title: Sample 2, 10µM vehicle Day 1


title: Sample 3, 10µM vehicle Day 1

status: Public on Mar 30 2023

type: SRA

city: Erlangen

first: Christian

last: Büttner

address: Schwabachanlage 10

department: Institut of Human Genetics

country: Germany

institute: University Hospital Erlangen

library_source: transcriptomic

data_processing:
After pooled sequencing 100 bp single-end reads on a HiSeq 2500 platform (Illumina) reads were converted to a FASTQ format with bcl2fastq (version 2.17.1.4).
Sequences were quality- and adapter-trimmed using cutadapt (version 1.18).
The pre-processed reads were mapped to the Mus musculus reference genome GRCm38.6 and Ensemble gene model 102, using spliced transcripts alignment to a reference (STAR) software (Version 2.7.8.a).
Strand specific gene level quantification with default parameters regarding overlap was performed using featureCounts (Version 2.0.1) relative to Ensembl gene model for mouse version 102.
Assembly: GRCm38.6
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Oli-Neu

growth_protocol: The mouse oligodendrocyte precurser cell line Oli-Neu was grown in T75 cell culture flasks (Thermo Fisher Scientific, Waltham, USA) using SATO medium containing Dulbecco’s modified Eagle’s medium (DMEM; Thermo Fisher Scientific) supplemented with 2 %. heat-inactivated horse serum (Themo Fisher Scientific), 5 µg/ml insuline (Merck, Darmstadt, Germany), 1% penicilline/streptomycine (10.000 U/ml) (Thermo Fisher Scientific), 1% N2 supplement (Thermo Fisher Scientific), 5 ng/ml sodium selenite (Merck), 25 µg/ml gentamicine (Merck, Darmstadt, Germany), 400 nM 3,3′,5-triiod-L-thyronine (T3) (Merck) and 520 nM L-thyroxine (T4) (Merck). Cells were maintained at 37 °C and 5% CO2 and passaged when confluency of 70–80% was reached. All cell culture materials were coated overnight at 37 °C with 0.0001 poly-ornithine (PORN) (Merck) solution. Oli-Neu cells were differentiated using PD 174265, and isolated primary OPCs using PDGF-AA (Miltenyi Biotech, Bergisch Gladbach, Germany) and FGF2 (Miltenyi Biotech). For RNA isolation, the PureLinkTM Mini Kit with PureLinkTM-DNase set (Thermo Fisher Scientific) were used according to the manufacturer’s suggestions.

extract_protocol:
Total RNA was extracted using the PureLink RNA Mini Kit (Thermo Fisher Scientific), followed by DNase treatment.
Sequencing libraries were generated from 1 mg of high-quality RNA using the TruSeq Stranded mRNA Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: Cells were treated with 10 µM Nimodipine or DMSO (Thermo Fisher Scientific) as a vehicle control.

tag: cell line

value: Oli-Neu

tag: cell type

value: oligodendrocyte precursor cells

tag: treatment

value: 10µM vehicle

tag: time

value: Day 1


title: 15: Asthma and lung cancer, unamplified

city: Sharjah

first: Rifat

last: Hamoudi

address: University city

country: United Arab Emirates

institute: University of Sharjah

description: column G

data_processing:
Ion Torrent Suite software version 5.12.1
Fragments per kilobase million (FPKM) normalization
Burrows-Wheeler Aligner (BWA)-short, BWA-long, Sequence Search and Alignment by Hashing Algorithm (SSAHA) and Super-maximal Exact Matching (SMEM), within the TMAP suite were implemented
Assembly: hg19_AmpliSeq_Transcriptome_21K_v1
Supplementary files format and content: tab-delimited read counts in one file

organism: Homo sapiens

source_name: Asthma and lung cancer, unamplified

extract_protocol:
RNA was extracted using recover all (Invitrogen) kit
10 ng of RNA was used to prepare library using Ion Ampliseq Human gene expression kit

tag: tissue

value: Adenocracinoma, stage 3


title: paVICs, DMSO+LPC, rep2

city: Houston

first: K.

middle: Jane

last: Grande-Allen

state: TX

address: 6500 Main St

department: Bioengineering

country: USA

institute: Rice University

data_processing:
Novogene in-house perl script for adapter trimming and filtering of low quality reads
Trimmed, high quality reads were mapped to Sscrofa11.1 using Hisat2 v2.0.5
In R (v4.1.1), gene count matrices were built with Rsamtools (v2.8.0) and GenomicFeatures (v1.44.2).
Batch correction was performed using Combat_seq function of sva (3.40.0)
Count normalization and differential gene expression was performed using DESeq2 (1.32.0)
Normalized counts and differential genes were annotated using biomaRt (2.48.3)
Assembly: Sscrofa11.1
Supplementary files format and content: comma-separated text files include normalized counts for each sample
Supplementary files format and content: comma-separated text files include differential gene expression

organism: Sus scrofa

source_name: primary isolation 2

growth_protocol: Primarily isolated paVICs were thawed from freezing, passaged once and then seed on 10 cm petri dishes with 10% bovine growth serum (BGS) in 1:1 DMEM:F12 with 10 mM HEPES and antibiotics in a humidified incubator at 37C at 5% CO2.

extract_protocol:
RNA was harvested into TRIzol and purfied using a Direct-zol RNA microprep spin kit with DNAse treatment. RNA was eluted into RNAse free water.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strandsynthesis was performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. 3’ ends of fragments were adenylated and Adaptor with hairpin loop structure were ligated. Library fragments (~370-420 bp) were purified with AMPure XP system (Beckman Coulter, Beverly, USA). PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCRprimers and Index (X) Primer. PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Cells were treated with 1:1 DMEM:F12 with 1%BGS, 10 mM HEPES and antibiotics with the listed treatments for 24 hours in a humidified incubator at 37C at 5% CO2.

value: aortic valve interstitial cells

tag: genotype

value: WT

value: 0.6% DMSO + 10 uM LPC in EtOH


title: Islet40

city: Farmington

first: Efthymios

last: Motakis

state: CT

address: 10 Farmington Drive

department: Computational Sciences

institute: The Jackson Laboratory

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Reads alignment with STARsolo
Estimation and removal of ambient RNA by SoupX
Genetic demultiplexing for the 12 mutiplexed libraries by Demuxlet and removal of doublets
Cluster-based cell QC: the cell clusters are generated by Seurat's processing pipeline and the cells with > 500 features & < 50% MT & >1000 UMIs are kept for further analysis
Doublet identification by Scrublet, DoubletFinder and doublet visualization in the cell clusters
Second step cluster-based cell QC: the cell clusters are re-generated with the cleaner data by Seurat's processing pipeline and the cells with > 1400 features & < 40% MT are kept for further analysis. Keep cells of particular cell types (marker-based pre-annotation) even if the do not satisfy the features criterion.
Data integration by Harmony and integrated data clustering
Visualize the estimated doublets on the integrated data clusters, remove all scrublet doublets plus while custers if they are enriched in such doublets
Keep the clean data for downstream analysis: final cell annotation, differential expression, subclustering
Assembly: HG38
Supplementary files format and content: CellRanger output files

source_name: Pancreatic islets

growth_protocol: Cultured overnight in PIM(S) [ProdoLabs] prior to dissociation and 10X Genomics single cell capture

extract_protocol:
10X Genomics standard procedures for sample dilution and single cell capture
10X Genomcis standard procedures for library construction

treatment_protocol: Islets treated with Accutase for 10 minutes at 37 degrees Celsius and gentle pipetting

value: Pancreatic islets

tag: chemistry

tag: disease state

value: PreDiabetic

tag: Sex

value: Female

tag: bmi

tag: race

value: Hispanic

tag: age

tag: unos

tag: center

value: Southern California IsletCell Resource Center

tag: Cause of death

value: Cerebrovascular/stroke

tag: library id


title: 13: Asthma and lung cancer, unamplified

description: column F


title: Sample 1, 10µM vehicle Day 1


title: Sample 4, 10µM Nimodipine, Day 1

value: 10µM Nimodipine


title: Islet39

description: 10x Genomics

value: White


title: 8: Lung cancer, unamplified

description: column E

source_name: Lung cancer, unamplified

value: Neoplasm malignant, stage 2


title: paVICs, DMSO+LPC, rep1

source_name: primary isolation 1


title: Islet38

description: 10x Genomics

value: NonDiabetic

value: Male

value: Scharp-Lacy

value: Head trauma


title: paVICs, DMSO+ethanol control, rep3

source_name: primary isolation 3


title: 19: Severe asthma, unamplified

description: column J

source_name: Severe asthma, unamplified

value: bronchial biopsy


title: Islet44

description: 10x Genomics

value: AfricanAmerican

value: UPenn


title: 5: Lung cancer, unamplified

description: column D

value: Squamous cell carcinoma, stage 4


title: Islet37

description: 10x Genomics

value: Pancreatic islets

value: Head trauma - gunshot wound/suicide


title: paVICs, DMSO+ethanol control, rep2

value: aortic valve interstitial cells

value: WT


title: 3: Lung cancer, unamplified

description: column C

value: Neoplasm malignant, stage 4


title: Islet34

description: 10x Genomics

value: Hispanic


title: Sample 2, 10µM Nimodipine, Day 1

value: Oli-Neu

value: oligodendrocyte precursor cells

value: 10µM Nimodipine

value: Day 1


title: 1: Lung cancer, unamplified

description: column B

value: NSCLC, stage 4


title: Sample 1, 10µM Nimodipine, Day 1


title: Islet33

description: 10x Genomics

value: Female

value: White

value: Cerebrovascular/stroke


title: paVICs, DMSO+ethanol control, rep1


title: 20: Severe asthma, Amplified

description: column J

source_name: Severe asthma, Amplified

value: bronchial biopsy


title: Islet31

description: 10x Genomics

value: Male

value: Scharp-Lacy


title: 18: Severe asthma, Amplified

description: column I


title: Islet30

description: 10x Genomics

value: Pancreatic islets


title: 14: Severe asthma, Amplified

description: column F


title: NRF2_ROM_H4ac_spikein

city: New York

first: Dimitris

last: Karagiannis

state: NY

institute: Columbia University

library_source: genomic

data_processing:
CUT&Tag reads of KP cell samples were mapped to the mouse genome assembly mm10 using Bowtie2 (v2.3.5.1, parameters: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700).
Potential PCR duplicates were removed by the function "MarkDuplicates" (parameter: REMOVE_DUPLICATES=true) of Picard (v2.24.2). Genomic enrichments of CUT&Tag signals were generated using deeptools (v3.3.2, parameters bamCoverage --normalizeUsing CPM --binSize 25 --smoothLength 100) and visualized using IGV.
Peaks were called using MACS2 (parameters: --f BAMPE -g mm --broad). Consensuses of H3K27ac, H4ac and BRD4 peaks across conditions were generated by the ‘cat’ function (Linux) and ‘sort’ and ‘merge’ functions of bedtools (v2.27.1).
The read counts of H3K27ac, H4ac and BRD4 CUT&Tag data in genomic elements were measured by featureCounts (v2.0.0). Differential analysis was performed using DEseq2(v1.32.0).
Peak annotation was done using ChIPseeker56(v1.28.3). Heatmaps were generated using deeptools (v3.3.2) functions computeMatrix and plotHeatmap.
Assembly: mm10
Supplementary files format and content: bam, bam index(bai) and bigWig for genomic distribution analysis, txt for spike-in scale factor determination
Library strategy: CUT&Tag

molecule: genomic DNA

growth_protocol: KP cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics (P/S) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
CUT&Tag was performed as described previously23, with an additional step of light fixation to better preserve histone acetylation/TF binding. In brief, 1 × 105 cells were lightly fixed with 0.1% paraformaldehyde 5’, neutralized by Glycine 125mM, and washed once with 1 ml of wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine (Sigma-Aldrich), 1× Protease inhibitor cocktail (Roche)). Concanavalin A-coated magnetic beads (Bangs Laboratories) were washed twice with binding buffer (20 mM HEPES pH 7.5, 10 mM KCl, 1 mM MnCl2, 1 mM CaCl2). 10 µl/sample of beads were added to cells in 400ul of wash buffer and incubated at room temperature for 15 min. Beads-bound cells were resuspended in 100 µl of antibody buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 0.06% Digitonin (Sigma-Aldrich), 2 mM EDTA, 0.1% BSA, 1× Protease inhibitor cocktail and incubated with indicated antibodies (Supplementary Table 3) or normal rabbit IgG (Cell Signaling) at 4 degrees overnight on nutator. After being washed once with Dig-wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 0.05% Digitonin, 1× Protease inhibitor cocktail), beads-bound cells were incubated with 1 µl Guinea pig anti-rabbit secondary antibody (Antibodies Online ABIN101961) and 2 µl  Hyperactive pA-Tn5 Transposase adapter complex in 100 µl Dig-300 buffer (20 mM HEPES•NaOH, pH 7.5, 0.5 mM Spermidine, 1× Protease inhibitor cocktail, 300 mM NaCl, 0.01% Digitonin) at room temperature for 1 h. Cells were washed three times with Dig-300 buffer to remove unbound antibody and Tn5 and then resuspended in 300 µl of tagmentation buffer (10 mM MgCl2 in Dig-300 buffer) and incubated at 37 °C for 1 h. 10 µl of 0.5 M EDTA, 3 µl of 10% SDS and 5 µl of 10 mg/ml Proteinase K were added to each sample and incubated at 50 °C for 1 h to terminate tagmentation. DNA was purified using chloroform isoamyl alcohol (Sigma Aldrich) and eluted with 25 µl ddH2O. For H3K27ac, 2ul of SNAP-ChIP K-AcylStat panel nucleosomes (EpiCypher) was added as spike-in control at the primary antibody incubation step. For H4ac, 5000 S2 Drosophila cells were added at the cell-bead binding step.
For library amplification, 21 µl of DNA was mixed with 2µL i5 unique index primer (10 µM), 2 µL i7 unique index primer (10 µM) and 25 µL NEBNext High-Fidelity 2X PCR Master Mix (NEB) and subjected to the following PCR program: 72℃, 5 min; 98℃, 30 sec; 13 cycles of 98℃, 10 sec and 63℃, 10 sec; 72℃, 1 min and hold at 10℃. To purify the PCR products, 1.1× volumes of pre-warmed Ampure XP beads (Beckman Coulter) were added and incubated at room temperature for 10 min. Libraries were washed twice with 80% ethanol and eluted in 20 µl of 10 mM Tris-HCl, pH 8.  Libraries were sequenced on an NextSeq 550 platform (Illumina, 75 cycles High Output Kit v2.0) and 75-bp paired-end reads were generated. To determine global level differences in histone acetylation signal we used spike-in controls.  Files resulting from 4 sequencing lanes were concatenated into a single file for each condition.

treatment_protocol: 200k KP cells were plated in 6-well plates in RPMI supplemented with 10% FBS and P/S. The next day cells were treated with DMSO or 5nM Romidepsin in RPMI for 16h. 3 biological replicates per condition are included

value: LUAD

value: NRF2 OE

value: ROM

tag: antibody


title: EV_ROM_H4ac_spikein

tag: cell line

value: Empty Vector


title: NRF2_DMSO_H4ac_spikein

tag: cell type

value: DMSO


title: 9: Lung cancer, Amplified

description: column D

source_name: Lung cancer, Amplified

value: Squamous cell carcinoma, stage 2


title: Sample 3, 10µM Nimodipine, Day 1

value: Oli-Neu

value: oligodendrocyte precursor cells

tag: treatment


title: Islet29

description: 10x Genomics

value: NonDiabetic

value: Wisconsin


title: Islet28

description: 10x Genomics

value: Hispanic


title: EV_DMSO_H4ac_spikein


title: NRF2_ROM_BRD4_rep1


title: NRF2_ROM_BRD4_rep2


title: 49333_LD7-2

first: Yuqi

last: Zhao

address: 273 Main Street A4

institute: City Of Hope

description:
49333_LD7-2
COHP_49333
LD7_vs_LT7_Diff_Peaks.bed

data_processing:
ATAC-seq reads were trimmed for adapters and cleaned up using fastp.
The clean reads were mapped with HISAT2 v2.1.0 in default paired-end mode to reference genome hg38.
Duplicated aligned reads were removed using Picard MarkDuplicates tool with the command REMOVE_DUPLICATES=true.
To detect and separate accessible loci in each sample, we used MACS version 2.2.5 with callpeak -g hs -B -q 0.01.
macs2 version 2.2.5 bdgdiff with deafaut parameters was adopted to detect the differential peaks between groups.
Assembly: hg38
Supplementary files format and content: The BED files from macs2 bdgdiff contains the differential analysis of ATAC-seq between two conditions.
Supplementary files format and content: The records in the BED files satisfy logLR =3, --min-len=200, and --max-gap=100 in macs2 bdgdiff.

source_name: CML patient blood leukapheresis

growth_protocol: Patient derived primary cells were kept in RPMI-1640 medium during imatinib treatment and switched to QBSF60 medium when treated with ICG-001 and DMSO.

extract_protocol:
Cell pellet of 50,000 cells per sample was used for library preparation
Sequencing libraries were constructed using a modified version of the Illumina Nextera DNA Sample prep kit.

treatment_protocol: CML cells were treated with 10 µM imatinib for 8 days and column enriched deep-quiescent subset of resistant (R) cells was treated with 10 µM ICG-001 and/or DMSO

value: CML patient blood leukapheresis

value: CML

value: CCR7+ LIs

value: CCR7+ LIs treated with DMSO for 6 days


title: 7: Lung cancer, Amplified

description: column C

value: Adeno carcinoma


title: 4: Lung cancer, Amplified

description: column B

value: Adeno carcinoma, stage 3


title: 49332_LD7-1

description:
49332_LD7-1
COHP_49332
LD7_vs_LT7_Diff_Peaks.bed


title: 49331_LT7-2

description:
49331_LT7-2
COHP_49331
LD7_vs_LT7_Diff_Peaks.bed

value: CCR7+ LIs treated with ICG-001 for 6 days


title: 10: Lung cancer, Amplified

description: column K

value: Squamous cell carcinoma, stage 4


title: NRF2_DMSO_BRD4_rep1

value: LUAD

value: NRF2 OE


title: NRF2_DMSO_BRD4_rep2

value: DMSO


title: R1

city: shanghai

first: li

last: li

state: c

address: kangxin

country: China

institute: university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to A. thaliana genome (downloaded from ENSEMBL, version 21) using Bowtie 1.0.0 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Trinity was used for assembly with the parameters --min_kmer_cov 3 --normalize_reads
The number of raw reads unambiguously aligned to ORFs in both RNA-Seq and ribosome profiling data sets from two biological replicates were used to generate gene read counts, which were normalized as reads per million of the total mapped reads (rpm) or reads per kilobase per million of the total mapped reads (rpkm)
Genome_build: A fasta file the generate with Trinity, named Trinity.fasta
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample ...

organism: Shiraia bambusicola

source_name: hypha

extract_protocol:
Purified polysomes were digested with RNAse I (1.5U/1OD/1 μl) at 22 °C for 10 min, loaded directly onto 15–60 % sucrose gradient and centrifuged at 4 °C, 237,000xg for 1.5 h.Total RNA was extracted using TRIzol reagent and spiked with ERCC RNA Spike-In Mix (Ambion). rRNA was depleted using RiboMinus Plant Kit (Ambion), and randomly fragmented by alkaline lysis in alkaline fragmentation solution (2 mM EDTA, 12 mM Na2CO3, 87 mM NaHCO3) at 95 °C for 40 min
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hypha

value: post natal day 21

value: experment type


title: D1

value: post natal day 22


title: EV_DMSO_BRD4_rep2

value: Empty Vector


title: EV_ROM_BRD4_rep1

value: ROM


title: 49330_LT7-1

description:
49330_LT7-1
COHP_49330
LD7_vs_LT7_Diff_Peaks.bed

value: CML patient blood leukapheresis


title: B1

value: wild type


title: Islet32

description: 10x Genomics

value: Pancreatic islets

value: Male

value: White

value: Scharp-Lacy

value: Cerebrovascular/stroke


title: EV_DMSO_BRD4_rep1


title: 49281_D7-2

description:
49281_D7-2
COHP_49281
DR_vs_D7_Diff_Peaks.bed

value: CML

value: CCR7+ LIs

value: R cells enriched for CCR7+ LIs


title: 49280_D7-1

description:
49280_D7-1
COHP_49280
DR_vs_D7_Diff_Peaks.bed


title: NRF2_ROM_H4ac_rep2

value: LUAD

value: NRF2 OE


title: NRF2_DMSO_H4ac_rep1

value: DMSO


title: NRF2_DMSO_H4ac_rep2


title: 49276_DR-1

description:
49276_DR-1
COHP_49276
UN_vs_DR_Diff_Peaks.bed

value: Resistant (R) cells

value: Treated with imatinib for 8 days


title: CantonS Heads, ZT22, Replicate 2

city: Waltham

first: Albert

middle: Dayuan

last: Yu

state: MA

address: 415 South St.

department: Molecular and Cell Biology

institute: Brandeis University

description:
CantonS Drosophila
BuTT-Seq Performed on CantonS Heads

data_processing:
Read 1 corresponds to Read 1, Read 2 corresponds to the UMI, and Read 3 corresponds to Read 2. UMIs were extracted from Read 2 and appended to Read 1 and 3 individually using umi_tools extract with the following command: extract -I READ2_UMI --extract-method=regex --bc-pattern='^(?P<umi_1>.{{8}})' --read2-in=READ1_OR_3  --stdout=/dev/null --read2-out=OUTPUT.fq.gz (Smith et al., 2017).
Reads were trimmed using fastp and the following settings: -trim_poly_g --trim_poly_x -F 1 --adapter_sequence AAGATCGGAAGAGC --adapter_sequence_r2 CTGTCTCTTATA (Chen et al., 2018).
Reads were subject to 2-pass mapping with STAR to dm6 using the following settings: --alignMatesGapMax 100000 --outSAMstrandField intronMotif --outFilterMismatchNoverLmax 0.05 --outFilterMultimapNmax 1 --outSJfilterReads Unique.
Aligned reads were converted to BAM files with Samtools, and deduplicated using umi_tools dedup (Li et al., 2009)
Small RNAs and exon 3’ ends were computationally removed using SAMtools and a bed file containing small RNAs and exon 3’ ends extracted from RefSeq gene annotations, and soft clipping was removed prior to single-nucleotide read conversion using a custom script modified from ngsutils (Breese & Liu, 2013)
Reads were truncated to the first nucleotide of Read 2 using a custom python script
Counts tables were generated using featurecounts raw count tables were imported into DESeq2, which we used to produce normalized count tables for correlation analyses and scaling factors (Liao et al, 2014)(Love et al, 2014).
Scaling factors were used to produce normalized bigwig files for data visualization using deepTool’s bamCoverage function (Ramirez et al, 2014).
Assembly: dm6
Supplementary files format and content: Positive and negative strand-separated bigWig files normalized by signal over regions of interest using DESeq2

organism: Drosophila melanogaster

source_name: Heads

growth_protocol: Flies were raised on standard-yeast agar up to an age of 10 days, where they were moved to entrainment incubators and left to entrain for 3 days. On the fourth day, timepoints were collected every six hours.

extract_protocol:
Nascent RNA was extracted as described in Yu and Rosbash, 2023. Flies were frozen on dry ice. 5 heads were removed on dry ice and transferred into a 2ml dounce homogenizer. 500µl cell lysis buffer (10mM Tris pH7.5, 2mM MgCl2, 10mM kCl, 0.6mM spermidine, 0.2mM spermine, 3mM TCEP, 0.03% Tween-20, and 0.1% BSA)was added to each homogenizer, and heads were dounced for 10 strokes with Pestle A and 20 strokes with Pestle B.
The resulting homogenate was first filtered through a 20µM filter, then a 10µM filter. Nuclei were spun down for 1000g for 5 minutes and washed once with 500µl nuclear lysis buffer.
Supernatant was removed and nuclei were resuspended in 100µl nuclear lysis buffer (10mM HEPES-KOH pH7.6, 100mM KCl, 0.1mM EDTA, 10% Glycerol, 0.15mM Spermine, 0.5mM Spermidine, 0.1mM NaF, 0.1mM Na3VO4, 0.1mM ZnCl2, 1mM TCEP, 0.1 units/µl SUPERaseIn, and 1x cOmplete protease inhibitor) and placed on a Thermomix set to 4°C and shaking at 1400 RPM.
100µl NUN buffer (25mM HEPES-KOH, pH7.6, 300mM NaCl, 1M Urea, 1% NP-40, 1mM TCEP, 3% Empigen, 0.1 units/µl SUPERaseIn, 1x cOmplete protease inhibitor) was added dropwise while shaking. Tubes were capped and left shaking at 4°C for 10 minutes. Chromatin was pelleted in the centrifuge at 21000g for 10 minutes, and the supernatant was discarded.
The resulting chromatin pellet was resuspended in 500µl TRIzol and incubated at 60°C for 10 minutes, then transferred to a phase lock tube.
RNA was then isolated with chloroform according to standard procedure and resuspended in a 10µl Turbo DNAse reaction containing 1x Turbo DNase Buffer and 1.5µl Turbo DNase, and DNase treatment was done for 30 minutes according to protocol.
Libraries were prepared as described in Yu and Rosbash, 2023. First strand master mixes (FS-MM) were prepared with 0.5µl 10x TGIRT Buffer(100mM HEPES pH8, 500mM NaCl, 50mM MgCl2, 10mM TCEP), 0.2µl SCR2R, 0.2µl TGIRT, and 1.1µl 50% PEG3350. 2µl of FS-MM was added to 2µl RNA in a PCR strip tube, flicking and spinning down twice to mix
Assembled reactions were incubated on ice for 30 minutes. While incubating, 1µl 5mM dNTPs was mixed with 30µl 2M NaCl. After 30 minutes, 1µl dNTPs/NaCl mixture was added to TGIRT reactions and placed on the thermal cycler with the following program: 25°C for 1 minute, ramping to 60°C at 1°C/second, 60°C for 10 seconds, then holding at 4°C.
Reactions were moved on to ice and 2µl Exonuclease III, 2µl H2O, and 1µl NEBuffer 1 were added. Reactions were incubated at 37°C for 8 minutes, then moved onto ice.
To eliminate RNA from downstream reactions and disassociate TGIRT, 3µl 1M NaOH was added to each sample and heated at 95°C for 5 minutes. After cooling to room temperature, 3µl 1M HCl was added to each sample to neutralize the reaction. 24µl 95% EtOH and 24µl Ampure XP beads were added to each sample, flicked to mix, and left to incubate for 10 minutes at room temperature. Beads were washed twice with 200µl 80% EtOH and resuspended in 4.2µl H2O and 4µl supernatant was moved to fresh PCR tubes.
Second-strand synthesis master mixes (SS-MM) were prepared with 1µl TGIRT Buffer, 0.3µl MER1R, 0.3µl TGIRT, 2µl 50% PEG3350, and 0.4µl H2O. 4µl SS-MM was added to cDNA samples and assembled reactions were left to incubate on ice for 30 minutes. While incubating, 1µl 20mM dNTPs was mixed with 10µl 2M NaCl.
After 30 minutes, 2µl dNTPs/NaCl mixture was added to TGIRT and placed on the thermal cycler with the following program: 25°C for 1 minute, ramping to 60°C at 1°C/second, 60°C for 30 seconds, then holding at 4°C.
Reactions were moved on to ice, and 1µl 0.2% SDS was added to each reaction to disassociate TGIRT. Reactions were incubated 55°C, then moved to room temperature.
30µl Ampure XP beads were added to each reaction, incubated for 5 minutes at room temperature, washed twice, and then eluted in 9µl H2O.
dsDNA was added to PCR reactions containing 25µl 2x NEBNext Ultra II Q5 Master mix, 2.5µl P7 primer, 2.5µl barcoded Ad1 primer, and 11µl H2O.
The assembled PCR reaction was subject to the following PCR program: 72°C for 3 minutes, 98°C for 30 seconds, 9-15 cycles of 98°C for 15 seconds and 65°C for 30 seconds, a final extension of 72°C for 2 minutes, and hold at 10°C.
PCR reactions were cleaned with 65µl Ampure XP beads following the standard protocol and resuspended in 10µl 1x Purple Loading Dye. Samples were loaded onto an 8% TBE gel alongside 1µl of TriDye Ultra Low Range DNA ladder mixed with 9µl 1x Purple Loading Dye and run at 180v for 45 minutes. Gels were post-stained with 1x Sybr Gold for 5 minutes, and the smear above 150nt were excised into a 0.5ml tube.
0.5ml tubes had a hole poked in the bottom with a 21-gauge needle and nested inside a 2.0ml tube and centrifuged for 21000g for 3 minutes. 600µl 300mM NaCl was added to each tube, and tubes were incubated at 75°C for 15 minutes or 4°C overnight.
Supernatant and gel fragments were transferred into a Costar Spin-X Centrifuge Tube Filter with a wide-bore 1000µl pipette tip and spun for 2 minutes at 21000g. Filters were discarded and 600µl isopropanol and 0.7µl GlycoBlue was added to each tube, and left to incubate for at least 15 minutes at room temperature or in -20°C for up to overnight.
Samples were spun at 21000g for 30 minutes, washed twice with 80% EtOH, and resuspended in 7-10µl MilliQ H2O. 2µl was used for analysis on a Tapestation 4200 D1000 tape and quantified using peak quantification centered around 170nt. Samples were sequenced on a NextSeq 500 with 8bp dual index reads.
BuTT-Seq (Bulk analysis of nascent Transcript Termini)

value: Heads

tag: timepoint


title: CantonS Heads, ZT22, Replicate 1


title: CantonS Heads, ZT18, Replicate 1


title: CantonS Heads, ZT18, Replicate 2


title: EV_ROM_H4ac_rep2

value: Empty Vector

value: ROM


title: old3

city: Charleston

first: Heehwa

last: Son

address: 149 13 street

institute: MASSACHUSETTS GENERAL HOSPITAL

data_processing:
The raw fastq files were aligned using CellRanger-6.0 count with human reference (GRCh38)
Seurat package-4.3.0 in R-4.2.2 was used for downstream analysis
Assembly: GRCh38
Supplementary files format and content: Output files from Cellranger count

source_name: skin

extract_protocol:
To isolate single cell suspension, we used Whole Skin Dissociation Kit (Miltenyi Biotec 130-101-540). We excluded enzyme P. We incubated skin biopsy for 15 hrs and stained with CD45 and propidium iodide and sorted CD45+ PI- cells. Immediately after sorting, we went to the scRNA seq.
For scRNA seq step, we followed instruction of Chromium Next GEM single cell3 3' Reagent Kits v3.1 (10x Genomic). We used NextSeq 500/550 Hi Output Kit v2.5 150 cycle (illumina) for sequencing.

treatment_protocol: No treatment was done

tag: tissue

value: skin

value: CD45+ immune cells

value: No treatment


title: CantonS Heads, ZT14, Replicate 1


title: hBHD_T7

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

description: Transcriptome profile of BHD-associated kidney tumors, biological rep7

data_processing:
For the analysis, the sequence reads were trimmed BBDuk (sourceforge.net/projects/bbmap/) to remove adapter sequences and low-quality end bases (Q < 20). Alignment was performed with STAR 2.6.0a on the Hg38 reference provided by UCSC Genome Browser. the reads were trimmed toremove adapter sequences and low-quality ends and reads mapping to contaminating  sequences (e.g., ribosomal RNA, phIX control) were filtered-out.
Assembly: Hg38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: BHD kidney tumor sample

growth_protocol: The tumor/normal tissues were surgical specimens from partial and full nephrectomies performed at the Urologic Oncology Branch, National Cancer Institute.

extract_protocol:
RNA was quantified and mixed at 10ng/µl
Total RNA (100 ng) from each sample was prepared using QuantSeq 3'mRNA-Seq Library prep kit  (Lexogen, Vienna, Austria) according to manufacturer's instructions
The amplified fragmented cDNA of 300 bp in size were sequenced in single-end mode using the NovaSeq 6000(Illumina) with a read length of 100 bp

treatment_protocol: Pieces of tumor (partial or radical nephrectomy) or control kidney tissues at the time of surgery were snap frozen in liquid nitrogen and stored at -80 C.

value: kidney tumor

value: BHD

tag: gender

value: not collected


title: old2

tag: genotype


title: hBHD_T6

description: Transcriptome profile of BHD-associated kidney tumors, biological rep6

tag: disease state


title: 49327_UN-2

description:
49327_UN-2
COHP_49327
UN_vs_D7_Diff_Peaks.bed

value: CML patient blood leukapheresis

value: CML

value: Untreated bulk cells

value: Untreated


title: old1


title: hBHD_T5

description: Transcriptome profile of BHD-associated kidney tumors, biological rep5


title: EV_ROM_H4ac_rep1

value: LUAD


title: CantonS Heads, ZT10, Replicate 1


title: EV_DMSO_H4ac_rep1

value: DMSO


title: CantonS Heads, ZT10, Replicate 2


title: 49326_UN-1

description:
49326_UN-1
COHP_49326
UN_vs_D7_Diff_Peaks.bed


title: EV_DMSO_H4ac_rep2


title: CantonS Heads, ZT6, Replicate 2


title: 49277_DR-2

description:
49277_DR-2
COHP_49277
UN_vs_DR_Diff_Peaks.bed

value: Resistant (R) cells


title: CantonS Heads, ZT14, Replicate 2


title: hBHD_T4

description: Transcriptome profile of BHD-associated kidney tumors, biological rep4


title: NRF2_ROM_H4ac_rep1

value: NRF2 OE


title: NRF2_ROM_K27ac_rep2


title: WT_CNCC_4C_VP5_Rep2

first: Justin

last: Cotney

address: 400 Farmington Avenue

department: Genetics and Genome Sciences

institute: UConn Health

description: 4C-seq from CNCCs derived from WT H9 hESCs

data_processing:
Library strategy: 4C
as in GSE98251 and accompanying manuscript

source_name: H9-derived CNCC

growth_protocol: Cultured in Essential 8 media (Gibco, A1517001) on Matrigel substrate (Corning,  354277)

extract_protocol: as in GSE98251

treatment_protocol: CNCC derivation as in Leung, A.W., Murdoch, B., Salem, A.F., Prasad, M.S., Gomez, G.A., and García-Castro, M.I. (2016). WNT/β-catenin signaling mediates human neural crest induction via a pre-neural border intermediate. Development 143, 398–410.

value: H9-derived CNCC

value: WT

tag: differentiation day

tag: 4c viewpoint

value: Viewpoint 5


title: CantonS Heads, ZT6, Replicate 1

value: Heads


title: WT_CNCC_4C_VP6_Rep2

value: Viewpoint 6


title: hBHD_T2

description: Transcriptome profile of BHD-associated kidney tumors, biological rep2


title: hBHD_T3

description: Transcriptome profile of BHD-associated kidney tumors, biological rep3


title: WT_CNCC_4C_VP3_Rep2

value: Viewpoint 3


title: NRF2_DMSO_K27ac_rep2


title: CantonS Heads, ZT2, Replicate 2


title: WT_CNCC_4C_VP4_Rep2

value: Viewpoint 4


title: NRF2_ROM_K27ac_rep1

value: ROM


title: CantonS Heads, ZT2, Replicate 1


title: WT_CNCC_4C_VP2_Rep2

value: Viewpoint 2


title: hBHD_T1

description: Transcriptome profile of BHD-associated kidney tumors, biological rep1

value: kidney tumor

value: BHD

value: not collected


title: WT_CNCC_4C_VP1_Rep2

value: Viewpoint 1


title: hBHD_C5

description: Transcriptome profile of normal kidney, biological rep5

source_name: control kidney sample

value: kidney

value: control


title: EV_ROM_K27ac_rep1

value: LUAD

value: Empty Vector


title: WT_CNCC_4C_VP6_Rep1

value: H9-derived CNCC


title: KL-1 Treated S2 Cells, BuTT-Seq, Replicate 2

description:
Drosophila
BuTT-Seq Performed On S2 Cells treated with 20µM KL-1 for 6 hours

growth_protocol: S2 Cells were cultured in Schneider's Medium supplemented with 10% FBS and 1x AA.

extract_protocol:
Nascent RNA was extracted as described in Yu and Rosbash, 2023. Cells were resuspended in 500µl cell lysis buffer (10mM Tris pH7.5, 2mM MgCl2, 10mM kCl, 0.6mM spermidine, 0.2mM spermine, 3mM TCEP, 0.03% Tween-20, and 0.1% BSA) and transferred into 2ml dounce homogenizers.
Cells were homogenized with 10 strokes with Pestle A and 15 strokes with Pestle B. Homogenized cells were passed through a 10µM filter (Sysmex, 04-0042-2314) and centrifuged at 1000g for 5 minutes.
Supernatant was removed and nuclei were resuspended in 100µl nuclear lysis buffer (10mM HEPES-KOH pH7.6, 100mM KCl, 0.1mM EDTA, 10% Glycerol, 0.15mM Spermine, 0.5mM Spermidine, 0.1mM NaF, 0.1mM Na3VO4, 0.1mM ZnCl2, 1mM TCEP, 0.1 units/µl SUPERaseIn, and 1x cOmplete protease inhibitor) and placed on a Thermomix set to 4°C and shaking at 1400 RPM.
100µl NUN buffer (25mM HEPES-KOH, pH7.6, 300mM NaCl, 1M Urea, 1% NP-40, 1mM TCEP, 3% Empigen, 0.1 units/µl SUPERaseIn, 1x cOmplete protease inhibitor) was added dropwise while shaking. Tubes were capped and left shaking at 4°C for 10 minutes. Chromatin was pelleted in the centrifuge at 21000g for 10 minutes, and the supernatant was discarded.
The resulting chromatin pellet was resuspended in 500µl TRIzol and incubated at 60°C for 10 minutes, then transferred to a phase lock tube.
RNA was then isolated with chloroform according to standard procedure and resuspended in a 10µl Turbo DNAse reaction containing 1x Turbo DNase Buffer and 1.5µl Turbo DNase, and DNase treatment was done for 30 minutes according to protocol.
Libraries were prepared as described in Yu and Rosbash, 2023. First strand master mixes (FS-MM) were prepared with 0.5µl 10x TGIRT Buffer(100mM HEPES pH8, 500mM NaCl, 50mM MgCl2, 10mM TCEP), 0.2µl SCR2R, 0.2µl TGIRT, and 1.1µl 50% PEG3350. 2µl of FS-MM was added to 2µl RNA in a PCR strip tube, flicking and spinning down twice to mix
Assembled reactions were incubated on ice for 30 minutes. While incubating, 1µl 5mM dNTPs was mixed with 30µl 2M NaCl. After 30 minutes, 1µl dNTPs/NaCl mixture was added to TGIRT reactions and placed on the thermal cycler with the following program: 25°C for 1 minute, ramping to 60°C at 1°C/second, 60°C for 10 seconds, then holding at 4°C.
Reactions were moved on to ice and 2µl Exonuclease III, 2µl H2O, and 1µl NEBuffer 1 were added. Reactions were incubated at 37°C for 8 minutes, then moved onto ice.
To eliminate RNA from downstream reactions and disassociate TGIRT, 3µl 1M NaOH was added to each sample and heated at 95°C for 5 minutes. After cooling to room temperature, 3µl 1M HCl was added to each sample to neutralize the reaction. 24µl 95% EtOH and 24µl Ampure XP beads were added to each sample, flicked to mix, and left to incubate for 10 minutes at room temperature. Beads were washed twice with 200µl 80% EtOH and resuspended in 4.2µl H2O and 4µl supernatant was moved to fresh PCR tubes.
Second-strand synthesis master mixes (SS-MM) were prepared with 1µl TGIRT Buffer, 0.3µl MER1R, 0.3µl TGIRT, 2µl 50% PEG3350, and 0.4µl H2O. 4µl SS-MM was added to cDNA samples and assembled reactions were left to incubate on ice for 30 minutes. While incubating, 1µl 20mM dNTPs was mixed with 10µl 2M NaCl.
After 30 minutes, 2µl dNTPs/NaCl mixture was added to TGIRT and placed on the thermal cycler with the following program: 25°C for 1 minute, ramping to 60°C at 1°C/second, 60°C for 30 seconds, then holding at 4°C.
Reactions were moved on to ice, and 1µl 0.2% SDS was added to each reaction to disassociate TGIRT. Reactions were incubated 55°C, then moved to room temperature.
30µl Ampure XP beads were added to each reaction, incubated for 5 minutes at room temperature, washed twice, and then eluted in 9µl H2O.
dsDNA was added to PCR reactions containing 25µl 2x NEBNext Ultra II Q5 Master mix, 2.5µl P7 primer, 2.5µl barcoded Ad1 primer, and 11µl H2O.
The assembled PCR reaction was subject to the following PCR program: 72°C for 3 minutes, 98°C for 30 seconds, 9-15 cycles of 98°C for 15 seconds and 65°C for 30 seconds, a final extension of 72°C for 2 minutes, and hold at 10°C.
PCR reactions were cleaned with 65µl Ampure XP beads following the standard protocol and resuspended in 10µl 1x Purple Loading Dye. Samples were loaded onto an 8% TBE gel alongside 1µl of TriDye Ultra Low Range DNA ladder mixed with 9µl 1x Purple Loading Dye and run at 180v for 45 minutes. Gels were post-stained with 1x Sybr Gold for 5 minutes, and the smear above 150nt were excised into a 0.5ml tube.
0.5ml tubes had a hole poked in the bottom with a 21-gauge needle and nested inside a 2.0ml tube and centrifuged for 21000g for 3 minutes. 600µl 300mM NaCl was added to each tube, and tubes were incubated at 75°C for 15 minutes or 4°C overnight.
Supernatant and gel fragments were transferred into a Costar Spin-X Centrifuge Tube Filter with a wide-bore 1000µl pipette tip and spun for 2 minutes at 21000g. Filters were discarded and 600µl isopropanol and 0.7µl GlycoBlue was added to each tube, and left to incubate for at least 15 minutes at room temperature or in -20°C for up to overnight.
Samples were spun at 21000g for 30 minutes, washed twice with 80% EtOH, and resuspended in 7-10µl MilliQ H2O. 2µl was used for analysis on a Tapestation 4200 D1000 tape and quantified using peak quantification centered around 170nt. Samples were sequenced on a NextSeq 500 with 8bp dual index reads.
BuTT-Seq (Bulk analysis of nascent Transcript Termini)

treatment_protocol: Cells were untreated or treated with DMSO or 20µM KL-1 by addition to media for 6 hours

value: 20 uM KL-1


title: hBHD_C4

description: Transcriptome profile of normal kidney, biological rep4


title: KL-1 Treated S2 Cells, BuTT-Seq, Replicate 1


title: EV_DMSO_K27ac_rep1

value: DMSO


title: WT_CNCC_4C_VP5_Rep1

value: WT

value: Viewpoint 5


title: DMSO Treated S2 Cells, BuTT-Seq, Replicate 2

description:
Drosophila
BuTT-Seq Performed On S2 Cells treated with DMSO for 6 hours


title: WT_CNCC_4C_VP4_Rep1


title: DMSO Treated S2 Cells, BuTT-Seq, Replicate 1


title: hBHD_C2

description: Transcriptome profile of normal kidney, biological rep2


title: EV_DMSO_IgG_rep1

value: IgG


title: LDLR-/-, PCSK9_4

city: Boston

first: Masanori

last: Aikawa

state: Massachusetts

address: 77 Avenue Louis Pasteur, NRB741

department: Department of Medicine

institute: Brigham and Women's Hospital

data_processing:
VIPER analysis pipeline for mapping and read counts
We normalized the raw read count data using DESeq2
The Wald test of DESeq2 was used to compare the RNA abundances and identify transcripts that were differentially abundant (increase/decrease by 2-fold) between two groups (control (no stimulus) versus PCSK9) (adjusted p-values <0.001).
The FDR was used for adjusted p-values. The data were imported into Excel to make the volcano plot. We used Qlucore for drawing principal component analysis (PCA) plots and heatmaps
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Peritoneal macrophage

growth_protocol: Mice peritoneal macrophage cells were maintained in RPMI 1640 containing 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using illustra RNAspin Mini kit (GE Healthecare, Little Chalfont, UK)
poly(A) enriched

value: Peritoneal macrophage

value: LDLR-/-

value: recombinant mice PCSK9


title: BuTT-Seq of 10,000 S2 Cells

description:
Drosophila
BuTT-Seq performed on 10,000 S2 Cells

value: Untreated


title: WT_CNCC_4C_VP3_Rep1

value: Viewpoint 3


title: NRF2_DMSO_K27ac_rep1

value: NRF2 OE


title: WT_CNCC_4C_VP2_Rep1

value: Viewpoint 2


title: hBHD_C1

description: Transcriptome profile of normal kidney, biological rep1

value: kidney

value: not collected


title: LDLR-/-, PCSK9_3


title: SMF016 sgSPOP-5 CHIR-98014 and ABBV-744 Replicate #2

city: Memphis

first: Wojciech

last: Rosikiewicz

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St. Jude Childrens Research Hospital

description: Total RNA was extracted by TRIzol (Thermo Fisher Scientific, 15596026) from replicate samples of cells treated with DMSO, CHIR98014, ABBV-744, or a combination thereof. About 200 ng total RNA was treated using Kapa rRNA depletion reagents to remove ribosomal RNA, then converted into cDNA libraries using Kapa RNA HyperPrep Kit with RiboErase (HMR). After end repair, dA-tailing, and adapter ligation, each cDNA library was purified and enriched by 11 cycles of PCR amplification.

data_processing:
Quality control filtering and adapter trimming of fastq files was performed with trim_galore.
Paired-end reads were mapped by STAR (v2.7.1a) using parameters "-c -p 4 --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJstitchMismatchNmax 5 -1 5 5 --alignSJDBoverhangMin 10 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 100000 --alignMatesGapMax 100000 --outSAMmapqUnique 60 --outSAMmultNmax 1 --outSAMstrandField intronMotif --outSAMattributes NH HI AS nM NM MD --outSAMunmapped Within --outSAMtype BAM SortedByCoordinate --outReadsUnmapped None --chimJunctionOverhangMin 12 --chimSegmentReadGapMax 3 --chimMultimapNmax 10 --chimMultimapScoreRange 10 --chimNonchimScoreDropMin 10 --chimOutJunctionFormat 1 --quantMode TranscriptomeSAM GeneCounts --twopassMode Basic --peOverlapNbasesMin 12 --peOverlapMMp 0.1 --outWigType wiggle --outWigStrand Stranded --outWigNorm RPM".
Read duplication was marked with MarkDuplicates from GATK (v4.1.2.0).
RSEM was used to quantify read counts per gene.
Assembly: hg19 (GRCh37.p13)
Supplementary files format and content: Gene-based raw counts as well as FPKM and TPM normalized txt files.

source_name: SEM cells

growth_protocol: SEM cells (ACC-546, DSMZ) were maintained in RPMI-1640 medium (Lonza) containing 10% fetal bovine serum (FBS) (HyClone) and 1% penicillin/streptomycin (Thermo Fisher Scientific); hTERT mesenchymal stem cells (MSCs; ABM, #T0529) were maintained in MSC culture medium made from RPMI-1640 (Gibco, #11875093), 10% heat-inactivated FBS (Gibco, #10082-147), and 1μM hydrocortisone (Sigma, #H0396); all cells were incubated at 37 °C, 5% CO2 atmosphere, and 95% humidity. The basal medium for maintaining 293T cells in culture was DMEM (HyClone). All passages of cells used in this study were mycoplasma-free. Cell identity was confirmed by STR analysis.

extract_protocol:
Total RNA was extracted by TRIzol (Thermo Fisher Scientific, 15596026).
About 200 ng total RNA was treated using Kapa rRNA depletion reagents to remove ribosomal RNA, then converted into cDNA libraries using Kapa RNA HyperPrep Kit with RiboErase (HMR). After end repair, dA-tailing, and adapter ligation, each cDNA library was purified and enriched by 11 cycles of PCR amplification.

treatment_protocol: Samples were treated with DMSO, CHIR98014, ABBV-744, or a combination thereof, with or without SPOP KO.

value: SEM (ACC-546, DSMZ)

value: human B cell precursor leukemia

value: SPOP KO; Treatment with GSK3 inhibitor (CHIR-98014, 400nM) and BET inhibitor (ABBV-744, 250nM)


title: LDLR-/-, PCSK9_2


title: SMF015 sgSPOP-5 CHIR-98014 and ABBV-744 Replicate #1


title: LDLR-/-, PCSK9_1


title: INV_CNCC_4C_VP6_Rep2

description: 4C-seq from CNCCs derived from H9 hESCs with an inversion on Chr7 due to CRISPR/Cas9 editing

source_name: CNCC derived from edited H9 hESC

treatment_protocol: Gene editing by nucleofection, CNCC derivation as in Leung, A.W., Murdoch, B., Salem, A.F., Prasad, M.S., Gomez, G.A., and García-Castro, M.I. (2016). WNT/β-catenin signaling mediates human neural crest induction via a pre-neural border intermediate. Development 143, 398–410.

value: CNCC derived from edited H9 hESC

value: Hemizygous inversion

value: Viewpoint 6


title: WT_CNCC_4C_VP1_Rep1

value: H9-derived CNCC

value: WT

value: Viewpoint 1


title: hBHD_C3

description: Transcriptome profile of normal kidney, biological rep3

value: control


title: Spleen, WT, Rep2, mRNA-derived cDNA

city: Zwijnaarde

first: Sophie

last: Janssens

address: Technologiepark 71

department: Inflammation Research Center

country: Belgium

institute: VIB/UGhent

description:
SAM3_cDNA
seuratObj_paper_dietSAM2and3_WT_subset_2023.rds
seuratObj_paper_dietSAM2and3_WT_subset2_v2_2023.rds
barcodes_SAM_2and3_WT_aggr.tsv.gz
features_SAM_2and3_WT_aggr.tsv.gz
matrix_SAM_2and3_WT_aggr.mtx.gz

data_processing:
The Cell Ranger pipeline (10x Genomics, v3.1.0) was used to perform sample demultiplexing and to generate FASTQ files for read 1, read 2 and the i7 sample index for the gene expression and cell surface protein libraries. Read 2 of the gene expression libraries was mapped to the reference genome (mouse mm10) using STAR. Subsequent barcode processing, unique molecular identifiers filtering and gene counting was performed using the Cell Ranger suite. CITE-seq reads were quantified using the feature-barcoding functionality. The cellranger aggr pipeline was used to aggregate the two WT samples into one feature-barcode matrix.
Pre-processing of the RNA UMI matrix was done by the scater and scran R packages (v1.14.6) according to the workflow proposed by the Marioni lab. Subsequent processing was done with Seurat v3.1.4 (gene filtering, SCTransform, clustering, dimensionality reduction, differential gene expression analysis).
DoubletFinder (v2.0.2) was performed to predict any remaining doublets in the dataset.
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes_SAM_2and3_WT_aggr.tsv.gz (barcode-1 correspond to SAM2, barcode-2 correspond to SAM3), features_SAM_2and3_WT_aggr.tsv.gz, matrix_SAM_2and3_WT_aggr.mtx.gz
Supplementary files format and content: Seurat objects for cDC1 and cDC2 subsets from the two WT samples merged together
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

molecule: polyA RNA

source_name: Spleen

extract_protocol:
DCs from two WT mice were enriched by magnisort negative selection and 4 million cells were stained with FACS antibodies, TruStain FcX Block (BioLegend, 101320) and the mouse cell surface protein antibody panel containing 160 oligo-conjugated antibodies (TotalSeq-A, BioLegend) and 9 TotalSeq-A isotype controls. 50.000 to 60.000 cDC1s (CD64negCD11cposMHCIIposXCR1posCD172aneg), 10.000 cDC2s (CD64negCD11cposMHCIIposXCR1negCD172apos) and 10,000 random live cells were FACS sorted and loaded into a Chromium Controller (10X Genomics).
Sorted single-cell suspensions were resuspended at an estimated final concentration of 1000 cells/µl and loaded on a Chromium GemCode Single Cell Instrument (10x Genomics) to generate single-cell gel beads-in-emulsion (GEM). The scRNA-Seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead and Library kit, version NextGEM 3.1 (10x Genomics) according to the manufacturer’s instructions with the addition of amplification primer (3 nM, 5’CCTTGGCACCCGAGAATT*C*C) during cDNA amplification to enrich the TotalSeq-A cell surface protein oligos. Size selection with SPRIselect Reagent Kit (Beckman Coulter) was used to separate amplified cDNA molecules for 3’ gene expression and cell surface protein construction. TotalSeq-A protein library construction including sample index PCR using Illumina’s Truseq Small RNA primer sets and SPRIselect size selection was performed according to the manufacturer’s instructions. The cDNA content of pre-fragmentation and post-sample index PCR samples was analyzed using the 2100 BioAnalyzer (Agilent).
Sequencing libraries were loaded on an Illumina NovaSeq flow cell at VIB Nucleomics core with sequencing settings according to the recommendations of 10x Genomics, pooled in an 85:15 ratio for the combined 3’ gene expression and cell surface protein samples, respectively.

value: Spleen

tag: strain

value: Splenocytes

value: steady-state


title: Spleen, WT, Rep2, ADT-derived cDNA

description:
SAM3_ADT
seuratObj_paper_dietSAM2and3_WT_subset_2023.rds
seuratObj_paper_dietSAM2and3_WT_subset2_v2_2023.rds
barcodes_SAM_2and3_WT_aggr.tsv.gz
features_SAM_2and3_WT_aggr.tsv.gz
matrix_SAM_2and3_WT_aggr.mtx.gz

library_source: other

molecule: protein


title: SMF014 sgSPOP-5 ABBV-744 250nM Replicate #2

value: SPOP KO; Treatment with BET inhibitor (ABBV-744, 250nM)


title: LDLR-/-, Control 3

value: Peritoneal macrophage

value: LDLR-/-

value: Control


title: INV_CNCC_4C_VP4_Rep2

value: Viewpoint 4


title: Spleen, WT, Rep1, ADT-derived cDNA

description:
SAM2_ADT
seuratObj_paper_dietSAM2and3_WT_subset_2023.rds
seuratObj_paper_dietSAM2and3_WT_subset2_v2_2023.rds
barcodes_SAM_2and3_WT_aggr.tsv.gz
features_SAM_2and3_WT_aggr.tsv.gz
matrix_SAM_2and3_WT_aggr.mtx.gz


title: SMF013 sgSPOP-5 ABBV-744 250nM Replicate #1

value: SEM (ACC-546, DSMZ)

value: human B cell precursor leukemia


title: SMF012 sgSPOP-5 CHIR-98014 400nM Replicate #2

value: SPOP KO; Treatment with GSK3 inhibitor (CHIR-98014, 400nM)


title: LDLR-/-, Control 2


title: Spleen, WT, Rep1, mRNA-derived cDNA

description:
SAM2_cDNA
seuratObj_paper_dietSAM2and3_WT_subset_2023.rds
seuratObj_paper_dietSAM2and3_WT_subset2_v2_2023.rds
barcodes_SAM_2and3_WT_aggr.tsv.gz
features_SAM_2and3_WT_aggr.tsv.gz
matrix_SAM_2and3_WT_aggr.mtx.gz


title: LDLR-/-, Control 1


title: INV_CNCC_4C_VP3_Rep2

value: CNCC derived from edited H9 hESC

value: Hemizygous inversion

value: Viewpoint 3


title: BuTT-Seq of 50,000 S2 Cells

description:
Drosophila
BuTT-Seq performed on 50,000 S2 Cells

value: Untreated


title: BuTT-Seq of 500,000 S2 Cells

description:
Drosophila
BuTT-Seq performed on 500,000 S2 Cells


title: SMF011 sgSPOP-5 CHIR-98014 400nM Replicate #1


title: INV_CNCC_4C_VP2_Rep2

value: Viewpoint 2


title: SMF010 sgSPOP-5 DMSO Replicate #2

value: SPOP KO; DMSO control


title: Cordycepin+αCD47, scRNAseq

city: Chang Zhou

first: Rongzhang

last: Chen

address: 185 Juqian Street

institute: Soochow University

description: 10x Genomics

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: subcutaneous tumors

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

tag: age

value: 6-8 weeks old

value: subcutaneous tumors


title: Mouse_WT_heart_RNA-seq_rep2 [Sample2_S2]

description: RNA-seq from mouse E11.5 heart tissue (WT)

data_processing:
STAR (v. 2.7.1a ) example command: STAR --runThreadN 8 --outTmpDir ~/STARtemp --genomeDir $GENOMEDIR --readFilesIn $FASTQDIR/paired_Sample11_S11_R1.fastq.gz $FASTQDI  R/paired_Sample11_S11_R2.fastq.gz --outFileNamePrefix $ANALYSISDIR/paired_Sample11_S11 --readFilesCommand zcat --sjdbGTFfile $GTFF  ILE --outSAMprimaryFlag OneBestScore --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhang  Min 2 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMtype B  AM SortedByCoordinate --outSAMattributes Standard --outWigType bedGraph --outWigStrand Stranded --outWigNorm RPM   rm -r ~/STARtemp
featureCounts (subread v. 2.0)
Differential gene expression with DESeq2 (v. 1.26.0)
Correction for surrogate variables with sva (3.34.0)
mm10 or hg19
text files of counts to be used with DESeq2

source_name: Embryonic heart tissue

growth_protocol: Timed matings and harvest of tissue according to approved University of Connecticut Health Center IACUC protocols

extract_protocol:
miRNeasy kit (Qiagen, 217004) with on-column DNAse I treatment (RNase-free DNase Set (Qiagen, 79254) )
Illumina TruSeq stranded RNA-seq library preparation kit (Illumina, RS-122-2101)

treatment_protocol: Tissue flash frozen immediately after collection

value: Embryonic heart tissue

value: WT

tag: developmental stage


title: Cordycepin, scRNAseq

description: 10x Genomics

value: Cordycepin


title: INV_CNCC_4C_VP1_Rep2

value: Viewpoint 1


title: SMF009 sgSPOP-5 DMSO Replicate #1


title: LDLR-/-, Control 4

value: Peritoneal macrophage

value: LDLR-/-

value: Control


title: INV_CNCC_4C_VP6_Rep1

value: Viewpoint 6


title: retina, 3dpc, Eif2ak3 cKO, rep4

city: San Francisco

first: Trent

middle: A

last: Watkins

email: trentw@bcm.edu, trent.watkins@ucsf.edu

state: CA

address: 675 Nelson Rising Lane, Rm 214A

department: Neurology

institute: University of California at San Francisco

data_processing:
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: Mus Musculus(GRCm38/mm10)
Supplementary files format and content: A single tab-delimited text file contains counts, FPKM, and differential expression for all samples.

source_name: retina

extract_protocol:
At 3 days post-crush (dpc), the retinae were quickly dissected out in 1X PBS and snap frozen in dry ice-ethanol bath and stored in -80°C until ready to be processed for RNA extraction. RNA was extracted using the Qiagen RNeasy micro kit (#74004).
RNA libraries were prepared according to Novogene procedures by polyA capture (or rRNA removal) and reverse transcription of cDNA.

value: retina

tag: time

value: 3 d

value: optic n. crush


title: SMF008 CFP CHIR-98014 and ABBV-744 Replicate #2

value: SEM (ACC-546, DSMZ)

value: human B cell precursor leukemia

value: sgRNA control; Treatment with GSK3 inhibitor (CHIR-98014, 400nM) and BET inhibitor (ABBV-744, 250nM)


title: INV_CNCC_4C_VP5_Rep2

value: CNCC derived from edited H9 hESC

value: Hemizygous inversion

value: Viewpoint 5


title: Mouse_WT_heart_RNA-seq_rep1 [Sample1_S1]

value: Embryonic heart tissue


title: Mouse_deltaGCR_heart_RNA-seq_rep3 [Sample14_S14]

description: RNA-seq from mouse E11.5 heart tissue (homozygous for deletion on Chr6)

value: Homozygous for deletion


title: retina, 3dpc, Eif2ak3 cKO, rep3


title: retina, 3dpc, Eif2ak3 cKO, rep2


title: SMF007 CFP CHIR-98014 and ABBV-744 Replicate #1


title: INV_CNCC_4C_VP4_Rep1

value: Viewpoint 4


title: Mouse_deltaGCR_heart_RNA-seq_rep2 [Sample12_S12]


title: SMF006 CFP ABBV-744 250nM Replicate #2

value: sgRNA control; Treatment with BET inhibitor (ABBV-744, 250nM)


title: retina, 3dpc, Eif2ak3 cKO, rep1


title: INV_CNCC_4C_VP3_Rep1

value: Viewpoint 3


title: SMF005 CFP ABBV-744 250nM Replicate #1


title: Mouse_WT_heart_RNA-seq_rep3 [Sample3_S3]

value: WT


title: retina, 3dpc, Ddit3 cKO, rep5


title: Mouse_deltaGCR_heart_RNA-seq_rep1 [Sample11_S11]


title: INV_CNCC_4C_VP2_Rep1

value: Viewpoint 2


title: Mouse_WT_limb_RNA-seq_rep3 [Sample9_S9]

description: RNA-seq from mouse E11.5 limb tissue (WT)

source_name: Embryonic limb tissue

value: Embryonic limb tissue


title: SMF004 CFP CHIR-98014 400nM Replicate #2

value: sgRNA control; Treatment with GSK3 inhibitor (CHIR-98014, 400nM)


title: retina, 3dpc, Ddit3 cKO, rep4

value: retina

value: 3 d


title: INV_CNCC_4C_VP1_Rep1

value: Viewpoint 1


title: SMF003 CFP CHIR-98014 400nM Replicate #1

value: SEM (ACC-546, DSMZ)

value: human B cell precursor leukemia


title: Mouse_deltaGCR_limb_RNA-seq_rep3 [Sample8_S8]

description: RNA-seq from mouse E11.5 limb tissue (homozygous for deletion on Chr6)


title: retina, 3dpc, Ddit3 cKO, rep3

value: optic n. crush


title: SMF002 CFP DMSO Replicate #2

value: sgRNA control; DMSO control


title: WT_CNCC_ChIP-seq_H3K27ac_rep2

description: H3K27ac ChIP-seq from WT H9-derived CNCCs

data_processing: as in GSE137731

extract_protocol: as in GSE137731

value: H9-derived CNCC

tag: chip antibody


title: Mouse_WT_limb_RNA-seq_rep2 [Sample7_S7]


title: INV_CNCC_4C_VP5_Rep1

value: CNCC derived from edited H9 hESC

value: Hemizygous inversion

value: Viewpoint 5


title: SMF001 CFP DMSO Replicate #1


title: WT_CNCC_ChIP-seq_H3K27me3_rep2

description: H3K27me3 ChIP-seq from WT H9-derived CNCCs


title: Mouse_deltaGCR_limb_RNA-seq_rep2 [Sample6_S6]

value: Homozygous for deletion


title: WT_CNCC_ChIP-seq_H3K9me3_rep2

description: H3K9me3 ChIP-seq from WT H9-derived CNCCs


title: Mouse_WT_limb_RNA-seq_rep1 [Sample5_S5]


title: retina, 3dpc, Atf4 cKO, rep5


title: P4_4: Non-senescent-induced human dermal fibroblast

first: Tomonori

last: Oka

department: CBRC

institute: Massachusetts general hospital

data_processing:
The raw files were aligned to human genome/GRCh38 using STAR-2.5.3.
Sequences located at transcripts were quantified by using RSEM-1.3.1.
Differentially expressed genes (DEG) analysis was performed using DESeq2-1.24.0.
genome build: Human genome/GRCh38
processed data files format and content: DEG analyzed by DESeq2-1.24.0.

source_name: normal human dermal fibroblast

extract_protocol: Used RNAeasy mini kit (Qiagen) and followed instruction

value: normal human dermal fibroblast

value: 4 times passsaged


title: retina, 3dpc, Ddit3 cKO, rep1


title: WT_CNCC_ChIP-seq_H3K36me3_rep2

description: H3K36me3 ChIP-seq from WT H9-derived CNCCs

value: WT


title: retina, 3dpc, Atf4 cKO, rep4


title: P4_3: Non-senescent-induced human dermal fibroblast


title: Mouse_deltaGCR_limb_RNA-seq_rep1 [Sample4_S4]

value: Embryonic limb tissue


title: WT_CNCC_ChIP-seq_H3K4me3_rep2

description: H3K4me3 ChIP-seq from WT H9-derived CNCCs


title: retina, 3dpc, Atf4 cKO, rep3


title: WT_CNCC_ChIP-seq_H3K4me2_rep2

description: H3K4me2 ChIP-seq from WT H9-derived CNCCs


title: P4_2: Non-senescent-induced human dermal fibroblast


title: Mouse_deltaGCR_face_RNA-seq_rep6 [Mouse_m14_S6]

description: RNA-seq from mouse E11.5 craniofacial tissue (homozygous for deletion on Chr6)

source_name: Embryonic craniofacial tissue

value: Embryonic craniofacial tissue


title: Mouse_WT_face_RNA-seq_rep8 [Mouse_m13_S5]

description: RNA-seq from mouse E11.5 craniofacial tissue (WT)


title: retina, 3dpc, Atf4 cKO, rep2

value: retina


title: retina, 3dpc, Ddit3 cKO, rep2

value: 3 d


title: P27_8: Senescent-induced human dermal fibroblast

value: 27 times passaged


title: WT_CNCC_ChIP-seq_Input_rep2

description: ChIP-seq Input from WT H9-derived CNCCs

value: none(input)


title: P27_7: Senescent-induced human dermal fibroblast


title: P4_1: Non-senescent-induced human dermal fibroblast


title: WT_CNCC_ChIP-seq_H3K27ac_rep1


title: P27_6: Senescent-induced human dermal fibroblast


title: Mouse_deltaGCR_face_RNA-seq_rep3 [Mouse_m10_S2]


title: retina, 3dpc, wildtype, rep4

value: wildtype


title: retina, 3dpc, wildtype, rep5

value: optic n. crush


title: retina, 3dpc, Atf4 cKO, rep1


title: P27_5: Senescent-induced human dermal fibroblast


title: retina, 3dpc, wildtype, rep3


title: WT_CNCC_ChIP-seq_H3K9me3_rep1


title: Mouse_deltaGCR_face_RNA-seq_rep2 [Mouse_m9_S1]


title: Young skin

data_processing:
The raw files were aligned to human genome/GRCh38 using STAR-2.5.1b
Sequences located at transcripts were quantified by using RSEM-1.2.3.1.
Differentially expressed genes (DEG) analysis was performed using DESeq2-1.24.0.
US law does not allow us to upload raw data files of human samples following guidelines for Human Genomic Data Submitted to Unrestricted-Access Repositories, so we upload only processed data.
genome build: hg19 (GENCODE v19)
processed data files format and content: Read counts estimated by using RSEM

source_name: normal young breast skin

value: normal young breast skin


title: Mouse_deltaGCR_face_RNA-seq_rep1 [AWIL085_m8-118_S1]


title: WT_CNCC_ChIP-seq_H3K36me3_rep1

value: H9-derived CNCC


title: retina, 3dpc, wildtype, rep2


title: WT_CNCC_ChIP-seq_H3K4me1_rep2

description: H3K4me1 ChIP-seq from WT H9-derived CNCCs


title: Old skin

source_name: normal old breast skin

value: normal old breast skin


title: Mouse_deltaGCR_face_RNA-seq_rep5 [Mouse_m12_S4]


title: Mouse_WT_face_RNA-seq_rep7 [AWIL084_m7-117_S5]


title: retina, uninjured, wildtype, rep4

value: 0 d

value: uninjured


title: retina, 3dpc, wildtype, rep1


title: WT_CNCC_ChIP-seq_H3K4me3_rep1


title: Mouse_WT_face_RNA-seq_rep6 [AWIL083_m6-116_S2]


title: WT_CNCC_ChIP-seq_H3K4me2_rep1


title: Mouse_deltaGCR_face_RNA-seq_rep4 [Mouse_m11_S3]

value: Homozygous for deletion


title: WT_CNCC_ChIP-seq_H3K4me1_rep1


title: Patient15_pre_BCG7 (RNA-seq)

city: Parkville

first: Boris

last: Novakovic

state: Victoria

address: Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road

country: Australia

institute: Murdoch Children's Research Institute

data_processing:
Fastq files were assessed for quality using the FastQC package and no samples were excluded from analysis. Bowtie was used to map 100-bp paired end reads to the human transcriptome (Ensembl, GRCh37v70), and gene expression estimates were derived using the mmseq pipeline. DESeq2  was used to normalise count data and determine gene expression differences between treatments.
Genome_build: hg19
Supplementary_files_format_and_content: .gene.mmseq files contain counts per gene

source_name: Adult Human Peripheral Blood

growth_protocol: We performed a prospective cohort study (‘Tribute’) and isolated PBMCs collected before BCG therapy and at 8 time points during BCG therapy. Following PBMC isolation we further purified the monocytes using an isolation protocol with a ficoll gradient.

extract_protocol:
1 – 5 x 10^6 cells of the monocyte-enriched cell suspension were used for RNA extraction. The cells were spun down at 500g for 5 minutes. Supernatant was removed and the cell pellet was resuspended with 500µL RNAlater solution (Thermo Fisher Scientific) and kept at room temperature for 20 minutes. The resuspended solution was stored at -80C until RNA isolation. The cell pellets which were frozen in RNAlater solution were thawed to RT and centrifuged for 5 minutes at 300g. The cell pellets were then dissolved in RLT buffer (Qiagen) for 20 minutes. RNA was isolated using RNeasy Mini Kit (Qiagen) according to manufacturer’s protocol, and including DNAse treatment.
Library preparation was performed using the Illumina TruSeq stranded mRNA kit with a starting input of 300ng and libraries were sequenced on the IlluminaNovaSeq 6000 instrument generating an average of 20 million reads per sample.
To infer gene expression levels, RNA-seq reads were aligned to hg19 human transcriptome using Bowtie. Quantification of gene expression levels as RPKM was performed using MMSEQ. Reads/transcripts were normalized using DEseq2 and pair-wise comparisons were performed.

tag: individual

value: Monocyte

value: Exposed monocytes. Collected on the day of and before the 7th intravesical BCG instillation, approximately 6 weeks after 6th instillation (pre-BCG7).


title: Patient15_BCG6 (RNA-seq)

value: Exposed monocytes. Collected on the day of the 6th intravesical BCG instillation (BCG6).


title: WT_CNCC_ChIP-seq_H3K27me3_rep1

value: WT


title: Mouse_WT_face_RNA-seq_rep4 [AWIL081_m4-114_S8]

value: Embryonic craniofacial tissue


title: retina, uninjured, wildtype, rep2

value: retina


title: WT_CNCC_ChIP-seq_Input_rep1

description: ChIP-seq Input from WT H9-derived CNCCs


title: Mouse_WT_face_RNA-seq_rep5 [AWIL082_m5-115_S6]


title: Patient14_pre_BCG10 (RNA-seq)

value: Exposed monocytes. Collected on the day of and before the 10th intravesical BCG instillation, approximately 12 weeks after 9th instillation (pre-BCG10).


title: Patient15_pre_BCG1 (RNA-seq)

value: Baseline monocytes. Collected before the 1st intravesical BCG instillation (pre-BCG1).


title: Mouse_WT_face_RNA-seq_rep2 [AWIL079_m2-112_S3]


title: INV_CNCC_RNA-seq_rep2 [AWIL097]

description: RNA-seq from CNCCs derived from H9 hESCs with an inversion on Chr7 due to CRISPR/Cas9 editing

value: CNCC derived from edited H9 hESC

value: Hemizygous inversion


title: INV_CNCC_RNA-seq_rep3 [AWIL098]


title: Mouse_WT_face_RNA-seq_rep1 [AWIL078_m1-111_S4]


title: Patient14_pre_BCG7 (RNA-seq)


title: Patient14_BCG6 (RNA-seq)


title: INV_CNCC_RNA-seq_rep1 [AWIL096]


title: Patient14_pre_BCG1 (RNA-seq)


title: ZT70, dermis, WT, ZT22, Replicate 3, scRNAseq

city: Irvine

first: Bogi

last: Andersen

address: Sprague Hall Rm 206

institute: University of California, Irvine

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: dorsal dermis

extract_protocol:
Immediately after sacrificing a mouse with CO2, hair on dorsal skin was removed with an electric razor and Nair Hair Removal cream. After the dorsal skin is isolated from the body, fat and remaining blood vessels were scrapped away. A circular piece of skin was obtained with a 12mm biopsy punch, and minced into tiny pieces. 1x collagenase was then added to the minced skin and the suspension was incubated at 37 °C for 1.5 hours. The suspension is then filtered with a 70μm and a 40μm cell strainers to obtain single cells. SYTOX blue viability dye was then added to the cell suspension and live cells were sorted out using FACS at the UCI Institute for Immunology Flow Cytometry Facility.
The Chromium Single Cell 3’ v3 (10x Genomics) libraries were prepared and sequenced by University of California Irvine Genomic High Throughput Facility with Illumina NovaSeq6000.

value: dorsal dermis

tag: Sex

value: male

value: dermal skin cells

tag: time point


title: Mouse_deltaGCR_HiC

description: HiC from mouse E11.5 craniofacial tissue (Homozygous for a deletion on Chr 6)

data_processing:
HiC-Pro (v. 2.10.0)
hicexplorer (v. 3.7.1)
convert data processed by HiC-Pro to .hic format: java -Xmx48g -jar ${JUICERTOOLS} pre ${SAMPLE}.bsorted.pairs.gz ${SAMPLE}.hic ${GENOME_SIZE} -f ${REFILE}" > ${JOB_NAME}.slurm
mm10 or hg19
.hic files compatible with juicer or .fastq files for analysis with other hic pipelines

extract_protocol:
Nuclear extraction-see accompanying manuscript
as per Belaghzal, H., Dekker, J., and Gibcus, J.H. (2017). Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation. Methods 123, 56–65.

treatment_protocol: Tissue  crosslinked and frozen immediately after collection


title: retina, uninjured, wildtype, rep3

value: wildtype


title: ZT22, dermis, WT, ZT22, Replicate 1, scRNAseq

tag: cell type


title: Mouse_WT_HiC

description: HiC from mouse E11.5 craniofacial tissue (WT)


title: Patient9_pre_BCG7 (RNA-seq)


title: INV_H9_RNA-seq_rep2 [AWIL094]

description: RNA-seq from H9 hESCs with an inversion on Chr7 due to CRISPR/Cas9 editing

source_name: edited H9 hESC

treatment_protocol: Gene editing by nucleofection

value: edited H9 hESC


title: ZT66, dermis, WT, ZT18, Replicate 3, scRNAseq


title: SC5314 Dipeptides III

city: Paris

first: Philipp

last: Brandt

address: 25-28 Rue du Dr Roux

department: Mycology

country: France

institute: Institut Pasteur

data_processing:
Fastq files were assessed for sequence quality using FastQC (version 0.11.9) and a genome index from file C_albicans_SC5314_version_A22-s07-m01-r44_chromosomes.fasta fom http://www.candidagenome.org/ was created with bowtie2 (version 2.3.5.1). Mapping of reads to the index was performed with bowtie2. Reads were counted and assigned to the corresponding genome using function featureCounts of R package Rsubread (version 2.2.6). Contrasts were calculated using R package DESeq2 (version 1.28.1). R version 4.0.4 was used.
Assembly: C_albicans_SC5314_version_A22-s07-m01-r44_chromosomes.fasta
Supplementary files format and content: Raw.counts.SC5314.S70.90.csv, Comma seperated text file containing counts of all samples

organism: Candida albicans

source_name: Planktonic cells

growth_protocol: C. albicans was pre-grown overnight at 37°C in YPD (1% yeast extract, 2% peptone, 2% glucose) and used to set log-cultures in SD (0.17 yeast nitrogen base w/o ammonium sulfate and w/o amino cids, 0.5% ammonium sulfate, 2% glucose) at OD600 0.2. Log-cultures were incubated at 37°C until OD600 of ~1 was reached. Cells were collected, washed twice with PBS and resuspended in PBS and used to set OD600 to 0.2 in the respective test medium and incubated for 4 h at 37°C and shaking at 180 rpm.

extract_protocol:
For total RNA isolation cells were resuspended in 440 µl AE buffer with 10% SDS and 440 µl of Acid-phenol:Chloroform with isoamyl alcohol (Ambion, Germany) was added. The suspension was thoroughly mixed and incubated for 5 min at 65°C, frozen at -80°C for 30 min and subsequently thawed at 65°C for 5 min. The phases were separated via 4 min centrifugation at 13,000 g, the upper aqueous phase transferred and 1/10 of the volume sodium acetate (pH 5.3) and 1 volume of 2 propanol was added to precipitate the RNA overnight at -20°C. The supernatant was discarded after 10 min centrifugation at 12,000 g, the RNA pellet washed twice with 70 % ethanol and finally solved in 300 µl nuclease free H2O. Quality and quantity of the RNA was assessed using 2100 Bioanalyzer (Agilent Technologies, California, USA) and Nanodrop (Thermo Fischer Scientific, Massachusetts, USA) measurements.
A total amount of 0.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA. Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA by mRNAusing poly-T oligo-attached magnetic beads. Fragmentation was carried out by Covaris sonication. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using dTTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality and quantity are assessed by Qubit and real-time PCR. Sequencing platform was Illumina Novaseq 6000 PE150.
Paired end RNA sequencing of cDNA fragments of preferentially 150~200 bp in length.

treatment_protocol: Cells were separated from test medium by centrifugation 4 min at 4000g and 4ºC. Cells were shock frozen in liquid nitrogen and stored at -80°C until further processing.

value: yeast cells

tag: genotype/variation

value: wild type

tag: medium type

value: 0.17% YNB w/o ammonium sulfate and w/o amino acids; 3.4 mM Ala-Gln, 3.3 mM Ala-Ser, 3.3 mM Arg-Asp; 1% Glucose; pH 5

value: 4 h


title: ZT42, dermis, WT, ZT18, Replicate 2, scRNAseq

tag: tissue


title: Mouse_WT_face_RNA-seq_rep3 [AWIL080_m3-113_S7]


title: ZT46, dermis, WT, ZT22, Replicate 2, scRNAseq


title: INV_H9_RNA-seq_rep1 [AWIL093]


title: ZT18, dermis, WT, ZT18, Replicate 1, scRNAseq


title: SC5314 Dipeptides II


title: retina, uninjured, wildtype, rep1

value: 0 d

tag: treatment

value: uninjured


title: WT_CNCC_RNA-seq_rep3 [AWIL092]

description: RNA-seq from WT H9-derived CNCCs

source_name: H9-derived CNCC

value: H9-derived CNCC

tag: genotype

value: WT


title: Patient9_pre_BCG1 (RNA-seq)

value: Monocyte


title: Patient7_pre_BCG7 (RNA-seq)

value: Exposed monocytes. Collected on the day of and before the 7th intravesical BCG instillation, approximately 6 weeks after 6th instillation (pre-BCG7).


title: Patient9_BCG6 (RNA-seq)

value: Exposed monocytes. Collected on the day of the 6th intravesical BCG instillation (BCG6).


title: WT_CNCC_RNA-seq_rep2 [AWIL091]

description: RNA-seq from WT H9-derived CNCCs


title: SC5314 Dipeptides I


title: INV_H9_RNA-seq_rep3 [AWIL095]

value: Hemizygous inversion


title: Patient7_BCG6 (RNA-seq)


title: ZT62, dermis, WT, ZT14, Replicate 3, scRNAseq

value: dorsal dermis


title: SC5314 Proline II

value: 0.17% YNB w/o ammonium sulfate and w/o amino acids; 0.5% ammonium sulfate; 1% Proline; pH 5


title: SC5314 Proline III


title: ZT38, dermis, WT, ZT14, Replicate 2, scRNAseq

value: male

value: dermal skin cells


title: WT_CNCC_RNA-seq_rep1 [AWIL090]

description: RNA-seq from WT H9-derived CNCCs


title: ZT14, dermis, WT, ZT14, Replicate 1, scRNAseq


title: WT_H9_RNA-seq_rep3 [AWIL089]

description: RNA-seq from WT H9

source_name: H9 hESC

treatment_protocol: No treatment

value: H9 hESC


title: SC5314 Proline I

value: yeast cells


title: Patient7_pre_BCG1 (RNA-seq)

value: Baseline monocytes. Collected before the 1st intravesical BCG instillation (pre-BCG1).


title: Patient2_pre_BCG10 (RNA-seq)

value: Exposed monocytes. Collected on the day of and before the 10th intravesical BCG instillation, approximately 12 weeks after 9th instillation (pre-BCG10).


title: WT_H9_RNA-seq_rep2 [AWIL088]

description: RNA-seq from WT H9


title: WT_H9_RNA-seq_rep1 [AWIL087]

description: RNA-seq from WT H9


title: ZT58, dermis, WT, ZT10, Replicate 3, scRNAseq


title: Patient2_pre_BCG7 (RNA-seq)


title: SC5314 α-ketoglutarate III

value: wild type

value: 0.17% YNB w/o ammonium sulfate and w/o amino acids; 0.5% ammonium sulfate; 1% α-ketoglutarate; pH 5

value: 4 h


title: ZT34, dermis, WT, ZT10, Replicate 2, scRNAseq


title: SC5314 α-ketoglutarate II


title: ZT10, dermis, WT, ZT10, Replicate 1, scRNAseq


title: HiC_NCC_INV_rep2

description: HiC from H9-derived CNCCs (Hemizygous for an inversion on Chr7)

value: CNCC derived from edited H9 hESC


title: Patient2_BCG6 (RNA-seq)


title: Patient2_pre_BCG1 (RNA-seq)


title: HiC_NCC_INV_rep1


title: Patient1_pre_BCG10 (RNA-seq)


title: SC5314 Malic acid III

value: 0.17% YNB w/o ammonium sulfate and w/o amino acids; 0.5% ammonium sulfate; 1% malic acid; pH 5


title: SC5314 α-ketoglutarate I


title: ZT30, dermis, WT, ZT6, Replicate 2, scRNAseq

value: WT


title: HiC_NCC_WT_rep2

description: HiC from H9-derived CNCCs (WT)

value: H9-derived CNCC


title: HiC_NCC_WT_rep1

description: HiC from H9-derived CNCCs (WT)


title: Patient1_pre_BCG7 (RNA-seq)

value: Monocyte

value: Exposed monocytes. Collected on the day of and before the 7th intravesical BCG instillation, approximately 6 weeks after 6th instillation (pre-BCG7).


title: SC5314 Malic acid II


title: Patient1_BCG6 (RNA-seq)

value: Exposed monocytes. Collected on the day of the 6th intravesical BCG instillation (BCG6).


title: ZT6, dermis, WT, ZT6, Replicate 1, scRNAseq

value: dorsal dermis


title: ZT50, dermis, WT, ZT2, Replicate 3, scRNAseq

value: male


title: Patient1_pre_BCG1 (RNA-seq)


title: ZT26, dermis, WT, ZT2, Replicate 2, scRNAseq

value: dermal skin cells


title: SC5314 Glucose III

value: 0.17% YNB w/o ammonium sulfate and w/o amino acids; 0.5% ammonium sulfate; 1% glucose; pH 5


title: Patient15_BCG9 (ChIP-seq)

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using bwa. For peak calling the BAM files were first filtered to remove the reads with mapping quality less than 15. The peak calling algorithm MACS2 http://github.com/taoliu/MACS/) was used to detect the genomic regions enriched for histone marks at p-value of 10-5. H3K4me1 peaks were called using the broad setting of MACS2 while H3K27ac peaks were called using the default (narrow) setting.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files for visualization

extract_protocol:
Purified cells were fixed with 1% formaldehyde (Sigma) at a concentration of approximately 10 million cells/ml. Fixed cell preparations were sonicated and 1ug of chromatin (~1 million cells) was incubated with 1µg of H3K27ac or H3K4me1 antibodies (Diagenode) and incubated overnight at 4ºC with rotation. Protein A/G magnetic beads were washed in dilution buffer with 0.15% SDS and 0.1% BSA, added to the chromatin/antibody mix and rotated for 60 minutes at 4°C. Beads were washed with 400µl buffer for 5 minutes at 4°C with five rounds of washes. After washing chromatin was eluted using elution buffer for 20 minutes. Supernatant was collected, 8µl 5M NaCl, 3µl proteinase K were added and samples were incubated for 4 hours at 65°C.Finally samples were purified using Qiagen; Qiaquick MinElute PCR purification Kit and eluted in 20µl EB.
Library preparation was performed using the Ovation Ultralow DNA-seq library preparation kit and libraries were sequenced on the IlluminaNovaSeq 6000 instrument generating an average of 30 million reads per sample.

value: Exposed monocytes. Collected on the day of the 9th intravesical BCG instillation (BCG9).

value: Rabbit anti-H3K4me3 Antibody (Cell Signaling Technology #9727)


title: SC5314 Glucose II

value: yeast cells


title: Patient15_pre_BCG7 (ChIP-seq)


title: ZT54, dermis, WT, ZT6, Replicate 3, scRNAseq


title: ZT2, dermis, WT, ZT2, Replicate 1, scRNAseq


title: SC5314 Glucose I

value: wild type


title: Patient15_BCG6 (ChIP-seq)


title: NRF2_ROM_3

data_processing:
We used RTA (Illumina) for base calling and bcl2fastq2 (version 2.19) for converting BCL to fastq format, coupled with adaptor trimming.
We performed a pseudoalignment to a kallisto index created from transcriptomes(Mouse: GRCm38 ) using kallisto (0.44.0).
We tested for differentially expressed genes under various conditions using DESeq2 in R.
Assembly: GRCm38
Supplementary files format and content: Gene counts for each condition; output from pseudoalignment in tab-delimited text
Supplementary files format and content: Normalized gene counts for each condition, output from DESeq2 in tab-delimited text

extract_protocol:
RNA extraction was done by Trizol (Sigma) following the manufacturers instructions
Poly-A pull-down to enrich mRNAs from total RNA samples, then proceed with library construction using Illumina TruSeq chemistry

treatment_protocol: 200k KP cells were plated in 6-well plates in RPMI supplemented with 10% FBS and P/S. The next day cells were treated with DMSO or 5nM Romidepsin in RPMI for 16h

tag: cell line

value: LUAD

value: NRF2 OE

value: ROMIDEPSIN


title: Spleen, Xbp1flIre1fl, Immature, Rep4

data_processing:
Illumina software was used for basecalling.
Sequenced reads were inspected with FastQC v0.11.4, trimmed for adaptor sequences with Trimmomatic v0.35, then mapped to mm10 whole genome using TopHat2 v2.1.0, converted to BAM-files with Samtools v0.1.19 and finally counted with HTSeqCount v0.6.1
Limma v3.42.2 was used to normalize the count data.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with log-CPM values for all biologically meaningfully expressed genes for each sample

extract_protocol:
Different cDC1 maturation subsets (5,000 – 50,000 cells) were FACS sorted directly into RLT Plus buffer (Qiagen; 74034) supplemented with ß-mercaptoethanol (1/100) and stored at −80 °C until further processing. RNA was obtained using the RNeasy Plus Micro Kit (Qiagen; 74034) according to manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Spleen

tag: maturity

value: Immature

value: steady-state

tag: condition


title: NRF2_ROM_1


title: Spleen, Xbp1flIre1fl, Immature, Rep1

tag: strain

value: WT


title: Spleen, Xbp1flIre1fl, Immature, Rep3


title: Spleen, Xbp1flIre1fl, Mature, Rep4

value: Mature


title: Patient15_pre_BCG1 (ChIP-seq)

value: Monocyte

value: Baseline monocytes. Collected before the 1st intravesical BCG instillation (pre-BCG1).


title: CS17_HiC

description: HiC from human CS17 craniofacial tissue

growth_protocol: Samples flash frozen immediately after collection by HDBR

treatment_protocol: Crosslinked after thawing

value: Embryonic craniofacial tissue

value: karyotypically normal

value: Carnegie stage 17 (CS17)


title: control Ab, scRNAseq

city: Tokushima

first: atsushi

last: mitsuhashi

address: 3-18-15 Kuramoto-cho

department: Department of Respiratory Medicine and Rheumatology

country: Japan

institute: Tokushima university

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: mesothelioma

extract_protocol:
The tumor tissues  from mouse mesothelioma AB1-HA cell-bearing mice were minced with scissors and incubated with RPMI including 1 mg/ml BSA (Sigma), 1 mg/ml collagenase A (Roche) and 10 U/ml DNase 1 (Roche) . The number of whole cells was counted using a hemocytometer, and the suspended cells were labeled with PE-Cy7 conjugated anti-mouse CD45 antibody (Invitrogen). Dead cells were removed by ReadiDrop PI staining (Bio-Rad). Tumor-infiltrating CD45+ immune cells were sorted by LE-SH800BC (Sony).
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, isolated cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: mesothelioma

value: CD45+ cells


title: EV_ROM_3

first: Dimitris

last: Karagiannis

institute: Columbia University

value: Empty Vector


title: anti-VEGF Ab, scRNAseq

description: 10x Genomics


title: Patient14_BCG9 (ChIP-seq)

value: Exposed monocytes. Collected on the day of the 9th intravesical BCG instillation (BCG9).

value: Rabbit anti-H3K4me3 Antibody (Cell Signaling Technology #9727)


title: SC5314 Malic acid I

value: yeast cells

value: wild type

value: 0.17% YNB w/o ammonium sulfate and w/o amino acids; 0.5% ammonium sulfate; 1% malic acid; pH 5

value: 4 h


title: Liver_GRff_CORT

city: Tokyo

first: Hiroki

last: Yamazaki

address: 35 Shinanomachi, Shinjuku-ku

department: Department of Biochemistry

institute: Keio University School of Medicine

data_processing:
Library construction and sequencing were performed on DNBSEQ-G400, and 100-bp paired-end reads were generated (Beijing Genomics Institute, China).
After data filtering, mapping of reads and quantification was performed using Salmon (v1.2.1) and a fasta file (protein-coding transcript sequences) downloaded from GENCODE (https://www.gencodegenes.org/mouse/release_M20.html) as reference.
The output files were imported to R (v3.5.0) by tximport package, and the parameter of countsFromAbundance in summarizeToGene function was set to "lengthScaledTPM".
Ensembl transcript IDs were converted to official gene name using biomaRt (v2.38.0).
Duplicated gene names were removed if the same gene name were present, where the one with larger total counts of all samples was left.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes ensemble gene IDs, gene names, and expected counts for each sample.

source_name: liver

extract_protocol: none provided by the submitter

value: GRf/f

value: corticosterone


title: Patient14_pre_BCG10 (ChIP-seq)

value: Exposed monocytes. Collected on the day of and before the 10th intravesical BCG instillation, approximately 12 weeks after 9th instillation (pre-BCG10).


title: Spleen, Xbp1flIre1fl, Mature, Rep2

source_name: Spleen

value: Spleen

value: Mature

value: steady-state

value: WT


title: Gas_obob_GRmKO

source_name: gastrocnemius muscle


title: EV_ROM_1

value: LUAD

value: ROMIDEPSIN


title: Spleen, Xbp1flIre1fl, Immature, Rep2

value: Immature


title: Spleen, Xbp1flIre1fl, Mature, Rep3


title: Gas_obob_GRff


title: NRF2_ROM_2

value: NRF2 OE


title: Patient14_BCG6 (ChIP-seq)

value: Monocyte

value: Exposed monocytes. Collected on the day of the 6th intravesical BCG instillation (BCG6).


title: Spleen, Xbp1flIre1fl, Mature, Rep1


title: Spleen, Xbp1fl, Immature, Rep4


title: Liver_GRff_vehicle

value: vehicle


title: NRF2_DMSO_3

value: DMSO


title: Patient14_pre_BCG1 (ChIP-seq)

value: Baseline monocytes. Collected before the 1st intravesical BCG instillation (pre-BCG1).

value: Rabbit anti-H3K4me3 Antibody (Cell Signaling Technology #9727)


title: Patient10_pre_BCG10 (ChIP-seq)


title: Gas_lean_GRff


title: Spleen, Xbp1fl, Immature, Rep3


title: Gas_lean_GRmKO


title: NRF2_DMSO_1


title: NRF2_DMSO_2


title: Patient10_BCG9 (ChIP-seq)

value: Exposed monocytes. Collected on the day of the 9th intravesical BCG instillation (BCG9).


title: Spleen, Xbp1fl, Immature, Rep2


title: EV_ROM_2

value: Empty Vector


title: WAT_GRmKO_CORT

source_name: gonadal white adipose tissue

value: GRmKO

value: corticosterone


title: EV_DMSO_2


title: EV_DMSO_3


title: Spleen, Xbp1fl, Immature, Rep1

value: Spleen


title: WAT_GRmKO_vehicle


title: Patient14_pre_BCG7 (ChIP-seq)

value: Exposed monocytes. Collected on the day of and before the 7th intravesical BCG instillation, approximately 6 weeks after 6th instillation (pre-BCG7).


title: Spleen, Xbp1fl, Mature, Rep4

value: Mature

value: steady-state

value: WT


title: WAT_GRff_CORT

value: GRf/f


title: Patient10_BCG6 (ChIP-seq)


title: DKO_Flcn-Tfe3_10

description:
CDM_FLCN_TFE3_DKO5
Transcriptome profile of mouse_DKO_Flcn-Tfe3_kidney, biological rep10
CDM_FLCN_TFE3_DKOp2_rawCounts.txt

data_processing:
Sequence reads were trimmed using Trim Galore software (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove adapter sequences and low-quality end bases and then aligned on mm10 reference sequence using STAR.
Assembly: mm10
Supplementary files format and content: *.txt: Tab-delimited text files include raw counts for each Sample.

source_name: mouse kidney sample

growth_protocol: All mice used were maintained in a C57BL/6 strain background.

extract_protocol:
RNA was quantified and mixed at 10ng/µl.
Total RNA (100 ng) from each sample was prepared using QuantSeq 3'mRNA-Seq Library prep kit (Lexogen, Vienna, Austria) according to manufacturer's instructions.
The amplified fragmented cDNA of 300 bp in size were sequenced in single-end mode using the NovaSeq 6000 (Illumina) with a read length of 100 bp.

treatment_protocol: RNA samples from mouse kidneys were extracted using RNeasy plus Mini kit (Qiagen) according to the manufacturer’s instructions.

value: kidney

tag: age

value: postnatal day 2


title: Patient10_pre_BCG1 (ChIP-seq)

value: Monocyte


title: Spleen, Xbp1fl, Mature, Rep3


title: EV_DMSO_1

value: LUAD


title: WAT_GRff_vehicle

value: vehicle


title: Spleen, Xbp1fl, Mature, Rep1


title: Patient9_pre_BCG10 (ChIP-seq)

value: Exposed monocytes. Collected on the day of and before the 10th intravesical BCG instillation, approximately 12 weeks after 9th instillation (pre-BCG10).


title: Spleen, Xbp1fl, Mature, Rep2


title: Patient9_BCG9 (ChIP-seq)

value: Rabbit anti-H3K4me3 Antibody (Cell Signaling Technology #9727)


title: Liver_GRmKO_CORT


title: Patient9_pre_BCG7 (ChIP-seq)


title: DKO_Flcn-Tfe3_8

description:
CDM_FLCN_TFE3_DKO3
Transcriptome profile of mouse_DKO_Flcn-Tfe3_kidney, biological rep8
CDM_FLCN_TFE3_DKOp2_rawCounts.txt


title: DKO_Flcn-Tfe3_7

description:
CDM_FLCN_TFE3_DKO1
Transcriptome profile of mouse_DKO_Flcn-Tfe3_kidney, biological rep7
CDM_FLCN_TFE3_DKOp2_rawCounts.txt


title: Control

city: Yokohama

first: Taishin

last: Akiyama

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

institute: RIKEN

description: 10x Genomics

data_processing: The demultiplexing, barcoded processing, gene counting and aggregation were done using the Cell Ranger software v5.1

source_name: Thymus

extract_protocol:
The thymus of 4-week-old mice was dissected and minced with a razor. Thymic fragments were pipetted up and down in 1 mL of Hepes-RPMI (Wako). The supernatant was used as lymphocytes, and the remaining fragments were digested by incubation in RPMI 1640 medium containing 0.05 U/mL Liberase (Roche) and 0.01% w/v DNase I (Sigma-Aldrich) at 37°C for 12 min x3 times after each incubation and Pipetting. Reactions were stopped by adding an equal volume of FACS buffer containing 1 mM ethylenediaminetetraacetic acid and washing with FACS buffer. Total cell count was calculated as the sum of lymphocytes and digested cells.
Single-cell emulsions were obtained using a 10x Genomics Controller and a v2 Library and Gel Bead kit (10X Genomics). RNA-sequencing libraries were prepared according to the 10x 3′ v2 kit protocol.

value: Thymus

value: Thymic epithelial cells

value: control


title: Patient10_pre_BCG7 (ChIP-seq)


title: Gas_GRmKO_vehicle

value: GRmKO


title: Gas_GRff_CORT

value: corticosterone


title: DKO_Flcn-Tfe3_6

description:
DKO_2015_6
Transcriptome profile of mouse_DKO_Flcn-Tfe3_kidney, biological rep6
raw_counts_FLCN_TFE3_invivo.txt


title: Patient9_pre_BCG1 (ChIP-seq)

value: Baseline monocytes. Collected before the 1st intravesical BCG instillation (pre-BCG1).


title: Patient7_pre_BCG10 (ChIP-seq)


title: Patient9_BCG6 (ChIP-seq)

value: Exposed monocytes. Collected on the day of the 6th intravesical BCG instillation (BCG6).


title: KPK2_t0_rep3

data_processing:
Computational analysis was done using MAGeCK. Briefly, the sequencing data were de-barcoded and the 20 bp sgRNA sequence was mapped to the reference sgRNA library without allowing for any mismatches.
The read counts were calculated for each individual sgRNA and normalized, and differential analysis was done between KP and KPK samples
Quality control, gene hit identification and graphs were generated using MAGeCKFlute.
Assembly: sgRNA library
Supplementary files format and content: sgRNA.raw.counts.txt: sgRNA raw counts for each sample
Supplementary files format and content: KP_KPK_mle_normalized3.sgrna_summary.txt; sgRNA - gene correspondence
Supplementary files format and content: KP_KPK_mle_normalized3.gene_summary.txt: Comparative analysis between KP and KPK cells in sgRNA enrichment for each gene

growth_protocol: KP and KPK cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics (P/S) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Genomic DNA from collected cell pellets were prepared with purelink mini kit (ThermoFisher) according to the manufacturer’s suggested protocol.
Libraries were generated by amplification from genomic DNA using a modified 2-step PCR   version of the protocol published by Doench et al. Briefly, we perform an initial “enrichment” PCR, whereby the integrated sgRNA cassettes are amplified from gDNA, followed by a second PCR to append Illumina sequencing adapters on the 5’- and 3’-ends of the amplicon, as well as a random nucleotide stagger and unique demultiplexing barcode on the 5’ end. Each “PCR1” reaction contains 25µL of Q5 High-Fidelity 2X Master Mix (NEB), 2.5µL of Nuc PCR#1 Fwd Primer (10µM), 2.5µL of Nuc PCR#1 Rev Primer (10µM), and 5µg of gDNA in 20µL of water (for a total volume of 50µL per reaction). The number of PCR1 reactions is scaled accordingly; therefore, we performed six PCR1 reactions per technical replicate, per time point (T0 or TF), and per condition. PCR1 amplicons were purified using the QIAquick PCR Purification Kit (Qiagen) and used as template for “PCR2” reactions. Each PCR2 reaction contains 25µL of Q5 High-Fidelity 2X Master Mix (NEB), 2.5µL of a unique Nuc PCR#2 Fwd Primer (10µM), 2.5µL of Nuc PCR#2 Rev Primer (10µM), and 300ng of PCR1 product in 20µL of water (for a total volume of 50µL per reaction). We performed two PCR2 reactions per PCR1 product.   PCR Program for PCR1 and PCR2: 1) 98°C x 30s; 2) 98°C x 10s; 3) 65°C x 30s; 4) 72°C x 30s; 5) Go to step 2 x 24 cycles; 6) 72°C x 2 min; 7) 4°C forever. Library amplicons were size-selected on a 2.5% agarose gel, purified using the QIAquick Gel Extraction Kit (Qiagen), and sequenced on an Illumina NextSeq500 instrument (75nt single end reads). Files resulting from 4 sequencing lanes were concatenated into a single file for each condition.

treatment_protocol: Derivatives of KP and KPK cells were generated by stable lentiviral transduction of Cas9 with blasticidin resistance (Addgene#52962). Cells were maintained with blasticidin selection throughout the experiment. Transduction of Cas9-expressing KP/KPK cells was performed at an MOI of approximately 0.2 by incubating cell suspension in lentiviral supernatant and centrifugation at 1500 rpm for 1.5 hours at room temperature before being returned to a humidified incubator. An initial population was infected to represent a 2500x representation of the epigenetic library; 36 hours post-transduction cells were resuspended and replated in 10 ug/mL puromycin and selected for another 48 hours. After complete puromycin selection cells were trypsinized, pooled, a cell sample representing time-0hr (t0) of the screen was reserved and stored at -20C. Each condition was performed in technical triplicate for the entire screen and maintained in 15 cm tissue culture dishes (Corning) with at least 2500x library representation maintained throughout all culture and library preparation steps. Population doublings for each cell line and condition were recorded and a sample was collected when a particular condition had reached 14 cumulative population doublings(t1) and stored at -20o C. At t1 cells were treated with DMSO as a control to other conditions that were not included in the final analysis. 3 biological replicates per condition are included.

value: Mouse LUAD

value: 0 doublings


title: Radiation

description: 10x Genomics

value: radiation


title: Gas_GRff_vehicle

value: GRf/f


title: KPK2_t1_rep3

value: 14 doublings


title: KPK2_t1_rep2


title: KPK2_t0_rep2


title: DKO_Flcn-Tfe3_5

description:
DKO_2015_5
Transcriptome profile of mouse_DKO_Flcn-Tfe3_kidney, biological rep5
raw_counts_FLCN_TFE3_invivo.txt

value: kidney

value: postnatal day 2


title: Patient7_BCG9 (ChIP-seq)

value: Monocyte

value: Exposed monocytes. Collected on the day of the 9th intravesical BCG instillation (BCG9).


title: DKO_Flcn-Tfe3_2

description:
DKO_2015_2
Transcriptome profile of mouse_DKO_Flcn-Tfe3_kidney, biological rep2
raw_counts_FLCN_TFE3_invivo.txt


title: DKO_Flcn-Tfe3_9

description:
CDM_FLCN_TFE3_DKO4
Transcriptome profile of mouse_DKO_Flcn-Tfe3_kidney, biological rep9
CDM_FLCN_TFE3_DKOp2_rawCounts.txt


title: KPK2_t1_rep1


title: Liver_GRmKO_vehicle

value: vehicle


title: Patient7_BCG6 (ChIP-seq)

value: Rabbit anti-H3K4me3 Antibody (Cell Signaling Technology #9727)


title: Patient7_pre_BCG1 (ChIP-seq)


title: Gas_GRmKO_CORT