title: PN H3K4me3 biol rep 2

data_processing:
Data was processed from Basepair Tech's CUT&RUN pipeline. Raw reads were trimmed using fastp to remove low-quality bases from reads (quality < 20) and adapter sequences. Trimmed reads were aligned using Bowtie2 [1] to UCSC genome assembly   mm10. Duplicate reads were removed using Sambamba [2] and bigwig files were created for   visualization using deeptools [3]. Peaks were identified with MACS2 [4] and transcription factor   binding motifs were detected with Homer [5]. Peaks overlapping with Satellite repeat regions   were discarded and remaining filtered peaks were annotated using custom scripts based on   UCSC gene models, where peaks between −2500 and 2500 bp of a transcription start site were   marked as “Promoter”, the overlapping gene body were marked as “Gene body” and the rest   were marked as “Intergenic”. For intergenic peaks, a gene was considered a target if it was   within 1 Mb of the peak.
Supplementary files format and content: bigwig
Library strategy: CUT&RUN

extract_protocol:
Extraction was prepared using Epicypher CUT&RUN Kit using the protocol for nuclei extraction (appendix I)
Library was prepared using Epicypher CUT&RUN Kit

treatment_protocol: 4T1 cells were treated with 0.5 µM Reversine for 48 hours before micronuclei isolation (Toufektchan E and Maciejowski J, STAR Protoc. 2021)

tag: cut&run antibody

value: H3K4me3 (Epicypher #13-0041)

value: Reversine 0.5 uM 48 hours


title: PN H3K4me3 biol rep 1

status: Public on Mar 13 2023

type: SRA

city: New York

first: Albert

middle: S

last: Agustinus

state: New York

address: 408 East 69th Street, Room 419-G

country: USA

institute: Memorial Sloan Kettering Cancer Center

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

growth_protocol: 4T1 cells were grown in RPMI media supplemented with 10% FBS and 1X Pen-Strep in 245x245 mm dish (Corning   Corning™ TC-Treated Culture Dishes)

tag: strain

value: BALB/c

tag: cell line

tag: cell type

value: 4T1 TNBC Breast Cancer Cells

tag: treatment


title: MN ruptured H3K4me3 biol rep 2


title: A97

type: genomic

city: Utrecht

first: Judith

middle: M.

last: Boer

address: Heidelberglaan 25

country: Netherlands

institute: Prinses Maxima Centrum

hyb_protocol: Agilent Oligo aCGH Hybridization Kit was used according to manufacturer's protocol.

scan_protocol: The Agilent G4449A arrays were scanned using an Agilent scanner. Agilent feature extraction software (version 10.5.1.1) was used to extract the data.

data_processing:
Data was processed using R-version 2.14.1. Limma version 3.10.2 (Bioconductor) was used to generate a logRatio matrix for unique probes. CGHcall version 2.14.0 (Bioconductor) was used to normalize the data, NoWave (from: van de Wiel et al., 2009, Bioinformatics) was used to dewave the data, CGHnormaliter version 1.9.1 (Bioconductor) was used to centralize the data (see Ratios.txt file). CGHcall was further used to segment the data (see Segmented.txt file).
Normalized signal intensity, log2 scale

organism: Homo sapiens

source_name: leukemic blast, blast percentage >90%

label_protocol: 1 ug of DNA was labelled using the Agilent Genomic DNA ULS Labeling kit 5190-0420, according to manufacturer's protocol.

growth_protocol: Primary human leukemic cells were isolated at initial diagnosis (blast percentage >90%).

extract_protocol: Trizol extraction of gDNA was performed according to the manufacturer's instructions.

tag: diagnosis

value: pediatric acute lymphoblastic leukemia

tag: all subtype

value: B-other

value: primary leukemic cells

source_name: reference genomic DNA male pool

tag: sample type

value: reference

tag: Sex

value: male


title: A94


title: MN ruptured H3K4me3 biol rep 1


title: A103


title: A93


title: A95


title: A96


title: A92


title: MN intact H3K4me3 biol rep 1


title: MN intact H3K4me3 biol rep 2


title: A91


title: A89


title: STW1

city: Changsha

first: Kailin

last: Yang

state: Hunan

address: Xueshi Road No. 300

country: China

institute: Hunan University of Chinese Medicine

library_source: transcriptomic

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.

molecule: total RNA

source_name: decidual tissue

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

tag: tissue

value: decidual tissue

tag: genotype

value: CBA/J mice x  DBA/2 mice

value: STW + Recurrent miscarriage model


title: A88


title: Model3

value: Recurrent miscarriage model


title: Model1


title: Model2


title: A84


title: A87


title: STW2


title: Control3

value: CBA/J mice x BALB/c mice


title: A83


title: Control2


title: A85


title: Control1


title: Model4


title: A86


title: Scramble-treated Sample 4

city: Dublin

last: Sanfeliu

address: 123 St. Stephen's Green

country: Ireland

institute: Royal College of Surgeons in Ireland

description:
Scr4
gene_count.xls
gene_count.csv
gene_FPKM.xls
gene_FPKM.csv

data_processing:
Base Calling using Casava 1.8
Filtering: Removal of reads containing adapters, reads containing N > 10% and reads with Q Score < 5 in > 50% of nucleotides
Alingment to mm10 genome using HISAT2 v2.0.5
Quantification of gene expression using featureCounts v1.5.0-p3
Fragments per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) calculated using a protocol by Trapnell et al. Nature Biotechnology 2010
Assembly: mm10
Supplementary files format and content: .csv and .xlsx files containing matrices with raw count and FPKM values corresponding to each gene and sample

source_name: Hippocampus

extract_protocol:
Trizol-chlorophorm extraction
Standard Illumina Protocol

value: Hippocampus

value: N4 Ube3am-/p+

value: Scramble

tag: procedure

value: Audiogenic seizure induction


title: A78


title: A79


title: A82


title: Littlemate control

city: Boston

first: jinzhi

last: duan

state: Massachusetts

address: 6th Floor, Room 641, NRB, 77 Louis Pasteur Avenue

institute: Brigham and Women' hospital

library_source: transcriptomic single cell

data_processing:
Cellranger count 3.1.0
Assembly: mm10
Supplementary files format and content: h5 Expression Matrices

source_name: small intestine epithelial cell

extract_protocol:
20k SI  (CD45-EpCAM+) small intestine epithelial cells from  SubAA273IEC and littermate control  were FACS-sorted for sequencing.
The sorted live cells were separated into a single droplet using the Chromium Single Cell 3' v3 kit  according to the manufacturer’s instruction (10x Genomics) and RNA libraries were prepared for sequencing using standard protocols.


title: A80


title: A77


title: Scramble-treated Sample 2

description:
Scr2
gene_count.xls
gene_count.csv
gene_FPKM.xls
gene_FPKM.csv


title: A76


title: A75


title: AML4_shELAV1-7_2

city: Toronto

first: Kristin

last: Hope

address: 101 College St.

country: Canada

institute: University of Toronto

data_processing:
Reads were quality checked using fastQC
Sequencing reads were aligned to the hg38 reference genome using STAR (v2.7.2c)
Gene-level quantification was performed using RSEM (v1.3.1)
Assembly: hg38
Supplementary files format and content: count_matrix.tsv (matrix of gene counts)

molecule: polyA RNA

source_name: Bone Marrow

growth_protocol: Cells were cultured for 48h in SFEM II supplemented with IL-6, TPO, SCF, FLT3-L and IL-3

extract_protocol:
RNA from 100k sorted transduced cells were extracted using Trizol LS according to manufacturer’s protocol
PolyA+ RNA libraries were generated using NEBNext PolyA mRNA Magnetic Isolation Module (E7490) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760L) and indexed using NEBNext Multiplex Oligos for Illumina (E6440L).

treatment_protocol: Lentiviral infection with shScramble or shELAVL1 for 48h

value: Bone Marrow

value: Bulk AML cells


title: AML4_shELAV1-7_3


title: Scramble-treated Sample 3

description:
Scr3
gene_count.xls
gene_count.csv
gene_FPKM.xls
gene_FPKM.csv


title: Scramble-treated Sample 1

description:
Scr1
gene_count.xls
gene_count.csv
gene_FPKM.xls
gene_FPKM.csv


title: A72


title: AML4_shELAV1-7_1


title: A71


title: A70


title: Antagomir-134-treated Sample 5

description:
Ant5
gene_count.xls
gene_count.csv
gene_FPKM.xls
gene_FPKM.csv

value: Antagomir 134


title: AML4_shScr_2

value: shScr


title: AML4_shScr_3


title: Antagomir-134-treated Sample 4

description:
Ant4
gene_count.xls
gene_count.csv
gene_FPKM.xls
gene_FPKM.csv


title: SubAA273IEC

source_name: small intestine epithelial  cell


title: AML4_shScr_1


title: A68

value: pediatric acute lymphoblastic leukemia

value: B-other


title: A81

value: primary leukemic cells

value: reference


title: A67

value: male


title: Antagomir-134-treated Sample 3

description:
Ant3
gene_count.xls
gene_count.csv
gene_FPKM.xls
gene_FPKM.csv


title: A65


title: CD8 T cell_Gal3 KO

type: RNA

city: Buffalo

first: Hemn

last: Mohammadpour

state: NY

address: Elm and Carlton Sts.

institute: Roswell Park Comprehensive Cancer Center

description: sorted live, H-2Kb+CD45+CD3+

hyb_protocol: Samples were submitted to the Roswell Park Genomic Shared Resources; Follow manufacturer's specification (Nanostring Technologies)

scan_protocol: nCounter™ Digital Analyzer

data_processing: Nanostring Nsolver software

source_name: spleen

growth_protocol: BALB/c mice were irradiated with a single dose of irradiation at 8.5 Gy from a Cs-137 source. One day after irradiation, mice received tail vein injections of 3.5x10^6 T cell depleted bone marrow cells from a WT C57BL/6 mice and 0.7x10^6 pan T cells isolated from the spleen of WT or Gal3-/- C57BL/6 mice.

extract_protocol: The purification of total and small RNAs is prepared using the miRNeasy mini kit (Qiagen).  10-50 mg of frozen samples, with the addition of 700 ul of Qiazol reagent, are first homogenized using Navy Rhino tubes in a Bullet Blender Homogenizer (Next Advance) for 5 minutes.  RNA is isolated by chloroform extraction, and ethanol is added to provide appropriate binding conditions for all RNA molecules from 18 nucleotides upwards. The sample is then applied to the miRNeasy Mini spin column.  On-column DNAse digestion is also performed to remove any residual genomic DNA contamination followed by additional washes.  High quality RNA is then eluted in 60 ul of RNase-free water.  Quantitative assessment of the purified total RNA is then accomplished by using a Qubit Broad Range RNA kit (Thermofisher), and concentration is determined by Ribogreen fluorescent binding to isolated RNA.  The RNA is further evaluated qualitatively using RNA Nanotape on the 4200 Tapestation (Agilent technologies), where sizing of the RNA is determined, and a qualitative numerical score (RINe) is assigned.

treatment_protocol: At D7 after allo-HCT, CD4+ and CD8+ T cells (live, H-2Kb+CD45+CD3+)  were sorted from the spleen using BD FACSAria. 5-6 mice were pooled prior to sorting. Sorted cells were immediately frozen in liquid nitrogen and stored at -80C or on dry ice.

tag: host strain

value: BALB/c

tag: donor strain


title: A64


title: A61


title: A74


title: CD8 T cell_WT

description: sorted live, H-2Kb+CD45+CD3+

label_protocol: Samples were submitted to the Roswell Park Genomic Shared Resources; Follow manufacturer's specification (Nanostring Technologies)


title: A63


title: Antagomir-134-treated Sample 2

description:
Ant2
gene_count.xls
gene_count.csv
gene_FPKM.xls
gene_FPKM.csv


title: A58


title: A60


title: SF1KO_MaleMouse8

city: Los Angeles

first: Michel

middle: A

last: Zamojski

state: California

address: 8700 Beverly Boulevard

department: Regenerative Medicine Institute

institute: Cedars-Sinai Medical Center

data_processing:
Single Nuclei ATAC-seq data of snap-frozen pituitary samples were processed using Cell Ranger-ATAC pipeline version 1.2.0 with mm10 as the reference genome.
Assembly: mm10
Supplementary files format and content: Peak accessibility count matrices in Hierarchical Data Format HDF5 for cell barcodes.
Supplementary files format and content: Metadata files that include per barcode QC, ATAC signal and cell calling metrics in comma-separated values (CSV) format.
Supplementary files format and content: BED-like tabular files listing all unique fragments captured by the assay in tab-separated values (TSV) format.

source_name: Pituitary gland

growth_protocol: Animals were on a 12-hour on, 12-hour off light cycle, with lights on at 7 AM and off at 7 PM. Pituitaries were collected from male mice aged 10-12 weeks of mixed C57BL/6 x 129sv/ev background strains.

extract_protocol:
Snap-frozen pituitaries were thawed on ice. For nuclei isolation, a modified protocol from Mathys et al Nat 2019 was followed, all on ice. RNAse inhibitor (NEB MO314L) was added to the homogenization buffer (0.32 M sucrose, 1 mM EDTA, 10 mM Tris-HCl, pH 7.4, 5mM CaCL2, 3mM Mg(Ac)2, 0.1% IGEPAL CA-630), 50% OptiPrep (Stock is 60% Media from Sigma; cat# D1556), 35% OptiPrep and 30% OptiPrep right before isolation. Each pituitary was homogenized with 10 strokes (loose pestle) in an individual autoclaved dounce glass homogenizer (1ml, VWR cat# 71000-514). The homogenate was filtered through a 40-micrometer cell strainer. The volume was measured and an equal volume of 50% OptiPrep was added. The gradient was centrifuged using an SW41 rotor at 9200 rpm and at 4C for 25 min. Nuclei were collected from the interphase between 30% and 35% OptiPrep. The nuclei were washed, resuspended either in 1x nuclei dilution buffer for snATACseq (10X Genomics) or in 1X PBS/0.04% BSA for snRNAseq, and counted on an Invitrogen Countess II cell counter. ii) Dissociated pituitary cells were cryopreserved in 90% FBS/10% DMSO and shipped to New York on dry-ice. Upon arrival, cells were stored in liquid nitrogen. On the day of an experiment, the vial was removed from liquid nitrogen on dry-ice, thawed quickly in a 37C waterbath, and cells were serially diluted with 10% FBS /DMEM until a minimum volume of 8ml was reached. Cells were centrifuged at 300xg for 5min, resuspended in 1ml of medium and counted. Nuclei were isolated from all cells remaining after the scGEM Drop-seq RNA-seq assay was done. Cells were centrifuged at 500g for 5min at 4C. The supernatant was carefully removed and 0.1X lysis buffer (1x: 10mM Tris-HCL pH 7.5, 10mM NaCl, 3mM MgCl2, nuclease-free H2O, 0.1% v/v NP-40, 0.1% v/v Tween-20, 0.01% v/v digitonin) was added. After 5min incubation on ice, 1ml of wash buffer was added. The nuclei were pelleted at 500xg for 5min at RT, resuspended either in 1X PBS/0.04% BSA for scGEM Drop-seq RNA-seq or in diluted nuclei buffer for snATAC-seq. Nuclei were counted and the concentration adjusted to run the given assay.
snATACseq was performed as described (10x Genomics, Pleasanton, CA), following the Chromium Single Cell ATAC Reagent Kits V1 User Guide. Nuclei were counted on a Nexclome instrument, and the final concentration was used to calculate the volume of nuclei stock to use. Transposition was performed in 10 microliter at 37C for 60min. Then the Chromium Chip E (PN-2000121) was loaded to target up to 10,000 nuclei. Barcoding was performed in the emulsion for 12 cycles following the Chromium protocol. Each library was tagged with a different index for multiplexing (Chromium i7 Sample Index N, Set A kit PN-3000262). Quality control and quantification of the libraries were assessed on a Bioanalyzer (High-Sensitivity DNA Bioanalyzer kit). Sequencing was carried out at the NYGC on Illumina Novaseq using 98+26 paired-end reads.

value: C57BL/6 x 129sv/ev

tag: age

value: 10-12 weeks

tag: genotype/variation

value: gonadotrope-specific SF-1 (Nr5a1) knockout

value: snap-frozen pituitaries


title: CD4 T cell_Gal3 KO

description: sorted live, H-2Kb+CD45+CD3+


title: CD4 T cell_WT

description: sorted live, H-2Kb+CD45+CD3+


title: SF1Cont_MaleMouse4

value: control


title: A69


title: A57


title: A55


title: A56


title: FAPs_cKO_7dpi_rep2

city: Berlin

first: Georgios

last: Kotsaris

address: Thielallee, 63

country: Germany

institute: Freie Universität Berlin

data_processing:
Read mapping to the mouse genome (mm10) was performed using STAR in the Galaxy Europe platform, and differential gene expression analysis was performed using DESeq2. Transcripts per million (TPM) abundances were calculated from the mean normalized fragment counts given by DESeq2 for all samples.
Supplementary files format and content: mm10
Supplementary files format and content: Tab-delimited text files include TPM values for each Sample.

source_name: Tibialis anterior muscle

extract_protocol:
RNA was isolated using the Micro RNA Kit (Zymo Research), the RNA concentration was measured using a QubitFluorometer (Invitrogen), and the quality of the RNA yield was measured with the Bioanalyzer 2100 (Agilent).
After quality control using Agilent’s Bioanalyzer sequencing libraries were prepared from 100ng of total RNA per sample following Roche’s stranded “KAPA RNA HyperPrep” library preparation protocol for dual indexed Illumina libraries: First the polyA‐RNA fraction was enriched using oligo‐dT‐probed paramagnetic beads. Enriched RNA was heat‐fragmented and subjected to first strand synthesis using random priming. The second strand was synthesized incorporating dUTP instead of dTTP to preserve strand information. After A‐tailing Illumina sequencing compatible unique dual index adapters were ligated. Following bead‐based clean‐up steps the libraries were amplified using 11‐12 cycles of PCR. Library quality and size was checked with qBit, Agilent Bioanalyzer and qPCR. Sequencing was carried out on an Illumina HiSeq 4000 system in PE75bp mode

value: Tibialis anterior muscle

value: FAPs

value: Osr1 flox/flox CAGG Cre+

value: 7 days post injury


title: FAPs_cKO_7dpi_rep1


title: A54


title: SF1Cont_MaleMouse1


title: VTCN1 Knocked down 72h, replicate 2, RNAseq

city: Durham

first: Jie

last: Zhou

state: North Carolina

address: The Chesterfield Building 701 W. Main Street, Suite 510

department: OBGYN

institute: Duke University

description: Human human embryonic stem cell derived trophoblast

data_processing:
Initial base calling and quality filtering of the mRNA-seq reads generated with the Illumina analysis pipeline (fastQ format) were performed with the FastxToolkit (http://hannonlab.cshl.edu/fastx_toolkit/) and adapters trimmed by using CutAdapt (https://cutadapt.readthedocs.org/en/stable/).
Reads that mapped either to the human mitochondrial genome or to the internal Phix standard were removed through use of Bowtie software (http://bowtie-bio.sourceforge.net/index.shtml).
Reads were mapped (TopHat v2.0.13; http://ccb.jhu.edu/software/tophat/index.shtml) to the reference genome (from Ensembl, v78; http://www.ensembl.org/index.html; Homo_sapiens.GRCh38.dna.primary assembly.fa with Homo_sapiens.GRCh38.78.gtf as annotation).
Tests for differential expression were made by using cuffdiff v2.2.1. Uniquely mapped reads were counted with htseq-count v.011.1.
Gene expression levels were calculated in FPKM, considering gene length as a sum of all exonic nonoverlapping sequences of all isoforms of a given gene.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Human human embryonic stem cell

growth_protocol: Human ESCs (H1, WA01) were cultured in Matrigel (BD Bioscience)-coated, six-well tissue culture plates (Thermo Scientific) under an atmosphere of 5% (vol/vol) CO2/air at 37 °C in mTeSR1 medium (STEMCELL Technologies). The culture medium was changed daily and the cells were passaged every 5-6 days. The method for TB differentiation has been described previously[19]. Briefly, on the day after passaging onto Matrigel-coated dishes at 1.2 × 104 cells/cm2, the culture medium was changed to DMEM/F-12 medium (Thermo Scientific) with knock-out serum replacement (KOSR, Invitrogen) that had been conditioned by mouse embryonic fibroblasts (MEF) and supplemented with FGF2 (4 ng/mL).  After 24 h, the conditioned medium was replaced with daily changes of nonconditioned DME/F12/KOSR medium lacking FGF2, but containing BMP4 (10 ng/mL), A83-01 (1 μM), and PD173074 (0.1 μM) (BAP treatment) for up to 8 days. Control cultures were maintained in conditioned medium containing 4 ng/mL FGF2.

extract_protocol:
RNA was obtained from VTCN1 knock down or negative control siRNA transfected cells 24 h, 48 h and 72 h after transfection. RNA was extracted in STAT60 containing 1-bromo-3-chloro-propane (Sigma-Aldrich), and DNA removed by using the TURBO-DNA-free kit (Ambion Inc.).
cDNA libraries were constructed by standard methods (Illumina TruSeq mRNA stranded kit) with index adapters (Illumina TruSeq indexes).

treatment_protocol: For small interfering RNA (siRNA)-mediated knockdown of VTCN1, differentiated hESCs were transfected with either a VTCN1 human siRNA oligo duplex (Origene, SR312516, 10nM) or a control, Trilencer-27 Universal scrambled negative control siRNA duplex (Origene, SR30004, 10 nM) on BAP treatment d 3 by using Lipofectamine 2000 (Invitrogen). After 6 h, the medium was replaced with BAP medium.

value: Human human embryonic stem cell

value: VTCN1 knockdown

value: BMP4, A83-01 and PD173074 treatment

tag: time

value: Day 6


title: VTCN1 Knocked down 72h, replicate 3, RNAseq


title: VTCN1 Knocked down 72h, replicate 1, RNAseq


title: Antagomir-134-treated Sample 1

description:
Ant1
gene_count.xls
gene_count.csv
gene_FPKM.xls
gene_FPKM.csv

value: Hippocampus

value: N4 Ube3am-/p+

value: Antagomir 134

value: Audiogenic seizure induction


title: FAPs_Ctrl_7dpi_rep2

value: Osr1 flox/+ CAGG Cre+


title: control 72h, replicate 3, RNAseq

value: WT


title: OVA Mcemp1-/- 4 [OVA_KO4]

city: Cleveland

first: Youn Jung

last: Choi

email: choiy4@ccf.org, younjung514@gmail.com

state: OH

address: 9500 Euclid Ave, NE2-251

department: Cancer biology

institute: Cleveland Clinic Lerner Research Institute

data_processing:
Fastq files were analyzed with Partek Flow (Build 10.0.21.1026). This includes quality control, alignment to mm10 with STAR, peak filtering, normalization, and differential gene expression.
Genome_build: mm10

source_name: lung

extract_protocol:
RNA from PCMC was extracted using RNeasy Mini Kit (74104) from QIAGEN.
The RNA-seq library was prepared using the KAPA mRNA HyperPrep Kit (KR1352), according to manufacturers’ instructions.

value: lung


title: A52

value: pediatric acute lymphoblastic leukemia

value: primary leukemic cells

value: reference

value: male


title: FAPs_Ctrl_7dpi_rep1

value: Tibialis anterior muscle

value: FAPs


title: control 72h, replicate 2, RNAseq

value: Human human embryonic stem cell


title: OVA Mcemp1-/- 3 [OVA_KO3]


title: A51


title: control 72h, replicate 1, RNAseq


title: OVA Mcemp1-/- 1 [OVA_KO1]


title: OVA Mcemp1-/- 2 [OVA_KO2]


title: A59


title: FAPs_Ctrl_3dpi_rep2

value: 3 days post injury


title: VTCN1 Knocked down 48h, replicate 3, RNAseq

value: VTCN1 knockdown

value: BMP4, A83-01 and PD173074 treatment

value: Day 5


title: Saline Mcemp1-/- 3 [SAL_KO3]


title: VTCN1 Knocked down 48h, replicate 2, RNAseq


title: FAPs_Ctrl_3dpi_rep1


title: A48

value: B-other


title: Saline Mcemp1-/- 2 [SAL_KO2]


title: VTCN1 Knocked down 48h, replicate 1, RNAseq


title: A47


title: A46


title: Saline Mcemp1-/- 1 [SAL_KO1]


title: Sciatic nerve 5 month WT - control - rep6 [SK24]

first: Diane

middle: Berengere

last: Re

address: 630 West 168th Street

department: Environmental Health Sciences

institute: Columbia University

data_processing:
RTA software (Illumina) was used for base-calling.
bcl2fastq2 (version 2.17) was used for converting BCL to fastq format, coupled with adaptor trimming.
Reads passing quality control (Phred score > 30) were mapped to a reference genome (Mouse: UCSC/mm10) using STAR (2.5.2b) and featureCounts (v1.5.0-p3) with the following parameters:
STAR:  STAR --genomeDir $genomeDir \  --readFilesCommand zcat \  --runThreadN 8 --outSAMtype BAM SortedByCoordinate \  --outSAMunmapped Within \  --quantMode GeneCounts \  --outReadsUnmapped Fastx \  --outFilterType BySJout \  --alignSJoverhangMin 8 \  --alignSJDBoverhangMin 1 \  --outFilterMismatchNmax 999 \  --outFilterMismatchNoverLmax 0.04 \  --readFilesIn "${fastqOneList[*]}" "${fastqPairList[*]}" \  --outFileNamePrefix $outputDir/${sample}. \  --outTmpDir $tmpdir    FeatureCounts:   featureCounts -T 4 -t $feature -a $annotation -s $str -g $grouper -o $outputDir/$sample.counts $bam
Raw counts were normalized using DESeq2 (v1.34.0).
Features with no counts or only a single count across all samples were filtered. Additional filtering was performed using the mean of normalized counts as a filter statistic.
Perform additional filtering to specify that at least 4 samples have a feature count of 10 or higher.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file with raw gene counts for every gene and every sample.
Supplementary files format and content: Comma-separated values (.csv) file of normalized counts for N=22 samples included in analysis (exclude sample SK05 and SK16), for genes passing filters.

source_name: Sciatic nerve 5 month WT - control

extract_protocol:
Total RNA (~200 ng per sample) was extracted from freshly removed sciatic nerves using the Invitrogen PureLink™ RNA Mini Kit (Cat#12183018A) following the manufacturer's instructions.
RNA libraries were prepared for sequencing according to Illumina's instructions accompanying the TruSeq Stranded mRNA kit (Cat#20020594), which uses poly-A pull-down to enrich mRNAs from total RNA samples.

value: sciatic nerve

value: 5 months

value: wild type


title: Sciatic nerve 5 month WT - control - rep5 [SK23]


title: A45


title: FAPs_cKO_3dpi_rep2

value: Osr1 flox/flox CAGG Cre+


title: control48h, replicate 3, RNAseq

value: WT


title: control 48h, replicate 2, RNAseq


title: A50

value: pediatric acute lymphoblastic leukemia


title: OVA wild-type 4 [OVA_WT4]

value: Wild type

value: lung


title: OVA wild-type 3 [OVA_WT3]


title: FAPs_cKO_3dpi_rep1


title: control 48h, replicate 1, RNAseq


title: A43

value: primary leukemic cells

value: reference

value: male


title: Sciatic nerve 5 month WT - control - rep3 [SK21]


title: OVA wild-type 1 [OVA_WT1]


title: A42


title: Sciatic nerve 5 month WT - control - rep2 [SK20]


title: VTCN1 Knocked down 24h, replicate 2, RNAseq

value: Human human embryonic stem cell

value: Day 4


title: Saline wild-type 3 [SAL_WT3]


title: Sciatic nerve 5 month WT - control - rep1 [SK19]


title: A41


title: A40


title: Sciatic nerve 24 month WT rep6 [SK18]

source_name: Sciatic nerve 24 month WT

value: 24 months


title: Saline wild-type 2 [SAL_WT2]


title: control 24h, replicate 3, RNAseq

value: BMP4, A83-01 and PD173074 treatment


title: VTCN1 Knocked down 24h, replicate 1, RNAseq

value: VTCN1 knockdown


title: Sciatic nerve 24 month WT rep5 [SK17]


title: Saline wild-type 1 [SAL_WT1]


title: A39

value: B-other


title: OVA wild-type 2 [OVA_WT2]


title: A44


title: Hypoxic renal single cell multiome ATAC

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

data_processing:
bcl2fastq/2.15.0.4
cellranger-arc/2.0.0
Genome_build: base on 10x refdata-cellranger-mm10-1.2.0
Genome_build: The tail of gene Epo was elongated by 1kb chr5:137,481,020-137,485,852
Supplementary_files_format_and_content: tab-delimited text files include ATAC peak read count values and mRNA molecule count values for each Sample

source_name: Hypoxia treated Epo-Norn cell enriched sample

extract_protocol:
Mice exposed to 4 hours of CO (0.1%) induced hypoxia. Kidney FACS sorted cells merged from 5 mice.
Sorted cells were processed according to 10x Genomics Chromium Single Cell Multiome ATAC+ Gene Expression low cell number protocol according to protocol number CG000365_DemonstratedProtocol_NucleiIsolation_ATAC_GEX_Sequencing_RevB used for cell lysis (0.1x lysis buffer and lysed for 7 min) to obtain intact nuclei. Single cell ATAC and RNA-seq libraries were prepared using the Chromium single cell multiome ATAC + gene expression platform (10x Genomics). Nuclei were prepared and counted to ensure quality and concentration. Nuclei were then transposed according to the manufacturer’s protocol.  Transposed nuclei suspension was loaded onto Next GEM Chip J targeting 5000 nuclei and then ran on a Chromium Controller instrument to generate GEM emulsion (10x Genomics). Single-cell gene expression libraries, as well as single cell ATAC-seq libraries, were generated according to the manufacturer’s protocol using the Chromium Next GEM Single Cell multiome ATAC+ gene expression kit. Final libraries were quantified using NEBNext Library Quant Kit for Illumina (NEB) and high sensitivity D1000 TapeStation (Agilent). Each library was sequenced separately on a NovaSeq 6000 instrument using an SP 100 cycles reagent kit (Illumina), targeting 25,000 reads/nuclei for ATAC-seq and a minimum of 20,000 reads/nuclei for gene expression.

tag: clinic status

value: Mouse kidney tissue

tag: sofa score

value: Epo-tdTomato transgenic mice

value: 10-12 weeks

value: male and female

tag: clinical outcome


title: Sciatic nerve 5 month WT - control - rep4 [SK22]

tag: strain

value: sciatic nerve

value: 5 months

value: wild type


title: Sciatic nerve 24 month WT rep3 [SK15]


title: A38

value: pediatric acute lymphoblastic leukemia

tag: cell type


title: Hypoxic renal single cell multiome RNA


title: A37

tag: diagnosis

value: high hyperdiploid

value: primary leukemic cells


title: control 24h, replicate 2, RNAseq

tag: cell line

value: WT

tag: treatment


title: Sciatic nerve 24 month WT rep2 [SK14]


title: A49

tag: all subtype

tag: sample type

value: reference

tag: Sex

value: male


title: GenolabM_B1-2

city: Tomsk

first: Irina

last: Larionova

state: Tomsk oblast

address: Lenin Ave, 36, Tomsk, Tomsk Oblast, Russia

country: Russia

institute: Tomsk State University

description:
Whole transcriptome probes
Instrument model used to produce the reads: GeneMind Genolab M
GenolabM_B1-2
Please note that the assigned instrument model "Illumina NovaSeq 6000" is a placeholder. The correct instrument model is: Genolab M

data_processing:
Raw sequencing reads were primary processed in the Space Ranger v.1.3 using the count command with default parameters. Raw reads were additionally assessed with FastQC quality control algorithm, and results were visualized with MultiQC tool.
After read mapping and counting, resulted feature-barcode matrix was uploaded into R environment and processed via the Seurat R package.
Normalization of the raw read counts in feature-barcode matrix was performed with the SCTransform function in the Seurat package.
Following dimension reduction and clusterization steps, the SCT normalized counts were used in Wilcoxon rank sum test to find differentially expressed genes.
Assembly: hg38
Supplementary files format and content: .h5 Filtered HDF5 Feature-Barcode Matrix
Supplementary files format and content: .json Scale factors for slide images
Supplementary files format and content: .png High resolution slide images
Supplementary files format and content: .png Low resolution slide images
Supplementary files format and content: .csv Tissue spot positions
Library strategy: Spatial Transcriptomics

source_name: Ovarian cancer

extract_protocol:
Three tumor FFPE samples obtained from patients with high-grade serous ovarian cancer were analyzed. Patients were treated in the Department of Gynecological Oncology, Cancer Research Institute of Tomsk National Research Medical Center (Tomsk, Russia). The study was carried out according to Declaration of Helsinki (from 1964, revised in 1975 and 1983) and was approved by the local committee of Medical Ethics of Tomsk Cancer Research Institute; all patients signed informed consent for the study. Shortly, FFPE tissue sections were placed on the Capture Areas of 10x Genomics Visium slides, deparaffinized, and stained by hematoxylin and eosin. Tumor tissue slides were scanned using the Leica Aperio AT2 station (Leica, Germany) and images were processed with Aperio ScanScope.
Libraries were prepared using standard protocol provided by 10x Genomics (User Guide | CG000407). The obtained cDNA libraries were analyzed following 10x Genomics sequencing recommendation for FFPE Visium libraries. Sequencing cycles comprised 28 bp (Read 1), 10 bp (Index 1 and 2) and 50 bp (Read 2). Illumina NextSeq 2000 sequencing was performed using NextSeq 1000/2000 P2 reagents (100 cycles), whereas GeneMind Genolab M used FCM reagents (150 cycles).

tag: tissue

value: Ovarian cancer

tag: disease state

tag: patient

tag: slide

tag: area


title: A36


title: VTCN1 Knocked down 24h, replicate 3, RNAseq

value: Human human embryonic stem cell

tag: genotype

value: BMP4, A83-01 and PD173074 treatment

tag: time

value: Day 4


title: Sciatic nerve 24 month WT rep1 [SK13]

tag: age

value: 24 months


title: GenolabM_A1-2

description:
Whole transcriptome probes
Instrument model used to produce the reads: GeneMind Genolab M
GenolabM_A1-2
Please note that the assigned instrument model "Illumina NovaSeq 6000" is a placeholder. The correct instrument model is: Genolab M


title: Kim_Sp_PC_VDJ

city: Saskatoon

first: Peter

middle: Dion

last: Pioli

state: SK

address: 107 Wiggins Rd

department: Biochemistry, Microbiology and Immunology

institute: University of Saskatchewan

description: VDJ Library.

data_processing:
cellranger count (v6.0.2) using the 'refdata-gex-mm10-2020-A' reference provided by 10x.
cellranger vdj (v6.0.2) using the 'refdata-cellranger-vdj-GRCm38-alts-ensembl-5.0.0' reference provided by 10x.
Genome_build: mm10

source_name: ASCs from spleen

extract_protocol:
ASCs from the bone marrow, spleen and thymus of 3 months old female and male Prdm1-eYFP mice were sorted on a BD Melody instrument. Each sort consisted of a pool of 3 mice and ASCs were gated as B220+/- CD138HI IgD- CD90.2- Prdm1-eYFP+. Sorted ASCs from each sex and organ were processed in individual GEM wells as separate samples on a 10x Genomics Chromium Controller.
5' Gene Expression (GEX) Libraries and VDJ Libraries were constructed following the manufacturer's guidelines using the Chromium Next GEM Single Cell 5' Library and Gel Bead Kit v1.1 (Catolog # 1000165) and Chromium Single Cell V(D)J Enrichment Kit, Mouse B Cell (Catolog # 1000072). VDJ Libraries were sequenced on an Illumina MiSeq. GEX Libraries were sequenced on a NovaSeq.

value: Prdm1-eYFP (The Jackson Laboratory, Strain # 008828)

value: Male

tag: background

value: spleen

value: antibody-secreting cells (ASCs)


title: A35

source_name: leukemic blast, blast percentage >90%

value: B-other


title: Kim_Thy_PC_VDJ

description: VDJ Library.

source_name: ASCs from thymus

tag: strain

value: thymus


title: Sciatic nerve 24 month WT rep4 [SK16]

description: excluded from analysis due to low mapping

value: sciatic nerve

value: wild type


title: Sciatic nerve 21 month WT rep6 [SK12]

source_name: Sciatic nerve 21 month WT

value: 21 months


title: A34

value: pediatric acute lymphoblastic leukemia

tag: cell type

value: primary leukemic cells

source_name: reference genomic DNA male pool


title: Sciatic nerve 21 month WT rep5 [SK11]


title: Kim_BM_PC_VDJ

description: VDJ Library.

source_name: ASCs from bone marrow

value: bone marrow


title: control 24h, replicate 1, RNAseq

value: WT


title: GenolabM_A1-1

description:
Whole transcriptome probes
Instrument model used to produce the reads: GeneMind Genolab M
GenolabM_A1-1
Please note that the assigned instrument model "Illumina NovaSeq 6000" is a placeholder. The correct instrument model is: Genolab M

value: Ovarian cancer


title: Bethyl_NIPBL RNAi r2

city: Vienna

first: Roman

middle: R

last: Stocsits

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP - Research Institute of Molecular Pathology

description: q-value (min. FDR) cutoff for significant regions is 0.05

data_processing:
Basecalling software: Illumina RTA
RNA polymerase II ChIP-Seq in mouse cells was performed without spike-in, and short-read sequencing data were mapped against the mm9 template using bowtie2
Illumina short read sequencing data for NIPBL/MAU2 were performed using calibration spike-ins (mouse) and aligned against a fusion genome template consisting of merged hg19 and mm9 assemblies.
NIPBL/MAU2 calibration by random subsampling of read counts after deduplication
Peak callings with MACS software versions 1.4 and 2 were applied on full, merged, filtered, and deduplicated replicate data sets of HA-tagged samples with corresponding depleted conditions (+dTAG) as input controls.
Assembly: hg19
Assembly: mm9
Supplementary files format and content: bigwig (*.bw) files containing ChIP-Seq profiles after full processing as described.
Supplementary files format and content: bedGraph (*.bdg) files containing ChIP-Seq profiles after full processing as described.

source_name: cervical carcinoma

growth_protocol: HeLa Kyoto (RRID:CVCL_1922) were got from Narumiya S (Kyoto University; Kyoto; Japan). MEFs were generated in the lab by 3T3 methods.

extract_protocol:
ChIP-Seq: Cells were cross-linked and scrapped of the plate. The DNA was fragmented and the protein of interest was immunoprecipitated with indicated antibodies; Adaptors were ligated to the 5' and 3' ends and the library was prepared for Illumina sequencing by a qPCR amplification step.
Libraries were prepared for sequencing using standard Illumina protocols. All antibodies used in this study were listed in Online Methods section 'Antibodies and Reagents'.

value: HeLa Kyoto

value: NIPBL knockdown

tag: chip antibody

value: NIPBL (Bethyl)


title: Bethyl_control r2

tag: cell line


title: Sciatic nerve 21 month WT rep4 [SK10]


title: A33

tag: diagnosis

value: high hyperdiploid

value: reference

value: male


title: Pete_Sp_PC_VDJ

description: VDJ Library.

value: Prdm1-eYFP (The Jackson Laboratory, Strain # 008828)

value: Female

value: spleen

value: antibody-secreting cells (ASCs)


title: Pete_Thy_PC_VDJ

description: VDJ Library.

value: thymus


title: A32

tag: all subtype

value: B-other


title: Bethyl_NIPBL RNAi r1

tag: treatment


title: Pete_BM_PC VDJ

description: VDJ Library.

tag: Sex


title: A31

value: pediatric acute lymphoblastic leukemia

tag: sample type


title: Bethyl_control r1


title: Sciatic nerve 21 month WT rep2 [SK08]

tag: tissue

value: sciatic nerve

value: 21 months

value: wild type


title: Kim_Thy_PC_GEX

description: Gene Expression Library.

value: Male


title: Sciatic nerve 21 month WT rep1 [SK07]


title: NCI-H520 cells, SIA-cIgG low, biol rep 2 [RNA-seq]

city: Nanjing

first: Xinmei

last: Huang

address: Zhongshan Road

institute: Nanjing Drum Tower Hospital

data_processing:
STAR v2.5.2b
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence by STAR.
Picard - tools v1.41 and samtools v0.1.18 were used to sort, remove duplicated reads and merge the bam alignment results of each sample. GATK3 or Samtools software was used to perform SNP calling.
HTSeq(v 0.5.4) was used to count the reads numbers mapped to each gene. Gene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped (FPKM).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Cell line

growth_protocol: NCI-H520 cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
RNA was quantified using Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA), the quality and integrity were assessed by NanoDrop spectrophotometer (Thermo Scientific). A total amount of 1.5 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB) following manufacturer’s recommendations.

treatment_protocol: NCI-H520 Cells were sorted by FACS into different bins based on their levels of SIA-cIgG.

value: Cell line

value: lung squamous carcinoma cells

value: SIA-cIgG low

value: FACS sorting


title: NCI-H520 cells, SIA-cIgG low, biol rep 3 [RNA-seq]


title: Kim_Sp_PC_GEX

description: Gene Expression Library.


title: A29

value: primary leukemic cells

value: reference


title: Kim_BM_PC_GEX

description: Gene Expression Library.

value: Prdm1-eYFP (The Jackson Laboratory, Strain # 008828)

value: bone marrow


title: Sciatic nerve 18 month WT rep6 [SK06]

source_name: Sciatic nerve 18 month WT

value: 18 months


title: A28

value: male


title: NCI-H520 cells, SIA-cIgG low, biol rep 1 [RNA-seq]


title: A27


title: NCI-H520 cells, SIA-cIgG high, biol rep 3 [RNA-seq]

value: SIA-cIgG high


title: A26

value: B-other


title: Pete_Sp_PC_GEX

description: Gene Expression Library.

value: Female

value: spleen

value: antibody-secreting cells (ASCs)


title: Sciatic nerve 18 month WT rep3 [SK03]

value: sciatic nerve

value: wild type


title: Pete_Thy_PC_GEX

description: Gene Expression Library.

value: thymus


title: NCI-H520 cells, SIA-cIgG high, biol rep 2 [RNA-seq]

value: Cell line

value: lung squamous carcinoma cells


title: Pete_BM_PC GEX

description: Gene Expression Library.


title: A24

value: pediatric acute lymphoblastic leukemia


title: Sciatic nerve 21 month WT rep3 [SK09]

value: 21 months


title: NCI-H520 cells, SIA-cIgG high, biol rep 1 [RNA-seq]

value: FACS sorting


title: A30

value: primary leukemic cells

value: reference


title: Sciatic nerve 18 month WT rep2 [SK02]

value: 18 months


title: A23

value: male


title: AB14044

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Well-barcode-RMT are extracted from the 7 first base pairs in the R2 fastq sequences. Unique-molecular-identifier are extracted from the subsequent 8 base pairs in the R2 sequences. R1 contains the genomic sequences.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error.
Genome_build: mm10
Genome_build: The tail of gene Epo was elongated by 1kb chr5:137,481,020-137,485,852
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

source_name: Epo-secreting Norn cells

extract_protocol:
Kidney single cell suspension: renal capsule was removed and the tissue minced with razor blades into 1 mm pieces. Each minced kidney was placed in 1 ml DMEM medium containing collagenase IV (Worthington Biochemical Cat no. LS004188, final concentration 0.25 mg/ml), neutral protease (Worthington Biochemical Cat no. LS02106, final concentration 0.25 mg/ml), and DNase (Roche Cat. no. 10104159001, final concentration 2000 U/ml), and incubated in a thermomixer at 37°C, 300 RPM, for 25-30 min. During this time, the suspension was passed 10 times through a 18G syringe and 8 times a 21 G syringe.
Single-cell RNA-seq libraries were prepared as previously described {Jaitin, 2014}. In brief, mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription, and the resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during ligation, RT, and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin, 2014}

tag: organ

value: kidney

value: Enriched gating for Epo-secreting Norn cells

tag: selection marker

value: normoxia

tag: mouse age

value: 6-8 weeks


title: A22

data_processing:
Data was processed using R-version 2.14.1. Limma version 3.10.2 (Bioconductor) was used to generate a logRatio matrix for unique probes. CGHcall version 2.14.0 (Bioconductor) was used to normalize the data, NoWave (from: van de Wiel et al., 2009, Bioinformatics) was used to dewave the data, CGHnormaliter version 1.9.1 (Bioconductor) was used to centralize the data (see Ratios.txt file). CGHcall was further used to segment the data (see Segmented.txt file).
Normalized signal intensity, log2 scale

extract_protocol: Trizol extraction of gDNA was performed according to the manufacturer's instructions.

value: B-other


title: AB14043


title: Sciatic nerve 18 month WT rep4 [SK04]

value: sciatic nerve

tag: genotype


title: Sciatic nerve 18 month WT rep5 [SK05]

description: excluded from analysis due to low RIN

value: wild type


title: A20


title: AB14041


title: T47D E2 + X15695 rep3

city: Nantes

first: Victor

last: GOURAIN

address: 30 Bd Jean Monnet

country: France

institute: Centre de recherche en transplantation et immunologie

data_processing:
read mapping with HISAT2 (v2.0.5)
gene expression quantification with featureCounts (v1.5.0-p3)
Assembly: GRCh38.p12
Supplementary files format and content: Count (quantification of reads at gene level)

growth_protocol: MCF-7, T47D, and LNCaP cells were cultured in RPMI 1640 supplemented with 10% FBS, 1% penicillin/streptomycin at 37°C in an incubator with 5% CO2 and 90% humidity. For experiments requiring hormone starvation, cells were cultured for 72 h in phenol red-free RPMI 1640 medium, supplemented with 3% charcoal-stripped fetal calf serum (CCS).

extract_protocol:
RNA was extracted using innuPREP RNA mini Kit 2.0 (Analytic Jena, Berlin, Germany). 1 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.

treatment_protocol: MCF-7 and T47D cells were treated with 10 nM 17-β-estradiol (E2) or dihydrotestosterone (DHT) for the LNCaP cells, 1 µM X15695 (for the MCF-7 and T47D cells) or 5 µM for LNCaP cells and X15695 together with E2 or DHT for the breast or prostate cancer cells.

value: Breast cancer cells

value: Estradiol + X15695


title: AB14040


title: Renal single cell mRNA1

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: refdata-cellranger-GRCh38-1.2.0
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: 10x_metadata_by_cell.txt

source_name: non-tumour kidney

extract_protocol:
Non-tumour portion were derived from partial or radical nephrectomies and collected into PBS on ice. Kidney samples were minced into 2-4mm and dissociated according to the manufacturer’s protocol of Multi Tissue Dissociation Kit 1 (Miltenyi Biotech, Cat# 130-110-201). Red blood cells (RBC) were removed by incubating the sample with 2mL RBC lysis for 3 minutes on ice. The sample was enriched to live cells using Dead Cell Removal Kit (Miltenyi Biotech, Cat# 130-090-101), centrifuged at 300G for 7min, resuspended in MACS buffer (PBS containing 2% FBS and 5 mM EDTA pH 8.0)
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Assortment of kidney cell types

value: non-tumour kidney

tag: indication

value: RCC


title: Renal single cell mRNA3

description: 10x Genomics


title: T47D E2 + X15695 rep2


title: T47D E2 + X15695 rep1


title: A18

last: Boer

address: Heidelberglaan 25

institute: Prinses Maxima Centrum

value: pediatric acute lymphoblastic leukemia


title: THP1 differentiated macrophages, treated with LN-18 glioma supernatant, rep 3

city: Clemson

first: Micaela

last: Scobie

state: SC

address: Clemson University

department: Biological Sciences

institute: Clemson University

data_processing:
Data quality control performed using FastQC and trimmed for paired end data with Trimmomatic v-0.36.
Reads were aligned to human reference genome GRCh38.p12 using GSNAP (Ensembl release 95 annotation), and mapped counts were summarized using Subread featureCounts (fragment length 50 – 600 base pairs).
Raw counts were analyzed with edgeR to estimate the common negative binomial dispersion by conditional maximum likelihood (CML).
Treatment effect was measured by calculating the log2 counts per million (CPM) of each gene and then using glm.ft to fit the generalized linear model.
Assembly: GRCh38.p12
Supplementary files format and content: counts_macro.txt: Tab-delimited text file includes logCPM values for each Sample.

extract_protocol:
mRNA was extracted and purified by poly-a-tail enrichment.
Strand-specific libraries were prepared by kit NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (NEB E7760).

value: monocyte cell line derived from acute monocytic leukemia patient

tag: condition

value: differentiated to macrophages with PMA

value: LN-18 supernatant

tag: time

value: Day 0


title: THP1 differentiated macrophages, treated with T98G glioma supernatant, rep 3

value: T98G supernatant


title: A19

city: Utrecht

first: Judith

value: primary leukemic cells

value: reference

value: male


title: THP1 differentiated macrophages, treated with LN-18 glioma supernatant, rep 2


title: A17


title: Sciatic nerve 18 month WT rep1 [SK01]

city: New York

tag: strain

tag: age

value: 18 months


title: AB14038

value: kidney

tag: cell type

value: Enriched gating for Epo-secreting Norn cells

value: Daily doses of tamoxifen for 5 days

value: normoxia

value: 6-8 weeks


title: AB14039


title: THP1 differentiated macrophages, treated with LN-18 glioma supernatant, rep 1

tag: cell line


title: SF1Cont_MaleMouse2

source_name: Pituitary gland

value: C57BL/6 x 129sv/ev

value: 10-12 weeks

tag: genotype/variation

value: control

value: snap-frozen pituitaries


title: THP1 differentiated macrophages, treated with T98G glioma supernatant, rep 1

value: monocyte cell line derived from acute monocytic leukemia patient

value: differentiated to macrophages with PMA


title: T47D X15695 rep3

value: Breast cancer cells


title: AB14037


title: THP1 differentiated macrophages, treated with T98G glioma supernatant, rep 2

value: T98G supernatant

value: Day 0


title: A16

tag: diagnosis

value: pediatric acute lymphoblastic leukemia

tag: all subtype

value: primary leukemic cells

value: reference


title: A21

tag: Sex

value: male


title: T47D X15695 rep2

tag: treatment


title: Renal single cell mRNA2

description: 10x Genomics

value: Assortment of kidney cell types

tag: tissue

value: non-tumour kidney

value: RCC


title: AB14042

tag: organ

value: kidney

value: Enriched gating for Epo-secreting Norn cells

value: normoxia

value: 6-8 weeks


title: THP1 differentiated macrophages, control, rep 3


title: AB14036

tag: selection marker

value: Daily doses of tamoxifen for 5 days


title: T47D X15695 rep1


title: THP1 differentiated macrophages, control, rep 2

value: monocyte cell line derived from acute monocytic leukemia patient


title: A14

value: B-other

tag: sample type


title: AB14035

tag: mouse age


title: THP1 differentiated macrophages, control, rep 1

value: differentiated to macrophages with PMA


title: T47D E2 rep3

value: Breast cancer cells

value: Estradiol


title: A13

value: pediatric acute lymphoblastic leukemia


title: A12

value: low hypodiploid (<39)

value: primary leukemic cells


title: THP1 cells, undifferentiated monocytes, rep 3

value: undifferentiated

value: Day 0


title: AB14034


title: T47D E2 rep2


title: THP1 cells, undifferentiated monocytes, rep 2


title: A11

value: reference

value: male


title: T47D E2 rep1


title: A10


title: AB14032

value: kidney


title: AB14031

value: Enriched gating for Epo-secreting Norn cells


title: T47D Vehicle rep2

value: Vehicle (DMSO)


title: AB14030

value: normoxia

value: 6-8 weeks


title: A9


title: DLD-1 Clone 36

first: Albert

last: Agustinus

address: 408 East 69th Street, Room 419-G

institute: Memorial Sloan Kettering Cancer Center

data_processing:
The raw reads were trimmed using fastp to remove low-quality bases from reads (quality < 20) and adapter sequences. The trimmed reads were aligned using Bowtie2 [PMID: 22388286 ] to UCSC genome assembly (hg38)
Filter aligned atac reads: 1) Reads aligning to mitochrondrial DNA were removed using the removeChrom.py script at https://github.com/harvardinformatics/ATAC-seq/blob/master/atacseq/removeChrom.py. 2) Reads with low mapping quality score (MAPQ < 15) were removed using samtools (version 1.13) view with the - q parameter set to 15.
Genome_build: hg38
Supplementary_files_format_and_content: BigWig for visualization

source_name: DLD-1 Cells

growth_protocol: DLD-1 cells were grown in RPMI supplemented with 10% FBS and 1X Pen-Strep in 100 mm dish (Corning   Corning™ 100 mm TC-Treated Culture Dishes)

extract_protocol:
Extraction was performed according to Buenrostro et. al. 2015
Library prepared according to Buenrostro et. al. 2015

treatment_protocol: n/a (clones and parental cells were obtained from the authors of Ly et al., Nat. Genet. 2019)

value: neo-DLD + CENP-A C-H3 - p6-derived clones - Clone 36


title: DLD-1 Clone 32

value: neo-DLD + CENP-A C-H3 - p6-derived clones - Clone 32


title: T47D Vehicle rep1


title: A15

value: B-other


title: A8


title: MCF-7 Vehicle rep3

value: Breast cancer cells


title: AB14029

value: Daily doses of tamoxifen for 5 days


title: DLD-1 Clone 26

value: neo-DLD + CENP-A C-H3 - p6-derived clones - Clone 26


title: AB14028


title: AB14033


title: DLD-1 Clone 22

value: neo-DLD + CENP-A C-H3 - p6-derived clones - Clone 22


title: A7

value: pediatric acute lymphoblastic leukemia

value: primary leukemic cells


title: MCF-7 Vehicle rep2


title: AB14027


title: T47D Vehicle rep3


title: THP1 cells, undifferentiated monocytes, rep 1

value: monocyte cell line derived from acute monocytic leukemia patient

value: undifferentiated

value: Day 0


title: MCF-7 Vehicle rep1


title: AB13723

value: kidney


title: A5

value: reference

value: male


title: MCF-7 E2 rep3

value: Estradiol


title: A6


title: DLD-1 Clone 19

value: neo-DLD + CENP-A C-H3 - p6-derived clones - Clone 19


title: A4


title: MCF-7 E2 rep2


title: DLD-1 Clone 17

value: neo-DLD + CENP-A C-H3 - p6-derived clones - Clone 17


title: AB13722

value: Enriched gating for Epo-secreting Norn cells

value: normoxia

value: 6-8 weeks


title: AB13721

value: Daily doses of tamoxifen for 5 days


title: MCF-7 E2 rep1

value: Breast cancer cells


title: DLD-1 Clone 16

value: neo-DLD + CENP-A C-H3 - p6-derived clones - Clone 16


title: A3

value: pediatric acute lymphoblastic leukemia


title: A2

value: B-other

value: primary leukemic cells


title: A1


title: AB13719


title: MCF-7 E2 + X15695 rep3

value: Estradiol + X15695


title: AB13720


title: MCF-7 E2 + X15695 rep2


title: MCF-7 E2 + X15695 rep1


title: AB13718


title: MCF-7 X15695 rep3


title: AB13717


title: DLD-1 Clone 13

value: neo-DLD + CENP-A C-H3 - p6-derived clones - Clone 13


title: DLD-1 Clone 18

value: neo-DLD + CENP-A C-H3 - p6-derived clones - Clone 18


title: DLD-1 Clone 9

value: neo-DLD + CENP-A C-H3 - p6-derived clones - Clone 9


title: DLD-1 Clone 6

value: neo-DLD + CENP-A C-H3 - p6-derived clones - Clone 6


title: MCF-7 X15695 rep2


title: AB13716

value: kidney


title: DLD-1 Clone 15

value: neo-DLD + CENP-A C-H3 - p6-derived clones - Clone 15


title: AB13715


title: DLD-1 Clone 8

value: neo-DLD + CENP-A C-H3 - p6-derived clones - Clone 8


title: AB13714

value: Enriched gating for Epo-secreting Norn cells


title: AB13561

value: 4 hours hypoxia induced by 0.1% CO


title: Parental Control of DLD-1

value: neo-DLD + CENP-A C-H3 - Clone 4 (Parental Clone) - passage 0 start point


title: MCF-7 X15695 rep1


title: LNCaP X15695 rep3

source_name: LNCaP

value: LNCaP

value: Prostate cancer cells


title: LNCaP X15695 rep2


title: LNCaP X15695 rep1


title: AB12895

value: Daily doses of tamoxifen for 5 days

value: 6-8 weeks


title: EBV-positive cancer cell [SNU-719cell_R1]

city: Fuzhou

first: Shun

last: Hu

state: Fujian

address: Chazhong Road

department: Department of Pathology

institute: The First Affiliated Hospital of Fujian Medical University

data_processing:
The raw data (raw reads) obtained by llumina HiSegTM2500 sequencing should be filtered first: remove the connectors at both ends of the reads, remove the reads with fragment length<17nt and low-quality reads, etc., complete the preliminary filtering of the data and obtain high-quality data (clean reads).
The expression of miRNAs can be obtained by comparing the clean reads obtained by sequencing with all EBV miRNA mature body sequences in the miRBase.v22 database.
The expression of miRNAs can be obtained by comparing the clean reads obtained by sequencing with all human miRNA mature body sequences in the miRBase.v22 database.
Assembly: hg18
Supplementary files format and content: miRNA counts

growth_protocol: SNU-719 (EBV-positive gastric cancer cell line), AGS(EBV-negative gastric cancer cell line) were cultured in PMI-1640 and F12, respectively. 5% fetal bovine serum without exosome and penicillin and streptomycin (100U/mL) were added to the medium prior to use. The supernatant was collected when the cells were growing vigorously (up to about 70% fusion).

extract_protocol:
Total RNA was extracted from cells and exosomes using a high purity RNA extraction kit (TRIzol) according to the manufacturer's protocol. The OD260 and OD280 values and ratios of 1 μl extracted samples were determined by ultraviolet spectrophotometer to determine the concentration and purity of extracted samples.
The miRNA library was prepared using an RNA sample preparation kit (Epicenter, San Diego, CA, USA) according to the manufacturer's instructions. As outlined below, small RNAs were attached to 3 and 5 splices for reverse transcription to produce single-stranded cDNA. Then PCR amplification was performed. The constructed library was tested for quality and yield using the Agilent 2100 bioanalyzer and ABI StepOnePlus real-time fluorescence quantitative PCR system. Four small RNA libraries were constructed from RNA samples extracted from EBV-positive gastric cancer cell lines (SNU-719) and EBV-negative gastric cancer cell lines (AGS) and their exosomes. The library was sequenced on Illumina HiSeq 2500 platform.

value: cell line

value: EBV-positive cancer cell


title: exosomes of EBV-positive cancer cell [SNU-719_exo-2_R1]

source_name: exosome

value: exosome

value: exosomes of EBV-positive cancer cell


title: exosomes of EBV-positive cancer cell [SNU-719Exo_R1]


title: AB12894


title: LNCaP DHT + X15695 rep3


title: DLD-1 Clone 12

value: neo-DLD + CENP-A C-H3 - p6-derived clones - Clone 12


title: LNCaP DHT + X15695 rep2


title: AB12893


title: exosomes of EBV-positive cancer cell [SNU-719_exo-1_R1]


title: AB12892


title: AB12891


title: LNCaP DHT rep3

value: DHT (10 nM)


title: EBV-positive cancer cell [SNU-719_cell-1_R1]


title: EBV-positive cancer cell [SNU-719_cell-2_R1]


title: LNCaP DHT + X15695 rep1


title: LNCaP DHT rep1


title: LNCaP DHT rep2


title: exosomes of EBV-negative cancer cell [AGS_Exo-2_R1]

value: exosomes of EBV-negative cancer cell


title: AB12890

value: kidney


title: LNCaP Vehicle rep3

value: Vehicle (DMSO)


title: AB12035


title: exosomes of EBV-negative cancer cell [AGS_Exo_R1]


title: LNCaP Vehicle rep2


title: AB12032


title: H3K27ac CUT&Tag KO rep 1

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

description: CUT&Tag for H3K27ac; antibody: Millipore-Sigma MABE647

data_processing:
Paired-end Mus musculus reads were mapped to UCSC mm10 using Bowtie2 version 2.2.2 (Langmead and Salzberg, 2012) with parameters --end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700.
Continuous-valued data tracks (bedGraph and bigWig) were generated using genomecov in bedtools v2.30.0 (-bg option) and normalized as fraction of total counts.
Assembly: mm10
Supplementary files format and content: bigWig, spike-in calibration, or, read-depth normalization
Library strategy: CUT&Tag

source_name: Organoid culture of bladder urothelium

extract_protocol:
Beads (with bound nuclei) were magnetized, supernatants were removed, beads were washed once with 400 ìl antibody buffer (Wash buffer supplemented with 2 mM EDTA and 0.05% Digitonin), and resuspended in 200 ìl antibody buffer containing the primary antibody in 1:100 v/v dilution (H3K27me3 - rabbit monoclonal, Cell Signaling Technology, cat. no. 9733). Primary antibody incubations were performed on a rotating platform overnight at 4oC. Beads were magnetized, supernatant removed, washed once with 400 ìl Dig-Wash (Wash buffer supplemented with 0.05% Digitonin), resuspended in 200 ìl Dig-Wash containing guinea pig á-rabbit IgG secondary antibody (Antibodies online cat. no. ABIN101961) at 1:00 dilution. Secondary antibody incubations were performed on a rotating platform for 30 min to 1 hr at room temperature. Beads were magnetized, supernatant removed, washed twice with 400 ìl Dig-Wash to remove unbound antibodies, and resuspended in 200 ìl Dig-Med buffer (Dig-Wash buffer, except contai  ning 300 mM NaCl) with 1:200 dilution (~0.04 ìM) of pA-Tn5 pre-loaded with double-stranded adapters with 19mer mosaic ends (Kaya-Okur et al., 2019). pA-Tn5 incubations were performed on a rotating platform for 1 hr at room temperature. Beads were magnetized, supernatant removed, washed three times with 400 ìl Dig-Med to remove unbound pA-Tn5, and resuspended in 300 ìl Tagmentation buffer (Dig-Med supplemented with 10 mM MgCl2). Tagmentation reactions were performed by incubating samples at 37oC on a rotating platform for 1 hr.
Tagmentation reactions were stopped by sequentially adding 10 μl of 0.5 mM EDTA, 3.1 μl of 10% SDS (1% final), and 2 uL of 20 mg/mL Proteinase K, mixed well, and incubated in 50oC water bath for 1 hr. DNA was extracted using phenolchloroform-isoamyl alcohol (25:24:1), re-extracted with one volume CHCl3, aqueous phase (~300 μl) was transferred to fresh tube, and DNA was precipitated by adding 900 μl ethanol overnight at -20°C followed by centrifugation for 45 min at 13,000 rpm and 4°C. Pellets were rinsed with 100% ice-cold ethanol, air-dried, dissolved in 30 μL 0.1 x TE (1 mM Tris pH 8, 0.1 mM EDTA) supplemented with RNase A, and incubated in 37°C water bath for 15 min. To amplify libraries, 21 μL DNA was mixed with 2 μL each of a universal i5 primer and a uniquely barcoded i7 primer, using a different barcode for each sample, and 25 μL of NEBNext HiFi 2x PCR Master mix. Samples were placed in a thermocycler with heated lid using the following cycling conditions: 72°C for 5 min (gap filling); 98°C for 30 sec (denaturation); 13 cycles of 98°C for 10 sec and 63°C for 10 sec (combined annealing and extension); final extension at 72°C for 1 min, and held at 8oC. Post-PCR clean-up was performed using a double-sided clean-up method. 25 μL (0.5 X) of Ampure XP beads (Beckman Counter) was mixed with the libraries and incubated for 10 min at room temperature to remove large DNA fragments (>1300 bp). Beads were magnetized, supernatants were removed to fresh tubes and mixed with 45 μL (1.4 X - 0.5 X = 0.9 X) of Ampure XP beads and incubated for 10 min at room temperature. Beads were magnetized and the supernatants containing unused PCR primers were discarded. Beads were washed three times with 80% ethanol and eluted in 30 μL 10 mM Tris pH 8.0. Libraries were sequenced for 25 cycles in 25bp paired-end mode on the Illumina HiSeq 2500 platform at the Fred Hutchinson Cancer Research Center Genomics Shared Resource. The detailed, step-by-step original protocol can be found at https://www.protocols.io/view/bench-top-cut-amp-tag-kqdg34qdpl25/v3
PCR amplification using indexed primers PMID: 26083756

tag: genotype

value: ARID1A KO


title: EBV-negative cancer cell [AGS_cell-2_R1]

source_name: AGS

value: AGS

value: EBV-negative cancer cell


title: H3K27me3 CUT&Tag KO DMSO

description: CUT&Tag for H3K27me3; antibody: CST 9733


title: AB12031

value: Enriched gating for Epo-secreting Norn cells

value: 4 hours hypoxia induced by 0.1% CO


title: LNCaP Vehicle rep1

value: LNCaP

value: Prostate cancer cells


title: EBV-negative cancer cell [AGS_cell_R1]


title: patient with Tetralogy of Fallot, 5 (RNA-seq)

city: Chongqing

first: Quan

last: Wang

address: Zhongshan 2nd Road

department: Department of Cardiothoracic Surgery

institute: Children’s Hospital of Chongqing Medical University

description:
treat5
lncRNA_count.txt
mRNA_count.txt

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Homo sapiens GRCh38.p13 genome (downloaded from ENSEMBL, version 105) using  Hisat, Finally, new transcripts of each sample were assembled using StringTie software
Download the reported lncRNA sequences from lncRNA-related databases, which mainly includes the collection of NONCODE, Ensembl and NCBI database, and then conduct the identification of known lncrnas based on these databases
The new lnc_RNA transcripts were selected transcripts with length ≥200 bp, Exon number ≥2, ORF length ≤300bp  as candidates for preliminary screening ，Whether the transcript has coding potential is a key condition to determine whether the transcript is lncRNA. lncRNA screening was conducted by integrating the most widely used coding potential analysis methods in studies, which mainly include: CPC analysis, CNCI analysis, CPAT analysis and Pfam protein domain analysis.
RSEM software was used to calculate the expression of transcripts
Assembly: GRCh38.p13
Supplementary files format and content: mRNA_count.txt: tab-delimited text files include mRNA count values for each Sample
Supplementary files format and content: lncRNA_count.txt: tab-delimited text files include lnc_RNA count values for each Sample

source_name: right ventricle

extract_protocol: RNA libraries for RNA-seq were prepared using ribo-off&VZ6SS Kit following manufacturer's protocols.

value: right ventricle

tag: condition

value: Tetralogy of Fallot


title: EBV-negative cancer cell [AGS_cell-1_R1]

value: cell line


title: EWS894 cells, UNC0621 treatment, 16 hr 3

city: Chapel Hill

first: Ian

middle: J

last: Davis

state: NC

address: 450 West Drive

department: Genetics

institute: University of North Carolina at Chapel Hill

data_processing:
Adaptor sequences were removed from reads using cutadapt (v.1.12).
High quality reads were isolated using FASTX-Toolkit (v0.0.12) passing options -Q 33, -p 90, and q 20.
Reads were aligned to the hg38 genome using STAR(v2.5.2b) (Dobin et al. 2013) with the following options: --quantMode TranscriptomeSAM, --alignIntronMax 1000000, --outFilterMismatchNmax 2, --alignIntronMin 20, --chimSegmentMin 15, --outSAMtype BAM Unsorted, --chimJunctionOverhangMin 15, --outFilterType BySJout, --outFilterScoreMin 1. GENCODE V41 GTF file was used for annotation.
Gene expression estimates (TPM) were calculated using Salmon (v.1.6.0).
Differentially expressed genes were identified using DESeq2 (Love et al. 2014)
Assembly: hg38
Supplementary files format and content: The DESeq2 file contains relevant data necessary to determine differential genes via DESeq2
Supplementary files format and content: The TPM file contains a combined expression matrix calculated by Salmon for each gene across all samples.
Supplementary files format and content: The SE_transcriptLevel.MATS.JCEC.txt file contains relevant data necessary to determine differential Skipped Exon alternative splicing events via rMATS in transcripts
Supplementary files format and content: The SE.MATS.JCEC.txt file contains relevant data necessary to determine differential Skipped Exons alternative splicing events via rMATS
Supplementary files format and content: The RI.MATS.JCEC.txt file contains relevant data necessary to determine differential Retained Intron alternative splicing events  via rMATS
Supplementary files format and content: The MXE.MATS.JCEC.txt file contains relevant data necessary to determine differential Mutually Exclusive Exon alternative splicing events via rMATS
Supplementary files format and content: The A3SS.MATS.JCEC.txt file contains relevant data necessary to determine differential Alternative 3' Splice Site splicing events  via rMATS
Supplementary files format and content: The A5SS.MATS.JCEC.txt file contains relevant data necessary to determine differential Alternative 5' Splice Site splicing events via rMATS

source_name: cell line

growth_protocol: EWS894 cells were  cultured in RPMI-1640 supplemented with 15%  fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
EWS894 cells were washed in PBS and harvested in Trizol (Invitrogen).
Poly-A selected sequencing libraries were generated using the KAPA Stranded mRNA-Seq Kit for Illumina platforms (KAPA Biosystems) according to manufacturer’s protocol.

treatment_protocol: Cells were treated with UNC0621 5 μM or Vehicle control (DMSO) for 16 hours prior to collection.

value: Ewing sarcoma cell line

value: UNC0621 5 μM

tag: time

value: 16 hour


title: pMEF_G0_Wapl-CTCF-KO_DRB-release

description: Hi-C, 1Kb resolution

data_processing:
Basecalling software: Illumina RTA
RNA polymerase II ChIP-Seq in mouse cells was performed without spike-in, and short-read sequencing data were mapped against the mm9 template using bowtie2
Illumina short read sequencing data for NIPBL/MAU2 were performed using calibration spike-ins (mouse) and aligned against a fusion genome template consisting of merged hg19 and mm9 assemblies.
NIPBL/MAU2 calibration by random subsampling of read counts after deduplication
Peak callings with MACS software versions 1.4 and 2 were applied on full, merged, filtered, and deduplicated replicate data sets of HA-tagged samples with corresponding depleted conditions (+dTAG) as input controls.
Hi-C data were mapped to 1 kb resolution coolers using the mm9 genome assembly and distiller pipeline (https://github.com/mirnylab/distiller-nf; version 0.0.3 for all datasets except for DRB and DRB release, which used version 0.3.1).
Assembly: mm9
Supplementary files format and content: cooler (.cool format) files with 1kb resolution, generated with distiller

source_name: mouse embryonic fibroblasts

value: mouse embryonic fibroblasts

value: Ctcf/Wapl-KO

tag: chip antibody


title: AB12034

tag: strain

value: kidney

value: Daily doses of tamoxifen for 5 days

value: 6-8 weeks


title: AB12030

tag: cell type

value: normoxia


title: pMEF_G0_Wapl-CTCF-KO_DRB

description: Hi-C, 1Kb resolution


title: patient with Tetralogy of Fallot, 4 (RNA-seq)

description:
treat4
lncRNA_count.txt
mRNA_count.txt


title: EWS894 cells, UNC0621 treatment, 16 hr 2

tag: cell line


title: pMEF_G0_wt_DRB-release

description: Hi-C, 1Kb resolution


title: patient with Tetralogy of Fallot, 2 (RNA-seq)

description:
treat2
lncRNA_count.txt
mRNA_count.txt


title: AB12033


title: exosomes of EBV-negative cancer cell [AGS_Exo-1_R1]

value: exosome

value: exosomes of EBV-negative cancer cell


title: EWS894 cells, UNC0621 treatment, 16 hr 1


title: pMEF_G0_wt_DRB

description: Hi-C, 1Kb resolution


title: EWS894 cells, Vehicle treatment, 16 hr 3

value: DMSO


title: patient with Tetralogy of Fallot, 1 (RNA-seq)

description:
treat1
lncRNA_count.txt
mRNA_count.txt


title: AB12027

value: Enriched gating for Epo-secreting Norn cells


title: AB12029


title: AB12026


title: AB12028


title: pMEF_G0_Smc3-KO

description: Hi-C, 1Kb resolution


title: healthy unaffected individual, 5 (RNA-seq)

description:
control5
lncRNA_count.txt
mRNA_count.txt

value: healthy


title: healthy unaffected individual, 4 (RNA-seq)

description:
control4
lncRNA_count.txt
mRNA_count.txt

value: right ventricle


title: EWS894 cells, Vehicle treatment, 16 hr 1


title: AB12025


title: AB12024


title: healthy unaffected individual, 3 (RNA-seq)

description:
control3
lncRNA_count.txt
mRNA_count.txt


title: pMEF_G0_Wapl-KO

description: Hi-C, 1Kb resolution

value: Wapl-KO


title: patient with Tetralogy of Fallot, 3 (RNA-seq)

description:
treat3
lncRNA_count.txt
mRNA_count.txt

value: Tetralogy of Fallot


title: 133M_NIPBL RNAi r1

description:
q-value (min. FDR) cutoff for significant regions is 0.05
HeLa_NIPBL-RNAi.bw

data_processing:
Basecalling software: Illumina RTA
RNA polymerase II ChIP-Seq in mouse cells was performed without spike-in, and short-read sequencing data were mapped against the mm9 template using bowtie2
Illumina short read sequencing data for NIPBL/MAU2 were performed using calibration spike-ins (mouse) and aligned against a fusion genome template consisting of merged hg19 and mm9 assemblies.
NIPBL/MAU2 calibration by random subsampling of read counts after deduplication
Peak callings with MACS software versions 1.4 and 2 were applied on full, merged, filtered, and deduplicated replicate data sets of HA-tagged samples with corresponding depleted conditions (+dTAG) as input controls.
Genome_build: hg19
Genome_build: mm9
Supplementary_files_format_and_content: bigwig (*.bw) files containing ChIP-Seq profiles after full processing as described.
Supplementary_files_format_and_content: bedGraph (*.bedgraph) files containing ChIP-Seq profiles after full processing as described.

growth_protocol: HeLa Kyoto (RRID:CVCL_1922) were from Narumiya S (Kyoto University; Kyoto; Japan). MEFs were generated in the lab by 3T3 methods.

value: HeLa Kyoto

value: NIPBL knockdown

value: NIPBL (Peters laboratory A870 or 133M)


title: AB12023


title: pMEF_G0_CTCF-KO

description: Hi-C, 1Kb resolution

value: mouse embryonic fibroblasts

value: Ctcf-KO


title: AB11641

value: kidney

value: 4 hours hypoxia induced by 0.1% CO


title: 133M_control r1

description:
q-value (min. FDR) cutoff for significant regions is 0.05
HeLa_ctrl.bw

value: wildtype


title: healthy unaffected individual, 1 (RNA-seq)

description:
control1
lncRNA_count.txt
mRNA_count.txt


title: healthy unaffected individual, 2 (RNA-seq)

description:
control2
lncRNA_count.txt
mRNA_count.txt


title: pMEF_wt

description: Hi-C, 1Kb resolution


title: AB11640

value: Daily doses of tamoxifen for 5 days

value: 6-8 weeks


title: patient with Tetralogy of Fallot, 5 (miRNA-seq)

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Homo sapiens GRCh38.p13 genome (downloaded from ENSEMBL, version 105) using  bowtie2 software.
Reads on the reference genome were compared with Homo sapiens miRNA sequences in the miRBase database.
The sRNA that could not be compared with Rfam and miRBase was compared to the reference genome, and the surrounding sequences were intercepted and the miRDeep2 software was used to predict the secondary structure. According to the predicted results, the Dicer enzyme restriction site information, energy value and other characteristics were used to filter and identify new miRNA
quantifier script in miRDeep2 software was used to calculate mirna expression
Assembly: GRCh38.p13
Supplementary files format and content: miRNA_count.txt: tab-delimited text files include miRNA count values for each Sample

extract_protocol: RNA libraries for miRNA-seq were prepared using bioov3 Kit following manufacturer's protocols.


title: GFP-WAPL

description:
q-value (min. FDR) cutoff for significant regions is 0.05
GFP-WAPL.bw

value: GFP (Abcam, ab290)


title: PIL C4

first: Yu-Jui

last: Ho

address: 417 E 68th St

department: Cancer Biology & Genetics Program

data_processing:
Illumina read quality was checked for each sample using FastQC v0.11.5.
Raw fastq files were analyzed by removing adaptor sequences using Trimmomatic (0.36), aligned to the mouse genome using STAR (2.5.3a), and quantified transcript counts using featureCounts (1.6.3).
Assembly: Reads were aligned to the mouse transcriptome (mm10, GRCm38)
Supplementary files format and content: Tab-delimited text file includes raw count table for each sample

source_name: tumor cells from KPCmut PDAC tumors transplanted into lungs (PIL)

growth_protocol: To generate pancreatic tumors, 5x104 KrasG12D/+;Trp53R172H/wt (KPCmut) PDAC cells (PIP) or KrasG12D/+;p53-/- (KP) lung cancer cells expressing luciferase and GFP (LUC-GFP) were transplanted into the pancreas of 8-10 week old C57BL/6 female mice. Mice were monitored for tumor development (5-8 days post-transplantation) by bioluminescence imaging (BLI) on a Xenogen IVIS Spectrum imager (PerkinElmer) before being randomized into various study cohorts. To generate lung tumors, 5x105 KPCmut PDAC cells (PIL) or 4x104 KP lung cancer cells expressing luciferase and GFP (LUC-GFP) were tail vein injected into 8-10 week old C57BL/6 female mice. Mice were monitored for tumor development (5-8 days post-transplantation) by bioluminescence imaging (BLI) on a Xenogen IVIS Spectrum imager (PerkinElmer) before being randomized into various study cohorts.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen)
PolyA mRNA was selected using beads coated with polyT oligonucleotides. Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.
For sequencing, pooled multiplexed libraries were run on a HiSeq 2500 machine on RAPID mode. Approximately 10 million 76bp single-end reads were retrieved per replicate  condition. Resulting RNA-Seq data was analyzed by removing adaptor sequences using Trimmomatic, aligning sequencing data to GRCh37.75(hg19) with STAR, and genome wide transcript counting using HTSeq to generate a RPKM matrix of transcript counts.

treatment_protocol: Tumor-bearing mice were treated with vehicle or combined trametinib (1 mg/kg body weight), and palbociclib (100 mg/kg body weight) per os for 4 consecutive days followed by 3 days off treatment for 2 weeks before sacrafice.

value: tumor cells

value: T/P (C)


title: SCC1-GFP

description:
q-value (min. FDR) cutoff for significant regions is 0.05
SCC1-GFP.bw


title: CTCF-GFP

description:
q-value (min. FDR) cutoff for significant regions is 0.05
CTCF-GFP.bw


title: EWS894 cells, Vehicle treatment, 16 hr 2

value: cell line

value: Ewing sarcoma cell line

value: DMSO

value: 16 hour


title: pMEF_G0_Wapl-CTCF-KO

description: Hi-C, 1Kb resolution

value: Ctcf/Wapl-KO


title: patient with Tetralogy of Fallot, 4 (miRNA-seq)

value: right ventricle

value: Tetralogy of Fallot


title: MAU2-HA SCC1 knockdown r1

description:
q-value (min. FDR) cutoff for significant regions is 0.05
MAU2-HA_SCC1-kd_treat_pileup.bedgraph

value: HeLa Kyoto

value: SCC1 knockdown

value: HA (Abcam, ab9110)

value: HA-tagged


title: AB11638

value: kidney

value: Enriched gating for Epo-secreting Norn cells

value: 4 hours hypoxia induced by 0.1% CO


title: AB11639

value: Daily doses of tamoxifen for 5 days

value: 6-8 weeks


title: PIL C2

value: tumor cells

value: T/P (C)


title: AB11637

value: normoxia


title: PIL C1


title: patient with Tetralogy of Fallot, 3 (miRNA-seq)


title: patient with Tetralogy of Fallot, 2 (miRNA-seq)


title: MAU2-HA control r1

description:
q-value (min. FDR) cutoff for significant regions is 0.05
MAU2-HA_ctrl_treat_pileup.bedgraph

value: wildtype


title: AB11636


title: PIL V4

value: Vehicle (V)


title: patient with Tetralogy of Fallot, 1 (miRNA-seq)


title: AB11635


title: HA-NIPBL SCC1 knockdown r1

description:
q-value (min. FDR) cutoff for significant regions is 0.05
HA-NIPBL_SCC1-kd_treat_pileup.bedgraph


title: PIL V3


title: healthy unaffected individual, 5 (miRNA-seq)

value: healthy


title: PIL V2


title: healthy unaffected individual, 4 (miRNA-seq)

value: right ventricle


title: HA-WAPL +dTAG r2

description:
n.a.
HA-WAPL_control_lambda.bedgraph

value: dTAG


title: HA-NIPBL control r1

description:
q-value (min. FDR) cutoff for significant regions is 0.05
HA-NIPBL_ctrl_treat_pileup.bedgraph

value: HeLa Kyoto


title: PIL C3


title: AB11634


title: HA-WAPL -dTAG r2

description:
q-value (min. FDR) cutoff for significant regions is 0.05
HA-WAPL_treat_pileup.bedgraph


title: healthy unaffected individual, 2 (miRNA-seq)


title: MAU2-HA +dTAG r2

description:
n.a.
HA-MAU2_control_lambda.bedgraph


title: PIL V1


title: LIL C4

source_name: tumor cells from KP lung tumors transplanted into lungs (LIL)


title: LIL C3


title: AB11631


title: LIL C2


title: healthy unaffected individual, 1 (miRNA-seq)


title: AB11630


title: HCT116 21-1 ATAC-Seq

data_processing:
The raw reads were trimmed using fastp to remove low-quality bases from reads (quality < 20) and adapter sequences. The trimmed reads were aligned using BWA to UCSC genome assembly (hg38)
Duplicate reads were removed using Sambamba [2] and bigwig files were created for visualization using deeptools [3]. Peaks were identified with MACS2 [4] and transcription factor binding motifs were detected with Homer [5]. Peaks overlapping with Satellite repeat regions were discarded and remaining filtered peaks were annotated using custom scripts based on publicly available gene models, where peaks between −2500 and 2500 bp of a transcription start site were marked as “Promoter”, the overlapping gene body were marked as “Gene body” and the rest were marked as “Intergenic”. For intergenic peaks, a gene was considered a target if it was within 1 Mb of the peak.
Assembly: hg38
Supplementary files format and content: bigwig, bai

growth_protocol: HCT116 cells were grown in RPMI media supplemented with 10% FBS and 1X Pen-Strep in 100 mmx 100 mm Falcon TC-Treated Culture Dishes

value: male


title: healthy unaffected individual, 3 (miRNA-seq)


title: AB11416


title: HCT116 18-2 ATAC-Seq


title: LIL C1


title: HA-NIPBL -dTAG r2

description:
q-value (min. FDR) cutoff for significant regions is 0.05
HA-NIPBL_treat_pileup.bedgraph

value: HA (Abcam, ab9110)


title: LIL V2


title: AB11415


title: HA-WAPL +dTAG r1

description:
n.a.
HA-WAPL_control_lambda.bedgraph


title: HCT116 13-2 ATAC-Seq


title: AB11633


title: AB11414


title: AB11632


title: HCT116 5-18 ATAC-Seq


title: AB11413


title: LIP C4

source_name: tumor cells from KP lung tumors transplanted into pancreas (LIP)


title: LIL V1


title: HCT116 5-17 ATAC-Seq


title: MAU2-HA -dTAG r2

description:
q-value (min. FDR) cutoff for significant regions is 0.05
HA-MAU2_treat_pileup.bedgraph

source_name: cervical carcinoma

value: HA-tagged


title: HA-NIPBL +dTAG r2

description:
n.a.
HA-NIPBL_control_lambda.bedgraph


title: HCT116 Parental Control ATAC-Seq Biol Rep 2


title: AB11412

value: kidney


title: AB11411

value: Enriched gating for Epo-secreting Norn cells


title: LIP C2


title: AB11410

value: 4 hours hypoxia induced by 0.1% CO


title: MAU2-HA +dTAG r1

description:
n.a.
HA-MAU2_control_lambda.bedgraph


title: LIP C3


title: HA-NIPBL +dTAG r1

description:
n.a.
HA-NIPBL_control_lambda.bedgraph


title: MAU2-HA -dTAG r1


title: HCT116 Parental Control ATAC-Seq Biol Rep 1


title: RPE-1 Chr4 misseg B biol rep 3

source_name: Retina (female)

growth_protocol: RPE-1 cells were grown in DMEM media supplemented with 10% FBS and 1X Pen-Strep in 100x100 mm dish (Falcon TC-Treated Culture Dishes)

value: Retina (female)

value: hTERT-immortalized retinal pigment epithelial cell line


title: LIP C1

value: tumor cells


title: LIP V4


title: HA-WAPL -dTAG r1


title: F0(Express617 x G3D001 ),30 days ovule,rep2 [F0_Rep3_E30 WGBS]

city: Wuhan

first: Hao

address: No. 1, Shizishan Street, Hongshan District

department: National Key Laboratory of Crop Genetic Improvement

institute: Huazhong Agricultural University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using  fastp 0.23.1 and TrimGalore-0.6.6
Sequence reads were mapped to Express617 using Bismark 0.23.0
Alignments were then deduplicated with the "deduplicate_bismark"  tool  in Bismark 0.23.0
Methylated regions were extracted and converted to bed format with the  "bismark_methylation_extractor" and "bismark2bedGraph" tools from Bismark 0.23.0 respectively.
The "coverage2cytosine" tool from Bismark 0.23.0 was run to  determine the DNA methylation context. Regions in unassigned scaffolds were discarded
Assembly: Express617_v1

organism: Brassica napus

source_name: ovule

growth_protocol: Express617, G3D001 and its F1 plants were planted in the natural environment of the potting field in Huazhong Agricultural University

extract_protocol:
DNA was extracted using CTAB method . 2.5 ug of total DNA was used for the construction of sequencing libraries.
DNA libraries for Bisulfite-seq were prepared using TruSeq Nano DNA LT Sample Prep Kit for Illumina following manufacturer's protocols.

value: ovule

value: F0(Express617 x G3D001 )

value: 30 days after ovule fertilization


title: AB11313

source_name: Epo-secreting Norn cells

value: Daily doses of tamoxifen for 5 days

value: 6-8 weeks


title: RPE-1 Chr4 misseg B biol rep 1


title: LIP V3

value: Vehicle (V)


title: F0(Express617 x G3D001 ),30 days ovule,rep1 [F0_Rep1_E30 WGBS]


title: AB11312


title: LIP V2


title: G3D001,30 days ovule,rep2 [20N1090_Rep3_E30 WGBS]


title: RPE-1 Chr4 misseg A biol rep 3


title: AB11311


title: LIP V1


title: RPE-1 Chr4 misseg A biol rep 2


title: Express617,30 days ovule,rep2 [20N1087_Rep3_E30 WGBS]


title: HA-NIPBL -dTAG r1

value: wildtype


title: RPE-1 Chr4 misseg A biol rep 1


title: H3K27me3 CUT&Tag KO rep 3

description: CUT&Tag for H3K27me3; antibody: CST 9733

data_processing:
Paired-end Mus musculus reads were mapped to UCSC mm10 using Bowtie2 version 2.2.2 (Langmead and Salzberg, 2012) with parameters --end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700.
Continuous-valued data tracks (bedGraph and bigWig) were generated using genomecov in bedtools v2.30.0 (-bg option) and normalized as fraction of total counts.
Assembly: mm10
Supplementary files format and content: bigWig, read-depth normalization

growth_protocol: CUT&Tag was performed following the published protocol (Kaya-Okur et al., 2019), with some modifications. Briefly, urothelial organoid cultures were harvested and prepared into homogenous suspension of cells in phosphate-buffered saline (PBS), aliquoted with 10% DMSO and slow-frozen to −80oC in isopropanol freezing chambers. CUT&Tag was performed with native nuclei. For nuclei preparation (see (Henikoff et al., 2021), cells were thawed at 37oC for 1 min, washed twice with PBS and centrifugation at 600 rcf for 3 min, and resuspended into ice-cold NE1 buffer (20mM K-HEPES pH 7.9, 10mM KCl, 10% Triton X-100, 20% Glycerol, 0.5 mM spermidine, and Roche complete EDTA-free protease inhibitor). Cells were kept on ice for 10 min, centrifuged at 1400 rcf for 3 min using a swinging-bucket rotor, pellets were resuspended in Wash buffer (20 mM Na- HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, and Roche complete EDTA-free protease inhibitor), nuclei were counted using Vi-CELL Cell Viability Analyzer (Beckman Coulter) and aliquoted into 0.6 mL low-binding flip-cap tubes for CUT&Tag experiments. 500,000 nuclei were used for each CUT&Tag experiment (sample). Bio-Mag Plus Concanavalin

value: ARID1A KO


title: AB11309

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Well-barcode-RMT are extracted from the 7 first base pairs in the R2 fastq sequences. Unique-molecular-identifier are extracted from the subsequent 8 base pairs in the R2 sequences. R1 contains the genomic sequences.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error.
Genome_build: mm10
Genome_build: The tail of gene Epo was elongated by 1kb chr5:137,481,020-137,485,852
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample


title: RPE-1 Chr4 misseg control biol rep 3


title: H3K27me3 CUT&Tag KO rep 2


title: F1(Express617 x G3D001 ),30 days ovule,rep2 [20N1084_Rep3_E30 WGBS]

value: F1(Express617 x G3D001 )


title: AB11310


title: AB11409


title: F1(Express617 x G3D001 ),30 days ovule,rep1 [20N1070_Rep1_E30 WGBS]


title: RPE-1 Chr4 misseg control biol rep 2


title: RPE-1 Chr4 misseg B biol rep 2


title: H3K27me3 CUT&Tag KO rep 1


title: Express617,30 days ovule,rep1 [20N1068_Rep1_E30 WGBS]


title: RPE-1 Chr4 misseg control biol rep 1


title: AB11306


title: AB11307


title: SUN1, STATIC biol rep 3

city: WAUWATOSA

first: ZIQING

last: LIU

state: WI

address: 8701 W Watertown Plank Rd, BSB 5320

department: Biology

institute: Medical College of Wisconsin

data_processing:
Fastq data quality was checked by fastqc and no trimming was performed because the data quality looks great. Sequencing depth ~ 20-30 million paired end reads/sample.
Fastq reads were mapped to hg38 genome by STAR with mismatch =1. All files has over 80% mapping rate.
Aligned reads were counted by Htseq-count with union mode. Over 80% mapped reads are from mRNA.
Assembly: hg38
Supplementary files format and content: a csv file containing Htseq counts for all genes in all samples

source_name: Human umbilical vein endothelial cells (HUVEC)

growth_protocol: HUVEC were cultured in EBM-2 (Lonza) supplemented with Endothelial Growth Medium bullet kit (Lonza) and 1x antibiotic-antimycotic (Gibco) at 5% CO2 and 37°C

extract_protocol:
RNA was extracted using TRIzol (Invitrogen)
KAPA mRNA HyperPrep Kit (Roche) was used to construct stranded libraries

treatment_protocol: HUVEC were treated with indicated siRNA at ~80% confluency using Lipofectamine 2000 or 3000 (ThermoFisher) for 24 h. Cells were cultured onto µ-Slides (Ibidi) then exposed to either static conditions for 48h or 15dyn/cm2 shear stress for 72 h on an Ibidi flow pump.

value: SUN1 siRNA

value: SUN1 KD

tag: stress

value: static condition


title: H3K27me3 CUT&Tag WT rep 2

value: ARID1A WT


title: H3K27me3 CUT&Tag WT rep 3


title: G3D001,30 days ovule,rep1 [20N1067_Rep1_E30 WGBS]


title: F0(Express617 x G3D001 ),15 days ovule,rep2 [F0_Rep3_E15 WGBS]

value: 15 days after ovule fertilization


title: SUN1, STATIC biol rep 2

value: Human umbilical vein endothelial cells (HUVEC)


title: H3K27me3 CUT&Tag WT rep 1


title: AB11066

value: kidney

value: Enriched gating for Epo-secreting Norn cells

value: 4 hours hypoxia induced by 0.1% CO


title: F0(Express617 x G3D001 ),15 days ovule,rep1 [F0_Rep1_E15 WGBS]

value: ovule

value: F0(Express617 x G3D001 )


title: AB11308

value: Daily doses of tamoxifen for 5 days


title: AB11065

value: 6-8 weeks


title: CANCER ARID1A KO rep 2 [RNA Seq]

description: ARID1A Cancer KO rep 2

data_processing:
Sequencing was performed using an Illumina HiSeq 2500 in Rapid Run mode and  employed a single-end, 50 base read length (SE50) sequencing strategy.
Files were then aligned to mm10 using STAR2 and counts  per gene were generated using HTSeq.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw values for each Sample.

source_name: tissue

extract_protocol:
RNA was extracted from isogenic bladder cancer organoids. Total RNA was prepared using RNeasy Mini Kit with DNase I (Qiagen). RNA concentration and quality (A260/A280) was measured using a NanoDrop 1000 Spectrophotometer (Thermo Scientific).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: bladder cancer tissue

tag: genotype/variation


title: SUN1, STATIC biol rep 1


title: G3D001,15 days ovule,rep2 [20N1090_Rep3_E15 WGBS]


title: SUN1, FLOW biol rep 3

value: 72h shear stress at 15 dyn/cm2


title: Express617,15 days ovule,rep2 [20N1087_Rep3_E15 WGBS]


title: F1(Express617 x G3D001 ),15 days ovule,rep2 [20N1084_Rep3_E15 WGBS]


title: SUN1, FLOW biol rep 1


title: CANCER ARID1A WT rep 2 [RNA Seq]

description: ARID1A Cancer WT rep 2


title: SUN1, FLOW biol rep 2


title: CANCER ARID1A WT rep 1 [RNA Seq]

description: ARID1A Cancer WT rep 1


title: F1(Express617 x G3D001 ),15 days ovule,rep1 [20N1070_Rep1_E15 WGBS]


title: AB11063


title: MEF_input

description:
n.a.
input.bedgraph

extract_protocol:
ChIP-Seq: Cells were cross-linked and scrapped of the plate. The DNA was fragmented and the protein of interest was immunoprecipitated with indicated antibodies; Adaptors were ligated to the 5' and 3' ends and the library was prepared for Illumina sequencing by a qPCR amplification step.
Libraries were prepared for sequencing using standard Illumina protocols. All antibodies used in this study were listed in Online Methods section 'Antibodies and Reagents'.

value: mouse embryonic fibroblasts (MEFs)

value: wildtype


title: PolII-S2__Smc3-KO

description:
p-val. threshold 1e-10
PolII-S2__Smc3-KO.bedgraph

value: RNA polymerase II S2 (Abcam, ab5095)


title: NT, STATIC biol rep 3

value: Non-targeting siRNA

value: control


title: AB11060


title: G3D001,15 days ovule,rep1 [20N1067_Rep1_E15 WGBS]


title: Express617,15 days ovule,rep1 [20N1068_Rep1_E15 WGBS]


title: AB11061


title: NT, STATIC biol rep 2

value: static condition


title: AB10929


title: PolII-S2__CW-dKO

description:
p-val. threshold 1e-10
PolII-S2__CW-dKO.bedgraph

value: Ctcf/Wapl-KO


title: NT, STATIC biol rep 1

value: Human umbilical vein endothelial cells (HUVEC)


title: AB10928

value: kidney


title: AB11064

value: Enriched gating for Epo-secreting Norn cells


title: NT, FLOW biol rep 3


title: PolII-S2__Wapl-KO

description:
p-val. threshold 1e-10
PolII-S2__Wapl-KO.bedgraph

value: Wapl-KO


title: Express617,six-leaf stage,rep2 [20N1087_Rep3_L WGBS]

source_name: leaf

value: leaf

value: six-leaf stage


title: G3D001,six-leaf stage,rep2 [20N1090_Rep3_L WGBS]


title: CANCER ARID1A KO rep 1 [RNA Seq]

description: ARID1A Cancer KO rep 1

value: ARID1A KO


title: AB10927

value: Daily doses of tamoxifen for 5 days

value: 4 hours hypoxia induced by 0.1% CO

value: 6-8 weeks