title: nTERT-BP-IgG2


title: Cisplatin stim, replicate 3

status: Public on Dec 04 2024

type: SRA

city: Cambridge

first: Benjamin

last: James

state: MA

address: 32 Vassar St

country: USA

institute: Massachusetts Institute of Technology

description:
10x Genomics
D21-2753

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcode processing, gene counting, and aggregation were performed with the Cell Ranger software 5.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Further data analysis was performed using Scanpy
Assembly: mm10
Supplementary files format and content: AnnData (H5AD) containing counts, cell metadata, cell type assignments, and dimensionality reduction; MatrixMarket (MTX) file containing raw counts; tab-separated value (TSV) files containing metadata

molecule: total RNA

organism: Mus musculus

source_name: Hippocampus

extract_protocol:
On the 22nd day from the first cisplatin/GENUS treatment, samples were anesthetized with isofluoren and cardiac perfused with ice cold DPBS (Thermo Fisher ScientificScienctific, 14190235). Two hippocampi per animal were isolated and four hippocampi from two animals were homogenized using adult neural tissue dissociation kit (Miltenyi bio, 130-092-628).
The resulting single cell suspension was processed to generate a cDNA library with targeted recovery of 5000 cells using 10x Genomics Chromium™ Single Cell 3' Library & Gel Bead Kit v3.1 (1000215, 1000268, 1000127). The library was sequenced with NovaSeq 6000 (Illumina) and NovaSeq S4 Flow Cell at MIT bioinformatics core.

tag: tissue

value: Hippocampus

tag: strain

tag: age

value: 9 weeks old

tag: Sex

value: female

tag: treatment

value: Cisplatin stim


title: DDX50 STAU1 dms15

city: Stanford

first: Douglas

last: Porter

state: CA

address: 269 Campus Drive

department: Dermatology

institute: Stanford

library_source: other

data_processing:
UMIs were moved to read name and fixed sequenced removed using umi_tools extract, after which bbduk.sh removed adapters AGA TCG GAA GAG CGT CGT GTA GGG AAA GAG TGT and AGA TCG GAA GAG CAC ACG TCT GAA CTC CAG TCA. Reads were then mapped to a bowtie2 genome of stabilized RNAs and expression-matched random RNAs using RNAFramework rf-map. Mapped reads were deduplicated with umi_tools, quantified with RNAFramework/rf-count, then normalized. For comparison of unnormalized reaction rates between conditions, the quantifications output from rf-count were used. Finally, RNAs were folded with the parameters --temperature 37 --dotplot -sh --vienna-rnasubopt ViennaRNA/bin/RNAsubopt --vienna-rnafold ViennaRNA/bin/RNAfold.
Assembly: hg38
Supplementary files format and content: TPM at the subset of genes investigated for structure.
Library strategy: DMS-seq

molecule: other

organism: Homo sapiens

source_name: Primary keratinocytes

growth_protocol: Primary human keratinocytes were isolated from fresh surgically discarded newborn foreskin, and progenitor cells cultured in complete Keratinocyte-SFM (Life Technologies, #17005-142) and Medium 154 (Life Technologies #M-154-500). Cells were induced to differentiate by the addition of 1.2 mM calcium for 4 days at full confluence.

extract_protocol:
Total RNA was extracted from day 4 differentiated keratinocytes using RNeasy Plus (QIAGEN, 74136).
DMS labeled RNA was first purified using the Dynabeads™ mRNA DIRECT™ Purification Kit (Invitrogen, 61012). 12 μL poly(A) beads per sample were washed twice with binding buffer (100 mM Tris-HCl pH 7.5, 500 mM NaCl, 10 mM EDTA, 1% SDS), then added to purified RNA in 600 μL of binding buffer, incubated for 3-5 minutes at room temperature with mixing to bind RNA to the beads, washed with the kit’s buffers according to the kit’s instructions, and eluted in 11 μL of 10 mM Tris-HCl (pH 7.5) by heating at 65-80°C for 2 minutes. Purified poly(A) RNA was converted to a sequencing library with the SMARTer® Stranded Total RNA-SeqKit v3 Pico Input Mammalian kit (Takara, 634485) following the manufacturer’s instructions and using a 1.5 min 94°C initial incubation in First-Strand buffer and 7 cycles during the first PCR reaction.

treatment_protocol: Total RNA was extracted from day 4 differentiated keratinocytes using RNeasy Plus (QIAGEN, 74136). 1 µg of total RNA was used for each experiment. RNA was diluted to 200ng/µL with RNase free water and heated for 1 min at 95 °C, then placed on ice. RNA was subsequentially diluted in refolding buffer to 90 µL before protein or glucose were added to the mix. A total of 6 conditions were explored (DMS was not added at this step): 1. No DMS+200ng BSA; 2. DMS+200ng BSA; 3. DMS+200ng BSA+1 mM glucose; 4. DMS+200ng DDX50; 5. DMS+150ng STAU1; 6. DMS+200ng DDX50+150ng STAU1+1mM glucose. Mixtures were incubated at 37 °C for 10 min on thermomixer. After incubation, 10 μL 1.7M DMS (diluted in ethanol) or 10 μL ethanol (for no DMS samples) was added to the mixtures and RNA labeled by incubation at 37 °C for 5 min on a thermomixer while shaking at 500rpm. To quench, 60 μL β-mercaptoethanol was added to the mixture immediately and labeled RNA was purified.

tag: cell type

value: Primary keratinocytes


title: GBCT11

city: Shanghai

first: Shengli

last: Li

address: 650 Xinsongjiang Road

country: China

institute: Shanghai Jiao Tong University School of Medicine

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using STAR
Stringtie was used to assemble transcripts from mapped reads.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample ...

source_name: Gallbladder tissue

extract_protocol:
Tissues were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent. NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (Cat#E7420L) was used with 3 ug of total RNA for the construction of sequencing libraries. RNA-seq libraries were prepared using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (Cat#E7420L) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using RNAseq protocols

value: Gallbladder

tag: tumor status

value: Primary tumor

tag: gender

value: Male

tag: patient age

tag: tumor stage


title: STAU1 dms13


title: Cisplatin stim, replicate 2

description:
10x Genomics
D21-2752


title: STAU1 dms14


title: PHK-Ctrl-IgG4

city: Chicago

first: kyle

last: amber

state: IL

address: 707 S Wood St

institute: Rush University

data_processing:
Bowtie (version 1.2.3), RSEM (version 1.3.3) with standard parameters
Assembly: Hg38/gencode.v42
Supplementary files format and content: TXT file, raw TPM, FPKM, counts

molecule: polyA RNA

source_name: Skin

growth_protocol: EpiLife Medium with Human Keratinocyte Growth Supplement (Thermo Fisher Scientific, Waltham, MA, USA) in a humidified atmosphere of 5% CO2 at 37°

extract_protocol:
Qiagen RNeasy Mini Kit
Poly (A) mRNA was subsequently extracted and enriched from total RNA utilizing oligo (dT)-attached magnetic beads according to the manufacturer’s (Illumina) instructions. Enriched and purified mRNA was fragmented into approximately 200 nt short mRNA, followed by first-strand cDNA synthesis using random hexamers as primers. Second-strand cDNA was constructed in a buffer containing dNTPs, DNA polymerase I and RNaseH. Appropriate fragments were isolated and enriched by PCR amplification.

treatment_protocol: Treated overnight with affinity purified BP-IgG or Ctrl-IgG

value: Skin

tag: cell line

value: Primary human Keratinocye

value: keratinocyte

value: Ctrl-IgG 4mg/mL


title: GBCT10


title: shDDX50-1 biorep1 adipocyte

description: NovaSeq X Plus

data_processing:
Lexogen reads were processed according to the manufacturer’s recommendation, mapped with STAR (v. 2.7) to the Gencode M32 genome (“basic” annotations), and genes quantified with FeatureCounts (from Rsubread v.2.10.5). Quantifications were analyzed with DESeq2 (v.1.38.3), with apeGLM shrinkage.
Assembly: GRCm39 (M32)
Supplementary files format and content: Reads per gene quantified with FeatureCounts (from Rsubread v.2.10.5).

growth_protocol: 3T3-L1 (ATCC, CL-173) cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) media (Gibco, #11995-065) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin–streptomycin at 37°C with 5% CO2. 3T3-L1 cells were induced to differentiation in DMEM supplied with 10% FBS, 1% penicillin–streptomycin, 0.5 mM IBMX, 1 µM dexamethasone, 10 µg/mL insulin.

extract_protocol:
Total RNA was extracted using the RNeasy Plus kit (QIAGEN, 74136).
QuantSeq 3’ mRNA-Seq V2 Library Prep Kit FWD with UDI (Lexogen, 191.96) following manufacturer’s protocol with UMI Second Strand Synthesis Module for QuantSeq FWD (Lexogen, 018.96)

value: Adipocyte

value: shRNA against DDX50, #1


title: GBCT9


title: PHK-Ctrl-IgG3


title: Cisplatin nonstim, replicate 2

description:
10x Genomics
D21-2750

value: Cisplatin nonstim


title: DDX50 dms11


title: PHK-Ctrl-IgG2


title: PBS stim, replicate 3

description:
10x Genomics
D21-2749

value: PBS stim


title: GBCT8


title: PHK-Ctrl-IgG1


title: GBCT7


title: PHK-BP-IgG-4

value: BP-IgG 4mg/mL


title: Glc dms10


title: PBS stim, replicate 2

description:
10x Genomics
D21-2748

value: Hippocampus


title: siLDHB_r3

city: Bern

first: Liang

last: Zhao

address: Murtenstrasse 24

country: Switzerland

institute: DBMR

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: DEResults.xlsx

source_name: lung

growth_protocol: cells were maintained in RPMI-1640 suppleemented with 10% FBS and incubated in humidited atmosphere with 5% CO2 at 37 degree.

extract_protocol: Total RNA was isolated and purified using RNeasy Mini Kit (Qiagen, Hilden, Germany)

treatment_protocol: cells were first transfected with siRNA against non-targeted control or LDHB for 48 hours and then treated with Erastin for another 20 hours.

value: lung

tag: genotype

value: siLDHB

value: DMSO

tag: time

value: 20 hours


title: GBCT6

value: Gallbladder


title: PHK-BP-IgG-3


title: nTERT-BP-IgG1

data_processing:
Bowtie (version 1.2.3), RSEM (version 1.3.3) with standard parameters
Assembly: Hg38/gencode.v42
Supplementary files format and content: TXT file containing raw TPM, FPKM, counts

growth_protocol: Cells were grown in KC-SFM medium (ThermoFisher) supplemented with 30 μg/ml bovine pituitary extract, 0.2 ng/ml epidermal growth factor, and 0.3 mM calcium chloride.

value: nTERT

value: BP-IgG


title: PBS nonstim, replicate 3

description:
10x Genomics
D21-2747

value: 9 weeks old

value: female

value: PBS nonstim


title: Glc dms9

value: Primary keratinocytes


title: GBCT5

value: Primary tumor

value: Female


title: DDX50 dms12


title: Cisplatin nonstim, replicate 3

description:
10x Genomics
D21-2751

value: Cisplatin nonstim


title: BSA dms8


title: PBS nonstim, replicate 2

description:
10x Genomics
D21-2746


title: BSA dms7


title: PHK-BP-IgG-2

value: Skin

value: Primary human Keratinocye

value: keratinocyte


title: GBCT4

value: Male


title: PHK-BP-IgG-1

value: BP-IgG 4mg/mL


title: Cisplatin stim, replicate 1

description:
10x Genomics
D20-6410

value: Hippocampus

value: Cisplatin stim


title: GBCT3

value: Gallbladder


title: No DMS dms6


title: Cisplatin nonstim, replicate 1

description:
10x Genomics
D20-6409


title: GBCT2


title: No DMS dms5


title: CD5_2

city: East Lansing

first: Rance

last: Nault

state: United States

address: 1355 Bogue St. B403

department: Department of Pharmacology and Toxicology

institute: Michigan State University

data_processing:
Following sequencing quality control, CellRanger v2.1 (10X Genomics) was used to align reads and integrate the two donor data sets
Raw counts were further analysed using Seurat v4.0.0. Each sample was filtered for (i) unique feature counts >4000, (ii) RNA count parameters <20000, and (iii) ≤15% mitochondrial genes or cell cycle-associated genes.
Clustering of cells was performed using Seurat integration tools at a resolution of 0.2 and 0.9
Assembly: Human Genome GRCh38 using STAR
Supplementary files format and content: Processed data files for individual sample are CellRanger filtered_feature_bc_matrix outputs which includes barcodes (barcodes.tsv.gz),  features (features.tsv.gz), and the matrix (matrix.mtx.gz).
Supplementary files format and content: Sparse matrices for log normalized and raw data

source_name: PBMC

extract_protocol:
PBMC were isolated by ficoll density gradient from 2 anonymous platelet donor leukapheresis packs naïve B cells were isolated by magnetic assisted cell sorting via negative selection. CD5 expressing B cells were enriched by positive selection for CD5 protein and then added back into a 1:1 ratio with CD5 negative B cells.
Libraries were prepared using the 10X Genomics Chromium Single Cell 3’ v3 kit and Chromium i7 Multiplex Kit.

value: PBMC

value: Unknown

value: Gulf Coast Blood Bank


title: DDX50 dms3


title: GBCT1


title: PBS stim, replicate 1

description:
10x Genomics
D20-6408

value: 9 weeks old

value: female

value: PBS stim


title: PBS nonstim, replicate 1

description:
10x Genomics
D20-6407

value: PBS nonstim


title: fur A18 F18 I1 R2

city: La Jolla

first: Bernhard

last: Palsson

address: 9500 Gilman Dr

institute: UCSD

data_processing:
RNA-sequencing reads were processed using https://github.com/avsastry/modulome-workflow.
Assembly: NC_000913
Supplementary files format and content: log_tpm_all_TF_KALEs.csv contains the log tpm values of all of the samples included in this submission

organism: Escherichia coli str. K-12 substr. MG1655

source_name: bacterial culture

extract_protocol:
All samples from both rounds were prepared and collected in biological duplicates at UCSD. 3 ml of culture sampled from an overnight grown culture at an OD600 nm = 0.5 was added to 6 ml of Qiagen RNA-protect Bacteria Reagent after sample collection. This solution was then vortexed for 5 seconds, incubated at room temperature for 5 minutes, and then centrifuged. The supernatant was then removed and the cell pellet was stored at -80° C. The Zymo Research Quick-RNA MicroPrep Kit was used to extract RNA from the cell pellets per vendor protocol. On-columns DNase treatment was performed for 30 minutes at room temperature. Anti-rRNA DNA Oligo mix and Hybridase Thermostable RNase H31 was used to remove ribosomal RNA.
Sequencing libraries were created using a Kapa Biosystems RNA HyperPrep per vendor protocol.

value: bacterial culture

value: fur KO, midpoint


title: GBCN20

value: Benign adjacent

value: Female


title: fur A18 F18 I1 R1


title: RNA-seq replicate2 of OxDRM2 LR stage 1

city: Wuhan

first: shaoli

last: zhou

state: Hubei

address: shizishan street

department: National Key Laboratory of Crop Genetic Improvement

institute: Huazhong Agricultural University

description: Library name: ZZSZ073

data_processing:
For RNA-seq analysis, HISAT (v0.1.6) was used to map clean reads to rice reference genome (RGAP version 7.0). Cufflinks (v2.2.1) and Cuffdiff (v2.2.1) were used to splice transcripts and find differential expressed genes. A strict criteria (fold change>4, q value<0.01) was used to filter differentially expressed genes. For BS-seq analysis, clean reads were mapped to rice reference genome (RGAP version 7.0) by BS-seeker2 (v2.1.8). MethylKit (v3.6) was used to identify differentially methylated regions (DMRs) with win.size equal to 1000 and step.size equal to 100. To avoid bins with few cytosines, we selected bins with at least four cytosines and covered by at least ten reads. Q value less than 0.01 as well as absolute methylation difference of 0.7, 0.5, and 0.1 for CG, CHG, and CHH, respectively, were selected as Tan et al. (2016) suggested. Adjacent bins with overlapping were merged into one DMR.
Assembly: RGAP version 7.0
Supplementary files format and content: The processed data is the standard output format of cuffnorm software, which contains the normalized transcription profiles of genomic genes of wild type and indicated mutants.

organism: Oryza sativa Japonica Group

source_name: root

growth_protocol: Rice (Oryza sativa spp japonica) material used in this study is from ‘Zhonghua 11’ (ZH11) background. For germination culture, seeds were surface-sterilized and germinated in medium containing 0.8% agar supplemented with 3% (w/v) sucrose at 28°C (in light) and 24°C (in dark) with a 14-h-light/10-h-dark cycle. For growth in field, germinated rice seedling was transferred to greenhouse at 25–30 °C under 14-h-light followed by 10-h-dark.

extract_protocol:
Twelve µm sections of crown, lateral, and embryonic root initials tissues were put onto RNase-free PEN membrane glass slide (Carl Zeiss, 415190-9041-000). Lasser catpture microdissection (LCM) was performed using the ZEISS PALM MicroBeam system.The RNA of dissected tissues was isolated with RNeasy Plus Micro Kit (Qiagen, 74034). The DNA of dissected tissues was isolated with DNA Micro Kit (Qiagen, 56304). For RNA-seq library construction, Smart-seq v4 Ultra Low Input RNA Kit (Takara, 091817) was used for amplifying purified mRNA. The amplified DNA was sheared to 200-500 bp range by sonication and purified with AMPure XP beads. 1 μg DNA was used for following library construction. Purified DNA was end repaired, added with adenylate in the 3’ ends, ligated with adapters, and amplified with PCR for 7-8 cycles with the reagents from TruSeq® ChIP Sample Preparation Kit (Illumina). For BS-seq library construction, Bisulfite conversion was performed by utilizing Zymo EZ Methylation Direct Kit (Zymo, D5020). Converted DNA was purified with PureLink PCR Purification Column Kit (Invitrogen, K210012) with minor modification (add M-Desulphonation Buffer to the column and hold for 15 mins before washing) as Clark et al. (2017) suggested. The converted ssDNA was then used for following BS-seq libraries construction with TruSeq® DNA Methylation Kit (Illumina).
RNA libraries for RNA-seq were prepared using TruePrep DNA Library Prep Kit V2 for Illumina following manufacturer's protocols. DNA libraries for BS-seq were prepared using KAPA following manufacturer's protocols

value: root

value: stage 1 of LR

value: root initials


title: GBCN19


title: RNA-seq replicate1 of OxDRM2 LR stage 1

description: Library name: ZZSZ072


title: CD5_1

value: 10X Genomics Chromium Single Cell 3’ v3 kit


title: No DMS dms1

value: Primary keratinocytes


title: fur A18 F110 I3 R2

value: fur KO, endpoint


title: siCTR_E_r3

value: lung

value: siCTRL

value: Erastin

value: 20 hours


title: GBCN18

value: Gallbladder

value: Male


title: HA STAU1 L gluc 1

data_processing:
STAR (Love et al., 2014) (v. 2.7) was used to map raw, paired-end, fastq files to the rDNA locus, then to a genome of repetitive elements, then to the genome. Custom scripts were used for read processing (https://github.com/dfporter/easyclip-snakemake). Reads were assigned to genes, separating exons and introns, using HTSeq (v. 0.13.5).
Assembly: hg38
Supplementary files format and content: Text file of read counts per million reads mapping to the indicated elements.
Library strategy: CLIP-seq

growth_protocol: Primary human keratinocytes were isolated from fresh surgically discarded newborn foreskin, and progenitor cells cultured in complete Keratinocyte-SFM (Life Technologies, #17005-142) and Medium 154 (Life Technologies #M-154-500). Cells were induced to differentiate by the addition of 1.2 mM calcium for 3 days at full confluence. Cells with low glucose and the corresponding normal glucose condition were maintained in glucose-free DMEM (Gibco, #11966025) supplied with SFM supplement (rEGF: Gibco, #10450-013; BPE: 13028-014), 1X Sodium Pyruvate (Gibco, 11360070) and a final concentration of 0.5 g/L (“low” glucose, Gibco, A2494001) or 4.5 g/L glucose (“normal” glucose) with adding 1.2 mM calcium during differentiation for 3 days. All the “low” and “normal” conditions indicated referred to day 3 differentiated cells if not specified.

extract_protocol:
Cells were lysed by lysis buffer and sonication, followed by immunopurification of the protein of interest, according to the easyCLIP protocol (https://doi.org/https://doi.org/10.1002/cpz1.659).
Libraries were constructed with the easyCLIP protocol (https://doi.org/10.1038/s41467-021-21623-4 and https://doi.org/https://doi.org/10.1002/cpz1.659).

value: Lentiviral integration of HA-tagged STAU1


title: GBCN17


title: fur A18 F110 I3 R1

value: bacterial culture


title: shDDX50-4 4h biorep2 stability DDX50

data_processing:
Salmon (v.1.4) was used to quantify gene abundances using only “basic” tagged Gencode v.39 transcripts. Quantifications analyzed with DESeq2 (v.1.38.3), with apeGLM shrinkage.
Assembly: hg38
Supplementary files format and content: VST quantification by DESeq2.

growth_protocol: Primary human keratinocytes were isolated from fresh surgically discarded newborn foreskin, and progenitor cells cultured in complete Keratinocyte-SFM (Life Technologies, #17005-142) and Medium 154 (Life Technologies #M-154-500). Human skin keratinocyte cells were induced to differentiate by the addition of 1.2 mM calcium for 3 days at full confluence in the 50/50 media. Biological replicates were performed in all cases using primary cells from at least 2 independent, unrelated donors.

extract_protocol:
Total RNA was extracted using the RNeasy Plus kit (QIAGEN, 74136), followed by poly(A) enrichment and library preparation using the NEB Ultra II (non-directional) kit (E6111).
NEB Ultra II (non-directional) kit (E6111)

treatment_protocol: For actinomycin D treatment, differentiated keratinocytes were treated with 5 µg/mL actinomycin D (~4 µM) or DMSO for the indicated time before harvesting the cells.

tag: replicate

value: Biological replicate 2

value: shRNA against DDX50, #4


title: shDDX50-4 0h biorep2 stability DDX50


title: GBCN16

value: Benign adjacent


title: shDDX50-1 4h biorep2 stability DDX50

value: shRNA against DDX50, #1


title: fur A14 F18 I1 R1

value: fur KO, midpoint


title: RNA-seq replicate2 of ta2 LR stage 1

description: Library name: ZZSZ069

value: root

value: stage 1 of LR

value: root initials


title: shDDX50-1 0h biorep2 stability DDX50

value: Primary keratinocytes


title: shControl 4h biorep2 stability DDX50

value: Control shRNA


title: BSA dms2


title: RNA-seq replicate1 of ta2 LR stage 1

description: Library name: ZZSZ068


title: fur A14 F113 I3 R2

value: fur KO, endpoint


title: fur A14 F113 I3 R1


title: GBCN15


title: GBCN14


title: shDDX50-4 4h biorep1 stability DDX50

value: Biological replicate 1


title: fur A13 F18 I6 R2


title: RNA-seq replicate2 of ta2 CR stage 1

description: Library name: ZZSZ067

value: stage 1 of CR


title: BAPN, Bio Replicate 3, scRNAseq

city: Houston

first: Cynthia

last: Reinhart-King

state: TX

address: 6100 Main Street

department: Biomedical Engineering

institute: Rice University

description:
Library name: Sample 6
custom inDrops

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the inDrops method [https://github.com/indrops/indrops].
Assembly: Mus musculus GRCm38 [ENSEMBL release 85]
Supplementary files format and content: Comma-separated values files

source_name: mammary tumor

extract_protocol:
Fresh tumors were isolated in a sterile biosafety cabinet and placed in ice cold HBSS during transit from mouse facility to laboratory. Tumors were rinsed several times in ice cold HBSS and minced with sterile scalpels. Minced tumor was then enzymatically digested using the Human Tumor Dissociation Kit from Milytenyi Biotec (130-095-929). Post-enzymatic digestion, cells were passed through 100µm and 70 µm strainers (Miltenyi Biotec 130-110-916) to remove debris and undigested fragments. Cell suspensions then underwent several brief rounds of washing in 1X PBS with 3mM EDTA and an incubation in TrypLE (ThermoFisher Scientific 12604013) for 10 min to break apart cell clusters. Cells were suspended in PBS without EDTA and diluted to a concentration of 150k cells/ml for encapsulation.
(1CellBio) with an in vitro transcription library preparation protocol (Klein et al., 2015). As per Klein et al., the CEL-Seq work flow is summarized: 1) RT, 2) ExoI, 3) SPRI purification (SPRIP), 4) SSS, 5) SPRIP, 6) T7 in vitro transcription linear Amplification, 7) SPRIP, 8) RNA Fragmentation, 9) SPRIP, 10) primer ligation, 11) RT, 12) library enrichment PCR.

treatment_protocol: Mice were treated with control or BAPN in drinking water once per week starting at week 6 until endpoint.

value: mammary tumor

value: MMTV-PyMT positive

value: BAPN

tag: batch


title: shControl 0h biorep2 stability DDX50


title: RNA-seq replicate2 of OxDRM2 CR stage 1

description: Library name: ZZSZ071


title: fur A13 F18 I6 R1

value: bacterial culture


title: GBCN13

value: Gallbladder

value: Male


title: RNA-seq replicate1 of OxDRM2 CR stage 1

description: Library name: ZZSZ070


title: fur A14 F18 I1 R2


title: GBCN11

value: Benign adjacent


title: RNA-seq replicate1 of ta2 CR stage 1

description: Library name: ZZSZ066


title: Affected, bird # A73

city: Stony Brook

first: Addolorata

last: Pisconti

address: 100 Nicolls Rd

department: Biochemistry and Cell Biology

institute: Stony Brook University

data_processing:
Sequencing QC was performed with FastQC v0.12.1 (Andrews, 2023), Trim Galore v0.6.7 (Krueger et al., 2021) (and Cutadapt v3.4 (Martin, 2011). Reads were mapped to the GRCg7b version of the Gallus gallus reference genome using STAR v2.7.9a (Dobin et al., 2013). Alignments were converted to BAM format and sorted using samtools v1.17 (Li et al., 2009).  Transcript expression was then quantified with Salmon v1.10.1 (Patro et al., 2017) and converted to gene-level counts with Tximport v1.12.0 (Soneson et al., 2015). Differential expression analysis comparing the affected and not affected groups was next performed using the nf-core differential abundance pipeline v1.4.0 (O Wacker, 2023), with read count normalization and statistical analysis performed with DESeq2 v1.34.0 (Love et al., 2014). Initial exploratory analysis showed that two samples from the “not affected” group were statistical outliers based on the median absolute deviation of their normalized read counts, and these samples were excluded from further analysis. This left 9 remaining samples in the not affected group and 10 samples in the affected group.  The results of the differential expression analysis were visualized using the Enhanced Volcano R package v1.20.0 (Blighe and Lun, 2018). Gene set enrichment analysis (GSEA) was performed with the ClusterProfiler R package v4.10.1  (Yu et al., 2012; Wu et al., 2021) using the fgsea algorithm (Korotkevich et al., 2016). Log2 fold-change scores were used to rank genes, and the results were visualized with the Enrichplot package v1.22.0 (Wu et al., 2021). Network analysis to find genes with correlated expression levels was performed with WGCNA v.1.72.5 (Langfelder and Horvath, 2008) using normalized and variance-stabilized read counts and a soft-thresholding power value of 10.  The genes present in selected modules were then subject to functional overrepresentation analysis (ORA) using ClusterProfiler v4.10.1. For the ORA, the background gene list was defined as the set of genes used in the differential expression analysis that also possessed relevant functional annotations.
Assembly: GRCg7b version of the Gallus gallus
Supplementary files format and content: TSV read counts

organism: Gallus gallus

source_name: pectoralis muscle

extract_protocol:
Qiagen Rneasy Mini Kit
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification

value: pectoralis muscle

tag: breed

value: primary skeletal myoblasts

tag: group

value: Affected


title: fur A13 F114 I1 R2

tag: tissue


title: shDDX50-1 4h biorep1 stability DDX50

value: shRNA against DDX50, #1


title: GBCN10


title: GBCN12


title: fur A13 F114 I1 R1


title: Non Affected, bird # NA61B

value: Non Affected


title: GBCN9


title: shDDX50-1 0h biorep1 stability DDX50

value: Primary keratinocytes


title: fur A0 F0 I1 R2

value: fur KO, unevolved


title: shControl 4h biorep1 stability DDX50

value: Control shRNA


title: fur A0 F0 I1 R1


title: GBCN8


title: Non Affected, bird # NA64B


title: GBCN7


title: Affected, bird # A16B


title: shControl 0h biorep1 stability DDX50

value: Biological replicate 1


title: shDDX50-4 0h biorep1 stability DDX50

value: shRNA against DDX50, #4


title: GBCN6


title: crp A4 F86 I1 R1

value: crp KO, endpoint


title: GBCN5

value: Female


title: crp A4 F20 I1 R2

value: crp KO, midpoint


title: crp A4 F86 I1 R2

value: bacterial culture


title: Affected, bird # A79


title: shDDX50-4 biorep4 techrep2 organoid

data_processing:
Lexogen reads were processed according to the manufacturer’s recommendation, mapped with STAR (v. 2.7) to the Gencode v39 genome (“basic” annotations), and genes quantified with FeatureCounts (from Rsubread v.2.10.5). Quantifications were analyzed with DESeq2 (v.1.38.3), with apeGLM shrinkage.
Assembly: hg38
Supplementary files format and content: Reads per gene quantified with FeatureCounts (from Rsubread v.2.10.5).

growth_protocol: Primary human keratinocytes were isolated from fresh surgically discarded newborn foreskin, and progenitor cells cultured in complete Keratinocyte-SFM (Life Technologies, #17005-142) and Medium 154 (Life Technologies #M-154-500). Organotypic regeneration of human epidermal and cervical tissues were performed as previously described (https://doi.org/10.1101/gad.1463206) using KGM media. Day 7 epidermal and cervical tissues were collected.

extract_protocol:
Total RNA was extracted using the RNeasy Plus kit (QIAGEN, 74136).
QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, 015.96)

value: Skin organoid

value: Biological replicate 4


title: Affected, bird # A85


title: GBCN4

value: Gallbladder

value: Benign adjacent

value: Male


title: shDDX50-4 biorep4 techrep1 organoid


title: Affected, bird # A76

value: pectoralis muscle

value: primary skeletal myoblasts

value: Affected


title: shDDX50-4 biorep3 techrep2 organoid

value: Primary keratinocytes

value: Biological replicate 3


title: crp A4 F20 I1 R1


title: Affected, bird # A76B


title: Affected, bird # A72


title: GBCN3


title: shDDX50-4 biorep3 techrep1 organoid


title: GBCN2


title: shDDX50-3 biorep2 techrep2 organoid

value: Biological replicate 2

value: shRNA against DDX50, #3


title: Affected, bird # A16


title: Affected, bird # A4


title: GBCN1


title: shDDX50-3 biorep2 techrep1 organoid


title: Non Affected, bird # NA70

value: Non Affected


title: shDDX50-3 biorep1 techrep2 organoid

value: Biological replicate 1


title: crp A2 F19 I1 R2


title: Non Affected, bird # NA69


title: crp A2 F19 I1 R1


title: shDDX50-3 biorep1 techrep1 organoid


title: crp A1 F86 I4 R2

value: crp KO, endpoint


title: OGD-R-1

city: Nanjing

first: Zhongyuan

address: Changle Road No.68

institute: Nanjing First Hospital

data_processing:
Firstly, we obtained raw data through high-throughput sequencing (Model: PE150, Sequencing data volume: 12G/15G) supporting by Ribobio Company (Guangzhou, China). Then, we filtered Raw Data, remove adapter sequences and low-quality reads to obtain high-quality data (Clean Data). Next, by aligning with the ribosomal database, rRNA sequences were removed to obtain effective reads. The effective reads were mapped to the reference genome, and the alignment results were used for the identification of circular RNAs in the next step. Two circRNA analysis toolsets, CIRI2 and CIRCexplorer2 were utilized to comprehensively identify RNA-seq reads, resulting in highly reliable circRNAs.
We identified the genomic origin regions of RNA sequences flanking the circRNA junction site. Subsequently, we predicted the functional elements, including exons, introns, 5'UTR, 3'UTR, and intergenic regions, as well as the source genes in which the circRNAs were situated.
Sequence prediction. Firstly, we selected an optimal transcript. The screening criteria were as follows: (1) Priority was given to selecting a linear transcript that was consistent with the circular RNA splicing site; (2) Among transcripts with consistent splicing sites, priority was given to selecting the transcript with the longest total length of exon sequences; (3) If the total exon length was the same, priority was given to selecting the transcript with the longest coding region. Then, splicing was performed according to the following criteria: (1) If the position of the circular RNA splicing site was consistent with the corresponding linear transcript splicing site, the intron sequence between the two splicing points was normally spliced out, and the exon sequences were concatenated to form a circular RNA sequence; (2) If the circRNA splicing site was located in an intron, the nearest exon was extended to the splicing site position, and the intermediate intron was normally spliced out; (3) If the splicing site exceeded the transcript boundary, the boundary exon was extended to the splicing site position, and the intermediate intron was normally spliced out.
Expression value calculation. Based on the predicted junction reads of circRNAs, we calculated the expression values of circRNAs. The junction reads were corrected using RPM normalization, and the normalized data were used for comparison between samples or groups. The calculation formula for RPM value was as follows:
circRNAs differential expression analysis was performed by DEGseq software between two different groups or samples.We identified circRNAs with a |log2FoldChange| > 1 and P value < 0.05 in a comparison as significant circRNAs
Assembly: mm10

source_name: microglia

extract_protocol:
Total RNA was extracted from the exosomes of M0 microglia(Ctrl) and M1 microglia(OGD-R) using miRNeasy Mini Kit, and the RNA molecules in a size range of 18-30 nt were enriched by polyacrylamide gel electrophoresis.
After a quality inspection of total RNA, rRNA was removed using a Ribo zero rRNA removal kit (Ribobio, Guangzhou, China). Subsequently, RNase R was used to digest linear RNA, and the reverse transcription was performed to synthesize dsDNA. Next, the end repair was carried out, followed by the ligation of sequencing adapters. Finally, after the PCR amplification and library quality inspection, the library was constructed..
circular RNA-Seq

value: microglia

value: OGD-R


title: Non Affected, bird # NA68


title: shDDX50-1 biorep2 techrep2 organoid

value: Skin organoid

value: shRNA against DDX50, #1


title: Ctrl-2

value: control


title: crp A2 F85 I1 R2

value: bacterial culture


title: crp A1 F86 I4 R1


title: shDDX50-1 biorep2 techrep1 organoid


title: crp A0 F0 I1 R2

value: crp KO, unevolved


title: T5

city: Boston

first: Mark

middle: W

last: Feinberg

address: 77 Avenue Louis Pasteur

department: Medicine

institute: Brigham and Women's Hospital

data_processing:
Sequence reads were trimmed to remove adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36
The trimmed reads were mapped to the Mus musculus GRCm38 reference genome using the STAR aligner v.2.5.2b
Unique gene hit counts were calculated by Subread package v.1.5.2
The hit counts were summarized and reported using the gene_id feature in the annotation file
Assembly: mm10
Supplementary files format and content: raw_counts.csv

source_name: Macrophages

extract_protocol:
Samples were lysed in Trizol LS reagent and total RNA was extracted using Direct-zolTM RNA Microprep kit (Zymo Research)
RNA liberaries were prepared using Illumina's ultra low input RNA

treatment_protocol: Mice were injected intravenously with 2 nmole of NS or miR-369-3p mimic twice weekly for four weeks

value: Macrophages

tag: strain background

value: Ldlr-/-


title: crp A0 F0 I1 R1


title: shDDX50-1 biorep1 techrep2 organoid


title: Non Affected, bird # NA66

value: pectoralis muscle

value: primary skeletal myoblasts


title: Ctrl-1


title: Non Affected, bird # NA65


title: crp A2 F85 I1 R1


title: shDDX50-1 biorep1 techrep1 organoid

value: Primary keratinocytes


title: Non Affected, bird # NA64


title: OGD-R-2


title: T3


title: T4


title: BS-seq replicate1 of ta2 LR stage 1

description: Library name: ZZSZ080

library_source: genomic

molecule: genomic DNA

value: root

value: stage 1 of LR

value: root initials


title: T2


title: Non Affected, bird # NA62

value: Non Affected


title: Non Affected, bird # NA67


title: BS-seq replicate2 of ta2 CR stage 1

description: Library name: ZZSZ079

value: stage 1 of CR


title: shControl biorep4 techrep1 organoid

value: Biological replicate 4

value: Control shRNA


title: shControl biorep3 techrep2 organoid

value: Skin organoid

value: Biological replicate 3


title: shControl biorep3 techrep1 organoid


title: Non Affected, bird # NA61


title: C5

value: NS control


title: BS-seq replicate1 of ta2 CR stage 1

description: Library name: ZZSZ078


title: T1


title: Mex-Gal4-GFPdsRNA-D

city: Reading

first: Justin

last: DiAngelo

state: PA

address: 2100 Stoudt Rd

institute: Penn State Berks

description: Library name: Sample 6

data_processing:
Base calling using Illumina HiSeq software
Sequence reads were trimmed using Trimmomatic v.0.36
Trimmed reads were mapped to the Drosophila melanogaster BDGP6 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b (BAM files were generated as a result)
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2
Assembly: BDGP6 Drosophila melanogaster reference genome
Supplementary files format and content: Unique reads that fell within exon regions of genes for each sample

organism: Drosophila melanogaster

source_name: control fat bodies

extract_protocol:
Total RNA was extracted using VWR Life Science RiboZol RNA Extraction Reagent
mRNA was enriched using polyA selection, mRNA was fragmented and first and second strand cDNA synthesis was performed, adaptors were ligated and samples PCR enriched before Illumina sequencing.

value: control fat bodies


title: Mex-Gal4-GFPdsRNA-B

description: Library name: Sample 5


title: C4


title: shControl biorep2 techrep2 organoid

value: Biological replicate 2


title: BS-seq replicate2 of OxDRM2 LR stage 1

description: Library name: ZZSZ065


title: Mex-Gal4-GFPdsRNA-A

description: Library name: Sample 4


title: BS-seq replicate2 of OxDRM2 CR stage 1

description: Library name: ZZSZ063


title: shControl biorep2 techrep1 organoid


title: BS-seq replicate1 of OxDRM2 LR stage 1

description: Library name: ZZSZ064


title: BS-seq replicate2 of ta2 LR stage 1

description: Library name: ZZSZ081


title: shControl biorep4 techrep2 organoid


title: Mex-Gal4-9G8RNAi-D

description: Library name: Sample 3

source_name: intestines

value: intestines


title: BS-seq replicate1 of OxDRM2 CR stage 1

description: Library name: ZZSZ062


title: shControl biorep1 techrep2 organoid

value: Biological replicate 1


title: shControl biorep1 techrep1 organoid


title: Mex-Gal4-9G8RNAi-B

description: Library name: Sample 2


title: Mex-Gal4-9G8RNAi-A

description: Library name: Sample 1


title: NonTRM

city: Hamburg

first: Nicola

last: Wanner

address: Martinistr

country: Germany

institute: UKE Hamburg-Eppendorf

data_processing:
RNA sequencing was performed by the core facility of the Leibniz Institute of Virology, Hamburg. Quality control was done with FastQC. Raw reads were trimmed using TrimGalore!  and mapped with RNA Star to mm9 using Galaxy Freiburg. Read counts were extracted with htseq-count, rlog transformation was done with DESeq2.
Assembly: mm9
Supplementary files format and content: raw gene counts, csv

source_name: non TRM CD1dtet-/CD69-

extract_protocol:
Mice were injected i.p. with αP2X7 HLE Nb-dimer 1 hour and  CD45-PerCP i.v. 3 min before sacrifice, respectively. Kidneys were isolated, minced and leucocytes collected using a Percoll gradient. T cell subpopulations (vascular CD4+, parenchymal NKT CD1dtet+/CD69+, TRM CD1dtet-/CD4+/CD69+ and non TRM CD1dtet-/CD69-) were sorted by FACS and total RNA was extracted using the Qiagen RNeasy Micro Kit.
RNA libraries for RNA-seq were prepared using Clonetech RNA with Nextera following manufacturer's protocols.

value: non TRM CD1dtet-/CD69-

value: WT


title: shDDX50-4 cervical 2

source_name: Primary cervical epithelial cells

growth_protocol: Primary cervical epithelial cells (ATCC, PCS-480-011) were cultured in cervical epithelial cell basal medium (ATCC, PCS-480-032) supplied with cervical epithelial growth kit (ATCC, PCS-480-042).

treatment_protocol: Human cervical primary cells were induced to differentiate by the addition of 1.2 mM calcium for 3 days at full confluence in the cervical media. Organotypic regeneration of human epidermal and cervical tissues were performed as previously described47 using KGM media. Day 7 epidermal and cervical tissues were collected.

value: Primary cervical epithelial cells

value: shRNA against DDX50, #4


title: TRM

source_name: TRM CD1dtet-/CD4+/CD69+

value: TRM CD1dtet-/CD4+/CD69+


title: cr_38_3

first: Ruohe

last: Yin

address: 800 Dongchuan RD. Minhang District

institute: Shanghai Jiao Tong University

data_processing:
fastp (version0.23.1) -g-q5-u50-n15-l150 --overlap_diff_limit1--overlap_diff_percent_limit10
Comparative analysis: hisat2 (version 2.0.5)
Quantitative analysis: featureCounts (version 1.5.0-p3)
GEAS analysis: gsea (version 3.0)
Difference analysis: DESeq2 (version 1.20.0); edgeR (version 3.22.5)
Assembly: https://solgenomics.net/ftp/tomato_genome/Heinz1706/assembly/build_4.00/S_lycopersicum_chromosomes.4.00.fa.gz; https://solgenomics.net/ftp/tomato_genome/Heinz1706/annotation/ITAG4.1_release/ITAG4.1_gene_models.gff
Supplementary files format and content: tab-delimited text files include readcount values (gene_count) and  FPKM values (gene_fpkm) for each sample.

organism: Solanum lycopersicum

source_name: Fruit pericarp

extract_protocol:
Fruit pericarps were flash frozen in liquid nitrogen, and RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard illumina protocols.

value: Fruit pericarp

value: mutant (cr)

tag: Stage

value: breaker (38) stage


title: NKT

source_name: parenchymal NKT CD1dtet+/CD69+

value: parenchymal NKT CD1dtet+/CD69+


title: cr_38_2


title: shControl cervical 2

value: Control shRNA


title: Sample56_Passage5, luciferase siRNA, 20X

city: San Francisco

first: Emily

last: Wong

address: 1800 Owens St

institute: VIR BIOTECHNOLOGY, INC.

data_processing:
Paired-end reads were trimmed to 2X150 upon inspection with FastQC to retain segments of high quality (>Q30). Illumina adapters were clipped using Trimmomatic. Read alignment to SARS-CoV-2 Wuhan-Hu-1 reference (NCBI: NC_045512.2) was performed with Burrows-Wheeler Aligner (BWA). Variants were called with LoFreq upon indel realignment and base quality recalibration, using a frequency threshold of 1%. Primers were excluded from variant calling. A consensus sequence was generated, mapped back to reference sequence coordinates and used to align reads a second time. The incorporation of variants from the first mapping iteration into a consensus sequence facilitates read alignment in case of mismatches with the reference. Variants were called again against the reference sequence from reads mapped to the consensus sequence. A third iteration of consensus generation read alignment and variant calling was performed. The variant call set from this last iteration was retained as final. Nucleotide variants were annotated with SnpEff to generate amino acid variants. Extensive QCs were performed at read, alignment and variant level using FastQC, samtools, picard, mosdepth, bcftools and MultiQC. An end-to-end workflow was automated using NextFlow. All programs are available through the Bioconda Initiative (bioconda.github.io).
Assembly: SARS-CoV-2 Wuhan-Hu-1 reference (NCBI: NC_045512.2)
Supplementary files format and content: The processed data contains the variant calls from the bioinformatics pipeline, together with variant annotation.

organism: Severe acute respiratory syndrome coronavirus 2

source_name: Vero E6

growth_protocol: Vero E6 cells cultured in DMEM supplemented with 10% FBS (VWR) and 1x Penicillin/Streptomycin (Thermo Fisher Scientific)

extract_protocol:
300 μL of cell supernatant was added to 900 μL of Trizol and stored at -80°C for further analysis. Trizol collected samples were subjected to RNA isolation using PureLink RNA Mini Kit with the incorporation of on-column PureLink DNase Treatment. Reverse transcription reactions were performed with 6 μL of purified RNA and random hexamer primers using the NEB ProtoScript II First Strand cDNA Synthesis kit.
The resulting cDNA was used as a template for PCR amplification of the siRNA binding sites, two primer pairs per site, using KapaBiosystems polymerase (KAPA HiFi HotStart ReadyMix) with primers, 5’-acgctgcttctggtaatc-3’ plus 5’-agaaacccttagacacagc-3’, and 5’-ctagataaacgcactacgtg-3’ and 5’-cctgagcaaagaagaagtg-3’ for the COV-siRNA1 binding site, and  5’-agatgccttcaaactcaac-3’ plus 5’-ttctactctgagttgttgc-3’, and 5’-ttggtggcaaaccttgtatc-3’ plus 5’-tgtgtaactggacacattg-3’ for the COV-siRNA2 binding site. Each PCR with a primer pair was carried out independently, then PCR products from each treatment were pooled for purification and subsequent library preparation. Amplification conditions included an initial 3 min at 95°C, followed by 24 cycles with 20 sec at 98°C, 15 sec at 60°C and 72°C for 15 sec, with a final 1 min at 72°C. Pooled PCR products were purified using AMPure XP beads. The size of the amplicon was confirmed by analyzing 2 μL of PCR products using the Agilent D1000 ScreenTape System. Products were quantified by analyzing 1 μL with the Quant-iT dsDNA High-Sensitivity Assay Kit. Fifty ng of purified PCR product was used as input for library construction using the NEBNext Ultra II DNA Library Prep kit. NEBNext Multiplex Oligos for Illumina Dual Index Primer Set 1 was used for library construction, with a total of 4 PCR cycles. Library size was determined using the Agilent D1000 ScreenTape System and quantified with the Quant-iT dsDNA High-Sensitivity Assay Kit.
Equal amounts of each library were pooled together for multiplexing and ‘Protocol A: Standard Normalization Method’ of the Illumina library preparation guide was used to prepare 8 pM final multiplexed libraries with 1% PhiX spike-in for sequencing. The MiSeq Reagent Kit v3 (600-cycle) was used for sequencing the libraries on the Illumina MiSeq platform, with 150 cycles for Read 1, 150 cycles for Read 2, 8 cycles for Index 1, and 8 cycles for Index 2. Illumina sequencing for COV-siRNA2 resistance studies was conducted by Genewiz/Azenta using an equivalent protocol.

treatment_protocol: 1.2 x 105 Vero E6 cells per well in a 24-well plate were reverse transfected with 5x, 10x or 20x EC50 of COV-siRNA1 (330 pM, 660 pM or 1320 pM, respectively) or of an equimolar combination of COV-siRNA1 and COV-siRNA2 at the same combined total concentrations. As a non-targeting control, cells were reverse transfected with 1320 pM of a control siRNA targeting the luciferase gene. All transfections used RNAiMax (Thermo Fisher Scientific) according to the manufacturer’s instructions. Six hours post reverse transfection, cells were incubated with SARS-CoV-2 (USA-WA1/2020, passage 2) at an MOI of 0.01 in infection medium (DMEM, 10% FBS) for 1 h at 37°C. After viral adsorption, cells were washed with DMEM and overlaid with infection media. For each condition, three independent wells were transfected and infected, and the supernatants were pooled together at the time of harvest. Infected cells were monitored visually for cytopathic effect (CPE) daily. When the cells in the luciferase-targeting control wells exhibited > 50% CPE, the culture supernatants were harvested, diluted 1:10 and added to fresh Vero E6 cells in 24-well plates that had been reverse-transfected with the equivalent amounts of siRNA(s) as used for the initial passage. Selection continued for a total of 5 passages. At each passage, supernatant was aliquoted and frozen at -80°C for further analyses. The same protocol was followed for resistance selection studies with COV-siRNA2.

value: Vero E6

value: kidney epithelialcellsof the African green monkey


title: shDDX50-13 cervical 2

value: shRNA against DDX50, #1,3


title: C2

value: Macrophages

value: Ldlr-/-

value: NS control


title: Sample54_Passage5, COV-siRNA2, 20X


title: Sample55_Passage5, COV-siRNA2, 5X


title: CD45Tvasc

source_name: vascular CD4+

value: vascular CD4+


title: C3


title: cr_38_1


title: shDDX50-4 cervical 1

value: Biological replicate 1


title: shDDX50-13 cervical 1


title: NOK_RNA_NT_8h_4_S44

city: LYON

first: Samrat

last: Das

address: 25 avenue Tony Garnier

country: France

institute: International Agency for Research on Cancer (IARC)

data_processing:
Read trimming : trimgalore=v0.6.2; Alignment : Star=2.7.3a; htseq=0.12.4
Assembly: hg38
Supplementary files format and content: TSV

source_name: hTERT Normal oral keratinocytes cells

extract_protocol:
After exposure, the media containing the test substances were removed from the flasks and the cellular RNA was extracted using standard methods (TRIzol™ Reagent, Cat. No. 15596026, Invitrogen). Estimation of yield was done by Qubit analysis (Qubit 3.0 Fluorometer, Life Technologies, Invitrogen™, Thermo Scientific Fisher) . RNA integrity was analysed on High Sensitivity RNA ScreenTape (Cat. No. 5067- 5579, Agilent), using the 4200 TapeStation automated electrophoresis instrument (Agilent). All samples exhibited RNA Integrity Number (RIN) above 8.4. 500 ng RNA per sample was used to prepare libraries (QuantSeq 3’ mRNA-Seq Library Prep Kit for Illumina (FWD)), Cat. No. 015, Lexogen).
QuantSeq 3‘ mRNA-Seq Library Prep Kit for Illumina (FWD)) (Lexogen)

value: hTERT Normal oral keratinocytes cells

value: Untreated (8h), REP4


title: cr_35_2

value: mature green (35) stage


title: C1


title: shControl cervical 1

value: Primary cervical epithelial cells


title: cr_35_3

value: Fruit pericarp


title: Sample51_Passage4, COV-siRNA2, 5X


title: Sample53_Passage5, COV-siRNA2, 10X


title: Sample50_Passage4, COV-siRNA2, 20X


title: Sample52_Passage4, luciferase siRNA, 20X


title: cr_35_1

value: mutant (cr)


title: NOK_RNA_NT_8h_3_S43

value: Untreated (8h), REP3


title: Exp115 DDX50 H gluc KC 312

source_name: Primary keratinocytes

growth_protocol: Primary human keratinocytes were isolated from fresh surgically discarded newborn foreskin, and progenitor cells cultured in complete Keratinocyte-SFM (Life Technologies, #17005-142) and Medium 154 (Life Technologies #M-154-500). Cells were induced to differentiate by the addition of 1.2 mM calcium for 3 days at full confluence.

value: Primary keratinocytes

value: UV cross-linked at 253 nm on plates.


title: Sample49_Passage4, COV-siRNA2, 10X

value: Vero E6


title: A_38_3

value: wild-type (A)

value: breaker (38) stage


title: NOK_RNA_SASLT_8h_3_S41

value: SA+ SLT, Sodium arsenite +Smokeless tobacco (8h), REP3


title: Exp115 DDX50 H gluc KC 212


title: A_38_2


title: Sample48_Passage3, luciferase siRNA, 20X

value: kidney epithelialcellsof the African green monkey


title: NOK_RNA_SLT_8h_4_S40

value: SLT, Smokeless tobacco (8h), REP4


title: Exp115 DDX50 L gluc KC 312


title: A_38_1


title: Sample47_Passage3, COV-siRNA2, 5X


title: Exp115 DDX50 H gluc KC 112


title: NOK_RNA_SLT_8h_3_S39

value: SLT, Smokeless tobacco (8h), REP3


title: Sample46_Passage3, COV-siRNA2, 20X


title: A_35_3


title: NOK_RNA_SASLT_8h_4_S42

value: SA+ SLT, Sodium arsenite +Smokeless tobacco (8h), REP4


title: Exp115 DDX50 L gluc KC 112


title: A_35_1


title: A_35_2


title: NOK_RNA_SASLT_4h_4_S36

value: hTERT Normal oral keratinocytes cells

value: SA+ SLT, Sodium arsenite +Smokeless tobacco (4h), REP4


title: Exp115 DDX50 L gluc KC 212


title: NOK_RNA_SA_8h_3_S37

value: SA, Sodium arsenite (8h), REP3


title: Sample44_Passage2, luciferase siRNA, 20X


title: wt A3 F70 I1 R2

organism: Escherichia coli BW25113

source_name: bacterial culture

value: bacterial culture

value: wt KO, endpoint


title: Sample45_Passage3, COV-siRNA2, 10X


title: Sample42_Passage2, COV-siRNA2, 20X


title: Sample43_Passage2, COV-siRNA2, 5X


title: Exp115 DDX50 Prog KC 212


title: NOK_RNA_SLT_4h_4_S34

value: SLT, Smokeless tobacco (4h), REP4


title: Exp115 DDX50 Prog KC 112


title: Sample41_Passage2, COV-siRNA2, 10X


title: NOK_RNA_SA_8h_4_S38

value: SA, Sodium arsenite (8h), REP4


title: wt A0 F0 I1 R2

value: wt KO, unevolved


title: Exp119 DDX50 H gluc KC 309

value: Primary keratinocytes

value: UV cross-linked at 253 nm on plates.


title: wt A3 F70 I1 R1


title: wt A0 F0 I1 R1


title: Sample40_Passage1, luciferase siRNA, 20X

value: Vero E6


title: Exp119 DDX50 H gluc KC 209


title: NOK_RNA_SA_4h_3_S31

value: SA, Sodium arsenite (4h), REP3


title: NOK_RNA_SLT_4h_3_S33

value: SLT, Smokeless tobacco (4h), REP3


title: Sample39_Passage1, COV-siRNA2, 5X

value: kidney epithelialcellsof the African green monkey


title: mlrA A15 F65 I1 R2

value: mlrA KO, endpoint


title: NOK_RNA_SASLT_4h_3_S35

value: SA+ SLT, Sodium arsenite +Smokeless tobacco (4h), REP3


title: Exp115 DDX50 Prog KC 312


title: Sample38_Passage1, COV-siRNA2, 20X


title: Exp119 DDX50 H gluc KC 109


title: Exp119 DDX50 L gluc KC 309


title: mlrA A0 F0 I1 R2

value: mlrA KO, unevolved


title: NOK_RNA_SASLT_2h_4_S30

value: hTERT Normal oral keratinocytes cells

value: SA+ SLT, Sodium arsenite +Smokeless tobacco (2h), REP4


title: Exp119 DDX50 L gluc KC 209


title: NOK_RNA_SASLT_2h_3_S29

value: SA+ SLT, Sodium arsenite +Smokeless tobacco (2h), REP3


title: mlrA A15 F65 I1 R1

value: bacterial culture


title: Sample36_Passage0, Null


title: Sample37_Passage1, COV-siRNA2, 10X


title: mlrA A0 F0 I1 R1


title: NOK_RNA_SLT_2h_4_S28

value: SLT, Smokeless tobacco (2h), REP4


title: Exp119 DDX50 L gluc KC 109


title: lrp A23 F97 I4 R2

value: lrp KO, endpoint


title: NOK_RNA_SA_4h_4_S32

value: SA, Sodium arsenite (4h), REP4


title: Exp119 DDX50 Prog KC 309


title: Sample35_Passage5, COV-siRNA1+2, 5X


title: NOK_RNA_SLT_2h_3_S27

value: SLT, Smokeless tobacco (2h), REP3


title: lrp A0 F0 I1 R2

value: lrp KO, unevolved


title: NOK_RNA_SA_2h_4_S26

value: SA, Sodium arsenite (2h), REP4


title: Exp119 DDX50 Prog KC 209

value: Primary keratinocytes

value: UV cross-linked at 253 nm on plates.


title: Sample34_Passage5, COV-siRNA1+2, 10X

value: Vero E6


title: Sample33_Passage5, COV-siRNA1+2, 20X

value: kidney epithelialcellsof the African green monkey


title: lrp A0 F0 I1 R1


title: Exp119 DDX50 Prog KC 109


title: lon A17 F62 I1 R2

value: lon KO, endpoint


title: NOK_RNA_NA_0h_4_S24

value: Untreated (0h), REP4


title: NOK_RNA_SA_2h_3_S25

value: SA, Sodium arsenite (2h), REP3


title: Sample31_Passage5, COV-siRNA1, 5X


title: NOK_RNA_NA_0h_3_S23

value: hTERT Normal oral keratinocytes cells

value: Untreated (0h), REP3


title: PCIF1 KO polysome fraction 5 rep2

city: New York

first: Ben

middle: R

last: Hawley

state: New York

address: 1300 York Avenue

institute: Weill Cornell Medicine

data_processing:
Reads with the 5' UMI and linker sequence were identified and UMI placed in FASTQ headers. Remaining 5' and 3' adaptor sequences trimmed using cutadapt. Reads aligned to GRCh38 using STAR and demultiplexed using UMI tools. 5' end of demultiplexed aligned reads were assigned as TSS.
For SLAM-seq reads, C to T transitions in the sense direction were identifed using samtools mpileup and converted to a transition rate using custom scripts. Half-life per TSS isoform calculated by first-order decay kinetics.
For polysome reads, mean ribosome load (MRL) for each TSS isoform was calculated.
Genome_build: GRCh38
Supplementary_files_format_and_content: Half-lives and Rsq values of lm fit for each TSS isoform
Supplementary_files_format_and_content: Mean ribosome load values for each TSS isoform
Supplementary_files_format_and_content: HEK293T_MRL.txt: Translational efficiency
Supplementary_files_format_and_content: MRL_change_PCIF1KO.txt: differential analysis
Supplementary_files_format_and_content: TSS_halflives.txt: Half-lives
Supplementary_files_format_and_content: WT_KO_halflife.txt: differential analysis

growth_protocol: HEK293T cells were cultured in DMEM supplemented with 10% FBS.

extract_protocol:
Polysome samples were prepared by lysis in polysome lysis buffer. Following fractionation, RNA was extracted from sucrose by the addition of 50 mM EDTA and an equal volume TRIZOL LS, and homogenised for 20 minutes at 50°C with frequent mixing. For 5'UTR-SLAM-seq, 4SU-containing RNAs were directly extracted by a standard TRIZOL protocol.
ReCappable-seq

value: PCIF1 knockout


title: Sample30_Passage5, COV-siRNA1, 10X


title: PCIF1 KO polysome fraction 4 rep2


title: Sample29_Passage5, COV-siRNA1, 20X


title: NOK_RNA_NT_8h_2_S22

value: Untreated (8h), REP2


title: NOK_RNA_NT_8h_1_S21

value: Untreated (8h), REP1


title: lon A0 F0 I1 R2

value: bacterial culture

value: lon KO, unevolved


title: Sample28_Passage4, COV-siRNA1+2, 5X


title: lon A0 F0 I1 R1


title: lrp A23 F97 I4 R1

value: lrp KO, endpoint


title: NOK_RNA_SASLT_8h_2_S20

value: SA+ SLT, Sodium arsenite +Smokeless tobacco (8h), REP2


title: PCIF1 KO polysome fraction 1 rep2


title: Sample27_Passage4, COV-siRNA1+2, 10X


title: basR A7 F63 I1 R2

value: basR KO, endpoint


title: Sample32_Passage5, luciferase siRNA, 20X


title: NOK_RNA_SASLT_8h_1_S19

value: SA+ SLT, Sodium arsenite +Smokeless tobacco (8h), REP1


title: Sample26_Passage4, COV-siRNA1+2, 20X


title: PCIF1 KO input rep2


title: NOK_RNA_SLT_8h_2_S18

value: SLT, Smokeless tobacco (8h), REP2


title: lon A17 F62 I1 R1


title: WT polysome fraction 5 rep2

value: wild-type


title: PCIF1 KO polysome fraction 3 rep2


title: basR A7 F63 I1 R1


title: basR A0 F0 I1 R2

value: basR KO, unevolved


title: Sample24_Passage4, COV-siRNA1, 5X

value: Vero E6

value: kidney epithelialcellsof the African green monkey


title: basR A0 F0 I1 R1


title: WT polysome fraction 4 rep2


title: NOK_RNA_SLT_8h_1_S17

value: SLT, Smokeless tobacco (8h), REP1


title: WT polysome fraction 3 rep2


title: Sample25_Passage4, luciferase siRNA, 20X


title: PCIF1 KO polysome fraction 2 rep2


title: NOK_RNA_SA_8h_1_S16

value: hTERT Normal oral keratinocytes cells

value: SA, Sodium arsenite (8h), REP2


title: Sample23_Passage4, COV-siRNA1, 10X


title: NOK_RNA_SA_8h_1_S15

value: SA, Sodium arsenite (8h), REP1


title: Zfp622_KO_Mor_3

first: Juan

last: Meng

address: Yueyang Road Street

institute: Center for Excellence in Brain Science and Intelligence Technology, Chineses Academy of Sciences

description: Library name: Mor_Zfp622_KO_3

data_processing:
Qualified reads were mapped to the reference genome (GRCm38.99) by Hisat2 (v2.2.1) and the read counts for each transcript were quantified by featureCounts (v2.0.1).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: embryo

extract_protocol:
For RNA sequencing, 10 embryos were used per reaction. Wild-type (WT), Ttf1 KO and Zfp622 KO embryos were collected at the L2C and morula stages, and four replicates were performed for each stage. The embryos were lysed in 3.45 μL lysis buffer (1 μl Oligo-dT30VN (10 μM), 1 μl dNTPs (10 mM), 0.05 μl RNase inhibitor (40 U/μL), 0.2 μL NP40 (10%) and 1.2 μL nuclease-free water) for 3 min at 72 ℃.
The released RNA was reverse transcribed in RT mix (0.5 μL HiScript III reverse transcriptase (200 U/μL), 0.25 μl RNase inhibitor (40 U/μL), 2 μL 5× First-strand buffer, 2 μL Betaine (5M), 1 μL template switching oligos (TSOs, 10 μM), 0.5 μL dithiothreitol (DTT, 100 mM) and 0.3 μL MgCl2 (300 mM)). cDNA was amplified with the ISPCR primers (10 μM) by KAPA HiFi HotStart ReadyMix and purified using NovoNGS DNA Clean Beads. RNA-seq libraries were prepared using TruePrep DNA Library Prep Kit V2 for Illumina and TruePrep Index Kit V2 for Illumina. The libraries were pair-end sequenced on Illumina HiSeq X Ten sequencing platform with paired-ended 150-bp reads.

value: embryo

value: Zfp628 knock out


title: Sample22_Passage4, COV-siRNA1, 20X


title: NOK_RNA_SASLT_4h_2_S14

value: SA+ SLT, Sodium arsenite +Smokeless tobacco (4h), REP2


title: Sample21_Passage3, COV-siRNA1+2, 5X


title: WT polysome fraction 1 rep2


title: Zfp622_KO_Mor_2

description: Library name: Mor_Zfp622_KO_2

value: Zfp627 knock out


title: NOK_RNA_SASLT_4h_1_S13

value: SA+ SLT, Sodium arsenite +Smokeless tobacco (4h), REP1


title: WT input rep2


title: PCIF1 KO polysome fraction 5 rep1

value: PCIF1 knockout


title: NOK_RNA_SLT_4h_2_S12

value: SLT, Smokeless tobacco (4h), REP2


title: Sample20_Passage3, COV-siRNA1+2, 10X


title: Zfp622_KO_Mor_1

description: Library name: Mor_Zfp622_KO_1

value: Zfp626 knock out


title: Sample19_Passage3, COV-siRNA1+2, 20X


title: Zfp622_KO_L2C_4

description: Library name: L2C_Zfp622_KO_4

value: Zfp625 knock out


title: Zfp622_KO_Mor_4

description: Library name: Mor_Zfp622_KO_4

value: Zfp629 knock out


title: WT polysome fraction 2 rep2

value: wild-type


title: PCIF1 KO polysome fraction 4 rep1


title: NOK_RNA_SLT_4h_1_S11

value: SLT, Smokeless tobacco (4h), REP1


title: PCIF1 KO polysome fraction 3 rep1


title: Zfp622_KO_L2C_3

description: Library name: L2C_Zfp622_KO_3

value: Zfp624 knock out


title: Zfp622_KO_L2C_2

description: Library name: L2C_Zfp622_KO_2

value: Zfp623 knock out


title: PCIF1 KO polysome fraction 2 rep1


title: NOK_RNA_SA_4h_1_S9

value: hTERT Normal oral keratinocytes cells

value: SA, Sodium arsenite (4h), REP1


title: Sample17_Passage3, COV-siRNA1, 5X

value: Vero E6

value: kidney epithelialcellsof the African green monkey


title: Sample16_Passage3, COV-siRNA1, 10X


title: NOK_RNA_SASLT_2h_2_S8

value: SA+ SLT, Sodium arsenite +Smokeless tobacco (2h), REP2


title: NOK_RNA_SA_4h_2_S10

value: SA, Sodium arsenite (4h), REP2


title: Sample15_Passage3, COV-siRNA1, 20X


title: NOK_RNA_SASLT_2h_1_S7

value: SA+ SLT, Sodium arsenite +Smokeless tobacco (2h), REP1


title: PCIF1 KO input rep1


title: Ttf1_KO_Mor_3

description: Library name: Mor_Ttf1_KO_3

value: embryo

value: Ttf1 knock out


title: PCIF1 KO polysome fraction 1 rep1

value: PCIF1 knockout


title: NOK_RNA_SLT_2h_2_S6

value: SLT, Smokeless tobacco (2h), REP2


title: Zfp622_KO_L2C_1

description: Library name: L2C_Zfp622_KO_1

value: Zfp622 knock out


title: Sample14_Passage2, COV-siRNA1+2, 5X


title: Sample18_Passage3, luciferase siRNA, 20X


title: WT polysome fraction 5 rep1


title: Ttf1_KO_Mor_2

description: Library name: Mor_Ttf1_KO_2


title: NOK_RNA_SLT_2h_1_S5

value: SLT, Smokeless tobacco (2h), REP1


title: Sample13_Passage2, COV-siRNA1+2, 10X


title: Sample12_Passage2, COV-siRNA1+2, 20X


title: WT polysome fraction 4 rep1

value: wild-type


title: WT polysome fraction 3 rep1


title: NOK_RNA_SA_2h_2_S4

value: SA, Sodium arsenite (2h), REP2


title: Ttf1_KO_Mor_1

description: Library name: Mor_Ttf1_KO_1


title: NOK_RNA_SA_2h_1_S3

value: SA, Sodium arsenite (2h), REP1


title: Sample11_Passage2, luciferase siRNA, 20X


title: Ttf1_KO_L2C_3

description: Library name: L2C_Ttf1_KO_3


title: NOK_RNA_NA_0h_2_S2

value: Untreated (0h), REP2


title: WT polysome fraction 1 rep1


title: Ttf1_KO_L2C_4

description: Library name: L2C_Ttf1_KO_4


title: WT polysome fraction 2 rep1


title: NOK_RNA_NA_0h_1_S1

value: hTERT Normal oral keratinocytes cells

value: Untreated (0h), REP1


title: Ttf1_KO_Mor_4

description: Library name: Mor_Ttf1_KO_4


title: Ttf1_KO_L2C_2

description: Library name: L2C_Ttf1_KO_2


title: Sample10_Passage2, COV-siRNA1, 5X

value: Vero E6


title: Sample9_Passage2, COV-siRNA1, 10X

value: kidney epithelialcellsof the African green monkey


title: Sample8_Passage2, COV-siRNA1, 20X


title: WT input rep1


title: PCIF1 KO 5' SLAM-seq 12 h rep2


title: Ttf1_KO_L2C_1

description: Library name: L2C_Ttf1_KO_1


title: NC_Mor_4

description: Library name: Mor_NC_4

value: WT


title: Sample7_Passage1, COV-siRNA1+2, 5X


title: gingival fibroblasts,  - Celastrol - TGFβ1_2

city: Saskatoon

first: Andrew

last: Leask

state: Saskatchewan

address: 105 wiggins road

department: Dentistry

country: Canada

institute: university of saskatchewan

data_processing:
Partek Flow v10.0.22
fastq files were aligned to hg38 using Star 2.7.3a and annotated with Ensembl Transcripts release 106
Features were excluded if maximum reads <= 8.0
Reads were normalized using Median ratio (DESeq2 only)
Fold changes and p-values were calculated using DESeq2.
Assembly: hg38
Supplementary files format and content: Excel file including fold change and statistical significance value for each gene, txt files reporting counts

source_name: Gingiva

growth_protocol: PCS-201-018 cells (>P8) was cultured in high glucose DMEM+10%FBS+1%anti-anti until 60% confluency and then starved overnight in low glucose DMEM+0.5%FBS+1% anti-anti till treatement

extract_protocol: The RNA was extracted using the TriZol extraction method.

treatment_protocol: Cells were pretreated with either DMSO or Celastrol (500nM) for 45 minutes followed by treatment with or without TGFβ1 (4 ng/ml) for an additional 6h

value: Gingiva

value: Fibroblasts

value: Primary cells

value: BSA+Citric Acid+DMSO


title: gingival fibroblasts,  - Celastrol - TGFβ1


title: PCIF1 KO 5' SLAM-seq 6 h rep2

value: PCIF1 knockout


title: gingival fibroblasts,  + Celastrol - TGFβ1_2

value: BSA+Citric Acid+Celastrol


title: NC_Mor_3

description: Library name: Mor_NC_3

value: embryo


title: PCIF1 KO 5' SLAM-seq 2 h rep2


title: Sample4_Passage1, luciferase siRNA, 20X


title: gingival fibroblasts,  + Celastrol - TGFβ1


title: NC_Mor_1

description: Library name: Mor_NC_1


title: PCIF1 KO 5' SLAM-seq 0 h rep2


title: gingival fibroblasts,  - Celastrol + TGFβ1_2

value: TGFB+DMSO


title: gingival fibroblasts,  - Celastrol + TGFβ1


title: WT 5' SLAM-seq 6 h rep2

value: wild-type


title: Sample2_Passage1, COV-siRNA1, 10X


title: NC_L2C_4

description: Library name: L2C_NC_4


title: WT 5' SLAM-seq 2 h rep2


title: Sample1_Passage1, COV-siRNA1, 20X


title: NC_L2C_2

description: Library name: L2C_NC_2


title: NC_L2C_3

description: Library name: L2C_NC_3


title: gingival fibroblasts,  + Celastrol + TGFβ1_2

value: TGFB+Celastrol


title: gingival fibroblasts,  + Celastrol + TGFβ1


title: WT 5' SLAM-seq 0 h rep2


title: Sample5_Passage1, COV-siRNA1+2, 20X


title: NC_Mor_2

description: Library name: Mor_NC_2


title: NC_L2C_1

description: Library name: L2C_NC_1


title: ATCC 8739, pulsed electric field, 70 kJ/kg, rep1

status: Public on Dec 03 2024

first: Astrid

last: Gedas

address: Ohnhorststrasse 18

department: Department of Chemistry

institute: Universität Hamburg

description: Library name: P7A

data_processing:
Quantified libraries were pooled and sequenced on an Illumina platform NovaSeq X Plus Series
Raw data (raw reads) in FASTQ format was first processed through fastp
The cleaned reads were aligned to reference genome of E. coli ATCC 8739 (GCA_016864475.1) using Bowtie2
To count the reads numbers mapped to each gene, FeatureCounts was used
Differential expression analysis was performed using the DESeq2 R package, and the p-values were adjusted using the Benjamini and Hochberg’s approach to control the false discovery rate.
Assembly: Reference genome: GCA_016864475.1
Supplementary files format and content: csv files include FPKM values for each samples

organism: Escherichia coli

source_name: bacterial cells

growth_protocol: E. coli ATCC 8739 culture in LB medium at 37°C for 16±1 h

extract_protocol:
RNA was harvested using Rneasy Mini Kit from Qiagen.
Firstly, ribosomal RNA was removed from total RNA, followed by ethanol precipitation. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. During the second strand cDNA synthesis, dUTPs were replaced with dTTPs in the reaction buffer. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.

value: bacterial cells

tag: strain

value: ATCC 8739

value: pulsed electric field, 70 kJ/kg, 6 kV/cm


title: Sample6_Passage1, COV-siRNA1+2, 10X


title: ATCC 8739, pulsed electric field, 70 kJ/kg, rep2

description: Library name: P7B

tag: treatment


title: WT 5' SLAM-seq 12 h rep2


title: ATCC 8739, pulsed electric field, 50 kJ/kg, rep2

description: Library name: P6B

tag: cell type

value: pulsed electric field, 50 kJ/kg, 6 kV/cm


title: ATCC 8739, high pressure, 400 MPa, rep3

description: Library name: H5C

value: high pressure processing, 400 MPa, 1 min


title: ATCC 8739, high pressure, 400 MPa, rep2

description: Library name: H5B


title: Sample3_Passage1, COV-siRNA1, 5X

value: Vero E6

value: kidney epithelialcellsof the African green monkey


title: ATCC 8739, pulsed electric field, 50 kJ/kg, rep3

description: Library name: P6C


title: ATCC 8739, pulsed electric field, 50 kJ/kg, rep1

description: Library name: P6A


title: ATCC 8739, high pressure, 300 MPa, rep2

description: Library name: H4B

value: high pressure processing, 300 MPa, 3 min


title: ATCC 8739, high pressure, 400 MPa, rep1

description: Library name: H5A


title: ATCC 8739, high pressure, 300 MPa, rep3

description: Library name: H4C


title: ATCC 8739, high pressure, 300 MPa, rep1

description: Library name: H4A


title: ATCC 8739, thermal 72°C, rep2

description: Library name: T3B

value: thermal treatment 72°C, 50 s


title: ATCC 8739, thermal, 72°C, rep1

description: Library name: T3A


title: ATCC 8739, thermal, 60°C, rep3

description: Library name: T2C

value: thermal treatment 60°C, 200 s


title: ATCC 8739, control, rep1

description: Library name: C1A

value: control


title: ATCC 8739, thermal 60°C, rep2

description: Library name: T2B


title: ATCC 8739, thermal, 60°C, rep1

description: Library name: T2A


title: ATCC 8739, control, rep2

description: Library name: C1B


title: ATCC 8739, pulsed electric field, 70 kJ/kg, rep3

description: Library name: P7C


title: Pool of 12-16 larvae after chronic stress

city: Irkutsk

first: Tuyana

last: Sidorova

address: 3, Ulan-Batorskaya

department: Siberian Branch of the Russian Academy of Sciences

country: Russia

institute: Limnological Institute

description: Library name: Sample 3

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v. 0.36.
The preprocessed reads were subjected to a de novo assembly procedure the Trinity v.2.13.2. software package
Read count extrraction and normalization were perfomed using the R package EdgeR v4.0.3.
Assembly: de novo assembly
Supplementary files format and content: tab-delimited text file includes normalized FPKM values for each sample

organism: Coregonus migratorius

source_name: whole larvae

extract_protocol:
Total RNA was isolated with TRIzol reagent (Ambion) from each individual sample (the whole larvae). RNA samples from the same group (12-16 individuals) have been combined into mixtures to obtain four RNA pools.
The library was examined using Qubit and real-time PCR for quantification and size distribution detection. Quantified libraries were pooled in equimolar amounts and sequenced on Illumina NovaSeq 6000 High Throughput Sequencer using a NovaSeq 6000 Reagent Kit v1.5 in 150 bp paired-end reads at Novogen company (China).

value: whole larvae

value: chronic stress


title: Pool of 12-16 larvae after acute stress

description: Library name: Sample 2

value: acute stress


title: Pool of 12-16 control larvae

description: Library name: Sample 1


description: Library name: Sample 3

organism: Coregonus peled


title: TCF21 V4

city: Cincinnati

first: Jeffery

middle: D

last: Molkentin

state: Ohio

address: 240 Albert Sabin Way MLC 7020

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Raw sequencing data in a form of FASTQ files were processed in the SciDAP data analysis platform (https://scidap.com/) using the "Trim Galore ChIP-Seq pipeline paired-end" pipeline. The minimum FDR (q-value) cutoff for peak detection was set to 0.001, while all other parameters were left at their default values.
Assembly: mm10
Supplementary files format and content: narrowPeak - MACS2 called peaks
Supplementary files format and content: bigWig - normalized genome coverage

source_name: Heart

growth_protocol: Cardiac fibroblasts were isolated from male and female Col1a1-TCF21 hearts as described above. Each sample prepared consisted of fibroblasts from 3 independent mice. To induce the expression of TCF21, cells were infected with an adenovirus encoding Cre recombinase in 2% BGS containing media overnight. Cells were then expanded for 5 additional days to generate 4 confluent 10 cm dishes per sample. Transforming growth factor b1 (10 ng/mL, 101-B1-010, R&D Systems) was added for the last 24 hours in 2% BGS to further induce fibroblast activation.

extract_protocol:
Cardiac fibroblasts were cross-linked for 10 minutes on ice in fixing solution (0.88% formaldehyde, 0.1 M sodium chloride (NaCl), 1 mM EDTA, 0.5 mM EGTA and 50 mM Hepes-KOH (pH 8.0)). The cross-linking reaction was quenched for 5 minutes at room temperature by adding glycine directly to the cell culture plates to achieve a final concentration of 0.125 M. The cells were washed twice with PBS, scraped and pelleted at 2000 g in a centrifuge at 4 °C. The supernatant was removed and cell pellets were frozen at -80 °C until use. All buffers used in the following procedures apart from the sonication buffer were supplemented with protease inhibitors (PIA32955; Thermo Fisher Scientific) and 0.1 mM sodium butyrate before use. To obtain nuclei, frozen cell pellets were incubated in cell lysis buffer 1 (50 mM Hepes, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40 and 0.25% Triton) for 10 minutes on ice. The lysed cells were Dounce homogenized using a piston A and then centrifuged at 2000 g for 5 minutes at 4 °C. After centrifugation, the pellet was incubated in cell lysis buffer 2 (200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA and 10 mM Tris pH7.2) at room temperature for 10 minutes to separate the cytoplasm from the nuclei. The samples were Dounce homogenized again using a piston A and then centrifuged at 2000 g for 5 minutes at 4°C to pellet the cell nuclei. The supernatant was removed, and the nuclei were washed and resuspended with cold sonication buffer (TE with 0.1% sodium dodecyl sulfate (SDS)). The samples were sonicated on a Covaris S2 Sonicator (Covaris Inc.) for 5 minutes with SDS (peak power: 105, 10% duty factor and 200 cycles/burst) until DNA fragments were in the 400-800 base-pair range (settings: duty cycle 10%, peak incident power 105 Watts, 200 cycles per burst). Triton, glycerol, NaCl and sodium deoxycholate were added to the chromatin samples to achieve final concentrations of 1%, 5%, 150 mM and 0.1%, respectively. Samples were centrifuged at 14,000 g for 10 minutes at 4 °C and the supernatant containing the chromatin was collected and transferred to a new tube. The chromatin was pre-cleared with 15 µl Protein-A Dynabeads (10001D, Thermo Fisher Scientific) for 45 minutes under rotation at 4 °C, after which the beads were removed. ChIP for TCF21 was performed using an IP-Star Compact automation system (Diagenode) with 3 µg of chromatin solution, 3 µg of antibody (HPA013189; Sigma-Aldrich) and 12 µl of Protein-A Dynabeads. The Dynabeads were sequentially washed with buffer 1 (RIPA 150 mM NaCl: 10 mM Tris-HCl, pH 8.0, 150 mM NaCl, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate and 1% Triton X-100), buffer 2 (RIPA 250 mM NaCl), buffer 3 (50 mM Tris-HCl, pH 8.0, 2 mM EDTA and 0.2% N-lauroylsarcosine sodium salt) and buffer 4 (Tris-EDTA (TE) and 0.2% Triton X-100) for 15 minutes each. The immunoprecipitated chromatin was then subjected to ChIPmentation on the beads as previously described15. Tagmented DNA was incubated with proteinase K in elution buffer (TE with 250 mM NaCl and 0.3% SDS) to disrupt the crosslinks, for 4 hours at 65 °C.
The DNA was purified using theQiagenMinEluteDNA kit. Library preparationand PCR amplificationoftheeluted DNA was prepared aspreviouslydescribed by Buenrostro, D. etal, 2013. Paired-end sequencing was obtained for pooled libraries using a NovaSeq 6000 instrument (Illumina, USA).

value: Heart

value: Mouse Primary cell

value: Cardiac Fibroblast


title: Pool of 12-16 larvae after acute stress

description: Library name: Sample 2


title: Pool of 12-16 control larvae

description: Library name: Sample 1


title: monocultured and co-cultured TE-9 cells

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

description: normalized log2 ratio (TE9co/TE9mo)

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: MSCs were seeded at a density of 3 × 105 cells per 100 mm dish and cultured for 3 hours in high-glucose DMEM (Wako) supplemented with 10% FBS and 1% Penicillin-Streptomycin-Amphotericin B suspension. Subsequently, ESCC cells were seeded at a density of 2 × 105 cells per dish and co-cultured with MSCs for 4 days. Monocultures of both cell types served as controls and were cultured under the same conditions.

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

value: monoculture

value: co-cultured


title: TCF21 V3


title: TCF21 V1


title: ATCC 8739, thermal, 72°C, rep3

description: Library name: T3C

value: bacterial cells

value: ATCC 8739


title: MPRA FIRE SM BV2 cDNA Rep3

city: Leuven

first: Gert

last: Hulselmans

address: Herestraat 49 PO Box 602

department: Center for Brain and Disease Research

country: Belgium

institute: VIB

data_processing:
Enhancer - barcode assignment files are processed with a custom script. Enhancers and barcodes are separated with cutadapt.
Raw cDNA and gDNA reads are first processed with a custom script to extract and count each barcode before associating them to the corresponding enhancer based on the enhancer - bc assignment list.
Enhancer activity from MPRA assay is estimated via a custom R script. Enhancers are first filtered based on the number of BCs identified in the sequencing reads. Thresholds of 4 BCs per enhancer are selected based on the complexity of the library and the sequencing saturation of the enhancer - BC assignment samples. For the remaining enhancers, BC counts are aggregated per enhancer and then a count per million (CPM) normalisation is applied. gDNA (input) and cDNA (output) samples are merged by keeping only enhancers remaining in both samples after filtering. Input normalisation is done by dividing CPM normalised cDNA counts by CPM normalised plasmid counts resulting in a FC value.
Assembly: mm10
Supplementary files format and content: FIRE saturation mutagenesis table has 2 columns: Region; LogFC

growth_protocol: BV2 cells were cultured with DMEM + 10% FBS + 0.5% penicillin/streptomycin in an incubator at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted from the cell with the innuPREP RNA Mini Kit 2.0 (Analytik Jena) , followed by mRNA isolation using the Dynabeads mRNA purification kit (Ambion). cDNA synthesis was performed with the GoScript RT kit and oligo dT primer (Promega). Genomic DNA was extracted with Blood and Tissue kit from Qiagen.
Plasmid libraries, extracted genomic DNA and cDNA were prepared for sequencing with two rounds of PCR. The first PCR targets the random barcode present within the transcript. The second PCR adds sequencing indexes to the PCR product.
DNA sequencing; targeted RNA-seq


title: MPRA FIRE SM BV2 gDNA Rep3


title: MPRA FIRE SM BV2 cDNA Rep2


title: MPRA FIRE SM BV2 gDNA Rep1


title: hNSC MEIS1/2 ChIP rep1

city: Neuherberg

first: Juliane

last: Winkelmann

address: Ingolstaedter Landstr. 1

department: Institute of Neurogenomics

institute: Helmholtz-Zentrum München

data_processing:
adapter trimming with cutadapt (v1.16), without quality-based trimming
Reads  mapped to GRCh37 (hg19) using bowtie2 (v2.3.0) and samtools (v1.2) at a cutoff of mapq >=30
PCR duplicate removal with Picard tools (v 2.15.0)
Peaks called by MACS2 in paired-end mode with a P-value cut-off of 0.01
IDR analysis (v.2.0.3) was used to determine reproducible peaks between the two replicates.
Assembly: hg19
Supplementary files format and content: bigwig files were generated by MACS2, treatment pileup (IP) and background (input)
Supplementary files format and content: narrowPeak files were generated with the MACS2 (p<0.01) and used as input for IDR analysis

source_name: hNSC

growth_protocol: Human Neural Stem Cells (hNSC) from Gibco™ (N7800-100) were cultured in StemPro® NSC SFM in dishes were coated with Geltrex

extract_protocol:
Cells were dissociated with Accutase and porcessed with the truChIP Chromatin Shearing Kit (Covaris). Chromatin of 30 mio cells was sonicated in a E220 Focused Ultrasonicator (Covaris). 1.5 µg of anti-MEISa (K830) and 1.5 µg of anti-MEIS1 (K844) were used for immunoprecipitation via Dynabeads Proein-A beads over night at 4°C. Eluted and de-crosslinked DNA was was purified by MinElute columns (Qiagen).
Illumina sequencing libraries were generated using the NEBNext Ultra II Library Prep Kit for Illumina (E7645) with NEBNext Multiplex Oligos for Illumina (Dual Index Set1, E7600). Size selection after PCR was performed by Pippin Prep (Sage Science), using a 2% cassette with size window set to 300-750 bp. Samples were sequenced 36bp paired-end on an Illumina NextSeq550.

value: hNSC

value: human neural stem cell

tag: antibody

value: anti-MEISa


title: hNSC MEIS1/2 Input rep2


title: ATCC 8739, control, rep3

description: Library name: C1C


title: MPRA FIRE SM BV2 gDNA Rep2


title: NCCIT-2

city: Utrecht

first: Joaquin

last: Montilla Rojo

address: Yalelaan 1

country: Netherlands

institute: Utrecht University

description: Library name: NCCIT-2

data_processing:
Quality control on the sequence reads from the raw FASTQ files was done with FastQC (v0.11.8). TrimGalore (v0.6.5) as used to trim reads based on quality and adapter presence after which FastQC was again used to check the resulting quality. rRNA reads were filtered out using SortMeRNA (v4.3.3) after which the resulting reads were aligned to the GRCh37 reference genome and Homo_sapiens.GRCh37.74.gtf annotation data using the STAR (v2.7.3a) aligner. Followup QC on the mapped (bam) files was done using Sambamba (v0.7.0), RSeQC (v3.0.1) and PreSeq (v2.0.3). Readcounts were then generated using the Subread FeatureCounts module (v2.0.0) with the Homo_sapiens.GRCh37.74.gtf file as annotation.
CPM and RPKM Normalized versions of the counts table were generated using the R-packages edgeR (v3.28) as well as a normalized version using DEseq2 (v1.28).
Assembly: Human - GRCh37
Supplementary files format and content: tab-delimited text file including counts as generated by DEseq2 (v1.28)

source_name: NCCIT

growth_protocol: Human pluripotent stem cells were maintained over vitronectin-coated plates and cultured with mTESR-PLUS. Embryonal carcinoma lines were maintained using DMEM-10%FCS

extract_protocol:
Total RNA was isolated using TRIzol (Thermo Fischer Scientific) following manufacturer’s recommendations. RNA quality was checked with the Agilent Fragment Analyzer 5300 system using the RNA Kit (15nt) (Cat. DNF-471-1000). RNA quantity was measured with the Invitrogen™ Qubit ™ Fluorometer using the Qubit RNA HS Assay Kit (Cat. Q32855).
100ng of total RNA was used to prepare TruSeq Stranded mRNA libraries (Cat. 20020594) following the manufacturers protocol with custom 384 xGen UDI-UMI adapters from IDT.

value: NCCIT

value: human embryonal carcinoma

value: WT


title: Lu07-p71plus2

description: Library name: Lu07-p71plus2

value: human pluripotent stem cell


title: NCCIT-TP53-KO-2

description: Library name: NCCIT-TP53-KO-2


title: Lu07-p71plus4

description: Library name: Lu07-p71plus4


title: NCCIT-1

description: Library name: NCCIT-1


title: Lu07-p66plus5

description: Library name: Lu07-p66plus5


title: NCCIT-TP53-KO-1

description: Library name: NCCIT-TP53-KO-1


title: LKO5-p72plus3

description: Library name: LKO5-p72plus3


title: hNSC MEIS1/2 Input rep1


title: LKO3-p79plus5

description: Library name: LKO3-p79plus5


title: LKO3-p77plus6

description: Library name: LKO3-p77plus6


title: HKO-p79plus2

description: Library name: HKO-p79plus2


title: HKO-p79plus13

description: Library name: HKO-p79plus13


title: hNSC MEIS1/2 ChIP rep2


title: H9-p69plus9

description: Library name: H9-p69plus9


title: HKO-p79plus7

description: Library name: HKO-p79plus7


title: 2102Ep-TP53-KO-2

description: Library name: 2102Ep-TP53-KO-2


title: 2102Ep-TP53-KO-1

description: Library name: 2102Ep-TP53-KO-1


title: 2102Ep-2

description: Library name: 2102Ep-2


title: LKO3-p77plus4

description: Library name: LKO3-p77plus4


title: H9-p69plus8

description: Library name: H9-p69plus8


title: H9-p69plus5

description: Library name: H9-p69plus5


title: 2102Ep-1

description: Library name: 2102Ep-1


title: EBNALP_WT_RNA_Rep2

city: Minneapolis

first: Chong

last: Wang

state: MINNESOTA

institute: University of Minnesota

data_processing:
ATAC-seq and Cut&Run reads were aligned to humen genome (hg19) using Bowtie v2.4.1. ATAC-seq and Cut&Run peaks were called on each replicate samples using MACS v2.2.7.1
RNA-seq reads were aligned to human (hg19) genome using STAR v2.7.3a. featureCounts v1.6.1 was used to calculate gene expression reads counts based on GENCODE v34 annotation.
HiChIP paired-end reads were mapped to human (hg19) genome using HiC-Pro v2.11.4 (default settings with LIGATION_SITE set as GATCGATC for MboI) All valid interaction read pairs were then analyzed with hichipper v0.7.7 for detection of significant long-range interactions.
Assembly: hg19
Supplementary files format and content: ATAC_seq and Cut&Run peaks
Supplementary files format and content: HiChIP long range interactions
Supplementary files format and content: Gene expression files

source_name: Human naive B cell

growth_protocol: Wild-type or EBNALP mutant EBV virus infectd naïve B cells were rountinly cultured in RPMI1640 supplemented with 10% FCS.

extract_protocol: RNA was extracted using RNeasy kit (Qiagen); RNA-seq library was constructed using kit NEBNext® Ultra™ II Directional RNA Library Prep with Sample Purification Beads

treatment_protocol: Naïve B cells extracted from blood were infected with either wild-type or EBNALP mutant EBV virus

value: Human naive B cell

value: B cell

value: Wild-type EBV virus infection of naïve B cells RNA-seq replication 2


title: GM12878_YY1KO_HiChIP_Rep1

data_processing:
ATAC-seq and Cut&Run reads were aligned to humen genome (hg19) using Bowtie v2.4.1. ATAC-seq and Cut&Run peaks were called on each replicate samples using MACS v2.2.7.1
RNA-seq reads were aligned to human (hg19) genome using STAR v2.7.3a. featureCounts v1.6.1 was used to calculate gene expression reads counts based on GENCODE v34 annotation.
HiChIP paired-end reads were mapped to human (hg19) genome using HiC-Pro v2.11.4 (default settings with LIGATION_SITE set as GATCGATC for MboI) All valid interaction read pairs were then analyzed with hichipper v0.7.7 for detection of significant long-range interactions.
Assembly: hg19
Supplementary files format and content: ATAC_seq and Cut&Run peaks
Supplementary files format and content: HiChIP long range interactions
Supplementary files format and content: Gene expression files
Library strategy: HiChIP

source_name: GM12878 cell line

extract_protocol: Following HiChIP protocal, enriched DNA was amplified with  High-Fidelity DNA Polymerase (NEB). Ampure XP beads were used for library DNA size selection

value: GM12878 cell line

value: GM12878 cells in which YY1 was deleted


title: EBNALP_WT_RNA_Rep3

value: Wild-type EBV virus infection of naïve B cells RNA-seq replication 3


title: GM12878_Ctrl_HiChIP_Rep2

value: GM12878 cells transfected with control sgRNA


title: EBNALP_KO_RNA_Rep3

value: EBNALP mutant EBV virus infection of naïve B cells RNA-seq replication 3


title: EBNALP_WT_RNA_Rep1

value: Wild-type EBV virus infection of naïve B cells RNA-seq replication 1


title: GM12878_YY1KO_HiChIP_Rep2


title: LKO5-p71plus3

description: Library name: LKO5-p71plus3


title: EBNALP_WT_YY1_CnR_Rep1

data_processing:
ATAC-seq and Cut&Run reads were aligned to humen genome (hg19) using Bowtie v2.4.1. ATAC-seq and Cut&Run peaks were called on each replicate samples using MACS v2.2.7.1
RNA-seq reads were aligned to human (hg19) genome using STAR v2.7.3a. featureCounts v1.6.1 was used to calculate gene expression reads counts based on GENCODE v34 annotation.
HiChIP paired-end reads were mapped to human (hg19) genome using HiC-Pro v2.11.4 (default settings with LIGATION_SITE set as GATCGATC for MboI) All valid interaction read pairs were then analyzed with hichipper v0.7.7 for detection of significant long-range interactions.
Assembly: hg19
Supplementary files format and content: ATAC_seq and Cut&Run peaks
Supplementary files format and content: HiChIP long range interactions
Supplementary files format and content: Gene expression files
Library strategy: Cut&Run

extract_protocol: CUT&RUN library was constructed using CUTANA™ ChIC/CUT&RUN Kit

value: Wild-type EBV virus infection of naïve B cells YY1 CUT&RUN replication 2


title: EBNALP_KO_HiChIP_Rep2

value: EBNALP mutant EBV virus infection of naïve B cells H3K27ac HiChIP replication 2


title: LKO5-p71plus7

description: Library name: LKO5-p71plus7


title: EBNALP_WT_HiChIP_Rep1

value: Wild-type EBV virus infection of naïve B cells H3K27ac HiChIP replication 1


title: EBNALP_KO_YY1_CnR_Rep2

value: EBNALP mutant EBV virus infection of naïve B cells YY1 CUT&RUN replication 2


title: EBNALP_KO_HiChIP_Rep1

value: EBNALP mutant EBV virus infection of naïve B cells H3K27ac HiChIP replication 1


title: EBNALP_WT_HiChIP_Rep2

value: Wild-type EBV virus infection of naïve B cells H3K27ac HiChIP replication 2


title: s42001.na.37.4.YPD, rep2

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

data_processing:
Illumina NovaSeq 6000 using NovaSeq Control Software v1.7.0, RTA v3.4.4. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
RNASeq analysis was conducted using the nf-core/rnaseq pipeline (version 3.11.1), with STAR for genome alignment and Salmon for transcript quantification. The bioconductor package tximport (version 1.28.0) was used to prepare gene-level summaries.
Assembly: S288c R64-1-1 version 109
Supplementary files format and content: charliew_julietb_081724_IntCt.txt.gz is a tab-delimited text file of integer count data
Supplementary files format and content: charliew_julietb_081724_l2tpm.txt.gz  is a tab-delimited text file of log 2 TPM values with a +1 offset.

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown in yeast extract and peptone supplemented with adenine (0.055 mg/mL) and either 2% dextrose (YPD), 2% dextrose and 1M sorbitol (YPD + sorbitol), or 2% dextrose and 0.5M NaCl (YPD + NaCl). All time-course experiments were initiated with cells growing in log phase (0.2 < OD600 < 0.8) in their respective media and diluted to OD600 of 0.2 in equivalent, sterile media. All cultures of cells were maintained in log-phase growth throughout the duration of time-course experiments by diluting the culture with sterile medium. This sterile medium contained 15 ug/mL nocodazole when added to mad1∆ bub2∆ cells. Cell culture was conducted at 30C for mad1∆ bub2∆ cells, 24C for exponentially-growing, haploid cdc24-1 swe1∆ cells. To induce genome duplication in cdc24-1 swe1∆ cells, cells were cultured at 37C, in a shaking water bath.

extract_protocol:
Cells were collected for RNA extraction by centrifugation, resuspension in diethyl pyrocarbonate-treated water, and immediately flash-freezing in liquid nitrogen. Total RNA was extracted from cells using an RNEasy Mini kit (QIAGEN) and the manufacturer’s protocol for RNA extraction from yeast with the following specifications. Cells were mechanically lysed by bead milling, using a FastPrep-24 5G instrument (MP Biomedicals). Samples contained between 0.5 X 106 and 2 X 107 cells, 600 uL of acid-washed glass beads (Sigma-Aldrich) and 600 uL lysis buffer (with -mercaptoethanol), in 2 mL tubes, and were agitated for 2-8 rounds of 60 seconds at 6.5 m/s, with chilling on ice for 5 minutes intervening rounds, until cells were completely lysed. Complete lysis was confirmed by microscopy. The concentration and integrity of the extracted total RNA was determined using a 2100 BioAnalyzer (Agilent).
mRNA was isolated and fragmented using an NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs) and cDNA was synthesized, ligated to adaptors, and PCR- amplified for sequencing using an NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs). Sequencing was conducted on NovaSeq6000 using an S4 flow cell (Illumina).

treatment_protocol: To induce genome duplication in mad1∆ bub2∆ cells, the cells were treated with 15 ug/mL nocodazole (Millipore Sigma) at the initiation of each experiment. Nocodazole was dissolved to a concentration of 10 mg/mL in DMSO (Millipore Sigma). To prevent the effects of cells’ adaptation to the presence of nocodazole, an additional 7.5 ug/mL of nocodazole was added to cultures every 4 hrs. Volume-equivalents of DMSO were added to all exponentially-growing mad1∆ bub2∆ control cultures. To induce genome duplication in cdc24-1 swe1∆ cells, the cells were added to flasks pre-warmed to 37°C in a shaking water bath at the initiation of each experiment, and grown at 37°C for the durations of the experiments. Exponentially-growing cdc24-1 swe1∆ control cultures were maintained at 24°C, in a shaker with air-cooling.

tag: temperature (degrees_c)

tag: time (hours)

value: CCS

tag: mean dna_content_(arbitrary_units)


title: s42001.na.37.8.YPD, rep3


title: EBNALP_KO_YY1_CnR_Rep1

value: EBNALP mutant EBV virus infection of naïve B cells YY1 CUT&RUN replication 1


title: EBNALP_KO_DPF2_CnR_Rep2

value: Human naive B cell

value: EBNALP mutant EBV virus infection of naïve B cells DPF2 CUT&RUN replication 2


title: EBNALP_WT_YY1_CnR_Rep2

value: B cell


title: s42001.na.37.4.YPD, rep3


title: EBNALP_WT_DPF2_CnR_Rep2

value: Wild-type EBV virus infection of naïve B cells DPF2 CUT&RUN replication 2


title: EBNALP_WT_DPF2_CnR_Rep1


title: EBNALP_KO_RNA_Rep1

value: EBNALP mutant EBV virus infection of naïve B cells RNA-seq replication 1


title: GM12878_Ctrl_HiChIP_Rep1

value: GM12878 cell line

tag: cell line


title: s42001.na.37.16.YPD, rep3

tag: genotype


title: EBNALP_WT_ATAC_Rep2

extract_protocol: ATAC-seq library was constructed using kit NEBNext® Ultra™II DNA Library Prep Kit for Illumina Beads

value: Wild-type EBV virus infection of naïve B cells ATAC-seq replication 2


title: s42001.na.37.16.YPD, rep1


title: s42001.na.37.12.YPD, rep3


title: EBNALP_WT_ATAC_Rep1

value: Wild-type EBV virus infection of naïve B cells ATAC-seq replication 1


title: EBNALP_KO_DPF2_CnR_Rep1

value: EBNALP mutant EBV virus infection of naïve B cells DPF2 CUT&RUN replication 1


title: s42001.na.37.8.YPD, rep1


title: s42001.na.37.4.YPD, rep1


title: EBNALP_KO_RNA_Rep2

value: EBNALP mutant EBV virus infection of naïve B cells RNA-seq replication 2


title: s42001.na.37.8.YPD, rep2


title: s42001.na.37.0.YPD, rep1


title: EBNALP_KO_ATAC_Rep2

value: EBNALP mutant EBV virus infection of naïve B cells ATAC-seq replication 2


title: s42001.na.37.12.YPD, rep2