title: Del14-4N24 DnybWX PkasOP::nybF::zwf, 70 h , replicate 3 [NYB-10_t3_C]

city: Bielefeld

first: Christian

last: Ruckert-Reed

address: Sequenz 1

department: Medical School OWL

country: Germany

institute: Bielefeld University

data_processing:
Basecalls were performed using RTA v 1.18.66.3
Sequenced reads were mapped to the C113229.1 whole genome using bowtie2 v2.3.2 with parameters -X 600
Raw read counts per gene were calculated using featureCounts v2.0.0 with parameters -O -M -t gene -g locus_tag -s 1
Read cound normalization and data analysis were performed using DESeq2
Assembly: CP113229.1
Supplementary files format and content: tab-delimited matrix table with raw read counts for every gene and every sample
Supplementary files format and content: tab-delimited matrix table with normalized read counts derived via DESeq2 for each gene

organism: Streptomyces albidoflavus

source_name: liquid culture

growth_protocol: Main cultures to overproduce nybomycin were grown in chemically defined minimal medium containing per liter: 10 g of D-mannitol, 15 g of (NH4)2SO4, 20.9 g of MOPS, 0.5 g of K2HPO4, 1 g of NaCl, 0.55 g of  CaCl2, 0.2 g of MgSO4·7H2O, 0.02 g of FeSO4·7H2O, 2 mg of FeCl3·6H2O, 2 mg of MnSO4·H2O, 0.5 mg of ZnSO4·H2O, 0.5 mg of CuCl2·2H2O, 0.2 mg of Na2B4O7·10H2O, 0.1 mg of (NH4)6Mo7O24·4H2O, 1 mg of nicotinamide, 1 mg of riboflavin, 0.5 mg of thiamine hydrochloride, 0.5 mg of pyridoxine hydrochloride, 0.2 mg of biotin and 0.1 mg of p-aminobenzoic acid. Liquid cultures were incubated in 500 mL baffled shake flasks (10% filing volume) on an orbital shaker at 230 rpm, 75% relative humidity, and 28 °C (5 cm shaking diameter). The medium was supplemented with 30 g 5mm soda-lime glass beads. Samples were taken after 12, 46, and 70 hours of cultivation.

extract_protocol:
Total RNA was isolated using the Quick-RNA Miniprep Plus kit (Zymo Research, Freiburg, Germany). After DNase treatment, the obtained RNA was purified (RNA Clean & Concentrator-5 kit, Zymo Research) and quantified (DropSense 16, Trinean NV, Gent, Belgium).
To construct whole transcriptome cDNA libraries, 2.5 μg of total RNA each was depleted of rRNA (Ribo-Zero rRNA Removal Kit (Bacteria), Illumina, San Diego, CA, USA). Successful rRNA removal was validated (Agilent RNA Pico 6000 kit, Agilent 2100 Bioanalyzer, Agilent Technologies). The obtained mRNA was converted into a cDNA library according to the TruSeq Stranded mRNA Sample Preparation guide (Illumina). Appropriate cDNA quality and quantity was validated (Agilent High Sensitivity DNA kit, Agilent 2100 Bioanalyzer, Agilent Technologies). Sequencing was performed on an Illumina NextSeq 500 instrument using 75 bases read length (Illumina).

value: liquid culture

value: Del14-4N24 DnybWX PkasOP::nybF::zwf

tag: time


title: mouse_14

status: Public on Nov 07 2023

type: SRA

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

library_source: transcriptomic

data_processing:
RNA preparation, library construction and sequencing on DNBSEQ platform was performed at Beijing Genomics Institute.
Reads were aligned to the mouse genome (GRCm39.104) using STAR  (-runThreadN 2 --genomeDir --readFilesIn  --readFilesCommand gunzip -c --outFileNamePrefix  --outSAMtype BAM SortedByCoordinate --outSAMunmapped None --outSAMattrIHstart 0 --outFilterType BySJout --sjdbGTFfile /Mus_musculus.GRCm39.104.gtf --quantMode TranscriptomeSAM
Reads were quantified using Htseq
Genome_build: Mus_musculus.GRCm39.104
Supplementary_files_format_and_content: Raw counts using HTSeq

molecule: total RNA

organism: Mus musculus

source_name: proximal small intestine scraping

extract_protocol:
21 days old mice were stratified by body weight and divided into the two dietary groups. The galactose group received a pelleted diet containing 16 en% in galactose + 16 en% in glucose, the glucose group was fed with a pelleted diet containing 32 en% in glucose. The two diets were otherwise identical. The mice were fed for 3 weeks with the intervention diet and sacrificed on day PN42. The RNA used for the analysis was obtained from the scraping of the proximal part of the small intestine. Collected tissue was snap frozen in liquid nitrogen and stored at -80°C until further analysis. Total RNA was isolated with RNeasy columns (Qiagen, Venlo, TheNetherlands). RNA integrity was checked on an Agilent 2200 Tapestation according to the manufacturer's instructions (Agilent Technologies Inc., Santa Clara, CA, USA).
RNA preparation, library construction and sequencing on DNBSEQ platform was performed at Beijing Genomics Institute.

tag: Sex

value: female

tag: strain

tag: diet

tag: age

value: 42 days

tag: tissue

value: proximal small intestine scraping


title: 22Rv1_GR_siARV7_Dex_rep2

city: Kuopio

first: Ville

last: Paakinaho

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

library_source: genomic

data_processing:
Basecalls performed using CASAVA, and FASTX-toolkit was used to trim low quality reads.
The reads were aligned to human reference genome version hg38 by using Bowtie2 software version 2.3.4.1. with end-to-end sensitive mode allowing no mismatches.
Peaks were called using HOMER program version 4.10. using findPeaks with style factor, FDR<0.01, >25 tags, >4-fold over control sample and local background. Corresponding EtOH sample was used as the control sample.
Assembly: hg38
Supplementary files format and content: bedGraph (HOMER makeUCSCfile command) from alignment file.

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: 22Rv1 cells were grown in RPMI-1640 medium supplemented with 10% fetal bovine serum, 1 U/µl penicillin, 1 µg/ml streptomycin and 2 mM L-glutamine. All cells were kept at 37 °C in a humidified 95% air/ 5% CO2 incubator.

extract_protocol:
For ChIP-seq, after 1% formaldehyde crosslinking, cells were harvested, chromatin was sonicated to 100-300 bp fragments, and protein-DNA complexes were isolated with specified antibody.
ChIP-seq libraries were prepared with NEBNext Ultra II DNA Library Prep Kit according to instructions.

treatment_protocol: 22Rv1 cells were grown in the presence or absence of 10 µM enzalutamide (ENZ) for at least 21 days (ENZ3w) before the start of hormone treatments. For siRNA treatments, the 22Rv1 cells were transfected with 80 nM siRNA using Lipofectamine RNAiMAX reagent 96 h before hormone treatments. 22Rv1 cells were treated with vehicle (EtOH) or 100 nM of Dexamethasone (Dex) for 1 h before the start of ChIPs.

tag: cell type

value: CWR22 xenograft derived human prostate carcinoma epithelial cell line

tag: cell line

tag: enz treatment

tag: sirna treatment

value: Custom AR-V7 siRNA (Dharmacon)

tag: hormone treatment

value: dexamethasone

tag: hormone concentration

tag: chip antibody

value: GR (Cell Signaling, 12041)


title: 22Rv1_RNA_siNON_EtOH_rep3

data_processing:
Basecalls performed using CASAVA
Alignment of RNA-seq data to human reference genome version hg38 was done with STAR. Differential expression of genes was analyzed using DESeq2 using HOMER.
Assembly: hg38
Supplementary files format and content: bedGraph (HOMER makeUCSCfile command) from alignment file.

molecule: polyA RNA

extract_protocol:
The isolation of RNA was conducted using NEB Monarch Total RNA Miniprep Kit following manufacturer’s protocol.
NEBNext Poly(A) mRNA Magnetic Isolation Module kit and NEBNext Ultra II Directional RNA Library Prep kit.

treatment_protocol: 22Rv1 cells were grown in the presence or absence of 10 µM enzalutamide (ENZ) for at least 21 days (ENZ3w) before the start of hormone treatments. For siRNA treatments, the 22Rv1 cells were transfected with 80 nM siRNA using Lipofectamine RNAiMAX reagent 96 h before hormone treatments. 22Rv1 cells were treated with vehicle (EtOH) or 100 nM of Dexamethasone (Dex) for 18 h before the start of RNA extraction.

value: Non-targeting control siRNA (Dharmacon, D-001810-10)

value: EtOH vehicle


title: Del14-4N24 DnybWX PkasOP::nybF::zwf, 70 h , replicate 1 [NYB-10_t3_A]

tag: genotype


title: Del14-4N24 DnybWX PkasOP::nybF::zwf, 70 h , replicate 2 [NYB-10_t3_B]


title: 22Rv1_GR_siARV7_Dex_rep1


title: 22Rv1_GR_siARV7_EtOH_rep2


title: 22Rv1_GR_siARV7_EtOH_rep1


title: Del14-4N24 DnybWX PkasOP::nybF::zwf, 12 h, replicate 2 [NYB-10_t1_B]


title: mouse_7


title: 22Rv1_GR_ENZ3w-siNON_Dex_rep2

value: 3 weeks


title: 22Rv1_GR_ENZ3w-siNON_Dex_rep1


title: 22Rv1_GR_siNON_Dex_rep2


title: 22Rv1_GR_ENZ3w-siNON_EtOH_rep2


title: mouse_4


title: 22Rv1_GR_ENZ3w-siNON_EtOH_rep1


title: 22Rv1_GR_siNON_Dex_rep1


title: 22Rv1_GR_siNON_EtOH_rep2


title: 22Rv1_GR_siNON_EtOH_rep1


title: Del14-4N24 DnybWX PkasOP::nybF::zwf, 12 h, replicate 3 [NYB-10_t1_C]


title: PLC-R

type: RNA

city: Chengdu City

first: Dingzhong

last: Peng

state: Sichuan Province

address: No. 37, Guoxue Alley

country: China

institute: West China Hospital of Sichuan University

description: circular RNA

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA

scan_protocol: 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing: Quantile normalization of raw data and subsequent data processing were performed using the R software limma package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 1 out of 6 samples have flags in “P” or “M” (“All Targets Value”) were retained for further analyses.

source_name: Exosomes from supernatant of sorafenib-resistant PLC/PRF/5 (PLC/PRF/5-R) cells

label_protocol: Circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Exosomes were isolated by standard centrifugation steps. Total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs

treatment_protocol: Dulbecco's Modified Eagle's Media supplemented with 10% FBS (v/v), and sorafenib (6 μM)

value: PLC/PRF/5-R (sorafenib-resistant) cells

tag: treatment

tag: group

value: R (sorafenib resistant)


title: Del14-4N24 DnybWX PkasOP::nybF::zwf, 12 h, replicate 1 [NYB-10_t1_A]


title: IR6h-2

city: beijing

first: zhu

last: shuolin

state: 北京市

address: Anzhen Street

institute: capital medical university

description: 10× Genomics

library_source: transcriptomic single cell

data_processing:
Illumina Casava219 software used for basecalling
UCSC mm10 reference genome, provided by 10x Genomics, was used for alignment and unique molecular identifier (UMI) quantification.
Gene level quantification was completed using Cellranger count.
Raw counts data was imported into R for downstream processing.
Assembly: mm10，Supplementary files format and content: Matrix table with raw read count values for every gene and every cell.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matix files

source_name: heart

extract_protocol:
Six hours after IR or sham operation, left ventricle tissues of three hearts were isolated, minced with fine scissors, and digested using the Neonatal Heart Dissociation Kit (Miltenyi Biotec; 130-098-373) in a 37°C water bath and the gentleMACS Dissociator according to manufacturer’s protocol. Digested cells were filtered through a 100 μm cell strainer and centrifuged at 300 × g for 10 min to obtain a single-cell suspension. Then, cell debris was removed by resuspending cells in 3100 µL of cold Dulbecco’s phosphate-buffered saline (DPBS) and 900 µL of Debris Removal Solution (Miltenyi Biotec, 130-109-398), mixing gently, followed by the addition of 4 mL of cold DPBS. The cells were centrifuged at 4°C and 3000 × g for 10 min, and the two upper phases were aspirated and washed with cold DPBS. The suspension was resuspended in DPBS containing 0.04% bovine serum albumin (BSA).
After determining the number of cells and viability, the single-cell suspension was loaded into a 10× Chromium Controller (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed, and sequencing libraries were constructed with reagents from a 10× Chromium Single Cell 30 v2 reagent kit (10X Genomics) according to the manufacturer’s protocol. The resulting libraries were sequenced on an Illumina NovaSeq6000 platform

value: heart


title: IR0h-4

description: 10× Genomics


title: IR6h-3

description: 10× Genomics


title: IR6h-4

description: 10× Genomics


title: Hep3B

description: circular RNA

source_name: Exosomes from supernatant of parental Hep3B cells

growth_protocol: Dulbecco's Modified Eagle's Media supplemented with 10% FBS (v/v)

value: Hep3B cells

value: control


title: Hep3B-R

description: circular RNA

source_name: Exosomes from supernatant of sorafenib-resistant Hep3B (Hep3B-R) cells

value: Hep3B-R (sorafenib-resistant) cells

value: Dulbecco's Modified Eagle's Media supplemented with 10% FBS (v/v), and sorafenib (6 μM)


title: IR0h-2

description: 10× Genomics


title: PLC

description: circular RNA

source_name: Exosomes from supernatant of parental PLC/PRF/5 cells

value: PLC/PRF/5 cells

value: Dulbecco's Modified Eagle's Media supplemented with 10% FBS (v/v)


title: Huh7-R

description: circular RNA

source_name: Exosomes from supernatant of sorafenib-resistant Huh7 (Huh7-R) cells

value: Huh7-R (sorafenib-resistant) cells


title: Huh7

description: circular RNA

source_name: Exosomes from supernatant of parental Huh7 cells

value: Huh7 cells


title: IR6h-1

description: 10× Genomics


title: MCUknockout_TA_muscle_rep3

city: Cincinnati

first: Jeffery

middle: D

last: Molkentin

state: Ohio

address: 240 Albert Sabin Way MLC 7020

department: Molecular Cardiovascular Biology

country: USA

institute: Cincinnati Children's Hospital Medical Center

description: Gene expression data from MCU knockout TA muscle

hyb_protocol: 3.0 ug of fragmented cDNA were hybridized to Clariom S Arrays, Mouse (Applied Biosystems). Probe arrays were incubated at 45°C for 17 hrs in the Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Probe arrays were washed and stained using the Fluidics Station 450 (Affymetrix), utilizing the fluidics protocol FS450-0007. The Stain and Antibody solutions are produced by Applied Biosystems and contained in the Genechip Hybridization Wash and Stain Kit.

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

data_processing: The .cel were created by Command Console (Affymetrix). The .cel files were analyzed by Expression Console (Affymetrix) to create .sst-rma-gene-full.chp files.

label: biotin

source_name: Tibialis anterior (TA) muscle

label_protocol: The GeneChip 3’ IVT Pico Reagent Kit is used to create biotin – labeled double -strand cDNA targets for hybridization to the Clariom S Arrays, Mouse.

extract_protocol:
cell isolation protocol: Tibialis anterior (TA) muscles were harvested from euthanized mice and flash-frozen
Trizol-based extraction of total RNA was performed according to the manufacturer's instructions.

value: MCU-/-/MCUb+/+; MCU knockout

value: Skeletal muscle


title: GC-JC-8721-1

city: London

first: Vlatka

last: Antolovic

address: Gower Street

department: MRC Laboratory for Molecular Cell Biology

country: United Kingdom

institute: University College London

description: 10x Genomics

data_processing:
Alignment, barcode counting, UMI counting, and filtering was performed by Cell Ranger v3.1.0 using default parameters.  For the two bioliogical replicates, totals of 2925 and 2404 single cell libraries passed the filter, with a median of around 15000 and 13000 transcripts per cell, and 2200 and 2300 genes per cell, for replicate one and two, respectively.
We excluded outliers with extremely high total UMI counts (1.5 interquartile ranges above the third quartile), cells with less than 3000 total UMI counts, and cells with less than 800 mapped genes. A total of 2671 and 2072 cells, from replicate one and two, respectively, were used for further analysis. Molecular counts of cells were normalised using size factors calculated with ‘scran’ package (Lun et al. Genome Biology, 2016). The processing steps were performed in R.
Supplementary files format and content: Tab-separated values files

organism: Dictyostelium discoideum

growth_protocol: Wild-type NC4 cells were cultured on lawns of Kelbsiella pneumoniae.

extract_protocol:
Cell suspensions were loaded to the 10X Chromium Single Cell A Chip (PN-1000009) using the Chromium 3’ Library and Gel Bead Kit v2 (PN-120267) as described by the manufacturers (10X Genomics, California).
14 cycles of cDNA amplification were performed on the purified GEM-RT product, and cDNA was examined for quality using the Agilent 2200 Tapestation with the High-sensitivity D5000 screentape and reagents (Agilent Technologies, Waldbronn, Germany), and the Qubit 2.0 Fluorometer and Qubit dsDNA HS Assay Kit (Life Technologies, California, USA). 35 µL of cDNA was used to prepare the 10x 3’RNA library and 12 and 13 cycles were used for sample index PCR of replicates 1 and 2 respectively. Final cleaned libraries were quantified using the Qubit 2.0 Fluorometer and Qubit dsDNA HS Assay Kit and average fragment size checked using the Agilent D1000 screentape and reagents. The final library was run on a NextSeq500 Mid-output 150-cycle kit with a 26[8]98 cycle configuration to generate 130 million read pairs in total.

treatment_protocol: For single cell RNAseq of a continuous developmental transition, we took a scrape of a feeding front of NC4 cells, from inside the bacterial zone through to the mound stage of development.  Cells were immediately inoculated into ice-cold KK2 buffer (20mM KPO4, pH 6.0), and disaggregated by gentle pipetting.  To remove the bacteria, cells were centrifuged at 720g for 2 minutes, then resuspended in ice-cold KK2.


title: GC-JC-8721-2

description: 10x Genomics

data_processing:
Alignment, barcode counting, UMI counting, and filtering was performed by Cell Ranger v3.1.0 using default parameters.  For the two biological replicates, totals of 2925 and 2404 single cell libraries passed the filter, with a median of around 15000 and 13000 transcripts per cell, and 2200 and 2300 genes per cell, for replicate one and two, respectively.
We excluded outliers with extremely high total UMI counts (1.5 interquartile ranges above the third quartile), cells with less than 3000 total UMI counts, and cells with less than 800 mapped genes. A total of 2671 and 2072 cells, from replicate one and two, respectively, were used for further analysis. Molecular counts of cells were normalised using size factors calculated with ‘scran’ package (Lun et al. Genome Biology, 2016). The processing steps were performed in R.
Supplementary files format and content: Tab-separated values files


title: MCUbknockout_TA_muscle_rep1

description: Gene expression data from MCUb knockout TA muscle

value: MCU+/+/MCUb-/-; MCUb knockout


title: IR0h-3

description: 10× Genomics


title: MCUbknockout_TA_muscle_rep3


title: Control_TA_muscle_rep2

description: Gene expression data from control TA muscle

value: MCU+/+/MCUb+/+; control


title: Control_TA_muscle_rep3


title: flox_unsti bio rep2

city: Shanghai

first: Yiheng

last: Yang

address: 1239 SIPING ROAD

institute: Tongji University

data_processing:
1. Quality control and mapping The transcriptome sequencing and analysis were conducted by OE biotech Co., Ltd. (Shanghai, China). Raw data (raw reads) were processed using Trimmomatic . The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2
2. Gene-level quantification, analysis of differentially expressed genes (DEGs), cluster analysis, GO and KEGG enrichment FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count . DEGs were identified using the DESeq(2012) R package functions estimateSizeFactors and nbinomTest. Pvalue < 0.05 and foldChange >2 or foldChange < 0.5 was set as the threshold for significantly differential expression. Hierarchical cluster analysis of DEGs was performed to explore genes expression pattern. GO enrichment and KEGG[7] pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution
3. Transcript-level quantification, analysis of differentially expressed transcript (DEGs), cluster analysis, GO and KEGG enrichment If it was transcript-level quantification, FPKMand read counts value of each transcript (protein_coding) was calculated using bowtie2 and eXpress . DEGs were identified using the DESeq (2012) functions estimateSizeFactors and nbinomTest. P value < 0.05 and foldChange >2 or foldChange < 0.5 was set as the threshold for significantly differential expression. Hierarchical cluster analysis of DEGs was performed to explore transcripts expression pattern. GO enrichment and KEGG pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution.
4. Gene structure extension and novel transcripts identification The reads were reassembled using StringTie . Then gene structure extension and novel transcripts identification were performed by comparing the reference genome and the known annotated genes using cuffcompare software.
5. Alternatively splicing analysis and SNP-INDEL calling The alternatively splicing analysis of differentially regulated transcripts isoforms or exons was performed using ASprofile[11] . SNP and INDEL were called using samtools and bcftools , and the details were shown on samtools webpage (http://samtools.sourceforge.net/mpileup.shtml). Then snpeff annotates and predicts the effects of variants on genes
Assembly: GRCm39
Supplementary files format and content: matrix tables with raw genes counts for every gene and every sample

source_name: bone marrow derived macrophages

extract_protocol:
A. Add 600 μL Lysis/Binding Buffer to the cell or tissue lysate. Then add 30 μL miRNA Homogenate Additive to homogenate, and mix well by vortexing or inverting the tube several times. Leave the mixture on ice for 10 min. B. Add a volume of Acid-Phenol: Chloroform that is equal to the lysate volume before addition of the miRNA Homogenate Additive. Centrifuge for 5 min at maximum speed (10,000 x g) to separate the aqueous and organic phases. Carefully remove the aqueous (upper) phase without disturbing the lower phase, and transfer it to a fresh tube. C. Add 1.25 volumes of room temperature 100% ethanol to the aqueous phase. D. Pipet the lysate/ethanol mixture (from the previous step) onto the Filter Cartridge (Note: Up to 700 μL can be applied to a Filter Cartridge at a time.). Centrifuge for 30 sec at 13,000 rpm to pass the mixture through the filter. Discard the flow-through. 5 E. Apply 350 μL miRNA Wash Solution 1 to the Filter Cartridge and centrifuge for 30 sec at 13,000 rpm. Discard the flow-through from the Collection Tube, and replace the Filter Cartridge into the same Collection Tube. F. The 10 μL DNase I and 70 μL Buffer RDD QIAGEN (#79254) were mixed. Then the mixture was added to the Filter Cartridge. Leave it at the room temperature for 15 min. G. Apply 350 μL miRNA Wash Solution 1 to the Filter Cartridge and centrifuge for 30 sec at 13,000 rpm. Discard the flow-through from the Collection Tube, and replace the Filter Cartridge into the same Collection Tube. H. Apply 500 μL Wash Solution 2/3 and centrifuge for 30 sec at 13,000 rpm. Draw it through the Filter Cartridge as in the previous step. Repeat with a second 500 μL aliquot of Wash Solution 2/3. I. Spin the assembly for 1 min to remove residual fluid from the filter. Transfer the Filter Cartridge into a fresh Collection Tube. Apply 100 μL of pre-heated (95°C) Elution Solution to the center of the filter. Leave it at the room temperature for 2 min. Spin for ~20–30 sec at maximum speed to recover the RNA. Collect the eluate (which contains the RNA) and store it at –70°C.
a. Add 50 μL RNA Purification Beads to each well with 50 μL total RNA (4μg) and mix thoroughly. b. Incubate at 65°C for 5 min, remove at 4°C, and then place at room temperaturefor 5 min. c. Place it on the magnetic stand at room temperature for 5 min. Remove and discard all of the supernatant from each well. d. Remove the magnetic stand, add 200 μL of Bead Washing Buffer in each well, and mix thoroughly. e. Place it on the magnetic stand at room temperature for 5 min. Remove and discard all of the supernatant from each well. f. Add 50 μL of Elution Buffer in each well and mix thoroughly. g. Incubate at 80°C for 2 min, remove at 25°C, and then place at room temperature. h. Add 50 μL of Beads Binding Buffer in each well and mix thoroughly. The mixture was placed at room temperature for 5 min. i. Place it on the magnetic stand at room temperature for 5 min. Remove and discard all of the supernatant from each well. j. Remove the magnetic stand, add 200 μL of Bead Washing Buffer in each well, and mix thoroughly. k. Place it on the magnetic stand at room temperature for 5 min. Remove and discard all of the supernatant from each well. l. Remove the magnetic stand, add 19.5 μL of Elute, Primer,Fragment Mix in each well and mix thoroughly. m. Incubate at 94°C for 8 min, remove at 4°C, and then centrifuge. 2.2 Synthesize First Strand cDNA a. Add 8 μL First Strand Synthesis Act D Mix and SuperScript II Reverse Transcriptase in each well and mix thoroughly. 8 b. The mixture was incubated in the following progress: 25°C for 10 min, 42°C for 15 min, 70°C for 15 min, hold at 4°C. 2.3 Synthesize Second Strand cDNA a. Add 5 μL End Repair Control (2 μL End Repair Control + 98 μL Resuspension Buffer) in each well. b. Add 20 μL Second Strand Marking Master Mix and mix thoroughly. b. The mixture was incubated at 16°C for 60 min. 2.3.1 Purification a. Add 90 μL mixed AMPure XP beads, mix thoroughly, and then place at room temperature for 15 min. b. Place it on the magnetic stand at room temperature for 5 min. c. Remove and discard all of the supernatant from each well. d. Place the plate on the magnetic stand. Add 200 μL of 80% ethyl alcohol and place at room temperature for 30 sec. Remove and discard all of the supernatant from each well. e. Repeat the above progress: place the plate on the magnetic stand; add 200 μL of 80% ethyl alcohol and place at room temperature for 30 sec; remove and discard all of the supernatant from each well. f. Place at room temperature for 15 min for air drying. Remove the plate from the magnetic stand. g. Add 17.5 μL Resuspension Buffer and mix thoroughly. h. Incubate the mixture at room temperature for 2 min. Place it on the magnetic stand at room temperature for 5 min. 9 i. Transfer 15 μL the supernatant from each well into the new PCR plate. 2.4 Adenylate 3’Ends a. Add 2.5 μL diluted A-Tailing Control (1 μL A-Tailing Control + 99 μL Resuspension Buffer) in each well. b. Add 12.5 μL A-Tailing Mix and mix thoroughly. c. The mixture was incubated in the following progress: 37°C for 30 min, 70°C for 5 min, hold at 4°C. 2.5 Ligate Adapters a. Add 2.5 μL diluted Ligation Control (1 μL Ligation Control + 99 μL Resuspension Buffer) in each well. b. Add 2.5 μL Ligation Mix. c. Add 2.5 μL RNA Adapter Index and mix thoroughly. d. The mixture was incubated at 30°C for 10 min. e. Add 5 μL Stop Ligation Buffer in each well and mix thoroughly. 2.5.1 Purification a. Add 42 μL mixed AMPure XP beads, mix thoroughly, and then place at room temperature for 15 min. b. Place it on the magnetic stand at room temperature for 15 min. c. Remove and discard 79.5 μL of the supernatant from each well. d. Place the plate on the magnetic stand. Add 200 μL of 80% ethyl alcohol and place at room temperature for 30 sec. Remove and discard all of the supernatant from each well. e. Repeat the above progress: place the plate on the magnetic stand; add 200 μL of 10 80% ethyl alcohol and place at room temperature for 30 sec; remove and discard all of the supernatant from each well. f. Place at room temperature for 15 min for air drying. Remove the plate from the magnetic stand. g. Add 52.5 μL Resuspension Buffer and mix thoroughly. h. Incubate the mixture at room temperature for 2 min. Place it on the magnetic stand at room temperature for 5 min. i. Transfer 50 μL the supernatant from each well into the new PCR plate. j. Add 50 μL mixed AMPure XP beads, mix thoroughly, and then place at room temperature for 15 min. k. Place it on the magnetic stand at room temperature for 15 min. l. Remove and discard 95 μL of the supernatant from each well. m. Place the plate on the magnetic stand. Add 200 μL of 80% ethyl alcohol and place at room temperature for 30 sec. Remove and discard all of the supernatant from each well. n. Repeat the above progress: place the plate on the magnetic stand; add 200 μL of 80% ethyl alcohol and place at room temperature for 30 sec; remove and discard all of the supernatant from each well. o. Place at room temperature for 15 min for air drying. Remove the plate from the magnetic stand. p. Add 22.5 μL Resuspension Buffer and mix thoroughly. q. Incubate the mixture at room temperature for 2 min. Place it on the magnetic stand at room temperature for 5 min. 11 r. Transfer 20 μL the supernatant from each well into the new PCR plate. 2.6 Enrich DNA Fragments a. Add 5 μL PCR Primer Cocktail. b. Add 25 μL PCR Master Mix and mix thoroughly. c. The mixture was incubated in the following progress: 1 cycle 98°C for 30 sec; 15 cycles 98°C for 10 sec, 60°C for 30 sec, 72°C for 30 sec; 1 cycle 72°C for 5 min; hold at 10°C. 2.7.1 Purification a. Add 50 μL mixed AMPure XP beads, mix thoroughly, and then place at room temperature for 15 min. b. Place it on the magnetic stand at room temperature for 15 min. c. Remove and discard 95 μL of the supernatant from each well. d. Place the plate on the magnetic stand. Add 200 μL of 80% ethyl alcohol and place at room temperature for 30 sec. Remove and discard all of the supernatant from each well. e. Repeat the above progress: place the plate on the magnetic stand; add 200 μL of 80% ethyl alcohol and place at room temperature for 30 sec; remove and discard all of the supernatant from each well. f. Place at room temperature for 15 min for air drying. Remove the plate from the magnetic stand. g. Add 32.5 μL Resuspension Buffer and mix thoroughly. h. Incubate the mixture at room temperature for 2 min. Place it on the magnetic stand at room temperature for 5 min. 12 i. Transfer 30 μL the supernatant from each well into the new PCR plate. 2.8 Validate library a. Load 1 μL sample on an Agilent 2100 Bioanalyzer. b. Check the size and purity of the library.

value: bone marrow derived macrophages


title: flox_unsti bio rep3


title: flox_Hyphae bio rep3


title: flox_unsti bio rep1


title: Control_TA_muscle_rep1


title: MCUknockout_TA_muscle_rep2


title: flox_Hyphae bio rep2


title: G10v1_m3-1_S7

city: Cambridge

first: Won

last: Jung

state: Massachusetts

address: 12 Oxford Street, NAITO 032D

department: CCB

institute: Harvard University

data_processing:
TopHat was used to align reads to the mm10 genome database and discover transcript splice sites. Cufflinks was used to assemble the reads to transcripts.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes tracking_ids, gene_ids and FPKM values for each sample

extract_protocol:
RNA was extracted and isolated using RNAqueous Micro total RNA isolation kit (Thermo Fisher, AM1931) following manufacturer’s instructions
RNA sequencing libraries were constructed using the Kapa mRNA HyperPrep Kits

treatment_protocol: Mice were maintained on a 12 hour:12 hour light/dark cycle (2pm-2am dark period) with at a temperature of 22 ± 1°C, a humidity of 30–70%, with ad libitum access to food and water

value: 56-62 days old

tag: mouse id


title: MCUknockout_TA_muscle_rep1


title: MCUbknockout_TA_muscle_rep2


title: H10v1_m3-2_S8


title: F10v1_m2-3_S6


title: IR0h-1

description: 10× Genomics


title: flox_Hyphae bio rep1


title: cre_unsti bio rep3


title: D10v1_m2-1_S4


title: mouse_45

value: female

value: 42 days

value: proximal small intestine scraping


title: E10v1_m2-2_S5


title: cre_unsti bio rep2


title: B10v1_m1-2_S2


title: C10v1_m1-3_S3


title: A10v1_m1-1_S1


title: cre_Hyphae bio rep2


title: cre_Hyphae bio rep3


title: MZ_15 (sgPrkcz )

city: New York

first: Jorge

last: Moscat

state: NY

address: 1188 York Avenue

department: Pathology and Laboratory Medicine

institute: WEILL CORNELL MEDICINE

description:
MZ_15
sgPrkcz

data_processing:
Read data was processed with the BlueBee Genomics Platform (BlueBee, San Mateo, CA).
Reads were aligned using Lexogen Quantseq 2.3.1 FWD UMI pipeline, and differential transcript expression was determined using Lexogen QuantSeq DE 1.3.1 pipeline. Both pipelines are from BluBee Genomics Platform.
Counts were normalized by total number of reads per each samples and multiplied by 10E6.
Assembly: Mus musculus - mouse (GRCm38)
Supplementary files format and content: Counts matrix with gene expression value for all samples.

source_name: MTO

growth_protocol: MTOs were cultured in advanced DMEM/F12 medium supplemented with 10 mM HEPES, Glutamax, B-27, and 50 ng/ml recombinant human EGF.

extract_protocol:
RNA was harvested using Trizol reagent and purified using Quick-RNA MiniPrep kit (Zymo Research).
Libraries were prepared from 200 ng of total RNA using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina from Lexogen, and optional UMIs (Vienna, Austria). Barcoded libraries were pooled, and single end sequenced (1X75) on the Illumina NextSeq 500 using the High output V2.5 kit (Illumina Inc., San Diego CA).

treatment_protocol: No treatment

value: MTO

value: sgPrkcz


title: cre_unsti bio rep1


title: MZ_14 (sgPrkcz )

description:
MZ_14
sgPrkcz


title: MZ_13 (sgPrkcz )

description:
MZ_13
sgPrkcz


title: ML_12 (sgPrkci)

description:
ML_12
sgPrkci

value: sgPrkci


title: ML_10 (sgPrkci)

description:
ML_10
sgPrkci


title: ML_11 (sgPrkci)

description:
ML_11
sgPrkci


title: dipc-mouse-cerebellum-p056-f1hybrid

city: Stanford

first: Siavash

last: Moghadami

state: CA

address: 299 Campus Drive, Fairchild Science Building, Room D236

department: Neurobiology

institute: Stanford University

description:
mouse.contacts_female.pairs.gz.tar.gz
mouse.contacts_female.seg.gz.tar.gz
mouse.contacts_male.pairs.gz.tar.gz
mouse.contacts_male.seg.gz.tar.gz
mouse.contacts_unisex.info.tar.gz
mouse.contacts_unisex.pairs.gz.tar.gz
mouse.contacts_unisex.seg.gz.tar.gz
mouse.cpg_b1m.color2.tar.gz
mouse.x2a.txt.tar.gz
mouse.contacts_male_with_haplotypes.pairs.gz.tar.gz
mouse.contacts_female_with_haplotypes.pairs.gz.tar.gz
mouse.contacts_male_with_haplotypes.seg.gz.tar.gz
mouse.contacts_female_with_haplotypes.seg.gz.tar.gz
mouse.contacts_male_with_imputed_haplotypes.pairs.gz.tar.gz
mouse.contacts_female_with_imputed_haplotypes.pairs.gz.tar.gz
mouse.3d_model_male.1m.tar.gz
mouse.3d_model_male.200k.tar.gz
mouse.3d_model_male.50k.tar.gz
mouse.3d_model_male.20k.tar.gz
mouse.3d_model_male_clean.20k.tar.gz
mouse.3d_model_male_clean.20k.rmsd.info.tar.gz
mouse.3d_model_female.1m.tar.gz
mouse.3d_model_female.200k.tar.gz
mouse.3d_model_female.50k.tar.gz
mouse.3d_model_female.20k.tar.gz
mouse.3d_model_female_clean.20k.tar.gz
mouse.3d_model_female_clean.20k.rmsd.info.tar.gz
mouse.C_male.color.tar.gz
mouse.C_female.color.tar.gz

data_processing:
For 10x Multiome data, please see README_multiome.md. For Dip-C data, please see https://github.com/tanlongzhi/dip-c.
Assembly: hg19 and mm10
Supplementary files format and content: For 10x Multiome data, data are in ArchR (https://www.archrproject.com) and LIGER (https://github.com/welch-lab/liger) formats. For Dip-C data, data are in pairs (https://github.com/4dn-dcic/pairix), hic (https://www.aidenlab.org/juicebox), and Dip-C (https://github.com/tanlongzhi/dip-c) formats.

source_name: cerebellum

extract_protocol: Dip-C

value: cerebellum

value: pooled male and female


title: dipc-mouse-cerebellum-p064-p084-diverse

value: male


title: dipc-mouse-cerebellum-p056-purkinje


title: dipc-mouse-cerebellum-p000-f1hybrid


title: dipc-mouse-cerebellum-p028


title: dipc-mouse-cerebellum-p000


title: dipc-mouse-cerebellum-p021


title: Yap1_KD3

city: Clayton

first: Wei

last: Shi

state: Victoria

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute

country: Australia

institute: Monash University

data_processing:
The libraries were aligned to the GRCm38/mm10 genome using Rsubread_2.2.6; only uniquely mapped read-pairs were allowed. The mapped read-pairs in each library were assigned to the NCBI RefSeq gene annotation for mm10 (build 38.1) by using featureCounts.
Genes were excluded from downstream analysis if they failed to achieve a CPM (counts per million mapped reads) value of at least 0.5 in at least 4 libraries. Counts were quantile normalized, precision weighted with the “voom” function of the limma package and converted to log2 counts per kilobase per million(log2 FKPM).
A linear model was fitted to each gene, and empirical Bayes moderated t-statistics were used to assess differences in expression. Genes were called differentially expressed if they achieved a false discovery rate of 0.05 or less.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized log2-FPKM values for each library. The supplementary file, Supp_Raw_Counts.txt, includes raw read counts for genes in all the libraries.

source_name: antral gastric tumor; 18-week-old  gp130FF;Yap1 flox mice

extract_protocol:
Gastric tumors were dissected from  gp130FF and  and gp130;Yap1floxed mice. Cells expressing EpCAM were isolated using flow cytometry and RNA was extracted from samples  using the RN-easy Mini Plus kit (Qiagen). RNA quality was validated using the RNA Tapestation.
Libraries were generated following the manufacturer's protocol using the TruSeq RNA Library Preparation Kit (Illumina, San Diego, USA)

value: gp130FF;Yap1 flox/flox

value: antral gastric tumor

tag: time

value: 3 days after tamoxifen treatment


title: IEC_ZKO_rep0

description: Small intestinal tissue from intestinal epithelial cell-specific PKCzeta-KO mouse

data_processing:
FASTQ.gz files were concatenated into two files per sample and used as input for Taiji software (https://taiji-pipeline.github.io/documentation/)
Taiji software uses BWA to allign the data to mm10 genome.
Taiji uses samtools, bedGraphToBigWig to generate bigwig files, and MACS2 to call peaks.
Assembly: mm10
Supplementary files format and content: processed data file consist of a bigwig file per sample

source_name: Small intestinal epithelial cell

extract_protocol:
Small intestines were isolated using EDTA, frozen on dry ice, and pellet was kept at -80C.
The cell pellet was resuspended in 50 μl lysis buffer and then spun down 500 × g for 10 min at 4 °C. The nuclei pellet was resuspended into 50 μl transposition reaction mixture containing Tn5 transposase from Nextera DNA Library Prep Kit (Illumina) and incubated at 37 °C for 30 min. Then the transposase-associated DNA was purified using MinElute PCR purification kit (QIAGEN). To amplify the library, the DNA was first amplified for 5 cycles using indexing primer from Nextera kit and NEBNext High-Fidelity 2X PCR master mix. To reduce the PCR amplification bias, 5 μl of amplified DNA after the first 5 cycles was used to do qPCR of 20 cycles to decide the number of cycles for the second round of PCR.
The total amplified DNA was size selected to fragments less than 800 bp using SPRI beads. Quantification of the ATAC-seq library was done with QuBit. The size of the pooled library was examined by TapeStation. Barcoded ATAC-seq libraries were pooled and paired end sequenced (sX75) on the Illumina NextSeq 500 using the High output V2.5 kit (Illumina Inc., San Diego, CA).

value: Small intestine

value: 8 weeks old

value: Villincre-negative, PKCzetaa f/f


title: dipc-mouse-cerebellum-p017

tag: Sex


title: dipc-mouse-cerebellum-p021-f1hybrid


title: Yap1_KD4


title: dipc-mouse-cerebellum-p014


title: dipc-mouse-cerebellum-p014-f1hybrid


title: Yap1_KD1


title: cre_Hyphae bio rep1

value: bone marrow derived macrophages


title: Yap1_KD2


title: IEC_DKO_rep0

description: Small intestinal tissue from intestinal epithelial cell-specific PKCLambdaPKCzeta-DKO mouse

tag: strain

value: Villincre-positive, PKClambda f/f, PKCzeta f/f


title: dipc-mouse-cerebellum-p007

value: female


title: WT3

source_name: antral gastric tumor; 18-week-old  gp130FF mice

value: gp130FF; Yap1WT


title: WT4


title: WT2


title: multiome-mouse-cerebellum-p014

library_source: other

data_processing:
library strategy: scRNA-seq/scATAC-seq
For 10x Multiome data, please see README_multiome.md. For Dip-C data, please see https://github.com/tanlongzhi/dip-c.
Assembly: hg19 and mm10
Supplementary files format and content: For 10x Multiome data, data are in ArchR (https://www.archrproject.com) and LIGER (https://github.com/welch-lab/liger) formats. For Dip-C data, data are in pairs (https://github.com/4dn-dcic/pairix), hic (https://www.aidenlab.org/juicebox), and Dip-C (https://github.com/tanlongzhi/dip-c) formats.

molecule: other


title: dipc-mouse-cerebellum-p010


title: WT1


title: dipc-mouse-cerebellum-p056


title: dipc-mouse-cerebellum-p003


title: bulk-mouse-cerebellum_p057-arid1b-wildtype


title: bulk-mouse-cerebellum_p057-arid1b-heterozygote


title: dipc-mouse-cerebellum-p637


title: bulk-mouse-cerebellum_p070-chd8-heterozygote


title: bulk-mouse-cerebellum_p070-chd8-wildtype


title: dipc-mouse-cerebellum-p385


title: dipc-mouse-cerebellum-p365


title: WT_RNA-seq

first: Mo

last: Zhang

address: 800 Dongchuan Road

institute: Shanghai Jiaotong University

data_processing:
RNA-seq raw FASTQ files were aligned to GRCh37/hg19 using STAR (v2.7.3a) with the default parameters.
The bam files were feed to Cufflinks (v2.2.1) to generate expression levels of transcripts in FPKM (fragments per kilobase of exon per million fragments mapped).
Deeptools was used to convert the bam file to bedGraph file for visualizing in UCSC genome browser.
Assembly: hg19
Supplementary files format and content: bigWig

growth_protocol: Human HEC-1-B cells and derived cell lines were cultured in MEM, 200mM L-Glutamine, Earle’s Balanced Salts (Hyclone) supplemented with 1mM sodium pyruvate (Sigma), 1% penicillin-streptomycin (Gibco) and 10% fetal bovine serum (Gibco). Human HCT-116 RAD21-AID-mClover cells (Natsume et al., 2016) were cultured in RPMI Medium 1640 L-Glutamine (Gibco), 1% penicillin-streptomycin (Gibco 15140122) and 10% fetal bovine serum (Gibco). The cells were cultured at 37°C in the incubator supplied with 5% (v/v) of CO2.

extract_protocol:
About 1 million cells were used for each RNA-seq experiment. Cells were washed twice using PBS and lysed by 1 mL Trizol (Invitrogen 15596026) for 15 min at room temperature. 0.2 mL chloroform was added and incubated for 2-3 minutes at room temperature. The upper phase was transferred into a new tube after centrifuged at 12,000rpm for 15 min at 4°C, and mixed with 0.5 mL isopropanol. After incubation at room temperature for 10 minutes, the total RNA was precipitated by centrifuging at 12,000 rpm for 10 minutes at 4°C. The precipitated DNA was washed by 75% ethanol to remove salt. Air-dried RNA was dissolved by 100 nuclease-free H2O.
The RNA was purified using the RNeasy kit (QIAGEN 75142) to remove residual DNA. 1ug RNA was used for extract mRNA by NEBNext poly(A) mRNA Magnetic Isolation Module (NEB E7490S), and RNA-seq library was constructed using NEBNext®Ultra™II RNA Library Prep Kit. The library was sequenced on the Illumina HiSeq platform.

value: Human Uterine Adenocarcinoma Cells

value: wild type


title: dipc-mouse-cerebellum-p175


title: ZNF143KO_RNA-seq


title: AID-CTCFd_ZNF143,ChIP-nexus

data_processing:
*library strategy: ChIP-nexus
Raw reads were trimmed to remove first 10bp barcode and adaptor. The reads were shorter than 20 bp will be discarded using cutadapt (v2.10) with the parameter -m 20.
Trimmed reads were aligned to the human GRCh37/hg19 genome using bowtie2 (v2.3.5.1).
Repeat samples were merged together, sorted, and indexed using samtools (v1.12).
NarrowPeak was called using MACS2 (v2.2.7.1) with the parameter -q 0.001.
The mapped reads normalization method is RPKM using deeptools bamCoverage function with the bin-size as 20 to generate bigwig files
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
Cells were crosslinked with 1% formaldehyde and quenched with glycine. Crosslinked cells were lysed twice with ChIP buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 150 mM NaCl, 1x protease inhibitors), and then were sonicated to fragmentize DNA. After centrifugation at 12000rpm for 10 min, supernatant was transferred into new tubes and incubated with an antibody overnight at 4℃ with slow rotation. Magnetic protein A/G beads were used to enrichment targeted chromatin, and the beads were sequentially washed to remove nonspecific binding protein or DNA.
The NEB end-repair module (NEB E6050S) was used to blunt the DNA ends, and Klenow exo- (NEB M0212S) to add dATP at the end of DNA. Nexus adaptors were ligated into DNA using Blunt/TA Ligase Master Mix (NEB M0367L), and Klenow exo- (NEB M0212S) and T4 DNA polymerase (NEB M0203S) were sequentially used to generate blunt-end DNA. The blunt-end DNA was digested with Lambda Exonuclease (NEB M0262S) and RecJf exonuclease (NEB M0264S). After reverse-crosslinking at 65℃for overnight, the DNA fragment were extracted using phenol-chloroform and precipitated with ethanol contains sodium acetate. DNA fragment were denatured to generate ssDNA and then cyclized with ssDNA Ligase (Epicentre CL4111K). The circular DNA were annealed with oligonucleotides contain BamHI endonuclease recognition sites. After digestion with BamHI and re-precipitation using ethanol, the ChIP-nexus library was constructed with PCR.

treatment_protocol: In order to degrade protein labeled with AID in TiR1 expression cells, IAA was added to final concentration of 500 μM for 6-24 hours.

value: ZNF143 (Proteintech, #16618-1-AP)

value: CTCF-AID

value: IAA, 24h


title: AID-WT_ZNF143,ChIP-nexus

value: IAA, 0h


title: WT_RAD21,ChIP-nexus

value: RAD21 (Abcam, #Ab992)


title: ZNF143KO_CTCF,ChIP-nexus

value: CTCF (Abcam, #Ab70303)


title: WT_CTCF,ChIP-nexus


title: ZNF143KO_RAD21,ChIP-nexus


title: AID-CTCFd_CTCF,ChIP-nexus


title: ZNF143KO_H3K4me3,ChIP

data_processing:
Reads of ChIP-seq were mapped to human genome GRCh37/hg19 with bowtie2.
The peaks were called by MACS2 with default parameters.
All of the mapped Sam files were sorted and indexed by Samtools (v1.12) and normalized to RPKM by Deeptools BamCoverage function.
The BedGraph file generated from Deeptools was uploaded into USCS browser for visualizing.
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak

growth_protocol: Human HEC-1-B cells and derived cell lines were cultured in MEM, 200mM L-Glutamine, Earle’s Balanced Salts (Hyclone) supplemented with 1mM sodium pyruvate (Sigma), 1% penicillin-streptomycin (Gibco) and 10% fetal bovine serum (Gibco). The cells were cultured at 37°C in the incubator supplied with 5% (v/v) of CO2.

extract_protocol:
After washed twice by PBS, ~10-20 million cells digested by trypsin and resuspended by 10mL medium. Formaldehyde (Thermo 28908) was added to a final concentration of 1% to cross-link protein and DNA. After incubation at room temperature for 10 minutes, the glycine solution reached a final concentration of 125mM and incubated at room temperature for 5 minutes to quench the cross-linking reaction. Cells were centrifuged at 2,500g for 10 minutes at 4°C to precipitate cells. The cell pellet was washed by ice-cold PBS and quickly frozen by liquid nitrogen. The cell pellet was stored at -80°C until the next step. Cell pellet was resuspended by 1mL ice-cold ChIP buffer 1 (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 150 mM NaCl, 1x protease inhibitors), and lysed twice by ChIP buffer 1 at 4°C for 10 minutes with slow rotation. After centrifuged at 2,500g for 5 minutes at 4°C, the pellet was resuspended by 0.7mL ChIP buffer 1 and incubated at ice for 10 minutes. The cell suspension was sonicated to fragment DNA using Bioruptor Plus Sonicator by high intensity (30 seconds on, 30 seconds rest, 30 cycles), and the DNA size should be 100-10000 bp. After spinning at 14,000g for 10 minutes at 4°C, the supernatant was transferred to a new tube with 50 μL agarose protein A beads (16-157 Millipore) were added. After incubation at 4°C with slow rotation for 1 hour, the supernatant was transferred into a new tube and the primary antibody was added to incubate it at 4°C with slow rotation overnight. 50 μL agarose protein A beads were added and incubated at 4°C with slow rotation for 3 hours. The protein-DNA complexes were sequenced and washed by ChIP buffer 1, ChIP buffer 2 (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 400 mM NaCl), ChIP buffer 3 (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate) and ChIP buffer 4 (50 mM HEPES pH 7.5, 1 mM EDTA, 1% NP-40, 0.7% sodium deoxycholate, 500 mM LiCl). DNA-protein complexes were eluted using 100 μL elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS) by incubation at 65°C for 30 minutes. The above step was repeated again and a total of 200 μL solution of DNA-protein complexes was collected. The DNA-protein complexes solution was mixed with 200 μL TE buffer, and incubated at 65°C overnight to be reversely cross-linked. The DNA-protein complexes were digested by 2 μL RNase A at 37°C for 2 hours and 8 μL proteinase K at 55°C for 2 hours. The DNA was purified using 400μl of phenol-chloroform. The DNA was precipitated by adding 40 μL 3M NaAc pH 5.2, 1.5 μL glycogen (Thermo R0561), and 1mL absolute ethanol, and frozen at -80°C for 30 minutes. After centrifuged at 17,000g for 30 minutes at 4°C, the DNA pellet was washed by 75% ethanol, air-dried, and then solved by 20 μL nuclease-free water.
DNA concentration was measured by PicoGreen reagents. 10 ng DNA was used for the library constructed with NEBNext®Ultra™ II DNA Library Prep Kit for Illumina. Library was sequenced on the Illumina HiSeq platform.

value: H3K4me3 (cell signaling #9751T)


title: WT_H3K4me3,ChIP


title: CTCFd_SWT1,4C

data_processing:
*library strategy: 4C-seq
QHR-4C FASTQ raw reads were aligned to GRCh37/hg19 genome using bowtie2 with default parameters.
The reads per million (RPM) interaction values were calculated by r3Cseq program (v1.38.0).
The Bedgraph files generated by r3Cseq package were used for visualizing in UCSC genome browser.
Assembly: hg19
Supplementary files format and content: bedGraph

extract_protocol:
~2 million cells were fixed by 2% formaldehyde and permeabilized by ice-cold 4C permeabilization buffer (50 mM Tris–HCl pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% Triton X-100, and 1× protease inhibitors). Chromatin was digested by DpnII (NEB R0543S), proximal ligated by T4 ligase (NEB M0202S), reverse cross-linked, purified using phenol-chloroform, and finally precipitated.
DNA sizes were 200-600bp through sonication and linear-amplified using 5’ biotin-labeled primers near viewpoint. ssDNA was connected with adapter, amplification using PCR, and sequenced on the Illumina HiSeq platform.

treatment_protocol: In order to degrade protein labeled with AID in TiR1 expression cells, IAA was added to final concentration of 500 μM for 0 or 24 hours.


title: WT_ZNF143,ChIP-nexus


title: Adult_rete_ovarii_rep2 _bulkRNA-seq

city: Aurora

first: Jennifer

last: McKey

state: CO

address: 1775 Aurora Ct Barbara Davis Center, M20-3202G

institute: CU Anschutz medical campus

data_processing:
For sc(sn)RNA-seq fastq sequence files were demultiplexed, aligned and the single cell or nucleotide gene expression matrix, features and barcodes files generated with 10X Genomics Cellranger (v?) count
For sc(sn)RNA-seq used Seurat v? CreateSeuratObject() to generate single cell SeuratObject from Cellranger output
For sc(sn)RNA-seq filtered cells for nFeatures > and percent mitochrondial expression <
For sc(sn)RNA-seq processed filtred SeuratObject with NormalizeData(), FindVariableFeatures(), ScaleData(), RunPCA(), RunUMAP(dims=1:20), FindNeighbors(dims=1:20) and FindClusters() with default parameters except as noted
For bulk RNA-seq gene expression for each library was quantified with Salmon quant
Assembly: GRCm39 (mm10)
Supplementary files format and content: gzipped mtx file of matrix of normalized gene expression by cell for sc(sn)RNA-seq
Supplementary files format and content: gzipped tsv files of metadata for cells for sc(sn)RNA-seq
Supplementary files format and content: salmon quantification tab separated file for bulkRNA-seq

source_name: rete ovarii

extract_protocol:
Pooled ROs (4-5 ROs for each replicate) were washed in RNase-free PBS-/- and incubated at 37°C in fresh 1X TrypLE (Thermo Fisher Scientific, catalog #12563029) for 20 minutes. TrypLE was then aspirated off, and samples were then resuspended in chilled RNase-free PBS with 3% bovine serum albumin (BSA) and pipetted gently up and down for about 2 min to disaggregate cells. Cells were pipetted through a 0.32μm cell strainer into FAC-sorting filter tubes (Corning Falcon cat # 352235). Single-cell suspensions were then FAC-sorted at the Duke Flow Cytometry Shared Resource core on a B-C Astrios Sorter, based on presence or absence of GFP. Cells were sorted into PBS, pelleted, and resuspended in 10.5ul Clontech Lysis buffer (Takara Bio Inc. Cat # 635013).
Sample libraries were prepared with SMART-Seq v4 Ultra Low Input RNA Kit (Takara Clontech Kit Cat# 63488)
Embryonic day (E)16.5 fetuses were harvested from pregnant Tre-H2BGFPtg/tg dams crossed to a Pax8rtTAtg/+ male. Embryos positive for both alleles were identified by presence of green fluorescence in the urogenital epithelia. Male fetuses were discarded, and ovary/mesonephros/oviduct complexes from females were dissected in RNAse-free PBS-/-, with as little removal of surrounding tissue as possible to ensure retention and survival of RO cells. The GFP signal was then used to perform close dissection of the RO and surrounding ovarian capsule, and the oviduct was discarded.
Ovaries and periovarian fat pads (in which the adult RO is embedded) were harvested from Pax8rtTA; Tre-H2BGFPtg/tg adult females. The RO was located within the fat pad by green fluorescence and closely dissected in RNase-free PBS-/-, with as much removal of surrounding tissue as possible to ensure enrichment in RO cells. To ensure capture of the IOR and CR, the dorso-lateral-most portion of the ovary was conserved, and the rest of the ovary was discarded. The samples were kept on ice until all samples were dissected. For snRNAseq analysis of the adult RO, samples were collected from 5 mice in early diestrus and 5 mice in estrus (total of 10 ROs in each group) and were snap frozen in an Ethanol/dry ice slush and stored at -80ºC until further processing.

value: rete ovarii

tag: developmental stage

value: 2 month old


title: Adult_rete_ovarii_rep1 _bulkRNA-seq


title: Fetal_rete_ovarii_rep1 _bulkRNA-seq

source_name: rete ovarii and ovarian capsule

value: rete ovarii and ovarian capsule


title: Fetal_rete_ovarii_rep2 _bulkRNA-seq


title: Adult_rete_ovarii_diestrus_snRNAseq

description:
10X Genomics scRNAseq
2M_Diestrus_scRNAseq

molecule: nuclear RNA

extract_protocol:
Pooled snap frozen ROs at diestrus (N=10) were further separated into two subgroups for gentle (N=5) and harsh (N=5) dissociation to ensure sensitive and highly adherent cell types were present in the final single nucleus suspension. Samples were then processed independently as described in the demonstrated protocol for nuclei isolation provided by 10X Genomics
To capture, label, and generate cDNA libraries of individual cells and nuclei, the 10X genomics Chromium Single Cell 3’ Library and Gel Bead Kit v3 following the 10X Genomics User Guide was used.
Embryonic day (E)16.5 fetuses were harvested from pregnant Tre-H2BGFPtg/tg dams crossed to a Pax8rtTAtg/+ male. Embryos positive for both alleles were identified by presence of green fluorescence in the urogenital epithelia. Male fetuses were discarded, and ovary/mesonephros/oviduct complexes from females were dissected in RNAse-free PBS-/-, with as little removal of surrounding tissue as possible to ensure retention and survival of RO cells. The GFP signal was then used to perform close dissection of the RO and surrounding ovarian capsule, and the oviduct was discarded.
Ovaries and periovarian fat pads (in which the adult RO is embedded) were harvested from Pax8rtTA; Tre-H2BGFPtg/tg adult females. The RO was located within the fat pad by green fluorescence and closely dissected in RNase-free PBS-/-, with as much removal of surrounding tissue as possible to ensure enrichment in RO cells. To ensure capture of the IOR and CR, the dorso-lateral-most portion of the ovary was conserved, and the rest of the ovary was discarded. The samples were kept on ice until all samples were dissected. For snRNAseq analysis of the adult RO, samples were collected from 5 mice in early diestrus and 5 mice in estrus (total of 10 ROs in each group) and were snap frozen in an Ethanol/dry ice slush and stored at -80ºC until further processing.

tag: estrus stage

value: diestrus


title: Adult_rete_ovarii_estrus_snRNAseq

description:
10X Genomics scRNAseq
2M_Estrus_scRNAseq

extract_protocol:
Pooled snap frozen ROs at estrus (N=10) were further separated into two subgroups for gentle (N=5) and harsh (N=5) dissociation to ensure sensitive and highly adherent cell types were present in the final single nucleus suspension. Samples were then processed independently as described in the demonstrated protocol for nuclei isolation provided by 10X Genomics
To capture, label, and generate cDNA libraries of individual cells and nuclei, the 10X genomics Chromium Single Cell 3’ Library and Gel Bead Kit v3 following the 10X Genomics User Guide was used.
Embryonic day (E)16.5 fetuses were harvested from pregnant Tre-H2BGFPtg/tg dams crossed to a Pax8rtTAtg/+ male. Embryos positive for both alleles were identified by presence of green fluorescence in the urogenital epithelia. Male fetuses were discarded, and ovary/mesonephros/oviduct complexes from females were dissected in RNAse-free PBS-/-, with as little removal of surrounding tissue as possible to ensure retention and survival of RO cells. The GFP signal was then used to perform close dissection of the RO and surrounding ovarian capsule, and the oviduct was discarded.
Ovaries and periovarian fat pads (in which the adult RO is embedded) were harvested from Pax8rtTA; Tre-H2BGFPtg/tg adult females. The RO was located within the fat pad by green fluorescence and closely dissected in RNase-free PBS-/-, with as much removal of surrounding tissue as possible to ensure enrichment in RO cells. To ensure capture of the IOR and CR, the dorso-lateral-most portion of the ovary was conserved, and the rest of the ovary was discarded. The samples were kept on ice until all samples were dissected. For snRNAseq analysis of the adult RO, samples were collected from 5 mice in early diestrus and 5 mice in estrus (total of 10 ROs in each group) and were snap frozen in an Ethanol/dry ice slush and stored at -80ºC until further processing.

tag: tissue

value: estrus


title: Liver, Y_Mal_F_11N

city: Madison

first: Cara

middle: Leanne

last: Green

state: Wisconsin

address: 2214 Kendall Ave

department: Medicine

institute: University of Wisconsin-Madisin

data_processing:
To remove any genes that exhibited no or a very low number of mapped reads, only genes that had more than 1 count per million in at least 6 samples across all treatments were retained for further analysis. This resulted in a total of 17,738 genes  retained in females and 17,757 genes in males. Raw counts were normalized using the trimmed mean of M values (TMM normalization) (Robinson and Oshlack 2010). Differential gene expression was modeled using the edgeR package (Robinson, McCarthy et al. 2010) in R (version 3.4.3) and pairwise comparisons were conducted between Control and Low AA or low Ile in each age/sex group. To control for type I errors, the Benjamini Hochberg adjusted p-value was used (5% FDR). We tested for over-representation of gene ontology (GO) terms or KEGG pathways in each comparison, using the limma package (Ritchie, Phipson et al. 2015).
Reads were aligned to the mouse (Mus musculus) with genome-build GRCm38.p5 of accession NCBI:GCA_000001635.7 and expected counts were generated with ensembl gene IDs (Zerbino et al., 2018).
Assembly: genome-build GRCm38.p5 of accession NCBI:GCA_000001635.7
Supplementary files format and content: Files include male and female analyzed data, with effective log2 fold-changes, p-values and adjusted p-values for each contrast of interest and the raw unanalyzed data that was imported into R for analysis.

source_name: Liver, Fasted

growth_protocol: Diet started at 9 weeks of age (Euthanized at 6 months) or 6 months of age (euthanized at 24 months)

extract_protocol:
Liver tissues were harvested and snap frozen in liquid nitrogen. Transcriptional profiling: RNA was extracted from liver as previously described (Cummings et al., 2018). Concentration and purity of RNA was initially determined using a Nanodrop 2000c, and then submitted to the University of Wisconsin-Madison Biotechnology Center Gene Expression Center & DNA Sequencing Facility. RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide Rev. E.
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide Rev. E.
Sample libraries were combined andstripedacross two lanes, the data from each lane was merged into a single samplefile prior to expression estimation

treatment_protocol: Mice were placed on either a control, low amino acid or low isoleucine

value: Liver, Fasted

tag: age (euthanized)

value: 6 months

tag: diet

value: Control

value: Male


title: WT_SWT1,4C

tag: cell line

tag: cell type

value: Human Uterine Adenocarcinoma Cells


title: SBSd_SBS,4C

value: SBS deletion


title: Liver, O_Mal_H_105N

value: 24 months

value: Low Amino Acid


title: Liver, O_Mal_F_113N


title: Liver, O_Fem_F_74R

value: Female


title: AID-WT_CTCF,ChIP-nexus

value: CTCF-AID

value: IAA, 0h


title: ZNF143KO_SWT1,4C

value: CTCF-AID, ZNF143KO


title: Liver, Y_Fem_HH_9R

value: Low Isoleucine


title: PBMC from healthy control 2

city: Xi'an

first: Pengju

state: Shaanxi

address: No. 277, Yanta West Road, Xi'an

institute: The First Affiliated Hospital of Xi’an Jiaotong University

data_processing:
Use CeleScope® for processing raw data to take double-ended FASTQ files as input and generate files and QC metrics that can be used for downstream data analysis.
Use fastQC and fastp to process raw reads to remove low sequencing quality reads, and removed poly-A tails and adaptor sequences using cutadapt.
The STAR Genome Mapper was applied to map the extracted reads to the reference genome GRCh38(ensembl version 92 annotation)
UMI counts and gene counts for each cell were obtained using featureCounts v1.6.2 software
Assembly: GRCh38
Supplementary files format and content: matrix files

source_name: PBMC

extract_protocol:
Collect 2 mL of peripheral venous blood from each sample in EDTA-anticoagulant tubes and dilute with 2 mL of PBS. The blood was layered onto the 3mL Ficoll-Paque (GE Healthcare, Sweden) in a 10 ml centrifuge tube and centrifuged at 400 g, 18˚C for 30 min. The PBMC fraction was transferred to another tube and washed 2 times with PBS to obtain a single cell suspension.
The final single cell suspension is loaded onto a microfluidic device the protocol of the Singleron GEXSCOPE Single Cell RNA Library Kit (Singleron Biotechnologies) according to the protocol of the Singleron GEXSCOPE Single Cell RNA Library Kit (Singleron Biotechnologies), which involves cell lysis, mRNA capture, labeling cells (barcode) and mRNA (UMI), reverse transcription of mRNA into cDNA and amplification, and finally cDNA fragmentation. Individual libraries were diluted to 4 nM and pooled for sequencing. Pools were sequenced on an Illumina HiSeq X with 150 bp paired end reads.

tag: age

tag: gender

tag: diagnosis

value: healthy control

value: PBMC


title: PBMC from healthy control 1


title: WT_SBS,4C

tag: genotype

value: wild type


title: PBMC from PV patient 5

value: progressive non-segmental vitiligo


title: PBMC from PV patient 3


title: Liver, Y_Fem_F_25R

value: Liver, Fasted


title: Liver, O_Fem_H_81N


title: Liver, Y_Fem_H_13R

value: 6 months


title: PBMC from PV patient 1


title: CTCFd_HS5-1,4C

tag: treatment

value: IAA, 24h


title: Liver, Y_Fem_F_12N

value: Control


title: WT_HS5-1,4C

value: Human Uterine Adenocarcinoma Cells


title: Liver, O_Mal_HH_93R

value: Male


title: Liver, Y_Mal_F_18N


title: PBMC from healthy control 3


title: Liver, Y_Fem_HH_2R


title: PBMC from PV patient 4


title: Liver, O_Mal_H_108N

value: 24 months


title: RNAseq_SKNMC_shCHD4#2_48h_rep2

city: Boston

first: Joana

middle: Graca

last: Marques

state: MA

address: 360 Longwood Avenue

institute: Dana-Farber Cancer Institute

description: ES_gtf101_DE_48hshCHD4#2_vs_48hshScramble_logFC.txt

data_processing:
Illumina adaptors were trimmed off and quality control was performed with FastQC v0.11.7.
Paired-end RNA-seq reads were aligned to the GRCh38 reference genome using Hisat2 v2.1.0 with the options ‘--rna-strandness RF --fr’ and Samtools v1.7.
Mapping quality was assessed by QualiMap v2.2.1.
Read counts were measured at the gene level and annotated according to Ensembl101, using featureCounts v1.6.0 with the options ‘-p -B -O -M --fraction’.
Genes with less than a sum of 10 reads were filtered out and differential gene expression analysis was conducted in RStudio v 4.1.1 using DESeq2 v 1.34.0.
Assembly: GRCh38
Supplementary files format and content: txt files with log2 fold change values depicting differential transcript expression between knockdown conditions and scramble control for both time points.
Supplementary files format and content: txt files with normalized filtered counts for all conditions in both the 24h and 48h time points.

source_name: SKNMC

growth_protocol: SKNMC cells were cultured in RPMI (Roswell Park Memorial Institute, Sigma-Aldrich) supplemented with 10% fetal bovine serum (#F7524, Sigma-Aldrich), 2 mM L-glutamine (Bioconcept AG) and 100 U/ml penicillin/streptomycin (Thermo Fisher Scientific AG), in 5% CO2 at 37°C.

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (#74104, Qiagen Instruments AG), including the DNase digestion step, according to the manufacturer`s instructions.
Library preparation and sequencing was performed by ATLAS Biolabs GmbH, Berlin, Germany. Briefly, cDNA libraries were prepared with the Illumina® TruSeq® Stranded Total RNA Sample Preparation Kits and paired-end sequenced on an Illumina HiSeq2000.

treatment_protocol: SKNMC shScramble, shCHD4#1, shCHD4#2, and shFLI1 cells were cultured in the presence of 100ng/ml doxycycline (Sigma-Aldrich) for 24 or 48 hours to induce shRNA expression. For each assay, at least three biological replicates were performed.

value: SKNMC

value: Ewing Sarcoma

value: CHD4 knockdown


title: RNAseq_SKNMC_shCHD4#2_48h_rep1


title: PBMC from PV patient 2


title: Liver, O_Fem_HH_90N

value: Female


title: RNAseq_SKNMC_shFLI1_48h_rep3

description: ES_gtf101_DE_48hshFLI_vs_48hshScramble_logFC.txt

value: EWS-FLI1 knockdown


title: Fetal_rete_ovarii_scRNAseq

description:
10X Genomics scRNAseq
Fetal_scRNAseq

extract_protocol:
28 ROs at E16.5 and E17.5 were collected as described above, pooled and incubated for 12 min in 450ul Trypsin 0.05% with 50ul 2.5% Collagenase Type IV at 37ºC. 500ul of chilled PBS 0.3% BAS were then added for mechanical disaggregation by pipetting gently up and down for about 2 min. Some tissue chunks were still present, thus the sample was incubated for another 6 min in 100ul Trypsin 0.05% with 50ul 2.5% Collagenase Type IV at 37ºC. The sample was then pelleted by gentle centrifugation (5 min 500 x g 4ºC) and resuspended in 500ul Red Blood Cell lysis buffer (eBioscience, cat #00-4333-57) and incubated for 3 min at room temperature. Cells were pelleted by gentle centrifugation and resuspended in 120ul PBS 0.3% BSA before passing through a 0.32um cell strainer into a clean 1.5mL tube.
To capture, label, and generate cDNA libraries of individual cells and nuclei, the 10X genomics Chromium Single Cell 3’ Library and Gel Bead Kit v3 following the 10X Genomics User Guide was used.
Embryonic day (E)16.5 fetuses were harvested from pregnant Tre-H2BGFPtg/tg dams crossed to a Pax8rtTAtg/+ male. Embryos positive for both alleles were identified by presence of green fluorescence in the urogenital epithelia. Male fetuses were discarded, and ovary/mesonephros/oviduct complexes from females were dissected in RNAse-free PBS-/-, with as little removal of surrounding tissue as possible to ensure retention and survival of RO cells. The GFP signal was then used to perform close dissection of the RO and surrounding ovarian capsule, and the oviduct was discarded.
Ovaries and periovarian fat pads (in which the adult RO is embedded) were harvested from Pax8rtTA; Tre-H2BGFPtg/tg adult females. The RO was located within the fat pad by green fluorescence and closely dissected in RNase-free PBS-/-, with as much removal of surrounding tissue as possible to ensure enrichment in RO cells. To ensure capture of the IOR and CR, the dorso-lateral-most portion of the ovary was conserved, and the rest of the ovary was discarded. The samples were kept on ice until all samples were dissected. For snRNAseq analysis of the adult RO, samples were collected from 5 mice in early diestrus and 5 mice in estrus (total of 10 ROs in each group) and were snap frozen in an Ethanol/dry ice slush and stored at -80ºC until further processing.

value: rete ovarii and ovarian capsule


title: RNAseq_SKNMC_shFLI1_48h_rep1


title: Liver, Y_Mal_HH_22R

value: Low Isoleucine


title: Liver, Y_Mal_H_1R

value: Low Amino Acid


title: RNAseq_SKNMC_shCHD4#1_48h_rep1

description: ES_gtf101_DE_48hshCHD4#1_vs_48hshScramble_logFC.txt


title: RNAseq_SKNMC_shCHD4#2_48h_rep3


title: RNAseq_SKNMC_shFLI1_48h_rep2


title: Liver, O_Fem_H_72R


title: RNAseq_SKNMC_shScramble_48h_rep5

description: ES_gtf101_FilteredNormalizedCounts_48h.txt

value: shScramble


title: RNAseq_SKNMC_shScramble_48h_rep4


title: Liver, O_Mal_F_112R


title: Liver, O_Fem_F_119R


title: RNAseq_SKNMC_shCHD4#1_48h_rep3


title: Liver, O_Fem_H_117R


title: RNAseq_SKNMC_shCHD4#1_48h_rep2


title: Liver, O_Fem_HH_120L


title: Liver, O_Mal_H_107L


title: Liver, Y_Mal_F_11L


title: Liver, Y_MAL_H_28R


title: Liver, O_Mal_H_106N


title: RNAseq_SKNMC_shScramble_48h_rep3


title: Liver, Y_Mal_HH_20N


title: Liver, Y_Mal_H_1L


title: RNAseq_SKNMC_shFLI1_24h_rep2

description: ES_gtf101_DE_24hshFLI_vs_24hshScramble_logFC.txt


title: Liver, O_Mal_H_103N


title: RNAseq_SKNMC_shScramble_48h_rep1


title: RNAseq_SKNMC_shFLI1_24h_rep3


title: Liver, O_Mal_HH_102N


title: Liver, O_Fem_F_71N


title: Liver, O_Fem_HH_84N


title: Liver, O_FEM_HH_76L


title: Liver, Y_Fem_HH_9L


title: RNAseq_SKNMC_shFLI1_24h_rep1


title: RNAseq_SKNMC_shCHD4#2_24h_rep3

description: ES_gtf101_DE_24hshCHD4#2_vs_24hshScramble_logFC.txt


title: Liver, O_Fem_H_87R


title: RNAseq_SKNMC_shCHD4#2_24h_rep2


title: RNAseq_SKNMC_shScramble_48h_rep2


title: Liver, Y_Mal_F_10N


title: RNAseq_SKNMC_shCHD4#1_24h_rep3

description: ES_gtf101_DE_24hshCHD4#1_vs_24hshScramble_logFC.txt


title: RNAseq_SKNMC_shScramble_24h_rep5

description: ES_gtf101_FilteredNormalizedCounts_24h.txt

value: wildtype


title: RNAseq_SKNMC_shCHD4#1_24h_rep2


title: Liver, O_Fem_HH_114R

value: Liver, Fasted


title: Liver, Y_Fem_HH_3N

value: 6 months


title: RNAseq_SKNMC_shScramble_24h_rep4


title: RNAseq_SKNMC_shScramble_24h_rep3


title: Liver, Y_Fem_HH_30N


title: Liver, O_Mal_F_91R


title: RNAseq_SKNMC_shScramble_24h_rep2


title: Liver, O_Fem_F_116R


title: Liver, Y_Fem_F_5R


title: Liver, Y_Fem_H_24N


title: RNAseq_SKNMC_shCHD4#2_24h_rep1


title: RNAseq_SKNMC_shScramble_24h_rep1


title: Liver, Y_Mal_F_10R


title: Liver, Y_FEM_F_5L


title: Liver, Y_Mal_HH_22N


title: Liver, Y_FEM_HH_14N


title: TPHP 50uM rep3 [S22]

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

data_processing:
*library strategy: TempO-Seq (Templated Oligo assay with Sequencing readout)
Reads were demultiplexed from the BCL files and processed into FASTQ files using bcl2fastq v2.20.0.422.
FASTQ files were aligned to the Human Surrogate+ Tox Panel (S1500+) v2.0 probes reference sequences using STAR 2.7.8a.
The qCount function from QuasR was used to extract feature counts specified in a GTF file (provided by BioSpyder) from the aligned reads.
Normalization was performed with DESeq2 R package v1.30.1
Log2 fold change shrinkage was performed using the ashr method.
Potential false positive DEGs were removed using filtering criteria defined in the Omics Data Analysis Frameworks for Regulatory application
Assembly: Genome_build: Biospyder S1500 Gene Set
Supplementary files format and content: Comma-delimited text file with genes by counts matrix

source_name: KGN

growth_protocol: KGN cells were maintained in DMEM/F12 medium supplemented with 10% charcoal-stripped fetal bovine serun (FBS) and 0.5% penicillin/streptomycin at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol: No RNA extraction was done. Cells were directly lysed with 1X TempO-Seq lysis buffer and TempO-Seq libraries were constructed directly from cell lysates according to the TempO-Seq Assay User Guide (Version 2.1)

treatment_protocol: Cells were exposed for 48 h to vehicle control (0.5% dimethyl sulfoxide; DMSO) or various concentrations of test chemicals (ranging from 0.1 to 50 μM).

value: KGN

value: Human ovarian granulosa cells

value: TPHP 50uM


title: TPHP 3.2uM rep5 [S67]

value: TPHP 3.2uM


title: TPHP 50uM rep1 [S146]


title: TPHP 50uM rep5 [S70]


title: TPHP 3.2uM rep4 [S24]


title: TPHP 50uM rep4 [S48]


title: TPHP 50uM rep2 [S190]


title: Liver, O_Fem_H_75N

value: 24 months


title: Liver, Y_Mal_HH_23L

value: Male


title: TPHP 3.2uM rep1 [S122]


title: Liver, Y_Fem_F_5N

value: Control


title: TPHP 3.2uM rep2 [S187]


title: Liver, O_Fem_H_85N


title: TPHP 20uM rep5 [S69]

value: TPHP 20uM


title: Liver, Y_Fem_H_24R

value: Female


title: Liver, O_Fem_HH_122L


title: TPHP 20uM rep4 [S40]


title: Liver, Y_Fem_H_8R


title: Liver, O_Mal_H_92N


title: TPHP 20uM rep3 [S21]


title: TPHP 20uM rep2 [S189]


title: Liver, O_Mal_F_101R


title: Liver, O_FEM_H_83R


title: TPHP 1uM rep5 [S66]

value: TPHP 1uM


title: TPHP 20uM rep1 [S138]


title: TPHP 3.2uM rep3 [S19]


title: Liver, O_Fem_F_116L


title: Liver, Y_Fem_H_4R


title: Liver, Y_Mal_F_11R


title: TPHP 1uM rep2 [S16]


title: Liver, Y_Fem_F_12R


title: TPHP 10uM rep4 [S32]

value: TPHP 10uM


title: Liver, O_Mal_HH_109N

value: Low Isoleucine


title: TPHP 1uM rep3 [S18]


title: Liver, O_Mal_H_96N

value: Low Amino Acid


title: TPHP 1uM rep1 [S114]


title: TPHP 10uM rep2 [S188]


title: Liver, Y_Mal_H_7N


title: TPHP 10uM rep1 [S130]


title: TPHP 0.32uM rep5 [S8]

value: TPHP 0.32uM


title: TPHP 0.32uM rep4 [S65]


title: Liver, O_Mal_HH_104L


title: TPHP 0.32uM rep3 [S185]


title: Liver, O_Mal_F_91L


title: TPHP 10uM rep3 [S20]


title: TPHP 0.32uM rep2 [S17]


title: Liver, O_Fem_F_86R


title: TPHP 0.32uM rep1 [S106]


title: TPHP 1uM rep4 [S186]


title: TMPP 3.2uM rep5 [S60]

value: TMPP 3.2uM


title: Liver, Y_Mal_H_29R

value: Liver, Fasted


title: TPHP 10uM rep5 [S68]


title: Liver, Y_Mal_H_29L

value: 6 months


title: Liver, Y_Mal_HH_20R


title: Liver, O_Fem_F_88R


title: Liver, O_Mal_HH_99R


title: TMPP 3.2uM rep4 [S31]

value: KGN


title: Liver, O_Mal_F_101N


title: TMPP 3.2uM rep2 [S129]

value: Human ovarian granulosa cells


title: Liver, O_Mal_F_95R


title: Liver, O_Mal_H_97N


title: Liver, Y_Fem_H_13N


title: TMPP 20uM rep4 [S47]

value: TMPP 20uM


title: TMPP 20uM rep5 [S62]


title: TMPP 20uM rep2 [S145]


title: TMPP 3.2uM rep1 [S12]


title: Liver, Y_Fem_F_15N


title: Liver, O_Mal_HH_98N


title: Liver, O_Mal_HH_109R


title: TMPP 20uM rep3 [S174]


title: TMPP 1uM rep5 [S59]

value: TMPP 1uM


title: Liver, Y_Mal_HH_17L


title: Liver, Y_Fem_HH_3R


title: TMPP 1uM rep3 [S171]


title: TMPP 1uM rep4 [S23]


title: Liver, O_Fem_HH_122N

value: 24 months


title: TMPP 1uM rep2 [S121]


title: TMPP 1uM rep1 [S11]


title: Liver, Y_Fem_HH_3L


title: TMPP 10uM rep5 [S61]

value: TMPP 10uM


title: Liver, Y_Mal_H_28N

value: Male


title: TMPP 3.2uM rep3 [S172]


title: Liver, Y_Mal_F_19R

value: Control


title: Liver, Y_Fem_H_27L

value: Female


title: Liver, O_Mal_HH_104N


title: Liver, Y_Fem_H_13L


title: TMPP 20uM rep1 [S14]


title: TMPP 10uM rep3 [S173]


title: TMPP 10uM rep2 [S137]


title: TMPP 10uM rep1 [S13]


title: Liver, O_Fem_F_118L


title: Liver, Y_Mal_HH_6N


title: Liver, Y_Mal_F_21L


title: Liver, O_Fem_HH_123R


title: TMPP 0.32uM rep4 [S170]

value: TMPP 0.32uM


title: TMPP 0.32uM rep2 [S113]


title: TMPP 0.32uM rep5 [S58]


title: TMPP 0.32uM rep3 [S15]


title: TMPP 0.1uM rep4 [S7]

value: TMPP 0.1uM


title: Liver, Y_Fem_F_26N


title: TMPP 0.1uM rep2 [S169]


title: B16_F10 cells, CTRL_additional sequencing,H3K27ac, ChIP

city: Hangzhou

first: Liyuan

last: Zhou

state: 杭州市

address: 国科大杭州高等研究院

institute: University of Chinese Academy of Sciences

data_processing:
The skewer(0.2.2) was used to remove low quality, splice fragments and too short sequences (less than 50bp) of raw paired-end reads  and FastQC were then used to qualified the reads.
The filtered reads were mapped on mouse genome mm10 by Bowtie (2.4.3) and Picard (2.26.5) was used to further remove duplicates due to PCR amplification.
To validate the distribution of H3K27ac signaling in genome, reads were extended to 200bp and normalized(reads per kilobase per million) to genarate bigwig files using deepTools. The bigwig files were visualized using IGV.
To analyze the enhancer signal intensity changes, the bam files were used to determine enhancers using ROSE_main.py and the enhancers of nearby genes were annotated with ROSE_geneMapper.py. The intensity curves of ChIP-seq signals for H3K27ac on enhancer regions were generated by deepTools (2.0).
Assembly: mm10
Supplementary files format and content: bigWig,bam

source_name: cell line

growth_protocol: B16-F10 and A375 cells were maintained in DMEM medium containing 1% Penicillin/Streptomycin  and 10% FBS andcultured in 37°C incubator with 5%CO2.

extract_protocol:
The total RNA from B16-F10 or A375 cells was extracted by trizol(Vazyme) according to manufacturer’s protocol for RNA-seq.  For chip-seq, B16-F10 cells were fixed by 1% formaldehyde for 10 minutes. Then, chromatin from cells lysate was digested by Micrococcal Nuclease  into DNA fragments between 150-900 bp in length and released by sonication for antibody enrichment.
DNA libraries for chip-seq were estabished using VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme) following the manufacturer’s guidelines. Equal amount of each library was sequencing on lIIumina NovaSeq 6000. The first sequencing data was not sufficient for data analysis, the second sequencing was performed.

value: cell line

value: melanoma cells

value: WT

value: H3K27ac(abcam, #ab4729)


title: B16_F10 cells, CTRL,Input


title: B16_F10 cells, PRMT1_sg1,H3K27ac, ChIP

value: PRMT1 knockout


title: TMPP 0.1uM rep5 [S9]


title: TMPP 0.1uM rep3 [S57]


title: B16_F10 cells, PRMT1_sg1_additional sequencing,H3K27ac, ChIP


title: TMPP 0.32uM rep1 [S10]


title: B16_F10 cells, CTRL_additional sequencing,Input


title: TMPP 10uM rep4 [S39]


title: B16_F10 cells, CTRL,H3K27ac, ChIP


title: TBOEP 50uM rep5 [S94]

value: TBOEP 50uM


title: TMPP 0.1uM rep1 [S105]

value: KGN


title: B16_F10 cells, PRMT1_sg1,rep3

data_processing:
FastQC was used to qualified the reads.
The  qualified reads were mapped on mouse genome mm10 by STAR(2.7.10b).
The gene counts were quantified  by featureCounts (subread 2.0.1).
Assembly: mm10

extract_protocol:
The total RNA from B16-F10 or A375 cells was extracted by trizol(Vazyme) according to manufacturer’s protocol for RNA-seq.  For chip-seq, B16-F10 cells were fixed by 1% formaldehyde for 10 minutes. Then, chromatin from cells lysate was digested by Micrococcal Nuclease  into DNA fragments between 150-900 bp in length and released by sonication for antibody enrichment.
RNA libraries for RNA-seq were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina(Vazyme) following manfacturer's protocl.


title: B16_F10 cells, PRMT1_sg1,Input


title: TBOEP 50uM rep3 [S158]

value: Human ovarian granulosa cells


title: B16_F10 cells, PRMT1_sg1,rep1


title: B16_F10 cells, CTRL,rep3


title: B16_F10 cells, CTRL,rep2


title: TBOEP 50uM rep2 [S147]


title: TBOEP 50uM rep1 [S143]


title: DKO

description: Prkcif/fPrkcif/f;Villin-Cre Small intestine Jejunum

data_processing:
Raw data was downloaded in Ubuntu using BaseSpaceCLI.
We used cellranger mkfastqto demultiplex raw base call (BCL) files generated by Illumina sequencers into FASTQ files
We used cellranger countto take FASTQ files fromcellranger mkfastqand perform alignment to mm10, filtering, barcode counting, and UMI counting
We used  harmony and cellranger aggrto aggregate both sample outputs ofcellranger count, normalizing  to the same sequencing depth and then recomputing the feature-barcode matrices and analysis on the combined data
We used Seurat in R to analyze the aggregated data
Assembly: mm10
Supplementary files format and content: RDS

source_name: Prkcif/fPrkcif/f;Villin-Cre

growth_protocol: In vivo endogenous mouse model

extract_protocol:
To prepare crypt-enriched intestinal epithelial cell suspension, isolated crypts were digested with digestion buffer (0.4 mg/ml Dispase and 0.1 mg/ml DNase in HBSS) for 20 min at 37°C with agitation, filtered through 70- and 40-μm-mesh cell strainers, washed with HBSS and resuspended with Advanced DMEM-F12 containing 10 mM HEPES, 1X Glutamax, 1X B27 supplement, 50 ng/ml EGF and 10 mM Y-27632. Dead cells were removed by EasySep Dead Cell Removal (Annexin V) kit (STEMCELL technologies).
scRNA-seq libraries were generated using the Chromium Single Cell 30 Reagent Kit v2 (10X Genomics). Cells were loaded onto the 10X Chromium Single Cell Platform (10X Genomics),  (Single Cell 3′ library and Gel Bead Kit v.2) as described in the manufacturer’s protocol (10x User Guide, Revision B). On average, approximately 10,000 cells were loaded. Generation of gel beads in emulsion (GEMs), barcoding, GEM-RT clean-up, complementary DNA amplification and library construction were all performed as per the manufacturer’s protocol. Individual sample quality was checked using a Bioanalyzer Tapestation (Agilent). Qubit was used for library quantification before pooling. The final library pool was sequenced on an Illumina NovaSeq6000 instrument using a S1 flowcell.Average cell recovery for Prkcif/fPrkcif/f (WT1) was 13018 cells with 18442 mean reads per cell and 2390 median genes per cell. Average cell recovery for Prkczf/f(WT2) was 12670 cells with 43035 mean reads per cell and 2848 median genes per cell. Average cell recovery for Prkcif/f(WT3) was 18194 cells with 9809 mean reads per cell and 882 median genes per cell. Average cell recovery for Prkczf/f;Villin-Cre(ZKO) was 13546 cells with 47238 mean reads per cell and 3110 median genes per cell. Average cell recovery for Prkcif/f;Villin-Cre(LKO) was 17991 cells with 8902 mean reads per cell and 769 median genes per cell. Average cell recovery for Prkcif/fPrkcif/f;Villin-Cre(DKO) was 20848 cells with 11700 mean reads per cell and 1974 median genes per cell

value: Small intestine Jejunum

value: 14 weeks old

value: Prkcif/fPrkcif/f;Villin-Cre


title: B16_F10 cells, PRMT1_sg1_additional sequencing,Input


title: B16_F10 cells, CTRL, rep1


title: TBOEP 3.2uM rep5 [S91]

value: TBOEP 3.2uM


title: TBOEP 3.2uM rep3 [S155]


title: TBOEP 3.2uM rep2 [S123]


title: TBOEP 3.2uM rep1 [S119]


title: WT1

description: Prkcif/fPrkcif/f Small intestine Jejunum

source_name: Prkcif/fPrkcif/f

value: Prkcif/fPrkcif/f


title: WT2

description: Prkczf/f Small intestine Jejunum

source_name: Prkczf/f

value: Prkczf/f


title: ZKO

description: Prkczf/f;Villin-Cre Small intestine Jejunum

source_name: Prkczf/f;Villin-Cre

value: Prkczf/f;Villin-Cre


title: TBOEP 20uM rep4 [S45]

value: TBOEP 20uM


title: TBOEP 20uM rep5 [S93]


title: 22_16

city: Glasgow

first: Payam

middle: A.

last: Gammage

address: Garscube Estate, Switchback Road

institute: CRUK Beatson Institute

description: 10X Chromium

data_processing: Cell Ranger was used to align the reads followed by Seurat R package for analysis.

source_name: B78 mt.12436 80% tumour sample n=1

extract_protocol:
Single cell suspensions were processed through 10X Genomics Chromium controller using the Single Cell Gene Expression kit (10X Genomics, Chromium Next GEM Single Cell 3’ Kit v3.1) to generate emulsions which were first reverse transcribed and then PCR amplified to generate cDNA. Sequencing libraries were then generated using 10µl of cDNA as outlined in the 10X Genomics protocol (CG000315 Rev C). Briefly, cDNA was first fragmented, end repaired and adaptors ligated, followed by PCR amplification and size selection to generate final libraries.
Libraries were sequenced on a NovaSeq S4 flowcell (Illumina) to a depth of 25,000 reads per cell.

value: 8-11 weeks

value: Male

value: fragment from a subcutaneous tumour


title: TBOEP 20uM rep3 [S157]


title: 22_15

description: 10X Chromium

source_name: B78 mt.12436 80% tumour sample n=2


title: B16_F10 cells, PRMT1_sg1,rep2

value: cell line

value: melanoma cells


title: 22_17

description: 10X Chromium

source_name: B78 mt.12436 80% tumour sample n=3


title: TBOEP 50uM rep4 [S46]


title: TBOEP 20uM rep2 [S139]


title: TBOEP 20uM rep1 [S135]


title: 22_14

description: 10X Chromium

source_name: B78 control sample n=6

value: WT


title: TBOEP 3.2uM rep4 [S43]


title: TBOEP 1uM rep4 [S42]

value: TBOEP 1uM


title: LKO

description: Prkcif/f;Villin-Cre Small intestine Jejunum

source_name: Prkcif/f;Villin-Cre

value: 16 weeks old

value: Prkcif/f;Villin-Cre


title: 22_13

description: 10X Chromium

source_name: B78 control sample n=5


title: TBOEP 1uM rep5 [S90]

value: KGN

value: Human ovarian granulosa cells


title: 22_10

description: 10X Chromium

source_name: B78 mt.12436 60% tumour sample n=2


title: TBOEP 1uM rep1 [S111]


title: TBOEP 1uM rep2 [S115]


title: 22_9

description: 10X Chromium

source_name: B78 control sample n=4


title: 22_7

description: 10X Chromium

source_name: B78 mt.12436 60% tumour sample n=3


title: WT3

description: Prkcif/f Small intestine Jejunum

source_name: Prkcif/f

value: Small intestine Jejunum

value: Prkcif/f


title: 22_8

description: 10X Chromium

source_name: B78 control sample n=7


title: 22_6

description: 10X Chromium

source_name: B78 control sample n=3


title: TBOEP 10uM rep5 [S92]

source_name: KGN

value: TBOEP 10uM


title: TBOEP 10uM rep4 [S44]


title: 22_4

description: 10X Chromium

source_name: B78 control sample n=2


title: TBOEP 10uM rep2 [S131]


title: TBOEP 10uM rep1 [S127]


title: RNAseq_SKNMC_shCHD4#1_24h_rep1

source_name: SKNMC

value: SKNMC

value: Ewing Sarcoma

value: CHD4 knockdown


title: TBOEP 0.32uM rep5 [S89]

value: TBOEP 0.32uM


title: TBOEP 0.32uM rep4 [S41]


title: 22_5

description: 10X Chromium

source_name: B78 mt.11944 60% tumour sample n=3

value: 8-11 weeks

value: Male


title: TBOEP 10uM rep3 [S156]


title: 22_3

description: 10X Chromium

source_name: B78 control sample n=1

value: fragment from a subcutaneous tumour


title: 22_1

description: 10X Chromium

source_name: B78 mt.11944 60% tumour sample n=1


title: 22_11

description: 10X Chromium

source_name: B78 mt.12436 60% tumour sample n=1


title: TBOEP 0.32uM rep2 [S107]


title: TBOEP 0.32uM rep3 [S153]


title: 22_2

description: 10X Chromium

source_name: B78 mt.11944 60% tumour sample n=2


title: TBOEP 0.32uM rep1 [S103]


title: 1399P1, RPR2;Nfibf/f, lung tumor, rep2

first: Julie

last: Ko

address: 265 Campus Drive G2065

data_processing:
Raw sequencing reads were demultiplexed and trimmed using CutAdapt (v2.10) in paired-end mode with the forward and reverse Nextera sequencing adapters (Fwd – CTGTCTCTTATACACATCT, Rev- AGATGTGTATAAGAGACAG) and a minimum read length of at least 25.
Next, Bowtie2 (Langmead & Salzberg, 2012) was used to align paired-end reads to the ENSEMBL mm10 genome (GRCm38), with the following settings: “--local --very-sensitive-local --no-unal --no-mixed --no-discordant”.
PicardTools (https://github.com/broadinstitute/picard) was used to mark duplicates, which were then filtered from the BAM files using samtools (Li et al., 2009).
MACS2 was used to call peaks genome-wide, with a q value of 0.05 and the arguments “-f BAMPE -g $GENOME_SIZE --nomodel --shift 37 --extsize 73” (Zhang et al., 2008).
Supplementary files format and content: bigWig, narrowPeak

growth_protocol: Cells were grown in DMEM with 10% BGS and 1X PSQ at 37C.

extract_protocol:
To perform ATAC-seq with mouse SCLC cell lines, ~100,000 suspension cells/cell line were collected trypsinized and processed using the OMNI-ATAC-Seq protocol (Corces et al., 2017). Briefly, cells were washed with 1 ml of ice-cold ATAC-RSB buffer, centrifuged at 500rcf for 5 minutes at 4℃. Next, the pellets were resuspended in 100µl of chilled ATAC-RSB-LYSIS and incubated on ice for 3 minutes. Lysis was stopped by adding 1mL of ATAC-RSB-WASH to each sample which were again centrifuged for 5 minutes at 500rcf. The supernatant was removed, and the pellet was resuspended in 50µl of OMNI-ATAC Mix and incubated in a mixing (500rpm) thermoblock at 37℃ for one hour. Tagmented DNA was purified using a Qiagen MinElute Kit (#28204), with 21µl of elution buffer warmed to 55℃.
Library amplification PCR was performed with the NEBNext Ultra II Q5 2X Master Mix (NEB #M0544S) using Nextera primers for 12 cycles. DNA concentration was measured using a Qubit DNA HS Assay (ThermoFisher #Q33230). Individual samples were pooled sequenced on an Illumina NextSeq500 using the 75bp kit in a paired end configuration.

tag: originating tissue

value: lung tumor


title: N2N1G, RPR2, LN metastasis, rep1

value: lymph node metastasis


title: 1399M4, RPR2;Nfibf/f, liver metastasis, rep2

value: liver metastasis


title: N2N1G, RPR2, LN metastasis, rep2


title: TBOEP 1uM rep3 [S154]

value: TBOEP 1uM


title: Pos Control HUMAN BRAIN rep4 [S99]

value: Pos Control HUMAN BRAIN


title: Pos Control HUMAN UNIVERSAL rep3 [S5]

value: KGN

value: Pos Control HUMAN UNIVERSAL


title: 1399M4, RPR2;Nfibf/f, liver metastasis, rep1


title: Pos Control HUMAN UNIVERSAL rep1 [S101]

value: Human ovarian granulosa cells


title: Pos Control HUMAN BRAIN rep3 [S6]


title: 1398P2, RPR2;Nfibf/f, lung tumor, rep2


title: 1398P2, RPR2;Nfibf/f, lung tumor, rep1


title: 1398M1, RPR2;Nfibf/f, liver metastasis, rep1


title: 1373M1, RPR2, liver metastasis, rep2


title: Neg Control LYIS BUFFER rep4 [S97]

value: Neg Control LYIS BUFFER


title: Pos Control HUMAN BRAIN rep2 [S3]


title: 12N1G, RPR2, LN metastasis, rep2


title: Pos Control HUMAN BRAIN rep1 [S102]


title: Neg Control LYIS BUFFER rep3 [S4]


title: 1373M1, RPR2, liver metastasis, rep1


title: 1398M1, RPR2;Nfibf/f, liver metastasis, rep2


title: Neg Control LYIS BUFFER rep2 [S100]


title: 12N1G, RPR2, LN metastasis, rep1


title: Pos Control HUMAN UNIVERSAL rep4 [S98]


title: IPPP 3.2uM rep5 [S84]

value: IPPP 3.2uM


title: Neg Control LYIS BUFFER rep1 [S1]


title: Pos Control HUMAN UNIVERSAL rep2 [S2]


title: 1399P1, RPR2;Nfibf/f, lung tumor, rep1


title: B78 mt.12436 40% tumour sample n=6

data_processing:
featureCounts
Supplementary files format and content: featureCounts

source_name: fragment from a subcutaneous tumour

extract_protocol:
Samples were extracted by GeneWIZ
Library was constructed by GeneWIZ


title: B78 mt.12436 40% tumour sample n=7


title: IPPP 3.2uM rep4 [S52]


title: IPPP 3.2uM rep2 [S175]


title: B78 mt.12436 40% tumour sample n=5


title: IPPP 3.2uM rep3 [S180]


title: B78 mt.12436 40% tumour sample n=4


title: B78 mt.12436 40% tumour sample n=3


title: B78 mt.12436 40% tumour sample n=2


title: IPPP 3.2uM rep1 [S132]


title: IPPP 20uM rep4 [S54]

value: IPPP 20uM


title: IPPP 20uM rep3 [S191]


title: B78 mt.12436 60% tumour sample n=7


title: IPPP 20uM rep2 [S182]


title: B78 mt.12436 60% tumour sample n=6


title: B78 mt.12436 40% tumour sample n=1


title: IPPP 1uM rep4 [S51]

value: IPPP 1uM


title: IPPP 20uM rep5 [S86]


title: IPPP 20uM rep1 [S148]


title: IPPP 1uM rep5 [S83]


title: B78 mt.12436 60% tumour sample n=1


title: B78 mt.12436 60% tumour sample n=4


title: B78 control tumour sample n=004

value: WT


title: IPPP 1uM rep1 [S124]


title: B78 mt.12436 60% tumour sample n=3


title: B78 control tumour sample n=003


title: IPPP 1uM rep3 [S179]


title: B78 mt.12436 60% tumour sample n=2


title: IPPP 10uM rep5 [S85]

value: IPPP 10uM


title: B78 control tumour sample n=002


title: IPPP 1uM rep2 [S167]


title: B78 control tumour sample n=001


title: IPPP 10uM rep4 [S53]


title: B78 mt.11944 60% tumour sample n=5


title: IPPP 10uM rep2 [S181]


title: B78 mt.12436 60% tumour sample n=5


title: IPPP 10uM rep3 [S183]


title: B78 mt.11944 60% tumour sample n=4


title: IPPP 10uM rep1 [S140]


title: IPPP 0.32uM rep3 [S178]

value: IPPP 0.32uM


title: IPPP 0.32uM rep5 [S82]


title: B78 mt.11944 60% tumour sample n=2


title: IPPP 0.32uM rep4 [S50]


title: IPPP 0.32uM rep2 [S159]


title: B78 mt.11944 60% tumour sample n=1


title: B78 mt.11944 40% tumour sample n=6


title: B78 mt.11944 40% tumour sample n=5


title: BPDP 3.2uM rep5 [S79]

value: BPDP 3.2uM


title: B78 mt.11944 60% tumour sample n=3

value: fragment from a subcutaneous tumour


title: BPDP 3.2uM rep3 [S28]


title: B78 mt.11944 40% tumour sample n=1


title: B78 mt.11944 40% tumour sample n=4


title: IPPP 0.32uM rep1 [S116]


title: B78 mt.11944 40% tumour sample n=2


title: BPDP 3.2uM rep4 [S76]


title: BPDP 3.2uM rep2 [S164]


title: BPDP 3.2uM rep1 [S134]


title: B78 control tumour sample n=5


title: BPDP 20uM rep5 [S95]

value: BPDP 20uM


title: B78 control tumour sample n=4


title: B78 control tumour sample n=3


title: BPDP 20uM rep3 [S30]


title: B78 control tumour sample n=2


title: B78 control tumour sample n=1


title: BPDP 20uM rep1 [S150]


title: B78 control cells n=4

value: Melanoma cells


title: B78 control cells n=3


title: B78 mt.11944 40% tumour sample n=3


title: B78 control cells n=2


title: BPDP 1uM rep5 [S75]

value: BPDP 1uM


title: BPDP 1uM rep2 [S163]


title: BPDP 1uM rep3 [S27]


title: B78 control cells n=1


title: BPDP 1uM rep1 [S126]


title: BPDP 1uM rep4 [S71]


title: B78 control tumour sample n=6


title: B78 mt.11944 60% cells n=2


title: BPDP 10uM rep4 [S77]

value: BPDP 10uM


title: BPDP 10uM rep5 [S87]


title: BPDP 20uM rep4 [S78]


title: B78 mt.11944 60% cells n=3


title: BPDP 10uM rep3 [S29]


title: BPDP 10uM rep1 [S142]


title: B78 mt.12436 60% cells n=4


title: B78 mt.12436 60% cells n=3


title: BPDP 10uM rep2 [S165]


title: BPDP 20uM rep2 [S166]


title: BPDP 0.32uM rep5 [S74]

value: BPDP 0.32uM


title: B78 mt.11944 60% cells n=4


title: B78 mt.12436 60% cells n=2


title: BPDP 0.32uM rep4 [S63]

value: KGN


title: B78 mt.11944 60% cells n=1


title: RNASeq, Yap-activated tumor, rep2

city: TORONTO

first: Haiyang

last: Guo

address: 101 College Street, 11-601D, TMDT, 11-601D, TMDT

department: Princess Margaret Cancer Centre

institute: UNIV HEALTH NETWORK

data_processing:
The trimmed pair-end reads were aligned to mouse reference genome (GRCm38) with STAR (version 2.4.2a), and the raw read count matrix was used for differential gene expression analysis by DESeq2.
Assembly: mm10
Supplementary files format and content: The .txt file contains raw read counts of all RNASeq samples.

source_name: Gastric corpus epithelial cells

growth_protocol: Cells were isolated without culturing

extract_protocol:
Gastric corpus is dissected and epithelial cells are isolated using EDTA. Total RNA was then extracted using RNeasy mini kit (QIAGEN, 74104).
Whole transcriptome sequencing libraries were prepared using TruSeq® Stranded mRNA Library Prep Kit (RS-122-2101, Illumina, San Diego, CA, USA) by following the manufacturer’s instructions.
RNA-Seq (50bp PE)

treatment_protocol: Mice were administered 2mg tamoxifen intraperitoneally for 5 consecutive days, and were subsequently fed DOX food for 14 days directly before endpoint

tag: disease state

value: Yap-activated gastric cancer

value: Gastric corpus epithelium


title: BPDP 0.32uM rep2 [S162]

value: Human ovarian granulosa cells


title: RNASeq, Yap-activated tumor, rep3


title: BPDP 0.32uM rep3 [S26]


title: RNASeq, Normal Stomach, rep3

value: Normal Stomach


title: 0.5% DMSO rep10 [S81]

value: 0.5% DMSO


title: RNASeq, Normal Stomach, rep1


title: RNASeq, Yap-activated tumor, rep1


title: B78 mt.12436 60% cells n=1