title: r03_35wpi

description:
RW-208-R
Frequency table Rats.xlsx

treatment_protocol: Mice and rats were infected by intrahepatic inoculation of 10 µg in vitro-transcribed viral genomic RNA.


title: r09_45wpi

status: Public on Feb 27 2023

type: SRA

city: Copenhagen N

first: Troels

middle: K H

last: Scheel

state: Copenhagen

address: Blegdamsvej 3

department: Institute for Immunology and Microbiology

country: Denmark

institute: University of Copenhagen

description:
MIB66-10
Frequency table Rats.xlsx

library_source: transcriptomic

data_processing:
The obtained reads were analyzed using the previously published VirVarSeq analysis pipeline (Verbist 2015 Bioinformatics, PMID: 25178459) with a set fixed quality value of 30 to call variation at the codon level. This package is available at http://sourceforge.net/projects/virtools/?source=directory. All samples had minimum coverage of 4,000 reads per position over the entire ORF. Variant calling frequency tables from VirVarSeq from samples of relevance were merged and filtered in R.
Assembly: NrHV-A: MF113386, NrHV-B: ON758386, RHV-rn1: KX905133
Supplementary files format and content: Frequency table NRG mice.xlsx lists viral substitutions as observed in NRG mice. For NRG mice where variation was less, substitutions with frequency of >20% in at least one sample were included in the processed data file.
Supplementary files format and content: Frequency table Rats.xlsx lists viral substitutions as observed in rats. For rats where variation was greater, positions with a combined frequency of one or several mutations >50% in at least two rats were kept. Individual substitutions with minimal contribution (<20%) at such position were not included.

molecule: total RNA

organism: Rattus norvegicus

source_name: Serum

extract_protocol:
Viral RNA was extracted using TRIzol, followed by standard on-column purification procedure. The wole ORF was reverse transcribed to generate viral cDNA. Samples were pre-incubated at 65ºC for 5 min prior to the reaction. RT was carried out at 50ºC for 2 h in the presence of RNase inhibitors using 0.1 μM primer TS-O-00319 (GCTTCCTGGAGCGGGCTAGATACTG). Amplification of the complete ORF was performed using Q5 High-Fidelity Hot start DNA Polymerase (NEB), including high GC Enhancer, and the primer pair TS-O-00318 (CCAAGCCCCAATGCCGTCCGGCACCGCTGCCCTTTTCGG) and TS-O-00361 (AGGTGAAGGGGGCATCGATG). Amplified DNA was purified using DNA Clean & Concentrator (Zymo Research).
Libraries were constructed using the NebNext Ultra II FS DNA Library Prep Kit for Illumina (New England Biolabs), using dual indices. cDNA input: 25ng, adapter ligation, bead-based size selection (AMPure XP beads; 200-350 bp), PCR enrichment using i7/i5 index primer set. Enriched libraries were washed twice using AMPure XP beads for complete depletion of residual adapter.
Libraries were sequenced paried-end on a Illumina Miseq using 500 PE V2 kit (Illumina).

tag: strain

value: Lewis rat

tag: immunodeficient

value: NO

tag: tissue

value: Serum

tag: virus

tag: molecule subtype

value: viral RNA


title: RNA-Seq of Huh7 cells treated with 400ug/ml GO-Rg3-rep1 [P19760_117_S38]

city: Goteborg

first: Shadi

last: Rahimi

address: Kemivägen 10

department: Department of Biology and Biological Engineering

country: Sweden

institute: Chalmers University of Technology

data_processing:
The raw reads were processed with the NGI RNAseq Pipeline (https://github.com/SciLifeLab/NGI-RNAseq). The GRCh37 reference genome was used to map the reads (https://support.illumina.com/sequencing/sequencing_software/igenome.html), and the percentage of uniquely mapped reads was between 79.7–83.6%. Raw read counts were calculated with feature Counts. In total 448,620,449 reads were uniquely mapped on the reference genomes. Samples contained between 8,598,597 to 14,340,446 unique reads.
Genome_build: GRCh37
Supplementary_files_format_and_content: txt file including raw gene counts

organism: Homo sapiens

source_name: Tretaed Huh7 cells with 400ug/ml GO-Rg3

growth_protocol: Cells were seeded onto 6-well plates at a density of 4 × 105 cells per well and cultured for 24 h before treatment with GO, GO-Rg3-GO-Rg3-DOX, and DOX for 6 h.

extract_protocol:
Total RNA extraction was performed through RNeasy Mini Kit (Qiagen), and the quality examination was performed by Bioanalyzer (Agilent) through Agilent RNA 6000 Nano Kit.
Library was prepared through Illumina TruSeq Stranded mRNA.

tag: cell line

tag: cell type

value: Hepatocarcinoma cells

tag: treatment

value: 400 ug/ml GO-Rg3


title: N15 NRK-49F cells, pH6

city: Halle (Saale)

first: Virginie

last: Dubourg

address: Magdeburger Str. 6

department: Julius Bernstein Institute for Physiology

country: Germany

institute: Martin Luther University - Halle-Wittenberg

data_processing:
Read alignment (HISAT2 2.1.0)
Read counting (featureCounts - 2.0.0)
Annotation with biomaRt and Ensembl 99
Assembly: rn6
Supplementary files format and content: .csv file including annotation raw counts (output of featureCounts) for each sample

growth_protocol: NRK-52E and NRK-49F were cultivated with DMEM medium (5% FCS, 1.5g/L NaHCO3), at 37°C, 5% CO2. For co-culture conditions, NRK-49F were directly sed in wells of 6-well plates, while NRK-52E were grown on permeable filter inserts that were embed onto the 6-well plates with the NRK-49F.

extract_protocol:
Total RNA was isolated with BluZol Reagent, following the manufacturer's instructions. Eventual gDNA contaminations were removed using Turbo DNAse (ambion, Life Technologies).
polyA enrichment (performed by Novogene Europe)

treatment_protocol: Cells were synchronized for 24h with medium without FCS. The incubation with pH 7.4 or 6.0 was then started and was maintained for 48h

value: Fibroblast


title: FGK_5_30min [DE54NGSUKBR107550]

city: Bonn

first: Susanne

last: Schmidt

address: Venusberg-Campus 1

department: Institute of Clin. Chemistry and Clin. Pharmacology

institute: University Hospital Bonn

data_processing:
Alignment with STAR against the mm10 reference genome
quantification of gene counts via Partek's E/M algorithm
normalized as Counts per million (CPM)
Flooring
Genome_build: mm10
Supplementary_files_format_and_content: normalized as Counts per million (CPM)

organism: Mus musculus

source_name: primary cDC1/APC_FGK_30min

growth_protocol: In vitro generation of bone marrow-derived DCs using Flt3 ligand followed by sort of cDC1

extract_protocol:
TRIzol - Direct-zolTM RNA MicroPrep kit (Zymo Research)
performed by the NGS Core Facility University Hospital Bonn according to the maufacturers' user guide for the QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (https://www.lexogen.com/quantseq-3mrna-sequencing/#quantseqdownloads/)
1x 50bp single reads, 10mio reads deep per sample, Illumina HiSeq2500

treatment_protocol: In vitro stimulation of cDC1 with IFN-⍺A in the presence or the absence of anti-CD40 monoclonal antibody (FGK45.5).

tag: strain background

value: Bone-marrow

value: primary cDC1/APC


title: r09_35wpi

description:
RW-212
Frequency table Rats.xlsx


title: RNA-Seq of Huh7 cells treated with 400ug/ml GO-rep2 [P19760_110_S36]

source_name: Tretaed Huh7 cells with 400ug/ml GO

value: 400 ug/ml GO


title: N14 NRK-49F cells, pH7


title: r09_08wpi

description:
MIB37-20
Frequency table Rats.xlsx


title: r09_22wpi

description:
RW-212-H
Frequency table Rats.xlsx


title: IFN_FGK_6_30min [DE59NGSUKBR107557]

source_name: primary cDC1/APC_IFN_FGK_30min


title: r09_01wpi

description:
MIB37-7
Frequency table Rats.xlsx


title: N12 NRK-49F cells, pH6


title: RNA-Seq of Huh7 cells treated with 400ug/ml GO-rep1 [P19760_109_S35]


title: RNA-Seq of Huh7 cells control non-treated-rep3 [P19760_103_S34]

source_name: Non-tretaed Huh7 cells


title: FGK_6_15min [DE43NGSUKBR107554]

source_name: primary cDC1/APC_FGK_15min


title: RNA-Seq of Huh7 cells control non-treated-rep1 [P19760_101_S32]


title: RNA-Seq of Huh7 cells control non-treated-rep2 [P19760_102_S33]


title: N11 NRK-49F cells, pH6


title: RNA-Seq of Huh7 cells treated with 400ug/ml GO-Rg3-rep3 [P19760_119_S40]


title: N13 NRK-49F cells, pH7


title: IFN_5_240min [DE38NGSUKBR107547]

source_name: primary cDC1/APC_IFN_240min


title: r06_40wpi

description:
RW-208-U
Frequency table Rats.xlsx


title: r06_46wpi

description:
MIB66-9
Frequency table Rats.xlsx


title: Unstim_4_240min [DE33NGSUKBR107540]

source_name: primary cDC1/APC_Unstim_240min


title: N10 NRK-49F cells, pH7


title: IFN_FGK_5_30min [DE27NGSUKBR107551]


title: N9 NRK-49F cells, pH7


title: RNA-Seq of Huh7 cells treated with 400ug/ml GO-rep3 [P19760_111_S37]


title: RFe_BiPS2-M-3

city: New York

first: Thomas

last: Zwaka

state: NY

address: 1 Gustave L. Levy Pl

country: USA

institute: Icahn School of Medicine

data_processing:
100 bp paired-end sequencing reads (PE100) were generated by Illumina NovaSeq 6000 S1 sequenicng
Samples 10 - 21 reads were processed with Trimmomatic v0.39
The reads were mapped with HISAT2 v2.2.1, the .sam files resulting from each mapping were converted into .bam files and indexed using samtools v1.10 , and the reads mapped against each gene were counted using featureCounts v2.0.1.
Assembly: RefSeq assembly accession GCF_004115265.1, assembled and annotated by the Vertebrate Genomes Project (https://vertebrategenomesproject.org)
The differential expression analysis was performed with DESeq2
bigwig files were generated using the bamCoverage command from deepTools (https://deeptools.readthedocs.io/en/ develop/content/tools/bamCoverage.html)
Text file with raw counts of sequencing reads.

organism: Rhinolophus ferrumequinum

source_name: M Replicate 3: Gene expression data of wildtype bat iPS cells following mesoderm differentiation

extract_protocol:
Qiagen RNeasy
SMART-Seq v4 Ultra Low Input kit (Takara Bio)

value: differentiated reprogrammed embryonic fibroblasts

tag: genotype

value: wildtype


title: r06_27wpi

description:
MIB53-20
Frequency table Rats.xlsx


title: IFN_FGK_4_15min [DE49NGSUKBR107543]

source_name: primary cDC1/APC_IFN_FGK_15min


title: FGK_4_30min [DE22NGSUKBR107544]


title: N8 NRK-52E cells, pH6

value: Epithelial


title: RFe_BiPS2-M-2

source_name: M Replicate 2: Gene expression data of wildtype bat iPS cells following mesoderm differentiation


title: RFe_BiPS2-M-1

source_name: M Replicate 1: Gene expression data of wildtype bat iPS cells following mesoderm differentiation


title: IFN_FGK_6_15min [DE16NGSUKBR107555]


title: r06_08wpi

description:
MIB37-17
Frequency table Rats.xlsx


title: N7 NRK-52E cells, pH6


title: N6 NRK-52E cells, pH7


title: r06_01wpi

description:
MIB37-4
Frequency table Rats.xlsx


title: FGK_5_15min [DE11NGSUKBR107548]


title: r05_45wpi

description:
MIB80-2
Frequency table Rats.xlsx


title: RFe_BiPS2-EN-2

source_name: EN Replicate 2: Gene expression data of wildtype bat iPS cells following endoderm differentiation


title: RFe_BiPS2-EN-3

source_name: EN Replicate 3: Gene expression data of wildtype bat iPS cells following endoderm differentiation


title: r05_35wpi

description:
RW-208-T
Frequency table Rats.xlsx


title: IFN_4_240min [DE06NGSUKBR107541]


title: r05_22wpi

description:
MIB53-19
Frequency table Rats.xlsx


title: N4 NRK-52E cells, pH6


title: RFe_BiPS2-EC-3

source_name: EC Replicate 3: Gene expression data of wildtype bat iPS cells following ectoderm differentiation


title: r05_08wpi

description:
MIB37-16
Frequency table Rats.xlsx


title: N5 NRK-52E cells, pH7


title: RFe_BiPS2-EN-1

source_name: EN Replicate 1: Gene expression data of wildtype bat iPS cells following endoderm differentiation


title: WT adult rep2 [miRNA-Seq]

city: Beijing

first: Jie

state: Beijing

address: Tsinghua University

department: Basic Medical Sciences, School of Medicine

country: China

institute: Tsinghua University

data_processing:
Sequenced reads were trimmed for adaptor sequences, and masked for low-complexity or low-quality sequences, Clean reads were mapped to mouse genome (mm10) using miRdeep2 software.
Fragments Per Kilobase per Million mapped reads (FPKM) of Refseq genes were caculated.
mm10
read counts number for each sample.
Supplementary_files_format_and_content: read counts

source_name: heart

extract_protocol:
Total RNA was extracted using TRIZOL and treated with RNase free DNase.
RNA library was prepared following the instruction of NEXTFLEX Small RNA seq Kit for Illumina® Sequencing.（Bioo Scientific）

value: cardiomyocyte

value: wild type


title: WT adult rep1 [miRNA-Seq]


title: N3 NRK-52E cells, pH6


title: RFe_BiPS2-EC-2

source_name: EC Replicate 2: Gene expression data of wildtype bat iPS cells following ectoderm differentiation


title: WT e13.5  [miRNA-Seq]


title: N2 NRK-52E cells, pH7


title: r05_01wpi

description:
MIB37-3
Frequency table Rats.xlsx

source_name: Serum


title: RFe_BiPS2-EC-1

source_name: EC Replicate 1: Gene expression data of wildtype bat iPS cells following ectoderm differentiation


title: KO adult rep1 [miRNA-Seq]

value: LncSync-/-


title: Unstim_3_240min [MED_no3_C9WE3ANXX_ATCACG]


title: N1 NRK-52E cells, pH7


title: Unstim_2_240min [MED_no2_C9WE3ANXX_CGTACG]


title: Sorghum bicolor Root Nuclei_3

first: Bruno

last: Guillotin

address: 12 Waverly Place, Floor 6

department: Biology

institute: NYU-Biology-CGSB

description:
10x Genomics 3' RNA seq V3
Maize_Sorghum_Setaria_Cells_Nuclei_Seurat_Obj.RData
Maize_Sorghum_Setaria_Cells_Nuclei_expression_matrix_raw_counts.RData
Maize_Sorghum_Setaria_Cells_Nuclei_expression_matrix_Norm_counts.RData

library_source: transcriptomic single cell

data_processing:
Cell Ranger 5.0.1 (10x Genomics) to generate gene-cell matrices. Gene reads were aligned to the Arabidopsis TAIR10.38, Maize B73 v4, Sorghum bicolor v3 and Setaria viridis v2 reference genomes.
Replicates (see Supplementary Table 1) were integrated and cells mapped using the Seurat package v4.0 66 as follows: first, genes with counts in fewer than three cells were excluded from the analysis and their counts were removed. Second, low-quality cells were removed using threshold variable depending on the library quality (see supplementary Table 1). Clustering of cells or nuclei separately were done by log-normalized raw counts and the 2000 most variable genes were identified for each replicate using the “vst” method in Seurat. Next, we used the FindIntegrationAnchors function to identify anchors between the three datasets, using 20 dimensions. A new profile with an integrated expression matrix containing cells from all replicates was produced with the IntegrateData function. For dimensionality reduction, the integrated expression matrix was scaled (linear transformed) using the ScaleData function, and Principal Component analysis (PCA) performed. The top 30 principal components were selected. Cells or nuclei were clustered using a K-nearest neighbor (KNN) graph, which is based on the Euclidean distance in PCA space. The FindNeighbors and FindClusters function with a resolution of 0.5. was applied. Next, non-linear dimensional reduction was performed using the UMAP algorithm with the top 30 PCs.
For the co-clustering of cells and nuclei, either dataset were treated similarly, all replicates were integrated at once using the seurat 'SCT' approach. First raw reads were normalized using the SCTransform function, then SelectIntegrationFeatures was used to identify anchors between the datasets, using 3000 features.
For multiple species clustering, all orthologous genes names from were replaced by their corresponding maize ID in sorghum and setaria raw features.tsv.gz files (Gene conversion in Supplementary Table 1). Anchors are combined using PrepSCTIntegration and selected using FindIntegrationAnchors. For clustering of maize, sorghum and setaria together, all species were considered equally using the FindIntegrationAnchors function. Finally, a Principal Component analysis (PCA) is performed using the first 100 principal components and a non-linear dimensional reduction was performed using the UMAP algorithm with the top 100 PCs.
Supplementary files format and content: Processed data include, R Seurat Objects of integrated datasets, expression matrices normalized and raw count extracted from the Seurat objects, and a metadata containing the cell identities, genes or UMI per cell.

organism: Sorghum bicolor

source_name: root meristem

growth_protocol: Arabidopsis seeds were imbibed for 48h at 4°C before being surface sterilized and placed on a nylon mesh (110um) and agar plates-1/2 × Murashige and Skoog salts (Sigma M5524), 0.5% sucrose, 0.8% Agar (Sigma A1296). Plant were transferred vertically in growth chambers set to 23°C and a 16 h light/8 h dark cycle (400 μmol m−2 s−1). Root tips were collected 7 days after transfer, cut with a feather scalpel at 150um from the tip and directly transferred to either the protoplast solution at room temperature or the nuclei lysis buffer at 4°C. Maize, Sorghum seeds were sterilized using bleach (1.5% active chloride) and 0.001% tween 20 for 20mins then 4% chloramine T for 20mins. Setaria seed germination was induced by incubation in 4% liquid smoke (Colgin, Authentic Natural Hickory) at 29°C for 24h.Then setaria seeds were sterilized using bleach (1.5% active chloride) and 0.001% tween 20 for 20mins. All seeds were placed between two layers of brown paper (Anchor Paper&Cie., 38# regular), rolled and covered with aluminum foil to prevent roots from exposure to direct light. Rolls were placed in a bucket of tap water at 28/24°C at 16 h light/8 h dark cycle (250 μmol m−2 s−1) for 7 days (15days for Setaria) before harvesting the root tips. Primary and seminal root tips were cut using a fine scalpel at 0.5 cm form the tip for Maize and Sorghum, 0.2cm from the tip for Setaria and transferred either to the pre-incubation solution for single cell or to the nuclei lysis buffer.

extract_protocol:
Root tip were incubated in a enzymatic solution to digest cell walls and produce protoplasts, or in lysis buffer for nuclei extraction. Protoplasts or nuclei were filtered using a cell strainer and used as input for the 10x Chromium Single Cell 3' kit
Libraries were prepared using Chromium Single Cell 3' Reagent Kit V2 and V3 protocol

value: Nuclei

value: root meristem

tag: age

value: 10 days old


title: KO adult rep2 [miRNA-Seq]


title: RFe_BiPS2-EB-3

source_name: EB Replicate 3: Gene expression data of wildtype iPS cells differentiated as bat embryonic bodies


title: KO e13.5 [miRNA-Seq]


title: Sorghum bicolor Root Nuclei_2


title: Unstim_1_240min [MED_no1_C8TR7ANXX_ACAGTG]


title: RFe_BiPS2-EB-2

source_name: EB Replicate 2: Gene expression data of wildtype iPS cells differentiated as bat embryonic bodies


title: KO e13.5 rep2

description:
total RNA
KO2-e13.5

data_processing:
Sequenced reads were trimmed for adaptor sequences, and masked for low-complexity or low-quality sequences, Clean reads were mapped to mouse genome (mm10) using RSEM software.
Fragments Per Kilobase per Million mapped reads (FPKM) of Refseq genes were caculated.
mm10
normalized expression for each sample.
Supplementary_files_format_and_content: FPKM

extract_protocol:
Total RNA was extracted using TRIZOL and treated with RNase free DNase.
200 ng total RNA was reverse transcribed and amplified using Smart-seq2, and RNA library was prepared following the instruction of SMARTer® Ultra™ Low RNA Kit for Illumina® Sequencing（Clontech）


title: Sorghum bicolor Root Nuclei_1


title: KO e13.5 rep1

description:
total RNA
KO1-e13.5


title: Sorghum bicolor Root Cell_1

description:
10x Genomics 3' RNA seq V2
Maize_Sorghum_Setaria_Cells_Nuclei_Seurat_Obj.RData
Maize_Sorghum_Setaria_Cells_Nuclei_expression_matrix_raw_counts.RData
Maize_Sorghum_Setaria_Cells_Nuclei_expression_matrix_Norm_counts.RData

value: Protoplast


title: RFe_BiPS2-EB-1

source_name: EB Replicate 1: Gene expression data of wildtype iPS cells differentiated as bat embryonic bodies


title: RFe_BiPS2-3

source_name: BiPS2 Replicate 3: Gene expression data of wildtype bat induced pluripotent stem cells

value: reprogrammed embryonic fibroblasts


title: KO adult rep1

description:
total RNA
KO1-adult


title: IFN_2_240min [IFN_no2_C9WE3ANXX_ACTGAT]

source_name: primary cDC1/APC_IFN_240min


title: KO adult rep2

description:
total RNA
KO2-adult


title: IFN_1_240min [IFN_no1_C8TR7ANXX_CTTGTA]


title: RFe_BiPS2-2

source_name: BiPS2 Replicate 2: Gene expression data of wildtype bat induced pluripotent stem cells


title: RFe_BiPS2-1

source_name: BiPS2 Replicate 1: Gene expression data of wildtype bat induced pluripotent stem cells


title: WT adult rep1

description:
total RNA
WT1-adult


title: IFN_FGK_3_240min [IFFG_no3_C9WE3ANXX_TGACCA]

source_name: primary cDC1/APC_IFN_FGK_240min


title: RFe_BiPS1-3

source_name: BiPS1 Replicate 3: Gene expression data of wildtype bat induced pluripotent stem cells


title: IFN_FGK_2_240min [IFFG_no2_C9WE3ANXX_ATTCCT]


title: RFe_BiPS1-2

source_name: BiPS1 Replicate 2: Gene expression data of wildtype bat induced pluripotent stem cells


title: Pistia Root 3

city: Sutton Bonington

first: Alexander

middle: George

last: Ware

state: Leicestershire

address: Sutton Bonington Campus

country: United Kingdom

institute: University of Nottingham

data_processing:
raw reads (.fastq) were processed using Perl. Clean reads were obtained by removing reads containing adapters and poly-N.
Reads from each sample were pseudoaligned against Pistia stratiotes v1, (Qian et al., 2022) using Salmon (Patro et al., 2017) with k-value set at the default level (31) and the --gcbias flag passed for all samples. The entire genome was concatenated to the transcriptome (cds.fa)  and passed to salmon as a decoy
differential expression analysis was performed on the using the package DESeq2 (Love et al., 2014)
Assembly: Pistia stratiotes V1, Qian et al., 2022
Supplementary files format and content: Normalised count matrix exported from DeSeq2

organism: Pistia stratiotes

source_name: Root

growth_protocol: Pistia stratiotes was seeded  (1 mature individual per flask) into 500ml flasks and grown for 10 days on 200ml SH-media. Emerging plants with 3-4 leaves were selected for sampling. For the leaf  sample, the largest emerged leaf was harvested from all the plants in a flask, pooled and snap frozen.  For the root sample, roots with the apex and laterals removed were harvested in the same manner.  Pooled tissue from a flask represented a biological replicate (4 total per tissue type).

extract_protocol:
TRIZOL/Qiagen RNEasy
RNA integrity was assessed using the RNA Nano 6000 Assay Kit on a Bioanalyzer 2100 (Agilent Technologies, CA, USA). Total RNA was used as input. 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, adaptors with hairpin loop structure were ligated to prepare for hybridization. In order to preferentially select cDNA fragments of 370~420 bp in length, library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. Clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to manufacturer’s instructions. After cluster generation, library preparations were sequenced on an Illumina Novaseq platform generating 150 bp paired-end reads

value: Root


title: Pistia Root 2


title: Pistia Root 4


title: WT e13.5 rep2

description:
total RNA
WT2-e13.5


title: WT adult rep2

description:
total RNA
WT2-adult


title: RFe_BiPS1-1

source_name: BiPS1 Replicate 1: Gene expression data of wildtype bat induced pluripotent stem cells


title: IFN_3_240min [IFN_no3_C9WE3ANXX_TTAGGC]


title: FGK_3_240min [FGK_no3_C9WE3ANXX_CGATGT]

source_name: primary cDC1/APC_FGK_240min


title: Pistia Root 1


title: RFe_BEF-3

source_name: BEF Replicate 3: Gene expression data of wildtype bat fibroblasts

value: embyronic fibroblasts


title: Pistia Leaf 5

source_name: Leaf

value: Leaf


title: Pistia Leaf 4


title: RFe_BEF-2

source_name: BEF Replicate 2: Gene expression data of wildtype bat fibroblasts


title: FGK_1_240min [FGK_no1_C8TR7ANXX_GCCAAT]

value: Bone-marrow


title: QS_B

city: Helsinki

first: Päivi

last: Saavalainen

address: Haartmaninkatu 8

department: TRIMM

country: Finland

institute: University of Helsinki

data_processing:
Sequencing in 75 cycles produced 20 bp Read 1 (bases 1-12 sample barcode, bases 13-20 UMI) and 55 bp Read 2 (sequence derived from the mRNA).
Raw sequence data was filtered to remove reads shorter than 20 bp.
The original pipeline suggested in (Macosko EZ et al. Cell 2015; https://github.com/broadinstitute/Drop-seq) for processing of drop-seq data was used. Briefly, reads were additionally filtered to remove polyA tails of length 6 or greater, then aligned to the human genome using STAR aligner, with default settings. Uniquely mapped reads were grouped according to the 1-12 barcode, and gene transcripts were counted by their Unique Molecular Identifiers (UMIs) to reduce bias emerging from the PCR amplification. Digital expression matrices (DGE) reported the number of transcripts per gene in a given sample (according to the distinct UMI sequences counted).
Differentially expressed genes were identified using edgeR
Supplementary_files_format_and_content: Digital Gene Expression (DGE): tab-delimited text file containing UMI read counts for each sample

source_name: A549 cell line

growth_protocol: A549 cells were grown 16h at 37°C in DMEM with the following additives: 10% fetal bovine serum (Gibco), 1× PenStep (Sigma) and 1× GlutaMAX (Gibco).

extract_protocol:
RNA was extracted from the A549 cells incubated under different conditions using an RNeasy Mini Kit (Qiagen) following manufacturer’s guidelines. Cells were homogenized with QIAshredder columns (Qiagen). After extraction, RNA was quantified using a Qubit 2 fluorometer (Thermo Fisher Scientific) with the Qubit RNA HS Assay Kit (Thermo Fisher Scientific), and stored at -70°C.
RNA sequencing method was designed based on the Drop-seq protocol described in (Macosko EZ et al. Cell 2015). Briefly, 10 ng of RNA was mixed with Indexing Oligonucleotides. After 5 minutes of incubation the RNA was combined with RT mix (1 x Maxima RT buffer, 1 mM dNTPs, 10 U/µl Maxima H- RTase, 1 U/µl RNase inhibitor and 2.5 µM Template Switch Oligo). Samples were incubated for 30 minutes at 22°C and 90 minutes at 42°C. The constructed cDNA was amplified by PCR. The PCR products were pooled together in sets of 12 samples containing different Indexing Oligos and purified with Agencourt AMPure XP Beads according to the manufacturer’s instructions. The 3’-end cDNA fragments for sequencing were prepared using the Nextera XT (Illumina) tagmentation reaction. The reaction was performed according to manufacturer’s instruction, with the exception of the P5 SMART primer that was used instead of S5xx Nextera primer. Each set of 12 samples that was pooled after the PCR reaction was tagmented with a different Nextera N7xx index. Subsequently, the samples were PCR amplified and purified twice using Agencourt AMPure Beads. The libraries were sequenced on a Illumina NextSeq 500, with a custom primer producing read 1 of 20 bp and read 2 (paired end) of 50 bp. Sequencing was performed at the Functional Genomics Unit of the University of Helsinki, Finland.

treatment_protocol: The cells were washed with 37°C PBS, and DMSO, PAO1 cells in DMEM, 2.5 mM or 100 µM of P[5]a, or combination of these factors were added to the culture. Such cultures were incubated overnight at 37°C.

value: lung epithelial cells


title: RFe_BEF-1

source_name: BEF Replicate 1: Gene expression data of wildtype bat fibroblasts


title: QS_A


title: FGK_2_240min [FGK_no2_C9WE3ANXX_GAGTGG]

value: primary cDC1/APC


title: Pistia Leaf 1


title: AC_B2_2

status: Public on Feb 26 2023

city: Changchun

first: Xue-song

last: Li

address: Xincheng Street No. 2888

institute: Jilin Agricultural University

data_processing:
The raw paired end reads were trimmed and quality controlled by Trimmomatic with parameters (SLIDINGWINDOW:4:15 MINLEN:75) (version 0.36 http://www.usadellab.org/cms/uploads/supplementar /Trimmomatic).Then clean reads were separately aligned to reference genome with orientation mode using Rockhopper (http://cs.wellesley.edu/~btjaden/Rockhopper/) software. Rockhopper was a comprehensive and user-friendly system for computational analysis of bacterial RNA-seq data. As input, Rockhopper takes RNA sequencing reads generated by high-throughput sequencing technology. This software was used to calculate gene expression levels with default parameter.
Assembly: not provided
Supplementary files format and content: tab-delimited text files include abundance values for each Sample

organism: Escherichia coli

source_name: Clinical separation

growth_protocol: E. coli B2 was cultured in Luria-Bertani (LB) liquid medium under aerobic condition at 37 ℃.

extract_protocol: Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed usingDNase I (TaKara). Then RNA quality was determined using 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). High-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0,>10μg) is used to construct sequencing library.

treatment_protocol: The strain E.coli B2 was cultured overnight and added 1% citric acid for 6 hours. After the citric acid was removed by centrifugation, the strain was suspended overnight.

value: E. coli B2

value: bacteria culture

value: 1% citric acid for 6 h


title: AC_B2_3


title: AC_B2_1


title: B2_3

value: none; control


title: B2_2


title: B2_1


title: IFN_FGK_1_240min [IFFG_no1_C8TR7ANXX_GTGAAA]


title: HG2 [RNA-Seq]

city: Wuxi

first: Jun

last: Qiang

state: Jiangsu

address: 9 Shanshi East road

institute: Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences

description: The acute experimental group reduced the dissolved oxygen to (1. 02 ± 0. 10) mg · L- within 30 minutes

data_processing:
Using the Illumina paired-end RNA-seq approach
We aligned reads of  all samples to the reference genome using HISAT package
StringTie and Ballgown was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM
The differentially expressed mRNAs and genes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package – Ballgown.
Genome_build: http://asia.ensembl.org/Oreochromis_niloticus/Info/Index
Supplementary_files_format_and_content: xls include FPKM values for each Sample

organism: Oreochromis niloticus

source_name: Gill

growth_protocol: A total of 90 experimental fish were used for the main acute hypoxic stress experiment. Ninety experimental fish were randomly placed in six tanks (15 fish per tank), three treatment tanks and three 5mg/L control tanks.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The DO of the three treatment tanks was rapidly reduced to 96h-LH50 by pumping nitrogen into water from a nitrogen gas cylinder. Real-time reading with a DO meter were used to control the DO in water by adjusting oxygen intake. The sampling time was 96h.

value: hypoxia stress

value: Gill


title: HG3 [RNA-Seq]


title: HG1 [RNA-Seq]


title: WT e13.5 rep1

description:
total RNA
WT1-e13.5

source_name: heart

value: cardiomyocyte

value: wild type


title: CG3 [RNA-Seq]

description: The culture conditions of the control group were the same as acclimation condition,

value: control


title: CG1 [RNA-Seq]


title: CG2 [RNA-Seq]


title: Pistia Leaf 3


title: GGOH_Rep2

city: Shanghai

first: Qian

last: Bian

state: Shanghai

address: Pudong New District, Jinzun Rd, No.115

department: Ninth People’s Hospital

institute: Shanghai Jiao Tong University School of Medicine

library_source: genomic

data_processing:
Hi-C reads were mapped to the mm10 genome and filtered using the hiclib pipeline (https://bitbucket.org/mirnylab/hiclib) as described previously (Crane et al.).
The mapped Hi-C fragments of replicates were combined and converted into cooler format using the cooler package (https://github.com/mirnylab/cooler, Abdennur & Mirny, 2020).
Assembly: mm10
Supplementary files format and content: cool

molecule: genomic DNA

source_name: oocytes

extract_protocol:
Ovaries were separated and transferred into M2 medium (Sigma). For oocyte and GCs at growing stage (GO and GCs), the follicles with a diameter of 200-250 μm were isolated using insulin syringe under stereoscope. Full-grown oocytes and GCs (FGO and FGCs) were obtained 48 h after pregnant mare serum gonadotropin (PMSG) priming. For oocyte and GCs at MI stage (MIO and MIGCs), C57BL/6 female mice were intraperitoneally injected with 10 units PMSG, and 48 h later injected with 10 units human chorionic gonadotropin (hCG). After 9 h, the mice were sacrificed by cervical dislocation and the ovaries were separated. The pre-ovulatory follicles were punctured using a 1 mL disposable syringe under stereoscope, and COCs were transferred into new hyaluronidase droplets with the mouth pipette for 5 minutes of digestion. For oocyte and GCs at MII stage (MIIO and MIIGCs), the COCs were isolated from oviduct after 13 h and cumulus masses were separated in hyaluronidase medium. Oocytes and GCs from young (6 weeks old ) and aged (10 months old) mice at four stages were collected and processed for smart RNA-seq.
Hi-C libraries of different cell types were prepared using a previously described in situ Hi-C protocol with minor modifications. Isolated oocytes were fixed with 920 μl 1% v/v formaldehyde in 1x HBSS at room temperature for 10 minutes. 2.5M Glycine was added to the cells to make the final concentration of Glycine 0.2 M. Cells were incubated at RT for 5 min and on ice for at least 15 min to quench crosslinking. The fixed cells were collected with oral siphon and washed twice in Hanks Buffer. Purified oocytes were lysed with 100 μl ice-cold Hi-C lysis buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% Igepal CA630) with protease inhibitors. Samples were incubated on ice for 15 minutes and centrifuged for 5 minutes at 3,000xg at 4°C to isolate nuclei. The nuclei pellets were washed once with 100 μl 1x NEB Buffer 3.1, resuspended in 2 μl 10x NEB Buffer 3.1, 14 μl ddH2O, and 4 μl of 0.5% SDS and then incubated at 65°C for 5 min to open up chromatin. 2.2 μl of 10% Triton X-100 (Sigma, 93443) was added to the samples, and samples were incubated at 37°C for 15 minutes to quench SDS. To digest chromatin, 0.5 μl of 10X NEB 3.1 Buffer, 1.5 μl ddH2O, and 1 μl (50 U) of DpnII restriction were added into the samples to bring total reaction volume to ~25 μl. Digestion was performed overnight at 37°C on a thermomixer with interval shaking (shake at 950 rpm for 10 sec with 5 min intervals). Following digestion, samples were incubated at 65°C for 20 min to inactivate the restriction enzyme, then cool to RT on ice. To fill the restriction overhangs, 6μl of fill-in master mix (3.75 μl of 0.4 mM biotin- 14-dATP (Life Technologies, 19524-016), 0.15 μl of 10 mM dCTP/dGTP/dTTP, 1 μl of 5 U/μl Klenow fragment (3’→5’ exo-), 0.6 μl 10X NEB 3.1, 0.2 μl Milli-Q water) was added to the reaction and samples were incubated at 37°C for 1 hr in thermomixer (shake at 950 rpm for 10 sec with 5 min intervals). 90 μl of ligation master mix (49.8 μl of water, 24 μl of 5X T4 DNA ligase buffer (Invitrogen), 10 μl of 10% Triton X-100, 1.2 μl of 10mg/ml Bovine Serum Albumin (100X BSA), 5 μl of 1 U/ μl T4 DNA Ligase (Invitrogen)) was then added and samples were mixed by inverting and incubated at 16 °C for 4 hours. After ligation, samples were centrifuged for 5 min at 3,000g. The pellets were washed with 100 μl 1X NEB buffer 3 and resuspended with 50 μl 1X NEB buffer. To reverse crosslinking, 3 μl 20mg/ml proteinase K (NEB, P8102) and 5μl of 10% SDS were added into the samples and then incubated at 65°C for 2hrs. Phenol- chloroform extraction and ethanol precipitation were performed. The purified DNA was dissolved in 130 μl 1x Tris Buffer and sheared by Covaris M220 (Peak Incident Power: 50W; Duty factor: 20%; Cycles per Burst: 200; Treatment Time: 65s). To minimize sample loss, size selection was not performed after shearing. End repair of DNA fragments and ligation with Illumina Truseq adapters was performed using End Repair/dA-Tailing Module (NEB, E7442L) and Ligation Module (NEB, E7445L) according to product manuals. Following adaptor ligation, the total volume of DNA samples was brought to 300 μl with Milli-Q H2O. To purify biotinylated DNA fragments, 50 μl Dynabeads MyOne Streptavidin T1 beads (Life technologies, 65602) were washed twice with 100 μl 1X Tween Washing Buffer (TWB, 5 mM Tris-HCl (pH 7.5); 0.5 mM EDTA; 1 M NaCl; 0.05% Tween 20), and then resuspended in 300 μl 2X Binding Buffer (10 mM Tris-HCl (pH 7.5); 1 mM EDTA; 2 M NaCl) before being added to DNA samples. The samples were incubated at RT for 15 minutes with rotation to bind biotinylated DNA to the streptavidin beads. Beads were washed twice with 100 μl 1X TWB on a Thermomixer at 55°C for 2 min with mixing and resuspended in 50 μl Milli-Q water. Samples were amplified with Phusion High-Fidelity DNA Polymerase (Thermo, F-530L) for 14-16 cycles. For size selection, 0.6X volumes of AMPure XP beads (Beckman Coulter, A63881) prewarmed to RT was added to the PCR products and samples were incubated at RT for 5 minutes. Samples were then separated on a magnet. The clear solution was mixed with another 0.2X volumes of AMPure XP beads by pipetting and incubated at RT for 5 minutes. Samples were again separated on a magnet and the clear solution was discarded. Beads were washed once with 700 μl freshly made 70% ethanol without mixing. After removing ethanol, tubes containing beads were left on the magnet for 5 minutes with lids open to allow the remaining ethanol to evaporate completely. DNA was eluted from beads with 25-50 μl of 1X Tris buffer. All Hi-C libraries were sequenced on Illumina Nova Seq 6000 platform at PE150 mode.

value: 10 months

value: metaphase I oocytes

value: GGOH treated


title: Control_Rep2

value: Control


title: Control_Rep1


title: OMIIO_1

data_processing:
All RNA-seq raw data were trimmed to remove low-quality reads and adapters with Trim Galore (Version 0.6.5).
The clean reads were then mapped to the mouse reference genome (mm10) using the STAR aligner(Dobin et al., 2013) with default parameters and the annotated genes were counted by HTSeq (Anders, Pyl, & Huber, 2015).
The raw counts files were normalized using the DESeq2 package and heatmaps was generated using the ggplot2 and pheatmap packages in R.
Genome_build: mm10
Supplementary_files_format_and_content: counts

extract_protocol:
Ovaries were separated and transferred into M2 medium (Sigma). For oocyte and GCs at growing stage (GO and GCs), the follicles with a diameter of 200-250 μm were isolated using insulin syringe under stereoscope. Full-grown oocytes and GCs (FGO and FGCs) were obtained 48 h after pregnant mare serum gonadotropin (PMSG) priming. For oocyte and GCs at MI stage (MIO and MIGCs), C57BL/6 female mice were intraperitoneally injected with 10 units PMSG, and 48 h later injected with 10 units human chorionic gonadotropin (hCG). After 9 h, the mice were sacrificed by cervical dislocation and the ovaries were separated. The pre-ovulatory follicles were punctured using a 1 mL disposable syringe under stereoscope, and COCs were transferred into new hyaluronidase droplets with the mouth pipette for 5 minutes of digestion. For oocyte and GCs at MII stage (MIIO and MIIGCs), the COCs were isolated from oviduct after 13 h and cumulus masses were separated in hyaluronidase medium. Oocytes and GCs from young (6 weeks old ) and aged (10 months old) mice at four stages were collected and processed for smart RNA-seq.
RNA-seq libraries were constructed as previously described (Liu et al., 2021). Discover-scTM WTA Kit V2 (Vazyme, N711) was used to obtain cDNA from single oocyte and GCs. The TruePrepTM DNA Library Prep Kit V2 for Illumina (Vazyme, TD503) was used for the purpose of constructing libraries. An Illumina HiSeq X platform (Shanghai, China) performs libraries sequencing. High-quality reads were aligned to Mus musculus UCSC mm9 references and FPKM value of each gene was calculated.

value: oocytes

value: wt


title: OMIO_3


title: OMIIO_3


title: OMIO_2


title: OMIIO_2


title: OGO_4


title: OGO_2


title: OGO_1


title: OGO_3


title: OFGO_3


title: OFGO_2


title: YMIIO_3

value: 6 weeks


title: OFGO_1


title: YMIIO_2


title: GGOH_Rep1


title: YMIO_1


title: YGO_4


title: YMIIO_1


title: YMIO_2


title: YMIO_3


title: YGO_3


title: YGO_2


title: YGO_1


title: OMIO_1


title: YFGO_3


title: YFGO_2


title: OMIIOGC_3

data_processing:
All RNA-seq raw data were trimmed to remove low-quality reads and adapters with Trim Galore (Version 0.6.5).
The clean reads were then mapped to the mouse reference genome (mm10) using the STAR aligner(Dobin et al., 2013) with default parameters and the annotated genes were counted by HTSeq (Anders, Pyl, & Huber, 2015).
The raw counts.txt files were normalized using the DESeq2 package and heatmaps was generated using the ggplot2 and pheatmap packages in R.
Genome_build: mm10
Supplementary_files_format_and_content: counts.txt

source_name: granulosa cells

value: granulosa cells


title: YFGO_1


title: OMIIOGC_2


title: OMIIOGC_1


title: liver_R636Q_hom_mouse_PBS_rep3

city: Heidelberg

first: Shengdi

address: Meyerhofstraße 1

institute: EMBL

data_processing:
Paired-end RNA sequencing reads were aligned to the mouse genome using STAR and processed into count tables using DEXEQ.
Assembly: GRCm39

molecule: polyA RNA

source_name: liver

extract_protocol:
RNA isolation was perfomed on 200 ul of homogenized tissue with 1 ml TRIzol (ThermoFisher), and then processed using the Direct-zol RNA Miniprep Kit with on-column DnaseI digestion. 200-500 ng RNA was used as input for reverse transcription with SuperScript IV (ThermoFisher).
RNA sequencing libraries were prepared using the NEBNext Ultra II Directinal RNA Library Prep Kit following manufactrurer's instruction.

value: liver

value: PBS


title: liver_R636Q_hom_mouse_PBS_rep2


title: liver_R636Q_hom_mouse_NRCH_gRNA6_rep3


title: liver_R636Q_hom_mouse_NRCH_gRNA6_rep2


title: OMIOGC_3


title: liver_P635L_hom_mouse_PBS_rep3


title: liver_P635L_hom_mouse_NRCH_gRNA5_rep3


title: OMIOGC_2


title: liver_R636Q_hom_mouse_PBS_rep1


title: liver_P635L_hom_mouse_NRCH_gRNA5_rep2


title: OMIOGC_1


title: liver_P635L_hom_mouse_NRCH_gRNA5_rep1


title: Replicate2

city: Paris

first: Laure

last: Bally-Cuif

address: 25 Rue du Docteur Roux

department: Developmental and stem cell biology department

country: France

institute: Institut Pasteur

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing and gene countings were made using the Cell Ranger software. We did not use the implemented aggregation method and the data provided here corresponds to individual replicates.
Assembly: GRCz11
Supplementary files format and content: Tab-separated values files and matrix files

organism: Danio rerio

source_name: Telencephalon

extract_protocol: Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Telencephalon

value: 12 weeks


title: Replicate1

description: 10x Genomics


title: Replicate3

description: 10x Genomics


title: liver_P635L_hom_mouse_PBS_rep2


title: OGOGC_4


title: liver_P635L_hom_mouse_SpRY_gRNA5_rep3


title: liver_P635L_hom_mouse_PBS_rep1


title: OGOGC_3


title: HBV infected human sample #46

city: Kansas City

first: Sumedha

middle: S

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using the TrimGalore software.
Reads were mapped to the human genome (GRCh38) using the STAR software.
Raw read counts per genne were estimated using the featureCounts software.
Assembly: Homo_sapiens (GRCh38.rel92)
Supplementary files format and content: Excel file containing raw read counts

source_name: Liver

extract_protocol:
Total RNA was extracted using TRI reagent
Total RNA was enriched for messenger RNA (mRNA) by oligo dT capture using the NuGEN Universal Plus mRNA-seq + UDI library kit (NuGEN 9144-96). Captured mRNAs were fragmented, reverse transcribed into cDNA and ligated with unique dual indexed (UDI) sequence adapters and PCR amplified to generate indexed libraries. Validation of library preparations was performed using the Agilent Bioanalyzer. Prior to pooling, quantification of the indexed libraries was performed using the Roche LightCycler96 RealTime PCR system.

tag: Sex

value: M

tag: ethnicity

value: Asian

value: Liver

tag: infection

value: HBV

tag: sample type

value: serum


title: HBV infected human sample #52


title: Huh7 cells transfected with the plasmid pTHBV1.3

source_name: Huh7 cells

value: Japanese

value: Huh7 cells

value: plasmid pTHBV1.3


title: HBV infected human sample #44

value: F

value: Other¸ Hispanic, Latino or Spanish Origin


title: liver_R636Q_hom_mouse_NRCH_gRNA6_rep1


title: HBV infected human sample #50

value: Other, Non Hispanic, Latino or Spanish Origin


title: liver_P635L_hom_mouse_SpRY_gRNA5_rep2


title: HBV infected human sample #43


title: liver_P635L_hom_mouse_SpRY_gRNA5_rep1


title: OGOGC_2

value: wt

value: 10 months


title: heart_wt_mouse_afterBE_rep8

value: heart


title: heart_wt_mouse_afterBE_rep7


title: OGOGC_1

value: granulosa cells


title: heart_wt_mouse_afterBE_rep6


title: HBV infected human sample #41


title: OFGOGC_4


title: HBV infected human sample #35


title: heart_wt_mouse_afterBE_rep5


title: OFGOGC_3


title: OFGOGC_2


title: heart_R636Q_hom_mouse_PBS_rep2

value: PBS


title: heart_R636Q_hom_mouse_NRCH_gRNA6_rep1


title: HBV infected human sample #40


title: heart_R636Q_hom_mouse_PBS_rep1


title: heart_R636Q_hom_mouse_NRCH_gRNA6_rep2


title: OFGOGC_1


title: HBV infected human sample #33


title: heart_R636Q_hom_mouse_PBS_rep3


title: heart_wt_mouse_afterBE_rep4


title: HBV infected human sample #32


title: heart_wt_mouse_afterBE_rep3


title: heart_R636Q_hom_mouse_NRCH_gRNA6_rep3


title: heart_wt_mouse_afterBE_rep2


title: YMIIOGC_3

value: 6 weeks


title: HBV infected human sample #27

value: White or Caucasian


title: HBV infected human sample #24

value: M

value: Asian


title: heart_P635L_hom_mouse_NRCH_gRNA5_rep2


title: HBV infected human sample #18

value: Liver

value: HBV


title: YMIOGC_3


title: YMIOGC_2


title: heart_P635L_hom_mouse_PBS_rep3


title: heart_P635L_hom_mouse_NRCH_gRNA5_rep3


title: YMIIOGC_2


title: HBV infected human sample #20

value: serum


title: heart_P635L_hom_mouse_PBS_rep1


title: heart_P635L_hom_mouse_PBS_rep2


title: heart_P635L_hom_mouse_SpRY_gRNA5_rep4


title: heart_P635L_hom_mouse_SpRY_gRNA5_rep3


title: heart_P635L_hom_mouse_NRCH_gRNA5_rep1


title: HBV infected human sample #17

value: Other¸ Non Hispanic, Latino or Spanish Origin


title: heart_P635L_hom_mouse_SpRY_gRNA5_rep5


title: YMIOGC_1


title: YMIIOGC_1


title: HBV infected human sample #15


title: YGOGC_4


title: heart_P635L_hom_mouse_SpRY_gRNA5_rep2


title: HBV infected human sample #02


title: HBV infected human sample #07


title: LB3 RNA-seq

city: Daejeon

first: Inkyung

last: Jung

address: KAIST, 291 Daehak-ro, Yuseong-gu

department: Biological Sciences

country: South Korea

institute: KAIST

data_processing:
RNA sequencing reads were aligned to the hg38 reference genome using HISAT2 with the parameters ‘--dta --known-splicesite-infile’. Gene abundance information is obtained from the aligned bam files using stringTie with the parameters '-G -e -A'. Human GENCODE v32 gtf file was used as a reference transcript annotation.
Assembly: GRCh38
Supplementary files format and content: StringTie tab-delimited gene abundances output

source_name: Substantia nigra

extract_protocol:
Total RNA was extracted from flash-frozen postmortem SN tissues using NucleoSpin RNA XS (Macherey-Nagel, 740902)
RNA sequencing libraries were generated using the TruSeq stranded mRNA library prep kit (Illumina, 20020594). Using the Illumina HiSeq 4000 or NextSeq High, RNA sequencing libraries were sequenced in 75 or 76 bp paired-end.

value: Substantia nigra

tag: subject status

value: Lewy body case


title: YGOGC_3


title: HBV infected human sample #03

value: F


title: YGOGC_1


title: NP69T_K27ac_rep2

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
ChIP-seq reads were aligned to hg19 reference human genome, using bowtie2.3.4.1.
Alignments were filtered for ENCODE blacklisted regions (ENCODE Project Consortium, 2012, doi: 10.1038/nature11247).
Duplication reads were removed from aligned file by using picard-tools-2.18.21.
The mapped sequence reads were extended to 100 bp and converted to the continuous signal data in bedGraph format using HOMER4.10 makeUCSCfile command.  BedGraph files were converted to bigwig files using UCSC BedGraphToBigWig program.
Assembly: hg19
Supplementary files format and content: bigwig

source_name: Nasophryngeal epithelial cell line

growth_protocol: These cells were cultured in K-SFM with supplement at 37 °C in 5% CO2 incubator.

extract_protocol:
For ChIP-seq, sonicated nuclear fraction was incubated with each antibody and histone-DNA complexes were isolated.
ChIP-seq libraries were prepared using KAPA Hyper Prep Kit (KAPA Biosystems) following the manufacturer’s protocol.

value: Nasophryngeal epithelial cell line

tag: chip antibody


title: LB2 RNA-seq


title: NP69T_K4me3_rep2

value: H3K4me3_ChIP (Active Motif, 39159, lot 25817005)


title: YFGOGC_4

tag: strain

value: wt


title: HOMIIO4

data_processing:
All RNA-seq raw data were trimmed to remove low-quality reads and adapters with Trim Galore (Version 0.6.5).
The clean reads were then mapped to the human reference genome (hg38) using the STAR aligner(Dobin et al., 2013) with default parameters and the annotated genes were counted by HTSeq (Anders, Pyl, & Huber, 2015).
The raw counts files were normalized using the DESeq2 package and heatmaps was generated using the ggplot2 and pheatmap packages in R.
Genome_build: hg38
Supplementary_files_format_and_content: counts

extract_protocol:
Human MII oocytes were obtained from patients undergoing in vitro fertilization and embryo transfer procedure due to a sperm quality issue or tubal obstruction.
RNA-seq libraries were constructed as previously described (Liu et al., 2021). Discover-scTM WTA Kit V2 (Vazyme, N711) was used to obtain cDNA from single oocyte and GCs. The TruePrepTM DNA Library Prep Kit V2 for Illumina (Vazyme, TD503) was used for the purpose of constructing libraries. An Illumina HiSeq X platform (Shanghai, China) performs libraries sequencing. High-quality reads were aligned to Mus musculus UCSC mm9 references and FPKM value of each gene was calculated.

treatment_protocol: Oocytes were isolated from donors under 28 (21-28) [HY] or over 38 (38-42) years old [HO].

value: oocytes

tag: patient age

value: over 38


title: AD6 RNA-seq

tag: tissue

value: Alzheimer's disease


title: heart_P635L_hom_mouse_SpRY_gRNA5_rep1

value: heart


title: HOMIIO3


title: LB5 RNA-seq


title: LB4 RNA-seq


title: YGOGC_2

value: granulosa cells

value: 6 weeks


title: LB1 RNA-seq


title: AD5 RNA-seq


title: genomic DNA from normal nasopharyegal epithelial tissue-1

type: genomic

description: SAMPLE 3

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC Beadchip Kit using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from cell lines or clinical samples using QIAquick DNA mini kit according to standard instructions

tag: gender

value: Male

value: clinical sample

tag: disease state

value: normal

value: normal nasopharyngeal epithelial tissue


title: HOMIIO2


title: YFGOGC_3


title: AD2 RNA-seq


title: genomic DNA from normal nasopharyegal epithelial tissue-3

description: SAMPLE 5

value: Female


title: genomic DNA from normal nasopharyegal epithelial tissue-2

description: SAMPLE 4


title: AD3 RNA-seq

value: Substantia nigra


title: PSME4KD_replicate2

city: Rehovot

first: Aaron

last: Javitt

state: Other/International

address: Herzl St 234,

country: Israel

institute: Weizmann Institute of Science

data_processing:
Analysis of RNA-seq data was carried out in User-friendly Transcriptome Analysis Pipeline UTAP version 1.10.2
Reads were trimmed using the Cutadapt function. Reads were then mapped to the mouse genome hg38 using STAR method. Followed by quantification with RefSeq annotated genes. Counting was performed using STAR. Subsequently, the analysis was carried out for genes that have at least 5 reads in at least one sample.
Normalization of the counts was done using DESeq2 with the parameters: betaPrior=True, cooksCutoff=FALSE, independentFiltering=FALSE.
Raw p-values were adjusted for multiple testing using Benjamini and Hochberg.
The adjusted p-value was corrected with FDR tools with the normal null model used for statistics.
Assembly: hg38

source_name: lung

growth_protocol: A549 cells were grown in DMEM

extract_protocol:
Total RNA was extracted from cells using Trizol (Ambion Life Technologies) and chloroform, followed by washes with isopropanol and 70% ethanol. Next, 1 ug of extracted RNA was used as an input for mRNA isolation using polyA beads (Lexogen’s SENSETM mRNA-Seq Kit V2).
libraries were prepared using the Lexogen’s SENSETM mRNA-Seq Kit V2, according to the manufacturer’s instructions.

value: lung

tag: cell line

value: lung carcinoma epithelial cells

value: PSME4 KD


title: HOMIIO1


title: genomic DNA from Low-NPC-2

description: SAMPLE 2

value: nasopharyngeal cancer

tag: cell type

value: low methylation nasoharyngeal cancer case


title: genomic DNA from NP69T-LMP1

description: SAMPLE 7

value: Unknown

value: cell line

value: immortalised normal nasopharyngeal epithelial cell


title: CTRLKD_replicate1

value: RFP KD


title: HYMIIO7

value: oocytes

value: under 28


title: CTRLKD_replicate2


title: NP69T-LMP1

data_processing:
Illumina bcl2fastq2.20.0 software used for basecalling.
Read were aligned with HISAT v2.1.0.
Fragments per kilobase of exon model per million mapped fragments (FPKM) were calculated using Cufflinks v2.2.1. Command line options for cufflinks were '--max-bundle-flags 4000000' for RNA-seq
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.

growth_protocol: NP69T and NP69T-LMP1 cells were cultured in K-SFM with supplement.

extract_protocol:
Total RNA was collected using Direct-zol RNA MiniPrep Kit (Zymo Research, Irvine, CA)
Libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina).


title: Hi-C_OMIIO_2

data_processing:
Hi-C reads were mapped to the mm10 genome and filtered using the hiclib pipeline (https://bitbucket.org/mirnylab/hiclib) as described previously (Crane et al.).
The mapped Hi-C fragments of replicates were combined and converted into cooler format using the cooler package (https://github.com/mirnylab/cooler, Abdennur & Mirny, 2020).
Genome_build: mm10
Supplementary_files_format_and_content: cool

value: 10 months

value: metaphase II oocytes


title: genomic DNA from Low-NPC-1

description: SAMPLE 1

value: Male

value: clinical sample


title: genomic DNA from NP69T

description: SAMPLE 6

value: normal

value: immortalised normal nasopharynegal epithelial cell


title: HYMIIO6


title: NP69T


title: PSME4KD_replicate1

value: lung


title: NP69T_K27ac_rep1

value: Nasophryngeal epithelial cell line


title: YFGOGC_1

value: granulosa cells

value: wt

value: 6 weeks


title: Hi-C_OMIIO_1


title: NP69T_K4me3_rep1

value: H3K4me3_ChIP (Active Motif, 39159, lot 25817005)


title: HYMIIO5


title: HYMIIO4


title: heart_wt_mouse_beforeBE_rep10

value: heart

tag: treatment


title: heart_R636Q_hom_mouse_beforeBE_rep5


title: heart_R636Q_hom_mouse_beforeBE_rep4


title: Hi-C_OMIO_1

value: metaphase I oocytes


title: Hi-C_OMIO_2


title: HYMIIO3


title: Hi-C_OFGO_2

value: full-grown oocytes


title: HYMIIO2

value: oocytes


title: heart_R636Q_hom_mouse_beforeBE_rep3


title: HYMIIO1

value: under 28


title: heart_R636Q_het_mouse_beforeBE_rep4


title: heart_wt_mouse_beforeBE_rep8


title: Hi-C_OGO_2

value: 10 months

value: germinal vesicle oocytes


title: heart_R636Q_het_mouse_beforeBE_rep5


title: HOMIIGC3

data_processing:
All RNA-seq raw data were trimmed to remove low-quality reads and adapters with Trim Galore (Version 0.6.5).
The clean reads were then mapped to the human reference genome (hg38) using the STAR aligner(Dobin et al., 2013) with default parameters and the annotated genes were counted by HTSeq (Anders, Pyl, & Huber, 2015).
The raw counts.txt files were normalized using the DESeq2 package and heatmaps was generated using the ggplot2 and pheatmap packages in R.
Genome_build: hg38
Supplementary_files_format_and_content: counts

extract_protocol:
hGCs were isolated from donors under 28 (21-28) [HY] or over 38 (38-42) years old [HO]. The hGCs were washed with 500 μL phosphate buffered saline (PBS) (Gibco) and centrifuged at 3,000 rpm for 5 min. Then 50 μL hyaluronidase (Sigma) was added to digest hGCs at 37oC for 5 min. The cell suspensions were washed with 100 μL PBS and then 20 μL PBS was added to resuspend cell pellet.
RNA-seq libraries were constructed as previously described (Liu et al., 2021). Discover-scTM WTA Kit V2 (Vazyme, N711) was used to obtain cDNA from single oocyte and GCs. The TruePrepTM DNA Library Prep Kit V2 for Illumina (Vazyme, TD503) was used for the purpose of constructing libraries. An Illumina HiSeq X platform (Shanghai, China) performs libraries sequencing. High-quality reads were aligned to Mus musculus UCSC mm9 references and FPKM value of each gene was calculated.

value: over 38


title: heart_R636Q_hom_mouse_beforeBE_rep2


title: heart_R636Q_hom_mouse_beforeBE_rep1


title: Hi-C_OGO_1


title: heart_wt_mouse_beforeBE_rep7


title: heart_R636Q_het_mouse_beforeBE_rep3


title: HOMIIGC2


title: heart_wt_mouse_beforeBE_rep6


title: HOMIIGC1


title: Hi-C_YMIIO_2

value: metaphase II oocytes


title: heart_wt_mouse_beforeBE_rep9


title: HBV infected human sample #34

value: M

value: Asian

value: Liver

value: HBV

value: serum


title: heart_R636Q_het_mouse_beforeBE_rep2


title: HYMIIGC9

value: granulosa cells


title: heart_wt_mouse_beforeBE_rep5

value: wt


title: Hi-C_OFGO_1


title: heart_R636Q_het_mouse_beforeBE_rep1


title: heart_wt_mouse_beforeBE_rep4


title: Hi-C_YMIIO_1

value: 6 weeks


title: heart_wt_mouse_afterBE_rep1

value: heart


title: HYMIIGC7


title: Hi-C_YMIO_2

value: metaphase I oocytes


title: HYMIIGC8


title: heart_wt_mouse_beforeBE_rep1


title: Hi-C_YMIO_1


title: heart_wt_mouse_beforeBE_rep2


title: Hi-C_YFGO_2

value: full-grown oocytes


title: heart_P635L_het_mouse_beforeBE_rep5


title: HYMIIGC6


title: heart_P635L_het_mouse_beforeBE_rep4


title: HYMIIGC5


title: heart_P635L_het_mouse_beforeBE_rep2


title: heart_P635L_het_mouse_beforeBE_rep3


title: Hi-C_YFGO_1


title: Hi-C_YGO_2


title: HYMIIGC4


title: heart_P635L_hom_mouse_beforeBE_rep5


title: heart_P635L_het_mouse_beforeBE_rep1


title: Hi-C_YGO_1


title: HYMIIGC3


title: AD4 RNA-seq

value: Substantia nigra

value: Alzheimer's disease


title: heart_P635L_hom_mouse_beforeBE_rep3


title: heart_wt_mouse_beforeBE_rep3


title: heart_P635L_hom_mouse_beforeBE_rep2


title: CITE-seq ADT (breast cancer)

city: Dallas

first: Siyuan

last: Zhang

address: 6001 Forest Park Rd

department: Department of Pathology

institute: UT Southwestern Medical Center

description: ADT

data_processing:
Demultiplexing: cellranger mkfastq
10x genomics Cellranger V3.1 was used for alignment, filtering, barcoding Counting and UMI Counting.
HTO1-6 were used for sample level demultiplexing and group assignment. We stained each sample with it's own unique hashing antibody so that we could subsequently pool the samples for loading onto the 10x Chromium and later prepare one library consisting of all sight samples and finally separate each sample in silico by it's unique hashing antibody. The samples are as follows: (1) HTO1: tumor of PBS treated C3-1-TAg mouse; (2) HTO2: tumor of PBS treated C3-1-TAg mouse;  (3) HTO3: tumor of PBS treated C3-1-TAg mouse;  (4) HTO4: tumor of MCT treated C3-1-TAg mouse;  (5) HTO5: tumor of MCT treated C3-1-TAg mouse; (6) HTO6: tumor of MCT treated C3-1-TAg mouse. The following sample comparisons were made: HTO1, HTO2, and HTO3 versus HTO4, HTO5, and HTO6.
After generating the digital gene expression data matrices, the Seurat R package V3.1.1 (Satija, 2015) was used to perform data normalization, dimension reduction, clustering and differential expression analysis.
Genome_build: mm10-3.0.0
Supplementary_files_format_and_content: tab-delimited text files that include UMI values for gene UMI, HTO and ADT counts

source_name: CITE-seq ADT

growth_protocol: Spontaneous breast tumor bearing C3-1-TAg mice were used.

extract_protocol:
Breast tumors were digested using collagenase enzyme. Immune cells were enriched using CD45 magnetic beads (Miltenyi).
cite-seq_and_hashing_protocol_190213.pdf
10x genomics single cell 3’ v3 assay

treatment_protocol: The tumor bearing mice (5mm*5mm) were treated intravenously with either PBS or a combination of Doxorubicin and Cyclophosphamide thrice a week for four weeks.

tag: mouse strain

value: 1 mouse tumor per HTO


title: CITE-seq HTO (breast cancer)

source_name: CITE-seq HTO


title: AD1 RNA-seq


title: HYMIIGC1

value: under 28


title: cDNA (breast cancer)

description: cDNA

source_name: cDNA


title: PD6 RNA-seq

value: Parkinson's disease


title: heart_P635L_hom_mouse_beforeBE_rep1

tag: genotype


title: I: XIPO323_24hr_r3

status: Public on Feb 25 2023

city: Harpenden

first: Daniel

last: Smith

state: Hertfordshire

address: West Common

department: IDE

institute: Rothamsted Research

data_processing:
Quality control of reads was performed using MultiQC. Sequence trimming of recognised adaptors was performed using Trimmomatic (Bolger et al., 2014) v0.39-Java-11. Reads were mapped to the Z. tritici IPO323 genome using HiSat2 (Kim et al., 2019) v2.2.1-foss-2019b. Principal Component Analysis (PCA) was performed on sample differences of variance stabilising transformed (vsd) gene count data to confirm that biological replicates clustered together. Count determination was performed using featureCounts (Liao et al., 2014), part of the SubRead package v2.0.0-GCC-8.3.0. Library normalisation and differential expression (DE) calling were done using the Bioconductor package v3.16 DESeq2 (Love et al., 2014; https://bioconductor.org/packages/release/bioc/html/DESeq2.html) in R.
Assembly: Triticum aestivum Chinese Spring IWGSC v2.1; Zymoseptoria_tritici MYCGR v2.0
Supplementary files format and content: taestivumCellWallRNAStringent.txt tab is delimited plain text listing gene counts generated using SubRead FeatureCounts

organism:
Triticum aestivum
Zymoseptoria tritici IPO323

source_name: Triticum aestivum (NCBI:txid4565), Zymoseptoria tritici  (NCBI:txid336722)

extract_protocol:
Infected leaf tissues were excised at 6 and 24 h and immediately snap frozen. Each technical and biological replicate incorporated five leaves. Total RNA was isolated using the TRIZOL procedure (Invitrogen) and RNA quality was assessed using Nanodrop and gel electrophoresis.
The library construction protocol was carried out by the contractor Novogen.  They report they did the following. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.

treatment_protocol: Second leaves of wheat cv. Riband seedlings grown for 21 days in complete compost were inoculated with spores of mutant isolates collected from YPD cultures, which had been washed and re-suspended in dH2O+0.01% Tween 20 to a density of 1x107 spores ml-1

value: infected leaf

value: T. aestivum cv. Riband, Z. tritici IPO323 (NCBI:txid336722)

value: 24 hours post infection


title: J: Y4124_24hr_r1

value: T. aestivum cv. Riband, Z. tritici IPO323 mutant 4-124 (NCBI:SAMN33272755)


title: H: XIPO323_24hr_r2


title: K: Y4124_24hr_r2


title: L: Y4124_24hr_r3


title: G: XIPO323_24hr_r1


title: E: Y4124_6hr_r2

value: 6 hours post infection


title: F: Y4124_6hr_r3


title: C: XIPO323_6hr_r3


title: D: Y4124_6hr_r1


title: heart_P635L_hom_mouse_beforeBE_rep4


title: A: XIPO323_6hr_r1


title: B: XIPO323_6hr_r2

description: PCA identifes sample B as a bad replicate (possible contamination)


title: DM210930_A_S1

city: Waltham

first: Michael

last: Rosbash

address: 415 South street

institute: HHMI/Brandeis University

data_processing:
For CEL-seq2 libraries, bcl2fastq v2.20 was used to convert the raw sequencing files into fastq files, zUMI v2.1.1 was used to align the reads to Drosophila genome
For 10X libraries, Cellranger-6.0.2 was used to map and count the reads
Assembly: dm6
Supplementary files format and content: raw read counts in rds file
Supplementary files format and content: raw read counts in matrix
Supplementary files format and content: raw read counts in csv

organism: Drosophila melanogaster

extract_protocol: CEL-seq2 and 10X Chromium

value: Adult neurons

value: TH-Gal4 and Clk856-Gal4 labeled neurons

tag: method

value: 10X Chromium

tag: Stage


title: HYMIIGC2

value: granulosa cells


title: th_ZT22_AR15_0627

source_name: TH neurons CEL-seq2 ZT22

value: TH-Gal4 labeled neurons


title: DM210930_B_S2


title: th_ZT22_AR16_0627


title: th_ZT22_AR14_0627


title: th_ZT22_AR13_0627


title: th_ZT18_AR16_0624

source_name: TH neurons CEL-seq2 ZT18


title: th_ZT18_AR15_0624


title: th_ZT14_AR06_0611

source_name: TH neurons CEL-seq2 ZT14


title: th_ZT18_AR13_0624


title: th_ZT10_AR19_0624

source_name: TH neurons CEL-seq2 ZT10


title: th_ZT14_AR05_0611


title: th_ZT14_AR08_0611


title: th_ZT6_AR04_0627

source_name: TH neurons CEL-seq2 ZT06


title: th_ZT10_AR18_0624


title: th_ZT6_AR05_0627


title: th_ZT18_AR14_0624


title: th_ZT10_AR17_0624


title: th_ZT6_AR02_0627


title: th_ZT6_AR03_0627


title: th_ZT02_AR04_0611

source_name: TH neurons CEL-seq2 ZT02


title: th_ZT02_AR02_0611


title: th_ZT02_AR01_0611


title: th_ZT14_AR07_0611


title: th_ZT02_AR03_0611


title: Bladder_tumor_S33_exp1 short-term

type: RNA

city: Lund

first: Ines

last: Ambite

address: Klinikgatan 28

department: Laboratory Medicine

institute: Lund University

description: Gene expression data from MB49-induced murine bladder cancer

hyb_protocol: 15ug cRNA was used for 2nd-cycle ss-cDNA of which 3ug cDNA was fragmented and hybridized onto Mouse Clariom S HT 24-array plates.

scan_protocol: Scanning was done using the GeneTitan Scanner systems (Thermo Fisher).

data_processing: Transcriptomic data was normalized using Robust Multi Average implemented in the Transcriptome Analysis Console software (v.4.0.1.36, Applied Biosystems, ThermoFisher Scientific).

label: biotin

source_name: Mice bladder cancer 4w 1 treatment

label_protocol: 100 ng of total RNA was amplified, labeled and fragmented using the Affy WT PLUS Reagent Kit ( ThermoFisher Scientific). Biotinylated cRNA was prepared according to the standard Affymetrix's protocol.

growth_protocol: Bladder cancer was induced in C57BL/6J female mice by intravesical instillation of MB49 cells. On day 0, bladders were emptied and preconditioned by intravesical instillation of 100 μl poly-L-lysine solution (0.1 mg/ml) for 30 minutes followed by instillation of MB49 mouse bladder carcinoma cells (2 × 10^5 in 100 μl PBS).

extract_protocol: At sacrifice, bladders were aseptically harvested for mRNA extraction and and analysis. Total RNA was extracted (RNeasy Mini kit, Qiagen) according to the manufacturer's instructions.

treatment_protocol: Treatment groups received 100 μl intravesical instillations with alpha1-oleate (1.7 mM or 8.5 mM) or chemotherapeutic drugs (MMC 25 μg, Epirubicin 25 μg), alone or in combination (2 -3  hours) on days 3, 5, 7, 9 and 11. Sham treated animals received PBS and healthy mice bladders were used as control. Bladder samples were collected after 12 days and 27 days (4w, follow-up).

value: female

value: bladder

tag: experiment

value: 4w 1T


title: Bladder_tumor_S28_exp1 short-term


title: Bladder_tumor_S18_exp1 short-term

source_name: Mice bladder cancer 12d 1 treatment


title: Bladder_tumor_S30_exp1 short-term


title: YFGOGC_2

source_name: granulosa cells

value: wt

tag: age

value: 6 weeks


title: Bladder_tumor_S25_exp1 short-term

source_name: Mice bladder healthy


title: Bladder_tumor_S20_exp1 short-term


title: Bladder_tumor_S31_exp1 short-term


title: Bladder_tumor_S23_exp1 short-term


title: Bladder_tumor_S15_exp1 short-term


title: Zinc deficient mice Zn6

city: Miyagi

first: Hiroyuki

last: Ikushima

address: 1-1 Seiryotyou Aobaku Sendai

institute: Tohoku Univercity

data_processing:
NextSeq500/550 version 2.5 and the NextSeq 500 System (Illumina)
Sequencing was performed using paired-end reads of 36 bases.
The basic information of the next-generation sequencing run data was checked using CLC Genomics Workbench 20.0.3 software (QIAGEN).
During the quality assessment of the reads, a PHRED score >20 was confirmed for 99.97% of all reads, indicating the success of the run.
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample, Zn vs. Con - FDR p-value, and Zn vs. Con - Fold change

source_name: nasal mucosa

growth_protocol: Control mice were reared on a control diet and zinc-deficient mice were reared on a zinc-deficient diet from 4 to 8 weeks of age.

extract_protocol:
RNA was harvested using RNAiso Blood (Takara Bio). 500 ng of RNA from each sample was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina and NEBNext rRNA Depletion Kit version 2.

treatment_protocol: Tissue samples were taken from the posterior nasal septum, including mucosa and bone.

value: nasal mucosa

value: Zinc-deficient


title: Zinc deficient mice Zn5


title: Zinc deficient mice Zn4


title: Control mice C6

value: Sufficient zinc


title: Bladder_tumor_S19_exp1 short-term

value: Epi


title: Bladder_tumor_S14_exp1 short-term


title: Bladder_tumor_S27_exp1 short-term

value: PBS


title: Bladder_tumor_S26_exp1 short-term


title: Bladder_tumor_S21_exp1 short-term


title: Bladder_tumor_S10_exp3 long term

hyb_protocol: 6ug of fragmented and labelled cRNA was hybridized onto Mouse Genome 430 PM array strips (Affymetrix) for 16 hours at 45 °C, washed, stained (Applied Biosystems, ThermoFisher Scientific).

scan_protocol: Scanning was done using the GeneAtlas systems (Thermo Fisher).

label_protocol: 100 ng of total RNA was amplified, labeled and fragmented using the GeneChip 3´IVT PLUS Kit ( ThermoFisher Scientific). Biotinylated cRNA was prepared according to the standard Affymetrix's protocol.

treatment_protocol: Treatment groups received 100 μl intravesical instillations with alpha1-oleate (8.5 mM) alone or in combination with chemotherapeutic drugs (MMC 25 μg, Epirubicin 25 μg). The catheter was left in place for about one minute and the time to voiding was 2 - 3 hours. Mice were subjected to 2 or 3  treatment rounds (5 treatments, 1 every other day), starting on days 3, 28 and 56. Bladder samples were then collected on days 56 (8 weeks) and 84 (12 weeks), respectively. Sham treated animals received PBS and healthy mice bladders were used as control.


title: Bladder_tumor_S6_exp3 long term

source_name: Mice bladder cancer 8w 2 treatments

value: 8w 2T


title: Bladder_tumor_S9_exp3 long term


title: Bladder_tumor_S22_exp1 short-term


title: Bladder_tumor_S32_exp1 short-term


title: Bladder_tumor_S17_exp1 short-term


title: Bladder_tumor_S29_exp1 short-term

value: MMC


title: Bladder_tumor_S24_exp1 short-term


title: Bladder_tumor_S16_exp1 short-term


title: Bladder_tumor_S7_exp3 long term


title: Bladder_tumor_S8_exp3 long term


title: Control mice C5


title: Control mice C4


title: Bladder_tumor_S13_exp1 short-term


title: T-STEM-like CAR-T cells donor B262

city: Melbourne

first: Paul

middle: J

last: Neeson

state: Victoria

address: 305 Grattan Street

department: Cancer Research

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
Sequencing data was demultiplexed and base call files (BCL) were converted into FASTQ files using bcl2fastq v2.20.0.422
Sequence reads were trimmed for low quality and minimum length using cutadapt v2.1 (parameter -q 15 -m 50)
Trimmed sequence reads were mapped to GRCh37 release 75, using hisat v2.0.4
Gene quantification was performed using htseq v0.11.2 (parameter -m intersection-nonempty -s reverse -t exon -i gene_name)
Assembly: GRCh37
Supplementary files format and content: tab-delimited text files include raw count for each Sample

source_name: T-STEM-like CAR-T cells

extract_protocol:
RNAEasy mini-kit QIAGEN
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina and NEBNext Poly(A) mRNA Magnetic Isolation Module, NEB

value: T-STEM-like CAR-T cells

value: WT


title: Conventional CAR-T cells donor B266

source_name: Conventional CAR-T cells

value: Conventional CAR-T cells


title: T-STEM-like CAR-T cells donor B264


title: Conventional CAR-T cells donor B262


title: T-STEM-like CAR-T cells donor B266


title: Conventional CAR-T cells donor B264


title: upf1KO,20mM H2O2,rep2

city: Beijing

first: Yuanhao

last: Meng

address: China Agricultural University (West Campus), No. 2, Yuanmingyuan West Road

institute: China Agricultural University

data_processing:
Fastqc was used to detect the quality of sequencing data,
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Hisat2 (version 2.2.1) was used as the aligner to map the reads to the reference genome [N. crassa OR74A (NC12)]
FeatureCounts (subread, version 2.0.1) was used to count the reads
Assembly: NC12
Supplementary files format and content: TXT,Text file, Recording the gene expression data of each sample

organism: Neurospora crassa OR74A

source_name: Mycelium

extract_protocol:
Total RNA was extracted by Trizol (water saturated phenol, guanidine isothiocyanate, ammonium thiocyanate, sodium acetate, glycerin) method, and then standard Illumina protocols were used to build the RNA library
Following standard Illumina protocols

treatment_protocol: The wild type and upf1 knockout strains were cultured in the same condition, with no or 20mM H2O2 treatment.

value: Mycelium

value: Hyphal cell

value: 20mM H2O2 treatment


title: T3

city: Xi'an

first: huayu

last: Zhu

address: No. 28 Road

institute: Fourth

description: microRNA expression after triamcinolone acetonide and lidocaine injection

hyb_protocol: After purification the labeled RNAs were hybridized onto the microarray.

scan_protocol: After washing, the arrays were scanned with the Agilent Scanner G2505C (Agilent Technologies).

data_processing:
Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data.
Next, the raw data was normalized with the quantile algorithm. The probes that at least 100.0 percent of samples in any 1 condition out of 2 conditions have flags in Detected were chosen for further data analysis. Differentially expressed miRNAs were then identified through fold change as well as P value calculated using t-test. The threshold set for up- and down-regulated genes was a fold change >= 2.0 and a P value <= 0.05.

source_name: hypertrophic scar

label_protocol: The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols. Briefly, total RNA were dephosphorylated, denaturated and then labeled with Cyanine-3-CTP.

extract_protocol: Patients received surgical treatment to resect the HS tissues. Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific) and the RNA integrity(RIN) was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: These patients were diagnosed by routine pathological examination and were given local injections of glucocorticoid triamcinolone acetonide mixed with lidocaine in for more than 3 months. Patients who had received lidocaine treatment were enrolled as controls. Patients received surgical treatment to resect the HS tissues.

value: hypertrophic scar

tag: agent


title: Bladder_tumor_S12_exp1 short-term

value: female

value: bladder


title: upf1KO,20mM H2O2,rep3


title: T1

value: glucocorticoid triamcinolone acetonide mixed with lidocaine


title: C2

description: microRNA expression after lidocaine injection

value: lidocaine


title: C3


title: Bladder_tumor_S11_exp1 short-term

value: 4w 1T


title: Bladder_tumor_S9_exp1 short-term


title: Bladder_tumor_S3_exp3 long term


title: Bladder_tumor_S2_exp3 long term


title: Bladder_tumor_S7_exp1 short-term


title: Bladder_tumor_S8_exp1 short-term


title: Bladder_tumor_S1_exp3 long term


title: Bladder_tumor_S7_exp2 long term

source_name: Mice bladder cancer 12w 3 treatments


title: upf1KO,20mM H2O2,rep1


title: Bladder_tumor_S5_exp3 long term


title: Bladder_tumor_S4_exp3 long term


title: C1


title: WT,20mM H2O2,rep3


title: WT,20mM H2O2,rep2


title: T2


title: Bladder_tumor_S6_exp1 short-term


title: WT,20mM H2O2,rep1


title: Bladder_tumor_S10_exp1 short-term


title: Bladder_tumor_S8_exp2 long term


title: upf1KO.no treatment,rep3

value: No treatment


title: upf1KO.no treatment,rep2


title: WT,no treatment,rep3


title: Bladder_tumor_S5_exp1 short-term


title: Bladder_tumor_S4_exp1 short-term


title: Bladder_tumor_S6_exp2 long term


title: Bladder_tumor_S4_exp2 long term


title: WT,no treatment,rep1


title: Bladder_tumor_S5_exp2 long term


title: 3T3-L1 cells,  Control (CTRL-GFP), Day 2 3

status: Public on Feb 24 2023

city: Amsterdam

first: Carlie

last: de Vries

address: Meibergdreef 15

department: Medical Biochemistry

country: Netherlands

institute: Amsterdam University Medical Center

data_processing:
Analysis was performed using R v4.1.0 and Bioconductor v3.13.
Reads were subjected to quality control (FastQC v0.11.9 and dupRadar v1.12.1), trimmed using Trimmomatic v0.39 and aligned to the genomes using HISAT2 (v2.2.1).
Counts were obtained using HTSeq (v0.11.0) using the corresponding GTFs (Mus_musculus.GRCm39.105.gtf). Genes were reannotated using biomaRt, using Ensembl (v105)
The count data was transformed to log2-counts per million (logCPM) using voom, estimating the mean-variance relationship.
Differential expression was assessed using a moderated t-test using the linear model framework from the limma package.
Assembly: mm39
Supplementary files format and content: .txt files contain counts of sequencing reads for each ENSEMBL transcript.

growth_protocol: 3T3-L1 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA isolation from these cultured cells was performed using TRI Reagent (Sigma) according to manufacturer’s protocol.
Libraries were generated using Truseq RNA stranded polyA (Illumina)

treatment_protocol: Adipogenic differentiation was induced by treatment of post confluent cells (Day 0) with 170 nM insulin, 1uM dexamethasone, and 0.5mM isobutylmethylxanthine in the presence of 10% FBS until day 2

value: mesenchymal stem cells

value: Control

value: adipogenic differentiation

tag: time

value: Day 2


title: 3T3-L1 cells,  Control (CTRL-GFP), Day 0 3

value: Day 0


title: 3T3-L1 cells,  Control (CTRL-GFP), Day 0 1


title: 3T3-L1 cells,  Control (CTRL-GFP), Day 0 2


title: Bladder_tumor_S1_exp1 short-term

value: PBS


title: 3T3-L1 cells,  FHL2 (FHL2-GFP), Day 2 3

value: FHL2 overexpression


title: Bladder_tumor_S3_exp2 long term


title: 3T3-L1 cells,  FHL2 (FHL2-GFP), Day 2 2


title: 3T3-L1 cells,  FHL2 (FHL2-GFP), Day 0 3


title: 3T3-L1 cells,  FHL2 (FHL2-GFP), Day 0 1


title: 3T3-L1 cells,  FHL2 (FHL2-GFP), Day 2 1


title: Bladder_tumor_S2_exp2 long term


title: WT,no treatment,rep2

value: Mycelium

value: WT


title: Bladder_tumor_S2_exp1 short-term


title: RW3 WT

city: Hangzhou

first: Xiaoyu

last: Wang

state: Zhejiang

address: Yuhangtang Road

department: College of Life Sciences

institute: Zhejiang University

data_processing:
Raw data were firstly processed through in-house perl scripts as a quality control. Demultiplexed and quality filtered reads were then aligned to S. melonis TY genome sequence using Bowtie2-2.2.3. HTSeq 0.6.1 was used to count the reads numbers mapped to each gene.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions was performed using the DESeq Rpackage (1.18.0).
The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate.
Assembly: ASM176134v1
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Sphingomonas melonis TY

source_name: TY

growth_protocol: shake-flask culture, LB culture, 30℃, 200 rpm

extract_protocol:
Total bacterial samples were collected (A600 = 0.6 at the time of collected), mixed with 0.2 volumes of stop-mix (95% ethanol and 5% phenol, v/v) and snap-frozen in liquid nitrogen. Pellets were resuspended in 100 μl lysozyme solution (15 mg/ml lysozyme in TE buffer, pH = 8.0). Total RNA was isolated with Omega-E.Z.N.A.® Bacterial RNA Kit.
Briefly, RNA degradation and contamination were monitored on 1% agarose gels. The integrity of RNA sample was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, USA). Sequencing libraries were generated from rRNA-depleted RNA using the RiboMinus Bacteria 2.0 Transcriptome Isolation Kit (Thermo Scientific, USA) following the manufacturer’s recommendations.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. The library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated. Before data analysis, raw data were firstly processed through in-house perl scripts as a quality control. Demultiplexed and quality filtered reads were then aligned to S. melonis TY genome sequence using Bowtie2-2.2.3. HTSeq 0.6.1 was used to count the reads numbers mapped to each gene.

treatment_protocol: The wild type (WT) of S. melonis TY and snc137 deleted cells carrying either a plasmid overexpressing SNC137 (Δsnc137 comp.), or an empty control vector (Δsnc137) were grown in Luria-Bertani (LB) culture to an OD600 of 0.6.

value: TY

value: wild type


title: RSNC137C-2

value: comp.


title: RSNC137C-3


title: RW2 WT


title: RSNC137-1


title: RSNC137C-1


title: RSNC137-2


title: RSNC137-3


title: 3T3-L1 cells,  Control (CTRL-GFP), Day 2 2


title: 3T3-L1 cells,  Control (CTRL-GFP), Day 2 1


title: RW1 WT


title: LGG, Patient_6

city: Kaunas

first: Dovydas

last: Širvinskas

address: Eivenių st. 4

country: Lithuania

institute: Lithuanian University of Health Sciences

data_processing:
Fast5 files were base-called with high accuracy mode on using ONT's Guppy software (v5.0.11), applying a configuration file for dRNA-seq ("rna_r9.4.1_70bps_hac.cfg")
Base-called fast5 files processed with Poreplex software (Version 0.5) to extract FASTQ files
FASTQ files alligned to the full Ensembl reference transcriptome (GRCh38.p13; Version 105, cDNA + ncRNA) using Minimap2 software (ver. 2.17-r941)
Aligned SAM files were sorted and indexed with Samtools (ver. 1.15.1) and quantified using NanoCount (ver. 1.0.0.post6)
Assembly: full Ensembl reference transcriptome (GRCh38.p13; Version 105, cDNA + ncRNA)
Supplementary files format and content: Processed file NAT_lnc.csv contains calculated tpm for each sample: lncRNA and overlapping gene are provided in one row

source_name: Glioma surgical sample

extract_protocol:
RNA isolated with TRIzol. Poly-A enrichment using Dynabeads mRNA DIRECT purification kit
Libraries prepared applying Direct RNA sequencing kit

value: Glioma surgical sample

tag: disease

value: LGG

tag: survival (months)

tag: status alive_(0)/dead_(1)


title: LGG, Patient_8

tag: tissue


title: 3T3-L1 cells,  FHL2 (FHL2-GFP), Day 0 2


title: Bladder_tumor_S1_exp2 long term

tag: gender

value: female

value: bladder


title: GB, Patient_17

value: GB


title: GB, Patient_16


title: GB, Patient_15


title: GB, Patient_13


title: GB, Patient_11


title: LGG, Patient_7


title: GB, Patient_14


title: GB, Patient_10


title: GB, Patient_12


title: GB, Patient_8


title: Healthy_Brain, Control

source_name: Normal Brain

value: Normal Brain

value: Healthy


title: LGG, Patient_4


title: GB, Patient_7


title: GB, Patient_9


title: GB, Patient_6


title: GB, Patient_4


title: LGG, Patient_3


title: LGG, Patient_9


title: LGG, Patient_2


title: GB, Patient_5


title: LGG, Patient_5


title: GB, Patient_3


title: LGG, Patient_1


title: GB, Patient_2


title: GB, Patient_1


title: i2_NHS_IgG_rep2

city: Stockholm

first: Anniina

last: Vihervaara

address: Tomtebodavägen 23A

department: Gene Technology

institute: KTH Royal Institute of Technology

description:
nascent RNA
iPRO_NHS_IgG_BRs_normalized_pl.bigWig
iPRO_NHS_IgG_BRs_normalized_mn.bigWig

data_processing:
The reads were sorted into distinct samples using fastx barcode splitter (http://hannonlab.cshl.edu/fastx_toolkit/).
For paired-end reads, the R1 and R2 reads were paired using fastq_pair (https://github.com/linsalrob/fastq-pair). Reads from multiple sequencing runs (re-sequencing) were combined.
The adapter sequences were removed and UMI indicated in fastp (Chen et al., 2019).
The reads were mapped to mm10 spike-in genome (masked not to recognise run-on reads from the human genome) using Bowtie2 (Langmead and Saltzberg, 2012)
The reads were mapped to hg19 using Bowtie2 (Langmead and Saltzberg, 2012), and sam files converted to bam files with samtools (Danecek et al., 2021).
bed files and begraph files were generated using bedtools (Quinlan and Hall, 2010).
BigWig files were generated using bedGraphToBigWig
Assembly: hg19
Supplementary files format and content: Normalized, replicate-combined bigWig files are provided.

growth_protocol: Human K562 erythroleukemia cells were maintained at 37°C in a humidified 5% CO2 atmosphere and cultured in RPMI medium (Sigma), containing 10% fetal calf serum, 2 mM L-glutamate, 100 μg/ml streptomycin, and 100 U/ml penicillin. The cells were grown below 5x10^5 cells/ml confluency.

extract_protocol:
Chromatin isolation: Cells were transferred into a large volume of ice-cold PBS to instantly bring the temperature below 8°C. The cells were pelleted by centrifugation and washed with ice cold PBS. The cell pellets were resuspended in ice-cold NUN buffer and the samples vortexed and centrifuged at 12 500 G at 4°C for 30 minutes. The chromatin pellet was washed once in ice cold 50 mM Tris-HCl (pH 7.5) and stored at -80°C.
PRO-IP-seq: Fragmented chromatin was subjected to a run-on reaction with biotinylated rA/rC/rG/rUTP. After the run-on reaction the samples was divided into distinct tubes for antibody-specific immunoprecipitation. After 3'-ligation of barcoded adapters (6nt barcode + constant G at the ligation site), the samples were re-pooled into a single tube. The nascet RNA was selected with streptavidin beads (x3 during the PRO-IP-seq protocol). The 5'-ends of nascent transcripts were decapped, repaired and ligated to UMI-containing adapters (6-nt UMI + constant C at the ligation site). The nascent RNA was reverse-transcribed, quality controlled and amplified to final sequencing library (Illumina TruSeq small RNA).
Illumina NextSeq 500 and Illumina NovaSeq6000

treatment_protocol: The cells were maintained at 37°C (NHS) or heat treated for 30 min at 42°C (HS30). The heat shock was conducted in pre-conditioned pre-warmed media. The control cells (NHS) were treated as the heat shocked (HS30) cells but using preconditioned media pre-warmed to 37°C.

tag: protocol

value: No heat shock, maintained at 37degreeC (NHS)

tag: antibody

value: SantaCruz sc2027

tag: antibody epitope

value: unspecific IgG

tag: library preparation

value: PRO-IP-seq


title: i2_HS30_S5_rep2

description:
nascent RNA
iPRO_HS30_S5_BRs_normalized_pl.bigWig
iPRO_HS30_S5_BRs_normalized_mn.bigWig

value: Heat treated at 42degreeC for 30 minutes (HS30)

value: Millipore 04-1572

value: serine-5-phosphorylated CTD (ser5PhCTD)


title: i2_HS30_IgG_rep2

description:
nascent RNA
iPRO_HS30_IgG_BRs_normalized_pl.bigWig
iPRO_HS30_IgG_BRs_normalized_mn.bigWig


title: i2_HS30_CTD_rep2

description:
nascent RNA
iPRO_HS30_CTD_BRs_normalized_pl.bigWig
iPRO_HS30_CTD_BRs_normalized_mn.bigWig

value: AbCam YWG16

value: unphosphorylated CTD (unPhCTD)


title: i2_NHS_input_rep2

description:
nascent RNA
iPRO_NHS_input_BRs_normalized_pl.bigWig
iPRO_NHS_input_BRs_normalized_mn.bigWig

value: no antibody


title: i2_NHS_S2_rep2

description:
nascent RNA
iPRO_NHS_S2_BRs_normalized_pl.bigWig
iPRO_NHS_S2_BRs_normalized_mn.bigWig

value: Millipore 04-1571

value: serine-2-phosphorylated CTD (ser2PhCTD)


title: i2_NHS_CTD_rep2

description:
nascent RNA
iPRO_NHS_CTD_BRs_normalized_pl.bigWig
iPRO_NHS_CTD_BRs_normalized_mn.bigWig


title: i2_NHS_S5_rep2

description:
nascent RNA
iPRO_NHS_S5_BRs_normalized_pl.bigWig
iPRO_NHS_S5_BRs_normalized_mn.bigWig


title: i1_HS30_IgG_rep1


title: i1_HS30_input_rep1

description:
nascent RNA
iPRO_HS30_input_BRs_normalized_pl.bigWig
iPRO_HS30_input_BRs_normalized_mn.bigWig


title: i1_HS30_S7_rep1

description:
nascent RNA
iPRO_HS30_S7_BRs_normalized_pl.bigWig
iPRO_HS30_S7_BRs_normalized_mn.bigWig

value: Millipore 04-1570

value: serine-7-phosphorylated CTD (ser7PhCTD)


title: i1_HS30_S5_rep1


title: i1_HS30_S2_rep1

description:
nascent RNA
iPRO_HS30_S2_BRs_normalized_pl.bigWig
iPRO_HS30_S2_BRs_normalized_mn.bigWig


title: i1_NHS_input_rep1


title: i1_HS30_CTD_rep1


title: ChIPseq_GRHL2_H9_day7_rep1

city: Stanford

first: Anthony

last: Oro

state: CA

address: 269 Campus Drvie

department: Dermatology

institute: Stanford University

data_processing:
bowtie2.3.4.1 used for alignment.
duplicate fragments were removed using samtools1.8
macs2 used for peak calling
Genome_build: hg38
Supplementary_files_format_and_content: narrowPeak

source_name: H9 day7

growth_protocol: Human embryonic stem cells (H9, female) were maintained in E8 medium (Life Technologies) on Matrigel (Stem Cell Technologies) coated plates, dissociated using 0.5mM EDTA, and passaged at 1:10 ratio.

extract_protocol:
Cells were grown on 15-cm dishes (25 million cells per replicate), singularized by Accutase (Innovative Cell Technologies), crosslinked by 1% formaldehyde for 10 minutes, lysed (50mM Tris-HCl pH 8.0, 10mM EDTA, 0.5% SDS, 1X protease inhibitors), and sonicated to 200-300 bp size using a Bioeruptor (Diagenode). Samples were centrifuged to remove insoluble debris and diluted in dilution buffer (50 mM Tris-HCl pH 8.0, 10mM EDTA, 1X protease inhibitors) to final concentration of 0.1% SDS.
Sheared chromatin was incubated overnight at 4°C with appropriate antibodies, followed by incubation on rotator with 30μL of pre-washed agarose G beads (Invitrogen) for 4h at 4°C. AP2A ChIP antibody (Santa Cruz: sc-12726) used at 20μg per 25 million cells and GRHL2 ChIP antibody (Sigma Prestige: HPA004820) used at 6μg per 25 million cells. Beads were washed twice each with low salt buffer (50 mM Tris-HCl pH 8.0, 0.15M NaCl, 1mM EDTA pH 8.0, 0.1% SDS, 1% triton X-100, 0.1% sodium deoxycholate), high salt buffer (50mM Tris-HCl pH 8.0, 0.5M NaCl, 1mM EDTA pH 8.0, 0.1% SDS, 1% triton X-100, 0.1% sodium deoxycholate), and LiCl buffer (50mM Tris-HCl pH 8.0, 0.15M LiCl, 1mM EDTA pH 8.0, 1% NP-40, 0.1% sodium deoxycholate). DNA was eluted in 100μL of elution buffer (50mM NaHCO3, 1% SDS) and crosslinks were reversed with 4μL of 5M NaCl incubated overnight at 67°C. RNA was removed by adding 1μL of 10 mg/mL RNase A and incubating for 30 min at 37°C. DNA was cleaned using the Qiagen Qiaquick PCR purification kit and quantified using Qubit (Invitrogen). Between 5ng and 1μg of pooled DNA were used for library preparation using NEBNext Ultra™ II DNA Library Prep Kit for Illumina kit (New England Biolabs) and AMPure XP beads (Beckman) according to the manufacturer’s protocol. Single-read libraries were sequenced on Illumina NextSeq or NovaSeq sequencer. Two independent, biological replicates were sequenced per cell type.

treatment_protocol: For differentiations, the media was changed to Essential 6 (Life Technologies) supplemented with 1μM retinoic acid (Sigma) and 5ng/mL Recombinant Human BMP4 (R&D Systems) and replaced every two days for seven days. On day 7, cells were collected for downstream analysis.

tag: treatment

value: 7 days RA/BMP4

tag: chip antibody

value: GRHL2, Sigma, AB_1857928


title: i2_HS30_S2_rep2


title: i1_NHS_S2_rep1


title: i1_NHS_S5_rep1


title: i1_NHS_CTD_rep1


title: ChIPseq_2AKO_GRHL2_H9_d7_rep2


title: i1_NHS_S7_rep1

description:
nascent RNA
iPRO_NHS_S7_BRs_normalized_pl.bigWig
iPRO_NHS_S7_BRs_normalized_mn.bigWig


title: ChIPseq_2AKO_GRHL2_H9_d7_rep1


title: ChIPseq_GRHL2KO_AP2A_H9_day7_rep2

value: AP2a, Santa Cruz, AB_667767


title: ChIPseq_GRHL2KO_AP2A_H9_day7_rep1


title: ATACseq_d7_GRHL2_KO_r2

data_processing:
bowtie2.3.4.1 used for alignment.
duplicate fragments were removed using samtools1.8
macs2 used for peak calling
bedtools2.27.1 multicov to generate normalized counts
DESEQ2 used for differential peak calling
Genome_build: hg38
Supplementary_files_format_and_content: narrowPeak

extract_protocol:
ES cells were removed from the tissue culture plate and singularized by Accutase treatment.
ATAC-seq was performed as described previously (Buenrostro et al., 2015). Briefly, 7x104 cells were washed with cold PBS and lysed in 0.1% NP40 RSB buffer. Nuclei were transposed with Nextera Transposase at 37°C for 30 minutes, then purified with the Qiagen MinElute PCR Purification Kit. Libraries were amplified for 9 total cycles using the Nextera Ad1 and Ad 2.1-2.16 barcodes. Libraries were purified and eluted using the MinElute columns (Qiagen). Library concentrations were determined with Bioanalyzer High-Sensitivity DNA analysis (Agilent). Paired-end libraries for all samples analyzed were pooled and sequenced on an Illumina NextSeq 500 and two independent, biological replicates were sequenced per sample.

tag: genotype

value: GRHL2 KO


title: ATACseq_d7_GRHL2_KO_r1


title: ATACseq_d7_AP2A_KO_r2

value: TFAP2A KO