title: hITM_HTO

city: Würzburg

first: Antoine-Emmanuel

last: Saliba

address: Josef-Schneider-Straße 2 / D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

description: Hashtag library (Hashtag1 = Replicate1; Hashtag2 = Replicate2)

library_source: transcriptomic single cell

data_processing:
FASTQ files were aligned and counted using the CellRanger count pipeline against the GRCh38 human genome reference as well as the TotalSeqA Hashtags 1 and 2.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: epithelial cells

extract_protocol:
Single cells were dissociated from the hITM as described. The cells of two different models were hashtagged with TotalSeq-A antibodies (Biolegend) following the manufacturer's protocol for TotalSeqTM-A antibodies and cell hashing with 10X Single Cell 3’ Reagent kit v3.1 (10x Genomics). Approximately 400.000 cells per sample were resuspended in 100 µl Cell Staining Buffer (Biolegend) and 5 µl Human TruStain FcXTM FcBlocking (Biolegend) reagent were added. For the blocking reaction, the cells were kept at 4°C for 10 minutes. 1 µg of TotalSeqTM-Antibody was added to each sample, followed by 30-minutes incubation at 4°C. Afterwards, cells were washed three times with 1 ml Cell Staining Buffer and spun down for 5 min at 350xg and 4°C. Finally, the cells were resuspended in an appropriate volume of PBS- and passed through a 40 µm cell strainer (FlowmiTM Cell Strainer, Merck). Cells were counted in a Neubauer Hemacytometer (Marienfeld) and concentration was adjusted to 1000 cells/µl with PBS-. The hashtagged cells were pooled equally and ~20.000 cells were loaded in the ChromiumTM Controller. The machine creates Gel Bead-In-Emulsions (GEMs) to separate single cells into a nanoliter compartment together with an individual barcode. Reverse transcription, cDNA amplification and the construction of gene expression libraries was performed using the 10x Single Cell 3’ reaction kit v3.1 (10x Genomics). Incubation and amplification steps were carried out using a SimpliAmp Thermal Cycler (ThermoFisher). Library quantification and quality control was observed using a QubitTM 4.0 Fluorometer (ThermoFisher) and a 2100 Bioanalyzer with High Sensitivity DNA kit (Agilent). Sequencing was performed on a NextSeq 500 sequencer (Illumina).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: For analyses of the hITM 0-24h post infection, supernatants of the apical and basolateral compartments were discarded, followed by washing the models with 1x PBS + 1mM EDTA (ThermoFisher) and incubation with Accutase (Gibco), added to both compartments, incubating for 10 min at 37°C. To detach the cells from the scaffold, the Accutase suspension in the apical compartment was vigorously resuspended and transferred to a 2 ml reaction tube. The Accutase solution of the basolateral compartment was discarded and the SIS scaffold was transferred to the 2 ml reaction tube containing the Accutase solution harvested from the apical site of the model with subsequent incubation on a shaker for 10 minutes, 37°C at 1000 rpm. After careful resuspension using a 1 ml Pipet and 10 min incubation at RT to allow settling of the cells by gravitation, the scaffold was removed. Next, the cells were centrifuged at 500xg for 3 min, RT and the supernatant was discarded. Afterwards, the pellet was washed twice with 1x PBS-. Finally, cells were resuspended in 1x PBS- and stored on ice for further analysis. Before flow cytometry and Drop-seq were performed, the cells were filtered through a 40 µm Strainer (Miltenyi).

value: epithelial cells

tag: cell line

value: small intestine


title: 11J_M_240

status: Public on Apr 25 2023

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

tag: age

tag: strain


title: hITM_GEX

description: Gene expression library

molecule: polyA RNA

organism: Homo sapiens

tag: tissue


title: VSMCs, 21d

city: Barcelona

first: Winona

middle: Oliveros

last: Diez

state: Barcelona

address: C. Maria Cubi 92, 2-2

country: Spain

institute: BSC

description: OmniC data

data_processing:
4D Nucleome pipeline was used. More details on OmniC analysis are described in the paper.
Assembly: hg38
Supplementary files format and content: cool files including interaction matrix
Library strategy: OmniC

source_name: VSMCs

extract_protocol:
Mapping Hi-C/OmniC protocol is described in the manuscript.
Details on library preparation are described in the manuscript.

tag: cell type

value: VSMCs


title: GFLV_heso1_3urt1_1_Plant1

city: Strasbourg

first: Dominique

last: Gagliardi

address: 12, rue du General Zimmer

department: IBMP

country: France

institute: CNRS

description:
3' RACE-seq
Processed_data_GFLV_B1B2.txt

library_source: transcriptomic

data_processing:
Fastq files were analyzed by a homemade pipeline adapted from Scheer et al. 2021 composed of scripts using python (v2.7), biopython (v1.63) and regex (v2.4) libraries.
Python and bash source code are available in github (https://github.com/hzuber67/RACEseq_virus)
Assembly: cf the associated publication
Supplementary files format and content: Three processed data files are given. They includes the processed data for the analyzed GFLV  (Processed_data_GFLV_B1B2.txt), TuMV (Processed_data_TuMV_B1B2.txt) and TCV (Processed_data_TCV_A.txt) for each genotype and biological replicate. Each line corresponds to one individual reads.
Supplementary files format and content: For each read, we indicate read ID (read.ID), Virus RNA name (Target), poly(A) tail sequence (polyA), poly(A) tail length (polyA.size), non-A extension sequence (modification), length of the non-A extension (modification.size), tail sequence (extension),  tail size (extension.size), a tag (classification) indicating the category of the tail, the 15N random sequence used for deduplication (random), barcode, biological replicate (Plant), Virus RNA (RNA), infected plant (Host) and Virus name (Virus).

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Infected leaves

growth_protocol: Leaves from GFLV, TuMV and TCV infected Arabidpsis plants (genotype WT, urt1-1, heso1-3 and heso1-3 urt1-1)

extract_protocol:
Total RNA of Arabidopsis infected leaves was extracted using Tri-Reagent (Molecular Research Center).
3'RACEseq
3'RACEseq protocol is based on the ligation of a primer at the 3’ end of RNA, and the subsequent targeted amplification by PCR of amplicons suitable for Illumina sequencing.

value: Infected leaves

tag: genotype

value: heso1-3 urt1-1

tag: treatment

value: GFLV


title: ATH1037

city: Newark

first: Pamela

middle: J

last: Green

state: DE

address: 15 Innovation Way

department: Plant and Soil Sciences

institute: Delaware Biotechnology Institute

description:
PARE
Leaf_PARE_Scores.bg

data_processing:
PARE libraries (Illumina HiSeq 2500); GMUCT and RNA-seq libraries (Illumina NextSeq 550)
Reads were mapped to Arabidopsis TAIR10 genome using Tophat v2.0
PARE and GMUCT libraries were analyzed as per Hurtig et al., 2021 (PNAS) using the ComPARE pipeline
Bedgraph files contain ComPARE scores from PARE and GMUCT libraries comparing normalized abundances (expressed as counts per million, CPM) at every 5'P site between Col-0, xrn4 and mfl1xrn4
Genome_build: Arabidopsis TAIR10 (Ensemble v49)
Supplementary_files_format_and_content: RNA-seq: gene_exp.diff is a cuffdiff output file; PARE and GMUCT: Genomic coordinate file (with annotations) containing RNA Degradome scores where 5'P site CPM >= 1 in xrn4 in both replicates (bedgraph files)

source_name: six-week-old rosette leaves

growth_protocol: Seedlings grown on 1X MS, 1% (w/v) sucrose, 1% (w/v) agar for two-weeks in a climate-controlled growth chamber (21C; 16h day: 8h night); Fully expanded rosette leaves were collected from adult plants grown in soil under long day growth chamber conditions at 21/22C

extract_protocol: PARE libraries were prepared as per Nagarajan et al., (2019); GMUCT libraries were prepared according to Wilmann et al., 2014 with modifications suggested in Carpentier et al., 2021; RNA-seq libraries: 50 ug polyA+ RNA (2x enriched) prepared as per NEBNext Ultra II Directional Library Preparation kit;

tag: ecotype

tag: genotype/variation

tag: rep


title: ATH1036

description:
PARE
Leaf_PARE_Scores.bg


title: ATH1039

description:
PARE
Leaf_PARE_Scores.bg


title: GFLV_heso1_3urt1_1_Plant3


title: OCIAML3_SLC2A3_3

city: Seoul

first: Junshik

last: Hong

state: Seoul

address: 101 Daehak-ro, Jongno-gu

department: Department of Internal Medicine

country: South Korea

institute: Seoul National University

data_processing:
Trim adaptors and low quality regions
Map reads using bwa
Sort bam file
Map reads using tophat2
Counts reads mapped to genes
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Blood

growth_protocol: OCI-AML3 cell lines were cultured according to DSMZ user manuals.

extract_protocol:
The GLUT3 overexpressed and empty control OCI-AML3 cell lines were collected, and RNA was harvested using Trizol reagent. NEBNext ultra II Directional RNA-seq kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 250 µM vitamin C

value: Blood

value: AML cell line

value: SLC2A3 overexpressed

value: 250 µM vitamin C


title: ATH1038

description:
PARE
Leaf_PARE_Scores.bg


title: 11J_M_236


title: OCIAML3_SLC2A3_2


title: OCIAML3_pLenti_3

value: empty vector


title: 11J_M_235


title: GFLV_heso1_3_Plant3


title: OCIAML3_pLenti_2


title: 11J_M_237


title: 11J_M_238


title: Hs578T siFOXD1-2 48hr RNA 1

city: Tokyo

first: Kohei

last: Kumegawa

address: 3-8-31 Ariake, Koto-ku

country: Japan

institute: Japanese Foundation for Cancer Research

data_processing:
The row reads were trimmed to remove adaptor sequences using Skewer (v0.2.2).
The reads were mapped to the hg38 genome using STAR (v.2.7.8a).
The mapped reads were then counted using featureCounts (v.2.0.10).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include counts for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA-seq libraries were prepared with 10 ng of total RNA using a SMARTer Stranded Total RNA-Seq Kit v2-Pico Input Mammalian (Takara)

value: basal-like breast cancer

value: FOXD1 knockdown


title: Hs578T siFOXD1-2 48hr RNA 2


title: GFLV_heso1_3_Plant2


title: GFLV_heso1_3_Plant1


title: GFLV_heso1_3urt1_1_Plant2


title: Hs578T siFOXD1-1 48hr RNA 2


title: OCIAML3_pLenti_1


title: s_138232

city: Ann Arbor

first: Antonio

middle: Marcondes

last: Lerario

state: MI

address: 109 Zina Pitcher Place, 1528 BSRB

department: MEND

institute: University of Michigan

data_processing:
Reads were aligned to the hg38 assembly of the human genome using STAR (Dobin et al., 2013)
Gene expression was quantified by featureCounts (Liao et al., 2014).
Supplementary files format and content: count table, tab-delimited text

source_name: NCI-H295R, FSK

growth_protocol: NCI-H295R were cultured in DMEM/F12 supplemented with 10% Nu serum, 1% ITS-X, and 1% penicillin/streptomycin in a humidified tissue culture incubator with 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted using Qiagen AllPrep kit with optional on column nuclease treatment.
Library was prepared by the University of Michigan Advanced Genomics Core using the NEBNExt polyA Ultra II RNA Library Prep Kit for Illumina.

treatment_protocol: NCI-H295R were plated in 6 well plates and treated for 96 hours with EZH2i at the IC-50 dose (62 μM EPZ-6438), CBPi at the IC-50 dose (26 μM PRI-724), or the vehicle (equivalent volume of DMSO, these are "baseline") in 3 biological replicates. Alternatively, NCI-H295R were plated in 6 well plates and treated with equivalent volume of  vehicle (DMSO) for 48 hours and then treated with 10 μM forskolin for 48 hours as above in 3 biological replicates. mRNA was extracted at endpoint for RNA-seq.

value: human adrenocortical carcinoma

value: Forskolin


title: Hs578T siFOXD1-1 48hr RNA 1


title: 11J_M_232


title: s_138231


title: GFLV_urt1_1_Plant4


title: GFLV_urt1_1_Plant3


title: 11J_M_231


title: Hs578T siNC 48hr RNA 1

value: WT


title: 11J_M_233


title: Hs578T siNC 48hr RNA 2


title: OCIAML3_SLC2A3_1


title: s_138230


title: GFLV_heso1_3_Plant4


title: BT549 siFOXD1-2 48hr RNA 2


title: s_138229

source_name: NCI-H295R, CBPi


title: 11J_M_234


title: GFLV_urt1_1_Plant2


title: 11J_M_229


title: GFLV_urt1_1_Plant1


title: GFLV_WT_Plant4


title: s_138228


title: BT549 siFOXD1-2 48hr RNA 1


title: 11J_M_228


title: s_138227


title: 11J_M_227


title: s_138226

source_name: NCI-H295R, EZH2i


title: GFLV_WT_Plant3


title: GFLV_WT_Plant2


title: BT549 siFOXD1-1 48hr RNA 1


title: 11J_M_226


title: BT549 siNC 48hr RNA 2


title: 11J_M_230


title: TuMV biol rep 2

description:
3' RACE-seq
Processeddata_polyA_allvirus_B1B2.txt

data_processing:
Fastq files were analyzed by a homemade pipeline adapted from Scheer et al. 2021 composed of scripts using python (v2.7), biopython (v1.63) and regex (v2.4) libraries.
Python and bash source code are available in github (https://github.com/hzuber67/RACEseq_virus)
Assembly: cf the associated publication
Supplementary files format and content: Two processed data file is given. They includes the processed data for the analyzed 21 virus, the poladenylated RNA virus  (Processeddata_polyA_allvirus_B1B2.txt), and the non polyadenylated virus (Processeddata_nonpolyA_allvirus_A.txt) for each genotype and biological replicate. Each line corresponds to one individual reads.
Supplementary files format and content: For each read, we indicate read ID (read.ID), Virus RNA name (Target), poly(A) tail sequence (polyA), poly(A) tail length (polyA.size), non-A extension sequence (modification), length of the non-A extension (modification.size), tail sequence (extension),  tail size (extension.size), a tag (classification) indicating the category of the tail, the 15N random sequence used for deduplication (random), barcode, biological replicate (Plant), Virus RNA (RNA), infected plant (Host) and Virus name (Virus).

source_name: Infected leaves of A. thaliana

growth_protocol: Leaves from virus infected plants

extract_protocol:
Total RNA from infected leaves of C. quinoa, N. benthamiana and grapevine were extracted using the RNeasy plant Mini Kit (Qiagen). Total RNA of Arabidopsis infected leaves was extracted using Tri-Reagent (Molecular Research Center).
3' RACE-seq
3'RACEseq protocol is based on the ligation of a primer at the 3’ end of RNA, and the subsequent targeted amplification by PCR of amplicons suitable for Illumina sequencing.

value: Infected leaves of A. thaliana

value: TuMV


title: GFLV_WT_Plant1


title: BT549 siNC 48hr RNA 1


title: s_138224


title: TuMV biol rep 3


title: Hs578T siFOXD1-2 48hr H3K27ac 1

data_processing:
The sequenced reads were mapped to the hg38 genome using bowtie2 (v.2.4.2).
Multi-mapped reads and PCR duplicates were removed using Picard (v.2.25.3).
Overlapping reads according to the ENCODE blacklist were filtered out using bedtools (2.30.0).
MACS2 (v.2.2.7.1) was used for calling peaks with the ”--keep-dup auto -q 0.1” parameter.
Assembly: hg38
Supplementary files format and content: peak summit files

extract_protocol:
Cells were fixed with 0.5% formaldehyde for 10 min at room temperature, quenched with 1.25 M glycine, washed, and lysed. The chromatin was sheared using S220 Focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using ThruPLEX DNA-seq Kit (Takara)

tag: chip antibody

value: H3K27ac (Cell Signaling Technology, 8173S)


title: 11J_M_223


title: 11J_M_224


title: s_138223

source_name: NCI-H295R, baseline

value: DMSO


title: s_138222


title: s_138221


title: TYMV biol rep 3

description:
3' RACE-seq
Processeddata_nonpolyA_allvirus_A.txt

value: TYMV


title: 11J_M_222


title: Hs578T siFOXD1-1 48hr H3K27ac 2


title: Hs578T siFOXD1-2 48hr H3K27ac 2


title: BT549 siFOXD1-1 48hr RNA 2


title: Hs578T siFOXD1-1 48hr H3K27ac 1


title: 11J_M_221


title: 11J_M_220


title: 27-CLP-9

description: Peak files are narrowPeak

data_processing:
We used bowtie2 (Langmead and Salzberg, 2012) to align the reads to the hg38 version of the human genome.
Reads overlapping with blacklisted regions (defined by ENCODE (Consortium, 2012; Davis et al., 2018)), and reads with a mapping score < 20 were filtered.
For ATAC-seq peak calling, we used genrich (Gaspar, 2018).
BigWig files were generating using deepTools 2.0 (Ramírez et al., 2016) with RPGC normalization
Assembly: hg38
Supplementary files format and content: BigWig
Supplementary files format and content: narrowPeaks - called peaks

extract_protocol:
At endpoint, cells were harvested for ATAC-seq. ATAC-seq was performed as previously described (Corces et al., 2017) with modifications. Specifically, 50,000 cells were resuspended in 500 μL resuspension buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2 in water). Cells were centrifuged at 50xg for 10 min in a pre-chilled (4°C) fixed-angle centrifuge.
Lysis and transposition were performed simultaneously by resuspending cells in 25 μL tagmentation mix (12.5 μL 2xTD buffer [Illumina, Cat. No. 15027866], 1.25 μL Tn5 enzyme [Illumina, Cat. No. 15027865], 9.25 μL PBS, 0.5 μL 1% digitonin, 0.5 μL Tween-20, 0.5 μL NP40, and 0.5 μL 100x protease inhibitors), and incubating at 37°C for 30 min in a thermomixer with shaking at 1,000 rpm. Tn5 transposase-tagged DNA was amplified by PCR and purified using AMPure XP magnetic beads. ATAC-seq reads were sequenced 2x150 bp using a NovaSeq 6000. Sequencing of ATAC-seq libraries was performed by the University of Michigan Advanced Genomics Core.

treatment_protocol: NCI-H295R were plated in 6 well plates and treated for 96 hours with EZH2i at the IC-50 dose (62 μM EPZ-6438), CBPi at the IC-50 dose (26 μM PRI-724), or the vehicle (equivalent volume of DMSO, these are "baseline") in 2 biological replicates. Alternatively, NCI-H295R were plated in 6 well plates and treated with equivalent volume of  vehicle (DMSO) for 48 hours and then treated with 10 μM forskolin for 48 hours as above in 2 biological replicates.


title: 11J_M_225


title: Hs578T siNC 48hr H3K27ac 2


title: s_138225


title: TYMV biol rep 2


title: 27-CLP-10

description: Peak files are narrowPeak


title: Hs578T siNC 48hr H3K27ac 1


title: 27-CLP-8

description: Peak files are narrowPeak


title: Hep3B cells, shDAGLA, rep3

city: Jinan

first: Yu-Chuan

last: Yan

state: Shandong

address: 107 West Wen Hua Road

country: China

institute: Qilu Hospital of Shandong University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing low-quality sequences and adapter contamination.
The reference genome was indexed using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene, considering the effect of sequencing depth and gene length for the reads count.
Assembly: Genome Reference Consortium Human Build 37 (GRCh37)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: Hep3B cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using RNA Fast200 kit (fastagen). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared for sequencing using standard illumina protocols.

treatment_protocol: Hep3B cells were infected with control and shDAGLA lentivirus, respectively (multiplicity of infection=5). Subsequently, puromycin was used to select stable knockdown cells.

value: Human hepatocellular carcinoma (HCC) cells

value: DAGLA knockdown


title: Hep3B cells, shDAGLA, rep2


title: 11J_M_218


title: BT549 siFOXD1-2 48hr H3K27ac 2


title: 11J_M_217


title: BT549 siFOXD1-2 48hr H3K27ac 1


title: Hep3B cells, shDAGLA, rep1


title: 11J_M_216


title: Hep3B cells, shControl, rep3

value: control


title: BT549 siFOXD1-1 48hr H3K27ac 2


title: Hep3B cells, shControl, rep2


title: TYMV biol rep 1


title: 27-CLP-5

description: Peak files are narrowPeak


title: 11J_M_215


title: 27-CLP-6

description: Peak files are narrowPeak


title: BT549 siFOXD1-1 48hr H3K27ac 1


title: 27-CLP-4

description: Peak files are narrowPeak


title: 11J_M_219


title: Hep3B cells, shControl, rep1


title: 11J_M_214


title: BT549 siNC 48hr H3K27ac 2


title: 11J_M_213


title: DRIP - shMEPCE.Input

city: Toronto

first: Razq

last: Hakem

state: Ontario

address: TMDT, 101 College Street. Rm13-310

department: Princess Margaret Cancer Centre

country: Canada

institute: University Health Network

data_processing:
Reads were aligned to the hg38 genome using Bowtie2 (v. 2.2.6)
Low-quality reads and multimappers were removed (MapQ < 40)
Duplicates were marked and removed using Picard (v. 2.10.9)
Bigwig files were generated using deeptools (v. 3.5.1) bamCoverage normalizing to inputs and sequencing depth (DRIP-seq) or to CPM (ChIP-seq)
Please note that each *.mean.bw was generated from both replicates and is linked to the corresponding rep1 sample records.
Assembly: hg38
Supplementary files format and content: Bigwig files of normalized reads in 5bp bins

source_name: MDA MB 436

growth_protocol: MDA-MB-436 cells were cultured in high-glucose Dulbecco's Modified Eagle Medium containing HEPES buffer, penicillin, and streptomycin supplemented with 10% fetal bovine serum.

extract_protocol:
RNA pol II (total or pSer2) was immunoprecipitated from sonicated chromatin for ChIP-seq Samples. DNA-RNA hybrid was immunoprecipitated from sonicated chromatin using S9.6 antibody for DRIP-seq Samples.
ChIP-seq samples were prepared as outlined by Takara Bio USA Inc’s ThruPLEX DNA-seq Kit user guide and DRIP-seq samples were prepared and sequenced by Novogene using their ChIP-seq protocols (NEB Next Ultra II DNA Library preparatino kit).

treatment_protocol: Lentiviral transduction of shScr or shMEPCE in MDA-MB-436 cells

value: MDA MB 436

value: MEPCE-KD


title: BT549 siNC 48hr H3K27ac 1


title: 11J_M_212


title: CTRL_NC7

city: Gainesville

first: Alberto

last: Riva

state: FL

address: 2033 Mowry Rd

department: ICBR

institute: University of Florida

description:
processed data file:
FPKM.matrix.csv

data_processing:
Short reads were trimmed with trimmomatic and quality control on the trimmed reads was performed with FastQC.
Reads were mapped to the human transcriptome using STAR, and gene expression was quantified with RSEM.
Differential expression analysis was performed using DESeq2.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited table of FPKM values; DESeq2 output

source_name: alveolar macrophage

growth_protocol: Ex vivo

extract_protocol:
RTL plus lysis & Rneasy extraction
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 1 hour plastic adherence at 37C

value: Lung

tag: aatd emphysema

value: Normal Control

tag: cell isolation

value: Bronchoalveolar Lavage


title: DRIP - shScr.Input


title: 27-CLP-7

description: Peak files are narrowPeak


title: 11J_M_211


title: CTRL_NC6

description:
processed data file:
FPKM.matrix.csv


title: DRIP - shMEPCE.RNase.rep1


title: CTRL_NC5

description:
processed data file:
FPKM.matrix.csv


title: HEK293, PE, rs4631439, VAF 100, clone 1

data_processing:
For MPRA RNA-Seq: trimmed and quality-filtered DNA and RNA reads using cutadapt, Then, we mapped reads to the barcodes and 10 upstream nucleotides of GFP requiring an exact match.
for CRISPR/Cas9 experiments: After read trimming using trim galore, we aligned reads to hg38 using Hisat2115, and we used FeatureCounts to count reads aligning to genes in GENCODE v26 (human)
Assembly: hg19
Supplementary files format and content: matrix of barcodes counts for MPRA single-end
Supplementary files format and content: matrix of gene counts for CRISPR-Cas9 paired-end analysis

extract_protocol:
Total RNA was extracted from MPRA-transfected cells using the phenol-chloroform extraction method according to standard protocols
cDNA was synthesized using SuperScript III First Strand Synthesis System (Invitrogen).


title: HEK293, PE, rs4631439, VAF 60, clone 2


title: DRIP - shScr.RNase.rep2


title: HEK293, PE, rs4631439, VAF 100, clone 2


title: 11J_M_210


title: HEK293, PE, rs4631439, VAF 60, clone 1


title: CTRL_NC3

description:
processed data file:
FPKM.matrix.csv


title: HEK293, PE, rs6712094, VAF 80, clone 1


title: 27-CLP-3

description: Peak files are narrowPeak


title: HEK293, PE, rs6712094, VAF 86, clone 2


title: HEK293, PE, rs4631439, VAF 30, clone 2


title: CTRL_NC1

description:
processed data file:
FPKM.matrix.csv


title: CTRL_NC2

description:
processed data file:
FPKM.matrix.csv


title: DRIP - shScr.RNase.rep1


title: 11J_M_207


title: HEK293, PE, rs4631439, VAF 30, clone 1


title: DRIP - shMEPCE.rep2


title: DRIP - shMEPCE.rep1


title: HEK293, PE, rs3824754, VAF 58, clone 2


title: 11J_M_205


title: 11J_M_206


title: AATD2_15

description:
processed data file:
FPKM.matrix.csv
allcodingdiff_case2.xlsx

value: Patient


title: DRIP - shMEPCE.RNase.rep2


title: AATD2_07


title: DRIP - shScr.rep2


title: 11J_M_209


title: HEK293, PE, rs3824754, VAF 58, clone 1


title: 11J_M_208


title: 11J_M_204


title: HEK293, PE, rs3824754, VAF 37, clone 2


title: AATD2_04


title: Pol II pSer2 - shMEPCE

data_processing:
Reads were aligned to the hg38 genome using Bowtie2 (v. 2.2.6)
Low-quality reads and multimappers were removed (MapQ < 40)
Duplicates were marked and removed using Picard (v. 2.10.9)
Bigwig files were generated using deeptools (v. 3.5.1) bamCoverage normalizing to CPM
Genome_build: hg38
Supplementary_files_format_and_content: bam files of high-quality reads aligning to one locus and duplicates removed sorted by position. Bigwig files of reads in 5bp bins normalized to counts per million

extract_protocol:
RNA pol II (total or pSer2) was immunoprecipitated from sonicated chromatin.
Samples were prepared as outlined by Takara Bio USA Inc’s ThruPLEX DNA-seq Kit user guide

tag: condition

value: anti-RNAPII CTD pSer2 (Abcam cat:ab5095)


title: 11J_M_203


title: AATD1_13

description:
processed data file:
FPKM.matrix.csv
allcodingdiff_case1.xlsx


title: Pol II pSer2 - shScr


title: AATD1_02


title: 11J_M_202


title: HEK293, PE, rs3753326, VAF 74, clone 2


title: Total Pol II - shMEPCE

value: anti-RNAPII CTD pSer5 (Abcam cat:ab5131)


title: HEK293, PE, rs3824754, VAF 37, clone 1


title: 11J_M_200


title: 11J_M_201


title: AATD1_01


title: HEK293, PE, rs3753326, VAF 70, clone 1


title: Total Pol II - shScr

value: WT


title: 11J_M_199


title: CNDV biol rep 3

organism: Nicotiana benthamiana

source_name: Infected leaves of N. benthamiana

value: Infected leaves of N. benthamiana

value: CNDV


title: 11J_M_198


title: HEK293, PE, rs3753326, VAF 50, clone 1


title: CNDV Plant3 N. benthamiana

description:
3' RACE-seq
Processed_Data_SECO_B2.txt

data_processing:
Fastq files were analyzed by a homemade pipeline adapted from Scheer et al. 2021 composed of scripts using python (v2.7), biopython (v1.63) and regex (v2.4) libraries.
Python and bash source code are available in github (https://github.com/hzuber67/RACEseq_virus)
Assembly: cf the associated publication
Supplementary files format and content: A processed data file is given. It includes the processed data for the analyzed Secoviridae viruses for each biological replicate. Each line corresponds to one individual reads.
Supplementary files format and content: For each read, we indicate read ID (read.ID), Virus RNA name (Target), poly(A) tail sequence (polyA), poly(A) tail length (polyA.size), non-A extension sequence (modification), length of the non-A extension (modification.size), tail sequence (extension),  tail size (extension.size), a tag (classification) indicating the category of the tail, the 15N random sequence used for deduplication (random), barcode, plant genotype (WT, urt1-1, heso1-3, heso1-3 urt1-1), biological replicate (Plant), Virus RNA (RNA), infected plant (Host) and Virus name (Virus).

growth_protocol: Leaves from plants infected by Secoviruses

extract_protocol:
Total RNA from infected leaves were extracted using the RNeasy plant Mini Kit (Qiagen).
3'RACE-seq
3'RACEseq protocol is based on the ligation of a primer at the 3’ end of RNA, and the subsequent targeted amplification by PCR of amplicons suitable for Illumina sequencing.


title: 11J_M_197


title: DRIP - shScr.rep1


title: HEK293, PE, rs3753326, VAF 33, clone 2


title: AVPV-3_ERalpha

city: Innsbruck

first: Jose Miguel

last: Ramos Pittol

address: Innrain 80-82

department: Institute of Biochemistry

country: Austria

institute: University of Innsbruck

data_processing:
ChIP-seq reads were aligned to the mm10 genome using Bowtie version 2.5.0. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to counts per million, cpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.2.7.1 with the significance cut-off q-value <=0.05
bigWig files were generated using the DeepTools 3.5 package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
A pooled bigWig track of ERalpha binding events was generated for each nucleus by pooling the data from all 4 replicates each (Arcuate-all_ERalpha.bw and AVPV-all_ERalpha.bw)
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak (except for Input samples)

source_name: AVPVnucleusof thehypothalamus

extract_protocol:
Tissues were fixed with 1% formaldehyde for 15 minutes, followed by quenching and cell lysis. 25 ng of pooled chromatin DNA was used as starting material for input and ip samples.
ChIP-seq libraries were prepared using the TruSeq ChIP Library Preparation Kit by ActiveMotif

treatment_protocol: Animals were ovariectomised and implanted with 2cm sub-cutaneous Silastic tubes (Dow Corning 508-005) containing 17β-estradiol (Merk) in sesame oil (0.1mg/mL). One week later, they were injected at 09:00 with either vehicle (sesame oil) or estradiol benzoate (0.05 mg/kg), and tissues were collected 28h after the injection.

value: AVPVnucleusof thehypothalamus

tag: Sex

value: Female

value: Estradiol benzoate (0.05 mg/kg) in sesame oil

value: ERalpha (SantaCruz, sc-543)


title: AVPV-4_ERalpha


title: AVPV-2_ERalpha


title: HEK293, PE, rs3753326, VAF 33, clone 1


title: 11J_M_196

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.


title: PVX biol rep 1

value: PVX


title: AVPV-1_ERalpha


title: 11J_M_195


title: Arcuate-pool_Input

source_name: Arcuatenucleusof thehypothalamus

value: Arcuatenucleusof thehypothalamus

value: input


title: PVX biol rep2


title: sc_ctrl_11d

city: Beijing

first: Bao-Fa

last: Sun

address: Da-Tun Road

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

data_processing:
Reads were processed using the Cell Ranger 3.0.0 pipeline (Zheng et al., 2017) with default and recommended parameters. FASTQ files generated from Illumina sequencing were aligned to the Schmidtea mediterranea transcriptome smed_20140614 using the STAR algorithm (Dobin et al., 2013). Next, Gene-Barcode matrices were generated for each individual sample by counting unique molecular identifiers (UMIs) and filtering non-cell associated barcodes. Only genes that can be translated into proteins were retained.
The output was then imported into the Seurat (v3.1.2) (Hao et al., 2020) R toolkit for quality control and downstream analysis of single cell RNA-seq data. All functions were run with default parameters, unless specified otherwise. Low quality cells (<500 genes/cell, >6000 genes/cell, <15 cells/ gene and >20% mitochondrial genes) were excluded. In order to exclude multiple captures, which is a major concern in microdroplet-based experiments, DoubletFinder (version 2.0.2) (McGinnis et al., 2019) was employed to remove top N cells with the highest pANN score for each library separately, where N represents the doublet rates. Then all the datasets were merged using the “merge” function in Seurat.
Assembly: Smed_20140614
Supplementary files format and content: counts for each cell

organism: Schmidtea mediterranea

extract_protocol: For single cell RNA-seq from 10x Chromium platform, Hoechst-stained and PI negative cells (200,000 cells) from wild-type animals, and from cells from wtap knockdown animals were collected on ice using Influx sorter. Approximately 9000 counted cells were loaded per channel. The libraries were made using the Chromium platform and Chromium Single Cell 3’ v3 chemistry. Sequencing libraries were loaded on an Illumina nova 6000 flowcell with two 150bp paired-end kits.

value: planarian whole body

value: wild type

value: 11 dpa


title: HEK293, PE, WT, clone 2


title: sc_ctrl_7d

value: 7 dpa


title: HEK293, PE, rs3753326, VAF 50, clone 2


title: AVPV-pool_Input


title: Arcuate-4_ERalpha


title: sc_ctrl_3d

value: 3 dpa


title: 11J_M_193


title: Arcuate-3_ERalpha


title: HEK293, PE, WT, clone 1


title: DNA input

source_name: plasmid pool

value: plasmid pool


title: 11J_M_192


title: VSMCs, replicate 4

value: VSMCs

value: MPRA


title: 11J_M_191


title: VSMCs, replicate 3, 2


title: Arcuate-2_ERalpha


title: sc_ctrl_0h

value: 0 hpa


title: VSMCs, replicate 3, 1


title: Arcuate-1_ERalpha


title: sc_kd_11d

value: wtap knockdown


title: 11J_M_190


title: 11J_M_189


title: 11J_M_188


title: 11J_M_194


title: sc_kd_3d


title: VSMCs, replicate 2, 1


title: VSMCs, replicate 1, 2


title: sc_kd_6h

value: 6 hpa


title: VSMCs, replicate 1, 1


title: PI3Ki+SHP2i_3

city: Basel

first: Mohamed

last: Bentires-Alj

address: Hebelstrasse 20

department: DBM

country: Switzerland

institute: University Hospital Basel

data_processing:
Standard Illumina software was used for base calling
Trimmed reads were aligned to the GRCm38 genome using the two-pass approach of STAR
Genome_build: hg19

source_name: Mammary carcinoma

growth_protocol: 4T1 cells (300,000 cells) were resuspendend in 50 µL PBS and injected into the mammary fat-pad of 8 weeks old female Balb/c mice. Tumors were collected 21 days after injection.

extract_protocol:
RNeasy Plus Mini Kit (Qiagen, #74136) and sample quality controlled on an Agilent 2100 Bioanalyzer system with the RNA6000 Nano kit (Agilent, #5067-1511).  mRNA isolation was performed with the NEBNext Poly(A) mRNA magnetic isolation module (NEB, #E7490) and libraries prepared with the NEBNext Ultra II Directional RNA Library Prep kit (NEB, #E7765) according to the manufacturer’s recommendations
Samples were individually barcoded during library preparation using NEBNext Multiplex Oligos for Illumina Index Primers Sets 1 and 2 (NEB, #E7335 and #E7500). Library quality control was performed with the DNA1000 kit (Agilent, #5067-1504) on the Agilent 2100 Bioanalyzer system.

treatment_protocol: Mice were treated with CLR457 and/or SHP099 from day 7 to day 21 after cell injection.

tag: breast cancer model

value: Balb/c

value: Mammary carcinoma


title: PI3Ki+SHP2i_5


title: PI3Ki+SHP2i_2


title: 11J_M_187

source_name: C57BL/6J Male P56 Mouse Brain


title: sc_ctrl_6h


title: sc_kd_0h


title: PI3Ki+SHP2i_1


title: 11J_M_185


title: 11J_M_186


title: 11J_M_184


title: CMs, replicate 5, 2

source_name: CMs

value: CMs


title: CMs, replicate 5, 1


title: merip_ctrl_11d_rep2

description:
merip_ctrl_11d_rep2
total-Ctrl-11d.txt

data_processing:
For MeRIP-seq, the m6A-enriched peaks in each m6A immunoprecipitation sample were identified by MACS2 peak-calling software (version 2.0.10).
MACS2 was run with default options except for nomodel to turn off fragment size estimation. A stringent cutoff threshold for P value of 0.001 was used to obtain high-confidence peaks. In each stage, peaks with over 50% overlap in 3 biological replicates were used in the downstream analysis.
Genome_build: Smed_20140614
Supplementary_files_format_and_content: peaks files

extract_protocol:
For m6A immunoprecipitation, the procedure was modified from the previously reported methods. In brief, purified mRNAs from control and mettl3 morphants were digested by DNase I and then fragmented into around 100-nt fragments by incubation at 94 °C for 1 min in fragmentation buffer (10 mM ZnCl2, 10 mM Tris-HCl, pH 7.0). The reaction was then stopped with 0.05 M EDTA (Ambion, AM8740), followed by standard ethanol precipitation and collection. Anti-m6A polyclonal antibody (12 μg antibody for 6 μg mRNAs; Synaptic Systems, 202003) was incubated with 50 μl Protein A beads (Sigma, P9424) in IPP buffer (150 mM NaCl, 0.1% NP-40, 10 mM Tris-HCl, pH 7.4) for 1 h at room temperature. Then the mRNAs (6 μg) were incubated with the prepared antibody-beads mixture for 4 h at 4 °C. After washing, bound RNAs were extracted by TRNzol.
Fragmented mRNA was used for library construction using the KAPA Stranded mRNA-Seq Kit (KAPA, K8401) according to the manufacturer’s protocol.

tag: rip antibody

value: anti-m6A polyclonal antibody (Synaptic Systems, 202003)


title: SHP2i_4


title: 11J_M_183

tag: brain region


title: VSMCs, replicate 2, 2

source_name: VSMCs


title: CMs, replicate 4, 2


title: sc_kd_7d

tag: age


title: CMs, replicate 4, 1


title: 11J_M_182

tag: strain


title: SHP2i_3

tag: tissue


title: PI3Ki+SHP2i_4


title: merip_ctrl_11d_rep1

description:
merip_ctrl_11d_rep1
total-Ctrl-11d.txt


title: merip_ctrl_7d_rep3

description:
merip_ctrl_7d_rep3
total-Ctrl-7d.txt


title: 11J_M_181


title: CMs, replicate 3, 2

tag: cell type


title: SHP2i_2


title: merip_ctrl_7d_rep2

description:
merip_ctrl_7d_rep2
total-Ctrl-7d.txt

tag: genotype


title: 11J_M_180


title: merip_ctrl_11d_rep3

description:
merip_ctrl_11d_rep3
total-Ctrl-11d.txt


title: merip_ctrl_3d_rep3

description:
merip_ctrl_3d_rep3
total-Ctrl-3d.txt


title: SHP2i_5


title: CMs, replicate 3, 1

tag: treatment


title: PI3Ki_5


title: PI3Ki_3


title: CMs, replicate 2, 2


title: PI3Ki_2


title: merip_ctrl_3d_rep2

description:
merip_ctrl_3d_rep2
total-Ctrl-3d.txt


title: CMs, replicate 2, 1


title: 11J_M_179


title: 11J_M_177


title: PI3Ki_1


title: 11J_M_178


title: CMs, replicate 1, 2


title: Vhc_5


title: merip_ctrl_3d_rep1

description:
merip_ctrl_3d_rep1
total-Ctrl-3d.txt


title: merip_ctrl_6h_rep3

description:
merip_ctrl_6h_rep3
total-Ctrl-6h.txt


title: 11J_M_176


title: Vhc_4


title: CMs, replicate 1, 1


title: merip_ctrl_6h_rep2

description:
merip_ctrl_6h_rep2
total-Ctrl-6h.txt


title: NCI-H295R, H3K27ac, EZH2i

description:
8_0695_00SUMichigan_Treated_H3K27Ac_hs-dm
Peak files are formatted as broadPeak

data_processing:
We used bowtie2 (Langmead and Salzberg, 2012) to align the reads to the hg38 and dm10 version of the human and fly genomes, respectively. Reads overlapping with blacklisted regions (defined by ENCODE), and reads with a mapping score < 20 were filtered.
BAM files were down-sampled to account for Drosophila spike-in control, enabling quantitative comparison of epitopes accounting for net chromatin recruitment across treatment conditions.
To perform ChIP-seq peak calling, we used SPAN and the JBR browser (Shpynov et al., 2021). These tools allow for empirical parameter adjustment after visual inspection of the peaks to obtain the best possible signal-to-noise ratio (FRIP).
BigWigs files were generated using deepTools 2.0 (Ramírez et al., 2016) with RPGC normalization.
Assembly: hg38/dm10
Supplementary files format and content: BigWig
Supplementary files format and content: broadPeaks - called peaks

organism:
Drosophila melanogaster
Homo sapiens

extract_protocol:
Cells were harvested for ChIP-seq with Drosophila melanogaster histone spike-in for all epitopes according to Active Motif's Epigenetic Services ChIP Cell Fixation protocol. Briefly, media was supplemented with 1/10 media volume of freshly prepared Formaldehyde Solution (11% formaldehyde, 0.1 M NaCl, 0.5 M EDTA pH 8.0, 1 M HEPES pH 7.9 in nuclease-free water), and plate was agitated for 15 minutes at room temperature. Fixation was stopped with addition of 1/20 volume of Glycine Solution (2.5 M Glycine, MW 75 in nuclease-free water) and incubating at room temperature for 5 minutes. Cells were then scraped, collected into a conical tube, and pelleted at 800xg at 4°C for 10 minutes. Supernatant was aspirated and each tube of cells was re-suspended in 10 mL chilled PBS-Igepal (0.5% Igepal CA-630 in PBS). Cell were pelleted again, supernatant aspirated, and cells resuspended in 10 mL chilled PBS-Igepal supplemented with 100 μL of 100 mM PMSF in ethanol. Cells were pelleted again, supernatant aspirated, snap frozen on dry ice, stored at -80°C, and shipped on dry ice to Active Motif Services (Carlsbad, CA) for chromatin preparation and ChIP-seq. Chromatin was isolated by addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and DNA sheared to an average length of 300-500 bp. Genomic DNA (Input) was prepared by treating aliquots of chromatin (pooled from all submitted samples) with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 μg) was precleared with protein A agarose beads (Invitrogen). Genomic DNA regions of interest were immunoprecipitated using the following antibodies: EZH2 (Active Motif, Cat. No. 39901; concentration 8 μL Ab/30 μg chromatin), H3K27me3 (ActiveMotif, Cat. No. 39155; concentration 4 μg Ab/30 μg chromatin), H3K27ac (ActiveMotif, Cat. No. 39133; concentration 4 μg Ab/30 μg chromatin), SF1 (EMD Millipore, Cat. No. 07-618; concentration 5 μg Ab/30 μg chromatin) and β-catenin (Invitrogen, Cat. No. 71-2700; concentration 4 μg Ab/30 μg chromatin). Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. Steps were performed on an automated system (Apollo 342, Wafergen Biosystems/Takara). After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina's NextSeq 500 (75 nt reads, single end).

treatment_protocol: NCI-H295R were plated in standard culture medium in 10 cm dishes at a density of 2.4 million cells per plate. To best account for biological variability, experiment was performed using 24 plates of cells total, where 16 plates were reserved for EZH2i administration at the IC-50 dose (62 μM EPZ-6438) and 8 plates were reserved for vehicle administration (equivalent volume of DMSO, these are considered "baseline" NCI-H295R). 24 hours after plating and daily thereafter, media was changed for media containing IC-50 EZH2i or vehicle. After approximately 96 hours of drug administration (120 hours post-plating), cells were harvested for ChIP-seq.

tag: cell line

value: human adrenocortical carcinoma

value: H3K27ac (Active Motif 39133)


title: 11J_M_175


title: Vhc_3


title: 11J_M_174


title: merip_ctrl_6h_rep1

description:
merip_ctrl_6h_rep1
total-Ctrl-6h.txt

value: planarian whole body


title: Vhc_2


title: merip_ctrl_7d_rep1

description:
merip_ctrl_7d_rep1
total-Ctrl-7d.txt

value: wild type


title: 11J_M_173


title: merip_ctrl_0d_rep3

description:
merip_ctrl_0d_rep3
total-Ctrl-0h.txt


title: NCI-H295R, H3K27ac, baseline

description:
7_0694_00SUMichigan_Untreated_H3K27Ac_hs-dm
Peak files are formatted as broadPeak

value: DMSO


title: Vhc_1


title: NCI-H295R, H3K27me3, EZH2i

description:
6_068M_00SUMichigan_Treated_H3K27me3_hs-dm
Peak files are formatted as broadPeak

value: H3K27me3 (Active Motif 39155)


title: merip_ctrl_0d_rep2

description:
merip_ctrl_0d_rep2
total-Ctrl-0h.txt


title: 11J_M_172


title: NCI-H295R, EZH2, EZH2i

description:
4_068K_00SUMichigan_Treated_EZH2_hs-dm
Peak files are formatted as broadPeak

value: EZH2 (Active Motif 39901)


title: NCI-H295R, H3K27me3, baseline

description:
5_068L_00SUMichigan_Untreated_H3K27me3_hs-dm
Peak files are formatted as broadPeak


title: 11J_M_171


title: merip_ctrl_0d_rep1

description:
merip_ctrl_0d_rep1
total-Ctrl-0h.txt


title: 11J_M_170


title: merip_kd_11d_rep3

description:
merip_kd_11d_rep3
total-kd-11d.txt

value: 11 dpa


title: NCI-H295R, EZH2, baseline

description:
3_068J_00SUMichigan_Untreated_EZH2_hs-dm
Peak files are formatted as broadPeak


title: NCI-H295R, β-catenin, EZH2i

description:
2_068I_00SUMichigan_Treated_bCatenin_hs-dm
Peak files are formatted as broadPeak

value: β-catenin (Invitrogen 71-2700)


title: merip_kd_11d_rep2

description:
merip_kd_11d_rep2
total-kd-11d.txt


title: 11J_M_169


title: merip_kd_11d_rep1

description:
merip_kd_11d_rep1
total-kd-11d.txt


title: NCI-H295R, β-catenin, baseline

description:
1_068H_00SUMichigan_Untreated_bCatenin_hs-dm
Peak files are formatted as broadPeak


title: 11J_M_168


title: 11J_M_167


title: NCI-H295R, SF1, EZH2i

description:
10_075I_00YIMichigan_Treated_SF-1_hs-dm
Peak files are formatted as broadPeak

value: SF1 (EMD Millipore 07-618)


title: merip_kd_7d_rep3

description:
merip_kd_7d_rep3
total-kd-7d.txt

value: 7 dpa


title: 11J_M_166


title: merip_kd_7d_rep2

description:
merip_kd_7d_rep2
total-kd-7d.txt

value: wtap knockdown


title: NCI-H295R, SF1, baseline

description:
09_075H_00YIMichigan_Untreated_SF-1_hs-dm
Peak files are formatted as broadPeak


title: 11J_M_165


title: renal cortex_db/db -rep2

type: RNA

city: Shanghai

first: Aili

last: Cao

state: Shanghai

address: 600 Yishan Road

institute: Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

description: Gene expression

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 22.5ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (4X44K) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Genespring(version13.1,Agilent Technologies)were employed to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the quantile algorithm. The probes that at least 100% of the values in any 1 out of all conditions have flags in Detected were chosen for further data analysis. Differentially expressed genes were then identified through fold change as well as P value calculated with t-test. The threshold set for up- and down-regulated genes was a fold change>= 2.0 and a P value<= 0.05. Afterwards, GO analysis and KEGG analysis were applied to determine the roles of these differentially expressed mRNAs. Finally, Hierarchical Clustering was performed to display the distinguishable genes' expression pattern among samples.

source_name: renal cortex, model gourp2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Micro-array gene expression analysis was used to identify the DEGs in renal cortex after HQD treatment. The samples (n=3 for each group) with TNA integrity number above 7 were accepted and performed by Wanyen Biotechnologies Inc. (Shanghai).

extract_protocol: Total RNA was extracted using a Trizol reagent (Invitrogen) and purified by Rnasey Mini Kit (Qiagen p/n 74104).

treatment_protocol: To further investigate the mechanism by which HQD exerts its reno-protective effects, we examined the changes in the glomerular transcriptome in db/db mice after 8 weeks of treatment with HQD using the high-throughput method.

value: renal cortex

value: db/db

tag: gender

value: male

value: 16 weeks


title: renal cortex_db/db -rep3

description: Gene expression

source_name: renal cortex, model gourp3


title: merip_kd_3d_rep3

description:
merip_kd_3d_rep3
total-kd-3d.txt

value: 3 dpa

value: anti-m6A polyclonal antibody (Synaptic Systems, 202003)


title: SLRSV_RNA2_Plant2 V.vinifera

description:
3' RACE-seq
Processed_Data_SECO_B2.txt

organism: Vitis vinifera

source_name: Infected leaves of V. vinifera

value: Infected leaves of V. vinifera

value: WT

value: SLRSV


title: merip_kd_7d_rep1

description:
merip_kd_7d_rep1
total-kd-7d.txt

value: planarian whole body


title: lmo1_TATATATA_MYCN_2

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

data_processing:
RNA-Seq reads were aligned to the danRer10 revision of the zebrafish reference genome using hisat2 version 2.1.0 (PMID 31375807) in paired-end mode. Reads in v90 of GRCz10 Ensembl genes were quantified using htseq-count (PMID 25260700) with parameters -i gene_name --stranded=reverse -m intersection-strict. Expression as reads normalized by kilobase of exon per million mapped reads (RPKM) were calculated by counting the number of non-redundant basepairs in all isoforms of each gene with the same gene name.
Assembly: danRer10
Supplementary files format and content: RPKM files contain gene name, read count, total exon length, and reads-per-kilobase-of-exon-per-million-reads--normalized values

organism: Danio rerio

source_name: neuroblastoma

growth_protocol: All zebrafish studies and maintenance were done in accord with Dana-Farber Cancer Institute IACUC-approved protocol (#02-107). EGFP+ neuroblastoma cells were harvested from tumor-bearing MYCN transgenic zebrafish. Tumors were mechanically homogenized and EGFP+ cells were sorted.

extract_protocol:
Tumors were extractyed and EGFP+ cells were sorted. Total RNA was extracted using the QIAzol lysis reagent (Qiagen) and was cleaned using the RNeasy kit (Qiagen). Samples were treated with the TURBO DNase (TURBO DNA-free Kit; Ambion) and cleaned using the RNeasy MinElute Cleanup kit (Qiagen).Total RNA was depleted of ribosomal RNA with the SMARTer Universal Low Input RNA Kit (Clontech). Enriched mRNA was then applied to library preparation according to manufacturer’s protocol (NEBNext Ultra). Strand-specific library construction and Illumina NextSeq 500 sequencing of paired-end 100-bp-long reads were performed.
Library preparation, quality control, and next-generation sequencing were conducted by the Molecular Biology Core Facility of the Dana-Farber Cancer Institute following standard protocols.

treatment_protocol: To generate stable zebrafish lines carrying the TATA allele in the first intron of lmo1, Transcription Activator-Like Effector Nuclease (TALEN) recognition sequences were designed to bind to the first intron of lmo1 surrounding the GATA site: TALEN1 5'-TACGACTGATTTGATTTT-3' and TALEN2 5'-TTCATTTCAAGTTCCAT-3'. TALEN expression vectors harboring a wild-type FokI nuclease were generated as previously described (Cade et al., Nucleic Acids Res., 2012 ), linearized by PmeI and used as templates for TALEN mRNA synthesis using the mMessage mMachine T3 Kit (Ambion). For the targeted integration of the TATA allele, a 41-nucleotide single-stranded oligonucleotide containing the T-allele sequence with 20 flanking nucleotides on either side of the T was designed. Equal amounts of TALEN1 and 2 mRNA (100 ng/L) together with 100pg of oligonucleotide were injected together into 1-cell-stage zebrafish embryos. To identify positive founder fish with a successful TATA knock-in, germline DNA was extracted by tail clip, and the DNA fragment surrounding the TATA site was amplified by PCR and analyzed.  The lmo1 knockout zebrafish line (lmo1-/-) was generated by using CRISPR-Cas9 genome editing technology, targeting exon 2 (Hwang et al., Nature Biotechnology, 2013). The following lmo1 exon 2 CRISPR site was designed using a CRISPR Design web tool (http://crispr.mit.edu):  5′-GGAGAGGGAGATCAGATCGA-3′, CRISPR gRNA was prepared by the cloning-free, single-guide RNA synthesis method (61) using the Ambion T7 MEGAscript Kit (AM1334M, Ambion) and purified with the Qiagen miRNeasy Kit (217004, Qiagen). Cas9 nuclease was purchased from New England Biolabs (M0386T). Each embryo was injected with 1 nl of solution containing lmo1-specific gRNA (60 ng/ul) and Cas9 (30 ng/ul) at the one-cell stage. Mosaic F0 fish with germline mutation were identified, and stable mutant lines were established by outcrossing.

value: neuroblastoma

value: EGFP+ neuroblastoma cells


title: lmo1_TATATATA_MYCN_1


title: SLRSV_RNA2_Plant1 V.vinifera

description:
3' RACE-seq
Processed_Data_SECO_B2.txt


title: 11J_M_163


title: lmo1_KO_MYCN_3


title: renal cortex_db/m -rep3

description: Gene expression

source_name: renal cortex, control gourp3

value: db/m


title: merip_kd_3d_rep2

description:
merip_kd_3d_rep2
total-kd-3d.txt


title: 11J_M_162


title: lmo1_KO_MYCN_2


title: merip_kd_3d_rep1

description:
merip_kd_3d_rep1
total-kd-3d.txt


title: GFLV_B844_RNA1&2 V. vinifera_Plant3

description:
3' RACE-seq
Processed_Data_SECO_B2.txt

value: GFLV


title: GFLV_B844_RNA1&2 V. vinifera_Plant2

description:
3' RACE-seq
Processed_Data_SECO_B2.txt


title: lmo1_KO_MYCN_1


title: 11J_M_161


title: renal cortex_db/m -rep2

description: Gene expression

source_name: renal cortex, control gourp2


title: merip_kd_6h_rep3

description:
merip_kd_6h_rep3
total-kd-6h.txt

value: 6 hpa


title: 11J_M_160


title: renal cortex_db/db -rep1

description: Gene expression

source_name: renal cortex, model gourp1


title: GFLV_B844_RNA1&2 V. vinifera_Plant1

description:
3' RACE-seq
Processed_Data_SECO_B2.txt


title: renal cortex_db/m -rep1

description: Gene expression

source_name: renal cortex, control gourp1


title: 11J_M_159


title: merip_kd_6h_rep2

description:
merip_kd_6h_rep2
total-kd-6h.txt


title: SLRSV_RNA2_Plant3 V.vinifera

description:
3' RACE-seq
Processed_Data_SECO_B2.txt


title: ARMV_RNA1&2 V. vinifera_Plant2

description:
3' RACE-seq
Processed_Data_SECO_B2.txt

value: ARMV


title: merip_kd_6h_rep1

description:
merip_kd_6h_rep1
total-kd-6h.txt

value: wtap knockdown


title: 11J_M_158


title: 11J_M_164


title: merip_kd_0h_rep3

description:
merip_kd_0h_rep3
total-kd-0h.txt

value: 0 hpa


title: merip_kd_0h_rep2

description:
merip_kd_0h_rep2
total-kd-0h.txt


title: merip_kd_0h_rep1

description:
merip_kd_0h_rep1
total-kd-0h.txt


title: TBRV_RNA2_Plant2

description:
3' RACE-seq
Processed_Data_SECO_B2.txt

value: TBRV


title: ARMV_RNA1&2 V. vinifera_Plant1

description:
3' RACE-seq
Processed_Data_SECO_B2.txt


title: TBRV_RNA1&2_Plant1

description:
3' RACE-seq
Processed_Data_SECO_B2.txt


title: GFLV B844 biol rep 3

data_processing:
Fastq files were analyzed by a homemade pipeline adapted from Scheer et al. 2021 composed of scripts using python (v2.7), biopython (v1.63) and regex (v2.4) libraries.
Python and bash source code are available in github (https://github.com/hzuber67/RACEseq_virus)
Assembly: cf the associated publication
Supplementary files format and content: Two processed data file is given. They includes the processed data for the analyzed 21 virus, the poladenylated RNA virus  (Processeddata_polyA_allvirus_B1B2.txt), and the non polyadenylated virus (Processeddata_nonpolyA_allvirus_A.txt) for each genotype and biological replicate. Each line corresponds to one individual reads.
Supplementary files format and content: For each read, we indicate read ID (read.ID), Virus RNA name (Target), poly(A) tail sequence (polyA), poly(A) tail length (polyA.size), non-A extension sequence (modification), length of the non-A extension (modification.size), tail sequence (extension),  tail size (extension.size), a tag (classification) indicating the category of the tail, the 15N random sequence used for deduplication (random), barcode, biological replicate (Plant), Virus RNA (RNA), infected plant (Host) and Virus name (Virus).

extract_protocol:
Total RNA from infected leaves of C. quinoa, N. benthamiana and grapevine were extracted using the RNeasy plant Mini Kit (Qiagen). Total RNA of Arabidopsis infected leaves was extracted using Tri-Reagent (Molecular Research Center).
3' RACE-seq
3'RACEseq protocol is based on the ligation of a primer at the 3’ end of RNA, and the subsequent targeted amplification by PCR of amplicons suitable for Illumina sequencing.

value: GFLV B844


title: RNA_kd_11d_rep3

description:
RNA_kd_11d_rep3
all_rpkm.txt

data_processing:
Adaptor sequences were trimmed off for all raw reads using the Cutadapt software (version 1.2.1). Reads that were less than 18 nt in length or contained an ambiguous nucleotide were discarded by Trimmomatic (version 0.30) .
The remaining reads were   aligned to the Schmidtea mediterranea transcriptome smed_20140614 using Bowtie2 v2.2.9 default parameters.
Genome_build: Smed_20140614
Supplementary_files_format_and_content: rpkm for samples

extract_protocol:
Total RNA was isolated from planarain at different time points with TRIzol reagent and mRNA was further purified using Dynabeads mRNA purification kit (Ambion, 61006). Fragmented mRNA was used for library construction using the KAPA Stranded mRNA-Seq Kit (KAPA, K8401) according to the manufacturer’s protocol.
Fragmented mRNA was used for library construction using the KAPA Stranded mRNA-Seq Kit (KAPA, K8401) according to the manufacturer’s protocol.

value: 11 dpa


title: GFLV B844 biol rep 2


title: RNA_kd_11d_rep2

description:
RNA_kd_11d_rep2
all_rpkm.txt


title: RNA_kd_11d_rep1

description:
RNA_kd_11d_rep1
all_rpkm.txt


title: GFLV B844 biol rep 1


title: GRGV biol rep 2

value: GRGV


title: 11J_M_152


title: 11J_M_155


title: 11J_M_153


title: RNA_kd_7d_rep3

description:
RNA_kd_7d_rep3
all_rpkm.txt

value: 7 dpa


title: 11J_M_151


title: GRGV biol rep 1

value: Infected leaves of V. vinifera


title: GPGV biol rep 3

value: WT

value: GPGV


title: 11J_M_150


title: RNA_kd_7d_rep2

description:
RNA_kd_7d_rep2
all_rpkm.txt

value: planarian whole body


title: RNA_kd_7d_rep1

description:
RNA_kd_7d_rep1
all_rpkm.txt


title: GPGV biol rep 2


title: 11J_M_148


title: 11J_M_149


title: 11J_M_157


title: RNA_kd_3d_rep2

description:
RNA_kd_3d_rep2
all_rpkm.txt

value: 3 dpa


title: GVB biol rep 2

value: GVB


title: 11J_M_147


title: RNA_kd_3d_rep3

description:
RNA_kd_3d_rep3
all_rpkm.txt


title: RNA_kd_3d_rep1

description:
RNA_kd_3d_rep1
all_rpkm.txt


title: GVB biol rep 1, GPGV biol rep 1

value: GVB, GPGV


title: 11J_M_156


title: 11J_M_146


title: RNA_kd_6h_rep3

description:
RNA_kd_6h_rep3
all_rpkm.txt


title: 11J_M_145


title: GRSPaV biol rep 1

value: GRSPaV


title: ATH1057

description:
RNA-seq
gene_exp.diff

data_processing:
PARE libraries (Illumina HiSeq 2500); GMUCT and RNA-seq libraries (Illumina NextSeq 550)
Reads were mapped to Arabidopsis TAIR10 genome using Tophat v2.0
PARE and GMUCT libraries were analyzed as per Hurtig et al., 2021 (PNAS) using the ComPARE pipeline
Bedgraph files contain ComPARE scores from PARE and GMUCT libraries comparing normalized abundances (expressed as counts per million, CPM) at every 5'P site between Col-0, xrn4 and mfl1xrn4
Genome_build: Arabidopsis TAIR10 (Ensemble v49)
Supplementary_files_format_and_content: RNA-seq: gene_exp.diff is a cuffdiff output file; PARE and GMUCT: Genomic coordinate file (with annotations) containing RNA Degradome scores where 5'P site CPM >= 1 in xrn4 in both replicates (bedgraph files)

source_name: two-week-old seedlings

extract_protocol: PARE libraries were prepared as per Nagarajan et al., (2019); GMUCT libraries were prepared according to Wilmann et al., 2014 with modifications suggested in Carpentier et al., 2021; RNA-seq libraries: 50 ug polyA+ RNA (2x enriched) prepared as per NEBNext Ultra II Directional Library Preparation kit;

tag: ecotype

tag: genotype/variation

tag: rep


title: 11J_M_154


title: RNA_kd_6h_rep2

description:
RNA_kd_6h_rep2
all_rpkm.txt

value: 6 hpa


title: 11J_M_144


title: ATH1056

description:
RNA-seq
gene_exp.diff


title: RNA_kd_0d_rep3

description:
RNA_kd_0d_rep3
all_rpkm.txt


title: ATH1055

description:
RNA-seq
gene_exp.diff


title: ATH1054

description:
RNA-seq
gene_exp.diff


title: 11J_M_142


title: RNA_kd_0d_rep2

description:
RNA_kd_0d_rep2
all_rpkm.txt


title: 11J_M_141


title: RNA_kd_6h_rep1

description:
RNA_kd_6h_rep1
all_rpkm.txt


title: 11J_M_143


title: RNA_kd_0d_rep1

description:
RNA_kd_0d_rep1
all_rpkm.txt


title: 11J_M_140


title: ATH1052

description:
RNA-seq
gene_exp.diff


title: 11J_M_139


title: RNA_11d_rep2

description:
RNA_11d_rep2
all_rpkm.txt

value: wild type


title: 11J_M_136


title: ATH1050

description:
RNA-seq
gene_exp.diff


title: ATH1048

description:
RNA-seq
gene_exp.diff


title: 11J_M_135


title: 11J_M_137


title: RNA_11d_rep1

description:
RNA_11d_rep1
all_rpkm.txt


title: RNA_7d_rep1

description:
RNA_7d_rep1
all_rpkm.txt


title: Head input, standard conditions, rep 3

first: Monica

last: Dus

address: 1150 N. University Ave.

department: Department of Molecular, Cellular and Developmental Biology

institute: The University of Michigan

description:
input
3749_CLIP-3.096-onecovary-log.bed
DW-2C

data_processing:
Trim adaptors, fastx clipper v. 0.0.14
Remove PCR duplicates and remove UMI
Map reads to genome dm6, STAR v 2.7.5a
Peak call, Piranha v 1.2.1
Assembly: Ensembl/BDGP6
Supplementary files format and content: peak calls modified bed format
Supplementary files format and content: normalized bigwig data

organism: Drosophila melanogaster

source_name: Heads

growth_protocol: All flies were maintained at 25°C in a humidity-controlled incubator with a 12:12 hr light/dark cycle. Animals were fed Bloomington Food B (cornmeal-glucose) ad-lib and provided fresh food every other day.

extract_protocol:
800 fly heads were isolated from bodies by sieving for CLIP. All samples were stored at -80 C. Phenol-chloroform (Invitrogen 15596018) and RIPA buffer (150 mm NaCl, 1% Nonidet P-40, 0.5% Sodium deoxycholate, 0.1% SDS, 50mM Tris pH 7.5) were added to frozen samples and homogenized by bead bashing (Bead Ruptor, 19-040E). Phenol-chloroform extracted RNA was precipitated by isopropanol with GlycoBlue coprecipitant (Invitrogen AM9515). RNA was stored at -80C until further processing.
20 ug of poly(A) selected (Invitrogen, 61012) RNA for each biological replicate from heads (~800, W1118cs) of flies was used as input to the CLIP reaction. Fragmented RNA (Ambion E6150S) was incubated for 2 hr at 4 C with antibody against m6A (Abcam, ab151230), UV-crosslinked, then immunoprecipated with magnetic beads (Invitrogen, 10004D). Pre-adenylated dye-conjugated linkers were ligated (NEB M0351S) to dephysophorylated 3’ ends of RNA fragments overnight at 16 C. RNA was extracted with NuPAGE SDS buffer and separated by NuPAGE gel (Invitrogen, NP0321), transferred to nitrocellulose membrane and visualized for excision at 800 nm. RNA-antibody complexes were released from the membrane by proteinase K digestion and RNA was purified with phenol chloroform extraction. RNA was reverse transcribed (Invitrogen, 18080085), circulized (Lucigen, CL4111K), PCR-amplified (Thermo Scientific, F530S). Libraries were subjected to 151bp paired-end sequencing according to the manufacturer’s protocol on an Illumina NovaSeq 6000 at the University of Michigan sequencing core.
CLIP-seq

value: Heads

value: male and female

value: neurons

value: standard diet


title: ATH1049

description:
RNA-seq
gene_exp.diff


title: RNA_7d_rep3

description:
RNA_7d_rep3
all_rpkm.txt


title: RNA_3d_rep3

description:
RNA_3d_rep3
all_rpkm.txt


title: RNA_7d_rep2

description:
RNA_7d_rep2
all_rpkm.txt


title: Head input, standard conditions, rep 2

description:
input
3749_CLIP-2.099-onecovary-log.bed
DW-2B


title: ATH1046

description:
RNA-seq
gene_exp.diff


title: ATH1047

description:
RNA-seq
gene_exp.diff


title: 11J_M_133


title: 11J_M_134


title: RNA_3d_rep2

description:
RNA_3d_rep2
all_rpkm.txt


title: ATH1087

description:
GMUCT
Seedling_PARE_scores.bg


title: ATH1086

description:
GMUCT
Seedling_PARE_scores.bg


title: ATH1053

description:
RNA-seq
gene_exp.diff


title: 11J_M_132


title: Head input, standard conditions, rep 1

description:
input
3749_CLIP-1.093-onecovary-log.bed
DW-2A


title: RNA_11d_rep3

description:
RNA_11d_rep3
all_rpkm.txt

value: 11 dpa


title: ATH1051

description:
RNA-seq
gene_exp.diff


title: Head, standard conditions, rep 3

description:
clip
3749_CLIP-3.096-onecovary-log.bed
DW-1C


title: 11J_M_131


title: ATH1085

description:
GMUCT
Seedling_PARE_scores.bg


title: 11J_M_138


title: RNA_6h_rep3

description:
RNA_6h_rep3
all_rpkm.txt


title: Head, standard conditions, rep 2

description:
clip
3749_CLIP-2.099-onecovary-log.bed
DW-1B


title: Head, standard conditions, rep 1

description:
clip
3749_CLIP-1.093-onecovary-log.bed
DW-1A


title: RNA_6h_rep2

description:
RNA_6h_rep2
all_rpkm.txt


title: ATH1084

description:
GMUCT
Seedling_PARE_scores.bg


title: 11J_M_129


title: RNA_6h_rep1

description:
RNA_6h_rep1
all_rpkm.txt


title: ATH1082

description:
GMUCT
Seedling_PARE_scores.bg


title: RNA_0d_rep3

description:
RNA_0d_rep3
all_rpkm.txt

value: 0 hpa


title: OS10

city: Fort Collins

first: Dylan

middle: T

last: Ammons

state: CO

address: 200 W Lake St

department: MIP

institute: Colorado State University

description: 10x Genomics

data_processing:
Demultiplexing, barcode processing, and gene counting was completed using Cell Ranger software v7.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). Data were loaded in as a Seurat object then QC filtered to only retain cells which met the following requirements: 200 < nFeature_RNA < 3500, percent.mt < 20, and 100 < nCount_RNA < 15000. Unsupervised clustering was completed on the complete dataset, then on each major immune cell type (CD4 T cells, CD8/NK cells, Myeloid, and B cells). The final processed Seurat objects are provided as 'final_dataSet_H.rds' (Healthy only) and 'final_dataSet_HvO.rds' (Healthy and osteosarcoma PBMCs). Each major immune cell type subset is provided where 'cytotoxic.rds' = CD8/NK cell, 'helper.rds' = CD4 T cells, 'myeloid.rds' = Myeloid, and 'bcell.rds' = B cells. All analysis code used to complete the analysis can be found at: https://github.com/dyammons/Canine_Leukocyte_scRNA .
Assembly: canFam3.1
Supplementary files format and content: Tab-separated values files and matrix files

organism: Canis lupus familiaris

source_name: PBMC

extract_protocol:
Approximately 10-mL of canine whole blood was obtained in EDTA collection tubes then processed within 30 minutes using Ficoll Paque to complete density gradient centrifugation. Whole blood was mixed with 12 mL of phosphate buffered saline, pH = 7.40, then layered onto 12 mL of Ficoll Paque. To isolated leukocytes, the layered sample was then centrifugated at room temperature for 40 minutes at 500 rcf with acceleration at maximum and brake off. Cells were washed, red blood cells lysed, and the sample prepared to be run on a Chromium iX instrument by resuspending in 0.04% molecular grade BSA. The instrument was loaded to target 5,000 cells per sample.
Library construction was performed according to the manufacturer’s instructions (Chromium Next GEM Single Cell 3ʹ Kit v3.1 protocol, 10x Genomics). Briefly, a Chromium iX instrument was used to pass cells and oligonucleotide coated gel beads at a limiting dilution to obtain a coupling of cells and beads in a 1:1 ratio. The cell-bead pair was then passed from an aqueous phase to an oil phase to form an emulsion. Within the emulsions, cells were lysed, and the oligonucleotide sequences on the gel beads pull down message RNA and other RNA molecules that have long adenosine stretches with an oligo-d(T) pull down. After hybridization, reverse transcription is completed to generate a cDNA library with each transcript now associated with a unique cell barcode and an Illumina R1 primer sequence.  Once cells were barcoded and unique molecular identifiers (UMIs) added, a standard Illumina library preparation kit was completed with SPRIselect used for fragment size selection. During the library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: PBMC

value: Primary

value: Immune

value: Wt

tag: disease state

value: osteosarcoma


title: RNA_0d_rep2

description:
RNA_0d_rep2
all_rpkm.txt

value: planarian whole body


title: A9161 ssKECs

city: Boston

first: Robert

last: Policastro

state: Massachusetts

address: 451 D St Unit #600

institute: Ensoma Inc.

data_processing:
Transcript sequences were generated with gffread (0.12.7) using a modified ENSEMBL Sscrofa11.1 FASTA assembly and v105 GTF annotation with unplaced contigs/scaffolds removed, and PL15S FASTA sequence and GTF annotation added as needed as a separate contig.
RNA-seq read counts were quantified at the transcript level with Salmon (1.6.0) with custom settings: whole genome used as decoy, 100 bootstrap replicates, and GC content and sequence bias correction applied.
Transcript abundances were aggregated to gene level using tximport (1.22.0) and only protein coding and lncRNA genes were retained.
Normalized rlog counts were generated with DESeq2 (1.34.0) using sample type (I.e. CD31-, ssKEC) and Pig ID as unblinded covariates.
Assembly: Sscrofa 11.1
Supplementary files format and content: TAR directory containing standard Salmon quantification output.
Supplementary files format and content: R RDS format file containing a DESeq2 dataset with metadata, raw, and rlog normalized counts.

organism: Sus scrofa

source_name: Kidney

extract_protocol:
Media was aspirated, plates were washed with 1X PBS, then treated with TrypLE Express (12604013, ThermoFisher) at 37 °C for 3 minutes. Detachment was facilitated by gentle tapping on the sides of the dish, and cells were checked under a microscope to ensure complete lifting. Cells were suspended in pre-warmed endothelial cell media to neutralize the trypsin and centrifuged at 400xg at RT for 4 minutes. Supernatant was aspirated. Cell pellets were resuspended in 1-2 mL 1X PBS, counted via trypan blue exclusion on the LUNA-II Automated Cell Counter (L40002, Logos Biosystems), and centrifuged again at 400xg at RT for 4 minutes. Supernatants were aspirated and the pellets were lysed directly in 350 µL Buffer RLT Plus (1053393, QIAGEN). Each sample was then passed through a QIAshredder (79656, QIAGEN) by centrifuging at 18,000 rcf for 2 minutes. Total RNA was isolated from each homogenized lysate using the RNeasy Plus Mini Kit (74134, QIAGEN) following manufacturer’s protocol. Purified RNA were eluted in 30-50 µL RNAse-free water.
RNA integrity and quantity was assessed using an automatic electronic Electrophoresis system (4200 Tapestation, Agilent) and reagents (5067-5578, Agilent), and spectrophotometer (DS-11 Spectrophotometer, DeNovix). Upon passing quality checks, library was generated using the Illumina Stranded mRNA kit (20040534, Illumina) on 500 ng of total RNA input. Library concentrations were quantified by using the Qubit 3 (Q33216, Invitrogen) high sensitivity dsDNA assay (Q33231, Invitrogen), diluted to a final loading concentration of 650 pM, and sequenced on an Illumina NextSeq 2000 using a P3 100 cycle reagent kit (20040559, Illumina).

value: Kidney

value: Endothelial

value: 3KO, PL15S, RI

value: CD31+ Double sorted


title: 11J_M_128

city: La Jolla

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute


title: OS8

description: 10x Genomics


title: RNA_0d_rep1

description:
RNA_0d_rep1
all_rpkm.txt

value: wild type


title: A9161 CD31-neg KCs

value: Non-endothelial

value: CD31- Single sorted


title: SV40 MEF E2f1-ko Q 4 (16koQ4)

city: Lausanne

first: Lluis

last: Fajas

address: UNIL Sorge

institute: UNIL

data_processing:
Sequencing data were demultiplexed using the bcl2fastq2 Conversion Software (version 2.20, Illumina).
Assembly: Mus_musculus.GRCm38.102
Supplementary files format and content: .txt
Supplementary files format and content: FPKM of all samples

source_name: SV40-immortalized MEF

growth_protocol: MEFs were maintained in standard growth media (DMEM 41966-062, Thermo Fisher Scientific) supplemented with 10% heat-inactivated fetal bovine serum (FBS, SV30160.03, Lot No. RB35956, HyClone, GE Healthcare Life Sciences) at 37°C in a 5% CO2 incubator.

extract_protocol:
To investigate gene expression, SV40 immortalized MEFs were plated in triplicates in 60 mm dishes (430166, Corning) in 4 ml standard growth media. After 24 hours, MEFs were washed once with 4 ml D-PBS (14190169, Thermo Fisher Scientific) and RNA was isolated using the TRI reagent (T9424, Sigma-Aldrich, Thermo Fisher Scientific) according to the manufacturer's protocols. RNA concentrations were determined with a NanoDrop 8000 (Thermo Fisher Scientific).
RNA quality was assessed on a Fragment Analyzer (Agilent Technologies) and all RNAs had a RQN above 9.3. RNA-seq libraries were prepared from 500 ng of total RNA with the Illumina TruSeq Stranded mRNA reagents (Illumina) using a unique dual indexing strategy, and following the official protocol.
Libraries were quantified by a fluorimetric method (QubIT, Life Technologies) and their quality assessed on a Fragment Analyzer (Agilent Technologies). Sequencing was performed on an Illumina NovaSeq 6000 for 100 cycles single read.

treatment_protocol: MEFs were cultivated with DMEM without glucose, glutamine, phenol red, and sodium pyruvate (A14430-01, Thermo Fisher Scientific) supplemented with 10% dialyzed and filtered FBS (26-400-044, Thermo Fisher Scientific), and either 25 mM glucose (G8769, Sigma-Aldrich) and 4 mM glutamine (25030-024, Thermo Fisher Scientific) or only 4 mM glutamine for 16 hours.

value: SV40-immortalized MEF

value: mouse embryonic fibroblasts

value: depletion media (DMEM 4mM glutamine no glucose)


title: SV40 MEF E2f1-ko Q 3 (15koQ3)


title: 9-3 ssKECs

value: WT


title: SV40 MEF E2f1-ko Q 2 (14koQ2)


title: sheep3-RAD.RNAseq

city: Chengdu

first: jin

last: long

address: Hui ming

institute: Sichuan Agricultural University

data_processing:
Contacts matrix were generated by using Juicer pipeline.
Gene-level expression was estimated as transcripts per million (TPM) using the high-speed transcript quantification tool Kallisto (version 0.43.0).
Tpm and counts matrixs were generated using R vresion 3.6.1.
TADs were identified using  Insulation Score.
Compartment A/B were defined by A-B index.
Assembly: Susscrofa11.1
Supplementary files format and content: Binned raw and normalized 2D contact matrices text files
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Genes expression level (TPM) and counts text file
Supplementary files format and content: TAD files
Supplementary files format and content: ABindex files

organism: Ovis aries

source_name: retroperitoneal adipose

extract_protocol:
Briefly, total RNA was extracted from each sample using the RNeasy Mini Kit (Qiagen, Valencia, CA, USA). Concentration and purity were quantified by Nanodrop, and integrity was evaluated using an Agilent 2000.
Then, RNA-seq libraries were generated using a rRNA depletion method (Globin-Zero Gold rRNA Removal Kit, Illumina, San Diego, CA, USA) coupled with a NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, Ipswich, MA, USA). The libraries were sequenced by the HiSeq X Ten platform (Illumina) with a paired-end sequencing length of 150 bp.

tag: breed

value: Small-tail Han sheep

tag: developmental stage

value: Adult

value: retroperitoneal adipose


title: RNA_3d_rep1

description:
RNA_3d_rep1
all_rpkm.txt

value: 3 dpa


title: OS6

description: 10x Genomics

value: PBMC

value: Primary

value: Immune

value: Wt

value: osteosarcoma


title: sheep3-MAD.RNAseq

source_name: mesenteric adipose

value: mesenteric adipose


title: SV40 MEF E2f1-ko Q 1 (13koQ1)


title: 21287 ssKECs

value: Kidney

value: Endothelial

value: CD31+ Double sorted


title: OS5

description: 10x Genomics


title: 11J_M_130

source_name: C57BL/6J Male P56 Mouse Brain


title: SV40 MEF E2f1-wt Q 3 (11wtQ3)

value: SV40-immortalized MEF


title: CPMV_RNA2_Plant3; BBWV_RNA1_Plant3; RpRSV_RNA1&2_Plant3

city: Strasbourg

first: Dominique

last: Gagliardi

address: 12, rue du General Zimmer

institute: CNRS

description:
3' RACE-seq
Processed_Data_SECO_B2.txt

data_processing:
Fastq files were analyzed by a homemade pipeline adapted from Scheer et al. 2021 composed of scripts using python (v2.7), biopython (v1.63) and regex (v2.4) libraries.
Python and bash source code are available in github (https://github.com/hzuber67/RACEseq_virus)
Assembly: cf the associated publication
Supplementary files format and content: A processed data file is given. It includes the processed data for the analyzed Secoviridae viruses for each biological replicate. Each line corresponds to one individual reads.
Supplementary files format and content: For each read, we indicate read ID (read.ID), Virus RNA name (Target), poly(A) tail sequence (polyA), poly(A) tail length (polyA.size), non-A extension sequence (modification), length of the non-A extension (modification.size), tail sequence (extension),  tail size (extension.size), a tag (classification) indicating the category of the tail, the 15N random sequence used for deduplication (random), barcode, plant genotype (WT, urt1-1, heso1-3, heso1-3 urt1-1), biological replicate (Plant), Virus RNA (RNA), infected plant (Host) and Virus name (Virus).

organism:
Nicotiana benthamiana
Vitis vinifera
Chenopodium quinoa

source_name: Infected leaves of C. quinoa, N. benthamiana and V. vinifera

extract_protocol:
Total RNA from infected leaves were extracted using the RNeasy plant Mini Kit (Qiagen).
3'RACE-seq
3'RACEseq protocol is based on the ligation of a primer at the 3’ end of RNA, and the subsequent targeted amplification by PCR of amplicons suitable for Illumina sequencing.

value: CPMV; BBWV; RpRSV; TBRV


title: OS4

description: 10x Genomics


title: sheep3-GOM.RNAseq

source_name: greater omentum fat

value: greater omentum fat


title: ATH1083

city: Newark

first: Pamela

last: Green

address: 15 Innovation Way

institute: Delaware Biotechnology Institute

description:
GMUCT
Seedling_PARE_scores.bg


title: OS3

description: 10x Genomics


title: SV40 MEF E2f1-wt Q 2 (10wtQ2)

value: mouse embryonic fibroblasts

value: depletion media (DMEM 4mM glutamine no glucose)


title: CPMV_RNA2_Plant2; BBWV_RNA1_Plant2; RpRSV_RNA1&2_Plant2

description:
3' RACE-seq
Processed_Data_SECO_B2.txt

value: Infected leaves of C. quinoa, N. benthamiana and V. vinifera

value: WT


title: sheep2-MAD.RNAseq

value: Small-tail Han sheep

value: Adult


title: OS9

description: 10x Genomics

value: PBMC

value: Primary


title: OS2

description: 10x Genomics

value: Immune

value: Wt


title: SV40 MEF E2f1-wt Q 1 (9wtQ1)


title: sheep2-GOM.RNAseq


title: CPMV_RNA2_Plant1; BBWV_RNA1_Plant1; RpRSV_RNA1&2_Plant1; TBRV_RNA2_Plant2

description:
3' RACE-seq
Processed_Data_SECO_B2.txt


title: OS7

description: 10x Genomics

value: osteosarcoma


title: OS1

description: 10x Genomics


title: SV40 MEF E2f1-ko GQ 4 (8koGQ4)

value: standard growth media (DMEM 25 mM glucose and 4 mM glutamine)


title: sheep1-RAD.RNAseq

value: retroperitoneal adipose


title: sheep1-MAD.RNAseq

value: mesenteric adipose


title: H7

description: 10x Genomics

value: healthy


title: H6

description: 10x Genomics


title: SV40 MEF E2f1-ko GQ 3 (7koGQ3)

value: SV40-immortalized MEF


title: SV40 MEF E2f1-ko GQ 2 (6koGQ2)


title: sheep1-GOM.RNAseq

value: greater omentum fat


title: 21287 CD31-neg KCs

value: Kidney

value: Non-endothelial

value: CD31- Single sorted


title: SV40 MEF E2f1-ko GQ 1 (5koGQ1)

value: mouse embryonic fibroblasts


title: SV40 MEF E2f1-wt Q 4 (12wtQ4)

value: depletion media (DMEM 4mM glutamine no glucose)


title: H5

description: 10x Genomics


title: SV40 MEF E2f1-wt GQ 4 (4wtGQ4)


title: sheep2-RAD.RNAseq

value: Small-tail Han sheep

value: Adult


title: SV40 MEF E2f1-wt GQ 3 (3wtGQ3)


title: H3

description: 10x Genomics

value: PBMC

value: Primary


title: H4

description: 10x Genomics

value: Immune

value: Wt


title: TRSV_RNA1_Plant1; CLRV_RNA1_Plant1; SLRSV_RNA1_Plant1_C.quinoa

description:
3' RACE-seq
Processed_Data_SECO_B2.txt

organism:
Vitis vinifera
Chenopodium quinoa

source_name: Infected leaves of C. quinoa and V. vinifera

value: WT

value: TRSV; CLRV; SLRSV


title: H2

description: 10x Genomics


title: ARMV_RNA1&2 V. vinifera_Plant3, SLRV_RNA1 Plant3 V.vinifera; CNDV Plant2 N. benthamiana

description:
3' RACE-seq
Processed_Data_SECO_B2.txt

value: Infected leaves of C. quinoa and V. vinifera

value: ARMV; SLRSV; CNDV


title: H1

description: 10x Genomics

value: healthy


title: SV40 MEF E2f1-wt GQ 2 (2wtGQ2)

value: SV40-immortalized MEF

value: standard growth media (DMEM 25 mM glucose and 4 mM glutamine)


title: SV40 MEF E2f1-wt GQ 1 (1wtGQ1)


title: KNO3_3_1_4

city: BeiJing

first: huairong

last: cao

state: Haidian

address: West Yuanmingyuan Road

institute: China Agricultural University

data_processing:
The library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
The paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach.
Assembly: B73RefGen_v4
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Zea mays

source_name: root

extract_protocol:
Total RNA was extracted with RNAiso Plus (Takara Biomedical Technology Co., Ltd., Beijing). 1.5 ug of total RNA was used for the construction of sequencing libraries.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA).

value: root

value: NLP3.1 knockdown


title: ARMV_RNA1&2 C. quinoa_Plant3;  SLRSV_RNA1_Plant2 V.vinifera; CNDV Plant1 N. benthamiana

description:
3' RACE-seq
Processed_Data_SECO_B2.txt


title: KNO3_3_1_3


title: CD8+ T-cells, KO_Rig1_4

city: zhuhai

first: zhang

last: yuncong

state: guangdong

address: 79 kangning road

institute: Jinan University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp (parameter- Quality limit: 0.05)
Clean reads were mapped to mouse genomic mm39
Read count extraction was performed by featureCounts
Assembly: mm39/GRCm39
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: spleens

extract_protocol:
Samples were ground under liquid nitrogen in a mortar and pestle, and the resulting powder dissolved in TRIzol™ Reagent (Invitrogen, Carlsbad, CA, USA), then extracted total RNA.The quality and purity of RNA were examined by a NanoDrop™ One/OneC spectrophotometer (Thermo Scientific, Waltham, MA, USA) and Life Invitrogen Qubit RNA BR (Broad-Range) Assay Kit. RNA integrity was analyzed using Agilent 4200 TapeStation system (Agilent, Santa Clara, CA, USA).
0.1-1 μg of total RNA per sample was prepared for library preparation. The NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® Ultra™ II mRNA Library Prep Kit for Illumina® were used for mRNA isolation and library construction following the manufacturers’ protocols.

value: spleens

value: CD8+ T cells

value: Rig1 KO


title: CD8+ T-cells, KO_Rig1_3


title: CD8+ T-cells, KO_Rig1_2


title: ARMV_RNA1&2 C. quinoa_Plant2; SLRSV_RNA1_Plant1 V.vinifera

description:
3' RACE-seq
Processed_Data_SECO_B2.txt

value: ARMV; SLRSV


title: KCl_3_1_4

value: KCl


title: KNO3_3_1_2


title: TRSV_RNA1_Plant3; CLRV_RNA1_Plant3; SLRSV_RNA1_Plant3_C.quinoa

description:
3' RACE-seq
Processed_Data_SECO_B2.txt


title: GFLV_B844_RNA1&2 C.quinoa_Plant3

description:
3' RACE-seq
Processed_Data_SECO_B2.txt

organism: Chenopodium quinoa

source_name: Infected leaves of C. quinoa

value: Infected leaves of C. quinoa

value: GFLV


title: TRSV_RNA1_Plant2; CLRV_RNA1_Plant2; SLRSV_RNA1_Plant2_C.quinoa

description:
3' RACE-seq
Processed_Data_SECO_B2.txt


title: KCl_3_1_3


title: KCl_3_1_1


title: GFLV_B844_RNA1&2 C.quinoa_Plant2

description:
3' RACE-seq
Processed_Data_SECO_B2.txt


title: CD8+ T-cells, KO_Rig1_1


title: CD8+ T-cells, WT_5


title: 205291550049_R06C01

type: genomic

city: Bari

first: Fabio

last: Sallustio

state: Bari

address: Piazza G. Cesare N°11

country: Italy

institute: University of Bari

description:
Genomic DNA from Mice
205291550049_R06C01_Grn.idat
205291550049_R06C01_Red.idat

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MouseMethylation array (MouseMethylation-12v1-0_A2) BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using the HiScan SQ platform using standard recommended Illumina scanner setting

data_processing: Genome Studio v1 Software

label: Cy5 and Cy3

source_name: Control mice

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from mice samples using Qiagen DNeasy Kit according to standard instructions

value: melanoma

tag: sample id


title: 205291550049_R06C02

description:
Genomic DNA from Mice
205291550049_R06C02_Grn.idat
205291550049_R06C02_Red.idat


title: KNO3_1_1b_5

value: NRT1.1B knockdown


title: 205291550049_R05C02

description:
Genomic DNA from Mice
205291550049_R05C02_Grn.idat
205291550049_R05C02_Red.idat


title: 205291550049_R03C02

description:
Genomic DNA from Mice
205291550049_R03C02_Grn.idat
205291550049_R03C02_Red.idat

source_name: mice treated with  guadecitabine


title: TRSV_RNA2_Plant2; CLRV_RNA2_Plant2

description:
3' RACE-seq
Processed_Data_SECO_B2.txt

value: WT

value: TRSV; CLRV


title: KNO3_1_1b_4


title: 205291550049_R03C01

description:
Genomic DNA from Mice
205291550049_R03C01_Grn.idat
205291550049_R03C01_Red.idat


title: 205291550049_R05C01

description:
Genomic DNA from Mice
205291550049_R05C01_Grn.idat
205291550049_R05C01_Red.idat


title: CD8+ T-cells, WT_1


title: 205291550049_R01C02

description:
Genomic DNA from Mice
205291550049_R01C02_Grn.idat
205291550049_R01C02_Red.idat

source_name: mice treated with guadecitabine/anti-PD-1/anti-CTLA-4


title: CD8+ T-cells, WT_4


title: ARMV_RNA1&2 C. quinoa_Plant1

description:
3' RACE-seq
Processed_Data_SECO_B2.txt

value: ARMV


title: 205291550049_R04C01

description:
Genomic DNA from Mice
205291550049_R04C01_Grn.idat
205291550049_R04C01_Red.idat


title: SLRSV_RNA2_Plant2 C.quinoa

description:
3' RACE-seq
Processed_Data_SECO_B2.txt

value: SLRSV


title: TRSV_RNA2_Plant1; CLRV_RNA2_Plant1

description:
3' RACE-seq
Processed_Data_SECO_B2.txt


title: 205291550049_R04C02

description:
Genomic DNA from Mice
205291550049_R04C02_Grn.idat
205291550049_R04C02_Red.idat


title: 205291550049_R02C02

description:
Genomic DNA from Mice
205291550049_R02C02_Grn.idat
205291550049_R02C02_Red.idat


title: TRSV_RNA2_Plant3; CLRV_RNA2_Plant3

description:
3' RACE-seq
Processed_Data_SECO_B2.txt


title: SLRSV_RNA2_Plant3 C.quinoa

description:
3' RACE-seq
Processed_Data_SECO_B2.txt


title: 205291550049_R02C01

description:
Genomic DNA from Mice
205291550049_R02C01_Grn.idat
205291550049_R02C01_Red.idat


title: CD8+ T-cells, WT_3


title: CD8+ T-cells, WT_2


title: 205291550049_R01C01

description:
Genomic DNA from Mice
205291550049_R01C01_Grn.idat
205291550049_R01C01_Red.idat


title: KCl_1_1b_2


title: 205291550023_R06C02

description:
Genomic DNA from Mice
205291550023_R06C02_Grn.idat
205291550023_R06C02_Red.idat

source_name: mice treated with guadecitabine/anti-CTLA-4


title: 205291550023_R05C02

description:
Genomic DNA from Mice
205291550023_R05C02_Grn.idat
205291550023_R05C02_Red.idat


title: KNO3_1_1b_2


title: KCl_1_1b_4


title: 205291550023_R06C01

description:
Genomic DNA from Mice
205291550023_R06C01_Grn.idat
205291550023_R06C01_Red.idat


title: CGN, GSK-126, RNA-seq, Rep 3

city: Durham

first: Anne

middle: E

last: West

state: NC

address: 311 Research Dr

department: Neurobiology

institute: Duke University

data_processing:
RNA-seq raw fastq read files were analyzed with FastQC and processed with Trimmomatic 0.38 for quality control and adapter trimming
Trimmed reads were then aligned to the mm10 reference genome using STAR 2.7.2b. Duplicates were filtered from the resulting alignments with macs2 2.1 filterdup keeping only one duplicate
Read counts for genes were generated using the count command of the HTseq2 package, with feature type set to ‘exon’, and the Gencode mm10 GTF annotation file
DESeq2 was used for read-count normalization and differential expression analysis.
Assembly: mm10
Supplementary files format and content: exon.reads

source_name: Cerebellum

extract_protocol:
Cerebellar tissue was lysed in Trizol reagent, after which chloroform was added and phase separation was performed. The resulting aqueous layer was further processed using the Zymo Direct-zol RNA miniprep kit (Zymo #R2052). RNA purity was then measured to make sure samples had A260/280 and A260/230 values > 1.9.
Novogene mRNA library preparation
poly A enrichment

value: Cerebellum

tag: agent


title: CGN, DMSO, RNA-seq, Rep 3

value: DMSO


title: CPMV_RNA1_Plant2

description:
3' RACE-seq
Processed_Data_SECO_B2.txt

value: CPMV


title: KCl_1_1b_3

value: root


title: SLRSV_RNA2_Plant1 C.quinoa

description:
3' RACE-seq
Processed_Data_SECO_B2.txt


title: CGN, GSK-126, RNA-seq, Rep 1


title: GFLV_B844_RNA1&2 C.quinoa_Plant1

description:
3' RACE-seq
Processed_Data_SECO_B2.txt


title: CPMV_RNA1_Plant3

description:
3' RACE-seq
Processed_Data_SECO_B2.txt


title: KCl_WT_2


title: KNO3_WT_4


title: CGN, GSK-126, RNA-seq, Rep 2