title: Male, dsx-RNAi, 7 day, replicate 2

city: Wageningen

first: Julien

last: Rougeot

address: Droevendaalsesteeg 1

institute: Wageningen University and Research (Netherlands)

data_processing:
Raw data filtering was performed to remove reads with adaptor contamination, uncertain nucleotides on more than 10% of the sequence (N>10%) and reads with low-quality nucleotides (<20) on more than 50% of the sequence.
Clean paired-end reads were mapped on the Nasonia vitripennis genome Nvit_psr_1.1 (GCA_009193385.2 Nvit_psr_1.1) using HISAT2 (v2.0.5) and default parameters.
Gene counts were obtained using HTSeq (v0.6.1) and the union method on the annotation GCF_009193385.1_Nvit_psr_1.
Assembly: Nvit_psr_1.1
Supplementary files format and content: tab-delimited text file includes raw counts for each samples

source_name: larvae

extract_protocol:
After 3 days post-injection, five samples with three individuals were collected for each time point and sex and flash-frozen in liquid nitrogen. For adult parts, seven adults were collected one day after emergence, between 7 and 8 days after pupae injection. Adults were flash-frozen in liquid nitrogen, then immediately dissected apart on ice into head, thorax, and abdomen, and finally flash-frozen back in liquid nitrogen. All samples were stored at −80 °C until RNA extraction. For 1 day-old embryo (parental RNAi), F0 female pupae 8 days after oviposition were injected as described above, kept until emergence, and then crossed with uninjected AsymCX males or kept virgin. Every female was then set up individually with one host, changed every 4 hours. Virgin females produce only male progeny while mated females produce between 90-95% females. Batches of 100 embryos were collected  24 hours later by dissecting the host, transfer into a microcentrifugation tube on ice without buffer, flash-frozen in liquid nitrogen, and stored at −80 °C until RNA extraction. Total RNA was extracted with Quick-RNA Tissue/Insect Kit coupled with on column DNase treatment (ZymoResearch - R2030) according to manufacturer's protocol.
Library preparation was performed at the Novogene (HK) Company Limited. Sequencing libraries were generated using NEBNext® Ultra TM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Sequencing libraries were paired-end sequenced (150 bp read-length) on an Illumina NovaSeq platform.

value: larvae

tag: strain

value: AsymCX

tag: Sex

value: Male

value: 7 day

value: dsx-RNAi


title: ATRT-MYC cell line CHLA-266 after treatment

status: Public on Jul 08 2026

type: SRA

city: Hamburg

first: Lea

last: Altendorf

address: Martinistraße 52

country: Germany

institute: Universitätsklinikum Hamburg-Eppendorf

description: Library name: CHLA-266 treated

library_source: transcriptomic

data_processing:
Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq (version 2.20) and adapters were trimmed with Skewer (version 0.2.2)
Trimmed sequence reads were aligned to the human genome hg38 using STAR
The transcripts were counted as feature counts and these were used as input for the raw count table
Assembly: hg38
Supplementary files format and content: CSV file containing the filtered count table after removing repetitively counted genes and genes from sex chromosomes and only keeping protein-coding transcripts
Supplementary files format and content: CSV file containing the VST-normalized filtered count table

molecule: total RNA

organism: Homo sapiens

growth_protocol: BT-16 and CHLA-266 were grown in DMEM +  20% Fetal Bovine Serum, 4mM L-Glutamine, 1X ITS (5 µg/mL insulin, 5 µg/mL transferrin, 5 ng/mL selenous acid), 1% Pen/Strep at 37.0°C, 5% CO2, 20% O2

extract_protocol:
Cell pellets were resuspended in Trizol and RNA was extracted according to standard protocols. 10 ng were used as input for library construction.
RNA libraries for RNA-seq were constructed using the SMART-Seq Stranded kit (Takara Bio) according to the manufacturer’s specifications

treatment_protocol: 1 µM doxorubicin + 5 µM etoposide + 1 µm vincristine at three consecutive days

tag: cell line

tag: treatment

tag: batch

value: C


title: Hi-C of Homo sapiens: D20 of atrial cardiomyocyte (CM) differentiation with 500 nM dTAGv-1 ligand treated for 24h rep1

city: San Francisco

first: Benoit

middle: G.

last: Bruneau

state: CA

address: 1650 Owens St

country: USA

institute: Gladstone Institutes

description: Library name: dTAG_24h_rep1

library_source: genomic

data_processing:
Hi-C 3.0 data were processed using 4D Nucleome (4DN) Hi-C data Processing Pipeline (v0.2.7) (https://data.4dnucleome.org/resources/data-analysis/hi_c-processing-pipeline), which generated .mcool file with iterative correction and eigenvector decomposition (ICE) normalization.
Reads were mapped to GRCh38 using bwa.
Valid HiC alignments were filtered using pairtools.
Biological replicates were merged using https://github.com/4dn-dcic/docker-4dn-hic/blob/master/scripts/run-merge-pairs.s
The pairs files were converted to cool files using cooler.
Assembly: hg38
Supplementary files format and content: .mcool file of interaction contact frequencies at different resolutions

molecule: genomic DNA

growth_protocol: An FKBP12F36V with 2x HA (DOI: 10.1038/s41589-018-0021-8) tag was used to generate a cell line in which TBX5 could be induced for degradation. The tag was inserted immediately after the start methionine codon in the N-terminus of the endogenous TBX5 locus using ribonucleoprotein (RNP) complexes of sgRNA (GCCCTCGTCTGCGTCGGCCA, ordered from Synthego) and SpCas9-NLS ‘HiFi’ protein (QB3 MacroLab, University of California Berkeley). Donor template sequences for each were provided by using HDR Alt-R gene blocks (IDT). 250,000 WTc11 iPSCs were resuspended in 12.2 µl Lonza P3 transfection buffer and nucleofected with 1 µg donor template and 10 µl RNPs using Lonza Nucleofector 4D system in 96-well format using DS-138 settings. Single cell colonies were screened by PCR using primers pairs flanking the whole insertion site (F: 5’-TCCTCAGAGCAGAACCTTGC, R: 5’-CTTACCTGCTGGGTGAAGG). Amplicon from whole insertion site PCR was amplified and verified by Sanger sequencing. All clones used were determined to have a normal karyotype.  Atrial (StemCell Technologies #100-0215) kits were used to differentate iPSCs into cardiomyocytes. At d20, each sample was treated with DMSO or dTAGv-1 (Tocris, #6914) ligand for 24 h before harvesting.

extract_protocol:
CMs were grown in 3 wells of a 6-well dish per replicate, with all 3 wells pooled together after dissociation for the crosslinking step (approximately 10 million cells). CMs were dissociated in 0.25% Trypsin-EDTA for 10 mins, followed by quenching in 15%FBS in DPBS. CMs were lifted off the dish and resuspended to single cells by repeatedly using P1000 pipette and then transferred to a 15 ml tube and centrifuged at 800 rpm for 5 min at room temperature. Pellets were washed once in 5 ml HBSS before resuspending entire cell pellet in exactly 10 ml HBSS. 16% methanol-free formaldehyde was added to a final concentration of 1% and samples incubated on nutator at room temperature for 10 min. Samples were quenched with 2.5 M glycine to a final concentration of 0.125 M and incubated on nutator at room temperature for 5 min, then 15 min at 4˚C and followed by centrifugation at 1000 x g for 5 min at room temperature. Samples were washed once in DPBS. Pellets were resuspended in 1 ml of 3 mM DSG in PBS, transferred to 1.5 ml tubes and incubated on nutator for 40 min. Samples were quenched with 2.5 M glycine to a final concentration of 0.125 M and incubated on nutator at room temperature for 5 min. Samples were centrifuged at 2000 x g for 5 min at RT. Cell pellets were resuspended in 5 mg/ml BSA in DPBS, to prevent cells sticking to tube after DSG crosslinking, and centrifuged at 2000 x g for 5 min at 4˚C. Supernatant was carefully removed and cell pellets were snap frozen in liquid nitrogen and stored at -80˚C.
Samples were processed for Hi-C using Arima-HiC+ kit (Arima Genomics). >1 µg per sample was used as determined by Arima’s Estimating Input Amount Protocol using Qubit Fluorometer and dsDNA HS Assay Kit (ThermoFisher Scientific #Q32854) Samples were processed by following manufacturer’s user guide for mammalian cell lines with one exception: DNA was digested using 50 U DpnII (New England Biolabs #R0543M) and 50 U DdeI (New England Biolabs #R0175L) restriction enzymes in 1x NEB Buffer 3.1 for 60 min at 37˚C. All samples passed Arima-QC1 Quality Control. Sequencing libraries were prepared by following Arima’s user guide for Library Prep Using KAPA Hyper Prep Kit (Roche #7962347001). Between 1.5-4 µg of DNA was fragmented in 130 µl microtube (Covaris #520045) using a Covaris S2 sonicator for 55s at 10% duty cycle, intensity 4, 200 cycles per burst in a water bath maintained at 4˚C. An average fragment size of 400 bp was verified using Agilent 2100 Bioanalyzer. Between 400-1000 ng of size-selected DNA was used for biotin enrichment, end repair, dA-tailing and adapter ligation. The number of PCR cycles was determined following Arima-QC2 Quality Control using KAPA Library Quantification Kit (Roche KK4824) and libraries were amplified to at least 10 nM. All samples passed Arima-QC2 Quality Control. DNA cleanup steps were done using Ampure XP beads (Beckman Coulter #A63881). Final libraries were quantified using Qubit Fluorometer and dsDNA HS Assay Kit and assessed on Agilent BioAnalyzer. Pooled, equimolar libraries were sequenced using NovaSeq technology (Illumina).

tag: cell type

value: cardiomyocyte

tag: genotype

value: WT

value: 500 nM dTAGv-1 ligand


title: Organoids_SOX2_ASO_Macrophages

city: Boston

first: Evgeny

last: Deforzh

state: MA

address: 60 Fenwood Rd, Brigham and Women's Hospital Neurology Department, 9th Floor

department: Neurology

institute: Brigham and Women's Hospital

description: Library name: Sample 12

data_processing:
Resulting fastq files were demultiplexed based on cell barcodes
Quantification of unique 25 nt long random sequences [Barcode] for each cell
Assembly: GRCh38/hg38

source_name: human brain organoids with glioma stem cells

extract_protocol:
Both dead and viable cell populations were single-cell deposited into individual wells of a 96-well plate, having a PCR-compatible Proteinase K-based lysis buffer (10 mM Tris-HCl (pH 8.0), 50 mM KCl, 2.5 mM MgCl2, 0.45% NP-40, 0.45% Tween-20, Proteinase K (100 µg/mL)), followed by 55°C, 30 min incubation to disrupt both cell and nuclear membranes and then heat-inactivation of the Proteinase K at 95°C for 10 minutes.
ASO Barcodes (DNA) from different wells were amplified for Illumina sequencing with the combination of cell barcodes unique for each well (Illumina DNA/RNA Unique Dual Indexes (UDI)

tag: tissue


title: RTX_TS_RIP

city: Budapest

first: Angela

last: Bekesi

address: Műegyetem rakpart 3.

department: Department of Applied Biotechnology and Food Science

country: Hungary

institute: Budapest University of Technology and Economics, Faculty of Chemical Technology and Biotechnology

description: Library name: UPL24-005157

data_processing:
Quality was checked using fastQC, residual rRNA-related reads were removed in silico, then polyG, adapter, and low-quality sequences were trimmed using the fastp tool.
A subsampling by random selection of half of the reads (A50) was performed to produce pseudoreplicates for the statistical analysis.
Clean reads were aligned to the human reference genome GRCh38  using HiSAT2 aligner.
Aligned data were filtered for the core chromosomes.
Samples were compared to the corresponding RIPctr samples using the Cufflinks package (cuffnorm and cuffdiff).
Read coverage and log2(fold change) tracks were calculated for the forward and reverse strands, respectively, using the deeptools package. From these tracks, TS-RIP enrichment was also calculated for exons.
Assembly: GRCh38
Supplementary files format and content: The *reverse.filtered.bw and *forward.filtered.bw files contain the strand-selective coverage tracks in bigwig format.
Supplementary files format and content: The *log2.filtered.bw files contain the log2(fold change) signal tracks calculated from the coverage of TS-RIP vs RIPctr samples in bigwig format.
Supplementary files format and content: The *.diff files contain the results of the Cuffdiff analysis comparing TS-RIP and RIPctr samples.

growth_protocol: Cells were maintained in McCoy’s 5A medium supplemented with 10% FBS and 1% PenStrep.

extract_protocol:
Cells were harvested, counted, and resuspended in cytoplasmic extraction buffer then centrifuged; the pellet was extracted with nuclear extraction buffer. Cytoplasmic and nuclear extracts were combined, and glycerol was added. Lysates were pre-cleared with magnetic Protein A/G beads, then subjected to RIP with anti-TS antibody (Proteintech 15047-1-AP) and captured on Protein A/G beads. Beads were washed, eluted in elution buffer (also containing proteinase K) at 60 °C for 30 min, and RNA was purified using the Geneaid VR050 kit. RNA concentration was measured by Qubit and integrity checked by agarose gelelectrophoresis.
The libraries for Illumina sequencing were prepared using xGen RNA Lib Prep Kit (Integrated DNA Technologies, Iowa, USA) according to the Manufacturer's suggestions.

treatment_protocol: Cells were cultured in 6-well plates, treated with 100 nM RTX or 20 µM 5FdUR for 48 hours.

value: colon adenocarcinoma

value: MMR deficient, UGI inhibited

value: 100 nM RTX


title: I-epi-4w-WT-1-734

city: Taipei

first: Linda

last: Yu

address: 1 Jen-Ai Rd. Sec. 1

country: Taiwan

institute: National Taiwan University

data_processing:
The library was loaded onto the instrument with Sequel Sequencing Kit 2.1 (4 rxn) (Part Number PB 101-310-500) and a Sequel™ SMRT® Cell 1M v2 Tray (4 cells) (Part Number PB101-008-000) for sequencing.
Assembly: The training method of the QIIME2 classifier follows these steps: - Extract all the read datafrom a reference database, in our report, SILVA version 138 with 99% similarity was used.
Supplementary files format and content: File name = abs-abund-table-7 (all 90 samples); Format = excel (.xlsx); Content = raw counts of sequencing reads for the bacteria strain
Supplementary files format and content: File name = rel-table-7 (all 90 samples); Format = excel (.xlsx); Content=relative abundance of sequencing reads for the bacteria strain

organism: Mus musculus

source_name: ileum epithelial cell

extract_protocol:
Fecalpellets werecollected asepticallyand placed in sterile eppendorf. Immediately freezing stool in liquid nitrogen (LN) and store at -80°C. Extract stool bacterial DNA followed by QIAamp Fast DNA Stool Kit protocol.
For the PacBio library construction and sequencing, 16S rRNA was amplified by using primer set 27F: AGRGTTYGATYMTGGCTCAG and 1492R: RGYTACCTTGTTACGACTT followed by purification via binding to pre-washed AMPure PB beads (Part Number PB100-265-900)
16S ribosomal RNA (rRNA) gene sequencing

value: ileum epithelial cell

value: Untreated

tag: time

value: 4 weeks old


title: Hi-C of Homo sapiens: D20 of atrial cardiomyocyte (CM) differentiation with DMSO vehicle treated for 24h rep2

description: Library name: DMSO_24h_rep2

value: DMSO vehicle


title: ATRT-MYC cell line CHLA-266 before treatment

description: Library name: CHLA-266 untreated

value: no


title: Organoids_SOX2_ASO_GSC_DEAD

description: Library name: Sample 11

value: human brain organoids with glioma stem cells


title: SCP_4

city: Qingdao

first: yinghuan

last: jing

address: No. 238, Songling Road, Laoshan District

department: College of Food Science and Engineering

country: China

institute: Ocean University of China

description:
Library name: SCP_4
The SCPs group was the intervention group. Human chondrocytes were first treated with 20 ng/mL IL-1β for 24 hours to induce an inflammatory model. After the induction, the medium was replaced with complete medium supplemented with 600 μg/mL sturgeon cartilage protein peptides (SCPs). The cells were then cultured for an additional 48 hours before being harvested for sampling.

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to hg38  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text files include gene count, fpkm value and TPM value for each Sample

source_name: Human Primary Chondrocytes

extract_protocol:
RNA was extracted from cell culture using TRIzol reagent. Briefly, cell culture samples were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA is enriched for small RNAs, followed by 3' and 5' adapter ligation. Reverse transcription generates cDNA, which is then PCR amplified with indexed primers. The final library is size-selected (typically ~150 bp) and validated by Bioanalyzer before sequencing on an Illumina flow cell.

value: Human Primary Chondrocytes


title: ATRT-MYC cell line BT-16 after treatment

description: Library name: BT-16 treated

value: 1 µM doxorubicin + 5 µM etoposide + 1 µm vincristine


title: Organoids_SOX2_ASO_GSC

description: Library name: Sample 10


title: SCP_3

description:
Library name: SCP_3
The SCPs group was the intervention group. Human chondrocytes were first treated with 20 ng/mL IL-1β for 24 hours to induce an inflammatory model. After the induction, the medium was replaced with complete medium supplemented with 600 μg/mL sturgeon cartilage protein peptides (SCPs). The cells were then cultured for an additional 48 hours before being harvested for sampling.


title: ATRT-MYC cell line BT-16 before treatment

description: Library name: BT-16 untreated


title: Hi-C of Homo sapiens: D20 of atrial cardiomyocyte (CM) differentiation with DMSO vehicle treated for 24h rep1

description: Library name: DMSO_24h_rep1


title: ChIP-seq of Homo sapiens: atrial cardiomyocyte differentiation at D20 from WT WTC11 rep2 - RAD21

description: Library name: TBX5_WT_RAD21_rep2

data_processing:
Fastq files were aligned to the hg38 reference genome using bowtie2. Reads were filtered to include of those with a mapq score of 30 or greater and removing duplicate reads using SAMtools. Blacklisted regions were removed using BEDtools. RAD21 and WT H3K27ac ChIP-seq peaks were called on each individual replicate relative to input using macs2 and the broadpeaks parameter. H3K27ac ChIP-seq data used for differential analysis between WT, TBX5in/+ and TBX5in/del samples were analyzed using the nextflow chip-seq pipeline with the macs2 broadpeaks parameter (DOI: 10.1038/s41587-020-0439-x)
Assembly: hg38
Supplementary files format and content: .narrowPeak of peaks and .bw of signal profiles
Supplementary files format and content: .bed for consensus or merged peaks

growth_protocol: Atrial (StemCell Technologies #100-0215) kits were used to differentate iPSCs into cardiomyocytes. Cells were grown in one 6-well plate per replicate, with all 6 wells pooled together after dissociation for the crosslinking step (approximately 20 million cells). Each plate was one biological replicate.

extract_protocol:
Cells were grown in one 6-well dish per replicate, with all 6 wells pooled together after dissociation for the crosslinking step (approximately 20 million cells). Cells were dissociated in 0.25% Trypsin-EDTA for 10 mins, followed by quenching in 15%FBS in DPBS. Cells were lifted off the dish and resuspended to single cells by repeatedly using P1000 pipette and then transferred to a 15 ml tube and centrifuged at 800 rpm for 5 min at room temperature. Pellets were washed once in 10 ml DPBS plus 1x protease inhibitors (DBPS+PI) before resuspending entire cell pellet in exactly 10 ml DPBS+PI. 16% methanol-free formaldehyde was added to a final concentration of 1% and samples incubated on nutator at room temperature for 10 min. Samples were quenched with 2.5 M glycine to a final concentration of 0.125 M and incubated on nutator at room temperature for 5 min, followed by centrifugation at 500 x g for 5 min at 4˚C. Samples were washed once in ice cold DPBS+PI, before being transferred to 2 ml protein lo-bind tubes, centrifuged at 2500 x g at 4˚C. for 5 min and cell pellets were snap frozen in liquid nitrogen and stored at -80˚C. Cell lysis for 10 min at 4˚C (cell lysis buffer recipe: 20 mM Tris-HCl pH 8.0, 85 mM KCl, 0.5% IGEPAL CA-630 and 1x protease inhibitors in ddH2O). Nuclear lysis for 30 min on ice  (nuclear lysis buffer recipe: 1% SDS, 10 mM EDTA, 50 mM Tris-HCl, pH 8.0, and 1x protease inhibitors in ddH2O). Samples were transferred to 1 ml millitube (Covaris #520130) and sheared using a Covaris S2 sonicator for 15 min at 5% duty cycle, intensity 5, 200 cycles per burst in a water bath maintained at 4˚C. 60 µg of chromatin was used per sample. After diluting in dilution buffer, each ChIP sample was incubated rotating at 4˚C overnight with antibodies (9 µg rabbit anti-RAD21 [Abcam, #ab992] or 10 µg rabbit anti-H3K27ac [Active Motif, #39133] and the following day incubated with 50 µl prewashed Pierce protein A/G beads for 4 hours at 4˚C. Bead washes were performed by resuspending beads in 1 ml buffer using P1000 pipette, spinning briefly and collecting on magnet. Wash buffer 1 recipe (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 0.1% SDS and 1% Triton X-100 in ddH2O), wash buffer 2 recipe (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2 mM EDTA, 0.1% SDS and 1% Triton X-100 in ddH2O) and wash buffer 3 (250 mM LiCl, 1% IGEPAL CA-630 [Sigma #I8896], 1% sodium deoxycholate, 1 mM EDTA and 10 mM Tris-HCl pH 8.0 in ddH2O) and elution buffer (1% SDS, 100 mM NaHCO3 in ddH2O). Following the bead washes, DNA was eluted in 50 µl shaking at 37˚C, transferring to new tube and repeating bead elution to pool eluates to a total volume of 100 µl. Both ChIP and input samples were incubated at 37˚C for 30 min at 37˚C with 1 µl RNase A, followed addition of 12 µl 5 M NaCl and reverse crosslinking with 1 µl proteinase K at 65˚C overnight. DNA was purified using ChIP DNA Clean and Concentrator kit (Zymo Research #D5205).
For Illumina sequencing library preparation, the entire ChIP sample or 2 µl of each input was used. End repair was performed in a 100 µl reaction with 15 U T4 DNA polymerase (New England Biolabs #M0203L), 5 U Klenow fragment DNA polymerase (New England Biolabs, #M0210L), 50 U T4 PNK (New England Biolabs #M0201L), 400 µM dNTP (Promega #U1511) and 1x T4 DNA ligase buffer w 10 mM ATP (New England Biolabs #B0202S) in nuclease-free water for 30 min at room temperature, followed by 1.6x bead:sample AmpureXP purification. Entire eluate was used for A-tailing in a 50 µl reaction with 1 mM dATP (New England Biolabs #N0440S), 15 U Klenow 3’>5’ exonuclease (New England Biolabs #M0212L) and 1x NEB buffer 2 in nuclease-free water for 30 min at 37˚C, followed by 1.6x bead:sample AMPureXP purification. Entire eluate was used for adapter ligation in a 50 µl reaction with 6000 U T4 DNA ligase (New England Biolabs #M0202L), 20 nM annealed and uniquely indexed adapters and 1x T4 DNA ligase buffer with 10 mM ATP (New England Biolabs #B0202S) in nuclease-free water for 2 hours at room temperature, followed by 1x bead:sample AMPureXP purification. Adapters were prepared by annealing following HPLC purified oligos: 5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC*T and 5’Phos-GATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG where * represents a phosphothiorate bond and NNNNNN is a Truseq index sequence.The entire eluate was used for PCR amplification in a 50 µl reaction with 1x NEB Next High-Fidelity 2x PCR master mix (New England Biolabs #M0541L), 10 µM primers (F: 5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGA, R: 5’-CAAGCAGAAGACGGCATACGAGAT) in nuclease free water, using thermocycler settings 98˚C for 30 sec; 16 cycles of 98˚C for 10 sec, 58˚C for 40 sec and 72˚C for 30 sec; 72˚C for 5 min and followed by 0.8x bead:sample AMPureXP purification. DNA was quantified using Qubit Fluorometer and dsDNA HS Assay Kit and quality assessed on Agilent Bioanalyzer. ChIP-seq libraries were sequenced on a NovaSeq X (Illumina) using 50 bp paired-end reads.

value: atrial cardiomyocyte differentation


title: C50D50-AF

city: Daejeon

first: In-Hwan

last: Jang

address: 125, Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea

department: Immunotherapy Research Center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

description: Library name: Samples 3

data_processing:
HISAT2 software (ver. 2.2.0) was used to index the reference genome and map sequencing reads of samples.
Samtools (ver. 1.15.1) was used to convert BAM files
FeatureCounts (ver. 2.0.1) software was used to calculate the generated BAM files
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: A549 cells and human lung fibroblasts (HLFs) were used in this sample; the cells were mixed with 1% collagen and lung-derived dECM to form spheroids.

growth_protocol: The non-small cell lung cell line (A549, H460, PC-9, H1650) was cultured in Roswell Park Memorial Institute (RPMI; Welgen, South Korea) medium 1640 containing 10% fetal bovine serum (FBS; R&D Systems, USA) and 1% antibiotic-antimycotic (anti-anti-; Gibco, USA). The human lung fibroblast was cultured in DMEM (Gibco) with 10% FBS and 1% penicillin.

extract_protocol:
Total RNA was extracted using an RNA extraction kit (#74104, QUIAGEN, Germany) following the manufacturer’s instructions. The separated cells were used for the RT-qPCR of the tumor and NK cells. RNA was extracted, and complementary deoxyribonucleic acid (cDNA) was synthesized using a cDNA synthesis kit (#PSK-101, Toyobo, Japan).
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA with Ribo-Zero H/M/R_Gold

treatment_protocol: A hydrogel was prepared using 1% collagen and dECM from the lung of a porcine. The prepared hydrogel and cell (A549, fibroblast) were mixed at a density of 1×10^7. The ratio of tumor cells to fibroblasts was 2:1.

value: A549 + HLF

value: lung cancer + fibroblast


title: Organoids_SOX2_ASO_Endothelial

description: Library name: Sample 9


title: ChIP-seq of Homo sapiens: atrial cardiomyocyte differentiation at D20 from WT WTC11 rep1 - RAD21

description: Library name: TBX5_WT_RAD21_rep1

value: cardiomyocyte


title: SCP_2

description:
Library name: SCP_2
The SCPs group was the intervention group. Human chondrocytes were first treated with 20 ng/mL IL-1β for 24 hours to induce an inflammatory model. After the induction, the medium was replaced with complete medium supplemented with 600 μg/mL sturgeon cartilage protein peptides (SCPs). The cells were then cultured for an additional 48 hours before being harvested for sampling.


title: C50D50-A

description: Library name: Samples 2

source_name: A549 cell line was used in this sample; the spheroids were formed by mixing the cells with 1% collagen and lung-derived dECM.

value: lung cancer


title: ATRT-MYC primary tumor #12

description: Library name: MYC #12

source_name: FFPE AT/RT primary tumor

extract_protocol:
RNA isolation from FFPE tissue samples was performed using “Maxwell® RSC RNA FFPE Kit” (Promega). 10 ng were used as input for library construction.
RNA libraries for RNA-seq were constructed using the SMART-Seq Stranded kit (Takara Bio) according to the manufacturer’s specifications

value: FFPE AT/RT primary tumor

value: A


title: I-epi-20w-WT-5-777

value: 20 weeks old


title: SCP_1

description:
Library name: SCP_1
The SCPs group was the intervention group. Human chondrocytes were first treated with 20 ng/mL IL-1β for 24 hours to induce an inflammatory model. After the induction, the medium was replaced with complete medium supplemented with 600 μg/mL sturgeon cartilage protein peptides (SCPs). The cells were then cultured for an additional 48 hours before being harvested for sampling.


title: Organoids_SOX2_ASO_Astrocytes

description: Library name: Sample 8

value: WT


title: ATRT-MYC primary tumor #11

description: Library name: MYC #11


title: C100-A

description: Library name: Samples 1

source_name: A549 cell line was used to form spheroids, prepared by mixing the cells with 1% collagen.


title: NT_negative_control

description: Library name: UPL24-005153

value: colon adenocarcinoma

value: MMR deficient, UGI inhibited


title: TBX5 degron + 500 nM dTAGv-1 ligand (24 h) rep 1 - RNAseq

description:
Library name: dTAGv1_TBX5-degron_24h_RNAseq_rep1
TBX5-degron_dTAGv-1_24h_rep1

data_processing:
The .fastq files were aligned to hg38 reference genome using HISAT2 for alignment and featureCounts (2.0.6) was used to count the reads numbers mapped to each gene. Differential expression analysis for two conditions/groups was performed using the DESeq2 R package(1.42.0). DESeq2 provides statistical programs for determining differential expression in digital gene expression data using models based on negative binomial distribution. The resulting P-value is adjusted using the Benjamini and Hochberg’s methods to control the error discovery rate.
Assembly: hg38
Supplementary files format and content: .txt format of gene counts and fpkm values

molecule: polyA RNA

source_name: atrial cardiomyocyte differentation

growth_protocol: An FKBP12F36V with 2x HA (DOI: 10.1038/s41589-018-0021-8) tag was used to generate a cell line in which TBX5 could be induced for degradation. The tag was inserted immediately after the start methionine codon in the N-terminus of the endogenous TBX5 locus using ribonucleoprotein (RNP) complexes of sgRNA (GCCCTCGTCTGCGTCGGCCA, ordered from Synthego) and SpCas9-NLS ‘HiFi’ protein (QB3 MacroLab, University of California Berkeley). Donor template sequences for each were provided by using HDR Alt-R gene blocks (IDT). 250,000 WTc11 iPSCs were resuspended in 12.2 µl Lonza P3 transfection buffer and nucleofected with 1 µg donor template and 10 µl RNPs using Lonza Nucleofector 4D system in 96-well format using DS-138 settings. Single cell colonies were screened by PCR using primers pairs flanking the whole insertion site (F: 5’-TCCTCAGAGCAGAACCTTGC, R: 5’-CTTACCTGCTGGGTGAAGG). Amplicon from whole insertion site PCR was amplified and verified by Sanger sequencing. All clones used were determined to have a normal karyotype. Cells were grown in 1 well of a 12-well dish per replicate. Atrial (StemCell Technologies #100-0215) kits were used to differentate iPSCs into cardiomyocytes. DMSO or dTAGv-1 samples were treated at d20 with DMSO or 500 nM dTAGv-1 (Tocris, #6914) ligand for 24 h before harvesting.

extract_protocol:
Cells were dissociated in 0.25% Trypsin-EDTA for 10 mins, followed by quenching in 15%FBS in DPBS. Cells were lifted off the dish and resuspended to single cells by repeatedly using P1000 pipette and then transferred to a 1.5 ml tube and centrifuged at 300 x g for 5 min at room temperature. Pellets were snap frozen in dry ice. Total RNA was isolated using Qiagen RNeasy micro kit (Qiagen #74004) with QIAshredder (Qiagen #79656) and eluted in 25 µl water. RNA concentration was determined using Nanodrop and quality was checked using Agilent Bioanalyzer.
Messenger RNA was purified from total RNA using poly-T oligo-attachedmagnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the secondstrand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

value: TBX5-FKBP12-F36V edited WTC11

value: 500 nM dTAGv-1 ligand (24 h)


title: Organoids_Control_ASO_OPC

description: Library name: Sample 7


title: MO_4

description:
Library name: MO_4
The MO group served as the model group. Human chondrocytes were first treated with 20 ng/mL interleukin-1β (IL-1β) for 24 hours to induce an inflammatory model. After the induction, the medium was replaced with fresh complete medium, and the cells were cultured for an additional 24 hours. The cells were then collected for sampling.


title: ATRT-MYC primary tumor #10

description: Library name: MYC #10


title: D5_ki67-myc+_ROI11_S1_Milademetan

city: Umeå

first: Lixiao

last: Wang

state: Sverige

address: Medicinsk biovetenskap, M21, Försörjningsvägen 1

department: Department of Medical Biosciences

country: Sweden

institute: Umeå University

description:
Library name: DSP-1001660037306-B-B09
Tumor D5, Slide S1, ROI 11, Segment ki67-myc+, Replicate D5_ki67-myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.

data_processing:
FASTQ files were converted to DCC count files via NanoString GeoMx NGS Pipeline. DCC files loaded into R using GeomxTools (Bioconductor). Segment QC: min 1,000 reads, 75% alignment, 50% saturation, 20 nuclei, 1,000 um2 area. Probe QC: ratio >0.1, Grubbs outlier removal. Aggregated to gene-level by geometric mean.
Counts imported into standR (Bioconductor) as SpatialExperiment. Low-expression genes filtered (sample_fraction=0.9, min_count=5). TMM normalization (edgeR). Batch effects assessed by PCA.
DE analysis: limma-voom with duplicateCorrelation (tumor as block). Treatment comparisons per cell population. Gene set analysis: limma::camera for MYC targets, ribosomal, cell cycle, apoptosis pathways. Significance: BH-adjusted P < 0.05 and |log2FC| > 0.5.
R (v4.4.2), GeomxTools, standR, limma, edgeR, SpatialExperiment (Bioconductor).
Assembly: hg38 (GRCh38)
Supplementary files format and content: DCC files: per-AOI probe-level count files from NanoString GeoMx NGS Pipeline, containing raw/trimmed/stitched/aligned read counts and per-probe expression values
Supplementary files format and content: standR_counts.txt: tab-delimited gene-level raw count matrix (genes x 92 AOIs)
Library strategy: Spatial Transcriptomics

source_name: Raji Burkitt lymphoma xenograft

growth_protocol: Raji Burkitt lymphoma cells (ATCC CCL-86, p53 R213Q) were harvested during logarithmic growth, washed, and resuspended in serum-free media. A total of 5x10^6 cells in 200 uL of a 1:1 mixture of Matrigel and medium were injected subcutaneously into the right flank of 6-8-week-old NSG mice (Charles River). Tumors grew to approximately 100-150 mm3 before randomization.

extract_protocol:
FFPE tumor sections were processed on the NanoString GeoMx Digital Spatial Profiler (DSP) at the Genomic Medicine Sweden Center North / Clinical Genomics Umea. Sections were stained with fluorescent antibodies against Ki67 and c-Myc. Within each ROI, cells were segmented into four populations: Ki67+MYC+, Ki67-MYC+, Ki67-MYC-, and Ki67+MYC-. UV-cleavable oligonucleotide tags from each segment (AOI) were collected for library preparation.
Libraries were prepared using the NanoString GeoMx NGS Library Preparation Kit per manufacturer protocol. Human NGS Whole Transcriptome Atlas (WTA v1.0) panel (~18,000 genes). Each AOI received a unique indexing barcode. 92 AOIs across 10 tumors on four slides (S1-S4), each slide containing both conditions.

treatment_protocol: Mice were randomized into milademetan-treated (n=5) and vehicle control (n=5) groups. Milademetan (20 mg/kg) or vehicle was administered daily by oral gavage for 15 days. Tumors were harvested, formalin-fixed, and paraffin-embedded (FFPE).

value: Raji Burkitt lymphoma xenograft

value: Raji (ATCC CCL-86)

value: Milademetan 20mg/kg


title: ChIP siHJ H3K9me3 465

city: Yonago

first: Junichiro

last: Ohzeki

address: 86 Nishi-cho

department: Chromosome Engineering Research Center

country: Japan

institute: Tottori University

description:
Library name: PC count ChIP siHJ H3K9me3 465
Competitive PCR product derived from ChIP DNA

data_processing:
Fastq files were generated by Miseq base calling.
Sequencing reads were trimmed with cutadapt 4.0 using Python 3.9.13.
Trimmed reads were matched against the indexed list of the position code DNA using bowtie.
The number of reads for each the position code was obtained using samtools idxstats (1.11).
Assembly: The index list of the position code DNA (See also supplementary Inofrmation)
Supplementary files format and content: Tab-delimited text file includes raw counts for each the position code.

source_name: Connective tissue

growth_protocol: Human HT1080 and derived cells were cultured in the DMEM Glutamax I (10569010, Gibco) supplemented with the 10% tet-system approved Fetal Bovine Serum (631101, TAKARA) at 37˚ C and 5% CO2

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes at RT. After quenching and hypotonic treatment, then cells were sonicated using a picoruptor 2 apparatus (Diagenode).
A DNA pool of triplicate ChIP was prepared and 10 μl of the pool was used for competitive PCR to the construction of sequencing library.

value: Connective tissue

value: Fibrosarcoma

value: carrying HAC 4-65

value: siHJURP

tag: chip antibody


title: Organoids_Control_ASO_Oligodendrocyte

description: Library name: Sample 6

value: human brain organoids with glioma stem cells


title: MO_3

description:
Library name: MO_3
The MO group served as the model group. Human chondrocytes were first treated with 20 ng/mL interleukin-1β (IL-1β) for 24 hours to induce an inflammatory model. After the induction, the medium was replaced with fresh complete medium, and the cells were cultured for an additional 24 hours. The cells were then collected for sampling.

value: Human Primary Chondrocytes


title: ATRT-MYC primary tumor #9

description: Library name: MYC #9

value: FFPE AT/RT primary tumor


title: ChIP siHJ H3K36me2 465

description:
Library name: PC count ChIP siHJ H3K36me2 465
Competitive PCR product derived from ChIP DNA


title: Organoids_Control_ASO_Neurons

description: Library name: Sample 5


title: I-epi-8w-Apc-5-757

value: ileum epithelial cell

value: ApcMin

value: Untreated

value: 8 weeks old


title: Shg_rep1

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

description: Library name: Shg_rep1

data_processing:
Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome dm6 with TopHat v2.0.13 , default parameters , using Ensembl 87 gene models. FPKM values were generated using Cufflinks v2.2.1 with “-u –max-bundle-frags 100000000”. Read counts were generated using HTSeq-count with “-m intersection-nonempty”.
Assembly: dm6
Supplementary files format and content: FPKM expression table in csv file

organism: Drosophila melanogaster

source_name: Ovary

extract_protocol:
Newly emerged flies expressing UAS-GFP and E-cadherin RNAi driven by c587ts in IGS cells were cultured for 1 week at 29°C. The ovaries were then dissected, placed in Grace’s medium, washed twice with 1X DPBS, and centrifuged at 700 g for 1 minute. Next, the ovaries were incubated in prewarmed collagenase solution at 37°C in a water bath for 3 minutes with gentle shaking, after which the enzymatic reaction was stopped by adding cold 1X DPBS containing 2% FBS. The dissociated samples were washed with 1X DPBS and centrifuged at 700 g and 4°C for 5 minutes. The cell pellet was resuspended in 1X DPBS, filtered through a 70 µm cell strainer, pelleted again by centrifugation, and finally resuspended in 200 µl of 1X DPBS for immediate sorting of GFP-positive cells.
1,000 cells from each of three biological replicates for both the control and E-cadherin RNAi groups were collected. cDNA was synthesized using the SMART-seq v4 Ultra Low Input RNA kit, and libraries were prepared with the Nextera XT DNA Sample Preparation Kit and Index kits. Both cDNA samples and libraries were quality-checked on a Bioanalyzer 2100 before RNA sequencing. Libraries were sequenced as 75-bp paired-end reads on an Illumina NextSeq platform, generating over 20 million FASTQ reads per sample.

value: Ovary

value: IGS cell

value: RNAi knockdown of shg


title: MO_2

description:
Library name: MO_2
The MO group served as the model group. Human chondrocytes were first treated with 20 ng/mL interleukin-1β (IL-1β) for 24 hours to induce an inflammatory model. After the induction, the medium was replaced with fresh complete medium, and the cells were cultured for an additional 24 hours. The cells were then collected for sampling.


title: ATRT-MYC primary tumor #8

description: Library name: MYC #8

value: B


title: ChIP siHJ K4K20me1 465

description:
Library name: PC count ChIP siHJ K4K20me1 465
Competitive PCR product derived from ChIP DNA


title: Organoids_Control_ASO_Macrophages

description: Library name: Sample 4

value: WT


title: OPC_RNA_SCIENCE

description: Library name: Sample 15

data_processing:
Duplicate reads were collapsed into a fasta file, with duplicate counts per read calculated using fastx_toolkit (version 0.0.14).
Chimeric reads were aligned to a reference fasta file containing transcript sequences (hg38_Homo_sapiens.GRCh38.100.fasta) using BWA-MEM in local alignment mode considered transcript strand only
Pairs of genes from each chimeric read were identified, and the number of reads for each gene pair was quantified with ChiRA
Assembly: GRCh38/hg38

source_name: primary glioma tumors

extract_protocol:
Nuclei were distributed into 96-well plates by limiting dilution. Nuclear membranes were lysed and chromatin was reverse-crosslinked by incubation with Proteinase K for 4 h at 65 °C followed by 15 min 95 °C to deactivate Proteinase K.  Biotinylated RNA complexes were captured using streptavidin magnetic beads and transferred to fresh wells. For 3′ RNA end repair, bead-enriched RNA–RNA crosslinked material was washed in ice-cold T4 polynucleotide kinase (PNK) buffer and treated with 0.5 U T4 PNK (NEB) in an 80-µL reaction at 37 °C for 4 h. Subsequently, fresh ATP (1 mM final) and an additional 0.5 U T4 PNK were added in a total volume of 100 µL and incubated for 1 h at 37 °C to repair 5′ RNA ends, followed by the removal of the buffer. RNA–RNA chimeras were generated by ligation in T4 RNA ligase buffer (NEB) supplemented with 1 mM ATP, 0.5 U/µL RNase inhibitor, and 2.5 U/µL T4 RNA ligase 1 (NEB) at 37 °C for 1 h with continuous agitation. Reverse crosslinking was completed by UV irradiation at 254 nm for 5 min on ice. RNA on Streptavidine beads was washed once with 1x scRT Buffer (Takara, #634444).
RT and subsequent steps were performed using the SMART-Seq® Stranded Kit (Takara, #634444), following the manufacturer’s instructions.

value: primary glioma tumors


title: I-epi-8w-Apc-4-756


title: ATRT-MYC primary tumor #7

description: Library name: MYC #7


title: ChIP siHJ H4K8ac 465

description:
Library name: PC count ChIP siHJ H4K8ac 465
Competitive PCR product derived from ChIP DNA

value: Connective tissue


title: MO_1

description:
Library name: MO_1
The MO group served as the model group. Human chondrocytes were first treated with 20 ng/mL interleukin-1β (IL-1β) for 24 hours to induce an inflammatory model. After the induction, the medium was replaced with fresh complete medium, and the cells were cultured for an additional 24 hours. The cells were then collected for sampling.


title: Organoids_Control_ASO_GSC

description: Library name: Sample 3


title: Con_4

description:
Library name: Con_4
The CON group consisted of human chondrocytes cultured in complete medium for 48 hours. After the 48-hour culture period, the cells were harvested for sampling.


title: ATRT-MYC primary tumor #6

description: Library name: MYC #6


title: D5_ki67+myc+_ROI9_S1_Milademetan

description:
Library name: DSP-1001660037306-B-B06
Tumor D5, Slide S1, ROI 9, Segment ki67+myc+, Replicate D5_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.

value: Raji Burkitt lymphoma xenograft

value: Raji (ATCC CCL-86)

value: Milademetan 20mg/kg


title: Oligodendrocytes_RNA_SCIENCE

description: Library name: Sample 14


title: ChIP siHJ H3K14ac 465

description:
Library name: PC count ChIP siHJ H3K14ac 465
Competitive PCR product derived from ChIP DNA

value: Fibrosarcoma

value: carrying HAC 4-65

value: siHJURP

value: H3K14ac (7G8, Kimura Lab.)


title: Organoids_Control_ASO_Endothelial

description: Library name: Sample 2

value: human brain organoids with glioma stem cells


title: ATRT-MYC primary tumor #5

description: Library name: MYC #5

value: FFPE AT/RT primary tumor


title: ChIP siHJ H3K4me2 465

description:
Library name: PC count ChIP siHJ H3K4me2 465
Competitive PCR product derived from ChIP DNA


title: Con_3

description:
Library name: Con_3
The CON group consisted of human chondrocytes cultured in complete medium for 48 hours. After the 48-hour culture period, the cells were harvested for sampling.

value: Human Primary Chondrocytes


title: Organoids_Control_ASO_Astrocytes

description: Library name: Sample 1


title: ATRT-MYC primary tumor #4

description: Library name: MYC #4


title: Con_2

description:
Library name: Con_2
The CON group consisted of human chondrocytes cultured in complete medium for 48 hours. After the 48-hour culture period, the cells were harvested for sampling.


title: ChIP siHJ CENPA 465

description:
Library name: PC count ChIP siHJ CENPA 465
Competitive PCR product derived from ChIP DNA

value: CENP-A (A1, Masumoto Lab.)


title: Con_1

description:
Library name: Con_1
The CON group consisted of human chondrocytes cultured in complete medium for 48 hours. After the 48-hour culture period, the cells were harvested for sampling.


title: ATRT-MYC primary tumor #3

description: Library name: MYC #3


title: scRNAseq_organoids_SOX2_ASO_treatment_7

description: Library name: Sample 35

library_source: transcriptomic single cell

data_processing:
Forward and Reverse reads of each fastq file were merged with FLASH (v1.2.11, Minimum overlap=1)
Resulting reads were aligned to GRCh38/hg38 genome assembly with Hisat2 (v2.2.1; default parameters)
Number of reads in genes were quantified with featureCounts for each cell (v2.1.1; using Comprehensive Gencode gene annotation v29)
Assembly: GRCh38/hg38

source_name: brain organoids with glioma stem cells

extract_protocol:
Both dead and viable cell populations were single-cell deposited into individual wells of a 96-well plate, having a PCR-compatible Proteinase K-based lysis buffer (10 mM Tris-HCl (pH 8.0), 50 mM KCl, 2.5 mM MgCl2, 0.45% NP-40, 0.45% Tween-20, Proteinase K (100 µg/mL)), followed by 55°C, 30 min incubation to disrupt both cell and nuclear membranes and then heat-inactivation of the Proteinase K at 95°C for 10 minutes. Polyadenylated (polyA) messenger RNA (mRNA and lncRNA) was captured using Dynabeads Oligo(dT)25 magnetic beads (Thermo Fisher Scientific, Cat. No. 61002) and transferred to a separate 96-well processing plate for transcriptome library preparation.
Reverse transcription (RT), template switching, and secondary cDNA amplification of the isolated polyA-selected mRNA fractions were conducted using the SMART-Seq Stranded Kit (Takara Bio, Cat. No. 634444) in strict accordance with instructions.

value: brain organoids with glioma stem cells


title: scRNAseq_organoids_SOX2_ASO_treatment_6

description: Library name: Sample 34


title: ChIP siK7 H3K9me3 465

description:
Library name: PC count ChIP siK7 H3K9me3 465
Competitive PCR product derived from ChIP DNA


title: 786-O cells, sgPLOD2, rep3

city: Beijing

first: Jian

last: Liu

state: Beijing

address: hujialou

institute: Beijing Chaoyang Hospital

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCH38 whole genome using hisat2 v2.1.0 with default parameters.
Transcript FPKM were calculated using Stringtie v1.3.4 with default parameters.
Assembly: GRCH38
Supplementary files format and content: comma-separated values (CSV) file includes FPKM values for each sample

source_name: kidney

growth_protocol: 786-O cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Trizol reagent. 3 ug of total was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: kidney

value: Adenocarcinoma; Renal Cell

value: PLOD2 knockout


title: ATRT-MYC primary tumor #2

description: Library name: MYC #2

value: A


title: 786-O cells, sgPLOD2, rep2


title: scRNAseq_organoids_SOX2_ASO_treatment_5

description: Library name: Sample 33

value: WT


title: ChIP siK7 K4K20me1 465

description:
Library name: PC count ChIP siK7 K4K20me1 465
Competitive PCR product derived from ChIP DNA

value: Connective tissue


title: 786-O cells, sgPLOD2, rep1


title: WT F6, rep3

city: Stockholm

first: Sören

last: Lehmann

address: Blickagången 16

department: the Department of Medicine

institute: Karolinska Institute

description:
Library name: 4C_EC_12
other

data_processing:
Demultiplexing was performed using bcl2fastq (v2.20.0). Reads were aligned to the GRCh38 reference genome from Ensembl using STAR (v2.7.9a). Aligned reads were assigned to coding regions of various biotypes defined in Homo_sapiens.GRCh38.111.gtf from Ensembl using featureCounts (v1.5.1).
Gene annotations were retrieved from Ensembl BioMart via the biomaRt R package. Differential ex-pression analysis was performed using the DESeq2 R package. P-values were computed using the Wald test and adjusted for multiple testing with the Benjamini–Hochberg correction.
Assembly: GRCh38
Supplementary files format and content: excle file includes raw read count, normalized count and differential expression analysis result

source_name: Hematopoietic system

growth_protocol: HL60 cells were cultured in RPMI-1640 with GlutaMAX and HEPES (Gibco) supplemented with 10% heat-inactivated fetal bovine serum (FBS, Thermo Scien-tific). The cell line was mycoplasma-free and grown in a humidified incubator at 37ºC and 5% CO2.

extract_protocol:
RNA sequencing of CATG00000106133.1 knockout (KO) HL60 clones was performed by extracting total RNA from HL60 KO and wild-type (WT) clones using the RNeasy Mini Kit (Qiagen). Total RNA was subjected to quality control with Agilent Tapestation according to the manufacturer’s instructions.
To construct libraries suitable for Illumina sequencing, the Illumina stranded mRNA prep ligation sample preparation protocol was used with starting concentration between 25-1000 ng total RNA. The protocol includes mRNA isolation, cDNA synthesis, ligation of adapters and amplification of indexed libraries. The yield and quality of the amplified libraries were analyzed using Qubit by Thermo Fisher and quality was checked by using Agilent Tapestation. The indexed cDNA libraries were normalized and combined, and the pools were sequenced on the Illumina Nextseq 2000 P2 100 cycles kit sequencing run, generating 58 base-paired end reads with dual index 10+10 base pairs.

value: Hematopoietic system

value: promyeloblast


title: scRNAseq_organoids_SOX2_ASO_treatment_3

description: Library name: Sample 31


title: 786-O cells, sgControl, rep3

value: Control


title: ChIP siK7 H4K8ac 465

description:
Library name: PC count ChIP siK7 H4K8ac 465
Competitive PCR product derived from ChIP DNA

value: Fibrosarcoma

value: carrying HAC 4-65


title: ChIP siK7 H3K14ac 465

description:
Library name: PC count ChIP siK7 H3K14ac 465
Competitive PCR product derived from ChIP DNA

value: H3K14ac (7G8, Kimura Lab.)


title: 786-O cells, sgControl, rep2


title: WT F6, rep1

description:
Library name: 4A_EC_4
other


title: ChIP siK7 H3K4me2 465

description:
Library name: PC count ChIP siK7 H3K4me2 465
Competitive PCR product derived from ChIP DNA


title: scRNAseq_organoids_SOX2_ASO_treatment_2

description: Library name: Sample 30


title: scRNAseq_organoids_SOX2_ASO_treatment_1

description: Library name: Sample 29


title: KO D10, rep3

description:
Library name: 2C_EC_10
other

value: HL60 KO


title: ChIP siK7 CENPA 465

description:
Library name: PC count ChIP siK7 CENPA 465
Competitive PCR product derived from ChIP DNA


title: scRNAseq_organoids_LINC01116_ASO_treatment_7

description: Library name: Sample 28


title: Rhesus macaque airway epithelial cells, WGBS, Wood smoke, 5 day, S4

city: Davis

first: Hong

last: Ji

state: California

address: One Shields Avenue

department: California National Primate Research Center

institute: University of California, Davis

description:
Library name: Sample 8
Whole genome bisulfite sequencing

data_processing:
Trim Galore used for adapter trimming
Bismark used for alignment to Mmul10 genome
Deduplication performed using Bismark
DMRs identified using DMRichR
Assembly: Mmul10
Supplementary files format and content: bedGraph files (compressed .bedGraph.gz) containing genome-wide CpG methylation levels (percent methylation) for each sample

organism: Macaca mulatta

source_name: Airway epithelium

growth_protocol: Primary tracheobronchial epithelial cells isolated from adult female rhesus macaques were expanded and cultured on Transwell inserts. Upon reaching confluence, cells were differentiated at air–liquid interface using BEGM:DMEM (1:1) supplemented with retinoic acid, with media changes every 2–3 days.

extract_protocol:
Genomic DNA was extracted using the Qiagen AllPrep DNA/RNA Micro Kit following manufacturer’s instructions and quantified using Qubit fluorometry.
Whole genome bisulfite sequencing libraries were prepared using Swift Accel-NGS Methyl-Seq Kit. Libraries were quality checked using Bioanalyzer and sequenced on an Illumina NovaSeq 6000 platform (paired-end 150 bp).

treatment_protocol: Differentiated primary tracheobronchial epithelial cells cultured at air–liquid interface were exposed to filtered air or diluted whole wood smoke for 6 hours per day for 5 consecutive days prior to DNA extraction.

value: Airway epithelium

value: female

tag: age days

tag: weight kgs

tag: animal id


title: ChIP siC H3K9me3 465

description:
Library name: PC count ChIP siC H3K9me3 465
Competitive PCR product derived from ChIP DNA

value: siControl


title: KO D10, rep2

description:
Library name: 2B_EC_6
other


title: ChIP siC H3K36me2 465

description:
Library name: PC count ChIP siC H3K36me2 465
Competitive PCR product derived from ChIP DNA


title: TTchem, INTS12_PHD_siINTS12_+DOX_REP3

city: Copenhagen N

first: Jesper

last: Svejstrup

state: Denmark

address: Blegdamsvej 3, 18.6

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

description:
Library name: INTS12_PHD_REP3
Nascent RNA

library_source: other

data_processing:
Reads were processed using the publicly available nf-core rnseq pipeline v3.3 with the STAR (Dobin et al., 2012)
RPKM normalised bigwig files generated using deepTools bamCoverage function with options: --normalizeUsing RPKM --exactScaling –effectiveGenomeSize (Ramirez et al., 2014)
NOTE: The 11 nt UMIs are provided in separate 'R2' fastq files
Assembly: GRCh38
Supplementary files format and content: bigwig files for forward and reverse strands

molecule: other

source_name: HEK293 FlpIn-TREx

extract_protocol:
As descriebd in Gregersen et al., 2020, Nat Protoc.
NEBNext Ultra II Direcional RNA Library Prep Kit for Illumina with UMI Adaptors

value: HEK293 FlpIn-TREx

value: Inducible INTS12 (dPHD)


title: KO D10, rep1

description:
Library name: 2A_EC_2
other


title: scRNAseq_organoids_LINC01116_ASO_treatment_5

description: Library name: Sample 26

value: brain organoids with glioma stem cells


title: ChIP siC K4K20me1 465

description:
Library name: PC count ChIP siC K4K20me1 465
Competitive PCR product derived from ChIP DNA


title: Rhesus macaque airway epithelial cells, WGBS, Wood smoke, 5 day, S1

description:
Library name: Sample 5
Whole genome bisulfite sequencing


title: scRNAseq_organoids_LINC01116_ASO_treatment_4

description: Library name: Sample 25


title: TTchem, INTS12_PHD_siINTS12_+DOX_REP2

description:
Library name: INTS12_PHD_REP2
Nascent RNA


title: ChIP siC H4K8ac 465

description:
Library name: PC count ChIP siC H4K8ac 465
Competitive PCR product derived from ChIP DNA


title: scRNAseq_organoids_LINC01116_ASO_treatment_3

description: Library name: Sample 24


title: Rhesus macaque airway epithelial cells, WGBS, Filtered air, 5 day, S4

description:
Library name: Sample 4
Whole genome bisulfite sequencing


title: scRNAseq_organoids_LINC01116_ASO_treatment_2

description: Library name: Sample 23


title: 786-O cells, sgControl, rep1

value: kidney

value: Adenocarcinoma; Renal Cell


title: TTchem, INTS12_PHD_siINTS12_+DOX_REP1

description:
Library name: INTS12_PHD_REP1
Nascent RNA


title: ChIP siC H3K14ac 465

description:
Library name: PC count ChIP siC H3K14ac 465
Competitive PCR product derived from ChIP DNA


title: TTchem, INTS12_WT_siINTS12_+DOX_REP3

description:
Library name: INTS12_WT_REP3
Nascent RNA

value: Inducible INTS12 (WT)


title: ChIP siC H3K4me2 465

description:
Library name: PC count ChIP siC H3K4me2 465
Competitive PCR product derived from ChIP DNA

value: Connective tissue


title: scRNAseq_organoids_LINC01116_ASO_treatment_1

description: Library name: Sample 22

value: WT


title: Rhesus macaque airway epithelial cells, WGBS, Filtered air, 5 day, S2

description:
Library name: Sample 2
Whole genome bisulfite sequencing


title: TTchem, INTS12_WT_siINTS12_+DOX_REP2

description:
Library name: INTS12_WT_REP2
Nascent RNA


title: ChIP siC CENPA 465

description:
Library name: PC count ChIP siC CENPA 465
Competitive PCR product derived from ChIP DNA

value: CENP-A (A1, Masumoto Lab.)


title: scRNAseq_organoids_Control_ASO_treatment_7

description: Library name: Sample 21


title: ChIP siHJ H3K9me3 120

description:
Library name: PC count ChIP siHJ H3K9me3 120
Competitive PCR product derived from ChIP DNA

value: carrying HAC 1-20

value: siHJURP


title: TTchem, INTS12_WT_siINTS12_+DOX_REP1

description:
Library name: INTS12_WT_REP1
Nascent RNA


title: Rhesus macaque airway epithelial cells, WGBS, Filtered air, 5 day, S1

description:
Library name: Sample 1
Whole genome bisulfite sequencing


title: scRNAseq_organoids_Control_ASO_treatment_6

description: Library name: Sample 20


title: Rhesus macaque airway epithelial cells, Wood smoke, Recovery, S4

description:
Library name: Sample 24
Column name in raw_counts_All_Samples.csv: WSR_4

data_processing:
Quality control performed using FastQC
Adapter and quality trimming performed using Trim Galore (adapter stringency = 6, quality cutoff = 20, 10 bp trimmed from 5′ ends, minimum length = 50 bp)
Reads aligned to the rhesus macaque transcriptome (Mmul10) using Bowtie2
Transcript quantification performed using RSEM
Gene-level counts generated using tximport for downstream analysis
Assembly: Mmul10
Supplementary files format and content: comma-delimited text file includes raw counts for each Sample

extract_protocol:
Cells were lysed using buffer RLT with beta-mercaptoethanol. RNA was extracted using the Qiagen AllPrep DNA/RNA Micro Kit according to manufacturer’s instructions. RNA quantity was measured using Qubit fluorometry.
Poly-A selected RNA libraries were prepared from 0.5 µg total RNA per sample using standard protocols. RNA quality (RIN ≥ 7) was confirmed prior to library preparation.

treatment_protocol: Differentiated primary tracheobronchial epithelial cells cultured at air–liquid interface were exposed to filtered air or diluted whole wood smoke for 6 hours per day for 1 day or 5 consecutive days. A subset of cells exposed for 5 days was allowed to recover for 7 days under standard culture conditions prior to sample collection.

value: Recovery


title: ChIP siHJ H3K36me2 120

description:
Library name: PC count ChIP siHJ H3K36me2 120
Competitive PCR product derived from ChIP DNA

value: Fibrosarcoma


title: TTchem, Parental_siINTS12_REP3

description:
Library name: INTS12_REP3
Nascent RNA

value: Parental


title: scRNAseq_organoids_Control_ASO_treatment_5

description: Library name: Sample 19


title: TTchem, Parental_siINTS12_REP1

description:
Library name: INTS12_REP1
Nascent RNA


title: ChIP siHJ H4K8ac 120

description:
Library name: PC count ChIP siHJ H4K8ac 120
Competitive PCR product derived from ChIP DNA


title: TTchem, Parental_siCTRL_REP3

description:
Library name: CTRL_REP3
Nascent RNA


title: scRNAseq_organoids_Control_ASO_treatment_3

description: Library name: Sample 17


title: Rhesus macaque airway epithelial cells, Wood smoke, Recovery, S1

description:
Library name: Sample 21
Column name in raw_counts_All_Samples.csv: WSR_1

value: Airway epithelium


title: ChIP siHJ H3K14ac 120

description:
Library name: PC count ChIP siHJ H3K14ac 120
Competitive PCR product derived from ChIP DNA

value: H3K14ac (7G8, Kimura Lab.)


title: scRNAseq_organoids_Control_ASO_treatment_2

description: Library name: Sample 16


title: Rhesus macaque airway epithelial cells, Filtered air, Recovery, S4

description:
Library name: Sample 20
Column name in raw_counts_All_Samples.csv: FAR_4

value: female


title: ChIP siHJ H3K4me2 120

description:
Library name: PC count ChIP siHJ H3K4me2 120
Competitive PCR product derived from ChIP DNA


title: TTchem, Parental_siCTRL_REP1

description:
Library name: CTRL_REP1
Nascent RNA

value: HEK293 FlpIn-TREx


title: scRNAseq_organoids_Control_ASO_treatment_1

description: Library name: Sample 15


title: Rhesus macaque airway epithelial cells, Filtered air, Recovery, S3

description:
Library name: Sample 19
Column name in raw_counts_All_Samples.csv: FAR_3


title: ChIP siHJ CENPA 120

description:
Library name: PC count ChIP siHJ CENPA 120
Competitive PCR product derived from ChIP DNA


title: scRNAseq_organoids_CDC42_ASO_treatment_7

description: Library name: Sample 14


title: Rhesus macaque airway epithelial cells, Filtered air, Recovery, S2

description:
Library name: Sample 18
Column name in raw_counts_All_Samples.csv: FAR_2


title: RNA-Seq, NELFA_R453A_siNELFA_+DOX_45'DRB_REP1

description:
Library name: NELFA_R453A_45_DRB_REP1
Nascent RNA

data_processing:
Reads were processed using the publicly available nf-core rnseq pipeline v3.3 with the STAR (Dobin et al., 2012)
RPKM normalised bigwig files generated using deepTools bamCoverage function with options: --normalizeUsing RPKM --exactScaling –effectiveGenomeSize (Ramirez et al., 2014)
Note: The first 11nt in the 5'-end of reads are the UMIs
Assembly: GRCh38
Supplementary files format and content: bigwig files for forward and reverse strands

value: Inducible NELFA (R453A)


title: scRNAseq_organoids_CDC42_ASO_treatment_6

description: Library name: Sample 13

value: brain organoids with glioma stem cells


title: Rhesus macaque airway epithelial cells, Filtered air, Recovery, S1

description:
Library name: Sample 17
Column name in raw_counts_All_Samples.csv: FAR_1


title: RNA-Seq, NELFA_R453A_siNELFA_+DOX_30'DRB_REP2

description:
Library name: NELFA_R453A_30_DRB_REP2
Nascent RNA


title: ChIP siK7 H3K36me2 120

description:
Library name: PC count ChIP siK7 H3K36me2 120
Competitive PCR product derived from ChIP DNA


title: scRNAseq_organoids_CDC42_ASO_treatment_5

description: Library name: Sample 12


title: Rhesus macaque airway epithelial cells, Wood smoke, 5 day, S4

description:
Library name: Sample 16
Column name in raw_counts_All_Samples.csv: WS5D_4


title: ChIP siK7 K4K20me1 120

description:
Library name: PC count ChIP siK7 K4K20me1 120
Competitive PCR product derived from ChIP DNA


title: scRNAseq_organoids_CDC42_ASO_treatment_4

description: Library name: Sample 11


title: Rhesus macaque airway epithelial cells, Wood smoke, 5 day, S3

description:
Library name: Sample 15
Column name in raw_counts_All_Samples.csv: WS5D_3


title: RNA-Seq, NELFA_R453A_siNELFA_+DOX_45'DRB_REP2

description:
Library name: NELFA_R453A_45_DRB_REP2
Nascent RNA


title: RNA-Seq, NELFA_R453A_siNELFA_+DOX_15'DRB_REP2

description:
Library name: NELFA_R453A_15_DRB_REP2
Nascent RNA


title: ChIP siK7 H4K8ac 120

description:
Library name: PC count ChIP siK7 H4K8ac 120
Competitive PCR product derived from ChIP DNA


title: Rhesus macaque airway epithelial cells, Wood smoke, 5 day, S2

description:
Library name: Sample 14
Column name in raw_counts_All_Samples.csv: WS5D_2


title: scRNAseq_organoids_CDC42_ASO_treatment_3

description: Library name: Sample 10


title: ChIP siK7 H3K9me3 120

description:
Library name: PC count ChIP siK7 H3K9me3 120
Competitive PCR product derived from ChIP DNA


title: RNA-Seq, NELFA_R453A_siNELFA_+DOX_15'DRB_REP1

description:
Library name: NELFA_R453A_15_DRB_REP1
Nascent RNA


title: scRNAseq_organoids_CDC42_ASO_treatment_2

description: Library name: Sample 9


title: ChIP siK7 H3K14ac 120

description:
Library name: PC count ChIP siK7 H3K14ac 120
Competitive PCR product derived from ChIP DNA


title: ChIP siK7 H3K36me2 465

description:
Library name: PC count ChIP siK7 H3K36me2 465
Competitive PCR product derived from ChIP DNA

value: carrying HAC 4-65


title: Rhesus macaque airway epithelial cells, Wood smoke, 5 day, S1

description:
Library name: Sample 13
Column name in raw_counts_All_Samples.csv: WS5D_1


title: ATRT-MYC primary tumor #1

description: Library name: MYC #1

data_processing:
Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq (version 2.20) and adapters were trimmed with Skewer (version 0.2.2)
Trimmed sequence reads were aligned to the human genome hg38 using STAR
The transcripts were counted as feature counts and these were used as input for the raw count table
Assembly: hg38
Supplementary files format and content: CSV file containing the filtered count table after removing repetitively counted genes and genes from sex chromosomes and only keeping protein-coding transcripts
Supplementary files format and content: CSV file containing the VST-normalized filtered count table

value: FFPE AT/RT primary tumor

value: A


title: RNA-Seq, NELFA_R453A_siNELFA_+DOX_REP2

description:
Library name: NELFA_R453A_REP2
Nascent RNA


title: ChIP siK7 H3K4me2 120

description:
Library name: PC count ChIP siK7 H3K4me2 120
Competitive PCR product derived from ChIP DNA

value: Connective tissue


title: scRNAseq_organoids_CDC42_ASO_treatment_1

description: Library name: Sample 8

value: WT


title: scRNAseq_organoids_SOX2_ASO_treatment_4

description: Library name: Sample 32


title: RNA-Seq, NELFA_R453A_siNELFA_+DOX_30'DRB_REP1

description:
Library name: NELFA_R453A_30_DRB_REP1
Nascent RNA


title: WT F6, rep2

description:
Library name: 4B_EC_8
other

value: Hematopoietic system

value: promyeloblast


title: Rhesus macaque airway epithelial cells, Filtered air, 5 day, S4

description:
Library name: Sample 12
Column name in raw_counts_All_Samples.csv: FA5D_4


title: RNA-Seq, NELFA_R453A_siNELFA_+DOX_REP1

description:
Library name: NELFA_R453A_REP1
Nascent RNA


title: ChIP siK7 CENPA 120

description:
Library name: PC count ChIP siK7 CENPA 120
Competitive PCR product derived from ChIP DNA

value: carrying HAC 1-20

value: CENP-A (A1, Masumoto Lab.)


title: scRNAseq_organoids_CD47_ASO_treatment_7

description: Library name: Sample 7


title: Rhesus macaque airway epithelial cells, Filtered air, 5 day, S3

description:
Library name: Sample 11
Column name in raw_counts_All_Samples.csv: FA5D_3


title: ChIP siC H3K9me3 120

description:
Library name: PC count ChIP siC H3K9me3 120
Competitive PCR product derived from ChIP DNA

value: Fibrosarcoma

value: siControl


title: RNA-Seq, NELFA_WT_siNELFA_+DOX_45'DRB_REP2

description:
Library name: NELFA_WT_45_DRB_REP2
Nascent RNA

value: Inducible NELFA (WT)


title: scRNAseq_organoids_LINC01116_ASO_treatment_6

description: Library name: Sample 27


title: Rhesus macaque airway epithelial cells, WGBS, Wood smoke, 5 day, S3

description:
Library name: Sample 7
Whole genome bisulfite sequencing

value: Airway epithelium


title: scRNAseq_organoids_CD47_ASO_treatment_6

description: Library name: Sample 6


title: Rhesus macaque airway epithelial cells, Filtered air, 5 day, S2

description:
Library name: Sample 10
Column name in raw_counts_All_Samples.csv: FA5D_2

value: female


title: RNA-Seq, NELFA_WT_siNELFA_+DOX_45'DRB_REP1

description:
Library name: NELFA_WT_45_DRB_REP1
Nascent RNA

value: HEK293 FlpIn-TREx


title: Rhesus macaque airway epithelial cells, WGBS, Wood smoke, 5 day, S2

description:
Library name: Sample 6
Whole genome bisulfite sequencing


title: ChIP siC H3K36me2 120

description:
Library name: PC count ChIP siC H3K36me2 120
Competitive PCR product derived from ChIP DNA


title: scRNAseq_organoids_CD47_ASO_treatment_5

description: Library name: Sample 5


title: RNA-Seq, NELFA_WT_siNELFA_+DOX_30'DRB_REP2

description:
Library name: NELFA_WT_30_DRB_REP2
Nascent RNA


title: Rhesus macaque airway epithelial cells, Filtered air, 5 day, S1

description:
Library name: Sample 9
Column name in raw_counts_All_Samples.csv: FA5D_1


title: ChIP siC K4K20me1 120

description:
Library name: PC count ChIP siC K4K20me1 120
Competitive PCR product derived from ChIP DNA


title: scRNAseq_organoids_CD47_ASO_treatment_4

description: Library name: Sample 4


title: scRNAseq_organoids_CD47_ASO_treatment_3

description: Library name: Sample 3


title: Rhesus macaque airway epithelial cells, Wood smoke, 1 day, S4

description:
Library name: Sample 8
Column name in raw_counts_All_Samples.csv: WS1D_4


title: ChIP siC H4K8ac 120

description:
Library name: PC count ChIP siC H4K8ac 120
Competitive PCR product derived from ChIP DNA


title: RNA-Seq, NELFA_WT_siNELFA_+DOX_30'DRB_REP1

description:
Library name: NELFA_WT_30_DRB_REP1
Nascent RNA


title: Rhesus macaque airway epithelial cells, Wood smoke, 1 day, S3

description:
Library name: Sample 7
Column name in raw_counts_All_Samples.csv: WS1D_3


title: Rhesus macaque airway epithelial cells, WGBS, Filtered air, 5 day, S3

description:
Library name: Sample 3
Whole genome bisulfite sequencing


title: RNA-Seq, NELFA_WT_siNELFA_+DOX_15'DRB_REP2

description:
Library name: NELFA_WT_15_DRB_REP2
Nascent RNA


title: ChIP siC H3K14ac 120

description:
Library name: PC count ChIP siC H3K14ac 120
Competitive PCR product derived from ChIP DNA

value: H3K14ac (7G8, Kimura Lab.)


title: scRNAseq_organoids_CD47_ASO_treatment_2

description: Library name: Sample 2

value: brain organoids with glioma stem cells


title: Rhesus macaque airway epithelial cells, Wood smoke, 1 day, S2

description:
Library name: Sample 6
Column name in raw_counts_All_Samples.csv: WS1D_2


title: RNA-Seq, NELFA_WT_siNELFA_+DOX_15'DRB_REP1

description:
Library name: NELFA_WT_15_DRB_REP1
Nascent RNA


title: ChIP siC H3K4me2 120

description:
Library name: PC count ChIP siC H3K4me2 120
Competitive PCR product derived from ChIP DNA


title: scRNAseq_organoids_CD47_ASO_treatment_1

description: Library name: Sample 1


title: Rhesus macaque airway epithelial cells, Wood smoke, 1 day, S1

description:
Library name: Sample 5
Column name in raw_counts_All_Samples.csv: WS1D_1


title: RNA-Seq, NELFA_WT_siNELFA_+DOX_REP2

description:
Library name: NELFA_WT_REP2
Nascent RNA


title: GROseq_NHA_RA_24h_rep2

description: Library name: Sample 6

data_processing:
Sequencing reads were aligned to the human reference genome (hg38) and Transcriptomic annotation Gencode Release 49 using STAR v2.5 (Dobin et al., 2013) in 2-pass mode.
BAM files were filtered for mapping quality (q >= 10) using SAMtools v0.1.19 (Li et al., 2009).
BAM files were normalized by dilution using a scaling factor derived from the ratio of Drosophila spike-in reads to the total number of mapped reads.
bigWig tracks were generated for visualization using deepTools v3.3.1
Assembly: GRCh38/hg38
Supplementary files format and content: bigwig
Library strategy: GRO-Seq

source_name: NHA

growth_protocol: Normal human astrocytes, immortalized via E6/E7 and hTERT expression (a generous gift from Dr. Yukihiko Sonoda), served as non-malignant controls. These cells were cultured in Astrocyte Medium (ScienCell, Cat# 1801) according to the manufacturer’s instructions.

extract_protocol:
RNA was extracted using TRIzol LS reagent (Invitrogen) according to the manufacturer’s instructions and recovered by ethanol precipitation.
Eluted RNA was quantified by Qubit and used for strand-specific library construction using the NEBNext Ultra II Directional RNA Library Prep kit (New England Biolabs). Libraries were sequenced on the Illumina NextSeq 500 platform.

treatment_protocol: Normal human astrocytes (NHAs) were seeded in 6-well plates and treated with All trans retinoic acid (SigmaAldrich,  R2500-25MG) diluted in DMSO according to manufacturer's protocol.

value: NHA

value: immortalized human astrocytes


title: ChIP siC CENPA 120

description:
Library name: PC count ChIP siC CENPA 120
Competitive PCR product derived from ChIP DNA


title: RNA-Seq, NELFA_WT_siNELFA_+DOX_REP1

description:
Library name: NELFA_WT_REP1
Nascent RNA


title: ChIP CR3 H3K9me3 465

description:
Library name: PC count ChIP CR3 H3K9me3 465
Competitive PCR product derived from ChIP DNA

value: carrying HAC 4-65

value: 3 hr after colcemid release


title: Rhesus macaque airway epithelial cells, Filtered air, 1 day, S4

description:
Library name: Sample 4
Column name in raw_counts_All_Samples.csv: FA1D_4


title: Rhesus macaque airway epithelial cells, Filtered air, 1 day, S3

description:
Library name: Sample 3
Column name in raw_counts_All_Samples.csv: FA1D_3


title: GROseq_NHA_RA_24h_rep1

description: Library name: Sample 5

value: WT


title: RNA-Seq, Parental_siNELFA_45'DRB_REP2

description:
Library name: NELFA_45_DRB_REP2
Nascent RNA

value: Parental


title: ChIP CR3 H3K36me2 465

description:
Library name: PC count ChIP CR3 H3K36me2 465
Competitive PCR product derived from ChIP DNA

value: Connective tissue


title: GROseq_NHA_RA_12h_rep2

description: Library name: Sample 4


title: Rhesus macaque airway epithelial cells, Filtered air, 1 day, S2

description:
Library name: Sample 2
Column name in raw_counts_All_Samples.csv: FA1D_2


title: ChIP CR3 K4K20me1 465

description:
Library name: PC count ChIP CR3 K4K20me1 465
Competitive PCR product derived from ChIP DNA


title: RNA-Seq, Parental_siNELFA_45'DRB_REP1

description:
Library name: NELFA_45_DRB_REP1
Nascent RNA


title: Rhesus macaque airway epithelial cells, Filtered air, 1 day, S1

description:
Library name: Sample 1
Column name in raw_counts_All_Samples.csv: FA1D_1


title: GROseq_NHA_RA_12h_rep1

description: Library name: Sample 3


title: Rhesus macaque airway epithelial cells, Wood smoke, Recovery, S3

description:
Library name: Sample 23
Column name in raw_counts_All_Samples.csv: WSR_3

value: Recovery


title: RNA-Seq, Parental_siNELFA_30'DRB_REP2

description:
Library name: NELFA_30_DRB_REP2
Nascent RNA


title: ChIP CR3 H4K8ac 465

description:
Library name: PC count ChIP CR3 H4K8ac 465
Competitive PCR product derived from ChIP DNA


title: GROseq_NHA_DMSO_rep2

description: Library name: Sample 2

value: DMSO


title: scRNAseq_organoids_Control_ASO_treatment_4

description: Library name: Sample 18


title: ChIP siHJ K4K20me1 120

description:
Library name: PC count ChIP siHJ K4K20me1 120
Competitive PCR product derived from ChIP DNA

value: Fibrosarcoma

value: carrying HAC 1-20

value: siHJURP


title: RNA-Seq, Parental_siNELFA_30'DRB_REP1

description:
Library name: NELFA_30_DRB_REP1
Nascent RNA


title: ChIP CR3 H3K14ac 465

description:
Library name: PC count ChIP CR3 H3K14ac 465
Competitive PCR product derived from ChIP DNA


title: GROseq_NHA_DMSO_rep1

description: Library name: Sample 1


title: RNA-Seq, Parental_siNELFA_15'DRB_REP2

description:
Library name: NELFA_15_DRB_REP2
Nascent RNA


title: Treated with 7,17-diHDPAn-3 Sample7

city: Jackson

first: Bioinformatics

last: Core

state: MISSISSIPPI

address: 2500 N state street

institute: Molecular and Genomics Core Facility

description: Library name: S_7_plusgata_1

data_processing:
Signal intensities were converted to individual base calls during a run using the system's Real Time Analysis (RTA) software.  Base calls are transferred from the machine's dedicated personal computer to the Yale High Performance Computing cluster via a 1 Gigabit network mount for downstream analysis. Primary analysis - sample de-multiplexing and alignment to the Zebrafish genome - is performed using Illumina's CASAVA 1.8.2 software suite. The data is returned to the user if the sample error rate is less than 2% and the distribution of reads per sample in a lane is within reasonable tolerance. Data is retained on the cluster for at least 6 months, after which it is transferred to a tape backup system. For RNA-seq data analysis, low quality reads were trimmed, and adaptor contamination was removed using Trim Galore (v0.5.0). Trimmed reads were mapped to the Zebrafish reference genome (GRCz11) using HISAT2 (v2.1.0). Gene expression levels were quantified using StringTie (v1.3.3b). Differentially expressed genes were identified using DESeq2 (v 1.22.1).
Assembly: Zebrafish reference genome: Danio rerio (GRCz11)
Supplementary files format and content: Gene level count data; gene_count_matrix.csv

organism: Danio rerio

source_name: Embryo

extract_protocol:
Total RNA was isolated from control and embryos treated with 7,17-diHDPAn-3 with Quick-RNA Miniprep Kit (Zymo Research), and cDNA was synthesized using iScript reverse transcription supermix (Bio-Rad). Total RNA quality was determined by measuring the A260/A280 and A260/A230 ratios by nanodrop. RNA integrity was determined by running an Agilent Bioanalyzer gel, which measures the ratio of ribosomal peaks.
Using the SMARTer Stranded Total RNA-Seq Kit v3- Pico Input Mammalian from Takara and a normalized RNA input between 250pg-10ng, the RNA was first fragmented prior to first strand cDNA synthesis. Next indexing and PCR1 was performed. After bead clean-up, ribosomal cDNA was depleted by ZapR v3 in the presence of mammalian specific R-probes. Next, fragments that were not cleaved in the depletion step were enriched in a second PCR before a final bead clean-up was performed. Indexed libraries that met appropriate cut-offs for both quantity and quality were quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the LabChip GX or Agilent Bioanalyzer. Samples with a yield of ≥0.5 ng/µl were used for sequencing. Sample concentrations were normalized to 2.0 nM and loaded onto an Illumina NovaSeq flow cell at a concentration that yields 25 million passing filter clusters per sample. Samples were sequenced using 100bp paired-end sequencing on an Illumina NovaSeq according to Illumina protocols. The 10bp unique dual index was read during additional sequencing reads that automatically follow the completion of read 1. Data generated during sequencing runs was simultaneously transferred to the Yale Center for Genome Analysis (YCGA) cluster. A positive control (prepared bacteriophage Phi X library) provided by Illumina is spiked into every lane at a concentration of 0.3% to monitor sequencing quality in real time.

value: Embryo

value: erythrocyte progenitors and erythrocytes

value: embryos treated with 7,17-diHDPAn-3


title: OPC_DNA_SCIENCE

description: Library name: Sample 7

data_processing:
Chimeric DNA–DNA reads consist of a viewpoint-specific sequence followed by one or more genomic fragments separated by CATG sites. Reads were split at CATG motifs using a custom awk script (deposited on Zenodo)
individual DNA segments were aligned to the human hg38 genome using Bowtie2 (default parameters)
Assembly: GRCh38/hg38
Supplementary files format and content: Interacting DNA segments with their genomic coordinates

extract_protocol:
Nuclei were distributed into 96-well plates by limiting dilution. Nuclear membranes were lysed and chromatin was reverse-crosslinked by incubation with Proteinase K for 4 h at 65 °C followed by 15 min 95 °C to deactivate Proteinase K.
DNA interactomic library preparation was performed using a two-step PCR approach. Locus-specific amplification was conducted using custom primers (Supplemental Table 1, PCR Round 1) containing Nextera-compatible universal adapter handles. Multiplexing was achieved in a second PCR step using Illumina DNA/RNA Unique Dual Indexes (UDI) Set A barcodes (Supplemental Table 1, PCR Round 2).

value: primary glioma tumors

value: OPC


title: RNA-Seq, Parental_siNELFA_15'DRB_REP1

description:
Library name: NELFA_15_DRB_REP1
Nascent RNA

value: HEK293 FlpIn-TREx


title: ChIP CR3 CENPA 465

description:
Library name: PC count ChIP CR3 CENPA 465
Competitive PCR product derived from ChIP DNA

value: CENP-A (A1, Masumoto Lab.)


title: Oligodendrocytes_DNA_SCIENCE

description: Library name: Sample 6

value: Oligodendrocytes


title: RNA-Seq, Parental_siNELFA_REP2

description:
Library name: NELFA_REP2
Nascent RNA


title: Treated with 7,17-diHDPAn-3 Sample5

description: Library name: S_5_plusgata_1


title: ChIP COL H3K9me3 465

description:
Library name: PC count ChIP COL H3K9me3 465
Competitive PCR product derived from ChIP DNA

value: carrying HAC 4-65

value: Colcemid


title: Neurons_DNA_SCIENCE

description: Library name: Sample 5

value: Neurons

value: WT


title: Control Sample4

description: Library name: S_4_ctr_2b_gata_1

value: Control


title: ChIP COL H3K36me2 465

description:
Library name: PC count ChIP COL H3K36me2 465
Competitive PCR product derived from ChIP DNA

value: Connective tissue


title: RNA-Seq, Parental_siNELFA_REP1

description:
Library name: NELFA_REP1
Nascent RNA

value: Parental


title: Control Sample3

description: Library name: S_3_ctr_gata_1


title: Macrophages_DNA_SCIENCE

description: Library name: Sample 4

value: Macrophages


title: RNA-Seq, Parental_siCTRL_45'DRB_REP2

description:
Library name: CTRL_45_DRB_REP2
Nascent RNA


title: ChIP COL K4K20me1 465

description:
Library name: PC count ChIP COL K4K20me1 465
Competitive PCR product derived from ChIP DNA

value: Fibrosarcoma


title: GSC_DNA_SCIENCE

description: Library name: Sample 3

value: GSC


title: RNA-Seq, Parental_siCTRL_45'DRB_REP1

description:
Library name: CTRL_45_DRB_REP1
Nascent RNA


title: Encothelial_DNA_SCIENCE

description: Library name: Sample 2

value: Encothelial


title: Control Sample1

description: Library name: S_1_ctr_gata_1

value: Embryo

value: erythrocyte progenitors and erythrocytes


title: ChIP COL H4K8ac 465

description:
Library name: PC count ChIP COL H4K8ac 465
Competitive PCR product derived from ChIP DNA


title: RNA-Seq, Parental_siCTRL_30'DRB_REP2

description:
Library name: CTRL_30_DRB_REP2
Nascent RNA


title: ChIP COL H3K14ac 465

description:
Library name: PC count ChIP COL H3K14ac 465
Competitive PCR product derived from ChIP DNA

value: H3K14ac (7G8, Kimura Lab.)


title: Astrocytes_DNA_SCIENCE

description: Library name: Sample 1

value: primary glioma tumors

value: Astrocytes


title: Mouse sperm, Untreated, 1.5ul Tn5, rep2

city: Atlanta

first: Katerina

last: Tsimaratou

state: GA

address: Whitehead Biomedical Research Building,615 Michael Street

department: Human Genetics

institute: Emory Univeristy

description: Library name: Sperm_ATAC_Untreated_1.5ul_rep2

data_processing:
All libraries were sequenced on an Illumina NovaSeq X Plus platform using 150-bp paired-end sequencing. Adapter sequences were trimmed using Trim Galore. Paired-end reads were aligned to the mouse reference genome (mm10) using Bowtie2 with default parameters except -X 2000. PCR duplicates were removed using Picard Tools. BAM files were filtered to retain properly paired reads with mapping quality ≥30 while excluding reads mapping to mitochondrial DNA (chrM), chromosome Y (chrY), unplaced contigs, and ENCODE mm10 blacklist regions. Read alignments were adjusted by offsetting reads mapped to the positive strand by +4 bp and reads mapped to the negative strand by −5 bp. Reads were separated into 50–115 bp and 180–247 bp fragment-size classes. Peaks were identified from the 50–115 bp fragments using MACS2 with the parameters --nomodel --nolambda. Genome-wide normalized bigWig tracks were generated from filtered BAM files using deepTools bamCoverage with RPKM normalization, a bin size of 10 bp, --ignoreForNormalization chrY chrM, and --minMappingQuality 30. Biological replicates were merged to generate the processed bigWig files deposited in GEO. Mono-nucleosomal occupancy profiles were generated using DANPOS2.
Assembly: mm10
Supplementary files format and content: bigWig (.bw) files containing genome-wide normalized ATAC-seq signal tracks generated from merged biological replicates. Signal tracks were generated separately for the 50–115 bp and 180–247 bp fragment-size classes from filtered, deduplicated alignments and normalized using deepTools bamCoverage with RPKM normalization (10-bp bins). The files are aligned to the mouse mm10 reference genome.

source_name: cauda epididymal sperm

extract_protocol:
After sperm counting, nuclei were isolated from 100,000 untreated or treated mouse sperm by centrifugation and lysis in buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl₂) containing 0.1% NP-40, 0.1% Tween-20, and 0.01% digitonin. Lysis was terminated with lysis buffer containing 0.1% Tween-20, and nuclei were pelleted by centrifugation. Purified nuclei were resuspended in the transposase reaction mixture containing 0.05% digitonin and incubated at 37°C for 35 min with shaking (1,000 rpm). Following transposition, genomic DNA was purified using proteinase K digestion followed by phenol:chloroform:isoamyl alcohol extraction and ethanol precipitation
Libraries were PCR-amplified using the 2× KAPA SYBR FAST ABI Prism Kit (Kapa Biosystems) and 2.5 µM indexed primers under the following conditions: 72°C for 5 min, 98°C for 30 s, followed by 13 cycles of 98°C for 10 s, 63°C for 30 s, and 72°C for 1 min. Libraries were sequenced on an Illumina NovaSeq X Plus platform using 150-bp paired-end sequencing.

value: cauda epididymal sperm

value: Untreated, 1.5ul Tn5


title: RNA-Seq, Parental_siCTRL_30'DRB_REP1

description:
Library name: CTRL_30_DRB_REP1
Nascent RNA

value: HEK293 FlpIn-TREx


title: ChIP COL H3K4me2 465

description:
Library name: PC count ChIP COL H3K4me2 465
Competitive PCR product derived from ChIP DNA

value: carrying HAC 4-65

value: Colcemid


title: Mouse sperm, Untreated, 1.5ul Tn5, rep1

description: Library name: Sperm_ATAC_Untreated_1.5ul_rep1


title: ChIP COL CENPA 465

description:
Library name: PC count ChIP COL CENPA 465
Competitive PCR product derived from ChIP DNA

value: CENP-A (A1, Masumoto Lab.)


title: 4Cseq_bulk_NHA_RA_24h_HOXDas2_viewpoint

description: Library name: Sample 29

data_processing:
First 20 nucleotides were trimmed from Forward Read
Trimmed reads were aligned with Bowtie2 (defaults)
Resulting BAMs were processed with r3Cseq (Thongjuea et al., 2013)
Assembly: GRCh37 (hg19)
Supplementary files format and content: bedgraph.gz
Library strategy: 4C-Seq

growth_protocol: GBM8 were maintained as neurospheres in serum-free Neurobasal medium (Gibco) supplemented with: B-27 Plus and N-2 supplements (Gibco), 3 mM GlutaMAX (Gibco), 20 ng/mL recombinant human FGF2 and EGF (Sigma-Aldrich), 2 μg/mL heparin (Sigma-Aldrich), 50 units/mL penicillin/streptomycin (Gibco). Normal human astrocytes, immortalized via E6/E7 and hTERT expression (a generous gift from Dr. Yukihiko Sonoda), served as non-malignant controls. These cells were cultured in Astrocyte Medium (ScienCell, Cat# 1801) according to the manufacturer’s instructions.

extract_protocol:
described in Peter Krijger et al., 2020
described in Peter Krijger et al., 2020

treatment_protocol: GBM8 or NHA cells were treated with siRNAs for 48 hours. NHA cells were treated with All trans retinoic acid (SigmaAldrich,  R2500-25MG) diluted in DMSO according to manufacturer's protocol. GBM8 cells were incubated with Proteinase K (Thermo Scientific, EO0491) for 48 hours

value: NHA

value: immortalized human astrocytes

value: WT

value: All Trans Retinoic Acid


title: Mouse sperm, Untreated, 2.5ul Tn5, rep2

description: Library name: Sperm_ATAC_Untreated_2.5ul_rep2

value: Untreated, 2.5ul Tn5


title: RNA-Seq, Parental_siCTRL_15'DRB_REP1

description:
Library name: CTRL_15_DRB_REP1
Nascent RNA

value: Parental


title: ChIP THYM H3K9me3 465

description:
Library name: PC count ChIP THYM H3K9me3 465
Competitive PCR product derived from ChIP DNA

value: Connective tissue

value: Fibrosarcoma

value: Thymdine


title: 4Cseq_bulk_NHA_RA_24h_HOXBas1_viewpoint

description: Library name: Sample 28


title: RNA-Seq, Parental_siCTRL_REP2

description:
Library name: CTRL_REP2
Nascent RNA


title: ChIP THYM H3K36me2 465

description:
Library name: PC count ChIP THYM H3K36me2 465
Competitive PCR product derived from ChIP DNA


title: 4Cseq_bulk_NHA_RA_24h_HOTAIRM1_viewpoint

description: Library name: Sample 27


title: Mouse sperm, SCLB+DNase I+DTT, rep2

description: Library name: Sperm_ATAC_SCLB_DNaseI_DTT_rep2

value: SCLB+DNase I+DTT


title: ChIP THYM K4K20me1 465

description:
Library name: PC count ChIP THYM K4K20me1 465
Competitive PCR product derived from ChIP DNA


title: 4Cseq_bulk_NHA_RA_24h_HOTAIR_viewpoint

description: Library name: Sample 26


title: Mouse sperm, SCLB+DNase I+DTT, rep1

description: Library name: Sperm_ATAC_SCLB_DNaseI_DTT_rep1


title: NELFA_R453A_siNELFA_+DOX_REP2

description: Library name: NELFA_R453A_REP2_PRO-seq

data_processing:
Illumina adapters were trimmed from the 3' ends of paired-end reads using Cutadapt, employing the parameters: '-a GNNNNNNTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC -A TNNNNNNGATCGTCGGACTGTAGAACTCTGAACGTGT -O 10 --minimum-length 10 --pair-filter=any'.
Unique Molecular Identifiers (UMIs) located at the first 7 bases of both reads were extracted using UMI-tools ('umi_tools extract --quality-filter-mask=10 --quality-encoding="phred33" --extract-method=string --bc-pattern=NNNNNNN --bc-pattern2=NNNNNNN').
The processed reads were aligned to the hg38 reference genome using Bowtie2 in '--very-sensitive' mode with '--non-deterministic --no-discordant --no-unal' flags. Reads with low mapping quality (MAPQ < 10) were removed via SAMtools. PCR duplicates were then identified and collapsed based on UMIs using the command: 'umi-tools dedup --paired'.
To determine the precise location of active RNAPII, single-base resolution BigWig files were generated from the first base of Read 1 using the bamCoverage function (deepTools) with parameters '--samFlagInclude 64 --offset 1 1 --binSize 1'.  Forward and reverse strand BigWig files were generated separately using the '--filterRNAstrand' option.
Assembly: hg38
Supplementary files format and content: bigwig files for forward and reverse strands
Library strategy: PRO-Seq

extract_protocol:
Nuclei were extracted following the 'Cell Permeabilization for PRO-seq' protocol from Nascent Transcriptomics Core at Harvard Medical School (https://ntc.hms.harvard.edu/file_url/141).
Quick PRO-seq libraries were prepared from 1 million nuclei following the protocol described by Judd et al. (bioRxiv, 2020). Four biotin-11-NTPs were used in the run-on reaction.


title: ChIP THYM H4K8ac 465

description:
Library name: PC count ChIP THYM H4K8ac 465
Competitive PCR product derived from ChIP DNA

data_processing:
Fastq files were generated by Miseq base calling.
Sequencing reads were trimmed with cutadapt 4.0 using Python 3.9.13.
Trimmed reads were matched against the indexed list of the position code DNA using bowtie.
The number of reads for each the position code was obtained using samtools idxstats (1.11).
Assembly: The index list of the position code DNA (See also supplementary Inofrmation)
Supplementary files format and content: Tab-delimited text file includes raw counts for each the position code.


title: Mouse sperm, SCLB+DNase I, rep2

description: Library name: Sperm_ATAC_SCLB_DNaseI_rep2

value: SCLB+DNase I


title: 4Cseq_bulk_NHA_RA_12h_LINC01116_viewpoint

description: Library name: Sample 25


title: ChIP THYM H3K14ac 465

description:
Library name: PC count ChIP THYM H3K14ac 465
Competitive PCR product derived from ChIP DNA

value: H3K14ac (7G8, Kimura Lab.)


title: NELFA_R453A_siNELFA_+DOX_REP1

description: Library name: NELFA_R453A_REP1_PRO-seq


title: 4Cseq_bulk_NHA_RA_12h_HOXDas2_viewpoint

description: Library name: Sample 24


title: Mouse sperm, SCLB+DNase I, rep1

description: Library name: Sperm_ATAC_SCLB_DNaseI_rep1

value: cauda epididymal sperm


title: NELFA_WT_siNELFA_+DOX_REP2

description: Library name: NELFA_WT_REP2_PRO-seq

value: HEK293 FlpIn-TREx


title: ChIP THYM H3K4me2 465

description:
Library name: PC count ChIP THYM H3K4me2 465
Competitive PCR product derived from ChIP DNA

value: carrying HAC 4-65


title: 4Cseq_bulk_NHA_RA_12h_HOXBas1_viewpoint

description: Library name: Sample 23


title: Mouse sperm, SCLB, rep2

description: Library name: Sperm_ATAC_SCLB_rep2

value: SCLB


title: Treated with 7,17-diHDPAn-3 Sample6

description: Library name: S_6_plusgata_1

value: Embryo

value: erythrocyte progenitors and erythrocytes

value: embryos treated with 7,17-diHDPAn-3


title: ChIP CR3 H3K4me2 465

description:
Library name: PC count ChIP CR3 H3K4me2 465
Competitive PCR product derived from ChIP DNA

value: 3 hr after colcemid release


title: NELFA_WT_siNELFA_+DOX_REP1

description: Library name: NELFA_WT_REP1_PRO-seq


title: ChIP THYM CENPA 465

description:
Library name: PC count ChIP THYM CENPA 465
Competitive PCR product derived from ChIP DNA

value: CENP-A (A1, Masumoto Lab.)


title: 4Cseq_bulk_NHA_RA_12h_HOTAIRM1_viewpoint

description: Library name: Sample 22

value: NHA

value: immortalized human astrocytes

value: WT

value: All Trans Retinoic Acid


title: INTS12_PHD_siINTS12_+DOX_REP2

description: Library name: INTS12_PHD_REP2_PRO-seq


title: Mouse sperm, SCLB, rep1

description: Library name: Sperm_ATAC_SCLB_rep1


title: ChIP CR3 H3K9me3 120

description:
Library name: PC count ChIP CR3 H3K9me3 120
Competitive PCR product derived from ChIP DNA

value: Connective tissue

value: Fibrosarcoma

value: carrying HAC 1-20


title: Mouse sperm, DNase I, rep2

description: Library name: Sperm_ATAC_DNaseI_rep2

value: DNase I


title: 4Cseq_bulk_NHA_RA_12h_HOTAIR_viewpoint

description: Library name: Sample 21


title: INTS12_PHD_siINTS12_+DOX_REP1

description: Library name: INTS12_PHD_REP1_PRO-seq


title: ChIP CR3 H3K36me2 120

description:
Library name: PC count ChIP CR3 H3K36me2 120
Competitive PCR product derived from ChIP DNA


title: Control Sample2

description: Library name: S_2_ctr_gata_1

value: Control


title: 4Cseq_bulk_NHA_DMSO_LINC01116_viewpoint

description: Library name: Sample 20

value: DMSO


title: INTS12_WT_siINTS12_+DOX_REP2

description: Library name: INTS12_WT_REP2_PRO-seq

value: HEK293 FlpIn-TREx


title: Mouse sperm, DNase I, rep1

description: Library name: Sperm_ATAC_DNaseI_rep1

value: cauda epididymal sperm


title: ChIP CR3 K4K20me1 120

description:
Library name: PC count ChIP CR3 K4K20me1 120
Competitive PCR product derived from ChIP DNA


title: 4Cseq_bulk_NHA_DMSO_HOXDas2_viewpoint

description: Library name: Sample 19


title: 4Cseq_bulk_NHA_RA_24h_LINC01116_viewpoint

description: Library name: Sample 30


title: Mouse sperm, Untreated, rep2

description: Library name: Sperm_ATAC_Untreated_rep2

value: Untreated


title: 4Cseq_bulk_NHA_DMSO_HOXBas1_viewpoint

description: Library name: Sample 18


title: INTS12_WT_siINTS12_+DOX_REP1

description: Library name: INTS12_WT_REP1_PRO-seq


title: ChIP CR3 H4K8ac 120

description:
Library name: PC count ChIP CR3 H4K8ac 120
Competitive PCR product derived from ChIP DNA


title: Mouse sperm, Untreated, rep1

description: Library name: Sperm_ATAC_Untreated_rep1


title: RNA-Seq, Parental_siCTRL_15'DRB_REP2

description:
Library name: CTRL_15_DRB_REP2
Nascent RNA

value: Parental


title: Parental_siNELFA_REP2

description: Library name: NELFA_REP2_PRO-seq


title: ChIP CR3 H3K14ac 120

description:
Library name: PC count ChIP CR3 H3K14ac 120
Competitive PCR product derived from ChIP DNA

value: H3K14ac (7G8, Kimura Lab.)


title: 4Cseq_bulk_NHA_DMSO_HOTAIRM1_viewpoint

description: Library name: Sample 17