title: MDA-MB-231_KO6h_rep2_RNA-seq

first: Kei-ichiro

last: Arimoto

address: 3855 Health Sciences Dr

institute: UCSD Moores Cancer Center

data_processing:
First, raw RNA-sequencing reads without adaptors or those containing greater than 10% undetermined bases were removed.
Clean RNA-sequencing reads were mapped to the reference genome using STAR software.
Aligned read counts were further used for downstream differential gene expression analysis using the DESeq2 software.
Genome_build: hg19
Supplementary_files_format_and_content: The text file, 'MDA gene.description.csv', contains reads per gene as is conventional for RNA-sequencing analysis.

growth_protocol: MDA-MB-231 cells were maintained in DMEM supplemented with 10% FBS.

extract_protocol:
RNA was extracted using Trizol reagent per the manufacturer's instructions.
Sequencing libraries were prepared  using the Nextera DNA Flex Library Prep Kit.

treatment_protocol: MDA-MB-231  cells were transduced with lentivirus containing control sgRNA or sgRNAs targeting USP18. WT and USP18KO cells were confirmed by PCR and western blot.WT and USP18KO were treated with or without IFNa (1000U/ml) for 6 hours.

value: breast cancer Cell Line

value: Crispr USP18KO

value: DMEM + 10% FBS


title: C50a [High-risk prostate cancer]

status: Public on Nov 09 2022

type: SRA

city: Fuzhou

first: Yu

middle: hua

last: Wang

address: 1 Keji Road, Shangjie Town, Minhou County, Fujian Province, China

country: China

institute: Fujian Normal University

description: High-risk prostate cancer

library_source: transcriptomic

data_processing:
FastQC (version 0.11.2) was used for evaluating the quality of sequenced data. Raw reads were filtered by Trimmomatic (version 0.36) according to several steps: 1) Removing adaptor sequence if reads contains; 2) Removing low quality bases from reads 3’ to 5’ (Q < 20); 3) Removing low quality bases from reads 5’ to 3’ (Q < 20); 4) Using a sliding window method to remove the base value less than 20 of reads tail (window size is 5 bp); 5) Removing reads with reads length less than 35 nt and its pairing reads. And the remaining clean data was used for further analysis.
Using String Tie for readcount and TPM calculation.
Differential expression analyses were performed using the DEGseq package.
Assembly: GRCh38
Supplementary files format and content: tab_delimited text files include TPM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: homo  prostate glands

extract_protocol:
The puncture biopsies samples were collected and  stored with TRIzol® Reagent (Invitrogen,USA) and stored in liquid nitrogen.  Total RNA was extracted with Hieff NGS™ MaxUp Dual-mode mRNA Library Prep Kit for Illumina®(Yeasen ,China) .  RNA integrity was assessed with a 1.0% agarose gel.  RNA concentration was measured by a Qubit® 2.0 Flurometer (Life, USA).
A total amount of 1 μg RNA per sample was used.    The V AHTSTM mRNA-seq V2 Library Prep Kit for Illumina® (vazyme, China)for Illumina was used to construct the libraries for sequencing following the manufacturer’s instructions.

tag: tissue

value: Prostate cancer

tag: age

tag: gleason score

tag: isup grade_group

value: Ⅴ

tag: proportion of_tumor


title: C50c [High-risk prostate cancer]

description: High-risk prostate cancer


title: C20c [High-risk prostate cancer]

description: High-risk prostate cancer


title: Pan02 whole tumor, Arg2-derived peptide vaccine, mouse 2 [Tumor_6]

city: Odense

first: Lars

last: Grøntved

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

data_processing:
Reads were aligned to mm10 using STAR
Reads at genes were quantified by featureCount

molecule: polyA RNA

organism: Mus musculus

source_name: Subcutaneous whole tumor, C57BL/6, female

growth_protocol:
Pan02 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin in humidified atmosphere with 5% CO2 at 37C.
Mice were injected subcutaneously (s.c.) on the right flank with 0.5 million  Pan02 cancer cells.

extract_protocol:
Tumor fragments (≤ 20 mg) in RNAlater (Invitrogen) were transferred to RLT buffer (Qiagen) and mechanically homogenized with a Tissue Lyser (Qiagen). RNA was extracted with the RNEasy Plus Mini Kit (Qiagen),
500ng purified RNA (RIN score > 7) was enriched for polyadenylated mRNA followed by fragmentation. Random primmed cDNA synthesis was performed using NEBNext kits. This was followed by hairpin adaptor ligation and PCR mediated indexing (NEBNext). The library was size selected using AMPure beads and quantified by KAPA (Roche).

treatment_protocol: Mice were vaccinated on day 11 and 17 post-inoculation with a control vaccine (sterile water emulsified 1:1 with Montanide) or an Arg2-derived peptide solution adjuvanted  1:1 with Montanide.

tag: strain

tag: cell line

tag: cell type

value: pancreatic ductal adenocarcinoma

tag: genotype

value: WT

tag: treatment

value: Arg2-derived peptide vaccine


title: 30-MB002-1-AAVS1-t8_S30

city: Hamilton

first: Sheila

last: Singh

state: ON

address: 1280 Main Street West

department: Biochemistry and Biomedical Sciences

country: Canada

institute: McMaster University

description:
AAVS1-KO day 8 post-transduction (replicate 1)
WG_S30

data_processing:
RNA sequencing reads were trimmed and filtered using BBDukfrom the BBTools package (REF: Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2012))
Sequencing reads were aligned using STAR aligner version 2.6.0 and Ensembl reference genome GRC38.
Expression levels were quantified as TMM based usingedgeR 3.26.4 using the ‘calcNormFactors’ and ‘cpm’ functions. The pre-processing pipeline is published and freely available on GitHub for reproducibility.
Differential gene expression analysis was performed using Limma with Benjamini and Hochberg correction for multiple comparisons.
Read counts less than 10 were filtered prior to analysis. Gene set enrichment analysis was carried out using the GSEAv4.2.1(Broad Institute) (REF:Subramanian, A. et al. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. 102, 15545–15550 (2005)). Gene sets enriched with FDR <0.05 and p<0.05 were considered statistically significant.
Assembly: GRC38
Supplementary files format and content: counts (WG_count_matrix.txt)

extract_protocol:
Total RNA was isolated from 200,000-300,000 viable tumor cells (RNeasy Midi Kit, Qiagen) and then sequenced using Illumina HiSeq.
NEBNext® Ultra™ II Directional RNA Library kit

value: brain cancer

value: medulloblastoma

tag: karyotype

value: XX

tag: time

value: day 8 post-transduction


title: THP-1_KO6h_rep1_ATAC-seq

city: La Jolla

state: CA

country: USA

library_source: genomic

data_processing:
Preprocessing: FASTQ files from sequencing experiments were mapped to the hg38 genome. Bowtie2 with default parameters was used to map ATAC-seq experiments (Langmead and Salzberg, 2012). HOMER was used to convert aligned reads into “tag directories” for further analysis (Heinz et al., 2010).
ATAC-seq experiments were performed in replicates. Peaks were called with HOMER for each data set using findPeaks with parameters -L 0 -C 0 -fdr 0.9 -minDist 200 - size 200. Peaks were combined using HOMER mergePeaks for downstream analysis. The pooled data from two replicates was used for track visualization using the UCSC Genome Browser.
Genome_build: hg38
Supplementary_files_format_and_content: Tab delimited text files of replicate ATAC-seq peaks and and the overall merger of all identified peaks.

molecule: genomic DNA

growth_protocol: THP-1 cells were maintained in RPMI supplemented with 10% FBS.

extract_protocol:
Permeabilized nuclei were obtained by resuspending cells in 250 µL Nuclear Permeabilization Buffer (10 mM Tris-HCL [pH 7.5], 10 mM NaCl, 3mM MgCl2, 0.1% Tween-20 [Sigma], 0.1% IGEPAL-CA630 [Sigma] and 0.01% Digitonin [Promega] in water) and incubating for 10 minutes on a rotator at 4°C. Nuclei were then pelleted by centrifugation for 5 minutes at 500 x g at 4°C. The pellet was resuspended in 20 µL ice-cold Tagmentation Buffer (33 mM Tris-acetate [pH 7.8] [BP-152, Thermo Fisher Scientific], 66 mM K-acetate [P5708, Sigma], 11 mM Mg-acetate [M2545, Sigma], 16% DMF [DX1730, EMD Millipore] in Molecular biology water [46000-CM, Corning]). An aliquot was then counted to determine nuclei concentration. Approximately 50,000 nuclei were resuspended in 10 µL ice-cold Tagmentation Buffer and incubated with 1 µL Tagmentation enzyme (FC-121-1030; Illumina) at 37°C for 30 minutes while shaking at 500 rpm. The tagmentated DNA was purified using the MinElute PCR purification kit (28004, Qiagen).
The libraries were amplified using NEBNext High-Fidelity 2X PCR Master Mix (M0541, NEB) with primer extension at 72°C for 5 minutes and denaturation at 98°C for 30 seconds, followed by 8 cycles of denaturation at 98°C for 10 seconds, annealing at 63°C for 30 seconds, and extension at 72°C for 60 seconds. Amplified libraries were then purified using the MinElute PCR purification kit (28004, Qiagen) and two size selection steps were performed using SPRIselect bead (B23317, Beckman Coulter) with 0.55X and 1.5X bead-to-sample volume ratios, respectively.

treatment_protocol: THP-1  cells were transduced with lentivirus containing control sgRNA or sgRNAs targeting USP18. WT and USP18KO cells were confirmed by PCR and western blot.WT and USP18KO were treated with or without IFNa (1000U/ml) for 6 hours.

value: AML Cell Line

value: IFN α 1000U/ml for 6 hours


title: MDA-MB-231_KO6h_rep1_RNA-seq


title: iSLK cells, BAC16-2

city: Guangzhou

first: Ersheng

last: Kuang

state: Guangdong

address: 74 Zhongshan 2nd Rd

department: Zhongshan School of Medicine

institute: Sun Yat-Sen University

data_processing:
The clustering of the index-coded samples was performed on a cBot cluster generation system using HiSeq PE Cluster Kit v4-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on an Illumina platform and 150 bp paired-end reads were generated
The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample
Under the assumption that the number of reads derived from a gene (or transcript isoform) follows abinomial distribution, DEGseq is proposed based on MA-plot and widely used for differential gene expression analysis. The P-value could be assigned to each gene and adjusted by the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with q≤0.05 and |log2_ratio|≥1 are identified as differentially expressed genes (DEGs)
The KEGG enrichment of DEGs was implemented by the hypergeometric test, in which p-value was adjusted by multiple comparisons as q-value. KEGG terms with q<0.05 were considered to be significantly enriched.
Genome_build: Homo_sapiens.GRCh38.94.chr
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

source_name: iSLK

extract_protocol:
Discard the supernatant, flash frozen on dry ice, and RNA was harvested using Trizol reagent.NEBNext® Ultra™ RNA Library Prep Kit for Illumina®（Cat #E7530L，NEB)was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: iSLK

value: wild type

tag: infection

value: Kaposi's sarcoma associated herpesvirus (KSHV)

value: under lytic induction for 72h


title: C20b [High-risk prostate cancer]

description: High-risk prostate cancer


title: THP-1_KO6h_rep2_ATAC-seq

value: Crispr USP18KO


title: Pan02 whole tumor, Arg2-derived peptide vaccine, mouse 1 [Tumor_5]


title: 28-MB002-2-DHODH-3-t8_S28

description:
DHODH-KO day 8 post-transduction (replicate 2)
WG_S28

value: DHODH-KO


title: MDA-MB-231_KO0h_rep1_RNA-seq

value: breast cancer Cell Line

value: DMEM + 10% FBS


title: THP-1_KO0h_rep2_ATAC-seq

value: untreated


title: Pan02 whole tumor, control vaccine, mouse 4 [Tumor_4]

value: pancreatic ductal adenocarcinoma

value: WT

value: Control vaccine


title: C20a [High-risk prostate cancer]

description: High-risk prostate cancer

value: Prostate cancer

value: Ⅴ


title: THP-1_KO0h_rep1_ATAC-seq


title: C14b [High-risk prostate cancer]

description: High-risk prostate cancer


title: MDA-MB-231_WT6h_rep3_RNA-seq

value: Cas9 only


title: Pan02 whole tumor, control vaccine, mouse 3 [Tumor_3]


title: THP-1_WT6h_rep2_ATAC-seq

value: AML Cell Line


title: C14a [High-risk prostate cancer]

description: High-risk prostate cancer


title: 27-MB002-1-DHODH-3-t8_S27

description:
DHODH-KO day 8 post-transduction (replicate 1)
WG_S27

value: brain cancer

value: medulloblastoma

value: XX

value: day 8 post-transduction


title: MDA-MB-231_WT6h_rep2_RNA-seq


title: MDA-MB-231_KO0h_rep3_RNA-seq


title: THP-1_WT6h_rep1_ATAC-seq

value: IFN α 1000U/ml for 6 hours


title: Pan02 whole tumor, control vaccine, mouse 2 [Tumor_2]


title: MDA-MB-231_KO6h_rep3_RNA-seq

value: Crispr USP18KO


title: Pan02 whole tumor, Arg2-derived peptide vaccine, mouse 3 [Tumor_7]

value: Arg2-derived peptide vaccine


title: C8c [High-risk prostate cancer]

description: High-risk prostate cancer


title: THP-1_WT0h_rep2_ATAC-seq


title: Pan02 whole tumor, control vaccine, mouse 1 [Tumor_1]

tag: Sex

value: female


title: C8b [High-risk prostate cancer]

description: High-risk prostate cancer


title: MDA-MB-231_WT6h_rep1_RNA-seq

value: breast cancer Cell Line

value: DMEM + 10% FBS


title: MDA-MB-231_WT0h_rep3_RNA-seq


title: THP-1_WT0h_rep1_ATAC-seq

value: untreated


title: Ter119 experiment: Ter119

city: Schlieren

first: Marc

last: Pfefferle

state: Schweiz

address: Wagistrasse 12

country: Switzerland

institute: University hospital Zürich (USZ)

library_source: transcriptomic single cell

data_processing:
The Cell Ranger Single-Cell Software Suite (version 4.0.0) was used for cDNA oligopeptide alignment, barcode assignment and UMI counting from fastq files obtained from the Illumina sequencing. For each sample, the cell-containing droplets were filtered from the empty droplets, and this step was followed by the generation of an expression matrix using Cell Ranger Count (version 4.0.0).
The resulting gene expression matrices were further analyzed with Python (version 3.8.8) using the Scanpy (version 1.7.0) (Wolf et al. 2018) library. Low-quality cells were defined as expressing more than 5000 or less than 500 genes, more than 40% proportion of mitochondrial genes or more than 30% ribosomal genes, and excluded from downstream analysis. Genes expressed in less than 20 cells were also removed. Normalization was performed using the pool-based size factor estimation implemented in the scran R package (version 1.14.1)(Lun et al. 2016; Lun et al. 2016). Size factors were determined using the function and normalization was performed by dividing in each cell the total gene count by the cell specific size-factor, deconvoluted from the pool size factor. Data was log transformed. Principal component analysis (PCA) was performed using the tl.pca function (Scanpy 1.7.0) with default settings followed by nearest neighbor graph construction using the pp.neighbors (Scanpy 1.7.0) function with the first 15 PCAs. Further dimension reduction was performed using the Leiden algorithm and cells plotted in 2 dimensions using UMAP plots. Differential gene expression was calculated using the tl.rank_genes_group function (Scanpy 1.7.0) or DEseq2 (1.26.0) (Love et al. 2014) implemented in the FindMarkers function of the Seurat package (3.2.3).
Assembly: Ensembl GRCm38.p6 Release M23

source_name: Liver macrophages

growth_protocol: Specific-pathogen-free (SPF) housed  7-10 week old C57BL/6J (JAXTM strain) mice obtained from Charles River Laboratories were used for the experiment.

extract_protocol:
At 24 after the last injection, mice were euthanized and their liver digested into a non-parenchymal single-cell suspension. Cells were enriched for macofphages using a mixture of anti-F4/80 and anti-CD11b coated magnetic beads (Anti-Rat IgG Dynabeads), stained with Totalseq B hashtag antibodies (Biolegend) and pooled together at equal cell count before processing for single-cell RNA sequencing.
Cells were processed according to the Chromium Single Cell 3' Reagent Kits User Guide (v3.1 Chemistry Dual Index) with Feature Barcoding technology for Cell Surface Protein. For all experiments, the sample volume was adjusted to a target capture of 10,000 cells and loaded on the 10x Genomics chromium next-GEM chip G to generate gel-beads-in-emulsion (GEMs). The GEM solution was placed in a Applied Biosystems Veriti 96 well thermal cycler for reverse transcription as described by the 10x Genomics instruction guide (53:00 min at 53°C followed by 5:00 min at 85°C). The resulting barcoded cDNA was then cleaned using Dynabeads MyOne Silane and amplified for 11 cycles (as recommended by the 10x Genomics user guide for a target cell recovery of >6,000 cells).  The quality and concentration of cDNA was assessed using High-Sensitivity D5000 ScreenTape (Agilent). All samples presented product sizes with a narrow distribution centered around 2000 pb and yielded between 50 and 800 ng cDNA (manually selecting products between 100-250 and 5000-6000 bp).  cDNA was  then subjected to enzymatic fragmentation, end repair and A-tailing. Adaptors were ligated to the fragmented cDNA and DNA, and the sample index was added during sample index PCR (set for 12 cycles, as recommended by the 10x Genomics user guide to correlate with a cDNA/DNA input of 12-150 ng). Library quality and concentration were assessed using High-Sensitivity D5000 ScreenTape (Agilent). All gene expression libraries showed an average fragment size of around 400 pb. For non multiplexed runs, 3ʹ Gene Expression libraries for each sample were pooled at an equimolar amount and sequenced using the Illumina NovaSeq 6000 system with a sequencing depth of 50,000 reads per cell (paired-end reads, single indexing, read 1 = 28 cycles, i7 = 8 cycles, i5 = 0 cycles and read 2 = 91 cycles).

treatment_protocol: A C57BL/6J mouse was injected with a single injection of murine Ter119 antibody subcutaneously (35 ug) followed by 10 daily injections at lower dose (10 ug). Another C57BL/6J mouse was injected with similar volume of saline solution.

value: Liver macrophages

tag: culture supplement


title: MDA-MB-231_WT0h_rep2_RNA-seq


title: C8a [High-risk prostate cancer]

description: High-risk prostate cancer


title: Ter119 experiment: Control

value: Saline


title: E34c [Medium-risk prostate cancer]

description: Medium-risk prostate cancer

value: Prostate cancer

value: Ⅲ


title: MDA-MB-231_WT0h_rep1_RNA-seq

value: Cas9 only


title: Control [AB05]

city: Madrid

first: Alberto

last: Bartolomé

state: Madrid

address: Arturo Duperier 4

country: Spain

institute: Instituto de Investigaciones Biomédicas Alberto Sols (CSIC/UAM)

data_processing:
The Illumina sequencer generates raw images utilizing sequencing control software for system control and base calling through an integrated primary analysis software called RTA (Real Time Analysis). The BCL (base calls) binary is converted into FASTQ utilizing Illumina package bcl2fastq. Adapters are not trimmed away from the reads.
Raw counts were pseudoaligned to the mouse transcriptome (GRCm38) by Kallisto and gene count tables generated.
Differential gene expression analyses were performed with limma, implemented in the BioJupies application.
Assembly: mm10, GCRm38
Supplementary files format and content: OIO counts_table.txt: Tab-delimited text file includes gene count table.
Supplementary files format and content: DEGs-OIO.xlsx: Excel file includes differential gene expression.

source_name: pancreatic islets

extract_protocol:
Islets were isolated from mice after 9-day overfeeding protocol. RNA was harvested using Trizol reagent.
Library preparation by using Illumina TruSeq RNA prep kit.

tag: gastric infusion

value: 9 day, saline

value: Pancreatic islets


title: Multiplexed CD40 liver experiment

description: multiplexed experiment with the following ADT_classification allocation to treatment:  - Ctrl.1 (B0301-TotalSeq) = Control (saline)  - CD40 7h (B0302-TotalSeq) = CD40 7h  - CD40 14h (B0303-TotalSeq) = CD40 14h  - CD40 22h (B0303-TotalSeq) = CD40 22h

data_processing:
The Cell Ranger Single-Cell Software Suite (version 4.0.0) was used for cDNA oligopeptide alignment, barcode assignment and UMI counting from fastq files obtained from the Illumina sequencing. For each sample, the cell-containing droplets were filtered from the empty droplets, and this step was followed by the generation of an expression matrix using Cell Ranger Count (version 4.0.0). Demultiplexing of the cells within each sample was performed with the filtered matrix produced by Cell Ranger in R (version 4.4) using Seurat (version 3.2.3) (Hao et al. 2021) and the HTODemux function (positive quantile set at 0.99).
The resulting gene expression matrices were further analyzed with Python (version 3.8.8) using the Scanpy (version 1.7.0) (Wolf et al. 2018) library. Low-quality cells were defined as expressing more than 5000 or less than 500 genes, more than 40% proportion of mitochondrial genes or more than 30% ribosomal genes, and excluded from downstream analysis. Genes expressed in less than 20 cells were also removed. Normalization was performed using the pool-based size factor estimation implemented in the scran R package (version 1.14.1)(Lun et al. 2016; Lun et al. 2016). Size factors were determined using the function and normalization was performed by dividing in each cell the total gene count by the cell specific size-factor, deconvoluted from the pool size factor. Data was log transformed. Principal component analysis (PCA) was performed using the tl.pca function (Scanpy 1.7.0) with default settings followed by nearest neighbor graph construction using the pp.neighbors (Scanpy 1.7.0) function with the first 15 PCAs. Further dimension reduction was performed using the Leiden algorithm and cells plotted in 2 dimensions using UMAP plots. Differential gene expression was calculated using the tl.rank_genes_group function (Scanpy 1.7.0) or DEseq2 (1.26.0) (Love et al. 2014) implemented in the FindMarkers function of the Seurat package (3.2.3).
Assembly: Ensembl GRCm38.p6 Release M23

source_name: Liver leucocytes

extract_protocol:
At 7, 14 or 22 hours post injection, mice were euthanized and their liver digested into a non-parenchymal single-cell suspension. Cells were enriched for leucocytes using CD45+ coated magnetic beads (MagniSort™ Mouse CD45 Positive Selection Kit, 8802-6865-74), stained with Totalseq B hashtag antibodies (Biolegend) and pooled together at equal cell count before processing for single-cell RNA sequencing.
Cells were processed according to the Chromium Single Cell 3' Reagent Kits User Guide (v3.1 Chemistry Dual Index) with Feature Barcoding technology for Cell Surface Protein. For all experiments, the sample volume was adjusted to a target capture of 10,000 cells and loaded on the 10x Genomics chromium next-GEM chip G to generate gel-beads-in-emulsion (GEMs). The GEM solution was placed in a Applied Biosystems Veriti 96 well thermal cycler for reverse transcription as described by the 10x Genomics instruction guide (53:00 min at 53°C followed by 5:00 min at 85°C). The resulting barcoded cDNA was then cleaned using Dynabeads MyOne Silane and amplified for 11 cycles (as recommended by the 10x Genomics user guide for a target cell recovery of >6,000 cells). After amplification, for multiplexed experiments, cDNA generated from polyadenylated mRNA for the 3’ gene expression library was separated from DNA from the Cell Surface Protein Feature Barcode for the Cell Surface Protein library with Dynabeads MyOne Silane and SPRIselect reagents based on size. The quality and concentration of both cDNA and DNA were assessed using High-Sensitivity D5000 ScreenTape (Agilent). All samples presented product sizes with a narrow distribution centered around 2000 pb and yielded between 50 and 800 ng cDNA (manually selecting products between 100-250 and 5000-6000 bp).  cDNA and DNA were  then subjected to enzymatic fragmentation, end repair and A-tailing. Adaptors were ligated to the fragmented cDNA and DNA, and the sample index was added during sample index PCR (set for 12 cycles, as recommended by the 10x Genomics user guide to correlate with a cDNA/DNA input of 12-150 ng). Library quality and concentration were assessed using High-Sensitivity D5000 ScreenTape (Agilent). All gene expression libraries showed an average fragment size of around 400 pb. For multiplexed runs, 3ʹ Gene Expression and Cell Surface Protein libraries were pooled at a ratio of 4:1 and sequenced using the Illumina NovaSeq 6000 system with a sequencing depth of 50,000 and 12,500 reads per cell, respectively, following the recommendations of 10X Genomics (paired-end reads, single indexing, read 1 = 28 cycles, i7 = 8 cycles, i5 = 0 cycles and read 2 = 91 cycles). For non multiplexed runs, 3ʹ Gene Expression libraries for each sample were pooled at an equimolar amount and sequenced using the Illumina NovaSeq 6000 system with a sequencing depth of 50,000 reads per cell, following the same recommendations of 10x Genomics.

treatment_protocol: Mice were injected with 20 mg/kg anti-CD40 antibody (InVivoPlus BP0016-2) intraveinously or saline (Control mouse).

value: Liver leucocytes

value: Anti-CD40 ((InVivoPlus BP0016-2) or saline (control mouse)


title: E34b [Medium-risk prostate cancer]

description: Medium-risk prostate cancer


title: THP-1_KO6h_rep3_RNA-seq

data_processing:
First, raw RNA-sequencing reads without adaptors or those containing greater than 10% undetermined bases were removed.
Clean RNA-sequencing reads were mapped to the reference genome using STAR software.
Aligned read counts were further used for downstream differential gene expression analysis using the DESeq2 software.
Genome_build: hg19
Supplementary_files_format_and_content: The text file, 'THP gene.description.csv', contains reads per gene as is conventional for RNA-sequencing analysis.

value: AML Cell Line

value: RPMI + 10% FBS


title: Control [AB04]


title: E24b [Medium-risk prostate cancer]

description: Medium-risk prostate cancer

value: Ⅱ


title: THP-1_KO6h_rep2_RNA-seq

value: Crispr USP18KO


title: Isolated Islets, WC, Rep3

city: Nashville

first: Matthew

middle: A

last: Cottam

state: TN

address: 2301 Vanderbilt Place

department: Surgical Sciences

institute: Vanderbilt University Medical Center

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using FastP
Quantification of sequences was performed using transcript-aware alignment with Salmon version 1.5.2
Read count extraction was performed using tximport v1.20.0
Assembly: mm10
Supplementary files format and content: tab-delimited text files include abundance values for each sample

source_name: Pancreatic Islets

growth_protocol: Obese mice were placed on 10% LFD (Research Diets) for 9 weeks followed by 60% HFD (Research Diets) for 18 weeks. Weight cycled mice were placed on 60% HFD for 9 weeks, then 10% LFD for 9 weeks, and then 60% HFD for the final 9 weeks.

extract_protocol:
Mouse islets were dissociated using collagenase P and hand picked from residual debris. RNA was harvested using Rneasy mini plus kit (Qiagen).
Poly-A selection for enrichment of mRNA was performed using poly-A magnetic beads (New England Biolabs) and cDNA library preparation was performed using the NEBNext Ultra kit (New England Biolabs).

value: Pancreatic Islets

tag: diet

value: Weight-cycled

tag: gender

value: Male


title: Isolated Islets, WC, Rep4

tag: tissue


title: OIO [AB02]

value: 9 day, Ensure 13-18.5 kcal/day


title: MDA-MB-231_KO0h_rep2_RNA-seq

value: breast cancer Cell Line

value: DMEM + 10% FBS


title: THP-1_KO6h_rep1_RNA-seq


title: OIO [AB03]


title: E19c [Medium-risk prostate cancer]

description: Medium-risk prostate cancer

value: Prostate cancer

tag: age

tag: gleason score

value: Ⅰ


title: E19b [Medium-risk prostate cancer]

description: Medium-risk prostate cancer

tag: isup grade_group

tag: proportion of_tumor


title: THP-1_KO0h_rep3_RNA-seq

tag: cell line


title: 2yr Mouse Liver, CgA KO, Replicate 2

first: Shandy

last: Shahabi

address: 9500 Gilman Dr

department: Chemistry

institute: UCSD

data_processing:
Illumina NovaSeq S2 reads were quantified at the transcript level and aligned to the GRCm38 mouse transcriptome using Salmon v1.4.0.
Raw count files were imported into R program using DESeq2 and annotated to genes based on RefSeq annotation. Read counts less than 1 were excluded in analysis.
Assembly: mm10

source_name: Liver

growth_protocol: Male WT and CgA-KO C57BL/6 mice were kept in a 12 hr dark/light cycle and fed a normal chow diet (NCD: 13.5% calorie from fat; LabDiet 5001, TX).

extract_protocol:
Total RNA was isolated from approximately 30 mg of liver tissue from 3 wild type and 3 CgA knockout mice using RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions. Total RNA was quantified by nanodrop and was quality checked by Tapestation (Agilent).
Poly(A) selected mRNA libraries were prepared from 500 ng of total RNA using KAPA mRNA HyperPrep kit (KAPA Biosystems) and dsDNA libraries were quantified using Qubit 2.0 fluorometer (Invitrogen).

value: Liver

value: CgA KO


title: OIO [AB01]

tag: strain

value: Pancreatic islets


title: Isolated Islets, WC, Rep1


title: E15c [Medium-risk prostate cancer]

description: Medium-risk prostate cancer


title: Isolated Islets, WC, Rep2


title: Isolated Islets, Obese, Rep4

value: Obese


title: THP-1_KO0h_rep2_RNA-seq

tag: cell type

tag: genotype


title: THP-1_KO0h_rep1_RNA-seq

tag: treatment


title: E1c [Medium-risk prostate cancer]

description: Medium-risk prostate cancer

value: Ⅲ


title: oil_scRNA-seq batch 2

data_processing:
Single cell sequencing libraries were prepared following the 10X Genomics V3 kit protocol and sequenced using an illumina Hiseq 4000.
Raw data was multiplexed. Data was demultiplexed and mapped using Cell Ranger (10X Genomics) to mm10 and analyzed using the Seurat R for single cell genomics.
Genome_build: mm10
Supplementary_files_format_and_content: Counts matrics consisting of three files: matrix.mtx, features.tsv, barcodes.tsv.

source_name: Splenocytes

growth_protocol: Lin- c-Kit+ GFP(AML cells) were sorted from recipient mice

extract_protocol:
Eight-thousand cells per genotype were targeted for single-cell RNA-sequencing on a Chromium Single Cell System (10x Genomics).
Single cell sequencing libraries were prepared following the 10X Genomics V3 kit protocol.

treatment_protocol: Usp18+/f UBCER-Cre  AE9a leukemia cells were transplanted into recipient mice. After mice become sick, oil or tamoxifen were injected to heterozygously deplete Usp18. Three days after first injection, Lin- c-kit+ AML cells were sorted from mouse splenocytes.

value: Lin- c-Kit+ GFP(AML cells) were sorted

value: GFP+Lin-c-Kit+ Usp18f/f

value: Usp18f/f UBCER-Cre  AE9a leukemia cells recipient mice were injected with oil


title: Isolated Islets, Obese, Rep3


title: Tam_scRNA-seq batch 2

value: Usp18f/f UBCER-Cre  AE9a leukemia cells recipient mice were injected with tamoxifen


title: THP-1_WT6h_rep3_RNA-seq

value: AML Cell Line

value: Cas9 only

value: RPMI + 10% FBS


title: A21b [BPH]

description: BPH

value: Benign Prostate Hyperplasia(BPH)

value: BPH


title: THP-1_WT6h_rep2_RNA-seq


title: Isolated Islets, Obese, Rep1

value: Pancreatic Islets

value: Male


title: Isolated Islets, Obese, Rep2


title: tam3_ATAC-seq

data_processing:
Preprocessing: FASTQ files from sequencing experiments were mapped to the mm10 genome. Bowtie2 with default parameters was used to map ATAC-seq experiments (Langmead and Salzberg, 2012). HOMER was used to convert aligned reads into “tag directories” for further analysis (Heinz et al., 2010).
ATAC-seq experiments were performed in replicates. Peaks were called with HOMER for each data set using findPeaks with parameters -L 0 -C 0 -fdr 0.9 -minDist 200 - size 200. Peaks were combined using HOMER mergePeaks for downstream analysis. The pooled data from two replicates was used for track visualization using the UCSC Genome Browser.
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited text files of overall merger of all identified peaks.

growth_protocol: Lin- c-Kit+ GFP(AML cells) were sorted

value: Usp18+/f UBCER-Cre  AE9a leukemia cells recipient mice were injected with tamoxifen


title: THP-1_WT6h_rep1_RNA-seq


title: A21a [BPH]

description: BPH


title: Control [AB06]

value: 9 day, saline


title: A16c [BPH]

description: BPH


title: tam3_RNA-seq batch 2

data_processing:
First, raw RNA-sequencing reads without adaptors or those containing greater than 10% undetermined bases were removed.
Clean RNA-sequencing reads were mapped to the reference genome using STAR software.
Aligned read counts were further used for downstream differential gene expression analysis using the DESeq2 software.
Genome_build: mm10
Supplementary_files_format_and_content: The csv file, 'Paired Usp18 heterozygous AE9a RNA-seq raw counts.csv', contains reads per gene as is conventional for RNA-sequencing analysis.


title: oil4_ATAC-seq

value: GFP+Lin-c-Kit+ Usp18+/f

value: Usp18+/f UBCER-Cre  AE9a leukemia cells recipient mice were injected with oil


title: oil2_ATAC-seq


title: tam4_RNA-seq batch 2


title: A16b [BPH]

description: BPH


title: tam1_ATAC-seq


title: tam1_RNA-seq batch 2


title: A16a [BPH]

description: BPH


title: THP-1_WT0h_rep1_RNA-seq


title: oil1_ATAC-seq


title: THP-1_KO6hinp_rep2_ChIP-seq

data_processing:
Preprocessing: FASTQ files from sequencing experiments were mapped to the hg38 genome. Bowtie2 with default parameters was used to map ChIP-seq experiments (Langmead and Salzberg, 2012). HOMER was used to convert aligned reads into “tag directories” for further analysis (Heinz et al., 2010).
ATAC-seq experiments were performed in replicates. Peaks were called with HOMER for each data set using findPeaks with parameters -L 0 -C 0 -fdr 0.9 -minDist 200 - size 200. Peaks were combined using HOMER mergePeaks for downstream analysis. The pooled data from two replicates was used for track visualization using the UCSC Genome Browser.
H3K27ac analysis: To annotate H3K27ac signal around ATAC-seq peaks the parameter -size 1000 was used. Subsequently, DESeq2 (Love et al., 2014) was used to identify differential H3K27ac signal or chromatin accessibility with > 2 fold-change and p-adj < 0.05, unless stated otherwise in the text.
To identify motifs enriched in peak regions over the background, HOMER’s motif analysis (findMotifsGenome.pl) including known default motifs and de novo motifs was used. The background sequences were from random genome sequences.
Genome_build: hg38
Supplementary_files_format_and_content: Tab delimited text file of normalized ChIP-seq signal in a 1000 bp window centered on the merged ATAC-seq peaks.

extract_protocol:
Untreated and IFN treated cells were crosslinked by adding 1% paraformaldehyde to the culture media and incubating at room temperature for 10 minutes. The crosslinked cells were quenched by adding ice-cold glycine to a final concentration of 125mM and incubating for 5 minutes. Cells were then washed with PBS, resuspended in Supplement Cell Lysis buffer (5 mM PIPES [pH 8.0], 85 mM KCl, 0.5% NP-40) supplemented with 1 X proteinase inhibitor cocktail (Roche), and incubated on ice for 10 minutes. Nuclear pellets were lysed with SDS lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl, pH 8.1) containing 1 X proteinase inhibitor cocktail for 15 minutes prior to sonication. Cells were sonicated using the Bioruptor plus (Diagenode) on the High setting: 30 seconds On, 30 seconds Off for 20 cycles. SDS was removed from the chromatin solution by centrifugation for 10 minutes at 4°C. The sheared chromatin was measured, diluted with ChIP Dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl, pH 8.1, 167 mM NaCl), and incubated with Protein A agarose beads for 1 hour at 4°C. An aliquot was removed as input from the pre-cleared chromatin and 300 ug of each sample was then incubated with H3K27Ac antibody (Active Motif #91193) overnight at 4°C. Then, Protein A agarose beads were added for 1 hour at 4 °C. The immune complexes were washed once with low salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, pH 8.1, 150 mM NaCl), once with high salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, pH 8.1, 500 mM NaCl), once with LiCl wash buffer (0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl, pH 8.1), and twice with 1x TE buffer (10 mM Tris-HCl, 1 mM EDTA [pH 8.0]). The complexes were eluted with elution buffer (1% SDS, 0.1 M NaHCO3). The eluates (200 µl) were reverse crosslinked at 65°C overnight by adding 8 µl of 5 M NaCl, followed by RNase A treatment for one hour at 37°C. The samples were mixed with 4 µl of 0.5 M EDTA, 8 µl of 1 M Tris-HCl pH 8.0, and 1 µl of Proteinase K for two hours at 45°C. The ChIPed DNA was purified using ChIP DNA clean & Concentrator (Zymo Research).
Sequencing libraries were prepared  using the Nextera DNA Flex Library Prep Kit.

value: Crispr USP18KO

value: IFN α 1000U/ml for 6 hours

tag: chip antibody


title: A21c [BPH]

description: BPH


title: A6c [BPH]

description: BPH


title: oil2_RNA-seq batch 2

value: Lin- c-Kit+ GFP(AML cells) were sorted


title: A6b [BPH]

description: BPH


title: tam4_ATAC-seq


title: THP-1_KO6hinp_rep1_ChIP-seq


title: oil1_RNA-seq batch 2


title: A6a [BPH]

description: BPH


title: THP-1_KO6hIP_rep2_ChIP-seq

value: H3K27Ac antibody (Active Motif #91193)


title: mESC_ATAC-seq_TERRA_KD_rep2

city: Taipei

first: Hsueh-Ping

last: Chu

address: No. 1 Sec. 4 Roosevelt Road

department: Molecular and Cellular Biology

country: Taiwan

institute: National Taiwan University

data_processing:
For ChIP-seq and ATAC-seq paired-end reads, adapter sequence and low-quality reads were removed by Trimgalore (v0.5.0) using options: --fastq -q 30.
Paired-end reads were mapped to the Mus musculus mm10 reference genome using bowtie2 (v2.3.4.1) with default parameters.
BAM files were sorted and deduplicated by SamTools (v1.9)
Bigwig files were generated by deepTools (v3.1.1) bamCoverage with parameters: --normalizeUsing CPM, --centerReads, --extendReads 150.
Normalized bigwig files were generated by deepTools (v3.1.1) bamCompare with parameters: --scaleFactorsMethod None, --normalizeUsing CPM, --smoothLength 250, --centerReads.
For ATRX, H3K9me3, and G4, peaks were called by MACS1.4 with p value < 0.01 cutoff and default parameters, using input as control. For ATAC-seq, peak calling was performed with MACS2 with p value < 0.01 cutoff.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig and peak bed

source_name: TERRA KD mESCs

growth_protocol: Cells were cultured in regular ES medium (15% FBS) with LIF

extract_protocol:
For ATAC-seq, accessible chromatin extraction, library construction, and size-selection (200 bp) were conducted using ATAC-seq kit (Active Motif, 53150) following manufacturer' s protocol (version B5).
For ATAC-seq, accessible chromatin extraction and DNA library construction were conducted using ATAC-seq kit (Active Motif, 53150) according to manufacturer's protocol (version B5).

treatment_protocol: TERRA LNA knockdown for 12 hours

tag: strain background

value: CAST/Ei x 129/Sv/Jae

value: Embryonic stem cells

tag: capture antibody

tag: knockdown

value: TERRA LNA knockdown for 12 hours


title: THP-1_WT0h_rep2_RNA-seq

value: AML Cell Line

value: Cas9 only


title: THP-1_WT0h_rep3_RNA-seq

value: RPMI + 10% FBS


title: WT_R3

city: Shinjukuku

first: Ayako

last: Nakamura-Ishizu

state: Tokyo

address: 8-1 Kawadacho

country: Japan

institute: Tokyo Women's Medical University

data_processing:
Reads were aligned to the Mus musculus genome (mm10) using TopHat2
differentially expressed genes (DEGs) between Thpo treatment groups were determined using Cufflinks v2.2.1.
Read counts were normalized to Fragments Per Kilobase of transcript sequence per Millions (FPKM).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
hematopoietic stem cells from treated and untreated mice were isolated through flow cytometry and sorted directly into TRIzol Reagent (Thermo Fisher), and RNA was extracted. RNA quality and concentration were assessed using an RNA 6000 bioanalyzer pico kit (Agilent Technologies), and samples with an RNA integrity number more than 8 were used.
Complementary DNA was amplied by the SMARTer Ultra Low RNA Kit (Clontech), and sequencing was performed on an Illumina HiSeq with 150 bp paired-end reads
Library preparation and sequencing was conducted at Novogene on a HiSeq4000 sequencing (Illumina) platform (150bp paired-end).

treatment_protocol: Romiplostim (Kyowa Kirin) or PBS for control was administered intravenously at a dose of 100μg/kg per day

value: primary hematopoietic stem cells

tag: genotype/variation

value: WT; Thpo+/+

value: 10 days of Thpo receptor agonist (Romiplostim)


title: THP-1_KO6hIP_rep1_ChIP-seq


title: KO_R1

value: KO; Thpo-/-


title: mESC_ATAC-seq_scramble_KD_rep2

treatment_protocol: scramble LNA knockdown for 12 hours

value: scramble LNA knockdown for 12 hours


title: Post2

city: Yangsan

first: Hansong

last: Lee

address: 49 Busandaehak-ro

country: South Korea

institute: Pusan National University

data_processing:
FastQC v0.11.7 was used to check the quality of raw sequences. Cell Ranger 3.1.0 was performed to demultiplex cellular barcodes (with Illumina's bcl2fastq v2.20.0), align reads and generate feature-barcode matrices.
The Seurat (v3.2.2) R package was used for integrating, scaling, clustering, and visualizing data.
Scrublet was used for estimating and removing possible doublets.
Genome_build: GRCh38, v3.0.0
Supplementary_files_format_and_content: csv file include matrix table with raw gene counts for every gene and cell

extract_protocol:
All samples were prepared using the Chromium controller according to the 10x chromium Next GEM Single Cell 3’ v3.1 protocol. The cell suspensions were diluted in nuclease-free water to achieve a targeted cell count of 10,000. Cell suspension was mixed with master mix and loaded with Single Cell 3’ v3.1 Gel Beads and Partitioning Oil into a chromium Next GEM chip G Single Cell kit.
RNA transcripts from single cells were uniquely barcoded and reverse-transcribed within droplets. cDNA molecules were pooled and  then went through an end repair process, the addition of a single ‘A’ base, and ligation of the adapters. The products were purified and enriched with PCR to create the final cDNA library. The purified libraries were quantified using qPCR according to the qPCR Quantification Protocol Guide and qualified using the Agilent Technologies 4200 TapeStation. Finally, the libraries were sequenced using Illumina HiSeq platform.

treatment_protocol: The peripheral blood samples were obtained from the volunteers using plastic blood collection tubes with EDTA and inverted multiple times to prevent clotting. The PBMCs were isolated using SepMate (Stemcell Technologies) within 30 min of the collection according to the manufacturer’s instruction. The density gradient media and diluted blood samples were added to the SepMate tube. After mixing the media and samples carefully, the tubes were centrifuged at 1200 x g for 10 min. Top layers were poured off into a new tube and washed twice with PBS containing 2% FBS. The tubes were centrifuged at 300 x g for 8 min at RT. The collected PBMCs were frozen and stored at - 80 °C before use.

tag: subject status

value: periodontitis patient

tag: time point

value: post-treatment

value: PBMC


title: THP-1_KO0hinp_rep1_ChIP-seq

value: Crispr USP18KO

value: untreated


title: mESC_ATAC-seq_TERRA_KD_rep1


title: KO_R2


title: Post4


title: WT_R2


title: oil4_RNA-seq batch 2

value: Lin- c-Kit+ GFP(AML cells) were sorted

value: GFP+Lin-c-Kit+ Usp18+/f

value: Usp18+/f UBCER-Cre  AE9a leukemia cells recipient mice were injected with oil


title: WT_R1


title: THP-1_KO0hinp_rep2_ChIP-seq


title: mESC_ATAC-seq_scramble_KD_rep1

value: CAST/Ei x 129/Sv/Jae

value: Embryonic stem cells


title: Post1


title: THP-1_KO0hIP_rep2_ChIP-seq

value: AML Cell Line

value: H3K27Ac antibody (Active Motif #91193)


title: KO3

value: primary hematopoietic stem cells


title: KO_R3


title: Pre4

value: pre-treatment


title: THP-1_KO0hIP_rep1_ChIP-seq


title: mESC_ChIP-seq_G4_scramble_KD_rep1

extract_protocol:
For G4 ChIP-seq experiments, TERRA KD or scramble KD cells were fixed with 1% formaldehyde for 5 min at RT. Chromatin were sonicated to ~250 bp by Covaris S220. Immunoprecipitations were performed overnight at 4℃. Sample without antibody capture was used as input control. After incubation overnight, immunocomplexes were incubated with Dynabeads Protein G (Thermo Fisher Scientific, 10004D) for 2 hours at 4℃. Immunocomplexes were washed by RIPA buffer containing 500 mM of LiCl. Immunoprecipitated DNA were purified by using PCR DNA isolation system (Viogene, GP1001) following manufacturer' s protocol.
For ChIP-seq, DNA library were constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S) according to manufacturer' s protocol.

value: Anti-DNA/RNA G-quadruplex [BG4] (absolute antibody, Ab00174-1.1)


title: KO2

value: KO; Thpo-/-


title: KO1


title: mESC_ChIP-seq_G4_TERRA_KD_rep1

value: TERRA LNA knockdown for 12 hours


title: THP-1_WT6hinp_rep2_ChIP-seq

value: Cas9 only

value: IFN α 1000U/ml for 6 hours


title: Pre3

value: periodontitis patient

value: PBMC


title: Post3

value: post-treatment


title: Pre2


title: mESC_ChIP-seq_input_TERRA_KD_rep3

description: TERRA KD input rep3 specific to TERRA KD G4 ChIP-seq rep1 and rep2


title: WT3

value: WT; Thpo+/+

value: untreated


title: THP-1_WT6hIP_rep2_ChIP-seq


title: tam3_RNA-seq

data_processing:
First, raw RNA-sequencing reads without adaptors or those containing greater than 10% undetermined bases were removed.
Clean RNA-sequencing reads were mapped to the reference genome using STAR software.
Aligned read counts were further used for downstream differential gene expression analysis using the DESeq2 software.
Genome_build: mm10
Supplementary_files_format_and_content: The csv file, 'fplus RNAseq counts.csv', contains reads per gene as is conventional for RNA-sequencing analysis.

source_name: tamoxifen_Lin- c-kit+ AML

extract_protocol:
RNA was extracted using Trizol reagent per the manufacturer's instructions.
Sequencing libraries were prepared  using the Nextera DNA Flex Library Prep Kit.

value: Usp18+/f UBCER-Cre  AE9a leukemia cells recipient mice were injected with tamoxifen

value: Splenocytes

tag: cell subtype

value: Lin- c-Kit+ GFP(AML cells) were sorted


title: THP-1_WT6hinp_rep1_ChIP-seq

value: AML Cell Line


title: WT2


title: Pre1


title: mESC_ChIP-seq_input_scramble_KD_rep3

description: scramble KD input rep3 specific to scramble KD G4 ChIP-seq rep1 and rep2

value: CAST/Ei x 129/Sv/Jae

value: Embryonic stem cells

value: scramble LNA knockdown for 12 hours


title: tam2_RNA-seq


title: Ctrl4

value: healthy


title: WT1

value: primary hematopoietic stem cells


title: Ctrl3


title: tam1_RNA-seq


title: THP-1_WT6hIP_rep1_ChIP-seq

value: H3K27Ac antibody (Active Motif #91193)


title: THP-1_WT0hinp_rep2_ChIP-seq

value: Cas9 only


title: Tam_scRNA-seq


title: THP-1_WT0hinp_rep1_ChIP-seq


title: Ctrl2


title: oil_scRNA-seq

source_name: control_Lin- c-kit+ AML

value: GFP+Lin-c-Kit+ Usp18+/f

value: Usp18+/f UBCER-Cre  AE9a leukemia cells recipient mice were injected with oil


title: oil3_RNA-seq


title: oil2_RNA-seq


title: Ctrl1

value: PBMC


title: THP-1_WT0hIP_rep2_ChIP-seq


title: oil1_RNA-seq


title: at_embryo-RNAseq-replicate2-Col-0 2n_x_pol4 4n

city: Uppsala

first: Juan

middle: C

last: Santos-González

state: Uppsala

address: Almas Allé 5

department: Department of Plant Biology and Forest Genetics

country: Sweden

institute: SLU

description: Arabidopsis thaliana F1-8DAP embryo of Columbia-0 (female) crossed with pol4 4n Columbia-0 (male)

data_processing:
Reads were quality trimmed using Trimmomatic (Bolger et al, 2014) and mapped to the Arabidopsis (TAIR10) genome masked for rRNA genes, in pair-end mode using TopHat2 (parameters adjusted as -g 1 -a 10 -i 40 -I 5000 -F 0 -r 130) (Trapnell et al., 2009). Transcript counts and RPKM values were calculated using GFOLD (Feng et al, 2012).
Genome_build: TAIR10
Supplementary_files_format_and_content: RNA-seq: expression levels (RPKM) are shown for genes in TAIR10 for each condition and replicate.

organism: Arabidopsis thaliana

source_name: AT F1-Embryo 2n Columbia x 4n pol4 Columbia

growth_protocol: All seeds were surface sterilized (5% sodium hypochlorite, 0.05% Triton X-100) for 10 min, washed three times in sterile ddH2O and then plated on half Murashige and Skoog (MS) medium containing 1% sucrose. After stratification for 3 day at 4°C, plants were grown in a growth room under long-day photoperiod (16 hours light and 8 hours darkness) at 22°C. Eight-day-old seedlings were transferred to soil and plants were grown in a growth room at 60% humidity and daily cycles of 16 hours light at 22°C and 8 hours darkness at 18°C. For crosses, designated female flower buds were emasculated, and the pistils hand-pollinated at 2 days after emasculation.

extract_protocol:
RNA was extracted using the MagJET plant RNA purification kit (Thermo Fisher Scientific). We then purified messenger RNA using the NEBNext poly(A) mRNA magnetic isolation module.
Samples were sequenced at the National Genomic Infrastructure (NGI) from SciLife Laboratory (Uppsala, Sweden) on an Illumina HiSeq2000 in paired-end 125bp read length.

treatment_protocol: Embryos were dissected in 0.3 M sorbitol and 5 mM Mes (pH 5.7) on a slide under a dissecting microscope 6 d for diploids and 8 d for triploids after pollination, which corresponded to the torpedo stage of embryogenesis. Embryos were washed three times to remove contaminating endosperm. Approximately 150 embryos per sample were dissected in three biological replicates.

tag: ecotype

value: Columbia

tag: developmental stage

tag: tissue

value: Embryo

value: Col-0 2n x pol4 4n


title: PV Vγ9Vδ2T-2

city: Shanghai

first: Jiaqing

last: Zhou

address: Yixueyuan road No.138

institute: Fudan university

description: Vγ9Vδ2 T cells

data_processing:
Illumina Casava1.7 software used for basecalling.
The raw reads were aligned to the human reference genome (version hg19) by using Hisat2 RNASeq alignment software.
Quantitated relative mRNA expression levels (FPKM) were calculated based on exon regions using Cufflinks and the hg19 reference genome annotations.
Genome_build: hg19
Supplementary_files_format_and_content: comma-separated values files include readcounts (column J-M) and FPKM values (column N-Q) for each Sample and every gene

source_name: peripheral blood

extract_protocol:
The purified Vγ9Vδ2 T cells (1*104) from psoriasis vulgaris (PV) patients and healthy controls (HC) were processed with the SMART‐Seq HT Kit (Takara) by the following manufacturer's instructions to generate high-quality, full-length cDNA. Libraries were generated using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme) following manufacturer’s protocol. The obtained libraries were sequenced on Illumina Hiseq X Ten system. The raw reads were aligned to the human reference genome by using Hisat2 RNASeq alignment software.
Libraries were generated using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme) following manufacturer’s protocol.

value: Vgamma9Vdelta2 T cells

tag: disease state

value: psoriasis vulgaris


title: PV Vγ9Vδ2T-1

description: Vγ9Vδ2 T cells


title: at_embryo-RNAseq-replicate1-Col-0 2n_x_pol4 4n


title: at_embryo-RNAseq-replicate3-Col-0 2n_x_pol4 4n


title: Rpb4-TAP RIP rep2

city: Solna

first: Vicent

last: Pelechano

address: Nobels väg 16

department: MTC

institute: ScilifeLab - Karolinska Institutet

data_processing:
Base-calling was done during processing of sequencing data with the Illumina HiSeq2000
Sequencing reads were aligned using the GSNAP aligner (Wu & Watanabe, 2005).
The aligned reads were further filtered to remove potential false positive poly(A) site calls arising from internal mispriming as previously described (Wilkening et al, 2013). Poly(A) sites were assigned based on the first base of each read.
Genome_build: R64-1-1
Supplementary_files_format_and_content: Bedgraph files

organism: Saccharomyces cerevisiae

growth_protocol: Saccharomyces cerevisiae  grown in YPD at 30°C.

extract_protocol:
RIP samples were obtained as described previously (PMID: 24569168). Briefly Flash‐frozen pellets of exponentially growing Rpb4‐TAP‐tagged cells (OD600 0.5–0.8) were mechanically lysed with glass beads using a FastPrep24 agitator. An aliquot of each cell lysate was used as an input control. Cell lysates were subjected to immunoprecipitation with Dyna M280 sheep anti‐rabbit IgG beads (Invitrogen) for 2 h at 4˚C. RNA‐protein complex was released by TEV protease cleavage of the TAP‐tag. The input and immunoprecipitated RNA were purified by phenol:chloroform:isoamyl alcohol extraction.
Libraries were constructed using 3'T-Fill protocol as previously described (PMID: 23295673)

value: MATa his3-{delta}200 leu2-3,112 trp1-{delta}63 ura3-52 rpb1-{delta}187::HIS3 + pYEB220 (2um LEU2 RPB1) RPB4::TAP::TRP1

tag: rip antibody


title: at_embryo-RNAseq-replicate3-Col-0 2n_x_Col-0 4n

description: Arabidopsis thaliana F1-8DAP embryo of Columbia-0 (female) crossed with 4n Columbia-0 (male)

source_name: AT F1-Embryo 2n Columbia x 4n Columbia

value: Col-0 2n x Col-0 4n


title: at_embryo-RNAseq-replicate2-Col-0 2n_x_Col-0 4n


title: Rpb4-TAP input rep2


title: in vitro cultured Bb enriched with aBb, rep 3

city: San Francisco

first: Seemay

last: Chou

address: 499 Illinois St, 4th Floor

institute: Chan Zuckerberg Biohub

data_processing:
Reads were trimmed of bases with quality scores less than 20 using Trim Galore v0.6.5
Read counts per Borrelia burgdorferi gene were calculated using Salmon v1.2.1 mapping to Borrelia burgdorferi cDNA sequences (GCA_000008685.2 ASM868v2 without lp5, cp9, and lp56 plasmids) with parameters: --validateMappings --seqBias --gcBias
Rounded counts were used as input to DESeq2 v1.24.0 for differential expression analysis
Assembly: NCBI Genbank GCA_000008685.2 ASM868v2 (without lp5, cp9, and lp56 plasmids)
Supplementary files format and content: Read counts for each gene are provided in .txt files with the output from Salmon

organism: Borreliella burgdorferi

growth_protocol: Bb strain B31-S9 was cultured in BSK II media at 35°C, 2.5% CO2.

extract_protocol:
Total RNA was extracted from immunomagnetically separated samples using the Zymo Direct-zol RNA Microprep Kit with on-column DNase treatment.
RNA-seq libraries were constructed from 50 ng of total RNA using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs). Borrelia rRNAs were depleted from the libraries using Depletion of Abundant Sequences by Hybridization (DASH)(Gu et al. 2016). Libraries were mixed with Cas9 and custom dgRNAs (Ring et al. 2022) for a total of 2 hours at 37°C to deplete rRNAs, purified 0.9X sparQ PureMag Beads (QuantaBio) then reamplified with the Kapa HiFi Real-Time Amplification Kit before sequencing.

treatment_protocol: Bb culture in BSK II was spun down three times at 8000xg for 7 minutes with two washes in PBS. Input samples were created from pellets after second wash. Enriched samples were resuspended in 1 mL PBS. aBb antibody (RRID: AB_1016668) was added with rotation for 30 minutes at 4°C. Bb and antibody mixture was added to 50 µL of PBS-washed Dynabeads Protein G (Invitrogen) and rotated for 30 minutes at 4°C. Beads were washed twice in PBS, the supernatant was removed, and 500 µL of Trizol (Invitrogen) was added to the beads.

tag: strain

value: cultured Bb were enriched by immunomagnetic separation with anti-Bb antibody

tag: molecule type

value: rRNA-depleted RNA


title: Rpb4-TAP RIP rep1

tag: genotype

value: Dyna M280 sheep anti‐rabbit IgG beads (Invitrogen)


title: HC Vγ9Vδ2T-2

description: Vγ9Vδ2 T cells

tag: cell type

value: healthy control


title: at_embryo-RNAseq-replicate3-Col-0 2n_x_pol4 2n

description: Arabidopsis thaliana F1-6DAP embryo of Columbia-0 (female) crossed with pol4 Columbia-0 (male)

source_name: AT F1-Embryo 2n Columbia x 2n pol4 Columbia

value: Col-0 2n x pol4 2n


title: aBb enriched from tick, 3 days after mouse attachment, rep 4

description: I. scapularis sourced from Oklahoma State University were infected with B. burgdorferi as larvae and fed on C3H/HeJ female mice as nymphs

source_name: Bb+ whole nymphal tick

growth_protocol: I. scapularis sourced from Oklahoma State University were infected with B. burgdorferi as larvae, and fed on 4-6 week old C3H/HeJ female mice as nymphs. Before feeding, ticks were maintained in glass jars with a relative humidity of 95% (saturated solution of potassium nitrate) in a sealed incubator at 22°C with a light cycle of 16h/8h (light/dark).

extract_protocol:
Total RNA was extracted from immunomagnetically separated samples using the Zymo Direct-zol RNA Microprep Kit with on-column DNase treatment.
RNA-seq libraries were constructed from 50 ng of total RNA using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs). Tick, mouse, and Borrelia rRNAs were depleted from the libraries using Depletion of Abundant Sequences by Hybridization (DASH)(Gu et al. 2016). Libraries were mixed with Cas9 and custom dgRNAs (Ring et al. 2022) for a total of 2 hours at 37°C to deplete rRNAs, purified 0.9X sparQ PureMag Beads (QuantaBio) then reamplified with the Kapa HiFi Real-Time Amplification Kit before sequencing.

treatment_protocol: Ticks were pulled off of mice 1 day, 2 days, or 3 days after attachment, or collected from cages 4 days after attachment. 6-14 ticks per replicate were homogenized in 1 mL PBS. aBb antibody (RRID: AB_1016668) was added to homogenates with rotation for 30 minutes at 4°C. Homogenate antibody mixture was added to 50 µL of PBS-washed Dynabeads Protein G (Invitrogen) and rotated for 30 minutes at 4°C. Beads were washed twice in PBS, the supernatant was removed, and 500 µL of Trizol (Invitrogen) was added to the beads.

value: Borrelia burgdorferi B31-S9

tag: tick vector

value: Ixodes scapularis

value: Bb+ whole nymphal tick

tag: time

value: 3 days after mouse attachment by ticks

tag: treatment

value: Borrelia burdorferi were enriched by immunomagnetic separation from ticks feeding on mice


title: aBb enriched from tick, 4 days after mouse attachment, rep 4

value: 4 days after mouse attachment by ticks


title: aBb enriched from tick, 4 days after mouse attachment, rep 2


title: aBb enriched from tick, 4 days after mouse attachment, rep 3


title: HC Vγ9Vδ2T-1

description: Vγ9Vδ2 T cells


title: in vitro cultured Bb enriched with aBb, rep 1


title: THP-1_WT0hIP_rep1_ChIP-seq

tag: cell line

value: AML Cell Line

value: Cas9 only

value: untreated

tag: chip antibody

value: H3K27Ac antibody (Active Motif #91193)


title: Rpb4-TAP input rep1

value: MATa his3-{delta}200 leu2-3,112 trp1-{delta}63 ura3-52 rpb1-{delta}187::HIS3 + pYEB220 (2um LEU2 RPB1) RPB4::TAP::TRP1


title: aBb enriched from tick, 4 days after mouse attachment, rep 1


title: at_embryo-RNAseq-replicate2-Col-0 2n_x_pol4 2n

value: Columbia

value: Embryo


title: at_embryo-RNAseq-replicate1-Col-0 2n_x_Col-0 4n

value: Col-0 2n x Col-0 4n


title: aBb enriched from tick, 3 days after mouse attachment, rep 3


title: in vitro cultured Bb, rep 3

value: cultured Bb were pelleted before enrichment

value: rRNA-depleted RNA


title: LLG-10-Month-3

city: Nanning

first: Sanbao

last: Zhang

address: No.100,Daxue East Road

institute: Guangxi University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to capra hircus  whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments per Kilobase per Million Mapped Fragments (FPKM)were calculated using a protocol from Trapnell, C. et al, 2010.Spliced Reads per Billion Mapping (SRPBM)  calculated using a protocol from Li, et al. 2015 . In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
MiRNA cannot be directly enriched and analyzed; so two *DEG_GO_enrichment_result.xls files represent target genes of DEM.
Assembly: ARS1.2
Supplementary files format and content: tab-delimited text files include FPKM/TPM/SRPBM values for each Sample
Supplementary files format and content: Matrix table with raw miRNA counts for every miRNA and every sample

organism: Capra hircus

source_name: longissimus dorsi muscle

extract_protocol:
Fresh adipose tissues were collected and stored in liquid nitrogen at −80 ℃, and RNA was harvested using Trizol reagent(Invitrogen，Carlsbad，CA，USA). A total amount of 3 μg RNA per sample was used as an initial material for the RNA sample preparation. The library was prepared according to the method and process of lncRNA sample preparation kit (Illumina, NEB) and Small RNA Sample Preparation Kit (Illumina, RS-200-0048) at Annoroad Gene Technology Corporation (Beijing, China).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: longissimus dorsi muscle

tag: breed

value: Longlin

tag: age


title: aBb enriched from tick, 3 days after mouse attachment, rep 2

value: Borrelia burgdorferi B31-S9

value: Ixodes scapularis


title: at_embryo-RNAseq-replicate1-Col-0 2n_x_pol4 2n

value: Col-0 2n x pol4 2n


title: in vitro cultured Bb, rep 2


title: LLG-10-Month-1


title: LLG-10-Month-2


title: aBb enriched from tick, 3 days after mouse attachment, rep 1

value: Bb+ whole nymphal tick

value: 3 days after mouse attachment by ticks

value: Borrelia burdorferi were enriched by immunomagnetic separation from ticks feeding on mice


title: LLG-1-Month-3


title: in vitro cultured Bb, rep 1


title: in vitro cultured Bb enriched with aBb, rep 2

value: cultured Bb were enriched by immunomagnetic separation with anti-Bb antibody


title: at_embryo-RNAseq-replicate3-Col-0 2n_x_Col-0 2n

description: Arabidopsis thaliana F1-6DAP embryo of Columbia-0 (female) crossed with Columbia-0 (male)

source_name: AT F1-Embryo 2n Columbia x 2n Columbia

value: Col-0 2n x Col-0 2n


title: at_embryo-RNAseq-replicate2-Col-0 2n_x_Col-0 2n


title: aBb enriched from tick, 2 days after mouse attachment, rep 4

value: 2 days after mouse attachment by ticks


title: LLG-1-Month-2


title: aBb enriched from tick, 2 days after mouse attachment, rep 3


title: at_embryo-RNAseq-replicate1-Col-0 2n_x_Col-0 2n


title: alveolar macrophage, NC-2, miRNA-seq

city: 扬州

first: 靳

last: 健

state: 江苏

address: 扬州大学荷花池校区

institute: 扬州大学

data_processing:
Data quality control was performed on ATAC-seq raw reads obtained from the sequencer before information analysis, and low-quality reads containing adapter reads, reads containing more than 10% unknown nucleotides (N), and low-quality reads containing more than 50% low quality (Q-value≤20) bases were removed to obtain high quality clean reads. The processed reads were aligned to the pig reference genome (release Sscrofa11.1) using Bowtie2 v2.2.8 with reads aligned to mitochondrial genome discarded, and reads that are uniquely aligned were used for subsequent analysis. The distribution map of insert fragments of each sample was drawn by ATACseqQC. DeepTools was used to visualize the read distribution flanking transcription start sites (TSSs). Peak calling was performed using MACS v2.1.2 with a threshold of q-value < 0.05. Only the common peaks among replicates (with overlap more than 50%) were retained for analysis. Peak annotation was performed using ChIPseeker v1.16.1.
We used fastp v0.18.0for quality control and data filtering of raw reads from rRNA-depleted library, to remove reads containing adapters, with a N-containing proportion greater than 10%, with all A bases, or with bases with Q-value≤20 accounting for more than 50% of the whole reads. The processed reads were aligned to the pig reference genome (release Sscrofa11.1) using HISAT2 v2.1.0. To examine the relationship among different samples, Principal component analysis (PCA) was performed using R package gmodels (http://www.rproject.org/). Differentially expressed genes were identified by DESeq2, with cut-off: FDR<0.05 and foldChange≥2. The raw data of small RNA library was filtered to remove low quality reads containing more than one low quality (Q-value≤20) base or containing unknown nucleotides (N) in the data, to filter out reads without 3 'adapters, to filter out reads containing 5' adapters, and to filter out reads containing poly A. All clean tags were searched to identify known porcine miRNAs (exist miRNAs) using the miRbase database (release 22).
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: Peak calling was performed using MACS v2.1.2. Peak annotation was performed using ChIPseeker v1.16.1
Supplementary_files_format_and_content: LncRNA_CodeGenesExpression_fpkm.csv
Supplementary_files_format_and_content: all_mirna_tpm.xlsx

organism: Sus scrofa

growth_protocol: Porcine alveolar macrophages (3D4/21) were cultured in RPMI-1640 (Gibco) medium containing 10% fetal bovine serum (Gibco) and 1% antibiotics (penicillin (100 U/mL), streptomycin (0.1 mg/mL) (Beijing Solarbio Science & Technology Co., Ltd.) at 37℃ in a saturated humidity constant temperature incubator continuously supplied with 5% CO2.

extract_protocol:
Total RNA was extracted from the experimental samples using the Trizol (Invitrogen, USA) kit according to the instructions.
The RNA of the size of 18-30 nt was enriched by polyacrylamide gel electrophoresis (PAGE). The 3' adapter and 5' adapter were connected respectively, and the small RNA connected with the two adapters was reverse transcribed. The bands of 140-160 bp in size were amplified by PCR and recovered and purified to complete the library construction. The constructed library was quality controlled using an Agilent 2100 (Agilent Technologies, CA, USA) and sequenced by Illumina HiSeqTM4000.

treatment_protocol: The cell viability of porcine alveolar macrophages (3D4/21) cells treated with different concentrations (0, 10, 20, 30, 40, 50, and 60μg/mL) of FB1 at different culture time points (24, 48, and 72 h) was measured on a Tecan Infinit 200 microplate reader (Tecan) platform using the Cell CountingKit-8 (CCK-8) kit (Dojindo), and finally 50μg/mL FB1 was induced for 24 h as the optimal treatment concentration and action time to investigate the cytotoxicity of FB1 on 3D4/21 cells. Porcine alveolar macrophages were seeded in 6-well plates at a density of 5 × 105 cells/mL and cultured in a 5% CO2 incubator at 37℃ for 24 h. FB1 at a final concentration of 50 µg/mL was added to the culture medium of the experimental wells, and the same amount of enzyme-free water was added to the culture medium of the control wells.

value: alveolar macrophage

value: control


title: alveolar macrophage, FB1-2, miRNA-seq

value: Fumonisin B1 (FB1)


title: aBb enriched from tick, 2 days after mouse attachment, rep 2


title: LLG-1-Month-1


title: NBG-10-Month-3

value: Nubian


title: NBG-10-Month-1


title: aBb enriched from tick, 2 days after mouse attachment, rep 1


title: NBG-10-Month-2


title: aBb enriched from tick, 1 day after mouse attachment, rep 4

value: 1 day after mouse attachment by ticks


title: alveolar macrophage, NC-1, miRNA-seq


title: alveolar macrophage, FB1-1, miRNA-seq


title: U87_Input

city: Suzhou

first: Gen

last: Li

state: Jiangsu

address: No. 92 Zhongnan Street

institute: Children's Hospital of Soochow University

data_processing:
Raw Data of ChIP-Seq was aligned to the reference genome (UCSC hg38) using BWA-MEM (v0.7.17)
Peaks were identified using MACS2 (v2.2.7)
Assembly: hg38
Supplementary files format and content: peak text files
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a sonicator (M220, Covaris).
Libraries were prepared for sequencing using standard MGI 2000 protocols

value: Glioblastoma


title: aBb enriched from tick, 1 day after mouse attachment, rep 3


title: CD45+ 7 Days post injury

city: Rensselaer

first: Thomas

middle: R

last: Kiehl

state: NY

address: One Discovery Drive

institute: Neural Stem Cell Institute

data_processing:
De-multiplex per Takara iCell8 guidelines
Mapping
normalization and quality control conducted using Seurat R toolkit for single cell genomics
Assembly: mm10
Supplementary files format and content: sci-cd45.csv contains RNA assay exported from Seurat

source_name: Spinal cord

extract_protocol:
After T9 thoracic contusion spinal sections were collected three, seven and sixty days post-injury. Sections were pooled and dissociated, FACS sorted to collect CD45+ cells. Collected cells were dispesed using a Takara iCell8 nanowell system.
Libraries prepared on the iCell8 5184 well chip according to the iCell8 single-cell SMART-seq 3' DE library preparation kits.

value: Spinal cord

value: 7 days post injury

value: female Swiss Webster

value: T9 Thoracic contusion


title: NBG-1-Month-3

value: longissimus dorsi muscle


title: CD45+ 60 Days post injury

value: 60 days post injury


title: aBb enriched from tick, 1 day after mouse attachment, rep 2

value: Borrelia burgdorferi B31-S9

value: Ixodes scapularis

value: Bb+ whole nymphal tick


title: U87_GNE987_H3K27Ac

value: GNE987 for 48h

value: H3K27Ac (Abcam, #ab4730)


title: NBG-1-Month-2


title: aBb enriched from tick, 1 day after mouse attachment, rep 1

value: Borrelia burdorferi were enriched by immunomagnetic separation from ticks feeding on mice


title: CD45+ 3 Days post-injury

value: 3 days post injury


title: CD45+ Uninjured

value: uninjured


title: U87_DMSO_H3K27ac

value: control (DMSO) for 48h

value: H3K27Ac (Abcam, #ab4729)


title: NBG-1-Month-1

value: Nubian


title: SKNO1-no drug biol rep 3

status: Public on Nov 08 2022

first: Bogdan

last: Popescu

address: 513 Parnassus Ave.

institute: UCSF

data_processing:
Quality metrics were evaluated for raw sequencing data using FastQC and thorough inspection of the alignment statistics
Reads were aligned to the human reference genome GRCh38 and gene counts were quantified using STAR
data from each sample were subjected to quality evaluation tests: manually inspecting the density plot, MA plots, principal component analysis (PCA) plots, correlation heatmap and PCA association plots and through automated outlier tests:distance, Kolmogorov-Smirnov, correlation and Hoeffding’s D
ample data were subsequently normalised using the trimmed mean of M-values normalisation method and subjected to the same quality control tests
Differential gene expression analysis was carried out using limma-voom. Functional geneset enrichment analysis was performed using GSEA v4.2.3
Assembly: GRCh38
Supplementary files format and content: tab delimited text files containing normalized counts (TMM)

source_name: SKNO-1 cells, treated with DMSO

growth_protocol: Molm-14 and MV4-11 human AML cell lines were grown in RPMI culture media supplemented with 10% fetal bovine serum (FBS) and 1% Pen-Strep-Glutamine. SKNO-1 cells were grown in same media, enriched with 10 ng/mL of hGM-CSF. All cells were grown at 37C in humidified atmosphere and 5% CO2 concentration.

extract_protocol:
total RNA was isolated using RNeasy mini kit. mRNA was purified from using oligo(dT)-attached magnetic beads.
mRNA was fragmented, reverse transcribed to cDNA which was end-repaired, 3'-adenylated for adapter ligation, then PCR amplified. PCR products were purified using Ampure XP beads, then heat denatured and circularized using a splint oligo sequence. The resulted ssCir DNA library was amplified with phi29 to generate DNA nanoballs (DNB), which were loaded into patterned nanoarrays and sequenced using Probe-Anchor Synthesis technology (cPAS).

treatment_protocol: Three replicates of each cell line were treated with either DMSO or RMC-4550 at a concentration of 500 nM for 24 hours. After 24 hours, cells were collected, centrifuged, washed once in PBS and pelleted for RNA isolation. All subsequent steps from RNA isolation to RNA sequencing were performed by BGI Genomics.

value: blood

value: acute myeloid leukemia

value: KIT N822K

value: DMSO


title: SKNO1-RMC biol rep 3

source_name: SKNO-1 cells, treated with RMC-4550 500nM


title: Molm14-RMC biol rep 3

source_name: Molm14 cells, treated with RMC-4550 500nM


title: Molm14-no drug biol rep 3

source_name: Molm14 cells, treated with DMSO


title: HeLa vs WTC11

type: genomic

city: Setagaya-ku

first: Gou

last: Takahashi

address: 2-1-6 Kamikitazawa

institute: Tokyo Metropolitan Institute of Medical Science

description: Genomic DNA from HeLa cells and WTC11 cells was labeled with Cy5 and Cy3, respectively.

hyb_protocol: Samples were hybridized to Agilent SurePrint G3 Human CGH Microarray (4x180k; G4449A) using Agilent Oligo aCGH/ChIP-on-Chip Hybridization Kit. Hybridization was performed for 24 hours at 67ºC at 20 rpm in a rotating hybridization oven.

scan_protocol: Slides were scanned with SureScan Microarray Scanner (Agilent Technologies) using a scan resolution of 3µm and dye channel of Green and Red with PMT set to 100%, respectively.

data_processing: The scan images were analyzed using the Agilent Feature Extraction software (v12.1.1.1) with set to default for all parameters.

source_name: HeLa

label_protocol: 500 ng of genomic DNA was labeled using the Sure Tag DNA Labeling Kit (Agilent Technologies) according to the manufacturer's protocol.

growth_protocol: HEK293T cells and HeLa cells were maintained in DMEM with high glucose, sodium pyruvate, and L-glutamine supplemented with 10% FBS and 1% Pen-Strep. PC9 cells were maintained in RPMI1640 medium with L-glutamine supplemented with 10% FBS and 1% Pen-Strep. WTC11 iPS cells were maintained on GFR Matrigel in mTeSR Plus medium supplemented with 1% PenStrep. To passaged wells, we added 10 μM Y-27632, a Rho-associated kinase inhibitor, to promote cell survival.

extract_protocol: Genomic DNA extracted using DNeasy Blood & Tissue Kit  (Qiagen) following manufacturer's instructions.

value: HeLa

source_name: Human iPS cells


title: MV411-no drug biol rep 2

source_name: MV4-11 cells, treated with DMSO


title: MV411-RMC biol rep 2

source_name: MV4-11 cell, treated with RMC-4550 500nM


title: SKNO1-RMC biol rep 2


title: Molm14-RMC biol rep 2


title: SKNO1-no drug biol rep 2


title: Molm14-no drug biol rep 2


title: SKNO1-no drug biol rep 1


title: SKNO1-RMC biol rep 1


title: Molm14-RMC biol rep 1


title: Molm14-no drug biol rep 1


title: MV411-RMC biol rep 1


title: HEK293T vs WTC11

description: Genomic DNA from HEK293T cells and WTC11 cells was labeled with Cy5 and Cy3, respectively.


title: PC9 vs WTC11

description: Genomic DNA from PC9 cells and WTC11 cells was labeled with Cy5 and Cy3, respectively.


title: MV411-RMC biol rep 3


title: MV411-no drug biol rep 3


title: MV411-no drug biol rep 1


title: LeafBlade_IR64_77DAT_HP_2016

type: RNA

city: Tsukuba

first: Hinako

last: Takehisa

address: 2-1-2 Kannondai

institute: National Institute of Agrobiological Sciences (NIAS)

description: Gene expression of leaf blade of IR64 at 77 days after transplanting under high available phosphate condition in 2016

hyb_protocol: For hybridization, 1650 ng of cyanine 3-labeled cRNA is fragmented and hybridized on the slide of rice 4x44K microarray RAP-DB (G2519F#15241) at 65°C for 17 hours using the Agilent Gene Expression Hybridization Kit.

scan_protocol: Slides were scanned on an Agilent G2505B DNA microarray scanner using one-color scan setting for 4x44K array slides (Scan Area 61x21.6 mm, Scan resolution 5um,  Dye channel is set to Green PMT: XDR Hi 100%; XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended processed signal intensities. The processed signal intensities were used for 75 percentile normalization and log2 transformation.

organism: Oryza sativa Indica Group

source_name: Leaf blade, IR64, 77 days after transplanting, high available phosphate, 2016

label_protocol: 400 ng of total RNA was added with one-color spike-mix and labeling was performed using Quick Amp Labeling Kit, One-Color (Agilent) in the presence of cyanine-3-CTP accoring to the manufacturer's protocol. The cyanine-3-labeled cRNA was purified by RNeasy Mini Kit (QIAGEN), and quantified using NanoDrop ND-1000 UV-VIS spectrophotometer.

growth_protocol: All plants were grown in paddy field in Tsukuba, Japan (~36o N latitude) during a normal rice growing season in 2012, 2014, 2015 and 2016.

extract_protocol: Total RNA was extracted using RNeasy Plant Mini Kit (QIAGEN) according to the manufacturer's protocol, quantitied using NanoDrop ND-1000 UV-VIS spectrophotometer (NanoDrop) and quality-checked using Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).

tag: cultivar

tag: organ/tissue

value: Leaf blade

tag: growth stage

value: 77 days after transplanting

tag: field soil type

value: high available phosphate

tag: year


title: LeafBlade_IR64_62DAT_HP_2016

description: Gene expression of leaf blade of IR64 at 62 days after transplanting under high available phosphate condition in 2016

source_name: Leaf blade, IR64, 62 days after transplanting, high available phosphate, 2016

value: 62 days after transplanting


title: LeafBlade_IR64_56DAT_HP_2016

description: Gene expression of leaf blade of IR64 at 56 days after transplanting under high available phosphate condition in 2016

source_name: Leaf blade, IR64, 56 days after transplanting, high available phosphate, 2016

value: 56 days after transplanting


title: LeafBlade_IR64_49DAT_HP_2016

description: Gene expression of leaf blade of IR64 at 49 days after transplanting under high available phosphate condition in 2016

source_name: Leaf blade, IR64, 49 days after transplanting, high available phosphate, 2016

value: 49 days after transplanting


title: LeafBlade_IR64_21DAT_HP_2016

description: Gene expression of leaf blade of IR64 at 21 days after transplanting under high available phosphate condition in 2016

source_name: Leaf blade, IR64, 21 days after transplanting, high available phosphate, 2016

value: 21 days after transplanting


title: LeafBlade_IR64_70DAT_LP_2016

description: Gene expression of leaf blade of IR64 at 70 days after transplanting under low available phosphate condition in 2016

source_name: Leaf blade, IR64, 70 days after transplanting, low available phosphate, 2016

value: 70 days after transplanting

value: low available phosphate


title: LeafBlade_IR64_77DAT_LP_2016

description: Gene expression of leaf blade of IR64 at 77 days after transplanting under low available phosphate condition in 2016

source_name: Leaf blade, IR64, 77 days after transplanting, low available phosphate, 2016


title: LeafBlade_IR64_28DAT_HP_2016

description: Gene expression of leaf blade of IR64 at 28 days after transplanting under high available phosphate condition in 2016

source_name: Leaf blade, IR64, 28 days after transplanting, high available phosphate, 2016

value: 28 days after transplanting


title: LeafBlade_IR64_56DAT_LP_2016

description: Gene expression of leaf blade of IR64 at 56 days after transplanting under low available phosphate condition in 2016

source_name: Leaf blade, IR64, 56 days after transplanting, low available phosphate, 2016


title: LeafBlade_IR64_42DAT_HP_2016

description: Gene expression of leaf blade of IR64 at 42 days after transplanting under high available phosphate condition in 2016

source_name: Leaf blade, IR64, 42 days after transplanting, high available phosphate, 2016

value: 42 days after transplanting


title: LeafBlade_IR64_28DAT_LP_2016

description: Gene expression of leaf blade of IR64 at 28 days after transplanting under low available phosphate condition in 2016

source_name: Leaf blade, IR64, 28 days after transplanting, low available phosphate, 2016


title: LeafBlade_IR64_70DAT_HP_2016

description: Gene expression of leaf blade of IR64 at 70 days after transplanting under high available phosphate condition in 2016

source_name: Leaf blade, IR64, 70 days after transplanting, high available phosphate, 2016


title: LeafBlade_IR64_14DAT_LP_2016

description: Gene expression of leaf blade of IR64 at 14 days after transplanting under low available phosphate condition in 2016

source_name: Leaf blade, IR64, 14 days after transplanting, low available phosphate, 2016

value: 14 days after transplanting


title: LeafBlade_IR64_42DAT_LP_2016

description: Gene expression of leaf blade of IR64 at 42 days after transplanting under low available phosphate condition in 2016

source_name: Leaf blade, IR64, 42 days after transplanting, low available phosphate, 2016


title: LeafBlade_IR64_35DAT_HP_2016

description: Gene expression of leaf blade of IR64 at 35 days after transplanting under high available phosphate condition in 2016

source_name: Leaf blade, IR64, 35 days after transplanting, high available phosphate, 2016

value: 35 days after transplanting


title: LeafBlade_IR64_35DAT_LP_2016

description: Gene expression of leaf blade of IR64 at 35 days after transplanting under low available phosphate condition in 2016

source_name: Leaf blade, IR64, 35 days after transplanting, low available phosphate, 2016


title: LeafBlade_IR64_62DAT_LP_2016

description: Gene expression of leaf blade of IR64 at 62 days after transplanting under low available phosphate condition in 2016

source_name: Leaf blade, IR64, 62 days after transplanting, low available phosphate, 2016


title: LeafBlade_IR64_49DAT_LP_2016

description: Gene expression of leaf blade of IR64 at 49 days after transplanting under low available phosphate condition in 2016

source_name: Leaf blade, IR64, 49 days after transplanting, low available phosphate, 2016


title: LeafBlade_Takanari_42DAT_HP_2016

description: Gene expression of leaf blade of Takanari at 42 days after transplanting under high available phosphate condition in 2016

source_name: Leaf blade, Takanari, 42 days after transplanting, high available phosphate, 2016

value: Takanari


title: LeafBlade_Takanari_62DAT_HP_2016

description: Gene expression of leaf blade of Takanari at 62 days after transplanting under high available phosphate condition in 2016

source_name: Leaf blade, Takanari, 62 days after transplanting, high available phosphate, 2016


title: LeafBlade_Takanari_49DAT_HP_2016

description: Gene expression of leaf blade of Takanari at 49 days after transplanting under high available phosphate condition in 2016

source_name: Leaf blade, Takanari, 49 days after transplanting, high available phosphate, 2016


title: LeafBlade_Takanari_56DAT_HP_2016

description: Gene expression of leaf blade of Takanari at 56 days after transplanting under high available phosphate condition in 2016

source_name: Leaf blade, Takanari, 56 days after transplanting, high available phosphate, 2016


title: LeafBlade_Takanari_77DAT_HP_2016

description: Gene expression of leaf blade of Takanari at 77 days after transplanting under high available phosphate condition in 2016

source_name: Leaf blade, Takanari, 77 days after transplanting, high available phosphate, 2016


title: LeafBlade_Takanari_70DAT_HP_2016

description: Gene expression of leaf blade of Takanari at 70 days after transplanting under high available phosphate condition in 2016

source_name: Leaf blade, Takanari, 70 days after transplanting, high available phosphate, 2016


title: LeafBlade_IR64_21DAT_LP_2016

description: Gene expression of leaf blade of IR64 at 21 days after transplanting under low available phosphate condition in 2016

source_name: Leaf blade, IR64, 21 days after transplanting, low available phosphate, 2016


title: LeafBlade_IR64_14DAT_HP_2016

description: Gene expression of leaf blade of IR64 at 14 days after transplanting under high available phosphate condition in 2016

source_name: Leaf blade, IR64, 14 days after transplanting, high available phosphate, 2016


title: LeafBlade_Takanari_21DAT_HP_2016

description: Gene expression of leaf blade of Takanari at 21 days after transplanting under high available phosphate condition in 2016

source_name: Leaf blade, Takanari, 21 days after transplanting, high available phosphate, 2016


title: LeafBlade_Takanari_28DAT_HP_2016

description: Gene expression of leaf blade of Takanari at 28 days after transplanting under high available phosphate condition in 2016

source_name: Leaf blade, Takanari, 28 days after transplanting, high available phosphate, 2016


title: LeafBlade_Takanari_14DAT_HP_2016

description: Gene expression of leaf blade of Takanari at 14 days after transplanting under high available phosphate condition in 2016

source_name: Leaf blade, Takanari, 14 days after transplanting, high available phosphate, 2016


title: LeafBlade_Takanari_77DAT_LP_2016

description: Gene expression of leaf blade of Takanari at 77 days after transplanting under low available phosphate condition in 2016

source_name: Leaf blade, Takanari, 77 days after transplanting, low available phosphate, 2016


title: LeafBlade_Takanari_35DAT_HP_2016

description: Gene expression of leaf blade of Takanari at 35 days after transplanting under high available phosphate condition in 2016

source_name: Leaf blade, Takanari, 35 days after transplanting, high available phosphate, 2016


title: LeafBlade_Takanari_56DAT_LP_2016

description: Gene expression of leaf blade of Takanari at 56 days after transplanting under low available phosphate condition in 2016

source_name: Leaf blade, Takanari, 56 days after transplanting, low available phosphate, 2016


title: LeafBlade_Takanari_49DAT_LP_2016

description: Gene expression of leaf blade of Takanari at 49 days after transplanting under low available phosphate condition in 2016

source_name: Leaf blade, Takanari, 49 days after transplanting, low available phosphate, 2016


title: LeafBlade_Koshihikari_77DAT_HP_2016

description: Gene expression of leaf blade of Koshihikari at 77 days after transplanting under high available phosphate condition in 2016

organism: Oryza sativa Japonica Group

source_name: Leaf blade, Koshihikari, 77 days after transplanting, high available phosphate, 2016

value: Koshihikari


title: LeafBlade_Koshihikari_70DAT_HP_2016

description: Gene expression of leaf blade of Koshihikari at 70 days after transplanting under high available phosphate condition in 2016

source_name: Leaf blade, Koshihikari, 70 days after transplanting, high available phosphate, 2016


title: LeafBlade_Takanari_28DAT_LP_2016

description: Gene expression of leaf blade of Takanari at 28 days after transplanting under low available phosphate condition in 2016

source_name: Leaf blade, Takanari, 28 days after transplanting, low available phosphate, 2016


title: LeafBlade_Takanari_14DAT_LP_2016

description: Gene expression of leaf blade of Takanari at 14 days after transplanting under low available phosphate condition in 2016

source_name: Leaf blade, Takanari, 14 days after transplanting, low available phosphate, 2016


title: LeafBlade_Takanari_42DAT_LP_2016

description: Gene expression of leaf blade of Takanari at 42 days after transplanting under low available phosphate condition in 2016

source_name: Leaf blade, Takanari, 42 days after transplanting, low available phosphate, 2016


title: LeafBlade_Koshihikari_35DAT_HP_2016

description: Gene expression of leaf blade of Koshihikari at 35 days after transplanting under high available phosphate condition in 2016

source_name: Leaf blade, Koshihikari, 35 days after transplanting, high available phosphate, 2016


title: LeafBlade_Takanari_35DAT_LP_2016

description: Gene expression of leaf blade of Takanari at 35 days after transplanting under low available phosphate condition in 2016

source_name: Leaf blade, Takanari, 35 days after transplanting, low available phosphate, 2016


title: LeafBlade_Koshihikari_77DAT_LP_2016

description: Gene expression of leaf blade of Koshihikari at 77 days after transplanting under low available phosphate condition in 2016

source_name: Leaf blade, Koshihikari, 77 days after transplanting, low available phosphate, 2016


title: LeafBlade_Takanari_62DAT_LP_2016

description: Gene expression of leaf blade of Takanari at 62 days after transplanting under low available phosphate condition in 2016

source_name: Leaf blade, Takanari, 62 days after transplanting, low available phosphate, 2016


title: LeafBlade_Takanari_21DAT_LP_2016

description: Gene expression of leaf blade of Takanari at 21 days after transplanting under low available phosphate condition in 2016

source_name: Leaf blade, Takanari, 21 days after transplanting, low available phosphate, 2016


title: LeafBlade_Koshihikari_28DAT_HP_2016

description: Gene expression of leaf blade of Koshihikari at 28 days after transplanting under high available phosphate condition in 2016

source_name: Leaf blade, Koshihikari, 28 days after transplanting, high available phosphate, 2016


title: LeafBlade_Takanari_70DAT_LP_2016

description: Gene expression of leaf blade of Takanari at 70 days after transplanting under low available phosphate condition in 2016

source_name: Leaf blade, Takanari, 70 days after transplanting, low available phosphate, 2016


title: LeafBlade_Koshihikari_62DAT_HP_2016

description: Gene expression of leaf blade of Koshihikari at 62 days after transplanting under high available phosphate condition in 2016

source_name: Leaf blade, Koshihikari, 62 days after transplanting, high available phosphate, 2016


title: LeafBlade_Koshihikari_49DAT_HP_2016

description: Gene expression of leaf blade of Koshihikari at 49 days after transplanting under high available phosphate condition in 2016

source_name: Leaf blade, Koshihikari, 49 days after transplanting, high available phosphate, 2016


title: LeafBlade_Koshihikari_56DAT_HP_2016

description: Gene expression of leaf blade of Koshihikari at 56 days after transplanting under high available phosphate condition in 2016

source_name: Leaf blade, Koshihikari, 56 days after transplanting, high available phosphate, 2016


title: LeafBlade_Koshihikari_21DAT_HP_2016

description: Gene expression of leaf blade of Koshihikari at 21 days after transplanting under high available phosphate condition in 2016

source_name: Leaf blade, Koshihikari, 21 days after transplanting, high available phosphate, 2016


title: LeafBlade_Koshihikari_42DAT_HP_2016

description: Gene expression of leaf blade of Koshihikari at 42 days after transplanting under high available phosphate condition in 2016

source_name: Leaf blade, Koshihikari, 42 days after transplanting, high available phosphate, 2016


title: LeafBlade_Koshihikari_70DAT_LP_2016

description: Gene expression of leaf blade of Koshihikari at 70 days after transplanting under low available phosphate condition in 2016

source_name: Leaf blade, Koshihikari, 70 days after transplanting, low available phosphate, 2016


title: LeafBlade_Koshihikari_56DAT_LP_2016

description: Gene expression of leaf blade of Koshihikari at 56 days after transplanting under low available phosphate condition in 2016

source_name: Leaf blade, Koshihikari, 56 days after transplanting, low available phosphate, 2016


title: LeafBlade_Koshihikari_62DAT_LP_2016

description: Gene expression of leaf blade of Koshihikari at 62 days after transplanting under low available phosphate condition in 2016

source_name: Leaf blade, Koshihikari, 62 days after transplanting, low available phosphate, 2016


title: LeafBlade_Koshihikari_49DAT_LP_2016

description: Gene expression of leaf blade of Koshihikari at 49 days after transplanting under low available phosphate condition in 2016

source_name: Leaf blade, Koshihikari, 49 days after transplanting, low available phosphate, 2016


title: LeafBlade_Koshihikari_42DAT_LP_2016

description: Gene expression of leaf blade of Koshihikari at 42 days after transplanting under low available phosphate condition in 2016

source_name: Leaf blade, Koshihikari, 42 days after transplanting, low available phosphate, 2016


title: LeafBlade_Koshihikari_14DAT_HP_2016

description: Gene expression of leaf blade of Koshihikari at 14 days after transplanting under high available phosphate condition in 2016

source_name: Leaf blade, Koshihikari, 14 days after transplanting, high available phosphate, 2016


title: LeafBlade_Koshihikari_21DAT_LP_2016

description: Gene expression of leaf blade of Koshihikari at 21 days after transplanting under low available phosphate condition in 2016

source_name: Leaf blade, Koshihikari, 21 days after transplanting, low available phosphate, 2016


title: LeafBlade_Koshihikari_28DAT_LP_2016

description: Gene expression of leaf blade of Koshihikari at 28 days after transplanting under low available phosphate condition in 2016

source_name: Leaf blade, Koshihikari, 28 days after transplanting, low available phosphate, 2016


title: LeafBlade_Koshihikari_14DAT_LP_2016

description: Gene expression of leaf blade of Koshihikari at 14 days after transplanting under low available phosphate condition in 2016

source_name: Leaf blade, Koshihikari, 14 days after transplanting, low available phosphate, 2016


title: LeafBlade_Koshihikari_35DAT_LP_2016

description: Gene expression of leaf blade of Koshihikari at 35 days after transplanting under low available phosphate condition in 2016

source_name: Leaf blade, Koshihikari, 35 days after transplanting, low available phosphate, 2016


title: LeafBlade_Nipponbare_70DAT_HP_2016

description: Gene expression of leaf blade of Nipponbare at 70 days after transplanting under high available phosphate condition in 2016

source_name: Leaf blade, Nipponbare, 70 days after transplanting, high available phosphate, 2016

value: Nipponbare


title: LeafBlade_Nipponbare_56DAT_HP_2016

description: Gene expression of leaf blade of Nipponbare at 56 days after transplanting under high available phosphate condition in 2016

source_name: Leaf blade, Nipponbare, 56 days after transplanting, high available phosphate, 2016


title: LeafBlade_Nipponbare_35DAT_HP_2016

description: Gene expression of leaf blade of Nipponbare at 35 days after transplanting under high available phosphate condition in 2016

source_name: Leaf blade, Nipponbare, 35 days after transplanting, high available phosphate, 2016


title: LeafBlade_Nipponbare_62DAT_HP_2016

description: Gene expression of leaf blade of Nipponbare at 62 days after transplanting under high available phosphate condition in 2016

source_name: Leaf blade, Nipponbare, 62 days after transplanting, high available phosphate, 2016


title: LeafBlade_Nipponbare_14DAT_HP_2016

description: Gene expression of leaf blade of Nipponbare at 14 days after transplanting under high available phosphate condition in 2016

source_name: Leaf blade, Nipponbare, 14 days after transplanting, high available phosphate, 2016


title: LeafBlade_Nipponbare_56DAT_LP_2016

description: Gene expression of leaf blade of Nipponbare at 56 days after transplanting under low available phosphate condition in 2016

source_name: Leaf blade, Nipponbare, 56 days after transplanting, low available phosphate, 2016


title: LeafBlade_Nipponbare_70DAT_LP_2016

description: Gene expression of leaf blade of Nipponbare at 70 days after transplanting under low available phosphate condition in 2016

source_name: Leaf blade, Nipponbare, 70 days after transplanting, low available phosphate, 2016


title: LeafBlade_Nipponbare_49DAT_HP_2016

description: Gene expression of leaf blade of Nipponbare at 49 days after transplanting under high available phosphate condition in 2016

source_name: Leaf blade, Nipponbare, 49 days after transplanting, high available phosphate, 2016


title: LeafBlade_Nipponbare_21DAT_HP_2016

description: Gene expression of leaf blade of Nipponbare at 21 days after transplanting under high available phosphate condition in 2016

source_name: Leaf blade, Nipponbare, 21 days after transplanting, high available phosphate, 2016


title: LeafBlade_Nipponbare_77DAT_HP_2016

description: Gene expression of leaf blade of Nipponbare at 77 days after transplanting under high available phosphate condition in 2016

source_name: Leaf blade, Nipponbare, 77 days after transplanting, high available phosphate, 2016


title: LeafBlade_Nipponbare_62DAT_LP_2016

description: Gene expression of leaf blade of Nipponbare at 62 days after transplanting under low available phosphate condition in 2016

source_name: Leaf blade, Nipponbare, 62 days after transplanting, low available phosphate, 2016


title: LeafBlade_Nipponbare_42DAT_LP_2016

description: Gene expression of leaf blade of Nipponbare at 42 days after transplanting under low available phosphate condition in 2016

source_name: Leaf blade, Nipponbare, 42 days after transplanting, low available phosphate, 2016


title: LeafBlade_Nipponbare_61DAT_HP_2015

description: Gene expression of leaf blade of Nipponbare at 61 days after transplanting under high available phosphate condition in 2015

source_name: Leaf blade, Nipponbare, 61 days after transplanting, high available phosphate, 2015

value: 61 days after transplanting


title: LeafBlade_Nipponbare_21DAT_LP_2016

description: Gene expression of leaf blade of Nipponbare at 21 days after transplanting under low available phosphate condition in 2016

source_name: Leaf blade, Nipponbare, 21 days after transplanting, low available phosphate, 2016

value: Leaf blade


title: LeafBlade_Nipponbare_47DAT_HP_2015

description: Gene expression of leaf blade of Nipponbare at 47 days after transplanting under high available phosphate condition in 2015

source_name: Leaf blade, Nipponbare, 47 days after transplanting, high available phosphate, 2015

value: 47 days after transplanting