title: E. coli C3000 5 min - targeting - rep 2


title: Bone Marrow Derived Macrophage - Room Air exposure 1

status: Public on Jun 23 2023

type: SRA

city: Santa Cruz

first: Susan

last: Carpenter

state: CA

address: Red Hill Rd, Biomedical Sciences

department: MCD

country: USA

institute: UC Santa Cruz

description:
macviv_air_ctl_er051
DESeq2_results.txt
juncBASE_Output.txt
rMATS_RI_JCEC.txt

library_source: transcriptomic

data_processing:
All samples were sequenced together on an Illumina HiSeq system (paired-end 150bp), and sequencing reads were mapped to mm10 using STAR. For analysis of differential genes, STAR outputs were processed using DESeq2.
Prior to alternative splicing steps (rMATS, juncBASE ), non-canonical chromosome reads were removed with Samtools v1.9 as samtools view -b -@ 8 <in.bam> chr{1..19} chrX chrY > chr_$<in.bam>
rMATS v4.1.1 was run as: rmats_turbo_v4_1_1/rmats.py --b1 <samples1.txt> --b2 <samples2.txt> --nthread 4 -t paired --readLength 100 --gtf merged.gtf --od <out> --libType fr-unstranded --allow-clipping
juncBASE was run using Docker container "mgmarin/juncbase:0.9" with the "--by_chr" option used wherever allowed. The full list of commands is available here: https://github.com/ericmalekos/alt_splicing_scripts/blob/main/tool_usage.txt
juncBASE counts were used as input to DRIMSeq v1.2. DRIMSeq was run as described in the manual with default settings except the filter step which was run as dmFilter(d, min_samps_gene_expr = 6, min_samps_feature_expr = 3, min_gene_expr = 10, min_feature_expr = 0)
Events from both rMATS and DRIMSeq statistical analysis were kept if they met the following criteria: FDR < 0.1, |PSI| > 0.1, number of reads supporting event > 10
Common retained intron events were identified with Bedtools v2.27.1 bedtools intersect -wa -u -f -r 0.85 -a <rmatsIR.bed> -b <drimIR.bed>
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2, juncBASE, rMATS files are TSV format containing the direct output of above commands
Supplementary_files_format_and_content: merged_annotations.gtf is GTF format
Supplementary_files_format_and_content: DESeq2 normalized gene counts and statistics
Supplementary_files_format_and_content: juncBASE event counts
Supplementary_files_format_and_content: rMATS retained intron counts and statistics

molecule: total RNA

organism: Mus musculus

source_name: Bone Marrow Derived Macrophage

growth_protocol: Mouse bone marrow-derived macrophages (BMDMs) were generated by culturing erythrocyte-depleted bone-marrow cells in DMEM medium supplemented with 10% FCS, 5 mL pen/strep (100X), 500μl ciprofloxacin (10mg/ml) and 10% L929 supernatant for 7-12 days, with the replacement of culture medium every 2-3 days.

extract_protocol:
Total RNA was purified from bone marrow cells or BMDMs using Direct-zol RNA MiniPrep Kit (Zymo Research) and TRIzol reagent (Ambion) according to the manufacturer’s instructions.
Total RNA was used to generate libraries using a NEXTflex Rapid Directional RNA-Seq kit (Bioo Scientific, $5138-07) according to the manufacturer’s instructions. Samples were quality assessed using TapeStation (Agilent, Santa Clara, CA) and read on a High-Seq System (Illumina, San Diego, CA.

treatment_protocol: Bone marrow erythrocyte-depleted cells from each mouse were split into two fractions, 1) to be immediately harvested in Trizol for RNA isolation (Day 0), and 2) to be differentiated into BMDMs upon addition of 10% L929 in culture media until harvest (Day 11).

tag: cell type

value: Bone Marrow Derived Macrophage

tag: treatment

value: Room Air Exposure

tag: genotype

value: Wild-type (WT)

tag: strain


title: T9_AM3

city: Nagoya

first: Hiroyuki

last: Tsuji

address: Furocho

department: Bioscience and Biotechnology Center

country: Japan

institute: Nagoya University

data_processing:
[Read alignment software]  Bowtie2
[Feature count]  Subread 2.1
Genome_build: Oryza sativa MSU7
Supplementary_files_format_and_content: 03-201130-TakaNIL-task.11v02.make_UMIcounts_matrix.pl.stdout.txt

organism: Oryza sativa

growth_protocol: Plants were grown in climate chambers at 70% humidity under short day conditions with daily cycles of 10 h of light at 27 °C and 14 h of dark at 25 °C. Light was provided by fluorescent white light tubes (400–700 nm, 100 μmol m-2·s-1).

extract_protocol:
Total RNA was extracted from the tissue using Plant Total RNA Mini Kit (Favogen)
Library construction was conducted according to the CEL-Seq2 method (10) with modifications. Briefly, 100 pg of RNA were used for amplification by in vitro transcription. Libraries were amplified by 11 -15 cycles of PCR, which was empirically determined.

tag: cultivar

value: Takanari

tag: tissue

value: axillary meristems


title: E. coli C3000 5 min - targeting - rep 1

city: Skolkovo

first: Matvei

last: Kolesnik

address: 3 Nobel str

department: Life Sciences

country: Russia

institute: Skoltech

data_processing:
Raw RNA sequencing reads were filtered by quality with the simultaneous adapters removal using trimmomatic v. 0.36. The exact parameters of trimmomatic run could be found in raw_data_processing.sh file.
Processed reads were mapped onto reference sequences (RefSeq: NC_000913.3 supplemented with pC002 and pC008 plasmids in case of nontargeting samples and NC_000913.3 supplemented with pC003_RFP_spacer and pC008 plasmids in case of targeting samples) using bowtie2 v. 2.3.4.3 producing corresponding SAM files. In case of the analysis of data obtained from in vitro experiments on isolated E. coli total RNAб reads were mapped only onto the NC_000913.3 sequence. The exact parameters of bowtie2 run could be found in read_mapping.sh file.
For each nucleotide position of each strand of reference sequences the number of 5’ ends of aligned fragments were counted producing corresponding tables (see return_fragment_coords_table.py file for details).
The obtained tables were joined using merge_ends_count_tables.py script. The differences between the numbers of mapped 5’ ends in targeting and nontargeting samples were analyzed using edgeR package v.  3.26.3. The features (here, strand specific nucleotide positions) with low counts were excluded from the analysis. The TMM normalization method implemented in edgeR was applied. Next, the edgeR likelihood ratio test was performed. The obtained p-values were corrected using Benjamini-Hochberg method, and the result tables containing analyzed features with assigned log2FC and adjusted p-values were written to separate files (see TCS_calling.R file for details). The obtained trascript cleavage sites were overlapped with annotated genomic features using GenomicRanges package.
Assembly: NC_000913.3

organism: Escherichia coli

growth_protocol: E. coli cells were grown overnight in LB supplemented with 25 µg/ml chloramphenicol and 100 µg/ml ampicillin. Cell cultures were diluted 1:100 in fresh LB with double selection and grown for 1 hour at 37 °C with continuous shaking. After 1 hour, target expression was induced with 500 ng/ml anhydrotetracyline.

extract_protocol:
Total RNA was isolated from cells pelleted at 5 minutes (E. coli C3000 5 min samples) or 30 minutes (E. coli C3000 + M13 phage samples) post RFP induction. Cell lysis was done using Max Bacterial Enhancement Reagent (Invitrogen) for 4 min and then with TRIzol reagent (Invitrogen) for 5 min. RNA was extracted by chloroform and precipitated with isopropanol. RNA pellets were washed with 70% ethanol and then dissolved in nuclease free water and then treated with Turbo DNA-free kit (Invitrogen).
Total RNA samples were treated with MICROBExpress Bacterial mRNA Enrichment Kit (Invitrogen) for rRNA depletion prior to library preparation. To obtain both primary (5’ PPP) and processed (5’ P/5’ OH) transcripts, RNA samples were treated with RNA 5' Pyrophosphohydrolase (RppH) (NEB) for 30 min at 37C which removes pyrophosphate from 5’ end from triphosphorylated RNA to leave a 5’ monophoshphate RNA. Fragmentation was carried out by sonication using the Covaris protocol to obtain fragments of 200 nt size. T4 PNK (NEB) treatment was done to obtain 5’P ends for adapter ligation during library preparation. Samples were purified using the Zymo Research Oligo Clean and Concentrator kit. Library preparation for RNA sequencing was done using the NEBNext Multiplex Small RNA Library Prep Set for Illumina according to manufacturer’s protocol. BluePippin size selection was done using 2% agarose gel cassette (Sage Science) to select for 100 - 600 bp products. QC at each step was carried out by both Qubit and fragment analyzer.

treatment_protocol: Expression of target transcript was induced with 500 ng/ml anhydrotetracyline


title: E. coli C3000 + M13 phage - targeting - rep 1


title: T8_AM4


title: CTCF_DNR_ML792_3

city: Montpellier

first: Denis

last: Tempé

address: 1919 route de Mende

country: France

institute: CNRS

description: PE50 on SP flow cell

library_source: genomic

data_processing:
Basecalls were performed using Illumina RTA software for Novaseq output.
Reads were trimmed using Trimmomatic v0.39 with paramaters ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50
Reads were aligned using Bowtie2 v2.3.5.
Reads were wig-converted and scaled using the PASHA pipeline (doi:10.1093/bioinformatics/btw206. PMID: 27153642.) with settings --threshold 70000 --bin 50
Wig files were merged from triplicates using the mergeWigs Rscript
Peaks were called and using the PASHA pipeline with settings --threshold 360 --minRun 50 --maxGap 50
BigWig files were generated using the UCSC wigToBigWig tool (doi: 10.1093/bioinformatics/btq351.PMID: 20639541; PMCID: PMC2922891).
Assembly: hg38
Supplementary files format and content: bigWig
Supplementary files format and content: bed
Library strategy: Cut&Run

molecule: genomic DNA

organism: Homo sapiens

source_name: peripheral blood

growth_protocol: HL-60 cells were cultured at 37°C in the presence of 5% CO2 in RPMI (Eurobio) medium supplemented with 10% decomplemented (30 min at 56°C) fetal bovine serum (FBS) and penicillin and streptomycin.

extract_protocol:
Cut&Run DNA fragments were extracted using Monarch®PCR & DNA Cleanup Kit (catalog #T1030).
Sequencing libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit (Illumina, catalog #E7645) with fragments amplification for 15 cycles and purification using cleanNGS beads (CleanNA, catalog #CNGS-0001).
Librarieswerequality-checked and quntified by capillary electrophoresis (Fragment Analyzer, NGS HS kit) and sequenced by Illumina Novaseq 6000 sequencer as paired-end 50 base reads.

treatment_protocol: HL-60 cells were seeded at 0.3 x 10^6/mL the day before treatment for 2hrs with 1 µM DNR and 2 µM Ara-C.

value: peripheral blood

tag: cell line

value: promyeoloblasts

tag: cut&run antibody

value: Millipore, Catalog #07-729


title: CTCF_ML792_3

description: PE50 on SP flow cell


title: WT3 [HiSeq]

city: Baltimore

first: Xingliang

last: Zhu

state: Maryland

address: 251 Bayview Blvd

institute: National Institute on Aging, National Institutes of Health

data_processing:
RNAseq raw data were removed adaptor by TrimGalore
Data quality was checked by FastQC
Trimmed data were mapped to mm10 using RSEM with the STAR alignments
The bedgraph files were produced by BEDTools.
Read counts were normalized and caluculated by RSEM
Assembly: mm10
Supplementary files format and content: each sample contains a bedgraph file.

source_name: Brain

growth_protocol: 10-12 week old mice

extract_protocol:
RNA was extracted by Trizol.
RNA libraries for RNA-seq were prepared using published protocols (Joo et al., Nature Communications, 2020).

value: Brain

value: Whole brain

value: WT


title: Bone Marrow Derived Macrophage - Room Air exposure 2

description:
macviv_air_ctl_er052
DESeq2_results.txt
juncBASE_Output.txt
rMATS_RI_JCEC.txt


title: mRNA_Control8

type: RNA

city: Amsterdam

first: Silvia

last: D'Ambrosi

address: De Boelelaan 1118

country: Netherlands

institute: Amsterdam UMC

description: RNA hybridization with Human Immunology V2 Panel

hyb_protocol: Two different nCounter panels for the analysis of platelet-derived RNA. The Human Immunology V2 Panel (NanoString Technologies) targets 594 genes involved in the immune response such as cytokines, enzymes, interferons, and their receptors. For each sample, 6 ng of total platelet RNA was hybridized with the biotinylated capture probe and the reporter probe attached to color-barcode tags for 18 hours at 65°C. The second panel was a custom-made panel targeting 78 circRNAs (78-circRNA Panel), 6 linear reference genes and 4 mRNAs. For this analysis, 8 ng of total platelet RNA from each sample was hybridized with the capture and reporter probes for 18 hours at 67°C.

scan_protocol: The automated nCounter® Prep Station was used to process the samples. The samples were purified and immobilized in a sample cartridge for data collection, where the target mRNA and circRNA in each hybridized sample were quantified, using the nCounter Digital Analyzer.

data_processing:
Pre-processing and normalization of the data were performed using R (version 4.0.3) and Rstudio as graphical interface (version 2022.02.2). The quality of the raw RCC proprietary format data was initially assessed by using the NanoStringQCPro (version 1.22.0) package. Standard control metrics embedded by NanoString, such as Imaging, Binding Density, Positive Control Linearity, and Limit of Detection, were used to search for any potential outlier samples.
Additionally, all samples were also subjected to supplementary exploratory examination, including Principal Component Analysis (PCA) and Inter Quartile Range (IQR) method for outlier detection. Samples higher than the upper bound (Q3 + 1.5 * IQR) or lower than the lower bound (Q1 - 1.5 * IQR) were excluded from subsequent analysis.
Prior to normalization, negative control probes embedded to each panel were used to filter out targets with poor expression and high background noise. Consequently, the background values were firstly calculated, by taking the mean of each sample’s Negative Controls increased by two times the standard deviation, and then removed from each sample. Any transcript that indicated a score of less or equal to 0 in more than 75% of the examined samples, was excluded from further examination. After this filtering steps, the data was again evaluated using a PCA plot. Two different packages were compared for the normalization of the data: DESeq2 (version 1.30.1) and edgeR (version 3.32.1). The normalization performance was assessed using the standard relative log expression (RLE) plot. DESeq2 was chosen as default to perform the normalization of the data. Differential expression (DE) analysis was performed to find significantly differentially (|FC|>0.5 and p-adj < 0.05) expressed genes between the cancer and control groups.

label: biotin

molecule: polyA RNA

source_name: platelets

label_protocol: According to the manufacturer’s instructions (NanoStrings Technologies, Seattle, WA).

extract_protocol: Platelets isolation from the whole blood specimens was performed by separating platelet-rich plasma (PRP) and nucleated blood cells, by centrifugation at 120 g for 20 minutes, followed by PRP centrifugation at 360 g for 20 minutes at room temperature. Resulting platelets pellet was re-suspended in RNAlater. Total RNA isolation was carried out using the mirVana RNA isolation kit according to the manufacturer's instructions (Ambion, Thermo Scientific, cat. no. AM1560). Extracted RNA was eluded in 30 μl of mirVana buffer

tag: disease state

value: control

tag: Stage

value: platelets

value: whole blood

tag: fraction

value: mRNA


title: 13-treatment1

city: London

first: Efthymia

last: Papaevangelou

address: Guy's Hospital

department: Peter Gorer Department of Immunobiology

country: United Kingdom

institute: King's College London

description: subcutaneous tumor model

data_processing:
Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq program version 2.20. One mis-match was allowed for index sequence identification.
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mus musculus reference genome GRCm38 using the STAR aligner v.2.5.2b. The STAR aligner uses a splice aligner that detects intron/exon junctions and helps align the entire read sequences.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
The gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the groups of samples was performed.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include hit counts for each sample
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 TPM values for every gene and every sample

source_name: TRAMP-C2 tumor

growth_protocol: Male C57BL/6J mice, 6–8 weeks old, were injected with 5 x 10^6 TRAMP-C2 cells in 0.1 mL PBS subcutaneously into the right flank.

extract_protocol:
At day 6, tumors were removed, flash frozen on dry ice, and RNA was harvested using an RNeasy Mini Kit (Qiagen). NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice with tumors of an approximate 200mm^3 volume were randomly divided into four treatment cohorts and treated intratumorally with 3 doses (every other day) of 50 µl HBSS (Hank’s balanced salt solution, vehicle control) or 2 doses of 10µg cyto-IL-15 or with 3 doses of 50µg (in 50µl) of ADU-S100 or combination of ADU-S100 (3 doses) and cyto-IL-15 (2 doses). Treatments were given as three doses injected at days 0, 2 and 4 for ADU-S100 and at days 0 and 4 for cyto-IL-15.

value: tumor

tag: tumor type

value: prostate


title: CTCF_DMSO_3

description: PE50 on SP flow cell

value: DMSO


title: HEK293A-GNB1L-dTAG cells, dTAGv-1_rep2

city: Shenzhen

first: Fuwen

last: Yao

address: Sungang Road 3001

country: China

institute: Shenzhen Second People's Hospital

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequance using Trimmomatic
Trimmed sequence reads were mapped to GRCh38/hg38 using hisat2
Reads count extraction and normalization were performed using HTseq
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

source_name: Kidney

growth_protocol: HEK293A-GNB1L-dTAG cells were cultured in Dulbecco’s modified Eagle’s medium with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was extracted  by   the Qiagen; 217004 kit
RNA libraries for RNA-seq were performed by NEB mRNAseq library preparation kit

treatment_protocol: HEK293A-GNB1L-dTAG cells were seeded at lower confluence (about 15%) and maintained with DMEM containing 10% FBS and either 1 uM NEG or 1 uM dTAGv-1 for 3 days

value: Kidney

value: human embryonic kidney cells

value: GNB1L depletion


title: HEK293A-GNB1L-dTAG cells, dTAGv-1_rep3


title: HEK293A-GNB1L-dTAG cells, dTAG-NEG_rep3

value: NEG


title: CTCF_DNR_3

description: PE50 on SP flow cell

value: peripheral blood

value: DNR


title: T5_AM1

value: Takanari

value: axillary meristems


title: T6_SAM

source_name: SAM


title: 9R-treatment1

description: subcutaneous tumor model


title: 22LL-control

description: subcutaneous tumor model

value: HBSS (control)


title: HEK293A-GNB1L-dTAG cells, dTAGv-1_rep1


title: T4_AM2


title: HEK293A-GNB1L-dTAG cells, dTAG-NEG_rep2

value: WT


title: 22R-control

description: subcutaneous tumor model


title: CTCF_ML792_2

description: PE50 on SP flow cell

value: promyeoloblasts

value: Millipore, Catalog #07-729


title: CTCF_DNR_2

description: PE50 on SP flow cell


title: 19-control

description: subcutaneous tumor model


title: 20LL-treatment1

description: subcutaneous tumor model


title: T3_AM3


title: T2_AM4


title: T7_AM5


title: ChIP-seq_BMDM_DexLPS_BRG1_rep2

city: Freising

first: Franziska

last: Greulich

address: Gregor-Mendel-Str. 2

department: Metabolic Programming

country: Germany

institute: TU München

data_processing:
Paired-end reads were mapped to the murine reference genome mm10 (Ensembl GRCm38.p6 (https://nov2020.archive.ensembl.org/Mus_musculus/Info/Index)) with BWA-MEM version 0.7.13 (https://github.com/lh3/bwa).
PCR duplicates were removed using Picard Tools version 2.0.1 (http://picard.sourceforge.net/).
Singeltons and multimappers were removed with Samtools version 1.11 (https://github.com/samtools/samtools).
Alignments were converted to bigwig files, merging 10 bp per bin using ‘bamCoverage’ from the Deeptools package version 3.5.0 (https://github.com/deeptools/deepTools).
Peaks were called with MACS version 3.0.0a5 in BAMPE mode and an FDR cutoff of 0.05 (https://github.com/macs3-project/MACS).
Blacklisted regions (https://github.com/Boyle-Lab/Blacklist/tree/master/lists: mm10-blacklist.v2.bed.gz) were removed from the called peaks.
Peaks were annotated to the closest TSS using UCSC gene annotation (TxDb.Mmusculus.UCSC.mm10.knownGene) and the ChiPpeakAnno R package v3.24.1. (doi: 10.1186/1471-2105-11-237)
Genome_build: mm10 (GRC38.p6)
Supplementary_files_format_and_content: NarrowPeak (.narrowpeak) files contain MACS3-called peak positions and scores (headers: A- chromosome, B-start, C-end, D-name, E-score, F-strand, G-signalValue, H-"-log10(pValue)", I-"-log10(qValue)", J-peakSummit (0-based from start)). Note, those peaklists are not cleaned of blacklisted regions. ; BigWig (.bw) files containing individual unscaled or mean coverage (scaled mean for all four replicates per treatment)  summarized at 10bp resolution for visualizetion in the genome browser.

source_name: bone marrow derived macrophages

growth_protocol: Bone marrow from male wild type mice was flushed with RPMI (Thermo Scientific) into Falcon tubes. Erythrocytes were removed with AKC lycis.Afterwards the cells were purified on a Ficoll gradient (GE Healthcare, 17-5442-02) and incubated with differentiation medium (DMEM (4.5g/l glucose,Sigma ), 30% supernatant of L929 cells, 20% FBS and 1% Pen/Strep) for 7 days in non cell culture treated plates. Differentiated macrophages were dissociated with Versene (Gibco) and seeded in cell culture treated plates in serum free medium (macrophage SFM, ThermoScientific) for further treatments.

extract_protocol:
ChIP-sequencing was performed as previously described  (doi: 10.1016/j.molcel.2012.10.013 ). In brief, 40 million cells were fixed with 2mM disuccinimidyl glutarate (DSG) at 4oC followed by 10 minutes fixation with 1% formaldehyde at RT. Cells were lysed in Fast IP buffer (150mM NaCl, 5mM EDTA, 5mM Tris, 1% Triton X-100 and 0.5% NP40) and cromatin was sheared with a Bioruptor in shearing buffer (1% SDS, 10µM EDTA and 0.05% Tris) until the majority of fragments were between 200-1000bp. Sheared chromatin was diluted 1:10 in Dilution buffer( 167mM NaCl, 16.7mM Tris, 1.2mM EDTA, 1.1% Triton X-100 and 0.01% SDS) and the IP was perfomed with 8µg of a-GR (Proteintech 24050-1-AP) and 16µg of a-BRG1(Cell Signalling #49360S and BRG1#abcam ab110641, 8µg from each) overnight. In the next day the IPs were incubated with Dynabeads (Invitrogen) for 6 hours. Afterwards the beads were washed with the FAST-IP budder and DNA was eluted in elution buffer (100mM NaHCO3 and 1%SDS).
Library preperation was performed from 5 ng of ChIP DNA using the Kapa Hyper Prep Kit with PCR library amplification (#KK8504, KapaBiosystems) according to the manufactur's protocol. Shortly, ChIP DNA was end-repaired and A-tailed before adapter ligation. After adapter ligation, the ChIP DNA was purified with Agencourt AMPure XP beads (#A63880, Beckman Coulter) and size-selected for 360-600 bp using the Pippin Prep System from Saga Science. The size-selected library is amplified by PCR using the Kapa Hyper Prep Kit (#KK8504,KapaBiosystems) and purified terminally with Agencourt AMPure XP beads (#A63880, Beckman Coulter).

treatment_protocol: 3 hours  LPS (100ng/ml LPS and 0.1% EtoH) or 3 hours LPS+Dex (100ng/ml LPS and 1µM Dex)

tag: antibody

value: BRG1 (D1Q7F)-Cell Signalling 49360S         BRG1- abcam ab110641

tag: Sex

value: male

value: 3h 100 ng/ml LPS and 1uM Dex

value: wildtype


title: CTCF_DMSO_2

description: PE50 on SP flow cell

value: DMSO


title: HEK293A-GNB1L-dTAG cells, dTAG-NEG_rep1

value: Kidney


title: IgG_Sin3a_CUTnTag

city: New York

first: Meelad

middle: M

last: Dawlaty

state: New York

address: 1301 Morris Park Ave, Price 419, Bronx

department: Genetics

institute: Albert Einstein College of Medicine

description: CUT&Tag with anti IgG antibody

data_processing:
For RNA-seq RNA was extracted using Omega E.Z.N.A. Total RNA kit I (R6834). Library preparation and mRNA sequencing were performed at Novogene using their Illumina Novoseq 6000 platform. Adaptors were trimmed using trim galore (v0.6.5) and clean reads were mapped to the mouse genome (mm10) using STAR (v2.7.3a) with default parameters. Gene counts were extracted from mapped reads using featureCounts with --largestOverlap parameter. Raw counts were used to identify differentially expressed genes with DESeq2 (FDR <0.05 and fold-change >1.5), following the standard package documentation.
For CUT&Tag cleaned reads were mapped to the mouse genome (mm10) using Bowtie2 (Version 2.2.3) (Langmead and Salzberg, 2012) with options: --local --very-sensitive-local --no-unal --no-mixed --no-discordant -I 10 -X 700. Peak calling was performed using MACS2 (Version 2.1.0) (Zhang et al., 2008) with options -f BAMPE --keep-dup all.
For WGBS, DNA was extracted by Quick-DNA miniprep kit (Zymo, D3024) following the manufacturer’s instructions. Bisulfite conversion and sequencing were performed at BGI Genomics (https://en.genomics.cn/). Lamda DNA spike-in confirmed a >99.4% bisulfite conversion efficiency. The libraries were subjected to 100 bp pair-end sequencing on a HiSeq 4000 Illumina platform. The raw reads were filtered by SOAPnuke (v1.5.5) (https://github.com/BGI-flexlab/SOAPnuke) with the parameters -n 0.001 -l 20 -q 0.4 -A 0.25 -Q 2 -G to remove adaptors and filter out low-quality reads. Clean reads were mapped to mouse genome mm10 using Bismark (v0.22.3) with default parameters. Duplicated reads were removed using deduplicate_bismark and methylation status of each cytosine extracted with bismark_methylation_extractor
Samtools was used to convert SAM to BAM, sort and index corresponding BAM files. Bigwig files were generated using bamCoverage from deepTools, and bigwig files were analyzed using plotProfile and plotHeatmap.Peaks annotation were implemented by R package "ChIPseeker".
Assembly: mm10
Supplementary files format and content: bigwig

source_name: Mouse ESCs

growth_protocol: ESCs were cultured on gelatin in serum/LIF and then harvested for subsequent high-throughput sequencing.

extract_protocol:
For RNA-seq, RNA extraction was performed using Omega E.Z.N.A Total RNA kit. For WGBS, DNA extraction was performed using Zymo Quick-DNA Miniprep Kit.
RNA-seq libraries were prepared by Novogene (https://en.novogene.com/). WGBS libraries were prepared by BGI company (https://en.genomics.cn/). CUT&Tag libraries were prepared by NEBNext HiFi 2x PCR Master mix.
RNA-seq, CUT&Tag, WGBS

treatment_protocol: For CUT&Tag, ESCs were crosslinked, bound to Con-A beads, incubated with primary antibody and treated with pre-loaded pA-Tn5 adapter complex.

value: Embryonic stem cells

value: V6.5 Male mixed 129/C57BL/6

value: Anti IgG Antibody (CST, 3900)


title: ChIP-seq_BMDM_DexLPS_BRG1_rep1


title: Tet1_Tet2_knockout_Sin3a_CUTnTag_rep2

description: CUT&Tag with anti Sin3a antibody

value: Anti Sin3a Antibody (Abcam, ab3479)

value: Tet1 Tet2 knockout


title: T18_SAM

description: T18.SAM.5.1 was omitted from the processed data because the reads from this sample were not aligned. The reason may be technical, as our protocol used very-low-amount of RNA.

value: Takanari


title: CTCF_DNR_ML792_2

description: PE50 on SP flow cell

value: peripheral blood


title: CTCF_DNR_ML792_1

description: PE50 on SP flow cell


title: T17_AM1

value: axillary meristems


title: Tet1_Tet2_knockout_Sin3a_CUTnTag_rep1

description: CUT&Tag with anti Sin3a antibody


title: CTCF_DNR_1

description: PE50 on SP flow cell

value: DNR


title: ChIP-seq_BMDM_LPS_BRG1_rep1

value: 3h 100 ng/ml LPS and 0.1% EtoH


title: CTCF_ML792_1

description: PE50 on SP flow cell

value: promyeoloblasts

value: Millipore, Catalog #07-729


title: ChIP-seq_BMDM_LPS_BRG1_rep2

value: BRG1 (D1Q7F)-Cell Signalling 49360S         BRG1- abcam ab110641

value: male


title: T16_AM2


title: ChIP-seq_BMDM_DexLPS_GR_rep2

value: Glucocorticoid Receptor- Proteintech 24050-1-AP

value: 3h 100 ng/ml LPS and 1uM Dex

value: wildtype


title: Tet1_Tet2_mutant_Sin3a_CUTnTag_rep2

description: CUT&Tag with anti Sin3a antibody

value: Embryonic stem cells

value: Tet1 Tet2 mutant


title: CTCF_DMSO_1

description: PE50 on SP flow cell

value: DMSO


title: T15_AM3


title: Tet1_Tet2_mutant_Sin3a_CUTnTag_rep1

description: CUT&Tag with anti Sin3a antibody

value: V6.5 Male mixed 129/C57BL/6

value: Anti Sin3a Antibody (Abcam, ab3479)


title: T14_AM4

value: Takanari


title: Tet1_Tet2_wildtype_Sin3a_CUTnTag_rep2

description: CUT&Tag with anti Sin3a antibody

value: Tet1 Tet2 wildtype


title: ChIP-seq_BMDM_DexLPS_GR_rep1


title: T13_AM5

value: axillary meristems


title: ATAC-seq_LPS_rep4

data_processing:
Paired-end reads were mapped to the mm10 (GRCm38.p6) reference genome obtained from Ensembl with Bowtie2 version 2.4.2 (https://github.com/BenLangmead/bowtie2).
PCR duplicates were removed with Picard tools version 2.0.1 (http://picard.sourceforge.net/).
Multi-mapping and non-paired reads were removed with samtools version 1.22 (https://github.com/samtools/samtools).
Alignments are converted to BigWig files and scaled in accordance to their reads-in-peaks fraction with Deeptools version 3.5.0 (https://github.com/deeptools/deepTools).
Peakss were called with MACS version 3.0.0a5 (https://github.com/macs3-project/MACS).
Genome_build: mm10 (GRCm38.p6)
Supplementary_files_format_and_content: .narrowPeak for MACS3-called peak positions and scores (headers: A- chromosome, B-start, C-end, D-name, E-score, F-strand, G-signalValue, H-"-log10(pValue)", I-"-log10(qValue)", J-peakSummit (0-based from start)). Note, those peaklists are not cleaned of blacklisted regions. ; BigWig (.bw) files containing individual unscaled or mean coverage (scaled mean for all four replicates per treatment)  summarized at 10bp resolution for visualizetion in the genome browser.

growth_protocol: Bone marrow from male wild type mice (C57BL6/J, 6-12 week) was flushed with RPMI (Thermo Scientific) into Falcon tubes. Erythrocytes were removed with the AKC lycis. Afterwards the cells were purified on a Ficoll gradient ( GE Healthcare, 17-5442-02) and incubated with differentiation medium (DMEM (4.5g/l glucose,Sigma ), 30% supernatant of L929 cells, 20% FBS and 1% Pen/Strep) for 7 days in non-cell culture treated plates. Differentiated macrophages were dissociated with Versene (Gibco) and seeded in cell culture dishes in serum free medium (macrophage SFM, ThermoScientific) for 16-24 hours before treatment.

extract_protocol:
ATAC seq was performed as previously described (doi: 10.1038/nmeth.4396). In brief, 50.000 viable cells were lysed in 50µL resuspension buffer 1 (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40,0.1% Tween-20 and 0.01% Digitonin) on ice for 3 mins. The lysates were washed with resuspension buffer 2 ( 10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2,0.1% Tween-20). The nuclei were pelleted and resuspended in 50µL transposition mixture ( 25µL 2xTD buffer, 2.5µL Tn5 transposase (Illumina Tagment DNA enzyme and buffer kit #20034197), 16.5µL PBS, 0.5µL 1% digitonin, 0,5µL 10% Tween-20 and 5µL H2O). The reactions were incubated for 30 minutes at 37oC  agitating at 1000rpm and the transposed DNA was subsequently purified using the PCR MinElute purification kit (Qiagen).
The tagmented DNA was initially amplified for 4 cycles using the NEBNext 2x PCR master mix (NEB) and Illumina compatible primers as described (https://doi.org/10.1038/nmeth.2688). The additional number of cycles for the amplification of the libraries were determined by a qPCR reaction using the amplified DNA as template and the Kappa SYBR Green (Roche) as indicated (doi: 10.1002/0471142727.mb2129s109). Libraries were further amplified and purified using the PCR MinElute kit (Qiagen). Size selection  was performed on purified libraries for fragments between 150-600bp the Agecount AMPure XP beads (Beckman Coulter)  and their quality was determined by the Qubit dsDNA HS kit (Thermo Scientific) and the Agilent High Sensitivity DNA kit on a  Bioanalyzer 2100.

treatment_protocol: Differentiated macrophages were either treated for 3 h  LPS (100ng/ml LPS and 0.1% EtoH) or 3 hLPS+Dex (100ng/ml LPS and 1µM Dex).

value: bone marrow derived macrophages


title: H9 Day 5 Chondrocyte, Undigested, H3K27ac, bio rep 4 [HiChIP]

city: Stanford

first: Jaaved

last: Mohammed

address: 265 Campus Drive

department: Chemical and Systems Biology

institute: Stanford University

data_processing:
Illumina NovoSeq 6000 sequencing produced 3 reads: first mate pair (99bp), second mate pair (99bp), and UMI sequence (9bp). To process reads, first and second mate pair reads were processed with fastp paired-end default settings in order to trim adaptor sequences. To deduplicate reads using UMIs, we first aligned trimmed paired-end reads to the hg38 genome using "bwa mem" with "-SP5M" option. Next, we used the program "umi_tools dedup" with default settings to process the aligned BAM files in order to remove duplicated reads originating from PCR amplification. Unfiltered BAM records corresponding to unique first and second mate pairs were written to corresponding read1 and read2 fastq files using "samtools collate" and "samtools fastq".
Deduplicated read1 and read2 sequences were processed with HiC-Pro without additional software deduplication. Reads were aligned to hg38 reference assembly with MboI ligation sites. HiC-Pro's .allvalidpairs files were converted to GInteraction format using HiCExplorer tool hicConvertFormat and provided as *.tsv.gz files.
For identifying HiChIP interactions, we used the MAPS program without additional software deduplication. MAPS aligns reads and identifies significant interactions. For individual samples, we used the hg38 genome assembly, 10K resolution, MboI ligation sites, and provide all interactions in *.sig3Dinteractions.bedpe.gz files. However, we recommend combining data across biological replicates, and using MAPS to identify significant interactions for a given cell type.
Assembly: hg38
Supplementary files format and content: .tsv files are Ginteraction format files output produced from hicConvertFormat using HiC-Pro allvalidpairs file as input
Supplementary files format and content: .bedpe files are paired-end BED format files produced from MAPS
Library strategy: HiChIP

source_name: Chondrocytes

growth_protocol: H9 hESC line was cultured and differentiation to CNCCs using protocol previously described in (Prescott et al. 2015) [PMID 26365491]. Passage 4 CNCCs were either harvested for experiments, or differentiated further to cranial chondrocytes using protocol described in (Long et al. 2020) [PMID: 32991838]

extract_protocol:
HiChIP experiments were performed following protocol described in (Mumbach et al. 2016) [PMID 27643841], using MboI digestion and sonication using Covaris E220 sonicator with settings power, 140 W; duty factor, 10%; cycle per burst, 200; time, 4 minutes; temp, 4°C, for an intended fragment target size between 200-700bp . For each biological replicate, 10 million CNCCs were fixed in suspension in 1% methanol-free formaldehyde diluted in serum-free medium with end-over-end rotation, quenched with 0.2M Glycine (final concentration), washed twice with ice-cold PBS, pelleted by centrifugation, and snap-frozen in liquid nitrogen. For cranial chondrocytes, cell were fixed similar to CNCCs as either single-cell chondrocytes after ECM digestion according to (Makki et al. 2017) [PMID 28315317], or as undigested "sheets" of chondrocytic tissue, both following 5 days of in vitro differentiation from CNCCs.
Libraries were constructed using protocol recommended by NEBNext Ultra II DNA Library Prep Kit for Illumina (Cat No. E7645). We substituted adaptors recommended by this kit with adaptors consisting of unique dual-index barcodes and unique molecular identifiers (IDT xGen UDI-UMI Adapters Cat No 10005925).

value: Chondrocytes

value: H9-derived cranial chondrocytes

value: WT

tag: chip antibody

value: Active Motif 39133


title: H9 Day 5 Chondrocyte, Undigested, H3K27ac, bio rep 3 [HiChIP]


title: T12_SAM


title: Tet1_Tet2_wildtype_Sin3a_CUTnTag_rep1

description: CUT&Tag with anti Sin3a antibody


title: IgG_Sin3a_Sap30_CUTnTag

description: CUT&Tag with anti IgG antibody

value: Anti IgG Antibody (CST, 3900)


title: H9 Day 5 Chondrocyte, Undigested, H3K27ac, bio rep 2 [HiChIP]


title: ATAC-seq_LPS_rep3

value: male

value: 3h 100 ng/ml LPS and 0.1% EtoH


title: Tet2_knockout_Sap30_CUTnTag

description: CUT&Tag with anti Sap30 antibody

value: Anti Sap30 Antibody (Novus, NBP2-99031)

value: Tet2 knockout


title: T11_AM1


title: H9 Day 5 Chondrocyte, Undigested, H3K27ac, bio rep 1 [HiChIP]


title: T10_AM2


title: ATAC-seq_LPS_rep2

value: wildtype


title: Tet2_mutant_Sap30_CUTnTag

description: CUT&Tag with anti Sap30 antibody

value: Embryonic stem cells

value: Tet2 mutant


title: ATAC-seq_LPS_rep1


title: N9_AM3


title: T1_AM5


title: Tet2_wildtype_Sap30_CUTnTag

description: CUT&Tag with anti Sap30 antibody

value: V6.5 Male mixed 129/C57BL/6

value: Tet2 wildtype


title: H9 Day 5 Chondrocyte, H3K27ac, bio rep 8 [HiChIP]


title: Tet2_knockout_Sin3a_CUTnTag

description: CUT&Tag with anti Sin3a antibody

value: Anti Sin3a Antibody (Abcam, ab3479)


title: H9 Day 5 Chondrocyte, H3K27ac, bio rep 7 [HiChIP]


title: N8_AM4

value: axillary meristems


title: ATAC-seq_DexLPS_rep2

value: bone marrow derived macrophages

value: 3h 100 ng/ml LPS and 1uM Dex


title: H9 Day 5 Chondrocyte, H3K27ac, bio rep 6 [HiChIP]

value: Chondrocytes

value: H9-derived cranial chondrocytes


title: IgG_H3K27ac_CUTnTag

description: CUT&Tag with anti IgG antibody


title: Tet2_mutant_Sin3a_CUTnTag

description: CUT&Tag with anti Sin3a antibody


title: Tet2_wildtype_Sin3a_CUTnTag

description: CUT&Tag with anti Sin3a antibody


title: N7_AM5


title: ATAC-seq_DexLPS_rep4


title: ATAC-seq_DexLPS_rep3


title: H9 Day 5 Chondrocyte, H3K27ac, bio rep 3 [HiChIP]

value: WT

value: Active Motif 39133


title: N5_AM1


title: H9 Day 5 Chondrocyte, H3K27ac, bio rep 5 [HiChIP]


title: Tet2_mutant_H3K27ac_CUTnTag

description: CUT&Tag with anti H3K27ac antibody

value: Anti H3K27ac Antibody (Abcam, ab4729)


title: N2_AM4


title: CLIP_QKI5_KD_IP_rep2

city: Beijing

first: Yue

last: Huo

state: Beijing

address: Dongcheng District, Dongdan 3 Tiao 5 Hao

department: State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences

institute: Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College

data_processing:
library strategy: CLIP-seq
Peaks were called with Homer software for ChIP-seq.
Peaks were called with clipper software for CLIP-seq.
Genome_build: Ensembl GRCh38.p5
Supplementary_files_format_and_content: peaks bed file for ChIP-seq and CLIP-seq.

source_name: THP-1 cell line

extract_protocol:
ChIP-seq: THP-1 cell lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with indicated antibody.
ChIP-seq: Libraries were prepared according to NEB's instructions accompanying the NEBNext Ultra II DNA Library Prep Kit (E7103S) and NEBNext Multiplex Oligos for Illumina (E7600S).
CLIP-seq: THP-1 cells were UV-crosslinked and lysed, then protein-RNA complexed were isolated with indicated antibody.
CLIP-seq: Libraries were prepared and sequenced using standard Illumina protocols.

treatment_protocol: THP-1 cells were infected with lenti-virus carrying sh-QKI5 sequence to knock down QKI5 or sh-control sequence.

value: infected with lenti-virus carrying sh-QKI5 sequence to knockdown QKI5

value: QKI5 (Millipore, AB9904, lot 3231958)


title: Lung benzene-exposed sample #6

city: Louisville

first: Sanjay

last: Srivastava

state: Kentucky

address: 302 E. Muhammad Ali

department: Medicine

institute: University of Louisville

data_processing:
Fastq files were trimmed using fastp version 0.20.0 and the following prameters: --cut_by_quality5 --cut_by_quality3 --detect_adapter_for_pe  --overrepresentation_analysis --correction  --trim_front1 7 --trim_front2 7
Alignment was performed using STAR version 020201 and the following parameters: --runMode alignReads --runThreadN 8  --outSAMstrandField intronMotif --outSAMmode Full --outSAMattributes All {params.stranded} --outSAMattrRGline {params.readgroup} --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 45000000000 --quantMode GeneCounts --outReadsUnmapped Fastx  -outSAMunmapped Within {params.keepPairs}
Differential expression analysis was perfomred using edgeR version 3.10 . The RLE method was used to normalize the data.
Genome_build: GRCm38.90
Supplementary_files_format_and_content: tab-delimited text file including CPM values and statistics based outputted by edgeR.

source_name: Lung

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instruction.
mRNA RNA-seq was performed by Novogene (California, U.S.A.) for poly-A mRNAs and sequenced with Illumina NovaSeq 6000 system (pair-end, 2 × 150 bp).

value: C57BL/6J background

tag: age

value: 14 weeks old

value: Male

value: Lung

value: 50ppm benzene (6hr/day, 5 days a week) for 6 weeks


title: N6_SAM


title: H9 Day 5 Chondrocyte, Undigested, Input, bio rep 1 [HiChIP]


title: KO_1

city: Rochester

first: Cameron

last: Baker

state: NY

address: 601 Elmwood Ave

institute: University of Rochester

data_processing:
DEMULTIPLEXING - cellranger 3.1 mkfastq --use-bases-mask y*,I8,y* --nopreflight
COUNTING - cellranger-3.1.0 count --fastqs=./fastq_path --jobmode=slurm --maxjobs=100 --nopreflight --transcriptome=refdata-cellranger-mm10-3.0.0/ --project=${PROJECT} --indices=SI-GA-${INDEX} --id=Sample_${SAMPLEPREFIX} --sample=${SAMPLEPREFIX}
Genome_build: mm10
Supplementary_files_format_and_content: filtered feature bc matrices

source_name: Heart

extract_protocol:
Enzymatic digestion with collagenase/dispase followed by RBC lysis in ACK buffer and multiple washes in FACS buffer.  Flow cytometric sorting for GFP+/DAPI- populations and post-sort for viability.
Chromium Next GEM Single Cell 3′ GEM, Library & Gel Bead Kit v3.1 with NovaSeq: Cellular suspensions were loaded on a Chromium Single-Cell Instrument (10x Genomics, Pleasanton, CA, USA) to generate single-cell Gel Bead-in-Emulsions (GEMs). Single-cell RNA-Seq libraries were prepared using Chromium Next GEM Single Cell 3′ GEM, Library & Gel Bead Kit v3.1 (10x Genomics). The beads were dissolved and cells were lysed per manufacturer’s recommendations. GEM reverse transcription (GEM-RT) was performed to produce a barcoded, full-length cDNA from poly-adenylated mRNA. After incubation, GEMs were broken and the pooled post-GEM-RT reaction mixtures were recovered and cDNA was purified with silane magnetic beads (DynaBeads MyOne Silane Beads, PN37002D, ThermoFisher Scientific). The entire purified post GEM-RT product was amplified by PCR. This amplification reaction generated sufficient material to construct a 3’ cDNA library.  Enzymatic fragmentation and size selection was used to optimize the cDNA amplicon size and indexed sequencing libraries were constructed by End Repair, A-tailing, Adaptor Ligation, and PCR. Final libraries contain the P5 and P7 priming sites used in Illumina bridge amplification. Sequence data was generated using Illumina’s NovaSeq 6000.

value: Cardiac fibroblast

tag: cellranger index


title: KO_2

tag: cell type


title: Tet2_knockout_H3K27ac_CUTnTag

description: CUT&Tag with anti H3K27ac antibody

value: Embryonic stem cells

value: V6.5 Male mixed 129/C57BL/6

value: Tet2 knockout


title: N4_AM2

value: axillary meristems


title: CLIP_QKI5_KD_IP_rep1

tag: treatment


title: H9 Day 5 Chondrocyte, Input, bio rep 1 [HiChIP]

value: Chondrocytes

tag: genotype


title: N16_AM2


title: H9 Day 5 Chondrocyte, H3K27ac, bio rep 2 [HiChIP]

value: H9-derived cranial chondrocytes


title: WT_2


title: CLIP_QKI5_KD_input_rep2


title: WT_1


title: H9 Day 5 Chondrocyte, Input, bio rep 5 [HiChIP]

value: WT


title: Tet2_wildtype_H3K27ac_CUTnTag

description: CUT&Tag with anti H3K27ac antibody

tag: strain

value: Tet2 wildtype


title: ATAC-seq_DexLPS_rep1

value: bone marrow derived macrophages

value: male

value: 3h 100 ng/ml LPS and 1uM Dex

value: wildtype


title: N18_SAM

tag: cultivar


title: H9 Day 5 Chondrocyte, H3K27ac, bio rep 4 [HiChIP]

tag: tissue

value: Active Motif 39133


title: H9 Passage 4 CNCC, H3K27ac, bio rep 8 [HiChIP]

source_name: Neural Crest Cells

value: Neural Crest Cells

tag: cell line

value: H9-derived cranial neural crest cells


title: CLIP_ctrl_IP_rep2

value: infected with lenti-virus carrying sh-control sequence

value: QKI5 (Millipore, AB9904, lot 3231958)


title: Lung benzene-exposed sample #5

value: C57BL/6J background

value: 14 weeks old

value: Male

value: Lung

value: 50ppm benzene (6hr/day, 5 days a week) for 6 weeks


title: Lung benzene-exposed sample #4


title: N14_AM4

value: axillary meristems


title: N17_AM1


title: Lung benzene-exposed sample #1


title: N3_AM3


title: N13_AM5


title: H9 Passage 4 CNCC, H3K27ac, bio rep 6 [HiChIP]

value: WT


title: H9 Passage 4 CNCC, H3K27ac, bio rep 5 [HiChIP]


title: Lung benzene-exposed sample #3


title: CLIP_QKI5_KD_input_rep1

value: infected with lenti-virus carrying sh-QKI5 sequence to knockdown QKI5


title: Lung benzene-exposed sample #2


title: N15_AM3


title: H9 Passage 4 CNCC, H3K27ac, bio rep 4 [HiChIP]


title: H9 Passage 4 CNCC, H3K27ac, bio rep 7 [HiChIP]


title: H9 Day 5 Chondrocyte, H3K27ac, bio rep 1 [HiChIP]

value: Chondrocytes

value: H9-derived cranial chondrocytes


title: CLIP_ctrl_IP_rep1


title: Lung air control sample #6

value: carbon and HEPA filters purified air


title: Lung air control sample #3


title: N10_AM2


title: CLIP_ctrl_input_rep2


title: QKI5_KD_Pol II_ChIP_rep1

data_processing:
Peaks were called with Homer software for ChIP-seq.
Peaks were called with clipper software for CLIP-seq.
Genome_build: Ensembl GRCh38.p5
Supplementary_files_format_and_content: peaks bed file for ChIP-seq and CLIP-seq.


title: N12_SAM


title: H9 Passage 4 CNCC, H3K27ac, bio rep 2 [HiChIP]


title: CLIP_ctrl_input_rep1


title: H9 Passage 4 CNCC, H3K27ac, bio rep 1 [HiChIP]


title: H9 Passage 4 CNCC, H3K27ac, bio rep 3 [HiChIP]


title: Lung air control sample #5


title: N11_AM1


title: Lung air control sample #4


title: Lung air control sample #2


title: QKI5_KD_H3K4me3_ChIP_rep2


title: H9 Passage 4 CNCC, Input, bio rep 5 [HiChIP]


title: QKI5_KD_Pol II_ChIP_rep2


title: QKI5_KD_ChIP_input_rep4


title: A.ostoyae C2 fresh stems 3

city: Sopron

first: Boris

last: Indic

address: Bajcsy-Zsilinszky u. 4

department: Functional Genomics and Bioinformatics Group

country: Hungary

institute: Institute of Forest and Natural Resource Management, University of Sopron

data_processing:
100 ng RNA was enriched using RiboCop rRNA Depletion Kits (Lexogen, Austria).
The RNA was fragmented, end prepped and adapter-ligated.
The libraries were amplified according to the manufacturers instructions.
The quality of the libraries was checked on Agilent 4200 TapeSation System using D1000 Screen Tape (Agilent Technologies, Palo Alto, CA, USA), the quantity was measured on Qubit 3.0. Illumina sequencing was performed on the NovaSeq 6000 instrument (Illumina, San Diego, CA, USA) with 2 151 run configuration.
Raw RNA-Seq reads were aligned against the A. ostoyae (NCBI genome GCA_900157425.1 version 2) genome using STAR v2.7 .5a.
The level of expression was estimated using RSEM v1.3.9
Assembly: NCBI genome GCA_900157425.1 version 2

organism: Armillaria ostoyae

extract_protocol:
RNA was isolated from the frozen samples using the RNeasy Plant Midi Kit (Qiagen Inc.) according to the manufacturer’s protocol
The libraries for Illumina sequencing were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, Ipswitch, MA, USA)

value: low virulent

value: fresh stems


title: QKI5_KD_H3K4me3_ChIP_rep1


title: H9 Passage 4 CNCC, Input, bio rep 1 [HiChIP]

value: Neural Crest Cells


title: A.ostoyae C2 fresh stems 2


title: Liver benzene-exposed sample #4

source_name: Liver

value: Liver


title: Liver benzene-exposed sample #5


title: QKI5_KD_ChIP_input_rep2


title: A.ostoyae C2 fresh stems 1


title: QKI5_KD_ChIP_input_rep3


title: A.ostoyae C2 control 2

value: control


title: H9 Day 5 Chondrocyte, Input, for tracks [ChIP]

data_processing:
Illumina adaptors were trimmed using fastp with default options for paired-end reads. Reads were aligned to the hg38 reference assembly using "bwa mem" with default settings.
Duplicate reads were identified and removed from alignment files using "java -jar picard.jar MarkDuplicates", and alignment files were sorted and indexed with samtools.
Alignment BAM files were converted to coverage bigWig files using bamCoverage with options "--binSize 10 --normalizeUsing RPGC --effectiveGenomeSize 2805636331 --ignoreForNormalization chrX --extendReads"
Broad H3K27ac ChIP peaks were identified using macs3 with option "callpeak --broad -g hs --broad-cutoff 0.1"
Assembly: hg38
Supplementary files format and content: .bw files are bigWig format files produced from bamCoverage
Supplementary files format and content: .broadPeak files are BED format files produced from macs3

source_name: Chondrocyte

extract_protocol:
ChIP experiments were performed as described in (Long et al. 2020) [PMID: 32991838]. For each biological replicate, 10 million single-cell CNCCs or post-ECM-digested chondrocytes were fixed in suspension in 1% methanol-free formaldehyde diluted in serum-free medium with end-over-end rotation, quenched with 0.125M Glycine (final concentration), washed twice with ice-cold PBS, pelleted by centrifugation, and snap-frozen in liquid nitrogen. 1mL of lysed cells was sonicated on a Bioruptor sonicator 4 times (8-cycles; power, high; "on" interval, 30 sec; "off" interval, 45 seconds; temperature 4°C).
Libraries were constructed using protocol recommended by NEBNext Ultra II DNA Library Prep Kit for Illumina (Cat No. E7645) with unique dual indexes. We used adaptors consisting of unique i5 and i7 barcodes and unique molecular identifiers (IDT xGen UDI-UMI Adapters Cat No 10005925)

value: Chondrocyte


title: N1_AM5

data_processing:
[Read alignment software]  Bowtie2
[Feature count]  Subread 2.1
Genome_build: Oryza sativa MSU7
Supplementary_files_format_and_content: 03-201130-TakaNIL-task.11v02.make_UMIcounts_matrix.pl.stdout.txt


title: H9 Passage 4 CNCC, H3K27ac, for tracks [ChIP]

value: H9-derived cranial neural crest cells

value: Active Motif 39133


title: Ctrl_Pol II_ChIP_rep2

value: infected with lenti-virus carrying sh-control sequence


title: A.ostoyae C2 control 3


title: Liver benzene-exposed sample #3

value: C57BL/6J background

value: 14 weeks old

value: Male


title: H9 Day 5 Chondrocyte, H3K27ac, for tracks [ChIP]

value: WT


title: Liver benzene-exposed sample #2

value: 50ppm benzene (6hr/day, 5 days a week) for 6 weeks


title: H9 Day 5 Chondrocyte, Input, bio rep 2 [ChIP]


title: A.ostoyae C18 fresh stems 3

value: high virulent


title: A.ostoyae C18 fresh stems 2


title: Ctrl_Pol II_ChIP_rep1


title: Lung air control sample #1

value: Lung


title: QKI5_KD_ChIP_input_rep1

value: infected with lenti-virus carrying sh-QKI5 sequence to knockdown QKI5


title: A.ostoyae C2 control 1

value: low virulent


title: H9 Day 5 Chondrocyte, Input, bio rep 1 [ChIP]

value: H9-derived cranial chondrocytes


title: Liver benzene-exposed sample #1


title: H9 Day 5 Chondrocyte, Input, bio rep 3 [ChIP]


title: H9 Passage 4 CNCC, Input, for tracks [ChIP]

value: Neural Crest Cells


title: Liver air control sample #3

value: Liver

value: carbon and HEPA filters purified air


title: Liver air control sample #5


title: Liver air control sample #4


title: Liver air control sample #2


title: Ctrl_H3K4me3_ChIP_rep2


title: Ctrl_ChIP_input_rep2


title: A.ostoyae C18 fresh stems 1

value: fresh stems


title: Ctrl_H3K4me3_ChIP_rep1


title: H9 Day 5 Chondrocyte, H3K27ac, bio rep 3 [ChIP]

value: Chondrocyte


title: A.ostoyae C18 control 3

value: control


title: H9 Day 5 Chondrocyte, H3K27ac, bio rep 2 [ChIP]

value: Active Motif 39133


title: Liver air control sample #1

value: C57BL/6J background


title: Ctrl_ChIP_input_rep1

value: infected with lenti-virus carrying sh-control sequence


title: C28mono2A

status: Public on Jun 22 2023

first: Yan

last: WANG

address: 1068 Xueyuan Ave

institute: Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences

data_processing:
Raw sequencing reads (fastq) were quality checked using SOAPnuke (v1.5.2).
Bowtie2 (v2.2.5) was applied to align the clean reads to the genomes.
The expression level of gene was calculated by RSEM (v1.2.12).
Differential expression analysis was performed using DESeq2 (v1.4.5)
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: excel

source_name: chondrocyte

growth_protocol: C28/I2 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin–streptomycin.

extract_protocol:
RNAs were extracted from culture tissues. The samples were homogenized in Trizol (Invitrogen) and processed for RNA extraction according to the manufacturer’s instructions.
BGI in-house kit (BGI-Shenzhen, China)

treatment_protocol: C28/I2 cells were treated with FABP4 for 48 h and then collected for bulk RNA sequencing.

value: chondrocyte


title: A.ostoyae C18 control 1


title: H9 Day 5 Chondrocyte, H3K27ac, bio rep 1 [ChIP]

value: WT


title: C28FABP41A

value: FABP4 25 ng/mL, 48 h


title: C28mono1A


title: C28FABP42A


title: SR9243-Ocellaris-5dpt-I10

city: Onna-son

first: Natacha

last: Roux

state: Okinaw

address: 1919-1 Tancha

institute: OIST

description: PE 2*150, 1.0 Lane(s)

data_processing:
Read quality was checked using FastQC v0.11.8
Gene expression quantification was done using Kallisto v0.46.1
Assembly Amphiprion_ocellaris.AmpOce1.0.cds from Ensembl 109 was used to make transcriptome index file for kallisto

organism: Amphiprion ocellaris

source_name: entire larvae

growth_protocol: Larvae were maintained in beakers filled with sea water and appropriate treatment and kept at 27°C

extract_protocol:
RNA was extracted using a Maxwell®16 System with RNA extraction kit
(S-Sa) Stranded RNA Lib Prep, Poly-A

treatment_protocol:
DMSO control at 0.0001%
SR9243 at 10-7M T3 at 10-7M

value: entire larvae

tag: time

value: 5 days post treatment


title: T3-IOP-Ocellaris-5dpt-I7

description: PE 2*150, 1.0 Lane(s)


title: T3-IOP-Ocellaris-5dpt-I9

description: PE 2*150, 1.0 Lane(s)


title: T3-IOP-Ocellaris-5dpt-I5

description: PE 2*150, 1.0 Lane(s)


title: T3-IOP-Ocellaris-5dpt-I10

description: PE 2*150, 1.0 Lane(s)


title: T3-IOP-Ocellaris-5dpt-I6

description: PE 2*150, 1.0 Lane(s)


title: T3-IOP-Ocellaris-5dpt-I8

description: PE 2*150, 1.0 Lane(s)


title: SR9243-Ocellaris-5dpt-I6

description: PE 2*150, 1.0 Lane(s)


title: T3-IOP-Ocellaris-5dpt-I4

description: PE 2*150, 1.0 Lane(s)


title: SR9243-Ocellaris-5dpt-I3

description: PE 2*150, 1.0 Lane(s)


title: T3-IOP-Ocellaris-5dpt-I1

description: PE 2*150, 1.0 Lane(s)


title: T3-IOP-Ocellaris-5dpt-I2

description: PE 2*150, 1.0 Lane(s)


title: A.ostoyae C18 control 2

value: high virulent


title: T3-IOP-Ocellaris-5dpt-I3

description: PE 2*150, 1.0 Lane(s)


title: SR9243-Ocellaris-5dpt-I9

description: PE 2*150, 1.0 Lane(s)


title: SR9243-Ocellaris-5dpt-I1

description: PE 2*150, 1.0 Lane(s)


title: SR9243-Ocellaris-5dpt-I5

description: PE 2*150, 1.0 Lane(s)


title: DMSO-Ocellaris-5dpt-I10

description: PE 2*150, 1.0 Lane(s)

value: DMSO


title: DMSO-Ocellaris-5dpt-I7

description: PE 2*150, 1.0 Lane(s)


title: SR9243-Ocellaris-5dpt-I4

description: PE 2*150, 1.0 Lane(s)


title: DMSO-Ocellaris-5dpt-I6

description: PE 2*150, 1.0 Lane(s)


title: DMSO-Ocellaris-5dpt-I9

description: PE 2*150, 1.0 Lane(s)


title: DMSO-Ocellaris-5dpt-I5

description: PE 2*150, 1.0 Lane(s)


title: DMSO-Ocellaris-5dpt-I8

description: PE 2*150, 1.0 Lane(s)


title: DMSO-Ocellaris-5dpt-I3

description: PE 2*150, 1.0 Lane(s)


title: DMSO-Ocellaris-5dpt-I2

description: PE 2*150, 1.0 Lane(s)


title: DMSO-Ocellaris-5dpt-I1

description: PE 2*150, 1.0 Lane(s)


title: SR9243-Ocellaris-5dpt-I8

description: PE 2*150, 1.0 Lane(s)


title: DMSO-Ocellaris-5dpt-I4

description: PE 2*150, 1.0 Lane(s)


title: T3 9

city: Lyon

first: Simon

last: de Bernard

address: 30 rue Pré Gaudry

institute: AltraBio

description: PE 2*150, 1.0 Lane(s)

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp v0.23.2
Transcript expression quantification was performed using Salmon v1.7.0 and Ensembl annotations v105
Gene counts were derived using function tximport (with countsFromAbundance="lengthScaledTPM")
Assembly: AmpOce1.0
Supplementary files format and content: xlsx file includes estimated counts for each sample

treatment_protocol:
DMSO control at 0.0001%
T3 at 10-7M

value: 2 days post treatment


title: T3 10

description: PE 2*150, 1.0 Lane(s)


title: T3 8

description: PE 2*150, 1.0 Lane(s)


title: SR9243-Ocellaris-5dpt-I7

description: PE 2*150, 1.0 Lane(s)


title: SR9243-Ocellaris-5dpt-I2

description: PE 2*150, 1.0 Lane(s)


title: T3 5

description: PE 2*150, 1.0 Lane(s)


title: T3 4

description: PE 2*150, 1.0 Lane(s)


title: T3 1

description: PE 2*150, 1.0 Lane(s)


title: T3 7

description: PE 2*150, 1.0 Lane(s)


title: Control (T3) 10

description: PE 2*150, 1.0 Lane(s)


title: Control (T3) 9

description: PE 2*150, 1.0 Lane(s)


title: Control (T3) 5

description: PE 2*150, 1.0 Lane(s)


title: T3 2

description: PE 2*150, 1.0 Lane(s)


title: Control (T3) 7

description: PE 2*150, 1.0 Lane(s)


title: Control (T3) 6

description: PE 2*150, 1.0 Lane(s)


title: Control (T3) 1

description: PE 2*150, 1.0 Lane(s)


title: Control (T3) 2

description: PE 2*150, 1.0 Lane(s)


title: T3 6

description: PE 2*150, 1.0 Lane(s)


title: MPI 10

description: PE 2*150, 1.0 Lane(s)

treatment_protocol:
DMSO control at 0.0001%
MPI diluted at 1/1000

value: 19 days post treatment


title: MPI 8

description: PE 2*150, 1.0 Lane(s)


title: MPI 9

description: PE 2*150, 1.0 Lane(s)


title: Control (T3) 3

description: PE 2*150, 1.0 Lane(s)


title: Control (T3) 8

description: PE 2*150, 1.0 Lane(s)


title: T3 3

description: PE 2*150, 1.0 Lane(s)


title: MPI 6

description: PE 2*150, 1.0 Lane(s)


title: MPI 4

description: PE 2*150, 1.0 Lane(s)


title: MPI 7

description: PE 2*150, 1.0 Lane(s)


title: MPI 3

description: PE 2*150, 1.0 Lane(s)


title: Control (MPI) 9

description: PE 2*150, 1.0 Lane(s)


title: MPI 2

description: PE 2*150, 1.0 Lane(s)


title: MPI 1

description: PE 2*150, 1.0 Lane(s)


title: Control (MPI) 5

description: PE 2*150, 1.0 Lane(s)


title: Control (MPI) 8

description: PE 2*150, 1.0 Lane(s)


title: Control (MPI) 6

description: PE 2*150, 1.0 Lane(s)


title: Control (MPI) 4

description: PE 2*150, 1.0 Lane(s)


title: Control (MPI) 3

description: PE 2*150, 1.0 Lane(s)


title: Control (MPI) 7

description: PE 2*150, 1.0 Lane(s)


title: Control (MPI) 2

description: PE 2*150, 1.0 Lane(s)


title: Control (T3) 4

description: PE 2*150, 1.0 Lane(s)


title: Control (MPI) 1

description: PE 2*150, 1.0 Lane(s)


title: MPI 5

description: PE 2*150, 1.0 Lane(s)


title: Control (MPI) 10

description: PE 2*150, 1.0 Lane(s)


title: 48hc rep 2

city: Muenster

first: Marcos

middle: J.

last: Araúzo-Bravo

address: Rogentstrasse

department: Cell and Developmental Biology

institute: Max Planck Institute for Molecular Biomedicine

description: replicate 2

hyb_protocol: Purified and labeled cRNA was then hybridized for 18 hrs onto MouseRef-8 v2 expression BeadChips (Illumina, USA) following the manufacturer’s instructions

scan_protocol: After the recommended washing, the chips were stained with streptavidin-Cy3 (GE Healthcare) and scanned using the iScan reader (Illumina) and the accompanying software.

data_processing:
The bead intensities were mapped to gene information using BeadStudio 3.2 (Illumina),
background correction was perform using the Affymetrix Robust Multi-array Analysis (RMA) background correction model,
variance stabilization was performed using the log2 scaling and gene expression normalization was calculated with the quantile method implemented in the lumi package of R-Bioconductor.
Data post-processing and graphics were performed with in-house developed functions in MATLAB.
Hierarchical clusters of genes and samples were performed with the one minus the sample correlation metric and the
Unweighted Pair-Group Method using Average (UPGMA) linkage method

source_name: 48hc rep 2

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays.

extract_protocol: 300 ng of total DNA-free RNA was used as input for labelled cRNA synthesis (Illumina TotalPrep RNA Amplification Kit - Ambion) following the manufacturer's instructions (IVT: 14h)

value: embryonic stem cell

value: E1A induction

tag: harvest time after induction

value: 48h control

tag: genetic background

value: mixed C57BL/6, C3H and CD1


title: 9h rep 2

description: replicate 2

source_name: 9h rep 2


title: 6h rep 1

description: replicate 1

source_name: 6h rep 1


title: iBAT, HFD, WT (Axl-floxed Cre-) rep 5

city: Schwerzenbach

first: Adhideb

last: Ghosh

address: Schorenstrasse 16

department: Health Sciences and Technology

country: Switzerland

institute: ETH Zurich

description:
poly-A-enriched RNA
Arion_308

data_processing:
bcl2Fastq v2.20 software used for demultiplexing + basecalling
reads trimmed with fastp 0.20.0 and a custom adapter reference, options: --trim_front1 0 --trim_tail1 0 --average_qual 0 --max_len1 0 --max_len2 0 --disable_trim_poly_g --trim_poly_x --poly_x_min_len 10 --length_required 18 --compression 4
Alignments generated with STAR 2.7.4a, options: --twopassMode None --runThreadN 8 --sjdbOverhang 150 --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --outMultimapperOrder Random --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 100000 --alignMatesGapMax 100000  --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif --alignEndsProtrude 3 ConcordantPair --outSAMattributes All --outStd BAM_Unsorted --outSAMtype BAM Unsorted
Feature counts generated with Rsubread 2.8.1
Differential expression analysis: DESeq2
Assembly: GENCODE/GRCm38.p6/Release_M23-2019-11-05
Supplementary files format and content: Tab-separated raw counts

source_name: interscapular brown adipose tissue (iBAT)

growth_protocol: Mice were on ad lib HFD and non-restricted access to water, room temperature conditions, both groups were treated with tamoxifen once every 3 weeks

extract_protocol:
iBAT was dissected and snap-frozen. Total RNA was extracted using the Trizol-chloroform method and was Dnase treated for genomic DNA removal.
Libraries were constructed using TruSeq RNA Sample preparation kit (Illumina)

treatment_protocol: Different genotype, we compare floxed-Axl Cre- (wild-type controls) to iFAXLKO (floxed-Axl Cre+) mice

value: loxP-Axl-loxP Cre-

value: HFD challenge - Tamoxifen

tag: replicate


title: iBAT, HFD, WT (Axl-floxed Cre-) rep 4

description:
poly-A-enriched RNA
Arion_302

value: interscapular brown adipose tissue (iBAT)


title: iBAT, HFD, iFAXLKO (Axl-floxed Cre+) rep 8

description:
poly-A-enriched RNA
Arion_313

value: loxP-Axl-loxP Cre+


title: iBAT, HFD, iFAXLKO (Axl-floxed Cre+) rep 7

description:
poly-A-enriched RNA
Arion_304


title: iBAT, HFD, WT (Axl-floxed Cre-) rep 3

description:
poly-A-enriched RNA
Arion_297


title: iBAT, HFD, iFAXLKO (Axl-floxed Cre+) rep 6

description:
poly-A-enriched RNA
Arion_303


title: iBAT, HFD, iFAXLKO (Axl-floxed Cre+) rep 5

description:
poly-A-enriched RNA
Arion_301


title: 24h rep 1

description: replicate 1

source_name: 24h rep 1


title: iBAT, HFD, WT (Axl-floxed Cre-) rep 1

description:
poly-A-enriched RNA
Arion_291


title: iBAT, HFD, WT (Axl-floxed Cre-) rep 2

description:
poly-A-enriched RNA
Arion_292


title: 48h rep 1

description: replicate 1

source_name: 48h rep 1


title: iBAT, HFD, iFAXLKO (Axl-floxed Cre+) rep 4

description:
poly-A-enriched RNA
Arion_290


title: 3h rep 1

description: replicate 1

source_name: 3h rep 1


title: Neuron, motor, KO, rep2

city: Mississauga

first: Ho Sung

last: Rhee

state: ON

address: 3359 Mississauga Rd

department: Cell and Systems Biology

country: Canada

institute: University of Toronto

data_processing:
To remove adapter sequences from the sequencing data, raw sequencing reads were trimmed using Trim Galore (www.bioinformatics.babraham.ac.uk/).
The raw trimmed reads were aligned to the mm10 mouse genome using the RNA STAR using Galaxy (www.usegalaxy.org).
BAM files were generated using Galaxy (www.usegalaxy.org)
FPKM values were generated using Cufflinks using Galaxy (www.usegalaxy.org)
Tabular files were generated using Galaxy (www.usegalaxy.org)
Assembly: mm10
Supplementary files format and content: FPKM (Fragments Per Kilobase per Million mapped fragments)
Supplementary files format and content: Tabular file format (FPKM values are sorted in a raw and column format)

source_name: mESC-derived motor neuron

growth_protocol: Motor neuron differentiation of mouse embryonic stem (ES) cells was performed as described previously (Jaura and Yeh et al., Nat. Commun, 2022) with some modifications.

extract_protocol:
Cells were collected, poly(A)+ RNA was homogenized in a phenol-containing solution, and the sample was isolated by standard ethanol precipitation.
RNA-seq libraries were prepared according to the standard Illumina protocols. Briefly, cDNA was synthesized from RNA, end-repaired, and ligated to sequencing adaptors, then PCR amplified and gel purified. The purified DNA libraries were sequenced following the manufacturer's protocols.

treatment_protocol: ES cells were trypsinized and seeded at 8 x 10^4 cells per mL on day 0. 1 uM retinoic acid and 0.25 uM Sonic Hedgehog Agonist were added to the medium on day 2. 5 uM gamma-secretase inhibitors were added on days 4 and 5.

value: mESC-derived motor neuron


title: Neuron, motor, KO, rep1


title: Neuron, motor, KO, rep3


title: 24h rep 2

description: replicate 2

source_name: 24h rep 2


title: 0h rep 2

description: replicate 2

source_name: 0h rep 2


title: 0h rep 1

description: replicate 1

source_name: 0h rep 1


title: 9h rep 1

description: replicate 1

source_name: 9h rep 1


title: 6h rep 2

description: replicate 2

source_name: 6h rep 2


title: 48hc rep 1

description: replicate 1

source_name: 48hc rep 1


title: 12h rep 2

description: replicate 2

source_name: 12h rep 2


title: iBAT, HFD, iFAXLKO (Axl-floxed Cre+) rep 3

description:
poly-A-enriched RNA
Arion_289


title: 48h rep 2

description: replicate 2

source_name: 48h rep 2


title: 12h rep 1

description: replicate 1

source_name: 12h rep 1


title: iBAT, HFD, iFAXLKO (Axl-floxed Cre+) rep 1

description:
poly-A-enriched RNA
Arion_287


title: iBAT, HFD, iFAXLKO (Axl-floxed Cre+) rep 2

description:
poly-A-enriched RNA
Arion_288


title: KO_ActD_8h_Rep2

city: Monrovia

first: Jianjun

last: Chen

department: Systems Biology

institute: Beckman Research Institute of City of Hope

description: KO ActD 8h Rep2

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Reads were mapped to the mouse mm10 using the STAR aligner. The aligned reads were then assigned to genes using RSEM.
The aligned reads were then assigned to genes using RSEM
Assembly: mm10
Supplementary files format and content: table delimited text file containing the expression of genes

source_name: NRAS/AE9a leukemic cells

growth_protocol: Cells were cultured in RPMI 1640 medium supplied with murine 50 ng/ml SCF, 10 ng/ml IL-3 and IL-6, 1 mg/mL G418, and 2 µg/mL puromycin

extract_protocol:
The total RNA were extracted with TRIzol lysis reagent.
RNA library preparation was conducted usingKAPA Stranded mRNA-Seq Kit (Illumina Platforms) following manufacturer's protocols.

treatment_protocol: 5 µg/mL actinomycin D

value: NRAS/AE9a leukemic cells

value: AML cells

value: Tet2 KO

value: 5 µg/ml actinomycin D for 8h


title: 3h rep 2

description: replicate 2

source_name: 3h rep 2


title: KO_ActD_4h_Rep1

description: KO ActD 4h Rep1

value: 5 µg/ml actinomycin D for 4h


title: WT_ActD_0h_Rep2

description: WT ActD 0h Rep2

value: WT

value: 5 µg/ml actinomycin D for 0h


title: WT_ActD_4h_Rep2

description: WT ActD 4h Rep2


title: WT_ActD_4h_Rep1

description: WT ActD 4h Rep1


title: KO_ActD_4h_Rep2

description: KO ActD 4h Rep2


title: Zbtb46GFP_Flt3L+IL-6_2

city: Saint Louis

first: Sunkyung

last: KIM

state: MO

address: 660 S. Euclid Ave.

department: Pathology and Immunology

institute: Washington University in Saint Louis

data_processing:
The adaptor sequences were removed before alignment to the mouse reference genome using Trimmomatic53 with the arguments as followings:  java -jar trimmomatic-0.39.jar PE -threads 30 -phred33 sample1_R1.fastq.gz sample1_R2.fastq.gz -baseout sample1.fastq.gz ILLUMINACLIP:Truseq3.PE.fa:2:15:4:4:true LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:25
The trimmed reads were aligned and mapped to the mouse reference genome (GRCm38/mm10) using Bowtie2 software version 2.2.5 with the arguments as followings: bowtie2 -p 30 --dovetail --phred33 -x mm10 -1 sample1_1P.fastq.gz -2 sample1_2P.fastq.gz > sample1.sam
Duplicated reads are discarded using 'make tag directory' of Homer software package (version 4.9) with the parameter -tbp 1: makeTagDirectory sample1.tags sample1.sam -fragLength given -tbp 1
Data were visualized with the 'makeUCSCfile' of Homer: makeUCSCfile sample1.tags -o auto -fragLength given -tbp 1 -fsize 5e7
Peak calling was performed with Homer software package: findPeaks sample1.tag -style factor -size 400 -o sample1.peak -i isotypectl_for_sample1.tag -poisson 1e-10
Assembly: mm10
Supplementary files format and content: bedGraph.gz files were generated with Homer software package using the "makeUCSCfile".
Supplementary files format and content: Peak files were generated with Homer software package using "findPeaks" commands.
Library strategy: CUT&RUN

source_name: bone marrow

growth_protocol: BM cells were isolated from 8-week-old Zbtb46GPF/+ mice and CD3-, CD19-, CD105-, TER-119-, Ly-6G- and NK1.1-expressing lineage-committed cells were depleted. Sort-purified lineage– cKithi Flt3+ M-CSFR– BM progenitors BM progenitor cells were retrovirally transduced with MSCV-Neo-ER-Hoxb8 then cultured in complete IMDM supplemented with1 μM β-estradiol (Sigma Aldrich), 5% SCF-conditioned mediaum and 5% Flt3L-conditioned medium more than 3 weeks to enrich Hoxb8-transduced cells only.

extract_protocol:
The stimulated 5 x 105 cells were harvested and adsorbed to activated Concanavalin A (ConA) beads, permeabilized with 0.01% digitonin, and incubated with 0.5 mg C/EBPβ antibody or mouse IgG2a isotype control antibody at 4 °C on a nutator overnight. After antibody binding, the target-DNA complex is cleaved by the Protein A/Protein G-Micrococc al Nuclease (pAG-MNase) for 2 hours at 4 °C. 0.05 ng E. coli Spike-in DNA was added before releasing CUT&RUN fragments at 37°C for 10 min. The CUT&RUN enriched DNA is collected and purified from the supernatant.
Libraries were prepared with a NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) and cleaned-up with AMPureXP.

treatment_protocol: The Hoxb8-transformed BM progenitor cell lines were washed with PBS twice to remove the residual estradiole. The cells (5 x 105 cells/500 μl) were cultured with Flt3L conditioned media (5%) alone or Flt3L (5%) and IL-6 (25 ng/ml) for 24 h.

value: bone marrow

value: Hoxb8-transformed cell line

value: bone marrow progenitor

value: Flt3L-conditioned media (5%)+IL-6 (25ng/ml)


title: WT_ActD_8h_Rep2

description: WT ActD 8h Rep2


title: KO_ActD_0h_Rep1

description: KO ActD 0h Rep1


title: WT_ActD_0h_Rep1

description: WT ActD 0h Rep1


title: WT_ActD_8h_Rep1

description: WT ActD 8h Rep1


title: KO_ActD_8h_Rep1

description: KO ActD 8h Rep1


title: Zbtb46GFP_Flt3L_1

value: Flt3L-conditioned media (5%)


title: Zbtb46GFP_Flt3L+IL-6_1


title: Zbtb46GFP_Flt3L+IL-6_Ctl


title: Zbtb46GFP_Flt3L_Ctl


title: Mouse CD4+ T cells, acetate 2

city: St. Petersburg

first: Jianhua

last: Xiong

state: FL

address: 600 Fifth Street S

institute: Johns Hopkins University

data_processing:
Quality control of raw reads was carried out using FastQC v0.11.9. Adapter and low-quality sequences were trimmed from raw reads using Trim Galore! v0.6.6. Trimmed reads were aligned to the reference genome using STAR v2.6.1d.
Assembly: GRCm39
Supplementary files format and content: The processed data file was in txt format.

source_name: CD4+ T

extract_protocol:
RNA was harvested using Direct-zol RNA Miniprep Plus Kits (Zymo Research).
RNA libraries for RNA-seq were prepared using Zymo-Seq RiboFree Total RNA Library Kit following manufacturer's protocols.

value: CD4+ T

value: Acetate


title: Zbtb46GFP_Flt3L_2


title: Mouse CD4+ T cells, control 2

value: Control


title: Mouse CD4+ T cells, control 3


title: OSN_WaplXP

city: SAN FRANCISCO

first: Lea

last: Kiefer

address: 1651 4th Street, Weill Neurosci RM 471A

institute: UCSF

description: 10x scRNA-seq

data_processing:
Adapter Sequences were trimmed with cutadapt (v1.9.1) (--minimum-length 18)
Alignment: All samples were aligned to mm10. For paired-end data sets, only read 1 was used for alignment and downstream analysis. RNA-seq samples were aligned with STAR (v2.5.3a) with the following parameters:  --outFilterIntronMotifs RemoveNoncanonical --outFilterType BySJout --outFilterMultimapNmax 20. HiC samples were aligned and processed using HiC-Pro (Servant et al. 2015 Genome Biology). 10x single cell RNA-seq was processed using cellranger.
Filtering: Unmapped reads and reads with a mapping quality below 30 were removed with Samtools (1.3.1).
For RNA-Seq, bigWig files were generated with RSeQC (2.6.4).
10x scRNAseq data were analyzed using 10x Genomics Cell Ranger 6.0.1 with a recovery of 4000-8000 cells per experiment. Data analysis was performed using Seurat(55–58) and custom scripts.
Assembly: mm10
Supplementary files format and content: bigWig files at base pair resolution normalized to a library size of 10,000,000 reads

source_name: Olfactory epithilium

extract_protocol:
For RNA-seq: RNA  was  isolated  from  tissue  using  TRIzol.  Cell  lysate  was  extracted  with  bromo-chloropropane and RNA was precipitated with 100% isopropanol supplemented with 10 μg of glycobluefor 10 min at room temperature and then pelleted at 16,000 x g for 30 min at  4°C.  The  RNA  pellet  was  washed  once  with  75%  ethanol  and  then  resuspended  in RNase-free water to a maximal concentration of 200 ng/μl. Genomic DNA contaminants were   removed   by   Turbo   DNase.   Removal   of   Turbo   DNase   was   performed   by phenol:chloroform  extraction  and  RNA  was  precipitated  as  described  above  and resuspended in RNase-free water and stored at -80°C.   For Raphe RNA-seq: RNA  was  isolated  from  coronal  sections  of  the  Raphe  (20  μm  thick)  obtainedfrom paraformaldehyde-fixed   brain   (described   in   more   detail   below,   see   paragraph “Preparation of Mouse Brain Tissue Sections”). After 3x 5 minutes washes of the slides with 1X PBS, a small portion of each section containing approximately the Raphe region was extracted. Then, the RNA was isolated using  RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE (Invitrogen) as instructed by the manufacturer.   For in situ HiC was carried out according to Rao et al. 2014.  For ChIP-seq: Cells were crosslinked with 1% formaldehyde for  10 minutes  at room  temperature. Formaldehyde  was  quenched  by  adding  glycine to  a  final concentration of 0.125 M for 5 minutes at room temperature. Cells were then washed with 1X cold PBS with protein inhibitors twice and pelleted. Cell pellets were stored at -80°C till use. Cells were lysed in lysis buffer (50 mM Tris pH 7.5, 140 mM NaCl, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100) for 10 minutes. Nuclei were spun for 10 minutes at 1000 x g and resuspended in the sonication buffer (10 mM Tris pH 7.5, 0.5% SDS) as 5million nuclei per 300 μl sonication buffer. Chromatin was sheared by Covaris (Peak power 105.0; Duty Factor 2.0; Cycle/Burst 200; Treatment 960 sec; Temperature 4-8°C). Following a spin at 13,000 x g for 10 minutes to remove debris, the sheared chromatin was diluted such that the final binding buffer concentration was 15 mM Tris-HCl pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS) and incubated for 2 hours with dynabeads G pre-equilibrated in the binding buffer for pre-clearing of the chromatin. Post-cleared chromatin was then incubated with the specific antibody overnight (1 μg of antibody was used per 5 million nuclei). The next day, dynabeads G were added to the chromatin-antibody mix for 2 hours. A total of four washes with 1X wash buffer (100 mM Tris pH 7.5, 500 mM LiCl, 1% NP-40, 1% sodium deoxycholate) and one wash with TE buffer (10 mM Tris pH 7.5, 1 mM EDTA) were performed. The elution was performed at65°C for 1 hour in the elution buffer (1% SDS, 250 mM NaCl, 2 mM DTT).  All steps, with the exception of the elution, were performed at 4°C. All buffers, with the exception of the TE and elution buffer contained 1X protease inhibitors. The eluted chromatin was reverse-crosslinked overnight at 65°C and the DNA was purified with AMPure  XP  beads  (Beckman  Coulter).
For RNA-Seq experiments, raw FASTQ files were aligned with either Tophat or STAR using hg19 or mm10 reference genomes. When libraries were made following the SMARTer Stranded Total RNA-Seq, the initial 4 base pairs of both paired reads were trimmed prior to alignment.   For single cell RNA-seq, raw FASTQ files were analyzed using cellranger.    For in situ Hi-C experiments, raw FASTQ files were analyzed using HiC-Pro and hic files were generated (Servant et al. 2015).

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The main olfactory epithelium (MOE) was dissected and transferred to ice-cold PBS. The MOE was cut in to small pieces with a razor blade, and then dissociated with a papain dissociation system (Worthington Biochemical). For RNA-seq, dissociated cells were washed once with sort media (PBS + 2% Fetal Bovine Serum) and then resuspended in sort media supplemented with 100 U/mL DNase I (Worthington Biochemical)  and 500ng/mL DAPI (Invitrogen). For  HiC samples, cells were fixed prior to sorting. For fixation, dissociated cells were resuspended in PBS + 1% methanol-free formaldehyde (Pierce). Cells were fixed at room temperature for 10 minutes, and then fixation was quenched by adding 1/10th volume of 1.25M glycine. Fixed cells were pelleted (500 rcf, 5 minutes, room temperature), washed once with PBS + 2% FBS, and then resuspended in sort media. All cells were passed through a 40uM cell strainer prior to sorting.

value: Olfactory epithilium


title: Mouse CD4+ T cells, acetate 1


title: Mouse CD4+ T cells, control 1


title: scMultiome_sgArid2 [ATAC]

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

description:
Single-Cell Multiome (RNA and ATAC) sequencing
sgArid2_ATAC

library_source: genomic single cell

data_processing:
Reads were aligned to mouse reference genome mm10.
Assembly: mm10
Supplementary files format and content: Matrix files were generated using Cell Ranger (10x Genomics). GEX: h5 files; ATAC: fragments.tsv files.

source_name: CD8 T cells

extract_protocol: 10x Genomics; each sample generated one gene expression library (GEX) and one ATAC library (ATAC).

value: P14 CD8 T cells

value: Arid2 CRISPR knock out

value: sgArid2 RNP

tag: infection

value: Day 21 p.i.


title: scMultiome_sgPbrm1 [ATAC]

description:
Single-Cell Multiome (RNA and ATAC) sequencing
sgPbrm1_ATAC

value: Pbrm1 CRISPR knock out

value: sgPbrm1 RNP


title: Mouse CD4+ T cells, acetate 3

value: WT


title: scMultiome_Control [ATAC]

description:
Single-Cell Multiome (RNA and ATAC) sequencing
sgCtrl_ATAC

value: CRISPR control

value: sgCtrl RNP


title: WT keratinocyte H3K27ac

city: San Francisco

first: Yuko

last: Oda

address: 111N-MB 360 1700 Owens St, Suite 360

department: Endocrine Research

institute: VA Medical Center UCSF

data_processing:
Quality and adapter trimming was performed with Trim Galore! (version 0.4.3.1)
Trimmed Fastq files were mapped to the mouse genome (mm10) with BWA (version 0.7.15.1), PCR duplicates were removed with RmDup (version 2.0) and filtered to remove mitochondrial DNA and not properly aligned sequnces.
Peaks were called with MACS2 callpeak (version 2.1.1.20160309.6) and Bigwig files were created with multiBigwigSummary (version 3.1.2.0.0)
5hmC coverage over defined regions was analyzed with the CEAS package (version 1.0.2)
Libraries were sequenced on an Illumina HiSeq 4000 instrument and Fastq file quality was checked with FastQC (version 0.72).
Quality and adapter trimming was performed with Trim Galore! (version 0.4.3.1)
Peaks were called with MACS2 callpeak (version 2.1.1.20160309.6)
H3K27ac coverage over defined regions was analyzed with the CEAS package (version 1.0.2)
Super-enhancers are analyzed by NaviSE
Assembly: mm10
Supplementary files format and content: bigWig

source_name: Skin

growth_protocol: Krt14Cre driven Med1 conditional knockout (cKO) and  littermate control (Ctrl) mice (n=3) were maintained on regular diet in animal center in VA Medical Center San Francisco.

extract_protocol:
Dissected CLH or CLT tissues were homogenized and cross-linked with 1% paraformaldehyde for 8 min (H3K27ac) or for 15 min (MED1), sonicated using a ultrasonicator (Covaris) to obtain DNA fragments with an average length of 300±50 bp. Sheared chromatin was thereafter immunoprecipitated with Protein A-coated magnetic beads (Diagenode) preincubated with 4.5 microgram/IP MED1 antibody (Bethyl A300-793A) or 3 ug/IP H3K27ac antibody (ab4729, Abcam). Chromatin input samples were used as reference. Complexes were then washed and eluted from the beads with washing buffer and crosslinks were reversed by incubation at 65°C for 4 hours. Immunoprecipitated DNA along with genomic DNA (Inputs) were purified using the IPure v2 kit (Diagenode). IP efficiency was confirmed by qPCR using primers provided in the kits. Experiments were carried out in duplicates.
ChIP-Seq libraries were generated using the Accel-NGS 2S Plus DNA library kits (Swift Sciences) and amplified by PCR for 11-13 cycles. High molecular weight smear was removed in the library by right side size selection using SPRI beads (Beckman Coulter). The libraries were quantified by Agilent 2100 Bioanalyzer with the high sensitivity DNA assay and sequenced on an Illumina HiSeq 4000 (UCSF Center of advanced technology) in a single strand 50 bp run.

treatment_protocol: No treatment

value: Skin

value: 9 week old (telogen)

value: H3K27ac Abcam ab 4729


title: Ctrl CLH Med1

source_name: Mandible

value: Mandible

value: 4 week old

value: Floxed Med1 (Ctrl)

value: Med1 Bethyl, A300-793A


title: Med1 cKO CLH H3K27ac


title: Input CL


title: Med1 cKO CLT H3K27ac


title: Ctrl CLT H3K27ac


title: Ctrl CLT Med1


title: Ctrl CLH H3K27ac


title: SCLC Lung Tumor 7 month HW1534

city: Sioux Falls

first: Michael

last: Kareta

state: SD

address: 2301 East 60th Street North

department: Genetics & Genomics

institute: Sanford Research

description: SCLC Lung Tumor 7 month

library_source: transcriptomic single cell

data_processing:
The data was processed using CellRanger  (10X Genomics, version 6.0.1). Initially CellRanger count was run on each sample followed by CellRanger aggregate to generate one expression matrix, a vector of genes and a vector of barcodes. CellRanger was run with the –expect-cells parameter set to the expected number of cells.
Assembly: Mus_musculus_GRCm39 or Homo_sapiens_GRCh38, both appended with the sequence for eGFP.

source_name: Lung Tumor

growth_protocol: Cell lines were grown in RPMI with 10% BGS and penicillin/streptomycin. All cell lines were validated and regularly tested for mycoplasma.

extract_protocol:
Samples were harvested and processed according to either the mouse or human tumor dissociation kit (Miltenyi Biotec).
Performed on a 10X Chromium Controller using standard protocol (version 3 chemistry).

treatment_protocol: For cell lines, cisplatin = 2.876 uM and etoposide = 0.110 uM. For mice, cisplatin = 5 mg/kg and etoposide = 10 mg/kg on day one. On days two and three they were treated with etoposide = 10 mg/kg.

value: Lung Tumor

value: 7 months

value: Cisplatin/Etoposide


title: SCLC Lung Tumor 6 month HW1673

description: SCLC Lung Tumor 6 month

value: 6 months

value: Untreated


title: SCLC Lung Tumor 6 month HW1645

description: SCLC Lung Tumor 6 month


title: SCLC Lung Tumor 5 month HW1553

description: SCLC Lung Tumor 5 month

value: 5 months


title: SCLC Lung Tumor 6 month HW1672

description: SCLC Lung Tumor 6 month


title: Mouse CD8+ T cells, acetate 1

state: Florida

address: 600 5th Street S

data_processing:
Quality control of raw reads was carried out using FastQC v0.11.9. Adapter and low-quality sequences were trimmed from raw reads using Trim Galore! v0.6.6. Trimmed reads were aligned to the reference genome using STAR v2.6.1d.
Assembly: GRCm39
Supplementary files format and content: The processed data file was in txt format.
Supplementary files format and content: raw counts

source_name: Mouse CD8+ T cells

value: Mouse CD8+ T cells

value: Acetate


title: Mouse CD8+ T cells, acetate 2

value: WT


title: SCLC Lung Tumor 3 month HW1604

description: SCLC Lung Tumor 3 month

value: 3 months


title: SCLC Lung Tumor 4 month HW1602

description: SCLC Lung Tumor 4 month

value: 4 months


title: Mouse CD8+ T cells, control 2

value: Control


title: SCLC Lung Tumor 4 month HW1614

description: SCLC Lung Tumor 4 month


title: SCLC Lung Tumor 4 month HW1656

description: SCLC Lung Tumor 4 month


title: SCLC Lung Tumor 5 month HW1641

description: SCLC Lung Tumor 5 month


title: SCLC Lung Tumor 2 month HW1603

description: SCLC Lung Tumor 2 month

value: 2 months


title: KO_ActD_0h_Rep2

description: KO ActD 0h Rep2

value: NRAS/AE9a leukemic cells

value: AML cells

value: Tet2 KO

value: 5 µg/ml actinomycin D for 0h


title: Input_keratinocyte

value: Skin

value: 9 week old (telogen)


title: CDP_Flt3L+IL-6_6h_3

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5. Isoform expression of known Ensembl transcripts were estimated with Salmon version 0.8.2.
All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis.  The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples with the voomWithQualityWeights.  The performance of all genes was assessed with plots of the residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals. Differential expression analysis was then performed to analyze for differences between conditions and the results were filtered for only those genes with Benjamini-Hochberg false-discovery rate adjusted p-values less than or equal to 0.05.
Assembly: Mouse Ensembl GRCm38.76 (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 merged differential expression results

source_name: Bone marrow

growth_protocol: BM cells were isolated from 8 week old WT mice and CD3-, CD19-, CD105-, NK1.1-, TER-119-, Ly-6G- and B220-expressing lineage-committed cells were depleted. The CDP (lineage– cKitint Flt3+ M-CSFR+ MHCII–, CD11c–) were sort-purified and cultured in Iscove’s Modified Dulbecco’s Medium (IMDM) supplemented with 10% FBS, 1% Penicilin Streptomycin solution, 1% Sodium Pyruvate, 1% MEM non-essention amino acid, 1% L-glutamine solution, and 55 mL β-mercaptoethanol (complete IMDM) cultured in the presence of Flt3L or Flt3L with murine recombinant IL-6 for 6 h.

extract_protocol:
RNA was isolated from 50,000 CDPs after 6 h stimulation using NucleoSpin RNA XS Kit (Macherey-Nagel).
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 10ng of total RNA using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

treatment_protocol: The sort-purified CDPs (50,000 cells) were (1) untreated, (2) Flt3L (conditioned medium 5%), or (3) Flt3L (conditioned medium 5%) and IL-6 (25 ng/ml) for 6 h.

value: Bone marrow

value: Common dendritic cell progenitor

value: Flt3L conditioned media (5%)+IL-6 (25 ng/ml)


title: CDP_Flt3L+IL-6_6h_2


title: Mouse CD8+ T cells, control 1


title: CDP_Flt3L+IL-6_6h_1


title: CDP_Flt3L_6h_2

value: Flt3L conditioned media (5%)


title: SCLC Lung Tumor 5 month HW1640

description: SCLC Lung Tumor 5 month

value: Lung Tumor

value: 5 months

value: Untreated


title: CDP_Flt3L_6h_1

value: WT


title: CDP_untreated_2


title: ptenca [scRNA-Seq]

city: Shanghai

first: Hanling

last: Wang

address: Shanghai

institute: Shanghai Institute of Nutrition and Health, Chinese Academy of Science

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: features, barcodes and matrix files

source_name: prostate

extract_protocol:
Mice prostates were dissociated into single cells in 5 mg/ml Collagenase Type II and TryPLE at first, and then stained with AO/PI for viability assessment using Countstar Fluorescence Cell Analyzer.
The scRNA-seq libraries were generated using the 10´ Genomics Chromium Controller Instrument and Chromium Single Cell 3’ V3 Reagent Kits (10X Genomics, Pleasanton, CA) according to the manufacturer’s recommendations. The experiments were performed by NovelBio Bio-Pharm Technology Co., Ltd.

value: prostate cells

value: prostate

value: PtenPC-/- ADT mice

value: 5.5 Mths old


title: CDP_untreated_1


title: p53ca [scRNA-Seq]

description: 10x Genomics

value: PtenPC-/-; Trp53PC-/- ADT mice


title: pten [scRNA-Seq]

description: 10x Genomics

value: PtenPC-/- mice

value: 4 Mths old


title: OSN_WaplcKO_scRNA

data_processing:
For single cell RNA-seq, raw FASTQ files were analyzed using cellranger.
Adapter Sequences were trimmed with cutadapt (v1.9.1) (--minimum-length 18)
Alignment: All samples were aligned to mm10. For paired-end data sets, only read 1 was used for alignment and downstream analysis. Crosslinked ChIP-Seq samples were aligned with Bowtie2 (2.3.2) with default parameters. RNA-seq samples were aligned with STAR (v2.5.3a) with the following parameters:  --outFilterIntronMotifs RemoveNoncanonical --outFilterType BySJout --outFilterMultimapNmax 20. HiC samples were aligned and processed using HiC-Pro (Servant et al. 2015 Genome Biology). 10x single cell RNA-seq was processed using cellranger.
Filtering: Unmapped reads and reads with a mapping quality below 30 were removed with Samtools (1.3.1). For ChIP-seq, duplicate reads were marked with Picard and removed with samtools.
For ChIP-Seq, bigWig files  were generated using HOMER (4.7) (-fsize 1e20 -fragLength given). For RNA-Seq, bigWig files were generated with RSeQC (2.6.4).
Assembly: mm10
Supplementary files format and content: bigWig files at base pair resolution normalized to a library size of 10,000,000 reads

extract_protocol: For RNA-seq: RNA  was  isolated  from  tissue  using  TRIzol.  Cell  lysate  was  extracted  with  bromo-chloropropane and RNA was precipitated with 100% isopropanol supplemented with 10 μg of glycobluefor 10 min at room temperature and then pelleted at 16,000 x g for 30 min at  4°C.  The  RNA  pellet  was  washed  once  with  75%  ethanol  and  then  resuspended  in RNase-free water to a maximal concentration of 200 ng/μl. Genomic DNA contaminants were   removed   by   Turbo   DNase.   Removal   of   Turbo   DNase   was   performed   by phenol:chloroform  extraction  and  RNA  was  precipitated  as  described  above  and resuspended in RNase-free water and stored at -80°C.   For Raphe RNA-seq: RNA  was  isolated  from  coronal  sections  of  the  Raphe  (20  μm  thick)  obtainedfrom paraformaldehyde-fixed   brain   (described   in   more   detail   below,   see   paragraph “Preparation of Mouse Brain Tissue Sections”). After 3x 5 minutes washes of the slides with 1X PBS, a small portion of each section containing approximately the Raphe region was extracted. Then, the RNA was isolated using  RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE (Invitrogen) as instructed by the manufacturer.   For in situ HiC was carried out according to Rao et al. 2014.  For ChIP-seq: Cells were crosslinked with 1% formaldehyde for  10 minutes  at room  temperature. Formaldehyde  was  quenched  by  adding  glycine to  a  final concentration of 0.125 M for 5 minutes at room temperature. Cells were then washed with 1X cold PBS with protein inhibitors twice and pelleted. Cell pellets were stored at -80°C till use. Cells were lysed in lysis buffer (50 mM Tris pH 7.5, 140 mM NaCl, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100) for 10 minutes. Nuclei were spun for 10 minutes at 1000 x g and resuspended in the sonication buffer (10 mM Tris pH 7.5, 0.5% SDS) as 5million nuclei per 300 μl sonication buffer. Chromatin was sheared by Covaris (Peak power 105.0; Duty Factor 2.0; Cycle/Burst 200; Treatment 960 sec; Temperature 4-8°C). Following a spin at 13,000 x g for 10 minutes to remove debris, the sheared chromatin was diluted such that the final binding buffer concentration was 15 mM Tris-HCl pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS) and incubated for 2 hours with dynabeads G pre-equilibrated in the binding buffer for pre-clearing of the chromatin. Post-cleared chromatin was then incubated with the specific antibody overnight (1 μg of antibody was used per 5 million nuclei). The next day, dynabeads G were added to the chromatin-antibody mix for 2 hours. A total of four washes with 1X wash buffer (100 mM Tris pH 7.5, 500 mM LiCl, 1% NP-40, 1% sodium deoxycholate) and one wash with TE buffer (10 mM Tris pH 7.5, 1 mM EDTA) were performed. The elution was performed at65°C for 1 hour in the elution buffer (1% SDS, 250 mM NaCl, 2 mM DTT).  All steps, with the exception of the elution, were performed at 4°C. All buffers, with the exception of the TE and elution buffer contained 1X protease inhibitors. The eluted chromatin was reverse-crosslinked overnight at 65°C and the DNA was purified with AMPure  XP  beads  (Beckman  Coulter).

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The main olfactory epithelium (MOE) was dissected and transferred to ice-cold PBS. The MOE was cut in to small pieces with a razor blade, and then dissociated with a papain dissociation system (Worthington Biochemical). For RNA-seq, dissociated cells were washed once with sort media (PBS + 2% Fetal Bovine Serum) and then resuspended in sort media supplemented with 100 U/mL DNase I (Worthington Biochemical)  and 500ng/mL DAPI (Invitrogen). For Crosslinked-ChIP and HiC samples, cells were fixed prior to sorting. For fixation, dissociated cells were resuspended in PBS + 1% methanol-free formaldehyde (Pierce). Cells were fixed at room temperature for 10 minutes, and then fixation was quenched by adding 1/10th volume of 1.25M glycine. Fixed cells were pelleted (500 rcf, 5 minutes, room temperature), washed once with PBS + 2% FBS, and then resuspended in sort media. All cells were passed through a 40uM cell strainer prior to sorting.

value: Olfactory epithilium


title: p53 [scRNA-Seq]

description: 10x Genomics

value: PtenPC-/-; Trp53PC-/- mice

value: 3.5 Mths old