title: snATAC Isl.15337453 3cyt-hi 24h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
"Bulk-like" matrices of read counts, but are derived from single cell data.
snATAC-seq of islet SAMN15337453 treatment: 10 ng/mL IFN-γ, 0.5 ng/mL IL-1β, 1 ng/mL TNF-α (high dose) for 24h
Islet_cytokine_responsive_cCREs.xlsx
Coaccessible_sites_cytokine-treated_beta_cells.tsv
Coaccessible_sites_cytokine-treated_and_untreated_beta_cells.tsv
stellate.snATAC_count.matrix.txt
endothelial.snATAC_count.matrix.txt
delta.snATAC_count.matrix.txt
alpha.snATAC_count.matrix.txt
acinar.snATAC_count.matrix.txt
beta.snATAC_count.matrix.txt
snATAC_barcodes_and_metadata.csv


title: du145_DU145PS1B_C9_Osimertinib_0.36_24

status: Public on Oct 31 2022

type: SRA

city: New York City

first: Alessandro

last: Vasciaveo

state: NY

address: 1130 Saint Nicholas Ave., 910

department: Department of Systems Biology

country: USA

institute: Columbia University

library_source: transcriptomic

data_processing:
Sequencing was performed in a Hi Seq 2500 sequencer (Illumina) and base calling was performed with Illumina HCS software.
RNASeq reads were mapped for each well to the human reference genome assembly 38 using the STAR aligner (Dobin et al., 2013), version 2.5.2b
Individual counts files were combined across genes and ERCC2 spike-in counts removed, yielding the raw counts file for each cell-line experiment.
Assembly: hg38
Supplementary files format and content: 2 semicolon delinated text files (for 2 cell-lines) with raw gene counts for every gene and every sample

molecule: total RNA

organism: Homo sapiens

source_name: prostate cancer

extract_protocol:
Cells are lysed for PLATE-Seq in Buffer TCL (Qiagen) supplemented with 2-mercaptoethanol in 96-well plates. We transfer 30 μl of cell lysate from each well to a 96-well plate with oligo(dT) grafted to the wells (mRNA TurboCapture Plate, Qiagen) and added 1 μl of 1:100 dilution of ERCC Ex-Fold Spike-Ins (ThermoFisher) to a subset of the sample wells. The plate is then centrifuged at 295 × g for 1 min to eliminate air bubbles followed by incubation for 90 min at room temperature with shaking at 200 rpm. Lysate is then removed from the oligo(dT) capture plate and wells are washed three times with Buffer TCW (Qiagen) using the 96 CO-RE Head of a Hamilton Microlab STAR automated liquid handling system. After drying the plate, mRNA is then eluted by adding 30 μl of elution buffer (nuclease-free water supplemented with 0.4 U μl−1 SUPERaseIN (ThermoFisher)), incubation at 65 °C for 5 min, and incubation at room temperature for 5 min. mRNA samples are then transferred to a new PCR plate (Hard-Shell PCR plate, 96-well, Bio-Rad) using sterile-filter 96-well, 50 μl tips on the Hamilton STAR. To anneal primers for reverse transcription, 3 μl of 100 μM adapter-linked oligo(dT) primers are added to each well along with 10 μl of 5× ProtoScript RT Buffer (New England BioLabs) with the Hamilton STAR CO-RE Head and 1000 μl channel pipetting system (see Supplementary Table 2 for “PLATEseq_oligodTBC” sequences). The plate is then heated to 94 °C for 2 min and placed immediately on ice for 5 min. The remaining components of the reverse transcription master mix including 0.5 mM of each dNTP, 10 mM DTT, 35.8 U of Protoscript II Reverse Transcriptase (New England BioLabs), and water are then added to bring the final reaction volume to 50 μl per well. The plate is then centrifuged at 295 × g for 1 min and incubated at 42 °C for 2 h. At this point, the samples can optionally be frozen at −80 °C. To remove excess primer, 1 μl of a fourfold dilution of Exonuclease I (New England BioLabs) is added to each sample. The Exonculease I reaction is incubated at 25 °C for 1 h. To hydrolyze the RNA, we add 20 μl of a 1:1 mixture of 1 M sodium hydroxide and 0.5 M EDTA to each well and incubate at 65 °C for 15 min. The wells are then pooled together into a single tube to which 80 μl of 12 M hydrochloric acid are added to neutralize the sample. At this point, the pooled sample can optionally be frozen at −80 °C. The pooled, neutralized sample is purified and concentrated using a Qiagen MinElute column using a vacuum apparatus according to the manufacturer’s instructions, and pooled cDNA is eluted in 15 μl of nuclease-free water. For second-strand synthesis, 1 μl of 10 mM dNTP mixture and 1 μl of 100 mM adapter-linked random hexamer primers are added to the pooled cDNA sample. The mixture is then heated to 70 °C for 2 min and immediately placed on ice for 5 min. Next, 2 μl of NEB Buffer 2 (New England BioLabs) and 1 μl of Klenow large fragment DNA polymerase (New England BioLabs) are added and the reaction is incubated at room temperature for 30 min. The reaction is then stopped by addition of EDTA to a final concentration of 50 μM the double-stranded cDNA is purified with two rounds of bead clean-up using AMPure XP beads (Beckman Counter) at a 1:1 bead-to-sample ratio. Finally, the double-stranded cDNA pool is amplified by PCR using Phusion DNA Polymerase (New England BioLabs)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cell-lines were treated at a 48-hour IC20 for each drug and RNA was collected at 24 hours to minimize cell-death.

tag: treatment

value: Osimertinib

tag: cell line

tag: provider

value: ATCC

tag: vendor id

tag: age

tag: Sex

value: male


title: Apex,F7,F2,scRNAseq

city: Cambridge

first: Vincent

last: Knight-Schrijver

address: Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Puddicombe Way

country: United Kingdom

institute: University Of Cambridge

description:
SINHA_F2_s1
Second sequencing run
Adult_Foetal_Integrated_Hearts_VKS2022.rds

library_source: transcriptomic single cell

data_processing:
Demultiplexed using bcl2fastq by sequencing CRUK.
Mutiple fastq files for I1, R1 and R2 reads were concatenated into a single file and aligned using Illumina CellRanger 6.1 with default parameters.
Filtered matrices were read in R and processed, retaining only cells with between 1000 and 15000 UMIs, over 300 uniquely expressed genes, or under 15 % UMIs within mitochondrial features.
Red Blood Cells were removed using a two-compartment Gaussian Mixture Model on the mean cellular expression of haemoglobin and erythrocyte-associated gene features, following by clustering and RBC cluster removal.
Doublets were detected and removed after QC steps using scrublet with default parameters.
Assembly: GRCh38-2020-A
Supplementary files format and content: Processed data files are provided in two forms. Firstly the filtered output for each foetal sample resulting from alignment in CellRanger 6.1, prior to any filtering or data processing steps  (*barcodes.tsv.gz, *features.tsv.gz, *matrix.mtx.gz).
Supplementary files format and content: Secondly, the sub-sampled and integrated object containing both foetal, and adult cells, as an .rds file including raw counts, log-normalised counts, integrated object dimemsion reduction embeddings and residuals matrix, and annotations produced during the analysis.

source_name: Heart

extract_protocol:
Tissue was dissociated using 6.6 mg/ml Bacillus Licheniformis protease, 5 mM CaCl2 and 20 U/ml DNase I, where the mixture was triturated on ice for 20 s every 5 minutes until clumps of tissue were no longer visible.
Chromium Single Cell 3' Library Construction Kit v3 and v3.1 (10x Genomics)

tag: tissue

value: Heart

value: Primary Tissue

value: F

tag: region

value: Apex

tag: developmental stage_(days)


title: snATAC Isl.15314807 untreat 24h

city: La Jolla

first: Paola

last: Benaglio

state: CA

address: 9500 Gilman Drive #0761

department: Pediatrics

institute: University of California San Diego

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
"Bulk-like" matrices of read counts, but are derived from single cell data.
snATAC-seq of islet SAMN15314807 treatment: untreated for 24h
Islet_cytokine_responsive_cCREs.xlsx
Coaccessible_sites_untreated_beta_cells.tsv
Coaccessible_sites_cytokine-treated_and_untreated_beta_cells.tsv
snATAC_barcodes_and_metadata.csv

library_source: genomic

data_processing:
Processing. 10x Genomics Cell Ranger ATAC v1.1 and multiplet removal script (version 1.1) were used to process 10x fastq files for each sample and perform alignment to the hg19 reference genome. BAM files were filtered for PCR duplicates, converted into tagAlign files, and intersected with a reference set of islet ATAC-seq peaks. Each experiment was clustered separately using scanpy following the procedure described in Chiou et al. 2021 (PMID: 33795864). Demuxlet was used to deconvolute the two-samples snATAC pool using genotyping data from Illumina Infinium Omni 2.5-8 array imputed into the HRC r1.1 panel.
Clustering. The filtered assays were merged and combined with 3 existing islet snATAC datasets previously processed using the same method; and the top 50 PCs were obtained. Harmony was used to batch correct PCs for experiments followed by UMAP dimensionality reduction and clustering using the Leiden algorithm (Resolution = 0.5), and sub-clustered using the Louvain algorithm (Resolution = 1.5). Low-quality cells from the merged clusters were iteratively removed and manual doublet removal was performed on sub-clusters with above average high usable read depth or those that expressed multiple marker genes. Cell type of each cluster was assigned based on chromatin accessibility at promoter regions of known marker genes. The remaining cells excluding samples used for reference were used for downstream analysis.
Differential chromatin accessibility in islet cell types. Accessible sites the individual cell types were identified as described in Chiou et al. 2021 (PMID: 33795864) and then used to annotate the consensus set of peaks identified in bulk islet ATAC using bedtools intersect. Duplicate-removed BAM files from each assay were used to generate a bulk-like matrix of read counts mapping to the consensus islet peaks in each cell type using featureCounts. Each celltype matrix was filtered for an average read depth of 1 per sample/condition and DESeq2 was used to identify differentially accessible sites between cytokine treated and untreated samples with the donor as covariate.
Co-accessibility. Cicero (version 1.4.4), was used to calculate co-accessibility between pairs of snATAC peaks in either untreated beta cells, cytokine-treated beta cells or merged treated-untreated beta cells, following the method described in Chiou et al. 2021 (PMID: 33795864). To annotate co-accessibility links between distal and promoter peaks, we annotated peaks within a 5kb window of a transcription start site (+/- 2.5 kb from GENCOVEv19 TSS).
Assembly: hg19
Supplementary files format and content: Matrix tables with raw gene or peak counts for every gene/peak and every sample
Supplementary files format and content: Co-accessible sites are provided for beta cells and annotated with gene promter within a 5kb window
Supplementary files format and content: List of islet candidate regulatory elements coordinates annotated with cell type and cytokine response
Supplementary files format and content: List of final barcodes and cell type assignments of the snATAC experiments

molecule: genomic DNA

source_name: Pancreatic islets

growth_protocol: Human islet samples were enriched using a dithizone stain and cultured in CMRL 1066 supplemented with 10% FBS, 1X pen-strep, 8mM glucose, 2mM L-glutamine, 1mM sodium pyruvate, 10mM HEPES, and 250ng/mL Amphotericin B.

extract_protocol:
Cells were collected from culture and homogenized in permeabilization buffer consisting of 5% BSA, 0.2% IGEPAL-CA630, 1mM DTT, and 1X cOmplete EDTA-free protease inhibitor (Sigma) in 1X PBS. Isolated nuclei were resuspended in 1X TDE1 buffer (Illumina) and quantified using a Countess II Automated Cell Counter (Thermo).
Islet nuclei were adjusted to a concentration of approximately 3000 nuclei/uL. We targeted 5000 nuclei per assay for use in the 10X Genomics Chromium Single Cell ATAC assay, v1 chemistry. Sequencing was performed at the UCSD Institute for Genomic Medicine on an Illumina NovaSeq using a specific paired-end 10X ATAC run configuration with reads of 50bp.
snATAC-seq

treatment_protocol: For cytokine-treated samples, human cytokines were added to the culture media for the indicated duration and concentration as follows: for high doses, 10ng/mL and IFN-g, 0.5ng/mL IL-1B (2 cytokines), with 1ng/mL TNF-α where indicated (3 cytokines); for low doses, 0.2ng/mL IFN-g and 0.01ng/mL IL-1B (2 cytokines), with 0.02ng/mL TNF-α where indicated (3 cytokines).

value: Pancreatic islets

tag: source id

value: no treatment

tag: treatment duration

tag: experiment label

value: untreat


title: snATAC Isl.12833535+12889245 untreat 24h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
"Bulk-like" matrices of read counts, but are derived from single cell data.
snATAC-seq of islet SAMN12833535+SAMN12889245 treatment: untreated for 24h
Islet_cytokine_responsive_cCREs.xlsx
Coaccessible_sites_untreated_beta_cells.tsv
Coaccessible_sites_cytokine-treated_and_untreated_beta_cells.tsv
stellate.snATAC_count.matrix.txt
endothelial.snATAC_count.matrix.txt
delta.snATAC_count.matrix.txt
alpha.snATAC_count.matrix.txt
acinar.snATAC_count.matrix.txt
beta.snATAC_count.matrix.txt
snATAC_barcodes_and_metadata.csv


title: Cdc14ab KO clon 3 time 0

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

country: Spain

institute: CNIO

description: mESC Cdc14ab KO not differentiated

data_processing:
RNA-seq processing:
Read adapters and polyA tails were removed with bbduk.sh, following the Lexogen recommendations. Processed reads were analysed with the nextpresso pipeline, as follows: Sequencing quality was checked with FastQC v0.11.7 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were aligned to the mouse reference genome (GRCm38) with TopHat-2.0.10 using Bowtie 1.0.0 and Samtools 0.1.19 (--library-type fr-secondstrand in TopHat), allowing two mismatches and twenty multihits. Read counts were obtained with HTSeq-count v0.6.1 (--stranded=yes), using the mouse gene annotation from GENCODE (gencode.vM20.GRCm38.Ensembl95). Differential expression was performed with DESeq2, using a 0.05 FDR.  GSEAPreranked was used to perform gene set enrichment analysis for several gene signatures on a pre-ranked gene list, setting 1000 gene set permutations. Only those gene sets with significant enrichment levels (FDR q-value < 0.25) were considered.
Genome_build: GRCm38
Supplementary_files_format_and_content: Normalized counts obtained with DESeq2

organism: Mus musculus

source_name: ESC from mouse blastocysts

growth_protocol: mESCs were grown over feeders in LIF-containing DMEM. Medium was changed every day

extract_protocol:
Samples were collected at day 0, 2 and 7 of the differentiation protocol. RNA was extracted with miRVana RNA isolation kit (Ambion)
Total RNA samples were used (500 ng on average). Sequencing libraries were prepared with the "QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD) for Illumina" (Lexogen, Cat.No. 015) by following manufacturer instructions. Library generation is initiated by reverse transcription with oligodT priming, and a second strand synthesis is performed from random primers by a DNA polymerase. Primers from both steps contain Illumina-compatible sequences. Libraries are completed by PCR {This kit generates directional libraries stranded in the sense orientation (the read1 (the only read in single read format) has the sense orientation (--library-type fr-secondstrand in TopHat, --stranded=yes in HTSeq).}  cDNA libraries are purified, applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument (see below) by following manufacturer's protocols.
Quantseq 3’UTR

treatment_protocol: Prior extraction, ESCs were grown on gelatin-coated plates at low density to remove feeders. For differentiation induction, LIF-containing medium was replaced with N2B27 with growing factors EGF snd FGF2. Medium was changed every 2 days. At day 6, cells were seeded on laminin-coated plates at high density and growth factors were removed

tag: cell type

value: embryonic stem cells

value: LIF-containing ESC media

tag: clon/replicate


title: du145_DU145PS1B_C7_Doxorubicin_0.045_24

value: Doxorubicin


title: F_F_157_NC_NT

first: Tatiana

last: Kisseleva

address: 9500 Gilman Drive

institute: University of California, San Diego

data_processing:
Base-calling was performed using Illumina Real Time Analysis RTA 1.18.64 with default parameters
Sequenced reads were mapped to the Mouse Genomes Project GRCm38_68.fa reference genome using STAR v2.5.1a with default parameters
Read quantification was performed with RSEM v1.3.0 and Ensembl annotation Mus_musculus.GRCm38.68.gtf
Genome_build: GRCm38.68
Supplementary_files_format_and_content: processed data is in supplementary file, which is a comma-separated text file containing a matrix of read counts for each gene accession number and sample

molecule: polyA RNA

source_name: Liver

extract_protocol:
Total RNA was isolated using Purelink RNA Mini Kit (Life Technologies)
Illumina Stranded Total RNA (Illumina 20020597)

value: Liver

tag: injury model

value: DEN

value: chow

tag: genotype


title: du145_DU145PS1B_C8_Thioguanine_0.085_24

value: Thioguanine


title: snATAC Isl.12833535+12889245 3cyt-hi 24h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
"Bulk-like" matrices of read counts, but are derived from single cell data.
snATAC-seq of islet SAMN12833535+SAMN12889245 treatment: 10 ng/mL IFN-γ, 0.5 ng/mL IL-1β, 1 ng/mL TNF-α (high dose) for 24h
Islet_cytokine_responsive_cCREs.xlsx
Coaccessible_sites_cytokine-treated_beta_cells.tsv
Coaccessible_sites_cytokine-treated_and_untreated_beta_cells.tsv
stellate.snATAC_count.matrix.txt
endothelial.snATAC_count.matrix.txt
delta.snATAC_count.matrix.txt
alpha.snATAC_count.matrix.txt
acinar.snATAC_count.matrix.txt
beta.snATAC_count.matrix.txt
snATAC_barcodes_and_metadata.csv


title: du145_DU145PS1B_C5_Everolimus_0.5_24

value: Everolimus


title: F_F_167_NC_T

source_name: liver tumor

value: liver tumor


title: dHEP_164_NC_T


title: du145_DU145PS1B_C2_UNTREATED_0_24

value: UNTREATED

value: ATCC

value: male


title: du145_DU145PS1B_C3_Cabozantinib_1_24

value: Cabozantinib


title: F_F_595_A_NT


title: F_F_169_NC_T


title: du145_DU145PS1B_C4_Lomustine_7_24

value: Lomustine


title: Pcx liver, rep4

city: Baltimore

first: Michael

middle: J.

last: Wolfgang

state: MD

address: 855 N Wolfe Street

department: Institute for Basic Biomedical Sciences

institute: The Johns Hopkins University School of Medicine

description:
Pcx liver knockout RNA-seq in 24hr fasted liver
L_KO_821

data_processing:
Library construction, base calling, and mapping were performed according to Novogene company protocol.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Indexes of the reference genome was built using STAR (v2.5) and paired-end clean reads were aligned to the reference genome using STAR with mismatch=2.
HTSeq v0.6.1 with -m union was used to count the read numbers mapped of each gene. FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression was performed on raw read counts in R with DESeq2.
Assembly: mm10
Supplementary files format and content: CSV files containing raw gene read counts and gene FPKM values

growth_protocol: Mice were housed in a facility with ventilated racks on a 14h light/10h dark cycle with ad libitum access to a standard rodent chow.

extract_protocol:
Total RNA was isolated from flash-frozen liver tissue was using TRIzol reagent followed by additional purification using RNeasy Mini Kit.
Library construction and sequencing was performed by Novogene Corporation Inc.

treatment_protocol: 24 hour fast (3pm-3pm).

tag: strain

value: 24 hour fast

value: Pcx L-/-


title: du145_DU145PS1B_C1_Clofarabine_0.175_24

tag: treatment

value: Clofarabine


title: F_F_503_A_NT


title: dHEP_550_A_NT


title: Pcx liver, rep2

description:
Pcx liver knockout RNA-seq in 24hr fasted liver
L_KO_819


title: F_F_523_A_NT


title: du145_DU145PS1B_B11_Pralatrexate_0.005_24

value: Pralatrexate

tag: cell line


title: du145_DU145PS1B_B12_Fluorouracil_10_24

value: Fluorouracil

tag: provider


title: dHEP_155_NC_T


title: Pcx liver, rep1

description:
Pcx liver knockout RNA-seq in 24hr fasted liver
L_KO_564


title: F_F_168_NC_T


title: Pcx liver, rep3

description:
Pcx liver knockout RNA-seq in 24hr fasted liver
L_KO_820


title: dHEP_549_A_NT


title: du145_DU145PS1B_B9_Belinostat_0.13_24

value: Belinostat

tag: vendor id


title: WT liver, rep4

description:
WT RNA-seq in 24hr fasted liver
L_WT_856

value: Liver

value: WT


title: F_F_581_A_NT

value: DEN


title: WT liver, rep3

description:
WT RNA-seq in 24hr fasted liver
L_WT_854


title: du145_DU145PS1B_B8_Tretinoin_2_24

value: Tretinoin

tag: age


title: WT liver, rep2

description:
WT RNA-seq in 24hr fasted liver
L_WT_567


title: du145_DU145PS1B_B5_Crizotinib_0.19_24

value: Crizotinib

tag: Sex


title: dHEP_518_A_NT

tag: tissue


title: WT liver, rep1

description:
WT RNA-seq in 24hr fasted liver
L_WT_563


title: F_F_581_A_T

value: liver tumor


title: F_F_595_A_T


title: du145_DU145PS1B_B7_Mitomycin_0.055_24

value: Mitomycin


title: dHEP_520_A_NT


title: F_F_523_A_T1


title: du145_DU145PS1B_B4_Carboplatin_10_24

value: Carboplatin

value: ATCC


title: du145_DU145PS1B_B3_Vemurafenib_8_24

value: Vemurafenib

value: male


title: dHEP_550_A_T


title: F_F_503_A_T1


title: du145_DU145PS1B_B1_Pemetrexed_10_24

value: Pemetrexed


title: du145_DU145PS1B_B10_Ibrutinib_0.35_24

value: Ibrutinib


title: HIV+ART 4-8

city: Montréal

first: Jean-Philippe

last: Goulet

state: Québec

address: C.P. 6128, succursale Centre-ville

country: Canada

institute: Université de Montréal

description:
HIV+ART 4
8

data_processing:
Raw Count Matrix was obtained from the standard workflow used at The McGill University and Génome Québec Innovation Centre
Features with at least one count per million (CPM) were kept prior to transformation.
Raw Counts were transformed into log2-CPM values using the voom method from the limma Bioconductor R package.
Genome_build: GRCh37
Supplementary_files_format_and_content: Matrix table with features as rows. First column is the feature ID and each subsequent column represent one sample.

growth_protocol: N/Av

extract_protocol:
RNA extracted with RNeasy Mini kit plus (QIAGEN).
cDNA libraries and RNA-seq were performed by The McGill University and Génome Québec Innovation Centre, Montreal, QC. 100 bp paired-end sequencing was performed on an Illumina-NovaSeq(depth was above 150 million reads).
RNA-Seq (rRNA-depleted stranded (HMR))

treatment_protocol: Isolated cells were stimulated with CD3/CD28 antibodies and cultured in the presence/absence of the aryl hydrocarbon receptor (AhR) antagonist CH223191 (10 mM) for 18 hours

tag: barcode

tag: stimulation

tag: randomization code


title: dHEP_518_A_T1


title: HIV+ART 4-7

description:
HIV+ART 4
7

value: DMSO


title: du145_DU145PS1B_A12_Sorafenib_1_24

value: Sorafenib


title: du145_DU145PS1B_B6_Bexarotene_1.5_24

value: Bexarotene


title: dHEP_520_A_T


title: NTHWT3

extract_protocol:
Total RNA was isolated using Purelink RNA Mini Kit (Life Technologies)
Strand specific mRNA-sequencing libraries (polyA+) were generated using Illumina's TruSeq stranded mRNA library prep kits

value: HFD


title: du145_DU145PS1B_A11_Dasatinib_0.02_24

value: Dasatinib


title: du145_DU145PS1B_A10_Carfilzomib_0.005_24

value: Carfilzomib


title: HIV+ART 3-6

description:
HIV+ART 3
6


title: HIV+ART 3-5

description:
HIV+ART 3
5


title: NTHWT2

value: DEN

value: WT


title: dHEP_549_A_T


title: du145_DU145PS1B_B2_DMSO_0_24


title: du145_DU145PS1B_A8_Vinblastine_0.02_24

value: Vinblastine


title: du145_DU145PS1B_A7_Mitoxantrone_0.01_24

value: Mitoxantrone


title: HIV+ART 2-3

description:
HIV+ART 2
3


title: HIV+ART 1-2

description:
HIV+ART 1
2


title: HIV+ART 5-9

description:
HIV+ART 5
9


title: NTHWT1


title: du145_DU145PS1B_A9_Toremifene_1.5_24

value: Toremifene


title: NTHKO2


title: du145_DU145PS1B_A6_Imatinib_5_24

value: Imatinib


title: HIV+ART 6-12

description:
HIV+ART 6
12


title: du145_DU145PS1B_A5_Ixabepilone_0.0031_24

value: Ixabepilone

value: ATCC


title: NTHKO1


title: HIV+ART 6-11

description:
HIV+ART 6
11


title: HWT6


title: HIV+ART 5-10

description:
HIV+ART 5
10


title: du145_DU145PS1B_A3_Bendamustine_10_24

value: Bendamustine

value: male


title: du145_DU145PS1B_A2_DMSO_0_24


title: HIV+ART 1-1

description:
HIV+ART 1
1


title: HWT5


title: HKO6


title: HIV+ART 2-4

description:
HIV+ART 2
4


title: du145_DU145PS1B_A1_Lapatinib_7.5_24

value: Lapatinib


title: du145_DU145PS1A_H12_Cabazitaxel_0.00065_24

value: Cabazitaxel


title: HKO5


title: HKO4


title: du145_DU145PS1A_H11_UNTREATED_0_24

value: UNTREATED


title: AWT6


title: NTHKO3


title: 60min_4sU_rep2_Nadia

city: Copenhagen

first: Haiyue

last: Liu

address: Blegdamsvej 3B

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

data_processing:
Cell and molecular barcodes were extracted from read1 and added as tags using Drop-seq tools v2.0.0
Sequenced reads were trimmed for polyA stretches, SMART adaptor sequences and low quality filtering using Drop-seq tools v2.0.0
Reads were aligned to the GRCh38 genome using STAR version 2.6.0a with optional parameters:  --outFilterMismatchNmax 10 --outSAMtype BAM Unsorted --outSAMattributes AS NH nM NM MD
Aligned bam files were sorted using Picard tools provide in Drop-seq tools v2.0.0
Aligned and sorted bam files were merged with unaliged bam files that tagged with cell and molecular barcodes using Drop-seq tools v2.0.0
Gene annotation tags were added and bead synthesis errors were detected and corrected using Drop-seq tools v2.0.0
Estimated the number of barcodes was determined by a knee point in the cumulative curve using dropbead v0.25
The number for mismathces between sequenced reads and reference genome were tagged in the bam files using cumtom python script
The unique gene name annotation were tagged to each reads in the aligned sorted bam file using custom python script
The splicing status tag for each read were added to the bam file using custom bash script
Reads with the same molecular barcode were merged and T->C mismatch posiiton, coverage and numbers were counted using custom python script
Sequencing error and background conversions were corrected and newly synthesized RNA molecules were identified via merged reads using Baysian model implemented in R script
RNA counts of each gene in each cell for different types of classified RNAs (i.e. labeled precursor, unlabeled precusor, labeled mature and unlabeled mature) were counted by summing up all the counts of molecules mapped to each gene in each cell and the processed gene expression matrix csv files were generated using custom Rscript.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited txt files include the transcript counts for each gene in each cell of four RNA types (i.e, labled precursor, labeled mature, unlabeled precursor and unlabeled mature) in each sample
Supplementary_files_format_and_content: Tab-delimited txt files include the transcript counts for each gene in each sample

source_name: HEK293 cells

growth_protocol: Cells were grown in DMEM (Gibco, 41965039) supplememnted with 10% FBS (Gibco, 10270106) and 2mM L-Glutamine (Gibco, 25030081). Cells were split the day before the experiment and were at 60-70% confluency at the time of sample collection.

extract_protocol:
Fixed cell suspention was rehydrated and washed in DPBS - BSA 0.1% + 1 U/μL Ribolock RNAse Inhibitor (ThermoFisher, EO0382), passed through a 35 μm FACS tube cell strainer and counted.
For DropSeq library preparation we followed the protocol of: Alles et al BMC Biol 2017 doi: 10.1186/s12915-017-0383-5. For Nadia library preparation we followed the instuctions of the system manual for scRNA-seq.

treatment_protocol: Cells were  washed in DPBS (Gibco  14190144), dissociated with TrypLE Express Enzyme (Gibco, 12605036) and fixed in fixation buffer (80% methanol - 20% DPBS) at a concentration berween 1 and 2 million cells per mL. Samples were incubated overnight, in mild rotation and in dark with 10mM iodoacetamide (final concentration, Sigma-Aldrich, I6125) in fixation buffer. Samples were washed two times in fixation buffer, rehydrated in DPBS-0.1%BSA-1 U/uL Ribolock RNAse Inhibitor + 100Mm DTT for 5 minutes at room temperature and resuspended in fixation buffer. scRNAseq with the cell suspention was performed. All the centrifugation step for pelleting cells were performed at 300g, 2 minutes, 4°C.

value: Flp-In-293 Cell Line

value: 60 minutes 4sU + IAA


title: du145_DU145PS1A_H10_Bortezomib_0.015_24

value: Bortezomib


title: 30min_4sU_rep1_Nadia

value: 30 minutes 4sU + IAA


title: 60min_4sU_rep1_Nadia


title: AWT5

value: DEN


title: 30min_4sU_rep2_Nadia


title: du145_DU145PS1A_H9_Trifluridine_1.5_24

value: Trifluridine


title: no_4sU_rep1_Nadia

value: (no 4sU) + IAA


title: AWT4

value: WT


title: no_4sU_rep2_Nadia


title: du145_DU145PS1B_A4_Cisplatin_6_24

value: Cisplatin


title: HWT4

value: HFD


title: du145_DU145PS1A_H7_Exemestane_1.5_24

value: Exemestane


title: AKO7


title: AKO5


title: du145_DU145PS1A_H5_Tamoxifen_1_24

value: Tamoxifen

value: ATCC


title: AKO6


title: du145_DU145PS1A_H4_Estramustine_3.5_24

value: Estramustine

value: male


title: du145_DU145PS1A_H3_Abiraterone_10_24

value: Abiraterone


title: du145_DU145PS1A_H2_Decitabine_0.5_24

value: Decitabine


title: NTAWT4


title: NTAWT5


title: AKO4


title: NTAWT2


title: du145_DU145PS1A_H1_Anastrozole_10_24

value: Anastrozole


title: NTAWT1


title: du145_DU145PS1A_G12_Epirubicin_0.065_24

value: Epirubicin


title: NTAKO5


title: NTAWT3


title: du145_DU145PS1A_G10_Panobinostat_0.01_24

value: Panobinostat


title: du145_DU145PS1A_G11_UNTREATED_0_24

value: UNTREATED


title: du145_DU145PS1A_H8_Temozolomide_10_24

value: Temozolomide


title: NTAKO2

value: DEN


title: NTAKO3


title: du145_DU145PS1A_G7_Methotrexate_0.01_24

value: Methotrexate


title: NTAKO1


title: NTAKO4


title: du145_DU145PS1A_G8_Lenvatinib_0.5_24

value: Lenvatinib


title: du145_DU145PS1A_H6_Ifosfamide_6.5_24

value: Ifosfamide


title: du145_DU145PS1A_G3_Temsirolimus_0.09_24

value: Temsirolimus


title: du145_DU145PS1A_G4_Pentostatin_1_24

value: Pentostatin


title: du145_DU145PS1A_G2_Vismodegib_10_24

value: Vismodegib


title: ST3, shTXNIP, Day 7, rep 3

city: Ghent

first: Georges

last: Leclercq

address: C. Heymanslaan

country: Belgium

institute: Ghent University

description: Sample 38

data_processing:
Fastq files were aligned to human reference genome GRCh38 using STARv2.42 and gencode v35 as guide gtf
Counts were generated on the fly by STAR
QC of fastq files was done with FastQC
Assembly: Genome_build: GRCh38

source_name: umbilical cord blood

growth_protocol: CD34+ cells were isolated from human umbilical cord blood. After isolation of mononuclear cells by Lymphoprep density gradient centrifugation, CD34+ cells were purified using Magnetic Activated Cell Sorting (MACS). Followed by 48 h of preculture in Iscove’s Modified Dulbecco’s Medium (IMDM) containing foetal calf serum (FCS) (10%), penicillin (100 U/mL), streptomycin (100 µg/mL) and glutamine (2 mM), supplemented with thrombopoietin (TPO) (20 ng/mL), stem cell factor (SCF) (100 ng/mL) and FMS-like tyrosine kinase 3 ligand (Ftl3L) (100 ng/mL).

extract_protocol:
Total mRNA was extracted using the RNeasy micro kit (Qiagen). The concentration and quality of the total extracted RNA was checked by using the Quant-it ribogreen RNA assay (Life Technologies) and the RNA 6000 nano chip (Agilent Technologies), respectively.
Illumina sequencing library preparation was performed using the QuantSeq 3' mRNA-Seq Library Prep Kits (Lexogen, Vienna, Austria) according to manufacturer's protocol. Libraries were quantified by qPCR.

treatment_protocol: Precultured CD34+ cells were transferred to RetroNectin (2 µg/cm²) coated plates and lentiviral supernatant was added followed by spinoculation at 950 g during 90 min at 32°C in the presence of polybrene (8 µg/mL). 24 h after lentiviral transduction, the medium was refreshed to remove polybrene. eGFP+ hematopoietic stem cells (HSCs), defined as CD34+lineage-(CD3/CD14/CD19/CD56)CD45RA- cells, were sorted to high purity 48 h after transduction using a FACS ARIA II cell sorter. Following FACS sorting, eGFP+ HSCs were plated on the mitomycin C-inactivated murine embryonic liver cell line EL08-1D2. Cells were co-cultured in NK cell coculture medium (NKCC) containing Dulbecco’s Modified Eagle Medium (DMEM) and Ham’s F-12 nutrient mixture (2:1 ratio) (all from Thermo Fisher Scientific), supplemented with penicillin (100 U/mL), streptomycin (100 µg/mL), glutamine (2 mM), sodium pyruvate (10 mM), heat-inactivated human AB serum (20%), β-mercaptoethanol (24 µM), ascorbic acid (20 µg/mL), ethanolamine (50 µM) and sodium selenite (50 ng/mL). The cytokines IL-3 (5 ng/mL), IL-7 (20 ng/mL), IL-15 (10 ng/mL), SCF (20 ng/mL) and Ftl3L (10 ng/mL) were added to the culture medium. Cultures were maintained in a humidified atmosphere of 5% CO2 at 37°C. On day 3 HSCs, defined as CD34+lineage-(CD3/CD14/CD19/CD56)CD45RA- cells and on day 7 eGFP+ stage (ST)3 (CD34-CD94-CD117+HLA-DR-NKp44-) cells were sorted.

value: umbilical cord blood

value: NK cell progenitor cells

tag: shRNA

value: shTXNIP

value: Lentiviral transduction

tag: time

value: Day 7


title: ST3, shTXNIP, Day 7, rep 2

description: Sample 37

tag: cell type


title: ST3, shTXNIP, Day 7, rep 4

description: Sample 39


title: du145_DU145PS1A_G1_Enzalutamide_10_24

value: Enzalutamide

value: ATCC

value: male


title: du145_DU145PS1A_G9_Ixazomib_0.035_24

value: Ixazomib


title: GNAQ-Q209L-Rep2_ATAC

city: Atlanta

first: Yoonhee

last: Jung

state: Georgia

address: 615 Michael Street

department: Human Genetics

institute: Emory university

data_processing:
All libraries were sequenced using an Illumina sequencer and 50 bp paired-end format. Paired reads were aligned to mouse reference genome mm10 using Bowtie2. ATAC-seq reads were aligned using default parameters except -X 2000 -m 1. Duplicates were removed using Samtools. To adjust for fragment size, we aligned all reads as + strands offset by +4 bp and – strands offset by -5 bp (Buenrostro et al. 2013). To separate nucleosome-free (THSS) and mono-nucleosome (Nucleosome) fragments, we chose reads 50-115 bp 180-247 bp in length, respectively. Mono-nucleosome reads were analyzed using DANPOS2 (Chen et al. 2013). MACS was used for peak calling with nucleosome-free reads (Liu 2014). For generating wiggle files, we combined each replicates.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig files

extract_protocol:
ATAC-seq was carried out using the Omni-ATAC protocol. After cells were counted, the nuclei were isolated with Lysis Buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) containing 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin. The purified nuclei pellet was then resuspended in the transposase reaction mix containing 0.05% digitonin and incubated for 30 min at 37°C. Following incubation, cells were treated with Proteinase K at 55°C for 2 h, and gDNA was isolated by phenol:chloroform:isoamyl alcohol and EtOH precipitation.
Library amplification was done with 2x KAPA HiFi mix (Kapa Biosystems) and 1.25 µM indexed primers using the following PCR conditions: 72°C for 5 min; 98°C for 30 s; and 10-11 cycles at 98°C for 10 s, 63°C for 30 s, and 72°C for 1 min. Libraries were paired-end sequenced on Illumina NovaSeq 6000 instruments.

tag: strain background


title: CTL-Rep1_ATAC

source_name: CTL

value: CTL


title: CTL-Rep2_ATAC


title: du145_DU145PS1A_F12_Ponatinib_0.135_24

value: Ponatinib


title: du145_DU145PS1A_G6_Topotecan_0.065_24

value: Topotecan


title: ST3, Control, Day 7, rep 5

description: Sample 30

value: control


title: ST3, shTXNIP, Day 7, rep 5

description: Sample 40


title: ST3, Control, Day 7, rep 4

description: Sample 29


title: du145_DU145PS1A_F9_Trametinib_0.035_24

value: Trametinib


title: ST3, Control, Day 7, rep 2

description: Sample 27


title: CMZ322 [NPB-9]

city: New York

first: Juan

middle: M

last: Arriaga

address: 1425 Madison Ave

department: Oncological Sciences, Urology

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Libraries were sequenced using Illumina HiSeq2500/4000 or NovaSeq6000 at Columbia Genome Center, or Genewiz. We multiplex samples in each lane, which yields targeted number of single-end/paired-end 100bp or 150bp reads for each sample, as a fraction of 280-400 million reads for the whole lane.
Reads were pseudo-aligned to mouse reference genome version GRCm38 mm10, using kallisto v0.44.0 (Bray et al., 2016) with sequence-based bias correction.
Genome_build: Mouse: UCSC/mm10
Supplementary_files_format_and_content: Tab-delimited text files include kallisto estimated counts for each gene in each sample
Supplementary_files_format_and_content: Gemms_counts.xlsx: Includes 19 NPK samples from GSE143815

source_name: Mouse prostate primary tumor

extract_protocol:
RNA was prepared from snap-frozen tissues the using MagMAX-96 total RNA isolation kit and only RNA samples having between >200 ng and 1 ug and with an RNA integrity number (RIN) > 8 were used.
Libraries were prepared by the Columbia Genome Center or Genewiz. Poly-A pull-down was used to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required). Libraries were prepared using TruSeq RNA library prep kit v2 or TruSeq Stranded mRNA library prep kit.

value: Mouse prostate primary tumor

value: Nkx3.1CreERT2/+; Ptenflox/flox; B-RafV6E/+; R26RLSL-EYFP/+

value: castrated

tag: mouse id

tag: use

value: Interactome + VIPER analysis


title: ST3, Control, Day 7, rep 3

description: Sample 28

value: umbilical cord blood

value: NK cell progenitor cells


title: du145_DU145PS1A_G5_Nilotinib_2_24

value: Nilotinib


title: ST3, Control, Day 7, rep 1

description: Sample 26

value: Lentiviral transduction

value: Day 7


title: CMZ321 [NPB-8]

tag: genotype


title: du145_DU145PS1A_F8_Cytarabine_0.18_24

tag: treatment

value: Cytarabine

value: ATCC


title: ST3, shTXNIP, Day 7, rep 1

description: Sample 36

value: shTXNIP


title: CMZ320 [NPB-7]


title: du145_DU145PS1A_F7_Etoposide_0.5_24

value: Etoposide

tag: cell line

value: male


title: dHEP_165_NC_T

value: liver tumor

tag: injury model

value: DEN

value: chow


title: HSC, shTXNIP, Day 3, rep 5

description: Sample 15

value: hematopoietic stem cells

value: Day 3


title: HSC, shTXNIP, Day 3, rep 4

description: Sample 14


title: du145_DU145PS1B_C6_DMSO_0_24

value: DMSO

tag: provider

tag: vendor id


title: HSC, shTXNIP, Day 3, rep 3

description: Sample 13


title: GNAQ-Q209L-Rep1_ATAC


title: du145_DU145PS1A_F11_DMSO_0_24

tag: age

tag: Sex


title: du145_DU145PS1A_F6_UNTREATED_0_24

value: UNTREATED


title: du145_DU145PS1A_F10_Docetaxel_0.00165_24

value: Docetaxel


title: CMZ323 [NPB-5]

tag: tissue

value: Mouse prostate primary tumor

value: Nkx3.1CreERT2/+; Ptenflox/flox; B-RafV6E/+; R26RLSL-EYFP/+

value: castrated

value: Interactome + VIPER analysis


title: du145_DU145PS1A_F4_Pazopanib_10_24

value: Pazopanib


title: HSC, shTXNIP, Day 3, rep 2

description: Sample 12

value: umbilical cord blood

value: Lentiviral transduction


title: HSC, shTXNIP, Day 3, rep 1

description: Sample 11

value: shTXNIP


title: CMZ312 [NPM-8]

value: Nkx3.1CreERT2/+; Ptenflox/flox; ARR2/Pbsn-MYCTg/; R26R-CAGLSL-EYFP/+


title: du145_DU145PS1A_F3_Mitotane_10_24

value: Mitotane

value: ATCC

value: male


title: HSC, Control, Day 3, rep 5

description: Sample 5

value: hematopoietic stem cells

value: control


title: du145_DU145PS1A_F2_Letrozole_2_24

value: Letrozole


title: CMZ313 [NPM-6]


title: HSC, Control, Day 3, rep 4

description: Sample 4

value: Day 3


title: HSC, Control, Day 3, rep 3

description: Sample 3


title: du145_DU145PS1A_F1_Irinotecan_0.3_24

value: Irinotecan


title: CMZ310 [NPM-2]

value: Mouse prostate primary tumor

value: intact


title: HSC, Control, Day 3, rep 2

description: Sample 2


title: CMZ319 [NPB-6]

value: Nkx3.1CreERT2/+; Ptenflox/flox; B-RafV6E/+; R26RLSL-EYFP/+

value: castrated


title: du145_DU145PS1A_E12_Pomalidomide_0.21_24

value: Pomalidomide


title: CMZ315 [NPp53 H/L-5]

value: Nkx3.1CreERT2/+; Ptenflox/flox; Trp53LSL-R27H/flox; R26R-CAGLSL-EYFP/+

value: Interactome + VIPER analysis


title: CMZ318 [NPp53 H/L-4]

value: Nkx3.1CreERT2/+; Ptenflox/flox; Trp53LSL-R27H/flox; R26R+/+


title: du145_DU145PS1A_E11_DMSO_0_24

value: DMSO


title: du145_DU145PS1A_F5_Vandetanib_1.5_24

value: Vandetanib


title: du145_DU145PS1A_E10_Vinorelbine_0.005_24

value: Vinorelbine

value: ATCC


title: ST3, shIRF2, Day 7, rep 5

description: Sample 50

value: umbilical cord blood

value: NK cell progenitor cells

value: Lentiviral transduction

value: Day 7


title: CMZ317 [NPp53 H/L-3]


title: du145_DU145PS1A_E9_Cobimetinib_0.5_24

value: Cobimetinib

value: male


title: CMZ309 [NPp53-16]

value: Mouse prostate primary tumor

value: Nkx3.1CreERT2/+; Ptenflox/flox; Trp53flox/flox; R26R-CAGLSL-EYFP/+


title: ST3, shIRF2, Day 7, rep 4

description: Sample 49


title: CMZ314 [NPM-7]

value: Nkx3.1CreERT2/+; Ptenflox/flox; ARR2/Pbsn-MYCTg/; R26R-CAGLSL-EYFP/+

value: castrated


title: du145_DU145PS1A_E8_Raloxifene_0.01_24

value: Raloxifene


title: CMZ308 [NPp53-14]

value: Interactome + VIPER analysis


title: ST3, shIRF2, Day 7, rep 3

description: Sample 48


title: du145_DU145PS1A_E7_Mercaptopurine_0.24_24

value: Mercaptopurine


title: CMZ316 [NPp53 H/L-6]

value: Nkx3.1CreERT2/+; Ptenflox/flox; Trp53LSL-R27H/flox; R26R-CAGLSL-EYFP/+

value: intact


title: ST3, shIRF2, Day 7, rep 1

description: Sample 46


title: du145_DU145PS1A_E6_UNTREATED_0_24

value: UNTREATED


title: CMZ305 [NPp53-9]


title: CMZ307 [NPp53-8]


title: HSC, Control, Day 3, rep 1

description: Sample 1

value: hematopoietic stem cells

value: control

value: Day 3


title: CMZ306 [NPp53-7]


title: ST3, CTRL, Day 7, rep 5

description: Sample 30

value: umbilical cord blood

value: NK cell progenitor cells

value: Lentiviral transduction


title: ST3, CTRL, Day 7, rep 3

description: Sample 28

value: Day 7


title: du145_DU145PS1A_E4_Dabrafenib_1.5_24

value: Dabrafenib

value: ATCC

value: male


title: CMZ364 [NP-18]

value: Mouse prostate primary tumor

value: castrated


title: du145_DU145PS1A_E5_Mithramycin_0.18_24

value: Mithramycin


title: CMZ304 [NPp53-4]

value: Nkx3.1CreERT2/+; Ptenflox/flox; Trp53flox/flox; R26R-CAGLSL-EYFP/+

value: Interactome + VIPER analysis


title: ST3, CTRL, Day 7, rep 4

description: Sample 29


title: du145_DU145PS1A_E3_Capecitabine_10_24

value: Capecitabine


title: ST3, CTRL, Day 7, rep 2

description: Sample 27


title: du145_DU145PS1A_E2_Cladribine_0.5_24

value: Cladribine


title: CMZ363 [NP-17]


title: du145_DU145PS1A_E1_Regorafenib_5_24

value: Regorafenib


title: HSC, shIRF2, Day 3, rep 5

description: Sample 25

value: hematopoietic stem cells


title: du145_DU145PS1A_D11_Sunitinib_0.045_24

value: Sunitinib


title: CMZ362 [NP-16]


title: ST3, CTRL, Day 7, rep 1

description: Sample 26

value: umbilical cord blood

value: control


title: du145_DU145PS1A_D12_Bleomycin_0.275_24

value: Bleomycin


title: HSC, shIRF2, Day 3, rep 4

description: Sample 24

value: Lentiviral transduction

value: Day 3


title: CMZ301 [NP-9]

value: intact


title: HSC, shIRF2, Day 3, rep 2

description: Sample 22


title: CMZ360 [NP-15]


title: du145_DU145PS1A_D10_Fulvestrant_0.03_24

value: Fulvestrant

value: ATCC

value: male


title: CMZ302 [NP-10]

value: Mouse prostate primary tumor


title: CMZ303 [NP-4]


title: HSC, shIRF2, Day 3, rep 1

description: Sample 21


title: du145_DU145PS1A_D9_Ruxolitinib_10_24

value: Ruxolitinib


title: du145_DU145PS1A_D8_Ceritinib_0.5_24

value: Ceritinib


title: HSC, CTRL, Day 3, rep 4

description: Sample 4


title: HSC, CTRL, Day 3, rep 5

description: Sample 5


title: du145_DU145PS1A_D5_Olaparib_1_24

value: Olaparib


title: HSC, CTRL, Day 3, rep 3

description: Sample 3


title: du145_DU145PS1A_D6_DMSO_0_24

value: DMSO


title: du145_DU145PS1A_D4_Procarbazine_2_24

value: Procarbazine


title: HSC, shIRF2, Day 3, rep 3

description: Sample 23

value: hematopoietic stem cells


title: du145_DU145PS1A_D3_Nelarabine_10_24

value: Nelarabine


title: HSC, CTRL, Day 3, rep 2

description: Sample 2

value: umbilical cord blood


title: KO_C

city: Tianjin

first: Wenwen

last: Zhang

address: huanhuxi road

country: China

institute: Tianjin Medical University Cancer Institute and Hospital

description:
Whole RNA
processed data file: expression_file.txt

data_processing:
Reference genome and gene model annotation files were downloaded from genome website directly.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. FPKM of each gene was then calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: expression_file.txt: Gene IDs and FPKM values for each sample.

source_name: white cells

extract_protocol:
RNA was extracted with the Macherey-Nagel Nucleo-spin RNA kit.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using the TruSeq PE Cluster Kit v3-cBot-HS (Illumina NovaSeq 6000). After cluster generation, the library preparations were sequenced on an Illumina Novaseq 6000 platform, and 125 bp/150 bp paired-end reads were generated.

tag: strain/background

tag: genotype/variation

value: SOCS3 KO

value: 6-8 weeks

value: Myeloid cells


title: HSC, CTRL, Day 3, rep 1

description: Sample 1

tag: shRNA

value: control

value: Lentiviral transduction

value: Day 3


title: du145_DU145PS1A_D2_UNTREATED_0_24

value: UNTREATED

value: ATCC


title: KO_B


title: ST3, shIRF2, Day 7, rep 2

description: Sample 47

value: NK cell progenitor cells

tag: time

value: Day 7


title: fl_C

value: Wild type

tag: cell type


title: Patient 10, rep 2

city: Edinburgh

first: Jose

middle: Ignacio

last: de las Heras

address: Max Born Crescent

department: Wellcome Trust Centre

institute: University of Edinburgh

description:
small RNA
Sample 35

data_processing: QC, alignment and quantification performed with the miRNASeq analysis pipeline from nf-core (smrnaseq: https://nf-co.re/smrnaseq/1.1.0) with default parameters

source_name: myotubes

growth_protocol: Myoblasts isolated from muscle biopsies were grown in culture at 37oC and 5% CO2 using skeletal muscle growth medium (PELOBiotech #PB-MH-272-0090). When myoblasts reach confluency, differentiation was induced by changing to skeletal muscle cell differentiation medium (Cell Applications #151D-250) for six days, replacing the medium every 48 hours. Myotubes were selectively isolated by partial trypsinisation, where myotubes are gently detached in 0.1% Trypsin leaving myoblasts attached to the tissue culture dish.

extract_protocol:
RNA < 200nt was extracted using Qiagen miRNeasy RNA extraction kit (#1038703).
Sequencing libraries were prepared by RealSeq Biosciences with the Somagenics Low-bias RealSeq-AC miRNA library kit for small RNA (#500-00012).

tag: individual

value: Patient 10

value: myotubes

tag: condition

value: EDMD

tag: mutation

value: LMNA, p.R571S


title: Patient 10, rep 3

description:
small RNA
Sample 36


title: KO_A


title: du145_DU145PS1A_D7_Gemcitabine_0.00255_24

value: Gemcitabine

value: male


title: du145_DU145PS1A_C12_Paclitaxel_0.00225_24

value: Paclitaxel


title: du145_DU145PS1A_C11_Afatinib_0.185_24

value: Afatinib


title: fl_B

value: 6-8 weeks

value: Myeloid cells


title: Patient 10, rep 1

description:
small RNA
Sample 34


title: Gr_1_C


title: du145_DU145PS1A_C10_Leuprolide_0.075_24

value: Leuprolide


title: Patient 9, rep 3

description:
small RNA
Sample 33

value: Patient 9

value: LMNA, p.T528K


title: Patient 9, rep 2

description:
small RNA
Sample 32


title: du145_DU145PS1A_D1_Lenalidomide_1.5_24

value: Lenalidomide

value: ATCC


title: fl_A


title: Patient 9, rep 1

description:
small RNA
Sample 31


title: du145_DU145PS1A_C9_Osimertinib_0.36_24

value: Osimertinib


title: du145_DU145PS1A_C8_Thioguanine_0.085_24

value: Thioguanine


title: Patient 8, rep 3

description:
small RNA
Sample 30

value: Patient 8

value: FHL1, p.V280M


title: Patient 8, rep 2

description:
small RNA
Sample 29

value: myotubes

value: EDMD


title: du145_DU145PS1A_C6_DMSO_0_24

value: DMSO


title: du145_DU145PS1A_C7_Doxorubicin_0.045_24

value: Doxorubicin

value: male


title: Gr_1_A

value: Wild type


title: Patient 8, rep 1

description:
small RNA
Sample 28


title: du145_DU145PS1A_C5_Everolimus_0.5_24

value: Everolimus


title: Patient 7, rep 3

description:
small RNA
Sample 27

value: Patient 7

value: FHL1, p.C224W


title: du145_DU145PS1A_C4_Lomustine_7_24

value: Lomustine


title: du145_DU145PS1A_C3_Cabozantinib_1_24

value: Cabozantinib


title: Patient 7, rep 1

description:
small RNA
Sample 25


title: du145_DU145PS1A_C2_UNTREATED_0_24

value: UNTREATED


title: spleen, De_UL23_infected, Day5 rep1

city: Zhengzhou

first: ZHU Xiaojing

middle: Xiaojing

last: ZHU

state: Henan

address: 15 Longzihu University Park, Zhengdong New District

institute: Henan Agricultural University

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Gallus gallus

source_name: spleen

extract_protocol:
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.
RNA libraries for RNA-seq were prepared for sequencing using standard Illumina protocols.

treatment_protocol: One-day-old chickens were wing-banded at hatch, randomly sorted into six experimental groups, and maintained in modified HorsfallBauer isolators for the duration of animal experiment. One group of chickens was remained as the uninoculated control.  The rest of five groups were inoculated subcutaneously with 2,000 PFUs Md5BAC, or CVI988, or Md5BAC Δmeq Δpp38 or Md5BAC Δlorf9, or Md5BAC ΔUL23 virus. 3 chickens from each group were euthanatized at 5-days post infection (dpi). Spleen tissues were collected for splenocytes isolation followed by RNA extraction

value: spleen


title: spleen, De_lorf9_infected, Day5 rep3


title: spleen, De_lorf9_infected, Day5 rep2


title: spleen, De_lorf9_infected, Day5 rep1


title: spleen, De_UL23_infected, Day5 rep3


title: Patient 6, rep 3

description:
small RNA
Sample 24

value: Patient 6


title: du145_DU145PS1A_C1_Clofarabine_0.175_24

value: Clofarabine

value: ATCC


title: Patient 6, rep 2

description:
small RNA
Sample 23


title: Patient 7, rep 2

description:
small RNA
Sample 26


title: du145_DU145PS1A_B12_Fluorouracil_10_24

value: Fluorouracil


title: spleen, De_meq_pp38_infected, Day5 rep3


title: Patient 5, rep 2

description:
small RNA
Sample 20

value: Patient 5

value: myotubes

value: EMD, p.S58Sfs*1


title: spleen, De_meq_pp38_infected, Day5 rep1


title: Patient 5, rep 3

description:
small RNA
Sample 21

value: EDMD


title: spleen, De_meq_pp38_infected, Day5 rep2


title: Gr_1_B

value: 6-8 weeks

value: Myeloid cells


title: du145_DU145PS1A_B10_Ibrutinib_0.35_24

value: Ibrutinib

value: male


title: Patient 5, rep 1

description:
small RNA
Sample 19


title: du145_DU145PS1A_B9_Belinostat_0.13_24

value: Belinostat


title: spleen, De_UL23_infected, Day5 rep2


title: spleen, CVI988_infected, Day5 rep2


title: spleen, CVI988_infected, Day5 rep3


title: du145_DU145PS1A_B8_Tretinoin_2_24

value: Tretinoin


title: Patient 4, rep 3

description:
small RNA
Sample 18

value: Patient 4


title: spleen, CVI988_infected, Day5 rep1


title: du145_DU145PS1A_B7_Mitomycin_0.055_24

value: Mitomycin


title: du145_DU145PS1A_B11_Pralatrexate_0.005_24

value: Pralatrexate


title: H1650over-2

city: Fuzhou City

first: hongguang

last: Lin

state: Fujian Province

address: NO.29 of Xinquan Road, Gulou District

institute: Fujian Medical University Union Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed by fastp v0.20.1 for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using STAR v2.7.7a with default parameters.Annotation file of Ensembl release 76 (GRCh38) transcriptome gff file was provided to STAR as gene model.
raw reads count aligned to each gene were calculated by FeatureCount v2.0.0
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Lung cancer cell line

extract_protocol:
RNA was isolated from 1-2x106 cells stored in TRIzol reagent following manufacturer's instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: SRSF2 over-expressing

value: lung cancer cell line


title: Patient 4, rep 2

description:
small RNA
Sample 17


title: spleen, Md5_infected, Day5 rep3

value: spleen


title: H1650over-1


title: H1650NC-3

value: untreated


title: du145_DU145PS1A_B6_Bexarotene_1.5_24

value: Bexarotene

value: ATCC


title: H1650over-3


title: du145_DU145PS1A_B5_Crizotinib_0.19_24

value: Crizotinib


title: Patient 4, rep 1

description:
small RNA
Sample 16

value: myotubes

value: EDMD


title: spleen, Md5_infected, Day5 rep2


title: Patient 3, rep 3

description:
small RNA
Sample 15

value: Patient 3


title: spleen, Md5_infected, Day5 rep1


title: du145_DU145PS1A_B4_Carboplatin_10_24

value: Carboplatin


title: du145_DU145PS1A_B3_Vemurafenib_8_24

value: Vemurafenib

value: male


title: Patient 3, rep 1

description:
small RNA
Sample 13


title: Patient 3, rep 2

description:
small RNA
Sample 14


title: spleen, Negative, Day5 rep2

value: uninfected


title: du145_DU145PS1A_B2_DMSO_0_24

value: DMSO


title: H1650NC-2


title: A549over-3


title: A549over-2


title: spleen, Negative, Day5 rep1


title: spleen, Negative, Day5 rep3


title: Patient 2, rep 3

description:
small RNA
Sample 12

value: Patient 2

value: NET39, p.M92K


title: du145_DU145PS1A_B1_Pemetrexed_10_24

value: Pemetrexed


title: A549over-1

value: SRSF2 over-expressing

value: lung cancer cell line


title: Patient 2, rep 1

description:
small RNA
Sample 10


title: du145_DU145PS1A_A12_Sorafenib_1_24

value: Sorafenib


title: patient-17 NAT

city: Hengyang

first: Zhengqing

last: Wan

address: 28 West Changsheng Road

institute: University of South China

data_processing:
Adapter and low‑quality reads were first trimmed using Trim Galore (version 0.4.4) in paired‑end mode with default parameters.
Trimmed reads were then mapped to the hg19 reference genome to count mapped reads for all human transcripts.
Normalization and analysis of differentially expressed genes (DEGs) were carried out using multifactor analysis (tumor vs. NAT) in the DESeq2 R program package.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.

source_name: Oral cavity

extract_protocol:
Tissue blocks of about 30 mg were further dissected out and used for extraction of total RNA following the manufacturer’s instruction of the AllPrep DNA/RNA/miRNA Universal Kit (80224, Qiagen, USA)
1 μg of total RNA from each sample was depleted for rRNA using the Ribo‑Zero rRNA Removal Kit (RZH1046, EPICENTRE, USA), followed by construction of sequencing library using the TruSeq RNA Sample Prep Kit v2 (RS‑122, Illumina, USA).

value: normal adjacent tissue


title: A549NC-3

value: untreated


title: patient-17 tumor

value: OSCC tissue


title: A549NC-2


title: Patient 1, rep 2

description:
small RNA
Sample 8

value: Patient 1

value: myotubes


title: H1650NC-1


title: du145_DU145PS1A_A10_Carfilzomib_0.005_24

extract_protocol:
Cells are lysed for PLATE-Seq in Buffer TCL (Qiagen) supplemented with 2-mercaptoethanol in 96-well plates. We transfer 30 μl of cell lysate from each well to a 96-well plate with oligo(dT) grafted to the wells (mRNA TurboCapture Plate, Qiagen) and added 1 μl of 1:100 dilution of ERCC Ex-Fold Spike-Ins (ThermoFisher) to a subset of the sample wells. The plate is then centrifuged at 295 × g for 1 min to eliminate air bubbles followed by incubation for 90 min at room temperature with shaking at 200 rpm. Lysate is then removed from the oligo(dT) capture plate and wells are washed three times with Buffer TCW (Qiagen) using the 96 CO-RE Head of a Hamilton Microlab STAR automated liquid handling system. After drying the plate, mRNA is then eluted by adding 30 μl of elution buffer (nuclease-free water supplemented with 0.4 U μl−1 SUPERaseIN (ThermoFisher)), incubation at 65 °C for 5 min, and incubation at room temperature for 5 min. mRNA samples are then transferred to a new PCR plate (Hard-Shell PCR plate, 96-well, Bio-Rad) using sterile-filter 96-well, 50 μl tips on the Hamilton STAR. To anneal primers for reverse transcription, 3 μl of 100 μM adapter-linked oligo(dT) primers are added to each well along with 10 μl of 5× ProtoScript RT Buffer (New England BioLabs) with the Hamilton STAR CO-RE Head and 1000 μl channel pipetting system (see Supplementary Table 2 for “PLATEseq_oligodTBC” sequences). The plate is then heated to 94 °C for 2 min and placed immediately on ice for 5 min. The remaining components of the reverse transcription master mix including 0.5 mM of each dNTP, 10 mM DTT, 35.8 U of Protoscript II Reverse Transcriptase (New England BioLabs), and water are then added to bring the final reaction volume to 50 μl per well. The plate is then centrifuged at 295 × g for 1 min and incubated at 42 °C for 2 h. At this point, the samples can optionally be frozen at −80 °C. To remove excess primer, 1 μl of a fourfold dilution of Exonuclease I (New England BioLabs) is added to each sample. The Exonculease I reaction is incubated at 25 °C for 1 h. To hydrolyze the RNA, we add 20 μl of a 1:1 mixture of 1 M sodium hydroxide and 0.5 M EDTA to each well and incubate at 65 °C for 15 min. The wells are then pooled together into a single tube to which 80 μl of 12 M hydrochloric acid are added to neutralize the sample. At this point, the pooled sample can optionally be frozen at −80 °C. The pooled, neutralized sample is purified and concentrated using a Qiagen MinElute column using a vacuum apparatus according to the manufacturer’s instructions, and pooled cDNA is eluted in 15 μl of nuclease-free water. For second-strand synthesis, 1 μl of 10 mM dNTP mixture and 1 μl of 100 mM adapter-linked random hexamer primers are added to the pooled cDNA sample. The mixture is then heated to 70 °C for 2 min and immediately placed on ice for 5 min. Next, 2 μl of NEB Buffer 2 (New England BioLabs) and 1 μl of Klenow large fragment DNA polymerase (New England BioLabs) are added and the reaction is incubated at room temperature for 30 min. The reaction is then stopped by addition of EDTA to a final concentration of 50 μM the double-stranded cDNA is purified with two rounds of bead clean-up using AMPure XP beads (Beckman Counter) at a 1:1 bead-to-sample ratio. Finally, the double-stranded cDNA pool is amplified by PCR using Phusion DNA Polymerase (New England BioLabs)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Carfilzomib

value: ATCC


title: Patient 1, rep 3

description:
small RNA
Sample 9

value: EDMD


title: A549NC-1


title: du145_DU145PS1A_A11_Dasatinib_0.02_24

value: Dasatinib

value: male


title: patient-16 tumor


title: patient-16 NAT


title: Patient 1, rep 1

description:
small RNA
Sample 7


title: Healthy control 2, rep 3

description:
small RNA
Sample 6

value: Healthy control 2

value: control


title: du145_DU145PS1A_A8_Vinblastine_0.02_24

value: Vinblastine


title: Healthy control 2, rep 2

description:
small RNA
Sample 5


title: patient-15 tumor


title: du145_DU145PS1A_A7_Mitoxantrone_0.01_24

value: Mitoxantrone


title: patient-14 NAT


title: Healthy control 2, rep 1

description:
small RNA
Sample 4


title: du145_DU145PS1A_A6_Imatinib_5_24

value: Imatinib


title: Healthy control 1, rep 3

description:
small RNA
Sample 3

value: Healthy control 1


title: du145_DU145PS1A_A5_Ixabepilone_0.0031_24

value: Ixabepilone


title: Healthy control 1, rep 2

description:
small RNA
Sample 2


title: Fresh DTAN4047

city: Palo Alto

first: Siddhartha

last: Jaiswal

address: 240 Pasteur Dr

department: Pathology

institute: Stanford University School of Medicine

data_processing:
Gene counts quantified with CellRanger 3.0
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene counts

source_name: Carotid Artery

extract_protocol:
Vessels were digested into single cell suspensions using a simple Liberase digestion protocol. The cells were then sorted for CD45+ cells and a live/dead exclusion was performed using AQUA.
V3’ 10x Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit

value: Carotid

value: CD45+ hematopoetic cells

tag: plaque severity

value: moderate

value: Male

tag: diabetes

value: No

tag: chd

value: Yes


title: patient-14 tumor

value: OSCC tissue


title: Frozen ROB2026


title: du145_DU145PS1A_A4_Cisplatin_6_24

first: Alessandro

last: Vasciaveo

address: 1130 Saint Nicholas Ave., 910

institute: Columbia University

data_processing:
Sequencing was performed in a Hi Seq 2500 sequencer (Illumina) and base calling was performed with Illumina HCS software.
RNASeq reads were mapped for each well to the human reference genome assembly 38 using the STAR aligner (Dobin et al., 2013), version 2.5.2b
Individual counts files were combined across genes and ERCC2 spike-in counts removed, yielding the raw counts file for each cell-line experiment.
Assembly: hg38
Supplementary files format and content: 2 semicolon delinated text files (for 2 cell-lines) with raw gene counts for every gene and every sample

tag: treatment

value: Cisplatin

tag: cell line

value: ATCC


title: Healthy control 1, rep 1

description:
small RNA
Sample 1

value: myotubes


title: du145_DU145PS1A_A3_Bendamustine_10_24

value: Bendamustine

tag: provider

tag: vendor id

value: male


title: patient-13 NAT

value: normal adjacent tissue


title: patient-13 tumor


title: HCASMC-hTERT-FHL5-NLS_rep3

city: Charlottesville

first: Clint

middle: L

last: Miller

state: VA

department: Center for Public Health Genomics

institute: University of Virginia

data_processing:
Quantification of transcript expression was performed using Salmon version 1.2.0 based on  the GENCODEv38 transcriptome index.
Transcript-level quantifications were merged to gene-level quantifications and normalized to transcripts per million (TPM) in the R package tximport (v1.22.0).
Read counts were imported and converted into DESeq2 matrix using tximport (v1.22.0).
Assembly: hg38
Supplementary files format and content: tab delimited file containing normalized transcripts per million values (TPM) for each sample

source_name: HCASMC-hTERT

growth_protocol: HCASMC-hTERT were immortalized via lentiviral mediated hTERT overexpression from the primary HCASMC cell line (Cell Signaling , Lot 2105). Cells were maintained in complete SmGM-2 Smooth Muscle Growth Medium-2 supplemented with hEGF, insulin, hFGF-B, 5% FBS, and 1ug/ml puromycin (Gibco, A1113803).

extract_protocol:
RNA was extracted from ~500,000 HCASMC-hTERT using the Quick-RNA Miniprep Kit (Zymo Research).
Libraries were prepared using the polyA enrichment method using standard Illumina protocols.

value: hTERT immortalized coronary artery smooth muscle cell

tag: expressing


title: du145_DU145PS1A_A9_Toremifene_1.5_24

city: New York City

source_name: prostate cancer

value: Toremifene

tag: age

tag: Sex


title: HCASMC-hTERT-FHL5-NLS_rep2


title: patient-12 tumor

tag: tissue


title: Fresh 1667

source_name: Coronary Artery

value: Coronary

value: severe


title: Frozen DTAN4047

value: Carotid


title: patient-15 NAT


title: HCASMC-hTERT-FHL5-NLS_rep1


title: du145_DU145PS1A_A1_Lapatinib_7.5_24

value: Lapatinib


title: patient-11 NAT


title: DE_CRISPRi_rep3

city: Lausanne

first: Evarist

last: Planet

state: Vaud

address: Route Cantonale

country: Switzerland

institute: EPFL

data_processing:
Reads were mapped to the human (hg19) genome using Hisat2 for RNA-seq
Cell Ranger with default parameters was used for the single-cell
Genome_build: hg19 for RNA-seq and hg38 for the single-cell
Supplementary_files_format_and_content: The .txt files contain read counts on genes or TEs

growth_protocol: H9 human ESC line were maintained in mTSER plus on Matrigel and were passaged using TryplE in single cells.

extract_protocol:
Truseq stranded mRNA
Total RNA from cell lines was isolated with NucleoSpin™ RNA Plus kit (Machery-Nagel). cDNA was prepared with Maxima Reverse Transcriptase (Thermo Scientific). Sequencing libraries were performed with Illumina Truseq Stranded mRNA LT kit
Illumina Truseq Stranded mRNA LT kit for RNA-seq and Chromium Single Cell Multiome ATAC + Gene Expression

treatment_protocol: Endodermal differentiation was performed as in Lee et al. 2019. Briefly, hESC were passaged at 80k cells/cm2 density in 12-well Matrigel-coated plate. When cells reached 80 – 90% confluence at 48-76h post-splitting, endodermal differentiation was initiated with 100 ng/ml of Activin A for 3 days, 5 μM GSK-3 inhibitor (CHIR-99021) to activate the WNT pathway for the first day, and 0.5 μM for the second day. Gastruloid differentiation was performed as in {Moris:2020hv}. Briefly, hESC were passaged at 40k cells/cm2 in mTSER density and at 48-76h post-splitting, mTSER was replace with Nutristem media with 3 μM CHIR-99021. Then after 24h then through single-cell passaging with TryplE, embryoid bodies were formed with 800 cells per well of low adherence 96-well plate Cell Star in E6 media supplemented with 3 μM CHIR-99021 and 10 μM Rock inhibitor for 18 hours, then replace with E6 twice to be harvest 72h.

tag: source

value: Early Embryo

tag: culture media

value: Advance DMEM + CHIR + Activin

tag: status

value: Endoderm-derived hESC expressing dCAS9-KRAB with sgRNA


title: 40y_snRNAseq

city: Perth

first: Ryan

last: Lister

state: WA

address: 35 Stirling Highway

country: Australia

institute: The University of Western Australia

description:
nuclear RNA
same donor as RL2373

data_processing:
cellranger mkfastq with Cellranger v3.1 to generate fastq files as inout for count pipeline.
cellranger count with Cellranger v3.1 to generate feature-barcode matrices of gene expression.
cellranger-atac mkfastq with Cellranger-ATAC v1.2 to generate fastq files as input for count pipeline.
cellranger-atac count with Cellranger-ATAC v1.2 to generate BED-like tabular file with contains frgaments captured by the assay and barcode information in single cell output tables.
Genome_build: hg19
Supplementary_files_format_and_content: For snRNA-seq data: feature-barcode matrices in HDF5 format containing every barcode from the fixed list of known-good barcode sequences that has at least 1 read for raw_feature files, or only containing detected cellular barcodes for filtered_feature files. For snATAC, a BED-like tabular fragment file with each line representing a unique ATAC-seq fragment captured by the assay,  an index for the fragments file as well as a singlecell file containing cell barcodes, QC information and ATAC signal.

source_name: prefrontal cortex, BA9

extract_protocol:
Per sample, 50 mg of frozen brain tissue was lysed and nuclei extracted. Nuclei were then either enriched by DAPI-positive FANS for single cell gene expression library generation or cleaned with a sucrose gradient centrifugation for single cell ATAC library generation.
10X Genomics 3' Single Cell Gene Expression v2/v3 , 10X Genomics Single Cell ATAC
snRNA-seq, snATAC-seq

value: brain


title: patient-11 tumor

value: OSCC tissue


title: Patient 2, rep 2

description:
small RNA
Sample 11

tag: individual

value: Patient 2

value: EDMD

value: NET39, p.M92K


title: DE_CRISPRi_rep2


title: Fresh ROB2026

tag: cell type

value: CD45+ hematopoetic cells

value: moderate

value: Male

value: No


title: du145_DU145PS1A_A2_DMSO_0_24

value: DMSO

value: ATCC

value: male


title: 25y_snATAC

description:
genomic DNA
same donor as RL2132

source_name: prefrontal cortex, BA10


title: patient-12 NAT

value: normal adjacent tissue


title: 25y_snRNAseq

description:
nuclear RNA
same donor as RL2369


title: DE_CRISPRi_rep1


title: patient-10 NAT


title: HCASMC-hTERT-HA_rep1

value: hTERT immortalized coronary artery smooth muscle cell

value: HA


title: 20y_snATAC

description:
genomic DNA
same donor as RL2128

source_name: prefrontal cortex, BA8


title: HCASMC-hTERT-HA_rep2


title: patient-9 NAT


title: DE_ctl_rep3

value: Early Embryo

value: Advance DMEM + CHIR + Activin

value: Endoderm-derived hESC expressing dCAS9-KRAB without sgRNA


title: HCASMC-hTERT-FHL5_rep3


title: patient-10 tumor

value: OSCC tissue


title: DE_ctl_rep2


title: patient-9 tumor


title: HCASMC-hTERT-HA_rep3


title: 20y_b_snRNAseq

description:
nuclear RNA
same donor as RL2085

value: brain


title: HCASMC-hTERT-FHL5_rep2


title: HCASMC-hTERT-FHL5_rep1


title: DE_ctl_rep1


title: 20y_a_snRNAseq

description:
nuclear RNA
no paired snATAC data


title: patient-8 NAT


title: hESC_rep2

value: mTSER Plus on matrigel

value: hESC


title: patient-8 tumor


title: 17y_snRNAseq

description:
nuclear RNA
no paired snATAC data


title: patient-7 NAT


title: gastruloid_72h_ATAC

extract_protocol:
10X chronium
Total RNA from cell lines was isolated with NucleoSpin™ RNA Plus kit (Machery-Nagel). cDNA was prepared with Maxima Reverse Transcriptase (Thermo Scientific). Sequencing libraries were performed with Illumina Truseq Stranded mRNA LT kit
Illumina Truseq Stranded mRNA LT kit for RNA-seq and Chromium Single Cell Multiome ATAC + Gene Expression

value: 72h elongated gastruloid


title: gastruloid_72h_RNA


title: 16y_snRNAseq

description:
nuclear RNA
same donor as RL1785


title: patient-7 tumor


title: patient-6 NAT


title: RNAseq_CLT_C2_RTT

city: Toronto

first: James

last: Ellis

state: ON

address: 686 Bay Street

institute: Hospital for Sick Children

data_processing: Raw data files were used in Pluritest, so there are no processed files

source_name: induced pluripotent stem cells

growth_protocol: All iPSC lines were maintained on Matrigel (Corning) coated dishes using mTeSR1. Daily media changes were performed except for the day following passaging. ReLeSR (STEMCELL Technologies) was used to lift clumps of iPSCs for routine passaging.

extract_protocol:
RNA was collected from single wells of 6-well plates using RNA PureLink RNA mini kit (Life Technologies) as per supplied protocol.
RNA libraries were prepared using NEBNext Ultra RNA Library Preparation kit for Illumina, and total RNA was used for poly(A) mRNA enrichment

value: iPSC

tag: genotype/variation

value: CLT RTT missense


title: 14y_snRNAseq

description:
nuclear RNA
same donor as RL2372


title: patient-6 tumor


title: patient-5 NAT


title: 14y_snATAC

description:
genomic DNA
same donor as RL2130


title: RNAseq_CLT_C17_WT

value: CLT WT


title: RNAseq_CLT_C1_RTT


title: 10y_snATAC

description:
genomic DNA
same donor as RL2110


title: patient-4 NAT


title: RNAseq_CLT_C4_WT


title: patient-5 tumor


title: 10y_b_snRNAseq

description:
nuclear RNA
no paired snATAC data


title: 16y_snATAC

description:
genomic DNA
same donor as RL2102


title: 12y_snRNAseq

description:
nuclear RNA
no paired snATAC data


title: patient-4 tumor


title: patient-3 NAT


title: patient-3 tumor


title: MCF7_SMYD3_rep2

city: Seoul

first: Hee-Joo

last: Choi

address: 222 Yangshimri-ro, Seongdonggu

country: South Korea

institute: Hanyang University

data_processing:
Illumina bcl2fastq2 v2.17 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR v2.6.0c
Raw counts were calculated using featureCounts from Subread package v1.6.2
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file include raw counts for all samples

source_name: breast cancer cell line

extract_protocol:
Total RNA was extracted from control and SMYD3 overexpressed MCF7 stable cell lines tumors using TRIzol® RNA Isolation Reagents (Life technologies, Carlsbad, CA). RNA integrity was confirmed by a bioanalyzer using an Agilent RNA 6000 Pico Kit (Agilent, Santa Clara, CA). The isolated total RNA was processed for preparing mRNA sequencing library using TruSeq stranded mRNA sample preparation kit (illumina, San Diego, CA) according to manufacturer’s instruction. Simply, mRNAs were isolated from 400 ng total RNA by RNA purification bead using polyA capture, and followed by enzyme shearing.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tag

value: mammary gland/breast

value: epithelial

value: adenocarcinoma


title: MCF7_SMYD3_rep3


title: hESC_rep1


title: patient-2 NAT

value: normal adjacent tissue


title: patient-2 tumor


title: 4y_snATAC

description:
genomic DNA
same donor as RL2109

source_name: prefrontal cortex, BA46


title: MCF7_Con_rep2


title: MCF7_SMYD3_rep1


title: MCF7_Con_rep1


title: 3y_snRNAseq

description:
nuclear RNA
no paired snATAC data


title: 120min_4sU_rep2_bulk

data_processing:
Sequenced reads were converted to the reverse complementary sequences using custom python script
Reads were aligned to the GRCh38 genome using STAR version 2.6.0a with optional parameters:  --outFilterMismatchNmax 10 --outSAMtype BAM Unsorted --outSAMattributes AS NH nM NM MD
Aligned bam files were sorted using samtools  v1.9
Gene annotation tags were added using Drop-seq tools v2.0.0
The number for mismathces between sequenced reads and reference genome were tagged in the bam files using cumtom python script
The unique gene name annotation were tagged to each reads in the aligned sorted bam file using custom python script
RNA counts of each gene in each sample were counted by summing up all the reads that mapped to the gene using custom python script
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited txt files include the transcript counts for each gene in each cell of four RNA types (i.e, labled precursor, labeled mature, unlabeled precursor and unlabeled mature) in each sample
Supplementary_files_format_and_content: Tab-delimited txt files include the transcript counts for each gene in each sample

source_name: HEK293 cells

extract_protocol:
Fixed cell suspention was rehydrated and washed in DPBS - BSA 0.1% + 1 U/μL Ribolock RNAse Inhibitor (ThermoFisher, EO0382), passed through a 35 μm FACS tube cell strainer and counted.
For DropSeq library preparation we followed the protocol of: Alles et al BMC Biol 2017 doi: 10.1186/s12915-017-0383-5. For Nadia library preparation we followed the instuctions of the system manual for scRNA-seq.

value: Flp-In-293 Cell Line

value: 120 minutes 4sU + IAA


title: 10y_a_snRNAseq

description:
nuclear RNA
same donor as RL2368


title: MCF7_Con_rep3


title: 4y_snRNAseq

description:
nuclear RNA
same donor as RL2210


title: patient-1 tumor


title: 120min_4sU_rep1_bulk


title: 60min_4sU_rep2_bulk

value: 60 minutes 4sU + IAA


title: patient-1 NAT


title: 2y_snATAC

description:
genomic DNA
same donor as RL1613


title: 60min_4sU_rep1_bulk


title: 1y_b_snRNAseq

description:
nuclear RNA
same donor as RL2209


title: cis1-1_Blue_2

city: Shenzhen

first: Zhao

last: Zhiwei

state: Guangdong

address: 1066, Xueyuan Rd

department: College of Life Sciences and Oceanography

institute: Shenzhen univerisity

data_processing:
Illumina software used for basecalling.
Sequenced reads were processed using Trimmomatic(Version0.36), The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2(Version2.2.1.0).
abundance measurement step:
Then quantified read counts per gene and normalized Fragments Per Kilobase exon per Million reads mapped (FPKM) values using Cufflinks TopHat（version:2.2.1）
FPKM and read counts valueof each transcript (protein_coding) was calculated using bowtie2 and eXpress. DEGs were identified using the DESeq(Version1.18.0)(2012) functions estimateSizeFactors and nbinomTest.
Splice-site Strength Estimation step:
RNA-seq data were mapped with STAR v2.5.2 using minimum intron size 20, and maximum intron size 6000
A splice junction BED file was generated using RegTools v0.5.2 ‘junctions extract’ command with the same intron limits
Each mapped RNA-seq sample was processed with SpliSER v0.1.1
Genome_build: abundance measurement: TAIR10.1_NCBI
Supplementary_files_format_and_content: abundance measurement: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Splice-site Strength Estimation: tab-delimited text files include Splice-site Strength Estimates values for each Sample

organism: Arabidopsis thaliana

source_name: seedling

extract_protocol:
total RNA was isolated using RNAiso Plus kit (Takara Bio, Shiga, Japan)
The RNA library generation process followed the manufacturer’s protocol for the Illumina TruseqTM RNA sample prep Kit

value: seedling

value: 4 DAY OLD

tag: genotype

value: cis1-1 mutant


title: cis1-1_Dark_3


title: cis1-1_Blue_1


title: 8y_snATAC

description:
genomic DNA
same donor as RL1614

value: brain


title: cis1-1_Blue_3


title: 30min_4sU_rep1_bulk

city: Copenhagen

first: Haiyue

last: Liu

institute: University of Copenhagen

value: 30 minutes 4sU + IAA


title: 30min_4sU_rep2_bulk


title: 10m_snATAC

description:
genomic DNA
same donor as RL2122


title: cis1-1_Dark_1


title: cry1cry2_Blue_3

value: cry1cry2 mutant


title: no_4sU_rep2_bulk

value: (no 4sU) + IAA


title: cry1cry2_Blue_1


title: 6m_snRNAseq

description:
nuclear RNA
same donor as RL2208


title: 10m_snRNAseq

description:
nuclear RNA
same donor as RL2371


title: 6m_snATAC

description:
genomic DNA
same donor as RL2108


title: no_4sU_rep1_bulk


title: 15min_4sU_rep2_Nadia

data_processing:
Cell and molecular barcodes were extracted from read1 and added as tags using Drop-seq tools v2.0.0
Sequenced reads were trimmed for polyA stretches, SMART adaptor sequences and low quality filtering using Drop-seq tools v2.0.0
Reads were aligned to the GRCh38 genome using STAR version 2.6.0a with optional parameters:  --outFilterMismatchNmax 10 --outSAMtype BAM Unsorted --outSAMattributes AS NH nM NM MD
Aligned bam files were sorted using Picard tools provide in Drop-seq tools v2.0.0
Aligned and sorted bam files were merged with unaliged bam files that tagged with cell and molecular barcodes using Drop-seq tools v2.0.0
Gene annotation tags were added and bead synthesis errors were detected and corrected using Drop-seq tools v2.0.0
Estimated the number of barcodes was determined by a knee point in the cumulative curve using dropbead v0.25
The number for mismathces between sequenced reads and reference genome were tagged in the bam files using cumtom python script
The unique gene name annotation were tagged to each reads in the aligned sorted bam file using custom python script
The splicing status tag for each read were added to the bam file using custom bash script
Reads with the same molecular barcode were merged and T->C mismatch posiiton, coverage and numbers were counted using custom python script
Sequencing error and background conversions were corrected and newly synthesized RNA molecules were identified via merged reads using Baysian model implemented in R script
RNA counts of each gene in each cell for different types of classified RNAs (i.e. labeled precursor, unlabeled precusor, labeled mature and unlabeled mature) were counted by summing up all the counts of molecules mapped to each gene in each cell and the processed gene expression matrix csv files were generated using custom Rscript.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited txt files include the transcript counts for each gene in each cell of four RNA types (i.e, labled precursor, labeled mature, unlabeled precursor and unlabeled mature) in each sample
Supplementary_files_format_and_content: Tab-delimited txt files include the transcript counts for each gene in each sample

value: 15 minutes 4sU + IAA


title: 3m_snATAC

description:
genomic DNA
same donor as RL2100


title: cry1cry2_Dark_2


title: cry1cry2_Dark_1


title: cry1cry2_Dark_3


title: 1y_snATAC

description:
genomic DNA
same donor as RL2105


title: 24h_4sU_rep1_Nadia

value: 24 hours 4sU + IAA


title: 15min_4sU_rep1_Nadia


title: WT_Blue_3

value: Wild-type


title: cis1-1_Dark_2


title: 1y_a_snRNASeq

description:
nuclear RNA
no paired snATAC data


title: 1m_snATAC

description:
genomic DNA
no paired snRNAseq data


title: 6y_snRNAseq

description:
nuclear RNA
same donor as RL2364


title: mh2a2_with_serum_rep3

city: New york

first: DAN

last: SUN

address: 1468 Madison Avenue,

institute: Ichan School of Medicine at Mount Sinai

data_processing:
Quality control was performed using FastQC (v0.11.8).
Trim Galore! (version 0.6.5) was used to trim the adapter sequences with a quality threshold of 20. The human genome reference used was GRCh38.p13 and GENCODE release 36.
Alignment was performed using STAR aligner (v2.7.5b)
Gene level read counts were obtained by using Salmon (v1.2.1) for all libraries. All samples passed the quality control requirements with > 60% of reads uniquely mapping (>20M uniquely mapped reads for each library) using STAR.
Genome_build: Differential expression analysis was performed using the gene level read counts and the DESeq2 (v1.28.1) R package
Supplementary_files_format_and_content: GRCh38.p13
Supplementary_files_format_and_content: xlsx or CSV file of normalized gene counts from all replicates or differential gene expression

source_name: T-HEp3 cells

growth_protocol: T-HEp3 (P1) primary cells derived from chicken CAM model were engineered to stably express either H2B-GFP or macroH2A2-GFP. T-HEp3 cells with either H2B-GFP or macroH2A2-GFP expression  were grown on CAM for 7 days and then the tumors were dissociated and cultured in normal growth medium in vitro. After 24 hours in dish, cells were used for RNA extraction and sequencing.

extract_protocol:
RNA was extracted using Direct-zol RNA MiniPrep Kit and total RNA was selected for polyA+ RNAs.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: disease state

value: head and neck squamous cell carcinoma


title: mh2a2_with_serum_rep2


title: WT_Blue_1


title: ga34_snRNAseq

description:
nuclear RNA
no paired snATAC data


title: ga24_snATAC

description:
genomic DNA
same donor as RL2107


title: mh2a2_with_serum_rep1


title: WT_Dark_2


title: h2b_with_serum_rep2


title: WT_Dark_3


title: 4m_snRNAseq

description:
nuclear RNA
no paired snATAC data


title: ga24_snRNAseq

description:
nuclear RNA
same donor as RL2207


title: 3m_snRNAseq

description:
nuclear RNA
same donor as RL1914


title: WT_Dark_1


title: 24h_4sU_rep2_Nadia

address: Blegdamsvej 3B

tag: treatment


title: cry1cry2_Blue_2


title: WT_Blue_2


title: 999062_4

status: Public on Oct 30 2022

city: Houston

first: exRNA

last: BRL

state: TX

address: One Baylor Plaza

department: Molecular & Human Genetics - Milosavljevic

institute: Baylor College of Medicine

description:
EXR-DGALA1plasma999062t4-BS
Samples were collected sequentially at 1- to 3-month-intervals depending on the study logistic. Time value indicates the sequential sample on the subject.

data_processing:
All FASTQ files were processed uniformly through the extra-cellular RNA processing toolkit (exceRpt). Information about exceRpt is available at https://github.gersteinlab.org/exceRpt/.
Assembly: hg19
Supplementary files format and content: Each processed data file is a core results archive generated by exceRpt. The core results archive contains read counts for alignments to the different transcriptome libraries used by exceRpt (miRNA / piRNA / tRNA / GENCODE annotations / circRNA), taxonomy trees for exogenous rRNA and genomic reads aligned by exceRpt, and a variety of other files generated by exceRpt.

source_name: Plasma

extract_protocol:
RNA Isolation kit was Homebrew Kit.
Library construction kit was Homebrew Kit. Samples were multiplexed. Type of Starting Material was total RNA.

tag: donor

tag: diagnosis

value: Type 1 Diabetes Mellitus

value: Plasma

tag: anatomical location

value: Entire cardiovascular system

tag: time

tag: rna source

value: total cell-free biofluid RNA

tag: rna isolation kit

value: Homebrew Kit


title: 999112_6

description:
EXR-DGALA1plasma999112t6-BS
Samples were collected sequentially at 1- to 3-month-intervals depending on the study logistic. Time value indicates the sequential sample on the subject.

tag: tissue


title: 999090_5

description:
EXR-DGALA1plasma999090t5-BS
Samples were collected sequentially at 1- to 3-month-intervals depending on the study logistic. Time value indicates the sequential sample on the subject.


title: 999199_10

description:
EXR-DGALA1plasma999199t10-BS
Samples were collected sequentially at 1- to 3-month-intervals depending on the study logistic. Time value indicates the sequential sample on the subject.


title: 267416_7

description:
EXR-DGALA1plasma267416t7-BS
Samples were collected sequentially at 1- to 3-month-intervals depending on the study logistic. Time value indicates the sequential sample on the subject.


title: 945052_1

description:
EXR-DGALA1plasma945052t1-BS
Samples were collected sequentially at 1- to 3-month-intervals depending on the study logistic. Time value indicates the sequential sample on the subject.


title: 999253_13

description:
EXR-DGALA1plasma999253t13-BS
Samples were collected sequentially at 1- to 3-month-intervals depending on the study logistic. Time value indicates the sequential sample on the subject.


title: 267416_11

description:
EXR-DGALA1plasma267416t11-BS
Samples were collected sequentially at 1- to 3-month-intervals depending on the study logistic. Time value indicates the sequential sample on the subject.


title: 234171_9

description:
EXR-DGALA1plasma234171t9-BS
Samples were collected sequentially at 1- to 3-month-intervals depending on the study logistic. Time value indicates the sequential sample on the subject.


title: ga22_snATAC

description:
genomic DNA
same donor as RL2103

source_name: prefrontal cortex, BA9, 46


title: 999192_10

description:
EXR-DGALA1plasma999192t10-BS
Samples were collected sequentially at 1- to 3-month-intervals depending on the study logistic. Time value indicates the sequential sample on the subject.


title: 267416_3

description:
EXR-DGALA1plasma267416t3-BS
Samples were collected sequentially at 1- to 3-month-intervals depending on the study logistic. Time value indicates the sequential sample on the subject.


title: 999126_7

description:
EXR-DGALA1plasma999126t7-BS
Samples were collected sequentially at 1- to 3-month-intervals depending on the study logistic. Time value indicates the sequential sample on the subject.


title: 999156_7

description:
EXR-DGALA1plasma999156t7-BS
Samples were collected sequentially at 1- to 3-month-intervals depending on the study logistic. Time value indicates the sequential sample on the subject.


title: 999214_11

description:
EXR-DGALA1plasma999214t11-BS
Samples were collected sequentially at 1- to 3-month-intervals depending on the study logistic. Time value indicates the sequential sample on the subject.


title: 234171_2

description:
EXR-DGALA1plasma234171t2-BS
Samples were collected sequentially at 1- to 3-month-intervals depending on the study logistic. Time value indicates the sequential sample on the subject.


title: 234171_5

description:
EXR-DGALA1plasma234171t5-BS
Samples were collected sequentially at 1- to 3-month-intervals depending on the study logistic. Time value indicates the sequential sample on the subject.


title: 267416_2

description:
EXR-DGALA1plasma267416t2-BS
Samples were collected sequentially at 1- to 3-month-intervals depending on the study logistic. Time value indicates the sequential sample on the subject.


title: 983649_1

description:
EXR-DGALA1plasma983649t1-BS
Samples were collected sequentially at 1- to 3-month-intervals depending on the study logistic. Time value indicates the sequential sample on the subject.


title: ga22_snRNAseq

description:
nuclear RNA
same donor as RL2366


title: 267416_4

description:
EXR-DGALA1plasma267416t4-BS
Samples were collected sequentially at 1- to 3-month-intervals depending on the study logistic. Time value indicates the sequential sample on the subject.


title: 234171_4

description:
EXR-DGALA1plasma234171t4-BS
Samples were collected sequentially at 1- to 3-month-intervals depending on the study logistic. Time value indicates the sequential sample on the subject.


title: 999227_11

description:
EXR-DGALA1plasma999227t11-BS
Samples were collected sequentially at 1- to 3-month-intervals depending on the study logistic. Time value indicates the sequential sample on the subject.


title: h2b_with_serum_rep1

tag: expressing

tag: cell line


title: B73, mrna-26 rep2

city: wuhan

first: qian

middle: lin

last: han

state: hubei

address: Huazhong Agricultural University, No.1 Shizishan Street, Hongshan District

institute: Huazhong Agricultural University

description:
instrument model: BGISEQ-100
slim-transcriptome.tpm

data_processing:
Quality control: Raw RNA-seq and circRNA-Seq data were processed by SOAPnuke1.6.548 with the parameters “-n 0.01 -l 20 -q 0.3 -A 0.25” and used SOAPnuke1.6.548 filters RNA to process the raw sRNA-Seq data with the parameters “-p 1 -z 18 -s -Q 2 --sanger”. Ribo-Seq data was removed adaptors and controled low quality by FASTX_Toolkit-0.0.14 fastx_clipper with the parameters "-l 5 -c -n -v -Q33" and fastx_trimmer with the parameters "-f 1 -Q 33".
Alignment: Clean reads were aligned to the maize AGPv4 reference genome. Total RNA-seq data from the 26 tissues or stages were mapped to the B73 AGPv4 reference genome using the default parameters of HISAT and StringTie; small RNAs which size were 18–26 nt were mapped to the maize AGPv4 reference genome using Bowtie-1.1.2 with the parameters unique location and no mismatch; the Ribo-Seq reads were aligned to the rRNA reference sequence using Bowtie-1.1.267 to filter out reads derived from rRNAs and retained reads were mapped to the maize AGPv4 reference genome.
Identification of non-coding RNA: Mapsplice-v2.1.8 was used to identify fusion RNAs from total RNA-seq data from each tissue; and improved version of LncRNA_Finder was used to identify lncRNAs from total RNAs. CIRI v2.0.5 was used to identify circRNAs by aligning them to the maize AGPv4 reference genome.
Quantification of RNA: Total RNAs including lncRNAs and mRNAs bound by ribosome were calculated expression by RSEM. CIRCexplorer2 v2.0.1 was used quantify the expression levels of the circRNAs. The expression of fusion RNA and small RNA was calculated according to the TPM standard formula.
PPIs: The libraries were sequenced on the PacBio platform, and Circular Consensus Sequencing reads were called using SMRTLink-5.1.0.26412. The following analysis was performed to obtain PPIs: Firstly, reads in FASTA format were extracted from BAM files using SAMtools-1.9. Next, because ten barcoded samples were combined to generate each sequencing library, reads from each sample were divided based on their barcode sequences using Cutadapt-1.9.1. Parameters -e and -m for running reads separation were 0.3 and 200, respectively. The reads were aligned to the coding sequence data from the maize AGPv4 genome to identified candidate PPI genes using BLAST+/2.7.1. Only PPI genes with BLAST e-value < 1.0e−4 that matched to two genes were retained. If a CCS contained sequences from two different genes, and the primer sequence and the recombination sequence were aligned consistently, the proteins encoded by the two genes were considered to be interacting proteins.
Assembly: Zea_mays.B73_RefGen_v4
Supplementary files format and content: Files include expression values and identified protein-protein interactions
21tis-circ.tpm (abundance measurements)
21tis-fusion-per.txt (abundance measurements)
21tis-lnc.tpm (abundance measurements)
21tis-srna.tpm (abundance measurements)
circ.gff3 (a tab-delimited text file that holds information of circular RNA)
fusion.gff3 (a tab-delimited text file that holds information of fusion RNA)
lncrna.gff3 (a tab-delimited text file that holds information of lncRNA)
PPIs-highconf.txt (high confidence protein-protein interactions)
PPIs.txt (protein-protein interactions)
slim-transcriptome.tpm (abundance measurements)
srna.gff3 (a tab-delimited text file that holds information of sRNA)
translatome.tpm (abundance measurements)
sd-slimio-lowconf.txt (Shortest distances of slim integrative omics low confidence network)
sd-slimio-highconf.txt (Shortest distances of slim integrative omics high confidence network)
sd-slimcoexpression.txt (Shortest distances of slim co-expression network)
sd-PPIs-lowconf.txt (Shortest distances of low confidence interactome network)
sd-PPIs-highconf.txt (Shortest distances of high confidence interactome network)
sd-iowithncrna-lowconf.txt (Shortest distances of integrative omics with ncRNAs low confidence network)
sd-iowithncrna-highconf.txt (Shortest distances of integrative omics with ncRNAs high confidence network)
sd-cotranslation.txt (Shortest distances of co-translation network)
sd-coexpressionwithncrna.txt (Shortest distances of co-expression with ncRNA network)
edge-slimio-lowconf.txt (Edges of slim integrative omics low confidence network)
edge-slimio-highconf.txt (Edges of slim integrative omics high confidence network)
edge-slimcoexpression.txt (Edges of slim co-expression network)
edge-iowithncrna-lowconf.txt (Edges of integrative omics with ncRNAs low confidence network)
edge-iowithncrna-highconf.txt (Edges of integrative omics with ncRNAs high confidence network)
edge-cotranslation.txt (Edges of co-translation network)
edge-coexpressionwithncrna.txt (Edges of co-expression with ncRNA network)

organism: Zea mays

growth_protocol: Twenty-six tissues or stages were sampled from B73 maize plants in a greenhouse. The plants were cultivated under a 12-h light/12-h dark cycle at 25 ℃.

extract_protocol:
Two replicates were prepared per tissue. RNA was extracted from 5–10 individual plants per replicate. Equal amounts of the three replicates were used for sequencing. Total RNA was isolated from the 26 tissues using a Direct-zol RNA Microprep kit (Zymo Research) following the manufacturer’s guidelines.
RNA libraries were prepared for sequencing using corresponding standard protocols.
mRNA-Seq, circular RNA-Seq, small RNA-Seq, ribo-Seq and PacBio Sequel

treatment_protocol: No special treatment.

tag: cultivar

tag: Stage

tag: age

tag: fraction

value: mRNA


title: 234171_6

description:
EXR-DGALA1plasma234171t6-BS
Samples were collected sequentially at 1- to 3-month-intervals depending on the study logistic. Time value indicates the sequential sample on the subject.


title: 999017_3

description:
EXR-DGALA1plasma999017t3-BS
Samples were collected sequentially at 1- to 3-month-intervals depending on the study logistic. Time value indicates the sequential sample on the subject.


title: 999034_4

description:
EXR-DGALA1plasma999034t4-BS
Samples were collected sequentially at 1- to 3-month-intervals depending on the study logistic. Time value indicates the sequential sample on the subject.


title: B73, mrna-25 rep2


title: 234171_3

description:
EXR-DGALA1plasma234171t3-BS
Samples were collected sequentially at 1- to 3-month-intervals depending on the study logistic. Time value indicates the sequential sample on the subject.


title: 999004_2

description:
EXR-DGALA1plasma999004t2-BS
Samples were collected sequentially at 1- to 3-month-intervals depending on the study logistic. Time value indicates the sequential sample on the subject.


title: B73, mrna-24 rep2

description:
instrument model: BGISEQ-100
slim-transcriptome.tpm
fusion.gff3
21tis-fusion-per.txt
21tis-lnc.tpm
lncrna.gff3


title: 267416_1

description:
EXR-DGALA1plasma267416t1-BS
Samples were collected sequentially at 1- to 3-month-intervals depending on the study logistic. Time value indicates the sequential sample on the subject.