title: PAO1161 PA3973 overproducer, biological rep3

description:
PAO1161_PA3973oe_3
RNA-seq_PA3973overproduction_vs_cells_with_empty_vector.xlsx

tag: strain


title: AKI, GFP-, 6 months, GEX library

status: Public on Nov 22 2022

type: SRA

city: Los Angeles

first: Kari

middle: Ann

last: Koppitch

state: CA

address: 1425 San Pablo Street, BCC 312

department: Stem Cell

country: USA

institute: USC

description:
10X Chromium multiome ATAC + gene expression kit
library source: transcriptomic single nucleus

library_source: transcriptomic single cell

data_processing:
Sequencing reads were aligned to the mouse genome (mm10) including the INTACTGFP sequence with the Cell Ranger ARC software (version 2.0.1) using STAR aligner on the University of Southern California High Performance Cluster. The samples were aggregated using cellranger-arc aggr. The aggregated data files are provided (Aggregated_filtered_feature_bc_matrix.h5, Aggregated_atac_fragments.tsv.gz, Aggregated_atac_fragments.tsv.gz.tbi).
Assembly: mm10 including INTACTGFP sequence
Supplementary files format and content: H5 file containing the filtered gene by cell gene expression and peak by cell matrices
Supplementary files format and content: Tab-separated file containing fragment information
Supplementary files format and content: Index of the tab-separated file

molecule: polyA RNA

organism: Mus musculus

source_name: Kidney tissue

extract_protocol:
Nuclei were isolated from flash-frozen kidney tissue and processed for single cell multiome ATAC + gene expression sequencing according to the 10X Genomics protocol. All reagents were prepared according to the online protocol. In brief, the tissue of a half kidney was thawed and minced on ice, transferred into NP40 lysis buffer (including Nonidet P40 Substitute, Sigma-Aldrich, 74385), homogenized using a pellet pestle and incubated for 5 minutes on ice. Subsequently, the nuclear suspension was filtered through a 70µm strainer, the flow through was centrifuged, the supernatant removed and the pellet incubated with 1% BSA-PBS + 1U/ul Rnase Inhibitor (Sigma-Aldrich, 3335402001) for 5 minutes on ice. After centrifugation, the pellet was resuspended in 500ul 1% BSA-PBS + 1U/ul Rnase Inhibitor supplemented with 5 ul 7AAD ready made solution (Sigma-Aldrich, SML1633). Nuclei were sorted according to the gating strategy provided in supplemental Figure 3 on a cooled BD Aria I with a 100um nozzle into BSA-PBS + Rnase Inhibitor to achieve a final concentration of 1% BSA-PBS + 1U/ul Rnase Inhibitor.
10X Chromium Single Cell Multiome + Gene Expression protocol (CG000338 Rev E)

tag: tissue

value: Kidney tissue

tag: group

value: AKI, GFP-, 6 months

tag: cell type

value: Kidney cells

tag: genotype

tag: treatment

value: Tamoxifen (0.0375mg/g)


title: PAO1161 PA3973 deletion strain, biological rep3

city: Warszawa

first: Adam

last: Kawałek

address: Pawinskiego 5A

department: Department of Microbial Biochemistry

country: Poland

institute: Institute of Biochemistry and Biophysics, PAS

description:
PAO1161_dPA3973_3
RNA-seq_deltaPA3973_vs_WT.xlsx

library_source: transcriptomic

data_processing:
base calling: bcl2fastq v2.20 (Illumina)
Sequencing data were quality-checked and filtered using FASTP version 0.20.0.
Reads were mapped to P. aeruginosa PAO11161 genome (CP032126) using Bowtie2 version 2.3.4.3 using default settings.
The number of reads mapping to individual genes was counted using FeatureCounts v 2.0.1 (with the -s2 option).
Differential expression analysis was conducted using edgeR ver 3.28.0.
Assembly: CP032126
Supplementary files format and content: Raw counts of sequencing (FeatureCounts output summarized for all samples) (PA3973_raw_counts.csv).
Supplementary files format and content: A table with DE data for all genes and normalized abundance measurements (EdgeR output) (RNA-seq_deltaPA3973_vs_WT.xlsx).
Supplementary files format and content: A table with DE data for all genes and normalized abundance measurements (EdgeR output) (RNA-seq_PA3973overproduction_vs_cells_with_empty_vector.xlsx ).

molecule: total RNA

organism: Pseudomonas aeruginosa

source_name: logarithmic phase of liquid culture

growth_protocol: Cells of P. aeruginosa PAO1161 derivative strains were taken from a deep-frozen stock, spread on L-agar plates and grown overnight at 37oC. Bacteria from single colonies were then used to inoculate L broth (DifcoTM L Broth, Lennox, BD) liquid cultures and grown overnight with shaking at 37oC. Three independent overnight cultures for each strain were diluted 1:100 into fresh L broth and grown with shaking at 37oC.  For analysis of overexpression of strains P. aeruginosa PAO1161 cells were transformed (method of Irani and Rowe, 1997) with pKKB3.11 carrying lacIQ-tacp-PA3973 or empty vector pAMB9.37 (lacIQ-tacp) to obtain PAO1161/pKKB3.11 (lacIQ-tacp-PA3973) and PAO1161/pAMB9.37 (lacIQ-tacp), respectively. Transformants were selected on L agar plates supplemented with 150 μg/ml-1 chloramphenicol and were verified by isolation of plasmid DNA and its digestion. Bacteria from single colonies were used to inoculate L broth (DifcoTM L Broth, Lennox, BD) liquid cultures with supplementation (75 µg/ml-1 chloramphenicol) and grown overnight with shaking at 37oC. Three independent overnight cultures for each strain were diluted 1:100 into fresh L broth with chloramphenicol (75 µg/ml-1) and IPTG (0.05 mM) and grown with shaking at 37oC. Aliquots of 2 ml from logarithmic phase cultures (OD600 0.5) were subjected to RNA extraction.

extract_protocol:
2 ml of cultures which reached optical density 0.4-0.6 at 600 nm were mixed with 4 ml of RNAprotect Bacteria Reagent (Qiagen). RNA was isolated with an RNeasy mini-kit (Qiagen) according to the manufacturer’s protocol. Total RNA was digested with DNase (TURBO DNA-free Kit, Ambion) to eliminate genomic DNA.
rRNA was depleted using Ribo-Zero™ rRNA Removal Kit (Bacteria) (MRZMB126, Illumina) according to manufacturer instructions. Libraries were prepared according to instructions accompanying the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, E7420). Libraries were sequenced using standard Illumina protocols.

value: PAO1161 leu-

value: logarithmic phase of liquid culture


title: PAO1161 PA3973 deletion strain, biological rep2

description:
PAO1161_dPA3973_2
RNA-seq_deltaPA3973_vs_WT.xlsx


title: AKI, GFP+, 6 months, rep2, ATAC library

description: 10X Chromium multiome ATAC + gene expression kit

library_source: genomic

molecule: genomic DNA

value: AKI, GFP+, 6 months


title: AKI, GFP+, 6 months, rep3, GEX library


title: AKI, GFP+, 6 months, rep4, GEX library


title: PAO1161 PA3973 deletion strain, biological rep1

description:
PAO1161_dPA3973_1
RNA-seq_deltaPA3973_vs_WT.xlsx


title: AKI, GFP+ 6 months, rep3, ATAC library


title: PAO1161 WT, biological rep3

description:
PAO1161_WT_3
RNA-seq_deltaPA3973_vs_WT.xlsx

value: WT


title: PAO1161 WT, biological rep2

description:
PAO1161_WT_2
RNA-seq_deltaPA3973_vs_WT.xlsx


title: PAO1161 WT, biological rep1

description:
PAO1161_WT_1
RNA-seq_deltaPA3973_vs_WT.xlsx


title: AKI, GFP+, 6 months, rep2, GEX library


title: AKI, GFP+, 6 months, rep1, ATAC library


title: empty vector ChIP control, replicate 2

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
Sequencing data were quality-checked and filtered using FASTP version 0.20.0.
Reads were mapped to P. aeruginosa PAO1161 genome (CP032126) using Bowtie2 version 2.3.4.3 using default settings.
Obtained *.sam files were sorted (samtools sort -n), run through samtools fixmate with the -m option, again sorted (samtools sort) and duplicates were marked with samtools markdup. Samtools ver. 1.9 was used.
The files were indexed and used to generate coverage *.bigwig files, normalized to 1× sequencing depth (RPGC), without binning and smoothing using the bamCoverage tool ver 3.3.0 included in deepTools.
PA3973 peaks were identified by comparing combined replicates of IP samples (PA3973-FLAG) for each strain with negative control (empty vector EV-FLAG) samples using the callpeak function of MACS2 ver 2.1.2 with default options for paired-end .BAM files, and 0.05 as false discovery rate (FDR) cut off.
Assembly: CP032126
Supplementary files format and content: Processed files in bigwig format represent normalized coverages of individual base pairs in the P. aeruginosa PAO1161 genome. Reference genome is enclosed in fasta format (CP032126.fa) and the annotation used is enclosed as a .bed (CP032126.bed). A modified .bed file with PAO1161 feature names changed to the names of corresponding PAO1 genes (PA… format) is included for convenience of data browsing e.g. using IGV (CP032126_PA_names.bed).

growth_protocol: P. aeruginosa PAO1161 ΔPA3973 strain carrying pMEB1 (lacIQ-tacp-PA3973-flag) as well as control strain carrying pABB28.1 (lacIQ-tacp-flag) were obtained by conjugation of PAO1161 (leu-, r-, RifR) and E. coli S-17 donor strain carrying appropriate plasmid. Conjugants were selected on L agar plates supplemented with 300 μg/mL rifampicin and 150 μg/mL chloramphenicol. Two independent overnight cultures from each strain were inoculated from single colonies and grown overnight with shaking at 37oC. After that they were diluted 1:100 in L broth (DifcoTM L Broth, Lennox, BD) supplemented with 75 μg/mL chloramphenicol and 0.05 mM IPTG to induce the expression of PA3973-flag and grown with shaking at 37oC until reaching exponential phase with optical density about 0.5 (OD600).

extract_protocol:
Chromatin immunoprecipitation (ChIP) protocol was based on the method described earlier (Kawalek et al, 2018; Nucleic Acids Res. 46:9, 4592-4606; Modrzejewska et al, 2021; mSystems 6:4, e0001521). Two cultures of each strain with similar OD600 were combined, formaldehyde was added from a 37% stock to a final concentration of 1%, and the cultures were kept for 10 min at room temperature with gentle inverting. Glycine was added to a final concentration of 0.5 M and the cultures were incubated for 5 min at room temperature with gentle rotation. Cells were then harvested by centrifugation (20 min, 3000 x g, 25 mL of culture in 50 mL conical tubes, 4 tubes per strain), washed twice with ice-cold Tris-buffered saline (25 mM Tris-HCl, 150 mM NaCl, pH=7.6), resuspended in 1 mL of TBS, transferred to a fresh 1.5 mL tube and centrifuged (2 min, 6000 x g). The cell pellets were frozen at -70oC. The pellets were thawed on ice, suspended in 0.5 mL of lysis buffer [10 mM Tris-HCl, 20% (w/v) sucrose, 50 mM NaCl, 10 mM ethylenediaminetetraacetic acid (EDTA), pH=8.0] supplemented with 10 µl of Protease Inhibitor Cocktail (Sigma, PA8849) and 125 µL of lysozyme (20 mg/mL) and incubated for 30 min at 37oC. Four samples for each strain were combined in 15 mL. Subsequently, 1.5 mL of IP-buffer [50 mM Tris-HCl, pH=7.5, 150 mM NaCl, 1 mM EDTA, 1% (v/v) Triton X-100, 0.1% (m/v) sodium deoxycholate], 30 µL protease inhibitor cocktail, PMSF (phenylmethanesulfonyl fluoride) to a final concentration of 2 mM, SDS (sodium dodecyl sulphate) to a final concentration of 0.1% were added to each sample. The samples were sonicated 20 times for 20 s each with 1 min break on ice using a Microson ultrasonic cell disruptor Xl2000 (Misonix) with 5-mm tip and 90% of output power to obtain DNA fragments of an average length of 250-350 bp. DNA fragmentation was checked by agarose gel electrophoresis. After sonication, samples were aliquoted (1 mL in 1.5 mL tubes) and stored at -70oC. Sonicated lysate was thawed on ice and 150 μL of each strain variant was incubated with 20 μL of magnetic beads coupled with protein A (Dynabeads Protein A, Invitrogen, 10001D) previously separated from original suspension using Magnetic Separation Stand. Such pre-clearing step was performed for minimum 1 hour at 4oC with rotation of the mixtures. In the meantime 50 μL of magnetic beads were prepared for each reaction by separating from the suspension as above. It was then mixed with anti-FLAG mouse antibodies (1-10 μg per reaction, 4 μL for this procedure) [DYKDDDDK Tag polyclonal  antibodies; 1 mg/mL; PA1-985B; Invitrogen] diluted in 200 μL of PBS with 0.05% Tween-20. Mixtures of magnetic beads and antibodies were incubated for 10 minutes at 4oC with gentle rotation. Beads with bound antibodies were then separated from the supernatant, washed once with 200 μL of the PBS with 0.05% Tween-20 solution and stored on ice. Pre-cleared lysate was separated from the beads used for pre-incubation and added to the beads coated with antibodies. Mixture containing lysate and magnetic beads with antibodies was incubated at 4oC for 20 minutes with mixing on rotator. Beads were then collected and washed. Elution was performed twice for 15 minutes in 50 μL at 65oC in thermoblock with shaking (1400 rpm). All 100 μL of obtained eluates were incubated with 1 μL of RNase A (100 mg/mL, Qiagen, 19101) for 30 min at 65oC. Then, 5 μL of Proteinase K (20 mg/mL, Qiagen, 19133) was added and the samples were incubated for 1 h at 50oC followed by overnight incubation at 65oC. Such prepared probes were stored on ice and 3 μL of 3 M sodium acetate (pH=5) was added. DNA purification was performed using Qiaquick Qiagen PCR purification Kit according to manufacturer’s instructions. The DNA was stored at -20oC.
NGS library was constructed using QiaSeq Ultralow Input Library kit. Sample was further quality checked on 1% agarose gel and concentration was measured using qPCR KAPA Library Quantification Kit.

treatment_protocol: All cultures were incubated at 37°C in L broth (DifcoTM L Broth, Lennox, BD) supplemented with 75 μg/mL chloramphenicol and 0.05 mM IPTG with shaking until reaching exponential phase of growth (OD600 = 0.5).

value: pABB28.1 (lacIQ-tacp-flag)

tag: chip antibody

value: Anti-FLAG (Invitrogen, #PA1-985B)


title: Control, 6 months, ATAC library

value: Control, 6 months


title: empty vector ChIP control, replicate 1


title: PA3973_FLAG overproducer, replicate 2

value: pMEB1 (lacIQ-tacp-PA3973-flag)


title: Control, 6 months, GEX library


title: AKI, GFP-, 4 weeks, ATAC library

value: AKI, GFP-, 4 weeks


title: PA3973_FLAG overproducer, replicate 1


title: AKI, GFP-, 4 weeks, GEX library


title: OCI-AML3 + CDKN2A gRNA - WM R2

city: Brisbane

first: Jasmin

last: Straube

state: QLD

address: 300 Herston Rd

country: Australia

institute: QIMR Berghofer

data_processing:
Reads were trimmed for adapter sequences using Cutadapt (version 1.11) and aligned using STAR (version 2.5.2a) to the GRCh37 assembly using the gene, transcript, and exon features of Ensembl (release 70) gene model. Expression was estimated using RSEM (version 1.2.30).
Transcripts with zero read counts across all samples were removed prior analysis. Normalisation of RSEM expected read counts was performed by dividing by million reads mapped to generate counts per million (CPM), followed by the trimmed mean of M-values (TMM) method from the edgeR package.
Assembly: GRCh37
Supplementary files format and content: RSEM expected read counts

organism: Homo sapiens

source_name: Peripheral blood

extract_protocol:
Cells were harvested on Day 7. RNA was isolated from a maximum of 0.5 x 106 cells using the Qiagen microRNeasy kit according to manufacturer instructions
cDNA libraries were prepared using the NEBNext Ultra RNA Library Prep kit with the polyA selection module (New England Biolabs) and purified with AMPure beads (Agilent). Libraries were quantified with the KAPA Library Quantification Kit for Illumina (Kapa Biosystems) and pooled. Sequencing was performed on the Illumina NextSeq 550 Sequencer High Output mode (1 × 75 bp).

treatment_protocol: Cells were seeded at 0.5 x 106 cells/mL and treated with WM-1119 1 uM or vehicle (DMSO). Drug was refreshed every 2-3 days at each passage

value: Peripheral blood

tag: cell line

value: Myeloid

value: CDKN2A 'knockout'


title: AKI, GFP+, 4 weeks, rep3, ATAC library

value: AKI, GFP+, 4 weeks


title: AKI, GFP+, 4 weeks, rep2, GEX library

value: Kidney tissue


title: OCI-AML3 + CDKN2A gRNA - WM R1


title: AKI, GFP+, 4 weeks, rep3, GEX library


title: AKI, GFP+, 4 weeks, rep2, ATAC library


title: OCI-AML3 + CDKN2A gRNA - Veh R3

value: DMSO


title: AKI, GFP+, 6 months, rep1, GEX library

value: Kidney cells


title: OCI-AML3 unedited - WM R3

value: native


title: OCI-AML3 + CDKN2A gRNA - Veh R2


title: OCI-AML3 + CDKN2A gRNA - Veh R1


title: OCI-AML3 unedited - WM R1


title: OCI-AML3 unedited - WM R2


title: AKI, GFP+, 4 weeks, rep1, ATAC library

value: Tamoxifen (0.0375mg/g)


title: Control, 4 weeks, rep2, ATAC library

value: Control, 4 weeks


title: OCI-AML3 unedited - Veh R3


title: AKI, GFP+, 4 weeks, rep1, GEX library


title: Control, 4 weeks, rep1, GEX library


title: Control, 4 weeks, rep1, ATAC library


title: OCI-AML3 unedited - Veh R1


title: Control, 4 weeks, rep2, GEX library


title: MC38, SETDB1, Input

city: Paris

first: Sebastian

last: Amigorena

state: --- Select a state ---

address: 26 rue Ulm

department: Center of Immunotherapy

country: France

institute: Curie Institute

data_processing:
ChIP-seq reads were trimmed with Cutadapt  and mapped to mouse genome build mm10 with Bowtie2 (v2.1.0),We processed only mapped reads with high mapping quality (MAPQ>=10) using samtools (v0.1.8)
Peak calling was performed with SICER  v1.1, using parameters : '-W 200 -G 600', peaks selected at 5 % FDR threshold.
All Bigwig files were generated per sample, normalized over own input ChIP-seq files using --BamCompare (with options: --effectiveGenomeSize 2719482043 for mm10 and --binSize 50 and –normalizeUsing BPM) from deepTools (v3.1.1)
Assembly: mm10
Supplementary files format and content: SICER peak bed file,  bigwig

growth_protocol: Cells were grown in RPMI-1640 (Gibco), Glutamax, 10%FCS, 1%Penicillin/Streptomycin, 2µg/mL puromycin. 2x10^6 were used for H3K9Ac and 8x10^6 cells for H3K9me3.

extract_protocol:
2 x 10^6 cells were resuspended in room temperature hypotonic MNase digestion buffer (50mM Tris-HCl, Triton X-100, 1mM CaCl2) supplemented with MNase (Thermofischer, 0.5μl/ml digestion buffer) and EDTA-free protease inhibitors (Roche), and incubated at 37°C for 5 minutes with shaking.
Addition of 10x MNase stop buffer (110 Tris-HCl, 55mM EDTA) quenched the reaction before a 30 second sonication at 4°C (Picoruptor, Diagenode) to fragment any remaining DNA longer than 200bp and then clarified by centrifugation at 4°C for 10 minutes at 10,000 x g.
 Illumina TruSeq ChIP Sample Prep kit (following manufacturer's instructions). 15 programmed cycles for the final PCR

value: Colon Adenocarcinoma

value: Setdb1 KO

value: Transduction with Setdb1-guide containing pCRISPR-v2-puro construct


title: MC38, CTRL, Input

value: Ctrl

value: Transduction with empty pCRISPR-v2-puro construct


title: B16, CTRL, Input

value: Melanoma


title: MC38, CTRL, H3K9Ac, 3

value: anti-H3K9Ac (1:50, Cell Signaling Technologies #9469)


title: MC38, SETDB1, H3K9Ac, 3


title: B16, SETDB1, H3K9Ac, 3


title: ME15-E4M1R

city: Helsinki

first: Jukka

last: Jernvall

address: P.O. Box 56 (Viikinkaari 9)

country: Finland

institute: University of Helsinki

data_processing:
The RNAseq reads were evaluated and bad reads were filtered out using FastQC (version 0.11.8, Andrews et al., 2012), AfterQC (version 0.9.6, Chen et al., 2017) and Trimmomatic (version 0.39, Bolger et al., 2014), and ribosomal RNA was removed using Sortmerna (Kopylova et al., 2012). The number of remaining, good reads varied between 30M and 90M. Reads were aligned using Salmon (version 0.99.0, Patro et al., 2017) to GRCm38 (Ensembl release 100) cDNA. Only one-to-one orthologous genes between mouse and rat were selected for further analysis. 16,604 one-to-one orthologous genes were found between mouse and rat using Ensembl Biomart tool (Kinsella et al., 2011), 126 additional one-to-one orthologues were added using Inparanoid8 (Sonnhammer & Östlund, 2015) in which gene pairs with bootstrap scores of 100% were selected. The output transcript ID’s of Salmon were converted to mouse gene ID’s using Ensembldb (Rainer et al., 2019) and Tximport (Soneson et al., 2015), allowing comparison of mouse and rat read counts. Deseq2 (Love et al., 2014) was used to normalise the read counts by library size and composition as well as transcript length.
Assembly: GRCm38 (Ensembl release 100) cDNA
Supplementary files format and content: Tab-delimited gene expression count values of each samples

source_name: lower first molar

extract_protocol:
Embryonic mouse molars were dissected from jaws on embryonic day E15 (E0 being the vaginal plug appearance day). Minimal amount of surrounding tissue was left around the tooth germ, at the same time making sure that the tooth was not damaged in the process. The tissue was immediately stored in RNAlater (Qiagen, Düsseldorf, Germany) at −80°C for RNAseq. For RNAseq, each tooth was handled individually. Samples were homogenized using Precellys 24 homogenizer (Bertin instruments). RNA was extracted using guanidium thiocyanate-phenol-chloroform method and purified using RNeasy Plus micro kit (Qiagen GmbH) following manufacturer's protocol. The purity of RNA was measured using Nanodrop microvolume spectrophotometer (Thermo Fisher Scientific).
The complementary DNA (cDNA) libraries were prepared using Ovation Mouse RNAseq System.

value: lower first molar

tag: age

value: wild type


title: ME15-E8M1L


title: ME15-E3M1L


title: ME15-E1M1R


title: ME15-E5M1R


title: ME15-E5M1L


title: MC38, SETDB1, H3K9me3, 3

value: anti-H3K9me3 (Diagenode, C15500003)


title: B16, CTRL, H3K9Ac, 3


title: B16, SETDB1, H3K9me3, 3


title: Control-5

city: Guangzhou city

first: Bo

last: Huang

state: Guangdong Province

address: No.280, East Ring Road

country: China

institute: Guangdong Pharmaceutical University

description: Exosomes from serum of C57BL/6 mice infected without  P. berghei ANKA (namely u-Exos-5), Control C-5

data_processing:
CLC Genomics Workbench v 11.0.1
After sequencing, the Solexa CHASTITY quanlity filtered reads were harvested as Clean Reads. The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15nt) were left.
miRDeep2 software was used to predict the novel miRNAs with these trimmed reads. Then, the trimmed reads were aligned to merged pre-miRNA databases (known pre-miRNA from miRBase v21 plus the newly predicted pre-miRNAs) using Novoalign software (v2.07.11) with at most one mismatch. Reads (counts < 2) were discarded when calculating the miRNA expression.
In order to characterize the isomiR variability, sequences that matched the miRNA precursors in the mature miRNAs region ±4 nt (no more than 1 mismatch) were accepted as mature miRNA isomiRs, which were grouped according to the 5-prime (5p) or 3-prime (3p) arm of the precursor hairpin. The numbers of mapped tags that were defined as the raw expression levels of that miRNA. To correct for the difference in tag counts between samples, the tag counts were scaled to TPM (the copy number of transcripts per million) based on the total number of tag aligned.
Assembly: Choosing a different isomiR sequence for measuring miRNA expression can affect the ability to detect differential miRNA expression. We use the most abundant isomiR, the mature miRNA annotated in miRBase and all isoforms of miRNA(5p or 3p) to calculate the miRNAs expression.When comparing the differentially expressed miRNA profiles between two groups, fold change and p-value were calculated and used to identify significant differentially expressed miRNAs (Based on ALL_Isoform value). Differentially expressed miRNAs between two samples were filtered through Fold change (Based on ALL_Isoform value). Hierarchical clustering was performed.
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Female 6-week-old C57BL/6 mice (n = 4), intraperitoneal (i.p.) with PBS

extract_protocol:
Exosomes were isolated from serum of uninfected mice (n = 20; namely un-Exos) and PbA-infected mice (n = 20; namely inf-Exos) at ~40% parasitaemia using the Total Exosome Isolation Kit (from serum; No. 4478360#, Invitrogen) following the manufacturer’s protocol.
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Mice were intraperitoneally injected with 10^6 iRBC or PBS, respectivey.

value: serum exosomes

tag: Sex

value: female

value: Mice were injected with PBS

tag: time

value: Day 0


title: OCI-AML3 + CDKN2A gRNA - WM R3

value: Peripheral blood

value: Myeloid

value: CDKN2A 'knockout'


title: B16, SETDB1, Input


title: Control-4

description: Exosomes from serum of C57BL/6 mice infected without  P. berghei ANKA (namely un-Exos-4), Control C-4


title: MC38, CTRL, H3K9Ac, 2

value: Colon Adenocarcinoma


title: OCI-AML3 unedited - Veh R2

value: native

value: DMSO


title: Control-2

description: Exosomes from serum of C57BL/6 mice infected without P. berghei ANKA (namely un-Exos-2), Control C-2


title: MC38, CTRL, H3K9me3, 3

value: Ctrl


title: Control-3

description: Exosomes from serum of C57BL/6 mice infected without P. berghei ANKA (namely un-Exos-3), Control C-3


title: ME15-E6M1R


title: muscle, mdx, 3m age, antibiotics, rep1

city: Cincinnati

first: Mattia

last: Quattrocelli

state: OH

address: 240 Sabin Way

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Reads were trimmed using Trimmomatic
Alignment to mm10 and isoform TPM counts were obtained through Kallisto

source_name: tibialis anterior muscle

extract_protocol:
Total RNA was isolated through Trizol and purified through Qiagen Rneasy columns
True-Seq stranded mRNA library (Illumina)

value: tibialis anterior muscle

value: antibiotics


title: B16, CTRL, H3K9me3, 3

value: Melanoma

value: Transduction with empty pCRISPR-v2-puro construct


title: Test C-5

description: Exosomes from serum of C57BL/6 mice infected with P. berghei ANKA (namely inf-Exos-5), Test C-5

source_name: Female 6-week-old C57BL/6 mice (n = 4), intraperitoneal (i.p.) with 10^6 infected red cells.

value: Mice were infected with 10^6 infected red cells.

value: At 10-14 days post infection at ~40% parasitaemia


title: Test C-4

description: Exosomes from serum of C57BL/6 mice infected with P. berghei ANKA (namely inf-Exos-4), Test C-4

value: serum exosomes


title: MC38, SETDB1, H3K9Ac, 2

value: Setdb1 KO

value: Transduction with Setdb1-guide containing pCRISPR-v2-puro construct

value: anti-H3K9Ac (1:50, Cell Signaling Technologies #9469)


title: B16, CTRL, H3K9Ac, 2


title: B16, SETDB1, H3K9Ac, 2


title: Test C-2

description: Exosomes from serum of C57BL/6 mice infected with P. berghei ANKA (namely inf-Exos-2), Test C-2

value: female


title: MC38, SETDB1, H3K9me3, 2

value: anti-H3K9me3 (Diagenode, C15500003)


title: Test C-3

description: Exosomes from serum of C57BL/6 mice infected with P. berghei ANKA (namely inf-Exos-3), Test C-3


title: MC38, CTRL, H3K9me3, 2


title: B16, SETDB1, H3K9me3, 2


title: Test C-1

description: Exosomes from serum of C57BL/6 mice infected with P. berghei ANKA (namely inf-Exos-1), Test C-1


title: Ascl1+shTip60#3_day5_rep2

city: Stanford

first: Justyna

middle: A.

last: Janas

address: 265 Campus Drive

institute: Stanford University

data_processing:
Primary data processing, including adapter trimming, genomic alignment to mm10 using Bowtie2 (v 2.3.4.3), mitochondrial and duplicate read removal, peak calling and reproducibility analysis using MACS2 and IDR, respectively, were performed using ENCODE ATAC-seq pipeline v1.2.0 (Consortium, 2012) (https://github.com/ENCODE-DCC/atac-seq-pipeline).
Reproducible peaks selected with IDR (idr threshold ≤ 0.05) were aggregated. Read counts for each region were obtained using featureCounts package, followed by normalization and differential accessibility analysis using DESeq2.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text file containing normalized read counts determined for the aggregated peak set

source_name: Ascl1+shTip60#3 day5

growth_protocol: Homozygous TauEGFP knock-in mice (Tucker et al., 2001) were bred with C57B/6 mice (Jackson Laboratory). Mouse embryonic fibroblasts (MEFs) were isolated from embryonic day (E)13.5 heterozygous embryos and maintained in DMEM (Invitrogen) supplemented with 10% cosmic calf serum.

extract_protocol: ATAC-seq was performed based on previously described protocol (Corces et al., 2017).

treatment_protocol: MEFs were transduced with indicated lentiviruses. The cells were treated with doxycycline (dox) two days post-infection to induce transgene expression, and transferred into N3 medium (DMEM/F12, N2 supplement, insulin) containing dox the following day. The medium was refreshed every 3 days.

value: E13.5 fibroblast

tag: time post-induction

value: 5 days


title: B16, CTRL, H3K9me3, 2


title: Ascl1+shTip60#3_day5_rep1


title: Control-1

description: Exosomes from serum of C57BL/6 mice infected without  P. berghei ANKA (namely un-Exos-1), Control C-1

value: Mice were injected with PBS

value: Day 0


title: MC38, CTRL, H3K9Ac, 1

value: Colon Adenocarcinoma

value: Ctrl


title: MC38, SETDB1, H3K9Ac, 1


title: Ascl1+shTip60#2_day5_rep1

source_name: Ascl1+shTip60#2 day5


title: Ascl1+shNTC_day5_rep1

source_name: Ascl1+shNTC day5


title: B16, CTRL, H3K9Ac, 1


title: Ascl1+shNTC_day5_rep2


title: MC38, SETDB1, H3K9me3, 1


title: Ascl1+shTip60#3_day2_rep1

source_name: Ascl1+shTip60#3 day2

value: 2 days


title: MC38, CTRL, H3K9me3, 1


title: B16, SETDB1, H3K9me3, 1

value: Melanoma


title: Ascl1+shTip60#2_day2_rep2

source_name: Ascl1+shTip60#2 day2


title: B16, CTRL, H3K9me3, 1

value: Transduction with empty pCRISPR-v2-puro construct


title: Thymus [D804T348]

description:
STAR_GENECount_Matrix_105samples_rawcounts.txt
STAR_GENECount_Matrix_105samples_normlibsze.txt

data_processing:
Trimming done by the Curie Institut plateform using Antropos for D176 and B262 and B243 or using TrimGalore for D804 and D812
After the Curie Institut plateform pass the FastQC
Afterwards reads are aligned using STAR with the basic 2 pass mode: first the genomeGenerate and then GeneCounts.
We used the HTSeq count like gene cout normalized by the librarysize of unique mapped
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw gene values for each Sample
Supplementary files format and content: tab-delimited text files include normalized gene values by library size for each Sample

source_name: Thymus

growth_protocol: Tissues were collected from WT female mice, directly placed in RNAlater (Sigma), and cut into small pieces.

extract_protocol:
Tissue fragments were dissociated in RLT buffer + beta-mercaptoethanol using a Precellys homogenizer.  After passing through a QiaShredder column, RNA was extracted RNAseq mini kit columns following manufacturer's instructions, including on-column DNAse digestion. After elution, samples were treated with TurboDNAse I according to manufacturer's instructions
Illumina TruSeq Stranded mRNA Library preparation kit

value: Thymus

tag: cancer/healthy

value: Healthy

tag: condition

value: WT


title: Ascl1+shNTC_day2_rep2

source_name: Ascl1+shNTC day2


title: Ascl1+shTip60#2_day2_rep1


title: Ascl1+shNTC_day2_rep1


title: Stomach [D804T347]

source_name: Stomach

value: Stomach


title: rtTA+shNTC_day2_rep2

source_name: rtTA+shNTC day2


title: Ovary [D804T345]

source_name: Ovary

value: Ovary


title: Ascl1+shTip60#2_day5_rep2


title: Skin [D804T342]

source_name: Skin

value: Skin


title: rtTA+shNTC_day2_rep1


title: B16, SETDB1, H3K9Ac, 1

value: Setdb1 KO

value: Transduction with Setdb1-guide containing pCRISPR-v2-puro construct

value: anti-H3K9Ac (1:50, Cell Signaling Technologies #9469)


title: LN [D804T343]

source_name: LN

value: LN


title: Ascl1+shTip60#3_day2_rep2

value: E13.5 fibroblast


title: Colon [D804T344]

source_name: Colon

value: Colon


title: NPC43 EBV+ve, TNFα

city: Hong Kong

first: Wingchung

last: Tang

state: Hong Kong

address: Rm321, 3/F, Cancer Center, Prince of Wales Hospital, Sha Tin

country: Hong Kong

institute: CUHK ACP

description: E-plus-TNF

data_processing:
Use cutadapt to remove reads with adapters or low quality. HISAT2 was used to perform sequence alignment analysis using the reference sequence;. Based on the alignment results of HISAT2, we use stringtie to complete the quantitative expression analysis of genes, and use edgeR to perform differential expression analysis. ClusterProfiler was used for KEGG and GO enrichment analysis, and STRINGdb was used for protein interaction analysis.
Assembly: Homo_sapiens.GRCh37
Supplementary files format and content: all.fpkm_anno.txt

growth_protocol: NPC43 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS), 20µm ROCK inhibitor and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using 1 ml TRIzol.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.
The lysates were sent to a company (Genewiz, Suzhou, PR China) for library preparation, sequencing, and data analysis. In brief, the libraries were prepared using the Illumina TruSeq mRNA Library Prep Kit according to the manufacturer’s instructions. Sequencing was performed on an Illumina HiSeq2000 sequencing system (Illumina, San Diego, CA, USA).

treatment_protocol: Invadopodia was induced by treatment of 10ng/ml TNFα for 18 hours

value: nasopharyngeal carcinoma

value: 10ng/ml TNFα

value: 18 hours


title: Thymus [D812T324]


title: Lung [D804T341]

source_name: Lung

value: Lung


title: Thymus [D812T336]


title: NPC43 EBV-ve , TNFα

description: E-minus-TNF


title: NPC43 EBV-ve

description: E-minus

value: control


title: Thymus [D812T312]

value: Thymus


title: rtTA+shNTC_day2_rep3

value: 2 days


title: WB20_dKO-dual_Input  [SUM159(p63 and p73 KO) with exogenous p63/p73]

city: Cambridge

first: Matt

last: Guenther

state: MA

address: 35 Cambridge Park Dr 4th floor

institute: Syros Pharmaceuticals

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using BowTie version 2 using the parameters  -p 4 --sensitive
Peaks were called with MACS version 1.4 using the parameters p-value = 1e-9
Genome_build: hg19
Supplementary_files_format_and_content: peak files

source_name: SUM159 Cells ITGB4-High with p73 and p63 Knock-out + exogenous p63/p73 cDNA

growth_protocol: Chromatin was isolated from SUM159 cells cells grown under standard tissue culture conditions

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with indicated antibody.
Libraries were prepared according to Swift Biosciences instructions accompanying the ACCEL-NGS® 2S DNA LIBRARY KIT (Part# 20024) using primers and amplification of libraries from KAPA Biosystems HiFi library amp Kit (Part# KK2611).

treatment_protocol: ITGB4-hi p63 KO, p73 KO, or dKO were produced from CRISPR-mediated mutagenesis. SUM159 variants cells were engineered to constitutively express the indicated cDNAs through stable selection.

tag: parental cell line

tag: subline

value: SUM159 Cells ITGB4-High

tag: modification

value: mammary carcinoma cells


title: WB18_dKO-p73_Input  [SUM159(p63 and p73 KO) with exogenous p73]

source_name: SUM159 Cells ITGB4-High with p73 and p63 Knock-out + exogenous p73 cDNA


title: NPC43 EBV+ve

description: E-plus

value: WT


title: Stomach [D812T323]

tag: strain

value: Stomach

value: Healthy


title: WB16_dKO-p63_Input  [SUM159(p63 and p73 KO) with exogenous p63]

source_name: SUM159 Cells ITGB4-High with p73 and p63 Knock-out + exogenous p63 cDNA


title: Brain [D804T346]

source_name: Brain

tag: tissue

value: Brain


title: WB19_dKO-dual_H3K27ac  [SUM159(p63 and p73 KO) with exogenous p63/p73]

value: p73 and p63 Knock-out + exogenous p63/p73 cDNA

value: H3K27ac (Abcam ab4729)


title: Stomach [D812T335]


title: FK866, replicate 2, RNA_seq

city: Jinan

first: Jing

last: Shen

address: Wenhua West Road 44

institute: Shandong University

data_processing:
The raw reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version: cutadapt-1.9).
Filtered reads were mapped against the mm10 assembly of the Mus musculus genome (National Center for Biotechnology Information) using hisat2 (Version 2.2.1).
Assembly: mm10
Supplementary files format and content: Raw count matrix with rows as genes and columns as samples

source_name: colon

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.
Full-length cDNA was generated using SMART-Seq HT Kit (Takara), paired-end DNA libraries was generated and indexed using NexteraTM XT Library Prep Kit and then NexteraTM XT Index Kit.

value: colon


title: Spleen [D812T338]

source_name: Spleen

value: Spleen


title: WB15_dKO-p63_H3K27ac  [SUM159(p63 and p73 KO) with exogenous p63]

value: p73 and p63 Knock-out + exogenous p63 cDNA


title: FK866, replicate 1, RNA_seq


title: Spleen [D812T314]


title: CMO_pool4

city: South San Francisco

first: David

last: Tatarakis

email: tatarakis@dnli.com, genomics@dnli.com

state: California

address: 161 Oyster Point Blvd

department: Discovery Genomics

institute: Denali Therapeutics

description: 10X Genomics

data_processing:
Mapping, demultiplexing, hash demultiplexing, and gene counting were performed using Cell Ranger v6.1.1. The 'cellranger multi' pipeline was used.
Assembly: mm10
Supplementary files format and content: Matrix Market format counts matrix
Supplementary files format and content: Comma seperated values format files for genes, cell barcodes, and cell-level meta data

extract_protocol:
Mice were perfused with cold PBS and cortical and hippocampal tissues were dissected and dissociated into a single cell suspension using the Adult Brain Dissociation Kit (Miltenyi Biotec, 130-107-677), according to the manufacturer’s protocol.  Tissues were diced into 0.5 cm pieces and placed in the CTube contianing enzyme mix 1 followed by addition of enzyme mix 2.   Dissociation was performed by the gentleMACS Octo Dissociator using the 37C_ABDK_01 program.  Samples were filtered through a 70 µm strainer and sedimented at 300Xg for 10 minutes in 4C followed by centrifugation in debris removal solution at 3000Xg for 10 minutes in 4C.  After debris removal, cells were washed with cold D-PBS and centrifuged at 1000Xg for 10 mintues in 4C and resuspended in FACS buffer.  Four batches of single cell suspensions, with one replicate of each condition, were labeled with CD11b antibody and cell multiplex oligos per user guide (10X Genomics, CG000391 Rev A).  Equal proportions of cells from each sample were combined into one pool per batch and 100,000 live, CD11b+ cells were FACS sorted on FACS Aria III (BD Biosciences with a 100 μm nozzle) into 1% BSA in PBS.
Single cell capture and library preparation was performed using Chromium Next GEM Single Cell 3ʹ Kit v3.1 per user guide (10X genomics, CG000388 Rev A).  Briefly, gel bead-in-emulsion (GEM) were generated by loading single cells in RT master mix onto the Chip G microfluidic along with partitioning oil and gel beads that contain an Illumina R1 primer sequence, Unique Moldecular Identifier, 10X barcode, and capture sequences for either mRNA transcripts or cell multiplex oligos.  After cDNA amplification of RT materials from the GEMs, transcriptional cDNA was separated from cell multiplex oligo cDNA via NucleoMag bead purification (Takara, 7444970.50), proceeded by library preparation of both sets of cDNA.  Transcriptional libraries were pooled equimolar for a sequencing run on an Illumina MiSeq instrument to estimate the number of cells captured in each library.  This MiSeq capture information was used to pool libraries in equal proportions for sequencing coverage of 50,000 reads per cell across libraries and 5000 reads per Cell multiplex oligo.  Sequencing on the Illumina NovaSeq 6000 instrument generating paired-end reads (28x10x10x90 bases) was performed by SeqMatic (Fremont, CA).

value: myeloid

value: mixed sample (non-demultiplexed)


title: WB14_dKO-EV_Input  [SUM159(p63 and p73 KO) with exogenous Empty vector]

source_name: SUM159 Cells ITGB4-High with p73 and p63 Knock-out + exogenous empty expression vector


title: Skin [D812T330]

value: Skin


title: Skin [D812T318]


title: Control, replicate 2, RNA_seq

value: Control


title: WB17_dKO-p73_H3K27ac  [SUM159(p63 and p73 KO) with exogenous p73]

value: p73 and p63 Knock-out + exogenous p73 cDNA


title: Ovary [D812T321]

value: Ovary


title: Ovary [D812T333]


title: Control, replicate 1, RNA_seq


title: Ovary [D812T309]


title: WB7_dKO_H3K27ac  [SUM159(p63 and p73 KO)]

source_name: SUM159 Cells ITGB4-High with p73 and p63 Knock-out

value: SUM159 Cells ITGB4-High

value: p73 and p63 Knock-out


title: Skin [D812T306]

value: WT


title: Lung [D812T329]

value: Lung


title: WB8_dKO_Input  [SUM159(p63 and p73 KO)]

value: mammary carcinoma cells


title: Spleen [D812T326]

value: Healthy


title: P1 2

city: Bethesda

first: Robert

last: Morell

state: MD

address: 35A Convent Drive, Room 1F-103

institute: National Institute on Deafness and Other Communication Disorders

description: Sample 14 P1_2

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sample demultiplexing, alignment and gene counts were performed using the 10X Genomics CellRanger pipeline v3.0.1 using default settings.
Downstream data analysis was performed on the CellRanger cell-gene filtered matrix, using the Seurat R package V3.2
Cell Ranger outputs were imported into Seurat (v3.2) using the ‘Read10x’ and ‘CreateSeuratObject’ functions with the parameters min.cells = 3, min.features = 200. Cells with > 15,000 total RNA molecules and >5% hemoglobin or mitochondrial transcripts were also removed. Data were normalized, scaled and underwent dimensional reduction using the standard Seurat workflow. Predicted doublets were removed with DoubletFinder and a predicted doublet rate of 5%. Each dataset was then re-normalized, scaled and dimensionally reduced using standard Seurat workflow. The top 20 principal components from Seurat’s “RunPCA” function were used to define the dimensions of the UMAP non-linear dimensional reduction analysis which was then viewed on a 2D UMAP plot. An unsupervised clustering analysis was also carried out using the same number of principal components. Neuronal clusters were identified using known neuronal marker genes (Tubb3, Snhg11, Nefl, Nefm, Nefh) and genes known to be expressed early in the SGNs (Pou4f1, Gata3, Neurod1). Neuronal clusters were subset from each individual dataset for further analysis.
At each individual timepoint isolated neuron clusters were merged using Seurat’s standard integration workflow to account for batch effects. For the integration of all timepoints together, neuron datasets for each timepoint were merged before carrying out standard Seurat work flow for PCA analysis. Harmony (v1.0) integration was then applied to this dimensionally reduced object to account for batch effects between the individual datasets. For all merged objects clustering analysis was re-done. Clusters were checked for quality and were removed if their identity could not be determined (< 3 significant genes defining their expression, low or no expression of neuronal marker genes, and/or top 10 marker genes matching > 1 cell type (eg: a mixture of glial and neuronal genes).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Matrices of raw and normalized counts, generated from Seurat. The barcode names in SGN_Combined_counts.csv and SGN_Combined_counts_norm.csv are formatted such that the number after the "1_" corresponds to the "Sample *", so that e.g., GTAATGCGTTGCCAAT-1_6,GTACAACGTGGCCCAT-1_6, correspond to "Sample 6 E16_2A".

source_name: Spiral ganglion

extract_protocol:
spiral ganglia (SG) were roughly dissected out of the cochlea with some sensory epithelia and mesenchyme still attached. At E16 SG were separated into basal and apical portions by cutting through the middle turn. At E14, E16 and E18, three biological replicates were collected containing pooled tissue from sperate litters. At P1, two biological replicates were collected.
Dissociation at E14 and E16: Pooled SG were dissociated for 14 minutes in 0.05% Trypsin-EDTA at 37˚C, with two vigorous triturations. Trypsin was neutralized with the addition of an equal volume of FBS.
Dissociation at E18 and P1: Pooled SG were dissociated for 25 minutes in Papain (20U/mL) at 37˚C, with triturations every 5 mins. Papain was neutralized with the addition of Ovomucoid inhibitor.
Dissociated cells were passed through a 20μm strainer, spun down at 300 x g and then resuspended in PBS with 0.4mg/mL BSA and 0.2U/mL RNase inhibitor at a density of 1,100 cells/ml
The single-cell suspension was loaded onto the droplet-based single-cell barcoding system (10x Chromium Controller, 10x Genomics) and a Chromium NextGEM Single Cell 3’ Reagent Kit v3.1 (10x Genomics) was used to prepare single-cell, barcoded 3’ cDNA libraries according to the manufacturer’s instructions. The libraries were sequenced on a NextSeq2000 instrument (Illumina).
scRNA-Seq

value: cochlea

value: Spiral Ganglion Neurons

tag: location

value: whole ganglion


title: Spleen [D812T302]

value: Spleen


title: Adrenal gland, Female, Senp2cKO, 554

city: Clermont-Ferrand

first: Antoine

last: Martinez

address: Faculté de Médecine, CRBC, 28 place Henri Dunant

department: GReD

institute: CNRS, INSERM, Université Clermont Auvergne

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Adapter dimer reads were removed using DimerRemover
Reads were mapped onto the mm10 assembly of Mus musculus genome using STAR version 2.5.3a. Gene expression quantification was performed from uniquely aligned reads using htseq-count version 0.6.1p1,
Read counts have been normalized across samples with the median-of-ratios method proposed by Anders and Huber
Differential expression have been implemented using the Bioconductor package DESeq2 version 1.16.1.
Genome_build: mm10
Supplementary_files_format_and_content: tsv file represents read raw and normalized read count for every sample and every gene and comparisons between conditions with log2FC, p-values, adjusted p-values

source_name: Adrenal gland, Female, Senp2cKO

extract_protocol:
Adrenal glands were removed, flash frozen on dry ice, and RNA was extracted using Rneasy micro kit from QIAGEN
RNA-Seq libraries were generated according to manufacturer's instructions from 100 ng of total RNA using the Illumina Stranded mRNA Prep, Ligation kit and IDT for Illumina RNA UD Indexes Ligation (Illumina, San Diego, USA). Briefly, Oligo(dT) magnetic beads were used to purify and capture the mRNA molecules containing polyA tails.The purified mRNA were then fragmented at 94oC for 8 min and copied into first strand complementary DNA (cDNA) using reverse transcriptase and random primers. Second strand cDNA synthesis further generated blunt-ended double-stranded cDNA and incorporated dTTP in place of dUTP to achieve strand specificity by quenching the second strand during amplification. Following A-tailing of DNA fragments and ligation of pre-index anchors, PCR amplification was used to add indexes and primer sequences and to enrich DNA libraries (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 13 cycles; 5 min at 72oC). Surplus PCR primers were further removed by purification using SPRIselect beads (Beckman-Coulter, Villepinte, France) and the final libraries were checked for quality and quantified using capillary electrophoresis.

value: Adrenal gland

value: Female


title: Adrenal gland, Female, Senp2cKO, 598


title: Lung [D812T317]


title: Stomach [D812T311]

source_name: Stomach

value: Stomach


title: LN [D812T331]

value: LN


title: Adrenal gland, Female, Senp2cKO, 549


title: WB6_p73_KO_Input  [SUM159(p73 KO)]

source_name: SUM159 Cells ITGB4-High with p73 Knock-out

value: p73 Knock-out

tag: cell type


title: WB5_p73_KO_H3K27ac  [SUM159(p73 KO)]

value: H3K27ac (Abcam ab4729)


title: Lung [D812T305]


title: WB13_dKO-EV_H3K27ac   [SUM159(p63 and p73 KO) with exogenous Empty vector]

value: p73 and p63 Knock-out + exogenous empty expression vector


title: LN [D812T307]


title: WB4_p63_KO_Input [SUM159(p3 KO)]

source_name: SUM159 Cells ITGB4-High with p63 Knock-out

value: SUM159 Cells ITGB4-High

value: p63 Knock-out


title: Adrenal gland, Female, WT, 529

source_name: Adrenal gland, Female, WT

tag: genotype

value: WT


title: Liver [D812T313]

source_name: Liver

value: Liver


title: WB3_p63_KO_H3K27ac [SUM159(p63 KO)]

value: mammary carcinoma cells


title: Liver [D812T337]

value: Healthy


title: Liver [D812T325]


title: Liver [D812T301]


title: Adrenal gland, Female, WT, 538


title: Adrenal gland, Female, WT, 536


title: WB2_NT_Input [SUM159(Non-targeting control)]

source_name: SUM159 Cells ITGB4-High with non-targeting control gRNA

value: non-targeting control gRNA


title: Kidney [D812T315]

source_name: Kidney

value: Kidney


title: Kidney [D812T339]


title: WB1_NT_H3K27ac [SUM159(Non-targeting control)]


title: Adrenal gland, Female, WT, 531


title: MWC229 SUM159 CD104-high Input

source_name: SUM159 Cells ITGB4-High


title: Kidney [D812T303]


title: Heart [D812T340]

source_name: Heart

value: Heart


title: Kidney [D812T327]


title: Adrenal gland, Male, Senp2cKO, 576

source_name: Adrenal gland, Male, Senp2cKO

value: Male


title: Heart [D812T328]


title: Adrenal gland, Male, Senp2cKO, 575

value: Adrenal gland


title: MWC228 SUM159 CD104-high H3K27Ac


title: Adrenal gland, Female, Senp2cKO, 548

value: Female


title: Heart [D812T304]


title: Heart [D812T316]


title: MWC227 SUM159 CD104-low Input

source_name: SUM159 Cells ITGB4-Low

value: SUM159 Cells ITGB4-Low


title: Colon [D812T332]

source_name: Colon

value: Colon


title: Adrenal gland, Male, Senp2cKO, 555


title: LN [D812T319]

source_name: LN

value: LN


title: MWC211_SUM159 CD104-high_Input


title: Colon [D812T320]


title: Brain [D812T334]

source_name: Brain

value: Brain


title: Colon [D812T308]


title: Adrenal gland, Male, Senp2cKO, 534


title: MWC226 SUM159 CD104-low H3K27Ac

value: H3K27ac (Abcam ab4729)


title: Adrenal gland, Male, WT, 543

source_name: Adrenal gland, Male, WT


title: Brain [D812T322]


title: Adrenal gland, Male, WT, 539


title: Mel_MB166 [D176T77]

source_name: Melanocyte

growth_protocol: Melanocytes were cultured from new-born C57BL6/J mice for 2-3 weeks, and cultures lysed directly in Trizol

extract_protocol:
After recovering the RNA-containing phase using chloroform + centrifugation, 100% ethanol was added to the samples, and samples were transferred to RNAseq mini kit columns. Extraction was performed following manufacturer's instructions, including on-column DNAse digestion. After elution, samples were treated with TurboDNAse I according to manufacturer's instructions.
Illumina TruSeq Stranded mRNA Library preparation kit

value: Melanocyte


title: MWC210_SUM159 CD104-high_H3K27Ac

value: SUM159 Cells ITGB4-High


title: YC15 (p63 CST) SUM159 ITGB4-Hi

source_name: SUM159 Cells ITGB4-Hi

value: p63 (Cell Signalling 13109S)


title: Adrenal gland, Male, WT, 532

value: WT


title: YC20 (p63 CST) SUM159 ITGB4-Low

value: mammary carcinoma cells


title: Mel_MB163 [D176T75]

value: Healthy


title: Adrenal gland, Male, WT, 533


title: IgG_day5_rep2

data_processing:
Library strategy: Cut&Tag
Reads were trimmed using cutadapt and aligned with Bowtie2 (v 2.3.5.1) to mm10 reference genome.
Peaks were called using MACS2. Reproducible peaks for each condition were identified using IDR (idr≤0.1) or by overlap thresholding (for histone Cut&Tag). Reproducible peaks were aggregated, read counts for each region were obtained using featureCounts package followed by normalization and differential accessibility analysis using DESeq2.
Bigwig files were produced with deepTools (Ramirez et al., 2014).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text file containing normalized read counts as determined for the aggregated peak set; tar containing normalized average signal files

source_name: IgG day5

growth_protocol: Mouse embryonic fibroblasts (MEFs) were isolated from embryonic day (E)13.5 heterozygous TauEGFP embryos, or E13.5 homozygous Tip60/Kat5 conditional KO (cKO) embryos, and maintained in DMEM (Invitrogen) supplemented with 10% cosmic calf serum.

extract_protocol: Cells at different times of neuronal induction were subjected to Cut&Tag following the previously described protocol (Kaya-Okur et al., 2019). Where indicated, day5 TauEGFP cells were sorted using BD FACS-Aria II sorter.

treatment_protocol: MEFs were transduced with indicated lentiviruses. shRNA-infected populations were selected for 2 days in 2 mg/ml puromycin. The cells were treated with doxycycline (dox) two days post-infection to induce transgene expression, and transferred into N3 medium (DMEM/F12, N2 supplement, insulin) containing dox the following day. The medium was refreshed every 3 days.

value: Kat5 cKO

value: E13.5 fibroblast

tag: antibody

value: IgG


title: IgG_day2_rep2

source_name: IgG day2


title: YC12 p73 Bethyl SUM159 ITGB4-Hi

tag: chip antibody


title: MWC209_SUM159 CD104-low_Input


title: Mel_161A [D176T74]

tag: cell line


title: Mel_160B [D176T73]


title: Brain [D812T310]


title: YC17 (p73 Bethyl) SUM159 ITGB4-Low


title: MWC208_SUM159 CD104-low_H3K27Ac


title: MC38_Setdb1 [D176T72]

source_name: colon adenocarcinoma

growth_protocol: Cells were cultured (RPMI, Glutamax, 10%FCS, 1%P/S, 2µg/mL Puromycing), detached using trypsin, and 2-3 million lysed in Trizol.

value: colon adenocarcinoma

value: Cancercells


title: Ascl1_Cre_h3k4me3_day5_rep2

source_name: Ascl1_Cre_h3k4me3 day5

value: H3K4me3 (Active Motif, 39060)


title: IgG_day2_rep1


title: Mel_7_12_18 [D176T76]


title: MWC91.ATAC SUM159 CD104-high Rep2

data_processing:
Encode ATAC-seq pipeline (https://github.com/kundajelab/atac_dnase_pipelines)
Genome_build: hg19
Supplementary_files_format_and_content: peak files
Supplementary_files_format_and_content: excel files
Supplementary_files_format_and_content: bigwig files

growth_protocol:
Chromatin was isolated from SUM159 cells cells grown under standard tissue culture conditions
ITGB4-hi and ITGB4-lo cells were grown under standard tissue culture conditions

extract_protocol:
Chromatin was fragmented using transposase
Libraries were prepared according to Illumina's instructions accompanying the Illumina Tagment DNA TDE1 Enzyme and Buffer Kit (Part# 20034198).

tag: dna extraction

value: Transposase insertion


title: YC16  SUM159 ITGB4-Hi Input


title: MC38_Setdb1 [D176T71]


title: MWC90.ATAC SUM159 CD104-high Rep1


title: MC38_Setdb1 [D176T70]


title: MWC89.ATAC SUM159 CD104-low Rep2

value: SUM159 Cells ITGB4-Low


title: Ascl1_dCre_h3k4me3_day5_rep2

source_name: Ascl1_dCre_h3k4me3 day5


title: MC38_Ctrl [D176T65]

value: Ctrl


title: MC38_Ctrl [D176T64]


title: MC38_Ctrl [D176T66]


title: Ascl1_Cre_h3k4me3_day5_rep1


title: Ascl1_dCre_h3k4me3_day5_rep1


title: YC21  SUM159 ITGB4-Low Input


title: MWC88.ATAC SUM159 CD104-low Rep1


title: Ascl1_Cre_h3k4me3_day2_rep2

source_name: Ascl1_Cre_h3k4me3 day2


title: MC38 [D176T62]


title: Ascl1_dCre_h3k4me3_day2_rep1

source_name: Ascl1_dCre_h3k4me3 day2


title: Ascl1_Cre_h3k4me3_day2_rep1


title: RC_j

city: Koto-ku

first: Osamu

last: Gotoh

state: Tokyo

address: Ariake 3-8-31

country: Japan

institute: Japanese Foundation For Cancer Research

description: The file supplementary_table.xlsx contains individual sample metadata.

data_processing:
Demultiplexing, alignment, filtering, and annotation was performed by iRepertoire (http://www.irepertoire.com) using a proprietary pipeline.
Raw files were submitted without demultiplexing.  This is required for use with the iRepertoire protocol.
Assembly: IMGT database
Supplementary files format and content: TCR CDR3 nucleotide and amino acid sequences, and V-D-J gene segment usage lists generated by iRepertoire.
Library strategy: TCR-seq

source_name: rectal cancer

extract_protocol:
Total RNA was extracted using RNeasy Micro kit (Qiagen).
The CDR3 region of the T-cell receptor (TCR) chain was amplified using the iRepertoire multiplex primer set (HTBI-M; iRepertoire, Huntsville, AL, USA) following the manufacturer’s instructions. The Qiagen OneStep RT-PCR kit (Qiagen, Valencia, CA, USA) was used for reverse transcription. Amplification and library preparation were performed with the iR-Processor and iRock 2.0 (iRepertoire, Huntsville, AL, USA).  Paired-end sequencing was performed on the purified libraries using the Illumina MiSeq v2 500-cycle Reagent Kit (Illumina, San Diego, CA, USA).

value: rectal cancer

tag: treatment

value: multiplexed sample:pre- and post-CRT

tag: age

value: multiplexed sample:45-64


title: MC38 [D176T63]


title: MC38 [D176T61]


title: Ascl1_dCre_h3k4me3_day2_rep2

tag: time post-induction


title: RC_i

value: multiplexed sample:45-74


title: rtTA_dCre_h3k4me3_day2_rep2

source_name: rtTA_dCre_h3k4me3 day2


title: B16OVA_Setdb1 [D176T59]

source_name: Melanoma

value: Melanoma

tag: cancer/healthy


title: RC_h

value: multiplexed sample:45-84


title: rtTA_dCre_h3k4me3_day2_rep1


title: IgG_b2_day5_rep3

source_name: IgG_b2 day5


title: RC_f

value: multiplexed sample:45-69


title: RC_e

value: multiplexed sample:30-84


title: B16OVA_Ctrl [D176T53]

tag: condition


title: RC_d

value: multiplexed sample:30-74


title: B16OVA_Setdb1 [D176T60]


title: IgG_b2_day5_rep1

value: E13.5 fibroblast


title: B16-OVA_RNA [B176T3]

value: WT


title: Ce-49 sh 5

type: genomic

city: Duarte

first: Haiqing

last: Li

address: 1500 E Durate Rd

department: Shared Resources Department

institute: City of Hope National Medical Center

description: genomic DNA from xenografted tumor

hyb_protocol: Standard Illumina Protocol by Diagenode

scan_protocol: Protocol by Diagenode

data_processing: The EPIC methylation array was analysed using the Bioconductor package RnBeads (v2.4.0) using the hg19 annotations.

label: Standard Illumina

label_protocol: Standard Illumina Protocol by Diagenode

growth_protocol: K562 cells grown in RPMI supplemented with 10% FBS and injected subcutaneously into the flank of NGS mice

extract_protocol: Genomic DNA was extracted using Qiagen DNeasy Kit according to standard instructions

treatment_protocol: 1) PBS group received PBS (100 μL/injection); 2) AZA group received intra-tumoural injections of 5-Aza (Sigma) (1 mg/kg injection/mouse in 100 μL/injection); 3) Ce-49 sh group received intra-tumoural injections of Ce-49 sh loaded GenVoy LNPs (0.3 mg/kg injection/mouse in 100 μL/injection). Treatments were performed daily for 10 days.

tag: disease

value: leukemia


title: IgG_b2_day2_rep2

source_name: IgG_b2 day2

value: IgG


title: RC_g

value: multiplexed sample:45-79


title: MCA101-OVA_RNA [B176T2]

source_name: Fibrosarcoma

value: Fibrosarcoma

value: Cancercells


title: B16_RNA [B176T4]


title: MCA101_RNA [B176T8]


title: B16OVA_Ctrl [D176T54]

value: Ctrl


title: B16OVA [D176T51]


title: IgG_day5_rep1

value: Kat5 cKO


title: RC_b

value: rectal cancer

value: multiplexed sample:pre- and post-CRT

value: multiplexed sample:30-79


title: Ce-49 sh 4

description: genomic DNA from xenografted tumor


title: MC38_RNA [B176T6]

value: colon adenocarcinoma


title: B16OVA_Setdb1 [D176T58]

value: Melanoma


title: IgG_b2_day2_rep1


title: IgG_b2_day5_rep2


title: B16OVA [D176T49]


title: MC38-GFP_RNA [B176T5]


title: Ce-49 sh 2

description: genomic DNA from xenografted tumor


title: B16OVA_Ctrl [D176T52]


title: MC38-OVA_RNA [B176T1]


title: RC_c


title: Ce-49 sh 3

description: genomic DNA from xenografted tumor


title: AZA 3

description: genomic DNA from xenografted tumor

value: AZA


title: 64-3P

city: Bar Harbor

first: Joel

middle: H

last: Graber

state: ME

address: 159 Old Bar Harbor Rd

department: Bioinformatics Core

institute: MDI Biological Laboratory

data_processing:
Fastq formatted read files were preprocessed with Trimmomatic version 0.36 with default options.
Fastq files were then aligned to the C. elegans genome version 235 from WormBase, as presented in Ensembl version 93, using the STAR aligner version 2.6.1b
The Ensembl transcriptome was preprocessed with a splice junction overhang of 100nt.
Following alignment, the resulting BAM files were preprocessed with RSEM version 1.3.0 for isoform and gene-level expression estimates.
The resulting gene-level expression values were merged into a single expression matrix with an in-house python script.
Differential expression analysis was carried out in R version 3.6.1 with the DESeq2 version 1.24.0.  DESeq2 was also used to generate an rlog-matrix which was Z-transformed to normalize each gene across all samples.
The Z-transformed rlog matrix was then loaded into JMP version 13 and used for PCA after thresholding to an average rlog expression value of 7.5
DESeq2 output tables were filtered with the following restrictions for the identification of statistically significant differentially expressed genes: BaseMean >= 75 (average of 5 counts per sample), padj <= 0.05, |log2foldchange| >= 0.5, estimated standard error of the log2foldchange < 1.0.
Genome_build: WBcel235 (Ensembl release 93), INSDC Assembly GCA_000002985.3
Supplementary_files_format_and_content: Tab-delimited text file includes rlog-normalized log2counts for each sample, and rsem expected counts, rounded to the nearest integer

organism: Caenorhabditis elegans

source_name: Whole embryo

growth_protocol: For each of three replicates, 25 plates of each strain were used to inoculate 1L of S Media containing 5 grams of freeze-dried OP50 (LabTie, Leiden, The Netherlands).  Liquid cultures were incubated in 4 1L beveled flasks at 20° C until worms were gravid, at which point embryos were harvested, washed, bleach-treated (Montserrat et al. 2012) and hatched overnight. The synchronized L1-staged worms were used to inoculate another 1L of S Media with OP50 and were grown for approximately 40 hours until the majority reached the young adult stage, where they were harvested, washed, pelleted and flash frozen in 1-ml aliquots.

extract_protocol:
mRNA was isolated from both total and polysome associated halves of the lysate using a TruSeq RNAv2 kit (Illumina) following the manufacturer’s protocol.  RNA quality was assessed on an Allegiant 2100 Bioanalyzer (Agilent, Palo Alto, CA) requiring an A260/A208 > 1.7 and RIN > 8.0.
All 12 samples were sent to the Jaxson laboratory (Bar Harbor, ME) for sequencing using a KAPA stranded mRNA sequencing kit (Roche), followed by 75 cycles on the NextSeq HO.

treatment_protocol: For each strain and replicate, approximately 800 microliters of lightly pelleted worms were lysed on ice by grinding in solubilization buffer (ground in aliquots of 100 μL pelleted worms per 350 μL buffer; 300 mM NaCl, 50 mM Tris–HCL pH 8, 10 mM MgCl2, 1 mM EGTA, 200 μg mL−1 heparin, 400 U mL−1 RNAsin, 1 mM PMSF, 0.2 mg mL−1 cycloheximide, 1% Triton X‐100, 0.1% sodium deoxycholate).  Half of the sample was used for total RNA isolation.  The other half of the lysate was loaded onto a 10-50% sucrose gradient in high salt resolving buffer (140 mM NaCl, 25 mM Tris–HCL pH 8, 10 mM MgCl2). Gradients were resolved by ultracentrifugation in a Beckman SW41Ti rotor at 38 000 × g at 4 °C for 2 h. Fractions of the gradients were continuously monitored at absorbance of 254 nm using a Teledyne density gradient fractionator collecting the polysome fraction.

value: whole embryo

value: wt

value: polysomal


title: Ascl1_shTip60#2_acH2AZ_day5_rep3

source_name: Ascl1_shTip60#2_acH2AZ day5

value: E13.5 fibroblast


title: B16OVA [D176T50]

value: WT


title: Ascl1_shTip60#3_acH2AZ_day5_rep3

source_name: Ascl1_shTip60#3_acH2AZ day5


title: 3T3-L1 cells, Ube3d-KO, biol rep 2

city: Boston

first: Daniel

last: Heller-Trulli

address: 136 Harrison Ave

department: Developmental, Molecular, and Chemical Biology

institute: Tufts University School of Medicine

data_processing:
Reads were aligned to the M. musculus genome (mm10/GRCm38) using STAR (2.6.1d) and quantified using featureCounts (v1.6.3).
Assembly: mm10
Supplementary files format and content: Tab delimited text file with read counts per gene for all samples.
Supplementary files format and content: Comma separated values file with read counts per DoG for all samples.

growth_protocol: Cells were cultured in DMEM, high glucose (4.5 g/L) supplemented with 10% FBS and antibiotics (100 U/mL penicillin, 100 μg/mL streptomycin). All cells were grown at 37°C with 5% CO2. Cells were subcultured every 2-3 days according to ATCC guidelines and never allowed to reach more than 80% confluence.

extract_protocol:
RNA was collected using the Quick-RNA™ Miniprep Kit (Zymo Research)
Library preparation was performed using a KAPA stranded RNAseq kit with rRNA depletion.

value: mouse embryonic fibroblast

value: Ube3d knockout


title: MCAOVA_Setdb1 [B262T24]

value: Fibrosarcoma


title: RC_a

value: multiplexed sample:45-79


title: Ascl1_shTip60#3_acH2AZ_day5_rep2


title: 64-2T

value: total


title: 64-3T


title: Ascl1_shTip60#2_acH2AZ_day5_rep2


title: AZA 2

description: genomic DNA from xenografted tumor

value: leukemia


title: 3T3-L1 cells, Ube3d-KO, biol rep 3


title: Ascl1_shTip60#3_acH2AZ_day5_rep1


title: Ascl1_shTip60#2_acH2AZ_day5_rep1


title: PBS 2

description: genomic DNA from xenografted tumor

value: PBS


title: PBS 3

description: genomic DNA from xenografted tumor


title: Ce-49 sh 1

description: genomic DNA from xenografted tumor


title: AZA 5

description: genomic DNA from xenografted tumor


title: 64-1P


title: MCAOVA_Ctrl [B262T22]

value: Cancercells

value: Ctrl


title: PBS 5

description: genomic DNA from xenografted tumor


title: 3T3-L1 cells, WT, biol rep 1


title: MCAOVA [B262T21]


title: 64-1T


title: Ascl1_shNTC_acH2AZ_day5_rep1

source_name: Ascl1_shNTC_acH2AZ day5


title: PBS 4

description: genomic DNA from xenografted tumor


title: Ascl1_shNTC_acH2AZ_day5_rep3


title: 3T3-L1 cells, WT, biol rep 2


title: AZA 4

description: genomic DNA from xenografted tumor


title: B16OVA_Setdb1 [B262T19]


title: Ascl1_shTip60#3_acH2AZ_day2_rep2

source_name: Ascl1_shTip60#3_acH2AZ day2


title: PBS 1

description: genomic DNA from xenografted tumor


title: EBF1-dTAG_N, 6h, rep3

city: Freiburg

first: Nikolay

last: Zolotarev

address: Stübeweg, 51

department: Cellular and Molecular Immunology

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description:
EBF1-dTAG_N_6h_rep3
exon_counts.tsv
gene_counts.tsv
DESeq2_results_Ex_In.csv

data_processing:
Quality control and read mapping was done using snakePipes (v2.5.1), an automatic pipeline for analysis of deep sequencing data.
Reads were mapped to the mouse genome (GRCm38 – mm10) using STAR (v2.7.4a).
Reads were sorted and indexed using samtools (v1.10) and duplicates were removed by sambamba_markdup.
Coverage bigwig files were created using bamCoverage from deeptools (v3.3.2) with RPKM normalization.
The expression level of the annotated genes (GRCm38.p4) was calculated by featureCounts (subread v2.0.0). The exon_count.tsv was obtained using default settings, and the gene_count.tsv was obtained using "-O" and "-t" options. Intron counts were calculated as the difference between gene counts and exon counts for each gene.
The differential gene expression was analyzed using the DESeq2 package, for exons and introns separately. Genes with a q-value < 0.05 were considered significantly differentially expressed.
Assembly: mm10
Supplementary files format and content: Two raw count matrices (for exons and entire genes) obtained from featureCounts are provided in tab-delimited format (.tsv).
Supplementary files format and content: Two separate bigwig files (.bw) for forward and reverse strand are provided for each sample.
Supplementary files format and content: One table (.csv) with combined DESeq2 results for exons and introns.

source_name: A-MuLV transformed pro-B cells

growth_protocol: Production of A-MuLV transformed cells with the replacement of endogenous EBF1 by exogenous modified genes was described in Boller et al. 2016. A-MuLV transformed cells were cultured in the RPMI 1640 medium with 10% FCS; 1x Penicillin-Streptomycin-Glutamine; 0.06 mM β-mercaptoethanol.

extract_protocol:
Total RNA was isolated using the RNeasy Micro Kit (Qiagen) according to the manufacturer's instructions.
Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit was used for library preparation according to the manufacturer's protocol.

treatment_protocol: Cells were treated with dTAG-13 (final concentration 0.5 uM) or DMSO for 6 hours.

value: A-MuLV transformed pro-B cells

value: dTAG-13 6h


title: 144-3P


title: AZA 1

description: genomic DNA from xenografted tumor

value: AZA


title: Ascl1_shNTC_acH2AZ_day5_rep2


title: 3T3-L1 cells, Ube3d-KO, biol rep 1


title: Ascl1_shTip60#3_acH2AZ_day2_rep1


title: B16OVA [B262T17]

value: Melanoma


title: B16_Setdb1 [B262T15]


title: EBF1-dTAG_N, 6h, rep2

description:
EBF1-dTAG_N_6h_rep2
exon_counts.tsv
gene_counts.tsv
DESeq2_results_Ex_In.csv


title: B16OVA_Ctrl [B262T18]


title: 144-3T

value: whole embryo


title: EBF1-dTAG_N, 6h, rep4

description:
EBF1-dTAG_N_6h_rep4
exon_counts.tsv
gene_counts.tsv
DESeq2_results_Ex_In.csv


title: 144-2T


title: 144-2P

value: polysomal


title: B16 [B262T13]


title: EBF1-dTAG_N, 6h, rep1

description:
EBF1-dTAG_N_6h_rep1
exon_counts.tsv
gene_counts.tsv
DESeq2_results_Ex_In.csv


title: MCAOVA_Setdb1 [B262T12]


title: 144-1T


title: Ascl1_shNTC_acH2AZ_day2_rep2

source_name: Ascl1_shNTC_acH2AZ day2

value: E13.5 fibroblast


title: 144-1P


title: MCAOVA_Ctrl [B262T10]


title: Ascl1_shTip60#2_acH2AZ_day2_rep1

source_name: Ascl1_shTip60#2_acH2AZ day2


title: EBF1-dTAG_N, 0h, rep4

description:
EBF1-dTAG_N_0h_rep4
exon_counts.tsv
gene_counts.tsv
DESeq2_results_Ex_In.csv

value: DMSO 6h


title: EBF1-dTAG_N, 0h, rep2

description:
EBF1-dTAG_N_0h_rep2
exon_counts.tsv
gene_counts.tsv
DESeq2_results_Ex_In.csv


title: MCAOVA [B262T09]

value: WT


title: Ascl1_shNTC_acH2AZ_day2_rep1


title: B16OVA_Setdb1 [B262T08]


title: EBF1-dTAG_N, 0h, rep1

description:
EBF1-dTAG_N_0h_rep1
exon_counts.tsv
gene_counts.tsv
DESeq2_results_Ex_In.csv


title: rtTA_shNTC_acH2AZ_day2_rep2

source_name: rtTA_shNTC_acH2AZ day2


title: B16OVA_Ctrl [B262T06]


title: Ascl1_shTip60#2_acH2AZ_day2_rep2


title: Rat-OH47-Emb5-M1-L-E18

data_processing:
The RNAseq reads were evaluated and bad reads were filtered out using FastQC (version 0.11.8, Andrews et al., 2012), AfterQC (version 0.9.6, Chen et al., 2017) and Trimmomatic (version 0.39, Bolger et al., 2014), and ribosomal RNA was removed using Sortmerna (Kopylova et al., 2012). The number of remaining, good reads varied between 30M and 90M. Reads were aligned using Salmon (version 0.99.0, Patro et al., 2017) to Rnor_6.0 (Ensembl release 99) cDNA. Only one-to-one orthologous genes between mouse and rat were selected for further analysis. 16,604 one-to-one orthologous genes were found between mouse and rat using Ensembl Biomart tool (Kinsella et al., 2011), 126 additional one-to-one orthologues were added using Inparanoid8 (Sonnhammer & Östlund, 2015) in which gene pairs with bootstrap scores of 100% were selected. The output transcript ID’s of Salmon were converted to mouse gene ID’s using Ensembldb (Rainer et al., 2019) and Tximport (Soneson et al., 2015), allowing comparison of mouse and rat read counts. Deseq2 (Love et al., 2014) was used to normalise the read counts by library size and composition as well as transcript length.
Assembly: Rnor_6.0 (Ensembl release 99) cDNA
Supplementary files format and content: Tab-delimited gene expression count values of each samples

organism: Rattus norvegicus

source_name: lower first molar

extract_protocol:
Embryonic rat molars were dissected from jaws on embryonic E18 (E0 being the vaginal plug appearance day). Minimal amount of surrounding tissue was left around the tooth germ, at the same time making sure that the tooth was not damaged in the process. The tissue was immediately stored in RNAlater (Qiagen, Düsseldorf, Germany) at −80°C for RNAseq. For RNAseq, each tooth was handled individually. Samples were homogenized using Precellys 24 homogenizer (Bertin instruments). RNA was extracted using guanidium thiocyanate-phenol-chloroform method and purified using RNeasy Plus micro kit (Qiagen GmbH) following manufacturer's protocol. The putiry of RNA was measured using Nanodrop microvolume spectrophotometer (Thermo Fisher Scientific).
The complementary DNA (cDNA) libraries were prepared using Ovation Rat RNAseq System (Tecan).

value: lower first molar

value: DA/HanRj

value: wild type


title: B16OVA [B262T05]


title: 3T3-L1 cells, WT, biol rep 3

value: mouse embryonic fibroblast


title: Rat-OH47-Emb6-M1-R-E18


title: EBF1-dTAG_C, 6h, input

data_processing:
Quality control and read mapping was done using snakePipes (v2.5.1), an automatic pipeline for analysis of deep sequencing data.
Reads were mapped to the mouse genome (GRCm38 – mm10) using bowtie2 (v2.3.5.1).
Reads were sorted and indexed using samtools (v1.10) and duplicates were removed by sambamba_markdup.
Coverage bigwig files were created using bamCoverage from deeptools (v3.3.2) with normalization on sequencing depth (CPM).
Peak calling was performed using MACS2 (v2.2.7.1) with default settings.
Assembly: mm10
Supplementary files format and content: One .narrowPeak file containing the MACS2 output for each ChIP sample.
Supplementary files format and content: One bigwig file (.bw) for each sample.

extract_protocol:
EBF1 ChIP was performed according to Boller et al. 2016 protocol with minor changes. Cells were crosslinked with formaldehyde. 4 µg rabbit a-EBF1 (1C) rabbit antibody per sample was used. Cells were harvested and washed with PBS. Cell pellet was resuspended in PBS with 2% FCS (4 mln cells per 1 ml buffer). Fresh formaldehyde mix (50mM HEPES-KOH pH8.0, 100mM NaCl, 0.5mM EGTA, 1mM EDTA, 11% (v/v) formaldehyde) was added to the cell suspension to a final concentration of 1% FA. Tubes were incubated on rotator for 10 min at RT. Quenching was performed by adding 2 M Glycine to the final concentration 0.2 M. Cell pellet was resuspended in Lysis buffer (50mM Tris-HCl pH 8.0, 1% (w/v) SDS, 10mM EDTA; PIM) (4 mln cells per 100 μl buffer). Chromatin was sheared the chromatin with a Bioruptor (20-25 cycles, output level "High", 30 sec ON, 30 sec OFF, 4°C). Fragment size and amount of chromatin was checked. 10-20 μg DNA was used for 1 ChIP reaction. Chromatin was mixed with 4 μg of EBF1 antibody or rabbit IgG and incubated on rotator ON at 4°C. Chromatin was incubated with 30 μl of Dynabeads Protein G (ThermoFisherScientific) suspension per sample on rotator for 4 hours at 4°C. Beads were washed 4 times with Wash buffer A (20mM Tris-HCl pH 8.0, 150mM NaCl, 1% (v/v) Triton X-100, 0.1% (w/v) SDS, 2mM EDTA); once with Final wash buffer A (20mM Tris-HCl pH 8.0, 500mM NaCl, 1% (v/v) Triton X-100, 0.1% (w/v) SDS, 2mM EDTA). Every wash was on rotator for 5 minutes at 4°C. Chromatin was eluted with 100 μl Elution buffer (10 mM Tris-HCl, pH 8.0; 0.5% SDS; 300 mM NaCl; 5 mM EDTA pH 8.0) by shaking vigorously at 65°C for 30 min. Samples were revese crosslinked, treated with RNase A and Proteinase K, and purified with QIAquick PCR Purification Kit.
NEBNext Ultra II DNA Library Prep Kit for Illumina was used for library preparation according to the manufacturer's protocol.


title: B16_Ctrl [B262T14]


title: Rat-OH47-Emb3-M1-R-E18


title: EBF1-dTAG_C, 6h, a-EBF1, ChIP

value: a-EBF1 (1C)


title: Ascl1_shTip60#3_H2AZ_day5_rep1

source_name: Ascl1_shTip60#3_H2AZ day5

value: H2A.Z (Active Motif, 39113)


title: EBF1-dTAG_N, 0h, rep3

description:
EBF1-dTAG_N_0h_rep3
exon_counts.tsv
gene_counts.tsv
DESeq2_results_Ex_In.csv


title: B16_Setdb1 [B262T04]

value: Cancercells


title: Rat-OH47-Emb7-M1-L-E18


title: Ascl1_shTip60#3_H2AZ_day5_rep2


title: EBF1-dTAG_C, 0h, a-EBF1, ChIP


title: rtTA_shNTC_acH2AZ_day2_rep1


title: EBF1-dTAG_N, 6h, rep2

data_processing:
Quality control and read mapping was done using snakePipes (v2.5.1), an automatic pipeline for analysis of deep sequencing data.
Reads were mapped to the mouse genome (GRCm38 – mm10) using bowtie2 (v2.3.5.1).
Reads were sorted and indexed using samtools (v1.10) and duplicates were removed by sambamba_markdup.
Coverage bigwig files were created using bamCoverage from deeptools (v3.3.2) with normalization on sequencing depth (CPM).
Peak calling and differential accessibility analysis were performed using the ATACofthesnake pipeline (https://github.com/maxplanck-ie/ATACofthesnake).
Peak calling was performed using MACS2 (v2.2.7.1).
Differential accessibility for the union of all peaks was analyzed with edgeR (3.32.0) for EBF1-dTAG_N and _C samples independently.
Differential motif analysis was performed using MEME (v5.0.2).
Assembly: mm10
Supplementary files format and content: Two tables (.csv) with edgeR results for EBF1-dTAG_N and _C.
Supplementary files format and content: One .narrowPeak file containing the MACS2 output for each ATAC sample.
Supplementary files format and content: One bigwig file (.bw) for each sample.

extract_protocol:
ATAC-seq was performed using loaded Tagmentase (Tn5 transposase) Diagenode according to the manufacturer protocol. 50000 cells were incubated with 2.5 μl loaded Tagmentase with the addition of 0.01% Digitonin and 0.1% Tween20 for 30 min at 37°C. Libraries were purified using Zymo DNA Clean and Concentration Kit.
Libraries were amplified using Nextera XT Index Kit v2, 9-10 cycles.


title: Nrf2 knockout bone marrow stromal/stem cells, #3

city: Nanjing

first: Renlei

last: Yang

address: Hanzhong Road 146

institute: Nanjing medical university

data_processing:
Mapping: Firstly, reference genome sequences and gene model annotation files of relative species were downloaded  from genome website, such as UCSC, NCBI, ENSEMBL.
Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence.
Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed  properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform  expression levels from the pair-end clean data.
Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative  binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate  data-driven prior distributions, Padj of genes were setted <0.05 to detect differential expressed ones.
Assembly: mm10
Supplementary files format and content: all.fpkm_anno.xls include FPKM values for each sample

source_name: bone marrow stromal/stem cells

growth_protocol: Bone marrow stromal/stem cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA of each sample was extracted using TRIzol Reagent/RNeasy Mini Kit (Qiagen). 1 μg total RNA was used  for following library preparation.
RNA libraries for RNA-seq were prepared using R8.VAHTS mRNA-seq V3 Library Prep Kit for Illumina following manufacturer's protocols.

value: bone marrow stromal/stem cells

value: Nrf2 knockout


title: B16_Ctrl [B262T02]

city: Paris

first: Sebastian

last: Amigorena

address: 26 rue Ulm

institute: Curie Institute

data_processing:
Trimming done by the Curie Institut plateform using Antropos for D176 and B262 and B243 or using TrimGalore for D804 and D812
After the Curie Institut plateform pass the FastQC
Afterwards reads are aligned using STAR with the basic 2 pass mode: first the genomeGenerate and then GeneCounts.
We used the HTSeq count like gene cout normalized by the librarysize of unique mapped
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw gene values for each Sample
Supplementary files format and content: tab-delimited text files include normalized gene values by library size for each Sample

value: Ctrl


title: EBF1-dTAG_C, 0h, input

value: A-MuLV transformed pro-B cells


title: B16 [B262T01]

value: Melanoma


title: Ascl1_shTip60#2_H2AZ_day5_rep2

source_name: Ascl1_shTip60#2_H2AZ day5


title: Ascl1_shTip60#3_H2AZ_day5_rep3


title: Nrf2 knockout bone marrow stromal/stem cells, #1


title: Ascl1_shTip60#2_H2AZ_day5_rep3


title: WT bone marrow stromal/stem cells, #3


title: Ascl1_shTip60#2_H2AZ_day5_rep1


title: MCAOVA_Setdb1 [B253T54]

value: Fibrosarcoma


title: MCAOVA_Ctrl [B253T52]


title: WT bone marrow stromal/stem cells, #2


title: Rat-OH47-Emb2-M1-L-E18

city: Helsinki

first: Jukka

last: Jernvall

address: P.O. Box 56 (Viikinkaari 9)

institute: University of Helsinki


title: Nrf2 knockout bone marrow stromal/stem cells, #2


title: Ascl1_shNTC_H2AZ_day5_rep3

source_name: Ascl1_shNTC_H2AZ day5


title: WT bone marrow stromal/stem cells, #1


title: EBF1-dTAG_N, 0h, rep1


title: Ascl1_shNTC_H2AZ_day5_rep2


title: MCAOVA [B253T51]


title: EBF1-dTAG_C, 6h, rep2

value: dTAG-13 6h


title: B16OVA_Setdb1 [B253T50]

source_name: Melanoma


title: Ascl1_shNTC_H2AZ_day5_rep1

value: E13.5 fibroblast


title: B16OVA_Ctrl [B253T48]


title: Ascl1_shTip60#3_H2AZ_day2_rep2

source_name: Ascl1_shTip60#3_H2AZ day2


title: EBF1-dTAG_C, 0h, rep2

value: DMSO 6h


title: EBF1-dTAG_N, 6h, rep1


title: EBF1-dTAG_C, 6h, rep1


title: B16OVA [B253T47]

value: WT


title: TAM_PP rep1

city: chengdu

first: Jue

last: Xu

address: 18# 3rd section, Renmin South Road

institute: Sichuan University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using HISAT2
Gene expression values were calculated as Fragments Per Kilobase of transcript per Million mapped reads (FPKM) using StringTie
Differential gene expression was determined using Ballgown
Genome_build: mm9
Supplementary_files_format_and_content: FPKM

source_name: posterior palate treated with tamoxifen

extract_protocol:
The anterior and posterior portions of the palatal shelves were dissected out from E13.5 TAM-treated mice and controls (n = 3 for each group), respectively, and subjected to total RNA extraction (RNeasy Micro Kit, cat. 74004; Qiagen). The quality and quantity of RNAs were determined by using a Qubit 2.0 Fluorometric Quantitation system (Life Technologies). Finally, the RNAs were subjected to RNA-Seq analysis. Gene Ontology and pathway categories were grouped according to functional theme and proportion of cases that were affected by individual pathway alterations was plotted per subgroup, and across series.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: posterior palate


title: TAM_PP rep3


title: B16_Setdb1 [B253T46]


title: TAM_PP rep2


title: EBF1-dTAG_C, 0h, rep1


title: Ascl1_shTip60#3_H2AZ_day2_rep1


title: Ascl1_shTip60#2_H2AZ_day2_rep2

source_name: Ascl1_shTip60#2_H2AZ day2


title: B16_Ctrl [B253T44]


title: 2D3: 2D cultured iRECs (p53), self assembly

city: Zurich

first: Soeren

middle: S.

last: Lienkamp

address: Winterthurerstrasse 190

department: Institute of Anatomy

country: Switzerland

institute: University of Zurich

data_processing:
Library preparation and RNA sequencing was performed by Novogene (HK).
Fastq files were uploaded on the Galaxy platform and further processed with the usegalaxy.eu server.
Sequencing quality check with FastQC (version 0.72)
Paired reads were trimmed with Trim Galore! (version 0.4.3)
Trimmed paired reads were aligned to the reference mouse genome mm10 with RNA STAR (version 2.6.0b-1)
Reades were counted with featureCounts (version 1.6.3)
Genome_build: mm10
Supplementary_files_format_and_content: Differential expression analysis was run with DESeq2 (version 1.22.1) considering each culturing condition and individual replicate (cell passage) as a factor, compared to the 2D control.

source_name: induced renal tubular epithelial cells

growth_protocol: 7 days incubation in Renal Epithelial Growth Medium (REGM) with media change every 48h.

extract_protocol: Total RNA was extracted using the QIAzol Lysis Reagent (Qiagen, no. 79306), and isolated with the RNeasy Plus Universal Mini Kit (Qiagen, no. 73404), according to the manufacturer’s instructions.

value: induced renal tubular epithelial cells

tag: passage

tag: culture condition

tag: dispensing method

value: manual

tag: microenvironment

value: REGM


title: EBF1-dTAG_N, 0h, rep2


title: con_PP rep3

source_name: posterior palate

tag: strain

tag: tissue


title: Ascl1_shTip60#2_H2AZ_day2_rep1

city: Stanford

first: Justyna

last: Janas

address: 265 Campus Drive

institute: Stanford University

tag: genotype

tag: cell type


title: con_PP rep2


title: 2D2: 2D cultured iRECs (p48), self assembly


title: B16 [B253T43]


title: Ascl1_shNTC_H2AZ_day2_rep2

source_name: Ascl1_shNTC_H2AZ day2

tag: antibody


title: 2D1: 2D cultured iRECs (p35), self assembly


title: TAM_AP rep3

source_name: anterior palate treated with tamoxifen

value: anterior palate


title: Ascl1_shNTC_H2AZ_day2_rep1

value: H2A.Z (Active Motif, 39113)


title: con_PP rep1


title: TAM_AP rep1


title: TAM_AP rep2


title: Printed2: 3D cultured, bioprinted iRECs (p48) in Fibrin/Collagen, guided-growth

value: inkjet bioprinting

value: REGM, Fibrin, Collagen I


title: DN_wt_d8_1

city: Freising

first: Gustavo

middle: P.

last: de Almeida

state: Bavaria

address: Liesel-Beckmann-Str. 1

department: Division of Animal Physiology and Immunology

institute: Technical University of Munich

description:
L20-Seq46_S8
counts_expression_matrix_batchB.tsv

data_processing:
Demultiplexing: Reads were demultipled with the bcl2fastq software (v2.20.0.422).
Pipeline: Reads were processed using snakemake pipelines as indicated under (https://gitlab.lrz.de/ImmunoPhysio/bulkSeqPipe). Parameters are provided in the configuration (see "config.yaml").
Filtering: Reads were filtered using Trimmomatic v0.36.
Mapping: STAR v2.5.3a was used for mapping to annotation release #91 and genome build #38 from Mus musculus (Ensembl). Multimapped reads were discarded.
Differential expression: DESeq2 v1.24.0 was used for differential expression analysis. Differences for genes with a Basemean > 50, an absolute log2 fold change >1, an adjusted p-value <0.05 and more than 10 counts in at least 2 samples were considered significant.
Assembly: GRCm38 (release 91)
Supplementary files format and content: The .tsv files contain the read counts for each gene (rows) in each sample (columns).

source_name: small intestine lamina propria

extract_protocol:
Small intestines were removed, digested using 240 mg/ml Liberase TL and 150 μg/mL DNase I, DPs and DNs were sorted with an Aria Fusion and RNA was harvested using Agencourt RNAdvance Cell v.2 kit.
TotalRNA was isolated using the RNAdvance Cell v2 kit (Beckmann-Coulter). cDNA synthesis was performed with the SMART-Seq v4 Ultra Low Input RNA kit (takara) following the manufacturers protocol with 14 cycles of PCR amplification. Input amount were 9.5µl of each RNA sample. cDNA was measured with Bioanalyzer DNA HS Chip (Agilent) and 300pg of amplified cDNA were used for library preparation with the Nextera XP DNA library Preparation Kit (Illumina). Libraries were analyzed with a Bioanalyzer DNA HS Chip (Agilent) and quantified by qPCR following guidelines from Illumina and using Kapa SYBR mastermix (Kapa Biosystems). After the normalization of all libraries to 2nM, 14 samples each were pooled and sequenced on three single-end runs (1x100bp, dual-index) on a HiSeq2500 (Illumina) using HiSeq Rapid v2 chemistry (Illumina).

treatment_protocol: C57BL/6 mice received 5x103 CD45.1 congenic INTEGRA OT-1 T-cells (day -1), an Lm-Ova infection (1000 cfu i.v., day 0), and tamoxifen (100 mg/kg in corn oil i.p.) on days 24 and 25. Mice were re-challenged with VSV-Ova (2x106 pfu i.v.) on day 32 and samples were collected after 2 and 8 days and for mice without re-infection.

value: small intestine lamina propria

tag: cell line

value: CD8+ T cell

value: CD103-ERT2-Cre-zsGreen (INTEGRA)

tag: group

value: VSV-wt

tag: subpopulation

value: DN

tag: time

tag: batch

value: B

tag: mouse

tag: replicate

tag: zsgreen

value: Neg

tag: lane

tag: ID


title: rtTA_shNTC_H2AZ_day2_rep2

source_name: rtTA_shNTC_H2AZ day2

value: E13.5 fibroblast

tag: time post-induction


title: rtTA_shNTC_H2AZ_day2_rep1


title: Collagen3: 3D cultured iRECs (p53) in Collagen, self assembly

tag: passage

tag: culture condition

tag: dispensing method

tag: microenvironment

value: REGM, Collagen I


title: con_AP rep3

source_name: anterior palate

tag: strain

tag: age

tag: tissue


title: DN_wt_d8_3

description:
L22-Seq46_S10
counts_expression_matrix_batchB.tsv

tag: cell line

tag: cell type

tag: genotype

tag: group


title: Printed1: 3D cultured, bioprinted iRECs (p35) in Fibrin/Collagen, guided-growth


title: DN_ova_d8_2

description:
L18-Seq46_S6
counts_expression_matrix_batchB.tsv

value: VSV-OVA

tag: subpopulation

tag: time

tag: batch

tag: mouse


title: IgG_b1_rep2

tag: antibody

value: IgG


title: IgG_b1_rep3

tag: time post-induction


title: DN_ova_d8_1

description:
L17-Seq46_S5
counts_expression_matrix_batchB.tsv

tag: replicate

tag: zsgreen

tag: lane

tag: ID


title: Collagen2: 3D cultured iRECs (p48) in Collagen, self assembly

value: induced renal tubular epithelial cells

tag: passage

tag: culture condition

tag: dispensing method

value: manual

tag: microenvironment


title: DN_ova_d8_3

description:
L19-Seq46_S7
counts_expression_matrix_batchB.tsv

tag: tissue

tag: cell line

tag: cell type


title: con_AP rep2

tag: strain

tag: age

value: anterior palate


title: Collagen1: 3D cultured iRECs (p35) in Collagen, self assembly


title: con_AP rep1


title: DP_wt_d8_5

description:
L8-Seq46_S8
counts_expression_matrix_batchB.tsv

tag: genotype

tag: group

tag: subpopulation

value: DP

tag: time

tag: batch

value: Pos


title: IgG_b1_rep1

tag: time post-induction

tag: antibody


title: Ascl1_acH2AZ_tauPos_day5_rep3

source_name: Ascl1_acH2AZ_tauPos day5


title: Ce-49 sh 5

description: BGI_Hong Kong

data_processing:
STAR v2.7.9
Sequence reads were mapped to referene sequene (hg19) with default setting
Read count extraction were performed using Subread (ver2.0.3)'s featureCount with Gencode v19 annoation database.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include gene id, gene length, and raw count values for each Sample

source_name: xenografted tumor

extract_protocol:
Total RNA extraction
Standard RNA-seq proocol

value: xenografted tumor

value: leukemia cells

value: wt

tag: treatment

value: Ce-49 sh aptaDiR


title: Printed3: 3D cultured, bioprinted iRECs (p53) in Fibrin/Collagen, guided-growth

tag: passage

value: inkjet bioprinting

value: REGM, Fibrin, Collagen I


title: Fibrin3: 3D cultured iRECs (p53) in Fibrin, self assembly

tag: culture condition

value: REGM, Fibrin


title: DP_wt_d8_3

description:
L6-Seq46_S6
counts_expression_matrix_batchB.tsv

value: small intestine lamina propria

value: CD8+ T cell

value: CD103-ERT2-Cre-zsGreen (INTEGRA)

value: VSV-wt

value: B

tag: mouse

tag: replicate

tag: zsgreen

tag: lane

tag: ID


title: Ce-49 sh 4

description: BGI_Hong Kong

tag: tissue

tag: cell line

tag: cell type


title: Ascl1_acH2AZ_tauPos_day5_rep2

tag: genotype

value: E13.5 fibroblast


title: Fibrin2: 3D cultured iRECs (p48) in Fibrin, self assembly

value: induced renal tubular epithelial cells

tag: dispensing method

value: manual

tag: microenvironment


title: Ce-49 sh 3

description: BGI_Hong Kong


title: Ascl1_acH2AZ_tauPos_day5_rep1


title: Fibrin1: 3D cultured iRECs (p35) in Fibrin, self assembly


title: DP_wt_d8_1

description:
L4-Seq46_S4
counts_expression_matrix_batchB.tsv

tag: group

tag: subpopulation

value: DP

tag: time

tag: batch


title: Ce-49 sh 2

description: BGI_Hong Kong

tag: treatment


title: Ascl1_acH2AZ_day2_rep3

source_name: Ascl1_acH2AZ day2

tag: time post-induction

tag: antibody


title: DP_ova_d8_2

description:
L2-Seq46_S2
counts_expression_matrix_batchB.tsv

value: VSV-OVA

tag: mouse

tag: replicate

value: Pos


title: Matrigel2: 3D cultured iRECs (p48) in Matrigel, self assembly

tag: passage

tag: culture condition

value: REGM, Matrigel


title: DP_ova_d8_1

description:
L1-Seq46_S1
counts_expression_matrix_batchB.tsv

tag: tissue

tag: zsgreen

tag: lane

tag: ID


title: Matrigel3: 3D cultured iRECs (p53) in Matrigel, self assembly

tag: cell type

tag: dispensing method


title: Ascl1_acH2AZ_day2_rep1

tag: genotype


title: AZA 5

description: BGI_Hong Kong

value: xenografted tumor

tag: cell line

value: leukemia cells

value: wt


title: Ascl1_acH2AZ_day2_rep2


title: Matrigel1: 3D cultured iRECs (p35) in Matrigel, self assembly

tag: microenvironment


title: DN_wt_d8_5

description:
L24-Seq46_S12
counts_expression_matrix_batchB.tsv

tag: group

tag: subpopulation

value: DN

tag: time

tag: batch

value: Neg


title: Ce-49 sh 1

description: BGI_Hong Kong

tag: treatment

value: Ce-49 sh aptaDiR


title: 64-2P

source_name: Whole embryo

value: whole embryo

value: polysomal


title: AZA 4

description: BGI_Hong Kong


title: rtTA_acH2AZ_day2_rep3

source_name: rtTA_acH2AZ day2

tag: time post-induction

tag: antibody


title: DN_ova_d2_4

description:
L42_S14
counts_expression_matrix_batchA.tsv

value: small intestine lamina propria

value: CD8+ T cell

value: CD103-ERT2-Cre-zsGreen (INTEGRA)

value: A

tag: mouse

tag: replicate


title: MEF+Ascl1+shTip60#3_day5_b2_rep2

data_processing:
Raw reads were trimmed for base call quality (PHRED score ≥ 21) using skewer 0.2.2 (Jiang et al., 2014).
Transcript quantification was performed using mm10 reference transcriptome and salmon 1.4.0 (Patro et al., 2017).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tsv files containig TPM values

source_name: MEF+Ascl1+shTip60#3 day5

extract_protocol:
RNA was harvested using Trizol.
Libraries were prepared using NEBNext Ultra DNA Library Prep Kit or TruSeq mRNA Library Prep Kit, following standard protocols.

treatment_protocol: MEFs were transduced with indicated lentiviruses. rtTA and Ascl1+rtTA transduced MEFs were treated with doxycycline (dox) two days post-infection to induce transgene expression. The cells were transferred into N3 medium (DMEM/F12, N2 supplement, insulin) containing dox the following day. The medium was refreshed every 3 days.

value: E13.5 fibroblast

tag: time post-infection

value: 7 days

tag: time post-dox

value: 5 days


title: AZA 3

description: BGI_Hong Kong

tag: tissue


title: DN_ova_d2_3

description:
L41_S13
counts_expression_matrix_batchA.tsv

tag: cell type

value: VSV-OVA

tag: zsgreen

tag: lane

tag: ID


title: rtTA_acH2AZ_day2_rep2

data_processing:
Library strategy: Cut&Tag
Reads were trimmed using cutadapt and aligned with Bowtie2 (v 2.3.5.1) to mm10 reference genome.
Peaks were called using MACS2. Reproducible peaks for each condition were identified using IDR (idr≤0.1) or by overlap thresholding (for histone Cut&Tag). Reproducible peaks were aggregated, read counts for each region were obtained using featureCounts package followed by normalization and differential accessibility analysis using DESeq2.
Bigwig files were produced with deepTools (Ramirez et al., 2014).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text file containing normalized read counts as determined for the aggregated peak set; tar containing normalized average signal files

tag: genotype


title: MEF+Ascl1+shTip60#3_day5_b2_rep1


title: DN_ova_d2_2

description:
L40_S12
counts_expression_matrix_batchA.tsv

tag: cell line

tag: group


title: AZA 2

description: BGI_Hong Kong


title: DP_ova_d8_3

description:
L3-Seq46_S3
counts_expression_matrix_batchB.tsv

tag: subpopulation

value: DP

tag: time

value: B

value: Pos


title: rtTA_acH2AZ_day2_rep1


title: DN_ova_d2_1

description:
L39_S11
counts_expression_matrix_batchA.tsv

tag: batch


title: MEF+Ascl1+shTip60#2_day5_b2_rep2

source_name: MEF+Ascl1+shTip60#2 day5


title: MEF+Ascl1+shTip60#2_day5_b2_rep1


title: AZA 1

description: BGI_Hong Kong

value: xenografted tumor

value: leukemia cells

value: wt

tag: treatment


title: Ascl1_H2AZ_tauPos_day5_rep2

source_name: Ascl1_H2AZ_tauPos day5

tag: time post-induction

tag: antibody

value: H2A.Z (Active Motif, 39113)


title: MEF+Ascl1+shNTC_day5_b2_rep2

source_name: MEF+Ascl1+shNTC day5


title: DN_wt_d2_5

description:
L38_S10
counts_expression_matrix_batchA.tsv

value: VSV-wt

value: DN

tag: mouse

tag: replicate

value: Neg


title: PBS 5

description: BGI_Hong Kong

value: PBS


title: Ascl1_H2AZ_tauPos_day5_rep1


title: DN_wt_d2_3

description:
L36_S8
counts_expression_matrix_batchA.tsv

value: small intestine lamina propria

value: CD8+ T cell

value: CD103-ERT2-Cre-zsGreen (INTEGRA)


title: PBS 3

description: BGI_Hong Kong


title: Ascl1_H2AZ_day2_rep3

source_name: Ascl1_H2AZ day2

value: E13.5 fibroblast


title: DN_wt_d2_4

description:
L37_S9
counts_expression_matrix_batchA.tsv

value: A


title: PBS 4

description: BGI_Hong Kong


title: MEF+Ascl1+shNTC_day5_b2_rep1

tag: time post-infection

value: 7 days

tag: time post-dox

value: 5 days


title: Ascl1_H2AZ_day2_rep2

tag: cell type


title: MEF+Ascl1+shNTC_day2_b2_rep1

source_name: MEF+Ascl1+shNTC day2

value: 4 days

value: 2 days


title: PBS 1

description: BGI_Hong Kong

tag: tissue

value: xenografted tumor


title: PBS 2

description: BGI_Hong Kong

value: leukemia cells


title: Ascl1_H2AZ_day2_rep1


title: MEF+shTip60#3_day7_rep2

source_name: MEF+shTip60#2 day7


title: DN_wt_d2_1

description:
L34_S6
counts_expression_matrix_batchA.tsv

tag: zsgreen

tag: lane


title: rtTA_H2AZ_day2_rep3

source_name: rtTA_H2AZ day2

tag: genotype