title: A549_HEK293T_15k_lib_polyIC_chx

first: Shira

last: Weingarten-Gabbay

address: 75 Ames St

institute: The Broad Institute

description:
Human+synthetic library
Table_S1_pan_viral_library_MPRP_ORFs_PRICE.txt

data_processing:
Illumina sequencing reads were preprocessed prior alignment using FASTX-Toolkit. Illumina adapters were removed using fastx_clipper, reads were split according to samples barcodes using fastx_barcode_splitter.pl and UMI sequence was trimmed using fastx_trimmer. Reads that were mapped to rRNA were removed using bowtie (version 1.2.2). Remaining reads were aligned to an artificial genome composed of all library oligos using bowtie. We used PRICE to identify ORFs from deep sequencing reads (version 1.0.3). We generated a chimeric reference genome composed of chromosome 1 in hg19 and an artificial chromosome composed of 15,000 oligos of the pan-viral library. In addition, we generated a gtf file with the annotations of hg19 and library oligos required for PRICE predictions. For each experiment, we mapped deep sequencing reads to the chimeric fasta file using Bowtie. We filtered ORFs a p-value ≤0.05 after correcting for false discovery rate (FDR). ORFs were then defined by extending each initiating codon to the next in-frame stop codon in the corresponding viral genome.
Assembly: Chr1 of hg19 + synthetic library
Supplementary files format and content: Tab-delimited text file containing PRICE predicted ORFs with p-value and total number of reads for each ORF
Library strategy: Ribo-seq

organism:
Homo sapiens
synthetic construct

source_name: HEK293T human embryonic kidny cells; A549 lung carcinoma cells

extract_protocol:
10cm dishes of library-transfected HEK293T or A549 cells were treated with 100µg/mL cycloheximide (CHX) for 1 min or 10uM LTM for 30 min prior lysis. Cells were washed with ice-cold PBS containing 100µg/mL CHX and lysed on ice by scraping in 400ul lysis buffer (20 mM Tris pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100µg/mL CHX, 1% Triton X-100, 25 U/mL Turbo DNase).
30µg total RNA was digested with 15 units of RNase I (Epicenter) in 200µl polysome buffer (20 mM Tris pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100µg/ml CHX) for 45 min at room temperature. 10uL SUPERase*In were added to stop RNase I digestion and tubes were transferred to ice. Ribosome protected mRNA fragments (RPFs) were enriched using MicroSpin S-400 columns (GE Healthcare, catalog # 27-5140-01). Columns were pre-washed with a 3mL polysome buffer. 100uL of RNAse I digested lysates were loaded to each column and purified RPFs were collected to a new tube by centrifuging the column at 600 x g for 2 min. 400ul TRIzol was added to purified RPFs and RNA was extracted using Direct-zol kit according to manufacturer's instructions, including on column DNase I treatment, and eluted in 50uL water. RNA was participated by adding 38.5ul water, 1.5uL GlycoBlue, 10uL 3M NaOAc pH 5.5 and 150uL isopropanol and incubating on ice for 1hr (or overnight at -20oC). RNA was pelleted by centrifugation for 30 min at 20,000 x g 4˚C, air dried for 10 min and resuspended in 5uL 10mM Tris pH 8. RPFs in the size of 26-34 nt were selected on a 15% polyacrylamide TBE-Urea. RNA was extracted from the gel by adding 400uL RNA gel extraction buffer (300mM NaOAc pH 5.5, 1mM EDTA, and 0.25% SDS), freezing samples for 30 min on dry ice and thawing overnight at room temperature with a gentle mixing nutator. RNA was participated, washed with ice-cold 75% EtOH buffer, air dried and resuspended in 3uL water.rRNA was depleted using an RNase H-based digestion protocol and samples were eluted in 4uL water. RNA was dephosphorylated using T4 PNK reaction and ligated to a pre-adenylated linker using T4 RNA ligase. Unligated linkers were depleted by adding 5'-deadenylase and RecJf to the ligation reaction. Ligation products were purified using the Oligo Clean & Concentrator kit and reverse transcribed using protoscript II and RT primer. cDNA was gel purified using 10% polyacrylamide TBE-Urea gel. cDNA was extracted from gel by adding 400uL DNA gel extraction buffer (300mM NaCl, 10mM Tris pH 8, and 1 mM EDTA), freezing samples for 30 min on dry ice and thawing overnight at room temperature with a gentle mixing nutator. cDNA was participated, washed with ice-cold 75% EtOH buffer, air dried and resuspended in 12uL 10mM Tris pH 8. cDNA was circularized using CircLigase II. Sequencing library was PCR amplified from circular DNA using Phusion polymerase and Illumina-adaptor containing primers (10-12 cycles). Amplified library was purified from E-gel EX Agarose Gels 4% followed by SPRI beads cleaning. Library was quantified using Qubit dsDNA-HS and analyzed on a TapeStation D1000.

tag: internal linker(s)

value: HEK293T_15k_lib_cntrl_chx:NI810 (ATCGT); HEK293T_15k_lib_polyIC_12h_chx:NI811 (AGCTA); A549_15k_lib_cntrl_chx:NI812 (CGTAA); A549_15k_lib_polyIC_12h_chx:NI813 (CTAGA)


title: A549_15k_lib_polyIC_Thapsigargin_chx

status: Public on Jun 12 2025

type: SRA

city: Cambridge

state: MA

country: USA

library_source: other

molecule: other

source_name: A549 lung carcinoma cells

tag: cell line

value: A549 lung carcinoma cells

value: 15k_lib_cntrl_chx:NI810 (ATCGT); 15k_lib_polyIC_12h_chx:NI811 (AGCTA); 15k_lilb_polyIC_6h_chx:NI812 (CGTAA); 15k_lib_Thapsigargin_chx:NI813 (CTAGA)


title: ARI-4206r.5192_01

city: Memphis

first: Richard

last: Lee

state: TN

address: 262 Danny Thomas Place

department: Department of Chemical Biology and Therapeutics

institute: St. Jude Children's Research Hospital

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
The resulting reads were saved in FASTQ format and data was processed through the High-Performance Computing Facility at St. Jude.
Adapter content and quality trimming was performed using Cutadapt. The quality of the raw and trimmed reads was assessed using FastQC and MultiQC.
The resulting processed reads were aligned to the reference Staphylococcus aureus subsp. aureus ATCC33591 genome (Reference genome downloaded from ATCC website: https://genomes.atcc.org/genomes/bfa4253471534524) using STAR2.5.3a and aligned reads were counted using featureCounts.
Differential gene expression analysis was analyzed using DESeq2 in the R statistical computing environment.
Assembly: Reference genome downloaded from ATCC website: https://genomes.atcc.org/genomes/bfa4253471534524
Supplementary files format and content: Binary Alignment Map (.bam) files include aligned reads to Staphylococcus aureus subsp. aureus ATCC33591 reference genome described above.
Supplementary files format and content: tab-delimitated text (.txt) files include raw counts for each Sample

molecule: total RNA

organism: Staphylococcus aureus

source_name: Planktonic

growth_protocol: S. aureus subsp. aureus ATCC 33591 was cultured in tryptic soy broth shaking at 210 rpm at 37 °C.

extract_protocol:
After 30 minutes treatment, 5 mL of Bacterial RNAprotect (Qiagen) was added for 5 minutes at room temperature. The culture was then centrifuged at 3214 xg for 10 minutes at 4 °C and the supernatant discarded. An RNAeasy Plus Mini Kit (Qiagen; Cat. No. 74134) was used to extract the RNA following the manufacturer’s instructions utilizing mechanical lysis for Gram-positive bacteria.
Libraries were prepared from ribosomal RNA-depleted total RNA using Illumina Stranded Total RNA Prep, ligation with Ribo-Zero Plus mRNA Library Prep Kit according to the manufacturer’s instructions (Illumina, PN 20037135). Libraries were analyzed for insert size distribution using the 2100 BioAnalyzer High Sensitivity kit (Agilent). Libraries were quantified using the Quant-iT PicoGreen ds DNA assay (ThermoFisher). Paired-end 100 cycle sequencing was performed on a NovaSeq X Plus (Illumina).

treatment_protocol: Five mL of mid-log cultures (OD600 0.4-0.6) were treated with 1/2 MIC of ARI-4206 (0.125 mg/L), ARI-5192 (0.5 mg/L), rifampin (0.004 mg/L), or equilalent vehicle control (DMSO) for 30 minutes shaking at 210 rpm at 37 °C.

tag: strain

value: ATCC 33591, ARI-4206 resistant

tag: cell type

value: Planktonic

tag: treatment


title: HEK293T_15k_lib_EMCV_IRES_Polio_IRES_MPRP_chx

description: Human+synthetic library

source_name: HEK293T human embryonic kidny cells

value: HEK293T human embryonic kidny cells

value: 15k_lib_EMCV_IRES_chx:NI811 (AGCTA); 15k_lib_Polio_IRES_chx:NI810 (ATCGT)


title: WT.4206_03


title: AB10037_SB202

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

library_source: transcriptomic single cell

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode used i5+i7 barcodes each of them is unique in run, 1 error was allowed.  well-barcode N7 folowed by UMI N8 in read 2.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary files format and content: metadata_q.txt

molecule: polyA RNA

organism: Homo sapiens

extract_protocol:
Synovial fluid mononuclear cells and blood mononuclear cells were isolated within maximum 4 hours of sample collection. Synovial fluid samples were first filtered by 100-micron strainer into 50 ml tube and diluted 1:1 with ice cold FACS buffer (2mM EDTA, Ph 8.0, 0.5% bovine serum albumin in PBS). Blood samples were diluted 1:1 with ice cold FACS buffer. Synovial fluid and blood mononuclear cell separation was performed using density centrifugation media (Ficol-paque, GE Life Sciences) in a 1:1 ratio with the diluted synovial fluid or blood sample. Centrifugation (460g, 25min) was performed at 10◦C and the mononuclear cells were carefully aspirated and washed with ice cold FACS buffer. After a short centrifuge (360g, 5min), we resuspended the cell pellet in cryopreservation media (FCS+10%DMSO) and stored the samples in cryotube at -80◦C. Prior to single-cell sorting, samples were quickly defrosted at 37◦C bath and washed with heated (37 ◦C) RPMI-1640. We resuspended the cells in FACS buffer for staining and sorting.
3' end mRNA libraries were prepared for sequencing using SPID-seq (Yofe et al, Cancer Discovery 2023)

tag: gating

tag: diagnosis

value: Control

tag: tissue

value: Blood

tag: pid


title: WT.RIF_03

value: Rifampin 0.004 mg/L


title: HEK293T_15k_lib_arsenite_chx

value: 15k_lib_cntrl_chx:NI810 (ATCGT); 15k_lib_arsenite_chx:NI813 (CTAGA)


title: AB10032_SB202


title: WT.5192_03


title: ARI-4206r.DMSO_02

value: DMSO


title: WT.DMSO_03


title: WT.RIF_02


title: batch3_Ctrl_RNaseH_rep2

city: Hangzhou

first: Dong

last: Fang

state: Zhejiang

address: 866 Yuhangtang Road

department: Life Sciences Institute

country: China

institute: Zhejiang University

library_source: genomic

data_processing:
Raw reads were trimmed to remove adapters and low-quality sequences using Trim Galore (version 0.6.7) with the parameters ‘-q 20 --paired’.
Trimmed reads were uniquely mapped to the human reference genome (hg19) using Bowtie2 (version 2.3.5.1). The output SAM files were converted to sorted BAM files using SAMtools  (version 1.9).
Peaks were identified using MACS2  (version 2.2.7.1) with the parameters ‘--nomodel -f BAMPE -g hg’.
Genome coverage bigwig files were generated by BEDtools (version 2.26.0) genomecov and bedGraphToBigWig (version 4) with the parameter ‘-scale 1e6/ (the number of reads mapped to ecoli genome)’.
To eliminate the batch effects between ctrl and ctrl_RNaseH samples, bigwig files were further normalized by multiplying the factor ratio of ctrl samples in two batches.
Assembly: hg19
Supplementary files format and content: BigWig files
Library strategy: CUT&Tag

molecule: genomic DNA

extract_protocol:
Cells were harvested in NE buffer and then nuclei were collected by ConA beads. The beads were blocked by blocking buffer.  S9.6 antibodies (Abcam, Cat. #ab234957) were added by 1:100 dilution and then secondary antibodies were added to each sample. PA-Tn5 transposase were added to each sample to bind with second antibodies and then the Tn5 were activated by adding MgCl2. This step was used to fragment the genome and add reads to the fragmented DNA. Reactions were stopped by adding stop buffer. 0.9X of VAHTS DNA clean beads were added to each sample to extract the fragmented DNA. For negative control, RNase H were added before the primary antibodies were added.
Custom Barcodes Adapters(i5: AATGATACGGCGACCACCGAGATCTACAC-NNNNNNNN-TCGTCGGCAGCGTCAGATGTGTAT; i7: CAAGCAGAAGACGGCATACGAGAT-NNNNNNNN-GTCTCGTGGGCTCGGAGATGTG) were used as primers to add different index to each sample. PCR Master Mix (NEB, Cat. #M0541S) were used to amplify DNA fragments.

value: HeLa

value: cervical adenocarcinoma cell line

tag: genotype

value: WT

value: RNaseH


title: HEK293T_15k_lib_ltm_Pilot_lib_chx_pilot_lib_ltm

value: 15k_lib_ltm:NI812 (CGTAA); Pilot_lib_chx:NI811 (AGCTA); Pilot_lib_ltm:NI813 (CTAGA)


title: batch2_Ctrl_RNaseH_rep1


title: batch3_Ctrl_no_RNaseH_rep2


title: HEK293T_15k_lib_chx

value: NI811 (AGCTA)


title: WT.4206_02


title: VHAS_2_rep_EPICv1_EPICv2

type: genomic

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 117-2194 Health Sciences Mall

department: Faculty of Medicine

country: Canada

institute: University of British Columbia

description: VHAS, EPICv2

hyb_protocol: DNA was bisulfite converted using EZ-96 DNA Methylation kits (Zymo Research, Irvine, CA), hybridized to the MethylationEPIC BeadChip Infinium microarray v1.0 B5 (EPICv1) and Infinium MethylationEPIC v2.0 (EPICv2) arrays using standard Illumina protocol

scan_protocol: arrays were scanned with an Illumina HiScan

data_processing:
Noob and functional normalized
*processed value definition: DNA methylation beta value

label: Cy3 and Cy5

source_name: Whole blood

label_protocol: Standard Illumnia protocol

extract_protocol: genomic DNA was extracted from whole blood using Qiagen DNeasy Kit according to standard instructions

value: Whole blood

tag: Sex

value: F

tag: age


title: AB10045_SB202


title: VHAS_22_EPICv1_EPICv2

description: VHAS, EPICv2

value: M


title: batch2_Ctrl_no_RNaseH_rep1


title: WT.DMSO_02

value: Planktonic


title: batch1_EXD2_KO2_MMS_rep2

value: MMS


title: VHAS_21_EPICv1_EPICv2

description: VHAS, EPICv2


title: batch1_EXD2_KO2_MMS_rep1


title: WT.RIF_01


title: AB10039_SB202


title: WT.4206_01


title: WT.5192_01


title: VHAS_20_EPICv1_EPICv2

description: VHAS, EPICv2


title: batch1_EXD2_KO1_MMS_rep2


title: VHAS_19_EPICv1_EPICv2

description: VHAS, EPICv2


title: batch1_EXD2_KO1_MMS_rep1


title: VHAS_18_EPICv1_EPICv2

description: VHAS, EPICv2


title: WT.DMSO_01


title: A549_15k_lib_chx

value: A549 lung carcinoma cells

value: NI812 (CGTAA)


title: VHAS_17_EPICv1_EPICv2

description: VHAS, EPICv2


title: Condition lung metastases. Cell Line  YEJH-M3. Rep n2

city: Glasgow

first: Robin

last: Shaw

address: Switchback Road

country: United Kingdom

institute: CRUK Scotland Institute

description: Library name: MGR20191213_S23_MG26_YEJH_M3_2

data_processing:
Quality Control with FastQC and FastQ Screen. Aligned to genome with version 2.1 of HiSat2 and sorted with Samtools version 1.2 using code following the format of `hisat2 -x path/to/index_hisat2/ --known-splicesite-infile path/to/mouse_38.95_splice_sites.txt --rna-strandness RF -1 path/to/{read1} -2 path/to/{read2} | samtools sort -o path/to/{samplename}.bam`. Counts tables for each bam file produced with version 0.11.2 of HTSeq Count. Format of code `htseq-count /path/to/{sample name}.bam -s reverse --mode=intersection-nonempty --type=exon --idattr=gene_id -f bam /path/to/Mus_musculus_GeneAnnot.GRCh38.95.gtf '>' tables/{sample name}.tsv`. Individual tables merged using base Linux commands.
Assembly: Ensemble 38.95 Mus Musculus.
Supplementary files format and content: raw_count_table.tsv file is a tab separated flat text file table of the counts for each sample of the Ensembl IDs.

organism: Mus musculus

extract_protocol:
For PyMT+ cell lines, cells lines were previously generated by Gounis et al., (Gounis et al, 2024), and plated at 0.5x106 - 1x106 cells per 10cm dish, 37°C/5% CO2 for 24 hours to achieve 80% confluence the next day. Cells were washed twice in ice-cold PBS, lysed into 1mL Trizol, and RNA prepped as manufacturer instructions.
RNA 6000 Pico Kit and Bioanalyzer (Agilent Technologies) was used to assess RNA integrity, sample library preparation was performed using the Illumina TruSeq RNA Library Prep kit v2, and sequencing was conducted on the NextSeq500 platform using a High Output 75 cycle kit.

value: lung metastases


title: WT.5192_02


title: batch1_Ctrl_rep2


title: VHAS_15_EPICv1_EPICv2

description: VHAS, EPICv2


title: Condition fat pad tumor. Cell Line  YEJH-FP2. Rep n1

description: Library name: MGR20191213_S21_MG8_YEJH_FP2_1

value: fat pad tumor


title: SMG organoids

city: Utrecht

first: Carla

last: Pou Casellas

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: 10X Genomics

data_processing:
The sequencing output was demultiplexed and converted to FASTQ files using the function mkfastq from the CellRanger toolkit (v5.0.1). Reads were then mapped to a custom variant of the GRCh38 human transcriptome, and feature count tables were generated using the CellRanger count function.
Assembly: GRCh38
Supplementary files format and content: The processed data files contain the barcodes (.tsv), features (.tsv), and matrix (.mtx) per sample.

source_name: Submucosal gland epithelium

extract_protocol:
Organoids were removed from BME (R&D Systems) and digested with TrypLE (Thermo Fisher Scientific) for 5 minutes into single cells using glass Pasteur pipettes. The cells were then washed with ice-cold AdDMEM/F12 (Thermo Fisher Scientific). Cells were resuspended in culture medium supplemented with Y-27632 dihydrochloride (10 µM, Abmole Bioscience) and filtered into FACS tubes through a cell strainer (Falcon). Cells were co-stained with DAPI (Sigma-Aldrich) and DRAQ5 (Biostatus), and subjected to FACS sorting for live cells. FACS was performed on a BD Influx™ cell sorter (BD Biosciences). 4,000 live cells per condition were subjected to droplet-based scRNA-seq using the 10x Genomics platform.
Libraries were prepared using the 10x Genomics Chromium 3’ Gene Expression solution v3.1 and sequenced on a NovaSeq 6000 (Illumina).

treatment_protocol: Untreated

value: Submucosal gland epithelium

value: Tissue-derived organoids

tag: condition

value: Healthy


title: batch1_Ctrl_rep1

value: HeLa

value: cervical adenocarcinoma cell line


title: Condition whole lung. Cell Line YEJG-M2. Rep n2

description: Library name: MGR20191213_S19_MG19_YEJG_M2_2

value: whole lung


title: SAE organoids

description: 10X Genomics

source_name: Surface airway epithelium

value: Surface airway epithelium


title: VHAS_14_EPICv1_EPICv2

description: VHAS, EPICv2


title: VHAS_13_EPICv1_EPICv2

description: VHAS, EPICv2


title: batch1_Ctrl_MMS_rep2

value: WT


title: Condition primary tumor (mammary gland/MG). Cell Line YEJH. Rep n3

description: Library name: MGR20191213_S18_MG35_YEJH_3

source_name: YEJH

value: YEJH

value: primary tumor (mammary gland/MG)


title: VHAS_12_EPICv1_EPICv2

description: VHAS, EPICv2

value: Whole blood

value: M


title: HFFs, WT HCMV, 12 hpi, SMI, replicate 2

city: Seoul

first: Hyejun

last: Kim

address: 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

description:
WT_D1D3G_rep1_vs_WT_SMI_rep2.odds_ratio.bedgraph
WT_D1D3G_rep1_vs_WT_SMI_rep2.p_value.bedgraph
WT_D1D3G_rep2_vs_WT_SMI_rep2.odds_ratio.bedgraph
WT_D1D3G_rep2_vs_WT_SMI_rep2.p_value.bedgraph
WT_E9G9G_rep1_vs_WT_SMI_rep2.odds_ratio.bedgraph
WT_E9G9G_rep1_vs_WT_SMI_rep2.p_value.bedgraph
WT_E9G9G_rep2_vs_WT_SMI_rep2.odds_ratio.bedgraph
WT_E9G9G_rep2_vs_WT_SMI_rep2.p_value.bedgraph

data_processing:
CLIP-Seq data were processed using fastp (Chen et al., 2018) for adapter trimming and merging of paired-end reads. Unique molecular identifier (UMI) sequences were removed and appended to the read names. The merged reads were aligned to the reference genomes, GRCh38 primary assembly (GENCODE V45) for host sequences and Human herpesvirus 5 strain Toledo (GenBank accession GU937742.2) for HCMV sequences, using GSNAP version 2016-11-07 with a 10% mismatch rate. Aligned reads were deduplicated using UMI-tools (Smith et al., 2017) with the “--method=directional” option.
Reads primarily aligned to the viral genome were collected using the “view” command in SAMtools 1.18 (Danecek et al., 2021) with the “-F 256” option to discard secondary alignments. Read coverage of each gene was calculated using the “genomecov” command in BEDTools v2.31.1 (Quinlan & Hall, 2010). Mean coverage depths were calculated using a sliding window size of 10 nt and a step size of 1 nt.
For each 10 nt window along the RNA4.9 region, coverage depths within the window were compared to those in the rest of the RNA4.9 region for both CLIP and SMI samples. Fisher's exact test was applied using SciPy 1.11.4 (Virtanen et al., 2020) to calculate the odds ratio and P-value of observing the given arrangement of coverage depths in two categories: sample type (CLIP vs. SMI) and region (in window vs. not in window). The odds ratio quantifies the association between the sample type and the region, with values greater than 1 indicating a higher likelihood of observing high coverage depths in the CLIP sample within the window compared to the SMI sample and the rest of the RNA4.9 region.
Assembly: GRCh38 and GU937742.2
Supplementary files format and content: bedGraph files include p-values / odd ratios for each 10 nt window in RNA4.9 of HCMV

source_name: Skin; Foreskin

growth_protocol: HFFs were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
For CLIP-libraries, the cells were cross-linked by UV irradiation and subjected to cell lysis. Purified cGAS-RNA complexes were treated with RNaseA. The fragmented RNAs were extracted and ligated with the adaptors. For SMI libraries, RNAs extracted from the non-cross-linked cells were subjected to rRNA depletion and fragmented by RNA fragmentation buffer. Fragmented RNAs with the size similar to the CLIPed RNAs were extracted and ligated with the adaptors.
Both libraries were prepared by TruSeq small RNA library kit (Illumina) through manafacturer's instrument. For SMI libraries, rRNA depletion was performed by Ribo-Zero Plus rRNA depletion kit (Illumina) through manafacturer's instrument.

treatment_protocol: HFFs with 90% confluency were infected with WT HCMV (1 MOI)

value: Skin; Foreskin

value: HFF-1 (Primary cell)

value: Fibroblast

value: Primary cell (WT)

value: WT HCMV infection, 12 hpi


title: 231 siEfp #B

type: RNA

city: Hidaka

first: Kazuhiro

last: Ikeda

state: Saitama

address: 1397-1 Yamane

country: Japan

institute: Saitama Medical University

description: Gene expression data from MDA-MB-231 cells treated with siRNA targeting Efp (siEfp #B)

hyb_protocol: Approximately 5.5 micro g of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45 degrees centigrade for 16 hour.

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: The microarray data were preprocessed with Affymetrix Expression Console software (TAC 4.0.2) using Affymetrix default Robust Multichip Analysis (RMA) sketch algorithm workflow.

label: biotin

source_name: MDA-MB-231 cells

label_protocol: cDNA was synthesized using the GeneChip WT (Whole Transcript) Amplification kit as described by the manufacturer. The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit.

growth_protocol: MDA-MB-231 and TNBC-PDC cells were maintained in Dulbecco's modified Eagle's medium (DMEM).

extract_protocol: Total RNA was extracted using ISOGEN reagent (Nippon Gene, Japan).

treatment_protocol: MDA-MB-231 and TNBC-PDC cells were treated with 10 nM either of siRNAs (siEfp #A, siEfp #B, or siCont) for 48 h.

tag: tumor

value: breast cancer

tag: transfected with

value: siEfp


title: batch1_Ctrl_MMS_rep1

value: MMS


title: HFFs, WT HCMV, 12 hpi, SMI, replicate 1

description:
WT_D1D3G_rep1_vs_WT_SMI_rep1.odds_ratio.bedgraph
WT_D1D3G_rep1_vs_WT_SMI_rep1.p_value.bedgraph
WT_D1D3G_rep2_vs_WT_SMI_rep1.odds_ratio.bedgraph
WT_D1D3G_rep2_vs_WT_SMI_rep1.p_value.bedgraph
WT_E9G9G_rep1_vs_WT_SMI_rep1.odds_ratio.bedgraph
WT_E9G9G_rep1_vs_WT_SMI_rep1.p_value.bedgraph
WT_E9G9G_rep2_vs_WT_SMI_rep1.odds_ratio.bedgraph
WT_E9G9G_rep2_vs_WT_SMI_rep1.p_value.bedgraph


title: TNBC-PDC siEfp #A

description: Gene expression data from TNBC-PDC cells treated with siRNA targeting Efp (siEfp #A)

source_name: TNBC-PDC cells

value: TNBC-PDC


title: TNBC-PDC siEfp #B

description: Gene expression data from TNBC-PDC cells treated with siRNA targeting Efp (siEfp #B)


title: Ubiquitous depletion of RPC-1, Day 1 adult hermaphrodites, NGM + 4mM auxin, rep 3

city: Bethesda

first: Katherine

last: McJunkin

state: Maryland

address: 50 South Dr

institute: NIDDK/ NIH

description:
sRNA libraries were constructed using NEBNext Small RNA Library Prep Set for Illumina with modifications. After reverse transcription, each sample was treated with 5000units of RNAse H (New England Biolabs) for 20 minutes at 37C. The treated samples were immediately run on 8% urea gels to purify and size select ~65-75nt RT products.
sRS253

data_processing:
Pooled samples were sequenced on a NextSeq 2000. Sequence analysis was performed on the NIH High Performance Computing Cluster. Small RNA libraries were trimmed using Cutadapt 4.4 (Martin, 2011), mapped using bowtie2 2.5.1 with settings ‘–no-unal –end-to-end –sensitive’ (Langmead et al., 2009), and the resulting bam files were sorted and indexed using samtools 1.19 (Danecek et al., 2021). Reads were assigned to miRNAs using htseq 2.0.4 with settings ‘--mode union --nonunique fraction -a 0’ (Anders et al., 2015). Analysis of miRNA expression using DESeq2 was performed as previously described (Kotagama et al., 2024).
Assembly: WS280
Supplementary files format and content: Excel file of raw miRNA and spike-in counts for each sample

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: For RNA sample collection for all strains, L1s were synchronized by alkaline hypochlorite lysis of gravid adults followed by hatching in M9 with 1 mM cholesterol at 20°C overnight. L1s were plated on NGM seeded with OP50 and maintained at 20°C until L4 (∼48hrs after plating). At this time point, L4s were transferred onto NGM with 4mM auxin and grown for 24hrs before harvesting (Day 1 adults).

extract_protocol:
Worm pellets of Day 1 adults were snap frozen and stored in -80C until samples were ready to be prepared. At the time of RNA isolation, worm pellets were resuspended in Trizol, followed by three freeze-thaw cycles on dry ice, and vortexing for 15 minutes at room temperature. Thereafter, total RNA was purified according to the Trizol manufacturer’s instructions (ThermoFisher).
Spike-ins were added at a final concentration of 0.1 pg/μl in 100 ng/μl total RNA.
sRNA libraries were constructed using NEBNext Small RNA Library Prep Set for Illumina with modifications. After reverse transcription, each sample was treated with 5000units of RNAse H (New England Biolabs) for 20 minutes at 37C. The treated samples were immediately run on 8% urea gels to purify and size select ~65-75nt RT products.

treatment_protocol: Worms were treated with auxin for 24hr starting at the L4 stage and grown to Day 1 adults.

value: whole animal

value: ieSi57 [eft-3p::TIR1::mRuby::unc-54 3'UTR + Cbr-unc-119(+)] II; ieSi38 [sun-1p::TIR1::mRuby::sun-1 3'UTR + Cbr-unc-119(+)] IV

value: 24hr auxin treatment


title: Condition whole lung. Cell Line  YEJH-M2. Rep n1

description: Library name: MGR20191213_S17_MG9_YEJH_M2_1

value: whole lung


title: TNBC-PDC siCont

description: Gene expression data from TNBC-PDC cells treated with control siRNA (siCont)

value: siCont


title: VHAS_11_EPICv1_EPICv2

description: VHAS, EPICv2

value: F


title: 231 siEfp #A

description: Gene expression data from MDA-MB-231 cells treated with siRNA targeting Efp (siEfp #A)


title: VHAS_16_EPICv1_EPICv2

description: VHAS, EPICv2

value: Whole blood


title: Condition whole lung. Cell Line  YEJH-M4. Rep n3

description: Library name: MGR20191213_S16_MG43_YEJH_M4_3


title: VHAS_1_EPICv1_EPICv2

description: VHAS, EPICv2


title: HFFs, WT HCMV, 12 hpi, CLIP by cGAS antibody (E9G9G), replicate 2

description:
WT_E9G9G_rep2_vs_WT_SMI_rep1.odds_ratio.bedgraph
WT_E9G9G_rep2_vs_WT_SMI_rep2.odds_ratio.bedgraph
WT_E9G9G_rep2_vs_WT_SMI_rep1.p_value.bedgraph
WT_E9G9G_rep2_vs_WT_SMI_rep2.p_value.bedgraph


title: Condition whole lung. Cell Line  YEJH-M1. Rep n3

description: Library name: MGR20191213_S20_MG37_YEJH_M1_3


title: Ubiquitous depletion of RPC-1, Day 1 adult hermaphrodites, NGM + 4mM auxin, rep 2

description:
sRNA libraries were constructed using NEBNext Small RNA Library Prep Set for Illumina with modifications. After reverse transcription, each sample was treated with 5000units of RNAse H (New England Biolabs) for 20 minutes at 37C. The treated samples were immediately run on 8% urea gels to purify and size select ~65-75nt RT products.
sRS243

value: ieSi57 [eft-3p::TIR1::mRuby::unc-54 3'UTR + Cbr-unc119(+)] II; rpc-1(cdb434) ieSi38 [sun-1p::TIR1::mRuby::sun-1 3'UTR + Cbr-unc-119(+)] IV


title: HFFs, WT HCMV, 12 hpi, CLIP by cGAS antibody (E9G9G), replicate 1

description:
WT_E9G9G_rep1_vs_WT_SMI_rep1.odds_ratio.bedgraph
WT_E9G9G_rep1_vs_WT_SMI_rep2.odds_ratio.bedgraph
WT_E9G9G_rep1_vs_WT_SMI_rep1.p_value.bedgraph
WT_E9G9G_rep1_vs_WT_SMI_rep2.p_value.bedgraph

value: Skin; Foreskin


title: VHAS_10_EPICv1_EPICv2

description: VHAS, EPICv2

value: M


title: TIR1-only strain (control for RPC-1 depletion), Day 1 adult hermaphrodites, NGM + 4mM auxin, rep 2

description:
sRNA libraries were constructed using NEBNext Small RNA Library Prep Set for Illumina with modifications. After reverse transcription, each sample was treated with 5000units of RNAse H (New England Biolabs) for 20 minutes at 37C. The treated samples were immediately run on 8% urea gels to purify and size select ~65-75nt RT products.
sRS239


title: Condition fat pad tumor. Cell Line  YEJH-FP5. Rep n3

description: Library name: MGR20191213_S14_MG44_YEJH_FP5_3

value: fat pad tumor


title: HFFs, WT HCMV, 12 hpi, CLIP by cGAS antibody (D1D3G), replicate 2

description:
WT_D1D3G_rep2_vs_WT_SMI_rep1.odds_ratio.bedgraph
WT_D1D3G_rep2_vs_WT_SMI_rep2.odds_ratio.bedgraph
WT_D1D3G_rep2_vs_WT_SMI_rep1.p_value.bedgraph
WT_D1D3G_rep2_vs_WT_SMI_rep2.p_value.bedgraph

value: HFF-1 (Primary cell)

value: Fibroblast

value: Primary cell (WT)


title: Ubiquitous depletion of RPC-1, Day 1 adult hermaphrodites, NGM + 4mM auxin, rep 1

description:
sRNA libraries were constructed using NEBNext Small RNA Library Prep Set for Illumina with modifications. After reverse transcription, each sample was treated with 5000units of RNAse H (New England Biolabs) for 20 minutes at 37C. The treated samples were immediately run on 8% urea gels to purify and size select ~65-75nt RT products.
sRS235


title: Condition fat pad tumor. Cell Line  YEJH-FP2. Rep n3

description: Library name: MGR20191213_S22_MG38_YEJH_FP2_3


title: VHAS_8_EPICv1_EPICv2

description: VHAS, EPICv2


title: Condition fat pad tumor. Cell Line  YEJH-FP4. Rep n1

description: Library name: MGR20191213_S13_MG12_YEJH_FP4_1


title: TIR1-only strain (control for RPC-1 depletion), Day 1 adult hermaphrodites, NGM + 4mM auxin, rep 1

description:
sRNA libraries were constructed using NEBNext Small RNA Library Prep Set for Illumina with modifications. After reverse transcription, each sample was treated with 5000units of RNAse H (New England Biolabs) for 20 minutes at 37C. The treated samples were immediately run on 8% urea gels to purify and size select ~65-75nt RT products.
sRS231


title: Condition whole lung. Cell Line YEJG-M1. Rep n2

description: Library name: MGR20191213_S15_MG18_YEJG_M1_2


title: Condition whole lung. Cell Line YEJG-M2. Rep n3

description: Library name: MGR20191213_S12_MG34_YEJG_M2_3


title: VHAS_9_EPICv1_EPICv2

description: VHAS, EPICv2


title: germline depletion of Dicer, Day 1 adult hermaphrodites, NGM + 4mM auxin, rep 3

description:
sRNA libraries were constructed using NEBNext Small RNA Library Prep Set for Illumina with modifications. After reverse transcription, each sample was treated with 5000units of RNAse H (New England Biolabs) for 20 minutes at 37C. The treated samples were immediately run on 8% urea gels to purify and size select ~65-75nt RT products.
sRS229

value: dcr-1(zen79) III; ieSi38 [sun-1p::TIR1::mRuby::sun-1 3'UTR + Cbr-unc-119(+)] IV


title: VHAS_7_EPICv1_EPICv2

description: VHAS, EPICv2


title: MHCC-97H cells, Vector_ip RNA

city: chongqing

first: bin

last: cheng

address: No. 1, Medical College Road, Yuzhong District, Chongqing

department: Department of Infectious Diseases, Key Laboratory of Molecular Biology for Infectious Diseases

institute: chongqing medical university

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed. Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing. In brief, clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the same cluster. Reads in the same cluster were compared to each other by pairwise alignment, and then reads with sequence identity over 95% were extracted to a new sub-cluster. After all sub-clusters were generated, multiple sequence alignment was performed to get one consensus sequence for each sub-clusters. After these steps, any errors and biases introduced by PCR amplification or sequencing were eliminated.
The de-duplicated consensus sequences were used for protein binding site analysis. They were mapped to the reference genome of XHuman from PHGDH using STAR software (version 2.5.3a) with default parameters. The RSeQC（version 2.6）was used for reads distribution analysis. The exomePeak（Version 3.8）software was used for peak calling. Peaks were annotated using bedtools（Version 2.25.0）. The deepTools（version 2.4.1）was used for peak distribution analysis. The differentially binding peaks were identified by a python script，using fisher test. Sequence motifs enriched in peak regions were identified using Homer（version 4.10）. Gene ontology (GO) analysis and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis for annotated genes were both implemented by KOBAS software (version: 2.1.1) with a corrected P-value cutoff of 0.05 to judge statistically significant enrichment.
Assembly: GRCh38
Supplementary files format and content: bigwig

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA), and the RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA). Poly (A) RNA was purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) by two rounds of purification.
the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. The cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). The IP RNA was reverse-transcribed to cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which was next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base was added to the blunt ends of each strand, preparing for ligation to the indexed adapters. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. At last, we performed paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 platform(LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol

value: control

tag: fraction

value: IP


title: MHCC-97H cells, Vector_input RNA

value: Input


title: VHAS_2_EPICv1_EPICv2

description: VHAS, EPICv2


title: TIR1-only strain (control for RPC-1 depletion), Day 1 adult hermaphrodites, NGM + 4mM auxin, rep 3

description:
sRNA libraries were constructed using NEBNext Small RNA Library Prep Set for Illumina with modifications. After reverse transcription, each sample was treated with 5000units of RNAse H (New England Biolabs) for 20 minutes at 37C. The treated samples were immediately run on 8% urea gels to purify and size select ~65-75nt RT products.
sRS249

value: whole animal

value: ieSi57 [eft-3p::TIR1::mRuby::unc-54 3'UTR + Cbr-unc-119(+)], II; ieSi38 [sun-1p::TIR1::mRuby::sun-1 3'UTR + Cbr-unc-119(+)], IV


title: MHCC-97H cells, PHGDH_ip RNA

value: overexpressed PHGDH


title: VHAS_6_EPICv1_EPICv2

description: VHAS, EPICv2


title: Condition fat pad tumor. Cell Line  YEJH-FP3. Rep n2

description: Library name: MGR20191213_S10_MG25_YEJH_FP3_2


title: 231 siCont

description: Gene expression data from MDA-MB-231 cells treated with control siRNA (siCont)

value: breast cancer

value: siCont


title: ubiquitous depletion of Dicer, Day 1 adult hermaphrodites, NGM + 4mM auxin, rep 3

description:
sRNA libraries were constructed using NEBNext Small RNA Library Prep Set for Illumina with modifications. After reverse transcription, each sample was treated with 5000units of RNAse H (New England Biolabs) for 20 minutes at 37C. The treated samples were immediately run on 8% urea gels to purify and size select ~65-75nt RT products.
sRS228

value: dcr-1(zen79) III; ieSi57 [eft-3p::TIR1::mRuby::unc-54 3'UTR + Cbr-unc119(+)] II; ieSi38 [sun-1p::TIR1::mRuby::sun-1 3'UTR + Cbr-unc-119(+)] IV

value: 24hr auxin treatment


title: MHCC-97H cells, PHGDH_input RNA


title: Condition fat pad tumor. Cell Line  YEJH-FP5. Rep n2

description: Library name: MGR20191213_S09_MG29_YEJH_FP5_2


title: VHAS_1_rep_EPICv1_EPICv2

description: VHAS, EPICv2

value: Whole blood

value: F


title: Dicer::AID tag control strain (no TIR1), Day 1 adult hermaphrodites, NGM + 4mM auxin, rep 3

description:
sRNA libraries were constructed using NEBNext Small RNA Library Prep Set for Illumina with modifications. After reverse transcription, each sample was treated with 5000units of RNAse H (New England Biolabs) for 20 minutes at 37C. The treated samples were immediately run on 8% urea gels to purify and size select ~65-75nt RT products.
sRS226

value: dcr-1(zen79) III


title: VHAS_2_rep_EPICv1

description: VHAS, EPICv1


title: germline depletion of Dicer, Day 1 adult hermaphrodites, NGM + 4mM auxin, rep 2

description:
sRNA libraries were constructed using NEBNext Small RNA Library Prep Set for Illumina with modifications. After reverse transcription, each sample was treated with 5000units of RNAse H (New England Biolabs) for 20 minutes at 37C. The treated samples were immediately run on 8% urea gels to purify and size select ~65-75nt RT products.
sRS222


title: Condition fat pad tumor. Cell Line  YEJH-FP1. Rep n2

description: Library name: MGR20191213_S08_MG21_YEJH_FP1_2

value: fat pad tumor


title: VHAS_5_EPICv1_EPICv2

description: VHAS, EPICv2

value: M


title: HFFs, WT HCMV, 12 hpi, CLIP by cGAS antibody (D1D3G), replicate 1

description:
WT_D1D3G_rep1_vs_WT_SMI_rep1.odds_ratio.bedgraph
WT_D1D3G_rep1_vs_WT_SMI_rep2.odds_ratio.bedgraph
WT_D1D3G_rep1_vs_WT_SMI_rep1.p_value.bedgraph
WT_D1D3G_rep1_vs_WT_SMI_rep2.p_value.bedgraph

value: Skin; Foreskin

value: HFF-1 (Primary cell)

value: Fibroblast

value: Primary cell (WT)

value: WT HCMV infection, 12 hpi


title: ubiquitous depletion of Dicer, Day 1 adult hermaphrodites, NGM + 4mM auxin, rep 2

description:
sRNA libraries were constructed using NEBNext Small RNA Library Prep Set for Illumina with modifications. After reverse transcription, each sample was treated with 5000units of RNAse H (New England Biolabs) for 20 minutes at 37C. The treated samples were immediately run on 8% urea gels to purify and size select ~65-75nt RT products.
sRS221

value: whole animal


title: VHAS_4_EPICv1_EPICv2

description: VHAS, EPICv2


title: Condition whole lung. Cell Line  YEJH-M1. Rep n1

description: Library name: MGR20191213_S07_MG7_YEJH_M1_1

value: whole lung


title: Condition fat pad tumor. Cell Line  YEJH-FP3. Rep n3

description: Library name: MGR20191213_S11_MG40_YEJH_FP3_3


title: VHAS_3_EPICv1_EPICv2

description: VHAS, EPICv2


title: VHAS_22_EPICv1

description: VHAS, EPICv1


title: Dicer::AID tag control strain (no TIR1), Day 1 adult hermaphrodites, NGM + 4mM auxin, rep 2

description:
sRNA libraries were constructed using NEBNext Small RNA Library Prep Set for Illumina with modifications. After reverse transcription, each sample was treated with 5000units of RNAse H (New England Biolabs) for 20 minutes at 37C. The treated samples were immediately run on 8% urea gels to purify and size select ~65-75nt RT products.
sRS219


title: VHAS_20_EPICv1

description: VHAS, EPICv1


title: VHAS_19_EPICv1

description: VHAS, EPICv1


title: ubiquitous depletion of Dicer, Day 1 adult hermaphrodites, NGM + 4mM auxin, rep 1

description:
sRNA libraries were constructed using NEBNext Small RNA Library Prep Set for Illumina with modifications. After reverse transcription, each sample was treated with 5000units of RNAse H (New England Biolabs) for 20 minutes at 37C. The treated samples were immediately run on 8% urea gels to purify and size select ~65-75nt RT products.
sRS214


title: Condition whole lung. Cell Line  YEJH-M5. Rep n3

description: Library name: MGR20191213_S05_MG45_YEJH_M5_3


title: VHAS_21_EPICv1

description: VHAS, EPICv1


title: CLHNS_1_rep_EPICv2

description: CLHNS, EPICv2


title: Condition primary tumor (mammary gland/MG). Cell Line YEJG. Rep n2

description: Library name: MGR20191213_S06_MG16_YEJG_2

source_name: YEJG

value: YEJG

value: primary tumor (mammary gland/MG)


title: Condition fat pad tumor. Cell Line YEJG-FP. Rep n1

description: Library name: MGR20191213_S04_MG2_YEJG_FP_1

source_name: YEJG-FP

value: YEJG-FP


title: VHAS_18_EPICv1

description: VHAS, EPICv1


title: Dicer::AID tag control strain (no TIR1), Day 1 adult hermaphrodites, NGM + 4mM auxin, rep 1

description:
sRNA libraries were constructed using NEBNext Small RNA Library Prep Set for Illumina with modifications. After reverse transcription, each sample was treated with 5000units of RNAse H (New England Biolabs) for 20 minutes at 37C. The treated samples were immediately run on 8% urea gels to purify and size select ~65-75nt RT products.
sRS212


title: CLHNS_15_EPICv2

description: CLHNS, EPICv2


title: Condition lung metastases. Cell Line  YEJH-M3. Rep n1

description: Library name: MGR20191213_S03_MG11_YEJH_M3_1

value: lung metastases


title: germline depletion of Dicer, Day 1 adult hermaphrodites, NGM + 4mM auxin, rep 1

description:
sRNA libraries were constructed using NEBNext Small RNA Library Prep Set for Illumina with modifications. After reverse transcription, each sample was treated with 5000units of RNAse H (New England Biolabs) for 20 minutes at 37C. The treated samples were immediately run on 8% urea gels to purify and size select ~65-75nt RT products.
sRS215

value: dcr-1(zen79) III; ieSi38 [sun-1p::TIR1::mRuby::sun-1 3'UTR + Cbr-unc-119(+)] IV

value: 24hr auxin treatment


title: CLHNS_14_EPICv2

description: CLHNS, EPICv2

value: Whole blood

value: F


title: VHAS_17_EPICv1

description: VHAS, EPICv1


title: Condition primary tumor (mammary gland/MG). Cell Line YEJH. Rep n1

description: Library name: MGR20191213_S02_MG5_YEJH_1

value: YEJH


title: CLHNS_13_EPICv2

description: CLHNS, EPICv2


title: VHAS_16_EPICv1

description: VHAS, EPICv1

value: M


title: CLHNS_12_EPICv2

description: CLHNS, EPICv2


title: Condition whole lung. Cell Line  YEJH-M4. Rep n2

description: Library name: MGR20191213_S01_MG28_YEJH_M4_2


title: VHAS_15_EPICv1

description: VHAS, EPICv1


title: A20ZF7_GEX

city: San Francisco

first: Averil

last: Ma

state: CA

address: 513 Parnassus Avenue

institute: University of California, San Francisco

description:
Library name: Sample2
10X Genomics

data_processing:
Sequences were aligned and processed using cellranger v7.1 using the mm10 reference genome and default parameters.
Cellranger output was further processed with R version 4.3.3 and Seurat version 4.3.
Assembly: mm10
Supplementary files format and content: tab-separated values and matrices of feature and cell barcodes

source_name: small intestine

extract_protocol:
Lamina propria cells were isolated from small intestines of two mice of each genotype. Isolated cells were negatively selected for T cells and ILCs (STEMCELL Technologies 19851) and stained with TotalSeq-C anti-mouse hash-tagged antibodies (BioLegend Totalseq-C; Hashtags 7 and 8 for WT; Hashtags 9 and 10 for A20ZF7 ). Cells from each animal were separately hashtagged.
WT cells hashtagged with barcodes GAGTCTGCCAGTATC and TATAGAACGCCAGGC
A20ZF7 cells hashtagged with barcodes TGCCTATGAAACAAG and CCGATTGTAACAGAC
For each genotype, a total of 60,000 cells were collected for processing using the 10X Genomics Chromium Next GEM Single Cell 5' Kit v1.1 per manufacturer's protocol.

value: small intestine

value: lamina propria cells


title: WT_GEX

description:
Library name: Sample1
10X Genomics

value: WT


title: Condition primary tumor (mammary gland/MG). Cell Line YEJG. Rep n3

description: Library name: MGR20191212_S22_MG31_YEJG_3


title: CLHNS_10_EPICv2

description: CLHNS, EPICv2


title: VHAS_14_EPICv1

description: VHAS, EPICv1


title: Condition fat pad tumor. Cell Line  YEJH-FP4. Rep n3

description: Library name: MGR20191212_S21_MG42_YEJH_FP4_3

value: fat pad tumor


title: CLHNS_11_EPICv2

description: CLHNS, EPICv2


title: CLHNS_9_EPICv2

description: CLHNS, EPICv2


title: VHAS_12_EPICv1

description: VHAS, EPICv1


title: mTH17_ZF7_FICZ_rep2

description: Library name: Sample11

data_processing:
Sequences were aligned to the GRCm38/mm10 mouse reference genome using Bowtie2 v2.4.5.
PCR duplicates were removed by samtools v1.15 followed by Picard v2.27.1 (MarkDuplicates).
Bigwig files were generated using UCSC’s bedGraphToBigWig script.
Assembly: mm10
Supplementary files format and content: BW (bigwig) files, normalized coverage

source_name: helper TH17, in vitro differentiated

growth_protocol: Naïve CD4 T cells were isolated from murine splenocytes using a Mouse CD4 naïve T cell negative selection kit (StemCell Technologies 19765) per manufacturer’s instructions. Isolated cells were subsequently differentiated in plates pre-coated with 2 µg/mL anti-CD3 in TH17 medium (IMDM with 10% FBS, 50 µM beta-mercaptoethanol, 2 µg/mL anti-CD28 (BioXCell BE0015, clone 37.51), 20 ng/mL recombinant murine IL-6 (R&D Biosystems 406-ML), 5 ng/mL recombinant human TGFbeta1 (PeproTech 100-21), 10 µg/mL anti-IL4 (BioXCell BE0045, clone 11B11), and 10 µg/mL anti-IFNgamma (BioXCell BE0055, clone XMG1.2)) at a density of 1 million cells per mL.

extract_protocol:
Nuclei were isolated in ATAC lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM sodium chloride, 3 mM magnesium chloride, 0.1% v/v IGEPAL-CA630, 0.1% v/v Tween-20, 0.01% w/v digitonin) for 3 min on ice. The nuclei were briefly rinsed in wash buffer (10 mM Tris-HCl pH 7.5, 10 mM sodium chloride, 3 mM magnesium chloride, 0.1% v/v Tween-20) before incubating in transposition buffer (10 mM Tris-HCl pH 7.6, 5 mM magnesium chloride, 10% v/v dimethyl formamide, 0.1% v/v Tween-20, 0.01% w/v digitonin) with 100 nM loaded hyperactive Tn5 transposase (Diagenode C01070012) for 30 min at 37 C at 1000 rpm. Transposed DNA was isolated from Qiagen MinElute columns.
Libraries were generated using published Illumina-compatible indexed oligonucleotides and 8 cycles of PCR amplification using NEBNext High-Fidelity 2X PCR Master Mix (NEB M0541). Libraries were purified from SPRIselect beads (Beckman Coulter B23317), and 51-bp paired-end sequences were sequenced on a NovaSeq X instrument.

value: helper TH17, in vitro differentiated

value: FICZ


title: VHAS_13_EPICv1

description: VHAS, EPICv1


title: mTH17_ZF7_rep3

description: Library name: Sample10


title: Condition fat pad tumor. Cell Line  YEJH-FP2. Rep n2

description: Library name: MGR20191212_S20_MG23_YEJH_FP2_2


title: VHAS_11_EPICv1

description: VHAS, EPICv1


title: CLHNS_8_EPICv2

description: CLHNS, EPICv2


title: mTH17_ZF7_rep2

description: Library name: Sample9

value: wild-type


title: CLHNS_7_EPICv2

description: CLHNS, EPICv2


title: Condition whole lung. Cell Line  YEJH-M1. Rep n2

description: Library name: MGR20191212_S18_MG22_YEJH_M1_2

value: whole lung


title: VHAS_1_EPICv1

description: VHAS, EPICv1


title: Condition fat pad tumor. Cell Line YEJG-FP. Rep n2

description: Library name: MGR20191212_S19_MG17_YEJG_FP_2


title: mTH17_WT_FICZ_rep3

description: Library name: Sample8


title: CLHNS_6_EPICv2

description: CLHNS, EPICv2


title: Condition whole lung. Cell Line YEJG-M2. Rep n1

description: Library name: MGR20191212_S17_MG4_YEJG_M2_1


title: WT_ADT

description:
Library name: Sample3
10X Genomics

data_processing:
Sequences were aligned and processed using cellranger v7.1 using the mm10 reference genome and default parameters.
Cellranger output was further processed with R version 4.3.3 and Seurat version 4.3.
Assembly: mm10
Supplementary files format and content: tab-separated values and matrices of feature and cell barcodes
Library strategy: CITE-seq

molecule: protein


title: VHAS_10_EPICv1

description: VHAS, EPICv1


title: Condition fat pad tumor. Cell Line  YEJH-FP1. Rep n3

description: Library name: MGR20191212_S16_MG36_YEJH_FP1_3


title: CLHNS_5_EPICv2

description: CLHNS, EPICv2


title: mTH17_WT_rep3

description: Library name: Sample6


title: CLHNS_1_EPICv2

description: CLHNS, EPICv2


title: CLHNS_4_EPICv2

description: CLHNS, EPICv2


title: Condition whole lung. Cell Line  YEJH-M4. Rep n1

description: Library name: MGR20191212_S15_MG13_YEJH_M4_1


title: VHAS_9_EPICv1

description: VHAS, EPICv1


title: Condition whole lung. Cell Line  YEJH-M5. Rep n1

description: Library name: MGR20191212_S14_MG15_YEJH_M5_1


title: Condition primary tumor (mammary gland/MG). Cell Line YEJG. Rep n1

description: Library name: MGR20191212_S13_MG1_YEJG_1

value: YEJG

value: primary tumor (mammary gland/MG)


title: VHAS_8_EPICv1

description: VHAS, EPICv1


title: mTH17_ZF7_rep1

description: Library name: Sample3


title: mTH17_ZF7_FICZ_rep1

description: Library name: Sample4


title: VHAS_7_EPICv1

description: VHAS, EPICv1


title: VHAS_2_EPICv1

description: VHAS, EPICv1


title: Condition whole lung. Cell Line  YEJH-M5. Rep n2

description: Library name: MGR20191212_S12_MG30_YEJH_M5_2


title: CLHNS_3_EPICv2

description: CLHNS, EPICv2


title: A20ZF7_ADT

description:
Library name: Sample4
10X Genomics


title: mTH17_WT_FICZ_rep1

description: Library name: Sample2


title: mTH17_WT_FICZ_rep2

description: Library name: Sample7


title: CALERIE_21_EPICv2

description: CALERIE, EPICv2


title: VHAS_6_EPICv1

description: VHAS, EPICv1


title: CALERIE_22_EPICv2

description: CALERIE, EPICv2


title: CLHNS_2_EPICv2

description: CLHNS, EPICv2


title: mTH17_WT_rep1

description: Library name: Sample1


title: Condition whole lung. Cell Line  YEJH-M2. Rep n2

description: Library name: MGR20191212_S11_MG24_YEJH_M2_2


title: Condition fat pad tumor. Cell Line  YEJH-FP1. Rep n1

description: Library name: MGR20191212_S10_MG6_YEJH_FP1_1


title: VHAS_1_rep_EPICv1

description: VHAS, EPICv1


title: VHAS_5_EPICv1

description: VHAS, EPICv1


title: Condition whole lung. Cell Line  YEJH-M2. Rep n3

description: Library name: MGR20191212_S09_MG39_YEJH_M2_3


title: CALERIE_20_EPICv2

description: CALERIE, EPICv2


title: mTH17_WT_rep2

description: Library name: Sample5


title: VHAS_4_EPICv1

description: VHAS, EPICv1


title: CALERIE_19_EPICv2

description: CALERIE, EPICv2


title: Condition fat pad tumor. Cell Line YEJG-FP. Rep n3

description: Library name: MGR20191212_S08_MG32_YEJG_FP_3

value: YEJG-FP


title: CUT&RUN in N2a cells for SIN3B, replicate 2

first: Igor

last: Ulitsky

address: Hertzl St.

description: Library name: CUT_RUN_SIN3B_2

data_processing:
RNA-seq: RNA-seq reads were mapped to the mouse genome (mm10 assembly) using STAR (Dobin et al., 2013) to generate read coverage tracks visualized using the UCSC genome browser. STAR -quant with RefSeq annotations and DESeq2 (Love et al., 2014) were used to call differential expression between samples
CUT&RUN: CUT&RUN reads were mapped to the human genome using Bowtie2 (Langmead and Salzberg, 2012) and peaks were called using all the samples together using MACS2 (Zhang et al., 2008)
Assembly: mm10
Supplementary files format and content: bigWig read coverage files are provided for all samples. STAR quantification is provided for the RNA-seq samples, MACS2-called peaks are provided for the CUT&RUN data.
Library strategy: CUT&Run

growth_protocol: Neuro2a (N2a) cells were cultured in DMEM supplemented with 4.5 g/L of glucose, 4 mM L-Glutamine, 10% FBS, 1% PenStrep solution, grown in incubators maintained at 37°C with 5% CO2, and were routinely passaged by gentle dissociation using a Trypsin (0.05%) – EDTA (0.02%) solution. DNA plasmid transfections were performed by using Lipofectamine 3000 (ThermoFisher Scientific), according to the respective protocols. For each transfection, the optimal DNA concentration and amount of transfection reagents were empirically determined to minimize cellular stress and maximize efficiency, to eventually ensure clean readouts. GapmeRs were transfected at the final concentration of 50 µM with Lipofectamine 3000, following the manufacturer’s guidelines. In all cases, cells were plated the day before the transfection in an antibiotic-free medium which was subsequently changed prior to adding the transfection mix, and again after 24h to minimize cell death. Finally, transfections were carried out for 72h, unless stated otherwise.

extract_protocol:
CUT&RUN reactions were performed as previously described (Meers et al., 2019), with the addition of 20mM sodium butyrate when profiling BAHCC1, SIN3A, SIN3B and H3K27ac
RNA-seq libraries were prepared using the CORALL mRNA-Seq Kit V2 (Lexogen), following the manufacturer’s instructions. CUT&RUN libraries were prepared as described previously (Meers et al., 2019).

treatment_protocol: Romidepsin (Sigma) was diluted in tissue culture-grade DMSO at a stock concentration of 10mM, and further diluted in cell media at a final concentration of 5 nM. As controls, cells were supplemented with an equal volume of DMSO. The treatments were performed for 24h in order to minimize indirect effects due to the extensive inhibition of deacetylation.

tag: cut&run antibody

value: SIN3B (ThermoFisher PA5-30680)

value: untreated


title: CUT&RUN in N2a cells for SIN3B, replicate 3

description: Library name: CUT_RUN_SIN3B_3


title: VHAS_3_EPICv1

description: VHAS, EPICv1

value: Whole blood


title: CUT&RUN in N2a cells for SIN3B, replicate 1

description: Library name: CUT_RUN_SIN3B_1


title: Condition fat pad tumor. Cell Line  YEJH-FP4. Rep n2

description: Library name: MGR20191212_S07_MG27_YEJH_FP4_2


title: CALERIE_18_EPICv2

description: CALERIE, EPICv2

value: F


title: CLHNS_15_EPICv1

description: CLHNS, EPICv1


title: RNA-seq in N2a cells after treatment for 24h with DMSO (Romidepsin control), replicate 3

description: Library name: RNA_DMSO_control_3

data_processing:
RNA-seq: RNA-seq reads were mapped to the mouse genome (mm10 assembly) using STAR (Dobin et al., 2013) to generate read coverage tracks visualized using the UCSC genome browser. STAR -quant with RefSeq annotations and DESeq2 (Love et al., 2014) were used to call differential expression between samples
CUT&RUN: CUT&RUN reads were mapped to the human genome using Bowtie2 (Langmead and Salzberg, 2012) and peaks were called using all the samples together using MACS2 (Zhang et al., 2008)
Assembly: mm10
Supplementary files format and content: bigWig read coverage files are provided for all samples. STAR quantification is provided for the RNA-seq samples, MACS2-called peaks are provided for the CUT&RUN data.

value: DMSO


title: RNA-seq in N2a cells after treatment for 24h with DMSO (Romidepsin control), replicate 2

description: Library name: RNA_DMSO_control_2


title: CLHNS_14_EPICv1

description: CLHNS, EPICv1


title: Condition whole lung. Cell Line YEJG-M1. Rep n3

description: Library name: MGR20191212_S05_MG33_YEJG_M1_3


title: CALERIE_17_EPICv2

description: CALERIE, EPICv2

value: M


title: CALERIE_2_rep_EPICv2

description: CALERIE, EPICv2


title: CLHNS_13_EPICv1

description: CLHNS, EPICv1


title: CALERIE_16_EPICv2

description: CALERIE, EPICv2


title: RNA-seq in N2a cells after treatment for 24h with DMSO (Romidepsin control), replicate 1

description: Library name: RNA_DMSO_control_1


title: Condition fat pad tumor. Cell Line  YEJH-FP3. Rep n1

description: Library name: MGR20191212_S06_MG10_YEJH_FP3_1


title: Condition fat pad tumor. Cell Line  YEJH-FP5. Rep n1

description: Library name: MGR20191212_S03_MG14_YRJH_FP5_1


title: Condition whole lung. Cell Line YEJG-M1. Rep n1

description: Library name: MGR20191212_S04_MG3_YEJH_M1_1


title: CALERIE_15_EPICv2

description: CALERIE, EPICv2


title: CLHNS_11_EPICv1

description: CLHNS, EPICv1


title: RNA-seq in N2a cells after treatment for 24h with 5nM Romidepsin, replicate 3

description: Library name: RNA_Romidepsin_5nM_3

value: Romidepsin


title: RNA-seq in N2a cells after treatment for 24h with 5nM Romidepsin, replicate 2

description: Library name: RNA_Romidepsin_5nM_2


title: CALERIE_14_EPICv2

description: CALERIE, EPICv2


title: Condition lung metastases. Cell Line  YEJH-M3. Rep n3

description: Library name: MGR20191212_S02_MG41_YEJH_M3_3

value: lung metastases


title: CLHNS_10_EPICv1

description: CLHNS, EPICv1


title: CALERIE_13_EPICv2

description: CALERIE, EPICv2


title: Condition primary tumor (mammary gland/MG). Cell Line YEJH. Rep n2

description: Library name: MGR20191212_S01_MG20_YRJH_2

value: YEJH


title: RNA-seq in N2a cells after transfection with the EV, replicate 3

description: Library name: RNA_EV_Bahcc1_OE_3


title: MEF n6 30uM Uracil  rep 6

description: Library name: CCR20200902_S18_CC18_MEF_n6_30uMUracil

source_name: Mouse embryonic fibroblasts Cultured Cells

extract_protocol:
MEFs were plated at 1x106 cells per 10cm2 dish in full growth media (DMEM (ThermoFisher) supplemented with 10% FBS, 2mM L-glutamine (ThermoFisher) and 100U/mL penicillin/streptomycin (ThermoFisher)) supplemented with 10 or 30µM uracil (Sigma) and incubated at 37°C/5% CO2 for 24 hours. Cells were then washed with ice cold PBS, scraped into Trizol, and RNA prepped as per manufacturers instructions.
Illumina TruSeq Stranded Total RNA Lib Prep, Gold kit. Quality and quantity of the DNA libraries was assessed on an Agilent 2200 Tapestation.


title: CALERIE_12_EPICv2

description: CALERIE, EPICv2


title: CLHNS_9_EPICv1

description: CLHNS, EPICv1


title: CLHNS_8_EPICv1

description: CLHNS, EPICv1


title: MEF n6 10uM Uracil  rep 6

description: Library name: CCR20200902_S17_CC17_MEF_n6_10uMUracil

value: Mouse embryonic fibroblasts Cultured Cells


title: RNA-seq in N2a cells after transfection with the EV, replicate 2

description: Library name: RNA_EV_Bahcc1_OE_2


title: CALERIE_11_EPICv2

description: CALERIE, EPICv2


title: CALERIE_10_EPICv2

description: CALERIE, EPICv2


title: RNA-seq in N2a cells after transfection with the EV, replicate 1

description: Library name: RNA_EV_Bahcc1_OE_1


title: MEF n6 control  rep 6

description: Library name: CCR20200902_S16_CC16_MEF_n6_CON


title: CLHNS_12_EPICv1

description: CLHNS, EPICv1


title: RNA-seq in N2a cells after transfection with the deltaBAH Bahcc1-HA vector, replicate 3

description: Library name: RNA_deltaBAH_Bahcc1_OE_3


title: CLHNS_6_EPICv1

description: CLHNS, EPICv1


title: MEF n5 30uM Uracil  rep 5

description: Library name: CCR20200902_S15_CC15_MEF_n5_30uMUracil


title: CLHNS_7_EPICv1

description: CLHNS, EPICv1


title: CLHNS_5_EPICv1

description: CLHNS, EPICv1


title: CALERIE_1_rep_EPICv2

description: CALERIE, EPICv2


title: RNA-seq in N2a cells after transfection with the deltaBAH Bahcc1-HA vector, replicate 2

description: Library name: RNA_deltaBAH_Bahcc1_OE_2


title: CALERIE_1_EPICv2

description: CALERIE, EPICv2


title: MEF n5 10uM Uracil  rep 5

description: Library name: CCR20200902_S14_CC14_MEF_n5_10uMUracil


title: CLHNS_1_EPICv1

description: CLHNS, EPICv1


title: RNA-seq in N2a cells after transfection with the deltaBAH Bahcc1-HA vector, replicate 1

description: Library name: RNA_deltaBAH_Bahcc1_OE_1


title: CALERIE_9_EPICv2

description: CALERIE, EPICv2


title: RNA-seq in N2a cells after transfection with the full-length Bahcc1-HA vector, replicate 3

description: Library name: RNA_FL_Bahcc1_OE_3


title: MEF n4 30uM Uracil  rep 4

description: Library name: CCR20200902_S12_CC12_MEF_n4_30uMUracil


title: CALERIE_8_EPICv2

description: CALERIE, EPICv2


title: CLHNS_3_EPICv1

description: CLHNS, EPICv1


title: RNA-seq in N2a cells after transfection with the full-length Bahcc1-HA vector, replicate 2

description: Library name: RNA_FL_Bahcc1_OE_2


title: CALERIE_7_EPICv2

description: CALERIE, EPICv2


title: MEF n4 10uM Uracil  rep 4

description: Library name: CCR20200902_S11_CC11_MEF_n4_10uMUracil


title: MEF n4 control  rep 4

description: Library name: CCR20200902_S10_CC10_MEF_n4_CON


title: CALERIE_6_EPICv2

description: CALERIE, EPICv2


title: CUT&RUN for BAHCC1 in primary mouse cortical neurons after control GapmeRs uptake, replicate 3

data_processing:
RNA-seq: RNA-seq reads were mapped to the mouse genome (mm10 assembly) using STAR (Dobin et al., 2013) to generate read coverage tracks visualized using the UCSC genome browser. RSEM (Li and Dewey, 2011) or STAR -quant with RefSeq annotations were used to call differential expression between samples
CUT&RUN: CUT&RUN reads were mapped to the mouse genome using Bowtie2 (Langmead and Salzberg, 2012) and peaks were called using all the samples together using MACS2 (Zhang et al., 2008) or epic2 (Stovner and Sætrom, 2019). HOMER (Heinz et al., 2011) was used to call differential expression between samples.
Assembly: mm10
Supplementary files format and content: bigWig read coverage files are provided for all samples. RSEM/STAR quantification is provided for the RNA-seq samples, and MACS2/epic2-called peaks are provided for the CUT&RUN data.
Library strategy: CUT&RUN

growth_protocol:
Neuro2a (N2a) cells were cultured in DMEM supplemented with 4.5 g/L of glucose, 4 mM L-Glutamine, 10% FBS, 1% PenStrep solution, grown in incubators maintained at 37°C with 5% CO2, and were routinely passaged by gentle dissociation using a Trypsin (0.05%) – EDTA (0.02%) solution. DNA plasmid transfections were performed by using Lipofectamine 3000 (ThermoFisher Scientific), according to the respective protocols. For each transfection, the optimal DNA concentration and amount of transfection reagents were empirically determined to minimize cellular stress and maximize efficiency, to eventually ensure clean readouts. SiRNAs were transfected using DharmaFECT reagents (DharmaFECT 2), at a final concentration of 25 µM concordantly to the manufacturer’s protocol. GapmeRs were transfected at the final concentration of 50 µM with Lipofectamine 3000, following the manufacturer’s guidelines. In all cases, cells were plated the day before the transfection in an antibiotic-free medium which was subsequently changed prior to adding the transfection mix, and again after 24h to minimize cell death. Finally, transfections were carried out for 72h, unless stated otherwise.
Primary neuronal culture Embryonic cortices (embryonic day 16.5–17) were dissected from 5–6 embryos of mixed sex and pooled for a single replicate culture. Trypsin (0.25%) was used to dissociate tissue through a 10 minutes incubation at 37°C. Digestion was terminated with the addition of ovomucoid (trypsin inhibitor, Worthington). Digested tissue was gently triturated through a P1000 pipette to release cells and passed through a 40 µm filter. After trituration, the cell suspension was transferred to a 15 mL Falcon tube and centrifuged for 5 minutes at RT / 154×g. After centrifugation, the cloudy supernatant was carefully removed with a pipette and discarded. The pellet was resuspended in 10 mL DMEM medium and added to uncoated 90 mm Petri dishes. The plates were incubated at 37°C, 5% CO2 humidified incubator for 30 minutes. During this incubation, glial cells and other unwanted debris adhere to the bottom of the plate while cortical cells are retained in the media and recover from the trituration. The supernatant was carefully removed, without disturbing attached glial cells and unwanted cell debris at the bottom of the plate, and moved into a new 15 mL Falcon tube using a pipette. The collected supernatant was then centrifuged for 5 minutes at RT / 154×g. Neurons were plated onto cell culture dishes pre-coated overnight with poly-d-lysine (20 µg/mL) and laminin (4 µg/mL) and were grown in neurobasal medium (Gibco) containing B27 supplement (2%), 1% PenStrep solution and glutaMAX (1 mM). Neurons were grown in incubators maintained at 37°C with a CO2 concentration of 5%. GapmeRs for unassisted uptake were added directly to the culture medium at a final concentration of 500 nM.

extract_protocol:
CUT&RUN reactions were performed as previously described (Meers et al., 2019), with the addition of 20mM sodium butyrate when profiling BAHCC1, SIN3A and H3K27ac
RNA-seq libraries were prepared using the CORALL mRNA-Seq Kit V2 (Lexogen), following the manufacturer’s instructions. CUT&RUN libraries were prepared as described previously (Meers et al., 2019)

treatment_protocol: Sodium Butyrate (Sigma) was diluted in sterile H2O at a stock concentration of 1M and added to the cell culture media at a final concentration of 5µM. As a control, cells were supplemented with an equal volume of H2O. All treatments were performed for 24h in order to minimize indirect effects due to the extensive inhibition of deacetylation. Retinoic Acid (Sigma) was diluted in DMSO at a stock concentration of 0.01M, and added to a complete media with reduced (1%) serum concentration at a final concentration of 10µM, with equal volumes of DMSO serving as vehicle controls. After three days of treatment, cells were transfected with GapmeRs as previously described, and incubated for three additional days in the retinoic acid medium.

value: Primary Mouse Cortical Neurons

value: BAHCC1 (this study)


title: CALERIE_22_EPICv1

description: CALERIE, EPICv1


title: MEF n3 30uM Uracil  rep 3

description: Library name: CCR20200902_S09_CC9_MEF_n3_30uMUracil


title: CALERIE_21_EPICv1

description: CALERIE, EPICv1


title: CALERIE_5_EPICv2

description: CALERIE, EPICv2


title: RNA-seq in N2a cells after treatment for 24h with 5nM Romidepsin, replicate 1

description: Library name: RNA_Romidepsin_5nM_1


title: CUT&RUN for BAHCC1 in primary mouse cortical neurons after control GapmeRs uptake, replicate 2


title: MEF n3 10uM Uracil  rep 3

description: Library name: CCR20200902_S08_CC8_MEF_n3_10uMUracil


title: CALERIE_20_EPICv1

description: CALERIE, EPICv1


title: MEF n5 control  rep 5

description: Library name: CCR20200902_S13_CC13_MEF_n5_CON


title: CUT&RUN for H3K27me3 in primary mouse cortical neurons after Bahcc1-targeting GapmeRs uptake, replicate 3


title: CLHNS_4_EPICv1

description: CLHNS, EPICv1


title: CALERIE_19_EPICv1

description: CALERIE, EPICv1


title: CALERIE_2_EPICv2

description: CALERIE, EPICv2


title: MEF n2 30uM Uracil  rep 2

description: Library name: CCR20200902_S06_CC6_MEF_n2_30uMUracil


title: RNA-seq in N2a cells after transfection with the full-length Bahcc1-HA vector, replicate 1

description: Library name: RNA_FL_Bahcc1_OE_1


title: CLHNS_2_EPICv1

description: CLHNS, EPICv1


title: MEF n2 10uM Uracil  rep 2

description: Library name: CCR20200902_S05_CC5_MEF_n2_10uMUracil


title: CALERIE_17_EPICv1

description: CALERIE, EPICv1


title: MEF n2 control  rep 2

description: Library name: CCR20200902_S04_CC4_MEF_n2_CON


title: BeCOME_7_EPICv2

description: BeCOME, EPICv2


title: CALERIE_4_EPICv2

description: CALERIE, EPICv2


title: CALERIE_2_rep_EPICv1

description: CALERIE, EPICv1


title: CUT&RUN for BAHCC1 in primary mouse cortical neurons after control GapmeRs uptake, replicate 1


title: MEF n1 30uM Uracil  rep 1

description: Library name: CCR20200902_S03_CC3_MEF_n1_30uMUracil


title: MEF n1 10uM Uracil  rep 1

description: Library name: CCR20200902_S02_CC2_MEF_n1_10uMUracil


title: BeCOME_5_EPICv2

description: BeCOME, EPICv2


title: MEF n3 control  rep 3

description: Library name: CCR20200902_S07_CC7_MEF_n3_CON


title: CALERIE_3_EPICv2

description: CALERIE, EPICv2


title: CUT&RUN for H3K27me3 in primary mouse cortical neurons after control GapmeRs uptake, replicate 2


title: CALERIE_16_EPICv1

description: CALERIE, EPICv1


title: MEF n1 control  rep 1

description: Library name: CCR20200902_S01_CC1_MEF_n1_CON


title: CALERIE_14_EPICv1

description: CALERIE, EPICv1


title: CALERIE_15_EPICv1

description: CALERIE, EPICv1


title: CUT&RUN for H3K27me3 in primary mouse cortical neurons after Bahcc1-targeting GapmeRs uptake, replicate 2


title: BeCOME_3_EPICv2

description: BeCOME, EPICv2


title: Lung-InVitro-Smad4OFF_r2

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

description: Library name: Lung-InVitro-Smad4OFF_r2

data_processing:
Illumina read quality was checked for each sample using FastQC v0.11.5.
FASTQ files were trimmed with trimGalore and cutadapt (PMID: 28715235), and the filtered, pair-ended reads were aligned to mm10 with Bowtie2 (PMID: 22388286).
Peaks were called over input using MACS2 (PMID: 18798982), and only peaks with a p-value of ≤ 0.001 and outside the ENCODE blacklist region were kept. All peaks from all samples were merged by combining peaks within 500 bp of each.
featureCounts (PMID: 24227677) was used to count the mapped reads for each sample. The resulting peak atlas was normalized using DESeq2 (PMID: 25516281). For comparison to DepthNorm, samples were normalized to 10 million mapped reads. Normalized bigWig files were created using the normalization factors from DESeq2 as previously described (PMID: 30429377) and BEDTools genomeCoverageBed (PMID: 20110278). Dynamic ATAC peaks were called if they had an absolute log2-transformed fold change ≥ 0.58 and FDR ≤ 0.1.
Assembly: Reads were aligned to the mouse genome (mm10, GRCm38.91)
Supplementary files format and content: Tab-delimited text file includes raw count table for each sample

source_name: Lung

growth_protocol: Cell lines were generated from tumor-bearing pancreata, livers, or lungs. Tumors were dissected, chopped with razor blades, and digested with 1 mg/ml collagenase V (Sigma-Aldrich) diluted in HBSS for 30-60 min, followed by 0.25% trypsin for 5-10 min. Digested tissues were washed with complete DMEM (DMEM, 10% FBS (Gibco), 1X penicillin–streptomycin), passed through a 100-μm filter, and cultured in complete DMEM on collagen-coated plates (0.1 mg/ml PurCol, Advanced Biomatrix) supplemented with 1 μg/ml doxycycline at 37°C. Cells were passaged at least five times to eliminate any non-tumor cells before using them in experiments.

extract_protocol:
Cells were harvested by trypsinization. Then, 60,000 mKate2+ cells per sample were isolated by FACS, washed once with 50 μl cold PBS and resuspended in 50 μl cold lysis buffer. Cells were then centrifuged immediately for 10 min at 500g at 4°C, and the pellet of nuclei was subjected to transposition with Nextera Tn5 transposase (Illumina #FC-121–1030) for 30 min at 37°C, according to the manufacturer’s instructions. DNA was eluted using a DNA Clean & Concentrator Kit in 21 μl elution buffer (Zymo Research #D4013).
ATAC-seq libraries were prepared using the NEBNext High-Fidelity 2X PCR Master Mix (NEB M0541) as previously described (PMID: 25559105). Purified libraries were assessed using a Bioanalyzer High-Sensitivity DNA Analysis kit (Agilent).
Approximately 50 million paired-end 150-bp reads (25 million each side) were sequenced per replicate on a HiSeq instrument (Illumina).

treatment_protocol: Cells were cultured under continunous treatment with 1 μg/ml doxycycline at 37°C.

value: Lung

value: PDAC Lung Metastasis Cells


title: CALERIE_18_EPICv1

description: CALERIE, EPICv1


title: BeCOME_4_EPICv2

description: BeCOME, EPICv2


title: BeCOME_8_EPICv2

description: BeCOME, EPICv2


title: CUT&RUN for H3K4me3 in primary mouse cortical neurons after Bahcc1-targeting GapmeRs uptake, replicate 3


title: CUT&RUN for H3K4me3 in primary mouse cortical neurons after Bahcc1-targeting GapmeRs uptake, replicate 2


title: CUT&RUN for H3K27me3 in primary mouse cortical neurons after Bahcc1-targeting GapmeRs uptake, replicate 1


title: CALERIE_13_EPICv1

description: CALERIE, EPICv1


title: CUT&RUN for H3K27me3 in primary mouse cortical neurons after control GapmeRs uptake, replicate 3


title: BeCOME_6_EPICv2

description: BeCOME, EPICv2


title: BeCOME_2_EPICv2

description: BeCOME, EPICv2


title: Lung-InVitro-Smad4OFF_r1

description: Library name: Lung-InVitro-Smad4OFF_r1


title: CALERIE_12_EPICv1

description: CALERIE, EPICv1


title: CUT&RUN for H3K4me3 in primary mouse cortical neurons after Bahcc1-targeting GapmeRs uptake, replicate 1


title: CALERIE_11_EPICv1

description: CALERIE, EPICv1


title: CUT&RUN for H3K4me3 in primary mouse cortical neurons after control GapmeRs uptake, replicate 3


title: Liv-InVitro-Smad4OFF_r2

description: Library name: Liv-InVitro-Smad4OFF_r2

source_name: Liver

value: Liver

value: PDAC Liver Metastasis Cells


title: BeCOME_1_EPICv2

description: BeCOME, EPICv2


title: Liv-InVitro-Smad4OFF_r1

description: Library name: Liv-InVitro-Smad4OFF_r1


title: CALERIE_10_EPICv1

description: CALERIE, EPICv1


title: mProxSmallIntestine_WT_rep5

description:
Library name: Sample18
7108

data_processing:
Sequenced reads were processed with fastp for quality control and adapter sequence trimming.
Trimmed reads were aligned to the Mus musculus mm10 genome using HISAT2.
Transcriptomes for each sample were assembled with StringTie2 and UCSC’s mm10 genes.gtf annotation, and all transciptomes for each samples were merged to construct non-redundant transcriptomes across all samples (stringtie --merge).
Expression counts were tabulated (stringtie -e) and used as input for downstream gene expression analyses.
DESeq2 was used for differential gene expression analyses.
Assembly: mm10
Supplementary files format and content: GTF, gene coverage and FPKM expression calculated from stringtie -e
Supplementary files format and content: CSV, gene expression counts used for DESeq2 analysis

source_name: proximal small intestine

extract_protocol:
Intact proximal small intestines were lysed in ice-cold TRIzol using Lysing matrix D (MP Biomedical 116913050-CF) with MP Biomedical FastPrep-24 Homogenizer (1 cycle of 20 s at 4 m/s). Total RNA was isolated from TRIzol using Zymo Research's Direct-zol kit per the manufacturer’s instructions.
One microgram of total RNA was depleted of ribosomal RNA (NEBNext rRNA Depletion Kit v2, NEB E7405) and subsequently fragmented, reverse-transcribed into cDNA, and amplified into barcoded libraries with NEBNext RNA Library Prep (NEB E7765) using custom barcoded Illumina-compatible primers.

value: proximal small intestine

value: Wild-type


title: Panc-InVitro-Smad4OFF_r2

description: Library name: Panc-InVitro-Smad4OFF_r2

source_name: Pancreas

value: Pancreas

value: PDAC Primary Tumor Cells


title: CUT&RUN for H3K4me3 in primary mouse cortical neurons after control GapmeRs uptake, replicate 2

value: untreated


title: CALERIE_1_rep_EPICv1

description: CALERIE, EPICv1

source_name: Whole blood

value: Whole blood


title: mProxSmallIntestine_A20ZF7_rep6

description:
Library name: Sample17
7102


title: CUT&RUN for H3K4me3 in primary mouse cortical neurons after control GapmeRs uptake, replicate 1


title: Panc-InVitro-Smad4OFF_r1

description: Library name: Panc-InVitro-Smad4OFF_r1


title: mProxSmallIntestine_A20ZF7_rep5

description:
Library name: Sample16
6636


title: KCS-B87_TGFb_DoxOff_24h

description: Library name: KCS-B87_TGFb_DoxOff_24h

data_processing:
Illumina read quality was checked for each sample using FastQC v0.11.5.
Raw fastq files were analyzed by removing adaptor sequences using Trimmomatic (0.36), aligned to the mouse genome using STAR (2.5.3a), and quantified transcript counts using featureCounts (1.6.3).
Assembly: Reads were aligned to the mouse transcriptome (mm10, GRCm38.91)
Supplementary files format and content: Tab-delimited text file includes raw count table for each sample

source_name: PDAC Primary Tumor

growth_protocol: Cell lines were generated from tumor-bearing pancreata. Tumors were dissected, chopped with razor blades, and digested with 1 mg/ml collagenase V (Sigma-Aldrich) diluted in HBSS for 30-60 min, followed by 0.25% trypsin for 5-10 min. Digested tissues were washed with complete DMEM (DMEM, 10% FBS (Gibco), 1X penicillin–streptomycin), passed through a 100-μm filter, and cultured in complete DMEM on collagen-coated plates (0.1 mg/ml PurCol, Advanced Biomatrix) supplemented with 1 μg/ml doxycycline at 37°C. Cells were passaged at least five times to eliminate any non-tumor cells before using them in experiments.

extract_protocol:
Total RNA was isolated using TRIzol LS (Thermo Fisher Scientific # 10296028) followed by column clean-up using an RNeasy kit (Qiagen #74106).
100-500 ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA HT Kit, Illumina #20020595), with 15 cycles of PCR.
Samples were barcoded and run on a HiSeq (Illumina) in a 75-bp SE run, with an average of 50 million reads per sample.

treatment_protocol: For ‘DoxOn’ conditions, cells were cultured under continuous Dox treatment (1 mg/ml). For ‘DoxOff’ conditions, cells were cultured in the absence of Dox for five days prior to the start of the experiment. Then, cells were treated for 24 h with either recombinant mouse TGFb-1 (100 pM; R&D Systems #7666-MB-005) or TGFb inhibitor SB505124 (2.5 µM; Sigma #S4696).

value: PDAC Primary Tumor

value: PDAC primary tumor cells

tag: time


title: mProxSmallIntestine_WT_rep4

description:
Library name: Sample15
6635


title: CUT&RUN for H3K27ac in primary mouse cortical neurons after Bahcc1-targeting GapmeRs uptake, replicate 2


title: CALERIE_9_EPICv1

description: CALERIE, EPICv1

value: M


title: CALERIE_8_EPICv1

description: CALERIE, EPICv1

value: F


title: mProxSmallIntestine_A20ZF7_Il22KO_rep4

description:
Library name: Sample14
4705

value: A20ZF7, Il22KO


title: KCS-B87_TGFb_DoxOn_24h

description: Library name: KCS-B87_TGFb_DoxOn_24h


title: KCS-B87_SB_DoxOff_24h

description: Library name: KCS-B87_SB_DoxOff_24h


title: CUT&RUN for H3K27ac in primary mouse cortical neurons after Bahcc1-targeting GapmeRs uptake, replicate 1

value: Primary Mouse Cortical Neurons


title: mProxSmallIntestine_A20ZF7_rep4

description:
Library name: Sample13
4703


title: CUT&RUN for H3K27ac in primary mouse cortical neurons after control GapmeRs uptake, replicate 3


title: KCS-B87_SB_DoxOn_24h

description: Library name: KCS-B87_SB_DoxOn_24h


title: CALERIE_6_EPICv1

description: CALERIE, EPICv1


title: CUT&RUN for H3K27ac in primary mouse cortical neurons after control GapmeRs uptake, replicate 2


title: mProxSmallIntestine_A20ZF7_rep3

description:
Library name: Sample11
4687


title: KCS-B73_TGFb_DoxOff_24h

description: Library name: KCS-B73_TGFb_DoxOff_24h


title: CUT&RUN for H3K27ac in primary mouse cortical neurons after control GapmeRs uptake, replicate 1


title: CALERIE_5_EPICv1

description: CALERIE, EPICv1


title: KCS-B73_TGFb_DoxOn_24h

description: Library name: KCS-B73_TGFb_DoxOn_24h


title: CALERIE_1_EPICv1

description: CALERIE, EPICv1


title: mProxSmallIntestine_A20ZF7_Il22KO_rep3

description:
Library name: Sample10
4219


title: CALERIE_4_EPICv1

description: CALERIE, EPICv1


title: RNA-seq in primary mouse cortical neurons after Bahcc1-targeting GapmeRs uptake, replicate 3

data_processing:
RNA-seq: RNA-seq reads were mapped to the mouse genome (mm10 assembly) using STAR (Dobin et al., 2013) to generate read coverage tracks visualized using the UCSC genome browser. RSEM (Li and Dewey, 2011) or STAR -quant with RefSeq annotations were used to call differential expression between samples
CUT&RUN: CUT&RUN reads were mapped to the mouse genome using Bowtie2 (Langmead and Salzberg, 2012) and peaks were called using all the samples together using MACS2 (Zhang et al., 2008) or epic2 (Stovner and Sætrom, 2019). HOMER (Heinz et al., 2011) was used to call differential expression between samples.
Assembly: mm10
Supplementary files format and content: bigWig read coverage files are provided for all samples. RSEM/STAR quantification is provided for the RNA-seq samples, and MACS2/epic2-called peaks are provided for the CUT&RUN data.


title: CUT&RUN for H3K27ac in primary mouse cortical neurons after Bahcc1-targeting GapmeRs uptake, replicate 3


title: KCS-B73_SB_DoxOff_24h

description: Library name: KCS-B73_SB_DoxOff_24h


title: mProxSmallIntestine_Il22KO_rep3

description:
Library name: Sample9
4214


title: RNA-seq in primary mouse cortical neurons after Bahcc1-targeting GapmeRs uptake, replicate 2


title: mProxSmallIntestine_A20ZF7_Il22KO_rep2

description:
Library name: Sample8
4213


title: RNA-seq in primary mouse cortical neurons after Bahcc1-targeting GapmeRs uptake, replicate 1


title: KCS-B73_SB_DoxOn_24h

description: Library name: KCS-B73_SB_DoxOn_24h


title: CALERIE_2_EPICv1

description: CALERIE, EPICv1

data_processing:
Noob and functional normalized
*processed value definition: DNA methylation beta value


title: CUT&RUN for H3K27me3 in primary mouse cortical neurons after control GapmeRs uptake, replicate 1


title: mProxSmallIntestine_Il22KO_rep2

description:
Library name: Sample7
4212


title: RNA-seq in primary mouse cortical neurons after control GapmeRs uptake, replicate 3


title: Muscle,knock down Hif-1α after hypoxia1,rep3 [K3]

city: Beijing

first: Yubing

last: Zeng

address: 9 Dongdan Santiao, Dongcheng District,

institute: Peking union medical college

data_processing:
raw data was created using bcl2fastq software from which the original image files of sequencing were identified and were transformed to sequenced reads.
Clean data was filtered from raw data. It was aligned to the reference sequence using Hisat2/Tophat. In this step, it was based on all subsequent analysis. Transcript assembly was performed using Stringtie software.
The expression level from readcount and the FPKMs of geneswas were then calculated. Differentially expressed gene (DEG) analysis and other bioinformatics analysis were counted using limma/DESeq software.
Genes with |Log2 fold change (Log2FC)| ≥1 and p-Value ≤ 0.05 were considered as DEGs in comparative analysis.
Assembly: mm10
Supplementary files format and content: genes.rawcount.anno.xlsx

source_name: lung

extract_protocol:
RNA was obtained using Rneasy mini plus kit (Qiagen). 2ug of total RNA was used for the construction of sequencing libraries.
The NEBNext Ultra RNA Library Prep Kit for llumina was used to build the RNA sequencing library according to manufacturer’s protocol.

value: lung

value: knock down Hif-1α after hypoxia


title: BeCOME_8_EPICv1

description: BeCOME, EPICv1


title: mProxSmallIntestine_WT_rep3

description:
Library name: Sample12
4701


title: CALERIE_7_EPICv1

description: CALERIE, EPICv1


title: Muscle,knock down Hif-1α after hypoxia1,rep2 [K2]


title: BeCOME_7_EPICv1

description: BeCOME, EPICv1


title: RNA-seq in primary mouse cortical neurons after control GapmeRs uptake, replicate 2


title: Muscle,knock down Hif-1α after hypoxia1,rep1 [K1]


title: BeCOME_6_EPICv1

description: BeCOME, EPICv1


title: mProxSmallIntestine_Il22KO_rep1

description:
Library name: Sample5
4208


title: CALERIE_3_EPICv1

description: CALERIE, EPICv1


title: Muscle,hypoxia1,rep2 [H2]

value: hypoxia


title: BeCOME_5_EPICv1

description: BeCOME, EPICv1


title: BeCOME_4_EPICv1

description: BeCOME, EPICv1


title: 3T3, GFP-Swi6, uninduced

city: Toulouse

first: Fabian

last: Erdel

address: 169 Avenue Grunberg-Manago

department: MCD

country: France

institute: CNRS, CBI Toulouse

data_processing:
After sequencing, the raw reads were filtered. Data filtering includes removing adapter sequences, contamination and low-quality reads from raw reads.
Reads were mapped to the mouse genome (GRCm39) using STAR
Count tables (considering genes and repetitive elements) were generated with TEtranscripts
Differential expression analysis was carried out using DESeq2
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file, containing counts for each gene or repetitive element

growth_protocol: 3T3 cells were cultured in DMEM supplemented with 10% fetal bovine serum, 1% Penicillin/Streptomycin and 1×GlutaMAX at 37°C in a humidified atmosphere with 5% CO2

extract_protocol:
Total RNA was purified using the MasterPure Complete DNA and RNA Purification Kit (Biosearch Technologies).
Libraries were prepared by BGI (rRNA Depletion stranded Library)

treatment_protocol: Expression of GFP-tagged HP1 variants was induced by addition of 500 ng/ml doxycycline

tag: cell line

value: fibroblast


title: 3T3, GFP-Swi6, induced

value: with dox


title: mProxSmallIntestine_WT_rep1

description:
Library name: Sample3
4199

value: proximal small intestine


title: mProxSmallIntestine_A20ZF7_rep2

description:
Library name: Sample2
4197


title: Muscle,hypoxia1,rep1 [H1]


title: BeCOME_3_EPICv1

description: BeCOME, EPICv1

extract_protocol: genomic DNA was extracted from whole blood using Qiagen DNeasy Kit according to standard instructions


title: Muscle,normoxia1,rep3 [N3]

value: normoxia


title: BeCOME_2_EPICv1

description: BeCOME, EPICv1


title: mProxSmallIntestine_A20ZF7_rep1

description:
Library name: Sample1
4195


title: Aorta_2nd 300 bp

city: Ann Arbor

first: Jun Hee

state: MI

address: 109 Zina Pitcher Pl

institute: University of Michigan

description: SeqScope 2nd-Seq library

data_processing:
Sequencing by Illumina HiSeqX, HiSeq4000 and NovaSeq platforms .
Seq-Scope data were initially processed using the STtools package, utilizing STAR/STARsolo 2.7.5c, with a modification to use hexagonal array, instead of square array. The processed DGE matrix, pooled in non-overlapping hexagons with 12 μm sides, was analyzed in the Seurat V4 package.
First, we removed all genes starting with mt and Gm to remove mitochondrial genes and hypothetical gene models. Then feature number <75 was removed, and data were normalized using regularized negative binomial repression implemented in Seurat’s SCTransform function.
Clustering analysis was performed using the shared nearest neighbor modularity optimization implemented in Seurat’s FindClusters function. The clusters were visualized in the UMAP (uniform manifold approximation and projection) manifold or the histological space using ggplot functions. The markers for each cluster were identified through the FindAllMarkers function and used to annotate cell types.
The clusters identified from initial non-overlapping hexagonal array were projected onto the multiscale sliding windows (MSSW) array, which has four-times higher resolution compared to the original non-overlapping array , using FindTransferAnchors, TransferData, and GetTransferPredictions functions, so that we can achieve higher resolution for cell type predictions.
Assembly: mm10
Supplementary files format and content: Digital expression matrix with barcode featuring spatial coordinates

source_name: Mouse Aorta

growth_protocol: Normal rearing condition

extract_protocol:
The experimental procedures were performed as we previously described, but it was adapted to HISEQ2500 flow cell system so that Seq-Scope has wider and continuous imaging area (1.5 mm × 60 mm in HISEQ2500, compared to 1 mm-diameter circles in MISEQ). A single imaging area was used for all 20 samples to minimize the experimental batch effects. In brief, HDMI32-Dral [Seed HDMI-oligo, containing the PCR/read adaptor sequences, the restriction enzyme-cleavable RNA-capture domain (olido-dT), the high-definition map coordinate identifier (HDMI), a spatial barcode composed of a 32 random nucleotide sequence] was amplified on a flow cell surface to generate HDMI-oligo cluster. The HDMI sequence and coordinates of each cluster were determined using the HISEQ2500 platform. Thumbnail images of clusters were visualized using Illumina Sequencing Analysis Viewer to inspect the cluster morphology and density. Next, the HISEQ2500 flow cell was processed to expose the oligo-dT and RNA-capture domain and generate an HDMI-encoded RNA-capturing array (HDMI-array). Subsequently, the HISEQ2500 flow cell was disassembled to expose the HDMI-array to the outside and used for tissue attachment. The OCT-mounted fresh frozen aortic tissue was sectioned 10 μm thickness in a cryostat (Leica CM3050S, -20°C) and the aortic sections were maneuvered onto the HDMI-array slide. After fixing in 4% formaldehyde for 10 min and incubating in isopropanol for 2 min, the tissue was stained with hematoxylin (Agilent, S3309) for 5 min, treated with bluing buffer (Agilent, CS702) for 2 min, and incubated with buffered eosin [1:9 = eosin (HT110216, Sigma): 0.45M Tris-Acetic buffer (pH 6.0)]. After mounting in 85% glycerol, the tissues were imaged under a digital imager (Keyence, BZ-X800).
Total RNAs released from the fixed tissues were performed as previously described13. Briefly, the fixed tissues attached on the HDMI-array slide were treated with 0.2 U/μl collagenase I (Thermo Fisher, 17018-029) at 37 °C for 20 min, and then incubated with 1mg/ml pepsin (Sigma, P7000) in 0.1M HCl at 37 °C for 10 min. The RNAs released from the tissue sections were captured by the HDMI-array and used as a template to generate cDNA footprints on the HDMI-barcoded RNA capturing molecule by reverse transcription. After overnight reverse transcription reaction at 37 °C, the tissues were incubated in exonuclease I cocktail [1U Exo I enzyme (M2903, NEB) in 1x Exo I buffer] and subsequently digested in 1x tissue digestion buffer [100 mM Tris pH8.0, 100mM NaCl, 2% SDS, 5mM EDTA, 16 U/ml Proteinase K (P8107S, NEB)]. After tissue digestion, the secondary strand, a chimeric molecule of HDMI and cDNA sequences, is synthesized on the cDNA footprint using an adaptor-tagged random primer (Truseq Read 2-conjugated Random Primer version 2 with TCA GAC GTG TGC TCT TCC GAT CTN NNN NNN NB sequence). After removing all DNAs that did not bind to the HDMI-array, the secondary strand product was eluted using NaOH, and after neutralization, purified using AMPure XP purification kit (A63881, Beckman Coulter). The secondary strand product was used as a template to construct library using Kapa HiFi Hotstart Readymix (KK2602, KAPA Biosystems) through two rounds of library PCR. After purification using Zymoclean Gel DNA recovery Kit (D4001, Zymo Research) and AMPure XP, the pooled libraries were subjected to paired-end (100-150bp) sequencing in the Illumina platform at Psomagen lnc.

treatment_protocol: Sixteen-week-old Apoe -/- male mice fed a normal diet were subcutaneously implanted minipumps to delivery AngII (1,000ng/ml, 5 mice) or saline (5 mice) for 4 weeks. No significant difference was found in body weight, TC, and TG between the two groups at 4 weeks after minipump implantation. The extraluminal diameters were significantly increased in AngII group, in which 3 mice developed AAA (60% incidence). The fresh frozen suprarenal abdominal aortas from 3 AAAs and 3 normal controls were pair-embedded in OCT and cut into 10 μm sections. A total of 20 aortic sections (10 normal aortic sections and 10 aneurysmal sections) were attached onto HDMI-array slide for histological staining, library preparation and sequencing.

value: Aorta

value: Normal and AAA, as indicated above

tag: platform

value: Seq-Scope


title: 3T3, GFP-dHP1, uninduced

tag: cell type


title: 3T3, GFP-mHP1, induced

tag: treatment


title: BeCOME_1_EPICv1

description: BeCOME, EPICv1

value: Whole blood


title: Muscle,normoxia1,rep2 [N2]


title: Muscle,normoxia1,rep1 [N1]


title: Muscle,hypoxia1,rep3 [H3]


title: Aorta_2nd

description: SeqScope 2nd-Seq library


title: mProxSmallIntestine_A20ZF7_Il22KO_rep1

description:
Library name: Sample6
4211


title: 3T3, GFP-mHP1, uninduced


title: mProxSmallIntestine_WT_rep2

description:
Library name: Sample4
4200

value: Wild-type


title: D7 ES Jpx KD Hi-C^2, rep1

status: Public on Jun 11 2025

city: Boston

first: Hyun Jung

last: Oh

address: 185 Cambridge St.

institute: MGH

description: Processed data:  d7.JpxKD.cas.combined.matrix.txt, d7.JpxKD.mus.combined.matrix.txt

data_processing:
Hi-C^2 reads were trimmed using cutadapt (v1.2.1) with the options --adapter=GATCGATC (MboI ligation junction) and --minimum-length=20. Reads of each pair were individually mapped to the mus and cas genomes using Novoalign (v3.00.02) and merged into Hi-C summary files and filtered using HOMER(v4.8) as previously described (Minajigi et al. Science 2015). To avoid computational complexities arising from normalization of sparse or non-enriched regions in the Hi-C contact map, we considered only Hi-C interactions falling within the capture region for further analysis. For each capture, the filtered Hi-C interactions falling within the target region (chrX:100,153,712-101,269,503) were pulled out from HOMER tag directories. Hi-C2 data of the capture regions in hic format were generated using the command  “pre” of Juicer tools (v1.5.3) and then converted into the matrices with “square root vanilla coverage” normalization using the command “dump” of Juicer tools and a custom script. The average interaction values of each library were obtained from the Juicebox tool (v1.9.8) and then used to normalize the interaction values among different libraries. The resulting Hi-C2 matrix values were used to generate the heatmaps. To generate allelic Hi-C^2 contact matrices for control and Jpx KD cells, allele-specific reads were combined from two biological replicates and converted into HOMER tag directories.
Assembly: mm9
Supplementary files format and content: Hi-C^2 probes (Xic_capture_probes.bed). Normalized Hi-C^2 contact matrices (*.txt).

source_name: Day 7 ES cells

growth_protocol: Undifferentiated female mouse embryonic stem cells were grown on the irradiated MEF feeders in regular DMEM medium (high-glucose) with 15% FBS and LIF. For differentiation, cells were trypsinizied and incubated in the medium at 37 °C for at least 40 min. After separation of ES cells from attached feeders, ES cells were re-plated on non-gelatinized petri dishes in the complete DMEM medium without LIF. Embryonic bodies (EB) formed from ES cells were transferred to the gelatinized cell culture plates on day 4 of differentiation. Cells were harvested on indicated days.

extract_protocol: Hi-C libraries were generated essentially based on the in-situ Hi-C protocol (Rao et al. Cell 2014; Oh et al. Cell 2021).  MboI (200U) was used for digestion of nuclei collected from 3 million cells.  The subsequent Hi-C^2 experiment was performed as descried previously (Sanborn et al.PNAS 2015). Briefly, 120 bp probes were designed around the MboI restriction sites in the region of interest: chrX:100,153,712-101,269,503 (mm9). Single stranded DNA oligos were amplified and biotinylated in a MAXIScript T7 transcription reaction (Ambion). The resulting biotinylated RNA probes were hybridized to 500 ng of in situ Hi-C libraries for 24 hours at 65°C. DNA hybridized to the RNA probes was pulled down by streptavidin beads, washed, and eluted as described (Sanborn et al. PNAS 2015). The resulting DNA was desalted with a cleanup using 1X AMPure beads and amplified with Illumina primers for 12 cycles of PCR to prepare for sequencing (paired-end 50bp).

treatment_protocol: LNA transfection: D7 ES cells were trypsinized, transfected with scrambled LNA or Jpx LNA using Mouse ES cell Nucleofector Kit (Lonza), transferred to the gelatinized plates and harvested after incubation at 37°C for 8 hr.

tag: strain

value: CAST/EiJ x 129S1

value: Differentiating mESC (day 7)

tag: transfection

value: Jpx LNA-transfected

tag: library strategy


title: D7 ES Jpx KD Hi-C^2, rep2