title: ZIKV_1to500_rep2

first: Roland

middle: G

last: Huber

address: 30 Biopolis Street

department: Bioinformatics Institute (BII)

institute: Agency for Science, Technology and Research (A*STAR)

description: Zika footprinting 1:500 replicate 2

data_processing:
illumina adapter removal using cutadapt
alignment with bowtie2 'very-sensitive-local' preset
calculation of SPMR from raw read counts
Genome_build: EU081177; KU497555
Supplementary_files_format_and_content: csv: nucleotide_coodinate, singal_per_million_reads (SPMR)

organism: Zika virus

source_name: Zika footprinting 1:500

growth_protocol: Following previous procedures,[16] DENV and ZIKV C proteins were expressed in Escherichia coli cells C43 (DE3) and C41 (DE3), transformed with the DENV 2 C protein gene and with the ZIKV Brazil C protein gene, respectively, cloned into a pET21a plasmid (ampicillin resistance). 6 mL LB medium with 100 μg/mL ampicillin were inoculated with a single E. coli colony, containing the pET21a, from LB-agar plates with 100 μg/mL ampicillin, and incubated overnight at 220 rpm, 37 °C. The overnight culture was used to inoculate LB with 100 μg/mL ampicillin, to a final dilution of 1:50. The main culture was incubated at 220 rpm and 37 °C, until the optical density at 600 nm (OD600) reaches 0.8. Protein expression was induced with 0.5 mM isopropyl β-D-1-thiogalactopyranoside (IPTG), at 25 °C overnight and with 220 rpm agitation. The overnight culture was centrifuged at 7000 × g for 40 min at 4 °C. Supernatants were discarded and the cell pellets were resuspended in 1/10 of the volume of the initial culture, in a buffer with 25 mM HEPES, pH 7.4, 0.2 M NaCl, 1 mM EDTA, 5% (v/v) glycerol (Buffer 0.2 M NaCl) and 10 μM protease inhibitor cocktail (Sigma). Cells were lysed by sonication, keeping the suspension on ice, with 5 to 7 pulses (1.5 min) and pauses of 2 min. Sodium chloride was added to the cell lysate to achieve a final concentration of 2 M NaCl, and incubated for at least 1 h, with agitation, at 4 °C. The suspension was centrifuged at 16100 × g for 30 min at 4 °C, and supernatants were collected. Before the first chromatography step, these supernatants were diluted fourfold with Buffer 0.2 M NaCl. The diluted supernatants were applied to a 5 mL HiTrap heparin column (HiTrapTM Heparin HP, GE Healthcare) coupled to an ÄKTA purifier system (ÄKTA explorer, GE Healthcare). The C protein was then eluted performing a NaCl gradient from 0.2 to 2 M NaCl. The fractions corresponding to the C protein were collected and injected in a size exclusion column (S200). C proteins were purified in a buffer with 55 mM KH2PO4 and 550 mM KCl, pH 6.0. DENV C protein purified fractions were concentrated with a Centriprep Centrifugal Filter (Millipore; 3 kDa cutoff) and stored at -80 °C. ZIKV C protein purified fractions were centrifuged at 13,400 × g to remove protein aggregates and the supernatants were stored at -80 °C. The purity of the purified recombinant C protein samples was assessed by 15% SDS-PAGE. Protein concentrations were determined from the sample absorbance at 280 nm, with extinction coefficients calculated from their primary structures (GenBank database: AAC59275.1 and KU497555.1, for DENV and ZIKV, respectively). Matrix-assisted laser desorption/ionization, time-of-flight mass spectrometry (MALDI-TOF MS) analysis showed one peak, with the expected mass of the protein monomer and much lower peaks corresponding to a very low degradation.

extract_protocol: 2 µl of 10× T4 polynucleotide kinase (PNK) buffer and 2 µL of T4 PNK were added to 14 µL of each vRNA sample. Reaction mixtures were incubated for 4 h at 37 °C. Then, additional 0.5 µL of T4 PNK and 2 µL of 10 mM ATP were added, and the mixture reactions were incubated for 1 h at 37 °C. The final volume of the mixtures was adjusted to 50 µL by adding nuclease-free water. Following, high-quality vRNA samples were prepared with an RNA Clean & Concentrator kit (RNA Clean & Concentrator-5, Zymo Research). Briefly, 100 μL of RNA binding buffer were added to each 50 μL of vRNA sample. Then, an equal volume of ethanol 100% was added and mixed. Samples were transferred to a column in a collection tube and centrifuged for 30 s at 12,000 × g. The flow-through was discarded and 400 μL of the second RNA buffer were added. Viral RNA bound to the columns were washed twice. A dry spin was made to completely remove the washing buffer. Columns were transferred into RNA-free tubes and the vRNA was eluted by adding 8 μL of RNase-free water to the column matrix. After 1 min incubation, columns were centrifuged for 30 s at 12,000 × g. The recovered vRNA was double eluted and samples were storage at -80 °C. Library preparation was made with a NEBNext Multiplex Small RNA Library Prep Set for Illumina kit (New England Biolabs), with small modifications to the protocol. 1 μL of 3’ SR Adaptor was added to 6 μL of the high-quality vRNA samples prepared, in nuclease-free PCR tubes. Reaction mixtures were incubated in a preheated thermal cycler for 2 min at 70 °C, and then transferred to ice. 10 μL of 3’ Ligation Reaction Buffer and 3 μL of 3’ Ligation Enzyme Mix were added to each reaction mixture. Samples were incubated in a thermal cycler for 1 h at 25°C. To prevent the formation of dimers of the remaining 3’ SR Adaptor, 4.5 μL of nuclease-free water and 1 μL of SR reverse transcription (RT) Primer for Illumina were added, and samples were incubated for 5 min at 75 °C, 15 min at 37 °C and 15 min at 25 °C. For the ligation of the 5’ SR Adaptor, an adaptor mix was prepared. For that, 5’ SR Adaptor was incubated in a thermal cycler at 70 °C for 2 min, and then immediately transferred to ice. Following, 1 μL of the denatured 5’ SR Adaptor was mixed with 1 μL of 5’ Ligation Reaction Buffer and 2.5 μL of 5’ Ligation Enzyme Mix. The adaptor mix was added to the samples with 3’ SR Adaptor and incubated in a thermal cycler for 1 h at 25 °C. To perform the RT of the adaptor ligated vRNA samples, 30 μL of these samples were mixed in nuclease-free tube with 8 μL of First Strand Synthesis Reaction Buffer, 1 μL of Murine RNase Inhibitor and 1 μL of ProtoScript II Reverse Transcriptase. Reaction mixtures were incubated at 50 °C for 60 min. Then, RT reactions were inactivated at 70 °C for 15 min and stored at -20 °C. A large-scale PCR amplification was performed using 12 PCR cycles, the number of cycles identified as enough to construct a library. For that, 10 μL of the cDNA were mixed, on ice, with 2.5 μL of F-primer (SR primer), 2.5 μL of R-primer (with different barcodes for each sample), 5 μL of nuclease-free water and 20 μL of 2X Q5 Master Mix. The barcoded cDNA samples were normalized to 1000 ng/mL and sent to next generation sequencing on the Illumina platform.

treatment_protocol: Eight reactions, four for DENV and four for ZIKV experiment, with 1 µg of vRNA in nuclease-free water were prepared in 0.2-ml PCR tubes. To renature the viral RNA, tubes were heated at 90 °C, for 2 min, in a thermal cycler with heated lid on and then transferred to ice for 2 min. 5 μL of 10× RNA structure buffer were added to the vRNA and gently homogenized by pipetting up and down. Then, tubes were placed into the thermal cycler and temperature increased from 4 °C to 37 °C over 35 min. DENV or ZIKV C proteins were added to the four reactions in increasing concentrations, to achieve different final ratios of C protein monomers to one molecule of vRNA (1:20, 1:100, 1:250 and 1:500). Samples were incubated at 37 °C for 30 min, to allow the interaction of the C protein with vRNA. 5 μl of RNase A/T1 Mix (RNase A 500 U/mL and RNase T1 20000 U/mL; Ambion AM2286) diluted 100 times were added to each tube, and incubated at 37 °C for 30 min. The dilution of RNase A/T1 Mix was previously determined with four serial 10 times dilutions of RNase A/T1 Mix from the stock solution. 45 µL of nuclease-free water were added to each sample to adjust the final volume of the reaction mixtures to 100 µL, and then transferred to 1.5 microfuge tubes with the same volume of phenol–chloroform–isoamyl alcohol. After mixing, tubes were centrifuged at 13,200 × g for 10 min at 4 °C. The aqueous phase of each sample was transferred to a new tube containing 10 µL sodium acetate 3 M and 1 µL glycogen 20 mg/mL. 300 µL of ethanol 100% were mixed with each aqueous solution and, to precipitate the vRNA, samples were stored at -20 °C overnight. To collect the vRNA, samples were spin at 13,200 × g for 30 min at 4 °C. Supernatants were discarded and 800 µL of ethanol 70% were added to the pellet. Samples were spin at 13,200 × g for 15 min at 4 °C and the supernatants removed. A dry spin at 13,200 × g for 1 min at 4 °C was made to completely remove ethanol. vRNA pellets were resuspend in 15 µL of nuclease-free water and stored at -80 °C.

value: viral RNA


title: ZIKV_1to500_rep1

status: Public on Dec 31 2022

type: SRA

city: Singapore

country: Singapore

description: Zika footprinting 1:500 replicate 1

library_source: transcriptomic

molecule: total RNA

tag: tissue


title: RCF-x192exo-2

city: Atlanta

first: Michael

middle: E.

last: Davis

address: 2015 Uppergate Dr NE

country: USA

institute: Emory University

description:
Sample 8
RCFcounts.csv

data_processing:
Base calling was conducted with RTA v3.4.4 and demultiplexing was performed with bcl2fastq v2.20.0.422
Total RNA was aligned and gene counts were determined with STAR aligner in the Illumina BaseSpace app, RNA-Seq Alignment.
Genome_build: Sample 1-~18 reads aligned with rn5 reference genome; sample 19-36 reads aligned with hg19 reference genome.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: Heart, left ventricular myocardium

growth_protocol: RCFs were cultured in Dulbecco’s modified Eagle’s medium (DMEM-ThermoFisher) supplemented with 10% FBS and 1% penstrep. THP-1 cells were cultured in Roswell Park Memorial Institute (RPMI) 1640 medium (ThermoFisher) supplemented with 10% FBS, 1% penstrep, and 1% L-glutamine.

extract_protocol:
Total RNA were isolated by using Qiagen RNeasy mini kit following manufacturer's protocol.
1 ng of RNA was used as input for library preparation with the Takaro Bio SMARTer Stranded Total RNA-Seq Kit v2 Pico Input Mammalian

treatment_protocol: To stimulate fibroblasts, RCFs were quiesced for 12 h, treated with 20 µg/mL sEVs for 12 h, and then treated with 10 ng/mL transforming growth factor beta (TGF-β; ThermoFisher) for another 12 h. THP-1 cells were then differentiated into macrophages by 24 h incubation with 150 nM phorbol 12-myristate 13-acetate (PMA; Sigma-Aldrich) followed by 24 h incubation in RPMI medium. Macrophages were then treated with 20 µg/mL sEVs for 12 h and activated with 20 ng/mL tissue necrosis factor alpha (TNF-⍺; R&D Systems, Minneapolis, MN, USA) for 12 h.

tag: cell type

value: Cardiac fibroblast

tag: strain

value: Heart, left ventricular myocardium

tag: treatment

value: miR-192-5p depleted CPC sEVs for 24 hours


title: ZIKV_1to100_rep1

description: Zika footprinting 1:100 replicate 1

source_name: Zika footprinting 1:100


title: ZIKV_1to20_rep1

description: Zika footprinting 1:20 replicate 1

source_name: Zika footprinting 1:20


title: RCF-x432-1

description:
Sample 16
RCFcounts.csv

value: miR-432-5p inhibitor for 24 hours


title: ZIKV_CONTROL_rep2

description: Zika footprinting control replicate 2

source_name: Zika footprinting control


title: ZIKV_1to250_rep2

description: Zika footprinting 1:250 replicate 2

source_name: Zika footprinting 1:250


title: ZIKV_1to100_rep2

description: Zika footprinting 1:100 replicate 2


title: MIA vehicle sample 3

city: Stony Brook

first: David

last: Carlson

state: NY

address: 100 Nicolls Rd

institute: Stony Brook University

data_processing:
Each set of paired-end RNA-Seq reads was processed with fastp v0.20.1 to generate quality control plots, remove adapter contamination, and filter and trim reads.
Transcript quantification was performed with Salmon v1.4.0 under the “selective alignment” mode with the “seqBias” and “gcBias” flags and using version mRatBN7.2 of the Rattus norvegicus genome assembly and gene annotation from Ensembl.
Transcript-level read counts were then converted to gene-level read counts with Tximport v1.18.0.
Differential gene expression (DEG) analysis was conducted independently for each treatment condition using DESeq2 v1.30.0 with the contralateral vehicle condition set as control.
Assembly: mRatBN7.2
Supplementary files format and content: Tab-delimited text files produced by Salmon, including raw counts and TPM normalized counts for each sample

source_name: Synovial

extract_protocol:
Rats were euthanized by exsanguination after deep isoflurane anesthesia. The synovial tissue was collected from the MIA injected ipsilateral knee and from the saline injected contralateral knee.  The synovial tissues were immediately preserved and stabilized in RNAlater (#R0901, Sigma).  Total RNA was extracted from each sample using the PureLink RNA Mini Kit (#12183018A, Invitrogen/Thermo Fisher Scientific) following the manufacturer’s instructions, and treated on column to degrade contaminating DNA with PureLink DNase (#12185-010, Invitrogen/Thermo Fisher Scientific). Purified total RNA was eluted from the column with RNase-free water. The RNA integrity number (RIN) was measured for each sample using a Bioanalyzer (Agilent 2100) and the sample RNA Quantification was determined with a Qubit Broad Range assay kit (#Q10210, Invitrogen/Thermo Fisher Scientific).
Library construction was performed with a NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7765S, New England Biolabs). Libraries were tested for quality on an Agilent Bioanalyzer High Sensitivity DNA chip followed by sequencing on an Illumina NextSeq 550 instrument.

treatment_protocol: Rats were anesthetized using 2-3 % isoflurane in O2 and subsequently injected with 2 mg of monoiodoacetate (MIA) (Sigma-Aldrich, St. Louis, MO) dissolved in 50 µl sterile saline percutaneously, through the patellar ligament using a 27-gauge needle. The contralateral knee received 50 µl saline as a control. After 4 weeks, the rats were euthanized by exsanguination after deep isoflurane anesthesia. The synovial membranes were collected from the MIA injected ipsilateral knees and from the saline injected contralateral knees.

value: Synovial

value: vehicle


title: MIA vehicle sample 1


title: MIA vehicle sample 4


title: contralateral vehicle sample 4


title: MIA vehicle sample 2


title: MIA inhibitor sample 3

value: inhibitor


title: ZIKV_1to20_rep2

description: Zika footprinting 1:20 replicate 2


title: MIA inhibitor sample 2


title: contralateral vehicle sample 1


title: contralateral vehicle sample 2


title: ZIKV_CONTROL_rep1

description: Zika footprinting control replicate 1


title: MIA inhibitor sample 4


title: Muscle-invasive bladder cancer [W006709T1PTa]

type: RNA

city: Bangor

first: Tim

last: Smith

address: Dean Street

department: School of Computer Science and Engineering

country: United Kingdom

institute: University of Bangor

hyb_protocol: Sample hybridisation on Clariom S arrays was carried out by Yourgene Health (Manchester, UK). Batches of CEL files were GC SST (Signal Space Transformation with probe Guanine Cytosine Count Correction) RNA normalised using Affymetrix Array Power Tools. (https://www.thermofisher.com/uk/en/home/life-science/microarray-analysis/microarray-analysis-partners-programs/affymetrix-developers-network.html)

data_processing: The log2-summarised gene level expression values generated were batch-corrected using the ComBat function from the Bioconductor package sva.

organism: Homo sapiens

source_name: Anonymised

label_protocol: RNA extracted from both sample cohorts were subject to Clariom S analysis. RNA (8 ng/µl in a 9 µl volume) was prepared for gene expression arrays with the Clariom S pico HT human assay (Thermo Fisher Scientific).

extract_protocol: Two 10µm sections from FFPE bladder cancer embodied blocks. RNA was extracted from the two 10 µm sections using the Roche High Pure FFPET RNA isolation kit. RNA yield was determined on Qubit fluorometer (Invitrogen, Paisley, UK).

tag: disease

value: Muscle-invasive bladder cancer


title: contralateral inhibitor sample 4


title: MIA inhibitor sample 1


title: Muscle-invasive bladder cancer [W6206T2PTa]


title: ZIKV_1to250_rep1

description: Zika footprinting 1:250 replicate 1


title: contralateral inhibitor sample 1


title: contralateral inhibitor sample 2


title: Dgcn5

city: Bangalore

first: Aditi

last: Gupta

state: Karnataka

address: FE-15, Biological Sciences Building, Indian Institute of Science

department: Biochemistry

country: India

institute: Indian Institute of Science

description: Sample 6

data_processing:
demultiplexing and base call to fastq conversion using illumina’s bcl2fastq v2.19.0.316
Adapter trimming using fastp 0.19.6
Read alignment to reference GCA_900235035.1_ASM90023503v1 using bowtie2
Counts per gene were obtained using featureCounts v1.6.4
Differential expression analysis was performed using DESeq2.
Genome_build: ASM90023503v1 (GCA_900235035.1)
Supplementary_files_format_and_content: read counts per gene in Excel file

organism: Komagataella pastoris

source_name: Cells cultured in YNBM for 14 hrs

growth_protocol: cells cultured in YNBM media for 14 hours

extract_protocol:
RNeasy Mini Kit Qiagen
NEBNext Ultra II RNA Library Prep Kit for Illumina was used to prepare the library after depleting rRNA from the total RNA  using RiboMinus™ Transcriptome Isolation Kit, bacteria.

tag: auxotroph

value: Histidine auxotroph

tag: antibiotic resistance

value: ZeocinTM

tag: genotype

value: Deletion mutant of Gcn5


title: contralateral vehicle sample 3


title: Muscle-invasive bladder cancer [W6150T1PTa]


title: M24

city: beijing

first: xiangying

last: yan

address: Dongzhimen Jiedao

country: China

institute: Institute of Chinese Medicine

data_processing:
Use fastp software to clean and filter the original offline data to obtain high-quality sequences (Clean Reads).
Use Hisat2 2.1.0 software to compare Clean Reads with reference genes (the reference genome version is GRnor_6.0.100).
Stringtie 1.3.3b software was used to compare the results and quantify the transcriptome expression; Normalize with TMM (trimmed mean of M values) algorithm, and finally calculate FPKM (Fragments Per Kilobase Million) value of each gene.
Differential analysis of gene expression between samples/groups using edgeR 3.30.3 software package.
Assembly: GRnor_6.0.100
Supplementary files format and content: gene_exp_add_all_diff.txt: Tab-delimited text file includes counts and FPKM values for each Sample.

source_name: liver

growth_protocol: All rats were housed under specific pathogens-free conditions, with a constant temperature of 24℃±1℃ in a 12-h light/12-h dark cycle room and were fed with ad libitum water and food access.

extract_protocol:
RNA was harvested using RNeasy Mini Kit (250) Qiagen #74106.
After the total RNA passes the quality inspection, it is further purified and reverse transcribed to obtain double stranded cDNA, which is used as a template for PCR amplification to construct a cDNA library.

treatment_protocol: Rats in the normal control group were fed a normal diet. DEN model, DEN+PZH low-dose and DEN+PZH high-dose groups were injected intraperitoneally with 0.01% DEN (catalog number N0756, Sigma Aldrich, St. Louis, MO, USA) weekly by the experimentalists for a period of 16 weeks.

value: liver

value: PZH


title: Dgal83

description: Sample 5

value: Deletion mutant of Gal83


title: GS115

description: Sample 3

value: Wild Type


title: contralateral inhibitor sample 3


title: Dmxr1

description: Sample 4

value: Deletion mutant of Mxr1


title: Muscle-invasive bladder cancer [H2714T1PTa]


title: RNA_sDH_rep2

city: Gatersleben, Stadt Seeland, Germany

first: Hua

last: Jiang

address: Corrensstraße 3

country: Germany

institute: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben

data_processing:
For RNA-seq analysis, reads were mapped to TAIR10 Col-0 and the Ler‐0 genomes with HISAT2 (Kim et al., 2019) in paired-end mode.
DEGs were analyzed via the Subread (Liao et al., 2019) and DESeq2 R packages (Love et al., 2014) with a 0.05 false discovery rate (FDR).
All the paired-end reads were aligned to TAIR10 Col-0 genome by Bismark (Krueger and Andrews, 2011) and Bowtie 2 (Langmead and Salzberg, 2012), with default parameter settings. PCR duplicates were removed after mapping. The unmethylated and methylated cytosine nucleotide(s) in every read was/were identified for all sequence contexts (CG, CHG, and CHH) by the “bismark_methylation_extractor” script in Bismark. The methylation ratio was calculated as the ratio between the total number of identified 5-methylcytosines and the total number of sequenced cytosine nucleotides. The correlation between two replicates for each sample was analyzed by pearson correlation with R. DMRs were identified by DMRcaller (Catoni et al., 2018). Methylation levels for each line were calculated by merging the two biological replicates. DMRs were defined by tiling the genome into 100- bp bins and comparing the number of called cytosine nucleotides and thiamine nucleotides in 1x Col-0, 2x Col-0, and DH Col-0. Bins with absolute methylation differences of 0.4, 0.2, and 0.1 for CG, CHG, and CHH, respectively, and a Benjamini-Hochberg-corrected FDR < 0.01 (Fisher’s exact test) were selected. To avoid 100-bp bins with few cytosine nucleotides, we selected bins with at least four cytosine nucleotides covered by at least four reads in the wild-type replicate.
Assembly: tair10

organism: Arabidopsis thaliana

source_name: 2-week-old seedlings

growth_protocol: Seeds were sown in soil and stratified for 2 days at 4°C. The plants were then grown in a growth chamber with a photoperiod of 16 h of light and 8 h of darkness at 22°C.

extract_protocol:
Total RNA from 6th, 7th and 8th leaves was extracted with a RNeasy Plant Mini kit (Qiagen). For RNA-seq analysis, the total RNA was treated with a Poly(A) mRNA Magnetic Isolation Module Kit (NEB #E7490). DNA of 6th, 7th and 8th leaves was purified using a DNeasy® Plant Mini Kit (Qiagen) and eluted in 150 µL of elution buffer. Experiments were performed for two biological replicates.
RNA-seq Libraries were prepared from the resulting mRNA with a NEBNext Ultra Kit (NEB #E7530). The libraries were constructed according to a standard protocol (Illumina). The RNA-seq libraries were sequenced at Novogene via a Novaseq instrument in 150-bp paired-end mode. For BS-seq libraries, The DNA was fragmented into 200-300 bp fragments using Covaris S220 and later Bioruptor® Plus from Diagenode (60 cycles, 30s on, 30s off). After adaptor ligation, bisulfite treatment was performed using the NEBNext® Enzymatic Methyl-seq Kit. PCR amplification of the library molecules was performed using Q5U Master Mix DNA polymerase (NEBNext®). Libraries were sequenced at Novogene (Hong kong, China) on a NovaSeq instrument in 150-bp paired-end mode. Experiments were performed on two biological replicates.

value: seedlings

tag: age

value: 2 weeks


title: RNA_sDH_rep1


title: RNA_DH14_rep2


title: RNA_DH14_rep1


title: RNA_DH6_rep2


title: RNA_DH9_rep1


title: RNA_DH6_rep1


title: Muscle-invasive bladder cancer [C8575T1PTa]


title: Muscle-invasive bladder cancer [W006687T1PTa]


title: Muscle-invasive bladder cancer [H2697T1PTa]


title: Muscle-invasive bladder cancer [W006703T1PTa]


title: RNA_2n_rep2


title: Muscle-invasive bladder cancer [H002769T1PTa]


title: Muscle-invasive bladder cancer [C8539T1PTa]


title: Muscle-invasive bladder cancer [C8547T1PTa]


title: Muscle-invasive bladder cancer [C8544T1PTa]


title: Muscle-invasive bladder cancer [C8541T1PTa]


title: Muscle-invasive bladder cancer [C8545TIPTa]


title: Muscle-invasive bladder cancer [C8546T1PTa]


title: Muscle-invasive bladder cancer [C8542T1PTa]


title: Muscle-invasive bladder cancer [H2426T1PTa]


title: RNA_2n_rep1


title: RNA_DH9_rep2


title: RNA_1n_rep2


title: Muscle-invasive bladder cancer [C8536T1PTa]


title: RNA_1n_rep1


title: Muscle-invasive bladder cancer [C8475T1PTa]


title: Muscle-invasive bladder cancer [C8540T1PTa]


title: Muscle-invasive bladder cancer [C8480T1PTa]


title: Muscle-invasive bladder cancer [H2711TPTa]


title: sDH_rep2

library_source: genomic

molecule: genomic DNA


title: Muscle-invasive bladder cancer [C8446T1PTa]


title: Muscle-invasive bladder cancer [C8458T1PTa]


title: Muscle-invasive bladder cancer [C8538T1PTa]


title: DH14_rep2


title: RCF-x432exo-1

description:
Sample 10
RCFcounts.csv

value: Cardiac fibroblast

value: Heart, left ventricular myocardium

value: miR-432-5p depleted CPC sEVs for 24 hours


title: DH14_rep1


title: DH6_rep2


title: DH6_rep1


title: 2n_rep2


title: DH9_rep2


title: Muscle-invasive bladder cancer [C8441T1PTa]


title: DH9_rep1


title: Muscle-invasive bladder cancer [C8425T1PTa]


title: 2n_rep1


title: 1n_rep1


title: 1n_rep2


title: Muscle-invasive bladder cancer [C8420T2PTa]


title: Muscle-invasive bladder cancer [C8315T1PTa]


title: Muscle-invasive bladder cancer [C008594T1PTa]


title: Muscle-invasive bladder cancer [C008543T1PTa]


title: Muscle-invasive bladder cancer [H002630T2PTa]


title: Muscle-invasive bladder cancer [C008586T1PTa]


title: xip_BLM_2

city: Shanghai

first: Yan

last: Zhu

address: 2005, Songhu Road

institute: Fudan University, School of life sciences

data_processing:
Raw data were filtered by using Skewer
Reads were mapped to the reference genome by using Bowtie2
Gene expression levels were estimated by using StringTie
Genome_build: Arabidopsis thaliana, version Araport11
Supplementary_files_format_and_content: TPM values with GTF format

source_name: 12-day-old xip seedling grown with BLM treatment

growth_protocol: 12-day-old seedling under normal growth condition

extract_protocol:
Total RNA was extracted from the snap-frozen tissues using TRIzol® Reagent according to the manufacturer’s instructions (Invitrogen).  PolyA+ RNA was enriched by selection with two rounds of oligo(dT) Dynabeads (Invitrogen).
Stranded RNA-seq library was constructed according to KAPA stranded mRNA-seq Kit instructions (Illumina® Platforms, KR0960-v5.17; www.kapabiosystems.com).

treatment_protocol: Seedlings were transferred to liquid medium (Mock), or medium with 1mM HU for 24 hours, or medium with 1mM BLM for 6 hours.

value: seedling

tag: development stage

value: xip mutant

value: BLM


title: xip_HU_1

source_name: 12-day-old xip seedling grown with HU treatment

value: HU


title: xip_HU_2


title: xip_BLM_1


title: Muscle-invasive bladder cancer [H002531T2PTa]

value: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer [C008599T1PTa]


title: Muscle-invasive bladder cancer [C8428T1PTa]


title: Muscle-invasive bladder cancer [H002588T1PTa]


title: xip_Mock_2

source_name: 12-day-old xip seedling grown under mock condition

value: mock


title: xip_Mock_1


title: WT_BLM_2

source_name: 12-day-old WT seedling grown with BLM treatment

value: WT


title: WT_BLM_1


title: WT_HU_1

source_name: 12-day-old WT seedling grown with HU treatment


title: WT_HU_2


title: Muscle-invasive bladder cancer [H002601T1PTa]


title: WT_Mock_1

source_name: 12-day-old WT seedling grown under mock condition


title: Muscle-invasive bladder cancer [H001286T2PTa]


title: Muscle-invasive bladder cancer [YPS10]


title: Muscle-invasive bladder cancer [YPS09]


title: Muscle-invasive bladder cancer [C007652T7PTa]


title: jmj29-1-3

city: Nanchang

first: Dong

last: Wang

state: JiangXi

address: Hong Gu Tan New Road, No. 999

institute: Nanchang University

data_processing:
Adaptors and low-quality sequences were trimmed using bbduk (version 38.90) with paramters: hdist=1 mink=11 ktrim=r qtrim=rl trimq=20 minlen=25 trimpolyg=20. Then clean reads were mapped to Arabidopsis reference genome (TAIR10) using STAR (2.7.6a) with following parameters:  --outSAMstrandField intronMotif --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.03 --alignIntronMax 10000 --quantMode GeneCounts.
Raw count table for all Arabidopsis reference genes were generated using STAR with --quantMode GeneCounts. DE (Differential expressed) genes were identified using edgeR with a cutoff Pvalue < 0.05.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab delimited text file with raw read counts for reference genes

source_name: seedlings

extract_protocol:
Total RNA was isolated using TRIzol according to the instructions.
Libraries were constructed through applying TruSeq Stranded mRNA (Illumina, San Diego, CA, USA) in accordance with the manufacturer’s instruction.


title: Muscle-invasive bladder cancer [C007477T7PTa]


title: Muscle-invasive bladder cancer [H002470T2PTa]


title: Muscle-invasive bladder cancer [C007967T6PTa]


title: Muscle-invasive bladder cancer [YPS06]


title: Muscle-invasive bladder cancer [YPS08]


title: Muscle-invasive bladder cancer [YPS07]


title: Muscle-invasive bladder cancer [YPS14]


title: dana2-1-3


title: Muscle-invasive bladder cancer [YPS05]


title: jmj29-1-1


title: jmj29-1-2


title: dana2-1-2


title: dana2-1-1


title: WT_Mock_2


title: Col 3

value: wild type


title: Col 1


title: Col 2


title: dana1-2-3

data_processing:
Adaptors and low-quality sequences were trimmed using Trim_galore (0.4.4_dev) with paramters: --stringency 6. Then clean reads were mapped to Arabidopsis reference genome (TAIR10) using STAR (2.7.6a) with following parameters:  --outSAMstrandField intronMotif --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.03 --alignIntronMax 10000 --quantMode GeneCounts.
Raw count table for all Arabidopsis reference genes were generated using STAR with --quantMode GeneCounts. DE (Differential expressed) genes were identified using edgeR with a cutoff Pvalue < 0.05.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab delimited text file with read counts for reference genes


title: Muscle-invasive bladder cancer [YPS01]


title: Muscle-invasive bladder cancer [BL270263(3)]


title: Muscle-invasive bladder cancer [BL270263(4)]


title: Muscle-invasive bladder cancer [BL270263(5)]


title: Muscle-invasive bladder cancer [YPS03]


title: Muscle-invasive bladder cancer [YPS04]


title: Muscle-invasive bladder cancer [BL270260]


title: Muscle-invasive bladder cancer [BL270263(2)]


title: dana1-2-1


title: dana1-2-2


title: Muscle-invasive bladder cancer [BL270263(1)]


title: Muscle-invasive bladder cancer [BL269678]


title: Col_2


title: Col_1


title: IBM1GFP_input_rep2

data_processing:
For RNA-seq analysis, reads were mapped to TAIR10 Col-0 and the Ler‐0 genomes with HISAT2 (Kim et al., 2019) in paired-end mode.
DEGs were analyzed via the Subread (Liao et al., 2019) and DESeq2 R packages (Love et al., 2014) with a 0.05 false discovery rate (FDR).
For ChIP-seq library preparation, the purified ChIP-ed DNA was utilized for the subsequent end repairing, A-tailing, adaptor ligation, and library amplification. The steps were performed with the NEBNext® Ultra™ II DNA Library Prep Kit (NEB).
The library was sequenced on an Illumina Novaseq instrument with 2 × 150 bp reads.
Genome_build: tair10
Supplementary_files_format_and_content: bedgraph

source_name: IBM1GFP_input_closed buds

growth_protocol: Seeds were sown in soil and stratified for 2 days at 4°C. The plants were then grown in a growth chamber with a photoperiod of 16 h of light and 8 h of darkness at 22°C (LDs) or in a chamber with a photoperiod of 8 h of light and 16 h of darkness at 22°C (SDs).

extract_protocol:
For RNA-seq library preparation, total RNA from closed buds was extracted with a RNeasy Plant Mini kit (Qiagen). Afterwards, the total RNA was treated with a Poly(A) mRNA Magnetic Isolation Module Kit (NEB #E7490). Libraries were prepared from the resulting mRNA with a VAHTS mRNA-seq V3 Library Prep Kit (Vazyme #NR611-01) . For ChIP-seq library preparation, closed buds were collected. Chip assay from cross-link to chromatin shearing was previously described by Lambing, et al (Lambing et al. 2020) with minor modifications. Briefly, the materials were firstly collected in liquid nitrogen and grind to fine powder. Nuclei isolation buffer (1M sucrose, 5mM KCl, 5mM MgCl2, 5 mM EDTA, 60 mM Hepes pH 8.0, 0.6% Triton X-100, 0.4 mM PMSF, 1 μM pepstatin A, 1X Protease Inhibitor Cocktail) and 1% final concentration formaldehyde solution were added to each sample. Incubating the sample on a Thermo roller mixer (cat number) at 12 rpm for 25 min for closed buds or 10 min for seedlings at room temperature. Cross-link was stopped by adding glycine to a final concentration of 130 mM for another 25 min for closed buds. After the isolation of nuclei, the chromatin was sonicated with Nuclei lysis buffer (50mMTris–HCl, pH 8.0, 10 mM EDTA, 1% SDS, 0.1 mM PMSF, 1 μM pepstatin A, Protease Inhibitor Cocktail) to obtain the desired DNA fragment (size enriched at 300 bp) by a Bioruptor® Plus sonication device. The following procedures were described by Moreno-Romero et al (Moreno-Romero et al. 2016). After the de-crosslinking, DNA was purified according to the manual of IPure kit v2 Kit (C03010015, Diagenode). Chip-seq libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit (NEB #E7645). The antibodies we used: anti-H3 (H9289, Sigma), anti-H3K9me2 (C15410060, Diagenode) and anti-GFP (A11122, Invitrogen). The library was sequenced on an Illumina Novaseq instrument with 2 × 150 bp reads..
Libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

value: closed buds


title: IBM1GFP_GFP_rep1

source_name: IBM1GFP_GFP_closed buds

tag: chip antibody

value: GFP

tag: chip antibody vendor

value: Invitrogen

tag: chip antibody cat. #


title: IBM1GFP_GFP_rep2


title: Muscle-invasive bladder cancer [BL265408]


title: pds5_H3K9me2_rep2

source_name: pds5_H3K9me2_closed buds

value: Diagenode


title: IBM1GFP_input_rep1


title: Muscle-invasive bladder cancer [BL264096(3)]


title: Muscle-invasive bladder cancer [BL265076 (2)]


title: Muscle-invasive bladder cancer [BL265076 (3)]


title: Muscle-invasive bladder cancer [BL264096(4)]


title: pds5_H3_rep2

source_name: pds5_H3_closed buds

value: Sigma


title: Col_3

value: seedlings


title: pds5_H3K9me2_rep1


title: pds5_H3_rep1


title: Muscle-invasive bladder cancer [BL263304]


title: Muscle-invasive bladder cancer [BL264096(1)]


title: ibm1 jmj27_H3_rep2

source_name: ibm1 jmj27_H3_closed buds

value: ibm1 jmj27


title: ibm1 jmj27_H3K9me2_rep1

source_name: ibm1 jmj27_H3K9me2_closed buds


title: ibm1 jmj27_H3K9me2_rep2


title: ibm1 jmj27_H3_rep1


title: Muscle-invasive bladder cancer [BL269435]

source_name: Anonymised


title: ibm1_H3K9me2_rep2

source_name: ibm1_H3K9me2_closed buds


title: Muscle-invasive bladder cancer [BL262760 (2)]


title: ibm1_H3_rep2

source_name: ibm1_H3_closed buds


title: Muscle-invasive bladder cancer [BL262229(5)]


title: Muscle-invasive bladder cancer [BL262229(3)]


title: Muscle-invasive bladder cancer [BL262229(2)]


title: Muscle-invasive bladder cancer [BL262229(1)]


title: Muscle-invasive bladder cancer [BL264096(2)]


title: Muscle-invasive bladder cancer [BL262229(4)]


title: ibm1_H3K9me2_rep1


title: Col_H3_rep2

source_name: Col_H3_closed buds

value: Col


title: ibm1_H3_rep1


title: Col_H3K9me2_rep2

source_name: Col_H3K9me2_closed buds


title: Muscle-invasive bladder cancer [BL251105(8)]


title: Col_H3K9me2_rep1


title: Col_H3_rep1


title: pds5_rep2

source_name: pds5_closed buds


title: Muscle-invasive bladder cancer [BL262760 (1)]


title: Muscle-invasive bladder cancer [BL251105(6)]


title: Muscle-invasive bladder cancer [BL251105(5)]


title: Muscle-invasive bladder cancer [BL251105(4)]


title: Muscle-invasive bladder cancer [BL260115]


title: ibm1 jmj27_rep2

source_name: ibm1 jmj27_closed buds


title: ibm1 jmj27_rep1


title: Muscle-invasive bladder cancer [BL251105(3)]


title: Muscle-invasive bladder cancer [BL251105(10)]


title: Muscle-invasive bladder cancer [BL250626(6)]


title: ibm1_rep2

source_name: ibm1_closed buds


title: Muscle-invasive bladder cancer [BL251105(2)]


title: erf4_2 rep2

city: Qingdao

first: Anming

last: Ding

state: Shandong

address: No.11 Keyuanjingsi Rd.

institute: Tobacco Research Institute of CAAS

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by Fastp (https://github.com/OpenGene/fastp )with parameters -q 20 --length_required 30 -5 20 -3 20 -W 4 -M 20 -n 0.
Then clean reads were separately aligned to reference genome with orientation mode using hisat software.
The expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FRKM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample.

source_name: 7 DAP seeds

extract_protocol:
Total RNA was extracted from seeds using Plant RNA Purification Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) was used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: erf4 mutant

value: developing seeds

tag: developmental stage

value: 7 day-post-anthesis (DPA)

tag: embryo stage

value: torpedo/linear


title: Col_rep2

source_name: Col_closed buds


title: erf4_2 rep1


title: Col_rep1


title: wild-type rep2

value: wild-type


title: wild-type rep1


title: Muscle-invasive bladder cancer [BL250626(5)]

value: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer [BL250626(2)]


title: Muscle-invasive bladder cancer [BL250626(3)]


title: ibm1_rep1


title: Muscle-invasive bladder cancer [BL247648]


title: pds5_rep1


title: Muscle-invasive bladder cancer [BL250626(4)]


title: Muscle-invasive bladder cancer [BL250052 (2)]


title: Muscle-invasive bladder cancer [BL248475]


title: MO-9-GMP

city: Paris

first: Hélène

last: CAVE

state: France

address: 48 Bd sérurier

department: Genetics

country: France

institute: APHP Hôpital Robert Debré

data_processing:
Full Fastq files were aligned to the reference human genome hg19/GRCh37 with tophat2 (-p 24 -r 150 -g 2 --library-type fr-firststrand). Gene expression was quantified using the full Gencode v26lift37. We used HTSeq (Anders et al., 2015) to obtain the number of reads associated to each gene in the Gencode v26lift37 database (restricted to protein-coding genes, antisense and lincRNAs). Bioconductor DESeq package (Anders and Huber, 2010) was used to import raw HTSeq counts for each sample into R statistical software and extract the count matrix.
Full Fastq files were aligned to the reference human genome hg19/GRCh37 with tophat2 (-p 24 -r 150 -g 2 --library-type fr-firststrand). Gene expression was quantified using the full Gencode v26lift37. We used HTSeq (Anders et al., 2015) to obtain the number of reads associated to each gene in the Gencode v26lift37 database (restricted to protein-coding genes, antisense and lincRNAs). Bioconductor DESeq package (Anders and Huber, 2010) was used to import raw HTSeq counts for each sample into R statistical software and extract the count matrix.
We used BS-Seeker2 (55) to map RRBS data to the Human hg38 genome and retrieve the number of methylated and unmethylated cytosines at each covered CpG site. Methylation rates were then integrated across CpG island (CGI)-based and gene-based features. CGI-based features were defined as follows: CpG islands (from UCSC database), shores (2 kb on each side of the island) and shelves (2 kb on each side of the shores). DNA methylation outside CpG islands was analyzed by grouping CpG sites not located in CGI-based features every 100kb window. Gene-based features were defined based on Gencode v26 assembly.

source_name: Bone Marrow

extract_protocol:
total RNA was extracted from mononuclear cells or sorted HSPC (1000 to 10000 cells) using the RNeasy Mini or Micro Kit (Qiagen).
Libraries were prepared with TruSeq® Stranded Total RNASample preparation kit (Illumina) according to supplier’s recommendations. Briefly the ribosomal RNA fraction was removed from 1μg of total RNA using the Ribo-Zero™ Gold Kit (Epicentre). Fragmentation was then achieved using divalent cations under elevated temperature to obtain approximately 300bp pieces. Double strand cDNA synthesis was performed using reverse transcriptase and random primers, Illumina adapters were ligated and cDNA library was PCR amplified for sequencing. Paired-end 75b sequencing was then carried out on a HiSeq4000 (Illumina).

treatment_protocol: CD34+ cells were selected from mononucleated cells using the Easysep Human CD34 positive selection kit and Easysep magnet (StemCell Technologies, Vancouver, Canada) following the manufacturer's instructions. Cells were phenotyped on a BD FACSCantoTM II analyzer (BD Biosciences) using marker combinations that have been validated in fetal and adult bone marrow (Notta et al., 2011, 2016): HSC CD34+CD38-CD45RA-CD90+, MPP CD34+CD38-CD45RA-CD90-CD49f-, CMP CD34+CD38+CD45RA-CD135+, GMP CD34+CD38+CD45RA+CD135+ and MEP CD34+CD38+CD45RA-CD135- .

value: Bone Marrow

value: Sorted  GMP

tag: disease state

value: Healthy postnatal sample

tag: jmml patients unique identifier


title: MO-9-MEP

tag: tissue

tag: cell type

value: Sorted  MEP


title: MO-6-MEP


title: Muscle-invasive bladder cancer [BL247303 (8)]


title: MO-6-CMP

value: Sorted  CMP


title: MO-05-MEP


title: Muscle-invasive bladder cancer [BL247303 (5)]


title: Muscle-invasive bladder cancer [BL247303 (7)]


title: Muscle-invasive bladder cancer [BL247303 (6)]


title: MO-05-GMP


title: Muscle-invasive bladder cancer [BL247303 (3)]


title: Muscle-invasive bladder cancer [BL247303 (20)]


title: Muscle-invasive bladder cancer [BL247303 (4)]


title: MO-05-CMP


title: MO-04-MEP


title: MO-04-GMP


title: Muscle-invasive bladder cancer [BL247303 (2)]


title: LMMJ-24-CMP

value: JMML_PTPN11 mutated


title: LMMJ-24-MEP


title: LMMJ-24-GMP


title: MO-04-CMP


title: Muscle-invasive bladder cancer [BL251105(7)]


title: Muscle-invasive bladder cancer [BL247303 (19)]


title: LMMJ-23-GMP

value: JMML_NRAS mutated


title: LMMJ-23-CMP


title: LMMJ-22-GMP


title: LMMJ-22-CMP


title: Muscle-invasive bladder cancer [BL247303 (17)]


title: LMMJ-23-MEP


title: Muscle-invasive bladder cancer [BL247303 (18)]


title: Muscle-invasive bladder cancer [BL247303 (13)]


title: Muscle-invasive bladder cancer [BL247303 (15)]


title: LMMJ-20-CMP


title: LMMJ-20-MEP


title: Muscle-invasive bladder cancer [BL247303 (12)]


title: Muscle-invasive bladder cancer [BL247303 (11)]


title: LMMJ-20-GMP


title: sDH_rep1

source_name: 2-week-old seedlings

value: 2 weeks


title: Muscle-invasive bladder cancer [BL247303 (10)]


title: Muscle-invasive bladder cancer [BL247303 (1)]


title: LMMJ-22-MEP


title: Muscle-invasive bladder cancer [BL246213(8)]


title: Muscle-invasive bladder cancer [BL246523]


title: Muscle-invasive bladder cancer [BL246546]


title: Muscle-invasive bladder cancer [BL246213(7)]


title: LMMJ-19-MEP


title: Muscle-invasive bladder cancer [BL246213(4)]


title: LMMJ-19-GMP


title: Muscle-invasive bladder cancer [BL246213(9)]


title: Muscle-invasive bladder cancer [BL246213(6)]


title: Muscle-invasive bladder cancer [BL246213(5)]


title: LMMJ-17-MEP

value: JMML_Other mutated


title: LMMJ-19-CMP


title: Muscle-invasive bladder cancer [BL246213(2)]


title: Muscle-invasive bladder cancer [BL246213(3)]


title: LMMJ-17-GMP


title: LMMJ-15-MEP


title: LMMJ-17-CMP


title: Muscle-invasive bladder cancer [BL246213(12)]


title: LMMJ-15-GMP


title: LMMJ-15-CMP


title: LMMJ-14-MEP

value: JMML_KRAS mutated


title: LMMJ-14-GMP

source_name: Peripheral blood

value: Peripheral blood


title: LMMJ-14-CMP


title: Muscle-invasive bladder cancer [BL246213(11)]


title: Muscle-invasive bladder cancer [BL244994 (2)]


title: Muscle-invasive bladder cancer [BL246213(10)]


title: Muscle-invasive bladder cancer [BL246211]


title: Muscle-invasive bladder cancer [BL267140]


title: LMMJ-12-MEP


title: Muscle-invasive bladder cancer [BL247303 (9)]


title: HCT116, extracted nuclei, cell 098

city: Hong Kong

first: Angela

middle: Ruohao

last: WU

address: Clear water bay street

department: LIFS

institute: HKUST

description: RNA+DNA

data_processing:
fastq files were filtered with fastp.
To process the raw sequencing data, please go to "https://github.com/0YuLei0/scONE-seq-data-processing" for the detailed analysis pipline.
RNA data were quantified with Kallisto.
RNA data from nuclei were quantified with Salmon to consider the pre-mature RNA.
RNA data from 10x were quantified with kb-python to consider the pre-mature RNA.
DNA data were mapped with BWA mem; filter reads with MAPQ higher than 59; transfered to bed files with bedtools; then used Ginkgo to get the normalized counts in 500kb genome bin size.
Assembly: hg38
Library strategy: scONE-seq

source_name: Colon

growth_protocol: HCT116 cells are cultured in DMEM

extract_protocol: Nuclei isolation from HCT116 is based on the TST protocol

value: Colon

tag: cell line

value: cancer cell

tag: treatment

value: Extracted nuclei


title: LMMJ-12-CMP


title: HCT116, extracted nuclei, cell 094

description: RNA+DNA


title: HCT116, extracted nuclei, cell 093

description: RNA+DNA


title: HCT116, extracted nuclei, cell 095

description: RNA+DNA


title: HCT116, extracted nuclei, cell 096

description: RNA+DNA


title: HCT116, extracted nuclei, cell 097

description: RNA+DNA


title: HCT116, extracted nuclei, cell 092

description: RNA+DNA


title: HCT116, extracted nuclei, cell 090

description: RNA+DNA


title: Muscle-invasive bladder cancer [BL243829]

tag: disease


title: Muscle-invasive bladder cancer [BL244994 (1)]


title: HCT116, extracted nuclei, cell 089

description: RNA+DNA


title: Muscle-invasive bladder cancer [BL266012]


title: LMMJ-12-GMP


title: LMMJ-10-GMP


title: Muscle-invasive bladder cancer [BL243157]


title: Muscle-invasive bladder cancer [BL251105(9)]


title: HCT116, extracted nuclei, cell 087

description: RNA+DNA


title: Muscle-invasive bladder cancer [BL266513]


title: HCT116, extracted nuclei, cell 086

description: RNA+DNA


title: LMMJ-07-MEP


title: Muscle-invasive bladder cancer [BL265174]


title: LMMJ-07-GMP


title: HCT116, extracted nuclei, cell 091

description: RNA+DNA


title: LMMJ-10-MEP


title: Muscle-invasive bladder cancer [BL262917]


title: Muscle-invasive bladder cancer [BL263217]


title: LMMJ-07-CMP


title: HCT116, extracted nuclei, cell 083

description: RNA+DNA


title: HCT116, extracted nuclei, cell 084

description: RNA+DNA


title: HCT116, extracted nuclei, cell 081

description: RNA+DNA


title: LMMJ-06-MEP


title: HCT116, extracted nuclei, cell 080

description: RNA+DNA


title: HCT116, extracted nuclei, cell 088

description: RNA+DNA


title: HCT116, extracted nuclei, cell 079

description: RNA+DNA


title: Muscle-invasive bladder cancer [BL262328]


title: HCT116, extracted nuclei, cell 078

description: RNA+DNA


title: Muscle-invasive bladder cancer [BL261796]


title: HCT116, extracted nuclei, cell 077

description: RNA+DNA


title: HCT116, extracted nuclei, cell 085

description: RNA+DNA


title: HCT116, extracted nuclei, cell 076

description: RNA+DNA


title: Muscle-invasive bladder cancer [BL262650]


title: Muscle-invasive bladder cancer [BL257542]


title: LMMJ-05-MEP


title: HCT116, extracted nuclei, cell 082

description: RNA+DNA


title: LMMJ-06-CMP


title: HCT116, extracted nuclei, cell 074

description: RNA+DNA


title: LMMJ-05-GMP


title: HCT116, extracted nuclei, cell 072

description: RNA+DNA


title: HCT116, extracted nuclei, cell 073

description: RNA+DNA


title: LMMJ-06-GMP


title: LMMJ-04-MEP


title: HCT116, extracted nuclei, cell 069

description: RNA+DNA


title: HCT116, extracted nuclei, cell 068

description: RNA+DNA


title: HCT116, extracted nuclei, cell 067

description: RNA+DNA


title: HCT116, extracted nuclei, cell 070

description: RNA+DNA


title: Muscle-invasive bladder cancer [BL261925]


title: Muscle-invasive bladder cancer [BL256588(2)]


title: LMMJ-04-GMP


title: HCT116, extracted nuclei, cell 075

description: RNA+DNA


title: HCT116, extracted nuclei, cell 066

description: RNA+DNA


title: LMMJ-04-CMP


title: Muscle-invasive bladder cancer [BL252613 (4)]


title: HCT116, extracted nuclei, cell 065

description: RNA+DNA


title: Muscle-invasive bladder cancer [BL256588(1)]


title: HCT116, extracted nuclei, cell 063

description: RNA+DNA


title: HCT116, extracted nuclei, cell 064

description: RNA+DNA


title: HCT116, extracted nuclei, cell 062

description: RNA+DNA


title: LMMJ-03-MEP


title: LMMJ-05-CMP


title: Muscle-invasive bladder cancer [BL256851]


title: HCT116, extracted nuclei, cell 071

description: RNA+DNA


title: Muscle-invasive bladder cancer [BL252613 (3)]


title: HCT116, extracted nuclei, cell 061

description: RNA+DNA


title: HCT116, extracted nuclei, cell 060

description: RNA+DNA


title: HCT116, extracted nuclei, cell 058

description: RNA+DNA


title: Muscle-invasive bladder cancer [BL252613 (2)]


title: Muscle-invasive bladder cancer [BL252613 (1)]


title: LMMJ-03-CMP


title: HCT116, extracted nuclei, cell 059

description: RNA+DNA


title: LMMJ-01-MEP


title: Muscle-invasive bladder cancer [BL255193]


title: HCT116, extracted nuclei, cell 055

description: RNA+DNA


title: LMMJ-03-GMP


title: LMMJ-01-GMP


title: HCT116, extracted nuclei, cell 054

description: RNA+DNA


title: HCT116, extracted nuclei, cell 053

description: RNA+DNA


title: HCT116, extracted nuclei, cell 057

description: RNA+DNA


title: EHRD29-MEP

value: Healthy prenatal sample


title: Muscle-invasive bladder cancer [BL251105(1)]


title: Muscle-invasive bladder cancer [BL250812(4)]


title: HCT116, extracted nuclei, cell 052

description: RNA+DNA


title: LMMJ-01-CMP


title: HCT116, extracted nuclei, cell 050

description: RNA+DNA


title: HCT116, extracted nuclei, cell 051

description: RNA+DNA


title: Muscle-invasive bladder cancer [BL251725]


title: Muscle-invasive bladder cancer [BL251476]


title: HCT116, extracted nuclei, cell 049

description: RNA+DNA


title: HCT116, extracted nuclei, cell 047

description: RNA+DNA


title: HCT116, extracted nuclei, cell 056

description: RNA+DNA


title: Muscle-invasive bladder cancer [BL250812(3)]


title: MO-6-GMP


title: HCT116, extracted nuclei, cell 048

description: RNA+DNA


title: EHRD29-CMP


title: Muscle-invasive bladder cancer [BL250812(1)]


title: HCT116, extracted nuclei, cell 045

description: RNA+DNA


title: EHRD23-MEP


title: EHRD29-GMP


title: HCT116, extracted nuclei, cell 044

description: RNA+DNA


title: Muscle-invasive bladder cancer [BL250626(7)]


title: HCT116, extracted nuclei, cell 043

description: RNA+DNA


title: EHRD23-GMP


title: HCT116, extracted nuclei, cell 041

description: RNA+DNA


title: HCT116, extracted nuclei, cell 039

description: RNA+DNA


title: EHAB72-MEP

source_name: Liver

value: Liver


title: EHRD23-CMP


title: HCT116, extracted nuclei, cell 040

description: RNA+DNA


title: HCT116, extracted nuclei, cell 046

description: RNA+DNA


title: EHAB72-CMP


title: EHAB72-GMP


title: HCT116, extracted nuclei, cell 034

description: RNA+DNA


title: Muscle-invasive bladder cancer [BL250626(1)]

value: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer [BL249167]


title: HCT116, extracted nuclei, cell 042

description: RNA+DNA


title: HCT116, extracted nuclei, cell 032

description: RNA+DNA


title: Muscle-invasive bladder cancer [BL250812(2)]


title: EHAB69-MEP


title: Muscle-invasive bladder cancer [BL248867]


title: Muscle-invasive bladder cancer [BL246213(1)]


title: EHAB69-GMP


title: Muscle-invasive bladder cancer [BL248796]


title: HCT116, extracted nuclei, cell 031

description: RNA+DNA


title: HCT116, extracted nuclei, cell 037

description: RNA+DNA


title: EHAB69-CMP


title: HCT116, extracted nuclei, cell 038

description: RNA+DNA


title: HCT116, extracted nuclei, cell 036

description: RNA+DNA


title: HCT116, extracted nuclei, cell 030

description: RNA+DNA


title: HCT116, extracted nuclei, cell 029

description: RNA+DNA


title: HCT116, extracted nuclei, cell 035

description: RNA+DNA


title: HCT116, extracted nuclei, cell 028

description: RNA+DNA


title: HCT116, extracted nuclei, cell 026

description: RNA+DNA


title: HCT116, extracted nuclei, cell 033

description: RNA+DNA


title: EHAB63-MEP


title: Muscle-invasive bladder cancer [BL246213 (2)]


title: HCT116, extracted nuclei, cell 025

description: RNA+DNA


title: EHAB63-GMP-ARN-1


title: Muscle-invasive bladder cancer [BL242476(1)]


title: Muscle-invasive bladder cancer [BL243554]


title: HCT116, extracted nuclei, cell 024

description: RNA+DNA


title: HCT116, extracted nuclei, cell 022

description: RNA+DNA


title: EHAB63-CMP


title: HCT116, extracted nuclei, cell 021

description: RNA+DNA


title: HCT116, extracted nuclei, cell 023

description: RNA+DNA


title: MO-9-CMP

value: Bone Marrow


title: HCT116, extracted nuclei, cell 020

description: RNA+DNA


title: Muscle-invasive bladder cancer [BL240835]


title: HCT116, extracted nuclei, cell 019

description: RNA+DNA


title: HCT116, extracted nuclei, cell 027

description: RNA+DNA


title: MO-27-MPP

value: Sorted  MPP


title: HCT116, extracted nuclei, cell 018

description: RNA+DNA


title: Transgenic, Citrus, rep1

city: Uttarakhand

first: Harsh

last: Chauhan

state: Haridwar

address: Roorkee-Haridwar Highway, Roorkee

department: Department of Biosciences and Bioengineering

institute: Indian Institute of Technology Roorkee

data_processing:
NGSQC toolkit (SQIT); tool used for QC
Alignment and mapping of reads was performed using Trinity platform (Bowtie2) (Hass et al., 2013; https://github.com/trinityrnaseq/trinityrnaseq).
Abundance estimation was calculated  using RSEM (RNA-Seq by Expectation-Maximization) method (Li and Dewey, 2011) and differential gene expression analysis was  performed using DESeq2 (Mi et al., 2014; https://bioconductor.org/packages/release/bioc/html/DESeq2.html).
Assembly: Denovo assembly
Supplementary files format and content: tab-delimited text files include COUNT matrix for each Sample
Supplementary files format and content: tab-delimited text files include TMM.EXPR matrix for each Sample

organism: Citrus x aurantiifolia

source_name: Leaves

extract_protocol:
Leaves of WT and PCR positive transgenic plants were used to extract the total RNA with RNeasy® plant mini kit (74904; Qiagen) as per the manufacturer’s instructions. During the total RNA extraction, RQ1 RNase-free DNase (M6101; Promega Corporation) was used to remove the genomic DNA. The RNA concentration was quantified by NanoDrop microvolume UV-Vis spectrophotometers (ND-ONE-W; Thermo Fisher Scientific), and total RNA (5µg) was separated on 1.2 % formaldehyde gel to determine concentration and integrity.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Leaves

tag: cultivar

value: Pramalini

value: overexpressing a novel trypsin inhibitor


title: HCT116, extracted nuclei, cell 016

description: RNA+DNA


title: HCT116, extracted nuclei, cell 017

description: RNA+DNA


title: Muscle-invasive bladder cancer [BL237270]


title: Transgenic, Citrus, rep2

tag: genotype


title: Muscle-invasive bladder cancer [BL242476(2)]


title: Muscle-invasive bladder cancer [BL237598]


title: Muscle-invasive bladder cancer [BL239562]


title: MO-24-CSH

value: Sorted  CSH

value: Healthy postnatal sample


title: MO-23-CSH


title: HCT116, extracted nuclei, cell 013

description: RNA+DNA


title: HCT116, extracted nuclei, cell 014

description: RNA+DNA


title: MO-06-CSH


title: Wild type, Citrus, rep1

value: wild type


title: HCT116, extracted nuclei, cell 012

description: RNA+DNA


title: HCT116, extracted nuclei, cell 010

description: RNA+DNA


title: HCT116, extracted nuclei, cell 011

description: RNA+DNA


title: HCT116, extracted nuclei, cell 009

description: RNA+DNA


title: MO-05-CSH


title: MO-04-CSH


title: HCT116, extracted nuclei, cell 008

description: RNA+DNA


title: Muscle-invasive bladder cancer [BL260841]


title: HCT116, extracted nuclei, cell 007

description: RNA+DNA


title: LMMJ-23-MPP

value: JMML_NRAS mutated


title: HCT116, extracted nuclei, cell 006

description: RNA+DNA


title: F4

city: Wuerzburg

first: Franziska

last: Faber

state: Bavaria

address: Josef-Schneider-Straße 2

department: Institute for Molecular Infection Biology

institute: University of Wuerzburg

data_processing:
Data analysis was performed as described in Melamed et al., with a few modifications. Briefly, raw reads were trimmed and quality filtered with BBDuk (min. phred-score of 20, min. read length of 25). First mapping was conducted with BWA provided by the RIL-seq computational pipeline. The map_chimeric_fragments.py script provided by the RIL-seq pipeline was used to classify fragments into single and chimeric. All parameters were set to default. Fragments that mapped within a distance of 1,000 nt or within the same transcript were considered single, whereas fragments that mapped to two different loci were considered chimeric. To test whether two fragments mapped within the same transcript, an additional annotation file for CP010905.2 was used. To decide if the replicates can be considered reproducible, their correlation was computed as described in Melamed et al. To be able to use the ribozero option of RILseq_significant_regions.py, which excludes rRNAs from the analysis, the necessary BioCyc database was generated with Pathway Tools based on the CP010905.2 annotation. The high correlation of all replicates allowed us to unify them for the final classification into S-chimeras. Fisher’s exact test was applied to assign an odds ratio and a p-value to each chimera. Chimeras with a minimum odds ratio of 1 and a p-value < 0.05 were considered significant. In addition, only chimeras covered by ≥ 25 chimeric reads were considered for further analysis.
Assembly: CP010905.2
Supplementary files format and content: text files with RIL-seq computational pipeline final output merged with CP010905.2 annotation
Library strategy: RIL-seq

organism: Clostridioides difficile

source_name: bacterial cell

growth_protocol: Cultures were grown in sterile filtered  TY liquid medium to transition phase (late exponential/early stationary)

extract_protocol:
RIL-seq was performed, following the original protocol published by Melamed and collogues with minor alterations. Briefly, C. difficile 630 WT and hfq::3XFLAG were grown in sterile filtered TY in four biological replicates until OD600 of ∼1.2. Of each replicate, 100 ODs were harvested (4,500 x g, 15min at 4 °C), resuspended in 10 ml ice-cold 1xPBS and irradiated with UV light (254 nm, 80,000 mJ/cm2). Following centrifugation (4,500 x g, 15min at 4 °C), pellets were resuspended in 800 µl of ice-cold wash buffer (50 mM NaH2PO4, 300 mM NaCl, 0.05% Tween, 1:200 diluted protease inhibitor cocktail set III (Calbiochem)) supplemented with 0.1 U/μL of recombinant RNase inhibitor (wash buffer-RIn, Takara). Mechanical cell lysis was achieved by mixing each sample with 0.1 mm glass beads and grinding in a Retsch mixer mill at a frequency of 30/s for 5 min. The grinding was repeated four times, after each step the adaptors were place on ice for 2 min. The resulting supernatant was transferred to a new tube (17,000 x g, 2 min at 4 °C), 400 µl wash buffer-RIn was added to the glass beads and the grinding was repeated once more. For Hfq co-immunoprecipitations, the accumulated lysates were incubated with protein A/G magnetic beads (Thermo-Fisher) pre-coupled with anti-Flag antibody (M2 monoclonal antibody, Sigma-Aldrich) for 2 h at 4°C with rotation, followed by three washing steps with wash buffer-RIn. Next, samples were treated with 480 µl of wash buffer supplemented with with RNase A/T1 (1:520, Thermo Fisher Scientific) for 5 min at 22°C, trimming any exposed RNA ends. The process was stopped by washing each sample with 200 µl of wash buffer supplemented with SUPERase In RNase inhibitor (final concentration of 0.1 U/μL, Ambion) three times for 5 min at 4 °C. Following PNK treatment for 2 h at 22 °C (1x PNK buffer A, 1 mM ATP, 1 U/µl recombinant RNAse inhibitor, 0.5 U/µl T4 PNK (New England BioLabs)), samples were washed again three times with wash buffer-RIn. Hfq-bound RNAs were then proximity ligated with T4 RNA ligase I (1x T4 RNA ligase buffer, 9% DMSO, 1 mM ATP, 20% PEG 8000, 0.6 U/µl recombinant RNase inhibitor, 2.7 U/µl T4 RNA ligase I (New England BioLabs)) overnight at 22°C with agitation, followed by 3 washing steps with wash buffer-RIn at 4 °C. Finally, RNA was eluted by incubating the beads with Proteinase K (50 mM Tris-HCl pH 7.8, 50 mM NaCl, 1% SDS, 5 mM EDTA pH 8.0, 5 mM β-mercaptoethanol, 0.1 U/µl recombinant RNase inhibitor, 0.33 mg/ml Proteinase K (Thermo Fisher Scientific)) for 2 h at 55 °C. RNA purification was achieved using TRIzol LS according to the manufacturer’s instructions.for 20 min at 4 °C and 4,000 g. Pellets were washed three times with ice-cold 1x TBS before resuspension in 500 µl ice-cold 1x lysis buffer (20 mM Tris-HCl (pH 7.5), 150 mM, KCl, 1 mM DTT, 1 mM PMSF, 0.2% Triton X 100, 20 U/ml DNase I (Thermo Fisher Scientific), 200 U/ml RNase inhibitor. Cell lysis was performed in 2 ml tubes containing Lysing matrix E (MP Biomedicals, 1.4 mm ceramic spheres, 0.1 mm silica spheres and one 4 mm glass bead) by using a FastPrep-24 (MP Biomedicals) machine at 6 m/s for 30 seconds. The lysate was centrifuged for 30 minutes at 4 °C and 4,000 g to remove beads and debris. For input controls 10 µl lysate was mixed with 1 ml TRIzol and 20 µl was mixed with 5x protein loading buffer. The 10 – 40% (w/v) glycerol gradient (in lysis buffer without DNase I or RNase inhibitor) was formed in an open-top polyallomer ultracentrifugation tube (Seton Scientific) by using a Gradient Station model 153 (Biocomp).  200 µl of the cleared cell lysate was layered on top of the gradient. The gradient was centrifuged for 17 h at 4 °C and 100,000 rcf (23,700 rpm) with an SW 40 Ti rotor (Beckman Coulter). Fractionation was done manually into 20 fractions with a volume of 590 µl.. For quality control, all fractions were analyzed with a NanoDrop (Thermo Fisher Scientific) Spectrophotometer at 260 nm. 90 µl of each fraction was mixed with 5x protein loading buffer to perform LC-MS/MS.500 µl of the fractions was used for total RNA isolation. Therefore, 50 µl 10% SDS (25 µl for the pellet) and 600 µl of acidic phenol/chloroform/isoamyl alcohol (P/C/I, Roth, 300 µl for the pellet) was added to the fractions. After mixing for 30 seconds the mixture was incubated for 5 minutes at room temperature. Additionally, 400 µl chloroform was added to the Trizol-dissolved lysate and mixed. The lysate was also incubated for 5 minutes at room temperature. Samples were centrifuged for 15 minutes at 4 °C and 13,000 rpm. The aqueous phase of all samples was collected. For RNA precipitation 1.4 ml ice-cold 30:1 Ethanol:3 M NaOAc (pH 6.5) and 1 µl GlycoBlue (Thermo Fisher Scientific) co-precipitant was added. RNA was precipitated over night at -20 °C. RNA was pelleted at 4 °C for 30 minutes and 13,000 rpm and washed with 70% ice-cold Ethanol, followed by centrifugation at 4 °C for 15 minutes and 13,000 rpm. The pellet was air-dryed and subsequently dissolved in 40 µl DEPC-H2O. To digest DNA 0.5 µl RNase inhibitor, 5 µl DNase I buffer with MgCl2 (Thermo Fisher Scientific), 4 µl DNase I (Thermo Fisher Scientific) and 0.5 µl DEPC-H2O was added to each RNA sample. Digestion was performed for 45 minutes at 37 °C. RNA was again purified as described above. This time 150 µl DEPC-H2O and 200 µl acidic P/C/I was added to the samples. RNA was finally dissolved in 35 µl DEPC-H2O and stored at -80 °C.
cDNA library preparation and sequencing were performed by Vertis Biotechnologie AG. First, oligonucleotide adapters were ligated to the RNA 5' and 3' ends followed by first-strand cDNA synthesis using M-MLV reverse transcriptase and the 3’ adapters as primers. The resulting cDNAs were PCR-amplified using a high fidelity DNA polymerase for 14-16 cycles. Next, cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and quality controlled by capillary electrophoresis on a Shimadzu MultiNA microchip electrophoresis system. For Illumina NextSeq sequencing, the samples were pooled in approximately equimolar amounts. The resulting cDNA pool was then size fractionated in the size range of 170 – 400 bp by polyacrylamide gel electrophoresis and paired-end sequenced on an Illumina HighSeq system using 2 x 150 bp read lengths.
RNA-seq (size fractionation)

tag: strain

value: RIL-seq FLAG

value: bacterial cell


title: HCT116, extracted nuclei, cell 015

description: RNA+DNA

value: Colon


title: LMMJ-23-CSH


title: HCT116, extracted nuclei, cell 005

description: RNA+DNA

value: cancer cell


title: HCT116, extracted nuclei, cell 003

description: RNA+DNA

value: Extracted nuclei


title: Wild type, Citrus, rep2


title: F2


title: WT4

value: RIL-seq control


title: F3


title: HCT116, extracted nuclei, cell 004

description: RNA+DNA


title: F1


title: LMMJ-20-MPP

value: JMML_PTPN11 mutated


title: HCT116, live whole cell, cell 091

description: RNA+DNA

value: no


title: LMMJ-20-MEP-cong

value: Bone Marrow

value: Sorted  MEP


title: HCT116, extracted nuclei, cell 001

description: RNA+DNA


title: HCT116, extracted nuclei, cell 002

description: RNA+DNA


title: WT3


title: HCT116, live whole cell, cell 092

description: RNA+DNA


title: HCT116, live whole cell, cell 090

description: RNA+DNA


title: HCT116, live whole cell, cell 089

description: RNA+DNA


title: LMMJ-20-CSH


title: LMMJ-20-CMP-cong

value: Sorted  CMP


title: HCT116, live whole cell, cell 088

description: RNA+DNA


title: LMMJ-20-GMP-cong

value: Sorted  GMP


title: WT1


title: WT2


title: HCT116, live whole cell, cell 087

description: RNA+DNA


title: HCT116, live whole cell, cell 086

description: RNA+DNA


title: HCT116, live whole cell, cell 085

description: RNA+DNA


title: LMMJ-15-MPP

value: Sorted  MPP


title: HCT116, live whole cell, cell 084

description: RNA+DNA


title: LMMJ-15-CSH

value: Sorted  CSH


title: UT-143 2 ATAC LNCaP

city: Memphis

first: Daniel

middle: Lee

last: Johnson

state: Tennessee

address: 71 S Manassas

department: Molecular Informatics Core

institute: UTHSC

data_processing:
QC performed using fastqc. Data trimmed for phred > 30
Alignment performed using STAR 2.7.10a and hg38 reference; Gapped mode for RNASeq; no gap for ATAC
RNASeq normalized count using CPM
Peaking calling using HOMER. BigWig files provided.
Supplementary files format and content: bw and  CPM normalized count table

source_name: LNCaP ATAC-Seq, prostate cancer

growth_protocol: Cells were grown in RPMI+10%FBS. Cells were treated with vehicle (DMSO) or 10 uM UT-143 for 20-24 hours. ATAC-Seq and RNA-Seq were performed

extract_protocol:
Cells were harvested for ATAC-Seq and RNA-Seq
DNA libraries were prepared using Swift Accel-NGS 2S Plus kit in an automated platform

treatment_protocol: Vehicle (DMSO): UT-143 (10 uM)

value: LNCaP

tag: agent


title: UT-143 3 ATAC LNCaP


title: UT-143 1 ATAC LNCaP


title: HCT116, live whole cell, cell 083

description: RNA+DNA


title: HCT116, live whole cell, cell 081

description: RNA+DNA


title: HCT116, live whole cell, cell 082

description: RNA+DNA


title: HCT116, live whole cell, cell 080

description: RNA+DNA


title: LMMJ-14-CSH

value: Peripheral blood

value: JMML_KRAS mutated


title: HCT116, live whole cell, cell 077

description: RNA+DNA


title: LMMJ-12-MPP


title: LMMJ-12-CSH


title: Vehicle 3 ATAC LNCaP

value: Vehicle


title: HCT116, live whole cell, cell 079

description: RNA+DNA


title: HCT116, live whole cell, cell 078

description: RNA+DNA


title: Vehicle 1 ATAC LNCaP


title: HCT116, live whole cell, cell 076

description: RNA+DNA


title: LMMJ-10-MPP

value: JMML_NRAS mutated


title: HCT116, live whole cell, cell 074

description: RNA+DNA

value: Colon


title: Vehicle 2 ATAC LNCaP


title: HCT116, live whole cell, cell 073

description: RNA+DNA

value: cancer cell


title: LMMJ-10-CMP


title: HCT116, live whole cell, cell 075

description: RNA+DNA


title: UT-143 2 RNASeq 22RV1

description:
RN5
cpm_normalized.tsv

source_name: 22RV1 RNA-Seq, prostate cancer


title: UT-143 3 RNASeq 22RV1

description:
RN6
cpm_normalized.tsv


title: HCT116, live whole cell, cell 071

description: RNA+DNA


title: LMMJ-04-MPP


title: HCT116, live whole cell, cell 070

description: RNA+DNA


title: UT-143 1 RNASeq 22RV1

description:
RN4
cpm_normalized.tsv


title: LMMJ-04-CSH


title: HCT116, live whole cell, cell 069

description: RNA+DNA


title: HCT116, live whole cell, cell 068

description: RNA+DNA


title: Vehicle 3 RNASeq 22RV1

description:
RN3
cpm_normalized.tsv


title: HCT116, live whole cell, cell 067

description: RNA+DNA


title: HCT116, live whole cell, cell 072

description: RNA+DNA


title: HCT116, live whole cell, cell 066

description: RNA+DNA


title: LMMJ-03-CSH


title: Vehicle 2 RNASeq 22RV1

description:
RN2
cpm_normalized.tsv


title: HCT116, live whole cell, cell 065

description: RNA+DNA


title: Vehicle 1 RNASeq 22RV1

description:
RN1
cpm_normalized.tsv


title: LMMJ-01-MPP


title: HCT116, live whole cell, cell 063

description: RNA+DNA


title: HCT116, live whole cell, cell 064

description: RNA+DNA


title: HCT116, live whole cell, cell 061

description: RNA+DNA


title: HCT116, live whole cell, cell 062

description: RNA+DNA


title: HCT116, live whole cell, cell 060

description: RNA+DNA


title: LMMJ-01-CSH


title: WT-M, CHLA Co-Culture, Rep 3

city: Madison

first: Jue

last: Zhang

state: WI

address: 330 N orchard st

institute: Morgridge Institute for Research

data_processing:
Basecalling via the standard Illumina Pipeline, version 1.8.2.
Trimming/Filtering for adapters and low quality via custom algorithm
Expression estimates via RSEM v1.3.0 under Python 2.7.15, using bowtie2-2.3.4.1. Executed command: rsem-calculate-expression --no-qualities --bowtie2 --bowtie2-k 200 --bowtie2-sensitivity-level sensitive --seed-length 20 --keep-intermediate-files --no-bam-output --paired-end [r1.fa.gz] [r2.fa.gz] [hg38 bowtie reference]
Assembly: hg38
Supplementary files format and content: genes.ec.tab : expected counts
Supplementary files format and content: genes.tpm.tab : transcripts per million

source_name: culture

growth_protocol:
CAR_M: We collected the hematopoietic cells on day 10 differentiation and cultured them in serum-free media containing GM-CSF for 3 days and then IL-1B and M-CSF for another 7 days.
WT_M: pnas.1702295114

extract_protocol:
Total RNA from cells were isolated with RNeasy Plus kit (QIAGEN).
Sequencing libraries were prepared following the LM-seq protocol (Hou et al., 2015).
Sequenced on Illumina NextSeq2000 at a depth of 19 samples per lane.

treatment_protocol:
CAR_M: Wild type (WT) or CAR-M were co-cultured with GD2-expressiong CHLA-20-AkaLuc-GFP neuroblastoma cells or WM266-4-AkaLuc-GFP melanoma cells
WT_M: Treated with FGF2, VEGFA, and RESV containing media (FVR) and cells were cultured for 4 days

value: culture

value: Macrophage


title: HCT116, live whole cell, cell 058

description: RNA+DNA


title: EHAB72-MPP

value: Liver

value: Healthy prenatal sample


title: HCT116, live whole cell, cell 059

description: RNA+DNA

value: no


title: WT-M, CHLA Co-Culture, Rep 1


title: WT-M, CHLA Co-Culture, Rep 2


title: HCT116, live whole cell, cell 056

description: RNA+DNA


title: WT-M, Rep 3


title: HCT116, live whole cell, cell 057

description: RNA+DNA


title: HCT116, live whole cell, cell 055

description: RNA+DNA


title: WT-M, Rep 2


title: HCT116, live whole cell, cell 053

description: RNA+DNA


title: EHAB65-MPP


title: 7_Patient 33_iReg__plus__G9ai

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

description: 7_Patien_33_iReg__plus__G9ai.FCHG3YCBBXY_L7_R*_IGTGGCC

data_processing:
Base calling was performed with the Illumina bcl2fastq
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by STAR 2.6.1c
Gene counts were generated using subread featureCounts
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files with FPKM values for each gene per sample

source_name: G9a inhibitor Treatment iReg

growth_protocol: 24 hour differentiation with cell media containing stimulating cytokines and antibodies.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Cat#74104)
Illumina TruSeq Stranded mRNA prep (Cat #20020594).

treatment_protocol:
Naive T cells treated with anti-CD3 and CD28 stimulation in addition to IL2 and TGFb for 24 hours with drug (UNC0642)
Plates coated with Anti-CD3. Media Contained anti-CD28 with ant without IL2 and TGFb in addiiton or not to vehicle and UNC0642

value: peripheral blood

value: Naive T cells

tag: treatment 1

value: Anti-CD3 + Anti CD28 treatment

tag: treatment 2

value: IL2 and TGFb

tag: treatment 3

value: UNC0642 2uM


title: EHAB65-CSH

value: Sorted  CSH


title: HCT116, live whole cell, cell 052

description: RNA+DNA


title: HCT116, live whole cell, cell 054

description: RNA+DNA


title: WT-M, Rep 1


title: CAR-M, CHLA Co-Culture, Rep 3


title: HCT116, live whole cell, cell 049

description: RNA+DNA


title: HCT116, live whole cell, cell 050

description: RNA+DNA


title: HCT116, live whole cell, cell 051

description: RNA+DNA


title: 3_Patient 29_iReg__plus__G9ai

description: 3_Patient_29_iReg__plus__G9ai.FCHG3YCBBXY_L7_R*_IACTTGA


title: 15_Donor 2_iReg__plus__G9ai

description: 15_Donor_2_iReg__plus__G9ai.FCHG3YCBBXY_L8_R*_IGATCAG


title: HCT116, live whole cell, cell 048

description: RNA+DNA


title: HCT116, live whole cell, cell 046

description: RNA+DNA


title: EHAB72-CSH


title: CAR-M, CHLA Co-Culture, Rep 2


title: CAR-M, CHLA Co-Culture, Rep 1


title: HCT116, live whole cell, cell 047

description: RNA+DNA


title: 4_Patient 29_iReg

description: 4_Patient_29_iReg.FCHG3YCBBXY_L7_R*_IGATCAG

source_name: Control iReg

treatment_protocol:
Naive T cells treated with anti-CD3 and CD28 stimulation in addition to IL2 and TGFb for 24 hours with vehicle (DMSO)
Plates coated with Anti-CD3. Media Contained anti-CD28 with ant without IL2 and TGFb in addiiton or not to vehicle and UNC0642


title: HCT116, live whole cell, cell 045

description: RNA+DNA


title: 8_Patient 33_iReg

description: 8_Patien_33_iReg.FCHG3YCBBXY_L7_R*_IGTTTCG


title: HCT116, live whole cell, cell 043

description: RNA+DNA


title: CAR-M, Rep 3


title: HCT116, live whole cell, cell 044

description: RNA+DNA


title: HCT116, live whole cell, cell 042

description: RNA+DNA


title: CAR-M, Rep 2


title: 16_Donor 2_iReg

description: 16_Donor_2_iReg.FCHG3YCBBXY_L8_R*_ITAGCTT


title: HCT116, live whole cell, cell 041

description: RNA+DNA


title: 6_Patient 33_Th0__plus__G9ai

description: 6_Patien_33_Th0__plus__G9ai.FCHG3YCBBXY_L7_R*_IGGCTAC

source_name: G9a inhibitor Treatment Th0

treatment_protocol:
Naive T cells treated with anti-CD3 and CD28 stimulation for 24 hours with drug (UNC0642)
Plates coated with Anti-CD3. Media Contained anti-CD28 with ant without IL2 and TGFb in addiiton or not to vehicle and UNC0642

value: Anti-CD3 treatment

value: Anti-CD28 treatment

value: DMSO


title: CAR-M, Rep 1


title: 2_Patient 29_Th0__plus__G9ai

description: 2_Patient_29_Th0__plus__G9ai.FCHG3YCBBXY_L7_R*_ITTAGGC


title: HCT116, live whole cell, cell 039

description: RNA+DNA


title: HCT116, live whole cell, cell 040

description: RNA+DNA


title: HCT116, live whole cell, cell 038

description: RNA+DNA


title: HCT116, live whole cell, cell 037

description: RNA+DNA


title: HCT116, live whole cell, cell 035

description: RNA+DNA


title: HCT116, live whole cell, cell 036

description: RNA+DNA


title: 5_Patient 33_Th0

description: 5_Patien_33_Th0.FCHG3YCBBXY_L7_R*_ITAGCTT

source_name: Control Th0

treatment_protocol:
Naive T cells treated with anti-CD3 and CD28 stimulation for 24 hours with vehicle (DMSO)
Plates coated with Anti-CD3. Media Contained anti-CD28 with ant without IL2 and TGFb in addiiton or not to vehicle and UNC0642


title: HCT116, live whole cell, cell 030

description: RNA+DNA


title: HCT116, live whole cell, cell 031

description: RNA+DNA


title: HCT116, live whole cell, cell 033

description: RNA+DNA


title: 1_Patient 29_Th0

description: 1_Patient_29_Th0.FCHG3YCBBXY_L7_R*_IATCACG


title: 13_Donor 2_Th0

description: 13_Donor_2_Th0.FCHG3YCBBXY_L8_R*_ITTAGGC


title: HCT116, live whole cell, cell 029

description: RNA+DNA


title: SKNMC_CBL0137 rep2

city: shanghai

first: Jialin

last: Mo

address: South Chongqing Road, Shanghai 200025. P.R. China

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Trim galore was used to automatically detect and trim adapters
Reads were mapped to mm10 reference genome using Hisat2
Read count was generated using HTSeq (version 0.11.1). Differentially expressed genes (DEGs) were calculated using DESeq2 (version 1.26.0).
FPKM (Fragments per Kilobase Million) was calculated from the number of reads that mapped to each particular gene sequence and the gene length and the sequencing depth were taken into account
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts and FPKM for every expressed gene and every sample

source_name: Ewing sarcoma cell line SKNMC

growth_protocol: SKNMC cells were cultured in Eagle's Minimum Essential Medium (MEM) (BasalMedia, L510KJ) supplemented with 10% FBS and 1×Penicillin Streptomycin Solution.

extract_protocol:
Total RNA was extracted with TRIzol Reagent (Thermo Fisher Scientific, 15596-026) according to the manufacturers’ protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: DMSO or CBL0137 (1μM) treatment for 24 h

value: Ewing sarcoma cell line SKNMC


title: HCT116, live whole cell, cell 032

description: RNA+DNA

value: Colon


title: HCT116, live whole cell, cell 028

description: RNA+DNA

value: cancer cell


title: RY_LP_R2

city: Haikou

first: Zhijian

last: Chen

email: jchen@scau.edu.cn, zjchen@catas.cn

address: Xueyuanlu 4

institute: Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences

data_processing:
The cDNA libraries of the three biological replicates were sequenced using an Illumina HiseqTM platform (Illumina, San Diego, USA) and paired-end, 150 nucleotide reads were generated
Remove contaminated Reads (the number of bases contaminated with Reads is greater than 5 bp. For double-stranded sequencing, if one end is affected Connector contamination, then remove both ends of the Reads). Remove low-quality Reads (Quality Q ≤ 19 bases in Reads account for more than 50% of total bases. For double-stranded sequencing, If one end has low quality Reads, both ends will be removed). Remove Reads containing more than 5% of N (for double-ended sequencing, if the ratio of N at one end is greater than 5%, both ends will be removed Reads)
As the genome sequence for stylo remains unavailable, a de novo assembly approach was conducted.The obtained clean reads were assembled into unigenes using the Trinity software with default parameters. The clean reads were mapped back to the assembled contigs by Bowtie2 v.2.2.3
Genome_build: All unigene sequences were aligned by BLAST search (E-value<1e-5) against the databases of the NCBI non-redundant protein sequences (Nr), the NCBI non-redundant nucleotide sequences (Nt), the Universal Protein (UniProt), the Gene Ontology (GO), the Clusters of Orthologous Groups of protein database (COG), the Functional Annotation (eggNOG), the Kyoto Encyclopedia of Genes and Genomes (KEGG) database and the Protein Family (Pfam).  FASTA files are available on the series record.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample .

organism: Stylosanthes guianensis

source_name: Root

extract_protocol:
Total RNA from leaves of stylo with 0 and 250 μM P treatments were extracted using TRIzol Reagent (Invitrogen, Carlsbad, USA) according to the manufacturer’s protocol. RNA integrity and concentration were determined using an Agilent 2100 RNA Nano 6000 Assay Kit (Agilent Technologies, California, USA).
Oligo (dT) magnetic beads are used to select mRNA with polyA tail.
RNA libraries were prepared for sequencing using standard Illumina protocols.
Sequencing libraries were generated using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, Ipswich, USA)

tag: phosphorus conccentration

value: root


title: HCT116, live whole cell, cell 026

description: RNA+DNA


title: HCT116, live whole cell, cell 025

description: RNA+DNA


title: SKNMC_DMSO rep2


title: RY_LP_R3


title: HCT116, live whole cell, cell 034

description: RNA+DNA


title: RY_LP_R1


title: HCT116, live whole cell, cell 024

description: RNA+DNA


title: CD8+Nrp_1+_2

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

hyb_protocol: 5.5 μg of biotinylated cDNA were fragmented and placed in a hybridization cocktail containing four biotinylated hybridization controls (BioB, BioC, BioD, and Cre) as recommended by the manufacturer. Samples were hybridized to an identical lot of Affymetrix Clariom™ S (mouse) for 17 hours at 45°C. Steps for washing and staining were processed on the fluidics station 450 using the GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix; Santa Clara, CA).

scan_protocol: Image Analysis was performed on GCOS3000 Scanner and GCOS1.2 Software Suite (Affymetrix; Santa Clara, CA).

data_processing: Signal intensities (raw data) were log2 transformed and normalized using RMA summarization method.

label: biotin

molecule: polyA RNA

organism: Mus musculus

source_name: sort-purified Nrp-1+ CD8+ T cells

label_protocol: 2-10 ng of total RNA were used for biotin labelling according GeneChip® Pico Kit (Affymetrix).

extract_protocol: RNAeasy (Qiagen). Quality and integrity of total RNA was controlled on Agilent Technologies 2100 Bioanalyzer (Agilent Technologies; Waldbronn, Germany).

treatment_protocol: Three C57BL/6 mice were infected with 1 x 10^5 P. berghei ANKA infected red blood cells intravenously. At day 6 post infection Nrp-1+ and Nrp-1- CD8+ T cells were isolated from spleen by FACS cell sorting (BD ARIA II). 2,000 splenocytes were directly sorted into 4.5µl cell lysis buffer with 0.5µL DNaseI and 0.5µL single cell stop solution from Invitrogen single cell lysis kit (Thermo Fisher Scientific, Waltham, USA) was added as recommended by the manufacturer. Samples were stored at -20°C until RNA isolation (RNeasy, Qiagen).

value: PbA-infected

value: spleen

value: sort-purified Nrp-1+ CD8+ T cells


title: CD8+Nrp_1__3

source_name: sort-purified Nrp-1- CD8+ T cells

value: sort-purified Nrp-1- CD8+ T cells


title: CD8+Nrp_1+_3


title: SKNMC_DMSO rep1


title: CD8+Nrp_1__1


title: CD8+Nrp_1__2


title: HCT116, live whole cell, cell 023

description: RNA+DNA

value: no


title: HCT116, live whole cell, cell 022

description: RNA+DNA


title: HCT116, live whole cell, cell 027

description: RNA+DNA


title: HCT116, live whole cell, cell 020

description: RNA+DNA


title: A673_CBL0137 rep1

source_name: Ewing sarcoma cell line A673

growth_protocol: A673 cells were cultured in Dulbecco’s modified Eagle medium/High glucose (DMEM) (BasalMedia, L110KJ) supplemented with 10% fetal bovine serum (FBS) (F2442, Sigma, St. Louis, MO, USA) and 1×Penicillin Streptomycin Solution (Gibco, 15240062).

value: Ewing sarcoma cell line A673


title: RY_CK_R2

value: 0 uM


title: SKNMC_CBL0137 rep1


title: HCT116, live whole cell, cell 019

description: RNA+DNA


title: A673_CBL0137 rep2


title: A673_DMSO rep2


title: HCT116, live whole cell, cell 018

description: RNA+DNA


title: A673_DMSO rep1


title: HCT116, live whole cell, cell 016

description: RNA+DNA


title: HCT116, live whole cell, cell 014

description: RNA+DNA


title: HCT116, live whole cell, cell 013

description: RNA+DNA


title: RY_CK_R3


title: HCT116, live whole cell, cell 021

description: RNA+DNA


title: HCT116, live whole cell, cell 015

description: RNA+DNA


title: HCT116, live whole cell, cell 011

description: RNA+DNA


title: HCT116, live whole cell, cell 012

description: RNA+DNA


title: Pinot noir berry sample collected at time point 10 (replicate 3) over ripening season 2014 - Crop thinned 75%

city: San Pietro in Cariano

first: Marianna

last: Fasoli

state: Verona

address: Via della Pieve 70

department: Biotechnology

country: Italy

institute: University of Verona

data_processing:
The reads were aligned onto the grapevine 12x reference genome PN40024 using TopHat v2.0.6 with default parameters
Mapped reads were used to reconstruct the transcripts using Cufflinks v2.0.2 and the reference genome annotation V1
The normalized expression of each transcript was calculated as RPKM (Reads Per Kilobase per Million mapped reads) for each sample.
Genome_build: 12X reference genome PN400024;
https://www.ncbi.nlm.nih.gov/assembly/GCF_000003745.3
Supplementary_files_format_and_content: tab delimited text file containing the normalized reads counts RPKM  for all the samples.

organism: Vitis vinifera

source_name: grape berry pericarp_time point 10_2014_Crop thinned 75%

growth_protocol: Vineyard Features: Vitis vinifera cultivar Pinot noir (clone FPS 23 grafted on rootstock Freedom and planted in 2001) was grown nearby Modesto (USA, CA) in sandy clay loam in an east-west orientation with 10 foot row spacing and 5 foot vine spacing.

extract_protocol:
Total RNA was isolated using the Spectrum Plant Total RNA kit (Sigma-Aldrich) following the manufacturer’s instructions with some modifications (Fasoli et al., 2012). RNA quality and quantity were determined using a Nanodrop 2000 spectrophotometer (Thermo Scientific) and a Bioanalyzer Chip RNA 7500 series II (Agilent).
165 non-directional cDNA libraries were prepared from 2.5 μg of total RNA using the Illumina TruSeq RNA Sample preparation protocol (Illumina Inc., San Diego, CA, USA). Library quality was determined using the Agilent High Sensitivity DNA kit on the Agilent 2100 bioanalyzer, and the quantity was determined by quantitative PCR using the KAPA Library Quantification kit (KapaBiosystems).

treatment_protocol: Cluster thinning treatments: Moderate thinning (50% crop load reduction) was achieved removing clusters to maintain one cluster per shoot; severe thinning (75% crop load reduction) consisted in mantaining one cluster every other shoot; control (0% crop load reduction) was unthinned vines.

value: cv Pinot noir

tag: year

tag: time point

tag: time point replicate

tag: day after veraison

tag: sugar content (g/100ml)

tag: treatment (cluster thinning)

value: Crop thinned 75%

value: grape berry pericarp


title: Pinot noir berry sample collected at time point 10 (replicate 2) over ripening season 2014 - Crop thinned 75%

tag: tissue


title: SKNMC_SSRP1

data_processing:
ChIP-seq data were first mapped against the human genome build hg19 using BowTie2 using the default settings
Then Model-based analysis of ChIP-seq (MACS2: v2.2.7.1) was used to identify peak regions of ChIP-seq enrichment comparing to input control with a q threshold of 0.05
Peak annotation and motifs finding was performed by HOMER Analysis
DeepTools was conducted to generate BigWig files and visualization
We explore Integrative Genome Viewer and WashU Epigenome Browse (http://epigenomegateway.wustl.edu/browser/) to visualize BigWig files on the hg19 genome track.
Genome_build: hg19
Supplementary_files_format_and_content: BW and BED

extract_protocol: Libraries were prepared for sequencing using standard Illumina protocols

tag: cell type


title: RY_CK_R1


title: HCT116, live whole cell, cell 017

description: RNA+DNA

source_name: Colon

tag: cell line

tag: treatment


title: SKNMC_H3K27ac


title: HCT116, live whole cell, cell 009

description: RNA+DNA


title: Pinot noir berry sample collected at time point 10 (replicate 3) over ripening season 2014 - Crop thinned 50%

source_name: grape berry pericarp_time point 10_2014_Crop thinned 50%

tag: cultivar

value: Crop thinned 50%


title: Pinot noir berry sample collected at time point 10 (replicate 2) over ripening season 2014 - Crop thinned 50%


title: HCT116, live whole cell, cell 008

description: RNA+DNA


title: SKNMC_Input


title: Pinot noir berry sample collected at time point 10 (replicate 1) over ripening season 2014 - Crop thinned 50%


title: HCT116, live whole cell, cell 006

description: RNA+DNA


title: SKNMC_FLI1


title: 7w_NC_Small

city: Beijing

first: Rui

last: WANG

address: No.5 Yiheyuan Road, Haidian District

department: Biodynamics Optical Imaging Center (BIOPIC)

institute: Peking University

data_processing:
For the data acquired by the modified STRT-seq method, paired-end sequencing reads were first split based on the cell barcodes in read 2. Then, the 8 bp UMI sequences located on read 2 were extracted and attached to the names of read 1. Next, low-quality reads and TSO-, polyA- and adapter-contaminated sequences were removed. Cleaned reads were mapped to the human genome(hg19) using TopHat (v.2.0.14)(Ghosh and Chan, 2016), and unique mapped reads were kept for further analysis. HTSeq (v0.6.1)(Anders et al., 2015) was used to calculate the transcript abundance of each gene and duplicated reads of each reads were removed based on the UMIs. The detailed code can be found on GitHub (https://github.com/WRui/Post_Implantation/tree/master/scRNA_UMI)
Genome_build: hg19
Supplementary_files_format_and_content: count and TPM gene expression matrix

extract_protocol:
The gonadal biopsies were isolated and washed twice with L15 medium with 10% FBS. Then, the samples were cut into small pieces under controlled cooling conditions and digested with 600 µl of Accutase Cell Detachment Solution (Millipore #SCR005) at 37°C and 850 rpm for 15 min. To ensure that the digestion was as thorough as possible, we pipetted the digestion mixture for at least 20 times. Then 500 µl of L15 medium with 10% PBS was added, and single gonadal cells were obtained by filtering through 50 mm Pre-Separation Filters (Miltenyi Biotec #130-041-407). Then, the cells were pelleted by centrifugation at 300 × g for 8 min and were resuspended in 500 µl of L15 medium with 10% PBS, at which point they were prepared for scRNA-seq. The cells were counted with a hemocytometer.
we performed scRNA-Seq on the cultured cells with a modified STRT-seq method as previously published(Li et al., 2021).

value: human embryo gonad

tag: developmental stage

value: 7 week

tag: experiment type

value: Modified STRT-seq


title: Pinot noir berry sample collected at time point 9 (replicate 3) over ripening season 2014 - Crop thinned 75%

source_name: grape berry pericarp_time point 9_2014_Crop thinned 75%


title: Pinot noir berry sample collected at time point 9 (replicate 2) over ripening season 2014 - Crop thinned 75%


title: HCT116, live whole cell, cell 010

description: RNA+DNA

value: Colon


title: HDLEC, p4, rep4

city: Guangzhou

first: lei

last: zeng

address: No. 74, Zhongshan 2nd Road, Yuexiu District

institute: SUN YAT-SEN UNIVERSITY

data_processing:
Sequencing was performed on the DNBSEQ platform.
Raw reads were aligned to the human genome using hierarchical indexing for spliced alignment of transcripts 2 (HISAT2) and Bowtie2.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include tpm values for all replicates.

source_name: human dermal lymphatic endothelial cells

growth_protocol: Human dermal lymphatic endothelial cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Plus Kit. To obtain sufficient quantitation of RNA, and a total of four relicate experiments were performed.
RNA quality was evaluated via Agilent 2100 Bioanalyzer. One microgram of qualified RNA was used to construct mRNA sequencing libraries.


title: Pinot noir berry sample collected at time point 10 (replicate 1) over ripening season 2014 - Crop thinned 75%


title: HCT116, live whole cell, cell 001

description: RNA+DNA

value: cancer cell


title: HCT116, live whole cell, cell 002

description: RNA+DNA


title: 7w_NC_Big


title: 7w_LDN_Small


title: HDLEC, p4, rep2

value: human dermal lymphatic endothelial cells


title: 7w_LDN_Big


title: HDLEC, p4, rep1


title: Pinot noir berry sample collected at time point 9 (replicate 3) over ripening season 2014 - Crop thinned 50%

source_name: grape berry pericarp_time point 9_2014_Crop thinned 50%


title: HCT116, live whole cell, cell 003

description: RNA+DNA


title: HDLEC, p4, rep3


title: HCT116, live whole cell, cell 007

description: RNA+DNA


title: HCT116, live whole cell, cell 005

description: RNA+DNA


title: 15w_24hNC_Both_B2_20210604

value: 15 week


title: C-5-GB miRNA miRNA

city: Chiba-City

first: Ariki

last: Nagashima

address: Inohana 1-8-1

department: Department of gastroenterology

country: Japan

institute: Graduate School of Medicine, Chiba University.

data_processing: The Deseq2 package version 1.34.0 was used for expression analysis.

source_name: Control patient 5

extract_protocol:
After the biopsy, samples were placed in a microtube containing All Protect Tissue Reagent (QIAGEN), stabilized, and stored at -80 °C. Total RNA was extracted using the miRNeasy Micro Kit (Qiagen).
RNA concentration and RNA integrity number (RIN) were measured, and micro RNA (miRNA)/messenger RNA (mRNA) sequences were performed on samples that met the criteria (total RNA >3 μg, RIN >8) for the following analysis. The extracted total RNA was sequenced for miRNA and mRNA using the Novaseq (Illumina) by GENEWIZ Japan (Tokyo, JP).

tag: phenotype

value: Control

tag: patient id

tag: biopsy site

value: GB


title: C-5-LB miRNA miRNA

value: LB


title: C-5-GA miRNA

value: GA


title: 15w_24hNC_Both_B1_20210604


title: C-5-LA miRNA

value: LA


title: 15w_24hLDN_Both_B2_20210604


title: C-4-GB miRNA miRNA

source_name: Control patient 4


title: HCT116, live whole cell, cell 004

description: RNA+DNA

value: no


title: Pinot noir berry sample collected at time point 9 (replicate 1) over ripening season 2014 - Crop thinned 50%

value: cv Pinot noir


title: Pinot noir berry sample collected at time point 8.5 (replicate 3) over ripening season 2014 - Crop thinned 75%

source_name: grape berry pericarp_time point 8.5_2014_Crop thinned 75%

value: Crop thinned 75%


title: Pinot noir berry sample collected at time point 9 (replicate 1) over ripening season 2014 - Crop thinned 75%

value: grape berry pericarp


title: 15w_24hLDN_Both_B1_20210604


title: C-4-LB miRNA miRNA


title: C-4-LA miRNA


title: C-4-GA miRNA


title: C-3-LB miRNA miRNA

source_name: Control patient 3


title: HCC827-siCDH3

city: beijing

first: wanru

last: ma

address: 52 Fucheng Road,Haidian District,Beijing

institute: beijing cancer hospital

data_processing:
Total RNA was extracted from cell/tissues using the Trizol (TsingKe) according to the manufacturer’s protocol.
Using the 3'-end polyA structure of messenger RNA and related molecular biology technology, mRNA separation, fragmentation, double-stranded cDNA synthesis, cDNA fragmentation modification, magnetic bead purification and fragmentation sorting were performed on the complete total RNA of the 4 RNA samples of this project. Library amplification and other processing. After testing and quality control, a sequencing library that can be used on the Illumina platform is finally obtained.
Differentially expressed genes were chosen according to the criteria of fold change > 2 and adjusted p-value < 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: The whole samples expression levels were presented as TPM

source_name: lung cancer cell line

extract_protocol:
RNA was extract though TsingKe Reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lung

value: treated with siCDH3 for 48 hours


title: H1299-siCDH3


title: Pinot noir berry sample collected at time point 9 (replicate 2) over ripening season 2014 - Crop thinned 50%

value: Crop thinned 50%


title: Pinot noir berry sample collected at time point 8.5 (replicate 1) over ripening season 2014 - Crop thinned 75%


title: HCC827-sictr

value: treated with siCTR for 48 hours


title: C-3-LA miRNA


title: Pinot noir berry sample collected at time point 8 (replicate 3) over ripening season 2014 - Crop thinned 75%

source_name: grape berry pericarp_time point 8_2014_Crop thinned 75%


title: C-2-LB miRNA miRNA

source_name: Control patient 2


title: C-3-GA miRNA


title: C-2-GA miRNA


title: C-2-LA miRNA


title: Pinot noir berry sample collected at time point 8 (replicate 1) over ripening season 2014 - Crop thinned 75%


title: C-2-GB miRNA miRNA


title: Pinot noir berry sample collected at time point 8 (replicate 2) over ripening season 2014 - Crop thinned 75%