title: STNT4

city: LA JOLLA

first: Edward

middle: M.

last: Callaway

state: CA

address: 10010 N Torrey Pines Rd

department: SNL-C

institute: Salk Institute

description: 10X Genomics V3.1

data_processing:
Raw read (fastq) files were aligned to the mouse pre-mRNA reference transcriptome (mm10) using the 10x Genomics CellRanger pipeline (version 6.0.). Intronic reads were included in expression quantification using the include-introns parameter.
Assembly: mm10
Supplementary files format and content: Processed data files are gene count matrices as output by CellRanger.

source_name: primary visual cortex

growth_protocol: All experimental procedures were approved by the Salk Institute Animal Care and Use Committee. C57BL/6J mice were used as wild-type. GENSAT BAC transgenic Sepw1-Cre NP39, Scnn1a-Tg3-Cre, Tlx3-Cre PL56, Npr3-IRES-Cre-neo, and Ntsr1-Cre GN220 mice have been previously described. Transgenic mice were maintained on C57BL/6J backgrounds. Mice were housed with a 12-hour light and 12-hour dark cycle and ad libitum access to food and water. Both male and female mice were used for RNA sequencing experiments.

extract_protocol:
Single nuclei preparations were performed as follows: the frozen brain tissues were transferred to pre-chilled dounce homogenizers with 1ml NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10ul of protease inhibitor (Sigma P8340), 1.5ul of RNasin Plus RNase inhibitor (Promega, N2611)), 0.1% Triton X-100, and 10 uM DAPI, and gently homogenized on ice with ice-cold pestles 10 - 15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 3000 rpm for 8 min at 4°C to pellet the nuclei. The supernatant was aspirated, the pellet gently resuspended in ice-cold 1ml NIM buffer, and again centrifuged at 3000 rpm for 8 min at 4°C. The pellet was then resuspended in 450ul of nuclei storage buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through a 40μM cell strainer. The sample was incubated with 50ul of nuclease-free BSA to prevent nuclei clumping. Fluorescence-activated nuclei sorting of single nuclei was performed using a FACS Aria Fusion sorter with a 70 μM nozzle at 22.5 PSI sheath pressure. DAPI+/mCherry+ rabies-infected nuclei were sorted into 0.2ml Eppendorf PCR tubes and immediately loaded onto the 10X Genomics Chromium Controller. Biological replicates were processed on different days.
For 10x processing, we used Chromium Next GEM single-cell 3’ Kit (v3.1 Dual Index) and Chromium Next GEM single-cell 3' LT Kit (v3.1 Dual Index) (10x Genomics, PN-1000127 and PN-1000325). We followed the manufacturer’s instructions for single-cell capture, barcoding, reverse transcription, cDNA amplification, and library construction. We targeted sequencing depth of 100,000 reads per cell. Pooled libraries were sequenced on Illumina NovaSeqTM 6000 Sequencing System (S4)

treatment_protocol: For rabies input tracing transgenic mice received AAV helper injections at P49 – P60. 100 nL of diluted AAV8-DIO-TC66T-2A-oG (4.31E+12 GC/mL, Addgene # 178430) was injected into the center of V1 0.5–0.7 mm ventral from the pia. Three weeks after AAV helper virus injection, 200 nL of EnvA+RVdG-H2BmCherry (7.43E+07 IU/ml) was injected into the same site in V1. Ten days after rabies injection,  brains were extracted and immediately submerged in ice-cold slicing solution. Coronal brain slices (400um thick) were cut using VF-300 CompresstomeTM (Precisionary Instruments, Greenville,NC) and submerged in ice-cold slicing solution. Subregions of V1 containing mCherry+ nuclei in brain slices were micro-dissected out under a fluorescent dissection microscope (Olympus SZX6).

value: primary visual cortex

value: cortical neurons

value: monosynaptic rabies tracing


title: 42-F

status: Public on Sep 19 2024

type: SRA

city: Linköping

first: CecilIa

last: Gunnarsson

address: Linköping University Hospital

country: Sweden

institute: Linköping University Hospital

library_source: transcriptomic

data_processing:
STAR (mapping)
nuDup (de-duplication algorithm for UMI provided by library manuyfacturer)
feautureCounts (counts)
DeSeq2 (statistics)
Assembly: GRCh38
Supplementary files format and content: raw counts

molecule: total RNA

organism: Homo sapiens

source_name: resected aortic coarctation

extract_protocol:
Samples were stored in DNA/RNA Shield (Zymo) , lysed using ZR BashingBead Lysis Tubes (Zymo) on a TissueLyser (Qiagen) set to 25Hz for 10 minutes and RNA was isolated using Quick-RNA Microprep kit (Zymo)
Ovation SoLo RNA-Seq System (Tecan)

tag: tissue

value: resected aortic coarctation

tag: patient biobank_id

tag: patient sex

value: female

tag: patient age_(days)

tag: bav/tav

value: tav

tag: biopsy location

value: coarctation

tag: biopsy group

tag: age group


title: STNT2

country: USA

description: 10X Genomics V3.1

library_source: transcriptomic single cell

molecule: polyA RNA

organism: Mus musculus

tag: cell type

tag: genotype

tag: treatment


title: 47-N

value: male

value: bav

value: proximal/distal


title: Wt_proB_1

city: Badalona

first: Alejandro

last: Vaquero

state: Barcelona

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

country: Spain

institute: Josep Carreras Leukemia Research Institute

description:
WT.10_ProB
Normalized_counts_RNA_seq_Sirt7

data_processing:
RNA-Seq: FastQ files were quality-checked using FastQC
RNA-Seq: raw counts were obtained by performing Salmon "quant" pseudoalignment (mm10 reference mouse genome, with fragment-level GC bias correction (--gcBias), eight threads (-p 8) and selective alignment enabled (--validateMappings)
RNA-Seq: The quant.sf files were used to import transcript-level quantification data into Summarized Experiment using Tximeta
RNA-Seq: Counts were normalized by DESeq2's median of ratios methods
ChIP-Seq: FastQ files were quality-checked using FastQC
ChIP-Seq: FastQ files were aligned onto a reference mouse genome (mm10) using Bowtie2 to generate SAM files
ChIP-Seq: SAM files were conerted to BAM files using SAMTools, skipping alignments with MAPQ smaller than 37
ChIP-Seq: BAM files were sorted and filtered using Sambamba, eliminating unmapped and duplicated reads.
ChIP-Seq: Index BAI files were generated using SAMTools "index"
ChIP_Seq: BigWig files were created using deepTools "bamCoverage"
Assembly: mm10
Supplementary files format and content: A ChIP-Seq .bigwig file for each sample
Supplementary files format and content: Two RNA-Seq DESeq2-normalized count files (.txt), one per experiment, containing the normalized counts for each RNA sample

source_name: Sorted bone marrow pro-B cells

growth_protocol: Pro-B cells were plated onto a layer of mitomycin C-inactivated OP9 feeder cells and grown on Opti-MEM supplemented with 10% heat-inactivated fetal bovine serum,  25 mM HEPES, 50 µg/mL Gentamicin and 50 µM β-mercaptoethanol in the presence of 10 ng/mL IL-7, 10 ng/mL SCF and 10 ng/mL FTL3-L

extract_protocol:
RNA was extracted from frozen cell pellets using the Maxwell RSC simplyRNA Tissue Kit; For anti-Pax5 ChIP-Seq, sheared DNA was washed after the ChIP, crosslink was reversed and DNA was purified using NucleoSpin Gel and PCR Clean-up columns.
For RNA-Seq, mRNA was enriched using oligo dT beads and fragmented. First strand cDNA was synthesized using random primers, and second strand cDNA was subjected to end-repair and 3' adenylated. Adaptors were ligated to the ends of the 3' adenylated cDNA fragments. U-labeled second-strand template was digested with UDG and amplified by PCR. After QC, library was circularized and amplified to make DNA nanoball before sequencing. For ChIP-Seq, IP-DNA and Input-DNA were 3' end repaired and adaptor-ligated before PCR amplification, purificaiton and sequencing.

treatment_protocol: Not appliable

value: Sorted bone marrow pro-B cells

value: Wt


title: D425_RNA_BFP3

city: Toronto

first: Michael

middle: D

last: Taylor

state: ON

address: 686 Bay St.

country: Canada

institute: Hospital for Sick Children

description: D425_BFP_vs_ZIC1_4_RNA_Seq_htseq_counts.txt

data_processing:
RNA-Seq - alignment with STAR, differential expression analysis with DESeq2
Counts were collected with htseq for RNA-Seq
Assembly: hg19 for human, mm10 for mouse
Supplementary files format and content: Raw counts for each sample for each gene

extract_protocol:
Rneasy purification kit for extraction of RNA.
NEB Ultra DNA library prep kit for ChIP-Seq (NEB7645), NEB Ultra II Directional mRNA kit for RNA-Seq

tag: cell line

value: Group 3 medulloblastoma

value: GFP-Luc-tagged

value: empty vector overexpression


title: STNT3

description: 10X Genomics V3.1


title: 28-N


title: D425_ev2_ZIC1_mut_constructs_RNA

description: D283_D425_ZIC1_mutant_constructs_RNA-Seq_htseq_counts.txt

value: WT


title: RE_WT_rep2

city: Wuhan

first: Yu

last: Chang

state: Hubei

address: No.1, Shizishan Street, Hongshan District

department: National Key Laboratory of Crop Genetic Improvement

country: China

institute: Huazhong Agricultural University

description:
column name in the processed data file: RE_WT_rep2
Count_matrix.txt

data_processing:
The raw reads were filtered and trimmed by fastp (v0.23.0) with parameters “-q 15” and then mapped to the MH63RS3 assembly using STAR software (v2.7.10a) with the default parameters.
Transcripts were assembled and quantified using StringTie (v2.1.7) with the reference-guide mode (“-e”).
Assembly: MH63RS3 (http://rice.hzau.edu.cn/rice_rs3/)
Supplementary files format and content: The Count_matrix.txt file records the raw read count of each gene in all samples.

organism: Oryza sativa

source_name: seedling

growth_protocol: Wild-type (WT) or osbzip23 seeds were soaked for 3 days until germination. Seedings with similar growth state were then planted in 12 buckets (30 / bucket) with equal amount of soil and water. The buckets were randomly placed in a growth chamber with the air temperature of 32°C (day) or 29°C (night), 12 hours of light (constant light intensity 15000 lux) per day, and the relative humidity of 80%. The weight of soil in each bucket was 2.1 kg, and the initial water is 800 mL.

extract_protocol:
Total RNA was isolated using the RNeasy Plant Mini Kit according to the manufacturer’s instructions (QIAGEN, 74904).
The isolated RNA (2 mg) was used for library construction using an Illumina TruSeq RNA kit according to the manufacturer’s recommendations.

treatment_protocol: After 14 days of normal growth with ample and equal watering, 8 buckets of the 4-leaf stage seedlings were randomly chosen for drought stress treatment while the other 4 buckets continued normal growth. The drought stress treatment was performed by cease watering for 15 days. The weights of the 8 buckets were adjusted in every of the 15 days with water to keep equal drought progress. During day 11–15, the relative soil water content (RSWC) was kept ~5% for each bucket. After that, half of the 8 buckets were randomly selected for re-watering, while the normally grown and drought-treated samples were harvested. Then after 4 days of equal and ample re-watering, the samples for recovery were harvested. The treastment was repeated twice with different batches of seedlings.

value: seedling

value: recovery


title: RE_WT_rep1

description:
column name in the processed data file: RE_WT_rep1
Count_matrix.txt


title: STNT1

description: 10X Genomics V3.1

value: primary visual cortex

value: cortical neurons


title: 28-F

value: resected aortic coarctation


title: STNP5

description: 10X Genomics V3.1

value: monosynaptic rabies tracing


title: N_WT_rep2

description:
column name in the processed data file: N_WT_rep2
Count_matrix.txt

value: normal


title: N_WT_rep1

description:
column name in the processed data file: N_WT_rep1
Count_matrix.txt


title: STNP4

description: 10X Genomics V3.1


title: D283_WT2_ZIC1_mut_constructs_RNA

value: WT ZIC1 overexpression


title: D283_WT1_ZIC1_mut_constructs_RNA


title: STNP3

description: 10X Genomics V3.1


title: DS_osbzip23_rep2

description:
column name in the processed data file: DS_osbzip23_rep2
Count_matrix.txt

value: drought


title: 26-N

value: male

value: bav


title: D283_S399F_ZIC1_mut_constructs_RNA

value: SHH medullo mutant ZIC1 overexpression


title: STNP1

description: 10X Genomics V3.1


title: D283_R294C_ZIC1_mut_constructs_RNA

value: Group 4 medullo mutant ZIC1 overexpression


title: DS_osbzip23_rep1

description:
column name in the processed data file: DS_osbzip23_rep1
Count_matrix.txt


title: D283_S403F_ZIC1_mut_constructs_RNA

value: Group 3 medulloblastoma


title: 22-N

value: tav

value: proximal/distal


title: 21-F

value: coarctation


title: 21-N

value: proximal


title: DS_WT_rep2

description:
column name in the processed data file: DS_WT_rep2
Count_matrix.txt

value: seedling


title: D283_P301S_ZIC1_mut_constructs_RNA

value: WT


title: D283_ev2_ZIC1_mut_constructs_RNA

value: empty vector overexpression


title: STNP2

description: 10X Genomics V3.1

value: primary visual cortex

value: cortical neurons


title: 26-F

value: resected aortic coarctation


title: DS_WT_rep1

description:
column name in the processed data file: DS_WT_rep1
Count_matrix.txt


title: STT3

description: 10X Genomics V3.1

value: monosynaptic rabies tracing


title: D283_ev1_ZIC1_mut_constructs_RNA


title: RE_WT_H3K9ac_ChIApet_rep1

library_source: genomic

data_processing:
The linker filtering, read mapping, redundancy removal, and chromatin interaction identification of the ChIA-PET data was processed using ChIA-PET tools v3, an updated version of the automatic ChIA-PET data processing pipeline previously applied in rice ChIA-PET data processing. We use the union H3K9ac ChIP-seq peak regions under all conditions as pre-defined candidate anchor regions for loop calling, so that loops under different conditions can be easily compared based on their anchors. Since the reproducibility between biological replicates were generally good (with Pearson correlation coefficient > 0.8 based on the intensity of inter-ligation PETs in 100k bp window), we perform the loop calling based on the pooled data of the two replicates. We defined the uniquely mapped, nonredundant pair-end tags (PETs) covering a genome span > 8000 bp as inter-ligation PETs (i-PETs). Considering the technical noise and the sequencing depth, candidate chromatin loops with false discovery rate (FDR) < 0.05 and unique i-PET counts > 5 were preserved as confident loops and passed to subsequent analysis. The sequencing signal tracks involving all uniquely mapped PETs were generated using bamCoverage in the deeptools kit (v3.5.1) with the RPGC (reads per genomic content) normalization and bin size of 10 bp.
Assembly: MH63RS3 (http://rice.hzau.edu.cn/rice_rs3/)
Supplementary files format and content: The bigwig (.bw) files record the coverage of uniquely mapped PETs, normalized by reads per genomic content with the bin size of  10 bp.

molecule: genomic DNA

extract_protocol:
Rice long-read ChIA-PET libraries were constructed with a modified ChIA-PET method. Tissues were dual cross-linked with 1% formaldehyde for 10 min and 1.5 mM ethylene glycol bis (succinimidylsuccinate) (Thermo Fisher Scientific, 21565) for 30 min at room temperature. After that, 0.2 M glycine was applied to halt the cross-linking reaction. Then, samples were ground in liquid nitrogen to a fine powder and approximately 5 g powder was lysed in 2× volume of buffer S. Next, each sample was applied with 8× volume of buffer F and sonicated in a Bioruptor® sonication system (Diagencode, UCD-200) to yield chromatin fragments with 1–3k bp in length.
The chromatin fragments were collected by centrifuging at 12,000× g for 10 min at 4°C. 800 μL protein G with 25 μg anti-Histone H3 acetyl K9 antibody (Abcam, ab10812) was applied to the chromatin fragments and incubated at 4°C overnight with gentle rotation. The supernatant was discarded and the beads were sequentially washed with 5 mL low-salt ChIP buffer for three times, 5 mL high-salt ChIP buffer twice, 5 mL ChIP wash buffer once and 5 mL 1× TE buffer twice. ChIP DNA was used for end-repair and A-tailing using T4 DNA polymerase (Promega, cat. no. M421F) and Klenow enzyme (NEB, cat. no. M0212L). Proximity ligation of ChIP DNA was performed using biotinylated bridge-linker (forward strand: 5′-[5Phos] CGCGATATC/iBIOdT/TATCTGACT-3′, reverse strand: 5′-[5Phos] GTCAGA- TAAGATATCGCGT-3′). Protein-DNA complex was reverse cross-linked and the ChIA-PET libraries were prepared by using Tn5 transposase (VAHTS, TD501).

tag: antibody

value: Anti-H3K9ac (Abcam, ab10812)

value: recovery


title: 17-N

value: male


title: RE_WT_H3K9ac_ChIApet_rep2


title: STT4

description: 10X Genomics V3.1


title: STT2

description: 10X Genomics V3.1


title: STT1

description: 10X Genomics V3.1


title: N_WT_H3K9ac_ChIApet_rep2

value: normal


title: N_WT_H3K9ac_ChIApet_rep1


title: UAS control male 3

city: Vancouver

first: Elizabeth

last: Rideout

state: BC

address: 2350 Health Sciences Mall

department: Department of Cell and Physiological Science

institute: University of British Columbia

data_processing:
Sample quality control was performed using the Agilent 2100 Bioanalyzer or the Agilent 4200 TapeStation. Qualifying samples were then prepped following the standard protocol for the Illumina Stranded mRNA prep (Illumina). Sequencing was performed on the Illumina NextSeq2000 with Paired End 59bp × 59bp reads.
Sequencing data was demultiplexed using Illumina's BCL Convert.
RNA-Seq Alignment (BaseSpace Workflow) v 1.1.0
Reads were aligned to reference genome (UCSC dm3) using STAR aligner (version STAR_2.5.0b).
Counts were quantified using Cufflinks (version 2.2.1).
Assembly: UCSC dm3
Supplementary files format and content: One tab-delineated text file containing raw counts for each sample

organism: Drosophila melanogaster

source_name: whole brain

growth_protocol: Fly strains were maintained on a 12 h:12 h light:dark cycle at 22°C. Larvae were reared on cornmeal-sugar-yeast 2-acid medium (Lewis, 1960; Wat et al., 2020) at a density of 50 larvae per 10 mL food. Male and female pupae were distinguished by the presence or absence of sex combs, respectively. Pupae eclosed into single-sex vials; adult flies were transferred into new vials every 2-3 days.

extract_protocol:
Adult whole brains of male and female flies at 5 to 6 days after eclosion were dissected into 1 mL Trizol and stored at -80℃. 30 brains were used in each biological replicate. RNA was isolated using RNeasy Mini Kit (Qiagen #74106) according to manufacturer's protocol. The isolated RNA samples were then send to UBC Biomedical Research Centre Sequencing Core for library prep and RNA sequencing.
Libraries were prepared for sequencing using Illumina Stranded mRNA Prep.

value: whole brain

value: + > UAS-bmm-RNAi


title: 16-F

value: bav


title: UAS control male 2


title: STSC3

description: 10X Genomics V3.1


title: DS_osbzip23_H3K9ac_ChIApet_rep2

value: drought


title: 1-N

value: proximal/distal


title: UAS control male 1


title: 1-F

value: coarctation


title: DS_osbzip23_H3K9ac_ChIApet_rep1

value: seedling


title: STSC2

description: 10X Genomics V3.1


title: UAS control female 3


title: 17-F

value: tav


title: STSC1

description: 10X Genomics V3.1


title: UAS control female 2


title: WT (ttchem) replicate 2

city: Mainz

first: Sergi

last: Sayols

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology, Mainz

data_processing:
TTchem-seq data were aligned on the Homo sapiens genome assembly hg38 from GENCODE (release 35) using STAR (v2.7.3a, parameters: --outMultimapperOrder Random --outSAMattributes NH HI AS nM MD –outSJfilterReads Unique --outSAMunmapped Within --outFilterMismatchNoverReadLmax 0.04 -outFilterMismatchNmax 999 –sjdbOverhang 74). The featureCounts program (v1.6, parameters: -t gene -s2) was used to count the number of reads overlapping genes.
Assembly: hg38
Supplementary files format and content: tab separated file with gene name and quantification (raw reads)

growth_protocol: HCT116, cultured in RPMI 1640 supplemented with 10% fetal bovine serum, L-glutamine, penicillin, and streptomycin. HEK293T cells were grown in DMEM (Gibco 41965062) supplemented with 10 % FBS, 100 U/mL penicillin/streptomycin and 2 mM L-glutamine. All the cells were cultured at 37°C under a humidified incubator with 5 % CO2. Cells were regularly tested for mycoplasma infection with a PCR-based method.

extract_protocol:
Cells were lysed with TRIzol (Invitrogen 15596026) directly on the plate to quench 4sU incorporation. Total RNA was extracted following manufacturer's instructions.
A total of66ng of 4sU-labeled RNA per sample was used for stranded RNA library preparation using the KAPA RNA HyperPrep kit (Roche KK8540) following the manufacturer’s instructions. Libraries were sequenced in a NextSeq550 illumina sequencer in 1x75bp mode

treatment_protocol: HCT116 TOP2A mAID and HCT116 TOP2A mAID/TOP2B -/- were synchronized in G1 by treating the cells with 2uM Palbociclib (Selleck Chemicals Cat #S1116) for a total of 28 hours. TOP2A degradation was achieved by treating HCT116 TOP2A mAID/TOP2B -/- cells with 500μM of indole-3-acetic acid (IAA, Auxin Sigma-Aldrich Cat# I5148-2G) for 8 hours. Cells were then pulsed with 1mM of 4-thiouridine (4sU, Jena Bioscience N-1090-100) for 30 minutes before being lysed with TRIzol (Invitrogen 15596026) directly on the plate to quench 4sU incorporation

value: human colorectal carcinoma

value: wildtype


title: DS_WT_H3K9ac_ChIApet_rep1


title: DS_WT_H3K9ac_ChIApet_rep2


title: STSC4

description: 10X Genomics V3.1

value: primary visual cortex

value: cortical neurons


title: H3K9ac_input

data_processing:
The raw reads were filtered and trimmed by fastp (v0.23.0) with parameters “-q 15” and mapped to the MH63RS3 assembly using Bowtie2 (v2.4.5) with parameters “--sensitive, --no-unal”. Uniquely mapped nonredundant reads were preserved by picard and were passed to macs2 (v2.2.7.1) for peaks calling (parameters “--call-summits, -f BAMPE, -p 0.01”). Peaks called by the two biological replicates were filtered by irreproducible discovery rate (IDR) framework with a threshold of 0.05 to yield high-fertility peaks. Differentially covered / shared (with at least 1-bp overlap) H3K9ac peak regions among conditions were identified using bedtools (v2.29.1). For quantitative analysis of differential occupation, uniquely mapped nonredundant reads with the union peak regions of all conditions were quantified and normalized (by library size) by R package DiffBind (v3.0). Then differential occupation was determined using the DEseq2 method with a threshold of |log2(fold change)| > 1 and FDR < 0.05. Annotation of the peak-flanking genes were done using R package ChIPseeker with the −1000 to +100 region relative to TSS as the promoter region. The sequencing signal tracks were generated using bamCoverage in the deeptools kit (v3.5.1) with the RPGC (reads per genomic content) normalization and bin size of 1 bp.
Assembly: MH63RS3 (http://rice.hzau.edu.cn/rice_rs3/)
Supplementary files format and content: The bigwig (.bw) files record the coverage of uniquely mapped reads, normalized by reads per genomic content with the bin size of  1 bp.

growth_protocol: Wild-type (WT)  seeds were soaked for 3 days until germination. Seedings with similar growth state were then planted in 12 buckets (30 / bucket) with equal amount of soil and water. The buckets were randomly placed in a growth chamber with the air temperature of 32°C (day) or 29°C (night), 12 hours of light (constant light intensity 15000 lux) per day, and the relative humidity of 80%. The weight of soil in each bucket was 2.1 kg, and the initial water is 800 mL.

extract_protocol:
Rice seedling strips were crosslinked with 1% formaldehyde (SIGMA, F8775) for 10–15 min at room temperature in a vacuum chamber, and 0.2 M glycine was applied to quench the reaction. For each reaction, ~0.1 g sample was ground in liquid nitrogen into fine powder and then lysed in 300 μL of Buffer S (50 mM HEPES-KOH (pH7.5), 150 mM NaCl, 1 mM Ethylene Diamine Tetraacetic Acid (EDTA), 1% Triton X-100, 0.1% sodium deoxycholate, 1% SDS) for 10 min at 4°C. The homogenate was mixed with 1.2 mL of Buffer F (50 mM HEPES-KOH (pH 7.5), 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate). After that, the chromatin in the homogenate was fragmented to 200–600 bp by sonication with a Bioruptor (Diagencode). Then, the mixture was centrifuged at 12000× g for 10 min at 4°C to recover the chromatin in the supernatant. 20 µL of the supernatant was reserved as input, and the remaining was used for ChIP.
50 μL Dynabeads® protein G beads (Life Technologies, 10003D) was balanced with PBST buffer (phosphate-buffered saline (PBS) with 0.1% Tween 20) twice before incubating with 1–2 μg anti-histone H3 acetyl K9 antibody (Abcam, ab10812) or previously approved anti-OsbZIP23 polyclonal antibody for 6–8 h on a rotator at 4°C. After removal of excessive antibody by washing with PBST twice, the antibody-conjugated beads were mixed with the sheared chromatin and incubated at 4°C overnight with gentle rotation. The immunoprecipitated chromatin was washed successively with low-salt ChIP buffer (50 mM HEPES-KOH, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, and 0.1% SDS) (three times), high-salt ChIP buffer (identical to low-salt ChIP buffer expect for the use of 350 mM NaCl) (twice), ChIP wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% NP-40, 1 mM EDTA, 0.1% sodium deoxycholate) (once), and TE buffer (10 mM Tris-HCl, pH 8.0, and 1 mM EDTA) (twice). The protein–DNA complex was eluted from the magnetic beads with 100 μL Elution Buffer (50 mM Tris-HCl pH 7.5, 10 mM EDTA, 1% SDS) at 65°C for 15 min and then reverse-cross-linked by overnight incubation with 20 mg/mL proteinase K and 5 M NaCl at 55°C. ChIP DNA libraries were prepared using the NEBNext® UltraTM II DNA library prep kit for Illumina® sequencing (New England BioLabs, E7645). Next, library DNA fragments with 250–650 bp in length were preserved using AMPure XP beads (Beckman, A63881).

tag: chip antibody

value: pooled


title: GAL4 control male 3

value: elav > +


title: STS3

description: 10X Genomics V3.1

value: monosynaptic rabies tracing


title: 16-N

value: resected aortic coarctation

value: male


title: UAS control female 1

value: whole brain


title: STS4

description: 10X Genomics V3.1


title: WT (ttchem) replicate 1


title: STS2

description: 10X Genomics V3.1


title: DKO (ttchem) replicate 2

value: TOP2A + TOP2B double knockout


title: DKO (ttchem) replicate 1


title: RE_H3K9ac_rep2_IP

value: Anti-H3K9ac (Abcam, ab10812)

value: recovery


title: STS1

description: 10X Genomics V3.1


title: GAL4 control male 1


title: WT (LaminB1) replicate 2

data_processing:
Lamin B1 Cut&Run data were mapped using Bowtie 2 (version 2.3.4.3 with params: --very-sensitive --end-to-end --maxins 1000 --minins 0) on the Homo sapiens genome assembly reference version hg38  provided by UCSC as of June 2016
Duplicated reads with the same sequence and sharing mapping coordinates were removed using Picard MarkDuplicates (version 2.20.3). Domains were called for each pair of replicates using the Epic 2 peak caller version 0.0.52 (Stovner EB and Sætrom (2019)) with a bin size of 1KB, and compared knock-out cells versus wildtype cells using the IGG sequenced libraries to control for the experiment background.
Assembly: hg38
Supplementary files format and content: tab separated Epic output with peak coordinates

extract_protocol:
Cells were trypsinized and incubated in lysis buffer for CUT&RUN as described by the manufacturer of the CUT&RUN Assay Kit (Cell signaling #86652).
Libraries were prepared using the SimpleChIP® ChIP-seq DNA Library Prep Kit for Illumina® (Cell signaling #56795) following manufacturer’s instructions. Indexed libraries were pooled at equimolar concentrations and sequenced in an illumina NextSeq550 in paired end mode (2x75bp)
CUT&RUN for LaminB1 with library preparation using the SimpleChIP® ChIP-seq DNA Library Prep Kit for Illumina® (Cell signaling #56795) following manufacturer’s instructions.

treatment_protocol: HCT116 TOP2A mAID and HCT116 TOP2A mAID/TOP2B -/- were synchronized in G1 by treating the cells with 2uM Palbociclib (Selleck Chemicals Cat #S1116) for a total of 28 hours. TOP2A degradation was achieved by treating HCT116 TOP2A mAID/TOP2B -/- cells with 500μM of indole-3-acetic acid (IAA, Auxin Sigma-Aldrich Cat# I5148-2G) for 8 hours.


title: GAL4 control male 2


title: N_bZIP23_input

value: normal


title: WT (LaminB1) replicate 1


title: GAL4 control female 3


title: Control

city: Turku

first: Varpu

last: Rinne

address: Kiinamyllynkatu 10, 20520

department: Institute of Biomedicine

country: Finland

institute: University of Turku

data_processing:
Raw data processing, including demultiplexing, read alignment, and quality control, was performed using the 10X Genomics Cell Ranger package version 3.1.0.
Supplementary files format and content: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lymph node

extract_protocol:
Single-cell suspension of lymphocytes was produced by mechanically homogenising the pooled popliteal lymph nodes with a custom-made metal cell strainer to detach cells from the stroma. Cells were washed twice with PBS with 2 % fetal calf serum (FCS) buffer and filtered through 77 µm silk. Cells were re-filtered through a 40 µm filter and suspended in RPMI medium with 2 % FCS buffer.
Extracted lymphocytes were processed with the Chromium platform (10X Genomics) for library preparation, and the barcoded scRNA-seq libraries were constructed using 10XGenomics Chromium Next GEM Single Cell 3', Reagent Kit v3.1. Briefly, reverse transcription was performed to specific single-cell gel beads in the emulsion to produce full-length 10X barcoded cDNA from polyadenylated mRNA. The cDNA was amplified with PCR, followed by enzymatic fragmentation, end repair and A-tailing, adaptor ligation, and sample index PCR. Qualities of cDNA were ensured with Agilent Bioanalyzer 2100, and index PCR was made using Chromium i7 Multiplex Kit. Prepared libraries were sequenced using the Illumina Novaseq6000 Sequencing System

value: lymph node

value: lymphocytes

value: Control


title: B. burgdorferi Infected

value: B. burgdorferi Infected


title: N_bZIP23_rep2_IP

value: seedling

value: Anti-OsbZIP23 (custom-made)


title: WT IgG control

value: human colorectal carcinoma

value: wildtype


title: GAL4 control female 2

value: elav > +


title: N_bZIP23_rep1_IP


title: ATOH1_GFP_RNA_ZIC1_sort_rep2

source_name: cerebellum

value: cerebellum

value: murine cerebellar primary granule cells

value: GFP-tagged

value: WT ZIC1 overexpression


title: DKO replicate 1

value: TOP2A + TOP2B double knockout


title: N_H3K9ac_rep1_IP

value: Anti-H3K9ac (Abcam, ab10812)


title: GAL4 control female 1

value: whole brain


title: N_H3K9ac_rep2_IP

value: normal


title: elav bmm KD male 2

value: elav > UAS-bmm-RNAi


title: ATOH1_GFP_RNA_ZIC1_sort_rep1


title: elav bmm KD male 3


title: RE_H3K9ac_rep1_IP

value: recovery


title: MT replicate 2

data_processing:
GapRUN data were mapped against hg38 using bowtie2 (v2.3.4, parameters: --very-sensitive –end-to-end --maxins 1000), the result was then filtered out for both multi-mapping and duplicated reads [4]. We used MACS2 (v2.1.2) to call peaks with the following parameters: “--min-length 150 --broad --keep-dup auto” [5]. Peaks identified by MACS2 were annotated using Chipseeker (v1.28.3)
Assembly: hg38
Supplementary files format and content: tab separated MACS2 output with peak coordinates

extract_protocol:
Cells were trypsinized and incubated in lysis buffer for CUT&RUN as described by the manufacturer of the CUT&RUN Assay Kit (Cell signaling #86652).
Libraries were prepared using the SimpleChIP® ChIP-seq DNA Library Prep Kit for Illumina® (Cell signaling #56795) following manufacturer’s instructions. Indexed libraries were pooled at equimolar concentrations and sequenced in an illumina NextSeq550 in paired end mode (2x75bp)

treatment_protocol: GapR-expressed cells were synchronized in G1 by treating the cells with 2uM Palbociclib (Selleck Chemicals Cat #S1116) for a total of 28 hours.


title: ATOH1_GFP_RNA_ZIC1_bulk_rep2


title: ATOH1_GFP_RNA_ZIC1_bulk_rep1


title: DKO IgG control


title: DS_bZIP23_input

value: drought


title: ATOH1_GFP_RNA_mch_sort_rep2

value: empty vector overexpression


title: DS_bZIP23_rep2_IP

value: seedling


title: elav bmm KD male 1


title: DKO replicate 2


title: MT replicate 1


title: ATOH1_GFP_RNA_mch_sort_rep1


title: elav bmm KD female 2


title: elav bmm KD female 3


title: DS_bZIP23_rep1_IP

value: Anti-OsbZIP23 (custom-made)


title: WT replicate 2

value: human colorectal carcinoma


title: ATOH1_GFP_RNA_mch_bulk_rep2


title: DS_H3K9ac_rep2_IP


title: elav bmm KD female 1


title: WT replicate 1

value: wildtype


title: ATOH1_GFP_RNA_mch_bulk_rep1


title: DS_H3K9ac_rep1_IP


title: GBS3_24, treatment, biol rep 3, 24 hour

status: Public on Sep 18 2024

city: Daegu

first: Hyung Soo

last: Han

state: Daegu

address: 680 Gukchaebosang-ro

country: South Korea

institute: Kyungpook National University

data_processing:
FASTQ files from the sequencer underwent quality assessment using FASTQC and Multiqc. To eliminate low-quality reads and sequencing adapters, Cutadapt was employed. The alignment and quantification of RNASeq data were facilitated by STAR.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: The tab-delimited text file contains raw counts for each sample
Supplementary files format and content: The comma-delimited text file includes raw count data for all samples

source_name: Uterus; Cervix

growth_protocol: Hela cells were cultured and maintained in T75 cell culture flasks using Minimum Essential Medium supplemented with 10% fetal bovine serum, within a humidified atmosphere of 5% CO2 at 37°C

extract_protocol:
The RNeasy Mini Kit (Qiagen) was employed to isolate total RNA in accordance with its protocol. Ribosomal RNA depletion was executed using the MGIEasy rRNA Depletion Kit. Quantitative and qualitative evaluations were performed using a Qubit 4 Fluorometer and Bioanalyzer
RNA libraries were prepared using the MGIEasy RNA Directional Library Prep Set

treatment_protocol: Hela cells were infected with GBS for 0, 2, 6, and 24 hours, with corresponding control groups treated solely with a bacteria-free human medium

value: Uterus; Cervix

value: Hela

value: epithelial cell

value: WT

value: infected with GBS in 24 hour


title: GBS2_24, treatment, biol rep 2, 24 hour


title: GBS3_06, treatment, biol rep 3, 06 hour

value: infected with GBS in 06 hour


title: GBS1_06, treatment, biol rep 1, 06 hour


title: GBS2_02, treatment, biol rep 2, 02 hour

value: infected with GBS in 02 hour


title: GBS1_02, treatment, biol rep 1, 02 hour


title: GBS3_02, treatment, biol rep 3, 02 hour


title: GBS3_00, treatment, biol rep 3, 00 hour

value: infected with GBS in 00 hour


title: C3_24, control, biol rep 3, 24 hour

value: human medium without bacteria


title: C2_24, control, biol rep 2, 24 hour


title: GBS1_00, treatment, biol rep 1, 00 hour


title: GBS2_00, treatment, biol rep 2, 00 hour


title: C1_06, control, biol rep 1, 06 hour


title: C1_24, control, biol rep 1, 24 hour


title: C3_02, control, biol rep 3, 02 hour


title: C2_00, control, biol rep 2, 00 hour


title: C1_00, control, biol rep 1, 00 hour


title: C2_02, control, biol rep 2, 02 hour


title: C2_06, control, biol rep 2, 06 hour


title: C3_00, control, biol rep 3, 00 hour


title: C1_02, control, biol rep 1, 02 hour


title: GBS2_06, treatment, biol rep 2, 06 hour


title: GBS1_24, treatment, biol rep 1, 24 hour


title: WT, scRNA

city: 重庆Chongqing

first: Zeyu

last: Fu

state: 重庆Chongqing

address: 高滩岩正街

department: College of Preventive Medicine

institute: AMU

description: 10X Genomics

data_processing:
Cellranger 7.0.1
Assembly: mm10
Supplementary files format and content: tsv files and matrix files

source_name: Bone marrow

extract_protocol:
To perform 10X Genomics single-cell sequencing on mouse bone marrow LSK cells, begin by euthanizing the mouse following ethical guidelines and extracting the femurs and tibias. Flush the bone marrow with  PBS with 2% FBS, to obtain a single-cell suspension. Filter this suspension through a 40 µm cell strainer to remove debris and clumps. Next, enrich the LSK (Lineage^-, Sca-1^+, c-Kit^+) cells using magnetic-activated cell sorting (MACS) or fluorescence-activated cell sorting (FACS). Count the cells and assess viability using trypan blue staining or a similar method. Adjust the concentration of LSK cells to the required density, typically 700-1200 cells/µL
Load the single-cell suspension, reagents, and gel beads into the appropriate wells of a 10X Genomics Single Cell 3' Chip and run the chip in the Chromium Controller to encapsulate single cells into nanoliter-scale Gel Bead-In-EMulsions (GEMs). Perform reverse transcription within the GEMs to generate barcoded cDNA from the mRNA of individual cells, then break the emulsion and clean up the barcoded cDNA. Amplify the cDNA via PCR and assess the quality and quantity using an Agilent Bioanalyzer or similar instrument. Construct sequencing libraries from the amplified cDNA, following the 10X Genomics protocol. Sequence the libraries on  Illumina 3000 platform.

value: Bone marrow

value: LSK phenotype HSCs

value: Wild type


title: aADM2tg5-MRNA-LFM18205

city: Beijng

first: Pengcheng

last: Wang

address: Huanyuan Road 49

institute: Peking University Third hospital

data_processing:
Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.2.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.2.1).
Assembly: In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: visceral adipose tissue

growth_protocol: 10 week old male mice were anesthetized and euthanized to obtain visceral adipose tissue samples

extract_protocol:
Total RNA from tissues or cells was isolated using TRIzol (Invitrogen, Darmstadt, Germany), following manufacturer’s instructions.1 ug of total RNA was used for the construction of sequencing libraries
The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature

treatment_protocol: We then performed gene expression profiling analysis using data obtained from RNA-seg of visceral adipose tissue from 5 mice per group

value: visceral adipose tissue

value: adipocyte

value: Muture adipocyte

value: 8 week Chow diet


title: DAPP1 KO, scRNA

description: 10X Genomics

value: DAPP1 gene knock out


title: aADM2tg4-MRNA-LFM18204


title: aADM2tg2-MRNA-LFM18202


title: aADM2tg3-MRNA-LFM18203


title: WT4-MRNA-LFM18210


title: WT2-MRNA-LFM18208


title: C3_06, control, biol rep 3, 06 hour

value: Uterus; Cervix


title: WT1-MRNA-LFM18207


title: genomic DNA from IRCC174_A_PDO

type: genomic

city: Candiolo

first: Federica

last: Di Nicolantonio

state: Torino

address: Candiolo Cancer Institute FPO-IRCCS, SP142, km 3.95

department: Department of Oncology

country: Italy

institute: University of Torino

description:
CRC patient derived organoid grown in vitro without any treatment
IRCC174_A_PDO

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip microarray using standard Illumina Infinium HD methylation protocol

scan_protocol: Arrays were imaged using iScan with the standard recommended Illumina scanner setting

data_processing:
EPIC raw data (IDAT files) were processed using the minfi R Bioconductor package and corresponding annotation packages. In each sample, probes with detection p-value > 0.05 were masked in the RGChannelSet. In addition, cross-reactivity probes and probes matching SNPs at the target CpG site were filtered using previously published lists. Then, methylation and unmethylation signals were obtained for each CpG site using the preprocessNoob function and beta-values were computed. Results obtained in all samples were subsequently merged in a single beta-matrix and CpG sites that are located on sex chromosomes or chrM were excluded.
Processed data matrix contains Beta-values and detection p-values for unfiltered probes in each sample

label: Cy5 and Cy3

source_name: CRC patient derived organoid

label_protocol: Standard Illumina labelling protocol

growth_protocol: All organoids were maintained in the media recommanded by supplier

extract_protocol: Genomic DNA was extracted Maxwell RSC Blood DNA kit (Promega)

treatment_protocol: All organoids were maintained in absence of drug

value: CRC patient derived organoids


title: genomic DNA from IRCC161_A_PDO

description:
CRC patient derived organoid grown in vitro without any treatment
IRCC161_A_PDO


title: E16.5 embryo, individual_1

type: RNA

city: Suita-shi

first: Manami

last: Nakai

state: Osaka-fu

address: 1-6 Yamadaoka

country: Japan

institute: Osaka University

description: Gene expression data in whole embryos during mouse development

hyb_protocol: Following fragmentation, 2.5 ug of cRNA were hybridized for 16 hr at 45C on Clariom S Array, mouse. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Transcriptome Analysis Console (Thermo Fisher Scientific) and global scaling as normalization method.

label: biotin

source_name: Mouse embryo at 16.5 days post-fertilization

label_protocol: Biotinylated cRNA were prepared according to the standard protocol from 2 ng total RNA (GeneChip WT Pico Kit, Thermo Fisher Scientific, 902622).

growth_protocol: Mice were housed under a 12-h light-dark cycle, provided with a standard diet, and maintained at a constant temperature. After inducing superovulation, natural mating was performed, and the day the vaginal plug was confirmed in the female mouse was designated as E0.5

extract_protocol: QIAzol (QIAGEN) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: On the same day the plug was confirmed, the pronucleus produced by copulation were washed in 100-μL KSOM (ARK Resource) drops twice and incubated at 37°C, 5% CO2. The collection of 2-cell embryos and morula were performed at 24 and 48 h after the plug-confirmation day. E10.5 and E16.5 were extracted from the mother mice from which the plugs were confirmed, and washed with PBS.

value: whole embryo


title: E16.5 embryo, individual_3


title: aADM2tg1-MRNA-LFM18201


title: genomic DNA from IRCC150_A_PDO

description:
CRC patient derived organoid grown in vitro without any treatment
IRCC150_A_PDO


title: WT5-MRNA-LFM18211

value: WT


title: genomic DNA from IRCC148_A_PDO

description:
CRC patient derived organoid grown in vitro without any treatment
IRCC148_A_PDO


title: genomic DNA from IRCC131_PDO

description:
CRC patient derived organoid grown in vitro without any treatment
IRCC131_PDO


title: E10.5 embryo, individual_3

source_name: Mouse embryo at 10.5 days post-fertilization


title: E10.5 embryo, individual_2


title: D425_ev1_ZIC1_mut_constructs_RNA

value: Group 3 medulloblastoma

value: empty vector overexpression


title: WT3-MRNA-LFM18209


title: genomic DNA from IRCC125_A_PDO

description:
CRC patient derived organoid grown in vitro without any treatment
IRCC125_A_PDO


title: genomic DNA from IRCC120_PDO

description:
CRC patient derived organoid grown in vitro without any treatment
IRCC120_PDO


title: genomic DNA from IRCC107_A_PDO

description:
CRC patient derived organoid grown in vitro without any treatment
IRCC107_A_PDO


title: morula stage embryo, biological rep1

source_name: Mouse embryo at 2.5 days post-fertilization


title: E16.5 embryo, individual_2


title: genomic DNA from IRCC166_PDO

description:
CRC patient derived organoid grown in vitro without any treatment
IRCC166_PDO


title: genomic DNA from IRCC105_E_PDO

description:
CRC patient derived organoid grown in vitro without any treatment
IRCC105_E_PDO


title: pronuclear stage embryo, biological rep2

source_name: Mouse embryo at 0.5 days post-fertilization


title: 22-F

value: resected aortic coarctation

value: male

value: tav

value: coarctation


title: 2-cell stage embryo, biological rep1

source_name: Mouse embryo at 1.5 days post-fertilization


title: E10.5 embryo, individual_1


title: pronuclear stage embryo, biological rep1


title: genomic DNA from IRCC105_A_PDO

description:
CRC patient derived organoid grown in vitro without any treatment
IRCC105_A_PDO


title: morula stage embryo, biological rep2


title: genomic DNA from IRCC105_C_PDO

description:
CRC patient derived organoid grown in vitro without any treatment
IRCC105_C_PDO


title: 2-cell stage embryo, biological rep2


title: 25mg SQ-diEG 1

city: Tsukuba

first: Yaman

middle: (Yaman

last: Zhang

state: Ibaraki

address: Amakubo 2-4-1

department: Comprehensive human science

institute: University of Tsukuba

description: Gene expression data from 25mg/kg SQ-diEG treated mice for 20 days

hyb_protocol: Following fragmentation, 250 ng of cRNA were hybridized for 16 hr at 45C on Clariom_S_Mouse Array. GeneChips were washed and stained in the GeneAtlas® Fluidics Station

scan_protocol: GeneChips were scanned using the GeneAtlas Imaging Station

data_processing:
The raw data were normalized using Expression Console Software provided by the Affymetrix following SST-RMA algorithm (http://www.affymetrix.com). Subsequent analysis of the gene expression data was carried out in the freely available Transcriptome Analysis Console (TAC) version 4 (Thermofisher inc.). Genes with a linear fold change >1.5 and p-value < 0.05(one-way between-subjects ANOVA) were considered as differentially expressed genes(DEGs). Further analysis was conducted using an online data mining tool DAVID (Database for Annotation, Visualization and Integrated Discovery, ver. 6.8). We used 'Functional Annotation' tool of DAVID to identify the most relevant biological terms, including gene ontology (GO) terms, biological pathways, tissue expression, and disease associations (Huang da et al., 2009).
Expression console signal intensity. For calculating average value, standard deviation, fold change, and Anova p-value of signal intensity of replicates, we used freely available Transcriptome Analysis Console software.
SST-RMA

source_name: Mice treated with 25mg/kg SQ-diEG

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 9.4 ug total RNA

growth_protocol: Eight per group, six-weeks old male C57BL/6J mice, total 40 mice (Charles River Laboratories Japan, Inc.) were housed individually in polycarbonate cage under 12-h light/dark cycle condition. Mice were allowed to access to food and water freely for 7 days acclimatization before the start of experiment. During the experiment, mice was housed as mentioned above.

extract_protocol: For RNA extraction from lung tissue was performed using Isogen (Nippon Gene Co. Ltd., Toyama, Japan) according to the protocol instructions.

treatment_protocol: Total 40 six years old male C57BL/6J mice were randomly divided into five groups (8 mice per group), including the control "(-)B16F10 injected and water treated"; the model "(+) B16F10 injected and water treated"; the positive control "(+) B16F10 injected and DTIC treated (Dacarbazine, 70 mg/kg/day)"; the SQ-diEG treatment "(+) B16F10 injected and SQ-diEG treated (5 mg/kg/day)"; the SQ-diEG treatment "(+) B16F10 injected and SQ-diEG treated (25 mg/kg/day)". Mice in each group was treated with water, DTIC or SQ-diEG accordingly for 20 days.

tag: gender

value: Male

tag: strain

value: Lung


title: 25mg SQ-diEG 2


title: NEVLPcty, scRNAseq

city: New Orleans

first: Ruoxin

last: Lan

state: LA

address: 204 S Saratoga St, Apt 316

institute: Tulane University

description: 10x Genomics

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

organism: Rattus norvegicus

source_name: liver

extract_protocol:
The perfusate was made up of 65mL William’s E Media (Quality Biological, Gaithersburg, MD), 3,250U each Penicillin/Streptomycin (Life Technologies Corporation, Grand Island, NY), 0.65mM sodium pyruvate (Sigma-Aldrich, St. Louis, MO), 1.30mM L-glutamine (Sigma-Aldrich), 1% human albumin (Baxter), 500U heparin, 15mg papaverine (American Regent, Inc., Shirley, NY), 1mg insulin (Sigma-Aldrich), 1.25mg hydrocortisone (Pfizer, New York, NY), and 30mL of leukoreduced, packed Lewis rat red blood cells.
Tulane Cypress high performance computer was used to process pair-ended raw fastq files generated from the sequencing experiments following the cellranger pipelines (10x Genomics), with a “filtered feature bc matrix” output folder that contains matrix.mtx.gz, barcodes.tsv.gz and features.tsv.gz files.

value: liver

value: Lewis

tag: condition

value: NEVLPcty


title: 5mg SQ-diEG 2

description: Gene expression data from 5mg/kg SQ-diEG treated mice for 20 days

source_name: Mice treated with 5mg/kg SQ-diEG

tag: tissue


title: NEVLP2, scRNAseq

description: 10x Genomics


title: Nave, scRNAseq

description: 10x Genomics

value: Nave


title: DTIC 2

description: Gene expression data from DTIC treated mice for 20 days

source_name: Mice treated with 70mg/kg DTIC


title: Con-exo3

city: Hefei

first: Hai-Juan

last: ZHU

state: Anhui

address: the 15th Yimin street

institute: Maternal and Child Medical Center of Anhui Medical University

data_processing:
The raw reads were processed by filtering out containing adapter, poly ’N’, low quality, smaller than 17nt reads by FASTQC to get clean reads. Mapping reads were obtained by mapping clean reads to reference genome of by BWA.
miRDeep2 was used to identify known mature miRNA based on miRBase21 (www.miRBase.org) and predict novel miRNA. Databases of Rfam12.1 (www.rfam.xfam.org) and pirnabank (www.pirnabank.ibab.ac.in) were used to identify rRNA, tRNA, snRNA, snoRNA and piRNA by BLAST. The miRNA expression were calculated by RPM (Reads Per Million) values (PRM=(number of reads mapping to miRNA/ number of reads in Clean data)×106 ).
The expression levels were normalized by RPM, RPM is equal to (number of reads mapping to miRNA/ number of reads in Clean data)×106. Differential expression between two sets of samples was calculated by edgeR algorithm according to the criteria of |log2(Fold Change)|≥1 and P-value < 0.05.
TargetScan, miRDB, miRTarBase and miRWalk were used to predict targets gene of selected miRNA. KOBAS was used to further Gene Ontology (GO) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis.
Assembly: rn6
Supplementary files format and content: all.miRNA.xls
Supplementary files format and content: xls

source_name: serum

growth_protocol: Adult male Sprague-Dawley (SD) rats (250-280 g) were obtained from the Experimental Animal Center of Anhui Medical University (China). The rats were given ad libitum access to standard rodent chow and water in a temperature-controlled room maintained at 22-24°C. All experimental procedures were conducted following the guidelines for the Care and Use of Laboratory Animals and were approved by the Institutional Animal Care and Use Committee of Anhui Medical University (approval number: LLSC20210983). Prior to experimentation, the rats were anesthetized with an intraperitoneal injection of 3% pentobarbital at a dosage of 50 mg/kg.

extract_protocol:
Total RNA was isolated by using Trizol (Invitrogen,USA). The quantity and integrity of RNA yield was as-sessed by using the Qubit®2.0 (Life Technologies, USA) and  Agilent 2200 TapeStation (Agilent Technologies, USA) separately. 1μg total RNA of each samples were used to prepare small RNA libraries by NEBNext® Multi- plex Small RNA Library Prep Set for Illumina (NEB,USA) according to manufacturer’s instructions.
The libraries were sequenced by HiSeq 2500 (Illumina,USA) with single-end 50bp at Ribobio Co. Ltd (Ribobio,China).

treatment_protocol: Following the administration of anesthesia, IPC was carried out by occluding the left anterior descending coronary artery (LAD) approximately 3 mm below the left atrium using a 6-0 nylon thread. This procedure involved three cycles of 5 minutes of ischemia alternated with 5 minutes of reperfusion. The induction of myocardial ischemia was verified by the pallor of the myocardial tissue beneath the suture and towards the heart's apex, coupled with S-T segment elevation observed in electrocardiograms. After this procedure, blood samples were drawn from the left ventricle using a sterile intravenous needle attached to a coagulation tube. Rats in the control group did not receive any processing , blood was taken in the same manner but without the ischemic preconditioning step.

value: serum

value: 9-10 weeks

value: Sprague-Dawley

value: Exosomes isolated from the serum of rats

value: The blood in the CON group was taken in the same manner as IPC group but without the ischemic preconditioning step.


title: Con-exo1


title: Con-exo2


title: IPC-exo3

value: The rats were treated with IPC, which was performed by ligating the left anterior descending coronary artery  with a 3-cycle procedure (5 min of ischemia followed by 5 min of reperfusion). Then blood samples were collected from the left ventricle and the exosomes were isolated.


title: Model 1

description: Gene expression data from water treated mice for 20 days

source_name: Mice treated with water


title: CS, scRNAseq

description: 10x Genomics

value: CS


title: IPC-exo1


title: DTIC 1


title: Control 1


title: 5mg SQ-diEG 1


title: WT, day 2

city: Aurora

first: Kristen

last: Wells

state: CO

address: 1775 Aurora Ct,

department: Barbara Davis Center

institute: University of Colorado Anschutz

description: 10x genomics

data_processing:
Sequences from scRNA-seq were processed using 10x Genomics Cellranger v 5.0.1 software {Zheng, 2017 #412} using the ferret ASM1176430v1.1 genome and gtf file. A recently described improved annotation of the ferret transcriptome was used which achieves a median read assignment in scRNA-seq studies of ~71% {Yuan, 2023 #414}. The genome and gtf file were made into a cellranger reference using the `mkref` command.
Raw data generated by Cellranger were then read into R v4.1.2 using the Seurat {Hao, 2021 #404} v4.1.1 R package with at least 200 genes per cell and at least 3 cells. Cells were further filtered based on the number of genes per cell and the percent of mitochondrial reads per cell (maximum 10%). The data were normalized by using `NormalizeData`. For each sample, variable genes were found by using `FindVariableFeatures` and data was scaled using `ScaleData`.
Doublets were removed using `DoubletFinder` {McGinnis, 2019 #407} using the default values except for pK, nExp, and PCs. The pK was identified using the pK associated with the maximum BCmetric value after running `find.pK` from doublet finder. All samples used PCs 1:20. After doublet removal, 4499 (CFKO_D2), 2750 (CFKO_D5), 1607 (CFKO_D7), 2489 (CFKO_D9), 6224 (WT_D2), 5326 (WT_D5), 4634 (WT_D7), 5416 (WT_D9) cells were used for downstream analysis.
The 8 samples were merged using the `merge` function from Seurat. The merged data was then normalized and scaled using `NormalizeData`, `FindVariableFeatures`, and `ScaleData` as described above. Dimensionality reduction and clustering were performed using `RunPCA`, `FindNeighbors`, `FindClusters`, and `RunUMAP`. `RunPCA` was run using the default values except all variable features were used for the features argument. `FindNeighbors` was run with default parameters except for the dims argument (dims=1:30). `FindClusters` was run with default parameters except for the resolution argument (resolution=0.6). `RunUMAP` was run with default parameters except for the dims and metric arguments (dims=1:30, metric=”correlation”). Because some clusters had good representation of all development days and we wanted to analyze the WT and KO separately, no batch correction was performed.
We made a first pass at naming clusters on the merged WT and merged CFKO samples separately using a mix of published single cell studies of mouse and human pancreas {Byrnes, 2018 #115;Baron, 2016 #114;Tabula Muris, 2018 #116;Qadir, 2020 #117;Muraro, 2016 #408;Krentz, 2018 #406} as a reference and determining cluster identity using `clustifyr` {Fu, 2020 #113}. For each reference, we used the top 2000 variable genes and found either the mouse or human ortholog. These orthologs were used as the `query_genes` and the clusters identified by `FindClusters` as the `cluster_col`. The top correlated cell type from any reference to each cluster was used as the first determination of cell type.
To identify markers of each cluster, `FindAllMarkers` was run on each merged dataset using default settings except we set only.pos to TRUE. Genes were called differentially expressed if the adjusted p-value was less than 0.05 and the log fold change was greater than 0.5. To generate a heatmap of gene sets, the average expression of all genes within each cluster was determined using `AverageExpression` from Seurat. Next, the average expression matrix was subset to only the genes in the gene set of interest. Finally, a z-score was computed, and the plot was generated with `pheatmap` (https://cran.r-project.org/web/packages/pheatmap/index.html).
Most figures were created using the `scAnalysisR` package available on github (https://github.com/CUAnschutzBDC/scAnalysisR). All scripts to replicate this analysis will be made public on github (https://github.com/cuAnschutzBDC) upon publication.
Trajectory analysis. To perform trajectory analysis, we used `slingshot`. We identified starting clusters based on the cluster containing the most D2 cells for each WT and CFKO. We then used `tradeseq` using the pseudotime scores generated by slingshot to identify genes that correlated with pseudotime. We used the function `evaluateK` to determine the number of knots (5 for the CFKO, 8 for WT) and the function `fitGAM` to identify correlated genes.
Assembly: Mustela purorius furo, assembly ASM1176430v1.1
Supplementary files format and content: Tab separated values, comma separated values, matrix files

organism: Mustela putorius furo

source_name: Polarized pancreatic ductal epithelia

growth_protocol: Pancreata were removed from 1-3 day old newborn WT and CF ferrets and digested in 5 mg/ml collagenase for 20 min at 37oC. The digested pancreas was incubated overnight in PneumaCult™-Ex Plus medium (STEMCELL Technologies, MA, USA) on 804G-coated culture dishes overnight at 37oC in a 5% CO2 incubator. The 804G coating procedure is as previously described for airway basal cells {Mou, 2016 #413}. Ductal structures that adhered to the plate were aspirated on the following day and cultured on fresh 804G-coated culture dishes in PneumaCult™-Ex Plus medium until near confluence. These cells were then passaged by incubating with Accutase (STEMCELL Technologies, MA, USA) for 5 min at 37oC. The cells were passaged continuously for 10 passages to eliminate contaminating cells and obtain a morphologically homogenous population of duct cells. Passage-10 cells were harvested using Accutase and transferred to 804G-coated transwell inserts (Corning, NY, USA) at a density of 100,000 cells per well. Following seeding, transwells were cultured in PneumaCult™-Ex Plus medium on both apical and basolateral chambers for 3 days. The medium in both the apical and basolateral chamber was then switched to PneumaCult™-ALI (STEMCELL Technologies, MA, USA) for 1 day. Air liquid interface (ALI) was established the following day by aspirating the medium from the apical chamber. Cultures were maintained at an ALI for 3 weeks before use in experiments at which time transepithelial resistance should be greater than 1000 ohms.

extract_protocol:
Fully differentiated WT and CF ferret PDE cultures grown at ALI for 2, 5, 7, and 9 days were dissociated using Accutase followed by DNase treatment. Cells were filtered through a 20 uM strainer and pelleted in 0.04% BSA PBS at 500 g for 10 min. Nonviable dead cells were removed by using MACS Dead Cell Removal Kit following 10X Genomics recommendations (Document CG00039). Single cells were counted on a Thermo countess cell counter and 0.04% BSA/PBS was added to achieve a targeted concentration of 1000 cells/ul.
Sequencing libraries were generated by following 10X Genomics recommendations (Document CG000315). Briefly, single cells and reverse transcription master mix were partitioned into Gel Beads in partitioning oil in the 10X Chromium controller. After reverse transcription, cDNA libraries were amplified and fragmentated, followed by adaptor ligation and sample index PCR reaction. Libraries were sequenced on NovaSeq 6000 platform by the University of Iowa Genomics Division.

value: Polarized pancreatic ductal epithelia

value: Ductal

value: WT


title: WT, day 5

description: 10x genomics


title: Model 2


title: WT, day 7

description: 10x genomics


title: WT, day 9

description: 10x genomics


title: Old 5

city: Kyoto

first: Masataka

last: Narukawa

state: Kyoto

address: 35 Kitahiyoshicho, Imakumano, Higashiyama, Department of Food and Nutrition, Kyoto Women's University

department: Department of Food and Nutrition

institute: Kyoto Women's University

hyb_protocol: Second strand cDNA 5.5 µg were flagmentated, and hybridized for 16hr at 45°C on Affymetrix Mouse Clariom S Array. GeneChips were washed and stained with Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were normalized using the statistical software R, and the qFARMS method.

label_protocol: Biotin-labeled single strand cDNA was synthesized from 100 ng total RNA according to the manufacture's protocol.

growth_protocol: Mice were housed under controlled conditions at a temperature of 23°C and humidity of 55% under a 12/12-h light-dark cycle, with ad libitum feed and water intake.

extract_protocol: Total RNA was isolated from the hypothalamus using ISOGEN (Nippon Gene, Tokyo, Japan), and then purified with a RNAeasy mini kit (QIAGEN, Hilden, Germany).

value: male

tag: age

value: 138 weeks old

value: hypothalamus


title: CFKO knockout, day 2

description: 10x genomics

value: CFTR KO/KO


title: CFKO knockout, day 5

description: 10x genomics


title: Old 3


title: Old 2


title: CFKO knockout, day 7

description: 10x genomics


title: Old 4


title: Control 2

value: Male

value: Lung


title: IPC-exo2


title: Young 5

value: 24 weeks old


title: Old 1


title: Young 4


title: Young 3


title: C12_20d_10Dol_3

city: Philadelphia

first: Yijing

last: Su

state: PA

address: Levy 326

department: Department of Oral Medicine

institute: University of Pennsylvania

data_processing:
Sequencing was performed on a NextSeq 550 (Illumina) with 3.0 pM loading, using 1x75bp reads.
Alignment was performed using STAR v.2.6.1d (Dobin et al 2013) with GRCh38 used as the reference genome and gencode v.28 GTF used as the annotation file.
Multimapping and chimeric alignments were discarded, and uniquely mapping reads were quantified at the exon level and summarized to gene counts using python package HTSeq v0.11.1 (Anders et al 2015).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

growth_protocol: Forebrain organoids were cultured from iPSCs as previously described (Qian et al 2018, Qian et al 2016), with some modifications. Briefly, hiPSC colonies were detached with collagenase type IV, washed with DMEM:F12, and transferred to an uncoated polystyrene petri dish (VWR) in neural induction medium containing DMEM:F12 supplemented with 20% KnockOut Serum Replacement, 1X MEM-NEAAs, 1X 2mM GlutaMax, 1X penicillin (100 units/mL)/-streptomycin (100 µg/mL), 1X 0.1mM 2-mercaptoethanol, 2 mM dorsomorphin and 2 mM A83-01. On Day 5 and Day 6, half of the medium was replaced with forebrain induction medium consisting of DMEM:F12 supplemented with 1X N2 supplement, 1X penicillin (100 units/mL)/streptomycin (100 µg/mL), 1X NEAA, 1X 2mM GlutaMax, 1 mM CHIR99021, and 1 mM SB-431542. On Day 7, organoids were embedded in Matrigel and cultured in forebrain induction medium with drug or vehicle supplementation for 7 more days. On Day 14, embedded organoids were dissociated from Matrigel by washing 3 times with 2 mL ice-cold DPBS (Gibco), incubated in 4 mL cell recovery solution (Corning) at 4ºC with gentle rotation or rocking, and finally washed 3 times with 2 mL ice-cold DPBS. Incubation time in cell recovery solution ranged from 15 to 30 minutes with periodic visual inspection to determine the optimal time for maximal Matrigel dissolution while maintaining good organoid integrity. Organoids were transferred to a 6 well-plate on a CO2 resistant orbital shaker (Thermo Scientific) and grown in differentiation medium consisting of DMEM:F12 supplemented with 1X N2 supplement, 1X B27 supplement, 1X penicillin (100 units/mL)/streptomycin (100 µg/mL), 0.1mM 2-mercaptoethanol, 1X NEAA, and 2.5 g/mL human insulin.

extract_protocol:
To minimize organoid-to-organoid variability, 5-10 organoids were pooled into one sample for analysis. Organoids were homogenized in 400 μL TRIzol (Invitrogen) by manual pipetting until complete lysis. RNA was isolated by addition of 80 μL chloroform (Sigma-Aldrich), vortex and centrifugation at 4ºC for 15 minutes at 12,000 g, and careful collection of 200 μL of the upper aqueous layer. RNA clean-up was performed using a silica spin column (Zymo) according to the manufacturer’s instructions, followed by elution in 15 μL water and analysis by NanoDrop 2000 (Thermo Scientific). RNA was immediately extracted, minimizing any additional steps that could lead to RNA degradation, which preserves RNA integrity for further processing.
RNA-seq library preparation was performed as previously described (Jacob et al 2020, Weng et al 2018).

treatment_protocol: Stocks of DTG (Cayman Chemical) were made in sterile DMSO (Sigma-Aldrich) at the following concentrations in aliquots at -20˚C:  DTG, 10mM. Aliquots were thawed and drugs were added to forebrain induction and differentiation media to achieve the following working concentrations: DTG: 0.1 μM, 1 μM, 10 μM.  During the drug treatment period (DIV 7 – DIV 19 or DIV 7 – DIV 39), media with the various drug concentrations  was changed every day and organoids were collected on DIV 20 or DIV 40 for tissue processing.

value: organoid

value: Dol


title: Young 2


title: C12_20d_DMSO_1

value: DMSO


title: C12_20d_DMSO_3


title: Young 1


title: C12_20d_10Dol_1


title: CFKO knockout, day 9

description: 10x genomics


title: C12_20d_10Dol_2


title: KO-KAP1-E2-1h-PolIIS5P-Rep2

city: SAN DIEGO

first: Lishuan

state: California

address: 9500 Gilman Drive

institute: UCSD

data_processing:
cutadapt: -u 15 -U 15 -a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT -b -B
Quality control: FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and TRIMMOMATIC (http://www.usadellab.org/cms/?page=trimmomatic) were used to inspect the quality of the sequencing reads, and to trim the sequencing adaptors, if necessary.
bowtie2:  -q --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700
makeTagDirectory: -format sam -keepAll -tbp 1 -checkGC -sspe -fragLength given
makeUCSCfile
Assembly: hg38
Supplementary files format and content: BedGraph
Library strategy: CUT&Tag

growth_protocol: MCF7 cells were maintained at 37°C and 5% CO2 in Dulbecco's modified Eagle's medium (DMEM, GIBCO/Invitrogen), supplemented with 10% fetal bovine serum (FBS, GIBCO/Invitrogen). For hormone treatments, cells were incubated at 37°C and 5% CO2 for at least 3 days in phenol red-free DMEM (GIBCO/Invitrogen) supplemented with 5% charcoal dextran-stripped FBS (GIBCO/Invitrogen). 17-β-Estradiol (E2; Steraloids, Inc.) was added to a final concentration of 100 nM.

extract_protocol:
CUT&Tag standard Protocol
PCR Ampfication

value: Human breast cancers

value: S5P(Active motif, 61085)


title: WT-E2-1h-PolIIS5P-Rep2

treatment_protocol: 17-β-Estradiol (E2; Steraloids, Inc.) was added to a final concentration of 100 nM.


title: P_24_small intestine stroma_1d

city: Wien

first: Andre

last: Oszwald

address: Währinger Gürtel 18-20

country: Austria

institute: Medical University of Vienna

description: EDTA_DSP_AO_P_24_small intestine stroma_1d

data_processing:
BCL files were converted to FASTQ files using the Illumina bcl2fastq app (v2.2)
FASTQ files were converted to .DCC files and extracted as a matrix using the Nanostring NGS pipeline and GeoMxTools R package, respectively.
Assembly: n.a. (barcodes only; corresponding to unique probes and regions)
Supplementary files format and content: .dcc: processed counts (used for input in GeoMxTools R package)
Supplementary files format and content: .stats: statistics output of Nanostring GeoMx NGS pipeline

source_name: small intestine stroma

extract_protocol:
Sections were deparaffinized and subjected to heat-induced protein epitope retrieval (using retrieval buffer at pH 9, Thermo Fisher Scientific, 00-4956-58) for 15 minutes at 100°C using a steam cooker. Retrieval for mRNA was performed using proteinase K (Thermo Fisher Scientific, 25530049) at 1µg/ml for 15 minutes. Slides were incubated with the human Whole Transcriptome Atlas (WTA) probe panel (Nanostring, NA-GMX-RNA-NGS-HuWTA-4, Lot HWTA21003) at 37°C in a humidified environment overnight. Sections were washed according to standard protocols and direct immunofluorescence was performed with antibodies against CD34 conjugated to Alexa-647 (Novus Biologicals, clone QBEnd-10, NBP2-34713AF647), Pan-cytokeratin conjugated to to Alexa532 (Novus Biologicals, clone AE1/AE3, NBP2-33200), CD45 conjugated to Alexa594 (clone 2B11 + PD7/26, Novus Biologicals, NBP2-34528), and a nuclear counterstain (Syto-13, Nanostring). DSP device run was performed according to the manufacturer's protocol (https://university.nanostring.com/geomx-dsp-ngs-readout-user-manual).
Library preparation and sequencing were performed according to the manufacturers’ protocol (https://university.nanostring.com/geomx-dsp-ngs-readout-user-manual). The library was sequenced using an Illumina NextSeq 550 sequencer with the specifications provided by Nanostring (paired-end reads at length 27, index length 8, PhiX 5%) at a final library concentration of 1.6 pM using a NextSeq 550 High Output 75-cycle kit (Illumina, 20024906).

value: small intestine stroma

tag: case

value: P

tag: specimen

tag: duration edta

tag: roi


title: P_24_small intestine stroma_7d

description: EDTA_DSP_AO_P_24_small intestine stroma_7d


title: KO-KAP1-E2-1h-ERα-Rep2

value: ERα(Santa Cruz; sc-8002)


title: WT-E2-1h-ERα-Rep2


title: P_24_small intestine stroma_0d

description: EDTA_DSP_AO_P_24_small intestine stroma_0d


title: C12_20d_DMSO_2


title: WT-Veh-1h-PolIIS5P-Rep2


title: WT-Veh-1h-ERα-Rep2


title: L_23_carcinoma immune_0d

description: EDTA_DSP_AO_L_23_carcinoma immune_0d

source_name: carcinoma immune

value: carcinoma immune

value: L


title: WT-E2-1h-GATA3-Rep2

value: GATA3(Santa Cruz, sc-268)


title: L_23_carcinoma immune_7d

description: EDTA_DSP_AO_L_23_carcinoma immune_7d


title: L_23_carcinoma immune_1d

description: EDTA_DSP_AO_L_23_carcinoma immune_1d


title: KO-KAP1-E2-1h-GATA3-Rep2


title: KO-KAP1-E2-1h-ELL2-Rep2

value: ELL2(Santa Cruz, sc-376611)


title: L_23_carcinoma immune_3d

description: EDTA_DSP_AO_L_23_carcinoma immune_3d


title: N_22_bronchus_7d

description:
sampling error; excluded from analysis in manuscript
EDTA_DSP_AO_N_22_bronchus_7d

source_name: bronchus

value: bronchus

value: N


title: N_22_bronchus_1d


title: WT-Veh-1h-GATA3-Rep2


title: N_22_bronchus_3d


title: WT-E2-1h-ELL2-Rep2


title: KO-KAP1-E2-1h-PAF1-Rep2

value: PAF1(Abcam, ab137519)


title: WT-Veh-1h-ELL2-Rep2


title: N_22_bronchus_0d


title: WT-E2-1h-PAF1-Rep2


title: T_21_foreskin_1d

source_name: foreskin

value: foreskin

value: T


title: T_21_foreskin_0d


title: T_21_foreskin_3d


title: WT-E2-1h-BRD4-Rep2

value: BRD4(Santa Cruz, sc-518021)


title: WT-Veh-1h-BRD4-Rep2


title: KO-KAP1-E2-1h-BRD4-Rep2


title: KO-KAP1-E2-1h-CDK9-Rep2

value: CDK9(Santa Cruz, sc-13130)


title: S_20_liver_7d

value: liver

value: S


title: S_20_liver_3d


title: WT-E2-1h-CDK9-Rep2

value: Human breast cancers


title: S_20_liver_0d


title: S_20_liver_1d


title: WT-Veh-1h-CDK9-Rep2


title: R_19_lung_7d

source_name: lung

value: lung

value: R


title: R_19_lung_3d


title: WT-E2-1h-H3K4me1-Rep2

value: H3K4me1(Abcam, ab8895)


title: R_19_lung_1d


title: WT-Veh-1h-H3K4me1-Rep2


title: WT-Veh-1h-PAF1-Rep2


title: KO-KAP1-E2-1h-H3K27Ac-Rep2

value: H3K27Ac(Active motif, 39085)


title: Q_18_colon_3d

source_name: colon

value: colon

value: Q


title: WT-E2-1h-H3K27Ac-Rep2


title: T_21_foreskin_7d


title: R_19_lung_0d


title: WT-Veh-1h-H3K27Ac-Rep2


title: Q_18_colon_0d


title: WT-E2-1h-PolIIS2P-Rep2

value: S2P(Active motif, 91116)


title: Q_18_colon_7d


title: Q_18_colon_1d


title: KO-KAP1-E2-1h-PolIIS2P-Rep2


title: P_17_small intestine_3d

description: EDTA_DSP_AO_P_17_small intestine_3d

source_name: small intestine

value: small intestine

value: P


title: WT-E2-1h-PolII-Rep2

value: PolII(Abcam, ab26721)


title: KO-KAP1-E2-1h-PolII-Rep2


title: P_17_small intestine_7d

description: EDTA_DSP_AO_P_17_small intestine_7d


title: O_16_artery_7d

source_name: artery

value: artery

value: O


title: P_17_small intestine_0d

description: EDTA_DSP_AO_P_17_small intestine_0d


title: KO-KAP1-E2-1h-H3K4me1-Rep2


title: P_17_small intestine_1d

description: EDTA_DSP_AO_P_17_small intestine_1d


title: O_16_artery_3d


title: KO-KAP1-E2-1h-rep2  [ATAC-Seq]

data_processing:
cutadapt: -u 15 -U 15 -a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT -b -B
Quality control: FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and TRIMMOMATIC (http://www.usadellab.org/cms/?page=trimmomatic) were used to inspect the quality of the sequencing reads, and to trim the sequencing adaptors, if necessary.
bowtie2:  -q --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700
makeTagDirectory: -format sam -keepAll -tbp 1 -checkGC -sspe -fragLength given
samtools; bamCoverage
Assembly: hg38
Supplementary files format and content: bigWig
Supplementary files format and content: BedGraph

extract_protocol:
ATAC-seq standard Protocol
PCR Ampfication


title: WT-Veh-1h-rep2  [ATAC-Seq]


title: O_16_artery_1d


title: KO-KAP1-E2-1h-rep2

data_processing:
cutadapt: -u 10 -U 10 -a AGATCGGAAGAG -A GATCGTCGGACT
Quality control: FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and TRIMMOMATIC (http://www.usadellab.org/cms/?page=trimmomatic) were used to inspect the quality of the sequencing reads, and to trim the sequencing adaptors, if necessary.
bowtie2: -q -5 10 --very-sensitive-local --no-unal -N 1 -p 24
makeTagDirectory: -format sam -keepAll -tbp 1 -checkGC -sspe -fragLength given
makeUCSCfile
Assembly: hg38
Supplementary files format and content: BedGraph
Library strategy: PRO-seq

molecule: nuclear RNA

growth_protocol: MCF7 cells were maintained at 37°C and 5% CO2 in Dulbecco's modified Eagle's medium (DMEM, GIBCO/Invitrogen), supplemented with 10% fetal bovine serum (FBS, GIBCO/Invitrogen). For hormone treatments, cells were incubated at 37°C and 5% CO2 for at least 3 days in phenol red-free DMEM (GIBCO/Invitrogen) supplemented with 5% charcoal dextran-stripped FBS (GIBCO/Invitrogen).

extract_protocol:
The resultant nuclei were washed two more times with 10ml lysis buffer and finally resuspended in 100 μl of freezing buffer (50mM Tris-HCl pH8.3, 40% glycerol, 5mM MgCl2, 0.1mM EDTA). For the run-on assay, resuspended nuclei were mixed with an equal volume of reaction buffer (10mM Tris-HCl pH 8.0, 5mM MgCl2, 1mM DTT, 300mM KCl, 20 units of SUPERase-In, 1% sarkosyl, 250 μM A/GTP, 50 µM biotin-11-C/UTP (Perkin-Elmer) and incubated for 5 min at 30°C. The resultant nuclear-run-on RNA (NRO-RNA) was then extracted with TRIzol® LS reagent (Life Technologies, Cat# 10296-028) following manufacturer’s instructions. NRO-RNA was fragmented to ∼200-500nt by alkaline base hydrolysis on ice for 30 min and and neutralized by adding 1× volume of 1 M Tris-HCl pH 6.8, Excessive salt and residual NTPs were removed by using P-30 column (Bio-Rad, Cat# 732-6250), followed by treatment with DNase I (Promega Cat# M6101) and antarctic phosphatase (NEB Cat# M0289L). Fragmented nascent RNA was bound to 10 µl of MyOne Streptavidin C1 dynabeads (Invitrogen, Cat# 65001) following the manufacturer’s instructions. The beads were washed twice in high salt (2 M NaCl, 50 mM Tris-HCl pH 7.5, 0.5% Triton X-100, 0.5 mM EDTA), once in medium salt (1M NaCl, 5 mM Tris-HCl pH 7.5, 0.1% Triton X-100, 0.5 mM EDTA), and once in low salt (5 mM Tris-HCl pH 7.5, 0.1% Triton X-100).
NEBNext® Small RNA Library Prep kit (NEB, Cat# E7330)


title: N_15_lung_7d

value: N


title: WT-Veh-1h-PolIIS2P-Rep2


title: WT-E2-1h-rep2


title: GBM_P4CC3_Droplet_Hi-C

city: La Jolla

first: Yang

last: Xie

address: Rm.2071, 9500 Gilman Dr

department: Department of Cellular and Molecular Medicine

institute: UC San Diego

description:
human patient sample with restricted access,  raw data will be deposited into dbGaP.
10XATAC_v2, single-cell Hi-C

library_source: genomic single cell

data_processing:
For read alignment and quantification for all libraries: All sequencing were performed with an Illumina NextSeq 2000 or NovaSeq 6000 sequencer. Fastq files are demultiplexed using cellranger-arc v2.0.0. Hi-C and RNA modalities were preprocessed using cellranger-atac v2.0.0 and cellranger v6.1.2, respectively, and barcodes were manually paired with custom script using the matching relationship provided in cellranger-arc. To select high-quality nuclei from DNA modality, we filtered barcodes based on the per cell contacts number, and then further selected nuclei by pairing pass-filtered nuclei from both Hi-C and RNA modality.
assembly: hg38
Supplementary files format and content:gzipped pairs file, txt file with valid cells entry

source_name: IDH-wildtype glioblastoma

growth_protocol: IDH-wildtype GBM tumor sample

extract_protocol: Following user guide of Chromium Next GEM Single Cell ATAC Reagent Kits v2

value: IDH-wildtype glioblastoma


title: M_14_ischaemic intestine_7d

description: EDTA_DSP_AO_M_14_ischaemic intestine_7d

source_name: ischaemic intestine

value: ischaemic intestine

value: M


title: BMMC_after_Paired_Hi-C_DNA

description:
human patient sample with restricted access,  raw data will be deposited into dbGaP.
10XMultiome, single-cell Hi-C
The library we generated is using the 10X Multiome kit, however RNA modalities were not generated or utilized in our studies so the data were not uploaded.

data_processing:
For read alignment and quantification for all libraries: All sequencing were performed with an Illumina NextSeq 2000 or NovaSeq 6000 sequencer. Fastq files are demultiplexed using cellranger-arc v2.0.0. Hi-C and RNA modalities were preprocessed using cellranger-atac v2.0.0 and cellranger v6.1.2, respectively, and barcodes were manually paired with custom script using the matching relationship provided in cellranger-arc. To select high-quality nuclei from DNA modality, we filtered barcodes based on the per cell contacts number, and then further selected nuclei by pairing pass-filtered nuclei from both Hi-C and RNA modality.
assembly: hg38
Supplementary files format and content:gzipped pairs file, txt file with valid cells entry
Library strategy: 10X Multiome

source_name: bone marrow mononuclear cells

growth_protocol: the bone marrow mononuclear cells (BMMC) from a myelodysplastic syndrome (MDS) patient manifesting secondary acute myeloid leukemia (AML), after treatment with azacitidine and ventoclax.

extract_protocol: Following user guide of Chromium Next GEM Single Cell Multiome ATAC + Gene Expression.

value: bone marrow mononuclear cells


title: N_15_lung_1d

value: lung


title: N_15_lung_3d


title: WT-Veh-1h-PolII-Rep2

value: Human breast cancers


title: BMMC_before_Paired_Hi-C_DNA

growth_protocol: the bone marrow mononuclear cells (BMMC) from a myelodysplastic syndrome (MDS) patient manifesting secondary acute myeloid leukemia (AML), before treatment with azacitidine and ventoclax.


title: N_15_lung_0d


title: WT-Veh-1h-rep2


title: L_13_carcinoma_7d

source_name: carcinoma

value: carcinoma

value: L


title: M_14_ischaemic intestine_0d

description: EDTA_DSP_AO_M_14_ischaemic intestine_0d


title: L_13_carcinoma_3d


title: Trip_K562_H2AZ_mildCHIP

city: Research Triangle Park

first: Jackson

middle: Andrew

last: Hoffman

state: North Carolina

address: 111 TW Alexander Dr, Building 101 Room C432

department: DIR

institute: NIEHS

data_processing:
ChIP-seq analysis. Reads were trimmed using Cutadapt and aligned to both hg19 and dm6 genomes using bowtie2. Aligned reads were deduplicated with picardtools. Scale factors were calculated for each sample by dividing the minimum number of dm6 reads for a given antibody by number of dm6 reads for each sample using the same antibody. Scaled and normalized coverage files were generated using deeptools with calculated scale factors and rpkm normalization.
Reads were trimmed using Cutadapt and aligned to both hg19 and mm10 genomes using bowtie2. Aligned reads were deduplicated with picardtools. Deduplicated read counts were used to calculate the human:mouse ratio, which was then used to calculate scaling factors for samples performed side by side with the same antibody. The scale factor was calculated by dividing the human:mouse read ratio for each sample using a given antibody by the maximum human:mouse read ratio from samples using the same antibody. Scaled and normalized coverage files were generated using deeptools with calculated scale factors and rpkm normalization.
Assembly: hg19
Supplementary files format and content: bigwig coverage files

growth_protocol: Human T47D A1-2 (Archer et al., 1994) and MCF-7 cell were grown in MEM (Gibco 10370) supplemented with 10% fetal bovine serum (Gibco 26140-079), GlutaMAX (Gibco 3505), HEPES (Sigma H0887), and Penicillin/Streptomycin (Sigma P0781).  HeLa, SW-13, U2OS, primary human fibroblast and mouse C127 cells were grown DMEM (Gibco 11965-092) supplemented with 10% fetal bovine serum (Gibco 26140-079), GlutaMAX (Gibco 3505), HEPES (Sigma H0887), and Penicillin/Streptomycin (Sigma P0781).  K562 cells were grown in suspension in RPMI Medium 1640 (Gibco 11875-093) supplemented with 10% fetal bovine serum (Gibco 26140-079), GlutaMAX (Gibco 3505), HEPES (Sigma H0887), and Penicillin/Streptomycin (Sigma P0781).  All cells were cultured in a humidified incubator at 37°C with 5% CO2 in the indicated growth medium with media changed every 2-3 days.  Cells were seeded in new tissue culture treated dishes when 80% confluency reached.

extract_protocol:
Cells were fixed in PBS with 1% methanol-free formaldehyde (ThermoFisher Scientific 28906) at 37C for 10 min and quenched with glycine (0.125M) for 5 min at room temperature.  After glycine quench, cells were washed three times and scraped into ice-cold PBS and pelleted by centrifugations at 500g for 5 min.  Compact cell pellets were resuspended in MNase swelling buffer (25 mM HEPES pH 7.9, 1.5 mM MgCl2, 10 mM KCl, 0.1% NP-40, 0.5 mM PMSF, and 1x cOmplete EDTA-free protease inhibitors (PIC)) (Roche), incubated on ice for 10 min then subjected to Dounce homogenization using 20-strokes with “tight” pestle (Duran Wheaton Kimble, 357542).  Nuclei were sedimented through digestion buffer (15mM Hepes pH 7.9, 60mM KCl, 15mM NaCl, 0.32M Sucrose, 0.5 mM PMSF, and PIC) by centrifugation for 930g for 7 min at 4C. Nuclei pellets were fully resuspended in digestion buffer containing 3.3 mM CaCl2 and digested with MNase (0.75U/1x10ˆ6 cells, Worthington, cat#) at 37C for 15min. MNase fragmentation was stopped by addition of 10 mM EGTA and incubation for 5 min on ice.  Digested nuclei were centrifuged at 930g for 7 min at 4C and compact nuclei pellets resuspended in 20 volumes (v/v) ChIP Shearing buffer (50 mM HEPES pH7.9, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.1% SDS containing spermidine, PIC and PMSF) and incubated on ice for 10 min.  Samples were subjected to sonication using PIXUL Multi-Sample Sonicator (Active Motif) at 12C using the following parameters: Pulse [N]: 50; PRF [kHz]: 1.00; Process Time: 10 min; Burst Rate [Hz]: 20.00.  After sonication, fragmented chromatin was recovered in supernatant after centrifugation at 18,000g for 10 min with extent of fragmentation determined by agarose gel electrophorese prior to immunoprecipitation.  The concentration of fragmentated chromatin determined by Bradford assay.  Fragmentated chromatin was diluted in two-fold in 2xIP buffer (20 mM Tris-HCl pH 8.0, 300 mM NaCl, 2 mM EDTA, 20% Glycerol, 1% Triton X-100, 0.5 mM PMSF and PIC) and immunoprecipitation performed with the indicated antibodies at a ratio of 1 ug antibody per 200 ug chromatin.  Equal amounts of Spike-IN antibody and Drosophila chromatin (Active Motif 61686 and 53083) added to each immunoprecipitation for normalization.  Immune complexes were captured using protein G dynabeads (Invitrogen 10004D), washed once each with low salt buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), high salt buffer (same as low salt buffer, except 500 mM NaCl), and LiCl buffer (Tris-HCl pH 8.0, 250 mM LiCl, 2 mM EDTA, 1 % NP-40, 1% (wt/vol) sodium deoxycholate), and twice with TE.  Immunoprecipitated DNA recovered from beads by incubation in ChIP Elution Buffer (1% SDS, 0.1M Sodium Bicarbonate) for 30 min at room temperature.  Eluted DNA was treated with RNaseA (Roche 10109169001) and Proteinase K (Invitrogen #25530015) and purified using Qiagen PCR purification columns.  ChIP-seq in K562 cells with milder cross-linking and fragmentation performed using a SimpleChIP Plus Enzymatic Chromatin IP Kit with Magnetic Beads (Cell Signaling Technologies #9005S) according to manufacturer’s protocol.
Cells were treated, harvested, and subjected to CUT&TAG analysis using a modified published protocol [Kaya-Okur et al., 2019].  Trypsinized cells were washed once with PBS and incubated with NE nuclear extraction buffer (20 mM HEPES-KOH, pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% Glycerol, 0.5 mM Spermidine, 100 uM PMSF, and 1x EDTA-free protease inhibitors (Roche cOmplete) for 30 min on ice followed by Dounce homogenization using 20-strokes from Dounce Tissue Grinder (Wheaton 357542) tight pestle.  Following homogenization, samples were centrifuged for 3 min at 600g, nuclei pellet resuspended in NE buffer supplemented with 0.1 % formaldehyde and incubated at room temperature for 2 minutes followed by quench with 0.125 M glycine.  Following formaldehyde cross-link, nuclei were re-centrifuged, resuspended in fresh NE buffer and counted with trypan blue dye using Bio-Rad TC20 Automated Cell Counter.   After isolation, 150,000 total nuclei [135,000 nuclei from experimental sample with 15,000 mouse spike-in nuclei] were incubated with activated concanavalin A-coated (ConA) magnetic beads (EpiCypher) in 0.2 ml thin-walled tubes for 10 min at room temperature.  Nuclei-bound ConA beads were resuspended in antibody incubation buffer (20 mM HEPES, pH 7.5, 150 mM NaCl, 0.01% Digitonin, 2 mM EDTA, 0.5 mM Spermidine, 100 uM PMSF, and 1x EDTA-free protease inhibitor), 0.75 ug indicated primary antibody (see Table S2) added and samples incubated overnight at 4C with gently rotation.  Primary antibody removed from ConA bead solution by placing samples on magnetic stand until clear followed by supernatant removal.  Samples were incubated with 0.75 ug species specific secondary antibody for 30 min at room temperature with gentle rotation followed by two washes with Digitonin150 wash buffer (20 mM HEPES, pH 7.5, 150 mM NaCl, 0.01% Digitonin, 0.5 mM Spermidine, 100 uM PMSF, and 1x EDTA-free protease inhibitor) then incubation with pAG-Tn5 in Digitonin300-wash buffer (20 mM HEPES, pH 7.5, 300 mM NaCl, 0.01% Digitonin, 0.5 mM Spermidine, 100 uM PMSF, and 1x EDTA-free protease inhibitor) for 1h at room temperature.   After pAG-Tn5 incubation, bound ConA beads were washed twice with Digitonin300-wash buffer then resuspended in Tagmentation buffer (Digitonin300 wash buffer containing 10 mM MgCl2) and incubated for 1h at 37C.  Beads were then pelleted, resuspended in TAPS buffer (10 mM TAPS pH 8.5, 0.2 mM EDTA).  TAPS buffer removed and beads carefully resuspended in SDS Release buffer (10 mM TAPS pH 8.5, 0.1% SDS) and incubated for 1 h at 58 C.  Following incubation, SDS Quench buffer (0.67% Triton X-100) was added to each sample along with 2 μl of a universal i5 and a uniquely barcoded i7 primers (from 10 μM stocks).  Equal volume (25 ul) NEBNext High-Fidelity 2x PCR Master mix (M0541, New England Biolabs) was added to each sample and mixed by gentle pipetting.  Samples subjected to DNA amplification using a thermocycler and the CUT&TAG-specific PCR cycling parameters: 58C for 5 min; 72C for 5 min; 98C for 45 sec; with 19 cycles of 98C for 15 sec and 60C for 10 sec; final extension at 72 °C for 1 min; and hold at 4C.  DNA clean-up performed by adding 1.3x AMPure XP beads (A63880, Beckman Coulter) to each sample, allowing libraries to incubated with beads for 10 min at room temperature, followed by two washes with 80% ethanol, then elution in 15 μl of 10 mM Tris pH 8.0.  While on magnetic stand, supernatant was carefully taken and transferred to a fresh tube.  Library size distribution determined by Agilent TapeStation 4200 (Agilent Technologies) and libraries mixed to yield equal representation prior to paired-end (2 x 50 bp) Illumina sequencing by NIEHS The Epigenomics and DNA Sequencing Core Facility.
Two replicates were used for each treatment condition. Cells were collected and subjected to the ATAC-seq protocol described by Buenrostro et al (2013).  Isolated cells were treated in 10 mM PIPES, pH 6.8, 100 mM NaCl, 300 mM sucrose, 3 mM MgCl2, and 0.1% Triton X-100 and then treated with the Illumina Tagment DNA TDE1 Enzyme and Buffer Kits for 30 min followed by mixing every 10 min. Libraries were sequenced at the NIEHS Epigenomics Core Facility on a NovaSeq instrument
ChIP-seq libraries were generated using the xGen ssDNA & Low-Input DNA Library Prep Kit and xGen CDI Primers (IDT 10009817 and 10009815) according to manufacturer’s protocol and sequenced on the Illumina NextSeq platforms.

treatment_protocol: Cells were treated for the indicated time individually, or in combination, with 100 nM Dexamethasone (Sigma D4902) or vehicle (equal volume EtOH or DMSO), 0.5 uM Triptolide (Tocris 3253), 0.5 uM Flavopiridol (Tocris 3094), 0.5 uM A485 (Tocris 6387), 0.1 uM Trichostatin A (Sigma T8552), 10 ug/ml Doxycycline (Sigma D9891), or 1 uM 5-Ph-IAA (AID) ligand (Sigma SML3574).

value: lymphoblast

tag: spike-in control

value: Drosophila chromatin

value: H2AZ (Diagenode C15410201)

tag: treatment 1

value: 0.5uM Triptolide


title: Trip_ATAC_rep2

tag: cell type

value: breast cancer

value: ATAC-seq


title: Untr_ATAC_rep2

value: DMSO


title: WT-E2-1h-rep2  [ATAC-Seq]


title: Untr_ATAC_rep1


title: Trip_ATAC_rep1


title: O_16_artery_0d

value: artery

value: O


title: Untr_K562_H2AZ_mildCHIP


title: L_13_carcinoma_0d


title: Trip_K562_H3K4me3_mildCHIP

value: H3K4me3 (Diagenode C15410003)


title: M_14_ischaemic intestine_3d

description: EDTA_DSP_AO_M_14_ischaemic intestine_3d

value: ischaemic intestine


title: Untr_K562_H3K4me3_mildCHIP


title: Trip_K562_K27ac_mildCHIP

value: K27ac (Abcam ab4729)


title: K_12_carcinoma_3d

description:
sampling error; excluded from analysis in manuscript
EDTA_DSP_AO_K_12_carcinoma_3d

value: K


title: M_14_ischaemic intestine_1d

description: EDTA_DSP_AO_M_14_ischaemic intestine_1d

value: M


title: K_12_carcinoma_1d


title: K_12_carcinoma_0d


title: J_11_seminal vesicle_7d

description: EDTA_DSP_AO_J_11_seminal vesicle_7d

source_name: seminal vesicle

value: seminal vesicle

value: J


title: Untr_K562_K27ac_mildCHIP


title: Trip_A485_A12_K27ac_CnT

data_processing:
ChIP-seq analysis. Reads were trimmed using Cutadapt and aligned to both hg19 and dm6 genomes using bowtie2. Aligned reads were deduplicated with picardtools. Scale factors were calculated for each sample by dividing the minimum number of dm6 reads for a given antibody by number of dm6 reads for each sample using the same antibody. Scaled and normalized coverage files were generated using deeptools with calculated scale factors and rpkm normalization.
Reads were trimmed using Cutadapt and aligned to both hg19 and mm10 genomes using bowtie2. Aligned reads were deduplicated with picardtools. Deduplicated read counts were used to calculate the human:mouse ratio, which was then used to calculate scaling factors for samples performed side by side with the same antibody. The scale factor was calculated by dividing the human:mouse read ratio for each sample using a given antibody by the maximum human:mouse read ratio from samples using the same antibody. Scaled and normalized coverage files were generated using deeptools with calculated scale factors and rpkm normalization.
Assembly: hg19
Supplementary files format and content: bigwig coverage files
Library strategy: CUT&TAG

value: Mouse nuclei

tag: treatment 2


title: J_11_seminal vesicle_3d

description: EDTA_DSP_AO_J_11_seminal vesicle_3d


title: TSA_A12_K27ac_CnT

value: 0.1 uM TSA


title: J_11_seminal vesicle_1d

description: EDTA_DSP_AO_J_11_seminal vesicle_1d


title: J_11_seminal vesicle_0d

description: EDTA_DSP_AO_J_11_seminal vesicle_0d


title: Flav_A12_RNAP2_CHIP

value: Drosophila chromatin

value: RNAP2 (ActiveMotif 39097)

value: 0.5uM Flavopiridol


title: Trip_TSA_A12_K27ac_CnT

value: breast cancer

value: 0.5uM Triptolide


title: Flav_A12_H2AZ_CnT

value: H2AZ (Diagenode C15410201)


title: I_10_carcinoma_3d

value: carcinoma

value: I


title: Untr_A12_RNAP2_CHIP

value: DMSO


title: Trip_A12_RNAP2_CHIP


title: I_10_carcinoma_1d


title: A485_A12_K27ac_CnT


title: I_10_carcinoma_7d


title: K_12_carcinoma_7d


title: Trip_HELA_H2AZ_CnT

source_name: HELA

value: HELA

value: cervical carcinoma


title: Untr_HELA_H2AZ_CnT


title: I_10_carcinoma_0d


title: H_9_small intestine_7d

description: EDTA_DSP_AO_H_9_small intestine_7d

value: small intestine

value: H


title: Untr_MCF7_H2AZ_CnT


title: H_9_small intestine_3d

description: EDTA_DSP_AO_H_9_small intestine_3d


title: Trip_MCF7_H2AZ_CnT


title: H_9_small intestine_1d

description: EDTA_DSP_AO_H_9_small intestine_1d


title: Untr_HELA_H3K4me3_CnT

value: H3K4me3 (Diagenode C15410003)


title: Trip_HELA_H3K4me3_CnT


title: Untr_MCF7_H3K4me3_CnT


title: G_8_lung_7d

value: lung

value: G


title: G_8_lung_3d


title: Trip_MCF7_H3K4me3_CnT

value: Mouse nuclei


title: G_8_lung_0d


title: Untr_HELA_K27ac_CnT

value: K27ac (Abcam ab4729)


title: G_8_lung_1d


title: Trip_HELA_K27ac_CnT


title: Trip_MCF7_K27ac_CnT


title: F_7_carcinoma_7d

value: F


title: Untr_A12_H3K27me3_CnT

value: H3K27me3 (Diagenode C15410195)


title: F_7_carcinoma_1d


title: Trip_A12_H3K4me3_CnT

value: breast cancer


title: F_7_carcinoma_3d


title: Trip_A12_H3K27me3_CnT

value: 0.5uM Triptolide


title: F_7_carcinoma_0d


title: Untr_A12_H3K4me3_CnT


title: F_6_spleen_7d

source_name: spleen

value: spleen


title: F_6_spleen_3d


title: F_6_spleen_0d


title: H_9_small intestine_0d

description: EDTA_DSP_AO_H_9_small intestine_0d


title: F_6_spleen_1d


title: E_5_salivary gland_7d

description: EDTA_DSP_AO_E_5_salivary gland_7d

source_name: salivary gland

value: salivary gland

value: E


title: Trip_A12_H2AZ_CnT

value: H2AZ (Diagenode C15410201)


title: Untr_A12_H2AZ_CnT

value: DMSO


title: Trip_A12_H3K18ac_CnT

value: H3K18ac (Diagenode C15410139)


title: E_5_salivary gland_3d

description: EDTA_DSP_AO_E_5_salivary gland_3d


title: E_5_salivary gland_0d

description: EDTA_DSP_AO_E_5_salivary gland_0d


title: D_4_colon_7d

value: colon

value: D


title: Trip_A12_H3K14ac_CnT

value: H3K14ac (Abcam ab 52946)


title: E_5_salivary gland_1d

description: EDTA_DSP_AO_E_5_salivary gland_1d


title: Untr_A12_H3K18ac_CnT


title: Untr_MCF7_K27ac_CnT


title: Untr_A12_H3K14ac_CnT


title: D_4_colon_3d


title: Trip_A12_H3K9ac_CnT

value: H3K9ac (Diagenode C15410004)


title: C_3_colon_7d

value: C


title: Untr_A12_K27ac_CnT_rep1

value: Mouse nuclei


title: D_4_colon_0d


title: B_2_lung_7d

value: lung

value: B


title: Untr_A12_K27ac_CHIP_rep4

value: Drosophila chromatin

value: K27ac (Abcam ab4729)


title: D_4_colon_1d


title: Untr_A12_H3K9ac_CnT

value: breast cancer


title: Untr_A12_K27ac_CnT_rep2


title: C_3_colon_3d


title: C_3_colon_1d


title: Trip_A12_K27ac_CnT_rep1

value: 0.5uM Triptolide


title: Trip_A12_K27ac_CHIP_rep4


title: Trip_A12_K27ac_CnT_rep2


title: B_2_lung_1d


title: C_3_colon_0d


title: B_2_lung_3d


title: B_2_lung_0d


title: Trip_A12_K27ac_CHIP_rep3


title: A_1_stomach_7d

source_name: stomach

value: stomach

value: A


title: Untr_A12_K27ac_CHIP_rep2


title: Trip_A12_K27ac_CHIP_rep2


title: DexTrip_A12_K27ac_CHIP_rep1

value: 100nM Dexamethasone


title: A_1_stomach_1d


title: A_1_stomach_3d


title: VehTrip_A12_K27ac_CHIP_rep1

value: EtOH Vehicle


title: Dex_A12_K27ac_CHIP_rep1

value: DMSO


title: NTC

description:
Only included as raw data, not included in matrix
EDTA_DSP_AO_NTC


title: Untr_A12_K27ac_CHIP_rep3


title: Veh_A12_K27ac_CHIP_rep1