520003_R06C02


title: Glomerulus_Obob_vehicle_3

description: Gene expression at the age of 22 weeks

source_name: Glomerulus, Obob, vehicle, 3


title: 201883520002_R11C01


title: 201883520003_R08C02


title: 201883520002_R07C01


title: Glomerulus_Obob_vehicle_2

description: Gene expression at the age of 22 weeks

source_name: Glomerulus, Obob, vehicle, 2


title: Glomerulus_Obob_enarodustat_2

description: Gene expression at the age of 22 weeks

source_name: Glomerulus, Obob, enarodusat, 2


title: 201883520003_R09C02


title: 201883520003_R05C02


title: 201883520003_R12C01


title: Glomerulus_Obob_enarodustat_3

description: Gene expression at the age of 22 weeks

source_name: Glomerulus, Obob, enarodusat, 3


title: Glomerulus_WT_vehicle_3

description: Gene expression at the age of 22 weeks

source_name: Glomerulus, WT, vehicle, 3

value: BTBR wild type


title: Glomerulus_WT_vehicle_2

description: Gene expression at the age of 22 weeks

source_name: Glomerulus, WT, vehicle, 2


title: Glomerulus_WT_vehicle_1

description: Gene expression at the age of 22 weeks

source_name: Glomerulus, WT, vehicle, 1


title: SNB19_shRNA-Luc_exp2

city: Amsterdam

first: Anton

last: Berns

state: Amsterdam

address: Plesmanlann 121

department: Division of Molecular Genetics

country: Netherlands

institute: NKI

description:
Human SNB19 and K562 cells bearing doxycycline-inducible short hairpin RNAs (shRNA) targeting CHD9 were induced with 1ug/ml doxycycline for 48 hours, harvested, and pellet was snap-frozen.
X2646_40

data_processing:
Illumina Casava1.7 software used for basecalling.
Tophat version: 2.1, HTSeq count (v0.5.3), DESeq2
Genome_build: mm9 (MEFs, ESCs), mm10 (ED15 brain and liver; EmuMyc  lymphomas), hg37 (K562 and SNB19 cells)
Supplementary_files_format_and_content: tab-delimited text files include raw read count values for each Sample

source_name: SNB19 cell line

extract_protocol:
Total RNA was extracted using Trizol, prepared using TruSeq protocol, and standard sample preparation protocols and RNA-seq was performed on a HiSeq2000 machine (Illumina) at the NKI Genomics Core Facility.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: glioblastoma multiforme


title: SNB19_shRNA-Luc_exp1

description:
Human SNB19 and K562 cells bearing doxycycline-inducible short hairpin RNAs (shRNA) targeting CHD9 were induced with 1ug/ml doxycycline for 48 hours, harvested, and pellet was snap-frozen.
X2646_39


title: Glomerulus_Obob_vehicle_1

description: Gene expression at the age of 22 weeks

source_name: Glomerulus, Obob, vehicle, 1


title: polarized M2-like BMM c-Maf KO, rep 2

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

hyb_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Low Input Quick Amp Labeling 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 Agilent 2100Bioanalyzer II (Agilent Technologies, Santa Clara, CA).

scan_protocol: Slides were washed by Gene Expression Was Buffer (Agilent) and scanned by on the Agilent Technologies Microarray Scanner (Scan Resolution; 3um, TIFF file dynamic range; 20bit)

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent).  Data was imported to GeneSpring and normalized by 75Percentile Shift.

source_name: M2-like BMM from c-Maf KO fetal liver

label_protocol: Total RNA was prepared using the RNeasy Mini kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

extract_protocol: RNAs were extracted with a QIAGEN RNeasy kit (QIAGEN).

treatment_protocol: Single-cell suspensions of fetal liver and bone marrow cells were prepared by mechanical disruption (grinding with a syringe insert against a 70-mm nylon cell strainer; BD Biosciences). Cells were re-suspended in DMEM supplemented with 10% FBS, 1% penicillin/streptomycin, and 10 ng ml−1 M-CSF (R&D Systems) and then seeded onto tissue culture dishes. The culture medium was not changed for the duration of the experiment. M-CSF (final concentration, 10 ng /ml) was added every day from day 4 onwards.

value: liver

tag: cell type

value: polarized M2-like BMM

value: c-Maf KO


title: 201883520003_R03C02

value: Int

value: High

value: saliva


title: SNB19_shRNA-CHD9#2_exp2

description:
Human SNB19 and K562 cells bearing doxycycline-inducible short hairpin RNAs (shRNA) targeting CHD9 were induced with 1ug/ml doxycycline for 48 hours, harvested, and pellet was snap-frozen.
X2646_34


title: SNB19_shRNA-CHD9#1_exp2

description:
Human SNB19 and K562 cells bearing doxycycline-inducible short hairpin RNAs (shRNA) targeting CHD9 were induced with 1ug/ml doxycycline for 48 hours, harvested, and pellet was snap-frozen.
X2646_30


title: polarized M2-like BMM c-Maf KO, rep 3


title: 201883520003_R04C02

value: Low


title: polarized M2-like BMM WT, rep 1

source_name: M2-like BMM from WT fetal liver

value: WT


title: polarized M2-like BMM c-Maf KO, rep 1


title: 201883520003_R08C01

value: Male


title: 201883520003_R01C02


title: SNB19_shRNA-CHD9#1_exp1

description:
Human SNB19 and K562 cells bearing doxycycline-inducible short hairpin RNAs (shRNA) targeting CHD9 were induced with 1ug/ml doxycycline for 48 hours, harvested, and pellet was snap-frozen.
X2646_29


title: K562_shRNA-Luc_exp1

description:
Human SNB19 and K562 cells bearing doxycycline-inducible short hairpin RNAs (shRNA) targeting CHD9 were induced with 1ug/ml doxycycline for 48 hours, harvested, and pellet was snap-frozen.
X2646_15

source_name: K562 cell line

value: chronic myelogenous leukemia


title: K562_shRNA-CHD9#2_exp1

description:
Human SNB19 and K562 cells bearing doxycycline-inducible short hairpin RNAs (shRNA) targeting CHD9 were induced with 1ug/ml doxycycline for 48 hours, harvested, and pellet was snap-frozen.
X2646_9


title: K562_shRNA-CHD9#1_exp1

description:
Human SNB19 and K562 cells bearing doxycycline-inducible short hairpin RNAs (shRNA) targeting CHD9 were induced with 1ug/ml doxycycline for 48 hours, harvested, and pellet was snap-frozen.
X2646_5


title: 201883520003_R09C01


title: K562_shRNA-CHD9#1_exp2

description:
Human SNB19 and K562 cells bearing doxycycline-inducible short hairpin RNAs (shRNA) targeting CHD9 were induced with 1ug/ml doxycycline for 48 hours, harvested, and pellet was snap-frozen.
X2646_6


title: 201883520003_R11C01

value: Female


title: K562_shRNA-CHD9#2_exp2

description:
Human SNB19 and K562 cells bearing doxycycline-inducible short hairpin RNAs (shRNA) targeting CHD9 were induced with 1ug/ml doxycycline for 48 hours, harvested, and pellet was snap-frozen.
X2646_10


title: polarized M2-like BMM WT, rep 3


title: SNB19_shRNA-CHD9#2_exp1

description:
Human SNB19 and K562 cells bearing doxycycline-inducible short hairpin RNAs (shRNA) targeting CHD9 were induced with 1ug/ml doxycycline for 48 hours, harvested, and pellet was snap-frozen.
X2646_33


title: 201883520003_R02C01


title: d9_Lung

first: Carolyn

last: King

address: Hebelstrasse 28

department: Department of Biomedicine

description: mice treated with NICD protector 15 mins prior to harvest

data_processing:
Single-cell sequencing files (basecalls) were processed using the Cell Ranger Single Cell Software Suite (v2.1.0) to perform quality control, sample de-multiplexing, barcode processing, alignment to mm10 genome with STAR (version 2.5.3a), and read counting on Ensembl 84 gene model (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome).
Default parameters were used for Cell Ranger, except for the STAR parameters outSAMmultNmax set to 1 and alignIntronMax set to 10000.
UMI were counted by extracting read counts from the .h5 files generated by Cell Ranger, using R and the cellrangerRkit package version 2.0.0. The UMI matrix was filtered to keep only cells with log library size > 2.9, log number of features > 2.6, % mitochondrial reads >= 6, % ribosomal protein reads >= 20. Genes with average counts < .007 were removed.  The UMI counts marices are tab-separated and gzipped in the processed data files.
Genome_build: mm10
Supplementary_files_format_and_content: TSV file (tab separated values) with raw UMI counts for ensembl release 84 gene models; columns correspond to: 1. ENSEMBL ID, 2. and remaining columns contain UMI counts for each cell; column headers include the cell barcode sequence and the sample ID separated by a dash (e.g., "AAAAAAAAAAAAAAAT-d30_Lung")

source_name: CD4+ T cells from pooled mice Lung extracts

growth_protocol: Mice were bred and kept in the animal facility of the Department of Biomedecine, University of Basel, Switzerland, under SPF conditions.

extract_protocol:
Single cells were extracted from pooled suspensions from lung (digested) or lymph node from 4-12 female individual litter-mate mice
Cells were sorted by flow cytometry (using a BD FACSAria III) and gated for dump- CD4+ CD44+ I-Ab NP311-325+ expression.
The sorted cell suspension from each sample was loaded into a single well of a 10× Genomics Chromium Single Cell Controller.
Single-cell capture and cDNA and library preparation were performed with a Single Cell 3’ v2 Reagent Kit (10× Genomics) according to manufacturer’s instructions.

treatment_protocol: For lung and lymph node samples, influenza A/PR8/34 OVAII was intranasally administered at 500-2000 TCID50. For liver sample, mice were infected by intraperitoneal (i.p.) injection with 2x105 focus forming units (FFU) of LCMV Armstrong.

value: CD4+ T cells

value: lung

tag: time post infection (days)

tag: Sex

value: female


title: d30_Lung


title: d9_LN

source_name: CD4+ T cells from pooled mice LN extracts

value: lymph node


title: K562_shRNA-Luc_exp2

description:
Human SNB19 and K562 cells bearing doxycycline-inducible short hairpin RNAs (shRNA) targeting CHD9 were induced with 1ug/ml doxycycline for 48 hours, harvested, and pellet was snap-frozen.
X2646_16


title: d14_LN


title: d30_LN


title: d14_Lung


title: 201883520003_R05C01


title: 201883520003_R07C01


title: polarized M2-like BMM WT, rep 2


title: MinigutsOld

city: Lausanne

first: Nicolas

last: Broguiere

address: AI 1208 Station 15

department: Sciences de la vie

institute: EPFL

description: Mini-guts differentiated in ENR for 20 days.

data_processing:
The reads were aligned to mm10 with cell ranger 3.0.1.
Raw count matrices were then imported in Seurat 2.3.4 using RStudio 1.1.463
Single live cells were selected based on number of detected genes (approx. 2500-5000) and fraction of mitochondrial genes (approx. 0.05-0.15)
Genome_build: mm10
Supplementary_files_format_and_content: Compressed (.gz) tab separated values (.tsv) file containing the raw counts from single live cells. The row names are gene names, and column names contain unique tags and annotations in the format SampleTitle_CellType_UniqueCellTag.

source_name: Small intestinal mini-guts

extract_protocol:
10x chromium
SingleCell 3' Reagent Kit v3, Official user guide, CG000183 Rev A, sequenced using Illumina protocol #15048776 using NextSeq v2.5 reagents with 56 nt read length (R2), 28 nt read length of barcode and UMI (R1), and 8 nt read length index (I1)

treatment_protocol: Enzymatic dissociation (TrypLE)

value: Small intestinal mini-guts

tag: days in differentiation medium

tag: c. parvum infected

value: No

tag: organ on a chip

value: Yes


title: MinigutsYoung

description: Mini-guts differentiated in ENR for 10 days.


title: MinigutsCrypto

description: Mini-guts differentiated in ENR for 10 days and infected with C. parvum.


title: Organoids

description: Small intestinal organoids grown in matrigel drops, differentiated in ENR for 10 days.

source_name: Small intestinal organoids

value: Small intestinal organoids


title: Ba/F3-P-K220 Dox(-) [EA2022_01]

city: Kyoto

first: Takuyo

last: Kanayama

address: 465, Kajii-cho, Kawaramachi-Hirokoji, Kamigyo-ku

department: Department of Pediatrics

institute: Kyoto Prefectural University of Medicine

hyb_protocol: cRNA was hybridized to GeneChip Mouse Genome 430 2.0 Array

scan_protocol: scanned with a Genechip 3000 7G Scanner (Thermo Fisher Scientific)

data_processing:
affymetrix-algorithm-name = ExpressionStat
affymetrix-algorithm-version = 5.0
program-name = Expression Console
program-id = 1.4.1.46

label: Biotin

label_protocol: Biotin-labeled cRNA

growth_protocol: RPMI-1640 medium supplemented with 10% FBS, penicillin (100 U/ml), streptomycin (10 mg/ml), and 20% of the supernatant in which the WEHI-3 were cultured, at 37℃ in a 5% CO2 humidified atmosphere.

extract_protocol: RNeasy mini kit (Qiagen) according to the manufacturer’s instructions

treatment_protocol: with or without 500 ng/mL of doxyxycline

tag: strain background

value: BALB/c

value: Ba/F3 murine leukemia cells

tag: genotype/variation


title: WT2 Treg3.22

city: Shanghai

first: Hui

last: Yang

address: Ruijin Second Road No.197

institute: Shanghai Jiaotong University, School of Medcine

description: Gene expression data from WT naïve T cells were stimulated under Treg-induction conditions

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization,Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instruction.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix,Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA,US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: Treg cells from WT2 mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: WT or KO naïve T cells were isolated from spleen of mice freshly.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Naïve T cells were stimulated under Treg-induction conditions for 3 days.

value: wild type naïve T cells

value: spleen


title: Ba/F3-P-K220 Dox(+) [EA1566_02]


title: Liver

description:
mice treated with NICD protector 15 mins prior to harvest
Liver4

data_processing:
Single-cell sequencing files (basecalls) were processed using the Cell Ranger Single Cell Software Suite (v2.1.0) to perform quality control, sample de-multiplexing, barcode processing, alignment to mm10 genome with STAR (version 2.5.3a), and read counting on Ensembl 84 gene model (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome).
Default parameters were used for Cell Ranger, except for the STAR parameters outSAMmultNmax set to 1 and alignIntronMax set to 10000.
For lung and LN cells, UMI were counted by extracting read counts from the .h5 files generated by Cell Ranger, using R and the cellrangerRkit package version 2.0.0. The UMI matrix was filtered to keep only cells with log library size > 2.9, log number of features > 2.6, % mitochondrial reads >= 6, % ribosomal protein reads >= 20. Genes with average counts < .007 were removed.  The UMI counts marices are tab-separated and gzipped in the processed data files.
For liver cells, UMI were counted by extracting read counts from the .h5 files generated by Cell Ranger, using R and the cellrangerRkit package version 2.0.0. The UMI matrix was filtered to keep only cells with log library size > 2.8, log number of features > 2.6, % mitochondrial reads >= 6, % ribosomal protein reads >= 20. Genes with average counts < .005 were removed. The UMI counts marices are tab-separated and gzipped in the processed data files.
Genome_build: mm10
Supplementary_files_format_and_content: TSV file (tab separated values) with raw UMI counts for ensembl release 84 gene models; columns correspond to: 1. ENSEMBL ID, 2. and remaining columns contain UMI counts for each cell; column headers include the cell barcode sequence and the sample ID separated by a dash (e.g., "AAAAAAAAAAAAAAAT-d30_Lung")

source_name: CD4+ T cells from pooled mice liver extracts

extract_protocol:
Lung and lymph node cells were extracted from pooled suspensions from lung (digested) or lymph node from 4-12 female individual litter-mate mice
Liver cells were extracted from pooled suspensions from liver from 3 female litter-mate mice
Lung and lymph node cells were sorted by flow cytometry (using a BD FACSAria III) and gated for dump- CD4+ CD44+ I-Ab NP311-325+ expression.
Liver cells were sorted by flow cytometry (using a BD FACSAria III) and gated for dump- CD4+ CD44+ GP66+ expression.
The sorted cell suspension from each sample was loaded into a single well of a 10× Genomics Chromium Single Cell Controller.
Single-cell capture and cDNA and library preparation were performed with a Single Cell 3’ v2 Reagent Kit (10× Genomics) according to manufacturer’s instructions.

treatment_protocol:
infection protocol: For lung and lymph node samples, influenza A/PR8/34 OVAII was intranasally administered at 500-2000 TCID50.
infection protocol: For liver sample, mice were infected by intraperitoneal (i.p.) injection with 2x105 focus forming units (FFU) of LCMV Armstrong

value: liver

value: C57/BL6 N


title: Ba/F3-P-K220 Dox(-) [EA1566_01]


title: Ba/F3-P-K220 Dox(-) [EA2021_01]


title: 201883520003_R03C01

description: Genomic DNA extracted from saliva was genotyped using Infinium DrugDev Consortium Array (Illumina).

tag: sex

tag: plasma thc - 5mg fast 2h

value: Int

tag: plasma thc - 10mg fast 2h

value: High

value: saliva


title: KO2 Treg3.22

description: Gene expression data from KO naïve T cells were stimulated under Treg-induction conditions

source_name: Treg cells from KO2 mice

value: KO naïve T cells

tag: tissue


title: Ba/F3-P-K220 Dox(+) [EA2019_01]


title: KO1 Treg3.22

source_name: Treg cells from KO1 mice


title: WT1Treg3.22

source_name: Treg cells from WT1 mice


title: G1E-ER4_Bcl11a+55KO_ATF4-r1

city: Guangzhou

first: Peng

last: Huang

state: Guangdong

address: Xinzao, Panyu District

department: GMU-GIBH Joint School of Life Sciences

institute: Guangzhou Medical University

data_processing:
Basecalls using bcl2fastq2 v2.15.0.4, and parameters --no-eamss --mismatches 1
 Mapping to reference genome mm10 with Bowtie 1.0.0 using parameters --chunkmbs 1024 -y -n 2 --best -k 1 --maxbts 800 -l 28 -e 80 --sam-nohead --sam
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files with read coverage; bed files of peaks

growth_protocol: G1E-ER4 cells were cultured with IMDM supplemented with 15% FBS, 2% penicillin/streptomycin, 0.6% Kit ligand conditioned medium, 0.15 mM monothioglycerol and 2 units/ml erythropoietin

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature. Fixed cells were lysised in 1mL Cell Lysis Buffer (10mM Tris-HCl pH 8, 10mM NaCl, 0.2% NP-40/Igepal). Nuclei were collected and lysised in 1mL Nuclear Lysis Buffer (50mM Tris-HCl pH 8, 10mM EDTA pH 8, 1% SDS). Chromatin was sonicated at 4 degrees C (Epishear, Active Motif). Chromatin was incubated with antibody and then decrosslink at 65C overnight.
Libraries were prepared using TruSeq ChIP-seq Sample Preparation Kit (Part# IP-202-1012) according to Illumina's instructions.

treatment_protocol: The ATF4 binding motif at the Bcl11a +55 enhancer was disrupted using a CRISPR-Cas9-mediated approach in pooled G1E-ER4 cells.

tag: cell line

value: Erythroid cells

tag: differentiation

value: Induced with 10 nM estradiol for 24 hours

tag: chip antibody

value: ATF4 (Cell Signaling Technology, 11815S, lot 4)


title: G1E-ER4_Bcl11a+55KO_input

data_processing:
Basecalls using bcl2fastq2 v2.15.0.4, and parameters --no-eamss --mismatches 1
Mapping to reference genome mm10 with Bowtie 1.0.0 using parameters --chunkmbs 1024 -y -n 2 --best -k 1 --maxbts 800 -l 28 -e 80 --sam-nohead --sam
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files with read coverage; bed files of peaks


title: G1E-ER4_Bcl11a+55KO_ATF4-r2


title: G1E-ER4_ATF4-r1


title: G1E-ER4_ATF4-r2


title: 201883520003_R01C01

value: Male

value: Low

tag: plasma thc - 5mg fed 5h

tag: plasma thc - 10mg fed 5h


title: RNA-seq_Runx1Evi1_PlusDox_HP_Rep1

city: Birmingham

last: Keane

address: Vincent Drive

department: Institute for Cancer and Genomic Sciences

institute: University of Birmingham

data_processing:
Raw paired-end sequencing data were processed to remove low quality sequences and adaptors with Trimmomatic v0.32.
The processed reads were then aligned to the mouse genome (version mm10) using Hisat2 v2.1.0 with default parameters
Gene expression was measured as Fragments Per Kilobase of transcript per Million mapped reads (FPKM) values with Stringtie v1.3.3 using gene models from RefSeq as the reference transcriptome.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited file containing gene name (column 1) and FPKM value (column 2)

source_name: A2lox.cre mESC

growth_protocol: RUNX1-EVI1 from the pME18s-RUNX1-EVI1 plasmid was cloned into the p2lox-targeting vector. A2lox ESCs were transduced with 20 µg of p2lox-RUNX-EVI1 using the 4D-Nucleofector (Lonza) with the mouse ES program, with the P3 primary cell kit. Individual colonies were expanded on mouse embryonic feeder cells in ES cell medium, comprising DMEM (Sigma D6546), 15% FCS (Sigma ES-009), 100 units/ml penicillin, 100 µg/ml streptomycin, 1 mM sodium pyruvate, 1mM L-glutamine, 0.15 mM monothioglycerol, 1x non-essential amino acids and  103 U/ml leukaemia inhibitory factor (ESGRO, Millipore) following 7 days of 300 µg/ml neomycin selection.

extract_protocol:
RNA was isolated from sorted cells using the NucleoSpin RNA kit (Macherey-Nagel).
RNA-seq libraries were prepared from two biological replicates using the True-Seq stranded total RNA kit (Illumina) and sequenced paired-end in a pool of 12 indexed libraries using a Next-Seq 500 high output kit v2 150 cycles (Illumina) at the Genomics Birmingham sequencing facility.

treatment_protocol: ESCs were passaged twice onto gelatine-coated tissue culture plastic without MEFs, on the second passage DMEM was substituted for IMDM (Sigma I3390). Cells were then plated into bacterial-grade dishes at a density of 2.5x104 cells/ml with IMDM, 15% FCS (Gibco), 100 units/ml penicillin, 100 µg/ml streptomycin, 1 mM sodium pyruvate, 1mM L-glutamine, 0.15 mM monothioglycerol, 0.18 mg/ml hTransferrin (Roche), 50 µg/ml ascorbic acid. After 3.25 days the resulting embryoid bodies were dispersed using TrypLE express (Gibco) to single cells and FLK1+ cells were purified by magnetic cells sorting, using biotin-conjugated CD309 antibody (eBioscience), anti-biotin microbeads (Miltenyi Biotec) and LS columns (Miltenyi Biotec). These FLK1+ cells were then cultured in gelatin-coated flasks – 1.4x106 cells in a T150 flask – in IMDM, 10% FCS (Gibco), 20% D4T condition media, 100 units/ml penicillin, 100 µg/ml streptomycin, 1 mM sodium pyruvate, 1mM L-glutamine, 0.45 mM monothioglycerol, 0.18 mg/ml hTransferrin (Roche), 25 µg/ml ascorbic acid, 5 ng/ml mVEGF (Peprotech) and 10 ng/ml mIL-6 (Peprotech). After 1 day 0.5 µg/ml doxycycline was added where appropriate and cells were cultured for a further 18 hours

tag: cell type

value: Hematpoietic progenitor

tag: construct

value: doxycycline inducible RUNX1-EVI1

tag: dox status

value: PlusDox


title: RNA-seq_Runx1Evi1_PlusDox_HP_Rep2


title: G1E-ER4_input


title: RNA-seq_Runx1Evi1_PlusDox_HE2_Rep1

value: Hemogenic endothelial 2


title: RNA-seq_Runx1Evi1_PlusDox_HE1_Rep2

value: Hemogenic endothelial 1


title: 201883520003_R10C01


title: RNA-seq_Runx1Evi1_NoDox_HP_Rep2

value: NoDox


title: RNA-seq_Runx1Evi1_NoDox_HE2_Rep2


title: RNA-seq_Runx1Evi1_NoDox_HE2_Rep1


title: 201883520003_R04C01


title: Runx1Evi1_PlusDox_Prog_DHS

data_processing:
Library strategy: DNaseI-seq
Raw single-end reads from DNaseI-seq experiments were processed with Trimmomatic v0.32.
The processed reads were aligned to the mouse genome (version mm10) using Bowtie2 v2.2.39 with the option --very-sensitive-local.
The resulting alignments were filtered to remove potentially PCR duplicated reads using the MarkDuplicates function in Picard v2.10.5
Peaks corresponding to regions of open chromatin were identified using MACS2 v2.1.1 with the options -g mm --keep-dup all -B --trackline --nomodel --shift -100 --extsize 200.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph files of read pileups generated by MACS v2.1.1

extract_protocol:
DNaseI was performed as previously described [Bert et al., 2007. PMID:17283044]. 3x10^5 sorted cells were added directly to DNaseI (Worthington Biochemical Corporation) used between 6 and 13 U/ml for 3 minutes at 22°C. The reaction was terminated by addition of SDS to 0.5% and cell lysates treated with 0.5 mg/ml proteinase K overnight at 45°C overnight then 0.2 mg/ml RNaseA for 1 hour at 37°C. DNA was isolated by phenol/chloroform extraction and level of DNaseI digestion was assessed using qRT-PCR for the active TBP promoter compared to an inactive region of chromosome 1 to ensure comparable digestion points were used.
DNaseI fragments were size selected on an agarose gel to between 50 and 250 bp then used to generate a library using the KAPA hyper prep kit, according to the manufacturer’s instructions.  These were then further size selected to obtain fragments between 200 and 300 bp and sequenced single-end in a pool of 12 indexed libraries using a Next-Seq 500 high output kit v2 75 cycles (Illumina) at the Genomics Birmingham sequencing facility.

value: Hematopoietic progenitor

value: doxycycline inducible RUNX1-EVI1 construct


title: RNA-seq_Runx1Evi1_NoDox_HE1_Rep2


title: RNA-seq_Runx1Evi1_PlusDox_HE2_Rep2


title: Runx1Evi1_PlusDox_HE_DHS

value: Hemogenic endothelial


title: RNA-seq_Runx1Evi1_PlusDox_HE1_Rep1


title: Ba/F3-P-K220 Dox(+) [EA2020_01]

value: BALB/c

value: Ba/F3 murine leukemia cells


title: Runx1Evi1_NoDox_HE_DHS


title: Runx1Evi1_plusDox_Runx1_ChIPseq

data_processing:
Raw single-end reads from ChIP-seq experiments were processed with Trimmomatic v0.32
The processed reads were aligned to the mouse genome (version mm10) using Bowtie2 v2.2.3 with the option --very-sensitive-local
The resulting alignments were filtered to remove potentially PCR duplicated reads using the MarkDuplicates function in Picard v2.10.5
Peaks were identified using MACS v2.1.1 with the options -g mm --keep-dup all -B --trackline
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph files of read pileups generated by MACS v2.1.1

extract_protocol:
KIT+ HP cells were purified as indicated above, then crosslinked for 45 minutes at room temperature in PBS with 0.83 mg/ml Di(N-succinimidyl) glutarate (Sigma), followed by a second crosslink for 10 minutes at room temperature in PBS with 1% formaldehyde (Pierce) which was quenched by adding 1/10th volume of 2M glycine. Nuclei were prepared as ref then sonicated for 8 cycles of 30s on/30s off using a Picoruptor (Diagenode), in 25 mM Tris 1 M pH 8.0, 150 mM NaCl, 2 mM EDTA pH 8.0, 1% TritonX-100 and 0.5% SDS. The chromatin fragments were diluted with 2 volumes of buffer containing 25 mM Tris pH 8.0, 150mM NaCl, 2 mM EDTA pH 8.0, 1% TritonX-100, 7.5% glycerol. Immunoprecipitation was carried out overnight at 4°C using 2 µg of RUNX1 (ab23980, Abcam) or EVI1 (2593, Cell Signalling Technologies) antibody coupled to 15 µg Dynabeads Protein G (Invitrogen) per 2 x 106 cells. The beads were then washed using low salt, high salt, LiCl and TE/NaCl buffers and eluted, the resulting material was incubated overnight with 0.25 mg/ml proteinase K.
DNA from 2-3 immunoprecipitations was pooled and extracted using Ampure beads (Beckman Coulter) and ChIP quality was assessed using qRT-PCR. ChIP libraries were generated and sequenced as for DNase I using the KAPA hyper prep kit, except libraries were size selected to obtain fragments between 150 and 450 bp.

value: hematopoietic progenitor cells

tag: chip target

value: abcam 23980


title: Runx1Evi1_noDox_Evi1_ChIPseq

value: cell signalling 2593


title: Runx1Evi1_plusDox_Evi1_ChIPseq


title: Runx1Evi1_noDox_Runx1_ChIPseq